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openmc-dev/openmc | 719 | openmc-dev__openmc-719 | [
"594"
] | d39d634a4009f8cfce127d7bab9588b8982b3bdb | diff --git a/examples/python/pincell_multigroup/build-xml.py b/examples/python/pincell_multigroup/build-xml.py
--- a/examples/python/pincell_multigroup/build-xml.py
+++ b/examples/python/pincell_multigroup/build-xml.py
@@ -21,44 +21,47 @@
# Instantiate the 7-group (C5G7) cross section data
uo2_xsdata = openmc.XSdata('UO2', groups)
uo2_xsdata.order = 0
-uo2_xsdata.total = [0.1779492, 0.3298048, 0.4803882, 0.5543674,
- 0.3118013, 0.3951678, 0.5644058]
-uo2_xsdata.absorption = [8.0248E-03, 3.7174E-03, 2.6769E-02, 9.6236E-02,
- 3.0020E-02, 1.1126E-01, 2.8278E-01]
-uo2_xsdata.scatter = [[[0.1275370, 0.0423780, 0.0000094, 0.0000000, 0.0000000, 0.0000000, 0.0000000],
- [0.0000000, 0.3244560, 0.0016314, 0.0000000, 0.0000000, 0.0000000, 0.0000000],
- [0.0000000, 0.0000000, 0.4509400, 0.0026792, 0.0000000, 0.0000000, 0.0000000],
- [0.0000000, 0.0000000, 0.0000000, 0.4525650, 0.0055664, 0.0000000, 0.0000000],
- [0.0000000, 0.0000000, 0.0000000, 0.0001253, 0.2714010, 0.0102550, 0.0000000],
- [0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0012968, 0.2658020, 0.0168090],
- [0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0085458, 0.2730800]]]
-uo2_xsdata.fission = [7.21206E-03, 8.19301E-04, 6.45320E-03,
- 1.85648E-02, 1.78084E-02, 8.30348E-02,
- 2.16004E-01]
-uo2_xsdata.nu_fission = [2.005998E-02, 2.027303E-03, 1.570599E-02,
- 4.518301E-02, 4.334208E-02, 2.020901E-01,
- 5.257105E-01]
-uo2_xsdata.chi = [5.8791E-01, 4.1176E-01, 3.3906E-04, 1.1761E-07,
- 0.0000E+00, 0.0000E+00, 0.0000E+00]
+uo2_xsdata.set_total(
+ [0.1779492, 0.3298048, 0.4803882, 0.5543674, 0.3118013, 0.3951678,
+ 0.5644058])
+uo2_xsdata.set_absorption([8.0248E-03, 3.7174E-03, 2.6769E-02, 9.6236E-02,
+ 3.0020E-02, 1.1126E-01, 2.8278E-01])
+uo2_xsdata.set_scatter_matrix(
+ [[[0.1275370, 0.0423780, 0.0000094, 0.0000000, 0.0000000, 0.0000000, 0.0000000],
+ [0.0000000, 0.3244560, 0.0016314, 0.0000000, 0.0000000, 0.0000000, 0.0000000],
+ [0.0000000, 0.0000000, 0.4509400, 0.0026792, 0.0000000, 0.0000000, 0.0000000],
+ [0.0000000, 0.0000000, 0.0000000, 0.4525650, 0.0055664, 0.0000000, 0.0000000],
+ [0.0000000, 0.0000000, 0.0000000, 0.0001253, 0.2714010, 0.0102550, 0.0000000],
+ [0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0012968, 0.2658020, 0.0168090],
+ [0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0085458, 0.2730800]]])
+uo2_xsdata.set_fission([7.21206E-03, 8.19301E-04, 6.45320E-03,
+ 1.85648E-02, 1.78084E-02, 8.30348E-02,
+ 2.16004E-01])
+uo2_xsdata.set_nu_fission([2.005998E-02, 2.027303E-03, 1.570599E-02,
+ 4.518301E-02, 4.334208E-02, 2.020901E-01,
+ 5.257105E-01])
+uo2_xsdata.set_chi([5.8791E-01, 4.1176E-01, 3.3906E-04, 1.1761E-07, 0.0000E+00,
+ 0.0000E+00, 0.0000E+00])
h2o_xsdata = openmc.XSdata('LWTR', groups)
h2o_xsdata.order = 0
-h2o_xsdata.total = [0.15920605, 0.412969593, 0.59030986, 0.58435,
- 0.718, 1.2544497, 2.650379]
-h2o_xsdata.absorption = [6.0105E-04, 1.5793E-05, 3.3716E-04,
- 1.9406E-03, 5.7416E-03, 1.5001E-02,
- 3.7239E-02]
-h2o_xsdata.scatter = [[[0.0444777, 0.1134000, 0.0007235, 0.0000037, 0.0000001, 0.0000000, 0.0000000],
- [0.0000000, 0.2823340, 0.1299400, 0.0006234, 0.0000480, 0.0000074, 0.0000010],
- [0.0000000, 0.0000000, 0.3452560, 0.2245700, 0.0169990, 0.0026443, 0.0005034],
- [0.0000000, 0.0000000, 0.0000000, 0.0910284, 0.4155100, 0.0637320, 0.0121390],
- [0.0000000, 0.0000000, 0.0000000, 0.0000714, 0.1391380, 0.5118200, 0.0612290],
- [0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0022157, 0.6999130, 0.5373200],
- [0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.1324400, 2.4807000]]]
+h2o_xsdata.set_total([0.15920605, 0.412969593, 0.59030986, 0.58435,
+ 0.718, 1.2544497, 2.650379])
+h2o_xsdata.set_absorption([6.0105E-04, 1.5793E-05, 3.3716E-04,
+ 1.9406E-03, 5.7416E-03, 1.5001E-02,
+ 3.7239E-02])
+h2o_xsdata.set_scatter_matrix(
+ [[[0.0444777, 0.1134000, 0.0007235, 0.0000037, 0.0000001, 0.0000000, 0.0000000],
+ [0.0000000, 0.2823340, 0.1299400, 0.0006234, 0.0000480, 0.0000074, 0.0000010],
+ [0.0000000, 0.0000000, 0.3452560, 0.2245700, 0.0169990, 0.0026443, 0.0005034],
+ [0.0000000, 0.0000000, 0.0000000, 0.0910284, 0.4155100, 0.0637320, 0.0121390],
+ [0.0000000, 0.0000000, 0.0000000, 0.0000714, 0.1391380, 0.5118200, 0.0612290],
+ [0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0022157, 0.6999130, 0.5373200],
+ [0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.1324400, 2.4807000]]])
mg_cross_sections_file = openmc.MGXSLibrary(groups)
mg_cross_sections_file.add_xsdatas([uo2_xsdata, h2o_xsdata])
-mg_cross_sections_file.export_to_xml()
+mg_cross_sections_file.export_to_hdf5()
###############################################################################
@@ -129,7 +132,7 @@
# Instantiate a Settings object, set all runtime parameters, and export to XML
settings_file = openmc.Settings()
settings_file.energy_mode = "multi-group"
-settings_file.cross_sections = "./mgxs.xml"
+settings_file.cross_sections = "./mgxs.h5"
settings_file.batches = batches
settings_file.inactive = inactive
settings_file.particles = particles
diff --git a/openmc/mesh.py b/openmc/mesh.py
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -286,10 +286,8 @@ def build_cells(self, bc=['reflective'] * 6):
openmc.XPlane(x0=self.upper_right[0],
boundary_type=bc[1])]
if len(self.dimension) == 1:
- yplanes = [openmc.YPlane(y0=np.finfo(np.float).min,
- boundary_type='reflective'),
- openmc.YPlane(y0=np.finfo(np.float).max,
- boundary_type='reflective')]
+ yplanes = [openmc.YPlane(y0=-1e10, boundary_type='reflective'),
+ openmc.YPlane(y0=1e10, boundary_type='reflective')]
else:
yplanes = [openmc.YPlane(y0=self.lower_left[1],
boundary_type=bc[2]),
@@ -297,10 +295,15 @@ def build_cells(self, bc=['reflective'] * 6):
boundary_type=bc[3])]
if len(self.dimension) <= 2:
- zplanes = [openmc.ZPlane(z0=np.finfo(np.float).min,
- boundary_type='reflective'),
- openmc.ZPlane(z0=np.finfo(np.float).max,
- boundary_type='reflective')]
+ # Would prefer to have the z ranges be the max supported float, but
+ # these values are apparently different between python and Fortran.
+ # Choosing a safe and sane default.
+ # Values of +/-1e10 are used here as there seems to be an
+ # inconsistency between what numpy uses as the max float and what
+ # Fortran expects for a real(8), so this avoids code complication
+ # and achieves the same goal.
+ zplanes = [openmc.ZPlane(z0=-1e10, boundary_type='reflective'),
+ openmc.ZPlane(z0=1e10, boundary_type='reflective')]
else:
zplanes = [openmc.ZPlane(z0=self.lower_left[2],
boundary_type=bc[4]),
diff --git a/openmc/mgxs/library.py b/openmc/mgxs/library.py
--- a/openmc/mgxs/library.py
+++ b/openmc/mgxs/library.py
@@ -822,11 +822,13 @@ def load_from_file(filename='mgxs', directory='mgxs'):
return pickle.load(open(full_filename, 'rb'))
def get_xsdata(self, domain, xsdata_name, nuclide='total', xs_type='macro',
- order=None, tabular_legendre=None, tabular_points=33,
- subdomain=None):
+ order=None, subdomain=None):
"""Generates an openmc.XSdata object describing a multi-group cross section
- data set for eventual combination in to an openmc.MGXSLibrary object
- (i.e., the library).
+ dataset for writing to an openmc.MGXSLibrary object.
+
+ Note that this method does not build an XSdata
+ object with nested temperature tables. The temperature of each
+ XSdata object will be left at the default value of 300K.
Parameters
----------
@@ -845,18 +847,6 @@ def get_xsdata(self, domain, xsdata_name, nuclide='total', xs_type='macro',
Scattering order for this data entry. Default is None,
which will set the XSdata object to use the order of the
Library.
- tabular_legendre : None or bool
- Flag to denote whether or not the Legendre expansion of the
- scattering angular distribution is to be converted to a tabular
- representation by OpenMC. A value of `True` means that it is to be
- converted while a value of `False` means that it will not be.
- Defaults to `None` which leaves the default behavior of OpenMC in
- place (the distribution is converted to a tabular representation).
- tabular_points : int
- This parameter is not used unless the ``tabular_legendre``
- parameter is set to `True`. In this case, this parameter sets the
- number of equally-spaced points in the domain of [-1,1] to be used
- in building the tabular distribution. Default is `33`.
subdomain : iterable of int
This parameter is not used unless using a mesh domain. In that
case, the subdomain is an [i,j,k] index (1-based indexing) of the
@@ -867,7 +857,7 @@ def get_xsdata(self, domain, xsdata_name, nuclide='total', xs_type='macro',
Returns
-------
xsdata : openmc.XSdata
- Multi-Group Cross Section data set object.
+ Multi-Group Cross Section dataset object.
Raises
------
@@ -890,10 +880,6 @@ def get_xsdata(self, domain, xsdata_name, nuclide='total', xs_type='macro',
if order is not None:
cv.check_greater_than('order', order, 0, equality=True)
cv.check_less_than('order', order, 10, equality=True)
- cv.check_type('tabular_legendre', tabular_legendre,
- (type(None), bool))
- if tabular_points is not None:
- cv.check_greater_than('tabular_points', tabular_points, 1)
if subdomain is not None:
cv.check_iterable_type('subdomain', subdomain, Integral,
max_depth=3)
@@ -910,7 +896,7 @@ def get_xsdata(self, domain, xsdata_name, nuclide='total', xs_type='macro',
# Build & add metadata to XSdata object
name = xsdata_name
- if nuclide is not 'total':
+ if nuclide != 'total':
name += '_' + nuclide
xsdata = openmc.XSdata(name, self.energy_groups)
@@ -922,14 +908,12 @@ def get_xsdata(self, domain, xsdata_name, nuclide='total', xs_type='macro',
# the provided order or the Library's order.
xsdata.order = min(order, self.legendre_order)
- # Set the tabular_legendre option if needed
- if tabular_legendre is not None:
- xsdata.tabular_legendre = {'enable': tabular_legendre,
- 'num_points': tabular_points}
+ # Right now only 'legendre' data and isotropic weighting is supported
+ self.scatter_format = 'legendre'
+ self.representation = 'isotropic'
- if nuclide is not 'total':
- xsdata.zaid = self._nuclides[nuclide][0]
- xsdata.awr = self._nuclides[nuclide][1]
+ if nuclide != 'total':
+ xsdata.atomic_weight_ratio = self._nuclides[nuclide][1]
if subdomain is None:
subdomain = 'all'
@@ -940,7 +924,7 @@ def get_xsdata(self, domain, xsdata_name, nuclide='total', xs_type='macro',
if 'nu-transport' in self.mgxs_types and self.correction == 'P0':
mymgxs = self.get_mgxs(domain, 'nu-transport')
xsdata.set_total_mgxs(mymgxs, xs_type=xs_type, nuclide=[nuclide],
- subdomains=subdomain)
+ subdomain=subdomain)
elif 'total' in self.mgxs_types:
mymgxs = self.get_mgxs(domain, 'total')
xsdata.set_total_mgxs(mymgxs, xs_type=xs_type, nuclide=[nuclide],
@@ -979,49 +963,55 @@ def get_xsdata(self, domain, xsdata_name, nuclide='total', xs_type='macro',
# If multiplicity matrix is available, prefer that
if 'multiplicity matrix' in self.mgxs_types:
mymgxs = self.get_mgxs(domain, 'multiplicity matrix')
- xsdata.set_multiplicity_mgxs(mymgxs, xs_type=xs_type,
- nuclide=[nuclide],
- subdomain=subdomain)
+ xsdata.set_multiplicity_matrix_mgxs(mymgxs, xs_type=xs_type,
+ nuclide=[nuclide],
+ subdomain=subdomain)
using_multiplicity = True
# multiplicity will fall back to using scatter and nu-scatter
elif ((('scatter matrix' in self.mgxs_types) and
('nu-scatter matrix' in self.mgxs_types))):
scatt_mgxs = self.get_mgxs(domain, 'scatter matrix')
nuscatt_mgxs = self.get_mgxs(domain, 'nu-scatter matrix')
- xsdata.set_multiplicity_mgxs(nuscatt_mgxs, scatt_mgxs,
- xs_type=xs_type, nuclide=[nuclide],
- subdomain=subdomain)
+ xsdata.set_multiplicity_matrix_mgxs(nuscatt_mgxs, scatt_mgxs,
+ xs_type=xs_type,
+ nuclide=[nuclide],
+ subdomain=subdomain)
using_multiplicity = True
else:
using_multiplicity = False
if using_multiplicity:
nuscatt_mgxs = self.get_mgxs(domain, 'nu-scatter matrix')
- xsdata.set_scatter_mgxs(nuscatt_mgxs, xs_type=xs_type,
- nuclide=[nuclide], subdomain=subdomain)
+ xsdata.set_scatter_matrix_mgxs(nuscatt_mgxs, xs_type=xs_type,
+ nuclide=[nuclide],
+ subdomain=subdomain)
else:
if 'nu-scatter matrix' in self.mgxs_types:
nuscatt_mgxs = self.get_mgxs(domain, 'nu-scatter matrix')
- xsdata.set_scatter_mgxs(nuscatt_mgxs, xs_type=xs_type,
- nuclide=[nuclide],
- subdomain=subdomain)
+ xsdata.set_scatter_matrix_mgxs(nuscatt_mgxs, xs_type=xs_type,
+ nuclide=[nuclide],
+ subdomain=subdomain)
# Since we are not using multiplicity, then
# scattering multiplication (nu-scatter) must be
# accounted for approximately by using an adjusted
# absorption cross section.
- if 'total' in self.mgxs_types:
- xsdata.absorption = \
- np.subtract(xsdata.total,
- np.sum(xsdata.scatter[0, :, :], axis=1))
+ if 'total' in self.mgxs_types or 'transport' in self.mgxs_types:
+ for i in range(len(xsdata.temperatures)):
+ xsdata._absorption[i] = \
+ np.subtract(xsdata._total[i], np.sum(
+ xsdata._scatter_matrix[i][0, :, :], axis=1))
return xsdata
- def create_mg_library(self, xs_type='macro', xsdata_names=None,
- tabular_legendre=None, tabular_points=33):
+ def create_mg_library(self, xs_type='macro', xsdata_names=None):
"""Creates an openmc.MGXSLibrary object to contain the MGXS data for the
Multi-Group mode of OpenMC.
+ Note that this library will not make use of nested temperature tables.
+ Every dataset in the library will be treated as if it was at the same
+ default temperature.
+
Parameters
----------
xs_type: {'macro', 'micro'}
@@ -1031,18 +1021,6 @@ def create_mg_library(self, xs_type='macro', xsdata_names=None,
xsdata_names : Iterable of str
List of names to apply to the "xsdata" entries in the
resultant mgxs data file. Defaults to 'set1', 'set2', ...
- tabular_legendre : None or bool
- Flag to denote whether or not the Legendre expansion of the
- scattering angular distribution is to be converted to a tabular
- representation by OpenMC. A value of `True` means that it is to be
- converted while a value of `False` means that it will not be.
- Defaults to `None` which leaves the default behavior of OpenMC in
- place (the distribution is converted to a tabular representation).
- tabular_points : int
- This parameter is not used unless the ``tabular_legendre``
- parameter is set to `True`. In this case, this parameter sets the
- number of equally-spaced points in the domain of [-1,1] to be used
- in building the tabular distribution. Default is `33`.
Returns
-------
@@ -1094,8 +1072,6 @@ def create_mg_library(self, xs_type='macro', xsdata_names=None,
# Create XSdata and Macroscopic for this domain
xsdata = self.get_xsdata(domain, xsdata_name,
- tabular_legendre=tabular_legendre,
- tabular_points=tabular_points,
subdomain=subdomain)
mgxs_file.add_xsdata(xsdata)
i += 1
@@ -1113,45 +1089,34 @@ def create_mg_library(self, xs_type='macro', xsdata_names=None,
xsdata_name = 'set' + str(i + 1)
else:
xsdata_name = xsdata_names[i]
- if nuclide is not 'total':
+ if nuclide != 'total':
xsdata_name += '_' + nuclide
xsdata = self.get_xsdata(domain, xsdata_name,
- nuclide=nuclide, xs_type=xs_type,
- tabular_legendre=tabular_legendre,
- tabular_points=tabular_points)
+ nuclide=nuclide, xs_type=xs_type)
mgxs_file.add_xsdata(xsdata)
return mgxs_file
- def create_mg_mode(self, xsdata_names=None, tabular_legendre=None,
- tabular_points=33, bc=['reflective'] * 6):
+ def create_mg_mode(self, xsdata_names=None, bc=['reflective'] * 6):
"""Creates an openmc.MGXSLibrary object to contain the MGXS data for the
Multi-Group mode of OpenMC as well as the associated openmc.Materials
- and openmc.Geometry objects. The created Geometry is the same as that
- used to generate the MGXS data, with the only differences being
- modifications to point to newly-created Materials which point to the
- multi-group data. This method only creates a macroscopic
- MGXS Library even if nuclidic tallies are specified in the Library.
+ and openmc.Geometry objects.
+
+ The created Geometry is the same as that used to generate the MGXS
+ data, with the only differences being modifications to point to
+ newly-created Materials which point to the multi-group data. This
+ method only creates a macroscopic MGXS Library even if nuclidic tallies
+ are specified in the Library. Note that this library will not make
+ use of nested temperature tables. Every dataset in the library will
+ be treated as if it was at the same default temperature.
Parameters
----------
xsdata_names : Iterable of str
List of names to apply to the "xsdata" entries in the
resultant mgxs data file. Defaults to 'set1', 'set2', ...
- tabular_legendre : None or bool
- Flag to denote whether or not the Legendre expansion of the
- scattering angular distribution is to be converted to a tabular
- representation by OpenMC. A value of `True` means that it is to be
- converted while a value of `False` means that it will not be.
- Defaults to `None` which leaves the default behavior of OpenMC in
- place (the distribution is converted to a tabular representation).
- tabular_points : int
- This parameter is not used unless the ``tabular_legendre``
- parameter is set to `True`. In this case, this parameter sets the
- number of equally-spaced points in the domain of [-1,1] to be used
- in building the tabular distribution. Default is `33`.
bc : iterable of {'reflective', 'periodic', 'transmission', or 'vacuum'}
Boundary conditions for each of the four faces of a rectangle
(if applying to a 2D mesh) or six faces of a parallelepiped
@@ -1198,8 +1163,7 @@ def create_mg_mode(self, xsdata_names=None, tabular_legendre=None,
cv.check_length("domains", self.domains, 1, 1)
# Get the MGXS File Data
- mgxs_file = self.create_mg_library('macro', xsdata_names,
- tabular_legendre, tabular_points)
+ mgxs_file = self.create_mg_library('macro', xsdata_names)
# Now move on the creating the geometry and assigning materials
if self.domain_type == 'mesh':
diff --git a/openmc/mgxs_library.py b/openmc/mgxs_library.py
--- a/openmc/mgxs_library.py
+++ b/openmc/mgxs_library.py
@@ -1,82 +1,22 @@
from collections import Iterable
from numbers import Real, Integral
-from xml.etree import ElementTree as ET
import sys
import numpy as np
+import h5py
import openmc
import openmc.mgxs
from openmc.checkvalue import check_type, check_value, check_greater_than, \
check_iterable_type
-from openmc.clean_xml import sort_xml_elements, clean_xml_indentation
if sys.version_info[0] >= 3:
basestring = str
# Supported incoming particle MGXS angular treatment representations
_REPRESENTATIONS = ['isotropic', 'angle']
-
-
-def ndarray_to_string(arr):
- """Converts a numpy ndarray in to a join with spaces between entries
- similar to ' '.join(map(str,arr)) but applied to all sub-dimensions.
-
- Parameters
- ----------
- arr : numpy.ndarray
- Array to combine in to a string
-
- Returns
- -------
- text : str
- String representation of array in arr
-
- """
-
- shape = arr.shape
- ndim = arr.ndim
- tab = ' '
- indent = '\n' + tab + tab
- text = indent
-
- if ndim == 1:
- text += tab
- for i in range(shape[0]):
- text += '{:.7E} '.format(arr[i])
- text += indent
- elif ndim == 2:
- for i in range(shape[0]):
- text += tab
- for j in range(shape[1]):
- text += '{:.7E} '.format(arr[i, j])
- text += indent
- elif ndim == 3:
- for i in range(shape[0]):
- for j in range(shape[1]):
- text += tab
- for k in range(shape[2]):
- text += '{:.7E} '.format(arr[i, j, k])
- text += indent
- elif ndim == 4:
- for i in range(shape[0]):
- for j in range(shape[1]):
- for k in range(shape[2]):
- text += tab
- for l in range(shape[3]):
- text += '{:.7E} '.format(arr[i, j, k, l])
- text += indent
- elif ndim == 5:
- for i in range(shape[0]):
- for j in range(shape[1]):
- for k in range(shape[2]):
- for l in range(shape[3]):
- text += tab
- for m in range(shape[4]):
- text += '{:.7E} '.format(arr[i, j, k, l, m])
- text += indent
-
- return text
+_SCATTER_TYPES = ['tabular', 'legendre', 'histogram']
+_SCATTER_SHAPES = ["[Order][G][G']"]
class XSdata(object):
@@ -85,162 +25,140 @@ class XSdata(object):
Parameters
----------
- name : str, optional
+ name : str
Name of the mgxs data set.
energy_groups : openmc.mgxs.EnergyGroups
- Energygroup structure
+ Energy group structure
representation : {'isotropic', 'angle'}, optional
Method used in generating the MGXS (isotropic or angle-dependent flux
weighting). Defaults to 'isotropic'
+ temperatures : Iterable of float
+ Temperatures (in units of Kelvin) of the provided datasets. Defaults
+ to a single temperature at 294K.
Attributes
----------
name : str
Unique identifier for the xsdata object
- alias : str
- Separate unique identifier for the xsdata object
- awr : float
+ aromic_weight_ratio : float
Atomic weight ratio of an isotope. That is, the ratio of the mass
of the isotope to the mass of a single neutron.
- kT : float
- Temperature (in units of MeV).
+ temperatures : numpy.ndarray
+ Temperatures (in units of Kelvin) of the provided datasets. Defaults
+ to a single temperature at 294K.
energy_groups : openmc.mgxs.EnergyGroups
Energy group structure
fissionable : bool
Whether or not this is a fissionable data set.
- scatt_type : {'legendre', 'histogram', or 'tabular'}
+ scatter_format : {'legendre', 'histogram', or 'tabular'}
Angular distribution representation (legendre, histogram, or tabular)
+ scatter_shapes : {"[Order][G][G']"}
+ Dimensionality of the scattering and multiplicity matrices
order : int
Either the Legendre order, number of bins, or number of points used to
describe the angular distribution associated with each group-to-group
transfer probability.
- tabular_legendre : dict
- Set how to treat the Legendre scattering kernel (tabular or leave in
- Legendre polynomial form). Dict contains two keys: 'enable' and
- 'num_points'. 'enable' is a boolean and 'num_points' is the
- number of points to use, if 'enable' is True.
representation : {'isotropic', 'angle'}
Method used in generating the MGXS (isotropic or angle-dependent flux
weighting).
num_azimuthal : int
Number of equal width angular bins that the azimuthal angular domain is
- subdivided into. This only applies when ``representation`` is "angle".
+ subdivided into. This only applies when :attr:`XSdata.representation`
+ is "angle".
num_polar : int
Number of equal width angular bins that the polar angular domain is
- subdivided into. This only applies when ``representation`` is "angle".
+ subdivided into. This only applies when :attr:`XSdata.representation`
+ is "angle".
use_chi : bool
Whether or not a chi vector or nu-fission matrix was used.
vector_shape : iterable of int
Dimensionality of vector multi-group cross sections (e.g., the total
cross section). The return result depends on the value of
- ``representation``.
+ :attr:`XSdata.representation`.
matrix_shape : iterable of int
Dimensionality of matrix multi-group cross sections (e.g., the
fission matrix cross section). The return result depends on the
- value of ``representation``.
+ value of :attr:`XSdata.representation`.
pn_matrix_shape : iterable of int
Dimensionality of scattering matrix data (e.g., the
scattering matrix cross section). The return result depends on the
- value of ``representation``.
- total : numpy.ndarray
- Group-wise total cross section ordered by increasing group index (i.e.,
- fast to thermal). If ``representation`` is "isotropic", then the length
- of this list should equal the number of groups described in the
- ``groups`` element. If ``representation`` is "angle", then the length
- of this list should equal the number of groups times the number of
- azimuthal angles times the number of polar angles, with the
- inner-dimension being groups, intermediate-dimension being azimuthal
- angles and outer-dimension being the polar angles.
- absorption : numpy.ndarray
- Group-wise absorption cross section ordered by increasing group index
- (i.e., fast to thermal). If ``representation`` is "isotropic", then the
- length of this list should equal the number of groups described in the
- ``groups`` attribute. If ``representation`` is "angle", then the length
- of this list should equal the number of groups times the number of
- azimuthal angles times the number of polar angles, with the
- inner-dimension being groups, intermediate-dimension being azimuthal
- angles and outer-dimension being the polar angles.
- scatter : numpy.ndarray
+ value of :attr:`XSdata.representation`.
+ total : dict of numpy.ndarray
+ Group-wise total cross section.
+ absorption : dict of numpy.ndarray
+ Group-wise absorption cross section.
+ scatter_matrix : dict of numpy.ndarray
Scattering moment matrices presented with the columns representing
incoming group and rows representing the outgoing group. That is,
- down-scatter will be above the diagonal of the resultant matrix. This
- matrix is repeated for every Legendre order (in order of increasing
- orders) if ``scatt_type`` is "legendre"; otherwise, this matrix is
- repeated for every bin of the histogram or tabular representation.
- Finally, if ``representation`` is "angle", the above is repeated for
- every azimuthal angle and every polar angle, in that order.
- multiplicity : numpy.ndarray
+ down-scatter will be above the diagonal of the resultant matrix.
+ multiplicity_matrix : dict of numpy.ndarray
Ratio of neutrons produced in scattering collisions to the neutrons
which undergo scattering collisions; that is, the multiplicity provides
the code with a scaling factor to account for neutrons produced in
- (n,xn) reactions. This information is assumed isotropic and therefore
- does not need to be repeated for every Legendre moment or
- histogram/tabular bin. This matrix follows the same arrangement as
- described for the ``scatter`` attribute, with the exception of the data
- needed to provide the scattering type information.
- fission : numpy.ndarray
- Group-wise fission cross section ordered by increasing group index
- (i.e., fast to thermal). If ``representation`` is "isotropic", then the
- length of this list should equal the number of groups described in the
- ``groups`` attribute. If ``representation`` is "angle", then the length
- of this list should equal the number of groups times the number of
- azimuthal angles times the number of polar angles, with the
- inner-dimension being groups, intermediate-dimension being azimuthal
- angles and outer-dimension being the polar angles.
- kappa_fission : numpy.ndarray
- Group-wise kappa-fission cross section ordered by increasing group
- index (i.e., fast to thermal). If ``representation`` is "isotropic",
- then the length of this list should equal the number of groups in the
- ``groups`` attribute. If ``representation`` is "angle", then the length
- of this list should equal the number of groups times the number of
- azimuthal angles times the number of polar angles, with the
- inner-dimension being groups, intermediate-dimension being azimuthal
- angles and outer-dimension being the polar angles.
- chi : numpy.ndarray
+ (n,xn) reactions.
+ fission : dict of numpy.ndarray
+ Group-wise fission cross section.
+ kappa_fission : dict of numpy.ndarray
+ Group-wise kappa-fission cross section.
+ chi : dict of numpy.ndarray
Group-wise fission spectra ordered by increasing group index (i.e.,
- fast to thermal). This attribute should be used if making the common
+ fast to thermal). This attribute should be used if making the common
approximation that the fission spectra does not depend on incoming
- energy. If the user does not wish to make this approximation, then
+ energy. If the user does not wish to make this approximation, then
this should not be provided and this information included in the
- ``nu_fission`` element instead. If ``representation`` is "isotropic",
- then the length of this list should equal the number of groups
- in the ``groups`` element. If ``representation`` is "angle", then the
- length of this list should equal the number of groups times the number
- of azimuthal angles times the number of polar angles, with the
- inner-dimension being groups, intermediate-dimension being azimuthal
- angles and outer-dimension being the polar angles.
- nu_fission : numpy.ndarray
- Group-wise fission production cross section vector (i.e., if ``chi`` is
- provided), or is the group-wise fission production matrix. If providing
- the vector, it should be ordered the same as the ``fission`` data. If
- providing the matrix, it should be ordered the same as the
- ``multiplicity`` matrix.
+ :attr:`XSdata.nu_fission` attribute instead.
+ nu_fission : dict of numpy.ndarray
+ Group-wise fission production cross section vector (i.e., if
+ :attr:`XSdata.chi` is provided), or is the group-wise fission
+ production matrix.
+ inverse_velocities : dict of numpy.ndarray
+ Inverse of velocities, in units of sec/cm.
+
+ Notes
+ -----
+ The parameters containing cross section data have dimensionalities which
+ depend upon the value of :attr:`XSdata.representation` as well as the
+ number of Legendre or other angular dimensions as described by
+ :attr:`XSdata.order`. The :attr:`XSdata.vector_shape`,
+ :attr:`XSdata.matrix_shape`, and :attr:`XSdata.pn_matrix_shape` properties
+ are provided to obtain the dimensionality of the data for each temperature.
+
+ The following are cross sections which should use each of these properties:
+
+ vector_shape :
+ total, absorption, fission, kappa_fission, chi, nu_fission (if chi is
+ provided), inverse_velocities
+ matrix_shape :
+ multiplicity_matrix, nu_fission (if chi is not provided)
+ pn_matrix_shape :
+ scatter_matrix
"""
- def __init__(self, name, energy_groups, representation='isotropic'):
+ def __init__(self, name, energy_groups, temperatures=[294.],
+ representation='isotropic'):
# Initialize class attributes
- self._name = name
- self._energy_groups = energy_groups
- self._representation = representation
- self._alias = None
- self._awr = None
- self._kT = None
+ self.name = name
+ self.energy_groups = energy_groups
+ self.temperatures = temperatures
+ self.representation = representation
+ self._atomic_weight_ratio = None
self._fissionable = False
- self._scatt_type = 'legendre'
+ self._scatter_format = 'legendre'
+ self._scatter_shape = "[Order][G][G']"
self._order = None
- self._tabular_legendre = None
self._num_polar = None
self._num_azimuthal = None
- self._total = None
- self._absorption = None
- self._scatter = None
- self._multiplicity = None
- self._fission = None
- self._nu_fission = None
- self._kappa_fission = None
- self._chi = None
self._use_chi = None
+ self._total = len(temperatures) * [None]
+ self._absorption = len(temperatures) * [None]
+ self._scatter_matrix = len(temperatures) * [None]
+ self._multiplicity_matrix = len(temperatures) * [None]
+ self._fission = len(temperatures) * [None]
+ self._nu_fission = len(temperatures) * [None]
+ self._kappa_fission = len(temperatures) * [None]
+ self._chi = len(temperatures) * [None]
+ self._inverse_velocities = len(temperatures) * [None]
@property
def name(self):
@@ -255,28 +173,28 @@ def representation(self):
return self._representation
@property
- def alias(self):
- return self._alias
+ def atomic_weight_ratio(self):
+ return self._atomic_weight_ratio
@property
- def awr(self):
- return self._awr
+ def fissionable(self):
+ return self._fissionable
@property
- def kT(self):
- return self._kT
+ def temperatures(self):
+ return self._temperatures
@property
- def scatt_type(self):
- return self._scatt_type
+ def scatter_format(self):
+ return self._scatter_format
@property
- def order(self):
- return self._order
+ def scatter_shape(self):
+ return self._scatter_shape
@property
- def tabular_legendre(self):
- return self._tabular_legendre
+ def order(self):
+ return self._order
@property
def num_polar(self):
@@ -299,12 +217,12 @@ def absorption(self):
return self._absorption
@property
- def scatter(self):
- return self._scatter
+ def scatter_matrix(self):
+ return self._scatter_matrix
@property
- def multiplicity(self):
- return self._multiplicity
+ def multiplicity_matrix(self):
+ return self._multiplicity_matrix
@property
def fission(self):
@@ -324,36 +242,36 @@ def chi(self):
@property
def num_orders(self):
- if (self._order is not None) and (self._scatt_type is not None):
- if self._scatt_type is 'legendre':
+ if self._order is not None:
+ if self._scatter_format in (None, 'legendre'):
return self._order + 1
else:
return self._order
@property
def vector_shape(self):
- if self.representation is 'isotropic':
+ if self.representation == 'isotropic':
return (self.energy_groups.num_groups,)
- elif self.representation is 'angle':
+ elif self.representation == 'angle':
return (self.num_polar, self.num_azimuthal,
self.energy_groups.num_groups)
@property
def matrix_shape(self):
- if self.representation is 'isotropic':
+ if self.representation == 'isotropic':
return (self.energy_groups.num_groups,
self.energy_groups.num_groups)
- elif self.representation is 'angle':
+ elif self.representation == 'angle':
return (self.num_polar, self.num_azimuthal,
self.energy_groups.num_groups,
self.energy_groups.num_groups)
@property
def pn_matrix_shape(self):
- if self.representation is 'isotropic':
+ if self.representation == 'isotropic':
return (self.num_orders, self.energy_groups.num_groups,
self.energy_groups.num_groups)
- elif self.representation is 'angle':
+ elif self.representation == 'angle':
return (self.num_polar, self.num_azimuthal, self.num_orders,
self.energy_groups.num_groups,
self.energy_groups.num_groups)
@@ -380,34 +298,30 @@ def representation(self, representation):
check_value('representation', representation, _REPRESENTATIONS)
self._representation = representation
- @alias.setter
- def alias(self, alias):
- if alias is not None:
- check_type('alias', alias, basestring)
- self._alias = alias
- else:
- self._alias = self._name
-
- @awr.setter
- def awr(self, awr):
- # Check validity of type and that the awr value is > 0
- check_type('awr', awr, Real)
- check_greater_than('awr', awr, 0.0)
- self._awr = awr
-
- @kT.setter
- def kT(self, kT):
- # Check validity of type and that the kT value is >= 0
- check_type('kT', kT, Real)
- check_greater_than('kT', kT, 0.0, equality=True)
- self._kT = kT
-
- @scatt_type.setter
- def scatt_type(self, scatt_type):
+ @atomic_weight_ratio.setter
+ def atomic_weight_ratio(self, atomic_weight_ratio):
+ # Check validity of type and that the atomic_weight_ratio value is > 0
+ check_type('atomic_weight_ratio', atomic_weight_ratio, Real)
+ check_greater_than('atomic_weight_ratio', atomic_weight_ratio, 0.0)
+ self._atomic_weight_ratio = atomic_weight_ratio
+
+ @temperatures.setter
+ def temperatures(self, temperatures):
+ check_iterable_type('temperatures', temperatures, Real)
+
+ self._temperatures = np.array(temperatures)
+
+ @scatter_format.setter
+ def scatter_format(self, scatter_format):
# check to see it is of a valid type and value
- check_value('scatt_type', scatt_type, ['legendre', 'histogram',
- 'tabular'])
- self._scatt_type = scatt_type
+ check_value('scatter_format', scatter_format, _SCATTER_TYPES)
+ self._scatter_format = scatter_format
+
+ @scatter_shape.setter
+ def scatter_shape(self, scatter_shape):
+ # check to see it is of a valid type and value
+ check_value('scatter_shape', scatter_shape, _SCATTER_SHAPES)
+ self._scatter_shape = scatter_shape
@order.setter
def order(self, order):
@@ -416,39 +330,16 @@ def order(self, order):
check_greater_than('order', order, 0, equality=True)
self._order = order
- @tabular_legendre.setter
- def tabular_legendre(self, tabular_legendre):
- # Check to make sure this is a dict and it has our keys with the
- # right values.
- check_type('tabular_legendre', tabular_legendre, dict)
- if 'enable' in tabular_legendre:
- enable = tabular_legendre['enable']
- check_type('enable', enable, bool)
- else:
- msg = 'The tabular_legendre dict must include a value keyed by ' \
- '"enable"'
- raise ValueError(msg)
- if 'num_points' in tabular_legendre:
- num_points = tabular_legendre['num_points']
- check_type('num_points', num_points, Integral)
- check_greater_than('num_points', num_points, 0)
- else:
- if not enable:
- num_points = 1
- else:
- num_points = 33
- self._tabular_legendre = {'enable': enable, 'num_points': num_points}
-
@num_polar.setter
def num_polar(self, num_polar):
# Make sure we have positive ints
- check_value('num_polar', num_polar, Integral)
+ check_type('num_polar', num_polar, Integral)
check_greater_than('num_polar', num_polar, 0)
self._num_polar = num_polar
@num_azimuthal.setter
def num_azimuthal(self, num_azimuthal):
- check_value('num_azimuthal', num_azimuthal, Integral)
+ check_type('num_azimuthal', num_azimuthal, Integral)
check_greater_than('num_azimuthal', num_azimuthal, 0)
self._num_azimuthal = num_azimuthal
@@ -457,102 +348,261 @@ def use_chi(self, use_chi):
check_type('use_chi', use_chi, bool)
self._use_chi = use_chi
- @total.setter
- def total(self, total):
+ def add_temperature(self, temperature):
+ """This method re-sizes the attributes of this XSdata object so that it
+ can accomodate an additional temperature. Note that the set_* methods
+ will still need to be executed.
+
+ Parameters
+ ----------
+ temperature : float
+ Temperature (in units of Kelvin) of the provided dataset.
+
+ """
+ check_type('temperature', temperature, Real)
+
+ temp_store = self.temperatures.tolist().append(temperature)
+ self.temperatures = temp_store
+
+ self._total.append(None)
+ self._absorption.append(None)
+ self._scatter_matrix.append(None)
+ self._multiplicity_matrix.append(None)
+ self._fission.append(None)
+ self._nu_fission.append(None)
+ self._kappa_fission.append(None)
+ self._chi.append(None)
+ self._inverse_velocities.append(None)
+
+ def set_total(self, total, temperature=294.):
+ """This method sets the cross section for this XSdata object at the
+ provided temperature.
+
+ Parameters
+ ----------
+ total: np.ndarray
+ Total Cross Section
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
+
+ See also
+ --------
+ openmc.mgxs_library.set_total_mgxs()
+
+ """
check_type('total', total, Iterable, expected_iter_type=Real)
- # Convert to a numpy array so we can easily get the shape for
- # checking
- nptotal = np.asarray(total)
- check_value('total shape', nptotal.shape, [self.vector_shape])
+ # Convert to a numpy array so we can easily get the shape for checking
+ total = np.asarray(total)
+ check_value('total shape', total.shape, [self.vector_shape])
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ i = np.where(self.temperatures == temperature)[0][0]
+ self._total[i] = total
+
+ def set_absorption(self, absorption, temperature=294.):
+ """This method sets the cross section for this XSdata object at the
+ provided temperature.
+
+ Parameters
+ ----------
+ absorption: np.ndarray
+ Absorption Cross Section
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
- self._total = nptotal
+ See also
+ --------
+ openmc.mgxs_library.set_absorption_mgxs()
- @absorption.setter
- def absorption(self, absorption):
+ """
check_type('absorption', absorption, Iterable, expected_iter_type=Real)
- # Convert to a numpy array so we can easily get the shape for
- # checking
- npabsorption = np.asarray(absorption)
- check_value('absorption shape', npabsorption.shape,
- [self.vector_shape])
+ # Convert to a numpy array so we can easily get the shape for checking
+ absorption = np.asarray(absorption)
+ check_value('absorption shape', absorption.shape, [self.vector_shape])
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ i = np.where(self.temperatures == temperature)[0][0]
+ self._absorption[i] = absorption
- self._absorption = npabsorption
+ def set_fission(self, fission, temperature=294.):
+ """This method sets the cross section for this XSdata object at the
+ provided temperature.
+
+ Parameters
+ ----------
+ fission: np.ndarray
+ Fission Cross Section
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
+
+ See also
+ --------
+ openmc.mgxs_library.set_fission_mgxs()
- @fission.setter
- def fission(self, fission):
+ """
check_type('fission', fission, Iterable, expected_iter_type=Real)
- # Convert to a numpy array so we can easily get the shape for
- # checking
- npfission = np.asarray(fission)
- check_value('fission shape', npfission.shape, [self.vector_shape])
+ # Convert to a numpy array so we can easily get the shape for checking
+ fission = np.asarray(fission)
+ check_value('fission shape', fission.shape, [self.vector_shape])
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
- self._fission = npfission
+ i = np.where(self.temperatures == temperature)[0][0]
+ self._fission[i] = fission
- if np.sum(self._fission) > 0.0:
+ if np.sum(fission) > 0.0:
self._fissionable = True
- @kappa_fission.setter
- def kappa_fission(self, kappa_fission):
+ def set_kappa_fission(self, kappa_fission, temperature=294.):
+ """This method sets the cross section for this XSdata object at the
+ provided temperature.
+
+ Parameters
+ ----------
+ kappa_fission: np.ndarray
+ Kappa-Fission Cross Section
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
+
+ See also
+ --------
+ openmc.mgxs_library.set_kappa_fission_mgxs()
+
+ """
check_type('kappa_fission', kappa_fission, Iterable,
expected_iter_type=Real)
- # Convert to a numpy array so we can easily get the shape for
- # checking
- npkappa_fission = np.asarray(kappa_fission)
- check_value('kappa fission shape', npkappa_fission.shape,
+ # Convert to a numpy array so we can easily get the shape for checking
+ kappa_fission = np.asarray(kappa_fission)
+ check_value('kappa fission shape', kappa_fission.shape,
[self.vector_shape])
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
- self._kappa_fission = npkappa_fission
+ i = np.where(self.temperatures == temperature)[0][0]
+ self._kappa_fission[i] = kappa_fission
- if np.sum(self._kappa_fission) > 0.0:
+ if np.sum(kappa_fission) > 0.0:
self._fissionable = True
- @chi.setter
- def chi(self, chi):
+ def set_chi(self, chi, temperature=294.):
+ """This method sets the cross section for this XSdata object at the
+ provided temperature.
+
+ Parameters
+ ----------
+ chi: np.ndarray
+ Fission Spectrum
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
+
+ See also
+ --------
+ openmc.mgxs_library.set_chi_mgxs()
+
+ """
if self.use_chi is not None:
if not self.use_chi:
- msg = 'Providing "chi" when "nu-fission" already provided as a' \
- 'matrix'
+ msg = 'Providing "chi" when "nu-fission" already provided ' \
+ 'as a matrix'
raise ValueError(msg)
check_type('chi', chi, Iterable, expected_iter_type=Real)
- # Convert to a numpy array so we can easily get the shape for
- # checking
- npchi = np.asarray(chi)
+ # Convert to a numpy array so we can easily get the shape for checking
+ chi = np.asarray(chi)
# Check the shape
- if npchi.shape != self.vector_shape:
+ if chi.shape != self.vector_shape:
msg = 'Provided chi iterable does not have the expected shape.'
raise ValueError(msg)
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
- self._chi = npchi
+ i = np.where(self.temperatures == temperature)[0][0]
+ self._chi[i] = chi
if self.use_chi is not None:
self.use_chi = True
- @scatter.setter
- def scatter(self, scatter):
- # Convert to a numpy array so we can easily get the shape for
- # checking
- npscatter = np.asarray(scatter)
- check_iterable_type('scatter', npscatter, Real,
- max_depth=len(npscatter.shape))
- check_value('scatter shape', npscatter.shape, [self.pn_matrix_shape])
-
- self._scatter = npscatter
-
- @multiplicity.setter
- def multiplicity(self, multiplicity):
- # Convert to a numpy array so we can easily get the shape for
- # checking
- npmultiplicity = np.asarray(multiplicity)
- check_iterable_type('multiplicity', npmultiplicity, Real,
- max_depth=len(npmultiplicity.shape))
- check_value('multiplicity shape', npmultiplicity.shape,
+ def set_scatter_matrix(self, scatter, temperature=294.):
+ """This method sets the cross section for this XSdata object at the
+ provided temperature.
+
+ Parameters
+ ----------
+ scatter: np.ndarray
+ Scattering Matrix Cross Section
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
+
+ See also
+ --------
+ openmc.mgxs_library.set_scatter_matrix_mgxs()
+
+ """
+ # Convert to a numpy array so we can easily get the shape for checking
+ scatter = np.asarray(scatter)
+ check_iterable_type('scatter', scatter, Real,
+ max_depth=len(scatter.shape))
+ check_value('scatter shape', scatter.shape, [self.pn_matrix_shape])
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ i = np.where(self.temperatures == temperature)[0][0]
+ self._scatter_matrix[i] = scatter
+
+ def set_multiplicity_matrix(self, multiplicity, temperature=294.):
+ """This method sets the cross section for this XSdata object at the
+ provided temperature.
+
+ Parameters
+ ----------
+ multiplicity: np.ndarray
+ Multiplicity Matrix Cross Section
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
+
+ See also
+ --------
+ openmc.mgxs_library.set_multiplicity_matrix_mgxs()
+
+ """
+ # Convert to a numpy array so we can easily get the shape for checking
+ multiplicity = np.asarray(multiplicity)
+ check_iterable_type('multiplicity', multiplicity, Real,
+ max_depth=len(multiplicity.shape))
+ check_value('multiplicity shape', multiplicity.shape,
[self.matrix_shape])
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ i = np.where(self.temperatures == temperature)[0][0]
+ self._multiplicity_matrix[i] = multiplicity
+
+ def set_nu_fission(self, nu_fission, temperature=294.):
+ """This method sets the cross section for this XSdata object at the
+ provided temperature.
+
+ Parameters
+ ----------
+ nu_fission: np.ndarray
+ Nu-fission Cross Section
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
- self._multiplicity = npmultiplicity
+ See also
+ --------
+ openmc.mgxs_library.set_nu_fission_mgxs()
- @nu_fission.setter
- def nu_fission(self, nu_fission):
+ """
# The NuFissionXS class does not have the capability to produce
# a fission matrix and therefore if this path is pursued, we know
# chi must be used.
@@ -563,33 +613,63 @@ def nu_fission(self, nu_fission):
# chi already has been set. If not, we just check that this is OK
# and set the use_chi flag accordingly
- # Convert to a numpy array so we can easily get the shape for
- # checking
- npnu_fission = np.asarray(nu_fission)
+ # Convert to a numpy array so we can easily get the shape for checking
+ nu_fission = np.asarray(nu_fission)
- check_iterable_type('nu_fission', npnu_fission, Real,
- max_depth=len(npnu_fission.shape))
+ check_iterable_type('nu_fission', nu_fission, Real,
+ max_depth=len(nu_fission.shape))
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
if self.use_chi is not None:
if self.use_chi:
- check_value('nu_fission shape', npnu_fission.shape,
+ check_value('nu_fission shape', nu_fission.shape,
[self.vector_shape])
else:
- check_value('nu_fission shape', npnu_fission.shape,
+ check_value('nu_fission shape', nu_fission.shape,
[self.matrix_shape])
else:
- check_value('nu_fission shape', npnu_fission.shape,
+ check_value('nu_fission shape', nu_fission.shape,
[self.vector_shape, self.matrix_shape])
# Find out if we have a nu-fission matrix or vector
# and set a flag to allow other methods to check this later.
- self.use_chi = (npnu_fission.shape == self.vector_shape)
+ if nu_fission.shape == self.vector_shape:
+ self.use_chi = True
+ else:
+ self.use_chi = False
- self._nu_fission = npnu_fission
- if np.sum(self._nu_fission) > 0.0:
+ i = np.where(self.temperatures == temperature)[0][0]
+ self._nu_fission[i] = nu_fission
+ if np.sum(nu_fission) > 0.0:
self._fissionable = True
- def set_total_mgxs(self, total, nuclide='total', xs_type='macro',
- subdomain='all'):
+ def set_inverse_velocities(self, inv_vel, temperature=294.):
+ """This method sets the inverse velocities for this XSdata object at the
+ provided temperature.
+
+ Parameters
+ ----------
+ inv_vel: np.ndarray
+ Inverse velocities in units of sec/cm.
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
+
+ """
+ check_type('inverse velocities', inv_vel, Iterable,
+ expected_iter_type=Real)
+ # Convert to a numpy array so we can easily get the shape for checking
+ inv_vel = np.asarray(inv_vel)
+ check_value('inverse velocities shape', inv_vel.shape,
+ [self.vector_shape])
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ i = np.where(self.temperatures == temperature)[0][0]
+ self._inverse_velocities[i] = inv_vel
+
+ def set_total_mgxs(self, total, temperature=294., nuclide='total',
+ xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.TotalXS or
openmc.mgxs.TransportXS to be used to set the total cross section
for this XSdata object.
@@ -599,6 +679,9 @@ def set_total_mgxs(self, total, nuclide='total', xs_type='macro',
total: openmc.mgxs.TotalXS or openmc.mgxs.TransportXS
MGXS Object containing the total or transport cross section
for the domain of interest.
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
nuclide : str
Individual nuclide (or 'total' if obtaining material-wise data)
to gather data for. Defaults to 'total'.
@@ -621,16 +704,19 @@ def set_total_mgxs(self, total, nuclide='total', xs_type='macro',
check_value('energy_groups', total.energy_groups, [self.energy_groups])
check_value('domain_type', total.domain_type,
['universe', 'cell', 'material', 'mesh'])
-
- if self.representation is 'isotropic':
- self._total = total.get_xs(nuclides=nuclide, xs_type=xs_type,
- subdomains=subdomain)
- elif self.representation is 'angle':
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ i = np.where(self.temperatures == temperature)[0][0]
+ if self.representation == 'isotropic':
+ self._total[i] = total.get_xs(nuclides=nuclide, xs_type=xs_type,
+ subdomains=subdomain)
+ elif self.representation == 'angle':
msg = 'Angular-Dependent MGXS have not yet been implemented'
raise ValueError(msg)
- def set_absorption_mgxs(self, absorption, nuclide='total',
- xs_type='macro', subdomain=None):
+ def set_absorption_mgxs(self, absorption, temperature=294.,
+ nuclide='total', xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.AbsorptionXS
to be used to set the absorption cross section for this XSdata object.
@@ -639,6 +725,9 @@ def set_absorption_mgxs(self, absorption, nuclide='total',
absorption: openmc.mgxs.AbsorptionXS
MGXS Object containing the absorption cross section
for the domain of interest.
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
nuclide : str
Individual nuclide (or 'total' if obtaining material-wise data)
to gather data for. Defaults to 'total'.
@@ -661,17 +750,20 @@ def set_absorption_mgxs(self, absorption, nuclide='total',
[self.energy_groups])
check_value('domain_type', absorption.domain_type,
['universe', 'cell', 'material', 'mesh'])
-
- if self.representation is 'isotropic':
- self._absorption = absorption.get_xs(nuclides=nuclide,
- xs_type=xs_type,
- subdomains=subdomain)
- elif self.representation is 'angle':
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ i = np.where(self.temperatures == temperature)[0][0]
+ if self.representation == 'isotropic':
+ self._absorption[i] = absorption.get_xs(nuclides=nuclide,
+ xs_type=xs_type,
+ subdomains=subdomain)
+ elif self.representation == 'angle':
msg = 'Angular-Dependent MGXS have not yet been implemented'
raise ValueError(msg)
- def set_fission_mgxs(self, fission, nuclide='total', xs_type='macro',
- subdomain=None):
+ def set_fission_mgxs(self, fission, temperature=294., nuclide='total',
+ xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.FissionXS
to be used to set the fission cross section for this XSdata object.
@@ -680,6 +772,9 @@ def set_fission_mgxs(self, fission, nuclide='total', xs_type='macro',
fission: openmc.mgxs.FissionXS
MGXS Object containing the fission cross section
for the domain of interest.
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
nuclide : str
Individual nuclide (or 'total' if obtaining material-wise data)
to gather data for. Defaults to 'total'.
@@ -702,17 +797,20 @@ def set_fission_mgxs(self, fission, nuclide='total', xs_type='macro',
[self.energy_groups])
check_value('domain_type', fission.domain_type,
['universe', 'cell', 'material', 'mesh'])
-
- if self.representation is 'isotropic':
- self._fission = fission.get_xs(nuclides=nuclide,
- xs_type=xs_type,
- subdomains=subdomain)
- elif self.representation is 'angle':
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ i = np.where(self.temperatures == temperature)[0][0]
+ if self.representation == 'isotropic':
+ self._fission[i] = fission.get_xs(nuclides=nuclide,
+ xs_type=xs_type,
+ subdomains=subdomain)
+ elif self.representation == 'angle':
msg = 'Angular-Dependent MGXS have not yet been implemented'
raise ValueError(msg)
- def set_nu_fission_mgxs(self, nu_fission, nuclide='total',
- xs_type='macro', subdomain=None):
+ def set_nu_fission_mgxs(self, nu_fission, temperature=294.,
+ nuclide='total', xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.NuFissionXS
to be used to set the nu-fission cross section for this XSdata object.
@@ -721,6 +819,9 @@ def set_nu_fission_mgxs(self, nu_fission, nuclide='total',
nu_fission: openmc.mgxs.NuFissionXS
MGXS Object containing the nu-fission cross section
for the domain of interest.
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
nuclide : str
Individual nuclide (or 'total' if obtaining material-wise data)
to gather data for. Defaults to 'total'.
@@ -744,12 +845,15 @@ def set_nu_fission_mgxs(self, nu_fission, nuclide='total',
[self.energy_groups])
check_value('domain_type', nu_fission.domain_type,
['universe', 'cell', 'material', 'mesh'])
-
- if self.representation is 'isotropic':
- self._nu_fission = nu_fission.get_xs(nuclides=nuclide,
- xs_type=xs_type,
- subdomains=subdomain)
- elif self.representation is 'angle':
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ i = np.where(self.temperatures == temperature)[0][0]
+ if self.representation == 'isotropic':
+ self._nu_fission[i] = nu_fission.get_xs(nuclides=nuclide,
+ xs_type=xs_type,
+ subdomains=subdomain)
+ elif self.representation == 'angle':
msg = 'Angular-Dependent MGXS have not yet been implemented'
raise ValueError(msg)
@@ -761,8 +865,9 @@ def set_nu_fission_mgxs(self, nu_fission, nuclide='total',
if np.sum(self._nu_fission) > 0.0:
self._fissionable = True
- def set_kappa_fission_mgxs(self, k_fission, nuclide='total',
- xs_type='macro', subdomain=None):
+ def set_kappa_fission_mgxs(self, k_fission, temperature=294.,
+ nuclide='total', xs_type='macro',
+ subdomain=None):
"""This method allows for an openmc.mgxs.KappaFissionXS
to be used to set the kappa-fission cross section for this XSdata
object.
@@ -772,6 +877,9 @@ def set_kappa_fission_mgxs(self, k_fission, nuclide='total',
kappa_fission: openmc.mgxs.KappaFissionXS
MGXS Object containing the kappa-fission cross section
for the domain of interest.
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
nuclide : str
Individual nuclide (or 'total' if obtaining material-wise data)
to gather data for. Defaults to 'total'.
@@ -794,17 +902,20 @@ def set_kappa_fission_mgxs(self, k_fission, nuclide='total',
[self.energy_groups])
check_value('domain_type', k_fission.domain_type,
['universe', 'cell', 'material', 'mesh'])
-
- if self.representation is 'isotropic':
- self._kappa_fission = k_fission.get_xs(nuclides=nuclide,
- xs_type=xs_type,
- subdomains=subdomain)
- elif self.representation is 'angle':
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ i = np.where(self.temperatures == temperature)[0][0]
+ if self.representation == 'isotropic':
+ self._kappa_fission[i] = k_fission.get_xs(nuclides=nuclide,
+ xs_type=xs_type,
+ subdomains=subdomain)
+ elif self.representation == 'angle':
msg = 'Angular-Dependent MGXS have not yet been implemented'
raise ValueError(msg)
- def set_chi_mgxs(self, chi, nuclide='total', xs_type='macro',
- subdomain=None):
+ def set_chi_mgxs(self, chi, temperature=294., nuclide='total',
+ xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.Chi
to be used to set chi for this XSdata object.
@@ -812,6 +923,9 @@ def set_chi_mgxs(self, chi, nuclide='total', xs_type='macro',
----------
chi: openmc.mgxs.Chi
MGXS Object containing chi for the domain of interest.
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
nuclide : str
Individual nuclide (or 'total' if obtaining material-wise data)
to gather data for. Defaults to 'total'.
@@ -839,19 +953,23 @@ def set_chi_mgxs(self, chi, nuclide='total', xs_type='macro',
check_value('energy_groups', chi.energy_groups, [self.energy_groups])
check_value('domain_type', chi.domain_type,
['universe', 'cell', 'material', 'mesh'])
-
- if self.representation is 'isotropic':
- self._chi = chi.get_xs(nuclides=nuclide,
- xs_type=xs_type, subdomains=subdomain)
- elif self.representation is 'angle':
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ i = np.where(self.temperatures == temperature)[0][0]
+ if self.representation == 'isotropic':
+ self._chi[i] = chi.get_xs(nuclides=nuclide,
+ xs_type=xs_type, subdomains=subdomain)
+ elif self.representation == 'angle':
msg = 'Angular-Dependent MGXS have not yet been implemented'
raise ValueError(msg)
if self.use_chi is not None:
self.use_chi = True
- def set_scatter_mgxs(self, scatter, nuclide='total', xs_type='macro',
- subdomain=None):
+ def set_scatter_matrix_mgxs(self, scatter, temperature=294.,
+ nuclide='total', xs_type='macro',
+ subdomain=None):
"""This method allows for an openmc.mgxs.ScatterMatrixXS
to be used to set the scatter matrix cross section for this XSdata
object. If the XSdata.order attribute has not yet been set, then
@@ -862,6 +980,9 @@ def set_scatter_mgxs(self, scatter, nuclide='total', xs_type='macro',
scatter: openmc.mgxs.ScatterMatrixXS
MGXS Object containing the scatter matrix cross section
for the domain of interest.
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
nuclide : str
Individual nuclide (or 'total' if obtaining material-wise data)
to gather data for. Defaults to 'total'.
@@ -884,8 +1005,10 @@ def set_scatter_mgxs(self, scatter, nuclide='total', xs_type='macro',
[self.energy_groups])
check_value('domain_type', scatter.domain_type,
['universe', 'cell', 'material', 'mesh'])
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
- if self.scatt_type != 'legendre':
+ if self.scatter_format != 'legendre':
msg = 'Anisotropic scattering representations other than ' \
'Legendre expansions have not yet been implemented in ' \
'openmc.mgxs.'
@@ -901,24 +1024,27 @@ def set_scatter_mgxs(self, scatter, nuclide='total', xs_type='macro',
check_value('legendre_order', scatter.legendre_order,
[self.order])
- if self.representation is 'isotropic':
+ i = np.where(self.temperatures == temperature)[0][0]
+ if self.representation == 'isotropic':
# Get the scattering orders in the outermost dimension
- self._scatter = np.zeros((self.num_orders,
- self.energy_groups.num_groups,
- self.energy_groups.num_groups))
+ self._scatter_matrix[i] = np.zeros((self.num_orders,
+ self.energy_groups.num_groups,
+ self.energy_groups.num_groups))
for moment in range(self.num_orders):
- self._scatter[moment, :, :] = \
+ self._scatter_matrix[i][moment, :, :] = \
scatter.get_xs(nuclides=nuclide, xs_type=xs_type,
moment=moment, subdomains=subdomain)
- elif self.representation is 'angle':
+ elif self.representation == 'angle':
msg = 'Angular-Dependent MGXS have not yet been implemented'
raise ValueError(msg)
- def set_multiplicity_mgxs(self, nuscatter, scatter=None, nuclide='total',
- xs_type='macro', subdomain=None):
+ def set_multiplicity_matrix_mgxs(self, nuscatter, scatter=None,
+ temperature=294., nuclide='total',
+ xs_type='macro', subdomain=None):
"""This method allows for either the direct use of only an
- openmc.mgxs.MultiplicityMatrixXS OR an openmc.mgxs.NuScatterMatrixXS and
+ openmc.mgxs.MultiplicityMatrixXS OR
+ an openmc.mgxs.NuScatterMatrixXS and
openmc.mgxs.ScatterMatrixXS to be used to set the scattering
multiplicity for this XSdata object. Multiplicity,
in OpenMC parlance, is a factor used to account for the production
@@ -935,6 +1061,9 @@ def set_multiplicity_mgxs(self, nuscatter, scatter=None, nuclide='total',
scatter: openmc.mgxs.ScatterMatrixXS
MGXS Object containing the scattering matrix cross section
for the domain of interest.
+ temperature : float
+ Temperature (in Kelvin) of the data. Defaults to room temperature
+ (294K).
nuclide : str
Individual nuclide (or 'total' if obtaining material-wise data)
to gather data for. Defaults to 'total'.
@@ -958,6 +1087,9 @@ def set_multiplicity_mgxs(self, nuscatter, scatter=None, nuclide='total',
[self.energy_groups])
check_value('domain_type', nuscatter.domain_type,
['universe', 'cell', 'material', 'mesh'])
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
if scatter is not None:
check_type('scatter', scatter, openmc.mgxs.ScatterMatrixXS)
if isinstance(nuscatter, openmc.mgxs.MultiplicityMatrixXS):
@@ -970,102 +1102,174 @@ def set_multiplicity_mgxs(self, nuscatter, scatter=None, nuclide='total',
check_value('domain_type', scatter.domain_type,
['universe', 'cell', 'material', 'mesh'])
- if self.representation is 'isotropic':
+ i = np.where(self.temperatures == temperature)[0][0]
+ if self.representation == 'isotropic':
nuscatt = nuscatter.get_xs(nuclides=nuclide,
xs_type=xs_type, moment=0,
subdomains=subdomain)
if isinstance(nuscatter, openmc.mgxs.MultiplicityMatrixXS):
- self._multiplicity = nuscatt
+ self._multiplicity_matrix[i] = nuscatt
else:
scatt = scatter.get_xs(nuclides=nuclide,
xs_type=xs_type, moment=0,
subdomains=subdomain)
- self._multiplicity = np.divide(nuscatt, scatt)
- elif self.representation is 'angle':
+ self._multiplicity_matrix[i] = np.divide(nuscatt, scatt)
+ elif self.representation == 'angle':
msg = 'Angular-Dependent MGXS have not yet been implemented'
raise ValueError(msg)
- self._multiplicity = np.nan_to_num(self._multiplicity)
-
- def _get_xsdata_xml(self):
- element = ET.Element('xsdata')
- element.set('name', self._name)
-
- if self._alias is not None:
- subelement = ET.SubElement(element, 'alias')
- subelement.text = self.alias
-
- if self._kT is not None:
- subelement = ET.SubElement(element, 'kT')
- subelement.text = str(self._kT)
-
- if self._awr is not None:
- subelement = ET.SubElement(element, 'awr')
- subelement.text = str(self._awr)
-
- if self._fissionable is not None:
- subelement = ET.SubElement(element, 'fissionable')
- subelement.text = str(self._fissionable)
-
- if self._representation is not None:
- subelement = ET.SubElement(element, 'representation')
- subelement.text = self._representation
-
- if self._representation == 'angle':
- if self._num_azimuthal is not None:
- subelement = ET.SubElement(element, 'num_azimuthal')
- subelement.text = str(self._num_azimuthal)
- if self._num_polar is not None:
- subelement = ET.SubElement(element, 'num_polar')
- subelement.text = str(self._num_polar)
-
- if self._scatt_type is not None:
- subelement = ET.SubElement(element, 'scatt_type')
- subelement.text = self._scatt_type
-
- if self._order is not None:
- subelement = ET.SubElement(element, 'order')
- subelement.text = str(self._order)
-
- if self._tabular_legendre is not None:
- subelement = ET.SubElement(element, 'tabular_legendre')
- subelement.set('enable', str(self._tabular_legendre['enable']))
- subelement.set('num_points',
- str(self._tabular_legendre['num_points']))
-
- if self._total is not None:
- subelement = ET.SubElement(element, 'total')
- subelement.text = ndarray_to_string(self._total)
-
- if self._absorption is not None:
- subelement = ET.SubElement(element, 'absorption')
- subelement.text = ndarray_to_string(self._absorption)
-
- if self._scatter is not None:
- subelement = ET.SubElement(element, 'scatter')
- subelement.text = ndarray_to_string(self._scatter)
-
- if self._multiplicity is not None:
- subelement = ET.SubElement(element, 'multiplicity')
- subelement.text = ndarray_to_string(self._multiplicity)
-
- if self._fissionable:
- if self._fission is not None:
- subelement = ET.SubElement(element, 'fission')
- subelement.text = ndarray_to_string(self._fission)
-
- if self._kappa_fission is not None:
- subelement = ET.SubElement(element, 'k_fission')
- subelement.text = ndarray_to_string(self._kappa_fission)
+ self._multiplicity_matrix[i] = \
+ np.nan_to_num(self._multiplicity_matrix[i])
- if self._nu_fission is not None:
- subelement = ET.SubElement(element, 'nu_fission')
- subelement.text = ndarray_to_string(self._nu_fission)
+ def to_hdf5(self, file):
+ """Write XSdata to an HDF5 file
- if self._chi is not None:
- subelement = ET.SubElement(element, 'chi')
- subelement.text = ndarray_to_string(self._chi)
+ Parameters
+ ----------
+ file : h5py.File
+ HDF5 File (a root Group) to write to
- return element
+ """
+ grp = file.create_group(self.name)
+ if self.atomic_weight_ratio is not None:
+ grp.attrs['atomic_weight_ratio'] = self.atomic_weight_ratio
+ if self.fissionable is not None:
+ grp.attrs['fissionable'] = self.fissionable
+ if self.representation is not None:
+ grp.attrs['representation'] = np.string_(self.representation)
+ if self.representation == 'angle':
+ if self.num_azimuthal is not None:
+ grp.attrs['num_azimuthal'] = self.num_azimuthal
+ if self.num_polar is not None:
+ grp.attrs['num_polar'] = self.num_polar
+ if self.scatter_format is not None:
+ grp.attrs['scatter_format'] = np.string_(self.scatter_format)
+ if self.scatter_shape is not None:
+ grp.attrs['scatter_shape'] = np.string_(self.scatter_shape)
+ if self.order is not None:
+ grp.attrs['order'] = self.order
+
+ ktg = grp.create_group('kTs')
+ for temperature in self.temperatures:
+ temp_label = str(int(np.round(temperature))) + "K"
+ kT = temperature * openmc.data.K_BOLTZMANN
+ ktg.create_dataset(temp_label, data=kT)
+
+ # Create the temperature datasets
+ for i, temperature in enumerate(self.temperatures):
+ xs_grp = grp.create_group(str(int(np.round(temperature))) + "K")
+ if self._total[i] is None:
+ raise ValueError('total data must be provided when writing '
+ 'the HDF5 library')
+ xs_grp.create_dataset("total", data=self._total[i])
+ if self._absorption[i] is None:
+ raise ValueError('absorption data must be provided when '
+ 'writing the HDF5 library')
+ xs_grp.create_dataset("absorption", data=self._absorption[i])
+ if self.fissionable:
+ if self._fission[i] is not None:
+ xs_grp.create_dataset("fission", data=self._fission[i])
+ if self._kappa_fission[i] is not None:
+ xs_grp.create_dataset("kappa-fission",
+ data=self._kappa_fission[i])
+ if self._chi[i] is not None:
+ xs_grp.create_dataset("chi", data=self._chi[i])
+ if self._nu_fission[i] is None:
+ raise ValueError('nu-fission data must be provided when '
+ 'writing the HDF5 library')
+ xs_grp.create_dataset("nu-fission", data=self._nu_fission[i])
+
+ if self._scatter_matrix[i] is None:
+ raise ValueError('Scatter matrix must be provided when '
+ 'writing the HDF5 library')
+
+ # Get the sparse scattering data to print to the library
+ G = self.energy_groups.num_groups
+ if self.representation == 'isotropic':
+ g_out_bounds = np.zeros((G, 2), dtype=np.int)
+ for g_in in range(G):
+ nz = np.nonzero(self._scatter_matrix[i][0, g_in, :])
+ g_out_bounds[g_in, 0] = nz[0][0]
+ g_out_bounds[g_in, 1] = nz[0][-1]
+ # Now create the flattened scatter matrix array
+ matrix = self._scatter_matrix[i]
+ flat_scatt = []
+ for g_in in range(G):
+ for g_out in range(g_out_bounds[g_in, 0],
+ g_out_bounds[g_in, 1] + 1):
+ for l in range(len(matrix[:, g_in, g_out])):
+ flat_scatt.append(matrix[l, g_in, g_out])
+ # And write it.
+ scatt_grp = xs_grp.create_group('scatter_data')
+ scatt_grp.create_dataset("scatter_matrix",
+ data=np.array(flat_scatt))
+ # Repeat for multiplicity
+ if self._multiplicity_matrix[i] is not None:
+ # Now create the flattened scatter matrix array
+ matrix = self._multiplicity_matrix[i][:, :]
+ flat_mult = []
+ for g_in in range(G):
+ for g_out in range(g_out_bounds[g_in, 0],
+ g_out_bounds[g_in, 1] + 1):
+ flat_mult.append(matrix[g_in, g_out])
+ scatt_grp.create_dataset("multiplicity_matrix",
+ data=np.array(flat_mult))
+
+ # And finally, adjust g_out_bounds for 1-based group counting
+ # and write it.
+ g_out_bounds[:, :] += 1
+ scatt_grp.create_dataset("g_min", data=g_out_bounds[:, 0])
+ scatt_grp.create_dataset("g_max", data=g_out_bounds[:, 1])
+
+ elif self.representation == 'angle':
+ Np = self.num_polar
+ Na = self.num_azimuthal
+ g_out_bounds = np.zeros((Np, Na, G, 2), dtype=np.int)
+ for p in range(Np):
+ for a in range(Na):
+ for g_in in range(G):
+ matrix = self._scatter_matrix[i][p, a, 0, g_in, :]
+ nz = np.nonzero(matrix)
+ g_out_bounds[p, a, g_in, 0] = nz[0][0]
+ g_out_bounds[p, a, g_in, 1] = nz[0][-1]
+ # Now create the flattened scatter matrix array
+ flat_scatt = []
+ for p in range(Np):
+ for a in range(Na):
+ matrix = self._scatter_matrix[i][p, a, :, :, :]
+ for g_in in range(G):
+ for g_out in range(g_out_bounds[p, a, g_in, 0],
+ g_out_bounds[p, a, g_in, 1] + 1):
+ for l in range(len(matrix[:, g_in, g_out])):
+ flat_scatt.append(matrix[l, g_in, g_out])
+ # And write it.
+ scatt_grp = xs_grp.create_group('scatter_data')
+ scatt_grp.create_dataset("scatter_matrix",
+ data=np.array(flat_scatt))
+ # Repeat for multiplicity
+ if self._multiplicity_matrix[i] is not None:
+ # Now create the flattened scatter matrix array
+ flat_mult = []
+ for p in range(Np):
+ for a in range(Na):
+ matrix = self._multiplicity_matrix[i][p, a, :, :]
+ for g_in in range(G):
+ for g_out in range(g_out_bounds[p, a, g_in, 0],
+ g_out_bounds[p, a, g_in, 1] + 1):
+ flat_mult.append(matrix[g_in, g_out])
+ # And write it.
+ scatt_grp.create_dataset("multiplicity_matrix",
+ data=np.array(flat_mult))
+
+ # And finally, adjust g_out_bounds for 1-based group counting
+ # and write it.
+ g_out_bounds[:, :, :, :] += 1
+ scatt_grp.create_dataset("g_min", data=g_out_bounds[:, :, :, 0])
+ scatt_grp.create_dataset("g_max", data=g_out_bounds[:, :, :, 1])
+
+ # Add the kinetics data
+ if self._inverse_velocities[i] is not None:
+ xs_grp.create_dataset("inverse_velocities",
+ data=self._inverse_velocities[i])
class MGXSLibrary(object):
@@ -1073,41 +1277,35 @@ class MGXSLibrary(object):
Corresponds directly to the MG version of the cross_sections.xml input
file.
+ Parameters
+ ----------
+ energy_groups : openmc.mgxs.EnergyGroups
+ Energy group structure
+
Attributes
----------
energy_groups : openmc.mgxs.EnergyGroups
Energy group structure.
- inverse_velocities : Iterable of Real
- Inverse of velocities, units of sec/cm
xsdatas : Iterable of openmc.XSdata
Iterable of multi-Group cross section data objects
"""
def __init__(self, energy_groups):
+ self.energy_groups = energy_groups
self._xsdatas = []
- self._energy_groups = energy_groups
- self._inverse_velocities = None
- self._cross_sections_file = ET.Element('cross_sections')
-
- @property
- def inverse_velocities(self):
- return self._inverse_velocities
@property
def energy_groups(self):
return self._energy_groups
+ @property
+ def temperatures(self):
+ return self._temperatures
+
@property
def xsdatas(self):
return self._xsdatas
- @inverse_velocities.setter
- def inverse_velocities(self, inverse_velocities):
- check_type('inverse_velocities', inverse_velocities, Iterable, Real)
- check_greater_than('number of inverse_velocities',
- len(inverse_velocities), 0.0)
- self._inverse_velocities = np.array(inverse_velocities)
-
@energy_groups.setter
def energy_groups(self, energy_groups):
check_type('energy groups', energy_groups, openmc.mgxs.EnergyGroups)
@@ -1163,52 +1361,24 @@ def remove_xsdata(self, xsdata):
self._xsdatas.remove(xsdata)
- def _create_groups_subelement(self):
- if self._energy_groups is not None:
- element = ET.SubElement(self._cross_sections_file, 'groups')
- element.text = str(self._energy_groups.num_groups)
-
- def _create_group_structure_subelement(self):
- if self._energy_groups is not None:
- element = ET.SubElement(self._cross_sections_file,
- 'group_structure')
- element.text = ' '.join(map(str, self._energy_groups.group_edges))
-
- def _create_inverse_velocities_subelement(self):
- if self._inverse_velocities is not None:
- element = ET.SubElement(self._cross_sections_file,
- 'inverse_velocities')
- element.text = ' '.join(map(str, self._inverse_velocities))
-
- def _create_xsdata_subelements(self):
- for xsdata in self._xsdatas:
- xml_element = xsdata._get_xsdata_xml()
- self._cross_sections_file.append(xml_element)
-
- def export_to_xml(self, filename='mgxs.xml'):
- """Create an mgxs.xml file that can be used for a
- simulation.
+ def export_to_hdf5(self, filename='mgxs.h5'):
+ """Create an hdf5 file that can be used for a simulation.
Parameters
----------
- filename : str, optional
- filename of file, default is mgxs.xml
+ filename : str
+ Filename of file, default is mgxs.h5.
"""
- # Reset xml element tree
- self._cross_sections_file.clear()
+ check_type('filename', filename, basestring)
- self._create_groups_subelement()
- self._create_group_structure_subelement()
- self._create_inverse_velocities_subelement()
- self._create_xsdata_subelements()
+ # Create and write to the HDF5 file
+ file = h5py.File(filename, "w")
+ file.attrs['groups'] = self.energy_groups.num_groups
+ file.attrs['group structure'] = self.energy_groups.group_edges
- # Clean the indentation in the file to be user-readable
- sort_xml_elements(self._cross_sections_file)
- clean_xml_indentation(self._cross_sections_file)
+ for xsdata in self._xsdatas:
+ xsdata.to_hdf5(file)
- # Write the XML Tree to the xsdatas.xml file
- tree = ET.ElementTree(self._cross_sections_file)
- tree.write(filename, xml_declaration=True,
- encoding='utf-8', method='xml')
+ file.close()
diff --git a/openmc/settings.py b/openmc/settings.py
--- a/openmc/settings.py
+++ b/openmc/settings.py
@@ -104,6 +104,13 @@ class Settings(object):
Coordinates of the lower-left point of the Shannon entropy mesh
entropy_upper_right : tuple or list
Coordinates of the upper-right point of the Shannon entropy mesh
+ tabular_legendre : dict
+ Determines if a multi-group scattering moment kernel expanded via
+ Legendre polynomials is to be converted to a tabular distribution or
+ not. Accepted keys are 'enable' and 'num_points'. The value for
+ 'enable' is a bool stating whether the conversion to tabular is
+ performed; the value for 'num_points' sets the number of points to use
+ in the tabular distribution, should 'enable' be True.
temperature : dict
Defines a default temperature and method for treating intermediate
temperatures at which nuclear data doesn't exist. Accepted keys are
@@ -206,6 +213,8 @@ def __init__(self):
self._trace = None
self._track = None
+ self._tabular_legendre = {}
+
self._temperature = {}
# Cutoff subelement
@@ -370,6 +379,10 @@ def no_reduce(self):
def verbosity(self):
return self._verbosity
+ @property
+ def tabular_legendre(self):
+ return self._tabular_legendre
+
@property
def temperature(self):
return self._temperature
@@ -687,6 +700,19 @@ def no_reduce(self, no_reduce):
cv.check_type('no reduction option', no_reduce, bool)
self._no_reduce = no_reduce
+ @tabular_legendre.setter
+ def tabular_legendre(self, tabular_legendre):
+ cv.check_type('tabular_legendre settings', tabular_legendre, Mapping)
+ for key, value in tabular_legendre.items():
+ cv.check_value('tabular_legendre key', key,
+ ['enable', 'num_points'])
+ if key == 'enable':
+ cv.check_type('enable tabular_legendre', value, bool)
+ elif key == 'num_points':
+ cv.check_type('num_points tabular_legendre', value, Integral)
+ cv.check_greater_than('num_points tabular_legendre', value, 0)
+ self._tabular_legendre = tabular_legendre
+
@temperature.setter
def temperature(self, temperature):
cv.check_type('temperature settings', temperature, Mapping)
@@ -1081,6 +1107,15 @@ def _create_no_reduce_subelement(self):
element = ET.SubElement(self._settings_file, "no_reduce")
element.text = str(self._no_reduce).lower()
+ def _create_tabular_legendre_subelements(self):
+ if self.tabular_legendre:
+ element = ET.SubElement(self._settings_file, "tabular_legendre")
+ subelement = ET.SubElement(element, "enable")
+ subelement.text = str(self._tabular_legendre['enable']).lower()
+ if 'num_points' in self._tabular_legendre:
+ subelement = ET.SubElement(element, "num_points")
+ subelement.text = str(self._tabular_legendre['num_points'])
+
def _create_temperature_subelements(self):
if self.temperature:
for key, value in sorted(self.temperature.items()):
@@ -1192,6 +1227,7 @@ def export_to_xml(self, path='settings.xml'):
self._create_no_reduce_subelement()
self._create_threads_subelement()
self._create_verbosity_subelement()
+ self._create_tabular_legendre_subelements()
self._create_temperature_subelements()
self._create_trace_subelement()
self._create_track_subelement()
| diff --git a/tests/1d_mgxs.h5 b/tests/1d_mgxs.h5
new file mode 100644
Binary files /dev/null and b/tests/1d_mgxs.h5 differ
diff --git a/tests/1d_mgxs.xml b/tests/1d_mgxs.xml
deleted file mode 100644
--- a/tests/1d_mgxs.xml
+++ /dev/null
@@ -1,9859 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<library>
- <groups> 1 </groups>
- <group_structure> 0.0000000E+00 2.0000000E+01 </group_structure>
-
- <xsdata>
- <name> uo2_iso </name>
- <alias> uo2_iso </alias>
- <kT> 2.5300000E-08 </kT>
- <order> 5 </order>
- <fissionable> true </fissionable>
- <representation> isotropic </representation>
- <total>
- 4.1022364E-01
- </total>
- <absorption>
- 3.4687432E-02
- </absorption>
- <nu_fission>
- 4.9631431E-02
- </nu_fission>
- <chi>
- 1.0000000E+00
- </chi>
- <fission>
- 2.0019027E-02
- </fission>
- <scatter>
- 3.7564339E-01
-
- 4.4983802E-02
-
- 2.2781624E-02
-
- 1.1639469E-02
-
- 7.1975833E-03
-
- 3.5887673E-03
- </scatter>
- <multiplicity>
- 1.0002764E+00
- </multiplicity>
- </xsdata>
-
- <xsdata>
- <name> clad_iso </name>
- <alias> clad_iso </alias>
- <kT> 2.5300000E-08 </kT>
- <order> 5 </order>
- <fissionable> false </fissionable>
- <representation> isotropic </representation>
- <total>
- 3.0736836E-01
- </total>
- <absorption>
- 1.7027907E-03
- </absorption>
- <scatter>
- 3.0566993E-01
-
- 4.1625057E-02
-
- 2.2287832E-02
-
- 3.9580806E-03
-
- 3.3420849E-03
-
- 1.3963828E-03
- </scatter>
- <multiplicity>
- 1.0000372E+00
- </multiplicity>
- </xsdata>
-
- <xsdata>
- <name> lwtr_iso </name>
- <alias> lwtr_iso </alias>
- <kT> 2.5300000E-08 </kT>
- <order> 5 </order>
- <fissionable> false </fissionable>
- <representation> isotropic </representation>
- <total>
- 9.6904862E-01
- </total>
- <absorption>
- 1.0230968E-02
- </absorption>
- <scatter>
- 9.5881780E-01
-
- 3.9202760E-01
-
- 1.2865356E-01
-
- 9.5231115E-03
-
- -1.9647208E-02
-
- 5.9291968E-04
- </scatter>
- <multiplicity>
- 1.0000000E+00
- </multiplicity>
- </xsdata>
-
- <xsdata>
- <name> uo2_iso_mu </name>
- <alias> uo2_iso_mu </alias>
- <kT> 2.5300000E-08 </kT>
- <order> 32 </order>
- <fissionable> true </fissionable>
- <representation> isotropic </representation>
- <scatt_type> histogram </scatt_type>
- <total>
- 4.1022364E-01
- </total>
- <absorption>
- 3.4687432E-02
- </absorption>
- <nu_fission>
- 4.9631431E-02
- </nu_fission>
- <chi>
- 1.0000000E+00
- </chi>
- <fission>
- 2.0019027E-02
- </fission>
- <scatter>
- 9.7621928E-03
-
- 9.6669975E-03
-
- 9.6217012E-03
-
- 9.6029285E-03
-
- 9.6155223E-03
-
- 9.6417022E-03
-
- 9.6845888E-03
-
- 9.7355785E-03
-
- 9.7971852E-03
-
- 9.8708684E-03
-
- 9.9451996E-03
-
- 1.0026273E-02
-
- 1.0121536E-02
-
- 1.0227606E-02
-
- 1.0340467E-02
-
- 1.0461281E-02
-
- 1.0600371E-02
-
- 1.0742182E-02
-
- 1.0892295E-02
-
- 1.1062409E-02
-
- 1.1236639E-02
-
- 1.1440302E-02
-
- 1.1662283E-02
-
- 1.1931512E-02
-
- 1.2259589E-02
-
- 1.2696194E-02
-
- 1.3272953E-02
-
- 1.4078939E-02
-
- 1.5238289E-02
-
- 1.6956791E-02
-
- 1.9602217E-02
-
- 2.3848802E-02
- </scatter>
- <multiplicity>
- 1.0002764E+00
- </multiplicity>
- </xsdata>
-
- <xsdata>
- <name> clad_iso_mu </name>
- <alias> clad_iso_mu </alias>
- <kT> 2.5300000E-08 </kT>
- <order> 32 </order>
- <fissionable> false </fissionable>
- <representation> isotropic </representation>
- <scatt_type> histogram </scatt_type>
- <total>
- 3.0736836E-01
- </total>
- <absorption>
- 1.7027907E-03
- </absorption>
- <scatter>
- 8.7275040E-03
-
- 8.3252599E-03
-
- 8.0120655E-03
-
- 7.7711039E-03
-
- 7.5947251E-03
-
- 7.4705350E-03
-
- 7.3804037E-03
-
- 7.3241515E-03
-
- 7.3010244E-03
-
- 7.3107188E-03
-
- 7.3487081E-03
-
- 7.4144814E-03
-
- 7.5104992E-03
-
- 7.6438156E-03
-
- 7.7974114E-03
-
- 7.9812213E-03
-
- 8.1816102E-03
-
- 8.4284406E-03
-
- 8.6892059E-03
-
- 8.9675370E-03
-
- 9.2626673E-03
-
- 9.6121293E-03
-
- 9.9669464E-03
-
- 1.0354054E-02
-
- 1.0794903E-02
-
- 1.1296566E-02
-
- 1.1883978E-02
-
- 1.2592532E-02
-
- 1.3494682E-02
-
- 1.4666635E-02
-
- 1.6229823E-02
-
- 1.8334594E-02
- </scatter>
- <multiplicity>
- 1.0000372E+00
- </multiplicity>
- </xsdata>
-
- <xsdata>
- <name> lwtr_iso_mu </name>
- <alias> lwtr_iso_mu </alias>
- <kT> 2.5300000E-08 </kT>
- <order> 32 </order>
- <fissionable> false </fissionable>
- <representation> isotropic </representation>
- <scatt_type> histogram </scatt_type>
- <total>
- 9.6904862E-01
- </total>
- <absorption>
- 1.0230968E-02
- </absorption>
- <scatter>
- 5.8755233E-03
-
- 1.0934725E-02
-
- 1.1142414E-02
-
- 1.0437139E-02
-
- 1.0756915E-02
-
- 1.0623054E-02
-
- 1.1295335E-02
-
- 1.1326212E-02
-
- 1.1795885E-02
-
- 1.2179916E-02
-
- 1.2528003E-02
-
- 1.3121696E-02
-
- 1.3563685E-02
-
- 1.4242846E-02
-
- 1.4567732E-02
-
- 1.5913317E-02
-
- 1.6851680E-02
-
- 2.0792196E-02
-
- 2.4129531E-02
-
- 2.8258248E-02
-
- 3.2040957E-02
-
- 3.6266761E-02
-
- 4.0455247E-02
-
- 4.4731350E-02
-
- 4.8820583E-02
-
- 5.3746086E-02
-
- 5.7743648E-02
-
- 6.3513540E-02
-
- 6.7353451E-02
-
- 7.2430683E-02
-
- 8.0723820E-02
-
- 8.0655621E-02
- </scatter>
- <multiplicity>
- 1.0000000E+00
- </multiplicity>
- </xsdata>
-
- <xsdata>
- <name> uo2_ang </name>
- <alias> uo2_ang </alias>
- <kT> 2.5300000E-08 </kT>
- <order> 5 </order>
- <fissionable> true </fissionable>
- <num_polar> 32 </num_polar>
- <num_azimuthal> 1 </num_azimuthal>
- <representation> angle </representation>
- <total>
- 4.0734790E-01
-
- 4.0709470E-01
-
- 4.0665280E-01
-
- 4.0605122E-01
-
- 4.0509226E-01
-
- 4.0399893E-01
-
- 4.0264927E-01
-
- 4.0112684E-01
-
- 3.9937450E-01
-
- 3.9743081E-01
-
- 3.9533879E-01
-
- 3.9307550E-01
-
- 3.9084961E-01
-
- 3.8878017E-01
-
- 3.8751931E-01
-
- 3.8693825E-01
-
- 3.9039929E-01
-
- 4.0037023E-01
-
- 4.1057791E-01
-
- 4.1924835E-01
-
- 4.2629128E-01
-
- 4.3202621E-01
-
- 4.3673213E-01
-
- 4.4062993E-01
-
- 4.4385222E-01
-
- 4.4647166E-01
-
- 4.4861335E-01
-
- 4.5026817E-01
-
- 4.5165329E-01
-
- 4.5255720E-01
-
- 4.5310208E-01
-
- 4.5337269E-01
- </total>
- <absorption>
- 3.1599020E-02
-
- 3.1371085E-02
-
- 3.1023091E-02
-
- 3.0539250E-02
-
- 2.9839460E-02
-
- 2.9013479E-02
-
- 2.8058288E-02
-
- 2.7047229E-02
-
- 2.5977776E-02
-
- 2.4952391E-02
-
- 2.4009896E-02
-
- 2.3244570E-02
-
- 2.2725200E-02
-
- 2.2489873E-02
-
- 2.2624168E-02
-
- 2.3059735E-02
-
- 2.4782557E-02
-
- 2.8553081E-02
-
- 3.3194318E-02
-
- 3.8038660E-02
-
- 4.2666012E-02
-
- 4.6923885E-02
-
- 5.0708283E-02
-
- 5.3996846E-02
-
- 5.6845491E-02
-
- 5.9213445E-02
-
- 6.1182604E-02
-
- 6.2742563E-02
-
- 6.3985293E-02
-
- 6.4852148E-02
-
- 6.5364227E-02
-
- 6.5703785E-02
- </absorption>
- <nu_fission>
- 4.5146530E-02
-
- 4.4766687E-02
-
- 4.4155441E-02
-
- 4.3323960E-02
-
- 4.2141314E-02
-
- 4.0739637E-02
-
- 3.9143652E-02
-
- 3.7465300E-02
-
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-
- 7.3188187E-02
-
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-
- 8.7933862E-02
-
- 8.7463314E-02
-
-
-
- 6.3504172E-03
-
- 1.2150642E-02
-
- 1.2387727E-02
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- 1.1620660E-02
-
- 1.2007755E-02
-
- 1.1841239E-02
-
- 1.2616226E-02
-
- 1.2659354E-02
-
- 1.3210608E-02
-
- 1.3647237E-02
-
- 1.4056090E-02
-
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-
- 1.5248667E-02
-
- 1.6022604E-02
-
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-
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-
- 1.8865800E-02
-
- 2.2962104E-02
-
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-
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-
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-
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-
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-
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-
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-
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-
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-
-
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-
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-
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-
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-
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-
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-
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- </scatter>
- <multiplicity>
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-
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-
-
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-
-
- 1.0000000E+00
-
-
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-
-
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-
-
- 1.0000000E+00
-
-
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-
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-
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- </multiplicity>
- </xsdata>
-
-
-</library>
\ No newline at end of file
diff --git a/tests/input_set.py b/tests/input_set.py
--- a/tests/input_set.py
+++ b/tests/input_set.py
@@ -1,8 +1,9 @@
+import numpy as np
+
import openmc
from openmc.source import Source
from openmc.stats import Box
-import numpy as np
class InputSet(object):
def __init__(self):
@@ -728,60 +729,59 @@ def build_defualt_plots(self):
class MGInputSet(InputSet):
- def build_default_materials_and_geometry(self):
+ def build_default_materials_and_geometry(self, reps=None, as_macro=True):
# Define materials needed for 1D/1G slab problem
- uo2_data = openmc.Macroscopic('uo2_iso')
- uo2 = openmc.Material(name='UO2', material_id=1)
- uo2.set_density('macro', 1.0)
- uo2.add_macroscopic(uo2_data)
-
- clad_data = openmc.Macroscopic('clad_ang_mu')
- clad = openmc.Material(name='Clad', material_id=2)
- clad.set_density('macro', 1.0)
- clad.add_macroscopic(clad_data)
-
- water_data = openmc.Macroscopic('lwtr_iso_mu')
- water = openmc.Material(name='LWTR', material_id=3)
- water.set_density('macro', 1.0)
- water.add_macroscopic(water_data)
-
- # Define the materials file.
- self.materials += (uo2, clad, water)
+ mat_names = ['uo2', 'clad', 'lwtr']
+ mgxs_reps = ['ang', 'ang_mu', 'iso', 'iso_mu']
+
+ if reps is None:
+ reps = mgxs_reps
+
+ xs = []
+ mats = []
+ i = 0
+ for mat in mat_names:
+ for rep in reps:
+ i += 1
+ if as_macro:
+ xs.append(openmc.Macroscopic(mat + '_' + rep))
+ mats.append(openmc.Material(name=str(i)))
+ mats[-1].set_density('macro', 1.)
+ mats[-1].add_macroscopic(xs[-1])
+ else:
+ xs.append(openmc.Nuclide(mat + '_' + rep))
+ mats.append(openmc.Material(name=str(i)))
+ mats[-1].set_density('atom/b-cm', 1.)
+ mats[-1].add_nuclide(xs[-1].name, 1.0, 'ao')
+
+ # Define the materials file
+ self.xs_data = xs
+ self.materials += mats
# Define surfaces.
-
# Assembly/Problem Boundary
- left = openmc.XPlane(x0=0.0, surface_id=200,
- boundary_type='reflective')
- right = openmc.XPlane(x0=10.0, surface_id=201,
- boundary_type='reflective')
- bottom = openmc.YPlane(y0=0.0, surface_id=300,
- boundary_type='reflective')
- top = openmc.YPlane(y0=10.0, surface_id=301,
- boundary_type='reflective')
-
- down = openmc.ZPlane(z0=0.0, surface_id=0,
- boundary_type='reflective')
- fuel_clad_intfc = openmc.ZPlane(z0=2.0, surface_id=1)
- clad_lwtr_intfc = openmc.ZPlane(z0=2.4, surface_id=2)
- up = openmc.ZPlane(z0=5.0, surface_id=3,
- boundary_type='reflective')
-
- # Define cells
- c1 = openmc.Cell(cell_id=1)
- c1.region = +left & -right & +bottom & -top & +down & -fuel_clad_intfc
- c1.fill = uo2
- c2 = openmc.Cell(cell_id=2)
- c2.region = +left & -right & +bottom & -top & +fuel_clad_intfc & -clad_lwtr_intfc
- c2.fill = clad
- c3 = openmc.Cell(cell_id=3)
- c3.region = +left & -right & +bottom & -top & +clad_lwtr_intfc & -up
- c3.fill = water
+ left = openmc.XPlane(x0=0.0, boundary_type='reflective')
+ right = openmc.XPlane(x0=10.0, boundary_type='reflective')
+ bottom = openmc.YPlane(y0=0.0, boundary_type='reflective')
+ top = openmc.YPlane(y0=10.0, boundary_type='reflective')
+ # for each material add a plane
+ planes = [openmc.ZPlane(z0=0.0, boundary_type='reflective')]
+ dz = round(5. / float(len(mats)), 4)
+ for i in range(len(mats) - 1):
+ planes.append(openmc.ZPlane(z0=dz * float(i + 1)))
+ planes.append(openmc.ZPlane(z0=5.0, boundary_type='reflective'))
+
+ # Define cells for each material
+ cells = []
+ xy = +left & -right & +bottom & -top
+ for i, mat in enumerate(mats):
+ cells.append(openmc.Cell())
+ cells[-1].region = xy & +planes[i] & -planes[i + 1]
+ cells[-1].fill = mat
# Define root universe.
root = openmc.Universe(universe_id=0, name='root universe')
-
- root.add_cells((c1, c2, c3))
+ root.add_cells(cells)
# Assign root universe to geometry
self.geometry.root_universe = root
@@ -791,9 +791,9 @@ def build_default_settings(self):
self.settings.inactive = 5
self.settings.particles = 100
self.settings.source = Source(space=Box([0.0, 0.0, 0.0],
- [10.0, 10.0, 2.0]))
+ [10.0, 10.0, 5.]))
self.settings.energy_mode = "multi-group"
- self.settings.cross_sections = "../1d_mgxs.xml"
+ self.settings.cross_sections = "../1d_mgxs.h5"
def build_defualt_plots(self):
plot = openmc.Plot()
diff --git a/tests/run_tests.py b/tests/run_tests.py
--- a/tests/run_tests.py
+++ b/tests/run_tests.py
@@ -117,7 +117,7 @@ def cleanup(path):
for dirpath, dirnames, filenames in os.walk(path):
for fname in filenames:
for ext in ['.h5', '.ppm', '.voxel']:
- if fname.endswith(ext):
+ if fname.endswith(ext) and fname != '1d_mgxs.h5':
os.remove(os.path.join(dirpath, fname))
diff --git a/tests/test_mg_basic/inputs_true.dat b/tests/test_mg_basic/inputs_true.dat
--- a/tests/test_mg_basic/inputs_true.dat
+++ b/tests/test_mg_basic/inputs_true.dat
@@ -1 +1 @@
-e843dbee8b989142d68e78f7a3e83309a9982c0127974ba4b6a58c823ce298e8fffc8828b48aa696f045818a2a80ef4003f5a191f33aacef7d7dd72c950855a6
\ No newline at end of file
+115218221500e60ea43145875324a9a6800366fcc97357ef4cd8182f9253e114cbe1c7481dd3bdd8d7dce5983e2cb757ae0a2e05ede236d94cba7909703ba7f7
\ No newline at end of file
diff --git a/tests/test_mg_basic/results_true.dat b/tests/test_mg_basic/results_true.dat
--- a/tests/test_mg_basic/results_true.dat
+++ b/tests/test_mg_basic/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.047136E+00 2.765964E-02
+1.160653E+00 6.227102E-02
diff --git a/tests/test_mg_max_order/inputs_true.dat b/tests/test_mg_max_order/inputs_true.dat
--- a/tests/test_mg_max_order/inputs_true.dat
+++ b/tests/test_mg_max_order/inputs_true.dat
@@ -1 +1 @@
-7d508b1f3a2661566b8e8cb76fee61aecb96e8b60d633b06f13c4600bd854ea3366cdebd033c0a71ffb8adb90a9aeb64fe5ac0ef3235260921f5689c93e54305
\ No newline at end of file
+139d760cd83eab001ed3fd52d7146fb5f30b7021b26ada6a1e425f5446185ac6fa61ac2ac58aa9e895981e10540160b7ae7428c833024679ef1ca762715e2d51
\ No newline at end of file
diff --git a/tests/test_mg_max_order/results_true.dat b/tests/test_mg_max_order/results_true.dat
--- a/tests/test_mg_max_order/results_true.dat
+++ b/tests/test_mg_max_order/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.102093E+00 4.962190E-02
+1.098323E+00 1.979833E-02
diff --git a/tests/test_mg_max_order/test_mg_max_order.py b/tests/test_mg_max_order/test_mg_max_order.py
--- a/tests/test_mg_max_order/test_mg_max_order.py
+++ b/tests/test_mg_max_order/test_mg_max_order.py
@@ -2,83 +2,26 @@
import os
import sys
+
sys.path.insert(0, os.pardir)
-from testing_harness import TestHarness, PyAPITestHarness
+from testing_harness import PyAPITestHarness
from input_set import MGInputSet
-import openmc
-
-class MGNuclideInputSet(MGInputSet):
- def build_default_materials_and_geometry(self):
- # Define materials needed for 1D/1G slab problem
- uo2_data = openmc.Macroscopic('uo2_iso')
- uo2 = openmc.Material(name='UO2', material_id=1)
- uo2.set_density('macro', 1.0)
- uo2.add_macroscopic(uo2_data)
-
- clad_data = openmc.Macroscopic('clad_iso')
- clad = openmc.Material(name='Clad', material_id=2)
- clad.set_density('macro', 1.0)
- clad.add_macroscopic(clad_data)
-
- water_data = openmc.Macroscopic('lwtr_iso')
- water = openmc.Material(name='LWTR', material_id=3)
- water.set_density('macro', 1.0)
- water.add_macroscopic(water_data)
-
- # Define the materials file.
- self.materials += (uo2, clad, water)
-
- # Define surfaces.
-
- # Assembly/Problem Boundary
- left = openmc.XPlane(x0=0.0, surface_id=200,
- boundary_type='reflective')
- right = openmc.XPlane(x0=10.0, surface_id=201,
- boundary_type='reflective')
- bottom = openmc.YPlane(y0=0.0, surface_id=300,
- boundary_type='reflective')
- top = openmc.YPlane(y0=10.0, surface_id=301,
- boundary_type='reflective')
- down = openmc.ZPlane(z0=0.0, surface_id=0,
- boundary_type='reflective')
- fuel_clad_intfc = openmc.ZPlane(z0=2.0, surface_id=1)
- clad_lwtr_intfc = openmc.ZPlane(z0=2.4, surface_id=2)
- up = openmc.ZPlane(z0=5.0, surface_id=3,
- boundary_type='reflective')
-
- # Define cells
- c1 = openmc.Cell(cell_id=1)
- c1.region = +left & -right & +bottom & -top & +down & -fuel_clad_intfc
- c1.fill = uo2
- c2 = openmc.Cell(cell_id=2)
- c2.region = +left & -right & +bottom & -top & +fuel_clad_intfc & -clad_lwtr_intfc
- c2.fill = clad
- c3 = openmc.Cell(cell_id=3)
- c3.region = +left & -right & +bottom & -top & +clad_lwtr_intfc & -up
- c3.fill = water
-
- # Define root universe.
- root = openmc.Universe(universe_id=0, name='root universe')
-
- root.add_cells((c1,c2,c3))
-
- # Define the geometry file.
- geometry = openmc.Geometry()
- geometry.root_universe = root
-
- self.geometry = geometry
class MGMaxOrderTestHarness(PyAPITestHarness):
def __init__(self, statepoint_name, tallies_present, mg=False):
PyAPITestHarness.__init__(self, statepoint_name, tallies_present)
- self._input_set = MGNuclideInputSet()
+ self._input_set = MGInputSet()
def _build_inputs(self):
+ """Write input XML files."""
+ reps = ['iso']
+ self._input_set.build_default_materials_and_geometry(reps=reps)
+ self._input_set.build_default_settings()
# Set P1 scattering
self._input_set.settings.max_order = 1
- # Call standard input build
- super(MGMaxOrderTestHarness, self)._build_inputs()
+ self._input_set.export()
+
if __name__ == '__main__':
harness = MGMaxOrderTestHarness('statepoint.10.*', False, mg=True)
diff --git a/tests/test_mg_nuclide/inputs_true.dat b/tests/test_mg_nuclide/inputs_true.dat
--- a/tests/test_mg_nuclide/inputs_true.dat
+++ b/tests/test_mg_nuclide/inputs_true.dat
@@ -1 +1 @@
-be296da93031694b2915e1a10e3e6fd663d612cdd29a84745e3ccb0065c088b4bcda45f6919962f6ee784efe52ebe178bf7d3ce019859637ae57c2da1e240a04
\ No newline at end of file
+6d03b988671fe21dfe2a908685536edb3059e5bdda7974ddfa65c7f63cecb7f6b3fce49bc1533ef2787e284121779653cb14a66cfd709258e4b07d8bd7571843
\ No newline at end of file
diff --git a/tests/test_mg_nuclide/results_true.dat b/tests/test_mg_nuclide/results_true.dat
--- a/tests/test_mg_nuclide/results_true.dat
+++ b/tests/test_mg_nuclide/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.047136E+00 2.765964E-02
+1.160653E+00 6.227102E-02
diff --git a/tests/test_mg_nuclide/test_mg_nuclide.py b/tests/test_mg_nuclide/test_mg_nuclide.py
--- a/tests/test_mg_nuclide/test_mg_nuclide.py
+++ b/tests/test_mg_nuclide/test_mg_nuclide.py
@@ -2,81 +2,22 @@
import os
import sys
+
sys.path.insert(0, os.pardir)
-from testing_harness import TestHarness, PyAPITestHarness
+from testing_harness import PyAPITestHarness
from input_set import MGInputSet
-import openmc
-
-class MGNuclideInputSet(MGInputSet):
- def build_default_materials_and_geometry(self):
- # Define materials needed for 1D/1G slab problem
- # This time do using nuclide, not macroscopic
- uo2 = openmc.Material(name='UO2', material_id=1)
- uo2.set_density('sum', 1.0)
- uo2.add_nuclide("uo2_iso", 1.0)
-
- clad = openmc.Material(name='Clad', material_id=2)
- clad.set_density('sum', 1.0)
- clad.add_nuclide("clad_ang_mu", 1.0)
-
- # water_data = openmc.Nuclide('lwtr_iso_mu', '71c')
- water = openmc.Material(name='LWTR', material_id=3)
- water.set_density('sum', 1.0)
- water.add_nuclide("lwtr_iso_mu", 1.0)
-
- # Define the materials file.
- self.materials.default_xs = '71c'
- self.materials += (uo2, clad, water)
-
- # Define surfaces.
-
- # Assembly/Problem Boundary
- left = openmc.XPlane(x0=0.0, surface_id=200,
- boundary_type='reflective')
- right = openmc.XPlane(x0=10.0, surface_id=201,
- boundary_type='reflective')
- bottom = openmc.YPlane(y0=0.0, surface_id=300,
- boundary_type='reflective')
- top = openmc.YPlane(y0=10.0, surface_id=301,
- boundary_type='reflective')
- down = openmc.ZPlane(z0=0.0, surface_id=0,
- boundary_type='reflective')
- fuel_clad_intfc = openmc.ZPlane(z0=2.0, surface_id=1)
- clad_lwtr_intfc = openmc.ZPlane(z0=2.4, surface_id=2)
- up = openmc.ZPlane(z0=5.0, surface_id=3,
- boundary_type='reflective')
-
- # Define cells
- c1 = openmc.Cell(cell_id=1)
- c1.region = +left & -right & +bottom & -top & +down & -fuel_clad_intfc
- c1.fill = uo2
- c2 = openmc.Cell(cell_id=2)
- c2.region = +left & -right & +bottom & -top & +fuel_clad_intfc & -clad_lwtr_intfc
- c2.fill = clad
- c3 = openmc.Cell(cell_id=3)
- c3.region = +left & -right & +bottom & -top & +clad_lwtr_intfc & -up
- c3.fill = water
-
- # Define root universe.
- root = openmc.Universe(universe_id=0, name='root universe')
-
- root.add_cells((c1,c2,c3))
-
- # Define the geometry file.
- geometry = openmc.Geometry()
- geometry.root_universe = root
-
- self.geometry = geometry
class MGNuclideTestHarness(PyAPITestHarness):
def __init__(self, statepoint_name, tallies_present, mg=False):
PyAPITestHarness.__init__(self, statepoint_name, tallies_present)
- self._input_set = MGNuclideInputSet()
+ self._input_set = MGInputSet()
def _build_inputs(self):
- super(MGNuclideTestHarness, self)._build_inputs()
-
+ """Write input XML files."""
+ self._input_set.build_default_materials_and_geometry(as_macro=False)
+ self._input_set.build_default_settings()
+ self._input_set.export()
if __name__ == '__main__':
diff --git a/tests/test_mg_tallies/inputs_true.dat b/tests/test_mg_tallies/inputs_true.dat
--- a/tests/test_mg_tallies/inputs_true.dat
+++ b/tests/test_mg_tallies/inputs_true.dat
@@ -1 +1 @@
-b607875dcaecb7110e396a62100182818b8b2853ec9921194b7ab00d6156373b01394ad8bd729babf7d258e6d9c599f6944c6857cd9d2f65ea98e245ee3cf010
\ No newline at end of file
+8c496e13f9456bedcc0789ffdca81913596cca3c7867717ced38c3063b6cdc8949bd204c98723b72c1b456e3fc85fc90e6710482b0c74e5e29283902a5d9ed50
\ No newline at end of file
diff --git a/tests/test_mg_tallies/results_true.dat b/tests/test_mg_tallies/results_true.dat
--- a/tests/test_mg_tallies/results_true.dat
+++ b/tests/test_mg_tallies/results_true.dat
@@ -1,2906 +1 @@
-k-combined:
-1.047136E+00 2.765964E-02
-tally 1:
-2.490837E+00
-1.335515E+00
-8.299408E-02
-1.628477E-03
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-tally 2:
-3.995283E+01
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-6.783537E+00
-9.416330E+00
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-3.134204E+03
+6ab4a178b642f886eea9fddbdf67a8d6d3e0d1968f06ee52d7fd5ecdc1b4a796398e9b3a8c15ac72fb1a011d13a5fcc59a868781d38fb11787e060bb2e602a7b
\ No newline at end of file
diff --git a/tests/test_mg_tallies/test_mg_tallies.py b/tests/test_mg_tallies/test_mg_tallies.py
--- a/tests/test_mg_tallies/test_mg_tallies.py
+++ b/tests/test_mg_tallies/test_mg_tallies.py
@@ -3,38 +3,84 @@
import os
import sys
sys.path.insert(0, os.pardir)
-from testing_harness import TestHarness, PyAPITestHarness
+from testing_harness import HashedPyAPITestHarness
import openmc
-class MGTalliesTestHarness(PyAPITestHarness):
+class MGTalliesTestHarness(HashedPyAPITestHarness):
def _build_inputs(self):
+ """Write input XML files."""
+ self._input_set.build_default_materials_and_geometry(as_macro=False)
+ self._input_set.build_default_settings()
+
# Instantiate a tally mesh
mesh = openmc.Mesh(mesh_id=1)
mesh.type = 'regular'
- mesh.dimension = [17, 17, 1]
+ mesh.dimension = [1, 1, 10]
mesh.lower_left = [0.0, 0.0, 0.0]
- mesh.upper_right = [21.42, 21.42, 100.0]
+ mesh.upper_right = [10, 10, 5]
# Instantiate some tally filters
energy_filter = openmc.EnergyFilter([0.0, 20.0])
energyout_filter = openmc.EnergyoutFilter([0.0, 20.0])
mesh_filter = openmc.MeshFilter(mesh)
- mat_filter = openmc.MaterialFilter([1,2,3])
+ mat_ids = [mat.id for mat in self._input_set.materials]
+ mat_filter = openmc.MaterialFilter(mat_ids)
+
+ nuclides = [xs.name for xs in self._input_set.xs_data]
+
+ scores= {False: ['total', 'absorption', 'flux', 'fission', 'nu-fission'],
+ True: ['total', 'absorption', 'fission', 'nu-fission']}
+
+ tallies = []
+ for do_nuclides in [False, True]:
+ tallies.append(openmc.Tally())
+ tallies[-1].filters = [mesh_filter]
+ tallies[-1].estimator = 'analog'
+ tallies[-1].scores = scores[do_nuclides]
+ if do_nuclides:
+ tallies[-1].nuclides = nuclides
+
+ tallies.append(openmc.Tally())
+ tallies[-1].filters = [mesh_filter]
+ tallies[-1].estimator = 'tracklength'
+ tallies[-1].scores = scores[do_nuclides]
+ if do_nuclides:
+ tallies[-1].nuclides = nuclides
+
+ tallies.append(openmc.Tally())
+ tallies[-1].filters = [mat_filter, energy_filter]
+ tallies[-1].estimator = 'analog'
+ tallies[-1].scores = scores[do_nuclides] + ['scatter',
+ 'nu-scatter']
+ if do_nuclides:
+ tallies[-1].nuclides = nuclides
+
+ tallies.append(openmc.Tally())
+ tallies[-1].filters = [mat_filter, energy_filter]
+ tallies[-1].estimator = 'collision'
+ tallies[-1].scores = scores[do_nuclides]
+ if do_nuclides:
+ tallies[-1].nuclides = nuclides
- tally1 = openmc.Tally(tally_id=1)
- tally1.filters = [mesh_filter]
- tally1.scores = ['total', 'absorption', 'flux',
- 'fission', 'nu-fission']
+ tallies.append(openmc.Tally())
+ tallies[-1].filters = [mat_filter, energy_filter]
+ tallies[-1].estimator = 'tracklength'
+ tallies[-1].scores = scores[do_nuclides]
+ if do_nuclides:
+ tallies[-1].nuclides = nuclides
- tally2 = openmc.Tally(tally_id=2)
- tally2.filters = [mat_filter, energy_filter, energyout_filter]
- tally2.scores = ['scatter', 'nu-scatter']
+ tallies.append(openmc.Tally())
+ tallies[-1].filters = [mat_filter, energy_filter,
+ energyout_filter]
+ tallies[-1].scores = ['scatter', 'nu-scatter', 'nu-fission']
+ if do_nuclides:
+ tallies[-1].nuclides = nuclides
- self._input_set.tallies = openmc.Tallies([tally1, tally2])
+ self._input_set.tallies = openmc.Tallies(tallies)
- super(MGTalliesTestHarness, self)._build_inputs()
+ self._input_set.export()
def _cleanup(self):
super(MGTalliesTestHarness, self)._cleanup()
diff --git a/tests/test_mgxs_library_ce_to_mg/results_true.dat b/tests/test_mgxs_library_ce_to_mg/results_true.dat
--- a/tests/test_mgxs_library_ce_to_mg/results_true.dat
+++ b/tests/test_mgxs_library_ce_to_mg/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.140804E+00 2.937150E-02
+1.140724E+00 2.952379E-02
diff --git a/tests/test_mgxs_library_ce_to_mg/test_mgxs_library_ce_to_mg.py b/tests/test_mgxs_library_ce_to_mg/test_mgxs_library_ce_to_mg.py
--- a/tests/test_mgxs_library_ce_to_mg/test_mgxs_library_ce_to_mg.py
+++ b/tests/test_mgxs_library_ce_to_mg/test_mgxs_library_ce_to_mg.py
@@ -61,14 +61,14 @@ def _run_openmc(self):
self._input_set.geometry = self.mgxs_lib.create_mg_mode()
# Modify settings so we can run in MG mode
- self._input_set.settings.cross_sections = './mgxs.xml'
+ self._input_set.settings.cross_sections = './mgxs.h5'
self._input_set.settings.energy_mode = 'multi-group'
# Write modified input files
self._input_set.settings.export_to_xml()
self._input_set.geometry.export_to_xml()
self._input_set.materials.export_to_xml()
- self._input_set.mgxs_file.export_to_xml()
+ self._input_set.mgxs_file.export_to_hdf5()
# Dont need tallies.xml, so remove the file
if os.path.exists('./tallies.xml'):
os.remove('./tallies.xml')
@@ -83,9 +83,8 @@ def _run_openmc(self):
returncode = openmc.run(openmc_exec=self._opts.exe)
def _cleanup(self):
- return
super(MGXSTestHarness, self)._cleanup()
- f = os.path.join(os.getcwd(), 'mgxs.xml')
+ f = os.path.join(os.getcwd(), 'mgxs.h5')
if os.path.exists(f):
os.remove(f)
| Implement HDF5-Based MGXS Library Format
As discussed in #336, it would be nice to have an HDF5-based mgxs input file format. This can be done in one of two ways:
1. We just take the current xml format as is and port it to HDF5.
2. Gain some experience with different use cases of the current capability and see if format changes exist which would be more useful.
I'm open to either an am curious to hear other's opinions. One facet to consider is if this should be included with 0.8 or not. If so, that would push us to #1.
| It would be nice to develop an HDF5 format consistent with OpenMOC, and perhaps MOCingjay (if @friedmud chooses to use HDF5). This doesn't mean that the format needs to be consistent with OpenMOC's currently accepted HDF5 format, but we would likely want to update our format there in lockstep with a format implemented here so the same files work with each code. Understandably our format in OpenMOC would probably be a subset of that for OpenMC, since the multi-group implementation here includes support for higher order scattering and angular-dependent MGXS. Anyway, I'm interested in participating in a conversation on this as you consider options @nelsonag.
That is a very good place to start, no reason to be different if we don't
have to be. What is MOCingjay anyways?
I should also add that while I don't know if it makes sense to attach it to
OpenMC directly, it would be awfully nice to have a generic MGXS converter
from external formats (HELIOS, WIMS, ANISN, DDX, whatever other
perturbations are common) to our own to help out with the researchers.
While everyone should use MC to generate their MGXS, not all may want to :-P
On Wed, Feb 24, 2016 at 8:17 AM, Will Boyd [email protected] wrote:
> It would be nice to develop an HDF5 format consistent with OpenMOC, and
> perhaps MOCingjay (if @friedmud https://github.com/friedmud chooses to
> use HDF5). This doesn't mean that the format needs to be consistent with
> OpenMOC's currently accepted HDF5 format, but we would likely want to
> update our format there in lockstep with a format implemented here so the
> same files work with each code. Understandably our format in OpenMOC would
> probably be a subset of that for OpenMC, since the multi-group
> implementation here includes support for higher order scattering and
> angular-dependent MGXS. Anyway, I'm interested in participating in a
> conversation on this as you consider options @nelsonag
> https://github.com/nelsonag.
>
> —
> Reply to this email directly or view it on GitHub
> https://github.com/mit-crpg/openmc/issues/594#issuecomment-188251459.
The latter issue sounds like something more suited for [pyne](https://github.com/pyne/pyne).
Good point.
On Wed, Feb 24, 2016 at 9:15 AM, Paul Romano [email protected]
wrote:
> The latter issue sounds like something more suited for pyne
> https://github.com/pyne/pyne.
>
> —
> Reply to this email directly or view it on GitHub
> https://github.com/mit-crpg/openmc/issues/594#issuecomment-188272552.
MOCingjay is a new MOC code I'm working on. I'm not at a point yet where I want to say too much about it :-). Hopefully soon!
@wbinventor I would definitely participate in trying to hammer out a consistent HDF5 format. I _do_ think that's what I'm going to use for MOCingjay. As always though: trying to satisfy the needs of many users can lead to a huge, nasty, specification. So we do need to weigh the pros and cons.
Have you seen the design documents for YakXS? That's the XML format Yaqi invented for Rattlesnake. It is huge, and exhaustive. Could be a good place to start. I think it's been openly published... I'll try to find a copy of it. Of course, we wouldn't use XML... but it's still a modern hierarchical XS storage plan.
I've never heard of YakXS and a scholar search came up with nothing
obvious. Interested to see any references you have though!
On Feb 24, 2016 10:23 AM, "Derek Gaston" [email protected] wrote:
> MOCingjay is a new MOC code I'm working on. I'm not at a point yet where I
> want to say too much about it :-). Hopefully soon!
>
> @wbinventor https://github.com/wbinventor I would definitely
> participate in trying to hammer out a consistent HDF5 format. I _do_
> think that's what I'm going to use for MOCingjay. As always though: trying
> to satisfy the needs of many users can lead to a huge, nasty,
> specification. So we do need to weigh the pros and cons.
>
> Have you seen the design documents for YakXS? That's the XML format Yaqi
> invented for Rattlesnake. It is huge, and exhaustive. Could be a good place
> to start. I think it's been openly published... I'll try to find a copy of
> it. Of course, we wouldn't use XML... but it's still a modern hierarchical
> XS storage plan.
>
> —
> Reply to this email directly or view it on GitHub
> https://github.com/mit-crpg/openmc/issues/594#issuecomment-188304288.
@wbinventor and @friedmud do you guys have any plans to support in-line self-shielding calculations? That is, do you expect your mgxs library format to include background cross sections, or subgroup data?
I ask because if not, then the current OpenMC MGXS data is very nearly a superset of all your needs. From the OpenMOC documentation it looks like you also would have a diffusion coefficient and buckling as user input. Those can be easily added, but is buckling a scalar or vector of length G?
My current plan is to ignore self-shielding all together... just do everything by generating XS directly using OpenMC. We'll see if I get tired of waiting ;-)
My main issues with the current format are that I need libraries that have multiple material temperature and densities in them. i.e.: I need to generate XS at 5 different temperatures and 5 different moderator densities and store all of that data in a way that I can quickly interpolate in-between it.
The YakXS format has that capability in it... I am realizing now that I still haven't posted any YakXS literature. Let me see if I can get something that has already been cleared for external release...
@nelsonag we have no plans to use OpenMOC as a traditional lattice physics code for in-line self-shielding, but rather as a high-fidelity full-core 3D analysis tool. @PrezNattyGibbs did work on some stuff along these lines early in his PhD, but determined it best to do it separately in his own code and it didn't make it into OpenMOC, nor do we have anyone lined up to continue to this area of work.
As for the OpenMOC MGXS data, be warned that our current documentation online is for v0.1.4 released nearly a year ago and is _very_ out-of-date. You should build our documentation locally which includes up-to-date guide on MGXS (though it is still lacking a _lot_ of details on bells and whistles in the code). Sorry for the confusion, our core code maintainer @geogunow should be releasing v0.2 and the respective documentation soon.
In short, you are correct in that data generated with `openmc.mgxs` fully meets the needs of OpenMOC. We no longer need bucklings or diffusion coefficients as input as these are computed on-the-fly for CMFD. The only things we need are constants for total/transport, nu-fission, (nu-)scattering and chi.
I do think that `openmc.mgxs` could be relatively easily extended to deal with both temperature (of interest to @friedmud) and angle (of interest to @nelsonag). This would account for 1) input generation, 2) (multi-)statepoint data processing, and 3) interpolation methods. If anyone wants to take a stab at implementing this I'd be happy to share my thoughts as a starting point.
Btw @nelsonag the process to build the OpenMOC docs locally is identical to that for OpenMC - simply run `make html` inside of our "docs" directory (with sphinx installed).
Also I'll add that density could be included in an extension to `openmc.mgxs` as well. I see temperature and densities as being additions to `openmc.mgxs.Library` while angle would be an addition to `openmc.mgxs.MGXS`.
@wbinventor & @friedmud I started a [gist](https://gist.github.com/nelsonag/2966440de322bca11a046cfb03cecbdd) to capture the format. Basically its the `mgxs_library.rst` file from our current docs directory, messed around a bit to represent what the h5 format would be. I based it off of the current mgxs.xml file, obviously, but also the OpenMOC documentation on the develop branch. By that I mean I use your naming of mgxs types where applicable.
When you get a chance can you take a look and let me know if it meets your needs?
@friedmud I'm clearly stil cogitating on your material temperature and density concern.
For now I did not include that in the format itself because the xs name gives all the flexibility you would need to store the multiple temps/densities. One thing I'm struggling with is what the density means to the user if they're using this library for microscopic data. I suppose a micro/macro attribute could be added, and if micro, then no density dimension to sub-xsdata objects are needed, but that sounds a bit messy.
Thanks for sharing your Gist @nelsonag, it is looking very nice! Although I don't have a near-term use case which calls for temperature- or density-dependence, I do have some thoughts on it which I thought I'd record here. As for density-dependence, I presume @friedmud was referring to functional form of pin cell MGXS on moderator density for coupled multi-physics simulation?
Just as the `MGXS` class serves as a "meta tally" leveraging tally arithmetic, we may consider implementing new class(es) which serve as "meta MGXS" to implement various functional approximations (_e.g._, point-wise linear) between `MGXS` at different temperatures and densities. These "meta MGXS" could also use tally arithmetic to implement their various functional approximations - for example, point-wise linear dependence would be very simple to implement to combine the `MGXS.xs_tally` objects from two or more `MGXS` tallied at different temperatures or densities. The "meta MGXS" classes could implement API(s) to output the predicted cross section values at different temperatures / densities, output the data at various temperatures / densities to HDF5, etc. This might not be what @friedmud would need, but just thought I'd throw it out there as a starting point.
Thanks @wbinventor! Right now I'm thinking the interpolation shouldnt be
up to the MGXS class, instead it should be on the code using the data to do
it internally. In my experience codes that would want to vary temperature,
density, burn-up, etc, will do it internally.
On May 30, 2016 8:46 AM, "Will Boyd" [email protected] wrote:
> Thanks for sharing your Gist @nelsonag https://github.com/nelsonag, it
> is looking very nice! Although I don't have a near-term use case which
> calls for temperature- or density-dependence, I do have some thoughts on it
> which I thought I'd record here. As for density-dependence, I presume
> @friedmud https://github.com/friedmud was referring to functional form
> of pin cell MGXS on moderator density for coupled multi-physics simulation?
>
> Just as the MGXS class serves as "meta tally" leveraging tally
> arithmetic, we may consider implementing new class(es) which serve as "meta
> MGXS" to implement various functional approximations (_e.g._, point-wise
> linear) between MGXS at different temperatures and densities. These "meta
> MGXS" could also use tally arithmetic to implement their various functional
> approximations - for example, point-wise linear dependence would be very
> simple to implement to combine the MGXS.xs_tally objects from two or more
> MGXS tallied at different temperatures or densities. The "meta MGXS"
> classes could implement API(s) to output the predicted cross section values
> at different temperatures / densities, output the data at various
> temperatures / densities to HDF5, etc. This might not be what @friedmud
> https://github.com/friedmud would need, but just thought I'd throw it
> out there as a starting point.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> https://github.com/mit-crpg/openmc/issues/594#issuecomment-222485188,
> or mute the thread
> https://github.com/notifications/unsubscribe/AA_TM4ZueSGMe78hoPGZx17BqjFGWukpks5qGtwlgaJpZM4HhqU4
> .
Ok - I finally got the go ahead to put out the YakXS format document. I'm attaching it here. Note that it's huge... and we probably don't want / need most of these features but it might give us some ideas...
[yakxs.pdf](https://github.com/mit-crpg/openmc/files/324194/yakxs.pdf)
Among the things I like about YakXS is the ability to specify sparse scattering matrices... that gets pretty important as group sizes get large.
@friedmud Do you like that feature due to the pain of writing all the zeros or the storage? I ask because its the former, then the user can always generate their hdf5 library with compression turned on. I think I prefer that route since I get the best of both worlds: I am able to see the complete matrix after its input in to the library so I can do a real quick check on if its been entered correctly, and I get the small storage footprint.
Also because it can reduce computation.... no need to multiply by those zeros either!
But yeah: memory is the big thing. If you're going to have separate XS for each material in each pin in a full reactor with 128 or 256 energy groups... that's a LOT of zeros...
I would be interested in seeing how effective HDF5 compression is for scattering matrices though....
Totally agree on the computation; didnt think of that though as OpenMC's MG
mode automatically takes the dense scattering matrix and converts it to
sparse.
My gut tells me its easy for a compression algorithm to compress a bunch of
0s. When I get this thing implemented I will include an option in the
Python API to choose some compression options. We shall see.
On Mon, Jun 20, 2016 at 5:14 PM, Derek Gaston [email protected]
wrote:
> Also because it can reduce computation.... no need to multiply by those
> zeros either!
>
> But yeah: memory is the big thing. If you're going to have separate XS for
> each material in each pin in a full reactor with 128 or 256 energy
> groups... that's a LOT of zeros...
>
> I would be interested in seeing how effective HDF5 compression is for
> scattering matrices though....
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> https://github.com/mit-crpg/openmc/issues/594#issuecomment-227271580,
> or mute the thread
> https://github.com/notifications/unsubscribe/AA_TM4QXGcqxZpbUYWeDKRtA0BnAW1xvks5qNwK6gaJpZM4HhqU4
> .
@friedmud: I just ran our MGXS example notebook #4 problem (a single 17x17 assembly with one MGXS set per material and p3 scattering), and running gzip compression at level 9 on the hdf5 MGXS library resulted in a 63% decrease in size. Thats not great but really not bad at all.
This compression performance should get better too as the library size grows too: I noticed a very small 2-grp library had an increase in size of ~100kb I guess just due to the compression table overhead (every dataset gets compressed independently...). This 63% number is from a library that, when compressed, is only 104kb, and therefore probably dominated by that overhead.
To be clear when I say I ran 'gzip compression at level 9' I mean that I told the HDF5 library itself to 'compress yourself, please'. I do _not_ mean that I ran gzip on the file from the command line.
@nelsonag interesting... but when is the decompression done? Is it done as the file is read? Because all of those zeros will still take up a lot of memory...
Eventually I really do want some sort of sparse storage for my XS... both for memory and computation.
I like the "format" that the YakXS guys came up with... it incorporates what we know about the physics: that there is a limited ability for upscatter and there is (possibly) a limit for downscatter. So, in their format you essentially specify the first column and last column of each row that will have values... and you provide a value for everything in between (keep in mind that YakXS uses "out on row" for it's scattering matrices). It's a very intuitive way to do it that maps well to the physics.
| 2016-09-11T10:39:14Z | [] | [] |
openmc-dev/openmc | 862 | openmc-dev__openmc-862 | [
"844"
] | 9d22f149d752397c71d2dcaa2d6789c839e9d474 | diff --git a/examples/python/basic/build-xml.py b/examples/python/basic/build-xml.py
--- a/examples/python/basic/build-xml.py
+++ b/examples/python/basic/build-xml.py
@@ -95,7 +95,7 @@
###############################################################################
# Instantiate some tally Filters
-cell_filter = openmc.CellFilter(100)
+cell_filter = openmc.CellFilter(cell2)
energy_filter = openmc.EnergyFilter([0., 20.e6])
energyout_filter = openmc.EnergyoutFilter([0., 20.e6])
diff --git a/examples/python/lattice/hexagonal/build-xml.py b/examples/python/lattice/hexagonal/build-xml.py
--- a/examples/python/lattice/hexagonal/build-xml.py
+++ b/examples/python/lattice/hexagonal/build-xml.py
@@ -153,7 +153,7 @@
# Instantiate a distribcell Tally
tally = openmc.Tally(tally_id=1)
-tally.filters = [openmc.DistribcellFilter(cell2.id)]
+tally.filters = [openmc.DistribcellFilter(cell2)]
tally.scores = ['total']
# Instantiate a Tallies collection and export to XML
diff --git a/openmc/filter.py b/openmc/filter.py
--- a/openmc/filter.py
+++ b/openmc/filter.py
@@ -434,54 +434,48 @@ def get_pandas_dataframe(self, data_size, **kwargs):
return df
-class IntegralFilter(Filter):
- """Tally modifier that describes phase-space and other characteristics.
-
- Parameters
- ----------
- bins : Integral or Iterable of Integral
- The bins for the filter. This takes on different meaning for different
- filters. See the docstrings for sublcasses of this filter or the online
- documentation for more details.
-
- Attributes
- ----------
- bins : Integral or Iterable of Integral
- The bins for the filter
- num_bins : Integral
- The number of filter bins
- stride : Integral
- The number of filter, nuclide and score bins within each of this
- filter's bins.
-
- """
+class WithIDFilter(Filter):
+ """Abstract parent for filters of types with ids (Cell, Material, etc.)."""
@property
def num_bins(self):
return len(self.bins)
+ # Since num_bins property is declared, also need a num_bins.setter, but
+ # we don't want it to do anything since num_bins is completely determined
+ # by len(self.bins). We also don't want to raise an error because that
+ # makes importing from HDF5 more complicated.
@num_bins.setter
- def num_bins(self, num_bins):
- cv.check_type('filter num_bins', num_bins, Integral)
- cv.check_greater_than('filter num_bins', num_bins, 0, equality=True)
- self._num_bins = num_bins
+ def num_bins(self, num_bins): pass
- def check_bins(self, bins):
- cv.check_iterable_type('filter bins', bins, Integral)
+ def _smart_set_bins(self, bins, bin_type):
+ # Format the bins as a 1D numpy array.
+ bins = np.atleast_1d(bins)
+
+ # Check the bin values.
+ cv.check_iterable_type('filter bins', bins, (Integral, bin_type))
for edge in bins:
- cv.check_greater_than('filter bin', edge, 0, equality=True)
+ if isinstance(edge, Integral):
+ cv.check_greater_than('filter bin', edge, 0, equality=True)
+ # Extract id values.
+ bins = np.atleast_1d([b if isinstance(b, Integral) else b.id
+ for b in bins])
+
+ self._bins = bins
-class UniverseFilter(IntegralFilter):
- """Bins tally event locations based on the universe they occured in.
+
+class UniverseFilter(WithIDFilter):
+ """Bins tally event locations based on the Universe they occured in.
Parameters
----------
- bins : Integral or Iterable of Integral
- openmc.Universe IDs.
+ bins : openmc.Universe, Integral, or iterable thereof
+ The Universes to tally. Either openmc.Universe objects or their
+ Integral ID numbers can be used.
Attributes
----------
- bins : Integral or Iterable of Integral
+ bins : Iterable of Integral
openmc.Universe IDs.
num_bins : Integral
The number of filter bins
@@ -490,19 +484,27 @@ class UniverseFilter(IntegralFilter):
filter's bins.
"""
+ @property
+ def bins(self):
+ return self._bins
+
+ @bins.setter
+ def bins(self, bins):
+ self._smart_set_bins(bins, openmc.Universe)
-class MaterialFilter(IntegralFilter):
- """Bins tally events based on which material they occured in.
+class MaterialFilter(WithIDFilter):
+ """Bins tally event locations based on the Material they occured in.
Parameters
----------
- bins : Integral or Iterable of Integral
- openmc.Material IDs.
+ bins : openmc.Material, Integral, or iterable thereof
+ The Materials to tally. Either openmc.Material objects or their
+ Integral ID numbers can be used.
Attributes
----------
- bins : Integral or Iterable of Integral
+ bins : Iterable of Integral
openmc.Material IDs.
num_bins : Integral
The number of filter bins
@@ -511,19 +513,27 @@ class MaterialFilter(IntegralFilter):
filter's bins.
"""
+ @property
+ def bins(self):
+ return self._bins
+ @bins.setter
+ def bins(self, bins):
+ self._smart_set_bins(bins, openmc.Material)
-class CellFilter(IntegralFilter):
- """Bins tally event locations based on which cell they occured in.
+
+class CellFilter(WithIDFilter):
+ """Bins tally event locations based on the Cell they occured in.
Parameters
----------
- bins : Integral or Iterable of Integral
- openmc.Cell IDs.
+ bins : openmc.Cell, Integral, or iterable thereof
+ The Cells to tally. Either openmc.Cell objects or their
+ Integral ID numbers can be used.
Attributes
----------
- bins : Integral or Iterable of Integral
+ bins : Iterable of Integral
openmc.Cell IDs.
num_bins : Integral
The number of filter bins
@@ -532,19 +542,27 @@ class CellFilter(IntegralFilter):
filter's bins.
"""
+ @property
+ def bins(self):
+ return self._bins
+
+ @bins.setter
+ def bins(self, bins):
+ self._smart_set_bins(bins, openmc.Cell)
-class CellbornFilter(IntegralFilter):
- """Bins tally events based on the cell that the particle was born in.
+class CellbornFilter(WithIDFilter):
+ """Bins tally events based on which Cell the neutron was born in.
Parameters
----------
- bins : Integral or Iterable of Integral
- openmc.Cell IDs.
+ bins : openmc.Cell, Integral, or iterable thereof
+ The birth Cells to tally. Either openmc.Cell objects or their
+ Integral ID numbers can be used.
Attributes
----------
- bins : Integral or Iterable of Integral
+ bins : Iterable of Integral
openmc.Cell IDs.
num_bins : Integral
The number of filter bins
@@ -553,9 +571,16 @@ class CellbornFilter(IntegralFilter):
filter's bins.
"""
+ @property
+ def bins(self):
+ return self._bins
+ @bins.setter
+ def bins(self, bins):
+ self._smart_set_bins(bins, openmc.Cell)
-class SurfaceFilter(IntegralFilter):
+
+class SurfaceFilter(Filter):
"""Bins particle currents on Mesh surfaces.
Parameters
@@ -576,6 +601,28 @@ class SurfaceFilter(IntegralFilter):
filter's bins.
"""
+ @property
+ def bins(self):
+ return self._bins
+
+ @property
+ def num_bins(self):
+ return len(self.bins)
+
+ @bins.setter
+ def bins(self, bins):
+ # Format the bins as a 1D numpy array.
+ bins = np.atleast_1d(bins)
+
+ # Check the bin values.
+ cv.check_iterable_type('filter bins', bins, Integral)
+ for edge in bins:
+ cv.check_greater_than('filter bin', edge, 0, equality=True)
+
+ self._bins = bins
+
+ @num_bins.setter
+ def num_bins(self, num_bins): pass
def get_pandas_dataframe(self, data_size, **kwargs):
"""Builds a Pandas DataFrame for the Filter's bins.
@@ -1082,14 +1129,14 @@ class DistribcellFilter(Filter):
Parameters
----------
- bins : Integral or Iterable of Integral or Iterable of Real
- The bins for the filter. This takes on different meaning for different
- filters. See the OpenMC online documentation for more details.
+ cell : openmc.Cell or Integral
+ The distributed cell to tally. Either an openmc.Cell or an Integral
+ cell ID number can be used.
Attributes
----------
- bins : Integral or Iterable of Integral or Iterable of Real
- The bins for the filter
+ bins : Iterable of Integral
+ An iterable with one element---the ID of the distributed Cell.
num_bins : Integral
The number of filter bins
stride : Integral
@@ -1101,9 +1148,9 @@ class DistribcellFilter(Filter):
"""
- def __init__(self, bins):
+ def __init__(self, cell):
self._paths = None
- super(DistribcellFilter, self).__init__(bins)
+ super(DistribcellFilter, self).__init__(cell)
@classmethod
def from_hdf5(cls, group, **kwargs):
@@ -1117,24 +1164,36 @@ def from_hdf5(cls, group, **kwargs):
return out
+ @property
+ def bins(self):
+ return self._bins
+
@property
def paths(self):
return self._paths
- @paths.setter
- def paths(self, paths):
- cv.check_iterable_type('paths', paths, str)
- self._paths = paths
+ @bins.setter
+ def bins(self, bins):
+ # Format the bins as a 1D numpy array.
+ bins = np.atleast_1d(bins)
- def check_bins(self, bins):
+ # Make sure there is only 1 bin.
if not len(bins) == 1:
msg = 'Unable to add bins "{0}" to a DistribcellFilter since ' \
'only a single distribcell can be used per tally'.format(bins)
raise ValueError(msg)
- cv.check_iterable_type('filter bins', bins, Integral)
- for edge in bins:
- cv.check_greater_than('filter bin', edge, 0, equality=True)
+ # Check the type and extract the id, if necessary.
+ cv.check_type('distribcell bin', bins[0], (Integral, openmc.Cell))
+ if isinstance(bins[0], openmc.Cell):
+ bins = np.atleast_1d(bins[0].id)
+
+ self._bins = bins
+
+ @paths.setter
+ def paths(self, paths):
+ cv.check_iterable_type('paths', paths, str)
+ self._paths = paths
def can_merge(self, other):
# Distribcell filters cannot have more than one bin
@@ -1608,7 +1667,7 @@ def get_pandas_dataframe(self, data_size, paths=True):
return df
-class DelayedGroupFilter(IntegralFilter):
+class DelayedGroupFilter(Filter):
"""Bins fission events based on the produced neutron precursor groups.
Parameters
@@ -1631,6 +1690,28 @@ class DelayedGroupFilter(IntegralFilter):
filter's bins.
"""
+ @property
+ def bins(self):
+ return self._bins
+
+ @property
+ def num_bins(self):
+ return len(self.bins)
+
+ @bins.setter
+ def bins(self, bins):
+ # Format the bins as a 1D numpy array.
+ bins = np.atleast_1d(bins)
+
+ # Check the bin values.
+ cv.check_iterable_type('filter bins', bins, Integral)
+ for edge in bins:
+ cv.check_greater_than('filter bin', edge, 0, equality=True)
+
+ self._bins = bins
+
+ @num_bins.setter
+ def num_bins(self, num_bins): pass
class EnergyFunctionFilter(Filter):
| diff --git a/tests/test_mg_tallies/test_mg_tallies.py b/tests/test_mg_tallies/test_mg_tallies.py
--- a/tests/test_mg_tallies/test_mg_tallies.py
+++ b/tests/test_mg_tallies/test_mg_tallies.py
@@ -26,8 +26,7 @@
matching_eout_filter = openmc.EnergyoutFilter(energies)
mesh_filter = openmc.MeshFilter(mesh)
- mat_ids = [mat.id for mat in model.materials]
- mat_filter = openmc.MaterialFilter(mat_ids)
+ mat_filter = openmc.MaterialFilter(model.materials)
nuclides = [xs.name for xs in model.xs_data]
diff --git a/tests/test_tallies/test_tallies.py b/tests/test_tallies/test_tallies.py
--- a/tests/test_tallies/test_tallies.py
+++ b/tests/test_tallies/test_tallies.py
@@ -43,7 +43,10 @@
azimuthal_tally3.estimator = 'tracklength'
cellborn_tally = Tally()
- cellborn_tally.filters = [CellbornFilter((10, 21, 22, 23))]
+ cellborn_tally.filters = [
+ CellbornFilter((model.geometry.get_all_cells()[10],
+ model.geometry.get_all_cells()[21],
+ 22, 23))] # Test both Cell objects and ids
cellborn_tally.scores = ['total']
dg_tally = Tally()
@@ -66,7 +69,10 @@
transfer_tally.scores = ['scatter', 'nu-fission']
material_tally = Tally()
- material_tally.filters = [MaterialFilter((1, 2, 3, 4))]
+ material_tally.filters = [
+ MaterialFilter((model.geometry.get_materials_by_name('UOX fuel')[0],
+ model.geometry.get_materials_by_name('Zircaloy')[0],
+ 3, 4))] # Test both Material objects and ids
material_tally.scores = ['total']
mu_bins = (-1.0, -0.5, 0.0, 0.5, 1.0)
@@ -97,10 +103,15 @@
polar_tally3.estimator = 'tracklength'
universe_tally = Tally()
- universe_tally.filters = [UniverseFilter((1, 2, 3, 4, 6, 8))]
+ universe_tally.filters = [
+ UniverseFilter((model.geometry.get_all_universes()[1],
+ model.geometry.get_all_universes()[2],
+ 3, 4, 6, 8))] # Test both Universe objects and ids
universe_tally.scores = ['total']
- cell_filter = CellFilter((10, 21, 22, 23, 60))
+ cell_filter = CellFilter((model.geometry.get_all_cells()[10],
+ model.geometry.get_all_cells()[21],
+ 22, 23, 60)) # Test both Cell objects and ids
score_tallies = [Tally(), Tally(), Tally()]
for t in score_tallies:
t.filters = [cell_filter]
| Use fewer `.id`s in the PythonAPI
Another tricky one to explain at workshops: We sort of try to hide the concept of `id` numbers from the user by making them an optional keyword argument in most of our constructors, but you still need to use them when you create a `TallyFilter` or specify a `Plot.col_spec`. I would like to make those objects accept e.g. `Cell` objects and grab their `id`s at export time.
| Totally agree -- let's fix that. The `Plot` one was already taken care of in #826, so specifying IDs when using filters is the last remaining area where you have to manually say `.id`. I guess the reason we use IDs is that if you read back a `Tally` object from a statepoint, it won't be able to recreate the same object unless the summary file is linked. These days that's usually a good assumption since we write summary.h5 by default, but the question then is what to store for filter bins when no geometry information is available.
Maybe we can avoid that question by only ever storing `id`s on the `TallyFilter`s. We can adjust the `bins.setter` method to simply strip the `id` numbers from e.g. `Cell`s passed to it. In other words, make these two options have identical effects:
```python
openmc.CellFilter([c.id for c in cells])
openmc.CellFilter(cells)
```
In the long run, there are probably advantages to storing the `Cell`s themselves, but I think we can quickly implement the `id` stripping now and have something which is better than the status quo.
Yeah, I was thinking that too. Do you want to implement this or should I take it?
Or, we can have a newcomer try to attack this since it is relatively simple.
I'm assigning @giudgiud. I don't see a way to assign him with the official GitHub thing. Maybe he has to be a collaborator first?
To be a little more explicit about the proposed change:
Consider this example of creating a CellFilter:
```python
filter = CellFilter([1, 2, 3])
```
That always calls this method you see defined for the `Filter` class in filter.py
```python
@bins.setter
def bins(self, bins):
# Format the bins as a 1D numpy array.
bins = np.atleast_1d(bins)
# Check the bin values.
self.check_bins(bins)
self._bins = bins
```
We want this method to be a little bit smarter so that we can do something like
```python
c1 = openmc.Cell(cell_id=1)
c2 = openmc.Cell(cell_id=2)
filt = openmc.CellFilter([c1, c2])
```
or
```python
m1 = openmc.Material(material_id=1)
m2 = openmc.Material(material_id=2)
filt = openmc.MaterialFilter([m1, m2])
```
The most obvious approach would be to overload the `bins.setter` method for each of the relevant filters. For every filter where we add a `bins.setter`, it probably doesn't make sense to keep a separate `check_bins` method. So for `CellFilter` you would define something like
```python
@bins.setter
def bins(self, bins):
# Format the bins as a 1D numpy array.
bins = np.atleast_1d(bins)
# Make sure the bins have the right content.
cv.check_iterable_type('filter bins', bins, (Integral, openmc.Cell))
# Strip ids from Cells.
if any([isinstance(b, openmc.Cell) for b in bins]):
if isinstance(bins[0], openmc.Cell)
bins = np.atleast_1d(
[b.id if isinstance(b, openmc.Cell) else b
for b in bins])
self._bins = bins
```
You would need to modify `UniverseFilter`, `MaterialFilter`, `CellFilter`, `CellbornFilter`, and `DistribcellFilter`. We should also probably modify test_tallies.py so that it tests this feature and the examples so that they demonstrate this feature.
Has there been any progress on this? I don't mean to rush it, but I would like to fix this before our next release and it is one of the last remaining issues tagged to v0.9. | 2017-04-13T21:43:03Z | [] | [] |
openmc-dev/openmc | 897 | openmc-dev__openmc-897 | [
"895"
] | e38bc516b783c5cd5e360efbe64c53b461f36d3e | diff --git a/openmc/material.py b/openmc/material.py
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -618,13 +618,18 @@ def remove_element(self, element):
if element == elm[0]:
self._elements.remove(elm)
- def add_s_alpha_beta(self, name):
+ def add_s_alpha_beta(self, name, fraction=1.0):
r"""Add an :math:`S(\alpha,\beta)` table to the material
Parameters
----------
name : str
Name of the :math:`S(\alpha,\beta)` table
+ fraction : float
+ The fraction of relevant nuclei that are affected by the
+ :math:`S(\alpha,\beta)` table. For example, if the material is a
+ block of carbon that is 60% graphite and 40% amorphous then add a
+ graphite :math:`S(\alpha,\beta)` table with fraction=0.6.
"""
@@ -638,13 +643,17 @@ def add_s_alpha_beta(self, name):
'non-string table name "{}"'.format(self._id, name)
raise ValueError(msg)
+ cv.check_type('S(a,b) fraction', fraction, Real)
+ cv.check_greater_than('S(a,b) fraction', fraction, 0.0, True)
+ cv.check_less_than('S(a,b) fraction', fraction, 1.0, True)
+
new_name = openmc.data.get_thermal_name(name)
if new_name != name:
msg = 'OpenMC S(a,b) tables follow the GND naming convention. ' \
'Table "{}" is being renamed as "{}".'.format(name, new_name)
warnings.warn(msg)
- self._sab.append(new_name)
+ self._sab.append((new_name, fraction))
def make_isotropic_in_lab(self):
for nuclide, percent, percent_type in self._nuclides:
@@ -972,7 +981,9 @@ def to_xml_element(self, cross_sections=None):
if len(self._sab) > 0:
for sab in self._sab:
subelement = ET.SubElement(element, "sab")
- subelement.set("name", sab)
+ subelement.set("name", sab[0])
+ if sab[1] != 1.0:
+ subelement.set("fraction", str(sab[1]))
return element
| diff --git a/tests/test_salphabeta/geometry.xml b/tests/test_salphabeta/geometry.xml
deleted file mode 100644
--- a/tests/test_salphabeta/geometry.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
- <surface id="1" type="x-plane" coeffs="-10" boundary="vacuum"/>
- <surface id="2" type="x-plane" coeffs="-5" />
- <surface id="3" type="x-plane" coeffs="0" />
- <surface id="4" type="x-plane" coeffs="5" />
- <surface id="5" type="x-plane" coeffs="10" boundary="vacuum"/>
-
- <cell id="1" material="1" region="1 -2" />
- <cell id="2" material="2" region="2 -3" />
- <cell id="3" material="3" region="3 -4" />
- <cell id="4" material="4" region="4 -5" />
-
-</geometry>
diff --git a/tests/test_salphabeta/inputs_true.dat b/tests/test_salphabeta/inputs_true.dat
new file mode 100644
--- /dev/null
+++ b/tests/test_salphabeta/inputs_true.dat
@@ -0,0 +1,60 @@
+<?xml version='1.0' encoding='utf-8'?>
+<geometry>
+ <cell id="1" material="1" region="1 -2" universe="1" />
+ <cell id="2" material="2" region="2 -3" universe="1" />
+ <cell id="3" material="3" region="3 -4" universe="1" />
+ <cell id="4" material="4" region="4 -5" universe="1" />
+ <surface boundary="vacuum" coeffs="-10" id="1" type="x-plane" />
+ <surface coeffs="-5" id="2" type="x-plane" />
+ <surface coeffs="0" id="3" type="x-plane" />
+ <surface coeffs="5" id="4" type="x-plane" />
+ <surface boundary="vacuum" coeffs="10" id="5" type="x-plane" />
+</geometry>
+<?xml version='1.0' encoding='utf-8'?>
+<materials>
+ <material id="1">
+ <density units="g/cc" value="4.5" />
+ <nuclide ao="1.0" name="U235" />
+ <nuclide ao="1.0" name="H1" />
+ <sab fraction="0.5" name="c_H_in_H2O" />
+ </material>
+ <material id="2">
+ <density units="g/cc" value="4.5" />
+ <nuclide ao="1.0" name="U235" />
+ <nuclide ao="1.0" name="C0" />
+ <sab name="c_Graphite" />
+ </material>
+ <material id="3">
+ <density units="g/cc" value="4.5" />
+ <nuclide ao="1.0" name="U235" />
+ <nuclide ao="1.0" name="Be9" />
+ <nuclide ao="1.0" name="O16" />
+ <sab name="c_Be_in_BeO" />
+ <sab name="c_O_in_BeO" />
+ </material>
+ <material id="4">
+ <density units="g/cm3" value="5.90168" />
+ <nuclide ao="0.3" name="H1" />
+ <nuclide ao="0.15" name="Zr90" />
+ <nuclide ao="0.1" name="Zr91" />
+ <nuclide ao="0.1" name="Zr92" />
+ <nuclide ao="0.05" name="Zr94" />
+ <nuclide ao="0.05" name="Zr96" />
+ <nuclide ao="0.1" name="U235" />
+ <nuclide ao="0.15" name="U238" />
+ <sab name="c_Zr_in_ZrH" />
+ <sab name="c_H_in_ZrH" />
+ </material>
+</materials>
+<?xml version='1.0' encoding='utf-8'?>
+<settings>
+ <run_mode>eigenvalue</run_mode>
+ <particles>1000</particles>
+ <batches>5</batches>
+ <inactive>0</inactive>
+ <source strength="1.0">
+ <space type="box">
+ <parameters>-4 -4 -4 4 4 4</parameters>
+ </space>
+ </source>
+</settings>
diff --git a/tests/test_salphabeta/materials.xml b/tests/test_salphabeta/materials.xml
deleted file mode 100644
--- a/tests/test_salphabeta/materials.xml
+++ /dev/null
@@ -1,41 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
- <material id="1">
- <density value="4.5" units="g/cc" />
- <nuclide name="U235" ao="1.0" />
- <nuclide name="H1" ao="1.0" />
- <sab name="c_H_in_H2O" />
- </material>
-
- <material id="2">
- <density value="4.5" units="g/cc" />
- <nuclide name="U235" ao="1.0" />
- <nuclide name="C0" ao="1.0" />
- <sab name="c_Graphite" />
- </material>
-
- <material id="3">
- <density value="4.5" units="g/cc" />
- <nuclide name="U235" ao="1.0" />
- <nuclide name="Be9" ao="1.0" />
- <nuclide name="O16" ao="1.0" />
- <sab name="c_Be_in_BeO" />
- <sab name="c_O_in_BeO" />
- </material>
-
- <material id="4">
- <density value="5.90168" units="g/cm3" />
- <nuclide name="H1" ao="0.3" />
- <nuclide name="Zr90" ao="0.15" />
- <nuclide name="Zr91" ao="0.1" />
- <nuclide name="Zr92" ao="0.1" />
- <nuclide name="Zr94" ao="0.05" />
- <nuclide name="Zr96" ao="0.05" />
- <nuclide name="U235" ao="0.1" />
- <nuclide name="U238" ao="0.15" />
- <sab name="c_Zr_in_ZrH" />
- <sab name="c_H_in_ZrH" />
- </material>
-
-</materials>
diff --git a/tests/test_salphabeta/results_true.dat b/tests/test_salphabeta/results_true.dat
--- a/tests/test_salphabeta/results_true.dat
+++ b/tests/test_salphabeta/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-8.544160E-01 1.274133E-02
+8.447580E-01 1.806149E-02
diff --git a/tests/test_salphabeta/settings.xml b/tests/test_salphabeta/settings.xml
deleted file mode 100644
--- a/tests/test_salphabeta/settings.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
- <run_mode>eigenvalue</run_mode>
- <batches>10</batches>
- <inactive>5</inactive>
- <particles>1000</particles>
-
- <source>
- <space type="box">
- <parameters>-4 -4 -4 4 4 4</parameters>
- </space>
- </source>
-
-</settings>
diff --git a/tests/test_salphabeta/test_salphabeta.py b/tests/test_salphabeta/test_salphabeta.py
--- a/tests/test_salphabeta/test_salphabeta.py
+++ b/tests/test_salphabeta/test_salphabeta.py
@@ -3,9 +3,82 @@
import os
import sys
sys.path.insert(0, os.pardir)
-from testing_harness import TestHarness
+
+from testing_harness import PyAPITestHarness
+import openmc
+import openmc.model
+
+
+def make_model():
+ model = openmc.model.Model()
+
+ # Materials
+ m1 = openmc.Material()
+ m1.set_density('g/cc', 4.5)
+ m1.add_nuclide('U235', 1.0)
+ m1.add_nuclide('H1', 1.0)
+ m1.add_s_alpha_beta('c_H_in_H2O', fraction=0.5)
+
+ m2 = openmc.Material()
+ m2.set_density('g/cc', 4.5)
+ m2.add_nuclide('U235', 1.0)
+ m2.add_nuclide('C0', 1.0)
+ m2.add_s_alpha_beta('c_Graphite')
+
+ m3 = openmc.Material()
+ m3.set_density('g/cc', 4.5)
+ m3.add_nuclide('U235', 1.0)
+ m3.add_nuclide('Be9', 1.0)
+ m3.add_nuclide('O16', 1.0)
+ m3.add_s_alpha_beta('c_Be_in_BeO')
+ m3.add_s_alpha_beta('c_O_in_BeO')
+
+ m4 = openmc.Material()
+ m4.set_density('g/cm3', 5.90168)
+ m4.add_nuclide('H1', 0.3)
+ m4.add_nuclide('Zr90', 0.15)
+ m4.add_nuclide('Zr91', 0.1)
+ m4.add_nuclide('Zr92', 0.1)
+ m4.add_nuclide('Zr94', 0.05)
+ m4.add_nuclide('Zr96', 0.05)
+ m4.add_nuclide('U235', 0.1)
+ m4.add_nuclide('U238', 0.15)
+ m4.add_s_alpha_beta('c_Zr_in_ZrH')
+ m4.add_s_alpha_beta('c_H_in_ZrH')
+
+ model.materials += [m1, m2, m3, m4]
+
+ # Geometry
+ x0 = openmc.XPlane(x0=-10, boundary_type='vacuum')
+ x1 = openmc.XPlane(x0=-5)
+ x2 = openmc.XPlane(x0=0)
+ x3 = openmc.XPlane(x0=5)
+ x4 = openmc.XPlane(x0=10, boundary_type='vacuum')
+
+ root_univ = openmc.Universe()
+
+ surfs = (x0, x1, x2, x3, x4)
+ mats = (m1, m2, m3, m4)
+ cells = []
+ for i in range(4):
+ cell = openmc.Cell()
+ cell.region = +surfs[i] & -surfs[i+1]
+ cell.fill = mats[i]
+ root_univ.add_cell(cell)
+
+ model.geometry.root_universe = root_univ
+
+ # Settings
+ model.settings.batches = 5
+ model.settings.inactive = 0
+ model.settings.particles = 1000
+ model.settings.source = openmc.Source(space=openmc.stats.Box(
+ [-4, -4, -4], [4, 4, 4]))
+
+ return model
if __name__ == '__main__':
- harness = TestHarness('statepoint.10.h5')
+ model = make_model()
+ harness = PyAPITestHarness('statepoint.5.h5', model)
harness.main()
| Nuclides with partial S(alpha, beta) tables
Some reactor materials have isotopes which appear in a mixture of different molecular structures. For example, the carbon in TREAT fuel assemblies is usually treated as a mixture of graphite and amorphus carbon. In these cases, we need to apply S(alpha, beta) tables to only a fraction of the atoms in that material.
I've made a [branch](https://github.com/smharper/openmc/tree/partial_sab) that I believe implements all the necessary code. I still need to update docs/relaxNG/tests, but that might take a while as I'll be out of town for a bit. @tjlaboss, can you test this branch and make sure it gives the expected results for your problem? To use it, set the optional `fraction` argument when calling `material.add_s_alpha_beta`.
| 2017-06-29T20:07:27Z | [] | [] |
|
openmc-dev/openmc | 918 | openmc-dev__openmc-918 | [
"549"
] | 39a02887d1a6ea0716996f18ba3a5d45b3f8159a | diff --git a/openmc/tallies.py b/openmc/tallies.py
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -4,7 +4,7 @@
import copy
import re
from functools import partial
-import itertools
+from itertools import product
from numbers import Integral, Real
import warnings
from xml.etree import ElementTree as ET
@@ -1329,7 +1329,7 @@ def get_filter_indices(self, filters=[], filter_bins=[]):
if isinstance(self_filter, openmc.MeshFilter):
dimension = self_filter.mesh.dimension
xyz = [range(1, x+1) for x in dimension]
- bins = list(itertools.product(*xyz))
+ bins = list(product(*xyz))
# Create list of 2-tuples for energy boundary bins
elif isinstance(self_filter, (openmc.EnergyFilter,
@@ -1364,7 +1364,7 @@ def get_filter_indices(self, filters=[], filter_bins=[]):
indices *= self_filter.num_bins
# Apply outer product sum between all filter bin indices
- filter_indices = list(map(sum, itertools.product(*filter_indices)))
+ filter_indices = list(map(sum, product(*filter_indices)))
# If user did not specify any specific Filters, use them all
else:
@@ -1880,7 +1880,7 @@ def hybrid_product(self, other, binary_op, filter_product=None,
new_tally.filters.append(self_filter)
else:
all_filters = [self_copy.filters, other_copy.filters]
- for self_filter, other_filter in itertools.product(*all_filters):
+ for self_filter, other_filter in product(*all_filters):
new_filter = openmc.CrossFilter(self_filter, other_filter,
binary_op)
new_tally.filters.append(new_filter)
@@ -1891,20 +1891,31 @@ def hybrid_product(self, other, binary_op, filter_product=None,
new_tally.nuclides.append(self_nuclide)
else:
all_nuclides = [self_copy.nuclides, other_copy.nuclides]
- for self_nuclide, other_nuclide in itertools.product(*all_nuclides):
- new_nuclide = \
- openmc.CrossNuclide(self_nuclide, other_nuclide, binary_op)
+ for self_nuclide, other_nuclide in product(*all_nuclides):
+ new_nuclide = openmc.CrossNuclide(self_nuclide, other_nuclide,
+ binary_op)
new_tally.nuclides.append(new_nuclide)
+ # Define helper function that handles score units appropriately
+ # depending on the binary operator
+ def cross_score(score1, score2, binary_op):
+ if binary_op == '+' or binary_op == '-':
+ if score1 == score2:
+ return score1
+ else:
+ return openmc.CrossScore(score1, score2, binary_op)
+ else:
+ return openmc.CrossScore(score1, score2, binary_op)
+
# Add scores to the new tally
if score_product == 'entrywise':
for self_score in self_copy.scores:
- new_tally.scores.append(self_score)
+ new_score = cross_score(self_score, self_score, binary_op)
+ new_tally.scores.append(new_score)
else:
all_scores = [self_copy.scores, other_copy.scores]
- for self_score, other_score in itertools.product(*all_scores):
- new_score = openmc.CrossScore(self_score, other_score,
- binary_op)
+ for self_score, other_score in product(*all_scores):
+ new_score = cross_score(self_score, other_score, binary_op)
new_tally.scores.append(new_score)
# Update the new tally's filter strides
@@ -2142,7 +2153,7 @@ def _swap_filters(self, filter1, filter2):
std_dev = {}
# Store the data from the misaligned structure
- for i, (bin1, bin2) in enumerate(itertools.product(filter1_bins, filter2_bins)):
+ for i, (bin1, bin2) in enumerate(product(filter1_bins, filter2_bins)):
filter_bins = [(bin1,), (bin2,)]
if self.mean is not None:
@@ -2163,7 +2174,7 @@ def _swap_filters(self, filter1, filter2):
self._update_filter_strides()
# Realign the data
- for i, (bin1, bin2) in enumerate(itertools.product(filter1_bins, filter2_bins)):
+ for i, (bin1, bin2) in enumerate(product(filter1_bins, filter2_bins)):
filter_bins = [(bin1,), (bin2,)]
indices = self.get_filter_indices(filters, filter_bins)
| diff --git a/tests/test_filter_energyfun/results_true.dat b/tests/test_filter_energyfun/results_true.dat
--- a/tests/test_filter_energyfun/results_true.dat
+++ b/tests/test_filter_energyfun/results_true.dat
@@ -1,2 +1,2 @@
- energyfunction nuclide score mean std. dev.
-0 02180f5f310ee4 Am241 (n,gamma) 1.00e-01 9.97e-03
+ energyfunction nuclide score mean std. dev.
+0 02180f5f310ee4 Am241 ((n,gamma) / (n,gamma)) 1.00e-01 9.97e-03
| Units on division of scores with tally arithmetic
When two scores are divided that have the same units, currently you get a derived score with the same units as the two scores, e.g. if you have an absorption score divided by another absorption score, the resulting quantity will be shown with units of absorption rather than absorption / absorption. This can be seen in Out[27] in the [tally arithmetic notebook](http://openmc.readthedocs.org/en/latest/pythonapi/examples/tally-arithmetic.html). This would be the correct behavior for addition and subtraction but for multiplication and division (and I suppose for exponentiation), having the same units doesn't mean the derived score should have the same units. As I understand, this should be a fairly trivial fix with @samuelshaner's new hybrid_product capability.
| Each value in a Tally will have "units" that describe the scores, nuclides, and filters used to produce the value. Currently, the units of a derived tally will depend on type of product performed, entrywise or tensor, over the scores, nuclides, and filters:
- **Entrywise Product**: An entrywise product is only performed on values that have the same units. For instances, cell [27] of tally-arithmetic.ipynb performs an entrywise product across scores, nuclides, and filters. The units from an entrywise product will always be the units of the common score/nuclide/filter.
- **Tensor Product**: A tensor product is performed on values irregardless of units. For instances, cell [30] of tally-arithmetic.ipynb performs a tensor product across scores and an entrywise product across nuclides and filters. The units from a tensor product will be `(units left) binary_op (units right)`.
As @paulromano alluded to, it would be better if the units took into account the operation being performed instead of the type of product, so:
- **\+ or -**: If the units of the operands are the same, the units of the derived tally are the common units. If the units are different, the units of the derived tally are `(units left) binary_op (units right)`.
- *** or /**: The units of the derived tally are `(units left) binary_op (units right)`.
- **^**: The units of the derived tally are `(units left) binary_op (exponent)`.
I'll submit a PR with these changes sometime this week.
| 2017-10-04T14:58:03Z | [] | [] |
openmc-dev/openmc | 1,147 | openmc-dev__openmc-1147 | [
"975"
] | 5f8f7d183c20403dcf8aed7409ddbd9f26789896 | diff --git a/openmc/settings.py b/openmc/settings.py
--- a/openmc/settings.py
+++ b/openmc/settings.py
@@ -11,7 +11,7 @@
from openmc import VolumeCalculation, Source, Mesh
_RUN_MODES = ['eigenvalue', 'fixed source', 'plot', 'volume', 'particle restart']
-_RES_SCAT_METHODS = ['dbrc', 'wcm', 'ares']
+_RES_SCAT_METHODS = ['dbrc', 'rvs']
class Settings(object):
@@ -82,14 +82,13 @@ class Settings(object):
Settings for resonance elastic scattering. Accepted keys are 'enable'
(bool), 'method' (str), 'energy_min' (float), 'energy_max' (float), and
'nuclides' (list). The 'method' can be set to 'dbrc' (Doppler broadening
- rejection correction), 'wcm' (weight correction method), and 'ares'
- (accelerated resonance elastic scattering). If not specified, 'ares' is
- the default method. The 'energy_min' and 'energy_max' values indicate
- the minimum and maximum energies above and below which the resonance
- elastic scattering method is to be applied. The 'nuclides' list
- indicates what nuclides the method should be applied to. In its absence,
- the method will be applied to all nuclides with 0 K elastic scattering
- data present.
+ rejection correction) or 'rvs' (relative velocity sampling). If not
+ specified, 'rvs' is the default method. The 'energy_min' and
+ 'energy_max' values indicate the minimum and maximum energies above and
+ below which the resonance elastic scattering method is to be
+ applied. The 'nuclides' list indicates what nuclides the method should
+ be applied to. In its absence, the method will be applied to all
+ nuclides with 0 K elastic scattering data present.
run_mode : {'eigenvalue', 'fixed source', 'plot', 'volume', 'particle restart'}
The type of calculation to perform (default is 'eigenvalue')
seed : int
| diff --git a/tests/regression_tests/resonance_scattering/inputs_true.dat b/tests/regression_tests/resonance_scattering/inputs_true.dat
--- a/tests/regression_tests/resonance_scattering/inputs_true.dat
+++ b/tests/regression_tests/resonance_scattering/inputs_true.dat
@@ -26,7 +26,7 @@
</source>
<resonance_scattering>
<enable>true</enable>
- <method>ares</method>
+ <method>rvs</method>
<energy_min>1.0</energy_min>
<energy_max>210.0</energy_max>
<nuclides>U238 U235 Pu239</nuclides>
diff --git a/tests/regression_tests/resonance_scattering/test.py b/tests/regression_tests/resonance_scattering/test.py
--- a/tests/regression_tests/resonance_scattering/test.py
+++ b/tests/regression_tests/resonance_scattering/test.py
@@ -28,7 +28,7 @@ def _build_inputs(self):
'enable': True,
'energy_min': 1.0,
'energy_max': 210.0,
- 'method': 'ares',
+ 'method': 'rvs',
'nuclides': ['U238', 'U235', 'Pu239']
}
diff --git a/tests/unit_tests/test_settings.py b/tests/unit_tests/test_settings.py
--- a/tests/unit_tests/test_settings.py
+++ b/tests/unit_tests/test_settings.py
@@ -40,7 +40,7 @@ def test_export_to_xml(run_in_tmpdir):
s.trace = (10, 1, 20)
s.track = [1, 1, 1, 2, 1, 1]
s.ufs_mesh = mesh
- s.resonance_scattering = {'enable': True, 'method': 'ares',
+ s.resonance_scattering = {'enable': True, 'method': 'rvs',
'energy_min': 1.0, 'energy_max': 1000.0,
'nuclides': ['U235', 'U238', 'Pu239']}
s.volume_calculations = openmc.VolumeCalculation(
| tallied weight w/ WCM resonance scattering
https://github.com/mit-crpg/openmc/blob/37c6d4a0f58a2143a51f7fd47689c6e492fdc024/src/tallies/tally.F90#L1015 needs to tally `wgt` instead of `last_wgt` for WCM resonance scattering to produce the correct fixed source answer for a tally with an elastic scattering score (specified using the MT number 2). I haven't checked if this is a subset of a larger bug or if this change would adversely affect anything but the case I described.
| 2019-01-11T14:25:31Z | [] | [] |
|
openmc-dev/openmc | 1,166 | openmc-dev__openmc-1166 | [
"1137",
"1137"
] | f5b1a39d4a55c8560bb9e6a2e305fb969c9817f5 | diff --git a/openmc/data/data.py b/openmc/data/data.py
--- a/openmc/data/data.py
+++ b/openmc/data/data.py
@@ -141,8 +141,8 @@
def atomic_mass(isotope):
"""Return atomic mass of isotope in atomic mass units.
- Atomic mass data comes from the `Atomic Mass Evaluation 2012
- <https://www-nds.iaea.org/amdc/ame2012/AME2012-1.pdf>`_.
+ Atomic mass data comes from the `Atomic Mass Evaluation 2016
+ <https://www-nds.iaea.org/amdc/ame2016/AME2016-a.pdf>`_.
Parameters
----------
@@ -157,8 +157,8 @@ def atomic_mass(isotope):
"""
if not _ATOMIC_MASS:
- # Load data from AME2012 file
- mass_file = os.path.join(os.path.dirname(__file__), 'mass.mas12')
+ # Load data from AME2016 file
+ mass_file = os.path.join(os.path.dirname(__file__), 'mass16.txt')
with open(mass_file, 'r') as ame:
# Read lines in file starting at line 40
for line in itertools.islice(ame, 39, None):
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -32,7 +32,7 @@
# Data files and librarries
'package_data': {
'openmc.capi': ['libopenmc.{}'.format(suffix)],
- 'openmc.data': ['mass.mas12', 'BREMX.DAT', '*.h5']
+ 'openmc.data': ['mass16.txt', 'BREMX.DAT', '*.h5']
},
# Metadata
| diff --git a/tests/unit_tests/test_data_misc.py b/tests/unit_tests/test_data_misc.py
--- a/tests/unit_tests/test_data_misc.py
+++ b/tests/unit_tests/test_data_misc.py
@@ -51,14 +51,14 @@ def test_thin():
def test_atomic_mass():
- assert openmc.data.atomic_mass('H1') == 1.00782503223
- assert openmc.data.atomic_mass('U235') == 235.043930131
+ assert openmc.data.atomic_mass('H1') == 1.00782503224
+ assert openmc.data.atomic_mass('U235') == 235.04392819
with pytest.raises(KeyError):
openmc.data.atomic_mass('U100')
def test_atomic_weight():
- assert openmc.data.atomic_weight('C') == 12.011115164862904
+ assert openmc.data.atomic_weight('C') == 12.011115164864455
with pytest.raises(ValueError):
openmc.data.atomic_weight('Qt')
| Update atomic mass evaluation to AME 2016
The atomic mass data we use for `openmc.data.atomic_mass(...)` is from the 2012 atomic mass evaluation. There is an updated evaluated from 2016 that is [available](https://www-nds.iaea.org/amdc/).
Update atomic mass evaluation to AME 2016
The atomic mass data we use for `openmc.data.atomic_mass(...)` is from the 2012 atomic mass evaluation. There is an updated evaluated from 2016 that is [available](https://www-nds.iaea.org/amdc/).
| 2019-02-13T23:47:45Z | [] | [] |
|
openmc-dev/openmc | 1,171 | openmc-dev__openmc-1171 | [
"859"
] | ef2767a127225e72c76a0170edaa05d606eaa2d6 | diff --git a/openmc/capi/core.py b/openmc/capi/core.py
--- a/openmc/capi/core.py
+++ b/openmc/capi/core.py
@@ -47,6 +47,7 @@ class _Bank(Structure):
c_double, _array_1d_int, _array_1d_int]
_dll.openmc_initialize_linsolver.argtypes = _init_linsolver_argtypes
_dll.openmc_initialize_linsolver.restype = None
+_dll.openmc_master.restype = c_bool
_dll.openmc_next_batch.argtypes = [POINTER(c_int)]
_dll.openmc_next_batch.restype = c_int
_dll.openmc_next_batch.errcheck = _error_handler
@@ -251,7 +252,7 @@ def master():
Whether is master processor or not
"""
- return c_bool.in_dll(_dll, 'openmc_master').value
+ return _dll.openmc_master()
def next_batch():
diff --git a/openmc/capi/filter.py b/openmc/capi/filter.py
--- a/openmc/capi/filter.py
+++ b/openmc/capi/filter.py
@@ -1,6 +1,6 @@
from collections.abc import Mapping
from ctypes import c_int, c_int32, c_double, c_char_p, POINTER, \
- create_string_buffer
+ create_string_buffer, c_size_t
from weakref import WeakValueDictionary
import numpy as np
@@ -34,9 +34,6 @@
_dll.openmc_energy_filter_set_bins.argtypes = [c_int32, c_int32, POINTER(c_double)]
_dll.openmc_energy_filter_set_bins.restype = c_int
_dll.openmc_energy_filter_set_bins.errcheck = _error_handler
-_dll.openmc_extend_filters.argtypes = [c_int32, POINTER(c_int32), POINTER(c_int32)]
-_dll.openmc_extend_filters.restype = c_int
-_dll.openmc_extend_filters.errcheck = _error_handler
_dll.openmc_filter_get_id.argtypes = [c_int32, POINTER(c_int32)]
_dll.openmc_filter_get_id.restype = c_int
_dll.openmc_filter_get_id.errcheck = _error_handler
@@ -46,9 +43,6 @@
_dll.openmc_filter_set_id.argtypes = [c_int32, c_int32]
_dll.openmc_filter_set_id.restype = c_int
_dll.openmc_filter_set_id.errcheck = _error_handler
-_dll.openmc_filter_set_type.argtypes = [c_int32, c_char_p]
-_dll.openmc_filter_set_type.restype = c_int
-_dll.openmc_filter_set_type.errcheck = _error_handler
_dll.openmc_get_filter_index.argtypes = [c_int32, POINTER(c_int32)]
_dll.openmc_get_filter_index.restype = c_int
_dll.openmc_get_filter_index.errcheck = _error_handler
@@ -77,6 +71,9 @@
_dll.openmc_meshsurface_filter_set_mesh.argtypes = [c_int32, c_int32]
_dll.openmc_meshsurface_filter_set_mesh.restype = c_int
_dll.openmc_meshsurface_filter_set_mesh.errcheck = _error_handler
+_dll.openmc_new_filter.argtypes = [c_char_p, POINTER(c_int32)]
+_dll.openmc_new_filter.restype = c_int
+_dll.openmc_new_filter.errcheck = _error_handler
_dll.openmc_spatial_legendre_filter_get_order.argtypes = [c_int32, POINTER(c_int)]
_dll.openmc_spatial_legendre_filter_get_order.restype = c_int
_dll.openmc_spatial_legendre_filter_get_order.errcheck = _error_handler
@@ -95,6 +92,7 @@
_dll.openmc_zernike_filter_set_order.argtypes = [c_int32, c_int]
_dll.openmc_zernike_filter_set_order.restype = c_int
_dll.openmc_zernike_filter_set_order.errcheck = _error_handler
+_dll.tally_filters_size.restype = c_size_t
class Filter(_FortranObjectWithID):
__instances = WeakValueDictionary()
@@ -111,13 +109,10 @@ def __new__(cls, obj=None, uid=None, new=True, index=None):
raise AllocationError('A filter with ID={} has already '
'been allocated.'.format(uid))
- # Resize internal array
- index = c_int32()
- _dll.openmc_extend_filters(1, index, None)
-
# Set the filter type -- note that the filter_type attribute
# only exists on subclasses!
- _dll.openmc_filter_set_type(index, cls.filter_type.encode())
+ index = c_int32()
+ _dll.openmc_new_filter(cls.filter_type.encode(), index)
index = index.value
else:
index = mapping[uid]._index
@@ -413,7 +408,7 @@ def __iter__(self):
yield _get_filter(i + 1).id
def __len__(self):
- return c_int32.in_dll(_dll, 'n_filters').value
+ return _dll.tally_filters_size()
def __repr__(self):
return repr(dict(self))
diff --git a/openmc/capi/nuclide.py b/openmc/capi/nuclide.py
--- a/openmc/capi/nuclide.py
+++ b/openmc/capi/nuclide.py
@@ -1,5 +1,5 @@
from collections.abc import Mapping
-from ctypes import c_int, c_char_p, POINTER
+from ctypes import c_int, c_char_p, POINTER, c_size_t
from weakref import WeakValueDictionary
import numpy as np
@@ -23,7 +23,7 @@
_dll.openmc_nuclide_name.argtypes = [c_int, POINTER(c_char_p)]
_dll.openmc_nuclide_name.restype = c_int
_dll.openmc_nuclide_name.errcheck = _error_handler
-_dll.nuclides_size.restype = c_int
+_dll.nuclides_size.restype = c_size_t
def load_nuclide(name):
diff --git a/openmc/capi/tally.py b/openmc/capi/tally.py
--- a/openmc/capi/tally.py
+++ b/openmc/capi/tally.py
@@ -26,13 +26,10 @@
_dll.openmc_global_tallies.argtypes = [POINTER(POINTER(c_double))]
_dll.openmc_global_tallies.restype = c_int
_dll.openmc_global_tallies.errcheck = _error_handler
-_dll.openmc_tally_allocate.argtypes = [c_int32, c_char_p]
-_dll.openmc_tally_allocate.restype = c_int
-_dll.openmc_tally_allocate.errcheck = _error_handler
_dll.openmc_tally_get_active.argtypes = [c_int32, POINTER(c_bool)]
_dll.openmc_tally_get_active.restype = c_int
_dll.openmc_tally_get_active.errcheck = _error_handler
-_dll.openmc_tally_get_estimator.argtypes = [c_int32, POINTER(c_int32)]
+_dll.openmc_tally_get_estimator.argtypes = [c_int32, POINTER(c_int)]
_dll.openmc_tally_get_estimator.restype = c_int
_dll.openmc_tally_get_estimator.errcheck = _error_handler
_dll.openmc_tally_get_id.argtypes = [c_int32, POINTER(c_int32)]
@@ -84,6 +81,7 @@
_dll.openmc_tally_set_type.argtypes = [c_int32, c_char_p]
_dll.openmc_tally_set_type.restype = c_int
_dll.openmc_tally_set_type.errcheck = _error_handler
+_dll.tallies_size.restype = c_size_t
_SCORES = {
@@ -195,7 +193,6 @@ def __new__(cls, uid=None, new=True, index=None):
index = c_int32()
_dll.openmc_extend_tallies(1, index, None)
- _dll.openmc_tally_allocate(index, b'generic')
index = index.value
else:
index = mapping[uid]._index
@@ -227,7 +224,7 @@ def type(self, type):
@property
def estimator(self):
- estimator = c_int32()
+ estimator = c_int()
_dll.openmc_tally_get_estimator(self._index, estimator)
return _ESTIMATORS[estimator.value]
@@ -387,7 +384,7 @@ def __iter__(self):
yield Tally(index=i + 1).id
def __len__(self):
- return c_int32.in_dll(_dll, 'n_tallies').value
+ return _dll.tallies_size()
def __repr__(self):
return repr(dict(self))
diff --git a/tools/ci/travis-install.py b/tools/ci/travis-install.py
--- a/tools/ci/travis-install.py
+++ b/tools/ci/travis-install.py
@@ -34,8 +34,6 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False):
# Use MPI wrappers when building in parallel
if mpi:
- os.environ['FC'] = 'mpifort' if which('mpifort') else 'mpif90'
- os.environ['CC'] = 'mpicc'
os.environ['CXX'] = 'mpicxx'
# Tell CMake to prefer parallel HDF5 if specified
@@ -49,7 +47,7 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False):
if dagmc:
cmake_cmd.append('-Ddagmc=ON')
-
+
# Build and install
cmake_cmd.append('..')
print(' '.join(cmake_cmd))
| diff --git a/tests/check_source.py b/tests/check_source.py
deleted file mode 100755
--- a/tests/check_source.py
+++ /dev/null
@@ -1,230 +0,0 @@
-#!/usr/bin/env python3
-
-import glob
-from string import whitespace
-from sys import exit
-from textwrap import TextWrapper
-
-
-################################################################################
-# Fortran reading/parsing backend.
-################################################################################
-
-
-class LineOfCode(object):
- """Contains and provides basic info about a line of Fortran 90 code."""
- def __init__(self, number, content, is_continuation=False,
- string_terminator=None):
- # Initialize member variables.
- self.number = number
- self.content = content
- self.is_continuation = is_continuation
- self.is_continued = False
- assert (string_terminator is None or
- string_terminator == "'" or
- string_terminator == '"')
- self.initial_string_terminator = string_terminator
- self.final_string_terminator = None
- self.is_comment_only = False
-
- # Parse the string.
- self.parse()
-
- def __repr__(self):
- rep = 'LineOfCode: line number = {0:d}\n'.format(self.number)
- rep += '\tis_continuation = ' + str(self.is_continuation) + '\n'
- rep += '\tis_continued = ' + str(self.is_continued) + '\n'
- rep += ('\tinitial_string_terminator = '
- + str(self.initial_string_terminator) + '\n')
- rep += ('\tfinal_string_terminator = '
- + str(self.final_string_terminator) + '\n')
- rep += '\tis_comment_only = ' + str(self.is_comment_only) + '\n'
- rep += '\tContent:\n' + self.content
- return rep
-
- def __str__(self):
- return repr(self)
-
- def parse(self):
- # Initialize the string variables.
- if self.initial_string_terminator == "'":
- in_a_single_quote = True
- in_a_double_quote = False
- elif self.initial_string_terminator == '"':
- in_a_single_quote = False
- in_a_double_quote = True
- else:
- in_a_single_quote = False
- in_a_double_quote = False
-
- # Initialize other variables.
- in_a_comment = False
- ends_with_ampersand = False
- has_real_content = False
-
- # Parse through the line.
- for char in self.content:
- # Check for the start or end of strings.
- if char == "'" and in_a_single_quote:
- in_a_single_quote = False
- elif char == "'" and not in_a_double_quote:
- in_a_single_quote = True
- elif char == '"' and in_a_double_quote:
- in_a_double_quote = False
- elif char == '"' and not in_a_single_quote:
- in_a_double_quote = True
-
- # Check for the start of a comment.
- if (char == "!" and not in_a_single_quote
- and not in_a_double_quote):
- in_a_comment = True
- break # Don't care about anything in a comment.
-
- # Check for a continuation ampersand.
- if char == "&":
- ends_with_ampersand = True
- elif all([char != w for w in whitespace]):
- ends_with_ampersand = False
-
- # Check to see if there is any real content (non-whitespace, not in
- # a comment)
- if (not in_a_comment) and all([char != w for w in whitespace]):
- has_real_content = True
-
- # Make sure nothing went terribly wrong.
- assert not (in_a_single_quote and in_a_double_quote)
- assert not (in_a_single_quote and in_a_comment)
- assert not (in_a_double_quote and in_a_comment)
-
- # Is this line continued onto the next?
- if ends_with_ampersand:
- self.is_continued = True
-
- # Is a multiline string continued on the next line?
- if in_a_single_quote:
- assert self.is_continued
- self.final_string_terminator = "'"
- if in_a_double_quote:
- assert self.is_continued
- self.final_string_terminator = '"'
-
- # Is this line a comment-only line?
- if (not has_real_content) and in_a_comment:
- self.is_comment_only = True
-
- def get_indent(self):
- """Return the number of indentation spaces prefixing this line."""
- return len(self.content) - len(self.content.lstrip(' '))
-
- def contains_whitespace_only(self):
- """Return True/False if all characters in the line are whitespace."""
- if len(self.content.strip('\n')) == 0: return False
- is_ws = [ any([char == ws for ws in whitespace])
- for char in self.content.strip('\n') ]
- return all(is_ws)
-
- def has_trailing_whitespace(self):
- """Return True/False if this line ends with a whitespace character."""
- stripped = self.content.strip('\n')
- if len(stripped) == 0: return False
- return any([stripped[-1] == ws for ws in whitespace])
-
- def contains_tab(self):
- """Return True/False if a tab character appears in the line."""
- return '\t' in self.content
-
-
-def read_lines_of_code(fname):
- line_num = 0
- cont = False
- str_term = None
- with open(fname) as fin:
- for line in fin:
- loc = LineOfCode(line_num, line, is_continuation=cont,
- string_terminator=str_term)
- cont = loc.is_continued
- str_term = loc.final_string_terminator
- line_num += 1
- yield loc
-
-
-################################################################################
-# Error checking.
-################################################################################
-
-
-def print_error(fname, line_number, err_msg):
- header = "Error in file {0}, line {1}:".format(fname, line_number + 1)
-
- tw = TextWrapper(width=80, initial_indent=' '*4, subsequent_indent=' '*4)
- body = '\n'.join(tw.wrap(err_msg))
-
- print(header + '\n' + body + '\n')
-
-
-def check_source(fname):
- """Make sure the given Fortran source file meets OpenMC standards.
-
- If errors are found, messages will be printed to the screen describing the
- error. The function will return True if no errors were found or False
- otherwise.
- """
- good_code = True
- base_indent = 0
-
- for loc in read_lines_of_code(fname):
- # Check for extra whitespace errors.
- if loc.contains_whitespace_only():
- good_code = False
- print_error(fname, loc.number, "Line contains whitespace "
- "characters but no content. Please remove whitespace.")
- elif loc.has_trailing_whitespace():
- good_code = False
- print_error(fname, loc.number, "Line has trailing whitespace after"
- " the content. Please remove trailing whitespace.")
- if loc.contains_tab():
- good_code = False
- print_error(fname, loc.number, "Line contains a tab character. "
- "Please replace with single whitespace characters.")
-
- # Check indentation.
- current_indent = loc.get_indent()
- if ((not loc.is_continuation) and (not loc.is_comment_only) and
- (not loc.contains_whitespace_only()) and current_indent % 2 != 0):
- good_code = False
- print_error(fname, loc.number, "Line is indented an odd number of "
- "spaces. All non-continuation lines should be indented an "
- "even number of spaces.")
- if loc.is_continuation and current_indent < base_indent + 5:
- good_code = False
- print_error(fname, loc.number, "Continuation lines must be "
- "indented by at least 5 spaces, but this line is indented {0}"
- " spaces.".format(current_indent - base_indent))
-
- # Set base indentation for next lines.
- if not loc.is_continuation:
- base_indent = current_indent
-
- return good_code
-
-
-################################################################################
-# Main loop.
-################################################################################
-
-
-if __name__ == '__main__':
- # Get a list of the F90 source files.
- f90_files = glob.glob('../src/*.F90')
-
- # Make sure we found the source files.
- assert len(f90_files) != 0, 'No .F90 source files found.'
-
- # Make sure all the F90 source files meet our standards.
- good_code = [check_source(fname) for fname in f90_files]
- if not all(good_code):
- print("ERROR: The Fortran source code does not meet OpenMC's standards")
- exit(-1)
- else:
- print("SUCCESS! Looks like the Fortran source meets our standards")
- exit(0)
diff --git a/tests/unit_tests/test_math.py b/tests/unit_tests/test_math.py
--- a/tests/unit_tests/test_math.py
+++ b/tests/unit_tests/test_math.py
@@ -108,7 +108,7 @@ def test_calc_zn():
rho = 0.5
phi = 0.5
- # Reference solution from running the Fortran implementation
+ # Reference solution from running the C++ implementation
ref_vals = np.array([
1.00000000e+00, 2.39712769e-01, 4.38791281e-01,
2.10367746e-01, -5.00000000e-01, 1.35075576e-01,
@@ -142,7 +142,7 @@ def test_calc_zn_rad():
n = 10
rho = 0.5
- # Reference solution from running the Fortran implementation
+ # Reference solution from running the C++ implementation
ref_vals = np.array([
1.00000000e+00, -5.00000000e-01, -1.25000000e-01,
4.37500000e-01, -2.89062500e-01,-8.98437500e-02])
| Runtime error with PGI community edition 17.10
PGI has a compiler bug that prevents OpenMC from compiling:
```
PGF90-S-0038-Symbol, size, has not been explicitly declared (/home/romano/openmc/src/stl_vector.F90)
1 inform, 0 warnings, 1 severes, 0 fatal for clear_int
```
I've run into problems with PGI before getting confused when you have local variables defined somewhere that have the same name as an intrinsic (preventing it from being used elsewhere even though it doesn't make any sense). I'm going to file a report with PGI and look into workaround ahead of our 0.9 release.
| Evidently the community edition also [doesn't work](https://www.pgroup.com/userforum/viewtopic.php?t=5442&view=previous&sid=ce9240125d2b931f57417ef29279246f) for C++ if the system you're compiling on uses GNU 6.0+ C++ headers. Supposed to be fixed in version 17 which has only been released as the professional edition (not the community edition).
I have a workaround for the PGF90-S-0038 error but now ran into:
```
PGF90-S-0155-Dummy argument names must be the same as those in parent's interface for type bound procedure get_next_bin_energyfunction (/home/romano/openmc/src/tally_filter.F90: 1649)
```
Doesn't make sense to me as the dummy argument names do match those of the parent's interface. I will file yet another bug report to PGI.
Evidently the first compiler bug is [already fixed](http://www.pgroup.com/userforum/viewtopic.php?p=21686) in the latest release and a new community edition will be out soon.
I've confirmed that both of the previous bugs mentioned are now fixed in PGI community edition 17.4. However, now that I've gotten past those issues, I've uncovered yet another bug, which I [just reported to PGI](http://www.pgroup.com/userforum/viewtopic.php?p=21785).
To elaborate on the problem a little bit: the compiler chokes when reading an internal file that has newline characters in it. This causes `get_node_array_*` from `xml_interface.F90` to fail because, e.g., it can't read an array like:
```XML
<universes>
11 10
12 13
</universes
```
The bug I reported previously in 17.4 has been [fixed in 17.10](http://www.pgroup.com/userforum/viewtopic.php?p=21785). That means that we can now at least build OpenMC using PGI, but using it is a different story. I'm getting all sorts of weird, un-debuggable segfaults and errors, and I can't get a proper traceback. I'm abandoning my efforts to compile with PGI; it's just not stable enough... | 2019-02-22T04:46:02Z | [] | [] |
openmc-dev/openmc | 1,191 | openmc-dev__openmc-1191 | [
"1027"
] | b2d6a06284a86a5dd645bd7c537252345d0c78c7 | diff --git a/openmc/data/endf.py b/openmc/data/endf.py
--- a/openmc/data/endf.py
+++ b/openmc/data/endf.py
@@ -66,7 +66,7 @@
106: list(range(750, 800)),
107: list(range(800, 850))}
-ENDF_FLOAT_RE = re.compile(r'([\s\-\+]?\d*\.\d+)([\+\-]\d+)')
+ENDF_FLOAT_RE = re.compile(r'([\s\-\+]?\d*\.\d+)([\+\-]) ?(\d+)')
def float_endf(s):
@@ -89,12 +89,15 @@ def float_endf(s):
The number
"""
- return float(ENDF_FLOAT_RE.sub(r'\1e\2', s))
+ return float(ENDF_FLOAT_RE.sub(r'\1e\2\3', s))
-def _int_endf(s):
- """Convert string to int. Used for INTG records where blank entries
- indicate a 0.
+def int_endf(s):
+ """Convert string of integer number in ENDF to int.
+
+ The ENDF-6 format technically allows integers to be represented by a field
+ of all blanks. This function acts like int(s) except when s is a string of
+ all whitespace, in which case zero is returned.
Parameters
----------
@@ -106,8 +109,7 @@ def _int_endf(s):
integer
The number or 0
"""
- s = s.strip()
- return int(s) if s else 0
+ return 0 if s.isspace() else int(s)
def get_text_record(file_obj):
@@ -127,35 +129,35 @@ def get_text_record(file_obj):
return file_obj.readline()[:66]
-def get_cont_record(file_obj, skipC=False):
+def get_cont_record(file_obj, skip_c=False):
"""Return data from a CONT record in an ENDF-6 file.
Parameters
----------
file_obj : file-like object
ENDF-6 file to read from
- skipC : bool
+ skip_c : bool
Determine whether to skip the first two quantities (C1, C2) of the CONT
record.
Returns
-------
- list
+ tuple
The six items within the CONT record
"""
line = file_obj.readline()
- if skipC:
+ if skip_c:
C1 = None
C2 = None
else:
C1 = float_endf(line[:11])
C2 = float_endf(line[11:22])
- L1 = int(line[22:33])
- L2 = int(line[33:44])
- N1 = int(line[44:55])
- N2 = int(line[55:66])
- return [C1, C2, L1, L2, N1, N2]
+ L1 = int_endf(line[22:33])
+ L2 = int_endf(line[33:44])
+ N1 = int_endf(line[44:55])
+ N2 = int_endf(line[55:66])
+ return (C1, C2, L1, L2, N1, N2)
def get_head_record(file_obj):
@@ -168,18 +170,18 @@ def get_head_record(file_obj):
Returns
-------
- list
+ tuple
The six items within the HEAD record
"""
line = file_obj.readline()
ZA = int(float_endf(line[:11]))
AWR = float_endf(line[11:22])
- L1 = int(line[22:33])
- L2 = int(line[33:44])
- N1 = int(line[44:55])
- N2 = int(line[55:66])
- return [ZA, AWR, L1, L2, N1, N2]
+ L1 = int_endf(line[22:33])
+ L2 = int_endf(line[33:44])
+ N1 = int_endf(line[44:55])
+ N2 = int_endf(line[55:66])
+ return (ZA, AWR, L1, L2, N1, N2)
def get_list_record(file_obj):
@@ -233,10 +235,10 @@ def get_tab1_record(file_obj):
line = file_obj.readline()
C1 = float_endf(line[:11])
C2 = float_endf(line[11:22])
- L1 = int(line[22:33])
- L2 = int(line[33:44])
- n_regions = int(line[44:55])
- n_pairs = int(line[55:66])
+ L1 = int_endf(line[22:33])
+ L2 = int_endf(line[33:44])
+ n_regions = int_endf(line[44:55])
+ n_pairs = int_endf(line[55:66])
params = [C1, C2, L1, L2]
# Read the interpolation region data, namely NBT and INT
@@ -247,8 +249,8 @@ def get_tab1_record(file_obj):
line = file_obj.readline()
to_read = min(3, n_regions - m)
for j in range(to_read):
- breakpoints[m] = int(line[0:11])
- interpolation[m] = int(line[11:22])
+ breakpoints[m] = int_endf(line[0:11])
+ interpolation[m] = int_endf(line[11:22])
line = line[22:]
m += 1
@@ -306,9 +308,9 @@ def get_intg_record(file_obj):
"""
# determine how many items are in list and NDIGIT
items = get_cont_record(file_obj)
- ndigit = int(items[2])
- npar = int(items[3]) # Number of parameters
- nlines = int(items[4]) # Lines to read
+ ndigit = items[2]
+ npar = items[3] # Number of parameters
+ nlines = items[4] # Lines to read
NROW_RULES = {2: 18, 3: 12, 4: 11, 5: 9, 6: 8}
nrow = NROW_RULES[ndigit]
@@ -316,13 +318,13 @@ def get_intg_record(file_obj):
corr = np.identity(npar)
for i in range(nlines):
line = file_obj.readline()
- ii = _int_endf(line[:5]) - 1 # -1 to account for 0 indexing
- jj = _int_endf(line[5:10]) - 1
+ ii = int_endf(line[:5]) - 1 # -1 to account for 0 indexing
+ jj = int_endf(line[5:10]) - 1
factor = 10**ndigit
for j in range(nrow):
if jj+j >= ii:
break
- element = _int_endf(line[11+(ndigit+1)*j:11+(ndigit+1)*(j+1)])
+ element = int_endf(line[11+(ndigit+1)*j:11+(ndigit+1)*(j+1)])
if element > 0:
corr[ii, jj] = (element+0.5)/factor
elif element < 0:
@@ -507,16 +509,7 @@ def _read_header(self):
# File numbers, reaction designations, and number of records
for i in range(NXC):
- line = file_obj.readline()
- mf = int(line[22:33])
- mt = int(line[33:44])
- nc = int(line[44:55])
- try:
- mod = int(line[55:66])
- except ValueError:
- # In JEFF 3.2, a few isotopes of U have MOD values that are
- # missing. This prevents failure on these isotopes.
- mod = 0
+ _, _, mf, mt, nc, mod = get_cont_record(file_obj, skip_c=True)
self.reaction_list.append((mf, mt, nc, mod))
@property
diff --git a/openmc/data/neutron.py b/openmc/data/neutron.py
--- a/openmc/data/neutron.py
+++ b/openmc/data/neutron.py
@@ -448,11 +448,13 @@ def export_to_hdf5(self, path, mode='a', libver='earliest'):
for rx in self.reactions.values():
# Skip writing redundant reaction if it doesn't have photon
# production or is a summed transmutation reaction. MT=4 is also
- # sometimes needed for probability tables.
+ # sometimes needed for probability tables. Also write gas
+ # production, heating, and damage energy production.
if rx.redundant:
photon_rx = any(p.particle == 'photon' for p in rx.products)
- transmutation_rx = (rx.mt in (16, 103, 104, 105, 106, 107))
- if not (photon_rx or transmutation_rx or rx.mt == 4):
+ keep_mts = (4, 16, 103, 104, 105, 106, 107,
+ 203, 204, 205, 206, 207, 301, 444)
+ if not (photon_rx or rx.mt in keep_mts):
continue
rx_group = rxs_group.create_group('reaction_{:03}'.format(rx.mt))
@@ -615,13 +617,14 @@ def from_ace(cls, ace_or_filename, metastable_scheme='nndc'):
# Read energy grid
n_energy = ace.nxs[3]
- energy = ace.xss[ace.jxs[1]:ace.jxs[1] + n_energy]*EV_PER_MEV
+ i = ace.jxs[1]
+ energy = ace.xss[i : i + n_energy]*EV_PER_MEV
data.energy[strT] = energy
- total_xs = ace.xss[ace.jxs[1] + n_energy:ace.jxs[1] + 2 * n_energy]
- absorption_xs = ace.xss[ace.jxs[1] + 2 * n_energy:ace.jxs[1] +
- 3 * n_energy]
+ total_xs = ace.xss[i + n_energy : i + 2*n_energy]
+ absorption_xs = ace.xss[i + 2*n_energy : i + 3*n_energy]
+ heating_number = ace.xss[i + 3*n_energy : i + 4*n_energy]*EV_PER_MEV
- # Create redundant reactions (total and absorption)
+ # Create redundant reactions (total, absorption, and heating)
total = Reaction(1)
total.xs[strT] = Tabulated1D(energy, total_xs)
total.redundant = True
@@ -633,13 +636,15 @@ def from_ace(cls, ace_or_filename, metastable_scheme='nndc'):
absorption.redundant = True
data.reactions[101] = absorption
+ heating = Reaction(301)
+ heating.xs[strT] = Tabulated1D(energy, heating_number)
+ heating.redundant = True
+ data.reactions[301] = heating
+
# Read each reaction
n_reaction = ace.nxs[4] + 1
for i in range(n_reaction):
rx = Reaction.from_ace(ace, i)
- # Don't include gas production / damage cross sections
- if 200 < rx.mt < 219 or rx.mt == 444:
- continue
data.reactions[rx.mt] = rx
# Some photon production reactions may be assigned to MTs that don't
@@ -690,6 +695,8 @@ def from_ace(cls, ace_or_filename, metastable_scheme='nndc'):
mts = data.get_reaction_components(rx.mt)
if mts != [rx.mt]:
rx.redundant = True
+ if rx.mt in (203, 204, 205, 206, 207, 444):
+ rx.redundant = True
# Read unresolved resonance probability tables
urr = ProbabilityTables.from_ace(ace)
@@ -784,16 +791,19 @@ def from_endf(cls, ev_or_filename, covariance=False):
return data
@classmethod
- def from_njoy(cls, filename, temperatures=None, **kwargs):
+ def from_njoy(cls, filename, temperatures=None, evaluation=None, **kwargs):
"""Generate incident neutron data by running NJOY.
Parameters
----------
filename : str
- Path to ENDF evaluation
+ Path to ENDF file
temperatures : iterable of float
Temperatures in Kelvin to produce data at. If omitted, data is
produced at room temperature (293.6 K)
+ evaluation : openmc.data.endf.Evaluation, optional
+ If the ENDF file contains multiple material evaluations, this
+ argument indicates which evaluation to use.
**kwargs
Keyword arguments passed to :func:`openmc.data.njoy.make_ace`
@@ -808,6 +818,7 @@ def from_njoy(cls, filename, temperatures=None, **kwargs):
ace_file = os.path.join(tmpdir, 'ace')
xsdir_file = os.path.join(tmpdir, 'xsdir')
pendf_file = os.path.join(tmpdir, 'pendf')
+ kwargs['evaluation'] = evaluation
make_ace(filename, temperatures, ace_file, xsdir_file,
pendf_file, **kwargs)
@@ -818,7 +829,7 @@ def from_njoy(cls, filename, temperatures=None, **kwargs):
data.add_temperature_from_ace(table)
# Add fission energy release data
- ev = Evaluation(filename)
+ ev = evaluation if evaluation is not None else Evaluation(filename)
if (1, 458) in ev.section:
data.fission_energy = FissionEnergyRelease.from_endf(ev, data)
diff --git a/openmc/data/njoy.py b/openmc/data/njoy.py
--- a/openmc/data/njoy.py
+++ b/openmc/data/njoy.py
@@ -72,8 +72,13 @@
_TEMPLATE_HEATR = """
heatr / %%%%%%%%%%%%%%%%%%%%%%%%% Add heating kerma %%%%%%%%%%%%%%%%%%%%%%%%%%%%
{nendf} {nheatr_in} {nheatr} /
-{mat} 3 /
-302 318 402 /
+{mat} 4 /
+302 318 402 444 /
+"""
+
+_TEMPLATE_GASPR = """
+gaspr / %%%%%%%%%%%%%%%%%%%%%%%%% Add gas production %%%%%%%%%%%%%%%%%%%%%%%%%%%
+{nendf} {ngaspr_in} {ngaspr} /
"""
_TEMPLATE_PURR = """
@@ -186,7 +191,7 @@ def run(commands, tapein, tapeout, input_filename=None, stdout=False,
def make_pendf(filename, pendf='pendf', error=0.001, stdout=False):
- """Generate ACE file from an ENDF file
+ """Generate pointwise ENDF file from an ENDF file
Parameters
----------
@@ -211,8 +216,8 @@ def make_pendf(filename, pendf='pendf', error=0.001, stdout=False):
def make_ace(filename, temperatures=None, ace='ace', xsdir='xsdir', pendf=None,
- error=0.001, broadr=True, heatr=True, purr=True, acer=True,
- **kwargs):
+ error=0.001, broadr=True, heatr=True, gaspr=True, purr=True,
+ acer=True, evaluation=None, **kwargs):
"""Generate incident neutron ACE file from an ENDF file
Parameters
@@ -234,10 +239,15 @@ def make_ace(filename, temperatures=None, ace='ace', xsdir='xsdir', pendf=None,
Indicating whether to Doppler broaden XS when running NJOY
heatr : bool, optional
Indicating whether to add heating kerma when running NJOY
+ gaspr : bool, optional
+ Indicating whether to add gas production data when running NJOY
purr : bool, optional
Indicating whether to add probability table when running NJOY
acer : bool, optional
Indicating whether to generate ACE file when running NJOY
+ evaluation : openmc.data.endf.Evaluation, optional
+ If the ENDF file contains multiple material evaluations, this argument
+ indicates which evaluation should be used.
**kwargs
Keyword arguments passed to :func:`openmc.data.njoy.run`
@@ -247,7 +257,7 @@ def make_ace(filename, temperatures=None, ace='ace', xsdir='xsdir', pendf=None,
If the NJOY process returns with a non-zero status
"""
- ev = endf.Evaluation(filename)
+ ev = evaluation if evaluation is not None else endf.Evaluation(filename)
mat = ev.material
zsymam = ev.target['zsymam']
@@ -285,6 +295,13 @@ def make_ace(filename, temperatures=None, ace='ace', xsdir='xsdir', pendf=None,
commands += _TEMPLATE_HEATR
nlast = nheatr
+ # gaspr
+ if gaspr:
+ ngaspr_in = nlast
+ ngaspr = ngaspr_in + 1
+ commands += _TEMPLATE_GASPR
+ nlast = ngaspr
+
# purr
if purr:
npurr_in = nlast
@@ -338,7 +355,8 @@ def make_ace(filename, temperatures=None, ace='ace', xsdir='xsdir', pendf=None,
def make_ace_thermal(filename, filename_thermal, temperatures=None,
- ace='ace', xsdir='xsdir', error=0.001, **kwargs):
+ ace='ace', xsdir='xsdir', error=0.001, evaluation=None,
+ evaluation_thermal=None, **kwargs):
"""Generate thermal scattering ACE file from ENDF files
Parameters
@@ -356,6 +374,12 @@ def make_ace_thermal(filename, filename_thermal, temperatures=None,
Path of xsdir file to write
error : float, optional
Fractional error tolerance for NJOY processing
+ evaluation : openmc.data.endf.Evaluation, optional
+ If the ENDF neutron sublibrary file contains multiple material
+ evaluations, this argument indicates which evaluation to use.
+ evaluation_thermal : openmc.data.endf.Evaluation, optional
+ If the ENDF thermal scattering sublibrary file contains multiple
+ material evaluations, this argument indicates which evaluation to use.
**kwargs
Keyword arguments passed to :func:`openmc.data.njoy.run`
@@ -365,11 +389,12 @@ def make_ace_thermal(filename, filename_thermal, temperatures=None,
If the NJOY process returns with a non-zero status
"""
- ev = endf.Evaluation(filename)
+ ev = evaluation if evaluation is not None else endf.Evaluation(filename)
mat = ev.material
zsymam = ev.target['zsymam']
- ev_thermal = endf.Evaluation(filename_thermal)
+ ev_thermal = (evaluation_thermal if evaluation_thermal is not None
+ else endf.Evaluation(filename_thermal))
mat_thermal = ev_thermal.material
zsymam_thermal = ev_thermal.target['zsymam']
diff --git a/openmc/data/reaction.py b/openmc/data/reaction.py
--- a/openmc/data/reaction.py
+++ b/openmc/data/reaction.py
@@ -51,7 +51,9 @@
189: '(n,nta)', 190: '(n,2n2p)', 191: '(n,p3He)',
192: '(n,d3He)', 193: '(n,3Hea)', 194: '(n,4n2p)',
195: '(n,4n2a)', 196: '(n,4npa)', 197: '(n,3p)',
- 198: '(n,n3p)', 199: '(n,3n2pa)', 200: '(n,5n2p)', 444: '(n,damage)',
+ 198: '(n,n3p)', 199: '(n,3n2pa)', 200: '(n,5n2p)', 203: '(n,Xp)',
+ 204: '(n,Xd)', 205: '(n,Xt)', 206: '(n,X3He)', 207: '(n,Xa)',
+ 301: 'heating', 444: 'damage-energy',
649: '(n,pc)', 699: '(n,dc)', 749: '(n,tc)', 799: '(n,3Hec)',
849: '(n,ac)', 891: '(n,2nc)'}
REACTION_NAME.update({i: '(n,n{})'.format(i - 50) for i in range(50, 91)})
@@ -988,6 +990,10 @@ def from_ace(cls, ace, i_reaction):
# Read reaction cross section
xs = ace.xss[ace.jxs[7] + loc + 1:ace.jxs[7] + loc + 1 + n_energy]
+ # For damage energy production, convert to eV
+ if mt == 444:
+ xs *= EV_PER_MEV
+
# Fix negatives -- known issue for Y89 in JEFF 3.2
if np.any(xs < 0.0):
warn("Negative cross sections found for MT={} in {}. Setting "
diff --git a/openmc/data/thermal.py b/openmc/data/thermal.py
--- a/openmc/data/thermal.py
+++ b/openmc/data/thermal.py
@@ -610,7 +610,8 @@ def from_ace(cls, ace_or_filename, name=None):
return table
@classmethod
- def from_njoy(cls, filename, filename_thermal, temperatures=None, **kwargs):
+ def from_njoy(cls, filename, filename_thermal, temperatures=None,
+ evaluation=None, evaluation_thermal=None, **kwargs):
"""Generate incident neutron data by running NJOY.
Parameters
@@ -623,6 +624,13 @@ def from_njoy(cls, filename, filename_thermal, temperatures=None, **kwargs):
Temperatures in Kelvin to produce data at. If omitted, data is
produced at all temperatures in the ENDF thermal scattering
sublibrary.
+ evaluation : openmc.data.endf.Evaluation, optional
+ If the ENDF neutron sublibrary file contains multiple material
+ evaluations, this argument indicates which evaluation to use.
+ evaluation_thermal : openmc.data.endf.Evaluation, optional
+ If the ENDF thermal scattering sublibrary file contains multiple
+ material evaluations, this argument indicates which evaluation to
+ use.
**kwargs
Keyword arguments passed to :func:`openmc.data.njoy.make_ace_thermal`
@@ -636,6 +644,8 @@ def from_njoy(cls, filename, filename_thermal, temperatures=None, **kwargs):
# Run NJOY to create an ACE library
ace_file = os.path.join(tmpdir, 'ace')
xsdir_file = os.path.join(tmpdir, 'xsdir')
+ kwargs['evaluation'] = evaluation
+ kwargs['evaluation_thermal'] = evaluation_thermal
make_ace_thermal(filename, filename_thermal, temperatures,
ace_file, xsdir_file, **kwargs)
| diff --git a/tests/regression_tests/tallies/inputs_true.dat b/tests/regression_tests/tallies/inputs_true.dat
--- a/tests/regression_tests/tallies/inputs_true.dat
+++ b/tests/regression_tests/tallies/inputs_true.dat
@@ -511,4 +511,7 @@
<scores>total</scores>
<estimator>tracklength</estimator>
</tally>
+ <tally id="33">
+ <scores>H1-production H2-production H3-production He3-production He4-production heating damage-energy</scores>
+ </tally>
</tallies>
diff --git a/tests/regression_tests/tallies/results_true.dat b/tests/regression_tests/tallies/results_true.dat
--- a/tests/regression_tests/tallies/results_true.dat
+++ b/tests/regression_tests/tallies/results_true.dat
@@ -1 +1 @@
-b5edf87cb58db29aa1c38203141df2f055b88aca675aee9673879b579391412abd232cb3d404f60840ac86b936384050576cccb1e3a1fc5c8290b6e890dda74c
\ No newline at end of file
+de773a799f84348241ebd65bf7beae8114861d8674b652bfd443d578c146a7d37ca38f2efc5d05124fdbb1cf12829907768351e6b2d6b5f4bd2c121417757507
\ No newline at end of file
diff --git a/tests/regression_tests/tallies/test.py b/tests/regression_tests/tallies/test.py
--- a/tests/regression_tests/tallies/test.py
+++ b/tests/regression_tests/tallies/test.py
@@ -165,6 +165,10 @@ def test_tallies():
all_nuclide_tallies[3].filters = [mesh_filter]
all_nuclide_tallies[3].nuclides = ['U235']
+ fusion_tally = Tally()
+ fusion_tally.scores = ['H1-production', 'H2-production', 'H3-production',
+ 'He3-production', 'He4-production', 'heating', 'damage-energy']
+
model.tallies += [
azimuthal_tally1, azimuthal_tally2, azimuthal_tally3,
cellborn_tally, dg_tally, energy_tally, energyout_tally,
@@ -174,5 +178,6 @@ def test_tallies():
model.tallies += score_tallies
model.tallies += flux_tallies
model.tallies += all_nuclide_tallies
+ model.tallies.append(fusion_tally)
harness.main()
diff --git a/tests/unit_tests/test_endf.py b/tests/unit_tests/test_endf.py
new file mode 100644
--- /dev/null
+++ b/tests/unit_tests/test_endf.py
@@ -0,0 +1,16 @@
+from openmc.data import endf
+from pytest import approx
+
+
+def test_float_endf():
+ assert endf.float_endf('+3.2146') == approx(3.2146)
+ assert endf.float_endf('.12345') == approx(0.12345)
+ assert endf.float_endf('6.022+23') == approx(6.022e23)
+ assert endf.float_endf('6.022-23') == approx(6.022e-23)
+ assert endf.float_endf(' +1.01+ 2') == approx(101.0)
+ assert endf.float_endf(' -1.01- 2') == approx(-0.0101)
+
+
+def test_int_endf():
+ assert endf.int_endf(' ') == 0
+ assert endf.int_endf('+4032') == 4032
| ENDF Parsing Blank Space
In the ENDF parsing routine there is a function to convert ENDF's odd format to floating point.
https://github.com/mit-crpg/openmc/blob/499f2f24944435c095d3d69acdd8fea98ddf1edd/openmc/data/endf.py#L71
The issue is that occasionally evaluations produced by SAMMY will contain white space indicating a 0. This is not currently the case for publicly distributed ENDF files but may rear its head in more specific use cases. For performance considerations it may be best to keep it as is, rather than eat the cost of a conditional for checking blank space. Maybe something like:
try:
return float(ENDF_FLOAT_RE.sub(r'\1e\2', s))
except:
if ENDF_FLOAT_RE.sub(r'\1e\2', s).isspace():
return 0
else:
raise TypeError('Expected float value or blank entry')
| Thanks for creating an issue for this @icmeyer. Looking at ENDF-102, here's what they have to say about integers:
> All numbers are given in fields of 11 columns. For fields representing integers, the fields have the following form:
>
> ±nnnnnnnnnn
>
> Here, n is a number between 0-9 or a space character and any leading “+” sign is optional. Therefore, integers are limited to a maximum absolute value of 9,999,999,999. Integers can be read by the FORTRAN77 “I11” format specification.
So, if you read it literally, technically all those `n`s could be spaces. I'm not sure if the intent is for that to be permissible. If you have a field of all blanks that is read by Fortran's I11 format spec, it looks like the Fortran standard does actually say that it's to be interpreted as zero (hence why Fortran-based codes don't choke on this). From section 10.7.2.1 in the F2008 standard:
> On input, leading blanks are not significant. When the input field is not an IEEE exceptional
specification (10.7.2.3.2), the interpretation of blanks, other than leading blanks, is determined by
the blank interpretation mode (10.8.6). Plus signs may be omitted. **A field containing only blanks
is considered to be zero.**
@brown170 Is the intent in ENDF-102 to allow fields of all whitespace to be interpreted as zeros? | 2019-03-10T20:05:59Z | [] | [] |
openmc-dev/openmc | 1,203 | openmc-dev__openmc-1203 | [
"1196"
] | e792fe72e57dc5c63d3546dde7e92691cb55cf3a | diff --git a/openmc/capi/tally.py b/openmc/capi/tally.py
--- a/openmc/capi/tally.py
+++ b/openmc/capi/tally.py
@@ -89,7 +89,7 @@
-5: 'absorption', -6: 'fission', -7: 'nu-fission', -8: 'kappa-fission',
-9: 'current', -10: 'events', -11: 'delayed-nu-fission',
-12: 'prompt-nu-fission', -13: 'inverse-velocity', -14: 'fission-q-prompt',
- -15: 'fission-q-recoverable', -16: 'decay-rate'
+ -15: 'fission-q-recoverable', -16: 'decay-rate', -17: 'heating'
}
_ESTIMATORS = {
1: 'analog', 2: 'tracklength', 3: 'collision'
diff --git a/openmc/data/function.py b/openmc/data/function.py
--- a/openmc/data/function.py
+++ b/openmc/data/function.py
@@ -3,6 +3,7 @@
from functools import reduce
from itertools import zip_longest
from numbers import Real, Integral
+from math import exp, log
import numpy as np
@@ -153,13 +154,11 @@ def __init__(self, x, y, breakpoints=None, interpolation=None):
self.y = np.asarray(y)
def __call__(self, x):
- # Check if input is array or scalar
- if isinstance(x, Iterable):
- iterable = True
- x = np.array(x)
- else:
- iterable = False
- x = np.array([x], dtype=float)
+ # Check if input is scalar
+ if not isinstance(x, Iterable):
+ return self._interpolate_scalar(x)
+
+ x = np.array(x)
# Create output array
y = np.zeros_like(x)
@@ -208,7 +207,46 @@ def __call__(self, x):
y[np.isclose(x, self.x[0], atol=1e-14)] = self.y[0]
y[np.isclose(x, self.x[-1], atol=1e-14)] = self.y[-1]
- return y if iterable else y[0]
+ return y
+
+ def _interpolate_scalar(self, x):
+ if x <= self._x[0]:
+ return self._y[0]
+ elif x >= self._x[-1]:
+ return self._y[-1]
+
+ # Get the index for interpolation
+ idx = np.searchsorted(self._x, x, side='right') - 1
+
+ # Loop over interpolation regions
+ for b, p in zip(self.breakpoints, self.interpolation):
+ if idx < b - 1:
+ break
+
+ xi = self._x[idx] # low edge of the corresponding bin
+ xi1 = self._x[idx + 1] # high edge of the corresponding bin
+ yi = self._y[idx]
+ yi1 = self._y[idx + 1]
+
+ if p == 1:
+ # Histogram
+ return yi
+
+ elif p == 2:
+ # Linear-linear
+ return yi + (x - xi)/(xi1 - xi)*(yi1 - yi)
+
+ elif p == 3:
+ # Linear-log
+ return yi + log(x/xi)/log(xi1/xi)*(yi1 - yi)
+
+ elif p == 4:
+ # Log-linear
+ return yi*exp((x - xi)/(xi1 - xi)*log(yi1/yi))
+
+ elif p == 5:
+ # Log-log
+ return yi*exp(log(x/xi)/log(xi1/xi)*log(yi1/yi))
def __len__(self):
return len(self.x)
diff --git a/openmc/data/photon.py b/openmc/data/photon.py
--- a/openmc/data/photon.py
+++ b/openmc/data/photon.py
@@ -3,12 +3,14 @@
from copy import deepcopy
from io import StringIO
from numbers import Integral, Real
+from math import pi, sqrt
import os
import h5py
import numpy as np
import pandas as pd
from scipy.interpolate import CubicSpline
+from scipy.integrate import quad
from openmc.mixin import EqualityMixin
import openmc.checkvalue as cv
@@ -19,6 +21,14 @@
from .function import Tabulated1D
+# Constants
+MASS_ELECTRON_EV = 0.5109989461e6 # Electron mass energy
+PLANCK_C = 1.2398419739062977e4 # Planck's constant times c in eV-Angstroms
+FINE_STRUCTURE = 137.035999139 # Inverse fine structure constant
+CM_PER_ANGSTROM = 1.0e-8
+# classical electron radius in cm
+R0 = CM_PER_ANGSTROM * PLANCK_C / (2.0 * pi * FINE_STRUCTURE * MASS_ELECTRON_EV)
+
# Electron subshell labels
_SUBSHELLS = [None, 'K', 'L1', 'L2', 'L3', 'M1', 'M2', 'M3', 'M4', 'M5',
'N1', 'N2', 'N3', 'N4', 'N5', 'N6', 'N7', 'O1', 'O2', 'O3',
@@ -33,6 +43,7 @@
516: ('Total pair production', 'pair_production_total'),
517: ('Pair production, nuclear field', 'pair_production_nuclear'),
522: ('Photoelectric absorption', 'photoelectric'),
+ 525: ('Heating', 'heating'),
526: ('Electro-atomic scattering', 'electro_atomic_scat'),
527: ('Electro-atomic bremsstrahlung', 'electro_atomic_brem'),
528: ('Electro-atomic excitation', 'electro_atomic_excit'),
@@ -150,6 +161,7 @@ def __init__(self, binding_energy, num_electrons, transitions):
self.binding_energy = binding_energy
self.num_electrons = num_electrons
self.transitions = transitions
+ self._e_fluorescence = {}
@property
def binding_energy(self):
@@ -379,6 +391,49 @@ def to_hdf5(self, group, shell):
_SUBSHELLS, range(len(_SUBSHELLS)))
group.create_dataset('transitions', data=df.values.astype(float))
+ def energy_fluorescence(self, shell):
+ """Compute expected energy of fluorescent photons for the shell
+
+ Parameters
+ ----------
+ shell : str
+ The subshell to compute
+
+ Returns
+ -------
+ float
+ Energy of fluorescent photons
+
+ """
+
+ if shell not in self.binding_energy:
+ raise KeyError('Invalid shell {}.'.format(shell))
+
+ if shell in self._e_fluorescence:
+ # Already computed
+ return self._e_fluorescence[shell]
+ e = 0.0
+ if shell not in self.transitions or self.transitions[shell].empty:
+ e = self.binding_energy[shell]
+ else:
+ df = self.transitions[shell]
+ for primary, secondary, energy, prob in df.itertuples(index=False):
+ e_row = 0.0
+ if secondary is None:
+ # Fluorescent photon release in radiative transition
+ e_row += energy
+ else:
+ # Fill the hole left by auger electron
+ e_row += self.energy_fluorescence(secondary)
+
+ # Fill the photoelectron hole
+ e_row += self.energy_fluorescence(primary)
+
+ # Expected fluorescent photon energy
+ e += e_row * prob
+
+ self._e_fluorescence[shell] = e
+ return e
class IncidentPhoton(EqualityMixin):
r"""Photon interaction data.
@@ -499,9 +554,14 @@ def from_ace(cls, ace_or_filename):
# Read each reaction
data = cls(Z)
- for mt in (502, 504, 515, 522):
+ for mt in (502, 504, 515, 522, 525):
data.reactions[mt] = PhotonReaction.from_ace(ace, mt)
+ # Get heating cross sections [eV-barn] from factors [eV per collision]
+ # by multiplying with total xs
+ data.reactions[525].xs.y *= sum([data.reactions[mt].xs.y for mt in
+ (502, 504, 515, 522)])
+
# Compton profiles
n_shell = ace.nxs[5]
if n_shell != 0:
@@ -631,6 +691,9 @@ def from_endf(cls, photoatomic, relaxation=None):
# Add bremsstrahlung DCS data
data._add_bremsstrahlung()
+ # Add heating cross sections
+ data._compute_heating()
+
return data
@classmethod
@@ -751,7 +814,7 @@ def export_to_hdf5(self, path, mode='a', libver='earliest'):
designators = []
for mt, rx in self.reactions.items():
name, key = _REACTION_NAME[mt]
- if mt in [502, 504, 515, 517, 522]:
+ if mt in (502, 504, 515, 517, 522, 525):
sub_group = group.create_group(key)
elif mt >= 534 and mt <= 572:
# Subshell
@@ -858,6 +921,80 @@ def _add_bremsstrahlung(self):
self.bremsstrahlung['photon_energy'] = _BREMSSTRAHLUNG['photon_energy']
self.bremsstrahlung.update(_BREMSSTRAHLUNG[self.atomic_number])
+ def _compute_heating(self):
+ r"""Compute heating cross sections (KERMA)
+
+ Photon energy is deposited as energy loss in three reactions:
+ incoherent scattering, pair production and photoelectric effect.
+ The point-wise heating cross section is calculated as:
+
+ .. math::
+ \sigma_{Hx}(E) &= (E - \overline{E}_x(E)) \cdot \sigma_x(E), x \in \left\{I, PP, PE \right\}
+
+ \overline{E}_I(E) &= \frac {\int E' \sigma_I (E,E',\mu) d\mu} {\int \sigma_I (E,E',\mu) d\mu}
+
+ \overline{E}_{PP} &= 2 m_e c^2 = 1.022 \times 10^6 eV
+
+ \overline{E}_{PE} &= E(\text{fluorescent photons})
+
+ The differential cross section representation for incoherent
+ scattering can be found in the theory manual.
+
+ """
+
+ # Determine a union energy grid
+ energy = np.array([])
+ for mt in (504, 515, 517, 522):
+ if mt in self:
+ energy = np.union1d(energy, self[mt].xs.x)
+
+ heating_xs = np.zeros_like(energy)
+
+ # Incoherent scattering
+ if 504 in self:
+ rx = self[504]
+
+ def dsigma_dmu(mu, E):
+ k = E / MASS_ELECTRON_EV
+ krat = 1.0 / (1.0 + k * (1.0 - mu))
+ x = E * sqrt(0.5 * (1.0 - mu)) / PLANCK_C
+ return pi * R0*R0 * krat*krat * (krat + 1/krat +
+ mu*mu - 1.0) * rx.scattering_factor(x)
+
+ def eout_dsigma_dmu(mu, E):
+ Eout = E / (1.0 + E / MASS_ELECTRON_EV * (1.0 - mu))
+ return Eout * dsigma_dmu(mu, E)
+
+ def eout_average(E):
+ integral_sigma = quad(dsigma_dmu, -1.0, 1.0,
+ args=(E,), epsabs=0.0, epsrel=1e-3)[0]
+ integral_sigma_e = quad(eout_dsigma_dmu, -1.0, 1.0,
+ args=(E,), epsabs=0.0, epsrel=1e-3)[0]
+ return integral_sigma_e / integral_sigma
+
+ e_out = np.vectorize(eout_average)(energy)
+ heating_xs += (energy - e_out) * rx.xs(energy)
+
+ # Pair production, electron field
+ if 515 in self:
+ heating_xs += (energy - 2*MASS_ELECTRON_EV)*self[515].xs(energy)
+
+ # Pair production, nuclear field
+ if 517 in self:
+ heating_xs += (energy - 2*MASS_ELECTRON_EV)*self[517].xs(energy)
+
+ # Photoelectric effect
+ if 522 in self:
+ # Account for fluorescent photons
+ for mt, rx in self.reactions.items():
+ if mt >= 534 and mt <= 572:
+ shell = _REACTION_NAME[mt][1]
+ e_f = self.atomic_relaxation.energy_fluorescence(shell)
+ heating_xs += (energy - e_f) * rx.xs(energy)
+
+ heat_rx = PhotonReaction(525)
+ heat_rx.xs = Tabulated1D(energy, heating_xs, [energy.size], [5])
+ self.reactions[525] = heat_rx
class PhotonReaction(EqualityMixin):
"""Photon-induced reaction
@@ -972,14 +1109,21 @@ def from_ace(cls, ace, mt):
elif mt == 522:
# Photoelectric
idx = ace.jxs[1] + 3*n
+ elif mt == 525:
+ # Heating
+ idx = ace.jxs[5]
else:
raise ValueError('ACE photoatomic cross sections do not have '
'data for MT={}.'.format(mt))
# Store cross section
xs = ace.xss[idx : idx+n].copy()
- nonzero = (xs != 0.0)
- xs[nonzero] = np.exp(xs[nonzero])
+ if mt == 525:
+ # Get heating factors in [eV per collision]
+ xs *= EV_PER_MEV
+ else:
+ nonzero = (xs != 0.0)
+ xs[nonzero] = np.exp(xs[nonzero])
rx.xs = Tabulated1D(energy, xs, [n], [5])
# Get form factors for incoherent/coherent scattering
| diff --git a/tests/regression_tests/photon_production/inputs_true.dat b/tests/regression_tests/photon_production/inputs_true.dat
--- a/tests/regression_tests/photon_production/inputs_true.dat
+++ b/tests/regression_tests/photon_production/inputs_true.dat
@@ -49,17 +49,20 @@
</tally>
<tally id="2">
<filters>2</filters>
- <scores>total</scores>
+ <nuclides>Al27 total</nuclides>
+ <scores>total heating</scores>
<estimator>tracklength</estimator>
</tally>
<tally id="3">
<filters>2</filters>
- <scores>total</scores>
+ <nuclides>Al27 total</nuclides>
+ <scores>total heating</scores>
<estimator>collision</estimator>
</tally>
<tally id="4">
<filters>2</filters>
- <scores>total</scores>
+ <nuclides>Al27 total</nuclides>
+ <scores>total heating</scores>
<estimator>analog</estimator>
</tally>
</tallies>
diff --git a/tests/regression_tests/photon_production/results_true.dat b/tests/regression_tests/photon_production/results_true.dat
--- a/tests/regression_tests/photon_production/results_true.dat
+++ b/tests/regression_tests/photon_production/results_true.dat
@@ -2,11 +2,29 @@ tally 1:
9.403000E-01
8.841641E-01
tally 2:
+1.819886E-01
+3.311985E-02
+1.960159E+05
+3.842224E+10
8.281718E-01
6.858685E-01
+1.960159E+05
+3.842224E+10
tally 3:
+1.799069E-01
+3.236650E-02
+1.945225E+05
+3.783901E+10
8.242000E-01
6.793056E-01
+1.945225E+05
+3.783901E+10
tally 4:
+2.308000E-01
+5.326864E-02
+1.988563E+05
+3.954384E+10
8.242000E-01
6.793056E-01
+1.988612E+05
+3.954578E+10
diff --git a/tests/regression_tests/photon_production/test.py b/tests/regression_tests/photon_production/test.py
--- a/tests/regression_tests/photon_production/test.py
+++ b/tests/regression_tests/photon_production/test.py
@@ -51,20 +51,23 @@ def _build_inputs(self):
current_tally = openmc.Tally()
current_tally.filters = [surface_filter, particle_filter]
current_tally.scores = ['current']
- total_tally_tracklength = openmc.Tally()
- total_tally_tracklength.filters = [particle_filter]
- total_tally_tracklength.scores = ['total']
- total_tally_tracklength.estimator = 'tracklength'
- total_tally_collision = openmc.Tally()
- total_tally_collision.filters = [particle_filter]
- total_tally_collision.scores = ['total']
- total_tally_collision.estimator = 'collision'
- total_tally_analog = openmc.Tally()
- total_tally_analog.filters = [particle_filter]
- total_tally_analog.scores = ['total']
- total_tally_analog.estimator = 'analog'
- tallies = openmc.Tallies([current_tally, total_tally_tracklength,
- total_tally_collision, total_tally_analog])
+ tally_tracklength = openmc.Tally()
+ tally_tracklength.filters = [particle_filter]
+ tally_tracklength.scores = ['total', 'heating']
+ tally_tracklength.nuclides = ['Al27', 'total']
+ tally_tracklength.estimator = 'tracklength'
+ tally_collision = openmc.Tally()
+ tally_collision.filters = [particle_filter]
+ tally_collision.scores = ['total', 'heating']
+ tally_collision.nuclides = ['Al27', 'total']
+ tally_collision.estimator = 'collision'
+ tally_analog = openmc.Tally()
+ tally_analog.filters = [particle_filter]
+ tally_analog.scores = ['total', 'heating']
+ tally_analog.nuclides = ['Al27', 'total']
+ tally_analog.estimator = 'analog'
+ tallies = openmc.Tallies([current_tally, tally_tracklength,
+ tally_collision, tally_analog])
tallies.export_to_xml()
def _get_results(self):
| Photon heating
We are reading [number 5 element of JXS when generating incident photon data from ACE for MT 515](https://github.com/openmc-dev/openmc/blob/develop/openmc/data/photon.py#L882-L884),
``` python
class PhotonReaction(EqualityMixin):
@classmethod
def from_ace(cls, ace, mt):
n = ace.nxs[3]
elif mt == 515:
# Pair production
idx = ace.jxs[1] + 4*n
# Store cross section
xs = ace.xss[idx : idx+n].copy()
```
However, the ACE format says the [number 5 element of JXS is the heating number](https://github.com/NuclearData/ACEFormat/blob/master/src/ContinuousEnergyPhoton.tex#L16-L27).
``` latex
1 & ESZG & Energy table \\
2 & JINC & Incoherent form factors \\
3 & JCOH & Coherent form factors \\
4 & JFLO & Fluorescence data \\
5 & LHNM & Heating numbers \\
6 & LNEPS & Number of electrons per shell \\
7 & LBEPS & Binding energy per shell \\
8 & LPIPS & Probability of interaction per shell \\
```
But I didn't see where the `pair production` should be from this table.
@amandalund @paulromano Did I miss something here? BTW I'm trying to add the heating number in the photon library so we can do neutron-photon coupled energy deposition tallies.
| It looks like the .tex documentation there for photoatomic data is incomplete. Pair production appears in the ESZG block starting at index `JXS(1) + 4*NXS(3)`. If you have a copy of MCNP5 user's manual, vol III, you'll see it there. Unfortunately that volume is under export control and can't be shared. You can find heating data in the ACE file starting at XSS(JXS(5)) and it is tabulated on the same energy grid as other cross sections. It's in units of MeV / collision, just like the neutron data. | 2019-03-21T22:20:43Z | [] | [] |
openmc-dev/openmc | 1,232 | openmc-dev__openmc-1232 | [
"161"
] | 2c0b16e73d5d81a2f849f4e2bfae5eb5319f2417 | diff --git a/openmc/__init__.py b/openmc/__init__.py
--- a/openmc/__init__.py
+++ b/openmc/__init__.py
@@ -32,6 +32,6 @@
from . import examples
# Import a few convencience functions that used to be here
-from openmc.model import get_rectangular_prism, get_hexagonal_prism
+from openmc.model import rectangular_prism, hexagonal_prism
__version__ = '0.10.0'
diff --git a/openmc/cell.py b/openmc/cell.py
--- a/openmc/cell.py
+++ b/openmc/cell.py
@@ -227,10 +227,6 @@ def fill(self, fill):
@rotation.setter
def rotation(self, rotation):
- if not isinstance(self.fill, openmc.Universe):
- raise TypeError('Cell rotation can only be applied if the cell '
- 'is filled with a Universe.')
-
cv.check_type('cell rotation', rotation, Iterable, Real)
cv.check_length('cell rotation', rotation, 3)
self._rotation = np.asarray(rotation)
diff --git a/openmc/mgxs/__init__.py b/openmc/mgxs/__init__.py
--- a/openmc/mgxs/__init__.py
+++ b/openmc/mgxs/__init__.py
@@ -7,6 +7,7 @@
GROUP_STRUCTURES = {}
"""Dictionary of commonly used energy group structures:
+
- "CASMO-X" (where X is 2, 4, 8, 16, 25, 40 or 70) from the CASMO_ lattice
physics code
- "XMAS-172_" designed for LWR analysis ([SAR1990]_, [SAN2004]_)
@@ -19,7 +20,7 @@
.. _XMAS-172: https://www-nds.iaea.org/wimsd/energy.htm
.. _SHEM-361: https://www.polymtl.ca/merlin/libraries.htm
.. _activation: https://fispact.ukaea.uk/wiki/Keyword:GETXS
-.. _CCFE-709: https://fispact.ukaea.uk/wiki/CCFE-709_group_structure
+.. _CCFE-709: https://fispact.ukaea.uk/wiki/CCFE-709_group_structure
.. _UKAEA-1102: https://fispact.ukaea.uk/wiki/UKAEA-1102_group_structure
.. [SAR1990] Sartori, E., OECD/NEA Data Bank: Standard Energy Group Structures
of Cross Section Libraries for Reactor Shielding, Reactor Cell and Fusion
diff --git a/openmc/model/funcs.py b/openmc/model/funcs.py
--- a/openmc/model/funcs.py
+++ b/openmc/model/funcs.py
@@ -3,6 +3,7 @@
from math import sqrt
from numbers import Real
from functools import partial
+from warnings import warn
from openmc import XPlane, YPlane, Plane, ZCylinder, Quadric
from openmc.checkvalue import check_type, check_value
@@ -101,10 +102,14 @@ def borated_water(boron_ppm, temperature=293., pressure=0.1013, temp_unit='K',
return out
-def get_rectangular_prism(width, height, axis='z', origin=(0., 0.),
- boundary_type='transmission', corner_radius=0.):
+def rectangular_prism(width, height, axis='z', origin=(0., 0.),
+ boundary_type='transmission', corner_radius=0.):
"""Get an infinite rectangular prism from four planar surfaces.
+ .. versionchanged:: 0.11
+ This function was renamed from `get_rectangular_prism` to
+ `rectangular_prism`.
+
Parameters
----------
width: float
@@ -202,10 +207,21 @@ def plane(axis, name, value):
return prism
-def get_hexagonal_prism(edge_length=1., orientation='y', origin=(0., 0.),
- boundary_type='transmission', corner_radius=0.):
+def get_rectangular_prism(*args, **kwargs):
+ warn("get_rectangular_prism(...) has been renamed rectangular_prism(...). "
+ "Future versions of OpenMC will not accept get_rectangular_prism.",
+ FutureWarning)
+ return rectangular_prism(*args, **kwargs)
+
+
+def hexagonal_prism(edge_length=1., orientation='y', origin=(0., 0.),
+ boundary_type='transmission', corner_radius=0.):
"""Create a hexagon region from six surface planes.
+ .. versionchanged:: 0.11
+ This function was renamed from `get_hexagonal_prism` to
+ `hexagonal_prism`.
+
Parameters
----------
edge_length : float
@@ -346,6 +362,13 @@ def get_hexagonal_prism(edge_length=1., orientation='y', origin=(0., 0.),
return prism
+def get_hexagonal_prism(*args, **kwargs):
+ warn("get_hexagonal_prism(...) has been renamed hexagonal_prism(...). "
+ "Future versions of OpenMC will not accept get_hexagonal_prism.",
+ FutureWarning)
+ return hexagonal_prism(*args, **kwargs)
+
+
def cylinder_from_points(p1, p2, r, **kwargs):
"""Return cylinder defined by two points passing through its center.
| diff --git a/tests/regression_tests/lattice_hex_coincident/test.py b/tests/regression_tests/lattice_hex_coincident/test.py
--- a/tests/regression_tests/lattice_hex_coincident/test.py
+++ b/tests/regression_tests/lattice_hex_coincident/test.py
@@ -103,10 +103,10 @@ def _build_inputs(self):
inf_mat_univ = openmc.Universe(cells=[inf_mat,])
# a hex surface for the core to go inside of
- hexprism = openmc.model.get_hexagonal_prism(edge_length=edge_length,
- origin=(0.0, 0.0),
- boundary_type = 'reflective',
- orientation='x')
+ hexprism = openmc.model.hexagonal_prism(edge_length=edge_length,
+ origin=(0.0, 0.0),
+ boundary_type = 'reflective',
+ orientation='x')
pincell_only_lattice = openmc.HexLattice(name="regular fuel assembly")
pincell_only_lattice.center = (0., 0.)
diff --git a/tests/regression_tests/lattice_hex_x/test.py b/tests/regression_tests/lattice_hex_x/test.py
--- a/tests/regression_tests/lattice_hex_x/test.py
+++ b/tests/regression_tests/lattice_hex_x/test.py
@@ -139,10 +139,10 @@ def _build_inputs(self):
# a hex surface for the core to go inside of
- hexprism = openmc.model.get_hexagonal_prism(edge_length=edge_length,
- origin=(0.0, 0.0),
- boundary_type='reflective',
- orientation='x')
+ hexprism = openmc.model.hexagonal_prism(edge_length=edge_length,
+ origin=(0.0, 0.0),
+ boundary_type='reflective',
+ orientation='x')
region = hexprism & +fuel_bottom & -fuel_top
inf_mat = openmc.Cell(cell_id=12)
diff --git a/tests/regression_tests/lattice_mixed/geometry.xml b/tests/regression_tests/lattice_mixed/geometry.xml
deleted file mode 100644
--- a/tests/regression_tests/lattice_mixed/geometry.xml
+++ /dev/null
@@ -1,156 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!--
- This geometry approximately describes a Russian-style VVER-1000 fuel assembly.
--->
-
-<geometry>
- <surface id="001" type="z-plane" coeffs="-10000"/>
-
- <!-- Universe 011: Fuel pellet -->
- <surface id="011" type="z-cylinder" coeffs="0.0 0.0 0.06"/>
- <surface id="012" type="z-cylinder" coeffs="0.0 0.0 0.378"/>
- <surface id="013" type="z-cylinder" coeffs="0.0 0.0 0.3865"/>
- <surface id="014" type="z-cylinder" coeffs="0.0 0.0 0.455"/>
- <surface id="015" type="sphere" coeffs="0.0 0.0 -2.5639 2.0"/>
- <surface id="016" type="sphere" coeffs="0.0 0.0 2.5639 2.0"/>
-
- <cell id="011" universe="011" material="void" region="-011"/>
- <cell id="012" universe="011" material="13" region="011 -012 015 016"/>
- <cell id="013" universe="011" material="void" region="011 -012 -015"/>
- <cell id="014" universe="011" material="void" region="011 -012 -016"/>
- <cell id="015" universe="011" material="void" region="012 -013"/>
- <cell id="016" universe="011" material="21" region="013 -014"/>
- <cell id="017" universe="011" material="01" region="014"/>
-
-
- <!-- Universe 051: Central guide tube -->
- <surface id="051" type="z-cylinder" coeffs="0.0 0.0 0.44"/>
- <surface id="052" type="z-cylinder" coeffs="0.0 0.0 0.515"/>
- <cell id="051" universe="051" material="01" region="-051"/>
- <cell id="052" universe="051" material="21" region="051 -052"/>
- <cell id="053" universe="051" material="01" region="052"/>
-
-
- <!-- Universe 055: Cluster tube -->
- <surface id="155" type="z-cylinder" coeffs="0.0 0.0 0.55"/>
- <surface id="156" type="z-cylinder" coeffs="0.0 0.0 0.63"/>
- <cell id="155" universe="055" material="01" region="-155"/>
- <cell id="156" universe="055" material="22" region="155 -156"/>
- <cell id="157" universe="055" material="01" region="156"/>
-
-
-
-
- <!-- Lattice 101: Fuel assembly pins -->
- <cell id="100" universe="100" material="01"/>
- <hex_lattice id="101" outer="100" n_rings="11"
- center="0.0 0.0" pitch="1.265">
- <universes>
- 011
- 011 011
- 011 011 011
- 011 011 011 011
- 011 011 011 011 011
- 011 011 011 011 011 011
- 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 055 011 011 011 011 011
- 011 011 011 055 011 011 055 011 011 011
- 011 011 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011 011 011
- 011 011 055 011 011 055 011 055 011 011
- 011 011 011 011 055 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 055 011 011 011
- 011 011 055 011 011 051 011 011 055 011 011
- 011 011 011 055 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 055 011 011 011 011
- 011 011 055 011 055 011 011 055 011 011
- 011 011 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011 011 011
- 011 011 011 055 011 011 055 011 011 011
- 011 011 011 011 011 055 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011 011
- 011 011 011 011 011 011 011
- 011 011 011 011 011 011
- 011 011 011 011 011
- 011 011 011 011
- 011 011 011
- 011 011
- 011
- </universes>
- </hex_lattice>
-
- <cell id="102" universe="102" fill="101"/>
-
- <lattice id="103" outer="100" dimension="1 1 294"
- lower_left="-25.0 -25.0 -177.0" pitch="50.0 50.0 1.2">
- <universes>
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
-
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
-
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102 102 102 102 102 102 102
- 102 102 102 102
- </universes>
- </lattice>
-
-
-
-
- <!-- Universe 0 -->
- <surface id="1001" type="plane" coeffs="1.0 0.0 0.0 11.8"
- boundary="reflective"/>
- <surface id="1002" type="plane" coeffs="0.5 0.866 0.0 11.8"
- boundary="reflective"/>
- <surface id="1003" type="plane" coeffs="-0.5 0.866 0.0 11.8"
- boundary="reflective"/>
- <surface id="1004" type="plane" coeffs="-1.0 0.0 0.0 11.8"
- boundary="reflective"/>
- <surface id="1005" type="plane" coeffs="-0.5 -0.866 0.0 11.8"
- boundary="reflective"/>
- <surface id="1006" type="plane" coeffs="0.5 -0.866 0.0 11.8"
- boundary="reflective"/>
- <surface id="1007" type="z-plane" coeffs="-177.4" boundary="vacuum"/>
- <surface id="1008" type="z-plane" coeffs="177.4" boundary="vacuum"/>
-
- <cell id="1001" universe="0" fill="103"
- region="-1001 -1002 -1003 -1004 -1005 -1006 1007 -1008"/>
-
-</geometry>
diff --git a/tests/regression_tests/lattice_mixed/materials.xml b/tests/regression_tests/lattice_mixed/materials.xml
deleted file mode 100644
--- a/tests/regression_tests/lattice_mixed/materials.xml
+++ /dev/null
@@ -1,42 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
- <!-- Material 01: Water -->
- <material id="01">
- <density value="0.998" units="g/cc"/>
- <nuclide name="H1" ao="2.0"/>
- <nuclide name="O16" ao="1.0"/>
- <nuclide name="B10" ao="0.00085"/>
- </material>
-
- <!-- Material 13: Fuel (3.30%) -->
- <material id="13">
- <density value="10.371" units="g/cc"/>
- <nuclide name="U235" ao="0.033408078"/>
- <nuclide name="U238" ao="0.966591922"/>
- <nuclide name="O16" ao="2.0"/>
- </material>
-
- <!-- Material 21: Zircaloy -->
- <material id="21">
- <density value="6.44" units="g/cc" />
- <nuclide name="Zr90" wo="0.501807"/>
- <nuclide name="Zr91" wo="0.110712"/>
- <nuclide name="Zr92" wo="0.170991"/>
- <nuclide name="Zr94" wo="0.177057"/>
- <nuclide name="Zr96" wo="0.029133"/>
- </material>
-
- <!-- Material 22: Steel -->
- <material id="22">
- <density value="7.9" units="g/cc"/>
- <nuclide name="Mn55" wo="2"/>
- <nuclide name="Ni58" wo="6.83"/>
- <nuclide name="Ni60" wo="2.61"/>
- <nuclide name="Cr53" wo="1.71"/>
- <nuclide name="Fe54" wo="3.98257"/>
- <nuclide name="Fe56" wo="63.03447"/>
- <nuclide name="Fe57" wo="1.4763"/>
- </material>
-
-</materials>
diff --git a/tests/regression_tests/lattice_mixed/plots.xml b/tests/regression_tests/lattice_mixed/plots.xml
deleted file mode 100644
--- a/tests/regression_tests/lattice_mixed/plots.xml
+++ /dev/null
@@ -1,32 +0,0 @@
-<?xml version="1.0"?>
-<plots>
-
- <plot id="1" type="slice" basis="xy" color_by="cell">
- <filename>xy_cell</filename>
- <origin>0 0 0</origin>
- <width>30 30</width>
- <pixels>500 500</pixels>
- </plot>
-
- <plot id="2" type="slice" basis="xy" color_by="material">
- <filename>xy_material</filename>
- <origin>0 0 0</origin>
- <width>30 30</width>
- <pixels>500 500</pixels>
- </plot>
-
- <plot id="3" type="slice" basis="yz" color_by="cell">
- <filename>yz_cell</filename>
- <origin>0 0 0</origin>
- <width>50 400</width>
- <pixels>500 4000</pixels>
- </plot>
-
- <plot id="4" type="slice" basis="yz" color_by="material">
- <filename>yz_material</filename>
- <origin>0 0 0</origin>
- <width>5 5</width>
- <pixels>500 500</pixels>
- </plot>
-
-</plots>
diff --git a/tests/regression_tests/lattice_mixed/results_true.dat b/tests/regression_tests/lattice_mixed/results_true.dat
deleted file mode 100644
--- a/tests/regression_tests/lattice_mixed/results_true.dat
+++ /dev/null
@@ -1,2 +0,0 @@
-k-combined:
-9.877395E-01 1.744626E-02
diff --git a/tests/regression_tests/lattice_mixed/settings.xml b/tests/regression_tests/lattice_mixed/settings.xml
deleted file mode 100644
--- a/tests/regression_tests/lattice_mixed/settings.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<settings>
- <run_mode>eigenvalue</run_mode>
- <batches>10</batches>
- <inactive>5</inactive>
- <particles>500</particles>
-
- <source>
- <space type="box">
- <parameters>-8.0 -8.0 -176
- 8.0 8.0 176</parameters>
- </space>
- </source>
-</settings>
diff --git a/tests/regression_tests/lattice_mixed/test.py b/tests/regression_tests/lattice_mixed/test.py
deleted file mode 100644
--- a/tests/regression_tests/lattice_mixed/test.py
+++ /dev/null
@@ -1,6 +0,0 @@
-from tests.testing_harness import TestHarness
-
-
-def test_lattice_mixed():
- harness = TestHarness('statepoint.10.h5')
- harness.main()
diff --git a/tests/regression_tests/lattice_mixed/__init__.py b/tests/regression_tests/lattice_rotated/__init__.py
similarity index 100%
rename from tests/regression_tests/lattice_mixed/__init__.py
rename to tests/regression_tests/lattice_rotated/__init__.py
diff --git a/tests/regression_tests/lattice_rotated/inputs_true.dat b/tests/regression_tests/lattice_rotated/inputs_true.dat
new file mode 100644
--- /dev/null
+++ b/tests/regression_tests/lattice_rotated/inputs_true.dat
@@ -0,0 +1,71 @@
+<?xml version='1.0' encoding='utf-8'?>
+<geometry>
+ <cell id="1" material="1" region="-1" universe="1" />
+ <cell id="2" material="3" region="1" universe="1" />
+ <cell id="3" material="2" region="-2" universe="2" />
+ <cell id="4" material="3" region="2" universe="2" />
+ <cell id="5" material="3" universe="30" />
+ <cell fill="4" id="6" region="-3" rotation="0.0 0.0 45.0" translation="-4.0 0.0 0.0" universe="5" />
+ <cell fill="3" id="7" region="-4" rotation="0.0 0.0 30.0" translation="4.0 0.0 0.0" universe="5" />
+ <cell id="8" material="3" region="-5 3 4" universe="5" />
+ <hex_lattice id="3" n_rings="3">
+ <pitch>1.25</pitch>
+ <outer>30</outer>
+ <center>0.0 0.0</center>
+ <universes>
+ 2
+ 1 1
+1 2 1
+ 1 1
+1 2 1
+ 1 1
+1 1 1
+ 1 1
+ 1</universes>
+ </hex_lattice>
+ <lattice id="4">
+ <pitch>1.25 1.25</pitch>
+ <outer>30</outer>
+ <dimension>4 4</dimension>
+ <lower_left>-2.5 -2.5</lower_left>
+ <universes>
+2 2 2 2
+1 1 1 1
+1 1 1 1
+1 1 1 1 </universes>
+ </lattice>
+ <surface coeffs="0.0 0.0 0.25" id="1" type="z-cylinder" />
+ <surface coeffs="0.0 0.0 0.5" id="2" type="z-cylinder" />
+ <surface coeffs="-4.0 0.0 4.0" id="3" type="z-cylinder" />
+ <surface coeffs="4.0 0.0 4.0" id="4" type="z-cylinder" />
+ <surface boundary="vacuum" coeffs="0.0 0.0 8.0" id="5" type="z-cylinder" />
+</geometry>
+<?xml version='1.0' encoding='utf-8'?>
+<materials>
+ <material depletable="true" id="1">
+ <density units="g/cm3" value="10.0" />
+ <nuclide ao="1.0" name="U235" />
+ </material>
+ <material depletable="true" id="2">
+ <density units="g/cm3" value="10.0" />
+ <nuclide ao="1.0" name="U238" />
+ </material>
+ <material id="3">
+ <density units="g/cm3" value="1.0" />
+ <nuclide ao="2.0" name="H1" />
+ <nuclide ao="1.0" name="O16" />
+ <sab name="c_H_in_H2O" />
+ </material>
+</materials>
+<?xml version='1.0' encoding='utf-8'?>
+<settings>
+ <run_mode>eigenvalue</run_mode>
+ <particles>1000</particles>
+ <batches>5</batches>
+ <inactive>0</inactive>
+ <source strength="1.0">
+ <space type="point">
+ <parameters>0.0 0.0 0.0</parameters>
+ </space>
+ </source>
+</settings>
diff --git a/tests/regression_tests/lattice_rotated/results_true.dat b/tests/regression_tests/lattice_rotated/results_true.dat
new file mode 100644
--- /dev/null
+++ b/tests/regression_tests/lattice_rotated/results_true.dat
@@ -0,0 +1,2 @@
+k-combined:
+4.538090E-01 2.452457E-02
diff --git a/tests/regression_tests/lattice_rotated/test.py b/tests/regression_tests/lattice_rotated/test.py
new file mode 100644
--- /dev/null
+++ b/tests/regression_tests/lattice_rotated/test.py
@@ -0,0 +1,85 @@
+import numpy as np
+import openmc
+
+from tests.testing_harness import PyAPITestHarness
+
+
+def rotated_lattice_model():
+ model = openmc.model.Model()
+
+ # Create some materials
+ fuel1 = openmc.Material()
+ fuel1.set_density('g/cm3', 10.0)
+ fuel1.add_nuclide('U235', 1.0)
+ fuel2 = openmc.Material()
+ fuel2.set_density('g/cm3', 10.0)
+ fuel2.add_nuclide('U238', 1.0)
+ water = openmc.Material()
+ water.set_density('g/cm3', 1.0)
+ water.add_nuclide('H1', 2.0)
+ water.add_nuclide('O16', 1.0)
+ water.add_s_alpha_beta('c_H_in_H2O')
+ model.materials.extend([fuel1, fuel2, water])
+
+ # Create universes for lattices
+ r_pin = openmc.ZCylinder(r=0.25)
+ fuel_cell = openmc.Cell(fill=fuel1, region=-r_pin)
+ water_cell = openmc.Cell(fill=water, region=+r_pin)
+ pin_universe = openmc.Universe(cells=(fuel_cell, water_cell))
+ r_big_pin = openmc.ZCylinder(r=0.5)
+ fuel2_cell = openmc.Cell(fill=fuel2, region=-r_big_pin)
+ water2_cell = openmc.Cell(fill=water, region=+r_big_pin)
+ big_pin_universe = openmc.Universe(cells=(fuel2_cell, water2_cell))
+ all_water_cell = openmc.Cell(fill=water)
+ outer_universe = openmc.Universe(30, cells=(all_water_cell,))
+
+ # Create hexagonal lattice
+ pitch = 1.25
+ hexlat = openmc.HexLattice()
+ hexlat.center = (0., 0.)
+ hexlat.pitch = [pitch]
+ hexlat.outer = outer_universe
+ outer_ring = [big_pin_universe] + [pin_universe]*11
+ middle_ring = [big_pin_universe] + [pin_universe]*5
+ inner_ring = [big_pin_universe]
+ hexlat.universes = [outer_ring, middle_ring, inner_ring]
+
+ # Create rectangular lattice
+ rectlat = openmc.RectLattice()
+ rectlat.center = (0., 0.)
+ rectlat.pitch = (pitch, pitch)
+ rectlat.lower_left = (-2*pitch, -2*pitch)
+ rectlat.outer = outer_universe
+ rectlat.universes = np.full((4, 4), pin_universe)
+ rectlat.universes[0] = big_pin_universe
+
+ # Create cell filled with translated/rotated rectangular lattice on left
+ left_cyl = openmc.ZCylinder(x0=-4.0, r=4.0)
+ left_cell = openmc.Cell(fill=rectlat, region=-left_cyl)
+ left_cell.translation = (-4.0, 0.0, 0.0)
+ left_cell.rotation = (0.0, 0.0, 45.0)
+
+ # Create cell filled with translated/rotated hexagonal lattice on right
+ right_cyl = openmc.ZCylinder(x0=4.0, r=4.0)
+ right_cell = openmc.Cell(fill=hexlat, region=-right_cyl)
+ right_cell.translation = (4.0, 0.0, 0.0)
+ right_cell.rotation = (0.0, 0.0, 30.0)
+
+ # Finish up with the geometry
+ outer_cyl = openmc.ZCylinder(r=8.0, boundary_type='vacuum')
+ main_cell = openmc.Cell(fill=water, region=-outer_cyl & +left_cyl & +right_cyl)
+ model.geometry = openmc.Geometry([main_cell, left_cell, right_cell])
+
+ model.settings.batches = 5
+ model.settings.inactive = 0
+ model.settings.particles = 1000
+ model.settings.source = openmc.Source(space=openmc.stats.Point())
+ model.settings.export_to_xml()
+
+ return model
+
+
+def test():
+ model = rotated_lattice_model()
+ harness = PyAPITestHarness('statepoint.5.h5', model)
+ harness.main()
diff --git a/tests/unit_tests/test_filters.py b/tests/unit_tests/test_filters.py
--- a/tests/unit_tests/test_filters.py
+++ b/tests/unit_tests/test_filters.py
@@ -11,7 +11,7 @@ def box_model():
m.add_nuclide('U235', 1.0)
m.set_density('g/cm3', 1.0)
- box = openmc.model.get_rectangular_prism(10., 10., boundary_type='vacuum')
+ box = openmc.model.rectangular_prism(10., 10., boundary_type='vacuum')
c = openmc.Cell(fill=m, region=box)
model.geometry.root_universe = openmc.Universe(cells=[c])
diff --git a/tests/unit_tests/test_geometry.py b/tests/unit_tests/test_geometry.py
--- a/tests/unit_tests/test_geometry.py
+++ b/tests/unit_tests/test_geometry.py
@@ -204,9 +204,9 @@ def test_get_by_name():
def test_hex_prism():
- hex_prism = openmc.model.get_hexagonal_prism(edge_length=5.0,
- origin=(0.0, 0.0),
- orientation='y')
+ hex_prism = openmc.model.hexagonal_prism(edge_length=5.0,
+ origin=(0.0, 0.0),
+ orientation='y')
# clear checks
assert (0.0, 0.0, 0.0) in hex_prism
assert (10.0, 10.0, 10.0) not in hex_prism
@@ -214,10 +214,10 @@ def test_hex_prism():
assert (0.0, 5.01, 0.0) not in hex_prism
assert (0.0, 4.99, 0.0) in hex_prism
- rounded_hex_prism = openmc.model.get_hexagonal_prism(edge_length=5.0,
- origin=(0.0, 0.0),
- orientation='y',
- corner_radius=1.0)
+ rounded_hex_prism = openmc.model.hexagonal_prism(edge_length=5.0,
+ origin=(0.0, 0.0),
+ orientation='y',
+ corner_radius=1.0)
# clear checks
assert (0.0, 0.0, 0.0) in rounded_hex_prism
| Lattice fill rotation
Rotation only seems to work for cells filled with regular universes - not for cells filled with lattices. In the example below, the only universe 0 cell (cell 1) is filled with the properly rotated universe 1000, which is filled with the lattice. However, if the rotation tag is removed from cell 1 and placed onto cell 10 (the one in universe 1000 filled with the lattice), the rotation is not applied.
``` xml
<?xml version="1.0"?>
<geometry>
<!-- Universe 2 -->
<surface id="2" type="y-plane" coeffs="-2" />
<surface id="3" type="y-plane" coeffs="2" />
<cell id="2" universe="2" material="1" surfaces="2 -3" />
<cell id="3" universe="2" material="2" surfaces="-2" />
<cell id="4" universe="2" material="2" surfaces="3" />
<!-- Fun Lattice -->
<lattice id="10" type="rectangular" dimension="2 2">
<lower_left> -7 -7 </lower_left>
<width> 7 7 </width>
<universes>
2 2
2 2
</universes>
</lattice>
<cell id="10" universe="1000" surfaces="" fill="10"/>
<!-- main universe -->
<surface id="1" type="sphere" coeffs="0 0 0 7" boundary="vacuum"/>
<cell id="1" fill="1000" surfaces="-1" rotation="0 0 45"/>
</geometry>
```
``` xml
<?xml version="1.0"?>
<plots>
<plot id="1" type="slice" basis="xy" color="cell">
<origin>0 0 0</origin>
<width>25 25</width>
<pixels>1000 1000</pixels>
</plot>
</plots>
```
| 2019-05-15T18:26:05Z | [] | [] |
|
openmc-dev/openmc | 1,247 | openmc-dev__openmc-1247 | [
"1239",
"1239"
] | cb9d0a92b0e5c3272282e70659878cf9301c1607 | diff --git a/openmc/data/library.py b/openmc/data/library.py
--- a/openmc/data/library.py
+++ b/openmc/data/library.py
@@ -1,5 +1,6 @@
import os
import xml.etree.ElementTree as ET
+import pathlib
import h5py
@@ -48,19 +49,30 @@ def register_file(self, filename):
Parameters
----------
- filename : str
+ filename : str or Path
Path to the file to be registered.
+ If an ``xml`` file, treat as the depletion chain file without
+ materials.
"""
- # Support pathlib
- # TODO: Remove when support is Python 3.6+ only
- filename = str(filename)
-
- with h5py.File(filename, 'r') as h5file:
- filetype = h5file.attrs['filetype'].decode()[5:]
- materials = list(h5file)
+ if not isinstance(filename, pathlib.Path):
+ path = pathlib.Path(filename)
+ else:
+ path = filename
+
+ if path.suffix == '.xml':
+ filetype = 'depletion_chain'
+ materials = []
+ elif path.suffix == '.h5':
+ with h5py.File(path, 'r') as h5file:
+ filetype = h5file.attrs['filetype'].decode()[5:]
+ materials = list(h5file)
+ else:
+ raise ValueError(
+ "File type {} not supported by {}"
+ .format(path.name, self.__class__.__name__))
- library = {'path': filename, 'type': filetype, 'materials': materials}
+ library = {'path': str(path), 'type': filetype, 'materials': materials}
self.libraries.append(library)
def export_to_xml(self, path='cross_sections.xml'):
@@ -85,8 +97,11 @@ def export_to_xml(self, path='cross_sections.xml'):
dir_element.text = os.path.realpath(common_dir)
for library in self.libraries:
- lib_element = ET.SubElement(root, "library")
- lib_element.set('materials', ' '.join(library['materials']))
+ if library['type'] == "depletion_chain":
+ lib_element = ET.SubElement(root, "depletion_chain")
+ else:
+ lib_element = ET.SubElement(root, "library")
+ lib_element.set('materials', ' '.join(library['materials']))
lib_element.set('path', os.path.relpath(library['path'], common_dir))
lib_element.set('type', library['type'])
@@ -106,7 +121,7 @@ def from_xml(cls, path=None):
----------
path : str, optional
Path to XML file to read. If not provided, the
- `OPENMC_CROSS_SECTIONS` environment variable will be used.
+ :envvar:`OPENMC_CROSS_SECTIONS` environment variable will be used.
Returns
-------
@@ -146,4 +161,13 @@ def from_xml(cls, path=None):
'materials': materials}
data.libraries.append(library)
+ # get depletion chain data
+
+ dep_node = root.find("depletion_chain")
+ if dep_node is not None:
+ filename = os.path.join(directory, dep_node.attrib['path'])
+ library = {'path': filename, 'type': 'depletion_chain',
+ 'materials': []}
+ data.libraries.append(library)
+
return data
diff --git a/openmc/deplete/abc.py b/openmc/deplete/abc.py
--- a/openmc/deplete/abc.py
+++ b/openmc/deplete/abc.py
@@ -8,7 +8,10 @@
import os
from pathlib import Path
from abc import ABCMeta, abstractmethod
+from xml.etree import ElementTree as ET
+from warnings import warn
+from openmc.data import DataLibrary
from .chain import Chain
OperatorResult = namedtuple('OperatorResult', ['k', 'rates'])
@@ -43,8 +46,9 @@ class TransportOperator(metaclass=ABCMeta):
Parameters
----------
chain_file : str, optional
- Path to the depletion chain XML file. Defaults to the
- :envvar:`OPENMC_DEPLETE_CHAIN` environment variable if it exists.
+ Path to the depletion chain XML file. Defaults to the file
+ listed under ``depletion_chain`` in
+ :envvar:`OPENMC_CROSS_SECTIONS` environment variable.
Attributes
----------
@@ -62,8 +66,21 @@ def __init__(self, chain_file=None):
if chain_file is None:
chain_file = os.environ.get("OPENMC_DEPLETE_CHAIN", None)
if chain_file is None:
- raise IOError("No chain specified, either manually or in "
- "environment variable OPENMC_DEPLETE_CHAIN.")
+ data = DataLibrary.from_xml()
+ # search for depletion_chain path from end of list
+ for lib in reversed(data.libraries):
+ if lib['type'] == 'depletion_chain':
+ break
+ else:
+ raise IOError(
+ "No chain specified, either manually or "
+ "under depletion_chain in environment variable "
+ "OPENMC_CROSS_SECTIONS.")
+ chain_file = lib['path']
+ else:
+ warn("Use of OPENMC_DEPLETE_CHAIN is deprecated in favor "
+ "of adding depletion_chain to OPENMC_CROSS_SECTIONS",
+ FutureWarning)
self.chain = Chain.from_xml(chain_file)
@abstractmethod
diff --git a/openmc/deplete/chain.py b/openmc/deplete/chain.py
--- a/openmc/deplete/chain.py
+++ b/openmc/deplete/chain.py
@@ -107,7 +107,8 @@ class Chain(object):
yield sublibrary files. The depletion chain used during a depletion
simulation is indicated by either an argument to
:class:`openmc.deplete.Operator` or through the
- :envvar:`OPENMC_DEPLETE_CHAIN` environment variable.
+ ``depletion_chain`` item in the :envvar:`OPENMC_CROSS_SECTIONS`
+ environment variable.
Attributes
----------
diff --git a/openmc/deplete/operator.py b/openmc/deplete/operator.py
--- a/openmc/deplete/operator.py
+++ b/openmc/deplete/operator.py
@@ -64,8 +64,9 @@ class Operator(TransportOperator):
settings : openmc.Settings
OpenMC Settings object
chain_file : str, optional
- Path to the depletion chain XML file. Defaults to the
- :envvar:`OPENMC_DEPLETE_CHAIN` environment variable if it exists.
+ Path to the depletion chain XML file. Defaults to the file
+ listed under ``depletion_chain`` in
+ :envvar:`OPENMC_CROSS_SECTIONS` environment variable.
prev_results : ResultsList, optional
Results from a previous depletion calculation. If this argument is
specified, the depletion calculation will start from the latest state
diff --git a/openmc/model/model.py b/openmc/model/model.py
--- a/openmc/model/model.py
+++ b/openmc/model/model.py
@@ -133,8 +133,9 @@ def deplete(self, timesteps, chain_file=None, method='cecm',
Array of timesteps in units of [s]. Note that values are not
cumulative.
chain_file : str, optional
- Path to the depletion chain XML file. Defaults to the
- :envvar:`OPENMC_DEPLETE_CHAIN` environment variable if it exists.
+ Path to the depletion chain XML file. Defaults to the chain
+ found under the ``depletion_chain`` in the
+ :envvar:`OPENMC_CROSS_SECTIONS` environment variable if it exists.
method : str
Integration method used for depletion (e.g., 'cecm', 'predictor')
**kwargs
| diff --git a/tests/unit_tests/test_data_misc.py b/tests/unit_tests/test_data_misc.py
--- a/tests/unit_tests/test_data_misc.py
+++ b/tests/unit_tests/test_data_misc.py
@@ -2,6 +2,7 @@
from collections.abc import Mapping
import os
+from pathlib import Path
import numpy as np
import pytest
@@ -33,6 +34,30 @@ def test_data_library(tmpdir):
assert new_lib.libraries[-1]['type'] == 'thermal'
+def test_depletion_chain_data_library(run_in_tmpdir):
+ dep_lib = openmc.data.DataLibrary.from_xml()
+ prev_len = len(dep_lib.libraries)
+ chain_path = Path(__file__).parents[1] / "chain_simple.xml"
+ dep_lib.register_file(chain_path)
+ assert len(dep_lib.libraries) == prev_len + 1
+ # Inspect
+ dep_dict = dep_lib.libraries[-1]
+ assert dep_dict['materials'] == []
+ assert dep_dict['type'] == 'depletion_chain'
+ assert dep_dict['path'] == str(chain_path)
+
+ out_path = "cross_section_chain.xml"
+ dep_lib.export_to_xml(out_path)
+
+ dep_import = openmc.data.DataLibrary.from_xml(out_path)
+ for lib in reversed(dep_import.libraries):
+ if lib['type'] == 'depletion_chain':
+ break
+ else:
+ raise IndexError("depletion_chain not found in exported DataLibrary")
+ assert os.path.exists(lib['path'])
+
+
def test_linearize():
"""Test linearization of a continuous function."""
x, y = openmc.data.linearize([-1., 1.], lambda x: 1 - x*x)
diff --git a/tests/unit_tests/test_deplete_operator.py b/tests/unit_tests/test_deplete_operator.py
new file mode 100644
--- /dev/null
+++ b/tests/unit_tests/test_deplete_operator.py
@@ -0,0 +1,70 @@
+"""Basic unit tests for openmc.deplete.Operator instantiation
+
+Modifies and resets environment variable OPENMC_CROSS_SECTIONS
+to a custom file with new depletion_chain node
+"""
+
+from os import environ
+from unittest import mock
+from pathlib import Path
+
+import pytest
+from openmc.deplete.abc import TransportOperator
+from openmc.deplete.chain import Chain
+
+BARE_XS_FILE = "bare_cross_sections.xml"
+CHAIN_PATH = Path(__file__).parents[1] / "chain_simple.xml"
+
+
[email protected]()
+def bare_xs(run_in_tmpdir):
+ """Create a very basic cross_sections file, return simple Chain.
+
+ """
+
+ bare_xs_contents = """<?xml version="1.0"?>
+<cross_sections>
+ <depletion_chain path="{}" />
+</cross_sections>
+""".format(CHAIN_PATH)
+
+ with open(BARE_XS_FILE, "w") as out:
+ out.write(bare_xs_contents)
+
+ yield
+
+
+class BareDepleteOperator(TransportOperator):
+ """Very basic class for testing the initialization."""
+
+ # declare abstract methods so object can be created
+ def __call__(self, *args, **kwargs):
+ pass
+
+ def initial_condition(self):
+ pass
+
+ def get_results_info(self):
+ pass
+
+
[email protected](environ, {"OPENMC_CROSS_SECTIONS": BARE_XS_FILE})
+def test_operator_init(bare_xs):
+ """The test will set and unset environment variable OPENMC_CROSS_SECTIONS
+ to point towards a temporary dummy file. This file will be removed
+ at the end of the test, and only contains a
+ depletion_chain node."""
+ # force operator to read from OPENMC_CROSS_SECTIONS
+ bare_op = BareDepleteOperator(chain_file=None)
+ act_chain = bare_op.chain
+ ref_chain = Chain.from_xml(CHAIN_PATH)
+ assert len(act_chain) == len(ref_chain)
+ for name in ref_chain.nuclide_dict:
+ # compare openmc.deplete.Nuclide objects
+ ref_nuc = ref_chain[name]
+ act_nuc = act_chain[name]
+ for prop in [
+ 'name', 'half_life', 'decay_energy', 'reactions',
+ 'decay_modes', 'yield_data', 'yield_energies',
+ ]:
+ assert getattr(act_nuc, prop) == getattr(ref_nuc, prop), prop
| Include path to depletion chain in cross_sections.xml
Right now, for depletion, it's necessary to either set an `OPENMC_DEPLETE_CHAIN` environment variable or the `chain_file` argument of `openmc.deplete.Operator`. It would be nice to also be able to specify the path in `cross_sections.xml` so that only a single environment variable is needed.
Include path to depletion chain in cross_sections.xml
Right now, for depletion, it's necessary to either set an `OPENMC_DEPLETE_CHAIN` environment variable or the `chain_file` argument of `openmc.deplete.Operator`. It would be nice to also be able to specify the path in `cross_sections.xml` so that only a single environment variable is needed.
| Would it be beneficial/helpful to first look for the chain file in the case `settings.xml` file/`openmc.deplete.Operator.settings` attribute, then the system `cross_sections.xml` file? This could allow _easy_ experimentation on the effect of the depletion chain.
Yes, I definitely agree that if we have the depletion chain specified in `cross_sections.xml`, we ought to retain some way to easily change the depletion chain for experimentation. Do you see any reason why the `chain_file` argument to `Operator` would not be adequate for that purpose?
I can't think of any, but I'm still working on familiarizing myself with the depletion capabilities.
The chain specified in `cross_sections.xml` could be the default and used unless `chain_file` is not passed. Something along these lines?
Yup, that's what I was thinking.
Would it be beneficial/helpful to first look for the chain file in the case `settings.xml` file/`openmc.deplete.Operator.settings` attribute, then the system `cross_sections.xml` file? This could allow _easy_ experimentation on the effect of the depletion chain.
Yes, I definitely agree that if we have the depletion chain specified in `cross_sections.xml`, we ought to retain some way to easily change the depletion chain for experimentation. Do you see any reason why the `chain_file` argument to `Operator` would not be adequate for that purpose?
I can't think of any, but I'm still working on familiarizing myself with the depletion capabilities.
The chain specified in `cross_sections.xml` could be the default and used unless `chain_file` is not passed. Something along these lines?
Yup, that's what I was thinking. | 2019-05-30T22:04:04Z | [] | [] |
openmc-dev/openmc | 1,254 | openmc-dev__openmc-1254 | [
"1253"
] | 1dd3ffbfcc85e7a8d148a77f2c11ffd2321da726 | diff --git a/openmc/capi/material.py b/openmc/capi/material.py
--- a/openmc/capi/material.py
+++ b/openmc/capi/material.py
@@ -32,6 +32,9 @@
POINTER(c_int)]
_dll.openmc_material_get_densities.restype = c_int
_dll.openmc_material_get_densities.errcheck = _error_handler
+_dll.openmc_material_get_density.argtypes = [c_int32, POINTER(c_double)]
+_dll.openmc_material_get_density.restype = c_int
+_dll.openmc_material_get_density.errcheck = _error_handler
_dll.openmc_material_get_volume.argtypes = [c_int32, POINTER(c_double)]
_dll.openmc_material_get_volume.restype = c_int
_dll.openmc_material_get_volume.errcheck = _error_handler
@@ -139,6 +142,15 @@ def nuclides(self):
return self._get_densities()[0]
return nuclides
+ @property
+ def density(self):
+ density = c_double()
+ try:
+ _dll.openmc_material_get_density(self._index, density)
+ except OpenMCError:
+ return None
+ return density.value
+
@property
def densities(self):
return self._get_densities()[1]
| diff --git a/tests/unit_tests/test_capi.py b/tests/unit_tests/test_capi.py
--- a/tests/unit_tests/test_capi.py
+++ b/tests/unit_tests/test_capi.py
@@ -120,6 +120,9 @@ def test_material(capi_init):
m.set_density(rho)
assert sum(m.densities) == pytest.approx(rho)
+ m.set_density(0.1, 'g/cm3')
+ assert m.density == pytest.approx(0.1)
+
def test_new_material(capi_init):
with pytest.raises(exc.AllocationError):
| Add method to get total material density
For multiphysics coupling, convergence between successive iterations of OpenMC with a T/H solver may be based on the densities, in which case we will need to make the initial density used in OpenMC available to a multiphysics driver.
There is an `openmc_material_get_densities()` method to get the density of each nuclide in a material, but it would be cleaner for a multiphysics driver to avoid doing a summation on this density and instead directly get the density in g/cm^3.
| 2019-06-09T23:56:58Z | [] | [] |
|
openmc-dev/openmc | 1,270 | openmc-dev__openmc-1270 | [
"1265"
] | 448b2ff82c1f64ddcc9e217b2da49b921a108c13 | diff --git a/openmc/deplete/__init__.py b/openmc/deplete/__init__.py
--- a/openmc/deplete/__init__.py
+++ b/openmc/deplete/__init__.py
@@ -8,6 +8,8 @@
from h5py import get_config
+from unittest.mock import Mock
+
from .dummy_comm import DummyCommunicator
try:
@@ -27,6 +29,7 @@
except ImportError:
comm = DummyCommunicator()
have_mpi = False
+ MPI = Mock()
from .nuclide import *
from .chain import *
diff --git a/openmc/deplete/integrator/cecm.py b/openmc/deplete/integrator/cecm.py
--- a/openmc/deplete/integrator/cecm.py
+++ b/openmc/deplete/integrator/cecm.py
@@ -3,7 +3,7 @@
import copy
from collections.abc import Iterable
-from .cram import deplete
+from .cram import timed_deplete
from ..results import Results
@@ -94,7 +94,8 @@ def cecm(operator, timesteps, power=None, power_density=None, print_out=True):
op_results[0].rates *= ratio_power[0]
# Deplete for first half of timestep
- x_middle = deplete(chain, x[0], op_results[0].rates, dt/2, print_out)
+ proc_time, x_middle = timed_deplete(
+ chain, x[0], op_results[0].rates, dt/2, print_out)
# Get middle-of-timestep reaction rates
x.append(x_middle)
@@ -102,10 +103,13 @@ def cecm(operator, timesteps, power=None, power_density=None, print_out=True):
# Deplete for full timestep using beginning-of-step materials
# and middle-of-timestep reaction rates
- x_end = deplete(chain, x[0], op_results[1].rates, dt, print_out)
+ pt_end, x_end = timed_deplete(
+ chain, x[0], op_results[1].rates, dt, print_out)
# Create results, write to disk
- Results.save(operator, x, op_results, [t, t + dt], p, i_res + i)
+ Results.save(
+ operator, x, op_results, [t, t + dt], p, i_res + i,
+ proc_time + pt_end)
# Advance time, update vector
t += dt
diff --git a/openmc/deplete/integrator/celi.py b/openmc/deplete/integrator/celi.py
--- a/openmc/deplete/integrator/celi.py
+++ b/openmc/deplete/integrator/celi.py
@@ -3,7 +3,7 @@
import copy
from collections.abc import Iterable
-from .cram import deplete
+from .cram import timed_deplete
from ..results import Results
@@ -149,19 +149,19 @@ def celi_inner(operator, vec, p, i, i_res, t, dt, print_out):
op_results[0].rates *= ratio_power[0]
# Deplete to end
- x_new = deplete(chain, x[0], op_results[0].rates, dt, print_out)
+ proc_time, x_new = timed_deplete(chain, x[0], op_results[0].rates, dt, print_out)
x.append(x_new)
op_results.append(operator(x[1], p))
# Deplete with two matrix exponentials
rates = list(zip(op_results[0].rates, op_results[1].rates))
- x_end = deplete(chain, x[0], rates, dt, print_out,
+ time_1, x_end = timed_deplete(chain, x[0], rates, dt, print_out,
matrix_func=_celi_f1)
- x_end = deplete(chain, x_end, rates, dt, print_out,
+ time_2, x_end = timed_deplete(chain, x_end, rates, dt, print_out,
matrix_func=_celi_f2)
# Create results, write to disk
- Results.save(operator, x, op_results, [t, t + dt], p, i_res + i)
+ Results.save(operator, x, op_results, [t, t + dt], p, i_res + i, proc_time + time_1 + time_2)
# return updated time and vectors
return x_end, t + dt, op_results[0]
diff --git a/openmc/deplete/integrator/cf4.py b/openmc/deplete/integrator/cf4.py
--- a/openmc/deplete/integrator/cf4.py
+++ b/openmc/deplete/integrator/cf4.py
@@ -3,7 +3,7 @@
import copy
from collections.abc import Iterable
-from .cram import deplete
+from .cram import timed_deplete
from ..results import Results
@@ -119,34 +119,38 @@ def cf4(operator, timesteps, power=None, power_density=None, print_out=True):
op_results[0].rates *= ratio_power[0]
# Step 1: deplete with matrix 1/2*A(y0)
- x_new = deplete(chain, x[0], op_results[0].rates, dt, print_out,
- matrix_func=_cf4_f1)
+ time_1, x_new = timed_deplete(
+ chain, x[0], op_results[0].rates, dt, print_out,
+ matrix_func=_cf4_f1)
x.append(x_new)
op_results.append(operator(x_new, p))
# Step 2: deplete with matrix 1/2*A(y1)
- x_new = deplete(chain, x[0], op_results[1].rates, dt, print_out,
- matrix_func=_cf4_f1)
+ time_2, x_new = timed_deplete(
+ chain, x[0], op_results[1].rates, dt, print_out,
+ matrix_func=_cf4_f1)
x.append(x_new)
op_results.append(operator(x_new, p))
# Step 3: deplete with matrix -1/2*A(y0)+A(y2)
rates = list(zip(op_results[0].rates, op_results[2].rates))
- x_new = deplete(chain, x[1], rates, dt, print_out,
- matrix_func=_cf4_f2)
+ time_3, x_new = timed_deplete(
+ chain, x[1], rates, dt, print_out, matrix_func=_cf4_f2)
x.append(x_new)
op_results.append(operator(x_new, p))
# Step 4: deplete with two matrix exponentials
rates = list(zip(op_results[0].rates, op_results[1].rates,
op_results[2].rates, op_results[3].rates))
- x_end = deplete(chain, x[0], rates, dt, print_out,
- matrix_func=_cf4_f3)
- x_end = deplete(chain, x_end, rates, dt, print_out,
- matrix_func=_cf4_f4)
+ time_4, x_end = timed_deplete(
+ chain, x[0], rates, dt, print_out, matrix_func=_cf4_f3)
+ time_5, x_end = timed_deplete(
+ chain, x_end, rates, dt, print_out, matrix_func=_cf4_f4)
# Create results, write to disk
- Results.save(operator, x, op_results, [t, t + dt], p, i_res + i)
+ Results.save(
+ operator, x, op_results, [t, t + dt], p, i_res + i,
+ time_1 + time_2 + time_3 + time_4 + time_5)
# Advance time, update vector
t += dt
diff --git a/openmc/deplete/integrator/cram.py b/openmc/deplete/integrator/cram.py
--- a/openmc/deplete/integrator/cram.py
+++ b/openmc/deplete/integrator/cram.py
@@ -53,6 +53,25 @@ def deplete(chain, x, rates, dt, print_out=True, matrix_func=None):
return x_result
+def timed_deplete(*args, **kwargs):
+ """Wrapper over :func:`deplete` that also returns process time
+
+ All arguments and keyword arguments are passed onto
+ :func:`deplete` directly.
+
+ Returns
+ -------
+ proc_time: float
+ Process time required to return from deplete
+ results: list of numpy arrays
+ Output from :func:`deplete` call
+ """
+
+ start = time.time()
+ results = deplete(*args, **kwargs)
+ return time.time() - start, results
+
+
def _cram_wrapper(chain, n0, rates, dt, matrix_func=None):
"""Wraps depletion matrix creation / CRAM solve for multiprocess execution
diff --git a/openmc/deplete/integrator/epc_rk4.py b/openmc/deplete/integrator/epc_rk4.py
--- a/openmc/deplete/integrator/epc_rk4.py
+++ b/openmc/deplete/integrator/epc_rk4.py
@@ -3,7 +3,7 @@
import copy
from collections.abc import Iterable
-from .cram import deplete
+from .cram import timed_deplete
from ..results import Results
@@ -105,30 +105,35 @@ def epc_rk4(operator, timesteps, power=None, power_density=None, print_out=True)
op_results[0].rates *= ratio_power[0]
# Step 1: deplete with matrix 1/2*A(y0)
- x_new = deplete(chain, x[0], op_results[0].rates, dt, print_out,
- matrix_func=_rk4_f1)
+ time_1, x_new = timed_deplete(
+ chain, x[0], op_results[0].rates, dt, print_out,
+ matrix_func=_rk4_f1)
x.append(x_new)
op_results.append(operator(x[1], p))
# Step 2: deplete with matrix 1/2*A(y1)
- x_new = deplete(chain, x[0], op_results[1].rates, dt, print_out,
- matrix_func=_rk4_f1)
+ time_2, x_new = timed_deplete(
+ chain, x[0], op_results[1].rates, dt, print_out,
+ matrix_func=_rk4_f1)
x.append(x_new)
op_results.append(operator(x[2], p))
# Step 3: deplete with matrix A(y2)
- x_new = deplete(chain, x[0], op_results[2].rates, dt, print_out)
+ time_3, x_new = timed_deplete(
+ chain, x[0], op_results[2].rates, dt, print_out)
x.append(x_new)
op_results.append(operator(x[3], p))
# Step 4: deplete with matrix 1/6*A(y0)+1/3*A(y1)+1/3*A(y2)+1/6*A(y3)
rates = list(zip(op_results[0].rates, op_results[1].rates,
op_results[2].rates, op_results[3].rates))
- x_end = deplete(chain, x[0], rates, dt, print_out,
- matrix_func=_rk4_f4)
+ time_4, x_end = timed_deplete(
+ chain, x[0], rates, dt, print_out, matrix_func=_rk4_f4)
# Create results, write to disk
- Results.save(operator, x, op_results, [t, t + dt], p, i_res + i)
+ Results.save(
+ operator, x, op_results, [t, t + dt], p, i_res + i,
+ time_1 + time_2 + time_3 + time_4)
# Advance time, update vector
t += dt
@@ -139,4 +144,5 @@ def epc_rk4(operator, timesteps, power=None, power_density=None, print_out=True)
op_results = [operator(x[0], power[-1])]
# Create results, write to disk
- Results.save(operator, x, op_results, [t, t], p, i_res + len(timesteps))
+ Results.save(
+ operator, x, op_results, [t, t], p, i_res + len(timesteps))
diff --git a/openmc/deplete/integrator/leqi.py b/openmc/deplete/integrator/leqi.py
--- a/openmc/deplete/integrator/leqi.py
+++ b/openmc/deplete/integrator/leqi.py
@@ -5,7 +5,7 @@
from itertools import repeat
from .celi import celi_inner
-from .cram import deplete
+from .cram import timed_deplete
from ..results import Results
@@ -137,22 +137,24 @@ def leqi(operator, timesteps, power=None, power_density=None, print_out=True):
inputs = list(zip(op_res_last.rates, op_results[0].rates,
repeat(dt_l), repeat(dt)))
- x_new = deplete(chain, x[0], inputs, dt, print_out,
- matrix_func=_leqi_f1)
- x_new = deplete(chain, x_new, inputs, dt, print_out,
- matrix_func=_leqi_f2)
+ time_1, x_new = timed_deplete(
+ chain, x[0], inputs, dt, print_out, matrix_func=_leqi_f1)
+ time_2, x_new = timed_deplete(
+ chain, x_new, inputs, dt, print_out, matrix_func=_leqi_f2)
x.append(x_new)
op_results.append(operator(x[1], p))
inputs = list(zip(op_res_last.rates, op_results[0].rates,
op_results[1].rates, repeat(dt_l), repeat(dt)))
- x_new = deplete(chain, x[0], inputs, dt, print_out,
- matrix_func=_leqi_f3)
- x_new = deplete(chain, x_new, inputs, dt, print_out,
- matrix_func=_leqi_f4)
+ time_3, x_new = timed_deplete(
+ chain, x[0], inputs, dt, print_out, matrix_func=_leqi_f3)
+ time_4, x_new = timed_deplete(
+ chain, x_new, inputs, dt, print_out, matrix_func=_leqi_f4)
# Create results, write to disk
- Results.save(operator, x, op_results, [t, t+dt], p, i_res+i)
+ Results.save(
+ operator, x, op_results, [t, t+dt], p, i_res+i,
+ time_1 + time_2 + time_3 + time_4)
# update results
op_res_last = copy.deepcopy(op_results[0])
@@ -164,4 +166,5 @@ def leqi(operator, timesteps, power=None, power_density=None, print_out=True):
op_results = [operator(x[0], power[-1])]
# Create results, write to disk
- Results.save(operator, x, op_results, [t, t], p, i_res + len(timesteps))
+ Results.save(
+ operator, x, op_results, [t, t], p, i_res + len(timesteps))
diff --git a/openmc/deplete/integrator/predictor.py b/openmc/deplete/integrator/predictor.py
--- a/openmc/deplete/integrator/predictor.py
+++ b/openmc/deplete/integrator/predictor.py
@@ -3,7 +3,7 @@
import copy
from collections.abc import Iterable
-from .cram import deplete
+from .cram import timed_deplete
from ..results import Results
@@ -53,6 +53,8 @@ def predictor(operator, timesteps, power=None, power_density=None,
if not isinstance(power, Iterable):
power = [power]*len(timesteps)
+ proc_time = None
+
# Generate initial conditions
with operator as vec:
# Initialize time and starting index
@@ -74,7 +76,7 @@ def predictor(operator, timesteps, power=None, power_density=None,
op_results = [operator(x[0], p)]
# Create results, write to disk
- Results.save(operator, x, op_results, [t, t + dt], p, i_res + i)
+ Results.save(operator, x, op_results, [t, t + dt], p, i_res + i, proc_time)
else:
# Get initial concentration
x = [operator.prev_res[-1].data[0]]
@@ -89,7 +91,8 @@ def predictor(operator, timesteps, power=None, power_density=None,
op_results[0].rates *= ratio_power[0]
# Deplete for full timestep
- x_end = deplete(chain, x[0], op_results[0].rates, dt, print_out)
+ proc_time, x_end = timed_deplete(
+ chain, x[0], op_results[0].rates, dt, print_out)
# Advance time, update vector
t += dt
@@ -100,4 +103,4 @@ def predictor(operator, timesteps, power=None, power_density=None,
op_results = [operator(x[0], power[-1])]
# Create results, write to disk
- Results.save(operator, x, op_results, [t, t], p, i_res + len(timesteps))
+ Results.save(operator, x, op_results, [t, t], p, i_res + len(timesteps), proc_time)
diff --git a/openmc/deplete/integrator/si_celi.py b/openmc/deplete/integrator/si_celi.py
--- a/openmc/deplete/integrator/si_celi.py
+++ b/openmc/deplete/integrator/si_celi.py
@@ -3,7 +3,7 @@
import copy
from collections.abc import Iterable
-from .cram import deplete
+from .cram import timed_deplete
from ..results import Results
from ..abc import OperatorResult
from .celi import _celi_f1, _celi_f2
@@ -94,7 +94,8 @@ def si_celi(operator, timesteps, power=None, power_density=None,
i, i_res, t, dt, print_out, m)
# Create results for last point, write to disk
- Results.save(operator, x, op_results, [t, t], p, i_res + len(timesteps))
+ Results.save(
+ operator, x, op_results, [t, t], p, i_res + len(timesteps))
def si_celi_inner(operator, x, op_results, p, i, i_res, t, dt, print_out, m=10):
@@ -136,7 +137,8 @@ def si_celi_inner(operator, x, op_results, p, i, i_res, t, dt, print_out, m=10):
chain = operator.chain
# Deplete to end
- x_new = deplete(chain, x[0], op_results[0].rates, dt, print_out)
+ proc_time, x_new = timed_deplete(
+ chain, x[0], op_results[0].rates, dt, print_out)
x.append(x_new)
for j in range(m + 1):
@@ -150,14 +152,15 @@ def si_celi_inner(operator, x, op_results, p, i, i_res, t, dt, print_out, m=10):
op_res_bar = OperatorResult(k, rates)
rates = list(zip(op_results[0].rates, op_res_bar.rates))
- x_new = deplete(chain, x[0], rates, dt, print_out,
- matrix_func=_celi_f1)
- x_new = deplete(chain, x_new, rates, dt, print_out,
- matrix_func=_celi_f2)
+ time_1, x_new = timed_deplete(
+ chain, x[0], rates, dt, print_out, matrix_func=_celi_f1)
+ time_2, x_new = timed_deplete(
+ chain, x_new, rates, dt, print_out, matrix_func=_celi_f2)
+ proc_time += time_1 + time_2
# Create results, write to disk
op_results.append(op_res_bar)
- Results.save(operator, x, op_results, [t, t+dt], p, i_res+i)
+ Results.save(operator, x, op_results, [t, t+dt], p, i_res+i, proc_time)
# return updated time and vectors
return [x_new], t + dt, [op_res_bar]
diff --git a/openmc/deplete/integrator/si_leqi.py b/openmc/deplete/integrator/si_leqi.py
--- a/openmc/deplete/integrator/si_leqi.py
+++ b/openmc/deplete/integrator/si_leqi.py
@@ -6,7 +6,7 @@
from .si_celi import si_celi_inner
from .leqi import _leqi_f1, _leqi_f2, _leqi_f3, _leqi_f4
-from .cram import deplete
+from .cram import timed_deplete
from ..results import Results
from ..abc import OperatorResult
@@ -112,12 +112,14 @@ def si_leqi(operator, timesteps, power=None, power_density=None,
# Perform remaining LE/QI
inputs = list(zip(op_res_last.rates, op_results[0].rates,
repeat(dt_l), repeat(dt)))
- x_new = deplete(chain, x[0], inputs, dt, print_out,
- matrix_func=_leqi_f1)
- x_new = deplete(chain, x_new, inputs, dt, print_out,
- matrix_func=_leqi_f2)
+ proc_time, x_new = timed_deplete(
+ chain, x[0], inputs, dt, print_out, matrix_func=_leqi_f1)
+ time_1, x_new = timed_deplete(
+ chain, x_new, inputs, dt, print_out, matrix_func=_leqi_f2)
x.append(x_new)
+ proc_time += time_1
+
# Loop on inner
for j in range(m + 1):
op_res = operator(x_new, p)
@@ -131,14 +133,17 @@ def si_leqi(operator, timesteps, power=None, power_density=None,
inputs = list(zip(op_res_last.rates, op_results[0].rates,
op_res_bar.rates, repeat(dt_l), repeat(dt)))
- x_new = deplete(chain, x[0], inputs, dt, print_out,
- matrix_func=_leqi_f3)
- x_new = deplete(chain, x_new, inputs, dt, print_out,
- matrix_func=_leqi_f4)
+ time_1, x_new = timed_deplete(
+ chain, x[0], inputs, dt, print_out, matrix_func=_leqi_f3)
+ time_2, x_new = timed_deplete(
+ chain, x_new, inputs, dt, print_out, matrix_func=_leqi_f4)
+
+ proc_time += time_1 + time_2
# Create results, write to disk
op_results.append(op_res_bar)
- Results.save(operator, x, op_results, [t, t+dt], p, i_res+i)
+ Results.save(
+ operator, x, op_results, [t, t+dt], p, i_res+i, proc_time)
# update results
x = [x_new]
@@ -148,4 +153,5 @@ def si_leqi(operator, timesteps, power=None, power_density=None,
dt_l = dt
# Create results for last point, write to disk
- Results.save(operator, x, op_results, [t, t], p, i_res+len(timesteps))
+ Results.save(
+ operator, x, op_results, [t, t], p, i_res+len(timesteps))
diff --git a/openmc/deplete/results.py b/openmc/deplete/results.py
--- a/openmc/deplete/results.py
+++ b/openmc/deplete/results.py
@@ -10,7 +10,7 @@
import numpy as np
import h5py
-from . import comm, have_mpi
+from . import comm, have_mpi, MPI
from .reaction_rates import ReactionRates
_VERSION_RESULTS = (1, 0)
@@ -47,6 +47,9 @@ class Results(object):
Number of stages in simulation.
data : numpy.ndarray
Atom quantity, stored by stage, mat, then by nuclide.
+ proc_time: int
+ Average time spent depleting a material across all
+ materials and processes
"""
def __init__(self):
@@ -55,6 +58,7 @@ def __init__(self):
self.power = None
self.rates = None
self.volume = None
+ self.proc_time = None
self.mat_to_ind = None
self.nuc_to_ind = None
@@ -245,6 +249,10 @@ def _write_hdf5_metadata(self, handle):
handle.create_dataset("power", (1, n_stages), maxshape=(None, n_stages),
dtype='float64')
+ handle.create_dataset(
+ "depletion time", (1,), maxshape=(None,),
+ dtype="float64")
+
def _to_hdf5(self, handle, index):
"""Converts results object into an hdf5 object.
@@ -268,6 +276,7 @@ def _to_hdf5(self, handle, index):
eigenvalues_dset = handle["/eigenvalues"]
time_dset = handle["/time"]
power_dset = handle["/power"]
+ proc_time_dset = handle["/depletion time"]
# Get number of results stored
number_shape = list(number_dset.shape)
@@ -296,6 +305,10 @@ def _to_hdf5(self, handle, index):
power_shape[0] = new_shape
power_dset.resize(power_shape)
+ proc_shape = list(proc_time_dset.shape)
+ proc_shape[0] = new_shape
+ proc_time_dset.resize(proc_shape)
+
# If nothing to write, just return
if len(self.mat_to_ind) == 0:
return
@@ -314,6 +327,10 @@ def _to_hdf5(self, handle, index):
if comm.rank == 0:
time_dset[index, :] = self.time
power_dset[index, :] = self.power
+ if self.proc_time is not None:
+ proc_time_dset[index] = (
+ self.proc_time / (comm.size * self.n_hdf5_mats)
+ )
@classmethod
def from_hdf5(cls, handle, step):
@@ -324,8 +341,7 @@ def from_hdf5(cls, handle, step):
handle : h5py.File or h5py.Group
An HDF5 file or group type to load from.
step : int
- What step is this?
-
+ Index for depletion step
"""
results = cls()
@@ -340,6 +356,14 @@ def from_hdf5(cls, handle, step):
results.time = time_dset[step, :]
results.power = power_dset[step, :]
+ if "depletion time" in handle:
+ proc_time_dset = handle["/depletion time"]
+ if step < proc_time_dset.shape[0]:
+ results.proc_time = proc_time_dset[step]
+
+ if results.proc_time is None:
+ results.proc_time = np.array([np.nan])
+
# Reconstruct dictionaries
results.volume = OrderedDict()
results.mat_to_ind = OrderedDict()
@@ -375,7 +399,7 @@ def from_hdf5(cls, handle, step):
return results
@staticmethod
- def save(op, x, op_results, t, power, step_ind):
+ def save(op, x, op_results, t, power, step_ind, proc_time=None):
"""Creates and writes depletion results to disk
Parameters
@@ -392,6 +416,10 @@ def save(op, x, op_results, t, power, step_ind):
Power during time step
step_ind : int
Step index.
+ proc_time : float or None
+ Total process time spent depleting materials. This may
+ be process-dependent and will be reduced across MPI
+ processes.
"""
# Get indexing terms
@@ -422,6 +450,9 @@ def save(op, x, op_results, t, power, step_ind):
results.rates = [r.rates for r in op_results]
results.time = t
results.power = power
+ results.proc_time = proc_time
+ if results.proc_time is not None:
+ results.proc_time = comm.reduce(proc_time, op=MPI.SUM)
results.export_to_hdf5("depletion_results.h5", step_ind)
diff --git a/openmc/deplete/results_list.py b/openmc/deplete/results_list.py
--- a/openmc/deplete/results_list.py
+++ b/openmc/deplete/results_list.py
@@ -105,3 +105,33 @@ def get_eigenvalue(self):
eigenvalue[i] = result.k[0]
return time, eigenvalue
+
+ def get_depletion_time(self):
+ """Return an array of the average time to deplete a material
+
+ ..note::
+
+ Will have one fewer row than number of other methods,
+ like :meth:`get_eigenvalues`, because no depletion
+ is performed at the final transport stage
+
+ Returns
+ -------
+
+ times : :class:`numpy.ndarray`
+ Vector of average time to deplete a single material
+ across all processes and materials.
+
+ """
+ times = np.empty(len(self) - 1)
+ # Need special logic because the predictor
+ # writes EOS values for step i as BOS values
+ # for step i+1
+ # The first proc_time may be zero
+ if self[0].proc_time > 0.0:
+ items = self[:-1]
+ else:
+ items = self[1:]
+ for ix, res in enumerate(items):
+ times[ix] = res.proc_time
+ return times
| diff --git a/tests/unit_tests/test_deplete_cecm.py b/tests/unit_tests/test_deplete_cecm.py
--- a/tests/unit_tests/test_deplete_cecm.py
+++ b/tests/unit_tests/test_deplete_cecm.py
@@ -35,3 +35,9 @@ def test_cecm(run_in_tmpdir):
assert y1[2] == approx(s2[0])
assert y2[2] == approx(s2[1])
+
+ # Test structure of depletion time dataset
+
+ dep_time = res.get_depletion_time()
+ assert dep_time.shape == (len(dt), )
+ assert all(dep_time > 0)
diff --git a/tests/unit_tests/test_deplete_celi.py b/tests/unit_tests/test_deplete_celi.py
--- a/tests/unit_tests/test_deplete_celi.py
+++ b/tests/unit_tests/test_deplete_celi.py
@@ -35,3 +35,9 @@ def test_celi(run_in_tmpdir):
assert y1[2] == approx(s2[0])
assert y2[2] == approx(s2[1])
+
+ # Test structure of depletion time dataset
+
+ dep_time = res.get_depletion_time()
+ assert dep_time.shape == (len(dt), )
+ assert all(dep_time > 0)
diff --git a/tests/unit_tests/test_deplete_cf4.py b/tests/unit_tests/test_deplete_cf4.py
--- a/tests/unit_tests/test_deplete_cf4.py
+++ b/tests/unit_tests/test_deplete_cf4.py
@@ -35,3 +35,9 @@ def test_cf4(run_in_tmpdir):
assert y1[2] == approx(s2[0])
assert y2[2] == approx(s2[1])
+
+ # Test structure of depletion time dataset
+
+ dep_time = res.get_depletion_time()
+ assert dep_time.shape == (len(dt), )
+ assert all(dep_time > 0)
diff --git a/tests/unit_tests/test_deplete_epc_rk4.py b/tests/unit_tests/test_deplete_epc_rk4.py
--- a/tests/unit_tests/test_deplete_epc_rk4.py
+++ b/tests/unit_tests/test_deplete_epc_rk4.py
@@ -35,3 +35,9 @@ def test_epc_rk4(run_in_tmpdir):
assert y1[2] == approx(s2[0])
assert y2[2] == approx(s2[1])
+
+ # Test structure of depletion time dataset
+
+ dep_time = res.get_depletion_time()
+ assert dep_time.shape == (len(dt), )
+ assert all(dep_time > 0)
diff --git a/tests/unit_tests/test_deplete_leqi.py b/tests/unit_tests/test_deplete_leqi.py
--- a/tests/unit_tests/test_deplete_leqi.py
+++ b/tests/unit_tests/test_deplete_leqi.py
@@ -35,3 +35,9 @@ def test_leqi(run_in_tmpdir):
assert y1[2] == approx(s2[0])
assert y2[2] == approx(s2[1])
+
+ # Test structure of depletion time dataset
+
+ dep_time = res.get_depletion_time()
+ assert dep_time.shape == (len(dt), )
+ assert all(dep_time > 0)
diff --git a/tests/unit_tests/test_deplete_predictor.py b/tests/unit_tests/test_deplete_predictor.py
--- a/tests/unit_tests/test_deplete_predictor.py
+++ b/tests/unit_tests/test_deplete_predictor.py
@@ -35,3 +35,9 @@ def test_predictor(run_in_tmpdir):
assert y1[2] == approx(s2[0])
assert y2[2] == approx(s2[1])
+
+ # Test structure of depletion time dataset
+
+ dep_time = res.get_depletion_time()
+ assert dep_time.shape == (len(dt), )
+ assert all(dep_time > 0)
diff --git a/tests/unit_tests/test_deplete_si_celi.py b/tests/unit_tests/test_deplete_si_celi.py
--- a/tests/unit_tests/test_deplete_si_celi.py
+++ b/tests/unit_tests/test_deplete_si_celi.py
@@ -35,3 +35,9 @@ def test_si_celi(run_in_tmpdir):
assert y1[2] == approx(s2[0])
assert y2[2] == approx(s2[1])
+
+ # Test structure of depletion time dataset
+
+ dep_time = res.get_depletion_time()
+ assert dep_time.shape == (len(dt), )
+ assert all(dep_time > 0)
diff --git a/tests/unit_tests/test_deplete_si_leqi.py b/tests/unit_tests/test_deplete_si_leqi.py
--- a/tests/unit_tests/test_deplete_si_leqi.py
+++ b/tests/unit_tests/test_deplete_si_leqi.py
@@ -35,3 +35,9 @@ def test_si_leqi(run_in_tmpdir):
assert y1[2] == approx(s2[0])
assert y2[2] == approx(s2[1])
+
+ # Test structure of depletion time dataset
+
+ dep_time = res.get_depletion_time()
+ assert dep_time.shape == (len(dt), )
+ assert all(dep_time > 0)
| Store total time for depletion in depletion results
Currently, every time the CRAM routine is called (if `comm == 0` and `print_out == True`), the time required to take the matrix exponential is printed to standard out. For schemes that have multiple matrix exponentials per step, `CELI`, `CF4`, etc. this is printed multiple times for each step if the given conditions are met.
For future performance studies, it would be nice to have a stored value of the total time required for depletion at each step. This could be done by having either a dedicated `depletion time` array in the `depletion_results.h5` file.
Care should be taken to ensure that the time entered in to this array is not the time to take the matrix exponential, but the **total** time required by the depletion routine at each step.
| 2019-06-21T19:39:03Z | [] | [] |
|
openmc-dev/openmc | 1,281 | openmc-dev__openmc-1281 | [
"1280"
] | 448b2ff82c1f64ddcc9e217b2da49b921a108c13 | diff --git a/openmc/material.py b/openmc/material.py
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -287,6 +287,8 @@ def from_hdf5(cls, group):
material.depletable = bool(group.attrs['depletable'])
if 'volume' in group.attrs:
material.volume = group.attrs['volume']
+ if "temperature" in group.attrs:
+ material.temperature = group.attrs["temperature"]
# Read the names of the S(a,b) tables for this Material and add them
if 'sab_names' in group:
@@ -841,8 +843,7 @@ def to_xml_element(self, cross_sections=None):
# Create temperature XML subelement
if self.temperature is not None:
- subelement = ET.SubElement(element, "temperature")
- subelement.text = str(self.temperature)
+ element.set("temperature", str(self.temperature))
# Create density XML subelement
if self._density is not None or self._density_units == 'sum':
@@ -931,8 +932,10 @@ def from_xml_element(cls, elem):
mat_id = int(elem.get('id'))
mat = cls(mat_id)
mat.name = elem.get('name')
- if 'temperature' in elem.attrib:
- mat.temperature = float(elem.get('temperature'))
+
+ if "temperature" in elem.attrib:
+ mat.temperature = float(elem.get("temperature"))
+
if 'volume' in elem.attrib:
mat.volume = float(elem.get('volume'))
mat.depletable = bool(elem.get('depletable'))
| diff --git a/tests/regression_tests/source/inputs_true.dat b/tests/regression_tests/source/inputs_true.dat
--- a/tests/regression_tests/source/inputs_true.dat
+++ b/tests/regression_tests/source/inputs_true.dat
@@ -5,8 +5,7 @@
</geometry>
<?xml version='1.0' encoding='utf-8'?>
<materials>
- <material depletable="true" id="1">
- <temperature>294</temperature>
+ <material depletable="true" id="1" temperature="294">
<density units="g/cm3" value="4.5" />
<nuclide ao="1.0" name="U235" />
</material>
diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -189,6 +189,8 @@ def test_from_xml(run_in_tmpdir):
m1.add_nuclide('H1', 1.0)
m1.add_nuclide('O16', 2.0)
m1.add_s_alpha_beta('c_H_in_H2O')
+ m1.temperature = 300
+ m1.volume = 100
m1.set_density('g/cm3', 0.9)
m1.isotropic = ['H1']
m2 = openmc.Material(2, 'zirc')
@@ -209,6 +211,8 @@ def test_from_xml(run_in_tmpdir):
assert m1.name == 'water'
assert m1.nuclides == [('H1', 1.0, 'ao'), ('O16', 2.0, 'ao')]
assert m1.isotropic == ['H1']
+ assert m1.temperature == 300
+ assert m1.volume == 100
m2 = mats[1]
assert m2.nuclides == [('Zr90', 1.0, 'wo')]
assert m2.density == 10.0
| Materials.from_xml not respecting temperature
Noticed that the newly generated material inputs when running depletion did not have any temperature tags. A simple working example
```
import openmc
mat0 = openmc.Material()
mat0.add_element("H", 2)
mat0.add_element("O", 1)
mat0.temperature = 600
openmc.Materials([mat0]).export_to_xml()
# can check to make sure the temperature tag is present
mat1 = openmc.Materials.from_xml()[0]
assert mat1.temperature is not None
```
| Looks like the error is due where `from_xml_element` expects to find temperature
https://github.com/openmc-dev/openmc/blob/448b2ff82c1f64ddcc9e217b2da49b921a108c13/openmc/material.py#L934-L935
and where it is written
https://github.com/openmc-dev/openmc/blob/448b2ff82c1f64ddcc9e217b2da49b921a108c13/openmc/material.py#L842-L845 | 2019-07-05T19:43:51Z | [] | [] |
openmc-dev/openmc | 1,287 | openmc-dev__openmc-1287 | [
"1283"
] | d6cbacf4b386fca86f3b5ec1d5a2cd33508d8bc7 | diff --git a/openmc/deplete/__init__.py b/openmc/deplete/__init__.py
--- a/openmc/deplete/__init__.py
+++ b/openmc/deplete/__init__.py
@@ -38,4 +38,4 @@
from .abc import *
from .results import *
from .results_list import *
-from .integrator import *
+from .integrators import *
diff --git a/openmc/deplete/_matrix_funcs.py b/openmc/deplete/_matrix_funcs.py
new file mode 100644
--- /dev/null
+++ b/openmc/deplete/_matrix_funcs.py
@@ -0,0 +1,79 @@
+"""Functions to form the special matrix for depletion"""
+
+
+def celi_f1(chain, rates):
+ return (5 / 12 * chain.form_matrix(rates[0])
+ + 1 / 12 * chain.form_matrix(rates[1]))
+
+
+def celi_f2(chain, rates):
+ return (1 / 12 * chain.form_matrix(rates[0])
+ + 5 / 12 * chain.form_matrix(rates[1]))
+
+
+def cf4_f1(chain, rates):
+ return 1 / 2 * chain.form_matrix(rates)
+
+
+def cf4_f2(chain, rates):
+ return -1 / 2 * chain.form_matrix(rates[0]) + chain.form_matrix(rates[1])
+
+
+def cf4_f3(chain, rates):
+ return (1 / 4 * chain.form_matrix(rates[0])
+ + 1 / 6 * chain.form_matrix(rates[1])
+ + 1 / 6 * chain.form_matrix(rates[2])
+ - 1 / 12 * chain.form_matrix(rates[3]))
+
+
+def cf4_f4(chain, rates):
+ return (-1 / 12 * chain.form_matrix(rates[0])
+ + 1 / 6 * chain.form_matrix(rates[1])
+ + 1 / 6 * chain.form_matrix(rates[2])
+ + 1 / 4 * chain.form_matrix(rates[3]))
+
+
+def rk4_f1(chain, rates):
+ return 1 / 2 * chain.form_matrix(rates)
+
+
+def rk4_f4(chain, rates):
+ return (1 / 6 * chain.form_matrix(rates[0])
+ + 1 / 3 * chain.form_matrix(rates[1])
+ + 1 / 3 * chain.form_matrix(rates[2])
+ + 1 / 6 * chain.form_matrix(rates[3]))
+
+
+def leqi_f1(chain, inputs):
+ f1 = chain.form_matrix(inputs[0])
+ f2 = chain.form_matrix(inputs[1])
+ dt_l, dt = inputs[2], inputs[3]
+ return -dt / (12 * dt_l) * f1 + (dt + 6 * dt_l) / (12 * dt_l) * f2
+
+
+def leqi_f2(chain, inputs):
+ f1 = chain.form_matrix(inputs[0])
+ f2 = chain.form_matrix(inputs[1])
+ dt_l, dt = inputs[2], inputs[3]
+ return -5 * dt / (12 * dt_l) * f1 + (5 * dt + 6 * dt_l) / (12 * dt_l) * f2
+
+
+def leqi_f3(chain, inputs):
+ f1 = chain.form_matrix(inputs[0])
+ f2 = chain.form_matrix(inputs[1])
+ f3 = chain.form_matrix(inputs[2])
+ dt_l, dt = inputs[3], inputs[4]
+ return (-dt ** 2 / (12 * dt_l * (dt + dt_l)) * f1
+ + (dt ** 2 + 6 * dt * dt_l + 5 * dt_l ** 2)
+ / (12 * dt_l * (dt + dt_l)) * f2 + dt_l / (12 * (dt + dt_l)) * f3)
+
+
+def leqi_f4(chain, inputs):
+ f1 = chain.form_matrix(inputs[0])
+ f2 = chain.form_matrix(inputs[1])
+ f3 = chain.form_matrix(inputs[2])
+ dt_l, dt = inputs[3], inputs[4]
+ return (-dt ** 2 / (12 * dt_l * (dt + dt_l)) * f1
+ + (dt ** 2 + 2 * dt * dt_l + dt_l ** 2)
+ / (12 * dt_l * (dt + dt_l)) * f2
+ + (4 * dt * dt_l + 5 * dt_l ** 2) / (12 * dt_l * (dt + dt_l)) * f3)
diff --git a/openmc/deplete/abc.py b/openmc/deplete/abc.py
--- a/openmc/deplete/abc.py
+++ b/openmc/deplete/abc.py
@@ -5,18 +5,22 @@
"""
from collections import namedtuple
+from collections.abc import Iterable
import os
from pathlib import Path
from abc import ABC, abstractmethod
-from xml.etree import ElementTree as ET
+from copy import deepcopy
from warnings import warn
-from numbers import Real
+from numbers import Real, Integral
from numpy import nonzero, empty
+from uncertainties import ufloat
from openmc.data import DataLibrary, JOULE_PER_EV
from openmc.checkvalue import check_type, check_greater_than
+from .results import Results
from .chain import Chain
+from .results_list import ResultsList
OperatorResult = namedtuple('OperatorResult', ['k', 'rates'])
OperatorResult.__doc__ = """\
@@ -24,8 +28,8 @@
Parameters
----------
-k : float
- Resulting eigenvalue
+k : uncertainties.ufloat
+ Resulting eigenvalue and standard deviation
rates : openmc.deplete.ReactionRates
Resulting reaction rates
@@ -43,8 +47,8 @@ class TransportOperator(ABC):
Each depletion integrator is written to work with a generic transport
operator that takes a vector of material compositions and returns an
- eigenvalue and reaction rates. This abstract class sets the requirements for
- such a transport operator. Users should instantiate
+ eigenvalue and reaction rates. This abstract class sets the requirements
+ for such a transport operator. Users should instantiate
:class:`openmc.deplete.Operator` rather than this class.
Parameters
@@ -61,6 +65,8 @@ class TransportOperator(ABC):
in initial condition to ensure they exist in the decay chain.
Only done for nuclides with reaction rates.
Defaults to 1.0e3.
+ prev_results : ResultsList, optional
+ Results from a previous depletion calculation.
Attributes
----------
@@ -68,8 +74,12 @@ class TransportOperator(ABC):
Initial atom density [atoms/cm^3] to add for nuclides that are zero
in initial condition to ensure they exist in the decay chain.
Only done for nuclides with reaction rates.
+ prev_res : ResultsList or None
+ Results from a previous depletion calculation. ``None`` if no
+ results are to be used.
"""
- def __init__(self, chain_file=None, fission_q=None, dilute_initial=1.0e3):
+ def __init__(self, chain_file=None, fission_q=None, dilute_initial=1.0e3,
+ prev_results=None):
self.dilute_initial = dilute_initial
self.output_dir = '.'
@@ -93,6 +103,11 @@ def __init__(self, chain_file=None, fission_q=None, dilute_initial=1.0e3):
"of adding depletion_chain to OPENMC_CROSS_SECTIONS",
FutureWarning)
self.chain = Chain.from_xml(chain_file, fission_q)
+ if prev_results is None:
+ self.prev_res = None
+ else:
+ check_type("previous results", prev_results, ResultsList)
+ self.prev_results = prev_results
@property
def dilute_initial(self):
@@ -106,15 +121,15 @@ def dilute_initial(self, value):
self._dilute_initial = value
@abstractmethod
- def __call__(self, vec, print_out=True):
+ def __call__(self, vec, power):
"""Runs a simulation.
Parameters
----------
vec : list of numpy.ndarray
Total atoms to be used in function.
- print_out : bool, optional
- Whether or not to print out time.
+ power : float
+ Power of the reactor in [W]
Returns
-------
@@ -122,7 +137,6 @@ def __call__(self, vec, print_out=True):
Eigenvalue and reaction rates resulting from transport operator
"""
- pass
def __enter__(self):
# Save current directory and move to specific output directory
@@ -157,8 +171,6 @@ def initial_condition(self):
Total density for initial conditions.
"""
- pass
-
@abstractmethod
def get_results_info(self):
"""Returns volume list, cell lists, and nuc lists.
@@ -170,16 +182,28 @@ def get_results_info(self):
nuc_list : list of str
A list of all nuclide names. Used for sorting the simulation.
burn_list : list of int
- A list of all cell IDs to be burned. Used for sorting the simulation.
+ A list of all cell IDs to be burned. Used for sorting the
+ simulation.
full_burn_list : list of int
All burnable materials in the geometry.
"""
- pass
-
def finalize(self):
pass
+ @abstractmethod
+ def write_bos_data(self, step):
+ """Document beginning of step data for a given step
+
+ Called at the beginning of a depletion step and at
+ the final point in the simulation.
+
+ Parameters
+ ----------
+ step : int
+ Current depletion step including restarts
+ """
+
class ReactionRateHelper(ABC):
"""Abstract class for generating reaction rates for operators
@@ -246,7 +270,8 @@ def divide_by_adens(self, number):
Parameters
----------
number : iterable of float
- Number density [atoms/b-cm] of each nuclide tracked in the calculation.
+ Number density [atoms/b-cm] of each nuclide tracked in the
+ calculation.
Returns
-------
@@ -337,3 +362,271 @@ def nuclides(self):
def nuclides(self, nuclides):
check_type("nuclides", nuclides, list, str)
self._nuclides = nuclides
+
+
+class Integrator(ABC):
+ """Abstract class for solving the time-integration for depletion
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ timesteps : iterable of float
+ Array of timesteps in units of [s]. Note that values are not
+ cumulative.
+ power : float or iterable of float, optional
+ Power of the reactor in [W]. A single value indicates that
+ the power is constant over all timesteps. An iterable
+ indicates potentially different power levels for each timestep.
+ For a 2D problem, the power can be given in [W/cm] as long
+ as the "volume" assigned to a depletion material is actually
+ an area in [cm^2]. Either ``power`` or ``power_density`` must be
+ specified.
+ power_density : float or iterable of float, optional
+ Power density of the reactor in [W/gHM]. It is multiplied by
+ initial heavy metal inventory to get total power if ``power``
+ is not speficied.
+
+ Attributes
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ chain : openmc.deplete.Chain
+ Depletion chain
+ timesteps : iterable of float
+ Size of each depletion interval in [s]
+ power : iterable of float
+ Power of the reactor in [W] for each interval in :attr:`timesteps`
+ """
+
+ def __init__(self, operator, timesteps, power=None, power_density=None):
+ # Check number of stages previously used
+ if operator.prev_res is not None:
+ res = operator.prev_res[-1]
+ if res.data.shape[0] != self._num_stages:
+ raise ValueError(
+ "{} incompatible with previous restart calculation. "
+ "Previous scheme used {} intermediate solutions, while "
+ "this uses {}".format(
+ self.__class__.__name__, res.data.shape[0],
+ self._num_stages))
+ self.operator = operator
+ self.chain = operator.chain
+ if not isinstance(timesteps, Iterable):
+ self.timesteps = [timesteps]
+ else:
+ self.timesteps = timesteps
+ if power is None:
+ if power_density is None:
+ raise ValueError("Either power or power density must be set")
+ if not isinstance(power_density, Iterable):
+ power = power_density * operator.heavy_metal
+ else:
+ power = [p * operator.heavy_metal for p in power_density]
+
+ if not isinstance(power, Iterable):
+ # Ensure that power is single value if that is the case
+ power = [power] * len(self.timesteps)
+ elif len(power) != len(self.timesteps):
+ raise ValueError(
+ "Number of time steps != number of powers. {} vs {}".format(
+ len(self.timesteps), len(power)))
+
+ self.power = power
+
+ @abstractmethod
+ def __call__(self, conc, rates, dt, power, i):
+ """Perform the integration across one time step
+
+ Parameters
+ ----------
+ conc : numpy.ndarray
+ Initial concentrations for all nuclides in [atom]
+ rates : openmc.deplete.ReactionRates
+ Reaction rates from operator
+ dt : float
+ Time in [s] for the entire depletion interval
+ power : float
+ Power of the system in [W]
+ i : int
+ Current depletion step index
+
+ Returns
+ -------
+ proc_time : float
+ Time spent in CRAM routines for all materials in [s]
+ conc_list : list of numpy.ndarray
+ Concentrations at each of the intermediate points with
+ the final concentration as the last element
+ op_results : list of openmc.deplete.OperatorResult
+ Eigenvalue and reaction rates from intermediate transport
+ simulations
+ """
+
+ @property
+ @abstractmethod
+ def _num_stages(self):
+ """Number of intermediate transport solutions
+
+ Needed to ensure schemes are consistent with restarts
+ """
+
+ def __iter__(self):
+ """Return pairs of time steps in [s] and powers in [W]"""
+ return zip(self.timesteps, self.power)
+
+ def __len__(self):
+ """Return integer number of depletion intervals"""
+ return len(self.timesteps)
+
+ def _get_bos_data_from_operator(self, step_index, step_power, bos_conc):
+ """Get beginning of step concentrations, reaction rates from Operator
+ """
+ x = deepcopy(bos_conc)
+ res = self.operator(x, step_power)
+ self.operator.write_bos_data(step_index + self._i_res)
+ return x, res
+
+ def _get_bos_data_from_restart(self, step_index, step_power, bos_conc):
+ """Get beginning of step concentrations, reaction rates from restart"""
+ res = self.operator.prev_res[-1]
+ # Depletion methods expect list of arrays
+ bos_conc = list(res.data[0])
+ rates = res.rates[0]
+ k = ufloat(res.k[0, 0], res.k[0, 1])
+
+ # Scale rates by ratio of powers
+ rates *= step_power / res.power[0]
+ return bos_conc, OperatorResult(k, rates)
+
+ def _get_start_data(self):
+ if self.operator.prev_res is None:
+ return 0.0, 0
+ return (self.operator.prev_res[-1].time[-1],
+ len(self.operator.prev_res) - 1)
+
+ def integrate(self):
+ """Perform the entire depletion process across all steps"""
+ with self.operator as conc:
+ t, self._i_res = self._get_start_data()
+
+ for i, (dt, p) in enumerate(self):
+ if i > 0 or self.operator.prev_res is None:
+ conc, res = self._get_bos_data_from_operator(i, p, conc)
+ else:
+ conc, res = self._get_bos_data_from_restart(i, p, conc)
+ proc_time, conc_list, res_list = self(conc, res.rates, dt, p, i)
+
+ # Insert BOS concentration, transport results
+ conc_list.insert(0, conc)
+ res_list.insert(0, res)
+
+ # Remove actual EOS concentration for next step
+ conc = conc_list.pop()
+
+ Results.save(self.operator, conc_list, res_list, [t, t + dt],
+ p, self._i_res + i, proc_time)
+
+ t += dt
+
+ # Final simulation
+ res_list = [self.operator(conc, p)]
+ Results.save(self.operator, [conc], res_list, [t, t],
+ p, self._i_res + len(self), proc_time)
+ self.operator.write_bos_data(len(self) + self._i_res)
+
+
+class SIIntegrator(Integrator):
+ """Abstract class for the Stochastic Implicit Euler integrators
+
+ Does not provide a ``__call__`` method, but scales and resets
+ the number of particles used in initial transport calculation
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ The operator object to simulate on.
+ timesteps : iterable of float
+ Array of timesteps in units of [s]. Note that values are not
+ cumulative.
+ power : float or iterable of float, optional
+ Power of the reactor in [W]. A single value indicates that
+ the power is constant over all timesteps. An iterable
+ indicates potentially different power levels for each timestep.
+ For a 2D problem, the power can be given in [W/cm] as long
+ as the "volume" assigned to a depletion material is actually
+ an area in [cm^2]. Either ``power`` or ``power_density`` must be
+ specified.
+ power_density : float or iterable of float, optional
+ Power density of the reactor in [W/gHM]. It is multiplied by
+ initial heavy metal inventory to get total power if ``power``
+ is not speficied.
+ n_steps : int, optional
+ Number of stochastic iterations per depletion interval.
+ Must be greater than zero. Default : 10
+
+ Attributes
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ chain : openmc.deplete.Chain
+ Depletion chain
+ timesteps : iterable of float
+ Size of each depletion interval in [s]
+ power : iterable of float
+ Power of the reactor in [W] for each interval in :attr:`timesteps`
+ n_steps : int
+ Number of stochastic iterations per depletion interval
+ """
+ def __init__(self, operator, timesteps, power=None, power_density=None,
+ n_steps=10):
+ check_type("n_steps", n_steps, Integral)
+ check_greater_than("n_steps", n_steps, 0)
+ super().__init__(operator, timesteps, power, power_density)
+ self.n_steps = n_steps
+
+ def _get_bos_data_from_operator(self, step_index, step_power, bos_conc):
+ reset_particles = False
+ if step_index == 0 and hasattr(self.operator, "settings"):
+ reset_particles = True
+ self.operator.settings.particles *= self.n_stages
+ inherited = super()._get_bos_data_from_operator(
+ step_index, step_power, bos_conc)
+ if reset_particles:
+ self.operator.settings.particles //= self.n_stages
+ return inherited
+
+ def integrate(self):
+ """Perform the entire depletion process across all steps"""
+ with self.operator as conc:
+ t, self._i_res = self._get_start_data()
+
+ for i, (dt, p) in enumerate(self):
+ if i == 0:
+ if self.operator.prev_res is None:
+ conc, res = self._get_bos_data_from_operator(i, p, conc)
+ else:
+ conc, res = self._get_bos_data_from_restart(i, p, conc)
+ else:
+ # Pull rates, k from previous iteration w/o
+ # re-running transport
+ res = res_list[-1] # defined in previous i iteration
+
+ proc_time, conc_list, res_list = self(conc, res.rates, dt, p, i)
+
+ # Insert BOS concentration, transport results
+ conc_list.insert(0, conc)
+ res_list.insert(0, res)
+
+ # Remove actual EOS concentration for next step
+ conc = conc_list.pop()
+
+ Results.save(self.operator, conc_list, res_list, [t, t + dt],
+ p, self._i_res + i, proc_time)
+
+ t += dt
+
+ # No final simulation for SIE, use last iteration results
+ Results.save(self.operator, [conc], [res_list[-1]], [t, t],
+ p, self._i_res + len(self), proc_time)
+ self.operator.write_bos_data(self._i_res + len(self))
diff --git a/openmc/deplete/integrator/cram.py b/openmc/deplete/cram.py
similarity index 95%
rename from openmc/deplete/integrator/cram.py
rename to openmc/deplete/cram.py
--- a/openmc/deplete/integrator/cram.py
+++ b/openmc/deplete/cram.py
@@ -11,10 +11,12 @@
import scipy.sparse as sp
import scipy.sparse.linalg as sla
-from .. import comm
+from . import comm
+__all__ = ["deplete", "timed_deplete", "CRAM16", "CRAM48"]
-def deplete(chain, x, rates, dt, print_out=True, matrix_func=None):
+
+def deplete(chain, x, rates, dt, matrix_func=None):
"""Deplete materials using given reaction rates for a specified time
Parameters
@@ -27,29 +29,22 @@ def deplete(chain, x, rates, dt, print_out=True, matrix_func=None):
Reaction rates (from transport operator)
dt : float
Time in [s] to deplete for
- print_out : bool, optional
- Whether to show elapsed time
- maxtrix_func : function, optional
- Function to form the depletion matrix
+ maxtrix_func : Callable, optional
+ Function of two variables: ``chain`` and ``rates``.
+ Expected to return the depletion matrix required by
+ :func:`CRAM48`.
Returns
-------
x_result : list of numpy.ndarray
Updated atom number vectors for each material
-
"""
- t_start = time.time()
# Use multiprocessing pool to distribute work
with Pool() as pool:
iters = zip(repeat(chain), x, rates, repeat(dt), repeat(matrix_func))
x_result = list(pool.starmap(_cram_wrapper, iters))
- t_end = time.time()
- if comm.rank == 0:
- if print_out:
- print("Time to matexp: ", t_end - t_start)
-
return x_result
diff --git a/openmc/deplete/integrator/__init__.py b/openmc/deplete/integrator/__init__.py
deleted file mode 100644
--- a/openmc/deplete/integrator/__init__.py
+++ /dev/null
@@ -1,16 +0,0 @@
-"""
-Integrator
-===========
-
-The integrator subcomponents.
-"""
-
-from .cf4 import *
-from .cecm import *
-from .celi import *
-from .cram import *
-from .epc_rk4 import *
-from .leqi import *
-from .predictor import *
-from .si_celi import *
-from .si_leqi import *
diff --git a/openmc/deplete/integrator/cecm.py b/openmc/deplete/integrator/cecm.py
deleted file mode 100644
--- a/openmc/deplete/integrator/cecm.py
+++ /dev/null
@@ -1,123 +0,0 @@
-"""The CE/CM integrator."""
-
-import copy
-from collections.abc import Iterable
-
-from .cram import timed_deplete
-from ..results import Results
-
-
-def cecm(operator, timesteps, power=None, power_density=None, print_out=True):
- r"""Deplete using the CE/CM algorithm.
-
- Implements the second order `CE/CM predictor-corrector algorithm
- <https://doi.org/10.13182/NSE14-92>`_.
-
- "CE/CM" stands for constant extrapolation on predictor and constant
- midpoint on corrector. This algorithm is mathematically defined as:
-
- .. math::
- \begin{aligned}
- y' &= A(y, t) y(t) \\
- A_p &= A(y_n, t_n) \\
- y_m &= \text{expm}(A_p h/2) y_n \\
- A_c &= A(y_m, t_n + h/2) \\
- y_{n+1} &= \text{expm}(A_c h) y_n
- \end{aligned}
-
- Parameters
- ----------
- operator : openmc.deplete.TransportOperator
- The operator object to simulate on.
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not cumulative.
- power : float or iterable of float, optional
- Power of the reactor in [W]. A single value indicates that the power is
- constant over all timesteps. An iterable indicates potentially different
- power levels for each timestep. For a 2D problem, the power can be given
- in [W/cm] as long as the "volume" assigned to a depletion material is
- actually an area in [cm^2]. Either `power` or `power_density` must be
- specified.
- power_density : float or iterable of float, optional
- Power density of the reactor in [W/gHM]. It is multiplied by initial
- heavy metal inventory to get total power if `power` is not speficied.
- print_out : bool, optional
- Whether or not to print out time.
-
- """
- if power is None:
- if power_density is None:
- raise ValueError(
- "Neither power nor power density was specified.")
- if not isinstance(power_density, Iterable):
- power = power_density*operator.heavy_metal
- else:
- power = [i*operator.heavy_metal for i in power_density]
-
- if not isinstance(power, Iterable):
- power = [power]*len(timesteps)
-
- # Generate initial conditions
- with operator as vec:
- # Initialize time and starting index
- if operator.prev_res is None:
- t = 0.0
- i_res = 0
- else:
- t = operator.prev_res[-1].time[-1]
- i_res = len(operator.prev_res)
-
- chain = operator.chain
-
- for i, (dt, p) in enumerate(zip(timesteps, power)):
- # Get beginning-of-timestep concentrations and reaction rates
- # Avoid doing first transport run if already done in previous
- # calculation
- if i > 0 or operator.prev_res is None:
- x = [copy.deepcopy(vec)]
- op_results = [operator(x[0], p)]
-
- else:
- # Get initial concentration
- x = [operator.prev_res[-1].data[0]]
-
- # Get rates
- op_results = [operator.prev_res[-1]]
- op_results[0].rates = op_results[0].rates[0]
-
- # Set first stage value of keff
- op_results[0].k = op_results[0].k[0]
-
- # Scale reaction rates by ratio of powers
- power_res = operator.prev_res[-1].power
- ratio_power = p / power_res
- op_results[0].rates *= ratio_power[0]
-
- # Deplete for first half of timestep
- proc_time, x_middle = timed_deplete(
- chain, x[0], op_results[0].rates, dt/2, print_out)
-
- # Get middle-of-timestep reaction rates
- x.append(x_middle)
- op_results.append(operator(x_middle, p))
-
- # Deplete for full timestep using beginning-of-step materials
- # and middle-of-timestep reaction rates
- pt_end, x_end = timed_deplete(
- chain, x[0], op_results[1].rates, dt, print_out)
-
- # Create results, write to disk
- Results.save(
- operator, x, op_results, [t, t + dt], p, i_res + i,
- proc_time + pt_end)
-
- # Advance time, update vector
- t += dt
- vec = copy.deepcopy(x_end)
-
- # Perform one last simulation
- x = [copy.deepcopy(vec)]
- op_results = [operator(x[0], power[-1])]
-
- # Create results, write to disk
- Results.save(operator, x, op_results, [t, t], p, i_res + len(timesteps))
diff --git a/openmc/deplete/integrator/celi.py b/openmc/deplete/integrator/celi.py
deleted file mode 100644
--- a/openmc/deplete/integrator/celi.py
+++ /dev/null
@@ -1,167 +0,0 @@
-"""The CE/LI CFQ4 integrator."""
-
-import copy
-from collections.abc import Iterable
-
-from .cram import timed_deplete
-from ..results import Results
-
-
-# Functions to form the special matrix for depletion
-def _celi_f1(chain, rates):
- return 5/12 * chain.form_matrix(rates[0]) + \
- 1/12 * chain.form_matrix(rates[1])
-
-
-def _celi_f2(chain, rates):
- return 1/12 * chain.form_matrix(rates[0]) + \
- 5/12 * chain.form_matrix(rates[1])
-
-
-def celi(operator, timesteps, power=None, power_density=None,
- print_out=True):
- r"""Deplete using the CE/LI CFQ4 algorithm.
-
- Implements the CE/LI Predictor-Corrector algorithm using the `fourth order
- commutator-free integrator <https://doi.org/10.1137/05063042>`_.
-
- "CE/LI" stands for constant extrapolation on predictor and linear
- interpolation on corrector. This algorithm is mathematically defined as:
-
- .. math::
- \begin{aligned}
- y' &= A(y, t) y(t) \\
- A_0 &= A(y_n, t_n) \\
- y_p &= \text{expm}(h A_0) y_n \\
- A_1 &= A(y_p, t_n + h) \\
- y_{n+1} &= \text{expm}(\frac{h}{12} A_0 + \frac{5h}{12} A1)
- \text{expm}(\frac{5h}{12} A_0 + \frac{h}{12} A1) y_n
- \end{aligned}
-
- Parameters
- ----------
- operator : openmc.deplete.TransportOperator
- The operator object to simulate on.
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not cumulative.
- power : float or iterable of float, optional
- Power of the reactor in [W]. A single value indicates that the power is
- constant over all timesteps. An iterable indicates potentially different
- power levels for each timestep. For a 2D problem, the power can be given
- in [W/cm] as long as the "volume" assigned to a depletion material is
- actually an area in [cm^2]. Either `power` or `power_density` must be
- specified.
- power_density : float or iterable of float, optional
- Power density of the reactor in [W/gHM]. It is multiplied by initial
- heavy metal inventory to get total power if `power` is not speficied.
- print_out : bool, optional
- Whether or not to print out time.
- """
- if power is None:
- if power_density is None:
- raise ValueError(
- "Neither power nor power density was specified.")
- if not isinstance(power_density, Iterable):
- power = power_density*operator.heavy_metal
- else:
- power = [i*operator.heavy_metal for i in power_density]
-
- if not isinstance(power, Iterable):
- power = [power]*len(timesteps)
-
- # Generate initial conditions
- with operator as vec:
- # Initialize time and starting index
- if operator.prev_res is None:
- t = 0.0
- i_res = 0
- else:
- t = operator.prev_res[-1].time[-1]
- i_res = len(operator.prev_res)
-
- for i, (dt, p) in enumerate(zip(timesteps, power)):
- vec, t, _ = celi_inner(operator, vec, p, i, i_res, t, dt,
- print_out)
-
- # Perform one last simulation
- x = [copy.deepcopy(vec)]
- op_results = [operator(x[0], power[-1])]
-
- # Create results, write to disk
- Results.save(operator, x, op_results, [t, t], p, i_res + len(timesteps))
-
-
-def celi_inner(operator, vec, p, i, i_res, t, dt, print_out):
- """ The inner loop of CE/LI CFQ4.
-
- Parameters
- ----------
- operator : Operator
- The operator object to simulate on.
- x : list of nuclide vector
- Nuclide vector, beginning of time.
- p : float
- Power of the reactor in [W]
- i : int
- Current iteration number.
- i_res : int
- Starting index, for restart calculation.
- t : float
- Time at start of step.
- dt : float
- Time step.
- print_out : bool
- Whether or not to print out time.
-
- Returns
- -------
- list of numpy.array
- Nuclide vector, end of time.
- float
- Next time
- OperatorResult
- Operator result from beginning of step.
- """
-
- chain = operator.chain
-
- # Get beginning-of-timestep concentrations and reaction rates
- # Avoid doing first transport run if already done in previous
- # calculation
- if i > 0 or operator.prev_res is None:
- x = [copy.deepcopy(vec)]
- op_results = [operator(x[0], p)]
-
- else:
- # Get initial concentration
- x = [operator.prev_res[-1].data[0]]
-
- # Get rates
- op_results = [operator.prev_res[-1]]
- op_results[0].rates = op_results[0].rates[0]
-
- # Set first stage value of keff
- op_results[0].k = op_results[0].k[0]
-
- # Scale reaction rates by ratio of powers
- power_res = operator.prev_res[-1].power
- ratio_power = p / power_res
- op_results[0].rates *= ratio_power[0]
-
- # Deplete to end
- proc_time, x_new = timed_deplete(chain, x[0], op_results[0].rates, dt, print_out)
- x.append(x_new)
- op_results.append(operator(x[1], p))
-
- # Deplete with two matrix exponentials
- rates = list(zip(op_results[0].rates, op_results[1].rates))
- time_1, x_end = timed_deplete(chain, x[0], rates, dt, print_out,
- matrix_func=_celi_f1)
- time_2, x_end = timed_deplete(chain, x_end, rates, dt, print_out,
- matrix_func=_celi_f2)
-
- # Create results, write to disk
- Results.save(operator, x, op_results, [t, t + dt], p, i_res + i, proc_time + time_1 + time_2)
-
- # return updated time and vectors
- return x_end, t + dt, op_results[0]
diff --git a/openmc/deplete/integrator/cf4.py b/openmc/deplete/integrator/cf4.py
deleted file mode 100644
--- a/openmc/deplete/integrator/cf4.py
+++ /dev/null
@@ -1,164 +0,0 @@
-"""The CF4 integrator."""
-
-import copy
-from collections.abc import Iterable
-
-from .cram import timed_deplete
-from ..results import Results
-
-
-# Functions to form the special matrix for depletion
-def _cf4_f1(chain, rates):
- return 1/2 * chain.form_matrix(rates)
-
-
-def _cf4_f2(chain, rates):
- return -1/2 * chain.form_matrix(rates[0]) + \
- chain.form_matrix(rates[1])
-
-
-def _cf4_f3(chain, rates):
- return 1/4 * chain.form_matrix(rates[0]) + \
- 1/6 * chain.form_matrix(rates[1]) + \
- 1/6 * chain.form_matrix(rates[2]) + \
- -1/12 * chain.form_matrix(rates[3])
-
-
-def _cf4_f4(chain, rates):
- return -1/12 * chain.form_matrix(rates[0]) + \
- 1/6 * chain.form_matrix(rates[1]) + \
- 1/6 * chain.form_matrix(rates[2]) + \
- 1/4 * chain.form_matrix(rates[3])
-
-
-def cf4(operator, timesteps, power=None, power_density=None, print_out=True):
- r"""Deplete using the CF4 algorithm.
-
- Implements the fourth order `commutator-free Lie algorithm
- <https://doi.org/10.1016/S0167-739X(02)00161-9>`_.
- This algorithm is mathematically defined as:
-
- .. math::
- \begin{aligned}
- F_1 &= h A(y_0) \\
- y_1 &= \text{expm}(1/2 F_1) y_0 \\
- F_2 &= h A(y_1) \\
- y_2 &= \text{expm}(1/2 F_2) y_0 \\
- F_3 &= h A(y_2) \\
- y_3 &= \text{expm}(-1/2 F_1 + F_3) y_1 \\
- F_4 &= h A(y_3) \\
- y_4 &= \text{expm}( 1/4 F_1 + 1/6 F_2 + 1/6 F_3 - 1/12 F_4)
- \text{expm}(-1/12 F_1 + 1/6 F_2 + 1/6 F_3 + 1/4 F_4) y_0
- \end{aligned}
-
- Parameters
- ----------
- operator : openmc.deplete.TransportOperator
- The operator object to simulate on.
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not cumulative.
- power : float or iterable of float, optional
- Power of the reactor in [W]. A single value indicates that the power is
- constant over all timesteps. An iterable indicates potentially different
- power levels for each timestep. For a 2D problem, the power can be given
- in [W/cm] as long as the "volume" assigned to a depletion material is
- actually an area in [cm^2]. Either `power` or `power_density` must be
- specified.
- power_density : float or iterable of float, optional
- Power density of the reactor in [W/gHM]. It is multiplied by initial
- heavy metal inventory to get total power if `power` is not speficied.
- print_out : bool, optional
- Whether or not to print out time.
- """
- if power is None:
- if power_density is None:
- raise ValueError(
- "Neither power nor power density was specified.")
- if not isinstance(power_density, Iterable):
- power = power_density*operator.heavy_metal
- else:
- power = [i*operator.heavy_metal for i in power_density]
-
- if not isinstance(power, Iterable):
- power = [power]*len(timesteps)
-
- # Generate initial conditions
- with operator as vec:
- # Initialize time and starting index
- if operator.prev_res is None:
- t = 0.0
- i_res = 0
- else:
- t = operator.prev_res[-1].time[-1]
- i_res = len(operator.prev_res)
-
- chain = operator.chain
-
- for i, (dt, p) in enumerate(zip(timesteps, power)):
- # Get beginning-of-timestep concentrations and reaction rates
- # Avoid doing first transport run if already done in previous
- # calculation
- if i > 0 or operator.prev_res is None:
- x = [copy.deepcopy(vec)]
- op_results = [operator(x[0], p)]
-
- else:
- # Get initial concentration
- x = [operator.prev_res[-1].data[0]]
-
- # Get rates
- op_results = [operator.prev_res[-1]]
- op_results[0].rates = op_results[0].rates[0]
-
- # Set first stage value of keff
- op_results[0].k = op_results[0].k[0]
-
- # Scale reaction rates by ratio of powers
- power_res = operator.prev_res[-1].power
- ratio_power = p / power_res
- op_results[0].rates *= ratio_power[0]
-
- # Step 1: deplete with matrix 1/2*A(y0)
- time_1, x_new = timed_deplete(
- chain, x[0], op_results[0].rates, dt, print_out,
- matrix_func=_cf4_f1)
- x.append(x_new)
- op_results.append(operator(x_new, p))
-
- # Step 2: deplete with matrix 1/2*A(y1)
- time_2, x_new = timed_deplete(
- chain, x[0], op_results[1].rates, dt, print_out,
- matrix_func=_cf4_f1)
- x.append(x_new)
- op_results.append(operator(x_new, p))
-
- # Step 3: deplete with matrix -1/2*A(y0)+A(y2)
- rates = list(zip(op_results[0].rates, op_results[2].rates))
- time_3, x_new = timed_deplete(
- chain, x[1], rates, dt, print_out, matrix_func=_cf4_f2)
- x.append(x_new)
- op_results.append(operator(x_new, p))
-
- # Step 4: deplete with two matrix exponentials
- rates = list(zip(op_results[0].rates, op_results[1].rates,
- op_results[2].rates, op_results[3].rates))
- time_4, x_end = timed_deplete(
- chain, x[0], rates, dt, print_out, matrix_func=_cf4_f3)
- time_5, x_end = timed_deplete(
- chain, x_end, rates, dt, print_out, matrix_func=_cf4_f4)
-
- # Create results, write to disk
- Results.save(
- operator, x, op_results, [t, t + dt], p, i_res + i,
- time_1 + time_2 + time_3 + time_4 + time_5)
-
- # Advance time, update vector
- t += dt
- vec = copy.deepcopy(x_end)
-
- # Perform one last simulation
- x = [copy.deepcopy(vec)]
- op_results = [operator(x[0], power[-1])]
-
- # Create results, write to disk
- Results.save(operator, x, op_results, [t, t], p, i_res + len(timesteps))
diff --git a/openmc/deplete/integrator/epc_rk4.py b/openmc/deplete/integrator/epc_rk4.py
deleted file mode 100644
--- a/openmc/deplete/integrator/epc_rk4.py
+++ /dev/null
@@ -1,148 +0,0 @@
-"""The EPC-RK4 integrator."""
-
-import copy
-from collections.abc import Iterable
-
-from .cram import timed_deplete
-from ..results import Results
-
-
-# Functions to form the special matrix for depletion
-def _rk4_f1(chain, rates):
- return 1/2 * chain.form_matrix(rates)
-
-def _rk4_f4(chain, rates):
- return 1/6 * chain.form_matrix(rates[0]) + \
- 1/3 * chain.form_matrix(rates[1]) + \
- 1/3 * chain.form_matrix(rates[2]) + \
- 1/6 * chain.form_matrix(rates[3])
-
-def epc_rk4(operator, timesteps, power=None, power_density=None, print_out=True):
- r"""Deplete using the EPC-RK4 algorithm.
-
- Implements an extended predictor-corrector algorithm with traditional
- Runge-Kutta 4 method.
- This algorithm is mathematically defined as:
-
- .. math::
- \begin{aligned}
- F_1 &= h A(y_0) \\
- y_1 &= \text{expm}(1/2 F_1) y_0 \\
- F_2 &= h A(y_1) \\
- y_2 &= \text{expm}(1/2 F_2) y_0 \\
- F_3 &= h A(y_2) \\
- y_3 &= \text{expm}(F_3) y_0 \\
- F_4 &= h A(y_3) \\
- y_4 &= \text{expm}(1/6 F_1 + 1/3 F_2 + 1/3 F_3 + 1/6 F_4) y_0
- \end{aligned}
-
- Parameters
- ----------
- operator : openmc.deplete.TransportOperator
- The operator object to simulate on.
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not cumulative.
- power : float or iterable of float, optional
- Power of the reactor in [W]. A single value indicates that the power is
- constant over all timesteps. An iterable indicates potentially different
- power levels for each timestep. For a 2D problem, the power can be given
- in [W/cm] as long as the "volume" assigned to a depletion material is
- actually an area in [cm^2]. Either `power` or `power_density` must be
- specified.
- power_density : float or iterable of float, optional
- Power density of the reactor in [W/gHM]. It is multiplied by initial
- heavy metal inventory to get total power if `power` is not speficied.
- print_out : bool, optional
- Whether or not to print out time.
-
- """
- if power is None:
- if power_density is None:
- raise ValueError(
- "Neither power nor power density was specified.")
- if not isinstance(power_density, Iterable):
- power = power_density*operator.heavy_metal
- else:
- power = [i*operator.heavy_metal for i in power_density]
-
- if not isinstance(power, Iterable):
- power = [power]*len(timesteps)
-
- # Generate initial conditions
- with operator as vec:
- # Initialize time and starting index
- if operator.prev_res is None:
- t = 0.0
- i_res = 0
- else:
- t = operator.prev_res[-1].time[-1]
- i_res = len(operator.prev_res)
-
- chain = operator.chain
-
- for i, (dt, p) in enumerate(zip(timesteps, power)):
- # Get beginning-of-timestep concentrations and reaction rates
- # Avoid doing first transport run if already done in previous
- # calculation
- if i > 0 or operator.prev_res is None:
- x = [copy.deepcopy(vec)]
- op_results = [operator(x[0], p)]
-
- else:
- # Get initial concentration
- x = [operator.prev_res[-1].data[0]]
-
- # Get rates
- op_results = [operator.prev_res[-1]]
- op_results[0].rates = op_results[0].rates[0]
-
- # Set first stage value of keff
- op_results[0].k = op_results[0].k[0]
-
- # Scale reaction rates by ratio of powers
- power_res = operator.prev_res[-1].power
- ratio_power = p / power_res
- op_results[0].rates *= ratio_power[0]
-
- # Step 1: deplete with matrix 1/2*A(y0)
- time_1, x_new = timed_deplete(
- chain, x[0], op_results[0].rates, dt, print_out,
- matrix_func=_rk4_f1)
- x.append(x_new)
- op_results.append(operator(x[1], p))
-
- # Step 2: deplete with matrix 1/2*A(y1)
- time_2, x_new = timed_deplete(
- chain, x[0], op_results[1].rates, dt, print_out,
- matrix_func=_rk4_f1)
- x.append(x_new)
- op_results.append(operator(x[2], p))
-
- # Step 3: deplete with matrix A(y2)
- time_3, x_new = timed_deplete(
- chain, x[0], op_results[2].rates, dt, print_out)
- x.append(x_new)
- op_results.append(operator(x[3], p))
-
- # Step 4: deplete with matrix 1/6*A(y0)+1/3*A(y1)+1/3*A(y2)+1/6*A(y3)
- rates = list(zip(op_results[0].rates, op_results[1].rates,
- op_results[2].rates, op_results[3].rates))
- time_4, x_end = timed_deplete(
- chain, x[0], rates, dt, print_out, matrix_func=_rk4_f4)
-
- # Create results, write to disk
- Results.save(
- operator, x, op_results, [t, t + dt], p, i_res + i,
- time_1 + time_2 + time_3 + time_4)
-
- # Advance time, update vector
- t += dt
- vec = copy.deepcopy(x_end)
-
- # Perform one last simulation
- x = [copy.deepcopy(vec)]
- op_results = [operator(x[0], power[-1])]
-
- # Create results, write to disk
- Results.save(
- operator, x, op_results, [t, t], p, i_res + len(timesteps))
diff --git a/openmc/deplete/integrator/leqi.py b/openmc/deplete/integrator/leqi.py
deleted file mode 100644
--- a/openmc/deplete/integrator/leqi.py
+++ /dev/null
@@ -1,170 +0,0 @@
-"""The LE/QI CFQ4 integrator."""
-
-import copy
-from collections.abc import Iterable
-from itertools import repeat
-
-from .celi import celi_inner
-from .cram import timed_deplete
-from ..results import Results
-
-
-# Functions to form the special matrix for depletion
-def _leqi_f1(chain, inputs):
- f1 = chain.form_matrix(inputs[0])
- f2 = chain.form_matrix(inputs[1])
- dt_l, dt = inputs[2], inputs[3]
- return -dt / (12 * dt_l) * f1 + (dt + 6 * dt_l) / (12 * dt_l) * f2
-
-
-def _leqi_f2(chain, inputs):
- f1 = chain.form_matrix(inputs[0])
- f2 = chain.form_matrix(inputs[1])
- dt_l, dt = inputs[2], inputs[3]
- return -5 * dt / (12 * dt_l) * f1 + (5 * dt + 6 * dt_l) / (12 * dt_l) * f2
-
-
-def _leqi_f3(chain, inputs):
- f1 = chain.form_matrix(inputs[0])
- f2 = chain.form_matrix(inputs[1])
- f3 = chain.form_matrix(inputs[2])
- dt_l, dt = inputs[3], inputs[4]
- return -dt**2 / (12 * dt_l * (dt + dt_l)) * f1 + \
- (dt**2 + 6*dt*dt_l + 5*dt_l**2) / (12 * dt_l * (dt + dt_l)) * f2 + \
- dt_l / (12 * (dt + dt_l)) * f3
-
-
-def _leqi_f4(chain, inputs):
- f1 = chain.form_matrix(inputs[0])
- f2 = chain.form_matrix(inputs[1])
- f3 = chain.form_matrix(inputs[2])
- dt_l, dt = inputs[3], inputs[4]
- return -dt**2 / (12 * dt_l * (dt + dt_l)) * f1 + \
- (dt**2 + 2*dt*dt_l + dt_l**2) / (12 * dt_l * (dt + dt_l)) * f2 + \
- (4 * dt * dt_l + 5 * dt_l**2) / (12 * dt_l * (dt + dt_l)) * f3
-
-
-def leqi(operator, timesteps, power=None, power_density=None, print_out=True):
- r"""Deplete using the LE/QI CFQ4 algorithm.
-
- Implements the LE/QI Predictor-Corrector algorithm using the `fourth order
- commutator-free integrator <https://doi.org/10.1137/05063042>`_.
-
- "LE/QI" stands for linear extrapolation on predictor and quadratic
- interpolation on corrector. This algorithm is mathematically defined as:
-
- .. math::
- \begin{aligned}
- y' &= A(y, t) y(t) \\
- A_{last} &= A(y_{n-1}, t_n - h_1) \\
- A_0 &= A(y_n, t_n) \\
- F_1 &= \frac{-h_2^2}{12h_1} A_{last} + \frac{h_2(6h_1+h_2)}{12h_1} A_0 \\
- F_2 &= \frac{-5h_2^2}{12h_1} A_{last} + \frac{h_2(6h_1+5h_2)}{12h_1} A_0 \\
- y_p &= \text{expm}(F_2) \text{expm}(F_1) y_n \\
- A_1 &= A(y_p, t_n + h_2) \\
- F_3 &= \frac{-h_2^3}{12 h_1 (h_1 + h_2)} A_{last} +
- \frac{h_2 (5 h_1^2 + 6 h_2 h_1 + h_2^2)}{12 h_1 (h_1 + h_2)} A_0 +
- \frac{h_2 h_1)}{12 (h_1 + h_2)} A_1 \\
- F_4 &= \frac{-h_2^3}{12 h_1 (h_1 + h_2)} A_{last} +
- \frac{h_2 (h_1^2 + 2 h_2 h_1 + h_2^2)}{12 h_1 (h_1 + h_2)} A_0 +
- \frac{h_2 (5 h_1^2 + 4 h_2 h_1)}{12 h_1 (h_1 + h_2)} A_1 \\
- y_{n+1} &= \text{expm}(F_4) \text{expm}(F_3) y_n
- \end{aligned}
-
- It is initialized using the CE/LI algorithm.
-
- Parameters
- ----------
- operator : openmc.deplete.TransportOperator
- The operator object to simulate on.
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not cumulative.
- power : float or iterable of float, optional
- Power of the reactor in [W]. A single value indicates that the power is
- constant over all timesteps. An iterable indicates potentially different
- power levels for each timestep. For a 2D problem, the power can be given
- in [W/cm] as long as the "volume" assigned to a depletion material is
- actually an area in [cm^2]. Either `power` or `power_density` must be
- specified.
- power_density : float or iterable of float, optional
- Power density of the reactor in [W/gHM]. It is multiplied by initial
- heavy metal inventory to get total power if `power` is not speficied.
- print_out : bool, optional
- Whether or not to print out time.
- """
- if power is None:
- if power_density is None:
- raise ValueError(
- "Neither power nor power density was specified.")
- if not isinstance(power_density, Iterable):
- power = power_density*operator.heavy_metal
- else:
- power = [i*operator.heavy_metal for i in power_density]
-
- if not isinstance(power, Iterable):
- power = [power]*len(timesteps)
-
- # Generate initial conditions
- with operator as vec:
- # Initialize time and starting index
- if operator.prev_res is None:
- t = 0.0
- i_res = 0
- else:
- t = operator.prev_res[-1].time[-1]
- i_res = len(operator.prev_res)
-
- chain = operator.chain
-
- for i, (dt, p) in enumerate(zip(timesteps, power)):
- # LE/QI needs the last step results to start
- # Perform CE/LI CFQ4 or restore results for the first step
- if i == 0:
- if i_res <= 1:
- dt_l = dt
- x_new, t, op_res_last = celi_inner(operator, vec, p, i,
- i_res, t, dt, print_out)
- continue
- else:
- dt_l = t - operator.prev_res[-2].time[0]
- op_res_last = operator.prev_res[-2]
- op_res_last.rates = op_res_last.rates[0]
- x_new = operator.prev_res[-1].data[0]
-
- # Perform remaining LE/QI
- x = [copy.deepcopy(x_new)]
- op_results = [operator(x[0], p)]
-
- inputs = list(zip(op_res_last.rates, op_results[0].rates,
- repeat(dt_l), repeat(dt)))
- time_1, x_new = timed_deplete(
- chain, x[0], inputs, dt, print_out, matrix_func=_leqi_f1)
- time_2, x_new = timed_deplete(
- chain, x_new, inputs, dt, print_out, matrix_func=_leqi_f2)
- x.append(x_new)
- op_results.append(operator(x[1], p))
-
- inputs = list(zip(op_res_last.rates, op_results[0].rates,
- op_results[1].rates, repeat(dt_l), repeat(dt)))
- time_3, x_new = timed_deplete(
- chain, x[0], inputs, dt, print_out, matrix_func=_leqi_f3)
- time_4, x_new = timed_deplete(
- chain, x_new, inputs, dt, print_out, matrix_func=_leqi_f4)
-
- # Create results, write to disk
- Results.save(
- operator, x, op_results, [t, t+dt], p, i_res+i,
- time_1 + time_2 + time_3 + time_4)
-
- # update results
- op_res_last = copy.deepcopy(op_results[0])
- t += dt
- dt_l = dt
-
- # Perform one last simulation
- x = [copy.deepcopy(x_new)]
- op_results = [operator(x[0], power[-1])]
-
- # Create results, write to disk
- Results.save(
- operator, x, op_results, [t, t], p, i_res + len(timesteps))
diff --git a/openmc/deplete/integrator/predictor.py b/openmc/deplete/integrator/predictor.py
deleted file mode 100644
--- a/openmc/deplete/integrator/predictor.py
+++ /dev/null
@@ -1,106 +0,0 @@
-"""First-order predictor algorithm."""
-
-import copy
-from collections.abc import Iterable
-
-from .cram import timed_deplete
-from ..results import Results
-
-
-def predictor(operator, timesteps, power=None, power_density=None,
- print_out=True):
- r"""Deplete using a first-order predictor algorithm.
-
- Implements the first-order predictor algorithm. This algorithm is
- mathematically defined as:
-
- .. math::
- \begin{aligned}
- y' &= A(y, t) y(t) \\
- A_p &= A(y_n, t_n) \\
- y_{n+1} &= \text{expm}(A_p h) y_n
- \end{aligned}
-
- Parameters
- ----------
- operator : openmc.deplete.TransportOperator
- The operator object to simulate on.
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not cumulative.
- power : float or iterable of float, optional
- Power of the reactor in [W]. A single value indicates that the power is
- constant over all timesteps. An iterable indicates potentially different
- power levels for each timestep. For a 2D problem, the power can be given
- in [W/cm] as long as the "volume" assigned to a depletion material is
- actually an area in [cm^2]. Either `power` or `power_density` must be
- specified.
- power_density : float or iterable of float, optional
- Power density of the reactor in [W/gHM]. It is multiplied by initial
- heavy metal inventory to get total power if `power` is not speficied.
- print_out : bool, optional
- Whether or not to print out time.
-
- """
- if power is None:
- if power_density is None:
- raise ValueError(
- "Neither power nor power density was specified.")
- if not isinstance(power_density, Iterable):
- power = power_density*operator.heavy_metal
- else:
- power = [i*operator.heavy_metal for i in power_density]
-
- if not isinstance(power, Iterable):
- power = [power]*len(timesteps)
-
- proc_time = None
-
- # Generate initial conditions
- with operator as vec:
- # Initialize time and starting index
- if operator.prev_res is None:
- t = 0.0
- i_res = 0
- else:
- t = operator.prev_res[-1].time[-1]
- i_res = len(operator.prev_res) - 1
-
- chain = operator.chain
-
- for i, (dt, p) in enumerate(zip(timesteps, power)):
- # Get beginning-of-timestep concentrations and reaction rates
- # Avoid doing first transport run if already done in previous
- # calculation
- if i > 0 or operator.prev_res is None:
- x = [copy.deepcopy(vec)]
- op_results = [operator(x[0], p)]
-
- # Create results, write to disk
- Results.save(operator, x, op_results, [t, t + dt], p, i_res + i, proc_time)
- else:
- # Get initial concentration
- x = [operator.prev_res[-1].data[0]]
-
- # Get rates
- op_results = [operator.prev_res[-1]]
- op_results[0].rates = op_results[0].rates[0]
-
- # Scale reaction rates by ratio of powers
- power_res = operator.prev_res[-1].power
- ratio_power = p / power_res
- op_results[0].rates *= ratio_power[0]
-
- # Deplete for full timestep
- proc_time, x_end = timed_deplete(
- chain, x[0], op_results[0].rates, dt, print_out)
-
- # Advance time, update vector
- t += dt
- vec = copy.deepcopy(x_end)
-
- # Perform one last simulation
- x = [copy.deepcopy(vec)]
- op_results = [operator(x[0], power[-1])]
-
- # Create results, write to disk
- Results.save(operator, x, op_results, [t, t], p, i_res + len(timesteps), proc_time)
diff --git a/openmc/deplete/integrator/si_celi.py b/openmc/deplete/integrator/si_celi.py
deleted file mode 100644
--- a/openmc/deplete/integrator/si_celi.py
+++ /dev/null
@@ -1,166 +0,0 @@
-"""The SI-CE/LI CFQ4 integrator."""
-
-import copy
-from collections.abc import Iterable
-
-from .cram import timed_deplete
-from ..results import Results
-from ..abc import OperatorResult
-from .celi import _celi_f1, _celi_f2
-
-
-def si_celi(operator, timesteps, power=None, power_density=None,
- print_out=True, m=10):
- r"""Deplete using the SI-CE/LI CFQ4 algorithm.
-
- Implements the Stochastic Implicit CE/LI Predictor-Corrector algorithm using
- the `fourth order commutator-free integrator <https://doi.org/10.1137/05063042>`_.
-
- Detailed algorithm can be found in Section 3.2 in `Colin Josey's thesis
- <http://hdl.handle.net/1721.1/113721>`_.
-
- Parameters
- ----------
- operator : openmc.deplete.TransportOperator
- The operator object to simulate on.
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not cumulative.
- power : float or iterable of float, optional
- Power of the reactor in [W]. A single value indicates that the power is
- constant over all timesteps. An iterable indicates potentially different
- power levels for each timestep. For a 2D problem, the power can be given
- in [W/cm] as long as the "volume" assigned to a depletion material is
- actually an area in [cm^2]. Either `power` or `power_density` must be
- specified.
- power_density : float or iterable of float, optional
- Power density of the reactor in [W/gHM]. It is multiplied by initial
- heavy metal inventory to get total power if `power` is not speficied.
- print_out : bool, optional
- Whether or not to print out time.
- m : int, optional
- Number of stages.
- """
- if power is None:
- if power_density is None:
- raise ValueError(
- "Neither power nor power density was specified.")
- if not isinstance(power_density, Iterable):
- power = power_density*operator.heavy_metal
- else:
- power = [i*operator.heavy_metal for i in power_density]
-
- if not isinstance(power, Iterable):
- power = [power]*len(timesteps)
-
- # Generate initial conditions
- with operator as vec:
- # Initialize time and starting index
- if operator.prev_res is None:
- t = 0.0
- i_res = 0
- else:
- t = operator.prev_res[-1].time[-1]
- i_res = len(operator.prev_res)
-
- # Get the concentrations and reaction rates for the first
- # beginning-of-timestep (BOS). Compute with m (stage number) times as
- # many neutrons as later simulations for statistics reasons if no
- # previous calculation results present
- if operator.prev_res is None:
- x = [copy.deepcopy(vec)]
- if hasattr(operator, "settings"):
- operator.settings.particles *= m
- op_results = [operator(x[0], power[0])]
- if hasattr(operator, "settings"):
- operator.settings.particles //= m
- else:
- # Get initial concentration
- x = [operator.prev_res[-1].data[0]]
-
- # Get rates
- op_results = [operator.prev_res[-1]]
- op_results[0].rates = op_results[0].rates[0]
-
- # Set first stage value of keff
- op_results[0].k = op_results[0].k[0]
-
- # Scale reaction rates by ratio of powers
- power_res = operator.prev_res[-1].power
- ratio_power = power[0] / power_res
- op_results[0].rates *= ratio_power[0]
-
- for i, (dt, p) in enumerate(zip(timesteps, power)):
- x, t, op_results = si_celi_inner(operator, x, op_results, p,
- i, i_res, t, dt, print_out, m)
-
- # Create results for last point, write to disk
- Results.save(
- operator, x, op_results, [t, t], p, i_res + len(timesteps))
-
-
-def si_celi_inner(operator, x, op_results, p, i, i_res, t, dt, print_out, m=10):
- """ The inner loop of SI-CE/LI CFQ4.
-
- Parameters
- ----------
- operator : Operator
- The operator object to simulate on.
- x : list of nuclide vector
- Nuclide vector, beginning of time.
- op_results : list of OperatorResult
- Operator result at BOS.
- p : float
- Power of the reactor in [W]
- i : int
- Current iteration number.
- i_res : int
- Starting index, for restart calculation.
- t : float
- Time at start of step.
- dt : float
- Time step.
- print_out : bool
- Whether or not to print out time.
- m : int, optional
- Number of stages.
-
- Returns
- -------
- list of nuclide vector (numpy.array)
- Nuclide vector, end of time.
- float
- Next time
- list of OperatorResult
- Operator result at end of time.
- """
-
- chain = operator.chain
-
- # Deplete to end
- proc_time, x_new = timed_deplete(
- chain, x[0], op_results[0].rates, dt, print_out)
- x.append(x_new)
-
- for j in range(m + 1):
- op_res = operator(x_new, p)
-
- if j <= 1:
- op_res_bar = copy.deepcopy(op_res)
- else:
- rates = 1/j * op_res.rates + (1 - 1/j) * op_res_bar.rates
- k = 1/j * op_res.k + (1 - 1/j) * op_res_bar.k
- op_res_bar = OperatorResult(k, rates)
-
- rates = list(zip(op_results[0].rates, op_res_bar.rates))
- time_1, x_new = timed_deplete(
- chain, x[0], rates, dt, print_out, matrix_func=_celi_f1)
- time_2, x_new = timed_deplete(
- chain, x_new, rates, dt, print_out, matrix_func=_celi_f2)
- proc_time += time_1 + time_2
-
- # Create results, write to disk
- op_results.append(op_res_bar)
- Results.save(operator, x, op_results, [t, t+dt], p, i_res+i, proc_time)
-
- # return updated time and vectors
- return [x_new], t + dt, [op_res_bar]
diff --git a/openmc/deplete/integrator/si_leqi.py b/openmc/deplete/integrator/si_leqi.py
deleted file mode 100644
--- a/openmc/deplete/integrator/si_leqi.py
+++ /dev/null
@@ -1,157 +0,0 @@
-"""The SI-LE/QI CFQ4 integrator."""
-
-import copy
-from collections.abc import Iterable
-from itertools import repeat
-
-from .si_celi import si_celi_inner
-from .leqi import _leqi_f1, _leqi_f2, _leqi_f3, _leqi_f4
-from .cram import timed_deplete
-from ..results import Results
-from ..abc import OperatorResult
-
-
-def si_leqi(operator, timesteps, power=None, power_density=None,
- print_out=True, m=10):
- r"""Deplete using the SI-LE/QI CFQ4 algorithm.
-
- Implements the Stochastic Implicit LE/QI Predictor-Corrector algorithm using
- the `fourth order commutator-free integrator <https://doi.org/10.1137/05063042>`_.
-
- Detailed algorithm can be found in Section 3.2 in `Colin Josey's thesis
- <http://hdl.handle.net/1721.1/113721>`_.
-
- Parameters
- ----------
- operator : openmc.deplete.TransportOperator
- The operator object to simulate on.
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not cumulative.
- power : float or iterable of float, optional
- Power of the reactor in [W]. A single value indicates that the power is
- constant over all timesteps. An iterable indicates potentially different
- power levels for each timestep. For a 2D problem, the power can be given
- in [W/cm] as long as the "volume" assigned to a depletion material is
- actually an area in [cm^2]. Either `power` or `power_density` must be
- specified.
- power_density : float or iterable of float, optional
- Power density of the reactor in [W/gHM]. It is multiplied by initial
- heavy metal inventory to get total power if `power` is not speficied.
- print_out : bool, optional
- Whether or not to print out time.
- m : int, optional
- Number of stages.
- """
- if power is None:
- if power_density is None:
- raise ValueError(
- "Neither power nor power density was specified.")
- if not isinstance(power_density, Iterable):
- power = power_density*operator.heavy_metal
- else:
- power = [i*operator.heavy_metal for i in power_density]
-
- if not isinstance(power, Iterable):
- power = [power]*len(timesteps)
-
- # Generate initial conditions
- with operator as vec:
- # Initialize time and starting index
- if operator.prev_res is None:
- t = 0.0
- i_res = 0
- else:
- t = operator.prev_res[-1].time[-1]
- i_res = len(operator.prev_res)
-
- # Get the concentrations and reaction rates for the first
- # beginning-of-timestep (BOS). Compute with m (stage number) times as
- # many neutrons as later simulations for statistics reasons if no
- # previous calculation results present
- if operator.prev_res is None:
- x = [copy.deepcopy(vec)]
- if hasattr(operator, "settings"):
- operator.settings.particles *= m
- op_results = [operator(x[0], power[0])]
- if hasattr(operator, "settings"):
- operator.settings.particles //= m
- else:
- # Get initial concentration
- x = [operator.prev_res[-1].data[0]]
-
- # Get rates
- op_results = [operator.prev_res[-1]]
- op_results[0].rates = op_results[0].rates[0]
-
- # Set first stage value of keff
- op_results[0].k = op_results[0].k[0]
-
- # Scale reaction rates by ratio of powers
- power_res = operator.prev_res[-1].power
- ratio_power = power[0] / power_res
- op_results[0].rates *= ratio_power[0]
-
- chain = operator.chain
-
- for i, (dt, p) in enumerate(zip(timesteps, power)):
- # LE/QI needs the last step results to start
- # Perform SI-CE/LI CFQ4 or restore results for the first step
- if i == 0:
- dt_l = dt
- if i_res <= 1:
- op_res_last = copy.deepcopy(op_results[0])
- x, t, op_results = si_celi_inner(operator, x, op_results, p,
- i, i_res, t, dt, print_out)
- continue
- else:
- dt_l = t - operator.prev_res[-2].time[0]
- op_res_last = operator.prev_res[-2]
- op_res_last.rates = op_res_last.rates[0]
- x = [operator.prev_res[-1].data[0]]
-
- # Perform remaining LE/QI
- inputs = list(zip(op_res_last.rates, op_results[0].rates,
- repeat(dt_l), repeat(dt)))
- proc_time, x_new = timed_deplete(
- chain, x[0], inputs, dt, print_out, matrix_func=_leqi_f1)
- time_1, x_new = timed_deplete(
- chain, x_new, inputs, dt, print_out, matrix_func=_leqi_f2)
- x.append(x_new)
-
- proc_time += time_1
-
- # Loop on inner
- for j in range(m + 1):
- op_res = operator(x_new, p)
-
- if j <= 1:
- op_res_bar = copy.deepcopy(op_res)
- else:
- rates = 1/j * op_res.rates + (1 - 1/j) * op_res_bar.rates
- k = 1/j * op_res.k + (1 - 1/j) * op_res_bar.k
- op_res_bar = OperatorResult(k, rates)
-
- inputs = list(zip(op_res_last.rates, op_results[0].rates,
- op_res_bar.rates, repeat(dt_l), repeat(dt)))
- time_1, x_new = timed_deplete(
- chain, x[0], inputs, dt, print_out, matrix_func=_leqi_f3)
- time_2, x_new = timed_deplete(
- chain, x_new, inputs, dt, print_out, matrix_func=_leqi_f4)
-
- proc_time += time_1 + time_2
-
- # Create results, write to disk
- op_results.append(op_res_bar)
- Results.save(
- operator, x, op_results, [t, t+dt], p, i_res+i, proc_time)
-
- # update results
- x = [x_new]
- op_res_last = copy.deepcopy(op_results[0])
- op_results = [op_res_bar]
- t += dt
- dt_l = dt
-
- # Create results for last point, write to disk
- Results.save(
- operator, x, op_results, [t, t], p, i_res+len(timesteps))
diff --git a/openmc/deplete/integrators.py b/openmc/deplete/integrators.py
new file mode 100644
--- /dev/null
+++ b/openmc/deplete/integrators.py
@@ -0,0 +1,836 @@
+import copy
+from itertools import repeat
+
+from .abc import Integrator, SIIntegrator, OperatorResult
+from .cram import timed_deplete
+from ._matrix_funcs import (
+ cf4_f1, cf4_f2, cf4_f3, cf4_f4, celi_f1, celi_f2,
+ leqi_f1, leqi_f2, leqi_f3, leqi_f4, rk4_f1, rk4_f4
+)
+
+__all__ = [
+ "PredictorIntegrator", "CECMIntegrator", "CF4Integrator",
+ "CELIIntegrator", "EPCRK4Integrator", "LEQIIntegrator",
+ "SICELIIntegrator", "SILEQIIntegrator"]
+
+
+class PredictorIntegrator(Integrator):
+ r"""Deplete using a first-order predictor algorithm.
+
+ Implements the first-order predictor algorithm. This algorithm is
+ mathematically defined as:
+
+ .. math::
+ \begin{aligned}
+ y' &= A(y, t) y(t) \\
+ A_p &= A(y_n, t_n) \\
+ y_{n+1} &= \text{expm}(A_p h) y_n
+ \end{aligned}
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ timesteps : iterable of float
+ Array of timesteps in units of [s]. Note that values are not
+ cumulative.
+ power : float or iterable of float, optional
+ Power of the reactor in [W]. A single value indicates that
+ the power is constant over all timesteps. An iterable
+ indicates potentially different power levels for each timestep.
+ For a 2D problem, the power can be given in [W/cm] as long
+ as the "volume" assigned to a depletion material is actually
+ an area in [cm^2]. Either ``power`` or ``power_density`` must be
+ specified.
+ power_density : float or iterable of float, optional
+ Power density of the reactor in [W/gHM]. It is multiplied by
+ initial heavy metal inventory to get total power if ``power``
+ is not speficied.
+
+ Attributes
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ chain : openmc.deplete.Chain
+ Depletion chain
+ timesteps : iterable of float
+ Size of each depletion interval in [s]
+ power : iterable of float
+ Power of the reactor in [W] for each interval in :attr:`timesteps`
+ """
+ _num_stages = 1
+
+ def __call__(self, conc, rates, dt, power, _i=None):
+ """Perform the integration across one time step
+
+ Parameters
+ ----------
+ conc : numpy.ndarray
+ Initial concentrations for all nuclides in [atom]
+ rates : openmc.deplete.ReactionRates
+ Reaction rates from operator
+ dt : float
+ Time in [s] for the entire depletion interval
+ power : float
+ Power of the system in [W]
+ _i : int or None
+ Iteration index. Not used
+
+ Returns
+ -------
+ proc_time : float
+ Time spent in CRAM routines for all materials in [s]
+ conc_list : list of numpy.ndarray
+ Concentrations at end of interval
+ op_results : empty list
+ Kept for consistency with API. No intermediate calls to
+ operator with predictor
+
+ """
+ proc_time, conc_end = timed_deplete(self.chain, conc, rates, dt)
+ return proc_time, [conc_end], []
+
+
+class CECMIntegrator(Integrator):
+ r"""Deplete using the CE/CM algorithm.
+
+ Implements the second order `CE/CM predictor-corrector algorithm
+ <https://doi.org/10.13182/NSE14-92>`_.
+
+ "CE/CM" stands for constant extrapolation on predictor and constant
+ midpoint on corrector. This algorithm is mathematically defined as:
+
+ .. math::
+ \begin{aligned}
+ y' &= A(y, t) y(t) \\
+ A_p &= A(y_n, t_n) \\
+ y_m &= \text{expm}(A_p h/2) y_n \\
+ A_c &= A(y_m, t_n + h/2) \\
+ y_{n+1} &= \text{expm}(A_c h) y_n
+ \end{aligned}
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ timesteps : iterable of float
+ Array of timesteps in units of [s]. Note that values are not
+ cumulative.
+ power : float or iterable of float, optional
+ Power of the reactor in [W]. A single value indicates that
+ the power is constant over all timesteps. An iterable
+ indicates potentially different power levels for each timestep.
+ For a 2D problem, the power can be given in [W/cm] as long
+ as the "volume" assigned to a depletion material is actually
+ an area in [cm^2]. Either ``power`` or ``power_density`` must be
+ specified.
+ power_density : float or iterable of float, optional
+ Power density of the reactor in [W/gHM]. It is multiplied by
+ initial heavy metal inventory to get total power if ``power``
+ is not speficied.
+
+ Attributes
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ chain : openmc.deplete.Chain
+ Depletion chain
+ timesteps : iterable of float
+ Size of each depletion interval in [s]
+ power : iterable of float
+ Power of the reactor in [W] for each interval in :attr:`timesteps`
+ """
+ _num_stages = 2
+
+ def __call__(self, conc, rates, dt, power, _i=None):
+ """Integrate using CE/CM
+
+ Parameters
+ ----------
+ conc : numpy.ndarray
+ Initial concentrations for all nuclides in [atom]
+ rates : openmc.deplete.ReactionRates
+ Reaction rates from operator
+ dt : float
+ Time in [s] for the entire depletion interval
+ power : float
+ Power of the system [W]
+ _i : int, optional
+ Current iteration count. Not used
+
+ Returns
+ -------
+ proc_time : float
+ Time spent in CRAM routines for all materials in [s]
+ conc_list : list of numpy.ndarray
+ Concentrations at each of the intermediate points with
+ the final concentration as the last element
+ op_results : list of openmc.deplete.OperatorResult
+ Eigenvalue and reaction rates from transport simulations
+ """
+ # deplete across first half of inteval
+ time0, x_middle = timed_deplete(self.chain, conc, rates, dt / 2)
+ res_middle = self.operator(x_middle, power)
+
+ # deplete across entire interval with BOS concentrations,
+ # MOS reaction rates
+ time1, x_end = timed_deplete(self.chain, conc, res_middle.rates, dt)
+
+ return time0 + time1, [x_middle, x_end], [res_middle]
+
+
+class CF4Integrator(Integrator):
+ r"""Deplete using the CF4 algorithm.
+
+ Implements the fourth order `commutator-free Lie algorithm
+ <https://doi.org/10.1016/S0167-739X(02)00161-9>`_.
+ This algorithm is mathematically defined as:
+
+ .. math::
+ \begin{aligned}
+ F_1 &= h A(y_0) \\
+ y_1 &= \text{expm}(1/2 F_1) y_0 \\
+ F_2 &= h A(y_1) \\
+ y_2 &= \text{expm}(1/2 F_2) y_0 \\
+ F_3 &= h A(y_2) \\
+ y_3 &= \text{expm}(-1/2 F_1 + F_3) y_1 \\
+ F_4 &= h A(y_3) \\
+ y_4 &= \text{expm}( 1/4 F_1 + 1/6 F_2 + 1/6 F_3 - 1/12 F_4)
+ \text{expm}(-1/12 F_1 + 1/6 F_2 + 1/6 F_3 + 1/4 F_4) y_0
+ \end{aligned}
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ timesteps : iterable of float
+ Array of timesteps in units of [s]. Note that values are not
+ cumulative.
+ power : float or iterable of float, optional
+ Power of the reactor in [W]. A single value indicates that
+ the power is constant over all timesteps. An iterable
+ indicates potentially different power levels for each timestep.
+ For a 2D problem, the power can be given in [W/cm] as long
+ as the "volume" assigned to a depletion material is actually
+ an area in [cm^2]. Either ``power`` or ``power_density`` must be
+ specified.
+ power_density : float or iterable of float, optional
+ Power density of the reactor in [W/gHM]. It is multiplied by
+ initial heavy metal inventory to get total power if ``power``
+ is not speficied.
+
+ Attributes
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ chain : openmc.deplete.Chain
+ Depletion chain
+ timesteps : iterable of float
+ Size of each depletion interval in [s]
+ power : iterable of float
+ Power of the reactor in [W] for each interval in :attr:`timesteps`
+ """
+ _num_stages = 4
+
+ def __call__(self, bos_conc, bos_rates, dt, power, _i=None):
+ """Perform the integration across one time step
+
+ Parameters
+ ----------
+ bos_conc : numpy.ndarray
+ Initial concentrations for all nuclides in [atom]
+ bos_rates : openmc.deplete.ReactionRates
+ Reaction rates from operator
+ dt : float
+ Time in [s] for the entire depletion interval
+ power : float
+ Power of the system in [W]
+ _i : int, optional
+ Current depletion step index. Not used
+
+ Returns
+ -------
+ proc_time : float
+ Time spent in CRAM routines for all materials in [s]
+ conc_list : list of numpy.ndarray
+ Concentrations at each of the intermediate points with
+ the final concentration as the last element
+ op_results : list of openmc.deplete.OperatorResult
+ Eigenvalue and reaction rates from intermediate transport
+ simulations
+ """
+ # Step 1: deplete with matrix 1/2*A(y0)
+ time1, conc_eos1 = timed_deplete(
+ self.chain, bos_conc, bos_rates, dt, matrix_func=cf4_f1)
+ res1 = self.operator(conc_eos1, power)
+
+ # Step 2: deplete with matrix 1/2*A(y1)
+ time2, conc_eos2 = timed_deplete(
+ self.chain, bos_conc, res1.rates, dt, matrix_func=cf4_f1)
+ res2 = self.operator(conc_eos2, power)
+
+ # Step 3: deplete with matrix -1/2*A(y0)+A(y2)
+ list_rates = list(zip(bos_rates, res2.rates))
+ time3, conc_eos3 = timed_deplete(
+ self.chain, conc_eos1, list_rates, dt, matrix_func=cf4_f2)
+ res3 = self.operator(conc_eos3, power)
+
+ # Step 4: deplete with two matrix exponentials
+ list_rates = list(zip(bos_rates, res1.rates, res2.rates, res3.rates))
+ time4, conc_inter = timed_deplete(
+ self.chain, bos_conc, list_rates, dt, matrix_func=cf4_f3)
+ time5, conc_eos5 = timed_deplete(
+ self.chain, conc_inter, list_rates, dt, matrix_func=cf4_f4)
+
+ return (time1 + time2 + time3 + time4 + time5,
+ [conc_eos1, conc_eos2, conc_eos3, conc_eos5],
+ [res1, res2, res3])
+
+
+class CELIIntegrator(Integrator):
+ r"""Deplete using the CE/LI CFQ4 algorithm.
+
+ Implements the CE/LI Predictor-Corrector algorithm using the `fourth order
+ commutator-free integrator <https://doi.org/10.1137/05063042>`_.
+
+ "CE/LI" stands for constant extrapolation on predictor and linear
+ interpolation on corrector. This algorithm is mathematically defined as:
+
+ .. math::
+ \begin{aligned}
+ y' &= A(y, t) y(t) \\
+ A_0 &= A(y_n, t_n) \\
+ y_p &= \text{expm}(h A_0) y_n \\
+ A_1 &= A(y_p, t_n + h) \\
+ y_{n+1} &= \text{expm}(\frac{h}{12} A_0 + \frac{5h}{12} A1)
+ \text{expm}(\frac{5h}{12} A_0 + \frac{h}{12} A1) y_n
+ \end{aligned}
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ timesteps : iterable of float
+ Array of timesteps in units of [s]. Note that values are not
+ cumulative.
+ power : float or iterable of float, optional
+ Power of the reactor in [W]. A single value indicates that
+ the power is constant over all timesteps. An iterable
+ indicates potentially different power levels for each timestep.
+ For a 2D problem, the power can be given in [W/cm] as long
+ as the "volume" assigned to a depletion material is actually
+ an area in [cm^2]. Either ``power`` or ``power_density`` must be
+ specified.
+ power_density : float or iterable of float, optional
+ Power density of the reactor in [W/gHM]. It is multiplied by
+ initial heavy metal inventory to get total power if ``power``
+ is not speficied.
+
+ Attributes
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ chain : openmc.deplete.Chain
+ Depletion chain
+ timesteps : iterable of float
+ Size of each depletion interval in [s]
+ power : iterable of float
+ Power of the reactor in [W] for each interval in :attr:`timesteps`
+ """
+ _num_stages = 2
+
+ def __call__(self, bos_conc, rates, dt, power, _i=None):
+ """Perform the integration across one time step
+
+ Parameters
+ ----------
+ bos_conc : numpy.ndarray
+ Initial concentrations for all nuclides in [atom]
+ rates : openmc.deplete.ReactionRates
+ Reaction rates from operator
+ dt : float
+ Time in [s] for the entire depletion interval
+ power : float
+ Power of the system in [W]
+ _i : int, optional
+ Current iteration count. Not used
+
+ Returns
+ -------
+ proc_time : float
+ Time spent in CRAM routines for all materials in [s]
+ conc_list : list of numpy.ndarray
+ Concentrations at each of the intermediate points with
+ the final concentration as the last element
+ op_results : list of openmc.deplete.OperatorResult
+ Eigenvalue and reaction rates from intermediate transport
+ simulation
+ """
+ # deplete to end using BOS rates
+ proc_time, conc_ce = timed_deplete(self.chain, bos_conc, rates, dt)
+ res_ce = self.operator(conc_ce, power)
+
+ # deplete using two matrix exponentials
+ list_rates = list(zip(rates, res_ce.rates))
+
+ time_le1, conc_inter = timed_deplete(
+ self.chain, bos_conc, list_rates, dt, matrix_func=celi_f1)
+
+ time_le2, conc_end = timed_deplete(
+ self.chain, conc_inter, list_rates, dt, matrix_func=celi_f2)
+
+ return proc_time + time_le1 + time_le1, [conc_ce, conc_end], [res_ce]
+
+
+class EPCRK4Integrator(Integrator):
+ r"""Deplete using the EPC-RK4 algorithm.
+
+ Implements an extended predictor-corrector algorithm with traditional
+ Runge-Kutta 4 method. This algorithm is mathematically defined as:
+
+ .. math::
+ \begin{aligned}
+ F_1 &= h A(y_0) \\
+ y_1 &= \text{expm}(1/2 F_1) y_0 \\
+ F_2 &= h A(y_1) \\
+ y_2 &= \text{expm}(1/2 F_2) y_0 \\
+ F_3 &= h A(y_2) \\
+ y_3 &= \text{expm}(F_3) y_0 \\
+ F_4 &= h A(y_3) \\
+ y_4 &= \text{expm}(1/6 F_1 + 1/3 F_2 + 1/3 F_3 + 1/6 F_4) y_0
+ \end{aligned}
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ timesteps : iterable of float
+ Array of timesteps in units of [s]. Note that values are not
+ cumulative.
+ power : float or iterable of float, optional
+ Power of the reactor in [W]. A single value indicates that
+ the power is constant over all timesteps. An iterable
+ indicates potentially different power levels for each timestep.
+ For a 2D problem, the power can be given in [W/cm] as long
+ as the "volume" assigned to a depletion material is actually
+ an area in [cm^2]. Either ``power`` or ``power_density`` must be
+ specified.
+ power_density : float or iterable of float, optional
+ Power density of the reactor in [W/gHM]. It is multiplied by
+ initial heavy metal inventory to get total power if ``power``
+ is not speficied.
+
+ Attributes
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ chain : openmc.deplete.Chain
+ Depletion chain
+ timesteps : iterable of float
+ Size of each depletion interval in [s]
+ power : iterable of float
+ Power of the reactor in [W] for each interval in :attr:`timesteps`
+ """
+ _num_stages = 4
+
+ def __call__(self, conc, rates, dt, power, _i=None):
+ """Perform the integration across one time step
+
+ Parameters
+ ----------
+ conc : numpy.ndarray
+ Initial concentrations for all nuclides in [atom]
+ rates : openmc.deplete.ReactionRates
+ Reaction rates from operator
+ dt : float
+ Time in [s] for the entire depletion interval
+ power : float
+ Power of the system in [W]
+ _i : int, optional
+ Current depletion step index, unused.
+
+ Returns
+ -------
+ proc_time : float
+ Time spent in CRAM routines for all materials in [s]
+ conc_list : list of numpy.ndarray
+ Concentrations at each of the intermediate points with
+ the final concentration as the last element
+ op_results : list of openmc.deplete.OperatorResult
+ Eigenvalue and reaction rates from intermediate transport
+ simulations
+ """
+
+ # Step 1: deplete with matrix A(y0) / 2
+ time1, conc1 = timed_deplete(
+ self.chain, conc, rates, dt, matrix_func=rk4_f1)
+ res1 = self.operator(conc1, power)
+
+ # Step 2: deplete with matrix A(y1) / 2
+ time2, conc2 = timed_deplete(
+ self.chain, conc, res1.rates, dt, matrix_func=rk4_f1)
+ res2 = self.operator(conc2, power)
+
+ # Step 3: deplete with matrix A(y2)
+ time3, conc3 = timed_deplete(
+ self.chain, conc, res2.rates, dt)
+ res3 = self.operator(conc3, power)
+
+ # Step 4: deplete with matrix built from weighted rates
+ list_rates = list(zip(rates, res1.rates, res2.rates, res3.rates))
+ time4, conc4 = timed_deplete(
+ self.chain, conc, list_rates, dt, matrix_func=rk4_f4)
+
+ return (time1 + time2 + time3 + time4, [conc1, conc2, conc3, conc4],
+ [res1, res2, res3])
+
+
+class LEQIIntegrator(Integrator):
+ r"""Deplete using the LE/QI CFQ4 algorithm.
+
+ Implements the LE/QI Predictor-Corrector algorithm using the `fourth order
+ commutator-free integrator <https://doi.org/10.1137/05063042>`_.
+
+ "LE/QI" stands for linear extrapolation on predictor and quadratic
+ interpolation on corrector. This algorithm is mathematically defined as:
+
+ .. math::
+ \begin{aligned}
+ y' &= A(y, t) y(t) \\
+ A_{last} &= A(y_{n-1}, t_n - h_1) \\
+ A_0 &= A(y_n, t_n) \\
+ F_1 &= \frac{-h_2^2}{12h_1} A_{last} + \frac{h_2(6h_1+h_2)}{12h_1} A_0 \\
+ F_2 &= \frac{-5h_2^2}{12h_1} A_{last} + \frac{h_2(6h_1+5h_2)}{12h_1} A_0 \\
+ y_p &= \text{expm}(F_2) \text{expm}(F_1) y_n \\
+ A_1 &= A(y_p, t_n + h_2) \\
+ F_3 &= \frac{-h_2^3}{12 h_1 (h_1 + h_2)} A_{last} +
+ \frac{h_2 (5 h_1^2 + 6 h_2 h_1 + h_2^2)}{12 h_1 (h_1 + h_2)} A_0 +
+ \frac{h_2 h_1)}{12 (h_1 + h_2)} A_1 \\
+ F_4 &= \frac{-h_2^3}{12 h_1 (h_1 + h_2)} A_{last} +
+ \frac{h_2 (h_1^2 + 2 h_2 h_1 + h_2^2)}{12 h_1 (h_1 + h_2)} A_0 +
+ \frac{h_2 (5 h_1^2 + 4 h_2 h_1)}{12 h_1 (h_1 + h_2)} A_1 \\
+ y_{n+1} &= \text{expm}(F_4) \text{expm}(F_3) y_n
+ \end{aligned}
+
+ It is initialized using the CE/LI algorithm.
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ timesteps : iterable of float
+ Array of timesteps in units of [s]. Note that values are not
+ cumulative.
+ power : float or iterable of float, optional
+ Power of the reactor in [W]. A single value indicates that
+ the power is constant over all timesteps. An iterable
+ indicates potentially different power levels for each timestep.
+ For a 2D problem, the power can be given in [W/cm] as long
+ as the "volume" assigned to a depletion material is actually
+ an area in [cm^2]. Either ``power`` or ``power_density`` must be
+ specified.
+ power_density : float or iterable of float, optional
+ Power density of the reactor in [W/gHM]. It is multiplied by
+ initial heavy metal inventory to get total power if ``power``
+ is not speficied.
+
+ Attributes
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ chain : openmc.deplete.Chain
+ Depletion chain
+ timesteps : iterable of float
+ Size of each depletion interval in [s]
+ power : iterable of float
+ Power of the reactor in [W] for each interval in :attr:`timesteps`
+ """
+ _num_stages = 2
+
+ def __call__(self, bos_conc, bos_rates, dt, power, i):
+ """Perform the integration across one time step
+
+ Parameters
+ ----------
+ conc : numpy.ndarray
+ Initial concentrations for all nuclides in [atom]
+ rates : openmc.deplete.ReactionRates
+ Reaction rates from operator
+ dt : float
+ Time in [s] for the entire depletion interval
+ power : float
+ Power of the system in [W]
+ i : int
+ Current depletion step index
+
+ Returns
+ -------
+ proc_time : float
+ Time spent in CRAM routines for all materials in [s]
+ conc_list : list of numpy.ndarray
+ Concentrations at each of the intermediate points with
+ the final concentration as the last element
+ op_results : list of openmc.deplete.OperatorResult
+ Eigenvalue and reaction rates from intermediate transport
+ simulation
+ """
+ if i == 0:
+ if self._i_res < 1: # need at least previous transport solution
+ self._prev_rates = bos_rates
+ return CELIIntegrator.__call__(
+ self, bos_conc, bos_rates, dt, power, i)
+ prev_res = self.operator.prev_res[-2]
+ prev_dt = self.timesteps[i] - prev_res.time[0]
+ self._prev_rates = prev_res.rates[0]
+ else:
+ prev_dt = self.timesteps[i - 1]
+
+ # Remaining LE/QI
+ bos_res = self.operator(bos_conc, power)
+
+ le_inputs = list(zip(
+ self._prev_rates, bos_res.rates, repeat(prev_dt), repeat(dt)))
+
+ time1, conc_inter = timed_deplete(
+ self.chain, bos_conc, le_inputs, dt, matrix_func=leqi_f1)
+ time2, conc_eos0 = timed_deplete(
+ self.chain, conc_inter, le_inputs, dt, matrix_func=leqi_f2)
+
+ res_inter = self.operator(conc_eos0, power)
+
+ qi_inputs = list(zip(
+ self._prev_rates, bos_res.rates, res_inter.rates,
+ repeat(prev_dt), repeat(dt)))
+
+ time3, conc_inter = timed_deplete(
+ self.chain, bos_conc, qi_inputs, dt, matrix_func=leqi_f3)
+ time4, conc_eos1 = timed_deplete(
+ self.chain, conc_inter, qi_inputs, dt, matrix_func=leqi_f4)
+
+ # store updated rates
+ self._prev_rates = copy.deepcopy(bos_res.rates)
+
+ return (
+ time1 + time2 + time3 + time4, [conc_eos0, conc_eos1],
+ [bos_res, res_inter])
+
+
+class SICELIIntegrator(SIIntegrator):
+ r"""Deplete using the SI-CE/LI CFQ4 algorithm.
+
+ Implements the stochastic implicit CE/LI predictor-corrector algorithm
+ using the `fourth order commutator-free integrator
+ <https://doi.org/10.1137/05063042>`_.
+
+ Detailed algorithm can be found in section 3.2 in `Colin Josey's thesis
+ <http://hdl.handle.net/1721.1/113721>`_.
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ The operator object to simulate on.
+ timesteps : iterable of float
+ Array of timesteps in units of [s]. Note that values are not
+ cumulative.
+ power : float or iterable of float, optional
+ Power of the reactor in [W]. A single value indicates that
+ the power is constant over all timesteps. An iterable
+ indicates potentially different power levels for each timestep.
+ For a 2D problem, the power can be given in [W/cm] as long
+ as the "volume" assigned to a depletion material is actually
+ an area in [cm^2]. Either ``power`` or ``power_density`` must be
+ specified.
+ power_density : float or iterable of float, optional
+ Power density of the reactor in [W/gHM]. It is multiplied by
+ initial heavy metal inventory to get total power if ``power``
+ is not speficied.
+ n_steps : int, optional
+ Number of stochastic iterations per depletion interval.
+ Must be greater than zero. Default : 10
+
+ Attributes
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ chain : openmc.deplete.Chain
+ Depletion chain
+ timesteps : iterable of float
+ Size of each depletion interval in [s]
+ power : iterable of float
+ Power of the reactor in [W] for each interval in :attr:`timesteps`
+ n_steps : int
+ Number of stochastic iterations per depletion interval
+ """
+ _num_stages = 2
+
+ def __call__(self, bos_conc, bos_rates, dt, power, _i=None):
+ """Perform the integration across one time step
+
+ Parameters
+ ----------
+ bos_conc : numpy.ndarray
+ Initial bos_concentrations for all nuclides in [atom]
+ bos_rates : openmc.deplete.ReactionRates
+ Reaction rates from operator
+ dt : float
+ Time in [s] for the entire depletion interval
+ power : float
+ Power of the system in [W]
+ _i : int, optional
+ Current depletion step index. Not used
+
+ Returns
+ -------
+ proc_time : float
+ Time spent in CRAM routines for all materials in [s]
+ bos_conc_list : list of numpy.ndarray
+ Concentrations at each of the intermediate points with
+ the final bos_concentration as the last element
+ op_results : list of openmc.deplete.OperatorResult
+ Eigenvalue and reaction rates from intermediate transport
+ simulations
+ """
+ proc_time, eos_conc = timed_deplete(
+ self.chain, bos_conc, bos_rates, dt)
+ inter_conc = copy.deepcopy(eos_conc)
+
+ # Begin iteration
+ for j in range(self.n_steps + 1):
+ inter_res = self.operator(inter_conc, power)
+
+ if j <= 1:
+ res_bar = copy.deepcopy(inter_res)
+ else:
+ rates = 1/j * inter_res.rates + (1 - 1 / j) * res_bar.rates
+ k = 1/j * inter_res.k + (1 - 1 / j) * res_bar.k
+ res_bar = OperatorResult(k, rates)
+
+ list_rates = list(zip(bos_rates, res_bar.rates))
+ time1, inter_conc = timed_deplete(
+ self.chain, bos_conc, list_rates, dt, matrix_func=celi_f1)
+ time2, inter_conc = timed_deplete(
+ self.chain, inter_conc, list_rates, dt, matrix_func=celi_f2)
+ proc_time += time1 + time2
+
+ # end iteration
+ return proc_time, [eos_conc, inter_conc], [res_bar]
+
+
+class SILEQIIntegrator(SIIntegrator):
+ r"""Deplete using the SI-LE/QI CFQ4 algorithm.
+
+ Implements the Stochastic Implicit LE/QI Predictor-Corrector algorithm
+ using the `fourth order commutator-free integrator
+ <https://doi.org/10.1137/05063042>`_.
+
+ Detailed algorithm can be found in Section 3.2 in `Colin Josey's thesis
+ <http://hdl.handle.net/1721.1/113721>`_.
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ The operator object to simulate on.
+ timesteps : iterable of float
+ Array of timesteps in units of [s]. Note that values are not
+ cumulative.
+ power : float or iterable of float, optional
+ Power of the reactor in [W]. A single value indicates that
+ the power is constant over all timesteps. An iterable
+ indicates potentially different power levels for each timestep.
+ For a 2D problem, the power can be given in [W/cm] as long
+ as the "volume" assigned to a depletion material is actually
+ an area in [cm^2]. Either ``power`` or ``power_density`` must be
+ specified.
+ power_density : float or iterable of float, optional
+ Power density of the reactor in [W/gHM]. It is multiplied by
+ initial heavy metal inventory to get total power if ``power``
+ is not speficied.
+ n_steps : int, optional
+ Number of stochastic iterations per depletion interval.
+ Must be greater than zero. Default : 10
+
+ Attributes
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator to perform transport simulations
+ chain : openmc.deplete.Chain
+ Depletion chain
+ timesteps : iterable of float
+ Size of each depletion interval in [s]
+ power : iterable of float
+ Power of the reactor in [W] for each interval in :attr:`timesteps`
+ n_steps : int
+ Number of stochastic iterations per depletion interval
+ """
+ _num_stages = 2
+
+ def __call__(self, bos_conc, bos_rates, dt, power, i):
+ """Perform the integration across one time step
+
+ Parameters
+ ----------
+ bos_conc : list of numpy.ndarray
+ Initial concentrations for all nuclides in [atom] for
+ all depletable materials
+ bos_rates : list of openmc.deplete.ReactionRates
+ Reaction rates from operator for all depletable materials
+ dt : float
+ Time in [s] for the entire depletion interval
+ power : float
+ Power of the system in [W]
+ i : int
+ Current depletion step index
+
+ Returns
+ -------
+ proc_time : float
+ Time spent in CRAM routines for all materials in [s]
+ conc_list : list of numpy.ndarray
+ Concentrations at each of the intermediate points with
+ the final concentration as the last element
+ op_results : list of openmc.deplete.OperatorResult
+ Eigenvalue and reaction rates from intermediate transport
+ simulation
+ """
+ if i == 0:
+ if self._i_res < 1:
+ self._prev_rates = bos_rates
+ # Perform CELI for initial steps
+ return SICELIIntegrator.__call__(
+ self, bos_conc, bos_rates, dt, power, i)
+ prev_res = self.operator.prev_res[-2]
+ prev_dt = self.timesteps[i] - prev_res.time[0]
+ self._prev_rates = prev_res.rates[0]
+ else:
+ prev_dt = self.timesteps[i - 1]
+
+ # Perform remaining LE/QI
+ inputs = list(zip(self._prev_rates, bos_rates,
+ repeat(prev_dt), repeat(dt)))
+ proc_time, inter_conc = timed_deplete(
+ self.chain, bos_conc, inputs, dt, matrix_func=leqi_f1)
+ time1, eos_conc = timed_deplete(
+ self.chain, inter_conc, inputs, dt, matrix_func=leqi_f2)
+
+ proc_time += time1
+ inter_conc = copy.deepcopy(eos_conc)
+
+ for j in range(self.n_steps + 1):
+ inter_res = self.operator(inter_conc, power)
+
+ if j <= 1:
+ res_bar = copy.deepcopy(inter_res)
+ else:
+ rates = 1 / j * inter_res.rates + (1 - 1 / j) * res_bar.rates
+ k = 1 / j * inter_res.k + (1 - 1 / j) * res_bar.k
+ res_bar = OperatorResult(k, rates)
+
+ inputs = list(zip(self._prev_rates, bos_rates, res_bar.rates,
+ repeat(prev_dt), repeat(dt)))
+ time1, inter_conc = timed_deplete(
+ self.chain, bos_conc, inputs, dt, matrix_func=leqi_f3)
+ time2, inter_conc = timed_deplete(
+ self.chain, inter_conc, inputs, dt, matrix_func=leqi_f4)
+ proc_time += time1 + time2
+
+ return proc_time, [eos_conc, inter_conc], [res_bar]
diff --git a/openmc/deplete/operator.py b/openmc/deplete/operator.py
--- a/openmc/deplete/operator.py
+++ b/openmc/deplete/operator.py
@@ -16,6 +16,7 @@
import h5py
import numpy as np
+from uncertainties import ufloat
import openmc
import openmc.capi
@@ -55,7 +56,7 @@ class Operator(TransportOperator):
Instances of this class can be used to perform depletion using OpenMC as the
transport operator. Normally, a user needn't call methods of this class
directly. Instead, an instance of this class is passed to an integrator
- function, such as :func:`openmc.deplete.integrator.cecm`.
+ class, such as :class:`openmc.deplete.CECMIntegrator`.
Parameters
----------
@@ -111,28 +112,24 @@ class Operator(TransportOperator):
Initial heavy metal inventory
local_mats : list of str
All burnable material IDs being managed by a single process
- prev_res : ResultsList
- Results from a previous depletion calculation
+ prev_res : ResultsList or None
+ Results from a previous depletion calculation. ``None`` if no
+ results are to be used.
diff_burnable_mats : bool
Whether to differentiate burnable materials with multiple instances
"""
def __init__(self, geometry, settings, chain_file=None, prev_results=None,
diff_burnable_mats=False, fission_q=None,
dilute_initial=1.0e3):
- super().__init__(chain_file, fission_q, dilute_initial)
+ super().__init__(chain_file, fission_q, dilute_initial, prev_results)
self.round_number = False
self.settings = settings
self.geometry = geometry
self.diff_burnable_mats = diff_burnable_mats
- if prev_results is not None:
+ if self.prev_res is not None:
# Reload volumes into geometry
- prev_results[-1].transfer_volumes(geometry)
-
- # Store previous results in operator
- self.prev_res = prev_results
- else:
- self.prev_res = None
+ self.prev_results[-1].transfer_volumes(geometry)
# Differentiate burnable materials with multiple instances
if self.diff_burnable_mats:
@@ -167,7 +164,7 @@ def __init__(self, geometry, settings, chain_file=None, prev_results=None,
self.reaction_rates.n_nuc, self.reaction_rates.n_react)
self._energy_helper = ChainFissionHelper()
- def __call__(self, vec, power, print_out=True):
+ def __call__(self, vec, power):
"""Runs a simulation.
Parameters
@@ -176,8 +173,6 @@ def __call__(self, vec, power, print_out=True):
Total atoms to be used in function.
power : float
Power of the reactor in [W]
- print_out : bool, optional
- Whether or not to print out time.
Returns
-------
@@ -207,14 +202,20 @@ def __call__(self, vec, power, print_out=True):
# Extract results
op_result = self._unpack_tallies_and_normalize(power)
- if comm.rank == 0:
- time_unpack = time.time()
+ return copy.deepcopy(op_result)
- if print_out:
- print("Time to openmc: ", time_openmc - time_start)
- print("Time to unpack: ", time_unpack - time_openmc)
+ @staticmethod
+ def write_bos_data(step):
+ """Write a state-point file with beginning of step data
- return copy.deepcopy(op_result)
+ Parameters
+ ----------
+ step : int
+ Current depletion step including restarts
+ """
+ openmc.capi.statepoint_write(
+ "openmc_simulation_n{}.h5".format(step),
+ write_source=False)
def _differentiate_burnable_mats(self):
"""Assign distribmats for each burnable material
@@ -525,7 +526,7 @@ def _unpack_tallies_and_normalize(self, power):
rates.fill(0.0)
# Get k and uncertainty
- k_combined = openmc.capi.keff()
+ k_combined = ufloat(*openmc.capi.keff())
# Extract tally bins
nuclides = self._rate_helper.nuclides
diff --git a/openmc/deplete/results.py b/openmc/deplete/results.py
--- a/openmc/deplete/results.py
+++ b/openmc/deplete/results.py
@@ -21,8 +21,8 @@ class Results(object):
Attributes
----------
- k : list of float
- Eigenvalue for each substep.
+ k : list of (float, float)
+ Eigenvalue and uncertainty for each substep.
time : list of float
Time at beginning, end of step, in seconds.
power : float
@@ -425,16 +425,7 @@ def save(op, x, op_results, t, power, step_ind, proc_time=None):
# Get indexing terms
vol_dict, nuc_list, burn_list, full_burn_list = op.get_results_info()
- # For a restart calculation, limit number of stages saved to meet the
- # format of the hdf5 file
stages = len(x)
- offset = 0
- if op.prev_res is not None and op.prev_res[0].n_stages < stages:
- offset = stages - op.prev_res[0].n_stages
- stages = min(stages, op.prev_res[0].n_stages)
- warn("Number of restart integrator stages saved limited by initial"
- " depletion integrator choice to {}"
- .format(op.prev_res[0].n_stages))
# Create results
results = Results()
@@ -444,9 +435,9 @@ def save(op, x, op_results, t, power, step_ind, proc_time=None):
for i in range(stages):
for mat_i in range(n_mat):
- results[i, mat_i, :] = x[offset + i][mat_i][:]
+ results[i, mat_i, :] = x[i][mat_i]
- results.k = [r.k for r in op_results]
+ results.k = [(r.k.nominal_value, r.k.std_dev) for r in op_results]
results.rates = [r.rates for r in op_results]
results.time = t
results.power = power
| diff --git a/tests/dummy_operator.py b/tests/dummy_operator.py
--- a/tests/dummy_operator.py
+++ b/tests/dummy_operator.py
@@ -1,5 +1,7 @@
import numpy as np
import scipy.sparse as sp
+from uncertainties import ufloat
+
from openmc.deplete.reaction_rates import ReactionRates
from openmc.deplete.abc import TransportOperator, OperatorResult
@@ -48,7 +50,7 @@ def __call__(self, vec, power, print_out=False):
reaction_rates[0, 1, 0] = vec[0][1]
# Create a fake rates object
- return OperatorResult(0.0, reaction_rates)
+ return OperatorResult(ufloat(0.0, 0.0), reaction_rates)
@property
def chain(self):
@@ -114,6 +116,9 @@ def burnable_mats(self):
"""Maps cell name to index in global geometry."""
return self.local_mats
+ @staticmethod
+ def write_bos_data(_step):
+ """Empty method but avoids calls to C API"""
@property
def reaction_rates(self):
diff --git a/tests/regression_tests/deplete/test.py b/tests/regression_tests/deplete/test.py
--- a/tests/regression_tests/deplete/test.py
+++ b/tests/regression_tests/deplete/test.py
@@ -39,7 +39,7 @@ def test_full(run_in_tmpdir):
space = openmc.stats.Box(lower_left, upper_right)
settings.source = openmc.Source(space=space)
settings.seed = 1
- settings.verbosity = 3
+ settings.verbosity = 1
# Create operator
chain_file = Path(__file__).parents[2] / 'chain_simple.xml'
@@ -54,7 +54,7 @@ def test_full(run_in_tmpdir):
power = 2.337e15*4*JOULE_PER_EV*1e6 # MeV/second cm from CASMO
# Perform simulation using the predictor algorithm
- openmc.deplete.integrator.predictor(op, dt, power)
+ openmc.deplete.PredictorIntegrator(op, dt, power).integrate()
# Get path to test and reference results
path_test = op.output_dir / 'depletion_results.h5'
@@ -101,3 +101,18 @@ def test_full(run_in_tmpdir):
assert correct, "Discrepancy in mat {} and nuc {}\n{}\n{}".format(
mat, nuc, y_old, y_test)
+
+ # Compare statepoint files with depletion results
+
+ t_test, k_test = res_test.get_eigenvalue()
+ t_ref, k_ref = res_ref.get_eigenvalue()
+ k_state = np.empty_like(k_ref)
+
+ # Get statepoint files for all BOS points and EOL
+ for n in range(N + 1):
+ statepoint = openmc.StatePoint("openmc_simulation_n{}.h5".format(n))
+ k_n = statepoint.k_combined
+ k_state[n] = [k_n.nominal_value, k_n.std_dev]
+ # Look for exact match pulling from statepoint and depletion_results
+ assert np.all(k_state == k_test)
+ assert np.allclose(k_test, k_ref)
diff --git a/tests/unit_tests/test_deplete_cecm.py b/tests/unit_tests/test_deplete_cecm.py
--- a/tests/unit_tests/test_deplete_cecm.py
+++ b/tests/unit_tests/test_deplete_cecm.py
@@ -5,6 +5,7 @@
from pytest import approx
import openmc.deplete
+from openmc.deplete import CECMIntegrator
from tests import dummy_operator
@@ -18,7 +19,8 @@ def test_cecm(run_in_tmpdir):
# Perform simulation using the MCNPX/MCNP6 algorithm
dt = [0.75, 0.75]
power = 1.0
- openmc.deplete.cecm(op, dt, power, print_out=False)
+ integrator = CECMIntegrator(op, dt, power)
+ integrator.integrate()
# Load the files
res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
diff --git a/tests/unit_tests/test_deplete_celi.py b/tests/unit_tests/test_deplete_celi.py
--- a/tests/unit_tests/test_deplete_celi.py
+++ b/tests/unit_tests/test_deplete_celi.py
@@ -4,7 +4,7 @@
"""
from pytest import approx
-import openmc.deplete
+from openmc.deplete import ResultsList, CELIIntegrator
from tests import dummy_operator
@@ -18,10 +18,10 @@ def test_celi(run_in_tmpdir):
# Perform simulation using the celi algorithm
dt = [0.75, 0.75]
power = 1.0
- openmc.deplete.celi(op, dt, power, print_out=False)
+ CELIIntegrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_cf4.py b/tests/unit_tests/test_deplete_cf4.py
--- a/tests/unit_tests/test_deplete_cf4.py
+++ b/tests/unit_tests/test_deplete_cf4.py
@@ -4,7 +4,7 @@
"""
from pytest import approx
-import openmc.deplete
+from openmc.deplete import CF4Integrator, ResultsList
from tests import dummy_operator
@@ -18,10 +18,10 @@ def test_cf4(run_in_tmpdir):
# Perform simulation using the cf4 algorithm
dt = [0.75, 0.75]
power = 1.0
- openmc.deplete.cf4(op, dt, power, print_out=False)
+ CF4Integrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_cram.py b/tests/unit_tests/test_deplete_cram.py
--- a/tests/unit_tests/test_deplete_cram.py
+++ b/tests/unit_tests/test_deplete_cram.py
@@ -6,7 +6,7 @@
from pytest import approx
import numpy as np
import scipy.sparse as sp
-from openmc.deplete.integrator import CRAM16, CRAM48
+from openmc.deplete.cram import CRAM16, CRAM48
def test_CRAM16():
diff --git a/tests/unit_tests/test_deplete_epc_rk4.py b/tests/unit_tests/test_deplete_epc_rk4.py
--- a/tests/unit_tests/test_deplete_epc_rk4.py
+++ b/tests/unit_tests/test_deplete_epc_rk4.py
@@ -4,7 +4,7 @@
"""
from pytest import approx
-import openmc.deplete
+from openmc.deplete import EPCRK4Integrator, ResultsList
from tests import dummy_operator
@@ -18,10 +18,10 @@ def test_epc_rk4(run_in_tmpdir):
# Perform simulation using the epc_rk4 algorithm
dt = [0.75, 0.75]
power = 1.0
- openmc.deplete.epc_rk4(op, dt, power, print_out=False)
+ EPCRK4Integrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_integrator.py b/tests/unit_tests/test_deplete_integrator.py
--- a/tests/unit_tests/test_deplete_integrator.py
+++ b/tests/unit_tests/test_deplete_integrator.py
@@ -11,8 +11,12 @@
from unittest.mock import MagicMock
import numpy as np
-from openmc.deplete import (ReactionRates, Results, ResultsList, comm,
- OperatorResult)
+from uncertainties import ufloat
+import pytest
+
+from openmc.deplete import (
+ ReactionRates, Results, ResultsList, comm, OperatorResult,
+ PredictorIntegrator, SICELIIntegrator)
def test_results_save(run_in_tmpdir):
@@ -74,8 +78,10 @@ def test_results_save(run_in_tmpdir):
t1 = [0.0, 1.0]
t2 = [1.0, 2.0]
- op_result1 = [OperatorResult(k, rates) for k, rates in zip(eigvl1, rate1)]
- op_result2 = [OperatorResult(k, rates) for k, rates in zip(eigvl2, rate2)]
+ op_result1 = [OperatorResult(ufloat(*k), rates)
+ for k, rates in zip(eigvl1, rate1)]
+ op_result2 = [OperatorResult(ufloat(*k), rates)
+ for k, rates in zip(eigvl2, rate2)]
Results.save(op, x1, op_result1, t1, 0, 0)
Results.save(op, x2, op_result2, t2, 0, 1)
@@ -95,3 +101,32 @@ def test_results_save(run_in_tmpdir):
np.testing.assert_array_equal(res[1].k, eigvl2)
np.testing.assert_array_equal(res[1].time, t2)
+
+
[email protected]("timesteps", (1, [1]))
+def test_bad_integrator_inputs(timesteps):
+ """Test failure modes for Integrator inputs"""
+
+ op = MagicMock()
+ op.prev_res = None
+ op.chain = None
+ op.heavy_metal = 1.0
+
+ # No power nor power density given
+ with pytest.raises(ValueError, match="Either power or power density"):
+ PredictorIntegrator(op, timesteps)
+
+ # Length of power != length time
+ with pytest.raises(ValueError, match="number of powers"):
+ PredictorIntegrator(op, timesteps, power=[1, 2])
+
+ # Length of power density != length time
+ with pytest.raises(ValueError, match="number of powers"):
+ PredictorIntegrator(op, timesteps, power_density=[1, 2])
+
+ # SI integrator with bad steps
+ with pytest.raises(TypeError, match="n_steps"):
+ SICELIIntegrator(op, timesteps, [1], n_steps=2.5)
+
+ with pytest.raises(ValueError, match="n_steps"):
+ SICELIIntegrator(op, timesteps, [1], n_steps=0)
diff --git a/tests/unit_tests/test_deplete_leqi.py b/tests/unit_tests/test_deplete_leqi.py
--- a/tests/unit_tests/test_deplete_leqi.py
+++ b/tests/unit_tests/test_deplete_leqi.py
@@ -4,7 +4,7 @@
"""
from pytest import approx
-import openmc.deplete
+from openmc.deplete import LEQIIntegrator, ResultsList
from tests import dummy_operator
@@ -18,10 +18,10 @@ def test_leqi(run_in_tmpdir):
# Perform simulation using the leqi algorithm
dt = [0.75, 0.75]
power = 1.0
- openmc.deplete.leqi(op, dt, power, print_out=False)
+ LEQIIntegrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_operator.py b/tests/unit_tests/test_deplete_operator.py
--- a/tests/unit_tests/test_deplete_operator.py
+++ b/tests/unit_tests/test_deplete_operator.py
@@ -37,14 +37,20 @@ def bare_xs(run_in_tmpdir):
class BareDepleteOperator(TransportOperator):
"""Very basic class for testing the initialization."""
- # declare abstract methods so object can be created
- def __call__(self, *args, **kwargs):
+ @staticmethod
+ def __call__(*args, **kwargs):
pass
- def initial_condition(self):
+ @staticmethod
+ def initial_condition():
pass
- def get_results_info(self):
+ @staticmethod
+ def get_results_info():
+ pass
+
+ @staticmethod
+ def write_bos_data():
pass
diff --git a/tests/unit_tests/test_deplete_predictor.py b/tests/unit_tests/test_deplete_predictor.py
--- a/tests/unit_tests/test_deplete_predictor.py
+++ b/tests/unit_tests/test_deplete_predictor.py
@@ -4,7 +4,7 @@
"""
from pytest import approx
-import openmc.deplete
+from openmc.deplete import PredictorIntegrator, ResultsList
from tests import dummy_operator
@@ -18,10 +18,11 @@ def test_predictor(run_in_tmpdir):
# Perform simulation using the predictor algorithm
dt = [0.75, 0.75]
power = 1.0
- openmc.deplete.predictor(op, dt, power, print_out=False)
+ PredictorIntegrator(op, dt, power).integrate()
+
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_restart.py b/tests/unit_tests/test_deplete_restart.py
--- a/tests/unit_tests/test_deplete_restart.py
+++ b/tests/unit_tests/test_deplete_restart.py
@@ -4,8 +4,12 @@
problem described in dummy_geometry.py.
"""
-from pytest import approx
+from pytest import approx, raises
import openmc.deplete
+from openmc.deplete import (
+ CECMIntegrator, PredictorIntegrator, CELIIntegrator, LEQIIntegrator,
+ EPCRK4Integrator, CF4Integrator, SICELIIntegrator, SILEQIIntegrator
+)
from tests import dummy_operator
@@ -20,7 +24,7 @@ def test_restart_predictor(run_in_tmpdir):
# Perform simulation using the predictor algorithm
dt = [0.75]
power = 1.0
- openmc.deplete.predictor(op, dt, power, print_out=False)
+ PredictorIntegrator(op, dt, power).integrate()
# Load the files
prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -30,7 +34,7 @@ def test_restart_predictor(run_in_tmpdir):
op.output_dir = output_dir
# Perform restarts simulation using the predictor algorithm
- openmc.deplete.predictor(op, dt, power, print_out=False)
+ PredictorIntegrator(op, dt, power).integrate()
# Load the files
res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -59,7 +63,8 @@ def test_restart_cecm(run_in_tmpdir):
# Perform simulation using the MCNPX/MCNP6 algorithm
dt = [0.75]
power = 1.0
- openmc.deplete.cecm(op, dt, power, print_out=False)
+ cecm = CECMIntegrator(op, dt, power)
+ cecm.integrate()
# Load the files
prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -69,7 +74,8 @@ def test_restart_cecm(run_in_tmpdir):
op.output_dir = output_dir
# Perform restarts simulation using the MCNPX/MCNP6 algorithm
- openmc.deplete.cecm(op, dt, power, print_out=False)
+ cecm_restart = CECMIntegrator(op, dt, power)
+ cecm_restart.integrate()
# Load the files
res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -84,13 +90,12 @@ def test_restart_cecm(run_in_tmpdir):
assert y1[1] == approx(s1[0])
assert y2[1] == approx(s1[1])
- assert y1[3] == approx(s2[0])
- assert y2[3] == approx(s2[1])
+ assert y1[2] == approx(s2[0])
+ assert y2[2] == approx(s2[1])
def test_restart_predictor_cecm(run_in_tmpdir):
- """Integral regression test of integrator algorithm using predictor
- for the first run then CE/CM for the restart run."""
+ """Test to ensure that schemes with different stages are not compatible"""
op = dummy_operator.DummyOperator()
output_dir = "test_restart_predictor_cecm"
@@ -99,7 +104,7 @@ def test_restart_predictor_cecm(run_in_tmpdir):
# Perform simulation using the predictor algorithm
dt = [0.75]
power = 1.0
- openmc.deplete.predictor(op, dt, power, print_out=False)
+ PredictorIntegrator(op, dt, power).integrate()
# Load the files
prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -108,24 +113,9 @@ def test_restart_predictor_cecm(run_in_tmpdir):
op = dummy_operator.DummyOperator(prev_res)
op.output_dir = output_dir
- # Perform restarts simulation using the MCNPX/MCNP6 algorithm
- openmc.deplete.cecm(op, dt, power, print_out=False)
-
- # Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
-
- _, y1 = res.get_atoms("1", "1")
- _, y2 = res.get_atoms("1", "2")
-
- # Test solution
- s1 = [2.46847546272295, 0.986431226850467]
- s2 = [3.09106948392, 0.607102912398]
-
- assert y1[1] == approx(s1[0])
- assert y2[1] == approx(s1[1])
-
- assert y1[2] == approx(s2[0])
- assert y2[2] == approx(s2[1])
+ # check ValueError is raised, indicating previous and current stages
+ with raises(ValueError, match="incompatible.* 1.*2"):
+ CECMIntegrator(op, dt, power)
def test_restart_cecm_predictor(run_in_tmpdir):
@@ -139,7 +129,8 @@ def test_restart_cecm_predictor(run_in_tmpdir):
# Perform simulation using the MCNPX/MCNP6 algorithm
dt = [0.75]
power = 1.0
- openmc.deplete.cecm(op, dt, power, print_out=False)
+ cecm = CECMIntegrator(op, dt, power)
+ cecm.integrate()
# Load the files
prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -148,25 +139,9 @@ def test_restart_cecm_predictor(run_in_tmpdir):
op = dummy_operator.DummyOperator(prev_res)
op.output_dir = output_dir
- # Perform restarts simulation using the predictor algorithm
- openmc.deplete.predictor(op, dt, power, print_out=False)
-
- # Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
-
- _, y1 = res.get_atoms("1", "1")
- _, y2 = res.get_atoms("1", "2")
-
- # Test solution
- s1 = [1.86872629872102, 1.395525772416039]
- s2 = [3.32776806576, 2.391425905]
-
- assert y1[1] == approx(s1[0])
- assert y2[1] == approx(s1[1])
-
- assert y1[2] == approx(s2[0])
- assert y2[2] == approx(s2[1])
-
+ # check ValueError is raised, indicating previous and current stages
+ with raises(ValueError, match="incompatible.* 2.*1"):
+ PredictorIntegrator(op, dt, power)
def test_restart_cf4(run_in_tmpdir):
"""Integral regression test of integrator algorithm using CF4."""
@@ -178,7 +153,7 @@ def test_restart_cf4(run_in_tmpdir):
# Perform simulation
dt = [0.75]
power = 1.0
- openmc.deplete.cf4(op, dt, power, print_out=False)
+ CF4Integrator(op, dt, power).integrate()
# Load the files
prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -188,7 +163,7 @@ def test_restart_cf4(run_in_tmpdir):
op.output_dir = output_dir
# Perform restarts simulation
- openmc.deplete.cf4(op, dt, power, print_out=False)
+ CF4Integrator(op, dt, power).integrate()
# Load the files
res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -203,8 +178,8 @@ def test_restart_cf4(run_in_tmpdir):
assert y1[1] == approx(s1[0])
assert y2[1] == approx(s1[1])
- assert y1[3] == approx(s2[0])
- assert y2[3] == approx(s2[1])
+ assert y1[2] == approx(s2[0])
+ assert y2[2] == approx(s2[1])
def test_restart_epc_rk4(run_in_tmpdir):
@@ -217,7 +192,7 @@ def test_restart_epc_rk4(run_in_tmpdir):
# Perform simulation
dt = [0.75]
power = 1.0
- openmc.deplete.epc_rk4(op, dt, power, print_out=False)
+ EPCRK4Integrator(op, dt, power).integrate()
# Load the files
prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -227,7 +202,7 @@ def test_restart_epc_rk4(run_in_tmpdir):
op.output_dir = output_dir
# Perform restarts simulation
- openmc.deplete.epc_rk4(op, dt, power, print_out=False)
+ EPCRK4Integrator(op, dt, power).integrate()
# Load the files
res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -242,8 +217,8 @@ def test_restart_epc_rk4(run_in_tmpdir):
assert y1[1] == approx(s1[0])
assert y2[1] == approx(s1[1])
- assert y1[3] == approx(s2[0])
- assert y2[3] == approx(s2[1])
+ assert y1[2] == approx(s2[0])
+ assert y2[2] == approx(s2[1])
def test_restart_celi(run_in_tmpdir):
@@ -256,7 +231,7 @@ def test_restart_celi(run_in_tmpdir):
# Perform simulation
dt = [0.75]
power = 1.0
- openmc.deplete.celi(op, dt, power, print_out=False)
+ CELIIntegrator(op, dt, power).integrate()
# Load the files
prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -266,7 +241,7 @@ def test_restart_celi(run_in_tmpdir):
op.output_dir = output_dir
# Perform restarts simulation
- openmc.deplete.celi(op, dt, power, print_out=False)
+ CELIIntegrator(op, dt, power).integrate()
# Load the files
res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -281,8 +256,8 @@ def test_restart_celi(run_in_tmpdir):
assert y1[1] == approx(s1[0])
assert y2[1] == approx(s1[1])
- assert y1[3] == approx(s2[0])
- assert y2[3] == approx(s2[1])
+ assert y1[2] == approx(s2[0])
+ assert y2[2] == approx(s2[1])
def test_restart_leqi(run_in_tmpdir):
@@ -295,7 +270,7 @@ def test_restart_leqi(run_in_tmpdir):
# Perform simulation
dt = [0.75]
power = 1.0
- openmc.deplete.leqi(op, dt, power, print_out=False)
+ LEQIIntegrator(op, dt, power).integrate()
# Load the files
prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -305,7 +280,7 @@ def test_restart_leqi(run_in_tmpdir):
op.output_dir = output_dir
# Perform restarts simulation
- openmc.deplete.leqi(op, dt, power, print_out=False)
+ LEQIIntegrator(op, dt, power).integrate()
# Load the files
res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -320,8 +295,8 @@ def test_restart_leqi(run_in_tmpdir):
assert y1[1] == approx(s1[0])
assert y2[1] == approx(s1[1])
- assert y1[3] == approx(s2[0])
- assert y2[3] == approx(s2[1])
+ assert y1[2] == approx(s2[0])
+ assert y2[2] == approx(s2[1])
def test_restart_si_celi(run_in_tmpdir):
"""Integral regression test of integrator algorithm using SI-CELI."""
@@ -333,7 +308,7 @@ def test_restart_si_celi(run_in_tmpdir):
# Perform simulation
dt = [0.75]
power = 1.0
- openmc.deplete.si_celi(op, dt, power, print_out=False)
+ SICELIIntegrator(op, dt, power).integrate()
# Load the files
prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -343,7 +318,7 @@ def test_restart_si_celi(run_in_tmpdir):
op.output_dir = output_dir
# Perform restarts simulation
- openmc.deplete.si_celi(op, dt, power, print_out=False)
+ SICELIIntegrator(op, dt, power).integrate()
# Load the files
res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -358,8 +333,8 @@ def test_restart_si_celi(run_in_tmpdir):
assert y1[1] == approx(s1[0])
assert y2[1] == approx(s1[1])
- assert y1[3] == approx(s2[0])
- assert y2[3] == approx(s2[1])
+ assert y1[2] == approx(s2[0])
+ assert y2[2] == approx(s2[1])
def test_restart_si_leqi(run_in_tmpdir):
@@ -372,7 +347,8 @@ def test_restart_si_leqi(run_in_tmpdir):
# Perform simulation
dt = [0.75]
power = 1.0
- openmc.deplete.si_leqi(op, dt, power, print_out=False)
+ nstages = 10
+ SILEQIIntegrator(op, dt, power, nstages).integrate()
# Load the files
prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -382,7 +358,7 @@ def test_restart_si_leqi(run_in_tmpdir):
op.output_dir = output_dir
# Perform restarts simulation
- openmc.deplete.si_leqi(op, dt, power, print_out=False)
+ SILEQIIntegrator(op, dt, power, nstages).integrate()
# Load the files
res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
@@ -397,5 +373,5 @@ def test_restart_si_leqi(run_in_tmpdir):
assert y1[1] == approx(s1[0])
assert y2[1] == approx(s1[1])
- assert y1[3] == approx(s2[0])
- assert y2[3] == approx(s2[1])
+ assert y1[2] == approx(s2[0])
+ assert y2[2] == approx(s2[1])
diff --git a/tests/unit_tests/test_deplete_si_celi.py b/tests/unit_tests/test_deplete_si_celi.py
--- a/tests/unit_tests/test_deplete_si_celi.py
+++ b/tests/unit_tests/test_deplete_si_celi.py
@@ -4,7 +4,7 @@
"""
from pytest import approx
-import openmc.deplete
+from openmc.deplete import SICELIIntegrator, ResultsList
from tests import dummy_operator
@@ -18,10 +18,10 @@ def test_si_celi(run_in_tmpdir):
# Perform simulation using the si_celi algorithm
dt = [0.75, 0.75]
power = 1.0
- openmc.deplete.si_celi(op, dt, power, print_out=False)
+ SICELIIntegrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_si_leqi.py b/tests/unit_tests/test_deplete_si_leqi.py
--- a/tests/unit_tests/test_deplete_si_leqi.py
+++ b/tests/unit_tests/test_deplete_si_leqi.py
@@ -4,7 +4,7 @@
"""
from pytest import approx
-import openmc.deplete
+from openmc.deplete import SILEQIIntegrator, ResultsList
from tests import dummy_operator
@@ -18,10 +18,10 @@ def test_si_leqi(run_in_tmpdir):
# Perform simulation using the si_leqi algorithm
dt = [0.75, 0.75]
power = 1.0
- openmc.deplete.si_leqi(op, dt, power, print_out=False)
+ SILEQIIntegrator(op, dt, power, 10).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_transfer_volumes.py b/tests/unit_tests/test_transfer_volumes.py
--- a/tests/unit_tests/test_transfer_volumes.py
+++ b/tests/unit_tests/test_transfer_volumes.py
@@ -4,7 +4,8 @@
"""
from pytest import approx
-import openmc.deplete
+import openmc
+from openmc.deplete import PredictorIntegrator, ResultsList
from tests import dummy_operator
@@ -18,13 +19,13 @@ def test_transfer_volumes(run_in_tmpdir):
# Perform simulation using the predictor algorithm
dt = [0.75]
power = 1.0
- openmc.deplete.predictor(op, dt, power, print_out=False)
+ PredictorIntegrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList(op.output_dir / "depletion_results.h5")
# Create a dictionary of volumes to transfer
- res[0].volume['1'] = 1.5
+ res[0].volume['1'] = 1.5
res[0].volume['2'] = 2.5
# Create dummy geometry
| Writing statepoint data through depletion
Currently, the statepoint files are lost/overwritten during the depletion process. This includes all tallies that one may want to compute over burnup. I propose that, at the end of transport simulation, the final statepoint file is moved to a name that reflects its point in the burnup sequence, e.g. `statepoint-s<N>.h5` where `<N>` is an indicator of the depletion step. Related PR: #857
In doing this, there may be additional information that could be added to this statepoint file, e.g. the point in calendar time (5.7 days), time integration scheme, etc. If there is other information people think may be useful, add it here.
Lastly, is there any sense in adding a new `StatepointList`-like structure that handles multiple such files?
| 2019-07-10T19:26:22Z | [] | [] |
|
openmc-dev/openmc | 1,312 | openmc-dev__openmc-1312 | [
"1275",
"1275"
] | 21fd9a8a13415e767ccc08a8edf9f3df0c23b2c2 | diff --git a/openmc/deplete/operator.py b/openmc/deplete/operator.py
--- a/openmc/deplete/operator.py
+++ b/openmc/deplete/operator.py
@@ -24,6 +24,7 @@
from .abc import TransportOperator, OperatorResult
from .atom_number import AtomNumber
from .reaction_rates import ReactionRates
+from .results_list import ResultsList
from .helpers import DirectReactionRateHelper, ChainFissionHelper
@@ -73,7 +74,8 @@ class Operator(TransportOperator):
specified, the depletion calculation will start from the latest state
in the previous results.
diff_burnable_mats : bool, optional
- Whether to differentiate burnable materials with multiple instances
+ Whether to differentiate burnable materials with multiple instances.
+ Default: False.
fission_q : dict, optional
Dictionary of nuclides and their fission Q values [eV]. If not given,
values will be pulled from the ``chain_file``.
@@ -123,14 +125,11 @@ def __init__(self, geometry, settings, chain_file=None, prev_results=None,
dilute_initial=1.0e3):
super().__init__(chain_file, fission_q, dilute_initial, prev_results)
self.round_number = False
+ self.prev_res = None
self.settings = settings
self.geometry = geometry
self.diff_burnable_mats = diff_burnable_mats
- if self.prev_res is not None:
- # Reload volumes into geometry
- self.prev_results[-1].transfer_volumes(geometry)
-
# Differentiate burnable materials with multiple instances
if self.diff_burnable_mats:
self._differentiate_burnable_mats()
@@ -144,6 +143,21 @@ def __init__(self, geometry, settings, chain_file=None, prev_results=None,
self._mat_index_map = {
lm: self.burnable_mats.index(lm) for lm in self.local_mats}
+ if self.prev_res is not None:
+ # Reload volumes into geometry
+ prev_results[-1].transfer_volumes(geometry)
+
+ # Store previous results in operator
+ # Distribute reaction rates according to those tracked
+ # on this process
+ if comm.size == 1:
+ self.prev_res = prev_results
+ else:
+ self.prev_res = ResultsList()
+ mat_indexes = _distribute(range(len(self.burnable_mats)))
+ for res_obj in prev_results:
+ new_res = res_obj.distribute(self.local_mats, mat_indexes)
+ self.prev_res.append(new_res)
# Determine which nuclides have incident neutron data
self.nuclides_with_data = self._get_nuclides_with_data()
diff --git a/openmc/deplete/results.py b/openmc/deplete/results.py
--- a/openmc/deplete/results.py
+++ b/openmc/deplete/results.py
@@ -153,6 +153,37 @@ def allocate(self, volume, nuc_list, burn_list, full_burn_list, stages):
# Create storage array
self.data = np.zeros((stages, self.n_mat, self.n_nuc))
+ def distribute(self, local_materials, ranges):
+ """Create a new object containing data for distributed materials
+
+ Parameters
+ ----------
+ local_materials : iterable of str
+ Materials for this process
+ ranges : iterable of int
+ Slice-like object indicating indicies of ``local_materials``
+ in the material dimension of :attr:`data` and each element
+ in :attr:`rates`
+
+ Returns
+ -------
+ Results
+ New results object
+ """
+ new = Results()
+ new.volume = {lm: self.volume[lm] for lm in local_materials}
+ new.mat_to_ind = dict(zip(
+ local_materials, range(len(local_materials))))
+ # Direct transfer
+ direct_attrs = ("time", "k", "power", "nuc_to_ind",
+ "mat_to_hdf5_ind", "proc_time")
+ for attr in direct_attrs:
+ setattr(new, attr, getattr(self, attr))
+ # Get applicable slice of data
+ new.data = self.data[:, ranges]
+ new.rates = [r[ranges] for r in self.rates]
+ return new
+
def export_to_hdf5(self, filename, step):
"""Export results to an HDF5 file
diff --git a/openmc/deplete/results_list.py b/openmc/deplete/results_list.py
--- a/openmc/deplete/results_list.py
+++ b/openmc/deplete/results_list.py
@@ -8,22 +8,34 @@
class ResultsList(list):
"""A list of openmc.deplete.Results objects
- Parameters
- ----------
- filename : str
- The filename to read from.
-
+ It is recommended to use :meth:`from_hdf5` over
+ direct creation.
"""
- def __init__(self, filename):
- super().__init__()
+
+ @classmethod
+ def from_hdf5(cls, filename):
+ """Load in depletion results from a previous file
+
+ Parameters
+ ----------
+ filename : str
+ Path to depletion result file
+
+ Returns
+ -------
+ new : ResultsList
+ New instance of depletion results
+ """
with h5py.File(str(filename), "r") as fh:
check_filetype_version(fh, 'depletion results', _VERSION_RESULTS[0])
+ new = cls()
# Get number of results stored
n = fh["number"][...].shape[0]
for i in range(n):
- self.append(Results.from_hdf5(fh, i))
+ new.append(Results.from_hdf5(fh, i))
+ return new
def get_atoms(self, mat, nuc):
"""Get number of nuclides over time from a single material
| diff --git a/tests/regression_tests/deplete/test.py b/tests/regression_tests/deplete/test.py
--- a/tests/regression_tests/deplete/test.py
+++ b/tests/regression_tests/deplete/test.py
@@ -66,8 +66,8 @@ def test_full(run_in_tmpdir):
return
# Load the reference/test results
- res_test = openmc.deplete.ResultsList(path_test)
- res_ref = openmc.deplete.ResultsList(path_reference)
+ res_test = openmc.deplete.ResultsList.from_hdf5(path_test)
+ res_ref = openmc.deplete.ResultsList.from_hdf5(path_reference)
# Assert same mats
for mat in res_ref[0].mat_to_ind:
diff --git a/tests/unit_tests/test_deplete_cecm.py b/tests/unit_tests/test_deplete_cecm.py
--- a/tests/unit_tests/test_deplete_cecm.py
+++ b/tests/unit_tests/test_deplete_cecm.py
@@ -4,8 +4,7 @@
"""
from pytest import approx
-import openmc.deplete
-from openmc.deplete import CECMIntegrator
+from openmc.deplete import CECMIntegrator, ResultsList
from tests import dummy_operator
@@ -23,7 +22,7 @@ def test_cecm(run_in_tmpdir):
integrator.integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_celi.py b/tests/unit_tests/test_deplete_celi.py
--- a/tests/unit_tests/test_deplete_celi.py
+++ b/tests/unit_tests/test_deplete_celi.py
@@ -21,7 +21,7 @@ def test_celi(run_in_tmpdir):
CELIIntegrator(op, dt, power).integrate()
# Load the files
- res = ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_cf4.py b/tests/unit_tests/test_deplete_cf4.py
--- a/tests/unit_tests/test_deplete_cf4.py
+++ b/tests/unit_tests/test_deplete_cf4.py
@@ -21,7 +21,7 @@ def test_cf4(run_in_tmpdir):
CF4Integrator(op, dt, power).integrate()
# Load the files
- res = ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_epc_rk4.py b/tests/unit_tests/test_deplete_epc_rk4.py
--- a/tests/unit_tests/test_deplete_epc_rk4.py
+++ b/tests/unit_tests/test_deplete_epc_rk4.py
@@ -21,7 +21,7 @@ def test_epc_rk4(run_in_tmpdir):
EPCRK4Integrator(op, dt, power).integrate()
# Load the files
- res = ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_integrator.py b/tests/unit_tests/test_deplete_integrator.py
--- a/tests/unit_tests/test_deplete_integrator.py
+++ b/tests/unit_tests/test_deplete_integrator.py
@@ -86,7 +86,7 @@ def test_results_save(run_in_tmpdir):
Results.save(op, x2, op_result2, t2, 0, 1)
# Load the files
- res = ResultsList("depletion_results.h5")
+ res = ResultsList.from_hdf5("depletion_results.h5")
for i in range(stages):
for mat_i, mat in enumerate(burn_list):
diff --git a/tests/unit_tests/test_deplete_leqi.py b/tests/unit_tests/test_deplete_leqi.py
--- a/tests/unit_tests/test_deplete_leqi.py
+++ b/tests/unit_tests/test_deplete_leqi.py
@@ -21,7 +21,7 @@ def test_leqi(run_in_tmpdir):
LEQIIntegrator(op, dt, power).integrate()
# Load the files
- res = ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_predictor.py b/tests/unit_tests/test_deplete_predictor.py
--- a/tests/unit_tests/test_deplete_predictor.py
+++ b/tests/unit_tests/test_deplete_predictor.py
@@ -22,7 +22,7 @@ def test_predictor(run_in_tmpdir):
# Load the files
- res = ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_restart.py b/tests/unit_tests/test_deplete_restart.py
--- a/tests/unit_tests/test_deplete_restart.py
+++ b/tests/unit_tests/test_deplete_restart.py
@@ -27,7 +27,7 @@ def test_restart_predictor(run_in_tmpdir):
PredictorIntegrator(op, dt, power).integrate()
# Load the files
- prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ prev_res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
# Re-create depletion operator and load previous results
op = dummy_operator.DummyOperator(prev_res)
@@ -37,7 +37,7 @@ def test_restart_predictor(run_in_tmpdir):
PredictorIntegrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
@@ -67,7 +67,7 @@ def test_restart_cecm(run_in_tmpdir):
cecm.integrate()
# Load the files
- prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ prev_res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
# Re-create depletion operator and load previous results
op = dummy_operator.DummyOperator(prev_res)
@@ -78,7 +78,7 @@ def test_restart_cecm(run_in_tmpdir):
cecm_restart.integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
@@ -107,7 +107,7 @@ def test_restart_predictor_cecm(run_in_tmpdir):
PredictorIntegrator(op, dt, power).integrate()
# Load the files
- prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ prev_res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
# Re-create depletion operator and load previous results
op = dummy_operator.DummyOperator(prev_res)
@@ -133,7 +133,7 @@ def test_restart_cecm_predictor(run_in_tmpdir):
cecm.integrate()
# Load the files
- prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ prev_res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
# Re-create depletion operator and load previous results
op = dummy_operator.DummyOperator(prev_res)
@@ -156,7 +156,7 @@ def test_restart_cf4(run_in_tmpdir):
CF4Integrator(op, dt, power).integrate()
# Load the files
- prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ prev_res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
# Re-create depletion operator and load previous results
op = dummy_operator.DummyOperator(prev_res)
@@ -166,7 +166,7 @@ def test_restart_cf4(run_in_tmpdir):
CF4Integrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
@@ -195,7 +195,7 @@ def test_restart_epc_rk4(run_in_tmpdir):
EPCRK4Integrator(op, dt, power).integrate()
# Load the files
- prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ prev_res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
# Re-create depletion operator and load previous results
op = dummy_operator.DummyOperator(prev_res)
@@ -205,7 +205,7 @@ def test_restart_epc_rk4(run_in_tmpdir):
EPCRK4Integrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
@@ -234,7 +234,7 @@ def test_restart_celi(run_in_tmpdir):
CELIIntegrator(op, dt, power).integrate()
# Load the files
- prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ prev_res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
# Re-create depletion operator and load previous results
op = dummy_operator.DummyOperator(prev_res)
@@ -244,7 +244,7 @@ def test_restart_celi(run_in_tmpdir):
CELIIntegrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
@@ -273,7 +273,7 @@ def test_restart_leqi(run_in_tmpdir):
LEQIIntegrator(op, dt, power).integrate()
# Load the files
- prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ prev_res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
# Re-create depletion operator and load previous results
op = dummy_operator.DummyOperator(prev_res)
@@ -283,7 +283,7 @@ def test_restart_leqi(run_in_tmpdir):
LEQIIntegrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
@@ -311,7 +311,7 @@ def test_restart_si_celi(run_in_tmpdir):
SICELIIntegrator(op, dt, power).integrate()
# Load the files
- prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ prev_res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
# Re-create depletion operator and load previous results
op = dummy_operator.DummyOperator(prev_res)
@@ -321,7 +321,7 @@ def test_restart_si_celi(run_in_tmpdir):
SICELIIntegrator(op, dt, power).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
@@ -351,7 +351,7 @@ def test_restart_si_leqi(run_in_tmpdir):
SILEQIIntegrator(op, dt, power, nstages).integrate()
# Load the files
- prev_res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ prev_res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
# Re-create depletion operator and load previous results
op = dummy_operator.DummyOperator(prev_res)
@@ -361,7 +361,7 @@ def test_restart_si_leqi(run_in_tmpdir):
SILEQIIntegrator(op, dt, power, nstages).integrate()
# Load the files
- res = openmc.deplete.ResultsList(op.output_dir / "depletion_results.h5")
+ res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_resultslist.py b/tests/unit_tests/test_deplete_resultslist.py
--- a/tests/unit_tests/test_deplete_resultslist.py
+++ b/tests/unit_tests/test_deplete_resultslist.py
@@ -12,7 +12,7 @@ def res():
"""Load the reference results"""
filename = (Path(__file__).parents[1] / 'regression_tests' / 'deplete'
/ 'test_reference.h5')
- return openmc.deplete.ResultsList(filename)
+ return openmc.deplete.ResultsList.from_hdf5(filename)
def test_get_atoms(res):
diff --git a/tests/unit_tests/test_deplete_si_celi.py b/tests/unit_tests/test_deplete_si_celi.py
--- a/tests/unit_tests/test_deplete_si_celi.py
+++ b/tests/unit_tests/test_deplete_si_celi.py
@@ -21,7 +21,7 @@ def test_si_celi(run_in_tmpdir):
SICELIIntegrator(op, dt, power).integrate()
# Load the files
- res = ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_deplete_si_leqi.py b/tests/unit_tests/test_deplete_si_leqi.py
--- a/tests/unit_tests/test_deplete_si_leqi.py
+++ b/tests/unit_tests/test_deplete_si_leqi.py
@@ -21,7 +21,7 @@ def test_si_leqi(run_in_tmpdir):
SILEQIIntegrator(op, dt, power, 10).integrate()
# Load the files
- res = ResultsList(op.output_dir / "depletion_results.h5")
+ res = ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
_, y1 = res.get_atoms("1", "1")
_, y2 = res.get_atoms("1", "2")
diff --git a/tests/unit_tests/test_transfer_volumes.py b/tests/unit_tests/test_transfer_volumes.py
--- a/tests/unit_tests/test_transfer_volumes.py
+++ b/tests/unit_tests/test_transfer_volumes.py
@@ -22,7 +22,7 @@ def test_transfer_volumes(run_in_tmpdir):
PredictorIntegrator(op, dt, power).integrate()
# Load the files
- res = ResultsList(op.output_dir / "depletion_results.h5")
+ res = openmc.deplete.ResultsList.from_hdf5(op.output_dir / "depletion_results.h5")
# Create a dictionary of volumes to transfer
res[0].volume['1'] = 1.5
| Restart depletion fails with MPI
When performing a restart run with multiple MPI processes, it appears that one operator tries building reaction rate data/material data before all the cross sections have been loaded.
## Steps to reproduce
1. Build a simple problem, and deplete for some period of time with some power
1. Create a new operator for restart mode by reading in from the previous `depletion_results.h5` file
1. Deplete again with some power and some time step but with multiple MPI processes.
I have two files: `start.py` and `restart.py` for the first depletion sequence and for the restart. Running `mpirun -n N restart.py` always fails, whether or not `start.py` used multiple processes.
## Error
`mpirun -n 2 restart.py 2>&1 > out.log`
```
Reading c_H_in_H2O from /home/drew/nndc_hdf5/c_H_in_H2O.h5
Maximum neutron transport energy: 20000000.000000 eV for U235
Reading tallies XML file...
Writing summary.h5 file...
Time to matexp: 0.1556260585784912
Traceback (most recent call last):
File "restart.py", line 20, in <module>
openmc.deplete.integrator.predictor(op, [time_steps[0]], power)
File "/home/drew/openmc/openmc/deplete/integrator/predictor.py", line 100, in predictor
op_results = [operator(x[0], power[-1])]
File "/home/drew/openmc/openmc/deplete/operator.py", line 175, in __call__
self.number.set_density(vec)
File "/home/drew/openmc/openmc/deplete/atom_number.py", line 214, in set_density
self.set_mat_slice(i, density_slice)
File "/home/drew/openmc/openmc/deplete/atom_number.py", line 199, in set_mat_slice
self[mat, :self.n_nuc_burn] = val
File "/home/drew/openmc/openmc/deplete/atom_number.py", line 104, in __setitem__
self.number[mat, nuc] = val
IndexError: index 0 is out of bounds for axis 0 with size 0
Reading I135 from /home/drew/nndc_hdf5/I135.h5
Reading Xe135 from /home/drew/nndc_hdf5/Xe135.h5
```
[Full error - pastebin](https://pastebin.com/RwaDfNc5)
The process also hung at the last line
Restart depletion fails with MPI
When performing a restart run with multiple MPI processes, it appears that one operator tries building reaction rate data/material data before all the cross sections have been loaded.
## Steps to reproduce
1. Build a simple problem, and deplete for some period of time with some power
1. Create a new operator for restart mode by reading in from the previous `depletion_results.h5` file
1. Deplete again with some power and some time step but with multiple MPI processes.
I have two files: `start.py` and `restart.py` for the first depletion sequence and for the restart. Running `mpirun -n N restart.py` always fails, whether or not `start.py` used multiple processes.
## Error
`mpirun -n 2 restart.py 2>&1 > out.log`
```
Reading c_H_in_H2O from /home/drew/nndc_hdf5/c_H_in_H2O.h5
Maximum neutron transport energy: 20000000.000000 eV for U235
Reading tallies XML file...
Writing summary.h5 file...
Time to matexp: 0.1556260585784912
Traceback (most recent call last):
File "restart.py", line 20, in <module>
openmc.deplete.integrator.predictor(op, [time_steps[0]], power)
File "/home/drew/openmc/openmc/deplete/integrator/predictor.py", line 100, in predictor
op_results = [operator(x[0], power[-1])]
File "/home/drew/openmc/openmc/deplete/operator.py", line 175, in __call__
self.number.set_density(vec)
File "/home/drew/openmc/openmc/deplete/atom_number.py", line 214, in set_density
self.set_mat_slice(i, density_slice)
File "/home/drew/openmc/openmc/deplete/atom_number.py", line 199, in set_mat_slice
self[mat, :self.n_nuc_burn] = val
File "/home/drew/openmc/openmc/deplete/atom_number.py", line 104, in __setitem__
self.number[mat, nuc] = val
IndexError: index 0 is out of bounds for axis 0 with size 0
Reading I135 from /home/drew/nndc_hdf5/I135.h5
Reading Xe135 from /home/drew/nndc_hdf5/Xe135.h5
```
[Full error - pastebin](https://pastebin.com/RwaDfNc5)
The process also hung at the last line
| The cause of the error is the distribution (or lack there of) of the previous results to multiple operators on different MPI processes.
Each operator/process [knows it's particular materials to deplete](https://github.com/openmc-dev/openmc/blob/a7d4dc0d5c4dd3546ad9e9c3b392f7c6ab7b3d9e/openmc/deplete/operator.py#L139), and creates corresponding `AtomNumber` objects to hold densities through time.
However, when the previous `ResultsList` is created with `ResultsList("depletion_results.h5")`, all MPI processes essentially share this object with knowledge of all materials, with no distribution. This is passed [directly on to the operator](https://github.com/openmc-dev/openmc/blob/develop/openmc/deplete/operator.py#L123-L128). At the start of the depletion routine, the initial concentrations are taken [directly from the operator](https://github.com/openmc-dev/openmc/blob/a7d4dc0d5c4dd3546ad9e9c3b392f7c6ab7b3d9e/openmc/deplete/integrator/cecm.py#L82). This puts all the processes in charge of depleting all materials, and then passing concentrations through `operator.__call__` to the `AtomNumber` objects, which are configured to only handle process-specific materials.
## Possible fixes
1) `ResultsList.__init__` handles the distribution, with a unique instance on each process, and these are passed directly to the `Operator`, or
2) When previous results are passed into `Operator`s, they distribute and create process-specific `prev_results` attributes.
My preference would be for path 2, because the `ResultsList` is not aware of what materials an `operator` may need at initialization.
Yes, I agree option 2 sounds better.
The cause of the error is the distribution (or lack there of) of the previous results to multiple operators on different MPI processes.
Each operator/process [knows it's particular materials to deplete](https://github.com/openmc-dev/openmc/blob/a7d4dc0d5c4dd3546ad9e9c3b392f7c6ab7b3d9e/openmc/deplete/operator.py#L139), and creates corresponding `AtomNumber` objects to hold densities through time.
However, when the previous `ResultsList` is created with `ResultsList("depletion_results.h5")`, all MPI processes essentially share this object with knowledge of all materials, with no distribution. This is passed [directly on to the operator](https://github.com/openmc-dev/openmc/blob/develop/openmc/deplete/operator.py#L123-L128). At the start of the depletion routine, the initial concentrations are taken [directly from the operator](https://github.com/openmc-dev/openmc/blob/a7d4dc0d5c4dd3546ad9e9c3b392f7c6ab7b3d9e/openmc/deplete/integrator/cecm.py#L82). This puts all the processes in charge of depleting all materials, and then passing concentrations through `operator.__call__` to the `AtomNumber` objects, which are configured to only handle process-specific materials.
## Possible fixes
1) `ResultsList.__init__` handles the distribution, with a unique instance on each process, and these are passed directly to the `Operator`, or
2) When previous results are passed into `Operator`s, they distribute and create process-specific `prev_results` attributes.
My preference would be for path 2, because the `ResultsList` is not aware of what materials an `operator` may need at initialization.
Yes, I agree option 2 sounds better. | 2019-08-05T21:34:19Z | [] | [] |
openmc-dev/openmc | 1,313 | openmc-dev__openmc-1313 | [
"1263"
] | 83028b8dcd810ed727102f7efdffba5254229d0f | diff --git a/openmc/deplete/_matrix_funcs.py b/openmc/deplete/_matrix_funcs.py
--- a/openmc/deplete/_matrix_funcs.py
+++ b/openmc/deplete/_matrix_funcs.py
@@ -1,77 +1,78 @@
"""Functions to form the special matrix for depletion"""
-def celi_f1(chain, rates):
- return (5 / 12 * chain.form_matrix(rates[0])
- + 1 / 12 * chain.form_matrix(rates[1]))
+def celi_f1(chain, rates, fission_yields=None):
+ return (5 / 12 * chain.form_matrix(rates[0], fission_yields)
+ + 1 / 12 * chain.form_matrix(rates[1], fission_yields))
-def celi_f2(chain, rates):
- return (1 / 12 * chain.form_matrix(rates[0])
- + 5 / 12 * chain.form_matrix(rates[1]))
+def celi_f2(chain, rates, fission_yields=None):
+ return (1 / 12 * chain.form_matrix(rates[0], fission_yields)
+ + 5 / 12 * chain.form_matrix(rates[1], fission_yields))
-def cf4_f1(chain, rates):
- return 1 / 2 * chain.form_matrix(rates)
+def cf4_f1(chain, rates, fission_yields=None):
+ return 1 / 2 * chain.form_matrix(rates, fission_yields)
-def cf4_f2(chain, rates):
- return -1 / 2 * chain.form_matrix(rates[0]) + chain.form_matrix(rates[1])
+def cf4_f2(chain, rates, fission_yields=None):
+ return (-1 / 2 * chain.form_matrix(rates[0], fission_yields)
+ + chain.form_matrix(rates[1], fission_yields))
-def cf4_f3(chain, rates):
- return (1 / 4 * chain.form_matrix(rates[0])
- + 1 / 6 * chain.form_matrix(rates[1])
- + 1 / 6 * chain.form_matrix(rates[2])
- - 1 / 12 * chain.form_matrix(rates[3]))
+def cf4_f3(chain, rates, fission_yields=None):
+ return (1 / 4 * chain.form_matrix(rates[0], fission_yields)
+ + 1 / 6 * chain.form_matrix(rates[1], fission_yields)
+ + 1 / 6 * chain.form_matrix(rates[2], fission_yields)
+ - 1 / 12 * chain.form_matrix(rates[3], fission_yields))
-def cf4_f4(chain, rates):
- return (-1 / 12 * chain.form_matrix(rates[0])
- + 1 / 6 * chain.form_matrix(rates[1])
- + 1 / 6 * chain.form_matrix(rates[2])
- + 1 / 4 * chain.form_matrix(rates[3]))
+def cf4_f4(chain, rates, fission_yields=None):
+ return (-1 / 12 * chain.form_matrix(rates[0], fission_yields)
+ + 1 / 6 * chain.form_matrix(rates[1], fission_yields)
+ + 1 / 6 * chain.form_matrix(rates[2], fission_yields)
+ + 1 / 4 * chain.form_matrix(rates[3], fission_yields))
-def rk4_f1(chain, rates):
- return 1 / 2 * chain.form_matrix(rates)
+def rk4_f1(chain, rates, fission_yields=None):
+ return 1 / 2 * chain.form_matrix(rates, fission_yields)
-def rk4_f4(chain, rates):
- return (1 / 6 * chain.form_matrix(rates[0])
- + 1 / 3 * chain.form_matrix(rates[1])
- + 1 / 3 * chain.form_matrix(rates[2])
- + 1 / 6 * chain.form_matrix(rates[3]))
+def rk4_f4(chain, rates, fission_yields=None):
+ return (1 / 6 * chain.form_matrix(rates[0], fission_yields)
+ + 1 / 3 * chain.form_matrix(rates[1], fission_yields)
+ + 1 / 3 * chain.form_matrix(rates[2], fission_yields)
+ + 1 / 6 * chain.form_matrix(rates[3], fission_yields))
-def leqi_f1(chain, inputs):
- f1 = chain.form_matrix(inputs[0])
- f2 = chain.form_matrix(inputs[1])
+def leqi_f1(chain, inputs, fission_yields):
+ f1 = chain.form_matrix(inputs[0], fission_yields)
+ f2 = chain.form_matrix(inputs[1], fission_yields)
dt_l, dt = inputs[2], inputs[3]
return -dt / (12 * dt_l) * f1 + (dt + 6 * dt_l) / (12 * dt_l) * f2
-def leqi_f2(chain, inputs):
- f1 = chain.form_matrix(inputs[0])
- f2 = chain.form_matrix(inputs[1])
+def leqi_f2(chain, inputs, fission_yields=None):
+ f1 = chain.form_matrix(inputs[0], fission_yields)
+ f2 = chain.form_matrix(inputs[1], fission_yields)
dt_l, dt = inputs[2], inputs[3]
return -5 * dt / (12 * dt_l) * f1 + (5 * dt + 6 * dt_l) / (12 * dt_l) * f2
-def leqi_f3(chain, inputs):
- f1 = chain.form_matrix(inputs[0])
- f2 = chain.form_matrix(inputs[1])
- f3 = chain.form_matrix(inputs[2])
+def leqi_f3(chain, inputs, fission_yields=None):
+ f1 = chain.form_matrix(inputs[0], fission_yields)
+ f2 = chain.form_matrix(inputs[1], fission_yields)
+ f3 = chain.form_matrix(inputs[2], fission_yields)
dt_l, dt = inputs[3], inputs[4]
return (-dt ** 2 / (12 * dt_l * (dt + dt_l)) * f1
+ (dt ** 2 + 6 * dt * dt_l + 5 * dt_l ** 2)
/ (12 * dt_l * (dt + dt_l)) * f2 + dt_l / (12 * (dt + dt_l)) * f3)
-def leqi_f4(chain, inputs):
- f1 = chain.form_matrix(inputs[0])
- f2 = chain.form_matrix(inputs[1])
- f3 = chain.form_matrix(inputs[2])
+def leqi_f4(chain, inputs, fission_yields=None):
+ f1 = chain.form_matrix(inputs[0], fission_yields)
+ f2 = chain.form_matrix(inputs[1], fission_yields)
+ f3 = chain.form_matrix(inputs[2], fission_yields)
dt_l, dt = inputs[3], inputs[4]
return (-dt ** 2 / (12 * dt_l * (dt + dt_l)) * f1
+ (dt ** 2 + 2 * dt * dt_l + dt_l ** 2)
diff --git a/openmc/deplete/abc.py b/openmc/deplete/abc.py
--- a/openmc/deplete/abc.py
+++ b/openmc/deplete/abc.py
@@ -13,10 +13,11 @@
from warnings import warn
from numbers import Real, Integral
-from numpy import nonzero, empty
+from numpy import nonzero, empty, asarray
from uncertainties import ufloat
from openmc.data import DataLibrary, JOULE_PER_EV
+from openmc.capi import MaterialFilter, Tally
from openmc.checkvalue import check_type, check_greater_than
from .results import Results
from .chain import Chain
@@ -364,6 +365,217 @@ def nuclides(self, nuclides):
self._nuclides = nuclides
+class FissionYieldHelper(ABC):
+ """Abstract class for processing energy dependent fission yields
+
+ Parameters
+ ----------
+ chain_nuclides : iterable of openmc.deplete.Nuclide
+ Nuclides tracked in the depletion chain. All nuclides are
+ not required to have fission yield data.
+
+ Attributes
+ ----------
+ constant_yields : dict of str to :class:`openmc.deplete.FissionYield`
+ Fission yields for all nuclides that only have one set of
+ fission yield data. Can be accessed as ``{parent: {product: yield}}``
+ """
+
+ def __init__(self, chain_nuclides):
+ self._chain_nuclides = {}
+ self._constant_yields = {}
+
+ # Get all nuclides with fission yield data
+ for nuc in chain_nuclides:
+ if nuc.yield_data is None:
+ continue
+ if len(nuc.yield_data) == 1:
+ self._constant_yields[nuc.name] = (
+ nuc.yield_data[nuc.yield_energies[0]])
+ elif len(nuc.yield_data) > 1:
+ self._chain_nuclides[nuc.name] = nuc
+ self._chain_set = set(self._chain_nuclides) | set(self._constant_yields)
+
+ @property
+ def constant_yields(self):
+ return deepcopy(self._constant_yields)
+
+ @abstractmethod
+ def weighted_yields(self, local_mat_index):
+ """Return fission yields for a specific material
+
+ Parameters
+ ----------
+ local_mat_index : int
+ Index for material tracked on this process that
+ exists in :attr:`local_mat_index` and fits within
+ the first axis in :attr:`results`
+
+ Returns
+ -------
+ library : dict
+ Dictionary of ``{parent: {product: fyield}}``
+ """
+
+ @staticmethod
+ def unpack():
+ """Unpack tally data prior to compute fission yields.
+
+ Called after a :meth:`openmc.deplete.Operator.__call__`
+ routine during the normalization of reaction rates.
+
+ Not necessary for all subclasses to implement, unless tallies
+ are used.
+ """
+
+ @staticmethod
+ def generate_tallies(materials, mat_indexes):
+ """Construct tallies necessary for computing fission yields
+
+ Called during the operator set up phase prior to depleting.
+ Not necessary for subclasses to implement
+
+ Parameters
+ ----------
+ materials : iterable of C-API materials
+ Materials to be used in :class:`openmc.capi.MaterialFilter`
+ mat_indexes : iterable of int
+ Indices of tallied materials that will have their fission
+ yields computed by this helper. Necessary as the
+ :class:`openmc.deplete.Operator` that uses this helper
+ may only burn a subset of all materials when running
+ in parallel mode.
+ """
+
+ def update_tally_nuclides(self, nuclides):
+ """Return nuclides with non-zero densities and yield data
+
+ Parameters
+ ----------
+ nuclides : iterable of str
+ Nuclides with non-zero densities from the
+ :class:`openmc.deplete.Operator`
+
+ Returns
+ -------
+ nuclides : list of str
+ Union of nuclides that the :class:`openmc.deplete.Operator`
+ says have non-zero densities at this stage and those that
+ have yield data. Sorted by nuclide name
+
+ """
+ return sorted(self._chain_set & set(nuclides))
+
+ @classmethod
+ def from_operator(cls, operator, **kwargs):
+ """Create a new instance by pulling data from the operator
+
+ All keyword arguments should be identical to their counterpart
+ in the main ``__init__`` method
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator with a depletion chain
+ kwargs: optional
+ Additional keyword arguments to be used in constuction
+ """
+ return cls(operator.chain.nuclides, **kwargs)
+
+
+class TalliedFissionYieldHelper(FissionYieldHelper):
+ """Abstract class for computing fission yields with tallies
+
+ Generates a basic fission rate tally in all burnable materials with
+ :meth:`generate_tallies`, and set nuclides to be tallied with
+ :meth:`update_tally_nuclides`. Subclasses will need to implement
+ :meth:`unpack` and :meth:`weighted_yields`.
+
+ Parameters
+ ----------
+ chain_nuclides : iterable of openmc.deplete.Nuclide
+ Nuclides tracked in the depletion chain. Not necessary
+ that all have yield data.
+
+ Attributes
+ ----------
+ constant_yields : dict of str to :class:`openmc.deplete.FissionYield`
+ Fission yields for all nuclides that only have one set of
+ fission yield data. Can be accessed as ``{parent: {product: yield}}``
+ results : None or numpy.ndarray
+ Tally results shaped in a manner useful to this helper.
+ """
+
+ _upper_energy = 20.0e6 # upper energy for tallies
+
+ def __init__(self, chain_nuclides):
+ super().__init__(chain_nuclides)
+ self._local_indexes = None
+ self._fission_rate_tally = None
+ self._tally_nucs = []
+ self.results = None
+
+ def generate_tallies(self, materials, mat_indexes):
+ """Construct the fission rate tally
+
+ Parameters
+ ----------
+ materials : iterable of :class:`openmc.capi.Material`
+ Materials to be used in :class:`openmc.capi.MaterialFilter`
+ mat_indexes : iterable of int
+ Indices of tallied materials that will have their fission
+ yields computed by this helper. Necessary as the
+ :class:`openmc.deplete.Operator` that uses this helper
+ may only burn a subset of all materials when running
+ in parallel mode.
+ """
+ self._local_indexes = asarray(mat_indexes)
+
+ # Tally group-wise fission reaction rates
+ self._fission_rate_tally = Tally()
+ self._fission_rate_tally.scores = ['fission']
+
+ self._fission_rate_tally.filters = [MaterialFilter(materials)]
+
+ def update_tally_nuclides(self, nuclides):
+ """Tally nuclides with non-zero density and multiple yields
+
+ Must be run after :meth:`generate_tallies`.
+
+ Parameters
+ ----------
+ nuclides : iterable of str
+ Potential nuclides to be tallied, such as those with
+ non-zero density at this stage.
+
+ Returns
+ -------
+ nuclides : list of str
+ Union of input nuclides and those that have multiple sets
+ of yield data. Sorted by nuclide name
+
+ Raises
+ ------
+ AttributeError
+ If tallies not generated
+ """
+ assert self._fission_rate_tally is not None, (
+ "Run generate_tallies first")
+ overlap = set(self._chain_nuclides).intersection(set(nuclides))
+ nuclides = sorted(overlap)
+ self._tally_nucs = [self._chain_nuclides[n] for n in nuclides]
+ self._fission_rate_tally.nuclides = nuclides
+ return nuclides
+
+ @abstractmethod
+ def unpack(self):
+ """Unpack tallies after a transport run.
+
+ Abstract because each subclass will need to arrange its
+ tally data.
+ """
+
+
class Integrator(ABC):
"""Abstract class for solving the time-integration for depletion
diff --git a/openmc/deplete/chain.py b/openmc/deplete/chain.py
--- a/openmc/deplete/chain.py
+++ b/openmc/deplete/chain.py
@@ -9,12 +9,13 @@
import math
import re
from collections import OrderedDict, defaultdict
-from collections.abc import Mapping
+from collections.abc import Mapping, Iterable
from numbers import Real
from warnings import warn
from openmc.checkvalue import check_type, check_greater_than
from openmc.data import gnd_name, zam
+from .nuclide import FissionYieldDistribution
# Try to use lxml if it is available. It preserves the order of attributes and
# provides a pretty-printer by default. If not available,
@@ -136,12 +137,22 @@ class Chain(object):
Reactions that are tracked in the depletion chain
nuclide_dict : OrderedDict of str to int
Maps a nuclide name to an index in nuclides.
+ fission_yields : None or iterable of dict
+ List of effective fission yields for materials. Each dictionary
+ should be of the form ``{parent: {product: yield}}`` with
+ types ``{str: {str: float}}``, where ``yield`` is the fission product
+ yield for isotope ``parent`` producing isotope ``product``.
+ A single entry indicates yields are constant across all materials.
+ Otherwise, an entry can be added for each material to be burned.
+ Ordering should be identical to how the operator orders reaction
+ rates for burnable materials.
"""
def __init__(self):
self.nuclides = []
self.reactions = []
self.nuclide_dict = OrderedDict()
+ self._fission_yields = None
def __contains__(self, nuclide):
return nuclide in self.nuclide_dict
@@ -209,8 +220,7 @@ def from_endf(cls, decay_files, fpy_files, neutron_files):
for idx, parent in enumerate(sorted(decay_data, key=openmc.data.zam)):
data = decay_data[parent]
- nuclide = Nuclide()
- nuclide.name = parent
+ nuclide = Nuclide(parent)
chain.nuclides.append(nuclide)
chain.nuclide_dict[parent] = idx
@@ -225,7 +235,8 @@ def from_endf(cls, decay_files, fpy_files, neutron_files):
if mode.daughter in decay_data:
target = mode.daughter
else:
- print('missing {} {} {}'.format(parent, ','.join(mode.modes), mode.daughter))
+ print('missing {} {} {}'.format(
+ parent, ','.join(mode.modes), mode.daughter))
target = replace_missing(mode.daughter, decay_data)
# Write branching ratio, taking care to ensure sum is unity
@@ -279,15 +290,16 @@ def from_endf(cls, decay_files, fpy_files, neutron_files):
fpy = fpy_data[parent]
if fpy.energies is not None:
- nuclide.yield_energies = fpy.energies
+ yield_energies = fpy.energies
else:
- nuclide.yield_energies = [0.0]
+ yield_energies = [0.0]
- for E, table in zip(nuclide.yield_energies, fpy.independent):
+ yield_data = {}
+ for E, table in zip(yield_energies, fpy.independent):
yield_replace = 0.0
yields = defaultdict(float)
for product, y in table.items():
- # Handle fission products that have no decay data available
+ # Handle fission products that have no decay data
if product not in decay_data:
daughter = replace_missing(product, decay_data)
product = daughter
@@ -297,10 +309,9 @@ def from_endf(cls, decay_files, fpy_files, neutron_files):
if yield_replace > 0.0:
missing_fp.append((parent, E, yield_replace))
+ yield_data[E] = yields
- nuclide.yield_data[E] = []
- for k in sorted(yields, key=openmc.data.zam):
- nuclide.yield_data[E].append((k, yields[k]))
+ nuclide.yield_data = FissionYieldDistribution(yield_data)
# Display warnings
if missing_daughter:
@@ -387,23 +398,56 @@ def export_to_xml(self, filename):
clean_indentation(root_elem)
tree.write(str(filename), encoding='utf-8')
- def form_matrix(self, rates):
+ def get_thermal_fission_yields(self):
+ """Return fission yields at lowest incident neutron energy
+
+ Used as the default set of fission yields for :meth:`form_matrix`
+ if ``fission_yields`` are not provided
+
+ Returns
+ -------
+ fission_yields : dict
+ Dictionary of ``{parent: {product: f_yield}}``
+ where ``parent`` and ``product`` are both string
+ names of nuclides with yield data and ``f_yield``
+ is a float for the fission yield.
+ """
+ out = {}
+ for nuc in self.nuclides:
+ if nuc.yield_data is None:
+ continue
+ yield_obj = nuc.yield_data[min(nuc.yield_energies)]
+ out[nuc.name] = dict(yield_obj)
+ return out
+
+ def form_matrix(self, rates, fission_yields=None):
"""Forms depletion matrix.
Parameters
----------
rates : numpy.ndarray
2D array indexed by (nuclide, reaction)
+ fission_yields : dict, optional
+ Option to use a custom set of fission yields. Expected
+ to be of the form ``{parent : {product : f_yield}}``
+ with string nuclide names for ``parent`` and ``product``,
+ and ``f_yield`` as the respective fission yield
Returns
-------
scipy.sparse.csr_matrix
Sparse matrix representing depletion.
+ See Also
+ --------
+ :meth:`get_thermal_fission_yields`
"""
matrix = defaultdict(float)
reactions = set()
+ if fission_yields is None:
+ fission_yields = self.get_thermal_fission_yields()
+
for i, nuc in enumerate(self.nuclides):
if nuc.n_decay_modes != 0:
@@ -448,11 +492,7 @@ def form_matrix(self, rates):
k = self.nuclide_dict[target]
matrix[k, i] += path_rate * br
else:
- # Assume that we should always use thermal fission
- # yields. At some point it would be nice to account
- # for the energy-dependence..
- energy, data = sorted(nuc.yield_data.items())[0]
- for product, y in data:
+ for product, y in fission_yields[nuc.name].items():
yield_val = y * path_rate
if yield_val != 0.0:
k = self.nuclide_dict[product]
@@ -678,6 +718,20 @@ def set_branch_ratios(self, branch_ratios, reaction="(n,gamma)",
parent.reactions.append(ReactionTuple(
reaction, ground_tgt, rxn_Q, ground_br))
+ @property
+ def fission_yields(self):
+ if self._fission_yields is None:
+ self._fission_yields = [self.get_thermal_fission_yields()]
+ return self._fission_yields
+
+ @fission_yields.setter
+ def fission_yields(self, yields):
+ if yields is not None:
+ if isinstance(yields, Mapping):
+ yields = [yields]
+ check_type("fission_yields", yields, Iterable, Mapping)
+ self._fission_yields = yields
+
def validate(self, strict=True, quiet=False, tolerance=1e-4):
"""Search for possible inconsistencies
diff --git a/openmc/deplete/cram.py b/openmc/deplete/cram.py
--- a/openmc/deplete/cram.py
+++ b/openmc/deplete/cram.py
@@ -30,7 +30,9 @@ def deplete(chain, x, rates, dt, matrix_func=None):
dt : float
Time in [s] to deplete for
maxtrix_func : Callable, optional
- Function of two variables: ``chain`` and ``rates``.
+ Function to form the depletion matrix after calling
+ ``matrix_func(chain, rates, fission_yields)``, where
+ ``fission_yields = {parent: {product: yield_frac}}``
Expected to return the depletion matrix required by
:func:`CRAM48`.
@@ -40,9 +42,19 @@ def deplete(chain, x, rates, dt, matrix_func=None):
Updated atom number vectors for each material
"""
+ fission_yields = chain.fission_yields
+ if len(fission_yields) == 1:
+ fission_yields = repeat(fission_yields[0])
+ elif len(fission_yields) != len(x):
+ raise ValueError(
+ "Number of material fission yield distributions {} is not equal "
+ "to the number of compositions {}".format(len(fission_yields),
+ len(x)))
+
# Use multiprocessing pool to distribute work
with Pool() as pool:
- iters = zip(repeat(chain), x, rates, repeat(dt), repeat(matrix_func))
+ iters = zip(repeat(chain), x, rates, repeat(dt),
+ fission_yields, repeat(matrix_func))
x_result = list(pool.starmap(_cram_wrapper, iters))
return x_result
@@ -67,7 +79,7 @@ def timed_deplete(*args, **kwargs):
return time.time() - start, results
-def _cram_wrapper(chain, n0, rates, dt, matrix_func=None):
+def _cram_wrapper(chain, n0, rates, dt, fission_yields, matrix_func=None):
"""Wraps depletion matrix creation / CRAM solve for multiprocess execution
Parameters
@@ -82,6 +94,9 @@ def _cram_wrapper(chain, n0, rates, dt, matrix_func=None):
Time to integrate to.
maxtrix_func : function, optional
Function to form the depletion matrix
+ fission_yields : dict
+ Single-energy fission yields of the form
+ ``{parent: {product: fission_yield}}``
Returns
-------
@@ -90,9 +105,9 @@ def _cram_wrapper(chain, n0, rates, dt, matrix_func=None):
"""
if matrix_func is None:
- A = chain.form_matrix(rates)
+ A = chain.form_matrix(rates, fission_yields)
else:
- A = matrix_func(chain, rates)
+ A = matrix_func(chain, rates, fission_yields)
return CRAM48(A, n0, dt)
diff --git a/openmc/deplete/helpers.py b/openmc/deplete/helpers.py
--- a/openmc/deplete/helpers.py
+++ b/openmc/deplete/helpers.py
@@ -1,12 +1,24 @@
"""
Class for normalizing fission energy deposition
"""
+from copy import deepcopy
from itertools import product
+from numbers import Real
+import bisect
-from numpy import dot, zeros
+from numpy import dot, zeros, newaxis
-from openmc.capi import Tally, MaterialFilter
-from .abc import ReactionRateHelper, EnergyHelper
+from openmc.checkvalue import check_type, check_greater_than
+from openmc.capi import (
+ Tally, MaterialFilter, EnergyFilter, EnergyFunctionFilter)
+from .abc import (
+ ReactionRateHelper, EnergyHelper, FissionYieldHelper,
+ TalliedFissionYieldHelper)
+
+__all__ = (
+ "DirectReactionRateHelper", "ChainFissionHelper",
+ "ConstantFissionYieldHelper", "FissionYieldCutoffHelper",
+ "AveragedFissionYieldHelper")
# -------------------------------------
# Helpers for generating reaction rates
@@ -142,3 +154,465 @@ def update(self, fission_rates, _mat_index):
isotopes in all materials have the same Q value.
"""
self._energy += dot(fission_rates, self._fission_q_vector)
+
+
+# ------------------------------------
+# Helper for collapsing fission yields
+# ------------------------------------
+
+
+class ConstantFissionYieldHelper(FissionYieldHelper):
+ """Class that uses a single set of fission yields on each isotope
+
+ Parameters
+ ----------
+ chain_nuclides : iterable of openmc.deplete.Nuclide
+ Nuclides tracked in the depletion chain. All nuclides are
+ not required to have fission yield data.
+ energy : float, optional
+ Key in :attr:`openmc.deplete.Nuclide.yield_data` corresponding
+ to the desired set of fission yield data. Typically one of
+ ``{0.0253, 500000, 14000000}`` corresponding to 0.0253 eV,
+ 500 keV, and 14 MeV yield libraries. If the specific key is not
+ found, will fall back to closest energy present.
+ Default: 0.0253 eV for thermal yields
+
+ Attributes
+ ----------
+ constant_yields : dict of str to :class:`openmc.deplete.FissionYield`
+ Fission yields for all nuclides that only have one set of
+ fission yield data. Can be accessed as ``{parent: {product: yield}}``
+ energy : float
+ Energy of fission yield libraries.
+ """
+
+ def __init__(self, chain_nuclides, energy=0.0253):
+ check_type("energy", energy, Real)
+ check_greater_than("energy", energy, 0.0, equality=True)
+ self._energy = energy
+ super().__init__(chain_nuclides)
+ # Iterate over all nuclides with > 1 set of yields
+ for name, nuc in self._chain_nuclides.items():
+ yield_data = nuc.yield_data.get(energy)
+ if yield_data is not None:
+ self._constant_yields[name] = yield_data
+ continue
+ # Specific energy not found, use closest energy
+ distances = [abs(energy - ene) for ene in nuc.yield_energies]
+ min_E = min(nuc.yield_energies, key=lambda e: abs(e - energy))
+ self._constant_yields[name] = nuc.yield_data[min_E]
+
+ @classmethod
+ def from_operator(cls, operator, **kwargs):
+ """Return a new ConstantFissionYieldHelper using operator data
+
+ All keyword arguments should be identical to their counterpart
+ in the main ``__init__`` method
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ operator with a depletion chain
+ kwargs:
+ Additional keyword arguments to be used in construction
+
+ Returns
+ -------
+ ConstantFissionYieldHelper
+ """
+ return cls(operator.chain.nuclides, **kwargs)
+
+ @property
+ def energy(self):
+ return self._energy
+
+ def weighted_yields(self, _local_mat_index=None):
+ """Return fission yields for all nuclides requested
+
+ Parameters
+ ----------
+ _local_mat_index : int, optional
+ Current material index. Not used since all yields are
+ constant
+
+ Returns
+ -------
+ library : dict
+ Dictionary of ``{parent: {product: fyield}}``
+ """
+ return self.constant_yields
+
+
+class FissionYieldCutoffHelper(TalliedFissionYieldHelper):
+ """Helper that computes fission yields based on a cutoff energy
+
+ Tally fission rates above and below the cutoff energy.
+ Assume that all fissions below cutoff energy have use thermal fission
+ product yield distributions, while all fissions above use a faster
+ set of yield distributions.
+
+ Uses a limit of 20 MeV for tallying fission.
+
+ Parameters
+ ----------
+ chain_nuclides : iterable of openmc.deplete.Nuclide
+ Nuclides tracked in the depletion chain. All nuclides are
+ not required to have fission yield data.
+ n_bmats : int, optional
+ Number of burnable materials tracked in the problem
+ cutoff : float, optional
+ Cutoff energy in [eV] below which all fissions will be
+ use thermal yields. All other fissions will use a
+ faster set of yields. Default: 112 [eV]
+ thermal_energy : float, optional
+ Energy of yield data corresponding to thermal yields.
+ Default: 0.0253 [eV]
+ fast_energy : float, optional
+ Energy of yield data corresponding to fast yields.
+ Default: 500 [kev]
+
+ Attributes
+ ----------
+ n_bmats : int
+ Number of burnable materials tracked in the problem.
+ Must be set prior to generating tallies
+ thermal_yields : dict
+ Dictionary of the form ``{parent: {product: yield}}``
+ with thermal yields
+ fast_yields : dict
+ Dictionary of the form ``{parent: {product: yield}}``
+ with fast yields
+ results : numpy.ndarray
+ Array of fission rate fractions with shape
+ ``(n_mats, 2, n_nucs)``. ``results[:, 0]``
+ corresponds to the fraction of all fissions
+ that occured below ``cutoff``. The number
+ of materials in the first axis corresponds
+ to the number of materials burned by the
+ :class:`openmc.deplete.Operator`
+ """
+
+ def __init__(self, chain_nuclides, n_bmats, cutoff=112.0,
+ thermal_energy=0.0253, fast_energy=500.0e3):
+ check_type("cutoff", cutoff, Real)
+ check_type("thermal_energy", thermal_energy, Real)
+ check_type("fast_energy", fast_energy, Real)
+ check_greater_than("thermal_energy", thermal_energy, 0.0, equality=True)
+ check_greater_than("cutoff", cutoff, thermal_energy, equality=False)
+ check_greater_than("fast_energy", fast_energy, cutoff, equality=False)
+ self.n_bmats = n_bmats
+ super().__init__(chain_nuclides)
+ self._cutoff = cutoff
+ self._thermal_yields = {}
+ self._fast_yields = {}
+ convert_to_constant = set()
+ for name, nuc in self._chain_nuclides.items():
+ yields = nuc.yield_data
+ energies = nuc.yield_energies
+ thermal = yields.get(thermal_energy)
+ fast = yields.get(fast_energy)
+ if thermal is None or fast is None:
+ if cutoff <= energies[0]:
+ # use lowest energy yields as constant
+ self._constant_yields[name] = yields[energies[0]]
+ convert_to_constant.add(name)
+ continue
+ if cutoff >= energies[-1]:
+ # use highest energy yields as constant
+ self._constant_yields[name] = yields[energies[-1]]
+ convert_to_constant.add(name)
+ continue
+ cutoff_ix = bisect.bisect_left(energies, cutoff)
+ # find closest energy to requested thermal, fast energies
+ if thermal is None:
+ min_E = min(energies[:cutoff_ix],
+ key=lambda e: abs(e - thermal_energy))
+ thermal = yields[min_E]
+ if fast is None:
+ min_E = min(energies[cutoff_ix:],
+ key=lambda e: abs(e - fast_energy))
+ fast = yields[min_E]
+ self._thermal_yields[name] = thermal
+ self._fast_yields[name] = fast
+ for name in convert_to_constant:
+ self._chain_nuclides.pop(name)
+
+ @classmethod
+ def from_operator(cls, operator, **kwargs):
+ """Construct a helper from an operator
+
+ All keyword arguments should be identical to their counterpart
+ in the main ``__init__`` method
+
+ Parameters
+ ----------
+ operator : openmc.deplete.Operator
+ Operator with a chain and burnable materials
+ kwargs:
+ Additional keyword arguments to be used in construction
+
+ Returns
+ -------
+ FissionYieldCutoffHelper
+
+ """
+ return cls(operator.chain.nuclides, len(operator.burnable_mats),
+ **kwargs)
+
+ def generate_tallies(self, materials, mat_indexes):
+ """Use C API to produce a fission rate tally in burnable materials
+
+ Include a :class:`openmc.capi.EnergyFilter` to tally fission rates
+ above and below cutoff energy.
+
+ Parameters
+ ----------
+ materials : iterable of :class:`openmc.capi.Material`
+ Materials to be used in :class:`openmc.capi.MaterialFilter`
+ mat_indexes : iterable of int
+ Indices of tallied materials that will have their fission
+ yields computed by this helper. Necessary as the
+ :class:`openmc.deplete.Operator` that uses this helper
+ may only burn a subset of all materials when running
+ in parallel mode.
+ """
+ super().generate_tallies(materials, mat_indexes)
+ energy_filter = EnergyFilter([0.0, self._cutoff, self._upper_energy])
+ self._fission_rate_tally.filters = (
+ self._fission_rate_tally.filters + [energy_filter])
+
+ def unpack(self):
+ """Obtain fast and thermal fission fractions from tally"""
+ if not self._tally_nucs:
+ self.results = None
+ return
+ fission_rates = self._fission_rate_tally.results[..., 1].reshape(
+ self.n_bmats, 2, len(self._tally_nucs))
+ self.results = fission_rates[self._local_indexes]
+ total_fission = self.results.sum(axis=1)
+ nz_mat, nz_nuc = total_fission.nonzero()
+ self.results[nz_mat, :, nz_nuc] /= total_fission[nz_mat, newaxis, nz_nuc]
+
+ def weighted_yields(self, local_mat_index):
+ """Return fission yields for a specific material
+
+ For nuclides with both yield data above and below
+ the cutoff energy, the effective yield for nuclide ``A``
+ will be a weighted sum of fast and thermal yields. The
+ weights will be the fraction of ``A`` fission events
+ in the above and below the cutoff energy.
+
+ If ``A`` has fission product distribution ``F``
+ for fast fissions and ``T`` for thermal fissions, and
+ 70% of ``A`` fissions are considered thermal, then
+ the effective fission product yield distributions
+ for ``A`` is ``0.7 * T + 0.3 * F``
+
+ Parameters
+ ----------
+ local_mat_index : int
+ Index for specific burnable material. Effective
+ yields will be produced using
+ ``self.results[local_mat_index]``
+
+ Returns
+ -------
+ library : dict
+ Dictionary of ``{parent: {product: fyield}}``
+ """
+ yields = self.constant_yields
+ if not self._tally_nucs:
+ return yields
+ rates = self.results[local_mat_index]
+ # iterate over thermal then fast yields, prefer __mul__ to __rmul__
+ for therm_frac, fast_frac, nuc in zip(rates[0], rates[1], self._tally_nucs):
+ yields[nuc.name] = (self._thermal_yields[nuc.name] * therm_frac
+ + self._fast_yields[nuc.name] * fast_frac)
+ return yields
+
+ @property
+ def thermal_yields(self):
+ return deepcopy(self._thermal_yields)
+
+ @property
+ def fast_yields(self):
+ return deepcopy(self._fast_yields)
+
+
+class AveragedFissionYieldHelper(TalliedFissionYieldHelper):
+ r"""Class that computes fission yields based on average fission energy
+
+ Computes average energy at which fission events occured with
+
+ .. math::
+
+ \bar{E} = \frac{
+ \int_0^\infty E\sigma_f(E)\phi(E)dE
+ }{
+ \int_0^\infty\sigma_f(E)\phi(E)dE
+ }
+
+ If the average energy for a nuclide is below the lowest energy
+ with yield data, that set of fission yields is taken.
+ Conversely, if the average energy is above the highest energy
+ with yield data, that set of fission yields is used.
+ For the case where the average energy is between two sets
+ of yields, the effective fission yield computed by
+ linearly interpolating between yields provided at the
+ nearest energies above and below the average.
+
+ Parameters
+ ----------
+ chain_nuclides : iterable of openmc.deplete.Nuclide
+ Nuclides tracked in the depletion chain. All nuclides are
+ not required to have fission yield data.
+
+ Attributes
+ ----------
+ constant_yields : dict of str to :class:`openmc.deplete.FissionYield`
+ Fission yields for all nuclides that only have one set of
+ fission yield data. Can be accessed as ``{parent: {product: yield}}``
+ results : None or numpy.ndarray
+ If tallies have been generated and unpacked, then the array will
+ have shape ``(n_mats, n_tnucs)``, where ``n_mats`` is the number
+ of materials where fission reactions were tallied and ``n_tnucs``
+ is the number of nuclides with multiple sets of fission yields.
+ Data in the array are the average energy of fission events for
+ tallied nuclides across burnable materials.
+ """
+
+ def __init__(self, chain_nuclides):
+ super().__init__(chain_nuclides)
+ self._weighted_tally = None
+
+ def generate_tallies(self, materials, mat_indexes):
+ """Construct tallies to determine average energy of fissions
+
+ Parameters
+ ----------
+ materials : iterable of :class:`openmc.capi.Material`
+ Materials to be used in :class:`openmc.capi.MaterialFilter`
+ mat_indexes : iterable of int
+ Indices of tallied materials that will have their fission
+ yields computed by this helper. Necessary as the
+ :class:`openmc.deplete.Operator` that uses this helper
+ may only burn a subset of all materials when running
+ in parallel mode.
+ """
+ super().generate_tallies(materials, mat_indexes)
+ fission_tally = self._fission_rate_tally
+ filters = fission_tally.filters
+
+ ene_filter = EnergyFilter([0, self._upper_energy])
+ fission_tally.filters = filters + [ene_filter]
+
+ func_filter = EnergyFunctionFilter()
+ func_filter.set_data((0, self._upper_energy), (0, self._upper_energy))
+ weighted_tally = Tally()
+ weighted_tally.scores = ['fission']
+ weighted_tally.filters = filters + [func_filter]
+ self._weighted_tally = weighted_tally
+
+ def update_tally_nuclides(self, nuclides):
+ """Tally nuclides with non-zero density and multiple yields
+
+ Must be run after :meth:`generate_tallies`.
+
+ Parameters
+ ----------
+ nuclides : iterable of str
+ Potential nuclides to be tallied, such as those with
+ non-zero density at this stage.
+
+ Returns
+ -------
+ nuclides : tuple of str
+ Union of input nuclides and those that have multiple sets
+ of yield data. Sorted by nuclide name
+
+ Raises
+ ------
+ AttributeError
+ If tallies not generated
+ """
+ tally_nucs = super().update_tally_nuclides(nuclides)
+ self._weighted_tally.nuclides = tally_nucs
+ return tally_nucs
+
+ def unpack(self):
+ """Unpack tallies and populate :attr:`results` with average energies"""
+ if not self._tally_nucs:
+ self.results = None
+ return
+ fission_results = (
+ self._fission_rate_tally.results[self._local_indexes, :, 1])
+ self.results = (
+ self._weighted_tally.results[self._local_indexes, :, 1]).copy()
+ nz_mat, nz_nuc = fission_results.nonzero()
+ self.results[nz_mat, nz_nuc] /= fission_results[nz_mat, nz_nuc]
+
+ def weighted_yields(self, local_mat_index):
+ """Return fission yields for a specific material
+
+ Use the computed average energy of fission
+ events to determine fission yields. If average
+ energy is between two sets of yields, linearly
+ interpolate bewteen the two.
+ Otherwise take the closet set of yields.
+
+ Parameters
+ ----------
+ local_mat_index : int
+ Index for specific burnable material. Effective
+ yields will be produced using
+ ``self.results[local_mat_index]``
+
+ Returns
+ -------
+ library : dict
+ Dictionary of ``{parent: {product: fyield}}``
+ """
+ if not self._tally_nucs:
+ return self.constant_yields
+ mat_yields = {}
+ average_energies = self.results[local_mat_index]
+ for avg_e, nuc in zip(average_energies, self._tally_nucs):
+ nuc_energies = nuc.yield_energies
+ if avg_e <= nuc_energies[0]:
+ mat_yields[nuc.name] = nuc.yield_data[nuc_energies[0]]
+ continue
+ if avg_e >= nuc_energies[-1]:
+ mat_yields[nuc.name] = nuc.yield_data[nuc_energies[-1]]
+ continue
+ # in-between two energies
+ # linear search since there are usually ~3 energies
+ for ix, ene in enumerate(nuc_energies[:-1]):
+ if nuc_energies[ix + 1] > avg_e:
+ break
+ lower, upper = nuc_energies[ix:ix + 2]
+ fast_frac = (avg_e - lower) / (upper - lower)
+ mat_yields[nuc.name] = (
+ nuc.yield_data[lower] * (1 - fast_frac)
+ + nuc.yield_data[upper] * fast_frac)
+ mat_yields.update(self.constant_yields)
+ return mat_yields
+
+ @classmethod
+ def from_operator(cls, operator, **kwargs):
+ """Return a new helper with data from an operator
+
+ All keyword arguments should be identical to their counterpart
+ in the main ``__init__`` method
+
+ Parameters
+ ----------
+ operator : openmc.deplete.TransportOperator
+ Operator with a depletion chain
+ kwargs :
+ Additional keyword arguments to be used in construction
+
+ Returns
+ -------
+ AveragedFissionYieldHelper
+ """
+ return cls(operator.chain.nuclides)
diff --git a/openmc/deplete/nuclide.py b/openmc/deplete/nuclide.py
--- a/openmc/deplete/nuclide.py
+++ b/openmc/deplete/nuclide.py
@@ -3,13 +3,20 @@
Contains the per-nuclide components of a depletion chain.
"""
+import bisect
+from collections.abc import Mapping
from collections import namedtuple, defaultdict
from warnings import warn
+from numbers import Real
try:
import lxml.etree as ET
except ImportError:
import xml.etree.ElementTree as ET
+from numpy import empty
+
+from openmc.checkvalue import check_type
+
DecayTuple = namedtuple('DecayTuple', 'type target branching_ratio')
DecayTuple.__doc__ = """\
@@ -62,11 +69,16 @@
class Nuclide(object):
"""Decay modes, reactions, and fission yields for a single nuclide.
+ Parameters
+ ----------
+ name : str, optional
+ GND name of this nuclide, e.g. ``"He4"``, ``"Am242_m1"``
+
Attributes
----------
- name : str
+ name : str or None
Name of nuclide.
- half_life : float
+ half_life : float or None
Half life of nuclide in [s].
decay_energy : float
Energy deposited from decay in [eV].
@@ -80,17 +92,16 @@ class Nuclide(object):
reactions : list of openmc.deplete.ReactionTuple
Reaction information. Each element of the list is a named tuple with
attribute 'type', 'target', 'Q', and 'branching_ratio'.
- yield_data : dict of float to list
- Maps tabulated energy to list of (product, yield) for all
- neutron-induced fission products.
- yield_energies : list of float
- Energies at which fission product yiels exist
-
+ yield_data : FissionYieldDistribution or None
+ Fission product yields at tabulated energies for this nuclide. Can be
+ treated as a nested dictionary ``{energy: {product: yield}}``
+ yield_energies : tuple of float or None
+ Energies at which fission product yields exist
"""
- def __init__(self):
+ def __init__(self, name=None):
# Information about the nuclide
- self.name = None
+ self.name = name
self.half_life = None
self.decay_energy = 0.0
@@ -101,8 +112,7 @@ def __init__(self):
self.reactions = []
# Neutron fission yields, if present
- self.yield_data = {}
- self.yield_energies = []
+ self._yield_data = None
@property
def n_decay_modes(self):
@@ -112,6 +122,29 @@ def n_decay_modes(self):
def n_reaction_paths(self):
return len(self.reactions)
+ @property
+ def yield_data(self):
+ if self._yield_data is None:
+ return None
+ return self._yield_data
+
+ @yield_data.setter
+ def yield_data(self, fission_yields):
+ if fission_yields is None:
+ self._yield_data = None
+ else:
+ check_type("fission_yields", fission_yields, Mapping)
+ if isinstance(fission_yields, FissionYieldDistribution):
+ self._yield_data = fission_yields
+ else:
+ self._yield_data = FissionYieldDistribution(fission_yields)
+
+ @property
+ def yield_energies(self):
+ if self._yield_data is None:
+ return None
+ return self.yield_data.energies
+
@classmethod
def from_xml(cls, element, fission_q=None):
"""Read nuclide from an XML element.
@@ -166,13 +199,7 @@ def from_xml(cls, element, fission_q=None):
fpy_elem = element.find('neutron_fission_yields')
if fpy_elem is not None:
- for yields_elem in fpy_elem.iter('fission_yields'):
- E = float(yields_elem.get('energy'))
- products = yields_elem.find('products').text.split()
- yields = [float(y) for y in
- yields_elem.find('data').text.split()]
- nuc.yield_data[E] = list(zip(products, yields))
- nuc.yield_energies = list(sorted(nuc.yield_data.keys()))
+ nuc.yield_data = FissionYieldDistribution.from_xml_element(fpy_elem)
return nuc
@@ -212,15 +239,7 @@ def to_xml_element(self):
fpy_elem = ET.SubElement(elem, 'neutron_fission_yields')
energy_elem = ET.SubElement(fpy_elem, 'energies')
energy_elem.text = ' '.join(str(E) for E in self.yield_energies)
-
- for E in self.yield_energies:
- yields_elem = ET.SubElement(fpy_elem, 'fission_yields')
- yields_elem.set('energy', str(E))
-
- products_elem = ET.SubElement(yields_elem, 'products')
- products_elem.text = ' '.join(x[0] for x in self.yield_data[E])
- data_elem = ET.SubElement(yields_elem, 'data')
- data_elem.text = ' '.join(str(x[1]) for x in self.yield_data[E])
+ self.yield_data.to_xml_element(fpy_elem)
return elem
@@ -304,8 +323,8 @@ def validate(self, strict=True, quiet=False, tolerance=1e-4):
valid = False
if self.yield_data:
- for energy, yield_list in self.yield_data.items():
- sum_yield = sum(y[1] for y in yield_list)
+ for energy, fission_yield in self.yield_data.items():
+ sum_yield = fission_yield.yields.sum()
stat = 2.0 - tolerance <= sum_yield <= 2.0 + tolerance
if stat:
continue
@@ -321,3 +340,227 @@ def validate(self, strict=True, quiet=False, tolerance=1e-4):
valid = False
return valid
+
+
+class FissionYieldDistribution(Mapping):
+ """Energy-dependent fission product yields for a single nuclide
+
+ Can be used as a dictionary mapping energies and products to fission
+ yields::
+
+ >>> fydist = FissionYieldDistribution{
+ ... {0.0253: {"Xe135": 0.021}})
+ >>> fydist[0.0253]["Xe135"]
+ 0.021
+
+ Parameters
+ ----------
+ fission_yields : dict
+ Dictionary of energies and fission product yields for that energy.
+ Expected to be of the form ``{float: {str: float}}``. The first
+ float is the energy, typically in eV, that represents this
+ distribution. The underlying dictionary maps fission products
+ to their respective yields.
+
+ Attributes
+ ----------
+ energies : tuple
+ Energies for which fission yields exist. Sorted by
+ increasing energy
+ products : tuple
+ Fission products produced at all energies. Sorted by name.
+ yield_matrix : numpy.ndarray
+ Array ``(n_energy, n_products)`` where
+ ``yield_matrix[g, j]`` is the fission yield of product
+ ``j`` for energy group ``g``.
+
+ See Also
+ --------
+ * :meth:`from_xml_element` - Construction methods
+ * :class:`FissionYield` - Class used for storing yields at a given energy
+ """
+
+ def __init__(self, fission_yields):
+ # mapping {energy: {product: value}}
+ energies = sorted(fission_yields)
+
+ # Get a consistent set of products to produce a matrix of yields
+ shared_prod = set.union(*(set(x) for x in fission_yields.values()))
+ ordered_prod = sorted(shared_prod)
+
+ yield_matrix = empty((len(energies), len(shared_prod)))
+
+ for g_index, energy in enumerate(energies):
+ prod_map = fission_yields[energy]
+ for prod_ix, product in enumerate(ordered_prod):
+ yield_val = prod_map.get(product)
+ yield_matrix[g_index, prod_ix] = (
+ 0.0 if yield_val is None else yield_val)
+ self.energies = tuple(energies)
+ self.products = tuple(ordered_prod)
+ self.yield_matrix = yield_matrix
+
+ def __len__(self):
+ return len(self.energies)
+
+ def __getitem__(self, energy):
+ if energy not in self.energies:
+ raise KeyError(energy)
+ return FissionYield(
+ self.products, self.yield_matrix[self.energies.index(energy)])
+
+ def __iter__(self):
+ return iter(self.energies)
+
+ def __repr__(self):
+ return "<{} with {} products at {} energies>".format(
+ self.__class__.__name__, self.yield_matrix.shape[1],
+ len(self.energies))
+
+ @classmethod
+ def from_xml_element(cls, element):
+ """Construct a distribution from a depletion chain xml file
+
+ Parameters
+ ----------
+ element : xml.etree.ElementTree.Element
+ XML element to pull fission yield data from
+
+ Returns
+ -------
+ FissionYieldDistribution
+ """
+ all_yields = {}
+ for elem_index, yield_elem in enumerate(element.iter("fission_yields")):
+ energy = float(yield_elem.get("energy"))
+ products = yield_elem.find("products").text.split()
+ yields = map(float, yield_elem.find("data").text.split())
+ # Get a map of products to their corresponding yield
+ all_yields[energy] = dict(zip(products, yields))
+
+ return cls(all_yields)
+
+ def to_xml_element(self, root):
+ """Write fission yield data to an xml element
+
+ Parameters
+ ----------
+ root : xml.etree.ElementTree.Element
+ Element to write distribution data to
+ """
+ for energy, yield_obj in self.items():
+ yield_element = ET.SubElement(root, "fission_yields")
+ yield_element.set("energy", str(energy))
+ product_elem = ET.SubElement(yield_element, "products")
+ product_elem.text = " ".join(map(str, yield_obj.products))
+ data_elem = ET.SubElement(yield_element, "data")
+ data_elem.text = " ".join(map(str, yield_obj.yields))
+
+
+class FissionYield(Mapping):
+ """Mapping for fission yields of a parent at a specific energy
+
+ Separated to support nested dictionary-like behavior for
+ :class:`FissionYieldDistribution`, and allowing math operations
+ on a single vector of yields. Can in turn be used like a
+ dictionary to fetch fission yields.
+ Supports multiplication of a scalar to scale the fission
+ yields and addition of another set of yields.
+
+ Does not support resizing / inserting new products that do
+ not exist.
+
+ Parameters
+ ----------
+ products : tuple of str
+ Products for this specific distribution
+ yields : numpy.ndarray
+ Fission product yields for each product in ``products``
+
+ Attributes
+ ----------
+ products : tuple of str
+ Products for this specific distribution
+ yields : numpy.ndarray
+ Fission product yields for each product in ``products``
+
+ Examples
+ --------
+ >>> import numpy
+ >>> fy_vector = FissionYield(
+ ... ("Xe135", "I129", "Sm149"),
+ ... numpy.array((0.002, 0.001, 0.0003)))
+ >>> fy_vector["Xe135"]
+ 0.002
+ >>> new = fy_vector.copy()
+ >>> fy_vector *= 2
+ >>> fy_vector["Xe135"]
+ 0.004
+ >>> new["Xe135"]
+ 0.002
+ >>> (new + fy_vector)["Sm149"]
+ 0.0009
+ >>> dict(new)
+ {"Xe135": 0.002, "I129": 0.001, "Sm149": 0.0003}
+ """
+
+ def __init__(self, products, yields):
+ self.products = products
+ self.yields = yields
+
+ def __contains__(self, product):
+ ix = bisect.bisect_left(self.products, product)
+ return ix != len(self.products) and self.products[ix] == product
+
+ def __getitem__(self, product):
+ ix = bisect.bisect_left(self.products, product)
+ if ix == len(self.products) or self.products[ix] != product:
+ raise KeyError(product)
+ return self.yields[ix]
+
+ def __len__(self):
+ return len(self.products)
+
+ def __iter__(self):
+ return iter(self.products)
+
+ def items(self):
+ """Return pairs of product, yield"""
+ return zip(self.products, self.yields)
+
+ def __add__(self, other):
+ if not isinstance(other, FissionYield):
+ return NotImplemented
+ new = FissionYield(self.products, self.yields.copy())
+ new += other
+ return new
+
+ def __iadd__(self, other):
+ """Increment value from other fission yield"""
+ if not isinstance(other, FissionYield):
+ return NotImplemented
+ self.yields += other.yields
+ return self
+
+ def __radd__(self, other):
+ return self + other
+
+ def __imul__(self, scalar):
+ if not isinstance(scalar, Real):
+ return NotImplemented
+ self.yields *= scalar
+ return self
+
+ def __mul__(self, scalar):
+ if not isinstance(scalar, Real):
+ return NotImplemented
+ new = FissionYield(self.products, self.yields.copy())
+ new *= scalar
+ return new
+
+ def __rmul__(self, scalar):
+ return self * scalar
+
+ def __repr__(self):
+ return "<{} containing {} products and yields>".format(
+ self.__class__.__name__, len(self))
diff --git a/openmc/deplete/operator.py b/openmc/deplete/operator.py
--- a/openmc/deplete/operator.py
+++ b/openmc/deplete/operator.py
@@ -25,7 +25,9 @@
from .atom_number import AtomNumber
from .reaction_rates import ReactionRates
from .results_list import ResultsList
-from .helpers import DirectReactionRateHelper, ChainFissionHelper
+from .helpers import (
+ DirectReactionRateHelper, ChainFissionHelper, ConstantFissionYieldHelper,
+ FissionYieldCutoffHelper, AveragedFissionYieldHelper)
def _distribute(items):
@@ -84,6 +86,21 @@ class Operator(TransportOperator):
in initial condition to ensure they exist in the decay chain.
Only done for nuclides with reaction rates.
Defaults to 1.0e3.
+ fission_yield_mode : {"constant", "cutoff", "average"}
+ Key indicating what fission product yield scheme to use. The
+ key determines what fission energy helper is used:
+
+ * "constant": :class:`~openmc.deplete.helpers.ConstantFissionYieldHelper`
+ * "cutoff": :class:`~openmc.deplete.helpers.FissionYieldCutoffHelper`
+ * "average": :class:`~openmc.deplete.helpers.AveragedFissionYieldHelper`
+
+ The documentation on these classes describe their methodology
+ and differences. Default: ``"constant"``
+ fission_yield_opts : dict of str to option, optional
+ Optional arguments to pass to the helper determined by
+ ``fission_yield_mode``. Will be passed directly on to the
+ helper. Passing a value of None will use the defaults for
+ the associated helper.
Attributes
----------
@@ -120,9 +137,20 @@ class Operator(TransportOperator):
diff_burnable_mats : bool
Whether to differentiate burnable materials with multiple instances
"""
+ _fission_helpers = {
+ "average": AveragedFissionYieldHelper,
+ "constant": ConstantFissionYieldHelper,
+ "cutoff": FissionYieldCutoffHelper,
+ }
+
def __init__(self, geometry, settings, chain_file=None, prev_results=None,
diff_burnable_mats=False, fission_q=None,
- dilute_initial=1.0e3):
+ dilute_initial=1.0e3, fission_yield_mode="constant",
+ fission_yield_opts=None):
+ if fission_yield_mode not in self._fission_helpers:
+ raise KeyError(
+ "fission_yield_mode must be one of {}, not {}".format(
+ ", ".join(self._fission_helpers), fission_yield_mode))
super().__init__(chain_file, fission_q, dilute_initial, prev_results)
self.round_number = False
self.prev_res = None
@@ -178,6 +206,13 @@ def __init__(self, geometry, settings, chain_file=None, prev_results=None,
self.reaction_rates.n_nuc, self.reaction_rates.n_react)
self._energy_helper = ChainFissionHelper()
+ # Select and create fission yield helper
+ fission_helper = self._fission_helpers[fission_yield_mode]
+ fission_yield_opts = (
+ {} if fission_yield_opts is None else fission_yield_opts)
+ self._yield_helper = fission_helper.from_operator(
+ self, **fission_yield_opts)
+
def __call__(self, vec, power):
"""Runs a simulation.
@@ -204,8 +239,10 @@ def __call__(self, vec, power):
# Update material compositions and tally nuclides
self._update_materials()
- self._rate_helper.nuclides = self._get_tally_nuclides()
- self._energy_helper.nuclides = self._rate_helper.nuclides
+ nuclides = self._get_tally_nuclides()
+ self._rate_helper.nuclides = nuclides
+ self._energy_helper.nuclides = nuclides
+ self._yield_helper.update_tally_nuclides(nuclides)
# Run OpenMC
openmc.capi.reset()
@@ -409,6 +446,10 @@ def initial_condition(self):
self._rate_helper.generate_tallies(materials, self.chain.reactions)
self._energy_helper.prepare(
self.chain.nuclides, self.reaction_rates.index_nuc, materials)
+ # Tell fission yield helper what materials this process is
+ # responsible for
+ self._yield_helper.generate_tallies(
+ materials, tuple(sorted(self._mat_index_map.values())))
# Return number density vector
return list(self.number.get_mat_slice(np.s_[:]))
@@ -554,6 +595,10 @@ def _unpack_tallies_and_normalize(self, power):
# Keep track of energy produced from all reactions in eV per source
# particle
self._energy_helper.reset()
+ self._yield_helper.unpack()
+
+ # Store fission yield dictionaries
+ fission_yields = []
# Create arrays to store fission Q values, reaction rates, and nuclide
# numbers, zeroed out in material iteration
@@ -576,6 +621,9 @@ def _unpack_tallies_and_normalize(self, power):
tally_rates = self._rate_helper.get_material_rates(
mat_index, nuc_ind, react_ind)
+ # Compute fission yields for this material
+ fission_yields.append(self._yield_helper.weighted_yields(i))
+
# Accumulate energy from fission
self._energy_helper.update(tally_rates[:, fission_ind], mat_index)
@@ -589,6 +637,9 @@ def _unpack_tallies_and_normalize(self, power):
# Scale reaction rates to obtain units of reactions/sec
rates *= power / energy
+ # Store new fission yields on the chain
+ self.chain.fission_yields = fission_yields
+
return OperatorResult(k_combined, rates)
def _get_nuclides_with_data(self):
| diff --git a/tests/dummy_operator.py b/tests/dummy_operator.py
--- a/tests/dummy_operator.py
+++ b/tests/dummy_operator.py
@@ -73,6 +73,49 @@
}
+class TestChain(object):
+ """Empty chain to assist with unit testing depletion routines
+
+ Only really provides the form_matrix function, but acts like
+ a real Chain
+ """
+
+ fission_yields = [None]
+
+ @staticmethod
+ def get_thermal_fission_yields():
+ return None
+
+ def form_matrix(self, rates, _fission_yields=None):
+ """Forms the f(y) matrix in y' = f(y)y.
+
+ Nominally a depletion matrix, this is abstracted on the off chance
+ that the function f has nothing to do with depletion at all.
+
+ Parameters
+ ----------
+ rates : numpy.ndarray
+ Slice of reaction rates for a single material
+ _fission_yields : optional
+ Not used
+
+ Returns
+ -------
+ scipy.sparse.csr_matrix
+ Sparse matrix representing f(y).
+ """
+
+ y_1 = rates[0, 0]
+ y_2 = rates[1, 0]
+
+ a11 = np.sin(y_2)
+ a12 = np.cos(y_1)
+ a21 = -np.cos(y_2)
+ a22 = np.sin(y_1)
+
+ return sp.csr_matrix(np.array([[a11, a12], [a21, a22]]))
+
+
class DummyOperator(TransportOperator):
"""This is a dummy operator class with no statistical uncertainty.
@@ -88,6 +131,7 @@ class DummyOperator(TransportOperator):
"""
def __init__(self, previous_results=None):
self.prev_res = previous_results
+ self.chain = TestChain()
self.output_dir = "."
def __call__(self, vec, power, print_out=False):
@@ -120,37 +164,6 @@ def __call__(self, vec, power, print_out=False):
# Create a fake rates object
return OperatorResult(ufloat(0.0, 0.0), reaction_rates)
- @property
- def chain(self):
- return self
-
- def form_matrix(self, rates):
- """Forms the f(y) matrix in y' = f(y)y.
-
- Nominally a depletion matrix, this is abstracted on the off chance
- that the function f has nothing to do with depletion at all.
-
- Parameters
- ----------
- rates : numpy.ndarray
- Slice of reaction rates for a single material
-
- Returns
- -------
- scipy.sparse.csr_matrix
- Sparse matrix representing f(y).
- """
-
- y_1 = rates[0, 0]
- y_2 = rates[1, 0]
-
- a11 = np.sin(y_2)
- a12 = np.cos(y_1)
- a21 = -np.cos(y_2)
- a22 = np.sin(y_1)
-
- return sp.csr_matrix(np.array([[a11, a12], [a21, a22]]))
-
@property
def volume(self):
"""
diff --git a/tests/unit_tests/test_deplete_chain.py b/tests/unit_tests/test_deplete_chain.py
--- a/tests/unit_tests/test_deplete_chain.py
+++ b/tests/unit_tests/test_deplete_chain.py
@@ -3,10 +3,11 @@
from collections.abc import Mapping
import os
from pathlib import Path
+from itertools import product
import numpy as np
from openmc.data import zam, ATOMIC_SYMBOL
-from openmc.deplete import comm, Chain, reaction_rates, nuclide
+from openmc.deplete import comm, Chain, reaction_rates, nuclide, cram
import pytest
from tests import cdtemp
@@ -128,9 +129,10 @@ def test_from_xml(simple_chain):
assert [r.branching_ratio for r in nuc.reactions] == [1.0, 0.7, 0.3]
# Yield tests
- assert nuc.yield_energies == [0.0253]
+ assert nuc.yield_energies == (0.0253,)
assert list(nuc.yield_data) == [0.0253]
- assert nuc.yield_data[0.0253] == [("A", 0.0292737), ("B", 0.002566345)]
+ assert nuc.yield_data[0.0253].products == ("A", "B")
+ assert (nuc.yield_data[0.0253].yields == [0.0292737, 0.002566345]).all()
def test_export_to_xml(run_in_tmpdir):
@@ -139,8 +141,7 @@ def test_export_to_xml(run_in_tmpdir):
# Prevent different MPI ranks from conflicting
filename = 'test{}.xml'.format(comm.rank)
- A = nuclide.Nuclide()
- A.name = "A"
+ A = nuclide.Nuclide("A")
A.half_life = 2.36520e4
A.decay_modes = [
nuclide.DecayTuple("beta1", "B", 0.6),
@@ -148,21 +149,19 @@ def test_export_to_xml(run_in_tmpdir):
]
A.reactions = [nuclide.ReactionTuple("(n,gamma)", "C", 0.0, 1.0)]
- B = nuclide.Nuclide()
- B.name = "B"
+ B = nuclide.Nuclide("B")
B.half_life = 3.29040e4
B.decay_modes = [nuclide.DecayTuple("beta", "A", 1.0)]
B.reactions = [nuclide.ReactionTuple("(n,gamma)", "C", 0.0, 1.0)]
- C = nuclide.Nuclide()
- C.name = "C"
+ C = nuclide.Nuclide("C")
C.reactions = [
nuclide.ReactionTuple("fission", None, 2.0e8, 1.0),
nuclide.ReactionTuple("(n,gamma)", "A", 0.0, 0.7),
nuclide.ReactionTuple("(n,gamma)", "B", 0.0, 0.3)
]
- C.yield_energies = [0.0253]
- C.yield_data = {0.0253: [("A", 0.0292737), ("B", 0.002566345)]}
+ C.yield_data = nuclide.FissionYieldDistribution({
+ 0.0253: {"A": 0.0292737, "B": 0.002566345}})
chain = Chain()
chain.nuclides = [A, B, C]
@@ -220,6 +219,13 @@ def test_form_matrix(simple_chain):
assert mat[1, 2] == mat12
assert mat[2, 2] == mat22
+ # Pass equivalent fission yields directly
+ # Ensure identical matrix is formed
+ f_yields = {"C": {"A": 0.0292737, "B": 0.002566345}}
+ new_mat = chain.form_matrix(react[0], f_yields)
+ for r, c in product(range(3), range(3)):
+ assert new_mat[r, c] == mat[r, c]
+
def test_getitem():
""" Test nuc_by_ind converter function. """
@@ -283,8 +289,7 @@ def test_capture_branch_infer_ground():
chain = Chain.from_xml(chain_file)
# Create nuclide to be added into the chain
- xe136m = nuclide.Nuclide()
- xe136m.name = "Xe136_m1"
+ xe136m = nuclide.Nuclide("Xe136_m1")
chain.nuclides.append(xe136m)
chain.nuclide_dict[xe136m.name] = len(chain.nuclides) - 1
@@ -301,8 +306,7 @@ def test_capture_branch_no_rxn():
chain_file = Path(__file__).parents[1] / "chain_simple.xml"
chain = Chain.from_xml(chain_file)
- u5m = nuclide.Nuclide()
- u5m.name = "U235_m1"
+ u5m = nuclide.Nuclide("U235_m1")
chain.nuclides.append(u5m)
chain.nuclide_dict[u5m.name] = len(chain.nuclides) - 1
@@ -378,6 +382,32 @@ def test_set_alpha_branches():
raise ValueError("Helium has been removed and should not have been")
+def test_simple_fission_yields(simple_chain):
+ """Check the default fission yields that can be used to form the matrix
+ """
+ fission_yields = simple_chain.get_thermal_fission_yields()
+ assert fission_yields == {"C": {"A": 0.0292737, "B": 0.002566345}}
+
+
+def test_fission_yield_attribute(simple_chain):
+ """Test the fission_yields property"""
+ thermal_yields = simple_chain.get_thermal_fission_yields()
+ # generate default with property
+ assert simple_chain.fission_yields[0] == thermal_yields
+ empty_chain = Chain()
+ empty_chain.fission_yields = thermal_yields
+ assert empty_chain.fission_yields[0] == thermal_yields
+ empty_chain.fission_yields = [thermal_yields] * 2
+ assert empty_chain.fission_yields[0] == thermal_yields
+ assert empty_chain.fission_yields[1] == thermal_yields
+
+ # test failure with deplete function
+ # number fission yields != number of materials
+ dummy_conc = [[1, 2]] * (len(empty_chain.fission_yields) + 1)
+ with pytest.raises(
+ ValueError, match="fission yield.*not equal.*compositions"):
+ cram.deplete(empty_chain, dummy_conc, None, 0.5)
+
def test_validate(simple_chain):
"""Test the validate method"""
@@ -394,7 +424,7 @@ def test_validate(simple_chain):
# Fix fission yields but keep to restore later
old_yields = simple_chain["C"].yield_data
- simple_chain["C"].yield_data = {0.0253: [("A", 1.4), ("B", 0.6)]}
+ simple_chain["C"].yield_data = {0.0253: {"A": 1.4, "B": 0.6}}
assert simple_chain.validate(strict=True, tolerance=0.0)
with pytest.warns(None) as record:
diff --git a/tests/unit_tests/test_deplete_fission_yields.py b/tests/unit_tests/test_deplete_fission_yields.py
new file mode 100644
--- /dev/null
+++ b/tests/unit_tests/test_deplete_fission_yields.py
@@ -0,0 +1,293 @@
+"""Test the FissionYieldHelpers"""
+
+import os
+from collections import namedtuple
+from unittest.mock import Mock
+import bisect
+
+import pytest
+import numpy as np
+import openmc
+from openmc import capi
+from openmc.deplete.nuclide import Nuclide, FissionYieldDistribution
+from openmc.deplete.helpers import (
+ FissionYieldCutoffHelper, ConstantFissionYieldHelper,
+ AveragedFissionYieldHelper)
+
+
[email protected](scope="module")
+def materials(tmpdir_factory):
+ """Use C API to construct realistic materials for testing tallies"""
+ tmpdir = tmpdir_factory.mktemp("capi")
+ orig = tmpdir.chdir()
+ # Create proxy problem to please openmc
+ mfuel = openmc.Material(name="test_fuel")
+ mfuel.volume = 1.0
+ for nuclide in ["U235", "U238", "Xe135", "Pu239"]:
+ mfuel.add_nuclide(nuclide, 1.0)
+ openmc.Materials([mfuel]).export_to_xml()
+ # Geometry
+ box = openmc.rectangular_prism(1.0, 1.0, boundary_type="reflective")
+ cell = openmc.Cell(fill=mfuel, region=box)
+ root = openmc.Universe(cells=[cell])
+ openmc.Geometry(root).export_to_xml()
+ # settings
+ settings = openmc.Settings()
+ settings.particles = 100
+ settings.inactive = 0
+ settings.batches = 10
+ settings.verbosity = 1
+ settings.export_to_xml()
+
+ try:
+ with capi.run_in_memory():
+ yield [capi.Material(), capi.Material()]
+ finally:
+ # Convert to strings as os.remove in py 3.5 doesn't support Paths
+ for file_path in ("settings.xml", "geometry.xml", "materials.xml",
+ "summary.h5"):
+ os.remove(str(tmpdir / file_path))
+ orig.chdir()
+ os.rmdir(str(tmpdir))
+
+
+def proxy_tally_data(tally, fill=None):
+ """Construct an empty matrix built from a C tally
+
+ The shape of tally.results will be
+ ``(n_bins, n_nuc * n_scores, 3)``
+ """
+ n_nucs = max(len(tally.nuclides), 1)
+ n_scores = max(len(tally.scores), 1)
+ n_bins = 1
+ for tfilter in tally.filters:
+ if not hasattr(tfilter, "bins"):
+ continue
+ this_bins = len(tfilter.bins)
+ if isinstance(tfilter, capi.EnergyFilter):
+ this_bins -= 1
+ n_bins *= max(this_bins, 1)
+ data = np.empty((n_bins, n_nucs * n_scores, 3))
+ if fill is not None:
+ data.fill(fill)
+ return data
+
+
[email protected](scope="module")
+def nuclide_bundle():
+ u5yield_dict = {
+ 0.0253: {"Xe135": 7.85e-4, "Gd155": 4.08e-12, "Sm149": 1.71e-12},
+ 5.0e5: {"Xe135": 7.85e-4, "Sm149": 1.71e-12},
+ 1.40e7: {"Xe135": 4.54e-3, "Gd155": 5.83e-8}}
+ u235 = Nuclide("U235")
+ u235.yield_data = FissionYieldDistribution(u5yield_dict)
+
+ u8yield_dict = {5.00e5: {"Xe135": 1.12e-3, "Gd155": 1.32e-12}}
+ u238 = Nuclide("U238")
+ u238.yield_data = FissionYieldDistribution(u8yield_dict)
+
+ xe135 = Nuclide("Xe135")
+
+ pu239 = Nuclide("Pu239")
+ pu239.yield_data = FissionYieldDistribution({
+ 5.0e5: {"Xe135": 6.14e-3, "Sm149": 9.429e-10, "Gd155": 5.24e-9},
+ 2e6: {"Xe135": 6.15e-3, "Sm149": 9.42e-10, "Gd155": 5.29e-9}})
+
+ NuclideBundle = namedtuple("NuclideBundle", "u235 u238 xe135 pu239")
+ return NuclideBundle(u235, u238, xe135, pu239)
+
+
[email protected](
+ "input_energy, yield_energy",
+ ((0.0253, 0.0253), (0.01, 0.0253), (4e5, 5e5)))
+def test_constant_helper(nuclide_bundle, input_energy, yield_energy):
+ helper = ConstantFissionYieldHelper(nuclide_bundle, energy=input_energy)
+ assert helper.energy == input_energy
+ assert helper.constant_yields == {
+ "U235": nuclide_bundle.u235.yield_data[yield_energy],
+ "U238": nuclide_bundle.u238.yield_data[5.00e5],
+ "Pu239": nuclide_bundle.pu239.yield_data[5e5]}
+ assert helper.constant_yields == helper.weighted_yields(1)
+
+
+def test_cutoff_construction(nuclide_bundle):
+ u235 = nuclide_bundle.u235
+ u238 = nuclide_bundle.u238
+ pu239 = nuclide_bundle.pu239
+
+ # defaults
+ helper = FissionYieldCutoffHelper(nuclide_bundle, 1)
+ assert helper.constant_yields == {
+ "U238": u238.yield_data[5.0e5],
+ "Pu239": pu239.yield_data[5e5]}
+ assert helper.thermal_yields == {"U235": u235.yield_data[0.0253]}
+ assert helper.fast_yields == {"U235": u235.yield_data[5e5]}
+
+ # use 14 MeV yields
+ helper = FissionYieldCutoffHelper(nuclide_bundle, 1, fast_energy=14e6)
+ assert helper.constant_yields == {
+ "U238": u238.yield_data[5.0e5],
+ "Pu239": pu239.yield_data[5e5]}
+ assert helper.thermal_yields == {"U235": u235.yield_data[0.0253]}
+ assert helper.fast_yields == {"U235": u235.yield_data[14e6]}
+
+ # specify missing thermal yields -> use 0.0253
+ helper = FissionYieldCutoffHelper(nuclide_bundle, 1, thermal_energy=1)
+ assert helper.thermal_yields == {"U235": u235.yield_data[0.0253]}
+ assert helper.fast_yields == {"U235": u235.yield_data[5e5]}
+
+ # request missing fast yields -> use epithermal
+ helper = FissionYieldCutoffHelper(nuclide_bundle, 1, fast_energy=1e4)
+ assert helper.thermal_yields == {"U235": u235.yield_data[0.0253]}
+ assert helper.fast_yields == {"U235": u235.yield_data[5e5]}
+
+ # higher cutoff energy -> obtain fast and "faster" yields
+ helper = FissionYieldCutoffHelper(nuclide_bundle, 1, cutoff=1e6,
+ thermal_energy=5e5, fast_energy=14e6)
+ assert helper.constant_yields == {"U238": u238.yield_data[5e5]}
+ assert helper.thermal_yields == {
+ "U235": u235.yield_data[5e5], "Pu239": pu239.yield_data[5e5]}
+ assert helper.fast_yields == {
+ "U235": u235.yield_data[14e6], "Pu239": pu239.yield_data[2e6]}
+
+ # test super low and super high cutoff energies
+ helper = FissionYieldCutoffHelper(
+ nuclide_bundle, 1, thermal_energy=0.001, cutoff=0.002)
+ assert helper.fast_yields == {}
+ assert helper.thermal_yields == {}
+ assert helper.constant_yields == {
+ "U235": u235.yield_data[0.0253], "U238": u238.yield_data[5e5],
+ "Pu239": pu239.yield_data[5e5]}
+
+ helper = FissionYieldCutoffHelper(
+ nuclide_bundle, 1, cutoff=15e6, fast_energy=17e6)
+ assert helper.thermal_yields == {}
+ assert helper.fast_yields == {}
+ assert helper.constant_yields == {
+ "U235": u235.yield_data[14e6], "U238": u238.yield_data[5e5],
+ "Pu239": pu239.yield_data[2e6]}
+
+
[email protected]("key", ("cutoff", "thermal_energy", "fast_energy"))
+def test_cutoff_failure(key):
+ with pytest.raises(TypeError, match=key):
+ FissionYieldCutoffHelper(None, None, **{key: None})
+ with pytest.raises(ValueError, match=key):
+ FissionYieldCutoffHelper(None, None, **{key: -1})
+
+
+# emulate some split between fast and thermal U235 fissions
[email protected]("therm_frac", (0.5, 0.2, 0.8))
+def test_cutoff_helper(materials, nuclide_bundle, therm_frac):
+ helper = FissionYieldCutoffHelper(nuclide_bundle, len(materials),
+ cutoff=1e6, fast_energy=14e6)
+ helper.generate_tallies(materials, [0])
+
+ non_zero_nucs = [n.name for n in nuclide_bundle]
+ tally_nucs = helper.update_tally_nuclides(non_zero_nucs)
+ assert tally_nucs == ["Pu239", "U235"]
+
+ # Check tallies
+ fission_tally = helper._fission_rate_tally
+ assert fission_tally is not None
+ filters = fission_tally.filters
+ assert len(filters) == 2
+ assert isinstance(filters[0], capi.MaterialFilter)
+ assert len(filters[0].bins) == len(materials)
+ assert isinstance(filters[1], capi.EnergyFilter)
+ # lower, cutoff, and upper energy
+ assert len(filters[1].bins) == 3
+
+ # Emulate building tallies
+ # material x energy, tallied_nuclides, 3
+ tally_data = proxy_tally_data(fission_tally)
+ helper._fission_rate_tally = Mock()
+ helper_flux = 1e6
+ tally_data[0, :, 1] = therm_frac * helper_flux
+ tally_data[1, :, 1] = (1 - therm_frac) * helper_flux
+ helper._fission_rate_tally.results = tally_data
+
+ helper.unpack()
+ # expected results of shape (n_mats, 2, n_tnucs)
+ expected_results = np.empty((1, 2, len(tally_nucs)))
+ expected_results[:, 0] = therm_frac
+ expected_results[:, 1] = 1 - therm_frac
+ assert helper.results == pytest.approx(expected_results)
+
+ actual_yields = helper.weighted_yields(0)
+ assert actual_yields["U238"] == nuclide_bundle.u238.yield_data[5e5]
+ for nuc in tally_nucs:
+ assert actual_yields[nuc] == (
+ helper.thermal_yields[nuc] * therm_frac
+ + helper.fast_yields[nuc] * (1 - therm_frac))
+
+
[email protected]("avg_energy", (0.01, 6e5, 15e6))
+def test_averaged_helper(materials, nuclide_bundle, avg_energy):
+ helper = AveragedFissionYieldHelper(nuclide_bundle)
+ helper.generate_tallies(materials, [0])
+ tallied_nucs = helper.update_tally_nuclides(
+ [n.name for n in nuclide_bundle])
+ assert tallied_nucs == ["Pu239", "U235"]
+
+ # check generated tallies
+ fission_tally = helper._fission_rate_tally
+ assert fission_tally is not None
+ fission_filters = fission_tally.filters
+ assert len(fission_filters) == 2
+ assert isinstance(fission_filters[0], capi.MaterialFilter)
+ assert len(fission_filters[0].bins) == len(materials)
+ assert isinstance(fission_filters[1], capi.EnergyFilter)
+ assert len(fission_filters[1].bins) == 2
+ assert fission_tally.scores == ["fission"]
+ assert fission_tally.nuclides == list(tallied_nucs)
+
+ weighted_tally = helper._weighted_tally
+ assert weighted_tally is not None
+ weighted_filters = weighted_tally.filters
+ assert len(weighted_filters) == 2
+ assert isinstance(weighted_filters[0], capi.MaterialFilter)
+ assert len(weighted_filters[0].bins) == len(materials)
+ assert isinstance(weighted_filters[1], capi.EnergyFunctionFilter)
+ assert len(weighted_filters[1].energy) == 2
+ assert len(weighted_filters[1].y) == 2
+ assert weighted_tally.scores == ["fission"]
+ assert weighted_tally.nuclides == list(tallied_nucs)
+
+ helper_flux = 1e16
+ fission_results = proxy_tally_data(fission_tally, helper_flux)
+ weighted_results = proxy_tally_data(
+ weighted_tally, helper_flux * avg_energy)
+
+ helper._fission_rate_tally = Mock()
+ helper._weighted_tally = Mock()
+ helper._fission_rate_tally.results = fission_results
+ helper._weighted_tally.results = weighted_results
+
+ helper.unpack()
+ expected_results = np.ones((1, len(tallied_nucs))) * avg_energy
+ assert helper.results == pytest.approx(expected_results)
+
+ actual_yields = helper.weighted_yields(0)
+ # constant U238 => no interpolation
+ assert actual_yields["U238"] == nuclide_bundle.u238.yield_data[5e5]
+ # construct expected yields
+ exp_u235_yields = interp_average_yields(nuclide_bundle.u235, avg_energy)
+ assert actual_yields["U235"] == exp_u235_yields
+ exp_pu239_yields = interp_average_yields(nuclide_bundle.pu239, avg_energy)
+ assert actual_yields["Pu239"] == exp_pu239_yields
+
+
+def interp_average_yields(nuc, avg_energy):
+ """Construct a set of yields by interpolation between neighbors"""
+ energies = nuc.yield_energies
+ yields = nuc.yield_data
+ if avg_energy < energies[0]:
+ return yields[energies[0]]
+ if avg_energy > energies[-1]:
+ return yields[energies[-1]]
+ thermal_ix = bisect.bisect_left(energies, avg_energy)
+ thermal_E, fast_E = energies[thermal_ix - 1:thermal_ix + 1]
+ assert thermal_E < avg_energy < fast_E
+ split = (avg_energy - thermal_E)/(fast_E - thermal_E)
+ return yields[thermal_E]*(1 - split) + yields[fast_E]*split
diff --git a/tests/unit_tests/test_deplete_nuclide.py b/tests/unit_tests/test_deplete_nuclide.py
--- a/tests/unit_tests/test_deplete_nuclide.py
+++ b/tests/unit_tests/test_deplete_nuclide.py
@@ -2,8 +2,8 @@
import xml.etree.ElementTree as ET
+import numpy
import pytest
-
from openmc.deplete import nuclide
@@ -71,18 +71,20 @@ def test_from_xml():
nuclide.ReactionTuple('(n,gamma)', 'U236', 6545200.0, 1.0),
nuclide.ReactionTuple('fission', None, 193405400.0, 1.0),
]
- assert u235.yield_energies == [0.0253]
- assert u235.yield_data == {
- 0.0253: [('Te134', 0.062155), ('Zr100', 0.0497641),
- ('Xe138', 0.0481413)]
- }
+ expected_yield_data = nuclide.FissionYieldDistribution({
+ 0.0253: {"Xe138": 0.0481413, "Zr100": 0.0497641, "Te134": 0.062155}})
+ assert u235.yield_data == expected_yield_data
+ # test accessing the yield energies through the FissionYieldDistribution
+ assert u235.yield_energies == (0.0253,)
+ assert u235.yield_energies is u235.yield_data.energies
+ with pytest.raises(AttributeError): # not settable
+ u235.yield_energies = [0.0253, 5e5]
def test_to_xml_element():
"""Test writing nuclide data to an XML element."""
- C = nuclide.Nuclide()
- C.name = "C"
+ C = nuclide.Nuclide("C")
C.half_life = 0.123
C.decay_modes = [
nuclide.DecayTuple('beta-', 'B', 0.99),
@@ -92,8 +94,8 @@ def test_to_xml_element():
nuclide.ReactionTuple('fission', None, 2.0e8, 1.0),
nuclide.ReactionTuple('(n,gamma)', 'A', 0.0, 1.0)
]
- C.yield_energies = [0.0253]
- C.yield_data = {0.0253: [("A", 0.0292737), ("B", 0.002566345)]}
+ C.yield_data = nuclide.FissionYieldDistribution(
+ {0.0253: {"A": 0.0292737, "B": 0.002566345}})
element = C.to_xml_element()
assert element.get("half_life") == "0.123"
@@ -118,6 +120,57 @@ def test_to_xml_element():
assert element.find('neutron_fission_yields') is not None
+def test_fission_yield_distribution():
+ """Test an energy-dependent yield distribution"""
+ yield_dict = {
+ 0.0253: {"Xe135": 7.85e-4, "Gd155": 4.08e-12, "Sm149": 1.71e-12},
+ 1.40e7: {"Xe135": 4.54e-3, "Gd155": 5.83e-8, "Sm149": 2.69e-8},
+ 5.00e5: {"Xe135": 1.12e-3, "Gd155": 1.32e-12}, # drop Sm149
+ }
+ yield_dist = nuclide.FissionYieldDistribution(yield_dict)
+ assert len(yield_dist) == len(yield_dict)
+ assert yield_dist.energies == tuple(sorted(yield_dict.keys()))
+ for exp_ene, exp_dist in yield_dict.items():
+ act_dist = yield_dict[exp_ene]
+ for exp_prod, exp_yield in exp_dist.items():
+ assert act_dist[exp_prod] == exp_yield
+ exp_yield = numpy.array([
+ [4.08e-12, 1.71e-12, 7.85e-4],
+ [1.32e-12, 0.0, 1.12e-3],
+ [5.83e-8, 2.69e-8, 4.54e-3]])
+ assert numpy.array_equal(yield_dist.yield_matrix, exp_yield)
+
+ # Test the operations / special methods for fission yield
+ orig_yields = yield_dist[0.0253]
+ assert len(orig_yields) == len(yield_dict[0.0253])
+ for key, value in yield_dict[0.0253].items():
+ assert key in orig_yields
+ assert orig_yields[key] == value
+ # __getitem__ return yields as a view into yield matrix
+ assert orig_yields.yields.base is yield_dist.yield_matrix
+
+ # Fission yield feature uses scaled and incremented
+ mod_yields = orig_yields * 2
+ assert numpy.array_equal(orig_yields.yields * 2, mod_yields.yields)
+ mod_yields += orig_yields
+ assert numpy.array_equal(orig_yields.yields * 3, mod_yields.yields)
+
+ # Failure modes for adding, multiplying yields
+ similar = numpy.empty_like(orig_yields.yields)
+ with pytest.raises(TypeError):
+ orig_yields + similar
+ with pytest.raises(TypeError):
+ similar + orig_yields
+ with pytest.raises(TypeError):
+ orig_yields += similar
+ with pytest.raises(TypeError):
+ orig_yields * similar
+ with pytest.raises(TypeError):
+ similar * orig_yields
+ with pytest.raises(TypeError):
+ orig_yields *= similar
+
+
def test_validate():
nuc = nuclide.Nuclide()
@@ -141,8 +194,8 @@ def test_validate():
# fission yields
nuc.yield_data = {
- 0.0253: [("0", 1.5), ("1", 0.5)],
- 1e6: [("0", 1.5), ("1", 0.5)],
+ 0.0253: {"0": 1.5, "1": 0.5},
+ 1e6: {"0": 1.5, "1": 0.5},
}
# nuclide is good and should have no warnings raise
@@ -176,7 +229,7 @@ def test_validate():
# restore reactions, invalidate fission yields
nuc.reactions.append(reaction)
- nuc.yield_data[1e6].pop()
+ nuc.yield_data[1e6].yields *= 2
with pytest.raises(ValueError, match=r"fission yields.*1\.0*e"):
nuc.validate(strict=True, quiet=False, tolerance=0.0)
| Better handle fission product yield energy dependence
Right now, `openmc.deplete` is hardwired to use fission product yields for a thermal spectrum (see [here](https://github.com/openmc-dev/openmc/blob/develop/openmc/deplete/chain.py#L424-L427)). We need some way of having the code use different yields, either automatically or as a user option.
| 2019-08-08T14:39:40Z | [] | [] |
|
openmc-dev/openmc | 1,314 | openmc-dev__openmc-1314 | [
"1308"
] | f5c421d24efa10c9a068d340a5b54510c0798d96 | diff --git a/openmc/deplete/chain.py b/openmc/deplete/chain.py
--- a/openmc/deplete/chain.py
+++ b/openmc/deplete/chain.py
@@ -10,9 +10,10 @@
import re
from collections import OrderedDict, defaultdict
from collections.abc import Mapping
+from numbers import Real
from warnings import warn
-from openmc.checkvalue import check_type, check_less_than
+from openmc.checkvalue import check_type, check_less_than, check_greater_than
from openmc.data import gnd_name, zam
# Try to use lxml if it is available. It preserves the order of attributes and
@@ -613,3 +614,54 @@ def set_capture_branches(self, branch_ratios, strict=True):
new_ratios[ground_tgt] = ground_br
parent.reactions.append(ReactionTuple(
"(n,gamma)", ground_tgt, capt_Q, ground_br))
+
+ def validate(self, strict=True, quiet=False, tolerance=1e-4):
+ """Search for possible inconsistencies
+
+ The following checks are performed for all nuclides present:
+
+ 1) For all non-fission reactions, does the sum of branching
+ ratios equal about one?
+ 2) For fission reactions, does the sum of fission yield
+ fractions equal about two?
+
+ Parameters
+ ----------
+ strict : bool, optional
+ Raise exceptions at the first inconsistency if true.
+ Otherwise mark a warning
+ quiet : bool, optional
+ Flag to suppress warnings and return immediately at
+ the first inconsistency. Used only if
+ ``strict`` does not evaluate to ``True``.
+ tolerance : float, optional
+ Absolute tolerance for comparisons. Used to compare computed
+ value ``x`` to intended value ``y`` as::
+
+ valid = (y - tolerance <= x <= y + tolerance)
+
+ Returns
+ -------
+ valid : bool
+ True if no inconsistencies were found
+
+ Raises
+ ------
+ ValueError
+ If ``strict`` evaluates to ``True`` and an inconistency was
+ found
+
+ See Also
+ --------
+ openmc.deplete.Nuclide.validate
+ """
+ check_type("tolerance", tolerance, Real)
+ check_greater_than("tolerance", tolerance, 0.0, True)
+ valid = True
+ # Sort through nuclides by name
+ for name in sorted(self.nuclide_dict):
+ stat = self[name].validate(strict, quiet, tolerance)
+ if quiet and not stat:
+ return stat
+ valid = valid and stat
+ return valid
diff --git a/openmc/deplete/nuclide.py b/openmc/deplete/nuclide.py
--- a/openmc/deplete/nuclide.py
+++ b/openmc/deplete/nuclide.py
@@ -3,7 +3,8 @@
Contains the per-nuclide components of a depletion chain.
"""
-from collections import namedtuple
+from collections import namedtuple, defaultdict
+from warnings import warn
try:
import lxml.etree as ET
except ImportError:
@@ -222,3 +223,101 @@ def to_xml_element(self):
data_elem.text = ' '.join(str(x[1]) for x in self.yield_data[E])
return elem
+
+ def validate(self, strict=True, quiet=False, tolerance=1e-4):
+ """Search for possible inconsistencies
+
+ The following checks are performed:
+
+ 1) for all non-fission reactions and decay modes,
+ does the sum of branching ratios equal about one?
+ 2) for fission reactions, does the sum of fission yield
+ fractions equal about two?
+
+ Parameters
+ ----------
+ strict : bool, optional
+ Raise exceptions at the first inconsistency if true.
+ Otherwise mark a warning
+ quiet : bool, optional
+ Flag to suppress warnings and return immediately at
+ the first inconsistency. Used only if
+ ``strict`` does not evaluate to ``True``.
+ tolerance : float, optional
+ Absolute tolerance for comparisons. Used to compare computed
+ value ``x`` to intended value ``y`` as::
+
+ valid = (y - tolerance <= x <= y + tolerance)
+
+ Returns
+ -------
+ valid : bool
+ True if no inconsistencies were found
+
+ Raises
+ ------
+ ValueError
+ If ``strict`` evaluates to ``True`` and an inconistency was
+ found
+
+ See Also
+ --------
+ openmc.deplete.Chain.validate
+ """
+
+ msg_func = ("Nuclide {name} has {prop} that sum to {actual} "
+ "instead of {expected} +/- {tol:7.4e}").format
+ valid = True
+
+ # check decay modes
+ if self.decay_modes:
+ sum_br = sum(m.branching_ratio for m in self.decay_modes)
+ stat = 1.0 - tolerance <= sum_br <= 1.0 + tolerance
+ if not stat:
+ msg = msg_func(
+ name=self.name, actual=sum_br, expected=1.0, tol=tolerance,
+ prop="decay mode branch ratios")
+ if strict:
+ raise ValueError(msg)
+ elif quiet:
+ return False
+ warn(msg)
+ valid = False
+
+ if self.reactions:
+ type_map = defaultdict(set)
+ for reaction in self.reactions:
+ type_map[reaction.type].add(reaction)
+ for rxn_type, reactions in type_map.items():
+ sum_rxn = sum(rx.branching_ratio for rx in reactions)
+ stat = 1.0 - tolerance <= sum_rxn <= 1.0 + tolerance
+ if stat:
+ continue
+ msg = msg_func(
+ name=self.name, actual=sum_br, expected=1.0, tol=tolerance,
+ prop="{} reaction branch ratios".format(rxn_type))
+ if strict:
+ raise ValueError(msg)
+ elif quiet:
+ return False
+ warn(msg)
+ valid = False
+
+ if self.yield_data:
+ for energy, yield_list in self.yield_data.items():
+ sum_yield = sum(y[1] for y in yield_list)
+ stat = 2.0 - tolerance <= sum_yield <= 2.0 + tolerance
+ if stat:
+ continue
+ msg = msg_func(
+ name=self.name, actual=sum_yield,
+ expected=2.0, tol=tolerance,
+ prop="fission yields (E = {:7.4e} eV)".format(energy))
+ if strict:
+ raise ValueError(msg)
+ elif quiet:
+ return False
+ warn(msg)
+ valid = False
+
+ return valid
diff --git a/scripts/casl_chain.py b/scripts/casl_chain.py
--- a/scripts/casl_chain.py
+++ b/scripts/casl_chain.py
@@ -6,6 +6,8 @@
# Note 32 of the 255 nuclides appeare twice as they are both activation
# nuclides (category 1) and fission product nuclides (category 3).
+# Te129 has been added due to it's link to I129 production.
+
CASL_CHAIN = {
# Nuclide: (Stable, CAT, IFPY, Special yield treatment)
# Stable: True if nuclide has no decay reactions
@@ -187,6 +189,7 @@
'Sb127': (False, 3, 2, None),
'Te127': (False, 3, -1, None),
'Te127_m1': (False, 3, -1, None),
+ 'Te129': (False, 3, 1, None),
'Te129_m1': (False, 3, 2, None),
'Te132': (False, 3, 2, None),
'I127': (True, 3, 1, None),
| diff --git a/tests/unit_tests/test_deplete_chain.py b/tests/unit_tests/test_deplete_chain.py
--- a/tests/unit_tests/test_deplete_chain.py
+++ b/tests/unit_tests/test_deplete_chain.py
@@ -329,3 +329,55 @@ def test_capture_branch_failures(simple_chain):
br = {"C": {"A": 1.0, "B": 1.0}}
with pytest.raises(ValueError, match="C ratios"):
simple_chain.set_capture_branches(br)
+
+
+def test_validate(simple_chain):
+ """Test the validate method"""
+
+ # current chain is invalid
+ # fission yields do not sum to 2.0
+ with pytest.raises(ValueError, match="Nuclide C.*fission yields"):
+ simple_chain.validate(strict=True, tolerance=0.0)
+
+ with pytest.warns(UserWarning) as record:
+ assert not simple_chain.validate(strict=False, quiet=False, tolerance=0.0)
+ assert not simple_chain.validate(strict=False, quiet=True, tolerance=0.0)
+ assert len(record) == 1
+ assert "Nuclide C" in record[0].message.args[0]
+
+ # Fix fission yields but keep to restore later
+ old_yields = simple_chain["C"].yield_data
+ simple_chain["C"].yield_data = {0.0253: [("A", 1.4), ("B", 0.6)]}
+
+ assert simple_chain.validate(strict=True, tolerance=0.0)
+ with pytest.warns(None) as record:
+ assert simple_chain.validate(strict=False, quiet=False, tolerance=0.0)
+ assert len(record) == 0
+
+ # Mess up "earlier" nuclide's reactions
+ decay_mode = simple_chain["A"].decay_modes.pop()
+
+ with pytest.raises(ValueError, match="Nuclide A.*decay mode"):
+ simple_chain.validate(strict=True, tolerance=0.0)
+
+ # restore old fission yields
+ simple_chain["C"].yield_data = old_yields
+
+ with pytest.warns(UserWarning) as record:
+ assert not simple_chain.validate(strict=False, quiet=False, tolerance=0.0)
+ assert len(record) == 2
+ assert "Nuclide A" in record[0].message.args[0]
+ assert "Nuclide C" in record[1].message.args[0]
+
+ # restore decay modes
+ simple_chain["A"].decay_modes.append(decay_mode)
+
+
+def test_validate_inputs():
+ c = Chain()
+
+ with pytest.raises(TypeError, match="tolerance"):
+ c.validate(tolerance=None)
+
+ with pytest.raises(ValueError, match="tolerance"):
+ c.validate(tolerance=-1)
diff --git a/tests/unit_tests/test_deplete_nuclide.py b/tests/unit_tests/test_deplete_nuclide.py
--- a/tests/unit_tests/test_deplete_nuclide.py
+++ b/tests/unit_tests/test_deplete_nuclide.py
@@ -2,6 +2,8 @@
import xml.etree.ElementTree as ET
+import pytest
+
from openmc.deplete import nuclide
@@ -114,3 +116,92 @@ def test_to_xml_element():
assert float(rx_elems[1].get("Q")) == 0.0
assert element.find('neutron_fission_yields') is not None
+
+
+def test_validate():
+
+ nuc = nuclide.Nuclide()
+ nuc.name = "Test"
+
+ # decay modes: type, target, branching_ratio
+
+ nuc.decay_modes = [
+ nuclide.DecayTuple("type 0", "0", 0.5),
+ nuclide.DecayTuple("type 1", "1", 0.5),
+ ]
+
+ # reactions: type, target, Q, branching_ratio
+ nuc.reactions = [
+ nuclide.ReactionTuple("0", "0", 1000, 0.3),
+ nuclide.ReactionTuple("0", "1", 1000, 0.3),
+ nuclide.ReactionTuple("1", "2", 1000, 1.0),
+ nuclide.ReactionTuple("0", "3", 1000, 0.4),
+ ]
+
+ # fission yields
+
+ nuc.yield_data = {
+ 0.0253: [("0", 1.5), ("1", 0.5)],
+ 1e6: [("0", 1.5), ("1", 0.5)],
+ }
+
+ # nuclide is good and should have no warnings raise
+ with pytest.warns(None) as record:
+ assert nuc.validate(strict=True, quiet=False, tolerance=0.0)
+ assert len(record) == 0
+
+ # invalidate decay modes
+ decay = nuc.decay_modes.pop()
+ with pytest.raises(ValueError, match="decay mode"):
+ nuc.validate(strict=True, quiet=False, tolerance=0.0)
+
+ with pytest.warns(UserWarning) as record:
+ assert not nuc.validate(strict=False, quiet=False, tolerance=0.0)
+ assert not nuc.validate(strict=False, quiet=True, tolerance=0.0)
+ assert len(record) == 1
+ assert "decay mode" in record[0].message.args[0]
+
+ # restore decay modes, invalidate reactions
+ nuc.decay_modes.append(decay)
+ reaction = nuc.reactions.pop()
+
+ with pytest.raises(ValueError, match="0 reaction"):
+ nuc.validate(strict=True, quiet=False, tolerance=0.0)
+
+ with pytest.warns(UserWarning) as record:
+ assert not nuc.validate(strict=False, quiet=False, tolerance=0.0)
+ assert not nuc.validate(strict=False, quiet=True, tolerance=0.0)
+ assert len(record) == 1
+ assert "0 reaction" in record[0].message.args[0]
+
+ # restore reactions, invalidate fission yields
+ nuc.reactions.append(reaction)
+ nuc.yield_data[1e6].pop()
+
+ with pytest.raises(ValueError, match=r"fission yields.*1\.0*e"):
+ nuc.validate(strict=True, quiet=False, tolerance=0.0)
+
+ with pytest.warns(UserWarning) as record:
+ assert not nuc.validate(strict=False, quiet=False, tolerance=0.0)
+ assert not nuc.validate(strict=False, quiet=True, tolerance=0.0)
+ assert len(record) == 1
+ assert "1.0" in record[0].message.args[0]
+
+ # invalidate everything, check that error is raised at decay modes
+
+ decay = nuc.decay_modes.pop()
+ reaction = nuc.reactions.pop()
+
+ with pytest.raises(ValueError, match="decay mode"):
+ nuc.validate(strict=True, quiet=False, tolerance=0.0)
+
+ # check for warnings
+ # should be one warning for decay modes, reactions, fission yields
+
+ with pytest.warns(UserWarning) as record:
+ assert not nuc.validate(strict=False, quiet=False, tolerance=0.0)
+ assert not nuc.validate(strict=False, quiet=True, tolerance=0.0)
+ assert len(record) == 3
+ assert "decay mode" in record[0].message.args[0]
+ assert "0 reaction" in record[1].message.args[0]
+ assert "1.0" in record[2].message.args[0]
| Provide validation for depletion Chain
As it was pointed out in #1307, it is not unlikely for a depletion chain to have incomplete branches, where the sum of branching ratios for a given reaction, decay mode, or fission yield do not sum to unity [2 for fission yield distributions].
Solution / sanity check: provide a `Chain.validate` method that looks for potential inconsistencies. Warnings or Exceptions should be raised, depending on a simple setting.
| 2019-08-08T22:02:37Z | [] | [] |
|
openmc-dev/openmc | 1,357 | openmc-dev__openmc-1357 | [
"1327"
] | 384954b099d2786dc4687ce6528fb0708bf1d81a | diff --git a/openmc/deplete/abc.py b/openmc/deplete/abc.py
--- a/openmc/deplete/abc.py
+++ b/openmc/deplete/abc.py
@@ -539,6 +539,7 @@ def generate_tallies(self, materials, mat_indexes):
# Tally group-wise fission reaction rates
self._fission_rate_tally = Tally()
+ self._fission_rate_tally.writable = False
self._fission_rate_tally.scores = ['fission']
self._fission_rate_tally.filters = [MaterialFilter(materials)]
diff --git a/openmc/deplete/helpers.py b/openmc/deplete/helpers.py
--- a/openmc/deplete/helpers.py
+++ b/openmc/deplete/helpers.py
@@ -59,6 +59,7 @@ def generate_tallies(self, materials, scores):
``"(n, gamma)"``, needed for the reaction rate tally.
"""
self._rate_tally = Tally()
+ self._rate_tally.writable = False
self._rate_tally.scores = scores
self._rate_tally.filters = [MaterialFilter(materials)]
@@ -194,6 +195,7 @@ def prepare(self, *args, **kwargs):
"""
self._tally = Tally()
+ self._tally.writable = False
self._tally.scores = [self.score]
def reset(self):
@@ -570,6 +572,7 @@ def generate_tallies(self, materials, mat_indexes):
func_filter = EnergyFunctionFilter()
func_filter.set_data((0, self._upper_energy), (0, self._upper_energy))
weighted_tally = Tally()
+ weighted_tally.writable = False
weighted_tally.scores = ['fission']
weighted_tally.filters = filters + [func_filter]
self._weighted_tally = weighted_tally
diff --git a/openmc/lib/tally.py b/openmc/lib/tally.py
--- a/openmc/lib/tally.py
+++ b/openmc/lib/tally.py
@@ -53,6 +53,9 @@
_dll.openmc_tally_get_type.argtypes = [c_int32, POINTER(c_int32)]
_dll.openmc_tally_get_type.restype = c_int
_dll.openmc_tally_get_type.errcheck = _error_handler
+_dll.openmc_tally_get_writable.argtypes = [c_int32, POINTER(c_bool)]
+_dll.openmc_tally_get_writable.restype = c_int
+_dll.openmc_tally_get_writable.errcheck = _error_handler
_dll.openmc_tally_reset.argtypes = [c_int32]
_dll.openmc_tally_reset.restype = c_int
_dll.openmc_tally_reset.errcheck = _error_handler
@@ -81,6 +84,9 @@
_dll.openmc_tally_set_type.argtypes = [c_int32, c_char_p]
_dll.openmc_tally_set_type.restype = c_int
_dll.openmc_tally_set_type.errcheck = _error_handler
+_dll.openmc_tally_set_writable.argtypes = [c_int32, c_bool]
+_dll.openmc_tally_set_writable.restype = c_int
+_dll.openmc_tally_set_writable.errcheck = _error_handler
_dll.tallies_size.restype = c_size_t
@@ -344,6 +350,16 @@ def std_dev(self):
return std_dev
+ @property
+ def writable(self):
+ writable = c_bool()
+ _dll.openmc_tally_get_writable(self._index, writable)
+ return writable.value
+
+ @writable.setter
+ def writable(self, writable):
+ _dll.openmc_tally_set_writable(self._index, writable)
+
def reset(self):
"""Reset results and num_realizations of tally"""
_dll.openmc_tally_reset(self._index)
diff --git a/openmc/statepoint.py b/openmc/statepoint.py
--- a/openmc/statepoint.py
+++ b/openmc/statepoint.py
@@ -375,13 +375,18 @@ def tallies(self):
for tally_id in tally_ids:
group = tallies_group['tally {}'.format(tally_id)]
- # Read the number of realizations
- n_realizations = group['n_realizations'][()]
+ # Check if tally is internal and therefore has no data
+ if group.attrs.get("internal"):
+ continue
# Create Tally object and assign basic properties
tally = openmc.Tally(tally_id)
tally._sp_filename = self._f.filename
tally.name = group['name'][()].decode() if 'name' in group else ''
+
+ # Read the number of realizations
+ n_realizations = group['n_realizations'][()]
+
tally.estimator = group['estimator'][()].decode()
tally.num_realizations = n_realizations
| diff --git a/tests/regression_tests/deplete/test.py b/tests/regression_tests/deplete/test.py
--- a/tests/regression_tests/deplete/test.py
+++ b/tests/regression_tests/deplete/test.py
@@ -108,11 +108,17 @@ def test_full(run_in_tmpdir):
t_ref, k_ref = res_ref.get_eigenvalue()
k_state = np.empty_like(k_ref)
+ n_tallies = np.empty(N + 1, dtype=int)
+
# Get statepoint files for all BOS points and EOL
for n in range(N + 1):
statepoint = openmc.StatePoint("openmc_simulation_n{}.h5".format(n))
k_n = statepoint.k_combined
k_state[n] = [k_n.nominal_value, k_n.std_dev]
+ n_tallies[n] = len(statepoint.tallies)
# Look for exact match pulling from statepoint and depletion_results
assert np.all(k_state == k_test)
assert np.allclose(k_test, k_ref)
+
+ # Check that no additional tallies are loaded from the files
+ assert np.all(n_tallies == 0)
diff --git a/tests/unit_tests/test_lib.py b/tests/unit_tests/test_lib.py
--- a/tests/unit_tests/test_lib.py
+++ b/tests/unit_tests/test_lib.py
@@ -50,24 +50,24 @@ def pincell_model():
@pytest.fixture(scope='module')
-def capi_init(pincell_model, mpi_intracomm):
+def lib_init(pincell_model, mpi_intracomm):
openmc.lib.init(intracomm=mpi_intracomm)
yield
openmc.lib.finalize()
@pytest.fixture(scope='module')
-def capi_simulation_init(capi_init):
+def lib_simulation_init(lib_init):
openmc.lib.simulation_init()
yield
@pytest.fixture(scope='module')
-def capi_run(capi_simulation_init):
+def lib_run(lib_simulation_init):
openmc.lib.run()
-def test_cell_mapping(capi_init):
+def test_cell_mapping(lib_init):
cells = openmc.lib.cells
assert isinstance(cells, Mapping)
assert len(cells) == 3
@@ -76,7 +76,7 @@ def test_cell_mapping(capi_init):
assert cell_id == cell.id
-def test_cell(capi_init):
+def test_cell(lib_init):
cell = openmc.lib.cells[1]
assert isinstance(cell.fill, openmc.lib.Material)
cell.fill = openmc.lib.materials[1]
@@ -85,7 +85,7 @@ def test_cell(capi_init):
cell.name = "Not fuel"
assert cell.name == "Not fuel"
-def test_cell_temperature(capi_init):
+def test_cell_temperature(lib_init):
cell = openmc.lib.cells[1]
cell.set_temperature(100.0, 0)
assert cell.get_temperature(0) == 100.0
@@ -93,7 +93,7 @@ def test_cell_temperature(capi_init):
assert cell.get_temperature() == 200.0
-def test_new_cell(capi_init):
+def test_new_cell(lib_init):
with pytest.raises(exc.AllocationError):
openmc.lib.Cell(1)
new_cell = openmc.lib.Cell()
@@ -101,7 +101,7 @@ def test_new_cell(capi_init):
assert len(openmc.lib.cells) == 5
-def test_material_mapping(capi_init):
+def test_material_mapping(lib_init):
mats = openmc.lib.materials
assert isinstance(mats, Mapping)
assert len(mats) == 3
@@ -110,7 +110,7 @@ def test_material_mapping(capi_init):
assert mat_id == mat.id
-def test_material(capi_init):
+def test_material(lib_init):
m = openmc.lib.materials[3]
assert m.nuclides == ['H1', 'O16', 'B10', 'B11']
@@ -136,14 +136,14 @@ def test_material(capi_init):
m.name = "Not hot borated water"
assert m.name == "Not hot borated water"
-def test_material_add_nuclide(capi_init):
+def test_material_add_nuclide(lib_init):
m = openmc.lib.materials[3]
m.add_nuclide('Xe135', 1e-12)
assert m.nuclides[-1] == 'Xe135'
assert m.densities[-1] == 1e-12
-def test_new_material(capi_init):
+def test_new_material(lib_init):
with pytest.raises(exc.AllocationError):
openmc.lib.Material(1)
new_mat = openmc.lib.Material()
@@ -151,7 +151,7 @@ def test_new_material(capi_init):
assert len(openmc.lib.materials) == 5
-def test_nuclide_mapping(capi_init):
+def test_nuclide_mapping(lib_init):
nucs = openmc.lib.nuclides
assert isinstance(nucs, Mapping)
assert len(nucs) == 13
@@ -160,7 +160,7 @@ def test_nuclide_mapping(capi_init):
assert name == nuc.name
-def test_settings(capi_init):
+def test_settings(lib_init):
settings = openmc.lib.settings
assert settings.batches == 10
settings.batches = 10
@@ -175,7 +175,7 @@ def test_settings(capi_init):
settings.run_mode = 'eigenvalue'
-def test_tally_mapping(capi_init):
+def test_tally_mapping(lib_init):
tallies = openmc.lib.tallies
assert isinstance(tallies, Mapping)
assert len(tallies) == 3
@@ -184,7 +184,7 @@ def test_tally_mapping(capi_init):
assert tally_id == tally.id
-def test_energy_function_filter(capi_init):
+def test_energy_function_filter(lib_init):
"""Test special __new__ and __init__ for EnergyFunctionFilter"""
efunc = openmc.lib.EnergyFunctionFilter([0.0, 1.0], [0.0, 2.0])
assert len(efunc.energy) == 2
@@ -193,7 +193,7 @@ def test_energy_function_filter(capi_init):
assert (efunc.y == [0.0, 2.0]).all()
-def test_tally(capi_init):
+def test_tally(lib_init):
t = openmc.lib.tallies[1]
assert t.type == 'volume'
assert len(t.filters) == 2
@@ -239,7 +239,7 @@ def test_tally(capi_init):
assert len(t3_f.y) == 3
-def test_new_tally(capi_init):
+def test_new_tally(lib_init):
with pytest.raises(exc.AllocationError):
openmc.lib.Material(1)
new_tally = openmc.lib.Tally()
@@ -249,16 +249,25 @@ def test_new_tally(capi_init):
assert len(openmc.lib.tallies) == 5
-def test_tally_activate(capi_simulation_init):
+def test_tally_activate(lib_simulation_init):
t = openmc.lib.tallies[1]
assert not t.active
t.active = True
assert t.active
-def test_tally_results(capi_run):
+def test_tally_writable(lib_simulation_init):
t = openmc.lib.tallies[1]
- assert t.num_realizations == 10 # t was made active in test_tally
+ assert t.writable
+ t.writable = False
+ assert not t.writable
+ # Revert tally to writable state for lib_run fixtures
+ t.writable = True
+
+
+def test_tally_results(lib_run):
+ t = openmc.lib.tallies[1]
+ assert t.num_realizations == 10 # t was made active in test_tally_active
assert np.all(t.mean >= 0)
nonzero = (t.mean > 0.0)
assert np.all(t.std_dev[nonzero] >= 0)
@@ -269,26 +278,26 @@ def test_tally_results(capi_run):
assert t2.mean.size == (n + 1) * (n + 2) // 2 * 3 # Number of Zernike coeffs * 3 cells
-def test_global_tallies(capi_run):
+def test_global_tallies(lib_run):
assert openmc.lib.num_realizations() == 5
gt = openmc.lib.global_tallies()
for mean, std_dev in gt:
assert mean >= 0
-def test_statepoint(capi_run):
+def test_statepoint(lib_run):
openmc.lib.statepoint_write('test_sp.h5')
assert os.path.exists('test_sp.h5')
-def test_source_bank(capi_run):
+def test_source_bank(lib_run):
source = openmc.lib.source_bank()
assert np.all(source['E'] > 0.0)
assert np.all(source['wgt'] == 1.0)
assert np.allclose(np.linalg.norm(source['u'], axis=1), 1.0)
-def test_by_batch(capi_run):
+def test_by_batch(lib_run):
openmc.lib.hard_reset()
# Running next batch before simulation is initialized should raise an
@@ -313,7 +322,7 @@ def test_by_batch(capi_run):
openmc.lib.simulation_finalize()
-def test_reset(capi_run):
+def test_reset(lib_run):
# Init and run 10 batches.
openmc.lib.hard_reset()
openmc.lib.simulation_init()
@@ -344,7 +353,7 @@ def test_reset(capi_run):
openmc.lib.simulation_finalize()
-def test_reproduce_keff(capi_init):
+def test_reproduce_keff(lib_init):
# Get k-effective after run
openmc.lib.hard_reset()
openmc.lib.run()
@@ -357,7 +366,7 @@ def test_reproduce_keff(capi_init):
assert keff0 == pytest.approx(keff1)
-def test_find_cell(capi_init):
+def test_find_cell(lib_init):
cell, instance = openmc.lib.find_cell((0., 0., 0.))
assert cell is openmc.lib.cells[1]
cell, instance = openmc.lib.find_cell((0.4, 0., 0.))
@@ -366,14 +375,14 @@ def test_find_cell(capi_init):
openmc.lib.find_cell((100., 100., 100.))
-def test_find_material(capi_init):
+def test_find_material(lib_init):
mat = openmc.lib.find_material((0., 0., 0.))
assert mat is openmc.lib.materials[1]
mat = openmc.lib.find_material((0.4, 0., 0.))
assert mat is openmc.lib.materials[2]
-def test_mesh(capi_init):
+def test_mesh(lib_init):
mesh = openmc.lib.RegularMesh()
mesh.dimension = (2, 3, 4)
assert mesh.dimension == (2, 3, 4)
@@ -408,7 +417,7 @@ def test_mesh(capi_init):
assert msf.mesh == mesh
-def test_restart(capi_init, mpi_intracomm):
+def test_restart(lib_init, mpi_intracomm):
# Finalize and re-init to make internal state consistent with XML.
openmc.lib.hard_reset()
openmc.lib.finalize()
@@ -440,7 +449,7 @@ def test_restart(capi_init, mpi_intracomm):
assert keff0 == pytest.approx(keff1)
-def test_load_nuclide(capi_init):
+def test_load_nuclide(lib_init):
# load multiple nuclides
openmc.lib.load_nuclide('H3')
assert 'H3' in openmc.lib.nuclides
@@ -451,7 +460,7 @@ def test_load_nuclide(capi_init):
openmc.lib.load_nuclide('Pu3')
-def test_id_map(capi_init):
+def test_id_map(lib_init):
expected_ids = np.array([[(3, 3), (2, 2), (3, 3)],
[(2, 2), (1, 1), (2, 2)],
[(3, 3), (2, 2), (3, 3)]], dtype='int32')
@@ -469,7 +478,7 @@ def test_id_map(capi_init):
ids = openmc.lib.plot.id_map(s)
assert np.array_equal(expected_ids, ids)
-def test_property_map(capi_init):
+def test_property_map(lib_init):
expected_properties = np.array(
[[(293.6, 0.740582), (293.6, 6.55), (293.6, 0.740582)],
[ (293.6, 6.55), (293.6, 10.29769), (293.6, 6.55)],
@@ -489,7 +498,7 @@ def test_property_map(capi_init):
assert np.allclose(expected_properties, properties, atol=1e-04)
-def test_position(capi_init):
+def test_position(lib_init):
pos = openmc.lib.plot._Position(1.0, 2.0, 3.0)
@@ -502,7 +511,7 @@ def test_position(capi_init):
assert tuple(pos) == (1.3, 2.3, 3.3)
-def test_global_bounding_box(capi_init):
+def test_global_bounding_box(lib_init):
expected_llc = (-0.63, -0.63, -np.inf)
expected_urc = (0.63, 0.63, np.inf)
| Internal tallies for depletion
The depletion framework creates a collection of tallies in order to obtain reaction rates, fission yield weights, and energy deposition [soon]. Some of these tallies can get cumbersome, tallying values in every burnable material, for dozens to hundreds of nuclides per material, etc. Furthermore, these are not necessarily clear to the user, and can increase the size of the statepoint file created. The reaction rates are duplicated in the depletion results file as well. If I create a model that is highly discretized for depletion, it could be problematic to share the statepoint file that may contain tallies that I am more interested in [e.g. spatial power distribution]
I propose the depletion framework utilize "internal" tallies that are not written to the statepoint file at the end of the transport simulation. This could be done in one of two ways.
1) `writeable` attribute
In this manner, tallies created would have a boolean indicating if they should be written or not. By default this should be true. During the writing of the statepoint, tallies that are not marked as writable would be skipped. The depletion framework, through the C API, would mark the tallies created as not-writable to avoid bloating the statepoint file.
Alternatively the flag could be `internal` with the meaning flipped [default to False, only write if internal is False, depletion set the value to True]
2) New tally class
This one is a bit more dramatic and would involve creating a new subclass of tally that is not written to the statepoint file at all. The depletion framework would utilize these tallies rather than those created by the C API currently. The benefit of this is these tallies are more expressive by design: I know that an `openmc::InternalTally` behaves differently than a `openmc::Tally` class immediately. Since we also [usually] don't care about uncertainties in reaction rates or power for depletion, we could potentially alter how these are scored / stored to only provide the depletion interface with the tally results, rather than having to select the correct position in `tally.results`, seen as the third dimension below
https://github.com/openmc-dev/openmc/blob/d9c66fc13f31b7b0e8f60184a8b2da013b7cf56e/openmc/deplete/helpers.py#L83
| 2019-09-20T17:37:12Z | [] | [] |
|
openmc-dev/openmc | 1,380 | openmc-dev__openmc-1380 | [
"1379"
] | 6799da13f1af3ca4e468c58df5f70a9c057092dd | diff --git a/openmc/cell.py b/openmc/cell.py
--- a/openmc/cell.py
+++ b/openmc/cell.py
@@ -63,6 +63,10 @@ class Cell(IDManagerMixin):
\sin\phi \sin\theta \sin\psi & -\sin\phi \cos\psi + \cos\phi
\sin\theta \sin\psi \\ -\sin\theta & \sin\phi \cos\theta & \cos\phi
\cos\theta \end{array} \right ]
+
+ A rotation matrix can also be specified directly by setting this
+ attribute to a nested list (or 2D numpy array) that specifies each
+ element of the matrix.
rotation_matrix : numpy.ndarray
The rotation matrix defined by the angles specified in the
:attr:`Cell.rotation` property.
@@ -227,21 +231,24 @@ def fill(self, fill):
@rotation.setter
def rotation(self, rotation):
- cv.check_type('cell rotation', rotation, Iterable, Real)
cv.check_length('cell rotation', rotation, 3)
self._rotation = np.asarray(rotation)
# Save rotation matrix -- the reason we do this instead of having it be
# automatically calculated when the rotation_matrix property is accessed
# is so that plotting on a rotated geometry can be done faster.
- phi, theta, psi = self.rotation*(-pi/180.)
- c3, s3 = cos(phi), sin(phi)
- c2, s2 = cos(theta), sin(theta)
- c1, s1 = cos(psi), sin(psi)
- self._rotation_matrix = np.array([
- [c1*c2, c1*s2*s3 - c3*s1, s1*s3 + c1*c3*s2],
- [c2*s1, c1*c3 + s1*s2*s3, c3*s1*s2 - c1*s3],
- [-s2, c2*s3, c2*c3]])
+ if self._rotation.ndim == 2:
+ # User specified rotation matrix directly
+ self._rotation_matrix = self._rotation
+ else:
+ phi, theta, psi = self.rotation*(-pi/180.)
+ c3, s3 = cos(phi), sin(phi)
+ c2, s2 = cos(theta), sin(theta)
+ c1, s1 = cos(psi), sin(psi)
+ self._rotation_matrix = np.array([
+ [c1*c2, c1*s2*s3 - c3*s1, s1*s3 + c1*c3*s2],
+ [c2*s1, c1*c3 + s1*s2*s3, c3*s1*s2 - c1*s3],
+ [-s2, c2*s3, c2*c3]])
@translation.setter
def translation(self, translation):
@@ -516,7 +523,7 @@ def create_surface_elements(node, element):
element.set("translation", ' '.join(map(str, self.translation)))
if self.rotation is not None:
- element.set("rotation", ' '.join(map(str, self.rotation)))
+ element.set("rotation", ' '.join(map(str, self.rotation.ravel())))
return element
diff --git a/openmc/summary.py b/openmc/summary.py
--- a/openmc/summary.py
+++ b/openmc/summary.py
@@ -154,8 +154,9 @@ def _read_cells(self):
if 'rotation' in group:
rotation = group['rotation'][()]
- rotation = np.asarray(rotation, dtype=np.int)
- cell._rotation = rotation
+ if rotation.size == 9:
+ rotation.shape = (3, 3)
+ cell.rotation = rotation
elif fill_type == 'material':
cell.temperature = group['temperature'][()]
| diff --git a/tests/unit_tests/test_geometry.py b/tests/unit_tests/test_geometry.py
--- a/tests/unit_tests/test_geometry.py
+++ b/tests/unit_tests/test_geometry.py
@@ -280,3 +280,24 @@ def test_from_xml(run_in_tmpdir, mixed_lattice_model):
ll, ur = geom.bounding_box
assert ll == pytest.approx((-6.0, -6.0, -np.inf))
assert ur == pytest.approx((6.0, 6.0, np.inf))
+
+
+def test_rotation_matrix():
+ """Test ability to set a rotation matrix directly"""
+ y = openmc.YPlane()
+ cyl1 = openmc.ZCylinder(r=1.0)
+ cyl2 = openmc.ZCylinder(r=2.0, boundary_type='vacuum')
+
+ # Create a universe and then reflect in the y-direction
+ c1 = openmc.Cell(region=-cyl1 & +y)
+ c2 = openmc.Cell(region=+cyl1 & +y)
+ c3 = openmc.Cell(region=-y)
+ univ = openmc.Universe(cells=[c1, c2, c3])
+ c = openmc.Cell(fill=univ, region=-cyl2)
+ c.rotation = [[1, 0, 0], [0, -1, 0], [0, 0, 1]]
+ assert np.all(c.rotation_matrix == c.rotation)
+ geom = openmc.Geometry([c])
+
+ assert geom.find((0.0, 0.5, 0.0))[-1] == c3
+ assert geom.find((0.0, -0.5, 0.0))[-1] == c1
+ assert geom.find((0.0, -1.5, 0.0))[-1] == c2
| Allow explicit instanciation of rotation matrix
Using the Tait-Bryan angles we cannot represent reflection of universes, this is needed to represent some geometries, therefore allow explicit instanciation through overloading the read of the rotation element to allow full spec i.e. ```<rotation="1 0 0 0 -1 0 0 0 1"/>```
| I've confirmed that mathematically the rotation matrix you have there is indeed impossible to represent using Tait-Bryan angles, so I'm +1 on allowing explicit specification of the rotation matrix. Should be a simple change. | 2019-10-16T04:02:28Z | [] | [] |
openmc-dev/openmc | 1,481 | openmc-dev__openmc-1481 | [
"1410"
] | dfe4d911b556127800beeba5ffec1b0356d743fe | diff --git a/examples/python/pincell_depletion/restart_depletion.py b/examples/python/pincell_depletion/restart_depletion.py
--- a/examples/python/pincell_depletion/restart_depletion.py
+++ b/examples/python/pincell_depletion/restart_depletion.py
@@ -1,25 +1,7 @@
import openmc
import openmc.deplete
-import numpy as np
import matplotlib.pyplot as plt
-###############################################################################
-# Simulation Input File Parameters
-###############################################################################
-
-# OpenMC simulation parameters
-batches = 100
-inactive = 10
-particles = 1000
-
-# Depletion simulation parameters
-time_step = 1*24*60*60 # s
-final_time = 5*24*60*60 # s
-time_steps = np.full(final_time // time_step, time_step)
-
-chain_file = './chain_simple.xml'
-power = 174 # W/cm, for 2D simulations only (use W for 3D)
-
###############################################################################
# Load previous simulation results
###############################################################################
@@ -37,31 +19,34 @@
###############################################################################
# Instantiate a Settings object, set all runtime parameters
-settings_file = openmc.Settings()
-settings_file.batches = batches
-settings_file.inactive = inactive
-settings_file.particles = particles
+settings = openmc.Settings()
+settings.batches = 100
+settings.inactive = 10
+settings.particles = 10000
# Create an initial uniform spatial source distribution over fissionable zones
bounds = [-0.62992, -0.62992, -1, 0.62992, 0.62992, 1]
uniform_dist = openmc.stats.Box(bounds[:3], bounds[3:], only_fissionable=True)
-settings_file.source = openmc.source.Source(space=uniform_dist)
+settings.source = openmc.source.Source(space=uniform_dist)
entropy_mesh = openmc.RegularMesh()
entropy_mesh.lower_left = [-0.39218, -0.39218, -1.e50]
entropy_mesh.upper_right = [0.39218, 0.39218, 1.e50]
entropy_mesh.dimension = [10, 10, 1]
-settings_file.entropy_mesh = entropy_mesh
+settings.entropy_mesh = entropy_mesh
###############################################################################
# Initialize and run depletion calculation
###############################################################################
-op = openmc.deplete.Operator(geometry, settings_file, chain_file,
- previous_results)
+# Create depletion "operator"
+chain_file = './chain_simple.xml'
+op = openmc.deplete.Operator(geometry, settings, chain_file, previous_results)
# Perform simulation using the predictor algorithm
-integrator = openmc.deplete.PredictorIntegrator(op, time_steps, power)
+time_steps = [1.0, 1.0, 1.0, 1.0, 1.0] # days
+power = 174 # W/cm, for 2D simulations only (use W for 3D)
+integrator = openmc.deplete.PredictorIntegrator(op, time_steps, power, timestep_units='d')
integrator.integrate()
###############################################################################
@@ -77,27 +62,28 @@
# Obtain U235 concentration as a function of time
time, n_U235 = results.get_atoms('1', 'U235')
-# Obtain Xe135 absorption as a function of time
-time, Xe_gam = results.get_reaction_rate('1', 'Xe135', '(n,gamma)')
+# Obtain Xe135 capture reaction rate as a function of time
+time, Xe_capture = results.get_reaction_rate('1', 'Xe135', '(n,gamma)')
###############################################################################
# Generate plots
###############################################################################
+days = 24*60*60
plt.figure()
-plt.plot(time/(24*60*60), keff, label="K-effective")
+plt.plot(time/days, keff, label="K-effective")
plt.xlabel("Time (days)")
plt.ylabel("Keff")
plt.show()
plt.figure()
-plt.plot(time/(24*60*60), n_U235, label="U 235")
+plt.plot(time/days, n_U235, label="U 235")
plt.xlabel("Time (days)")
plt.ylabel("n U5 (-)")
plt.show()
plt.figure()
-plt.plot(time/(24*60*60), Xe_gam, label="Xe135 absorption")
+plt.plot(time/days, Xe_capture, label="Xe135 capture")
plt.xlabel("Time (days)")
plt.ylabel("RR (-)")
plt.show()
diff --git a/examples/python/pincell_depletion/run_depletion.py b/examples/python/pincell_depletion/run_depletion.py
--- a/examples/python/pincell_depletion/run_depletion.py
+++ b/examples/python/pincell_depletion/run_depletion.py
@@ -1,47 +1,31 @@
+from math import pi
+
import openmc
import openmc.deplete
-import numpy as np
import matplotlib.pyplot as plt
-###############################################################################
-# Simulation Input File Parameters
-###############################################################################
-
-# OpenMC simulation parameters
-batches = 100
-inactive = 10
-particles = 1000
-
-# Depletion simulation parameters
-time_step = 1*24*60*60 # s
-final_time = 5*24*60*60 # s
-time_steps = np.full(final_time // time_step, time_step)
-chain_file = './chain_simple.xml'
-power = 174 # W/cm, for 2D simulations only (use W for 3D)
-
###############################################################################
# Define materials
###############################################################################
# Instantiate some Materials and register the appropriate Nuclides
-uo2 = openmc.Material(material_id=1, name='UO2 fuel at 2.4% wt enrichment')
+uo2 = openmc.Material(name='UO2 fuel at 2.4% wt enrichment')
uo2.set_density('g/cm3', 10.29769)
uo2.add_element('U', 1., enrichment=2.4)
uo2.add_element('O', 2.)
-uo2.depletable = True
-helium = openmc.Material(material_id=2, name='Helium for gap')
+helium = openmc.Material(name='Helium for gap')
helium.set_density('g/cm3', 0.001598)
helium.add_element('He', 2.4044e-4)
-zircaloy = openmc.Material(material_id=3, name='Zircaloy 4')
+zircaloy = openmc.Material(name='Zircaloy 4')
zircaloy.set_density('g/cm3', 6.55)
-zircaloy.add_element('Sn', 0.014 , 'wo')
+zircaloy.add_element('Sn', 0.014, 'wo')
zircaloy.add_element('Fe', 0.00165, 'wo')
-zircaloy.add_element('Cr', 0.001 , 'wo')
+zircaloy.add_element('Cr', 0.001, 'wo')
zircaloy.add_element('Zr', 0.98335, 'wo')
-borated_water = openmc.Material(material_id=4, name='Borated water')
+borated_water = openmc.Material(name='Borated water')
borated_water.set_density('g/cm3', 0.740582)
borated_water.add_element('B', 4.0e-5)
borated_water.add_element('H', 5.0e-2)
@@ -52,87 +36,62 @@
# Create geometry
###############################################################################
-# Instantiate ZCylinder surfaces
-fuel_or = openmc.ZCylinder(surface_id=1, x0=0, y0=0, r=0.39218, name='Fuel OR')
-clad_ir = openmc.ZCylinder(surface_id=2, x0=0, y0=0, r=0.40005, name='Clad IR')
-clad_or = openmc.ZCylinder(surface_id=3, x0=0, y0=0, r=0.45720, name='Clad OR')
-left = openmc.XPlane(surface_id=4, x0=-0.62992, name='left')
-right = openmc.XPlane(surface_id=5, x0=0.62992, name='right')
-bottom = openmc.YPlane(surface_id=6, y0=-0.62992, name='bottom')
-top = openmc.YPlane(surface_id=7, y0=0.62992, name='top')
-
-left.boundary_type = 'reflective'
-right.boundary_type = 'reflective'
-top.boundary_type = 'reflective'
-bottom.boundary_type = 'reflective'
-
-# Instantiate Cells
-fuel = openmc.Cell(cell_id=1, name='cell 1')
-gap = openmc.Cell(cell_id=2, name='cell 2')
-clad = openmc.Cell(cell_id=3, name='cell 3')
-water = openmc.Cell(cell_id=4, name='cell 4')
-
-# Use surface half-spaces to define regions
-fuel.region = -fuel_or
-gap.region = +fuel_or & -clad_ir
-clad.region = +clad_ir & -clad_or
-water.region = +clad_or & +left & -right & +bottom & -top
-
-# Register Materials with Cells
-fuel.fill = uo2
-gap.fill = helium
-clad.fill = zircaloy
-water.fill = borated_water
-
-# Instantiate Universe
-root = openmc.Universe(universe_id=0, name='root universe')
-
-# Register Cells with Universe
-root.add_cells([fuel, gap, clad, water])
-
-# Instantiate a Geometry, register the root Universe
-geometry = openmc.Geometry(root)
+# Define surfaces
+pitch = 1.25984
+fuel_or = openmc.ZCylinder(r=0.39218, name='Fuel OR')
+clad_ir = openmc.ZCylinder(r=0.40005, name='Clad IR')
+clad_or = openmc.ZCylinder(r=0.45720, name='Clad OR')
+box = openmc.model.rectangular_prism(pitch, pitch, boundary_type='reflective')
+
+# Define cells
+fuel = openmc.Cell(fill=uo2, region=-fuel_or)
+gap = openmc.Cell(fill=helium, region=+fuel_or & -clad_ir)
+clad = openmc.Cell(fill=zircaloy, region=+clad_ir & -clad_or)
+water = openmc.Cell(fill=borated_water, region=+clad_or & box)
+
+# Define overall geometry
+geometry = openmc.Geometry([fuel, gap, clad, water])
###############################################################################
# Set volumes of depletable materials
###############################################################################
-# Compute cell areas
-area = {}
-area[fuel] = np.pi * fuel_or.coefficients['r'] ** 2
-
-# Set materials volume for depletion. Set to an area for 2D simulations
-uo2.volume = area[fuel]
+# Set material volume for depletion. For 2D simulations, this should be an area.
+uo2.volume = pi * fuel_or.r**2
###############################################################################
# Transport calculation settings
###############################################################################
# Instantiate a Settings object, set all runtime parameters, and export to XML
-settings_file = openmc.Settings()
-settings_file.batches = batches
-settings_file.inactive = inactive
-settings_file.particles = particles
+settings = openmc.Settings()
+settings.batches = 100
+settings.inactive = 10
+settings.particles = 1000
# Create an initial uniform spatial source distribution over fissionable zones
bounds = [-0.62992, -0.62992, -1, 0.62992, 0.62992, 1]
uniform_dist = openmc.stats.Box(bounds[:3], bounds[3:], only_fissionable=True)
-settings_file.source = openmc.source.Source(space=uniform_dist)
+settings.source = openmc.source.Source(space=uniform_dist)
entropy_mesh = openmc.RegularMesh()
entropy_mesh.lower_left = [-0.39218, -0.39218, -1.e50]
entropy_mesh.upper_right = [0.39218, 0.39218, 1.e50]
entropy_mesh.dimension = [10, 10, 1]
-settings_file.entropy_mesh = entropy_mesh
+settings.entropy_mesh = entropy_mesh
###############################################################################
# Initialize and run depletion calculation
###############################################################################
-op = openmc.deplete.Operator(geometry, settings_file, chain_file)
+# Create depletion "operator"
+chain_file = './chain_simple.xml'
+op = openmc.deplete.Operator(geometry, settings, chain_file)
# Perform simulation using the predictor algorithm
-integrator = openmc.deplete.PredictorIntegrator(op, time_steps, power)
+time_steps = [1.0, 1.0, 1.0, 1.0, 1.0] # days
+power = 174 # W/cm, for 2D simulations only (use W for 3D)
+integrator = openmc.deplete.PredictorIntegrator(op, time_steps, power, timestep_units='d')
integrator.integrate()
###############################################################################
@@ -148,27 +107,28 @@
# Obtain U235 concentration as a function of time
time, n_U235 = results.get_atoms('1', 'U235')
-# Obtain Xe135 absorption as a function of time
-time, Xe_gam = results.get_reaction_rate('1', 'Xe135', '(n,gamma)')
+# Obtain Xe135 capture reaction rate as a function of time
+time, Xe_capture = results.get_reaction_rate('1', 'Xe135', '(n,gamma)')
###############################################################################
# Generate plots
###############################################################################
+days = 24*60*60
plt.figure()
-plt.plot(time/(24*60*60), keff, label="K-effective")
+plt.plot(time/days, keff, label="K-effective")
plt.xlabel("Time (days)")
plt.ylabel("Keff")
plt.show()
plt.figure()
-plt.plot(time/(24*60*60), n_U235, label="U 235")
+plt.plot(time/days, n_U235, label="U235")
plt.xlabel("Time (days)")
plt.ylabel("n U5 (-)")
plt.show()
plt.figure()
-plt.plot(time/(24*60*60), Xe_gam, label="Xe135 absorption")
+plt.plot(time/days, Xe_capture, label="Xe135 capture")
plt.xlabel("Time (days)")
plt.ylabel("RR (-)")
plt.show()
diff --git a/openmc/deplete/abc.py b/openmc/deplete/abc.py
--- a/openmc/deplete/abc.py
+++ b/openmc/deplete/abc.py
@@ -31,6 +31,10 @@
"Integrator", "SIIntegrator", "DepSystemSolver"]
+_SECONDS_PER_MINUTE = 60
+_SECONDS_PER_HOUR = 60*60
+_SECONDS_PER_DAY = 24*60*60
+
OperatorResult = namedtuple('OperatorResult', ['k', 'rates'])
OperatorResult.__doc__ = """\
Result of applying transport operator
@@ -597,9 +601,11 @@ class Integrator(ABC):
----------
operator : openmc.deplete.TransportOperator
Operator to perform transport simulations
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not
- cumulative.
+ timesteps : iterable of float or iterable of tuple
+ Array of timesteps. Note that values are not cumulative. The units are
+ specified by the `timestep_units` argument when `timesteps` is an
+ iterable of float. Alternatively, units can be specified for each step
+ by passing an iterable of (value, unit) tuples.
power : float or iterable of float, optional
Power of the reactor in [W]. A single value indicates that
the power is constant over all timesteps. An iterable
@@ -612,6 +618,11 @@ class Integrator(ABC):
Power density of the reactor in [W/gHM]. It is multiplied by
initial heavy metal inventory to get total power if ``power``
is not speficied.
+ timestep_units : {'s', 'min', 'h', 'd', 'MWd/kg'}
+ Units for values specified in the `timesteps` argument. 's' means
+ seconds, 'min' means minutes, 'h' means hours, and 'MWd/kg' indicates
+ that the values are given in burnup (MW-d of energy deposited per
+ kilogram of initial heavy metal).
Attributes
----------
@@ -625,7 +636,8 @@ class Integrator(ABC):
Power of the reactor in [W] for each interval in :attr:`timesteps`
"""
- def __init__(self, operator, timesteps, power=None, power_density=None):
+ def __init__(self, operator, timesteps, power=None, power_density=None,
+ timestep_units='s'):
# Check number of stages previously used
if operator.prev_res is not None:
res = operator.prev_res[-1]
@@ -638,27 +650,59 @@ def __init__(self, operator, timesteps, power=None, power_density=None):
self._num_stages))
self.operator = operator
self.chain = operator.chain
- if not isinstance(timesteps, Iterable):
- self.timesteps = [timesteps]
- else:
- self.timesteps = timesteps
+
+ # Determine power and normalize units to W
if power is None:
if power_density is None:
raise ValueError("Either power or power density must be set")
if not isinstance(power_density, Iterable):
power = power_density * operator.heavy_metal
else:
- power = [p * operator.heavy_metal for p in power_density]
-
+ power = [p*operator.heavy_metal for p in power_density]
if not isinstance(power, Iterable):
# Ensure that power is single value if that is the case
- power = [power] * len(self.timesteps)
- elif len(power) != len(self.timesteps):
+ power = [power] * len(timesteps)
+
+ if len(power) != len(timesteps):
raise ValueError(
- "Number of time steps != number of powers. {} vs {}".format(
- len(self.timesteps), len(power)))
+ "Number of time steps ({}) != number of powers ({})".format(
+ len(timesteps), len(power)))
- self.power = power
+ # Get list of times / units
+ if isinstance(timesteps[0], Iterable):
+ times, units = zip(*timesteps)
+ else:
+ times = timesteps
+ units = [timestep_units] * len(timesteps)
+
+ # Determine number of seconds for each timestep
+ seconds = []
+ for time, unit, watts in zip(times, units, power):
+ # Make sure values passed make sense
+ check_type('timestep', time, Real)
+ check_greater_than('timestep', time, 0.0, False)
+ check_type('timestep units', unit, str)
+ check_type('power', watts, Real)
+ check_greater_than('power', watts, 0.0, True)
+
+ if unit in ('s', 'sec'):
+ seconds.append(time)
+ elif unit in ('min', 'minute'):
+ seconds.append(time*_SECONDS_PER_MINUTE)
+ elif unit in ('h', 'hr', 'hour'):
+ seconds.append(time*_SECONDS_PER_HOUR)
+ elif unit in ('d', 'day'):
+ seconds.append(time*_SECONDS_PER_DAY)
+ elif unit.lower() == 'mwd/kg':
+ watt_days_per_kg = 1e6*time
+ kilograms = 1e-3*operator.heavy_metal
+ days = watt_days_per_kg * kilograms / watts
+ seconds.append(days*_SECONDS_PER_DAY)
+ else:
+ raise ValueError("Invalid timestep unit '{}'".format(unit))
+
+ self.timesteps = asarray(seconds)
+ self.power = asarray(power)
@abstractmethod
def __call__(self, conc, rates, dt, power, i):
@@ -772,9 +816,11 @@ class SIIntegrator(Integrator):
----------
operator : openmc.deplete.TransportOperator
The operator object to simulate on.
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not
- cumulative.
+ timesteps : iterable of float or iterable of tuple
+ Array of timesteps. Note that values are not cumulative. The units are
+ specified by the `timestep_units` argument when `timesteps` is an
+ iterable of float. Alternatively, units can be specified for each step
+ by passing an iterable of (value, unit) tuples.
power : float or iterable of float, optional
Power of the reactor in [W]. A single value indicates that
the power is constant over all timesteps. An iterable
@@ -787,6 +833,11 @@ class SIIntegrator(Integrator):
Power density of the reactor in [W/gHM]. It is multiplied by
initial heavy metal inventory to get total power if ``power``
is not speficied.
+ timestep_units : {'s', 'min', 'h', 'd', 'MWd/kg'}
+ Units for values specified in the `timesteps` argument. 's' means
+ seconds, 'min' means minutes, 'h' means hours, and 'MWd/kg' indicates
+ that the values are given in burnup (MW-d of energy deposited per
+ kilogram of initial heavy metal).
n_steps : int, optional
Number of stochastic iterations per depletion interval.
Must be greater than zero. Default : 10
@@ -805,10 +856,10 @@ class SIIntegrator(Integrator):
Number of stochastic iterations per depletion interval
"""
def __init__(self, operator, timesteps, power=None, power_density=None,
- n_steps=10):
+ timestep_units='s', n_steps=10):
check_type("n_steps", n_steps, Integral)
check_greater_than("n_steps", n_steps, 0)
- super().__init__(operator, timesteps, power, power_density)
+ super().__init__(operator, timesteps, power, power_density, timestep_units)
self.n_steps = n_steps
def _get_bos_data_from_operator(self, step_index, step_power, bos_conc):
diff --git a/openmc/deplete/integrators.py b/openmc/deplete/integrators.py
--- a/openmc/deplete/integrators.py
+++ b/openmc/deplete/integrators.py
@@ -31,9 +31,11 @@ class PredictorIntegrator(Integrator):
----------
operator : openmc.deplete.TransportOperator
Operator to perform transport simulations
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not
- cumulative.
+ timesteps : iterable of float or iterable of tuple
+ Array of timesteps. Note that values are not cumulative. The units are
+ specified by the `timestep_units` argument when `timesteps` is an
+ iterable of float. Alternatively, units can be specified for each step
+ by passing an iterable of (value, unit) tuples.
power : float or iterable of float, optional
Power of the reactor in [W]. A single value indicates that
the power is constant over all timesteps. An iterable
@@ -46,6 +48,11 @@ class PredictorIntegrator(Integrator):
Power density of the reactor in [W/gHM]. It is multiplied by
initial heavy metal inventory to get total power if ``power``
is not speficied.
+ timestep_units : {'s', 'min', 'h', 'd', 'MWd/kg'}
+ Units for values specified in the `timesteps` argument. 's' means
+ seconds, 'min' means minutes, 'h' means hours, and 'MWd/kg' indicates
+ that the values are given in burnup (MW-d of energy deposited per
+ kilogram of initial heavy metal).
Attributes
----------
@@ -113,9 +120,11 @@ class CECMIntegrator(Integrator):
----------
operator : openmc.deplete.TransportOperator
Operator to perform transport simulations
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not
- cumulative.
+ timesteps : iterable of float or iterable of tuple
+ Array of timesteps. Note that values are not cumulative. The units are
+ specified by the `timestep_units` argument when `timesteps` is an
+ iterable of float. Alternatively, units can be specified for each step
+ by passing an iterable of (value, unit) tuples.
power : float or iterable of float, optional
Power of the reactor in [W]. A single value indicates that
the power is constant over all timesteps. An iterable
@@ -128,6 +137,11 @@ class CECMIntegrator(Integrator):
Power density of the reactor in [W/gHM]. It is multiplied by
initial heavy metal inventory to get total power if ``power``
is not speficied.
+ timestep_units : {'s', 'min', 'h', 'd', 'MWd/kg'}
+ Units for values specified in the `timesteps` argument. 's' means
+ seconds, 'min' means minutes, 'h' means hours, and 'MWd/kg' indicates
+ that the values are given in burnup (MW-d of energy deposited per
+ kilogram of initial heavy metal).
Attributes
----------
@@ -203,9 +217,11 @@ class CF4Integrator(Integrator):
----------
operator : openmc.deplete.TransportOperator
Operator to perform transport simulations
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not
- cumulative.
+ timesteps : iterable of float or iterable of tuple
+ Array of timesteps. Note that values are not cumulative. The units are
+ specified by the `timestep_units` argument when `timesteps` is an
+ iterable of float. Alternatively, units can be specified for each step
+ by passing an iterable of (value, unit) tuples.
power : float or iterable of float, optional
Power of the reactor in [W]. A single value indicates that
the power is constant over all timesteps. An iterable
@@ -218,6 +234,11 @@ class CF4Integrator(Integrator):
Power density of the reactor in [W/gHM]. It is multiplied by
initial heavy metal inventory to get total power if ``power``
is not speficied.
+ timestep_units : {'s', 'min', 'h', 'd', 'MWd/kg'}
+ Units for values specified in the `timesteps` argument. 's' means
+ seconds, 'min' means minutes, 'h' means hours, and 'MWd/kg' indicates
+ that the values are given in burnup (MW-d of energy deposited per
+ kilogram of initial heavy metal).
Attributes
----------
@@ -310,9 +331,11 @@ class CELIIntegrator(Integrator):
----------
operator : openmc.deplete.TransportOperator
Operator to perform transport simulations
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not
- cumulative.
+ timesteps : iterable of float or iterable of tuple
+ Array of timesteps. Note that values are not cumulative. The units are
+ specified by the `timestep_units` argument when `timesteps` is an
+ iterable of float. Alternatively, units can be specified for each step
+ by passing an iterable of (value, unit) tuples.
power : float or iterable of float, optional
Power of the reactor in [W]. A single value indicates that
the power is constant over all timesteps. An iterable
@@ -325,6 +348,11 @@ class CELIIntegrator(Integrator):
Power density of the reactor in [W/gHM]. It is multiplied by
initial heavy metal inventory to get total power if ``power``
is not speficied.
+ timestep_units : {'s', 'min', 'h', 'd', 'MWd/kg'}
+ Units for values specified in the `timesteps` argument. 's' means
+ seconds, 'min' means minutes, 'h' means hours, and 'MWd/kg' indicates
+ that the values are given in burnup (MW-d of energy deposited per
+ kilogram of initial heavy metal).
Attributes
----------
@@ -404,9 +432,11 @@ class EPCRK4Integrator(Integrator):
----------
operator : openmc.deplete.TransportOperator
Operator to perform transport simulations
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not
- cumulative.
+ timesteps : iterable of float or iterable of tuple
+ Array of timesteps. Note that values are not cumulative. The units are
+ specified by the `timestep_units` argument when `timesteps` is an
+ iterable of float. Alternatively, units can be specified for each step
+ by passing an iterable of (value, unit) tuples.
power : float or iterable of float, optional
Power of the reactor in [W]. A single value indicates that
the power is constant over all timesteps. An iterable
@@ -419,6 +449,11 @@ class EPCRK4Integrator(Integrator):
Power density of the reactor in [W/gHM]. It is multiplied by
initial heavy metal inventory to get total power if ``power``
is not speficied.
+ timestep_units : {'s', 'min', 'h', 'd', 'MWd/kg'}
+ Units for values specified in the `timesteps` argument. 's' means
+ seconds, 'min' means minutes, 'h' means hours, and 'MWd/kg' indicates
+ that the values are given in burnup (MW-d of energy deposited per
+ kilogram of initial heavy metal).
Attributes
----------
@@ -518,9 +553,11 @@ class LEQIIntegrator(Integrator):
----------
operator : openmc.deplete.TransportOperator
Operator to perform transport simulations
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not
- cumulative.
+ timesteps : iterable of float or iterable of tuple
+ Array of timesteps. Note that values are not cumulative. The units are
+ specified by the `timestep_units` argument when `timesteps` is an
+ iterable of float. Alternatively, units can be specified for each step
+ by passing an iterable of (value, unit) tuples.
power : float or iterable of float, optional
Power of the reactor in [W]. A single value indicates that
the power is constant over all timesteps. An iterable
@@ -533,6 +570,11 @@ class LEQIIntegrator(Integrator):
Power density of the reactor in [W/gHM]. It is multiplied by
initial heavy metal inventory to get total power if ``power``
is not speficied.
+ timestep_units : {'s', 'min', 'h', 'd', 'MWd/kg'}
+ Units for values specified in the `timesteps` argument. 's' means
+ seconds, 'min' means minutes, 'h' means hours, and 'MWd/kg' indicates
+ that the values are given in burnup (MW-d of energy deposited per
+ kilogram of initial heavy metal).
Attributes
----------
@@ -629,9 +671,11 @@ class SICELIIntegrator(SIIntegrator):
----------
operator : openmc.deplete.TransportOperator
The operator object to simulate on.
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not
- cumulative.
+ timesteps : iterable of float or iterable of tuple
+ Array of timesteps. Note that values are not cumulative. The units are
+ specified by the `timestep_units` argument when `timesteps` is an
+ iterable of float. Alternatively, units can be specified for each step
+ by passing an iterable of (value, unit) tuples.
power : float or iterable of float, optional
Power of the reactor in [W]. A single value indicates that
the power is constant over all timesteps. An iterable
@@ -644,6 +688,11 @@ class SICELIIntegrator(SIIntegrator):
Power density of the reactor in [W/gHM]. It is multiplied by
initial heavy metal inventory to get total power if ``power``
is not speficied.
+ timestep_units : {'s', 'min', 'h', 'd', 'MWd/kg'}
+ Units for values specified in the `timesteps` argument. 's' means
+ seconds, 'min' means minutes, 'h' means hours, and 'MWd/kg' indicates
+ that the values are given in burnup (MW-d of energy deposited per
+ kilogram of initial heavy metal).
n_steps : int, optional
Number of stochastic iterations per depletion interval.
Must be greater than zero. Default : 10
@@ -730,9 +779,11 @@ class SILEQIIntegrator(SIIntegrator):
----------
operator : openmc.deplete.TransportOperator
The operator object to simulate on.
- timesteps : iterable of float
- Array of timesteps in units of [s]. Note that values are not
- cumulative.
+ timesteps : iterable of float or iterable of tuple
+ Array of timesteps. Note that values are not cumulative. The units are
+ specified by the `timestep_units` argument when `timesteps` is an
+ iterable of float. Alternatively, units can be specified for each step
+ by passing an iterable of (value, unit) tuples.
power : float or iterable of float, optional
Power of the reactor in [W]. A single value indicates that
the power is constant over all timesteps. An iterable
@@ -745,6 +796,11 @@ class SILEQIIntegrator(SIIntegrator):
Power density of the reactor in [W/gHM]. It is multiplied by
initial heavy metal inventory to get total power if ``power``
is not speficied.
+ timestep_units : {'s', 'min', 'h', 'd', 'MWd/kg'}
+ Units for values specified in the `timesteps` argument. 's' means
+ seconds, 'min' means minutes, 'h' means hours, and 'MWd/kg' indicates
+ that the values are given in burnup (MW-d of energy deposited per
+ kilogram of initial heavy metal).
n_steps : int, optional
Number of stochastic iterations per depletion interval.
Must be greater than zero. Default : 10
| diff --git a/tests/unit_tests/test_deplete_integrator.py b/tests/unit_tests/test_deplete_integrator.py
--- a/tests/unit_tests/test_deplete_integrator.py
+++ b/tests/unit_tests/test_deplete_integrator.py
@@ -7,6 +7,7 @@
"""
import copy
+from random import uniform
from unittest.mock import MagicMock
import numpy as np
@@ -15,11 +16,24 @@
from openmc.deplete import (
ReactionRates, Results, ResultsList, comm, OperatorResult,
- PredictorIntegrator, SICELIIntegrator)
+ PredictorIntegrator, CECMIntegrator, CF4Integrator, CELIIntegrator,
+ EPCRK4Integrator, LEQIIntegrator, SICELIIntegrator, SILEQIIntegrator)
from tests import dummy_operator
+INTEGRATORS = [
+ PredictorIntegrator,
+ CECMIntegrator,
+ CF4Integrator,
+ CELIIntegrator,
+ EPCRK4Integrator,
+ LEQIIntegrator,
+ SICELIIntegrator,
+ SILEQIIntegrator
+]
+
+
def test_results_save(run_in_tmpdir):
"""Test data save module"""
@@ -105,14 +119,14 @@ def test_results_save(run_in_tmpdir):
np.testing.assert_array_equal(res[1].time, t2)
[email protected]("timesteps", (1, [1]))
-def test_bad_integrator_inputs(timesteps):
+def test_bad_integrator_inputs():
"""Test failure modes for Integrator inputs"""
op = MagicMock()
op.prev_res = None
op.chain = None
op.heavy_metal = 1.0
+ timesteps = [1]
# No power nor power density given
with pytest.raises(ValueError, match="Either power or power density"):
@@ -159,3 +173,62 @@ def test_integrator(run_in_tmpdir, scheme):
dep_time = res.get_depletion_time()
assert dep_time.shape == (2, )
assert all(dep_time > 0)
+
+
[email protected]("integrator", INTEGRATORS)
+def test_timesteps(integrator):
+ # Crate fake operator
+ op = MagicMock()
+ op.prev_res = None
+ op.chain = None
+
+ # Set heavy metal mass and power randomly
+ op.heavy_metal = uniform(0, 10000)
+ power = uniform(0, 1e6)
+
+ # Reference timesteps in seconds
+ day = 86400.0
+ ref_timesteps = [1*day, 2*day, 5*day, 10*day]
+
+ # Case 1, timesteps in seconds
+ timesteps = ref_timesteps
+ x = integrator(op, timesteps, power, timestep_units='s')
+ assert np.allclose(x.timesteps, ref_timesteps)
+
+ # Case 2, timesteps in minutes
+ minute = 60
+ timesteps = [t / minute for t in ref_timesteps]
+ x = integrator(op, timesteps, power, timestep_units='min')
+ assert np.allclose(x.timesteps, ref_timesteps)
+
+ # Case 3, timesteps in hours
+ hour = 60*60
+ timesteps = [t / hour for t in ref_timesteps]
+ x = integrator(op, timesteps, power, timestep_units='h')
+ assert np.allclose(x.timesteps, ref_timesteps)
+
+ # Case 4, timesteps in days
+ timesteps = [t / day for t in ref_timesteps]
+ x = integrator(op, timesteps, power, timestep_units='d')
+ assert np.allclose(x.timesteps, ref_timesteps)
+
+ # Case 5, timesteps in MWd/kg
+ kilograms = op.heavy_metal / 1000.0
+ days = [t/day for t in ref_timesteps]
+ megawatts = power / 1000000.0
+ burnup = [t * megawatts / kilograms for t in days]
+ x = integrator(op, burnup, power, timestep_units='MWd/kg')
+ assert np.allclose(x.timesteps, ref_timesteps)
+
+ # Case 6, mixed units
+ burnup_per_day = (1e-6*power) / kilograms
+ timesteps = [(burnup_per_day, 'MWd/kg'), (2*day, 's'), (5, 'd'),
+ (10*burnup_per_day, 'MWd/kg')]
+ x = integrator(op, timesteps, power)
+ assert np.allclose(x.timesteps, ref_timesteps)
+
+ # Bad units should raise an exception
+ with pytest.raises(ValueError, match="unit"):
+ integrator(op, ref_timesteps, power, timestep_units='🐨')
+ with pytest.raises(ValueError, match="unit"):
+ integrator(op, [(800.0, 'gorillas')], power)
| Allow depletion by burnup
Ideally, this could / should mimic the time steps, e.g.
```python
>>> pred = PredictorIntegrator(op, burnup=[0.5, 1.0, 2.0, ...], ...)
```
where `burnup` is in MWd/kgHM [kg heavy metal].
Looking over the `Integrator`, it would actually be a pretty straight forward inclusion. Given some power (or power density) and mass of initial heavy metal (through `operator.heavy_metal`) we can back calculate the corresponding step sizes in days.
If we want to add a regression test, it would probably benefit us to use the same HDF result file and specify the burnup steps to exactly match the current time steps. But these depletion tests are not super short...
I'm open to suggestions on testing this
| Good idea. I agree to add this kind of input parameters for burnup steps.
Serpent also supports "bustep", "butot", "daystep", "daytot", "decstep", "dectot", which mean that:
1. burnup interval
2. cumulative burnup
3. time step interval
4. cumulative time
5. pure decay time interval
6. pure decay cumulative time
BTW, no further comment on the regression test. It seems easier to use the same results file. ;-)
Agree, it would be really nice to support those settings as well. I think ultimately, the `Integrator`s should have two vectors: time [s] and power. Mainly because the `Integrator.__call__(...)` methods are already configured to accept a step size in seconds and step power. If we can compute those quantities during `Integrator.__init__`, then we don't have to compute those every step.
This also eases our testing, because we can throw a myriad of inputs at the `__init__` methods, and check their time and power vectors rather than run a full regression test [OpenMC + depletion]. The assumption here is that all the solutions would be the same if you had the same time and power vectors.
One thing worth noting, is that some additional changes may be required for decay. Technically, we could simulate a decay step with a zero power step to compute zero particle-induced reaction rates [fission, (n,2n), etc.]. But this would require running a useless transport simulation only to throw the reaction rates away. Maybe modifying
https://github.com/openmc-dev/openmc/blob/50a271bfda80be4be37e5cce514e022e79fd1899/openmc/deplete/abc.py#L739-L743
if the step power is zero?
I'm planning on implementing support for indicating steps by burnup rather than by time. My proposal is as follows:
- Have `Integrator` accept `(operator, timesteps, ..., timestep_units='s')`
- The user specifies either 's' or 'MWd/kg' for `timestep_units`.
- Decay timesteps are indicated by power=0
- Generally, `timesteps` is just a plain array/list with numeric values. However, in the case where a user wants to specify timesteps by burnup _and_ have decay timesteps, we can support this by having `timesteps` by an iterable of (value, unit) tuples, e.g. `timesteps=[(3.0, 'MWd/kg'), (3.0, 'MWd/kg'), (10*86400, 's')]` would mean two 3 MWd/kg timesteps and then a 10 day decay period (assuming the power associated with the third step was zero)
- For convenience, we might want to support alternate time units (day, year, etc.) in `timestep_units`
@drewejohnson @rockfool @pshriwise Let me know if any of you have objections or can think of a better way of supporting all the different cases.
> I'm planning on implementing support for indicating steps by burnup rather than by time. My proposal is as follows:
>
> * Have `Integrator` accept `(operator, timesteps, ..., timestep_units='s')`
> * The user specifies either 's' or 'MWd/kg' for `timestep_units`.
> * Decay timesteps are indicated by power=0
> * Generally, `timesteps` is just a plain array/list with numeric values. However, in the case where a user wants to specify timesteps by burnup _and_ have decay timesteps, we can support this by having `timesteps` by an iterable of (value, unit) tuples, e.g. `timesteps=[(3.0, 'MWd/kg'), (3.0, 'MWd/kg'), (10*86400, 's')]` would mean two 3 MWd/kg timesteps and then a 10 day decay period (assuming the power associated with the third step was zero)
> * For convenience, we might want to support alternate time units (day, year, etc.) in `timestep_units`
>
> @drewejohnson @rockfool @pshriwise Let me know if any of you have objections or can think of a better way of supporting all the different cases.
Agree. That would be much flexible. Just one idea to add kind of `cumulative-timesteps` to avoid the calc of time interval sometimes.
No need to reinvent the wheel -- we should just point users to [numpy.cumsum](https://docs.scipy.org/doc/numpy/reference/generated/numpy.cumsum.html) and [numpy.diff](https://docs.scipy.org/doc/numpy/reference/generated/numpy.diff.html) if they need to convert between cumulative / non-cumulative.
This sounds great; I really like the ability to support multiple units (days and years) :100: | 2020-02-11T13:18:17Z | [] | [] |
openmc-dev/openmc | 1,493 | openmc-dev__openmc-1493 | [
"1492"
] | 9a3574676125abe131796ab1f9b63702bb84fd16 | diff --git a/openmc/deplete/nuclide.py b/openmc/deplete/nuclide.py
--- a/openmc/deplete/nuclide.py
+++ b/openmc/deplete/nuclide.py
@@ -533,6 +533,7 @@ def items(self):
return zip(self.products, self.yields)
def __add__(self, other):
+ """Add one set of fission yields to this set, return new yields"""
if not isinstance(other, FissionYield):
return NotImplemented
new = FissionYield(self.products, self.yields.copy())
@@ -550,12 +551,14 @@ def __radd__(self, other):
return self + other
def __imul__(self, scalar):
+ """Scale these fission yields by a real scalar"""
if not isinstance(scalar, Real):
return NotImplemented
self.yields *= scalar
return self
def __mul__(self, scalar):
+ """Return a new set of yields scaled by a real scalar"""
if not isinstance(scalar, Real):
return NotImplemented
new = FissionYield(self.products, self.yields.copy())
@@ -568,3 +571,8 @@ def __rmul__(self, scalar):
def __repr__(self):
return "<{} containing {} products and yields>".format(
self.__class__.__name__, len(self))
+
+ # Avoid greedy numpy operations like np.float64 * fission_yield
+ # converting this to an array on the fly. Force __rmul__ and
+ # __radd__. See issue #1492
+ __array_ufunc__ = None
| diff --git a/tests/unit_tests/test_deplete_nuclide.py b/tests/unit_tests/test_deplete_nuclide.py
--- a/tests/unit_tests/test_deplete_nuclide.py
+++ b/tests/unit_tests/test_deplete_nuclide.py
@@ -149,12 +149,18 @@ def test_fission_yield_distribution():
# __getitem__ return yields as a view into yield matrix
assert orig_yields.yields.base is yield_dist.yield_matrix
- # Fission yield feature uses scaled and incremented
+ # Scale and increment fission yields
mod_yields = orig_yields * 2
assert numpy.array_equal(orig_yields.yields * 2, mod_yields.yields)
mod_yields += orig_yields
assert numpy.array_equal(orig_yields.yields * 3, mod_yields.yields)
+ mod_yields = 2.0 * orig_yields
+ assert numpy.array_equal(orig_yields.yields * 2, mod_yields.yields)
+
+ mod_yields = numpy.float64(2.0) * orig_yields
+ assert numpy.array_equal(orig_yields.yields * 2, mod_yields.yields)
+
# Failure modes for adding, multiplying yields
similar = numpy.empty_like(orig_yields.yields)
with pytest.raises(TypeError):
| numpy.floatX * FissionYield causes ufunc errors
tl;dr: ``w * fy == fy * w == fy * numpy.float64(w) != numpy.float64(w) * fy``
When computing the effective fission yields, a [collection of special methods](https://github.com/openmc-dev/openmc/blob/9a3574676125abe131796ab1f9b63702bb84fd16/openmc/deplete/nuclide.py#L535-L567) are provided that allow simple ``fy_collapsed = fy0 * w0 + w1 * f1 ...``. This is great, because one just has to compute the various scalar weights for each energy group, and we can compute a single fission yield that captures the correct spectrum.
However, if the weight is a special `numpy` float like `numpy.float64` __and__ is the first argument, the weighting errors. I've provided a small example to demonstrate
```python
import numpy
import openmc
import openmc.deplete
print(numpy.__version__)
print(openmc.__version__)
fy = openmc.deplete.FissionYield(("Xe135", "Sm155"), numpy.array((1.0, 1.0)))
print(fy * 0.2)
print(0.2 * fy)
print(fy * numpy.float64(0.2))
try:
print(numpy.float64(0.2) * fy)
except Exception as ee:
print(str(ee))
try:
print(numpy.float32(0.2) * fy)
except Exception as ee:
print(str(ee))
```
Output
```
1.18.1
0.12.0-dev
<FissionYield containing 2 products and yields>
<FissionYield containing 2 products and yields>
<FissionYield containing 2 products and yields>
ufunc 'multiply' did not contain a loop with signature matching types (dtype('<U32'), dtype('<U32')) -> dtype('<U32')
ufunc 'multiply' did not contain a loop with signature matching types (dtype('<U32'), dtype('<U32')) -> dtype('<U32')
```
Even though ``__rmul__`` is implemented, which should take over for ``w * fy``, it never gets called. Recent updates to numpy, I think 1.16(?), made it really easy to create an array from an arbitrary sequence. For example,
```python
print(numpy.asarray(fy))
['Xe135' 'Sm155']
```
It looks like numpy sees the left argument of the multiply, our fission yields, can be coerced into an array, and then multiplies that array by the scalar.
There are couple ways that we can fix this, and I'm not sure which is best. The numpy docs provide some instructions on [writing custom containers](https://docs.scipy.org/doc/numpy/user/basics.dispatch.html), or using some mixins [NDArrayOperatorMixin](https://docs.scipy.org/doc/numpy/reference/generated/numpy.lib.mixins.NDArrayOperatorsMixin.html#numpy.lib.mixins.NDArrayOperatorsMixin) that may work here. However, I don't think we want to lose the `Mapping` API, as the `Chain.form_matrix` relies on this
https://github.com/openmc-dev/openmc/blob/9a3574676125abe131796ab1f9b63702bb84fd16/openmc/deplete/chain.py#L534-L538
| Honestly this sounds like a numpy bug to me. The protocol is that if `x.__mul__(y)` doesn't work, it should return `NotImplemented` so that the interpreter will know to try `y.__rmul__(x)`. The reason it doesn't work even though we have `__rmul__` implemented is because `float64.__mul__` is just raising an exception rather than returning NotImplemented.
...after a little digging, found this: numpy/numpy#9677. A solution suggested there is to just add `__array_ufunc__ = None` to the `FissionYield` class. | 2020-02-25T15:01:09Z | [] | [] |
openmc-dev/openmc | 1,531 | openmc-dev__openmc-1531 | [
"1532"
] | a294172342e05c9fa856e5608ad51ae16aacf840 | diff --git a/openmc/_utils.py b/openmc/_utils.py
deleted file mode 100644
--- a/openmc/_utils.py
+++ /dev/null
@@ -1,70 +0,0 @@
-import hashlib
-import os.path
-from pathlib import Path
-from urllib.parse import urlparse
-from urllib.request import urlopen, Request
-
-_BLOCK_SIZE = 16384
-
-
-def download(url, checksum=None, as_browser=False, **kwargs):
- """Download file from a URL
-
- Parameters
- ----------
- url : str
- URL from which to download
- checksum : str or None
- MD5 checksum to check against
- as_browser : bool
- Change User-Agent header to appear as a browser
- kwargs : dict
- Keyword arguments passed to :func:urllib.request.urlopen
-
- Returns
- -------
- basename : str
- Name of file written locally
-
- """
- if as_browser:
- page = Request(url, headers={'User-Agent': 'Mozilla/5.0'})
- else:
- page = url
-
- with urlopen(page, **kwargs) as response:
- # Get file size from header
- file_size = response.length
-
- # Check if file already downloaded
- basename = Path(urlparse(url).path).name
- if os.path.exists(basename):
- if os.path.getsize(basename) == file_size:
- print('Skipping {}, already downloaded'.format(basename))
- return basename
-
- # Copy file to disk in chunks
- print('Downloading {}... '.format(basename), end='')
- downloaded = 0
- with open(basename, 'wb') as fh:
- while True:
- chunk = response.read(_BLOCK_SIZE)
- if not chunk:
- break
- fh.write(chunk)
- downloaded += len(chunk)
- status = '{:10} [{:3.2f}%]'.format(
- downloaded, downloaded * 100. / file_size)
- print(status + '\b'*len(status), end='', flush=True)
- print('')
-
- if checksum is not None:
- downloadsum = hashlib.md5(open(basename, 'rb').read()).hexdigest()
- if downloadsum != checksum:
- raise IOError("MD5 checksum for {} does not match. If this is "
- "your first time receiving this message, please "
- "re-run the script. Otherwise, please contact "
- "OpenMC developers by emailing "
- "[email protected].".format(basename))
-
- return basename
diff --git a/openmc/_xml.py b/openmc/_xml.py
--- a/openmc/_xml.py
+++ b/openmc/_xml.py
@@ -1,26 +1,20 @@
def clean_indentation(element, level=0, spaces_per_level=2):
"""
- copy and paste from http://effbot.org/zone/element-lib.htm#prettyprint
+ copy and paste from https://effbot.org/zone/element-lib.htm#prettyprint
it basically walks your tree and adds spaces and newlines so the tree is
printed in a nice way
"""
-
i = "\n" + level*spaces_per_level*" "
if len(element):
-
if not element.text or not element.text.strip():
element.text = i + spaces_per_level*" "
-
if not element.tail or not element.tail.strip():
element.tail = i
-
for sub_element in element:
clean_indentation(sub_element, level+1, spaces_per_level)
-
if not sub_element.tail or not sub_element.tail.strip():
sub_element.tail = i
-
else:
if level and (not element.tail or not element.tail.strip()):
element.tail = i
diff --git a/openmc/arithmetic.py b/openmc/arithmetic.py
--- a/openmc/arithmetic.py
+++ b/openmc/arithmetic.py
@@ -17,7 +17,7 @@
_TALLY_AGGREGATE_OPS = ['sum', 'avg']
-class CrossScore(object):
+class CrossScore:
"""A special-purpose tally score used to encapsulate all combinations of two
tally's scores as an outer product for tally arithmetic.
@@ -43,18 +43,10 @@ class CrossScore(object):
"""
- def __init__(self, left_score=None, right_score=None, binary_op=None):
-
- self._left_score = None
- self._right_score = None
- self._binary_op = None
-
- if left_score is not None:
- self.left_score = left_score
- if right_score is not None:
- self.right_score = right_score
- if binary_op is not None:
- self.binary_op = binary_op
+ def __init__(self, left_score, right_score, binary_op):
+ self.left_score = left_score
+ self.right_score = right_score
+ self.binary_op = binary_op
def __hash__(self):
return hash(repr(self))
@@ -62,13 +54,9 @@ def __hash__(self):
def __eq__(self, other):
return str(other) == str(self)
- def __ne__(self, other):
- return not self == other
-
def __repr__(self):
- string = '({0} {1} {2})'.format(self.left_score,
- self.binary_op, self.right_score)
- return string
+ return '({} {} {})'.format(self.left_score, self.binary_op,
+ self.right_score)
@property
def left_score(self):
@@ -101,7 +89,7 @@ def binary_op(self, binary_op):
self._binary_op = binary_op
-class CrossNuclide(object):
+class CrossNuclide:
"""A special-purpose nuclide used to encapsulate all combinations of two
tally's nuclides as an outer product for tally arithmetic.
@@ -127,18 +115,10 @@ class CrossNuclide(object):
"""
- def __init__(self, left_nuclide=None, right_nuclide=None, binary_op=None):
-
- self._left_nuclide = None
- self._right_nuclide = None
- self._binary_op = None
-
- if left_nuclide is not None:
- self.left_nuclide = left_nuclide
- if right_nuclide is not None:
- self.right_nuclide = right_nuclide
- if binary_op is not None:
- self.binary_op = binary_op
+ def __init__(self, left_nuclide, right_nuclide, binary_op):
+ self.left_nuclide = left_nuclide
+ self.right_nuclide = right_nuclide
+ self.binary_op = binary_op
def __hash__(self):
return hash(repr(self))
@@ -146,9 +126,6 @@ def __hash__(self):
def __eq__(self, other):
return str(other) == str(self)
- def __ne__(self, other):
- return not self == other
-
def __repr__(self):
return self.name
@@ -206,7 +183,7 @@ def binary_op(self, binary_op):
self._binary_op = binary_op
-class CrossFilter(object):
+class CrossFilter:
"""A special-purpose filter used to encapsulate all combinations of two
tally's filter bins as an outer product for tally arithmetic.
@@ -239,26 +216,10 @@ class CrossFilter(object):
"""
- def __init__(self, left_filter=None, right_filter=None, binary_op=None):
-
- left_type = left_filter.type
- right_type = right_filter.type
- self._type = '({0} {1} {2})'.format(left_type, binary_op, right_type)
-
- self._bins = {}
-
- self._left_filter = None
- self._right_filter = None
- self._binary_op = None
-
- if left_filter is not None:
- self.left_filter = left_filter
- self._bins['left'] = left_filter.bins
- if right_filter is not None:
- self.right_filter = right_filter
- self._bins['right'] = right_filter.bins
- if binary_op is not None:
- self.binary_op = binary_op
+ def __init__(self, left_filter, right_filter, binary_op):
+ self.left_filter = left_filter
+ self.right_filter = right_filter
+ self.binary_op = binary_op
def __hash__(self):
return hash((self.left_filter, self.right_filter))
@@ -266,21 +227,16 @@ def __hash__(self):
def __eq__(self, other):
return str(other) == str(self)
- def __ne__(self, other):
- return not self == other
-
def __repr__(self):
-
- string = 'CrossFilter\n'
- filter_type = '({0} {1} {2})'.format(self.left_filter.type,
- self.binary_op,
- self.right_filter.type)
- filter_bins = '({0} {1} {2})'.format(self.left_filter.bins,
- self.binary_op,
- self.right_filter.bins)
- string += '{0: <16}{1}{2}\n'.format('\tType', '=\t', filter_type)
- string += '{0: <16}{1}{2}\n'.format('\tBins', '=\t', filter_bins)
- return string
+ filter_bins = '({} {} {})'.format(self.left_filter.bins,
+ self.binary_op,
+ self.right_filter.bins)
+ parts = [
+ 'CrossFilter',
+ '{: <16}=\t{}'.format('\tType', self.type),
+ '{: <16}=\t{}'.format('\tBins', filter_bins)
+ ]
+ return '\n'.join(parts)
@property
def left_filter(self):
@@ -296,11 +252,13 @@ def binary_op(self):
@property
def type(self):
- return self._type
+ left_type = self.left_filter.type
+ right_type = self.right_filter.type
+ return '({} {} {})'.format(left_type, self.binary_op, right_type)
@property
def bins(self):
- return self._bins['left'], self._bins['right']
+ return self._left_filter.bins, self._right_filter.bins
@property
def num_bins(self):
@@ -309,28 +267,17 @@ def num_bins(self):
else:
return 0
- @type.setter
- def type(self, filter_type):
- if filter_type not in _FILTER_TYPES:
- msg = 'Unable to set CrossFilter type to "{0}" since it ' \
- 'is not one of the supported types'.format(filter_type)
- raise ValueError(msg)
-
- self._type = filter_type
-
@left_filter.setter
def left_filter(self, left_filter):
cv.check_type('left_filter', left_filter,
(openmc.Filter, CrossFilter, AggregateFilter))
self._left_filter = left_filter
- self._bins['left'] = left_filter.bins
@right_filter.setter
def right_filter(self, right_filter):
cv.check_type('right_filter', right_filter,
(openmc.Filter, CrossFilter, AggregateFilter))
self._right_filter = right_filter
- self._bins['right'] = right_filter.bins
@binary_op.setter
def binary_op(self, binary_op):
@@ -418,7 +365,8 @@ def get_pandas_dataframe(self, data_size, summary=None):
return df
-class AggregateScore(object):
+
+class AggregateScore:
"""A special-purpose tally score used to encapsulate an aggregate of a
subset or all of tally's scores for tally aggregation.
@@ -456,12 +404,9 @@ def __hash__(self):
def __eq__(self, other):
return str(other) == str(self)
- def __ne__(self, other):
- return not self == other
-
def __repr__(self):
string = ', '.join(map(str, self.scores))
- string = '{0}({1})'.format(self.aggregate_op, string)
+ string = '{}({})'.format(self.aggregate_op, string)
return string
@property
@@ -491,7 +436,7 @@ def aggregate_op(self, aggregate_op):
self._aggregate_op = aggregate_op
-class AggregateNuclide(object):
+class AggregateNuclide:
"""A special-purpose tally nuclide used to encapsulate an aggregate of a
subset or all of tally's nuclides for tally aggregation.
@@ -529,13 +474,10 @@ def __hash__(self):
def __eq__(self, other):
return str(other) == str(self)
- def __ne__(self, other):
- return not self == other
-
def __repr__(self):
# Append each nuclide in the aggregate to the string
- string = '{0}('.format(self.aggregate_op)
+ string = '{}('.format(self.aggregate_op)
names = [nuclide.name if isinstance(nuclide, openmc.Nuclide)
else str(nuclide) for nuclide in self.nuclides]
string += ', '.join(map(str, names)) + ')'
@@ -570,7 +512,7 @@ def aggregate_op(self, aggregate_op):
self._aggregate_op = aggregate_op
-class AggregateFilter(object):
+class AggregateFilter:
"""A special-purpose tally filter used to encapsulate an aggregate of a
subset or all of a tally filter's bins for tally aggregation.
@@ -600,17 +542,16 @@ class AggregateFilter(object):
"""
- def __init__(self, aggregate_filter=None, bins=None, aggregate_op=None):
+ def __init__(self, aggregate_filter, bins=None, aggregate_op=None):
- self._type = '{0}({1})'.format(aggregate_op,
- aggregate_filter.short_name.lower())
+ self._type = '{}({})'.format(aggregate_op,
+ aggregate_filter.short_name.lower())
self._bins = None
self._aggregate_filter = None
self._aggregate_op = None
- if aggregate_filter is not None:
- self.aggregate_filter = aggregate_filter
+ self.aggregate_filter = aggregate_filter
if bins is not None:
self.bins = bins
if aggregate_op is not None:
@@ -622,9 +563,6 @@ def __hash__(self):
def __eq__(self, other):
return str(other) == str(self)
- def __ne__(self, other):
- return not self == other
-
def __gt__(self, other):
if self.type != other.type:
if self.aggregate_filter.type in _FILTER_TYPES and \
@@ -641,10 +579,12 @@ def __lt__(self, other):
return not self > other
def __repr__(self):
- string = 'AggregateFilter\n'
- string += '{0: <16}{1}{2}\n'.format('\tType', '=\t', self.type)
- string += '{0: <16}{1}{2}\n'.format('\tBins', '=\t', self.bins)
- return string
+ parts = [
+ 'AggregateFilter',
+ '{: <16}=\t{}'.format('\tType', self.type),
+ '{: <16}=\t{}'.format('\tBins', self.bins)
+ ]
+ return '\n'.join(parts)
@property
def aggregate_filter(self):
@@ -669,7 +609,7 @@ def num_bins(self):
@type.setter
def type(self, filter_type):
if filter_type not in _FILTER_TYPES:
- msg = 'Unable to set AggregateFilter type to "{0}" since it ' \
+ msg = 'Unable to set AggregateFilter type to "{}" since it ' \
'is not one of the supported types'.format(filter_type)
raise ValueError(msg)
@@ -722,7 +662,7 @@ def get_bin_index(self, filter_bin):
if filter_bin not in self.bins:
msg = 'Unable to get the bin index for AggregateFilter since ' \
- '"{0}" is not one of the bins'.format(filter_bin)
+ '"{}" is not one of the bins'.format(filter_bin)
raise ValueError(msg)
else:
return self.bins.index(filter_bin)
@@ -800,12 +740,7 @@ def can_merge(self, other):
return False
# None of the bins in this filter should match in the other filter
- for bin in self.bins:
- if bin in other.bins:
- return False
-
- # If all conditional checks passed then filters are mergeable
- return True
+ return not any(b in other.bins for b in self.bins)
def merge(self, other):
"""Merge this aggregatefilter with another.
@@ -823,8 +758,8 @@ def merge(self, other):
"""
if not self.can_merge(other):
- msg = 'Unable to merge "{0}" with "{1}" ' \
- 'filters'.format(self.type, other.type)
+ msg = 'Unable to merge "{}" with "{}" filters'.format(
+ self.type, other.type)
raise ValueError(msg)
# Create deep copy of filter to return as merged filter
diff --git a/openmc/checkvalue.py b/openmc/checkvalue.py
--- a/openmc/checkvalue.py
+++ b/openmc/checkvalue.py
@@ -4,7 +4,7 @@
import numpy as np
-def check_type(name, value, expected_type, expected_iter_type=None):
+def check_type(name, value, expected_type, expected_iter_type=None, *, none_ok=False):
"""Ensure that an object is of an expected type. Optionally, if the object is
iterable, check that each element is of a particular type.
@@ -19,39 +19,44 @@ def check_type(name, value, expected_type, expected_iter_type=None):
expected_iter_type : type or Iterable of type or None, optional
Expected type of each element in value, assuming it is iterable. If
None, no check will be performed.
+ none_ok : bool, optional
+ Whether None is allowed as a value
"""
+ if none_ok and value is None:
+ return
if not isinstance(value, expected_type):
if isinstance(expected_type, Iterable):
- msg = 'Unable to set "{0}" to "{1}" which is not one of the ' \
- 'following types: "{2}"'.format(name, value, ', '.join(
+ msg = 'Unable to set "{}" to "{}" which is not one of the ' \
+ 'following types: "{}"'.format(name, value, ', '.join(
[t.__name__ for t in expected_type]))
else:
- msg = 'Unable to set "{0}" to "{1}" which is not of type "{2}"'.format(
+ msg = 'Unable to set "{}" to "{}" which is not of type "{}"'.format(
name, value, expected_type.__name__)
raise TypeError(msg)
if expected_iter_type:
if isinstance(value, np.ndarray):
if not issubclass(value.dtype.type, expected_iter_type):
- msg = 'Unable to set "{0}" to "{1}" since each item must be ' \
- 'of type "{2}"'.format(name, value,
- expected_iter_type.__name__)
+ msg = 'Unable to set "{}" to "{}" since each item must be ' \
+ 'of type "{}"'.format(name, value,
+ expected_iter_type.__name__)
+ raise TypeError(msg)
else:
return
for item in value:
if not isinstance(item, expected_iter_type):
if isinstance(expected_iter_type, Iterable):
- msg = 'Unable to set "{0}" to "{1}" since each item must be ' \
- 'one of the following types: "{2}"'.format(
+ msg = 'Unable to set "{}" to "{}" since each item must be ' \
+ 'one of the following types: "{}"'.format(
name, value, ', '.join([t.__name__ for t in
expected_iter_type]))
else:
- msg = 'Unable to set "{0}" to "{1}" since each item must be ' \
- 'of type "{2}"'.format(name, value,
- expected_iter_type.__name__)
+ msg = 'Unable to set "{}" to "{}" since each item must be ' \
+ 'of type "{}"'.format(name, value,
+ expected_iter_type.__name__)
raise TypeError(msg)
@@ -150,18 +155,18 @@ def check_length(name, value, length_min, length_max=None):
"""
if length_max is None:
- if len(value) != length_min:
- msg = 'Unable to set "{0}" to "{1}" since it must be of ' \
- 'length "{2}"'.format(name, value, length_min)
+ if len(value) < length_min:
+ msg = 'Unable to set "{}" to "{}" since it must be at least of ' \
+ 'length "{}"'.format(name, value, length_min)
raise ValueError(msg)
elif not length_min <= len(value) <= length_max:
if length_min == length_max:
- msg = 'Unable to set "{0}" to "{1}" since it must be of ' \
- 'length "{2}"'.format(name, value, length_min)
+ msg = 'Unable to set "{}" to "{}" since it must be of ' \
+ 'length "{}"'.format(name, value, length_min)
else:
- msg = 'Unable to set "{0}" to "{1}" since it must have length ' \
- 'between "{2}" and "{3}"'.format(name, value, length_min,
- length_max)
+ msg = 'Unable to set "{}" to "{}" since it must have length ' \
+ 'between "{}" and "{}"'.format(name, value, length_min,
+ length_max)
raise ValueError(msg)
@@ -184,6 +189,7 @@ def check_value(name, value, accepted_values):
name, value, accepted_values)
raise ValueError(msg)
+
def check_less_than(name, value, maximum, equality=False):
"""Ensure that an object's value is less than a given value.
@@ -211,6 +217,7 @@ def check_less_than(name, value, maximum, equality=False):
'or equal to "{2}"'.format(name, value, maximum)
raise ValueError(msg)
+
def check_greater_than(name, value, minimum, equality=False):
"""Ensure that an object's value is greater than a given value.
@@ -265,13 +272,13 @@ def check_filetype_version(obj, expected_type, expected_version):
if this_version[0] != expected_version:
raise IOError('{} file has a version of {} which is not '
'consistent with the version expected by OpenMC, {}'
- .format(this_filetype,
- '.'.join(str(v) for v in this_version),
- expected_version))
+ .format(this_filetype,
+ '.'.join(str(v) for v in this_version),
+ expected_version))
except AttributeError:
- raise IOError('Could not read {} file. This most likely means the {} '
+ raise IOError('Could not read {} file. This most likely means the '
'file was produced by a different version of OpenMC than '
- 'the one you are using.'.format(expected_type))
+ 'the one you are using.'.format(obj.filename))
class CheckedList(list):
@@ -288,12 +295,13 @@ class CheckedList(list):
"""
- def __init__(self, expected_type, name, items=[]):
+ def __init__(self, expected_type, name, items=None):
super().__init__()
self.expected_type = expected_type
self.name = name
- for item in items:
- self.append(item)
+ if items is not None:
+ for item in items:
+ self.append(item)
def __add__(self, other):
new_instance = copy.copy(self)
diff --git a/openmc/cmfd.py b/openmc/cmfd.py
--- a/openmc/cmfd.py
+++ b/openmc/cmfd.py
@@ -55,7 +55,7 @@
}
-class CMFDMesh(object):
+class CMFDMesh:
"""A structured Cartesian mesh used for CMFD acceleration.
Attributes
@@ -182,14 +182,14 @@ def albedo(self, albedo):
self._albedo = albedo
@map.setter
- def map(self, meshmap):
- check_type('CMFD mesh map', meshmap, Iterable, Integral)
- for m in meshmap:
+ def map(self, mesh_map):
+ check_type('CMFD mesh map', mesh_map, Iterable, Integral)
+ for m in mesh_map:
check_value('CMFD mesh map', m, [0, 1])
- self._map = meshmap
+ self._map = mesh_map
-class CMFDRun(object):
+class CMFDRun:
r"""Class for running CMFD acceleration through the C API.
Attributes
@@ -535,7 +535,6 @@ def solver_begin(self, begin):
check_greater_than('CMFD feedback begin batch', begin, 0)
self._solver_begin = begin
-
@ref_d.setter
def ref_d(self, diff_params):
check_type('Reference diffusion params', diff_params,
@@ -896,9 +895,8 @@ def _write_cmfd_statepoint(self, filename):
cmfd_group.create_dataset('total_rate',
data=self._total_rate)
elif openmc.settings.verbosity >= 5:
- print(' CMFD data not written to statepoint file'
- 'as it already exists in {}'.format(filename))
- sys.stdout.flush()
+ print(' CMFD data not written to statepoint file as it '
+ 'already exists in {}'.format(filename), flush=True)
def _initialize_linsolver(self):
# Determine number of rows in CMFD matrix
@@ -1185,7 +1183,6 @@ def _execute_cmfd(self):
# Write CMFD output if CMFD on for current batch
self._write_cmfd_output()
-
def _cmfd_tally_reset(self):
"""Resets all CMFD tallies in memory"""
# Print message
@@ -1753,7 +1750,7 @@ def _execute_power_iter(self, loss, prod):
# Compute new flux with C++ solver
innerits = openmc.lib._dll.openmc_run_linsolver(loss.data, s_o,
- phi_n, toli)
+ phi_n, toli)
# Compute new source vector
s_n = prod.dot(phi_n)
@@ -1785,7 +1782,7 @@ def _execute_power_iter(self, loss, prod):
# Update tolerance for inner iterations
toli = max(atoli, rtoli*norm_n)
- def _check_convergence(self, s_n, s_o, k_n, k_o, iter, innerits):
+ def _check_convergence(self, s_n, s_o, k_n, k_o, iteration, innerits):
"""Checks the convergence of the CMFD problem
Parameters
@@ -1798,9 +1795,9 @@ def _check_convergence(self, s_n, s_o, k_n, k_o, iter, innerits):
K-effective from current iteration
k_o : float
K-effective from previous iteration
- iter: int
+ iteration : int
Iteration number
- innerits: int
+ innerits : int
Number of iterations required for convergence in inner GS loop
Returns
@@ -1825,14 +1822,13 @@ def _check_convergence(self, s_n, s_o, k_n, k_o, iter, innerits):
# Print out to user
if self._power_monitor and openmc.lib.master():
- str1 = ' {:d}:'.format(iter)
- str2 = 'k-eff: {:0.8f}'.format(k_n)
- str3 = 'k-error: {:.5e}'.format(kerr)
- str4 = 'src-error: {:.5e}'.format(serr)
- str5 = ' {:d}'.format(innerits)
- print('{:8s}{:20s}{:25s}{:s}{:s}'.format(str1, str2, str3, str4,
- str5))
- sys.stdout.flush()
+ print('{:8s}{:20s}{:25s}{:s}{:s}'.format(
+ ' {:d}:'.format(iteration),
+ 'k-eff: {:0.8f}'.format(k_n),
+ 'k-error: {:.5e}'.format(kerr),
+ 'src-error: {:.5e}'.format(serr),
+ ' {:d}'.format(innerits)
+ ), flush=True)
return iconv, serr
@@ -1850,7 +1846,7 @@ def _set_coremap(self):
# Define coremap as cumulative sum over accelerated regions,
# otherwise set value to _CMFD_NOACCEL
self._coremap = np.where(self._coremap == 0, _CMFD_NOACCEL,
- np.cumsum(self._coremap)-1)
+ np.cumsum(self._coremap) - 1)
# Reshape coremap to three dimensional array
# Indices of coremap in user input switched in x and z axes
@@ -1929,19 +1925,19 @@ def _compute_xs(self):
') in group ' + str(ng-idx[-1])
raise OpenMCError(err_message)
- # Get total rr from CMFD tally 0
+ # Get total reaction rate (rr) from CMFD tally 0
totalrr = tallies[tally_id].results[:,1,1]
- # Reshape totalrr array to target shape. Swap x and z axes so that
- # shape is now [nx, ny, nz, ng, 1]
+ # Reshape total reaction rate array to target shape. Swap x and z axes
+ # so that shape is now [nx, ny, nz, ng, 1]
reshape_totalrr = np.swapaxes(totalrr.reshape(target_tally_shape),
0, 2)
- # Total rr is flipped in energy axis as tally results are given in
- # reverse order of energy group
+ # Total reaction rate is flipped in energy axis as tally results are
+ # given in reverse order of energy group
reshape_totalrr = np.flip(reshape_totalrr, axis=3)
- # Bank total rr to total_rate
+ # Bank total reaction rate to total_rate
self._total_rate = np.append(self._total_rate, reshape_totalrr,
axis=4)
@@ -2047,7 +2043,7 @@ def _compute_xs(self):
axis=5)
# Compute current as aggregate of banked current_rate over tally window
- self._current = np.where(is_accel[..., np.newaxis, np.newaxis],
+ self._current = np.where(is_accel[..., np.newaxis, np.newaxis],
np.sum(self._current_rate, axis=5), 0.0)
# Get p1 scatter rr from CMFD tally 3
diff --git a/openmc/data/endf.py b/openmc/data/endf.py
--- a/openmc/data/endf.py
+++ b/openmc/data/endf.py
@@ -370,7 +370,7 @@ def get_evaluations(filename):
return evaluations
-class Evaluation(object):
+class Evaluation:
"""ENDF material evaluation with multiple files/sections
Parameters
@@ -528,7 +528,7 @@ def gnd_name(self):
self.target['isomeric_state'])
-class Tabulated2D(object):
+class Tabulated2D:
"""Metadata for a two-dimensional function.
This is a dummy class that is not really used other than to store the
diff --git a/openmc/data/resonance.py b/openmc/data/resonance.py
--- a/openmc/data/resonance.py
+++ b/openmc/data/resonance.py
@@ -17,7 +17,7 @@
import openmc.checkvalue as cv
-class Resonances(object):
+class Resonances:
"""Resolved and unresolved resonance data
Parameters
@@ -119,7 +119,7 @@ def from_endf(cls, ev):
return cls(ranges)
-class ResonanceRange(object):
+class ResonanceRange:
"""Resolved resonance range
Parameters
@@ -867,7 +867,7 @@ def from_endf(cls, ev, file_obj, items):
return rml
-class ParticlePair(object):
+class ParticlePair:
def __init__(self, first, second, q_value, penetrability,
shift, mt):
self.first = first
@@ -878,7 +878,7 @@ def __init__(self, first, second, q_value, penetrability,
self.mt = mt
-class SpinGroup(object):
+class SpinGroup:
"""Resonance spin group
Attributes
diff --git a/openmc/deplete/atom_number.py b/openmc/deplete/atom_number.py
--- a/openmc/deplete/atom_number.py
+++ b/openmc/deplete/atom_number.py
@@ -7,7 +7,7 @@
import numpy as np
-class AtomNumber(object):
+class AtomNumber:
"""Stores local material compositions (atoms of each nuclide).
Parameters
diff --git a/openmc/deplete/chain.py b/openmc/deplete/chain.py
--- a/openmc/deplete/chain.py
+++ b/openmc/deplete/chain.py
@@ -141,7 +141,7 @@ def replace_missing(product, decay_data):
}
-class Chain(object):
+class Chain:
"""Full representation of a depletion chain.
A depletion chain can be created by using the :meth:`from_endf` method which
diff --git a/openmc/deplete/dummy_comm.py b/openmc/deplete/dummy_comm.py
--- a/openmc/deplete/dummy_comm.py
+++ b/openmc/deplete/dummy_comm.py
@@ -1,6 +1,7 @@
import sys
-class DummyCommunicator(object):
+
+class DummyCommunicator:
rank = 0
size = 1
diff --git a/openmc/deplete/nuclide.py b/openmc/deplete/nuclide.py
--- a/openmc/deplete/nuclide.py
+++ b/openmc/deplete/nuclide.py
@@ -75,7 +75,7 @@
pass
-class Nuclide(object):
+class Nuclide:
"""Decay modes, reactions, and fission yields for a single nuclide.
Parameters
diff --git a/openmc/deplete/results.py b/openmc/deplete/results.py
--- a/openmc/deplete/results.py
+++ b/openmc/deplete/results.py
@@ -19,7 +19,7 @@
__all__ = ["Results"]
-class Results(object):
+class Results:
"""Output of a depletion run
Attributes
diff --git a/openmc/element.py b/openmc/element.py
--- a/openmc/element.py
+++ b/openmc/element.py
@@ -40,7 +40,7 @@ def expand(self, percent, percent_type, enrichment=None,
cross_sections=None):
"""Expand natural element into its naturally-occurring isotopes.
- An optional cross_sections argument or the OPENMC_CROSS_SECTIONS
+ An optional cross_sections argument or the :envvar:`OPENMC_CROSS_SECTIONS`
environment variable is used to specify a cross_sections.xml file.
If the cross_sections.xml file is found, the element is expanded only
into the isotopes/nuclides present in cross_sections.xml. If no
@@ -132,7 +132,6 @@ def expand(self, percent, percent_type, enrichment=None,
# If a cross_sections library is present, check natural nuclides
# against the nuclides in the library
if cross_sections is not None:
-
library_nuclides = set()
tree = ET.parse(cross_sections)
root = tree.getroot()
@@ -174,14 +173,12 @@ def expand(self, percent, percent_type, enrichment=None,
# our knowledge of the common cross section libraries
# (ENDF, JEFF, and JENDL)
else:
-
# Add the mutual isotopes
for nuclide in mutual_nuclides:
abundances[nuclide] = NATURAL_ABUNDANCE[nuclide]
# Adjust the abundances for the absent nuclides
for nuclide in absent_nuclides:
-
if nuclide in ['O17', 'O18'] and 'O16' in mutual_nuclides:
abundances['O16'] += NATURAL_ABUNDANCE[nuclide]
elif nuclide == 'Ta180' and 'Ta181' in mutual_nuclides:
diff --git a/openmc/executor.py b/openmc/executor.py
--- a/openmc/executor.py
+++ b/openmc/executor.py
@@ -3,7 +3,6 @@
from numbers import Integral
import openmc
-from openmc import VolumeCalculation
def _run(args, output, cwd):
@@ -201,7 +200,7 @@ def run(particles=None, threads=None, geometry_debug=False,
if geometry_debug:
args.append('-g')
-
+
if event_based:
args.append('-e')
diff --git a/openmc/filter.py b/openmc/filter.py
--- a/openmc/filter.py
+++ b/openmc/filter.py
@@ -36,13 +36,16 @@
class FilterMeta(ABCMeta):
+ """Metaclass for filters that ensures class names are appropriate."""
+
def __new__(cls, name, bases, namespace, **kwargs):
# Check the class name.
- if not name.endswith('Filter'):
+ required_suffix = 'Filter'
+ if not name.endswith(required_suffix):
raise ValueError("All filter class names must end with 'Filter'")
# Create a 'short_name' attribute that removes the 'Filter' suffix.
- namespace['short_name'] = name[:-6]
+ namespace['short_name'] = name[:-len(required_suffix)]
# Subclass methods can sort of inherit the docstring of parent class
# methods. If a function is defined without a docstring, most (all?)
@@ -51,7 +54,7 @@ def __new__(cls, name, bases, namespace, **kwargs):
# use that docstring. However, Sphinx does not have that functionality.
# This chunk of code handles this docstring inheritance manually so that
# the autodocumentation will pick it up.
- if name != 'Filter':
+ if name != required_suffix:
# Look for newly-defined functions that were also in Filter.
for func_name in namespace:
if func_name in Filter.__dict__:
@@ -72,6 +75,12 @@ def __new__(cls, name, bases, namespace, **kwargs):
return super().__new__(cls, name, bases, namespace, **kwargs)
+def _repeat_and_tile(bins, repeat_factor, data_size):
+ filter_bins = np.repeat(bins, repeat_factor)
+ tile_factor = data_size // len(filter_bins)
+ return np.tile(filter_bins, tile_factor)
+
+
class Filter(IDManagerMixin, metaclass=FilterMeta):
"""Tally modifier that describes phase-space and other characteristics.
@@ -110,9 +119,6 @@ def __eq__(self, other):
else:
return np.allclose(self.bins, other.bins)
- def __ne__(self, other):
- return not self == other
-
def __gt__(self, other):
if type(self) is not type(other):
if self.short_name in _FILTER_TYPES and \
@@ -292,8 +298,8 @@ def is_subset(self, other):
if type(self) is not type(other):
return False
- for bin in other.bins:
- if bin not in self.bins:
+ for b in other.bins:
+ if b not in self.bins:
return False
return True
@@ -389,8 +395,7 @@ def __init__(self, bins, filter_id=None):
# Extract ID values
bins = np.array([b if isinstance(b, Integral) else b.id
for b in bins])
- self.bins = bins
- self.id = filter_id
+ super().__init__(bins, filter_id)
def check_bins(self, bins):
# Check the bin values.
@@ -663,6 +668,16 @@ class ParticleFilter(Filter):
The number of filter bins
"""
+ def __eq__(self, other):
+ if type(self) is not type(other):
+ return False
+ elif len(self.bins) != len(other.bins):
+ return False
+ else:
+ return np.all(self.bins == other.bins)
+
+ __hash__ = Filter.__hash__
+
@Filter.bins.setter
def bins(self, bins):
bins = np.atleast_1d(bins)
@@ -804,28 +819,16 @@ def get_pandas_dataframe(self, data_size, stride, **kwargs):
ny = nz = 1
# Generate multi-index sub-column for x-axis
- filter_bins = np.arange(1, nx + 1)
- repeat_factor = stride
- filter_bins = np.repeat(filter_bins, repeat_factor)
- tile_factor = data_size // len(filter_bins)
- filter_bins = np.tile(filter_bins, tile_factor)
- filter_dict[(mesh_key, 'x')] = filter_bins
+ filter_dict[mesh_key, 'x'] = _repeat_and_tile(
+ np.arange(1, nx + 1), stride, data_size)
# Generate multi-index sub-column for y-axis
- filter_bins = np.arange(1, ny + 1)
- repeat_factor = nx * stride
- filter_bins = np.repeat(filter_bins, repeat_factor)
- tile_factor = data_size // len(filter_bins)
- filter_bins = np.tile(filter_bins, tile_factor)
- filter_dict[(mesh_key, 'y')] = filter_bins
+ filter_dict[mesh_key, 'y'] = _repeat_and_tile(
+ np.arange(1, ny + 1), nx * stride, data_size)
# Generate multi-index sub-column for z-axis
- filter_bins = np.arange(1, nz + 1)
- repeat_factor = nx * ny * stride
- filter_bins = np.repeat(filter_bins, repeat_factor)
- tile_factor = data_size // len(filter_bins)
- filter_bins = np.tile(filter_bins, tile_factor)
- filter_dict[(mesh_key, 'z')] = filter_bins
+ filter_dict[mesh_key, 'z'] = _repeat_and_tile(
+ np.arange(1, nz + 1), nx * ny * stride, data_size)
# Initialize a Pandas DataFrame from the mesh dictionary
df = pd.concat([df, pd.DataFrame(filter_dict)])
@@ -933,37 +936,22 @@ def get_pandas_dataframe(self, data_size, stride, **kwargs):
ny = nz = 1
# Generate multi-index sub-column for x-axis
- filter_bins = np.arange(1, nx + 1)
- repeat_factor = n_surfs * stride
- filter_bins = np.repeat(filter_bins, repeat_factor)
- tile_factor = data_size // len(filter_bins)
- filter_bins = np.tile(filter_bins, tile_factor)
- filter_dict[(mesh_key, 'x')] = filter_bins
+ filter_dict[mesh_key, 'x'] = _repeat_and_tile(
+ np.arange(1, nx + 1), n_surfs * stride, data_size)
# Generate multi-index sub-column for y-axis
if len(self.mesh.dimension) > 1:
- filter_bins = np.arange(1, ny + 1)
- repeat_factor = n_surfs * nx * stride
- filter_bins = np.repeat(filter_bins, repeat_factor)
- tile_factor = data_size // len(filter_bins)
- filter_bins = np.tile(filter_bins, tile_factor)
- filter_dict[(mesh_key, 'y')] = filter_bins
+ filter_dict[mesh_key, 'y'] = _repeat_and_tile(
+ np.arange(1, ny + 1), n_surfs * nx * stride, data_size)
# Generate multi-index sub-column for z-axis
if len(self.mesh.dimension) > 2:
- filter_bins = np.arange(1, nz + 1)
- repeat_factor = n_surfs * nx * ny * stride
- filter_bins = np.repeat(filter_bins, repeat_factor)
- tile_factor = data_size // len(filter_bins)
- filter_bins = np.tile(filter_bins, tile_factor)
- filter_dict[(mesh_key, 'z')] = filter_bins
+ filter_dict[mesh_key, 'z'] = _repeat_and_tile(
+ np.arange(1, nz + 1), n_surfs * nx * ny * stride, data_size)
# Generate multi-index sub-column for surface
- repeat_factor = stride
- filter_bins = np.repeat(_CURRENT_NAMES[:n_surfs], repeat_factor)
- tile_factor = data_size // len(filter_bins)
- filter_bins = np.tile(filter_bins, tile_factor)
- filter_dict[(mesh_key, 'surf')] = filter_bins
+ filter_dict[mesh_key, 'surf'] = _repeat_and_tile(
+ _CURRENT_NAMES[:n_surfs], stride, data_size)
# Initialize a Pandas DataFrame from the mesh dictionary
return pd.concat([df, pd.DataFrame(filter_dict)])
@@ -1386,8 +1374,8 @@ def get_pandas_dataframe(self, data_size, stride, **kwargs):
Returns
-------
pandas.DataFrame
- A Pandas DataFrame with columns describing distributed cells. The
- for will be either:
+ A Pandas DataFrame with columns describing distributed cells. The
+ dataframe will have either:
1. a single column with the cell instance IDs (without summary info)
2. separate columns for the cell IDs, universe IDs, and lattice IDs
@@ -1479,10 +1467,8 @@ def get_pandas_dataframe(self, data_size, stride, **kwargs):
# Tile the Multi-index columns
for level_key, level_bins in level_dict.items():
- level_bins = np.repeat(level_bins, stride)
- tile_factor = data_size // len(level_bins)
- level_bins = np.tile(level_bins, tile_factor)
- level_dict[level_key] = level_bins
+ level_dict[level_key] = _repeat_and_tile(
+ level_bins, stride, data_size)
# Initialize a Pandas DataFrame from the level dictionary
if level_df is None:
@@ -1494,10 +1480,8 @@ def get_pandas_dataframe(self, data_size, stride, **kwargs):
# Create DataFrame column for distribcell instance IDs
# NOTE: This is performed regardless of whether the user
# requests Summary geometric information
- filter_bins = np.arange(self.num_bins)
- filter_bins = np.repeat(filter_bins, stride)
- tile_factor = data_size // len(filter_bins)
- filter_bins = np.tile(filter_bins, tile_factor)
+ filter_bins = _repeat_and_tile(
+ np.arange(self.num_bins), stride, data_size)
df = pd.DataFrame({self.short_name.lower() : filter_bins})
# Concatenate with DataFrame of distribcell instance IDs
@@ -1709,10 +1693,8 @@ def __eq__(self, other):
return False
elif not all(self.energy == other.energy):
return False
- elif not all(self.y == other.y):
- return False
else:
- return True
+ return all(self.y == other.y)
def __gt__(self, other):
if type(self) is not type(other):
@@ -1905,9 +1887,7 @@ def get_pandas_dataframe(self, data_size, stride, **kwargs):
# hex characters) of the digest are probably sufficient.
out = out[:14]
- filter_bins = np.repeat(out, stride)
- tile_factor = data_size // len(filter_bins)
- filter_bins = np.tile(filter_bins, tile_factor)
+ filter_bins = _repeat_and_tile(out, stride, data_size)
df = pd.concat([df, pd.DataFrame(
{self.short_name.lower(): filter_bins})])
diff --git a/openmc/geometry.py b/openmc/geometry.py
--- a/openmc/geometry.py
+++ b/openmc/geometry.py
@@ -11,7 +11,7 @@
from openmc.checkvalue import check_type
-class Geometry(object):
+class Geometry:
"""Geometry representing a collection of surfaces, cells, and universes.
Parameters
@@ -406,10 +406,27 @@ def get_redundant_surfaces(self):
coeffs = tuple(surf._coefficients[k] for k in surf._coeff_keys)
key = (surf._type,) + coeffs
tally[key].append(surf)
- return {replace.id: keep
+ return {replace.id: keep
for keep, *redundant in tally.values()
for replace in redundant}
+ def _get_domains_by_name(self, name, case_sensitive, matching, domain_type):
+ if not case_sensitive:
+ name = name.lower()
+
+ domains = []
+
+ func = getattr(self, 'get_all_{}s'.format(domain_type))
+ for domain in func().values():
+ domain_name = domain.name if case_sensitive else domain.name.lower()
+ if domain_name == name:
+ domains.append(domain)
+ elif not matching and name in domain_name:
+ domains.append(domain)
+
+ domains.sort(key=lambda x: x.id)
+ return domains
+
def get_materials_by_name(self, name, case_sensitive=False, matching=False):
"""Return a list of materials with matching names.
@@ -429,24 +446,7 @@ def get_materials_by_name(self, name, case_sensitive=False, matching=False):
Materials matching the queried name
"""
-
- if not case_sensitive:
- name = name.lower()
-
- all_materials = self.get_all_materials().values()
- materials = set()
-
- for material in all_materials:
- material_name = material.name
- if not case_sensitive:
- material_name = material_name.lower()
-
- if material_name == name:
- materials.add(material)
- elif not matching and name in material_name:
- materials.add(material)
-
- return sorted(materials, key=lambda x: x.id)
+ return self._get_domains_by_name(name, case_sensitive, matching, 'material')
def get_cells_by_name(self, name, case_sensitive=False, matching=False):
"""Return a list of cells with matching names.
@@ -467,24 +467,7 @@ def get_cells_by_name(self, name, case_sensitive=False, matching=False):
Cells matching the queried name
"""
-
- if not case_sensitive:
- name = name.lower()
-
- all_cells = self.get_all_cells().values()
- cells = set()
-
- for cell in all_cells:
- cell_name = cell.name
- if not case_sensitive:
- cell_name = cell_name.lower()
-
- if cell_name == name:
- cells.add(cell)
- elif not matching and name in cell_name:
- cells.add(cell)
-
- return sorted(cells, key=lambda x: x.id)
+ return self._get_domains_by_name(name, case_sensitive, matching, 'cell')
def get_cells_by_fill_name(self, name, case_sensitive=False, matching=False):
"""Return a list of cells with fills with matching names.
@@ -550,24 +533,7 @@ def get_universes_by_name(self, name, case_sensitive=False, matching=False):
Universes matching the queried name
"""
-
- if not case_sensitive:
- name = name.lower()
-
- all_universes = self.get_all_universes().values()
- universes = set()
-
- for universe in all_universes:
- universe_name = universe.name
- if not case_sensitive:
- universe_name = universe_name.lower()
-
- if universe_name == name:
- universes.add(universe)
- elif not matching and name in universe_name:
- universes.add(universe)
-
- return sorted(universes, key=lambda x: x.id)
+ return self._get_domains_by_name(name, case_sensitive, matching, 'universe')
def get_lattices_by_name(self, name, case_sensitive=False, matching=False):
"""Return a list of lattices with matching names.
@@ -588,24 +554,7 @@ def get_lattices_by_name(self, name, case_sensitive=False, matching=False):
Lattices matching the queried name
"""
-
- if not case_sensitive:
- name = name.lower()
-
- all_lattices = self.get_all_lattices().values()
- lattices = set()
-
- for lattice in all_lattices:
- lattice_name = lattice.name
- if not case_sensitive:
- lattice_name = lattice_name.lower()
-
- if lattice_name == name:
- lattices.add(lattice)
- elif not matching and name in lattice_name:
- lattices.add(lattice)
-
- return sorted(lattices, key=lambda x: x.id)
+ return self._get_domains_by_name(name, case_sensitive, matching, 'lattice')
def remove_redundant_surfaces(self):
"""Remove redundant surfaces from the geometry"""
@@ -613,7 +562,7 @@ def remove_redundant_surfaces(self):
# Get redundant surfaces
redundant_surfaces = self.get_redundant_surfaces()
- # Iterate through all cells contained in the geometry
+ # Iterate through all cells contained in the geometry
for cell in self.get_all_cells().values():
# Recursively remove redundant surfaces from regions
cell.region.remove_redundant_surfaces(redundant_surfaces)
diff --git a/openmc/lattice.py b/openmc/lattice.py
--- a/openmc/lattice.py
+++ b/openmc/lattice.py
@@ -101,187 +101,13 @@ def from_hdf5(group, universes):
Instance of lattice subclass
"""
- lattice_id = int(group.name.split('/')[-1].lstrip('lattice '))
- name = group['name'][()].decode() if 'name' in group else ''
lattice_type = group['type'][()].decode()
-
if lattice_type == 'rectangular':
- dimension = group['dimension'][...]
- lower_left = group['lower_left'][...]
- pitch = group['pitch'][...]
- outer = group['outer'][()]
- universe_ids = group['universes'][...]
-
- # Create the Lattice
- lattice = openmc.RectLattice(lattice_id, name)
- lattice.lower_left = lower_left
- lattice.pitch = pitch
-
- # If the Universe specified outer the Lattice is not void
- if outer >= 0:
- lattice.outer = universes[outer]
-
- # Build array of Universe pointers for the Lattice
- uarray = np.empty(universe_ids.shape, dtype=openmc.Universe)
-
- for z in range(universe_ids.shape[0]):
- for y in range(universe_ids.shape[1]):
- for x in range(universe_ids.shape[2]):
- uarray[z, y, x] = universes[universe_ids[z, y, x]]
-
- # Use 2D NumPy array to store lattice universes for 2D lattices
- if len(dimension) == 2:
- uarray = np.squeeze(uarray)
- uarray = np.atleast_2d(uarray)
-
- # Set the universes for the lattice
- lattice.universes = uarray
-
+ return openmc.RectLattice.from_hdf5(group, universes)
elif lattice_type == 'hexagonal':
- n_rings = group['n_rings'][()]
- n_axial = group['n_axial'][()]
- center = group['center'][()]
- pitch = group['pitch'][()]
- outer = group['outer'][()]
- if 'orientation' in group:
- orientation = group['orientation'][()].decode()
- else:
- orientation = "y"
-
- universe_ids = group['universes'][()]
-
- # Create the Lattice
- lattice = openmc.HexLattice(lattice_id, name)
- lattice.center = center
- lattice.pitch = pitch
- lattice.orientation = orientation
- # If the Universe specified outer the Lattice is not void
- if outer >= 0:
- lattice.outer = universes[outer]
- if orientation == "y":
- # Build array of Universe pointers for the Lattice. Note that
- # we need to convert between the HDF5's square array of
- # (x, alpha, z) to the Python API's format of a ragged nested
- # list of (z, ring, theta).
- uarray = []
- for z in range(n_axial):
- # Add a list for this axial level.
- uarray.append([])
- x = n_rings - 1
- a = 2*n_rings - 2
- for r in range(n_rings - 1, 0, -1):
- # Add a list for this ring.
- uarray[-1].append([])
-
- # Climb down the top-right.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, a, x])
- x += 1
- a -= 1
-
- # Climb down the right.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, a, x])
- a -= 1
-
- # Climb down the bottom-right.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, a, x])
- x -= 1
-
- # Climb up the bottom-left.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, a, x])
- x -= 1
- a += 1
-
- # Climb up the left.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, a, x])
- a += 1
-
- # Climb up the top-left.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, a, x])
- x += 1
-
- # Move down to the next ring.
- a -= 1
-
- # Convert the ids into Universe objects.
- uarray[-1][-1] = [universes[u_id]
- for u_id in uarray[-1][-1]]
-
- # Handle the degenerate center ring separately.
- u_id = universe_ids[z, a, x]
- uarray[-1].append([universes[u_id]])
- else:
- # Build array of Universe pointers for the Lattice. Note that
- # we need to convert between the HDF5's square array of
- # (alpha, y, z) to the Python API's format of a ragged nested
- # list of (z, ring, theta).
- uarray = []
- for z in range(n_axial):
- # Add a list for this axial level.
- uarray.append([])
- a = 2*n_rings - 2
- y = n_rings - 1
- for r in range(n_rings - 1, 0, -1):
- # Add a list for this ring.
- uarray[-1].append([])
-
- # Climb down the bottom-right.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, y, a])
- y -= 1
-
- # Climb across the bottom.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, y, a])
- a -= 1
-
- # Climb up the bottom-left.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, y, a])
- a -= 1
- y += 1
-
- # Climb up the top-left.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, y, a])
- y += 1
-
- # Climb across the top.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, y, a])
- a += 1
-
- # Climb down the top-right.
- for i in range(r):
- uarray[-1][-1].append(universe_ids[z, y, a])
- a += 1
- y -= 1
-
- # Move down to the next ring.
- a -= 1
-
- # Convert the ids into Universe objects.
- uarray[-1][-1] = [universes[u_id]
- for u_id in uarray[-1][-1]]
-
- # Handle the degenerate center ring separately.
- u_id = universe_ids[z, y, a]
- uarray[-1].append([universes[u_id]])
-
- # Add the universes to the lattice.
- if len(pitch) == 2:
- # Lattice is 3D
- lattice.universes = uarray
- else:
- # Lattice is 2D; extract the only axial level
- lattice.universes = uarray[0]
-
- return lattice
+ return openmc.HexLattice.from_hdf5(group, universes)
+ else:
+ raise ValueError('Unkown lattice type: {}'.format(lattice_type))
def get_unique_universes(self):
"""Determine all unique universes in the lattice
@@ -579,29 +405,22 @@ def __init__(self, lattice_id=None, name=''):
def __repr__(self):
string = 'RectLattice\n'
- string += '{0: <16}{1}{2}\n'.format('\tID', '=\t', self._id)
- string += '{0: <16}{1}{2}\n'.format('\tName', '=\t', self._name)
- string += '{0: <16}{1}{2}\n'.format('\tShape', '=\t',
- self.shape)
- string += '{0: <16}{1}{2}\n'.format('\tLower Left', '=\t',
- self._lower_left)
- string += '{0: <16}{1}{2}\n'.format('\tPitch', '=\t', self._pitch)
+ string += '{: <16}=\t{}\n'.format('\tID', self._id)
+ string += '{: <16}=\t{}\n'.format('\tName', self._name)
+ string += '{: <16}=\t{}\n'.format('\tShape', self.shape)
+ string += '{: <16}=\t{}\n'.format('\tLower Left', self._lower_left)
+ string += '{: <16}=\t{}\n'.format('\tPitch', self._pitch)
+ string += '{: <16}=\t{}\n'.format(
+ '\tOuter', self._outer._id if self._outer is not None else None)
- if self._outer is not None:
- string += '{0: <16}{1}{2}\n'.format('\tOuter', '=\t',
- self._outer._id)
- else:
- string += '{0: <16}{1}{2}\n'.format('\tOuter', '=\t',
- self._outer)
+ string += '{: <16}\n'.format('\tUniverses')
- string += '{0: <16}\n'.format('\tUniverses')
-
- # Lattice nested Universe IDs - column major for Fortran
+ # Lattice nested Universe IDs
for i, universe in enumerate(np.ravel(self._universes)):
- string += '{0} '.format(universe._id)
+ string += '{} '.format(universe._id)
# Add a newline character every time we reach end of row of cells
- if (i+1) % self.shape[0] == 0:
+ if (i + 1) % self.shape[0] == 0:
string += '\n'
string = string.rstrip('\n')
@@ -1141,6 +960,59 @@ def from_xml_element(cls, elem, get_universe):
lat.universes = uarray
return lat
+ @classmethod
+ def from_hdf5(cls, group, universes):
+ """Create rectangular lattice from HDF5 group
+
+ Parameters
+ ----------
+ group : h5py.Group
+ Group in HDF5 file
+ universes : dict
+ Dictionary mapping universe IDs to instances of
+ :class:`openmc.Universe`.
+
+ Returns
+ -------
+ openmc.RectLattice
+ Rectangular lattice
+
+ """
+ dimension = group['dimension'][...]
+ lower_left = group['lower_left'][...]
+ pitch = group['pitch'][...]
+ outer = group['outer'][()]
+ universe_ids = group['universes'][...]
+
+ # Create the Lattice
+ lattice_id = int(group.name.split('/')[-1].lstrip('lattice '))
+ name = group['name'][()].decode() if 'name' in group else ''
+ lattice = cls(lattice_id, name)
+ lattice.lower_left = lower_left
+ lattice.pitch = pitch
+
+ # If the Universe specified outer the Lattice is not void
+ if outer >= 0:
+ lattice.outer = universes[outer]
+
+ # Build array of Universe pointers for the Lattice
+ uarray = np.empty(universe_ids.shape, dtype=openmc.Universe)
+
+ for z in range(universe_ids.shape[0]):
+ for y in range(universe_ids.shape[1]):
+ for x in range(universe_ids.shape[2]):
+ uarray[z, y, x] = universes[universe_ids[z, y, x]]
+
+ # Use 2D NumPy array to store lattice universes for 2D lattices
+ if len(dimension) == 2:
+ uarray = np.squeeze(uarray)
+ uarray = np.atleast_2d(uarray)
+
+ # Set the universes for the lattice
+ lattice.universes = uarray
+
+ return lattice
+
class HexLattice(Lattice):
r"""A lattice consisting of hexagonal prisms.
@@ -1458,20 +1330,16 @@ def get_local_coordinates(self, point, idx):
"""
if self._orientation == 'x':
- x = point[0] - (self.center[0] + self.pitch[0]*idx[0] +
- 0.5*self.pitch[0]*idx[1])
- y = point[1] - (self.center[1] +
- sqrt(0.75)*self.pitch[0]*idx[1])
+ x = point[0] - (self.center[0] + (idx[0] + 0.5*idx[1])*self.pitch[0])
+ y = point[1] - (self.center[1] + sqrt(0.75)*self.pitch[0]*idx[1])
else:
- x = point[0] - (self.center[0]
- + sqrt(0.75)*self.pitch[0]*idx[0])
- y = point[1] - (self.center[1]
- + (0.5*idx[0] + idx[1])*self.pitch[0])
+ x = point[0] - (self.center[0] + sqrt(0.75)*self.pitch[0]*idx[0])
+ y = point[1] - (self.center[1] + (0.5*idx[0] + idx[1])*self.pitch[0])
if self._num_axial is None:
z = point[2]
else:
- z = point[2] - (self.center[2] + (idx[2] + 0.5 - 0.5*self.num_axial)*
+ z = point[2] - (self.center[2] + (idx[2] + 0.5 - 0.5*self.num_axial) *
self.pitch[1])
return (x, y, z)
@@ -2168,3 +2036,167 @@ def show_indices(num_rings, orientation="y"):
return HexLattice._show_indices_x(num_rings)
else:
return HexLattice._show_indices_y(num_rings)
+
+ @classmethod
+ def from_hdf5(cls, group, universes):
+ """Create rectangular lattice from HDF5 group
+
+ Parameters
+ ----------
+ group : h5py.Group
+ Group in HDF5 file
+ universes : dict
+ Dictionary mapping universe IDs to instances of
+ :class:`openmc.Universe`.
+
+ Returns
+ -------
+ openmc.RectLattice
+ Rectangular lattice
+
+ """
+ n_rings = group['n_rings'][()]
+ n_axial = group['n_axial'][()]
+ center = group['center'][()]
+ pitch = group['pitch'][()]
+ outer = group['outer'][()]
+ if 'orientation' in group:
+ orientation = group['orientation'][()].decode()
+ else:
+ orientation = "y"
+ universe_ids = group['universes'][()]
+
+ # Create the Lattice
+ lattice_id = int(group.name.split('/')[-1].lstrip('lattice '))
+ name = group['name'][()].decode() if 'name' in group else ''
+ lattice = openmc.HexLattice(lattice_id, name)
+ lattice.center = center
+ lattice.pitch = pitch
+ lattice.orientation = orientation
+ # If the Universe specified outer the Lattice is not void
+ if outer >= 0:
+ lattice.outer = universes[outer]
+ if orientation == "y":
+ # Build array of Universe pointers for the Lattice. Note that
+ # we need to convert between the HDF5's square array of
+ # (x, alpha, z) to the Python API's format of a ragged nested
+ # list of (z, ring, theta).
+ uarray = []
+ for z in range(n_axial):
+ # Add a list for this axial level.
+ uarray.append([])
+ x = n_rings - 1
+ a = 2*n_rings - 2
+ for r in range(n_rings - 1, 0, -1):
+ # Add a list for this ring.
+ uarray[-1].append([])
+
+ # Climb down the top-right.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, a, x])
+ x += 1
+ a -= 1
+
+ # Climb down the right.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, a, x])
+ a -= 1
+
+ # Climb down the bottom-right.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, a, x])
+ x -= 1
+
+ # Climb up the bottom-left.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, a, x])
+ x -= 1
+ a += 1
+
+ # Climb up the left.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, a, x])
+ a += 1
+
+ # Climb up the top-left.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, a, x])
+ x += 1
+
+ # Move down to the next ring.
+ a -= 1
+
+ # Convert the ids into Universe objects.
+ uarray[-1][-1] = [universes[u_id]
+ for u_id in uarray[-1][-1]]
+
+ # Handle the degenerate center ring separately.
+ u_id = universe_ids[z, a, x]
+ uarray[-1].append([universes[u_id]])
+ else:
+ # Build array of Universe pointers for the Lattice. Note that
+ # we need to convert between the HDF5's square array of
+ # (alpha, y, z) to the Python API's format of a ragged nested
+ # list of (z, ring, theta).
+ uarray = []
+ for z in range(n_axial):
+ # Add a list for this axial level.
+ uarray.append([])
+ a = 2*n_rings - 2
+ y = n_rings - 1
+ for r in range(n_rings - 1, 0, -1):
+ # Add a list for this ring.
+ uarray[-1].append([])
+
+ # Climb down the bottom-right.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, y, a])
+ y -= 1
+
+ # Climb across the bottom.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, y, a])
+ a -= 1
+
+ # Climb up the bottom-left.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, y, a])
+ a -= 1
+ y += 1
+
+ # Climb up the top-left.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, y, a])
+ y += 1
+
+ # Climb across the top.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, y, a])
+ a += 1
+
+ # Climb down the top-right.
+ for i in range(r):
+ uarray[-1][-1].append(universe_ids[z, y, a])
+ a += 1
+ y -= 1
+
+ # Move down to the next ring.
+ a -= 1
+
+ # Convert the ids into Universe objects.
+ uarray[-1][-1] = [universes[u_id]
+ for u_id in uarray[-1][-1]]
+
+ # Handle the degenerate center ring separately.
+ u_id = universe_ids[z, y, a]
+ uarray[-1].append([universes[u_id]])
+
+ # Add the universes to the lattice.
+ if len(pitch) == 2:
+ # Lattice is 3D
+ lattice.universes = uarray
+ else:
+ # Lattice is 2D; extract the only axial level
+ lattice.universes = uarray[0]
+
+ return lattice
diff --git a/openmc/lib/core.py b/openmc/lib/core.py
--- a/openmc/lib/core.py
+++ b/openmc/lib/core.py
@@ -400,7 +400,7 @@ def run_in_memory(**kwargs):
finalize()
-class _DLLGlobal(object):
+class _DLLGlobal:
"""Data descriptor that exposes global variables from libopenmc."""
def __init__(self, ctype, name):
self.ctype = ctype
@@ -413,7 +413,7 @@ def __set__(self, instance, value):
self.ctype.in_dll(_dll, self.name).value = value
-class _FortranObject(object):
+class _FortranObject:
def __repr__(self):
return "{}[{}]".format(type(self).__name__, self._index)
diff --git a/openmc/lib/settings.py b/openmc/lib/settings.py
--- a/openmc/lib/settings.py
+++ b/openmc/lib/settings.py
@@ -15,7 +15,7 @@
_dll.openmc_get_seed.restype = c_int64
-class _Settings(object):
+class _Settings:
# Attributes that are accessed through a descriptor
batches = _DLLGlobal(c_int32, 'n_batches')
cmfd_run = _DLLGlobal(c_bool, 'cmfd_run')
diff --git a/openmc/material.py b/openmc/material.py
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -1,4 +1,4 @@
-from collections import OrderedDict, defaultdict, Counter
+from collections import OrderedDict, defaultdict, namedtuple, Counter
from collections.abc import Iterable
from copy import deepcopy
from numbers import Real, Integral
@@ -21,6 +21,9 @@
'macro']
+NuclideTuple = namedtuple('NuclideTuple', ['name', 'percent', 'percent_type'])
+
+
class Material(IDManagerMixin):
"""A material composed of a collection of nuclides/elements.
@@ -56,9 +59,10 @@ class Material(IDManagerMixin):
applies in the case of a multi-group calculation.
depletable : bool
Indicate whether the material is depletable.
- nuclides : list of tuple
- List in which each item is a 3-tuple consisting of a nuclide string, the
- percent density, and the percent type ('ao' or 'wo').
+ nuclides : list of namedtuple
+ List in which each item is a namedtuple consisting of a nuclide string,
+ the percent density, and the percent type ('ao' or 'wo'). The namedtuple
+ has field names ``name``, ``percent``, and ``percent_type``.
isotropic : list of str
Nuclides for which elastic scattering should be treated as though it
were isotropic in the laboratory system.
@@ -75,7 +79,9 @@ class Material(IDManagerMixin):
instance. This property is initialized by calling the
:meth:`Geometry.determine_paths` method.
num_instances : int
- The number of instances of this material throughout the geometry.
+ The number of instances of this material throughout the geometry. This
+ property is initialized by calling the :meth:`Geometry.determine_paths`
+ method.
fissionable_mass : float
Mass of fissionable nuclides in the material in [g]. Requires that the
:attr:`volume` attribute is set.
@@ -109,12 +115,6 @@ def __init__(self, material_id=None, name='', temperature=None):
# If specified, a list of table names
self._sab = []
- # If true, the material will be initialized as distributed
- self._convert_to_distrib_comps = False
-
- # If specified, this file will be used instead of composition values
- self._distrib_otf_file = None
-
def __repr__(self):
string = 'Material\n'
string += '{: <16}=\t{}\n'.format('\tID', self._id)
@@ -184,31 +184,19 @@ def nuclides(self):
def isotropic(self):
return self._isotropic
- @property
- def convert_to_distrib_comps(self):
- return self._convert_to_distrib_comps
-
- @property
- def distrib_otf_file(self):
- return self._distrib_otf_file
-
@property
def average_molar_mass(self):
-
- # Get a list of all the nuclides, with elements expanded
- nuclide_densities = self.get_nuclide_densities()
-
# Using the sum of specified atomic or weight amounts as a basis, sum
# the mass and moles of the material
mass = 0.
moles = 0.
- for nuc, vals in nuclide_densities.items():
- if vals[2] == 'ao':
- mass += vals[1] * openmc.data.atomic_mass(nuc)
- moles += vals[1]
+ for nuc in self.nuclides:
+ if nuc.percent_type == 'ao':
+ mass += nuc.percent * openmc.data.atomic_mass(nuc.name)
+ moles += nuc.percent
else:
- moles += vals[1] / openmc.data.atomic_mass(nuc)
- mass += vals[1]
+ moles += nuc.percent / openmc.data.atomic_mass(nuc.name)
+ mass += nuc.percent
# Compute and return the molar mass
return mass / moles
@@ -331,9 +319,11 @@ def add_volume_information(self, volume_calc):
self._volume = volume_calc.volumes[self.id].n
self._atoms = volume_calc.atoms[self.id]
else:
- raise ValueError('No volume information found for this material.')
+ raise ValueError('No volume information found for material ID={}.'
+ .format(self.id))
else:
- raise ValueError('No volume information found for this material.')
+ raise ValueError('No volume information found for material ID={}.'
+ .format(self.id))
def set_density(self, units, density=None):
"""Set the density of the material
@@ -367,27 +357,6 @@ def set_density(self, units, density=None):
density, Real)
self._density = density
- @distrib_otf_file.setter
- def distrib_otf_file(self, filename):
- # TODO: remove this when distributed materials are merged
- warnings.warn('This feature is not yet implemented in a release '
- 'version of openmc')
-
- if not isinstance(filename, str) and filename is not None:
- msg = 'Unable to add OTF material file to Material ID="{}" with a ' \
- 'non-string name "{}"'.format(self._id, filename)
- raise ValueError(msg)
-
- self._distrib_otf_file = filename
-
- @convert_to_distrib_comps.setter
- def convert_to_distrib_comps(self):
- # TODO: remove this when distributed materials are merged
- warnings.warn('This feature is not yet implemented in a release '
- 'version of openmc')
-
- self._convert_to_distrib_comps = True
-
def add_nuclide(self, nuclide, percent, percent_type='ao'):
"""Add a nuclide to the material
@@ -420,7 +389,7 @@ def add_nuclide(self, nuclide, percent, percent_type='ao'):
if Z >= 89:
self.depletable = True
- self._nuclides.append((nuclide, percent, percent_type))
+ self._nuclides.append(NuclideTuple(nuclide, percent, percent_type))
def remove_nuclide(self, nuclide):
"""Remove a nuclide from the material
@@ -434,10 +403,9 @@ def remove_nuclide(self, nuclide):
cv.check_type('nuclide', nuclide, str)
# If the Material contains the Nuclide, delete it
- for nuc in self._nuclides:
- if nuclide == nuc[0]:
- self._nuclides.remove(nuc)
- break
+ for nuc in reversed(self.nuclides):
+ if nuclide == nuc.name:
+ self.nuclides.remove(nuc)
def add_macroscopic(self, macroscopic):
"""Add a macroscopic to the material. This will also set the
@@ -532,7 +500,7 @@ def add_element(self, element, percent, percent_type='ao', enrichment=None,
natural composition is added to the material.
"""
-
+
cv.check_type('nuclide', element, str)
cv.check_type('percent', percent, Real)
cv.check_value('percent type', percent_type, {'ao', 'wo'})
@@ -682,6 +650,7 @@ def add_elements_from_formula(self, formula, percent_type='ao', enrichment=None,
enrichment_target, enrichment_type)
else:
self.add_element(element, percent, percent_type)
+
def add_s_alpha_beta(self, name, fraction=1.0):
r"""Add an :math:`S(\alpha,\beta)` table to the material
@@ -720,7 +689,7 @@ def add_s_alpha_beta(self, name, fraction=1.0):
self._sab.append((new_name, fraction))
def make_isotropic_in_lab(self):
- self.isotropic = [x[0] for x in self._nuclides]
+ self.isotropic = [x.name for x in self._nuclides]
def get_nuclides(self):
"""Returns all nuclides in the material
@@ -731,7 +700,7 @@ def get_nuclides(self):
List of nuclide names
"""
- return [x[0] for x in self._nuclides]
+ return [x.name for x in self._nuclides]
def get_nuclide_densities(self):
"""Returns all nuclides in the material and their densities
@@ -744,10 +713,11 @@ def get_nuclide_densities(self):
"""
+ # keep ordered dictionary for testing purposes
nuclides = OrderedDict()
- for nuclide, density, density_type in self._nuclides:
- nuclides[nuclide] = (nuclide, density, density_type)
+ for nuclide in self._nuclides:
+ nuclides[nuclide.name] = nuclide
return nuclides
@@ -763,9 +733,6 @@ def get_nuclide_atom_densities(self):
"""
- # Expand elements in to nuclides
- nuclides = self.get_nuclide_densities()
-
sum_density = False
if self.density_units == 'sum':
sum_density = True
@@ -782,16 +749,15 @@ def get_nuclide_atom_densities(self):
density = 1.E-24 * self.density
# For ease of processing split out nuc, nuc_density,
- # and nuc_density_type in to separate arrays
+ # and nuc_density_type into separate arrays
nucs = []
nuc_densities = []
nuc_density_types = []
- for nuclide in nuclides.items():
- nuc, nuc_density, nuc_density_type = nuclide[1]
- nucs.append(nuc)
- nuc_densities.append(nuc_density)
- nuc_density_types.append(nuc_density_type)
+ for nuclide in self.nuclides:
+ nucs.append(nuclide.name)
+ nuc_densities.append(nuclide.percent)
+ nuc_density_types.append(nuclide.percent_type)
nucs = np.array(nucs)
nuc_densities = np.array(nuc_densities)
@@ -911,15 +877,14 @@ def clone(self, memo=None):
return memo[self]
- def _get_nuclide_xml(self, nuclide, distrib=False):
+ def _get_nuclide_xml(self, nuclide):
xml_element = ET.Element("nuclide")
- xml_element.set("name", nuclide[0])
+ xml_element.set("name", nuclide.name)
- if not distrib:
- if nuclide[2] == 'ao':
- xml_element.set("ao", str(nuclide[1]))
- else:
- xml_element.set("wo", str(nuclide[1]))
+ if nuclide.percent_type == 'ao':
+ xml_element.set("ao", str(nuclide.percent))
+ else:
+ xml_element.set("wo", str(nuclide.percent))
return xml_element
@@ -929,10 +894,10 @@ def _get_macroscopic_xml(self, macroscopic):
return xml_element
- def _get_nuclides_xml(self, nuclides, distrib=False):
+ def _get_nuclides_xml(self, nuclides):
xml_elements = []
for nuclide in nuclides:
- xml_elements.append(self._get_nuclide_xml(nuclide, distrib))
+ xml_elements.append(self._get_nuclide_xml(nuclide))
return xml_elements
def to_xml_element(self, cross_sections=None):
@@ -977,51 +942,15 @@ def to_xml_element(self, cross_sections=None):
raise ValueError('Density has not been set for material {}!'
.format(self.id))
- if not self._convert_to_distrib_comps:
- if self._macroscopic is None:
- # Create nuclide XML subelements
- subelements = self._get_nuclides_xml(self._nuclides)
- for subelement in subelements:
- element.append(subelement)
- else:
- # Create macroscopic XML subelements
- subelement = self._get_macroscopic_xml(self._macroscopic)
+ if self._macroscopic is None:
+ # Create nuclide XML subelements
+ subelements = self._get_nuclides_xml(self._nuclides)
+ for subelement in subelements:
element.append(subelement)
-
else:
- subelement = ET.SubElement(element, "compositions")
-
- comps = []
- allnucs = self._nuclides
- dist_per_type = allnucs[0][2]
- for nuc in allnucs:
- if nuc[2] != dist_per_type:
- msg = 'All nuclides and elements in a distributed ' \
- 'material must have the same type, either ao or wo'
- raise ValueError(msg)
- comps.append(nuc[1])
-
- if self._distrib_otf_file is None:
- # Create values and units subelements
- subsubelement = ET.SubElement(subelement, "values")
- subsubelement.text = ' '.join([str(c) for c in comps])
- subsubelement = ET.SubElement(subelement, "units")
- subsubelement.text = dist_per_type
- else:
- # Specify the materials file
- subsubelement = ET.SubElement(subelement, "otf_file_path")
- subsubelement.text = self._distrib_otf_file
-
- if self._macroscopic is None:
- # Create nuclide XML subelements
- subelements = self._get_nuclides_xml(self._nuclides,
- distrib=True)
- for subelement_nuc in subelements:
- subelement.append(subelement_nuc)
- else:
- # Create macroscopic XML subelements
- subsubelement = self._get_macroscopic_xml(self._macroscopic)
- subelement.append(subsubelement)
+ # Create macroscopic XML subelements
+ subelement = self._get_macroscopic_xml(self._macroscopic)
+ element.append(subelement)
if self._sab:
for sab in self._sab:
diff --git a/openmc/mgxs/groups.py b/openmc/mgxs/groups.py
--- a/openmc/mgxs/groups.py
+++ b/openmc/mgxs/groups.py
@@ -8,7 +8,7 @@
import openmc.checkvalue as cv
-class EnergyGroups(object):
+class EnergyGroups:
"""An energy groups structure used for multi-group cross-sections.
Parameters
@@ -57,9 +57,6 @@ def __eq__(self, other):
else:
return False
- def __ne__(self, other):
- return not self == other
-
def __hash__(self):
return hash(tuple(self.group_edges))
diff --git a/openmc/mgxs/library.py b/openmc/mgxs/library.py
--- a/openmc/mgxs/library.py
+++ b/openmc/mgxs/library.py
@@ -15,7 +15,7 @@
from openmc.tallies import ESTIMATOR_TYPES
-class Library(object):
+class Library:
"""A multi-energy-group and multi-delayed-group cross section library for
some energy group structure.
diff --git a/openmc/mgxs_library.py b/openmc/mgxs_library.py
--- a/openmc/mgxs_library.py
+++ b/openmc/mgxs_library.py
@@ -13,12 +13,25 @@
from openmc.checkvalue import check_type, check_value, check_greater_than, \
check_iterable_type, check_less_than, check_filetype_version
+ROOM_TEMPERATURE_KELVIN = 294.0
# Supported incoming particle MGXS angular treatment representations
-_REPRESENTATIONS = ['isotropic', 'angle']
+REPRESENTATION_ISOTROPIC = 'isotropic'
+REPRESENTATION_ANGLE = 'angle'
+_REPRESENTATIONS = [
+ REPRESENTATION_ISOTROPIC,
+ REPRESENTATION_ANGLE
+]
# Supported scattering angular distribution representations
-_SCATTER_TYPES = ['tabular', 'legendre', 'histogram']
+SCATTER_TABULAR = 'tabular'
+SCATTER_LEGENDRE = 'legendre'
+SCATTER_HISTOGRAM = 'histogram'
+_SCATTER_TYPES = [
+ SCATTER_TABULAR,
+ SCATTER_LEGENDRE,
+ SCATTER_HISTOGRAM
+]
# List of MGXS indexing schemes
_XS_SHAPES = ["[G][G'][Order]", "[G]", "[G']", "[G][G']", "[DG]", "[DG][G]",
@@ -34,7 +47,7 @@
_VERSION_MGXS_LIBRARY = 1
-class XSdata(object):
+class XSdata:
"""A multi-group cross section data set providing all the
multi-group data necessary for a multi-group OpenMC calculation.
@@ -168,8 +181,8 @@ class XSdata(object):
"""
- def __init__(self, name, energy_groups, temperatures=[294.],
- representation='isotropic', num_delayed_groups=0):
+ def __init__(self, name, energy_groups, temperatures=[ROOM_TEMPERATURE_KELVIN],
+ representation=REPRESENTATION_ISOTROPIC, num_delayed_groups=0):
# Initialize class attributes
self.name = name
@@ -179,7 +192,7 @@ def __init__(self, name, energy_groups, temperatures=[294.],
self.representation = representation
self._atomic_weight_ratio = None
self._fissionable = False
- self._scatter_format = 'legendre'
+ self._scatter_format = SCATTER_LEGENDRE
self._order = None
self._num_polar = None
self._num_azimuthal = None
@@ -340,11 +353,13 @@ def chi_delayed(self):
@property
def num_orders(self):
- if self._order is not None:
- if self._scatter_format in (None, 'legendre'):
- return self._order + 1
- else:
- return self._order
+ if self._order is None:
+ raise ValueError('Order has not been set.')
+
+ if self._scatter_format in (None, SCATTER_LEGENDRE):
+ return self._order + 1
+ else:
+ return self._order
@property
def xs_shapes(self):
@@ -370,7 +385,7 @@ def xs_shapes(self):
self.energy_groups.num_groups, self.num_orders)
# If representation is by angle prepend num polar and num azim
- if self.representation == 'angle':
+ if self.representation == REPRESENTATION_ANGLE:
for key, shapes in self._xs_shapes.items():
self._xs_shapes[key] \
= (self.num_polar, self.num_azimuthal) + shapes
@@ -483,7 +498,18 @@ def add_temperature(self, temperature):
self._decay_rate.append(None)
self._inverse_velocity.append(None)
- def set_total(self, total, temperature=294.):
+ def _check_temperature(self, temperature):
+ check_type('temperature', temperature, Real)
+ check_value('temperature', temperature, self.temperatures)
+
+ def _temperature_index(self, temperature):
+ return np.where(self.temperatures == temperature)[0][0]
+
+ def _set_fissionable(self, array):
+ if np.sum(array) > 0:
+ self._fissionable = True
+
+ def set_total(self, total, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -507,13 +533,12 @@ def set_total(self, total, temperature=294.):
# Convert to a numpy array so we can easily get the shape for checking
total = np.asarray(total)
check_value('total shape', total.shape, shapes)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._total[i] = total
- def set_absorption(self, absorption, temperature=294.):
+ def set_absorption(self, absorption, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -537,13 +562,12 @@ def set_absorption(self, absorption, temperature=294.):
# Convert to a numpy array so we can easily get the shape for checking
absorption = np.asarray(absorption)
check_value('absorption shape', absorption.shape, shapes)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._absorption[i] = absorption
- def set_fission(self, fission, temperature=294.):
+ def set_fission(self, fission, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -567,16 +591,14 @@ def set_fission(self, fission, temperature=294.):
# Convert to a numpy array so we can easily get the shape for checking
fission = np.asarray(fission)
check_value('fission shape', fission.shape, shapes)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._fission[i] = fission
- if np.sum(fission) > 0.0:
- self._fissionable = True
+ self._set_fissionable(fission)
- def set_kappa_fission(self, kappa_fission, temperature=294.):
+ def set_kappa_fission(self, kappa_fission, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -600,16 +622,14 @@ def set_kappa_fission(self, kappa_fission, temperature=294.):
# Convert to a numpy array so we can easily get the shape for checking
kappa_fission = np.asarray(kappa_fission)
check_value('kappa fission shape', kappa_fission.shape, shapes)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._kappa_fission[i] = kappa_fission
- if np.sum(kappa_fission) > 0.0:
- self._fissionable = True
+ self._set_fissionable(kappa_fission)
- def set_chi(self, chi, temperature=294.):
+ def set_chi(self, chi, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -633,13 +653,12 @@ def set_chi(self, chi, temperature=294.):
# Convert to a numpy array so we can easily get the shape for checking
chi = np.asarray(chi)
check_value('chi shape', chi.shape, shapes)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._chi[i] = chi
- def set_chi_prompt(self, chi_prompt, temperature=294.):
+ def set_chi_prompt(self, chi_prompt, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -663,13 +682,12 @@ def set_chi_prompt(self, chi_prompt, temperature=294.):
# Convert to a numpy array so we can easily get the shape for checking
chi_prompt = np.asarray(chi_prompt)
check_value('chi prompt shape', chi_prompt.shape, shapes)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._chi_prompt[i] = chi_prompt
- def set_chi_delayed(self, chi_delayed, temperature=294.):
+ def set_chi_delayed(self, chi_delayed, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -693,13 +711,14 @@ def set_chi_delayed(self, chi_delayed, temperature=294.):
# Convert to a numpy array so we can easily get the shape for checking
chi_delayed = np.asarray(chi_delayed)
check_value('chi delayed shape', chi_delayed.shape, shapes)
+ self._check_temperature(temperature)
check_type('temperature', temperature, Real)
check_value('temperature', temperature, self.temperatures)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._chi_delayed[i] = chi_delayed
- def set_beta(self, beta, temperature=294.):
+ def set_beta(self, beta, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -723,13 +742,12 @@ def set_beta(self, beta, temperature=294.):
# Convert to a numpy array so we can easily get the shape for checking
beta = np.asarray(beta)
check_value('beta shape', beta.shape, shapes)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._beta[i] = beta
- def set_decay_rate(self, decay_rate, temperature=294.):
+ def set_decay_rate(self, decay_rate, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -753,13 +771,12 @@ def set_decay_rate(self, decay_rate, temperature=294.):
# Convert to a numpy array so we can easily get the shape for checking
decay_rate = np.asarray(decay_rate)
check_value('decay rate shape', decay_rate.shape, shapes)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._decay_rate[i] = decay_rate
- def set_scatter_matrix(self, scatter, temperature=294.):
+ def set_scatter_matrix(self, scatter, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -785,13 +802,12 @@ def set_scatter_matrix(self, scatter, temperature=294.):
check_iterable_type('scatter', scatter, Real,
max_depth=len(scatter.shape))
check_value('scatter shape', scatter.shape, shapes)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._scatter_matrix[i] = scatter
- def set_multiplicity_matrix(self, multiplicity, temperature=294.):
+ def set_multiplicity_matrix(self, multiplicity, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -817,13 +833,12 @@ def set_multiplicity_matrix(self, multiplicity, temperature=294.):
check_iterable_type('multiplicity', multiplicity, Real,
max_depth=len(multiplicity.shape))
check_value('multiplicity shape', multiplicity.shape, shapes)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._multiplicity_matrix[i] = multiplicity
- def set_nu_fission(self, nu_fission, temperature=294.):
+ def set_nu_fission(self, nu_fission, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -849,15 +864,13 @@ def set_nu_fission(self, nu_fission, temperature=294.):
check_value('nu_fission shape', nu_fission.shape, shapes)
check_iterable_type('nu_fission', nu_fission, Real,
max_depth=len(nu_fission.shape))
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._nu_fission[i] = nu_fission
- if np.sum(nu_fission) > 0.0:
- self._fissionable = True
+ self._set_fissionable(nu_fission)
- def set_prompt_nu_fission(self, prompt_nu_fission, temperature=294.):
+ def set_prompt_nu_fission(self, prompt_nu_fission, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -883,15 +896,13 @@ def set_prompt_nu_fission(self, prompt_nu_fission, temperature=294.):
check_value('prompt_nu_fission shape', prompt_nu_fission.shape, shapes)
check_iterable_type('prompt_nu_fission', prompt_nu_fission, Real,
max_depth=len(prompt_nu_fission.shape))
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._prompt_nu_fission[i] = prompt_nu_fission
- if np.sum(prompt_nu_fission) > 0.0:
- self._fissionable = True
+ self._set_fissionable(prompt_nu_fission)
- def set_delayed_nu_fission(self, delayed_nu_fission, temperature=294.):
+ def set_delayed_nu_fission(self, delayed_nu_fission, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the cross section for this XSdata object at the
provided temperature.
@@ -918,15 +929,13 @@ def set_delayed_nu_fission(self, delayed_nu_fission, temperature=294.):
shapes)
check_iterable_type('delayed_nu_fission', delayed_nu_fission, Real,
max_depth=len(delayed_nu_fission.shape))
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._delayed_nu_fission[i] = delayed_nu_fission
- if np.sum(delayed_nu_fission) > 0.0:
- self._fissionable = True
+ self._set_fissionable(delayed_nu_fission)
- def set_inverse_velocity(self, inv_vel, temperature=294.):
+ def set_inverse_velocity(self, inv_vel, temperature=ROOM_TEMPERATURE_KELVIN):
"""This method sets the inverse velocity for this XSdata object at the
provided temperature.
@@ -946,13 +955,12 @@ def set_inverse_velocity(self, inv_vel, temperature=294.):
# Convert to a numpy array so we can easily get the shape for checking
inv_vel = np.asarray(inv_vel)
check_value('inverse_velocity shape', inv_vel.shape, shapes)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._inverse_velocity[i] = inv_vel
- def set_total_mgxs(self, total, temperature=294., nuclide='total',
+ def set_total_mgxs(self, total, temperature=ROOM_TEMPERATURE_KELVIN, nuclide='total',
xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.TotalXS or
openmc.mgxs.TransportXS to be used to set the total cross section for
@@ -987,14 +995,13 @@ def set_total_mgxs(self, total, temperature=294., nuclide='total',
openmc.mgxs.TransportXS))
check_value('energy_groups', total.energy_groups, [self.energy_groups])
check_value('domain_type', total.domain_type, openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._total[i] = total.get_xs(nuclides=nuclide, xs_type=xs_type,
subdomains=subdomain)
- def set_absorption_mgxs(self, absorption, temperature=294.,
+ def set_absorption_mgxs(self, absorption, temperature=ROOM_TEMPERATURE_KELVIN,
nuclide='total', xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.AbsorptionXS
to be used to set the absorption cross section for this XSdata object.
@@ -1029,15 +1036,14 @@ def set_absorption_mgxs(self, absorption, temperature=294.,
[self.energy_groups])
check_value('domain_type', absorption.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._absorption[i] = absorption.get_xs(nuclides=nuclide,
xs_type=xs_type,
subdomains=subdomain)
- def set_fission_mgxs(self, fission, temperature=294., nuclide='total',
+ def set_fission_mgxs(self, fission, temperature=ROOM_TEMPERATURE_KELVIN, nuclide='total',
xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.FissionXS
to be used to set the fission cross section for this XSdata object.
@@ -1072,15 +1078,14 @@ def set_fission_mgxs(self, fission, temperature=294., nuclide='total',
[self.energy_groups])
check_value('domain_type', fission.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._fission[i] = fission.get_xs(nuclides=nuclide,
xs_type=xs_type,
subdomains=subdomain)
- def set_nu_fission_mgxs(self, nu_fission, temperature=294.,
+ def set_nu_fission_mgxs(self, nu_fission, temperature=ROOM_TEMPERATURE_KELVIN,
nuclide='total', xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.FissionXS
to be used to set the nu-fission cross section for this XSdata object.
@@ -1118,18 +1123,16 @@ def set_nu_fission_mgxs(self, nu_fission, temperature=294.,
[self.energy_groups])
check_value('domain_type', nu_fission.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._nu_fission[i] = nu_fission.get_xs(nuclides=nuclide,
xs_type=xs_type,
subdomains=subdomain)
- if np.sum(self._nu_fission) > 0.0:
- self._fissionable = True
+ self._set_fissionable(self._nu_fission)
- def set_prompt_nu_fission_mgxs(self, prompt_nu_fission, temperature=294.,
+ def set_prompt_nu_fission_mgxs(self, prompt_nu_fission, temperature=ROOM_TEMPERATURE_KELVIN,
nuclide='total', xs_type='macro',
subdomain=None):
"""Sets the prompt-nu-fission cross section.
@@ -1170,17 +1173,15 @@ def set_prompt_nu_fission_mgxs(self, prompt_nu_fission, temperature=294.,
[self.energy_groups])
check_value('domain_type', prompt_nu_fission.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._prompt_nu_fission[i] = prompt_nu_fission.get_xs(
nuclides=nuclide, xs_type=xs_type, subdomains=subdomain)
- if np.sum(self._prompt_nu_fission) > 0.0:
- self._fissionable = True
+ self._set_fissionable(self._prompt_nu_fission)
- def set_delayed_nu_fission_mgxs(self, delayed_nu_fission, temperature=294.,
+ def set_delayed_nu_fission_mgxs(self, delayed_nu_fission, temperature=ROOM_TEMPERATURE_KELVIN,
nuclide='total', xs_type='macro',
subdomain=None):
"""This method allows for an openmc.mgxs.DelayedNuFissionXS or
@@ -1221,17 +1222,15 @@ def set_delayed_nu_fission_mgxs(self, delayed_nu_fission, temperature=294.,
[self.num_delayed_groups])
check_value('domain_type', delayed_nu_fission.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._delayed_nu_fission[i] = delayed_nu_fission.get_xs(
nuclides=nuclide, xs_type=xs_type, subdomains=subdomain)
- if np.sum(self._delayed_nu_fission) > 0.0:
- self._fissionable = True
+ self._set_fissionable(self._delayed_nu_fission)
- def set_kappa_fission_mgxs(self, k_fission, temperature=294.,
+ def set_kappa_fission_mgxs(self, k_fission, temperature=ROOM_TEMPERATURE_KELVIN,
nuclide='total', xs_type='macro',
subdomain=None):
"""This method allows for an openmc.mgxs.KappaFissionXS
@@ -1268,15 +1267,14 @@ def set_kappa_fission_mgxs(self, k_fission, temperature=294.,
[self.energy_groups])
check_value('domain_type', k_fission.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._kappa_fission[i] = k_fission.get_xs(nuclides=nuclide,
xs_type=xs_type,
subdomains=subdomain)
- def set_chi_mgxs(self, chi, temperature=294., nuclide='total',
+ def set_chi_mgxs(self, chi, temperature=ROOM_TEMPERATURE_KELVIN, nuclide='total',
xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.Chi
to be used to set chi for this XSdata object.
@@ -1308,14 +1306,13 @@ def set_chi_mgxs(self, chi, temperature=294., nuclide='total',
check_type('chi', chi, openmc.mgxs.Chi)
check_value('energy_groups', chi.energy_groups, [self.energy_groups])
check_value('domain_type', chi.domain_type, openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._chi[i] = chi.get_xs(nuclides=nuclide, xs_type=xs_type,
subdomains=subdomain)
- def set_chi_prompt_mgxs(self, chi_prompt, temperature=294.,
+ def set_chi_prompt_mgxs(self, chi_prompt, temperature=ROOM_TEMPERATURE_KELVIN,
nuclide='total', xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.Chi to be used to set
chi-prompt for this XSdata object.
@@ -1350,15 +1347,14 @@ def set_chi_prompt_mgxs(self, chi_prompt, temperature=294.,
[self.energy_groups])
check_value('domain_type', chi_prompt.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._chi_prompt[i] = chi_prompt.get_xs(nuclides=nuclide,
xs_type=xs_type,
subdomains=subdomain)
- def set_chi_delayed_mgxs(self, chi_delayed, temperature=294.,
+ def set_chi_delayed_mgxs(self, chi_delayed, temperature=ROOM_TEMPERATURE_KELVIN,
nuclide='total', xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.ChiDelayed
to be used to set chi-delayed for this XSdata object.
@@ -1394,15 +1390,14 @@ def set_chi_delayed_mgxs(self, chi_delayed, temperature=294.,
[self.num_delayed_groups])
check_value('domain_type', chi_delayed.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._chi_delayed[i] = chi_delayed.get_xs(nuclides=nuclide,
xs_type=xs_type,
subdomains=subdomain)
- def set_beta_mgxs(self, beta, temperature=294.,
+ def set_beta_mgxs(self, beta, temperature=ROOM_TEMPERATURE_KELVIN,
nuclide='total', xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.Beta
to be used to set beta for this XSdata object.
@@ -1435,15 +1430,14 @@ def set_beta_mgxs(self, beta, temperature=294.,
check_value('num_delayed_groups', beta.num_delayed_groups,
[self.num_delayed_groups])
check_value('domain_type', beta.domain_type, openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._beta[i] = beta.get_xs(nuclides=nuclide,
xs_type=xs_type,
subdomains=subdomain)
- def set_decay_rate_mgxs(self, decay_rate, temperature=294.,
+ def set_decay_rate_mgxs(self, decay_rate, temperature=ROOM_TEMPERATURE_KELVIN,
nuclide='total', xs_type='macro', subdomain=None):
"""This method allows for an openmc.mgxs.DecayRate
to be used to set decay rate for this XSdata object.
@@ -1477,15 +1471,14 @@ def set_decay_rate_mgxs(self, decay_rate, temperature=294.,
[self.num_delayed_groups])
check_value('domain_type', decay_rate.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._decay_rate[i] = decay_rate.get_xs(nuclides=nuclide,
xs_type=xs_type,
subdomains=subdomain)
- def set_scatter_matrix_mgxs(self, scatter, temperature=294.,
+ def set_scatter_matrix_mgxs(self, scatter, temperature=ROOM_TEMPERATURE_KELVIN,
nuclide='total', xs_type='macro',
subdomain=None):
"""This method allows for an openmc.mgxs.ScatterMatrixXS
@@ -1523,8 +1516,7 @@ def set_scatter_matrix_mgxs(self, scatter, temperature=294.,
[self.energy_groups])
check_value('domain_type', scatter.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
# Set the value of scatter_format based on the same value within
# scatter
@@ -1534,30 +1526,30 @@ def set_scatter_matrix_mgxs(self, scatter, temperature=294.,
# the order based on the data within scatter.
# Otherwise, we will check to see that XSdata.order matches
# the order of scatter
- if self.scatter_format == 'legendre':
+ if self.scatter_format == SCATTER_LEGENDRE:
if self.order is None:
self.order = scatter.legendre_order
else:
check_value('legendre_order', scatter.legendre_order,
[self.order])
- elif self.scatter_format == 'histogram':
+ elif self.scatter_format == SCATTER_HISTOGRAM:
if self.order is None:
self.order = scatter.histogram_bins
else:
check_value('histogram_bins', scatter.histogram_bins,
[self.order])
- i = np.where(self.temperatures == temperature)[0][0]
- if self.scatter_format == 'legendre':
+ i = self._temperature_index(temperature)
+ if self.scatter_format == SCATTER_LEGENDRE:
self._scatter_matrix[i] = \
np.zeros(self.xs_shapes["[G][G'][Order]"])
# Get the scattering orders in the outermost dimension
- if self.representation == 'isotropic':
+ if self.representation == REPRESENTATION_ISOTROPIC:
for moment in range(self.num_orders):
self._scatter_matrix[i][:, :, moment] = \
scatter.get_xs(nuclides=nuclide, xs_type=xs_type,
moment=moment, subdomains=subdomain)
- elif self.representation == 'angle':
+ elif self.representation == REPRESENTATION_ANGLE:
for moment in range(self.num_orders):
self._scatter_matrix[i][:, :, :, :, moment] = \
scatter.get_xs(nuclides=nuclide, xs_type=xs_type,
@@ -1568,7 +1560,7 @@ def set_scatter_matrix_mgxs(self, scatter, temperature=294.,
subdomains=subdomain)
def set_multiplicity_matrix_mgxs(self, nuscatter, scatter=None,
- temperature=294., nuclide='total',
+ temperature=ROOM_TEMPERATURE_KELVIN, nuclide='total',
xs_type='macro', subdomain=None):
"""This method allows for either the direct use of only an
openmc.mgxs.MultiplicityMatrixXS or an openmc.mgxs.ScatterMatrixXS and
@@ -1613,8 +1605,7 @@ def set_multiplicity_matrix_mgxs(self, nuscatter, scatter=None,
[self.energy_groups])
check_value('domain_type', nuscatter.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
if scatter is not None:
check_type('scatter', scatter, openmc.mgxs.ScatterMatrixXS)
@@ -1627,7 +1618,7 @@ def set_multiplicity_matrix_mgxs(self, nuscatter, scatter=None,
[self.energy_groups])
check_value('domain_type', scatter.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
nuscatt = nuscatter.get_xs(nuclides=nuclide,
xs_type=xs_type, moment=0,
subdomains=subdomain)
@@ -1637,16 +1628,16 @@ def set_multiplicity_matrix_mgxs(self, nuscatter, scatter=None,
scatt = scatter.get_xs(nuclides=nuclide,
xs_type=xs_type, moment=0,
subdomains=subdomain)
- if scatter.scatter_format == 'histogram':
+ if scatter.scatter_format == SCATTER_HISTOGRAM:
scatt = np.sum(scatt, axis=2)
- if nuscatter.scatter_format == 'histogram':
+ if nuscatter.scatter_format == SCATTER_HISTOGRAM:
nuscatt = np.sum(nuscatt, axis=2)
self._multiplicity_matrix[i] = np.divide(nuscatt, scatt)
self._multiplicity_matrix[i] = \
np.nan_to_num(self._multiplicity_matrix[i])
- def set_inverse_velocity_mgxs(self, inverse_velocity, temperature=294.,
+ def set_inverse_velocity_mgxs(self, inverse_velocity, temperature=ROOM_TEMPERATURE_KELVIN,
nuclide='total', xs_type='macro',
subdomain=None):
"""This method allows for an openmc.mgxs.InverseVelocity
@@ -1683,10 +1674,9 @@ def set_inverse_velocity_mgxs(self, inverse_velocity, temperature=294.,
[self.energy_groups])
check_value('domain_type', inverse_velocity.domain_type,
openmc.mgxs.DOMAIN_TYPES)
- check_type('temperature', temperature, Real)
- check_value('temperature', temperature, self.temperatures)
+ self._check_temperature(temperature)
- i = np.where(self.temperatures == temperature)[0][0]
+ i = self._temperature_index(temperature)
self._inverse_velocity[i] = inverse_velocity.get_xs(
nuclides=nuclide, xs_type=xs_type, subdomains=subdomain)
@@ -1727,7 +1717,7 @@ def convert_representation(self, target_representation, num_polar=None,
check_value('target_representation', target_representation,
_REPRESENTATIONS)
- if target_representation == 'angle':
+ if target_representation == REPRESENTATION_ANGLE:
check_type('num_polar', num_polar, Integral)
check_type('num_azimuthal', num_azimuthal, Integral)
check_greater_than('num_polar', num_polar, 0)
@@ -1739,7 +1729,7 @@ def convert_representation(self, target_representation, num_polar=None,
# representations are the same
if target_representation == self.representation:
# Check to make sure the num_polar and num_azimuthal values match
- if target_representation == 'angle':
+ if target_representation == REPRESENTATION_ANGLE:
if num_polar != self.num_polar or num_azimuthal != self.num_azimuthal:
raise ValueError("Cannot translate between `angle`"
" representations with different angle"
@@ -1749,13 +1739,13 @@ def convert_representation(self, target_representation, num_polar=None,
xsdata.representation = target_representation
# We have different actions depending on the representation conversion
- if target_representation == 'isotropic':
+ if target_representation == REPRESENTATION_ISOTROPIC:
# This is not needed for the correct functionality, but these
# values are changed back to None for clarity
xsdata._num_polar = None
xsdata._num_azimuthal = None
- elif target_representation == 'angle':
+ elif target_representation == REPRESENTATION_ANGLE:
xsdata.num_polar = num_polar
xsdata.num_azimuthal = num_azimuthal
@@ -1777,7 +1767,7 @@ def convert_representation(self, target_representation, num_polar=None,
# current data is just the average over the angle bins
new_data = orig_data.mean(axis=(0, 1))
- elif target_representation == 'angle':
+ elif target_representation == REPRESENTATION_ANGLE:
# Since we are going from isotropic to angle, the
# current data is just copied for every angle bin
new_shape = (num_polar, num_azimuthal) + \
@@ -1812,7 +1802,7 @@ def convert_scatter_format(self, target_format, target_order=None):
check_value('target_format', target_format, _SCATTER_TYPES)
check_type('target_order', target_order, Integral)
- if target_format == 'legendre':
+ if target_format == SCATTER_LEGENDRE:
check_greater_than('target_order', target_order, 0, equality=True)
else:
check_greater_than('target_order', target_order, 0)
@@ -1829,14 +1819,14 @@ def convert_scatter_format(self, target_format, target_order=None):
new_shape = orig_data.shape[:-1] + (xsdata.num_orders,)
new_data = np.zeros(new_shape)
- if self.scatter_format == 'legendre':
- if target_format == 'legendre':
+ if self.scatter_format == SCATTER_LEGENDRE:
+ if target_format == SCATTER_LEGENDRE:
# Then we are changing orders and only need to change
# dimensionality of the mu data and pad/truncate as needed
order = min(xsdata.num_orders, self.num_orders)
new_data[..., :order] = orig_data[..., :order]
- elif target_format == 'tabular':
+ elif target_format == SCATTER_TABULAR:
mu = np.linspace(-1, 1, xsdata.num_orders)
# Evaluate the legendre on the mu grid
for imu in range(len(mu)):
@@ -1845,7 +1835,7 @@ def convert_scatter_format(self, target_format, target_order=None):
(l + 0.5) * eval_legendre(l, mu[imu]) *
orig_data[..., l])
- elif target_format == 'histogram':
+ elif target_format == SCATTER_HISTOGRAM:
# This code uses the vectorized integration capabilities
# instead of having an isotropic and angle representation
# path.
@@ -1863,27 +1853,26 @@ def convert_scatter_format(self, target_format, target_order=None):
orig_data[..., l])
new_data[..., h_bin] = simps(table_fine, mu_fine)
- elif self.scatter_format == 'tabular':
+ elif self.scatter_format == SCATTER_TABULAR:
# Calculate the mu points of the current data
mu_self = np.linspace(-1, 1, self.num_orders)
- if target_format == 'legendre':
+ if target_format == SCATTER_LEGENDRE:
# Find the Legendre coefficients via integration. To best
# use the vectorized integration capabilities of scipy,
# this is done with fixed sample integration routines.
mu_fine = np.linspace(-1, 1, _NMU)
- y = [interp1d(mu_self, orig_data)(mu_fine) *
- eval_legendre(l, mu_fine)
- for l in range(xsdata.num_orders)]
for l in range(xsdata.num_orders):
- new_data[..., l] = simps(y[l], mu_fine)
+ y = (interp1d(mu_self, orig_data)(mu_fine) *
+ eval_legendre(l, mu_fine))
+ new_data[..., l] = simps(y, mu_fine)
- elif target_format == 'tabular':
+ elif target_format == SCATTER_TABULAR:
# Simply use an interpolating function to get the new data
mu = np.linspace(-1, 1, xsdata.num_orders)
new_data[..., :] = interp1d(mu_self, orig_data)(mu)
- elif target_format == 'histogram':
+ elif target_format == SCATTER_HISTOGRAM:
# Use an interpolating function to do the bin-wise
# integrals
mu = np.linspace(-1, 1, xsdata.num_orders + 1)
@@ -1897,7 +1886,7 @@ def convert_scatter_format(self, target_format, target_order=None):
mu_fine = np.linspace(mu[h_bin], mu[h_bin + 1], _NMU)
new_data[..., h_bin] = simps(interp(mu_fine), mu_fine)
- elif self.scatter_format == 'histogram':
+ elif self.scatter_format == SCATTER_HISTOGRAM:
# The histogram format does not have enough information to
# convert to the other forms without inducing some amount of
# error. We will make the assumption that the center of the bin
@@ -1914,22 +1903,21 @@ def convert_scatter_format(self, target_format, target_order=None):
# We now have a tabular distribution in tab_data on mu_self.
# We now proceed just like the tabular branch above.
- if target_format == 'legendre':
+ if target_format == SCATTER_LEGENDRE:
# find the legendre coefficients via integration. To best
# use the vectorized integration capabilities of scipy,
# this will be done with fixed sample integration routines.
mu_fine = np.linspace(-1, 1, _NMU)
- y = [interp(mu_fine) * norm * eval_legendre(l, mu_fine)
- for l in range(xsdata.num_orders)]
for l in range(xsdata.num_orders):
- new_data[..., l] = simps(y[l], mu_fine)
+ y = interp(mu_fine) * norm * eval_legendre(l, mu_fine)
+ new_data[..., l] = simps(y, mu_fine)
- elif target_format == 'tabular':
+ elif target_format == SCATTER_TABULAR:
# Simply use an interpolating function to get the new data
mu = np.linspace(-1, 1, xsdata.num_orders)
new_data[..., :] = interp(mu) * norm
- elif target_format == 'histogram':
+ elif target_format == SCATTER_HISTOGRAM:
# Use an interpolating function to do the bin-wise
# integrals
mu = np.linspace(-1, 1, xsdata.num_orders + 1)
@@ -1968,7 +1956,7 @@ def to_hdf5(self, file):
if self.representation is not None:
grp.attrs['representation'] = np.string_(self.representation)
- if self.representation == 'angle':
+ if self.representation == REPRESENTATION_ANGLE:
if self.num_azimuthal is not None:
grp.attrs['num_azimuthal'] = self.num_azimuthal
@@ -2055,10 +2043,10 @@ def to_hdf5(self, file):
# Get the sparse scattering data to print to the library
G = self.energy_groups.num_groups
- if self.representation == 'isotropic':
+ if self.representation == REPRESENTATION_ISOTROPIC:
Np = 1
Na = 1
- elif self.representation == 'angle':
+ elif self.representation == REPRESENTATION_ANGLE:
Np = self.num_polar
Na = self.num_azimuthal
@@ -2066,19 +2054,19 @@ def to_hdf5(self, file):
for p in range(Np):
for a in range(Na):
for g_in in range(G):
- if self.scatter_format == 'legendre':
- if self.representation == 'isotropic':
+ if self.scatter_format == SCATTER_LEGENDRE:
+ if self.representation == REPRESENTATION_ISOTROPIC:
matrix = \
self._scatter_matrix[i][g_in, :, 0]
- elif self.representation == 'angle':
+ elif self.representation == REPRESENTATION_ANGLE:
matrix = \
self._scatter_matrix[i][p, a, g_in, :, 0]
else:
- if self.representation == 'isotropic':
+ if self.representation == REPRESENTATION_ISOTROPIC:
matrix = \
np.sum(self._scatter_matrix[i][g_in, :, :],
axis=1)
- elif self.representation == 'angle':
+ elif self.representation == REPRESENTATION_ANGLE:
matrix = \
np.sum(self._scatter_matrix[i][p, a, g_in, :, :],
axis=1)
@@ -2096,9 +2084,9 @@ def to_hdf5(self, file):
flat_scatt = []
for p in range(Np):
for a in range(Na):
- if self.representation == 'isotropic':
+ if self.representation == REPRESENTATION_ISOTROPIC:
matrix = self._scatter_matrix[i][:, :, :]
- elif self.representation == 'angle':
+ elif self.representation == REPRESENTATION_ANGLE:
matrix = self._scatter_matrix[i][p, a, :, :, :]
for g_in in range(G):
for g_out in range(g_out_bounds[p, a, g_in, 0],
@@ -2118,9 +2106,9 @@ def to_hdf5(self, file):
flat_mult = []
for p in range(Np):
for a in range(Na):
- if self.representation == 'isotropic':
+ if self.representation == REPRESENTATION_ISOTROPIC:
matrix = self._multiplicity_matrix[i][:, :]
- elif self.representation == 'angle':
+ elif self.representation == REPRESENTATION_ANGLE:
matrix = self._multiplicity_matrix[i][p, a, :, :]
for g_in in range(G):
for g_out in range(g_out_bounds[p, a, g_in, 0],
@@ -2134,10 +2122,10 @@ def to_hdf5(self, file):
# And finally, adjust g_out_bounds for 1-based group counting
# and write it.
g_out_bounds[:, :, :, :] += 1
- if self.representation == 'isotropic':
+ if self.representation == REPRESENTATION_ISOTROPIC:
scatt_grp.create_dataset("g_min", data=g_out_bounds[0, 0, :, 0])
scatt_grp.create_dataset("g_max", data=g_out_bounds[0, 0, :, 1])
- elif self.representation == 'angle':
+ elif self.representation == REPRESENTATION_ANGLE:
scatt_grp.create_dataset("g_min", data=g_out_bounds[:, :, :, 0])
scatt_grp.create_dataset("g_max", data=g_out_bounds[:, :, :, 1])
@@ -2190,7 +2178,7 @@ def from_hdf5(cls, group, name, energy_groups, num_delayed_groups):
if 'representation' in attrs:
representation = group.attrs['representation'].decode()
else:
- representation = 'isotropic'
+ representation = REPRESENTATION_ISOTROPIC
data = cls(name, energy_groups, float_temperatures, representation,
num_delayed_groups)
@@ -2203,7 +2191,7 @@ def from_hdf5(cls, group, name, energy_groups, num_delayed_groups):
data.atomic_weight_ratio = group.attrs['atomic_weight_ratio']
if 'order' in attrs:
data.order = group.attrs['order']
- if data.representation == 'angle':
+ if data.representation == REPRESENTATION_ANGLE:
data.num_azimuthal = group.attrs['num_azimuthal']
data.num_polar = group.attrs['num_polar']
@@ -2230,28 +2218,28 @@ def from_hdf5(cls, group, name, energy_groups, num_delayed_groups):
flat_scatter = scatt_group['scatter_matrix'][()]
scatter_matrix = np.zeros(data.xs_shapes["[G][G'][Order]"])
G = data.energy_groups.num_groups
- if data.representation == 'isotropic':
+ if data.representation == REPRESENTATION_ISOTROPIC:
Np = 1
Na = 1
- elif data.representation == 'angle':
+ elif data.representation == REPRESENTATION_ANGLE:
Np = data.num_polar
Na = data.num_azimuthal
flat_index = 0
for p in range(Np):
for a in range(Na):
for g_in in range(G):
- if data.representation == 'isotropic':
+ if data.representation == REPRESENTATION_ISOTROPIC:
g_mins = g_min[g_in]
g_maxs = g_max[g_in]
- elif data.representation == 'angle':
+ elif data.representation == REPRESENTATION_ANGLE:
g_mins = g_min[p, a, g_in]
g_maxs = g_max[p, a, g_in]
for g_out in range(g_mins - 1, g_maxs):
for ang in range(data.num_orders):
- if data.representation == 'isotropic':
+ if data.representation == REPRESENTATION_ISOTROPIC:
scatter_matrix[g_in, g_out, ang] = \
flat_scatter[flat_index]
- elif data.representation == 'angle':
+ elif data.representation == REPRESENTATION_ANGLE:
scatter_matrix[p, a, g_in, g_out, ang] = \
flat_scatter[flat_index]
flat_index += 1
@@ -2265,17 +2253,17 @@ def from_hdf5(cls, group, name, energy_groups, num_delayed_groups):
for p in range(Np):
for a in range(Na):
for g_in in range(G):
- if data.representation == 'isotropic':
+ if data.representation == REPRESENTATION_ISOTROPIC:
g_mins = g_min[g_in]
g_maxs = g_max[g_in]
- elif data.representation == 'angle':
+ elif data.representation == REPRESENTATION_ANGLE:
g_mins = g_min[p, a, g_in]
g_maxs = g_max[p, a, g_in]
for g_out in range(g_mins - 1, g_maxs):
- if data.representation == 'isotropic':
+ if data.representation == REPRESENTATION_ISOTROPIC:
mult_matrix[g_in, g_out] = \
flat_mult[flat_index]
- elif data.representation == 'angle':
+ elif data.representation == REPRESENTATION_ANGLE:
mult_matrix[p, a, g_in, g_out] = \
flat_mult[flat_index]
flat_index += 1
@@ -2284,7 +2272,7 @@ def from_hdf5(cls, group, name, energy_groups, num_delayed_groups):
return data
-class MGXSLibrary(object):
+class MGXSLibrary:
"""Multi-Group Cross Sections file used for an OpenMC simulation.
Corresponds directly to the MG version of the cross_sections.xml input
file.
diff --git a/openmc/mixin.py b/openmc/mixin.py
--- a/openmc/mixin.py
+++ b/openmc/mixin.py
@@ -6,7 +6,7 @@
import openmc.checkvalue as cv
-class EqualityMixin(object):
+class EqualityMixin:
"""A Class which provides generic __eq__ and __ne__ functionality which
can easily be inherited by downstream classes.
"""
@@ -21,15 +21,12 @@ def __eq__(self, other):
return True
- def __ne__(self, other):
- return not self.__eq__(other)
-
class IDWarning(UserWarning):
pass
-class IDManagerMixin(object):
+class IDManagerMixin:
"""A Class which automatically manages unique IDs.
This mixin gives any subclass the ability to assign unique IDs through an
diff --git a/openmc/model/funcs.py b/openmc/model/funcs.py
--- a/openmc/model/funcs.py
+++ b/openmc/model/funcs.py
@@ -253,8 +253,8 @@ def hexagonal_prism(edge_length=1., orientation='y', origin=(0., 0.),
x, y = origin
if orientation == 'y':
- right = XPlane(x + sqrt(3.)/2*l, boundary_type)
- left = XPlane(x - sqrt(3.)/2*l, boundary_type)
+ right = XPlane(x + sqrt(3.)/2*l, boundary_type=boundary_type)
+ left = XPlane(x - sqrt(3.)/2*l, boundary_type=boundary_type)
c = sqrt(3.)/3.
# y = -x/sqrt(3) + a
diff --git a/openmc/model/model.py b/openmc/model/model.py
--- a/openmc/model/model.py
+++ b/openmc/model/model.py
@@ -5,7 +5,7 @@
from openmc.checkvalue import check_type, check_value
-class Model(object):
+class Model:
"""Model container.
This class can be used to store instances of :class:`openmc.Geometry`,
diff --git a/openmc/particle_restart.py b/openmc/particle_restart.py
--- a/openmc/particle_restart.py
+++ b/openmc/particle_restart.py
@@ -4,7 +4,8 @@
_VERSION_PARTICLE_RESTART = 2
-class Particle(object):
+
+class Particle:
"""Information used to restart a specific particle that caused a simulation to
fail.
diff --git a/openmc/polynomial.py b/openmc/polynomial.py
--- a/openmc/polynomial.py
+++ b/openmc/polynomial.py
@@ -29,7 +29,7 @@ def legendre_from_expcoef(coef, domain=(-1, 1)):
return np.polynomial.Legendre(c, domain)
-class Polynomial(object):
+class Polynomial:
"""Abstract Polynomial Class for creating polynomials.
"""
def __init__(self, coef):
@@ -82,24 +82,24 @@ def __call__(self, r):
class Zernike(Polynomial):
r"""Create Zernike polynomials given coefficients and domain.
-
+
The azimuthal Zernike polynomials are defined as in :class:`ZernikeFilter`.
-
+
Parameters
----------
coef : Iterable of float
A list of coefficients of each term in radial only Zernike polynomials
radius : float
Domain of Zernike polynomials to be applied on. Default is 1.
-
+
Attributes
----------
order : int
The maximum (even) order of Zernike polynomials.
radius : float
Domain of Zernike polynomials to be applied on. Default is 1.
- theta : float
- Azimuthal of Zernike polynomial to be applied on. Default is 0.
+ theta : float
+ Azimuthal of Zernike polynomial to be applied on. Default is 0.
norm_coef : iterable of float
The list of coefficients of each term in the polynomials after
normailization.
@@ -115,7 +115,7 @@ def __init__(self, coef, radius=1):
for m in range(-n, n + 1, 2):
j = int((n*(n + 2) + m)/2)
if m == 0:
- norm_vec[j] = n + 1
+ norm_vec[j] = n + 1
else:
norm_vec[j] = 2*n + 2
norm_vec /= (math.pi * radius**2)
diff --git a/openmc/region.py b/openmc/region.py
--- a/openmc/region.py
+++ b/openmc/region.py
@@ -41,9 +41,6 @@ def __eq__(self, other):
else:
return str(self) == str(other)
- def __ne__(self, other):
- return not self == other
-
def get_surfaces(self, surfaces=None):
"""Recursively find all surfaces referenced by a region and return them
diff --git a/openmc/settings.py b/openmc/settings.py
--- a/openmc/settings.py
+++ b/openmc/settings.py
@@ -1,4 +1,5 @@
from collections.abc import Iterable, MutableSequence, Mapping
+from enum import Enum
from pathlib import Path
from numbers import Real, Integral
import warnings
@@ -11,11 +12,19 @@
import openmc.checkvalue as cv
from openmc import VolumeCalculation, Source, RegularMesh
-_RUN_MODES = ['eigenvalue', 'fixed source', 'plot', 'volume', 'particle restart']
+
+class RunMode(Enum):
+ EIGENVALUE = 'eigenvalue'
+ FIXED_SOURCE = 'fixed source'
+ PLOT = 'plot'
+ VOLUME = 'volume'
+ PARTICLE_RESTART = 'particle restart'
+
+
_RES_SCAT_METHODS = ['dbrc', 'rvs']
-class Settings(object):
+class Settings:
"""Settings used for an OpenMC simulation.
Attributes
@@ -59,9 +68,9 @@ class Settings(object):
generations_per_batch : int
Number of generations per batch
max_lost_particles : int
- Maximum number of lost particles
+ Maximum number of lost particles
rel_max_lost_particles : int
- Maximum number of lost particles, relative to the total number of particles
+ Maximum number of lost particles, relative to the total number of particles
inactive : int
Number of inactive batches
keff_trigger : dict
@@ -174,9 +183,7 @@ class Settings(object):
"""
def __init__(self):
-
- # Run mode subelement (default is 'eigenvalue')
- self._run_mode = 'eigenvalue'
+ self._run_mode = RunMode.EIGENVALUE
self._batches = None
self._generations_per_batch = None
self._inactive = None
@@ -246,7 +253,7 @@ def __init__(self):
@property
def run_mode(self):
- return self._run_mode
+ return self._run_mode.value
@property
def batches(self):
@@ -262,11 +269,11 @@ def inactive(self):
@property
def max_lost_particles(self):
- return self._max_lost_particles
+ return self._max_lost_particles
@property
def rel_max_lost_particles(self):
- return self._rel_max_lost_particles
+ return self._rel_max_lost_particles
@property
def particles(self):
@@ -410,8 +417,10 @@ def max_particles_in_flight(self):
@run_mode.setter
def run_mode(self, run_mode):
- cv.check_value('run mode', run_mode, _RUN_MODES)
- self._run_mode = run_mode
+ cv.check_value('run mode', run_mode, {x.value for x in RunMode})
+ for mode in RunMode:
+ if mode.value == run_mode:
+ self._run_mode = mode
@batches.setter
def batches(self, batches):
@@ -435,14 +444,14 @@ def inactive(self, inactive):
def max_lost_particles(self, max_lost_particles):
cv.check_type('max_lost_particles', max_lost_particles, Integral)
cv.check_greater_than('max_lost_particles', max_lost_particles, 0)
- self._max_lost_particles = max_lost_particles
+ self._max_lost_particles = max_lost_particles
@rel_max_lost_particles.setter
def rel_max_lost_particles(self, rel_max_lost_particles):
cv.check_type('rel_max_lost_particles', rel_max_lost_particles, Real)
cv.check_greater_than('rel_max_lost_particles', rel_max_lost_particles, 0)
cv.check_less_than('rel_max_lost_particles', rel_max_lost_particles, 1)
- self._rel_max_lost_particles = rel_max_lost_particles
+ self._rel_max_lost_particles = rel_max_lost_particles
@particles.setter
def particles(self, particles):
@@ -769,7 +778,7 @@ def log_grid_bins(self, log_grid_bins):
def _create_run_mode_subelement(self, root):
elem = ET.SubElement(root, "run_mode")
- elem.text = self._run_mode
+ elem.text = self._run_mode.value
def _create_batches_subelement(self, root):
if self._batches is not None:
@@ -789,12 +798,12 @@ def _create_inactive_subelement(self, root):
def _create_max_lost_particles_subelement(self, root):
if self._max_lost_particles is not None:
element = ET.SubElement(root, "max_lost_particles")
- element.text = str(self._max_lost_particles)
+ element.text = str(self._max_lost_particles)
def _create_rel_max_lost_particles_subelement(self, root):
if self._rel_max_lost_particles is not None:
element = ET.SubElement(root, "rel_max_lost_particles")
- element.text = str(self._rel_max_lost_particles)
+ element.text = str(self._rel_max_lost_particles)
def _create_particles_subelement(self, root):
if self._particles is not None:
@@ -1069,12 +1078,12 @@ def _inactive_from_xml_element(self, root):
def _max_lost_particles_from_xml_element(self, root):
text = get_text(root, 'max_lost_particles')
if text is not None:
- self.max_lost_particles = int(text)
+ self.max_lost_particles = int(text)
def _rel_max_lost_particles_from_xml_element(self, root):
text = get_text(root, 'rel_max_lost_particles')
if text is not None:
- self.rel_max_lost_particles = float(text)
+ self.rel_max_lost_particles = float(text)
def _generations_per_batch_from_xml_element(self, root):
text = get_text(root, 'generations_per_batch')
diff --git a/openmc/statepoint.py b/openmc/statepoint.py
--- a/openmc/statepoint.py
+++ b/openmc/statepoint.py
@@ -14,7 +14,7 @@
_VERSION_STATEPOINT = 17
-class StatePoint(object):
+class StatePoint:
"""State information on a simulation at a certain point in time (at the end
of a given batch). Statepoints can be used to analyze tally results as well
as restart a simulation.
@@ -310,7 +310,7 @@ def n_inactive(self):
if self.run_mode == 'eigenvalue':
return self._f['n_inactive'][()]
else:
- return None
+ return None
@property
def n_particles(self):
diff --git a/openmc/summary.py b/openmc/summary.py
--- a/openmc/summary.py
+++ b/openmc/summary.py
@@ -12,7 +12,7 @@
_VERSION_SUMMARY = 6
-class Summary(object):
+class Summary:
"""Summary of geometry, materials, and tallies used in a simulation.
Attributes
diff --git a/openmc/tallies.py b/openmc/tallies.py
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -128,28 +128,18 @@ def __init__(self, tally_id=None, name=''):
self._results_read = False
def __repr__(self):
- string = 'Tally\n'
- string += '{: <16}=\t{}\n'.format('\tID', self.id)
- string += '{: <16}=\t{}\n'.format('\tName', self.name)
-
+ parts = ['Tally']
+ parts.append('{: <15}=\t{}'.format('ID', self.id))
+ parts.append('{: <15}=\t{}'.format('Name', self.name))
if self.derivative is not None:
- string += '{: <16}=\t{}\n'.format('\tDerivative ID',
- str(self.derivative.id))
-
+ parts.append('{: <15}=\t{}'.format('Derivative ID', self.derivative.id))
filters = ', '.join(type(f).__name__ for f in self.filters)
- string += '{: <16}=\t{}\n'.format('\tFilters', filters)
-
- string += '{: <16}=\t'.format('\tNuclides')
-
- for nuclide in self.nuclides:
- string += str(nuclide) + ' '
-
- string += '\n'
-
- string += '{: <16}=\t{}\n'.format('\tScores', self.scores)
- string += '{: <16}=\t{}\n'.format('\tEstimator', self.estimator)
-
- return string
+ parts.append('{: <15}=\t{}'.format('Filters', filters))
+ nuclides = ' '.join(str(nuclide) for nuclide in self.nuclides)
+ parts.append('{: <15}=\t{}'.format('Nuclides', nuclides))
+ parts.append('{: <15}=\t{}'.format('Scores', self.scores))
+ parts.append('{: <15}=\t{}'.format('Estimator', self.estimator))
+ return '\n\t'.join(parts)
@property
def name(self):
@@ -207,40 +197,40 @@ def num_realizations(self):
def with_summary(self):
return self._with_summary
- @property
- def sum(self):
- if not self._sp_filename or self.derived:
- return None
-
- if not self._results_read:
- # Open the HDF5 statepoint file
- f = h5py.File(self._sp_filename, 'r')
+ def _read_results(self):
+ if self._results_read:
+ return
+ # Open the HDF5 statepoint file
+ with h5py.File(self._sp_filename, 'r') as f:
# Extract Tally data from the file
- data = f['tallies/tally {0}/results'.format(self.id)]
- sum = data[:, :, 0]
+ data = f['tallies/tally {}/results'.format(self.id)]
+ sum_ = data[:, :, 0]
sum_sq = data[:, :, 1]
# Reshape the results arrays
- sum = np.reshape(sum, self.shape)
+ sum_ = np.reshape(sum_, self.shape)
sum_sq = np.reshape(sum_sq, self.shape)
# Set the data for this Tally
- self._sum = sum
+ self._sum = sum_
self._sum_sq = sum_sq
# Convert NumPy arrays to SciPy sparse LIL matrices
if self.sparse:
- self._sum = sps.lil_matrix(self._sum.flatten(),
- self._sum.shape)
- self._sum_sq = sps.lil_matrix(self._sum_sq.flatten(),
- self._sum_sq.shape)
+ self._sum = sps.lil_matrix(self._sum.flatten(), self._sum.shape)
+ self._sum_sq = sps.lil_matrix(self._sum_sq.flatten(), self._sum_sq.shape)
- # Indicate that Tally results have been read
- self._results_read = True
+ # Indicate that Tally results have been read
+ self._results_read = True
- # Close the HDF5 statepoint file
- f.close()
+ @property
+ def sum(self):
+ if not self._sp_filename or self.derived:
+ return None
+
+ # Make sure results have been read
+ self._read_results()
if self.sparse:
return np.reshape(self._sum.toarray(), self.shape)
@@ -252,9 +242,8 @@ def sum_sq(self):
if not self._sp_filename or self.derived:
return None
- if not self._results_read:
- # Force reading of sum and sum_sq
- self.sum
+ # Make sure results have been read
+ self._read_results()
if self.sparse:
return np.reshape(self._sum_sq.toarray(), self.shape)
@@ -332,16 +321,13 @@ def triggers(self, triggers):
@name.setter
def name(self, name):
- if name is not None:
- cv.check_type('tally name', name, str)
- self._name = name
- else:
- self._name = ''
+ cv.check_type('tally name', name, str, none_ok=True)
+ self._name = name
@derivative.setter
def derivative(self, deriv):
- if deriv is not None:
- cv.check_type('tally derivative', deriv, openmc.TallyDerivative)
+ cv.check_type('tally derivative', deriv, openmc.TallyDerivative,
+ none_ok=True)
self._derivative = deriv
@filters.setter
@@ -349,12 +335,14 @@ def filters(self, filters):
cv.check_type('tally filters', filters, MutableSequence)
# If the filter is already in the Tally, raise an error
- for i, f in enumerate(filters[:-1]):
- if f in filters[i+1:]:
- msg = 'Unable to add a duplicate filter "{0}" to Tally ID="{1}" ' \
+ visited_filters = set()
+ for f in filters:
+ if f in visited_filters:
+ msg = 'Unable to add a duplicate filter "{}" to Tally ID="{}" ' \
'since duplicate filters are not supported in the OpenMC ' \
'Python API'.format(f, self.id)
raise ValueError(msg)
+ visited_filters.add(f)
self._filters = cv.CheckedList(_FILTER_CLASSES, 'tally filters', filters)
@@ -363,12 +351,14 @@ def nuclides(self, nuclides):
cv.check_type('tally nuclides', nuclides, MutableSequence)
# If the nuclide is already in the Tally, raise an error
- for i, nuclide in enumerate(nuclides[:-1]):
- if nuclide in nuclides[i+1:]:
- msg = 'Unable to add a duplicate nuclide "{0}" to Tally ID="{1}" ' \
+ visited_nuclides = set()
+ for nuc in nuclides:
+ if nuc in visited_nuclides:
+ msg = 'Unable to add a duplicate nuclide "{}" to Tally ID="{}" ' \
'since duplicate nuclides are not supported in the OpenMC ' \
'Python API'.format(nuclide, self.id)
raise ValueError(msg)
+ visited_nuclides.add(nuc)
self._nuclides = cv.CheckedList(_NUCLIDE_CLASSES, 'tally nuclides',
nuclides)
@@ -377,13 +367,15 @@ def nuclides(self, nuclides):
def scores(self, scores):
cv.check_type('tally scores', scores, MutableSequence)
+ visited_scores = set()
for i, score in enumerate(scores):
# If the score is already in the Tally, raise an error
- if score in scores[i+1:]:
- msg = 'Unable to add a duplicate score "{0}" to Tally ID="{1}" ' \
+ if score in visited_scores:
+ msg = 'Unable to add a duplicate score "{}" to Tally ID="{}" ' \
'since duplicate scores are not supported in the OpenMC ' \
'Python API'.format(score, self.id)
raise ValueError(msg)
+ visited_scores.add(score)
# If score is a string, strip whitespace
if isinstance(score, str):
@@ -477,9 +469,9 @@ def remove_score(self, score):
"""
if score not in self.scores:
- msg = 'Unable to remove score "{0}" from Tally ID="{1}" since ' \
+ msg = 'Unable to remove score "{}" from Tally ID="{}" since ' \
'the Tally does not contain this score'.format(score, self.id)
- ValueError(msg)
+ raise ValueError(msg)
self._scores.remove(score)
@@ -494,9 +486,9 @@ def remove_filter(self, old_filter):
"""
if old_filter not in self.filters:
- msg = 'Unable to remove filter "{0}" from Tally ID="{1}" since the ' \
+ msg = 'Unable to remove filter "{}" from Tally ID="{}" since the ' \
'Tally does not contain this filter'.format(old_filter, self.id)
- ValueError(msg)
+ raise ValueError(msg)
self._filters.remove(old_filter)
@@ -511,9 +503,9 @@ def remove_nuclide(self, nuclide):
"""
if nuclide not in self.nuclides:
- msg = 'Unable to remove nuclide "{0}" from Tally ID="{1}" since the ' \
+ msg = 'Unable to remove nuclide "{}" from Tally ID="{}" since the ' \
'Tally does not contain this nuclide'.format(nuclide, self.id)
- ValueError(msg)
+ raise ValueError(msg)
self._nuclides.remove(nuclide)
@@ -539,33 +531,20 @@ def _can_merge_filters(self, other):
# Return False if only one tally has a delayed group filter
tally1_dg = self.contains_filter(openmc.DelayedGroupFilter)
tally2_dg = other.contains_filter(openmc.DelayedGroupFilter)
- if sum([tally1_dg, tally2_dg]) == 1:
+ if tally1_dg != tally2_dg:
return False
# Look to see if all filters are the same, or one or more can be merged
for filter1 in self.filters:
- merge_filters = False
- mergeable_filter = False
+ mergeable = False
for filter2 in other.filters:
-
- # If filters match, they are mergeable
- if filter1 == filter2:
- mergeable_filter = True
+ if filter1 == filter2 or filter1.can_merge(filter2):
+ mergeable = True
break
- # If filters are first mergeable filters encountered
- elif filter1.can_merge(filter2) and not merge_filters:
- merge_filters = True
- mergeable_filter = True
- break
-
- # If filters are the second mergeable filters encountered
- elif filter1.can_merge(filter2) and merge_filters:
- return False
-
# If no mergeable filter was found, the tallies are not mergeable
- if not mergeable_filter:
+ if not mergeable:
return False
# Tally filters are mergeable if all conditional checks passed
@@ -671,24 +650,22 @@ def can_merge(self, other):
equality = [equal_filters, equal_nuclides, equal_scores]
# If all filters, nuclides and scores match then tallies are mergeable
- if equal_filters and equal_nuclides and equal_scores:
+ if all(equality):
return True
# Variables to indicate filter bins, nuclides, and scores that can be merged
- merge_filters = self._can_merge_filters(other)
- merge_nuclides = self._can_merge_nuclides(other)
- merge_scores = self._can_merge_scores(other)
- mergeability = [merge_filters, merge_nuclides, merge_scores]
+ can_merge_filters = self._can_merge_filters(other)
+ can_merge_nuclides = self._can_merge_nuclides(other)
+ can_merge_scores = self._can_merge_scores(other)
+ mergeability = [can_merge_filters, can_merge_nuclides, can_merge_scores]
if not all(mergeability):
return False
- # If the tally results have been read from the statepoint, we can only
- # at least two of filters, nuclides and scores must match
- elif self._results_read and sum(equality) < 2:
- return False
+ # If the tally results have been read from the statepoint, at least two
+ # of filters, nuclides and scores must match
else:
- return True
+ return not self._results_read or sum(equality) >= 2
def merge(self, other):
"""Merge another tally with this one
@@ -709,8 +686,8 @@ def merge(self, other):
"""
if not self.can_merge(other):
- msg = 'Unable to merge tally ID="{0}" with ' \
- '"{1}"'.format(other.id, self.id)
+ msg = 'Unable to merge tally ID="{}" with "{}"'.format(
+ other.id, self.id)
raise ValueError(msg)
# Create deep copy of tally to return as merged tally
@@ -866,14 +843,14 @@ def to_xml_element(self):
# Scores
if len(self.scores) == 0:
- msg = 'Unable to get XML for Tally ID="{0}" since it does not ' \
+ msg = 'Unable to get XML for Tally ID="{}" since it does not ' \
'contain any scores'.format(self.id)
raise ValueError(msg)
else:
scores = ''
for score in self.scores:
- scores += '{0} '.format(score)
+ scores += '{} '.format(score)
subelement = ET.SubElement(element, "scores")
subelement.text = scores.rstrip(' ')
@@ -909,16 +886,10 @@ def contains_filter(self, filter_type):
otherwise false
"""
-
- filter_found = False
-
- # Look through all of this Tally's Filters for the type requested
for test_filter in self.filters:
if type(test_filter) is filter_type:
- filter_found = True
- break
-
- return filter_found
+ return True
+ return False
def find_filter(self, filter_type):
"""Return a filter in the tally that matches a specified type
@@ -941,28 +912,21 @@ def find_filter(self, filter_type):
"""
- filter_found = None
-
# Look through all of this Tally's Filters for the type requested
for test_filter in self.filters:
if type(test_filter) is filter_type:
- filter_found = test_filter
- break
+ return test_filter
# Also check to see if the desired filter is wrapped up in an
# aggregate
elif isinstance(test_filter, openmc.AggregateFilter):
if isinstance(test_filter.aggregate_filter, filter_type):
- filter_found = test_filter
- break
+ return test_filter
# If we did not find the Filter, throw an Exception
- if filter_found is None:
- msg = 'Unable to find filter type "{0}" in ' \
- 'Tally ID="{1}"'.format(filter_type, self.id)
- raise ValueError(msg)
-
- return filter_found
+ msg = 'Unable to find filter type "{}" in Tally ID="{}"'.format(
+ filter_type, self.id)
+ raise ValueError(msg)
def get_nuclide_index(self, nuclide):
"""Returns the index in the Tally's results array for a Nuclide bin
@@ -984,30 +948,21 @@ def get_nuclide_index(self, nuclide):
in the Tally.
"""
-
- nuclide_index = -1
-
# Look for the user-requested nuclide in all of the Tally's Nuclides
for i, test_nuclide in enumerate(self.nuclides):
-
# If the Summary was linked, then values are Nuclide objects
if isinstance(test_nuclide, openmc.Nuclide):
if test_nuclide.name == nuclide:
- nuclide_index = i
- break
+ return i
# If the Summary has not been linked, then values are ZAIDs
else:
if test_nuclide == nuclide:
- nuclide_index = i
- break
+ return i
- if nuclide_index == -1:
- msg = 'Unable to get the nuclide index for Tally since "{0}" ' \
- 'is not one of the nuclides'.format(nuclide)
- raise KeyError(msg)
- else:
- return nuclide_index
+ msg = ('Unable to get the nuclide index for Tally since "{}" '
+ 'is not one of the nuclides'.format(nuclide))
+ raise KeyError(msg)
def get_score_index(self, score):
"""Returns the index in the Tally's results array for a score bin
@@ -1034,7 +989,7 @@ def get_score_index(self, score):
score_index = self.scores.index(score)
except ValueError:
- msg = 'Unable to get the score index for Tally since "{0}" ' \
+ msg = 'Unable to get the score index for Tally since "{}" ' \
'is not one of the scores'.format(score)
raise ValueError(msg)
@@ -1076,48 +1031,44 @@ def get_filter_indices(self, filters=[], filter_bins=[]):
cv.check_type('filters', filters, Iterable, openmc.FilterMeta)
cv.check_type('filter_bins', filter_bins, Iterable, tuple)
- # Determine the score indices from any of the requested scores
- if filters:
- # Initialize empty list of indices for each bin in each Filter
- filter_indices = []
-
- # Loop over all of the Tally's Filters
- for i, self_filter in enumerate(self.filters):
- # If a user-requested Filter, get the user-requested bins
- for j, test_filter in enumerate(filters):
- if type(self_filter) is test_filter:
- bins = filter_bins[j]
- break
- else:
- # If not a user-requested Filter, get all bins
- if isinstance(self_filter, openmc.DistribcellFilter):
- # Create list of cell instance IDs for distribcell Filters
- bins = list(range(self_filter.num_bins))
+ # If user did not specify any specific Filters, use them all
+ if not filters:
+ return np.arange(self.num_filter_bins)
- elif isinstance(self_filter, openmc.EnergyFunctionFilter):
- # EnergyFunctionFilters don't have bins so just add a None
- bins = [None]
+ # Initialize empty list of indices for each bin in each Filter
+ filter_indices = []
- else:
- # Create list of IDs for bins for all other filter types
- bins = self_filter.bins
+ # Loop over all of the Tally's Filters
+ for i, self_filter in enumerate(self.filters):
+ # If a user-requested Filter, get the user-requested bins
+ for j, test_filter in enumerate(filters):
+ if type(self_filter) is test_filter:
+ bins = filter_bins[j]
+ break
+ else:
+ # If not a user-requested Filter, get all bins
+ if isinstance(self_filter, openmc.DistribcellFilter):
+ # Create list of cell instance IDs for distribcell Filters
+ bins = list(range(self_filter.num_bins))
- # Add indices for each bin in this Filter to the list
- indices = np.array([self_filter.get_bin_index(b) for b in bins])
- filter_indices.append(indices)
+ elif isinstance(self_filter, openmc.EnergyFunctionFilter):
+ # EnergyFunctionFilters don't have bins so just add a None
+ bins = [None]
- # Account for stride in each of the previous filters
- for indices in filter_indices[:i]:
- indices *= self_filter.num_bins
+ else:
+ # Create list of IDs for bins for all other filter types
+ bins = self_filter.bins
- # Apply outer product sum between all filter bin indices
- filter_indices = list(map(sum, product(*filter_indices)))
+ # Add indices for each bin in this Filter to the list
+ indices = np.array([self_filter.get_bin_index(b) for b in bins])
+ filter_indices.append(indices)
- # If user did not specify any specific Filters, use them all
- else:
- filter_indices = np.arange(self.num_filter_bins)
+ # Account for stride in each of the previous filters
+ for indices in filter_indices[:i]:
+ indices *= self_filter.num_bins
- return filter_indices
+ # Apply outer product sum between all filter bin indices
+ return list(map(sum, product(*filter_indices)))
def get_nuclide_indices(self, nuclides):
"""Get indices into the nuclide axis of this tally's data arrays.
@@ -1141,16 +1092,14 @@ def get_nuclide_indices(self, nuclides):
cv.check_iterable_type('nuclides', nuclides, str)
- # Determine the score indices from any of the requested scores
- if nuclides:
- nuclide_indices = np.zeros(len(nuclides), dtype=int)
- for i, nuclide in enumerate(nuclides):
- nuclide_indices[i] = self.get_nuclide_index(nuclide)
-
# If user did not specify any specific Nuclides, use them all
- else:
- nuclide_indices = np.arange(self.num_nuclides)
+ if not nuclides:
+ return np.arange(self.num_nuclides)
+ # Determine the score indices from any of the requested scores
+ nuclide_indices = np.zeros_like(nuclides, dtype=int)
+ for i, nuclide in enumerate(nuclides):
+ nuclide_indices[i] = self.get_nuclide_index(nuclide)
return nuclide_indices
def get_score_indices(self, scores):
@@ -1162,7 +1111,7 @@ def get_score_indices(self, scores):
Parameters
----------
- scores : list of str
+ scores : list of str or openmc.CrossScore
A list of one or more score strings
(e.g., ['absorption', 'nu-fission']; default is [])
@@ -1175,8 +1124,8 @@ def get_score_indices(self, scores):
for score in scores:
if not isinstance(score, (str, openmc.CrossScore)):
- msg = 'Unable to get score indices for score "{0}" in Tally ' \
- 'ID="{1}" since it is not a string or CrossScore'\
+ msg = 'Unable to get score indices for score "{}" in Tally ' \
+ 'ID="{}" since it is not a string or CrossScore'\
.format(score, self.id)
raise ValueError(msg)
@@ -1249,7 +1198,7 @@ def get_values(self, scores=[], filters=[], filter_bins=[],
(value == 'rel_err' and self.mean is None) or \
(value == 'sum' and self.sum is None) or \
(value == 'sum_sq' and self.sum_sq is None):
- msg = 'The Tally ID="{0}" has no data to return'.format(self.id)
+ msg = 'The Tally ID="{}" has no data to return'.format(self.id)
raise ValueError(msg)
# Get filter, nuclide and score indices
@@ -1272,8 +1221,8 @@ def get_values(self, scores=[], filters=[], filter_bins=[],
elif value == 'sum_sq':
data = self.sum_sq[indices]
else:
- msg = 'Unable to return results from Tally ID="{0}" since the ' \
- 'the requested value "{1}" is not \'mean\', \'std_dev\', ' \
+ msg = 'Unable to return results from Tally ID="{}" since the ' \
+ 'the requested value "{}" is not \'mean\', \'std_dev\', ' \
'\'rel_err\', \'sum\', or \'sum_sq\''.format(self.id, value)
raise LookupError(msg)
@@ -1325,7 +1274,7 @@ def get_pandas_dataframe(self, filters=True, nuclides=True, scores=True,
# Ensure that the tally has data
if self.mean is None or self.std_dev is None:
- msg = 'The Tally ID="{0}" has no data to return'.format(self.id)
+ msg = 'The Tally ID="{}" has no data to return'.format(self.id)
raise KeyError(msg)
# Initialize a pandas dataframe for the tally data
@@ -1352,7 +1301,7 @@ def get_pandas_dataframe(self, filters=True, nuclides=True, scores=True,
nuclides.append(nuclide.name)
elif isinstance(nuclide, openmc.AggregateNuclide):
nuclides.append(nuclide.name)
- column_name = '{0}(nuclide)'.format(nuclide.aggregate_op)
+ column_name = '{}(nuclide)'.format(nuclide.aggregate_op)
else:
nuclides.append(nuclide)
@@ -1371,7 +1320,7 @@ def get_pandas_dataframe(self, filters=True, nuclides=True, scores=True,
scores.append(str(score))
elif isinstance(score, openmc.AggregateScore):
scores.append(score.name)
- column_name = '{0}(score)'.format(score.aggregate_op)
+ column_name = '{}(score)'.format(score.aggregate_op)
tile_factor = data_size / len(self.scores)
df[column_name] = np.tile(scores, int(tile_factor))
@@ -1540,7 +1489,7 @@ def hybrid_product(self, other, binary_op, filter_product=None,
# Check that results have been read
if not other.derived and other.sum is None:
- msg = 'Unable to use tally arithmetic with Tally ID="{0}" ' \
+ msg = 'Unable to use tally arithmetic with Tally ID="{}" ' \
'since it does not contain any results.'.format(other.id)
raise ValueError(msg)
@@ -1554,7 +1503,7 @@ def hybrid_product(self, other, binary_op, filter_product=None,
# Construct a combined derived name from the two tally operands
if self.name != '' and other.name != '':
- new_name = '({0} {1} {2})'.format(self.name, binary_op, other.name)
+ new_name = '({} {} {})'.format(self.name, binary_op, other.name)
new_tally.name = new_name
# Query the mean and std dev so the tally data is read in from file
@@ -1850,11 +1799,11 @@ def _swap_filters(self, filter1, filter2):
if filter1 == filter2:
return
elif filter1 not in self.filters:
- msg = 'Unable to swap "{0}" filter1 in Tally ID="{1}" since it ' \
+ msg = 'Unable to swap "{}" filter1 in Tally ID="{}" since it ' \
'does not contain such a filter'.format(filter1.type, self.id)
raise ValueError(msg)
elif filter2 not in self.filters:
- msg = 'Unable to swap "{0}" filter2 in Tally ID="{1}" since it ' \
+ msg = 'Unable to swap "{}" filter2 in Tally ID="{}" since it ' \
'does not contain such a filter'.format(filter2.type, self.id)
raise ValueError(msg)
@@ -1932,7 +1881,7 @@ def _swap_nuclides(self, nuclide1, nuclide2):
# Check that results have been read
if not self.derived and self.sum is None:
- msg = 'Unable to use tally arithmetic with Tally ID="{0}" ' \
+ msg = 'Unable to use tally arithmetic with Tally ID="{}" ' \
'since it does not contain any results.'.format(self.id)
raise ValueError(msg)
@@ -1944,12 +1893,12 @@ def _swap_nuclides(self, nuclide1, nuclide2):
msg = 'Unable to swap a nuclide with itself'
raise ValueError(msg)
elif nuclide1 not in self.nuclides:
- msg = 'Unable to swap nuclide1 "{0}" in Tally ID="{1}" since it ' \
+ msg = 'Unable to swap nuclide1 "{}" in Tally ID="{}" since it ' \
'does not contain such a nuclide'\
.format(nuclide1.name, self.id)
raise ValueError(msg)
elif nuclide2 not in self.nuclides:
- msg = 'Unable to swap "{0}" nuclide2 in Tally ID="{1}" since it ' \
+ msg = 'Unable to swap "{}" nuclide2 in Tally ID="{}" since it ' \
'does not contain such a nuclide'\
.format(nuclide2.name, self.id)
raise ValueError(msg)
@@ -1999,17 +1948,17 @@ def _swap_scores(self, score1, score2):
# Check that results have been read
if not self.derived and self.sum is None:
- msg = 'Unable to use tally arithmetic with Tally ID="{0}" ' \
+ msg = 'Unable to use tally arithmetic with Tally ID="{}" ' \
'since it does not contain any results.'.format(self.id)
raise ValueError(msg)
# Check that the scores are valid
if not isinstance(score1, (str, openmc.CrossScore)):
- msg = 'Unable to swap score1 "{0}" in Tally ID="{1}" since it is ' \
+ msg = 'Unable to swap score1 "{}" in Tally ID="{}" since it is ' \
'not a string or CrossScore'.format(score1, self.id)
raise ValueError(msg)
elif not isinstance(score2, (str, openmc.CrossScore)):
- msg = 'Unable to swap score2 "{0}" in Tally ID="{1}" since it is ' \
+ msg = 'Unable to swap score2 "{}" in Tally ID="{}" since it is ' \
'not a string or CrossScore'.format(score2, self.id)
raise ValueError(msg)
@@ -2018,11 +1967,11 @@ def _swap_scores(self, score1, score2):
msg = 'Unable to swap a score with itself'
raise ValueError(msg)
elif score1 not in self.scores:
- msg = 'Unable to swap score1 "{0}" in Tally ID="{1}" since it ' \
+ msg = 'Unable to swap score1 "{}" in Tally ID="{}" since it ' \
'does not contain such a score'.format(score1, self.id)
raise ValueError(msg)
elif score2 not in self.scores:
- msg = 'Unable to swap score2 "{0}" in Tally ID="{1}" since it ' \
+ msg = 'Unable to swap score2 "{}" in Tally ID="{}" since it ' \
'does not contain such a score'.format(score2, self.id)
raise ValueError(msg)
@@ -2083,7 +2032,7 @@ def __add__(self, other):
# Check that results have been read
if not self.derived and self.sum is None:
- msg = 'Unable to use tally arithmetic with Tally ID="{0}" ' \
+ msg = 'Unable to use tally arithmetic with Tally ID="{}" ' \
'since it does not contain any results.'.format(self.id)
raise ValueError(msg)
@@ -2113,7 +2062,7 @@ def __add__(self, other):
new_tally.sparse = self.sparse
else:
- msg = 'Unable to add "{0}" to Tally ID="{1}"'.format(other, self.id)
+ msg = 'Unable to add "{}" to Tally ID="{}"'.format(other, self.id)
raise ValueError(msg)
return new_tally
@@ -2155,7 +2104,7 @@ def __sub__(self, other):
# Check that results have been read
if not self.derived and self.sum is None:
- msg = 'Unable to use tally arithmetic with Tally ID="{0}" ' \
+ msg = 'Unable to use tally arithmetic with Tally ID="{}" ' \
'since it does not contain any results.'.format(self.id)
raise ValueError(msg)
@@ -2184,8 +2133,7 @@ def __sub__(self, other):
new_tally.sparse = self.sparse
else:
- msg = 'Unable to subtract "{0}" from Tally ' \
- 'ID="{1}"'.format(other, self.id)
+ msg = 'Unable to subtract "{}" from Tally ID="{}"'.format(other, self.id)
raise ValueError(msg)
return new_tally
@@ -2227,7 +2175,7 @@ def __mul__(self, other):
# Check that results have been read
if not self.derived and self.sum is None:
- msg = 'Unable to use tally arithmetic with Tally ID="{0}" ' \
+ msg = 'Unable to use tally arithmetic with Tally ID="{}" ' \
'since it does not contain any results.'.format(self.id)
raise ValueError(msg)
@@ -2256,8 +2204,7 @@ def __mul__(self, other):
new_tally.sparse = self.sparse
else:
- msg = 'Unable to multiply Tally ID="{0}" ' \
- 'by "{1}"'.format(self.id, other)
+ msg = 'Unable to multiply Tally ID="{}" by "{}"'.format(self.id, other)
raise ValueError(msg)
return new_tally
@@ -2299,7 +2246,7 @@ def __truediv__(self, other):
# Check that results have been read
if not self.derived and self.sum is None:
- msg = 'Unable to use tally arithmetic with Tally ID="{0}" ' \
+ msg = 'Unable to use tally arithmetic with Tally ID="{}" ' \
'since it does not contain any results.'.format(self.id)
raise ValueError(msg)
@@ -2328,8 +2275,7 @@ def __truediv__(self, other):
new_tally.sparse = self.sparse
else:
- msg = 'Unable to divide Tally ID="{0}" ' \
- 'by "{1}"'.format(self.id, other)
+ msg = 'Unable to divide Tally ID="{}" by "{}"'.format(self.id, other)
raise ValueError(msg)
return new_tally
@@ -2374,7 +2320,7 @@ def __pow__(self, power):
# Check that results have been read
if not self.derived and self.sum is None:
- msg = 'Unable to use tally arithmetic with Tally ID="{0}" ' \
+ msg = 'Unable to use tally arithmetic with Tally ID="{}" ' \
'since it does not contain any results.'.format(self.id)
raise ValueError(msg)
@@ -2404,8 +2350,7 @@ def __pow__(self, power):
new_tally.sparse = self.sparse
else:
- msg = 'Unable to raise Tally ID="{0}" to ' \
- 'power "{1}"'.format(self.id, power)
+ msg = 'Unable to raise Tally ID="{}" to power "{}"'.format(self.id, power)
raise ValueError(msg)
return new_tally
@@ -2561,7 +2506,7 @@ def get_slice(self, scores=[], filters=[], filter_bins=[], nuclides=[],
# Ensure that the tally has data
if not self.derived and self.sum is None:
- msg = 'Unable to use tally arithmetic with Tally ID="{0}" ' \
+ msg = 'Unable to use tally arithmetic with Tally ID="{}" ' \
'since it does not contain any results.'.format(self.id)
raise ValueError(msg)
@@ -2994,8 +2939,8 @@ def diagonalize_filter(self, new_filter, filter_position=-1):
cv.check_type('filter_position', filter_position, Integral)
if new_filter in self.filters:
- msg = 'Unable to diagonalize Tally ID="{0}" which already ' \
- 'contains a "{1}" filter'.format(self.id, type(new_filter))
+ msg = 'Unable to diagonalize Tally ID="{}" which already ' \
+ 'contains a "{}" filter'.format(self.id, type(new_filter))
raise ValueError(msg)
# Add the new filter to a copy of this Tally
@@ -3073,7 +3018,7 @@ def append(self, tally, merge=False):
"""
if not isinstance(tally, Tally):
- msg = 'Unable to add a non-Tally "{0}" to the ' \
+ msg = 'Unable to add a non-Tally "{}" to the ' \
'Tallies instance'.format(tally)
raise TypeError(msg)
diff --git a/openmc/trigger.py b/openmc/trigger.py
--- a/openmc/trigger.py
+++ b/openmc/trigger.py
@@ -7,7 +7,7 @@
import openmc.checkvalue as cv
-class Trigger(object):
+class Trigger:
"""A criterion for when to finish a simulation based on tally uncertainties.
Parameters
@@ -38,9 +38,6 @@ def __init__(self, trigger_type, threshold):
def __eq__(self, other):
return str(self) == str(other)
- def __ne__(self, other):
- return not self == other
-
def __repr__(self):
string = 'Trigger\n'
string += '{0: <16}{1}{2}\n'.format('\tType', '=\t', self._trigger_type)
diff --git a/openmc/volume.py b/openmc/volume.py
--- a/openmc/volume.py
+++ b/openmc/volume.py
@@ -15,7 +15,7 @@
_VERSION_VOLUME = 1
-class VolumeCalculation(object):
+class VolumeCalculation:
"""Stochastic volume calculation specifications and results.
Parameters
| diff --git a/tests/dummy_operator.py b/tests/dummy_operator.py
--- a/tests/dummy_operator.py
+++ b/tests/dummy_operator.py
@@ -74,7 +74,7 @@
}
-class TestChain(object):
+class TestChain:
"""Empty chain to assist with unit testing depletion routines
Only really provides the form_matrix function, but acts like
diff --git a/tests/regression_tests/asymmetric_lattice/test.py b/tests/regression_tests/asymmetric_lattice/test.py
--- a/tests/regression_tests/asymmetric_lattice/test.py
+++ b/tests/regression_tests/asymmetric_lattice/test.py
@@ -25,12 +25,12 @@ def __init__(self, *args, **kwargs):
[water, water, water]]
# Create bounding surfaces
- min_x = openmc.XPlane(-32.13, 'reflective')
- max_x = openmc.XPlane(+32.13, 'reflective')
- min_y = openmc.YPlane(-32.13, 'reflective')
- max_y = openmc.YPlane(+32.13, 'reflective')
- min_z = openmc.ZPlane(0, 'reflective')
- max_z = openmc.ZPlane(+32.13, 'reflective')
+ min_x = openmc.XPlane(-32.13, boundary_type='reflective')
+ max_x = openmc.XPlane(+32.13, boundary_type='reflective')
+ min_y = openmc.YPlane(-32.13, boundary_type='reflective')
+ max_y = openmc.YPlane(+32.13, boundary_type='reflective')
+ min_z = openmc.ZPlane(0, boundary_type='reflective')
+ max_z = openmc.ZPlane(+32.13, boundary_type='reflective')
# Define root universe
root_univ = openmc.Universe(universe_id=0, name='root universe')
diff --git a/tests/regression_tests/deplete/example_geometry.py b/tests/regression_tests/deplete/example_geometry.py
--- a/tests/regression_tests/deplete/example_geometry.py
+++ b/tests/regression_tests/deplete/example_geometry.py
@@ -298,12 +298,12 @@ def generate_geometry(n_rings, n_wedges):
lattice.outer = all_water_u
# Bound universe
- x_low = openmc.XPlane(-pitch*n_pin/2, 'reflective')
- x_high = openmc.XPlane(pitch*n_pin/2, 'reflective')
- y_low = openmc.YPlane(-pitch*n_pin/2, 'reflective')
- y_high = openmc.YPlane(pitch*n_pin/2, 'reflective')
- z_low = openmc.ZPlane(-10, 'reflective')
- z_high = openmc.ZPlane(10, 'reflective')
+ x_low = openmc.XPlane(-pitch*n_pin/2, boundary_type='reflective')
+ x_high = openmc.XPlane(pitch*n_pin/2, boundary_type='reflective')
+ y_low = openmc.YPlane(-pitch*n_pin/2, boundary_type='reflective')
+ y_high = openmc.YPlane(pitch*n_pin/2, boundary_type='reflective')
+ z_low = openmc.ZPlane(-10, boundary_type='reflective')
+ z_high = openmc.ZPlane(10, boundary_type='reflective')
# Compute bounding box
lower_left = [-pitch*n_pin/2, -pitch*n_pin/2, -10]
diff --git a/tests/regression_tests/salphabeta/test.py b/tests/regression_tests/salphabeta/test.py
--- a/tests/regression_tests/salphabeta/test.py
+++ b/tests/regression_tests/salphabeta/test.py
@@ -44,11 +44,11 @@ def make_model():
model.materials += [m1, m2, m3, m4]
# Geometry
- x0 = openmc.XPlane(-10, 'vacuum')
+ x0 = openmc.XPlane(-10, boundary_type='vacuum')
x1 = openmc.XPlane(-5)
x2 = openmc.XPlane(0)
x3 = openmc.XPlane(5)
- x4 = openmc.XPlane(10, 'vacuum')
+ x4 = openmc.XPlane(10, boundary_type='vacuum')
root_univ = openmc.Universe()
diff --git a/tests/regression_tests/triso/test.py b/tests/regression_tests/triso/test.py
--- a/tests/regression_tests/triso/test.py
+++ b/tests/regression_tests/triso/test.py
@@ -54,12 +54,12 @@ def _build_inputs(self):
inner_univ = openmc.Universe(cells=[c1, c2, c3, c4, c5])
# Define box to contain lattice and to pack TRISO particles in
- min_x = openmc.XPlane(-0.5, 'reflective')
- max_x = openmc.XPlane(0.5, 'reflective')
- min_y = openmc.YPlane(-0.5, 'reflective')
- max_y = openmc.YPlane(0.5, 'reflective')
- min_z = openmc.ZPlane(-0.5, 'reflective')
- max_z = openmc.ZPlane(0.5, 'reflective')
+ min_x = openmc.XPlane(-0.5, boundary_type='reflective')
+ max_x = openmc.XPlane(0.5, boundary_type='reflective')
+ min_y = openmc.YPlane(-0.5, boundary_type='reflective')
+ max_y = openmc.YPlane(0.5, boundary_type='reflective')
+ min_z = openmc.ZPlane(-0.5, boundary_type='reflective')
+ max_z = openmc.ZPlane(0.5, boundary_type='reflective')
box_region = +min_x & -max_x & +min_y & -max_y & +min_z & -max_z
box = openmc.Cell(region=box_region)
diff --git a/tests/testing_harness.py b/tests/testing_harness.py
--- a/tests/testing_harness.py
+++ b/tests/testing_harness.py
@@ -30,7 +30,7 @@ def colorize(diff):
yield line
-class TestHarness(object):
+class TestHarness:
"""General class for running OpenMC regression tests."""
def __init__(self, statepoint_name):
diff --git a/tests/unit_tests/conftest.py b/tests/unit_tests/conftest.py
--- a/tests/unit_tests/conftest.py
+++ b/tests/unit_tests/conftest.py
@@ -108,11 +108,11 @@ def mixed_lattice_model(uo2, water):
[empty_univ, u]
]
- xmin = openmc.XPlane(-d, 'periodic')
- xmax = openmc.XPlane(d, 'periodic')
+ xmin = openmc.XPlane(-d, boundary_type='periodic')
+ xmax = openmc.XPlane(d, boundary_type='periodic')
xmin.periodic_surface = xmax
- ymin = openmc.YPlane(-d, 'periodic')
- ymax = openmc.YPlane(d, 'periodic')
+ ymin = openmc.YPlane(-d, boundary_type='periodic')
+ ymax = openmc.YPlane(d, boundary_type='periodic')
main_cell = openmc.Cell(fill=rect_lattice,
region=+xmin & -xmax & +ymin & -ymax)
diff --git a/tests/unit_tests/test_complex_cell_bb.py b/tests/unit_tests/test_complex_cell_bb.py
--- a/tests/unit_tests/test_complex_cell_bb.py
+++ b/tests/unit_tests/test_complex_cell_bb.py
@@ -27,20 +27,20 @@ def complex_cell(run_in_tmpdir, mpi_intracomm):
model.materials = (u235, u238, zr90, n14)
- s1 = openmc.XPlane(-10.0, 'vacuum')
+ s1 = openmc.XPlane(-10.0, boundary_type='vacuum')
s2 = openmc.XPlane(-7.0)
s3 = openmc.XPlane(-4.0)
s4 = openmc.XPlane(4.0)
s5 = openmc.XPlane(7.0)
- s6 = openmc.XPlane(10.0, 'vacuum')
+ s6 = openmc.XPlane(10.0, boundary_type='vacuum')
s7 = openmc.XPlane(0.0)
- s11 = openmc.YPlane(-10.0, 'vacuum')
+ s11 = openmc.YPlane(-10.0, boundary_type='vacuum')
s12 = openmc.YPlane(-7.0)
s13 = openmc.YPlane(-4.0)
s14 = openmc.YPlane(4.0)
s15 = openmc.YPlane(7.0)
- s16 = openmc.YPlane(10.0, 'vacuum')
+ s16 = openmc.YPlane(10.0, boundary_type='vacuum')
s17 = openmc.YPlane(0.0)
c1 = openmc.Cell(fill=u235)
diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -14,8 +14,8 @@ def test_attributes(uo2):
assert uo2.depletable
-def test_nuclides(uo2):
- """Test adding/removing nuclides."""
+def test_add_nuclide():
+ """Test adding nuclides."""
m = openmc.Material()
m.add_nuclide('U235', 1.0)
with pytest.raises(TypeError):
@@ -24,7 +24,18 @@ def test_nuclides(uo2):
m.add_nuclide(1.0, 'H1')
with pytest.raises(ValueError):
m.add_nuclide('H1', 1.0, 'oa')
- m.remove_nuclide('U235')
+
+
+def test_remove_nuclide():
+ """Test removing nuclides."""
+ m = openmc.Material()
+ for nuc, percent in [('H1', 1.0), ('H2', 1.0), ('H1', 2.0), ('H2', 2.0)]:
+ m.add_nuclide(nuc, percent)
+ m.remove_nuclide('H1')
+ assert len(m.nuclides) == 2
+ assert all(nuc.name == 'H2' for nuc in m.nuclides)
+ assert m.nuclides[0].percent == 1.0
+ assert m.nuclides[1].percent == 2.0
def test_elements():
diff --git a/tests/unit_tests/test_surface.py b/tests/unit_tests/test_surface.py
--- a/tests/unit_tests/test_surface.py
+++ b/tests/unit_tests/test_surface.py
@@ -67,7 +67,7 @@ def test_plane_from_points():
def test_xplane():
- s = openmc.XPlane(3., 'reflective')
+ s = openmc.XPlane(3., boundary_type='reflective')
assert s.x0 == 3.
assert s.boundary_type == 'reflective'
@@ -441,7 +441,7 @@ def test_cone():
assert_infinite_bb(s)
# evaluate method
- # cos^2(theta) * ((p - p1))**2 - (d @ (p - p1))^2
+ # cos^2(theta) * ((p - p1))**2 - (d @ (p - p1))^2
# The argument r2 for cones is actually tan^2(theta) so that
# cos^2(theta) = 1 / (1 + r2)
#
diff --git a/tests/unit_tests/test_utils.py b/tests/unit_tests/test_utils.py
deleted file mode 100644
--- a/tests/unit_tests/test_utils.py
+++ /dev/null
@@ -1,26 +0,0 @@
-import os
-import filecmp
-
-from openmc import _utils
-import pytest
-
[email protected]()
-def download_photos(run_in_tmpdir):
- """use _utils download() function to download the same picture three times,
- twice to get unique names, & a third time to use the already downloaded
- block of code"""
- _utils.download("https://i.ibb.co/HhKFc8x/small.jpg")
- _utils.download("https://tinyurl.com/y4t38ugb")
- _utils.download("https://tinyurl.com/y4t38ugb", as_browser=True)
-
-
-def test_checksum_error(run_in_tmpdir):
- """use download() in such a way that will test the checksum error line"""
- phrase = "MD5 checksum for y4t38ugb"
- with pytest.raises(OSError, match=phrase):
- _utils.download("https://tinyurl.com/y4t38ugb", as_browser=True,
- checksum="not none")
-
-
-def test_photos(download_photos):
- assert filecmp.cmp("small.jpg", "y4t38ugb")
| Material.remove only removing one isotope
Hi all,
I spotted what might be a bug in the openmc.Material.remove_nuclide() method
If there is a material with multiple entries for the same isotope then only the first matching nuclide is removed due to the [break line in the material.py code ](https://github.com/openmc-dev/openmc/blob/2160e6b156f8e01331c9177881570ef754399bde/openmc/material.py#L439)
This current behavior can be a little unpredictable as users might not know which nuclide in the material is going to be removed.
It probably was not a problem due to the construction of materials via add_nuclide and add_element. However multiple isotopes within the same occurs material often occur when mixing materials (recently implemented). Perhaps this remove_nuclide method should remove all matching nuclide from the material?
I can submit a PR for this behavior change if people think remove_nuclide should remove all entries of the nuclide from the material instead of just the first one?
| 2020-03-24T02:03:38Z | [] | [] |
|
openmc-dev/openmc | 1,588 | openmc-dev__openmc-1588 | [
"1587"
] | 2979cfa2f4a7c57b0374f21da93f90c7afc277a2 | diff --git a/openmc/_xml.py b/openmc/_xml.py
--- a/openmc/_xml.py
+++ b/openmc/_xml.py
@@ -43,3 +43,21 @@ def get_text(elem, name, default=None):
else:
child = elem.find(name)
return child.text if child is not None else default
+
+
+def reorder_attributes(root):
+ """Sort attributes in XML to preserve pre-Python 3.8 behavior
+
+ Parameters
+ ----------
+ root : xml.etree.ElementTree.Element
+ Root element
+
+ """
+ for el in root.iter():
+ attrib = el.attrib
+ if len(attrib) > 1:
+ # adjust attribute order, e.g. by sorting
+ attribs = sorted(attrib.items())
+ attrib.clear()
+ attrib.update(attribs)
diff --git a/openmc/data/library.py b/openmc/data/library.py
--- a/openmc/data/library.py
+++ b/openmc/data/library.py
@@ -5,7 +5,7 @@
import h5py
from openmc.mixin import EqualityMixin
-from openmc._xml import clean_indentation
+from openmc._xml import clean_indentation, reorder_attributes
class DataLibrary(EqualityMixin):
@@ -112,6 +112,7 @@ def export_to_xml(self, path='cross_sections.xml'):
clean_indentation(root)
# Write XML file
+ reorder_attributes(root) # TODO: Remove when support is Python 3.8+
tree = ET.ElementTree(root)
tree.write(str(path), xml_declaration=True, encoding='utf-8',
method='xml')
diff --git a/openmc/geometry.py b/openmc/geometry.py
--- a/openmc/geometry.py
+++ b/openmc/geometry.py
@@ -110,6 +110,7 @@ def export_to_xml(self, path='geometry.xml', remove_surfs=False):
p /= 'geometry.xml'
# Write the XML Tree to the geometry.xml file
+ xml.reorder_attributes(root_element) # TODO: Remove when support is Python 3.8+
tree = ET.ElementTree(root_element)
tree.write(str(p), xml_declaration=True, encoding='utf-8')
diff --git a/openmc/material.py b/openmc/material.py
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -12,7 +12,7 @@
import openmc
import openmc.data
import openmc.checkvalue as cv
-from ._xml import clean_indentation
+from ._xml import clean_indentation, reorder_attributes
from .mixin import IDManagerMixin
@@ -1239,6 +1239,7 @@ def export_to_xml(self, path='materials.xml'):
clean_indentation(element, level=1)
element.tail = element.tail.strip(' ')
fh.write(' ')
+ reorder_attributes(element) # TODO: Remove when support is Python 3.8+
ET.ElementTree(element).write(fh, encoding='unicode')
# Write the <material> elements.
@@ -1247,6 +1248,7 @@ def export_to_xml(self, path='materials.xml'):
clean_indentation(element, level=1)
element.tail = element.tail.strip(' ')
fh.write(' ')
+ reorder_attributes(element) # TODO: Remove when support is Python 3.8+
ET.ElementTree(element).write(fh, encoding='unicode')
# Write the closing tag for the root element.
diff --git a/openmc/mesh.py b/openmc/mesh.py
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -361,14 +361,14 @@ def build_cells(self, bc=None):
n_dim = len(self.dimension)
# Build the cell which will contain the lattice
- xplanes = [openmc.XPlane(self.lower_left[0], bc[0]),
- openmc.XPlane(self.upper_right[0], bc[1])]
+ xplanes = [openmc.XPlane(self.lower_left[0], boundary_type=bc[0]),
+ openmc.XPlane(self.upper_right[0], boundary_type=bc[1])]
if n_dim == 1:
- yplanes = [openmc.YPlane(-1e10, 'reflective'),
- openmc.YPlane(1e10, 'reflective')]
+ yplanes = [openmc.YPlane(-1e10, boundary_type='reflective'),
+ openmc.YPlane(1e10, boundary_type='reflective')]
else:
- yplanes = [openmc.YPlane(self.lower_left[1], bc[2]),
- openmc.YPlane(self.upper_right[1], bc[3])]
+ yplanes = [openmc.YPlane(self.lower_left[1], boundary_type=bc[2]),
+ openmc.YPlane(self.upper_right[1], boundary_type=bc[3])]
if n_dim <= 2:
# Would prefer to have the z ranges be the max supported float, but
@@ -378,11 +378,11 @@ def build_cells(self, bc=None):
# inconsistency between what numpy uses as the max float and what
# Fortran expects for a real(8), so this avoids code complication
# and achieves the same goal.
- zplanes = [openmc.ZPlane(-1e10, 'reflective'),
- openmc.ZPlane(1e10, 'reflective')]
+ zplanes = [openmc.ZPlane(-1e10, boundary_type='reflective'),
+ openmc.ZPlane(1e10, boundary_type='reflective')]
else:
- zplanes = [openmc.ZPlane(self.lower_left[2], bc[4]),
- openmc.ZPlane(self.upper_right[2], bc[5])]
+ zplanes = [openmc.ZPlane(self.lower_left[2], boundary_type=bc[4]),
+ openmc.ZPlane(self.upper_right[2], boundary_type=bc[5])]
root_cell = openmc.Cell()
root_cell.region = ((+xplanes[0] & -xplanes[1]) &
(+yplanes[0] & -yplanes[1]) &
diff --git a/openmc/plots.py b/openmc/plots.py
--- a/openmc/plots.py
+++ b/openmc/plots.py
@@ -8,7 +8,7 @@
import openmc
import openmc.checkvalue as cv
-from ._xml import clean_indentation
+from ._xml import clean_indentation, reorder_attributes
from .mixin import IDManagerMixin
@@ -844,5 +844,6 @@ def export_to_xml(self, path='plots.xml'):
p /= 'plots.xml'
# Write the XML Tree to the plots.xml file
+ reorder_attributes(self._plots_file) # TODO: Remove when support is Python 3.8+
tree = ET.ElementTree(self._plots_file)
tree.write(str(p), xml_declaration=True, encoding='utf-8')
diff --git a/openmc/settings.py b/openmc/settings.py
--- a/openmc/settings.py
+++ b/openmc/settings.py
@@ -6,7 +6,7 @@
import openmc.checkvalue as cv
from . import VolumeCalculation, Source, RegularMesh
-from ._xml import clean_indentation, get_text
+from ._xml import clean_indentation, get_text, reorder_attributes
class RunMode(Enum):
@@ -1375,6 +1375,7 @@ def export_to_xml(self, path='settings.xml'):
p /= 'settings.xml'
# Write the XML Tree to the settings.xml file
+ reorder_attributes(root_element) # TODO: Remove when support is Python 3.8+
tree = ET.ElementTree(root_element)
tree.write(str(p), xml_declaration=True, encoding='utf-8')
diff --git a/openmc/tallies.py b/openmc/tallies.py
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -14,7 +14,7 @@
import openmc
import openmc.checkvalue as cv
-from ._xml import clean_indentation
+from ._xml import clean_indentation, reorder_attributes
from .mixin import IDManagerMixin
@@ -3143,5 +3143,6 @@ def export_to_xml(self, path='tallies.xml'):
p /= 'tallies.xml'
# Write the XML Tree to the tallies.xml file
+ reorder_attributes(root_element) # TODO: Remove when support is Python 3.8+
tree = ET.ElementTree(root_element)
tree.write(str(p), xml_declaration=True, encoding='utf-8')
| diff --git a/tests/regression_tests/photon_production/test.py b/tests/regression_tests/photon_production/test.py
--- a/tests/regression_tests/photon_production/test.py
+++ b/tests/regression_tests/photon_production/test.py
@@ -13,9 +13,9 @@ def model():
model.materials.append(mat)
cyl = openmc.XCylinder(r=1.0, boundary_type='vacuum')
- x_plane_left = openmc.XPlane(-1.0, 'vacuum')
+ x_plane_left = openmc.XPlane(-1.0, boundary_type='vacuum')
x_plane_center = openmc.XPlane(1.0)
- x_plane_right = openmc.XPlane(1.0e9, 'vacuum')
+ x_plane_right = openmc.XPlane(1.0e9, boundary_type='vacuum')
inner_cyl_left = openmc.Cell()
inner_cyl_right = openmc.Cell()
diff --git a/tests/regression_tests/resonance_scattering/test.py b/tests/regression_tests/resonance_scattering/test.py
--- a/tests/regression_tests/resonance_scattering/test.py
+++ b/tests/regression_tests/resonance_scattering/test.py
@@ -17,7 +17,7 @@ def _build_inputs(self):
mats_file.export_to_xml()
# Geometry
- dumb_surface = openmc.XPlane(100, 'reflective')
+ dumb_surface = openmc.XPlane(100, boundary_type='reflective')
c1 = openmc.Cell(cell_id=1, fill=mat, region=-dumb_surface)
root_univ = openmc.Universe(universe_id=0, cells=[c1])
geometry = openmc.Geometry(root_univ)
| Tests fail when using Python 3.8
In Python 3.8, [xml.etree.ElementTree.dump](https://docs.python.org/3/library/xml.etree.elementtree.html#xml.etree.ElementTree.dump) now preserves attribute order specified by user, which is great but it also means that when our Python-based regression tests compare XML output in `inputs_true.dat`, the order is different when you are running with Python 3.8 versus an earlier version. Not sure what a good solution is yet :confused:
| Ok, so there's a really long discussion of this on the Python [bug tracker](https://bugs.python.org/issue34160), including a bunch of angry people who didn't appreciate Python 3.8 breaking their tests. It sounds like an easy fix for this is to have our code reorder attributes using a recipe found in the [Python docs](https://docs.python.org/3/library/xml.etree.elementtree.html#xml.etree.ElementTree.Element.remove). | 2020-06-18T03:31:35Z | [] | [] |
openmc-dev/openmc | 1,623 | openmc-dev__openmc-1623 | [
"1621"
] | c9120bafbcff2ce8d1bb2261f93193a1828a2ef4 | diff --git a/examples/parameterized_custom_source/build_xml.py b/examples/parameterized_custom_source/build_xml.py
new file mode 100644
--- /dev/null
+++ b/examples/parameterized_custom_source/build_xml.py
@@ -0,0 +1,37 @@
+import openmc
+
+# Create a single material
+iron = openmc.Material()
+iron.set_density('g/cm3', 5.0)
+iron.add_element('Fe', 1.0)
+mats = openmc.Materials([iron])
+mats.export_to_xml()
+
+# Create a 5 cm x 5 cm box filled with iron
+box = openmc.model.rectangular_prism(10.0, 10.0, boundary_type='vacuum')
+cell = openmc.Cell(fill=iron, region=box)
+geometry = openmc.Geometry([cell])
+geometry.export_to_xml()
+
+# Tell OpenMC we're going to use our custom source
+settings = openmc.Settings()
+settings.run_mode = 'fixed source'
+settings.batches = 10
+settings.particles = 1000
+source = openmc.Source()
+source.library = 'build/libparameterized_source.so'
+source.parameters = 'radius=3.0, energy=14.08e6'
+settings.source = source
+settings.export_to_xml()
+
+# Finally, define a mesh tally so that we can see the resulting flux
+mesh = openmc.RegularMesh()
+mesh.lower_left = (-5.0, -5.0)
+mesh.upper_right = (5.0, 5.0)
+mesh.dimension = (50, 50)
+
+tally = openmc.Tally()
+tally.filters = [openmc.MeshFilter(mesh)]
+tally.scores = ['flux']
+tallies = openmc.Tallies([tally])
+tallies.export_to_xml()
diff --git a/examples/parameterized_custom_source/show_flux.py b/examples/parameterized_custom_source/show_flux.py
new file mode 100644
--- /dev/null
+++ b/examples/parameterized_custom_source/show_flux.py
@@ -0,0 +1,14 @@
+import matplotlib.pyplot as plt
+import openmc
+
+# Get the flux from the statepoint
+with openmc.StatePoint('statepoint.10.h5') as sp:
+ flux = sp.tallies[1].mean
+ flux.shape = (50, 50)
+
+# Plot the flux
+fig, ax = plt.subplots()
+ax.imshow(flux, origin='lower', extent=(-5.0, 5.0, -5.0, 5.0))
+ax.set_xlabel('x [cm]')
+ax.set_ylabel('y [cm]')
+plt.show()
diff --git a/openmc/source.py b/openmc/source.py
--- a/openmc/source.py
+++ b/openmc/source.py
@@ -22,6 +22,8 @@ class Source:
Source file from which sites should be sampled
library : str
Path to a custom source library
+ parameters : str
+ Parameters to be provided to the custom source library
.. versionadded:: 0.12
strength : float
@@ -41,6 +43,8 @@ class Source:
Source file from which sites should be sampled
library : str or None
Path to a custom source library
+ parameters : str
+ Parameters to be provided to the custom source library
strength : float
Strength of the source
particle : {'neutron', 'photon'}
@@ -49,12 +53,13 @@ class Source:
"""
def __init__(self, space=None, angle=None, energy=None, filename=None,
- library=None, strength=1.0, particle='neutron'):
+ library=None, parameters=None, strength=1.0, particle='neutron'):
self._space = None
self._angle = None
self._energy = None
self._file = None
self._library = None
+ self._parameters = None
if space is not None:
self.space = space
@@ -66,6 +71,8 @@ def __init__(self, space=None, angle=None, energy=None, filename=None,
self.file = filename
if library is not None:
self.library = library
+ if parameters is not None:
+ self.parameters = parameters
self.strength = strength
self.particle = particle
@@ -77,6 +84,10 @@ def file(self):
def library(self):
return self._library
+ @property
+ def parameters(self):
+ return self._parameters
+
@property
def space(self):
return self._space
@@ -107,6 +118,11 @@ def library(self, library_name):
cv.check_type('library', library_name, str)
self._library = library_name
+ @parameters.setter
+ def parameters(self, parameters_path):
+ cv.check_type('parameters', parameters_path, str)
+ self._parameters = parameters_path
+
@space.setter
def space(self, space):
cv.check_type('spatial distribution', space, Spatial)
@@ -150,6 +166,8 @@ def to_xml_element(self):
element.set("file", self.file)
if self.library is not None:
element.set("library", self.library)
+ if self.parameters is not None:
+ element.set("parameters", self.parameters)
if self.space is not None:
element.append(self.space.to_xml_element())
if self.angle is not None:
@@ -191,6 +209,10 @@ def from_xml_element(cls, elem):
if library is not None:
source.library = library
+ parameters = get_text(elem, 'parameters')
+ if parameters is not None:
+ source.parameters = parameters
+
space = elem.find('space')
if space is not None:
source.space = Spatial.from_xml_element(space)
| diff --git a/tests/regression_tests/source_dlopen/source_sampling.cpp b/tests/regression_tests/source_dlopen/source_sampling.cpp
--- a/tests/regression_tests/source_dlopen/source_sampling.cpp
+++ b/tests/regression_tests/source_dlopen/source_sampling.cpp
@@ -1,11 +1,14 @@
#include <iostream>
+#include <memory>
+
#include "openmc/random_lcg.h"
#include "openmc/source.h"
#include "openmc/particle.h"
-// you must have external C linkage here otherwise
-// dlopen will not find the file
-extern "C" openmc::Particle::Bank sample_source(uint64_t *seed) {
+class Source : openmc::CustomSource
+{
+ openmc::Particle::Bank sample(uint64_t *seed)
+ {
openmc::Particle::Bank particle;
// wgt
particle.particle = openmc::Particle::Type::neutron;
@@ -20,4 +23,13 @@ extern "C" openmc::Particle::Bank sample_source(uint64_t *seed) {
particle.E = 14.08e6;
particle.delayed_group = 0;
return particle;
+ }
+};
+
+// A function to create a unique pointer to an instance of this class when generated
+// via a plugin call using dlopen/dlsym.
+// You must have external C linkage here otherwise dlopen will not find the file
+extern "C" std::unique_ptr<Source> openmc_create_source(std::string parameters)
+{
+ return std::make_unique<Source>();
}
diff --git a/tests/regression_tests/source_parameterized_dlopen/__init__.py b/tests/regression_tests/source_parameterized_dlopen/__init__.py
new file mode 100644
diff --git a/tests/regression_tests/source_parameterized_dlopen/inputs_true.dat b/tests/regression_tests/source_parameterized_dlopen/inputs_true.dat
new file mode 100644
--- /dev/null
+++ b/tests/regression_tests/source_parameterized_dlopen/inputs_true.dat
@@ -0,0 +1,23 @@
+<?xml version='1.0' encoding='utf-8'?>
+<geometry>
+ <cell id="1" material="1" region="-1" universe="1" />
+ <surface boundary="vacuum" coeffs="0.0 0.0 0.0 100" id="1" type="sphere" />
+</geometry>
+<?xml version='1.0' encoding='utf-8'?>
+<materials>
+ <material id="1" name="natural_lead">
+ <density units="g/cm3" value="11.34" />
+ <nuclide ao="0.014" name="Pb204" />
+ <nuclide ao="0.241" name="Pb206" />
+ <nuclide ao="0.221" name="Pb207" />
+ <nuclide ao="0.524" name="Pb208" />
+ </material>
+</materials>
+<?xml version='1.0' encoding='utf-8'?>
+<settings>
+ <run_mode>fixed source</run_mode>
+ <particles>1000</particles>
+ <batches>10</batches>
+ <inactive>0</inactive>
+ <source library="build/libsource.so" parameters="1e3" strength="1.0" />
+</settings>
diff --git a/tests/regression_tests/source_parameterized_dlopen/parameterized_source_sampling.cpp b/tests/regression_tests/source_parameterized_dlopen/parameterized_source_sampling.cpp
new file mode 100644
--- /dev/null
+++ b/tests/regression_tests/source_parameterized_dlopen/parameterized_source_sampling.cpp
@@ -0,0 +1,38 @@
+#include "openmc/source.h"
+#include "openmc/particle.h"
+
+class Source : public openmc::CustomSource {
+ public:
+ Source(double energy) : energy_(energy) { }
+
+ // Samples from an instance of this class.
+ openmc::Particle::Bank sample(uint64_t* seed)
+ {
+ openmc::Particle::Bank particle;
+ // wgt
+ particle.particle = openmc::Particle::Type::neutron;
+ particle.wgt = 1.0;
+ // position
+ particle.r.x = 0.0;
+ particle.r.y = 0.0;
+ particle.r.z = 0.0;
+ // angle
+ particle.u = {1.0, 0.0, 0.0};
+ particle.E = this->energy_;
+ particle.delayed_group = 0;
+
+ return particle;
+ }
+
+ private:
+ double energy_;
+};
+
+// A function to create a unique pointer to an instance of this class when generated
+// via a plugin call using dlopen/dlsym.
+// You must have external C linkage here otherwise dlopen will not find the file
+extern "C" std::unique_ptr<Source> openmc_create_source(std::string parameter)
+{
+ double energy = std::stod(parameter);
+ return std::make_unique<Source>(energy);
+}
diff --git a/tests/regression_tests/source_parameterized_dlopen/results_true.dat b/tests/regression_tests/source_parameterized_dlopen/results_true.dat
new file mode 100644
diff --git a/tests/regression_tests/source_parameterized_dlopen/test.py b/tests/regression_tests/source_parameterized_dlopen/test.py
new file mode 100644
--- /dev/null
+++ b/tests/regression_tests/source_parameterized_dlopen/test.py
@@ -0,0 +1,75 @@
+from pathlib import Path
+import os
+import shutil
+import subprocess
+import textwrap
+
+import openmc
+import pytest
+
+from tests.testing_harness import PyAPITestHarness
+
+
[email protected]
+def compile_source(request):
+ """Compile the external source"""
+
+ # Get build directory and write CMakeLists.txt file
+ openmc_dir = Path(str(request.config.rootdir)) / 'build'
+ with open('CMakeLists.txt', 'w') as f:
+ f.write(textwrap.dedent("""
+ cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
+ project(openmc_sources CXX)
+ add_library(source SHARED parameterized_source_sampling.cpp)
+ find_package(OpenMC REQUIRED HINTS {})
+ target_link_libraries(source OpenMC::libopenmc)
+ """.format(openmc_dir)))
+
+ # Create temporary build directory and change to there
+ local_builddir = Path('build')
+ local_builddir.mkdir(exist_ok=True)
+ os.chdir(str(local_builddir))
+
+ # Run cmake/make to build the shared libary
+ subprocess.run(['cmake', os.path.pardir], check=True)
+ subprocess.run(['make'], check=True)
+ os.chdir(os.path.pardir)
+
+ yield
+
+ # Remove local build directory when test is complete
+ shutil.rmtree('build')
+ os.remove('CMakeLists.txt')
+
+
[email protected]
+def model():
+ model = openmc.model.Model()
+ natural_lead = openmc.Material(name="natural_lead")
+ natural_lead.add_element('Pb', 1.0)
+ natural_lead.set_density('g/cm3', 11.34)
+ model.materials.append(natural_lead)
+
+ # geometry
+ surface_sph1 = openmc.Sphere(r=100, boundary_type='vacuum')
+ cell_1 = openmc.Cell(fill=natural_lead, region=-surface_sph1)
+ model.geometry = openmc.Geometry([cell_1])
+
+ # settings
+ model.settings.batches = 10
+ model.settings.inactive = 0
+ model.settings.particles = 1000
+ model.settings.run_mode = 'fixed source'
+
+ # custom source from shared library
+ source = openmc.Source()
+ source.library = 'build/libsource.so'
+ source.parameters = '1e3'
+ model.settings.source = source
+
+ return model
+
+
+def test_dlopen_source(compile_source, model):
+ harness = PyAPITestHarness('statepoint.10.h5', model)
+ harness.main()
| Add support for deserialization of custom source
The current implementation of a custom source is supported by the user providing a compiled shared object library, which implements the `sample_source` function, having a template providing an array of random seeds and returning a `Particle::Bank`. This is convenient for static sources, where the parametrisation of that source does not change but is less convenient is the source can vary e.g. between sequential runs. In this case the current solution would require the user to recompile their custom source with the new parametrisation and use the new library in the new run.
This Issue suggests to also attempt to dynamically load a `sample_source` function with an additional parameter that accepts a path to a file containing a serialised representation of the parameterised source. The existing function template would still be loadable, to avoid regression effects. This would allow the source to be deserialized before sampling, allowing for a more dynamic approach that does not require recompilation. Docs and tests relating to the custom source would also need to be updated to describe this alternative approach.
I'd be happy to put a PR together for this (assuming there is some availability to review that), but wanted to throw the issue out there first in case there are any comments or alternative suggestions before I get started.
| Of course the name of the new function would have to be different from `sample_source` to allow it to be a c-style function and avoid name mangling. I'd suggest something like `deserialize_sample_source`.
Why not just pass the parametrisation through the input xml (or equivalently through the serialised xml form the python interface)?
On 28 Jul 2020, at 19:50, DanShort12 <[email protected]<mailto:[email protected]>> wrote:
Of course the name of the new function would have to be different from sample_source to allow it to be a c-style function and avoid name mangling. I'd suggest something like deserialize_sample_source.
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Fair point, I was considering a couple of factors:
1. A general user might not want to serialise/deserialise to/from XML, in which case they'd have to embed their favoured format within the settings.xml, with appropriate escaping.
2. If the serialisation is passed into settings.xml as XML then the schema of the serialised source and the settings.xml get merged, so again unless the serialised representation is escaped there may be some unexpected interactions.
That being said, from the perspective of OpenMC the proposed new element in the settings.xml would have a string-like value so a user could in principle use whatever string they like, whether that be a file path of a direct injection of the serialised source. Perhaps a compromise would be to give that element a name that is not so specific (`serialised_source` rather than `serialised_source_path`, for example), then the implementation in OpenMC is agnostic to how the user wants to perform their serialisation/deserialisation routines? | 2020-07-31T16:57:25Z | [] | [] |
openmc-dev/openmc | 1,637 | openmc-dev__openmc-1637 | [
"1509"
] | 6aa1570c041b5ea6819b46884dace29acb5d8301 | diff --git a/openmc/lib/core.py b/openmc/lib/core.py
--- a/openmc/lib/core.py
+++ b/openmc/lib/core.py
@@ -17,6 +17,7 @@ class _Bank(Structure):
('E', c_double),
('wgt', c_double),
('delayed_group', c_int),
+ ('surf_id', c_int),
('particle', c_int),
('parent_id', c_int64),
('progeny_id', c_int64)]
diff --git a/openmc/settings.py b/openmc/settings.py
--- a/openmc/settings.py
+++ b/openmc/settings.py
@@ -143,6 +143,17 @@ class Settings:
Options for writing state points. Acceptable keys are:
:batches: list of batches at which to write source
+ surf_source_read : dict
+ Options for reading surface source points. Acceptable keys are:
+
+ :path: Path to surface source file (str).
+ surf_source_write : dict
+ Options for writing surface source points. Acceptable keys are:
+
+ :surface_ids: List of surface ids at which crossing particles are to be
+ banked (int)
+ :max_particles: Maximum number of particles to be banked on surfaces
+ per process (int)
survival_biasing : bool
Indicate whether survival biasing is to be used
tabular_legendre : dict
@@ -229,6 +240,9 @@ def __init__(self):
self._statepoint = {}
self._sourcepoint = {}
+ self._surf_source_read = {}
+ self._surf_source_write = {}
+
self._no_reduce = None
self._verbosity = None
@@ -356,6 +370,14 @@ def sourcepoint(self):
def statepoint(self):
return self._statepoint
+ @property
+ def surf_source_read(self):
+ return self._surf_source_read
+
+ @property
+ def surf_source_write(self):
+ return self._surf_source_write
+
@property
def no_reduce(self):
return self._no_reduce
@@ -567,6 +589,35 @@ def statepoint(self, statepoint):
"statepoint options.".format(key))
self._statepoint = statepoint
+ @surf_source_read.setter
+ def surf_source_read(self, surf_source_read):
+ cv.check_type('surface source reading options', surf_source_read, Mapping)
+ for key, value in surf_source_read.items():
+ cv.check_value('surface source reading key', key,
+ ('path'))
+ if key == 'path':
+ cv.check_type('path to surface source file', value, str)
+ self._surf_source_read = surf_source_read
+
+ @surf_source_write.setter
+ def surf_source_write(self, surf_source_write):
+ cv.check_type('surface source writing options', surf_source_write, Mapping)
+ for key, value in surf_source_write.items():
+ cv.check_value('surface source writing key', key,
+ ('surface_ids', 'max_particles'))
+ if key == 'surface_ids':
+ cv.check_type('surface ids for source banking', value,
+ Iterable, Integral)
+ for surf_id in value:
+ cv.check_greater_than('surface id for source banking',
+ surf_id, 0)
+ elif key == 'max_particles':
+ cv.check_type('maximum particle banks on surfaces per process',
+ value, Integral)
+ cv.check_greater_than('maximum particle banks on surfaces per process',
+ value, 0)
+ self._surf_source_write = surf_source_write
+
@confidence_intervals.setter
def confidence_intervals(self, confidence_intervals):
cv.check_type('confidence interval', confidence_intervals, bool)
@@ -889,6 +940,24 @@ def _create_sourcepoint_subelement(self, root):
subelement = ET.SubElement(element, "overwrite_latest")
subelement.text = str(self._sourcepoint['overwrite']).lower()
+ def _create_surf_source_read_subelement(self, root):
+ if self._surf_source_read:
+ element = ET.SubElement(root, "surf_source_read")
+ if 'path' in self._surf_source_read:
+ subelement = ET.SubElement(element, "path")
+ subelement.text = self._surf_source_read['path']
+
+ def _create_surf_source_write_subelement(self, root):
+ if self._surf_source_write:
+ element = ET.SubElement(root, "surf_source_write")
+ if 'surface_ids' in self._surf_source_write:
+ subelement = ET.SubElement(element, "surface_ids")
+ subelement.text = ' '.join(
+ str(x) for x in self._surf_source_write['surface_ids'])
+ if 'max_particles' in self._surf_source_write:
+ subelement = ET.SubElement(element, "max_particles")
+ subelement.text = str(self._surf_source_write['max_particles'])
+
def _create_confidence_intervals(self, root):
if self._confidence_intervals is not None:
element = ET.SubElement(root, "confidence_intervals")
@@ -1151,6 +1220,25 @@ def _sourcepoint_from_xml_element(self, root):
value = [int(x) for x in value.split()]
self.sourcepoint[key] = value
+ def _surf_source_read_from_xml_element(self, root):
+ elem = root.find('surf_source_read')
+ if elem is not None:
+ value = get_text(elem, 'path')
+ if value is not None:
+ self.surf_source_read['path'] = value
+
+ def _surf_source_write_from_xml_element(self, root):
+ elem = root.find('surf_source_write')
+ if elem is not None:
+ for key in ('surface_ids', 'max_particles'):
+ value = get_text(elem, key)
+ if value is not None:
+ if key == 'surface_ids':
+ value = [int(x) for x in value.split()]
+ elif key in ('max_particles'):
+ value = int(value)
+ self.surf_source_write[key] = value
+
def _confidence_intervals_from_xml_element(self, root):
text = get_text(root, 'confidence_intervals')
if text is not None:
@@ -1349,6 +1437,8 @@ def export_to_xml(self, path='settings.xml'):
self._create_output_subelement(root_element)
self._create_statepoint_subelement(root_element)
self._create_sourcepoint_subelement(root_element)
+ self._create_surf_source_read_subelement(root_element)
+ self._create_surf_source_write_subelement(root_element)
self._create_confidence_intervals(root_element)
self._create_electron_treatment_subelement(root_element)
self._create_energy_mode_subelement(root_element)
@@ -1422,6 +1512,8 @@ def from_xml(cls, path='settings.xml'):
settings._output_from_xml_element(root)
settings._statepoint_from_xml_element(root)
settings._sourcepoint_from_xml_element(root)
+ settings._surf_source_read_from_xml_element(root)
+ settings._surf_source_write_from_xml_element(root)
settings._confidence_intervals_from_xml_element(root)
settings._electron_treatment_from_xml_element(root)
settings._energy_mode_from_xml_element(root)
diff --git a/openmc/source.py b/openmc/source.py
--- a/openmc/source.py
+++ b/openmc/source.py
@@ -257,17 +257,20 @@ class SourceParticle:
Weight of the particle
delayed_group : int
Delayed group particle was created in (neutrons only)
+ surf_id : int
+ Surface ID where particle is at, if any.
particle : ParticleType
Type of the particle
"""
def __init__(self, r=(0., 0., 0.), u=(0., 0., 1.), E=1.0e6, wgt=1.0,
- delayed_group=0, particle=ParticleType.NEUTRON):
+ delayed_group=0, surf_id=0, particle=ParticleType.NEUTRON):
self.r = tuple(r)
self.u = tuple(u)
self.E = float(E)
self.wgt = float(wgt)
self.delayed_group = delayed_group
+ self.surf_id = surf_id
self.particle = particle
def to_tuple(self):
@@ -280,7 +283,7 @@ def to_tuple(self):
"""
return (self.r, self.u, self.E, self.wgt,
- self.delayed_group, self.particle.value)
+ self.delayed_group, self.surf_id, self.particle.value)
def write_source_file(source_particles, filename, **kwargs):
@@ -304,6 +307,7 @@ def write_source_file(source_particles, filename, **kwargs):
('E', '<f8'),
('wgt', '<f8'),
('delayed_group', '<i4'),
+ ('surf_id', '<i4'),
('particle', '<i4'),
])
diff --git a/openmc/statepoint.py b/openmc/statepoint.py
--- a/openmc/statepoint.py
+++ b/openmc/statepoint.py
@@ -94,9 +94,9 @@ class StatePoint:
Pseudorandom number generator seed
source : numpy.ndarray of compound datatype
Array of source sites. The compound datatype has fields 'r', 'u',
- 'E', 'wgt', 'delayed_group', and 'particle', corresponding to the
- position, direction, energy, weight, delayed group, and particle type
- of the source site, respectively.
+ 'E', 'wgt', 'delayed_group', 'surf_id', and 'particle', corresponding to
+ the position, direction, energy, weight, delayed group, surface ID and
+ particle type of the source site, respectively.
source_present : bool
Indicate whether source sites are present
sparse : bool
| diff --git a/tests/regression_tests/surface_source/__init__.py b/tests/regression_tests/surface_source/__init__.py
new file mode 100644
diff --git a/tests/regression_tests/surface_source/inputs_true_read.dat b/tests/regression_tests/surface_source/inputs_true_read.dat
new file mode 100644
--- /dev/null
+++ b/tests/regression_tests/surface_source/inputs_true_read.dat
@@ -0,0 +1,34 @@
+<?xml version='1.0' encoding='utf-8'?>
+<geometry>
+ <cell id="1" material="void" region="-1" universe="1" />
+ <cell id="2" material="void" region="1 -2" universe="1" />
+ <cell id="3" material="void" region="2 -3" universe="1" />
+ <cell id="4" material="void" region="3 -4" universe="1" />
+ <surface coeffs="0.0 0.0 0.0 1.0" id="1" type="sphere" />
+ <surface coeffs="0.0 0.0 0.0 2.0" id="2" type="sphere" />
+ <surface coeffs="0.0 0.0 0.0 2.5" id="3" type="sphere" />
+ <surface boundary="vacuum" coeffs="0.0 0.0 0.0 4.0" id="4" type="sphere" />
+</geometry>
+<?xml version='1.0' encoding='utf-8'?>
+<materials>
+</materials>
+<?xml version='1.0' encoding='utf-8'?>
+<settings>
+ <run_mode>fixed source</run_mode>
+ <particles>1000</particles>
+ <batches>10</batches>
+ <surf_source_read>
+ <path>surface_source_true.h5</path>
+ </surf_source_read>
+ <seed>1</seed>
+</settings>
+<?xml version='1.0' encoding='utf-8'?>
+<tallies>
+ <filter id="1" type="cell">
+ <bins>3</bins>
+ </filter>
+ <tally id="1">
+ <filters>1</filters>
+ <scores>flux</scores>
+ </tally>
+</tallies>
diff --git a/tests/regression_tests/surface_source/inputs_true_write.dat b/tests/regression_tests/surface_source/inputs_true_write.dat
new file mode 100644
--- /dev/null
+++ b/tests/regression_tests/surface_source/inputs_true_write.dat
@@ -0,0 +1,40 @@
+<?xml version='1.0' encoding='utf-8'?>
+<geometry>
+ <cell id="1" material="void" region="-1" universe="1" />
+ <cell id="2" material="void" region="1 -2" universe="1" />
+ <cell id="3" material="void" region="2 -3" universe="1" />
+ <cell id="4" material="void" region="3 -4" universe="1" />
+ <surface coeffs="0.0 0.0 0.0 1.0" id="1" type="sphere" />
+ <surface coeffs="0.0 0.0 0.0 2.0" id="2" type="sphere" />
+ <surface coeffs="0.0 0.0 0.0 2.5" id="3" type="sphere" />
+ <surface boundary="vacuum" coeffs="0.0 0.0 0.0 4.0" id="4" type="sphere" />
+</geometry>
+<?xml version='1.0' encoding='utf-8'?>
+<materials>
+</materials>
+<?xml version='1.0' encoding='utf-8'?>
+<settings>
+ <run_mode>fixed source</run_mode>
+ <particles>1000</particles>
+ <batches>10</batches>
+ <source strength="1.0">
+ <space type="point">
+ <parameters>0 0 0</parameters>
+ </space>
+ </source>
+ <surf_source_write>
+ <surface_ids>1</surface_ids>
+ <max_particles>1000</max_particles>
+ </surf_source_write>
+ <seed>1</seed>
+</settings>
+<?xml version='1.0' encoding='utf-8'?>
+<tallies>
+ <filter id="1" type="cell">
+ <bins>3</bins>
+ </filter>
+ <tally id="1">
+ <filters>1</filters>
+ <scores>flux</scores>
+ </tally>
+</tallies>
diff --git a/tests/regression_tests/surface_source/results_true.dat b/tests/regression_tests/surface_source/results_true.dat
new file mode 100644
--- /dev/null
+++ b/tests/regression_tests/surface_source/results_true.dat
@@ -0,0 +1,3 @@
+tally 1:
+5.000000E+00
+2.500000E+00
diff --git a/tests/regression_tests/surface_source/surface_source_true.h5 b/tests/regression_tests/surface_source/surface_source_true.h5
new file mode 100644
Binary files /dev/null and b/tests/regression_tests/surface_source/surface_source_true.h5 differ
diff --git a/tests/regression_tests/surface_source/test.py b/tests/regression_tests/surface_source/test.py
new file mode 100644
--- /dev/null
+++ b/tests/regression_tests/surface_source/test.py
@@ -0,0 +1,125 @@
+import os
+
+import h5py
+import numpy as np
+import pytest
+import openmc
+
+from tests.testing_harness import PyAPITestHarness
+
+
[email protected]
+def model(request):
+ openmc.reset_auto_ids()
+ marker = request.node.get_closest_marker("surf_source_op")
+ surf_source_op = marker.args[0]
+
+ openmc_model = openmc.model.Model()
+
+ # Materials
+ # None
+
+ # Geometry
+ # Concentric void spheres
+ # - Innermost sphere to bank surface sources
+ # - Second shell to tally cell flux
+ # - Outermost sphere as vacuum boundary
+ sph_1 = openmc.Sphere(r=1.0) # Surface to bank/write sources.
+ sph_2 = openmc.Sphere(r=2.0)
+ sph_3 = openmc.Sphere(r=2.5)
+ sph_4 = openmc.Sphere(r=4.0, boundary_type='vacuum')
+ cell_1 = openmc.Cell(region=-sph_1)
+ cell_2 = openmc.Cell(region=+sph_1&-sph_2)
+ cell_3 = openmc.Cell(region=+sph_2&-sph_3) # Cell to tally flux.
+ cell_4 = openmc.Cell(region=+sph_3&-sph_4)
+ root = openmc.Universe(cells=[cell_1, cell_2, cell_3, cell_4])
+ openmc_model.geometry = openmc.Geometry(root)
+
+ # Settings
+ openmc_model.settings.run_mode = 'fixed source'
+ openmc_model.settings.particles = 1000
+ openmc_model.settings.batches = 10
+ openmc_model.settings.seed = 1
+
+ if surf_source_op == 'write':
+ point = openmc.stats.Point((0, 0, 0))
+ pt_src = openmc.Source(space=point)
+ openmc_model.settings.source = pt_src
+
+ openmc_model.settings.surf_source_write = {'surface_ids': [1],
+ 'max_particles': 1000}
+ elif surf_source_op == 'read':
+ openmc_model.settings.surf_source_read = {'path': 'surface_source_true.h5'}
+
+ # Tallies
+ tal = openmc.Tally()
+ cell_filter = openmc.CellFilter(cell_3)
+ tal.filters = [cell_filter]
+ tal.scores = ['flux']
+ openmc_model.tallies.append(tal)
+
+ return openmc_model
+
+
+class SurfaceSourceTestHarness(PyAPITestHarness):
+ def _test_output_created(self):
+ """Make sure surface_source.h5 has also been created."""
+ super()._test_output_created()
+ # Check if 'surface_source.h5' has been created.
+ if self._model.settings.surf_source_write:
+ assert os.path.exists('surface_source.h5'), \
+ 'Surface source file does not exist.'
+
+ def _compare_output(self):
+ """Make sure the current surface_source.h5 agree with the reference."""
+ if self._model.settings.surf_source_write:
+ with h5py.File("surface_source_true.h5", 'r') as f:
+ source_true = f['source_bank'][()]
+ # Convert dtye from mixed to a float for comparison assertion
+ source_true.dtype = 'float64'
+ with h5py.File("surface_source.h5", 'r') as f:
+ source_test = f['source_bank'][()]
+ # Convert dtye from mixed to a float for comparison assertion
+ source_test.dtype = 'float64'
+ np.testing.assert_allclose(np.sort(source_true),
+ np.sort(source_test),
+ atol=1e-07)
+
+ def execute_test(self):
+ """Build input XMLs, run OpenMC, check output and results."""
+ try:
+ self._build_inputs()
+ inputs = self._get_inputs()
+ self._write_inputs(inputs)
+ self._compare_inputs()
+ self._run_openmc()
+ self._test_output_created()
+ self._compare_output()
+ results = self._get_results()
+ self._write_results(results)
+ self._compare_results()
+ finally:
+ self._cleanup()
+
+ def _cleanup(self):
+ """Delete statepoints, tally, and test files."""
+ super()._cleanup()
+ fs = 'surface_source.h5'
+ if os.path.exists(fs):
+ os.remove(fs)
+
+
[email protected]_source_op('write')
+def test_surface_source_write(model):
+ harness = SurfaceSourceTestHarness('statepoint.10.h5',
+ model,
+ 'inputs_true_write.dat')
+ harness.main()
+
+
[email protected]_source_op('read')
+def test_surface_source_read(model):
+ harness = SurfaceSourceTestHarness('statepoint.10.h5',
+ model,
+ 'inputs_true_read.dat')
+ harness.main()
diff --git a/tests/unit_tests/test_settings.py b/tests/unit_tests/test_settings.py
--- a/tests/unit_tests/test_settings.py
+++ b/tests/unit_tests/test_settings.py
@@ -20,6 +20,8 @@ def test_export_to_xml(run_in_tmpdir):
s.sourcepoint = {'batches': [50, 150, 500, 1000], 'separate': True,
'write': True, 'overwrite': True}
s.statepoint = {'batches': [50, 150, 500, 1000]}
+ s.surf_source_read = {'path': 'surface_source_1.h5'}
+ s.surf_source_write = {'surface_ids': [2], 'max_particles': 200}
s.confidence_intervals = True
s.ptables = True
s.seed = 17
@@ -76,6 +78,8 @@ def test_export_to_xml(run_in_tmpdir):
assert s.sourcepoint == {'batches': [50, 150, 500, 1000], 'separate': True,
'write': True, 'overwrite': True}
assert s.statepoint == {'batches': [50, 150, 500, 1000]}
+ assert s.surf_source_read == {'path': 'surface_source_1.h5'}
+ assert s.surf_source_write == {'surface_ids': [2], 'max_particles': 200}
assert s.confidence_intervals
assert s.ptables
assert s.seed == 17
| Feature addition: Surface source
Having the capability of banking particles crossing user-defined surfaces and reading them in different simulations as a source (similar to MCNP's SSW/SSR cards) would be useful in designing localized geometry without having to run the full geometry every time the local design changes.
Related paper: Paul P. H. Wilson and Patrick Snouffer, "A MONTE CARLO SURFACE SOURCE METHOD FOR ADVANCED TEST REACTOR EXPERIMENT PROTOTYPING", PHYSOR2010 (2010)
I am currently working on it, and I will create a relevant PR in the future.
Any comments or suggestions would be much appreciated!
| 2020-08-12T04:02:05Z | [] | [] |
|
openmc-dev/openmc | 1,679 | openmc-dev__openmc-1679 | [
"1672"
] | 8ed15a83e60847ee3ec45bb8176d7c20593ffc98 | diff --git a/openmc/data/decay.py b/openmc/data/decay.py
--- a/openmc/data/decay.py
+++ b/openmc/data/decay.py
@@ -298,6 +298,8 @@ class Decay(EqualityMixin):
applications.
decay_constant : uncertainties.UFloat
Decay constant in inverse seconds.
+ decay_energy : uncertainties.UFloat
+ Average energy in [eV] per decay for decay heat applications
half_life : uncertainties.UFloat
Half-life of the decay in seconds.
modes : list
@@ -347,7 +349,7 @@ def __init__(self, ev_or_filename):
items, values = get_list_record(file_obj)
self.half_life = ufloat(items[0], items[1])
NC = items[4]//2
- pairs = [x for x in zip(values[::2], values[1::2])]
+ pairs = list(zip(values[::2], values[1::2]))
ex = self.average_energies
ex['light'] = ufloat(*pairs[0])
ex['electromagnetic'] = ufloat(*pairs[1])
@@ -359,7 +361,7 @@ def __init__(self, ev_or_filename):
ex['conversion'] = ufloat(*pairs[6])
ex['gamma'] = ufloat(*pairs[7])
ex['xray'] = ufloat(*pairs[8])
- ex['Bremsstrahlung'] = ufloat(*pairs[9])
+ ex['bremsstrahlung'] = ufloat(*pairs[9])
ex['annihilation'] = ufloat(*pairs[10])
ex['alpha'] = ufloat(*pairs[11])
ex['recoil'] = ufloat(*pairs[12])
@@ -464,6 +466,14 @@ def decay_constant(self):
mu, sigma = self.half_life
return ufloat(log(2.)/mu, log(2.)/mu**2*sigma)
+ @property
+ def decay_energy(self):
+ energy = self.average_energies
+ if energy:
+ return energy['light'] + energy['electromagnetic'] + energy['heavy']
+ else:
+ return ufloat(0, 0)
+
@classmethod
def from_endf(cls, ev_or_filename):
"""Generate radioactive decay data from an ENDF evaluation
diff --git a/openmc/deplete/chain.py b/openmc/deplete/chain.py
--- a/openmc/deplete/chain.py
+++ b/openmc/deplete/chain.py
@@ -395,8 +395,7 @@ def from_endf(cls, decay_files, fpy_files, neutron_files,
if not data.nuclide['stable'] and data.half_life.nominal_value != 0.0:
nuclide.half_life = data.half_life.nominal_value
- nuclide.decay_energy = sum(E.nominal_value for E in
- data.average_energies.values())
+ nuclide.decay_energy = data.decay_energy.nominal_value
sum_br = 0.0
for i, mode in enumerate(data.modes):
type_ = ','.join(mode.modes)
| diff --git a/tests/unit_tests/test_data_decay.py b/tests/unit_tests/test_data_decay.py
--- a/tests/unit_tests/test_data_decay.py
+++ b/tests/unit_tests/test_data_decay.py
@@ -34,7 +34,7 @@ def u235_yields():
def test_nb90_halflife(nb90):
ufloat_close(nb90.half_life, ufloat(52560.0, 180.0))
ufloat_close(nb90.decay_constant, log(2.)/nb90.half_life)
-
+ ufloat_close(nb90.decay_energy, ufloat(2265527.5, 25159.400474401213))
def test_nb90_nuclide(nb90):
assert nb90.nuclide['atomic_number'] == 41
| Reading Beta-decay energies from ENDF format files
I'm currently working on my depletion code validation with residual heat tests and using data generated by `chain = openmc.deplete.Chain.from_endf(decay_files, nfy_files, neutron_files)`. I initially started with endfb-vii.1 library and results was fine except the first 10 seconds of heat measurement then i switched to jeff 3.3 lib and results have changed extrmely. As I supposed the main reason is the value of decay energy calculated as follows: `nuclide.decay_energy = sum(E.nominal_value for E in data.average_energies.values())` (openmc/depletion/chain.py:398) with average_energies were read from *.endf file `ex = self.average_energies
ex['light'] = ufloat(*pairs[0])
ex['electromagnetic'] = ufloat(*pairs[1])
ex['heavy'] = ufloat(*pairs[2])
if NC == 17:
ex['beta-'] = ufloat(*pairs[3])
ex['beta+'] = ufloat(*pairs[4])
ex['auger'] = ufloat(*pairs[5])
ex['conversion'] = ufloat(*pairs[6])
ex['gamma'] = ufloat(*pairs[7])
ex['xray'] = ufloat(*pairs[8])
ex['Bremsstrahlung'] = ufloat(*pairs[9])
ex['annihilation'] = ufloat(*pairs[10])
ex['alpha'] = ufloat(*pairs[11])
ex['recoil'] = ufloat(*pairs[12])
ex['SF'] = ufloat(*pairs[13])
ex['neutron'] = ufloat(*pairs[14])
ex['proton'] = ufloat(*pairs[15])
ex['neutrino'] = ufloat(*pairs[16])`
(openmc/data/decay.py:351)
Where the endfb lib contains only the first three records('light', 'electromagnetic', 'heavy') but the jeff along with these contains the rest 14 records.
It seems to me to duplicating take places by simple sum over these 17 values in the case with jeff3.3 lib.
I can fix it but i don't know how to do it properly.
@paulromano
@drewejohnson
| Thanks for reporting this @dryuri92. Your assessment is exactly right. I'll submit a pull request to fix this issue. | 2020-10-05T20:43:10Z | [] | [] |
openmc-dev/openmc | 1,732 | openmc-dev__openmc-1732 | [
"1713"
] | 18af12925a99866b6d07e6769ac2346b4c5085ba | diff --git a/openmc/deplete/results_list.py b/openmc/deplete/results_list.py
--- a/openmc/deplete/results_list.py
+++ b/openmc/deplete/results_list.py
@@ -1,8 +1,12 @@
+import numbers
+import bisect
+import math
+
import h5py
import numpy as np
from .results import Results, VERSION_RESULTS
-from openmc.checkvalue import check_filetype_version, check_value
+from openmc.checkvalue import check_filetype_version, check_value, check_type
__all__ = ["ResultsList"]
@@ -192,3 +196,103 @@ def get_depletion_time(self):
for ix, res in enumerate(items):
times[ix] = res.proc_time
return times
+
+ def get_times(self, time_units="d") -> np.ndarray:
+ """Return the points in time that define the depletion schedule
+
+
+ .. versionadded:: 0.12.1
+
+ Parameters
+ ----------
+ time_units : {"s", "d", "h", "min"}, optional
+ Return the vector in these units. Default is to
+ convert to days
+
+ Returns
+ -------
+ numpy.ndarray
+ 1-D vector of time points
+
+ """
+ check_type("time_units", time_units, str)
+
+ times = np.fromiter(
+ (r.time[0] for r in self),
+ dtype=self[0].time.dtype,
+ count=len(self),
+ )
+
+ if time_units == "d":
+ times /= (60 * 60 * 24)
+ elif time_units == "h":
+ times /= (60 * 60)
+ elif time_units == "min":
+ times /= 60
+ elif time_units != "s":
+ raise ValueError(
+ 'Unable to set "time_units" to {} since it is not '
+ 'in ("s", "d", "min", "h")'.format(time_units)
+ )
+ return times
+
+ def get_step_where(
+ self, time, time_units="d", atol=1e-6, rtol=1e-3
+ ) -> int:
+ """Return the index closest to a given point in time
+
+ In the event ``time`` lies exactly between two points, the
+ lower index will be returned. It is possible that the index
+ will be at most one past the point in time requested, but only
+ according to tolerances requested.
+
+ Passing ``atol=math.inf`` and ``rtol=math.inf`` will return
+ the closest index to the requested point.
+
+
+ .. versionadded:: 0.12.1
+
+ Parameters
+ ----------
+ time : float
+ Desired point in time
+ time_units : {"s", "d", "min", "h"}, optional
+ Units on ``time``. Default: days
+ atol : float, optional
+ Absolute tolerance (in ``time_units``) if ``time`` is not
+ found.
+ rtol : float, optional
+ Relative tolerance if ``time`` is not found.
+
+ Returns
+ -------
+ int
+
+ """
+ check_type("time", time, numbers.Real)
+ check_type("atol", atol, numbers.Real)
+ check_type("rtol", rtol, numbers.Real)
+
+ times = self.get_times(time_units)
+
+ if times[0] < time < times[-1]:
+ ix = bisect.bisect_left(times, time)
+ if ix == times.size:
+ ix -= 1
+ # Bisection will place us either directly on the point
+ # or one-past the first value less than time
+ elif time - times[ix - 1] <= times[ix] - time:
+ ix -= 1
+ elif times[0] >= time:
+ ix = 0
+ elif time >= times[-1]:
+ ix = times.size - 1
+
+ if math.isclose(time, times[ix], rel_tol=rtol, abs_tol=atol):
+ return ix
+
+ raise ValueError(
+ "A value of {} {} was not found given absolute and "
+ "relative tolerances {} and {}.".format(
+ time, time_units, atol, rtol)
+ )
| diff --git a/tests/unit_tests/test_deplete_resultslist.py b/tests/unit_tests/test_deplete_resultslist.py
--- a/tests/unit_tests/test_deplete_resultslist.py
+++ b/tests/unit_tests/test_deplete_resultslist.py
@@ -1,6 +1,7 @@
"""Tests the ResultsList class"""
from pathlib import Path
+from math import inf
import numpy as np
import pytest
@@ -65,3 +66,66 @@ def test_get_eigenvalue(res):
np.testing.assert_allclose(t, t_ref)
np.testing.assert_allclose(k[:, 0], k_ref)
np.testing.assert_allclose(k[:, 1], u_ref)
+
+
[email protected]("unit", ("s", "d", "min", "h"))
+def test_get_steps(unit):
+ # Make a ResultsList full of near-empty Result instances
+ # Just fill out a time schedule
+ results = openmc.deplete.ResultsList()
+ # Time in units of unit
+ times = np.linspace(0, 100, num=5)
+ if unit == "d":
+ conversion_to_seconds = 60 * 60 * 24
+ elif unit == "h":
+ conversion_to_seconds = 60 * 60
+ elif unit == "min":
+ conversion_to_seconds = 60
+ else:
+ conversion_to_seconds = 1
+
+ for ix in range(times.size):
+ res = openmc.deplete.Results()
+ res.time = times[ix:ix + 1] * conversion_to_seconds
+ results.append(res)
+
+ for expected, value in enumerate(times):
+ actual = results.get_step_where(
+ value, time_units=unit, atol=0, rtol=0)
+ assert actual == expected, (value, results[actual].time[0])
+
+ with pytest.raises(ValueError):
+ # Emulate a result file with a non-zero initial point in time
+ # as in starting from a restart
+ results.get_step_where(times[0] - 1, time_units=unit, atol=0, rtol=0)
+
+ with pytest.raises(ValueError):
+ results.get_step_where(times[-1] + 1, time_units=unit, atol=0, rtol=0)
+
+ # Grab intermediate points with a small offset
+ delta = (times[1] - times[0])
+ offset = delta * 0.1
+ for expected, value in enumerate(times[1:-1], start=1):
+ # Shoot a little low and a little high
+ for mult in (1, -1):
+ target = value + mult * offset
+ # Compare using absolute and relative tolerances
+ actual = results.get_step_where(
+ target, time_units=unit, atol=offset * 2, rtol=inf)
+ assert actual == expected, (
+ target, times[actual], times[expected], offset)
+
+ actual = results.get_step_where(
+ target, time_units=unit, atol=inf, rtol=offset / value)
+ assert actual == expected, (
+ target, times[actual], times[expected], offset)
+ # Check that the lower index is returned for the exact mid-point
+ target = value + delta * 0.5
+ actual = results.get_step_where(
+ target, time_units=unit, atol=delta, rtol=delta / value)
+ assert actual == expected
+
+ # Shoot way over with no tolerance -> just give closest value
+ actual = results.get_step_where(
+ times[-1] * 100, time_units=unit, atol=inf, rtol=inf)
+ assert actual == times.size - 1
| Feature: Easier indexing through ResultsList to find depletion step index
If a user wanted to perform a restart simulation not necessarily at the end point in time, there isn't a super simple way to do it from the API. Currently you would have to manually search through the `Result` instances and compare their time data one at a time.
This isn't a monumental task, and I think we could easily provide a method that would allow users to find the index corresponding to a specific point in time. Supporting similar `time_units` like we do for the `Operator` (days, seconds, MWd/kgHM) would also be super nice.
Looking at #1708, this would also be useful when exporting `material.xml` files either during the depletion run or after the fact. Either way, the user will need a way to link a depletion step to a point in calendar time for restarting or other analysis.
Other things to consider would be some tolerance on the search criteria. If I ask for the step where burnup was 12 MWd/kgHM, (for example), but the closest point is 12.1 MWd/kgHM, should that step be returned? Or error out?
| 2020-12-04T16:49:24Z | [] | [] |
|
openmc-dev/openmc | 1,931 | openmc-dev__openmc-1931 | [
"1653"
] | d12e390f1a365c8e5b92e586cb8dc7a4599e80d2 | diff --git a/openmc/lib/mesh.py b/openmc/lib/mesh.py
--- a/openmc/lib/mesh.py
+++ b/openmc/lib/mesh.py
@@ -11,7 +11,7 @@
from .core import _FortranObjectWithID
from .error import _error_handler
-__all__ = ['RegularMesh', 'RectilinearMesh', 'meshes']
+__all__ = ['RegularMesh', 'RectilinearMesh', 'CylindricalMesh', 'SphericalMesh', 'meshes']
# Mesh functions
_dll.openmc_extend_meshes.argtypes = [c_int32, c_char_p, POINTER(c_int32),
@@ -56,6 +56,26 @@
_dll.openmc_regular_mesh_set_params.restype = c_int
_dll.openmc_regular_mesh_set_params.errcheck = _error_handler
+_dll.openmc_cylindrical_mesh_get_grid.argtypes = [c_int32,
+ POINTER(POINTER(c_double)), POINTER(c_int), POINTER(POINTER(c_double)),
+ POINTER(c_int), POINTER(POINTER(c_double)), POINTER(c_int)]
+_dll.openmc_cylindrical_mesh_get_grid.restype = c_int
+_dll.openmc_cylindrical_mesh_get_grid.errcheck = _error_handler
+_dll.openmc_cylindrical_mesh_set_grid.argtypes = [c_int32, POINTER(c_double),
+ c_int, POINTER(c_double), c_int, POINTER(c_double), c_int]
+_dll.openmc_cylindrical_mesh_set_grid.restype = c_int
+_dll.openmc_cylindrical_mesh_set_grid.errcheck = _error_handler
+
+_dll.openmc_spherical_mesh_get_grid.argtypes = [c_int32,
+ POINTER(POINTER(c_double)), POINTER(c_int), POINTER(POINTER(c_double)),
+ POINTER(c_int), POINTER(POINTER(c_double)), POINTER(c_int)]
+_dll.openmc_spherical_mesh_get_grid.restype = c_int
+_dll.openmc_spherical_mesh_get_grid.errcheck = _error_handler
+_dll.openmc_spherical_mesh_set_grid.argtypes = [c_int32, POINTER(c_double),
+ c_int, POINTER(c_double), c_int, POINTER(c_double), c_int]
+_dll.openmc_spherical_mesh_set_grid.restype = c_int
+_dll.openmc_spherical_mesh_set_grid.errcheck = _error_handler
+
class Mesh(_FortranObjectWithID):
"""Base class to represent mesh objects
@@ -275,9 +295,184 @@ def set_grid(self, x_grid, y_grid, z_grid):
ny, z_grid, nz)
+class CylindricalMesh(Mesh):
+ """CylindricalMesh stored internally.
+
+ This class exposes a mesh that is stored internally in the OpenMC
+ library. To obtain a view of a mesh with a given ID, use the
+ :data:`openmc.lib.meshes` mapping.
+
+ Parameters
+ ----------
+ index : int
+ Index in the `meshes` array.
+
+ Attributes
+ ----------
+ id : int
+ ID of the mesh
+ dimension : iterable of int
+ The number of mesh cells in each direction.
+ lower_left : numpy.ndarray
+ The lower-left corner of the structured mesh.
+ upper_right : numpy.ndarray
+ The upper-right corner of the structrued mesh.
+ width : numpy.ndarray
+ The width of mesh cells in each direction.
+
+ """
+ mesh_type = 'cylindrical'
+
+ def __init__(self, uid=None, new=True, index=None):
+ super().__init__(uid, new, index)
+
+ @property
+ def lower_left(self):
+ return self._get_parameters()[0]
+
+ @property
+ def upper_right(self):
+ return self._get_parameters()[1]
+
+ @property
+ def dimension(self):
+ return self._get_parameters()[2]
+
+ @property
+ def width(self):
+ return self._get_parameters()[3]
+
+ def _get_parameters(self):
+ gx = POINTER(c_double)()
+ nx = c_int()
+ gy = POINTER(c_double)()
+ ny = c_int()
+ gz = POINTER(c_double)()
+ nz = c_int()
+ # Call C API to get grid parameters
+ _dll.openmc_cylindrical_mesh_get_grid(self._index, gx, nx, gy, ny, gz,
+ nz)
+
+ # Convert grid parameters to Numpy arrays
+ grid_x = as_array(gx, (nx.value,))
+ grid_y = as_array(gy, (ny.value,))
+ grid_z = as_array(gz, (nz.value,))
+
+ # Calculate lower_left, upper_right, width, and dimension from grid
+ lower_left = np.array((grid_x[0], grid_y[0], grid_z[0]))
+ upper_right = np.array((grid_x[-1], grid_y[-1], grid_z[-1]))
+ dimension = np.array((nx.value - 1, ny.value - 1, nz.value - 1))
+ width = np.zeros(list(dimension) + [3])
+
+ for i, diff_x in enumerate(np.diff(grid_x)):
+ for j, diff_y in enumerate(np.diff(grid_y)):
+ for k, diff_z in enumerate(np.diff(grid_z)):
+ width[i, j, k, :] = diff_x, diff_y, diff_z
+
+ return (lower_left, upper_right, dimension, width)
+
+ def set_grid(self, x_grid, y_grid, z_grid):
+ nx = len(x_grid)
+ x_grid = (c_double*nx)(*x_grid)
+ ny = len(y_grid)
+ y_grid = (c_double*ny)(*y_grid)
+ nz = len(z_grid)
+ z_grid = (c_double*nz)(*z_grid)
+ _dll.openmc_cylindrical_mesh_set_grid(self._index, x_grid, nx, y_grid,
+ ny, z_grid, nz)
+
+class SphericalMesh(Mesh):
+ """SphericalMesh stored internally.
+
+ This class exposes a mesh that is stored internally in the OpenMC
+ library. To obtain a view of a mesh with a given ID, use the
+ :data:`openmc.lib.meshes` mapping.
+
+ Parameters
+ ----------
+ index : int
+ Index in the `meshes` array.
+
+ Attributes
+ ----------
+ id : int
+ ID of the mesh
+ dimension : iterable of int
+ The number of mesh cells in each direction.
+ lower_left : numpy.ndarray
+ The lower-left corner of the structured mesh.
+ upper_right : numpy.ndarray
+ The upper-right corner of the structrued mesh.
+ width : numpy.ndarray
+ The width of mesh cells in each direction.
+
+ """
+ mesh_type = 'spherical'
+
+ def __init__(self, uid=None, new=True, index=None):
+ super().__init__(uid, new, index)
+
+ @property
+ def lower_left(self):
+ return self._get_parameters()[0]
+
+ @property
+ def upper_right(self):
+ return self._get_parameters()[1]
+
+ @property
+ def dimension(self):
+ return self._get_parameters()[2]
+
+ @property
+ def width(self):
+ return self._get_parameters()[3]
+
+ def _get_parameters(self):
+ gx = POINTER(c_double)()
+ nx = c_int()
+ gy = POINTER(c_double)()
+ ny = c_int()
+ gz = POINTER(c_double)()
+ nz = c_int()
+ # Call C API to get grid parameters
+ _dll.openmc_spherical_mesh_get_grid(self._index, gx, nx, gy, ny, gz,
+ nz)
+
+ # Convert grid parameters to Numpy arrays
+ grid_x = as_array(gx, (nx.value,))
+ grid_y = as_array(gy, (ny.value,))
+ grid_z = as_array(gz, (nz.value,))
+
+ # Calculate lower_left, upper_right, width, and dimension from grid
+ lower_left = np.array((grid_x[0], grid_y[0], grid_z[0]))
+ upper_right = np.array((grid_x[-1], grid_y[-1], grid_z[-1]))
+ dimension = np.array((nx.value - 1, ny.value - 1, nz.value - 1))
+ width = np.zeros(list(dimension) + [3])
+
+ for i, diff_x in enumerate(np.diff(grid_x)):
+ for j, diff_y in enumerate(np.diff(grid_y)):
+ for k, diff_z in enumerate(np.diff(grid_z)):
+ width[i, j, k, :] = diff_x, diff_y, diff_z
+
+ return (lower_left, upper_right, dimension, width)
+
+ def set_grid(self, x_grid, y_grid, z_grid):
+ nx = len(x_grid)
+ x_grid = (c_double*nx)(*x_grid)
+ ny = len(y_grid)
+ y_grid = (c_double*ny)(*y_grid)
+ nz = len(z_grid)
+ z_grid = (c_double*nz)(*z_grid)
+ _dll.openmc_spherical_mesh_set_grid(self._index, x_grid, nx, y_grid,
+ ny, z_grid, nz)
+
+
_MESH_TYPE_MAP = {
'regular': RegularMesh,
- 'rectilinear': RectilinearMesh
+ 'rectilinear': RectilinearMesh,
+ 'cylindrical': CylindricalMesh,
+ 'spherical': SphericalMesh
}
diff --git a/openmc/mesh.py b/openmc/mesh.py
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -79,6 +79,10 @@ def from_hdf5(cls, group):
return RegularMesh.from_hdf5(group)
elif mesh_type == 'rectilinear':
return RectilinearMesh.from_hdf5(group)
+ elif mesh_type == 'cylindrical':
+ return CylindricalMesh.from_hdf5(group)
+ elif mesh_type == 'spherical':
+ return SphericalMesh.from_hdf5(group)
elif mesh_type == 'unstructured':
return UnstructuredMesh.from_hdf5(group)
else:
@@ -624,6 +628,334 @@ def to_xml_element(self):
return element
+class CylindricalMesh(MeshBase):
+ """A 3D cylindrical mesh
+
+ Parameters
+ ----------
+ mesh_id : int
+ Unique identifier for the mesh
+ name : str
+ Name of the mesh
+
+ Attributes
+ ----------
+ id : int
+ Unique identifier for the mesh
+ name : str
+ Name of the mesh
+ dimension : Iterable of int
+ The number of mesh cells in each direction.
+ n_dimension : int
+ Number of mesh dimensions (always 3 for a CylindricalMesh).
+ r_grid : Iterable of float
+ Mesh boundary points along the r-axis.
+ Requirement is r >= 0.
+ phi_grid : Iterable of float
+ Mesh boundary points along the phi-axis.
+ The default value is [0, 360], i.e. the full phi range.
+ z_grid : Iterable of float
+ Mesh boundary points along the z-axis.
+ indices : Iterable of tuple
+ An iterable of mesh indices for each mesh element, e.g. [(1, 1, 1),
+ (2, 1, 1), ...]
+
+ """
+
+ def __init__(self, mesh_id=None, name=''):
+ super().__init__(mesh_id, name)
+
+ self._r_grid = None
+ self._phi_grid = [0, 360]
+ self._z_grid = None
+
+ @property
+ def dimension(self):
+ return (len(self.r_grid) - 1,
+ len(self.phi_grid) - 1,
+ len(self.z_grid) - 1)
+
+ @property
+ def n_dimension(self):
+ return 3
+
+ @property
+ def r_grid(self):
+ return self._r_grid
+
+ @property
+ def phi_grid(self):
+ return self._phi_grid
+
+ @property
+ def z_grid(self):
+ return self._z_grid
+
+ @property
+ def indices(self):
+ nr, np, nz = self.dimension
+ np = len(self.phi_grid) - 1
+ nz = len(self.z_grid) - 1
+ return ((r, p, z)
+ for z in range(1, nz + 1)
+ for p in range(1, np + 1)
+ for r in range(1, nr + 1))
+
+ @r_grid.setter
+ def r_grid(self, grid):
+ cv.check_type('mesh r_grid', grid, Iterable, Real)
+ self._r_grid = grid
+
+ @phi_grid.setter
+ def phi_grid(self, grid):
+ cv.check_type('mesh phi_grid', grid, Iterable, Real)
+ self._phi_grid = np.array(grid)
+
+ @z_grid.setter
+ def z_grid(self, grid):
+ cv.check_type('mesh z_grid', grid, Iterable, Real)
+ self._z_grid = np.array(grid)
+
+ def __repr__(self):
+ fmt = '{0: <16}{1}{2}\n'
+ string = super().__repr__()
+ string += fmt.format('\tDimensions', '=\t', self.n_dimension)
+ r_grid_str = str(self._r_grid) if self._r_grid is None else len(self._r_grid)
+ string += fmt.format('\tN R pnts:', '=\t', r_grid_str)
+ if self._r_grid is not None:
+ string += fmt.format('\tR Min:', '=\t', self._r_grid[0])
+ string += fmt.format('\tR Max:', '=\t', self._r_grid[-1])
+ phi_grid_str = str(self._phi_grid) if self._phi_grid is None else len(self._phi_grid)
+ string += fmt.format('\tN Phi pnts:', '=\t', phi_grid_str)
+ if self._phi_grid is not None:
+ string += fmt.format('\tPhi Min:', '=\t', self._phi_grid[0])
+ string += fmt.format('\tPhi Max:', '=\t', self._phi_grid[-1])
+ z_grid_str = str(self._z_grid) if self._z_grid is None else len(self._z_grid)
+ string += fmt.format('\tN Z pnts:', '=\t', z_grid_str)
+ if self._z_grid is not None:
+ string += fmt.format('\tZ Min:', '=\t', self._z_grid[0])
+ string += fmt.format('\tZ Max:', '=\t', self._z_grid[-1])
+ return string
+
+ @classmethod
+ def from_hdf5(cls, group):
+ mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
+
+ # Read and assign mesh properties
+ mesh = cls(mesh_id)
+ mesh.r_grid = group['r_grid'][()]
+ mesh.phi_grid = 180 / np.pi * group['phi_grid'][()]
+ mesh.z_grid = group['z_grid'][()]
+
+ return mesh
+
+ def to_xml_element(self):
+ """Return XML representation of the mesh
+
+ Returns
+ -------
+ element : xml.etree.ElementTree.Element
+ XML element containing mesh data
+
+ """
+
+ element = ET.Element("mesh")
+ element.set("id", str(self._id))
+ element.set("type", "cylindrical")
+
+ subelement = ET.SubElement(element, "r_grid")
+ subelement.text = ' '.join(map(str, self.r_grid))
+
+ subelement = ET.SubElement(element, "phi_grid")
+ subelement.text = ' '.join(map(str, self.phi_grid))
+
+ subelement = ET.SubElement(element, "z_grid")
+ subelement.text = ' '.join(map(str, self.z_grid))
+
+ return element
+
+ def calc_mesh_volumes(self):
+ """Return Volumes for every mesh cell
+
+ Returns
+ -------
+ volumes : Iterable of float
+ Volumes
+
+ """
+
+ V_r = np.diff(np.array(self.r_grid)**2 / 2)
+ V_p = np.diff(np.array(self.phi_grid) * np.pi / 180.0)
+ V_z = np.diff(np.array(self.z_grid))
+
+ return np.multiply.outer(np.outer(V_r, V_p), V_z)
+
+
+class SphericalMesh(MeshBase):
+ """A 3D spherical mesh
+
+ Parameters
+ ----------
+ mesh_id : int
+ Unique identifier for the mesh
+ name : str
+ Name of the mesh
+
+ Attributes
+ ----------
+ id : int
+ Unique identifier for the mesh
+ name : str
+ Name of the mesh
+ dimension : Iterable of int
+ The number of mesh cells in each direction.
+ n_dimension : int
+ Number of mesh dimensions (always 3 for a SphericalMesh).
+ r_grid : Iterable of float
+ Mesh boundary points along the r-axis.
+ Requirement is r >= 0.
+ theta_grid : Iterable of float
+ Mesh boundary points along the theta-axis in degrees.
+ The default value is [0, 180], i.e. the full theta range.
+ phi_grid : Iterable of float
+ Mesh boundary points along the phi-axis in degrees.
+ The default value is [0, 360], i.e. the full phi range.
+ indices : Iterable of tuple
+ An iterable of mesh indices for each mesh element, e.g. [(1, 1, 1),
+ (2, 1, 1), ...]
+
+ """
+
+ def __init__(self, mesh_id=None, name=''):
+ super().__init__(mesh_id, name)
+
+ self._r_grid = None
+ self._theta_grid = [0, 180]
+ self._phi_grid = [0, 360]
+
+ @property
+ def dimension(self):
+ return (len(self.r_grid) - 1,
+ len(self.theta_grid) - 1,
+ len(self.phi_grid) - 1)
+
+ @property
+ def n_dimension(self):
+ return 3
+
+ @property
+ def r_grid(self):
+ return self._r_grid
+
+ @property
+ def theta_grid(self):
+ return self._theta_grid
+
+ @property
+ def phi_grid(self):
+ return self._phi_grid
+
+ @property
+ def indices(self):
+ nr, nt, np = self.dimension
+ nt = len(self.theta_grid) - 1
+ np = len(self.phi_grid) - 1
+ return ((r, t, p)
+ for p in range(1, np + 1)
+ for t in range(1, nt + 1)
+ for r in range(1, nr + 1))
+
+ @r_grid.setter
+ def r_grid(self, grid):
+ cv.check_type('mesh r_grid', grid, Iterable, Real)
+ self._r_grid = grid
+
+ @theta_grid.setter
+ def theta_grid(self, grid):
+ cv.check_type('mesh theta_grid', grid, Iterable, Real)
+ self._theta_grid = np.array(grid)
+
+ @phi_grid.setter
+ def phi_grid(self, grid):
+ cv.check_type('mesh phi_grid', grid, Iterable, Real)
+ self._phi_grid = np.array(grid)
+
+ def __repr__(self):
+ fmt = '{0: <16}{1}{2}\n'
+ string = super().__repr__()
+ string += fmt.format('\tDimensions', '=\t', self.n_dimension)
+ r_grid_str = str(self._r_grid) if not self._r_grid else len(self._r_grid)
+ string += fmt.format('\tN R pnts:', '=\t', r_grid_str)
+ if self._r_grid:
+ string += fmt.format('\tR Min:', '=\t', self._r_grid[0])
+ string += fmt.format('\tR Max:', '=\t', self._r_grid[-1])
+ theta_grid_str = str(self._theta_grid) if not self._theta_grid else len(self._theta_grid)
+ string += fmt.format('\tN Theta pnts:', '=\t', theta_grid_str)
+ if self._theta_grid:
+ string += fmt.format('\tTheta Min:', '=\t', self._theta_grid[0])
+ string += fmt.format('\tTheta Max:', '=\t', self._theta_grid[-1])
+ phi_grid_str = str(self._phi_grid) if not self._phi_grid else len(self._phi_grid)
+ string += fmt.format('\tN Phi pnts:', '=\t', phi_grid_str)
+ if self._phi_grid:
+ string += fmt.format('\tPhi Min:', '=\t', self._phi_grid[0])
+ string += fmt.format('\tPhi Max:', '=\t', self._phi_grid[-1])
+ return string
+
+ @classmethod
+ def from_hdf5(cls, group):
+ mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
+
+ # Read and assign mesh properties
+ mesh = cls(mesh_id)
+ mesh.r_grid = group['r_grid'][()]
+ mesh.theta_grid = 180 / np.pi * group['theta_grid'][()]
+ mesh.phi_grid = 180 / np.pi * group['phi_grid'][()]
+
+ return mesh
+
+ def to_xml_element(self):
+ """Return XML representation of the mesh
+
+ Returns
+ -------
+ element : xml.etree.ElementTree.Element
+ XML element containing mesh data
+
+ """
+
+ element = ET.Element("mesh")
+ element.set("id", str(self._id))
+ element.set("type", "spherical")
+
+ subelement = ET.SubElement(element, "r_grid")
+ subelement.text = ' '.join(map(str, self.r_grid))
+
+ subelement = ET.SubElement(element, "theta_grid")
+ subelement.text = ' '.join(map(str, self.theta_grid))
+
+ subelement = ET.SubElement(element, "phi_grid")
+ subelement.text = ' '.join(map(str, self.phi_grid))
+
+ return element
+
+ def calc_mesh_volumes(self):
+ """Return Volumes for every mesh cell
+
+ Returns
+ -------
+ volumes : Iterable of float
+ Volumes
+
+ """
+
+ V_r = np.diff(np.array(self.r_grid)**3 / 3)
+ V_t = np.diff(-np.cos(np.pi * np.array(self.theta_grid) / 180.0))
+ V_p = np.diff(np.array(self.phi_grid) * np.pi / 180)
+
+ return np.multiply.outer(np.outer(V_r, V_t), V_p)
+
+
+
class UnstructuredMesh(MeshBase):
"""A 3D unstructured mesh
| diff --git a/tests/regression_tests/filter_mesh/inputs_true.dat b/tests/regression_tests/filter_mesh/inputs_true.dat
--- a/tests/regression_tests/filter_mesh/inputs_true.dat
+++ b/tests/regression_tests/filter_mesh/inputs_true.dat
@@ -53,36 +53,58 @@
<y_grid>-7.5 -6.617647058823529 -5.735294117647059 -4.852941176470589 -3.9705882352941178 -3.0882352941176467 -2.2058823529411766 -1.3235294117647065 -0.4411764705882355 0.4411764705882355 1.3235294117647065 2.2058823529411757 3.0882352941176467 3.9705882352941178 4.852941176470587 5.735294117647058 6.617647058823529 7.5</y_grid>
<z_grid>1.0 1.223224374241637 1.4962778697388448 1.8302835609029084 2.2388474634702153 2.7386127875258306 3.3499379133114306 4.09772570775871 5.012437964687018 6.131336292779302 7.500000000000001</z_grid>
</mesh>
+ <mesh id="5" type="cylindrical">
+ <r_grid>0.0 0.4411764705882353 0.8823529411764706 1.3235294117647058 1.7647058823529411 2.2058823529411766 2.6470588235294117 3.0882352941176467 3.5294117647058822 3.9705882352941178 4.411764705882353 4.852941176470588 5.294117647058823 5.735294117647059 6.1764705882352935 6.617647058823529 7.0588235294117645 7.5</r_grid>
+ <phi_grid>0.0 20.0 40.0 60.0 80.0 100.0 120.0 140.0 160.0 180.0 200.0 220.0 240.0 260.0 280.0 300.0 320.0 340.0 360.0</phi_grid>
+ <z_grid>-7.5 -6.5625 -5.625 -4.6875 -3.75 -2.8125 -1.875 -0.9375 0.0 0.9375 1.875 2.8125 3.75 4.6875 5.625 6.5625 7.5</z_grid>
+ </mesh>
+ <mesh id="6" type="spherical">
+ <r_grid>0.0 0.4411764705882353 0.8823529411764706 1.3235294117647058 1.7647058823529411 2.2058823529411766 2.6470588235294117 3.0882352941176467 3.5294117647058822 3.9705882352941178 4.411764705882353 4.852941176470588 5.294117647058823 5.735294117647059 6.1764705882352935 6.617647058823529 7.0588235294117645 7.5</r_grid>
+ <theta_grid>0.0 22.5 45.0 67.5 90.0 112.5 135.0 157.5 180.0</theta_grid>
+ <phi_grid>0.0 20.0 40.0 60.0 80.0 100.0 120.0 140.0 160.0 180.0 200.0 220.0 240.0 260.0 280.0 300.0 320.0 340.0 360.0</phi_grid>
+ </mesh>
<filter id="1" type="mesh">
<bins>1</bins>
</filter>
- <filter id="5" type="meshsurface">
+ <filter id="7" type="meshsurface">
<bins>1</bins>
</filter>
<filter id="2" type="mesh">
<bins>2</bins>
</filter>
- <filter id="6" type="meshsurface">
+ <filter id="8" type="meshsurface">
<bins>2</bins>
</filter>
<filter id="3" type="mesh">
<bins>3</bins>
</filter>
- <filter id="7" type="meshsurface">
+ <filter id="9" type="meshsurface">
<bins>3</bins>
</filter>
<filter id="4" type="mesh">
<bins>4</bins>
</filter>
- <filter id="8" type="meshsurface">
+ <filter id="10" type="meshsurface">
<bins>4</bins>
</filter>
+ <filter id="5" type="mesh">
+ <bins>5</bins>
+ </filter>
+ <filter id="11" type="meshsurface">
+ <bins>5</bins>
+ </filter>
+ <filter id="6" type="mesh">
+ <bins>6</bins>
+ </filter>
+ <filter id="12" type="meshsurface">
+ <bins>6</bins>
+ </filter>
<tally id="1">
<filters>1</filters>
<scores>total</scores>
</tally>
<tally id="2">
- <filters>5</filters>
+ <filters>7</filters>
<scores>current</scores>
</tally>
<tally id="3">
@@ -90,7 +112,7 @@
<scores>total</scores>
</tally>
<tally id="4">
- <filters>6</filters>
+ <filters>8</filters>
<scores>current</scores>
</tally>
<tally id="5">
@@ -98,7 +120,7 @@
<scores>total</scores>
</tally>
<tally id="6">
- <filters>7</filters>
+ <filters>9</filters>
<scores>current</scores>
</tally>
<tally id="7">
@@ -106,7 +128,23 @@
<scores>total</scores>
</tally>
<tally id="8">
- <filters>8</filters>
+ <filters>10</filters>
+ <scores>current</scores>
+ </tally>
+ <tally id="9">
+ <filters>5</filters>
+ <scores>total</scores>
+ </tally>
+ <tally id="10">
+ <filters>11</filters>
+ <scores>current</scores>
+ </tally>
+ <tally id="11">
+ <filters>6</filters>
+ <scores>total</scores>
+ </tally>
+ <tally id="12">
+ <filters>12</filters>
<scores>current</scores>
</tally>
</tallies>
diff --git a/tests/regression_tests/filter_mesh/results_true.dat b/tests/regression_tests/filter_mesh/results_true.dat
--- a/tests/regression_tests/filter_mesh/results_true.dat
+++ b/tests/regression_tests/filter_mesh/results_true.dat
@@ -1 +1 @@
-97cf099a24099d2af794752e145841a9ef9f24980c53ee71e3fdd400d4249a7e6f3f52f63132fe2fe8d1973604a72d87910ab13bc3721f7d0bec533b87756847
\ No newline at end of file
+6e02d01fc115c54e4c60477a9f963149bc83c82e6a7bdb2d29125b131546150c59de5ac3aae5b9469b89b343ecf2574f6c949b918ccb43231e8666ee2b7c1b7c
\ No newline at end of file
diff --git a/tests/regression_tests/filter_mesh/test.py b/tests/regression_tests/filter_mesh/test.py
--- a/tests/regression_tests/filter_mesh/test.py
+++ b/tests/regression_tests/filter_mesh/test.py
@@ -51,18 +51,32 @@ def model():
recti_mesh.y_grid = np.linspace(-7.5, 7.5, 18)
recti_mesh.z_grid = np.logspace(0, np.log10(7.5), 11)
+ cyl_mesh = openmc.CylindricalMesh()
+ cyl_mesh.r_grid = np.linspace(0, 7.5, 18)
+ cyl_mesh.phi_grid = np.linspace(0, 360, 19)
+ cyl_mesh.z_grid = np.linspace(-7.5, 7.5, 17)
+
+ sph_mesh = openmc.SphericalMesh()
+ sph_mesh.r_grid = np.linspace(0, 7.5, 18)
+ sph_mesh.theta_grid = np.linspace(0, 180, 9)
+ sph_mesh.phi_grid = np.linspace(0, 360, 19)
+
# Create filters
reg_filters = [
openmc.MeshFilter(mesh_1d),
openmc.MeshFilter(mesh_2d),
openmc.MeshFilter(mesh_3d),
- openmc.MeshFilter(recti_mesh)
+ openmc.MeshFilter(recti_mesh),
+ openmc.MeshFilter(cyl_mesh),
+ openmc.MeshFilter(sph_mesh)
]
surf_filters = [
openmc.MeshSurfaceFilter(mesh_1d),
openmc.MeshSurfaceFilter(mesh_2d),
openmc.MeshSurfaceFilter(mesh_3d),
- openmc.MeshSurfaceFilter(recti_mesh)
+ openmc.MeshSurfaceFilter(recti_mesh),
+ openmc.MeshSurfaceFilter(cyl_mesh),
+ openmc.MeshSurfaceFilter(sph_mesh)
]
# Create tallies
diff --git a/tests/regression_tests/mgxs_library_mesh/results_true.dat b/tests/regression_tests/mgxs_library_mesh/results_true.dat
--- a/tests/regression_tests/mgxs_library_mesh/results_true.dat
+++ b/tests/regression_tests/mgxs_library_mesh/results_true.dat
@@ -181,11 +181,11 @@
mesh 1 group in nuclide mean std. dev.
x y surf
3 1 1 x-max in 1 total 0.1816 0.006129
-2 1 1 x-max out 1 total 0.2718 0.095077
+2 1 1 x-max out 1 total 0.1730 0.004382
1 1 1 x-min in 1 total 0.0000 0.000000
0 1 1 x-min out 1 total 0.0000 0.000000
7 1 1 y-max in 1 total 0.1790 0.011921
-6 1 1 y-max out 1 total 0.2290 0.034821
+6 1 1 y-max out 1 total 0.1802 0.016599
5 1 1 y-min in 1 total 0.0000 0.000000
4 1 1 y-min out 1 total 0.0000 0.000000
19 1 2 x-max in 1 total 0.1872 0.012447
@@ -194,23 +194,23 @@
16 1 2 x-min out 1 total 0.0000 0.000000
23 1 2 y-max in 1 total 0.0000 0.000000
22 1 2 y-max out 1 total 0.0000 0.000000
-21 1 2 y-min in 1 total 0.2290 0.034821
+21 1 2 y-min in 1 total 0.1802 0.016599
20 1 2 y-min out 1 total 0.1790 0.011921
11 2 1 x-max in 1 total 0.0000 0.000000
10 2 1 x-max out 1 total 0.0000 0.000000
-9 2 1 x-min in 1 total 0.2718 0.095077
+9 2 1 x-min in 1 total 0.1730 0.004382
8 2 1 x-min out 1 total 0.1816 0.006129
15 2 1 y-max in 1 total 0.1778 0.009484
-14 2 1 y-max out 1 total 0.2326 0.042782
+14 2 1 y-max out 1 total 0.1822 0.010077
13 2 1 y-min in 1 total 0.0000 0.000000
12 2 1 y-min out 1 total 0.0000 0.000000
27 2 2 x-max in 1 total 0.0000 0.000000
-26 2 2 x-max out 1 total 0.0260 0.026000
+26 2 2 x-max out 1 total 0.0000 0.000000
25 2 2 x-min in 1 total 0.1952 0.015948
24 2 2 x-min out 1 total 0.1872 0.012447
31 2 2 y-max in 1 total 0.0000 0.000000
-30 2 2 y-max out 1 total 0.0244 0.024400
-29 2 2 y-min in 1 total 0.2326 0.042782
+30 2 2 y-max out 1 total 0.0000 0.000000
+29 2 2 y-min in 1 total 0.1822 0.010077
28 2 2 y-min out 1 total 0.1778 0.009484
mesh 1 group in nuclide mean std. dev.
x y z
diff --git a/tests/unit_tests/test_lib.py b/tests/unit_tests/test_lib.py
--- a/tests/unit_tests/test_lib.py
+++ b/tests/unit_tests/test_lib.py
@@ -580,6 +580,68 @@ def test_rectilinear_mesh(lib_init):
msf = openmc.lib.MeshSurfaceFilter(mesh)
assert msf.mesh == mesh
+def test_cylindrical_mesh(lib_init):
+ deg2rad = lambda deg: deg*np.pi/180
+ mesh = openmc.lib.CylindricalMesh()
+ x_grid = [0., 5., 10.]
+ y_grid = [0., 10., 20.]
+ z_grid = [10., 20., 30.]
+ mesh.set_grid(x_grid, y_grid, z_grid)
+ assert np.all(mesh.lower_left == (0., 0., 10.))
+ assert np.all(mesh.upper_right == (10., deg2rad(20.), 30.))
+ assert np.all(mesh.dimension == (2, 2, 2))
+ for i, diff_x in enumerate(np.diff(x_grid)):
+ for j, diff_y in enumerate(np.diff(y_grid)):
+ for k, diff_z in enumerate(np.diff(z_grid)):
+ assert np.all(mesh.width[i, j, k, :] == (5, deg2rad(10), 10))
+
+ with pytest.raises(exc.AllocationError):
+ mesh2 = openmc.lib.CylindricalMesh(mesh.id)
+
+ meshes = openmc.lib.meshes
+ assert isinstance(meshes, Mapping)
+ assert len(meshes) == 3
+
+ mesh = meshes[mesh.id]
+ assert isinstance(mesh, openmc.lib.CylindricalMesh)
+
+ mf = openmc.lib.MeshFilter(mesh)
+ assert mf.mesh == mesh
+
+ msf = openmc.lib.MeshSurfaceFilter(mesh)
+ assert msf.mesh == mesh
+
+def test_spherical_mesh(lib_init):
+ deg2rad = lambda deg: deg*np.pi/180
+ mesh = openmc.lib.SphericalMesh()
+ x_grid = [0., 5., 10.]
+ y_grid = [0., 10., 20.]
+ z_grid = [10., 20., 30.]
+ mesh.set_grid(x_grid, y_grid, z_grid)
+ assert np.all(mesh.lower_left == (0., 0., deg2rad(10.)))
+ assert np.all(mesh.upper_right == (10., deg2rad(20.), deg2rad(30.)))
+ assert np.all(mesh.dimension == (2, 2, 2))
+ for i, diff_x in enumerate(np.diff(x_grid)):
+ for j, diff_y in enumerate(np.diff(y_grid)):
+ for k, diff_z in enumerate(np.diff(z_grid)):
+ assert np.all(abs(mesh.width[i, j, k, :] - (5, deg2rad(10), deg2rad(10))) < 1e-16)
+
+ with pytest.raises(exc.AllocationError):
+ mesh2 = openmc.lib.SphericalMesh(mesh.id)
+
+ meshes = openmc.lib.meshes
+ assert isinstance(meshes, Mapping)
+ assert len(meshes) == 4
+
+ mesh = meshes[mesh.id]
+ assert isinstance(mesh, openmc.lib.SphericalMesh)
+
+ mf = openmc.lib.MeshFilter(mesh)
+ assert mf.mesh == mesh
+
+ msf = openmc.lib.MeshSurfaceFilter(mesh)
+ assert msf.mesh == mesh
+
def test_restart(lib_init, mpi_intracomm):
# Finalize and re-init to make internal state consistent with XML.
| [Feature request] Non-uniform cylindrical meshes
Those would be convenient to generate MGXS for 2D-RZ calculations mostly. Those could remain common for cylindrical reactors with highly heterogeneous geometries (TMSR, PB-FHR for example).
Also for tokamaks?
| I’d agree with this. Came across the need for this in a particular reactor analysis I’m working on now. The model of interest has R-Z symmetry that such a mesh is best suited for.
From: Giud <[email protected]>
Sent: Saturday, September 5, 2020 11:12 AM
To: openmc-dev/openmc <[email protected]>
Cc: Subscribed <[email protected]>
Subject: [openmc-dev/openmc] [Feature request] Rectilinear cylindrical meshes (#1653)
Those would be convenient to generate MGXS for 2D-RZ calculations mostly. Those could remain common for cylindrical reactors with highly heterogeneous geometries (TMSR, PB-FHR for example).
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub<https://github.com/openmc-dev/openmc/issues/1653>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAH5GM5PRVFQAUKUIYHZ4ODSEJPNPANCNFSM4Q3CERBA>.
| 2021-12-20T19:37:27Z | [] | [] |
openmc-dev/openmc | 1,948 | openmc-dev__openmc-1948 | [
"1939"
] | 34ec14c5ee2e9ea1f7518376e8b066d4ed140d9e | diff --git a/openmc/data/thermal.py b/openmc/data/thermal.py
--- a/openmc/data/thermal.py
+++ b/openmc/data/thermal.py
@@ -615,7 +615,8 @@ def from_ace(cls, ace_or_filename, name=None):
ace_name, xs = ace.name.split('.')
if not xs.endswith('t'):
raise TypeError("{} is not a thermal scattering ACE table.".format(ace))
- name = get_thermal_name(ace_name)
+ if name is None:
+ name = get_thermal_name(ace_name)
# Assign temperature to the running list
kTs = [ace.temperature*EV_PER_MEV]
@@ -783,9 +784,10 @@ def from_njoy(cls, filename, filename_thermal, temperatures=None,
# Create instance from ACE tables within library
lib = Library(kwargs['ace'])
- data = cls.from_ace(lib.tables[0])
+ name = kwargs.get('table_name')
+ data = cls.from_ace(lib.tables[0], name=name)
for table in lib.tables[1:]:
- data.add_temperature_from_ace(table)
+ data.add_temperature_from_ace(table, name=name)
# Load ENDF data to replace incoherent elastic
if use_endf_data:
diff --git a/openmc/deplete/abc.py b/openmc/deplete/abc.py
--- a/openmc/deplete/abc.py
+++ b/openmc/deplete/abc.py
@@ -19,7 +19,6 @@
from numpy import nonzero, empty, asarray
from uncertainties import ufloat
-from openmc.data import DataLibrary
from openmc.lib import MaterialFilter, Tally
from openmc.checkvalue import check_type, check_greater_than
from openmc.mpi import comm
@@ -70,10 +69,8 @@ class TransportOperator(ABC):
Parameters
----------
- chain_file : str, optional
- Path to the depletion chain XML file. Defaults to the file
- listed under ``depletion_chain`` in
- :envvar:`OPENMC_CROSS_SECTIONS` environment variable.
+ chain_file : str
+ Path to the depletion chain XML file
fission_q : dict, optional
Dictionary of nuclides and their fission Q values [eV]. If not given,
values will be pulled from the ``chain_file``.
@@ -95,30 +92,12 @@ class TransportOperator(ABC):
Results from a previous depletion calculation. ``None`` if no
results are to be used.
"""
- def __init__(self, chain_file=None, fission_q=None, dilute_initial=1.0e3,
+ def __init__(self, chain_file, fission_q=None, dilute_initial=1.0e3,
prev_results=None):
self.dilute_initial = dilute_initial
self.output_dir = '.'
# Read depletion chain
- if chain_file is None:
- chain_file = os.environ.get("OPENMC_DEPLETE_CHAIN", None)
- if chain_file is None:
- data = DataLibrary.from_xml()
- # search for depletion_chain path from end of list
- for lib in reversed(data.libraries):
- if lib['type'] == 'depletion_chain':
- break
- else:
- raise IOError(
- "No chain specified, either manually or "
- "under depletion_chain in environment variable "
- "OPENMC_CROSS_SECTIONS.")
- chain_file = lib['path']
- else:
- warn("Use of OPENMC_DEPLETE_CHAIN is deprecated in favor "
- "of adding depletion_chain to OPENMC_CROSS_SECTIONS",
- FutureWarning)
self.chain = Chain.from_xml(chain_file, fission_q)
if prev_results is None:
self.prev_res = None
diff --git a/openmc/deplete/chain.py b/openmc/deplete/chain.py
--- a/openmc/deplete/chain.py
+++ b/openmc/deplete/chain.py
@@ -7,6 +7,7 @@
from io import StringIO
from itertools import chain
import math
+import os
import re
from collections import OrderedDict, defaultdict, namedtuple
from collections.abc import Mapping, Iterable
@@ -14,7 +15,8 @@
from warnings import warn
from openmc.checkvalue import check_type, check_greater_than
-from openmc.data import gnd_name, zam
+from openmc.data import gnd_name, zam, DataLibrary
+from openmc.exceptions import DataError
from .nuclide import FissionYieldDistribution
# Try to use lxml if it is available. It preserves the order of attributes and
@@ -237,6 +239,24 @@ def replace_missing_fpy(actinide, fpy_data, decay_data):
return 'U235'
+def _find_chain_file(cross_sections=None):
+ # First check deprecated OPENMC_DEPLETE_CHAIN environment variable
+ chain_file = os.environ.get("OPENMC_DEPLETE_CHAIN")
+ if chain_file is not None:
+ warn("Use of OPENMC_DEPLETE_CHAIN is deprecated in favor of adding "
+ "depletion_chain to OPENMC_CROSS_SECTIONS", FutureWarning)
+ return chain_file
+
+ # Check for depletion chain in cross_sections.xml
+ data = DataLibrary.from_xml(cross_sections)
+ for lib in reversed(data.libraries):
+ if lib['type'] == 'depletion_chain':
+ return lib['path']
+
+ raise DataError("No depletion chain specified and could not find depletion "
+ f"chain in {cross_sections}")
+
+
class Chain:
"""Full representation of a depletion chain.
diff --git a/openmc/deplete/operator.py b/openmc/deplete/operator.py
--- a/openmc/deplete/operator.py
+++ b/openmc/deplete/operator.py
@@ -10,20 +10,20 @@
import copy
from collections import OrderedDict
import os
-from typing import Type
-import xml.etree.ElementTree as ET
from warnings import warn
-from pathlib import Path
import numpy as np
from uncertainties import ufloat
import openmc
from openmc.checkvalue import check_value
+from openmc.data import DataLibrary
+from openmc.exceptions import DataError
import openmc.lib
from openmc.mpi import comm
from .abc import TransportOperator, OperatorResult
from .atom_number import AtomNumber
+from .chain import _find_chain_file
from .reaction_rates import ReactionRates
from .results_list import ResultsList
from .helpers import (
@@ -58,6 +58,22 @@ def _distribute(items):
j += chunk_size
+def _find_cross_sections(model):
+ """Determine cross sections to use for depletion"""
+ if model.materials and model.materials.cross_sections is not None:
+ # Prefer info from Model class if available
+ return model.materials.cross_sections
+
+ # otherwise fallback to environment variable
+ cross_sections = os.environ.get("OPENMC_CROSS_SECTIONS")
+ if cross_sections is None:
+ raise DataError(
+ "Cross sections were not specified in Model.materials and "
+ "the OPENMC_CROSS_SECTIONS environment variable is not set."
+ )
+ return cross_sections
+
+
class Operator(TransportOperator):
"""OpenMC transport operator for depletion.
@@ -206,6 +222,11 @@ def __init__(self, model, chain_file=None, prev_results=None,
"to generate the depletion Operator."
raise TypeError(msg)
+ # Determine cross sections / depletion chain
+ cross_sections = _find_cross_sections(model)
+ if chain_file is None:
+ chain_file = _find_chain_file(cross_sections)
+
check_value('fission yield mode', fission_yield_mode,
self._fission_helpers.keys())
check_value('normalization mode', normalization_mode,
@@ -270,7 +291,7 @@ def __init__(self, model, chain_file=None, prev_results=None,
self.prev_res.append(new_res)
# Determine which nuclides have incident neutron data
- self.nuclides_with_data = self._get_nuclides_with_data()
+ self.nuclides_with_data = self._get_nuclides_with_data(cross_sections)
# Select nuclides with data that are also in the chain
self._burnable_nucs = [nuc.name for nuc in self.chain.nuclides
@@ -637,14 +658,6 @@ def _generate_materials_xml(self):
for mat in self.materials:
mat._nuclides.sort(key=lambda x: nuclides.index(x[0]))
- # Grab the cross sections tag from the existing file
- mfile = Path("materials.xml")
- if mfile.exists():
- tree = ET.parse(str(mfile))
- xs = tree.find('cross_sections')
- if xs is not None and self.materials.cross_sections is None:
- self.materials.cross_sections = xs.text
-
self.materials.export_to_xml()
def _get_tally_nuclides(self):
@@ -768,40 +781,14 @@ def _unpack_tallies_and_normalize(self, source_rate):
return OperatorResult(k_combined, rates)
- def _get_nuclides_with_data(self):
- """Loads a cross_sections.xml file to find participating nuclides.
-
- This allows for nuclides that are important in the decay chain but not
- important neutronically, or have no cross section data.
- """
-
- # Reads cross_sections.xml to create a dictionary containing
- # participating (burning and not just decaying) nuclides.
-
- try:
- filename = os.environ["OPENMC_CROSS_SECTIONS"]
- except KeyError:
- filename = None
-
+ def _get_nuclides_with_data(self, cross_sections):
+ """Loads cross_sections.xml file to find nuclides with neutron data"""
nuclides = set()
-
- try:
- tree = ET.parse(filename)
- except Exception:
- if filename is None:
- msg = "No cross_sections.xml specified in materials."
- else:
- msg = 'Cross section file "{}" is invalid.'.format(filename)
- raise IOError(msg)
-
- root = tree.getroot()
- for nuclide_node in root.findall('library'):
- mats = nuclide_node.get('materials')
- if not mats:
+ data_lib = DataLibrary.from_xml(cross_sections)
+ for library in data_lib.libraries:
+ if library['type'] != 'neutron':
continue
- for name in mats.split():
- # Make a burn list of the union of nuclides in cross_sections.xml
- # and nuclides in depletion chain.
+ for name in library['materials']:
if name not in nuclides:
nuclides.add(name)
diff --git a/openmc/material.py b/openmc/material.py
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -700,14 +700,7 @@ def add_s_alpha_beta(self, name, fraction=1.0):
cv.check_type('S(a,b) fraction', fraction, Real)
cv.check_greater_than('S(a,b) fraction', fraction, 0.0, True)
cv.check_less_than('S(a,b) fraction', fraction, 1.0, True)
-
- new_name = openmc.data.get_thermal_name(name)
- if new_name != name:
- msg = 'OpenMC S(a,b) tables follow the GND naming convention. ' \
- 'Table "{}" is being renamed as "{}".'.format(name, new_name)
- warnings.warn(msg)
-
- self._sab.append((new_name, fraction))
+ self._sab.append((name, fraction))
def make_isotropic_in_lab(self):
self.isotropic = [x.name for x in self._nuclides]
diff --git a/openmc/model/model.py b/openmc/model/model.py
--- a/openmc/model/model.py
+++ b/openmc/model/model.py
@@ -1,10 +1,11 @@
from collections.abc import Iterable
+from contextlib import contextmanager
from functools import lru_cache
import os
from pathlib import Path
from numbers import Integral
+from tempfile import NamedTemporaryFile
import time
-from contextlib import contextmanager
import h5py
@@ -528,8 +529,11 @@ def run(self, particles=None, threads=None, geometry_debug=False,
"""
# Setting tstart here ensures we don't pick up any pre-existing
- # statepoint files in the output directory
- tstart = time.time()
+ # statepoint files in the output directory -- just in case there are
+ # differences between the system clock and the filesystem, we get the
+ # time of a just-created temporary file
+ with NamedTemporaryFile() as fp:
+ tstart = Path(fp.name).stat().st_mtime
last_statepoint = None
# Operate in the provided working directory
| diff --git a/tests/unit_tests/test_deplete_operator.py b/tests/unit_tests/test_deplete_operator.py
--- a/tests/unit_tests/test_deplete_operator.py
+++ b/tests/unit_tests/test_deplete_operator.py
@@ -10,7 +10,7 @@
import pytest
from openmc.deplete.abc import TransportOperator
-from openmc.deplete.chain import Chain
+from openmc.deplete.chain import Chain, _find_chain_file
BARE_XS_FILE = "bare_cross_sections.xml"
CHAIN_PATH = Path(__file__).parents[1] / "chain_simple.xml"
@@ -31,7 +31,7 @@ def bare_xs(run_in_tmpdir):
with open(BARE_XS_FILE, "w") as out:
out.write(bare_xs_contents)
- yield
+ yield BARE_XS_FILE
class BareDepleteOperator(TransportOperator):
@@ -54,14 +54,10 @@ def write_bos_data():
pass
[email protected](environ, {"OPENMC_CROSS_SECTIONS": BARE_XS_FILE})
def test_operator_init(bare_xs):
- """The test will set and unset environment variable OPENMC_CROSS_SECTIONS
- to point towards a temporary dummy file. This file will be removed
- at the end of the test, and only contains a
- depletion_chain node."""
- # force operator to read from OPENMC_CROSS_SECTIONS
- bare_op = BareDepleteOperator(chain_file=None)
+ """The test uses a temporary dummy chain. This file will be removed
+ at the end of the test, and only contains a depletion_chain node."""
+ bare_op = BareDepleteOperator(_find_chain_file(bare_xs))
act_chain = bare_op.chain
ref_chain = Chain.from_xml(CHAIN_PATH)
assert len(act_chain) == len(ref_chain)
| model.run() can fail to return the statefile
I had a problem with running one of the tests, namely `trigger_statepoint_restart`. It crashed on the first assert of the statefile. I tracked it down to a problem with my setup and the logic in model.run(), that determines the last statefile.
The root cause is, that the time of the fileserver where my /home is located is ~30 s off the time of my compute-node (and I can't change that). The logic in model.run() looks for the newest statefile, that is newer than the starttime of `openmc`. Due to the time-difference of my machines and the short runtime this results in a `None` return value.
| Wow, that's definitely something I did not anticipate when writing that bit of code. One potential solution is instead of using `time.time()` as the starting time, we could create a temporary file and then look at the timestamp so that it's getting the 30 second behind time from the filesystem. Do you want to give that a shot and see if it works? Here's a patch:
```diff
diff --git a/openmc/model/model.py b/openmc/model/model.py
index d253bfb5b0..3c0dfcb871 100644
--- a/openmc/model/model.py
+++ b/openmc/model/model.py
@@ -4,6 +4,7 @@ from pathlib import Path
from numbers import Integral
import time
from contextlib import contextmanager
+from tempfile import NamedTemporaryFile
import h5py
@@ -508,7 +509,8 @@ class Model:
# Setting tstart here ensures we don't pick up any pre-existing
# statepoint files in the output directory
- tstart = time.time()
+ with NamedTemporaryFile() as fp:
+ tstart = Path(fp.name).stat().st_mtime
last_statepoint = None
# Operate in the provided working directory
```
Yes, it took me quite some time to figure out, what was happening ;-)
Unfortunately I destroyed my testing opportunity by asking our admins to update the timesource for the filer. But I did a test for the non-lib case and took `tstart` from the settings.xml. That worked. So I guess, your patch will work as well. | 2022-01-12T16:41:58Z | [] | [] |
openmc-dev/openmc | 1,955 | openmc-dev__openmc-1955 | [
"1951"
] | 3abf0a9f5b0119c4d37cbdf1948251651db0ee62 | diff --git a/openmc/filter.py b/openmc/filter.py
--- a/openmc/filter.py
+++ b/openmc/filter.py
@@ -16,6 +16,7 @@
from .mixin import IDManagerMixin
from .surface import Surface
from .universe import UniverseBase
+from ._xml import get_text
_FILTER_TYPES = (
@@ -231,9 +232,43 @@ def to_xml_element(self):
subelement = ET.SubElement(element, 'bins')
subelement.text = ' '.join(str(b) for b in self.bins)
-
return element
+ @classmethod
+ def from_xml_element(cls, elem, **kwargs):
+ """Generate a filter from an XML element
+
+ Parameters
+ ----------
+ elem : xml.etree.ElementTree.Element
+ XML element
+ **kwargs
+ Keyword arguments (e.g., mesh information)
+
+ Returns
+ -------
+ openmc.Filter
+ Filter object
+
+ """
+ filter_type = elem.get('type')
+
+ # If the filter type matches this class's short_name, then
+ # there is no overriden from_xml_element method
+ if filter_type == cls.short_name.lower():
+ # Get bins from element -- the default here works for any filters
+ # that just store a list of bins that can be represented as integers
+ filter_id = int(elem.get('id'))
+ bins = [int(x) for x in get_text(elem, 'bins').split()]
+ return cls(bins, filter_id=filter_id)
+
+ # Search through all subclasses and find the one matching the HDF5
+ # 'type'. Call that class's from_hdf5 method
+ for subclass in cls._recursive_subclasses():
+ if filter_type == subclass.short_name.lower():
+ return subclass.from_xml_element(elem, **kwargs)
+
+
def can_merge(self, other):
"""Determine if filter can be merged with another.
@@ -622,6 +657,13 @@ def to_xml_element(self):
subelement.text = ' '.join(str(i) for i in self.bins.ravel())
return element
+ @classmethod
+ def from_xml_element(cls, elem, **kwargs):
+ filter_id = int(elem.get('id'))
+ bins = [int(x) for x in get_text(elem, 'bins').split()]
+ cell_instances = list(zip(bins[::2], bins[1::2]))
+ return cls(cell_instances, filter_id=filter_id)
+
class SurfaceFilter(WithIDFilter):
"""Filters particles by surface crossing
@@ -661,8 +703,8 @@ class ParticleFilter(Filter):
Attributes
----------
- bins : Iterable of Integral
- The Particles to tally
+ bins : iterable of str
+ The particles to tally
id : int
Unique identifier for the filter
num_bins : Integral
@@ -698,6 +740,12 @@ def from_hdf5(cls, group, **kwargs):
filter_id = int(group.name.split('/')[-1].lstrip('filter '))
return cls(particles, filter_id=filter_id)
+ @classmethod
+ def from_xml_element(cls, elem, **kwargs):
+ filter_id = int(elem.get('id'))
+ bins = get_text(elem, 'bins').split()
+ return cls(bins, filter_id=filter_id)
+
class MeshFilter(Filter):
"""Bins tally event locations onto a regular, rectangular mesh.
@@ -877,6 +925,18 @@ def to_xml_element(self):
element.set('translation', ' '.join(map(str, self.translation)))
return element
+ @classmethod
+ def from_xml_element(cls, elem, **kwargs):
+ mesh_id = int(get_text(elem, 'bins'))
+ mesh_obj = kwargs['meshes'][mesh_id]
+ filter_id = int(elem.get('id'))
+ out = cls(mesh_obj, filter_id=filter_id)
+
+ translation = elem.get('translation')
+ if translation:
+ out.translation = [float(x) for x in translation.split()]
+ return out
+
class MeshSurfaceFilter(MeshFilter):
"""Filter events by surface crossings on a regular, rectangular mesh.
@@ -1019,35 +1079,12 @@ def __init__(self, bins, filter_id=None):
self.bins = np.asarray(bins)
self.id = filter_id
- def __repr__(self):
- string = type(self).__name__ + '\n'
- string += '{: <16}=\t{}\n'.format('\tValues', self.bins)
- string += '{: <16}=\t{}\n'.format('\tID', self.id)
- return string
-
- @Filter.bins.setter
- def bins(self, bins):
- Filter.bins.__set__(self, np.asarray(bins))
-
def check_bins(self, bins):
for x in bins:
# Values should be integers
cv.check_type('filter value', x, Integral)
cv.check_greater_than('filter value', x, 0, equality=True)
- def to_xml_element(self):
- """Return XML Element representing the Filter.
-
- Returns
- -------
- element : xml.etree.ElementTree.Element
- XML element containing filter data
-
- """
- element = super().to_xml_element()
- element[0].text = ' '.join(str(x) for x in self.bins)
- return element
-
class RealFilter(Filter):
"""Tally modifier that describes phase-space and other characteristics
@@ -1236,6 +1273,12 @@ def to_xml_element(self):
element[0].text = ' '.join(str(x) for x in self.values)
return element
+ @classmethod
+ def from_xml_element(cls, elem, **kwargs):
+ filter_id = int(elem.get('id'))
+ bins = [float(x) for x in get_text(elem, 'bins').split()]
+ return cls(bins, filter_id=filter_id)
+
class EnergyFilter(RealFilter):
"""Bins tally events based on incident particle energy.
@@ -1969,6 +2012,13 @@ def to_xml_element(self):
return element
+ @classmethod
+ def from_xml_element(cls, elem, **kwargs):
+ filter_id = int(elem.get('id'))
+ energy = [float(x) for x in get_text(elem, 'energy').split()]
+ y = [float(x) for x in get_text(elem, 'y').split()]
+ return cls(energy, y, filter_id=filter_id)
+
def can_merge(self, other):
return False
diff --git a/openmc/filter_expansion.py b/openmc/filter_expansion.py
--- a/openmc/filter_expansion.py
+++ b/openmc/filter_expansion.py
@@ -46,6 +46,12 @@ def to_xml_element(self):
return element
+ @classmethod
+ def from_xml_element(cls, elem, **kwargs):
+ filter_id = int(elem.get('id'))
+ order = int(elem.find('order').text)
+ return cls(order, filter_id=filter_id)
+
class LegendreFilter(ExpansionFilter):
r"""Score Legendre expansion moments up to specified order.
@@ -226,6 +232,15 @@ def to_xml_element(self):
return element
+ @classmethod
+ def from_xml_element(cls, elem, **kwargs):
+ filter_id = int(elem.get('id'))
+ order = int(elem.find('order').text)
+ axis = elem.find('axis').text
+ minimum = float(elem.find('min').text)
+ maximum = float(elem.find('max').text)
+ return cls(order, axis, minimum, maximum, filter_id=filter_id)
+
class SphericalHarmonicsFilter(ExpansionFilter):
r"""Score spherical harmonic expansion moments up to specified order.
@@ -316,6 +331,14 @@ def to_xml_element(self):
element.set('cosine', self.cosine)
return element
+ @classmethod
+ def from_xml_element(cls, elem, **kwargs):
+ filter_id = int(elem.get('id'))
+ order = int(elem.find('order').text)
+ filter = cls(order, filter_id=filter_id)
+ filter.cosine = elem.get('cosine')
+ return filter
+
class ZernikeFilter(ExpansionFilter):
r"""Score Zernike expansion moments in space up to specified order.
@@ -358,7 +381,7 @@ class ZernikeFilter(ExpansionFilter):
x-coordinate of center of circle for normalization
y : float
y-coordinate of center of circle for normalization
- r : int or None
+ r : float
Radius of circle for normalization
Attributes
@@ -369,7 +392,7 @@ class ZernikeFilter(ExpansionFilter):
x-coordinate of center of circle for normalization
y : float
y-coordinate of center of circle for normalization
- r : int or None
+ r : float
Radius of circle for normalization
id : int
Unique identifier for the filter
@@ -464,6 +487,15 @@ def to_xml_element(self):
return element
+ @classmethod
+ def from_xml_element(cls, elem, **kwargs):
+ filter_id = int(elem.get('id'))
+ order = int(elem.find('order').text)
+ x = float(elem.find('x').text)
+ y = float(elem.find('y').text)
+ r = float(elem.find('r').text)
+ return cls(order, x, y, r, filter_id=filter_id)
+
class ZernikeRadialFilter(ZernikeFilter):
r"""Score the :math:`m = 0` (radial variation only) Zernike moments up to
@@ -499,7 +531,7 @@ class ZernikeRadialFilter(ZernikeFilter):
x-coordinate of center of circle for normalization
y : float
y-coordinate of center of circle for normalization
- r : int or None
+ r : float
Radius of circle for normalization
Attributes
@@ -510,7 +542,7 @@ class ZernikeRadialFilter(ZernikeFilter):
x-coordinate of center of circle for normalization
y : float
y-coordinate of center of circle for normalization
- r : int or None
+ r : float
Radius of circle for normalization
id : int
Unique identifier for the filter
diff --git a/openmc/lib/mesh.py b/openmc/lib/mesh.py
--- a/openmc/lib/mesh.py
+++ b/openmc/lib/mesh.py
@@ -285,6 +285,18 @@ def _get_parameters(self):
return (lower_left, upper_right, dimension, width)
def set_grid(self, x_grid, y_grid, z_grid):
+ """Set grid values
+
+ Parameters
+ ----------
+ x_grid : iterable of float
+ Mesh boundary points along the x-axis
+ y_grid : iterable of float
+ Mesh boundary points along the y-axis
+ z_grid : iterable of float
+ Mesh boundary points along the z-axis
+
+ """
nx = len(x_grid)
x_grid = (c_double*nx)(*x_grid)
ny = len(y_grid)
@@ -371,15 +383,27 @@ def _get_parameters(self):
return (lower_left, upper_right, dimension, width)
- def set_grid(self, x_grid, y_grid, z_grid):
- nx = len(x_grid)
- x_grid = (c_double*nx)(*x_grid)
- ny = len(y_grid)
- y_grid = (c_double*ny)(*y_grid)
+ def set_grid(self, r_grid, phi_grid, z_grid):
+ """Set grid values
+
+ Parameters
+ ----------
+ r_grid : iterable of float
+ Mesh boundary points along the r-axis
+ phi_grid : Iterable of float
+ Mesh boundary points along the phi-axis
+ z_grid : Iterable of float
+ Mesh boundary points along the z-axis
+
+ """
+ nr = len(r_grid)
+ r_grid = (c_double*nr)(*r_grid)
+ nphi = len(phi_grid)
+ phi_grid = (c_double*nphi)(*phi_grid)
nz = len(z_grid)
z_grid = (c_double*nz)(*z_grid)
- _dll.openmc_cylindrical_mesh_set_grid(self._index, x_grid, nx, y_grid,
- ny, z_grid, nz)
+ _dll.openmc_cylindrical_mesh_set_grid(self._index, r_grid, nr, phi_grid,
+ nphi, z_grid, nz)
class SphericalMesh(Mesh):
"""SphericalMesh stored internally.
@@ -457,15 +481,27 @@ def _get_parameters(self):
return (lower_left, upper_right, dimension, width)
- def set_grid(self, x_grid, y_grid, z_grid):
- nx = len(x_grid)
- x_grid = (c_double*nx)(*x_grid)
- ny = len(y_grid)
- y_grid = (c_double*ny)(*y_grid)
- nz = len(z_grid)
- z_grid = (c_double*nz)(*z_grid)
- _dll.openmc_spherical_mesh_set_grid(self._index, x_grid, nx, y_grid,
- ny, z_grid, nz)
+ def set_grid(self, r_grid, theta_grid, phi_grid):
+ """Set grid values
+
+ Parameters
+ ----------
+ r_grid : iterable of float
+ Mesh boundary points along the r-axis
+ theta_grid : Iterable of float
+ Mesh boundary points along the theta-axis
+ phi_grid : Iterable of float
+ Mesh boundary points along the phi-axis
+
+ """
+ nr = len(r_grid)
+ r_grid = (c_double*nr)(*r_grid)
+ ntheta = len(theta_grid)
+ theta_grid = (c_double*ntheta)(*theta_grid)
+ nphi = len(phi_grid)
+ phi_grid = (c_double*nphi)(*phi_grid)
+ _dll.openmc_spherical_mesh_set_grid(self._index, r_grid, nr, theta_grid,
+ ntheta, phi_grid, nphi)
_MESH_TYPE_MAP = {
diff --git a/openmc/mesh.py b/openmc/mesh.py
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -1,5 +1,6 @@
from abc import ABC
from collections.abc import Iterable
+from math import pi
from numbers import Real, Integral
import warnings
from xml.etree import ElementTree as ET
@@ -89,7 +90,7 @@ def from_hdf5(cls, group):
raise ValueError('Unrecognized mesh type: "' + mesh_type + '"')
@classmethod
- def from_xml(cls, elem):
+ def from_xml_element(cls, elem):
"""Generates a mesh from an XML element
Parameters
@@ -109,6 +110,10 @@ def from_xml(cls, elem):
return RegularMesh.from_xml_element(elem)
elif mesh_type == 'rectilinear':
return RectilinearMesh.from_xml_element(elem)
+ elif mesh_type == 'cylindrical':
+ return CylindricalMesh.from_xml_element(elem)
+ elif mesh_type == 'spherical':
+ return SphericalMesh.from_xml_element(elem)
elif mesh_type == 'unstructured':
return UnstructuredMesh.from_xml_element(elem)
else:
@@ -697,11 +702,11 @@ class CylindricalMesh(MeshBase):
n_dimension : int
Number of mesh dimensions (always 3 for a CylindricalMesh).
r_grid : Iterable of float
- Mesh boundary points along the r-axis.
+ Mesh boundary points along the r-axis.
Requirement is r >= 0.
phi_grid : Iterable of float
- Mesh boundary points along the phi-axis.
- The default value is [0, 360], i.e. the full phi range.
+ Mesh boundary points along the phi-axis.
+ The default value is [0, 2π], i.e. the full phi range.
z_grid : Iterable of float
Mesh boundary points along the z-axis.
indices : Iterable of tuple
@@ -714,7 +719,7 @@ def __init__(self, mesh_id=None, name=''):
super().__init__(mesh_id, name)
self._r_grid = None
- self._phi_grid = [0, 360]
+ self._phi_grid = [0.0, 2*pi]
self._z_grid = None
@property
@@ -757,12 +762,12 @@ def r_grid(self, grid):
@phi_grid.setter
def phi_grid(self, grid):
cv.check_type('mesh phi_grid', grid, Iterable, Real)
- self._phi_grid = np.array(grid)
+ self._phi_grid = np.asarray(grid)
@z_grid.setter
def z_grid(self, grid):
cv.check_type('mesh z_grid', grid, Iterable, Real)
- self._z_grid = np.array(grid)
+ self._z_grid = np.asarray(grid)
def __repr__(self):
fmt = '{0: <16}{1}{2}\n'
@@ -792,7 +797,7 @@ def from_hdf5(cls, group):
# Read and assign mesh properties
mesh = cls(mesh_id)
mesh.r_grid = group['r_grid'][()]
- mesh.phi_grid = 180 / np.pi * group['phi_grid'][()]
+ mesh.phi_grid = group['phi_grid'][()]
mesh.z_grid = group['z_grid'][()]
return mesh
@@ -822,6 +827,29 @@ def to_xml_element(self):
return element
+ @classmethod
+ def from_xml_element(cls, elem):
+ """Generate a cylindrical mesh from an XML element
+
+ Parameters
+ ----------
+ elem : xml.etree.ElementTree.Element
+ XML element
+
+ Returns
+ -------
+ openmc.CylindricalMesh
+ Cylindrical mesh object
+
+ """
+
+ mesh_id = int(get_text(elem, 'id'))
+ mesh = cls(mesh_id)
+ mesh.r_grid = [float(x) for x in get_text(elem, "r_grid").split()]
+ mesh.phi_grid = [float(x) for x in get_text(elem, "phi_grid").split()]
+ mesh.z_grid = [float(x) for x in get_text(elem, "z_grid").split()]
+ return mesh
+
def calc_mesh_volumes(self):
"""Return Volumes for every mesh cell
@@ -832,9 +860,9 @@ def calc_mesh_volumes(self):
"""
- V_r = np.diff(np.array(self.r_grid)**2 / 2)
- V_p = np.diff(np.array(self.phi_grid) * np.pi / 180.0)
- V_z = np.diff(np.array(self.z_grid))
+ V_r = np.diff(np.asarray(self.r_grid)**2 / 2)
+ V_p = np.diff(self.phi_grid)
+ V_z = np.diff(self.z_grid)
return np.multiply.outer(np.outer(V_r, V_p), V_z)
@@ -864,10 +892,10 @@ class SphericalMesh(MeshBase):
Requirement is r >= 0.
theta_grid : Iterable of float
Mesh boundary points along the theta-axis in degrees.
- The default value is [0, 180], i.e. the full theta range.
+ The default value is [0, π], i.e. the full theta range.
phi_grid : Iterable of float
Mesh boundary points along the phi-axis in degrees.
- The default value is [0, 360], i.e. the full phi range.
+ The default value is [0, 2π], i.e. the full phi range.
indices : Iterable of tuple
An iterable of mesh indices for each mesh element, e.g. [(1, 1, 1),
(2, 1, 1), ...]
@@ -878,8 +906,8 @@ def __init__(self, mesh_id=None, name=''):
super().__init__(mesh_id, name)
self._r_grid = None
- self._theta_grid = [0, 180]
- self._phi_grid = [0, 360]
+ self._theta_grid = [0, pi]
+ self._phi_grid = [0, 2*pi]
@property
def dimension(self):
@@ -921,12 +949,12 @@ def r_grid(self, grid):
@theta_grid.setter
def theta_grid(self, grid):
cv.check_type('mesh theta_grid', grid, Iterable, Real)
- self._theta_grid = np.array(grid)
+ self._theta_grid = np.asarray(grid)
@phi_grid.setter
def phi_grid(self, grid):
cv.check_type('mesh phi_grid', grid, Iterable, Real)
- self._phi_grid = np.array(grid)
+ self._phi_grid = np.asarray(grid)
def __repr__(self):
fmt = '{0: <16}{1}{2}\n'
@@ -956,8 +984,8 @@ def from_hdf5(cls, group):
# Read and assign mesh properties
mesh = cls(mesh_id)
mesh.r_grid = group['r_grid'][()]
- mesh.theta_grid = 180 / np.pi * group['theta_grid'][()]
- mesh.phi_grid = 180 / np.pi * group['phi_grid'][()]
+ mesh.theta_grid = group['theta_grid'][()]
+ mesh.phi_grid = group['phi_grid'][()]
return mesh
@@ -986,6 +1014,29 @@ def to_xml_element(self):
return element
+ @classmethod
+ def from_xml_element(cls, elem):
+ """Generate a spherical mesh from an XML element
+
+ Parameters
+ ----------
+ elem : xml.etree.ElementTree.Element
+ XML element
+
+ Returns
+ -------
+ openmc.SphericalMesh
+ Spherical mesh object
+
+ """
+
+ mesh_id = int(get_text(elem, 'id'))
+ mesh = cls(mesh_id)
+ mesh.r_grid = [float(x) for x in get_text(elem, "r_grid").split()]
+ mesh.theta_grid = [float(x) for x in get_text(elem, "theta_grid").split()]
+ mesh.phi_grid = [float(x) for x in get_text(elem, "phi_grid").split()]
+ return mesh
+
def calc_mesh_volumes(self):
"""Return Volumes for every mesh cell
@@ -996,15 +1047,13 @@ def calc_mesh_volumes(self):
"""
- V_r = np.diff(np.array(self.r_grid)**3 / 3)
- V_t = np.diff(-np.cos(np.pi * np.array(self.theta_grid) / 180.0))
- V_p = np.diff(np.array(self.phi_grid) * np.pi / 180)
+ V_r = np.diff(np.asarray(self.r_grid)**3 / 3)
+ V_t = np.diff(-np.cos(self.theta_grid))
+ V_p = np.diff(self.phi_grid)
return np.multiply.outer(np.outer(V_r, V_t), V_p)
-
-
class UnstructuredMesh(MeshBase):
"""A 3D unstructured mesh
@@ -1017,6 +1066,8 @@ class UnstructuredMesh(MeshBase):
----------
filename : str
Location of the unstructured mesh file
+ library : {'moab', 'libmesh'}
+ Mesh library used for the unstructured mesh tally
mesh_id : int
Unique identifier for the mesh
name : str
@@ -1034,7 +1085,7 @@ class UnstructuredMesh(MeshBase):
Name of the file containing the unstructured mesh
length_multiplier: float
Multiplicative factor to apply to mesh coordinates
- library : str
+ library : {'moab', 'libmesh'}
Mesh library used for the unstructured mesh tally
output : bool
Indicates whether or not automatic tally output should
@@ -1291,4 +1342,4 @@ def from_xml_element(cls, elem):
library = get_text(elem, 'library')
length_multiplier = float(get_text(elem, 'length_multiplier', 1.0))
- return cls(filename, library, mesh_id, '', length_multiplier)
\ No newline at end of file
+ return cls(filename, library, mesh_id, '', length_multiplier)
diff --git a/openmc/model/model.py b/openmc/model/model.py
--- a/openmc/model/model.py
+++ b/openmc/model/model.py
@@ -5,7 +5,6 @@
from pathlib import Path
from numbers import Integral
from tempfile import NamedTemporaryFile
-import time
import h5py
@@ -204,10 +203,9 @@ def plots(self, plots):
@classmethod
def from_xml(cls, geometry='geometry.xml', materials='materials.xml',
- settings='settings.xml'):
+ settings='settings.xml', tallies='tallies.xml',
+ plots='plots.xml'):
"""Create model from existing XML files
- When initializing this way, the user must manually load plots and
- tallies.
Parameters
----------
@@ -217,6 +215,14 @@ def from_xml(cls, geometry='geometry.xml', materials='materials.xml',
Path to materials.xml file
settings : str
Path to settings.xml file
+ tallies : str
+ Path to tallies.xml file
+
+ .. versionadded:: 0.13.0
+ plots : str
+ Path to plots.xml file
+
+ .. versionadded:: 0.13.0
Returns
-------
@@ -227,7 +233,9 @@ def from_xml(cls, geometry='geometry.xml', materials='materials.xml',
materials = openmc.Materials.from_xml(materials)
geometry = openmc.Geometry.from_xml(geometry, materials)
settings = openmc.Settings.from_xml(settings)
- return cls(geometry, materials, settings)
+ tallies = openmc.Tallies.from_xml(tallies) if Path(tallies).exists() else None
+ plots = openmc.Plots.from_xml(plots) if Path(plots).exists() else None
+ return cls(geometry, materials, settings, tallies, plots)
def init_lib(self, threads=None, geometry_debug=False, restart_file=None,
tracks=False, output=True, event_based=None, intracomm=None):
diff --git a/openmc/plots.py b/openmc/plots.py
--- a/openmc/plots.py
+++ b/openmc/plots.py
@@ -684,6 +684,85 @@ def to_xml_element(self):
return element
+ @classmethod
+ def from_xml_element(cls, elem):
+ """Generate plot object from an XML element
+
+ Parameters
+ ----------
+ elem : xml.etree.ElementTree.Element
+ XML element
+
+ Returns
+ -------
+ openmc.Plot
+ Plot object
+
+ """
+ plot_id = int(elem.get("id"))
+ plot = cls(plot_id)
+ if "filename" in elem.keys():
+ plot.filename = elem.get("filename")
+ plot.color_by = elem.get("color_by")
+ plot.type = elem.get("type")
+ plot.basis = elem.get("basis")
+
+ # Helper function to get a tuple of values
+ def get_tuple(elem, name, dtype=int):
+ subelem = elem.find(name)
+ if subelem is not None:
+ return tuple([dtype(x) for x in subelem.text.split()])
+
+ plot.origin = get_tuple(elem, "origin", float)
+ plot.width = get_tuple(elem, "width", float)
+ plot.pixels = get_tuple(elem, "pixels")
+ plot._background = get_tuple(elem, "background")
+
+ # Set plot colors
+ colors = {}
+ for color_elem in elem.findall("color"):
+ uid = color_elem.get("id")
+ colors[uid] = tuple([int(x) for x in color_elem.get("rgb").split()])
+ # TODO: set colors (needs geometry information)
+
+ # Set masking information
+ mask_elem = elem.find("mask")
+ if mask_elem is not None:
+ mask_components = [int(x) for x in mask_elem.get("components").split()]
+ # TODO: set mask components (needs geometry information)
+ background = mask_elem.get("background")
+ if background is not None:
+ plot.mask_background = tuple([int(x) for x in background.split()])
+
+ # show overlaps
+ overlap_elem = elem.find("show_overlaps")
+ if overlap_elem is not None:
+ plot.show_overlaps = (overlap_elem.text in ('true', '1'))
+ overlap_color = get_tuple(elem, "overlap_color")
+ if overlap_color is not None:
+ plot.overlap_color = overlap_color
+
+ # Set universe level
+ level = elem.find("level")
+ if level is not None:
+ plot.level = int(level.text)
+
+ # Set meshlines
+ mesh_elem = elem.find("meshlines")
+ if mesh_elem is not None:
+ meshlines = {'type': mesh_elem.get('meshtype')}
+ if 'id' in mesh_elem.keys():
+ meshlines['id'] = int(mesh_elem.get('id'))
+ if 'linewidth' in mesh_elem.keys():
+ meshlines['linewidth'] = int(mesh_elem.get('linewidth'))
+ if 'color' in mesh_elem.keys():
+ meshlines['color'] = tuple(
+ [int(x) for x in mesh_elem.get('color').split()]
+ )
+ plot.meshlines = meshlines
+
+ return plot
+
def to_ipython_image(self, openmc_exec='openmc', cwd='.'):
"""Render plot as an image
@@ -848,3 +927,27 @@ def export_to_xml(self, path='plots.xml'):
reorder_attributes(self._plots_file) # TODO: Remove when support is Python 3.8+
tree = ET.ElementTree(self._plots_file)
tree.write(str(p), xml_declaration=True, encoding='utf-8')
+
+ @classmethod
+ def from_xml(cls, path='plots.xml'):
+ """Generate plots collection from XML file
+
+ Parameters
+ ----------
+ path : str, optional
+ Path to plots XML file
+
+ Returns
+ -------
+ openmc.Plots
+ Plots collection
+
+ """
+ tree = ET.parse(path)
+ root = tree.getroot()
+
+ # Generate each plot
+ plots = cls()
+ for elem in root.findall('plot'):
+ plots.append(Plot.from_xml_element(elem))
+ return plots
diff --git a/openmc/settings.py b/openmc/settings.py
--- a/openmc/settings.py
+++ b/openmc/settings.py
@@ -1247,6 +1247,12 @@ def _source_from_xml_element(self, root):
for elem in root.findall('source'):
self.source.append(Source.from_xml_element(elem))
+ def _volume_calcs_from_xml_element(self, root):
+ volume_elems = root.findall("volume_calc")
+ if volume_elems:
+ self.volume_calculations = [VolumeCalculation.from_xml_element(elem)
+ for elem in volume_elems]
+
def _output_from_xml_element(self, root):
elem = root.find('output')
if elem is not None:
@@ -1585,6 +1591,7 @@ def from_xml(cls, path='settings.xml'):
settings._generations_per_batch_from_xml_element(root)
settings._keff_trigger_from_xml_element(root)
settings._source_from_xml_element(root)
+ settings._volume_calcs_from_xml_element(root)
settings._output_from_xml_element(root)
settings._statepoint_from_xml_element(root)
settings._sourcepoint_from_xml_element(root)
diff --git a/openmc/stats/multivariate.py b/openmc/stats/multivariate.py
--- a/openmc/stats/multivariate.py
+++ b/openmc/stats/multivariate.py
@@ -492,6 +492,7 @@ def from_xml_element(cls, elem):
origin = [float(x) for x in elem.get('origin').split()]
return cls(r, theta, phi, origin=origin)
+
class CylindricalIndependent(Spatial):
r"""Spatial distribution represented in cylindrical coordinates.
diff --git a/openmc/tallies.py b/openmc/tallies.py
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -10,12 +10,14 @@
import h5py
import numpy as np
import pandas as pd
+from scipy.misc import derivative
import scipy.sparse as sps
import openmc
import openmc.checkvalue as cv
-from ._xml import clean_indentation, reorder_attributes
+from ._xml import clean_indentation, reorder_attributes, get_text
from .mixin import IDManagerMixin
+from .mesh import MeshBase
# The tally arithmetic product types. The tensor product performs the full
@@ -844,13 +846,8 @@ def to_xml_element(self):
'not contain any scores'
raise ValueError(msg)
- else:
- scores = ''
- for score in self.scores:
- scores += f'{score} '
-
- subelement = ET.SubElement(element, "scores")
- subelement.text = scores.rstrip(' ')
+ subelement = ET.SubElement(element, "scores")
+ subelement.text = ' '.join(str(x) for x in self.scores)
# Tally estimator type
if self.estimator is not None:
@@ -859,7 +856,7 @@ def to_xml_element(self):
# Optional Triggers
for trigger in self.triggers:
- trigger.get_trigger_xml(element)
+ element.append(trigger.to_xml_element())
# Optional derivatives
if self.derivative is not None:
@@ -868,6 +865,60 @@ def to_xml_element(self):
return element
+ @classmethod
+ def from_xml_element(cls, elem, **kwargs):
+ """Generate tally object from an XML element
+
+ Parameters
+ ----------
+ elem : xml.etree.ElementTree.Element
+ XML element
+
+ Returns
+ -------
+ openmc.Tally
+ Tally object
+
+ """
+ tally_id = int(elem.get('id'))
+ name = elem.get('name', '')
+ tally = cls(tally_id=tally_id, name=name)
+
+ # Read filters
+ filters_elem = elem.find('filters')
+ if filters_elem is not None:
+ filter_ids = [int(x) for x in filters_elem.text.split()]
+ tally.filters = [kwargs['filters'][uid] for uid in filter_ids]
+
+ # Read nuclides
+ nuclides_elem = elem.find('nuclides')
+ if nuclides_elem is not None:
+ tally.nuclides = nuclides_elem.text.split()
+
+ # Read scores
+ scores_elem = elem.find('scores')
+ if scores_elem is not None:
+ tally.scores = scores_elem.text.split()
+
+ # Set estimator
+ estimator_elem = elem.find('estimator')
+ if estimator_elem is not None:
+ tally.estimator = estimator_elem.text
+
+ # Read triggers
+ tally.triggers = [
+ openmc.Trigger.from_xml_element(trigger_elem)
+ for trigger_elem in elem.findall('trigger')
+ ]
+
+ # Read tally derivative
+ deriv_elem = elem.find('derivative')
+ if deriv_elem is not None:
+ deriv_id = int(deriv_elem.text)
+ tally.derivative = kwargs['derivatives'][deriv_id]
+
+ return tally
+
def contains_filter(self, filter_type):
"""Looks for a filter in the tally that matches a specified type
@@ -3143,3 +3194,49 @@ def export_to_xml(self, path='tallies.xml'):
reorder_attributes(root_element) # TODO: Remove when support is Python 3.8+
tree = ET.ElementTree(root_element)
tree.write(str(p), xml_declaration=True, encoding='utf-8')
+
+ @classmethod
+ def from_xml(cls, path='tallies.xml'):
+ """Generate tallies from XML file
+
+ Parameters
+ ----------
+ path : str, optional
+ Path to tallies XML file
+
+ Returns
+ -------
+ openmc.Tallies
+ Tallies object
+
+ """
+ tree = ET.parse(path)
+ root = tree.getroot()
+
+ # Read mesh elements
+ meshes = {}
+ for elem in root.findall('mesh'):
+ mesh = MeshBase.from_xml_element(elem)
+ meshes[mesh.id] = mesh
+
+ # Read filter elements
+ filters = {}
+ for elem in root.findall('filter'):
+ filter = openmc.Filter.from_xml_element(elem, meshes=meshes)
+ filters[filter.id] = filter
+
+ # Read derivative elements
+ derivatives = {}
+ for elem in root.findall('derivative'):
+ deriv = openmc.TallyDerivative.from_xml_element(elem)
+ derivatives[deriv.id] = deriv
+
+ # Read tally elements
+ tallies = []
+ for elem in root.findall('tally'):
+ tally = openmc.Tally.from_xml_element(
+ elem, filters=filters, derivatives=derivatives
+ )
+ tallies.append(tally)
+
+ return cls(tallies)
diff --git a/openmc/tally_derivative.py b/openmc/tally_derivative.py
--- a/openmc/tally_derivative.py
+++ b/openmc/tally_derivative.py
@@ -105,3 +105,24 @@ def to_xml_element(self):
if self.variable == 'nuclide_density':
element.set("nuclide", self.nuclide)
return element
+
+ @classmethod
+ def from_xml_element(cls, elem):
+ """Generate tally derivative from an XML element
+
+ Parameters
+ ----------
+ elem : xml.etree.ElementTree.Element
+ XML element
+
+ Returns
+ -------
+ openmc.TallyDerivative
+ Tally derivative object
+
+ """
+ derivative_id = int(elem.get("id"))
+ variable = elem.get("variable")
+ material = int(elem.get("material"))
+ nuclide = elem.get("nuclide") if variable == "nuclide_density" else None
+ return cls(derivative_id, variable, material, nuclide)
diff --git a/openmc/trigger.py b/openmc/trigger.py
--- a/openmc/trigger.py
+++ b/openmc/trigger.py
@@ -74,7 +74,7 @@ def scores(self, scores):
if score not in self._scores:
self._scores.append(score)
- def get_trigger_xml(self, element):
+ def to_xml_element(self):
"""Return XML representation of the trigger
Returns
@@ -84,8 +84,36 @@ def get_trigger_xml(self, element):
"""
- subelement = ET.SubElement(element, "trigger")
- subelement.set("type", self._trigger_type)
- subelement.set("threshold", str(self._threshold))
+ element = ET.Element("trigger")
+ element.set("type", self._trigger_type)
+ element.set("threshold", str(self._threshold))
if len(self._scores) != 0:
- subelement.set("scores", ' '.join(map(str, self._scores)))
+ element.set("scores", ' '.join(self._scores))
+ return element
+
+ @classmethod
+ def from_xml_element(cls, elem):
+ """Generate trigger object from an XML element
+
+ Parameters
+ ----------
+ elem : xml.etree.ElementTree.Element
+ XML element
+
+ Returns
+ -------
+ openmc.Trigger
+ Trigger object
+
+ """
+ # Generate trigger object
+ trigger_type = elem.get("type")
+ threshold = float(elem.get("threshold"))
+ trigger = cls(trigger_type, threshold)
+
+ # Add scores if present
+ scores = elem.get("scores")
+ if scores is not None:
+ trigger.scores = scores.split()
+
+ return trigger
diff --git a/openmc/volume.py b/openmc/volume.py
--- a/openmc/volume.py
+++ b/openmc/volume.py
@@ -11,6 +11,7 @@
import openmc
import openmc.checkvalue as cv
+from openmc._xml import get_text
_VERSION_VOLUME = 1
@@ -352,3 +353,49 @@ def to_xml_element(self):
trigger_elem.set("type", self.trigger_type)
trigger_elem.set("threshold", str(self.threshold))
return element
+
+ @classmethod
+ def from_xml_element(cls, elem):
+ """Generate volume calculation object from an XML element
+
+ Parameters
+ ----------
+ elem : xml.etree.ElementTree.Element
+ XML element
+
+ Returns
+ -------
+ openmc.VolumeCalculation
+ Volume calculation object
+
+ """
+ domain_type = get_text(elem, "domain_type")
+ domain_ids = get_text(elem, "domain_ids").split()
+ ids = [int(x) for x in domain_ids]
+ samples = int(get_text(elem, "samples"))
+ lower_left = get_text(elem, "lower_left").split()
+ lower_left = tuple([float(x) for x in lower_left])
+ upper_right = get_text(elem, "upper_right").split()
+ upper_right = tuple([float(x) for x in upper_right])
+
+ # Instantiate some throw-away domains that are used by the constructor
+ # to assign IDs
+ with warnings.catch_warnings():
+ warnings.simplefilter('ignore', openmc.IDWarning)
+ if domain_type == 'cell':
+ domains = [openmc.Cell(uid) for uid in ids]
+ elif domain_type == 'material':
+ domains = [openmc.Material(uid) for uid in ids]
+ elif domain_type == 'universe':
+ domains = [openmc.Universe(uid) for uid in ids]
+
+ vol = cls(domains, samples, lower_left, upper_right)
+
+ # Check for trigger
+ trigger_elem = elem.find("threshold")
+ if trigger_elem is not None:
+ trigger_type = get_text(trigger_elem, "type")
+ threshold = float(get_text(trigger_elem, "threshold"))
+ vol.set_trigger(threshold, trigger_type)
+
+ return vol
diff --git a/openmc/weight_windows.py b/openmc/weight_windows.py
--- a/openmc/weight_windows.py
+++ b/openmc/weight_windows.py
@@ -270,7 +270,7 @@ def from_xml_element(cls, elem, root):
path = f"./mesh[@id='{mesh_id}']"
mesh_elem = root.find(path)
if mesh_elem is not None:
- mesh = MeshBase.from_xml(mesh_elem)
+ mesh = MeshBase.from_xml_element(mesh_elem)
# Read all other parameters
lower_ww_bounds = [float(l) for l in get_text(elem, 'lower_ww_bounds').split()]
| diff --git a/tests/regression_tests/filter_mesh/inputs_true.dat b/tests/regression_tests/filter_mesh/inputs_true.dat
--- a/tests/regression_tests/filter_mesh/inputs_true.dat
+++ b/tests/regression_tests/filter_mesh/inputs_true.dat
@@ -55,13 +55,13 @@
</mesh>
<mesh id="5" type="cylindrical">
<r_grid>0.0 0.4411764705882353 0.8823529411764706 1.3235294117647058 1.7647058823529411 2.2058823529411766 2.6470588235294117 3.0882352941176467 3.5294117647058822 3.9705882352941178 4.411764705882353 4.852941176470588 5.294117647058823 5.735294117647059 6.1764705882352935 6.617647058823529 7.0588235294117645 7.5</r_grid>
- <phi_grid>0.0 20.0 40.0 60.0 80.0 100.0 120.0 140.0 160.0 180.0 200.0 220.0 240.0 260.0 280.0 300.0 320.0 340.0 360.0</phi_grid>
+ <phi_grid>0.0 0.3490658503988659 0.6981317007977318 1.0471975511965976 1.3962634015954636 1.7453292519943295 2.0943951023931953 2.443460952792061 2.792526803190927 3.141592653589793 3.490658503988659 3.839724354387525 4.1887902047863905 4.537856055185257 4.886921905584122 5.235987755982989 5.585053606381854 5.93411945678072 6.283185307179586</phi_grid>
<z_grid>-7.5 -6.5625 -5.625 -4.6875 -3.75 -2.8125 -1.875 -0.9375 0.0 0.9375 1.875 2.8125 3.75 4.6875 5.625 6.5625 7.5</z_grid>
</mesh>
<mesh id="6" type="spherical">
<r_grid>0.0 0.4411764705882353 0.8823529411764706 1.3235294117647058 1.7647058823529411 2.2058823529411766 2.6470588235294117 3.0882352941176467 3.5294117647058822 3.9705882352941178 4.411764705882353 4.852941176470588 5.294117647058823 5.735294117647059 6.1764705882352935 6.617647058823529 7.0588235294117645 7.5</r_grid>
- <theta_grid>0.0 22.5 45.0 67.5 90.0 112.5 135.0 157.5 180.0</theta_grid>
- <phi_grid>0.0 20.0 40.0 60.0 80.0 100.0 120.0 140.0 160.0 180.0 200.0 220.0 240.0 260.0 280.0 300.0 320.0 340.0 360.0</phi_grid>
+ <theta_grid>0.0 0.39269908169872414 0.7853981633974483 1.1780972450961724 1.5707963267948966 1.9634954084936207 2.356194490192345 2.748893571891069 3.141592653589793</theta_grid>
+ <phi_grid>0.0 0.3490658503988659 0.6981317007977318 1.0471975511965976 1.3962634015954636 1.7453292519943295 2.0943951023931953 2.443460952792061 2.792526803190927 3.141592653589793 3.490658503988659 3.839724354387525 4.1887902047863905 4.537856055185257 4.886921905584122 5.235987755982989 5.585053606381854 5.93411945678072 6.283185307179586</phi_grid>
</mesh>
<filter id="1" type="mesh">
<bins>1</bins>
diff --git a/tests/regression_tests/filter_mesh/test.py b/tests/regression_tests/filter_mesh/test.py
--- a/tests/regression_tests/filter_mesh/test.py
+++ b/tests/regression_tests/filter_mesh/test.py
@@ -1,4 +1,5 @@
import numpy as np
+from math import pi
import openmc
import pytest
@@ -53,13 +54,13 @@ def model():
cyl_mesh = openmc.CylindricalMesh()
cyl_mesh.r_grid = np.linspace(0, 7.5, 18)
- cyl_mesh.phi_grid = np.linspace(0, 360, 19)
+ cyl_mesh.phi_grid = np.linspace(0, 2*pi, 19)
cyl_mesh.z_grid = np.linspace(-7.5, 7.5, 17)
sph_mesh = openmc.SphericalMesh()
sph_mesh.r_grid = np.linspace(0, 7.5, 18)
- sph_mesh.theta_grid = np.linspace(0, 180, 9)
- sph_mesh.phi_grid = np.linspace(0, 360, 19)
+ sph_mesh.theta_grid = np.linspace(0, pi, 9)
+ sph_mesh.phi_grid = np.linspace(0, 2*pi, 19)
# Create filters
reg_filters = [
diff --git a/tests/unit_tests/test_filters.py b/tests/unit_tests/test_filters.py
--- a/tests/unit_tests/test_filters.py
+++ b/tests/unit_tests/test_filters.py
@@ -1,5 +1,4 @@
-from math import sqrt, pi
-
+import numpy as np
import openmc
from pytest import fixture, approx
@@ -38,6 +37,11 @@ def test_cell_instance():
assert all(x == c1.id for x in bins[:6:2])
assert all(x == c2.id for x in bins[6::2])
+ # from_xml_element()
+ new_f = openmc.Filter.from_xml_element(elem)
+ assert new_f.id == f.id
+ assert np.all(new_f.bins == f.bins)
+
# get_pandas_dataframe()
df = f.get_pandas_dataframe(f.num_bins, 1)
cells = df['cellinstance', 'cell']
@@ -61,6 +65,11 @@ def test_collision():
assert elem.tag == 'filter'
assert elem.attrib['type'] == 'collision'
+ # from_xml_element()
+ new_f = openmc.Filter.from_xml_element(elem)
+ assert new_f.id == f.id
+ assert np.all(new_f.bins == f.bins)
+
def test_legendre():
n = 5
@@ -79,6 +88,11 @@ def test_legendre():
assert elem.attrib['type'] == 'legendre'
assert elem.find('order').text == str(n)
+ # from_xml_element()
+ new_f = openmc.Filter.from_xml_element(elem)
+ assert new_f.id == f.id
+ assert new_f.bins, f.bins
+
def test_spatial_legendre():
n = 5
@@ -102,6 +116,12 @@ def test_spatial_legendre():
assert elem.find('order').text == str(n)
assert elem.find('axis').text == str(axis)
+ # from_xml_element()
+ new_f = openmc.Filter.from_xml_element(elem)
+ assert new_f.id == f.id
+ assert new_f.order == f.order
+ assert new_f.axis == f.axis
+
def test_spherical_harmonics():
n = 3
@@ -122,6 +142,12 @@ def test_spherical_harmonics():
assert elem.attrib['cosine'] == f.cosine
assert elem.find('order').text == str(n)
+ # from_xml_element()
+ new_f = openmc.Filter.from_xml_element(elem)
+ assert new_f.id == f.id
+ assert new_f.order == f.order
+ assert new_f.cosine == f.cosine
+
def test_zernike():
n = 4
@@ -140,6 +166,12 @@ def test_zernike():
assert elem.attrib['type'] == 'zernike'
assert elem.find('order').text == str(n)
+ # from_xml_element()
+ new_f = openmc.Filter.from_xml_element(elem)
+ for attr in ('id', 'order', 'x', 'y', 'r'):
+ assert getattr(new_f, attr) == getattr(f, attr)
+
+
def test_zernike_radial():
n = 4
f = openmc.ZernikeRadialFilter(n, 0., 0., 1.)
@@ -157,6 +189,11 @@ def test_zernike_radial():
assert elem.attrib['type'] == 'zernikeradial'
assert elem.find('order').text == str(n)
+ # from_xml_element()
+ new_f = openmc.Filter.from_xml_element(elem)
+ for attr in ('id', 'order', 'x', 'y', 'r'):
+ assert getattr(new_f, attr) == getattr(f, attr)
+
def test_first_moment(run_in_tmpdir, box_model):
plain_tally = openmc.Tally()
diff --git a/tests/unit_tests/test_lib.py b/tests/unit_tests/test_lib.py
--- a/tests/unit_tests/test_lib.py
+++ b/tests/unit_tests/test_lib.py
@@ -583,17 +583,17 @@ def test_rectilinear_mesh(lib_init):
def test_cylindrical_mesh(lib_init):
deg2rad = lambda deg: deg*np.pi/180
mesh = openmc.lib.CylindricalMesh()
- x_grid = [0., 5., 10.]
- y_grid = [0., 10., 20.]
+ r_grid = [0., 5., 10.]
+ phi_grid = np.radians([0., 10., 20.])
z_grid = [10., 20., 30.]
- mesh.set_grid(x_grid, y_grid, z_grid)
+ mesh.set_grid(r_grid, phi_grid, z_grid)
assert np.all(mesh.lower_left == (0., 0., 10.))
assert np.all(mesh.upper_right == (10., deg2rad(20.), 30.))
assert np.all(mesh.dimension == (2, 2, 2))
- for i, diff_x in enumerate(np.diff(x_grid)):
- for j, diff_y in enumerate(np.diff(y_grid)):
- for k, diff_z in enumerate(np.diff(z_grid)):
- assert np.all(mesh.width[i, j, k, :] == (5, deg2rad(10), 10))
+ for i, _ in enumerate(np.diff(r_grid)):
+ for j, _ in enumerate(np.diff(phi_grid)):
+ for k, _ in enumerate(np.diff(z_grid)):
+ assert np.allclose(mesh.width[i, j, k, :], (5, deg2rad(10), 10))
with pytest.raises(exc.AllocationError):
mesh2 = openmc.lib.CylindricalMesh(mesh.id)
@@ -614,17 +614,17 @@ def test_cylindrical_mesh(lib_init):
def test_spherical_mesh(lib_init):
deg2rad = lambda deg: deg*np.pi/180
mesh = openmc.lib.SphericalMesh()
- x_grid = [0., 5., 10.]
- y_grid = [0., 10., 20.]
- z_grid = [10., 20., 30.]
- mesh.set_grid(x_grid, y_grid, z_grid)
+ r_grid = [0., 5., 10.]
+ theta_grid = np.radians([0., 10., 20.])
+ phi_grid = np.radians([10., 20., 30.])
+ mesh.set_grid(r_grid, theta_grid, phi_grid)
assert np.all(mesh.lower_left == (0., 0., deg2rad(10.)))
assert np.all(mesh.upper_right == (10., deg2rad(20.), deg2rad(30.)))
assert np.all(mesh.dimension == (2, 2, 2))
- for i, diff_x in enumerate(np.diff(x_grid)):
- for j, diff_y in enumerate(np.diff(y_grid)):
- for k, diff_z in enumerate(np.diff(z_grid)):
- assert np.all(abs(mesh.width[i, j, k, :] - (5, deg2rad(10), deg2rad(10))) < 1e-16)
+ for i, _ in enumerate(np.diff(r_grid)):
+ for j, _ in enumerate(np.diff(theta_grid)):
+ for k, _ in enumerate(np.diff(phi_grid)):
+ assert np.allclose(mesh.width[i, j, k, :], (5, deg2rad(10), deg2rad(10)))
with pytest.raises(exc.AllocationError):
mesh2 = openmc.lib.SphericalMesh(mesh.id)
diff --git a/tests/unit_tests/test_model.py b/tests/unit_tests/test_model.py
--- a/tests/unit_tests/test_model.py
+++ b/tests/unit_tests/test_model.py
@@ -195,8 +195,8 @@ def test_from_xml(run_in_tmpdir, pin_model_attributes):
keys = sorted(k for k in settings.__dict__.keys() if k not in no_test)
for ref_k in keys:
assert test_model.settings.__dict__[ref_k] == settings.__dict__[ref_k]
- assert len(test_model.tallies) == 0
- assert len(test_model.plots) == 0
+ assert len(test_model.tallies) == 1
+ assert len(test_model.plots) == 2
assert test_model._materials_by_id == \
{1: test_model.materials[0], 2: test_model.materials[1],
3: test_model.materials[2]}
diff --git a/tests/unit_tests/test_plots.py b/tests/unit_tests/test_plots.py
--- a/tests/unit_tests/test_plots.py
+++ b/tests/unit_tests/test_plots.py
@@ -1,3 +1,4 @@
+import numpy as np
import openmc
import openmc.examples
import pytest
@@ -12,8 +13,8 @@ def myplot():
plot.filename = 'myplot'
plot.type = 'slice'
plot.basis = 'yz'
- plot.background = (0, 0, 0)
plot.background = 'black'
+ plot.background = (0, 0, 0)
plot.color_by = 'material'
m1, m2 = openmc.Material(), openmc.Material()
@@ -21,8 +22,8 @@ def myplot():
plot.colors = {m1: 'green', m2: 'blue'}
plot.mask_components = [openmc.Material()]
- plot.mask_background = (255, 255, 255)
plot.mask_background = 'white'
+ plot.mask_background = (255, 255, 255)
plot.overlap_color = (255, 211, 0)
plot.overlap_color = 'yellow'
@@ -70,7 +71,7 @@ def test_highlight_domains():
plots.highlight_domains(model.geometry, mats)
-def test_to_xml_element(myplot):
+def test_xml_element(myplot):
elem = myplot.to_xml_element()
assert 'id' in elem.attrib
assert 'color_by' in elem.attrib
@@ -80,10 +81,19 @@ def test_to_xml_element(myplot):
assert elem.find('pixels') is not None
assert elem.find('background').text == '0 0 0'
+ newplot = openmc.Plot.from_xml_element(elem)
+ attributes = ('id', 'color_by', 'filename', 'type', 'basis', 'level',
+ 'meshlines', 'show_overlaps', 'origin', 'width', 'pixels',
+ 'background', 'mask_background')
+ for attr in attributes:
+ assert getattr(newplot, attr) == getattr(myplot, attr), attr
+
def test_plots(run_in_tmpdir):
p1 = openmc.Plot(name='plot1')
+ p1.origin = (5., 5., 5.)
p2 = openmc.Plot(name='plot2')
+ p2.origin = (-3., -3., -3.)
plots = openmc.Plots([p1, p2])
assert len(plots) == 2
@@ -92,3 +102,9 @@ def test_plots(run_in_tmpdir):
assert len(plots) == 3
plots.export_to_xml()
+
+ # from_xml
+ new_plots = openmc.Plots.from_xml()
+ assert len(plots)
+ assert plots[0].origin == p1.origin
+ assert plots[1].origin == p2.origin
diff --git a/tests/unit_tests/test_settings.py b/tests/unit_tests/test_settings.py
--- a/tests/unit_tests/test_settings.py
+++ b/tests/unit_tests/test_settings.py
@@ -112,3 +112,10 @@ def test_export_to_xml(run_in_tmpdir):
assert not s.photon_transport
assert s.electron_treatment == 'led'
assert s.write_initial_source == True
+ assert len(s.volume_calculations) == 1
+ vol = s.volume_calculations[0]
+ assert vol.domain_type == 'cell'
+ assert len(vol.ids) == 1
+ assert vol.samples == 1000
+ assert vol.lower_left == (-10., -10., -10.)
+ assert vol.upper_right == (10., 10., 10.)
diff --git a/tests/unit_tests/test_tallies.py b/tests/unit_tests/test_tallies.py
new file mode 100644
--- /dev/null
+++ b/tests/unit_tests/test_tallies.py
@@ -0,0 +1,40 @@
+import numpy as np
+import openmc
+
+
+def test_xml_roundtrip(run_in_tmpdir):
+ # Create a tally with all possible gizmos
+ mesh = openmc.RegularMesh()
+ mesh.lower_left = (-10., -10., -10.)
+ mesh.upper_right = (10., 10., 10.,)
+ mesh.dimension = (5, 5, 5)
+ mesh_filter = openmc.MeshFilter(mesh)
+ tally = openmc.Tally()
+ tally.filters = [mesh_filter]
+ tally.nuclides = ['U235', 'I135', 'Li6']
+ tally.scores = ['total', 'fission', 'heating']
+ tally.derivative = openmc.TallyDerivative(
+ variable='nuclide_density', material=1, nuclide='Li6'
+ )
+ tally.triggers = [openmc.Trigger('rel_err', 0.025)]
+ tally.triggers[0].scores = ['total', 'fission']
+ tallies = openmc.Tallies([tally])
+
+ # Roundtrip through XML and make sure we get what we started with
+ tallies.export_to_xml()
+ new_tallies = openmc.Tallies.from_xml()
+ assert len(new_tallies) == 1
+ new_tally = new_tallies[0]
+ assert new_tally.id == tally.id
+ assert len(new_tally.filters) == 1
+ assert isinstance(new_tally.filters[0], openmc.MeshFilter)
+ assert np.allclose(new_tally.filters[0].mesh.lower_left, mesh.lower_left)
+ assert new_tally.nuclides == tally.nuclides
+ assert new_tally.scores == tally.scores
+ assert new_tally.derivative.variable == tally.derivative.variable
+ assert new_tally.derivative.material == tally.derivative.material
+ assert new_tally.derivative.nuclide == tally.derivative.nuclide
+ assert len(new_tally.triggers) == 1
+ assert new_tally.triggers[0].trigger_type == tally.triggers[0].trigger_type
+ assert new_tally.triggers[0].threshold == tally.triggers[0].threshold
+ assert new_tally.triggers[0].scores == tally.triggers[0].scores
| Add `from_xml_element` methods to spherical and cylindrical mesh objects...
...and update the `mesh.MeshBase.from_xml` method to include those types.
| 2022-01-21T04:29:04Z | [] | [] |
|
openmc-dev/openmc | 2,071 | openmc-dev__openmc-2071 | [
"1923"
] | 7752afb554aa05103ed8f62a3c26b12632bbac2c | diff --git a/openmc/__init__.py b/openmc/__init__.py
--- a/openmc/__init__.py
+++ b/openmc/__init__.py
@@ -30,6 +30,7 @@
from openmc.plotter import *
from openmc.search import *
from openmc.polynomial import *
+from openmc.tracks import *
from . import examples
# Import a few names from the model module
diff --git a/openmc/settings.py b/openmc/settings.py
--- a/openmc/settings.py
+++ b/openmc/settings.py
@@ -2,6 +2,7 @@
import typing # imported separately as py3.8 requires typing.Iterable
from collections.abc import Iterable, Mapping, MutableSequence
from enum import Enum
+import itertools
from math import ceil
from numbers import Integral, Real
from pathlib import Path
@@ -104,6 +105,10 @@ class Settings:
Maximum number of times a particle can split during a history
.. versionadded:: 0.13
+ max_tracks : int
+ Maximum number of tracks written to a track file (per MPI process).
+
+ .. versionadded:: 0.13.1
no_reduce : bool
Indicate that all user-defined and global tallies should not be reduced
across processes in a parallel calculation.
@@ -187,7 +192,7 @@ class Settings:
integers: the batch number, generation number, and particle number
track : tuple or list
Specify particles for which track files should be written. Each particle
- is identified by a triplet with the batch number, generation number, and
+ is identified by a tuple with the batch number, generation number, and
particle number.
trigger_active : bool
Indicate whether tally triggers are used
@@ -290,6 +295,7 @@ def __init__(self):
self._weight_windows = cv.CheckedList(WeightWindows, 'weight windows')
self._weight_windows_on = None
self._max_splits = None
+ self._max_tracks = None
@property
def run_mode(self):
@@ -475,6 +481,10 @@ def weight_windows_on(self):
def max_splits(self):
return self._max_splits
+ @property
+ def max_tracks(self):
+ return self._max_tracks
+
@run_mode.setter
def run_mode(self, run_mode: str):
cv.check_value('run mode', run_mode, {x.value for x in RunMode})
@@ -776,16 +786,18 @@ def trace(self, trace: Iterable):
self._trace = trace
@track.setter
- def track(self, track: typing.Iterable[int]):
- cv.check_type('track', track, Iterable, Integral)
- if len(track) % 3 != 0:
- msg = f'Unable to set the track to "{track}" since its length is ' \
- 'not a multiple of 3'
- raise ValueError(msg)
- for t in zip(track[::3], track[1::3], track[2::3]):
+ def track(self, track: typing.Iterable[typing.Iterable[int]]):
+ cv.check_type('track', track, Iterable)
+ for t in track:
+ if len(t) != 3:
+ msg = f'Unable to set the track to "{t}" since its length is not 3'
+ raise ValueError(msg)
cv.check_greater_than('track batch', t[0], 0)
- cv.check_greater_than('track generation', t[0], 0)
- cv.check_greater_than('track particle', t[0], 0)
+ cv.check_greater_than('track generation', t[1], 0)
+ cv.check_greater_than('track particle', t[2], 0)
+ cv.check_type('track batch', t[0], Integral)
+ cv.check_type('track generation', t[1], Integral)
+ cv.check_type('track particle', t[2], Integral)
self._track = track
@ufs_mesh.setter
@@ -881,9 +893,15 @@ def weight_windows_on(self, value):
@max_splits.setter
def max_splits(self, value: int):
cv.check_type('maximum particle splits', value, Integral)
- cv.check_greater_than('max particles in flight', value, 0)
+ cv.check_greater_than('max particle splits', value, 0)
self._max_splits = value
+ @max_tracks.setter
+ def max_tracks(self, value: int):
+ cv.check_type('maximum particle tracks', value, Integral)
+ cv.check_greater_than('maximum particle tracks', value, 0, True)
+ self._max_tracks = value
+
def _create_run_mode_subelement(self, root):
elem = ET.SubElement(root, "run_mode")
elem.text = self._run_mode.value
@@ -1110,7 +1128,7 @@ def _create_trace_subelement(self, root):
def _create_track_subelement(self, root):
if self._track is not None:
element = ET.SubElement(root, "track")
- element.text = ' '.join(map(str, self._track))
+ element.text = ' '.join(map(str, itertools.chain(*self._track)))
def _create_ufs_mesh_subelement(self, root):
if self.ufs_mesh is not None:
@@ -1196,6 +1214,11 @@ def _create_max_splits_subelement(self, root):
elem = ET.SubElement(root, "max_splits")
elem.text = str(self._max_splits)
+ def _create_max_tracks_subelement(self, root):
+ if self._max_tracks is not None:
+ elem = ET.SubElement(root, "max_tracks")
+ elem.text = str(self._max_tracks)
+
def _eigenvalue_from_xml_element(self, root):
elem = root.find('eigenvalue')
if elem is not None:
@@ -1424,7 +1447,8 @@ def _trace_from_xml_element(self, root):
def _track_from_xml_element(self, root):
text = get_text(root, 'track')
if text is not None:
- self.track = [int(x) for x in text.split()]
+ values = [int(x) for x in text.split()]
+ self.track = list(zip(values[::3], values[1::3], values[2::3]))
def _ufs_mesh_from_xml_element(self, root):
text = get_text(root, 'ufs_mesh')
@@ -1498,6 +1522,11 @@ def _max_splits_from_xml_element(self, root):
if text is not None:
self.max_splits = int(text)
+ def _max_tracks_from_xml_element(self, root):
+ text = get_text(root, 'max_tracks')
+ if text is not None:
+ self.max_tracks = int(text)
+
def export_to_xml(self, path: Union[str, os.PathLike] = 'settings.xml'):
"""Export simulation settings to an XML file.
@@ -1554,6 +1583,7 @@ def export_to_xml(self, path: Union[str, os.PathLike] = 'settings.xml'):
self._create_write_initial_source_subelement(root_element)
self._create_weight_windows_subelement(root_element)
self._create_max_splits_subelement(root_element)
+ self._create_max_tracks_subelement(root_element)
# Clean the indentation in the file to be user-readable
clean_indentation(root_element)
@@ -1633,6 +1663,7 @@ def from_xml(cls, path: Union[str, os.PathLike] = 'settings.xml'):
settings._write_initial_source_from_xml_element(root)
settings._weight_windows_from_xml_element(root)
settings._max_splits_from_xml_element(root)
+ settings._max_tracks_from_xml_element(root)
# TODO: Get volume calculations
diff --git a/openmc/source.py b/openmc/source.py
--- a/openmc/source.py
+++ b/openmc/source.py
@@ -298,6 +298,10 @@ def __init__(self, r=(0., 0., 0.), u=(0., 0., 1.), E=1.0e6, time=0.0, wgt=1.0,
self.surf_id = surf_id
self.particle = particle
+ def __repr__(self):
+ name = self.particle.name.lower()
+ return f'<SourceParticle: {name} at E={self.E:.6e} eV>'
+
def to_tuple(self):
"""Return source particle attributes as a tuple
diff --git a/openmc/tracks.py b/openmc/tracks.py
new file mode 100644
--- /dev/null
+++ b/openmc/tracks.py
@@ -0,0 +1,291 @@
+from collections import namedtuple
+from collections.abc import Sequence
+
+import h5py
+
+from .checkvalue import check_filetype_version
+from .source import SourceParticle, ParticleType
+
+
+ParticleTrack = namedtuple('ParticleTrack', ['particle', 'states'])
+ParticleTrack.__doc__ = """\
+Particle track information
+
+Parameters
+----------
+particle : openmc.ParticleType
+ Type of the particle
+states : numpy.ndarray
+ Structured array containing each state of the particle. The structured array
+ contains the following fields: ``r`` (position; each direction in [cm]),
+ ``u`` (direction), ``E`` (energy in [eV]), ``time`` (time in [s]), ``wgt``
+ (weight), ``cell_id`` (cell ID) , ``cell_instance`` (cell instance), and
+ ``material_id`` (material ID).
+
+"""
+def _particle_track_repr(self):
+ name = self.particle.name.lower()
+ return f"<ParticleTrack: {name}, {len(self.states)} states>"
+ParticleTrack.__repr__ = _particle_track_repr
+
+
+_VERSION_TRACK = 3
+
+
+def _identifier(dset_name):
+ """Return (batch, gen, particle) tuple given dataset name"""
+ _, batch, gen, particle = dset_name.split('_')
+ return (int(batch), int(gen), int(particle))
+
+
+class Track(Sequence):
+ """Tracks resulting from a single source particle
+
+ This class stores information for all tracks resulting from a primary source
+ particle and any secondary particles that it created. The track for each
+ primary/secondary particle is stored in the :attr:`particle_tracks`
+ attribute.
+
+ Parameters
+ ----------
+ dset : h5py.Dataset
+ Dataset to read track data from
+
+ Attributes
+ ----------
+ identifier : tuple
+ Tuple of (batch, generation, particle number)
+ particle_tracks : list
+ List of tuples containing (particle type, array of track states)
+ sources : list
+ List of :class:`SourceParticle` representing each primary/secondary
+ particle
+
+ """
+
+ def __init__(self, dset):
+ tracks = dset[()]
+ offsets = dset.attrs['offsets']
+ particles = dset.attrs['particles']
+ self.identifier = _identifier(dset.name)
+
+ # Construct list of track histories
+ tracks_list = []
+ for particle, start, end in zip(particles, offsets[:-1], offsets[1:]):
+ ptype = ParticleType(particle)
+ tracks_list.append(ParticleTrack(ptype, tracks[start:end]))
+ self.particle_tracks = tracks_list
+
+ def __repr__(self):
+ return f'<Track {self.identifier}: {len(self.particle_tracks)} particles>'
+
+ def __getitem__(self, index):
+ return self.particle_tracks[index]
+
+ def __len__(self):
+ return len(self.particle_tracks)
+
+ def filter(self, particle=None, state_filter=None):
+ """Filter particle tracks by given criteria
+
+ Parameters
+ ----------
+ particle : {'neutron', 'photon', 'electron', 'positron'}
+ Matching particle type
+ state_filter : function
+ Function that takes a state (structured datatype) and returns a bool
+ depending on some criteria.
+
+ Returns
+ -------
+ Track
+ New instance with only matching :class:`openmc.ParticleTrack` objects
+
+ Examples
+ --------
+ Get all particle tracks for photons:
+
+ >>> track.filter(particle='photon')
+
+ Get all particle tracks that entered cell with ID=15:
+
+ >>> track.filter(state_filter=lambda s: s['cell_id'] == 15)
+
+ Get all particle tracks in entered material with ID=2:
+
+ >>> track.filter(state_filter=lambda s: s['material_id'] == 2)
+
+ See Also
+ --------
+ openmc.ParticleTrack
+
+ """
+ matching = []
+ for t in self:
+ # Check for matching particle
+ if particle is not None:
+ if t.particle.name.lower() != particle:
+ continue
+
+ # Apply arbitrary state filter
+ match = True
+ if state_filter is not None:
+ for state in t.states:
+ if state_filter(state):
+ break
+ else:
+ match = False
+
+ if match:
+ matching.append(t)
+
+ # Return new Track instance with only matching particle tracks
+ track = type(self).__new__(type(self))
+ track.identifier = self.identifier
+ track.particle_tracks = matching
+ return track
+
+ def plot(self, axes=None):
+ """Produce a 3D plot of particle tracks
+
+ Parameters
+ ----------
+ axes : matplotlib.axes.Axes, optional
+ Axes for plot
+
+ Returns
+ -------
+ axes : matplotlib.axes.Axes
+ Axes for plot
+
+ """
+ import matplotlib.pyplot as plt
+
+ # Setup axes is one wasn't passed
+ if axes is None:
+ fig = plt.figure()
+ ax = plt.axes(projection='3d')
+ ax.set_xlabel('x [cm]')
+ ax.set_ylabel('y [cm]')
+ ax.set_zlabel('z [cm]')
+ else:
+ ax = axes
+
+ # Plot each particle track
+ for _, states in self:
+ r = states['r']
+ ax.plot3D(r['x'], r['y'], r['z'])
+
+ return ax
+
+ @property
+ def sources(self):
+ sources = []
+ for particle_track in self:
+ particle_type = ParticleType(particle_track.particle)
+ state = particle_track.states[0]
+ sources.append(
+ SourceParticle(
+ r=state['r'], u=state['u'], E=state['E'],
+ time=state['time'], wgt=state['wgt'],
+ particle=particle_type
+ )
+ )
+ return sources
+
+
+class Tracks(list):
+ """Collection of particle tracks
+
+ This class behaves like a list and can be indexed using the normal subscript
+ notation. Each element in the list is a :class:`openmc.Track` object.
+
+ Parameters
+ ----------
+ filepath : str or pathlib.Path
+ Path of file to load
+
+ """
+
+ def __init__(self, filepath='tracks.h5'):
+ # Read data from track file
+ with h5py.File(filepath, 'r') as fh:
+ # Check filetype and version
+ check_filetype_version(fh, 'track', _VERSION_TRACK)
+
+ for dset_name in sorted(fh, key=_identifier):
+ dset = fh[dset_name]
+ self.append(Track(dset))
+
+ def filter(self, particle=None, state_filter=None):
+ """Filter tracks by given criteria
+
+ Parameters
+ ----------
+ particle : {'neutron', 'photon', 'electron', 'positron'}
+ Matching particle type
+ state_filter : function
+ Function that takes a state (structured datatype) and returns a bool
+ depending on some criteria.
+
+ Returns
+ -------
+ Tracks
+ List of :class:`openmc.Track` objects
+
+ See Also
+ --------
+ openmc.Track.filter
+
+ """
+ # Create a new Tracks instance but avoid call to __init__
+ matching = type(self).__new__(type(self))
+
+ # Append matching Track objects
+ for track in self:
+ if track.filter(particle, state_filter):
+ matching.append(track)
+ return matching
+
+ def plot(self):
+ """Produce a 3D plot of particle tracks
+
+ Returns
+ -------
+ matplotlib.axes.Axes
+ Axes for plot
+
+ """
+ import matplotlib.pyplot as plt
+ fig = plt.figure()
+ ax = plt.axes(projection='3d')
+ ax.set_xlabel('x [cm]')
+ ax.set_ylabel('y [cm]')
+ ax.set_zlabel('z [cm]')
+ for track in self:
+ track.plot(ax)
+ return ax
+
+ @staticmethod
+ def combine(track_files, path='tracks.h5'):
+ """Combine multiple track files into a single track file
+
+ Parameters
+ ----------
+ track_files : list of path-like
+ Paths to track files to combine
+ path : path-like
+ Path of combined track file to create
+
+ """
+ with h5py.File(path, 'w') as h5_out:
+ for i, fname in enumerate(track_files):
+ with h5py.File(fname, 'r') as h5_in:
+ # Copy file attributes for first file
+ if i == 0:
+ h5_out.attrs['filetype'] = h5_in.attrs['filetype']
+ h5_out.attrs['version'] = h5_in.attrs['version']
+
+ # Copy each 'track_*' dataset from input file
+ for dset in h5_in:
+ h5_in.copy(dset, h5_out)
| diff --git a/tests/regression_tests/track_output/results_true.dat b/tests/regression_tests/track_output/results_true.dat
--- a/tests/regression_tests/track_output/results_true.dat
+++ b/tests/regression_tests/track_output/results_true.dat
@@ -1,9 +1,266 @@
-<?xml version="1.0"?>
-<VTKFile type="PPolyData" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
- <PPolyData GhostLevel="0">
- <PPoints>
- <PDataArray type="Float32" Name="Points" NumberOfComponents="3"/>
- </PPoints>
- <Piece Source="poly_0.vtp"/>
- </PPolyData>
-</VTKFile>
+ParticleType.NEUTRON [((-9.663085e-01, -6.616522e-01, -9.863690e-01), (-7.513921e-01, 4.140970e-01, 5.137447e-01), 5.293873e+06, 0.000000e+00, 1.000000e+00, 23, 2403, 1)
+ ((-1.281491e+00, -4.879529e-01, -7.708709e-01), (-7.513921e-01, 4.140970e-01, 5.137447e-01), 5.293873e+06, 1.323629e-10, 1.000000e+00, 22, 2403, 3)
+ ((-1.368452e+00, -4.400285e-01, -7.114141e-01), (-7.513921e-01, 4.140970e-01, 5.137447e-01), 5.293873e+06, 1.688824e-10, 1.000000e+00, 21, 2403, 2)
+ ((-2.150539e+00, -9.015151e-03, -1.766823e-01), (-7.513921e-01, 4.140970e-01, 5.137447e-01), 5.293873e+06, 4.973246e-10, 1.000000e+00, 22, 2403, 3)
+ ((-2.237499e+00, 3.890922e-02, -1.172255e-01), (-7.513921e-01, 4.140970e-01, 5.137447e-01), 5.293873e+06, 5.338441e-10, 1.000000e+00, 23, 2403, 1)
+ ((-2.453640e+00, 1.580257e-01, 3.055504e-02), (-7.513921e-01, 4.140970e-01, 5.137447e-01), 5.293873e+06, 6.246136e-10, 1.000000e+00, 23, 2402, 1)
+ ((-2.767485e+00, 3.309877e-01, 2.451383e-01), (-7.513921e-01, 4.140970e-01, 5.137447e-01), 5.293873e+06, 7.564146e-10, 1.000000e+00, 22, 2402, 3)
+ ((-2.825099e+00, 3.627392e-01, 2.845305e-01), (-6.842434e-01, 3.658561e-01, 6.308409e-01), 5.292729e+06, 7.806100e-10, 1.000000e+00, 22, 2402, 3)
+ ((-3.274427e+00, 6.029890e-01, 6.987901e-01), (-6.842434e-01, 3.658561e-01, 6.308409e-01), 5.292729e+06, 9.878481e-10, 1.000000e+00, 23, 2402, 1)
+ ((-3.676327e+00, 8.178800e-01, 1.069324e+00), (-6.842434e-01, 3.658561e-01, 6.308409e-01), 5.292729e+06, 1.173212e-09, 1.000000e+00, 23, 2416, 1)
+ ((-4.089400e+00, 1.038745e+00, 1.450158e+00), (-6.842434e-01, 3.658561e-01, 6.308409e-01), 5.292729e+06, 1.363728e-09, 1.000000e+00, 23, 2415, 1)
+ ((-4.456639e+00, 1.235102e+00, 1.788735e+00), (-6.842434e-01, 3.658561e-01, 6.308409e-01), 5.292729e+06, 1.533105e-09, 1.000000e+00, 22, 2415, 3)
+ ((-4.536974e+00, 1.278056e+00, 1.862800e+00), (-6.842434e-01, 3.658561e-01, 6.308409e-01), 5.292729e+06, 1.570157e-09, 1.000000e+00, 21, 2415, 2)
+ ((-5.410401e+00, 1.745067e+00, 2.668060e+00), (-6.842434e-01, 3.658561e-01, 6.308409e-01), 5.292729e+06, 1.972998e-09, 1.000000e+00, 22, 2415, 3)
+ ((-5.490736e+00, 1.788021e+00, 2.742125e+00), (-6.842434e-01, 3.658561e-01, 6.308409e-01), 5.292729e+06, 2.010050e-09, 1.000000e+00, 23, 2415, 1)
+ ((-5.576301e+00, 1.833771e+00, 2.821012e+00), (-2.881377e-01, 1.217316e-01, -9.498200e-01), 4.458753e+06, 2.049514e-09, 1.000000e+00, 23, 2415, 1)
+ ((-5.725160e+00, 1.896661e+00, 2.330311e+00), (-2.881377e-01, 1.217316e-01, -9.498200e-01), 4.458753e+06, 2.227030e-09, 1.000000e+00, 23, 2414, 1)
+ ((-6.116514e+00, 2.061999e+00, 1.040248e+00), (-2.881377e-01, 1.217316e-01, -9.498200e-01), 4.458753e+06, 2.693724e-09, 1.000000e+00, 22, 2414, 3)
+ ((-6.534762e+00, 2.238699e+00, -3.384686e-01), (-2.881377e-01, 1.217316e-01, -9.498200e-01), 4.458753e+06, 3.192489e-09, 1.000000e+00, 23, 2414, 1)
+ ((-7.043525e+00, 2.453640e+00, -2.015560e+00), (-2.881377e-01, 1.217316e-01, -9.498200e-01), 4.458753e+06, 3.799195e-09, 1.000000e+00, 23, 2428, 1)
+ ((-7.360920e+00, 2.587732e+00, -3.061825e+00), (-2.881377e-01, 1.217316e-01, -9.498200e-01), 4.458753e+06, 4.177692e-09, 1.000000e+00, 11, 1757, 1)
+ ((-8.996680e+00, 3.278803e+00, -8.453960e+00), (-2.881377e-01, 1.217316e-01, -9.498200e-01), 4.458753e+06, 6.128354e-09, 1.000000e+00, 23, 2427, 1)
+ ((-9.220205e+00, 3.373238e+00, -9.190791e+00), (-2.881377e-01, 1.217316e-01, -9.498200e-01), 4.458753e+06, 6.394910e-09, 1.000000e+00, 22, 2427, 3)
+ ((-9.320244e+00, 3.415502e+00, -9.520561e+00), (-2.881377e-01, 1.217316e-01, -9.498200e-01), 4.458753e+06, 6.514208e-09, 1.000000e+00, 21, 2427, 2)
+ ((-1.005591e+01, 3.726304e+00, -1.194562e+01), (-2.881377e-01, 1.217316e-01, -9.498200e-01), 4.458753e+06, 7.391498e-09, 1.000000e+00, 22, 2427, 3)
+ ((-1.015595e+01, 3.768569e+00, -1.227539e+01), (-2.881377e-01, 1.217316e-01, -9.498200e-01), 4.458753e+06, 7.510796e-09, 1.000000e+00, 23, 2427, 1)
+ ((-1.062054e+01, 3.964848e+00, -1.380687e+01), (-5.395885e-01, 2.109921e-01, -8.150623e-01), 4.068754e+06, 8.064826e-09, 1.000000e+00, 23, 2427, 1)
+ ((-1.063244e+01, 3.969501e+00, -1.382484e+01), (-5.395885e-01, 2.109921e-01, -8.150623e-01), 4.068754e+06, 8.072756e-09, 1.000000e+00, 23, 2426, 1)
+ ((-1.093907e+01, 4.089400e+00, -1.428802e+01), (-5.395885e-01, 2.109921e-01, -8.150623e-01), 4.068754e+06, 8.277097e-09, 1.000000e+00, 23, 2437, 1)
+ ((-1.108410e+01, 4.146112e+00, -1.450710e+01), (4.855193e-01, 3.316053e-01, -8.088937e-01), 8.856868e+05, 8.373750e-09, 1.000000e+00, 23, 2437, 1)
+ ((-1.080173e+01, 4.338973e+00, -1.497755e+01), (2.818553e-01, 5.419536e-02, -9.579251e-01), 7.653670e+05, 8.820862e-09, 1.000000e+00, 23, 2437, 1)
+ ((-1.063244e+01, 4.371524e+00, -1.555290e+01), (2.818553e-01, 5.419536e-02, -9.579251e-01), 7.653670e+05, 9.317522e-09, 1.000000e+00, 23, 2438, 1)
+ ((-1.041266e+01, 4.413783e+00, -1.629984e+01), (2.686183e-01, -3.269476e-01, -9.060626e-01), 6.562001e+05, 9.962308e-09, 1.000000e+00, 23, 2438, 1)
+ ((-1.016754e+01, 4.115428e+00, -1.712667e+01), (-6.340850e-01, -7.142137e-01, -2.963697e-01), 7.155058e+04, 1.077718e-08, 1.000000e+00, 23, 2438, 1)
+ ((-1.019064e+01, 4.089400e+00, -1.713747e+01), (-6.340850e-01, -7.142137e-01, -2.963697e-01), 7.155058e+04, 1.087569e-08, 1.000000e+00, 23, 2427, 1)
+ ((-1.024915e+01, 4.023496e+00, -1.716481e+01), (1.827568e-01, -7.452255e-01, -6.412791e-01), 2.628504e+04, 1.112511e-08, 1.000000e+00, 23, 2427, 1)
+ ((-1.018199e+01, 3.749638e+00, -1.740047e+01), (1.827568e-01, -7.452255e-01, -6.412791e-01), 2.628504e+04, 1.276389e-08, 1.000000e+00, 22, 2427, 3)
+ ((-1.015866e+01, 3.654498e+00, -1.748234e+01), (1.827568e-01, -7.452255e-01, -6.412791e-01), 2.628504e+04, 1.333321e-08, 1.000000e+00, 21, 2427, 2)
+ ((-1.009978e+01, 3.414404e+00, -1.768895e+01), (1.735861e-01, -9.678731e-01, 1.819053e-01), 2.620416e+04, 1.476994e-08, 1.000000e+00, 21, 2427, 2)
+ ((-9.994809e+00, 2.829099e+00, -1.757894e+01), (4.635724e-01, 5.558106e-01, 6.900545e-01), 2.214649e+04, 1.747088e-08, 1.000000e+00, 21, 2427, 2)
+ ((-9.553365e+00, 3.358379e+00, -1.692183e+01), (-5.990363e-01, 3.483710e-01, -7.209668e-01), 1.813617e+04, 2.209726e-08, 1.000000e+00, 21, 2427, 2)
+ ((-1.011854e+01, 3.687059e+00, -1.760205e+01), (-5.990363e-01, 3.483710e-01, -7.209668e-01), 1.813617e+04, 2.716243e-08, 1.000000e+00, 22, 2427, 3)
+ ((-1.020058e+01, 3.734765e+00, -1.770077e+01), (-5.990363e-01, 3.483710e-01, -7.209668e-01), 1.813617e+04, 2.789760e-08, 1.000000e+00, 23, 2427, 1)
+ ((-1.063244e+01, 3.985917e+00, -1.822054e+01), (-5.990363e-01, 3.483710e-01, -7.209668e-01), 1.813617e+04, 3.176800e-08, 1.000000e+00, 23, 2426, 1)
+ ((-1.081038e+01, 4.089400e+00, -1.843470e+01), (-5.990363e-01, 3.483710e-01, -7.209668e-01), 1.813617e+04, 3.336273e-08, 1.000000e+00, 23, 2437, 1)
+ ((-1.081564e+01, 4.092455e+00, -1.844103e+01), (-6.690877e-01, 6.718700e-01, -3.176671e-01), 1.355236e+04, 3.340982e-08, 1.000000e+00, 23, 2437, 1)
+ ((-1.096190e+01, 4.239327e+00, -1.851047e+01), (-5.904492e-01, 8.058629e-01, 4.421237e-02), 1.153343e+04, 3.476743e-08, 1.000000e+00, 23, 2437, 1)
+ ((-1.109457e+01, 4.420404e+00, -1.850054e+01), (-5.904492e-01, 8.058629e-01, 4.421237e-02), 1.153343e+04, 3.628014e-08, 1.000000e+00, 22, 2437, 3)
+ ((-1.113484e+01, 4.475368e+00, -1.849752e+01), (-3.382310e-01, -9.403895e-01, -3.560132e-02), 1.114105e+04, 3.673931e-08, 1.000000e+00, 22, 2437, 3)
+ ((-1.117187e+01, 4.372425e+00, -1.850142e+01), (-3.382310e-01, -9.403895e-01, -3.560132e-02), 1.114105e+04, 3.748914e-08, 1.000000e+00, 23, 2437, 1)
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+ ((-1.135375e+01, 3.866733e+00, -1.852056e+01), (-3.382310e-01, -9.403895e-01, -3.560132e-02), 1.114105e+04, 4.117251e-08, 1.000000e+00, 22, 2426, 3)
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+ ((-1.309582e+01, 2.150526e+00, -1.834143e+01), (1.090151e-01, 4.333767e-01, -8.945950e-01), 2.357642e+02, 2.808996e-07, 1.000000e+00, 22, 2100, 3)
+ ((-1.307365e+01, 2.238628e+00, -1.852329e+01), (1.090151e-01, 4.333767e-01, -8.945950e-01), 2.357642e+02, 2.904717e-07, 1.000000e+00, 23, 2100, 1)
+ ((-1.301957e+01, 2.453640e+00, -1.896713e+01), (1.090151e-01, 4.333767e-01, -8.945950e-01), 2.357642e+02, 3.138324e-07, 1.000000e+00, 23, 2101, 1)
+ ((-1.297913e+01, 2.614390e+00, -1.929896e+01), (6.012134e-01, 7.985735e-01, -2.868317e-02), 4.041011e+01, 3.312976e-07, 1.000000e+00, 23, 2101, 1)
+ ((-1.295975e+01, 2.640133e+00, -1.929988e+01), (6.762805e-01, -5.875192e-01, 4.443713e-01), 3.527833e+01, 3.349640e-07, 1.000000e+00, 23, 2101, 1)
+ ((-1.282907e+01, 2.526604e+00, -1.921402e+01), (-1.767101e-01, -9.842348e-01, 7.448995e-03), 6.258032e+00, 3.584852e-07, 1.000000e+00, 23, 2101, 1)
+ ((-1.284217e+01, 2.453640e+00, -1.921346e+01), (-1.767101e-01, -9.842348e-01, 7.448995e-03), 6.258032e+00, 3.799102e-07, 1.000000e+00, 23, 2100, 1)
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+ ((9.284015e+00, -1.058143e+01, 7.603793e+00), (3.963415e-01, -8.051509e-01, 4.411865e-01), 2.970280e-02, 8.283227e-05, 1.000000e+00, 23, 2328, 1)
+ ((9.309126e+00, -1.063244e+01, 7.631745e+00), (3.963415e-01, -8.051509e-01, 4.411865e-01), 2.970280e-02, 8.309804e-05, 1.000000e+00, 23, 2313, 1)
+ ((9.317824e+00, -1.065011e+01, 7.641427e+00), (7.190682e-01, 8.976507e-02, -6.891177e-01), 2.867417e-02, 8.319011e-05, 1.000000e+00, 23, 2313, 1)
+ ((9.459378e+00, -1.063244e+01, 7.505770e+00), (7.190682e-01, 8.976507e-02, -6.891177e-01), 2.867417e-02, 8.403060e-05, 1.000000e+00, 23, 2328, 1)
+ ((9.492454e+00, -1.062831e+01, 7.474071e+00), (4.092619e-03, -9.482095e-01, -3.176193e-01), 4.656141e-02, 8.422700e-05, 1.000000e+00, 23, 2328, 1)
+ ((9.492472e+00, -1.063244e+01, 7.472688e+00), (4.092619e-03, -9.482095e-01, -3.176193e-01), 4.656141e-02, 8.424159e-05, 1.000000e+00, 23, 2313, 1)
+ ((9.492761e+00, -1.069927e+01, 7.450302e+00), (9.457151e-01, -1.928731e-01, 2.615777e-01), 4.542312e-02, 8.447773e-05, 1.000000e+00, 23, 2313, 1)
+ ((9.890524e+00, -1.078039e+01, 7.560320e+00), (7.849118e-01, -1.237812e-01, -6.071175e-01), 5.609444e-02, 8.590450e-05, 1.000000e+00, 23, 2313, 1)
+ ((1.004645e+01, -1.080498e+01, 7.439717e+00), (7.849118e-01, -1.237812e-01, -6.071175e-01), 5.609444e-02, 8.651090e-05, 0.000000e+00, 23, 2313, 1)]
diff --git a/tests/regression_tests/track_output/settings.xml b/tests/regression_tests/track_output/settings.xml
--- a/tests/regression_tests/track_output/settings.xml
+++ b/tests/regression_tests/track_output/settings.xml
@@ -16,7 +16,8 @@
<track>
1 1 1
- 1 1 2
+ 1 1 30
+ 2 1 60
</track>
</settings>
diff --git a/tests/regression_tests/track_output/test.py b/tests/regression_tests/track_output/test.py
--- a/tests/regression_tests/track_output/test.py
+++ b/tests/regression_tests/track_output/test.py
@@ -1,11 +1,13 @@
import glob
import os
+from pathlib import Path
from subprocess import call
-import shutil
+import numpy as np
+import openmc
import pytest
-from tests.testing_harness import TestHarness
+from tests.testing_harness import TestHarness, config
class TrackTestHarness(TestHarness):
@@ -13,26 +15,33 @@ def _test_output_created(self):
"""Make sure statepoint.* and track* have been created."""
TestHarness._test_output_created(self)
- outputs = glob.glob('track_1_1_*.h5')
- assert len(outputs) == 2, 'Expected two track files.'
+ if config['mpi'] and int(config['mpi_np']) > 1:
+ outputs = Path.cwd().glob('tracks_p*.h5')
+ assert len(list(outputs)) == int(config['mpi_np'])
+ else:
+ assert Path('tracks.h5').is_file()
def _get_results(self):
- """Digest info in the statepoint and return as a string."""
- # Run the track-to-vtk conversion script.
- call(['../../../scripts/openmc-track-to-vtk', '-o', 'poly'] +
- glob.glob('track_1_1_*.h5'))
+ """Get data from track file and return as a string."""
- # Make sure the vtk file was created then return it's contents.
- assert os.path.isfile('poly.pvtp'), 'poly.pvtp file not found.'
+ # For MPI mode, combine track files
+ if config['mpi']:
+ call(['../../../scripts/openmc-track-combine', '-o', 'tracks.h5'] +
+ glob.glob('tracks_p*.h5'))
- with open('poly.pvtp', 'r') as fin:
- outstr = fin.read()
+ # Get string of track file information
+ outstr = ''
+ tracks = openmc.Tracks('tracks.h5')
+ for track in tracks:
+ with np.printoptions(formatter={'float_kind': '{:.6e}'.format}):
+ for ptrack in track:
+ outstr += f"{ptrack.particle} {ptrack.states}\n"
return outstr
def _cleanup(self):
TestHarness._cleanup(self)
- output = glob.glob('track*') + glob.glob('poly*')
+ output = glob.glob('tracks*') + glob.glob('poly*')
for f in output:
if os.path.exists(f):
os.remove(f)
diff --git a/tests/unit_tests/test_settings.py b/tests/unit_tests/test_settings.py
--- a/tests/unit_tests/test_settings.py
+++ b/tests/unit_tests/test_settings.py
@@ -14,6 +14,7 @@ def test_export_to_xml(run_in_tmpdir):
s.keff_trigger = {'type': 'std_dev', 'threshold': 0.001}
s.energy_mode = 'continuous-energy'
s.max_order = 5
+ s.max_tracks = 1234
s.source = openmc.Source(space=openmc.stats.Point())
s.output = {'summary': True, 'tallies': False, 'path': 'here'}
s.verbosity = 7
@@ -42,7 +43,7 @@ def test_export_to_xml(run_in_tmpdir):
s.temperature = {'default': 293.6, 'method': 'interpolation',
'multipole': True, 'range': (200., 1000.)}
s.trace = (10, 1, 20)
- s.track = [1, 1, 1, 2, 1, 1]
+ s.track = [(1, 1, 1), (2, 1, 1)]
s.ufs_mesh = mesh
s.resonance_scattering = {'enable': True, 'method': 'rvs',
'energy_min': 1.0, 'energy_max': 1000.0,
@@ -71,6 +72,7 @@ def test_export_to_xml(run_in_tmpdir):
assert s.keff_trigger == {'type': 'std_dev', 'threshold': 0.001}
assert s.energy_mode == 'continuous-energy'
assert s.max_order == 5
+ assert s.max_tracks == 1234
assert isinstance(s.source[0], openmc.Source)
assert isinstance(s.source[0].space, openmc.stats.Point)
assert s.output == {'summary': True, 'tallies': False, 'path': 'here'}
@@ -99,7 +101,7 @@ def test_export_to_xml(run_in_tmpdir):
assert s.temperature == {'default': 293.6, 'method': 'interpolation',
'multipole': True, 'range': [200., 1000.]}
assert s.trace == [10, 1, 20]
- assert s.track == [1, 1, 1, 2, 1, 1]
+ assert s.track == [(1, 1, 1), (2, 1, 1)]
assert isinstance(s.ufs_mesh, openmc.RegularMesh)
assert s.ufs_mesh.lower_left == [-10., -10., -10.]
assert s.ufs_mesh.upper_right == [10., 10., 10.]
diff --git a/tests/unit_tests/test_tracks.py b/tests/unit_tests/test_tracks.py
new file mode 100644
--- /dev/null
+++ b/tests/unit_tests/test_tracks.py
@@ -0,0 +1,143 @@
+from pathlib import Path
+
+import numpy as np
+import openmc
+import pytest
+
+from tests.testing_harness import config
+
+
[email protected]
+def sphere_model():
+ openmc.reset_auto_ids()
+ mat = openmc.Material()
+ mat.add_nuclide('Zr90', 1.0)
+ mat.set_density('g/cm3', 1.0)
+
+ model = openmc.Model()
+ sph = openmc.Sphere(r=25.0, boundary_type='vacuum')
+ cell = openmc.Cell(fill=mat, region=-sph)
+ model.geometry = openmc.Geometry([cell])
+
+ model.settings.run_mode = 'fixed source'
+ model.settings.batches = 2
+ model.settings.particles = 50
+
+ return model
+
+
+def generate_track_file(model, **kwargs):
+ # If running in MPI mode, setup proper keyword arguments for run()
+ kwargs.setdefault('openmc_exec', config['exe'])
+ if config['mpi']:
+ kwargs['mpi_args'] = [config['mpiexec'], '-n', config['mpi_np']]
+ model.run(**kwargs)
+
+ if config['mpi'] and int(config['mpi_np']) > 1:
+ # With MPI, we need to combine track files
+ track_files = Path.cwd().glob('tracks_p*.h5')
+ openmc.Tracks.combine(track_files, 'tracks.h5')
+ else:
+ track_file = Path('tracks.h5')
+ assert track_file.is_file()
+
+
[email protected]("particle", ["neutron", "photon"])
+def test_tracks(sphere_model, particle, run_in_tmpdir):
+ # Set track identifiers
+ sphere_model.settings.track = [(1, 1, 1), (1, 1, 10), (2, 1, 15)]
+
+ # Set source particle
+ sphere_model.settings.source = openmc.Source(particle=particle)
+
+ # Run OpenMC to generate tracks.h5 file
+ generate_track_file(sphere_model)
+
+ # Open track file and make sure we have correct number of tracks
+ tracks = openmc.Tracks('tracks.h5')
+ assert len(tracks) == len(sphere_model.settings.track)
+
+ for track, identifier in zip(tracks, sphere_model.settings.track):
+ # Check attributes on Track object
+ assert isinstance(track, openmc.Track)
+ assert track.identifier == identifier
+ assert isinstance(track.particle_tracks, list)
+ if particle == 'neutron':
+ assert len(track.particle_tracks) == 1
+
+ # Check attributes on ParticleTrack object
+ particle_track = track.particle_tracks[0]
+ assert isinstance(particle_track, openmc.ParticleTrack)
+
+ assert particle_track.particle.name.lower() == particle
+ assert isinstance(particle_track.states, np.ndarray)
+
+ # Sanity checks on actual data
+ for state in particle_track.states:
+ assert np.linalg.norm([*state['r']]) <= 25.0001
+ assert np.linalg.norm([*state['u']]) == pytest.approx(1.0)
+ assert 0.0 <= state['E'] <= 20.0e6
+ assert state['time'] >= 0.0
+ assert 0.0 <= state['wgt'] <= 1.0
+ assert state['cell_id'] == 1
+ assert state['material_id'] == 1
+
+ # Checks on 'sources' property
+ sources = track.sources
+ assert len(sources) == len(track.particle_tracks)
+ x = sources[0]
+ state = particle_track.states[0]
+ assert x.r == (*state['r'],)
+ assert x.u == (*state['u'],)
+ assert x.E == state['E']
+ assert x.time == state['time']
+ assert x.wgt == state['wgt']
+ assert x.particle == particle_track.particle
+
+
+def test_max_tracks(sphere_model, run_in_tmpdir):
+ # Set maximum number of tracks per process to write
+ sphere_model.settings.max_tracks = expected_num_tracks = 10
+ if config['mpi']:
+ expected_num_tracks *= int(config['mpi_np'])
+
+ # Run OpenMC to generate tracks.h5 file
+ generate_track_file(sphere_model, tracks=True)
+
+ # Open track file and make sure we have correct number of tracks
+ tracks = openmc.Tracks('tracks.h5')
+ assert len(tracks) == expected_num_tracks
+
+
+def test_filter(sphere_model, run_in_tmpdir):
+ # Set maximum number of tracks per process to write
+ sphere_model.settings.max_tracks = 25
+ sphere_model.settings.photon_transport = True
+
+ # Run OpenMC to generate tracks.h5 file
+ generate_track_file(sphere_model, tracks=True)
+
+ tracks = openmc.Tracks('tracks.h5')
+ for track in tracks:
+ # Test filtering by particle
+ matches = track.filter(particle='photon')
+ for x in matches:
+ assert x.particle == openmc.ParticleType.PHOTON
+
+ # Test general state filter
+ matches = track.filter(state_filter=lambda s: s['cell_id'] == 1)
+ assert isinstance(matches, openmc.Track)
+ assert matches.particle_tracks == track.particle_tracks
+ matches = track.filter(state_filter=lambda s: s['cell_id'] == 2)
+ assert matches.particle_tracks == []
+ matches = track.filter(state_filter=lambda s: s['E'] < 0.0)
+ assert matches.particle_tracks == []
+
+ # Test filter method on Tracks
+ matches = tracks.filter(particle='neutron')
+ assert isinstance(matches, openmc.Tracks)
+ assert matches == tracks
+ matches = tracks.filter(state_filter=lambda s: s['E'] > 0.0)
+ assert matches == tracks
+ matches = tracks.filter(particle='bunnytron')
+ assert matches == []
| Extend particle track files to include more than just position
Our particle track files currently only contain information on the spatial location (x,y,z) of particles as they are being simulated. For some applications, it would be useful to have additional information stored in particle track files (energy, direction, weight, time).
| Hello @paulromano, How to get energy of a particle at each position of spatial location in track file
@rihanafridi Right now it's not possible but I'm planning on adding this capability in the coming months
That would really assist!
Thank you @paulromano | 2022-05-20T17:17:05Z | [] | [] |
openmc-dev/openmc | 2,074 | openmc-dev__openmc-2074 | [
"2073"
] | 7752afb554aa05103ed8f62a3c26b12632bbac2c | diff --git a/openmc/cell.py b/openmc/cell.py
--- a/openmc/cell.py
+++ b/openmc/cell.py
@@ -690,7 +690,10 @@ def from_xml_element(cls, elem, surfaces, materials, get_universe):
for key in ('temperature', 'rotation', 'translation'):
value = get_text(elem, key)
if value is not None:
- setattr(c, key, [float(x) for x in value.split()])
+ values = [float(x) for x in value.split()]
+ if key == 'rotation' and len(values) == 9:
+ values = np.array(values).reshape(3, 3)
+ setattr(c, key, values)
# Add this cell to appropriate universe
univ_id = int(get_text(elem, 'universe', 0))
diff --git a/openmc/material.py b/openmc/material.py
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -29,9 +29,9 @@ class Material(IDManagerMixin):
To create a material, one should create an instance of this class, add
nuclides or elements with :meth:`Material.add_nuclide` or
- `Material.add_element`, respectively, and set the total material density
- with `Material.set_density()`. The material can then be assigned to a cell
- using the :attr:`Cell.fill` attribute.
+ :meth:`Material.add_element`, respectively, and set the total material
+ density with :meth:`Material.set_density()`. The material can then be
+ assigned to a cell using the :attr:`Cell.fill` attribute.
Parameters
----------
diff --git a/openmc/plots.py b/openmc/plots.py
--- a/openmc/plots.py
+++ b/openmc/plots.py
@@ -213,8 +213,8 @@ class Plot(IDManagerMixin):
The basis directions for the plot
background : Iterable of int or str
Color of the background
- mask_components : Iterable of openmc.Cell or openmc.Material
- The cells or materials to plot
+ mask_components : Iterable of openmc.Cell or openmc.Material or int
+ The cells or materials (or corresponding IDs) to mask
mask_background : Iterable of int or str
Color to apply to all cells/materials not listed in mask_components
show_overlaps : bool
@@ -222,8 +222,10 @@ class Plot(IDManagerMixin):
overlap_color : Iterable of int or str
Color to apply to overlapping regions
colors : dict
- Dictionary indicating that certain cells/materials (keys) should be
- displayed with a particular color.
+ Dictionary indicating that certain cells/materials should be
+ displayed with a particular color. The keys can be of type
+ :class:`~openmc.Cell`, :class:`~openmc.Material`, or int (ID for a
+ cell/material).
level : int
Universe depth to plot at
meshlines : dict
@@ -373,14 +375,15 @@ def background(self, background):
def colors(self, colors):
cv.check_type('plot colors', colors, Mapping)
for key, value in colors.items():
- cv.check_type('plot color key', key, (openmc.Cell, openmc.Material))
+ cv.check_type('plot color key', key,
+ (openmc.Cell, openmc.Material, Integral))
self._check_color('plot color value', value)
self._colors = colors
@mask_components.setter
def mask_components(self, mask_components):
cv.check_type('plot mask components', mask_components, Iterable,
- (openmc.Cell, openmc.Material))
+ (openmc.Cell, openmc.Material, Integral))
self._mask_components = mask_components
@mask_background.setter
@@ -634,11 +637,16 @@ def to_xml_element(self):
color = _SVG_COLORS[color.lower()]
subelement.text = ' '.join(str(x) for x in color)
+ # Helper function that returns the domain ID given either a
+ # Cell/Material object or the domain ID itself
+ def get_id(domain):
+ return domain if isinstance(domain, Integral) else domain.id
+
if self._colors:
for domain, color in sorted(self._colors.items(),
- key=lambda x: x[0].id):
+ key=lambda x: get_id(x[0])):
subelement = ET.SubElement(element, "color")
- subelement.set("id", str(domain.id))
+ subelement.set("id", str(get_id(domain)))
if isinstance(color, str):
color = _SVG_COLORS[color.lower()]
subelement.set("rgb", ' '.join(str(x) for x in color))
@@ -646,7 +654,7 @@ def to_xml_element(self):
if self._mask_components is not None:
subelement = ET.SubElement(element, "mask")
subelement.set("components", ' '.join(
- str(d.id) for d in self._mask_components))
+ str(get_id(d)) for d in self._mask_components))
color = self._mask_background
if color is not None:
if isinstance(color, str):
@@ -720,15 +728,14 @@ def get_tuple(elem, name, dtype=int):
# Set plot colors
colors = {}
for color_elem in elem.findall("color"):
- uid = color_elem.get("id")
+ uid = int(color_elem.get("id"))
colors[uid] = tuple([int(x) for x in color_elem.get("rgb").split()])
- # TODO: set colors (needs geometry information)
+ plot.colors = colors
# Set masking information
mask_elem = elem.find("mask")
if mask_elem is not None:
- mask_components = [int(x) for x in mask_elem.get("components").split()]
- # TODO: set mask components (needs geometry information)
+ plot.mask_components = [int(x) for x in mask_elem.get("components").split()]
background = mask_elem.get("background")
if background is not None:
plot.mask_background = tuple([int(x) for x in background.split()])
diff --git a/openmc/surface.py b/openmc/surface.py
--- a/openmc/surface.py
+++ b/openmc/surface.py
@@ -760,7 +760,7 @@ class XPlane(PlaneMixin, Surface):
Parameters
----------
x0 : float, optional
- Location of the plane. Defaults to 0.
+ Location of the plane in [cm]. Defaults to 0.
boundary_type : {'transmission, 'vacuum', 'reflective', 'periodic', 'white'}, optional
Boundary condition that defines the behavior for particles hitting the
surface. Defaults to transmissive boundary condition where particles
@@ -775,7 +775,7 @@ class XPlane(PlaneMixin, Surface):
Attributes
----------
x0 : float
- Location of the plane
+ Location of the plane in [cm]
boundary_type : {'transmission, 'vacuum', 'reflective', 'periodic', 'white'}
Boundary condition that defines the behavior for particles hitting the
surface.
@@ -819,7 +819,7 @@ class YPlane(PlaneMixin, Surface):
Parameters
----------
y0 : float, optional
- Location of the plane
+ Location of the plane in [cm]
boundary_type : {'transmission, 'vacuum', 'reflective', 'periodic', 'white'}, optional
Boundary condition that defines the behavior for particles hitting the
surface. Defaults to transmissive boundary condition where particles
@@ -834,7 +834,7 @@ class YPlane(PlaneMixin, Surface):
Attributes
----------
y0 : float
- Location of the plane
+ Location of the plane in [cm]
boundary_type : {'transmission, 'vacuum', 'reflective', 'periodic', 'white'}
Boundary condition that defines the behavior for particles hitting the
surface.
@@ -878,7 +878,7 @@ class ZPlane(PlaneMixin, Surface):
Parameters
----------
z0 : float, optional
- Location of the plane. Defaults to 0.
+ Location of the plane in [cm]. Defaults to 0.
boundary_type : {'transmission, 'vacuum', 'reflective', 'periodic', 'white'}, optional
Boundary condition that defines the behavior for particles hitting the
surface. Defaults to transmissive boundary condition where particles
@@ -893,7 +893,7 @@ class ZPlane(PlaneMixin, Surface):
Attributes
----------
z0 : float
- Location of the plane
+ Location of the plane in [cm]
boundary_type : {'transmission, 'vacuum', 'reflective', 'periodic', 'white'}
Boundary condition that defines the behavior for particles hitting the
surface.
@@ -991,8 +991,8 @@ def evaluate(self, point):
Parameters
----------
point : 3-tuple of float
- The Cartesian coordinates, :math:`(x',y',z')`, at which the surface
- equation should be evaluated.
+ The Cartesian coordinates, :math:`(x',y',z')`, in [cm] at which the
+ surface equation should be evaluated.
Returns
-------
@@ -1106,13 +1106,13 @@ class Cylinder(QuadricMixin, Surface):
Parameters
----------
x0 : float, optional
- x-coordinate for the origin of the Cylinder. Defaults to 0
+ x-coordinate for the origin of the Cylinder in [cm]. Defaults to 0
y0 : float, optional
- y-coordinate for the origin of the Cylinder. Defaults to 0
+ y-coordinate for the origin of the Cylinder in [cm]. Defaults to 0
z0 : float, optional
- z-coordinate for the origin of the Cylinder. Defaults to 0
+ z-coordinate for the origin of the Cylinder in [cm]. Defaults to 0
r : float, optional
- Radius of the cylinder. Defaults to 1.
+ Radius of the cylinder in [cm]. Defaults to 1.
dx : float, optional
x-component of the vector representing the axis of the cylinder.
Defaults to 0.
@@ -1136,13 +1136,13 @@ class Cylinder(QuadricMixin, Surface):
Attributes
----------
x0 : float
- x-coordinate for the origin of the Cylinder
+ x-coordinate for the origin of the Cylinder in [cm]
y0 : float
- y-coordinate for the origin of the Cylinder
+ y-coordinate for the origin of the Cylinder in [cm]
z0 : float
- z-coordinate for the origin of the Cylinder
+ z-coordinate for the origin of the Cylinder in [cm]
r : float
- Radius of the cylinder
+ Radius of the cylinder in [cm]
dx : float
x-component of the vector representing the axis of the cylinder
dy : float
@@ -1243,7 +1243,7 @@ def from_points(cls, p1, p2, r=1., **kwargs):
p1, p2 : 3-tuples
Points that pass through the plane, p1 will be used as (x0, y0, z0)
r : float, optional
- Radius of the cylinder. Defaults to 1.
+ Radius of the cylinder in [cm]. Defaults to 1.
kwargs : dict
Keyword arguments passed to the :class:`Cylinder` constructor
@@ -1288,11 +1288,11 @@ class XCylinder(QuadricMixin, Surface):
Parameters
----------
y0 : float, optional
- y-coordinate for the origin of the Cylinder. Defaults to 0
+ y-coordinate for the origin of the Cylinder in [cm]. Defaults to 0
z0 : float, optional
- z-coordinate for the origin of the Cylinder. Defaults to 0
+ z-coordinate for the origin of the Cylinder in [cm]. Defaults to 0
r : float, optional
- Radius of the cylinder. Defaults to 1.
+ Radius of the cylinder in [cm]. Defaults to 1.
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}, optional
Boundary condition that defines the behavior for particles hitting the
surface. Defaults to transmissive boundary condition where particles
@@ -1307,11 +1307,11 @@ class XCylinder(QuadricMixin, Surface):
Attributes
----------
y0 : float
- y-coordinate for the origin of the Cylinder
+ y-coordinate for the origin of the Cylinder in [cm]
z0 : float
- z-coordinate for the origin of the Cylinder
+ z-coordinate for the origin of the Cylinder in [cm]
r : float
- Radius of the cylinder
+ Radius of the cylinder in [cm]
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}
Boundary condition that defines the behavior for particles hitting the
surface.
@@ -1379,11 +1379,11 @@ class YCylinder(QuadricMixin, Surface):
Parameters
----------
x0 : float, optional
- x-coordinate for the origin of the Cylinder. Defaults to 0
+ x-coordinate for the origin of the Cylinder in [cm]. Defaults to 0
z0 : float, optional
- z-coordinate for the origin of the Cylinder. Defaults to 0
+ z-coordinate for the origin of the Cylinder in [cm]. Defaults to 0
r : float, optional
- Radius of the cylinder. Defaults to 1.
+ Radius of the cylinder in [cm]. Defaults to 1.
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}, optional
Boundary condition that defines the behavior for particles hitting the
surface. Defaults to transmissive boundary condition where particles
@@ -1398,11 +1398,11 @@ class YCylinder(QuadricMixin, Surface):
Attributes
----------
x0 : float
- x-coordinate for the origin of the Cylinder
+ x-coordinate for the origin of the Cylinder in [cm]
z0 : float
- z-coordinate for the origin of the Cylinder
+ z-coordinate for the origin of the Cylinder in [cm]
r : float
- Radius of the cylinder
+ Radius of the cylinder in [cm]
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}
Boundary condition that defines the behavior for particles hitting the
surface.
@@ -1470,11 +1470,11 @@ class ZCylinder(QuadricMixin, Surface):
Parameters
----------
x0 : float, optional
- x-coordinate for the origin of the Cylinder. Defaults to 0
+ x-coordinate for the origin of the Cylinder in [cm]. Defaults to 0
y0 : float, optional
- y-coordinate for the origin of the Cylinder. Defaults to 0
+ y-coordinate for the origin of the Cylinder in [cm]. Defaults to 0
r : float, optional
- Radius of the cylinder. Defaults to 1.
+ Radius of the cylinder in [cm]. Defaults to 1.
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}, optional
Boundary condition that defines the behavior for particles hitting the
surface. Defaults to transmissive boundary condition where particles
@@ -1489,11 +1489,11 @@ class ZCylinder(QuadricMixin, Surface):
Attributes
----------
x0 : float
- x-coordinate for the origin of the Cylinder
+ x-coordinate for the origin of the Cylinder in [cm]
y0 : float
- y-coordinate for the origin of the Cylinder
+ y-coordinate for the origin of the Cylinder in [cm]
r : float
- Radius of the cylinder
+ Radius of the cylinder in [cm]
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}
Boundary condition that defines the behavior for particles hitting the
surface.
@@ -1560,13 +1560,13 @@ class Sphere(QuadricMixin, Surface):
Parameters
----------
x0 : float, optional
- x-coordinate of the center of the sphere. Defaults to 0.
+ x-coordinate of the center of the sphere in [cm]. Defaults to 0.
y0 : float, optional
- y-coordinate of the center of the sphere. Defaults to 0.
+ y-coordinate of the center of the sphere in [cm]. Defaults to 0.
z0 : float, optional
- z-coordinate of the center of the sphere. Defaults to 0.
+ z-coordinate of the center of the sphere in [cm]. Defaults to 0.
r : float, optional
- Radius of the sphere. Defaults to 1.
+ Radius of the sphere in [cm]. Defaults to 1.
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}, optional
Boundary condition that defines the behavior for particles hitting the
surface. Defaults to transmissive boundary condition where particles
@@ -1580,13 +1580,13 @@ class Sphere(QuadricMixin, Surface):
Attributes
----------
x0 : float
- x-coordinate of the center of the sphere
+ x-coordinate of the center of the sphere in [cm]
y0 : float
- y-coordinate of the center of the sphere
+ y-coordinate of the center of the sphere in [cm]
z0 : float
- z-coordinate of the center of the sphere
+ z-coordinate of the center of the sphere in [cm]
r : float
- Radius of the sphere
+ Radius of the sphere in [cm]
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}
Boundary condition that defines the behavior for particles hitting the
surface.
@@ -1653,11 +1653,11 @@ class Cone(QuadricMixin, Surface):
Parameters
----------
x0 : float, optional
- x-coordinate of the apex. Defaults to 0.
+ x-coordinate of the apex in [cm]. Defaults to 0.
y0 : float, optional
- y-coordinate of the apex. Defaults to 0.
+ y-coordinate of the apex in [cm]. Defaults to 0.
z0 : float, optional
- z-coordinate of the apex. Defaults to 0.
+ z-coordinate of the apex in [cm]. Defaults to 0.
r2 : float, optional
Parameter related to the aperature. Defaults to 1.
dx : float, optional
@@ -1682,11 +1682,11 @@ class Cone(QuadricMixin, Surface):
Attributes
----------
x0 : float
- x-coordinate of the apex
+ x-coordinate of the apex in [cm]
y0 : float
- y-coordinate of the apex
+ y-coordinate of the apex in [cm]
z0 : float
- z-coordinate of the apex
+ z-coordinate of the apex in [cm]
r2 : float
Parameter related to the aperature
dx : float
@@ -1796,11 +1796,11 @@ class XCone(QuadricMixin, Surface):
Parameters
----------
x0 : float, optional
- x-coordinate of the apex. Defaults to 0.
+ x-coordinate of the apex in [cm]. Defaults to 0.
y0 : float, optional
- y-coordinate of the apex. Defaults to 0.
+ y-coordinate of the apex in [cm]. Defaults to 0.
z0 : float, optional
- z-coordinate of the apex. Defaults to 0.
+ z-coordinate of the apex in [cm]. Defaults to 0.
r2 : float, optional
Parameter related to the aperature. Defaults to 1.
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}, optional
@@ -1816,11 +1816,11 @@ class XCone(QuadricMixin, Surface):
Attributes
----------
x0 : float
- x-coordinate of the apex
+ x-coordinate of the apex in [cm]
y0 : float
- y-coordinate of the apex
+ y-coordinate of the apex in [cm]
z0 : float
- z-coordinate of the apex
+ z-coordinate of the apex in [cm]
r2 : float
Parameter related to the aperature
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}
@@ -1885,11 +1885,11 @@ class YCone(QuadricMixin, Surface):
Parameters
----------
x0 : float, optional
- x-coordinate of the apex. Defaults to 0.
+ x-coordinate of the apex in [cm]. Defaults to 0.
y0 : float, optional
- y-coordinate of the apex. Defaults to 0.
+ y-coordinate of the apex in [cm]. Defaults to 0.
z0 : float, optional
- z-coordinate of the apex. Defaults to 0.
+ z-coordinate of the apex in [cm]. Defaults to 0.
r2 : float, optional
Parameter related to the aperature. Defaults to 1.
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}, optional
@@ -1905,11 +1905,11 @@ class YCone(QuadricMixin, Surface):
Attributes
----------
x0 : float
- x-coordinate of the apex
+ x-coordinate of the apex in [cm]
y0 : float
- y-coordinate of the apex
+ y-coordinate of the apex in [cm]
z0 : float
- z-coordinate of the apex
+ z-coordinate of the apex in [cm]
r2 : float
Parameter related to the aperature
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}
@@ -1974,11 +1974,11 @@ class ZCone(QuadricMixin, Surface):
Parameters
----------
x0 : float, optional
- x-coordinate of the apex. Defaults to 0.
+ x-coordinate of the apex in [cm]. Defaults to 0.
y0 : float, optional
- y-coordinate of the apex. Defaults to 0.
+ y-coordinate of the apex in [cm]. Defaults to 0.
z0 : float, optional
- z-coordinate of the apex. Defaults to 0.
+ z-coordinate of the apex in [cm]. Defaults to 0.
r2 : float, optional
Parameter related to the aperature. Defaults to 1.
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}, optional
@@ -1994,11 +1994,11 @@ class ZCone(QuadricMixin, Surface):
Attributes
----------
x0 : float
- x-coordinate of the apex
+ x-coordinate of the apex in [cm]
y0 : float
- y-coordinate of the apex
+ y-coordinate of the apex in [cm]
z0 : float
- z-coordinate of the apex
+ z-coordinate of the apex in [cm]
r2 : float
Parameter related to the aperature
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}
@@ -2198,34 +2198,34 @@ class XTorus(TorusMixin, Surface):
Parameters
----------
x0 : float
- x-coordinate of the center of the axis of revolution
+ x-coordinate of the center of the axis of revolution in [cm]
y0 : float
- y-coordinate of the center of the axis of revolution
+ y-coordinate of the center of the axis of revolution in [cm]
z0 : float
- z-coordinate of the center of the axis of revolution
+ z-coordinate of the center of the axis of revolution in [cm]
a : float
- Major radius of the torus
+ Major radius of the torus in [cm]
b : float
- Minor radius of the torus (parallel to axis of revolution)
+ Minor radius of the torus in [cm] (parallel to axis of revolution)
c : float
- Minor radius of the torus (perpendicular to axis of revolution)
+ Minor radius of the torus in [cm] (perpendicular to axis of revolution)
kwargs : dict
Keyword arguments passed to the :class:`Surface` constructor
Attributes
----------
x0 : float
- x-coordinate of the center of the axis of revolution
+ x-coordinate of the center of the axis of revolution in [cm]
y0 : float
- y-coordinate of the center of the axis of revolution
+ y-coordinate of the center of the axis of revolution in [cm]
z0 : float
- z-coordinate of the center of the axis of revolution
+ z-coordinate of the center of the axis of revolution in [cm]
a : float
- Major radius of the torus
+ Major radius of the torus in [cm]
b : float
- Minor radius of the torus (parallel to axis of revolution)
+ Minor radius of the torus in [cm] (parallel to axis of revolution)
c : float
- Minor radius of the torus (perpendicular to axis of revolution)
+ Minor radius of the torus in [cm] (perpendicular to axis of revolution)
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}
Boundary condition that defines the behavior for particles hitting the
surface.
@@ -2269,32 +2269,32 @@ class YTorus(TorusMixin, Surface):
Parameters
----------
x0 : float
- x-coordinate of the center of the axis of revolution
+ x-coordinate of the center of the axis of revolution in [cm]
y0 : float
- y-coordinate of the center of the axis of revolution
+ y-coordinate of the center of the axis of revolution in [cm]
z0 : float
- z-coordinate of the center of the axis of revolution
+ z-coordinate of the center of the axis of revolution in [cm]
a : float
- Major radius of the torus
+ Major radius of the torus in [cm]
b : float
- Minor radius of the torus (parallel to axis of revolution)
+ Minor radius of the torus in [cm] (parallel to axis of revolution)
c : float
- Minor radius of the torus (perpendicular to axis of revolution)
+ Minor radius of the torus in [cm] (perpendicular to axis of revolution)
kwargs : dict
Keyword arguments passed to the :class:`Surface` constructor
Attributes
----------
x0 : float
- x-coordinate of the center of the axis of revolution
+ x-coordinate of the center of the axis of revolution in [cm]
y0 : float
- y-coordinate of the center of the axis of revolution
+ y-coordinate of the center of the axis of revolution in [cm]
z0 : float
- z-coordinate of the center of the axis of revolution
+ z-coordinate of the center of the axis of revolution in [cm]
a : float
- Major radius of the torus
+ Major radius of the torus in [cm]
b : float
- Minor radius of the torus (parallel to axis of revolution)
+ Minor radius of the torus in [cm] (parallel to axis of revolution)
c : float
Minor radius of the torus (perpendicular to axis of revolution)
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}
@@ -2340,34 +2340,34 @@ class ZTorus(TorusMixin, Surface):
Parameters
----------
x0 : float
- x-coordinate of the center of the axis of revolution
+ x-coordinate of the center of the axis of revolution in [cm]
y0 : float
- y-coordinate of the center of the axis of revolution
+ y-coordinate of the center of the axis of revolution in [cm]
z0 : float
- z-coordinate of the center of the axis of revolution
+ z-coordinate of the center of the axis of revolution in [cm]
a : float
- Major radius of the torus
+ Major radius of the torus in [cm]
b : float
- Minor radius of the torus (parallel to axis of revolution)
+ Minor radius of the torus in [cm] (parallel to axis of revolution)
c : float
- Minor radius of the torus (perpendicular to axis of revolution)
+ Minor radius of the torus in [cm] (perpendicular to axis of revolution)
kwargs : dict
Keyword arguments passed to the :class:`Surface` constructor
Attributes
----------
x0 : float
- x-coordinate of the center of the axis of revolution
+ x-coordinate of the center of the axis of revolution in [cm]
y0 : float
- y-coordinate of the center of the axis of revolution
+ y-coordinate of the center of the axis of revolution in [cm]
z0 : float
- z-coordinate of the center of the axis of revolution
+ z-coordinate of the center of the axis of revolution in [cm]
a : float
- Major radius of the torus
+ Major radius of the torus in [cm]
b : float
- Minor radius of the torus (parallel to axis of revolution)
+ Minor radius of the torus in [cm] (parallel to axis of revolution)
c : float
- Minor radius of the torus (perpendicular to axis of revolution)
+ Minor radius of the torus in [cm] (perpendicular to axis of revolution)
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}
Boundary condition that defines the behavior for particles hitting the
surface.
| diff --git a/tests/unit_tests/test_cell.py b/tests/unit_tests/test_cell.py
--- a/tests/unit_tests/test_cell.py
+++ b/tests/unit_tests/test_cell.py
@@ -297,3 +297,20 @@ def test_to_xml_element(cell_with_lattice):
elem = c.create_xml_subelement(root)
assert elem.get('region') == str(c.region)
assert elem.get('temperature') == str(c.temperature)
+
+
[email protected]("rotation", [
+ (90, 45, 0),
+ [[1.0, 0.0, 0.0], [0.0, 0.0, 1.0], [0.0, -1.0, 0.0]]
+])
+def test_rotation_from_xml(rotation):
+ # Make sure rotation attribute (matrix) round trips through XML correctly
+ s = openmc.ZCylinder(r=10.0)
+ cell = openmc.Cell(region=-s)
+ cell.rotation = rotation
+ root = ET.Element('geometry')
+ elem = cell.create_xml_subelement(root)
+ new_cell = openmc.Cell.from_xml_element(
+ elem, {s.id: s}, {'void': None}, openmc.Universe
+ )
+ np.testing.assert_allclose(new_cell.rotation, cell.rotation)
diff --git a/tests/unit_tests/test_plots.py b/tests/unit_tests/test_plots.py
--- a/tests/unit_tests/test_plots.py
+++ b/tests/unit_tests/test_plots.py
@@ -92,6 +92,8 @@ def test_xml_element(myplot):
def test_plots(run_in_tmpdir):
p1 = openmc.Plot(name='plot1')
p1.origin = (5., 5., 5.)
+ p1.colors = {10: (255, 100, 0)}
+ p1.mask_components = [2, 4, 6]
p2 = openmc.Plot(name='plot2')
p2.origin = (-3., -3., -3.)
plots = openmc.Plots([p1, p2])
@@ -107,4 +109,6 @@ def test_plots(run_in_tmpdir):
new_plots = openmc.Plots.from_xml()
assert len(plots)
assert plots[0].origin == p1.origin
+ assert plots[0].colors == p1.colors
+ assert plots[0].mask_components == p1.mask_components
assert plots[1].origin == p2.origin
| Plot.from_xml_element doesn't grab colors from XML file
Code to reproduce below. We really should set something up to avoid having to write all this XML I/O boilerplate, maybe something similar to the dataclass functionality introduced recently to python.
```
gpad% cat plots.xml
<?xml version='1.0' encoding='utf-8'?>
<plots>
<plot color_by="material" filename="radial_cells_midplane_proj" id="2" type="slice" basis="xy">
<origin>0 0 230.0</origin>
<pixels>200 200 </pixels>
<width>10.0 10.0</width>
<color id="1" rgb="255 255 255"/>
<color id="2" rgb="0 0 0"/>
<color id="3" rgb="255 0 0"/>
<color id="4" rgb="200 50 50"/>
<color id="5" rgb="255 218 185"/>
<color id="6" rgb="101 101 101"/>
<color id="7" rgb="111 111 111"/>
<color id="8" rgb="50 50 50"/>
<color id="9" rgb="142 35 35"/>
<color id="10" rgb="255 215 0"/>
<color id="11" rgb="0 0 128"/>
<color id="14" rgb="0 255 0"/>
<color id="15" rgb="198 226 255"/>
<color id="16" rgb="176 196 222"/>
<color id="17" rgb="112 128 144"/>
</plot>
</plots>
gpad% python
Python 3.10.4 (main, Mar 23 2022, 23:05:40) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import openmc
>>> p = openmc.Plots.from_xml()
>>> p
[Plot
ID = 2
Name =
Filename = radial_cells_midplane_proj
Type = slice
Basis = xy
Width = (10.0, 10.0)
Origin = (0.0, 0.0, 230.0)
Pixels = (200, 200)
Color by = material
Background = None
Mask components= None
Mask background= None
Overlap Color = None
Colors = {}
Level = None
Meshlines = None
]
```
| 2022-05-24T16:05:35Z | [] | [] |
|
openmc-dev/openmc | 2,081 | openmc-dev__openmc-2081 | [
"2082"
] | 50cafaf61c5cb937714316f3441a3b891daf832e | diff --git a/openmc/region.py b/openmc/region.py
--- a/openmc/region.py
+++ b/openmc/region.py
@@ -106,6 +106,11 @@ def from_expression(expression, surfaces):
# If special character appears immediately after a non-operator,
# create a token with the appropriate half-space
if i_start >= 0:
+ # When an opening parenthesis appears after a non-operator,
+ # there's an implicit intersection operator between them
+ if expression[i] == '(':
+ tokens.append(' ')
+
j = int(expression[i_start:i])
if j < 0:
tokens.append(-surfaces[abs(j)])
| diff --git a/tests/unit_tests/test_region.py b/tests/unit_tests/test_region.py
--- a/tests/unit_tests/test_region.py
+++ b/tests/unit_tests/test_region.py
@@ -204,3 +204,7 @@ def test_from_expression(reset):
# Make sure ")(" is handled correctly
r = openmc.Region.from_expression('(-1|2)(2|-3)', surfs)
assert str(r) == '((-1 | 2) (2 | -3))'
+
+ # Opening parenthesis immediately after halfspace
+ r = openmc.Region.from_expression('1(2|-3)', surfs)
+ assert str(r) == '(1 (2 | -3))'
| documentation missing factor in TSL eq 81
Eq. 81 in section 5.11.2 is missing a factor of 2. Code is correct, only a documentation bug.
https://github.com/openmc-dev/openmc/blob/2efe223404680099f9a77214e743ab78e37cd08c/src/secondary_thermal.cpp#L50
in docs/source/methods/neutron_physics.rst
this: "\mu = 1 - \frac{E_i}{E}"
should be "\mu = 1 - \frac{2E_i}{E}"
| 2022-06-09T17:49:33Z | [] | [] |
|
openmc-dev/openmc | 2,119 | openmc-dev__openmc-2119 | [
"1537"
] | bf6cf505cc2b59353dc9c803f7e2c5af195dda6e | diff --git a/openmc/lib/core.py b/openmc/lib/core.py
--- a/openmc/lib/core.py
+++ b/openmc/lib/core.py
@@ -1,8 +1,10 @@
from contextlib import contextmanager
from ctypes import (c_bool, c_int, c_int32, c_int64, c_double, c_char_p,
- c_char, POINTER, Structure, c_void_p, create_string_buffer)
+ c_char, POINTER, Structure, c_void_p, create_string_buffer,
+ c_uint64, c_size_t)
import sys
import os
+from random import getrandbits
import numpy as np
from numpy.ctypeslib import as_array
@@ -10,6 +12,7 @@
from . import _dll
from .error import _error_handler
import openmc.lib
+import openmc
class _SourceSite(Structure):
@@ -95,6 +98,9 @@ class _SourceSite(Structure):
POINTER(c_double)]
_dll.openmc_global_bounding_box.restype = c_int
_dll.openmc_global_bounding_box.errcheck = _error_handler
+_dll.openmc_sample_external_source.argtypes = [c_size_t, POINTER(c_uint64), POINTER(_SourceSite)]
+_dll.openmc_sample_external_source.restype = c_int
+_dll.openmc_sample_external_source.errcheck = _error_handler
def global_bounding_box():
@@ -415,6 +421,45 @@ def run(output=True):
_dll.openmc_run()
+def sample_external_source(n_samples=1, prn_seed=None):
+ """Sample external source
+
+ .. versionadded:: 0.13.1
+
+ Parameters
+ ----------
+ n_samples : int
+ Number of samples
+ prn_seed : int
+ Pseudorandom number generator (PRNG) seed; if None, one will be
+ generated randomly.
+
+ Returns
+ -------
+ list of openmc.SourceParticle
+ List of samples source particles
+
+ """
+ if n_samples <= 0:
+ raise ValueError("Number of samples must be positive")
+ if prn_seed is None:
+ prn_seed = getrandbits(63)
+
+ # Call into C API to sample source
+ sites_array = (_SourceSite * n_samples)()
+ _dll.openmc_sample_external_source(c_size_t(n_samples), c_uint64(prn_seed), sites_array)
+
+ # Convert to list of SourceParticle and return
+ return [
+ openmc.SourceParticle(
+ r=site.r, u=site.u, E=site.E, time=site.time, wgt=site.wgt,
+ delayed_group=site.delayed_group, surf_id=site.surf_id,
+ particle=openmc.ParticleType(site.particle)
+ )
+ for site in sites_array
+ ]
+
+
def simulation_init():
"""Initialize simulation"""
_dll.openmc_simulation_init()
diff --git a/openmc/lib/math.py b/openmc/lib/math.py
--- a/openmc/lib/math.py
+++ b/openmc/lib/math.py
@@ -1,12 +1,11 @@
from ctypes import c_int, c_double, POINTER, c_uint64
+from random import getrandbits
import numpy as np
from numpy.ctypeslib import ndpointer
from . import _dll
-from random import getrandbits
-
_dll.t_percentile.restype = c_double
_dll.t_percentile.argtypes = [c_double, c_int]
@@ -200,7 +199,8 @@ def rotate_angle(uvw0, mu, phi, prn_seed=None):
phi : float
Azimuthal angle; if None, one will be sampled uniformly
prn_seed : int
- PRNG seed; if None, one will be generated randomly
+ Pseudorandom number generator (PRNG) seed; if None, one will be
+ generated randomly.
Returns
-------
@@ -232,7 +232,8 @@ def maxwell_spectrum(T, prn_seed=None):
T : float
Spectrum parameter
prn_seed : int
- PRNG seed; if None, one will be generated randomly
+ Pseudorandom number generator (PRNG) seed; if None, one will be
+ generated randomly.
Returns
-------
@@ -240,10 +241,10 @@ def maxwell_spectrum(T, prn_seed=None):
Sampled outgoing energy
"""
-
+
if prn_seed is None:
prn_seed = getrandbits(63)
-
+
return _dll.maxwell_spectrum(T, c_uint64(prn_seed))
@@ -257,7 +258,8 @@ def watt_spectrum(a, b, prn_seed=None):
b : float
Spectrum parameter b
prn_seed : int
- PRNG seed; if None, one will be generated randomly
+ Pseudorandom number generator (PRNG) seed; if None, one will be
+ generated randomly.
Returns
-------
@@ -265,7 +267,7 @@ def watt_spectrum(a, b, prn_seed=None):
Sampled outgoing energy
"""
-
+
if prn_seed is None:
prn_seed = getrandbits(63)
@@ -282,7 +284,8 @@ def normal_variate(mean_value, std_dev, prn_seed=None):
std_dev : float
Standard deviation of the normal distribution
prn_seed : int
- PRNG seed; if None, one will be generated randomly
+ Pseudorandom number generator (PRNG) seed; if None, one will be
+ generated randomly.
Returns
-------
@@ -290,7 +293,7 @@ def normal_variate(mean_value, std_dev, prn_seed=None):
Sampled outgoing normally distributed value
"""
-
+
if prn_seed is None:
prn_seed = getrandbits(63)
| diff --git a/tests/unit_tests/test_lib.py b/tests/unit_tests/test_lib.py
--- a/tests/unit_tests/test_lib.py
+++ b/tests/unit_tests/test_lib.py
@@ -807,3 +807,46 @@ def test_cell_rotation(pincell_model_w_univ, mpi_intracomm):
cell.rotation = (180., 0., 0.)
assert cell.rotation == pytest.approx([180., 0., 0.])
openmc.lib.finalize()
+
+
+def test_sample_external_source(run_in_tmpdir, mpi_intracomm):
+ # Define a simple model and export
+ mat = openmc.Material()
+ mat.add_nuclide('U235', 1.0e-2)
+ sph = openmc.Sphere(r=100.0, boundary_type='vacuum')
+ cell = openmc.Cell(fill=mat, region=-sph)
+ model = openmc.Model()
+ model.geometry = openmc.Geometry([cell])
+ model.settings.source = openmc.Source(
+ space=openmc.stats.Box([-5., -5., -5.], [5., 5., 5.]),
+ angle=openmc.stats.Monodirectional((0., 0., 1.)),
+ energy=openmc.stats.Discrete([1.0e5], [1.0])
+ )
+ model.settings.particles = 1000
+ model.settings.batches = 10
+ model.export_to_xml()
+
+ # Sample some particles and make sure they match specified source
+ openmc.lib.init()
+ particles = openmc.lib.sample_external_source(10, prn_seed=3)
+ assert len(particles) == 10
+ for p in particles:
+ assert -5. < p.r[0] < 5.
+ assert -5. < p.r[1] < 5.
+ assert -5. < p.r[2] < 5.
+ assert p.u[0] == 0.0
+ assert p.u[1] == 0.0
+ assert p.u[2] == 1.0
+ assert p.E == 1.0e5
+
+ # Using the same seed should produce the same particles
+ other_particles = openmc.lib.sample_external_source(10, prn_seed=3)
+ assert len(other_particles) == 10
+ for p1, p2 in zip(particles, other_particles):
+ assert p1.r == p2.r
+ assert p1.u == p2.u
+ assert p1.E == p2.E
+ assert p1.time == p2.time
+ assert p1.wgt == p2.wgt
+
+ openmc.lib.finalize()
| optional writing of source for fixed_source simulations
A recent PR #1518 implemented a new bank model which is a nice improvement for fixed source simulations. Thanks @alex-lyons
The new bank model no longer exports source information like particle x,y,z, E and u,v,w to the statepoint file. This is great as we often run simulation with fixed_source mode with many particles and the automatic writing of this data to the statepoint file was generating large files and taking a long time.
However it would be nice to be able to optinally add source information in some cases so we can do things like plot the source locations, distributions etc
So I have been looking at the documentation the and it appears we have a `sourcepoint` setting called `write` in` openmc.settings ` that should control if we write the source to the h5 file or not.
https://docs.openmc.org/en/latest/pythonapi/generated/openmc.Settings.html
Then there is an additional check in the simulations.cpp that prohibit writing of source points for fixed source.
```
if (contains(settings::sourcepoint_batch, simulation::current_batch)
&& settings::source_write && !settings::source_separate) {
bool b = (settings::run_mode == RunMode::EIGENVALUE);
```
https://github.com/openmc-dev/openmc/blob/571ed3b6ab449e555fc9c8452106425d26b19bd3/src/simulation.cpp#L367
Perhaps we should just use the `openmc.settings sourcepoint write` to determine if source points should be writing and not involve the simulation type.
https://github.com/Shimwell/openmc/blob/8b8392f94326a965de47d3ba6fb010a9bbb8f922/src/simulation.cpp#L366-L367
Unfortunately this would not be enough to write the source points to the statepoint file and some additional code is probably needed in the bank model but I get a bit lost and was wondering if anyone has any suggestions or perhaps this is not an issue for anyone else?
| Just in case anyone else is looking for a solution to this there are a few work arounds, here is an example of getting data points by pretending to perform an eiganvalue simulation
```
import xml.etree.ElementTree as ET
import h5py
import openmc
import plotly.graph_objects as go
sett = openmc.Settings()
sett.run_mode = "eigenvalue" # this will fail but it will write the inital_source.h5 file first
sett.particles = 10
sett.batches = 3
sett.inactive = 0
sett.write_initial_source = True
# Create a DT point source
source = openmc.Source()
source.space = openmc.stats.Point((0, 0, 0))
source.angle = openmc.stats.Isotropic()
source.energy = openmc.stats.Muir(kt=10e3) # might want to change the 10KeV plasma temperature
sett.source = source
sett.export_to_xml()
# this just adds write_initial_source == True to the settings.xml
tree = ET.parse("settings.xml")
root = tree.getroot()
elem = ET.SubElement(root, "write_initial_source")
elem.text = "true"
tree.write("settings.xml")
# no materials needed
openmc.Materials([]).export_to_xml()
# simple geometry
outer_surface = openmc.Sphere(r=100, boundary_type='vacuum')
cell = openmc.Cell(region=-outer_surface)
universe = openmc.Universe(cells=[cell])
geom = openmc.Geometry(universe)
geom.export_to_xml()
# this will crash hence the try except loop, but it writes the inital source.h5
try:
openmc.run()
except:
pass
# Read the intial_source.h5 and pull the coordinates from the dataset
filename = "initial_source.h5"
x = []
y = []
z = []
dir_x = []
dir_y = []
dir_z = []
e = []
with h5py.File(filename, "r") as f:
dataset = f["source_bank"]
for data in dataset:
x += [data[0][0]]
y += [data[0][1]]
z += [data[0][2]]
e += [data[2]]
dir_x += [data[1][0]]
dir_y += [data[1][1]]
dir_z += [data[1][2]]
print('neutron x birth positions', x)
print('neutron y birth positions', y)
print('neutron z birth positions', z)
print('neutron dir_x birth positions', dir_x)
print('neutron dir_y birth positions', dir_y)
print('neutron dir_z birth positions', dir_z)
print('neutron birth energy', e)
```
Just a thought -- one of the simplest approaches here might be to expose the `sample_external_source` C++ function to Python via `openmc.lib`. This would give a power user the ability to sample the source as they wish completely separate from a simulation.
I am keen understand how to contribute to the openmc.lib so I had a little go and am wondering if I am on the right track.
Would core.py need these extra lines
https://github.com/shimwell/openmc-1/blob/f7b968663c098848e5f5da0f25ac50b61f3597d6/openmc/lib/core.py#L93-L95
Also would core.py need a function link this
https://github.com/shimwell/openmc-1/blob/f7b968663c098848e5f5da0f25ac50b61f3597d6/openmc/lib/core.py#L102-L111
We'll need these changes, but there's a bit more to it. We'll need to expose the function through the CAPI in `capi.h` and add a wrapper function `openmc_sample_external_source` that matches the C-style pattern we have in place for errorcodes and such.
Is [this line](https://github.com/shimwell/openmc-1/blob/254884576ea65705138d7d6742e53ed719ab2908/include/openmc/capi.h#L124) all that is needed to expose the function through the CAPI in ```capi.h``` | 2022-07-16T01:33:32Z | [] | [] |
openmc-dev/openmc | 2,129 | openmc-dev__openmc-2129 | [
"907"
] | 925a5f6bb6295eb71fa974066bc992476a13b63e | diff --git a/openmc/region.py b/openmc/region.py
--- a/openmc/region.py
+++ b/openmc/region.py
@@ -259,13 +259,16 @@ def clone(self, memo=None):
clone[:] = [n.clone(memo) for n in self]
return clone
- def translate(self, vector, memo=None):
+ def translate(self, vector, inplace=False, memo=None):
"""Translate region in given direction
Parameters
----------
vector : iterable of float
Direction in which region should be translated
+ inplace : bool
+ Whether or not to return a region based on new surfaces or one based
+ on the original surfaces that have been modified.
memo : dict or None
Dictionary used for memoization. This parameter is used internally
and should not be specified by the user.
@@ -279,7 +282,7 @@ def translate(self, vector, memo=None):
if memo is None:
memo = {}
- return type(self)(n.translate(vector, memo) for n in self)
+ return type(self)(n.translate(vector, inplace, memo) for n in self)
def rotate(self, rotation, pivot=(0., 0., 0.), order='xyz', inplace=False,
memo=None):
@@ -308,7 +311,7 @@ def rotate(self, rotation, pivot=(0., 0., 0.), order='xyz', inplace=False,
:math:`\psi` about z. This corresponds to an x-y-z extrinsic
rotation as well as a z-y'-x'' intrinsic rotation using Tait-Bryan
angles :math:`(\phi, \theta, \psi)`.
- inplace : boolean
+ inplace : bool
Whether or not to return a new instance of Surface or to modify the
coefficients of this Surface in place. Defaults to False.
memo : dict or None
@@ -622,10 +625,10 @@ def clone(self, memo=None):
clone.node = self.node.clone(memo)
return clone
- def translate(self, vector, memo=None):
+ def translate(self, vector, inplace=False, memo=None):
if memo is None:
memo = {}
- return type(self)(self.node.translate(vector, memo))
+ return type(self)(self.node.translate(vector, inplace, memo))
def rotate(self, rotation, pivot=(0., 0., 0.), order='xyz', inplace=False,
memo=None):
diff --git a/openmc/surface.py b/openmc/surface.py
--- a/openmc/surface.py
+++ b/openmc/surface.py
@@ -336,9 +336,9 @@ def translate(self, vector, inplace=False):
----------
vector : iterable of float
Direction in which surface should be translated
- inplace : boolean
+ inplace : bool
Whether or not to return a new instance of this Surface or to
- modify the coefficients of this Surface. Defaults to False
+ modify the coefficients of this Surface.
Returns
-------
@@ -374,7 +374,7 @@ def rotate(self, rotation, pivot=(0., 0., 0.), order='xyz', inplace=False):
:math:`\psi` about z. This corresponds to an x-y-z extrinsic
rotation as well as a z-y'-x'' intrinsic rotation using Tait-Bryan
angles :math:`(\phi, \theta, \psi)`.
- inplace : boolean
+ inplace : bool
Whether or not to return a new instance of Surface or to modify the
coefficients of this Surface in place. Defaults to False.
@@ -568,9 +568,9 @@ def translate(self, vector, inplace=False):
----------
vector : iterable of float
Direction in which surface should be translated
- inplace : boolean
+ inplace : bool
Whether or not to return a new instance of a Plane or to modify the
- coefficients of this plane. Defaults to False
+ coefficients of this plane.
Returns
-------
@@ -1012,9 +1012,8 @@ def translate(self, vector, inplace=False):
----------
vector : iterable of float
Direction in which surface should be translated
- inplace : boolean
+ inplace : bool
Whether to return a clone of the Surface or the Surface itself.
- Defaults to False
Returns
-------
@@ -2563,7 +2562,7 @@ def clone(self, memo=None):
clone.surface = self.surface.clone(memo)
return clone
- def translate(self, vector, memo=None):
+ def translate(self, vector, inplace=False, memo=None):
"""Translate half-space in given direction
Parameters
@@ -2585,7 +2584,7 @@ def translate(self, vector, memo=None):
# If translated surface not in memo, add it
key = (self.surface, tuple(vector))
if key not in memo:
- memo[key] = self.surface.translate(vector)
+ memo[key] = self.surface.translate(vector, inplace)
# Return translated half-space
return type(self)(memo[key], self.side)
@@ -2617,7 +2616,7 @@ def rotate(self, rotation, pivot=(0., 0., 0.), order='xyz', inplace=False,
:math:`\psi` about z. This corresponds to an x-y-z extrinsic
rotation as well as a z-y'-x'' intrinsic rotation using Tait-Bryan
angles :math:`(\phi, \theta, \psi)`.
- inplace : boolean
+ inplace : bool
Whether or not to return a new instance of Surface or to modify the
coefficients of this Surface in place. Defaults to False.
memo : dict or None
| diff --git a/tests/unit_tests/test_region.py b/tests/unit_tests/test_region.py
--- a/tests/unit_tests/test_region.py
+++ b/tests/unit_tests/test_region.py
@@ -208,3 +208,17 @@ def test_from_expression(reset):
# Opening parenthesis immediately after halfspace
r = openmc.Region.from_expression('1(2|-3)', surfs)
assert str(r) == '(1 (2 | -3))'
+
+
+def test_translate_inplace():
+ sph = openmc.Sphere()
+ x = openmc.XPlane()
+ region = -sph & +x
+
+ # Translating a region should produce new surfaces
+ region2 = region.translate((0.5, -6.7, 3.9), inplace=False)
+ assert str(region) != str(region2)
+
+ # Translating a region in-place should *not* produce new surfaces
+ region3 = region.translate((0.5, -6.7, 3.9), inplace=True)
+ assert str(region) == str(region3)
| Dimensional inconsistency for SLBW competitive width terms
The neutron wave number factor seems to be missing in the channel radius ratio (`rhoc`) and scattering radius ratio (`rhochat`) terms for the competitive width branch of `reconstruct_slbw`. See lines 302 and 303 of [openmc/data/reconstruct.pyx](https://github.com/mit-crpg/openmc/blob/1008ab8ea1509e17151a96b535c57b4f64831831/openmc/data/reconstruct.pyx#L302)
| Nice find @apmccartney. Do you know of any evaluations that have non-zero competitive widths for SLBW/MLBW?
Not yet, but I'm planning to build up a test suite as part the resonance reconstruction effort. Assuming I can find such an evaluation, it will be available there. I'll ping you if I come across one before then.
Yeah, I hadn't run into one either which is probably part of the reason this slipped through. I'd welcome a PR if you want "credit" for finding the bug. If you have better things to do though, I can put in a fix :)
I'll post a fix sometime this weekend =)
math for wavenumber in reconstruct.pyx seems to be wrong. Code looks ok though | 2022-07-21T12:24:36Z | [] | [] |
openmc-dev/openmc | 2,139 | openmc-dev__openmc-2139 | [
"2069"
] | f5bd55debd7c16560f5376cb4696b7c10abc3084 | diff --git a/openmc/material.py b/openmc/material.py
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -34,7 +34,9 @@ class Material(IDManagerMixin):
To create a material, one should create an instance of this class, add
nuclides or elements with :meth:`Material.add_nuclide` or
:meth:`Material.add_element`, respectively, and set the total material
- density with :meth:`Material.set_density()`. The material can then be
+ density with :meth:`Material.set_density()`. Alternatively, you can
+ use :meth:`Material.add_components()` to pass a dictionary
+ containing all the component information. The material can then be
assigned to a cell using the :attr:`Cell.fill` attribute.
Parameters
@@ -403,6 +405,54 @@ def add_nuclide(self, nuclide: str, percent: float, percent_type: str = 'ao'):
self._nuclides.append(NuclideTuple(nuclide, percent, percent_type))
+ def add_components(self, components: dict, percent_type: str = 'ao'):
+ """ Add multiple elements or nuclides to a material
+
+ .. versionadded:: 0.13.1
+
+ Parameters
+ ----------
+ components : dict of str to float or dict
+ Dictionary mapping element or nuclide names to their atom or weight
+ percent. To specify enrichment of an element, the entry of
+ ``components`` for that element must instead be a dictionary
+ containing the keyword arguments as well as a value for
+ ``'percent'``
+ percent_type : {'ao', 'wo'}
+ 'ao' for atom percent and 'wo' for weight percent
+
+ Examples
+ --------
+ >>> mat = openmc.Material()
+ >>> components = {'Li': {'percent': 1.0,
+ >>> 'enrichment': 60.0,
+ >>> 'enrichment_target': 'Li7'},
+ >>> 'Fl': 1.0,
+ >>> 'Be6': 0.5}
+ >>> mat.add_components(components)
+
+ """
+
+ for component, params in components.items():
+ cv.check_type('component', component, str)
+ if isinstance(params, float):
+ params = {'percent': params}
+
+ else:
+ cv.check_type('params', params, dict)
+ if 'percent' not in params:
+ raise ValueError("An entry in the dictionary does not have "
+ "a required key: 'percent'")
+
+ params['percent_type'] = percent_type
+
+ ## check if nuclide
+ if str.isdigit(component[-1]):
+ self.add_nuclide(component, **params)
+ else: # is element
+ kwargs = params
+ self.add_element(component, **params)
+
def remove_nuclide(self, nuclide: str):
"""Remove a nuclide from the material
| diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -25,6 +25,52 @@ def test_add_nuclide():
with pytest.raises(ValueError):
m.add_nuclide('H1', 1.0, 'oa')
+def test_add_components():
+ """Test adding multipe elements or nuclides at once"""
+ m = openmc.Material()
+ components = {'H1': 2.0,
+ 'O16': 1.0,
+ 'Zr': 1.0,
+ 'O': 1.0,
+ 'U': {'percent': 1.0,
+ 'enrichment': 4.5},
+ 'Li': {'percent': 1.0,
+ 'enrichment': 60.0,
+ 'enrichment_target': 'Li7'},
+ 'H': {'percent': 1.0,
+ 'enrichment': 50.0,
+ 'enrichment_target': 'H2',
+ 'enrichment_type': 'wo'}}
+ m.add_components(components)
+ with pytest.raises(ValueError):
+ m.add_components({'U': {'percent': 1.0,
+ 'enrichment': 100.0}})
+ with pytest.raises(ValueError):
+ m.add_components({'Pu': {'percent': 1.0,
+ 'enrichment': 3.0}})
+ with pytest.raises(ValueError):
+ m.add_components({'U': {'percent': 1.0,
+ 'enrichment': 70.0,
+ 'enrichment_target':'U235'}})
+ with pytest.raises(ValueError):
+ m.add_components({'He': {'percent': 1.0,
+ 'enrichment': 17.0,
+ 'enrichment_target': 'He6'}})
+ with pytest.raises(ValueError):
+ m.add_components({'li': 1.0}) # should fail as 1st char is lowercase
+ with pytest.raises(ValueError):
+ m.add_components({'LI': 1.0}) # should fail as 2nd char is uppercase
+ with pytest.raises(ValueError):
+ m.add_components({'Xx': 1.0}) # should fail as Xx is not an element
+ with pytest.raises(ValueError):
+ m.add_components({'n': 1.0}) # check to avoid n for neutron being accepted
+ with pytest.raises(TypeError):
+ m.add_components({'H1': '1.0'})
+ with pytest.raises(TypeError):
+ m.add_components({1.0: 'H1'}, percent_type = 'wo')
+ with pytest.raises(ValueError):
+ m.add_components({'H1': 1.0}, percent_type = 'oa')
+
def test_remove_nuclide():
"""Test removing nuclides."""
@@ -49,7 +95,7 @@ def test_remove_elements():
assert m.nuclides[0].percent == 1.0
-def test_elements():
+def test_add_element():
"""Test adding elements."""
m = openmc.Material()
m.add_element('Zr', 1.0)
@@ -74,7 +120,6 @@ def test_elements():
with pytest.raises(ValueError):
m.add_element('n', 1.0) # check to avoid n for neutron being accepted
-
def test_elements_by_name():
"""Test adding elements by name"""
m = openmc.Material()
@@ -441,7 +486,7 @@ def test_activity_of_tritium():
m1.add_nuclide("H3", 1)
m1.set_density('g/cm3', 1)
m1.volume = 1
- assert pytest.approx(m1.activity) == 3.559778e14
+ assert pytest.approx(m1.activity) == 3.559778e14
def test_activity_of_metastable():
| Add material nuclides using a dictionary.
At the PHYSOR '22 workshop, an attendee mentioned that it would be useful to specify nuclide by passing in a dictionary with nuclide strings as keys and tuples for the atom/weight percent or atom/b-cm. Something like:
```python
mat_dict = {'H1': (2.0, 'ao'),
'O16': (1.0, 'ao')}
material.add_nuclides(mat_dict)
```
| 2022-07-27T18:13:59Z | [] | [] |
|
openmc-dev/openmc | 2,161 | openmc-dev__openmc-2161 | [
"2155"
] | adbc9e0537fcaa71b36d3095d7cfcff706699026 | diff --git a/openmc/lib/tally.py b/openmc/lib/tally.py
--- a/openmc/lib/tally.py
+++ b/openmc/lib/tally.py
@@ -87,6 +87,9 @@
_dll.openmc_tally_set_writable.argtypes = [c_int32, c_bool]
_dll.openmc_tally_set_writable.restype = c_int
_dll.openmc_tally_set_writable.errcheck = _error_handler
+_dll.openmc_remove_tally.argtypes = [c_int32]
+_dll.openmc_remove_tally.restype = c_int
+_dll.openmc_remove_tally.errcheck = _error_handler
_dll.tallies_size.restype = c_size_t
@@ -405,4 +408,8 @@ def __len__(self):
def __repr__(self):
return repr(dict(self))
+ def __delitem__(self, key):
+ """Delete a tally from tally vector and remove the ID,index pair from tally"""
+ _dll.openmc_remove_tally(self[key]._index)
+
tallies = _TallyMapping()
| diff --git a/tests/unit_tests/test_lib.py b/tests/unit_tests/test_lib.py
--- a/tests/unit_tests/test_lib.py
+++ b/tests/unit_tests/test_lib.py
@@ -340,6 +340,20 @@ def test_new_tally(lib_init):
assert len(openmc.lib.tallies) == 5
+def test_delete_tally(lib_init):
+ # delete tally 10 which was added in the above test
+ # check length is one less than before
+ del openmc.lib.tallies[10]
+ assert len(openmc.lib.tallies) == 4
+
+
+def test_invalid_tally_id(lib_init):
+ # attempt to access a tally that is guaranteed not to have a valid index
+ max_id = max(openmc.lib.tallies.keys())
+ with pytest.raises(KeyError):
+ openmc.lib.tallies[max_id+1]
+
+
def test_tally_activate(lib_simulation_init):
t = openmc.lib.tallies[1]
assert not t.active
diff --git a/tests/unit_tests/test_tallies.py b/tests/unit_tests/test_tallies.py
--- a/tests/unit_tests/test_tallies.py
+++ b/tests/unit_tests/test_tallies.py
@@ -38,4 +38,4 @@ def test_xml_roundtrip(run_in_tmpdir):
assert len(new_tally.triggers) == 1
assert new_tally.triggers[0].trigger_type == tally.triggers[0].trigger_type
assert new_tally.triggers[0].threshold == tally.triggers[0].threshold
- assert new_tally.triggers[0].scores == tally.triggers[0].scores
+ assert new_tally.triggers[0].scores == tally.triggers[0].scores
\ No newline at end of file
| No extern function to delete a tally from a model in tally.cpp
During a simulation with adaptive mesh refinement, as well as in some other cases (e.g. FETs), it would be useful to delete a tally that will no longer be needed. For the adaptivity application, if a mesh changes, the tally need to be reinitialized with new bins that account for additions to and deletions from the mesh. To accomplish this, an `extern` function will be added to `openmc/src/tallies/tally.cpp`
I will look into how to do this and create a new PR. @aprilnovak @pshriwise let me know if I missed anything important to the description of this issue.
| 2022-08-10T22:12:05Z | [] | [] |
|
openmc-dev/openmc | 2,217 | openmc-dev__openmc-2217 | [
"2210"
] | aea56288198bb53ed753c6b3b48a7b767f4806ee | diff --git a/openmc/mesh.py b/openmc/mesh.py
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -279,6 +279,7 @@ def write_data_to_vtk(self, points, filename, datasets, volume_normalization=Tru
return vtk_grid
+
class RegularMesh(StructuredMesh):
"""A regular Cartesian mesh in one, two, or three dimensions
@@ -509,6 +510,49 @@ def from_rect_lattice(cls, lattice, division=1, mesh_id=None, name=''):
return mesh
+ @classmethod
+ def from_domain(
+ cls,
+ domain,
+ dimension=[100, 100, 100],
+ mesh_id=None,
+ name=''
+ ):
+ """Create mesh from an existing openmc cell, region, universe or
+ geometry by making use of the objects bounding box property.
+
+ Parameters
+ ----------
+ domain : {openmc.Cell, openmc.Region, openmc.Universe, openmc.Geometry}
+ The object passed in will be used as a template for this mesh. The
+ bounding box of the property of the object passed will be used to
+ set the lower_left and upper_right of the mesh instance
+ dimension : Iterable of int
+ The number of mesh cells in each direction.
+ mesh_id : int
+ Unique identifier for the mesh
+ name : str
+ Name of the mesh
+
+ Returns
+ -------
+ openmc.RegularMesh
+ RegularMesh instance
+
+ """
+ cv.check_type(
+ "domain",
+ domain,
+ (openmc.Cell, openmc.Region, openmc.Universe, openmc.Geometry),
+ )
+
+ mesh = cls(mesh_id, name)
+ mesh.lower_left = domain.bounding_box[0]
+ mesh.upper_right = domain.bounding_box[1]
+ mesh.dimension = dimension
+
+ return mesh
+
def to_xml_element(self):
"""Return XML representation of the mesh
| diff --git a/tests/unit_tests/test_mesh_from_domain.py b/tests/unit_tests/test_mesh_from_domain.py
new file mode 100644
--- /dev/null
+++ b/tests/unit_tests/test_mesh_from_domain.py
@@ -0,0 +1,63 @@
+import numpy as np
+import openmc
+import pytest
+
+
+def test_reg_mesh_from_cell():
+ """Tests a RegularMesh can be made from a Cell and the specified dimensions
+ are propagated through. Cell is not centralized"""
+ surface = openmc.Sphere(r=10, x0=2, y0=3, z0=5)
+ cell = openmc.Cell(region=-surface)
+
+ mesh = openmc.RegularMesh.from_domain(cell, dimension=[7, 11, 13])
+ assert isinstance(mesh, openmc.RegularMesh)
+ assert np.array_equal(mesh.dimension, (7, 11, 13))
+ assert np.array_equal(mesh.lower_left, cell.bounding_box[0])
+ assert np.array_equal(mesh.upper_right, cell.bounding_box[1])
+
+
+def test_reg_mesh_from_region():
+ """Tests a RegularMesh can be made from a Region and the default dimensions
+ are propagated through. Region is not centralized"""
+ surface = openmc.Sphere(r=1, x0=-5, y0=-3, z0=-2)
+ region = -surface
+
+ mesh = openmc.RegularMesh.from_domain(region)
+ assert isinstance(mesh, openmc.RegularMesh)
+ assert np.array_equal(mesh.dimension, (100, 100, 100)) # default values
+ assert np.array_equal(mesh.lower_left, region.bounding_box[0])
+ assert np.array_equal(mesh.upper_right, region.bounding_box[1])
+
+
+def test_reg_mesh_from_universe():
+ """Tests a RegularMesh can be made from a Universe and the default dimensions
+ are propagated through. Universe is centralized"""
+ surface = openmc.Sphere(r=42)
+ cell = openmc.Cell(region=-surface)
+ universe = openmc.Universe(cells=[cell])
+
+ mesh = openmc.RegularMesh.from_domain(universe)
+ assert isinstance(mesh, openmc.RegularMesh)
+ assert np.array_equal(mesh.dimension, (100, 100, 100)) # default values
+ assert np.array_equal(mesh.lower_left, universe.bounding_box[0])
+ assert np.array_equal(mesh.upper_right, universe.bounding_box[1])
+
+
+def test_reg_mesh_from_geometry():
+ """Tests a RegularMesh can be made from a Geometry and the default dimensions
+ are propagated through. Geometry is centralized"""
+ surface = openmc.Sphere(r=42)
+ cell = openmc.Cell(region=-surface)
+ universe = openmc.Universe(cells=[cell])
+ geometry = openmc.Geometry(universe)
+
+ mesh = openmc.RegularMesh.from_domain(geometry)
+ assert isinstance(mesh, openmc.RegularMesh)
+ assert np.array_equal(mesh.dimension, (100, 100, 100)) # default values
+ assert np.array_equal(mesh.lower_left, geometry.bounding_box[0])
+ assert np.array_equal(mesh.upper_right, geometry.bounding_box[1])
+
+
+def test_error_from_unsupported_object():
+ with pytest.raises(TypeError):
+ openmc.RegularMesh.from_domain("vacuum energy")
| feature request: RegularMesh from universe class method
I find myself making RegularMesh that encompass the entire geometry quite often. When making weight windows, flux maps or dose maps.
We have ```Universe.bounding_box``` property and I was wondering if anyone else would like a new class method on the ```RegularMesh``` class so that regular meshes can be made from a universe.
This would automatically set ```lower_left``` and the ```upper_right``` using the universe.bounding_box
Perhaps not a huge saving for the user but let me know if this is a worthwhile upgrade and I can make a PR
usage
```python
mesh = openmc.RegularMesh.from_universe(my_universe, dimension=[100, 100, 100])
```
current method
```python
mesh = openmc.RegularMesh()
mesh.dimension = [100, 100, 100]
mesh.lower_left = geometry.bounding_box[0]
mesh.upper_right = geometry.bounding_box[1]
```
additional code required in mesh.py
```python
@classmethod
def from_universe(cls, universe, dimension=[10, 10, 10], mesh_id=None, name=''):
"""Create mesh from an existing openmc universe
Parameters
----------
universe : openmc.Universe
Open used as a template for this mesh
dimension : Iterable of int
The number of mesh cells in each direction.
mesh_id : int
Unique identifier for the mesh
name : str
Name of the mesh
Returns
-------
openmc.RegularMesh
RegularMesh instance
"""
cv.check_type('rectangular lattice', universe, openmc.Universe)
mesh = cls(mesh_id, name)
mesh.lower_left = universe.bounding_box[0]
mesh.upper_right = universe.bounding_box[1]
mesh.dimension = dimension
return mesh
```
| `Universe` is one of several classes that has a `bounding_box` property (`Cell`, `Region`, `Geometry` also do), so if we were to do this, we'd probably want to make it more general
Agreed @paulromano. A few instance type checks, new parameter name for `universe`, and an update to the docstrings should get us pretty close I think. | 2022-09-09T13:50:09Z | [] | [] |
openmc-dev/openmc | 2,235 | openmc-dev__openmc-2235 | [
"1829"
] | 1d140e348d190fc50deebf76ea85162e018495da | diff --git a/openmc/source.py b/openmc/source.py
--- a/openmc/source.py
+++ b/openmc/source.py
@@ -1,10 +1,13 @@
+from collections.abc import Iterable
from enum import Enum
from numbers import Real
+import warnings
from xml.etree import ElementTree as ET
import numpy as np
import h5py
+import openmc
import openmc.checkvalue as cv
from openmc.stats.multivariate import UnitSphere, Spatial
from openmc.stats.univariate import Univariate
@@ -36,6 +39,9 @@ class Source:
Strength of the source
particle : {'neutron', 'photon'}
Source particle type
+ domains : iterable of openmc.Cell, openmc.Material, or openmc.Universe
+ Domains to reject based on, i.e., if a sampled spatial location is not
+ within one of these domains, it will be rejected.
Attributes
----------
@@ -57,11 +63,16 @@ class Source:
Strength of the source
particle : {'neutron', 'photon'}
Source particle type
+ ids : Iterable of int
+ IDs of domains to use for rejection
+ domain_type : {'cell', 'material', 'universe'}
+ Type of domain to use for rejection
"""
def __init__(self, space=None, angle=None, energy=None, time=None, filename=None,
- library=None, parameters=None, strength=1.0, particle='neutron'):
+ library=None, parameters=None, strength=1.0, particle='neutron',
+ domains=None):
self._space = None
self._angle = None
self._energy = None
@@ -87,6 +98,17 @@ def __init__(self, space=None, angle=None, energy=None, time=None, filename=None
self.strength = strength
self.particle = particle
+ self._domain_ids = []
+ self._domain_type = None
+ if domains is not None:
+ if isinstance(domains[0], openmc.Cell):
+ self.domain_type = 'cell'
+ elif isinstance(domains[0], openmc.Material):
+ self.domain_type = 'material'
+ elif isinstance(domains[0], openmc.Universe):
+ self.domain_type = 'universe'
+ self.domain_ids = [d.id for d in domains]
+
@property
def file(self):
return self._file
@@ -123,6 +145,24 @@ def strength(self):
def particle(self):
return self._particle
+ @property
+ def domain_ids(self):
+ return self._domain_ids
+
+ @property
+ def domain_type(self):
+ return self._domain_type
+
+ @domain_ids.setter
+ def domain_ids(self, ids):
+ cv.check_type('domain IDs', ids, Iterable, Real)
+ self._domain_ids = ids
+
+ @domain_type.setter
+ def domain_type(self, domain_type):
+ cv.check_value('domain type', domain_type, ('cell', 'material', 'universe'))
+ self._domain_type = domain_type
+
@file.setter
def file(self, filename):
cv.check_type('source file', filename, str)
@@ -196,6 +236,11 @@ def to_xml_element(self):
element.append(self.energy.to_xml_element('energy'))
if self.time is not None:
element.append(self.time.to_xml_element('time'))
+ if self.domain_ids:
+ dt_elem = ET.SubElement(element, "domain_type")
+ dt_elem.text = self.domain_type
+ id_elem = ET.SubElement(element, "domain_ids")
+ id_elem.text = ' '.join(str(uid) for uid in self.domain_ids)
return element
@classmethod
@@ -213,7 +258,24 @@ def from_xml_element(cls, elem):
Source generated from XML element
"""
- source = cls()
+ domain_type = get_text(elem, "domain_type")
+ if domain_type is not None:
+ domain_ids = [int(x) for x in get_text(elem, "domain_ids").split()]
+
+ # Instantiate some throw-away domains that are used by the
+ # constructor to assign IDs
+ with warnings.catch_warnings():
+ warnings.simplefilter('ignore', openmc.IDWarning)
+ if domain_type == 'cell':
+ domains = [openmc.Cell(uid) for uid in domain_ids]
+ elif domain_type == 'material':
+ domains = [openmc.Material(uid) for uid in domain_ids]
+ elif domain_type == 'universe':
+ domains = [openmc.Universe(uid) for uid in domain_ids]
+ else:
+ domains = None
+
+ source = cls(domains=domains)
strength = get_text(elem, 'strength')
if strength is not None:
| diff --git a/tests/unit_tests/test_source.py b/tests/unit_tests/test_source.py
--- a/tests/unit_tests/test_source.py
+++ b/tests/unit_tests/test_source.py
@@ -1,6 +1,7 @@
from math import pi
import openmc
+import openmc.lib
import openmc.stats
import numpy as np
from pytest import approx
@@ -96,3 +97,40 @@ def test_source_xml_roundtrip():
np.testing.assert_allclose(new_src.angle.reference_uvw, src.angle.reference_uvw)
assert new_src.particle == src.particle
assert new_src.strength == approx(src.strength)
+
+
+def test_rejection(run_in_tmpdir):
+ # Model with two spheres inside a box
+ mat = openmc.Material()
+ mat.add_nuclide('H1', 1.0)
+ sph1 = openmc.Sphere(x0=3, r=1.0)
+ sph2 = openmc.Sphere(x0=-3, r=1.0)
+ cube = openmc.model.RectangularParallelepiped(
+ -5., 5., -5., 5., -5., 5., boundary_type='reflective'
+ )
+ cell1 = openmc.Cell(fill=mat, region=-sph1)
+ cell2 = openmc.Cell(fill=mat, region=-sph2)
+ non_source_region = +sph1 & +sph2 & -cube
+ cell3 = openmc.Cell(region=non_source_region)
+ model = openmc.Model()
+ model.geometry = openmc.Geometry([cell1, cell2, cell3])
+ model.settings.particles = 100
+ model.settings.batches = 10
+ model.settings.run_mode = 'fixed source'
+
+ # Set up a box source with rejection on the spherical cell
+ space = openmc.stats.Box(*cell3.bounding_box)
+ model.settings.source = openmc.Source(space=space, domains=[cell1, cell2])
+
+ # Load up model via openmc.lib and sample source
+ model.export_to_xml()
+ openmc.lib.init()
+ particles = openmc.lib.sample_external_source(1000)
+
+ # Make sure that all sampled sources are within one of the spheres
+ joint_region = cell1.region | cell2.region
+ for p in particles:
+ assert p.r in joint_region
+ assert p.r not in non_source_region
+
+ openmc.lib.finalize()
| Generic filter for rejecting sources points when sampling
As originally discussed on Discourse https://openmc.discourse.group/t/source-uniform-sampling-in-cell-of-given-material/1062
It would be great to add generic filter to allow the rejection of source points when being sampled during the creation of particles.
Source sampling should allow for rejection of the proposed sampled coordinates if the coordinates are not in a user specified material or not in a user specified cell.
While the generic source sampling filter would be separate to the distributions themselves it could be passed to the distributions and the distributions should make use of the filter to ascertain if the sampling point results in a neutron or not.
Perhaps the best distribution to demonstrate this on is the ```openmc.stats.Box``` distribution as it already has a similar feature.
This will allow us to make interesting shaped sources like the example picture below which shows source sampling randomly across a openmc.stats.Box rejecting sample points that don't appear within a certain material / cell
There are some related lines in OpenMC relating to a similar feature that allows sampling points to be rejected if they are not within a fissionable material with the ```only_fissionable``` keyword that might be useful for anyone considering this feature.
https://github.com/openmc-dev/openmc/blob/efcc0c158edcc3e389eb20a5c5ffc4e0a65ef554/src/distribution_spatial.cpp#L187-L204
https://github.com/openmc-dev/openmc/blob/efcc0c158edcc3e389eb20a5c5ffc4e0a65ef554/src/source.cpp#L171-L173
https://github.com/openmc-dev/openmc/blob/efcc0c158edcc3e389eb20a5c5ffc4e0a65ef554/openmc/stats/multivariate.py#L617-L716
| I've issued a bounty reward for this issue https://www.bountysource.com/issues/98138076-generic-filter-for-rejecting-sources-points-when-sampling
Could the spawn probability be inhomogeneous and a function of x, y, z? | 2022-09-26T19:45:49Z | [] | [] |
openmc-dev/openmc | 2,252 | openmc-dev__openmc-2252 | [
"2250"
] | 9a86c9c065e545a7ece086c34dc7dca38cfa9892 | diff --git a/openmc/data/decay.py b/openmc/data/decay.py
--- a/openmc/data/decay.py
+++ b/openmc/data/decay.py
@@ -1,10 +1,9 @@
from collections.abc import Iterable
from io import StringIO
from math import log
-from pathlib import Path
import re
+from typing import Optional
from warnings import warn
-from xml.etree import ElementTree as ET
import numpy as np
from uncertainties import ufloat, UFloat
@@ -579,7 +578,7 @@ def sources(self):
_DECAY_PHOTON_ENERGY = {}
-def decay_photon_energy(nuclide: str) -> Univariate:
+def decay_photon_energy(nuclide: str) -> Optional[Univariate]:
"""Get photon energy distribution resulting from the decay of a nuclide
This function relies on data stored in a depletion chain. Before calling it
@@ -595,9 +594,10 @@ def decay_photon_energy(nuclide: str) -> Univariate:
Returns
-------
- openmc.stats.Univariate
- Distribution of energies in [eV] of photons emitted from decay. Note
- that the probabilities represent intensities, given as [decay/sec].
+ openmc.stats.Univariate or None
+ Distribution of energies in [eV] of photons emitted from decay, or None
+ if no photon source exists. Note that the probabilities represent
+ intensities, given as [decay/sec].
"""
if not _DECAY_PHOTON_ENERGY:
chain_file = openmc.config.get('chain_file')
diff --git a/openmc/material.py b/openmc/material.py
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -92,10 +92,11 @@ class Material(IDManagerMixin):
fissionable_mass : float
Mass of fissionable nuclides in the material in [g]. Requires that the
:attr:`volume` attribute is set.
- decay_photon_energy : openmc.stats.Univariate
+ decay_photon_energy : openmc.stats.Univariate or None
Energy distribution of photons emitted from decay of unstable nuclides
- within the material. The integral of this distribution is the total
- intensity of the photon source in [decay/sec].
+ within the material, or None if no photon source exists. The integral of
+ this distribution is the total intensity of the photon source in
+ [decay/sec].
.. versionadded:: 0.14.0
@@ -264,7 +265,7 @@ def fissionable_mass(self):
return density*self.volume
@property
- def decay_photon_energy(self) -> Univariate:
+ def decay_photon_energy(self) -> Optional[Univariate]:
atoms = self.get_nuclide_atoms()
dists = []
probs = []
@@ -273,7 +274,7 @@ def decay_photon_energy(self) -> Univariate:
if source_per_atom is not None:
dists.append(source_per_atom)
probs.append(num_atoms)
- return openmc.data.combine_distributions(dists, probs)
+ return openmc.data.combine_distributions(dists, probs) if dists else None
@classmethod
def from_hdf5(cls, group: h5py.Group):
| diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -573,3 +573,9 @@ def intensity(src):
assert src.integral() == pytest.approx(sum(
intensity(decay_photon_energy(nuc)) for nuc in m.get_nuclides()
))
+
+ # A material with no unstable nuclides should have no decay photon source
+ stable = openmc.Material()
+ stable.add_nuclide('Gd156', 1.0)
+ stable.volume = 1.0
+ assert stable.decay_photon_energy is None
| Error when calling decay_photon_energy on stable isotope
When calling ```decay_photon_energy``` on a material which has no gamma decays the code raises an indexError
in this case ```dists``` is ```[]``` so ```dists[0]``` is not possible
Perhaps we should add some error handling for empty lists to ```combine_distributions```
Code to reproduce
```python
import openmc
openmc.config['chain_file']='chain-endf.xml'
a=openmc.Material()
a.add_nuclide('Li6',1)
a.volume=1
a.decay_photon_energy
```
error message
```
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/openmc/openmc/material.py", line 276, in decay_photon_energy
return openmc.data.combine_distributions(dists, probs)
File "/home/openmc/openmc/stats/univariate.py", line 1252, in combine_distributions
return dist_list[0]
IndexError: list index out of range
```
| Oops! Thanks for reporting @shimwell. I'll submit a fix for this shortly. | 2022-10-05T19:29:41Z | [] | [] |
openmc-dev/openmc | 2,256 | openmc-dev__openmc-2256 | [
"2248"
] | 341cb9eb11c9d4e5637bc06ebfa312fe4ceb7491 | diff --git a/openmc/mesh.py b/openmc/mesh.py
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -1050,6 +1050,9 @@ class CylindricalMesh(StructuredMesh):
The default value is [0, 2π], i.e. the full phi range.
z_grid : numpy.ndarray
1-D array of mesh boundary points along the z-axis.
+ origin : numpy.ndarray
+ 1-D array of length 3 the (x,y,z) origin of the mesh in
+ cartesian coordinates
indices : Iterable of tuple
An iterable of mesh indices for each mesh element, e.g. [(1, 1, 1),
(2, 1, 1), ...]
@@ -1062,6 +1065,7 @@ def __init__(self, mesh_id=None, name=''):
self._r_grid = None
self._phi_grid = [0.0, 2*pi]
self._z_grid = None
+ self.origin = (0., 0., 0.)
@property
def dimension(self):
@@ -1073,6 +1077,10 @@ def dimension(self):
def n_dimension(self):
return 3
+ @property
+ def origin(self):
+ return self._origin
+
@property
def r_grid(self):
return self._r_grid
@@ -1099,6 +1107,12 @@ def indices(self):
for p in range(1, np + 1)
for r in range(1, nr + 1))
+ @origin.setter
+ def origin(self, coords):
+ cv.check_type('mesh origin', coords, Iterable, Real)
+ cv.check_length("mesh origin", coords, 3)
+ self._origin = np.asarray(coords)
+
@r_grid.setter
def r_grid(self, grid):
cv.check_type('mesh r_grid', grid, Iterable, Real)
@@ -1118,6 +1132,7 @@ def __repr__(self):
fmt = '{0: <16}{1}{2}\n'
string = super().__repr__()
string += fmt.format('\tDimensions', '=\t', self.n_dimension)
+ string += fmt.format('\tOrigin', '=\t', self.origin)
r_grid_str = str(self._r_grid) if self._r_grid is None else len(self._r_grid)
string += fmt.format('\tN R pnts:', '=\t', r_grid_str)
if self._r_grid is not None:
@@ -1144,6 +1159,8 @@ def from_hdf5(cls, group):
mesh.r_grid = group['r_grid'][()]
mesh.phi_grid = group['phi_grid'][()]
mesh.z_grid = group['z_grid'][()]
+ if 'origin' in group:
+ mesh.origin = group['origin'][()]
return mesh
@@ -1240,6 +1257,9 @@ def to_xml_element(self):
subelement = ET.SubElement(element, "z_grid")
subelement.text = ' '.join(map(str, self.z_grid))
+ subelement = ET.SubElement(element, "origin")
+ subelement.text = ' '.join(map(str, self.origin))
+
return element
@classmethod
@@ -1263,6 +1283,8 @@ def from_xml_element(cls, elem):
mesh.r_grid = [float(x) for x in get_text(elem, "r_grid").split()]
mesh.phi_grid = [float(x) for x in get_text(elem, "phi_grid").split()]
mesh.z_grid = [float(x) for x in get_text(elem, "z_grid").split()]
+ mesh.origin = [float(x) for x in get_text(elem, "origin", default=[0., 0., 0.]).split()]
+
return mesh
@property
@@ -1304,12 +1326,13 @@ def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
"""
# create points
pts_cylindrical = self.vertices.T.reshape(-1, 3)
-
pts_cartesian = np.copy(pts_cylindrical)
- r, phi = pts_cylindrical[:, 0], pts_cylindrical[:, 1]
- pts_cartesian[:, 0] = r * np.cos(phi)
- pts_cartesian[:, 1] = r * np.sin(phi)
+ r, phi = pts_cylindrical[:, 0], pts_cylindrical[:, 1]
+ pts_cartesian[:, 0] = r * np.cos(phi) + self.origin[0]
+ pts_cartesian[:, 1] = r * np.sin(phi) + self.origin[1]
+ pts_cartesian[:, 2] += self.origin[2]
+
return super().write_data_to_vtk(
points=pts_cartesian,
filename=filename,
@@ -1346,6 +1369,9 @@ class SphericalMesh(StructuredMesh):
phi_grid : numpy.ndarray
1-D array of mesh boundary points along the phi-axis in radians.
The default value is [0, 2π], i.e. the full phi range.
+ origin : numpy.ndarray
+ 1-D array of length 3 the (x,y,z) origin of the mesh in
+ cartesian coordinates
indices : Iterable of tuple
An iterable of mesh indices for each mesh element, e.g. [(1, 1, 1),
(2, 1, 1), ...]
@@ -1358,6 +1384,7 @@ def __init__(self, mesh_id=None, name=''):
self._r_grid = None
self._theta_grid = [0, pi]
self._phi_grid = [0, 2*pi]
+ self.origin = (0., 0., 0.)
@property
def dimension(self):
@@ -1369,6 +1396,10 @@ def dimension(self):
def n_dimension(self):
return 3
+ @property
+ def origin(self):
+ return self._origin
+
@property
def r_grid(self):
return self._r_grid
@@ -1395,6 +1426,12 @@ def indices(self):
for t in range(1, nt + 1)
for r in range(1, nr + 1))
+ @origin.setter
+ def origin(self, coords):
+ cv.check_type('mesh origin', coords, Iterable, Real)
+ cv.check_length("mesh origin", coords, 3)
+ self._origin = np.asarray(coords)
+
@r_grid.setter
def r_grid(self, grid):
cv.check_type('mesh r_grid', grid, Iterable, Real)
@@ -1414,6 +1451,7 @@ def __repr__(self):
fmt = '{0: <16}{1}{2}\n'
string = super().__repr__()
string += fmt.format('\tDimensions', '=\t', self.n_dimension)
+ string += fmt.format('\tOrigin', '=\t', self.origin)
r_grid_str = str(self._r_grid) if self._r_grid is None else len(self._r_grid)
string += fmt.format('\tN R pnts:', '=\t', r_grid_str)
if self._r_grid is not None:
@@ -1440,6 +1478,8 @@ def from_hdf5(cls, group):
mesh.r_grid = group['r_grid'][()]
mesh.theta_grid = group['theta_grid'][()]
mesh.phi_grid = group['phi_grid'][()]
+ if 'origin' in group:
+ mesh.origin = group['origin'][()]
return mesh
@@ -1466,6 +1506,9 @@ def to_xml_element(self):
subelement = ET.SubElement(element, "phi_grid")
subelement.text = ' '.join(map(str, self.phi_grid))
+ subelement = ET.SubElement(element, "origin")
+ subelement.text = ' '.join(map(str, self.origin))
+
return element
@classmethod
@@ -1489,6 +1532,8 @@ def from_xml_element(cls, elem):
mesh.r_grid = [float(x) for x in get_text(elem, "r_grid").split()]
mesh.theta_grid = [float(x) for x in get_text(elem, "theta_grid").split()]
mesh.phi_grid = [float(x) for x in get_text(elem, "phi_grid").split()]
+ mesh.origin = [float(x) for x in get_text(elem, "origin", default=[0., 0., 0.]).split()]
+
return mesh
@property
@@ -1530,12 +1575,13 @@ def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
"""
# create points
pts_spherical = self.vertices.T.reshape(-1, 3)
-
pts_cartesian = np.copy(pts_spherical)
+
r, theta, phi = pts_spherical[:, 0], pts_spherical[:, 1], pts_spherical[:, 2]
- pts_cartesian[:, 0] = r * np.sin(theta) * np.cos(phi)
- pts_cartesian[:, 1] = r * np.sin(theta) * np.sin(phi)
- pts_cartesian[:, 2] = r * np.cos(theta)
+
+ pts_cartesian[:, 0] = r * np.sin(phi) * np.cos(theta) + self.origin[0]
+ pts_cartesian[:, 1] = r * np.sin(phi) * np.sin(theta) + self.origin[1]
+ pts_cartesian[:, 2] = r * np.cos(phi) + self.origin[2]
return super().write_data_to_vtk(
points=pts_cartesian,
| diff --git a/tests/regression_tests/filter_mesh/inputs_true.dat b/tests/regression_tests/filter_mesh/inputs_true.dat
--- a/tests/regression_tests/filter_mesh/inputs_true.dat
+++ b/tests/regression_tests/filter_mesh/inputs_true.dat
@@ -57,11 +57,13 @@
<r_grid>0.0 0.4411764705882353 0.8823529411764706 1.3235294117647058 1.7647058823529411 2.2058823529411766 2.6470588235294117 3.0882352941176467 3.5294117647058822 3.9705882352941178 4.411764705882353 4.852941176470588 5.294117647058823 5.735294117647059 6.1764705882352935 6.617647058823529 7.0588235294117645 7.5</r_grid>
<phi_grid>0.0 0.3490658503988659 0.6981317007977318 1.0471975511965976 1.3962634015954636 1.7453292519943295 2.0943951023931953 2.443460952792061 2.792526803190927 3.141592653589793 3.490658503988659 3.839724354387525 4.1887902047863905 4.537856055185257 4.886921905584122 5.235987755982989 5.585053606381854 5.93411945678072 6.283185307179586</phi_grid>
<z_grid>-7.5 -6.5625 -5.625 -4.6875 -3.75 -2.8125 -1.875 -0.9375 0.0 0.9375 1.875 2.8125 3.75 4.6875 5.625 6.5625 7.5</z_grid>
+ <origin>0.0 0.0 0.0</origin>
</mesh>
<mesh id="6" type="spherical">
<r_grid>0.0 0.4411764705882353 0.8823529411764706 1.3235294117647058 1.7647058823529411 2.2058823529411766 2.6470588235294117 3.0882352941176467 3.5294117647058822 3.9705882352941178 4.411764705882353 4.852941176470588 5.294117647058823 5.735294117647059 6.1764705882352935 6.617647058823529 7.0588235294117645 7.5</r_grid>
<theta_grid>0.0 0.39269908169872414 0.7853981633974483 1.1780972450961724 1.5707963267948966 1.9634954084936207 2.356194490192345 2.748893571891069 3.141592653589793</theta_grid>
<phi_grid>0.0 0.3490658503988659 0.6981317007977318 1.0471975511965976 1.3962634015954636 1.7453292519943295 2.0943951023931953 2.443460952792061 2.792526803190927 3.141592653589793 3.490658503988659 3.839724354387525 4.1887902047863905 4.537856055185257 4.886921905584122 5.235987755982989 5.585053606381854 5.93411945678072 6.283185307179586</phi_grid>
+ <origin>0.0 0.0 0.0</origin>
</mesh>
<filter id="1" type="mesh">
<bins>1</bins>
diff --git a/tests/unit_tests/test_cylindrical_mesh.py b/tests/unit_tests/test_cylindrical_mesh.py
new file mode 100644
--- /dev/null
+++ b/tests/unit_tests/test_cylindrical_mesh.py
@@ -0,0 +1,105 @@
+from itertools import product, permutations
+
+import openmc
+import numpy as np
+
+import pytest
+
+geom_size = 5
+
[email protected]()
+def model():
+ openmc.reset_auto_ids()
+
+ water = openmc.Material(name='water')
+ water.add_element('H', 2.0)
+ water.add_element('O', 1.0)
+ water.set_density('g/cc', 1.0)
+
+ rpp = openmc.model.RectangularParallelepiped(*([-geom_size, geom_size] * 3),
+ boundary_type='vacuum')
+
+ cell = openmc.Cell(region=-rpp, fill=water)
+
+ geom = openmc.Geometry([cell])
+
+ source = openmc.Source()
+ source.space = openmc.stats.Point()
+ source.energy = openmc.stats.Discrete([10000], [1.0])
+
+ settings = openmc.Settings()
+ settings.particles = 2000
+ settings.batches = 10
+ settings.run_mode = 'fixed source'
+
+ # build
+ mesh = openmc.CylindricalMesh()
+ mesh.phi_grid = np.linspace(0, 2*np.pi, 21)
+ mesh.z_grid = np.linspace(-geom_size, geom_size, 11)
+ mesh.r_grid = np.linspace(0, geom_size, geom_size)
+
+ tally = openmc.Tally()
+
+ mesh_filter = openmc.MeshFilter(mesh)
+ tally.filters.append(mesh_filter)
+
+ tally.scores.append("flux")
+
+ tallies = openmc.Tallies([tally])
+
+ return openmc.Model(geometry=geom, settings=settings, tallies=tallies)
+
+def test_origin_read_write_to_xml(run_in_tmpdir, model):
+ """Tests that the origin attribute can be written and read back to XML
+ """
+ mesh = model.tallies[0].filters[0].mesh
+ mesh.origin = [0.1, 0.2, 0.3]
+ model.tallies.export_to_xml()
+
+ # read back
+ new_tallies = openmc.Tallies.from_xml()
+ new_tally = new_tallies[0]
+ new_mesh = new_tally.filters[0].mesh
+ np.testing.assert_equal(new_mesh.origin, mesh.origin)
+
+estimators = ('tracklength', 'collision')
+origins = set(permutations((-geom_size, 0, 0)))
+origins |= set(permutations((geom_size, 0, 0)))
+
+test_cases = product(estimators, origins)
+
+def label(p):
+ if isinstance(p, tuple):
+ return f'origin:{p}'
+ if isinstance(p, str):
+ return f'estimator:{p}'
+
[email protected]('estimator,origin', test_cases, ids=label)
+def test_offset_mesh(model, estimator, origin):
+ """Tests that the mesh has been moved based on tally results
+ """
+ mesh = model.tallies[0].filters[0].mesh
+ model.tallies[0].estimator = estimator
+ # move the center of the cylinder mesh upwards
+ mesh.origin = origin
+
+ sp_filename = model.run()
+
+ with openmc.StatePoint(sp_filename) as sp:
+ tally = sp.tallies[1]
+
+ # we've translated half of the cylinder mesh above the model,
+ # so ensure that half of the bins are populated
+ assert np.count_nonzero(tally.mean) == tally.mean.size / 2
+
+ # check that the half of the mesh that is outside of the geometry
+ # contains the zero values
+ mean = tally.get_reshaped_data('mean', expand_dims=True)
+ centroids = mesh.centroids
+ for ijk in mesh.indices:
+ i, j, k = np.array(ijk) - 1
+ print(centroids[:, i, j, k])
+ if model.geometry.find(centroids[:, i, j, k]):
+ mean[i, j, k] == 0.0
+ else:
+ mean[i, j, k] != 0.0
diff --git a/tests/unit_tests/test_deplete_activation.py b/tests/unit_tests/test_deplete_activation.py
--- a/tests/unit_tests/test_deplete_activation.py
+++ b/tests/unit_tests/test_deplete_activation.py
@@ -33,7 +33,7 @@ def model():
)
model.settings.run_mode = 'fixed source'
- rx_tally = openmc.Tally()
+ rx_tally = openmc.Tally(name='activation tally')
rx_tally.scores = ['(n,gamma)']
model.tallies.append(rx_tally)
@@ -53,7 +53,7 @@ def test_activation(run_in_tmpdir, model, reaction_rate_mode, reaction_rate_opts
# Determine (n.gamma) reaction rate using initial run
sp = model.run()
with openmc.StatePoint(sp) as sp:
- tally = sp.tallies[1]
+ tally = sp.get_tally(name='activation tally')
capture_rate = tally.mean.flat[0]
# Create one-nuclide depletion chain
diff --git a/tests/unit_tests/test_spherical_mesh.py b/tests/unit_tests/test_spherical_mesh.py
new file mode 100644
--- /dev/null
+++ b/tests/unit_tests/test_spherical_mesh.py
@@ -0,0 +1,109 @@
+from itertools import product, permutations
+
+import openmc
+import numpy as np
+
+import pytest
+
+geom_size = 5
+
[email protected]()
+def model():
+ openmc.reset_auto_ids()
+
+ water = openmc.Material(name='water')
+ water.add_element('H', 2.0)
+ water.add_element('O', 1.0)
+ water.set_density('g/cc', 1.0)
+
+ rpp = openmc.model.RectangularParallelepiped(*([-geom_size, geom_size] * 3),
+ boundary_type='vacuum')
+
+ cell = openmc.Cell(region=-rpp, fill=water)
+
+ geom = openmc.Geometry([cell])
+
+ source = openmc.Source()
+ source.space = openmc.stats.Point()
+ source.energy = openmc.stats.Discrete([10000], [1.0])
+
+ settings = openmc.Settings()
+ settings.particles = 2000
+ settings.batches = 10
+ settings.run_mode = 'fixed source'
+
+ # build
+ mesh = openmc.SphericalMesh()
+ mesh.phi_grid = np.linspace(0, 2*np.pi, 13)
+ mesh.theta_grid = np.linspace(0, np.pi, 7)
+ mesh.r_grid = np.linspace(0, geom_size, geom_size)
+
+ tally = openmc.Tally()
+
+ mesh_filter = openmc.MeshFilter(mesh)
+ tally.filters.append(mesh_filter)
+
+ tally.scores.append("flux")
+
+ tallies = openmc.Tallies([tally])
+
+ return openmc.Model(geometry=geom, settings=settings, tallies=tallies)
+
+def test_origin_read_write_to_xml(run_in_tmpdir, model):
+ """Tests that the origin attribute can be written and read back to XML
+ """
+ mesh = model.tallies[0].filters[0].mesh
+ mesh.origin = [0.1, 0.2, 0.3]
+ model.tallies.export_to_xml()
+
+ # read back
+ new_tallies = openmc.Tallies.from_xml()
+ new_tally = new_tallies[0]
+ new_mesh = new_tally.filters[0].mesh
+ np.testing.assert_equal(new_mesh.origin, mesh.origin)
+
+estimators = ('tracklength', 'collision')
+# TODO: determine why this is needed for spherical mesh
+# but not cylindrical mesh
+offset = geom_size + 0.001
+
+origins = set(permutations((-offset, 0, 0)))
+origins |= set(permutations((offset, 0, 0)))
+
+test_cases = product(estimators, origins)
+
+def label(p):
+ if isinstance(p, tuple):
+ return f'origin:{p}'
+ if isinstance(p, str):
+ return f'estimator:{p}'
+
[email protected]('estimator,origin', test_cases, ids=label)
+def test_offset_mesh(model, estimator, origin):
+ """Tests that the mesh has been moved based on tally results
+ """
+ mesh = model.tallies[0].filters[0].mesh
+ model.tallies[0].estimator = estimator
+ # move the center of the spherical mesh
+ mesh.origin = origin
+
+ sp_filename = model.run()
+
+ with openmc.StatePoint(sp_filename) as sp:
+ tally = sp.tallies[1]
+
+ # we've translated half of the spherical mesh above the model,
+ # so ensure that half of the bins are populated
+ assert np.count_nonzero(tally.mean) == tally.mean.size / 2
+
+ # check that the half of the mesh that is outside of the geometry
+ # contains the zero values
+ mean = tally.get_reshaped_data('mean', expand_dims=True)
+ centroids = mesh.centroids
+ for ijk in mesh.indices:
+ i, j, k = np.array(ijk) - 1
+ print(centroids[:, i, j, k])
+ if model.geometry.find(centroids[:, i, j, k]):
+ mean[i, j, k] == 0.0
+ else:
+ mean[i, j, k] != 0.0
| Cylinder meshes to allow non central location
As mentioned by @paulromano in PR #2233 the ```CylindricalMesh``` is central around a location.
We could allow for an x,y,z offset that defaults to (0,0,0).
Also tagging @RemDelaporteMathurin
| 2022-10-07T07:29:46Z | [] | [] |
|
openmc-dev/openmc | 2,265 | openmc-dev__openmc-2265 | [
"729"
] | b9c1eb34fb6bf548530572465eb8ef43ba477cff | diff --git a/openmc/settings.py b/openmc/settings.py
--- a/openmc/settings.py
+++ b/openmc/settings.py
@@ -186,13 +186,15 @@ class Settings:
'default', 'method', 'range', 'tolerance', and 'multipole'. The value
for 'default' should be a float representing the default temperature in
Kelvin. The value for 'method' should be 'nearest' or 'interpolation'.
- If the method is 'nearest', 'tolerance' indicates a range of temperature
- within which cross sections may be used. The value for 'range' should be
- a pair of minimum and maximum temperatures which are used to indicate
- that cross sections be loaded at all temperatures within the
- range. 'multipole' is a boolean indicating whether or not the windowed
- multipole method should be used to evaluate resolved resonance cross
- sections.
+ If the method is 'nearest', 'tolerance' indicates a range of
+ temperature within which cross sections may be used. If the method is
+ 'interpolation', 'tolerance' indicates the range of temperatures outside
+ of the available cross section temperatures where cross sections will
+ evaluate to the nearer bound. The value for 'range' should be a pair of
+ minimum and maximum temperatures which are used to indicate that cross
+ sections be loaded at all temperatures within the range. 'multipole' is
+ a boolean indicating whether or not the windowed multipole method should
+ be used to evaluate resolved resonance cross sections.
trace : tuple or list
Show detailed information about a single particle, indicated by three
integers: the batch number, generation number, and particle number
| diff --git a/tests/unit_tests/test_temp_interp.py b/tests/unit_tests/test_temp_interp.py
--- a/tests/unit_tests/test_temp_interp.py
+++ b/tests/unit_tests/test_temp_interp.py
@@ -10,7 +10,7 @@
def make_fake_cross_section():
- """Create fake U235 nuclide
+ """Create fake U235 nuclide with a fake thermal scattering library attached
This nuclide is designed to have k_inf=1 at 300 K, k_inf=2 at 600 K, and
k_inf=1 at 900 K. The absorption cross section is also constant with
@@ -81,8 +81,62 @@ def cross_section(value):
# Export HDF5 file
u235_fake.export_to_hdf5('U235_fake.h5', 'w')
+ # Create a fake thermal scattering library attached to the fake U235 data
+ c_U_fake = openmc.data.ThermalScattering("c_U_fake", 1.9968, 4.9, [0.0253])
+ c_U_fake.nuclides = ['U235']
+
+ # Create elastic reaction
+ bragg_edges = [0.00370672, 0.00494229]
+ factors = [0.00375735, 0.01386287]
+ coherent_xs = openmc.data.CoherentElastic(bragg_edges, factors)
+ incoherent_xs_294 = openmc.data.Tabulated1D([0.00370672, 0.00370672], [0.00370672, 0.00370672])
+ elastic_xs_base = openmc.data.Sum((coherent_xs, incoherent_xs_294))
+ elastic_xs = {'294K': elastic_xs_base, '600K': elastic_xs_base}
+ coherent_dist = openmc.data.CoherentElasticAE(coherent_xs)
+ incoherent_dist_294 = openmc.data.IncoherentElasticAEDiscrete([
+ [-0.6, -0.18, 0.18, 0.6], [-0.6, -0.18, 0.18, 0.6]
+ ])
+ incoherent_dist_600 = openmc.data.IncoherentElasticAEDiscrete([
+ [-0.1, -0.2, 0.2, 0.1], [-0.1, -0.2, 0.2, 0.1]
+ ])
+ elastic_dist = {
+ '294K': openmc.data.MixedElasticAE(coherent_dist, incoherent_dist_294),
+ '600K': openmc.data.MixedElasticAE(coherent_dist, incoherent_dist_600)
+ }
+ c_U_fake.elastic = openmc.data.ThermalScatteringReaction(elastic_xs, elastic_dist)
+
+ # Create inelastic reaction
+ inelastic_xs = {
+ '294K': openmc.data.Tabulated1D([1.0e-5, 4.9], [13.4, 3.35]),
+ '600K': openmc.data.Tabulated1D([1.0e-2, 10], [1.4, 5])
+ }
+ breakpoints = [3]
+ interpolation = [2]
+ energy = [1.0e-5, 4.3e-2, 4.9]
+ energy_out = [
+ openmc.data.Tabular([0.0002, 0.067, 0.146, 0.366], [0.25, 0.25, 0.25, 0.25]),
+ openmc.data.Tabular([0.0001, 0.009, 0.137, 0.277], [0.25, 0.25, 0.25, 0.25]),
+ openmc.data.Tabular([0.0579, 4.555, 4.803, 4.874], [0.25, 0.25, 0.25, 0.25]),
+ ]
+ for eout in energy_out:
+ eout.normalize()
+ eout.c = eout.cdf()
+ discrete = openmc.stats.Discrete([-0.9, -0.6, -0.3, -0.1, 0.1, 0.3, 0.6, 0.9], [1/8]*8)
+ discrete.c = discrete.cdf()[1:]
+ mu = [[discrete]*4]*3
+ dist = openmc.data.IncoherentInelasticAE(
+ breakpoints, interpolation, energy, energy_out, mu)
+ inelastic_dist = {'294K': dist, '600K': dist}
+ inelastic = openmc.data.ThermalScatteringReaction(inelastic_xs, inelastic_dist)
+ c_U_fake.inelastic = inelastic
+
+ # Export HDF5 file
+ c_U_fake.export_to_hdf5("c_U_fake.h5")
+
+ # Create a data library of the fake nuclide and its thermal scattering data
lib = openmc.data.DataLibrary()
lib.register_file('U235_fake.h5')
+ lib.register_file("c_U_fake.h5")
lib.export_to_xml('cross_sections_fake.xml')
@@ -119,21 +173,23 @@ def model(tmp_path_factory):
@pytest.mark.parametrize(
- ["method", "temperature", "fission_expected"],
+ ["method", "temperature", "fission_expected", "tolerance"],
[
- ("nearest", 300.0, 0.5),
- ("nearest", 600.0, 1.0),
- ("nearest", 900.0, 0.5),
- ("interpolation", 360.0, 0.6),
- ("interpolation", 450.0, 0.75),
- ("interpolation", 540.0, 0.9),
- ("interpolation", 660.0, 0.9),
- ("interpolation", 750.0, 0.75),
- ("interpolation", 840.0, 0.6),
+ ("nearest", 300.0, 0.5, 10),
+ ("nearest", 600.0, 1.0, 10),
+ ("nearest", 900.0, 0.5, 10),
+ ("interpolation", 360.0, 0.6, 10),
+ ("interpolation", 450.0, 0.75, 10),
+ ("interpolation", 540.0, 0.9, 10),
+ ("interpolation", 660.0, 0.9, 10),
+ ("interpolation", 750.0, 0.75, 10),
+ ("interpolation", 840.0, 0.6, 10),
+ ("interpolation", 295.0, 0.5, 10),
+ ("interpolation", 990.0, 0.5, 100),
]
)
-def test_interpolation(model, method, temperature, fission_expected):
- model.settings.temperature = {'method': method, 'default': temperature}
+def test_interpolation(model, method, temperature, fission_expected, tolerance):
+ model.settings.temperature = {'method': method, 'default': temperature, "tolerance": tolerance}
sp_filename = model.run()
with openmc.StatePoint(sp_filename) as sp:
t = sp.tallies[model.tallies[0].id]
@@ -152,3 +208,33 @@ def test_interpolation(model, method, temperature, fission_expected):
assert k.n == pytest.approx(nu*fission_expected)
else:
assert abs(k.n - nu*fission_expected) <= 3*k.s
+
+
+def test_temperature_interpolation_tolerance(model):
+ """Test applying global and cell temperatures with thermal scattering libraries
+ """
+ model.materials[0].add_s_alpha_beta("c_U_fake")
+
+ # Default k-effective, using the thermal scattering data's minimum available temperature
+ model.settings.temperature = {'method': "nearest", 'default': 294, "tolerance": 50}
+ sp_filename = model.run()
+ with openmc.StatePoint(sp_filename) as sp:
+ default_k = sp.keff.n
+
+ # Get k-effective with temperature below the minimum but in interpolation mode
+ model.settings.temperature = {'method': "interpolation", 'default': 255, "tolerance": 50}
+ sp_filename = model.run()
+ with openmc.StatePoint(sp_filename) as sp:
+ interpolated_k = sp.keff.n
+
+ # Get the k-effective with the temperature applied to the cell, instead of globally
+ model.settings.temperature = {'method': "interpolation", 'default': 500, "tolerance": 50}
+ for cell in model.geometry.get_all_cells().values():
+ cell.temperature = 275
+ sp_filename = model.run()
+ with openmc.StatePoint(sp_filename) as sp:
+ cell_k = sp.keff.n
+
+ # All calculated k-effectives should be equal
+ assert default_k == pytest.approx(interpolated_k)
+ assert interpolated_k == pytest.approx(cell_k)
| Handling temperatures just outside the library
I've run into an issue with the `interpolation` temperature method near 293.6 K. With the MCNP ENDF71 library, the coldest light water s(alpha, beta) table is at 293.606 K, above our default temperature of 293.600. So trying to use the MCNP s(a, b) with interpolation will give
```
ERROR: Nuclear data library does not contain cross sections for c_H_in_H2O at
temperatures that bound 294 K.
```
The error is technically correct, but it would be nice if we built in some tolerance for these tiny out-of-bounds errors. Maybe we also want some way to have the `interpolation` method revert back to `nearest` when the temperature of a cell is very close to a temperature in the data.
| @smharper One thought on this issue -- is it not sufficient to just change the default temperature to 293.606 K in this case? i.e.
```Python
settings.temperature = {'default': 293.606}
```
Setting the default to 293.606 does not work, but 293.607 does.
@johnnyliu27, you said you wanted to try a small OpenMC PR, right? This could be a good one to fix. If you're interested, maybe we could talk about how to add this tolerance to the interpolation code.
Thanks! @smharper I'll try to fix this one.
@johnnyliu27, you and I discussed whether or not we should output a warning for when the code substitutes 293.606 for 293.600. After thinking about it a little more, I don't think we should print out a warning. If we print too many warnings, we risk having users ignore them. If our tolerance for this substitution is something like 1 K, then I'm not worried about a "silent" adjustment because the uncertainty on the underlying data itself probably dwarfs the effects of a <1 K change.
@smharper Yes I agree, then the value for the tolerance might be the next thing to discuss, like 1.0 K or 0.5 K? As @paulromano mentioned in #838, the value for "default room temperature" could be either 293.15 K or 293.6 K, and a tolerance of 0.5 K will work for both values.
Let's use 1K. That makes the most sense to me since we round to the nearest K anyway in our programming structures.
I met some challenges when giving a second try to fix this issue. I was trying to fix it by a more flexible fix inside "_sab_header.F90_" than just changing the default temperature in OpenMC. My plan was to adjust the desired temperature (like 293.6 K, the default) to the coldest temperature (~293.6061 K) in the sab library if it’s below the coldest sab temperature by less than 1 K. However, this will cause problems when computing cross sections, because then we will need to use two different temperature values for sab isotopes and other isotopes. (I assume we don’t want to adjust the temperature for non-sab isotopes.) If so, we also have to modify the `temperature` variable in a more complex way.
As I talked with @smharper about this issue, an `if` statement in "_sab_header.F90_" can make the code more forgiving if the desired temperature is just slightly below the coldest sab temperature, but we don’t want to put the same `if` statement into the module for computing sab cross sections. Then in this case, maybe changing the default temperature is a better idea for this specific issue.
Any thoughts on this? Thanks! | 2022-10-14T01:44:18Z | [] | [] |
openmc-dev/openmc | 2,293 | openmc-dev__openmc-2293 | [
"2292"
] | 1a7762283df83d72deb2c1dc14904990abb038be | diff --git a/openmc/filter.py b/openmc/filter.py
--- a/openmc/filter.py
+++ b/openmc/filter.py
@@ -533,7 +533,7 @@ class CellFromFilter(WithIDFilter):
expected_type = Cell
-class CellbornFilter(WithIDFilter):
+class CellBornFilter(WithIDFilter):
"""Bins tally events based on which cell the particle was born in.
Parameters
@@ -557,6 +557,14 @@ class CellbornFilter(WithIDFilter):
expected_type = Cell
+# Temporary alias for CellbornFilter
+def CellbornFilter(*args, **kwargs):
+ warnings.warn('The name of "CellbornFilter" has changed to '
+ '"CellBornFilter". "CellbornFilter" will be '
+ 'removed in the future.', FutureWarning)
+ return CellBornFilter(*args, **kwargs)
+
+
class CellInstanceFilter(Filter):
"""Bins tally events based on which cell instance a particle is in.
| diff --git a/tests/regression_tests/tallies/test.py b/tests/regression_tests/tallies/test.py
--- a/tests/regression_tests/tallies/test.py
+++ b/tests/regression_tests/tallies/test.py
@@ -40,7 +40,7 @@ def test_tallies():
cellborn_tally = Tally()
cellborn_tally.filters = [
- CellbornFilter((model.geometry.get_all_cells()[10],
+ CellBornFilter((model.geometry.get_all_cells()[10],
model.geometry.get_all_cells()[21],
22, 23))] # Test both Cell objects and ids
cellborn_tally.scores = ['total']
| Enumerator for filter types
There are some cleverly-implemented `Filter::type` methods that allow a filter to return its type via a descriptive string, which is nice for use when writing out a mesh type as part of an error message or warning. To compare filter types (using two `Filter` pointers for instance) I think it would make sense to have a `FilterType` enumerator.
I'll propose changing the return type of `Filter::type()` from `std::string` to `FilterType` and adding a `Filter::type_str` method to replace the original.
| 2022-11-06T05:10:58Z | [] | [] |
|
openmc-dev/openmc | 2,302 | openmc-dev__openmc-2302 | [
"2289"
] | a17fe6cc828dd6a54166aa4065eafc0deb145dad | diff --git a/openmc/deplete/coupled_operator.py b/openmc/deplete/coupled_operator.py
--- a/openmc/deplete/coupled_operator.py
+++ b/openmc/deplete/coupled_operator.py
@@ -460,7 +460,6 @@ def __call__(self, vec, source_rate):
# Run OpenMC
openmc.lib.run()
- openmc.lib.reset_timers()
# Extract results
rates = self._calculate_reaction_rates(source_rate)
@@ -529,6 +528,8 @@ def write_bos_data(step):
"openmc_simulation_n{}.h5".format(step),
write_source=False)
+ openmc.lib.reset_timers()
+
def finalize(self):
"""Finalize a depletion simulation and release resources."""
if self.cleanup_when_done:
| diff --git a/tests/regression_tests/deplete_with_transport/test.py b/tests/regression_tests/deplete_with_transport/test.py
--- a/tests/regression_tests/deplete_with_transport/test.py
+++ b/tests/regression_tests/deplete_with_transport/test.py
@@ -3,6 +3,7 @@
from math import floor
import shutil
from pathlib import Path
+from collections import defaultdict
from difflib import unified_diff
import numpy as np
@@ -122,8 +123,11 @@ def test_full(run_in_tmpdir, problem, multiproc):
n_tallies = np.empty(N + 1, dtype=int)
# Get statepoint files for all BOS points and EOL
+ runtimes = defaultdict(list)
for n in range(N + 1):
statepoint = openmc.StatePoint(f"openmc_simulation_n{n}.h5")
+ for measure, time in statepoint.runtime.items():
+ runtimes[measure].append(time)
k_n = statepoint.keff
k_state[n] = [k_n.nominal_value, k_n.std_dev]
n_tallies[n] = len(statepoint.tallies)
@@ -134,6 +138,21 @@ def test_full(run_in_tmpdir, problem, multiproc):
# Check that no additional tallies are loaded from the files
assert np.all(n_tallies == 0)
+ # Convert values in runtimes to arrays
+ runtimes = {k: np.array(v) for k, v in runtimes.items()}
+
+ # Check that runtimes are qualitatively correct
+ assert runtimes['reading cross sections'][0] != 0
+ assert runtimes['total initialization'][0] != 0
+ assert np.all(runtimes['reading cross sections'][1:] == 0)
+ assert np.all(runtimes['total initialization'][1:] == 0)
+ assert np.all(runtimes['inactive batches'] == 0)
+ del runtimes['reading cross sections']
+ del runtimes['total initialization']
+ del runtimes['inactive batches']
+ for measure, times in runtimes.items():
+ assert np.all(times != 0)
+
def test_depletion_results_to_material(run_in_tmpdir, problem):
"""Checks openmc.Materials objects can be created from depletion results"""
| `StatePoint.runtime` incorrectly written from depletion simulation.
When running a depletion simulation, OpenMC generates a statepoint file for each depletion step.
The expected behavior is that OpenMC stores all data in these statepoint files that it normally would when running a transport simulation. However, I have noticed that this is not the case. On inspection of the `runtime` attribute, I get the following output:
```python
>>> sp = openmc.StatePoint('dep-res/openmc_simulation_n0.h5')
>>> sp.runtime
{'SEND-RECV source sites': 0.0, 'accumulating tallies': 0.0, 'active batches': 0.0, 'inactive batches': 0.0, 'reading cross sections': 0.0, 'sampling source sites': 0.0, 'simulation': 0.0, 'synchronizing fission bank': 0.0, 'total': 0.0, 'total initialization': 0.0, 'transport': 0.0, 'writing statepoints': 0.001705276}
>>> sp.close()
>>> sp = openmc.StatePoint('dep-res/openmc_simulation_n10.h5')
>>> sp.runtime
{'SEND-RECV source sites': 0.0, 'accumulating tallies': 0.0, 'active batches': 0.0, 'inactive batches': 0.0, 'reading cross sections': 0.0, 'sampling source sites': 0.0, 'simulation': 0.0, 'synchronizing fission bank': 0.0, 'total': 0.0, 'total initialization': 0.0, 'transport': 0.0, 'writing statepoints': 0.001968965}
```
wheras the output we get from a transport simulation is:
```python
sp2 = openmc.StatePoint('trans-res/statepoint.50.h5')
>>> sp2.runtime
{'SEND-RECV source sites': 0.00023556000000000006, 'accumulating tallies': 3.6788999999999996e-05, 'active batches': 0.294044768, 'inactive batches': 0.076043973, 'reading cross sections': 0.563972203, 'sampling source sites': 0.0023178319999999993, 'simulation': 0.369967645, 'synchronizing fission bank': 0.0026567239999999996, 'total': 0.948286129, 'total initialization': 0.573223358, 'transport': 0.36242318100000004, 'writing statepoints': 0.001678007}
```
It is possible that there are other attributes that are erroneously written as well.
The dummy model and depletion running script are below:
[dep-test.zip](https://github.com/openmc-dev/openmc/files/9922464/dep-test.zip)
### System Info:
OpenMC v0.13.3-dev
HDF5 1.12.1
Ubuntu 22.04
This issue can be closed when a PR exists that ensures that statepoint files from depletion simulations correctly store the `runtime` attribute.
## Update
I checked the statepoint files from my experiments this summer with the depletion module and all the statepoint files there have the same issue.
| Is anyone able to reproduce this? Pinging @paulromano @pshriwise @shimwell or others for support.
One item of note I found: the `CoupledOperator.write_bos_data()` function calls `openmc.lib.statepoint_write()` to write the `openmc_simulation_n{i}.h5` file. The `cmfd.py` file also uses this function, so that may be affected as well. | 2022-11-18T16:52:27Z | [] | [] |
openmc-dev/openmc | 2,320 | openmc-dev__openmc-2320 | [
"2317"
] | 743bb31f1fc5ab42616ba790d8c830f3627fbea9 | diff --git a/openmc/data/neutron.py b/openmc/data/neutron.py
--- a/openmc/data/neutron.py
+++ b/openmc/data/neutron.py
@@ -868,9 +868,8 @@ def get_file3_xs(ev, mt, E):
heatr_evals = get_evaluations(kwargs["heatr"])
heatr_local_evals = get_evaluations(kwargs["heatr"] + "_local")
- for ev, ev_local in zip(heatr_evals, heatr_local_evals):
- temp = "{}K".format(round(ev.target["temperature"]))
+ for ev, ev_local, temp in zip(heatr_evals, heatr_local_evals, data.temperatures):
# Get total KERMA (originally from ACE file) and energy grid
kerma = data.reactions[301].xs[temp]
E = kerma.x
| diff --git a/tests/unit_tests/test_data_neutron.py b/tests/unit_tests/test_data_neutron.py
--- a/tests/unit_tests/test_data_neutron.py
+++ b/tests/unit_tests/test_data_neutron.py
@@ -531,3 +531,12 @@ def test_ace_table_types():
assert TT.from_suffix('20t') == TT.THERMAL_SCATTERING
with pytest.raises(ValueError):
TT.from_suffix('z')
+
+
+@needs_njoy
+def test_high_temperature():
+ endf_data = os.environ['OPENMC_ENDF_DATA']
+ endf_file = os.path.join(endf_data, 'neutrons', 'n-001_H_001.endf')
+
+ # Ensure that from_njoy works when given a high temperature
+ openmc.data.IncidentNeutron.from_njoy(endf_file, temperatures=[123_456.0])
| High Temperature key error in from_njoy()
When using **openmc.data.IncidentNeutron.from_njoy()**, for high temperatures a python KeyError may arise.
For what I can say the problem arises from the following sequence of actions performed by this routine (in file neutron.py):
- Input temperature is taken in Kelvin.
- Temperature is converted to MeV and written to an .ace file by **njoy**, rounded to something like 6 digits.
- Data from the .ace file is read in by OpenMC and temperature is converted from MeV to K and rounded to an int - for temperatures above approx. 1e5 K this is not the same as the temperature int from the input.
`data = cls.from_ace(lib.tables[0])`
`data.add_temperature_from_ace(table)`
This temperature is stored in data.temperatures.
- A key for the data table is created using the "new" temperature after reading and rounding - but at a later point OpenMC tries to access the data table with a key from an evaluation object which seems to hold the "old" temperature from the input (or maybe it has been converted back and forth with higher precision, so rounding does not have an impact for the numbers I tested)
`temp = "{}K".format(round(ev.target["temperature"]))`
`kerma = data.reactions[301].xs[temp]`
- Consequently, a python KeyError arises.
As a workaround, one can use **openmc.data.njoy.make_ace** and subsequently **openmc.data.IncidentNeutron.from_ace** (in this case, the data table is created and accessed with the same key from the .ace file).
Nevertheless, I suppose that the observed behaviour is not intended, so you might want to have a look at that.
| Thanks for reporting this @teutebergt! Should be an easy fix; I'll try to get a PR submitted shortly. However, do note that NJOY itself also has some issues with [high temperatures](https://github.com/njoy/NJOY2016/issues/222). | 2022-12-06T05:13:44Z | [] | [] |
openmc-dev/openmc | 2,381 | openmc-dev__openmc-2381 | [
"2190"
] | c0d5efc3409e353db51ba308b60e38ce0fabc5e8 | diff --git a/openmc/cmfd.py b/openmc/cmfd.py
--- a/openmc/cmfd.py
+++ b/openmc/cmfd.py
@@ -246,7 +246,7 @@ def grid(self, grid):
Real)
check_greater_than('CMFD mesh {}-grid length'.format(dims[i]),
len(grid[i]), 1)
- self._grid = np.array(grid)
+ self._grid = [np.array(g) for g in grid]
self._display_mesh_warning('rectilinear', 'CMFD mesh grid')
def _display_mesh_warning(self, mesh_type, variable_label):
@@ -1382,9 +1382,7 @@ def _write_vector(self, vector, base_filename):
"""
# Write each element in vector to file
- with open(base_filename+'.dat', 'w') as fh:
- for val in vector:
- fh.write('{:0.8f}\n'.format(val))
+ np.savetxt(f'{base_filename}.dat', vector, fmt='%.8f')
# Save as numpy format
np.save(base_filename, vector)
diff --git a/openmc/filter.py b/openmc/filter.py
--- a/openmc/filter.py
+++ b/openmc/filter.py
@@ -1741,7 +1741,7 @@ def get_pandas_dataframe(self, data_size, stride, **kwargs):
# Concatenate with DataFrame of distribcell instance IDs
if level_df is not None:
level_df = level_df.dropna(axis=1, how='all')
- level_df = level_df.astype(np.int)
+ level_df = level_df.astype(int)
df = pd.concat([level_df, df], axis=1)
return df
diff --git a/openmc/mgxs/groups.py b/openmc/mgxs/groups.py
--- a/openmc/mgxs/groups.py
+++ b/openmc/mgxs/groups.py
@@ -164,7 +164,7 @@ def get_group_indices(self, groups='all'):
if groups == 'all':
return np.arange(self.num_groups)
else:
- indices = np.zeros(len(groups), dtype=np.int)
+ indices = np.zeros(len(groups), dtype=int)
for i, group in enumerate(groups):
cv.check_greater_than('group', group, 0)
diff --git a/openmc/mgxs/mdgxs.py b/openmc/mgxs/mdgxs.py
--- a/openmc/mgxs/mdgxs.py
+++ b/openmc/mgxs/mdgxs.py
@@ -586,7 +586,7 @@ def print_xs(self, subdomains='all', nuclides='all', xs_type='macro'):
if not isinstance(subdomains, str):
cv.check_iterable_type('subdomains', subdomains, Integral)
elif self.domain_type == 'distribcell':
- subdomains = np.arange(self.num_subdomains, dtype=np.int)
+ subdomains = np.arange(self.num_subdomains, dtype=int)
elif self.domain_type == 'mesh':
xyz = [range(1, x + 1) for x in self.domain.dimension]
subdomains = list(itertools.product(*xyz))
@@ -2473,7 +2473,7 @@ def print_xs(self, subdomains='all', nuclides='all', xs_type='macro'):
if not isinstance(subdomains, str):
cv.check_iterable_type('subdomains', subdomains, Integral)
elif self.domain_type == 'distribcell':
- subdomains = np.arange(self.num_subdomains, dtype=np.int)
+ subdomains = np.arange(self.num_subdomains, dtype=int)
elif self.domain_type == 'mesh':
xyz = [range(1, x + 1) for x in self.domain.dimension]
subdomains = list(itertools.product(*xyz))
diff --git a/openmc/mgxs/mgxs.py b/openmc/mgxs/mgxs.py
--- a/openmc/mgxs/mgxs.py
+++ b/openmc/mgxs/mgxs.py
@@ -918,7 +918,7 @@ def get_nuclide_densities(self, nuclides='all'):
# Sum the atomic number densities for all nuclides
if nuclides == 'sum':
nuclides = self.get_nuclides()
- densities = np.zeros(1, dtype=np.float)
+ densities = np.zeros(1, dtype=float)
for nuclide in nuclides:
densities[0] += self.get_nuclide_density(nuclide)
@@ -931,7 +931,7 @@ def get_nuclide_densities(self, nuclides='all'):
# Tabulate the atomic number densities for each specified nuclide
else:
- densities = np.zeros(len(nuclides), dtype=np.float)
+ densities = np.zeros(len(nuclides), dtype=float)
for i, nuclide in enumerate(nuclides):
densities[i] = self.get_nuclide_density(nuclide)
@@ -1720,7 +1720,7 @@ def print_xs(self, subdomains='all', nuclides='all', xs_type='macro'):
if not isinstance(subdomains, str):
cv.check_iterable_type('subdomains', subdomains, Integral)
elif self.domain_type == 'distribcell':
- subdomains = np.arange(self.num_subdomains, dtype=np.int)
+ subdomains = np.arange(self.num_subdomains, dtype=int)
elif self.domain_type == 'mesh':
subdomains = list(self.domain.indices)
else:
@@ -1887,7 +1887,7 @@ def build_hdf5_store(self, filename='mgxs.h5', directory='mgxs',
if not isinstance(subdomains, str):
cv.check_iterable_type('subdomains', subdomains, Integral)
elif self.domain_type == 'distribcell':
- subdomains = np.arange(self.num_subdomains, dtype=np.int)
+ subdomains = np.arange(self.num_subdomains, dtype=int)
elif self.domain_type == 'sum(distribcell)':
domain_filter = self.xs_tally.find_filter('sum(distribcell)')
subdomains = domain_filter.bins
@@ -1900,7 +1900,7 @@ def build_hdf5_store(self, filename='mgxs.h5', directory='mgxs',
if self.by_nuclide:
if nuclides == 'all':
nuclides = self.get_nuclides()
- densities = np.zeros(len(nuclides), dtype=np.float)
+ densities = np.zeros(len(nuclides), dtype=float)
elif nuclides == 'sum':
nuclides = ['sum']
else:
@@ -2447,7 +2447,7 @@ def print_xs(self, subdomains='all', nuclides='all', xs_type='macro'):
if not isinstance(subdomains, str):
cv.check_iterable_type('subdomains', subdomains, Integral)
elif self.domain_type == 'distribcell':
- subdomains = np.arange(self.num_subdomains, dtype=np.int)
+ subdomains = np.arange(self.num_subdomains, dtype=int)
elif self.domain_type == 'mesh':
subdomains = list(self.domain.indices)
else:
@@ -4785,7 +4785,7 @@ def print_xs(self, subdomains='all', nuclides='all',
if not isinstance(subdomains, str):
cv.check_iterable_type('subdomains', subdomains, Integral)
elif self.domain_type == 'distribcell':
- subdomains = np.arange(self.num_subdomains, dtype=np.int)
+ subdomains = np.arange(self.num_subdomains, dtype=int)
elif self.domain_type == 'mesh':
subdomains = list(self.domain.indices)
else:
| diff --git a/tests/regression_tests/adj_cell_rotation/results_true.dat b/tests/regression_tests/adj_cell_rotation/results_true.dat
--- a/tests/regression_tests/adj_cell_rotation/results_true.dat
+++ b/tests/regression_tests/adj_cell_rotation/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-4.381997E-01 1.286263E-03
+4.403987E-01 1.514158E-03
diff --git a/tests/regression_tests/asymmetric_lattice/results_true.dat b/tests/regression_tests/asymmetric_lattice/results_true.dat
--- a/tests/regression_tests/asymmetric_lattice/results_true.dat
+++ b/tests/regression_tests/asymmetric_lattice/results_true.dat
@@ -1 +1 @@
-73bae264aaca0988fd2ae207722461d161ddbcf9aef083b99a2efc536b09665bbe839d6cae89b32ebab3089a820a2c35ae63a88d5869f0c91b0d6c2f2e090e55
\ No newline at end of file
+b0ca1fb0436732188b1a199b3250ca9a33782f8fc379b0f7ff9c582e0c794b0a0470df063cafd0b05e802b26f61eaaf9ff5c0a8a672a933246acf49eed3ebf9f
\ No newline at end of file
diff --git a/tests/regression_tests/cmfd_feed/results_true.dat b/tests/regression_tests/cmfd_feed/results_true.dat
--- a/tests/regression_tests/cmfd_feed/results_true.dat
+++ b/tests/regression_tests/cmfd_feed/results_true.dat
@@ -1,117 +1,117 @@
k-combined:
-1.159021E+00 8.924006E-03
+1.164262E+00 9.207592E-03
tally 1:
-1.140162E+01
-1.306940E+01
-2.093739E+01
-4.404780E+01
-2.914408E+01
-8.521010E+01
-3.483677E+01
-1.216824E+02
-3.778463E+01
-1.429632E+02
-3.810371E+01
-1.455108E+02
-3.465248E+01
-1.207868E+02
-2.862033E+01
-8.218833E+01
-2.086025E+01
-4.365941E+01
-1.130798E+01
-1.286509E+01
+1.156972E+01
+1.339924E+01
+2.136306E+01
+4.567185E+01
+2.859527E+01
+8.195821E+01
+3.470754E+01
+1.207851E+02
+3.766403E+01
+1.422263E+02
+3.778821E+01
+1.432660E+02
+3.573197E+01
+1.278854E+02
+2.849979E+01
+8.135515E+01
+2.073803E+01
+4.303374E+01
+1.112117E+01
+1.242944E+01
tally 2:
-2.234393E+01
-2.516414E+01
-1.555024E+01
-1.218205E+01
-4.087743E+01
-8.401702E+01
-2.883717E+01
-4.185393E+01
-5.635166E+01
-1.595225E+02
-3.998857E+01
-8.040398E+01
-6.887126E+01
-2.379185E+02
-4.903103E+01
-1.206174E+02
-7.452051E+01
-2.785675E+02
-5.295380E+01
-1.406900E+02
-7.495422E+01
-2.819070E+02
-5.333191E+01
-1.427474E+02
-6.921815E+01
-2.408568E+02
-4.928246E+01
-1.221076E+02
-5.668548E+01
-1.612556E+02
-4.035856E+01
-8.181159E+01
-4.259952E+01
-9.112630E+01
-3.026717E+01
-4.600625E+01
-2.310563E+01
-2.688378E+01
-1.615934E+01
-1.315528E+01
+2.388054E+01
+2.875255E+01
+1.667791E+01
+1.403426E+01
+4.224771E+01
+8.942109E+01
+2.993088E+01
+4.490335E+01
+5.689839E+01
+1.625557E+02
+4.043633E+01
+8.212299E+01
+6.764024E+01
+2.297126E+02
+4.807902E+01
+1.161468E+02
+7.314835E+01
+2.684645E+02
+5.203584E+01
+1.359261E+02
+7.375727E+01
+2.733105E+02
+5.252944E+01
+1.386205E+02
+6.909571E+01
+2.397721E+02
+4.922548E+01
+1.217465E+02
+5.685978E+01
+1.621746E+02
+4.051938E+01
+8.237277E+01
+4.185562E+01
+8.784067E+01
+2.983570E+01
+4.467414E+01
+2.238373E+01
+2.520356E+01
+1.566758E+01
+1.234103E+01
tally 3:
-1.496375E+01
-1.128154E+01
-9.905641E-01
-5.125710E-02
-2.774937E+01
-3.877241E+01
-1.786861E+00
-1.627655E-01
-3.849739E+01
-7.453828E+01
-2.494135E+00
-3.158098E-01
-4.724085E+01
-1.119901E+02
-3.031174E+00
-4.653741E-01
-5.096719E+01
-1.303552E+02
-3.254375E+00
-5.351020E-01
-5.133808E+01
-1.322892E+02
-3.383595E+00
-5.798798E-01
-4.756072E+01
-1.137527E+02
-3.001917E+00
-4.558247E-01
-3.887437E+01
-7.593416E+01
-2.517908E+00
-3.221926E-01
-2.910687E+01
-4.255173E+01
-1.817765E+00
-1.678763E-01
-1.557241E+01
-1.222026E+01
-9.852737E-01
-5.002659E-02
+1.609520E+01
+1.307542E+01
+1.033429E+00
+5.510889E-02
+2.877073E+01
+4.149542E+01
+1.964219E+00
+1.954692E-01
+3.896816E+01
+7.629752E+01
+2.484053E+00
+3.103733E-01
+4.634285E+01
+1.079367E+02
+2.974750E+00
+4.468223E-01
+5.007964E+01
+1.259202E+02
+3.181802E+00
+5.103621E-01
+5.058915E+01
+1.286193E+02
+3.249442E+00
+5.337712E-01
+4.744464E+01
+1.131026E+02
+3.067644E+00
+4.736335E-01
+3.900632E+01
+7.634433E+01
+2.443552E+00
+3.028060E-01
+2.874166E+01
+4.146375E+01
+1.810421E+00
+1.671667E-01
+1.509222E+01
+1.145579E+01
+1.014919E+00
+5.391053E-02
tally 4:
-3.047490E+00
-4.661458E-01
+3.148231E+00
+4.974555E-01
0.000000E+00
0.000000E+00
-2.635775E+00
-3.524426E-01
-5.357229E+00
-1.440049E+00
+2.805439E+00
+3.982239E-01
+5.574031E+00
+1.561105E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -128,14 +128,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-5.357229E+00
-1.440049E+00
-2.635775E+00
-3.524426E-01
-4.982072E+00
-1.251449E+00
-7.228146E+00
-2.620353E+00
+5.574031E+00
+1.561105E+00
+2.805439E+00
+3.982239E-01
+5.171038E+00
+1.344877E+00
+7.372031E+00
+2.725420E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -152,14 +152,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.228146E+00
-2.620353E+00
-4.982072E+00
-1.251449E+00
-7.082265E+00
-2.520047E+00
-8.736529E+00
-3.831244E+00
+7.372031E+00
+2.725420E+00
+5.171038E+00
+1.344877E+00
+6.946847E+00
+2.424850E+00
+8.496610E+00
+3.627542E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -176,14 +176,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.736529E+00
-3.831244E+00
-7.082265E+00
-2.520047E+00
-8.474631E+00
-3.607043E+00
-9.346623E+00
-4.390819E+00
+8.496610E+00
+3.627542E+00
+6.946847E+00
+2.424850E+00
+8.479501E+00
+3.607280E+00
+9.261869E+00
+4.305912E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -200,14 +200,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-9.346623E+00
-4.390819E+00
-8.474631E+00
-3.607043E+00
-9.496684E+00
-4.522478E+00
-9.532822E+00
-4.559003E+00
+9.261869E+00
+4.305912E+00
+8.479501E+00
+3.607280E+00
+9.232858E+00
+4.278432E+00
+9.306384E+00
+4.348594E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -224,14 +224,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-9.532822E+00
-4.559003E+00
-9.496684E+00
-4.522478E+00
-9.404949E+00
-4.446260E+00
-8.550930E+00
-3.668401E+00
+9.306384E+00
+4.348594E+00
+9.232858E+00
+4.278432E+00
+9.299764E+00
+4.347828E+00
+8.511976E+00
+3.639893E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -248,14 +248,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.550930E+00
-3.668401E+00
-9.404949E+00
-4.446260E+00
-8.785273E+00
-3.874792E+00
-7.128863E+00
-2.554326E+00
+8.511976E+00
+3.639893E+00
+9.299764E+00
+4.347828E+00
+8.726086E+00
+3.819567E+00
+7.147277E+00
+2.562747E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -272,14 +272,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.128863E+00
-2.554326E+00
-8.785273E+00
-3.874792E+00
-7.408549E+00
-2.755885E+00
-5.094992E+00
-1.305737E+00
+7.147277E+00
+2.562747E+00
+8.726086E+00
+3.819567E+00
+7.218790E+00
+2.612243E+00
+5.018287E+00
+1.263077E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -296,14 +296,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-5.094992E+00
-1.305737E+00
-7.408549E+00
-2.755885E+00
-5.532149E+00
-1.537289E+00
-2.812344E+00
-3.997146E-01
+5.018287E+00
+1.263077E+00
+7.218790E+00
+2.612243E+00
+5.443494E+00
+1.487018E+00
+2.732334E+00
+3.773047E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -320,12 +320,12 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-2.812344E+00
-3.997146E-01
-5.532149E+00
-1.537289E+00
-3.063251E+00
-4.728672E-01
+2.732334E+00
+3.773047E-01
+5.443494E+00
+1.487018E+00
+3.044773E+00
+4.655756E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -345,144 +345,144 @@ tally 4:
0.000000E+00
0.000000E+00
tally 5:
-1.496000E+01
-1.127586E+01
-2.280081E+00
-2.675609E-01
-2.774503E+01
-3.876011E+01
-3.908836E+00
-7.703029E-01
-3.848706E+01
-7.449836E+01
-5.299924E+00
-1.422782E+00
-4.723172E+01
-1.119459E+02
-6.450156E+00
-2.105590E+00
-5.095931E+01
-1.303132E+02
-7.050681E+00
-2.515092E+00
-5.133412E+01
-1.322694E+02
-6.853429E+00
-2.384127E+00
-4.754621E+01
-1.136848E+02
-6.370026E+00
-2.058896E+00
-3.886829E+01
-7.591042E+01
-5.266816E+00
-1.400495E+00
-2.910277E+01
-4.253981E+01
-4.090844E+00
-8.442500E-01
-1.556949E+01
-1.221526E+01
-2.266123E+00
-2.641551E-01
+1.609029E+01
+1.306718E+01
+2.230601E+00
+2.559496E-01
+2.876780E+01
+4.148686E+01
+3.835952E+00
+7.456562E-01
+3.895738E+01
+7.625344E+01
+4.841024E+00
+1.197335E+00
+4.633595E+01
+1.079043E+02
+6.236821E+00
+1.963311E+00
+5.007472E+01
+1.258967E+02
+6.749745E+00
+2.297130E+00
+5.058336E+01
+1.285894E+02
+6.727612E+00
+2.315656E+00
+4.743869E+01
+1.130735E+02
+6.338193E+00
+2.042159E+00
+3.899838E+01
+7.631289E+01
+5.187573E+00
+1.359733E+00
+2.873434E+01
+4.144233E+01
+3.815610E+00
+7.367619E-01
+1.509020E+01
+1.145268E+01
+2.125767E+00
+2.341894E-01
cmfd indices
1.000000E+01
1.000000E+00
1.000000E+00
1.000000E+00
k cmfd
-1.161531E+00
-1.182724E+00
-1.169653E+00
-1.164722E+00
-1.164583E+00
-1.162952E+00
-1.167024E+00
-1.164509E+00
-1.165693E+00
-1.170623E+00
-1.166618E+00
-1.170805E+00
-1.170962E+00
-1.170964E+00
-1.168224E+00
-1.169864E+00
+1.129918E+00
+1.143848E+00
+1.147976E+00
+1.151534E+00
+1.152378E+00
+1.148219E+00
+1.150402E+00
+1.154647E+00
+1.156159E+00
+1.160048E+00
+1.167441E+00
+1.168163E+00
+1.168629E+00
+1.164120E+00
+1.165051E+00
+1.169177E+00
cmfd entropy
-3.206619E+00
-3.205815E+00
-3.208678E+00
-3.210820E+00
-3.217023E+00
-3.215014E+00
-3.214592E+00
-3.215913E+00
-3.214998E+00
-3.213644E+00
-3.210755E+00
-3.210496E+00
-3.212488E+00
-3.211553E+00
-3.212999E+00
-3.214052E+00
+3.224769E+00
+3.225945E+00
+3.227421E+00
+3.226174E+00
+3.224429E+00
+3.227049E+00
+3.230710E+00
+3.230315E+00
+3.226825E+00
+3.226655E+00
+3.226588E+00
+3.224155E+00
+3.223246E+00
+3.222640E+00
+3.223920E+00
+3.222838E+00
cmfd balance
-4.99833E-03
-5.64677E-03
-3.62795E-03
-3.91962E-03
-3.87172E-03
-2.48450E-03
-3.15554E-03
-2.49335E-03
-2.31973E-03
-2.19156E-03
-2.31352E-03
-2.03401E-03
-1.80242E-03
-1.65868E-03
-1.47543E-03
-1.49706E-03
+3.90454E-03
+4.08089E-03
+3.46511E-03
+4.09535E-03
+2.62009E-03
+2.23559E-03
+2.54033E-03
+2.12799E-03
+2.25864E-03
+1.85766E-03
+1.49916E-03
+1.63471E-03
+1.48377E-03
+1.59800E-03
+1.37354E-03
+1.32853E-03
cmfd dominance ratio
-5.283E-01
-5.289E-01
-5.305E-01
-5.327E-01
-5.377E-01
-5.360E-01
-5.353E-01
-4.983E-01
-5.379E-01
-5.370E-01
-5.359E-01
-5.349E-01
-5.364E-01
-5.347E-01
-5.360E-01
-5.378E-01
+5.539E-01
+5.537E-01
+5.536E-01
+5.515E-01
+5.512E-01
+5.514E-01
+5.518E-01
+5.507E-01
+5.500E-01
+5.497E-01
+5.477E-01
+5.461E-01
+5.444E-01
+5.445E-01
+5.454E-01
+5.441E-01
cmfd openmc source comparison
-1.291827E-02
-1.027137E-02
-8.738370E-03
-6.854409E-03
-4.188357E-03
-4.941359E-03
-5.139239E-03
-4.244784E-03
-4.240559E-03
-3.375424E-03
-3.716858E-03
-3.595700E-03
-3.626952E-03
-3.999302E-03
-2.431760E-03
-1.673200E-03
+9.875240E-03
+1.106163E-02
+9.847628E-03
+6.065921E-03
+5.772039E-03
+4.615656E-03
+4.244331E-03
+3.694299E-03
+3.545814E-03
+3.213063E-03
+3.467537E-03
+3.383489E-03
+3.697591E-03
+3.937358E-03
+3.369124E-03
+3.190359E-03
cmfd source
-4.185460E-02
-7.636314E-02
-1.075536E-01
-1.307167E-01
-1.400879E-01
-1.459944E-01
-1.297413E-01
-1.084649E-01
-7.772031E-02
-4.150306E-02
+4.360494E-02
+8.397599E-02
+1.074181E-01
+1.294531E-01
+1.385611E-01
+1.407934E-01
+1.325191E-01
+1.044311E-01
+7.660359E-02
+4.263941E-02
diff --git a/tests/regression_tests/cmfd_feed/test.py b/tests/regression_tests/cmfd_feed/test.py
--- a/tests/regression_tests/cmfd_feed/test.py
+++ b/tests/regression_tests/cmfd_feed/test.py
@@ -111,7 +111,7 @@ def test_cmfd_write_matrices():
# Load flux vector from numpy output file
flux_np = np.load('fluxvec.npy')
# Load flux from data file
- flux_dat = np.loadtxt("fluxvec.dat", delimiter='\n')
+ flux_dat = np.loadtxt("fluxvec.dat")
# Compare flux from numpy file, .dat file, and from simulation
assert(np.all(np.isclose(flux_np, cmfd_run._phi)))
diff --git a/tests/regression_tests/cmfd_feed_2g/results_true.dat b/tests/regression_tests/cmfd_feed_2g/results_true.dat
--- a/tests/regression_tests/cmfd_feed_2g/results_true.dat
+++ b/tests/regression_tests/cmfd_feed_2g/results_true.dat
@@ -1,112 +1,112 @@
k-combined:
-1.021592E+00 7.184545E-03
+1.035567E+00 9.463160E-03
tally 1:
-1.158654E+02
-1.342707E+03
-1.151877E+02
-1.327269E+03
-1.153781E+02
-1.331661E+03
-1.151151E+02
-1.325578E+03
+1.146535E+02
+1.315267E+03
+1.157458E+02
+1.340166E+03
+1.140491E+02
+1.301364E+03
+1.146589E+02
+1.315433E+03
tally 2:
-4.299142E+01
-9.258204E+01
-6.324043E+01
-2.003732E+02
-1.860419E+02
-1.731270E+03
-1.037502E+02
-5.383979E+02
-4.229132E+01
-8.952923E+01
-6.264581E+01
-1.965074E+02
-1.838340E+02
-1.690620E+03
-1.029415E+02
-5.299801E+02
-4.314759E+01
-9.337463E+01
-6.404361E+01
-2.056541E+02
-1.836548E+02
-1.687065E+03
-1.028141E+02
-5.287334E+02
-4.256836E+01
-9.079806E+01
-6.336524E+01
-2.012627E+02
-1.837730E+02
-1.689124E+03
-1.021852E+02
-5.222598E+02
+4.319968E+01
+9.360083E+01
+6.373035E+01
+2.038056E+02
+1.889646E+02
+1.812892E+03
+1.024866E+02
+5.254528E+02
+4.323262E+01
+9.360200E+01
+6.363111E+01
+2.028178E+02
+1.849746E+02
+1.711533E+03
+1.034532E+02
+5.352768E+02
+4.296541E+01
+9.249656E+01
+6.346919E+01
+2.018659E+02
+1.888697E+02
+1.812037E+03
+1.025707E+02
+5.262261E+02
+4.691085E+01
+1.269707E+02
+6.299377E+01
+1.990497E+02
+1.853864E+02
+1.719984E+03
+1.023015E+02
+5.235858E+02
tally 3:
-5.973628E+01
-1.787876E+02
+6.034963E+01
+1.827718E+02
0.000000E+00
0.000000E+00
-1.724004E-02
-2.766372E-05
-4.379655E+00
-9.682433E-01
-3.484795E+00
-6.104792E-01
+1.865665E-02
+4.244195E-05
+4.170941E+00
+8.769372E-01
+3.453368E+00
+5.989168E-01
0.000000E+00
0.000000E+00
-9.874445E+01
-4.877157E+02
-8.886034E-01
-4.009294E-02
-5.923584E+01
-1.757014E+02
+9.743205E+01
+4.749420E+02
+8.570316E-01
+3.807993E-02
+6.005903E+01
+1.807233E+02
0.000000E+00
0.000000E+00
-1.733168E-02
-3.950365E-05
-4.212697E+00
-8.996477E-01
-3.503046E+00
-6.150657E-01
+1.885450E-02
+3.653402E-05
+4.323863E+00
+9.447512E-01
+3.465465E+00
+6.022861E-01
0.000000E+00
0.000000E+00
-9.780995E+01
-4.784706E+02
-8.648283E-01
-3.899383E-02
-6.057017E+01
-1.839745E+02
+9.843481E+01
+4.846158E+02
+9.048150E-01
+4.205551E-02
+5.996660E+01
+1.802150E+02
0.000000E+00
0.000000E+00
-2.056597E-02
-3.726744E-05
-4.280120E+00
-9.288225E-01
-3.378205E+00
-5.730279E-01
+1.221444E-02
+2.263445E-05
+4.301287E+00
+9.309882E-01
+3.456076E+00
+5.992144E-01
0.000000E+00
0.000000E+00
-9.790474E+01
-4.794523E+02
-9.073765E-01
-4.204720E-02
-5.990874E+01
-1.799224E+02
+9.761231E+01
+4.765834E+02
+8.434644E-01
+3.728180E-02
+5.961891E+01
+1.783106E+02
0.000000E+00
0.000000E+00
-1.881508E-02
-4.239902E-05
-4.206916E+00
-8.926965E-01
-3.478009E+00
-6.067461E-01
+1.500709E-02
+3.541280E-05
+4.155669E+00
+8.713442E-01
+3.455342E+00
+6.006426E-01
0.000000E+00
0.000000E+00
-9.715787E+01
-4.721453E+02
-8.602457E-01
-3.786346E-02
+9.726798E+01
+4.733393E+02
+9.202611E-01
+4.390503E-02
tally 4:
0.000000E+00
0.000000E+00
@@ -116,14 +116,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.735001E+00
-3.821211E+00
-3.708124E+01
-6.880811E+01
-8.713175E+00
-3.807176E+00
-3.703536E+01
-6.862245E+01
+8.943264E+00
+4.008855E+00
+3.661063E+01
+6.704808E+01
+8.945553E+00
+4.011707E+00
+3.696832E+01
+6.835286E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -132,14 +132,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.851322E+00
-3.930766E+00
-3.716154E+01
-6.908449E+01
-8.892499E+00
-3.970458E+00
-3.718644E+01
-6.918810E+01
+8.844569E+00
+3.924591E+00
+3.666726E+01
+6.726522E+01
+8.769637E+00
+3.855006E+00
+3.654115E+01
+6.680777E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -156,14 +156,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.713175E+00
-3.807176E+00
-3.703536E+01
-6.862245E+01
-8.735001E+00
-3.821211E+00
-3.708124E+01
-6.880811E+01
+8.945553E+00
+4.011707E+00
+3.696832E+01
+6.835286E+01
+8.943264E+00
+4.008855E+00
+3.661063E+01
+6.704808E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -180,14 +180,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.915310E+00
-3.982710E+00
-3.682783E+01
-6.786998E+01
-8.800405E+00
-3.881868E+00
-3.692302E+01
-6.819716E+01
+8.648474E+00
+3.752219E+00
+3.689442E+01
+6.808997E+01
+8.757378E+00
+3.850408E+00
+3.716920E+01
+6.909715E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -212,22 +212,22 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.659918E+00
-3.761908E+00
-3.709957E+01
-6.884298E+01
-8.796329E+00
-3.881588E+00
-3.693599E+01
-6.825932E+01
-8.892499E+00
-3.970458E+00
-3.718644E+01
-6.918810E+01
-8.851322E+00
-3.930766E+00
-3.716154E+01
-6.908449E+01
+8.783669E+00
+3.870748E+00
+3.687358E+01
+6.802581E+01
+8.755250E+00
+3.846298E+00
+3.660278E+01
+6.704349E+01
+8.769637E+00
+3.855006E+00
+3.654115E+01
+6.680777E+01
+8.844569E+00
+3.924591E+00
+3.666726E+01
+6.726522E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -252,14 +252,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.796329E+00
-3.881588E+00
-3.693599E+01
-6.825932E+01
-8.659918E+00
-3.761908E+00
-3.709957E+01
-6.884298E+01
+8.755250E+00
+3.846298E+00
+3.660278E+01
+6.704349E+01
+8.783669E+00
+3.870748E+00
+3.687358E+01
+6.802581E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -268,14 +268,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.800405E+00
-3.881868E+00
-3.692302E+01
-6.819716E+01
-8.915310E+00
-3.982710E+00
-3.682783E+01
-6.786998E+01
+8.757378E+00
+3.850408E+00
+3.716920E+01
+6.909715E+01
+8.648474E+00
+3.752219E+00
+3.689442E+01
+6.808997E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -301,133 +301,133 @@ tally 4:
0.000000E+00
0.000000E+00
tally 5:
-5.975352E+01
-1.788900E+02
-1.022213E+02
-5.226556E+02
-1.378440E+01
-9.544964E+00
-4.668065E+01
-1.090372E+02
-5.925317E+01
-1.758044E+02
-1.013043E+02
-5.132587E+02
-1.356187E+01
-9.210736E+00
-4.606346E+01
-1.061497E+02
-6.059074E+01
-1.840993E+02
-1.012721E+02
-5.130091E+02
-1.356441E+01
-9.262377E+00
-4.634250E+01
-1.074283E+02
-5.992755E+01
-1.800342E+02
-1.006299E+02
-5.065012E+02
-1.370402E+01
-9.450980E+00
-4.575433E+01
-1.047310E+02
+6.036829E+01
+1.828885E+02
+1.008777E+02
+5.091033E+02
+1.353211E+01
+9.188155E+00
+4.618716E+01
+1.067410E+02
+6.007789E+01
+1.808371E+02
+1.018892E+02
+5.192269E+02
+1.357961E+01
+9.247052E+00
+4.618560E+01
+1.067058E+02
+5.997882E+01
+1.802895E+02
+1.010597E+02
+5.108478E+02
+1.374955E+01
+9.502494E+00
+4.619500E+01
+1.067547E+02
+5.963392E+01
+1.783999E+02
+1.007134E+02
+5.074700E+02
+1.319398E+01
+8.734106E+00
+4.586295E+01
+1.052870E+02
cmfd indices
2.000000E+00
2.000000E+00
1.000000E+00
2.000000E+00
k cmfd
-1.037231E+00
-1.035671E+00
-1.042384E+00
-1.033525E+00
-1.031304E+00
-1.029654E+00
-1.031704E+00
-1.032213E+00
-1.030500E+00
-1.036227E+00
-1.034924E+00
-1.035753E+00
-1.034679E+00
-1.035096E+00
-1.033818E+00
-1.030023E+00
+1.018115E+00
+1.022665E+00
+1.020323E+00
+1.020653E+00
+1.021036E+00
+1.020623E+00
+1.021482E+00
+1.025450E+00
+1.027292E+00
+1.028065E+00
+1.027065E+00
+1.024275E+00
+1.025309E+00
+1.026039E+00
+1.026700E+00
+1.023865E+00
cmfd entropy
-1.999702E+00
-1.999790E+00
-1.999713E+00
-1.999852E+00
-1.999820E+00
-1.999667E+00
-1.999553E+00
-1.999649E+00
-1.999398E+00
-1.999527E+00
-1.999648E+00
-1.999607E+00
+1.998965E+00
+1.999214E+00
+1.999348E+00
+1.999366E+00
+1.999564E+00
+1.999453E+00
1.999533E+00
-1.999684E+00
-1.999714E+00
-1.999812E+00
+1.999630E+00
+1.999739E+00
+1.999588E+00
+1.999581E+00
+1.999719E+00
+1.999773E+00
+1.999764E+00
+1.999821E+00
+1.999843E+00
cmfd balance
-7.33587E-04
-1.00987E-03
-8.26985E-04
-5.20809E-04
-6.47932E-04
-9.69990E-04
-8.62860E-04
-4.92175E-04
-5.80764E-04
-4.49167E-04
-4.05541E-04
-4.13811E-04
-4.27271E-04
-3.64944E-04
-3.43522E-04
-2.82842E-04
+5.73174E-04
+7.55398E-04
+1.46671E-03
+6.39625E-04
+8.19008E-04
+1.93449E-03
+1.15900E-03
+1.01690E-03
+5.62788E-04
+6.90450E-04
+6.01060E-04
+5.73418E-04
+4.37190E-04
+4.82966E-04
+4.09700E-04
+3.45096E-04
cmfd dominance ratio
-6.259E-03
-6.252E-03
-6.292E-03
-6.347E-03
-6.360E-03
-6.403E-03
-6.375E-03
-6.400E-03
-6.374E-03
-6.343E-03
-6.331E-03
-6.312E-03
-6.305E-03
-6.271E-03
-6.267E-03
-6.265E-03
+6.264E-03
+6.142E-03
+5.987E-03
+6.082E-03
+5.895E-03
+5.939E-03
+5.910E-03
+5.948E-03
+6.013E-03
+6.017E-03
+6.024E-03
+6.008E-03
+5.976E-03
+5.987E-03
+5.967E-03
+5.929E-03
cmfd openmc source comparison
-7.908947E-05
-7.452591E-05
-9.249409E-05
-8.223037E-05
-7.355125E-05
-8.926808E-05
-9.363510E-05
-7.628519E-05
-9.019193E-05
-7.130550E-05
-5.947633E-05
-5.744157E-05
-6.093797E-05
-4.505304E-05
-4.430670E-05
-3.019083E-05
+4.832872E-05
+6.552342E-05
+7.516800E-05
+7.916087E-05
+9.022260E-05
+8.574478E-05
+7.891622E-05
+7.281636E-05
+7.750571E-05
+6.565408E-05
+6.078665E-05
+5.834343E-05
+4.758176E-05
+5.723990E-05
+4.994116E-05
+4.116808E-05
cmfd source
-2.557606E-01
-2.464707E-01
-2.518098E-01
-2.459589E-01
+2.455663E-01
+2.553511E-01
+2.512257E-01
+2.478570E-01
0.000000E+00
0.000000E+00
0.000000E+00
diff --git a/tests/regression_tests/cmfd_feed_expanding_window/results_true.dat b/tests/regression_tests/cmfd_feed_expanding_window/results_true.dat
--- a/tests/regression_tests/cmfd_feed_expanding_window/results_true.dat
+++ b/tests/regression_tests/cmfd_feed_expanding_window/results_true.dat
@@ -1,117 +1,117 @@
k-combined:
-1.184725E+00 9.808181E-03
+1.167865E+00 7.492213E-03
tally 1:
-1.121111E+01
-1.261033E+01
-2.101271E+01
-4.433294E+01
-2.782926E+01
-7.776546E+01
-3.351044E+01
-1.125084E+02
-3.625691E+01
-1.319666E+02
-3.741881E+01
-1.403776E+02
-3.538049E+01
-1.255798E+02
-3.030311E+01
-9.228152E+01
-2.188389E+01
-4.811272E+01
-1.172417E+01
-1.379179E+01
+1.146860E+01
+1.318884E+01
+2.161527E+01
+4.685283E+01
+2.951158E+01
+8.733566E+01
+3.521610E+01
+1.242821E+02
+3.774236E+01
+1.426501E+02
+3.727918E+01
+1.391158E+02
+3.377176E+01
+1.143839E+02
+2.904497E+01
+8.452907E+01
+2.090871E+01
+4.384549E+01
+1.078642E+01
+1.168086E+01
tally 2:
-1.146940E+00
-1.315471E+00
-8.068187E-01
-6.509564E-01
-2.070090E+00
-4.285274E+00
-1.469029E+00
-2.158045E+00
-2.703224E+00
-7.307421E+00
-1.895589E+00
-3.593259E+00
-3.567634E+00
-1.272801E+01
-2.541493E+00
-6.459185E+00
-3.937463E+00
-1.550361E+01
-2.770463E+00
-7.675465E+00
-3.960472E+00
-1.568534E+01
-2.792668E+00
-7.798997E+00
-3.243459E+00
-1.052002E+01
-2.296673E+00
-5.274706E+00
-2.794726E+00
-7.810492E+00
-1.953143E+00
-3.814769E+00
-2.187302E+00
-4.784292E+00
-1.544500E+00
-2.385481E+00
-1.199609E+00
-1.439061E+00
-8.356062E-01
-6.982377E-01
+1.136810E+00
+1.292338E+00
+7.987303E-01
+6.379700E-01
+2.266938E+00
+5.139009E+00
+1.613483E+00
+2.603328E+00
+3.046349E+00
+9.280239E+00
+2.182459E+00
+4.763126E+00
+3.568068E+00
+1.273111E+01
+2.532456E+00
+6.413333E+00
+3.989504E+00
+1.591614E+01
+2.848301E+00
+8.112818E+00
+3.853133E+00
+1.484663E+01
+2.718493E+00
+7.390202E+00
+3.478138E+00
+1.209745E+01
+2.467281E+00
+6.087476E+00
+2.952220E+00
+8.715605E+00
+2.103261E+00
+4.423706E+00
+1.917459E+00
+3.676649E+00
+1.378369E+00
+1.899902E+00
+1.048240E+00
+1.098807E+00
+7.511947E-01
+5.642934E-01
tally 3:
-7.817522E-01
-6.111366E-01
-5.930056E-02
-3.516556E-03
-1.426374E+00
-2.034542E+00
-8.539281E-02
-7.291931E-03
-1.815687E+00
-3.296718E+00
-1.221592E-01
-1.492286E-02
-2.447191E+00
-5.988744E+00
-1.624835E-01
-2.640090E-02
-2.670084E+00
-7.129351E+00
-1.838317E-01
-3.379411E-02
-2.683007E+00
-7.198528E+00
-1.719716E-01
-2.957424E-02
-2.215446E+00
-4.908202E+00
-1.707856E-01
-2.916773E-02
-1.872330E+00
-3.505620E+00
-1.209731E-01
-1.463450E-02
-1.484167E+00
-2.202752E+00
-1.114851E-01
-1.242892E-02
-8.018653E-01
-6.429879E-01
-5.692854E-02
-3.240858E-03
+7.701233E-01
+5.930898E-01
+4.481585E-02
+2.008461E-03
+1.547307E+00
+2.394158E+00
+1.226539E-01
+1.504398E-02
+2.106373E+00
+4.436806E+00
+1.450618E-01
+2.104294E-02
+2.437654E+00
+5.942157E+00
+1.521380E-01
+2.314598E-02
+2.754639E+00
+7.588038E+00
+1.745460E-01
+3.046629E-02
+2.623852E+00
+6.884601E+00
+1.851602E-01
+3.428432E-02
+2.376886E+00
+5.649588E+00
+1.615729E-01
+2.610582E-02
+2.021856E+00
+4.087900E+00
+1.533174E-01
+2.350622E-02
+1.333190E+00
+1.777397E+00
+7.076188E-02
+5.007243E-03
+7.258527E-01
+5.268622E-01
+3.656030E-02
+1.336656E-03
tally 4:
-1.404203E-01
-1.971786E-02
+1.667432E-01
+2.780328E-02
0.000000E+00
0.000000E+00
-1.383954E-01
-1.915329E-02
-2.626162E-01
-6.896729E-02
+1.292567E-01
+1.670730E-02
+2.813370E-01
+7.915052E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -128,14 +128,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-2.626162E-01
-6.896729E-02
-1.383954E-01
-1.915329E-02
-2.300607E-01
-5.292793E-02
-3.213893E-01
-1.032911E-01
+2.813370E-01
+7.915052E-02
+1.292567E-01
+1.670730E-02
+2.670549E-01
+7.131835E-02
+4.055324E-01
+1.644566E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -152,14 +152,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-3.213893E-01
-1.032911E-01
-2.300607E-01
-5.292793E-02
-3.621797E-01
-1.311741E-01
-4.326081E-01
-1.871498E-01
+4.055324E-01
+1.644566E-01
+2.670549E-01
+7.131835E-02
+3.848125E-01
+1.480807E-01
+4.809430E-01
+2.313062E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -176,14 +176,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.326081E-01
-1.871498E-01
-3.621797E-01
-1.311741E-01
-4.274873E-01
-1.827454E-01
-4.701391E-01
-2.210307E-01
+4.809430E-01
+2.313062E-01
+3.848125E-01
+1.480807E-01
+4.543918E-01
+2.064719E-01
+5.106133E-01
+2.607260E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -200,14 +200,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.701391E-01
-2.210307E-01
-4.274873E-01
-1.827454E-01
-4.867763E-01
-2.369512E-01
-5.027339E-01
-2.527413E-01
+5.106133E-01
+2.607260E-01
+4.543918E-01
+2.064719E-01
+4.543120E-01
+2.063994E-01
+4.626328E-01
+2.140291E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -224,14 +224,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-5.027339E-01
-2.527413E-01
-4.867763E-01
-2.369512E-01
-4.679231E-01
-2.189520E-01
-4.504626E-01
-2.029166E-01
+4.626328E-01
+2.140291E-01
+4.543120E-01
+2.063994E-01
+4.827759E-01
+2.330726E-01
+4.442622E-01
+1.973689E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -248,14 +248,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.504626E-01
-2.029166E-01
-4.679231E-01
-2.189520E-01
-4.340994E-01
-1.884423E-01
-3.622741E-01
-1.312425E-01
+4.442622E-01
+1.973689E-01
+4.827759E-01
+2.330726E-01
+4.630420E-01
+2.144079E-01
+3.886524E-01
+1.510507E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -272,14 +272,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-3.622741E-01
-1.312425E-01
-4.340994E-01
-1.884423E-01
-3.743415E-01
-1.401316E-01
-2.666952E-01
-7.112632E-02
+3.886524E-01
+1.510507E-01
+4.630420E-01
+2.144079E-01
+3.535870E-01
+1.250237E-01
+2.530312E-01
+6.402478E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -296,14 +296,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-2.666952E-01
-7.112632E-02
-3.743415E-01
-1.401316E-01
-2.832774E-01
-8.024609E-02
-1.469617E-01
-2.159775E-02
+2.530312E-01
+6.402478E-02
+3.535870E-01
+1.250237E-01
+2.465524E-01
+6.078808E-02
+1.197152E-01
+1.433173E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -320,12 +320,12 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-1.469617E-01
-2.159775E-02
-2.832774E-01
-8.024609E-02
-1.514998E-01
-2.295220E-02
+1.197152E-01
+1.433173E-02
+2.465524E-01
+6.078808E-02
+1.369631E-01
+1.875888E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -345,119 +345,119 @@ tally 4:
0.000000E+00
0.000000E+00
tally 5:
-7.817522E-01
-6.111366E-01
-1.254009E-01
-1.572539E-02
-1.426374E+00
-2.034542E+00
-2.208879E-01
-4.879148E-02
-1.815687E+00
-3.296718E+00
-2.598747E-01
-6.753484E-02
-2.446236E+00
-5.984069E+00
-3.067269E-01
-9.408137E-02
-2.670084E+00
-7.129351E+00
-3.358701E-01
-1.128087E-01
-2.682078E+00
-7.193544E+00
-3.021763E-01
-9.131050E-02
-2.215446E+00
-4.908202E+00
-3.092066E-01
-9.560869E-02
-1.871260E+00
-3.501614E+00
-2.400592E-01
-5.762841E-02
-1.483097E+00
-2.199577E+00
-2.197780E-01
-4.830237E-02
-8.009060E-01
-6.414504E-01
-1.023121E-01
-1.046776E-02
+7.701233E-01
+5.930898E-01
+1.386250E-01
+1.921688E-02
+1.547307E+00
+2.394158E+00
+2.630277E-01
+6.918357E-02
+2.106373E+00
+4.436806E+00
+2.807880E-01
+7.884187E-02
+2.435849E+00
+5.933361E+00
+3.322060E-01
+1.103608E-01
+2.753634E+00
+7.582501E+00
+3.825922E-01
+1.463768E-01
+2.623852E+00
+6.884601E+00
+3.888710E-01
+1.512206E-01
+2.376886E+00
+5.649588E+00
+3.196217E-01
+1.021581E-01
+2.021856E+00
+4.087900E+00
+2.897881E-01
+8.397715E-02
+1.333190E+00
+1.777397E+00
+1.627110E-01
+2.647486E-02
+7.258527E-01
+5.268622E-01
+9.348666E-02
+8.739755E-03
cmfd indices
1.000000E+01
1.000000E+00
1.000000E+00
1.000000E+00
k cmfd
-1.165553E+00
-1.179705E+00
-1.191818E+00
-1.207372E+00
-1.203745E+00
-1.208055E+00
-1.208191E+00
-1.201797E+00
-1.201945E+00
-1.203753E+00
-1.209025E+00
+1.149077E+00
+1.156751E+00
+1.158648E+00
+1.159506E+00
+1.156567E+00
+1.160259E+00
+1.150345E+00
+1.149846E+00
+1.151606E+00
+1.164544E+00
+1.174648E+00
cmfd entropy
-3.217557E+00
-3.209881E+00
-3.204672E+00
-3.212484E+00
-3.217253E+00
-3.216845E+00
-3.219057E+00
-3.217057E+00
-3.223643E+00
-3.230985E+00
-3.230377E+00
+3.216173E+00
+3.228717E+00
+3.220402E+00
+3.214352E+00
+3.215636E+00
+3.213599E+00
+3.212854E+00
+3.213131E+00
+3.213196E+00
+3.205474E+00
+3.202869E+00
cmfd balance
-1.65304E-03
-2.29940E-03
-1.63416E-03
-1.39975E-03
-1.91312E-03
-1.62824E-03
-1.95516E-03
-2.02934E-03
-1.92846E-03
-2.33117E-03
-2.29845E-03
+3.08825E-03
+1.42345E-03
+1.21253E-03
+1.17694E-03
+1.05901E-03
+9.29611E-04
+1.35587E-03
+1.13579E-03
+1.14964E-03
+1.29313E-03
+1.46566E-03
cmfd dominance ratio
-5.465E-01
-5.481E-01
-5.432E-01
-5.459E-01
-5.463E-01
-5.486E-01
-5.515E-01
-5.493E-01
-5.511E-01
-5.518E-01
-5.499E-01
+5.524E-01
+5.614E-01
+5.522E-01
+5.487E-01
+5.482E-01
+5.446E-01
+5.437E-01
+5.429E-01
+5.407E-01
+5.380E-01
+5.377E-01
cmfd openmc source comparison
-6.499546E-03
-3.419761E-03
-4.342514E-03
-7.229618E-03
-9.943057E-03
-1.050086E-02
-1.055060E-02
-6.562146E-03
-7.232860E-03
-4.424331E-03
-2.531323E-03
+1.586045E-02
+6.953134E-03
+6.860419E-03
+6.198467E-03
+5.142854E-03
+4.373354E-03
+5.564831E-03
+4.184765E-03
+1.867780E-03
+2.734784E-03
+2.523985E-03
cmfd source
-4.224785E-02
-7.504165E-02
-1.009909E-01
-1.238160E-01
-1.301409E-01
-1.425954E-01
-1.353275E-01
-1.134617E-01
-8.830470E-02
-4.807346E-02
+4.241440E-02
+8.226026E-02
+1.180811E-01
+1.328433E-01
+1.412410E-01
+1.424902E-01
+1.269340E-01
+1.096490E-01
+6.953251E-02
+3.455422E-02
diff --git a/tests/regression_tests/cmfd_feed_ng/results_true.dat b/tests/regression_tests/cmfd_feed_ng/results_true.dat
--- a/tests/regression_tests/cmfd_feed_ng/results_true.dat
+++ b/tests/regression_tests/cmfd_feed_ng/results_true.dat
@@ -1,208 +1,208 @@
k-combined:
-1.027584E+00 1.502267E-02
+1.005987E+00 1.354263E-02
tally 1:
-1.148263E+02
-1.318910E+03
-1.144863E+02
-1.311468E+03
-1.163124E+02
-1.353643E+03
-1.149445E+02
-1.321759E+03
+1.140273E+02
+1.301245E+03
+1.147962E+02
+1.319049E+03
+1.151426E+02
+1.326442E+03
+1.149265E+02
+1.321518E+03
tally 2:
-3.397796E+01
-7.265736E+01
-5.019405E+01
-1.585764E+02
-1.053191E+01
-6.978659E+00
-8.739144E+00
-4.800811E+00
-1.368395E+02
-1.172003E+03
-7.370695E+01
-3.398875E+02
-3.374845E+01
-7.161454E+01
-5.011266E+01
-1.580982E+02
-1.014814E+01
-6.486800E+00
-8.590537E+00
-4.639730E+00
-1.379236E+02
-1.198395E+03
-7.277377E+01
-3.313373E+02
-3.554441E+01
-7.913690E+01
-5.224651E+01
-1.709692E+02
-1.050466E+01
-6.961148E+00
-8.866162E+00
-4.951519E+00
-1.388541E+02
-1.206000E+03
-7.399637E+01
-3.423642E+02
-3.479281E+01
-7.602778E+01
-5.139230E+01
-1.659298E+02
-1.026632E+01
-6.621042E+00
-8.649433E+00
-4.697954E+00
-1.402563E+02
-1.235504E+03
-7.374718E+01
-3.400080E+02
+3.462748E+01
+7.542476E+01
+5.129219E+01
+1.658142E+02
+1.034704E+01
+6.730603E+00
+8.672967E+00
+4.715295E+00
+1.344669E+02
+1.132019E+03
+7.262519E+01
+3.300787E+02
+3.447358E+01
+7.459545E+01
+5.075836E+01
+1.619570E+02
+1.080516E+01
+7.366369E+00
+8.908065E+00
+4.991975E+00
+1.354224E+02
+1.146824E+03
+7.300078E+01
+3.332531E+02
+3.432298E+01
+7.388666E+01
+5.096378E+01
+1.627979E+02
+1.053664E+01
+7.029789E+00
+8.826624E+00
+4.904429E+00
+1.388389E+02
+1.207280E+03
+7.376623E+01
+3.403211E+02
+4.383841E+01
+1.943331E+02
+5.165881E+01
+1.675923E+02
+1.059646E+01
+7.048052E+00
+8.763673E+00
+4.823505E+00
+1.378179E+02
+1.188104E+03
+7.431708E+01
+3.453746E+02
tally 3:
-4.748159E+01
-1.419494E+02
+4.858880E+01
+1.488705E+02
0.000000E+00
0.000000E+00
-8.132630E-03
-1.326503E-05
+8.148667E-03
+1.337050E-05
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-3.299481E+00
-6.900644E-01
-2.429296E+00
-3.713869E-01
+3.347376E+00
+7.045574E-01
+2.433484E+00
+3.727266E-01
0.000000E+00
0.000000E+00
-6.175576E+00
-2.403118E+00
+6.095478E+00
+2.332622E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-7.020357E-02
-6.481773E-04
-3.097931E-01
-6.853044E-03
+1.235421E-01
+1.205155E-03
+3.647699E-01
+8.953589E-03
0.000000E+00
0.000000E+00
-2.592969E+00
-4.215508E-01
+2.673965E+00
+4.517972E-01
0.000000E+00
0.000000E+00
-6.972257E+01
-3.041404E+02
-5.792796E-01
-2.191871E-02
-4.745221E+01
-1.418371E+02
+6.841105E+01
+2.929195E+02
+5.902473E-01
+2.307683E-02
+4.792291E+01
+1.444397E+02
0.000000E+00
0.000000E+00
-1.507569E-02
-3.140047E-05
+2.183275E-02
+8.061011E-05
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-3.307769E+00
-6.924370E-01
-2.473164E+00
-3.840166E-01
+3.435826E+00
+7.480244E-01
+2.450829E+00
+3.800327E-01
0.000000E+00
0.000000E+00
-5.967063E+00
-2.251947E+00
+6.331358E+00
+2.530492E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-9.143833E-02
-8.020544E-04
-3.234880E-01
-7.219562E-03
+1.012941E-01
+8.217580E-04
+2.981274E-01
+5.863186E-03
0.000000E+00
0.000000E+00
-2.477436E+00
-3.882619E-01
+2.535628E+00
+4.048310E-01
0.000000E+00
0.000000E+00
-6.888326E+01
-2.968630E+02
-5.925099E-01
-2.344632E-02
-4.946736E+01
-1.533087E+02
+6.912003E+01
+2.987684E+02
+5.984862E-01
+2.386115E-02
+4.822881E+01
+1.458309E+02
0.000000E+00
0.000000E+00
-1.369119E-02
-3.099298E-05
+1.525590E-02
+3.794082E-05
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-3.513467E+00
-7.852189E-01
-2.483110E+00
-3.901527E-01
+3.314494E+00
+6.944527E-01
+2.424209E+00
+3.691360E-01
0.000000E+00
0.000000E+00
-6.238898E+00
-2.455700E+00
+6.254897E+00
+2.474317E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-9.032973E-02
-6.677512E-04
-2.816159E-01
-5.349737E-03
+1.112542E-01
+1.051688E-03
+3.234880E-01
+7.156753E-03
0.000000E+00
0.000000E+00
-2.620828E+00
-4.350795E-01
+2.474142E+00
+3.837496E-01
0.000000E+00
0.000000E+00
-6.992910E+01
-3.057653E+02
-5.890670E-01
-2.307978E-02
-4.853121E+01
-1.480132E+02
+6.987095E+01
+3.053358E+02
+5.928782E-01
+2.368116E-02
+4.885415E+01
+1.499856E+02
0.000000E+00
0.000000E+00
-1.719291E-02
-4.141727E-05
+1.262416E-02
+2.486286E-05
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-3.490129E+00
-7.743548E-01
-2.381968E+00
-3.564896E-01
+3.426826E+00
+7.480396E-01
+2.487209E+00
+3.903882E-01
0.000000E+00
0.000000E+00
-6.151693E+00
-2.382656E+00
+6.127303E+00
+2.364605E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-8.653178E-02
-5.524601E-04
-3.307211E-01
-7.362512E-03
+9.439007E-02
+1.082564E-03
+2.963491E-01
+5.652952E-03
0.000000E+00
0.000000E+00
-2.566722E+00
-4.136929E-01
+2.620696E+00
+4.311792E-01
0.000000E+00
0.000000E+00
-6.968935E+01
-3.036323E+02
-6.295592E-01
-2.609911E-02
+7.030725E+01
+3.091241E+02
+5.986966E-01
+2.352487E-02
tally 4:
0.000000E+00
0.000000E+00
@@ -216,18 +216,18 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-6.910417E+00
-3.013908E+00
-2.099086E+00
-2.794191E-01
-2.725309E+01
-4.645663E+01
-7.076086E+00
-3.154776E+00
-2.051075E+00
-2.671542E-01
-2.737348E+01
-4.686718E+01
+7.028624E+00
+3.105990E+00
+2.154648E+00
+2.948865E-01
+2.714077E+01
+4.607926E+01
+7.035506E+00
+3.118549E+00
+2.085916E+00
+2.730884E-01
+2.750091E+01
+4.731304E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -240,18 +240,18 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.215131E+00
-3.265328E+00
-2.066108E+00
-2.704238E-01
-2.755564E+01
-4.753705E+01
-7.022836E+00
-3.102535E+00
-2.076586E+00
-2.741254E-01
-2.756981E+01
-4.756632E+01
+7.170567E+00
+3.240715E+00
+2.131758E+00
+2.862355E-01
+2.747702E+01
+4.722977E+01
+7.068817E+00
+3.139275E+00
+2.095865E+00
+2.762179E-01
+2.737835E+01
+4.688689E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -276,18 +276,18 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.076086E+00
-3.154776E+00
-2.051075E+00
-2.671542E-01
-2.737348E+01
-4.686718E+01
-6.910417E+00
-3.013908E+00
-2.099086E+00
-2.794191E-01
-2.725309E+01
-4.645663E+01
+7.035506E+00
+3.118549E+00
+2.085916E+00
+2.730884E-01
+2.750091E+01
+4.731304E+01
+7.028624E+00
+3.105990E+00
+2.154648E+00
+2.948865E-01
+2.714077E+01
+4.607926E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -312,18 +312,18 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.008937E+00
-3.087084E+00
-2.040640E+00
-2.622272E-01
-2.705295E+01
-4.578207E+01
-7.038404E+00
-3.111878E+00
-2.123591E+00
-2.840551E-01
-2.708214E+01
-4.588834E+01
+7.103896E+00
+3.171147E+00
+2.095666E+00
+2.756673E-01
+2.711842E+01
+4.600196E+01
+7.197270E+00
+3.255501E+00
+2.046179E+00
+2.630301E-01
+2.729901E+01
+4.662030E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -360,30 +360,30 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.286308E+00
-3.346248E+00
-2.108252E+00
-2.794781E-01
-2.738387E+01
-4.689407E+01
-7.108444E+00
-3.172810E+00
-2.111474E+00
-2.804633E-01
-2.737249E+01
-4.687424E+01
-7.022836E+00
-3.102535E+00
-2.076586E+00
-2.741254E-01
-2.756981E+01
-4.756632E+01
-7.215131E+00
-3.265328E+00
-2.066108E+00
-2.704238E-01
-2.755564E+01
-4.753705E+01
+7.240906E+00
+3.296285E+00
+2.130816E+00
+2.850713E-01
+2.761433E+01
+4.771548E+01
+7.126427E+00
+3.199209E+00
+2.177254E+00
+2.998765E-01
+2.754936E+01
+4.748447E+01
+7.068817E+00
+3.139275E+00
+2.095865E+00
+2.762179E-01
+2.737835E+01
+4.688689E+01
+7.170567E+00
+3.240715E+00
+2.131758E+00
+2.862355E-01
+2.747702E+01
+4.722977E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -420,18 +420,18 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.108444E+00
-3.172810E+00
-2.111474E+00
-2.804633E-01
-2.737249E+01
-4.687424E+01
-7.286308E+00
-3.346248E+00
-2.108252E+00
-2.794781E-01
-2.738387E+01
-4.689407E+01
+7.126427E+00
+3.199209E+00
+2.177254E+00
+2.998765E-01
+2.754936E+01
+4.748447E+01
+7.240906E+00
+3.296285E+00
+2.130816E+00
+2.850713E-01
+2.761433E+01
+4.771548E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -444,18 +444,18 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.038404E+00
-3.111878E+00
-2.123591E+00
-2.840551E-01
-2.708214E+01
-4.588834E+01
-7.008937E+00
-3.087084E+00
-2.040640E+00
-2.622272E-01
-2.705295E+01
-4.578207E+01
+7.197270E+00
+3.255501E+00
+2.046179E+00
+2.630301E-01
+2.729901E+01
+4.662030E+01
+7.103896E+00
+3.171147E+00
+2.095666E+00
+2.756673E-01
+2.711842E+01
+4.600196E+01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -493,124 +493,124 @@ tally 4:
0.000000E+00
0.000000E+00
tally 5:
-4.748972E+01
-1.419968E+02
-8.604872E+00
-4.655596E+00
-7.261430E+01
-3.298767E+02
-1.092092E+01
-7.540081E+00
-3.984923E+00
-1.000404E+00
-3.294804E+01
-6.794642E+01
-4.746728E+01
-1.419250E+02
-8.440227E+00
-4.478243E+00
-7.167598E+01
-3.214310E+02
-1.073385E+01
-7.257545E+00
-3.904158E+00
-9.587510E-01
-3.253492E+01
-6.626202E+01
-4.948105E+01
-1.533940E+02
-8.722008E+00
-4.791509E+00
-7.283154E+01
-3.316829E+02
-1.138387E+01
-8.162117E+00
-4.131397E+00
-1.078045E+00
-3.254336E+01
-6.624925E+01
-4.854840E+01
-1.481182E+02
-8.533661E+00
-4.573316E+00
-7.258180E+01
-3.293419E+02
-1.053673E+01
-7.002045E+00
-3.988151E+00
-1.001884E+00
-3.284213E+01
-6.749116E+01
+4.859695E+01
+1.489217E+02
+8.528963E+00
+4.561881E+00
+7.144500E+01
+3.194467E+02
+1.120265E+01
+7.944038E+00
+4.009821E+00
+1.012575E+00
+3.235456E+01
+6.558658E+01
+4.794474E+01
+1.445671E+02
+8.782187E+00
+4.852477E+00
+7.195036E+01
+3.237389E+02
+1.075572E+01
+7.333822E+00
+4.084680E+00
+1.054714E+00
+3.267154E+01
+6.675266E+01
+4.824407E+01
+1.459220E+02
+8.679106E+00
+4.742342E+00
+7.266858E+01
+3.302641E+02
+1.094872E+01
+7.536318E+00
+3.935828E+00
+9.749543E-01
+3.319517E+01
+6.894791E+01
+4.886677E+01
+1.500624E+02
+8.614512E+00
+4.662618E+00
+7.321408E+01
+3.352172E+02
+1.095123E+01
+7.574359E+00
+3.885927E+00
+9.539315E-01
+3.334065E+01
+6.953215E+01
cmfd indices
2.000000E+00
2.000000E+00
1.000000E+00
3.000000E+00
k cmfd
-1.026167E+00
-1.026753E+00
-1.034560E+00
-1.028298E+00
-1.029032E+00
-1.033531E+00
-1.034902E+00
-1.029837E+00
-1.025313E+00
-1.019855E+00
-1.021235E+00
+1.026473E+00
+1.024183E+00
+1.023151E+00
+1.025047E+00
+1.019801E+00
+1.020492E+00
+1.015249E+00
+1.016714E+00
+1.016047E+00
+1.019687E+00
+1.020955E+00
cmfd entropy
-1.998818E+00
-1.998853E+00
-1.999048E+00
-1.998864E+00
-1.998999E+00
-1.998789E+00
-1.998670E+00
-1.998822E+00
-1.998782E+00
-1.999027E+00
-1.999420E+00
+1.999640E+00
+1.999556E+00
+1.999484E+00
+1.999718E+00
+1.999697E+00
+1.999657E+00
+1.999883E+00
+1.999902E+00
+1.999977E+00
+1.999977E+00
+1.999906E+00
cmfd balance
-1.00064E-03
-6.95941E-04
-5.74967E-04
-4.34776E-04
-4.03288E-04
-4.32457E-04
-4.49075E-04
-3.57342E-04
-3.62891E-04
-2.86133E-04
-2.08678E-04
+8.10090E-04
+1.28103E-03
+7.97200E-04
+5.82188E-04
+7.20670E-04
+7.31475E-04
+5.71904E-04
+6.14057E-04
+6.00142E-04
+5.47870E-04
+3.53604E-04
cmfd dominance ratio
-3.759E-03
-3.706E-03
-3.719E-03
-3.796E-03
-3.724E-03
-3.809E-03
-3.792E-03
-3.782E-03
-3.841E-03
+3.977E-03
+4.018E-03
+3.950E-03
3.866E-03
-3.868E-03
+3.840E-03
+3.888E-03
+3.867E-03
+3.896E-03
+3.924E-03
+3.885E-03
+3.913E-03
cmfd openmc source comparison
-8.283222E-05
-6.636005E-05
-5.320110E-05
-4.474530E-05
-4.409263E-05
-4.914331E-05
-4.834447E-05
-4.040592E-05
-4.173469E-05
-3.118350E-05
-1.667967E-05
+4.787501E-05
+4.450525E-05
+2.532345E-05
+3.844307E-05
+4.821504E-05
+4.840760E-05
+3.739246E-05
+3.957960E-05
+4.521480E-05
+4.072007E-05
+2.532636E-05
cmfd source
-2.416781E-01
-2.442811E-01
-2.566121E-01
-2.574288E-01
+2.486236E-01
+2.531628E-01
+2.460219E-01
+2.521918E-01
0.000000E+00
0.000000E+00
0.000000E+00
diff --git a/tests/regression_tests/cmfd_feed_rectlin/results_true.dat b/tests/regression_tests/cmfd_feed_rectlin/results_true.dat
--- a/tests/regression_tests/cmfd_feed_rectlin/results_true.dat
+++ b/tests/regression_tests/cmfd_feed_rectlin/results_true.dat
@@ -1,149 +1,149 @@
k-combined:
-1.167761E+00 4.293426E-03
+1.160561E+00 1.029736E-02
tally 1:
-1.202277E+01
-1.452746E+01
-2.195725E+01
-4.835710E+01
-2.862021E+01
-8.215585E+01
-3.453333E+01
-1.196497E+02
-3.756803E+01
-1.414919E+02
-3.739045E+01
-1.403446E+02
-3.361501E+01
-1.134271E+02
-2.819861E+01
-7.968185E+01
-2.111919E+01
-4.472336E+01
-1.129975E+01
-1.280982E+01
+1.089904E+01
+1.193573E+01
+2.026534E+01
+4.113383E+01
+2.723584E+01
+7.440537E+01
+3.309956E+01
+1.101184E+02
+3.659327E+01
+1.341221E+02
+3.780158E+01
+1.430045E+02
+3.520883E+01
+1.241772E+02
+2.961801E+01
+8.784675E+01
+2.182029E+01
+4.781083E+01
+1.180347E+01
+1.399970E+01
tally 2:
-8.743037E+00
-3.861220E+00
-6.027264E+00
-1.836570E+00
-3.366159E+01
-5.708871E+01
-2.367086E+01
-2.824484E+01
-2.348709E+01
-2.777633E+01
-1.668756E+01
-1.403629E+01
-5.609969E+01
-1.580739E+02
-3.985682E+01
-7.985715E+01
-3.319543E+01
-5.528370E+01
-2.358360E+01
-2.791829E+01
-7.132407E+01
-2.550603E+02
-5.083603E+01
-1.296049E+02
-3.801086E+01
-7.257141E+01
-2.709688E+01
-3.686995E+01
-3.751307E+01
-7.073318E+01
-2.660859E+01
-3.559134E+01
-7.258292E+01
-2.644619E+02
-5.168044E+01
-1.340982E+02
-3.304423E+01
-5.486256E+01
-2.335526E+01
-2.742989E+01
-5.655005E+01
-1.603926E+02
-4.014572E+01
-8.087797E+01
-2.351019E+01
-2.776367E+01
-1.670083E+01
-1.401374E+01
-3.451886E+01
-5.983149E+01
-2.443300E+01
-2.997375E+01
-8.551177E+00
-3.691263E+00
-5.916124E+00
-1.768556E+00
+8.794706E+00
+3.939413E+00
+6.131113E+00
+1.913116E+00
+3.265522E+01
+5.364042E+01
+2.304238E+01
+2.672742E+01
+2.250225E+01
+2.541491E+01
+1.601668E+01
+1.288405E+01
+5.525355E+01
+1.531915E+02
+3.929637E+01
+7.748545E+01
+3.222711E+01
+5.216630E+01
+2.285375E+01
+2.623641E+01
+7.051908E+01
+2.495413E+02
+5.010064E+01
+1.259701E+02
+3.728726E+01
+6.974440E+01
+2.652872E+01
+3.530919E+01
+3.747306E+01
+7.058235E+01
+2.681415E+01
+3.613314E+01
+7.296802E+01
+2.669214E+02
+5.202502E+01
+1.356733E+02
+3.333947E+01
+5.579355E+01
+2.361733E+01
+2.800800E+01
+5.785916E+01
+1.680561E+02
+4.093282E+01
+8.410711E+01
+2.377151E+01
+2.842464E+01
+1.681789E+01
+1.423646E+01
+3.422028E+01
+5.880493E+01
+2.415199E+01
+2.930240E+01
+8.890608E+00
+3.986356E+00
+6.140159E+00
+1.897764E+00
tally 3:
-5.799161E+00
-1.702117E+00
-3.588837E-01
-7.127789E-03
-2.273477E+01
-2.606361E+01
-1.586822E+00
-1.296956E-01
-1.606466E+01
-1.300770E+01
-1.018209E+00
-5.281297E-02
-3.840128E+01
-7.415483E+01
-2.383738E+00
-2.877855E-01
-2.268388E+01
-2.583457E+01
-1.485208E+00
-1.122747E-01
-4.899435E+01
-1.204028E+02
-3.203505E+00
-5.163235E-01
-2.610714E+01
-3.423244E+01
-1.707156E+00
-1.476400E-01
-2.559242E+01
-3.293100E+01
-1.761813E+00
-1.597786E-01
-4.985698E+01
-1.248029E+02
-3.081386E+00
-4.824389E-01
-2.245777E+01
-2.536963E+01
-1.447127E+00
-1.065745E-01
-3.869628E+01
-7.516217E+01
-2.545419E+00
-3.270790E-01
-1.610401E+01
-1.303231E+01
-1.011897E+00
-5.274155E-02
-2.353410E+01
-2.781055E+01
-1.517873E+00
-1.184503E-01
-5.687356E+00
-1.636570E+00
-3.728435E-01
-7.203797E-03
+5.925339E+00
+1.788596E+00
+3.912632E-01
+8.061838E-03
+2.215544E+01
+2.471404E+01
+1.465191E+00
+1.092622E-01
+1.542988E+01
+1.195626E+01
+1.022876E+00
+5.356825E-02
+3.792029E+01
+7.218149E+01
+2.370476E+00
+2.839465E-01
+2.200154E+01
+2.432126E+01
+1.360836E+00
+9.402424E-02
+4.824980E+01
+1.168447E+02
+3.124366E+00
+4.907460E-01
+2.557420E+01
+3.282066E+01
+1.725855E+00
+1.519830E-01
+2.577963E+01
+3.341077E+01
+1.654042E+00
+1.386845E-01
+5.008220E+01
+1.257610E+02
+3.223857E+00
+5.237360E-01
+2.273380E+01
+2.595325E+01
+1.438369E+00
+1.050840E-01
+3.938822E+01
+7.789691E+01
+2.648324E+00
+3.559703E-01
+1.623604E+01
+1.327214E+01
+1.058882E+00
+5.680630E-02
+2.325730E+01
+2.717892E+01
+1.584276E+00
+1.275868E-01
+5.937929E+00
+1.774847E+00
+3.866918E-01
+7.994353E-03
tally 4:
-3.060660E+00
-4.703581E-01
+3.063235E+00
+4.714106E-01
0.000000E+00
0.000000E+00
-1.451637E+00
-1.081522E-01
-4.402560E+00
-9.746218E-01
+1.425705E+00
+1.043616E-01
+4.355515E+00
+9.538346E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -160,14 +160,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.402560E+00
-9.746218E-01
-1.451637E+00
-1.081522E-01
-3.903491E+00
-7.713768E-01
-6.448935E+00
-2.089570E+00
+4.355515E+00
+9.538346E-01
+1.425705E+00
+1.043616E-01
+3.859174E+00
+7.519499E-01
+6.350310E+00
+2.024214E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -184,14 +184,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-6.448935E+00
-2.089570E+00
-3.903491E+00
-7.713768E-01
-5.075609E+00
-1.297182E+00
-7.371853E+00
-2.729133E+00
+6.350310E+00
+2.024214E+00
+3.859174E+00
+7.519499E-01
+4.993073E+00
+1.258264E+00
+7.194275E+00
+2.596886E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -208,14 +208,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.371853E+00
-2.729133E+00
-5.075609E+00
-1.297182E+00
-7.015514E+00
-2.477295E+00
-8.723726E+00
-3.828466E+00
+7.194275E+00
+2.596886E+00
+4.993073E+00
+1.258264E+00
+6.786617E+00
+2.312259E+00
+8.306978E+00
+3.459668E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -232,14 +232,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.723726E+00
-3.828466E+00
-7.015514E+00
-2.477295E+00
-7.735344E+00
-3.007547E+00
-9.106625E+00
-4.165807E+00
+8.306978E+00
+3.459668E+00
+6.786617E+00
+2.312259E+00
+7.603410E+00
+2.905228E+00
+8.791222E+00
+3.882935E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -256,14 +256,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-9.106625E+00
-4.165807E+00
-7.735344E+00
-3.007547E+00
-9.026526E+00
-4.098261E+00
-9.551542E+00
-4.586695E+00
+8.791222E+00
+3.882935E+00
+7.603410E+00
+2.905228E+00
+8.867113E+00
+3.938503E+00
+9.302808E+00
+4.340042E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -280,14 +280,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-9.551542E+00
-4.586695E+00
-9.026526E+00
-4.098261E+00
-9.344096E+00
-4.384840E+00
-9.405215E+00
-4.441966E+00
+9.302808E+00
+4.340042E+00
+8.867113E+00
+3.938503E+00
+9.270113E+00
+4.306513E+00
+9.263471E+00
+4.302184E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -304,14 +304,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-9.405215E+00
-4.441966E+00
-9.344096E+00
-4.384840E+00
-9.390313E+00
-4.435716E+00
-9.011690E+00
-4.080913E+00
+9.263471E+00
+4.302184E+00
+9.270113E+00
+4.306513E+00
+9.348712E+00
+4.388570E+00
+8.977713E+00
+4.047349E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -328,14 +328,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-9.011690E+00
-4.080913E+00
-9.390313E+00
-4.435716E+00
-9.140785E+00
-4.195868E+00
-8.003067E+00
-3.218771E+00
+8.977713E+00
+4.047349E+00
+9.348712E+00
+4.388570E+00
+9.234380E+00
+4.280666E+00
+8.036978E+00
+3.239853E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -352,14 +352,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.003067E+00
-3.218771E+00
-9.140785E+00
-4.195868E+00
-8.629258E+00
-3.736554E+00
-7.133986E+00
-2.557637E+00
+8.036978E+00
+3.239853E+00
+9.234380E+00
+4.280666E+00
+8.713633E+00
+3.808850E+00
+7.160878E+00
+2.572915E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -376,14 +376,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.133986E+00
-2.557637E+00
-8.629258E+00
-3.736554E+00
-7.284136E+00
-2.659936E+00
-5.069993E+00
-1.289638E+00
+7.160878E+00
+2.572915E+00
+8.713633E+00
+3.808850E+00
+7.378538E+00
+2.732122E+00
+5.145728E+00
+1.329190E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -400,14 +400,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-5.069993E+00
-1.289638E+00
-7.284136E+00
-2.659936E+00
-6.585377E+00
-2.178573E+00
-4.109746E+00
-8.535283E-01
+5.145728E+00
+1.329190E+00
+7.378538E+00
+2.732122E+00
+6.660125E+00
+2.228506E+00
+4.087925E+00
+8.435381E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -424,14 +424,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.109746E+00
-8.535283E-01
-6.585377E+00
-2.178573E+00
-4.394913E+00
-9.694834E-01
-1.455260E+00
-1.073327E-01
+4.087925E+00
+8.435381E-01
+6.660125E+00
+2.228506E+00
+4.466295E+00
+1.002320E+00
+1.468481E+00
+1.099604E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -448,12 +448,12 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-1.455260E+00
-1.073327E-01
-4.394913E+00
-9.694834E-01
-3.054512E+00
-4.687172E-01
+1.468481E+00
+1.099604E-01
+4.466295E+00
+1.002320E+00
+3.139355E+00
+4.955456E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -473,164 +473,164 @@ tally 4:
0.000000E+00
0.000000E+00
tally 5:
-5.798163E+00
-1.701480E+00
-7.719076E-01
-3.205800E-02
-2.272861E+01
-2.604939E+01
-3.183925E+00
-5.123120E-01
-1.606367E+01
-1.300597E+01
-2.209506E+00
-2.514085E-01
-3.839444E+01
-7.412912E+01
-5.235063E+00
-1.389014E+00
-2.268086E+01
-2.582733E+01
-3.074902E+00
-4.810618E-01
-4.898566E+01
-1.203589E+02
-6.606838E+00
-2.201101E+00
-2.609836E+01
-3.420917E+01
-3.518842E+00
-6.264238E-01
-2.558605E+01
-3.291399E+01
-3.686659E+00
-6.942431E-01
-4.984902E+01
-1.247644E+02
-6.876822E+00
-2.400434E+00
-2.245394E+01
-2.536044E+01
-3.098158E+00
-4.940204E-01
-3.868744E+01
-7.512715E+01
-5.302748E+00
-1.428609E+00
-1.610093E+01
-1.302770E+01
-2.252209E+00
-2.578778E-01
-2.352951E+01
-2.779963E+01
-3.249775E+00
-5.380883E-01
-5.685356E+00
-1.635162E+00
-7.886630E-01
-3.440650E-02
+5.925339E+00
+1.788596E+00
+8.954773E-01
+4.217679E-02
+2.215054E+01
+2.470273E+01
+2.944747E+00
+4.443186E-01
+1.542658E+01
+1.195085E+01
+1.950262E+00
+1.946340E-01
+3.791137E+01
+7.214779E+01
+4.955741E+00
+1.254830E+00
+2.200054E+01
+2.431894E+01
+3.031040E+00
+4.685971E-01
+4.823946E+01
+1.167941E+02
+6.226321E+00
+1.956308E+00
+2.556930E+01
+3.280828E+01
+3.582546E+00
+6.505962E-01
+2.577249E+01
+3.339204E+01
+3.316825E+00
+5.676842E-01
+5.007249E+01
+1.257124E+02
+6.462364E+00
+2.120157E+00
+2.273285E+01
+2.595106E+01
+2.960964E+00
+4.496277E-01
+3.937362E+01
+7.783849E+01
+5.339336E+00
+1.449257E+00
+1.623315E+01
+1.326746E+01
+2.289661E+00
+2.698618E-01
+2.325250E+01
+2.716827E+01
+3.253010E+00
+5.413837E-01
+5.937929E+00
+1.774847E+00
+9.208589E-01
+4.421403E-02
cmfd indices
1.400000E+01
1.000000E+00
1.000000E+00
1.000000E+00
k cmfd
-1.154550E+00
-1.172635E+00
-1.171962E+00
-1.174888E+00
-1.182656E+00
-1.190779E+00
-1.200964E+00
-1.196775E+00
-1.190049E+00
-1.181514E+00
-1.180749E+00
-1.179370E+00
-1.177279E+00
-1.178924E+00
-1.177106E+00
-1.179987E+00
+1.125528E+00
+1.145509E+00
+1.158948E+00
+1.171983E+00
+1.180649E+00
+1.184072E+00
+1.188112E+00
+1.183095E+00
+1.182269E+00
+1.175467E+00
+1.175184E+00
+1.172637E+00
+1.171593E+00
+1.175439E+00
+1.174650E+00
+1.176474E+00
cmfd entropy
-3.598911E+00
-3.600560E+00
-3.599978E+00
-3.601027E+00
-3.599502E+00
-3.598849E+00
-3.601916E+00
-3.605728E+00
-3.607212E+00
-3.612277E+00
-3.615627E+00
-3.618446E+00
-3.615292E+00
-3.612951E+00
-3.610620E+00
-3.607388E+00
+3.607059E+00
+3.604890E+00
+3.601329E+00
+3.597776E+00
+3.597360E+00
+3.597387E+00
+3.595379E+00
+3.596995E+00
+3.600901E+00
+3.601832E+00
+3.601426E+00
+3.604521E+00
+3.602848E+00
+3.603875E+00
+3.605213E+00
+3.606699E+00
cmfd balance
-6.80696E-03
-7.03786E-03
-5.33837E-03
-5.39054E-03
-4.82209E-03
-4.46014E-03
-4.48076E-03
-3.31344E-03
-2.71476E-03
-2.03403E-03
-1.68070E-03
-1.38975E-03
-1.30457E-03
-1.29678E-03
-1.34009E-03
-1.43023E-03
+4.46212E-03
+4.66648E-03
+5.04274E-03
+5.21553E-03
+3.92498E-03
+2.97185E-03
+2.79785E-03
+2.66951E-03
+2.17472E-03
+1.98009E-03
+1.77035E-03
+1.51281E-03
+1.52807E-03
+1.33341E-03
+1.18155E-03
+1.07752E-03
cmfd dominance ratio
-5.913E-01
-5.946E-01
-5.961E-01
-5.995E-01
-6.024E-01
-6.050E-01
-6.056E-01
-6.062E-01
-6.064E-01
-6.087E-01
-6.117E-01
-6.120E-01
+6.136E-01
+6.127E-01
+6.137E-01
+6.102E-01
+6.067E-01
+6.061E-01
+6.031E-01
+6.046E-01
+6.071E-01
6.089E-01
-6.074E-01
-6.052E-01
-6.030E-01
+6.073E-01
+6.080E-01
+6.080E-01
+6.090E-01
+6.092E-01
+6.094E-01
cmfd openmc source comparison
-1.274461E-02
-9.191627E-03
-7.371466E-03
-4.977614E-03
-4.481864E-03
-3.396798E-03
-2.167863E-03
-4.137274E-03
-4.692749E-03
-2.955754E-03
-2.656269E-03
-2.241441E-03
-4.127496E-03
-3.040657E-03
-3.925292E-03
-3.183157E-03
+1.043027E-02
+1.278226E-02
+1.184867E-02
+1.017186E-02
+1.099696E-02
+7.955341E-03
+8.360344E-03
+6.875508E-03
+4.824018E-03
+4.915363E-03
+5.371647E-03
+4.593100E-03
+4.894955E-03
+4.928253E-03
+4.292171E-03
+4.018545E-03
cmfd source
-1.525739E-02
-6.776716E-02
-4.352345E-02
-1.020209E-01
-6.379967E-02
-1.378464E-01
-7.334653E-02
-7.562170E-02
-1.318340E-01
-6.145426E-02
-1.073314E-01
-4.229800E-02
-6.258388E-02
-1.531527E-02
+1.600876E-02
+6.000305E-02
+4.248071E-02
+9.935789E-02
+5.768092E-02
+1.338593E-01
+7.417398E-02
+7.102984E-02
+1.382563E-01
+6.181889E-02
+1.142473E-01
+4.571447E-02
+6.864655E-02
+1.672206E-02
diff --git a/tests/regression_tests/cmfd_feed_ref_d/results_true.dat b/tests/regression_tests/cmfd_feed_ref_d/results_true.dat
--- a/tests/regression_tests/cmfd_feed_ref_d/results_true.dat
+++ b/tests/regression_tests/cmfd_feed_ref_d/results_true.dat
@@ -1,117 +1,117 @@
k-combined:
-1.184724E+00 9.807415E-03
+1.167869E+00 7.492916E-03
tally 1:
-1.121178E+01
-1.261180E+01
-2.101384E+01
-4.433764E+01
-2.783041E+01
-7.777181E+01
-3.351124E+01
-1.125137E+02
-3.625716E+01
-1.319682E+02
-3.741849E+01
-1.403752E+02
-3.537964E+01
-1.255737E+02
-3.030185E+01
-9.227364E+01
-2.188275E+01
-4.810760E+01
-1.172353E+01
-1.379028E+01
+1.146821E+01
+1.318787E+01
+2.161476E+01
+4.685066E+01
+2.951084E+01
+8.733116E+01
+3.521523E+01
+1.242762E+02
+3.774181E+01
+1.426460E+02
+3.727924E+01
+1.391162E+02
+3.377236E+01
+1.143877E+02
+2.904590E+01
+8.453427E+01
+2.090941E+01
+4.384824E+01
+1.078680E+01
+1.168172E+01
tally 2:
-1.146903E+00
-1.315387E+00
-8.067939E-01
-6.509164E-01
-2.070041E+00
-4.285068E+00
-1.468994E+00
-2.157944E+00
-2.703198E+00
-7.307278E+00
-1.895572E+00
-3.593192E+00
-3.567627E+00
-1.272796E+01
-2.541486E+00
-6.459152E+00
-3.937479E+00
-1.550374E+01
-2.770473E+00
-7.675520E+00
-3.960493E+00
-1.568551E+01
-2.792683E+00
-7.799079E+00
-3.243496E+00
-1.052027E+01
-2.296698E+00
-5.274821E+00
-2.794771E+00
-7.810744E+00
-1.953175E+00
-3.814893E+00
-2.187333E+00
-4.784426E+00
-1.544523E+00
-2.385551E+00
-1.199628E+00
-1.439107E+00
-8.356207E-01
-6.982620E-01
+1.136805E+00
+1.292326E+00
+7.987282E-01
+6.379667E-01
+2.266961E+00
+5.139112E+00
+1.613498E+00
+2.603376E+00
+3.046379E+00
+9.280427E+00
+2.182480E+00
+4.763219E+00
+3.568101E+00
+1.273134E+01
+2.532478E+00
+6.413444E+00
+3.989532E+00
+1.591637E+01
+2.848319E+00
+8.112921E+00
+3.853139E+00
+1.484668E+01
+2.718497E+00
+7.390223E+00
+3.478134E+00
+1.209742E+01
+2.467279E+00
+6.087465E+00
+2.952214E+00
+8.715569E+00
+2.103257E+00
+4.423688E+00
+1.917446E+00
+3.676599E+00
+1.378361E+00
+1.899878E+00
+1.048230E+00
+1.098785E+00
+7.511876E-01
+5.642828E-01
tally 3:
-7.817283E-01
-6.110991E-01
-5.930048E-02
-3.516547E-03
-1.426340E+00
-2.034446E+00
-8.539269E-02
-7.291911E-03
-1.815669E+00
-3.296655E+00
-1.221590E-01
-1.492282E-02
-2.447185E+00
-5.988716E+00
-1.624833E-01
-2.640082E-02
-2.670094E+00
-7.129404E+00
-1.838315E-01
-3.379401E-02
-2.683021E+00
-7.198600E+00
-1.719714E-01
-2.957416E-02
-2.215470E+00
-4.908307E+00
-1.707854E-01
-2.916764E-02
-1.872360E+00
-3.505733E+00
-1.209730E-01
-1.463446E-02
-1.484189E+00
-2.202817E+00
-1.114849E-01
-1.242888E-02
-8.018794E-01
-6.430105E-01
-5.692846E-02
-3.240849E-03
+7.701212E-01
+5.930866E-01
+4.481580E-02
+2.008456E-03
+1.547321E+00
+2.394203E+00
+1.226538E-01
+1.504395E-02
+2.106393E+00
+4.436893E+00
+1.450617E-01
+2.104289E-02
+2.437675E+00
+5.942260E+00
+1.521379E-01
+2.314593E-02
+2.754657E+00
+7.588135E+00
+1.745458E-01
+3.046622E-02
+2.623856E+00
+6.884619E+00
+1.851600E-01
+3.428423E-02
+2.376884E+00
+5.649579E+00
+1.615728E-01
+2.610576E-02
+2.021851E+00
+4.087882E+00
+1.533172E-01
+2.350617E-02
+1.333182E+00
+1.777374E+00
+7.076179E-02
+5.007231E-03
+7.258458E-01
+5.268521E-01
+3.656026E-02
+1.336653E-03
tally 4:
-1.404164E-01
-1.971677E-02
+1.667426E-01
+2.780308E-02
0.000000E+00
0.000000E+00
-1.383903E-01
-1.915186E-02
-2.626104E-01
-6.896424E-02
+1.292556E-01
+1.670700E-02
+2.813401E-01
+7.915227E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -128,14 +128,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-2.626104E-01
-6.896424E-02
-1.383903E-01
-1.915186E-02
-2.300555E-01
-5.292554E-02
-3.213857E-01
-1.032888E-01
+2.813401E-01
+7.915227E-02
+1.292556E-01
+1.670700E-02
+2.670582E-01
+7.132006E-02
+4.055365E-01
+1.644599E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -152,14 +152,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-3.213857E-01
-1.032888E-01
-2.300555E-01
-5.292554E-02
-3.621759E-01
-1.311714E-01
-4.326073E-01
-1.871490E-01
+4.055365E-01
+1.644599E-01
+2.670582E-01
+7.132006E-02
+3.848164E-01
+1.480837E-01
+4.809472E-01
+2.313102E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -176,14 +176,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.326073E-01
-1.871490E-01
-3.621759E-01
-1.311714E-01
-4.274871E-01
-1.827452E-01
-4.701411E-01
-2.210326E-01
+4.809472E-01
+2.313102E-01
+3.848164E-01
+1.480837E-01
+4.543959E-01
+2.064756E-01
+5.106174E-01
+2.607301E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -200,14 +200,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.701411E-01
-2.210326E-01
-4.274871E-01
-1.827452E-01
-4.867793E-01
-2.369540E-01
-5.027352E-01
-2.527427E-01
+5.106174E-01
+2.607301E-01
+4.543959E-01
+2.064756E-01
+4.543155E-01
+2.064026E-01
+4.626331E-01
+2.140294E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -224,14 +224,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-5.027352E-01
-2.527427E-01
-4.867793E-01
-2.369540E-01
-4.679247E-01
-2.189535E-01
-4.504680E-01
-2.029214E-01
+4.626331E-01
+2.140294E-01
+4.543155E-01
+2.064026E-01
+4.827763E-01
+2.330729E-01
+4.442611E-01
+1.973679E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -248,14 +248,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.504680E-01
-2.029214E-01
-4.679247E-01
-2.189535E-01
-4.341058E-01
-1.884478E-01
-3.622812E-01
-1.312477E-01
+4.442611E-01
+1.973679E-01
+4.827763E-01
+2.330729E-01
+4.630415E-01
+2.144074E-01
+3.886521E-01
+1.510505E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -272,14 +272,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-3.622812E-01
-1.312477E-01
-4.341058E-01
-1.884478E-01
-3.743485E-01
-1.401368E-01
-2.666983E-01
-7.112801E-02
+3.886521E-01
+1.510505E-01
+4.630415E-01
+2.144074E-01
+3.535862E-01
+1.250232E-01
+2.530293E-01
+6.402384E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -296,14 +296,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-2.666983E-01
-7.112801E-02
-3.743485E-01
-1.401368E-01
-2.832798E-01
-8.024744E-02
-1.469655E-01
-2.159885E-02
+2.530293E-01
+6.402384E-02
+3.535862E-01
+1.250232E-01
+2.465508E-01
+6.078730E-02
+1.197139E-01
+1.433141E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -320,12 +320,12 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-1.469655E-01
-2.159885E-02
-2.832798E-01
-8.024744E-02
-1.515017E-01
-2.295275E-02
+1.197139E-01
+1.433141E-02
+2.465508E-01
+6.078730E-02
+1.369614E-01
+1.875841E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -345,119 +345,119 @@ tally 4:
0.000000E+00
0.000000E+00
tally 5:
-7.817283E-01
-6.110991E-01
-1.253966E-01
-1.572431E-02
-1.426340E+00
-2.034446E+00
-2.208824E-01
-4.878905E-02
-1.815669E+00
-3.296655E+00
-2.598719E-01
-6.753342E-02
-2.446230E+00
-5.984040E+00
-3.067264E-01
-9.408108E-02
-2.670094E+00
-7.129404E+00
-3.358723E-01
-1.128102E-01
-2.682092E+00
-7.193615E+00
-3.021784E-01
-9.131179E-02
-2.215470E+00
-4.908307E+00
-3.092112E-01
-9.561158E-02
-1.871290E+00
-3.501727E+00
-2.400626E-01
-5.763006E-02
-1.483119E+00
-2.199642E+00
-2.197799E-01
-4.830323E-02
-8.009200E-01
-6.414728E-01
-1.023113E-01
-1.046761E-02
+7.701212E-01
+5.930866E-01
+1.386254E-01
+1.921700E-02
+1.547321E+00
+2.394203E+00
+2.630318E-01
+6.918571E-02
+2.106393E+00
+4.436893E+00
+2.807911E-01
+7.884363E-02
+2.435870E+00
+5.933464E+00
+3.322093E-01
+1.103630E-01
+2.753652E+00
+7.582597E+00
+3.825961E-01
+1.463797E-01
+2.623856E+00
+6.884619E+00
+3.888719E-01
+1.512213E-01
+2.376884E+00
+5.649579E+00
+3.196211E-01
+1.021576E-01
+2.021851E+00
+4.087882E+00
+2.897873E-01
+8.397667E-02
+1.333182E+00
+1.777374E+00
+1.627096E-01
+2.647441E-02
+7.258458E-01
+5.268521E-01
+9.348575E-02
+8.739586E-03
cmfd indices
1.000000E+01
1.000000E+00
1.000000E+00
1.000000E+00
k cmfd
-1.165539E+00
-1.179703E+00
-1.191810E+00
-1.207373E+00
-1.203749E+00
-1.208059E+00
-1.208191E+00
-1.201767E+00
-1.201921E+00
-1.203758E+00
-1.209018E+00
+1.149087E+00
+1.156777E+00
+1.158641E+00
+1.159507E+00
+1.156564E+00
+1.160257E+00
+1.150344E+00
+1.149854E+00
+1.151616E+00
+1.164575E+00
+1.174683E+00
cmfd entropy
-3.217563E+00
-3.209882E+00
-3.204676E+00
-3.212483E+00
-3.217256E+00
-3.216849E+00
-3.219070E+00
-3.217085E+00
-3.223663E+00
-3.230980E+00
-3.230377E+00
+3.216202E+00
+3.228703E+00
+3.220414E+00
+3.214361E+00
+3.215642E+00
+3.213607E+00
+3.212862E+00
+3.213128E+00
+3.213189E+00
+3.205465E+00
+3.202859E+00
cmfd balance
-1.65304E-03
-2.29951E-03
-1.63426E-03
-1.40012E-03
-1.91396E-03
-1.62948E-03
-1.95633E-03
-2.03045E-03
-1.93004E-03
-2.33201E-03
-2.29894E-03
+3.08825E-03
+1.42554E-03
+1.21448E-03
+1.17859E-03
+1.06034E-03
+9.30949E-04
+1.35713E-03
+1.13694E-03
+1.14938E-03
+1.29296E-03
+1.46518E-03
cmfd dominance ratio
-5.460E-01
-5.473E-01
-5.415E-01
-5.446E-01
-5.451E-01
-5.475E-01
-5.502E-01
-5.474E-01
-5.498E-01
-5.502E-01
-5.483E-01
+5.503E-01
+5.596E-01
+5.505E-01
+5.471E-01
+5.468E-01
+5.427E-01
+5.421E-01
+5.412E-01
+5.389E-01
+5.371E-01
+5.329E-01
cmfd openmc source comparison
-6.484315E-03
-3.411419E-03
-4.321857E-03
-7.194272E-03
-9.907101E-03
-1.046661E-02
-1.050754E-02
-6.523687E-03
-7.212189E-03
-4.425062E-03
-2.540177E-03
+1.571006E-02
+6.945629E-03
+6.838511E-03
+6.183655E-03
+5.138825E-03
+4.362701E-03
+5.558586E-03
+4.188314E-03
+1.837101E-03
+2.737321E-03
+2.529244E-03
cmfd source
-4.224343E-02
-7.503541E-02
-1.009853E-01
-1.238103E-01
-1.301388E-01
-1.425912E-01
-1.353339E-01
-1.134730E-01
-8.830826E-02
-4.808031E-02
+4.240947E-02
+8.226746E-02
+1.180848E-01
+1.328470E-01
+1.412449E-01
+1.424870E-01
+1.269297E-01
+1.096476E-01
+6.953001E-02
+3.455212E-02
diff --git a/tests/regression_tests/cmfd_feed_rolling_window/results_true.dat b/tests/regression_tests/cmfd_feed_rolling_window/results_true.dat
--- a/tests/regression_tests/cmfd_feed_rolling_window/results_true.dat
+++ b/tests/regression_tests/cmfd_feed_rolling_window/results_true.dat
@@ -1,117 +1,117 @@
k-combined:
-1.169526E+00 5.973537E-03
+1.173626E+00 1.098719E-02
tally 1:
-1.115884E+01
-1.253283E+01
-2.176964E+01
-4.753045E+01
-2.988209E+01
-8.948736E+01
-3.426842E+01
-1.176956E+02
-3.817775E+01
-1.464502E+02
-3.802079E+01
-1.449155E+02
-3.407399E+01
-1.166067E+02
-2.938579E+01
-8.673128E+01
-2.126809E+01
-4.540856E+01
-1.105934E+01
-1.229825E+01
+1.101892E+01
+1.218768E+01
+2.036233E+01
+4.152577E+01
+2.937587E+01
+8.637268E+01
+3.502389E+01
+1.231700E+02
+3.804803E+01
+1.453948E+02
+3.822561E+01
+1.465677E+02
+3.456290E+01
+1.198651E+02
+2.904088E+01
+8.470264E+01
+2.111529E+01
+4.463713E+01
+1.147633E+01
+1.326012E+01
tally 2:
-1.064631E+00
-1.133439E+00
-7.584662E-01
-5.752710E-01
-1.898252E+00
-3.603361E+00
-1.330629E+00
-1.770573E+00
-2.737585E+00
-7.494369E+00
-1.949437E+00
-3.800303E+00
-3.313845E+00
-1.098157E+01
-2.356303E+00
-5.552166E+00
-3.735566E+00
-1.395445E+01
-2.657859E+00
-7.064213E+00
-4.052274E+00
-1.642093E+01
-2.864885E+00
-8.207568E+00
-3.385112E+00
-1.145899E+01
-2.358075E+00
-5.560519E+00
-2.776429E+00
-7.708560E+00
-1.960468E+00
-3.843434E+00
-2.240243E+00
-5.018688E+00
-1.549641E+00
-2.401386E+00
-1.092006E+00
-1.192478E+00
-7.441585E-01
-5.537719E-01
+1.010478E+00
+1.021066E+00
+6.902031E-01
+4.763804E-01
+1.899891E+00
+3.609584E+00
+1.322615E+00
+1.749312E+00
+2.756419E+00
+7.597845E+00
+1.955934E+00
+3.825676E+00
+3.818740E+00
+1.458278E+01
+2.704746E+00
+7.315652E+00
+3.920857E+00
+1.537312E+01
+2.843144E+00
+8.083470E+00
+3.835060E+00
+1.470768E+01
+2.728705E+00
+7.445831E+00
+3.510590E+00
+1.232424E+01
+2.497237E+00
+6.236191E+00
+2.717388E+00
+7.384198E+00
+1.903638E+00
+3.623837E+00
+2.207863E+00
+4.874659E+00
+1.563588E+00
+2.444808E+00
+1.289027E+00
+1.661591E+00
+9.022714E-01
+8.140937E-01
tally 3:
-7.295798E-01
-5.322866E-01
-4.986135E-02
-2.486155E-03
-1.280099E+00
-1.638654E+00
-9.022531E-02
-8.140606E-03
-1.859202E+00
-3.456630E+00
-1.234662E-01
-1.524390E-02
-2.274313E+00
-5.172502E+00
-1.234662E-01
-1.524390E-02
-2.548554E+00
-6.495129E+00
-1.531456E-01
-2.345357E-02
-2.773126E+00
-7.690228E+00
-1.733276E-01
-3.004244E-02
-2.270798E+00
-5.156524E+00
-1.673917E-01
-2.801998E-02
-1.887286E+00
-3.561849E+00
-1.507712E-01
-2.273196E-02
-1.480414E+00
-2.191625E+00
-1.127816E-01
-1.271970E-02
-7.126366E-01
-5.078509E-01
-6.054593E-02
-3.665809E-03
+6.593197E-01
+4.347024E-01
+5.216387E-02
+2.721069E-03
+1.266446E+00
+1.603885E+00
+8.298797E-02
+6.887003E-03
+1.888709E+00
+3.567222E+00
+1.398940E-01
+1.957033E-02
+2.616078E+00
+6.843867E+00
+1.588627E-01
+2.523735E-02
+2.733300E+00
+7.470927E+00
+1.944290E-01
+3.780262E-02
+2.643656E+00
+6.988917E+00
+1.612338E-01
+2.599633E-02
+2.410643E+00
+5.811199E+00
+1.754603E-01
+3.078631E-02
+1.838012E+00
+3.378288E+00
+1.126265E-01
+1.268473E-02
+1.500033E+00
+2.250100E+00
+1.102554E-01
+1.215626E-02
+8.750096E-01
+7.656418E-01
+6.757592E-02
+4.566505E-03
tally 4:
-1.416041E-01
-2.005172E-02
+1.490605E-01
+2.221904E-02
0.000000E+00
0.000000E+00
-1.118431E-01
-1.250887E-02
-2.419761E-01
-5.855243E-02
+1.139233E-01
+1.297851E-02
+2.549497E-01
+6.499934E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -128,14 +128,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-2.419761E-01
-5.855243E-02
-1.118431E-01
-1.250887E-02
-2.383966E-01
-5.683292E-02
-3.454391E-01
-1.193281E-01
+2.549497E-01
+6.499934E-02
+1.139233E-01
+1.297851E-02
+2.191337E-01
+4.801958E-02
+3.295187E-01
+1.085826E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -152,14 +152,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-3.454391E-01
-1.193281E-01
-2.383966E-01
-5.683292E-02
-3.449676E-01
-1.190027E-01
-4.324309E-01
-1.869965E-01
+3.295187E-01
+1.085826E-01
+2.191337E-01
+4.801958E-02
+3.872400E-01
+1.499548E-01
+4.595835E-01
+2.112170E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -176,14 +176,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.324309E-01
-1.869965E-01
-3.449676E-01
-1.190027E-01
-4.410209E-01
-1.944994E-01
-4.785286E-01
-2.289896E-01
+4.595835E-01
+2.112170E-01
+3.872400E-01
+1.499548E-01
+4.668106E-01
+2.179121E-01
+5.112307E-01
+2.613569E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -200,14 +200,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.785286E-01
-2.289896E-01
-4.410209E-01
-1.944994E-01
-5.038795E-01
-2.538945E-01
-5.028063E-01
-2.528142E-01
+5.112307E-01
+2.613569E-01
+4.668106E-01
+2.179121E-01
+4.716605E-01
+2.224636E-01
+4.916148E-01
+2.416851E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -224,14 +224,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-5.028063E-01
-2.528142E-01
-5.038795E-01
-2.538945E-01
-4.780368E-01
-2.285192E-01
-4.303602E-01
-1.852099E-01
+4.916148E-01
+2.416851E-01
+4.716605E-01
+2.224636E-01
+4.696777E-01
+2.205972E-01
+4.365150E-01
+1.905453E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -248,14 +248,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.303602E-01
-1.852099E-01
-4.780368E-01
-2.285192E-01
-4.183673E-01
-1.750312E-01
-3.317104E-01
-1.100318E-01
+4.365150E-01
+1.905453E-01
+4.696777E-01
+2.205972E-01
+4.179902E-01
+1.747158E-01
+3.350564E-01
+1.122628E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -272,14 +272,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-3.317104E-01
-1.100318E-01
-4.183673E-01
-1.750312E-01
-3.797671E-01
-1.442230E-01
-2.636003E-01
-6.948514E-02
+3.350564E-01
+1.122628E-01
+4.179902E-01
+1.747158E-01
+3.743487E-01
+1.401370E-01
+2.400661E-01
+5.763172E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -296,14 +296,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-2.636003E-01
-6.948514E-02
-3.797671E-01
-1.442230E-01
-2.686240E-01
-7.215888E-02
-1.324766E-01
-1.755005E-02
+2.400661E-01
+5.763172E-02
+3.743487E-01
+1.401370E-01
+3.063657E-01
+9.385994E-02
+1.605078E-01
+2.576275E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -320,12 +320,12 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-1.324766E-01
-1.755005E-02
-2.686240E-01
-7.215888E-02
-1.444839E-01
-2.087560E-02
+1.605078E-01
+2.576275E-02
+3.063657E-01
+9.385994E-02
+1.700639E-01
+2.892174E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -345,119 +345,119 @@ tally 4:
0.000000E+00
0.000000E+00
tally 5:
-7.285713E-01
-5.308161E-01
-1.056136E-01
-1.115423E-02
-1.280099E+00
-1.638654E+00
-1.717497E-01
-2.949797E-02
-1.859202E+00
-3.456630E+00
-2.285372E-01
-5.222927E-02
-2.274313E+00
-5.172502E+00
-2.636808E-01
-6.952757E-02
-2.547588E+00
-6.490203E+00
-2.914026E-01
-8.491545E-02
-2.773126E+00
-7.690228E+00
-3.908576E-01
-1.527696E-01
-2.269831E+00
-5.152135E+00
-3.279256E-01
-1.075352E-01
-1.886272E+00
-3.558024E+00
-2.679083E-01
-7.177487E-02
-1.479436E+00
-2.188731E+00
-2.362981E-01
-5.583681E-02
-7.126366E-01
-5.078509E-01
-1.015892E-01
-1.032038E-02
+6.593197E-01
+4.347024E-01
+1.314196E-01
+1.727112E-02
+1.266446E+00
+1.603885E+00
+2.002491E-01
+4.009970E-02
+1.888709E+00
+3.567222E+00
+2.444522E-01
+5.975686E-02
+2.616078E+00
+6.843867E+00
+3.234935E-01
+1.046481E-01
+2.733300E+00
+7.470927E+00
+3.309500E-01
+1.095279E-01
+2.643656E+00
+6.988917E+00
+4.025014E-01
+1.620074E-01
+2.410643E+00
+5.811199E+00
+3.050040E-01
+9.302747E-02
+1.838012E+00
+3.378288E+00
+2.800764E-01
+7.844279E-02
+1.500033E+00
+2.250100E+00
+2.324765E-01
+5.404531E-02
+8.750096E-01
+7.656418E-01
+1.256919E-01
+1.579844E-02
cmfd indices
1.000000E+01
1.000000E+00
1.000000E+00
1.000000E+00
k cmfd
-1.188625E+00
-1.172261E+00
-1.172154E+00
-1.176234E+00
-1.161072E+00
-1.174217E+00
-1.176208E+00
-1.183067E+00
-1.208406E+00
-1.220367E+00
-1.208889E+00
+1.166297E+00
+1.148237E+00
+1.162472E+00
+1.187078E+00
+1.188411E+00
+1.194879E+00
+1.216739E+00
+1.216829E+00
+1.196596E+00
+1.199223E+00
+1.211817E+00
cmfd entropy
-3.216548E+00
-3.213244E+00
-3.220132E+00
-3.216556E+00
-3.218184E+00
-3.208592E+00
-3.220641E+00
-3.217076E+00
-3.216257E+00
-3.212578E+00
-3.230102E+00
+3.215349E+00
+3.225577E+00
+3.223357E+00
+3.208828E+00
+3.211072E+00
+3.206578E+00
+3.195799E+00
+3.198236E+00
+3.220074E+00
+3.230249E+00
+3.238015E+00
cmfd balance
-1.65186E-03
-1.76715E-03
-2.25997E-03
-2.27924E-03
-1.67354E-03
-1.72671E-03
-1.79744E-03
-1.99065E-03
-2.56417E-03
-2.45718E-03
-3.26245E-03
+2.07468E-03
+2.39687E-03
+1.51020E-03
+2.07618E-03
+1.89367E-03
+2.00902E-03
+2.54856E-03
+2.43636E-03
+2.48527E-03
+3.07775E-03
+3.37967E-03
cmfd dominance ratio
-5.445E-01
-5.466E-01
-5.539E-01
-5.547E-01
-5.569E-01
-5.518E-01
-5.553E-01
-5.544E-01
-5.474E-01
-5.355E-01
-5.460E-01
+5.505E-01
+5.558E-01
+5.584E-01
+5.477E-01
+5.477E-01
+5.426E-01
+5.335E-01
+5.305E-01
+5.427E-01
+5.484E-01
+5.465E-01
cmfd openmc source comparison
-5.662096E-03
-3.660183E-03
-4.806643E-03
-2.475327E-03
-6.166988E-03
-2.205088E-03
-4.010491E-03
-6.270883E-03
-3.070427E-03
-5.679208E-03
-1.488803E-02
+5.598628E-03
+1.162952E-02
+1.083004E-02
+1.037470E-02
+5.649750E-03
+5.137914E-03
+3.868209E-03
+1.208756E-02
+5.398131E-03
+8.119598E-03
+4.573105E-03
cmfd source
-4.111004E-02
-7.023296E-02
-1.023250E-01
-1.185886E-01
-1.386562E-01
-1.392823E-01
-1.290017E-01
-1.147469E-01
-9.733704E-02
-4.871933E-02
+4.219187E-02
+8.692096E-02
+1.061389E-01
+1.199181E-01
+1.377328E-01
+1.326161E-01
+1.345872E-01
+1.112871E-01
+7.569533E-02
+5.291175E-02
diff --git a/tests/regression_tests/cmfd_nofeed/results_true.dat b/tests/regression_tests/cmfd_nofeed/results_true.dat
--- a/tests/regression_tests/cmfd_nofeed/results_true.dat
+++ b/tests/regression_tests/cmfd_nofeed/results_true.dat
@@ -1,117 +1,117 @@
k-combined:
-1.170405E+00 1.487119E-02
+1.172893E+00 8.095197E-03
tally 1:
-1.172722E+01
-1.378635E+01
-2.122139E+01
-4.511390E+01
-2.936481E+01
-8.649521E+01
-3.553909E+01
-1.265901E+02
-3.862903E+01
-1.497314E+02
-3.683895E+01
-1.358679E+02
-3.373597E+01
-1.140439E+02
-2.810435E+01
-7.932253E+01
-2.098314E+01
-4.409819E+01
-1.105096E+01
-1.224007E+01
+1.156995E+01
+1.347019E+01
+2.120053E+01
+4.531200E+01
+2.995993E+01
+8.997889E+01
+3.498938E+01
+1.226414E+02
+3.794510E+01
+1.442188E+02
+3.798115E+01
+1.446436E+02
+3.415954E+01
+1.171635E+02
+2.960329E+01
+8.785532E+01
+2.182231E+01
+4.782353E+01
+1.147379E+01
+1.321150E+01
tally 2:
-2.275408E+01
-2.603315E+01
-1.590700E+01
-1.273395E+01
-4.112322E+01
-8.498758E+01
-2.911800E+01
-4.264070E+01
-5.707453E+01
-1.638375E+02
-4.069300E+01
-8.336155E+01
-6.915962E+01
-2.399628E+02
-4.926800E+01
-1.218497E+02
-7.521027E+01
-2.842789E+02
-5.357900E+01
-1.443468E+02
-7.387401E+01
-2.738660E+02
-5.263400E+01
-1.390611E+02
-6.871266E+01
-2.368771E+02
-4.902000E+01
-1.205569E+02
-5.632046E+01
-1.592677E+02
-3.999300E+01
-8.035469E+01
-4.291289E+01
-9.245946E+01
-3.046000E+01
-4.661878E+01
-2.273666E+01
-2.598211E+01
-1.590800E+01
-1.271433E+01
+2.345900E+01
+2.783672E+01
+1.627300E+01
+1.339749E+01
+4.127267E+01
+8.563716E+01
+2.934800E+01
+4.334439E+01
+5.742644E+01
+1.658158E+02
+4.092600E+01
+8.423842E+01
+6.740126E+01
+2.279288E+02
+4.796500E+01
+1.154602E+02
+7.340327E+01
+2.701349E+02
+5.235900E+01
+1.374186E+02
+7.387392E+01
+2.740829E+02
+5.277400E+01
+1.398425E+02
+6.733428E+01
+2.274414E+02
+4.800100E+01
+1.156206E+02
+5.794970E+01
+1.685421E+02
+4.124600E+01
+8.540686E+01
+4.257013E+01
+9.092401E+01
+3.014500E+01
+4.566369E+01
+2.300274E+01
+2.659051E+01
+1.613400E+01
+1.307448E+01
tally 3:
-1.529800E+01
-1.178010E+01
-1.016076E+00
-5.280687E-02
-2.803900E+01
-3.955010E+01
-1.861024E+00
-1.765351E-01
-3.919400E+01
-7.734526E+01
-2.540695E+00
-3.268959E-01
-4.749400E+01
-1.132677E+02
-3.087604E+00
-4.837647E-01
-5.156500E+01
-1.337335E+02
-3.371014E+00
-5.734875E-01
-5.070500E+01
-1.290569E+02
-3.292766E+00
-5.489854E-01
-4.723400E+01
-1.119247E+02
-2.949932E+00
-4.381745E-01
-3.847900E+01
-7.441953E+01
-2.522868E+00
-3.218962E-01
-2.933900E+01
-4.325593E+01
-1.818016E+00
-1.672765E-01
-1.534700E+01
-1.183573E+01
-9.564025E-01
-4.735079E-02
+1.564900E+01
+1.239852E+01
+1.086873E+00
+6.047264E-02
+2.821700E+01
+4.006730E+01
+1.855830E+00
+1.755984E-01
+3.946300E+01
+7.833997E+01
+2.523142E+00
+3.210725E-01
+4.622500E+01
+1.072588E+02
+2.919735E+00
+4.340292E-01
+5.033400E+01
+1.270010E+02
+3.243022E+00
+5.318534E-01
+5.082400E+01
+1.297502E+02
+3.313898E+00
+5.546608E-01
+4.623700E+01
+1.072944E+02
+2.887766E+00
+4.203084E-01
+3.975000E+01
+7.934279E+01
+2.567158E+00
+3.333121E-01
+2.903500E+01
+4.237270E+01
+1.852070E+00
+1.733821E-01
+1.557800E+01
+1.219084E+01
+9.951884E-01
+5.121758E-02
tally 4:
-3.092000E+00
-4.809100E-01
+3.111000E+00
+4.872850E-01
0.000000E+00
0.000000E+00
-2.628000E+00
-3.509980E-01
-5.388000E+00
-1.458946E+00
+2.794000E+00
+3.972060E-01
+5.520000E+00
+1.535670E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -128,14 +128,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-5.388000E+00
-1.458946E+00
-2.628000E+00
-3.509980E-01
-5.063000E+00
-1.292417E+00
-7.312000E+00
-2.686738E+00
+5.520000E+00
+1.535670E+00
+2.794000E+00
+3.972060E-01
+5.071000E+00
+1.305697E+00
+7.303000E+00
+2.685365E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -152,14 +152,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.312000E+00
-2.686738E+00
-5.063000E+00
-1.292417E+00
-7.115000E+00
-2.542363E+00
-8.719000E+00
-3.819081E+00
+7.303000E+00
+2.685365E+00
+5.071000E+00
+1.305697E+00
+7.015000E+00
+2.471981E+00
+8.545000E+00
+3.670539E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -176,14 +176,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.719000E+00
-3.819081E+00
-7.115000E+00
-2.542363E+00
-8.483000E+00
-3.615549E+00
-9.255000E+00
-4.303287E+00
+8.545000E+00
+3.670539E+00
+7.015000E+00
+2.471981E+00
+8.431000E+00
+3.570057E+00
+9.224000E+00
+4.268004E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -200,14 +200,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-9.255000E+00
-4.303287E+00
-8.483000E+00
-3.615549E+00
-9.375000E+00
-4.416751E+00
-9.330000E+00
-4.375230E+00
+9.224000E+00
+4.268004E+00
+8.431000E+00
+3.570057E+00
+9.217000E+00
+4.259749E+00
+9.305000E+00
+4.340149E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -224,14 +224,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-9.330000E+00
-4.375230E+00
-9.375000E+00
-4.416751E+00
-9.346000E+00
-4.379220E+00
-8.458000E+00
-3.585930E+00
+9.305000E+00
+4.340149E+00
+9.217000E+00
+4.259749E+00
+9.374000E+00
+4.415290E+00
+8.611000E+00
+3.718227E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -248,14 +248,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.458000E+00
-3.585930E+00
-9.346000E+00
-4.379220E+00
-8.671000E+00
-3.770383E+00
-7.062000E+00
-2.505966E+00
+8.611000E+00
+3.718227E+00
+9.374000E+00
+4.415290E+00
+8.515000E+00
+3.639945E+00
+7.056000E+00
+2.501658E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -272,14 +272,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.062000E+00
-2.505966E+00
-8.671000E+00
-3.770383E+00
-7.279000E+00
-2.663587E+00
-4.994000E+00
-1.261468E+00
+7.056000E+00
+2.501658E+00
+8.515000E+00
+3.639945E+00
+7.385000E+00
+2.737677E+00
+5.194000E+00
+1.356022E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -296,14 +296,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-4.994000E+00
-1.261468E+00
-7.279000E+00
-2.663587E+00
-5.492000E+00
-1.515002E+00
-2.772000E+00
-3.896040E-01
+5.194000E+00
+1.356022E+00
+7.385000E+00
+2.737677E+00
+5.436000E+00
+1.481654E+00
+2.756000E+00
+3.843860E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -320,12 +320,12 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-2.772000E+00
-3.896040E-01
-5.492000E+00
-1.515002E+00
-3.022000E+00
-4.608940E-01
+2.756000E+00
+3.843860E-01
+5.436000E+00
+1.481654E+00
+3.030000E+00
+4.643920E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -345,144 +345,144 @@ tally 4:
0.000000E+00
0.000000E+00
tally 5:
-1.529600E+01
-1.177689E+01
-2.229624E+00
-2.514699E-01
-2.803300E+01
-3.953329E+01
-3.889856E+00
-7.678274E-01
-3.918900E+01
-7.732686E+01
-5.211188E+00
-1.378173E+00
-4.748700E+01
-1.132339E+02
-6.595911E+00
-2.211528E+00
-5.155000E+01
-1.336522E+02
-6.673103E+00
-2.248462E+00
-5.069800E+01
-1.290196E+02
-6.907470E+00
-2.412919E+00
-4.722500E+01
-1.118824E+02
-6.200070E+00
-1.954544E+00
-3.847200E+01
-7.439145E+01
-5.385095E+00
-1.462192E+00
-2.933600E+01
-4.324744E+01
-4.014057E+00
-8.142088E-01
-1.534200E+01
-1.182781E+01
-2.076271E+00
-2.273431E-01
+1.564300E+01
+1.238861E+01
+2.090227E+00
+2.262627E-01
+2.821400E+01
+4.005826E+01
+3.870834E+00
+7.614623E-01
+3.945400E+01
+7.830326E+01
+5.290557E+00
+1.422339E+00
+4.621500E+01
+1.072116E+02
+6.144745E+00
+1.903309E+00
+5.032900E+01
+1.269756E+02
+6.867524E+00
+2.373593E+00
+5.081000E+01
+1.296784E+02
+6.456283E+00
+2.130767E+00
+4.623000E+01
+1.072613E+02
+5.931623E+00
+1.776451E+00
+3.974500E+01
+7.932288E+01
+5.339603E+00
+1.456812E+00
+2.902800E+01
+4.235232E+01
+4.102240E+00
+8.519551E-01
+1.557800E+01
+1.219084E+01
+2.137954E+00
+2.347770E-01
cmfd indices
1.000000E+01
1.000000E+00
1.000000E+00
1.000000E+00
k cmfd
-1.161531E+00
-1.181707E+00
-1.176063E+00
-1.168433E+00
-1.173170E+00
-1.174671E+00
-1.176457E+00
-1.177540E+00
-1.180826E+00
-1.174158E+00
-1.171305E+00
-1.172618E+00
-1.170171E+00
-1.173235E+00
-1.172599E+00
-1.177343E+00
+1.129918E+00
+1.148352E+00
+1.143137E+00
+1.145795E+00
+1.147285E+00
+1.148588E+00
+1.148151E+00
+1.162118E+00
+1.165380E+00
+1.162851E+00
+1.163379E+00
+1.166986E+00
+1.167838E+00
+1.171743E+00
+1.170398E+00
+1.169773E+00
cmfd entropy
-3.206619E+00
-3.207385E+00
-3.208853E+00
-3.210825E+00
-3.214820E+00
-3.213490E+00
-3.212717E+00
-3.210590E+00
-3.211948E+00
-3.212156E+00
-3.212900E+00
-3.212275E+00
-3.212766E+00
-3.214205E+00
-3.212717E+00
-3.214169E+00
+3.224769E+00
+3.222795E+00
+3.221174E+00
+3.222164E+00
+3.221025E+00
+3.220967E+00
+3.223497E+00
+3.219213E+00
+3.221679E+00
+3.222084E+00
+3.222281E+00
+3.222540E+00
+3.224614E+00
+3.224193E+00
+3.224925E+00
+3.224367E+00
cmfd balance
-4.99833E-03
-5.81289E-03
-3.45193E-03
-2.84521E-03
-3.72331E-03
-3.07942E-03
-2.58676E-03
-2.19354E-03
-2.11522E-03
-2.02671E-03
-1.71439E-03
-1.62909E-03
-1.43261E-03
-1.26201E-03
-1.40167E-03
-1.26141E-03
+3.90454E-03
+4.33180E-03
+3.77057E-03
+3.16391E-03
+3.11765E-03
+2.59886E-03
+2.81060E-03
+3.25473E-03
+2.68544E-03
+2.01716E-03
+1.89350E-03
+1.79159E-03
+1.51353E-03
+1.48514E-03
+1.50207E-03
+1.44045E-03
cmfd dominance ratio
-5.283E-01
-5.304E-01
-5.310E-01
-5.324E-01
-5.372E-01
-5.369E-01
-5.367E-01
-5.341E-01
-5.353E-01
-5.375E-01
-5.379E-01
-5.372E-01
-5.379E-01
-5.393E-01
-5.384E-01
-5.382E-01
+5.539E-01
+5.522E-01
+5.491E-01
+5.511E-01
+5.506E-01
+5.523E-01
+5.523E-01
+5.473E-01
+5.478E-01
+5.461E-01
+5.462E-01
+5.459E-01
+5.475E-01
+5.463E-01
+5.466E-01
+5.469E-01
cmfd openmc source comparison
-1.291827E-02
-9.488059E-03
-8.538280E-03
-6.820006E-03
-4.300032E-03
-5.486871E-03
-4.493389E-03
-4.913340E-03
-5.132196E-03
-3.342331E-03
-3.094995E-03
-3.553279E-03
-3.284811E-03
-2.492272E-03
-3.062765E-03
-2.632092E-03
+9.875240E-03
+1.119358E-02
+8.513903E-03
+7.728971E-03
+5.993771E-03
+5.837301E-03
+4.861789E-03
+5.624038E-03
+4.297229E-03
+4.029732E-03
+3.669197E-03
+3.598834E-03
+3.023310E-03
+3.347346E-03
+2.943658E-03
+2.764986E-03
cmfd source
-4.280100E-02
-7.944783E-02
-1.091569E-01
-1.329540E-01
-1.451697E-01
-1.413526E-01
-1.258514E-01
-1.067698E-01
-7.656551E-02
-3.993138E-02
+4.561921E-02
+7.896381E-02
+1.084687E-01
+1.264057E-01
+1.408942E-01
+1.438180E-01
+1.247333E-01
+1.100896E-01
+7.897187E-02
+4.203556E-02
diff --git a/tests/regression_tests/cmfd_restart/results_true.dat b/tests/regression_tests/cmfd_restart/results_true.dat
--- a/tests/regression_tests/cmfd_restart/results_true.dat
+++ b/tests/regression_tests/cmfd_restart/results_true.dat
@@ -1,117 +1,117 @@
k-combined:
-1.159021E+00 8.924006E-03
+1.164262E+00 9.207592E-03
tally 1:
-1.140162E+01
-1.306940E+01
-2.093739E+01
-4.404780E+01
-2.914408E+01
-8.521010E+01
-3.483677E+01
-1.216824E+02
-3.778463E+01
-1.429632E+02
-3.810371E+01
-1.455108E+02
-3.465248E+01
-1.207868E+02
-2.862033E+01
-8.218833E+01
-2.086025E+01
-4.365941E+01
-1.130798E+01
-1.286509E+01
+1.156972E+01
+1.339924E+01
+2.136306E+01
+4.567185E+01
+2.859527E+01
+8.195821E+01
+3.470754E+01
+1.207851E+02
+3.766403E+01
+1.422263E+02
+3.778821E+01
+1.432660E+02
+3.573197E+01
+1.278854E+02
+2.849979E+01
+8.135515E+01
+2.073803E+01
+4.303374E+01
+1.112117E+01
+1.242944E+01
tally 2:
-2.234393E+01
-2.516414E+01
-1.555024E+01
-1.218205E+01
-4.087743E+01
-8.401702E+01
-2.883717E+01
-4.185393E+01
-5.635166E+01
-1.595225E+02
-3.998857E+01
-8.040398E+01
-6.887126E+01
-2.379185E+02
-4.903103E+01
-1.206174E+02
-7.452051E+01
-2.785675E+02
-5.295380E+01
-1.406900E+02
-7.495422E+01
-2.819070E+02
-5.333191E+01
-1.427474E+02
-6.921815E+01
-2.408568E+02
-4.928246E+01
-1.221076E+02
-5.668548E+01
-1.612556E+02
-4.035856E+01
-8.181159E+01
-4.259952E+01
-9.112630E+01
-3.026717E+01
-4.600625E+01
-2.310563E+01
-2.688378E+01
-1.615934E+01
-1.315528E+01
+2.388054E+01
+2.875255E+01
+1.667791E+01
+1.403426E+01
+4.224771E+01
+8.942109E+01
+2.993088E+01
+4.490335E+01
+5.689839E+01
+1.625557E+02
+4.043633E+01
+8.212299E+01
+6.764024E+01
+2.297126E+02
+4.807902E+01
+1.161468E+02
+7.314835E+01
+2.684645E+02
+5.203584E+01
+1.359261E+02
+7.375727E+01
+2.733105E+02
+5.252944E+01
+1.386205E+02
+6.909571E+01
+2.397721E+02
+4.922548E+01
+1.217465E+02
+5.685978E+01
+1.621746E+02
+4.051938E+01
+8.237277E+01
+4.185562E+01
+8.784067E+01
+2.983570E+01
+4.467414E+01
+2.238373E+01
+2.520356E+01
+1.566758E+01
+1.234103E+01
tally 3:
-1.496375E+01
-1.128154E+01
-9.905641E-01
-5.125710E-02
-2.774937E+01
-3.877241E+01
-1.786861E+00
-1.627655E-01
-3.849739E+01
-7.453828E+01
-2.494135E+00
-3.158098E-01
-4.724085E+01
-1.119901E+02
-3.031174E+00
-4.653741E-01
-5.096719E+01
-1.303552E+02
-3.254375E+00
-5.351020E-01
-5.133808E+01
-1.322892E+02
-3.383595E+00
-5.798798E-01
-4.756072E+01
-1.137527E+02
-3.001917E+00
-4.558247E-01
-3.887437E+01
-7.593416E+01
-2.517908E+00
-3.221926E-01
-2.910687E+01
-4.255173E+01
-1.817765E+00
-1.678763E-01
-1.557241E+01
-1.222026E+01
-9.852737E-01
-5.002659E-02
+1.609520E+01
+1.307542E+01
+1.033429E+00
+5.510889E-02
+2.877073E+01
+4.149542E+01
+1.964219E+00
+1.954692E-01
+3.896816E+01
+7.629752E+01
+2.484053E+00
+3.103733E-01
+4.634285E+01
+1.079367E+02
+2.974750E+00
+4.468223E-01
+5.007964E+01
+1.259202E+02
+3.181802E+00
+5.103621E-01
+5.058915E+01
+1.286193E+02
+3.249442E+00
+5.337712E-01
+4.744464E+01
+1.131026E+02
+3.067644E+00
+4.736335E-01
+3.900632E+01
+7.634433E+01
+2.443552E+00
+3.028060E-01
+2.874166E+01
+4.146375E+01
+1.810421E+00
+1.671667E-01
+1.509222E+01
+1.145579E+01
+1.014919E+00
+5.391053E-02
tally 4:
-3.047490E+00
-4.661458E-01
+3.148231E+00
+4.974555E-01
0.000000E+00
0.000000E+00
-2.635775E+00
-3.524426E-01
-5.357229E+00
-1.440049E+00
+2.805439E+00
+3.982239E-01
+5.574031E+00
+1.561105E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -128,14 +128,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-5.357229E+00
-1.440049E+00
-2.635775E+00
-3.524426E-01
-4.982072E+00
-1.251449E+00
-7.228146E+00
-2.620353E+00
+5.574031E+00
+1.561105E+00
+2.805439E+00
+3.982239E-01
+5.171038E+00
+1.344877E+00
+7.372031E+00
+2.725420E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -152,14 +152,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.228146E+00
-2.620353E+00
-4.982072E+00
-1.251449E+00
-7.082265E+00
-2.520047E+00
-8.736529E+00
-3.831244E+00
+7.372031E+00
+2.725420E+00
+5.171038E+00
+1.344877E+00
+6.946847E+00
+2.424850E+00
+8.496610E+00
+3.627542E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -176,14 +176,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.736529E+00
-3.831244E+00
-7.082265E+00
-2.520047E+00
-8.474631E+00
-3.607043E+00
-9.346623E+00
-4.390819E+00
+8.496610E+00
+3.627542E+00
+6.946847E+00
+2.424850E+00
+8.479501E+00
+3.607280E+00
+9.261869E+00
+4.305912E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -200,14 +200,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-9.346623E+00
-4.390819E+00
-8.474631E+00
-3.607043E+00
-9.496684E+00
-4.522478E+00
-9.532822E+00
-4.559003E+00
+9.261869E+00
+4.305912E+00
+8.479501E+00
+3.607280E+00
+9.232858E+00
+4.278432E+00
+9.306384E+00
+4.348594E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -224,14 +224,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-9.532822E+00
-4.559003E+00
-9.496684E+00
-4.522478E+00
-9.404949E+00
-4.446260E+00
-8.550930E+00
-3.668401E+00
+9.306384E+00
+4.348594E+00
+9.232858E+00
+4.278432E+00
+9.299764E+00
+4.347828E+00
+8.511976E+00
+3.639893E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -248,14 +248,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-8.550930E+00
-3.668401E+00
-9.404949E+00
-4.446260E+00
-8.785273E+00
-3.874792E+00
-7.128863E+00
-2.554326E+00
+8.511976E+00
+3.639893E+00
+9.299764E+00
+4.347828E+00
+8.726086E+00
+3.819567E+00
+7.147277E+00
+2.562747E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -272,14 +272,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-7.128863E+00
-2.554326E+00
-8.785273E+00
-3.874792E+00
-7.408549E+00
-2.755885E+00
-5.094992E+00
-1.305737E+00
+7.147277E+00
+2.562747E+00
+8.726086E+00
+3.819567E+00
+7.218790E+00
+2.612243E+00
+5.018287E+00
+1.263077E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -296,14 +296,14 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-5.094992E+00
-1.305737E+00
-7.408549E+00
-2.755885E+00
-5.532149E+00
-1.537289E+00
-2.812344E+00
-3.997146E-01
+5.018287E+00
+1.263077E+00
+7.218790E+00
+2.612243E+00
+5.443494E+00
+1.487018E+00
+2.732334E+00
+3.773047E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -320,12 +320,12 @@ tally 4:
0.000000E+00
0.000000E+00
0.000000E+00
-2.812344E+00
-3.997146E-01
-5.532149E+00
-1.537289E+00
-3.063251E+00
-4.728672E-01
+2.732334E+00
+3.773047E-01
+5.443494E+00
+1.487018E+00
+3.044773E+00
+4.655756E-01
0.000000E+00
0.000000E+00
0.000000E+00
@@ -345,144 +345,144 @@ tally 4:
0.000000E+00
0.000000E+00
tally 5:
-1.496000E+01
-1.127586E+01
-2.280081E+00
-2.675609E-01
-2.774503E+01
-3.876011E+01
-3.908836E+00
-7.703029E-01
-3.848706E+01
-7.449836E+01
-5.299924E+00
-1.422782E+00
-4.723172E+01
-1.119459E+02
-6.450156E+00
-2.105590E+00
-5.095931E+01
-1.303132E+02
-7.050681E+00
-2.515092E+00
-5.133412E+01
-1.322694E+02
-6.853429E+00
-2.384127E+00
-4.754621E+01
-1.136848E+02
-6.370026E+00
-2.058896E+00
-3.886829E+01
-7.591042E+01
-5.266816E+00
-1.400495E+00
-2.910277E+01
-4.253981E+01
-4.090844E+00
-8.442500E-01
-1.556949E+01
-1.221526E+01
-2.266123E+00
-2.641551E-01
+1.609029E+01
+1.306718E+01
+2.230601E+00
+2.559496E-01
+2.876780E+01
+4.148686E+01
+3.835952E+00
+7.456562E-01
+3.895738E+01
+7.625344E+01
+4.841024E+00
+1.197335E+00
+4.633595E+01
+1.079043E+02
+6.236821E+00
+1.963311E+00
+5.007472E+01
+1.258967E+02
+6.749745E+00
+2.297130E+00
+5.058336E+01
+1.285894E+02
+6.727612E+00
+2.315656E+00
+4.743869E+01
+1.130735E+02
+6.338193E+00
+2.042159E+00
+3.899838E+01
+7.631289E+01
+5.187573E+00
+1.359733E+00
+2.873434E+01
+4.144233E+01
+3.815610E+00
+7.367619E-01
+1.509020E+01
+1.145268E+01
+2.125767E+00
+2.341894E-01
cmfd indices
1.000000E+01
1.000000E+00
1.000000E+00
1.000000E+00
k cmfd
-1.161531E+00
-1.182724E+00
-1.169653E+00
-1.164722E+00
-1.164583E+00
-1.162952E+00
-1.167024E+00
-1.164509E+00
-1.165693E+00
-1.170623E+00
-1.166618E+00
-1.170805E+00
-1.170962E+00
-1.170964E+00
-1.168224E+00
-1.169864E+00
+1.129918E+00
+1.143848E+00
+1.147976E+00
+1.151534E+00
+1.152378E+00
+1.148219E+00
+1.150402E+00
+1.154647E+00
+1.156159E+00
+1.160048E+00
+1.167441E+00
+1.168163E+00
+1.168629E+00
+1.164120E+00
+1.165051E+00
+1.169177E+00
cmfd entropy
-3.206619E+00
-3.205815E+00
-3.208678E+00
-3.210820E+00
-3.217023E+00
-3.215014E+00
-3.214592E+00
-3.215913E+00
-3.214998E+00
-3.213644E+00
-3.210755E+00
-3.210496E+00
-3.212488E+00
-3.211553E+00
-3.212999E+00
-3.214052E+00
+3.224769E+00
+3.225945E+00
+3.227421E+00
+3.226174E+00
+3.224429E+00
+3.227049E+00
+3.230710E+00
+3.230315E+00
+3.226825E+00
+3.226655E+00
+3.226588E+00
+3.224155E+00
+3.223246E+00
+3.222640E+00
+3.223920E+00
+3.222838E+00
cmfd balance
-4.99833E-03
-5.64677E-03
-3.62795E-03
-3.91962E-03
-3.87172E-03
-2.48450E-03
-3.15554E-03
-2.49335E-03
-2.31973E-03
-2.19156E-03
-2.31352E-03
-2.03401E-03
-1.80242E-03
-1.65868E-03
-1.47543E-03
-1.49706E-03
+3.90454E-03
+4.08089E-03
+3.46511E-03
+4.09535E-03
+2.62009E-03
+2.23559E-03
+2.54033E-03
+2.12799E-03
+2.25864E-03
+1.85766E-03
+1.49916E-03
+1.63471E-03
+1.48377E-03
+1.59800E-03
+1.37354E-03
+1.32853E-03
cmfd dominance ratio
-5.283E-01
-5.289E-01
-5.305E-01
-5.327E-01
-5.377E-01
-5.360E-01
-5.353E-01
-4.983E-01
-5.379E-01
-5.370E-01
-5.359E-01
-5.349E-01
-5.364E-01
-5.347E-01
-5.360E-01
-5.378E-01
+5.539E-01
+5.537E-01
+5.536E-01
+5.515E-01
+5.512E-01
+5.514E-01
+5.518E-01
+5.507E-01
+5.500E-01
+5.497E-01
+5.477E-01
+5.461E-01
+5.444E-01
+5.445E-01
+5.454E-01
+5.441E-01
cmfd openmc source comparison
-1.291827E-02
-1.027137E-02
-8.738370E-03
-6.854409E-03
-4.188357E-03
-4.941359E-03
-5.139239E-03
-4.244784E-03
-4.240559E-03
-3.375424E-03
-3.716858E-03
-3.595700E-03
-3.626952E-03
-3.999302E-03
-2.431760E-03
-1.673200E-03
+9.875240E-03
+1.106163E-02
+9.847628E-03
+6.065921E-03
+5.772039E-03
+4.615656E-03
+4.244331E-03
+3.694299E-03
+3.545814E-03
+3.213063E-03
+3.467537E-03
+3.383489E-03
+3.697591E-03
+3.937358E-03
+3.369124E-03
+3.190359E-03
cmfd source
-4.185460E-02
-7.636314E-02
-1.075536E-01
-1.307167E-01
-1.400879E-01
-1.459944E-01
-1.297413E-01
-1.084649E-01
-7.772031E-02
-4.150306E-02
+4.360494E-02
+8.397599E-02
+1.074181E-01
+1.294531E-01
+1.385611E-01
+1.407934E-01
+1.325191E-01
+1.044311E-01
+7.660359E-02
+4.263941E-02
diff --git a/tests/regression_tests/complex_cell/results_true.dat b/tests/regression_tests/complex_cell/results_true.dat
--- a/tests/regression_tests/complex_cell/results_true.dat
+++ b/tests/regression_tests/complex_cell/results_true.dat
@@ -1,11 +1,11 @@
k-combined:
-2.490321E-01 1.083676E-03
+2.564169E-01 4.095378E-03
tally 1:
-2.617769E+00
-1.371478E+00
-2.716496E+00
-1.476169E+00
-1.005297E+00
-2.026100E-01
-1.075286E-01
-2.316593E-03
+2.607144E+00
+1.360414E+00
+2.681079E+00
+1.439354E+00
+9.627534E-01
+1.855496E-01
+1.123751E-01
+2.530233E-03
diff --git a/tests/regression_tests/confidence_intervals/results_true.dat b/tests/regression_tests/confidence_intervals/results_true.dat
--- a/tests/regression_tests/confidence_intervals/results_true.dat
+++ b/tests/regression_tests/confidence_intervals/results_true.dat
@@ -1,5 +1,5 @@
k-combined:
-2.679617E-01 1.158917E-02
+2.759923E-01 6.988588E-03
tally 1:
-6.693704E+01
-5.643483E+02
+6.167984E+01
+4.772717E+02
diff --git a/tests/regression_tests/cpp_driver/results_true.dat b/tests/regression_tests/cpp_driver/results_true.dat
--- a/tests/regression_tests/cpp_driver/results_true.dat
+++ b/tests/regression_tests/cpp_driver/results_true.dat
@@ -1,13 +1,13 @@
k-combined:
-1.902610E+00 1.901530E-02
+1.933305E+00 1.300360E-02
tally 1:
-9.580351E+01
-1.031580E+03
-2.745984E+01
-8.430494E+01
-9.422158E+01
-9.919885E+02
-2.174849E+02
-5.292948E+03
-2.174849E+02
-5.292948E+03
+9.552846E+01
+1.019358E+03
+2.887973E+01
+9.308509E+01
+9.732441E+01
+1.059022E+03
+2.217326E+02
+5.486892E+03
+2.217326E+02
+5.486892E+03
diff --git a/tests/regression_tests/dagmc/external/results_true.dat b/tests/regression_tests/dagmc/external/results_true.dat
--- a/tests/regression_tests/dagmc/external/results_true.dat
+++ b/tests/regression_tests/dagmc/external/results_true.dat
@@ -1,5 +1,5 @@
k-combined:
-8.426936E-01 5.715847E-02
+9.118190E-01 3.615552E-02
tally 1:
-8.093843E+00
-1.328829E+01
+8.430103E+00
+1.442878E+01
diff --git a/tests/regression_tests/dagmc/legacy/results_true.dat b/tests/regression_tests/dagmc/legacy/results_true.dat
--- a/tests/regression_tests/dagmc/legacy/results_true.dat
+++ b/tests/regression_tests/dagmc/legacy/results_true.dat
@@ -1,5 +1,5 @@
k-combined:
-8.426936E-01 5.715847E-02
+9.118190E-01 3.615552E-02
tally 1:
-8.093843E+00
-1.328829E+01
+8.430103E+00
+1.442878E+01
diff --git a/tests/regression_tests/dagmc/refl/results_true.dat b/tests/regression_tests/dagmc/refl/results_true.dat
--- a/tests/regression_tests/dagmc/refl/results_true.dat
+++ b/tests/regression_tests/dagmc/refl/results_true.dat
@@ -1,5 +1,5 @@
k-combined:
-2.130286E+00 2.412252E-02
+2.035173E+00 3.967029E-02
tally 1:
-1.177815E+01
-2.806871E+01
+1.064492E+01
+2.301019E+01
diff --git a/tests/regression_tests/dagmc/universes/results_true.dat b/tests/regression_tests/dagmc/universes/results_true.dat
--- a/tests/regression_tests/dagmc/universes/results_true.dat
+++ b/tests/regression_tests/dagmc/universes/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-9.436168E-01 2.905559E-02
+9.156561E-01 4.398617E-02
diff --git a/tests/regression_tests/density/results_true.dat b/tests/regression_tests/density/results_true.dat
--- a/tests/regression_tests/density/results_true.dat
+++ b/tests/regression_tests/density/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.097336E+00 2.305434E-02
+1.110057E+00 1.303260E-02
diff --git a/tests/regression_tests/deplete_with_transport/last_step_reference_materials.xml b/tests/regression_tests/deplete_with_transport/last_step_reference_materials.xml
--- a/tests/regression_tests/deplete_with_transport/last_step_reference_materials.xml
+++ b/tests/regression_tests/deplete_with_transport/last_step_reference_materials.xml
@@ -4,1001 +4,1001 @@
<density units="sum" />
<nuclide ao="0.046295399999999994" name="O16" />
<nuclide ao="0.00011276839999999999" name="O17" />
- <nuclide ao="4.62489782739765e-07" name="Cs135" />
- <nuclide ao="8.513845108222934e-09" name="Gd156" />
- <nuclide ao="3.6422790646859405e-10" name="Gd157" />
- <nuclide ao="1.2506256160444458e-08" name="I135" />
- <nuclide ao="1.0044833338996991e-05" name="U234" />
- <nuclide ao="0.0010135760878333647" name="U235" />
- <nuclide ao="0.022134354214267578" name="U238" />
- <nuclide ao="6.021515908249729e-09" name="Xe135" />
- <nuclide ao="1.8945262713301022e-06" name="Xe136" />
+ <nuclide ao="4.418048979824424e-07" name="Cs135" />
+ <nuclide ao="7.25497932072497e-09" name="Gd156" />
+ <nuclide ao="4.6150717323028846e-10" name="Gd157" />
+ <nuclide ao="8.610759132296853e-09" name="I135" />
+ <nuclide ao="1.0044759509631791e-05" name="U234" />
+ <nuclide ao="0.0010213199681434208" name="U235" />
+ <nuclide ao="0.022134492490418312" name="U238" />
+ <nuclide ao="4.8988835309280406e-09" name="Xe135" />
+ <nuclide ao="1.5016036273208697e-06" name="Xe136" />
</material>
<material depletable="true" id="2" temperature="293.6" volume="0.06674732823364922">
<density units="sum" />
<nuclide ao="0.046295399999999994" name="O16" />
<nuclide ao="0.00011276839999999999" name="O17" />
- <nuclide ao="4.1317192551597164e-07" name="Cs135" />
- <nuclide ao="7.1951197683939435e-09" name="Gd156" />
- <nuclide ao="4.554662978016352e-10" name="Gd157" />
- <nuclide ao="9.143600937356816e-09" name="I135" />
- <nuclide ao="1.004460107410099e-05" name="U234" />
- <nuclide ao="0.0010219836045364463" name="U235" />
- <nuclide ao="0.022134432003405754" name="U238" />
- <nuclide ao="4.881875416775785e-09" name="Xe135" />
- <nuclide ao="1.4950302645958752e-06" name="Xe136" />
+ <nuclide ao="4.7109992148358017e-07" name="Cs135" />
+ <nuclide ao="7.042063886012849e-09" name="Gd156" />
+ <nuclide ao="6.027071902372695e-10" name="Gd157" />
+ <nuclide ao="7.95412959144086e-09" name="I135" />
+ <nuclide ao="1.0044351820092838e-05" name="U234" />
+ <nuclide ao="0.001024086327318598" name="U235" />
+ <nuclide ao="0.0221342327478446" name="U238" />
+ <nuclide ao="4.9730371223377224e-09" name="Xe135" />
+ <nuclide ao="1.3283930207935904e-06" name="Xe136" />
</material>
<material depletable="true" id="3" temperature="293.6" volume="0.06674732823364922">
<density units="sum" />
<nuclide ao="0.046295399999999994" name="O16" />
<nuclide ao="0.00011276839999999999" name="O17" />
- <nuclide ao="4.4233023267926427e-07" name="Cs135" />
- <nuclide ao="7.650057506928347e-09" name="Gd156" />
- <nuclide ao="4.381381122619264e-10" name="Gd157" />
- <nuclide ao="1.1144702868821656e-08" name="I135" />
- <nuclide ao="1.0044728829940631e-05" name="U234" />
- <nuclide ao="0.0010193377809846768" name="U235" />
- <nuclide ao="0.022134335403001696" name="U238" />
- <nuclide ao="5.174637175809274e-09" name="Xe135" />
- <nuclide ao="1.6074048322782988e-06" name="Xe136" />
+ <nuclide ao="4.519688238646543e-07" name="Cs135" />
+ <nuclide ao="7.390520655992046e-09" name="Gd156" />
+ <nuclide ao="6.113962449652282e-10" name="Gd157" />
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+ <nuclide ao="1.4925022858546866e-06" name="Xe136" />
</material>
<material depletable="true" id="4" temperature="293.6" volume="0.06674732823364922">
<density units="sum" />
<nuclide ao="0.046295399999999994" name="O16" />
<nuclide ao="0.00011276839999999999" name="O17" />
- <nuclide ao="4.542189401531697e-07" name="Cs135" />
- <nuclide ao="7.626788139129838e-09" name="Gd156" />
- <nuclide ao="4.554036803723083e-10" name="Gd157" />
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- <nuclide ao="5.204386319535494e-09" name="Xe135" />
- <nuclide ao="1.584256968309388e-06" name="Xe136" />
+ <nuclide ao="4.6103855622977077e-07" name="Cs135" />
+ <nuclide ao="7.2542350965307454e-09" name="Gd156" />
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+ <nuclide ao="1.4782292624287545e-06" name="Xe136" />
</material>
<material depletable="true" id="5" temperature="293.6" volume="0.06674732823364922">
<density units="sum" />
<nuclide ao="0.0464035" name="O16" />
- <nuclide ao="4.2096758498059444e-07" name="Cs135" />
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- <nuclide ao="4.953957753020382e-09" name="Xe135" />
- <nuclide ao="4.2224989343743e-07" name="Xe136" />
+ <nuclide ao="4.606890661382998e-07" name="Cs135" />
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</material>
<material depletable="true" id="6" temperature="293.6" volume="0.06674732823364922">
<density units="sum" />
<nuclide ao="0.046295399999999994" name="O16" />
<nuclide ao="0.00011276839999999999" name="O17" />
- <nuclide ao="4.3856345758280014e-07" name="Cs135" />
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- <nuclide ao="5.070841178646676e-09" name="Xe135" />
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</material>
<material depletable="true" id="7" temperature="293.6" volume="0.06674732823364922">
<density units="sum" />
<nuclide ao="0.046295399999999994" name="O16" />
<nuclide ao="0.00011276839999999999" name="O17" />
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</material>
<material depletable="true" id="8" temperature="293.6" volume="0.06674732823364922">
<density units="sum" />
<nuclide ao="0.046295399999999994" name="O16" />
<nuclide ao="0.00011276839999999999" name="O17" />
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</material>
<material depletable="true" id="9" temperature="293.6" volume="0.06674732823364922">
<density units="sum" />
<nuclide ao="0.046295399999999994" name="O16" />
<nuclide ao="0.00011276839999999999" name="O17" />
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<material depletable="true" id="10" temperature="293.6" volume="0.06674732823364922">
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<material depletable="true" id="11" temperature="293.6" volume="0.06674732823364922">
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</material>
<material depletable="true" id="12" temperature="293.6" volume="0.06674732823364922">
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<material depletable="true" id="13" temperature="293.6" volume="0.06674732823364922">
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- <nuclide ao="5.264268767954928e-09" name="Xe135" />
- <nuclide ao="1.914549450091292e-06" name="Xe136" />
+ <nuclide ao="4.6223836643047225e-07" name="Cs135" />
+ <nuclide ao="7.953476977467476e-09" name="Gd156" />
+ <nuclide ao="4.1027175102378134e-10" name="Gd157" />
+ <nuclide ao="9.796423510520291e-09" name="I135" />
+ <nuclide ao="1.0044187649332334e-05" name="U234" />
+ <nuclide ao="0.0010170353834330855" name="U235" />
+ <nuclide ao="0.02213437255948415" name="U238" />
+ <nuclide ao="5.099103090678887e-09" name="Xe135" />
+ <nuclide ao="1.7121460729487166e-06" name="Xe136" />
</material>
<material depletable="true" id="70" temperature="293.6" volume="0.06674732823364922">
<density units="sum" />
<nuclide ao="0.046295399999999994" name="O16" />
<nuclide ao="0.00011276839999999999" name="O17" />
- <nuclide ao="4.3531353442394307e-07" name="Cs135" />
- <nuclide ao="7.81003289792918e-09" name="Gd156" />
- <nuclide ao="4.231882305801109e-10" name="Gd157" />
- <nuclide ao="9.994767275045177e-09" name="I135" />
- <nuclide ao="1.0044404992700028e-05" name="U234" />
- <nuclide ao="0.00101745168907518" name="U235" />
- <nuclide ao="0.02213450398339581" name="U238" />
- <nuclide ao="5.086631577630462e-09" name="Xe135" />
- <nuclide ao="1.714351229930211e-06" name="Xe136" />
+ <nuclide ao="4.6649971611519487e-07" name="Cs135" />
+ <nuclide ao="9.025781285565924e-09" name="Gd156" />
+ <nuclide ao="3.1907017092468375e-10" name="Gd157" />
+ <nuclide ao="1.4711477971416576e-08" name="I135" />
+ <nuclide ao="1.0043737061582427e-05" name="U234" />
+ <nuclide ao="0.0010106766372541289" name="U235" />
+ <nuclide ao="0.022134240991070177" name="U238" />
+ <nuclide ao="5.458886765350308e-09" name="Xe135" />
+ <nuclide ao="2.046679694527426e-06" name="Xe136" />
</material>
<material depletable="true" id="71" temperature="293.6" volume="0.06674732823364922">
<density units="sum" />
<nuclide ao="0.046295399999999994" name="O16" />
<nuclide ao="0.00011276839999999999" name="O17" />
- <nuclide ao="4.255300202203111e-07" name="Cs135" />
- <nuclide ao="7.426043977046747e-09" name="Gd156" />
- <nuclide ao="3.377872666455574e-10" name="Gd157" />
- <nuclide ao="1.1422719702197714e-08" name="I135" />
- <nuclide ao="1.0044829773222666e-05" name="U234" />
- <nuclide ao="0.001018948265719757" name="U235" />
- <nuclide ao="0.022134724441539442" name="U238" />
- <nuclide ao="5.2177995610820925e-09" name="Xe135" />
- <nuclide ao="1.6384969094902849e-06" name="Xe136" />
+ <nuclide ao="4.6163611951434233e-07" name="Cs135" />
+ <nuclide ao="8.092676349588978e-09" name="Gd156" />
+ <nuclide ao="4.0155978971538995e-10" name="Gd157" />
+ <nuclide ao="1.1255710238096574e-08" name="I135" />
+ <nuclide ao="1.004408015645573e-05" name="U234" />
+ <nuclide ao="0.0010160767932069026" name="U235" />
+ <nuclide ao="0.02213440485813173" name="U238" />
+ <nuclide ao="6.106545578915884e-09" name="Xe135" />
+ <nuclide ao="1.7613053602979686e-06" name="Xe136" />
</material>
<material depletable="true" id="72" temperature="293.6" volume="0.06674732823364922">
<density units="sum" />
<nuclide ao="0.046295399999999994" name="O16" />
<nuclide ao="0.00011276839999999999" name="O17" />
- <nuclide ao="4.298921456967344e-07" name="Cs135" />
- <nuclide ao="7.472175332876386e-09" name="Gd156" />
- <nuclide ao="4.695600230063656e-10" name="Gd157" />
- <nuclide ao="8.590922950164814e-09" name="I135" />
- <nuclide ao="1.0045021051031072e-05" name="U234" />
- <nuclide ao="0.0010198929186005497" name="U235" />
- <nuclide ao="0.02213446910874194" name="U238" />
- <nuclide ao="4.695283130627553e-09" name="Xe135" />
- <nuclide ao="1.5908358918951317e-06" name="Xe136" />
+ <nuclide ao="4.5571123667085124e-07" name="Cs135" />
+ <nuclide ao="6.92888783217973e-09" name="Gd156" />
+ <nuclide ao="4.375317133467861e-10" name="Gd157" />
+ <nuclide ao="8.93489066848444e-09" name="I135" />
+ <nuclide ao="1.004461017444276e-05" name="U234" />
+ <nuclide ao="0.0010236806449050182" name="U235" />
+ <nuclide ao="0.02213444447231895" name="U238" />
+ <nuclide ao="5.2257746760182805e-09" name="Xe135" />
+ <nuclide ao="1.360904087177153e-06" name="Xe136" />
</material>
<material id="73" temperature="293.6" volume="0.017528298008244847">
<density units="sum" />
diff --git a/tests/regression_tests/deplete_with_transport/test_reference.h5 b/tests/regression_tests/deplete_with_transport/test_reference.h5
Binary files a/tests/regression_tests/deplete_with_transport/test_reference.h5 and b/tests/regression_tests/deplete_with_transport/test_reference.h5 differ
diff --git a/tests/regression_tests/diff_tally/results_true.dat b/tests/regression_tests/diff_tally/results_true.dat
--- a/tests/regression_tests/diff_tally/results_true.dat
+++ b/tests/regression_tests/diff_tally/results_true.dat
@@ -1,27 +1,27 @@
d_material,d_nuclide,d_variable,score,mean,std. dev.
-3,,density,flux,-8.9862333e+00,2.7508460e+00
-3,,density,flux,-1.9778752e+01,3.5926341e+00
-1,,density,flux,-2.6861000e-01,3.8449483e-02
-1,,density,flux,-3.7643515e-01,1.8991066e-01
-1,O16,nuclide_density,flux,-2.5795663e+00,1.6620453e+01
-1,O16,nuclide_density,flux,7.2861106e+00,1.5941849e+01
-1,U235,nuclide_density,flux,-2.2849358e+03,3.9506163e+02
-1,U235,nuclide_density,flux,-2.7845978e+03,5.6693457e+02
-1,,temperature,flux,-1.8666344e-04,1.1088646e-04
-1,,temperature,flux,9.2264971e-05,8.7268407e-05
-3,,density,total,-4.1447663e+00,1.1453915e+00
-3,,density,absorption,-6.0174688e-01,1.0525787e-01
-3,,density,scatter,-3.5430194e+00,1.0499557e+00
-3,,density,fission,-2.8547461e-01,6.7402688e-02
-3,,density,nu-fission,-6.9988357e-01,1.6360007e-01
-3,,density,total,-3.7715161e-01,1.0166405e-01
-3,,density,absorption,-3.3327322e-01,8.9912373e-02
-3,,density,scatter,-4.3878393e-02,1.3801869e-02
-3,,density,fission,-2.7256167e-01,7.1483193e-02
-3,,density,nu-fission,-6.6439453e-01,1.7417261e-01
-3,,density,total,-2.3838461e+00,4.2331432e+00
-3,,density,absorption,-5.7877951e-02,5.3522562e-02
-3,,density,scatter,-2.3259682e+00,4.1799423e+00
+3,,density,flux,-8.7368155e+00,1.5577812e+00
+3,,density,flux,-1.4842625e+01,2.2947682e+00
+1,,density,flux,-2.0922686e-01,4.9935069e-02
+1,,density,flux,-3.4582490e-01,1.7454386e-01
+1,O16,nuclide_density,flux,1.1301782e+01,2.2440389e+01
+1,O16,nuclide_density,flux,3.2481563e+00,3.2342885e+01
+1,U235,nuclide_density,flux,-1.5048665e+03,5.9045681e+02
+1,U235,nuclide_density,flux,-1.6193231e+03,9.7230073e+02
+1,,temperature,flux,-1.0891931e-04,2.3076849e-04
+1,,temperature,flux,-1.3563853e-04,2.0952841e-04
+3,,density,total,-3.9155374e+00,5.4862771e-01
+3,,density,absorption,-4.9210534e-01,3.4700776e-02
+3,,density,scatter,-3.4234320e+00,5.1443821e-01
+3,,density,fission,-3.1088949e-01,8.0540906e-02
+3,,density,nu-fission,-7.6137447e-01,1.9548876e-01
+3,,density,total,-3.8615156e-01,1.0175701e-01
+3,,density,absorption,-3.4458071e-01,9.3381192e-02
+3,,density,scatter,-4.1570854e-02,8.6942039e-03
+3,,density,fission,-2.9864832e-01,8.4711885e-02
+3,,density,nu-fission,-7.2797006e-01,2.0640455e-01
+3,,density,total,1.0491251e+01,9.1787723e+00
+3,,density,absorption,2.9819000e-01,3.0887165e-01
+3,,density,scatter,1.0193061e+01,8.8715930e+00
3,,density,fission,0.0000000e+00,0.0000000e+00
3,,density,nu-fission,0.0000000e+00,0.0000000e+00
3,,density,total,0.0000000e+00,0.0000000e+00
@@ -29,19 +29,19 @@ d_material,d_nuclide,d_variable,score,mean,std. dev.
3,,density,scatter,0.0000000e+00,0.0000000e+00
3,,density,fission,0.0000000e+00,0.0000000e+00
3,,density,nu-fission,0.0000000e+00,0.0000000e+00
-1,,density,total,4.0520294e-01,3.3719992e-02
-1,,density,absorption,1.3915754e-02,1.3515385e-02
-1,,density,scatter,3.9128718e-01,2.2403876e-02
-1,,density,fission,2.4781454e-04,1.0189025e-02
-1,,density,nu-fission,1.2555927e-03,2.4804599e-02
-1,,density,total,5.1306892e-03,1.1784483e-02
-1,,density,absorption,6.1064429e-04,1.1572255e-02
-1,,density,scatter,4.5200449e-03,3.2228853e-04
-1,,density,fission,-1.5830325e-03,1.0334068e-02
-1,,density,nu-fission,-3.8226434e-03,2.5181192e-02
-1,,density,total,-6.6601129e-01,2.0465955e-01
-1,,density,absorption,-1.5334818e-02,4.0664980e-03
-1,,density,scatter,-6.5067647e-01,2.0153765e-01
+1,,density,total,4.7128871e-01,5.7197095e-02
+1,,density,absorption,2.1981833e-02,1.7427232e-02
+1,,density,scatter,4.4930687e-01,4.0030120e-02
+1,,density,fission,6.0712328e-03,1.3719512e-02
+1,,density,nu-fission,1.5474650e-02,3.3437103e-02
+1,,density,total,1.2203418e-02,1.5798741e-02
+1,,density,absorption,7.0228085e-03,1.5294984e-02
+1,,density,scatter,5.1806097e-03,5.0807003e-04
+1,,density,fission,4.1074923e-03,1.3759608e-02
+1,,density,nu-fission,1.0046778e-02,3.3529881e-02
+1,,density,total,-5.2100220e-01,2.7618985e-01
+1,,density,absorption,-1.1039048e-02,6.2043549e-03
+1,,density,scatter,-5.0996315e-01,2.7027892e-01
1,,density,fission,0.0000000e+00,0.0000000e+00
1,,density,nu-fission,0.0000000e+00,0.0000000e+00
1,,density,total,0.0000000e+00,0.0000000e+00
@@ -49,19 +49,19 @@ d_material,d_nuclide,d_variable,score,mean,std. dev.
1,,density,scatter,0.0000000e+00,0.0000000e+00
1,,density,fission,0.0000000e+00,0.0000000e+00
1,,density,nu-fission,0.0000000e+00,0.0000000e+00
-1,O16,nuclide_density,total,4.3895711e+01,8.6765744e+00
-1,O16,nuclide_density,absorption,-7.3377277e-01,1.1652783e+00
-1,O16,nuclide_density,scatter,4.4629484e+01,7.5113743e+00
-1,O16,nuclide_density,fission,-1.0525946e+00,6.2358336e-01
-1,O16,nuclide_density,nu-fission,-2.5950001e+00,1.5266115e+00
-1,O16,nuclide_density,total,-1.0686783e+00,8.1661764e-01
-1,O16,nuclide_density,absorption,-1.0549848e+00,7.2501792e-01
-1,O16,nuclide_density,scatter,-1.3693500e-02,9.5152724e-02
-1,O16,nuclide_density,fission,-9.8026040e-01,6.2874064e-01
-1,O16,nuclide_density,nu-fission,-2.3899304e+00,1.5323042e+00
-1,O16,nuclide_density,total,4.3744802e+00,1.8346830e+01
-1,O16,nuclide_density,absorption,-7.6879459e-03,1.9447931e-01
-1,O16,nuclide_density,scatter,4.3821681e+00,1.8168908e+01
+1,O16,nuclide_density,total,5.5744608e+01,1.3811361e+01
+1,O16,nuclide_density,absorption,2.1284059e+00,3.3353171e+00
+1,O16,nuclide_density,scatter,5.3616202e+01,1.0494347e+01
+1,O16,nuclide_density,fission,6.6058671e-01,1.9263932e+00
+1,O16,nuclide_density,nu-fission,1.5973305e+00,4.6977280e+00
+1,O16,nuclide_density,total,9.8433784e-01,2.4053581e+00
+1,O16,nuclide_density,absorption,9.1167507e-01,2.2565683e+00
+1,O16,nuclide_density,scatter,7.2662768e-02,1.5198625e-01
+1,O16,nuclide_density,fission,6.8845700e-01,1.9451444e+00
+1,O16,nuclide_density,nu-fission,1.6768628e+00,4.7395897e+00
+1,O16,nuclide_density,total,8.1604245e+00,3.7248338e+01
+1,O16,nuclide_density,absorption,2.4903834e-01,4.5609671e-01
+1,O16,nuclide_density,scatter,7.9113862e+00,3.6811434e+01
1,O16,nuclide_density,fission,0.0000000e+00,0.0000000e+00
1,O16,nuclide_density,nu-fission,0.0000000e+00,0.0000000e+00
1,O16,nuclide_density,total,0.0000000e+00,0.0000000e+00
@@ -69,19 +69,19 @@ d_material,d_nuclide,d_variable,score,mean,std. dev.
1,O16,nuclide_density,scatter,0.0000000e+00,0.0000000e+00
1,O16,nuclide_density,fission,0.0000000e+00,0.0000000e+00
1,O16,nuclide_density,nu-fission,0.0000000e+00,0.0000000e+00
-1,U235,nuclide_density,total,-6.4251150e+02,2.3106826e+02
-1,U235,nuclide_density,absorption,1.5311660e+02,8.7788828e+01
-1,U235,nuclide_density,scatter,-7.9562811e+02,1.5432248e+02
-1,U235,nuclide_density,fission,2.3667219e+02,6.4506235e+01
-1,U235,nuclide_density,nu-fission,5.7770896e+02,1.5738708e+02
-1,U235,nuclide_density,total,4.1238071e+02,7.5208565e+01
-1,U235,nuclide_density,absorption,3.0507276e+02,7.3015316e+01
-1,U235,nuclide_density,scatter,1.0730795e+02,3.4182980e+00
-1,U235,nuclide_density,fission,2.3734641e+02,6.4221163e+01
-1,U235,nuclide_density,nu-fission,5.7953503e+02,1.5657365e+02
-1,U235,nuclide_density,total,-5.5174298e+03,1.1185254e+03
-1,U235,nuclide_density,absorption,-1.3416339e+02,3.2272881e+01
-1,U235,nuclide_density,scatter,-5.3832664e+03,1.0864829e+03
+1,U235,nuclide_density,total,-2.8654443e+02,3.3721470e+02
+1,U235,nuclide_density,absorption,2.0329180e+02,1.0522263e+02
+1,U235,nuclide_density,scatter,-4.8983623e+02,2.3237977e+02
+1,U235,nuclide_density,fission,2.6089045e+02,7.2578344e+01
+1,U235,nuclide_density,nu-fission,6.3692044e+02,1.7710877e+02
+1,U235,nuclide_density,total,4.5611633e+02,9.1682367e+01
+1,U235,nuclide_density,absorption,3.3831545e+02,8.5035501e+01
+1,U235,nuclide_density,scatter,1.1780088e+02,7.4128809e+00
+1,U235,nuclide_density,fission,2.6094461e+02,7.2102445e+01
+1,U235,nuclide_density,nu-fission,6.3705705e+02,1.7578950e+02
+1,U235,nuclide_density,total,-4.1342174e+03,1.4666097e+03
+1,U235,nuclide_density,absorption,-1.1329170e+02,3.5066579e+01
+1,U235,nuclide_density,scatter,-4.0209257e+03,1.4320401e+03
1,U235,nuclide_density,fission,0.0000000e+00,0.0000000e+00
1,U235,nuclide_density,nu-fission,0.0000000e+00,0.0000000e+00
1,U235,nuclide_density,total,0.0000000e+00,0.0000000e+00
@@ -89,19 +89,19 @@ d_material,d_nuclide,d_variable,score,mean,std. dev.
1,U235,nuclide_density,scatter,0.0000000e+00,0.0000000e+00
1,U235,nuclide_density,fission,0.0000000e+00,0.0000000e+00
1,U235,nuclide_density,nu-fission,0.0000000e+00,0.0000000e+00
-1,,temperature,total,3.0892324e-05,5.5277596e-05
-1,,temperature,absorption,2.2324596e-05,2.6209954e-05
-1,,temperature,scatter,8.5677277e-06,6.2111314e-05
-1,,temperature,fission,-1.7715856e-05,1.2803586e-05
-1,,temperature,nu-fission,-4.3163971e-05,3.1203107e-05
-1,,temperature,total,-2.3895766e-05,1.6226810e-05
-1,,temperature,absorption,-2.2388970e-05,1.6503185e-05
-1,,temperature,scatter,-1.5067967e-06,8.6753589e-07
-1,,temperature,fission,-1.7806576e-05,1.2760443e-05
-1,,temperature,nu-fission,-4.3390060e-05,3.1095620e-05
-1,,temperature,total,1.3388075e-04,1.1361483e-04
-1,,temperature,absorption,1.3825063e-06,1.3898795e-06
-1,,temperature,scatter,1.3249824e-04,1.1224449e-04
+1,,temperature,total,5.3733744e-05,1.1785516e-04
+1,,temperature,absorption,-1.3987780e-05,1.9819801e-05
+1,,temperature,scatter,6.7721524e-05,9.9934995e-05
+1,,temperature,fission,-1.4882696e-05,1.6930666e-05
+1,,temperature,nu-fission,-3.6272065e-05,4.1250892e-05
+1,,temperature,total,-1.8119796e-05,2.2651409e-05
+1,,temperature,absorption,-1.7632076e-05,2.1825006e-05
+1,,temperature,scatter,-4.8771972e-07,1.4270133e-06
+1,,temperature,fission,-1.4890811e-05,1.6935899e-05
+1,,temperature,nu-fission,-3.6292215e-05,4.1263951e-05
+1,,temperature,total,-2.0776498e-04,2.9286552e-04
+1,,temperature,absorption,-3.9068381e-06,3.4912438e-06
+1,,temperature,scatter,-2.0385814e-04,2.8941307e-04
1,,temperature,fission,0.0000000e+00,0.0000000e+00
1,,temperature,nu-fission,0.0000000e+00,0.0000000e+00
1,,temperature,total,0.0000000e+00,0.0000000e+00
@@ -109,68 +109,68 @@ d_material,d_nuclide,d_variable,score,mean,std. dev.
1,,temperature,scatter,0.0000000e+00,0.0000000e+00
1,,temperature,fission,0.0000000e+00,0.0000000e+00
1,,temperature,nu-fission,0.0000000e+00,0.0000000e+00
-3,,density,absorption,-4.3471777e-01,1.4851761e-01
-3,,density,absorption,4.8155520e-02,1.3781656e-01
-1,,density,absorption,9.4994508e-03,2.4533642e-03
-1,,density,absorption,-1.0306958e-02,3.9360517e-03
-1,O16,nuclide_density,absorption,-1.6745789e+00,6.7608522e-01
-1,O16,nuclide_density,absorption,1.2254539e+00,7.5421132e-01
-1,U235,nuclide_density,absorption,7.1093314e+01,1.0278274e+02
-1,U235,nuclide_density,absorption,-1.3158317e+02,1.0057325e+01
-1,,temperature,absorption,-2.8254564e-05,2.2125234e-05
-1,,temperature,absorption,1.3248119e-05,8.9856151e-06
+3,,density,absorption,-4.5579543e-01,5.5532252e-02
+3,,density,absorption,-1.3526251e-02,1.3917291e-01
+1,,density,absorption,3.8695654e-02,1.5823093e-02
+1,,density,absorption,-1.8171150e-02,1.2999773e-03
+1,O16,nuclide_density,absorption,2.0992238e+00,2.7230754e+00
+1,O16,nuclide_density,absorption,-6.8956953e-01,3.3064989e-01
+1,U235,nuclide_density,absorption,2.5000417e+02,7.3334295e+01
+1,U235,nuclide_density,absorption,-1.0832917e+02,1.1517513e+01
+1,,temperature,absorption,1.1819459e-05,4.2090670e-05
+1,,temperature,absorption,-7.2302974e-06,1.5200299e-05
3,,density,nu-fission,0.0000000e+00,0.0000000e+00
-3,,density,scatter,-5.9591692e-01,1.8102644e-01
+3,,density,scatter,-7.6858714e-01,3.2467801e-01
3,,density,nu-fission,0.0000000e+00,0.0000000e+00
-3,,density,scatter,-1.0186140e-04,6.5335918e-04
-3,,density,nu-fission,-7.7216010e-01,6.6235203e-02
-3,,density,scatter,-3.1141316e+00,8.7438594e-01
-3,,density,nu-fission,-7.4472975e-01,6.8932536e-02
-3,,density,scatter,-1.0613299e-02,1.4747505e-02
+3,,density,scatter,3.2513857e-04,3.2513857e-04
+3,,density,nu-fission,-6.4963717e-01,1.8008086e-01
+3,,density,scatter,-2.6911548e+00,2.6336008e-01
+3,,density,nu-fission,-6.3014524e-01,1.8056453e-01
+3,,density,scatter,-3.4247012e-02,2.2649385e-02
3,,density,nu-fission,0.0000000e+00,0.0000000e+00
-3,,density,scatter,-2.3938461e+00,2.0442591e+00
+3,,density,scatter,1.0254549e+01,1.1054242e+01
3,,density,nu-fission,0.0000000e+00,0.0000000e+00
3,,density,scatter,0.0000000e+00,0.0000000e+00
3,,density,nu-fission,0.0000000e+00,0.0000000e+00
-3,,density,scatter,-3.8155549e-02,2.1549075e+00
+3,,density,scatter,2.5022850e-01,2.1207285e+00
3,,density,nu-fission,0.0000000e+00,0.0000000e+00
3,,density,scatter,0.0000000e+00,0.0000000e+00
1,,density,nu-fission,0.0000000e+00,0.0000000e+00
-1,,density,scatter,9.6114352e-03,3.0773624e-02
+1,,density,scatter,8.1153611e-03,3.1226564e-02
1,,density,nu-fission,0.0000000e+00,0.0000000e+00
-1,,density,scatter,-4.8445916e-04,4.1692636e-04
-1,,density,nu-fission,-2.0032982e-02,1.5628598e-02
-1,,density,scatter,3.8609205e-01,2.0651677e-02
-1,,density,nu-fission,-2.4325475e-02,1.6087936e-02
-1,,density,scatter,2.1127093e-03,1.1144847e-03
+1,,density,scatter,2.3728497e-04,9.7166041e-04
+1,,density,nu-fission,2.6248459e-02,3.9328080e-02
+1,,density,scatter,4.2447769e-01,1.2580873e-02
+1,,density,nu-fission,1.9600074e-02,3.8118776e-02
+1,,density,scatter,8.0978391e-03,2.6585488e-03
1,,density,nu-fission,0.0000000e+00,0.0000000e+00
-1,,density,scatter,-5.6312059e-01,1.2644279e-01
+1,,density,scatter,-3.8358302e-01,2.1525401e-01
1,,density,nu-fission,0.0000000e+00,0.0000000e+00
1,,density,scatter,0.0000000e+00,0.0000000e+00
1,,density,nu-fission,0.0000000e+00,0.0000000e+00
-1,,density,scatter,-9.2583739e-02,1.3802271e-01
+1,,density,scatter,-1.1924803e-01,9.1254221e-02
1,,density,nu-fission,0.0000000e+00,0.0000000e+00
1,,density,scatter,0.0000000e+00,0.0000000e+00
1,O16,nuclide_density,nu-fission,0.0000000e+00,0.0000000e+00
-1,O16,nuclide_density,scatter,2.8010197e-02,9.9675258e-02
-1,O16,nuclide_density,nu-fission,-2.7133439e+00,1.9638343e+00
-1,O16,nuclide_density,scatter,-5.8699167e-02,2.9596632e-01
+1,O16,nuclide_density,scatter,-1.6577061e-01,1.0793192e-01
+1,O16,nuclide_density,nu-fission,2.4995074e+00,5.7946039e+00
+1,O16,nuclide_density,scatter,5.5800956e-01,5.7675606e-01
1,O16,nuclide_density,nu-fission,0.0000000e+00,0.0000000e+00
1,O16,nuclide_density,scatter,0.0000000e+00,0.0000000e+00
1,O16,nuclide_density,nu-fission,0.0000000e+00,0.0000000e+00
1,O16,nuclide_density,scatter,0.0000000e+00,0.0000000e+00
1,U235,nuclide_density,nu-fission,0.0000000e+00,0.0000000e+00
-1,U235,nuclide_density,scatter,1.0007013e+01,5.9794002e+00
-1,U235,nuclide_density,nu-fission,4.3209054e+02,1.5648214e+02
-1,U235,nuclide_density,scatter,4.6100250e+01,2.3766583e+01
+1,U235,nuclide_density,scatter,5.8641633e+00,2.9488422e+00
+1,U235,nuclide_density,nu-fission,6.7444160e+02,1.1308014e+02
+1,U235,nuclide_density,scatter,1.1592472e+02,2.8886339e+01
1,U235,nuclide_density,nu-fission,0.0000000e+00,0.0000000e+00
1,U235,nuclide_density,scatter,0.0000000e+00,0.0000000e+00
1,U235,nuclide_density,nu-fission,0.0000000e+00,0.0000000e+00
1,U235,nuclide_density,scatter,0.0000000e+00,0.0000000e+00
1,,temperature,nu-fission,0.0000000e+00,0.0000000e+00
-1,,temperature,scatter,1.9350898e-06,2.0685006e-06
-1,,temperature,nu-fission,-6.5233572e-05,6.4075926e-05
-1,,temperature,scatter,-7.6629325e-07,7.6629325e-07
+1,,temperature,scatter,-7.7511866e-07,6.4761261e-07
+1,,temperature,nu-fission,-9.5466386e-05,3.1033330e-05
+1,,temperature,scatter,-2.7127084e-06,2.0699253e-07
1,,temperature,nu-fission,0.0000000e+00,0.0000000e+00
1,,temperature,scatter,0.0000000e+00,0.0000000e+00
1,,temperature,nu-fission,0.0000000e+00,0.0000000e+00
diff --git a/tests/regression_tests/distribmat/results_true.dat b/tests/regression_tests/distribmat/results_true.dat
--- a/tests/regression_tests/distribmat/results_true.dat
+++ b/tests/regression_tests/distribmat/results_true.dat
@@ -1,5 +1,5 @@
k-combined:
-1.234870E+00 1.724266E-02
+1.257344E+00 6.246360E-04
Cell
ID = 11
Name =
diff --git a/tests/regression_tests/eigenvalue_genperbatch/results_true.dat b/tests/regression_tests/eigenvalue_genperbatch/results_true.dat
--- a/tests/regression_tests/eigenvalue_genperbatch/results_true.dat
+++ b/tests/regression_tests/eigenvalue_genperbatch/results_true.dat
@@ -1,5 +1,5 @@
k-combined:
-3.029569E-01 9.632511E-05
+3.037481E-01 1.247474E-04
tally 1:
-3.226370E+01
-2.602467E+02
+3.211129E+01
+2.578396E+02
diff --git a/tests/regression_tests/eigenvalue_no_inactive/results_true.dat b/tests/regression_tests/eigenvalue_no_inactive/results_true.dat
--- a/tests/regression_tests/eigenvalue_no_inactive/results_true.dat
+++ b/tests/regression_tests/eigenvalue_no_inactive/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-3.066848E-01 7.260987E-03
+2.998284E-01 7.587782E-03
diff --git a/tests/regression_tests/energy_grid/results_true.dat b/tests/regression_tests/energy_grid/results_true.dat
--- a/tests/regression_tests/energy_grid/results_true.dat
+++ b/tests/regression_tests/energy_grid/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-3.317249E-01 1.079825E-02
+3.152586E-01 1.458068E-03
diff --git a/tests/regression_tests/entropy/results_true.dat b/tests/regression_tests/entropy/results_true.dat
--- a/tests/regression_tests/entropy/results_true.dat
+++ b/tests/regression_tests/entropy/results_true.dat
@@ -1,13 +1,13 @@
k-combined:
-2.987050E-01 1.827430E-03
+3.070134E-01 3.900396E-03
entropy:
7.688862E+00
-8.184416E+00
-8.363034E+00
-8.174200E+00
-8.243373E+00
-8.298547E+00
-8.267346E+00
-8.253347E+00
-8.329508E+00
-8.363320E+00
+8.237960E+00
+8.314772E+00
+8.285254E+00
+8.271486E+00
+8.291355E+00
+8.253349E+00
+8.336726E+00
+8.284741E+00
+8.328102E+00
diff --git a/tests/regression_tests/filter_cellinstance/results_true.dat b/tests/regression_tests/filter_cellinstance/results_true.dat
--- a/tests/regression_tests/filter_cellinstance/results_true.dat
+++ b/tests/regression_tests/filter_cellinstance/results_true.dat
@@ -1,84 +1,84 @@
k-combined:
-1.045340E+00 4.712608E-02
+1.050139E+00 1.886614E-02
tally 1:
-7.410456E-02
-1.481523E-03
-1.225401E-01
-3.736978E-03
-1.383468E-01
-4.249085E-03
-1.197994E-01
-3.155257E-03
-2.966893E-01
-2.045198E-02
-1.570258E-01
-5.313506E-03
-1.655546E-01
-6.093224E-03
-2.749756E-01
-1.582780E-02
-1.184686E-01
-3.543719E-03
-1.354860E-01
-3.990719E-03
-1.299309E-01
-3.988554E-03
-6.794395E-02
-1.135006E-03
-1.061333E+01
-2.508486E+01
-2.767786E+01
-1.781264E+02
-2.898957E+01
-2.015188E+02
-9.951936E+00
-2.345815E+01
-1.061333E+01
-2.508486E+01
-2.767786E+01
-1.781264E+02
-2.898957E+01
-2.015188E+02
-9.951936E+00
-2.345815E+01
+9.724996E-02
+2.784804E-03
+1.146976E-01
+3.173782E-03
+1.698297E-01
+6.569993E-03
+1.158802E-01
+2.959280E-03
+2.533354E-01
+1.539905E-02
+1.908717E-01
+8.360058E-03
+1.738899E-01
+6.713494E-03
+3.172247E-01
+2.124184E-02
+1.363012E-01
+4.653519E-03
+1.698720E-01
+6.753819E-03
+9.934671E-02
+2.371660E-03
+6.038075E-02
+1.204656E-03
+1.038793E+01
+2.590382E+01
+2.841397E+01
+1.865709E+02
+2.786916E+01
+1.923869E+02
+1.085149E+01
+2.907194E+01
+1.038793E+01
+2.590382E+01
+2.841397E+01
+1.865709E+02
+2.786916E+01
+1.923869E+02
+1.085149E+01
+2.907194E+01
tally 2:
-9.951936E+00
-2.345815E+01
-2.898957E+01
-2.015188E+02
-2.767786E+01
-1.781264E+02
-1.061333E+01
-2.508486E+01
-9.951936E+00
-2.345815E+01
-2.898957E+01
-2.015188E+02
-2.767786E+01
-1.781264E+02
-1.061333E+01
-2.508486E+01
-6.794395E-02
-1.135006E-03
-1.299309E-01
-3.988554E-03
-1.354860E-01
-3.990719E-03
-1.184686E-01
-3.543719E-03
-2.749756E-01
-1.582780E-02
-1.655546E-01
-6.093224E-03
-1.570258E-01
-5.313506E-03
-2.966893E-01
-2.045198E-02
-1.197994E-01
-3.155257E-03
-1.383468E-01
-4.249085E-03
-1.225401E-01
-3.736978E-03
-7.410456E-02
-1.481523E-03
+1.085149E+01
+2.907194E+01
+2.786916E+01
+1.923869E+02
+2.841397E+01
+1.865709E+02
+1.038793E+01
+2.590382E+01
+1.085149E+01
+2.907194E+01
+2.786916E+01
+1.923869E+02
+2.841397E+01
+1.865709E+02
+1.038793E+01
+2.590382E+01
+6.038075E-02
+1.204656E-03
+9.934671E-02
+2.371660E-03
+1.698720E-01
+6.753819E-03
+1.363012E-01
+4.653519E-03
+3.172247E-01
+2.124184E-02
+1.738899E-01
+6.713494E-03
+1.908717E-01
+8.360058E-03
+2.533354E-01
+1.539905E-02
+1.158802E-01
+2.959280E-03
+1.698297E-01
+6.569993E-03
+1.146976E-01
+3.173782E-03
+9.724996E-02
+2.784804E-03
diff --git a/tests/regression_tests/filter_distribcell/case-3/results_true.dat b/tests/regression_tests/filter_distribcell/case-3/results_true.dat
--- a/tests/regression_tests/filter_distribcell/case-3/results_true.dat
+++ b/tests/regression_tests/filter_distribcell/case-3/results_true.dat
@@ -1 +1 @@
-d3ecf354b33d09064f43816325f33ec1229d1258255ee8413e83f7ba96ca921b8f4be738c10af99c5376bfe2b6be45976595634efcafddec0d9296eb45ffed3e
\ No newline at end of file
+1d09084dc41305687d53d1e800fb3d0ac3949aa4e1cb0bfbb327d0ec1ad4b74fc97ee73da84b910529296b858aab9b8a5d0924d17ca2cc373625e1a9e197aa94
\ No newline at end of file
diff --git a/tests/regression_tests/filter_mesh/results_true.dat b/tests/regression_tests/filter_mesh/results_true.dat
--- a/tests/regression_tests/filter_mesh/results_true.dat
+++ b/tests/regression_tests/filter_mesh/results_true.dat
@@ -1 +1 @@
-70243ebdb882e4367bf821667a9f4d41dea03eaf8b27d734e014a13e14922b5158cd47b0a7edf3733d4e23ca6a5ab06457220c9138b7e9720acf547f2eaa06e2
\ No newline at end of file
+bd55ee25094f9ad04fda4439f58ef0fed718632c88b9fde411a484dc624dedcd45dee643e14d8b107d8b92757737b8bb3d9a667de5482457d6d8346afffdf657
\ No newline at end of file
diff --git a/tests/regression_tests/filter_translations/results_true.dat b/tests/regression_tests/filter_translations/results_true.dat
--- a/tests/regression_tests/filter_translations/results_true.dat
+++ b/tests/regression_tests/filter_translations/results_true.dat
@@ -1,342 +1,342 @@
k-combined:
-7.952381E-01 3.714273E-02
+2.298294E-01 3.256961E-01
tally 1:
-5.340506E-02
-5.744901E-04
-8.160966E-02
-1.360702E-03
-5.306458E-02
-5.712302E-04
-1.263577E-01
-3.302526E-03
-3.858930E-01
-3.008104E-02
-1.511449E-01
-4.656419E-03
-1.279399E-01
-3.429368E-03
-3.676349E-01
-2.739091E-02
-1.410822E-01
-4.100718E-03
-5.379722E-02
-5.997669E-04
-8.933947E-02
-1.635151E-03
-5.212766E-02
-5.497167E-04
-7.332108E-02
-1.098591E-03
-1.040477E-01
-2.211291E-03
-5.326449E-02
-5.881665E-04
-1.952299E-01
-7.733668E-03
-5.683168E-01
-6.600345E-02
-1.866765E-01
-7.004663E-03
-2.262997E-01
-1.033597E-02
-6.280081E-01
-7.932045E-02
-1.861170E-01
-6.952815E-03
-7.317076E-02
-1.109977E-03
-1.145829E-01
-2.646373E-03
-6.567032E-02
-8.836880E-04
-6.614241E-02
-8.902720E-04
-1.083575E-01
-2.356190E-03
-6.479323E-02
-8.604886E-04
-2.202887E-01
-9.846484E-03
-9.405324E-01
-2.263338E-01
-1.993991E-01
-7.984693E-03
-2.310168E-01
-1.084962E-02
-9.617014E-01
-2.432501E-01
-2.127786E-01
-9.085201E-03
-7.772444E-02
-1.217267E-03
-1.170744E-01
-2.791253E-03
-7.480464E-02
-1.126824E-03
-6.321842E-02
-8.234272E-04
-1.002360E-01
-2.026069E-03
-6.532157E-02
-8.622865E-04
-1.934126E-01
-7.639724E-03
-5.583838E-01
-6.274792E-02
-1.914812E-01
-7.440011E-03
-1.808706E-01
-6.774850E-03
-6.259735E-01
-7.874410E-02
-1.959623E-01
-7.771208E-03
-6.301362E-02
-8.178688E-04
-1.062362E-01
-2.292485E-03
-5.916939E-02
-7.078944E-04
-5.265976E-02
-5.634399E-04
-6.747063E-02
-9.141711E-04
-4.478697E-02
-4.077583E-04
-1.277486E-01
-3.308655E-03
-3.585674E-01
-2.641571E-02
-1.192882E-01
-2.901276E-03
-1.457696E-01
-4.299462E-03
-3.467377E-01
-2.463831E-02
-1.305729E-01
-3.605534E-03
-5.067715E-02
-5.273379E-04
-7.374940E-02
-1.102912E-03
-5.226497E-02
-5.649644E-04
+4.880089E-02
+4.894233E-04
+8.221192E-02
+1.373712E-03
+5.205261E-02
+5.584673E-04
+1.272758E-01
+3.371623E-03
+3.599375E-01
+2.655645E-02
+1.377572E-01
+3.835778E-03
+1.646205E-01
+5.916595E-03
+3.806765E-01
+2.947576E-02
+1.470573E-01
+4.360385E-03
+5.568294E-02
+6.368003E-04
+6.775790E-02
+9.447074E-04
+5.580909E-02
+6.303584E-04
+6.674847E-02
+9.080853E-04
+9.747628E-02
+1.934325E-03
+6.824062E-02
+9.908844E-04
+1.891692E-01
+7.211874E-03
+5.976566E-01
+7.206211E-02
+1.805640E-01
+6.599680E-03
+2.114692E-01
+9.202185E-03
+6.514433E-01
+8.523087E-02
+1.905740E-01
+7.287607E-03
+7.633486E-02
+1.216488E-03
+1.117747E-01
+2.538705E-03
+7.438042E-02
+1.127109E-03
+7.356007E-02
+1.090617E-03
+1.161258E-01
+2.734941E-03
+6.745417E-02
+9.371031E-04
+2.153323E-01
+9.293477E-03
+9.414362E-01
+2.261845E-01
+2.016933E-01
+8.270477E-03
+2.370758E-01
+1.150628E-02
+9.973982E-01
+2.489516E-01
+2.152505E-01
+9.424546E-03
+7.502684E-02
+1.208304E-03
+1.244515E-01
+3.168682E-03
+7.515812E-02
+1.151397E-03
+6.355178E-02
+8.423316E-04
+1.040915E-01
+2.224064E-03
+6.902234E-02
+9.843766E-04
+1.978591E-01
+7.894161E-03
+5.162186E-01
+5.357742E-02
+1.897326E-01
+7.231935E-03
+1.827950E-01
+6.839560E-03
+5.780661E-01
+6.799910E-02
+1.881215E-01
+7.093746E-03
+6.083700E-02
+7.861240E-04
+9.978991E-02
+2.022733E-03
+6.004653E-02
+7.428556E-04
+4.951220E-02
+4.952385E-04
+7.401227E-02
+1.124154E-03
+5.151090E-02
+5.339359E-04
+1.356118E-01
+3.711749E-03
+3.400140E-01
+2.367518E-02
+1.385305E-01
+4.060592E-03
+1.438711E-01
+4.191824E-03
+3.276170E-01
+2.210924E-02
+1.279501E-01
+3.435254E-03
+4.852204E-02
+4.919417E-04
+7.229090E-02
+1.062894E-03
+4.344414E-02
+3.825354E-04
tally 2:
-2.442367E-01
-1.209459E-02
-2.543262E-01
-1.314598E-02
-5.639744E-01
-6.449959E-02
-6.415410E-01
-8.269091E-02
-2.631124E-01
-1.406544E-02
-2.513955E-01
-1.285616E-02
-3.570608E-01
-2.559924E-02
-2.978502E-01
-1.787722E-02
-1.142500E+00
-2.799696E-01
-1.072656E+00
-2.465813E-01
-3.720711E-01
-2.776168E-02
-3.520288E-01
-2.482313E-02
-3.406093E-01
-2.332649E-02
-3.186893E-01
-2.046998E-02
-1.039053E+00
-2.337911E-01
-1.055863E+00
-2.442418E-01
-3.636093E-01
-2.679467E-02
-3.514845E-01
-2.481131E-02
-2.356811E-01
-1.112305E-02
-2.424590E-01
-1.205945E-02
-5.851380E-01
-6.974618E-02
-5.788717E-01
-6.882684E-02
-2.430058E-01
-1.205907E-02
-2.390704E-01
-1.167330E-02
+2.379877E-01
+1.141258E-02
+2.376600E-01
+1.137350E-02
+6.546514E-01
+8.852321E-02
+5.823862E-01
+6.810779E-02
+2.692631E-01
+1.479426E-02
+2.360469E-01
+1.124950E-02
+3.534788E-01
+2.528363E-02
+3.247931E-01
+2.160130E-02
+1.181513E+00
+2.959140E-01
+1.078874E+00
+2.467321E-01
+3.743375E-01
+2.859905E-02
+3.468123E-01
+2.427809E-02
+3.203903E-01
+2.109786E-02
+3.315547E-01
+2.216053E-02
+1.039077E+00
+2.294722E-01
+1.091786E+00
+2.572834E-01
+3.615960E-01
+2.678347E-02
+3.323317E-01
+2.226424E-02
+2.519726E-01
+1.279098E-02
+2.332385E-01
+1.101251E-02
+5.587247E-01
+6.293355E-02
+5.426859E-01
+6.010041E-02
+2.332981E-01
+1.097940E-02
+2.239951E-01
+1.043440E-02
tally 3:
-5.340506E-02
-5.744901E-04
-8.160966E-02
-1.360702E-03
-5.306458E-02
-5.712302E-04
-1.263577E-01
-3.302526E-03
-3.858930E-01
-3.008104E-02
-1.511449E-01
-4.656419E-03
-1.279399E-01
-3.429368E-03
-3.676349E-01
-2.739091E-02
-1.410822E-01
-4.100718E-03
-5.379722E-02
-5.997669E-04
-8.933947E-02
-1.635151E-03
-5.212766E-02
-5.497167E-04
-7.332108E-02
-1.098591E-03
-1.040477E-01
-2.211291E-03
-5.326449E-02
-5.881665E-04
-1.952299E-01
-7.733668E-03
-5.683168E-01
-6.600345E-02
-1.866765E-01
-7.004663E-03
-2.262997E-01
-1.033597E-02
-6.280081E-01
-7.932045E-02
-1.861170E-01
-6.952815E-03
-7.317076E-02
-1.109977E-03
-1.145829E-01
-2.646373E-03
-6.567032E-02
-8.836880E-04
-6.614241E-02
-8.902720E-04
-1.083575E-01
-2.356190E-03
-6.479323E-02
-8.604886E-04
-2.202887E-01
-9.846484E-03
-9.405324E-01
-2.263338E-01
-1.993991E-01
-7.984693E-03
-2.310168E-01
-1.084962E-02
-9.617014E-01
-2.432501E-01
-2.127786E-01
-9.085201E-03
-7.772444E-02
-1.217267E-03
-1.170744E-01
-2.791253E-03
-7.480464E-02
-1.126824E-03
-6.321842E-02
-8.234272E-04
-1.002360E-01
-2.026069E-03
-6.532157E-02
-8.622865E-04
-1.934126E-01
-7.639724E-03
-5.583838E-01
-6.274792E-02
-1.914812E-01
-7.440011E-03
-1.808706E-01
-6.774850E-03
-6.259735E-01
-7.874410E-02
-1.959623E-01
-7.771208E-03
-6.301362E-02
-8.178688E-04
-1.062362E-01
-2.292485E-03
-5.916939E-02
-7.078944E-04
-5.265976E-02
-5.634399E-04
-6.747063E-02
-9.141711E-04
-4.478697E-02
-4.077583E-04
-1.277486E-01
-3.308655E-03
-3.585674E-01
-2.641571E-02
-1.192882E-01
-2.901276E-03
-1.457696E-01
-4.299462E-03
-3.467377E-01
-2.463831E-02
-1.305729E-01
-3.605534E-03
-5.067715E-02
-5.273379E-04
-7.374940E-02
-1.102912E-03
-5.226497E-02
-5.649644E-04
+4.880089E-02
+4.894233E-04
+8.221192E-02
+1.373712E-03
+5.205261E-02
+5.584673E-04
+1.272758E-01
+3.371623E-03
+3.599375E-01
+2.655645E-02
+1.377572E-01
+3.835778E-03
+1.646205E-01
+5.916595E-03
+3.806765E-01
+2.947576E-02
+1.470573E-01
+4.360385E-03
+5.568294E-02
+6.368003E-04
+6.775790E-02
+9.447074E-04
+5.580909E-02
+6.303584E-04
+6.674847E-02
+9.080853E-04
+9.747628E-02
+1.934325E-03
+6.824062E-02
+9.908844E-04
+1.891692E-01
+7.211874E-03
+5.976566E-01
+7.206211E-02
+1.805640E-01
+6.599680E-03
+2.114692E-01
+9.202185E-03
+6.514433E-01
+8.523087E-02
+1.905740E-01
+7.287607E-03
+7.633486E-02
+1.216488E-03
+1.117747E-01
+2.538705E-03
+7.438042E-02
+1.127109E-03
+7.356007E-02
+1.090617E-03
+1.161258E-01
+2.734941E-03
+6.745417E-02
+9.371031E-04
+2.153323E-01
+9.293477E-03
+9.414362E-01
+2.261845E-01
+2.016933E-01
+8.270477E-03
+2.370758E-01
+1.150628E-02
+9.973982E-01
+2.489516E-01
+2.152505E-01
+9.424546E-03
+7.502684E-02
+1.208304E-03
+1.244515E-01
+3.168682E-03
+7.515812E-02
+1.151397E-03
+6.355178E-02
+8.423316E-04
+1.040915E-01
+2.224064E-03
+6.902234E-02
+9.843766E-04
+1.978591E-01
+7.894161E-03
+5.162186E-01
+5.357742E-02
+1.897326E-01
+7.231935E-03
+1.827950E-01
+6.839560E-03
+5.780661E-01
+6.799910E-02
+1.881215E-01
+7.093746E-03
+6.083700E-02
+7.861240E-04
+9.978991E-02
+2.022733E-03
+6.004653E-02
+7.428556E-04
+4.951220E-02
+4.952385E-04
+7.401227E-02
+1.124154E-03
+5.151090E-02
+5.339359E-04
+1.356118E-01
+3.711749E-03
+3.400140E-01
+2.367518E-02
+1.385305E-01
+4.060592E-03
+1.438711E-01
+4.191824E-03
+3.276170E-01
+2.210924E-02
+1.279501E-01
+3.435254E-03
+4.852204E-02
+4.919417E-04
+7.229090E-02
+1.062894E-03
+4.344414E-02
+3.825354E-04
tally 4:
-2.442367E-01
-1.209459E-02
-2.543262E-01
-1.314598E-02
-5.639744E-01
-6.449959E-02
-6.415410E-01
-8.269091E-02
-2.631124E-01
-1.406544E-02
-2.513955E-01
-1.285616E-02
-3.570608E-01
-2.559924E-02
-2.978502E-01
-1.787722E-02
-1.142500E+00
-2.799696E-01
-1.072656E+00
-2.465813E-01
-3.720711E-01
-2.776168E-02
-3.520288E-01
-2.482313E-02
-3.406093E-01
-2.332649E-02
-3.186893E-01
-2.046998E-02
-1.039053E+00
-2.337911E-01
-1.055863E+00
-2.442418E-01
-3.636093E-01
-2.679467E-02
-3.514845E-01
-2.481131E-02
-2.356811E-01
-1.112305E-02
-2.424590E-01
-1.205945E-02
-5.851380E-01
-6.974618E-02
-5.788717E-01
-6.882684E-02
-2.430058E-01
-1.205907E-02
-2.390704E-01
-1.167330E-02
+2.379877E-01
+1.141258E-02
+2.376600E-01
+1.137350E-02
+6.546514E-01
+8.852321E-02
+5.823862E-01
+6.810779E-02
+2.692631E-01
+1.479426E-02
+2.360469E-01
+1.124950E-02
+3.534788E-01
+2.528363E-02
+3.247931E-01
+2.160130E-02
+1.181513E+00
+2.959140E-01
+1.078874E+00
+2.467321E-01
+3.743375E-01
+2.859905E-02
+3.468123E-01
+2.427809E-02
+3.203903E-01
+2.109786E-02
+3.315547E-01
+2.216053E-02
+1.039077E+00
+2.294722E-01
+1.091786E+00
+2.572834E-01
+3.615960E-01
+2.678347E-02
+3.323317E-01
+2.226424E-02
+2.519726E-01
+1.279098E-02
+2.332385E-01
+1.101251E-02
+5.587247E-01
+6.293355E-02
+5.426859E-01
+6.010041E-02
+2.332981E-01
+1.097940E-02
+2.239951E-01
+1.043440E-02
diff --git a/tests/regression_tests/infinite_cell/results_true.dat b/tests/regression_tests/infinite_cell/results_true.dat
--- a/tests/regression_tests/infinite_cell/results_true.dat
+++ b/tests/regression_tests/infinite_cell/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-9.537627E-02 2.349145E-03
+9.589951E-02 8.489144E-04
diff --git a/tests/regression_tests/iso_in_lab/results_true.dat b/tests/regression_tests/iso_in_lab/results_true.dat
--- a/tests/regression_tests/iso_in_lab/results_true.dat
+++ b/tests/regression_tests/iso_in_lab/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-9.050918E-01 3.355799E-02
+9.015537E-01 1.086850E-01
diff --git a/tests/regression_tests/lattice/results_true.dat b/tests/regression_tests/lattice/results_true.dat
--- a/tests/regression_tests/lattice/results_true.dat
+++ b/tests/regression_tests/lattice/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.068493E+00 1.318070E-01
+9.610829E-01 2.522714E-02
diff --git a/tests/regression_tests/lattice_hex/results_true.dat b/tests/regression_tests/lattice_hex/results_true.dat
--- a/tests/regression_tests/lattice_hex/results_true.dat
+++ b/tests/regression_tests/lattice_hex/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-2.522694E-01 1.422929E-02
+2.566607E-01 9.207770E-03
diff --git a/tests/regression_tests/lattice_hex_coincident/results_true.dat b/tests/regression_tests/lattice_hex_coincident/results_true.dat
--- a/tests/regression_tests/lattice_hex_coincident/results_true.dat
+++ b/tests/regression_tests/lattice_hex_coincident/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.901983E+00 1.772999E-02
+1.917792E+00 4.329425E-02
diff --git a/tests/regression_tests/lattice_hex_x/results_true.dat b/tests/regression_tests/lattice_hex_x/results_true.dat
--- a/tests/regression_tests/lattice_hex_x/results_true.dat
+++ b/tests/regression_tests/lattice_hex_x/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.345955E+00 3.225468E-02
+1.367975E+00 2.264887E-02
diff --git a/tests/regression_tests/lattice_multiple/results_true.dat b/tests/regression_tests/lattice_multiple/results_true.dat
--- a/tests/regression_tests/lattice_multiple/results_true.dat
+++ b/tests/regression_tests/lattice_multiple/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.859909E+00 1.768384E-02
+1.859911E+00 8.282311E-03
diff --git a/tests/regression_tests/lattice_rotated/results_true.dat b/tests/regression_tests/lattice_rotated/results_true.dat
--- a/tests/regression_tests/lattice_rotated/results_true.dat
+++ b/tests/regression_tests/lattice_rotated/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-4.674233E-01 1.599236E-02
+4.426784E-01 6.627506E-03
diff --git a/tests/regression_tests/mgxs_library_ce_to_mg/results_true.dat b/tests/regression_tests/mgxs_library_ce_to_mg/results_true.dat
--- a/tests/regression_tests/mgxs_library_ce_to_mg/results_true.dat
+++ b/tests/regression_tests/mgxs_library_ce_to_mg/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.263928E+00 3.768356E-02
+1.158563E+00 3.354681E-02
diff --git a/tests/regression_tests/mgxs_library_ce_to_mg_nuclides/results_true.dat b/tests/regression_tests/mgxs_library_ce_to_mg_nuclides/results_true.dat
--- a/tests/regression_tests/mgxs_library_ce_to_mg_nuclides/results_true.dat
+++ b/tests/regression_tests/mgxs_library_ce_to_mg_nuclides/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-3.817369E-01 1.166296E-02
+6.025533E-01 1.157401E-02
diff --git a/tests/regression_tests/mgxs_library_condense/results_true.dat b/tests/regression_tests/mgxs_library_condense/results_true.dat
--- a/tests/regression_tests/mgxs_library_condense/results_true.dat
+++ b/tests/regression_tests/mgxs_library_condense/results_true.dat
@@ -1,362 +1,362 @@
mesh 1 group in nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.693468 0.019161
-2 1 2 1 1 total 0.694532 0.021411
-1 2 1 1 1 total 0.693746 0.023378
-3 2 2 1 1 total 0.697424 0.031315
+0 1 1 1 1 total 0.699306 0.028642
+2 1 2 1 1 total 0.687913 0.025966
+1 2 1 1 1 total 0.716035 0.018945
+3 2 2 1 1 total 0.702630 0.028574
mesh 1 group in nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.439784 0.020575
-2 1 2 1 1 total 0.427837 0.025828
-1 2 1 1 1 total 0.423294 0.027075
-3 2 2 1 1 total 0.433094 0.032674
+0 1 1 1 1 total 0.443642 0.030984
+2 1 2 1 1 total 0.429968 0.028072
+1 2 1 1 1 total 0.461535 0.021345
+3 2 2 1 1 total 0.439454 0.031232
mesh 1 group in nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.439784 0.020575
-2 1 2 1 1 total 0.427935 0.025836
-1 2 1 1 1 total 0.423294 0.027075
-3 2 2 1 1 total 0.433094 0.032674
+0 1 1 1 1 total 0.443642 0.030984
+2 1 2 1 1 total 0.429968 0.028072
+1 2 1 1 1 total 0.461535 0.021345
+3 2 2 1 1 total 0.439454 0.031232
mesh 1 group in nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.021509 0.001396
-2 1 2 1 1 total 0.020854 0.001436
-1 2 1 1 1 total 0.021469 0.001983
-3 2 2 1 1 total 0.022046 0.001594
+0 1 1 1 1 total 0.021895 0.001041
+2 1 2 1 1 total 0.021903 0.001108
+1 2 1 1 1 total 0.024895 0.001401
+3 2 2 1 1 total 0.022105 0.001198
mesh 1 group in nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.021489 0.001396
-2 1 2 1 1 total 0.020837 0.001436
-1 2 1 1 1 total 0.021454 0.001983
-3 2 2 1 1 total 0.022036 0.001594
+0 1 1 1 1 total 0.021883 0.001040
+2 1 2 1 1 total 0.021879 0.001108
+1 2 1 1 1 total 0.024875 0.001401
+3 2 2 1 1 total 0.022071 0.001197
mesh 1 group in nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.011598 0.001508
-2 1 2 1 1 total 0.010856 0.001613
-1 2 1 1 1 total 0.011622 0.002259
-3 2 2 1 1 total 0.012002 0.001685
+0 1 1 1 1 total 0.011219 0.000958
+2 1 2 1 1 total 0.011437 0.001013
+1 2 1 1 1 total 0.012947 0.001437
+3 2 2 1 1 total 0.011756 0.001144
mesh 1 group in nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.009911 0.000667
-2 1 2 1 1 total 0.009998 0.000859
-1 2 1 1 1 total 0.009847 0.001153
-3 2 2 1 1 total 0.010044 0.000939
+0 1 1 1 1 total 0.010676 0.000481
+2 1 2 1 1 total 0.010466 0.000446
+1 2 1 1 1 total 0.011948 0.000517
+3 2 2 1 1 total 0.010350 0.000547
mesh 1 group in nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.024369 0.001625
-2 1 2 1 1 total 0.024572 0.002095
-1 2 1 1 1 total 0.024189 0.002811
-3 2 2 1 1 total 0.024677 0.002291
+0 1 1 1 1 total 0.026218 0.001180
+2 1 2 1 1 total 0.025724 0.001093
+1 2 1 1 1 total 0.029326 0.001262
+3 2 2 1 1 total 0.025451 0.001338
mesh 1 group in nuclide mean std. dev.
x y z
-0 1 1 1 1 total 1.919781e+06 128933.976741
-2 1 2 1 1 total 1.936343e+06 166141.202022
-1 2 1 1 1 total 1.906964e+06 223076.300071
-3 2 2 1 1 total 1.945248e+06 181591.269295
+0 1 1 1 1 total 2.067337e+06 93152.452502
+2 1 2 1 1 total 2.026907e+06 86377.585629
+1 2 1 1 1 total 2.313358e+06 99980.823985
+3 2 2 1 1 total 2.004370e+06 105820.022073
mesh 1 group in nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.671959 0.018153
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mesh 1 group in nuclide mean std. dev.
x y z
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mesh 1 group in group out legendre nuclide mean std. dev.
x y z
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mesh 1 group in group out legendre nuclide mean std. dev.
x y z
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- mesh 1 group in group out nuclide mean std. dev.
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+ mesh 1 group in group out nuclide mean std. dev.
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mesh 1 group in group out nuclide mean std. dev.
x y z
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mesh 1 group in group out nuclide mean std. dev.
x y z
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mesh 1 group in group out legendre nuclide mean std. dev.
x y z
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mesh 1 group in group out legendre nuclide mean std. dev.
x y z
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mesh 1 group out nuclide mean std. dev.
x y z
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mesh 1 group out nuclide mean std. dev.
x y z
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mesh 1 group in nuclide mean std. dev.
x y z
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in group out nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
x y surf
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 delayedgroup group in nuclide mean std. dev.
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mesh 1 delayedgroup group out nuclide mean std. dev.
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mesh 1 delayedgroup group in nuclide mean std. dev.
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+14 1 2 1 3 1 total 0.001182 0.000051
+15 1 2 1 4 1 total 0.002744 0.000120
+16 1 2 1 5 1 total 0.001223 0.000056
+17 1 2 1 6 1 total 0.000509 0.000023
+6 2 1 1 1 1 total 0.000227 0.000013
+7 2 1 1 2 1 total 0.001207 0.000067
+8 2 1 1 3 1 total 0.001173 0.000065
+9 2 1 1 4 1 total 0.002710 0.000150
+10 2 1 1 5 1 total 0.001195 0.000066
+11 2 1 1 6 1 total 0.000498 0.000027
+18 2 2 1 1 1 total 0.000227 0.000014
+19 2 2 1 2 1 total 0.001212 0.000073
+20 2 2 1 3 1 total 0.001180 0.000071
+21 2 2 1 4 1 total 0.002740 0.000163
+22 2 2 1 5 1 total 0.001221 0.000073
+23 2 2 1 6 1 total 0.000508 0.000030
mesh 1 delayedgroup nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.013357 0.001250
-1 1 1 1 2 total 0.032589 0.002884
-2 1 1 1 3 total 0.121105 0.010300
-3 1 1 1 4 total 0.306138 0.024490
-4 1 1 1 5 total 0.862757 0.061312
-5 1 1 1 6 total 2.897868 0.207582
-12 1 2 1 1 total 0.013356 0.001625
-13 1 2 1 2 total 0.032597 0.003869
-14 1 2 1 3 total 0.121088 0.014125
-15 1 2 1 4 total 0.305963 0.034783
-16 1 2 1 5 total 0.862125 0.093434
-17 1 2 1 6 total 2.895716 0.314825
-6 2 1 1 1 total 0.013355 0.002181
-7 2 1 1 2 total 0.032604 0.005141
-8 2 1 1 3 total 0.121074 0.018615
-9 2 1 1 4 total 0.305828 0.045169
-10 2 1 1 5 total 0.861633 0.116817
-11 2 1 1 6 total 2.894042 0.394847
-18 2 2 1 1 total 0.013355 0.001620
-19 2 2 1 2 total 0.032602 0.003798
-20 2 2 1 3 total 0.121077 0.013715
-21 2 2 1 4 total 0.305857 0.033214
-22 2 2 1 5 total 0.861740 0.086567
-23 2 2 1 6 total 2.894407 0.292238
- mesh 1 delayedgroup group in group out nuclide mean std. dev.
- x y z
-0 1 1 1 1 1 1 total 0.000000 0.000000
-1 1 1 1 2 1 1 total 0.000000 0.000000
-2 1 1 1 3 1 1 total 0.000000 0.000000
-3 1 1 1 4 1 1 total 0.000172 0.000172
-4 1 1 1 5 1 1 total 0.000192 0.000192
-5 1 1 1 6 1 1 total 0.000000 0.000000
-12 1 2 1 1 1 1 total 0.000000 0.000000
-13 1 2 1 2 1 1 total 0.000000 0.000000
-14 1 2 1 3 1 1 total 0.000000 0.000000
-15 1 2 1 4 1 1 total 0.000000 0.000000
-16 1 2 1 5 1 1 total 0.000000 0.000000
-17 1 2 1 6 1 1 total 0.000000 0.000000
-6 2 1 1 1 1 1 total 0.000000 0.000000
-7 2 1 1 2 1 1 total 0.000000 0.000000
-8 2 1 1 3 1 1 total 0.000000 0.000000
-9 2 1 1 4 1 1 total 0.000000 0.000000
-10 2 1 1 5 1 1 total 0.000000 0.000000
-11 2 1 1 6 1 1 total 0.000000 0.000000
-18 2 2 1 1 1 1 total 0.000000 0.000000
-19 2 2 1 2 1 1 total 0.000186 0.000186
-20 2 2 1 3 1 1 total 0.000000 0.000000
-21 2 2 1 4 1 1 total 0.000000 0.000000
-22 2 2 1 5 1 1 total 0.000000 0.000000
-23 2 2 1 6 1 1 total 0.000000 0.000000
+0 1 1 1 1 total 0.013354 0.000674
+1 1 1 1 2 total 0.032612 0.001720
+2 1 1 1 3 total 0.121057 0.006579
+3 1 1 1 4 total 0.305656 0.017398
+4 1 1 1 5 total 0.861000 0.053768
+5 1 1 1 6 total 2.891889 0.179407
+12 1 2 1 1 total 0.013354 0.000497
+13 1 2 1 2 total 0.032605 0.001150
+14 1 2 1 3 total 0.121071 0.004175
+15 1 2 1 4 total 0.305792 0.010484
+16 1 2 1 5 total 0.861500 0.032627
+17 1 2 1 6 total 2.893589 0.108347
+6 2 1 1 1 total 0.013352 0.000663
+7 2 1 1 2 total 0.032625 0.001570
+8 2 1 1 3 total 0.121029 0.005721
+9 2 1 1 4 total 0.305375 0.014144
+10 2 1 1 5 total 0.859955 0.039608
+11 2 1 1 6 total 2.888337 0.132844
+18 2 2 1 1 total 0.013354 0.000892
+19 2 2 1 2 total 0.032606 0.002209
+20 2 2 1 3 total 0.121069 0.008302
+21 2 2 1 4 total 0.305776 0.021416
+22 2 2 1 5 total 0.861442 0.063571
+23 2 2 1 6 total 2.893392 0.212640
+ mesh 1 delayedgroup group in group out nuclide mean std. dev.
+ x y z
+0 1 1 1 1 1 1 total 0.0 0.0
+1 1 1 1 2 1 1 total 0.0 0.0
+2 1 1 1 3 1 1 total 0.0 0.0
+3 1 1 1 4 1 1 total 0.0 0.0
+4 1 1 1 5 1 1 total 0.0 0.0
+5 1 1 1 6 1 1 total 0.0 0.0
+12 1 2 1 1 1 1 total 0.0 0.0
+13 1 2 1 2 1 1 total 0.0 0.0
+14 1 2 1 3 1 1 total 0.0 0.0
+15 1 2 1 4 1 1 total 0.0 0.0
+16 1 2 1 5 1 1 total 0.0 0.0
+17 1 2 1 6 1 1 total 0.0 0.0
+6 2 1 1 1 1 1 total 0.0 0.0
+7 2 1 1 2 1 1 total 0.0 0.0
+8 2 1 1 3 1 1 total 0.0 0.0
+9 2 1 1 4 1 1 total 0.0 0.0
+10 2 1 1 5 1 1 total 0.0 0.0
+11 2 1 1 6 1 1 total 0.0 0.0
+18 2 2 1 1 1 1 total 0.0 0.0
+19 2 2 1 2 1 1 total 0.0 0.0
+20 2 2 1 3 1 1 total 0.0 0.0
+21 2 2 1 4 1 1 total 0.0 0.0
+22 2 2 1 5 1 1 total 0.0 0.0
+23 2 2 1 6 1 1 total 0.0 0.0
diff --git a/tests/regression_tests/mgxs_library_correction/results_true.dat b/tests/regression_tests/mgxs_library_correction/results_true.dat
--- a/tests/regression_tests/mgxs_library_correction/results_true.dat
+++ b/tests/regression_tests/mgxs_library_correction/results_true.dat
@@ -1,60 +1,60 @@
material group in group out nuclide mean std. dev.
-3 1 1 1 total 0.353219 0.011858
-2 1 1 2 total 0.000876 0.000554
+3 1 1 1 total 0.342252 0.023795
+2 1 1 2 total 0.000695 0.000327
1 1 2 1 total 0.000000 0.000000
-0 1 2 2 total 0.367572 0.024736
+0 1 2 2 total 0.388426 0.020840
material group in group out nuclide mean std. dev.
-3 1 1 1 total 0.353488 0.011854
-2 1 1 2 total 0.000876 0.000554
+3 1 1 1 total 0.342252 0.023795
+2 1 1 2 total 0.000695 0.000327
1 1 2 1 total 0.000000 0.000000
-0 1 2 2 total 0.367572 0.024736
+0 1 2 2 total 0.388426 0.020840
material group in group out nuclide mean std. dev.
-3 1 1 1 total 0.350138 0.017141
-2 1 1 2 total 0.000869 0.000551
+3 1 1 1 total 0.343021 0.031016
+2 1 1 2 total 0.000697 0.000329
1 1 2 1 total 0.000000 0.000000
-0 1 2 2 total 0.378130 0.046663
+0 1 2 2 total 0.376544 0.025156
material group in group out nuclide mean std. dev.
-3 1 1 1 total 0.350406 0.018910
-2 1 1 2 total 0.000869 0.000953
+3 1 1 1 total 0.343021 0.039761
+2 1 1 2 total 0.000697 0.000566
1 1 2 1 total 0.000000 0.000000
-0 1 2 2 total 0.378130 0.057580
+0 1 2 2 total 0.376544 0.032140
material group in group out nuclide mean std. dev.
-3 2 1 1 total 0.272853 0.018051
-2 2 1 2 total 0.000486 0.000486
+3 2 1 1 total 0.271174 0.022374
+2 2 1 2 total 0.000000 0.000000
1 2 2 1 total 0.000000 0.000000
-0 2 2 2 total 0.287308 0.063393
+0 2 2 2 total 0.295401 0.032831
material group in group out nuclide mean std. dev.
-3 2 1 1 total 0.272853 0.018051
-2 2 1 2 total 0.000486 0.000486
+3 2 1 1 total 0.271174 0.022374
+2 2 1 2 total 0.000000 0.000000
1 2 2 1 total 0.000000 0.000000
-0 2 2 2 total 0.287308 0.063393
+0 2 2 2 total 0.295401 0.032831
material group in group out nuclide mean std. dev.
-3 2 1 1 total 0.273465 0.021487
-2 2 1 2 total 0.000487 0.000487
+3 2 1 1 total 0.264654 0.028288
+2 2 1 2 total 0.000000 0.000000
1 2 2 1 total 0.000000 0.000000
-0 2 2 2 total 0.294966 0.065882
+0 2 2 2 total 0.295178 0.032530
material group in group out nuclide mean std. dev.
-3 2 1 1 total 0.273465 0.025834
-2 2 1 2 total 0.000487 0.000843
+3 2 1 1 total 0.264654 0.036081
+2 2 1 2 total 0.000000 0.000000
1 2 2 1 total 0.000000 0.000000
-0 2 2 2 total 0.294966 0.089321
- material group in group out nuclide mean std. dev.
-3 3 1 1 total 0.262301 0.012948
-2 3 1 2 total 0.029783 0.000974
-1 3 2 1 total 0.000000 0.000000
-0 3 2 2 total 1.418218 0.082199
- material group in group out nuclide mean std. dev.
-3 3 1 1 total 0.262301 0.012948
-2 3 1 2 total 0.029783 0.000974
-1 3 2 1 total 0.000000 0.000000
-0 3 2 2 total 1.418218 0.082199
- material group in group out nuclide mean std. dev.
-3 3 1 1 total 0.261486 0.022535
-2 3 1 2 total 0.029746 0.001063
-1 3 2 1 total 0.000000 0.000000
-0 3 2 2 total 1.432958 0.149985
- material group in group out nuclide mean std. dev.
-3 3 1 1 total 0.261486 0.026061
-2 3 1 2 total 0.029746 0.001468
-1 3 2 1 total 0.000000 0.000000
-0 3 2 2 total 1.432958 0.178757
+0 2 2 2 total 0.295178 0.044676
+ material group in group out nuclide mean std. dev.
+3 3 1 1 total 0.257831 0.014436
+2 3 1 2 total 0.030826 0.000973
+1 3 2 1 total 0.000467 0.000467
+0 3 2 2 total 1.443057 0.119909
+ material group in group out nuclide mean std. dev.
+3 3 1 1 total 0.257831 0.014436
+2 3 1 2 total 0.030826 0.000973
+1 3 2 1 total 0.000467 0.000467
+0 3 2 2 total 1.443057 0.119909
+ material group in group out nuclide mean std. dev.
+3 3 1 1 total 0.267025 0.029512
+2 3 1 2 total 0.031268 0.001416
+1 3 2 1 total 0.000466 0.000467
+0 3 2 2 total 1.440250 0.164573
+ material group in group out nuclide mean std. dev.
+3 3 1 1 total 0.267025 0.032860
+2 3 1 2 total 0.031268 0.001768
+1 3 2 1 total 0.000466 0.000808
+0 3 2 2 total 1.440250 0.212183
diff --git a/tests/regression_tests/mgxs_library_distribcell/results_true.dat b/tests/regression_tests/mgxs_library_distribcell/results_true.dat
--- a/tests/regression_tests/mgxs_library_distribcell/results_true.dat
+++ b/tests/regression_tests/mgxs_library_distribcell/results_true.dat
@@ -1,97 +1,97 @@
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.450382 0.010238
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.455527 0.009851
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.413436 0.011349
- sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.413276 0.011357
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.409242 0.011118
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.06484 0.002514
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.40929 0.011119
+ sum(distribcell) group in nuclide mean std. dev.
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.066934 0.002424
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.064761 0.002514
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.066764 0.002423
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.028638 0.002713
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.028358 0.002669
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.036203 0.001449
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.038576 0.001526
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.089088 0.003536
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.094817 0.003725
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 7.011996e+06 280281.488034
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 7.470225e+06 295170.385185
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.385542 0.008566
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.388593 0.008156
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.386602 0.013718
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.388874 0.013889
sum(distribcell) group in group out legendre nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P0 total 0.386439 0.013702
-1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P1 total 0.036946 0.004896
-2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P2 total 0.016245 0.003818
-3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P3 total 0.005544 0.003119
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P0 total 0.388711 0.013887
+1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P1 total 0.046285 0.005155
+2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P2 total 0.023632 0.003772
+3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P3 total 0.006997 0.003207
sum(distribcell) group in group out legendre nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P0 total 0.386602 0.013718
-1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P1 total 0.037106 0.004917
-2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P2 total 0.016398 0.003839
-3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P3 total 0.005688 0.003138
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P0 total 0.388874 0.013889
+1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P1 total 0.046237 0.005156
+2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P2 total 0.023571 0.003775
+3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P3 total 0.007058 0.003207
sum(distribcell) group in group out nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 1.000421 0.036026
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 1.000418 0.036246
sum(distribcell) group in group out nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 0.083975 0.005759
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 0.092139 0.005956
sum(distribcell) group in group out nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 1.0 0.035985
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 1.0 0.036242
sum(distribcell) group in group out legendre nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P0 total 0.385542 0.016305
-1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P1 total 0.036860 0.004958
-2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P2 total 0.016207 0.003827
-3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P3 total 0.005531 0.003114
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P0 total 0.388593 0.016275
+1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P1 total 0.046271 0.005251
+2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P2 total 0.023624 0.003806
+3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P3 total 0.006995 0.003209
sum(distribcell) group in group out legendre nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P0 total 0.385704 0.021424
-1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P1 total 0.036876 0.005135
-2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P2 total 0.016214 0.003873
-3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P3 total 0.005533 0.003122
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P0 total 0.388755 0.021528
+1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P1 total 0.046290 0.005515
+2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P2 total 0.023634 0.003903
+3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 P3 total 0.006998 0.003221
sum(distribcell) group out nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 1.0 0.090473
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 1.0 0.084366
sum(distribcell) group out nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 1.0 0.090571
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 1.0 0.084331
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 4.896406e-07 2.047455e-08
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 5.253873e-07 2.168461e-08
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.088451 0.003512
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.094147 0.003701
sum(distribcell) group in group out nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 0.082789 0.005683
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 0.091593 0.005919
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.806252 0.022131
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.814514 0.022129
sum(distribcell) group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.806564 0.022166
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.814419 0.022125
sum(distribcell) delayedgroup group in nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 0.000020 8.047454e-07
-1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 2 1 total 0.000108 4.184372e-06
-2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 3 1 total 0.000106 4.014315e-06
-3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 4 1 total 0.000246 9.085237e-06
-4 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 5 1 total 0.000111 3.832957e-06
-5 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 6 1 total 0.000046 1.601490e-06
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 0.000021 8.473275e-07
+1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 2 1 total 0.000115 4.405467e-06
+2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 3 1 total 0.000112 4.225826e-06
+3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 4 1 total 0.000259 9.559952e-06
+4 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 5 1 total 0.000115 4.025369e-06
+5 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 6 1 total 0.000048 1.682226e-06
sum(distribcell) delayedgroup group out nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 1.0 1.414214
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 0.0 0.000000
1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 2 1 total 0.0 0.000000
-2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 3 1 total 0.0 0.000000
-3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 4 1 total 1.0 0.708218
-4 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 5 1 total 1.0 1.414214
+2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 3 1 total 1.0 1.000002
+3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 4 1 total 1.0 1.414214
+4 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 5 1 total 0.0 0.000000
5 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 6 1 total 0.0 0.000000
sum(distribcell) delayedgroup group in nuclide mean std. dev.
0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 total 0.000227 0.000012
-1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 2 1 total 0.001216 0.000062
-2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 3 1 total 0.001187 0.000060
-3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 4 1 total 0.002764 0.000138
-4 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 5 1 total 0.001241 0.000060
-5 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 6 1 total 0.000516 0.000025
+1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 2 1 total 0.001210 0.000062
+2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 3 1 total 0.001177 0.000060
+3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 4 1 total 0.002728 0.000136
+4 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 5 1 total 0.001211 0.000059
+5 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 6 1 total 0.000504 0.000025
sum(distribcell) delayedgroup nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.013356 0.000697
-1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 2 total 0.032593 0.001644
-2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 3 total 0.121097 0.005963
-3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 4 total 0.306056 0.014519
-4 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 5 total 0.862463 0.037889
-5 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 6 total 2.896867 0.127967
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 total 0.013353 0.000692
+1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 2 total 0.032613 0.001644
+2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 3 total 0.121054 0.005983
+3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 4 total 0.305630 0.014645
+4 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 5 total 0.860903 0.038693
+5 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 6 total 2.891558 0.130564
sum(distribcell) delayedgroup group in group out nuclide mean std. dev.
-0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 1 total 0.000189 0.000189
+0 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 1 1 1 total 0.000000 0.000000
1 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 2 1 1 total 0.000000 0.000000
-2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 3 1 1 total 0.000000 0.000000
-3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 4 1 1 total 0.000807 0.000405
-4 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 5 1 1 total 0.000191 0.000191
+2 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 3 1 1 total 0.000362 0.000256
+3 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 4 1 1 total 0.000185 0.000185
+4 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 5 1 1 total 0.000000 0.000000
5 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, ...),) 6 1 1 total 0.000000 0.000000
diff --git a/tests/regression_tests/mgxs_library_hdf5/results_true.dat b/tests/regression_tests/mgxs_library_hdf5/results_true.dat
--- a/tests/regression_tests/mgxs_library_hdf5/results_true.dat
+++ b/tests/regression_tests/mgxs_library_hdf5/results_true.dat
@@ -1,201 +1,201 @@
domain=1 type=total
-[5.62093429e-01 1.47762208e+00]
-[1.25813379e-02 1.33969236e-01]
+[5.52629207e-01 1.46792426e+00]
+[2.73983948e-02 9.30468557e-02]
domain=1 type=transport
-[3.20646457e-01 1.15112225e+00]
-[1.43813685e-02 1.38168210e-01]
+[3.09650231e-01 1.14528468e+00]
+[2.96126059e-02 1.01957125e-01]
domain=1 type=nu-transport
-[3.20646457e-01 1.15112225e+00]
-[1.43813685e-02 1.38168210e-01]
+[3.09650231e-01 1.14528468e+00]
+[2.96126059e-02 1.01957125e-01]
domain=1 type=absorption
-[9.18204614e-03 9.50890834e-02]
-[1.02291781e-03 9.51211716e-03]
+[7.90251362e-03 9.52195503e-02]
+[7.77996866e-04 5.32017792e-03]
domain=1 type=reduced absorption
-[9.15806809e-03 9.50890834e-02]
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+[7.88836875e-03 9.52195503e-02]
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domain=1 type=capture
-[6.76780024e-03 4.04282690e-02]
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domain=1 type=fission
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domain=1 type=nu-fission
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domain=1 type=kappa-fission
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domain=1 type=scatter
-[5.52911383e-01 1.38253299e+00]
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domain=1 type=nu-scatter
-[5.53262132e-01 1.38285128e+00]
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domain=1 type=scatter matrix
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domain=1 type=nu-scatter matrix
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[[0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00]
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+ [9.59957737e-02 3.98634629e-02 1.79245433e-02 2.53788407e-02]]]
domain=1 type=multiplicity matrix
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domain=1 type=nu-fission matrix
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domain=1 type=scatter probability matrix
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[0.00000000e+00 1.00000000e+00]]
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domain=1 type=consistent scatter matrix
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[[0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00]
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[[0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00]
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+ [1.50979688e-01 4.66032426e-02 1.81833349e-02 2.51354735e-02]]]
domain=1 type=consistent nu-scatter matrix
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+ [2.09266366e-02 5.66365392e-03 -1.85639416e-03 -1.62637189e-03]]
[[0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00]
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+ [2.82310416e-03 1.19879975e-03 3.90317811e-04 8.45179676e-04]]
[[0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00]
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domain=1 type=chi
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domain=1 type=chi-prompt
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domain=1 type=inverse-velocity
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domain=1 type=prompt-nu-fission
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domain=1 type=prompt-nu-fission matrix
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domain=1 type=diffusion-coefficient
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+[1.07648340e+00 2.91048451e-01]
+[1.02946730e-01 2.59101197e-02]
domain=1 type=nu-diffusion-coefficient
-[1.03956656e+00 2.89572488e-01]
-[4.66257756e-02 3.47571359e-02]
+[1.07648340e+00 2.91048451e-01]
+[1.02946730e-01 2.59101197e-02]
domain=1 type=delayed-nu-fission
-[[1.37840363e-06 3.03296462e-05]
- [8.45663047e-06 1.56552364e-04]
- [8.84043266e-06 1.49458552e-04]
- [2.28234463e-05 3.35098665e-04]
- [1.25147617e-05 1.37385990e-04]
- [5.13410858e-06 5.75504990e-05]]
-[[2.55826273e-08 3.18690909e-06]
- [1.59619691e-07 1.64498503e-05]
- [2.08725713e-07 1.57044628e-05]
- [7.35913253e-07 3.52107280e-05]
- [6.08970534e-07 1.44359288e-05]
- [2.44376821e-07 6.04715887e-06]]
+[[1.27862358e-06 3.04521075e-05]
+ [7.84219053e-06 1.57184471e-04]
+ [8.19703020e-06 1.50062017e-04]
+ [2.11585246e-05 3.36451683e-04]
+ [1.15983232e-05 1.37940708e-04]
+ [4.75823112e-06 5.77828684e-05]]
+[[8.24665595e-08 1.78649023e-06]
+ [5.11270396e-07 9.22131636e-06]
+ [5.43215007e-07 8.80347339e-06]
+ [1.44919046e-06 1.97381285e-05]
+ [8.56858673e-07 8.09236929e-06]
+ [3.49663884e-07 3.38986452e-06]]
domain=1 type=chi-delayed
[[0.00000000e+00 0.00000000e+00]
[0.00000000e+00 0.00000000e+00]
[0.00000000e+00 0.00000000e+00]
- [1.00000000e+00 0.00000000e+00]
- [1.00000000e+00 0.00000000e+00]
+ [0.00000000e+00 0.00000000e+00]
+ [0.00000000e+00 0.00000000e+00]
[0.00000000e+00 0.00000000e+00]]
[[0.00000000e+00 0.00000000e+00]
[0.00000000e+00 0.00000000e+00]
[0.00000000e+00 0.00000000e+00]
- [1.41421356e+00 0.00000000e+00]
- [1.41421356e+00 0.00000000e+00]
+ [0.00000000e+00 0.00000000e+00]
+ [0.00000000e+00 0.00000000e+00]
[0.00000000e+00 0.00000000e+00]]
domain=1 type=beta
-[[2.24598146e-04 2.27713712e-04]
- [1.37792986e-03 1.17538858e-03]
- [1.44046689e-03 1.12212854e-03]
- [3.71886987e-03 2.51590672e-03]
- [2.03916489e-03 1.03148825e-03]
- [8.36555595e-04 4.32086733e-04]]
-[[2.89454288e-06 2.65002712e-05]
- [1.83788053e-05 1.36786298e-04]
- [2.80459046e-05 1.30588139e-04]
- [1.09140523e-04 2.92789605e-04]
- [9.54156078e-05 1.20039834e-04]
- [3.82194001e-05 5.02842563e-05]]
+[[2.24289169e-04 2.27713711e-04]
+ [1.37563425e-03 1.17538857e-03]
+ [1.43787829e-03 1.12212853e-03]
+ [3.71151288e-03 2.51590669e-03]
+ [2.03451453e-03 1.03148823e-03]
+ [8.34662928e-04 4.32086724e-04]]
+[[1.75760869e-05 1.28957660e-05]
+ [1.08591736e-04 6.65640010e-05]
+ [1.14785004e-04 6.35478047e-05]
+ [3.03169937e-04 1.42479528e-04]
+ [1.75476030e-04 5.84147049e-05]
+ [7.17094876e-05 2.44697107e-05]]
domain=1 type=decay-rate
-[1.33568264e-02 3.25888950e-02 1.21105369e-01 3.06137651e-01
- 8.62756682e-01 2.89786766e+00]
-[1.25011470e-03 2.88396059e-03 1.03002481e-02 2.44903689e-02
- 6.13119717e-02 2.07581680e-01]
+[1.33535692e-02 3.26115957e-02 1.21057117e-01 3.05655911e-01
+ 8.60999995e-01 2.89188863e+00]
+[6.74373067e-04 1.71978136e-03 6.57917554e-03 1.73982053e-02
+ 5.37683207e-02 1.79407115e-01]
domain=1 type=delayed-nu-fission matrix
[[[0.00000000e+00 0.00000000e+00]
[0.00000000e+00 0.00000000e+00]]
@@ -207,10 +207,10 @@ domain=1 type=delayed-nu-fission matrix
[0.00000000e+00 0.00000000e+00]]
[[0.00000000e+00 0.00000000e+00]
- [1.19201367e-03 0.00000000e+00]]
+ [0.00000000e+00 0.00000000e+00]]
[[0.00000000e+00 0.00000000e+00]
- [1.33749216e-03 0.00000000e+00]]
+ [0.00000000e+00 0.00000000e+00]]
[[0.00000000e+00 0.00000000e+00]
[0.00000000e+00 0.00000000e+00]]]
@@ -224,10 +224,10 @@ domain=1 type=delayed-nu-fission matrix
[0.00000000e+00 0.00000000e+00]]
[[0.00000000e+00 0.00000000e+00]
- [1.19567703e-03 0.00000000e+00]]
+ [0.00000000e+00 0.00000000e+00]]
[[0.00000000e+00 0.00000000e+00]
- [1.34160260e-03 0.00000000e+00]]
+ [0.00000000e+00 0.00000000e+00]]
[[0.00000000e+00 0.00000000e+00]
[0.00000000e+00 0.00000000e+00]]]
diff --git a/tests/regression_tests/mgxs_library_histogram/results_true.dat b/tests/regression_tests/mgxs_library_histogram/results_true.dat
--- a/tests/regression_tests/mgxs_library_histogram/results_true.dat
+++ b/tests/regression_tests/mgxs_library_histogram/results_true.dat
@@ -1,25 +1,25 @@
material group in group out mu bin nuclide mean std. dev.
-33 1 1 1 1 total 0.028385 0.002919
-34 1 1 1 2 total 0.031890 0.001548
-35 1 1 1 3 total 0.027684 0.002596
-36 1 1 1 4 total 0.035920 0.003337
-37 1 1 1 5 total 0.034343 0.001897
-38 1 1 1 6 total 0.032591 0.002289
-39 1 1 1 7 total 0.033467 0.002209
-40 1 1 1 8 total 0.031714 0.002398
-41 1 1 1 9 total 0.033467 0.003343
-42 1 1 1 10 total 0.041001 0.002362
-43 1 1 1 11 total 0.060801 0.003580
+33 1 1 1 1 total 0.032861 0.003703
+34 1 1 1 2 total 0.026428 0.003637
+35 1 1 1 3 total 0.029210 0.001648
+36 1 1 1 4 total 0.032513 0.004770
+37 1 1 1 5 total 0.030949 0.003129
+38 1 1 1 6 total 0.027124 0.004029
+39 1 1 1 7 total 0.030079 0.002186
+40 1 1 1 8 total 0.037034 0.002198
+41 1 1 1 9 total 0.038251 0.003825
+42 1 1 1 10 total 0.039294 0.003626
+43 1 1 1 11 total 0.062593 0.005934
22 1 1 2 1 total 0.000000 0.000000
-23 1 1 2 2 total 0.000350 0.000351
-24 1 1 2 3 total 0.000175 0.000175
-25 1 1 2 4 total 0.000000 0.000000
-26 1 1 2 5 total 0.000175 0.000175
+23 1 1 2 2 total 0.000174 0.000174
+24 1 1 2 3 total 0.000348 0.000213
+25 1 1 2 4 total 0.000174 0.000174
+26 1 1 2 5 total 0.000000 0.000000
27 1 1 2 6 total 0.000000 0.000000
28 1 1 2 7 total 0.000000 0.000000
29 1 1 2 8 total 0.000000 0.000000
30 1 1 2 9 total 0.000000 0.000000
-31 1 1 2 10 total 0.000175 0.000175
+31 1 1 2 10 total 0.000000 0.000000
32 1 1 2 11 total 0.000000 0.000000
11 1 2 1 1 total 0.000000 0.000000
12 1 2 1 2 total 0.000000 0.000000
@@ -32,39 +32,39 @@
19 1 2 1 9 total 0.000000 0.000000
20 1 2 1 10 total 0.000000 0.000000
21 1 2 1 11 total 0.000000 0.000000
-0 1 2 2 1 total 0.023599 0.005270
-1 1 2 2 2 total 0.036471 0.008401
-2 1 2 2 3 total 0.034325 0.003271
-3 1 2 2 4 total 0.030035 0.003674
-4 1 2 2 5 total 0.039688 0.001478
-5 1 2 2 6 total 0.033253 0.005499
-6 1 2 2 7 total 0.039688 0.004725
-7 1 2 2 8 total 0.031107 0.006458
-8 1 2 2 9 total 0.031107 0.005996
-9 1 2 2 10 total 0.052560 0.005543
-10 1 2 2 11 total 0.033253 0.002688
+0 1 2 2 1 total 0.032383 0.006826
+1 1 2 2 2 total 0.037146 0.001158
+2 1 2 2 3 total 0.036193 0.004463
+3 1 2 2 4 total 0.036193 0.007028
+4 1 2 2 5 total 0.038098 0.006769
+5 1 2 2 6 total 0.024764 0.004638
+6 1 2 2 7 total 0.034288 0.008049
+7 1 2 2 8 total 0.040003 0.007350
+8 1 2 2 9 total 0.032383 0.003211
+9 1 2 2 10 total 0.050480 0.005824
+10 1 2 2 11 total 0.045718 0.013291
material group in group out mu bin nuclide mean std. dev.
-33 1 1 1 1 total 0.028385 0.002919
-34 1 1 1 2 total 0.031890 0.001548
-35 1 1 1 3 total 0.027860 0.002738
-36 1 1 1 4 total 0.035920 0.003337
-37 1 1 1 5 total 0.034343 0.001897
-38 1 1 1 6 total 0.032591 0.002289
-39 1 1 1 7 total 0.033467 0.002209
-40 1 1 1 8 total 0.031714 0.002398
-41 1 1 1 9 total 0.033467 0.003343
-42 1 1 1 10 total 0.041001 0.002362
-43 1 1 1 11 total 0.060801 0.003580
+33 1 1 1 1 total 0.032861 0.003703
+34 1 1 1 2 total 0.026428 0.003637
+35 1 1 1 3 total 0.029210 0.001648
+36 1 1 1 4 total 0.032513 0.004770
+37 1 1 1 5 total 0.030949 0.003129
+38 1 1 1 6 total 0.027124 0.004029
+39 1 1 1 7 total 0.030079 0.002186
+40 1 1 1 8 total 0.037034 0.002198
+41 1 1 1 9 total 0.038251 0.003825
+42 1 1 1 10 total 0.039294 0.003626
+43 1 1 1 11 total 0.062593 0.005934
22 1 1 2 1 total 0.000000 0.000000
-23 1 1 2 2 total 0.000350 0.000351
-24 1 1 2 3 total 0.000175 0.000175
-25 1 1 2 4 total 0.000000 0.000000
-26 1 1 2 5 total 0.000175 0.000175
+23 1 1 2 2 total 0.000174 0.000174
+24 1 1 2 3 total 0.000348 0.000213
+25 1 1 2 4 total 0.000174 0.000174
+26 1 1 2 5 total 0.000000 0.000000
27 1 1 2 6 total 0.000000 0.000000
28 1 1 2 7 total 0.000000 0.000000
29 1 1 2 8 total 0.000000 0.000000
30 1 1 2 9 total 0.000000 0.000000
-31 1 1 2 10 total 0.000175 0.000175
+31 1 1 2 10 total 0.000000 0.000000
32 1 1 2 11 total 0.000000 0.000000
11 1 2 1 1 total 0.000000 0.000000
12 1 2 1 2 total 0.000000 0.000000
@@ -77,39 +77,39 @@
19 1 2 1 9 total 0.000000 0.000000
20 1 2 1 10 total 0.000000 0.000000
21 1 2 1 11 total 0.000000 0.000000
-0 1 2 2 1 total 0.023599 0.005270
-1 1 2 2 2 total 0.036471 0.008401
-2 1 2 2 3 total 0.034325 0.003271
-3 1 2 2 4 total 0.030035 0.003674
-4 1 2 2 5 total 0.039688 0.001478
-5 1 2 2 6 total 0.033253 0.005499
-6 1 2 2 7 total 0.039688 0.004725
-7 1 2 2 8 total 0.031107 0.006458
-8 1 2 2 9 total 0.031107 0.005996
-9 1 2 2 10 total 0.052560 0.005543
-10 1 2 2 11 total 0.033253 0.002688
+0 1 2 2 1 total 0.032383 0.006826
+1 1 2 2 2 total 0.037146 0.001158
+2 1 2 2 3 total 0.036193 0.004463
+3 1 2 2 4 total 0.036193 0.007028
+4 1 2 2 5 total 0.038098 0.006769
+5 1 2 2 6 total 0.024764 0.004638
+6 1 2 2 7 total 0.034288 0.008049
+7 1 2 2 8 total 0.040003 0.007350
+8 1 2 2 9 total 0.032383 0.003211
+9 1 2 2 10 total 0.050480 0.005824
+10 1 2 2 11 total 0.045718 0.013291
material group in group out mu bin nuclide mean std. dev.
-33 1 1 1 1 total 0.028162 0.003056
-34 1 1 1 2 total 0.031639 0.001886
-35 1 1 1 3 total 0.027466 0.002746
-36 1 1 1 4 total 0.035637 0.003533
-37 1 1 1 5 total 0.034072 0.002221
-38 1 1 1 6 total 0.032334 0.002532
-39 1 1 1 7 total 0.033203 0.002475
-40 1 1 1 8 total 0.031465 0.002617
-41 1 1 1 9 total 0.033203 0.003510
-42 1 1 1 10 total 0.040678 0.002734
-43 1 1 1 11 total 0.060322 0.004120
+33 1 1 1 1 total 0.032927 0.003848
+34 1 1 1 2 total 0.026481 0.003736
+35 1 1 1 3 total 0.029268 0.001884
+36 1 1 1 4 total 0.032578 0.004885
+37 1 1 1 5 total 0.031010 0.003280
+38 1 1 1 6 total 0.027177 0.004124
+39 1 1 1 7 total 0.030139 0.002382
+40 1 1 1 8 total 0.037108 0.002485
+41 1 1 1 9 total 0.038327 0.004013
+42 1 1 1 10 total 0.039372 0.003833
+43 1 1 1 11 total 0.062717 0.006256
22 1 1 2 1 total 0.000000 0.000000
-23 1 1 2 2 total 0.000348 0.000348
-24 1 1 2 3 total 0.000174 0.000174
-25 1 1 2 4 total 0.000000 0.000000
-26 1 1 2 5 total 0.000174 0.000174
+23 1 1 2 2 total 0.000174 0.000174
+24 1 1 2 3 total 0.000348 0.000214
+25 1 1 2 4 total 0.000174 0.000174
+26 1 1 2 5 total 0.000000 0.000000
27 1 1 2 6 total 0.000000 0.000000
28 1 1 2 7 total 0.000000 0.000000
29 1 1 2 8 total 0.000000 0.000000
30 1 1 2 9 total 0.000000 0.000000
-31 1 1 2 10 total 0.000174 0.000174
+31 1 1 2 10 total 0.000000 0.000000
32 1 1 2 11 total 0.000000 0.000000
11 1 2 1 1 total 0.000000 0.000000
12 1 2 1 2 total 0.000000 0.000000
@@ -122,39 +122,39 @@
19 1 2 1 9 total 0.000000 0.000000
20 1 2 1 10 total 0.000000 0.000000
21 1 2 1 11 total 0.000000 0.000000
-0 1 2 2 1 total 0.024246 0.005837
-1 1 2 2 2 total 0.037470 0.009265
-2 1 2 2 3 total 0.035266 0.004620
-3 1 2 2 4 total 0.030858 0.004684
-4 1 2 2 5 total 0.040777 0.003968
-5 1 2 2 6 total 0.034164 0.006431
-6 1 2 2 7 total 0.040777 0.006083
-7 1 2 2 8 total 0.031960 0.007230
-8 1 2 2 9 total 0.031960 0.006797
-9 1 2 2 10 total 0.054002 0.007483
-10 1 2 2 11 total 0.034164 0.004130
+0 1 2 2 1 total 0.031440 0.006860
+1 1 2 2 2 total 0.036063 0.002322
+2 1 2 2 3 total 0.035138 0.004763
+3 1 2 2 4 total 0.035138 0.007105
+4 1 2 2 5 total 0.036988 0.006894
+5 1 2 2 6 total 0.024042 0.004702
+6 1 2 2 7 total 0.033289 0.008036
+7 1 2 2 8 total 0.038837 0.007464
+8 1 2 2 9 total 0.031440 0.003585
+9 1 2 2 10 total 0.049009 0.006292
+10 1 2 2 11 total 0.044385 0.013144
material group in group out mu bin nuclide mean std. dev.
-33 1 1 1 1 total 0.028174 0.003144
-34 1 1 1 2 total 0.031653 0.002058
-35 1 1 1 3 total 0.027479 0.002838
-36 1 1 1 4 total 0.035653 0.003654
-37 1 1 1 5 total 0.034088 0.002392
-38 1 1 1 6 total 0.032348 0.002668
-39 1 1 1 7 total 0.033218 0.002621
-40 1 1 1 8 total 0.031479 0.002742
-41 1 1 1 9 total 0.033218 0.003616
-42 1 1 1 10 total 0.040696 0.002931
-43 1 1 1 11 total 0.060349 0.004409
+33 1 1 1 1 total 0.032927 0.004236
+34 1 1 1 2 total 0.026481 0.003998
+35 1 1 1 3 total 0.029268 0.002455
+36 1 1 1 4 total 0.032578 0.005190
+37 1 1 1 5 total 0.031010 0.003679
+38 1 1 1 6 total 0.027177 0.004376
+39 1 1 1 7 total 0.030139 0.002881
+40 1 1 1 8 total 0.037108 0.003187
+41 1 1 1 9 total 0.038327 0.004511
+42 1 1 1 10 total 0.039372 0.004379
+43 1 1 1 11 total 0.062717 0.007108
22 1 1 2 1 total 0.000000 0.000000
-23 1 1 2 2 total 0.000348 0.000451
-24 1 1 2 3 total 0.000174 0.000225
-25 1 1 2 4 total 0.000000 0.000000
-26 1 1 2 5 total 0.000174 0.000225
+23 1 1 2 2 total 0.000174 0.000209
+24 1 1 2 3 total 0.000348 0.000315
+25 1 1 2 4 total 0.000174 0.000209
+26 1 1 2 5 total 0.000000 0.000000
27 1 1 2 6 total 0.000000 0.000000
28 1 1 2 7 total 0.000000 0.000000
29 1 1 2 8 total 0.000000 0.000000
30 1 1 2 9 total 0.000000 0.000000
-31 1 1 2 10 total 0.000174 0.000225
+31 1 1 2 10 total 0.000000 0.000000
32 1 1 2 11 total 0.000000 0.000000
11 1 2 1 1 total 0.000000 0.000000
12 1 2 1 2 total 0.000000 0.000000
@@ -167,29 +167,29 @@
19 1 2 1 9 total 0.000000 0.000000
20 1 2 1 10 total 0.000000 0.000000
21 1 2 1 11 total 0.000000 0.000000
-0 1 2 2 1 total 0.024246 0.006112
-1 1 2 2 2 total 0.037470 0.009679
-2 1 2 2 3 total 0.035266 0.005319
-3 1 2 2 4 total 0.030858 0.005221
-4 1 2 2 5 total 0.040777 0.005003
-5 1 2 2 6 total 0.034164 0.006919
-6 1 2 2 7 total 0.040777 0.006803
-7 1 2 2 8 total 0.031960 0.007614
-8 1 2 2 9 total 0.031960 0.007205
-9 1 2 2 10 total 0.054002 0.008502
-10 1 2 2 11 total 0.034164 0.004856
+0 1 2 2 1 total 0.031440 0.007170
+1 1 2 2 2 total 0.036063 0.003334
+2 1 2 2 3 total 0.035138 0.005303
+3 1 2 2 4 total 0.035138 0.007478
+4 1 2 2 5 total 0.036988 0.007318
+5 1 2 2 6 total 0.024042 0.004965
+6 1 2 2 7 total 0.033289 0.008334
+7 1 2 2 8 total 0.038837 0.007896
+8 1 2 2 9 total 0.031440 0.004148
+9 1 2 2 10 total 0.049009 0.007083
+10 1 2 2 11 total 0.044385 0.013469
material group in group out mu bin nuclide mean std. dev.
-33 2 1 1 1 total 0.025262 0.003309
-34 2 1 1 2 total 0.023805 0.004083
-35 2 1 1 3 total 0.027205 0.001631
-36 2 1 1 4 total 0.021376 0.003175
-37 2 1 1 5 total 0.017489 0.002412
-38 2 1 1 6 total 0.024291 0.002862
-39 2 1 1 7 total 0.029634 0.005250
-40 2 1 1 8 total 0.025262 0.001228
-41 2 1 1 9 total 0.028663 0.003403
-42 2 1 1 10 total 0.034493 0.004425
-43 2 1 1 11 total 0.052467 0.006227
+33 2 1 1 1 total 0.026798 0.002892
+34 2 1 1 2 total 0.021339 0.003475
+35 2 1 1 3 total 0.021835 0.003963
+36 2 1 1 4 total 0.018361 0.006133
+37 2 1 1 5 total 0.023820 0.003932
+38 2 1 1 6 total 0.025805 0.003808
+39 2 1 1 7 total 0.026798 0.002299
+40 2 1 1 8 total 0.029279 0.003939
+41 2 1 1 9 total 0.034738 0.004323
+42 2 1 1 10 total 0.032753 0.006086
+43 2 1 1 11 total 0.057069 0.003798
22 2 1 2 1 total 0.000000 0.000000
23 2 1 2 2 total 0.000000 0.000000
24 2 1 2 3 total 0.000000 0.000000
@@ -199,7 +199,7 @@
28 2 1 2 7 total 0.000000 0.000000
29 2 1 2 8 total 0.000000 0.000000
30 2 1 2 9 total 0.000000 0.000000
-31 2 1 2 10 total 0.000486 0.000486
+31 2 1 2 10 total 0.000000 0.000000
32 2 1 2 11 total 0.000000 0.000000
11 2 2 1 1 total 0.000000 0.000000
12 2 2 1 2 total 0.000000 0.000000
@@ -212,29 +212,29 @@
19 2 2 1 9 total 0.000000 0.000000
20 2 2 1 10 total 0.000000 0.000000
21 2 2 1 11 total 0.000000 0.000000
-0 2 2 2 1 total 0.032689 0.010313
-1 2 2 2 2 total 0.035958 0.011071
-2 2 2 2 3 total 0.019614 0.012398
-3 2 2 2 4 total 0.022883 0.009072
-4 2 2 2 5 total 0.009807 0.009926
-5 2 2 2 6 total 0.029420 0.011781
-6 2 2 2 7 total 0.032689 0.014602
-7 2 2 2 8 total 0.019614 0.006844
-8 2 2 2 9 total 0.032689 0.010313
-9 2 2 2 10 total 0.022883 0.009072
-10 2 2 2 11 total 0.029420 0.005650
+0 2 2 2 1 total 0.032254 0.009449
+1 2 2 2 2 total 0.018815 0.005569
+2 2 2 2 3 total 0.032254 0.009449
+3 2 2 2 4 total 0.024191 0.006844
+4 2 2 2 5 total 0.013439 0.008563
+5 2 2 2 6 total 0.024191 0.005365
+6 2 2 2 7 total 0.043005 0.010420
+7 2 2 2 8 total 0.032254 0.012710
+8 2 2 2 9 total 0.034942 0.007365
+9 2 2 2 10 total 0.021503 0.007051
+10 2 2 2 11 total 0.018815 0.008193
material group in group out mu bin nuclide mean std. dev.
-33 2 1 1 1 total 0.025262 0.003309
-34 2 1 1 2 total 0.023805 0.004083
-35 2 1 1 3 total 0.027205 0.001631
-36 2 1 1 4 total 0.021376 0.003175
-37 2 1 1 5 total 0.017489 0.002412
-38 2 1 1 6 total 0.024291 0.002862
-39 2 1 1 7 total 0.029634 0.005250
-40 2 1 1 8 total 0.025262 0.001228
-41 2 1 1 9 total 0.028663 0.003403
-42 2 1 1 10 total 0.034493 0.004425
-43 2 1 1 11 total 0.052467 0.006227
+33 2 1 1 1 total 0.026798 0.002892
+34 2 1 1 2 total 0.021339 0.003475
+35 2 1 1 3 total 0.021835 0.003963
+36 2 1 1 4 total 0.018361 0.006133
+37 2 1 1 5 total 0.023820 0.003932
+38 2 1 1 6 total 0.025805 0.003808
+39 2 1 1 7 total 0.026798 0.002299
+40 2 1 1 8 total 0.029279 0.003939
+41 2 1 1 9 total 0.034738 0.004323
+42 2 1 1 10 total 0.032753 0.006086
+43 2 1 1 11 total 0.057069 0.003798
22 2 1 2 1 total 0.000000 0.000000
23 2 1 2 2 total 0.000000 0.000000
24 2 1 2 3 total 0.000000 0.000000
@@ -244,7 +244,7 @@
28 2 1 2 7 total 0.000000 0.000000
29 2 1 2 8 total 0.000000 0.000000
30 2 1 2 9 total 0.000000 0.000000
-31 2 1 2 10 total 0.000486 0.000486
+31 2 1 2 10 total 0.000000 0.000000
32 2 1 2 11 total 0.000000 0.000000
11 2 2 1 1 total 0.000000 0.000000
12 2 2 1 2 total 0.000000 0.000000
@@ -257,29 +257,29 @@
19 2 2 1 9 total 0.000000 0.000000
20 2 2 1 10 total 0.000000 0.000000
21 2 2 1 11 total 0.000000 0.000000
-0 2 2 2 1 total 0.032689 0.010313
-1 2 2 2 2 total 0.035958 0.011071
-2 2 2 2 3 total 0.019614 0.012398
-3 2 2 2 4 total 0.022883 0.009072
-4 2 2 2 5 total 0.009807 0.009926
-5 2 2 2 6 total 0.029420 0.011781
-6 2 2 2 7 total 0.032689 0.014602
-7 2 2 2 8 total 0.019614 0.006844
-8 2 2 2 9 total 0.032689 0.010313
-9 2 2 2 10 total 0.022883 0.009072
-10 2 2 2 11 total 0.029420 0.005650
+0 2 2 2 1 total 0.032254 0.009449
+1 2 2 2 2 total 0.018815 0.005569
+2 2 2 2 3 total 0.032254 0.009449
+3 2 2 2 4 total 0.024191 0.006844
+4 2 2 2 5 total 0.013439 0.008563
+5 2 2 2 6 total 0.024191 0.005365
+6 2 2 2 7 total 0.043005 0.010420
+7 2 2 2 8 total 0.032254 0.012710
+8 2 2 2 9 total 0.034942 0.007365
+9 2 2 2 10 total 0.021503 0.007051
+10 2 2 2 11 total 0.018815 0.008193
material group in group out mu bin nuclide mean std. dev.
-33 2 1 1 1 total 0.025312 0.003469
-34 2 1 1 2 total 0.023852 0.004203
-35 2 1 1 3 total 0.027259 0.001971
-36 2 1 1 4 total 0.021418 0.003297
-37 2 1 1 5 total 0.017524 0.002518
-38 2 1 1 6 total 0.024339 0.003032
-39 2 1 1 7 total 0.029693 0.005395
-40 2 1 1 8 total 0.025312 0.001600
-41 2 1 1 9 total 0.028719 0.003602
-42 2 1 1 10 total 0.034561 0.004648
-43 2 1 1 11 total 0.052571 0.006591
+33 2 1 1 1 total 0.026249 0.003012
+34 2 1 1 2 total 0.020902 0.003500
+35 2 1 1 3 total 0.021388 0.003971
+36 2 1 1 4 total 0.017986 0.006048
+37 2 1 1 5 total 0.023333 0.003958
+38 2 1 1 6 total 0.025277 0.003858
+39 2 1 1 7 total 0.026249 0.002473
+40 2 1 1 8 total 0.028680 0.004017
+41 2 1 1 9 total 0.034027 0.004437
+42 2 1 1 10 total 0.032082 0.006091
+43 2 1 1 11 total 0.055901 0.004311
22 2 1 2 1 total 0.000000 0.000000
23 2 1 2 2 total 0.000000 0.000000
24 2 1 2 3 total 0.000000 0.000000
@@ -289,7 +289,7 @@
28 2 1 2 7 total 0.000000 0.000000
29 2 1 2 8 total 0.000000 0.000000
30 2 1 2 9 total 0.000000 0.000000
-31 2 1 2 10 total 0.000487 0.000487
+31 2 1 2 10 total 0.000000 0.000000
32 2 1 2 11 total 0.000000 0.000000
11 2 2 1 1 total 0.000000 0.000000
12 2 2 1 2 total 0.000000 0.000000
@@ -302,29 +302,29 @@
19 2 2 1 9 total 0.000000 0.000000
20 2 2 1 10 total 0.000000 0.000000
21 2 2 1 11 total 0.000000 0.000000
-0 2 2 2 1 total 0.033560 0.010222
-1 2 2 2 2 total 0.036916 0.010953
-2 2 2 2 3 total 0.020136 0.012619
-3 2 2 2 4 total 0.023492 0.009111
-4 2 2 2 5 total 0.010068 0.010157
-5 2 2 2 6 total 0.030204 0.011837
-6 2 2 2 7 total 0.033560 0.014735
-7 2 2 2 8 total 0.020136 0.006828
-8 2 2 2 9 total 0.033560 0.010222
-9 2 2 2 10 total 0.023492 0.009111
-10 2 2 2 11 total 0.030204 0.005242
+0 2 2 2 1 total 0.032230 0.009604
+1 2 2 2 2 total 0.018801 0.005658
+2 2 2 2 3 total 0.032230 0.009604
+3 2 2 2 4 total 0.024172 0.006964
+4 2 2 2 5 total 0.013429 0.008588
+5 2 2 2 6 total 0.024172 0.005520
+6 2 2 2 7 total 0.042973 0.010671
+7 2 2 2 8 total 0.032230 0.012821
+8 2 2 2 9 total 0.034915 0.007601
+9 2 2 2 10 total 0.021486 0.007142
+10 2 2 2 11 total 0.018801 0.008251
material group in group out mu bin nuclide mean std. dev.
-33 2 1 1 1 total 0.025312 0.003700
-34 2 1 1 2 total 0.023852 0.004373
-35 2 1 1 3 total 0.027259 0.002407
-36 2 1 1 4 total 0.021418 0.003471
-37 2 1 1 5 total 0.017524 0.002670
-38 2 1 1 6 total 0.024339 0.003273
-39 2 1 1 7 total 0.029693 0.005602
-40 2 1 1 8 total 0.025312 0.002052
-41 2 1 1 9 total 0.028719 0.003886
-42 2 1 1 10 total 0.034561 0.004968
-43 2 1 1 11 total 0.052571 0.007110
+33 2 1 1 1 total 0.026249 0.003460
+34 2 1 1 2 total 0.020902 0.003754
+35 2 1 1 3 total 0.021388 0.004206
+36 2 1 1 4 total 0.017986 0.006160
+37 2 1 1 5 total 0.023333 0.004238
+38 2 1 1 6 total 0.025277 0.004192
+39 2 1 1 7 total 0.026249 0.003003
+40 2 1 1 8 total 0.028680 0.004427
+41 2 1 1 9 total 0.034027 0.004956
+42 2 1 1 10 total 0.032082 0.006437
+43 2 1 1 11 total 0.055901 0.005636
22 2 1 2 1 total 0.000000 0.000000
23 2 1 2 2 total 0.000000 0.000000
24 2 1 2 3 total 0.000000 0.000000
@@ -334,7 +334,7 @@
28 2 1 2 7 total 0.000000 0.000000
29 2 1 2 8 total 0.000000 0.000000
30 2 1 2 9 total 0.000000 0.000000
-31 2 1 2 10 total 0.000487 0.000843
+31 2 1 2 10 total 0.000000 0.000000
32 2 1 2 11 total 0.000000 0.000000
11 2 2 1 1 total 0.000000 0.000000
12 2 2 1 2 total 0.000000 0.000000
@@ -347,40 +347,40 @@
19 2 2 1 9 total 0.000000 0.000000
20 2 2 1 10 total 0.000000 0.000000
21 2 2 1 11 total 0.000000 0.000000
-0 2 2 2 1 total 0.033560 0.011889
-1 2 2 2 2 total 0.036916 0.012828
-2 2 2 2 3 total 0.020136 0.013135
-3 2 2 2 4 total 0.023492 0.010054
-4 2 2 2 5 total 0.010068 0.010319
-5 2 2 2 6 total 0.030204 0.013037
-6 2 2 2 7 total 0.033560 0.015937
-7 2 2 2 8 total 0.020136 0.007739
-8 2 2 2 9 total 0.033560 0.011889
-9 2 2 2 10 total 0.023492 0.010054
-10 2 2 2 11 total 0.030204 0.007573
+0 2 2 2 1 total 0.032230 0.010330
+1 2 2 2 2 total 0.018801 0.006077
+2 2 2 2 3 total 0.032230 0.010330
+3 2 2 2 4 total 0.024172 0.007526
+4 2 2 2 5 total 0.013429 0.008733
+5 2 2 2 6 total 0.024172 0.006213
+6 2 2 2 7 total 0.042973 0.011815
+7 2 2 2 8 total 0.032230 0.013373
+8 2 2 2 9 total 0.034915 0.008646
+9 2 2 2 10 total 0.021486 0.007579
+10 2 2 2 11 total 0.018801 0.008544
material group in group out mu bin nuclide mean std. dev.
-33 3 1 1 1 total 0.008818 0.001587
-34 3 1 1 2 total 0.006389 0.000610
-35 3 1 1 3 total 0.007288 0.000775
-36 3 1 1 4 total 0.008008 0.001111
-37 3 1 1 5 total 0.007828 0.000452
-38 3 1 1 6 total 0.011247 0.000473
-39 3 1 1 7 total 0.039411 0.002111
-40 3 1 1 8 total 0.071443 0.002082
-41 3 1 1 9 total 0.115713 0.004165
-42 3 1 1 10 total 0.164662 0.005479
-43 3 1 1 11 total 0.214060 0.006189
-22 3 1 2 1 total 0.000360 0.000090
-23 3 1 2 2 total 0.000810 0.000169
-24 3 1 2 3 total 0.000810 0.000331
-25 3 1 2 4 total 0.001440 0.000332
-26 3 1 2 5 total 0.002339 0.000267
-27 3 1 2 6 total 0.003149 0.000256
-28 3 1 2 7 total 0.004409 0.000601
-29 3 1 2 8 total 0.004139 0.000398
-30 3 1 2 9 total 0.004769 0.000639
-31 3 1 2 10 total 0.004769 0.000453
-32 3 1 2 11 total 0.002789 0.000630
+33 3 1 1 1 total 0.007006 0.000692
+34 3 1 1 2 total 0.006819 0.000431
+35 3 1 1 3 total 0.005511 0.000591
+36 3 1 1 4 total 0.006165 0.000470
+37 3 1 1 5 total 0.007660 0.000919
+38 3 1 1 6 total 0.012237 0.000938
+39 3 1 1 7 total 0.040914 0.002235
+40 3 1 1 8 total 0.074356 0.001968
+41 3 1 1 9 total 0.121622 0.004662
+42 3 1 1 10 total 0.158707 0.004147
+43 3 1 1 11 total 0.200742 0.007791
+22 3 1 2 1 total 0.000187 0.000187
+23 3 1 2 2 total 0.001028 0.000096
+24 3 1 2 3 total 0.000841 0.000176
+25 3 1 2 4 total 0.000841 0.000310
+26 3 1 2 5 total 0.001308 0.000274
+27 3 1 2 6 total 0.003736 0.000538
+28 3 1 2 7 total 0.003830 0.000703
+29 3 1 2 8 total 0.006259 0.000452
+30 3 1 2 9 total 0.005231 0.000510
+31 3 1 2 10 total 0.005044 0.000440
+32 3 1 2 11 total 0.002522 0.000194
11 3 2 1 1 total 0.000000 0.000000
12 3 2 1 2 total 0.000000 0.000000
13 3 2 1 3 total 0.000000 0.000000
@@ -390,42 +390,42 @@
17 3 2 1 7 total 0.000000 0.000000
18 3 2 1 8 total 0.000000 0.000000
19 3 2 1 9 total 0.000000 0.000000
-20 3 2 1 10 total 0.000000 0.000000
+20 3 2 1 10 total 0.000467 0.000467
21 3 2 1 11 total 0.000000 0.000000
-0 3 2 2 1 total 0.086327 0.004499
-1 3 2 2 2 total 0.088278 0.008634
-2 3 2 2 3 total 0.108275 0.008710
-3 3 2 2 4 total 0.115103 0.005859
-4 3 2 2 5 total 0.139489 0.012654
-5 3 2 2 6 total 0.152658 0.005193
-6 3 2 2 7 total 0.182897 0.007164
-7 3 2 2 8 total 0.202894 0.014663
-8 3 2 2 9 total 0.268249 0.019575
-9 3 2 2 10 total 0.294098 0.015467
-10 3 2 2 11 total 0.354088 0.012355
+0 3 2 2 1 total 0.084030 0.007630
+1 3 2 2 2 total 0.099902 0.010027
+2 3 2 2 3 total 0.112040 0.010928
+3 3 2 2 4 total 0.117642 0.008523
+4 3 2 2 5 total 0.139116 0.009002
+5 3 2 2 6 total 0.161057 0.013537
+6 3 2 2 7 total 0.180664 0.010135
+7 3 2 2 8 total 0.219411 0.014717
+8 3 2 2 9 total 0.239485 0.027005
+9 3 2 2 10 total 0.281033 0.021376
+10 3 2 2 11 total 0.369731 0.027200
material group in group out mu bin nuclide mean std. dev.
-33 3 1 1 1 total 0.008818 0.001587
-34 3 1 1 2 total 0.006389 0.000610
-35 3 1 1 3 total 0.007288 0.000775
-36 3 1 1 4 total 0.008008 0.001111
-37 3 1 1 5 total 0.007828 0.000452
-38 3 1 1 6 total 0.011247 0.000473
-39 3 1 1 7 total 0.039411 0.002111
-40 3 1 1 8 total 0.071443 0.002082
-41 3 1 1 9 total 0.115713 0.004165
-42 3 1 1 10 total 0.164662 0.005479
-43 3 1 1 11 total 0.214060 0.006189
-22 3 1 2 1 total 0.000360 0.000090
-23 3 1 2 2 total 0.000810 0.000169
-24 3 1 2 3 total 0.000810 0.000331
-25 3 1 2 4 total 0.001440 0.000332
-26 3 1 2 5 total 0.002339 0.000267
-27 3 1 2 6 total 0.003149 0.000256
-28 3 1 2 7 total 0.004409 0.000601
-29 3 1 2 8 total 0.004139 0.000398
-30 3 1 2 9 total 0.004769 0.000639
-31 3 1 2 10 total 0.004769 0.000453
-32 3 1 2 11 total 0.002789 0.000630
+33 3 1 1 1 total 0.007006 0.000692
+34 3 1 1 2 total 0.006819 0.000431
+35 3 1 1 3 total 0.005511 0.000591
+36 3 1 1 4 total 0.006165 0.000470
+37 3 1 1 5 total 0.007660 0.000919
+38 3 1 1 6 total 0.012237 0.000938
+39 3 1 1 7 total 0.040914 0.002235
+40 3 1 1 8 total 0.074356 0.001968
+41 3 1 1 9 total 0.121622 0.004662
+42 3 1 1 10 total 0.158707 0.004147
+43 3 1 1 11 total 0.200742 0.007791
+22 3 1 2 1 total 0.000187 0.000187
+23 3 1 2 2 total 0.001028 0.000096
+24 3 1 2 3 total 0.000841 0.000176
+25 3 1 2 4 total 0.000841 0.000310
+26 3 1 2 5 total 0.001308 0.000274
+27 3 1 2 6 total 0.003736 0.000538
+28 3 1 2 7 total 0.003830 0.000703
+29 3 1 2 8 total 0.006259 0.000452
+30 3 1 2 9 total 0.005231 0.000510
+31 3 1 2 10 total 0.005044 0.000440
+32 3 1 2 11 total 0.002522 0.000194
11 3 2 1 1 total 0.000000 0.000000
12 3 2 1 2 total 0.000000 0.000000
13 3 2 1 3 total 0.000000 0.000000
@@ -435,42 +435,42 @@
17 3 2 1 7 total 0.000000 0.000000
18 3 2 1 8 total 0.000000 0.000000
19 3 2 1 9 total 0.000000 0.000000
-20 3 2 1 10 total 0.000000 0.000000
+20 3 2 1 10 total 0.000467 0.000467
21 3 2 1 11 total 0.000000 0.000000
-0 3 2 2 1 total 0.086327 0.004499
-1 3 2 2 2 total 0.088278 0.008634
-2 3 2 2 3 total 0.108275 0.008710
-3 3 2 2 4 total 0.115103 0.005859
-4 3 2 2 5 total 0.139489 0.012654
-5 3 2 2 6 total 0.152658 0.005193
-6 3 2 2 7 total 0.182897 0.007164
-7 3 2 2 8 total 0.202894 0.014663
-8 3 2 2 9 total 0.268249 0.019575
-9 3 2 2 10 total 0.294098 0.015467
-10 3 2 2 11 total 0.354088 0.012355
+0 3 2 2 1 total 0.084030 0.007630
+1 3 2 2 2 total 0.099902 0.010027
+2 3 2 2 3 total 0.112040 0.010928
+3 3 2 2 4 total 0.117642 0.008523
+4 3 2 2 5 total 0.139116 0.009002
+5 3 2 2 6 total 0.161057 0.013537
+6 3 2 2 7 total 0.180664 0.010135
+7 3 2 2 8 total 0.219411 0.014717
+8 3 2 2 9 total 0.239485 0.027005
+9 3 2 2 10 total 0.281033 0.021376
+10 3 2 2 11 total 0.369731 0.027200
material group in group out mu bin nuclide mean std. dev.
-33 3 1 1 1 total 0.008807 0.001589
-34 3 1 1 2 total 0.006381 0.000614
-35 3 1 1 3 total 0.007279 0.000779
-36 3 1 1 4 total 0.007998 0.001113
-37 3 1 1 5 total 0.007818 0.000461
-38 3 1 1 6 total 0.011233 0.000491
-39 3 1 1 7 total 0.039362 0.002160
-40 3 1 1 8 total 0.071354 0.002246
-41 3 1 1 9 total 0.115569 0.004381
-42 3 1 1 10 total 0.164456 0.005812
-43 3 1 1 11 total 0.213793 0.006684
-22 3 1 2 1 total 0.000359 0.000090
-23 3 1 2 2 total 0.000809 0.000169
-24 3 1 2 3 total 0.000809 0.000331
-25 3 1 2 4 total 0.001438 0.000332
-26 3 1 2 5 total 0.002337 0.000269
-27 3 1 2 6 total 0.003145 0.000259
-28 3 1 2 7 total 0.004403 0.000603
-29 3 1 2 8 total 0.004134 0.000400
-30 3 1 2 9 total 0.004763 0.000640
-31 3 1 2 10 total 0.004763 0.000456
-32 3 1 2 11 total 0.002786 0.000630
+33 3 1 1 1 total 0.007106 0.000737
+34 3 1 1 2 total 0.006917 0.000488
+35 3 1 1 3 total 0.005590 0.000624
+36 3 1 1 4 total 0.006254 0.000516
+37 3 1 1 5 total 0.007770 0.000964
+38 3 1 1 6 total 0.012412 0.001029
+39 3 1 1 7 total 0.041501 0.002618
+40 3 1 1 8 total 0.075421 0.003106
+41 3 1 1 9 total 0.123365 0.006125
+42 3 1 1 10 total 0.160981 0.006595
+43 3 1 1 11 total 0.203618 0.010185
+22 3 1 2 1 total 0.000190 0.000190
+23 3 1 2 2 total 0.001042 0.000103
+24 3 1 2 3 total 0.000853 0.000180
+25 3 1 2 4 total 0.000853 0.000316
+26 3 1 2 5 total 0.001327 0.000281
+27 3 1 2 6 total 0.003790 0.000559
+28 3 1 2 7 total 0.003885 0.000724
+29 3 1 2 8 total 0.006348 0.000500
+30 3 1 2 9 total 0.005306 0.000544
+31 3 1 2 10 total 0.005117 0.000475
+32 3 1 2 11 total 0.002558 0.000213
11 3 2 1 1 total 0.000000 0.000000
12 3 2 1 2 total 0.000000 0.000000
13 3 2 1 3 total 0.000000 0.000000
@@ -480,42 +480,42 @@
17 3 2 1 7 total 0.000000 0.000000
18 3 2 1 8 total 0.000000 0.000000
19 3 2 1 9 total 0.000000 0.000000
-20 3 2 1 10 total 0.000000 0.000000
+20 3 2 1 10 total 0.000466 0.000467
21 3 2 1 11 total 0.000000 0.000000
-0 3 2 2 1 total 0.086966 0.006257
-1 3 2 2 2 total 0.088931 0.009752
-2 3 2 2 3 total 0.109076 0.010309
-3 3 2 2 4 total 0.115955 0.008241
-4 3 2 2 5 total 0.140521 0.014528
-5 3 2 2 6 total 0.153787 0.009249
-6 3 2 2 7 total 0.184250 0.011645
-7 3 2 2 8 total 0.204395 0.017916
-8 3 2 2 9 total 0.270233 0.023844
-9 3 2 2 10 total 0.296274 0.021418
-10 3 2 2 11 total 0.356708 0.021633
+0 3 2 2 1 total 0.083912 0.007782
+1 3 2 2 2 total 0.099762 0.010188
+2 3 2 2 3 total 0.111883 0.011115
+3 3 2 2 4 total 0.117477 0.008794
+4 3 2 2 5 total 0.138921 0.009363
+5 3 2 2 6 total 0.160831 0.013853
+6 3 2 2 7 total 0.180411 0.010676
+7 3 2 2 8 total 0.219104 0.015265
+8 3 2 2 9 total 0.239149 0.027341
+9 3 2 2 10 total 0.280639 0.021991
+10 3 2 2 11 total 0.369213 0.028038
material group in group out mu bin nuclide mean std. dev.
-33 3 1 1 1 total 0.008807 0.001597
-34 3 1 1 2 total 0.006381 0.000625
-35 3 1 1 3 total 0.007279 0.000790
-36 3 1 1 4 total 0.007998 0.001123
-37 3 1 1 5 total 0.007818 0.000482
-38 3 1 1 6 total 0.011233 0.000531
-39 3 1 1 7 total 0.039362 0.002274
-40 3 1 1 8 total 0.071354 0.002589
-41 3 1 1 9 total 0.115569 0.004852
-42 3 1 1 10 total 0.164456 0.006526
-43 3 1 1 11 total 0.213793 0.007718
-22 3 1 2 1 total 0.000359 0.000092
-23 3 1 2 2 total 0.000809 0.000174
-24 3 1 2 3 total 0.000809 0.000333
-25 3 1 2 4 total 0.001438 0.000340
-26 3 1 2 5 total 0.002337 0.000295
-27 3 1 2 6 total 0.003145 0.000306
-28 3 1 2 7 total 0.004403 0.000645
-29 3 1 2 8 total 0.004134 0.000454
-30 3 1 2 9 total 0.004763 0.000686
-31 3 1 2 10 total 0.004763 0.000519
-32 3 1 2 11 total 0.002786 0.000646
+33 3 1 1 1 total 0.007106 0.000751
+34 3 1 1 2 total 0.006917 0.000509
+35 3 1 1 3 total 0.005590 0.000635
+36 3 1 1 4 total 0.006254 0.000532
+37 3 1 1 5 total 0.007770 0.000977
+38 3 1 1 6 total 0.012412 0.001060
+39 3 1 1 7 total 0.041501 0.002755
+40 3 1 1 8 total 0.075421 0.003475
+41 3 1 1 9 total 0.123365 0.006634
+42 3 1 1 10 total 0.160981 0.007387
+43 3 1 1 11 total 0.203618 0.011019
+22 3 1 2 1 total 0.000190 0.000190
+23 3 1 2 2 total 0.001042 0.000114
+24 3 1 2 3 total 0.000853 0.000185
+25 3 1 2 4 total 0.000853 0.000319
+26 3 1 2 5 total 0.001327 0.000288
+27 3 1 2 6 total 0.003790 0.000588
+28 3 1 2 7 total 0.003885 0.000748
+29 3 1 2 8 total 0.006348 0.000587
+30 3 1 2 9 total 0.005306 0.000601
+31 3 1 2 10 total 0.005117 0.000535
+32 3 1 2 11 total 0.002558 0.000246
11 3 2 1 1 total 0.000000 0.000000
12 3 2 1 2 total 0.000000 0.000000
13 3 2 1 3 total 0.000000 0.000000
@@ -525,16 +525,16 @@
17 3 2 1 7 total 0.000000 0.000000
18 3 2 1 8 total 0.000000 0.000000
19 3 2 1 9 total 0.000000 0.000000
-20 3 2 1 10 total 0.000000 0.000000
+20 3 2 1 10 total 0.000466 0.000808
21 3 2 1 11 total 0.000000 0.000000
-0 3 2 2 1 total 0.086966 0.007070
-1 3 2 2 2 total 0.088931 0.010317
-2 3 2 2 3 total 0.109076 0.011105
-3 3 2 2 4 total 0.115955 0.009338
-4 3 2 2 5 total 0.140521 0.015472
-5 3 2 2 6 total 0.153787 0.010930
-6 3 2 2 7 total 0.184250 0.013575
-7 3 2 2 8 total 0.204395 0.019516
-8 3 2 2 9 total 0.270233 0.025947
-9 3 2 2 10 total 0.296274 0.024178
-10 3 2 2 11 total 0.356708 0.025503
+0 3 2 2 1 total 0.083912 0.008936
+1 3 2 2 2 total 0.099762 0.011448
+2 3 2 2 3 total 0.111883 0.012563
+3 3 2 2 4 total 0.117477 0.010731
+4 3 2 2 5 total 0.138921 0.011855
+5 3 2 2 6 total 0.160831 0.016211
+6 3 2 2 7 total 0.180411 0.014254
+7 3 2 2 8 total 0.219104 0.019093
+8 3 2 2 9 total 0.239149 0.030071
+9 3 2 2 10 total 0.280639 0.026447
+10 3 2 2 11 total 0.369213 0.034054
diff --git a/tests/regression_tests/mgxs_library_mesh/results_true.dat b/tests/regression_tests/mgxs_library_mesh/results_true.dat
--- a/tests/regression_tests/mgxs_library_mesh/results_true.dat
+++ b/tests/regression_tests/mgxs_library_mesh/results_true.dat
@@ -1,362 +1,362 @@
mesh 1 group in nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.102319 0.005483
-2 1 2 1 1 total 0.104659 0.002878
-1 2 1 1 1 total 0.107122 0.005105
-3 2 2 1 1 total 0.103856 0.003459
+0 1 1 1 1 total 0.102539 0.004894
+2 1 2 1 1 total 0.106476 0.007513
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in group out legendre nuclide mean std. dev.
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mesh 1 group in group out legendre nuclide mean std. dev.
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mesh 1 group in group out nuclide mean std. dev.
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mesh 1 group in group out nuclide mean std. dev.
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mesh 1 group in group out nuclide mean std. dev.
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mesh 1 group in group out legendre nuclide mean std. dev.
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mesh 1 group in group out legendre nuclide mean std. dev.
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mesh 1 group out nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in group out nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 group in nuclide mean std. dev.
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mesh 1 delayedgroup group out nuclide mean std. dev.
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-2 1 1 1 3 1 total 1.0 1.414214
-3 1 1 1 4 1 total 1.0 0.579241
+1 1 1 1 2 1 total 1.0 0.866877
+2 1 1 1 3 1 total 1.0 0.866877
+3 1 1 1 4 1 total 1.0 1.414214
4 1 1 1 5 1 total 1.0 1.414214
5 1 1 1 6 1 total 0.0 0.000000
-12 1 2 1 1 1 total 1.0 1.414214
+12 1 2 1 1 1 total 0.0 0.000000
13 1 2 1 2 1 total 0.0 0.000000
-14 1 2 1 3 1 total 1.0 0.866166
-15 1 2 1 4 1 total 1.0 0.868547
-16 1 2 1 5 1 total 1.0 0.873899
+14 1 2 1 3 1 total 0.0 0.000000
+15 1 2 1 4 1 total 1.0 0.579346
+16 1 2 1 5 1 total 1.0 1.414214
17 1 2 1 6 1 total 1.0 1.414214
-6 2 1 1 1 1 total 0.0 0.000000
-7 2 1 1 2 1 total 1.0 0.654642
-8 2 1 1 3 1 total 1.0 1.414214
-9 2 1 1 4 1 total 1.0 1.414214
+6 2 1 1 1 1 total 1.0 1.414214
+7 2 1 1 2 1 total 1.0 1.414214
+8 2 1 1 3 1 total 1.0 0.874781
+9 2 1 1 4 1 total 0.0 0.000000
10 2 1 1 5 1 total 0.0 0.000000
11 2 1 1 6 1 total 0.0 0.000000
-18 2 2 1 1 1 total 1.0 0.867501
-19 2 2 1 2 1 total 0.0 0.000000
-20 2 2 1 3 1 total 0.0 0.000000
-21 2 2 1 4 1 total 1.0 0.867501
+18 2 2 1 1 1 total 1.0 1.414214
+19 2 2 1 2 1 total 1.0 0.867902
+20 2 2 1 3 1 total 1.0 1.414214
+21 2 2 1 4 1 total 1.0 1.414214
22 2 2 1 5 1 total 1.0 1.414214
-23 2 2 1 6 1 total 1.0 1.414214
+23 2 2 1 6 1 total 0.0 0.000000
mesh 1 delayedgroup group in nuclide mean std. dev.
x y z
-0 1 1 1 1 1 total 0.000221 0.000018
-1 1 1 1 2 1 total 0.001141 0.000091
-2 1 1 1 3 1 total 0.001090 0.000087
-3 1 1 1 4 1 total 0.002443 0.000194
-4 1 1 1 5 1 total 0.001002 0.000080
-5 1 1 1 6 1 total 0.000420 0.000033
-12 1 2 1 1 1 total 0.000221 0.000011
-13 1 2 1 2 1 total 0.001142 0.000059
-14 1 2 1 3 1 total 0.001090 0.000056
-15 1 2 1 4 1 total 0.002444 0.000126
-16 1 2 1 5 1 total 0.001002 0.000052
-17 1 2 1 6 1 total 0.000420 0.000022
-6 2 1 1 1 1 total 0.000221 0.000013
-7 2 1 1 2 1 total 0.001140 0.000065
-8 2 1 1 3 1 total 0.001088 0.000062
-9 2 1 1 4 1 total 0.002440 0.000140
-10 2 1 1 5 1 total 0.001000 0.000057
-11 2 1 1 6 1 total 0.000419 0.000024
-18 2 2 1 1 1 total 0.000219 0.000014
-19 2 2 1 2 1 total 0.001132 0.000072
-20 2 2 1 3 1 total 0.001081 0.000069
-21 2 2 1 4 1 total 0.002424 0.000155
-22 2 2 1 5 1 total 0.000994 0.000064
-23 2 2 1 6 1 total 0.000416 0.000027
+0 1 1 1 1 1 total 0.000221 0.000016
+1 1 1 1 2 1 total 0.001138 0.000084
+2 1 1 1 3 1 total 0.001087 0.000080
+3 1 1 1 4 1 total 0.002437 0.000180
+4 1 1 1 5 1 total 0.000999 0.000074
+5 1 1 1 6 1 total 0.000418 0.000031
+12 1 2 1 1 1 total 0.000221 0.000014
+13 1 2 1 2 1 total 0.001138 0.000073
+14 1 2 1 3 1 total 0.001087 0.000069
+15 1 2 1 4 1 total 0.002436 0.000155
+16 1 2 1 5 1 total 0.000999 0.000064
+17 1 2 1 6 1 total 0.000418 0.000027
+6 2 1 1 1 1 total 0.000220 0.000014
+7 2 1 1 2 1 total 0.001137 0.000070
+8 2 1 1 3 1 total 0.001086 0.000067
+9 2 1 1 4 1 total 0.002435 0.000150
+10 2 1 1 5 1 total 0.000998 0.000062
+11 2 1 1 6 1 total 0.000418 0.000026
+18 2 2 1 1 1 total 0.000221 0.000015
+19 2 2 1 2 1 total 0.001141 0.000078
+20 2 2 1 3 1 total 0.001089 0.000074
+21 2 2 1 4 1 total 0.002442 0.000167
+22 2 2 1 5 1 total 0.001001 0.000068
+23 2 2 1 6 1 total 0.000419 0.000029
mesh 1 delayedgroup nuclide mean std. dev.
x y z
-0 1 1 1 1 total 0.013336 0.001054
-1 1 1 1 2 total 0.032739 0.002588
-2 1 1 1 3 total 0.120780 0.009548
-3 1 1 1 4 total 0.302780 0.023936
-4 1 1 1 5 total 0.849490 0.067157
-5 1 1 1 6 total 2.853000 0.225544
-12 1 2 1 1 total 0.013336 0.000716
-13 1 2 1 2 total 0.032739 0.001758
-14 1 2 1 3 total 0.120780 0.006485
-15 1 2 1 4 total 0.302780 0.016257
-16 1 2 1 5 total 0.849490 0.045611
-17 1 2 1 6 total 2.853000 0.153186
-6 2 1 1 1 total 0.013336 0.000744
-7 2 1 1 2 total 0.032739 0.001827
-8 2 1 1 3 total 0.120780 0.006740
-9 2 1 1 4 total 0.302780 0.016897
-10 2 1 1 5 total 0.849490 0.047407
-11 2 1 1 6 total 2.853000 0.159216
-18 2 2 1 1 total 0.013336 0.000872
-19 2 2 1 2 total 0.032739 0.002141
-20 2 2 1 3 total 0.120780 0.007899
-21 2 2 1 4 total 0.302780 0.019803
-22 2 2 1 5 total 0.849490 0.055560
-23 2 2 1 6 total 2.853000 0.186598
+0 1 1 1 1 total 0.013336 0.000997
+1 1 1 1 2 total 0.032739 0.002447
+2 1 1 1 3 total 0.120780 0.009028
+3 1 1 1 4 total 0.302780 0.022633
+4 1 1 1 5 total 0.849490 0.063500
+5 1 1 1 6 total 2.853000 0.213262
+12 1 2 1 1 total 0.013336 0.000866
+13 1 2 1 2 total 0.032739 0.002126
+14 1 2 1 3 total 0.120780 0.007843
+15 1 2 1 4 total 0.302780 0.019661
+16 1 2 1 5 total 0.849490 0.055163
+17 1 2 1 6 total 2.853000 0.185263
+6 2 1 1 1 total 0.013336 0.000814
+7 2 1 1 2 total 0.032739 0.001999
+8 2 1 1 3 total 0.120780 0.007373
+9 2 1 1 4 total 0.302780 0.018483
+10 2 1 1 5 total 0.849490 0.051857
+11 2 1 1 6 total 2.853000 0.174163
+18 2 2 1 1 total 0.013336 0.000896
+19 2 2 1 2 total 0.032739 0.002200
+20 2 2 1 3 total 0.120780 0.008117
+21 2 2 1 4 total 0.302780 0.020349
+22 2 2 1 5 total 0.849490 0.057091
+23 2 2 1 6 total 2.853000 0.191738
mesh 1 delayedgroup group in group out nuclide mean std. dev.
x y z
0 1 1 1 1 1 1 total 0.000000 0.000000
-1 1 1 1 2 1 1 total 0.000029 0.000030
-2 1 1 1 3 1 1 total 0.000028 0.000028
-3 1 1 1 4 1 1 total 0.000083 0.000034
-4 1 1 1 5 1 1 total 0.000028 0.000028
+1 1 1 1 2 1 1 total 0.000056 0.000034
+2 1 1 1 3 1 1 total 0.000056 0.000034
+3 1 1 1 4 1 1 total 0.000029 0.000029
+4 1 1 1 5 1 1 total 0.000026 0.000026
5 1 1 1 6 1 1 total 0.000000 0.000000
-12 1 2 1 1 1 1 total 0.000029 0.000029
+12 1 2 1 1 1 1 total 0.000000 0.000000
13 1 2 1 2 1 1 total 0.000000 0.000000
-14 1 2 1 3 1 1 total 0.000052 0.000032
-15 1 2 1 4 1 1 total 0.000055 0.000034
-16 1 2 1 5 1 1 total 0.000059 0.000037
-17 1 2 1 6 1 1 total 0.000033 0.000033
-6 2 1 1 1 1 1 total 0.000000 0.000000
-7 2 1 1 2 1 1 total 0.000113 0.000053
-8 2 1 1 3 1 1 total 0.000034 0.000034
-9 2 1 1 4 1 1 total 0.000029 0.000029
+14 1 2 1 3 1 1 total 0.000000 0.000000
+15 1 2 1 4 1 1 total 0.000079 0.000033
+16 1 2 1 5 1 1 total 0.000032 0.000032
+17 1 2 1 6 1 1 total 0.000032 0.000032
+6 2 1 1 1 1 1 total 0.000029 0.000029
+7 2 1 1 2 1 1 total 0.000027 0.000027
+8 2 1 1 3 1 1 total 0.000058 0.000036
+9 2 1 1 4 1 1 total 0.000000 0.000000
10 2 1 1 5 1 1 total 0.000000 0.000000
11 2 1 1 6 1 1 total 0.000000 0.000000
-18 2 2 1 1 1 1 total 0.000053 0.000033
-19 2 2 1 2 1 1 total 0.000000 0.000000
-20 2 2 1 3 1 1 total 0.000000 0.000000
-21 2 2 1 4 1 1 total 0.000053 0.000033
-22 2 2 1 5 1 1 total 0.000031 0.000031
-23 2 2 1 6 1 1 total 0.000025 0.000025
+18 2 2 1 1 1 1 total 0.000027 0.000027
+19 2 2 1 2 1 1 total 0.000056 0.000035
+20 2 2 1 3 1 1 total 0.000028 0.000028
+21 2 2 1 4 1 1 total 0.000030 0.000030
+22 2 2 1 5 1 1 total 0.000033 0.000033
+23 2 2 1 6 1 1 total 0.000000 0.000000
diff --git a/tests/regression_tests/mgxs_library_no_nuclides/results_true.dat b/tests/regression_tests/mgxs_library_no_nuclides/results_true.dat
--- a/tests/regression_tests/mgxs_library_no_nuclides/results_true.dat
+++ b/tests/regression_tests/mgxs_library_no_nuclides/results_true.dat
@@ -1,333 +1,333 @@
total
material group in nuclide mean std. dev.
-1 1 1 total 0.416386 0.014741
-0 1 2 total 0.658651 0.060521
+1 1 1 total 0.413814 0.018434
+0 1 2 total 0.663001 0.012535
transport
material group in nuclide mean std. dev.
-1 1 1 total 0.378343 0.016533
-0 1 2 total 0.641137 0.060797
+1 1 1 total 0.369730 0.019494
+0 1 2 total 0.643777 0.018246
nu-transport
material group in nuclide mean std. dev.
-1 1 1 total 0.378437 0.016556
-0 1 2 total 0.641137 0.060797
+1 1 1 total 0.369730 0.019494
+0 1 2 total 0.643777 0.018246
absorption
material group in nuclide mean std. dev.
-1 1 1 total 0.027335 0.002038
-0 1 2 total 0.263007 0.029616
+1 1 1 total 0.026013 0.001851
+0 1 2 total 0.267233 0.007475
reduced absorption
material group in nuclide mean std. dev.
-1 1 1 total 0.027278 0.002038
-0 1 2 total 0.263007 0.029616
+1 1 1 total 0.025932 0.001850
+0 1 2 total 0.267233 0.007475
capture
material group in nuclide mean std. dev.
-1 1 1 total 0.019722 0.001980
-0 1 2 total 0.071284 0.032059
+1 1 1 total 0.018869 0.001758
+0 1 2 total 0.072358 0.008204
fission
material group in nuclide mean std. dev.
-1 1 1 total 0.007613 0.000245
-0 1 2 total 0.191723 0.021698
+1 1 1 total 0.007144 0.000317
+0 1 2 total 0.194875 0.005528
nu-fission
material group in nuclide mean std. dev.
-1 1 1 total 0.019339 0.000628
-0 1 2 total 0.467173 0.052872
+1 1 1 total 0.018243 0.000827
+0 1 2 total 0.474851 0.013471
kappa-fission
material group in nuclide mean std. dev.
-1 1 1 total 1.482697e+06 4.755501e+04
-0 1 2 total 3.708035e+07 4.196524e+06
+1 1 1 total 1.391782e+06 6.192598e+04
+0 1 2 total 3.768981e+07 1.069211e+06
scatter
material group in nuclide mean std. dev.
-1 1 1 total 0.389051 0.013216
-0 1 2 total 0.395644 0.031715
+1 1 1 total 0.387802 0.017462
+0 1 2 total 0.395768 0.007541
nu-scatter
material group in nuclide mean std. dev.
-1 1 1 total 0.392313 0.009662
-0 1 2 total 0.385086 0.024132
+1 1 1 total 0.387032 0.024325
+0 1 2 total 0.407651 0.016266
scatter matrix
material group in group out legendre nuclide mean std. dev.
-12 1 1 1 P0 total 0.391262 0.009858
-13 1 1 1 P1 total 0.038043 0.007486
-14 1 1 1 P2 total 0.019717 0.003619
-15 1 1 1 P3 total 0.018917 0.001007
-8 1 1 2 P0 total 0.000876 0.000554
-9 1 1 2 P1 total -0.000275 0.000386
-10 1 1 2 P2 total 0.000074 0.000114
-11 1 1 2 P3 total 0.000141 0.000113
+12 1 1 1 P0 total 0.386336 0.024297
+13 1 1 1 P1 total 0.044084 0.006343
+14 1 1 1 P2 total 0.027336 0.006403
+15 1 1 1 P3 total 0.011672 0.004897
+8 1 1 2 P0 total 0.000695 0.000327
+9 1 1 2 P1 total -0.000359 0.000201
+10 1 1 2 P2 total -0.000047 0.000081
+11 1 1 2 P3 total 0.000239 0.000099
4 1 2 1 P0 total 0.000000 0.000000
5 1 2 1 P1 total 0.000000 0.000000
6 1 2 1 P2 total 0.000000 0.000000
7 1 2 1 P3 total 0.000000 0.000000
-0 1 2 2 P0 total 0.385086 0.024132
-1 1 2 2 P1 total 0.019196 0.005279
-2 1 2 2 P2 total -0.005654 0.006088
-3 1 2 2 P3 total 0.002768 0.007045
+0 1 2 2 P0 total 0.407651 0.016266
+1 1 2 2 P1 total 0.021192 0.013171
+2 1 2 2 P2 total 0.010327 0.017230
+3 1 2 2 P3 total 0.005148 0.013732
nu-scatter matrix
material group in group out legendre nuclide mean std. dev.
-12 1 1 1 P0 total 0.391437 0.009813
-13 1 1 1 P1 total 0.037949 0.007537
-14 1 1 1 P2 total 0.019705 0.003623
-15 1 1 1 P3 total 0.018991 0.001065
-8 1 1 2 P0 total 0.000876 0.000554
-9 1 1 2 P1 total -0.000275 0.000386
-10 1 1 2 P2 total 0.000074 0.000114
-11 1 1 2 P3 total 0.000141 0.000113
+12 1 1 1 P0 total 0.386336 0.024297
+13 1 1 1 P1 total 0.044084 0.006343
+14 1 1 1 P2 total 0.027336 0.006403
+15 1 1 1 P3 total 0.011672 0.004897
+8 1 1 2 P0 total 0.000695 0.000327
+9 1 1 2 P1 total -0.000359 0.000201
+10 1 1 2 P2 total -0.000047 0.000081
+11 1 1 2 P3 total 0.000239 0.000099
4 1 2 1 P0 total 0.000000 0.000000
5 1 2 1 P1 total 0.000000 0.000000
6 1 2 1 P2 total 0.000000 0.000000
7 1 2 1 P3 total 0.000000 0.000000
-0 1 2 2 P0 total 0.385086 0.024132
-1 1 2 2 P1 total 0.019196 0.005279
-2 1 2 2 P2 total -0.005654 0.006088
-3 1 2 2 P3 total 0.002768 0.007045
+0 1 2 2 P0 total 0.407651 0.016266
+1 1 2 2 P1 total 0.021192 0.013171
+2 1 2 2 P2 total 0.010327 0.017230
+3 1 2 2 P3 total 0.005148 0.013732
multiplicity matrix
- material group in group out nuclide mean std. dev.
-3 1 1 1 total 1.000448 0.020416
-2 1 1 2 total 1.000000 0.894427
-1 1 2 1 total 0.000000 0.000000
-0 1 2 2 total 1.000000 0.085266
+ material group in group out nuclide mean std. dev.
+3 1 1 1 total 1.0 0.064268
+2 1 1 2 total 1.0 0.661438
+1 1 2 1 total 0.0 0.000000
+0 1 2 2 total 1.0 0.050545
nu-fission matrix
material group in group out nuclide mean std. dev.
-3 1 1 1 total 0.017516 0.001935
+3 1 1 1 total 0.024633 0.002205
2 1 1 2 total 0.000000 0.000000
-1 1 2 1 total 0.498681 0.013398
+1 1 2 1 total 0.435159 0.014743
0 1 2 2 total 0.000000 0.000000
scatter probability matrix
material group in group out nuclide mean std. dev.
-3 1 1 1 total 0.997766 0.020541
-2 1 1 2 total 0.002234 0.001413
+3 1 1 1 total 0.998203 0.064101
+2 1 1 2 total 0.001797 0.000844
1 1 2 1 total 0.000000 0.000000
-0 1 2 2 total 1.000000 0.085266
+0 1 2 2 total 1.000000 0.050545
consistent scatter matrix
material group in group out legendre nuclide mean std. dev.
-12 1 1 1 P0 total 0.388182 0.015419
-13 1 1 1 P1 total 0.037744 0.007517
-14 1 1 1 P2 total 0.019562 0.003641
-15 1 1 1 P3 total 0.018769 0.001154
-8 1 1 2 P0 total 0.000869 0.000551
-9 1 1 2 P1 total -0.000273 0.000383
-10 1 1 2 P2 total 0.000073 0.000113
-11 1 1 2 P3 total 0.000140 0.000112
+12 1 1 1 P0 total 0.387105 0.030361
+13 1 1 1 P1 total 0.044172 0.006684
+14 1 1 1 P2 total 0.027391 0.006543
+15 1 1 1 P3 total 0.011695 0.004937
+8 1 1 2 P0 total 0.000697 0.000329
+9 1 1 2 P1 total -0.000360 0.000202
+10 1 1 2 P2 total -0.000047 0.000082
+11 1 1 2 P3 total 0.000239 0.000100
4 1 2 1 P0 total 0.000000 0.000000
5 1 2 1 P1 total 0.000000 0.000000
6 1 2 1 P2 total 0.000000 0.000000
7 1 2 1 P3 total 0.000000 0.000000
-0 1 2 2 P0 total 0.395644 0.046302
-1 1 2 2 P1 total 0.019723 0.005763
-2 1 2 2 P2 total -0.005809 0.006281
-3 1 2 2 P3 total 0.002843 0.007244
+0 1 2 2 P0 total 0.395768 0.021378
+1 1 2 2 P1 total 0.020575 0.012809
+2 1 2 2 P2 total 0.010026 0.016732
+3 1 2 2 P3 total 0.004998 0.013333
consistent nu-scatter matrix
material group in group out legendre nuclide mean std. dev.
-12 1 1 1 P0 total 0.388355 0.017343
-13 1 1 1 P1 total 0.037760 0.007560
-14 1 1 1 P2 total 0.019571 0.003664
-15 1 1 1 P3 total 0.018777 0.001216
-8 1 1 2 P0 total 0.000869 0.000953
-9 1 1 2 P1 total -0.000273 0.000454
-10 1 1 2 P2 total 0.000073 0.000131
-11 1 1 2 P3 total 0.000140 0.000168
+12 1 1 1 P0 total 0.387105 0.039252
+13 1 1 1 P1 total 0.044172 0.007262
+14 1 1 1 P2 total 0.027391 0.006776
+15 1 1 1 P3 total 0.011695 0.004994
+8 1 1 2 P0 total 0.000697 0.000566
+9 1 1 2 P1 total -0.000360 0.000313
+10 1 1 2 P2 total -0.000047 0.000087
+11 1 1 2 P3 total 0.000239 0.000187
4 1 2 1 P0 total 0.000000 0.000000
5 1 2 1 P1 total 0.000000 0.000000
6 1 2 1 P2 total 0.000000 0.000000
7 1 2 1 P3 total 0.000000 0.000000
-0 1 2 2 P0 total 0.395644 0.057288
-1 1 2 2 P1 total 0.019723 0.006004
-2 1 2 2 P2 total -0.005809 0.006300
-3 1 2 2 P3 total 0.002843 0.007248
+0 1 2 2 P0 total 0.395768 0.029278
+1 1 2 2 P1 total 0.020575 0.012851
+2 1 2 2 P2 total 0.010026 0.016739
+3 1 2 2 P3 total 0.004998 0.013335
chi
material group out nuclide mean std. dev.
-1 1 1 total 1.0 0.029903
+1 1 1 total 1.0 0.039887
0 1 2 total 0.0 0.000000
chi-prompt
material group out nuclide mean std. dev.
-1 1 1 total 1.0 0.028494
+1 1 1 total 1.0 0.039887
0 1 2 total 0.0 0.000000
inverse-velocity
material group in nuclide mean std. dev.
-1 1 1 total 6.148661e-08 3.647428e-09
-0 1 2 total 2.844242e-06 3.098230e-07
+1 1 1 total 5.956290e-08 2.255751e-09
+0 1 2 total 2.886630e-06 7.418455e-08
prompt-nu-fission
material group in nuclide mean std. dev.
-1 1 1 total 0.019154 0.000623
-0 1 2 total 0.464134 0.052528
+1 1 1 total 0.018067 0.000817
+0 1 2 total 0.471762 0.013383
prompt-nu-fission matrix
material group in group out nuclide mean std. dev.
-3 1 1 1 total 0.017516 0.001935
+3 1 1 1 total 0.024633 0.002205
2 1 1 2 total 0.000000 0.000000
-1 1 2 1 total 0.495450 0.012592
+1 1 2 1 total 0.435159 0.014743
0 1 2 2 total 0.000000 0.000000
diffusion-coefficient
material group in nuclide mean std. dev.
-1 1 1 total 0.881035 0.038500
-0 1 2 total 0.519910 0.049301
+1 1 1 total 0.901559 0.047536
+0 1 2 total 0.517778 0.014675
nu-diffusion-coefficient
material group in nuclide mean std. dev.
-1 1 1 total 0.880816 0.038534
-0 1 2 total 0.519910 0.049301
+1 1 1 total 0.901559 0.047536
+0 1 2 total 0.517778 0.014675
(n,elastic)
material group in nuclide mean std. dev.
-1 1 1 total 0.361427 0.011879
-0 1 2 total 0.395644 0.031715
+1 1 1 total 0.360179 0.016169
+0 1 2 total 0.395768 0.007541
(n,level)
material group in nuclide mean std. dev.
-1 1 1 total 0.000549 0.000035
+1 1 1 total 0.000568 0.000028
0 1 2 total 0.000000 0.000000
(n,2n)
material group in nuclide mean std. dev.
-1 1 1 total 0.000058 0.000012
+1 1 1 total 0.000079 0.000042
0 1 2 total 0.000000 0.000000
(n,na)
material group in nuclide mean std. dev.
-1 1 1 total 4.608391e-11 2.324841e-11
+1 1 1 total 8.510945e-07 8.515320e-07
0 1 2 total 0.000000e+00 0.000000e+00
(n,nc)
material group in nuclide mean std. dev.
-1 1 1 total 0.008349 0.000869
+1 1 1 total 0.008258 0.000928
0 1 2 total 0.000000 0.000000
(n,gamma)
material group in nuclide mean std. dev.
-1 1 1 total 0.019640 0.001935
-0 1 2 total 0.071284 0.007918
+1 1 1 total 0.018749 0.001838
+0 1 2 total 0.072358 0.001951
(n,a)
material group in nuclide mean std. dev.
-1 1 1 total 0.000082 0.000016
+1 1 1 total 0.000119 0.000023
0 1 2 total 0.000000 0.000000
(n,Xa)
- material group in nuclide mean std. dev.
-1 1 1 total 0.000082 0.000016
-0 1 2 total 0.000000 0.000000
+ material group in nuclide mean std. dev.
+1 1 1 total 0.00012 0.000022
+0 1 2 total 0.00000 0.000000
heating
- material group in nuclide mean std. dev.
-1 1 1 total 1.302118e+06 4.240633e+04
-0 1 2 total 3.235834e+07 3.683247e+06
+ material group in nuclide mean std. dev.
+1 1 1 total 1.216089e+06 54827.397330
+0 1 2 total 3.262993e+07 904277.817101
damage-energy
material group in nuclide mean std. dev.
-1 1 1 total 2323.848080 106.914413
-0 1 2 total 1349.749682 152.756195
+1 1 1 total 2317.176742 165.734097
+0 1 2 total 1371.933922 38.919660
(n,n1)
material group in nuclide mean std. dev.
-1 1 1 total 0.011709 0.000412
+1 1 1 total 0.012055 0.000759
0 1 2 total 0.000000 0.000000
(n,a0)
material group in nuclide mean std. dev.
-1 1 1 total 0.000076 0.000018
+1 1 1 total 0.000109 0.000028
0 1 2 total 0.000000 0.000000
(n,nc) matrix
material group in group out nuclide mean std. dev.
-3 1 1 1 total 0.007009 0.000797
+3 1 1 1 total 0.009563 0.001002
2 1 1 2 total 0.000000 0.000000
1 1 2 1 total 0.000000 0.000000
0 1 2 2 total 0.000000 0.000000
(n,n1) matrix
- material group in group out nuclide mean std. dev.
-3 1 1 1 total 0.01209 0.00108
-2 1 1 2 total 0.00000 0.00000
-1 1 2 1 total 0.00000 0.00000
-0 1 2 2 total 0.00000 0.00000
-(n,2n) matrix
material group in group out nuclide mean std. dev.
-3 1 1 1 total 0.000175 0.000175
-2 1 1 2 total 0.000000 0.000000
-1 1 2 1 total 0.000000 0.000000
-0 1 2 2 total 0.000000 0.000000
+3 1 1 1 total 0.013909 0.00145
+2 1 1 2 total 0.000000 0.00000
+1 1 2 1 total 0.000000 0.00000
+0 1 2 2 total 0.000000 0.00000
+(n,2n) matrix
+ material group in group out nuclide mean std. dev.
+3 1 1 1 total 0.0 0.0
+2 1 1 2 total 0.0 0.0
+1 1 2 1 total 0.0 0.0
+0 1 2 2 total 0.0 0.0
delayed-nu-fission
material delayedgroup group in nuclide mean std. dev.
-1 1 1 1 total 0.000004 1.358228e-07
-3 1 2 1 total 0.000027 8.873679e-07
-5 1 3 1 total 0.000028 1.017223e-06
-7 1 4 1 total 0.000071 3.064066e-06
-9 1 5 1 total 0.000039 2.180731e-06
-11 1 6 1 total 0.000016 8.808101e-07
-0 1 1 2 total 0.000106 1.203961e-05
-2 1 2 2 total 0.000549 6.214477e-05
-4 1 3 2 total 0.000524 5.932882e-05
-6 1 4 2 total 0.001175 1.330202e-04
-8 1 5 2 total 0.000482 5.453651e-05
-10 1 6 2 total 0.000202 2.284515e-05
+1 1 1 1 total 0.000004 1.857100e-07
+3 1 2 1 total 0.000025 1.293123e-06
+5 1 3 1 total 0.000026 1.448812e-06
+7 1 4 1 total 0.000068 4.132525e-06
+9 1 5 1 total 0.000037 2.670208e-06
+11 1 6 1 total 0.000015 1.084541e-06
+0 1 1 2 total 0.000108 3.067510e-06
+2 1 2 2 total 0.000558 1.583355e-05
+4 1 3 2 total 0.000533 1.511609e-05
+6 1 4 2 total 0.001195 3.389154e-05
+8 1 5 2 total 0.000490 1.389508e-05
+10 1 6 2 total 0.000205 5.820598e-06
chi-delayed
material delayedgroup group out nuclide mean std. dev.
-1 1 1 1 total 0.0 0.000000
-3 1 2 1 total 1.0 1.414214
-5 1 3 1 total 0.0 0.000000
-7 1 4 1 total 1.0 1.414214
-9 1 5 1 total 1.0 1.414214
-11 1 6 1 total 0.0 0.000000
-0 1 1 2 total 0.0 0.000000
-2 1 2 2 total 0.0 0.000000
-4 1 3 2 total 0.0 0.000000
-6 1 4 2 total 0.0 0.000000
-8 1 5 2 total 0.0 0.000000
-10 1 6 2 total 0.0 0.000000
+1 1 1 1 total 0.0 0.0
+3 1 2 1 total 0.0 0.0
+5 1 3 1 total 0.0 0.0
+7 1 4 1 total 0.0 0.0
+9 1 5 1 total 0.0 0.0
+11 1 6 1 total 0.0 0.0
+0 1 1 2 total 0.0 0.0
+2 1 2 2 total 0.0 0.0
+4 1 3 2 total 0.0 0.0
+6 1 4 2 total 0.0 0.0
+8 1 5 2 total 0.0 0.0
+10 1 6 2 total 0.0 0.0
beta
material delayedgroup group in nuclide mean std. dev.
-1 1 1 1 total 0.000225 0.000006
-3 1 2 1 total 0.001373 0.000038
-5 1 3 1 total 0.001433 0.000045
-7 1 4 1 total 0.003692 0.000142
-9 1 5 1 total 0.002016 0.000106
-11 1 6 1 total 0.000827 0.000043
-0 1 1 2 total 0.000228 0.000032
-2 1 2 2 total 0.001175 0.000163
-4 1 3 2 total 0.001122 0.000156
-6 1 4 2 total 0.002516 0.000349
-8 1 5 2 total 0.001031 0.000143
-10 1 6 2 total 0.000432 0.000060
+1 1 1 1 total 0.000223 0.000009
+3 1 2 1 total 0.001375 0.000067
+5 1 3 1 total 0.001439 0.000076
+7 1 4 1 total 0.003724 0.000217
+9 1 5 1 total 0.002049 0.000142
+11 1 6 1 total 0.000840 0.000058
+0 1 1 2 total 0.000228 0.000008
+2 1 2 2 total 0.001175 0.000041
+4 1 3 2 total 0.001122 0.000040
+6 1 4 2 total 0.002516 0.000089
+8 1 5 2 total 0.001031 0.000036
+10 1 6 2 total 0.000432 0.000015
decay-rate
material delayedgroup nuclide mean std. dev.
-0 1 1 total 0.013356 0.001466
-1 1 2 total 0.032598 0.003432
-2 1 3 total 0.121086 0.012382
-3 1 4 total 0.305945 0.029907
-4 1 5 total 0.862061 0.077144
-5 1 6 total 2.895499 0.260691
+0 1 1 total 0.013353 0.000379
+1 1 2 total 0.032612 0.001002
+2 1 3 total 0.121056 0.003938
+3 1 4 total 0.305642 0.010892
+4 1 5 total 0.860947 0.036893
+5 1 6 total 2.891708 0.122310
delayed-nu-fission matrix
- material delayedgroup group in group out nuclide mean std. dev.
-3 1 1 1 1 total 0.000000 0.000000
-7 1 2 1 1 total 0.000000 0.000000
-11 1 3 1 1 total 0.000000 0.000000
-15 1 4 1 1 total 0.000000 0.000000
-19 1 5 1 1 total 0.000000 0.000000
-23 1 6 1 1 total 0.000000 0.000000
-2 1 1 1 2 total 0.000000 0.000000
-6 1 2 1 2 total 0.000000 0.000000
-10 1 3 1 2 total 0.000000 0.000000
-14 1 4 1 2 total 0.000000 0.000000
-18 1 5 1 2 total 0.000000 0.000000
-22 1 6 1 2 total 0.000000 0.000000
-1 1 1 2 1 total 0.000000 0.000000
-5 1 2 2 1 total 0.001133 0.001133
-9 1 3 2 1 total 0.000000 0.000000
-13 1 4 2 1 total 0.000988 0.000989
-17 1 5 2 1 total 0.001109 0.001109
-21 1 6 2 1 total 0.000000 0.000000
-0 1 1 2 2 total 0.000000 0.000000
-4 1 2 2 2 total 0.000000 0.000000
-8 1 3 2 2 total 0.000000 0.000000
-12 1 4 2 2 total 0.000000 0.000000
-16 1 5 2 2 total 0.000000 0.000000
-20 1 6 2 2 total 0.000000 0.000000
+ material delayedgroup group in group out nuclide mean std. dev.
+3 1 1 1 1 total 0.0 0.0
+7 1 2 1 1 total 0.0 0.0
+11 1 3 1 1 total 0.0 0.0
+15 1 4 1 1 total 0.0 0.0
+19 1 5 1 1 total 0.0 0.0
+23 1 6 1 1 total 0.0 0.0
+2 1 1 1 2 total 0.0 0.0
+6 1 2 1 2 total 0.0 0.0
+10 1 3 1 2 total 0.0 0.0
+14 1 4 1 2 total 0.0 0.0
+18 1 5 1 2 total 0.0 0.0
+22 1 6 1 2 total 0.0 0.0
+1 1 1 2 1 total 0.0 0.0
+5 1 2 2 1 total 0.0 0.0
+9 1 3 2 1 total 0.0 0.0
+13 1 4 2 1 total 0.0 0.0
+17 1 5 2 1 total 0.0 0.0
+21 1 6 2 1 total 0.0 0.0
+0 1 1 2 2 total 0.0 0.0
+4 1 2 2 2 total 0.0 0.0
+8 1 3 2 2 total 0.0 0.0
+12 1 4 2 2 total 0.0 0.0
+16 1 5 2 2 total 0.0 0.0
+20 1 6 2 2 total 0.0 0.0
total
material group in nuclide mean std. dev.
-1 2 1 total 0.312441 0.009893
-0 2 2 total 0.300527 0.023155
+1 2 1 total 0.313574 0.016009
+0 2 2 total 0.300858 0.005911
transport
material group in nuclide mean std. dev.
-1 2 1 total 0.275347 0.016021
-0 2 2 total 0.300167 0.026917
+1 2 1 total 0.266154 0.017348
+0 2 2 total 0.300597 0.011062
nu-transport
material group in nuclide mean std. dev.
-1 2 1 total 0.275347 0.016021
-0 2 2 total 0.300167 0.026917
+1 2 1 total 0.266154 0.017348
+0 2 2 total 0.300597 0.011062
absorption
- material group in nuclide mean std. dev.
-1 2 1 total 0.001395 0.000129
-0 2 2 total 0.005202 0.000498
+ material group in nuclide mean std. dev.
+1 2 1 total 0.00150 0.000118
+0 2 2 total 0.00542 0.000201
reduced absorption
material group in nuclide mean std. dev.
-1 2 1 total 0.001390 0.000129
-0 2 2 total 0.005202 0.000498
+1 2 1 total 0.001481 0.000119
+0 2 2 total 0.005420 0.000201
capture
- material group in nuclide mean std. dev.
-1 2 1 total 0.001395 0.000129
-0 2 2 total 0.005202 0.000498
+ material group in nuclide mean std. dev.
+1 2 1 total 0.00150 0.000118
+0 2 2 total 0.00542 0.000201
fission
material group in nuclide mean std. dev.
1 2 1 total 0.0 0.0
@@ -342,54 +342,54 @@ kappa-fission
0 2 2 total 0.0 0.0
scatter
material group in nuclide mean std. dev.
-1 2 1 total 0.311046 0.009880
-0 2 2 total 0.295325 0.022678
+1 2 1 total 0.312074 0.015934
+0 2 2 total 0.295438 0.005743
nu-scatter
material group in nuclide mean std. dev.
-1 2 1 total 0.310433 0.013519
-0 2 2 total 0.287667 0.061288
+1 2 1 total 0.318594 0.023203
+0 2 2 total 0.295662 0.031486
scatter matrix
- material group in group out legendre nuclide mean std. dev.
-12 2 1 1 P0 total 3.099468e-01 1.368691e-02
-13 2 1 1 P1 total 3.709418e-02 1.260219e-02
-14 2 1 1 P2 total 2.620103e-02 2.237097e-03
-15 2 1 1 P3 total 1.039112e-02 2.917283e-03
-8 2 1 2 P0 total 4.858100e-04 4.860246e-04
-9 2 1 2 P1 total 3.762752e-04 3.764414e-04
-10 2 1 2 P2 total 1.942506e-04 1.943364e-04
-11 2 1 2 P3 total -9.482181e-08 9.486370e-08
-4 2 2 1 P0 total 0.000000e+00 0.000000e+00
-5 2 2 1 P1 total 0.000000e+00 0.000000e+00
-6 2 2 1 P2 total 0.000000e+00 0.000000e+00
-7 2 2 1 P3 total 0.000000e+00 0.000000e+00
-0 2 2 2 P0 total 2.876667e-01 6.128794e-02
-1 2 2 2 P1 total -2.172735e-03 1.616275e-02
-2 2 2 2 P2 total 9.596560e-03 1.756046e-02
-3 2 2 2 P3 total -5.006322e-03 1.249952e-02
+ material group in group out legendre nuclide mean std. dev.
+12 2 1 1 P0 total 0.318594 0.023203
+13 2 1 1 P1 total 0.047420 0.006684
+14 2 1 1 P2 total 0.029426 0.008048
+15 2 1 1 P3 total 0.007335 0.004092
+8 2 1 2 P0 total 0.000000 0.000000
+9 2 1 2 P1 total 0.000000 0.000000
+10 2 1 2 P2 total 0.000000 0.000000
+11 2 1 2 P3 total 0.000000 0.000000
+4 2 2 1 P0 total 0.000000 0.000000
+5 2 2 1 P1 total 0.000000 0.000000
+6 2 2 1 P2 total 0.000000 0.000000
+7 2 2 1 P3 total 0.000000 0.000000
+0 2 2 2 P0 total 0.295662 0.031486
+1 2 2 2 P1 total 0.000261 0.009350
+2 2 2 2 P2 total -0.004912 0.007866
+3 2 2 2 P3 total -0.018278 0.012339
nu-scatter matrix
- material group in group out legendre nuclide mean std. dev.
-12 2 1 1 P0 total 3.099468e-01 1.368691e-02
-13 2 1 1 P1 total 3.709418e-02 1.260219e-02
-14 2 1 1 P2 total 2.620103e-02 2.237097e-03
-15 2 1 1 P3 total 1.039112e-02 2.917283e-03
-8 2 1 2 P0 total 4.858100e-04 4.860246e-04
-9 2 1 2 P1 total 3.762752e-04 3.764414e-04
-10 2 1 2 P2 total 1.942506e-04 1.943364e-04
-11 2 1 2 P3 total -9.482181e-08 9.486370e-08
-4 2 2 1 P0 total 0.000000e+00 0.000000e+00
-5 2 2 1 P1 total 0.000000e+00 0.000000e+00
-6 2 2 1 P2 total 0.000000e+00 0.000000e+00
-7 2 2 1 P3 total 0.000000e+00 0.000000e+00
-0 2 2 2 P0 total 2.876667e-01 6.128794e-02
-1 2 2 2 P1 total -2.172735e-03 1.616275e-02
-2 2 2 2 P2 total 9.596560e-03 1.756046e-02
-3 2 2 2 P3 total -5.006322e-03 1.249952e-02
+ material group in group out legendre nuclide mean std. dev.
+12 2 1 1 P0 total 0.318594 0.023203
+13 2 1 1 P1 total 0.047420 0.006684
+14 2 1 1 P2 total 0.029426 0.008048
+15 2 1 1 P3 total 0.007335 0.004092
+8 2 1 2 P0 total 0.000000 0.000000
+9 2 1 2 P1 total 0.000000 0.000000
+10 2 1 2 P2 total 0.000000 0.000000
+11 2 1 2 P3 total 0.000000 0.000000
+4 2 2 1 P0 total 0.000000 0.000000
+5 2 2 1 P1 total 0.000000 0.000000
+6 2 2 1 P2 total 0.000000 0.000000
+7 2 2 1 P3 total 0.000000 0.000000
+0 2 2 2 P0 total 0.295662 0.031486
+1 2 2 2 P1 total 0.000261 0.009350
+2 2 2 2 P2 total -0.004912 0.007866
+3 2 2 2 P3 total -0.018278 0.012339
multiplicity matrix
material group in group out nuclide mean std. dev.
-3 2 1 1 total 1.0 0.046178
-2 2 1 2 total 1.0 1.414214
+3 2 1 1 total 1.0 0.071770
+2 2 1 2 total 0.0 0.000000
1 2 2 1 total 0.0 0.000000
-0 2 2 2 total 1.0 0.204230
+0 2 2 2 total 1.0 0.103652
nu-fission matrix
material group in group out nuclide mean std. dev.
3 2 1 1 total 0.0 0.0
@@ -397,47 +397,47 @@ nu-fission matrix
1 2 2 1 total 0.0 0.0
0 2 2 2 total 0.0 0.0
scatter probability matrix
- material group in group out nuclide mean std. dev.
-3 2 1 1 total 0.998435 0.046097
-2 2 1 2 total 0.001565 0.001566
-1 2 2 1 total 0.000000 0.000000
-0 2 2 2 total 1.000000 0.204230
+ material group in group out nuclide mean std. dev.
+3 2 1 1 total 1.0 0.071770
+2 2 1 2 total 0.0 0.000000
+1 2 2 1 total 0.0 0.000000
+0 2 2 2 total 1.0 0.103652
consistent scatter matrix
- material group in group out legendre nuclide mean std. dev.
-12 2 1 1 P0 total 3.105594e-01 1.740367e-02
-13 2 1 1 P1 total 3.716750e-02 1.269205e-02
-14 2 1 1 P2 total 2.625282e-02 2.417618e-03
-15 2 1 1 P3 total 1.041166e-02 2.945041e-03
-8 2 1 2 P0 total 4.867703e-04 4.872749e-04
-9 2 1 2 P1 total 3.770190e-04 3.774098e-04
-10 2 1 2 P2 total 1.946345e-04 1.948363e-04
-11 2 1 2 P3 total -9.500924e-08 9.510772e-08
-4 2 2 1 P0 total 0.000000e+00 0.000000e+00
-5 2 2 1 P1 total 0.000000e+00 0.000000e+00
-6 2 2 1 P2 total 0.000000e+00 0.000000e+00
-7 2 2 1 P3 total 0.000000e+00 0.000000e+00
-0 2 2 2 P0 total 2.953250e-01 6.443681e-02
-1 2 2 2 P1 total -2.230578e-03 1.659337e-02
-2 2 2 2 P2 total 9.852041e-03 1.803392e-02
-3 2 2 2 P3 total -5.139601e-03 1.283456e-02
+ material group in group out legendre nuclide mean std. dev.
+12 2 1 1 P0 total 0.312074 0.027487
+13 2 1 1 P1 total 0.046450 0.006939
+14 2 1 1 P2 total 0.028824 0.008012
+15 2 1 1 P3 total 0.007185 0.004024
+8 2 1 2 P0 total 0.000000 0.000000
+9 2 1 2 P1 total 0.000000 0.000000
+10 2 1 2 P2 total 0.000000 0.000000
+11 2 1 2 P3 total 0.000000 0.000000
+4 2 2 1 P0 total 0.000000 0.000000
+5 2 2 1 P1 total 0.000000 0.000000
+6 2 2 1 P2 total 0.000000 0.000000
+7 2 2 1 P3 total 0.000000 0.000000
+0 2 2 2 P0 total 0.295438 0.031157
+1 2 2 2 P1 total 0.000261 0.009343
+2 2 2 2 P2 total -0.004909 0.007859
+3 2 2 2 P3 total -0.018264 0.012327
consistent nu-scatter matrix
- material group in group out legendre nuclide mean std. dev.
-12 2 1 1 P0 total 3.105594e-01 2.255119e-02
-13 2 1 1 P1 total 3.716750e-02 1.280757e-02
-14 2 1 1 P2 total 2.625282e-02 2.704548e-03
-15 2 1 1 P3 total 1.041166e-02 2.984029e-03
-8 2 1 2 P0 total 4.867703e-04 8.434023e-04
-9 2 1 2 P1 total 3.770190e-04 6.532417e-04
-10 2 1 2 P2 total 1.946345e-04 3.372334e-04
-11 2 1 2 P3 total -9.500924e-08 1.646177e-07
-4 2 2 1 P0 total 0.000000e+00 0.000000e+00
-5 2 2 1 P1 total 0.000000e+00 0.000000e+00
-6 2 2 1 P2 total 0.000000e+00 0.000000e+00
-7 2 2 1 P3 total 0.000000e+00 0.000000e+00
-0 2 2 2 P0 total 2.953250e-01 8.826037e-02
-1 2 2 2 P1 total -2.230578e-03 1.659963e-02
-2 2 2 2 P2 total 9.852041e-03 1.814582e-02
-3 2 2 2 P3 total -5.139601e-03 1.287741e-02
+ material group in group out legendre nuclide mean std. dev.
+12 2 1 1 P0 total 0.312074 0.035456
+13 2 1 1 P1 total 0.046450 0.007699
+14 2 1 1 P2 total 0.028824 0.008274
+15 2 1 1 P3 total 0.007185 0.004057
+8 2 1 2 P0 total 0.000000 0.000000
+9 2 1 2 P1 total 0.000000 0.000000
+10 2 1 2 P2 total 0.000000 0.000000
+11 2 1 2 P3 total 0.000000 0.000000
+4 2 2 1 P0 total 0.000000 0.000000
+5 2 2 1 P1 total 0.000000 0.000000
+6 2 2 1 P2 total 0.000000 0.000000
+7 2 2 1 P3 total 0.000000 0.000000
+0 2 2 2 P0 total 0.295438 0.043686
+1 2 2 2 P1 total 0.000261 0.009343
+2 2 2 2 P2 total -0.004909 0.007876
+3 2 2 2 P3 total -0.018264 0.012471
chi
material group out nuclide mean std. dev.
1 2 1 total 0.0 0.0
@@ -448,8 +448,8 @@ chi-prompt
0 2 2 total 0.0 0.0
inverse-velocity
material group in nuclide mean std. dev.
-1 2 1 total 6.397205e-08 3.117085e-09
-0 2 2 total 2.875630e-06 2.751728e-07
+1 2 1 total 6.076563e-08 2.727519e-09
+0 2 2 total 2.996176e-06 1.110140e-07
prompt-nu-fission
material group in nuclide mean std. dev.
1 2 1 total 0.0 0.0
@@ -462,69 +462,69 @@ prompt-nu-fission matrix
0 2 2 2 total 0.0 0.0
diffusion-coefficient
material group in nuclide mean std. dev.
-1 2 1 total 1.210594 0.070439
-0 2 2 total 1.110491 0.099580
+1 2 1 total 1.252406 0.081631
+0 2 2 total 1.108904 0.040809
nu-diffusion-coefficient
material group in nuclide mean std. dev.
-1 2 1 total 1.210594 0.070439
-0 2 2 total 1.110491 0.099580
+1 2 1 total 1.252406 0.081631
+0 2 2 total 1.108904 0.040809
(n,elastic)
material group in nuclide mean std. dev.
-1 2 1 total 0.301494 0.009403
-0 2 2 total 0.295325 0.022678
+1 2 1 total 0.302664 0.015531
+0 2 2 total 0.295438 0.005743
(n,level)
material group in nuclide mean std. dev.
1 2 1 total 0.0 0.0
0 2 2 total 0.0 0.0
(n,2n)
material group in nuclide mean std. dev.
-1 2 1 total 0.000005 0.000003
+1 2 1 total 0.000019 0.000017
0 2 2 total 0.000000 0.000000
(n,na)
material group in nuclide mean std. dev.
-1 2 1 total 1.085156e-09 6.357350e-10
+1 2 1 total 4.892570e-09 4.436228e-09
0 2 2 total 0.000000e+00 0.000000e+00
(n,nc)
material group in nuclide mean std. dev.
-1 2 1 total 0.001947 0.000276
+1 2 1 total 0.001998 0.000408
0 2 2 total 0.000000 0.000000
(n,gamma)
material group in nuclide mean std. dev.
-1 2 1 total 0.001392 0.000128
-0 2 2 total 0.005201 0.000498
+1 2 1 total 0.001497 0.000118
+0 2 2 total 0.005419 0.000201
(n,a)
material group in nuclide mean std. dev.
-1 2 1 total 8.373873e-07 5.295954e-08
-0 2 2 total 2.735007e-07 2.100237e-08
+1 2 1 total 9.546292e-07 9.180854e-08
+0 2 2 total 2.736059e-07 5.318732e-09
(n,Xa)
material group in nuclide mean std. dev.
-1 2 1 total 8.384725e-07 5.277215e-08
-0 2 2 total 2.735007e-07 2.100237e-08
+1 2 1 total 9.595218e-07 9.558005e-08
+0 2 2 total 2.736059e-07 5.318732e-09
heating
material group in nuclide mean std. dev.
-1 2 1 total 2151.700349 142.319459
-0 2 2 total 1.947222 0.155279
+1 2 1 total 2551.878627 212.765665
+0 2 2 total 2.332139 0.087384
damage-energy
- material group in nuclide mean std. dev.
-1 2 1 total 1591.760682 90.145807
-0 2 2 total 0.284888 0.026354
+ material group in nuclide mean std. dev.
+1 2 1 total 1585.677533 130.382718
+0 2 2 total 0.295108 0.010079
(n,n1)
material group in nuclide mean std. dev.
-1 2 1 total 0.002962 0.00032
-0 2 2 total 0.000000 0.00000
+1 2 1 total 0.002835 0.000246
+0 2 2 total 0.000000 0.000000
(n,a0)
material group in nuclide mean std. dev.
-1 2 1 total 7.199126e-07 5.011215e-08
-0 2 2 total 2.732253e-07 2.098122e-08
+1 2 1 total 7.169006e-07 6.251188e-08
+0 2 2 total 2.733303e-07 5.313375e-09
(n,nc) matrix
material group in group out nuclide mean std. dev.
-3 2 1 1 total 0.002915 0.000493
+3 2 1 1 total 0.001489 0.001491
2 2 1 2 total 0.000000 0.000000
1 2 2 1 total 0.000000 0.000000
0 2 2 2 total 0.000000 0.000000
(n,n1) matrix
material group in group out nuclide mean std. dev.
-3 2 1 1 total 0.002429 0.001332
+3 2 1 1 total 0.001985 0.000507
2 2 1 2 total 0.000000 0.000000
1 2 2 1 total 0.000000 0.000000
0 2 2 2 total 0.000000 0.000000
@@ -612,28 +612,28 @@ delayed-nu-fission matrix
20 2 6 2 2 total 0.0 0.0
total
material group in nuclide mean std. dev.
-1 3 1 total 0.684512 0.015513
-0 3 2 total 2.038387 0.113839
+1 3 1 total 0.682896 0.024140
+0 3 2 total 2.032938 0.085675
transport
material group in nuclide mean std. dev.
-1 3 1 total 0.291947 0.019086
-0 3 2 total 1.464248 0.116005
+1 3 1 total 0.298986 0.026905
+0 3 2 total 1.471887 0.096907
nu-transport
material group in nuclide mean std. dev.
-1 3 1 total 0.291947 0.019086
-0 3 2 total 1.464248 0.116005
+1 3 1 total 0.298986 0.026905
+0 3 2 total 1.471887 0.096907
absorption
material group in nuclide mean std. dev.
-1 3 1 total 0.000715 0.000032
-0 3 2 total 0.031290 0.001882
+1 3 1 total 0.000693 0.000020
+0 3 2 total 0.031171 0.001403
reduced absorption
material group in nuclide mean std. dev.
-1 3 1 total 0.000715 0.000032
-0 3 2 total 0.031290 0.001882
+1 3 1 total 0.000693 0.000020
+0 3 2 total 0.031171 0.001403
capture
material group in nuclide mean std. dev.
-1 3 1 total 0.000715 0.000032
-0 3 2 total 0.031290 0.001882
+1 3 1 total 0.000693 0.000020
+0 3 2 total 0.031171 0.001403
fission
material group in nuclide mean std. dev.
1 3 1 total 0.0 0.0
@@ -648,54 +648,54 @@ kappa-fission
0 3 2 total 0.0 0.0
scatter
material group in nuclide mean std. dev.
-1 3 1 total 0.683797 0.015496
-0 3 2 total 2.007097 0.111979
+1 3 1 total 0.682202 0.024123
+0 3 2 total 2.001768 0.084281
nu-scatter
material group in nuclide mean std. dev.
-1 3 1 total 0.684650 0.017888
-0 3 2 total 1.992357 0.090997
+1 3 1 total 0.672567 0.017434
+0 3 2 total 2.004576 0.129211
scatter matrix
material group in group out legendre nuclide mean std. dev.
-12 3 1 1 P0 total 0.654867 0.017215
-13 3 1 1 P1 total 0.392566 0.011118
-14 3 1 1 P2 total 0.165345 0.005121
-15 3 1 1 P3 total 0.016963 0.003137
-8 3 1 2 P0 total 0.029783 0.000974
-9 3 1 2 P1 total 0.008810 0.000479
-10 3 1 2 P2 total -0.002652 0.000630
-11 3 1 2 P3 total -0.002872 0.000517
-4 3 2 1 P0 total 0.000000 0.000000
-5 3 2 1 P1 total 0.000000 0.000000
-6 3 2 1 P2 total 0.000000 0.000000
-7 3 2 1 P3 total 0.000000 0.000000
-0 3 2 2 P0 total 1.992357 0.090997
-1 3 2 2 P1 total 0.526383 0.022569
-2 3 2 2 P2 total 0.108016 0.009047
-3 3 2 2 P3 total 0.016856 0.010707
+12 3 1 1 P0 total 0.641741 0.016600
+13 3 1 1 P1 total 0.383841 0.011878
+14 3 1 1 P2 total 0.149909 0.005512
+15 3 1 1 P3 total 0.004238 0.002485
+8 3 1 2 P0 total 0.030826 0.000973
+9 3 1 2 P1 total 0.009943 0.000415
+10 3 1 2 P2 total -0.003002 0.000628
+11 3 1 2 P3 total -0.004234 0.000393
+4 3 2 1 P0 total 0.000467 0.000467
+5 3 2 1 P1 total 0.000345 0.000345
+6 3 2 1 P2 total 0.000149 0.000149
+7 3 2 1 P3 total -0.000047 0.000047
+0 3 2 2 P0 total 2.004109 0.129225
+1 3 2 2 P1 total 0.511363 0.043448
+2 3 2 2 P2 total 0.108599 0.014070
+3 3 2 2 P3 total 0.035733 0.021921
nu-scatter matrix
material group in group out legendre nuclide mean std. dev.
-12 3 1 1 P0 total 0.654867 0.017215
-13 3 1 1 P1 total 0.392566 0.011118
-14 3 1 1 P2 total 0.165345 0.005121
-15 3 1 1 P3 total 0.016963 0.003137
-8 3 1 2 P0 total 0.029783 0.000974
-9 3 1 2 P1 total 0.008810 0.000479
-10 3 1 2 P2 total -0.002652 0.000630
-11 3 1 2 P3 total -0.002872 0.000517
-4 3 2 1 P0 total 0.000000 0.000000
-5 3 2 1 P1 total 0.000000 0.000000
-6 3 2 1 P2 total 0.000000 0.000000
-7 3 2 1 P3 total 0.000000 0.000000
-0 3 2 2 P0 total 1.992357 0.090997
-1 3 2 2 P1 total 0.526383 0.022569
-2 3 2 2 P2 total 0.108016 0.009047
-3 3 2 2 P3 total 0.016856 0.010707
+12 3 1 1 P0 total 0.641741 0.016600
+13 3 1 1 P1 total 0.383841 0.011878
+14 3 1 1 P2 total 0.149909 0.005512
+15 3 1 1 P3 total 0.004238 0.002485
+8 3 1 2 P0 total 0.030826 0.000973
+9 3 1 2 P1 total 0.009943 0.000415
+10 3 1 2 P2 total -0.003002 0.000628
+11 3 1 2 P3 total -0.004234 0.000393
+4 3 2 1 P0 total 0.000467 0.000467
+5 3 2 1 P1 total 0.000345 0.000345
+6 3 2 1 P2 total 0.000149 0.000149
+7 3 2 1 P3 total -0.000047 0.000047
+0 3 2 2 P0 total 2.004109 0.129225
+1 3 2 2 P1 total 0.511363 0.043448
+2 3 2 2 P2 total 0.108599 0.014070
+3 3 2 2 P3 total 0.035733 0.021921
multiplicity matrix
material group in group out nuclide mean std. dev.
-3 3 1 1 total 1.0 0.020014
-2 3 1 2 total 1.0 0.034047
-1 3 2 1 total 0.0 0.000000
-0 3 2 2 total 1.0 0.048455
+3 3 1 1 total 1.0 0.022200
+2 3 1 2 total 1.0 0.033880
+1 3 2 1 total 1.0 1.414214
+0 3 2 2 total 1.0 0.066922
nu-fission matrix
material group in group out nuclide mean std. dev.
3 3 1 1 total 0.0 0.0
@@ -704,46 +704,46 @@ nu-fission matrix
0 3 2 2 total 0.0 0.0
scatter probability matrix
material group in group out nuclide mean std. dev.
-3 3 1 1 total 0.956499 0.018759
-2 3 1 2 total 0.043501 0.001202
-1 3 2 1 total 0.000000 0.000000
-0 3 2 2 total 1.000000 0.048455
+3 3 1 1 total 0.954167 0.020729
+2 3 1 2 total 0.045833 0.001296
+1 3 2 1 total 0.000233 0.000233
+0 3 2 2 total 0.999767 0.066899
consistent scatter matrix
material group in group out legendre nuclide mean std. dev.
-12 3 1 1 P0 total 0.654051 0.019602
-13 3 1 1 P1 total 0.392076 0.012456
-14 3 1 1 P2 total 0.165139 0.005640
-15 3 1 1 P3 total 0.016942 0.003143
-8 3 1 2 P0 total 0.029746 0.001063
-9 3 1 2 P1 total 0.008799 0.000495
-10 3 1 2 P2 total -0.002648 0.000631
-11 3 1 2 P3 total -0.002868 0.000518
-4 3 2 1 P0 total 0.000000 0.000000
-5 3 2 1 P1 total 0.000000 0.000000
-6 3 2 1 P2 total 0.000000 0.000000
-7 3 2 1 P3 total 0.000000 0.000000
-0 3 2 2 P0 total 2.007097 0.148316
-1 3 2 2 P1 total 0.530278 0.038286
-2 3 2 2 P2 total 0.108815 0.011091
-3 3 2 2 P3 total 0.016981 0.010831
+12 3 1 1 P0 total 0.650935 0.027014
+13 3 1 1 P1 total 0.389340 0.017459
+14 3 1 1 P2 total 0.152056 0.007457
+15 3 1 1 P3 total 0.004299 0.002525
+8 3 1 2 P0 total 0.031268 0.001416
+9 3 1 2 P1 total 0.010085 0.000533
+10 3 1 2 P2 total -0.003045 0.000645
+11 3 1 2 P3 total -0.004295 0.000423
+4 3 2 1 P0 total 0.000466 0.000467
+5 3 2 1 P1 total 0.000344 0.000345
+6 3 2 1 P2 total 0.000148 0.000149
+7 3 2 1 P3 total -0.000047 0.000047
+0 3 2 2 P0 total 2.001301 0.158219
+1 3 2 2 P1 total 0.510647 0.049275
+2 3 2 2 P2 total 0.108446 0.014900
+3 3 2 2 P3 total 0.035683 0.021951
consistent nu-scatter matrix
material group in group out legendre nuclide mean std. dev.
-12 3 1 1 P0 total 0.654051 0.023571
-13 3 1 1 P1 total 0.392076 0.014722
-14 3 1 1 P2 total 0.165139 0.006537
-15 3 1 1 P3 total 0.016942 0.003161
-8 3 1 2 P0 total 0.029746 0.001468
-9 3 1 2 P1 total 0.008799 0.000579
-10 3 1 2 P2 total -0.002648 0.000637
-11 3 1 2 P3 total -0.002868 0.000528
-4 3 2 1 P0 total 0.000000 0.000000
-5 3 2 1 P1 total 0.000000 0.000000
-6 3 2 1 P2 total 0.000000 0.000000
-7 3 2 1 P3 total 0.000000 0.000000
-0 3 2 2 P0 total 2.007097 0.177359
-1 3 2 2 P1 total 0.530278 0.046109
-2 3 2 2 P2 total 0.108815 0.012281
-3 3 2 2 P3 total 0.016981 0.010862
+12 3 1 1 P0 total 0.650935 0.030637
+13 3 1 1 P1 total 0.389340 0.019481
+14 3 1 1 P2 total 0.152056 0.008185
+15 3 1 1 P3 total 0.004299 0.002526
+8 3 1 2 P0 total 0.031268 0.001768
+9 3 1 2 P1 total 0.010085 0.000633
+10 3 1 2 P2 total -0.003045 0.000653
+11 3 1 2 P3 total -0.004295 0.000447
+4 3 2 1 P0 total 0.000466 0.000808
+5 3 2 1 P1 total 0.000344 0.000597
+6 3 2 1 P2 total 0.000148 0.000257
+7 3 2 1 P3 total -0.000047 0.000081
+0 3 2 2 P0 total 2.001301 0.207294
+1 3 2 2 P1 total 0.510647 0.059966
+2 3 2 2 P2 total 0.108446 0.016574
+3 3 2 2 P3 total 0.035683 0.022080
chi
material group out nuclide mean std. dev.
1 3 1 total 0.0 0.0
@@ -754,8 +754,8 @@ chi-prompt
0 3 2 total 0.0 0.0
inverse-velocity
material group in nuclide mean std. dev.
-1 3 1 total 6.447429e-08 2.866173e-09
-0 3 2 total 3.006810e-06 1.808750e-07
+1 3 1 total 6.023693e-08 1.678511e-09
+0 3 2 total 2.995346e-06 1.347817e-07
prompt-nu-fission
material group in nuclide mean std. dev.
1 3 1 total 0.0 0.0
@@ -768,60 +768,60 @@ prompt-nu-fission matrix
0 3 2 2 total 0.0 0.0
diffusion-coefficient
material group in nuclide mean std. dev.
-1 3 1 total 1.141761 0.074641
-0 3 2 total 0.227648 0.018035
+1 3 1 total 1.114881 0.100326
+0 3 2 total 0.226467 0.014910
nu-diffusion-coefficient
material group in nuclide mean std. dev.
-1 3 1 total 1.141761 0.074641
-0 3 2 total 0.227648 0.018035
+1 3 1 total 1.114881 0.100326
+0 3 2 total 0.226467 0.014910
(n,elastic)
material group in nuclide mean std. dev.
-1 3 1 total 0.683777 0.015496
-0 3 2 total 2.007097 0.111979
+1 3 1 total 0.682168 0.024125
+0 3 2 total 2.001768 0.084281
(n,level)
- material group in nuclide mean std. dev.
-1 3 1 total 0.00002 0.000006
-0 3 2 total 0.00000 0.000000
+ material group in nuclide mean std. dev.
+1 3 1 total 0.000033 0.000019
+0 3 2 total 0.000000 0.000000
(n,2n)
material group in nuclide mean std. dev.
1 3 1 total 0.0 0.0
0 3 2 total 0.0 0.0
(n,na)
material group in nuclide mean std. dev.
-1 3 1 total 3.714897e-11 2.058007e-11
+1 3 1 total 9.967562e-07 9.970492e-07
0 3 2 total 0.000000e+00 0.000000e+00
(n,nc)
- material group in nuclide mean std. dev.
-1 3 1 total 0.0 0.0
-0 3 2 total 0.0 0.0
+ material group in nuclide mean std. dev.
+1 3 1 total 8.867935e-07 8.870902e-07
+0 3 2 total 0.000000e+00 0.000000e+00
(n,gamma)
material group in nuclide mean std. dev.
-1 3 1 total 0.000234 0.000010
-0 3 2 total 0.010896 0.000655
+1 3 1 total 0.000219 0.000006
+0 3 2 total 0.010855 0.000488
(n,a)
material group in nuclide mean std. dev.
-1 3 1 total 0.000481 0.000022
-0 3 2 total 0.020394 0.001227
+1 3 1 total 0.000474 0.000015
+0 3 2 total 0.020316 0.000914
(n,Xa)
material group in nuclide mean std. dev.
-1 3 1 total 0.000481 0.000022
-0 3 2 total 0.020394 0.001227
+1 3 1 total 0.000475 0.000015
+0 3 2 total 0.020316 0.000914
heating
material group in nuclide mean std. dev.
-1 3 1 total 64982.284489 3654.924951
-0 3 2 total 49786.819570 2967.698779
+1 3 1 total 77986.174023 6103.108384
+0 3 2 total 59060.658662 3576.641806
damage-energy
material group in nuclide mean std. dev.
-1 3 1 total 1147.965123 36.313921
-0 3 2 total 332.961479 20.030541
+1 3 1 total 1107.847239 59.901669
+0 3 2 total 331.691439 14.926212
(n,n1)
- material group in nuclide mean std. dev.
-1 3 1 total 7.030461e-07 2.133325e-07
-0 3 2 total 0.000000e+00 0.000000e+00
+ material group in nuclide mean std. dev.
+1 3 1 total 0.000001 3.988839e-07
+0 3 2 total 0.000000 0.000000e+00
(n,a0)
material group in nuclide mean std. dev.
-1 3 1 total 0.000068 0.000011
-0 3 2 total 0.001283 0.000077
+1 3 1 total 0.000084 0.000016
+0 3 2 total 0.001278 0.000058
(n,nc) matrix
material group in group out nuclide mean std. dev.
3 3 1 1 total 0.0 0.0
diff --git a/tests/regression_tests/mgxs_library_nuclides/results_true.dat b/tests/regression_tests/mgxs_library_nuclides/results_true.dat
--- a/tests/regression_tests/mgxs_library_nuclides/results_true.dat
+++ b/tests/regression_tests/mgxs_library_nuclides/results_true.dat
@@ -1 +1 @@
-93ad567f1b36461a68d4ead0ff5cfa4a2003b05cf5241a232544545001a94a33fc7b99f21af277ea3a24861d38aac3a9ac36c8b1706c4b3b33caec589df2c90c
\ No newline at end of file
+c4a4cb4e00f09ef62222a0e66df817af87bf324a2ac0e57a82ff1337535a223c7077d660a60d0ce9ac7113c47d37b3296347f3ba212558ff09ef5fc586e1dd28
\ No newline at end of file
diff --git a/tests/regression_tests/microxs/test.py b/tests/regression_tests/microxs/test.py
--- a/tests/regression_tests/microxs/test.py
+++ b/tests/regression_tests/microxs/test.py
@@ -4,9 +4,10 @@
import numpy as np
import pytest
import openmc
-
from openmc.deplete import MicroXS
+from tests.regression_tests import config
+
CHAIN_FILE = Path(__file__).parents[2] / "chain_simple.xml"
@pytest.fixture(scope="module")
@@ -46,7 +47,10 @@ def model():
def test_from_model(model):
- ref_xs = MicroXS.from_csv('test_reference.csv')
test_xs = MicroXS.from_model(model, model.materials[0], CHAIN_FILE)
+ if config['update']:
+ test_xs.to_csv('test_reference.csv')
+
+ ref_xs = MicroXS.from_csv('test_reference.csv')
np.testing.assert_allclose(test_xs, ref_xs, rtol=1e-11)
diff --git a/tests/regression_tests/microxs/test_reference.csv b/tests/regression_tests/microxs/test_reference.csv
--- a/tests/regression_tests/microxs/test_reference.csv
+++ b/tests/regression_tests/microxs/test_reference.csv
@@ -1,13 +1,13 @@
nuclide,"(n,gamma)",fission
-U234,22.231989815372202,0.49620744658634824
-U235,10.479008966651142,48.417873345870724
-U238,0.8673334103130558,0.1046788058833928
-U236,8.651710443768728,0.3194839239606777
-O16,7.497850998328519e-05,0.0
-O17,0.0004079227795364271,0.0
-I135,6.842395320017149,0.0
-Xe135,227463.8640052883,0.0
-Xe136,0.023178960335476638,0.0
-Cs135,2.1721665579658485,0.0
-Gd157,12786.099387172428,0.0
-Gd156,3.4006085435237843,0.0
+U234,20.548033586079335,0.4951725071956495
+U235,10.593745111766133,48.86980740247932
+U238,0.8607296097035912,0.10623994948321437
+U236,8.697176401063281,0.32148140073986475
+O16,7.503456435273737e-05,0.0
+O17,0.0004107265933745623,0.0
+I135,6.896228129273278,0.0
+Xe135,229100.9245987756,0.0
+Xe136,0.02336047367105298,0.0
+Cs135,2.055822714073886,0.0
+Gd157,12927.465334134899,0.0
+Gd156,3.500756543915523,0.0
diff --git a/tests/regression_tests/multipole/results_true.dat b/tests/regression_tests/multipole/results_true.dat
--- a/tests/regression_tests/multipole/results_true.dat
+++ b/tests/regression_tests/multipole/results_true.dat
@@ -1,36 +1,36 @@
k-combined:
-1.377711E+00 1.297376E-02
+1.354889E+00 8.437211E-03
tally 1:
-3.861112E+00
-2.991150E+00
-2.787756E+00
-1.559383E+00
-5.422517E-01
-5.899488E-02
-4.575965E-01
-4.201819E-02
+3.869969E+00
+3.000421E+00
+2.800393E+00
+1.570851E+00
+5.399091E-01
+5.842233E-02
+4.577147E-01
+4.203362E-02
0.000000E+00
0.000000E+00
-2.250654E+01
-1.013609E+02
+2.286465E+01
+1.045869E+02
0.000000E+00
0.000000E+00
-6.830189E-04
-9.338756E-08
-2.248753E+01
-1.011895E+02
-1.147267E-05
-4.624497E-11
-3.580777E+02
-2.567385E+04
-2.787756E+00
-1.559383E+00
-2.157976E+00
-9.322753E-01
-3.530401E+02
-2.495723E+04
-1.147267E-05
-4.624497E-11
+6.971793E-04
+9.724819E-08
+2.283955E+01
+1.043576E+02
+4.659256E-06
+2.170865E-11
+3.663230E+02
+2.685383E+04
+2.800393E+00
+1.570851E+00
+2.204999E+00
+9.728014E-01
+3.612213E+02
+2.611152E+04
+4.659256E-06
+2.170865E-11
Cell
ID = 11
Name =
diff --git a/tests/regression_tests/output/results_true.dat b/tests/regression_tests/output/results_true.dat
--- a/tests/regression_tests/output/results_true.dat
+++ b/tests/regression_tests/output/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-2.987050E-01 1.827430E-03
+3.070134E-01 3.900396E-03
diff --git a/tests/regression_tests/particle_restart_eigval/results_true.dat b/tests/regression_tests/particle_restart_eigval/results_true.dat
--- a/tests/regression_tests/particle_restart_eigval/results_true.dat
+++ b/tests/regression_tests/particle_restart_eigval/results_true.dat
@@ -3,14 +3,14 @@ current batch:
current generation:
1.000000E+00
particle id:
-9.020000E+02
+2.540000E+02
run mode:
eigenvalue
particle weight:
1.000000E+00
particle energy:
-3.691964E+06
+2.220048E+06
particle xyz:
--5.047439E+01 2.730535E+01 -2.619863E+01
+-4.820850E+01 2.432936E+01 4.397668E+01
particle uvw:
--6.278670E-01 1.419818E-01 -7.652609E-01
+-3.148565E-01 9.184190E-01 2.395245E-01
diff --git a/tests/regression_tests/particle_restart_eigval/test.py b/tests/regression_tests/particle_restart_eigval/test.py
--- a/tests/regression_tests/particle_restart_eigval/test.py
+++ b/tests/regression_tests/particle_restart_eigval/test.py
@@ -2,5 +2,5 @@
def test_particle_restart_eigval():
- harness = ParticleRestartTestHarness('particle_11_902.h5')
+ harness = ParticleRestartTestHarness('particle_11_254.h5')
harness.main()
diff --git a/tests/regression_tests/periodic/results_true.dat b/tests/regression_tests/periodic/results_true.dat
--- a/tests/regression_tests/periodic/results_true.dat
+++ b/tests/regression_tests/periodic/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.654583E+00 1.501286E-02
+1.623300E+00 2.572983E-02
diff --git a/tests/regression_tests/periodic_6fold/results_true.dat b/tests/regression_tests/periodic_6fold/results_true.dat
--- a/tests/regression_tests/periodic_6fold/results_true.dat
+++ b/tests/regression_tests/periodic_6fold/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.845885E+00 1.472487E-02
+1.858730E+00 6.824588E-03
diff --git a/tests/regression_tests/periodic_6fold/test.py b/tests/regression_tests/periodic_6fold/test.py
--- a/tests/regression_tests/periodic_6fold/test.py
+++ b/tests/regression_tests/periodic_6fold/test.py
@@ -1,5 +1,6 @@
+from math import sin, cos, pi
+
import openmc
-import numpy as np
import pytest
from tests.testing_harness import PyAPITestHarness
@@ -24,17 +25,14 @@ def model():
# (it essentially defines a circle of half-cylinders), but it is
# designed so that periodic and reflective BCs will give different
# answers.
- theta1 = (-1/6 + 1/2) * np.pi
- theta2 = (1/6 - 1/2) * np.pi
- plane1 = openmc.Plane(a=np.cos(theta1), b=np.sin(theta1),
- boundary_type='periodic')
- plane2 = openmc.Plane(a=np.cos(theta2), b=np.sin(theta2),
- boundary_type='periodic')
+ theta1 = (-1/6 + 1/2) * pi
+ theta2 = (1/6 - 1/2) * pi
+ plane1 = openmc.Plane(a=cos(theta1), b=sin(theta1), boundary_type='periodic')
+ plane2 = openmc.Plane(a=cos(theta2), b=sin(theta2), boundary_type='periodic')
- x_max = openmc.XPlane(x0=5., boundary_type='reflective')
+ x_max = openmc.XPlane(5., boundary_type='reflective')
- z_cyl = openmc.ZCylinder(x0=3*np.cos(np.pi/6), y0=3*np.sin(np.pi/6),
- r=2.0)
+ z_cyl = openmc.ZCylinder(x0=3*cos(pi/6), y0=3*sin(pi/6), r=2.0)
outside_cyl = openmc.Cell(1, fill=water, region=(
+plane1 & +plane2 & -x_max & +z_cyl))
diff --git a/tests/regression_tests/periodic_hex/results_true.dat b/tests/regression_tests/periodic_hex/results_true.dat
--- a/tests/regression_tests/periodic_hex/results_true.dat
+++ b/tests/regression_tests/periodic_hex/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-2.271604E+00 1.159996E-02
+2.284468E+00 2.781588E-02
diff --git a/tests/regression_tests/photon_production_fission/results_true.dat b/tests/regression_tests/photon_production_fission/results_true.dat
--- a/tests/regression_tests/photon_production_fission/results_true.dat
+++ b/tests/regression_tests/photon_production_fission/results_true.dat
@@ -1,12 +1,12 @@
k-combined:
-2.294874E+00 2.454640E-02
+2.272421E+00 4.418825E-02
tally 1:
-2.691351E+00
-2.415076E+00
+2.665301E+00
+2.369839E+00
0.000000E+00
0.000000E+00
-2.691351E+00
-2.415076E+00
+2.665301E+00
+2.369839E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -18,52 +18,52 @@ tally 1:
0.000000E+00
0.000000E+00
tally 2:
-2.654218E+00
-2.348806E+00
-4.260252E+08
-6.051306E+16
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0.000000E+00
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tally 3:
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0.000000E+00
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diff --git a/tests/regression_tests/ptables_off/results_true.dat b/tests/regression_tests/ptables_off/results_true.dat
--- a/tests/regression_tests/ptables_off/results_true.dat
+++ b/tests/regression_tests/ptables_off/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-3.042885E-01 1.073889E-02
+2.978318E-01 1.560055E-03
diff --git a/tests/regression_tests/quadric_surfaces/results_true.dat b/tests/regression_tests/quadric_surfaces/results_true.dat
--- a/tests/regression_tests/quadric_surfaces/results_true.dat
+++ b/tests/regression_tests/quadric_surfaces/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.213534E+00 1.386061E-02
+1.193830E+00 1.824184E-02
diff --git a/tests/regression_tests/reflective_plane/results_true.dat b/tests/regression_tests/reflective_plane/results_true.dat
--- a/tests/regression_tests/reflective_plane/results_true.dat
+++ b/tests/regression_tests/reflective_plane/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-2.275423E+00 4.746681E-03
+2.276857E+00 8.776678E-03
diff --git a/tests/regression_tests/resonance_scattering/results_true.dat b/tests/regression_tests/resonance_scattering/results_true.dat
--- a/tests/regression_tests/resonance_scattering/results_true.dat
+++ b/tests/regression_tests/resonance_scattering/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.463226E+00 1.142843E-02
+1.462509E+00 2.205413E-02
diff --git a/tests/regression_tests/rotation/results_true.dat b/tests/regression_tests/rotation/results_true.dat
--- a/tests/regression_tests/rotation/results_true.dat
+++ b/tests/regression_tests/rotation/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-4.132181E-01 1.130226E-02
+4.175600E-01 1.117465E-02
diff --git a/tests/regression_tests/salphabeta/results_true.dat b/tests/regression_tests/salphabeta/results_true.dat
--- a/tests/regression_tests/salphabeta/results_true.dat
+++ b/tests/regression_tests/salphabeta/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-8.214164E-01 2.262776E-02
+8.694866E-01 2.033328E-02
diff --git a/tests/regression_tests/score_current/results_true.dat b/tests/regression_tests/score_current/results_true.dat
--- a/tests/regression_tests/score_current/results_true.dat
+++ b/tests/regression_tests/score_current/results_true.dat
@@ -1,58 +1,58 @@
k-combined:
-7.952381E-01 3.714273E-02
+2.298294E-01 3.256961E-01
tally 1:
0.000000E+00
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-4.016000E-03
-1.760000E-01
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@@ -61,430 +61,430 @@ tally 1:
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tally 2:
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@@ -1020,28 +1020,28 @@ tally 2:
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@@ -1052,12 +1052,12 @@ tally 2:
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@@ -1068,20 +1068,20 @@ tally 2:
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@@ -1092,12 +1092,12 @@ tally 2:
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@@ -1108,44 +1108,44 @@ tally 2:
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@@ -1156,36 +1156,36 @@ tally 2:
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@@ -1204,28 +1204,28 @@ tally 2:
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@@ -1236,100 +1236,100 @@ tally 2:
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0.000000E+00
0.000000E+00
-2.510000E-01
-1.270100E-02
+2.410000E-01
+1.168300E-02
0.000000E+00
0.000000E+00
-1.000000E-01
-2.154000E-03
+9.100000E-02
+1.807000E-03
0.000000E+00
0.000000E+00
-1.890000E-01
-7.267000E-03
+2.100000E-01
+8.928000E-03
0.000000E+00
0.000000E+00
-1.710000E-01
-5.975000E-03
+2.090000E-01
+8.775000E-03
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-1.250000E-01
-3.287000E-03
+1.320000E-01
+3.514000E-03
0.000000E+00
0.000000E+00
-1.260000E-01
-3.360000E-03
+1.490000E-01
+4.731000E-03
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1636,24 +1636,24 @@ tally 2:
0.000000E+00
0.000000E+00
0.000000E+00
-1.230000E-01
-3.143000E-03
+1.150000E-01
+2.891000E-03
0.000000E+00
0.000000E+00
-1.300000E-01
-3.454000E-03
+1.560000E-01
+5.154000E-03
0.000000E+00
0.000000E+00
-4.500000E-02
-4.390000E-04
+7.900000E-02
+1.495000E-03
0.000000E+00
0.000000E+00
-1.650000E-01
-5.497000E-03
+1.770000E-01
+6.293000E-03
0.000000E+00
0.000000E+00
-1.380000E-01
-3.946000E-03
+1.600000E-01
+5.352000E-03
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1668,88 +1668,88 @@ tally 2:
0.000000E+00
0.000000E+00
0.000000E+00
-1.840000E-01
-6.872000E-03
+1.610000E-01
+5.273000E-03
0.000000E+00
0.000000E+00
-2.440000E-01
-1.221200E-02
+2.310000E-01
+1.098100E-02
0.000000E+00
0.000000E+00
-1.370000E-01
-3.775000E-03
+1.610000E-01
+5.233000E-03
0.000000E+00
0.000000E+00
-1.220000E-01
-3.024000E-03
+1.370000E-01
+3.855000E-03
0.000000E+00
0.000000E+00
-1.560000E-01
-4.952000E-03
+1.760000E-01
+6.482000E-03
0.000000E+00
0.000000E+00
-1.210000E-01
-3.039000E-03
+1.340000E-01
+3.882000E-03
0.000000E+00
0.000000E+00
-1.010000E-01
-2.179000E-03
+1.030000E-01
+2.271000E-03
0.000000E+00
0.000000E+00
-2.020000E-01
-8.370000E-03
+2.090000E-01
+8.841000E-03
0.000000E+00
0.000000E+00
-1.800000E-01
-6.542000E-03
+1.830000E-01
+6.761000E-03
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-2.440000E-01
-1.221200E-02
+2.310000E-01
+1.098100E-02
0.000000E+00
0.000000E+00
-1.840000E-01
-6.872000E-03
+1.610000E-01
+5.273000E-03
0.000000E+00
0.000000E+00
-2.430000E-01
-1.197500E-02
+2.620000E-01
+1.380600E-02
0.000000E+00
0.000000E+00
1.700000E-01
-6.050000E-03
+5.970000E-03
0.000000E+00
0.000000E+00
-2.510000E-01
-1.270100E-02
+2.410000E-01
+1.168300E-02
0.000000E+00
0.000000E+00
-1.580000E-01
-5.108000E-03
+1.550000E-01
+4.921000E-03
0.000000E+00
0.000000E+00
-2.750000E-01
-1.589500E-02
+2.250000E-01
+1.014100E-02
0.000000E+00
0.000000E+00
-1.680000E-01
-5.858000E-03
+1.370000E-01
+3.805000E-03
0.000000E+00
0.000000E+00
-2.250000E-01
-1.096300E-02
+2.100000E-01
+1.004600E-02
0.000000E+00
0.000000E+00
-5.020000E-01
-5.764600E-02
+5.140000E-01
+5.890200E-02
0.000000E+00
0.000000E+00
-2.260000E-01
-1.039600E-02
+2.320000E-01
+1.093000E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1757,11 +1757,11 @@ tally 2:
0.000000E+00
0.000000E+00
1.700000E-01
-6.050000E-03
+5.970000E-03
0.000000E+00
0.000000E+00
-2.430000E-01
-1.197500E-02
+2.620000E-01
+1.380600E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1772,32 +1772,32 @@ tally 2:
0.000000E+00
0.000000E+00
0.000000E+00
-1.300000E-01
-3.454000E-03
+1.560000E-01
+5.154000E-03
0.000000E+00
0.000000E+00
-1.230000E-01
-3.143000E-03
+1.150000E-01
+2.891000E-03
0.000000E+00
0.000000E+00
-1.590000E-01
-5.219000E-03
+1.430000E-01
+4.163000E-03
0.000000E+00
0.000000E+00
-1.270000E-01
-3.447000E-03
+1.120000E-01
+2.640000E-03
0.000000E+00
0.000000E+00
1.030000E-01
2.191000E-03
0.000000E+00
0.000000E+00
-2.110000E-01
-8.999000E-03
+1.950000E-01
+7.705000E-03
0.000000E+00
0.000000E+00
-2.090000E-01
-9.091000E-03
+1.760000E-01
+6.392000E-03
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1812,20 +1812,20 @@ tally 2:
0.000000E+00
0.000000E+00
0.000000E+00
-1.150000E-01
-2.821000E-03
+9.200000E-02
+1.822000E-03
0.000000E+00
0.000000E+00
-1.610000E-01
-5.499000E-03
+1.370000E-01
+3.843000E-03
0.000000E+00
0.000000E+00
-1.210000E-01
-3.039000E-03
+1.340000E-01
+3.882000E-03
0.000000E+00
0.000000E+00
-1.560000E-01
-4.952000E-03
+1.760000E-01
+6.482000E-03
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1836,44 +1836,44 @@ tally 2:
0.000000E+00
0.000000E+00
0.000000E+00
-7.000000E-02
-1.284000E-03
+6.400000E-02
+9.460000E-04
0.000000E+00
0.000000E+00
-1.440000E-01
-4.264000E-03
+1.510000E-01
+4.845000E-03
0.000000E+00
0.000000E+00
-1.580000E-01
-5.002000E-03
+1.800000E-01
+6.520000E-03
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-1.610000E-01
-5.499000E-03
+1.370000E-01
+3.843000E-03
0.000000E+00
0.000000E+00
-1.150000E-01
-2.821000E-03
+9.200000E-02
+1.822000E-03
0.000000E+00
0.000000E+00
-1.630000E-01
-5.583000E-03
+1.300000E-01
+3.604000E-03
0.000000E+00
0.000000E+00
-1.270000E-01
-3.315000E-03
+1.170000E-01
+2.789000E-03
0.000000E+00
0.000000E+00
-1.680000E-01
-5.858000E-03
+1.370000E-01
+3.805000E-03
0.000000E+00
0.000000E+00
-2.750000E-01
-1.589500E-02
+2.250000E-01
+1.014100E-02
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1884,28 +1884,28 @@ tally 2:
0.000000E+00
0.000000E+00
0.000000E+00
-1.160000E-01
-3.278000E-03
+9.600000E-02
+2.024000E-03
0.000000E+00
0.000000E+00
-2.070000E-01
-8.695000E-03
+2.000000E-01
+8.202000E-03
0.000000E+00
0.000000E+00
-1.840000E-01
-6.908000E-03
+1.820000E-01
+6.660000E-03
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-1.270000E-01
-3.315000E-03
+1.170000E-01
+2.789000E-03
0.000000E+00
0.000000E+00
-1.630000E-01
-5.583000E-03
+1.300000E-01
+3.604000E-03
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1916,12 +1916,12 @@ tally 2:
0.000000E+00
0.000000E+00
0.000000E+00
-1.270000E-01
-3.447000E-03
+1.120000E-01
+2.640000E-03
0.000000E+00
0.000000E+00
-1.590000E-01
-5.219000E-03
+1.430000E-01
+4.163000E-03
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1932,16 +1932,16 @@ tally 2:
0.000000E+00
0.000000E+00
0.000000E+00
-5.400000E-02
-6.340000E-04
+4.900000E-02
+5.630000E-04
0.000000E+00
0.000000E+00
-1.600000E-01
-5.186000E-03
+1.670000E-01
+5.653000E-03
0.000000E+00
0.000000E+00
-1.920000E-01
-7.646000E-03
+1.670000E-01
+5.701000E-03
0.000000E+00
0.000000E+00
0.000000E+00
diff --git a/tests/regression_tests/seed/results_true.dat b/tests/regression_tests/seed/results_true.dat
--- a/tests/regression_tests/seed/results_true.dat
+++ b/tests/regression_tests/seed/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-2.961599E-01 2.921488E-03
+3.069730E-01 2.632099E-03
diff --git a/tests/regression_tests/source/results_true.dat b/tests/regression_tests/source/results_true.dat
--- a/tests/regression_tests/source/results_true.dat
+++ b/tests/regression_tests/source/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-3.073726E-01 2.535074E-03
+3.054101E-01 1.167865E-03
diff --git a/tests/regression_tests/source/test.py b/tests/regression_tests/source/test.py
--- a/tests/regression_tests/source/test.py
+++ b/tests/regression_tests/source/test.py
@@ -39,15 +39,15 @@ def _build_inputs(self):
spatial2 = openmc.stats.Box([-4., -4., -4.], [4., 4., 4.])
spatial3 = openmc.stats.Point([1.2, -2.3, 0.781])
spatial4 = openmc.stats.SphericalIndependent(r_dist, cos_theta_dist,
- phi_dist,
+ phi_dist,
origin=(1., 1., 0.))
- spatial5 = openmc.stats.CylindricalIndependent(r_dist, phi_dist,
+ spatial5 = openmc.stats.CylindricalIndependent(r_dist, phi_dist,
z_dist,
origin=(1., 1., 0.))
spatial6 = openmc.stats.SphericalIndependent(r_dist2, cos_theta_dist,
- phi_dist,
+ phi_dist,
origin=(1., 1., 0.))
- spatial7 = openmc.stats.CylindricalIndependent(r_dist1, phi_dist,
+ spatial7 = openmc.stats.CylindricalIndependent(r_dist1, phi_dist,
z_dist,
origin=(1., 1., 0.))
@@ -57,7 +57,10 @@ def _build_inputs(self):
angle2 = openmc.stats.Monodirectional(reference_uvw=[0., 1., 0.])
angle3 = openmc.stats.Isotropic()
- E = np.logspace(0, 7)
+ # Note that the definition for E is equivalent to logspace(0, 7) but we
+ # manually take powers because of last-digit differences that may cause
+ # test failures with different versions of numpy
+ E = np.array([10**x for x in np.linspace(0, 7)])
p = np.sin(np.linspace(0., pi))
p /= sum(np.diff(E)*p[:-1])
energy1 = openmc.stats.Maxwell(1.2895e6)
diff --git a/tests/regression_tests/source_file/results_true.dat b/tests/regression_tests/source_file/results_true.dat
--- a/tests/regression_tests/source_file/results_true.dat
+++ b/tests/regression_tests/source_file/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-3.009416E-01 3.229998E-03
+2.983135E-01 5.116978E-03
diff --git a/tests/regression_tests/source_mcpl_file/results_true.dat b/tests/regression_tests/source_mcpl_file/results_true.dat
--- a/tests/regression_tests/source_mcpl_file/results_true.dat
+++ b/tests/regression_tests/source_mcpl_file/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-3.009416E-01 3.229999E-03
+2.983135E-01 5.116978E-03
diff --git a/tests/regression_tests/sourcepoint_batch/results_true.dat b/tests/regression_tests/sourcepoint_batch/results_true.dat
--- a/tests/regression_tests/sourcepoint_batch/results_true.dat
+++ b/tests/regression_tests/sourcepoint_batch/results_true.dat
@@ -1,3 +1,3 @@
k-combined:
-3.003690E-01 3.923324E-03
--5.424825E+00 -4.990262E+00 -6.395029E+00
+3.074376E-01 3.049465E-03
+3.667754E+00 -7.701697E+00 2.213664E+00
diff --git a/tests/regression_tests/sourcepoint_latest/results_true.dat b/tests/regression_tests/sourcepoint_latest/results_true.dat
--- a/tests/regression_tests/sourcepoint_latest/results_true.dat
+++ b/tests/regression_tests/sourcepoint_latest/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-2.987050E-01 1.827430E-03
+3.070134E-01 3.900396E-03
diff --git a/tests/regression_tests/sourcepoint_restart/results_true.dat b/tests/regression_tests/sourcepoint_restart/results_true.dat
--- a/tests/regression_tests/sourcepoint_restart/results_true.dat
+++ b/tests/regression_tests/sourcepoint_restart/results_true.dat
@@ -1,126 +1,158 @@
k-combined:
-2.987050E-01 1.827430E-03
+3.070134E-01 3.900396E-03
tally 1:
-1.400000E-02
-5.000000E-05
-5.637968E-03
-7.140222E-06
+1.300000E-02
+4.700000E-05
+5.741381E-03
+9.030024E-06
+0.000000E+00
+0.000000E+00
+3.067112E-04
+9.407179E-08
+1.000000E-03
+1.000000E-06
+3.015814E-04
+9.095135E-08
0.000000E+00
0.000000E+00
-8.891645E-04
-4.440759E-07
0.000000E+00
0.000000E+00
+2.600000E-02
+1.420000E-04
+1.268989E-02
+3.464490E-05
0.000000E+00
0.000000E+00
+2.948908E-04
+8.696057E-08
+1.000000E-03
+1.000000E-06
+1.535009E-03
+1.224718E-06
+1.000000E-03
+1.000000E-06
0.000000E+00
0.000000E+00
+3.200000E-02
+2.760000E-04
+1.248507E-02
+3.714039E-05
0.000000E+00
0.000000E+00
-1.800000E-02
-7.200000E-05
-8.618270E-03
-1.620709E-05
+9.208601E-04
+4.708050E-07
0.000000E+00
0.000000E+00
-2.884266E-04
-8.318989E-08
0.000000E+00
0.000000E+00
-8.903211E-04
-7.926717E-07
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-3.300000E-02
-2.290000E-04
-1.685675E-02
-6.105228E-05
+1.900000E-02
+7.500000E-05
+8.218811E-03
+1.462963E-05
0.000000E+00
0.000000E+00
-6.007379E-04
-3.608860E-07
+9.070399E-04
+2.743247E-07
0.000000E+00
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-3.587866E-07
+9.047443E-04
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1.000000E-03
1.000000E-06
-2.884266E-04
-8.318989E-08
-1.500000E-02
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-7.665313E-03
-1.617331E-05
0.000000E+00
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0.000000E+00
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0.000000E+00
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0.000000E+00
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-1.100000E-02
-6.900000E-05
-5.663296E-03
-1.118218E-05
0.000000E+00
0.000000E+00
-1.198138E-03
-8.972573E-07
0.000000E+00
0.000000E+00
-5.989880E-04
-3.587866E-07
-1.000000E-03
-1.000000E-06
-0.000000E+00
-0.000000E+00
-1.300000E-02
-6.300000E-05
-5.687181E-03
-1.121031E-05
-0.000000E+00
-0.000000E+00
-5.963216E-04
-1.778036E-07
0.000000E+00
0.000000E+00
+3.100000E-02
+2.010000E-04
+1.336346E-02
+3.645780E-05
0.000000E+00
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+2.102710E-03
+1.524522E-06
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0.000000E+00
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+1.334578E-02
+3.590708E-05
0.000000E+00
0.000000E+00
-1.500000E-02
-6.100000E-05
-1.040584E-02
-2.402892E-05
+6.031628E-04
+3.638054E-07
+1.000000E-03
+1.000000E-06
+1.530605E-03
+1.035684E-06
+2.000000E-03
+2.000000E-06
+6.082927E-04
+1.850231E-07
+1.400000E-02
+4.200000E-05
+7.257468E-03
+1.221578E-05
0.000000E+00
0.000000E+00
-5.879206E-04
-1.728865E-07
+2.948908E-04
+8.696057E-08
0.000000E+00
0.000000E+00
-8.903211E-04
-7.926717E-07
-1.000000E-03
-1.000000E-06
+8.980536E-04
+4.507660E-07
+2.000000E-03
+4.000000E-06
0.000000E+00
0.000000E+00
-4.200000E-02
-3.880000E-04
-1.781042E-02
-7.329257E-05
+9.000000E-03
+2.700000E-05
+5.193169E-03
+1.187321E-05
0.000000E+00
0.000000E+00
-5.990419E-04
-1.794256E-07
+3.054379E-04
+9.329231E-08
0.000000E+00
0.000000E+00
0.000000E+00
@@ -129,12 +161,14 @@ tally 1:
0.000000E+00
0.000000E+00
0.000000E+00
-2.200000E-02
-1.220000E-04
-9.854350E-03
-2.671897E-05
+1.000000E-02
+2.400000E-05
+5.170002E-03
+7.361546E-06
0.000000E+00
0.000000E+00
+6.003287E-04
+1.802529E-07
0.000000E+00
0.000000E+00
0.000000E+00
@@ -143,12 +177,12 @@ tally 1:
0.000000E+00
0.000000E+00
0.000000E+00
+2.800000E-02
+1.720000E-04
+1.699195E-02
+6.267008E-05
0.000000E+00
0.000000E+00
-1.200000E-02
-4.400000E-05
-5.595730E-03
-9.201460E-06
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@@ -785,12 +799,12 @@ tally 1:
0.000000E+00
0.000000E+00
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@@ -801,12 +815,12 @@ tally 1:
0.000000E+00
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0.000000E+00
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@@ -817,60 +831,48 @@ tally 1:
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@@ -895,54 +897,52 @@ tally 1:
0.000000E+00
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@@ -962,11 +962,11 @@ tally 1:
0.000000E+00
0.000000E+00
tally 2:
-5.649702E-01
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diff --git a/tests/regression_tests/statepoint_batch/results_true.dat b/tests/regression_tests/statepoint_batch/results_true.dat
--- a/tests/regression_tests/statepoint_batch/results_true.dat
+++ b/tests/regression_tests/statepoint_batch/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-2.985923E-01 2.864193E-03
+3.048864E-01 1.689118E-03
diff --git a/tests/regression_tests/statepoint_restart/results_true.dat b/tests/regression_tests/statepoint_restart/results_true.dat
--- a/tests/regression_tests/statepoint_restart/results_true.dat
+++ b/tests/regression_tests/statepoint_restart/results_true.dat
@@ -1,95 +1,132 @@
k-combined:
-2.987050E-01 1.827430E-03
+3.070134E-01 3.900396E-03
tally 1:
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@@ -97,90 +134,103 @@ tally 1:
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@@ -191,16 +241,18 @@ tally 1:
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@@ -213,16 +265,16 @@ tally 1:
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@@ -237,122 +289,114 @@ tally 1:
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@@ -361,42 +405,24 @@ tally 1:
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0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-1.000000E-03
-1.000000E-06
-1.000000E-03
-1.000000E-06
-5.990959E-04
-3.589159E-07
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-2.400000E-02
-1.260000E-04
-2.400000E-02
-1.260000E-04
-1.220791E-02
-3.565074E-05
+1.100000E-02
+2.700000E-05
+1.100000E-02
+2.700000E-05
+3.927884E-03
+3.728010E-06
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-2.995479E-04
-8.972896E-08
+3.074376E-04
+9.451786E-08
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1057,12 +1081,6 @@ tally 1:
0.000000E+00
0.000000E+00
0.000000E+00
-9.000000E-03
-2.500000E-05
-9.000000E-03
-2.500000E-05
-3.572884E-03
-4.101061E-06
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1073,14 +1091,6 @@ tally 1:
0.000000E+00
0.000000E+00
0.000000E+00
-5.935474E-04
-3.522985E-07
-1.000000E-03
-1.000000E-06
-1.000000E-03
-1.000000E-06
-2.967737E-04
-8.807464E-08
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1095,76 +1105,88 @@ tally 1:
0.000000E+00
0.000000E+00
0.000000E+00
+9.000000E-03
+1.900000E-05
+9.000000E-03
+1.900000E-05
+4.217645E-03
+4.306910E-06
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
+6.128755E-04
+1.878102E-07
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-1.000000E-02
-3.800000E-05
-1.000000E-02
-3.800000E-05
-5.382607E-03
-1.128619E-05
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-1.000000E-03
-1.000000E-06
-1.000000E-03
-1.000000E-06
-2.994940E-04
-8.969666E-08
+1.700000E-02
+7.700000E-05
+1.700000E-02
+7.700000E-05
+7.235504E-03
+1.301737E-05
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
+3.054379E-04
+9.329231E-08
+0.000000E+00
+0.000000E+00
+0.000000E+00
+0.000000E+00
+1.531736E-03
+8.439742E-07
+3.000000E-03
+3.000000E-06
+3.000000E-03
+3.000000E-06
+3.074376E-04
+9.451786E-08
+9.000000E-03
+1.900000E-05
+9.000000E-03
+1.900000E-05
+3.018298E-03
+2.174671E-06
0.000000E+00
0.000000E+00
-1.200000E-02
-4.600000E-05
-1.200000E-02
-4.600000E-05
-6.554978E-03
-9.995681E-06
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-2.884266E-04
-8.318989E-08
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-2.994940E-04
-8.969666E-08
+6.141488E-04
+1.885896E-07
+1.000000E-03
+1.000000E-06
+1.000000E-03
+1.000000E-06
+3.074376E-04
+9.451786E-08
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-7.000000E-03
-1.100000E-05
-7.000000E-03
-1.100000E-05
-3.868525E-03
-3.829197E-06
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-5.935474E-04
-3.522985E-07
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1177,14 +1199,14 @@ tally 1:
0.000000E+00
0.000000E+00
0.000000E+00
-1.000000E-03
-1.000000E-06
-1.000000E-03
-1.000000E-06
-5.989880E-04
-3.587866E-07
0.000000E+00
0.000000E+00
+2.000000E-03
+2.000000E-06
+2.000000E-03
+2.000000E-06
+1.203204E-03
+7.241295E-07
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1201,14 +1223,14 @@ tally 1:
0.000000E+00
0.000000E+00
0.000000E+00
-1.000000E-03
-1.000000E-06
-1.000000E-03
-1.000000E-06
-2.994940E-04
-8.969666E-08
0.000000E+00
0.000000E+00
+7.000000E-03
+1.500000E-05
+7.000000E-03
+1.500000E-05
+4.818843E-03
+6.474375E-06
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1225,86 +1247,68 @@ tally 1:
0.000000E+00
0.000000E+00
0.000000E+00
-1.100000E-02
-3.100000E-05
-1.100000E-02
-3.100000E-05
-4.132972E-03
-4.495389E-06
0.000000E+00
0.000000E+00
+2.400000E-02
+1.180000E-04
+2.400000E-02
+1.180000E-04
+1.088639E-02
+2.567229E-05
0.000000E+00
0.000000E+00
-2.967737E-04
-8.807464E-08
0.000000E+00
0.000000E+00
+3.067112E-04
+9.407179E-08
0.000000E+00
0.000000E+00
-6.007379E-04
-3.608860E-07
-1.000000E-03
-1.000000E-06
-1.000000E-03
-1.000000E-06
-2.967737E-04
-8.807464E-08
-2.000000E-02
-9.200000E-05
-2.000000E-02
-9.200000E-05
-8.597951E-03
-1.801722E-05
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-5.989880E-04
-3.587866E-07
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
+1.300000E-02
+5.100000E-05
+1.300000E-02
+5.100000E-05
+6.002667E-03
+1.149916E-05
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
+3.015814E-04
+9.095135E-08
0.000000E+00
0.000000E+00
-1.200000E-02
-3.200000E-05
-1.200000E-02
-3.200000E-05
-6.509749E-03
-9.403130E-06
0.000000E+00
0.000000E+00
+3.067112E-04
+9.407179E-08
0.000000E+00
0.000000E+00
-3.003690E-04
-9.022151E-08
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-5.990959E-04
-3.589159E-07
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
+2.948908E-04
+8.696057E-08
0.000000E+00
0.000000E+00
-1.000000E-03
-1.000000E-06
-1.000000E-03
-1.000000E-06
-2.884266E-04
-8.318989E-08
0.000000E+00
0.000000E+00
+2.948908E-04
+8.696057E-08
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1341,22 +1345,22 @@ tally 1:
0.000000E+00
0.000000E+00
0.000000E+00
+1.300000E-02
+4.700000E-05
+1.300000E-02
+4.700000E-05
+5.486562E-03
+7.965488E-06
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-7.000000E-03
-2.100000E-05
-7.000000E-03
-2.100000E-05
-3.890163E-03
-6.545535E-06
+3.054379E-04
+9.329231E-08
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-2.995479E-04
-8.972896E-08
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1365,22 +1369,22 @@ tally 1:
0.000000E+00
0.000000E+00
0.000000E+00
+8.000000E-03
+1.800000E-05
+8.000000E-03
+1.800000E-05
+3.334317E-03
+3.609712E-06
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-1.300000E-02
-4.300000E-05
-1.300000E-02
-4.300000E-05
-6.485840E-03
-1.112994E-05
+2.948908E-04
+8.696057E-08
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-5.989880E-04
-3.587866E-07
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1389,32 +1393,28 @@ tally 1:
0.000000E+00
0.000000E+00
0.000000E+00
+2.000000E-02
+1.080000E-04
+2.000000E-02
+1.080000E-04
+9.741552E-03
+2.552400E-05
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-1.500000E-02
-4.900000E-05
-1.500000E-02
-4.900000E-05
-7.442524E-03
-1.164759E-05
+3.015814E-04
+9.095135E-08
0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
-2.994940E-04
-8.969666E-08
+1.800986E-03
+1.622276E-06
1.000000E-03
1.000000E-06
1.000000E-03
1.000000E-06
-5.768531E-04
-3.327596E-07
-0.000000E+00
-0.000000E+00
-0.000000E+00
-0.000000E+00
0.000000E+00
0.000000E+00
0.000000E+00
@@ -1442,11 +1442,11 @@ tally 1:
0.000000E+00
0.000000E+00
tally 2:
-5.649702E-01
-6.385502E-02
-6.158199E-01
-7.586795E-02
-3.579551E+00
-2.563396E+00
-3.982345E+01
-3.172536E+02
+5.818100E-01
+6.772558E-02
+6.344749E-01
+8.054355E-02
+3.690180E+00
+2.724752E+00
+4.102635E+01
+3.367908E+02
diff --git a/tests/regression_tests/statepoint_sourcesep/results_true.dat b/tests/regression_tests/statepoint_sourcesep/results_true.dat
--- a/tests/regression_tests/statepoint_sourcesep/results_true.dat
+++ b/tests/regression_tests/statepoint_sourcesep/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-2.987050E-01 1.827430E-03
+3.070134E-01 3.900396E-03
diff --git a/tests/regression_tests/surface_source/surface_source_true.h5 b/tests/regression_tests/surface_source/surface_source_true.h5
Binary files a/tests/regression_tests/surface_source/surface_source_true.h5 and b/tests/regression_tests/surface_source/surface_source_true.h5 differ
diff --git a/tests/regression_tests/surface_tally/results_true.dat b/tests/regression_tests/surface_tally/results_true.dat
--- a/tests/regression_tests/surface_tally/results_true.dat
+++ b/tests/regression_tests/surface_tally/results_true.dat
@@ -1,52 +1,52 @@
mean,std. dev.
-1.9600000e-02,1.5719768e-03
-7.3700000e-02,1.9382122e-03
-1.7130000e-01,4.0907755e-03
-6.3490000e-01,8.8197380e-03
-2.5000000e-03,5.2174919e-04
-6.0000000e-03,1.6799471e-03
-1.0600000e-02,1.8749815e-03
-4.0200000e-02,1.6852300e-03
-1.9600000e-02,1.5719768e-03
-7.3700000e-02,1.9382122e-03
-1.7130000e-01,4.0907755e-03
-6.3490000e-01,8.8197380e-03
-2.5000000e-03,5.2174919e-04
-6.0000000e-03,1.6799471e-03
-1.0600000e-02,1.8749815e-03
-4.0200000e-02,1.6852300e-03
-4.7000000e-03,9.1954095e-04
-4.5400000e-02,2.4413111e-03
-4.2800000e-02,2.2150997e-03
-4.2460000e-01,7.3017502e-03
-0.0000000e+00,0.0000000e+00
-1.6000000e-03,2.6666667e-04
-4.0000000e-04,1.6329932e-04
-1.5700000e-02,1.1551816e-03
--4.7000000e-03,9.1954095e-04
--4.5400000e-02,2.4413111e-03
--4.2800000e-02,2.2150997e-03
--4.2460000e-01,7.3017502e-03
-0.0000000e+00,0.0000000e+00
--1.6000000e-03,2.6666667e-04
--4.0000000e-04,1.6329932e-04
--1.5700000e-02,1.1551816e-03
-1.4900000e-02,1.5235193e-03
-2.8300000e-02,2.0925795e-03
-1.2850000e-01,4.0613353e-03
-2.1030000e-01,5.4955538e-03
-2.5000000e-03,5.2174919e-04
-4.4000000e-03,1.4847372e-03
-1.0200000e-02,1.8903263e-03
-2.4500000e-02,1.7966017e-03
-0.0000000e+00,0.0000000e+00
--3.0900000e-02,2.0518285e-03
-0.0000000e+00,0.0000000e+00
--3.4370000e-01,4.5093730e-03
-0.0000000e+00,0.0000000e+00
--2.9000000e-03,8.0897741e-04
-0.0000000e+00,0.0000000e+00
--2.2200000e-02,2.0210009e-03
+2.1200000e-02,1.8366636e-03
+7.4900000e-02,2.2083176e-03
+1.6220000e-01,2.8079253e-03
+6.4010000e-01,8.6838931e-03
+2.1000000e-03,3.7859389e-04
+5.6000000e-03,6.8637534e-04
+1.1700000e-02,1.4456832e-03
+4.1700000e-02,2.7041121e-03
+2.1200000e-02,1.8366636e-03
+7.4900000e-02,2.2083176e-03
+1.6220000e-01,2.8079253e-03
+6.4010000e-01,8.6838931e-03
+2.1000000e-03,3.7859389e-04
+5.6000000e-03,6.8637534e-04
+1.1700000e-02,1.4456832e-03
+4.1700000e-02,2.7041121e-03
+5.2000000e-03,5.9254629e-04
+3.9200000e-02,2.5508169e-03
+4.0200000e-02,1.9310331e-03
+4.1360000e-01,8.0072190e-03
+0.0000000e+00,0.0000000e+00
+1.9000000e-03,3.7859389e-04
+1.0000000e-04,1.0000000e-04
+1.6400000e-02,1.2840907e-03
+-5.2000000e-03,5.9254629e-04
+-3.9200000e-02,2.5508169e-03
+-4.0200000e-02,1.9310331e-03
+-4.1360000e-01,8.0072190e-03
+0.0000000e+00,0.0000000e+00
+-1.9000000e-03,3.7859389e-04
+-1.0000000e-04,1.0000000e-04
+-1.6400000e-02,1.2840907e-03
+1.6000000e-02,2.1602469e-03
+3.5700000e-02,2.9441090e-03
+1.2200000e-01,3.5932035e-03
+2.2650000e-01,9.2463206e-03
+2.1000000e-03,3.7859389e-04
+3.7000000e-03,8.1717671e-04
+1.1600000e-02,1.4772347e-03
+2.5300000e-02,1.9723083e-03
+0.0000000e+00,0.0000000e+00
+-2.9700000e-02,2.4587711e-03
+0.0000000e+00,0.0000000e+00
+-3.5090000e-01,3.7161808e-03
+0.0000000e+00,0.0000000e+00
+-2.1000000e-03,4.8189441e-04
+0.0000000e+00,0.0000000e+00
+-2.1400000e-02,1.7397318e-03
0.0000000e+00,0.0000000e+00
0.0000000e+00,0.0000000e+00
0.0000000e+00,0.0000000e+00
diff --git a/tests/regression_tests/survival_biasing/results_true.dat b/tests/regression_tests/survival_biasing/results_true.dat
--- a/tests/regression_tests/survival_biasing/results_true.dat
+++ b/tests/regression_tests/survival_biasing/results_true.dat
@@ -1,20 +1,20 @@
k-combined:
-9.826269E-01 1.626276E-02
+9.879232E-01 8.097582E-03
tally 1:
-4.209907E+01
-3.546281E+02
-1.759415E+01
-6.197412E+01
-2.165888E+00
-9.392975E-01
-1.873459E+00
-7.025989E-01
-4.850267E+00
-4.708899E+00
-3.397795E-02
-2.310621E-04
-3.628554E+08
-2.635633E+16
+4.295331E+01
+3.691096E+02
+1.802724E+01
+6.501934E+01
+2.193500E+00
+9.627609E-01
+1.893529E+00
+7.174104E-01
+4.902380E+00
+4.808570E+00
+3.418014E-02
+2.337353E-04
+3.667128E+08
+2.690758E+16
tally 2:
-1.759415E+01
-6.197412E+01
+1.802724E+01
+6.501934E+01
diff --git a/tests/regression_tests/tallies/results_true.dat b/tests/regression_tests/tallies/results_true.dat
--- a/tests/regression_tests/tallies/results_true.dat
+++ b/tests/regression_tests/tallies/results_true.dat
@@ -1 +1 @@
-ad28e723270c25dc46f27f1482052e381c802cb111ea8224368d4ea3d903eeaba1a3dce541957f24ec0634ed2ada6f20f97c0270c269b9bcae4b34a1b317a165
\ No newline at end of file
+6b1d8d6f4d7a70af6c39cc76b9267a61ba9a9d0c14b75a4df6f83e72a2bfaf1533caaf936c2185f0a158443eb9da266bd5a77b7996020fd638551ea841d821e0
\ No newline at end of file
diff --git a/tests/regression_tests/tally_aggregation/results_true.dat b/tests/regression_tests/tally_aggregation/results_true.dat
--- a/tests/regression_tests/tally_aggregation/results_true.dat
+++ b/tests/regression_tests/tally_aggregation/results_true.dat
@@ -1,97 +1,97 @@
-[[1.6100557e-05 5.2845844e-04]
- [3.1178030e-01 1.6963068e-01]
- [1.8103970e-02 7.1792000e-01]], [[1.6327747e-05 5.3562414e-04]
- [3.2299959e-01 1.7506573e-01]
- [1.8518775e-02 7.2159429e-01]], [[1.5779072e-05 5.7847880e-04]
- [3.1206099e-01 1.6937953e-01]
- [1.7615699e-02 6.9887963e-01]], [[1.6129040e-05 5.2214564e-04]
- [3.3116549e-01 1.7924984e-01]
- [1.8339236e-02 7.1809645e-01]][[2.5070599e-07 4.1541177e-05]
- [8.8868371e-03 4.3482360e-03]
- [4.2929455e-04 5.1166511e-03]], [[2.6348920e-07 4.0911978e-05]
- [9.5560259e-03 4.6948487e-03]
- [5.1500008e-04 8.2022796e-03]], [[2.8482730e-07 5.2369388e-05]
- [5.9366950e-03 2.9803949e-03]
- [3.5036278e-04 7.1193378e-03]], [[4.9529279e-07 5.2183723e-05]
- [1.1645140e-02 5.7325245e-03]
- [9.3005699e-04 9.2536054e-03]][[1.0276552e-06 8.0660598e-04]
- [1.1192721e+00 5.5462743e-01]
- [1.3911834e-06 5.0699881e-01]], [[1.9629638e-06 1.0409504e-03]
- [1.4059305e-01 9.8087142e-02]
- [2.9492646e-05 7.8705320e-01]], [[1.5107402e-05 2.2995488e-04]
- [1.3135825e-02 2.9816182e-02]
- [3.2964785e-04 1.1215217e+00]], [[4.6238395e-05 8.7195730e-05]
- [5.0054342e-03 1.0795027e-02]
- [7.2217149e-02 4.4091666e-01]][[1.6532673e-08 1.2337935e-05]
- [1.8386631e-02 9.0206165e-03]
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\ No newline at end of file
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\ No newline at end of file
diff --git a/tests/regression_tests/tally_arithmetic/results_true.dat b/tests/regression_tests/tally_arithmetic/results_true.dat
--- a/tests/regression_tests/tally_arithmetic/results_true.dat
+++ b/tests/regression_tests/tally_arithmetic/results_true.dat
@@ -1,49 +1,49 @@
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+ 6.18150e-03 4.97869e-03 3.17279e-03 2.55542e-03 2.36089e-03 4.46651e-05
+ 1.02263e-02 1.93469e-04 1.18179e-04 2.62375e-05 5.11897e-04 1.13649e-04
+ 2.56040e-02 4.84394e-04 4.55595e-02 8.61927e-04 1.28165e-03 2.84546e-04
+ 2.28056e-03 5.06320e-04 2.29877e-03 4.53056e-05 9.95724e-03 1.96244e-04
+ 1.14803e-04 2.57898e-05 4.97276e-04 1.11710e-04 2.49302e-02 4.91340e-04
+ 4.43606e-02 8.74289e-04 1.24504e-03 2.79691e-04 2.21542e-03 4.97680e-04
+ 2.31940e-03 4.34238e-05 1.00466e-02 1.88093e-04 1.17620e-04 2.69280e-05
+ 5.09479e-04 1.16640e-04 2.51540e-02 4.70932e-04 4.47588e-02 8.37974e-04
+ 1.27560e-03 2.92034e-04 2.26979e-03 5.19644e-04 2.19212e-03 4.53914e-05
+ 9.49530e-03 1.96615e-04 1.09609e-04 2.41615e-05 4.74778e-04 1.04657e-04
+ 2.37736e-02 4.92271e-04 4.23026e-02 8.75944e-04 1.18871e-03 2.62032e-04
+ 2.11519e-03 4.66257e-04][0.0057 0.00454 0.00293 0.00233 0.00568 0.00451 0.00292 0.00232 0.00574
+ 0.00461 0.00295 0.00236 0.00618 0.00498 0.00317 0.00256 0.00128 0.00028
+ 0.00228 0.00051 0.00125 0.00028 0.00222 0.0005 0.00128 0.00029 0.00227
+ 0.00052 0.00119 0.00026 0.00212 0.00047][0.00018 0.00017 0.00315 0.00293 0.00018 0.00017 0.00325 0.00292 0.00017
+ 0.00017 0.00303 0.00295 0.00018 0.00018 0.00317 0.00317 0.01023 0.00051
+ 0.04556 0.00228 0.00996 0.0005 0.04436 0.00222 0.01005 0.00051 0.04476
+ 0.00227 0.0095 0.00047 0.0423 0.00212][0.00293 0.00292 0.00295 0.00317 0.00228 0.00222 0.00227 0.00212]
\ No newline at end of file
diff --git a/tests/regression_tests/tally_assumesep/results_true.dat b/tests/regression_tests/tally_assumesep/results_true.dat
--- a/tests/regression_tests/tally_assumesep/results_true.dat
+++ b/tests/regression_tests/tally_assumesep/results_true.dat
@@ -1,11 +1,11 @@
k-combined:
-6.353587E-01 1.925016E-02
+5.683578E-01 1.129170E-02
tally 1:
-7.878503E+00
-1.242768E+01
+6.753950E+00
+9.188305E+00
tally 2:
-2.687214E-01
-1.487262E-02
+2.278558E-01
+1.052944E-02
tally 3:
-1.344654E+01
-3.630145E+01
+1.179091E+01
+2.795539E+01
diff --git a/tests/regression_tests/tally_nuclides/results_true.dat b/tests/regression_tests/tally_nuclides/results_true.dat
--- a/tests/regression_tests/tally_nuclides/results_true.dat
+++ b/tests/regression_tests/tally_nuclides/results_true.dat
@@ -1,28 +1,28 @@
k-combined:
-9.655280E-01 1.463557E-02
+1.132463E+00 5.721067E-02
tally 1:
-6.932814E+00
-9.650528E+00
-1.591338E+00
-5.075076E-01
-1.541515E+00
-4.761914E-01
-5.341475E+00
-5.732892E+00
-6.932814E+00
-9.650528E+00
-1.591338E+00
-5.075076E-01
-1.541515E+00
-4.761914E-01
-5.341475E+00
-5.732892E+00
+7.310528E+00
+1.080411E+01
+1.664215E+00
+5.567756E-01
+1.609340E+00
+5.205634E-01
+5.646313E+00
+6.459724E+00
+7.310528E+00
+1.080411E+01
+1.664215E+00
+5.567756E-01
+1.609340E+00
+5.205634E-01
+5.646313E+00
+6.459724E+00
tally 2:
-6.932814E+00
-9.650528E+00
-1.591338E+00
-5.075076E-01
-1.541515E+00
-4.761914E-01
-5.341475E+00
-5.732892E+00
+7.310528E+00
+1.080411E+01
+1.664215E+00
+5.567756E-01
+1.609340E+00
+5.205634E-01
+5.646313E+00
+6.459724E+00
diff --git a/tests/regression_tests/tally_slice_merge/results_true.dat b/tests/regression_tests/tally_slice_merge/results_true.dat
--- a/tests/regression_tests/tally_slice_merge/results_true.dat
+++ b/tests/regression_tests/tally_slice_merge/results_true.dat
@@ -1,45 +1,45 @@
cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 21 0.00e+00 6.25e-01 U235 fission 1.77e-01 1.81e-02 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 21 0.00e+00 6.25e-01 U235 nu-fission 4.32e-01 4.42e-02 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 21 0.00e+00 6.25e-01 U238 fission 2.43e-07 2.40e-08 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 21 0.00e+00 6.25e-01 U238 nu-fission 6.07e-07 5.97e-08 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 21 6.25e-01 2.00e+07 U235 fission 3.03e-02 1.93e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 21 6.25e-01 2.00e+07 U235 nu-fission 7.41e-02 4.67e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 21 6.25e-01 2.00e+07 U238 fission 1.65e-02 1.61e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 21 6.25e-01 2.00e+07 U238 nu-fission 4.61e-02 4.87e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 27 0.00e+00 6.25e-01 U235 fission 1.31e-01 2.54e-02 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 27 0.00e+00 6.25e-01 U235 nu-fission 3.18e-01 6.19e-02 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 27 0.00e+00 6.25e-01 U238 fission 1.80e-07 3.46e-08 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 27 0.00e+00 6.25e-01 U238 nu-fission 4.49e-07 8.62e-08 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 27 6.25e-01 2.00e+07 U235 fission 2.34e-02 1.23e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 27 6.25e-01 2.00e+07 U235 nu-fission 5.72e-02 2.99e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 27 6.25e-01 2.00e+07 U238 fission 1.24e-02 9.35e-04 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 27 6.25e-01 2.00e+07 U238 nu-fission 3.44e-02 2.73e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 21 0.00e+00 6.25e-01 U235 fission 1.77e-01 1.81e-02
-1 21 0.00e+00 6.25e-01 U235 nu-fission 4.32e-01 4.42e-02
-2 21 0.00e+00 6.25e-01 U238 fission 2.43e-07 2.40e-08
-3 21 0.00e+00 6.25e-01 U238 nu-fission 6.07e-07 5.97e-08
-4 21 6.25e-01 2.00e+07 U235 fission 3.03e-02 1.93e-03
-5 21 6.25e-01 2.00e+07 U235 nu-fission 7.41e-02 4.67e-03
-6 21 6.25e-01 2.00e+07 U238 fission 1.65e-02 1.61e-03
-7 21 6.25e-01 2.00e+07 U238 nu-fission 4.61e-02 4.87e-03
-8 27 0.00e+00 6.25e-01 U235 fission 1.31e-01 2.54e-02
-9 27 0.00e+00 6.25e-01 U235 nu-fission 3.18e-01 6.19e-02
-10 27 0.00e+00 6.25e-01 U238 fission 1.80e-07 3.46e-08
-11 27 0.00e+00 6.25e-01 U238 nu-fission 4.49e-07 8.62e-08
-12 27 6.25e-01 2.00e+07 U235 fission 2.34e-02 1.23e-03
-13 27 6.25e-01 2.00e+07 U235 nu-fission 5.72e-02 2.99e-03
-14 27 6.25e-01 2.00e+07 U238 fission 1.24e-02 9.35e-04
-15 27 6.25e-01 2.00e+07 U238 nu-fission 3.44e-02 2.73e-03
+0 21 0.00e+00 6.25e-01 U235 fission 1.75e-01 1.20e-02 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 21 0.00e+00 6.25e-01 U235 nu-fission 4.26e-01 2.92e-02 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 21 0.00e+00 6.25e-01 U238 fission 2.41e-07 1.61e-08 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 21 0.00e+00 6.25e-01 U238 nu-fission 6.00e-07 4.01e-08 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 21 6.25e-01 2.00e+07 U235 fission 2.89e-02 2.07e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 21 6.25e-01 2.00e+07 U235 nu-fission 7.07e-02 5.06e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 21 6.25e-01 2.00e+07 U238 fission 1.41e-02 5.76e-04 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 21 6.25e-01 2.00e+07 U238 nu-fission 3.95e-02 1.90e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 27 0.00e+00 6.25e-01 U235 fission 1.51e-01 1.17e-02 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 27 0.00e+00 6.25e-01 U235 nu-fission 3.69e-01 2.86e-02 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 27 0.00e+00 6.25e-01 U238 fission 2.07e-07 1.47e-08 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 27 0.00e+00 6.25e-01 U238 nu-fission 5.17e-07 3.66e-08 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 27 6.25e-01 2.00e+07 U235 fission 2.57e-02 2.43e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 27 6.25e-01 2.00e+07 U235 nu-fission 6.30e-02 5.92e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 27 6.25e-01 2.00e+07 U238 fission 1.47e-02 1.41e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 27 6.25e-01 2.00e+07 U238 nu-fission 4.12e-02 4.02e-03 cell energy low [eV] energy high [eV] nuclide score mean std. dev.
+0 21 0.00e+00 6.25e-01 U235 fission 1.75e-01 1.20e-02
+1 21 0.00e+00 6.25e-01 U235 nu-fission 4.26e-01 2.92e-02
+2 21 0.00e+00 6.25e-01 U238 fission 2.41e-07 1.61e-08
+3 21 0.00e+00 6.25e-01 U238 nu-fission 6.00e-07 4.01e-08
+4 21 6.25e-01 2.00e+07 U235 fission 2.89e-02 2.07e-03
+5 21 6.25e-01 2.00e+07 U235 nu-fission 7.07e-02 5.06e-03
+6 21 6.25e-01 2.00e+07 U238 fission 1.41e-02 5.76e-04
+7 21 6.25e-01 2.00e+07 U238 nu-fission 3.95e-02 1.90e-03
+8 27 0.00e+00 6.25e-01 U235 fission 1.51e-01 1.17e-02
+9 27 0.00e+00 6.25e-01 U235 nu-fission 3.69e-01 2.86e-02
+10 27 0.00e+00 6.25e-01 U238 fission 2.07e-07 1.47e-08
+11 27 0.00e+00 6.25e-01 U238 nu-fission 5.17e-07 3.66e-08
+12 27 6.25e-01 2.00e+07 U235 fission 2.57e-02 2.43e-03
+13 27 6.25e-01 2.00e+07 U235 nu-fission 6.30e-02 5.92e-03
+14 27 6.25e-01 2.00e+07 U238 fission 1.47e-02 1.41e-03
+15 27 6.25e-01 2.00e+07 U238 nu-fission 4.12e-02 4.02e-03
sum(distribcell) energy low [eV] energy high [eV] nuclide score mean std. dev.
0 (0, 100, 2000, 30000) 0.00e+00 6.25e-01 U235 fission 0.00e+00 0.00e+00
1 (0, 100, 2000, 30000) 0.00e+00 6.25e-01 U235 nu-fission 0.00e+00 0.00e+00
2 (0, 100, 2000, 30000) 0.00e+00 6.25e-01 U238 fission 0.00e+00 0.00e+00
3 (0, 100, 2000, 30000) 0.00e+00 6.25e-01 U238 nu-fission 0.00e+00 0.00e+00
-4 (0, 100, 2000, 30000) 6.25e-01 2.00e+07 U235 fission 0.00e+00 0.00e+00
-5 (0, 100, 2000, 30000) 6.25e-01 2.00e+07 U235 nu-fission 0.00e+00 0.00e+00
-6 (0, 100, 2000, 30000) 6.25e-01 2.00e+07 U238 fission 0.00e+00 0.00e+00
-7 (0, 100, 2000, 30000) 6.25e-01 2.00e+07 U238 nu-fission 0.00e+00 0.00e+00
+4 (0, 100, 2000, 30000) 6.25e-01 2.00e+07 U235 fission 9.53e-07 9.53e-07
+5 (0, 100, 2000, 30000) 6.25e-01 2.00e+07 U235 nu-fission 2.37e-06 2.37e-06
+6 (0, 100, 2000, 30000) 6.25e-01 2.00e+07 U238 fission 1.25e-08 1.25e-08
+7 (0, 100, 2000, 30000) 6.25e-01 2.00e+07 U238 nu-fission 3.15e-08 3.15e-08
8 (500, 5000, 50000) 0.00e+00 6.25e-01 U235 fission 0.00e+00 0.00e+00
9 (500, 5000, 50000) 0.00e+00 6.25e-01 U235 nu-fission 0.00e+00 0.00e+00
10 (500, 5000, 50000) 0.00e+00 6.25e-01 U238 fission 0.00e+00 0.00e+00
@@ -49,19 +49,19 @@
14 (500, 5000, 50000) 6.25e-01 2.00e+07 U238 fission 0.00e+00 0.00e+00
15 (500, 5000, 50000) 6.25e-01 2.00e+07 U238 nu-fission 0.00e+00 0.00e+00
sum(mesh) energy low [eV] energy high [eV] nuclide score mean std. dev.
-0 ((1, 1), (1, 2)) 0.00e+00 6.25e-01 U235 fission 2.75e-02 4.32e-03
-1 ((1, 1), (1, 2)) 0.00e+00 6.25e-01 U235 nu-fission 6.71e-02 1.05e-02
-2 ((1, 1), (1, 2)) 0.00e+00 6.25e-01 U238 fission 3.78e-08 5.83e-09
-3 ((1, 1), (1, 2)) 0.00e+00 6.25e-01 U238 nu-fission 9.42e-08 1.45e-08
-4 ((1, 1), (1, 2)) 6.25e-01 2.00e+07 U235 fission 3.96e-03 7.84e-04
-5 ((1, 1), (1, 2)) 6.25e-01 2.00e+07 U235 nu-fission 9.71e-03 1.91e-03
-6 ((1, 1), (1, 2)) 6.25e-01 2.00e+07 U238 fission 3.92e-03 8.53e-04
-7 ((1, 1), (1, 2)) 6.25e-01 2.00e+07 U238 nu-fission 1.08e-02 2.25e-03
-8 ((2, 1), (2, 2)) 0.00e+00 6.25e-01 U235 fission 5.42e-02 2.50e-02
-9 ((2, 1), (2, 2)) 0.00e+00 6.25e-01 U235 nu-fission 1.32e-01 6.10e-02
-10 ((2, 1), (2, 2)) 0.00e+00 6.25e-01 U238 fission 7.47e-08 3.42e-08
-11 ((2, 1), (2, 2)) 0.00e+00 6.25e-01 U238 nu-fission 1.86e-07 8.53e-08
-12 ((2, 1), (2, 2)) 6.25e-01 2.00e+07 U235 fission 6.58e-03 2.03e-03
-13 ((2, 1), (2, 2)) 6.25e-01 2.00e+07 U235 nu-fission 1.61e-02 4.95e-03
-14 ((2, 1), (2, 2)) 6.25e-01 2.00e+07 U238 fission 3.74e-03 1.12e-03
-15 ((2, 1), (2, 2)) 6.25e-01 2.00e+07 U238 nu-fission 1.05e-02 3.20e-03
+0 ((1, 1), (1, 2)) 0.00e+00 6.25e-01 U235 fission 6.73e-03 3.04e-03
+1 ((1, 1), (1, 2)) 0.00e+00 6.25e-01 U235 nu-fission 1.64e-02 7.40e-03
+2 ((1, 1), (1, 2)) 0.00e+00 6.25e-01 U238 fission 8.80e-09 3.84e-09
+3 ((1, 1), (1, 2)) 0.00e+00 6.25e-01 U238 nu-fission 2.19e-08 9.56e-09
+4 ((1, 1), (1, 2)) 6.25e-01 2.00e+07 U235 fission 9.89e-04 3.53e-04
+5 ((1, 1), (1, 2)) 6.25e-01 2.00e+07 U235 nu-fission 2.42e-03 8.60e-04
+6 ((1, 1), (1, 2)) 6.25e-01 2.00e+07 U238 fission 5.01e-04 2.13e-04
+7 ((1, 1), (1, 2)) 6.25e-01 2.00e+07 U238 nu-fission 1.36e-03 5.86e-04
+8 ((2, 1), (2, 2)) 0.00e+00 6.25e-01 U235 fission 1.63e-02 4.21e-03
+9 ((2, 1), (2, 2)) 0.00e+00 6.25e-01 U235 nu-fission 3.98e-02 1.02e-02
+10 ((2, 1), (2, 2)) 0.00e+00 6.25e-01 U238 fission 2.28e-08 5.90e-09
+11 ((2, 1), (2, 2)) 0.00e+00 6.25e-01 U238 nu-fission 5.67e-08 1.47e-08
+12 ((2, 1), (2, 2)) 6.25e-01 2.00e+07 U235 fission 1.79e-03 4.31e-04
+13 ((2, 1), (2, 2)) 6.25e-01 2.00e+07 U235 nu-fission 4.37e-03 1.05e-03
+14 ((2, 1), (2, 2)) 6.25e-01 2.00e+07 U238 fission 7.51e-04 2.51e-04
+15 ((2, 1), (2, 2)) 6.25e-01 2.00e+07 U238 nu-fission 2.02e-03 6.71e-04
diff --git a/tests/regression_tests/torus/results_true.dat b/tests/regression_tests/torus/results_true.dat
--- a/tests/regression_tests/torus/results_true.dat
+++ b/tests/regression_tests/torus/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-7.628424E-01 2.557300E-02
+7.667201E-01 1.136882E-02
diff --git a/tests/regression_tests/trace/results_true.dat b/tests/regression_tests/trace/results_true.dat
--- a/tests/regression_tests/trace/results_true.dat
+++ b/tests/regression_tests/trace/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-2.987050E-01 1.827430E-03
+3.070134E-01 3.900396E-03
diff --git a/tests/regression_tests/track_output/results_true.dat b/tests/regression_tests/track_output/results_true.dat
--- a/tests/regression_tests/track_output/results_true.dat
+++ b/tests/regression_tests/track_output/results_true.dat
@@ -143,124 +143,76 @@ ParticleType.NEUTRON [((-9.469716e-01, -2.580266e-01, 1.414357e-01), (1.438873e-
((-3.920090e+00, -9.211794e-01, 2.908406e+00), (9.094673e-01, -3.659267e-01, -1.974002e-01), 9.547085e+00, 1.260840e-07, 1.000000e+00, 23, 2387, 1)
((-3.729948e+00, -9.976834e-01, 2.867135e+00), (-2.916959e-01, -6.494657e-01, -7.022164e-01), 8.590591e+00, 1.750036e-07, 1.000000e+00, 23, 2387, 1)
((-3.744933e+00, -1.031047e+00, 2.831062e+00), (-2.916959e-01, -6.494657e-01, -7.022164e-01), 8.590591e+00, 1.876753e-07, 0.000000e+00, 23, 2387, 1)]
-ParticleType.NEUTRON [((6.474155e+00, -5.192870e+00, 5.413003e+00), (-3.042035e-02, -9.914979e-01, 1.265170e-01), 2.052226e+06, 4.450859e-05, 1.000000e+00, 21, 2367, 2)
- ((6.467293e+00, -5.416535e+00, 5.441544e+00), (-3.042035e-02, -9.914979e-01, 1.265170e-01), 2.052226e+06, 4.450870e-05, 1.000000e+00, 22, 2367, 3)
- ((6.464574e+00, -5.505149e+00, 5.452851e+00), (-3.042035e-02, -9.914979e-01, 1.265170e-01), 2.052226e+06, 4.450874e-05, 1.000000e+00, 23, 2367, 1)
- ((6.461877e+00, -5.593034e+00, 5.464065e+00), (6.364108e-01, -7.713322e-01, 5.284745e-03), 1.141417e+06, 4.450879e-05, 1.000000e+00, 23, 2367, 1)
- ((6.570892e+00, -5.725160e+00, 5.464970e+00), (6.364108e-01, -7.713322e-01, 5.284745e-03), 1.141417e+06, 4.450891e-05, 1.000000e+00, 32, 7, 1)
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- ((7.101210e+00, -6.367908e+00, 5.469374e+00), (6.364108e-01, -7.713322e-01, 5.284745e-03), 1.141417e+06, 4.450947e-05, 1.000000e+00, 32, 7, 1)
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+ ((-3.697811e+00, -7.360920e+00, -1.449560e+00), (-4.275550e-01, 8.441443e-01, 3.234457e-01), 1.848049e-02, 5.193299e-05, 1.000000e+00, 23, 2347, 1)
+ ((-3.703436e+00, -7.349814e+00, -1.445305e+00), (-7.832167e-01, 5.713670e-01, 2.451762e-01), 1.861705e-02, 5.200296e-05, 1.000000e+00, 23, 2347, 1)
+ ((-3.823243e+00, -7.262414e+00, -1.407801e+00), (-9.917106e-01, 5.069164e-02, 1.180695e-01), 4.703334e-02, 5.281350e-05, 1.000000e+00, 23, 2347, 1)
+ ((-4.089400e+00, -7.248809e+00, -1.376113e+00), (-9.917106e-01, 5.069164e-02, 1.180695e-01), 4.703334e-02, 5.370820e-05, 1.000000e+00, 23, 2346, 1)
+ ((-4.131081e+00, -7.246679e+00, -1.371151e+00), (9.108632e-01, -4.018526e-01, 9.403556e-02), 8.057393e-02, 5.384831e-05, 1.000000e+00, 23, 2346, 1)
+ ((-4.089400e+00, -7.265067e+00, -1.366848e+00), (9.108632e-01, -4.018526e-01, 9.403556e-02), 8.057393e-02, 5.396486e-05, 1.000000e+00, 23, 2347, 1)
+ ((-3.872134e+00, -7.360920e+00, -1.344418e+00), (9.108632e-01, -4.018526e-01, 9.403556e-02), 8.057393e-02, 5.457239e-05, 1.000000e+00, 11, 1750, 1)
+ ((-3.673062e+00, -7.448746e+00, -1.323866e+00), (2.976906e-01, 8.174443e-01, -4.931178e-01), 5.538060e-02, 5.512905e-05, 1.000000e+00, 11, 1750, 1)
+ ((-3.658580e+00, -7.408978e+00, -1.347855e+00), (-5.409120e-01, 8.345378e-01, -1.046943e-01), 8.122576e-02, 5.527851e-05, 1.000000e+00, 11, 1750, 1)
+ ((-3.682981e+00, -7.371331e+00, -1.352578e+00), (-5.409120e-01, 8.345378e-01, -1.046943e-01), 8.122576e-02, 5.539294e-05, 0.000000e+00, 11, 1750, 1)]
diff --git a/tests/regression_tests/translation/results_true.dat b/tests/regression_tests/translation/results_true.dat
--- a/tests/regression_tests/translation/results_true.dat
+++ b/tests/regression_tests/translation/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-4.003951E-01 7.739871E-03
+4.087580E-01 4.466279E-03
diff --git a/tests/regression_tests/trigger_batch_interval/results_true.dat b/tests/regression_tests/trigger_batch_interval/results_true.dat
--- a/tests/regression_tests/trigger_batch_interval/results_true.dat
+++ b/tests/regression_tests/trigger_batch_interval/results_true.dat
@@ -1,28 +1,28 @@
k-combined:
-9.764624E-01 8.747085E-03
+9.767929E-01 5.327552E-03
tally 1:
-1.408588E+01
-1.985937E+01
-3.194837E+00
-1.021391E+00
-3.096170E+00
-9.592197E-01
-1.089104E+01
-1.187349E+01
-1.408588E+01
-1.985937E+01
-3.194837E+00
-1.021391E+00
-3.096170E+00
-9.592197E-01
-1.089104E+01
-1.187349E+01
+1.405471E+01
+1.976444E+01
+3.186139E+00
+1.015515E+00
+3.088643E+00
+9.542994E-01
+1.086857E+01
+1.182011E+01
+1.405471E+01
+1.976444E+01
+3.186139E+00
+1.015515E+00
+3.088643E+00
+9.542994E-01
+1.086857E+01
+1.182011E+01
tally 2:
-1.408588E+01
-1.985937E+01
-3.194837E+00
-1.021391E+00
-3.096170E+00
-9.592197E-01
-1.089104E+01
-1.187349E+01
+1.405471E+01
+1.976444E+01
+3.186139E+00
+1.015515E+00
+3.088643E+00
+9.542994E-01
+1.086857E+01
+1.182011E+01
diff --git a/tests/regression_tests/trigger_no_batch_interval/results_true.dat b/tests/regression_tests/trigger_no_batch_interval/results_true.dat
--- a/tests/regression_tests/trigger_no_batch_interval/results_true.dat
+++ b/tests/regression_tests/trigger_no_batch_interval/results_true.dat
@@ -1,28 +1,28 @@
k-combined:
-9.764624E-01 8.747085E-03
+9.767929E-01 5.327552E-03
tally 1:
-1.408588E+01
-1.985937E+01
-3.194837E+00
-1.021391E+00
-3.096170E+00
-9.592197E-01
-1.089104E+01
-1.187349E+01
-1.408588E+01
-1.985937E+01
-3.194837E+00
-1.021391E+00
-3.096170E+00
-9.592197E-01
-1.089104E+01
-1.187349E+01
+1.405471E+01
+1.976444E+01
+3.186139E+00
+1.015515E+00
+3.088643E+00
+9.542994E-01
+1.086857E+01
+1.182011E+01
+1.405471E+01
+1.976444E+01
+3.186139E+00
+1.015515E+00
+3.088643E+00
+9.542994E-01
+1.086857E+01
+1.182011E+01
tally 2:
-1.408588E+01
-1.985937E+01
-3.194837E+00
-1.021391E+00
-3.096170E+00
-9.592197E-01
-1.089104E+01
-1.187349E+01
+1.405471E+01
+1.976444E+01
+3.186139E+00
+1.015515E+00
+3.088643E+00
+9.542994E-01
+1.086857E+01
+1.182011E+01
diff --git a/tests/regression_tests/trigger_no_status/results_true.dat b/tests/regression_tests/trigger_no_status/results_true.dat
--- a/tests/regression_tests/trigger_no_status/results_true.dat
+++ b/tests/regression_tests/trigger_no_status/results_true.dat
@@ -1,28 +1,28 @@
k-combined:
-9.688702E-01 2.263104E-02
+9.682315E-01 3.302924E-03
tally 1:
-7.069810E+00
-1.000691E+01
-1.597648E+00
-5.109653E-01
-1.547262E+00
-4.792189E-01
-5.472161E+00
-5.995488E+00
-7.069810E+00
-1.000691E+01
-1.597648E+00
-5.109653E-01
-1.547262E+00
-4.792189E-01
-5.472161E+00
-5.995488E+00
+7.046510E+00
+9.932168E+00
+1.591675E+00
+5.067777E-01
+1.541572E+00
+4.753743E-01
+5.454835E+00
+5.951990E+00
+7.046510E+00
+9.932168E+00
+1.591675E+00
+5.067777E-01
+1.541572E+00
+4.753743E-01
+5.454835E+00
+5.951990E+00
tally 2:
-7.069810E+00
-1.000691E+01
-1.597648E+00
-5.109653E-01
-1.547262E+00
-4.792189E-01
-5.472161E+00
-5.995488E+00
+7.046510E+00
+9.932168E+00
+1.591675E+00
+5.067777E-01
+1.541572E+00
+4.753743E-01
+5.454835E+00
+5.951990E+00
diff --git a/tests/regression_tests/trigger_statepoint_restart/results_true.dat b/tests/regression_tests/trigger_statepoint_restart/results_true.dat
--- a/tests/regression_tests/trigger_statepoint_restart/results_true.dat
+++ b/tests/regression_tests/trigger_statepoint_restart/results_true.dat
@@ -1,5 +1,5 @@
k-combined:
-2.963805E-01 2.986351E-03
+3.014717E-01 2.864764E-03
tally 1:
-8.017826E+01
-6.436316E+02
+8.946107E+01
+7.281263E+02
diff --git a/tests/regression_tests/trigger_tallies/results_true.dat b/tests/regression_tests/trigger_tallies/results_true.dat
--- a/tests/regression_tests/trigger_tallies/results_true.dat
+++ b/tests/regression_tests/trigger_tallies/results_true.dat
@@ -1,28 +1,28 @@
k-combined:
-9.764624E-01 8.747085E-03
+9.767929E-01 5.327552E-03
tally 1:
-1.408588E+01
-1.985937E+01
-3.194837E+00
-1.021391E+00
-3.096170E+00
-9.592197E-01
-1.089104E+01
-1.187349E+01
-1.408588E+01
-1.985937E+01
-3.194837E+00
-1.021391E+00
-3.096170E+00
-9.592197E-01
-1.089104E+01
-1.187349E+01
+1.405471E+01
+1.976444E+01
+3.186139E+00
+1.015515E+00
+3.088643E+00
+9.542994E-01
+1.086857E+01
+1.182011E+01
+1.405471E+01
+1.976444E+01
+3.186139E+00
+1.015515E+00
+3.088643E+00
+9.542994E-01
+1.086857E+01
+1.182011E+01
tally 2:
-1.408588E+01
-1.985937E+01
-3.194837E+00
-1.021391E+00
-3.096170E+00
-9.592197E-01
-1.089104E+01
-1.187349E+01
+1.405471E+01
+1.976444E+01
+3.186139E+00
+1.015515E+00
+3.088643E+00
+9.542994E-01
+1.086857E+01
+1.182011E+01
diff --git a/tests/regression_tests/triso/results_true.dat b/tests/regression_tests/triso/results_true.dat
--- a/tests/regression_tests/triso/results_true.dat
+++ b/tests/regression_tests/triso/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-1.406055E+00 9.581396E-02
+1.716873E+00 5.266107E-02
diff --git a/tests/regression_tests/uniform_fs/results_true.dat b/tests/regression_tests/uniform_fs/results_true.dat
--- a/tests/regression_tests/uniform_fs/results_true.dat
+++ b/tests/regression_tests/uniform_fs/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-3.643255E-01 1.041799E-02
+3.685309E-01 1.861720E-03
diff --git a/tests/regression_tests/universe/results_true.dat b/tests/regression_tests/universe/results_true.dat
--- a/tests/regression_tests/universe/results_true.dat
+++ b/tests/regression_tests/universe/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-2.987050E-01 1.827430E-03
+3.070134E-01 3.900396E-03
diff --git a/tests/regression_tests/unstructured_mesh/results_true.dat b/tests/regression_tests/unstructured_mesh/results_true.dat
--- a/tests/regression_tests/unstructured_mesh/results_true.dat
+++ b/tests/regression_tests/unstructured_mesh/results_true.dat
@@ -1,26002 +1,4002 @@
tally 1:
-4.873713E-02
-2.881006E-04
-7.388548E-02
-6.421281E-04
-8.309847E-02
-8.079791E-04
-8.802030E-02
-8.590396E-04
-6.935977E-02
-5.711723E-04
-7.203243E-02
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-8.146742E-02
-8.422730E-04
-7.112287E-02
-5.331461E-04
-6.944025E-02
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-4.605581E-02
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-1.761591E-03
-1.244445E-01
-1.714565E-03
-1.324446E-01
-2.041161E-03
-1.110879E-01
-1.399393E-03
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diff --git a/tests/regression_tests/white_plane/results_true.dat b/tests/regression_tests/white_plane/results_true.dat
--- a/tests/regression_tests/white_plane/results_true.dat
+++ b/tests/regression_tests/white_plane/results_true.dat
@@ -1,2 +1,2 @@
k-combined:
-2.279902E+00 3.262078E-03
+2.279719E+00 5.380792E-03
diff --git a/tests/testing_harness.py b/tests/testing_harness.py
--- a/tests/testing_harness.py
+++ b/tests/testing_harness.py
@@ -276,6 +276,13 @@ def _get_results(self):
return outstr
+ def _cleanup(self):
+ """Delete particle restart files."""
+ super()._cleanup()
+ output = glob.glob('particle*.h5')
+ for f in output:
+ os.remove(f)
+
class PyAPITestHarness(TestHarness):
def __init__(self, statepoint_name, model=None, inputs_true=None):
diff --git a/tests/unit_tests/test_deplete_resultslist.py b/tests/unit_tests/test_deplete_resultslist.py
--- a/tests/unit_tests/test_deplete_resultslist.py
+++ b/tests/unit_tests/test_deplete_resultslist.py
@@ -22,7 +22,7 @@ def test_get_atoms(res):
t_ref = np.array([0.0, 1296000.0, 2592000.0, 3888000.0])
n_ref = np.array(
- [6.67473282e+08, 3.72442707e+14, 3.61129692e+14, 4.01920099e+14])
+ [6.67473282e+08, 3.88942731e+14, 3.73091215e+14, 3.26987387e+14])
np.testing.assert_allclose(t, t_ref)
np.testing.assert_allclose(n, n_ref)
@@ -48,8 +48,8 @@ def test_get_reaction_rate(res):
t, r = res.get_reaction_rate("1", "Xe135", "(n,gamma)")
t_ref = [0.0, 1296000.0, 2592000.0, 3888000.0]
- n_ref = [6.67473282e+08, 3.72442707e+14, 3.61129692e+14, 4.01920099e+14]
- xs_ref = [5.10301159e-05, 3.19379638e-05, 4.50543806e-05, 4.71004301e-05]
+ n_ref = [6.67473282e+08, 3.88942731e+14, 3.73091215e+14, 3.26987387e+14]
+ xs_ref = [2.53336104e-05, 4.21747011e-05, 3.48616127e-05, 3.61775563e-05]
np.testing.assert_allclose(t, t_ref)
np.testing.assert_allclose(r, np.array(n_ref) * xs_ref)
@@ -61,8 +61,8 @@ def test_get_keff(res):
t_min, k = res.get_keff(time_units='min')
t_ref = [0.0, 1296000.0, 2592000.0, 3888000.0]
- k_ref = [1.21409662, 1.16518654, 1.25357797, 1.22611968]
- u_ref = [0.0278795195, 0.0233141097, 0.0167899218, 0.0246734716]
+ k_ref = [1.1596402556, 1.1914183335, 1.2292570871, 1.1797030302]
+ u_ref = [0.0270680649, 0.0219163444, 0.024268508 , 0.0221401194]
np.testing.assert_allclose(t, t_ref)
np.testing.assert_allclose(t_min * 60, t_ref)
| Last decimal place disagreements causing failed tests with numpy 1.22.0 or later
When testing from a clean copy of the `develop` branch of OpenMC (from the main fork) in debug mode, a few tests fail due to last decimal place or near it disagreements about values in a diff. The `-v` output from `test_lethargy_bin_width` shows one such example
```
test_lethargy_bin_width
def test_lethargy_bin_width():
f = openmc.EnergyFilter.from_group_structure('VITAMIN-J-175')
assert len(f.lethargy_bin_width) == 175
energy_bins = openmc.mgxs.GROUP_STRUCTURES['VITAMIN-J-175']
assert f.lethargy_bin_width[0] == math.log10(energy_bins[1]/energy_bins[0])
> assert f.lethargy_bin_width[-1] == math.log10(energy_bins[-1]/energy_bins[-2])
E assert 0.05429280308859366 == 0.05429280308859367
E + where 0.05429280308859367 = <built-in function log10>((19640000.0 / 17332000.0))
E + where <built-in function log10> = math.log10
unit_tests/test_filters.py:257: AssertionError
```
This test and a few others fail for me when I was using `python 3.10.5` and `numpy 1.23.0`. Did some digging with @pshriwise and we determined that with `python 3.8.3` and `numpy 1.21.0` these tests pass, but as soon as `numpy` is increased to or beyond `1.22.0`, the assertions fail.
I was wondering if the appropriate fix would be to allow `assert` to vary with a certain tolerance (say like `1e-15`) or if something else should be done with the environment to make sure they exactly agree.
| Perhaps replacing ```math.log10``` with ```numpy.log10``` for this test would also work
I'll try this locally and see if it passes
@shimwell Looks like that did the trick for `test_lethargy_bin_width`. Just out of curiosity I grep'd for more `math.` and these came up. Do you think it would be worth PRing to change all these to `numpy` if a similar `numpy` function exists? This assumes `numpy` is always better to use and has an equivalent function, so maybe there reasons to keep some of these as `math.` ?
At the least, I can PR to change this one test.
```
lgross@ulam:~/openmc (lethargy_test_fix) $ grep -rI "= math."
tests/unit_tests/test_surface.py: psi = math.degrees(math.atan2(1, 2))
tests/unit_tests/test_surface.py: phi = math.degrees(math.atan2(1, math.sqrt(5)))
tests/unit_tests/test_surface.py: phi = math.degrees(math.atan2(1, math.sqrt(2)))
tests/regression_tests/deplete_with_transport/example_geometry.py: v_fuel = math.pi * r_fuel**2
tests/regression_tests/deplete_with_transport/example_geometry.py: v_gap = math.pi * r_gap**2 - v_fuel
tests/regression_tests/deplete_with_transport/example_geometry.py: v_clad = math.pi * r_clad**2 - v_fuel - v_gap
tests/regression_tests/deplete_with_transport/example_geometry.py: r_rings[i] = math.sqrt(1.0/(math.pi) * v_ring * (i+1))
openmc/deplete/chain.py: decay_constant = math.log(2) / nuc.half_life
openmc/deplete/chain.py: level = math.inf
openmc/surface.py: cx, sx = math.cos(phi), math.sin(phi)
openmc/surface.py: cy, sy = math.cos(theta), math.sin(theta)
openmc/surface.py: cz, sz = math.cos(psi), math.sin(psi)
vendor/xtensor/include/xtensor/xmath.hpp: auto d = math::abs(internal_type(a) - internal_type(b));
vendor/xtensor/include/xtensor/xcomplex.hpp: using functor = math::conj_impl_fun;
vendor/xtensor/include/xtensor/xcomplex.hpp: using functor = math::arg_fun;
vendor/xtensor/include/xtensor/xcomplex.hpp: using functor = math::norm_fun;
vendor/xtensor/include/xtensor/xio.hpp: m_max = math::abs(val);
vendor/xtensor/include/xtensor/xio.hpp: m_max = math::abs(val);
```
EDIT: looks like some of these actually shouldn't be changed. Like the vendor ones for sure shouldn't. But the tests potentially could
Switching lethargy test to numpy worked because the lethargy function uses numpy. Not sure about the others, I just happened to have written the lethargy function.
> maybe there reasons to keep some of these as `math`
@lewisgross1296 If you are evaluating the function on a scalar value, it is generally preferable to use `math.func(...)` instead of `numpy.func(...)` because the latter has to do extra work to check the type of its argument (to differentiate between an array and a scalar), whereas `math.func(...)` always assumes its argument scalar and returns a scalar.
Gotcha, to clarify, would this be a case where `math.log10` is better?
```
a = numpy.log10(array[-1])
```
Or is `numpy` better since it is doing an operation involving an array? In my head, `array[-1]` is a scalar, but maybe I'm misunderstanding.
If `array[-1]` is a scalar, I would pass it to `math.log10`
Closed by #2193
There actually were other tests that were failing when using numpy 1.22.0 or later but passing with 1.21.0 or earlier. This was just a good example since there was only one comparison in the diff. I can always revert my numpy version, but I'd think we eventually will upgrade?
Ah, sorry. Yes, numpy changed something in 1.22 that results in numbers being displayed slightly differently. The easiest thing would be for us to just update the failing tests and force anyone who wants to test locally to update to 1.22+
I think I have been seeing this same issue with tests on a server and just confirmed that I am indeed using numpy 1.23.2. Is the current recommendation to just accept theses floating point errors in the tests or to bump numpy down to 1.21 for reliable usage? (this may be a vague question without additional context)
For the purpose of having my local tests pass, I just downgraded to 1.21.0. I do think we want to eventually upgrade our numpy version though.
I'm guessing your GitHub Actions tests would still pass when you push to a PR. I think since that is the requirement for merging, it is up to you whether to downgrade wherever your tests are running.
I am not using GH actions, but I am trying to get the newest version up and running on a cluster for people and haven't been able to get the tests to pass. I think this is the reason. I will downgrade and see if that helps. | 2023-02-10T20:46:35Z | [] | [] |
openmc-dev/openmc | 2,388 | openmc-dev__openmc-2388 | [
"2387"
] | fa4aa4ad21172815a8b77fecfb75f1f6e453abaa | diff --git a/openmc/universe.py b/openmc/universe.py
--- a/openmc/universe.py
+++ b/openmc/universe.py
@@ -91,6 +91,23 @@ def add_volume_information(self, volume_calc):
else:
raise ValueError('No volume information found for this universe.')
+ def get_all_universes(self):
+ """Return all universes that are contained within this one.
+
+ Returns
+ -------
+ universes : collections.OrderedDict
+ Dictionary whose keys are universe IDs and values are
+ :class:`Universe` instances
+
+ """
+ # Append all Universes within each Cell to the dictionary
+ universes = OrderedDict()
+ for cell in self.get_all_cells().values():
+ universes.update(cell.get_all_universes())
+
+ return universes
+
@abstractmethod
def create_xml_subelement(self, xml_element, memo=None):
"""Add the universe xml representation to an incoming xml element
@@ -538,23 +555,6 @@ def get_all_materials(self, memo=None):
return materials
- def get_all_universes(self):
- """Return all universes that are contained within this one.
-
- Returns
- -------
- universes : collections.OrderedDict
- Dictionary whose keys are universe IDs and values are
- :class:`Universe` instances
-
- """
- # Append all Universes within each Cell to the dictionary
- universes = OrderedDict()
- for cell in self.get_all_cells().values():
- universes.update(cell.get_all_universes())
-
- return universes
-
def create_xml_subelement(self, xml_element, memo=None):
# Iterate over all Cells
for cell in self._cells.values():
| diff --git a/tests/unit_tests/test_universe.py b/tests/unit_tests/test_universe.py
--- a/tests/unit_tests/test_universe.py
+++ b/tests/unit_tests/test_universe.py
@@ -93,10 +93,12 @@ def test_get_all_universes():
u2 = openmc.Universe(cells=[c2])
c3 = openmc.Cell(fill=u1)
c4 = openmc.Cell(fill=u2)
- u3 = openmc.Universe(cells=[c3, c4])
+ u3 = openmc.DAGMCUniverse(filename="")
+ c5 = openmc.Cell(fill=u3)
+ u4 = openmc.Universe(cells=[c3, c4, c5])
- univs = set(u3.get_all_universes().values())
- assert not (univs ^ {u1, u2})
+ univs = set(u4.get_all_universes().values())
+ assert not (univs ^ {u1, u2, u3})
def test_clone():
| Feature request: DAGMCUniverse to support get_all_universes
When we call ```.get_all_universes()``` on a ```Geometry``` that is a ```Universe``` that is filled with a DAGMC cell we get this error. ```Universe``` has the attribute but as the code cycles through the individual parts it calls ```.get_all_universes()``` on each part and fails when it reaches the DAGMCUniverse
```python
>>>AttributeError: 'DAGMCUniverse' object has no attribute 'get_all_universes'
```
code to reproduce
```python
import openmc
bound_dag_univ = openmc.DAGMCUniverse(filename='dagmc.h5m').bounded_universe()
my_geometry = openmc.Geometry(root=bound_dag_univ)
my_geometry.get_all_universes()
```
Could we add the same ```get_all_universes()``` method that is in ```Universe``` to the ```DAGMCUniverse```?
Alternatively could we move ```get_all_universes()``` from ```UniverseBase``` to ```Universe``` so that the ```DAGMCUniverse``` inherits it?
| Happy to put in a PR to move the ```get_all_universes``` method to the ```UniverseBase``` class if others think that is the way to go?
Sounds reasonable to me, but @pshriwise is the DAGMC god so I defer to him on this
Totally reasonable @shimwell. I ran into this as well and have a change to this effect in a local branch. A PR that addresses this specifically would be most welcome. | 2023-02-16T16:25:07Z | [] | [] |
openmc-dev/openmc | 2,390 | openmc-dev__openmc-2390 | [
"2389"
] | 6e2a9add5ef5019147e20422c380900c9b4a21a4 | diff --git a/openmc/executor.py b/openmc/executor.py
--- a/openmc/executor.py
+++ b/openmc/executor.py
@@ -1,5 +1,6 @@
from collections.abc import Iterable
from numbers import Integral
+import os
import subprocess
import openmc
@@ -23,7 +24,7 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None,
Number of particles to simulate per generation.
plot : bool, optional
Run in plotting mode. Defaults to False.
- restart_file : str, optional
+ restart_file : str or PathLike
Path to restart file to use
threads : int, optional
Number of OpenMP threads. If OpenMC is compiled with OpenMP threading
@@ -42,7 +43,7 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None,
mpi_args : list of str, optional
MPI execute command and any additional MPI arguments to pass,
e.g., ['mpiexec', '-n', '8'].
- path_input : str or Pathlike
+ path_input : str or PathLike
Path to a single XML file or a directory containing XML files for the
OpenMC executable to read.
@@ -73,8 +74,8 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None,
if event_based:
args.append('-e')
- if isinstance(restart_file, str):
- args += ['-r', restart_file]
+ if isinstance(restart_file, (str, os.PathLike)):
+ args += ['-r', str(restart_file)]
if tracks:
args.append('-t')
@@ -230,7 +231,7 @@ def calculate_volumes(threads=None, output=True, cwd='.',
cwd : str, optional
Path to working directory to run in. Defaults to the current working
directory.
- path_input : str or Pathlike
+ path_input : str or PathLike
Path to a single XML file or a directory containing XML files for the
OpenMC executable to read.
@@ -270,7 +271,7 @@ def run(particles=None, threads=None, geometry_debug=False,
:envvar:`OMP_NUM_THREADS` environment variable).
geometry_debug : bool, optional
Turn on geometry debugging during simulation. Defaults to False.
- restart_file : str, optional
+ restart_file : str or PathLike
Path to restart file to use
tracks : bool, optional
Enables the writing of particles tracks. The number of particle tracks
@@ -291,7 +292,7 @@ def run(particles=None, threads=None, geometry_debug=False,
.. versionadded:: 0.12
- path_input : str or Pathlike
+ path_input : str or PathLike
Path to a single XML file or a directory containing XML files for the
OpenMC executable to read.
diff --git a/openmc/filter.py b/openmc/filter.py
--- a/openmc/filter.py
+++ b/openmc/filter.py
@@ -258,6 +258,8 @@ def from_xml_element(cls, elem, **kwargs):
"""
filter_type = elem.get('type')
+ if filter_type is None:
+ filter_type = elem.find('type').text
# If the filter type matches this class's short_name, then
# there is no overridden from_xml_element method
diff --git a/openmc/geometry.py b/openmc/geometry.py
--- a/openmc/geometry.py
+++ b/openmc/geometry.py
@@ -278,7 +278,7 @@ def from_xml(
"""
- # Using str and os.Pathlike here to avoid error when using just the imported PathLike
+ # Using str and os.PathLike here to avoid error when using just the imported PathLike
# TypeError: Subscripted generics cannot be used with class and instance checks
check_type('materials', materials, (str, os.PathLike, openmc.Materials))
diff --git a/openmc/model/model.py b/openmc/model/model.py
--- a/openmc/model/model.py
+++ b/openmc/model/model.py
@@ -248,7 +248,7 @@ def from_model_xml(cls, path='model.xml'):
Parameters
----------
- path : str or Pathlike
+ path : str or PathLike
Path to model.xml file
"""
tree = ET.parse(path)
@@ -473,7 +473,7 @@ def export_to_model_xml(self, path='model.xml', remove_surfs=False):
Parameters
----------
- path : str or Pathlike
+ path : str or PathLike
Location of the XML file to write (default is 'model.xml'). Can be a
directory or file path.
remove_surfs : bool
@@ -620,7 +620,7 @@ def run(self, particles=None, threads=None, geometry_debug=False,
value set by the :envvar:`OMP_NUM_THREADS` environment variable).
geometry_debug : bool, optional
Turn on geometry debugging during simulation. Defaults to False.
- restart_file : str, optional
+ restart_file : str or PathLike
Path to restart file to use
tracks : bool, optional
Enables the writing of particles tracks. The number of particle
| diff --git a/tests/regression_tests/statepoint_restart/test.py b/tests/regression_tests/statepoint_restart/test.py
--- a/tests/regression_tests/statepoint_restart/test.py
+++ b/tests/regression_tests/statepoint_restart/test.py
@@ -1,11 +1,11 @@
-import glob
-import os
+from pathlib import Path
import openmc
+import pytest
from tests.testing_harness import TestHarness
from tests.regression_tests import config
-
+from tests import cdtemp
class StatepointRestartTestHarness(TestHarness):
def __init__(self, final_sp, restart_sp):
@@ -42,7 +42,7 @@ def update_results(self):
def _run_openmc_restart(self):
# Get the name of the statepoint file.
- statepoint = glob.glob(os.path.join(os.getcwd(), self._restart_sp))
+ statepoint = list(Path.cwd().glob(self._restart_sp))
assert len(statepoint) == 1
statepoint = statepoint[0]
@@ -59,3 +59,26 @@ def test_statepoint_restart():
harness = StatepointRestartTestHarness('statepoint.10.h5',
'statepoint.07.h5')
harness.main()
+
+
+def test_batch_check(request):
+ xmls = list(request.path.parent.glob('*.xml'))
+
+ with cdtemp(xmls):
+ model = openmc.Model.from_xml()
+ model.settings.particles = 100
+ # run the model
+ sp_file = model.run()
+
+ # run a restart with the resulting statepoint
+ # and the settings unchanged
+ with pytest.raises(RuntimeError, match='is smaller than the number of batches'):
+ model.run(restart_file=sp_file)
+
+ # update the number of batches and run again
+ model.settings.batches = 15
+ model.settings.statepoint = {}
+ sp_file = model.run(restart_file=sp_file)
+
+ sp = openmc.StatePoint(sp_file)
+ assert sp.n_batches == 15
| Simulation restart isn't terminated correctly
As @eepeterson and I were discussing restart capabilities today, I noted that the restart of a problem without editing the number of batches in the `settings.xml` file results in an unbounded simulation. I believe this is caused by the following lines in `simulation.cpp`:
https://github.com/openmc-dev/openmc/blob/6e2a9add5ef5019147e20422c380900c9b4a21a4/src/simulation.cpp#L238-L246
When a restart occurs and the initial number of batches read from the statepoint file is equal to `settings::n_max_batches` set by the `settings.xml` file, the simulation will continue indefinitely.
This probably should be caught here:
https://github.com/openmc-dev/openmc/blob/6e2a9add5ef5019147e20422c380900c9b4a21a4/src/state_point.cpp#L406-L409
I think a couple of changes are in order:
- change the check in `simulation.cpp` from `==` to `>=`
- change the check in `state_point.cpp` from `>` to `>=` and update the error message appropriately
| 2023-02-16T19:53:44Z | [] | [] |
|
openmc-dev/openmc | 2,464 | openmc-dev__openmc-2464 | [
"2219"
] | 82ccbe07386adb134ccd497b703788686764f77e | diff --git a/openmc/plots.py b/openmc/plots.py
--- a/openmc/plots.py
+++ b/openmc/plots.py
@@ -1,15 +1,18 @@
from collections.abc import Iterable, Mapping
-from numbers import Real, Integral
+from numbers import Integral, Real
from pathlib import Path
+from typing import Optional
from xml.etree import ElementTree as ET
+import h5py
import numpy as np
import openmc
import openmc.checkvalue as cv
-from ._xml import clean_indentation, reorder_attributes, get_elem_tuple
-from .mixin import IDManagerMixin
+from openmc.checkvalue import PathLike
+from ._xml import clean_indentation, get_elem_tuple, reorder_attributes
+from .mixin import IDManagerMixin
_BASES = ['xy', 'xz', 'yz']
@@ -178,6 +181,78 @@ def _get_plot_image(plot, cwd):
return Image(str(png_file))
+def voxel_to_vtk(voxel_file: PathLike, output: PathLike = 'plot.vti'):
+ """Converts a voxel HDF5 file to a VTK file
+
+ .. versionadded:: 0.13.4
+
+ Parameters
+ ----------
+ voxel_file : path-like
+ Path of the input h5 to convert
+ output : path-like
+ Path of the output vti file produced
+
+ Returns
+ -------
+ Path
+ Path of the .vti file produced
+ """
+
+ # imported vtk only if used as vtk is an option dependency
+ import vtk
+
+ _min_version = (2, 0)
+
+ # Read data from voxel file
+ with h5py.File(voxel_file, "r") as fh:
+ # check version
+ version = tuple(fh.attrs["version"])
+ if version < _min_version:
+ old_version = ".".join(map(str, version))
+ min_version = ".".join(map(str, _min_version))
+ err_msg = (
+ f"This voxel file's version is {old_version}. This function only "
+ f" supports voxel files with version {min_version} or higher. "
+ "Please generate a new voxel file using a newer version of OpenMC."
+ )
+ raise ValueError(err_msg)
+
+ dimension = fh.attrs["num_voxels"]
+ width = fh.attrs["voxel_width"]
+ lower_left = fh.attrs["lower_left"]
+
+ nx, ny, nz = dimension
+
+ grid = vtk.vtkImageData()
+ grid.SetDimensions(nx + 1, ny + 1, nz + 1)
+ grid.SetOrigin(*lower_left)
+ grid.SetSpacing(*width)
+
+ # transpose data from OpenMC ordering (zyx) to VTK ordering (xyz)
+ # and flatten to 1-D array
+ h5data = fh["data"][...]
+
+ data = vtk.vtkIntArray()
+ data.SetName("id")
+ # set the array using the h5data array
+ data.SetArray(h5data, h5data.size, True)
+ # add data to image grid
+ grid.GetCellData().AddArray(data)
+
+ writer = vtk.vtkXMLImageDataWriter()
+ if vtk.vtkVersion.GetVTKMajorVersion() > 5:
+ writer.SetInputData(grid)
+ else:
+ writer.SetInput(grid)
+ if not output.endswith(".vti"):
+ output += ".vti"
+ writer.SetFileName(str(output))
+ writer.Write()
+
+ return output
+
+
class PlotBase(IDManagerMixin):
"""
Parameters
@@ -512,7 +587,7 @@ def origin(self, origin):
@type.setter
def type(self, plottype):
- cv.check_value('plot type', plottype, ['slice', 'voxel', 'projection'])
+ cv.check_value('plot type', plottype, ['slice', 'voxel'])
self._type = plottype
@basis.setter
@@ -831,6 +906,45 @@ def to_ipython_image(self, openmc_exec='openmc', cwd='.'):
# Return produced image
return _get_plot_image(self, cwd)
+ def to_vtk(self, output: Optional[PathLike] = None,
+ openmc_exec: str = 'openmc', cwd: str = '.'):
+ """Render plot as an voxel image
+
+ This method runs OpenMC in plotting mode to produce a .vti file.
+
+ .. versionadded:: 0.13.4
+
+ Parameters
+ ----------
+ output : path-like
+ Path of the output .vti file produced
+ openmc_exec : str
+ Path to OpenMC executable
+ cwd : str, optional
+ Path to working directory to run in
+
+ Returns
+ -------
+ Path
+ Path of the .vti file produced
+
+ """
+ if self.type != 'voxel':
+ raise ValueError('Generating a VTK file only works for voxel plots')
+
+ # Create plots.xml
+ Plots([self]).export_to_xml(cwd)
+
+ # Run OpenMC in geometry plotting mode and produces a h5 file
+ openmc.plot_geometry(False, openmc_exec, cwd)
+
+ stem = self.filename if self.filename is not None else f'plot_{self.id}'
+ h5_voxel_file = Path(cwd) / f'{stem}.h5'
+ if output is None:
+ output = h5_voxel_file.with_suffix('.vti')
+
+ return voxel_to_vtk(h5_voxel_file, output)
+
class ProjectionPlot(PlotBase):
"""Definition of a camera's view of OpenMC geometry
@@ -880,7 +994,7 @@ class ProjectionPlot(PlotBase):
wireframe_domains : iterable of either Material or Cells
If provided, the wireframe is only drawn around these.
If color_by is by material, it must be a list of materials, else cells.
- xs : dict
+ xs : dict
A mapping from cell/material IDs to floats. The floating point values
are macroscopic cross sections influencing the volume rendering opacity
of each geometric region. Zero corresponds to perfect transparency, and
| diff --git a/tests/unit_tests/test_plots.py b/tests/unit_tests/test_plots.py
--- a/tests/unit_tests/test_plots.py
+++ b/tests/unit_tests/test_plots.py
@@ -1,3 +1,5 @@
+from pathlib import Path
+
import openmc
import openmc.examples
import pytest
@@ -37,6 +39,7 @@ def myplot():
}
return plot
+
@pytest.fixture(scope='module')
def myprojectionplot():
plot = openmc.ProjectionPlot(name='myprojectionplot')
@@ -66,6 +69,35 @@ def myprojectionplot():
return plot
+def test_voxel_plot(run_in_tmpdir):
+ surf1 = openmc.Sphere(r=500, boundary_type='vacuum')
+ cell1 = openmc.Cell(region=-surf1)
+ geometry = openmc.Geometry([cell1])
+ geometry.export_to_xml()
+ materials = openmc.Materials()
+ materials.export_to_xml()
+ vox_plot = openmc.Plot()
+ vox_plot.type = 'voxel'
+ vox_plot.id = 12
+ vox_plot.width = (1500., 1500., 1500.)
+ vox_plot.pixels = (200, 200, 200)
+ vox_plot.color_by = 'cell'
+ vox_plot.to_vtk('test_voxel_plot.vti')
+
+ assert Path('plot_12.h5').is_file()
+ assert Path('test_voxel_plot.vti').is_file()
+
+ vox_plot.filename = 'h5_voxel_plot'
+ vox_plot.to_vtk('another_test_voxel_plot.vti')
+
+ assert Path('h5_voxel_plot.h5').is_file()
+ assert Path('another_test_voxel_plot.vti').is_file()
+
+ slice_plot = openmc.Plot()
+ with pytest.raises(ValueError):
+ slice_plot.to_vtk('shimmy.vti')
+
+
def test_attributes(myplot):
assert myplot.name == 'myplot'
| Feature request: voxel plots from within the python API
Everyone loves a nice voxel plot
:black_square_button: :red_square: :red_square: :red_square: :black_square_button:
:red_square: :red_square: :red_square: :red_square: :red_square:
:black_square_button: :black_square_button: :black_square_button: :red_square: :red_square:
:brown_square: :brown_square: :black_square_button: :red_square: :red_square:
:black_square_button: :brown_square: :black_square_button: :red_square: :black_square_button:
The current method requires a mixture of the python API and running the ```openmc-voxel-to-vtk``` script.
```python
vox_plot = openmc.Plot()
vox_plot.type = 'voxel'
vox_plot.width = (1500., 1500., 1500.)
vox_plot.pixels = (200, 200, 200)
vox_plot.filename = 'output_file' # used for the h5 filename
plots = openmc.Plots([vox_plot])
plots.export_to_xml()
openmc.plot_geometry()
os.system('openmc-voxel-to-vtk output_h5_file.h5 -o plot_3d_tokamak.vti')
```
I would be keen to move some of the functionally into the the Python API so that the voxel vti file can be make entirely from within the Python API. This could also be accessed from the script so we wouldn't lose functionality. Similar to the #2171 PR where we moved the track writing from the script file to the Python track object. The above user code would then look a bit more like this ...
```python
vox_plot = openmc.Plot()
vox_plot.type = 'voxel'
vox_plot.width = (1500., 1500., 1500.)
vox_plot.pixels = (200, 200, 200)
vox_plot.filename = 'output_file' # used for the h5 and vti filename
plots = openmc.Plots([vox_plot])
plots.export_to_xml()
openmc.plot_geometry() # produces the vti file as well as the h5 file
```
Having suggested this movement of code I'm not entirely sure how to go about it but I'm taking a look at the openmc.plot_geometry and I'm sure it would be possible. Any comments on if this would be a welcome improvement or hints about how this could be done are most welcome.
| Looking into this and I think issue #2384 would need solving first so that the plot filename can be found. | 2023-04-11T17:07:21Z | [] | [] |
openmc-dev/openmc | 2,538 | openmc-dev__openmc-2538 | [
"2416"
] | 74fb2801c26b748eccc76c4a3d584e084b17ed9f | diff --git a/openmc/mesh.py b/openmc/mesh.py
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -1338,7 +1338,7 @@ def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
pts_cartesian[:, 0] = r * np.cos(phi) + self.origin[0]
pts_cartesian[:, 1] = r * np.sin(phi) + self.origin[1]
pts_cartesian[:, 2] += self.origin[2]
-
+
return super().write_data_to_vtk(
points=pts_cartesian,
filename=filename,
@@ -1585,9 +1585,9 @@ def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
r, theta, phi = pts_spherical[:, 0], pts_spherical[:, 1], pts_spherical[:, 2]
- pts_cartesian[:, 0] = r * np.sin(phi) * np.cos(theta) + self.origin[0]
- pts_cartesian[:, 1] = r * np.sin(phi) * np.sin(theta) + self.origin[1]
- pts_cartesian[:, 2] = r * np.cos(phi) + self.origin[2]
+ pts_cartesian[:, 0] = r * np.sin(theta) * np.cos(phi) + self.origin[0]
+ pts_cartesian[:, 1] = r * np.sin(theta) * np.sin(phi) + self.origin[1]
+ pts_cartesian[:, 2] = r * np.cos(theta) + self.origin[2]
return super().write_data_to_vtk(
points=pts_cartesian,
| diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -273,3 +273,45 @@ def in_geom(cell):
# need to get flat index with axes reversed due to ordering passed into the VTK file
flat_idx = np.ravel_multi_index(tuple(ijk[::-1]), mesh.dimension[::-1])
assert vtk_data[flat_idx] == 0.0, err_msg
+
+
+def test_sphere_mesh_coordinates(run_in_tmpdir):
+ mesh = openmc.SphericalMesh()
+ mesh.r_grid = np.linspace(0.1, 10, 30)
+ mesh.phi_grid = np.linspace(0, 1.5*np.pi, 25)
+ mesh.theta_grid = np.linspace(0, np.pi / 2, 15)
+
+ # write the data to a VTK file (no data)
+ vtk_filename = 'test.vtk'
+ mesh.write_data_to_vtk(vtk_filename, {})
+
+ # read file
+ reader = vtk.vtkStructuredGridReader()
+ reader.SetFileName(str(vtk_filename))
+ reader.Update()
+
+ vtk_grid = reader.GetOutput()
+
+ # create a region that matches the spherical mesh description
+ x = openmc.XPlane()
+ z = openmc.ZPlane()
+ y = openmc.YPlane()
+ s = openmc.Sphere(r=10.0)
+
+ region = +z & +y & -s | -x & -y & +z & -s
+
+ # the VTK interface will update this list when GetCentroid is called
+ centroid = np.zeros(3)
+
+ # ensure all centroids of the sphere mesh are inside the cell region
+ for i in range(vtk_grid.GetNumberOfCells()):
+ # get the cell from the stuctured mesh object
+ cell = vtk_grid.GetCell(i)
+ cell.GetCentroid(centroid)
+
+ # if the coordinate conversion is happening correctly,
+ # every one of the cell centroids should be in the CSG region
+ assert centroid in region, \
+ f'Cell centroid {centroid} not in equivalent ' \
+ f'CSG region for spherical mesh {mesh}'
+
| Spherical mesh VTK coordinates bug
As I was working on #2397, I noticed that spherical meshes with a `theta_grid` property covering only part of [0, $\pi$] resulted in an incorrect mesh
```python
import openmc
import numpy as np
sphere_mesh = openmc.SphericalMesh()
sphere_mesh.r_grid = np.linspace(0, 50, 31)
sphere_mesh.theta_grid = np.linspace(0, 0.5 * np.pi, 11)
sphere_mesh.phi_grid = np.linspace(0, 2*np.pi, 21)
sphere_mesh.write_data_to_vtk('test.vtk', datasets={})
```
This is caused by incorrect use of $\phi$ and $\theta$ in the `SphericalMesh.write_data_to_vtk` method:
https://github.com/openmc-dev/openmc/blob/9768e34b869e9d698282778d2397bf9a982ed24f/openmc/mesh.py#L1536-L1538
The meaning of these variables in spherical coordinates have opposite conventions in mathematics and physics. This can be confusing. Our implementation adopts the one used in physics. After correcting these lines, the VTK file is correct:
I'll submit a PR with this fix and some additional test coverage shortly.
| Closed by #2417
This bug was reintroduced in #2256. I'll open a PR shortly to correct the issue.
And I suppose I'll improve the related test since reverting the code didn't trigger a failure... | 2023-05-31T19:17:18Z | [] | [] |
openmc-dev/openmc | 2,595 | openmc-dev__openmc-2595 | [
"2580"
] | eea52238dac0162a8b7924b81800af4a3c78798e | diff --git a/openmc/deplete/helpers.py b/openmc/deplete/helpers.py
--- a/openmc/deplete/helpers.py
+++ b/openmc/deplete/helpers.py
@@ -196,13 +196,13 @@ def reset_tally_means(self):
"""
self._rate_tally_means_cache = None
- def get_material_rates(self, mat_id, nuc_index, rx_index):
+ def get_material_rates(self, mat_index, nuc_index, rx_index):
"""Return an array of reaction rates for a material
Parameters
----------
- mat_id : int
- Unique ID for the requested material
+ mat_index : int
+ Index for the material
nuc_index : iterable of int
Index for each nuclide in :attr:`nuclides` in the
desired reaction rate matrix
@@ -216,7 +216,7 @@ def get_material_rates(self, mat_id, nuc_index, rx_index):
reaction rates in this material
"""
self._results_cache.fill(0.0)
- full_tally_res = self.rate_tally_means[mat_id]
+ full_tally_res = self.rate_tally_means[mat_index]
for i_tally, (i_nuc, i_rx) in enumerate(product(nuc_index, rx_index)):
self._results_cache[i_nuc, i_rx] = full_tally_res[i_tally]
diff --git a/openmc/deplete/independent_operator.py b/openmc/deplete/independent_operator.py
--- a/openmc/deplete/independent_operator.py
+++ b/openmc/deplete/independent_operator.py
@@ -5,8 +5,10 @@
"""
+from __future__ import annotations
+from collections.abc import Iterable
import copy
-from itertools import product
+from typing import List, Set
import numpy as np
from uncertainties import ufloat
@@ -37,14 +39,20 @@ class IndependentOperator(OpenMCOperator):
.. versionadded:: 0.13.1
+ .. versionchanged:: 0.13.4
+ Arguments updated to include list of fluxes and microscopic cross
+ sections.
+
Parameters
----------
materials : openmc.Materials
Materials to deplete.
- micro_xs : MicroXS
- One-group microscopic cross sections in [b]. If the
- :class:`~openmc.deplete.MicroXS` object is empty, a decay-only calculation will
- be run.
+ fluxes : list of numpy.ndarray
+ Flux in each group in [n-cm/src] for each domain
+ micros : list of MicroXS
+ Cross sections in [b] for each domain. If the
+ :class:`~openmc.deplete.MicroXS` object is empty, a decay-only
+ calculation will be run.
chain_file : str
Path to the depletion chain XML file. Defaults to
``openmc.config['chain_file']``.
@@ -109,7 +117,8 @@ class IndependentOperator(OpenMCOperator):
def __init__(self,
materials,
- micro_xs,
+ fluxes,
+ micros,
chain_file=None,
keff=None,
normalization_mode='fission-q',
@@ -120,7 +129,7 @@ def __init__(self,
fission_yield_opts=None):
# Validate micro-xs parameters
check_type('materials', materials, openmc.Materials)
- check_type('micro_xs', micro_xs, MicroXS)
+ check_type('micros', micros, Iterable, MicroXS)
if keff is not None:
check_type('keff', keff, tuple, float)
keff = ufloat(*keff)
@@ -132,10 +141,15 @@ def __init__(self,
helper_kwargs = {'normalization_mode': normalization_mode,
'fission_yield_opts': fission_yield_opts}
- cross_sections = micro_xs * 1e-24
+ # Sort fluxes and micros in same order that materials get sorted
+ index_sort = np.argsort([mat.id for mat in materials])
+ fluxes = [fluxes[i] for i in index_sort]
+ micros = [micros[i] for i in index_sort]
+
+ self.fluxes = fluxes
super().__init__(
materials,
- cross_sections,
+ micros,
chain_file,
prev_results,
fission_q=fission_q,
@@ -145,6 +159,7 @@ def __init__(self,
@classmethod
def from_nuclides(cls, volume, nuclides,
+ flux,
micro_xs,
chain_file=None,
nuc_units='atom/b-cm',
@@ -163,10 +178,11 @@ def from_nuclides(cls, volume, nuclides,
nuclides : dict of str to float
Dictionary with nuclide names as keys and nuclide concentrations as
values.
+ flux : numpy.ndarray
+ Flux in each group in [n-cm/src]
micro_xs : MicroXS
- One-group microscopic cross sections in [b]. If the
- :class:`~openmc.deplete.MicroXS` object is empty, a decay-only calculation
- will be run.
+ Cross sections in [b]. If the :class:`~openmc.deplete.MicroXS`
+ object is empty, a decay-only calculation will be run.
chain_file : str, optional
Path to the depletion chain XML file. Defaults to
``openmc.config['chain_file']``.
@@ -203,8 +219,11 @@ def from_nuclides(cls, volume, nuclides,
"""
check_type('nuclides', nuclides, dict, str)
materials = cls._consolidate_nuclides_to_material(nuclides, nuc_units, volume)
+ fluxes = [flux]
+ micros = [micro_xs]
return cls(materials,
- micro_xs,
+ fluxes,
+ micros,
chain_file,
keff=keff,
normalization_mode=normalization_mode,
@@ -256,9 +275,9 @@ def _load_previous_results(self):
self.prev_res.append(new_res)
- def _get_nuclides_with_data(self, cross_sections):
+ def _get_nuclides_with_data(self, cross_sections: List[MicroXS]) -> Set[str]:
"""Finds nuclides with cross section data"""
- return set(cross_sections.index)
+ return set(cross_sections[0].nuclides)
class _IndependentRateHelper(ReactionRateHelper):
"""Class for generating one-group reaction rates with flux and
@@ -285,7 +304,7 @@ class _IndependentRateHelper(ReactionRateHelper):
"""
- def __init__(self, op):
+ def __init__(self, op: IndependentOperator):
rates = op.reaction_rates
super().__init__(rates.n_nuc, rates.n_react)
@@ -301,13 +320,13 @@ def reset_tally_means(self):
"""Unused in this case"""
pass
- def get_material_rates(self, mat_id, nuc_index, react_index):
+ def get_material_rates(self, mat_index, nuc_index, react_index):
"""Return 2D array of [nuclide, reaction] reaction rates
Parameters
----------
- mat_id : int
- Unique ID for the requested material
+ mat_index : int
+ Index for the material
nuc_index : list of str
Ordering of desired nuclides
react_index : list of str
@@ -315,20 +334,18 @@ def get_material_rates(self, mat_id, nuc_index, react_index):
"""
self._results_cache.fill(0.0)
- # Get volume in units of [b-cm]
- volume_b_cm = 1e24 * self._op.number.get_mat_volume(mat_id)
+ # Get flux and microscopic cross sections from operator
+ flux = self._op.fluxes[mat_index]
+ xs = self._op.cross_sections[mat_index]
- for i_nuc, i_react in product(nuc_index, react_index):
+ for i_nuc in nuc_index:
nuc = self.nuc_ind_map[i_nuc]
- rx = self.rx_ind_map[i_react]
-
- # OK, this is kind of weird, but we multiply by volume in [b-cm]
- # only because OpenMCOperator._calculate_reaction_rates has to
- # divide it out later. It might make more sense to account for
- # the source rate (flux) here rather than in the normalization
- # helper.
- self._results_cache[i_nuc, i_react] = \
- self._op.cross_sections[rx][nuc] * volume_b_cm
+ for i_rx in react_index:
+ rx = self.rx_ind_map[i_rx]
+
+ # Determine reaction rate by multiplying xs in [b] by flux
+ # in [n-cm/src] to give [(reactions/src)*b-cm/atom]
+ self._results_cache[i_nuc, i_rx] = (xs[nuc, rx] * flux).sum()
return self._results_cache
diff --git a/openmc/deplete/microxs.py b/openmc/deplete/microxs.py
--- a/openmc/deplete/microxs.py
+++ b/openmc/deplete/microxs.py
@@ -1,15 +1,17 @@
"""MicroXS module
-A pandas.DataFrame storing microscopic cross section data with
-nuclide names as row indices and reaction names as column indices.
+A class for storing microscopic cross section data that can be used with the
+IndependentOperator class for depletion.
"""
+from __future__ import annotations
import tempfile
+from typing import List, Tuple, Iterable, Optional, Union
-from pandas import DataFrame, read_csv, Series
+import pandas as pd
import numpy as np
-from openmc.checkvalue import check_type, check_value, check_iterable_type
+from openmc.checkvalue import check_type, check_value, check_iterable_type, PathLike
from openmc.exceptions import DataError
from openmc import StatePoint
import openmc
@@ -20,168 +22,178 @@
_valid_rxns.append('fission')
-class MicroXS(DataFrame):
- """Microscopic cross section data for use in transport-independent depletion.
-
- .. versionadded:: 0.13.1
+def get_microxs_and_flux(
+ model: openmc.Model,
+ domains,
+ nuclides: Optional[Iterable[str]] = None,
+ reactions: Optional[Iterable[str]] = None,
+ energies: Optional[Union[Iterable[float], str]] = None,
+ chain_file: Optional[PathLike] = None,
+ run_kwargs=None
+ ) -> Tuple[List[np.ndarray], List[MicroXS]]:
+ """Generate a microscopic cross sections and flux from a Model
+
+ .. versionadded:: 0.13.4
+
+ Parameters
+ ----------
+ model : openmc.Model
+ OpenMC model object. Must contain geometry, materials, and settings.
+ domains : list of openmc.Material or openmc.Cell or openmc.Universe
+ Domains in which to tally reaction rates.
+ nuclides : list of str
+ Nuclides to get cross sections for. If not specified, all burnable
+ nuclides from the depletion chain file are used.
+ reactions : list of str
+ Reactions to get cross sections for. If not specified, all neutron
+ reactions listed in the depletion chain file are used.
+ energies : iterable of float or str
+ Energy group boundaries in [eV] or the name of the group structure
+ chain_file : str, optional
+ Path to the depletion chain XML file that will be used in depletion
+ simulation. Used to determine cross sections for materials not
+ present in the inital composition. Defaults to
+ ``openmc.config['chain_file']``.
+ run_kwargs : dict, optional
+ Keyword arguments passed to :meth:`openmc.Model.run`
+
+ Returns
+ -------
+ list of numpy.ndarray
+ Flux in each group in [n-cm/src] for each domain
+ list of MicroXS
+ Cross section data in [b] for each domain
"""
+ # Save any original tallies on the model
+ original_tallies = model.tallies
- @classmethod
- def from_model(cls,
- model,
- domain,
- nuclides=None,
- reactions=None,
- chain_file=None,
- energy_bounds=(0, 20e6),
- run_kwargs=None):
- """Generate a one-group cross-section dataframe using OpenMC.
-
- Note that the ``openmc`` executable must be compiled.
-
- Parameters
- ----------
- model : openmc.Model
- OpenMC model object. Must contain geometry, materials, and settings.
- domain : openmc.Material or openmc.Cell or openmc.Universe
- Domain in which to tally reaction rates.
- nuclides : list of str
- Nuclides to get cross sections for. If not specified, all burnable
- nuclides from the depletion chain file are used.
- reactions : list of str
- Reactions to get cross sections for. If not specified, all neutron
- reactions listed in the depletion chain file are used.
- chain_file : str, optional
- Path to the depletion chain XML file that will be used in depletion
- simulation. Used to determine cross sections for materials not
- present in the inital composition. Defaults to
- ``openmc.config['chain_file']``.
- energy_bound : 2-tuple of float, optional
- Bounds for the energy group.
- run_kwargs : dict, optional
- Keyword arguments passed to :meth:`openmc.model.Model.run`
-
- Returns
- -------
- MicroXS
- Cross section data in [b]
-
- """
- # Save any original tallies on the model
- original_tallies = model.tallies
-
- # Determine what reactions and nuclides are available in chain
+ # Determine what reactions and nuclides are available in chain
+ if chain_file is None:
+ chain_file = openmc.config.get('chain_file')
if chain_file is None:
- chain_file = openmc.config.get('chain_file')
- if chain_file is None:
- raise DataError(
- "No depletion chain specified and could not find depletion "
- "chain in openmc.config['chain_file']"
- )
- chain = Chain.from_xml(chain_file)
- if reactions is None:
- reactions = chain.reactions
- if not nuclides:
- cross_sections = _find_cross_sections(model)
- nuclides_with_data = _get_nuclides_with_data(cross_sections)
- nuclides = [nuc.name for nuc in chain.nuclides
- if nuc.name in nuclides_with_data]
-
- # Set up the reaction rate and flux tallies
- energy_filter = openmc.EnergyFilter(energy_bounds)
- if isinstance(domain, openmc.Material):
- domain_filter = openmc.MaterialFilter([domain])
- elif isinstance(domain, openmc.Cell):
- domain_filter = openmc.CellFilter([domain])
- elif isinstance(domain, openmc.Universe):
- domain_filter = openmc.UniverseFilter([domain])
+ raise DataError(
+ "No depletion chain specified and could not find depletion "
+ "chain in openmc.config['chain_file']"
+ )
+ chain = Chain.from_xml(chain_file)
+ if reactions is None:
+ reactions = chain.reactions
+ if not nuclides:
+ cross_sections = _find_cross_sections(model)
+ nuclides_with_data = _get_nuclides_with_data(cross_sections)
+ nuclides = [nuc.name for nuc in chain.nuclides
+ if nuc.name in nuclides_with_data]
+
+ # Set up the reaction rate and flux tallies
+ if energies is None:
+ energy_filter = openmc.EnergyFilter([0.0, 100.0e6])
+ elif isinstance(energies, str):
+ energy_filter = openmc.EnergyFilter.from_group_structure(energies)
+ else:
+ energy_filter = openmc.EnergyFilter(energies)
+ if isinstance(domains[0], openmc.Material):
+ domain_filter = openmc.MaterialFilter(domains)
+ elif isinstance(domains[0], openmc.Cell):
+ domain_filter = openmc.CellFilter(domains)
+ elif isinstance(domains[0], openmc.Universe):
+ domain_filter = openmc.UniverseFilter(domains)
+ else:
+ raise ValueError(f"Unsupported domain type: {type(domains[0])}")
+
+ rr_tally = openmc.Tally(name='MicroXS RR')
+ rr_tally.filters = [domain_filter, energy_filter]
+ rr_tally.nuclides = nuclides
+ rr_tally.multiply_density = False
+ rr_tally.scores = reactions
+
+ flux_tally = openmc.Tally(name='MicroXS flux')
+ flux_tally.filters = [domain_filter, energy_filter]
+ flux_tally.scores = ['flux']
+ model.tallies = openmc.Tallies([rr_tally, flux_tally])
+
+ # create temporary run
+ with tempfile.TemporaryDirectory() as temp_dir:
+ if run_kwargs is None:
+ run_kwargs = {}
else:
- raise ValueError(f"Unsupported domain type: {type(domain)}")
-
- rr_tally = openmc.Tally(name='MicroXS RR')
- rr_tally.filters = [domain_filter, energy_filter]
- rr_tally.nuclides = nuclides
- rr_tally.multiply_density = False
- rr_tally.scores = reactions
+ run_kwargs = dict(run_kwargs)
+ run_kwargs.setdefault('cwd', temp_dir)
+ statepoint_path = model.run(**run_kwargs)
- flux_tally = openmc.Tally(name='MicroXS flux')
- flux_tally.filters = [domain_filter, energy_filter]
- flux_tally.scores = ['flux']
- tallies = openmc.Tallies([rr_tally, flux_tally])
+ with StatePoint(statepoint_path) as sp:
+ rr_tally = sp.tallies[rr_tally.id]
+ rr_tally._read_results()
+ flux_tally = sp.tallies[flux_tally.id]
+ flux_tally._read_results()
- model.tallies = tallies
+ # Get reaction rates and flux values
+ reaction_rates = rr_tally.get_reshaped_data() # (domains, groups, nuclides, reactions)
+ flux = flux_tally.get_reshaped_data() # (domains, groups, 1, 1)
- # create temporary run
- with tempfile.TemporaryDirectory() as temp_dir:
- if run_kwargs is None:
- run_kwargs = {}
- run_kwargs.setdefault('cwd', temp_dir)
- statepoint_path = model.run(**run_kwargs)
+ # Make energy groups last dimension
+ reaction_rates = np.moveaxis(reaction_rates, 1, -1) # (domains, nuclides, reactions, groups)
+ flux = np.moveaxis(flux, 1, -1) # (domains, 1, 1, groups)
- with StatePoint(statepoint_path) as sp:
- rr_tally = sp.tallies[rr_tally.id]
- rr_tally._read_results()
- flux_tally = sp.tallies[flux_tally.id]
- flux_tally._read_results()
+ # Divide RR by flux to get microscopic cross sections
+ xs = np.empty_like(reaction_rates) # (domains, nuclides, reactions, groups)
+ d, _, _, g = np.nonzero(flux)
+ xs[d, ..., g] = reaction_rates[d, ..., g] / flux[d, :, :, g]
- # Get reaction rates and flux values
- reaction_rates = rr_tally.mean.sum(axis=0) # (nuclides, reactions)
- flux = flux_tally.mean[0, 0, 0]
+ # Reset tallies
+ model.tallies = original_tallies
- # Divide RR by flux to get microscopic cross sections
- xs = reaction_rates / flux
+ # Create lists where each item corresponds to one domain
+ fluxes = list(flux.squeeze((1, 2)))
+ micros = [MicroXS(xs_i, nuclides, reactions) for xs_i in xs]
+ return fluxes, micros
- # Build Series objects
- series = {}
- for i, rx in enumerate(reactions):
- series[rx] = Series(xs[..., i], index=rr_tally.nuclides)
- # Revert to the original tallies and materials
- model.tallies = original_tallies
-
- return cls(series).rename_axis('nuclide')
+class MicroXS:
+ """Microscopic cross section data for use in transport-independent depletion.
- @classmethod
- def from_array(cls, nuclides, reactions, data):
- """
- Creates a ``MicroXS`` object from arrays.
+ .. versionadded:: 0.13.1
- Parameters
- ----------
- nuclides : list of str
- List of nuclide symbols for that have data for at least one
- reaction.
- reactions : list of str
- List of reactions. All reactions must match those in
- :data:`openmc.deplete.chain.REACTIONS`
- data : ndarray of floats
- Array containing one-group microscopic cross section values for
- each nuclide and reaction. Cross section values are assumed to be
- in [b].
-
- Returns
- -------
- MicroXS
- """
+ .. versionchanged:: 0.13.4
+ Class was heavily refactored and no longer subclasses pandas.DataFrame.
+
+ Parameters
+ ----------
+ data : numpy.ndarray of floats
+ 3D array containing microscopic cross section values for each
+ nuclide, reaction, and energy group. Cross section values are assumed to
+ be in [b], and indexed by [nuclide, reaction, energy group]
+ nuclides : list of str
+ List of nuclide symbols for that have data for at least one
+ reaction.
+ reactions : list of str
+ List of reactions. All reactions must match those in
+ :data:`openmc.deplete.chain.REACTIONS`
+ """
+ def __init__(self, data: np.ndarray, nuclides: List[str], reactions: List[str]):
# Validate inputs
- if data.shape != (len(nuclides), len(reactions)):
+ if data.shape[:2] != (len(nuclides), len(reactions)):
raise ValueError(
f'Nuclides list of length {len(nuclides)} and '
f'reactions array of length {len(reactions)} do not '
f'match dimensions of data array of shape {data.shape}')
+ check_iterable_type('nuclides', nuclides, str)
+ check_iterable_type('reactions', reactions, str)
+ check_type('data', data, np.ndarray, expected_iter_type=float)
+ for reaction in reactions:
+ check_value('reactions', reaction, _valid_rxns)
- cls._validate_micro_xs_inputs(
- nuclides, reactions, data)
- micro_xs = cls(index=nuclides, columns=reactions, data=data)
+ self.data = data
+ self.nuclides = nuclides
+ self.reactions = reactions
- return micro_xs
+ # TODO: Add a classmethod for generating MicroXS directly from cross section
+ # data using a known flux spectrum
@classmethod
def from_csv(cls, csv_file, **kwargs):
- """
- Load a ``MicroXS`` object from a ``.csv`` file.
+ """Load data from a comma-separated values (csv) file.
Parameters
----------
@@ -199,17 +211,37 @@ def from_csv(cls, csv_file, **kwargs):
if 'float_precision' not in kwargs:
kwargs['float_precision'] = 'round_trip'
- micro_xs = cls(read_csv(csv_file, index_col=0, **kwargs))
+ df = pd.read_csv(csv_file, **kwargs)
+ df.set_index(['nuclides', 'reactions', 'groups'], inplace=True)
+ nuclides = list(df.index.unique(level='nuclides'))
+ reactions = list(df.index.unique(level='reactions'))
+ groups = list(df.index.unique(level='groups'))
+ shape = (len(nuclides), len(reactions), len(groups))
+ data = df.values.reshape(shape)
+ return cls(data, nuclides, reactions)
- cls._validate_micro_xs_inputs(list(micro_xs.index),
- list(micro_xs.columns),
- micro_xs.to_numpy())
- return micro_xs
+ def __getitem__(self, index):
+ nuc, rx = index
+ i_nuc = self.nuclides.index(nuc)
+ i_rx = self.reactions.index(rx)
+ return self.data[i_nuc, i_rx]
+
+ def to_csv(self, *args, **kwargs):
+ """Write data to a comma-separated values (csv) file
+
+ Parameters
+ ----------
+ *args
+ Positional arguments passed to :meth:`pandas.DataFrame.to_csv`
+ **kwargs
+ Keyword arguments passed to :meth:`pandas.DataFrame.to_csv`
+
+ """
+ groups = self.data.shape[2]
+ multi_index = pd.MultiIndex.from_product(
+ [self.nuclides, self.reactions, range(1, groups + 1)],
+ names=['nuclides', 'reactions', 'groups']
+ )
+ df = pd.DataFrame({'xs': self.data.flatten()}, index=multi_index)
+ df.to_csv(*args, **kwargs)
- @staticmethod
- def _validate_micro_xs_inputs(nuclides, reactions, data):
- check_iterable_type('nuclides', nuclides, str)
- check_iterable_type('reactions', reactions, str)
- check_type('data', data, np.ndarray, expected_iter_type=float)
- for reaction in reactions:
- check_value('reactions', reaction, _valid_rxns)
diff --git a/openmc/deplete/openmc_operator.py b/openmc/deplete/openmc_operator.py
--- a/openmc/deplete/openmc_operator.py
+++ b/openmc/deplete/openmc_operator.py
@@ -6,6 +6,7 @@
"""
from abc import abstractmethod
+from typing import List, Tuple, Dict
import numpy as np
@@ -31,9 +32,9 @@ class OpenMCOperator(TransportOperator):
----------
materials : openmc.Materials
List of all materials in the model
- cross_sections : str or pandas.DataFrame
- Path to continuous energy cross section library, or object containing
- one-group cross-sections.
+ cross_sections : str or list of MicroXS
+ Path to continuous energy cross section library, or list of objects
+ containing cross sections.
chain_file : str, optional
Path to the depletion chain XML file. Defaults to
openmc.config['chain_file'].
@@ -60,9 +61,9 @@ class OpenMCOperator(TransportOperator):
----------
materials : openmc.Materials
All materials present in the model
- cross_sections : str or MicroXS
- Path to continuous energy cross section library, or object
- containing one-group cross-sections.
+ cross_sections : str or list of MicroXS
+ Path to continuous energy cross section library, or list of objects
+ containing cross sections.
output_dir : pathlib.Path
Path to output directory to save results.
round_number : bool
@@ -164,7 +165,7 @@ def _differentiate_burnable_mats(self):
"""Assign distribmats for each burnable material"""
pass
- def _get_burnable_mats(self):
+ def _get_burnable_mats(self) -> Tuple[List[str], Dict[str, float], List[str]]:
"""Determine depletable materials, volumes, and nuclides
Returns
diff --git a/openmc/deplete/reaction_rates.py b/openmc/deplete/reaction_rates.py
--- a/openmc/deplete/reaction_rates.py
+++ b/openmc/deplete/reaction_rates.py
@@ -2,6 +2,8 @@
An ndarray to store reaction rates with string, integer, or slice indexing.
"""
+from typing import Dict
+
import numpy as np
@@ -51,6 +53,10 @@ class ReactionRates(np.ndarray):
# the __array_finalize__ method (discussed here:
# https://docs.scipy.org/doc/numpy/user/basics.subclassing.html)
+ index_mat: Dict[str, int]
+ index_nuc: Dict[str, int]
+ index_rx: Dict[str, int]
+
def __new__(cls, local_mats, nuclides, reactions, from_results=False):
# Create appropriately-sized zeroed-out ndarray
shape = (len(local_mats), len(nuclides), len(reactions))
| diff --git a/tests/micro_xs_simple.csv b/tests/micro_xs_simple.csv
--- a/tests/micro_xs_simple.csv
+++ b/tests/micro_xs_simple.csv
@@ -1,13 +1,25 @@
-nuclide,"(n,gamma)",fission
-U234,22.231989822002454,0.4962074466374984
-U235,10.479008971197121,48.41787337164606
-U238,0.8673334105437321,0.1046788058876236
-U236,8.651710446071224,0.31948392400019293
-O16,7.497851000107522e-05,0.0
-O17,0.0004079227797153372,0.0
-I135,6.842395323713929,0.0
-Xe135,227463.8642699061,0.0
-Xe136,0.023178960347535887,0.0
-Cs135,2.1721665580713623,0.0
-Gd157,12786.099392370175,0.0
-Gd156,3.4006085445846983,0.0
+nuclides,reactions,groups,xs
+U234,"(n,gamma)",1,22.23198982200245
+U234,fission,1,0.4962074466374984
+U235,"(n,gamma)",1,10.47900897119712
+U235,fission,1,48.41787337164606
+U238,"(n,gamma)",1,0.8673334105437321
+U238,fission,1,0.1046788058876236
+U236,"(n,gamma)",1,8.651710446071224
+U236,fission,1,0.3194839240001929
+O16,"(n,gamma)",1,7.497851000107522e-05
+O16,fission,1,0.0
+O17,"(n,gamma)",1,0.0004079227797153
+O17,fission,1,0.0
+I135,"(n,gamma)",1,6.842395323713929
+I135,fission,1,0.0
+Xe135,"(n,gamma)",1,227463.8642699061
+Xe135,fission,1,0.0
+Xe136,"(n,gamma)",1,0.0231789603475358
+Xe136,fission,1,0.0
+Cs135,"(n,gamma)",1,2.1721665580713623
+Cs135,fission,1,0.0
+Gd157,"(n,gamma)",1,12786.099392370175
+Gd157,fission,1,0.0
+Gd156,"(n,gamma)",1,3.4006085445846983
+Gd156,fission,1,0.0
diff --git a/tests/regression_tests/deplete_no_transport/test.py b/tests/regression_tests/deplete_no_transport/test.py
--- a/tests/regression_tests/deplete_no_transport/test.py
+++ b/tests/regression_tests/deplete_no_transport/test.py
@@ -36,13 +36,16 @@ def chain_file():
return Path(__file__).parents[2] / 'chain_simple.xml'
[email protected]("multiproc, from_nuclides, normalization_mode, power, flux", [
- (True, True, 'source-rate', None, 1164719970082145.0),
- (False, True, 'source-rate', None, 1164719970082145.0),
+neutron_per_cm2_sec = 1164719970082145.0
+
+
[email protected]("multiproc, from_nuclides, normalization_mode, power, source_rate", [
+ (True, True, 'source-rate', None, 1.0),
+ (False, True, 'source-rate', None, 1.0),
(True, True, 'fission-q', 174, None),
(False, True, 'fission-q', 174, None),
- (True, False, 'source-rate', None, 1164719970082145.0),
- (False, False, 'source-rate', None, 1164719970082145.0),
+ (True, False, 'source-rate', None, 1.0),
+ (False, False, 'source-rate', None, 1.0),
(True, False, 'fission-q', 174, None),
(False, False, 'fission-q', 174, None)])
def test_against_self(run_in_tmpdir,
@@ -53,7 +56,7 @@ def test_against_self(run_in_tmpdir,
from_nuclides,
normalization_mode,
power,
- flux):
+ source_rate):
"""Transport free system test suite.
Runs an OpenMC transport-free depletion calculation and verifies
@@ -61,8 +64,10 @@ def test_against_self(run_in_tmpdir,
"""
# Create operator
+ flux = neutron_per_cm2_sec * fuel.volume
op = _create_operator(from_nuclides,
fuel,
+ flux,
micro_xs,
chain_file,
normalization_mode)
@@ -75,12 +80,12 @@ def test_against_self(run_in_tmpdir,
openmc.deplete.PredictorIntegrator(op,
dt,
power=power,
- source_rates=flux,
+ source_rates=source_rate,
timestep_units='s').integrate()
# Get path to test and reference results
path_test = op.output_dir / 'depletion_results.h5'
- if flux is not None:
+ if power is None:
ref_path = 'test_reference_source_rate.h5'
else:
ref_path = 'test_reference_fission_q.h5'
@@ -99,8 +104,8 @@ def test_against_self(run_in_tmpdir,
_assert_same_mats(res_test, res_ref)
tol = 1.0e-14
- assert_atoms_equal(res_test, res_ref, tol)
- assert_reaction_rates_equal(res_test, res_ref, tol)
+ assert_atoms_equal(res_ref, res_test, tol)
+ assert_reaction_rates_equal(res_ref, res_test, tol)
@pytest.mark.parametrize("multiproc, dt, time_units, time_type, atom_tol, rx_tol ", [
@@ -123,7 +128,8 @@ def test_against_coupled(run_in_tmpdir,
atom_tol,
rx_tol):
# Create operator
- op = _create_operator(False, fuel, micro_xs, chain_file, 'fission-q')
+ flux = neutron_per_cm2_sec * fuel.volume
+ op = _create_operator(False, fuel, flux, micro_xs, chain_file, 'fission-q')
# Power and timesteps
dt = [dt] # single step
@@ -151,12 +157,13 @@ def test_against_coupled(run_in_tmpdir,
# Assert same mats
_assert_same_mats(res_test, res_ref)
- assert_atoms_equal(res_test, res_ref, atom_tol)
- assert_reaction_rates_equal(res_test, res_ref, rx_tol)
+ assert_atoms_equal(res_ref, res_test, atom_tol)
+ assert_reaction_rates_equal(res_ref, res_test, rx_tol)
def _create_operator(from_nuclides,
fuel,
+ flux,
micro_xs,
chain_file,
normalization_mode):
@@ -167,13 +174,15 @@ def _create_operator(from_nuclides,
op = IndependentOperator.from_nuclides(fuel.volume,
nuclides,
+ flux,
micro_xs,
chain_file,
normalization_mode=normalization_mode)
else:
op = IndependentOperator(openmc.Materials([fuel]),
- micro_xs,
+ [flux],
+ [micro_xs],
chain_file,
normalization_mode=normalization_mode)
diff --git a/tests/regression_tests/microxs/test.py b/tests/regression_tests/microxs/test.py
--- a/tests/regression_tests/microxs/test.py
+++ b/tests/regression_tests/microxs/test.py
@@ -4,7 +4,7 @@
import numpy as np
import pytest
import openmc
-from openmc.deplete import MicroXS
+from openmc.deplete import MicroXS, get_microxs_and_flux
from tests.regression_tests import config
@@ -47,13 +47,13 @@ def model():
def test_from_model(model):
- fuel = model.materials[0]
+ domains = model.materials[:1]
nuclides = ['U234', 'U235', 'U238', 'U236', 'O16', 'O17', 'I135', 'Xe135',
'Xe136', 'Cs135', 'Gd157', 'Gd156']
- test_xs = MicroXS.from_model(model, fuel, nuclides, chain_file=CHAIN_FILE)
+ _, test_xs = get_microxs_and_flux(model, domains, nuclides, chain_file=CHAIN_FILE)
if config['update']:
- test_xs.to_csv('test_reference.csv')
+ test_xs[0].to_csv('test_reference.csv')
ref_xs = MicroXS.from_csv('test_reference.csv')
- np.testing.assert_allclose(test_xs, ref_xs, rtol=1e-11)
+ np.testing.assert_allclose(test_xs[0].data, ref_xs.data, rtol=1e-11)
diff --git a/tests/regression_tests/microxs/test_reference.csv b/tests/regression_tests/microxs/test_reference.csv
--- a/tests/regression_tests/microxs/test_reference.csv
+++ b/tests/regression_tests/microxs/test_reference.csv
@@ -1,13 +1,25 @@
-nuclide,"(n,gamma)",fission
-U234,21.418670317831197,0.5014588470882195
-U235,10.343944102483244,47.46718472611891
-U238,0.8741166723597251,0.10829568455139126
-U236,9.083486784689326,0.3325287927011428
-O16,7.548646353912453e-05,0.0
-O17,0.0004018486221310307,0.0
-I135,6.6912565089429235,0.0
-Xe135,223998.64185667288,0.0
-Xe136,0.022934362666193576,0.0
-Cs135,2.28453952223533,0.0
-Gd157,12582.079620036275,0.0
-Gd156,2.9421127515332417,0.0
+nuclides,reactions,groups,xs
+U234,"(n,gamma)",1,21.418670317831076
+U234,fission,1,0.5014588470882162
+U235,"(n,gamma)",1,10.343944102483215
+U235,fission,1,47.46718472611895
+U238,"(n,gamma)",1,0.8741166723597229
+U238,fission,1,0.10829568455139067
+U236,"(n,gamma)",1,9.08348678468935
+U236,fission,1,0.3325287927011424
+O16,"(n,gamma)",1,7.548646353912426e-05
+O16,fission,1,0.0
+O17,"(n,gamma)",1,0.00040184862213103105
+O17,fission,1,0.0
+I135,"(n,gamma)",1,6.691256508942912
+I135,fission,1,0.0
+Xe135,"(n,gamma)",1,223998.6418566729
+Xe135,fission,1,0.0
+Xe136,"(n,gamma)",1,0.022934362666193503
+Xe136,fission,1,0.0
+Cs135,"(n,gamma)",1,2.2845395222353204
+Cs135,fission,1,0.0
+Gd157,"(n,gamma)",1,12582.07962003624
+Gd157,fission,1,0.0
+Gd156,"(n,gamma)",1,2.942112751533234
+Gd156,fission,1,0.0
diff --git a/tests/unit_tests/test_deplete_decay_products.py b/tests/unit_tests/test_deplete_decay_products.py
--- a/tests/unit_tests/test_deplete_decay_products.py
+++ b/tests/unit_tests/test_deplete_decay_products.py
@@ -1,4 +1,5 @@
import openmc.deplete
+import numpy as np
import pytest
@@ -16,11 +17,14 @@ def test_deplete_decay_products(run_in_tmpdir):
</depletion_chain>
""")
+ # Create MicroXS object with no cross sections
+ micro_xs = openmc.deplete.MicroXS(np.empty((0, 0)), [], [])
+
# Create depletion operator with no reactions
- micro_xs = openmc.deplete.MicroXS()
op = openmc.deplete.IndependentOperator.from_nuclides(
volume=1.0,
nuclides={'Li5': 1.0},
+ flux=0.0,
micro_xs=micro_xs,
chain_file='test_chain.xml',
normalization_mode='source-rate'
diff --git a/tests/unit_tests/test_deplete_independent_operator.py b/tests/unit_tests/test_deplete_independent_operator.py
--- a/tests/unit_tests/test_deplete_independent_operator.py
+++ b/tests/unit_tests/test_deplete_independent_operator.py
@@ -4,14 +4,13 @@
from pathlib import Path
-import pytest
from openmc.deplete import IndependentOperator, MicroXS
from openmc import Material, Materials
-import numpy as np
CHAIN_PATH = Path(__file__).parents[1] / "chain_simple.xml"
ONE_GROUP_XS = Path(__file__).parents[1] / "micro_xs_simple.csv"
+
def test_operator_init():
"""The test uses a temporary dummy chain. This file will be removed
at the end of the test, and only contains a depletion_chain node."""
@@ -22,15 +21,18 @@ def test_operator_init():
'U236': 4.5724195495061115e+18,
'O16': 4.639065406771322e+22,
'O17': 1.7588724018066158e+19}
+ flux = 1.0
micro_xs = MicroXS.from_csv(ONE_GROUP_XS)
IndependentOperator.from_nuclides(
- volume, nuclides, micro_xs, CHAIN_PATH, nuc_units='atom/cm3')
+ volume, nuclides, flux, micro_xs, CHAIN_PATH, nuc_units='atom/cm3')
fuel = Material(name="uo2")
fuel.add_element("U", 1, percent_type="ao", enrichment=4.25)
fuel.add_element("O", 2)
fuel.set_density("g/cc", 10.4)
- fuel.depletable=True
+ fuel.depletable = True
fuel.volume = 1
materials = Materials([fuel])
- IndependentOperator(materials, micro_xs, CHAIN_PATH)
+ fluxes = [1.0]
+ micros = [micro_xs]
+ IndependentOperator(materials, fluxes, micros, CHAIN_PATH)
diff --git a/tests/unit_tests/test_deplete_microxs.py b/tests/unit_tests/test_deplete_microxs.py
--- a/tests/unit_tests/test_deplete_microxs.py
+++ b/tests/unit_tests/test_deplete_microxs.py
@@ -43,17 +43,18 @@ def test_from_array():
[0., 0.],
[0., 0.1],
[0., 0.1]])
+ data.shape = (12, 2, 1)
- MicroXS.from_array(nuclides, reactions, data)
+ MicroXS(data, nuclides, reactions)
with pytest.raises(ValueError, match=r'Nuclides list of length \d* and '
r'reactions array of length \d* do not '
- r'match dimensions of data array of shape \(\d*\,d*\)'):
- MicroXS.from_array(nuclides, reactions, data[:, 0])
+ r'match dimensions of data array of shape \(\d*\, \d*\)'):
+ MicroXS(data[:, 0], nuclides, reactions)
def test_csv():
ref_xs = MicroXS.from_csv(ONE_GROUP_XS)
ref_xs.to_csv('temp_xs.csv')
temp_xs = MicroXS.from_csv('temp_xs.csv')
- assert np.all(ref_xs == temp_xs)
+ assert np.all(ref_xs.data == temp_xs.data)
remove('temp_xs.csv')
| Design of the `MicroXS` and `IndependentOperator` classes
I'm currently working on refactoring the `MicroXS` and `IndependentOperator` classes to support a wider variety of use cases. Namely, the `MicroXS` class currently stores one-group microscopic cross sections that are to be paired with one-group fluxes. For our [FES shutdown dose rate project](https://github.com/openmc-dev/fes-sdr-project), we need the ability to do activation calculations using a multigroup flux spectrum / cross sections. Furthermore, the `MicroXS` and `IndependentOperator` class are not currently structured to support multiple materials very well (you can have multiple materials in `IndependentOperator` but only a single `MicroXS`).
As I'm envisioning a refactor of these two classes, one issue I'm having trouble resolving in my mind is how to handle multiple materials. For example, I can imagine something like the following
```Python
# This involves running an OpenMC model to get microscopic cross sections
# by (material, nuclide, reaction, energy group) and fluxes by (material, energy group)
micros, fluxes = get_micros_and_fluxes(model)
op = openmc.deplete.IndependentOperator(materials, micros, fluxes)
timesteps = [...]
source_rates = [...]
integrator = openmc.deplete.PredictorIntegrator(op, timesteps, source_rates=source_rates)
```
The main issue is: _how do we specify the source rates for multiple materials_? The options are:
1. The source rate is specified as the actual fixed source rate in [neutrons/sec]. In this case, it would make sense for us to pass `fluxes` to the independent operator corresponding to a unity source rate, and then all the reaction rates would be scaled accordingly.
2. The source rate is the one-group flux in [neutrons/cm²-s]. This implies that we would have to have a separate instance of the integrator and operator for each material, so the code above would become:
```Python
timesteps = [...]
for mat, micro_xs, flux in zip(materials, micros, fluxes):
op = openmc.deplete.IndependentOperator(mat, micro_xs, flux)
source_rate = flux.sum()
integrator = openmc.deplete.PredictorIntegrator(op, timesteps, source_rates=source_rate)
```
Option 2 is arguably closer to how codes like FISPACT work. The multigroup flux provided to the operator has arbitrary units and everything is normalized to the total flux in [n/cm²-s]. Option 1 feels syntactically cleaner and more consistent with `CoupledOperator`, but it does imply that the units on `fluxes` matter.
Anyone have thoughts on this? @eepeterson @shimwell @yardasol @pshriwise
| Thanks for starting this @paulromano! I think if we look at the highest level and go from there the thought process might be something like this:
1. `CoupledOperator` allows you to deplete an entire model (currently across all materials).
2. Do we want the same interpretation for `IndependentOperator`? My gut says yes, which means that it too should be able to deplete across all materials (or cells, or mesh voxels, etc) for an entire model.
3. This means the source rate should be for the model i.e. the actual source rate in [neutrons/sec] in `IndependentOperator`
4. Under the hood, I think we need a helper function to do the Bateman solve for all the cells/materials/voxels independently where each solve uses the local source rate derived from the global source rate (essentially how FISPACT does a single calculation).
5. Maybe in some sense the `IndependentOperator` becomes a wrapper for other operators. I think it's important to have the functionality to do a FISPACT-like calculation given any arbitrary multigroup spectrum and material composition and then to be able to dispatch that helper function over whatever discretization of your model you want.
I guess when I start thinking about it a bit more I wonder if we need to add an `Integrator` class to facilitate this or refactor current `Integrators` to have a method that just does the time integration without needing to know where the burnup matrix came from.
Being able to easily compare with inventory codes that don't handle transport like would be really helpful. I'm often asked to compared code outputs and was actually thinking of comparing with [ALARA ](https://svalinn.github.io/ALARA/) as it is open source.
I guess it is double the work but would it be worth fleshing out both approaches as skeleton PRs in case we discover any performance or usability benefits of one approach over the other.
Thanks for starting an in-depth conversation about this @paulromano!
My thoughts on this are pretty in-line with @eepeterson's on this. It would be very convenient to have our `IndependentOperator` class handle the bookkeeping for the domain-specific flux based on a global source term with a lower-level class or function that performs calculations domain-by-domain.
In my head, this would mean that the loop from option 2 above would exist inside the `IndependentOperator` class after some pre-computation of the source rates for each domain. This would be paired with an internal refactor of `IndependentOperator` to allow for the depletion/activation of individual domains based on the XS, flux, and a user-specified source rate. Given this, it would be easier for us to enforce the flux units when depleting with the higher-level `IndependentOperator` functionality since we're handling that ourselves.
As @eepeterson said, an additional step might be to separate burnup matrices from the operators fo for each domain. I'm curious as to whether or not we would be able to "stack" those to perform the Bateman solve more efficiently than repeated calls. In this case, it would be nice to be able to detect when we can avoid duplication of these matrices (i.e. when doing cell-based depletion with cells containing the same material).
A good deal of that is probably me just rephrasing previous thoughts as I understand them 😄 but let me know if I'm missing the mark here.
Responding to @shimwell:
> I guess it is double the work but would it be worth fleshing out both approaches as skeleton PRs in case we discover any performance or usability benefits of one approach over the other.
I don't think it's going to be double the work. It just requires careful thought about the normalization of the multigroup flux being passed to the operator and similarly the source rate passed to the integrator. Clearly in the case where you just have a flux spectrum (absolute units) and you want to activate a material, the source rate will not just be [neutrons/sec] anymore. So, either we need very good documentation and/or some helper functions/classes to ease the burden.
<hr>
Responding to @pshriwise:
> In my head, this would mean that the loop from option 2 above would exist inside the `IndependentOperator` class after some pre-computation of the source rates for each domain.
In fact, `IndependentOperator` and the integrators are already set up to work with multiple materials, so not too much is needed there. The main change is to allow reaction rates to be calculated with separate flux spectra / cross sections for each material since right now the same ones are used for all materials.
<hr>
Thanks all for the (very prompt) feedback! I agree with the points and it sounds like we're converging around the idea of `IndependentOperator` handling multiple materials with a global source rate specified for the integrator. I'll start moving in that direction with my refactor; hoping to break it up into smaller chunks as much as possible.
Hopefully I'm not too late on this @paulromano. To answer your question
>how do we specify the source rates for multiple materials?
I think option 1 is more in line with the design goals we initially had for `IndependentOperator`. I think it's reasonable to assert that units for flux matters! AFAIK that's how the rest of the code behaves as well. Option 2 feels a bit clunky to me, but I'm sure there are use cases that demand it. Maybe as @eepeterson suggested, we could add this functionality through a subclass of `IndependentOperator`?
In response to the additonal discussion, I have some additional points for consideration in the context of how `IndependentOperator` was designed:
1. The [docstring for `IndependentOperator`](https://docs.openmc.org/en/stable/pythonapi/generated/openmc.deplete.IndependentOperator.html) specifies that `source-rate` normalization option assumes the values being passed are the neutron flux [n/cm^2-s]. This option should probably be changed to make this assumption clearer. The reason I used the term `source-rate` was that the `SourceRateHelper` had the correct algorithm set up for calculating the reaction rate by multiplying macroscopic cross sections with a neutron flux. We will probably need to change how we implement the `source-rate` normalization when adding to multi-group flux and cross section capabilities.
2. It's been a while since I've looked at the code, but I believe `IndependentOperator` already handles depletion of multiple materials with a single source rate (either a power/power density or a single-group flux). If we look at [the User Guide section on Transport-independent depletion,](https://docs.openmc.org/en/stable/usersguide/depletion.html#multiple-materials):
>A transport-independent depletion simulation using source-rate normalization will calculate reaction rates for each material independently... A transport-independent depletion simulation using fission-q normalization will sum the fission energy values across all materials into $Q_i$ in Equation [(1)](https://docs.openmc.org/en/stable/usersguide/depletion.html#equation-fission-q), and Equation [(1)](https://docs.openmc.org/en/stable/usersguide/depletion.html#equation-fission-q) provides the flux we use to calculate the reaction rates in each material.
Based on this description, it sounds like it wouldn't be super complicated to add functionality where we use a local flux/power/source-rate for different materials, but it's hard to say for sure without analyzing the code itself. Currently, `IndependentOperator` currently doesn't do *anything* with the geometry, so adding some machinery to allow localized fluxes/powers/source-rates would be a way to kind of shoehorn the geometry component into the calculation.
3. @pshriwise @eepeterson I think the idea of using a global-source term to create domain-specific fluxes is interesting. Do we need to do a transport simulation to get such quantities? Or is it enough to have the multi-group cross sections and a global source rate? | 2023-07-13T11:57:04Z | [] | [] |
openmc-dev/openmc | 2,647 | openmc-dev__openmc-2647 | [
"2646"
] | 1d29adc0808a726fba93ad687fcce7b1b6632f66 | diff --git a/openmc/settings.py b/openmc/settings.py
--- a/openmc/settings.py
+++ b/openmc/settings.py
@@ -133,6 +133,8 @@ class Settings:
Number of particles per generation
photon_transport : bool
Whether to use photon transport.
+ plot_seed : int
+ Initial seed for randomly generated plot colors.
ptables : bool
Determine whether probability tables are used.
resonance_scattering : dict
@@ -270,6 +272,7 @@ def __init__(self, **kwargs):
self._confidence_intervals = None
self._electron_treatment = None
self._photon_transport = None
+ self._plot_seed = None
self._ptables = None
self._seed = None
self._survival_biasing = None
@@ -504,6 +507,16 @@ def photon_transport(self, photon_transport: bool):
cv.check_type('photon transport', photon_transport, bool)
self._photon_transport = photon_transport
+ @property
+ def plot_seed(self):
+ return self._plot_seed
+
+ @plot_seed.setter
+ def plot_seed(self, seed):
+ cv.check_type('random plot color seed', seed, Integral)
+ cv.check_greater_than('random plot color seed', seed, 0)
+ self._plot_seed = seed
+
@property
def seed(self) -> int:
return self._seed
@@ -1118,6 +1131,11 @@ def _create_photon_transport_subelement(self, root):
element = ET.SubElement(root, "photon_transport")
element.text = str(self._photon_transport).lower()
+ def _create_plot_seed_subelement(self, root):
+ if self._plot_seed is not None:
+ element = ET.SubElement(root, "plot_seed")
+ element.text = str(self._plot_seed)
+
def _create_ptables_subelement(self, root):
if self._ptables is not None:
element = ET.SubElement(root, "ptables")
@@ -1491,6 +1509,11 @@ def _photon_transport_from_xml_element(self, root):
if text is not None:
self.photon_transport = text in ('true', '1')
+ def _plot_seed_from_xml_element(self, root):
+ text = get_text(root, 'plot_seed')
+ if text is not None:
+ self.plot_seed = int(text)
+
def _ptables_from_xml_element(self, root):
text = get_text(root, 'ptables')
if text is not None:
@@ -1706,6 +1729,7 @@ def to_xml_element(self, mesh_memo=None):
self._create_energy_mode_subelement(element)
self._create_max_order_subelement(element)
self._create_photon_transport_subelement(element)
+ self._create_plot_seed_subelement(element)
self._create_ptables_subelement(element)
self._create_seed_subelement(element)
self._create_survival_biasing_subelement(element)
@@ -1802,6 +1826,7 @@ def from_xml_element(cls, elem, meshes=None):
settings._energy_mode_from_xml_element(elem)
settings._max_order_from_xml_element(elem)
settings._photon_transport_from_xml_element(elem)
+ settings._plot_seed_from_xml_element(elem)
settings._ptables_from_xml_element(elem)
settings._seed_from_xml_element(elem)
settings._survival_biasing_from_xml_element(elem)
diff --git a/openmc/universe.py b/openmc/universe.py
--- a/openmc/universe.py
+++ b/openmc/universe.py
@@ -423,7 +423,7 @@ def plot(self, origin=None, width=None, pixels=40000,
model = openmc.Model()
model.geometry = openmc.Geometry(self)
if seed is not None:
- model.settings.seed = seed
+ model.settings.plot_seed = seed
# Determine whether any materials contains macroscopic data and if
# so, set energy mode accordingly
| diff --git a/tests/unit_tests/test_settings.py b/tests/unit_tests/test_settings.py
--- a/tests/unit_tests/test_settings.py
+++ b/tests/unit_tests/test_settings.py
@@ -23,6 +23,7 @@ def test_export_to_xml(run_in_tmpdir):
s.surf_source_write = {'surface_ids': [2], 'max_particles': 200}
s.confidence_intervals = True
s.ptables = True
+ s.plot_seed = 100
s.survival_biasing = True
s.cutoff = {'weight': 0.25, 'weight_avg': 0.5, 'energy_neutron': 1.0e-5,
'energy_photon': 1000.0, 'energy_electron': 1.0e-5,
@@ -82,6 +83,7 @@ def test_export_to_xml(run_in_tmpdir):
assert s.surf_source_write == {'surface_ids': [2], 'max_particles': 200}
assert s.confidence_intervals
assert s.ptables
+ assert s.plot_seed == 100
assert s.seed == 17
assert s.survival_biasing
assert s.cutoff == {'weight': 0.25, 'weight_avg': 0.5,
@@ -108,7 +110,7 @@ def test_export_to_xml(run_in_tmpdir):
'energy_min': 1.0, 'energy_max': 1000.0,
'nuclides': ['U235', 'U238', 'Pu239']}
assert s.create_fission_neutrons
- assert not s.create_delayed_neutrons
+ assert not s.create_delayed_neutrons
assert s.log_grid_bins == 2000
assert not s.photon_transport
assert s.electron_treatment == 'led'
| `Universe.plot` seed does not change color behavior.
## Bug Description
I noticed today that setting the `seed` parameter when calling `Universe.plot` doesn't affect the colors in a plot.
## Steps to Reproduce
Run the following in a notebook for the assembly model located at `examples/assembly` in the repo.
<img width="1067" alt="Screenshot 2023-08-13 at 2 57 47 PM" src="https://github.com/openmc-dev/openmc/assets/4563941/06afb0a2-7d19-43e2-8d3b-4c6470a15c1c">
| 2023-08-13T20:08:31Z | [] | [] |
|
openmc-dev/openmc | 2,685 | openmc-dev__openmc-2685 | [
"2563"
] | a125f815002a24fab02a62b847cd0d240ff994d4 | diff --git a/openmc/region.py b/openmc/region.py
--- a/openmc/region.py
+++ b/openmc/region.py
@@ -4,7 +4,6 @@
import numpy as np
-from .checkvalue import check_type
from .bounding_box import BoundingBox
@@ -362,6 +361,9 @@ class Intersection(Region, MutableSequence):
def __init__(self, nodes):
self._nodes = list(nodes)
+ for node in nodes:
+ if not isinstance(node, Region):
+ raise ValueError('Intersection operands must be of type Region')
def __and__(self, other):
new = Intersection(self)
@@ -450,6 +452,9 @@ class Union(Region, MutableSequence):
def __init__(self, nodes):
self._nodes = list(nodes)
+ for node in nodes:
+ if not isinstance(node, Region):
+ raise ValueError('Union operands must be of type Region')
def __or__(self, other):
new = Union(self)
@@ -566,7 +571,8 @@ def node(self):
@node.setter
def node(self, node):
- check_type('node', node, Region)
+ if not isinstance(node, Region):
+ raise ValueError('Complement operand must be of type Region')
self._node = node
@property
| diff --git a/tests/unit_tests/test_region.py b/tests/unit_tests/test_region.py
--- a/tests/unit_tests/test_region.py
+++ b/tests/unit_tests/test_region.py
@@ -222,3 +222,21 @@ def test_translate_inplace():
# Translating a region in-place should *not* produce new surfaces
region3 = region.translate((0.5, -6.7, 3.9), inplace=True)
assert str(region) == str(region3)
+
+
+def test_invalid_operands():
+ s = openmc.Sphere()
+ z = 3
+
+ # Intersection with invalid operand
+ with pytest.raises(ValueError, match='must be of type Region'):
+ -s & +z
+
+ # Union with invalid operand
+ with pytest.raises(ValueError, match='must be of type Region'):
+ -s | +z
+
+ # Complement with invalid operand
+ with pytest.raises(ValueError, match='must be of type Region'):
+ openmc.Complement(z)
+
| Potential for error check when region uses intersection or union operations between surface objects and integers
I mistakenly tried to create a region that was the intersection of an `openmc.ZCylinder` and two integers when I actually meant to intersect with two `openmc.ZPlane` objects at those integer heights.
OpenMC allowed me to
- create a cell with this defective region
- create a geometry using that cell
but then failed when I attempted to export the geometry. I believe that maybe some error checking could be added to [region.py](https://github.com/openmc-dev/openmc/blob/610a5d8c3485034626ce54ce87a88eaa8071cc23/openmc/region.py)
I created an MWE
```python
import openmc
cyl = openmc.ZCylinder(r=1.0)
z_lower_coord = 1
z_upper_coord = 2
region = -cyl & +z_lower_coord & +z_upper_coord
finite_cylinder = openmc.Cell(region=region)
geom = openmc.Geometry([finite_cylinder])
geom.export_to_xml()
```
which generates this error for me
```
Traceback (most recent call last):
File "fake_region_mwe.py", line 9, in <module>
geom.export_to_xml()
File "openmc/openmc/geometry.py", line 158, in export_to_xml
root_element = self.to_xml_element(remove_surfs)
File "openmc/openmc/geometry.py", line 132, in to_xml_element
self.root_universe.create_xml_subelement(element, memo=set())
File "openmc/openmc/universe.py", line 689, in create_xml_subelement
cell_element = cell.create_xml_subelement(xml_element, memo)
File "openmc/openmc/cell.py", line 630, in create_xml_subelement
create_surface_elements(self.region, xml_element, memo)
File "openmc/openmc/cell.py", line 627, in create_surface_elements
create_surface_elements(subnode, element, memo)
File "openmc/openmc/cell.py", line 626, in create_surface_elements
for subnode in node:
TypeError: 'int' object is not iterable
```
Tagging @pshriwise who understands the inner workings better in case anyone wants to have a discussion on more error checking.
| 2023-09-06T02:51:50Z | [] | [] |
|
openmc-dev/openmc | 2,694 | openmc-dev__openmc-2694 | [
"2692"
] | 7b0eb9d4026bcd461b9abf6ed721ee6ad0d63873 | diff --git a/openmc/deplete/helpers.py b/openmc/deplete/helpers.py
--- a/openmc/deplete/helpers.py
+++ b/openmc/deplete/helpers.py
@@ -268,6 +268,11 @@ def nuclides(self, nuclides):
if self._reactions_direct and self._nuclides_direct is None:
self._rate_tally.nuclides = nuclides
+ # Make sure nuclide data is loaded
+ for nuclide in self.nuclides:
+ if nuclide not in openmc.lib.nuclides:
+ openmc.lib.load_nuclide(nuclide)
+
def generate_tallies(self, materials, scores):
"""Produce multigroup flux spectrum tally
| diff --git a/tests/unit_tests/test_deplete_activation.py b/tests/unit_tests/test_deplete_activation.py
--- a/tests/unit_tests/test_deplete_activation.py
+++ b/tests/unit_tests/test_deplete_activation.py
@@ -11,7 +11,7 @@
@pytest.fixture
def model():
"""Sphere of single nuclide"""
- model = openmc.model.Model()
+ model = openmc.Model()
w = openmc.Material(name='tungsten')
w.add_nuclide('W186', 1.0)
@@ -161,3 +161,30 @@ def test_decay(run_in_tmpdir):
# Ensure density goes down by a factor of 2 after each half-life
assert atoms[1] / atoms[0] == pytest.approx(0.5)
assert atoms[2] / atoms[1] == pytest.approx(0.25)
+
+
+def test_flux_rr_missing_nuclide(run_in_tmpdir, model):
+ # Create two-nuclide depletion chain -- since W184 is not in the model, this
+ # test ensures that FluxCollapseHelper loads missing nuclides appropriately
+ chain = openmc.deplete.Chain()
+ w184 = openmc.deplete.Nuclide('W184')
+ w184.add_reaction('(n,gamma)', None, 0.0, 1.0)
+ chain.add_nuclide(w184)
+ w186 = openmc.deplete.Nuclide('W186')
+ w186.add_reaction('(n,gamma)', None, 0.0, 1.0)
+ chain.add_nuclide(w186)
+ chain.export_to_xml('test_chain.xml')
+
+ # Create transport operator
+ op = openmc.deplete.CoupledOperator(
+ model, 'test_chain.xml',
+ normalization_mode="source-rate",
+ reaction_rate_mode="flux",
+ reaction_rate_opts={'energies': [0.0, 20.0e6]},
+ )
+
+ # Deplete with two decay steps
+ integrator = openmc.deplete.PredictorIntegrator(
+ op, [100.0], source_rates=[10.0]
+ )
+ integrator.integrate()
| Depletion flux mode reaction rate reconstruction broken
<!--
If you are a user of OpenMC and are running into trouble with the code or are
seeking general user support, we highly recommend posting on the OpenMC
discourse forum first. GitHub issues should be used specifically for bug reports
and feature requests.
https://openmc.discourse.group/
-->
## Bug Description
<!--A clear and concise description of the problem (Note: A missing feature is not a bug).-->
The flux mode reaction rate reconstruction method causes OpenMC to crash after step 0, because other nuclides from the chain are not being loaded.
## Steps to Reproduce
<!--Steps to reproduce the behavior (input file, or modifications to an existing input file, etc.)-->
Go to `examples/pincell_depletion`, and define the depletion operator as:
```
chain_file = 'chain_simple.xml'
op = openmc.deplete.CoupledOperator(model, chain_file,
reaction_rate_mode="flux", reaction_rate_opts=
{'energies':openmc.mgxs.GROUP_STRUCTURES['SHEM-361']})
```
The simulation crashes with the message:
```
k-effective (Collision) = 1.16273 +/- 0.00361
k-effective (Track-length) = 1.15901 +/- 0.00440
k-effective (Absorption) = 1.16493 +/- 0.00321
Combined k-effective = 1.16348 +/- 0.00277
Leakage Fraction = 0.00000 +/- 0.00000
Traceback (most recent call last):
File "/home/gavin/Code/openmc/openmc/lib/nuclide.py", line 115, in __getitem__
_dll.openmc_get_nuclide_index(key.encode(), index)
File "/home/gavin/Code/openmc/openmc/lib/error.py", line 33, in _error_handler
raise exc.DataError(msg)
openmc.exceptions.DataError: No nuclide named 'I135' has been loaded.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/gavin/Code/openmc/examples/pincell_depletion/run_depletion.py", line 100, in <module>
integrator.integrate()
File "/home/gavin/Code/openmc/openmc/deplete/abc.py", line 790, in integrate
n, res = self._get_bos_data_from_operator(i, source_rate, n)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gavin/Code/openmc/openmc/deplete/abc.py", line 743, in _get_bos_data_from_operator
res = self.operator(x, source_rate)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gavin/Code/openmc/openmc/deplete/coupled_operator.py", line 457, in __call__
rates = self._calculate_reaction_rates(source_rate)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gavin/Code/openmc/openmc/deplete/openmc_operator.py", line 502, in _calculate_reaction_rates
tally_rates = self._rate_helper.get_material_rates(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gavin/Code/openmc/openmc/deplete/helpers.py", line 391, in get_material_rates
nuc = openmc.lib.nuclides[name]
~~~~~~~~~~~~~~~~~~~^^^^^^
File "/home/gavin/Code/openmc/openmc/lib/nuclide.py", line 118, in __getitem__
raise KeyError(str(e))
KeyError: "No nuclide named 'I135' has been loaded."
```
## Environment
<!--Operating system, OpenMC version, how OpenMC was installed, nuclear data being used, etc.-->
"I use arch btw"
```
gpad% openmc -v
OpenMC version 0.13.4
Git SHA1: bf7a079b2c84d02f3636dd1bd185e1e326469189
Copyright (c) 2011-2023 MIT, UChicago Argonne LLC, and contributors
MIT/X license at <https://docs.openmc.org/en/latest/license.html>
Build type: RelWithDebInfo
Compiler ID: GNU 13.2.1
MPI enabled: no
Parallel HDF5 enabled: no
PNG support: yes
DAGMC support: no
libMesh support: no
MCPL support: no
NCrystal support: no
Coverage testing: no
Profiling flags: no
```
| 2023-09-14T22:50:46Z | [] | [] |
|
openmc-dev/openmc | 2,730 | openmc-dev__openmc-2730 | [
"2720"
] | e851c57b7bc77d059ed15244ac4891aaead8c726 | diff --git a/openmc/mesh.py b/openmc/mesh.py
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -179,18 +179,18 @@ def vertices(self):
-------
vertices : numpy.ndarray
Returns a numpy.ndarray representing the coordinates of the mesh
- vertices with a shape equal to (ndim, dim1 + 1, ..., dimn + 1). Can be
- unpacked along the first dimension with xx, yy, zz = mesh.vertices.
+ vertices with a shape equal to (dim1 + 1, ..., dimn + 1, ndim). X, Y, Z values
+ can be unpacked with xx, yy, zz = np.rollaxis(mesh.vertices, -1).
"""
return self._generate_vertices(*self._grids)
@staticmethod
def _generate_vertices(i_grid, j_grid, k_grid):
- """Returns an array with shape (3, i_grid.size+1, j_grid.size+1, k_grid.size+1)
+ """Returns an array with shape (i_grid.size, j_grid.size, k_grid.size, 3)
containing the corner vertices of mesh elements.
"""
- return np.stack(np.meshgrid(i_grid, j_grid, k_grid, indexing='ij'), axis=0)
+ return np.stack(np.meshgrid(i_grid, j_grid, k_grid, indexing='ij'), axis=-1)
@staticmethod
def _generate_edge_midpoints(grids):
@@ -206,7 +206,7 @@ def _generate_edge_midpoints(grids):
midpoint_grids : list of numpy.ndarray
The edge midpoints for the i, j, and k midpoints of each element in
i, j, k ordering. The shapes of the resulting grids are
- [(3, ni-1, nj, nk), (3, ni, nj-1, nk), (3, ni, nj, nk-1)]
+ [(ni-1, nj, nk, 3), (ni, nj-1, nk, 3), (ni, nj, nk-1, 3)]
"""
# generate a set of edge midpoints for each dimension
midpoint_grids = []
@@ -216,7 +216,7 @@ def _generate_edge_midpoints(grids):
# each grid is comprised of the mid points for one dimension and the
# corner vertices of the other two
for dims in ((0, 1, 2), (1, 0, 2), (2, 0, 1)):
- # compute the midpoints along the first dimension
+ # compute the midpoints along the last dimension
midpoints = grids[dims[0]][:-1] + 0.5 * np.diff(grids[dims[0]])
coords = (midpoints, grids[dims[1]], grids[dims[2]])
@@ -251,17 +251,16 @@ def centroids(self):
-------
centroids : numpy.ndarray
Returns a numpy.ndarray representing the mesh element centroid
- coordinates with a shape equal to (ndim, dim1, ..., dimn). Can be
- unpacked along the first dimension with xx, yy, zz = mesh.centroids.
-
-
+ coordinates with a shape equal to (dim1, ..., dimn, ndim). X,
+ Y, Z values can be unpacked with xx, yy, zz =
+ np.rollaxis(mesh.centroids, -1).
"""
ndim = self.n_dimension
# this line ensures that the vertices aren't adjusted by the origin or
# converted to the Cartesian system for cylindrical and spherical meshes
vertices = StructuredMesh.vertices.fget(self)
- s0 = (slice(None),) + (slice(0, -1),)*ndim
- s1 = (slice(None),) + (slice(1, None),)*ndim
+ s0 = (slice(0, -1),)*ndim + (slice(None),)
+ s1 = (slice(1, None),)*ndim + (slice(None),)
return (vertices[s0] + vertices[s1]) / 2
@property
@@ -351,10 +350,8 @@ def _create_vtk_structured_grid(self):
import vtk
from vtk.util import numpy_support as nps
- vertices = self.vertices.T.reshape(-1, 3)
-
vtkPts = vtk.vtkPoints()
- vtkPts.SetData(nps.numpy_to_vtk(vertices, deep=True))
+ vtkPts.SetData(nps.numpy_to_vtk(np.swapaxes(self.vertices, 0, 2).reshape(-1, 3), deep=True))
vtk_grid = vtk.vtkStructuredGrid()
vtk_grid.SetPoints(vtkPts)
vtk_grid.SetDimensions(*[dim + 1 for dim in self.dimension])
@@ -373,7 +370,7 @@ def _create_vtk_unstructured_grid(self):
import vtk
from vtk.util import numpy_support as nps
- corner_vertices = self.vertices.T.reshape(-1, 3)
+ corner_vertices = np.swapaxes(self.vertices, 0, 2).reshape(-1, 3)
vtkPts = vtk.vtkPoints()
vtk_grid = vtk.vtkUnstructuredGrid()
@@ -415,7 +412,7 @@ def _insert_point(pnt):
# list of point IDs
midpoint_vertices = self.midpoint_vertices
for edge_grid in midpoint_vertices:
- for pnt in edge_grid.T.reshape(-1, 3):
+ for pnt in np.swapaxes(edge_grid, 0, 2).reshape(-1, 3):
point_ids.append(_insert_point(pnt))
# determine how many elements in each dimension
@@ -448,7 +445,7 @@ def _insert_point(pnt):
# initial offset for corner vertices and midpoint dimension
flat_idx = corner_vertices.shape[0] + sum(n_midpoint_vertices[:dim])
# generate a flat index into the table of point IDs
- midpoint_shape = midpoint_vertices[dim].shape[1:]
+ midpoint_shape = midpoint_vertices[dim].shape[:-1]
flat_idx += np.ravel_multi_index((i+di, j+dj, k+dk),
midpoint_shape,
order='F')
@@ -1178,7 +1175,7 @@ class CylindricalMesh(StructuredMesh):
Parameters
----------
r_grid : numpy.ndarray
- 1-D array of mesh boundary points along the r-axis.
+ 1-D array of mesh boundary points along the r-axis
Requirement is r >= 0.
z_grid : numpy.ndarray
1-D array of mesh boundary points along the z-axis relative to the
@@ -1543,14 +1540,14 @@ def centroids_cylindrical(self):
@staticmethod
def _convert_to_cartesian(arr, origin: Sequence[float]):
- """Converts an array with xyz values in the first dimension (shape (3, ...))
+ """Converts an array with r, phi, z values in the last dimension (shape (..., 3))
to Cartesian coordinates.
"""
- x = arr[0, ...] * np.cos(arr[1, ...]) + origin[0]
- y = arr[0, ...] * np.sin(arr[1, ...]) + origin[1]
- arr[0, ...] = x
- arr[1, ...] = y
- arr[2, ...] += origin[2]
+ x = arr[..., 0] * np.cos(arr[..., 1]) + origin[0]
+ y = arr[..., 0] * np.sin(arr[..., 1]) + origin[1]
+ arr[..., 0] = x
+ arr[..., 1] = y
+ arr[..., 2] += origin[2]
return arr
@@ -1839,16 +1836,16 @@ def centroids_spherical(self):
@staticmethod
def _convert_to_cartesian(arr, origin: Sequence[float]):
- """Converts an array with xyz values in the first dimension (shape (3, ...))
+ """Converts an array with r, theta, phi values in the last dimension (shape (..., 3))
to Cartesian coordinates.
"""
- r_xy = arr[0, ...] * np.sin(arr[1, ...])
- x = r_xy * np.cos(arr[2, ...])
- y = r_xy * np.sin(arr[2, ...])
- z = arr[0, ...] * np.cos(arr[1, ...])
- arr[0, ...] = x + origin[0]
- arr[1, ...] = y + origin[1]
- arr[2, ...] = z + origin[2]
+ r_xy = arr[..., 0] * np.sin(arr[..., 1])
+ x = r_xy * np.cos(arr[..., 2])
+ y = r_xy * np.sin(arr[..., 2])
+ z = arr[..., 0] * np.cos(arr[..., 1])
+ arr[..., 0] = x + origin[0]
+ arr[..., 1] = y + origin[1]
+ arr[..., 2] = z + origin[2]
return arr
@@ -1891,14 +1888,14 @@ class UnstructuredMesh(MeshBase):
volumes : Iterable of float
Volumes of the unstructured mesh elements
centroids : numpy.ndarray
- Centroids of the mesh elements with array shape (3, n_elements)
+ Centroids of the mesh elements with array shape (n_elements, 3)
vertices : numpy.ndarray
- Coordinates of the mesh vertices with array shape (3, n_elements)
+ Coordinates of the mesh vertices with array shape (n_elements, 3)
.. versionadded:: 0.13.1
connectivity : numpy.ndarray
- Connectivity of the elements with array shape (8, n_elements)
+ Connectivity of the elements with array shape (n_elements, 8)
.. versionadded:: 0.13.1
element_types : Iterable of integers
@@ -1985,11 +1982,11 @@ def total_volume(self):
@property
def vertices(self):
- return self._vertices.T
+ return self._vertices
@property
def connectivity(self):
- return self._connectivity.T
+ return self._connectivity
@property
def element_types(self):
@@ -1997,7 +1994,7 @@ def element_types(self):
@property
def centroids(self):
- return np.array([self.centroid(i) for i in range(self.n_elements)]).T
+ return np.array([self.centroid(i) for i in range(self.n_elements)])
@property
def n_elements(self):
@@ -2053,11 +2050,11 @@ def centroid(self, bin: int):
x, y, z values of the element centroid
"""
- conn = self.connectivity[:, bin]
+ conn = self.connectivity[bin]
# remove invalid connectivity values
conn = conn[conn >= 0]
- coords = self.vertices[:, conn]
- return coords.mean(axis=1)
+ coords = self.vertices[conn]
+ return coords.mean(axis=0)
def write_vtk_mesh(self, **kwargs):
"""Map data to unstructured VTK mesh elements.
@@ -2120,12 +2117,12 @@ def write_data_to_vtk(
grid = vtk.vtkUnstructuredGrid()
vtk_pnts = vtk.vtkPoints()
- vtk_pnts.SetData(nps.numpy_to_vtk(self.vertices.T))
+ vtk_pnts.SetData(nps.numpy_to_vtk(self.vertices))
grid.SetPoints(vtk_pnts)
n_skipped = 0
elems = []
- for elem_type, conn in zip(self.element_types, self.connectivity.T):
+ for elem_type, conn in zip(self.element_types, self.connectivity):
if elem_type == self._LINEAR_TET:
elem = vtk.vtkTetra()
elif elem_type == self._LINEAR_HEX:
| diff --git a/tests/regression_tests/unstructured_mesh/test.py b/tests/regression_tests/unstructured_mesh/test.py
--- a/tests/regression_tests/unstructured_mesh/test.py
+++ b/tests/regression_tests/unstructured_mesh/test.py
@@ -54,7 +54,7 @@ def _compare_results(self):
exp_vertex = (-10.0, -10.0, 10.0)
exp_centroid = (-9.0, -9.0, 9.0)
- np.testing.assert_array_equal(umesh.vertices[:, 0], exp_vertex)
+ np.testing.assert_array_equal(umesh.vertices[0], exp_vertex)
np.testing.assert_array_equal(umesh.centroid(0), exp_centroid)
# loop over the tallies and get data
diff --git a/tests/unit_tests/test_cylindrical_mesh.py b/tests/unit_tests/test_cylindrical_mesh.py
--- a/tests/unit_tests/test_cylindrical_mesh.py
+++ b/tests/unit_tests/test_cylindrical_mesh.py
@@ -98,7 +98,7 @@ def test_offset_mesh(run_in_tmpdir, model, estimator, origin):
centroids = mesh.centroids
for ijk in mesh.indices:
i, j, k = np.array(ijk) - 1
- if model.geometry.find(centroids[:, i, j, k]):
+ if model.geometry.find(centroids[i, j, k]):
mean[i, j, k] == 0.0
else:
mean[i, j, k] != 0.0
diff --git a/tests/unit_tests/test_mesh.py b/tests/unit_tests/test_mesh.py
--- a/tests/unit_tests/test_mesh.py
+++ b/tests/unit_tests/test_mesh.py
@@ -4,6 +4,7 @@
import pytest
import openmc
+from openmc import RegularMesh, RectilinearMesh, CylindricalMesh, SphericalMesh
@pytest.mark.parametrize("val_left,val_right", [(0, 0), (-1., -1.), (2.0, 2)])
def test_raises_error_when_flat(val_left, val_right):
@@ -162,29 +163,80 @@ def test_centroids():
mesh.lower_left = (1., 2., 3.)
mesh.upper_right = (11., 12., 13.)
mesh.dimension = (1, 1, 1)
- np.testing.assert_array_almost_equal(mesh.centroids[:, 0, 0, 0], [6., 7., 8.])
+ np.testing.assert_array_almost_equal(mesh.centroids[0, 0, 0], [6., 7., 8.])
# rectilinear mesh
mesh = openmc.RectilinearMesh()
mesh.x_grid = [1., 11.]
mesh.y_grid = [2., 12.]
mesh.z_grid = [3., 13.]
- np.testing.assert_array_almost_equal(mesh.centroids[:, 0, 0, 0], [6., 7., 8.])
+ np.testing.assert_array_almost_equal(mesh.centroids[0, 0, 0], [6., 7., 8.])
# cylindrical mesh
mesh = openmc.CylindricalMesh(r_grid=(0, 10), z_grid=(0, 10), phi_grid=(0, np.pi))
- np.testing.assert_array_almost_equal(mesh.centroids[:, 0, 0, 0], [0.0, 5.0, 5.0])
+ np.testing.assert_array_almost_equal(mesh.centroids[0, 0, 0], [0.0, 5.0, 5.0])
# ensure that setting an origin is handled correctly
mesh.origin = (5.0, 0, -10)
- np.testing.assert_array_almost_equal(mesh.centroids[:, 0, 0, 0], [5.0, 5.0, -5.0])
+ np.testing.assert_array_almost_equal(mesh.centroids[0, 0, 0], [5.0, 5.0, -5.0])
# spherical mesh, single element xyz-positive octant
mesh = openmc.SphericalMesh(r_grid=[0, 10], theta_grid=[0, 0.5*np.pi], phi_grid=[0, np.pi])
x = 5.*np.cos(0.5*np.pi)*np.sin(0.25*np.pi)
y = 5.*np.sin(0.5*np.pi)*np.sin(0.25*np.pi)
z = 5.*np.sin(0.25*np.pi)
- np.testing.assert_array_almost_equal(mesh.centroids[:, 0, 0, 0], [x, y, z])
+ np.testing.assert_array_almost_equal(mesh.centroids[0, 0, 0], [x, y, z])
mesh.origin = (-5.0, -5.0, 5.0)
- np.testing.assert_array_almost_equal(mesh.centroids[:, 0, 0, 0], [x-5.0, y-5.0, z+5.0])
+ np.testing.assert_array_almost_equal(mesh.centroids[0, 0, 0], [x-5.0, y-5.0, z+5.0])
+
+
[email protected]('mesh_type', ('regular', 'rectilinear', 'cylindrical', 'spherical'))
+def test_mesh_vertices(mesh_type):
+
+ ijk = (2, 3, 2)
+
+ # create a new mesh object
+ if mesh_type == 'regular':
+ mesh = openmc.RegularMesh()
+ ll = np.asarray([0.]*3)
+ width = np.asarray([0.5]*3)
+ mesh.lower_left = ll
+ mesh.width = width
+ mesh.dimension = (5, 7, 9)
+
+ # spot check that an element has the correct vertex coordinates asociated with it
+ # (using zero-indexing here)
+ exp_i_j_k = ll + np.asarray(ijk, dtype=float) * width
+ np.testing.assert_equal(mesh.vertices[ijk], exp_i_j_k)
+
+ # shift the mesh using the llc
+ shift = np.asarray((3.0, 6.0, 10.0))
+ mesh.lower_left += shift
+ np.testing.assert_equal(mesh.vertices[ijk], exp_i_j_k+shift)
+ elif mesh_type == 'rectilinear':
+ mesh = openmc.RectilinearMesh()
+ w = np.asarray([0.5] * 3)
+ ll = np.asarray([0.]*3)
+ dims = (5, 7, 9)
+ mesh.x_grid = np.linspace(ll[0], w[0]*dims[0], dims[0])
+ mesh.y_grid = np.linspace(ll[1], w[1]*dims[1], dims[1])
+ mesh.z_grid = np.linspace(ll[2], w[2]*dims[2], dims[2])
+ exp_vert = np.asarray((mesh.x_grid[2], mesh.y_grid[3], mesh.z_grid[2]))
+ np.testing.assert_equal(mesh.vertices[ijk], exp_vert)
+ elif mesh_type == 'cylindrical':
+ r_grid = np.linspace(0, 5, 10)
+ z_grid = np.linspace(-10, 10, 20)
+ phi_grid = np.linspace(0, 2*np.pi, 8)
+ mesh = openmc.CylindricalMesh(r_grid=r_grid, z_grid=z_grid, phi_grid=phi_grid)
+ exp_vert = np.asarray((mesh.r_grid[2], mesh.phi_grid[3], mesh.z_grid[2]))
+ np.testing.assert_equal(mesh.vertices_cylindrical[ijk], exp_vert)
+ elif mesh_type == 'spherical':
+ r_grid = np.linspace(0, 13, 14)
+ theta_grid = np.linspace(0, np.pi, 11)
+ phi_grid = np.linspace(0, 2*np.pi, 7)
+ mesh = openmc.SphericalMesh(r_grid=r_grid, theta_grid=theta_grid, phi_grid=phi_grid)
+ exp_vert = np.asarray((mesh.r_grid[2], mesh.theta_grid[3], mesh.phi_grid[2]))
+ np.testing.assert_equal(mesh.vertices_spherical[ijk], exp_vert)
+
+
diff --git a/tests/unit_tests/test_spherical_mesh.py b/tests/unit_tests/test_spherical_mesh.py
--- a/tests/unit_tests/test_spherical_mesh.py
+++ b/tests/unit_tests/test_spherical_mesh.py
@@ -102,7 +102,7 @@ def test_offset_mesh(run_in_tmpdir, model, estimator, origin):
centroids = mesh.centroids
for ijk in mesh.indices:
i, j, k = np.array(ijk) - 1
- if model.geometry.find(centroids[:, i, j, k]):
+ if model.geometry.find(centroids[i, j, k]):
mean[i, j, k] == 0.0
else:
mean[i, j, k] != 0.0
| Shuffle array shapes returned from mesh classes
Based on discussion with @paulromano and @eepeterson:
The shape of vertices, and centroids returned from our mesh classes is currently `(ndim, dim0, ..., dimn)`. While this is convenient for unpacking x, y, and z coordinates in a way that is useful for some plotting operations,
```python
xx, yy, zz = mesh.vertices
```
it makes what indexing a centroid or vertex by an `ijk` tuple (i.e. `(2, 3, 6)` counterintuitive
```python
centroid = mesh.centroids[(:, *ijk)]
```
These properties of the mesh class will be updated to a shape of `(dim0, ..., dimn, ndim)` to allow indexing to occur more naturally:
```python
centroid = mesh.centroids[ijk]
```
Note that x, y, z values can still be unpacked fairly easily with the following command:
```python
xx, yy, zz = np.rollaxis(mesh.vertices, -1)
```
| 2023-10-17T18:09:03Z | [] | [] |
|
openmc-dev/openmc | 2,840 | openmc-dev__openmc-2840 | [
"2839"
] | d8e9d58c5e461b3b16345f25c4741027c915a297 | diff --git a/openmc/deplete/coupled_operator.py b/openmc/deplete/coupled_operator.py
--- a/openmc/deplete/coupled_operator.py
+++ b/openmc/deplete/coupled_operator.py
@@ -178,10 +178,6 @@ class CoupledOperator(OpenMCOperator):
----------
model : openmc.model.Model
OpenMC model object
- geometry : openmc.Geometry
- OpenMC geometry object
- settings : openmc.Settings
- OpenMC settings object
output_dir : pathlib.Path
Path to output directory to save results.
round_number : bool
@@ -242,8 +238,6 @@ def __init__(self, model, chain_file=None, prev_results=None,
warn("Fission Q dictionary will not be used")
fission_q = None
self.model = model
- self.settings = model.settings
- self.geometry = model.geometry
# determine set of materials in the model
if not model.materials:
@@ -358,7 +352,7 @@ def _get_helper_classes(self, helper_kwargs):
if normalization_mode == "fission-q":
self._normalization_helper = ChainFissionHelper()
elif normalization_mode == "energy-deposition":
- score = "heating" if self.settings.photon_transport else "heating-local"
+ score = "heating" if self.model.settings.photon_transport else "heating-local"
self._normalization_helper = EnergyScoreHelper(score)
else:
self._normalization_helper = SourceRateHelper()
@@ -380,8 +374,12 @@ def initial_condition(self):
# Create XML files
if comm.rank == 0:
- self.geometry.export_to_xml()
- self.settings.export_to_xml()
+ self.model.geometry.export_to_xml()
+ self.model.settings.export_to_xml()
+ if self.model.plots:
+ self.model.plots.export_to_xml()
+ if self.model.tallies:
+ self.model.tallies.export_to_xml()
self._generate_materials_xml()
# Initialize OpenMC library
@@ -528,6 +526,36 @@ def finalize(self):
if self.cleanup_when_done:
openmc.lib.finalize()
+ # The next few class variables and methods should be removed after one
+ # release cycle or so. For now, we will provide compatibility to
+ # accessing CoupledOperator.settings and CoupledOperator.geometry. In
+ # the future these should stay on the Model class.
+
+ var_warning_msg = "The CoupledOperator.{0} variable should be \
+accessed through CoupledOperator.model.{0}."
+ geometry_warning_msg = var_warning_msg.format("geometry")
+ settings_warning_msg = var_warning_msg.format("settings")
+
+ @property
+ def settings(self):
+ warn(self.settings_warning_msg, FutureWarning)
+ return self.model.settings
+
+ @settings.setter
+ def settings(self, new_settings):
+ warn(self.settings_warning_msg, FutureWarning)
+ self.model.settings = new_settings
+
+ @property
+ def geometry(self):
+ warn(self.geometry_warning_msg, FutureWarning)
+ return self.model.geometry
+
+ @geometry.setter
+ def geometry(self, new_geometry):
+ warn(self.geometry_warning_msg, FutureWarning)
+ self.model.geometry = new_geometry
+
# Retain deprecated name for the time being
def Operator(*args, **kwargs):
| diff --git a/tests/unit_tests/test_deplete_coupled_operator.py b/tests/unit_tests/test_deplete_coupled_operator.py
--- a/tests/unit_tests/test_deplete_coupled_operator.py
+++ b/tests/unit_tests/test_deplete_coupled_operator.py
@@ -38,7 +38,8 @@ def model():
pin_surfaces = [openmc.ZCylinder(r=r) for r in radii]
pin_univ = openmc.model.pin(pin_surfaces, materials)
- bound_box = openmc.model.RectangularPrism(1.24, 1.24, boundary_type="reflective")
+ bound_box = openmc.model.RectangularPrism(
+ 1.24, 1.24, boundary_type="reflective")
root_cell = openmc.Cell(fill=pin_univ, region=-bound_box)
geometry = openmc.Geometry([root_cell])
@@ -95,7 +96,7 @@ def test_diff_volume_method_match_cell(model_with_volumes):
chain_file=CHAIN_PATH
)
- all_cells = list(operator.geometry.get_all_cells().values())
+ all_cells = list(operator.model.geometry.get_all_cells().values())
assert all_cells[0].fill.volume == 4.19
assert all_cells[1].fill.volume == 33.51
# mat2 is not depletable
@@ -112,9 +113,8 @@ def test_diff_volume_method_divide_equally(model_with_volumes):
chain_file=CHAIN_PATH
)
- all_cells = list(operator.geometry.get_all_cells().values())
+ all_cells = list(operator.model.geometry.get_all_cells().values())
assert all_cells[0].fill[0].volume == 51
assert all_cells[1].fill[0].volume == 51
# mat2 is not depletable
assert all_cells[2].fill.volume is None
-
diff --git a/tests/unit_tests/test_model.py b/tests/unit_tests/test_model.py
--- a/tests/unit_tests/test_model.py
+++ b/tests/unit_tests/test_model.py
@@ -457,6 +457,20 @@ def test_deplete(run_in_tmpdir, pin_model_attributes, mpi_intracomm):
assert after_xe + after_u == pytest.approx(initial_u, abs=1e-15)
assert test_model.is_initialized is False
+ # check the tally output
+ def check_tally_output():
+ with openmc.StatePoint('openmc_simulation_n0.h5') as sp:
+ flux = sp.get_tally(id=1).get_values(scores=['flux'])[0, 0, 0]
+ fission = sp.get_tally(id=1).get_values(
+ scores=['fission'])[0, 0, 0]
+
+ # we're mainly just checking that the result was produced,
+ # so a rough numerical comparison doesn't hurt to have.
+ assert flux == pytest.approx(13.1, abs=0.2)
+ assert fission == pytest.approx(0.47, abs=0.2)
+
+ check_tally_output()
+
# Reset the initial material densities
mats[0].nuclides.clear()
densities = initial_mat.get_nuclide_atom_densities()
@@ -481,6 +495,8 @@ def test_deplete(run_in_tmpdir, pin_model_attributes, mpi_intracomm):
assert after_xe == pytest.approx(after_lib_xe, abs=1e-15)
assert after_u == pytest.approx(after_lib_u, abs=1e-15)
+ check_tally_output()
+
test_model.finalize_lib()
@@ -531,6 +547,7 @@ def test_calc_volumes(run_in_tmpdir, pin_model_attributes, mpi_intracomm):
test_model.finalize_lib()
+
def test_model_xml(run_in_tmpdir):
# load a model from examples
@@ -549,6 +566,7 @@ def test_model_xml(run_in_tmpdir):
# XML files
new_model.export_to_xml()
+
def test_single_xml_exec(run_in_tmpdir):
pincell_model = openmc.examples.pwr_pin_cell()
| Tallies ignored or not output in depletion calculations
<!--
If you are a user of OpenMC and are running into trouble with the code or are
seeking general user support, we highly recommend posting on the OpenMC
discourse forum first. GitHub issues should be used specifically for bug reports
and feature requests.
https://openmc.discourse.group/
-->
## Bug Description
The expected behavior of OpenMC when run via the `CoupledOperator` for depletion is to output the tallies from the beginning of each time step in files named `openmc_simulation_n{i}.h5` where i is the time step. However, NO tallies are ever present.
## Steps to Reproduce
<!--Steps to reproduce the behavior (input file, or modifications to an existing input file, etc.)-->
Go to the classic pincell_depletion problem, and modify the steps leading to the time integration to read as:
```
tallies = openmc.Tallies()
abs_235 = openmc.Tally()
abs_235.name = 'U235 absorption'
abs_235.nuclides = ['U235']
abs_235.scores = ['absorption']
tallies.append(abs_235)
model = openmc.Model(geometry=geometry, settings=settings, tallies=tallies)
```
You're in for a big disappointment if you want to check the absorption fraction into U235 at timestep 2 though, because:
```
In [1]: import openmc
In [2]: sp = openmc.StatePoint('./openmc_simulation_n2.h5')
In [3]: sp.tallies
Out[3]: {}
```
😢
## Environment
<!--Operating system, OpenMC version, how OpenMC was installed, nuclear data being used, etc.-->
Arch linux, latest commit.
| 2024-01-14T05:20:01Z | [] | [] |
|
openmc-dev/openmc | 2,906 | openmc-dev__openmc-2906 | [
"2896"
] | 0f07420af217e2f5c6c526edbbcb45a0a6ff9394 | diff --git a/openmc/bounding_box.py b/openmc/bounding_box.py
--- a/openmc/bounding_box.py
+++ b/openmc/bounding_box.py
@@ -95,9 +95,23 @@ def __or__(self, other: BoundingBox) -> BoundingBox:
new |= other
return new
- def __contains__(self, point):
- """Check whether or not a point is in the bounding box"""
- return all(point > self.lower_left) and all(point < self.upper_right)
+ def __contains__(self, other):
+ """Check whether or not a point or another bounding box is in the bounding box.
+
+ For another bounding box to be in the parent it must lie fully inside of it.
+ """
+ # test for a single point
+ if isinstance(other, (tuple, list, np.ndarray)):
+ point = other
+ check_length("Point", point, 3, 3)
+ return all(point > self.lower_left) and all(point < self.upper_right)
+ elif isinstance(other, BoundingBox):
+ return all([p in self for p in [other.lower_left, other.upper_right]])
+ else:
+ raise TypeError(
+ f"Unable to determine if {other} is in the bounding box."
+ f" Expected a tuple or a bounding box, but {type(other)} given"
+ )
@property
def center(self) -> np.ndarray:
| diff --git a/tests/unit_tests/test_bounding_box.py b/tests/unit_tests/test_bounding_box.py
--- a/tests/unit_tests/test_bounding_box.py
+++ b/tests/unit_tests/test_bounding_box.py
@@ -78,9 +78,9 @@ def test_bounding_box_input_checking():
def test_bounding_box_extents():
- assert test_bb_1.extent['xy'] == (-10., 1., -20., 2.)
- assert test_bb_1.extent['xz'] == (-10., 1., -30., 3.)
- assert test_bb_1.extent['yz'] == (-20., 2., -30., 3.)
+ assert test_bb_1.extent["xy"] == (-10.0, 1.0, -20.0, 2.0)
+ assert test_bb_1.extent["xz"] == (-10.0, 1.0, -30.0, 3.0)
+ assert test_bb_1.extent["yz"] == (-20.0, 2.0, -30.0, 3.0)
def test_bounding_box_methods():
@@ -156,3 +156,35 @@ def test_bounding_box_methods():
assert all(test_bb[0] == [-50.1, -50.1, -12.1])
assert all(test_bb[1] == [50.1, 14.1, 50.1])
+
+
[email protected](
+ "bb, other, expected",
+ [
+ (test_bb_1, (0, 0, 0), True),
+ (test_bb_2, (3, 3, 3), False),
+ # completely disjoint
+ (test_bb_1, test_bb_2, False),
+ # contained but touching border
+ (test_bb_1, test_bb_3, False),
+ # Fully contained
+ (test_bb_1, openmc.BoundingBox((-9, -19, -29), (0, 0, 0)), True),
+ # intersecting boxes
+ (test_bb_1, openmc.BoundingBox((-9, -19, -29), (1, 2, 5)), False),
+ ],
+)
+def test_bounding_box_contains(bb, other, expected):
+ assert (other in bb) == expected
+
+
[email protected](
+ "invalid, ex",
+ [
+ ((1, 0), ValueError),
+ ((1, 2, 3, 4), ValueError),
+ ("foo", TypeError),
+ ],
+)
+def test_bounding_box_contains_checking(invalid, ex):
+ with pytest.raises(ex):
+ invalid in test_bb_1
| Implement contains for BoundingBox
## Description
Implement `__contains__` for `BoundingBox` containing either a point, or another `BoundingBox`. This means that users could then write:
`if point in box:` or `if little_box in big_box`.
## Alternatives
It is possible for users to accomplish this currently but requires some clever coding to avoid becoming difficult to read:
``` python
def in_box(point, box):
for min_p, p, max_p in zip(box.lower_left, point, box.upper_right):
if p < min_p or > max_p:
return False
return True
```
## Compatibility
This would be an enhancement, and would not alter the behavior of the existing API.
There is a risk though that users will misinterpret the results. A point in the bounding box of a volume *may* be in the volume, but not necessarily. A user could misuse this information and create problems for themselves. Also a small volume's bounding box can be completely contained in another volume's bounding box, and be completely outside that other volume.
| Turns out this was added for points in #2759 e0d03812, or 0.14.1dev. I will still implement this for nested bounding boxes. | 2024-03-11T02:40:22Z | [] | [] |
openmc-dev/openmc | 2,935 | openmc-dev__openmc-2935 | [
"2931"
] | 1a34ddf121cf3ec4929ba7cef160c96a3896dbd9 | diff --git a/openmc/model/surface_composite.py b/openmc/model/surface_composite.py
--- a/openmc/model/surface_composite.py
+++ b/openmc/model/surface_composite.py
@@ -635,7 +635,7 @@ class XConeOneSided(CompositeSurface):
z-coordinate of the apex. Defaults to 0.
r2 : float, optional
Parameter related to the aperture [:math:`\\rm cm^2`].
- It can be interpreted as the increase in the radius squared per cm along
+ It can be interpreted as the increase in the radius squared per cm along
the cone's axis of revolution.
up : bool
Whether to select the side of the cone that extends to infinity in the
@@ -695,7 +695,7 @@ class YConeOneSided(CompositeSurface):
z-coordinate of the apex. Defaults to 0.
r2 : float, optional
Parameter related to the aperture [:math:`\\rm cm^2`].
- It can be interpreted as the increase in the radius squared per cm along
+ It can be interpreted as the increase in the radius squared per cm along
the cone's axis of revolution.
up : bool
Whether to select the side of the cone that extends to infinity in the
@@ -749,7 +749,7 @@ class ZConeOneSided(CompositeSurface):
z-coordinate of the apex. Defaults to 0.
r2 : float, optional
Parameter related to the aperture [:math:`\\rm cm^2`].
- It can be interpreted as the increase in the radius squared per cm along
+ It can be interpreted as the increase in the radius squared per cm along
the cone's axis of revolution.
up : bool
Whether to select the side of the cone that extends to infinity in the
@@ -1029,9 +1029,9 @@ def _constrain_triangulation(self, points, depth=0):
-------
None
"""
- # Only attempt the triangulation up to 3 times.
- if depth > 2:
- raise RuntimeError('Could not create a valid triangulation after 3'
+ # Only attempt the triangulation up to 5 times.
+ if depth > 4:
+ raise RuntimeError('Could not create a valid triangulation after 5'
' attempts')
tri = Delaunay(points, qhull_options='QJ')
@@ -1039,7 +1039,7 @@ def _constrain_triangulation(self, points, depth=0):
# included in the triangulation, break it into two line segments.
n = len(points)
new_pts = []
- for i, j in zip(range(n), range(1, n +1)):
+ for i, j in zip(range(n), range(1, n + 1)):
# If both vertices of any edge are not found in any simplex, insert
# a new point between them.
if not any([i in s and j % n in s for s in tri.simplices]):
@@ -1077,7 +1077,8 @@ def _group_simplices(self, neighbor_map, group=None):
return group
# If group is empty, grab the next simplex in the dictionary and recurse
if group is None:
- sidx = next(iter(neighbor_map))
+ # Start with smallest neighbor lists
+ sidx = sorted(neighbor_map.items(), key=lambda item: len(item[1]))[0][0]
return self._group_simplices(neighbor_map, group=[sidx])
# Otherwise use the last simplex in the group
else:
@@ -1087,13 +1088,16 @@ def _group_simplices(self, neighbor_map, group=None):
# For each neighbor check if it is part of the same convex
# hull as the rest of the group. If yes, recurse. If no, continue on.
for n in neighbors:
- if n in group or neighbor_map.get(n, None) is None:
+ if n in group or neighbor_map.get(n) is None:
continue
test_group = group + [n]
test_point_idx = np.unique(self._tri.simplices[test_group, :])
test_points = self.points[test_point_idx]
- # If test_points are convex keep adding to this group
- if len(test_points) == len(ConvexHull(test_points).vertices):
+ test_hull = ConvexHull(test_points, qhull_options='Qc')
+ pts_on_hull = len(test_hull.vertices) + len(test_hull.coplanar)
+ # If test_points are convex (including coplanar) keep adding to
+ # this group
+ if len(test_points) == pts_on_hull:
group = self._group_simplices(neighbor_map, group=test_group)
return group
| diff --git a/tests/unit_tests/test_surface_composite.py b/tests/unit_tests/test_surface_composite.py
--- a/tests/unit_tests/test_surface_composite.py
+++ b/tests/unit_tests/test_surface_composite.py
@@ -399,6 +399,32 @@ def test_polygon():
with pytest.raises(ValueError):
openmc.model.Polygon(rz_points)
+ # Test "M" shaped polygon
+ points = np.array([[8.5151581, -17.988337],
+ [10.381711000000001, -17.988337],
+ [12.744357, -24.288728000000003],
+ [15.119406000000001, -17.988337],
+ [16.985959, -17.988337],
+ [16.985959, -27.246687],
+ [15.764328, -27.246687],
+ [15.764328, -19.116951],
+ [13.376877, -25.466951],
+ [12.118039, -25.466951],
+ [9.7305877, -19.116951],
+ [9.7305877, -27.246687],
+ [8.5151581, -27.246687]])
+
+ # Test points inside and outside by using offset method
+ m_polygon = openmc.model.Polygon(points, basis='xz')
+ inner_pts = m_polygon.offset(-0.1).points
+ assert all([(pt[0], 0, pt[1]) in -m_polygon for pt in inner_pts])
+ outer_pts = m_polygon.offset(0.1).points
+ assert all([(pt[0], 0, pt[1]) in +m_polygon for pt in outer_pts])
+
+ # Offset of -0.2 will cause self-intersection
+ with pytest.raises(ValueError):
+ m_polygon.offset(-0.2)
+
@pytest.mark.parametrize("axis", ["x", "y", "z"])
def test_cruciform_prism(axis):
| Polygon can't handle colinear points.
## Bug Description
When multiple points for `openmc.model.Polygon` are colinear the polygon decomposes in part into a line and breaks the underlying geometry engine. The question though is why would you ever specify colinear points? I was working on hackily creating polygons from an SVG file. In this case SVG interpreters don't care about colinearity, and this can happen.
I was attempting to create this:
The problematic polygon looks like:
## Steps to Reproduce
MWE:
``` python
import openmc
openmc.model.Polygon([
(43.08936, -13.206429),
(43.08936, -22.855452),
(44.236576, -22.855452),
(44.236576, -18.930111),
(44.236576, -16.989144),
(44.236576, -13.206429),
(43.08936, -13.206429),
])
```
This leads to:
``` python
QhullError Traceback (most recent call last)
Cell In[1], line 2
1 import openmc
----> 2 openmc.model.Polygon([
3 (43.08936, -13.206429),
4 (43.08936, -22.855452),
5 (44.236576, -22.855452),
6 (44.236576, -18.930111),
7 (44.236576, -16.989144),
8 (44.236576, -13.206429),
9 (43.08936, -13.206429),
10 ])
File ~/mambaforge/lib/python3.10/site-packages/openmc/model/surface_composite.py:818, in Polygon.__init__(self, points, basis)
814 self._constrain_triangulation(self._validate_points(points))
816 # Decompose the polygon into groups of simplices forming convex subsets
817 # and get the sets of (surface, operator) pairs defining the polygon
--> 818 self._surfsets = self._decompose_polygon_into_convex_sets()
820 # Set surface names as required by CompositeSurface protocol
821 surfnames = []
File ~/mambaforge/lib/python3.10/site-packages/openmc/model/surface_composite.py:1190, in Polygon._decompose_polygon_into_convex_sets(self)
1188 groups = []
1189 while neighbor_map:
-> 1190 groups.append(self._group_simplices(neighbor_map))
1191 self._groups = groups
1193 # Generate lists of (surface, operator) pairs for each convex
1194 # sub-region.
File ~/mambaforge/lib/python3.10/site-packages/openmc/model/surface_composite.py:1075, in Polygon._group_simplices(self, neighbor_map, group)
1073 if group is None:
1074 sidx = next(iter(neighbor_map))
-> 1075 return self._group_simplices(neighbor_map, group=[sidx])
1076 # Otherwise use the last simplex in the group
1077 else:
1078 sidx = group[-1]
File ~/mambaforge/lib/python3.10/site-packages/openmc/model/surface_composite.py:1090, in Polygon._group_simplices(self, neighbor_map, group)
1088 test_points = self.points[test_point_idx]
1089 # If test_points are convex keep adding to this group
-> 1090 if len(test_points) == len(ConvexHull(test_points).vertices):
1091 group = self._group_simplices(neighbor_map, group=test_group)
1092 return group
File _qhull.pyx:2431, in scipy.spatial._qhull.ConvexHull.__init__()
File _qhull.pyx:353, in scipy.spatial._qhull._Qhull.__init__()
QhullError: QH6013 qhull input error: input is less than 2-dimensional since all points have the same x coordinate 44.24
While executing: | qhull i Qt
Options selected for Qhull 2019.1.r 2019/06/21:
run-id 179452238 incidence Qtriangulate _pre-merge _zero-centrum
_max-width 9.6 Error-roundoff 3.8e-14 _one-merge 1.9e-13
_near-inside 9.5e-13 Visible-distance 7.6e-14 U-max-coplanar 7.6e-14
Width-outside 1.5e-13 _wide-facet 4.5e-13 _maxoutside 2.3e-13
```
## Environment
Openmc 0.14. See #2930 for details.
| 2024-04-03T03:39:46Z | [] | [] |
|
openmc-dev/openmc | 2,945 | openmc-dev__openmc-2945 | [
"2944"
] | c85ba93040433ee2d4be7f17d37d0831da14d2f0 | diff --git a/openmc/settings.py b/openmc/settings.py
--- a/openmc/settings.py
+++ b/openmc/settings.py
@@ -109,6 +109,10 @@ class Settings:
parallelism.
.. versionadded:: 0.12
+ max_particle_events : int
+ Maximum number of allowed particle events per source particle.
+
+ .. versionadded:: 0.14.1
max_order : None or int
Maximum scattering order to apply globally when in multi-group mode.
max_splits : int
@@ -334,6 +338,7 @@ def __init__(self, **kwargs):
self._event_based = None
self._max_particles_in_flight = None
+ self._max_particle_events = None
self._write_initial_source = None
self._weight_windows = cv.CheckedList(WeightWindows, 'weight windows')
self._weight_window_generators = cv.CheckedList(WeightWindowGenerator, 'weight window generators')
@@ -938,6 +943,16 @@ def max_particles_in_flight(self, value: int):
cv.check_greater_than('max particles in flight', value, 0)
self._max_particles_in_flight = value
+ @property
+ def max_particle_events(self) -> int:
+ return self._max_particle_events
+
+ @max_particle_events.setter
+ def max_particle_events(self, value: int):
+ cv.check_type('max particle events', value, Integral)
+ cv.check_greater_than('max particle events', value, 0)
+ self._max_particle_events = value
+
@property
def write_initial_source(self) -> bool:
return self._write_initial_source
@@ -1341,6 +1356,11 @@ def _create_max_particles_in_flight_subelement(self, root):
elem = ET.SubElement(root, "max_particles_in_flight")
elem.text = str(self._max_particles_in_flight).lower()
+ def _create_max_events_subelement(self, root):
+ if self._max_particle_events is not None:
+ elem = ET.SubElement(root, "max_particle_events")
+ elem.text = str(self._max_particle_events).lower()
+
def _create_material_cell_offsets_subelement(self, root):
if self._material_cell_offsets is not None:
elem = ET.SubElement(root, "material_cell_offsets")
@@ -1719,6 +1739,11 @@ def _max_particles_in_flight_from_xml_element(self, root):
if text is not None:
self.max_particles_in_flight = int(text)
+ def _max_particle_events_from_xml_element(self, root):
+ text = get_text(root, 'max_particle_events')
+ if text is not None:
+ self.max_particle_events = int(text)
+
def _material_cell_offsets_from_xml_element(self, root):
text = get_text(root, 'material_cell_offsets')
if text is not None:
@@ -1820,6 +1845,7 @@ def to_xml_element(self, mesh_memo=None):
self._create_delayed_photon_scaling_subelement(element)
self._create_event_based_subelement(element)
self._create_max_particles_in_flight_subelement(element)
+ self._create_max_events_subelement(element)
self._create_material_cell_offsets_subelement(element)
self._create_log_grid_bins_subelement(element)
self._create_write_initial_source_subelement(element)
@@ -1923,6 +1949,7 @@ def from_xml_element(cls, elem, meshes=None):
settings._delayed_photon_scaling_from_xml_element(elem)
settings._event_based_from_xml_element(elem)
settings._max_particles_in_flight_from_xml_element(elem)
+ settings._max_particle_events_from_xml_element(elem)
settings._material_cell_offsets_from_xml_element(elem)
settings._log_grid_bins_from_xml_element(elem)
settings._write_initial_source_from_xml_element(elem)
| diff --git a/tests/unit_tests/test_settings.py b/tests/unit_tests/test_settings.py
--- a/tests/unit_tests/test_settings.py
+++ b/tests/unit_tests/test_settings.py
@@ -27,8 +27,8 @@ def test_export_to_xml(run_in_tmpdir):
s.survival_biasing = True
s.cutoff = {'weight': 0.25, 'weight_avg': 0.5, 'energy_neutron': 1.0e-5,
'energy_photon': 1000.0, 'energy_electron': 1.0e-5,
- 'energy_positron': 1.0e-5, 'time_neutron': 1.0e-5,
- 'time_photon': 1.0e-5, 'time_electron': 1.0e-5,
+ 'energy_positron': 1.0e-5, 'time_neutron': 1.0e-5,
+ 'time_photon': 1.0e-5, 'time_electron': 1.0e-5,
'time_positron': 1.0e-5}
mesh = openmc.RegularMesh()
mesh.lower_left = (-10., -10., -10.)
@@ -59,6 +59,8 @@ def test_export_to_xml(run_in_tmpdir):
s.write_initial_source = True
s.weight_window_checkpoints = {'surface': True, 'collision': False}
+ s.max_particle_events = 100
+
# Make sure exporting XML works
s.export_to_xml()
@@ -92,7 +94,7 @@ def test_export_to_xml(run_in_tmpdir):
assert s.cutoff == {'weight': 0.25, 'weight_avg': 0.5,
'energy_neutron': 1.0e-5, 'energy_photon': 1000.0,
'energy_electron': 1.0e-5, 'energy_positron': 1.0e-5,
- 'time_neutron': 1.0e-5, 'time_photon': 1.0e-5,
+ 'time_neutron': 1.0e-5, 'time_photon': 1.0e-5,
'time_electron': 1.0e-5, 'time_positron': 1.0e-5}
assert isinstance(s.entropy_mesh, openmc.RegularMesh)
assert s.entropy_mesh.lower_left == [-10., -10., -10.]
@@ -128,3 +130,4 @@ def test_export_to_xml(run_in_tmpdir):
assert vol.lower_left == (-10., -10., -10.)
assert vol.upper_right == (10., 10., 10.)
assert s.weight_window_checkpoints == {'surface': True, 'collision': False}
+ assert s.max_particle_events == 100
| Expose a `max_events` setting.
## Description
For deep shielding problems and/or problems using weight windows, particles may exceed the maximum number of allowed events. This value is currently hard-coded in https://github.com/openmc-dev/openmc/blob/87e00f76ed6fd30b0dc10e8c86daba1f4ff7dff5/include/openmc/particle_data.h#L31-L32.
## Compatibility
Exposing this setting should be an additive change and won't break backward compatibility.
| 2024-04-08T12:02:25Z | [] | [] |
|
openmc-dev/openmc | 2,949 | openmc-dev__openmc-2949 | [
"2929"
] | fea90e0926be94627b67f9d9d2500d0def7d17ce | diff --git a/openmc/filter.py b/openmc/filter.py
--- a/openmc/filter.py
+++ b/openmc/filter.py
@@ -864,10 +864,10 @@ def mesh(self, mesh):
cv.check_type('filter mesh', mesh, openmc.MeshBase)
self._mesh = mesh
if isinstance(mesh, openmc.UnstructuredMesh):
- if mesh.volumes is None:
- self.bins = []
- else:
+ if mesh.has_statepoint_data:
self.bins = list(range(len(mesh.volumes)))
+ else:
+ self.bins = []
else:
self.bins = list(mesh.indices)
@@ -982,7 +982,7 @@ def from_xml_element(cls, elem, **kwargs):
if translation:
out.translation = [float(x) for x in translation.split()]
return out
-
+
class MeshBornFilter(MeshFilter):
"""Filter events by the mesh cell a particle originated from.
diff --git a/openmc/mesh.py b/openmc/mesh.py
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -3,6 +3,7 @@
import warnings
from abc import ABC, abstractmethod
from collections.abc import Iterable
+from functools import wraps
from math import pi, sqrt, atan2
from numbers import Integral, Real
from pathlib import Path
@@ -39,7 +40,8 @@ class MeshBase(IDManagerMixin, ABC):
bounding_box : openmc.BoundingBox
Axis-aligned bounding box of the mesh as defined by the upper-right and
lower-left coordinates.
-
+ indices : Iterable of tuple
+ An iterable of mesh indices for each mesh element, e.g. [(1, 1, 1), (2, 1, 1), ...]
"""
next_id = 1
@@ -66,6 +68,11 @@ def name(self, name: str):
def bounding_box(self) -> openmc.BoundingBox:
return openmc.BoundingBox(self.lower_left, self.upper_right)
+ @property
+ @abstractmethod
+ def indices(self):
+ pass
+
def __repr__(self):
string = type(self).__name__ + '\n'
string += '{0: <16}{1}{2}\n'.format('\tID', '=\t', self._id)
@@ -1914,6 +1921,17 @@ def _convert_to_cartesian(arr, origin: Sequence[float]):
return arr
+def require_statepoint_data(func):
+ @wraps(func)
+ def wrapper(self: UnstructuredMesh, *args, **kwargs):
+ if not self._has_statepoint_data:
+ raise AttributeError(f'The "{func.__name__}" property requires '
+ 'information about this mesh to be loaded '
+ 'from a statepoint file.')
+ return func(self, *args, **kwargs)
+ return wrapper
+
+
class UnstructuredMesh(MeshBase):
"""A 3D unstructured mesh
@@ -1990,6 +2008,7 @@ def __init__(self, filename: PathLike, library: str, mesh_id: Optional[int] = No
self.library = library
self._output = False
self.length_multiplier = length_multiplier
+ self._has_statepoint_data = False
@property
def filename(self):
@@ -2010,6 +2029,7 @@ def library(self, lib: str):
self._library = lib
@property
+ @require_statepoint_data
def size(self):
return self._size
@@ -2028,6 +2048,7 @@ def output(self, val: bool):
self._output = val
@property
+ @require_statepoint_data
def volumes(self):
"""Return Volumes for every mesh cell if
populated by a StatePoint file
@@ -2046,26 +2067,32 @@ def volumes(self, volumes: typing.Iterable[Real]):
self._volumes = volumes
@property
+ @require_statepoint_data
def total_volume(self):
return np.sum(self.volumes)
@property
+ @require_statepoint_data
def vertices(self):
return self._vertices
@property
+ @require_statepoint_data
def connectivity(self):
return self._connectivity
@property
+ @require_statepoint_data
def element_types(self):
return self._element_types
@property
+ @require_statepoint_data
def centroids(self):
return np.array([self.centroid(i) for i in range(self.n_elements)])
@property
+ @require_statepoint_data
def n_elements(self):
if self._n_elements is None:
raise RuntimeError("No information about this mesh has "
@@ -2096,6 +2123,15 @@ def dimension(self):
def n_dimension(self):
return 3
+ @property
+ @require_statepoint_data
+ def indices(self):
+ return [(i,) for i in range(self.n_elements)]
+
+ @property
+ def has_statepoint_data(self) -> bool:
+ return self._has_statepoint_data
+
def __repr__(self):
string = super().__repr__()
string += '{: <16}=\t{}\n'.format('\tFilename', self.filename)
@@ -2106,13 +2142,16 @@ def __repr__(self):
return string
@property
+ @require_statepoint_data
def lower_left(self):
return self.vertices.min(axis=0)
@property
+ @require_statepoint_data
def upper_right(self):
return self.vertices.max(axis=0)
+ @require_statepoint_data
def centroid(self, bin: int):
"""Return the vertex averaged centroid of an element
@@ -2257,6 +2296,7 @@ def from_hdf5(cls, group: h5py.Group):
library = group['library'][()].decode()
mesh = cls(filename=filename, library=library, mesh_id=mesh_id)
+ mesh._has_statepoint_data = True
vol_data = group['volumes'][()]
mesh.volumes = np.reshape(vol_data, (vol_data.shape[0],))
mesh.n_elements = mesh.volumes.size
diff --git a/openmc/source.py b/openmc/source.py
--- a/openmc/source.py
+++ b/openmc/source.py
@@ -500,9 +500,13 @@ def populate_xml_element(self, elem: ET.Element):
elem.set("mesh", str(self.mesh.id))
# write in the order of mesh indices
- for idx in self.mesh.indices:
- idx = tuple(i - 1 for i in idx)
- elem.append(self.sources[idx].to_xml_element())
+ if isinstance(self.mesh, openmc.UnstructuredMesh):
+ for s in self.sources:
+ elem.append(s.to_xml_element())
+ else:
+ for idx in self.mesh.indices:
+ idx = tuple(i - 1 for i in idx)
+ elem.append(self.sources[idx].to_xml_element())
@classmethod
def from_xml_element(cls, elem: ET.Element, meshes) -> openmc.MeshSource:
| diff --git a/tests/unit_tests/test_mesh.py b/tests/unit_tests/test_mesh.py
--- a/tests/unit_tests/test_mesh.py
+++ b/tests/unit_tests/test_mesh.py
@@ -298,3 +298,22 @@ def test_CylindricalMesh_get_indices_at_coords():
assert mesh.get_indices_at_coords([98, 200.1, 299]) == (0, 1, 0) # second angle quadrant
assert mesh.get_indices_at_coords([98, 199.9, 299]) == (0, 2, 0) # third angle quadrant
assert mesh.get_indices_at_coords([102, 199.1, 299]) == (0, 3, 0) # forth angle quadrant
+
+def test_umesh_roundtrip(run_in_tmpdir, request):
+ umesh = openmc.UnstructuredMesh(request.path.parent / 'test_mesh_tets.e', 'moab')
+ umesh.output = True
+
+ # create a tally using this mesh
+ mf = openmc.MeshFilter(umesh)
+ tally = openmc.Tally()
+ tally.filters = [mf]
+ tally.scores = ['flux']
+
+ tallies = openmc.Tallies([tally])
+ tallies.export_to_xml()
+
+ xml_tallies = openmc.Tallies.from_xml()
+ xml_tally = xml_tallies[0]
+ xml_mesh = xml_tally.filters[0].mesh
+
+ assert umesh.id == xml_mesh.id
diff --git a/tests/unit_tests/test_source_mesh.py b/tests/unit_tests/test_source_mesh.py
--- a/tests/unit_tests/test_source_mesh.py
+++ b/tests/unit_tests/test_source_mesh.py
@@ -208,23 +208,29 @@ def test_roundtrip(run_in_tmpdir, model, request):
###################
# MeshSource tests
###################
[email protected]('mesh_type', ('rectangular', 'cylindrical'))
-def test_mesh_source_independent(run_in_tmpdir, mesh_type):
[email protected]
+def void_model():
"""
A void model containing a single box
"""
- min, max = -10, 10
- box = openmc.model.RectangularParallelepiped(
- min, max, min, max, min, max, boundary_type='vacuum')
+ model = openmc.Model()
- geometry = openmc.Geometry([openmc.Cell(region=-box)])
+ box = openmc.model.RectangularParallelepiped(*[-10, 10]*3, boundary_type='vacuum')
+ model.geometry = openmc.Geometry([openmc.Cell(region=-box)])
- settings = openmc.Settings()
- settings.particles = 100
- settings.batches = 10
- settings.run_mode = 'fixed source'
+ model.settings.particles = 100
+ model.settings.batches = 10
+ model.settings.run_mode = 'fixed source'
+
+ return model
- model = openmc.Model(geometry=geometry, settings=settings)
+
[email protected]('mesh_type', ('rectangular', 'cylindrical'))
+def test_mesh_source_independent(run_in_tmpdir, void_model, mesh_type):
+ """
+ A void model containing a single box
+ """
+ model = void_model
# define a 2 x 2 x 2 mesh
if mesh_type == 'rectangular':
@@ -310,6 +316,41 @@ def test_mesh_source_independent(run_in_tmpdir, mesh_type):
assert mesh_source.strength == 1.0
[email protected]("library", ('moab', 'libmesh'))
+def test_umesh_source_independent(run_in_tmpdir, request, void_model, library):
+ import openmc.lib
+ # skip the test if the library is not enabled
+ if library == 'moab' and not openmc.lib._dagmc_enabled():
+ pytest.skip("DAGMC (and MOAB) mesh not enabled in this build.")
+
+ if library == 'libmesh' and not openmc.lib._libmesh_enabled():
+ pytest.skip("LibMesh is not enabled in this build.")
+
+ model = void_model
+
+ mesh_filename = Path(request.fspath).parent / "test_mesh_tets.e"
+ uscd_mesh = openmc.UnstructuredMesh(mesh_filename, library)
+ ind_source = openmc.IndependentSource()
+ n_elements = 12_000
+ model.settings.source = openmc.MeshSource(uscd_mesh, n_elements*[ind_source])
+ model.export_to_model_xml()
+ try:
+ openmc.lib.init()
+ openmc.lib.simulation_init()
+ sites = openmc.lib.sample_external_source(10)
+ openmc.lib.statepoint_write('statepoint.h5')
+ finally:
+ openmc.lib.finalize()
+
+ with openmc.StatePoint('statepoint.h5') as sp:
+ uscd_mesh = sp.meshes[uscd_mesh.id]
+
+ # ensure at least that all sites are inside the mesh
+ bounding_box = uscd_mesh.bounding_box
+ for site in sites:
+ assert site.r in bounding_box
+
+
def test_mesh_source_file(run_in_tmpdir):
# Creating a source file with a single particle
source_particle = openmc.SourceParticle(time=10.0)
| get UnstructuredMesh centroids and volumes without loading from statepoint
## Description
It would be useful if we can get mesh information such as volumes and centroids of the unstructured mesh. Currently this is possible if one loads in an unstructured mesh from a statepoint file but not if an UnstructuredMesh is instantiated in python like this
```
umesh = openmc.UnstructuredMesh(filename="umesh.h5m",library='moab')
umesh.centroids
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/j/openmc/openmc/mesh.py", line 2066, in centroids
return np.array([self.centroid(i) for i in range(self.n_elements)])
File "/home/j/openmc/openmc/mesh.py", line 2071, in n_elements
raise RuntimeError("No information about this mesh has "
RuntimeError: No information about this mesh has been loaded from a statepoint file.
```
This would be useful as knowing the centroids or volumes could help with defining a openmc.MeshSource. It would also bring the UnstructuredMesh behaviour more inline with the other meshes such as RegularMesh
## Alternatives
We write the UnstructuredMesh to a statepoint file, then read in the statepoint file and get the UnstructuredMesh from hdf5 then it contains centroids and volume information
## Compatibility
this would maintain the same api usage
| A good thought. I'm sure you can imagine why this is difficult from the Python API as the libraries we rely on for unstructured mesh (MOAB and libMesh) interact with OpennMC through a C++ interface. The mesh volumes are already exposed through the CAPI in the `openmc.lib` module. If the `centroids` were also to be added would that suit your needs?
A valid OpenMC problem would still need to be defined and loaded before determining your mesh source strengths, but maybe it's still useful?
latest attempt
```
import openmc
import openmc.lib
openmc.config['cross_sections'] = '/home/j/endf-b8.0-hdf5/endfb-viii.0-hdf5/cross_sections.xml'
umesh = openmc.UnstructuredMesh(filename="umesh.h5m",library='moab')
surf1 = openmc.Sphere(r=50000, boundary_type="vacuum")
region1 = -surf1
cell1 = openmc.Cell(region=region1)
my_geometry = openmc.Geometry([cell1])
my_source = openmc.IndependentSource()
my_source.space = openmc.stats.Point((0, 0, 0))
my_source.angle = openmc.stats.Isotropic()
my_source.energy = openmc.stats.Discrete([14e6], [1])
all_sources = [my_source] * 308
mesh_source = openmc.MeshSource(
mesh=umesh,
sources=all_sources,
)
my_settings = openmc.Settings()
my_settings.batches = 1
my_settings.particles = 1
my_settings.run_mode = "fixed source"
my_settings.source = mesh_source
model = openmc.model.Model(my_geometry, None, my_settings )
model.export_to_model_xml()
openmc.lib.init()
openmc.lib.UnstructuredMesh()
```
At the end, perhaps try: `unstructured_mesh = openmc.lib.meshes[umesh.id]`
Thanks Patrick
It is a bit tricky with the need to include the mesh in the model so that openmc.lib can find it.
Originally I tried to include it in the model via a MeshSource but that didn't work and raised the error
```
"/home/j/openmc/openmc/source.py", line 503, in populate_xml_element
for idx in self.mesh.indices:
AttributeError: 'UnstructuredMesh' object has no attribute 'indices'
```
```
umesh = openmc.UnstructuredMesh(filename="umesh.h5m",library='moab')
mesh_source = openmc.MeshSource(
mesh=umesh,
sources=all_sources,
)
settings.source = mesh_source # this line raises the error
```
So I shall include the mesh via a tally and then I should be able to get the fully populated unstrucutred mesh object and then I should be able to make a meshSource from it.
Adding centroids would be great. I think longer term we might want to add some extra code to meshSource or settings.source to simplify the process of having a meshsource with and unstrucutred mesh
update. I tried reading the unstructured mesh in from the statepoint and did get populated centroids and volumes. However it appears that an unstrucutred mesh can't be used as a mesh for an openmc.MeshSource. When trying to use a umesh read in from the statepoint we get the AttributeError
```
model_gamma.run(cwd="photons")
File "/home/j/openmc/openmc/model/model.py", line 712, in run
self.export_to_model_xml(**export_kwargs)
File "/home/j/openmc/openmc/model/model.py", line 509, in export_to_model_xml
settings_element = self.settings.to_xml_element(mesh_memo)
File "/home/j/openmc/openmc/settings.py", line 1791, in to_xml_element
self._create_source_subelement(element, mesh_memo)
File "/home/j/openmc/openmc/settings.py", line 1076, in _create_source_subelement
root.append(source.to_xml_element())
File "/home/j/openmc/openmc/source.py", line 77, in to_xml_element
self.populate_xml_element(element)
File "/home/j/openmc/openmc/source.py", line 503, in populate_xml_element
for idx in self.mesh.indices:
AttributeError: 'UnstructuredMesh' object has no attribute 'indices'
```
I tried to add that attribute with
```umesh_from_sp.indices = [i+1 for i in range(len(mesh_vols))]```
but this just raised a type error when trying to write the xml
```
model_gamma.run(cwd="photons")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/j/openmc/openmc/model/model.py", line 712, in run
self.export_to_model_xml(**export_kwargs)
File "/home/j/openmc/openmc/model/model.py", line 509, in export_to_model_xml
settings_element = self.settings.to_xml_element(mesh_memo)
File "/home/j/openmc/openmc/settings.py", line 1791, in to_xml_element
self._create_source_subelement(element, mesh_memo)
File "/home/j/openmc/openmc/settings.py", line 1076, in _create_source_subelement
root.append(source.to_xml_element())
File "/home/j/openmc/openmc/source.py", line 77, in to_xml_element
self.populate_xml_element(element)
File "/home/j/openmc/openmc/source.py", line 504, in populate_xml_element
idx = tuple(i - 1 for i in idx)
TypeError: 'int' object is not iterable
```
I have a not so minimal example over [here](https://github.com/fusion-energy/neutronics-workshop/blob/3173f5b59ec1359367932cea898a7f2dff6c8422/tasks/task_18_CAD_shut_down_dose_rate/1_unstrucutred_mesh_R2S_shut_down_dose_rate_concise.py) if it helps
Glad to hear that reading the volumes and centroids went alright @shimwell!
It seems we are in fact missing the indices property for the `UnstructuredMesh` class. This should really be present on the `MeshBase` class as an abstract method to protect from this as we expect all mesh implementations to have it. Should be an easy fix and I can update it shortly.
The reason that the population of the indices attribute you have above isn't working is because that property is expected to be a tuple of indices. See https://docs.openmc.org/en/latest/pythonapi/generated/openmc.RegularMesh.html?highlight=meshbase#openmc-regularmesh
Hopefully that helps you move forward in the meantime.
Thanks Patrick and Paul (on slack), I appreciate your help going through some of these less trodden workflows.
I changed
```
umesh_from_sp.indices = [i+1 for i in range(len(mesh_vols))]
```
to
```
umesh_from_sp.indices = [(i+1, i+1, i+1) for i in range(len(mesh_vols))]
```
in my example and it now writes the model.xml file, so it does get past that indices check. The code still fails on the run command as now later in the code it recieves a tuple with three values when unstructured meshes have 1D indexing.
```
gamma_sp_filename = model_gamma.run(cwd="photons")
File "/home/j/openmc/openmc/model/model.py", line 712, in run
self.export_to_model_xml(**export_kwargs)
File "/home/j/openmc/openmc/model/model.py", line 509, in export_to_model_xml
settings_element = self.settings.to_xml_element(mesh_memo)
File "/home/j/openmc/openmc/settings.py", line 1791, in to_xml_element
self._create_source_subelement(element, mesh_memo)
File "/home/j/openmc/openmc/settings.py", line 1076, in _create_source_subelement
root.append(source.to_xml_element())
File "/home/j/openmc/openmc/source.py", line 77, in to_xml_element
self.populate_xml_element(element)
File "/home/j/openmc/openmc/source.py", line 505, in populate_xml_element
elem.append(self.sources[idx].to_xml_element())
IndexError: too many indices for array: array is 1-dimensional, but 3 were indexed
>>>
```
So I guess the ```indices``` could be moved to ```MeshBase``` and used by regular mesh, spherical mesh etc but it the UnstrucutreMesh class might need its own implementation as it's indices appear to be 1D in places
| 2024-04-09T10:07:54Z | [] | [] |
openmc-dev/openmc | 2,966 | openmc-dev__openmc-2966 | [
"2968",
"2968"
] | 2974d53b3c07dc1a822f2b31ecd27b6553cbd458 | diff --git a/openmc/deplete/abc.py b/openmc/deplete/abc.py
--- a/openmc/deplete/abc.py
+++ b/openmc/deplete/abc.py
@@ -848,7 +848,7 @@ def integrate(
print(f"[openmc.deplete] t={t} (final operator evaluation)")
res_list = [self.operator(n, source_rate if final_step else 0.0)]
StepResult.save(self.operator, [n], res_list, [t, t],
- source_rate, self._i_res + len(self), proc_time)
+ source_rate, self._i_res + len(self), proc_time, path)
self.operator.write_bos_data(len(self) + self._i_res)
self.operator.finalize()
diff --git a/openmc/deplete/independent_operator.py b/openmc/deplete/independent_operator.py
--- a/openmc/deplete/independent_operator.py
+++ b/openmc/deplete/independent_operator.py
@@ -241,7 +241,6 @@ def from_nuclides(cls, volume, nuclides,
reduce_chain_level=reduce_chain_level,
fission_yield_opts=fission_yield_opts)
-
@staticmethod
def _consolidate_nuclides_to_material(nuclides, nuc_units, volume):
"""Puts nuclide list into an openmc.Materials object.
@@ -270,7 +269,6 @@ def _load_previous_results(self):
self.prev_res[-1].transfer_volumes(model)
self.materials = model.materials
-
# Store previous results in operator
# Distribute reaction rates according to those tracked
# on this process
@@ -282,7 +280,6 @@ def _load_previous_results(self):
new_res = res_obj.distribute(self.local_mats, mat_indexes)
self.prev_res.append(new_res)
-
def _get_nuclides_with_data(self, cross_sections: List[MicroXS]) -> Set[str]:
"""Finds nuclides with cross section data"""
return set(cross_sections[0].nuclides)
@@ -412,6 +409,12 @@ def __call__(self, vec, source_rate):
self._update_materials_and_nuclides(vec)
+ # If the source rate is zero, return zero reaction rates
+ if source_rate == 0.0:
+ rates = self.reaction_rates.copy()
+ rates.fill(0.0)
+ return OperatorResult(ufloat(0.0, 0.0), rates)
+
rates = self._calculate_reaction_rates(source_rate)
keff = self._keff
| diff --git a/tests/unit_tests/test_deplete_decay_products.py b/tests/unit_tests/test_deplete_decay.py
similarity index 55%
rename from tests/unit_tests/test_deplete_decay_products.py
rename to tests/unit_tests/test_deplete_decay.py
--- a/tests/unit_tests/test_deplete_decay_products.py
+++ b/tests/unit_tests/test_deplete_decay.py
@@ -1,3 +1,5 @@
+from pathlib import Path
+
import openmc.deplete
import numpy as np
import pytest
@@ -45,3 +47,37 @@ def test_deplete_decay_products(run_in_tmpdir):
# H1 and He4
assert h1[1] == pytest.approx(1e24)
assert he4[1] == pytest.approx(1e24)
+
+
+def test_deplete_decay_step_fissionable(run_in_tmpdir):
+ """Ensures that power is not computed in zero power cases with
+ fissionable material present. This tests decay calculations without
+ power, although this specific example does not exhibit any decay.
+
+ Proves github issue #2963 is fixed
+ """
+
+ # Set up a pure decay operator
+ micro_xs = openmc.deplete.MicroXS(np.empty((0, 0)), [], [])
+ mat = openmc.Material()
+ mat.name = 'I do not decay.'
+ mat.add_nuclide('U238', 1.0, 'ao')
+ mat.volume = 10.0
+ mat.set_density('g/cc', 1.0)
+ original_atoms = mat.get_nuclide_atoms()['U238']
+
+ mats = openmc.Materials([mat])
+ op = openmc.deplete.IndependentOperator(
+ mats, [1.0], [micro_xs], Path(__file__).parents[1] / "chain_simple.xml")
+
+ # Create time integrator and integrate
+ integrator = openmc.deplete.PredictorIntegrator(
+ op, [1.0], power=[0.0], timestep_units='s'
+ )
+ integrator.integrate()
+
+ # Get concentration of U238. It should be unchanged since this chain has no U238 decay.
+ results = openmc.deplete.Results('depletion_results.h5')
+ _, u238 = results.get_atoms("1", "U238")
+
+ assert u238[1] == pytest.approx(original_atoms)
| Final step in depletion being written to depletion_results.h5 regardless of filename given to integrator
<!--
If you are a user of OpenMC and are running into trouble with the code or are
seeking general user support, we highly recommend posting on the OpenMC
discourse forum first. GitHub issues should be used specifically for bug reports
and feature requests.
https://openmc.discourse.group/
-->
## Bug Description
The last step always tries to write to an h5 file called depletion_results.h5, even if a user gave something like my_decay.h5 to Integrator.integrate. This is because the kwarg for the file name is written at all steps but the last in the integrator base class.
It throws an exception as a result that looks like:
```
bigrig% python decay_mwe.py
/usr/lib/python3/dist-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.17.3 and <1.25.0 is required for this version of SciPy (detected version 1.26.2
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
[openmc.deplete] t=0.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=50.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=100.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=150.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=200.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=250.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=300.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=350.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=400.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=450.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=500.0 (final operator evaluation)
Traceback (most recent call last):
File "/home/gavin/Scratch/decay_mwe.py", line 28, in <module>
integ.integrate(path='decaystep.h5')
File "/home/gavin/Code/openmc/openmc/deplete/abc.py", line 850, in integrate
StepResult.save(self.operator, [n], res_list, [t, t],
File "/home/gavin/Code/openmc/openmc/deplete/stepresult.py", line 570, in save
results.export_to_hdf5(path, step_ind)
File "/home/gavin/Code/openmc/openmc/deplete/stepresult.py", line 271, in export_to_hdf5
res._to_hdf5(handle, step, parallel=False)
File "/home/gavin/Code/openmc/openmc/deplete/stepresult.py", line 426, in _to_hdf5
number_dset[index, i, low:high+1] = self.data[i]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/home/gavin/.local/lib/python3.10/site-packages/h5py/_hl/dataset.py", line 997, in __setitem__
mspace = h5s.create_simple(selection.expand_shape(mshape))
File "/home/gavin/.local/lib/python3.10/site-packages/h5py/_hl/selections.py", line 264, in expand_shape
raise TypeError("Can't broadcast %s -> %s" % (source_shape, self.array_shape)) # array shape
TypeError: Can't broadcast (1, 3820) -> (1, 3819)
```
## Steps to Reproduce
<!--Steps to reproduce the behavior (input file, or modifications to an existing input file, etc.)-->
See the MWE in #2966 and set the path as follows:
```
integ.integrate(path='decaystep.h5')
results = openmc.deplete.Results('decaystep.h5')
```
## Environment
<!--Operating system, OpenMC version, how OpenMC was installed, nuclear data being used, etc.-->
Does not matter.
Final step in depletion being written to depletion_results.h5 regardless of filename given to integrator
<!--
If you are a user of OpenMC and are running into trouble with the code or are
seeking general user support, we highly recommend posting on the OpenMC
discourse forum first. GitHub issues should be used specifically for bug reports
and feature requests.
https://openmc.discourse.group/
-->
## Bug Description
The last step always tries to write to an h5 file called depletion_results.h5, even if a user gave something like my_decay.h5 to Integrator.integrate. This is because the kwarg for the file name is written at all steps but the last in the integrator base class.
It throws an exception as a result that looks like:
```
bigrig% python decay_mwe.py
/usr/lib/python3/dist-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.17.3 and <1.25.0 is required for this version of SciPy (detected version 1.26.2
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
[openmc.deplete] t=0.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=50.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=100.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=150.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=200.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=250.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=300.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=350.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=400.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=450.0 s, dt=50.0 s, source=0.0
[openmc.deplete] t=500.0 (final operator evaluation)
Traceback (most recent call last):
File "/home/gavin/Scratch/decay_mwe.py", line 28, in <module>
integ.integrate(path='decaystep.h5')
File "/home/gavin/Code/openmc/openmc/deplete/abc.py", line 850, in integrate
StepResult.save(self.operator, [n], res_list, [t, t],
File "/home/gavin/Code/openmc/openmc/deplete/stepresult.py", line 570, in save
results.export_to_hdf5(path, step_ind)
File "/home/gavin/Code/openmc/openmc/deplete/stepresult.py", line 271, in export_to_hdf5
res._to_hdf5(handle, step, parallel=False)
File "/home/gavin/Code/openmc/openmc/deplete/stepresult.py", line 426, in _to_hdf5
number_dset[index, i, low:high+1] = self.data[i]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/home/gavin/.local/lib/python3.10/site-packages/h5py/_hl/dataset.py", line 997, in __setitem__
mspace = h5s.create_simple(selection.expand_shape(mshape))
File "/home/gavin/.local/lib/python3.10/site-packages/h5py/_hl/selections.py", line 264, in expand_shape
raise TypeError("Can't broadcast %s -> %s" % (source_shape, self.array_shape)) # array shape
TypeError: Can't broadcast (1, 3820) -> (1, 3819)
```
## Steps to Reproduce
<!--Steps to reproduce the behavior (input file, or modifications to an existing input file, etc.)-->
See the MWE in #2966 and set the path as follows:
```
integ.integrate(path='decaystep.h5')
results = openmc.deplete.Results('decaystep.h5')
```
## Environment
<!--Operating system, OpenMC version, how OpenMC was installed, nuclear data being used, etc.-->
Does not matter.
| 2024-04-17T19:21:10Z | [] | [] |
|
openmc-dev/openmc | 3,003 | openmc-dev__openmc-3003 | [
"3002"
] | a7d6939c11a2d905d0aab3c57a97cd82e7018b3a | diff --git a/openmc/lattice.py b/openmc/lattice.py
--- a/openmc/lattice.py
+++ b/openmc/lattice.py
@@ -1564,6 +1564,7 @@ def from_xml_element(cls, elem, get_universe):
alpha -= 1
if not lat.is_valid_index((x, alpha, z)):
# Reached the bottom
+ j += 1
break
j += 1
else:
@@ -1583,6 +1584,7 @@ def from_xml_element(cls, elem, get_universe):
# Check if we've reached the bottom
if y == -n_rings:
+ j += 1
break
while not lat.is_valid_index((alpha, y, z)):
| diff --git a/tests/unit_tests/test_lattice.py b/tests/unit_tests/test_lattice.py
--- a/tests/unit_tests/test_lattice.py
+++ b/tests/unit_tests/test_lattice.py
@@ -377,3 +377,46 @@ def test_unset_universes():
hex_lattice.pitch = (1.,)
with pytest.raises(ValueError):
hex_lattice.create_xml_subelement(elem)
+
+
[email protected]("orientation", ['x', 'y'])
+def test_hex_lattice_roundtrip(orientation):
+ openmc.reset_auto_ids()
+
+ # ensure that the lattice universes are the same on all axial levels
+ def check_lattice_universes(og_lattice, xml_lattice):
+ for axial_og, axial_rt in zip(og_lattice.universes, xml_lattice.universes):
+ for ring_og, ring_rt in zip(axial_og, axial_rt):
+ assert [u.id for u in ring_og] == [u.id for u in ring_rt]
+
+ latt = openmc.HexLattice()
+ latt.pitch = (1.0, 1.0)
+ latt.center = (0.0, 0.0, 0.0)
+ latt.orientation = orientation
+
+ # fill the lattice with universes in increasing order and repeat for
+ # the second actial level
+ lvl_one_univs = [openmc.Universe(cells=[openmc.Cell()]) for _ in range(19)]
+ lvl_one_univs = [lvl_one_univs[-12:], lvl_one_univs[1:7], lvl_one_univs[:1]]
+ latt.universes = [lvl_one_univs, lvl_one_univs]
+
+ geom = openmc.Geometry([openmc.Cell(fill=latt)])
+ geom.export_to_xml()
+
+ xml_geom = openmc.Geometry.from_xml(materials=openmc.Materials())
+
+ xml_latt = xml_geom.get_all_lattices()[latt.id]
+
+ check_lattice_universes(latt, xml_latt)
+
+ # same test but with unique universes for each axial level
+ lvl_two_univs = [openmc.Universe(cells=[openmc.Cell()]) for _ in range(19)]
+ lvl_two_univs = [lvl_two_univs[-12:], lvl_two_univs[1:7], lvl_two_univs[:1]]
+ latt.universes = [lvl_one_univs, lvl_two_univs]
+
+ geom.export_to_xml()
+
+ xml_geom = openmc.Geometry.from_xml(materials=openmc.Materials())
+ xml_latt = xml_geom.get_all_lattices()[latt.id]
+
+ check_lattice_universes(latt, xml_latt)
| Hexagonal Lattices Don't Roundtrip
## Bug Description
Our hexagonal lattices don't currently roundtrip from XML correctly for multiple axial layers. The first layer is fine, but layers beyond that are incorrect.
```
<hex_lattice id="100" n_axial="2" n_rings=" <hex_lattice id="100" n_axial="2" n_rings="
<pitch>1.0 1.0</pitch> <pitch>1.0 1.0</pitch>
<center>0.0 0.0 0.0</center> <center>0.0 0.0 0.0</center>
<universes> <universes>
16 17 18 16 17 18
15 6 7 19 15 6 7 19
14 5 1 2 8 14 5 1 2 8
13 4 3 9 13 4 3 9
12 11 10 12 11 10
10 16 17 | 16 17 18
18 15 6 7 | 15 6 7 19
19 14 5 1 2 | 14 5 1 2 8
8 13 4 3 | 13 4 3 9
9 12 11</universes> | 12 11 10</universes>
</hex_lattice> </hex_lattice>
</geometry> </geometry>
````
<!--A clear and concise description of the problem (Note: A missing feature is not a bug).-->
## Steps to Reproduce
```python
# coding: utf-8
import openmc
openmc.reset_auto_ids()
latt = openmc.HexLattice(lattice_id=100)
latt.pitch = (1.0, 1.0)
latt.center = (0.0, 0.0, 0.0)
u19 = [openmc.Universe(cells=[openmc.Cell()]) for i in range(19)]
axial_one = [u19[-12:], u19[1:7], u19[0:1]]
latt.orientation = 'x'
u19 = [openmc.Universe(cells=[openmc.Cell()]) for i in range(19)]
axial_two = [u19[-12:], u19[1:7], u19[0:1]]
latt.universes = [axial_one, axial_one]
outer_univ = openmc.Universe(cells=[openmc.Cell(fill=latt)])
geom = openmc.Geometry(root=outer_univ)
geom.export_to_xml()
geom2 = openmc.Geometry.from_xml(materials=openmc.Materials())
print("Original Lattice:")
print(latt)
print("Roundtrip Lattice:")
print(geom2.get_all_lattices()[latt.id])
rt_latt = geom2.get_all_lattices()[latt.id]
for aixal_og, axial_rt in zip(latt.universes, rt_latt.universes):
for ring_og, ring_rt in zip(aixal_og, axial_rt):
assert [u.id for u in ring_og] == [u.id for u in ring_rt]
```
| 2024-05-14T20:25:33Z | [] | [] |
|
zalando/patroni | 171 | zalando__patroni-171 | [
"167"
] | 24a2ea6cefd9dec31b4081472dd087dcbb710c90 | diff --git a/patroni/ha.py b/patroni/ha.py
--- a/patroni/ha.py
+++ b/patroni/ha.py
@@ -106,12 +106,6 @@ def bootstrap(self):
return 'waiting for leader to bootstrap'
def recover(self):
- # try to see if we are the former master that crashed. If so - we likely need to run pg_rewind
- # in order to join the former standby being promoted.
- if self.state_handler.role == 'master':
- pg_controldata = self.state_handler.controldata()
- if pg_controldata and pg_controldata.get('Database cluster state', '') == 'in production': # crashed master
- self.state_handler.require_rewind()
self.recovering = True
return self.follow("starting as readonly because i had the session lock", "starting as a secondary", True, True)
diff --git a/patroni/postgresql.py b/patroni/postgresql.py
--- a/patroni/postgresql.py
+++ b/patroni/postgresql.py
@@ -73,14 +73,13 @@ def __init__(self, config):
self._connection = None
self._cursor_holder = None
- self._need_rewind = False
self._sysid = None
self.replication_slots = [] # list of already existing replication slots
self.retry = Retry(max_tries=-1, deadline=5, max_delay=1, retry_exceptions=PostgresConnectionException)
self._state = 'stopped'
self._state_lock = Lock()
- self._role = 'replica'
+ self._role = self.get_postgres_role_from_data_directory()
self._role_lock = Lock()
if self.is_running():
@@ -115,9 +114,6 @@ def sysid(self):
self._sysid = data.get('Database system identifier', "")
return self._sysid
- def require_rewind(self):
- self._need_rewind = True
-
def get_local_address(self):
listen_addresses = self.listen_addresses.split(',')
local_address = listen_addresses[0].strip() # take first address from listen_addresses
@@ -128,6 +124,9 @@ def get_local_address(self):
break
return local_address + ':' + self.port
+ def get_postgres_role_from_data_directory(self):
+ return 'replica' if os.path.exists(self.recovery_conf) else 'master'
+
@property
def _connect_kwargs(self):
r = parseurl('postgres://{0}/postgres'.format(self.local_address))
@@ -351,7 +350,7 @@ def start(self, block_callbacks=False):
logger.error('Cannot start PostgreSQL because one is already running.')
return True
- self.set_role('replica' if os.path.exists(self.recovery_conf) else 'master')
+ self.set_role(self.get_postgres_role_from_data_directory())
if os.path.exists(self.postmaster_pid):
os.remove(self.postmaster_pid)
logger.info('Removed %s', self.postmaster_pid)
@@ -564,13 +563,12 @@ def cleanup_archive_status(self):
def follow(self, leader, recovery=False):
if self.check_recovery_conf(leader) and not recovery:
return True
-
change_role = self.role == 'master'
- self._need_rewind = (self._need_rewind or change_role) and self.can_rewind
- if self._need_rewind:
+ need_rewind = change_role and self.can_rewind
+ if need_rewind:
logger.info("set the rewind flag after demote")
self.write_recovery_conf(leader)
- if leader and self._need_rewind: # we have a leader and need to rewind
+ if leader and need_rewind: # we have a leader and need to rewind
if self.is_running():
self.stop()
# at present, pg_rewind only runs when the cluster is shut down cleanly
@@ -594,7 +592,6 @@ def follow(self, leader, recovery=False):
logger.error("unable to rewind the former master")
self.remove_data_directory()
ret = True
- self._need_rewind = False
else: # do not rewind until the leader becomes available
ret = self.restart()
if change_role and ret:
@@ -630,7 +627,6 @@ def promote(self):
if ret:
self.set_role('master')
logger.info("cleared rewind flag after becoming the leader")
- self._need_rewind = False
self.call_nowait(ACTION_ON_ROLE_CHANGE)
return ret
| diff --git a/tests/test_ha.py b/tests/test_ha.py
--- a/tests/test_ha.py
+++ b/tests/test_ha.py
@@ -91,6 +91,7 @@ def setUp(self):
'data_dir': 'data/postgresql0', 'superuser': {}, 'admin': {},
'replication': {'username': '', 'password': '', 'network': ''}})
self.p.set_state('running')
+ self.p.set_role('replica')
self.p.check_replication_lag = true
self.p.can_create_replica_without_replication_connection = MagicMock(return_value=False)
self.e = Etcd('foo', {'ttl': 30, 'host': 'ok:2379', 'scope': 'test'})
diff --git a/tests/test_postgresql.py b/tests/test_postgresql.py
--- a/tests/test_postgresql.py
+++ b/tests/test_postgresql.py
@@ -257,12 +257,10 @@ def test_follow(self, mock_pg_rewind):
self.p.follow(Leader(-1, 28, self.other))
self.p.rewind = mock_pg_rewind
self.p.follow(self.leader)
- self.p.require_rewind()
with mock.patch('os.path.islink', MagicMock(return_value=True)):
with mock.patch('patroni.postgresql.Postgresql.can_rewind', new_callable=PropertyMock(return_value=True)):
with mock.patch('os.unlink', MagicMock(return_value=True)):
self.p.follow(self.leader, recovery=True)
- self.p.require_rewind()
with mock.patch('patroni.postgresql.Postgresql.can_rewind', new_callable=PropertyMock(return_value=True)):
self.p.rewind.return_value = True
self.p.follow(self.leader, recovery=True)
| rejoin former master fails
I'm not entirely sure if this is expected behaviour or not. If I stop a master (systemctl stop patroni) a slave takes over. This works fine. If I then want to rejoin the master as slave using just systemctl start patroni it fails:
> < 2016-03-31 09:13:38.119 CEST >ERROR: requested starting point 0/26000000 on timeline 5 is not in this server's history
> < 2016-03-31 09:13:38.119 CEST >DETAIL: This server's history forked from timeline 5 at 0/250001A8.
I can fix it by manually running pg_rewind on the former master:
`sudo -u postgres pg_rewind -D /var/lib/pgsql/9.5/data --source-server='host=currentmaster password=pwforpostgres'
`
After running that command the former master can join again as slave and everything appears to work. Looking at the code I see that there is quite a bit of code there for running pg_rewind already so I am wondering if I have hit a bug or if this is how it is expected to work and I should always manually intervene before rejoining a former master even if it was shut down manually (not crashed.)
| You have to configure the username and the password for pg_rewind first (i.e. https://github.com/zalando/patroni/blob/master/postgres0.yml). Create a pg_rewind section in the patroni configuration file and specify there the superuser username and the password, i.e.
pg_rewind:
username: postgres
password: pwforpostgres
I assume you have set either the wal_log_hints or enabled the checksum, because this is a prerequisite to running pg_rewind.
Hmm, usually pg_rewind is not necessary if patroni (postgres) was shut down cleanly.
How it works:
1. `systemctl stop patroni` sends (hopefully) `SIGTERM` to patroni
2. patroni handles this signal and shuts down postgres with: `pg_ctl stop -m fast`
3. after clean shutdown of postgres patroni removes `leader` lock from etcd (or zookeeper)
4. one of replicas acquires leader lock and promote.
What can go wrong?
It could happen that patroni was not able to shut down postgres during 10 seconds (https://github.com/zalando/patroni/blob/master/extras/startup-scripts/patroni.service#L21) and was killed with `SIGKILL`. In this case replica has a chance to promote earlier then former master was shut down.
In order to get full picture and answer all questions I need to get:
1. config yaml file from the former master
2. patroni logs from the former master (starting from the moment when you run `systemctl stop patroni`)
3. postgres logs from the former master (starting from the moment when you run `systemctl stop patroni`)
And also please check, that after execution of `systemctl stop patroni` there is no postgres running on this host any more.
@alexeyklyukin Yes wal_log_hints is on and I have tried with both data-checksums of and on. The pg_rewind settings are also there (assuming that is supposed to be the postgres pasword for the database, not for the OS user.)
@CyberDem0n Sorry for the delay, found the time to get all the requested info:
[logfiles.txt](https://github.com/zalando/patroni/files/204181/logfiles.txt)
[patroni.yaml.txt](https://github.com/zalando/patroni/files/204183/patroni.yaml.txt)
ps.: I can reproduce this every time (you can actually see from the logfile the slave is just starting for the first time and creating the new replication slot.)
**< 2016-04-05 11:11:11.130 CEST >LOG: received smart shutdown request**
< 2016-04-05 11:11:11.130 CEST >LOG: autovacuum launcher shutting down
< 2016-04-05 11:11:11.130 CEST >FATAL: terminating connection due to administrator command
< 2016-04-05 11:11:11.130 CEST >FATAL: terminating connection due to administrator command
< 2016-04-05 11:11:11.137 CEST >LOG: shutting down
< 2016-04-05 11:11:11.147 CEST >FATAL: the database system is shutting down
**< 2016-04-05 11:11:11.232 CEST >LOG: received fast shutdown request**
Somehow postgres received two shutdown requests. But only one of then actually was initiated by patroni, the last one (fast shutdown).
Replica stopped streaming right after the first shutdown request (smart) and didn't got latest changes. Actually it should be solved by pg_rewind, but somehow it was not called...
Now we need to figure out who and why sends smart shutdown request. I guess it was sent by `systemctl`
```
KillMode=
Specifies how processes of this unit shall be killed. One of control-group, process, mixed, none.
If set to control-group, all remaining processes in the control group of this unit will be killed on unit stop (for services: after the stop command is executed, as configured with ExecStop=). If set to process, only the main process itself is killed. If set to mixed, the SIGTERM signal (see below) is sent to the main process while the subsequent SIGKILL signal (see below) is sent to all remaining processes of the unit's control group. If set to none, no process is killed. In this case, only the stop command will be executed on unit stop, but no process be killed otherwise. Processes remaining alive after stop are left in their control group and the control group continues to exist after stop unless it is empty.
Processes will first be terminated via SIGTERM (unless the signal to send is changed via KillSignal=). Optionally, this is immediately followed by a SIGHUP (if enabled with SendSIGHUP=). If then, after a delay (configured via the TimeoutStopSec= option), processes still remain, the termination request is repeated with the SIGKILL signal (unless this is disabled via the SendSIGKILL= option). See kill(2) for more information.
Defaults to control-group.
```
At least in our example we didn't changed KillMode, so probably it defaults to `control-group`.
If you are using not the latest version of patroni (which doesn't include https://github.com/zalando/patroni/commit/7b524bc5571f2c49d7375d2cbd4eb3c7d303dca8), then it could explain such behaviour.
In any case please try to update your service file and set `KillMode=process`, hopefully it should help.
Thanks, this does indeed solve the problem!
For me it is still not clear why patroni was not calling pg_rewind...
True, it is still reproducible by sending the kill signals systemd is sending manually.
So first ps -ef | grep postgres (assuming patroni and postgres run as postgres user) and then a single kill command with a list of all the pid's.
| 2016-04-12T08:13:45Z | [] | [] |
zalando/patroni | 295 | zalando__patroni-295 | [
"283"
] | c6417b2558d7de4358287a305e75e203aef5e309 | diff --git a/patroni/__init__.py b/patroni/__init__.py
--- a/patroni/__init__.py
+++ b/patroni/__init__.py
@@ -143,8 +143,30 @@ def patroni_main():
patroni.dcs.delete_leader()
+def pg_ctl_start(args):
+ import subprocess
+ postmaster = subprocess.Popen(args)
+ print(postmaster.pid)
+
+
+def call_self(args, **kwargs):
+ """This function executes Patroni once again with provided arguments.
+
+ :args: list of arguments to call Patroni with.
+ :returns: `Popen` object"""
+
+ exe = [sys.executable]
+ if not getattr(sys, 'frozen', False): # Binary distribution?
+ exe.append(sys.argv[0])
+
+ import subprocess
+ return subprocess.Popen(exe + args, **kwargs)
+
+
def main():
if os.getpid() != 1:
+ if len(sys.argv) > 5 and sys.argv[1] == 'pg_ctl_start':
+ return pg_ctl_start(sys.argv[2:])
return patroni_main()
pid = 0
@@ -173,7 +195,6 @@ def passtochild(signo, stack_frame):
signal.signal(signal.SIGQUIT, passtochild)
signal.signal(signal.SIGTERM, passtochild)
- import subprocess
- patroni = subprocess.Popen([sys.executable] + sys.argv)
+ patroni = call_self(sys.argv[1:])
pid = patroni.pid
patroni.wait()
diff --git a/patroni/api.py b/patroni/api.py
--- a/patroni/api.py
+++ b/patroni/api.py
@@ -8,7 +8,7 @@
import datetime
from patroni.exceptions import PostgresConnectionException
-from patroni.utils import deep_compare, patch_config, Retry, RetryFailedError, is_valid_pg_version, tzutc
+from patroni.utils import deep_compare, patch_config, Retry, RetryFailedError, is_valid_pg_version, parse_int, tzutc
from six.moves.BaseHTTPServer import BaseHTTPRequestHandler, HTTPServer
from six.moves.socketserver import ThreadingMixIn
from threading import Thread
@@ -223,6 +223,12 @@ def do_POST_restart(self):
status_code = 400
data = "PostgreSQL version should be in the first.major.minor format"
break
+ elif k == 'timeout':
+ request[k] = parse_int(request[k], 's')
+ if request[k] is None or request[k] <= 0:
+ status_code = 400
+ data = "Timeout should be a positive number of seconds"
+ break
elif k != 'restart_pending':
status_code = 400
data = "Unknown filter for the scheduled restart: {0}".format(k)
@@ -236,7 +242,6 @@ def do_POST_restart(self):
logger.exception('Exception during restart')
status_code = 400
else:
- request['postmaster_start_time'] = self.server.patroni.ha.state_handler.postmaster_start_time()
if self.server.patroni.ha.schedule_future_restart(request):
data = "Restart scheduled"
status_code = 202
@@ -379,7 +384,8 @@ def get_postgresql_status(self, retry=False):
THEN 0
ELSE pg_xlog_location_diff(pg_current_xlog_location(), '0/0')::bigint
END,
- pg_xlog_location_diff(pg_last_xlog_receive_location(), '0/0')::bigint,
+ pg_xlog_location_diff(COALESCE(pg_last_xlog_receive_location(),
+ pg_last_xlog_replay_location()), '0/0')::bigint,
pg_xlog_location_diff(pg_last_xlog_replay_location(), '0/0')::bigint,
to_char(pg_last_xact_replay_timestamp(), 'YYYY-MM-DD HH24:MI:SS.MS TZ'),
pg_is_in_recovery() AND pg_is_xlog_replay_paused(),
diff --git a/patroni/config.py b/patroni/config.py
--- a/patroni/config.py
+++ b/patroni/config.py
@@ -41,6 +41,7 @@ class Config(object):
__DEFAULT_CONFIG = {
'ttl': 30, 'loop_wait': 10, 'retry_timeout': 10,
'maximum_lag_on_failover': 1048576,
+ 'master_start_timeout': 300,
'synchronous_mode': False,
'postgresql': {
'bin_dir': '',
diff --git a/patroni/ctl.py b/patroni/ctl.py
--- a/patroni/ctl.py
+++ b/patroni/ctl.py
@@ -439,9 +439,11 @@ def parse_scheduled(scheduled):
@click.option('--pg-version', 'version', help='Restart if the PostgreSQL version is less than provided (e.g. 9.5.2)',
default=None)
@click.option('--pending', help='Restart if pending', is_flag=True)
[email protected]('--timeout',
+ help='Return error and fail over if necessary when restarting takes longer than this.')
@option_force
@click.pass_obj
-def restart(obj, cluster_name, member_names, force, role, p_any, scheduled, version, pending):
+def restart(obj, cluster_name, member_names, force, role, p_any, scheduled, version, pending, timeout):
cluster = get_dcs(obj, cluster_name).get_cluster()
members = get_members(cluster, cluster_name, member_names, role, force, 'restart')
@@ -473,6 +475,9 @@ def restart(obj, cluster_name, member_names, force, role, p_any, scheduled, vers
raise PatroniCtlException("Can't schedule restart in the paused state")
content['schedule'] = scheduled_at.isoformat()
+ if timeout is not None:
+ content['timeout'] = timeout
+
for member in members:
if 'schedule' in content:
if force and member.data.get('scheduled_restart'):
diff --git a/patroni/ha.py b/patroni/ha.py
--- a/patroni/ha.py
+++ b/patroni/ha.py
@@ -7,6 +7,7 @@
import sys
import time
+from collections import namedtuple
from multiprocessing.pool import ThreadPool
from patroni.async_executor import AsyncExecutor
from patroni.exceptions import DCSError, PostgresConnectionException
@@ -17,6 +18,35 @@
logger = logging.getLogger(__name__)
+class _MemberStatus(namedtuple('_MemberStatus', 'member,reachable,in_recovery,xlog_location,tags')):
+ """Node status distilled from API response:
+
+ member - dcs.Member object of the node
+ reachable - `!False` if the node is not reachable or is not responding with correct JSON
+ in_recovery - `!True` if pg_is_in_recovery() == true
+ xlog_location - value of `replayed_location` or `location` from JSON, dependin on its role.
+ is_lagging - `True` if node considers itself too far behind to promote
+ tags - dictionary with values of different tags (i.e. nofailover)
+ """
+ @classmethod
+ def from_api_response(cls, member, json):
+ is_master = json['role'] == 'master'
+ xlog_location = None if is_master else json['xlog']['received_location']
+ return cls(member, True, not is_master, xlog_location, json.get('tags', {}))
+
+ @classmethod
+ def unknown(cls, member):
+ return cls(member, False, None, 0, {})
+
+ def failover_limitation(self):
+ """Returns reason why this node can't promote or None if everything is ok."""
+ if not self.reachable:
+ return 'not reachable'
+ if self.tags.get('nofailover', False):
+ return 'not allowed to promote'
+ return None
+
+
class Ha(object):
def __init__(self, patroni):
@@ -26,6 +56,7 @@ def __init__(self, patroni):
self.cluster = None
self.old_cluster = None
self.recovering = False
+ self._start_timeout = None
self._async_executor = AsyncExecutor(self.wakeup)
# Each member publishes various pieces of information to the DCS using touch_member. This lock protects
@@ -140,8 +171,21 @@ def bootstrap(self):
return 'waiting for leader to bootstrap'
def recover(self):
+ if self.has_lock() and self.update_lock():
+ timeout = self.patroni.config['master_start_timeout']
+ if timeout == 0:
+ # We are requested to prefer failing over to restarting master. But see first if there
+ # is anyone to fail over to.
+ if self.is_failover_possible(self.cluster.members):
+ logger.info("Master crashed. Failing over.")
+ self.demote('immediate')
+ return 'stopped PostgreSQL to fail over after a crash'
+ else:
+ timeout = None
+
self.recovering = True
- return self.follow("starting as readonly because i had the session lock", "starting as a secondary", True, True)
+ return self.follow("starting as readonly because i had the session lock",
+ "starting as a secondary", True, True, None, timeout)
def _get_node_to_follow(self, cluster):
# determine the node to follow. If replicatefrom tag is set,
@@ -153,7 +197,7 @@ def _get_node_to_follow(self, cluster):
return node_to_follow if node_to_follow and node_to_follow.name != self.state_handler.name else None
- def follow(self, demote_reason, follow_reason, refresh=True, recovery=False, need_rewind=None):
+ def follow(self, demote_reason, follow_reason, refresh=True, recovery=False, need_rewind=None, timeout=None):
if refresh:
self.load_cluster_from_dcs()
@@ -172,7 +216,8 @@ def follow(self, demote_reason, follow_reason, refresh=True, recovery=False, nee
elif not node_to_follow:
return 'no action'
- self.state_handler.follow(node_to_follow, self.cluster.leader, recovery, self._async_executor, need_rewind)
+ self.state_handler.follow(node_to_follow, self.cluster.leader, recovery,
+ self._async_executor, need_rewind, timeout)
return ret
@@ -282,24 +327,16 @@ def enforce_master_role(self, message, promote_message):
@staticmethod
def fetch_node_status(member):
"""This function perform http get request on member.api_url and fetches its status
- :returns: tuple(`member`, reachable, in_recovery, xlog_location)
-
- reachable - `!False` if the node is not reachable or is not responding with correct JSON
- in_recovery - `!True` if pg_is_in_recovery() == true
- xlog_location - value of `replayed_location` or `location` from JSON, dependin on its role.
- tags - dictionary with values of different tags (i.e. nofailover)
+ :returns: `_MemberStatus` object
"""
try:
response = requests.get(member.api_url, timeout=2, verify=False)
logger.info('Got response from %s %s: %s', member.name, member.api_url, response.content)
- json = response.json()
- is_master = json['role'] == 'master'
- xlog_location = None if is_master else json['xlog']['replayed_location']
- return (member, True, not is_master, xlog_location, json.get('tags', {}))
+ return _MemberStatus.from_api_response(member, response.json())
except Exception as e:
logger.warning("request failed: GET %s (%s)", member.api_url, e)
- return (member, False, None, 0, {})
+ return _MemberStatus.unknown(member)
def fetch_nodes_statuses(self, members):
pool = ThreadPool(len(members))
@@ -308,23 +345,32 @@ def fetch_nodes_statuses(self, members):
pool.join()
return results
+ def is_lagging(self, xlog_location):
+ """Returns if instance with an xlog should consider itself unhealthy to be promoted due to replication lag.
+
+ :param xlog_location: Current xlog location.
+ :returns True when node is lagging
+ """
+ lag = (self.cluster.last_leader_operation or 0) - xlog_location
+ return lag > self.state_handler.config.get('maximum_lag_on_failover', 0)
+
def _is_healthiest_node(self, members, check_replication_lag=True):
"""This method tries to determine whether I am healthy enough to became a new leader candidate or not."""
- if check_replication_lag and not self.state_handler.check_replication_lag(self.cluster.last_leader_operation):
+ my_xlog_location = self.state_handler.xlog_position()
+ if check_replication_lag and self.is_lagging(my_xlog_location):
return False # Too far behind last reported xlog location on master
# Prepare list of nodes to run check against
members = [m for m in members if m.name != self.state_handler.name and not m.nofailover and m.api_url]
if members:
- my_xlog_location = self.state_handler.xlog_position()
- for member, reachable, in_recovery, xlog_location, tags in self.fetch_nodes_statuses(members):
- if reachable and not tags.get('nofailover', False): # If the node is unreachable it's not healhy
- if not in_recovery:
- logger.warning('Master (%s) is still alive', member.name)
+ for st in self.fetch_nodes_statuses(members):
+ if st.failover_limitation() is None:
+ if not st.in_recovery:
+ logger.warning('Master (%s) is still alive', st.member.name)
return False
- if my_xlog_location < xlog_location:
+ if my_xlog_location < st.xlog_location:
return False
return True
@@ -332,13 +378,14 @@ def is_failover_possible(self, members):
ret = False
members = [m for m in members if m.name != self.state_handler.name and not m.nofailover and m.api_url]
if members:
- for member, reachable, _, _, tags in self.fetch_nodes_statuses(members):
- if reachable and not tags.get('nofailover', False):
- ret = True # TODO: check xlog_location
- elif not reachable:
- logger.info('Member %s is not reachable', member.name)
- elif tags.get('nofailover', False):
- logger.info('Member %s is not allowed to promote', member.name)
+ for st in self.fetch_nodes_statuses(members):
+ not_allowed_reason = st.failover_limitation()
+ if not_allowed_reason:
+ logger.info('Member %s is %s', st.member.name, not_allowed_reason)
+ elif self.is_lagging(st.xlog_location):
+ logger.info('Member %s exceeds maximum replication lag', st.member.name)
+ else:
+ ret = True
else:
logger.warning('manual failover: members list is empty')
return ret
@@ -361,15 +408,13 @@ def manual_failover_process_no_leader(self):
# find specific node and check that it is healthy
member = self.cluster.get_member(failover.candidate, fallback_to_leader=False)
if member:
- member, reachable, _, _, tags = self.fetch_node_status(member)
- if reachable and not tags.get('nofailover', False): # node is healthy
- logger.info('manual failover: to %s, i am %s', member.name, self.state_handler.name)
+ st = self.fetch_node_status(member)
+ not_allowed_reason = st.failover_limitation()
+ if not_allowed_reason is None: # node is healthy
+ logger.info('manual failover: to %s, i am %s', st.member.name, self.state_handler.name)
return False
# we wanted to failover to specific member but it is not healthy
- if not reachable:
- logger.warning('manual failover: member %s is unhealthy', member.name)
- elif tags.get('nofailover', False):
- logger.warning('manual failover: member %s is not allowed to promote', member.name)
+ logger.warning('manual failover: member %s is %s', st.member.name, not_allowed_reason)
# at this point we should consider all members as a candidates for failover
# i.e. we assume that failover.candidate is None
@@ -399,6 +444,9 @@ def is_healthiest_node(self):
if ret is not None: # continue if we just deleted the stale failover key as a master
return ret
+ if self.state_handler.is_starting(): # postgresql still starting up is unhealthy
+ return False
+
if self.state_handler.is_leader(): # leader is always the healthiest
return True
@@ -424,18 +472,45 @@ def is_healthiest_node(self):
return self._is_healthiest_node(members.values())
- def demote(self, delete_leader=True):
- if delete_leader:
- self.state_handler.stop()
+ def release_leader_key_voluntarily(self):
+ self.dcs.delete_leader()
+ self.touch_member()
+ self.dcs.reset_cluster()
+ logger.info("Leader key released")
+
+ def demote(self, mode):
+ """Demote PostgreSQL running as master.
+
+ :param mode: One of offline, graceful or immediate.
+ offline is used when connection to DCS is not available.
+ graceful is used when failing over to another node due to user request. May only be called running async.
+ immediate is used when we determine that we are not suitable for master and want to failover quickly
+ without regard for data durability. May only be called synchronously.
+ """
+ assert mode in ['offline', 'graceful', 'immediate']
+ if mode != 'offline':
+ if mode == 'immediate':
+ self.state_handler.stop('immediate', checkpoint=False)
+ else:
+ self.state_handler.stop()
self.state_handler.set_role('demoted')
- self.dcs.delete_leader()
- self.dcs.reset_cluster()
+ self.release_leader_key_voluntarily()
time.sleep(2) # Give a time to somebody to take the leader lock
cluster = self.dcs.get_cluster()
node_to_follow = self._get_node_to_follow(cluster)
- return self.state_handler.follow(node_to_follow, cluster.leader, recovery=True, need_rewind=True)
+ if mode == 'immediate':
+ # We will try to start up as a standby now. If no one takes the leader lock before we finish
+ # recovery we will try to promote ourselves.
+ self._async_executor.schedule('waiting for failover to complete')
+ self._async_executor.run_async(self.state_handler.follow,
+ (node_to_follow, cluster.leader, True, None, True))
+ else:
+ return self.state_handler.follow(node_to_follow, cluster.leader, recovery=True, need_rewind=True)
else:
- self.state_handler.follow(None, None)
+ # Need to become unavailable as soon as possible, so initiate a stop here. However as we can't release
+ # the leader key we don't care about confirming the shutdown quickly and can use a regular stop.
+ self.state_handler.stop(checkpoint=False)
+ self.state_handler.follow(None, None, recovery=True)
def should_run_scheduled_action(self, action_name, scheduled_at, cleanup_fn):
if scheduled_at and not self.is_paused():
@@ -454,6 +529,9 @@ def should_run_scheduled_action(self, action_name, scheduled_at, cleanup_fn):
action_name, scheduled_at.isoformat(), delta)
return False
elif delta < - int(self.dcs.loop_wait * 1.5):
+ # This means that if run_cycle gets delayed for 2.5x loop_wait we skip the
+ # scheduled action. Probably not a problem, if things are that bad we don't
+ # want to be restarting or failing over anyway.
logger.warning('Found a stale %s value, cleaning up: %s',
action_name, scheduled_at.isoformat())
cleanup_fn()
@@ -492,7 +570,7 @@ def process_manual_failover_from_leader(self):
if not failover.candidate or m.name == failover.candidate]
if self.is_failover_possible(members): # check that there are healthy members
self._async_executor.schedule('manual failover: demote')
- self._async_executor.run_async(self.demote)
+ self._async_executor.run_async(self.demote, ('graceful',))
return 'manual failover: demoting myself'
else:
logger.warning('manual failover: no healthy members found, failover is not possible')
@@ -559,7 +637,7 @@ def process_healthy_cluster(self):
else:
# Either there is no connection to DCS or someone else acquired the lock
logger.error('failed to update leader lock')
- self.demote(delete_leader=False)
+ self.demote('offline')
return 'demoted self because failed to update leader lock in DCS'
else:
logger.info('does not have lock')
@@ -614,6 +692,7 @@ def restart_matches(self, role, postgres_version, pending_restart):
def schedule_future_restart(self, restart_data):
with self._async_executor:
+ restart_data['postmaster_start_time'] = self.state_handler.postmaster_start_time()
if not self.patroni.scheduled_restart:
self.patroni.scheduled_restart = restart_data
self.touch_member()
@@ -636,10 +715,11 @@ def future_restart_scheduled(self):
def restart_scheduled(self):
return self._async_executor.scheduled_action == 'restart'
- def restart(self, restart_data=None, run_async=False):
+ def restart(self, restart_data, run_async=False):
""" conditional and unconditional restart """
- if (restart_data and isinstance(restart_data, dict) and
- not self.restart_matches(restart_data.get('role'),
+ assert isinstance(restart_data, dict)
+
+ if (not self.restart_matches(restart_data.get('role'),
restart_data.get('postgres_version'),
('restart_pending' in restart_data))):
return (False, "restart conditions are not satisfied")
@@ -649,17 +729,32 @@ def restart(self, restart_data=None, run_async=False):
if prev is not None:
return (False, prev + ' already in progress')
- do_restart = self.state_handler.restart
+ # Make the main loop to think that we were recovering dead postgres. If we fail
+ # to start postgres after a specified timeout (see below), we need to remove
+ # leader key (if it belong to us) rather than trying to start postgres once again.
+ self.recovering = True
+
+ # No that restart is scheduled we can set timeout for startup, it will get reset
+ # once async executor runs and main loop notices PostgreSQL as up.
+ timeout = restart_data.get('timeout', self.patroni.config['master_start_timeout'])
+ self.set_start_timeout(timeout)
+
+ # For non async cases we want to wait for restart to complete or timeout before returning.
+ do_restart = functools.partial(self.state_handler.restart, timeout)
if self.is_synchronous_mode() and not self.has_lock():
do_restart = functools.partial(self.while_not_sync_standby, do_restart)
if run_async:
self._async_executor.run_async(do_restart)
return (True, 'restart initiated')
- elif self._async_executor.run(do_restart):
- return (True, 'restarted successfully')
else:
- return (False, 'restart failed')
+ res = self._async_executor.run(do_restart)
+ if res:
+ return (True, 'restarted successfully')
+ elif res is None:
+ return (False, 'postgres is still starting')
+ else:
+ return (False, 'restart failed')
def _do_reinitialize(self, cluster):
self.state_handler.stop('immediate')
@@ -712,6 +807,49 @@ def post_recover(self):
return 'failed to start postgres'
return None
+ def handle_starting_instance(self):
+ """Starting up PostgreSQL may take a long time. In case we are the leader we may want to
+ fail over to."""
+
+ # Check if we are in startup, when paused defer to main loop for manual failovers.
+ if not self.state_handler.check_for_startup() or self.is_paused():
+ self.set_start_timeout(None)
+ return None
+
+ # state_handler.state == 'starting' here
+ if self.has_lock():
+ if not self.update_lock():
+ logger.info("Lost lock while starting up. Demoting self.")
+ self.demote('immediate')
+ return 'stopped PostgreSQL while starting up because leader key was lost'
+
+ timeout = self._start_timeout or self.patroni.config['master_start_timeout']
+ time_left = timeout - self.state_handler.time_in_state()
+
+ if time_left <= 0:
+ if self.is_failover_possible(self.cluster.members):
+ logger.info("Demoting self because master startup is taking too long")
+ self.demote('immediate')
+ return 'stopped PostgreSQL because of startup timeout'
+ else:
+ return 'master start has timed out, but continuing to wait because failover is not possible'
+ else:
+ msg = self.process_manual_failover_from_leader()
+ if msg is not None:
+ return msg
+
+ return 'PostgreSQL is still starting up, {0:.0f} seconds until timeout'.format(time_left)
+ else:
+ # Use normal processing for standbys
+ logger.info("Still starting up as a standby.")
+ return None
+
+ def set_start_timeout(self, value):
+ """Sets timeout for starting as master before eligible for failover.
+
+ Must be called when async_executor is busy or in the main thread."""
+ self._start_timeout = value
+
def _run_cycle(self):
dcs_failed = False
try:
@@ -731,6 +869,10 @@ def _run_cycle(self):
if self._async_executor.busy:
return self.handle_long_action_in_progress()
+ msg = self.handle_starting_instance()
+ if msg is not None:
+ return msg
+
# we've got here, so any async action has finished.
if self.recovering and not self.state_handler.need_rewind:
self.recovering = False
@@ -774,7 +916,7 @@ def _run_cycle(self):
# we might not have a valid PostgreSQL connection here if another thread
# stops PostgreSQL, therefore, we only reload replication slots if no
# asynchronous processes are running (should be always the case for the master)
- if not self._async_executor.busy:
+ if not self._async_executor.busy and not self.state_handler.is_starting():
if not self.state_handler.cb_called:
self.state_handler.call_nowait(ACTION_ON_START)
self.state_handler.sync_replication_slots(self.cluster)
@@ -782,7 +924,7 @@ def _run_cycle(self):
dcs_failed = True
logger.error('Error communicating with DCS')
if not self.is_paused() and self.state_handler.is_running() and self.state_handler.is_leader():
- self.demote(delete_leader=False)
+ self.demote('offline')
return 'demoted self because DCS is not accessible and i was a leader'
return 'DCS is not accessible'
except (psycopg2.Error, PostgresConnectionException):
diff --git a/patroni/postgresql.py b/patroni/postgresql.py
--- a/patroni/postgresql.py
+++ b/patroni/postgresql.py
@@ -1,4 +1,3 @@
-from collections import defaultdict
import logging
import os
import psycopg2
@@ -9,10 +8,12 @@
import tempfile
import time
+from collections import defaultdict
+from patroni import call_self
from patroni.exceptions import PostgresConnectionException, PostgresException
-from patroni.utils import compare_values, parse_bool, parse_int, Retry, RetryFailedError
+from patroni.utils import compare_values, parse_bool, parse_int, Retry, RetryFailedError, polling_loop
from six import string_types
-from threading import Lock
+from threading import current_thread, Lock
logger = logging.getLogger(__name__)
@@ -22,6 +23,11 @@
ACTION_ON_RELOAD = "on_reload"
ACTION_ON_ROLE_CHANGE = "on_role_change"
+STATE_RUNNING = 'running'
+STATE_REJECT = 'rejecting connections'
+STATE_NO_RESPONSE = 'not responding'
+STATE_UNKNOWN = 'unknown'
+
def slot_name_from_member_name(member_name):
"""Translate member name to valid PostgreSQL slot name.
@@ -80,6 +86,7 @@ def __init__(self, config):
self._database = config.get('database', 'postgres')
self._data_dir = config['data_dir']
self._pending_restart = False
+ self.__thread_ident = current_thread().ident
self._version_file = os.path.join(self._data_dir, 'PG_VERSION')
self._major_version = self.get_major_version()
@@ -97,6 +104,7 @@ def __init__(self, config):
self._pgpass = config.get('pgpass') or os.path.join(os.path.expanduser('~'), 'pgpass')
self.__cb_called = False
+ self.__cb_pending = None
config_base_name = config.get('config_base_name', 'postgresql')
self._postgresql_conf = os.path.join(self._data_dir, config_base_name + '.conf')
self._postgresql_base_conf_name = config_base_name + '.base.conf'
@@ -113,11 +121,17 @@ def __init__(self, config):
self.retry = Retry(max_tries=-1, deadline=config['retry_timeout']/2.0, max_delay=1,
retry_exceptions=PostgresConnectionException)
+ # Retry 'pg_is_in_recovery()' only once
+ self._is_leader_retry = Retry(max_tries=1, deadline=config['retry_timeout']/2.0, max_delay=1,
+ retry_exceptions=PostgresConnectionException)
+
self._state_lock = Lock()
self.set_state('stopped')
self._role_lock = Lock()
self.set_role(self.get_postgres_role_from_data_directory())
+ self._state_entry_timestamp = None
+
if self.is_running():
self.set_state('running')
self.set_role('master' if self.is_leader() else 'replica')
@@ -179,7 +193,7 @@ def pg_ctl(self, cmd, *args, **kwargs):
:returns: `!True` when return_code == 0, otherwise `!False`"""
pg_ctl = [self._pgcommand('pg_ctl'), cmd]
- if cmd in ('start', 'stop', 'restart'):
+ if cmd == 'stop':
pg_ctl += ['-w']
timeout = self.config.get('pg_ctl_timeout')
if timeout:
@@ -189,11 +203,31 @@ def pg_ctl(self, cmd, *args, **kwargs):
logger.error('Bad value of pg_ctl_timeout: %s', timeout)
return subprocess.call(pg_ctl + ['-D', self._data_dir] + list(args), **kwargs) == 0
+ def pg_isready(self):
+ """Runs pg_isready to see if PostgreSQL is accepting connections.
+
+ :returns: 'ok' if PostgreSQL is up, 'reject' if starting up, 'no_resopnse' if not up."""
+
+ cmd = [self._pgcommand('pg_isready'),
+ '-h', self._local_address['host'],
+ '-p', self._local_address['port'],
+ '-d', self._database]
+ # We only need the username because pg_isready does not try to authenticate
+ if 'username' in self._superuser:
+ cmd.extend(['-U', self._superuser['username']])
+
+ ret = subprocess.call(cmd)
+ return_codes = {0: STATE_RUNNING,
+ 1: STATE_REJECT,
+ 2: STATE_NO_RESPONSE,
+ 3: STATE_UNKNOWN}
+ return return_codes.get(ret, STATE_UNKNOWN)
+
def reload_config(self, config):
server_parameters = self.get_server_parameters(config)
listen_address_changed = pending_reload = pending_restart = False
- if self.is_healthy():
+ if self.state == 'running':
changes = {p: v for p, v in server_parameters.items() if '.' not in p}
changes.update({p: None for p, v in self._server_parameters.items() if not ('.' in p or p in changes)})
if changes:
@@ -250,7 +284,7 @@ def reload_config(self, config):
if pending_reload:
self._write_postgresql_conf()
self.reload()
- self.retry.deadline = config['retry_timeout']/2.0
+ self._is_leader_retry.deadline = self.retry.deadline = config['retry_timeout']/2.0
@property
def pending_restart(self):
@@ -334,6 +368,9 @@ def close_connection(self):
self._cursor_holder = self._connection = None
def _query(self, sql, *params):
+ """We are always using the same cursor, therefore this method is not thread-safe!!!
+ You can call it from different threads only if you are holding explicit `AsyncExecutor` lock,
+ because the main thread is always holding this lock when running HA cycle."""
cursor = None
try:
cursor = self._cursor()
@@ -412,6 +449,9 @@ def run_bootstrap_post_init(self, config):
connstring = 'postgres://{user}@{host}:{port}/{database}'.format(**r)
else:
connstring = 'postgres://{host}:{port}/{database}'.format(**r)
+ if 'password' in r:
+ import getpass
+ r.setdefault('user', os.environ.get('PGUSER', getpass.getuser()))
env = self.write_pgpass(r) if 'password' in r else None
try:
@@ -521,17 +561,37 @@ def create_replica(self, clone_member):
return ret
def is_leader(self):
- return not self.query('SELECT pg_is_in_recovery()').fetchone()[0]
+ try:
+ return not self._is_leader_retry(self._query, 'SELECT pg_is_in_recovery()').fetchone()[0]
+ except RetryFailedError as e: # SELECT pg_is_in_recovery() failed two times
+ if not self.is_starting() and self.pg_isready() == STATE_REJECT:
+ self.set_state('starting')
+ raise PostgresConnectionException(str(e))
def is_running(self):
if not (self._version_file_exists() and os.path.isfile(self._postmaster_pid)):
return False
+ return self.is_pid_running(self.read_pid_file().get('pid', 0))
+
+ def read_pid_file(self):
+ """Reads and parses postmaster.pid from the data directory
+
+ :returns dictionary of values if successful, empty dictionary otherwise
+ """
+ pid_line_names = ['pid', 'data_dir', 'start_time', 'port', 'socket_dir', 'listen_addr', 'shmem_key']
try:
with open(self._postmaster_pid) as f:
- pid = int(f.readline())
- if pid < 0:
- pid = -pid
- return pid > 0 and pid != os.getpid() and pid != os.getppid() and (os.kill(pid, 0) or True)
+ return {name: line.rstrip("\n") for name, line in zip(pid_line_names, f)}
+ except IOError:
+ return {}
+
+ @staticmethod
+ def is_pid_running(pid):
+ try:
+ pid = int(pid)
+ if pid < 0:
+ pid = -pid
+ return pid > 0 and pid != os.getpid() and pid != os.getppid() and (os.kill(pid, 0) or True)
except Exception:
return False
@@ -571,8 +631,48 @@ def state(self):
def set_state(self, value):
with self._state_lock:
self._state = value
+ self._state_entry_timestamp = time.time()
+
+ def time_in_state(self):
+ return time.time() - self._state_entry_timestamp
+
+ def is_starting(self):
+ return self.state == 'starting'
+
+ def wait_for_port_open(self, pid, initiated, timeout):
+ """Waits until PostgreSQL opens ports."""
+ for _ in polling_loop(timeout):
+ pid_file = self.read_pid_file()
+ if len(pid_file) > 5:
+ try:
+ pmpid = int(pid_file['pid'])
+ pmstart = int(pid_file['start_time'])
+
+ if pmstart >= initiated - 2 and pmpid == pid:
+ isready = self.pg_isready()
+ if isready != STATE_NO_RESPONSE:
+ if isready not in [STATE_REJECT, STATE_RUNNING]:
+ logger.warning("Can't determine PostgreSQL startup status, assuming running")
+ return True
+ except ValueError:
+ # Garbage in the pid file
+ pass
+
+ if not self.is_pid_running(pid):
+ logger.error('postmaster is not running')
+ self.set_state('start failed')
+ return False
+
+ logger.warning("Timed out waiting for PostgreSQL to start")
+ return False
+
+ def start(self, timeout=None, block_callbacks=False):
+ """Start PostgreSQL
- def start(self, block_callbacks=False):
+ Waits for postmaster to open ports or terminate so pg_isready can be used to check startup completion
+ or failure.
+
+ :returns: True if start was initiated and postmaster ports are open, False if start failed"""
# make sure we close all connections established against
# the former node, otherwise, we might get a stalled one
# after kill -9, which would report incorrect data to
@@ -583,18 +683,13 @@ def start(self, block_callbacks=False):
logger.error('Cannot start PostgreSQL because one is already running.')
return True
- self.set_role(self.get_postgres_role_from_data_directory())
- if os.path.exists(self._postmaster_pid):
- os.remove(self._postmaster_pid)
- logger.info('Removed %s', self._postmaster_pid)
-
if not block_callbacks:
- self.set_state('starting')
+ self.__cb_pending = ACTION_ON_START
+
+ self.set_role(self.get_postgres_role_from_data_directory())
- env = {'PATH': os.environ.get('PATH')}
- # pg_ctl will write a FATAL if the username is incorrect. exporting PGUSER if necessary
- if 'username' in self._superuser and self._superuser['username'] != os.environ.get('USER'):
- env['PGUSER'] = self._superuser['username']
+ self.set_state('starting')
+ self._pending_restart = False
self._write_postgresql_conf()
self.resolve_connection_addresses()
@@ -602,20 +697,45 @@ def start(self, block_callbacks=False):
opts = {p: self._server_parameters[p] for p, v in self.CMDLINE_OPTIONS.items() if self._major_version >= v[2]}
if self._major_version >= 9.6 and opts['wal_level'] == 'hot_standby':
opts['wal_level'] = 'replica'
- options = ' '.join("--{0}='{1}'".format(p, v) for p, v in opts.items())
-
- ret = self.pg_ctl('start', '-o', options, env=env, preexec_fn=os.setsid)
- self._pending_restart = False
+ options = ['--{0}={1}'.format(p, v) for p, v in opts.items()]
+
+ start_initiated = time.time()
+
+ # Unfortunately `pg_ctl start` does not return postmaster pid to us. Without this information
+ # it is hard to know the current state of postgres startup, so we had to reimplement pg_ctl start
+ # in python. It will start postgres, wait for port to be open and wait until postgres will start
+ # accepting connections.
+ # Important!!! We can't just start postgres using subprocess.Popen, because in this case it
+ # will be our child for the rest of our live and we will have to take care of it (`waitpid`).
+ # So we will use the same approach as pg_ctl uses: start a new process, which will start postgres.
+ # This process will write postmaster pid to stdout and exit immediately. Now it's responsibility
+ # of init process to take care about postmaster.
+ # In order to make everything portable we can't use fork&exec approach here, so we will call
+ # ourselves and pass list of arguments which must be used to start postgres.
+ proc = call_self(['pg_ctl_start', self._pgcommand('postgres'), '-D', self._data_dir] + options, close_fds=True,
+ preexec_fn=os.setsid, stdout=subprocess.PIPE, env={'PATH': os.environ.get('PATH')})
+ pid = int(proc.stdout.readline().strip())
+ proc.wait()
+ logger.info('postmaster pid=%s', pid)
+
+ start_timeout = timeout
+ if not start_timeout:
+ try:
+ start_timeout = float(self.config.get('pg_ctl_timeout', 60))
+ except ValueError:
+ start_timeout = 60
- self.set_state('running' if ret else 'start failed')
+ # We want postmaster to open ports before we continue
+ if not self.wait_for_port_open(pid, start_initiated, start_timeout):
+ return False
- self._schedule_load_slots = ret and self.use_slots
- self.save_configuration_files()
- # block_callbacks is used during restart to avoid
- # running start/stop callbacks in addition to restart ones
- if ret and not block_callbacks:
- self.call_nowait(ACTION_ON_START)
- return ret
+ ret = self.wait_for_startup(start_timeout)
+ if ret is not None:
+ return ret
+ elif timeout is not None:
+ return False
+ else:
+ return None
def checkpoint(self, connect_kwargs=None):
check_not_is_in_recovery = connect_kwargs is not None
@@ -642,7 +762,7 @@ def stop(self, mode='fast', block_callbacks=False, checkpoint=True):
self.set_state('stopped')
return True
- if checkpoint:
+ if checkpoint and not self.is_starting():
self.checkpoint()
if not block_callbacks:
@@ -665,12 +785,70 @@ def reload(self):
self.call_nowait(ACTION_ON_RELOAD)
return ret
- def restart(self):
- self.set_state('restarting')
- ret = self.stop(block_callbacks=True) and self.start(block_callbacks=True)
- if ret:
- self.call_nowait(ACTION_ON_RESTART)
+ def check_for_startup(self):
+ """Checks PostgreSQL status and returns if PostgreSQL is in the middle of startup."""
+ return self.is_starting() and not self.check_startup_state_changed()
+
+ def check_startup_state_changed(self):
+ """Checks if PostgreSQL has completed starting up or failed or still starting.
+
+ Should only be called when state == 'starting'
+
+ :returns: True iff state was changed from 'starting'
+ """
+ ready = self.pg_isready()
+
+ if ready == STATE_REJECT:
+ return False
+ elif ready == STATE_NO_RESPONSE:
+ self.set_state('start failed')
+ self._schedule_load_slots = False # TODO: can remove this?
+ self.save_configuration_files() # TODO: maybe remove this?
+ return True
else:
+ if ready != STATE_RUNNING:
+ # Bad configuration or unexpected OS error. No idea of PostgreSQL status.
+ # Let the main loop of run cycle clean up the mess.
+ logger.warning("%s status returned from pg_isready",
+ "Unknown" if ready == STATE_UNKNOWN else "Invalid")
+ self.set_state('running')
+ self._schedule_load_slots = self.use_slots
+ self.save_configuration_files()
+ # TODO: __cb_pending can be None here after PostgreSQL restarts on its own. Do we want to call the callback?
+ # Previously we didn't even notice.
+ action = self.__cb_pending or ACTION_ON_START
+ self.call_nowait(action)
+ self.__cb_pending = None
+
+ return True
+
+ def wait_for_startup(self, timeout=None):
+ """Waits for PostgreSQL startup to complete or fail.
+
+ :returns: True if start was successful, False otherwise"""
+ if not self.is_starting():
+ # Should not happen
+ logger.warning("wait_for_startup() called when not in starting state")
+
+ while not self.check_startup_state_changed():
+ if timeout and self.time_in_state() > timeout:
+ return None
+ time.sleep(1)
+
+ return self.state == 'running'
+
+ def restart(self, timeout=None):
+ """Restarts PostgreSQL.
+
+ When timeout parameter is set the call will block either until PostgreSQL has started, failed to start or
+ timeout arrives.
+
+ :returns: True when restart was successful and timeout did not expire when waiting.
+ """
+ self.set_state('restarting')
+ self.__cb_pending = ACTION_ON_RESTART
+ ret = self.stop(block_callbacks=True) and self.start(timeout=timeout, block_callbacks=True)
+ if not ret and not self.is_starting():
self.set_state('restart failed ({0})'.format(self.state))
return ret
@@ -691,9 +869,6 @@ def is_healthy(self):
return False
return True
- def check_replication_lag(self, last_leader_operation):
- return (last_leader_operation or 0) - self.xlog_position() <= self.config.get('maximum_lag_on_failover', 0)
-
def write_pg_hba(self, config):
with open(os.path.join(self._data_dir, 'pg_hba.conf'), 'a') as f:
f.write('\n{}\n'.format('\n'.join(config)))
@@ -804,7 +979,7 @@ def cleanup_archive_status(self):
def need_rewind(self):
return self._need_rewind
- def follow(self, member, leader, recovery=False, async_executor=None, need_rewind=None):
+ def follow(self, member, leader, recovery=False, async_executor=None, need_rewind=None, timeout=None):
if need_rewind is not None:
self._need_rewind = need_rewind
@@ -815,11 +990,11 @@ def follow(self, member, leader, recovery=False, async_executor=None, need_rewin
if async_executor:
async_executor.schedule('changing primary_conninfo and restarting')
- async_executor.run_async(self._do_follow, (primary_conninfo, leader, recovery))
+ async_executor.run_async(self._do_follow, (primary_conninfo, leader, recovery, timeout))
else:
- return self._do_follow(primary_conninfo, leader, recovery)
+ return self._do_follow(primary_conninfo, leader, recovery, timeout)
- def _do_follow(self, primary_conninfo, leader, recovery=False):
+ def _do_follow(self, primary_conninfo, leader, recovery=False, timeout=None):
change_role = self.role in ('master', 'demoted')
if leader and leader.name == self.name:
@@ -830,12 +1005,13 @@ def _do_follow(self, primary_conninfo, leader, recovery=False):
elif change_role:
self._need_rewind = True
- self._need_rewind &= bool(leader and leader.conn_url) and self.can_rewind
+ if self._need_rewind and not self.can_rewind:
+ logger.warning("Data directory may be out of sync master, rewind may be needed.")
- if self._need_rewind:
+ if self._need_rewind and leader and leader.conn_url and self.can_rewind:
logger.info("rewind flag is set")
- if self.is_running() and not self.stop():
+ if self.is_running() and not self.stop(checkpoint=False):
return logger.warning('Can not run pg_rewind because postgres is still running')
# prepare pg_rewind connection
@@ -874,12 +1050,13 @@ def _do_follow(self, primary_conninfo, leader, recovery=False):
else:
self.write_recovery_conf(primary_conninfo)
if recovery:
- self.start()
+ self.start(timeout=timeout)
else:
self.restart()
self.set_role('replica')
if change_role:
+ # TODO: postpone this until start completes, or maybe do even earlier
self.call_nowait(ACTION_ON_ROLE_CHANGE)
return True
@@ -935,10 +1112,19 @@ def create_or_update_role(self, name, password, options):
def xlog_position(self, retry=True):
stmt = """SELECT pg_xlog_location_diff(CASE WHEN pg_is_in_recovery()
- THEN pg_last_xlog_replay_location()
+ THEN COALESCE(pg_last_xlog_receive_location(),
+ pg_last_xlog_replay_location())
ELSE pg_current_xlog_location()
END, '0/0')::bigint"""
- return (self.query(stmt) if retry else self._query(stmt)).fetchone()[0]
+
+ # This method could be called from different threads (simultaneously with some other `_query` calls).
+ # If it is called not from main thread we will create a new cursor to execute statement.
+ if current_thread().ident == self.__thread_ident:
+ return (self.query(stmt) if retry else self._query(stmt)).fetchone()[0]
+
+ with self.connection().cursor() as cursor:
+ cursor.execute(stmt)
+ return cursor.fetchone()[0]
def load_replication_slots(self):
if self.use_slots and self._schedule_load_slots:
@@ -1093,7 +1279,7 @@ def pick_synchronous_standby(self, cluster):
# TODO: for synchronous_commit = remote_write we actually want to order on write_location
for app_name, state, sync_state in self.query(
"""SELECT application_name, state, sync_state
- FROM pg_stat_replication
+ FROM pg_stat_replication
ORDER BY flush_location DESC"""):
member = members.get(app_name)
if state != 'streaming' or not member or member.tags.get('nosync', False):
| diff --git a/tests/test_api.py b/tests/test_api.py
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -63,6 +63,10 @@ def fetch_nodes_statuses(members):
def schedule_future_restart(data):
return True
+ @staticmethod
+ def is_lagging(xlog):
+ return False
+
@staticmethod
def get_effective_tags():
return {'nosync': True}
@@ -233,6 +237,10 @@ def make_request(request=None, **kwargs):
mock_dcs.get_cluster.return_value.is_paused.return_value = True
MockRestApiServer(RestApiHandler, make_request(schedule='2016-08-42 12:45TZ+1', role='master'))
+ # Valid timeout
+ MockRestApiServer(RestApiHandler, make_request(timeout='60s'))
+ # Invalid timeout
+ MockRestApiServer(RestApiHandler, make_request(timeout='42towels'))
def test_do_DELETE_restart(self):
for retval in (True, False):
diff --git a/tests/test_config.py b/tests/test_config.py
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -20,9 +20,10 @@ def setUp(self):
def test_no_config(self):
self.assertRaises(SystemExit, Config)
- @patch.object(Config, '_build_effective_configuration', Mock(side_effect=Exception))
def test_set_dynamic_configuration(self):
- self.assertIsNone(self.config.set_dynamic_configuration({'foo': 'bar'}))
+ with patch.object(Config, '_build_effective_configuration', Mock(side_effect=Exception)):
+ self.assertIsNone(self.config.set_dynamic_configuration({'foo': 'bar'}))
+ self.assertTrue(self.config.set_dynamic_configuration({'synchronous_mode': True}))
def test_reload_local_configuration(self):
os.environ.update({
diff --git a/tests/test_ctl.py b/tests/test_ctl.py
--- a/tests/test_ctl.py
+++ b/tests/test_ctl.py
@@ -237,6 +237,9 @@ def test_restart_reinit(self, mock_get_dcs):
assert 'Error: PostgreSQL version' in result.output
assert result.exit_code == 1
+ result = self.runner.invoke(ctl, ['restart', 'alpha', '--pending', '--force', '--timeout', '10min'])
+ assert result.exit_code == 0
+
with patch('requests.delete', Mock(return_value=MockResponse(500))):
# normal restart, the schedule is actually parsed, but not validated in patronictl
result = self.runner.invoke(ctl, ['restart', 'alpha', 'other', '--force',
diff --git a/tests/test_etcd.py b/tests/test_etcd.py
--- a/tests/test_etcd.py
+++ b/tests/test_etcd.py
@@ -42,7 +42,7 @@ def requests_get(url, **kwargs):
if url.startswith('http://local'):
raise requests.exceptions.RequestException()
elif ':8011/patroni' in url:
- response.content = '{"role": "replica", "xlog": {"replayed_location": 0}, "tags": {}}'
+ response.content = '{"role": "replica", "xlog": {"received_location": 0}, "tags": {}}'
elif url.endswith('/members'):
response.content = '[{}]' if url.startswith('http://error') else members
elif url.startswith('http://exhibitor'):
diff --git a/tests/test_ha.py b/tests/test_ha.py
--- a/tests/test_ha.py
+++ b/tests/test_ha.py
@@ -8,7 +8,7 @@
from patroni.dcs import Cluster, ClusterConfig, Failover, Leader, Member, get_dcs, SyncState
from patroni.dcs.etcd import Client
from patroni.exceptions import DCSError, PostgresException
-from patroni.ha import Ha
+from patroni.ha import Ha, _MemberStatus
from patroni.postgresql import Postgresql
from patroni.utils import tzutc
from test_etcd import socket_getaddrinfo, etcd_read, etcd_write, requests_get
@@ -53,6 +53,15 @@ def get_cluster_initialized_with_only_leader(failover=None):
l = get_cluster_initialized_without_leader(leader=True, failover=failover).leader
return get_cluster(True, l, [l], failover, None)
+
+def get_node_status(reachable=True, in_recovery=True, xlog_location=10, nofailover=False):
+ def fetch_node_status(e):
+ tags = {}
+ if nofailover:
+ tags['nofailover'] = True
+ return _MemberStatus(e, reachable, in_recovery, xlog_location, tags)
+ return fetch_node_status
+
future_restart_time = datetime.datetime.now(tzutc) + datetime.timedelta(days=5)
postmaster_start_time = datetime.datetime.now(tzutc)
@@ -100,7 +109,7 @@ def run_async(self, func, args=()):
@patch.object(Postgresql, 'is_running', Mock(return_value=True))
@patch.object(Postgresql, 'is_leader', Mock(return_value=True))
[email protected](Postgresql, 'xlog_position', Mock(return_value=0))
[email protected](Postgresql, 'xlog_position', Mock(return_value=10))
@patch.object(Postgresql, 'call_nowait', Mock(return_value=True))
@patch.object(Postgresql, 'data_directory_empty', Mock(return_value=False))
@patch.object(Postgresql, 'controldata', Mock(return_value={'Database system identifier': '1234567890'}))
@@ -126,6 +135,7 @@ def setUp(self):
mock_machines.__get__ = Mock(return_value=['http://remotehost:2379'])
self.p = Postgresql({'name': 'postgresql0', 'scope': 'dummy', 'listen': '127.0.0.1:5432',
'data_dir': 'data/postgresql0', 'retry_timeout': 10,
+ 'maximum_lag_on_failover': 5,
'authentication': {'superuser': {'username': 'foo', 'password': 'bar'},
'replication': {'username': '', 'password': ''}},
'parameters': {'wal_level': 'hot_standby', 'max_replication_slots': 5, 'foo': 'bar',
@@ -133,7 +143,6 @@ def setUp(self):
self.p.set_state('running')
self.p.set_role('replica')
self.p.postmaster_start_time = MagicMock(return_value=str(postmaster_start_time))
- self.p.check_replication_lag = true
self.p.can_create_replica_without_replication_connection = MagicMock(return_value=False)
self.e = get_dcs({'etcd': {'ttl': 30, 'host': 'ok:2379', 'scope': 'test',
'name': 'foo', 'retry_timeout': 10}})
@@ -292,18 +301,20 @@ def test_reinitialize(self):
self.assertIsNotNone(self.ha.reinitialize())
def test_restart(self):
- self.assertEquals(self.ha.restart(), (True, 'restarted successfully'))
+ self.assertEquals(self.ha.restart({}), (True, 'restarted successfully'))
+ self.p.restart = Mock(return_value=None)
+ self.assertEquals(self.ha.restart({}), (False, 'postgres is still starting'))
self.p.restart = false
- self.assertEquals(self.ha.restart(), (False, 'restart failed'))
+ self.assertEquals(self.ha.restart({}), (False, 'restart failed'))
self.ha.cluster = get_cluster_initialized_with_leader()
self.ha.reinitialize()
- self.assertEquals(self.ha.restart(), (False, 'reinitialize already in progress'))
+ self.assertEquals(self.ha.restart({}), (False, 'reinitialize already in progress'))
with patch.object(self.ha, "restart_matches", return_value=False):
self.assertEquals(self.ha.restart({'foo': 'bar'}), (False, "restart conditions are not satisfied"))
def test_restart_in_progress(self):
with patch('patroni.async_executor.AsyncExecutor.busy', PropertyMock(return_value=True)):
- self.ha.restart(run_async=True)
+ self.ha.restart({}, run_async=True)
self.assertTrue(self.ha.restart_scheduled())
self.assertEquals(self.ha.run_cycle(), 'not healthy enough for leader race')
@@ -319,6 +330,7 @@ def test_restart_in_progress(self):
@patch('requests.get', requests_get)
@patch('time.sleep', Mock())
def test_manual_failover_from_leader(self):
+ self.ha.fetch_node_status = get_node_status()
self.ha.has_lock = true
self.ha.cluster = get_cluster_initialized_with_leader(Failover(0, 'blabla', '', None))
self.assertEquals(self.ha.run_cycle(), 'no action. i am the leader with the lock')
@@ -329,7 +341,9 @@ def test_manual_failover_from_leader(self):
f = Failover(0, self.p.name, '', None)
self.ha.cluster = get_cluster_initialized_with_leader(f)
self.assertEquals(self.ha.run_cycle(), 'manual failover: demoting myself')
- self.ha.fetch_node_status = lambda e: (e, True, True, 0, {'nofailover': 'True'})
+ self.ha.fetch_node_status = get_node_status(nofailover=True)
+ self.assertEquals(self.ha.run_cycle(), 'no action. i am the leader with the lock')
+ self.ha.fetch_node_status = get_node_status(xlog_location=1)
self.assertEquals(self.ha.run_cycle(), 'no action. i am the leader with the lock')
# manual failover from the previous leader to us won't happen if we hold the nofailover flag
self.ha.cluster = get_cluster_initialized_with_leader(Failover(0, 'blabla', self.p.name, None))
@@ -375,17 +389,17 @@ def test_manual_failover_process_no_leader(self):
self.ha.cluster = get_cluster_initialized_without_leader(failover=Failover(0, '', 'leader', None))
self.p.set_role('replica')
self.assertEquals(self.ha.run_cycle(), 'promoted self to leader by acquiring session lock')
- self.ha.fetch_node_status = lambda e: (e, True, True, 0, {}) # accessible, in_recovery
+ self.ha.fetch_node_status = get_node_status() # accessible, in_recovery
self.assertEquals(self.ha.run_cycle(), 'following a different leader because i am not the healthiest node')
self.ha.cluster = get_cluster_initialized_without_leader(failover=Failover(0, self.p.name, '', None))
self.assertEquals(self.ha.run_cycle(), 'following a different leader because i am not the healthiest node')
- self.ha.fetch_node_status = lambda e: (e, False, True, 0, {}) # inaccessible, in_recovery
+ self.ha.fetch_node_status = get_node_status(reachable=False) # inaccessible, in_recovery
self.p.set_role('replica')
self.assertEquals(self.ha.run_cycle(), 'promoted self to leader by acquiring session lock')
# set failover flag to True for all members of the cluster
# this should elect the current member, as we are not going to call the API for it.
self.ha.cluster = get_cluster_initialized_without_leader(failover=Failover(0, '', 'other', None))
- self.ha.fetch_node_status = lambda e: (e, True, True, 0, {'nofailover': 'True'}) # accessible, in_recovery
+ self.ha.fetch_node_status = get_node_status(nofailover=True) # accessible, in_recovery
self.p.set_role('replica')
self.assertEquals(self.ha.run_cycle(), 'promoted self to leader by acquiring session lock')
# same as previous, but set the current member to nofailover. In no case it should be elected as a leader
@@ -409,22 +423,24 @@ def test_manual_failover_process_no_leader_in_pause(self):
def test_is_healthiest_node(self):
self.ha.state_handler.is_leader = false
self.ha.patroni.nofailover = False
- self.ha.fetch_node_status = lambda e: (e, True, True, 0, {})
+ self.ha.fetch_node_status = get_node_status()
self.assertTrue(self.ha.is_healthiest_node())
+ with patch('patroni.postgresql.Postgresql.is_starting', return_value=True):
+ self.assertFalse(self.ha.is_healthiest_node())
self.ha.is_paused = true
self.assertFalse(self.ha.is_healthiest_node())
def test__is_healthiest_node(self):
self.assertTrue(self.ha._is_healthiest_node(self.ha.old_cluster.members))
self.p.is_leader = false
- self.ha.fetch_node_status = lambda e: (e, True, True, 0, {}) # accessible, in_recovery
+ self.ha.fetch_node_status = get_node_status() # accessible, in_recovery
self.assertTrue(self.ha._is_healthiest_node(self.ha.old_cluster.members))
- self.ha.fetch_node_status = lambda e: (e, True, False, 0, {}) # accessible, not in_recovery
- self.assertFalse(self.ha._is_healthiest_node(self.ha.old_cluster.members))
- self.ha.fetch_node_status = lambda e: (e, True, True, 1, {}) # accessible, in_recovery, xlog location ahead
+ self.ha.fetch_node_status = get_node_status(in_recovery=False) # accessible, not in_recovery
self.assertFalse(self.ha._is_healthiest_node(self.ha.old_cluster.members))
- self.p.check_replication_lag = false
+ self.ha.fetch_node_status = get_node_status(xlog_location=11) # accessible, in_recovery, xlog location ahead
self.assertFalse(self.ha._is_healthiest_node(self.ha.old_cluster.members))
+ with patch('patroni.postgresql.Postgresql.xlog_position', return_value=1):
+ self.assertFalse(self.ha._is_healthiest_node(self.ha.old_cluster.members))
self.ha.patroni.nofailover = True
self.assertFalse(self.ha._is_healthiest_node(self.ha.old_cluster.members))
self.ha.patroni.nofailover = False
@@ -514,6 +530,70 @@ def test_no_etcd_connection_in_pause(self):
self.ha.load_cluster_from_dcs = Mock(side_effect=DCSError('Etcd is not responding properly'))
self.assertEquals(self.ha.run_cycle(), 'PAUSE: DCS is not accessible')
+ @patch('patroni.ha.Ha.update_lock', return_value=True)
+ @patch('patroni.ha.Ha.demote')
+ def test_starting_timeout(self, demote, update_lock):
+ def check_calls(seq):
+ for mock, called in seq:
+ if called:
+ mock.assert_called_once()
+ else:
+ mock.assert_not_called()
+ mock.reset_mock()
+ self.ha.has_lock = true
+ self.ha.cluster = get_cluster_initialized_with_leader()
+ self.p.check_for_startup = true
+ self.p.time_in_state = lambda: 30
+ self.assertEquals(self.ha.run_cycle(), 'PostgreSQL is still starting up, 270 seconds until timeout')
+ check_calls([(update_lock, True), (demote, False)])
+
+ self.p.time_in_state = lambda: 350
+ self.ha.fetch_node_status = get_node_status(reachable=False) # inaccessible, in_recovery
+ self.assertEquals(self.ha.run_cycle(),
+ 'master start has timed out, but continuing to wait because failover is not possible')
+ check_calls([(update_lock, True), (demote, False)])
+
+ self.ha.fetch_node_status = get_node_status() # accessible, in_recovery
+ self.assertEquals(self.ha.run_cycle(), 'stopped PostgreSQL because of startup timeout')
+ check_calls([(update_lock, True), (demote, True)])
+
+ update_lock.return_value = False
+ self.assertEquals(self.ha.run_cycle(), 'stopped PostgreSQL while starting up because leader key was lost')
+ check_calls([(update_lock, True), (demote, True)])
+
+ self.ha.has_lock = false
+ self.p.is_leader = false
+ self.assertEquals(self.ha.run_cycle(), 'no action. i am a secondary and i am following a leader')
+ check_calls([(update_lock, False), (demote, False)])
+
+ @patch('time.sleep', Mock())
+ def test_manual_failover_while_starting(self):
+ self.ha.has_lock = true
+ self.p.check_for_startup = true
+ f = Failover(0, self.p.name, '', None)
+ self.ha.cluster = get_cluster_initialized_with_leader(f)
+ self.ha.fetch_node_status = get_node_status() # accessible, in_recovery
+ self.assertEquals(self.ha.run_cycle(), 'manual failover: demoting myself')
+
+ @patch('patroni.ha.Ha.demote')
+ def test_failover_immediately_on_zero_master_start_timeout(self, demote):
+ self.p.is_running = false
+ self.ha.cluster = get_cluster_initialized_with_leader()
+ self.ha.patroni.config.set_dynamic_configuration({'master_start_timeout': 0})
+ self.ha.has_lock = true
+ self.ha.update_lock = true
+ self.ha.fetch_node_status = get_node_status() # accessible, in_recovery
+ self.assertEquals(self.ha.run_cycle(), 'stopped PostgreSQL to fail over after a crash')
+ demote.assert_called_once()
+
+ @patch('time.sleep', Mock())
+ @patch('patroni.postgresql.Postgresql.follow')
+ def test_demote_immediate(self, follow):
+ self.ha.has_lock = true
+ self.e.get_cluster = Mock(return_value=get_cluster_initialized_without_leader())
+ self.ha.demote('immediate')
+ follow.assert_called_once_with(None, None, True, None, True)
+
@patch('time.sleep', Mock())
def test_process_sync_replication(self):
self.ha.has_lock = true
@@ -648,7 +728,7 @@ def test_disable_sync_when_restarting(self, mock_sleep):
get_cluster_initialized_with_leader(sync=('leader', syncstandby))
for syncstandby in ['other', None]])
- self.ha.restart()
+ self.ha.restart({})
mock_restart.assert_called_once()
mock_sleep.assert_called()
@@ -656,7 +736,7 @@ def test_disable_sync_when_restarting(self, mock_sleep):
# Restart is still called when DCS connection fails
mock_restart.reset_mock()
self.ha.dcs.get_cluster = Mock(side_effect=DCSError("foo"))
- self.ha.restart()
+ self.ha.restart({})
mock_restart.assert_called_once()
@@ -665,7 +745,7 @@ def test_disable_sync_when_restarting(self, mock_sleep):
self.ha.dcs.get_cluster.reset_mock()
self.ha.touch_member = Mock(return_value=False)
- self.ha.restart()
+ self.ha.restart({})
mock_restart.assert_called_once()
self.ha.dcs.get_cluster.assert_not_called()
diff --git a/tests/test_patroni.py b/tests/test_patroni.py
--- a/tests/test_patroni.py
+++ b/tests/test_patroni.py
@@ -4,7 +4,7 @@
import time
import unittest
-from mock import Mock, patch
+from mock import Mock, PropertyMock, patch
from patroni.api import RestApiServer
from patroni.async_executor import AsyncExecutor
from patroni.dcs.etcd import Client
@@ -72,6 +72,10 @@ def test_patroni_main(self, mock_popen, mock_getpid):
mock_getpid.return_value = 2
_main()
+ with patch('sys.frozen', Mock(return_value=True), create=True):
+ sys.argv = ['/patroni', 'pg_ctl_start', 'postgres', '-D', '/data', '--max_connections=100']
+ _main()
+
mock_getpid.return_value = 1
def mock_signal(signo, handler):
@@ -98,6 +102,7 @@ def mock_wait():
@patch('patroni.config.Config.save_cache', Mock())
@patch('patroni.config.Config.reload_local_configuration', Mock(return_value=True))
+ @patch.object(Postgresql, 'state', PropertyMock(return_value='running'))
def test_run(self):
self.p.sighup_handler()
self.p.ha.dcs.watch = Mock(side_effect=SleepException)
diff --git a/tests/test_postgresql.py b/tests/test_postgresql.py
--- a/tests/test_postgresql.py
+++ b/tests/test_postgresql.py
@@ -8,9 +8,10 @@
from mock import Mock, MagicMock, PropertyMock, patch, mock_open
from patroni.dcs import Cluster, Leader, Member, SyncState
from patroni.exceptions import PostgresException, PostgresConnectionException
-from patroni.postgresql import Postgresql
+from patroni.postgresql import Postgresql, STATE_REJECT, STATE_NO_RESPONSE
from patroni.utils import RetryFailedError
from six.moves import builtins
+from threading import Thread
class MockCursor(object):
@@ -204,19 +205,64 @@ def test_get_initdb_options(self):
def test_delete_trigger_file(self):
self.p.delete_trigger_file()
+ @patch('subprocess.Popen')
+ @patch.object(Postgresql, 'wait_for_startup')
+ @patch.object(Postgresql, 'wait_for_port_open')
@patch.object(Postgresql, 'is_running')
- def test_start(self, mock_is_running):
+ def test_start(self, mock_is_running, mock_wait_for_port_open, mock_wait_for_startup, mock_popen):
mock_is_running.return_value = True
+ mock_wait_for_port_open.return_value = True
+ mock_wait_for_startup.return_value = False
+ mock_popen.stdout.readline.return_value = '123'
self.assertTrue(self.p.start())
mock_is_running.return_value = False
open(os.path.join(self.data_dir, 'postmaster.pid'), 'w').close()
pg_conf = os.path.join(self.data_dir, 'postgresql.conf')
open(pg_conf, 'w').close()
- self.assertTrue(self.p.start())
+ self.assertFalse(self.p.start())
with open(pg_conf) as f:
lines = f.readlines()
self.assertTrue("f.oo = 'bar'\n" in lines)
+ mock_wait_for_startup.return_value = None
+ self.assertFalse(self.p.start(10))
+ self.assertIsNone(self.p.start())
+
+ mock_wait_for_port_open.return_value = False
+ self.assertFalse(self.p.start())
+
+ @patch.object(Postgresql, 'pg_isready')
+ @patch.object(Postgresql, 'read_pid_file')
+ @patch.object(Postgresql, 'is_pid_running')
+ @patch('patroni.postgresql.polling_loop', Mock(return_value=range(1)))
+ def test_wait_for_port_open(self, mock_is_pid_running, mock_read_pid_file, mock_pg_isready):
+ mock_is_pid_running.return_value = False
+ mock_pg_isready.return_value = STATE_NO_RESPONSE
+
+ # No pid file and postmaster death
+ mock_read_pid_file.return_value = {}
+ self.assertFalse(self.p.wait_for_port_open(42, 100., 1))
+
+ mock_is_pid_running.return_value = True
+
+ # timeout
+ mock_read_pid_file.return_value = {'pid', 1}
+ self.assertFalse(self.p.wait_for_port_open(42, 100., 1))
+
+ # Garbage pid
+ mock_read_pid_file.return_value = {'pid': 'garbage', 'start_time': '101', 'data_dir': '',
+ 'socket_dir': '', 'port': '', 'listen_addr': ''}
+ self.assertFalse(self.p.wait_for_port_open(42, 100., 1))
+
+ # Not ready
+ mock_read_pid_file.return_value = {'pid': '42', 'start_time': '101', 'data_dir': '',
+ 'socket_dir': '', 'port': '', 'listen_addr': ''}
+ self.assertFalse(self.p.wait_for_port_open(42, 100., 1))
+
+ # pg_isready failure
+ mock_pg_isready.return_value = 'garbage'
+ self.assertTrue(self.p.wait_for_port_open(42, 100., 1))
+
@patch.object(Postgresql, 'is_running')
def test_stop(self, mock_is_running):
mock_is_running.return_value = True
@@ -342,8 +388,11 @@ def test_query(self):
self.assertRaises(PostgresConnectionException, self.p.query, 'RetryFailedError')
self.assertRaises(psycopg2.OperationalError, self.p.query, 'blabla')
+ @patch.object(Postgresql, 'pg_isready', Mock(return_value=STATE_REJECT))
def test_is_leader(self):
self.assertTrue(self.p.is_leader())
+ with patch.object(Postgresql, '_query', Mock(side_effect=RetryFailedError(''))):
+ self.assertRaises(PostgresConnectionException, self.p.is_leader)
def test_reload(self):
self.assertTrue(self.p.reload())
@@ -362,6 +411,7 @@ def test_promote(self):
def test_last_operation(self):
self.assertEquals(self.p.last_operation(), '0')
+ Thread(target=self.p.last_operation).start()
@patch('os.path.isfile', Mock(return_value=True))
@patch('os.kill', Mock(side_effect=Exception))
@@ -385,9 +435,6 @@ def test_is_leader_exception(self):
self.p.query = Mock(side_effect=psycopg2.OperationalError("not supported"))
self.assertTrue(self.p.stop())
- def test_check_replication_lag(self):
- self.assertTrue(self.p.check_replication_lag(0))
-
@patch('os.rename', Mock())
@patch('os.path.isdir', Mock(return_value=True))
def test_move_data_directory(self):
@@ -421,12 +468,13 @@ def test_run_bootstrap_post_init(self):
self.assertFalse(self.p.run_bootstrap_post_init({'post_init': '/bin/false'}))
with patch('subprocess.call', Mock(return_value=0)) as mock_method:
+ self.p._superuser.pop('username')
self.assertTrue(self.p.run_bootstrap_post_init({'post_init': '/bin/false'}))
mock_method.assert_called()
args, kwargs = mock_method.call_args
assert 'PGPASSFILE' in kwargs['env'].keys()
- self.assertEquals(args[0], ['/bin/false', 'postgres://test@localhost:5432/postgres'])
+ self.assertEquals(args[0], ['/bin/false', 'postgres://localhost:5432/postgres'])
@patch('patroni.postgresql.Postgresql.create_replica', Mock(return_value=0))
def test_clone(self):
@@ -573,6 +621,88 @@ def test_postmaster_start_time(self):
with patch.object(MockCursor, "execute", side_effect=psycopg2.Error):
self.assertIsNone(self.p.postmaster_start_time())
+ def test_check_for_startup(self):
+ with patch('subprocess.call', return_value=0):
+ self.p._state = 'starting'
+ self.assertFalse(self.p.check_for_startup())
+ self.assertEquals(self.p.state, 'running')
+
+ with patch('subprocess.call', return_value=1):
+ self.p._state = 'starting'
+ self.assertTrue(self.p.check_for_startup())
+ self.assertEquals(self.p.state, 'starting')
+
+ with patch('subprocess.call', return_value=2):
+ self.p._state = 'starting'
+ self.assertFalse(self.p.check_for_startup())
+ self.assertEquals(self.p.state, 'start failed')
+
+ with patch('subprocess.call', return_value=0):
+ self.p._state = 'running'
+ self.assertFalse(self.p.check_for_startup())
+ self.assertEquals(self.p.state, 'running')
+
+ with patch('subprocess.call', return_value=127):
+ self.p._state = 'running'
+ self.assertFalse(self.p.check_for_startup())
+ self.assertEquals(self.p.state, 'running')
+
+ self.p._state = 'starting'
+ self.assertFalse(self.p.check_for_startup())
+ self.assertEquals(self.p.state, 'running')
+
+ def test_wait_for_startup(self):
+ state = {'sleeps': 0, 'num_rejects': 0, 'final_return': 0}
+
+ def increment_sleeps(*args):
+ print("Sleep")
+ state['sleeps'] += 1
+
+ def isready_return(*args):
+ ret = 1 if state['sleeps'] < state['num_rejects'] else state['final_return']
+ print("Isready {0} {1}".format(ret, state))
+ return ret
+
+ def time_in_state(*args):
+ return state['sleeps']
+
+ with patch('subprocess.call', side_effect=isready_return):
+ with patch('time.sleep', side_effect=increment_sleeps):
+ self.p.time_in_state = Mock(side_effect=time_in_state)
+
+ self.p._state = 'stopped'
+ self.assertTrue(self.p.wait_for_startup())
+ self.assertEquals(state['sleeps'], 0)
+
+ self.p._state = 'starting'
+ state['num_rejects'] = 5
+ self.assertTrue(self.p.wait_for_startup())
+ self.assertEquals(state['sleeps'], 5)
+
+ self.p._state = 'starting'
+ state['sleeps'] = 0
+ state['final_return'] = 2
+ self.assertFalse(self.p.wait_for_startup())
+
+ self.p._state = 'starting'
+ state['sleeps'] = 0
+ state['final_return'] = 0
+ self.assertFalse(self.p.wait_for_startup(timeout=2))
+ self.assertEquals(state['sleeps'], 3)
+
+ def test_read_pid_file(self):
+ pidfile = os.path.join(self.data_dir, 'postmaster.pid')
+ if os.path.exists(pidfile):
+ os.remove(pidfile)
+ self.assertEquals(self.p.read_pid_file(), {})
+
+ @patch('os.kill')
+ def test_is_pid_running(self, mock_kill):
+ mock_kill.return_value = True
+ self.assertTrue(self.p.is_pid_running(-100))
+ self.assertFalse(self.p.is_pid_running(0))
+ self.assertFalse(self.p.is_pid_running(None))
+
def test_pick_sync_standby(self):
cluster = Cluster(True, None, self.leader, 0, [self.me, self.other, self.leadermem], None,
SyncState(0, self.me.name, self.leadermem.name))
diff --git a/tests/test_utils.py b/tests/test_utils.py
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -2,7 +2,13 @@
from mock import Mock, patch
from patroni.exceptions import PatroniException
-from patroni.utils import Retry, RetryFailedError
+from patroni.utils import Retry, RetryFailedError, polling_loop
+
+
+class TestUtils(unittest.TestCase):
+
+ def test_polling_loop(self):
+ self.assertEquals(list(polling_loop(0.001, interval=0.001)), [0])
@patch('time.sleep', Mock())
| PostgreSQL taking a long time to start up is considered running and healthy
When PostgreSQL is taking a long time to start up either due to crash recovery or WAL needed to reach consistent state not being available pg_ctl -w will timeout and return with error code 0. Postgresql.start() will happily consider such server to be running. This is, at best, misleading.
There seems to be at least one race condition here.
1. Master boots up and starts Patroni
2. In first iteration of run_cycle Ha.recover() is called, this asynchronously starts postgres.
3. Lock ttl expires.
4. The master is now starting up, will not participate in the race due to async action.
5. Standby will consider itself healthiest because master is not reachable (xlog key missing from JSON) acquires leader key, promotes itself.
6. pg_ctl start timeout expires on old master, it sets role to be replica in Postgresql._do_follow need_rewind == False branch.
7. run_cycle calls follow to restart master with new primary_conninfo while in the middle of recovery, because role != master it will not get rewound.
Basically 3 possible outcomes after a crash
1. Master manages to reacquire the lock in handle_long_action_in_progress in second iteration of run_cycle, will continue to be master once recovery completes. Although it is marked as running when pg_ctl timeout expires, despite not yet accepting connections. Somewhat confusing, but does not require administrator intervention.
2. Lock times out after first but before second iteration, leading to rewind not getting called.
3. Lock times out before first iteration, rewind will get called, everything is peachy.
In some cases (huge checkpoint_timeout, availability is priority over durability) it might be preferrable to refrain from acquiring leader lock before crash recovery is completed.
| > In some cases (huge checkpoint_timeout, availability is priority over durability) it might be preferrable to refrain from acquiring leader lock before crash recovery is completed.
Agree. And it looks like the only way to solve it would be having the option which will switch the behaviour.
In one case it should update the lock even before starting dead postgres, in other case it should remove the leader lock immediately, wait couple of seconds (until someboody else will take the lock) and try to rewind and start.
| 2016-09-08T08:48:09Z | [] | [] |
zalando/patroni | 296 | zalando__patroni-296 | [
"291"
] | 0d701999417877af58f64a9257b6bf0011e08fc4 | diff --git a/patroni/postgresql.py b/patroni/postgresql.py
--- a/patroni/postgresql.py
+++ b/patroni/postgresql.py
@@ -389,6 +389,30 @@ def _initialize(self, config):
self.set_state('initdb failed')
return ret
+ def run_bootstrap_post_init(self, config):
+ """
+ runs a script after initdb is called and waits until completion.
+ passed: cluster name, parameters
+ """
+ if 'post_init' in config:
+ cmd = config['post_init']
+ r = self._local_connect_kwargs
+ if 'user' in r:
+ connstring = 'postgres://{user}@{host}:{port}/{database}'.format(**r)
+ else:
+ connstring = 'postgres://{host}:{port}/{database}'.format(**r)
+
+ env = self.write_pgpass(r) if 'password' in r else None
+ try:
+ ret = subprocess.call(shlex.split(cmd) + [connstring], env=env)
+ except OSError:
+ logger.error('post_init script %s failed', cmd)
+ return False
+ if ret != 0:
+ logger.error('post_init script %s returned non-zero code %d', cmd, ret)
+ return False
+ return True
+
def delete_trigger_file(self):
if os.path.exists(self._trigger_file):
os.unlink(self._trigger_file)
@@ -971,7 +995,7 @@ def clone(self, clone_member):
def bootstrap(self, config):
""" Initialize a new node from scratch and start it. """
- if self._initialize(config) and self.start():
+ if self._initialize(config) and self.start() and self.run_bootstrap_post_init(config):
for name, value in config['users'].items():
if name not in (self._superuser.get('username'), self._replication['username']):
self.create_or_update_role(name, value['password'], value.get('options', []))
| diff --git a/tests/test_postgresql.py b/tests/test_postgresql.py
--- a/tests/test_postgresql.py
+++ b/tests/test_postgresql.py
@@ -395,15 +395,34 @@ def test_bootstrap(self):
with patch('subprocess.call', Mock(return_value=1)):
self.assertRaises(PostgresException, self.p.bootstrap, {})
+ with patch.object(Postgresql, 'run_bootstrap_post_init', Mock(return_value=False)):
+ self.assertRaises(PostgresException, self.p.bootstrap, {})
+
self.p.bootstrap({'users': {'replicator': {'password': 'rep-pass', 'options': ['replication']}},
'pg_hba': ['host replication replicator 127.0.0.1/32 md5',
'hostssl all all 0.0.0.0/0 md5',
- 'host all all 0.0.0.0/0 md5']})
+ 'host all all 0.0.0.0/0 md5'],
+ 'post_init': '/bin/false'})
with open(os.path.join(self.data_dir, 'pg_hba.conf')) as f:
lines = f.readlines()
assert 'host replication replicator 127.0.0.1/32 md5\n' in lines
assert 'host all all 0.0.0.0/0 md5\n' in lines
+ def test_run_bootstrap_post_init(self):
+ with patch('subprocess.call', Mock(return_value=1)):
+ self.assertFalse(self.p.run_bootstrap_post_init({'post_init': '/bin/false'}))
+
+ with patch('subprocess.call', Mock(side_effect=OSError)):
+ self.assertFalse(self.p.run_bootstrap_post_init({'post_init': '/bin/false'}))
+
+ with patch('subprocess.call', Mock(return_value=0)) as mock_method:
+ self.assertTrue(self.p.run_bootstrap_post_init({'post_init': '/bin/false'}))
+
+ mock_method.assert_called()
+ args, kwargs = mock_method.call_args
+ assert 'PGPASSFILE' in kwargs['env'].keys()
+ self.assertEquals(args[0], ['/bin/false', 'postgres://test@localhost:5432/postgres'])
+
@patch('patroni.postgresql.Postgresql.create_replica', Mock(return_value=0))
def test_clone(self):
self.p.clone(self.leader)
| Callback for custom operations after initial bootstrap
Our usecase involves creating a lot of database clusters that need to have some initial database setup (some specific databases with extensions) created on the cluster (so, only once after the initial initdb bootstrapping) before becoming usable.
So we would like to have a way for Patroni to invoke the running of these tasks after the db is created but before the node is deemed ready.
I was thinking on adding a new `on_bootstrap` hook that gets executed after the initial bootstrap currently done [here](https://github.com/zalando/patroni/blob/master/patroni/postgresql.py#L973) and blocks until completion.
Would this make sense?, can you think of any other way to achieve this?
| > I was thinking on adding a new on_bootstrap hook that gets executed after the initial bootstrap currently done here and blocks until completion.
Since there is already `bootstrap` section in the configuration file, probably something like (see below) would be better than `on_bootstrap`
``` yaml
bootstrap:
post_init: /your/script/or/binary
```
Patroni should run this executable and pass connection string as an argument. I think this step should be done right after starting up freshly initialized cluster: [patroni/postgresql.py#L975](https://github.com/zalando/patroni/blob/39d16fe2f95c87793a9227f6c32f2d0953a057b7/patroni/postgresql.py#L975), but before creation of all kind of additional users and roles.
Ok, we're going to work on adding it that way then.
Wouldn't it make sense to execute it _after_ the creation of roles? - so then we can pass the superuser info in the connection string.
> so then we can pass the superuser info in the connection string.
Superuser is created by initdb.
Please never pass password in the connection string. It has to be written into file with the permissions 0600 and filename should be exported as environment variable `PGPASSFILE`. This way any application using `libpq` will be able to "catch" it.
You can take [create_replica](https://github.com/zalando/patroni/blob/master/patroni/postgresql.py#L415) method as an example.
| 2016-09-08T14:54:27Z | [] | [] |
zalando/patroni | 420 | zalando__patroni-420 | [
"419"
] | 875e450ff876f65fa0b6dcf91475453903d164ca | diff --git a/patroni/ha.py b/patroni/ha.py
--- a/patroni/ha.py
+++ b/patroni/ha.py
@@ -886,6 +886,11 @@ def _run_cycle(self):
# is data directory empty?
if self.state_handler.data_directory_empty():
+ # is this instance the leader?
+ if self.has_lock():
+ self.release_leader_key_voluntarily()
+ return 'released leader key voluntarily as data dir empty and currently leader'
+
return self.bootstrap() # new node
# "bootstrap", but data directory is not empty
elif not self.sysid_valid(self.cluster.initialize) and self.cluster.is_unlocked() and not self.is_paused():
| diff --git a/tests/test_ha.py b/tests/test_ha.py
--- a/tests/test_ha.py
+++ b/tests/test_ha.py
@@ -771,3 +771,14 @@ def test_watch(self):
def test_wakup(self):
self.ha.wakeup()
+
+ def test_leader_with_empty_directory(self):
+ self.ha.cluster = get_cluster_initialized_with_leader()
+ self.ha.has_lock = true
+ self.p.data_directory_empty = true
+ self.assertEquals(self.ha.run_cycle(), 'released leader key voluntarily as data dir empty and currently leader')
+
+ # as has_lock is mocked out, we need to fake the leader key release
+ self.ha.has_lock = false
+ # will not say bootstrap from leader as replica can't self elect
+ self.assertEquals(self.ha.run_cycle(), "trying to bootstrap from replica 'other'")
| No election after loss of leader
I am trying to get patroni setup in Kubernetes (well minikube right now) by [adapting](https://github.com/abkfenris/atomicdb) @jberkus [atomicbd](https://github.com/jberkus/atomicdb/tree/master/patroni_petset).
When I kill the leader pod it will restart fast enough that it reacquires the leader key so their is no failover. It then will try to bootstrap from itself.
```sh
2017-03-24 13:11:11,066 INFO: Selected new etcd server http://172.17.0.6:2379
2017-03-24 13:11:11,066 INFO: Starting new HTTP connection (1): 172.17.0.6
2017-03-24 13:11:11,087 INFO: trying to bootstrap from leader 'patroni_0'
2017-03-24 13:11:11,089 INFO: Lock owner: patroni_0; I am patroni_0
2017-03-24 13:11:11,096 INFO: updated leader lock during bootstrap from leader 'patroni_0'
pg_basebackup: could not connect to server: could not translate host name "patroni-0.patroni" to address: Name or service not known
2017-03-24 13:11:11,129 ERROR: Error when fetching backup: pg_basebackup exited with code=1
2017-03-24 13:11:11,130 WARNING: Trying again in 5 seconds
2017-03-24 13:11:16,090 INFO: Lock owner: patroni_0; I am patroni_0
2017-03-24 13:11:16,097 INFO: updated leader lock during bootstrap from leader 'patroni_0'
pg_basebackup: could not connect to server: could not connect to server: Connection refused
Is the server running on host "patroni-0.patroni" (172.17.0.7) and accepting
TCP/IP connections on port 5432?
2017-03-24 13:11:16,146 ERROR: Error when fetching backup: pg_basebackup exited with code=1
2017-03-24 13:11:16,146 ERROR: failed to bootstrap from leader 'patroni_0'
```
The other two pods don't realize that the leader is trying to bootstrap and try to keep following it rather than having an election.
```sh
[patroni-2] 2017-03-24 13:23:56,100 INFO: Lock owner: patroni_0; I am patroni_2
[patroni-2] 2017-03-24 13:23:56,100 INFO: does not have lock
[patroni-1] 2017-03-24 13:23:56,097 INFO: Lock owner: patroni_0; I am patroni_1
[patroni-1] 2017-03-24 13:23:56,098 INFO: does not have lock
[patroni-1] 2017-03-24 13:23:56,108 INFO: no action. i am a secondary and i am following a leader
[patroni-2] 2017-03-24 13:23:56,110 INFO: no action. i am a secondary and i am following a leader
[patroni-2] FATAL: could not connect to the primary server: could not connect to server: Connection refused
[patroni-2] Is the server running on host "patroni-0.patroni" (172.17.0.7) and accepting
[patroni-2] TCP/IP connections on port 5432?
[patroni-2]
[patroni-1] FATAL: could not connect to the primary server: could not connect to server: Connection refused
[patroni-1] Is the server running on host "patroni-0.patroni" (172.17.0.7) and accepting
[patroni-1] TCP/IP connections on port 5432?
```
As far as I can tell, there is a method ([ha.release_leader_key_voluntarily](https://github.com/zalando/patroni/blob/8fda95780451029cee6b9dc3fdcf9f71ab4480a6/patroni/ha.py#L474)) for the leader to give up the key but it doesn't look like there is a check if a newly created instance is the leader and to release the key.
| Yeah, the lock should be released if the master doesn't have data. I'll look into it.
This hasn't come up previously because in a multi-machine configuration the original leader node never comes back that fast unless it's mounting the same storage (in which case it's still the master). However, it should Do The Right Thing regardless. | 2017-03-28T10:26:48Z | [] | [] |
zalando/patroni | 466 | zalando__patroni-466 | [
"465"
] | 23e6f65156256b45fe55c1508ae7e20303831a03 | diff --git a/patroni/postgresql.py b/patroni/postgresql.py
--- a/patroni/postgresql.py
+++ b/patroni/postgresql.py
@@ -99,6 +99,7 @@ def __init__(self, config):
self._bin_dir = config.get('bin_dir') or ''
self._database = config.get('database', 'postgres')
self._data_dir = config['data_dir']
+ self._config_dir = config.get('config_dir') or self._data_dir
self._pending_restart = False
self.__thread_ident = current_thread().ident
@@ -120,9 +121,9 @@ def __init__(self, config):
self.__cb_called = False
self.__cb_pending = None
config_base_name = config.get('config_base_name', 'postgresql')
- self._postgresql_conf = os.path.join(self._data_dir, config_base_name + '.conf')
+ self._postgresql_conf = os.path.join(self._config_dir, config_base_name + '.conf')
self._postgresql_base_conf_name = config_base_name + '.base.conf'
- self._postgresql_base_conf = os.path.join(self._data_dir, self._postgresql_base_conf_name)
+ self._postgresql_base_conf = os.path.join(self._config_dir, self._postgresql_base_conf_name)
self._recovery_conf = os.path.join(self._data_dir, 'recovery.conf')
self._postmaster_pid = os.path.join(self._data_dir, 'postmaster.pid')
self._trigger_file = config.get('recovery_conf', {}).get('trigger_file') or 'promote'
@@ -162,11 +163,11 @@ def __init__(self, config):
@property
def _configuration_to_save(self):
- configuration = [self._postgresql_conf]
+ configuration = [os.path.basename(self._postgresql_conf)]
if 'custom_conf' not in self.config:
- configuration.append(self._postgresql_base_conf)
+ configuration.append(os.path.basename(self._postgresql_base_conf))
if not self.config['parameters'].get('hba_file'):
- configuration.append(os.path.join(self._data_dir, 'pg_hba.conf'))
+ configuration.append('pg_hba.conf')
return configuration
@property
@@ -826,8 +827,9 @@ def start(self, timeout=None, block_callbacks=False, task=None):
return False
start_initiated = time.time()
- proc = call_self(['pg_ctl_start', self._pgcommand('postgres'), '-D', self._data_dir] + options,
- close_fds=True, preexec_fn=os.setsid, stdout=subprocess.PIPE,
+ proc = call_self(['pg_ctl_start', self._pgcommand('postgres'), '-D', self._data_dir,
+ '--config-file={}'.format(self._postgresql_conf)] + options, close_fds=True,
+ preexec_fn=os.setsid, stdout=subprocess.PIPE,
env={p: os.environ[p] for p in ('PATH', 'LC_ALL', 'LANG') if p in os.environ})
pid = int(proc.stdout.readline().strip())
proc.wait()
@@ -1060,6 +1062,9 @@ def _write_postgresql_conf(self):
with open(self._postgresql_conf, 'w') as f:
f.write('# Do not edit this file manually!\n# It will be overwritten by Patroni!\n')
f.write("include '{0}'\n\n".format(self.config.get('custom_conf') or self._postgresql_base_conf_name))
+ f.write("data_directory = '{}'\n".format(self._data_dir))
+ f.write("hba_file = '{}'\n".format(os.path.join(self._config_dir, 'pg_hba.conf')))
+ f.write("ident_file = '{}'\n".format(os.path.join(self._config_dir, 'pg_ident.conf')))
for name, value in sorted(self._server_parameters.items()):
f.write("{0} = '{1}'\n".format(name, value))
@@ -1070,7 +1075,7 @@ def is_healthy(self):
return True
def write_pg_hba(self, config):
- with open(os.path.join(self._data_dir, 'pg_hba.conf'), 'a') as f:
+ with open(os.path.join(self._config_dir, 'pg_hba.conf'), 'a') as f:
f.write('\n{}\n'.format('\n'.join(config)))
def _replace_pg_hba(self):
@@ -1081,7 +1086,7 @@ def _replace_pg_hba(self):
:returns: True if pg_hba.conf was rewritten.
"""
if not self.config['parameters'].get('hba_file') and self.config.get('pg_hba'):
- with open(os.path.join(self._data_dir, 'pg_hba.conf'), 'w') as f:
+ with open(os.path.join(self._config_dir, 'pg_hba.conf'), 'w') as f:
f.write('# Do not edit this file manually!\n# It will be overwritten by Patroni!\n')
for line in self.config['pg_hba']:
f.write('{0}\n'.format(line))
@@ -1366,8 +1371,10 @@ def save_configuration_files(self):
"""
try:
for f in self._configuration_to_save:
- if os.path.isfile(f):
- shutil.copy(f, f + '.backup')
+ config_file = os.path.join(self._config_dir, f)
+ backup_file = os.path.join(self._data_dir, f + '.backup')
+ if os.path.isfile(config_file):
+ shutil.copy(config_file, backup_file)
except IOError:
logger.exception('unable to create backup copies of configuration files')
@@ -1375,8 +1382,10 @@ def restore_configuration_files(self):
""" restore a previously saved postgresql.conf """
try:
for f in self._configuration_to_save:
- if not os.path.isfile(f) and os.path.isfile(f + '.backup'):
- shutil.copy(f + '.backup', f)
+ config_file = os.path.join(self._config_dir, f)
+ backup_file = os.path.join(self._data_dir, f + '.backup')
+ if not os.path.isfile(config_file) and os.path.isfile(backup_file):
+ shutil.copy(backup_file, config_file)
except IOError:
logger.exception('unable to restore configuration files from backup')
| diff --git a/tests/test_config.py b/tests/test_config.py
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -39,6 +39,7 @@ def test_reload_local_configuration(self):
'PATRONI_POSTGRESQL_LISTEN': '0.0.0.0:5432',
'PATRONI_POSTGRESQL_CONNECT_ADDRESS': '127.0.0.1:5432',
'PATRONI_POSTGRESQL_DATA_DIR': 'data/postgres0',
+ 'PATRONI_POSTGRESQL_CONFIG_DIR': 'data/postgres0',
'PATRONI_POSTGRESQL_PGPASS': '/tmp/pgpass0',
'PATRONI_ETCD_HOST': '127.0.0.1:2379',
'PATRONI_ETCD_URL': 'https://127.0.0.1:2379',
diff --git a/tests/test_postgresql.py b/tests/test_postgresql.py
--- a/tests/test_postgresql.py
+++ b/tests/test_postgresql.py
@@ -168,9 +168,11 @@ class TestPostgresql(unittest.TestCase):
@patch.object(Postgresql, 'is_running', Mock(return_value=True))
def setUp(self):
self.data_dir = 'data/test0'
+ self.config_dir = self.data_dir
if not os.path.exists(self.data_dir):
os.makedirs(self.data_dir)
- self.p = Postgresql({'name': 'test0', 'scope': 'batman', 'data_dir': self.data_dir, 'retry_timeout': 10,
+ self.p = Postgresql({'name': 'test0', 'scope': 'batman', 'data_dir': self.data_dir,
+ 'config_dir': self.config_dir, 'retry_timeout': 10,
'listen': '127.0.0.2, 127.0.0.3:5432', 'connect_address': '127.0.0.2:5432',
'authentication': {'superuser': {'username': 'test', 'password': 'test'},
'replication': {'username': 'replicator', 'password': 'rep-pass'}},
@@ -502,7 +504,7 @@ def test_bootstrap(self):
config = {'users': {'replicator': {'password': 'rep-pass', 'options': ['replication']}}}
self.p.bootstrap(config)
- with open(os.path.join(self.data_dir, 'pg_hba.conf')) as f:
+ with open(os.path.join(self.config_dir, 'pg_hba.conf')) as f:
lines = f.readlines()
self.assertTrue('host all all 0.0.0.0/0 md5\n' in lines)
| Set different directory for configuration files
Hello,
On debian, the configuration files (`postgresql.conf`, `pg_hba.conf`, etc) are not stored in the data directory. It would be great to be able to configure the location of this separate directory. Patroni could override existing configuration files where they are used to be.
It's quite confusing to see configuration files created in the data directory as a debian sysadmin. We are tempted to ignore them but they are effectively used by Patroni. On the other hand, Patroni ignores the configuration files in `/etc`. Using only one location should avoid confusion.
I will understand if you are not agree with this. I was a CentOS administrator few years ago, configuration files where stored in the data directory and everything was ok. Now that I have to manage plenty of debian systems with PostgreSQL running on it, things have changed. This pull request is reflecting this feeling.
The default is to store configuration files in the data directory. This setting is targeting custom installations like debian and any others moving configuration files out of the data directory.
| 2017-07-01T17:20:37Z | [] | [] |
|
zalando/patroni | 531 | zalando__patroni-531 | [
"528"
] | 8a584f7a61581b647900e2c0b2571f714946622b | diff --git a/features/steps/watchdog.py b/features/steps/watchdog.py
--- a/features/steps/watchdog.py
+++ b/features/steps/watchdog.py
@@ -31,7 +31,7 @@ def watchdog_was_closed(context, name):
assert context.pctl.get_watchdog(name).was_closed
-@step('I wait for next {name:w} watchdog ping')
+@step('I reset {name:w} watchdog state')
def watchdog_reset_pinged(context, name):
context.pctl.get_watchdog(name).reset()
diff --git a/patroni/watchdog/base.py b/patroni/watchdog/base.py
--- a/patroni/watchdog/base.py
+++ b/patroni/watchdog/base.py
@@ -133,6 +133,7 @@ def _activate(self):
try:
self.impl.open()
+ actual_timeout = self._set_timeout()
except WatchdogError as e:
logger.warning("Could not activate %s: %s", self.impl.describe(), e)
self.impl = NullWatchdog()
@@ -141,8 +142,6 @@ def _activate(self):
logger.warning("Watchdog implementation can't be disabled."
" Watchdog will trigger after Patroni loses leader key.")
- actual_timeout = self._set_timeout()
-
if not self.impl.is_running or actual_timeout > self.config.timeout:
if self.config.mode == MODE_REQUIRED:
if self.impl.is_null:
diff --git a/patroni/watchdog/linux.py b/patroni/watchdog/linux.py
--- a/patroni/watchdog/linux.py
+++ b/patroni/watchdog/linux.py
@@ -155,21 +155,25 @@ def close(self):
def can_be_disabled(self):
return self.get_support().has_MAGICCLOSE
- def _ioctl(self, func, arg, mutate_arg=False):
+ def _ioctl(self, func, arg):
+ """Runs the specified ioctl on the underlying fd.
+
+ Raises WatchdogError if the device is closed.
+ Raises OSError or IOError (Python 2) when the ioctl fails."""
if self._fd is None:
raise WatchdogError("Watchdog device is closed")
-
- result = fcntl.ioctl(self._fd, func, arg, mutate_arg)
- if result < 0:
- raise IOError(result)
+ fcntl.ioctl(self._fd, func, arg, True)
def get_support(self):
if self._support_cache is None:
info = watchdog_info()
- self._ioctl(WDIOC_GETSUPPORT, info, True)
+ try:
+ self._ioctl(WDIOC_GETSUPPORT, info)
+ except (WatchdogError, OSError, IOError) as e:
+ raise WatchdogError("Could not get information about watchdog device: {}".format(e))
self._support_cache = WatchdogInfo(info.options,
info.firmware_version,
- str(bytearray(info.identity)).rstrip('\x00'))
+ bytearray(info.identity).decode(errors='ignore').rstrip('\x00'))
return self._support_cache
def describe(self):
@@ -180,7 +184,7 @@ def describe(self):
try:
_, version, identity = self.get_support()
ver_str = " (firmware {0})".format(version) if version else ""
- except WatchdogError: # XXX: Can it really be raise when self._fd is not None?
+ except WatchdogError:
pass
return identity + ver_str + dev_str
@@ -199,11 +203,17 @@ def set_timeout(self, timeout):
timeout = int(timeout)
if not 0 < timeout < 0xFFFF:
raise WatchdogError("Invalid timeout {0}. Supported values are between 1 and 65535".format(timeout))
- self._ioctl(WDIOC_SETTIMEOUT, ctypes.c_int(timeout))
+ try:
+ self._ioctl(WDIOC_SETTIMEOUT, ctypes.c_int(timeout))
+ except (WatchdogError, OSError, IOError) as e:
+ raise WatchdogError("Could not set timeout on watchdog device: {}".format(e))
def get_timeout(self):
timeout = ctypes.c_int()
- self._ioctl(WDIOC_GETTIMEOUT, timeout, True)
+ try:
+ self._ioctl(WDIOC_GETTIMEOUT, timeout)
+ except (WatchdogError, OSError, IOError) as e:
+ raise WatchdogError("Could not get timeout on watchdog device: {}".format(e))
return timeout.value
| diff --git a/tests/test_watchdog.py b/tests/test_watchdog.py
--- a/tests/test_watchdog.py
+++ b/tests/test_watchdog.py
@@ -194,15 +194,24 @@ def test_basics(self):
self.assertRaises(WatchdogError, self.impl.set_timeout, -1)
@patch('os.open', Mock(return_value=3))
- @patch('fcntl.ioctl', Mock(return_value=-1))
+ @patch('fcntl.ioctl', Mock(side_effect=OSError))
def test__ioctl(self):
self.assertRaises(WatchdogError, self.impl.get_support)
self.impl.open()
- self.assertRaises(IOError, self.impl.get_support)
+ self.assertRaises(WatchdogError, self.impl.get_support)
def test_is_healthy(self):
self.assertFalse(self.impl.is_healthy)
+ @patch('os.open', Mock(return_value=3))
+ @patch('fcntl.ioctl', Mock(side_effect=OSError))
+ def test_error_handling(self):
+ self.impl.open()
+ self.assertRaises(WatchdogError, self.impl.get_timeout)
+ self.assertRaises(WatchdogError, self.impl.set_timeout, 10)
+ # We still try to output a reasonable string even if getting info errors
+ self.assertEquals(self.impl.describe(), "Linux watchdog device")
+
@patch('os.open', Mock(side_effect=OSError))
def test_open(self):
self.assertRaises(WatchdogError, self.impl.open)
| Patroni python3 watchdog problem
Centos 7, python3
Using watchdog in configuration, the supposed to be leader does not properly start. Issue can be repeated by patronictl failover too.
```
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: Traceback (most recent call last):
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/bin/patroni", line 11, in <module>
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: sys.exit(main())
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/__init__.py", line 173, in main
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: return patroni_main()
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/__init__.py", line 142, in patroni_main
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: patroni.run()
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/__init__.py", line 114, in run
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: logger.info(self.ha.run_cycle())
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/ha.py", line 1056, in run_cycle
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: info = self._run_cycle()
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/ha.py", line 1027, in _run_cycle
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: return self.process_unhealthy_cluster()
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/ha.py", line 657, in process_unhealthy_cluster
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: 'promoted self to leader by acquiring session lock')
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/ha.py", line 345, in enforce_master_role
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: if not self.watchdog.activate():
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/watchdog/base.py", line 36, in wrapped
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: return func(self, *args, **kwargs)
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/watchdog/base.py", line 124, in activate
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: return self._activate()
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/watchdog/base.py", line 144, in _activate
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: actual_timeout = self._set_timeout()
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/watchdog/base.py", line 172, in _set_timeout
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: self.impl.set_timeout(self.config.timeout)
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/watchdog/linux.py", line 202, in set_timeout
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: self._ioctl(WDIOC_SETTIMEOUT, ctypes.c_int(timeout))
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: File "/usr/lib/python3.4/site-packages/patroni/watchdog/linux.py", line 163, in _ioctl
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: if result < 0:
Sep 22 08:39:02 pgdron002d1vteo patroni[2707]: TypeError: unorderable types: bytes() < int()
```
| Hi @DeathBorn,
what patroni version do you use?
Sorry. Patroni 1.3.3. The same was with 1.3.4
@ants, I think this is something for you.
Taking a look at it now. `fcntl.ioctl()` is somehow returning a `bytes` object. Python's documentation says that it is supposed to return an int...
Pythons [HTML documentation](https://docs.python.org/3/library/fcntl.html#fcntl.ioctl) and [source code](https://github.com/python/cpython/blob/master/Modules/fcntlmodule.c#L110) don't match. Fix coming up soon, I need to dig through source history to see how this has changed over the versions.
Until the fix is available the workaround is to just disable watchdog in config:
watchdog:
mode: off | 2017-09-25T09:28:48Z | [] | [] |
zalando/patroni | 544 | zalando__patroni-544 | [
"542"
] | cfdda23e2781558fbfa1341a814fa34719be9c16 | diff --git a/patroni/ha.py b/patroni/ha.py
--- a/patroni/ha.py
+++ b/patroni/ha.py
@@ -1014,6 +1014,7 @@ def _run_cycle(self):
# is data directory empty?
if self.state_handler.data_directory_empty():
+ self.state_handler.set_role('uninitialized')
# In case datadir went away while we were master. TODO: check for this and try to stop postgresql.
self.watchdog.disable()
diff --git a/patroni/version.py b/patroni/version.py
--- a/patroni/version.py
+++ b/patroni/version.py
@@ -1 +1 @@
-__version__ = '1.3.4'
+__version__ = '1.3.5'
| diff --git a/tests/test_ha.py b/tests/test_ha.py
--- a/tests/test_ha.py
+++ b/tests/test_ha.py
@@ -862,6 +862,7 @@ def test_leader_with_empty_directory(self):
self.ha.has_lock = true
self.p.data_directory_empty = true
self.assertEquals(self.ha.run_cycle(), 'released leader key voluntarily as data dir empty and currently leader')
+ self.assertEquals(self.p.role, 'uninitialized')
# as has_lock is mocked out, we need to fake the leader key release
self.ha.has_lock = false
diff --git a/tests/test_postgresql.py b/tests/test_postgresql.py
--- a/tests/test_postgresql.py
+++ b/tests/test_postgresql.py
@@ -905,6 +905,7 @@ def test_single_user_mode(self, subprocess_popen_mock):
self.assertEquals(self.p.single_user_mode(command="CHECKPOINT"), 0)
subprocess_popen_mock.return_value = None
self.assertEquals(self.p.single_user_mode(), 1)
+ self.assertEquals(self.p.single_user_mode(options={'archive_mode': 'on'}), 1)
@patch('os.listdir', Mock(side_effect=[OSError, ['a', 'b']]))
@patch('os.unlink', Mock(side_effect=OSError))
| Patroni does not perform failover if master lost data directory
We are migrating from 1.2 to 1.3.4 and one of our tests fails - we removed data directory and are expecting failover to replica and master reinitialization. But with new version master detects empty dir, releases key and .. wait for leader to bootstrap. Meanwhile replica is considering master as "master" and wait for master too.
From master:
> 2017-10-11 11:35:27,431 ERROR: get_postgresql_status
> Traceback (most recent call last):
> File "/patroni/patroni/api.py", line 405, in get_postgresql_status
> retry=retry)[0]
> File "/patroni/patroni/api.py", line 381, in query
> return retry(self.server.query, sql, *params)
> File "/patroni/patroni/utils.py", line 259, in __call__
> return func(*args, **kwargs)
> File "/patroni/patroni/api.py", line 452, in query
> raise e
> OperationalError: could not open file "base/12404/2600": No such file or directory
>
> 2017-10-11 11:35:27,433 INFO: released leader key voluntarily as data dir empty and currently leader
> ...
> 2017-10-11 11:35:37,416 INFO: Lock owner: None; I am node1
> 2017-10-11 11:35:37,420 INFO: waiting for leader to bootstrap
From slave:
> 2017-10-11 14:20:50,223 INFO: Got response from node1 http://10.129.1.63:8008/patroni: {"state": "unknown", "database_system_identifier": "6475561736777527351", "role": "master", "patroni": {"scope": "common", "version": "1.3.4"}}
> 2017-10-11 14:20:50,262 WARNING: Master (node1) is still alive
> 2017-10-11 14:20:50,267 INFO: following a different leader because i am not the healthiest node
I suppose that replica cannot promote itself because broken master declares wrong status. Broken master declares wrong status because it released key but never update `postgresql.role` value.
| Good catch, will fix it tomorrow. | 2017-10-12T08:27:28Z | [] | [] |
zalando/patroni | 549 | zalando__patroni-549 | [
"548"
] | 7c000f1519955cce6f1ae720ceb6ecead4fa5aef | diff --git a/patroni/postgresql.py b/patroni/postgresql.py
--- a/patroni/postgresql.py
+++ b/patroni/postgresql.py
@@ -17,7 +17,7 @@
from patroni import call_self
from patroni.callback_executor import CallbackExecutor
from patroni.exceptions import PostgresConnectionException
-from patroni.utils import compare_values, parse_bool, parse_int, Retry, RetryFailedError, polling_loop
+from patroni.utils import compare_values, parse_bool, parse_int, Retry, RetryFailedError, polling_loop, int_or_none
from six import string_types
from six.moves.urllib.parse import quote_plus
from threading import current_thread, Lock
@@ -707,7 +707,10 @@ def is_running(self):
if not (self._version_file_exists() and os.path.isfile(self._postmaster_pid)):
# XXX: This is dangerous in case somebody deletes the data directory while PostgreSQL is still running.
return False
- return self.is_pid_running(self.get_pid())
+
+ pidfile = self.read_pid_file()
+ return self._is_postmaster_pid_running(int_or_none(pidfile.get('pid')),
+ start_time=int_or_none(pidfile.get('start_time')))
def read_pid_file(self):
"""Reads and parses postmaster.pid from the data directory
@@ -734,14 +737,29 @@ def get_pid(self):
return 0
@staticmethod
- def is_pid_running(pid):
+ def _is_postmaster_pid_running(pid, start_time=None):
+ # Normalize pid handling missing values and negative pids from postmaster.pid
+ if not pid:
+ return False
+ if pid < 0:
+ pid = -pid
+
try:
- if pid < 0:
- pid = -pid
- return pid > 0 and pid != os.getpid() and pid != os.getppid() and (os.kill(pid, 0) or True)
- except Exception:
+ proc = psutil.Process(pid)
+ except psutil.NoSuchProcess:
return False
+ # If the process is Patroni or Patronis host process or Patronis child process then it's a false positive
+ my_pid = os.getpid()
+ if pid == my_pid or pid == os.getppid() or proc.parent() == my_pid:
+ return False
+
+ # If process start time differs by more than 3 seconds it's a false positive
+ if start_time is not None and abs(proc.create_time() - start_time) > 3:
+ return False
+
+ return True
+
@property
def cb_called(self):
return self.__cb_called
@@ -805,7 +823,7 @@ def wait_for_port_open(self, pid, initiated, timeout):
# Garbage in the pid file
pass
- if not self.is_pid_running(pid):
+ if not self._is_postmaster_pid_running(pid, start_time=initiated):
logger.error('postmaster is not running')
self.set_state('start failed')
return False
@@ -964,7 +982,7 @@ def _do_stop(self, mode, block_callbacks, checkpoint, on_safepoint):
def _wait_for_postmaster_stop(self, pid):
# This wait loop differs subtly from pg_ctl as we check for both the pid file going
# away and if the pid is running. This seems safer.
- while pid == self.get_pid() and self.is_pid_running(pid):
+ while pid == self.get_pid() and self._is_postmaster_pid_running(pid):
time.sleep(STOP_POLLING_INTERVAL)
def _signal_postmaster_stop(self, mode):
@@ -994,13 +1012,13 @@ def terminate_starting_postmaster(self, pid):
return
logger.warning("Could not send stop signal to PostgreSQL (error: {0})".format(e.errno))
- while self.is_pid_running(pid):
+ while self._is_postmaster_pid_running(pid):
time.sleep(STOP_POLLING_INTERVAL)
def _wait_for_connection_close(self, pid):
try:
with self.connection().cursor() as cur:
- while pid == self.get_pid() and self.is_pid_running(pid): # Need a timeout here?
+ while pid == self.get_pid() and self._is_postmaster_pid_running(pid): # Need a timeout here?
cur.execute("SELECT 1")
time.sleep(STOP_POLLING_INTERVAL)
except psycopg2.Error:
diff --git a/patroni/utils.py b/patroni/utils.py
--- a/patroni/utils.py
+++ b/patroni/utils.py
@@ -280,3 +280,11 @@ def polling_loop(timeout, interval=1):
yield iteration
iteration += 1
time.sleep(interval)
+
+
+def int_or_none(val):
+ """Returns integer value of the parameter if convertible to int, None otherwise."""
+ try:
+ return int(val)
+ except (ValueError, TypeError):
+ return None
| diff --git a/tests/test_postgresql.py b/tests/test_postgresql.py
--- a/tests/test_postgresql.py
+++ b/tests/test_postgresql.py
@@ -2,6 +2,7 @@
import mock # for the mock.call method, importing it without a namespace breaks python3
import os
import psycopg2
+import psutil
import shutil
import subprocess
import unittest
@@ -238,17 +239,17 @@ def test_start(self, mock_is_running, mock_wait_for_port_open, mock_wait_for_sta
@patch.object(Postgresql, 'pg_isready')
@patch.object(Postgresql, 'read_pid_file')
- @patch.object(Postgresql, 'is_pid_running')
+ @patch.object(Postgresql, '_is_postmaster_pid_running')
@patch('patroni.postgresql.polling_loop', Mock(return_value=range(1)))
- def test_wait_for_port_open(self, mock_is_pid_running, mock_read_pid_file, mock_pg_isready):
- mock_is_pid_running.return_value = False
+ def test_wait_for_port_open(self, mock_is_postmaster_pid_running, mock_read_pid_file, mock_pg_isready):
+ mock_is_postmaster_pid_running.return_value = False
mock_pg_isready.return_value = STATE_NO_RESPONSE
# No pid file and postmaster death
mock_read_pid_file.return_value = {}
self.assertFalse(self.p.wait_for_port_open(42, 100., 1))
- mock_is_pid_running.return_value = True
+ mock_is_postmaster_pid_running.return_value = True
# timeout
mock_read_pid_file.return_value = {'pid', 1}
@@ -289,7 +290,7 @@ def test_stop(self, mock_get_pid, mock_is_running):
self.assertFalse(self.p.stop())
self.assertTrue(self.p.stop())
with patch.object(Postgresql, '_signal_postmaster_stop', Mock(return_value=(123, None))):
- with patch.object(Postgresql, 'is_pid_running', Mock(side_effect=[True, False, False])):
+ with patch.object(Postgresql, '_is_postmaster_pid_running', Mock(side_effect=[True, False, False])):
self.assertTrue(self.p.stop())
def test_restart(self):
@@ -772,12 +773,13 @@ def test_read_pid_file(self):
os.remove(pidfile)
self.assertEquals(self.p.read_pid_file(), {})
- @patch('os.kill')
- def test_is_pid_running(self, mock_kill):
- mock_kill.return_value = True
- self.assertTrue(self.p.is_pid_running(-100))
- self.assertFalse(self.p.is_pid_running(0))
- self.assertFalse(self.p.is_pid_running(None))
+ @patch('psutil.Process')
+ def test_is_postmaster_pid_running(self, mock_psutil):
+ mock_proc = Mock()
+ mock_psutil.return_value = mock_proc
+ self.assertTrue(self.p._is_postmaster_pid_running(-100))
+ self.assertFalse(self.p._is_postmaster_pid_running(0))
+ self.assertFalse(self.p._is_postmaster_pid_running(None))
def test_pick_sync_standby(self):
cluster = Cluster(True, None, self.leader, 0, [self.me, self.other, self.leadermem], None,
@@ -855,20 +857,20 @@ def test_get_pid(self):
@patch.object(Postgresql, '_signal_postmaster_stop', Mock(return_value=(123, None)))
@patch.object(Postgresql, 'get_pid', Mock(return_value=123))
@patch('time.sleep', Mock())
- @patch.object(Postgresql, 'is_pid_running')
- def test__wait_for_connection_close(self, mock_is_pid_running):
- mock_is_pid_running.side_effect = [True, False, False]
+ @patch.object(Postgresql, '_is_postmaster_pid_running')
+ def test__wait_for_connection_close(self, mock_is_postmaster_pid_running):
+ mock_is_postmaster_pid_running.side_effect = [True, False, False]
mock_callback = Mock()
self.p.stop(on_safepoint=mock_callback)
- mock_is_pid_running.side_effect = [True, False, False]
+ mock_is_postmaster_pid_running.side_effect = [True, False, False]
with patch.object(MockCursor, "execute", Mock(side_effect=psycopg2.Error)):
self.p.stop(on_safepoint=mock_callback)
@patch.object(Postgresql, 'is_running', Mock(return_value=True))
@patch.object(Postgresql, '_signal_postmaster_stop', Mock(return_value=(123, None)))
@patch.object(Postgresql, 'get_pid', Mock(return_value=123))
- @patch.object(Postgresql, 'is_pid_running', Mock(return_value=False))
+ @patch.object(Postgresql, '_is_postmaster_pid_running', Mock(return_value=False))
@patch('psutil.Process')
def test__wait_for_user_backends_to_close(self, mock_psutil):
child = Mock()
@@ -878,8 +880,9 @@ def test__wait_for_user_backends_to_close(self, mock_psutil):
self.p.stop(on_safepoint=mock_callback)
@patch('os.kill', Mock(side_effect=[OSError(errno.ESRCH, ''), OSError]))
+ @patch('psutil.Process', Mock(side_effect=[psutil.NoSuchProcess]))
@patch('time.sleep', Mock())
- @patch.object(Postgresql, 'is_pid_running', Mock(side_effect=[True, False]))
+ @patch.object(Postgresql, '_is_postmaster_pid_running', Mock(side_effect=[True, False]))
def test_terminate_starting_postmaster(self):
self.p.terminate_starting_postmaster(123)
self.p.terminate_starting_postmaster(123)
| is_pid_running() needs to check if the process is actually postgres
Debugged a system where async executor was stuck in `_wait_for_postmaster_stop()`. There was a postmaster.pid left over from before power loss, the pid it contained was the same as the async executor threads PID, but different from Patroni pid. This means that the pid didn't match os.getpid(), but os.kill still succeeded.
I think we should also compare the start time in the pid file with the start time of the running process.
| 2017-10-24T11:25:14Z | [] | [] |
|
zalando/patroni | 578 | zalando__patroni-578 | [
"415"
] | 84de53603fba8ab89934d9c30771d6f71b5b3810 | diff --git a/patroni/api.py b/patroni/api.py
--- a/patroni/api.py
+++ b/patroni/api.py
@@ -80,6 +80,14 @@ def do_GET(self, write_status_code_only=False):
patroni = self.server.patroni
cluster = patroni.dcs.cluster
+
+ def is_synchronous():
+ return (cluster.is_synchronous_mode() and cluster.sync
+ and cluster.sync.sync_standby == patroni.postgresql.name)
+
+ def is_balanceable_replica():
+ return response.get('role') == 'replica' and not patroni.noloadbalance
+
if cluster: # dcs available
if cluster.leader and cluster.leader.name == patroni.postgresql.name: # is_leader
status_code = 200 if 'master' in path else 503
@@ -87,6 +95,10 @@ def do_GET(self, write_status_code_only=False):
status_code = 503
elif response['role'] == 'master': # running as master but without leader lock!!!!
status_code = 503
+ elif path in ('/sync', '/synchronous'):
+ status_code = 200 if is_balanceable_replica() and is_synchronous() else 503
+ elif path in ('/async', '/asynchronous'):
+ status_code = 200 if is_balanceable_replica() and not is_synchronous() else 503
elif response['role'] in path: # response['role'] != 'master'
status_code = 503 if patroni.noloadbalance else 200
else:
| diff --git a/tests/test_api.py b/tests/test_api.py
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -92,7 +92,7 @@ class MockPatroni(object):
dcs = Mock()
tags = {}
version = '0.00'
- noloadbalance = Mock(return_value=False)
+ noloadbalance = PropertyMock(return_value=False)
scheduled_restart = {'schedule': future_restart_time,
'postmaster_start_time': postgresql.postmaster_start_time()}
@@ -140,6 +140,12 @@ def test_do_GET(self):
with patch.object(RestApiHandler, 'get_postgresql_status', Mock(return_value={'role': 'master'})):
MockRestApiServer(RestApiHandler, 'GET /replica')
MockRestApiServer(RestApiHandler, 'GET /master')
+ MockPatroni.dcs.cluster.sync.sync_standby = MockPostgresql.name
+ MockPatroni.dcs.cluster.is_synchronous_mode = Mock(return_value=True)
+ with patch.object(RestApiHandler, 'get_postgresql_status', Mock(return_value={'role': 'replica'})):
+ MockRestApiServer(RestApiHandler, 'GET /synchronous')
+ with patch.object(RestApiHandler, 'get_postgresql_status', Mock(return_value={'role': 'replica'})):
+ MockRestApiServer(RestApiHandler, 'GET /asynchronous')
MockPatroni.dcs.cluster.leader.name = MockPostgresql.name
MockRestApiServer(RestApiHandler, 'GET /replica')
MockPatroni.dcs.cluster = None
| Add new healthcheck endpoint to Patroni api
It should return 200 only if the node is running as a synchronous replica (when it's exposed as synchronous in `sync` key in the DCS).
| 2017-12-19T14:43:11Z | [] | [] |
|
zalando/patroni | 695 | zalando__patroni-695 | [
"694"
] | e5f25117642478bba6ae50514d948b2056417bc3 | diff --git a/patroni/api.py b/patroni/api.py
--- a/patroni/api.py
+++ b/patroni/api.py
@@ -8,7 +8,8 @@
import datetime
from patroni.postgresql import PostgresConnectionException, PostgresException, Postgresql
-from patroni.utils import deep_compare, parse_bool, patch_config, Retry, RetryFailedError, parse_int, tzutc
+from patroni.utils import deep_compare, parse_bool, patch_config, Retry, \
+ RetryFailedError, parse_int, split_host_port, tzutc
from six.moves.BaseHTTPServer import BaseHTTPRequestHandler, HTTPServer
from six.moves.socketserver import ThreadingMixIn
from threading import Thread
@@ -473,6 +474,7 @@ class RestApiServer(ThreadingMixIn, HTTPServer, Thread):
def __init__(self, patroni, config):
self.patroni = patroni
+ self.__listen = None
self.__initialize(config)
self.__set_config_parameters(config)
self.daemon = True
@@ -507,18 +509,25 @@ def check_auth_header(self, auth_header):
def __get_ssl_options(config):
return {option: config[option] for option in ['certfile', 'keyfile'] if option in config}
- def __set_connection_string(self, connect_address):
- self.connection_string = '{0}://{1}/patroni'.format(self.__protocol, connect_address or self.__listen)
-
def __set_config_parameters(self, config):
self.__auth_key = base64.b64encode(config['auth'].encode('utf-8')).decode('utf-8') if 'auth' in config else None
- self.__set_connection_string(config.get('connect_address'))
+ self.connection_string = '{0}://{1}/patroni'.format(self.__protocol,
+ config.get('connect_address') or self.__listen)
def __initialize(self, config):
- self.__ssl_options = self.__get_ssl_options(config)
+ try:
+ host, port = split_host_port(config['listen'], None)
+ except Exception:
+ raise ValueError('Invalid "restapi" config: expected <HOST>:<PORT> for "listen", but got "{0}"'
+ .format(config['listen']))
+
+ if self.__listen is not None: # changing config in runtime
+ self.shutdown()
+
self.__listen = config['listen']
- host, port = config['listen'].rsplit(':', 1)
- HTTPServer.__init__(self, (host, int(port)), RestApiHandler)
+ self.__ssl_options = self.__get_ssl_options(config)
+
+ HTTPServer.__init__(self, (host, port), RestApiHandler)
Thread.__init__(self, target=self.serve_forever)
self._set_fd_cloexec(self.socket)
@@ -530,11 +539,13 @@ def __initialize(self, config):
import ssl
self.socket = ssl.wrap_socket(self.socket, server_side=True, **self.__ssl_options)
self.__protocol = 'https'
- self.__set_connection_string(config.get('connect_address'))
+ return True
def reload_config(self, config):
- self.__set_config_parameters(config)
- if self.__listen != config['listen'] or self.__ssl_options != self.__get_ssl_options(config):
- self.shutdown()
- self.__initialize(config)
+ if 'listen' not in config: # changing config in runtime
+ raise ValueError('Can not find "restapi.listen" config')
+
+ elif (self.__listen != config['listen'] or self.__ssl_options != self.__get_ssl_options(config)) \
+ and self.__initialize(config):
self.start()
+ self.__set_config_parameters(config)
| diff --git a/tests/test_api.py b/tests/test_api.py
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -123,16 +123,14 @@ def sendall(self, *args, **kwargs):
class MockRestApiServer(RestApiServer):
- def __init__(self, Handler, request):
+ def __init__(self, Handler, request, config=None):
self.socket = 0
self.serve_forever = Mock()
BaseHTTPServer.HTTPServer.__init__ = Mock()
MockRestApiServer._BaseServer__is_shut_down = Mock()
MockRestApiServer._BaseServer__shutdown_request = True
- config = {'listen': '127.0.0.1:8008', 'auth': 'test:test'}
+ config = config or {'listen': '127.0.0.1:8008', 'auth': 'test:test', 'certfile': 'dumb'}
super(MockRestApiServer, self).__init__(MockPatroni(), config)
- config['certfile'] = 'dumb'
- self.reload_config(config)
Handler(MockRequest(request), ('0.0.0.0', 8080), self)
@@ -380,3 +378,15 @@ def test_do_POST_failover(self):
post = 'POST /failover HTTP/1.0' + self._authorization + '\nContent-Length: '
MockRestApiServer(RestApiHandler, post + '14\n\n{"leader":"1"}')
MockRestApiServer(RestApiHandler, post + '37\n\n{"candidate":"2","scheduled_at": "1"}')
+
+
+@patch('ssl.wrap_socket', Mock(return_value=0))
+class TestRestApiServer(unittest.TestCase):
+
+ def test_reload_config(self):
+ bad_config = {'listen': 'foo'}
+ self.assertRaises(ValueError, MockRestApiServer, None, '', bad_config)
+ srv = MockRestApiServer(lambda a1, a2, a3: None, '')
+ self.assertRaises(ValueError, srv.reload_config, bad_config)
+ self.assertRaises(ValueError, srv.reload_config, {})
+ srv.reload_config({'listen': '127.0.0.2:8008'})
| Fails with error on start
Patroni terminates with the following error messages on startup:
2018-06-05 21:41:41,692 INFO: Selected new etcd server http://192.168.221.45:2379
Traceback (most recent call last):
File "/usr/local/bin/patroni", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python2.7/dist-packages/patroni/__init__.py", line 176, in main
return patroni_main()
File "/usr/local/lib/python2.7/dist-packages/patroni/__init__.py", line 143, in patroni_main
patroni = Patroni()
File "/usr/local/lib/python2.7/dist-packages/patroni/__init__.py", line 30, in __init__
self.api = RestApiServer(self, self.config['restapi'])
File "/usr/local/lib/python2.7/dist-packages/patroni/api.py", line 476, in __init__
self.__initialize(config)
File "/usr/local/lib/python2.7/dist-packages/patroni/api.py", line 520, in __initialize
host, port = config['listen'].rsplit(':', 1)
ValueError: need more than 1 value to unpack
I have the following setup:
- Fresh Ubuntu 18.04 (running in LXD containers)
- stock postgreSQL
- followed the instructions on [linode.com:](https://www.linode.com/docs/databases/postgresql/create-a-highly-available-postgresql-cluster-using-patroni-and-haproxy/)
PS: I had a version conflict warning in this setup:
/usr/local/lib/python2.7/dist-packages/requests/__init__.py:80: RequestsDependencyWarning: urllib3 (1.23) or chardet (3.0.4) doesn't match a supported version!
which I've found a work around for:
pip uninstall requests
pip install requests
pip uninstall docopt
pip install docopt
Source: [here](https://medium.com/@gloriapalmagonzalez/urllib3-1-22-or-chardet-2-2-1-doesnt-match-a-supported-version-requestsdependencywarning-97c36e0cb561)
No effect on the above error though
| Please check your "listen" configuration option, it apparently needs host/IP + port separated by colon. I flag this as bug as `api.py` should handle this configuration error gracefully. | 2018-06-05T22:11:39Z | [] | [] |
zalando/patroni | 1,191 | zalando__patroni-1191 | [
"1133"
] | f4623c4e8e6aa50d522620a9b9744088d58c10e2 | diff --git a/patroni/api.py b/patroni/api.py
--- a/patroni/api.py
+++ b/patroni/api.py
@@ -13,7 +13,7 @@
from patroni.postgresql import PostgresConnectionException
from patroni.postgresql.misc import postgres_version_to_int, PostgresException
from patroni.utils import deep_compare, parse_bool, patch_config, Retry, \
- RetryFailedError, parse_int, split_host_port, tzutc, uri
+ RetryFailedError, parse_int, split_host_port, tzutc, uri, cluster_as_json
from six.moves.BaseHTTPServer import BaseHTTPRequestHandler, HTTPServer
from six.moves.socketserver import ThreadingMixIn
from threading import Thread
@@ -133,6 +133,14 @@ def do_GET_patroni(self):
response = self.get_postgresql_status(True)
self._write_status_response(200, response)
+ def do_GET_cluster(self):
+ cluster = self.server.patroni.dcs.cluster or self.server.patroni.dcs.get_cluster()
+ self._write_json_response(200, cluster_as_json(cluster))
+
+ def do_GET_history(self):
+ cluster = self.server.patroni.dcs.cluster or self.server.patroni.dcs.get_cluster()
+ self._write_json_response(200, cluster.history and cluster.history.lines or [])
+
def do_GET_config(self):
cluster = self.server.patroni.dcs.cluster or self.server.patroni.dcs.get_cluster()
if cluster.config:
@@ -415,10 +423,7 @@ def get_postgresql_status(self, retry=False):
if self.server.patroni.postgresql.state not in ('running', 'restarting', 'starting'):
raise RetryFailedError('')
- stmt = ("WITH replication_info AS ("
- "SELECT usename, application_name, client_addr, state, sync_state, sync_priority"
- " FROM pg_catalog.pg_stat_replication) SELECT"
- " pg_catalog.to_char(pg_catalog.pg_postmaster_start_time(), 'YYYY-MM-DD HH24:MI:SS.MS TZ'),"
+ stmt = ("SELECT pg_catalog.to_char(pg_catalog.pg_postmaster_start_time(), 'YYYY-MM-DD HH24:MI:SS.MS TZ'),"
" CASE WHEN pg_catalog.pg_is_in_recovery() THEN 0"
" ELSE ('x' || pg_catalog.substr(pg_catalog.pg_{0}file_name("
"pg_catalog.pg_current_{0}_{1}()), 1, 8))::bit(32)::int END,"
@@ -429,8 +434,10 @@ def get_postgresql_status(self, retry=False):
" pg_catalog.pg_{0}_{1}_diff(pg_catalog.pg_last_{0}_replay_{1}(), '0/0')::bigint,"
" pg_catalog.to_char(pg_catalog.pg_last_xact_replay_timestamp(), 'YYYY-MM-DD HH24:MI:SS.MS TZ'),"
" pg_catalog.pg_is_in_recovery() AND pg_catalog.pg_is_{0}_replay_paused(), "
- "(SELECT pg_catalog.array_to_json(pg_catalog.array_agg("
- "pg_catalog.row_to_json(ri))) FROM replication_info ri)")
+ " pg_catalog.array_to_json(pg_catalog.array_agg(pg_catalog.row_to_json(ri))) "
+ "FROM (SELECT (SELECT rolname FROM pg_authid WHERE oid = usesysid) AS usename,"
+ " application_name, client_addr, w.state, sync_state, sync_priority"
+ " FROM pg_catalog.pg_stat_get_wal_senders() w, pg_catalog.pg_stat_get_activity(pid)) AS ri")
row = self.query(stmt.format(self.server.patroni.postgresql.wal_name,
self.server.patroni.postgresql.lsn_name), retry=retry)[0]
diff --git a/patroni/ctl.py b/patroni/ctl.py
--- a/patroni/ctl.py
+++ b/patroni/ctl.py
@@ -14,6 +14,7 @@
import logging
import os
import random
+import six
import subprocess
import sys
import tempfile
@@ -28,12 +29,11 @@
from patroni.exceptions import PatroniException
from patroni.postgresql import Postgresql
from patroni.postgresql.misc import postgres_version_to_int
+from patroni.utils import cluster_as_json, patch_config, polling_loop
from patroni.request import PatroniRequest
-from patroni.utils import patch_config, polling_loop
from patroni.version import __version__
from prettytable import PrettyTable
from six.moves.urllib_parse import urlparse
-from six import text_type
CONFIG_DIR_PATH = click.get_app_dir('patroni')
CONFIG_FILE_PATH = os.path.join(CONFIG_DIR_PATH, 'patronictl.yaml')
@@ -705,80 +705,51 @@ def switchover(obj, cluster_name, master, candidate, force, scheduled):
def output_members(cluster, name, extended=False, fmt='pretty'):
rows = []
logging.debug(cluster)
- leader_name = None
- if cluster.leader:
- leader_name = cluster.leader.name
-
- xlog_location_cluster = cluster.last_leader_operation or 0
-
- # Mainly for consistent pretty printing and watching we sort the output
- cluster.members.sort(key=lambda x: x.name)
+ cluster = cluster_as_json(cluster)
- has_scheduled_restarts = any(m.data.get('scheduled_restart') for m in cluster.members)
- has_pending_restarts = any(m.data.get('pending_restart') for m in cluster.members)
+ columns = ['Cluster', 'Member', 'Host', 'Role', 'State', 'TL', 'Lag in MB']
+ for c in ('Pending restart', 'Scheduled restart'):
+ if extended or any(m.get(c.lower().replace(' ', '_')) for m in cluster['members']):
+ columns.append(c)
# Show Host as 'host:port' if somebody is running on non-standard port or two nodes are running on the same host
- append_port = any(str(m.conn_kwargs()['port']) != '5432' for m in cluster.members) or\
- len(set(m.conn_kwargs()['host'] for m in cluster.members)) < len(cluster.members)
+ append_port = any(m['port'] != 5432 for m in cluster['members']) or\
+ len(set(m['host'] for m in cluster['members'])) < len(cluster['members'])
- for m in cluster.members:
+ for m in cluster['members']:
logging.debug(m)
- role = ''
- if m.name == leader_name:
- role = 'Leader'
- elif m.name == cluster.sync.sync_standby:
- role = 'Sync standby'
+ lag = m.get('lag', '')
+ m.update(cluster=name, member=m['name'], tl=m.get('timeline', ''),
+ role='' if m['role'] == 'replica' else m['role'].replace('_', ' ').title(),
+ lag_in_mb=round(lag/1024/1024) if isinstance(lag, six.integer_types) else lag,
+ pending_restart='*' if m.get('pending_restart') else '')
- xlog_location = m.data.get('xlog_location')
- lag = ''
- if xlog_location is None:
- lag = 'unknown'
- elif xlog_location_cluster >= xlog_location:
- lag = round((xlog_location_cluster - xlog_location)/1024/1024)
-
- host = m.conn_kwargs()['host']
if append_port:
- host += ':{0}'.format(m.conn_kwargs()['port'])
-
- row = [name, m.name, host, role, m.data.get('state', ''), m.data.get('timeline', ''), lag]
-
- if extended or has_pending_restarts:
- row.append('*' if m.data.get('pending_restart') else '')
+ m['host'] = ':'.join([m['host'], str(m['port'])])
- if extended or has_scheduled_restarts:
- value = ''
- scheduled_restart = m.data.get('scheduled_restart')
- if scheduled_restart:
- value = scheduled_restart['schedule']
- if 'postgres_version' in scheduled_restart:
- value += ' if version < {0}'.format(scheduled_restart['postgres_version'])
+ if 'scheduled_restart' in m:
+ value = m['scheduled_restart']['schedule']
+ if 'postgres_version' in m['scheduled_restart']:
+ value += ' if version < {0}'.format(m['scheduled_restart']['postgres_version'])
+ m['scheduled_restart'] = value
- row.append(value)
+ rows.append([m.get(n.lower().replace(' ', '_'), '') for n in columns])
- rows.append(row)
-
- columns = ['Cluster', 'Member', 'Host', 'Role', 'State', 'TL', 'Lag in MB']
- alignment = {'Lag in MB': 'r', 'TL': 'r'}
+ print_output(columns, rows, {'Lag in MB': 'r', 'TL': 'r'}, fmt)
- if extended or has_pending_restarts:
- columns.append('Pending restart')
-
- if extended or has_scheduled_restarts:
- columns.append('Scheduled restart')
-
- print_output(columns, rows, alignment, fmt)
+ if fmt != 'pretty': # Omit service info when using machine-readable formats
+ return
service_info = []
- if cluster.is_paused():
+ if cluster.get('pause'):
service_info.append('Maintenance mode: on')
- if cluster.failover and cluster.failover.scheduled_at:
- info = 'Switchover scheduled at: ' + cluster.failover.scheduled_at.isoformat()
- if cluster.failover.leader:
- info += '\n from: ' + cluster.failover.leader
- if cluster.failover.candidate:
- info += '\n to: ' + cluster.failover.candidate
+ if 'scheduled_switchover' in cluster:
+ info = 'Switchover scheduled at: ' + cluster['scheduled_switchover']['at']
+ for name in ('from', 'to'):
+ if name in cluster['scheduled_switchover']:
+ info += '\n{0:>24}: {1}'.format(name, cluster['scheduled_switchover'][name])
service_info.append(info)
if service_info:
@@ -998,7 +969,7 @@ def listify(string):
buf = io.StringIO()
for line in unified_diff:
# Force cast to unicode as difflib on Python 2.7 returns a mix of unicode and str.
- buf.write(text_type(line))
+ buf.write(six.text_type(line))
buf.seek(0)
class opts:
@@ -1217,6 +1188,19 @@ def version(obj, cluster_name, member_names):
click.echo("{0}: failed to get version: {1}".format(m.name, e))
[email protected]('history', help="Show the history of failovers/switchovers")
+@arg_cluster_name
+@option_format
[email protected]_obj
+def history(obj, cluster_name, fmt):
+ cluster = get_dcs(obj, cluster_name).get_cluster()
+ history = cluster.history and cluster.history.lines or []
+ for line in history:
+ if len(line) < 4:
+ line.append('')
+ print_output(['TL', 'LSN', 'Reason', 'Timestamp'], history, {'TL': 'r', 'LSN': 'r'}, fmt)
+
+
def format_pg_version(version):
if version < 100000:
return "{0}.{1}.{2}".format(version // 10000, version // 100 % 100, version % 100)
diff --git a/patroni/ha.py b/patroni/ha.py
--- a/patroni/ha.py
+++ b/patroni/ha.py
@@ -14,7 +14,7 @@
from patroni.postgresql import ACTION_ON_START, ACTION_ON_ROLE_CHANGE
from patroni.postgresql.misc import postgres_version_to_int
from patroni.postgresql.rewind import Rewind
-from patroni.utils import polling_loop, tzutc
+from patroni.utils import polling_loop, tzutc, is_standby_cluster as _is_standby_cluster
from patroni.dcs import RemoteMember
from threading import RLock
@@ -108,9 +108,7 @@ def get_standby_cluster_config(self):
return config.get('standby_cluster')
def is_standby_cluster(self):
- config = self.get_standby_cluster_config()
- # Check whether or not provided configuration describes a standby cluster
- return isinstance(config, dict) and (config.get('host') or config.get('port') or config.get('restore_command'))
+ return _is_standby_cluster(self.get_standby_cluster_config())
def is_leader(self):
with self._is_leader_lock:
@@ -580,6 +578,7 @@ def is_lagging(self, wal_position):
def _is_healthiest_node(self, members, check_replication_lag=True):
"""This method tries to determine whether I am healthy enough to became a new leader candidate or not."""
+ # We don't call `last_operation()` here because it returns a string
_, my_wal_position = self.state_handler.timeline_wal_position()
if check_replication_lag and self.is_lagging(my_wal_position):
logger.info('My wal position exceeds maximum replication lag')
diff --git a/patroni/postgresql/__init__.py b/patroni/postgresql/__init__.py
--- a/patroni/postgresql/__init__.py
+++ b/patroni/postgresql/__init__.py
@@ -37,15 +37,6 @@
STOP_POLLING_INTERVAL = 1
-cluster_info_query = ("SELECT CASE WHEN pg_catalog.pg_is_in_recovery() THEN 0 "
- "ELSE ('x' || pg_catalog.substr(pg_catalog.pg_{0}file_name("
- "pg_catalog.pg_current_{0}_{1}()), 1, 8))::bit(32)::int END, "
- "CASE WHEN pg_catalog.pg_is_in_recovery() THEN GREATEST("
- " pg_catalog.pg_{0}_{1}_diff(COALESCE("
- "pg_catalog.pg_last_{0}_receive_{1}(), '0/0'), '0/0')::bigint,"
- " pg_catalog.pg_{0}_{1}_diff(pg_catalog.pg_last_{0}_replay_{1}(), '0/0')::bigint)"
- "ELSE pg_catalog.pg_{0}_{1}_diff(pg_catalog.pg_current_{0}_{1}(), '0/0')::bigint END")
-
@contextmanager
def null_context():
@@ -139,6 +130,18 @@ def wal_name(self):
def lsn_name(self):
return 'lsn' if self._major_version >= 100000 else 'location'
+ @property
+ def cluster_info_query(self):
+ return ("SELECT CASE WHEN pg_catalog.pg_is_in_recovery() THEN 0 "
+ "ELSE ('x' || pg_catalog.substr(pg_catalog.pg_{0}file_name("
+ "pg_catalog.pg_current_{0}_{1}()), 1, 8))::bit(32)::int END, "
+ "CASE WHEN pg_catalog.pg_is_in_recovery() THEN GREATEST("
+ " pg_catalog.pg_{0}_{1}_diff(COALESCE("
+ "pg_catalog.pg_last_{0}_receive_{1}(), '0/0'), '0/0')::bigint,"
+ " pg_catalog.pg_{0}_{1}_diff(pg_catalog.pg_last_{0}_replay_{1}(), '0/0')::bigint)"
+ "ELSE pg_catalog.pg_{0}_{1}_diff(pg_catalog.pg_current_{0}_{1}(), '0/0')::bigint "
+ "END").format(self.wal_name, self.lsn_name)
+
def _version_file_exists(self):
return not self.data_directory_empty() and os.path.isfile(self._version_file)
@@ -275,9 +278,8 @@ def reset_cluster_info_state(self):
def _cluster_info_state_get(self, name):
if not self._cluster_info_state:
- stmt = cluster_info_query.format(self.wal_name, self.lsn_name)
try:
- result = self._is_leader_retry(self._query, stmt).fetchone()
+ result = self._is_leader_retry(self._query, self.cluster_info_query).fetchone()
self._cluster_info_state = dict(zip(['timeline', 'wal_position'], result))
except RetryFailedError as e: # SELECT failed two times
self._cluster_info_state = {'error': str(e)}
@@ -721,7 +723,7 @@ def timeline_wal_position(self):
return self._cluster_info_state_get('timeline'), self._cluster_info_state_get('wal_position')
with self.connection().cursor() as cursor:
- cursor.execute(cluster_info_query.format(self.wal_name, self.lsn_name))
+ cursor.execute(self.cluster_info_query)
return cursor.fetchone()[:2]
def postmaster_start_time(self):
diff --git a/patroni/postgresql/config.py b/patroni/postgresql/config.py
--- a/patroni/postgresql/config.py
+++ b/patroni/postgresql/config.py
@@ -118,7 +118,7 @@ def parse_dsn(value):
>>> r == {'application_name': 'mya/pp', 'host': ',/host2', 'sslmode': 'require',\
'password': 'pass', 'port': '/123', 'user': 'u/se'}
True
- >>> r = parse_dsn(" host = 'host' dbname = db\\ name requiressl=1 ")
+ >>> r = parse_dsn(" host = 'host' dbname = db\\\\ name requiressl=1 ")
>>> r == {'host': 'host', 'sslmode': 'require'}
True
>>> parse_dsn('requiressl = 0\\\\') == {'sslmode': 'prefer'}
diff --git a/patroni/utils.py b/patroni/utils.py
--- a/patroni/utils.py
+++ b/patroni/utils.py
@@ -352,3 +352,52 @@ def uri(proto, netloc, path='', user=None):
path = '/{0}'.format(path) if path and not path.startswith('/') else path
user = '{0}@'.format(user) if user else ''
return '{0}://{1}{2}{3}{4}'.format(proto, user, host, port, path)
+
+
+def is_standby_cluster(config):
+ # Check whether or not provided configuration describes a standby cluster
+ return isinstance(config, dict) and (config.get('host') or config.get('port') or config.get('restore_command'))
+
+
+def cluster_as_json(cluster):
+ leader_name = cluster.leader.name if cluster.leader else None
+ xlog_location_cluster = cluster.last_leader_operation or 0
+
+ ret = {'members': []}
+ for m in cluster.members:
+ if m.name == leader_name:
+ config = cluster.config.data if cluster.config and cluster.config.modify_index else {}
+ role = 'standby_leader' if is_standby_cluster(config.get('standby_cluster')) else 'leader'
+ elif m.name == cluster.sync.sync_standby:
+ role = 'sync_standby'
+ else:
+ role = 'replica'
+
+ conn_kwargs = m.conn_kwargs()
+ member = {'name': m.name, 'host': conn_kwargs['host'], 'port': int(conn_kwargs['port']),
+ 'role': role, 'state': m.data.get('state', ''), 'api_url': m.api_url}
+ optional_attributes = ('timeline', 'pending_restart', 'scheduled_restart', 'tags')
+ member.update({n: m.data[n] for n in optional_attributes if n in m.data})
+
+ if m.name != leader_name:
+ xlog_location = m.data.get('xlog_location')
+ if xlog_location is None:
+ member['lag'] = 'unknown'
+ elif xlog_location_cluster >= xlog_location:
+ member['lag'] = xlog_location_cluster - xlog_location
+ else:
+ member['lag'] = 0
+
+ ret['members'].append(member)
+
+ # sort members by name for consistency
+ ret['members'].sort(key=lambda m: m['name'])
+ if cluster.is_paused():
+ ret['pause'] = True
+ if cluster.failover and cluster.failover.scheduled_at:
+ ret['scheduled_switchover'] = {'at': cluster.failover.scheduled_at.isoformat()}
+ if cluster.failover.leader:
+ ret['scheduled_switchover']['from'] = cluster.failover.leader
+ if cluster.failover.candidate:
+ ret['scheduled_switchover']['to'] = cluster.failover.candidate
+ return ret
| diff --git a/tests/__init__.py b/tests/__init__.py
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -100,7 +100,7 @@ def execute(self, sql, *params):
self.results = [(1, 2)]
elif sql.startswith('SELECT pg_catalog.pg_is_in_recovery()'):
self.results = [(False, 2)]
- elif sql.startswith('WITH replication_info AS ('):
+ elif sql.startswith('SELECT pg_catalog.to_char'):
replication_info = '[{"application_name":"walreceiver","client_addr":"1.2.3.4",' +\
'"state":"streaming","sync_state":"async","sync_priority":0}]'
self.results = [('', 0, '', '', '', '', False, replication_info)]
diff --git a/tests/test_api.py b/tests/test_api.py
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -12,6 +12,7 @@
from six import BytesIO as IO
from six.moves import BaseHTTPServer
from . import psycopg2_connect, MockCursor
+from .test_ha import get_cluster_initialized_without_leader
future_restart_time = datetime.datetime.now(tzutc) + datetime.timedelta(days=5)
@@ -159,6 +160,7 @@ class TestRestApiHandler(unittest.TestCase):
def test_do_GET(self):
MockRestApiServer(RestApiHandler, 'GET /replica')
+ MockRestApiServer(RestApiHandler, 'GET /read-only')
with patch.object(RestApiHandler, 'get_postgresql_status', Mock(return_value={})):
MockRestApiServer(RestApiHandler, 'GET /replica')
with patch.object(RestApiHandler, 'get_postgresql_status', Mock(return_value={'role': 'master'})):
@@ -197,6 +199,17 @@ def test_basicauth(self):
self.assertIsNotNone(MockRestApiServer(RestApiHandler, 'POST /restart HTTP/1.0'))
MockRestApiServer(RestApiHandler, 'POST /restart HTTP/1.0\nAuthorization:')
+ @patch.object(MockPatroni, 'dcs')
+ def test_do_GET_cluster(self, mock_dcs):
+ mock_dcs.cluster = get_cluster_initialized_without_leader()
+ mock_dcs.cluster.members[1].data['xlog_location'] = 11
+ self.assertIsNotNone(MockRestApiServer(RestApiHandler, 'GET /cluster'))
+
+ @patch.object(MockPatroni, 'dcs')
+ def test_do_GET_history(self, mock_dcs):
+ mock_dcs.cluster = get_cluster_initialized_without_leader()
+ self.assertIsNotNone(MockRestApiServer(RestApiHandler, 'GET /history'))
+
@patch.object(MockPatroni, 'dcs')
def test_do_GET_config(self, mock_dcs):
mock_dcs.cluster.config.data = {}
diff --git a/tests/test_ctl.py b/tests/test_ctl.py
--- a/tests/test_ctl.py
+++ b/tests/test_ctl.py
@@ -566,6 +566,13 @@ def test_version(self, mock_get_dcs):
result = self.runner.invoke(ctl, ['version', 'dummy'])
assert 'failed to get version' in result.output
+ @patch('patroni.ctl.get_dcs')
+ def test_history(self, mock_get_dcs):
+ mock_get_dcs.return_value.get_cluster = Mock()
+ mock_get_dcs.return_value.get_cluster.return_value.history.lines = [[1, 67176, 'no recovery target specified']]
+ result = self.runner.invoke(ctl, ['history'])
+ assert 'Reason' in result.output
+
def test_format_pg_version(self):
self.assertEqual(format_pg_version(100001), '10.1')
self.assertEqual(format_pg_version(90605), '9.6.5')
diff --git a/tests/test_log.py b/tests/test_log.py
--- a/tests/test_log.py
+++ b/tests/test_log.py
@@ -19,7 +19,6 @@ def tearDown(self):
logging.getLogger().handlers[:] = self._handlers
@patch('logging.FileHandler._open', Mock())
- @patch('logging.Handler.close', Mock(side_effect=Exception))
def test_patroni_logger(self):
config = {
'log': {
@@ -47,13 +46,14 @@ def test_patroni_logger(self):
self.assertEqual(logger.log_handler.backupCount, config['log']['file_num'])
config['log'].pop('dir')
- logger.reload_config(config['log'])
- with patch.object(logging.Logger, 'makeRecord',
- Mock(side_effect=[logging.LogRecord('', logging.INFO, '', 0, '', (), None), Exception])):
+ with patch('logging.Handler.close', Mock(side_effect=Exception)):
+ logger.reload_config(config['log'])
+ with patch.object(logging.Logger, 'makeRecord',
+ Mock(side_effect=[logging.LogRecord('', logging.INFO, '', 0, '', (), None), Exception])):
+ logging.error('test')
logging.error('test')
- logging.error('test')
- with patch.object(Queue, 'put_nowait', Mock(side_effect=Full)):
- self.assertRaises(SystemExit, logger.shutdown)
- self.assertRaises(Exception, logger.shutdown)
+ with patch.object(Queue, 'put_nowait', Mock(side_effect=Full)):
+ self.assertRaises(SystemExit, logger.shutdown)
+ self.assertRaises(Exception, logger.shutdown)
self.assertLessEqual(logger.queue_size, 2) # "Failed to close the old log handler" could be still in the queue
self.assertEqual(logger.records_lost, 0)
| Add 'list' method to API
Currently Patroni cluster can be mostly managed via API, almost all commands from `patronictl` is available. Although not of them documented. But I'm really missing `list` command. It would be great if it will be implemented in foreseeable future.
I.e. for restart cluster nodes in correct order after changing `max_connections` PostgreSQL option, I need to get all nodes and then restart master first an then slaves or vice versa depending on increasing or decreasing the `max_connections` value.
Currently direct DCS (consul in my case) request can be used as workaround, but due different DCS supported by Patroni it is not versatile and pretty hard to support, while Patroni already have all required code.
| Hi @hatifnatt,
feel free to contribute it. | 2019-09-23T15:06:27Z | [] | [] |
zalando/patroni | 1,197 | zalando__patroni-1197 | [
"898"
] | c95275665fca23643591f589d1d237879c274fba | diff --git a/patroni/__init__.py b/patroni/__init__.py
--- a/patroni/__init__.py
+++ b/patroni/__init__.py
@@ -16,6 +16,7 @@ def __init__(self):
from patroni.ha import Ha
from patroni.log import PatroniLogger
from patroni.postgresql import Postgresql
+ from patroni.request import PatroniRequest
from patroni.version import __version__
from patroni.watchdog import Watchdog
@@ -31,6 +32,7 @@ def __init__(self):
self.postgresql = Postgresql(self.config['postgresql'])
self.api = RestApiServer(self, self.config['restapi'])
+ self.request = PatroniRequest(self.config, True)
self.ha = Ha(self)
self.tags = self.get_tags()
@@ -71,6 +73,8 @@ def reload_config(self, sighup=False):
self.tags = self.get_tags()
self.logger.reload_config(self.config.get('log', {}))
self.watchdog.reload_config(self.config)
+ if sighup:
+ self.request.reload_config(self.config)
self.api.reload_config(self.config['restapi'])
self.postgresql.reload_config(self.config['postgresql'], sighup)
self.dcs.reload_config(self.config)
diff --git a/patroni/api.py b/patroni/api.py
--- a/patroni/api.py
+++ b/patroni/api.py
@@ -7,6 +7,7 @@
import dateutil.parser
import datetime
import os
+import six
import socket
from patroni.postgresql import PostgresConnectionException
@@ -20,20 +21,6 @@
logger = logging.getLogger(__name__)
-def check_auth(func):
- """Decorator function to check authorization header.
-
- Usage example:
- @check_auth
- def do_PUT_foo():
- pass
- """
- def wrapper(handler, *args, **kwargs):
- if handler.check_auth_header():
- return func(handler, *args, **kwargs)
- return wrapper
-
-
class RestApiHandler(BaseHTTPRequestHandler):
def _write_response(self, status_code, body, content_type='text/html', headers=None):
@@ -49,14 +36,20 @@ def _write_response(self, status_code, body, content_type='text/html', headers=N
def _write_json_response(self, status_code, response):
self._write_response(status_code, json.dumps(response), content_type='application/json')
- def send_auth_request(self, body):
- headers = {'WWW-Authenticate': 'Basic realm="' + self.server.patroni.__class__.__name__ + '"'}
- self._write_response(401, body, headers=headers)
+ def check_auth(func):
+ """Decorator function to check authorization header or client certificates
+
+ Usage example:
+ @check_auth
+ def do_PUT_foo():
+ pass
+ """
- def check_auth_header(self):
- auth_header = self.headers.get('Authorization')
- status = self.server.check_auth_header(auth_header)
- return not status or self.send_auth_request(status)
+ def wrapper(self, *args, **kwargs):
+ if self.server.check_auth(self):
+ return func(self, *args, **kwargs)
+
+ return wrapper
def _write_status_response(self, status_code, response):
patroni = self.server.patroni
@@ -488,8 +481,8 @@ class RestApiServer(ThreadingMixIn, HTTPServer, Thread):
def __init__(self, patroni, config):
self.patroni = patroni
self.__listen = None
- self.__initialize(config)
- self.__set_config_parameters(config)
+ self.__ssl_options = None
+ self.reload_config(config)
self.daemon = True
def query(self, sql, *params):
@@ -520,13 +513,16 @@ def check_auth_header(self, auth_header):
if not auth_header.startswith('Basic ') or not self.check_basic_auth_key(auth_header[6:]):
return 'not authenticated'
- @staticmethod
- def __get_ssl_options(config):
- return {option: config[option] for option in ['certfile', 'keyfile'] if option in config}
+ def check_auth(self, rh):
+ if not hasattr(rh.request, 'getpeercert') or not rh.request.getpeercert(): # valid client cert isn't present
+ if self.__protocol == 'https' and self.__ssl_options.get('verify_client') in ('required', 'optional'):
+ return rh._write_response(403, 'client certificate required')
- def __set_config_parameters(self, config):
- self.__auth_key = base64.b64encode(config['auth'].encode('utf-8')).decode('utf-8') if 'auth' in config else None
- self.connection_string = uri(self.__protocol, config.get('connect_address') or self.__listen, 'patroni')
+ reason = self.check_auth_header(rh.headers.get('Authorization'))
+ if reason:
+ headers = {'WWW-Authenticate': 'Basic realm="' + self.patroni.__class__.__name__ + '"'}
+ return rh._write_response(401, reason, headers=headers)
+ return True
@staticmethod
def __has_dual_stack():
@@ -545,7 +541,7 @@ def __has_dual_stack():
def __httpserver_init(self, host, port):
dual_stack = self.__has_dual_stack()
- if host == '':
+ if host in ('', '*'):
host = None
info = socket.getaddrinfo(host, port, socket.AF_UNSPEC, socket.SOCK_STREAM, 0, socket.AI_PASSIVE)
@@ -555,43 +551,56 @@ def __httpserver_init(self, host, port):
self.address_family = info[0][0]
HTTPServer.__init__(self, info[0][-1][:2], RestApiHandler)
- def __initialize(self, config):
+ def __initialize(self, listen, ssl_options):
try:
- host, port = split_host_port(config['listen'], None)
+ host, port = split_host_port(listen, None)
except Exception:
raise ValueError('Invalid "restapi" config: expected <HOST>:<PORT> for "listen", but got "{0}"'
- .format(config['listen']))
+ .format(listen))
- if self.__listen is not None: # changing config in runtime
+ reloading_config = self.__listen is not None # changing config in runtime
+ if reloading_config:
self.shutdown()
- self.__listen = config['listen']
- self.__ssl_options = self.__get_ssl_options(config)
+ self.__listen = listen
+ self.__ssl_options = ssl_options
self.__httpserver_init(host, port)
Thread.__init__(self, target=self.serve_forever)
self._set_fd_cloexec(self.socket)
- self.__protocol = 'http'
-
# wrap socket with ssl if 'certfile' is defined in a config.yaml
# Sometime it's also needed to pass reference to a 'keyfile'.
- if self.__ssl_options.get('certfile'):
+ self.__protocol = 'https' if ssl_options.get('certfile') else 'http'
+ if self.__protocol == 'https':
import ssl
- ctx = ssl.create_default_context(ssl.Purpose.CLIENT_AUTH)
- ctx.load_cert_chain(**self.__ssl_options)
+ ctx = ssl.create_default_context(ssl.Purpose.CLIENT_AUTH, cafile=ssl_options.get('cafile'))
+ ctx.load_cert_chain(certfile=ssl_options['certfile'], keyfile=ssl_options.get('keyfile'))
+ verify_client = ssl_options.get('verify_client')
+ if verify_client:
+ modes = {'none': ssl.CERT_NONE, 'optional': ssl.CERT_OPTIONAL, 'required': ssl.CERT_REQUIRED}
+ if verify_client in modes:
+ ctx.verify_mode = modes[verify_client]
+ else:
+ logger.error('Bad value in the "restapi.verify_client": %s', verify_client)
self.socket = ctx.wrap_socket(self.socket, server_side=True)
- self.__protocol = 'https'
- return True
+ if reloading_config:
+ self.start()
def reload_config(self, config):
if 'listen' not in config: # changing config in runtime
raise ValueError('Can not find "restapi.listen" config')
- elif (self.__listen != config['listen'] or self.__ssl_options != self.__get_ssl_options(config)) \
- and self.__initialize(config):
- self.start()
- self.__set_config_parameters(config)
+ ssl_options = {n: config[n] for n in ('certfile', 'keyfile', 'cafile') if n in config}
+
+ if isinstance(config.get('verify_client'), six.string_types):
+ ssl_options['verify_client'] = config['verify_client'].lower()
+
+ if self.__listen != config['listen'] or self.__ssl_options != ssl_options:
+ self.__initialize(config['listen'], ssl_options)
+
+ self.__auth_key = base64.b64encode(config['auth'].encode('utf-8')).decode('utf-8') if 'auth' in config else None
+ self.connection_string = uri(self.__protocol, config.get('connect_address') or self.__listen, 'patroni')
@staticmethod
def handle_error(request, client_address):
diff --git a/patroni/config.py b/patroni/config.py
--- a/patroni/config.py
+++ b/patroni/config.py
@@ -236,7 +236,8 @@ def _set_section_values(section, params):
if value:
ret[section][param] = value
- _set_section_values('restapi', ['listen', 'connect_address', 'certfile', 'keyfile'])
+ _set_section_values('restapi', ['listen', 'connect_address', 'certfile', 'keyfile', 'cafile', 'verify_client'])
+ _set_section_values('ctl', ['insecure', 'cacert', 'certfile', 'keyfile'])
_set_section_values('postgresql', ['listen', 'connect_address', 'config_dir', 'data_dir', 'pgpass', 'bin_dir'])
_set_section_values('log', ['level', 'format', 'dateformat', 'max_queue_size',
'dir', 'file_size', 'file_num', 'loggers'])
diff --git a/patroni/ctl.py b/patroni/ctl.py
--- a/patroni/ctl.py
+++ b/patroni/ctl.py
@@ -2,7 +2,6 @@
Patroni Control
'''
-import base64
import click
import codecs
import datetime
@@ -15,7 +14,6 @@
import logging
import os
import random
-import requests
import subprocess
import sys
import tempfile
@@ -30,6 +28,7 @@
from patroni.exceptions import PatroniException
from patroni.postgresql import Postgresql
from patroni.postgresql.misc import postgres_version_to_int
+from patroni.request import PatroniRequest
from patroni.utils import patch_config, polling_loop
from patroni.version import __version__
from prettytable import PrettyTable
@@ -135,36 +134,12 @@ def get_dcs(config, scope):
raise PatroniCtlException(str(e))
-def auth_header(config):
- if config.get('restapi', {}).get('auth', ''):
- return {'Authorization': 'Basic ' + base64.b64encode(config['restapi']['auth'].encode('utf-8')).decode('utf-8')}
-
-
-def request_patroni(member, request_type, endpoint, content=None, headers=None):
+def request_patroni(member, method='GET', endpoint=None, data=None):
ctx = click.get_current_context() # the current click context
- headers = headers or {}
- url_parts = urlparse(member.api_url)
- logging.debug(url_parts)
- if 'Content-Type' not in headers:
- headers['Content-Type'] = 'application/json'
-
- url = '{0}://{1}/{2}'.format(url_parts.scheme, url_parts.netloc, endpoint)
-
- insecure = ctx.obj.get('ctl', {}).get('insecure', False)
- # Get certfile if any from several configuration namespace
- cert = ctx.obj.get('ctl', {}).get('cacert') or \
- ctx.obj.get('restapi', {}).get('cacert') or \
- ctx.obj.get('restapi', {}).get('certfile')
- # In the case we specificaly disable SSL cert verification we don't want to have the warning
- if insecure:
- verify = False
- elif cert:
- verify = cert
- else:
- verify = True
- return getattr(requests, request_type)(url, headers=headers,
- data=json.dumps(content) if content else None, timeout=60,
- verify=verify)
+ request_executor = ctx.obj.get('__request_patroni')
+ if not request_executor:
+ request_executor = ctx.obj['__request_patroni'] = PatroniRequest(ctx.obj)
+ return request_executor(member, method, endpoint, data)
def print_output(columns, rows=None, alignment=None, fmt='pretty', header=True, delimiter='\t'):
@@ -457,9 +432,9 @@ def remove(obj, cluster_name, fmt):
def check_response(response, member_name, action_name, silent_success=False):
- if response.status_code >= 400:
+ if response.status >= 400:
click.echo('Failed: {0} for member {1}, status code={2}, ({3})'.format(
- action_name, member_name, response.status_code, response.text
+ action_name, member_name, response.status, response.data.decode('utf-8')
))
return False
elif not silent_success:
@@ -493,18 +468,17 @@ def reload(obj, cluster_name, member_names, force, role):
members = get_members(cluster, cluster_name, member_names, role, force, 'reload')
- content = {}
for member in members:
- r = request_patroni(member, 'post', 'reload', content, auth_header(obj))
- if r.status_code == 200:
+ r = request_patroni(member, 'post', 'reload')
+ if r.status == 200:
click.echo('No changes to apply on member {0}'.format(member.name))
- elif r.status_code == 202:
+ elif r.status == 202:
click.echo('Reload request received for member {0} and will be processed within {1} seconds'.format(
member.name, cluster.config.data.get('loop_wait'))
)
else:
click.echo('Failed: reload for member {0}, status code={1}, ({2})'.format(
- member.name, r.status_code, r.text)
+ member.name, r.status, r.data.decode('utf-8'))
)
@@ -565,19 +539,19 @@ def restart(obj, cluster_name, member_names, force, role, p_any, scheduled, vers
for member in members:
if 'schedule' in content:
if force and member.data.get('scheduled_restart'):
- r = request_patroni(member, 'delete', 'restart', headers=auth_header(obj))
+ r = request_patroni(member, 'delete', 'restart')
check_response(r, member.name, 'flush scheduled restart', True)
- r = request_patroni(member, 'post', 'restart', content, auth_header(obj))
- if r.status_code == 200:
+ r = request_patroni(member, 'post', 'restart', content)
+ if r.status == 200:
click.echo('Success: restart on member {0}'.format(member.name))
- elif r.status_code == 202:
+ elif r.status == 202:
click.echo('Success: restart scheduled on member {0}'.format(member.name))
- elif r.status_code == 409:
+ elif r.status == 409:
click.echo('Failed: another restart is already scheduled on member {0}'.format(member.name))
else:
click.echo('Failed: restart for member {0}, status code={1}, ({2})'.format(
- member.name, r.status_code, r.text)
+ member.name, r.status, r.data.decode('utf-8'))
)
@@ -593,8 +567,8 @@ def reinit(obj, cluster_name, member_names, force):
for member in members:
body = {'force': force}
while True:
- r = request_patroni(member, 'post', 'reinitialize', body, auth_header(obj))
- if not check_response(r, member.name, 'reinitialize') and r.text.endswith(' already in progress') \
+ r = request_patroni(member, 'post', 'reinitialize', body)
+ if not check_response(r, member.name, 'reinitialize') and r.data.endswith(b' already in progress') \
and not force and click.confirm('Do you want to cancel it and reinitialize anyway?'):
body['force'] = True
continue
@@ -682,19 +656,19 @@ def _do_failover_or_switchover(obj, action, cluster_name, master, candidate, for
try:
member = cluster.leader.member if cluster.leader else cluster.get_member(candidate, False)
- r = request_patroni(member, 'post', action, failover_value, auth_header(obj))
+ r = request_patroni(member, 'post', action, failover_value)
# probably old patroni, which doesn't support switchover yet
- if r.status_code == 501 and action == 'switchover' and 'Server does not support this operation' in r.text:
- r = request_patroni(member, 'post', 'failover', failover_value, auth_header(obj))
+ if r.status == 501 and action == 'switchover' and b'Server does not support this operation' in r.data:
+ r = request_patroni(member, 'post', 'failover', failover_value)
- if r.status_code in (200, 202):
+ if r.status in (200, 202):
logging.debug(r)
cluster = dcs.get_cluster()
logging.debug(cluster)
- click.echo('{0} {1}'.format(timestamp(), r.text))
+ click.echo('{0} {1}'.format(timestamp(), r.data.decode('utf-8')))
else:
- click.echo('{0} failed, details: {1}, {2}'.format(action.title(), r.status_code, r.text))
+ click.echo('{0} failed, details: {1}, {2}'.format(action.title(), r.status, r.data.decode('utf-8')))
return
except Exception:
logging.exception(r)
@@ -919,7 +893,7 @@ def flush(obj, cluster_name, member_names, force, role, target):
for member in members:
if target == 'restart':
if member.data.get('scheduled_restart'):
- r = request_patroni(member, 'delete', 'restart', None, auth_header(obj))
+ r = request_patroni(member, 'delete', 'restart')
check_response(r, member.name, 'flush scheduled restart')
else:
click.echo('No scheduled restart for member {0}'.format(member.name))
@@ -956,20 +930,20 @@ def toggle_pause(config, cluster_name, paused, wait):
for member in members:
try:
- r = request_patroni(member, 'patch', 'config', {'pause': paused or None}, auth_header(config))
+ r = request_patroni(member, 'patch', 'config', {'pause': paused or None})
except Exception as err:
logging.warning(str(err))
logging.warning('Member %s is not accessible', member.name)
continue
- if r.status_code == 200:
+ if r.status == 200:
if wait:
wait_until_pause_is_applied(dcs, paused, cluster)
else:
click.echo('Success: cluster management is {0}'.format(paused and 'paused' or 'resumed'))
else:
click.echo('Failed: {0} cluster management status code={1}, ({2})'.format(
- paused and 'pause' or 'resume', r.status_code, r.text))
+ paused and 'pause' or 'resume', r.status, r.data.decode('utf-8')))
break
else:
raise PatroniCtlException('Can not find accessible cluster member')
@@ -1233,8 +1207,8 @@ def version(obj, cluster_name, member_names):
if m.api_url:
if not member_names or m.name in member_names:
try:
- response = request_patroni(m, 'get', 'patroni')
- data = response.json()
+ response = request_patroni(m)
+ data = json.loads(response.data)
version = data.get('patroni', {}).get('version')
pg_version = data.get('server_version')
pg_version_str = " PostgreSQL {0}".format(format_pg_version(pg_version)) if pg_version else ""
diff --git a/patroni/ha.py b/patroni/ha.py
--- a/patroni/ha.py
+++ b/patroni/ha.py
@@ -3,7 +3,6 @@
import json
import logging
import psycopg2
-import requests
import sys
import time
import uuid
@@ -558,16 +557,15 @@ def on_success():
args=(self.dcs.loop_wait, on_success, self._leader_access_is_restricted))
return promote_message
- @staticmethod
- def fetch_node_status(member):
+ def fetch_node_status(self, member):
"""This function perform http get request on member.api_url and fetches its status
:returns: `_MemberStatus` object
"""
try:
- response = requests.get(member.api_url, timeout=2, verify=False)
- logger.info('Got response from %s %s: %s', member.name, member.api_url, response.content)
- return _MemberStatus.from_api_response(member, response.json())
+ response = self.patroni.request(member, timeout=2, retries=0)
+ logger.info('Got response from %s %s: %s', member.name, member.api_url, response.data.decode('utf-8'))
+ return _MemberStatus.from_api_response(member, json.loads(response.data))
except Exception as e:
logger.warning("Request failed to %s: GET %s (%s)", member.name, member.api_url, e)
return _MemberStatus.unknown(member)
diff --git a/patroni/request.py b/patroni/request.py
new file mode 100644
--- /dev/null
+++ b/patroni/request.py
@@ -0,0 +1,47 @@
+import json
+import urllib3
+
+from six.moves.urllib_parse import urlparse, urlunparse
+
+
+class PatroniRequest(object):
+
+ def __init__(self, config, insecure=False):
+ cert_reqs = 'CERT_NONE' if insecure or config.get('ctl', {}).get('insecure', False) else 'CERT_REQUIRED'
+ self._pool = urllib3.PoolManager(cert_reqs=cert_reqs)
+ self.reload_config(config)
+
+ @staticmethod
+ def _get_cfg_value(config, name):
+ return config.get('ctl', {}).get(name) or config.get('restapi', {}).get(name)
+
+ def _apply_pool_param(self, param, value):
+ if value:
+ self._pool.connection_pool_kw[param] = value
+ else:
+ self._pool.connection_pool_kw.pop(param, None)
+
+ def _apply_ssl_file_param(self, config, name):
+ value = self._get_cfg_value(config, name + 'file')
+ self._apply_pool_param(name + '_file', value)
+ return value
+
+ def reload_config(self, config):
+ self._pool.headers = urllib3.make_headers(basic_auth=self._get_cfg_value(config, 'auth'))
+
+ if self._apply_ssl_file_param(config, 'cert'):
+ self._apply_ssl_file_param(config, 'key')
+ else:
+ self._pool.connection_pool_kw.pop('key_file', None)
+
+ cacert = config.get('ctl', {}).get('cacert') or config.get('restapi', {}).get('cafile')
+ self._apply_pool_param('ca_certs', cacert)
+
+ def __call__(self, member, method='GET', endpoint=None, data=None, **kwargs):
+ url = member.api_url
+ if endpoint:
+ scheme, netloc, _, _, _, _ = urlparse(url)
+ url = urlunparse((scheme, netloc, endpoint, '', '', ''))
+ if data is not None:
+ kwargs['body'] = json.dumps(data)
+ return self._pool.request(method.upper(), url, **kwargs)
| diff --git a/tests/test_api.py b/tests/test_api.py
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -145,7 +145,7 @@ def __init__(self, Handler, request, config=None):
self.serve_forever = Mock()
MockRestApiServer._BaseServer__is_shut_down = Mock()
MockRestApiServer._BaseServer__shutdown_request = True
- config = config or {'listen': '127.0.0.1:8008', 'auth': 'test:test', 'certfile': 'dumb'}
+ config = config or {'listen': '127.0.0.1:8008', 'auth': 'test:test', 'certfile': 'dumb', 'verify_client': 'a'}
super(MockRestApiServer, self).__init__(MockPatroni(), config)
Handler(MockRequest(request), ('0.0.0.0', 8080), self)
@@ -408,12 +408,18 @@ class TestRestApiServer(unittest.TestCase):
def test_reload_config(self):
bad_config = {'listen': 'foo'}
self.assertRaises(ValueError, MockRestApiServer, None, '', bad_config)
- srv = MockRestApiServer(lambda a1, a2, a3: None, '')
+ srv = MockRestApiServer(Mock(), '', {'listen': '*:8008', 'certfile': 'a', 'verify_client': 'required'})
self.assertRaises(ValueError, srv.reload_config, bad_config)
self.assertRaises(ValueError, srv.reload_config, {})
with patch.object(socket.socket, 'setsockopt', Mock(side_effect=socket.error)):
srv.reload_config({'listen': ':8008'})
+ def test_check_auth(self):
+ srv = MockRestApiServer(Mock(), '', {'listen': '*:8008', 'certfile': 'a', 'verify_client': 'required'})
+ mock_rh = Mock()
+ mock_rh.request.getpeercert.return_value = None
+ self.assertIsNot(srv.check_auth(mock_rh), True)
+
def test_handle_error(self):
try:
raise Exception()
diff --git a/tests/test_ctl.py b/tests/test_ctl.py
--- a/tests/test_ctl.py
+++ b/tests/test_ctl.py
@@ -1,20 +1,21 @@
import etcd
+import json
import os
-import requests
import sys
import unittest
from click.testing import CliRunner
from datetime import datetime, timedelta
from mock import patch, Mock
-from patroni.ctl import ctl, store_config, load_config, output_members, request_patroni, get_dcs, parse_dcs, \
+from patroni.ctl import ctl, store_config, load_config, output_members, get_dcs, parse_dcs, \
get_all_members, get_any_member, get_cursor, query_member, configure, PatroniCtlException, apply_config_changes, \
format_config_for_editing, show_diff, invoke_editor, format_pg_version, find_executable
from patroni.dcs.etcd import Client, Failover
from patroni.utils import tzutc
from psycopg2 import OperationalError
+from urllib3 import PoolManager
-from . import MockConnect, MockCursor, MockResponse, psycopg2_connect, requests_get
+from . import MockConnect, MockCursor, MockResponse, psycopg2_connect
from .test_etcd import etcd_read, socket_getaddrinfo
from .test_ha import get_cluster_initialized_without_leader, get_cluster_initialized_with_leader, \
get_cluster_initialized_with_only_leader, get_cluster_not_initialized_without_leader, get_cluster, Member
@@ -35,7 +36,7 @@ def test_rw_config():
@patch('patroni.ctl.load_config',
Mock(return_value={'scope': 'alpha', 'postgresql': {'data_dir': '.', 'parameters': {}, 'retry_timeout': 5},
- 'restapi': {'auth': 'u:p', 'listen': ''}, 'etcd': {'host': 'localhost:2379'}}))
+ 'restapi': {'listen': '::', 'certfile': 'a'}, 'etcd': {'host': 'localhost:2379'}}))
class TestCtl(unittest.TestCase):
@patch('socket.getaddrinfo', socket_getaddrinfo)
@@ -75,7 +76,7 @@ def test_output_members(self):
self.assertIsNone(output_members(cluster, name='abc', fmt='tsv'))
@patch('patroni.ctl.get_dcs')
- @patch('patroni.ctl.request_patroni', Mock(return_value=MockResponse()))
+ @patch.object(PoolManager, 'request', Mock(return_value=MockResponse()))
def test_switchover(self, mock_get_dcs):
mock_get_dcs.return_value = self.e
mock_get_dcs.return_value.get_cluster = get_cluster_initialized_with_leader
@@ -125,18 +126,18 @@ def test_switchover(self, mock_get_dcs):
result = self.runner.invoke(ctl, ['switchover', 'dummy'], input='dummy')
assert result.exit_code == 1
- with patch('patroni.ctl.request_patroni', Mock(side_effect=Exception)):
+ with patch.object(PoolManager, 'request', Mock(side_effect=Exception)):
# Non-responding patroni
result = self.runner.invoke(ctl, ['switchover', 'dummy'], input='leader\nother\n2300-01-01T12:23:00\ny')
assert 'falling back to DCS' in result.output
- with patch('patroni.ctl.request_patroni') as mocked:
- mocked.return_value.status_code = 500
+ with patch.object(PoolManager, 'request') as mocked:
+ mocked.return_value.status = 500
result = self.runner.invoke(ctl, ['switchover', 'dummy'], input='leader\nother\n\ny')
assert 'Switchover failed' in result.output
- mocked.return_value.status_code = 501
- mocked.return_value.text = 'Server does not support this operation'
+ mocked.return_value.status = 501
+ mocked.return_value.data = b'Server does not support this operation'
result = self.runner.invoke(ctl, ['switchover', 'dummy'], input='leader\nother\n\ny')
assert 'Switchover failed' in result.output
@@ -151,7 +152,7 @@ def test_switchover(self, mock_get_dcs):
assert result.exit_code == 1
@patch('patroni.ctl.get_dcs')
- @patch('patroni.ctl.request_patroni', Mock(return_value=MockResponse()))
+ @patch.object(PoolManager, 'request', Mock(return_value=MockResponse()))
def test_failover(self, mock_get_dcs):
mock_get_dcs.return_value = self.e
mock_get_dcs.return_value.get_cluster = get_cluster_initialized_with_leader
@@ -231,7 +232,7 @@ def test_dsn(self, mock_get_dcs):
result = self.runner.invoke(ctl, ['dsn', 'alpha', '--member', 'dummy'])
assert result.exit_code == 1
- @patch('requests.post')
+ @patch.object(PoolManager, 'request')
@patch('patroni.ctl.get_dcs')
def test_reload(self, mock_get_dcs, mock_post):
mock_get_dcs.return_value.get_cluster = get_cluster_initialized_with_leader
@@ -239,18 +240,19 @@ def test_reload(self, mock_get_dcs, mock_post):
result = self.runner.invoke(ctl, ['reload', 'alpha'], input='y')
assert 'Failed: reload for member' in result.output
- mock_post.return_value.status_code = 200
+ mock_post.return_value.status = 200
result = self.runner.invoke(ctl, ['reload', 'alpha'], input='y')
assert 'No changes to apply on member' in result.output
- mock_post.return_value.status_code = 202
+ mock_post.return_value.status = 202
result = self.runner.invoke(ctl, ['reload', 'alpha'], input='y')
assert 'Reload request received for member' in result.output
- @patch('requests.post', requests_get)
+ @patch.object(PoolManager, 'request')
@patch('patroni.ctl.get_dcs')
- def test_restart_reinit(self, mock_get_dcs):
+ def test_restart_reinit(self, mock_get_dcs, mock_post):
mock_get_dcs.return_value.get_cluster = get_cluster_initialized_with_leader
+ mock_post.return_value.status = 503
result = self.runner.invoke(ctl, ['restart', 'alpha'], input='now\ny\n')
assert 'Failed: restart for' in result.output
assert result.exit_code == 0
@@ -285,58 +287,49 @@ def test_restart_reinit(self, mock_get_dcs):
result = self.runner.invoke(ctl, ['restart', 'alpha', '--pending', '--force', '--timeout', '10min'])
assert result.exit_code == 0
- with patch('requests.delete', Mock(return_value=MockResponse(500))):
- # normal restart, the schedule is actually parsed, but not validated in patronictl
- result = self.runner.invoke(ctl, ['restart', 'alpha', 'other', '--force',
- '--scheduled', '2300-10-01T14:30'])
- assert 'Failed: flush scheduled restart' in result.output
+ # normal restart, the schedule is actually parsed, but not validated in patronictl
+ result = self.runner.invoke(ctl, ['restart', 'alpha', 'other', '--force', '--scheduled', '2300-10-01T14:30'])
+ assert 'Failed: flush scheduled restart' in result.output
with patch('patroni.dcs.Cluster.is_paused', Mock(return_value=True)):
result = self.runner.invoke(ctl,
['restart', 'alpha', 'other', '--force', '--scheduled', '2300-10-01T14:30'])
assert result.exit_code == 1
- with patch('requests.post', Mock(return_value=MockResponse())):
- # normal restart, the schedule is actually parsed, but not validated in patronictl
- result = self.runner.invoke(ctl, ['restart', 'alpha', '--pg-version', '42.0.0',
- '--scheduled', '2300-10-01T14:30'], input='y')
- assert result.exit_code == 0
+ # force restart with restart already present
+ result = self.runner.invoke(ctl, ['restart', 'alpha', 'other', '--force', '--scheduled', '2300-10-01T14:30'])
+ assert result.exit_code == 0
- with patch('requests.post', Mock(return_value=MockResponse(204))):
- # get restart with the non-200 return code
- # normal restart, the schedule is actually parsed, but not validated in patronictl
- result = self.runner.invoke(ctl, ['restart', 'alpha', '--pg-version', '42.0',
- '--scheduled', '2300-10-01T14:30'], input='y')
- assert result.exit_code == 0
+ ctl_args = ['restart', 'alpha', '--pg-version', '99.0', '--scheduled', '2300-10-01T14:30']
+ # normal restart, the schedule is actually parsed, but not validated in patronictl
+ mock_post.return_value.status = 200
+ result = self.runner.invoke(ctl, ctl_args, input='y')
+ assert result.exit_code == 0
- # force restart with restart already present
- with patch('patroni.ctl.request_patroni', Mock(return_value=MockResponse(204))):
- result = self.runner.invoke(ctl, ['restart', 'alpha', 'other', '--force',
- '--scheduled', '2300-10-01T14:30'])
- assert result.exit_code == 0
+ # get restart with the non-200 return code
+ # normal restart, the schedule is actually parsed, but not validated in patronictl
+ mock_post.return_value.status = 204
+ result = self.runner.invoke(ctl, ctl_args, input='y')
+ assert result.exit_code == 0
- with patch('requests.post', Mock(return_value=MockResponse(202))):
- # get restart with the non-200 return code
- # normal restart, the schedule is actually parsed, but not validated in patronictl
- result = self.runner.invoke(
- ctl, ['restart', 'alpha', '--pg-version', '99.0.0', '--scheduled', '2300-10-01T14:30'], input='y'
- )
- assert 'Success: restart scheduled' in result.output
- assert result.exit_code == 0
+ # get restart with the non-200 return code
+ # normal restart, the schedule is actually parsed, but not validated in patronictl
+ mock_post.return_value.status = 202
+ result = self.runner.invoke(ctl, ctl_args, input='y')
+ assert 'Success: restart scheduled' in result.output
+ assert result.exit_code == 0
- with patch('requests.post', Mock(return_value=MockResponse(409))):
- # get restart with the non-200 return code
- # normal restart, the schedule is actually parsed, but not validated in patronictl
- result = self.runner.invoke(
- ctl, ['restart', 'alpha', '--pg-version', '99.0.0', '--scheduled', '2300-10-01T14:30'], input='y'
- )
- assert 'Failed: another restart is already' in result.output
- assert result.exit_code == 0
+ # get restart with the non-200 return code
+ # normal restart, the schedule is actually parsed, but not validated in patronictl
+ mock_post.return_value.status = 409
+ result = self.runner.invoke(ctl, ctl_args, input='y')
+ assert 'Failed: another restart is already' in result.output
+ assert result.exit_code == 0
@patch('patroni.ctl.get_dcs')
def test_remove(self, mock_get_dcs):
mock_get_dcs.return_value.get_cluster = get_cluster_initialized_with_leader
- result = self.runner.invoke(ctl, ['remove', 'alpha'], input='alpha\nslave')
+ result = self.runner.invoke(ctl, ['-k', 'remove', 'alpha'], input='alpha\nslave')
assert 'Please confirm' in result.output
assert 'You are about to remove all' in result.output
# Not typing an exact confirmation
@@ -353,17 +346,6 @@ def test_remove(self, mock_get_dcs):
result = self.runner.invoke(ctl, ['remove', 'alpha'], input='alpha\nYes I am aware\nleader')
assert result.exit_code == 0
- @patch('requests.post', Mock(side_effect=requests.exceptions.ConnectionError('foo')))
- @patch('click.get_current_context')
- def test_request_patroni(self, mock_context):
- member = get_cluster_initialized_with_leader().leader.member
-
- mock_context.return_value.obj = {'ctl': {'cacert': 'cert.pem'}}
- self.assertRaises(requests.exceptions.ConnectionError, request_patroni, member, 'post', 'dummy', {})
-
- mock_context.return_value.obj = {'ctl': {'insecure': True}}
- self.assertRaises(requests.exceptions.ConnectionError, request_patroni, member, 'post', 'dummy', {})
-
def test_ctl(self):
self.runner.invoke(ctl, ['list'])
@@ -437,7 +419,7 @@ def test_list_extended(self, mock_get_dcs):
assert 'Scheduled restart' in result.output
@patch('patroni.ctl.get_dcs')
- @patch('requests.delete', Mock(return_value=MockResponse()))
+ @patch.object(PoolManager, 'request', Mock(return_value=MockResponse()))
def test_flush(self, mock_get_dcs):
mock_get_dcs.return_value = self.e
mock_get_dcs.return_value.get_cluster = get_cluster_initialized_with_leader
@@ -447,58 +429,58 @@ def test_flush(self, mock_get_dcs):
result = self.runner.invoke(ctl, ['flush', 'dummy', 'restart', '--force'])
assert 'Success: flush scheduled restart' in result.output
- with patch.object(requests, 'delete', return_value=MockResponse(404)):
+ with patch.object(PoolManager, 'request', return_value=MockResponse(404)):
result = self.runner.invoke(ctl, ['flush', 'dummy', 'restart', '--force'])
assert 'Failed: flush scheduled restart' in result.output
+ @patch.object(PoolManager, 'request')
@patch('patroni.ctl.get_dcs')
@patch('patroni.ctl.polling_loop', Mock(return_value=[1]))
- def test_pause_cluster(self, mock_get_dcs):
+ def test_pause_cluster(self, mock_get_dcs, mock_post):
mock_get_dcs.return_value = self.e
mock_get_dcs.return_value.get_cluster = get_cluster_initialized_with_leader
- with patch('requests.patch', Mock(return_value=MockResponse(500))):
- result = self.runner.invoke(ctl, ['pause', 'dummy'])
- assert 'Failed' in result.output
+ mock_post.return_value.status = 500
+ result = self.runner.invoke(ctl, ['pause', 'dummy'])
+ assert 'Failed' in result.output
- with patch('requests.patch', Mock(return_value=MockResponse(200))),\
- patch('patroni.dcs.Cluster.is_paused', Mock(return_value=True)):
+ mock_post.return_value.status = 200
+ with patch('patroni.dcs.Cluster.is_paused', Mock(return_value=True)):
result = self.runner.invoke(ctl, ['pause', 'dummy'])
assert 'Cluster is already paused' in result.output
- with patch('requests.patch', Mock(return_value=MockResponse(200))):
- result = self.runner.invoke(ctl, ['pause', 'dummy', '--wait'])
- assert "'pause' request sent" in result.output
- mock_get_dcs.return_value.get_cluster = Mock(side_effect=[get_cluster_initialized_with_leader(),
- get_cluster(None, None, [], None, None)])
- self.runner.invoke(ctl, ['pause', 'dummy', '--wait'])
- member = Member(1, 'other', 28, {})
- mock_get_dcs.return_value.get_cluster = Mock(side_effect=[get_cluster_initialized_with_leader(),
- get_cluster(None, None, [member], None, None)])
- self.runner.invoke(ctl, ['pause', 'dummy', '--wait'])
-
+ result = self.runner.invoke(ctl, ['pause', 'dummy', '--wait'])
+ assert "'pause' request sent" in result.output
+ mock_get_dcs.return_value.get_cluster = Mock(side_effect=[get_cluster_initialized_with_leader(),
+ get_cluster(None, None, [], None, None)])
+ self.runner.invoke(ctl, ['pause', 'dummy', '--wait'])
+ member = Member(1, 'other', 28, {})
+ mock_get_dcs.return_value.get_cluster = Mock(side_effect=[get_cluster_initialized_with_leader(),
+ get_cluster(None, None, [member], None, None)])
+ self.runner.invoke(ctl, ['pause', 'dummy', '--wait'])
+
+ @patch.object(PoolManager, 'request')
@patch('patroni.ctl.get_dcs')
- def test_resume_cluster(self, mock_get_dcs):
+ def test_resume_cluster(self, mock_get_dcs, mock_post):
mock_get_dcs.return_value = self.e
mock_get_dcs.return_value.get_cluster = get_cluster_initialized_with_leader
- with patch('patroni.dcs.Cluster.is_paused', Mock(return_value=True)):
- with patch('requests.patch', Mock(return_value=MockResponse(200))):
- result = self.runner.invoke(ctl, ['resume', 'dummy'])
- assert 'Success' in result.output
+ mock_post.return_value.status = 200
+ with patch('patroni.dcs.Cluster.is_paused', Mock(return_value=False)):
+ result = self.runner.invoke(ctl, ['resume', 'dummy'])
+ assert 'Cluster is not paused' in result.output
- with patch('requests.patch', Mock(return_value=MockResponse(500))):
- result = self.runner.invoke(ctl, ['resume', 'dummy'])
- assert 'Failed' in result.output
+ with patch('patroni.dcs.Cluster.is_paused', Mock(return_value=True)):
+ result = self.runner.invoke(ctl, ['resume', 'dummy'])
+ assert 'Success' in result.output
- with patch('requests.patch', Mock(return_value=MockResponse(200))),\
- patch('patroni.dcs.Cluster.is_paused', Mock(return_value=False)):
- result = self.runner.invoke(ctl, ['resume', 'dummy'])
- assert 'Cluster is not paused' in result.output
+ mock_post.return_value.status = 500
+ result = self.runner.invoke(ctl, ['resume', 'dummy'])
+ assert 'Failed' in result.output
- with patch('requests.patch', Mock(side_effect=Exception)):
- result = self.runner.invoke(ctl, ['resume', 'dummy'])
- assert 'Can not find accessible cluster member' in result.output
+ mock_post.side_effect = Exception
+ result = self.runner.invoke(ctl, ['resume', 'dummy'])
+ assert 'Can not find accessible cluster member' in result.output
def test_apply_config_changes(self):
config = {"postgresql": {"parameters": {"work_mem": "4MB"}, "use_pg_rewind": True}, "ttl": 30}
@@ -574,13 +556,13 @@ def test_edit_config(self, mock_get_dcs):
def test_version(self, mock_get_dcs):
mock_get_dcs.return_value = self.e
mock_get_dcs.return_value.get_cluster = get_cluster_initialized_with_leader
- with patch('patroni.ctl.request_patroni') as mocked:
+ with patch.object(PoolManager, 'request') as mocked:
result = self.runner.invoke(ctl, ['version'])
assert 'patronictl version' in result.output
- mocked.return_value.json = lambda: {'patroni': {'version': '1.2.3'}, 'server_version': 100001}
+ mocked.return_value.data = json.dumps({'patroni': {'version': '1.2.3'}, 'server_version': 100001})
result = self.runner.invoke(ctl, ['version', 'dummy'])
assert '1.2.3' in result.output
- with patch('requests.get', Mock(side_effect=Exception)):
+ with patch.object(PoolManager, 'request', Mock(side_effect=Exception)):
result = self.runner.invoke(ctl, ['version', 'dummy'])
assert 'failed to get version' in result.output
diff --git a/tests/test_ha.py b/tests/test_ha.py
--- a/tests/test_ha.py
+++ b/tests/test_ha.py
@@ -137,6 +137,7 @@ def __init__(self, p, d):
self.scheduled_restart = {'schedule': future_restart_time,
'postmaster_start_time': str(postmaster_start_time)}
self.watchdog = Watchdog(self.config)
+ self.request = lambda member, **kwargs: requests_get(member.api_url, **kwargs)
def run_async(self, func, args=()):
@@ -464,7 +465,6 @@ def test_restart_in_progress(self):
self.assertEqual(self.ha.run_cycle(), 'lost leader lock during restart')
mock_terminate.assert_called()
- @patch('requests.get', requests_get)
def test_manual_failover_from_leader(self):
self.ha.fetch_node_status = get_node_status()
self.ha.has_lock = true
@@ -512,7 +512,6 @@ def test_manual_failover_from_leader(self):
self.ha.cluster = get_cluster_initialized_with_leader(Failover(0, 'blabla', self.p.name, scheduled))
self.assertEqual('no action. i am the leader with the lock', self.ha.run_cycle())
- @patch('requests.get', requests_get)
def test_manual_failover_from_leader_in_pause(self):
self.ha.has_lock = true
self.ha.is_paused = true
@@ -522,7 +521,6 @@ def test_manual_failover_from_leader_in_pause(self):
self.ha.cluster = get_cluster_initialized_with_leader(Failover(0, self.p.name, '', None))
self.assertEqual('PAUSE: no action. i am the leader with the lock', self.ha.run_cycle())
- @patch('requests.get', requests_get)
def test_manual_failover_from_leader_in_synchronous_mode(self):
self.p.is_leader = true
self.ha.has_lock = true
@@ -535,7 +533,6 @@ def test_manual_failover_from_leader_in_synchronous_mode(self):
self.ha.is_failover_possible = true
self.assertEqual('manual failover: demoting myself', self.ha.run_cycle())
- @patch('requests.get', requests_get)
def test_manual_failover_process_no_leader(self):
self.p.is_leader = false
self.ha.cluster = get_cluster_initialized_without_leader(failover=Failover(0, '', self.p.name, None))
@@ -585,7 +582,6 @@ def test_is_healthiest_node(self):
self.ha.is_paused = true
self.assertFalse(self.ha.is_healthiest_node())
- @patch('requests.get', requests_get)
def test__is_healthiest_node(self):
self.ha.cluster = get_cluster_initialized_without_leader(sync=('postgresql1', self.p.name))
self.assertTrue(self.ha._is_healthiest_node(self.ha.old_cluster.members))
@@ -607,7 +603,6 @@ def test__is_healthiest_node(self):
self.assertFalse(self.ha._is_healthiest_node(self.ha.old_cluster.members))
self.ha.patroni.nofailover = False
- @patch('requests.get', requests_get)
def test_fetch_node_status(self):
member = Member(0, 'test', 1, {'api_url': 'http://127.0.0.1:8011/patroni'})
self.ha.fetch_node_status(member)
@@ -696,7 +691,6 @@ def test_process_healthy_standby_cluster_as_cascade_replica(self):
with patch.object(Leader, 'conn_url', PropertyMock(return_value='')):
self.assertEqual(self.ha.run_cycle(), 'continue following the old known standby leader')
- @patch('requests.get', requests_get)
def test_process_unhealthy_standby_cluster_as_standby_leader(self):
self.p.is_leader = false
self.p.name = 'leader'
@@ -1027,7 +1021,6 @@ def test_update_cluster_history(self):
self.assertEqual(self.ha.run_cycle(), 'no action. i am the leader with the lock')
@patch('sys.exit', return_value=1)
- @patch('requests.get', requests_get)
def test_abort_join(self, exit_mock):
self.ha.cluster = get_cluster_not_initialized_without_leader()
self.p.is_leader = false
| InsecureRequestWarning on fetch_node_status when performing failover
Hello!
After testing one of the failover scenarios (power cut on primary node), the log output following warning:
```
/usr/lib/python2.7/site-packages/urllib3/connectionpool.py:847: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
2018-12-19 14:06:20,805 INFO: Got response from db-03 https://db-03:8008/patroni: {"database_system_identifier": "6396680538100349567", "postmaster_start_time": "2018-11-23 11:50:01.615 CET", "timeline": 3, "cluster_unlocked": true, "patroni": {"scope": "tags", "version": "1.5.1"}, "state": "running", "role": "replica", "xlog": {"received_location": 207004628544, "replayed_timestamp": "2018-12-19 14:04:28.135 CET", "paused": false, "replayed_location": 207004628544}, "server_version": 90610}
InsecureRequestWarning)
```
The first and third line is the problematic warning. Warning itself seems to be harmless, however it taints the logs and makes the troubleshooting more confusing.
I've looked around the code and I believe this is what is called, when the warning is output.
```
@staticmethod
def fetch_node_status(member):
"""This function perform http get request on member.api_url and fetches its status
:returns: `_MemberStatus` object
"""
try:
response = requests.get(member.api_url, timeout=2, verify=False)
logger.info('Got response from %s %s: %s', member.name, member.api_url, response.content)
return _MemberStatus.from_api_response(member, response.json())
except Exception as e:
logger.warning("Request failed to %s: GET %s (%s)", member.name, member.api_url, e)
return _MemberStatus.unknown(member)
```
Is there any particular reason `verify=False` is left in instead of relying to the configured cacert entry in `restapi.cacert` ?
If we can not / do not want to use cert verification when checking other nodes cert in same cluster, then would it be possible to suppress this warning or have an option to do so ?
Thanks in advance!
| > Is there any particular reason verify=False is left in instead of relying to the configured cacert entry in restapi.cacert
There is no such configuration parameter like `restapi.cacert`. Maybe you mix it with `ctl.cacert`, which actually was added only recently https://github.com/zalando/patroni/pull/790/files
Indeed, it would be good to enable certificate verification, but there is another side of this problem. Patroni is doing such api calls during leader elections in order to make sure that the old master is not running anymore. In the case if somebody messed up with configuration, api request will fail even if the master is still running. Potentially this is a very big foot gun.
We mostly need to protect rest api with certificates and basic-auth due to some management endpoints, e.g. POST|PATCH|PUT /restart, /switchover, /failover, /config /reload and so on.
Running health-checks via https sometimes leads to a problem like here: https://github.com/zalando/patroni/issues/857, therefore I am thinking about making it possible to optionally run health-check endpoints on a different port without ssl.
Thanks, @CyberDem0n
> Indeed, it would be good to enable certificate verification, but there is another side of this problem. Patroni is doing such api calls during leader elections in order to make sure that the old master is not running anymore. In the case if somebody messed up with configuration, api request will fail even if the master is still running. Potentially this is a very big foot gun.
This is a fair point and one of the reasons I had in back of my mind as well.
> I am thinking about making it possible to optionally run health-check endpoints on a different port without ssl.
That may be one way to do it. To add to this, do you think we should have this warning from urllib3 suppressed and a disclaimer added somewhere in docs instead (for current implementation and if user has chosen to run it via SSL, when / if this setting has been introduced) ?
This is not high priority issue by no means, now that I understand this is intended and why.. | 2019-09-27T15:03:25Z | [] | [] |
zalando/patroni | 1,279 | zalando__patroni-1279 | [
"1278",
"1278"
] | 66d77697ae12113dcff28982a2aaee6bd40d2c29 | diff --git a/patroni/__init__.py b/patroni/__init__.py
--- a/patroni/__init__.py
+++ b/patroni/__init__.py
@@ -176,6 +176,13 @@ def fatal(string, *args):
sys.exit(1)
+def use_spawn_start_method():
+ if sys.version_info >= (3, 4):
+ # The default, forking, method is not a good idea in a multithreaded process: https://bugs.python.org/issue6721
+ import multiprocessing
+ multiprocessing.set_start_method('spawn')
+
+
def check_psycopg2():
min_psycopg2 = (2, 5, 4)
min_psycopg2_str = '.'.join(map(str, min_psycopg2))
@@ -198,6 +205,7 @@ def parse_version(version):
def main():
+ use_spawn_start_method()
check_psycopg2()
if os.getpid() != 1:
return patroni_main()
| diff --git a/tests/test_patroni.py b/tests/test_patroni.py
--- a/tests/test_patroni.py
+++ b/tests/test_patroni.py
@@ -83,6 +83,7 @@ def test_patroni_patroni_main(self, mock_machines):
@patch('os.getpid')
@patch('multiprocessing.Process')
+ @patch('patroni.use_spawn_start_method', Mock())
@patch('patroni.patroni_main', Mock())
def test_patroni_main(self, mock_process, mock_getpid):
mock_getpid.return_value = 2
| Postmaster starting process hangs because sys.stderr is locked after fork
In version `v1.6.0` Patroni uses forking `multiprocessing.Process` for creating a postmaster parent.
Unfortunately there are other threads which may hold some locks during `fork()` call.
```
$ docker-compose exec patroni2 ps xaf
PID TTY STAT TIME COMMAND
382 pts/0 Rs+ 0:00 ps xaf
1 ? Ss 0:00 python3 /patroni.py postgres0.yml
8 ? Sl 0:00 python3 /patroni.py postgres0.yml
24 ? Ss 0:00 \_ python3 /patroni.py postgres0.yml
25 ? S 0:00 \_ postgres -D /var/lib/postgresql/data/pgdata -
26 ? Ss 0:00 \_ postgres: batman: startup process recov
27 ? Ss 0:00 \_ postgres: batman: checkpointer process
28 ? Ss 0:00 \_ postgres: batman: writer process
29 ? Ss 0:00 \_ postgres: batman: stats collector process
31 ? Ss 0:00 \_ postgres: batman: postgres postgres 127.0
```
The postmaster parent hangs on lock on stderr:
```
Thread 0x7fbf86ffd700
File "/usr/lib/python3.5/threading.py", line 882, in _bootstrap
self._bootstrap_inner()
File "/usr/lib/python3.5/threading.py", line 914, in _bootstrap_inner
self.run()
File "/usr/lib/python3.5/threading.py", line 862, in run
self._target(*self._args, **self._kwargs)
File "/patroni/async_executor.py", line 97, in run
wakeup = func(*args) if args else func()
File "/patroni/postgresql/__init__.py", line 728, in follow
self.start(timeout=timeout, block_callbacks=change_role, role=role)
File "/patroni/postgresql/__init__.py", line 434, in start
options)
File "/patroni/postgresql/postmaster.py", line 175, in start
proc.start()
File "/usr/lib/python3.5/multiprocessing/process.py", line 105, in start
self._popen = self._Popen(self)
File "/usr/lib/python3.5/multiprocessing/context.py", line 212, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/usr/lib/python3.5/multiprocessing/context.py", line 267, in _Popen
return Popen(process_obj)
File "/usr/lib/python3.5/multiprocessing/popen_fork.py", line 20, in __init__
self._launch(process_obj)
File "/usr/lib/python3.5/multiprocessing/popen_fork.py", line 74, in _launch
code = process_obj._bootstrap()
File "/usr/lib/python3.5/multiprocessing/process.py", line 269, in _bootstrap
sys.stderr.flush()
File "<string>", line 1, in <module>
File "<string>", line 7, in <module>
```
While a bootstrap thread waits for child to finish:
```
Thread 0x7fbf86ffd700
File "/usr/lib/python3.5/threading.py", line 882, in _bootstrap
self._bootstrap_inner()
File "/usr/lib/python3.5/threading.py", line 914, in _bootstrap_inner
self.run()
File "/usr/lib/python3.5/threading.py", line 862, in run
self._target(*self._args, **self._kwargs)
File "/patroni/async_executor.py", line 97, in run
wakeup = func(*args) if args else func()
File "/patroni/postgresql/__init__.py", line 728, in follow
self.start(timeout=timeout, block_callbacks=change_role, role=role)
File "/patroni/postgresql/__init__.py", line 434, in start
options)
File "/patroni/postgresql/postmaster.py", line 177, in start
proc.join()
File "/usr/lib/python3.5/multiprocessing/process.py", line 121, in join
res = self._popen.wait(timeout)
File "/usr/lib/python3.5/multiprocessing/popen_fork.py", line 51, in wait
return self.poll(os.WNOHANG if timeout == 0.0 else 0)
File "/usr/lib/python3.5/multiprocessing/popen_fork.py", line 29, in poll
pid, sts = os.waitpid(self.pid, flag)
```
The hanging patroni process repeatedly logs: `INFO: restarting after failure in progress`.
It is a known issue in Python that threading and multiprocessing do not mix well: [https://bugs.python.org/issue6721](url)
While the issue with logging lock might have been fixed in Python 3.7 the recommended workaround is to use `spawn` of `forkserver` start methods, e.g. by adding `multiprocessing.set_start_method('spawn')` at the beggining of `main()`.
This can be quickly reproduced using following `docker-compose.yml`:
```
version: "2.1"
volumes:
patroni1_volume:
patroni2_volume:
services:
zookeeper:
image: zookeeper:3.4.10
patroni1:
build:
context: https://github.com/zalando/patroni.git
depends_on:
- zookeeper
environment:
PATRONI_POSTGRESQL_DATA_DIR: /var/lib/postgresql/data/pgdata
PATRONI_ZOOKEEPER_HOSTS: "[\"zookeeper:2181\"]"
volumes:
- patroni1_volume:/var/lib/postgresql/data
healthcheck:
test: "curl --fail localhost:8008/health && (curl --fail localhost:8008/sync || curl --fail localhost:8008/master)"
interval: 10s
timeout: 5s
retries: 30
patroni2:
build:
context: https://github.com/zalando/patroni.git
depends_on:
- zookeeper
environment:
PATRONI_POSTGRESQL_DATA_DIR: /var/lib/postgresql/data/pgdata
PATRONI_ZOOKEEPER_HOSTS: "[\"zookeeper:2181\"]"
volumes:
- patroni2_volume:/var/lib/postgresql/data
healthcheck:
test: "curl --fail localhost:8008/health && (curl --fail localhost:8008/sync || curl --fail localhost:8008/master)"
interval: 10s
timeout: 5s
retries: 30
```
and following shell script:
```
#!/bin/bash
docker-compose up -d
docker-compose exec patroni1 patronictl edit-config -s synchronous_mode=true -q --force batman
CHECK() { ! docker-compose ps | grep patroni[12] | tee /dev/stderr | grep -v '(healthy)' > /dev/null; }
WAIT() { for ((i=0;i<300;i++)); do ! CHECK || break; sleep 1; done; CHECK; }
while WAIT; do docker-compose restart patroni{1,2}; done
```
Postmaster starting process hangs because sys.stderr is locked after fork
In version `v1.6.0` Patroni uses forking `multiprocessing.Process` for creating a postmaster parent.
Unfortunately there are other threads which may hold some locks during `fork()` call.
```
$ docker-compose exec patroni2 ps xaf
PID TTY STAT TIME COMMAND
382 pts/0 Rs+ 0:00 ps xaf
1 ? Ss 0:00 python3 /patroni.py postgres0.yml
8 ? Sl 0:00 python3 /patroni.py postgres0.yml
24 ? Ss 0:00 \_ python3 /patroni.py postgres0.yml
25 ? S 0:00 \_ postgres -D /var/lib/postgresql/data/pgdata -
26 ? Ss 0:00 \_ postgres: batman: startup process recov
27 ? Ss 0:00 \_ postgres: batman: checkpointer process
28 ? Ss 0:00 \_ postgres: batman: writer process
29 ? Ss 0:00 \_ postgres: batman: stats collector process
31 ? Ss 0:00 \_ postgres: batman: postgres postgres 127.0
```
The postmaster parent hangs on lock on stderr:
```
Thread 0x7fbf86ffd700
File "/usr/lib/python3.5/threading.py", line 882, in _bootstrap
self._bootstrap_inner()
File "/usr/lib/python3.5/threading.py", line 914, in _bootstrap_inner
self.run()
File "/usr/lib/python3.5/threading.py", line 862, in run
self._target(*self._args, **self._kwargs)
File "/patroni/async_executor.py", line 97, in run
wakeup = func(*args) if args else func()
File "/patroni/postgresql/__init__.py", line 728, in follow
self.start(timeout=timeout, block_callbacks=change_role, role=role)
File "/patroni/postgresql/__init__.py", line 434, in start
options)
File "/patroni/postgresql/postmaster.py", line 175, in start
proc.start()
File "/usr/lib/python3.5/multiprocessing/process.py", line 105, in start
self._popen = self._Popen(self)
File "/usr/lib/python3.5/multiprocessing/context.py", line 212, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/usr/lib/python3.5/multiprocessing/context.py", line 267, in _Popen
return Popen(process_obj)
File "/usr/lib/python3.5/multiprocessing/popen_fork.py", line 20, in __init__
self._launch(process_obj)
File "/usr/lib/python3.5/multiprocessing/popen_fork.py", line 74, in _launch
code = process_obj._bootstrap()
File "/usr/lib/python3.5/multiprocessing/process.py", line 269, in _bootstrap
sys.stderr.flush()
File "<string>", line 1, in <module>
File "<string>", line 7, in <module>
```
While a bootstrap thread waits for child to finish:
```
Thread 0x7fbf86ffd700
File "/usr/lib/python3.5/threading.py", line 882, in _bootstrap
self._bootstrap_inner()
File "/usr/lib/python3.5/threading.py", line 914, in _bootstrap_inner
self.run()
File "/usr/lib/python3.5/threading.py", line 862, in run
self._target(*self._args, **self._kwargs)
File "/patroni/async_executor.py", line 97, in run
wakeup = func(*args) if args else func()
File "/patroni/postgresql/__init__.py", line 728, in follow
self.start(timeout=timeout, block_callbacks=change_role, role=role)
File "/patroni/postgresql/__init__.py", line 434, in start
options)
File "/patroni/postgresql/postmaster.py", line 177, in start
proc.join()
File "/usr/lib/python3.5/multiprocessing/process.py", line 121, in join
res = self._popen.wait(timeout)
File "/usr/lib/python3.5/multiprocessing/popen_fork.py", line 51, in wait
return self.poll(os.WNOHANG if timeout == 0.0 else 0)
File "/usr/lib/python3.5/multiprocessing/popen_fork.py", line 29, in poll
pid, sts = os.waitpid(self.pid, flag)
```
The hanging patroni process repeatedly logs: `INFO: restarting after failure in progress`.
It is a known issue in Python that threading and multiprocessing do not mix well: [https://bugs.python.org/issue6721](url)
While the issue with logging lock might have been fixed in Python 3.7 the recommended workaround is to use `spawn` of `forkserver` start methods, e.g. by adding `multiprocessing.set_start_method('spawn')` at the beggining of `main()`.
This can be quickly reproduced using following `docker-compose.yml`:
```
version: "2.1"
volumes:
patroni1_volume:
patroni2_volume:
services:
zookeeper:
image: zookeeper:3.4.10
patroni1:
build:
context: https://github.com/zalando/patroni.git
depends_on:
- zookeeper
environment:
PATRONI_POSTGRESQL_DATA_DIR: /var/lib/postgresql/data/pgdata
PATRONI_ZOOKEEPER_HOSTS: "[\"zookeeper:2181\"]"
volumes:
- patroni1_volume:/var/lib/postgresql/data
healthcheck:
test: "curl --fail localhost:8008/health && (curl --fail localhost:8008/sync || curl --fail localhost:8008/master)"
interval: 10s
timeout: 5s
retries: 30
patroni2:
build:
context: https://github.com/zalando/patroni.git
depends_on:
- zookeeper
environment:
PATRONI_POSTGRESQL_DATA_DIR: /var/lib/postgresql/data/pgdata
PATRONI_ZOOKEEPER_HOSTS: "[\"zookeeper:2181\"]"
volumes:
- patroni2_volume:/var/lib/postgresql/data
healthcheck:
test: "curl --fail localhost:8008/health && (curl --fail localhost:8008/sync || curl --fail localhost:8008/master)"
interval: 10s
timeout: 5s
retries: 30
```
and following shell script:
```
#!/bin/bash
docker-compose up -d
docker-compose exec patroni1 patronictl edit-config -s synchronous_mode=true -q --force batman
CHECK() { ! docker-compose ps | grep patroni[12] | tee /dev/stderr | grep -v '(healthy)' > /dev/null; }
WAIT() { for ((i=0;i<300;i++)); do ! CHECK || break; sleep 1; done; CHECK; }
while WAIT; do docker-compose restart patroni{1,2}; done
```
| Interesting, somehow we have never seen it in the wild.
Maybe because we don't run Patroni with PID=1?
@maciejkowalczyk9ld could you please prepare a fix?
> Interesting, somehow we have never seen it in the wild.
> Maybe because we don't run Patroni with PID=1?
It occurs even if you add some proper init process with PID=1 above Patroni:
```diff
--- docker-compose.yml
+++ docker-compose.yml
@@ -1,4 +1,4 @@
-version: "2.1"
+version: "2.2"
volumes:
patroni1_volume:
patroni2_volume:
@@ -6,6 +6,7 @@ services:
zookeeper:
image: zookeeper:3.4.10
patroni1:
+ init: true
build:
context: https://github.com/zalando/patroni.git
depends_on:
@@ -21,6 +22,7 @@ services:
timeout: 5s
retries: 30
patroni2:
+ init: true
build:
context: https://github.com/zalando/patroni.git
depends_on:
```
> @maciejkowalczyk9ld could you please prepare a fix?
Do you still support Python 2.7?
I'm not sure this bug also occurs there and it does not have capability of setting `spawn` start method.
So my fix would set the start method conditionally.
> Do you still support Python 2.7?
Yes, we do. Despite all attempts to make 2.7 die some enterprises continue using it :(
> I'm not sure this bug also occurs there and it does not have capability of setting spawn start method.
Yes, I know that it lacks such capability, and probably it was a reason why I didn't set it myself.
Before going the `multiprocessing` way we tried to use `subprocess.Popen` to execute itself and send the postmaster pid via stdout-stdin. It was sort of working, but closing the stdout of postgres process :(
> So my fix would set the start method conditionally.
I am fine with it.
Interesting, somehow we have never seen it in the wild.
Maybe because we don't run Patroni with PID=1?
@maciejkowalczyk9ld could you please prepare a fix?
> Interesting, somehow we have never seen it in the wild.
> Maybe because we don't run Patroni with PID=1?
It occurs even if you add some proper init process with PID=1 above Patroni:
```diff
--- docker-compose.yml
+++ docker-compose.yml
@@ -1,4 +1,4 @@
-version: "2.1"
+version: "2.2"
volumes:
patroni1_volume:
patroni2_volume:
@@ -6,6 +6,7 @@ services:
zookeeper:
image: zookeeper:3.4.10
patroni1:
+ init: true
build:
context: https://github.com/zalando/patroni.git
depends_on:
@@ -21,6 +22,7 @@ services:
timeout: 5s
retries: 30
patroni2:
+ init: true
build:
context: https://github.com/zalando/patroni.git
depends_on:
```
> @maciejkowalczyk9ld could you please prepare a fix?
Do you still support Python 2.7?
I'm not sure this bug also occurs there and it does not have capability of setting `spawn` start method.
So my fix would set the start method conditionally.
> Do you still support Python 2.7?
Yes, we do. Despite all attempts to make 2.7 die some enterprises continue using it :(
> I'm not sure this bug also occurs there and it does not have capability of setting spawn start method.
Yes, I know that it lacks such capability, and probably it was a reason why I didn't set it myself.
Before going the `multiprocessing` way we tried to use `subprocess.Popen` to execute itself and send the postmaster pid via stdout-stdin. It was sort of working, but closing the stdout of postgres process :(
> So my fix would set the start method conditionally.
I am fine with it. | 2019-11-14T16:54:06Z | [] | [] |
zalando/patroni | 1,392 | zalando__patroni-1392 | [
"280"
] | 7e170928093f31da7b64086d515108f1fd7efab1 | diff --git a/patroni/dcs/__init__.py b/patroni/dcs/__init__.py
--- a/patroni/dcs/__init__.py
+++ b/patroni/dcs/__init__.py
@@ -449,21 +449,21 @@ def is_paused(self):
def is_synchronous_mode(self):
return self.check_mode('synchronous_mode')
- def get_replication_slots(self, name, role):
+ def get_replication_slots(self, my_name, role):
# if the replicatefrom tag is set on the member - we should not create the replication slot for it on
# the current master, because that member would replicate from elsewhere. We still create the slot if
# the replicatefrom destination member is currently not a member of the cluster (fallback to the
# master), or if replicatefrom destination member happens to be the current master
use_slots = self.config and self.config.data.get('postgresql', {}).get('use_slots', True)
if role in ('master', 'standby_leader'):
- slot_members = [m.name for m in self.members if use_slots and m.name != name and
- (m.replicatefrom is None or m.replicatefrom == name or
+ slot_members = [m.name for m in self.members if use_slots and m.name != my_name and
+ (m.replicatefrom is None or m.replicatefrom == my_name or
not self.has_member(m.replicatefrom))]
permanent_slots = (self.config and self.config.permanent_slots or {}).copy()
else:
# only manage slots for replicas that replicate from this one, except for the leader among them
slot_members = [m.name for m in self.members if use_slots and
- m.replicatefrom == name and m.name != self.leader.name]
+ m.replicatefrom == my_name and m.name != self.leader.name]
permanent_slots = {}
slots = {slot_name_from_member_name(name): {'type': 'physical'} for name in slot_members}
@@ -484,22 +484,21 @@ def get_replication_slots(self, name, role):
logger.error("Slot name may only contain lower case letters, numbers, and the underscore chars")
continue
- if name in slots:
- logger.error("Permanent replication slot {'%s': %s} is conflicting with" +
- " physical replication slot for cluster member", name, value)
- continue
-
- value = deepcopy(value)
- if not value:
- value = {'type': 'physical'}
-
+ value = deepcopy(value) if value else {'type': 'physical'}
if isinstance(value, dict):
if 'type' not in value:
value['type'] = 'logical' if value.get('database') and value.get('plugin') else 'physical'
- if value['type'] == 'physical' or value['type'] == 'logical' \
- and value.get('database') and value.get('plugin'):
- slots[name] = value
+ if value['type'] == 'physical':
+ if name != my_name: # Don't try to create permanent physical replication slot for yourself
+ slots[name] = value
+ continue
+ elif value['type'] == 'logical' and value.get('database') and value.get('plugin'):
+ if name in slots:
+ logger.error("Permanent logical replication slot {'%s': %s} is conflicting with" +
+ " physical replication slot for cluster member", name, value)
+ else:
+ slots[name] = value
continue
logger.error("Bad value for slot '%s' in permanent_slots: %s", name, permanent_slots[name])
| diff --git a/tests/test_postgresql.py b/tests/test_postgresql.py
--- a/tests/test_postgresql.py
+++ b/tests/test_postgresql.py
@@ -281,8 +281,8 @@ def test_follow(self):
@patch.object(Postgresql, 'is_running', Mock(return_value=True))
def test_sync_replication_slots(self):
self.p.start()
- config = ClusterConfig(1, {'slots': {'ls': {'database': 'a', 'plugin': 'b'},
- 'A': 0, 'test_3': 0, 'b': {'type': 'logical', 'plugin': '1'}}}, 1)
+ config = ClusterConfig(1, {'slots': {'test_3': {'database': 'a', 'plugin': 'b'},
+ 'A': 0, 'ls': 0, 'b': {'type': 'logical', 'plugin': '1'}}}, 1)
cluster = Cluster(True, config, self.leader, 0, [self.me, self.other, self.leadermem], None, None, None)
with mock.patch('patroni.postgresql.Postgresql._query', Mock(side_effect=psycopg2.OperationalError)):
self.p.slots_handler.sync_replication_slots(cluster)
| Replication slots don't prevent recycling of WAL when standby goes offline
When standby goes offline for a while the member key will expire and Patroni will happily remove its replication slot. Having an archive works around this, but it would be nice to make simple deployments more resilient too. Probably needs some kind of persistent flag, or offline_ttl for cluster members so Patroni knows they will be coming back and doesn't remove their replication slots. And a corresponding administration command to kick them out when they actually need to go away.
| Is this problem solved?
This issue is still active, patches are welcome.
While this is not done, `wal_keep_segments` is a decent workaround. I think in most cases an upper limit for how far behind a replication slot can be would be needed anyway because having the master go down due to full disk is worse than having to reinit a standby. And you need to keep the disk space available for that purpose, so it doesn't matter too much if you are using that disk space even if you don't actually need to. | 2020-02-14T15:15:37Z | [] | [] |
zalando/patroni | 1,696 | zalando__patroni-1696 | [
"1695"
] | 4dd902fbf13ea9be81b652e28e1e84725cb6779d | diff --git a/patroni/ctl.py b/patroni/ctl.py
--- a/patroni/ctl.py
+++ b/patroni/ctl.py
@@ -7,7 +7,6 @@
import datetime
import dateutil.parser
import dateutil.tz
-import cdiff
import copy
import difflib
import io
@@ -34,6 +33,10 @@
from patroni.version import __version__
from prettytable import ALL, FRAME, PrettyTable
from six.moves.urllib_parse import urlparse
+try:
+ from ydiff import markup_to_pager, PatchStream
+except ImportError: # pragma: no cover
+ from cdiff import markup_to_pager, PatchStream
CONFIG_DIR_PATH = click.get_app_dir('patroni')
CONFIG_FILE_PATH = os.path.join(CONFIG_DIR_PATH, 'patronictl.yaml')
@@ -1086,7 +1089,14 @@ class opts:
side_by_side = False
width = 80
tab_width = 8
- cdiff.markup_to_pager(cdiff.PatchStream(buf), opts)
+ wrap = True
+ if find_executable('less'):
+ pager = None
+ else:
+ pager = 'more.com' if sys.platform == 'win32' else 'more'
+ pager_options = None
+
+ markup_to_pager(PatchStream(buf), opts)
else:
for line in unified_diff:
click.echo(line.rstrip('\n'))
| diff --git a/tests/test_ctl.py b/tests/test_ctl.py
--- a/tests/test_ctl.py
+++ b/tests/test_ctl.py
@@ -561,7 +561,7 @@ def test_apply_config_changes(self):
self.assertRaises(PatroniCtlException, apply_config_changes, before_editing, config, ['a'])
@patch('sys.stdout.isatty', return_value=False)
- @patch('cdiff.markup_to_pager')
+ @patch('patroni.ctl.markup_to_pager')
def test_show_diff(self, mock_markup_to_pager, mock_isatty):
show_diff("foo:\n bar: 1\n", "foo:\n bar: 2\n")
mock_markup_to_pager.assert_not_called()
@@ -570,6 +570,9 @@ def test_show_diff(self, mock_markup_to_pager, mock_isatty):
show_diff("foo:\n bar: 1\n", "foo:\n bar: 2\n")
mock_markup_to_pager.assert_called_once()
+ with patch('patroni.ctl.find_executable', Mock(return_value=None)):
+ show_diff("foo:\n bar: 1\n", "foo:\n bar: 2\n")
+
# Test that unicode handling doesn't fail with an exception
show_diff(b"foo:\n bar: \xc3\xb6\xc3\xb6\n".decode('utf-8'),
b"foo:\n bar: \xc3\xbc\xc3\xbc\n".decode('utf-8'))
| patronictl edit-config fails under Windows
The python library `cdiff` (or as it's now known, `ydiff`) is hardwired to use `less` in version <1.2.0
Regular Windows installs only have `more` and that is not enough.
When running `edit-config` in quiet mode, no diffs are generated, thus this option is currently the only one that works on Windows.
When running in regular mode `FileNotFoundError` raised:
```
...
File "C:\Program Files\Python38\lib\subprocess.py", line 854, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "C:\Program Files\Python38\lib\subprocess.py", line 1307, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
File "c:\Users\pasha\.vscode\extensions\ms-python.python-2020.8.108011\pythonFiles\lib\python\debugpy\_vendored\pydevd\_pydev_bundle\pydev_monkey.py", line 632, in new_CreateProcess
return getattr(_subprocess, original_name)(app_name, cmd_line, *args)
FileNotFoundError: [WinError 2] The system cannot find the file specified
```
| 2020-09-15T11:50:52Z | [] | [] |
|
zalando/patroni | 1,991 | zalando__patroni-1991 | [
"1990"
] | 77382e75dc0574419d97ace4c9f8941c2b036e2c | diff --git a/patroni/ha.py b/patroni/ha.py
--- a/patroni/ha.py
+++ b/patroni/ha.py
@@ -1002,7 +1002,7 @@ def process_healthy_cluster(self):
else:
return self.enforce_master_role(
'no action. I am ({0}) the leader with the lock'.format(self.state_handler.name),
- 'promoted self to leader because i had the session lock'
+ 'promoted self to leader because I had the session lock'
)
else:
# Either there is no connection to DCS or someone else acquired the lock
| diff --git a/tests/test_ha.py b/tests/test_ha.py
--- a/tests/test_ha.py
+++ b/tests/test_ha.py
@@ -300,7 +300,7 @@ def test_start_as_readonly(self):
self.p.is_healthy = true
self.ha.has_lock = true
self.p.controldata = lambda: {'Database cluster state': 'in production', 'Database system identifier': SYSID}
- self.assertEqual(self.ha.run_cycle(), 'promoted self to leader because i had the session lock')
+ self.assertEqual(self.ha.run_cycle(), 'promoted self to leader because I had the session lock')
@patch('psycopg2.connect', psycopg2_connect)
def test_acquire_lock_as_master(self):
@@ -354,7 +354,7 @@ def test_promote_because_have_lock(self):
self.ha.cluster.is_unlocked = false
self.ha.has_lock = true
self.p.is_leader = false
- self.assertEqual(self.ha.run_cycle(), 'promoted self to leader because i had the session lock')
+ self.assertEqual(self.ha.run_cycle(), 'promoted self to leader because I had the session lock')
def test_promote_without_watchdog(self):
self.ha.cluster.is_unlocked = false
| minor typo in logging message
`promoted self to leader because i had the session lock` instead of `promoted self to leader because I had the session lock` (note the capitalization of `I`) in `patroni/patroni/ha.py` and `patroni/tests/test_ha.py`.
| 2021-06-30T15:11:57Z | [] | [] |
|
zalando/patroni | 1,993 | zalando__patroni-1993 | [
"1988"
] | 77382e75dc0574419d97ace4c9f8941c2b036e2c | diff --git a/patroni/dcs/consul.py b/patroni/dcs/consul.py
--- a/patroni/dcs/consul.py
+++ b/patroni/dcs/consul.py
@@ -227,12 +227,11 @@ def __init__(self, config):
self._last_session_refresh = 0
self.__session_checks = config.get('checks', [])
self._register_service = config.get('register_service', False)
+ self._previous_loop_register_service = self._register_service
+ self._service_tags = sorted(config.get('service_tags', []))
+ self._previous_loop_service_tags = self._service_tags
if self._register_service:
- self._service_tags = config.get('service_tags', [])
- self._service_name = service_name_from_scope_name(self._scope)
- if self._scope != self._service_name:
- logger.warning('Using %s as consul service name instead of scope name %s', self._service_name,
- self._scope)
+ self._set_service_name()
self._service_check_interval = config.get('service_check_interval', '5s')
if not self._ctl:
self.create_session()
@@ -250,7 +249,18 @@ def create_session(self):
def reload_config(self, config):
super(Consul, self).reload_config(config)
- self._client.reload_config(config.get('consul', {}))
+
+ consul_config = config.get('consul', {})
+ self._client.reload_config(consul_config)
+ self._previous_loop_service_tags = self._service_tags
+ self._service_tags = sorted(consul_config.get('service_tags', []))
+
+ should_register_service = consul_config.get('register_service', False)
+ if should_register_service and not self._register_service:
+ self._set_service_name()
+
+ self._previous_loop_register_service = self._register_service
+ self._register_service = should_register_service
def set_ttl(self, ttl):
if self._client.http.set_ttl(ttl/2.0): # Consul multiplies the TTL by 2x
@@ -402,14 +412,18 @@ def touch_member(self, data, permanent=False):
self._client.kv.delete(self.member_path)
create_member = True
+ if self._register_service or self._previous_loop_register_service:
+ try:
+ self.update_service(not create_member and member and member.data or {}, data)
+ except Exception:
+ logger.exception('update_service')
+
if not create_member and member and deep_compare(data, member.data):
return True
try:
args = {} if permanent else {'acquire': self._session}
self._client.kv.put(self.member_path, json.dumps(data, separators=(',', ':')), **args)
- if self._register_service:
- self.update_service(not create_member and member and member.data or {}, data)
return True
except InvalidSession:
self._session = None
@@ -418,6 +432,11 @@ def touch_member(self, data, permanent=False):
logger.exception('touch_member')
return False
+ def _set_service_name(self):
+ self._service_name = service_name_from_scope_name(self._scope)
+ if self._scope != self._service_name:
+ logger.warning('Using %s as consul service name instead of scope name %s', self._service_name, self._scope)
+
@catch_consul_errors
def register_service(self, service_name, **kwargs):
logger.info('Register service %s, params %s', service_name, kwargs)
@@ -441,17 +460,22 @@ def _update_service(self, data):
deregister='{0}s'.format(self._client.http.ttl * 10))
tags = self._service_tags[:]
tags.append(role)
+ self._previous_loop_service_tags = self._service_tags
+
params = {
'service_id': '{0}/{1}'.format(self._scope, self._name),
'address': conn_parts.hostname,
'port': conn_parts.port,
'check': check,
- 'tags': tags
+ 'tags': tags,
+ 'enable_tag_override': True,
}
- if state == 'stopped':
+ if state == 'stopped' or (not self._register_service and self._previous_loop_register_service):
+ self._previous_loop_register_service = self._register_service
return self.deregister_service(params['service_id'])
+ self._previous_loop_register_service = self._register_service
if role in ['master', 'replica', 'standby-leader']:
if state != 'running':
return
@@ -470,7 +494,10 @@ def update_service(self, old_data, new_data, force=False):
if old_data.get(key) != new_data[key]:
update = True
- if force or update:
+ if (
+ force or update or self._register_service != self._previous_loop_register_service
+ or self._service_tags != self._previous_loop_service_tags
+ ):
return self._update_service(new_data)
@catch_consul_errors
| diff --git a/tests/test_consul.py b/tests/test_consul.py
--- a/tests/test_consul.py
+++ b/tests/test_consul.py
@@ -215,4 +215,50 @@ def test_update_service(self):
self.assertIsNone(self.c.update_service({}, d))
def test_reload_config(self):
- self.c.reload_config({'consul': {'token': 'foo'}, 'loop_wait': 10, 'ttl': 30, 'retry_timeout': 10})
+ self.assertEqual([], self.c._service_tags)
+ self.c.reload_config({'consul': {'token': 'foo', 'register_service': True, 'service_tags': ['foo']},
+ 'loop_wait': 10, 'ttl': 30, 'retry_timeout': 10})
+ self.assertEqual(["foo"], self.c._service_tags)
+
+ self.c.refresh_session = Mock(return_value=False)
+
+ d = {'role': 'replica', 'api_url': 'http://a/t', 'conn_url': 'pg://c:1', 'state': 'running'}
+
+ # Changing register_service from True to False calls deregister()
+ self.c.reload_config({'consul': {'register_service': False}, 'loop_wait': 10, 'ttl': 30, 'retry_timeout': 10})
+ with patch('consul.Consul.Agent.Service.deregister') as mock_deregister:
+ self.c.touch_member(d)
+ mock_deregister.assert_called_once()
+
+ self.assertEqual([], self.c._service_tags)
+
+ # register_service staying False between reloads does not call deregister()
+ self.c.reload_config({'consul': {'register_service': False}, 'loop_wait': 10, 'ttl': 30, 'retry_timeout': 10})
+ with patch('consul.Consul.Agent.Service.deregister') as mock_deregister:
+ self.c.touch_member(d)
+ self.assertFalse(mock_deregister.called)
+
+ # Changing register_service from False to True calls register()
+ self.c.reload_config({'consul': {'register_service': True}, 'loop_wait': 10, 'ttl': 30, 'retry_timeout': 10})
+ with patch('consul.Consul.Agent.Service.register') as mock_register:
+ self.c.touch_member(d)
+ mock_register.assert_called_once()
+
+ # register_service staying True between reloads does not call register()
+ self.c.reload_config({'consul': {'register_service': True}, 'loop_wait': 10, 'ttl': 30, 'retry_timeout': 10})
+ with patch('consul.Consul.Agent.Service.register') as mock_register:
+ self.c.touch_member(d)
+ self.assertFalse(mock_deregister.called)
+
+ # register_service staying True between reloads does calls register() if other service data has changed
+ self.c.reload_config({'consul': {'register_service': True}, 'loop_wait': 10, 'ttl': 30, 'retry_timeout': 10})
+ with patch('consul.Consul.Agent.Service.register') as mock_register:
+ self.c.touch_member(d)
+ mock_register.assert_called_once()
+
+ # register_service staying True between reloads does calls register() if service_tags have changed
+ self.c.reload_config({'consul': {'register_service': True, 'service_tags': ['foo']}, 'loop_wait': 10,
+ 'ttl': 30, 'retry_timeout': 10})
+ with patch('consul.Consul.Agent.Service.register') as mock_register:
+ self.c.touch_member(d)
+ mock_register.assert_called_once()
| sighup doesnt reload consul.register_service
**Describe the bug**
The register_service setting for Consul isn't dynamically adjustable.
**To Reproduce**
1. Start Patroni with Consul as the DCS and without setting consul.register_service in patroni.yml, so it defaults to false
2. set consul.register_service: true in patroni.yml
3. reload patroni (either by sighup or by the reload endpoint)
**Expected behavior**
I'd expect this to enable Consul service registration
**Environment**
- Patroni version: 2.0.2
- PostgreSQL version: 13..3
- DCS (and its version): Consul 1.10.0
I'm happy to put together a PR if this is something that yall are interested in accepting
| @tommyzli please, go ahead. | 2021-06-30T21:50:46Z | [] | [] |
zalando/patroni | 2,029 | zalando__patroni-2029 | [
"2028"
] | c81391e3148dad86adbb79e017cf105b61c8d869 | diff --git a/patroni/config.py b/patroni/config.py
--- a/patroni/config.py
+++ b/patroni/config.py
@@ -347,7 +347,7 @@ def _get_auth(name, params=None):
if param.startswith(PATRONI_ENV_PREFIX):
# PATRONI_(ETCD|CONSUL|ZOOKEEPER|EXHIBITOR|...)_(HOSTS?|PORT|..)
name, suffix = (param[8:].split('_', 1) + [''])[:2]
- if suffix in ('HOST', 'HOSTS', 'PORT', 'USE_PROXIES', 'PROTOCOL', 'SRV', 'URL', 'PROXY',
+ if suffix in ('HOST', 'HOSTS', 'PORT', 'USE_PROXIES', 'PROTOCOL', 'SRV', 'SRV_SUFFIX', 'URL', 'PROXY',
'CACERT', 'CERT', 'KEY', 'VERIFY', 'TOKEN', 'CHECKS', 'DC', 'CONSISTENCY',
'REGISTER_SERVICE', 'SERVICE_CHECK_INTERVAL', 'NAMESPACE', 'CONTEXT',
'USE_ENDPOINTS', 'SCOPE_LABEL', 'ROLE_LABEL', 'POD_IP', 'PORTS', 'LABELS',
diff --git a/patroni/dcs/etcd.py b/patroni/dcs/etcd.py
--- a/patroni/dcs/etcd.py
+++ b/patroni/dcs/etcd.py
@@ -283,13 +283,14 @@ def get_srv_record(host):
except DNSException:
return []
- def _get_machines_cache_from_srv(self, srv):
+ def _get_machines_cache_from_srv(self, srv, srv_suffix=None):
"""Fetch list of etcd-cluster member by resolving _etcd-server._tcp. SRV record.
This record should contain list of host and peer ports which could be used to run
'GET http://{host}:{port}/members' request (peer protocol)"""
ret = []
for r in ['-client-ssl', '-client', '-ssl', '', '-server-ssl', '-server']:
+ r = r.format('{0}-{1}', r, srv_suffix) if srv_suffix else r
protocol = 'https' if '-ssl' in r else 'http'
endpoint = '/members' if '-server' in r else ''
for host, port in self.get_srv_record('_etcd{0}._tcp.{1}'.format(r, srv)):
@@ -326,7 +327,7 @@ def _get_machines_cache_from_config(self):
machines_cache = []
if 'srv' in self._config:
- machines_cache = self._get_machines_cache_from_srv(self._config['srv'])
+ machines_cache = self._get_machines_cache_from_srv(self._config['srv'], self._config.get('srv_suffix'))
if not machines_cache and 'hosts' in self._config:
machines_cache = list(self._config['hosts'])
diff --git a/patroni/validator.py b/patroni/validator.py
--- a/patroni/validator.py
+++ b/patroni/validator.py
@@ -302,10 +302,11 @@ def assert_(condition, message="Wrong value"):
validate_host_port_listen_multiple_hosts.expected_type = string_types
validate_data_dir.expected_type = string_types
validate_etcd = {
- Or("host", "hosts", "srv", "url", "proxy"): Case({
+ Or("host", "hosts", "srv", "srv_suffix", "url", "proxy"): Case({
"host": validate_host_port,
"hosts": Or(comma_separated_host_port, [validate_host_port]),
"srv": str,
+ "srv_suffix": str,
"url": str,
"proxy": str})
}
| diff --git a/tests/test_etcd.py b/tests/test_etcd.py
--- a/tests/test_etcd.py
+++ b/tests/test_etcd.py
@@ -87,7 +87,8 @@ def dns_query(name, _):
raise DNSException()
srv = Mock()
srv.port = 2380
- srv.target.to_text.return_value = 'localhost' if name == '_etcd-server._tcp.foobar' else '127.0.0.1'
+ srv.target.to_text.return_value = \
+ 'localhost' if name in ['_etcd-server._tcp.foobar', '_etcd-server-baz._tcp.foobar'] else '127.0.0.1'
return [srv]
@@ -183,6 +184,7 @@ def test_get_srv_record(self):
def test__get_machines_cache_from_srv(self):
self.client._get_machines_cache_from_srv('foobar')
+ self.client._get_machines_cache_from_srv('foobar', 'baz')
self.client.get_srv_record = Mock(return_value=[('localhost', 2380)])
self.client._get_machines_cache_from_srv('blabla')
| Add ETCD srv_name config parametter
Please consider adding ETCD SRV name config parameter to Patroni.
As per ETCD documentation:
> The -discovery-srv-name flag additionally configures a suffix to the SRV name that is queried during discovery. Use this flag to differentiate between multiple etcd clusters under the same domain. For example, if discovery-srv=example.com and -discovery-srv-name=foo are set, the following DNS SRV queries are made:
>
> _etcd-server-ssl-foo._tcp.example.com
> _etcd-server-foo._tcp.example.com
we use SRV name suffixes to differentiate ETCD clusters in our private domain (around 40k users) and there is no simple way how to point Patroni to a specific ETCD cluster using SRV.
| It is perfectly supported, please read the docs: https://patroni.readthedocs.io/en/latest/SETTINGS.html#etcd
https://github.com/zalando/patroni/blob/c81391e3148dad86adbb79e017cf105b61c8d869/patroni/dcs/etcd.py#L287-L313
OK then, how I can configure Patroni to retrieve _etcd-server-gis._tcp.ourdomain.org SRV records from DNS? (Note the -gis part of the url) Because it is not obvious from docs or even source code.
I see, discovery-srv-name is something that didn't exist 6 years ago.
If you want to have it supported - please feel free to implement the support. | 2021-08-11T10:16:02Z | [] | [] |
zalando/patroni | 2,185 | zalando__patroni-2185 | [
"2184"
] | 3e1076a5746b4d7f313eaba0ff374824644c8ab1 | diff --git a/patroni/api.py b/patroni/api.py
--- a/patroni/api.py
+++ b/patroni/api.py
@@ -768,6 +768,8 @@ def __initialize(self, listen, ssl_options):
reloading_config = self.__listen is not None # changing config in runtime
if reloading_config:
self.shutdown()
+ # Rely on ThreadingMixIn.server_close() to have all requests terminate before we continue
+ self.server_close()
self.__listen = listen
self.__ssl_options = ssl_options
| diff --git a/tests/test_api.py b/tests/test_api.py
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -549,7 +549,8 @@ def test_reload_config(self):
self.assertRaises(ValueError, MockRestApiServer, None, '', bad_config)
self.assertRaises(ValueError, self.srv.reload_config, bad_config)
self.assertRaises(ValueError, self.srv.reload_config, {})
- with patch.object(socket.socket, 'setsockopt', Mock(side_effect=socket.error)):
+ with patch.object(socket.socket, 'setsockopt', Mock(side_effect=socket.error)), \
+ patch.object(MockRestApiServer, 'server_close', Mock()):
self.srv.reload_config({'listen': ':8008'})
@patch.object(MockPatroni, 'dcs')
| Rest API somtimes stops responding when switching certificates
Switching REST API certificates while there is a concurrent API request active results in the following error:
2022-01-25 14:14:37,739 ERROR: Failed to reload config_file=postgres0.yml
Traceback (most recent call last):
File "/home/ants/work/patroni/patroni/patroni/__main__.py", line 74, in reload_config
self.api.reload_config(self.config['restapi'])
File "/home/ants/work/patroni/patroni/patroni/api.py", line 871, in reload_config
self.__initialize(config['listen'], ssl_options)
File "/home/ants/work/patroni/patroni/patroni/api.py", line 776, in __initialize
self.__httpserver_init(host, port)
File "/home/ants/work/patroni/patroni/patroni/api.py", line 755, in __httpserver_init
HTTPServer.__init__(self, info[0][-1][:2], RestApiHandler)
File "/usr/lib/python3.8/socketserver.py", line 452, in __init__
self.server_bind()
File "/usr/lib/python3.8/http/server.py", line 138, in server_bind
socketserver.TCPServer.server_bind(self)
File "/usr/lib/python3.8/socketserver.py", line 466, in server_bind
self.socket.bind(self.server_address)
OSError: [Errno 98] Address already in use
After this REST API is stuck in a state where it is not responding.
To reproduce:
* Create two keypairs {cert,key}{1,2}.pem, one with EE as country other with AU
* Configure postgres0.yml to use the keypair.
* Run attached python script to create a load on the API.
* Run attached shell script to swap between the certs continuously. Should get stuck within a few tries.
| 2022-01-25T15:01:19Z | [] | [] |
|
zalando/patroni | 2,287 | zalando__patroni-2287 | [
"2286"
] | 5f6197aaad3ab0fb6c7eea9b8dd3cf6f141a616e | diff --git a/patroni/dcs/kubernetes.py b/patroni/dcs/kubernetes.py
--- a/patroni/dcs/kubernetes.py
+++ b/patroni/dcs/kubernetes.py
@@ -48,14 +48,29 @@ class ConfigException(Exception):
def __init__(self):
self.pool_config = {'maxsize': 10, 'num_pools': 10} # configuration for urllib3.PoolManager
+ self._token_expires_at = datetime.datetime.max
self._make_headers()
+ def _set_token(self, token):
+ self._headers['authorization'] = 'Bearer ' + token
+
def _make_headers(self, token=None, **kwargs):
self._headers = urllib3.make_headers(user_agent=USER_AGENT, **kwargs)
if token:
- self._headers['authorization'] = 'Bearer ' + token
+ self._set_token(token)
- def load_incluster_config(self, ca_certs=SERVICE_CERT_FILENAME):
+ def _read_token_file(self):
+ if not os.path.isfile(SERVICE_TOKEN_FILENAME):
+ raise self.ConfigException('Service token file does not exists.')
+ with open(SERVICE_TOKEN_FILENAME) as f:
+ token = f.read()
+ if not token:
+ raise self.ConfigException('Token file exists but empty.')
+ self._token_expires_at = datetime.datetime.now() + self._token_refresh_interval
+ return token
+
+ def load_incluster_config(self, ca_certs=SERVICE_CERT_FILENAME,
+ token_refresh_interval=datetime.timedelta(minutes=1)):
if SERVICE_HOST_ENV_NAME not in os.environ or SERVICE_PORT_ENV_NAME not in os.environ:
raise self.ConfigException('Service host/port is not set.')
if not os.environ[SERVICE_HOST_ENV_NAME] or not os.environ[SERVICE_PORT_ENV_NAME]:
@@ -67,14 +82,9 @@ def load_incluster_config(self, ca_certs=SERVICE_CERT_FILENAME):
if not f.read():
raise self.ConfigException('Cert file exists but empty.')
self.pool_config['ca_certs'] = ca_certs
-
- if not os.path.isfile(SERVICE_TOKEN_FILENAME):
- raise self.ConfigException('Service token file does not exists.')
- with open(SERVICE_TOKEN_FILENAME) as f:
- token = f.read()
- if not token:
- raise self.ConfigException('Token file exists but empty.')
- self._make_headers(token=token)
+ self._token_refresh_interval = token_refresh_interval
+ token = self._read_token_file()
+ self._make_headers(token=token)
self._server = uri('https', (os.environ[SERVICE_HOST_ENV_NAME], os.environ[SERVICE_PORT_ENV_NAME]))
@staticmethod
@@ -109,6 +119,11 @@ def server(self):
@property
def headers(self):
+ if self._token_expires_at <= datetime.datetime.now():
+ try:
+ self._set_token(self._read_token_file())
+ except Exception as e:
+ logger.error('Failed to refresh service account token: %r', e)
return self._headers.copy()
| diff --git a/tests/test_kubernetes.py b/tests/test_kubernetes.py
--- a/tests/test_kubernetes.py
+++ b/tests/test_kubernetes.py
@@ -1,3 +1,4 @@
+import datetime
import json
import socket
import time
@@ -79,6 +80,28 @@ def test_load_incluster_config(self):
self.assertRaises(k8s_config.ConfigException, k8s_config.load_incluster_config)
k8s_config.load_incluster_config()
self.assertEqual(k8s_config.server, 'https://a:1')
+ self.assertEqual(k8s_config.headers.get('authorization'), 'Bearer a')
+
+ def test_refresh_token(self):
+ with patch('os.environ', {SERVICE_HOST_ENV_NAME: 'a', SERVICE_PORT_ENV_NAME: '1'}),\
+ patch('os.path.isfile', Mock(side_effect=[True, True, False, True, True, True])),\
+ patch.object(builtins, 'open', Mock(side_effect=[
+ mock_open(read_data='cert')(), mock_open(read_data='a')(),
+ mock_open()(), mock_open(read_data='b')(), mock_open(read_data='c')()])):
+ k8s_config.load_incluster_config(token_refresh_interval=datetime.timedelta(milliseconds=100))
+ self.assertEqual(k8s_config.headers.get('authorization'), 'Bearer a')
+ time.sleep(0.1)
+ # token file doesn't exist
+ self.assertEqual(k8s_config.headers.get('authorization'), 'Bearer a')
+ # token file is empty
+ self.assertEqual(k8s_config.headers.get('authorization'), 'Bearer a')
+ # token refreshed
+ self.assertEqual(k8s_config.headers.get('authorization'), 'Bearer b')
+ time.sleep(0.1)
+ # token refreshed
+ self.assertEqual(k8s_config.headers.get('authorization'), 'Bearer c')
+ # no need to refresh token
+ self.assertEqual(k8s_config.headers.get('authorization'), 'Bearer c')
def test_load_kube_config(self):
config = {
| kubernetes: Refresh service account tokens by reloading from the projected volume
**Describe the bug**
Patroni loads a service account token [on initialization](https://github.com/zalando/patroni/blob/04c6f58b2b60a8620bc15deaeb819b205fb8f93b/patroni/dcs/kubernetes.py#L71-L77) and use the same token across its lifetime.
If the apiserver flag `--service-account-extend-token-expiration` is turned on (the default). Apiserver will log a stale-token event in audit log for each request. If the apiserver flag `--service-account-extend-token-expiration` is turned off, the request will be rejected.
Since Kubernetes v1.21, [projected service account tokens](https://kubernetes.io/docs/reference/access-authn-authz/service-accounts-admin/#bound-service-account-token-volume) are enable by default. The token expiry is 1 hour and a client is expected to reload the token upon expiry.
**Expected behavior**
Examine service account token's expiry when making requests to apiserver and reload the token if expired.
**Environment**
- Patroni version: 2.1.2
**Have you tried to use GitHub issue search?**
Yes
**Additional context**
Details about kubernetes service account token feature:
https://github.com/kubernetes/enhancements/blob/master/keps/sig-auth/1205-bound-service-account-tokens/README.md
| Good catch @hligit!
It seems that the official python client uses a very simple strategy, refresh the token every minute: https://github.com/kubernetes-client/python/commit/3cfc41ea9e94ca6c865d4149dcd64f24412221ce
We can do exactly the same.
Thanks for the pointer @CyberDem0n. Raised a PR #2287 | 2022-05-04T02:41:59Z | [] | [] |
zalando/patroni | 2,304 | zalando__patroni-2304 | [
"2302"
] | 96b75fa7cbf43f185642cf7d5e5b6b57ecf231bc | diff --git a/patroni/ha.py b/patroni/ha.py
--- a/patroni/ha.py
+++ b/patroni/ha.py
@@ -315,8 +315,7 @@ def _handle_rewind_or_reinitialize(self):
msg = 'running pg_rewind from ' + leader.name
return self._async_executor.try_run_async(msg, self._rewind.execute, args=(leader,)) or msg
- # remove_data_directory_on_diverged_timelines is set
- if not self.is_standby_cluster():
+ if self._rewind.should_remove_data_directory_on_diverged_timelines and not self.is_standby_cluster():
msg = 'reinitializing due to diverged timelines'
return self._async_executor.try_run_async(msg, self._do_reinitialize, args=(self.cluster,)) or msg
diff --git a/patroni/postgresql/rewind.py b/patroni/postgresql/rewind.py
--- a/patroni/postgresql/rewind.py
+++ b/patroni/postgresql/rewind.py
@@ -46,9 +46,13 @@ def can_rewind(self):
return False
return self.configuration_allows_rewind(self._postgresql.controldata())
+ @property
+ def should_remove_data_directory_on_diverged_timelines(self):
+ return self._postgresql.config.get('remove_data_directory_on_diverged_timelines')
+
@property
def can_rewind_or_reinitialize_allowed(self):
- return self._postgresql.config.get('remove_data_directory_on_diverged_timelines') or self.can_rewind
+ return self.should_remove_data_directory_on_diverged_timelines or self.can_rewind
def trigger_check_diverged_lsn(self):
if self.can_rewind_or_reinitialize_allowed and self._state != REWIND_STATUS.NEED:
@@ -374,19 +378,22 @@ def execute(self, leader):
if self.pg_rewind(r):
self._state = REWIND_STATUS.SUCCESS
- elif not self.check_leader_is_not_in_recovery(r):
- logger.warning('Failed to rewind because master %s become unreachable', leader.name)
else:
- logger.error('Failed to rewind from healty master: %s', leader.name)
-
- for name in ('remove_data_directory_on_rewind_failure', 'remove_data_directory_on_diverged_timelines'):
- if self._postgresql.config.get(name):
- logger.warning('%s is set. removing...', name)
- self._postgresql.remove_data_directory()
- self._state = REWIND_STATUS.INITIAL
- break
+ if not self.check_leader_is_not_in_recovery(r):
+ logger.warning('Failed to rewind because master %s become unreachable', leader.name)
+ if not self.can_rewind: # It is possible that the previous attempt damaged pg_control file!
+ self._state = REWIND_STATUS.FAILED
else:
+ logger.error('Failed to rewind from healty master: %s', leader.name)
self._state = REWIND_STATUS.FAILED
+
+ if self.failed:
+ for name in ('remove_data_directory_on_rewind_failure', 'remove_data_directory_on_diverged_timelines'):
+ if self._postgresql.config.get(name):
+ logger.warning('%s is set. removing...', name)
+ self._postgresql.remove_data_directory()
+ self._state = REWIND_STATUS.INITIAL
+ break
return False
def reset_state(self):
| diff --git a/tests/test_ha.py b/tests/test_ha.py
--- a/tests/test_ha.py
+++ b/tests/test_ha.py
@@ -314,6 +314,7 @@ def test_recover_with_rewind(self):
self.assertEqual(self.ha.run_cycle(), 'fake')
@patch.object(Rewind, 'rewind_or_reinitialize_needed_and_possible', Mock(return_value=True))
+ @patch.object(Rewind, 'should_remove_data_directory_on_diverged_timelines', PropertyMock(return_value=True))
@patch.object(Bootstrap, 'create_replica', Mock(return_value=1))
def test_recover_with_reinitialize(self):
self.p.is_running = false
| Removed data directory
**Describe the bug**
We had networking issues and Patroni switched the primary sql server multiple times (40+).
The timelines diverged and the following was in the log files:
2022-05-15 14:13:05,019 INFO: reinitializing due to diverged timelines
2022-05-15 14:13:08,613 INFO: Removing data directory: /var/lib/pgsql/13/data
We don't have the following parameters set in any configuration:
remove_data_directory_on_rewind_failure
remove_data_directory_on_diverged_timelines
And by default, the values should be 'false' according to https://patroni.readthedocs.io/en/latest/SETTINGS.html#postgresql
**Expected behavior**
Data directory should not be removed since "remove_data_directory_on_diverged_timelines" is not set
**Environment**
- Patroni version: 2.1.3
- PostgreSQL version: 13.5
- DCS (and its version): etcd 3.5.2
**Patroni configuration file**
```
scope: 'patroni_env'
namespace: '/patroni/'
name: 'envdb2'
log:
dir: '/var/log/pgsql/'
file_size: 2097152
file_num: 5
restapi:
listen: '192.168.1.12:8008'
connect_address: '192.168.1.12:8008'
# certfile: /etc/ssl/certs/ssl-cert.pem
# keyfile: /etc/ssl/private/ssl-cert.key
# authentication:
# username: username
# password: password
# ctl:
# insecure: false # Allow connections to SSL sites without certs
# certfile: /etc/ssl/certs/ssl-cert.pem
# cacert: /etc/ssl/certs/ssl-cacert.pem
etcd:
hosts: "192.168.1.10:2379,192.168.1.12:2379,192.168.1.2:2379,192.168.1.3:2379,192.168.1.6:2379,192.168.1.7:2379"
protocol: http
# cacert: /etc/patroni/certs/ca.crt
# cert: /etc/patroni/certs/client.crt
# key: /etc/patroni/certs/client.key
bootstrap:
# this section will be written into Etcd:/<namespace>/<scope>/config after initializing new cluster
# and all other cluster members will use it as a `global configuration`
dcs:
ttl: 30
loop_wait: 10
retry_timeout: 10
maximum_lag_on_failover: 536870912
# master_start_timeout: 300
# synchronous_mode: false
#standby_cluster:
#host: 127.0.0.1
#port: 1111
#primary_slot_name: patroni
postgresql:
use_pg_rewind: true
# use_slots: true
parameters:
max_locks_per_transaction: 2000
wal_log_hints: on
hot_standby: on
max_connections: 150
wal_keep_size: 5120MB
max_replication_slots: 5
max_wal_senders: 10
# some desired options for 'initdb'
# initdb: # Note: It needs to be a list (some options need values, others are switches)
# - encoding: UTF8
# - data-checksums
# pg_hba: # Add following lines to pg_hba.conf after running 'initdb'
# - local all all peer
# - host all all 127.0.0.1/32 md5
# - host all all ::1/128 ident
# - host all all 0.0.0.0/0 md5
# - host all all ::0/0 md5
# - host replication replication 0.0.0.0/0 md5
# - host replication replication ::0/0 md5
# Additional script to be launched after initial cluster creation (will be passed the connection URL as parameter)
# post_init: /usr/local/bin/setup_cluster.sh
# Some additional users users which needs to be created after initializing new cluster
# users:
# admin:
# password: admin
# options:
# - createrole
postgresql:
listen: '*:5432'
connect_address: '192.168.1.12:5432'
use_unix_socket: true
data_dir: /var/lib/pgsql/13/data
bin_dir: /usr/pgsql-13/bin
# config_dir:
#pgpass_patroni is dynamically created on the replica during patroni start. Do not use the standard .pgpass file because it will overwrite the file
pgpass: /var/lib/pgsql/.pgpass_patroni
authentication:
replication:
username: replication
password: PASSWORD
superuser:
username: postgres
password: PASSWORD
# Server side kerberos spn
# krbsrvname: postgres
parameters:
unix_socket_directories: '/var/run/postgresql'
watchdog:
mode: off # Allowed values: off, automatic, required
# device: /dev/watchdog
# safety_margin: 5
tags:
nofailover: false
noloadbalance: false
clonefrom: false
nosync: false
```
**patronictl show-config**
```
loop_wait: 10
maximum_lag_on_failover: 536870912
postgresql:
parameters:
hot_standby: true
max_connections: 150
max_locks_per_transaction: 2000
max_replication_slots: 5
max_wal_senders: 10
wal_keep_size: 5120MB
wal_log_hints: true
use_pg_rewind: true
retry_timeout: 10
ttl: 30
```
**Have you checked Patroni logs?**
2022-05-15 14:13:05,019 INFO: reinitializing due to diverged timelines
2022-05-15 14:13:08,613 INFO: Removing data directory: /var/lib/pgsql/13/data
**Have you tried to use GitHub issue search?**
Yes
| Unfortunately, just two lines of logs aren't enough.
You need to provide more lines from this node or describe how it could be reproduced.
[patroni.log](https://github.com/zalando/patroni/files/8715840/patroni.log)
Sorry. Here is the log file from the time it happened
Thank, it helps.
Here is what happened:
```
2022-05-15 14:08:40,358 INFO: running pg_rewind from envdb1
...
2022-05-15 14:11:47,956 INFO: running pg_rewind from envdb1 in progress
2022-05-15 14:11:57,097 INFO: pg_rewind exit code=1
2022-05-15 14:11:57,098 INFO: stdout=
2022-05-15 14:11:57,098 INFO: stderr=pg_rewind: servers diverged at WAL location 35A8/D4373518 on timeline 35
pg_rewind: rewinding from last common checkpoint at 35A8/CD30C0C0 on timeline 34
WARNING: terminating connection because of crash of another server process
DETAIL: The postmaster has commanded this server process to roll back the current transaction and exit, because another server process exited abnormally and possibly corrupted shared memory.
HINT: In a moment you should be able to reconnect to the database and repeat your command.
pg_rewind: fatal: unexpected result while fetching remote files: SSL SYSCALL error: EOF detected
2022-05-15 14:12:00,103 WARNING: Failed to rewind because master envdb1 become unreachable
```
That failed attempt damaged `pg_control` file:
```
2022-05-15 14:12:05,780 ERROR: Error when calling pg_controldata
Traceback (most recent call last):
File "/opt/patroni/patroni/lib/python3.9/site-packages/patroni/postgresql/__init__.py", line 816, in controldata
data = subprocess.check_output([self.pgcommand('pg_controldata'), self._data_dir], env=env)
File "/opt/patroni/lib/python3.9/subprocess.py", line 420, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/opt/patroni/lib/python3.9/subprocess.py", line 524, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/usr/pgsql-13/bin/pg_controldata', '/var/lib/pgsql/13/data']' returned non-zero exit status 1.
2022-05-15 14:12:11,770 INFO: pg_controldata:
```
That's it, $PGDATA became totally broken.
Patroni still keeps the state that `pg_rewind` is required, but the next attempt can't be executed anymore. And yes, it falsly removes $PGDATA. | 2022-05-18T12:38:03Z | [] | [] |
zalando/patroni | 2,344 | zalando__patroni-2344 | [
"2345"
] | b8a6387236d619345c2f72f2f8e858dc7a2bd791 | diff --git a/patroni/config.py b/patroni/config.py
--- a/patroni/config.py
+++ b/patroni/config.py
@@ -102,9 +102,9 @@ def __init__(self, configfile, validator=default_validator):
config_env = os.environ.pop(self.PATRONI_CONFIG_VARIABLE, None)
self._local_configuration = config_env and yaml.safe_load(config_env) or self.__environment_configuration
if validator:
- error = validator(self._local_configuration)
- if error:
- raise ConfigParseError(error)
+ errors = validator(self._local_configuration)
+ if errors:
+ raise ConfigParseError("\n".join(errors))
self.__effective_configuration = self._build_effective_configuration({}, self._local_configuration)
self._data_dir = self.__effective_configuration.get('postgresql', {}).get('data_dir', "")
diff --git a/patroni/daemon.py b/patroni/daemon.py
--- a/patroni/daemon.py
+++ b/patroni/daemon.py
@@ -1,3 +1,5 @@
+from __future__ import print_function
+
import abc
import os
import signal
@@ -83,16 +85,18 @@ def abstract_main(cls, validator=None):
help='Patroni may also read the configuration from the {0} environment variable'
.format(Config.PATRONI_CONFIG_VARIABLE))
args = parser.parse_args()
+ validate_config = validator and args.validate_config
try:
- if validator and args.validate_config:
+ if validate_config:
Config(args.configfile, validator=validator)
sys.exit()
config = Config(args.configfile)
except ConfigParseError as e:
if e.value:
- print(e.value)
- parser.print_help()
+ print(e.value, file=sys.stderr)
+ if not validate_config:
+ parser.print_help()
sys.exit(1)
controller = cls(config)
diff --git a/patroni/validator.py b/patroni/validator.py
--- a/patroni/validator.py
+++ b/patroni/validator.py
@@ -178,9 +178,11 @@ def __init__(self, validator):
self.validator = validator
def __call__(self, data):
+ errors = []
for i in self.validate(data):
if not i.status:
- print(i)
+ errors.append(str(i))
+ return errors
def validate(self, data):
self.data = data
| diff --git a/tests/test_validator.py b/tests/test_validator.py
--- a/tests/test_validator.py
+++ b/tests/test_validator.py
@@ -141,14 +141,14 @@ def setUp(self):
del directories[:]
def test_empty_config(self, mock_out, mock_err):
- schema({})
- output = mock_out.getvalue()
+ errors = schema({})
+ output = "\n".join(errors)
expected = list(sorted(['name', 'postgresql', 'restapi', 'scope'] + available_dcs))
self.assertEqual(expected, parse_output(output))
def test_complete_config(self, mock_out, mock_err):
- schema(config)
- output = mock_out.getvalue()
+ errors = schema(config)
+ output = "\n".join(errors)
self.assertEqual(['postgresql.bin_dir', 'raft.bind_addr', 'raft.self_addr'], parse_output(output))
def test_bin_dir_is_file(self, mock_out, mock_err):
@@ -158,8 +158,8 @@ def test_bin_dir_is_file(self, mock_out, mock_err):
c["restapi"]["connect_address"] = 'False:blabla'
c["etcd"]["hosts"] = ["127.0.0.1:2379", "1244.0.0.1:2379", "127.0.0.1:invalidport"]
c["kubernetes"]["pod_ip"] = "127.0.0.1111"
- schema(c)
- output = mock_out.getvalue()
+ errors = schema(c)
+ output = "\n".join(errors)
self.assertEqual(['etcd.hosts.1', 'etcd.hosts.2', 'kubernetes.pod_ip', 'postgresql.bin_dir',
'postgresql.data_dir', 'raft.bind_addr', 'raft.self_addr',
'restapi.connect_address'], parse_output(output))
@@ -176,8 +176,8 @@ def test_bin_dir_is_empty(self, mock_out, mock_err):
c["etcd"]["host"] = "127.0.0.1:237"
c["postgresql"]["listen"] = "127.0.0.1:5432"
with patch('patroni.validator.open', mock_open(read_data='9')):
- schema(c)
- output = mock_out.getvalue()
+ errors = schema(c)
+ output = "\n".join(errors)
self.assertEqual(['consul.host', 'etcd.host', 'postgresql.bin_dir', 'postgresql.data_dir', 'postgresql.listen',
'raft.bind_addr', 'raft.self_addr', 'restapi.connect_address'], parse_output(output))
@@ -195,8 +195,8 @@ def test_data_dir_contains_pg_version(self, mock_out, mock_err):
files.append(os.path.join(config["postgresql"]["bin_dir"], "postgres"))
files.append(os.path.join(config["postgresql"]["bin_dir"], "pg_isready"))
with patch('patroni.validator.open', mock_open(read_data='12')):
- schema(config)
- output = mock_out.getvalue()
+ errors = schema(config)
+ output = "\n".join(errors)
self.assertEqual(['raft.bind_addr', 'raft.self_addr'], parse_output(output))
@patch('subprocess.check_output', Mock(return_value=b"postgres (PostgreSQL) 12.1"))
@@ -210,8 +210,8 @@ def test_pg_version_missmatch(self, mock_out, mock_err):
c["etcd"]["hosts"] = []
del c["postgresql"]["bin_dir"]
with patch('patroni.validator.open', mock_open(read_data='11')):
- schema(c)
- output = mock_out.getvalue()
+ errors = schema(c)
+ output = "\n".join(errors)
self.assertEqual(['etcd.hosts', 'postgresql.data_dir',
'raft.bind_addr', 'raft.self_addr'], parse_output(output))
@@ -224,8 +224,8 @@ def test_pg_wal_doesnt_exist(self, mock_out, mock_err):
c = copy.deepcopy(config)
del c["postgresql"]["bin_dir"]
with patch('patroni.validator.open', mock_open(read_data='11')):
- schema(c)
- output = mock_out.getvalue()
+ errors = schema(c)
+ output = "\n".join(errors)
self.assertEqual(['postgresql.data_dir', 'raft.bind_addr', 'raft.self_addr'], parse_output(output))
def test_data_dir_is_empty_string(self, mock_out, mock_err):
@@ -236,7 +236,7 @@ def test_data_dir_is_empty_string(self, mock_out, mock_err):
c["postgresql"]["pg_hba"] = ""
c["postgresql"]["data_dir"] = ""
c["postgresql"]["bin_dir"] = ""
- schema(c)
- output = mock_out.getvalue()
+ errors = schema(c)
+ output = "\n".join(errors)
self.assertEqual(['kubernetes', 'postgresql.bin_dir', 'postgresql.data_dir',
'postgresql.pg_hba', 'raft.bind_addr', 'raft.self_addr'], parse_output(output))
| 'patroni --validate-config' exists 0 upon invalid configuration
`patroni --validate-config` exists 0 upon invalid configuration:
```
$ patroni --validate-config postgres0.yml
restapi.connect_address 127.0.0.1:8008 didn't pass validation: 'must not contain "127.0.0.1", "0.0.0.0", "*", "::1", "localhost"'
etcd.host 127.0.0.1:2379 didn't pass validation: '127.0.0.1:2379 is not reachable'
postgresql.connect_address 127.0.0.1:5432 didn't pass validation: 'must not contain "127.0.0.1", "0.0.0.0", "*", "::1", "localhost"'
$ echo $?
0
```
This is misleading since one cannot rely on exit code to detect an error; also errors are printed to stdout whereas stderr would be more appropriate.
I'd suggest to:
* exit 1 upon invalid configuration
* print errors to stderr
and I'm willing to prepare a PR for this.
**Environment**
- Patroni version: master at b8a6387236d619345c2f72f2f8e858dc7a2bd791
- PostgreSQL version: n/a
- DCS (and its version): n/a
| 2022-06-17T12:56:40Z | [] | [] |
|
zalando/patroni | 2,391 | zalando__patroni-2391 | [
"2239"
] | f92d975e7b05141fe24983029c81a648c926402b | diff --git a/patroni/postgresql/slots.py b/patroni/postgresql/slots.py
--- a/patroni/postgresql/slots.py
+++ b/patroni/postgresql/slots.py
@@ -5,6 +5,7 @@
from collections import defaultdict
from contextlib import contextmanager
+from threading import Condition, Thread
from .connection import get_connection_cursor
from .misc import format_lsn
@@ -31,10 +32,94 @@ def fsync_dir(path):
os.close(fd)
+class SlotsAdvanceThread(Thread):
+
+ def __init__(self, slots_handler):
+ super(SlotsAdvanceThread, self).__init__()
+ self.daemon = True
+ self._slots_handler = slots_handler
+
+ # _copy_slots and _failed are used to asynchronously give some feedback to the main thread
+ self._copy_slots = []
+ self._failed = False
+
+ self._scheduled = defaultdict(dict) # {'dbname1': {'slot1': 100, 'slot2': 100}, 'dbname2': {'slot3': 100}}
+ self._condition = Condition() # protect self._scheduled from concurrent access and to wakeup the run() method
+
+ self.start()
+
+ def sync_slot(self, cur, database, slot, lsn):
+ failed = copy = False
+ try:
+ cur.execute("SELECT pg_catalog.pg_replication_slot_advance(%s, %s)", (slot, format_lsn(lsn)))
+ except Exception as e:
+ logger.error("Failed to advance logical replication slot '%s': %r", slot, e)
+ failed = True
+ copy = isinstance(e, OperationalError) and e.diag.sqlstate == '58P01' # WAL file is gone
+ with self._condition:
+ if self._scheduled and failed:
+ if copy and slot not in self._copy_slots:
+ self._copy_slots.append(slot)
+ self._failed = True
+
+ new_lsn = self._scheduled.get(database, {}).get(slot, 0)
+ # remove slot from the self._scheduled structure only if it wasn't changed
+ if new_lsn == lsn and database in self._scheduled:
+ self._scheduled[database].pop(slot)
+ if not self._scheduled[database]:
+ self._scheduled.pop(database)
+
+ def sync_slots_in_database(self, database, slots):
+ with self._slots_handler.get_local_connection_cursor(dbname=database, options='-c statement_timeout=0') as cur:
+ for slot in slots:
+ with self._condition:
+ lsn = self._scheduled.get(database, {}).get(slot, 0)
+ if lsn:
+ self.sync_slot(cur, database, slot, lsn)
+
+ def sync_slots(self):
+ with self._condition:
+ databases = list(self._scheduled.keys())
+ for database in databases:
+ with self._condition:
+ slots = list(self._scheduled.get(database, {}).keys())
+ if slots:
+ try:
+ self.sync_slots_in_database(database, slots)
+ except Exception as e:
+ logger.error('Failed to advance replication slots in database %s: %r', database, e)
+
+ def run(self):
+ while True:
+ with self._condition:
+ if not self._scheduled:
+ self._condition.wait()
+
+ self.sync_slots()
+
+ def schedule(self, advance_slots):
+ with self._condition:
+ for database, values in advance_slots.items():
+ self._scheduled[database].update(values)
+ ret = (self._failed, self._copy_slots)
+ self._copy_slots = []
+ self._failed = False
+ self._condition.notify()
+
+ return ret
+
+ def on_promote(self):
+ with self._condition:
+ self._scheduled.clear()
+ self._failed = False
+ self._copy_slots = []
+
+
class SlotsHandler(object):
def __init__(self, postgresql):
self._postgresql = postgresql
+ self._advance = None
self._replication_slots = {} # already existing replication slots
self._unready_logical_slots = {}
self.schedule()
@@ -143,7 +228,7 @@ def _ensure_physical_slots(self, slots):
self._schedule_load_slots = True
@contextmanager
- def _get_local_connection_cursor(self, **kwargs):
+ def get_local_connection_cursor(self, **kwargs):
conn_kwargs = self._postgresql.config.local_connect_kwargs
conn_kwargs.update(kwargs)
with get_connection_cursor(**conn_kwargs) as cur:
@@ -162,7 +247,7 @@ def _ensure_logical_slots_primary(self, slots):
# Create new logical slots
for database, values in logical_slots.items():
- with self._get_local_connection_cursor(dbname=database) as cur:
+ with self.get_local_connection_cursor(dbname=database) as cur:
for name, value in values.items():
try:
cur.execute("SELECT pg_catalog.pg_create_logical_replication_slot(%s, %s)" +
@@ -175,6 +260,11 @@ def _ensure_logical_slots_primary(self, slots):
slots.pop(name)
self._schedule_load_slots = True
+ def schedule_advance_slots(self, slots):
+ if not self._advance:
+ self._advance = SlotsAdvanceThread(self)
+ return self._advance.schedule(slots)
+
def _ensure_logical_slots_replica(self, cluster, slots):
advance_slots = defaultdict(dict) # Group logical slots to be advanced by database name
create_slots = [] # And collect logical slots to be created on the replica
@@ -186,25 +276,16 @@ def _ensure_logical_slots_replica(self, cluster, slots):
if name in cluster.slots:
try: # Skip slots that doesn't need to be advanced
if value['confirmed_flush_lsn'] < int(cluster.slots[name]):
- advance_slots[value['database']][name] = value
+ advance_slots[value['database']][name] = int(cluster.slots[name])
except Exception as e:
logger.error('Failed to parse "%s": %r', cluster.slots[name], e)
elif name in cluster.slots: # We want to copy only slots with feedback in a DCS
create_slots.append(name)
- # Advance logical slots
- for database, values in advance_slots.items():
- with self._get_local_connection_cursor(dbname=database, options='-c statement_timeout=0') as cur:
- for name, value in values.items():
- try:
- cur.execute("SELECT pg_catalog.pg_replication_slot_advance(%s, %s)",
- (name, format_lsn(int(cluster.slots[name]))))
- except Exception as e:
- logger.error("Failed to advance logical replication slot '%s': %r", name, e)
- if isinstance(e, OperationalError) and e.diag.sqlstate == '58P01': # WAL file is gone
- create_slots.append(name)
- self._schedule_load_slots = True
- return create_slots
+ error, copy_slots = self.schedule_advance_slots(advance_slots)
+ if error:
+ self._schedule_load_slots = True
+ return create_slots + copy_slots
def sync_replication_slots(self, cluster, nofailover, replicatefrom=None, paused=False):
ret = None
@@ -331,6 +412,9 @@ def schedule(self, value=None):
self._schedule_load_slots = self._force_readiness_check = value
def on_promote(self):
+ if self._advance:
+ self._advance.on_promote()
+
if self._unready_logical_slots:
logger.warning('Logical replication slots that might be unsafe to use after promote: %s',
set(self._unready_logical_slots))
| diff --git a/tests/test_slots.py b/tests/test_slots.py
--- a/tests/test_slots.py
+++ b/tests/test_slots.py
@@ -4,17 +4,19 @@
from mock import Mock, PropertyMock, patch
+from threading import Thread
from patroni import psycopg
from patroni.dcs import Cluster, ClusterConfig, Member
from patroni.postgresql import Postgresql
-from patroni.postgresql.slots import SlotsHandler, fsync_dir
+from patroni.postgresql.slots import SlotsAdvanceThread, SlotsHandler, fsync_dir
from . import BaseTestPostgresql, psycopg_connect, MockCursor
@patch('subprocess.call', Mock(return_value=0))
@patch('patroni.psycopg.connect', psycopg_connect)
[email protected](Thread, 'start', Mock())
@patch.object(Postgresql, 'is_running', Mock(return_value=True))
class TestSlotsHandler(BaseTestPostgresql):
@@ -91,6 +93,7 @@ def test__ensure_logical_slots_replica(self):
self.assertEqual(self.s.sync_replication_slots(self.cluster, False), [])
self.s._schedule_load_slots = False
with patch.object(MockCursor, 'execute', Mock(side_effect=psycopg.OperationalError)),\
+ patch.object(SlotsAdvanceThread, 'schedule', Mock(return_value=(True, ['ls']))),\
patch.object(psycopg.OperationalError, 'diag') as mock_diag:
type(mock_diag).sqlstate = PropertyMock(return_value='58P01')
self.assertEqual(self.s.sync_replication_slots(self.cluster, False), ['ls'])
@@ -123,6 +126,7 @@ def test_check_logical_slots_readiness(self):
@patch.object(Postgresql, 'start', Mock(return_value=True))
@patch.object(Postgresql, 'is_leader', Mock(return_value=False))
def test_on_promote(self):
+ self.s.schedule_advance_slots({'foo': {'bar': 100}})
self.s.copy_logical_slots(self.cluster, ['ls'])
self.s.on_promote()
@@ -132,3 +136,18 @@ def test_on_promote(self):
@patch('os.fsync', Mock(side_effect=OSError))
def test_fsync_dir(self):
self.assertRaises(OSError, fsync_dir, 'foo')
+
+ def test_slots_advance_thread(self):
+ with patch.object(MockCursor, 'execute', Mock(side_effect=psycopg.OperationalError)),\
+ patch.object(psycopg.OperationalError, 'diag') as mock_diag:
+ type(mock_diag).sqlstate = PropertyMock(return_value='58P01')
+ self.s.schedule_advance_slots({'foo': {'bar': 100}})
+ self.s._advance.sync_slots()
+
+ with patch.object(SlotsAdvanceThread, 'sync_slots', Mock(side_effect=Exception)):
+ self.s._advance._condition.wait = Mock()
+ self.assertRaises(Exception, self.s._advance.run)
+
+ with patch.object(SlotsHandler, 'get_local_connection_cursor', Mock(side_effect=Exception)):
+ self.s.schedule_advance_slots({'foo': {'bar': 100}})
+ self.s._advance.sync_slots()
| Permanent replication slot not progressing
```
patronictl version
patronictl version 2.1.2
```
We have a number of patroni clusters which maintain multiple replication slots. Cluster has three nodes:
```
+ Cluster: cluster-1 (7072422856714349561) -------+---------+---------+----+-----------+------------------+
| Member | Host | Role | State | TL | Lag in MB | Tags |
+----------------------------------+--------------+---------+---------+----+-----------+------------------+
| node-2 | 10.1.0.3 | Replica | running | 2 | 0 | nofailover: true |
| | | | | | | nosync: true |
+----------------------------------+--------------+---------+---------+----+-----------+------------------+
| node-0 | 10.1.0.1 | Leader | running | 2 | | |
+----------------------------------+--------------+---------+---------+----+-----------+------------------+
| node-1 | 10.1.0.2 | Replica | running | 2 | 0 | |
+----------------------------------+--------------+---------+---------+----+-----------+------------------+
```
One of the standbys randomly stopped progressing at least one replication slot. You could see it attempting to do so in:
```
pid | left | datname | usename | application_name | age | wait_event
-------+----------------------------------------------------------------------------------+-------------+----------+------------------+-----------------+------------
17804 | SELECT pg_catalog.pg_replication_slot_advance('bad_slot2', '199/65915E78') | db5 | pgadmin | Patroni | 00:19:38.426721 | WALRead
```
This leads to wal files not being removed on a secondary and slowly filling the disk.
Replication slots stats:
```
slot_name | plugin | slot_type | datoid | database | temporary | active | active_pid | xmin | catalog_xmin | restart_lsn | confirmed_flush_lsn | wal_status | safe_wal_size | two_phase
-----------------------+----------+-----------+---------+-------------------+-----------+--------+------------+------+--------------+--------------+---------------------+------------+---------------+-----------
bad_slot1 | wal2json | logical | 32273 | db1 | f | f | | | 6457848 | 15C/EA222C90 | 199/65B5FBE8 | reserved | | f
good_slot1 | wal2json | logical | 4624065 | db2 | f | f | | | 6529903 | 18F/D1D5BB0 | 199/65A9B820 | reserved | | f
good_slot2 | wal2json | logical | 5265720 | db3 | f | f | | | 6529903 | 18F/D1D5BB0 | 199/6578D8D0 | reserved | | f
good_slot3 | wal2json | logical | 6664819 | db4 | f | f | | | 6529903 | 18F/D1D5BB0 | 199/657A7928 | reserved | | f
bad_slot2 | wal2json | logical | 8515756 | db5 | f | t | 17804 | | 6529654 | 18F/CFFFB08 | 18F/D4988C0 | reserved | | f
```
Logs:
```
Mar 11 00:26:34 node-1 patroni: 2022-03-11 00:26:34,128 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 00:26:49 node-1 patroni: 2022-03-11 00:26:49,528 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 00:27:07 node-1 patroni: 2022-03-11 00:27:07,713 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 00:27:07 node-1 patroni: 2022-03-11 00:27:07,714 WARNING: Loop time exceeded, rescheduling immediately.
Mar 11 00:27:42 node-1 patroni: 2022-03-11 00:27:42,944 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 00:27:42 node-1 patroni: 2022-03-11 00:27:42,946 WARNING: Loop time exceeded, rescheduling immediately.
Mar 11 00:28:46 node-1 patroni: 2022-03-11 00:28:46,002 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 00:28:46 node-1 patroni: 2022-03-11 00:28:46,004 WARNING: Loop time exceeded, rescheduling immediately.
Mar 11 00:30:50 node-1 patroni: 2022-03-11 00:30:50,153 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 00:30:50 node-1 patroni: 2022-03-11 00:30:50,154 WARNING: Loop time exceeded, rescheduling immediately.
Mar 11 00:35:20 node-1 patroni: 2022-03-11 00:35:20,798 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 00:35:20 node-1 patroni: 2022-03-11 00:35:20,799 WARNING: Loop time exceeded, rescheduling immediately.
Mar 11 00:42:35 node-1 patroni: 2022-03-11 00:42:35,619 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 00:42:35 node-1 patroni: 2022-03-11 00:42:35,620 WARNING: Loop time exceeded, rescheduling immediately.
Mar 11 00:54:12 node-1 patroni: 2022-03-11 00:54:12,748 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 00:54:12 node-1 patroni: 2022-03-11 00:54:12,749 WARNING: Loop time exceeded, rescheduling immediately.
Mar 11 01:14:27 node-1 patroni: 2022-03-11 01:14:27,781 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 01:14:27 node-1 patroni: 2022-03-11 01:14:27,782 WARNING: Loop time exceeded, rescheduling immediately.
Mar 11 01:49:01 node-1 patroni: 2022-03-11 01:49:01,098 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 01:49:01 node-1 patroni: 2022-03-11 01:49:01,100 WARNING: Loop time exceeded, rescheduling immediately.
Mar 11 03:23:20 node-1 patroni: 2022-03-11 03:23:20,014 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 03:23:20 node-1 patroni: 2022-03-11 03:23:20,016 WARNING: Loop time exceeded, rescheduling immediately.
Mar 11 15:59:16 node-1 patroni: 2022-03-11 15:59:16,008 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
Mar 11 15:59:16 node-1 patroni: 2022-03-11 15:59:16,010 WARNING: Loop time exceeded, rescheduling immediately.
Mar 12 01:49:10 node-1 patroni: 2022-03-11 15:59:16,014 INFO: Lock owner: node-0; I am node-1
Mar 12 01:49:10 node-1 patroni: 2022-03-12 01:49:10,266 ERROR: Failed to advance logical replication slot 'bad_slot2': AdminShutdown('terminating connection due to administrator command\nSSL connection has been closed unexpectedly\n',)
```
The last message is me terminating the backend from postgres, which did not alleviate the issue.
During the issue, the node was not reported in `patronictl list` at all, though patroni service was up and running. The command returned the master and the `no_failover: true` replica, which never has any slots on it (that seems like a feature):
```
+ Cluster: cluster-1 (7072422856714349561) -------+---------+---------+----+-----------+------------------+
| Member | Host | Role | State | TL | Lag in MB | Tags |
+----------------------------------+--------------+---------+---------+----+-----------+------------------+
| node-2 | 10.1.0.3 | Replica | running | 2 | 0 | nofailover: true |
| | | | | | | nosync: true |
+----------------------------------+--------------+---------+---------+----+-----------+------------------+
| node-0 | 10.1.0.1 | Leader | running | 2 | | |
+----------------------------------+--------------+---------+---------+----+-----------+------------------+
```
All the slots are configured as follows:
```yaml
slots:
bad_slot2:
database: db5
plugin: wal2json
type: logical
...
```
We recently upgraded patroni version on our clusters. We were aware that the persistent slot feature was changed in the last update, so we tested it prior to the upgrade and it worked just fine. However, within the last two weeks this happened twice and I'm wondering if there's something that could prevent patroni from progressing the slot.
The only solution that I found effective was to completely stop patroni and postgres and drop all the files from `$PGDATA/pg_replslot/` folder and restart patroni.
| What is in postgres logs?
It is also not clear whether it is completely stale or slowly moving forward.
> What is in postgres logs?
Postgres logs don't really show anything. There's no errors, no messages other than the fact that the `pg_replication_slot_advance` statement has been started. This is the extract from when I terminated the session running the advance function:
```
2022-03-12 01:49:10.265 UTC [17804] (user=pgadmin) (db=db5) (rhost=::1) (app=Patroni) [vxid:25/23577 txid:0] [SELECT] FATAL: terminating connection due to administrator command
2022-03-12 01:49:10.265 UTC [17804] (user=pgadmin) (db=db5) (rhost=::1) (app=Patroni) [vxid:25/23577 txid:0] [SELECT] STATEMENT: SELECT pg_catalog.pg_replication_slot_advance('slot_db5', '199/65915E78')
2022-03-12 01:49:10.265 UTC [17804] (user=pgadmin) (db=db5) (rhost=::1) (app=Patroni) [vxid: txid:0] [SELECT] LOG: disconnection: session time: 0:21:19.803 user=pgadmin database=db5 host=::1 port=40284
2022-03-12 01:49:10.268 UTC [26458] (user=[unknown]) (db=[unknown]) (rhost=::1) (app=[unknown]) [vxid: txid:0] [] LOG: connection received: host=::1 port=48062
2022-03-12 01:49:10.277 UTC [26458] (user=pgadmin) (db=db2) (rhost=::1) (app=[unknown]) [vxid:25/23578 txid:0] [authentication] LOG: connection authenticated: identity="pgadmin" method=md5 (/pgsql/cluster/data/pg_hba.conf:14)
2022-03-12 01:49:10.420 UTC [26458] (user=pgadmin) (db=db2) (rhost=::1) (app=Patroni) [vxid:25/23579 txid:0] [SELECT] LOG: starting logical decoding for slot "slot_db2"
2022-03-12 01:49:10.420 UTC [26458] (user=pgadmin) (db=db2) (rhost=::1) (app=Patroni) [vxid:25/23579 txid:0] [SELECT] DETAIL: Streaming transactions committing after 18F/D824C38, reading WAL from 15C/EA222C90.
2022-03-12 01:49:10.420 UTC [26458] (user=pgadmin) (db=db2) (rhost=::1) (app=Patroni) [vxid:25/23579 txid:0] [SELECT] STATEMENT: SELECT pg_catalog.pg_replication_slot_advance('slot_db2', '199/657A7928')
2022-03-12 01:49:10.558 UTC [26458] (user=pgadmin) (db=db2) (rhost=::1) (app=Patroni) [vxid:25/23579 txid:0] [SELECT] LOG: logical decoding found consistent point at 15C/EA222C90
2022-03-12 01:49:10.558 UTC [26458] (user=pgadmin) (db=db2) (rhost=::1) (app=Patroni) [vxid:25/23579 txid:0] [SELECT] DETAIL: Logical decoding will begin using saved snapshot.
2022-03-12 01:49:10.558 UTC [26458] (user=pgadmin) (db=db2) (rhost=::1) (app=Patroni) [vxid:25/23579 txid:0] [SELECT] STATEMENT: SELECT pg_catalog.pg_replication_slot_advance('slot_db2', '199/657A7928')
```
> It is also not clear whether it is completely stale or slowly moving forward.
As far as my terminal log goes, the slot was stuck at the same LSN and was not progressing.
> no messages other than the fact that the pg_replication_slot_advance statement has been started
Well, pg_replication_slot_advance() doesn't run instantly, it has to actually read and process WAL records.
Your pg_stat_activity query actually proves it, because `wait_event` is `WALRead`.
According to the pg_replication_slots view, the current lsn of this slot is `18F/CFFFB08` and it is being advanced to the `199/65915E78`. That requires to process 44GB of WAL files and of course it takes time.
It does take time, but I'd imagine it is not supposed to take more than 24 hours. Seeing how the slot wasn't progressing, I'm inclined to believe that it was stuck for whatever reason.
This is the count of wal files from our monitoring:
Replication slot on the replica is only advanced when it is moving forward on the primary. Are you sure that a client was connected to the slot and more important it was periodically updating the flush lsn?
Yes, we monitor the replication slot lag on a primary. If the LSN wasn't updated on primary, removing the slot on the secondary would not impact the slot lag and it would still be stuck, even after re-creating. To the same extent, the number of wal files on the leader would also increase at the similar rate, while in reality this happened:
The wal files on primary grew together with the wal files on secondary, but then got properly removed. The secondary got stuck in a weird state. What could have impacted this: at midnight, a logical backup kicks off, which enables the hot_standby_feedback for the replica to prevent backup termination. But I'm not sure how a replication slot progress could be affected by this.
> which enables the hot_standby_feedback for the replica
Hmm, the `hot_standby_feedback` is already enabled on replicas that are either supposed to be failover targets or doing cascading replication for failover targets.
Without the `hot_standby_feedback` logical slots are not guaranteed to work because the primary might have cleaned some dead tuples in pg_catalog that are required for logical decoding to work.
In any case, according to Patroni logs it was correctly calling `pg_replication_slot_advance()`. Hence, you have to examine postgres logs from the moment when lag started accumulating.
Small update: we have experienced this problem once more since this issue was opened. We decided to enable `hot_standby_feedback` everywhere and see if it alleviates the issue. I'll make another update in a couple of months.
Update: Enabling `hot_standby_feedback` did not help, and after having a few more issues like the one described we decided to stop using the permanent slots feature. It would be cool if we could get back to the old slot recreation logic instead of the current logic.
As for the symptoms, whatever patroni is doing during the slot progression, it seems that this is a synchronous operation, and the whole the main failover loop/healthchecks are not running while the slot advancement is in progress. This might explain why the replica is removed from the cluster node list and why we're seeing a lot of messages like these in patroni logs:
```
May 11 16:26:43 node-1 patroni: 2022-05-11 16:26:43,731 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
May 11 16:26:43 node-1 patroni: 2022-05-11 16:26:43,733 WARNING: Loop time exceeded, rescheduling immediately.
May 11 16:27:12 node-1 patroni: 2022-05-11 16:27:12,842 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
May 11 16:27:12 node-1 patroni: 2022-05-11 16:27:12,844 WARNING: Loop time exceeded, rescheduling immediately.
May 11 16:28:13 node-1 patroni: 2022-05-11 16:28:13,370 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
May 11 16:28:13 node-1 patroni: 2022-05-11 16:28:13,371 WARNING: Loop time exceeded, rescheduling immediately.
May 11 16:30:45 node-1 patroni: 2022-05-11 16:30:45,542 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
May 11 16:30:45 node-1 patroni: 2022-05-11 16:30:45,544 WARNING: Loop time exceeded, rescheduling immediately.
May 11 16:36:10 node-1 patroni: 2022-05-11 16:36:10,325 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
May 11 16:36:10 node-1 patroni: 2022-05-11 16:36:10,327 WARNING: Loop time exceeded, rescheduling immediately.
May 11 16:43:48 node-1 patroni: 2022-05-11 16:43:48,736 INFO: no action. I am (node-1), a secondary, and following a leader (node-0)
May 11 16:43:48 node-1 patroni: 2022-05-11 16:43:48,737 WARNING: Loop time exceeded, rescheduling immediately.
```
> Update: Enabling hot_standby_feedback did not help
Well, according to logs that you post here slot is certainly moving forward. In the opposite case Patroni would log an error or an exception.
> t would be cool if we could get back to the old slot recreation logic instead of the current logic.
It would be not. In case if you really want it is possible to mimic the old behavior by using `ignore_slots` and `callbacks`.
> whatever patroni is doing during the slot progression, it seems that this is a synchronous operation, and the whole the main failover loop/healthchecks are not running while the slot advancement is in progress. This might explain why the replica is removed from the cluster node list and why we're seeing a lot of messages like these in patroni logs:
It is indeed calling `pg_advance_replication_slot()` from the main thread. We certainly can improve it by starting a dedicated thread for that. But, what I find really bad is that the replica can't keep up with the pace of the primary in your case. I.e., if the logical slot in the primary moved forward X bytes in 10 seconds it shouldn't be taking much longer to do the same on the replica or the replica isn't running on a hardware that is comparable with the primary. | 2022-08-23T09:07:03Z | [] | [] |
zalando/patroni | 2,398 | zalando__patroni-2398 | [
"2397"
] | 4a854a71c087a315e3d8697fa824e9714e6db7b2 | diff --git a/patroni/validator.py b/patroni/validator.py
--- a/patroni/validator.py
+++ b/patroni/validator.py
@@ -37,6 +37,10 @@ def validate_host_port(host_port, listen=False, multiple_hosts=False):
hosts = hosts.split(",")
else:
hosts = [hosts]
+ if "*" in hosts:
+ if len(hosts) != 1:
+ raise ConfigParseError("expecting '*' alone")
+ hosts = [p[-1][0] for p in socket.getaddrinfo(None, port, 0, socket.SOCK_STREAM, 0, socket.AI_PASSIVE)]
for host in hosts:
proto = socket.getaddrinfo(host, "", 0, socket.SOCK_STREAM, 0, socket.AI_PASSIVE)
s = socket.socket(proto[0][0], socket.SOCK_STREAM)
| diff --git a/tests/test_validator.py b/tests/test_validator.py
--- a/tests/test_validator.py
+++ b/tests/test_validator.py
@@ -156,6 +156,7 @@ def test_bin_dir_is_file(self, mock_out, mock_err):
files.append(config["postgresql"]["bin_dir"])
c = copy.deepcopy(config)
c["restapi"]["connect_address"] = 'False:blabla'
+ c["postgresql"]["listen"] = '*:543'
c["etcd"]["hosts"] = ["127.0.0.1:2379", "1244.0.0.1:2379", "127.0.0.1:invalidport"]
c["kubernetes"]["pod_ip"] = "127.0.0.1111"
errors = schema(c)
@@ -208,11 +209,12 @@ def test_pg_version_missmatch(self, mock_out, mock_err):
files.append(os.path.join(config["postgresql"]["data_dir"], "PG_VERSION"))
c = copy.deepcopy(config)
c["etcd"]["hosts"] = []
+ c["postgresql"]["listen"] = '127.0.0.2,*:543'
del c["postgresql"]["bin_dir"]
with patch('patroni.validator.open', mock_open(read_data='11')):
errors = schema(c)
output = "\n".join(errors)
- self.assertEqual(['etcd.hosts', 'postgresql.data_dir',
+ self.assertEqual(['etcd.hosts', 'postgresql.data_dir', 'postgresql.listen',
'raft.bind_addr', 'raft.self_addr'], parse_output(output))
@patch('subprocess.check_output', Mock(return_value=b"postgres (PostgreSQL) 12.1"))
| Accept *:port as a valid entry for postgresql.listen in patroni --validate-config
**Describe the bug**
If `postgresql.listen` is set to `*:port`, `patroni --validate-config` complains.
I understand that security wise choosing the interface explicitly is better and that patroni's documentation
doesn't state that it's possible but it's a valid (and wide spread) postgresql.conf value.
If you're ok with allowing this, we can do the PR.
**To Reproduce**
1 ) configure `postgresql.listen` to `*:5432` in the yaml
2 ) run `patroni --validate-config` on the config file
**Expected behavior**
No errors.
**Screenshots**
```
postgresql.listen *:5432 didn't pass validation: gaierror(-2, 'Name or service not known')
```
**Environment**
- Patroni version: 2.1.4
- PostgreSQL version: 14.5
- DCS (and its version): 3.4.20
**Patroni configuration file**
```
scope: pgdemo
name: pg1
bootstrap:
dcs:
postgresql:
parameters:
cluster_name: pg1
lc_messages: C
lc_monetary: C
lc_numeric: C
lc_time: C
listen_addresses: '*'
log_destination: stderr
logging_collector: true
port: 5432
unix_socket_directories: /run/user/1000/pglift/postgresql
initdb:
- locale: C
- encoding: UTF8
pg_hba:
- local all postgres trust
- local all all trust
- host all all 127.0.0.1/32 trust
- host all all ::1/128 trust
- local replication replication trust
- host replication replication 127.0.0.1/32 trust
- host replication replication ::1/128 trust
pg_ident:
- '# MAPNAME SYSTEM-USERNAME PG-USERNAME'
restapi:
connect_address: 127.0.1.1:8008
listen: 127.0.1.1:8008
etcd3:
host: 10.20.60.99:2379
postgresql:
authentication:
superuser:
username: postgres
replication:
username: replication
rewind:
username: postgres
connect_address: 127.0.1.1:5432
data_dir: /home/vagrant/.local/share/pglift/srv/pgsql/14/pg1/data
bin_dir: /usr/pgsql-14/bin
listen: 127.0.1.1:5432
use_unix_socket: true
use_unix_socket_repl: true
pgpass: /home/vagrant/.pgpass
parameters:
cluster_name: pg1
lc_messages: C
lc_monetary: C
lc_numeric: C
lc_time: C
listen_addresses: '*'
log_destination: stderr
logging_collector: true
port: 5432
unix_socket_directories: /run/user/1000/pglift/postgresql
pg_hba:
- local all postgres trust
- local all all trust
- host all all 127.0.0.1/32 trust
- host all all ::1/128 trust
- local replication replication trust
- host replication replication 127.0.0.1/32 trust
- host replication replication ::1/128 trust
pg_ident:
- '# MAPNAME SYSTEM-USERNAME PG-USERNAME'
```
**patronictl show-config**
```
(.venv) [vagrant@pat1 pglift]$ patronictl show-config
postgresql:
parameters:
cluster_name: pg1
lc_messages: C
lc_monetary: C
lc_numeric: C
lc_time: C
listen_addresses: '*'
log_destination: stderr
logging_collector: true
port: 5432
unix_socket_directories: /run/user/1000/pglift/postgresql
```
**Have you checked Patroni logs?**
N/A
**Have you checked PostgreSQL logs?**
N/A
**Have you tried to use GitHub issue search?**
I didn't find one.
**Additional context**
N/A
| 2022-08-25T09:34:33Z | [] | [] |
|
zalando/patroni | 2,471 | zalando__patroni-2471 | [
"1421"
] | 838653325a2bfa2080d3ba11fced1bd1921ae4bb | diff --git a/patroni/postgresql/__init__.py b/patroni/postgresql/__init__.py
--- a/patroni/postgresql/__init__.py
+++ b/patroni/postgresql/__init__.py
@@ -1053,13 +1053,15 @@ def pg_tblspc_realpaths(self):
def move_data_directory(self):
if os.path.isdir(self._data_dir) and not self.is_running():
try:
- postfix = time.strftime('%Y-%m-%d-%H-%M-%S')
+ postfix = 'failed'
# let's see if the wal directory is a symlink, in this case we
# should move the target
for (source, pg_wal_realpath) in self.pg_wal_realpath().items():
logger.info('renaming WAL directory and updating symlink: %s', pg_wal_realpath)
- new_name = '{0}_{1}'.format(pg_wal_realpath, postfix)
+ new_name = '{0}.{1}'.format(pg_wal_realpath, postfix)
+ if os.path.exists(new_name):
+ shutil.rmtree(new_name)
os.rename(pg_wal_realpath, new_name)
os.unlink(source)
os.symlink(new_name, source)
@@ -1067,13 +1069,17 @@ def move_data_directory(self):
# Move user defined tablespace directory
for (source, pg_tsp_rpath) in self.pg_tblspc_realpaths().items():
logger.info('renaming user defined tablespace directory and updating symlink: %s', pg_tsp_rpath)
- new_name = '{0}_{1}'.format(pg_tsp_rpath, postfix)
+ new_name = '{0}.{1}'.format(pg_tsp_rpath, postfix)
+ if os.path.exists(new_name):
+ shutil.rmtree(new_name)
os.rename(pg_tsp_rpath, new_name)
os.unlink(source)
os.symlink(new_name, source)
- new_name = '{0}_{1}'.format(self._data_dir, postfix)
+ new_name = '{0}.{1}'.format(self._data_dir, postfix)
logger.info('renaming data directory to %s', new_name)
+ if os.path.exists(new_name):
+ shutil.rmtree(new_name)
os.rename(self._data_dir, new_name)
except OSError:
logger.exception("Could not rename data directory %s", self._data_dir)
| diff --git a/tests/test_postgresql.py b/tests/test_postgresql.py
--- a/tests/test_postgresql.py
+++ b/tests/test_postgresql.py
@@ -438,6 +438,8 @@ def test_is_leader_exception(self):
self.assertTrue(self.p.stop())
@patch('os.rename', Mock())
+ @patch('os.path.exists', Mock(return_value=True))
+ @patch('shutil.rmtree', Mock())
@patch('os.path.isdir', Mock(return_value=True))
@patch('os.unlink', Mock())
@patch('os.symlink', Mock())
| Standby failed bootstrap fills up disk with timestamped directories
Hi,
We've got a standby cluster where we're clearly doing something wrong in our bootstrap script (a wal-g hack of your wal-e one), but on failure the postgres/current directory is renamed with a timestamp, and the process starts again. This soon fills up a disk.
Is there any reason not to just rename once to `current.failed` as if this is a repeated problem then only the last failure is really relevant?
Thanks.
| Maybe you are right. It was just easier to implement back than.
If you want to change it - please open a PR. | 2022-12-01T14:35:49Z | [] | [] |
zalando/patroni | 2,659 | zalando__patroni-2659 | [
"2495"
] | 06db2966122cc3bf0291169b3cd2a2e93a522445 | diff --git a/patroni/config.py b/patroni/config.py
--- a/patroni/config.py
+++ b/patroni/config.py
@@ -475,7 +475,8 @@ def _get_auth(name: str, params: Optional[Collection[str]] = None) -> Dict[str,
'REGISTER_SERVICE', 'SERVICE_CHECK_INTERVAL', 'SERVICE_CHECK_TLS_SERVER_NAME',
'SERVICE_TAGS', 'NAMESPACE', 'CONTEXT', 'USE_ENDPOINTS', 'SCOPE_LABEL', 'ROLE_LABEL',
'POD_IP', 'PORTS', 'LABELS', 'BYPASS_API_SERVICE', 'RETRIABLE_HTTP_CODES', 'KEY_PASSWORD',
- 'USE_SSL', 'SET_ACLS', 'GROUP', 'DATABASE') and name:
+ 'USE_SSL', 'SET_ACLS', 'GROUP', 'DATABASE', 'LEADER_LABEL_VALUE', 'FOLLOWER_LABEL_VALUE',
+ 'STANDBY_LEADER_LABEL_VALUE', 'TMP_ROLE_LABEL') and name:
value = os.environ.pop(param)
if name == 'CITUS':
if suffix == 'GROUP':
diff --git a/patroni/dcs/kubernetes.py b/patroni/dcs/kubernetes.py
--- a/patroni/dcs/kubernetes.py
+++ b/patroni/dcs/kubernetes.py
@@ -752,6 +752,10 @@ def __init__(self, config: Dict[str, Any]) -> None:
self._label_selector = ','.join('{0}={1}'.format(k, v) for k, v in self._labels.items())
self._namespace = config.get('namespace') or 'default'
self._role_label = config.get('role_label', 'role')
+ self._leader_label_value = config.get('leader_label_value', 'master')
+ self._follower_label_value = config.get('follower_label_value', 'replica')
+ self._standby_leader_label_value = config.get('standby_leader_label_value', 'standby-leader')
+ self._tmp_role_label = config.get('tmp_role_label')
self._ca_certs = os.environ.get('PATRONI_KUBERNETES_CACERT', config.get('cacert')) or SERVICE_CERT_FILENAME
super(Kubernetes, self).__init__({**config, 'namespace': ''})
if self._citus_group:
@@ -1263,19 +1267,30 @@ def set_config_value(self, value: str, version: Optional[str] = None) -> bool:
def touch_member(self, data: Dict[str, Any]) -> bool:
cluster = self.cluster
if cluster and cluster.leader and cluster.leader.name == self._name:
- role = 'master'
+ role = self._leader_label_value
+ tmp_role = 'master'
elif data['state'] == 'running' and data['role'] not in ('master', 'primary'):
- role = data['role']
+ role = {
+ 'replica': self._follower_label_value,
+ 'standby-leader': self._standby_leader_label_value,
+ }.get(data['role'], data['role'])
+ tmp_role = data['role']
else:
role = None
+ tmp_role = None
+
+ role_labels = {self._role_label: role}
+ if self._tmp_role_label:
+ role_labels[self._tmp_role_label] = tmp_role
member = cluster and cluster.get_member(self._name, fallback_to_leader=False)
pod_labels = member and member.data.pop('pod_labels', None)
ret = member and pod_labels is not None\
- and pod_labels.get(self._role_label) == role and deep_compare(data, member.data)
+ and all(pod_labels.get(k) == v for k, v in role_labels.items())\
+ and deep_compare(data, member.data)
if not ret:
- metadata = {'namespace': self._namespace, 'name': self._name, 'labels': {self._role_label: role},
+ metadata = {'namespace': self._namespace, 'name': self._name, 'labels': role_labels,
'annotations': {'status': json.dumps(data, separators=(',', ':'))}}
body = k8s_client.V1Pod(metadata=k8s_client.V1ObjectMeta(**metadata))
ret = self._api.patch_namespaced_pod(self._name, self._namespace, body)
diff --git a/patroni/validator.py b/patroni/validator.py
--- a/patroni/validator.py
+++ b/patroni/validator.py
@@ -995,6 +995,10 @@ def validate_watchdog_mode(value: Any) -> None:
Optional("namespace"): str,
Optional("scope_label"): str,
Optional("role_label"): str,
+ Optional("leader_label_value"): str,
+ Optional("follower_label_value"): str,
+ Optional("standby_leader_label_value"): str,
+ Optional("tmp_role_label"): str,
Optional("use_endpoints"): bool,
Optional("pod_ip"): Or(is_ipv4_address, is_ipv6_address),
Optional("ports"): [{"name": str, "port": int}],
| diff --git a/tests/test_kubernetes.py b/tests/test_kubernetes.py
--- a/tests/test_kubernetes.py
+++ b/tests/test_kubernetes.py
@@ -298,6 +298,28 @@ def test_touch_member(self, mock_patch_namespaced_pod):
self.k.touch_member({'state': 'running', 'role': 'replica'})
self.k.touch_member({'state': 'stopped', 'role': 'primary'})
+ self.k._role_label = 'isMaster'
+ self.k._leader_label_value = 'true'
+ self.k._follower_label_value = 'false'
+ self.k._standby_leader_label_value = 'false'
+ self.k._tmp_role_label = 'tmp_role'
+
+ self.k.touch_member({'state': 'running', 'role': 'replica'})
+ mock_patch_namespaced_pod.assert_called()
+ self.assertEqual(mock_patch_namespaced_pod.call_args.args[2].metadata.labels['isMaster'], 'false')
+ self.assertEqual(mock_patch_namespaced_pod.call_args.args[2].metadata.labels['tmp_role'], 'replica')
+
+ self.k.touch_member({'state': 'running', 'role': 'standby-leader'})
+ mock_patch_namespaced_pod.assert_called()
+ self.assertEqual(mock_patch_namespaced_pod.call_args.args[2].metadata.labels['isMaster'], 'false')
+ self.assertEqual(mock_patch_namespaced_pod.call_args.args[2].metadata.labels['tmp_role'], 'standby-leader')
+
+ self.k._name = 'p-0'
+ self.k.touch_member({'role': 'primary'})
+ mock_patch_namespaced_pod.assert_called()
+ self.assertEqual(mock_patch_namespaced_pod.call_args.args[2].metadata.labels['isMaster'], 'true')
+ self.assertEqual(mock_patch_namespaced_pod.call_args.args[2].metadata.labels['tmp_role'], 'master')
+
def test_initialize(self):
self.k.initialize()
| Feature request: make value of replication role labels configurable
**Describe the feature**
Currently, on K8s the value of the labels that identify the replication role of each patroni/postgresql Pod is hardcoded to be "master" for the leader and "replica" for the followers.
I would like to make those values configurable.
That allows us to stop using the non-inclusive "master" term and replace it with something like "leader" or primary.
I would also like to opt out from using "replica". The reason is that I'm running patroni/spilo in a context where "replica" is already widely used to describe something different than postgresql's replication replicas. So currently there's a name overloading that causes confusion.
If there's consensus and someone can work on it it'd be great. I might also do this, but I'm not a python expert (at all) and have never touched patroni's codebase so I'd need guidance.
| Getting rif from non-inclusive terms is in our radar.
The thing is that the problem is much deeper than just labels.
There are plenty of internal checks on the "master" and we can't rename it without doing an intermediate release (compatible between old and new terms).
Even with labels it is much harder than you probably anticipate. If Patroni is managing the endpoint on it's own - everything will be fine. If Patroni is using configmaps and there is a Service with label selector, then they could not be migrated to the new scheme without a downtime, because set-based requirements aren't supported for Services: https://kubernetes.io/docs/concepts/overview/working-with-objects/labels/#resources-that-support-set-based-requirements
@CyberDem0n thank you for your reply. I now have a better understanding of the problem and its caveats.
Strictly speaking my change request is not for Patroni to replace the non-inclusive terms. It's just to make the values of the replication role label for both master and replica pods configurable. This could be implemented in a backward-compatible way with a change that:
1. adds two env variables/config parameters that determine the value of the replication role label for leader and followers, respecitvely (e.g. `PATRONI_KUBERNETES_LEADER_LABEL_VALUE` and `PATRONI_KUBERNETES_FOLLOWER_LABEL_VALUE`
2. keeps the defaults for the two aforementioned env vars/config parameters to the legacy values (`master` and `replica`); this is what ensures backward compatibility
3. makes patroni's code use the value of the aforementioned config parameters rather than the hardcoded current values.
For my use case this would be already enough.
The change I described could be the intermediate non-breaking release you mentioned. Its release notes could advertise that in a few releases the defaults would be changed to the inclusive terms, so users could get ready.
> If Patroni is using configmaps and there is a Service with label selector, then they could not be migrated to the new scheme without a downtime, because set-based requirements aren't supported for Services
A couple of random thoughts on this (not sure whether they make sense):
1. No matter how this change is done, it would involve updating patroni's version. It would mean that all the pg pods would be restarted (likely 1 at a time if they run a statefulset). Given this, isn't there some downtime anyway, from when the old master goes down to when a new one is elected? I suspect this downtime would be comparable in duration to the one caused by updating the primary pod label and the service selector non-atomically (granted, this is an unproven claim though).
2. I'm thinking about a fairly convoluted way to update both the pod label and the service selector to minimize downtime:
a. t0: add to the leader pod a temporary master label with a different key while also keeping the old one (i.e. the pod would have both labels at this point in time, `role: master`and `tmp-role: leader`
b. t1: update the service selector to select the leader only via `tmp-role: leader`
c. t2: update the leader pod by updating the usual master label's value to the new inclusive value (after this step the leader has labels `role: leader` and `tmp-role: leader`
d. t3: update the service selector to select only on `role: leader`
e. t4: update the leader pod by removing the temporary label `tmp-role`.
It might take too long but there's also the option to wait for K8s to add set-based selectors to services, a K8s enhancement proposal should be filed at some point: https://github.com/kubernetes/kubernetes/issues/48528#issuecomment-1256458873
> isn't there some downtime anyway, from when the old master goes down to when a new one is elected?
I wouldn't call a switchover a "real" downtime. Typically it takes just a couple of seconds. If someone screwed up with the label selector it is a toally different story. Applications will not be able to connect for a much longer time, until someone fixes the service.
> I'm thinking about a fairly convoluted way to update both the pod label and the service selector to minimize downtime
Yes, I was thinking exactly about the same process.
> It might take too long but there's also the option to wait for K8s to add set-based selectors to services, a K8s enhancement proposal should be filed at some point: https://github.com/kubernetes/kubernetes/issues/48528#issuecomment-1256458873
Taking into account that the issue was open more than 5 years ago...
> Strictly speaking my change request is not for Patroni to replace the non-inclusive terms. It's just to make the values of the replication role label for both master and replica pods configurable. This could be implemented in a backward-compatible way with a change that:
Yes, it will make life easier for people not wanting to go through the complex-multi-step migration process. Instead they could just opt in using old terms.
> I might also do this, but I'm not a python expert (at all) and have never touched patroni's codebase so I'd need guidance.
It shoudn't be hard. First, there is a short doc describing how to setup dev environment and run test: https://patroni.readthedocs.io/en/latest/CONTRIBUTING.html
After that you'll have to touch only two files: [config.py](https://github.com/zalando/patroni/blob/e5d750e9b8f7fc6a4172932056eddeb3fc892e7f/patroni/config.py#L351-L357) and [kubernetes.py](https://github.com/zalando/patroni/blob/master/patroni/dcs/kubernetes.py)
I will begin implementing the proposed change 2 weeks from now (unless you want to go ahead before that).
Really sorry for the long delay and silence, I've been busier than anticipated with other work. I'm starting on this now.
@matteoolivi is there any progress?
Maybe you need some help?
I had started to look into this, then got pulled into a different project and completely forgot to provide updates on this.
Really really sorry for the wast of time and lack of professionalism.
Unfortunately I won't have time to do this for a long time - whoever can take over this should do that.
@CyberDem0n I can help with this, It just so happens that my colleague also asked for this feature this week
Dear Patroni Team. Polite ping: any progress here/ETA? | 2023-04-28T07:24:41Z | [] | [] |
zalando/patroni | 2,724 | zalando__patroni-2724 | [
"1804"
] | 1c36112b44b62bb668f0f23f8ad1ff9b1cff5561 | diff --git a/features/environment.py b/features/environment.py
--- a/features/environment.py
+++ b/features/environment.py
@@ -52,10 +52,9 @@ def start(self, max_wait_limit=5):
self._log = open(os.path.join(self._output_dir, self._name + '.log'), 'a')
self._handle = self._start()
- assert self._has_started(), "Process {0} is not running after being started".format(self._name)
-
max_wait_limit *= self._context.timeout_multiplier
for _ in range(max_wait_limit):
+ assert self._has_started(), "Process {0} is not running after being started".format(self._name)
if self._is_accessible():
break
time.sleep(1)
@@ -344,6 +343,13 @@ def backup(self, dest=os.path.join('data', 'basebackup')):
'--datadir=' + os.path.join(self._work_directory, dest),
'--dbname=' + self.backup_source])
+ def read_patroni_log(self, level):
+ try:
+ with open(str(os.path.join(self._output_dir or '', self._name + ".log"))) as f:
+ return [line for line in f.readlines() if line[24:24 + len(level)] == level]
+ except IOError:
+ return []
+
class ProcessHang(object):
@@ -827,7 +833,7 @@ def start(self, name, max_wait_limit=40, custom_config=None):
def __getattr__(self, func):
if func not in ['stop', 'query', 'write_label', 'read_label', 'check_role_has_changed_to',
- 'add_tag_to_config', 'get_watchdog', 'patroni_hang', 'backup']:
+ 'add_tag_to_config', 'get_watchdog', 'patroni_hang', 'backup', 'read_patroni_log']:
raise AttributeError("PatroniPoolController instance has no attribute '{0}'".format(func))
def wrapper(name, *args, **kwargs):
diff --git a/features/steps/basic_replication.py b/features/steps/basic_replication.py
--- a/features/steps/basic_replication.py
+++ b/features/steps/basic_replication.py
@@ -9,6 +9,22 @@ def start_patroni(context, name):
return context.pctl.start(name)
+@step('I start duplicate {name:w} on port {port:d}')
+def start_duplicate_patroni(context, name, port):
+ config = {
+ "name": name,
+ "restapi": {
+ "listen": "127.0.0.1:{0}".format(port)
+ }
+ }
+ try:
+ context.pctl.start('dup-' + name, custom_config=config)
+ assert False, "Process was expected to fail"
+ except AssertionError as e:
+ assert 'is not running after being started' in str(e),\
+ "No error was raised by duplicate start of {0} ".format(name)
+
+
@step('I shut down {name:w}')
def stop_patroni(context, name):
return context.pctl.stop(name, timeout=60)
@@ -90,3 +106,10 @@ def replication_works(context, primary, replica, time_limit):
When I add the table test_{0} to {1}
Then table test_{0} is present on {2} after {3} seconds
""".format(int(time()), primary, replica, time_limit))
+
+
+@then('there is a "{message}" {level:w} in the {node} patroni log')
+def check_patroni_log(context, message, level, node):
+ messsages_of_level = context.pctl.read_patroni_log(node, level)
+ assert any(message in line for line in messsages_of_level),\
+ "There was no {0} {1} in the {2} patroni log".format(message, level, node)
diff --git a/patroni/__main__.py b/patroni/__main__.py
--- a/patroni/__main__.py
+++ b/patroni/__main__.py
@@ -30,12 +30,15 @@ def __init__(self, config: 'Config') -> None:
self.version = __version__
self.dcs = get_dcs(self.config)
+ self.request = PatroniRequest(self.config, True)
+
+ self.ensure_unique_name()
+
self.watchdog = Watchdog(self.config)
self.load_dynamic_configuration()
self.postgresql = Postgresql(self.config['postgresql'])
self.api = RestApiServer(self, self.config['restapi'])
- self.request = PatroniRequest(self.config, True)
self.ha = Ha(self)
self.tags = self.get_tags()
@@ -60,6 +63,23 @@ def load_dynamic_configuration(self) -> None:
logger.warning('Can not get cluster from dcs')
time.sleep(5)
+ def ensure_unique_name(self) -> None:
+ """A helper method to prevent splitbrain from operator naming error."""
+ from patroni.dcs import Member
+
+ cluster = self.dcs.get_cluster()
+ if not cluster:
+ return
+ member = cluster.get_member(self.config['name'], False)
+ if not isinstance(member, Member):
+ return
+ try:
+ _ = self.request(member, endpoint="/liveness")
+ logger.fatal("Can't start; there is already a node named '%s' running", self.config['name'])
+ sys.exit(1)
+ except Exception:
+ return
+
def get_tags(self) -> Dict[str, Any]:
return {tag: value for tag, value in self.config.get('tags', {}).items()
if tag not in ('clonefrom', 'nofailover', 'noloadbalance', 'nosync') or value}
| diff --git a/tests/test_patroni.py b/tests/test_patroni.py
--- a/tests/test_patroni.py
+++ b/tests/test_patroni.py
@@ -10,6 +10,7 @@
from mock import Mock, PropertyMock, patch
from patroni.api import RestApiServer
from patroni.async_executor import AsyncExecutor
+from patroni.dcs import Cluster, Member
from patroni.dcs.etcd import AbstractEtcdClientWithFailover
from patroni.exceptions import DCSError
from patroni.postgresql import Postgresql
@@ -202,3 +203,36 @@ def test_check_psycopg(self):
self.assertRaises(SystemExit, check_psycopg)
with patch('builtins.__import__', mock_import):
self.assertRaises(SystemExit, check_psycopg)
+
+ def test_ensure_unique_name(self):
+ # None/empty cluster implies unique name
+ with patch('patroni.dcs.AbstractDCS.get_cluster', Mock(return_value=None)):
+ self.assertIsNone(self.p.ensure_unique_name())
+ empty_cluster = Cluster.empty()
+ with patch('patroni.dcs.AbstractDCS.get_cluster', Mock(return_value=empty_cluster)):
+ self.assertIsNone(self.p.ensure_unique_name())
+ without_members = empty_cluster._asdict()
+ del without_members['members']
+
+ # Cluster with members with different names implies unique name
+ okay_cluster = Cluster(
+ members=[Member(version=1, name="distinct", session=1, data={})],
+ **without_members
+ )
+ with patch('patroni.dcs.AbstractDCS.get_cluster', Mock(return_value=okay_cluster)):
+ self.assertIsNone(self.p.ensure_unique_name())
+
+ # Cluster with a member with the same name that is running
+ bad_cluster = Cluster(
+ members=[Member(version=1, name="postgresql0", session=1, data={
+ "api_url": "https://127.0.0.1:8008",
+ })],
+ **without_members
+ )
+ with patch('patroni.dcs.AbstractDCS.get_cluster', Mock(return_value=bad_cluster)):
+ # If the api of the running node cannot be reached, this implies unique name
+ with patch.object(self.p, 'request', Mock(side_effect=ConnectionError)):
+ self.assertIsNone(self.p.ensure_unique_name())
+ # Only if the api of the running node is reachable do we throw an error
+ with patch.object(self.p, 'request', Mock()):
+ self.assertRaises(SystemExit, self.p.ensure_unique_name)
| Split-brain possible on simple configuration mistake
Currently Patroni will happily launch a 2nd primary if the "member" name is by accident a duplicate of the current leader.
Sure it's an operator error...but I think would be relatively easy to avoid it by first checking the current leader's (if exists) role directly over the Patroni API.
This situation won't happen on new setups as there's seems to be a check against that (although the message "released leader key voluntarily as data dir empty and currently leader" hints that the new duplicate node still grabbed the key), but rather with a "takeover" of some old Postgres clusters where the PGDATA exists.
**To Reproduce**
1. Start the 1st node as leader.
2. Start a 2nd node that will be bootstrapped as replica.
3. Change the replica config so that the member name (`name`) matches the leader's name.
4. Restart Patroni on 2nd node
| I was able to reproduce this on the current version. I agree that it's operator error, but seems logical to check that a new node's name is unique when adding to a cluster. Am starting on a simple fix now.
So far, I've been working on a fix that involves a pre-check during the initialization of a new-node to make sure there aren't any existing nodes in the cluster with the same name. However, it struck me that the root cause of the issue seems to be that in the DCS, nodes are simply storing their name, which causes two nodes to have the view of being the leader. Another solution is to make it so that instead of writing name to the DCS, there's some way of assigning UUIDs to nodes automatically, so two nodes can have the same name and be fine.
Was curious what people thought was the better solution here. Personally, I'm inclined to stick with the simple pre-check when adding a node to an existing cluster. I think the UUID is a bit of an overkill, given that patroni _probably_ isn't used for more than a few tens of nodes, max. I'm also not sure if this is an operator error we want to correct for, vs just error out + notify that the configuration is incorrect. Also UUIDs in general seem like more headaches down the road.
_But_, I can see how a UUID approach might get more at the "core" of the issue. Open to input! | 2023-06-26T20:37:18Z | [] | [] |
aws-cloudformation/cfn-lint | 43 | aws-cloudformation__cfn-lint-43 | [
"41"
] | 7b2875a27ffec75d0fa4f30af6a7fa6d779938aa | diff --git a/src/cfnlint/__init__.py b/src/cfnlint/__init__.py
--- a/src/cfnlint/__init__.py
+++ b/src/cfnlint/__init__.py
@@ -576,22 +576,34 @@ def get_condition_values(self, template, path=[]):
result = {}
result['Path'] = path[:] + [index + 1]
if not isinstance(item, (dict, list)):
+ # Just straight values and pass them through
result['Value'] = item
matches.append(result)
elif len(item) == 1:
- for sub_key, sub_value in item.items():
- if sub_key in cfnlint.helpers.CONDITION_FUNCTIONS:
- results = self.get_condition_values(sub_value, result['Path'] + [sub_key])
- if isinstance(results, list):
- matches.extend(results)
- elif sub_key == 'Ref':
- if sub_value != 'AWS::NoValue':
- result['Value'] = sub_value
- result['Path'] += ['Ref']
+ # Checking for conditions inside of conditions
+ if isinstance(item, dict):
+ for sub_key, sub_value in item.items():
+ if sub_key in cfnlint.helpers.CONDITION_FUNCTIONS:
+ results = self.get_condition_values(sub_value, result['Path'] + [sub_key])
+ if isinstance(results, list):
+ matches.extend(results)
+ elif sub_key == 'Ref':
+ if sub_value != 'AWS::NoValue':
+ result['Value'] = sub_value
+ result['Path'] += ['Ref']
+ matches.append(result)
+ else:
+ # Return entire Item
+ result['Value'] = item
matches.append(result)
- else:
- result['Value'] = sub_value
- matches.append(result)
+ else:
+ # Return entire Item
+ result['Value'] = item
+ matches.append(result)
+ else:
+ # Length longer than 1 means a list or object that should be fully returned
+ result['Value'] = item
+ matches.append(result)
return matches
| diff --git a/test/module/test_cfn_json.py b/test/module/test_cfn_json.py
--- a/test/module/test_cfn_json.py
+++ b/test/module/test_cfn_json.py
@@ -49,7 +49,7 @@ def setUp(self):
},
"vpc": {
"filename": 'templates/quickstart/vpc.json',
- "failures": 1
+ "failures": 0
}
}
diff --git a/test/module/test_template.py b/test/module/test_template.py
--- a/test/module/test_template.py
+++ b/test/module/test_template.py
@@ -66,3 +66,65 @@ def test_get_valid_refs(self):
""" Get Valid REFs"""
refs = self.template.get_valid_refs()
assert len(refs) == 20
+
+ def test_conditions_return_object_success(self):
+ """Test condition object response and nested IFs"""
+ template = [
+ 'isProd',
+ {
+ 'Key': 'Environment1',
+ 'Value': 'Prod'
+ },
+ {
+ 'Fn::If': [
+ 'isDev',
+ {
+ 'Key': 'Environment2',
+ 'Value': 'Dev'
+ },
+ {
+ "Ref": "AWS::NoValue"
+ }
+ ]
+ }
+ ]
+
+ results = self.template.get_condition_values(template, [])
+ self.assertEqual(results, [
+ {'Path': [1], 'Value': {'Value': 'Prod', 'Key': 'Environment1'}},
+ {'Path': [2, 'Fn::If', 1], 'Value': {'Value': 'Dev', 'Key': 'Environment2'}}
+ ])
+
+ def test_conditions_return_list_success(self):
+ """Test condition list response"""
+ template = [
+ 'PrimaryRegion',
+ [
+ 'EN'
+ ],
+ [
+ 'BE',
+ 'LU',
+ 'NL'
+ ]
+ ]
+
+ results = self.template.get_condition_values(template, [])
+ self.assertEqual(results, [
+ {'Value': ['EN'], 'Path': [1]}, {'Value': ['BE', 'LU', 'NL'], 'Path': [2]}
+ ])
+
+ def test_conditions_return_string_success(self):
+ """Test condition object response and nested IFs"""
+ template = [
+ 'isProd',
+ {
+ 'Ref': 'Sample'
+ },
+ 'String'
+ ]
+
+ results = self.template.get_condition_values(template, [])
+ self.assertEqual(results, [
+ {'Path': [1, 'Ref'], 'Value': 'Sample'}, {'Path': [2], 'Value': 'String'}
+ ])
diff --git a/test/templates/bad/conditions.yaml b/test/templates/bad/conditions.yaml
--- a/test/templates/bad/conditions.yaml
+++ b/test/templates/bad/conditions.yaml
@@ -34,12 +34,15 @@ Parameters:
- prod
- test
ConstraintDescription: must specify prod or test.
+ EnableGeoBlocking:
+ Type: String
Conditions:
CreateProdResources: !Equals [ !Ref EnvType, prod ]
BadCondition: String
TooManyConditions:
Fn::Equals: [ !Ref EnvType, prod ]
Fn::Not: !Equals [ !Ref EnvType, prod ]
+ EnableGeoBlocking: !Equals [ !Ref EnableGeoBlocking, "true" ]
Resources:
EC2Instance:
Type: "AWS::EC2::Instance"
@@ -74,6 +77,27 @@ Resources:
Size: 100
AvailabilityZone:
!GetAtt EC2Instance.AvailabilityZone
+ CloudFrontDistribution:
+ Type: "AWS::CloudFront::Distribution"
+ Properties:
+ DistributionConfig:
+ Enabled: true
+ Restrictions:
+ GeoRestriction:
+ !If
+ - EnableGeoBlocking
+ -
+ RestrictionType:
+ !If
+ - EnableGeoBlocking
+ -
+ - whitelist
+ - whitelist
+ BadLocations:
+ - BE
+ - LU
+ - NL
+ - RestrictionType: none
Outputs:
VolumeId:
Condition: CreateProdResources
diff --git a/test/templates/good/conditions.yaml b/test/templates/good/conditions.yaml
--- a/test/templates/good/conditions.yaml
+++ b/test/templates/good/conditions.yaml
@@ -8,6 +8,8 @@ Parameters:
AllowedValues:
- prod
- dev
+ EnableGeoBlocking:
+ Type: String
Conditions:
isProd:
"Fn::Equals":
@@ -17,6 +19,11 @@ Conditions:
"Fn::Equals":
- !Ref myEnvironment
- "dev"
+ EnableGeoBlocking: !Equals [ !Ref EnableGeoBlocking, "true" ]
+ PrimaryRegion:
+ "Fn::Equals":
+ - !Ref AWS::Region
+ - 'us-east-1'
Resources:
myInstance:
Type: AWS::EC2::Instance
@@ -35,3 +42,22 @@ Resources:
- Key: Environment2
Value: Dev
- !Ref AWS::NoValue
+ CloudFrontDistribution:
+ Type: "AWS::CloudFront::Distribution"
+ Properties:
+ DistributionConfig:
+ Enabled: true
+ Restrictions:
+ GeoRestriction:
+ !If
+ - EnableGeoBlocking
+ -
+ RestrictionType: whitelist
+ Locations:
+ !If
+ - PrimaryRegion
+ - - EN
+ - - BE
+ - LU
+ - NL
+ - RestrictionType: none
| Complex Condition breaks Properties check (E3002)
Properties check breaks on complex Conditions that return multiple sub-properties. Example:
```
AWSTemplateFormatVersion: "2010-09-09"
Description: A sample template
Parameters:
EnableGeoBlocking:
Type: String
Conditions:
EnableGeoBlocking: !Equals [ !Ref EnableGeoBlocking, "true" ]
Resources:
CloudFrontDistribution:
Type: "AWS::CloudFront::Distribution"
Properties:
DistributionConfig:
Enabled: true
Restrictions:
GeoRestriction:
!If
- EnableGeoBlocking
-
RestrictionType: whitelist
Locations:
- BE
- LU
- NL
- RestrictionType: none
```
This returns an error on the `!If`:
```
E3002 Expecting an object at Resources/CloudFrontDistribution/Properties/DistributionConfig/Restrictions/GeoRestriction/Fn::If/2
template.yaml:15:11
```
| Shoot. Yea those conditions can be tricky. I'll take a look at this. | 2018-05-07T13:59:24Z | [] | [] |
aws-cloudformation/cfn-lint | 55 | aws-cloudformation__cfn-lint-55 | [
"54"
] | 8a2e86f58b719814312a41c7a3ef3cdea8e1e3d3 | diff --git a/src/cfnlint/rules/parameters/LambdaMemorySize.py b/src/cfnlint/rules/parameters/LambdaMemorySize.py
--- a/src/cfnlint/rules/parameters/LambdaMemorySize.py
+++ b/src/cfnlint/rules/parameters/LambdaMemorySize.py
@@ -26,6 +26,9 @@ class LambdaMemorySize(CloudFormationLintRule):
' should have a min and max size that matches Lambda constraints'
tags = ['base', 'parameters', 'lambda']
+ min_memory = 128
+ max_memory = 3008
+
def __init__(self):
"""Init"""
resource_type_specs = [
@@ -39,18 +42,22 @@ def __init__(self):
def check_lambda_memory_size_ref(self, value, path, parameters, resources):
"""Check ref for VPC"""
matches = list()
- min_value = 1
- max_value = 3
if value in parameters:
parameter = parameters.get(value)
min_value = parameter.get('MinValue', 0)
max_value = parameter.get('MaxValue', 999999)
- if min_value < 128 or max_value > 1536:
+ if min_value < self.min_memory or max_value > self.max_memory:
param_path = ['Parameters', value, 'Type']
message = 'Type for Parameter should be Integer, MinValue should be ' \
- 'at least 128, and MaxValue equal or less than 1536 at {0}'
- matches.append(RuleMatch(param_path, message.format(('/'.join(param_path)))))
+ 'at least {0}, and MaxValue equal or less than {1} at {0}'
+ matches.append(
+ RuleMatch(
+ param_path,
+ message.format(
+ self.min_memory,
+ self.max_memory,
+ ('/'.join(param_path)))))
return matches
diff --git a/src/cfnlint/rules/resources/lambda/FunctionMemorySize.py b/src/cfnlint/rules/resources/lmbd/FunctionMemorySize.py
similarity index 79%
rename from src/cfnlint/rules/resources/lambda/FunctionMemorySize.py
rename to src/cfnlint/rules/resources/lmbd/FunctionMemorySize.py
--- a/src/cfnlint/rules/resources/lambda/FunctionMemorySize.py
+++ b/src/cfnlint/rules/resources/lmbd/FunctionMemorySize.py
@@ -24,24 +24,35 @@ class FunctionMemorySize(CloudFormationLintRule):
shortdesc = 'Check Lambda Memory Size Properties'
description = 'See if Lambda Memory Size is valid'
tags = ['base', 'resources', 'lambda']
+ min_memory = 128
+ max_memory = 3008
def check_value(self, value, path):
""" Check memory size value """
matches = list()
- message = 'You must specify a value that is greater than or equal to 128, ' \
+ message = 'You must specify a value that is greater than or equal to {0}, ' \
'and it must be a multiple of 64. You cannot specify a size ' \
- 'larger than 1536. The default value is 128 MB at {0}'
+ 'larger than {1}. Error at {2}'
try:
value = int(value)
- if value < 128 or value > 1536:
- matches.append(RuleMatch(path, message.format(value, ('/'.join(path)))))
+ if value < self.min_memory or value > self.max_memory:
+ matches.append(
+ RuleMatch(
+ path, message.format(
+ self.min_memory, self.max_memory, ('/'.join(path)))))
elif value % 64 != 0:
- matches.append(RuleMatch(path, message.format(value, ('/'.join(path)))))
+ matches.append(
+ RuleMatch(
+ path, message.format(
+ self.min_memory, self.max_memory, ('/'.join(path)))))
except ValueError:
- matches.append(RuleMatch(path, message.format(value, ('/'.join(path)))))
+ matches.append(
+ RuleMatch(
+ path, message.format(
+ self.min_memory, self.max_memory, ('/'.join(path)))))
return matches
diff --git a/src/cfnlint/rules/resources/lambda/FunctionRuntime.py b/src/cfnlint/rules/resources/lmbd/FunctionRuntime.py
similarity index 100%
rename from src/cfnlint/rules/resources/lambda/FunctionRuntime.py
rename to src/cfnlint/rules/resources/lmbd/FunctionRuntime.py
diff --git a/src/cfnlint/rules/resources/lambda/__init__.py b/src/cfnlint/rules/resources/lmbd/__init__.py
similarity index 100%
rename from src/cfnlint/rules/resources/lambda/__init__.py
rename to src/cfnlint/rules/resources/lmbd/__init__.py
| diff --git a/test/rules/resources/lmbd/__init__.py b/test/rules/resources/lmbd/__init__.py
new file mode 100644
--- /dev/null
+++ b/test/rules/resources/lmbd/__init__.py
@@ -0,0 +1,16 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
diff --git a/test/rules/resources/lmbd/test_memory_size.py b/test/rules/resources/lmbd/test_memory_size.py
new file mode 100644
--- /dev/null
+++ b/test/rules/resources/lmbd/test_memory_size.py
@@ -0,0 +1,34 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+from cfnlint.rules.resources.lmbd.FunctionMemorySize import FunctionMemorySize # pylint: disable=E0401
+from ... import BaseRuleTestCase
+
+
+class TestFunctionMemorySize(BaseRuleTestCase):
+ """Test Lambda Memory Size Property Configuration"""
+ def setUp(self):
+ """Setup"""
+ super(TestFunctionMemorySize, self).setUp()
+ self.collection.register(FunctionMemorySize())
+
+ def test_file_positive(self):
+ """Test Positive"""
+ self.helper_file_positive()
+
+ def test_file_negative(self):
+ """Test failure"""
+ self.helper_file_negative('templates/bad/resources_lambda.yaml', 2)
diff --git a/test/rules/resources/lmbd/test_runtime.py b/test/rules/resources/lmbd/test_runtime.py
new file mode 100644
--- /dev/null
+++ b/test/rules/resources/lmbd/test_runtime.py
@@ -0,0 +1,34 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+from cfnlint.rules.resources.lmbd.FunctionRuntime import FunctionRuntime # pylint: disable=E0401
+from ... import BaseRuleTestCase
+
+
+class TestFunctionRuntime(BaseRuleTestCase):
+ """Test Lambda Memory Size Property Configuration"""
+ def setUp(self):
+ """Setup"""
+ super(TestFunctionRuntime, self).setUp()
+ self.collection.register(FunctionRuntime())
+
+ def test_file_positive(self):
+ """Test Positive"""
+ self.helper_file_positive()
+
+ def test_file_negative(self):
+ """Test failure"""
+ self.helper_file_negative('templates/bad/resources_lambda.yaml', 1)
diff --git a/test/templates/bad/resources_lambda.yaml b/test/templates/bad/resources_lambda.yaml
--- a/test/templates/bad/resources_lambda.yaml
+++ b/test/templates/bad/resources_lambda.yaml
@@ -34,7 +34,7 @@ Resources:
S3Key: "amilookup.zip"
Runtime: !Ref myParameterRuntime
Timeout: "25"
- MemorySize: "1537"
+ MemorySize: "3072"
myLambdaTwo:
Type: AWS::Lambda::Function
Properties:
| E2530: Support Lambda Memory values up to 3008
E2530 warns that Lambda memory capacity must not be greater than 1536. This should now be 3008 since Lambda doubled the maximum memory capacity.
https://aws.amazon.com/about-aws/whats-new/2017/11/aws-lambda-doubles-maximum-memory-capacity-for-lambda-functions/
| Thanks. Good call. I wasn't thinking when I followed this. https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-resource-lambda-function.html#cfn-lambda-function-memorysize
I'll fix this and send a pull request for the documentation. | 2018-05-11T14:14:55Z | [] | [] |
aws-cloudformation/cfn-lint | 58 | aws-cloudformation__cfn-lint-58 | [
"57"
] | 07e250f01bf100842d4d85371b25c358685f2430 | diff --git a/src/cfnlint/__init__.py b/src/cfnlint/__init__.py
--- a/src/cfnlint/__init__.py
+++ b/src/cfnlint/__init__.py
@@ -569,6 +569,9 @@ def _search_deep_keys(self, searchText, cfndict, path):
if key == searchText:
pathprop.append(cfndict[key])
keys.append(pathprop)
+ # pop the last element off for nesting of found elements for
+ # dict and list checks
+ pathprop = pathprop[:-1]
if isinstance(cfndict[key], dict):
keys.extend(self._search_deep_keys(searchText, cfndict[key], pathprop))
elif isinstance(cfndict[key], list):
diff --git a/src/cfnlint/rules/functions/FindInMap.py b/src/cfnlint/rules/functions/FindInMap.py
--- a/src/cfnlint/rules/functions/FindInMap.py
+++ b/src/cfnlint/rules/functions/FindInMap.py
@@ -26,19 +26,35 @@ class FindInMap(CloudFormationLintRule):
description = 'Making sure the function is a list of appropriate config'
tags = ['base', 'functions', 'getatt']
- def check_ref(self, obj, tree):
+ supported_functions = [
+ 'Fn::FindInMap',
+ 'Ref'
+ ]
+
+ def check_dict(self, obj, tree):
"""
Check that obj is a dict with Ref as the only key
Mappings only support Ref inside them
"""
matches = list()
+
if isinstance(obj, dict):
if len(obj) == 1:
for key_name, _ in obj.items():
- if key_name not in ['Ref', 'Fn::FindInMap']:
- message = 'FindInMap only supports Ref and Fn::FindInMap for {0}'
+ if key_name not in self.supported_functions:
+ message = 'FindInMap only supports [{0}] functions at {1}'
matches.append(RuleMatch(
- tree[:] + [key_name], message.format('/'.join(map(str, tree)))))
+ tree[:] + [key_name],
+ message.format(
+ ', '.join(map(str, self.supported_functions)),
+ '/'.join(map(str, tree)))))
+ else:
+ message = 'FindInMap only supports an object of 1 of [{0}] functions at {1}'
+ matches.append(RuleMatch(
+ tree[:],
+ message.format(
+ ', '.join(map(str, self.supported_functions)),
+ '/'.join(map(str, tree)))))
return matches
@@ -61,31 +77,44 @@ def match(self, cfn):
map_name = map_obj[0]
first_key = map_obj[1]
second_key = map_obj[2]
- if not isinstance(map_name, six.string_types):
- message = 'Map Name should be a string for {0}'
- matches.append(RuleMatch(
- tree[:] + [0], message.format('/'.join(map(str, tree)))))
+
+ if isinstance(map_name, (six.string_types, six.text_type, dict)):
+ if isinstance(map_name, dict):
+ matches.extend(self.check_dict(map_name, tree[:] + [0]))
+ else:
+ if map_name not in mappings:
+ message = 'Map Name {0} doesnt exist for {0}'
+ matches.append(RuleMatch(
+ tree[:] + [0], message.format(map_name, '/'.join(map(str, tree)))))
else:
- if map_name not in mappings:
- message = 'Map Name {0} doesnt exist for {0}'
- matches.append(RuleMatch(
- tree[:] + [0], message.format(map_name, '/'.join(map(str, tree)))))
+ message = 'Map Name should be a {0}, or string at {1}'
+ matches.append(RuleMatch(
+ tree[:] + [0],
+ message.format(
+ ', '.join(map(str, self.supported_functions)),
+ '/'.join(map(str, tree)))))
- if isinstance(first_key, (six.string_types, dict, int)):
+ if isinstance(first_key, (six.text_type, six.string_types, dict, int)):
if isinstance(first_key, dict):
- matches.extend(self.check_ref(first_key, tree[:] + [1]))
+ matches.extend(self.check_dict(first_key, tree[:] + [1]))
else:
- message = 'Map Name should be a string, int, FindInMap, or Ref for {0}'
+ message = 'Map first key should be a {0}, string, or int at {1}'
matches.append(RuleMatch(
- tree[:] + [1], message.format('/'.join(map(str, tree)))))
+ tree[:] + [1],
+ message.format(
+ ', '.join(map(str, self.supported_functions)),
+ '/'.join(map(str, tree)))))
- if isinstance(second_key, (six.string_types, dict, int)):
+ if isinstance(second_key, (six.text_type, six.string_types, dict, int)):
if isinstance(second_key, dict):
- matches.extend(self.check_ref(second_key, tree[:] + [2]))
+ matches.extend(self.check_dict(second_key, tree[:] + [2]))
else:
- message = 'Map Name should be a string, int, FindInMap, or Ref for {0}'
+ message = 'Map second key should be a {0}, string, or int at {1}'
matches.append(RuleMatch(
- tree[:] + [2], message.format('/'.join(tree))))
+ tree[:] + [2],
+ message.format(
+ ', '.join(map(str, self.supported_functions)),
+ '/'.join(tree))))
else:
message = 'FindInMap is a list with 3 values for {0}'
| diff --git a/test/rules/__init__.py b/test/rules/__init__.py
--- a/test/rules/__init__.py
+++ b/test/rules/__init__.py
@@ -39,6 +39,7 @@ class BaseRuleTestCase(BaseTestCase):
'templates/good/properties_elb.yaml',
'templates/good/functions_sub.yaml',
'templates/good/functions_cidr.yaml',
+ 'templates/good/functions_findinmap.yaml',
'templates/good/resources_lambda.yaml',
'templates/good/transform_serverless_api.yaml',
'templates/good/transform_serverless_function.yaml',
diff --git a/test/rules/functions/test_find_in_map.py b/test/rules/functions/test_find_in_map.py
--- a/test/rules/functions/test_find_in_map.py
+++ b/test/rules/functions/test_find_in_map.py
@@ -31,4 +31,4 @@ def test_file_positive(self):
def test_file_negative(self):
"""Test failure"""
- self.helper_file_negative('templates/bad/functions_findinmap.yaml', 3)
+ self.helper_file_negative('templates/bad/functions_findinmap.yaml', 5)
diff --git a/test/templates/bad/functions_findinmap.yaml b/test/templates/bad/functions_findinmap.yaml
--- a/test/templates/bad/functions_findinmap.yaml
+++ b/test/templates/bad/functions_findinmap.yaml
@@ -21,3 +21,16 @@ Resources:
- azmap
- !Ref "AWS::Region"
- 0
+ myInstance2:
+ Type: AWS::EC2::Instance
+ Properties:
+ ImageId: !FindInMap [ !FindInMap [ myMapDne, !Ref 'AWS::Region', !Ref 'AWS::Region' ], !Ref 'AWS::Region', 32 ]
+ myInstance3:
+ Type: AWS::EC2::Instance
+ Properties:
+ ImageId:
+ Fn::FindInMap:
+ - Ref: myInstance
+ Fn::FindInMap: [ amimap, !Ref 'AWS::Region', !Ref 'AWS::Region' ]
+ - TopLevelKey
+ - SecondLevelKey
diff --git a/test/templates/bad/issues.yaml b/test/templates/bad/issues.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/bad/issues.yaml
@@ -0,0 +1,16 @@
+AWSTemplateFormatVersion: 2010-09-09
+Resources:
+ RDSOptionGroup:
+ Type: "AWS::RDS::OptionGroup"
+ Properties:
+ EngineName: "oracle-se2"
+ MajorEngineVersion: "12.1"
+ OptionGroupDescription: "SSL and Timezone options"
+ OptionConfigurations:
+ - OptionName: "SSL"
+ VpcSecurityGroupMemberships:
+ - !Ref "PrivateSecurityGroup"
+ - OptionName: "Timezone"
+ OptionSettings:
+ - Name: "TIME_ZONE"
+ Value: "Europe/Amsterdam"
diff --git a/test/templates/good/functions_findinmap.yaml b/test/templates/good/functions_findinmap.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/good/functions_findinmap.yaml
@@ -0,0 +1,30 @@
+---
+AWSTemplateFormatVersion: "2010-09-09"
+Description: >
+ Test Good Sub Strings
+Mappings:
+ myMap:
+ us-east-1:
+ 32: ami-1234567
+ 64: ami-abcdefg
+Resources:
+ myInstance1:
+ Type: AWS::EC2::Instance
+ Properties:
+ ImageId: !FindInMap [ !FindInMap [ myMap, !Ref 'AWS::Region', !Ref 'AWS::Region' ], !Ref 'AWS::Region', 32 ]
+ myInstance2:
+ Type: AWS::EC2::Instance
+ Properties:
+ ImageId:
+ Fn::FindInMap:
+ - !FindInMap [ myMap, !Ref 'AWS::Region', !Ref 'AWS::Region' ]
+ - !FindInMap [ myMap, !Ref 'AWS::Region', !Ref 'AWS::Region' ]
+ - !FindInMap [ myMap, !Ref 'AWS::Region', !Ref 'AWS::Region' ]
+ myInstance3:
+ Type: AWS::EC2::Instance
+ Properties:
+ ImageId:
+ Fn::FindInMap:
+ - !Ref myInstance1
+ - !Ref myInstance1
+ - !Ref myInstance1
| Nesting FindInMap not supported
Don't ask why, but we have the following CloudFormation:
```
CidrBlock: !FindInMap [!FindInMap ["Environment", !Ref "Environment", "Subnets"], "eu-west-1a", "Management"]
```
Which causes an error:
```
E1011 Map Name should be a string for Resources/XXX/Properties/CidrBlock/Fn::FindInMap
../xxx.yaml:
```
The FindInMap rule does not support recursive FindInMaps.
| Should work though. Fixing shortly. Ref and FindInMap are the documented approved functions and should work for all 3 properties for findinmap.
https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/intrinsic-function-reference-findinmap.html#w2ab2c21c28c26c13
| 2018-05-14T14:06:32Z | [] | [] |
aws-cloudformation/cfn-lint | 67 | aws-cloudformation__cfn-lint-67 | [
"66"
] | c5816491198b317309eee8d2a5edb47359aa83ed | diff --git a/src/cfnlint/__init__.py b/src/cfnlint/__init__.py
--- a/src/cfnlint/__init__.py
+++ b/src/cfnlint/__init__.py
@@ -482,10 +482,15 @@ def get_valid_getatts(self):
resourcetypes = cfnlint.helpers.RESOURCE_SPECS['us-east-1'].get('ResourceTypes')
results = {}
resources = self.template.get('Resources', {})
+
+ astrik_types = (
+ 'Custom::', 'AWS::CloudFormation::Stack',
+ 'AWS::Serverless::', 'AWS::CloudFormation::CustomResource'
+ )
for name, value in resources.items():
if 'Type' in value:
valtype = value['Type']
- if valtype.startswith(('Custom::', 'AWS::CloudFormation::Stack', 'AWS::Serverless::')):
+ if valtype.startswith(astrik_types):
LOGGER.debug('Cant build an appropriate getatt list from %s', valtype)
results[name] = {'*': {'PrimitiveItemType': 'String'}}
else:
diff --git a/src/cfnlint/rules/functions/Sub.py b/src/cfnlint/rules/functions/Sub.py
--- a/src/cfnlint/rules/functions/Sub.py
+++ b/src/cfnlint/rules/functions/Sub.py
@@ -51,17 +51,23 @@ def _test_string(self, cfn, sub_string, parameters, tree):
valid_params.extend(cfn.get_resource_names())
for key, _ in parameters.items():
valid_params.append(key)
- for resource, attributes in get_atts.items():
- for attribute_name, _ in attributes.items():
- valid_params.append('%s.%s' % (resource, attribute_name))
for string_param in string_params:
string_param = string_param[2:-1]
- if isinstance(string_param, six.string_types):
+ if isinstance(string_param, (six.string_types, six.text_type)):
if string_param not in valid_params:
- message = 'String parameter {0} not found in string for {1}'
- matches.append(RuleMatch(
- tree, message.format(string_param, '/'.join(map(str, tree)))))
+ found = False
+ for resource, attributes in get_atts.items():
+ for attribute_name, _ in attributes.items():
+ if resource == string_param.split('.')[0] and attribute_name == '*':
+ found = True
+ elif (resource == string_param.split('.')[0] and
+ attribute_name == '.'.join(string_param.split('.')[1:])):
+ found = True
+ if not found:
+ message = 'String parameter {0} not found in string for {1}'
+ matches.append(RuleMatch(
+ tree, message.format(string_param, '/'.join(map(str, tree)))))
return matches
| diff --git a/test/rules/functions/test_sub.py b/test/rules/functions/test_sub.py
--- a/test/rules/functions/test_sub.py
+++ b/test/rules/functions/test_sub.py
@@ -31,4 +31,4 @@ def test_file_positive(self):
def test_file_negative(self):
"""Test failure"""
- self.helper_file_negative('templates/bad/functions_sub.yaml', 4)
+ self.helper_file_negative('templates/bad/functions_sub.yaml', 7)
diff --git a/test/templates/bad/functions_sub.yaml b/test/templates/bad/functions_sub.yaml
--- a/test/templates/bad/functions_sub.yaml
+++ b/test/templates/bad/functions_sub.yaml
@@ -5,6 +5,18 @@ Description: >
Resources:
myInstance:
Type: AWS::EC2::Instance
+ Metadata:
+ AWS::CloudFormation::Init:
+ config:
+ files:
+ /etc/aws-signing-proxy.yml:
+ content: !Sub |
+ listen-address: 127.0.0.1
+ port: 9200
+ target: https://${mySubStack.Outputs.DomainEndpoint}
+ region: ${AWS::Region}
+ loadbalancer: ${myInstance3.PublicDnsName1}
+ badresource: ${myInstance5.PublicDnsName}
Properties:
ImageId: ami-asdfef
UserData:
diff --git a/test/templates/good/functions_sub.yaml b/test/templates/good/functions_sub.yaml
--- a/test/templates/good/functions_sub.yaml
+++ b/test/templates/good/functions_sub.yaml
@@ -11,9 +11,22 @@ Parameters:
Type: String
Default: java
Description: App Package
+ mySubnets:
+ Type: List<AWS::EC2::Subnet::Id>
Resources:
myInstance:
Type: AWS::EC2::Instance
+ Metadata:
+ AWS::CloudFormation::Init:
+ config:
+ files:
+ /etc/aws-signing-proxy.yml:
+ content: !Sub |
+ listen-address: 127.0.0.1
+ port: 9200
+ target: https://${mySubStack.Outputs.DomainEndpoint}
+ region: ${AWS::Region}
+ loadbalancer: ${myAlb.DNSName}
Properties:
ImageId: String
UserData:
@@ -21,4 +34,19 @@ Resources:
Fn::Sub:
- yum install ${myPackage}
yum install ${package}
+ yum install ${myCustomResource.Package}
- package: !Ref myAppPackage
+ mySubStack:
+ Type: AWS::CloudFormation::Stack
+ Properties:
+ TemplateURL: String
+ myCustomResource:
+ Type: Custom::Test
+ Properties:
+ ServiceToken: Arn
+
+ myAlb:
+ Type: "AWS::ElasticLoadBalancingV2::LoadBalancer"
+ Properties:
+ Name: !Sub ${AWS::StackName}-lb
+ Subnets: !Ref mySubnets
| Best way to handle parameters from nested stacks?
This project is awesome and super useful!
I can imagine the complexity of linting nested stacks is super high and wouldn't expect that, but how are folks handling situations where Outputs from nested stacks are being used?
For example, given this code:
```
/etc/aws-signing-proxy.yml:
content: !Sub |
listen-address: 127.0.0.1
port: 9200
target: https://${ElasticsearchStack.Outputs.DomainEndpoint}
region: ${AWS::Region}
```
always throws:
```
E1019 String parameter ElasticsearchStack.Outputs.DomainEndpoint not found in string for Resources/ServerLaunchConfig/Metadata/AWS::CloudFormation::Init/es_proxy_setup/files//etc/aws-signing-proxy.yml/content/Fn::Sub
```
I don't want to disable all E1019 checks because they're useful. Would it maybe be right, for now, to exclude all parameters that have `/.Outputs./` in their name?
| Let me check on that and add tests for this going forward. I thought I had this working but I'm guessing I forgot to write the test to make sure that change stayed permanent. Now its been a while.
The best I had at the time was to ignore GetAtts to resources that that are of type AWS::CloudFormation::Stack. The same applies to custom:: resources. Would that make sense to you? | 2018-05-15T20:46:57Z | [] | [] |
aws-cloudformation/cfn-lint | 77 | aws-cloudformation__cfn-lint-77 | [
"76"
] | 0495d106b0cdc0b0ec93d1f151c3091b1c76a700 | diff --git a/src/cfnlint/helpers.py b/src/cfnlint/helpers.py
--- a/src/cfnlint/helpers.py
+++ b/src/cfnlint/helpers.py
@@ -39,6 +39,8 @@
'ap-northeast-2', 'ap-southeast-1', 'ap-southeast-2', 'ap-south-1',
'sa-east-1']
+REGEX_ALPHANUMERIC = re.compile('^[a-zA-Z0-9_]*$')
+
AVAILABILITY_ZONES = [
'us-east-1a', 'us-east-1b', 'us-east-1c', 'us-east-1d', 'us-east-1e', 'us-east-1f',
'us-east-2a' 'us-east-2b' 'us-east-2c',
diff --git a/src/cfnlint/rules/mappings/Name.py b/src/cfnlint/rules/mappings/Name.py
new file mode 100644
--- /dev/null
+++ b/src/cfnlint/rules/mappings/Name.py
@@ -0,0 +1,44 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+import re
+from cfnlint import CloudFormationLintRule
+from cfnlint import RuleMatch
+from cfnlint.helpers import REGEX_ALPHANUMERIC
+
+
+class Name(CloudFormationLintRule):
+ """Check if Mappings are named correctly"""
+ id = 'E7002'
+ shortdesc = 'Mappings have appropriate names'
+ description = 'Check if Mappings are properly named (A-Za-z0-9)'
+ tags = ['base', 'mapping']
+
+ def match(self, cfn):
+ """Check CloudFormation Mapping"""
+
+ matches = list()
+
+ mappings = cfn.template.get('Mappings', {})
+ for mapping_name, _ in mappings.items():
+ if not re.match(REGEX_ALPHANUMERIC, mapping_name):
+ message = 'Mapping {0} has invalid name. Name has to be alphanumeric.'
+ matches.append(RuleMatch(
+ ['Mappings', mapping_name],
+ message.format(mapping_name)
+ ))
+
+ return matches
diff --git a/src/cfnlint/rules/outputs/Name.py b/src/cfnlint/rules/outputs/Name.py
new file mode 100644
--- /dev/null
+++ b/src/cfnlint/rules/outputs/Name.py
@@ -0,0 +1,44 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+import re
+from cfnlint import CloudFormationLintRule
+from cfnlint import RuleMatch
+from cfnlint.helpers import REGEX_ALPHANUMERIC
+
+
+class Name(CloudFormationLintRule):
+ """Check if Outputs are named correctly"""
+ id = 'E6004'
+ shortdesc = 'Outputs have appropriate names'
+ description = 'Check if Outputs are properly named (A-Za-z0-9)'
+ tags = ['base', 'outputs']
+
+ def match(self, cfn):
+ """Check CloudFormation Mapping"""
+
+ matches = list()
+
+ outputs = cfn.template.get('Outputs', {})
+ for output_name, _ in outputs.items():
+ if not re.match(REGEX_ALPHANUMERIC, output_name):
+ message = 'Output {0} has invalid name. Name has to be alphanumeric.'
+ matches.append(RuleMatch(
+ ['Outputs', output_name],
+ message.format(output_name)
+ ))
+
+ return matches
diff --git a/src/cfnlint/rules/parameters/Name.py b/src/cfnlint/rules/parameters/Name.py
new file mode 100644
--- /dev/null
+++ b/src/cfnlint/rules/parameters/Name.py
@@ -0,0 +1,44 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+import re
+from cfnlint import CloudFormationLintRule
+from cfnlint import RuleMatch
+from cfnlint.helpers import REGEX_ALPHANUMERIC
+
+
+class Name(CloudFormationLintRule):
+ """Check if Parameters are named correctly"""
+ id = 'E2003'
+ shortdesc = 'Parameters have appropriate names'
+ description = 'Check if Parameters are properly named (A-Za-z0-9)'
+ tags = ['base', 'parameters']
+
+ def match(self, cfn):
+ """Check CloudFormation Mapping"""
+
+ matches = list()
+
+ parameters = cfn.template.get('Parameters', {})
+ for parameter_name, _ in parameters.items():
+ if not re.match(REGEX_ALPHANUMERIC, parameter_name):
+ message = 'Parameter {0} has invalid name. Name has to be alphanumeric.'
+ matches.append(RuleMatch(
+ ['Parameters', parameter_name],
+ message.format(parameter_name)
+ ))
+
+ return matches
diff --git a/src/cfnlint/rules/resources/Name.py b/src/cfnlint/rules/resources/Name.py
new file mode 100644
--- /dev/null
+++ b/src/cfnlint/rules/resources/Name.py
@@ -0,0 +1,44 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+import re
+from cfnlint import CloudFormationLintRule
+from cfnlint import RuleMatch
+from cfnlint.helpers import REGEX_ALPHANUMERIC
+
+
+class Name(CloudFormationLintRule):
+ """Check if Resources are named correctly"""
+ id = 'E3006'
+ shortdesc = 'Resources have appropriate names'
+ description = 'Check if Resources are properly named (A-Za-z0-9)'
+ tags = ['base', 'resources']
+
+ def match(self, cfn):
+ """Check CloudFormation Mapping"""
+
+ matches = list()
+
+ resources = cfn.template.get('Resources', {})
+ for resource_name, _ in resources.items():
+ if not re.match(REGEX_ALPHANUMERIC, resource_name):
+ message = 'Resources {0} has invalid name. Name has to be alphanumeric.'
+ matches.append(RuleMatch(
+ ['Resources', resource_name],
+ message.format(resource_name)
+ ))
+
+ return matches
| diff --git a/test/module/test_main.py b/test/module/test_main.py
deleted file mode 100644
diff --git a/test/rules/mappings/test_name.py b/test/rules/mappings/test_name.py
new file mode 100644
--- /dev/null
+++ b/test/rules/mappings/test_name.py
@@ -0,0 +1,38 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+from cfnlint.rules.mappings.Name import Name # pylint: disable=E0401
+from .. import BaseRuleTestCase
+
+
+class TestName(BaseRuleTestCase):
+ """Test template Condition Names"""
+ def setUp(self):
+ """Setup"""
+ super(TestName, self).setUp()
+ self.collection.register(Name())
+
+ def test_file_positive(self):
+ """Test Positive"""
+ self.helper_file_positive()
+
+ def test_file_success(self):
+ """Test success"""
+ self.helper_file_positive_template('templates/good/mappings/name.yaml')
+
+ def test_file_negative(self):
+ """Test failure"""
+ self.helper_file_negative('templates/bad/mappings/name.yaml', 1)
diff --git a/test/rules/outputs/test_name.py b/test/rules/outputs/test_name.py
new file mode 100644
--- /dev/null
+++ b/test/rules/outputs/test_name.py
@@ -0,0 +1,38 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+from cfnlint.rules.outputs.Name import Name # pylint: disable=E0401
+from .. import BaseRuleTestCase
+
+
+class TestName(BaseRuleTestCase):
+ """Test template outputs Names"""
+ def setUp(self):
+ """Setup"""
+ super(TestName, self).setUp()
+ self.collection.register(Name())
+
+ def test_file_positive(self):
+ """Test Positive"""
+ self.helper_file_positive()
+
+ def test_file_success(self):
+ """Test success"""
+ self.helper_file_positive_template('templates/good/outputs/name.yaml')
+
+ def test_file_negative(self):
+ """Test failure"""
+ self.helper_file_negative('templates/bad/outputs/name.yaml', 1)
diff --git a/test/rules/parameters/test_name.py b/test/rules/parameters/test_name.py
new file mode 100644
--- /dev/null
+++ b/test/rules/parameters/test_name.py
@@ -0,0 +1,38 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+from cfnlint.rules.parameters.Name import Name # pylint: disable=E0401
+from .. import BaseRuleTestCase
+
+
+class TestName(BaseRuleTestCase):
+ """Test template parameters Names"""
+ def setUp(self):
+ """Setup"""
+ super(TestName, self).setUp()
+ self.collection.register(Name())
+
+ def test_file_positive(self):
+ """Test Positive"""
+ self.helper_file_positive()
+
+ def test_file_success(self):
+ """Test success"""
+ self.helper_file_positive_template('templates/good/parameters/name.yaml')
+
+ def test_file_negative(self):
+ """Test failure"""
+ self.helper_file_negative('templates/bad/parameters/name.yaml', 1)
diff --git a/test/rules/resources/test_name.py b/test/rules/resources/test_name.py
new file mode 100644
--- /dev/null
+++ b/test/rules/resources/test_name.py
@@ -0,0 +1,38 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+from cfnlint.rules.resources.Name import Name # pylint: disable=E0401
+from .. import BaseRuleTestCase
+
+
+class TestName(BaseRuleTestCase):
+ """Test template resources Names"""
+ def setUp(self):
+ """Setup"""
+ super(TestName, self).setUp()
+ self.collection.register(Name())
+
+ def test_file_positive(self):
+ """Test Positive"""
+ self.helper_file_positive()
+
+ def test_file_success(self):
+ """Test success"""
+ self.helper_file_positive_template('templates/good/resources/name.yaml')
+
+ def test_file_negative(self):
+ """Test failure"""
+ self.helper_file_negative('templates/bad/resources/name.yaml', 1)
diff --git a/test/templates/bad/mappings/name.yaml b/test/templates/bad/mappings/name.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/bad/mappings/name.yaml
@@ -0,0 +1,10 @@
+AWSTemplateFormatVersion: "2010-09-09"
+Mappings:
+ Bad.Name:
+ us-east-1:
+ AMI: "ami-7f418316"
+ TestAz: "us-east-1a"
+ us-west-1:
+ AMI: "ami-951945d0"
+ TestAz: "us-west-1a"
+Resources: {}
diff --git a/test/templates/bad/outputs/name.yaml b/test/templates/bad/outputs/name.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/bad/outputs/name.yaml
@@ -0,0 +1,9 @@
+AWSTemplateFormatVersion: "2010-09-09"
+Resources:
+ myInstance:
+ Type: AWS::EC2::Instance
+ Properties:
+ ImageId: ami-123456
+Outputs:
+ dns.Name:
+ Value: !GetAtt myInstance.PrivateDnsName
diff --git a/test/templates/bad/parameters/name.yaml b/test/templates/bad/parameters/name.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/bad/parameters/name.yaml
@@ -0,0 +1,9 @@
+AWSTemplateFormatVersion: "2010-09-09"
+Parameters:
+ image.Id:
+ Type: AWS::EC2::Image::Id
+Resources:
+ myInstance:
+ Type: AWS::EC2::Instance
+ Properties:
+ ImageId: !Ref image.Id
diff --git a/test/templates/bad/resources/name.yaml b/test/templates/bad/resources/name.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/bad/resources/name.yaml
@@ -0,0 +1,6 @@
+AWSTemplateFormatVersion: "2010-09-09"
+Resources:
+ my.Instance:
+ Type: AWS::EC2::Instance
+ Properties:
+ ImageId: ami-123456
diff --git a/test/templates/good/mappings/name.yaml b/test/templates/good/mappings/name.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/good/mappings/name.yaml
@@ -0,0 +1,10 @@
+AWSTemplateFormatVersion: "2010-09-09"
+Mappings:
+ RegionMap:
+ us-east-1:
+ AMI: "ami-7f418316"
+ TestAz: "us-east-1a"
+ us-west-1:
+ AMI: "ami-951945d0"
+ TestAz: "us-west-1a"
+Resources: {}
diff --git a/test/templates/good/outputs/name.yaml b/test/templates/good/outputs/name.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/good/outputs/name.yaml
@@ -0,0 +1,9 @@
+AWSTemplateFormatVersion: "2010-09-09"
+Resources:
+ myInstance:
+ Type: AWS::EC2::Instance
+ Properties:
+ ImageId: ami-123456
+Outputs:
+ dnsName:
+ Value: !GetAtt myInstance.PrivateDnsName
diff --git a/test/templates/good/parameters/name.yaml b/test/templates/good/parameters/name.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/good/parameters/name.yaml
@@ -0,0 +1,9 @@
+AWSTemplateFormatVersion: "2010-09-09"
+Parameters:
+ imageId:
+ Type: AWS::EC2::Image::Id
+Resources:
+ myInstance:
+ Type: AWS::EC2::Instance
+ Properties:
+ ImageId: !Ref imageId
diff --git a/test/templates/good/properties_ec2_vpc.yaml b/test/templates/good/properties_ec2_vpc.yaml
--- a/test/templates/good/properties_ec2_vpc.yaml
+++ b/test/templates/good/properties_ec2_vpc.yaml
@@ -22,7 +22,7 @@ Resources:
Properties:
InstanceTenancy: !Ref vpcTenancy
CidrBlock: !Ref cidrBlock
- mySubnet2-1:
+ mySubnet21:
Type: AWS::EC2::Subnet
Properties:
CidrBlock:
@@ -30,7 +30,7 @@ Resources:
- 0
- !Cidr [!Ref cidrBlock, 3, 16]
VpcId: vpc-1234567
- mySubnet2-2:
+ mySubnet22:
Type: AWS::EC2::Subnet
Properties:
CidrBlock: !Ref cidrBlock
diff --git a/test/templates/good/resources/name.yaml b/test/templates/good/resources/name.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/good/resources/name.yaml
@@ -0,0 +1,6 @@
+AWSTemplateFormatVersion: "2010-09-09"
+Resources:
+ myInstance:
+ Type: AWS::EC2::Instance
+ Properties:
+ ImageId: ami-123456
| Naming standards for Names of Items.
The following elements support (A-Za-z0-9) names:
- [x] Resources
- [x] Mappings
- [x] Parameters
- [x] Outputs
- [ ] Conditions
| 2018-05-18T02:41:26Z | [] | [] |
|
aws-cloudformation/cfn-lint | 80 | aws-cloudformation__cfn-lint-80 | [
"69"
] | 18a46848a2c7402764e04930a716b675780dc1cb | diff --git a/src/cfnlint/__init__.py b/src/cfnlint/__init__.py
--- a/src/cfnlint/__init__.py
+++ b/src/cfnlint/__init__.py
@@ -20,15 +20,11 @@
from datetime import datetime
from yaml.parser import ParserError
import cfnlint.helpers
-import cfnlint.parser
import cfnlint.transforms
LOGGER = logging.getLogger(__name__)
-DEFAULT_RULESDIR = os.path.join(os.path.dirname(cfnlint.helpers.__file__), 'rules')
-DEFAULT_TRANSFORMSDIR = os.path.join(os.path.dirname(cfnlint.helpers.__file__), 'transforms')
-
class CloudFormationLintRule(object):
"""CloudFormation linter rules"""
diff --git a/src/cfnlint/__main__.py b/src/cfnlint/__main__.py
--- a/src/cfnlint/__main__.py
+++ b/src/cfnlint/__main__.py
@@ -15,188 +15,22 @@
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
import sys
-import argparse
import logging
-import json
-import cfnlint.helpers
-from cfnlint import RulesCollection, TransformsCollection, Match
-import cfnlint.formatters as formatters
-import cfnlint.cfn_json
-from cfnlint.version import __version__
-
-LOGGER = logging.getLogger('cfnlint')
-
-
-class ArgumentParser(argparse.ArgumentParser):
- """ Override Argument Parser so we can control the exit code"""
- def error(self, message):
- self.print_help(sys.stderr)
- self.exit(32, '%s: error: %s\n' % (self.prog, message))
+import cfnlint.core
-def configure_logging(log_level):
- """Setup Logging"""
- ch = logging.StreamHandler()
- ch.setLevel(logging.DEBUG)
- if log_level == 'info':
- LOGGER.setLevel(logging.INFO)
- elif log_level == 'debug':
- LOGGER.setLevel(logging.DEBUG)
- else:
- LOGGER.setLevel(logging.ERROR)
- log_formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
- ch.setFormatter(log_formatter)
- LOGGER.addHandler(ch)
+LOGGER = logging.getLogger('cfnlint')
def main():
- """Main Function"""
- parser = ArgumentParser(description='CloudFormation Linter')
- parser.add_argument(
- '--template', help='CloudFormation Template')
- parser.add_argument(
- '--ignore-bad-template', help='Ignore failures with Bad template',
- action='store_true'
- )
- parser.add_argument(
- '--log-level', help='Log Level', choices=['info', 'debug']
- )
- parser.add_argument(
- '--format', help='Output Format', choices=['quiet', 'parseable', 'json']
- )
-
- defaults = {}
- args = parser.parse_known_args()
- template = {}
-
- configure_logging(vars(args[0])['log_level'])
-
- if vars(args[0])['template']:
- (defaults, template) = cfnlint.helpers.get_template_default_args(
- vars(args[0])['template'],
- vars(args[0])['ignore_bad_template'])
-
- parser.add_argument(
- '--list-rules', dest='listrules', default=False,
- action='store_true', help='list all the rules'
- )
- parser.add_argument(
- '--regions', dest='regions', default=['us-east-1'], nargs='*',
- help='list the regions to validate against.'
- )
- parser.add_argument(
- '--append-rules', dest='rulesdir', default=[], nargs='*',
- help='specify one or more rules directories using '
- 'one or more --append-rules arguments. '
- )
- parser.add_argument(
- '--ignore-checks', dest='ignore_checks', default=[], nargs='*',
- help='only check rules whose id do not match these values'
- )
-
- parser.add_argument(
- '--override-spec', dest='override_spec',
- help='A CloudFormation Spec override file that allows customization'
- )
-
- parser.add_argument(
- '--version', help='Version of cfn-lint', action='version',
- version='%(prog)s {version}'.format(version=__version__)
- )
- parser.add_argument(
- '--update-specs', help='Update the CloudFormation Specs',
- action='store_true'
- )
-
- parser.set_defaults(**defaults)
- args = parser.parse_args()
-
- if vars(args)['format']:
- if vars(args)['format'] == 'quiet':
- formatter = formatters.QuietFormatter()
- elif vars(args)['format'] == 'parseable':
- # pylint: disable=bad-option-value
- formatter = formatters.ParseableFormatter()
- else:
- formatter = formatters.Formatter()
-
- if vars(args)['override_spec']:
- cfnlint.helpers.override_specs(vars(args)['override_spec'])
-
- if vars(args)['update_specs']:
- cfnlint.helpers.update_resource_specs()
- exit(0)
-
- rules = RulesCollection()
- rulesdirs = [cfnlint.DEFAULT_RULESDIR] + vars(args)['rulesdir']
- for rulesdir in rulesdirs:
- rules.extend(
- RulesCollection.create_from_directory(rulesdir))
-
- if vars(args)['listrules']:
- print(rules)
- return 0
-
- transforms = TransformsCollection()
- transformdirs = [cfnlint.DEFAULT_TRANSFORMSDIR]
- for transformdir in transformdirs:
- transforms.extend(
- TransformsCollection.create_from_directory(transformdir))
-
- if not vars(args)['template']:
- parser.print_help()
- exit(1)
-
- matches = cfnlint.helpers.run_checks(
- vars(args)['template'], template, rules, transforms, vars(args)['ignore_checks'],
- vars(args)['regions'])
-
- exit_code = 0
- for match in matches:
- if match.rule.id[0] == 'W':
- exit_code = exit_code | 4
- elif match.rule.id[0] == 'E':
- exit_code = exit_code | 2
- if vars(args)['format'] == 'json':
- print(json.dumps(matches, indent=4, cls=CustomEncoder))
- else:
- for match in matches:
- print(formatter.format(match))
-
- return exit_code
-
-
-class CustomEncoder(json.JSONEncoder):
- """Custom Encoding for the Match Object"""
- # pylint: disable=E0202
- def default(self, o):
- if isinstance(o, Match):
- if o.rule.id[0] == 'W':
- level = 'Warning'
- else:
- level = 'Error'
-
- return {
- 'Rule': {
- 'Id': o.rule.id,
- 'Description': o.rule.description,
- 'ShortDescription': o.rule.shortdesc,
- },
- 'Location': {
- 'Start': {
- 'ColumnNumber': o.columnnumber,
- 'LineNumber': o.linenumber,
- },
- 'End': {
- 'ColumnNumber': o.columnnumberend,
- 'LineNumber': o.linenumberend,
- }
- },
- 'Level': level,
- 'Message': o.message,
- 'Filename': o.filename,
- }
- return {'__{}__'.format(o.__class__.__name__): o.__dict__}
+ """Main function"""
+ (args, template, rules) = cfnlint.core.get_template_args_rules(sys.argv[1:])
+
+ return(
+ cfnlint.core.run_cli(
+ vars(args)['template'], template, rules, vars(args)['format'],
+ vars(args)['ignore_checks'], vars(args)['regions'],
+ vars(args)['override_spec']))
if __name__ == '__main__':
diff --git a/src/cfnlint/cfn_json.py b/src/cfnlint/cfn_json.py
--- a/src/cfnlint/cfn_json.py
+++ b/src/cfnlint/cfn_json.py
@@ -18,7 +18,7 @@
import json
from json.decoder import WHITESPACE, WHITESPACE_STR, BACKSLASH, STRINGCHUNK
from json.scanner import NUMBER_RE
-from cfnlint.parser import DuplicateError, NullError
+from cfnlint.cfn_yaml import DuplicateError, NullError
LOGGER = logging.getLogger(__name__)
diff --git a/src/cfnlint/parser.py b/src/cfnlint/cfn_yaml.py
similarity index 100%
rename from src/cfnlint/parser.py
rename to src/cfnlint/cfn_yaml.py
diff --git a/src/cfnlint/core.py b/src/cfnlint/core.py
new file mode 100644
--- /dev/null
+++ b/src/cfnlint/core.py
@@ -0,0 +1,350 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+import logging
+import sys
+import os
+import json
+import argparse
+import six
+from yaml.parser import ParserError, ScannerError
+from cfnlint import RulesCollection, TransformsCollection, Match
+import cfnlint.formatters as formatters
+import cfnlint.cfn_yaml
+import cfnlint.cfn_json
+from cfnlint.version import __version__
+from cfnlint.helpers import REGIONS
+
+LOGGER = logging.getLogger('cfnlint')
+DEFAULT_RULESDIR = os.path.join(os.path.dirname(__file__), 'rules')
+DEFAULT_TRANSFORMSDIR = os.path.join(os.path.dirname(__file__), 'transforms')
+
+
+class ArgumentParser(argparse.ArgumentParser):
+ """ Override Argument Parser so we can control the exit code"""
+ def error(self, message):
+ self.print_help(sys.stderr)
+ self.exit(32, '%s: error: %s\n' % (self.prog, message))
+
+
+def run_cli(filename, template, rules, fmt, ignore_checks, regions, override_spec):
+ """Process args and run"""
+
+ formatter = get_formatter(fmt)
+
+ if override_spec:
+ cfnlint.helpers.override_specs(override_spec)
+
+ transforms = get_transforms()
+ matches = run_checks(
+ filename, template, rules, transforms, ignore_checks,
+ regions)
+
+ if fmt == 'json':
+ print(json.dumps(matches, indent=4, cls=CustomEncoder))
+ else:
+ for match in matches:
+ print(formatter.format(match))
+
+ return get_exit_code(matches)
+
+
+def get_exit_code(matches):
+ """ Determine exit code """
+ exit_code = 0
+ for match in matches:
+ if match.rule.id[0] == 'W':
+ exit_code = exit_code | 4
+ elif match.rule.id[0] == 'E':
+ exit_code = exit_code | 2
+
+ return exit_code
+
+
+def configure_logging(log_level):
+ """Setup Logging"""
+ ch = logging.StreamHandler()
+ ch.setLevel(logging.DEBUG)
+ if log_level == 'info':
+ LOGGER.setLevel(logging.INFO)
+ elif log_level == 'debug':
+ LOGGER.setLevel(logging.DEBUG)
+ else:
+ LOGGER.setLevel(logging.ERROR)
+ log_formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+ ch.setFormatter(log_formatter)
+
+ # make sure all other log handlers are removed before adding it back
+ for handler in LOGGER.handlers:
+ LOGGER.removeHandler(handler)
+ LOGGER.addHandler(ch)
+
+
+def create_parser():
+ """Do first round of parsing parameters to set options"""
+ parser = ArgumentParser(description='CloudFormation Linter')
+ parser.add_argument(
+ '--template', help='CloudFormation Template')
+ parser.add_argument(
+ '--ignore-bad-template', help='Ignore failures with Bad template',
+ action='store_true'
+ )
+ parser.add_argument(
+ '--log-level', help='Log Level', choices=['info', 'debug']
+ )
+ parser.add_argument(
+ '--format', help='Output Format', choices=['quiet', 'parseable', 'json']
+ )
+
+ return parser
+
+
+def get_formatter(fmt):
+ """ Get Formatter"""
+ formatter = {}
+ if fmt:
+ if fmt == 'quiet':
+ formatter = formatters.QuietFormatter()
+ elif fmt == 'parseable':
+ # pylint: disable=bad-option-value
+ formatter = formatters.ParseableFormatter()
+ else:
+ formatter = formatters.Formatter()
+
+ return formatter
+
+
+def get_rules(rulesdir):
+ """Get rules"""
+ rules = RulesCollection()
+ rules_dirs = [DEFAULT_RULESDIR] + rulesdir
+ for rules_dir in rules_dirs:
+ rules.extend(
+ RulesCollection.create_from_directory(rules_dir))
+
+ return rules
+
+
+def get_transforms():
+ """Get Transforms"""
+ transforms = TransformsCollection()
+ transformdirs = [DEFAULT_TRANSFORMSDIR]
+ for transformdir in transformdirs:
+ transforms.extend(
+ TransformsCollection.create_from_directory(transformdir))
+
+ return transforms
+
+
+def append_parser(parser, defaults):
+ """Append arguments to parser"""
+ parser.add_argument(
+ '--list-rules', dest='listrules', default=False,
+ action='store_true', help='list all the rules'
+ )
+ parser.add_argument(
+ '--regions', dest='regions', default=['us-east-1'], nargs='*',
+ help='list the regions to validate against.'
+ )
+ parser.add_argument(
+ '--append-rules', dest='append_rules', default=[], nargs='*',
+ help='specify one or more rules directories using '
+ 'one or more --append-rules arguments. '
+ )
+ parser.add_argument(
+ '--ignore-checks', dest='ignore_checks', default=[], nargs='*',
+ help='only check rules whose id do not match these values'
+ )
+
+ parser.add_argument(
+ '--override-spec', dest='override_spec',
+ help='A CloudFormation Spec override file that allows customization'
+ )
+
+ parser.add_argument(
+ '--version', help='Version of cfn-lint', action='version',
+ version='%(prog)s {version}'.format(version=__version__)
+ )
+ parser.add_argument(
+ '--update-specs', help='Update the CloudFormation Specs',
+ action='store_true'
+ )
+
+ parser.set_defaults(**defaults)
+
+
+def get_template_args_rules(cli_args):
+ """ Get Template Configuration items and set them as default vales"""
+ defaults = {}
+ template = {}
+ parser = create_parser()
+
+ args = parser.parse_known_args(cli_args)
+ configure_logging(vars(args[0])['log_level'])
+
+ if vars(args[0])['template']:
+ filename = vars(args[0])['template']
+ ignore_bad_template = vars(args[0])['ignore_bad_template']
+ try:
+ fp = open(filename)
+ loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
+ loader.add_multi_constructor('!', cfnlint.cfn_yaml.multi_constructor)
+ template = loader.get_single_data()
+ defaults = get_default_args(template)
+ except IOError as e:
+ if e.errno == 2:
+ LOGGER.error('Template file not found: %s', filename)
+ sys.exit(1)
+ elif e.errno == 21:
+ LOGGER.error('Template references a directory, not a file: %s', filename)
+ sys.exit(1)
+ elif e.errno == 13:
+ LOGGER.error('Permission denied when accessing template file: %s', filename)
+ sys.exit(1)
+ except cfnlint.cfn_yaml.DuplicateError as err:
+ LOGGER.error('Template %s contains duplicates: %s', filename, err)
+ sys.exit(1)
+ except cfnlint.cfn_yaml.NullError as err:
+ LOGGER.error('Template %s contains nulls: %s', filename, err)
+ sys.exit(1)
+ except (ParserError, ScannerError) as err:
+ try:
+ template = json.load(open(filename), cls=cfnlint.cfn_json.CfnJSONDecoder)
+ except cfnlint.cfn_json.JSONDecodeError as json_err:
+ if ignore_bad_template:
+ LOGGER.info('Template %s is malformed: %s', filename, err.problem)
+ LOGGER.error('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
+ else:
+ LOGGER.error('Template %s is malformed: %s', filename, err.problem)
+ LOGGER.error('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
+ sys.exit(1)
+ except Exception as json_err: # pylint: disable=W0703
+ if ignore_bad_template:
+ LOGGER.info('Template %s is malformed: %s', filename, err.problem)
+ LOGGER.info('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
+ else:
+ LOGGER.error('Template %s is malformed: %s', filename, err.problem)
+ LOGGER.error('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
+ sys.exit(1)
+
+ append_parser(parser, defaults)
+ args = parser.parse_args(cli_args)
+
+ if vars(args)['update_specs']:
+ cfnlint.helpers.update_resource_specs()
+ exit(0)
+
+ rules = cfnlint.core.get_rules(vars(args)['append_rules'])
+
+ if vars(args)['listrules']:
+ print(rules)
+ exit(0)
+
+ if not vars(args)['template']:
+ parser.print_help()
+ exit(1)
+
+ return(args, template, rules)
+
+
+def get_default_args(template):
+ """ Parse and validate default args """
+ defaults = {}
+ if isinstance(template, dict):
+ configs = template.get('Metadata', {}).get('cfn-lint', {}).get('config', {})
+
+ if isinstance(configs, dict):
+ for config_name, config_value in configs.items():
+ if config_name == 'ignore_checks':
+ if isinstance(config_value, list):
+ defaults['ignore_checks'] = config_value
+ if config_name == 'regions':
+ if isinstance(config_value, list):
+ defaults['regions'] = config_value
+ if config_name == 'append_rules':
+ if isinstance(config_value, list):
+ defaults['override_spec'] = config_value
+ if config_name == 'override_spec':
+ if isinstance(config_value, (six.string_types, six.text_type)):
+ defaults['override_spec'] = config_value
+ if config_name == 'ignore_bad_template':
+ if isinstance(config_value, bool):
+ defaults['ignore_bad_template'] = config_value
+ if config_name == 'log_level':
+ if isinstance(config_value, (six.string_types, six.text_type)):
+ defaults['log_level'] = config_value
+
+ return defaults
+
+
+def run_checks(filename, template, rules, transforms, ignore_checks, regions):
+ """Run Checks against the template"""
+ if regions:
+
+ for region in regions:
+ if region not in REGIONS:
+ LOGGER.error('Supported regions are %s', REGIONS)
+ exit(32)
+
+ matches = list()
+
+ runner = cfnlint.Runner(
+ rules, transforms, filename, template,
+ ignore_checks, regions)
+ matches.extend(runner.transform())
+ # Only do rule analysis if Transform was successful
+ if not matches:
+ try:
+ matches.extend(runner.run())
+ except Exception as err: # pylint: disable=W0703
+ LOGGER.error('Tried to process rules on file %s but got an error: %s', filename, str(err))
+ exit(1)
+ matches.sort(key=lambda x: (x.filename, x.linenumber, x.rule.id))
+
+ return(matches)
+
+
+class CustomEncoder(json.JSONEncoder):
+ """Custom Encoding for the Match Object"""
+ # pylint: disable=E0202
+ def default(self, o):
+ if isinstance(o, Match):
+ if o.rule.id[0] == 'W':
+ level = 'Warning'
+ else:
+ level = 'Error'
+
+ return {
+ 'Rule': {
+ 'Id': o.rule.id,
+ 'Description': o.rule.description,
+ 'ShortDescription': o.rule.shortdesc,
+ },
+ 'Location': {
+ 'Start': {
+ 'ColumnNumber': o.columnnumber,
+ 'LineNumber': o.linenumber,
+ },
+ 'End': {
+ 'ColumnNumber': o.columnnumberend,
+ 'LineNumber': o.linenumberend,
+ }
+ },
+ 'Level': level,
+ 'Message': o.message,
+ 'Filename': o.filename,
+ }
+ return {'__{}__'.format(o.__class__.__name__): o.__dict__}
diff --git a/src/cfnlint/helpers.py b/src/cfnlint/helpers.py
--- a/src/cfnlint/helpers.py
+++ b/src/cfnlint/helpers.py
@@ -22,10 +22,7 @@
import logging
import re
import requests
-from yaml.parser import ParserError, ScannerError
import pkg_resources
-from cfnlint.parser import DuplicateError, NullError
-import cfnlint.parser
LOGGER = logging.getLogger(__name__)
@@ -243,95 +240,3 @@ def override_specs(override_spec_file):
except (ValueError) as err:
LOGGER.error('Override spec file %s is malformed: %s', filename, err)
sys.exit(1)
-
-
-def get_template_default_args(filename, ignore_bad_template):
- """ Get Template Configuration items and set them as default vales"""
- defaults = {}
- template = {}
- try:
- fp = open(filename)
- loader = cfnlint.parser.MarkedLoader(fp.read())
- loader.add_multi_constructor('!', cfnlint.parser.multi_constructor)
- template = loader.get_single_data()
- if isinstance(template, dict):
- defaults = template.get('Metadata', {}).get('cfn-lint', {}).get('config', {})
- except IOError as e:
- if e.errno == 2:
- LOGGER.error('Template file not found: %s', filename)
- sys.exit(1)
- elif e.errno == 21:
- LOGGER.error('Template references a directory, not a file: %s', filename)
- sys.exit(1)
- elif e.errno == 13:
- LOGGER.error('Permission denied when accessing template file: %s', filename)
- sys.exit(1)
- except DuplicateError as err:
- LOGGER.error('Template %s contains duplicates: %s', filename, err)
- sys.exit(1)
- except NullError as err:
- LOGGER.error('Template %s contains nulls: %s', filename, err)
- sys.exit(1)
- except (ParserError, ScannerError) as err:
- try:
- template = json.load(open(filename), cls=cfnlint.cfn_json.CfnJSONDecoder)
- except cfnlint.cfn_json.JSONDecodeError as json_err:
- if ignore_bad_template:
- LOGGER.info('Template %s is malformed: %s', filename, err.problem)
- LOGGER.error('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
- else:
- LOGGER.error('Template %s is malformed: %s', filename, err.problem)
- LOGGER.error('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
- sys.exit(1)
- except Exception as json_err: # pylint: disable=W0703
- if ignore_bad_template:
- LOGGER.info('Template %s is malformed: %s', filename, err.problem)
- LOGGER.info('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
- else:
- LOGGER.error('Template %s is malformed: %s', filename, err.problem)
- LOGGER.error('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
- sys.exit(1)
-
- return(defaults, template)
-
-
-def run_checks(filename, template, rules, transforms, ignore_checks, regions):
- """Run Checks against the template"""
- if regions:
- supported_regions = [
- 'ap-south-1',
- 'sa-east-1',
- 'ap-northeast-1',
- 'ap-northeast-2',
- 'ap-southeast-1',
- 'ap-southeast-2',
- 'ca-central-1',
- 'eu-central-1',
- 'eu-west-1',
- 'eu-west-2',
- 'us-west-2',
- 'us-east-1',
- 'us-east-2',
- 'us-west-1'
- ]
- for region in regions:
- if region not in supported_regions:
- LOGGER.error('Supported regions are %s', supported_regions)
- exit(32)
-
- matches = list()
-
- runner = cfnlint.Runner(
- rules, transforms, filename, template,
- ignore_checks, regions)
- matches.extend(runner.transform())
- # Only do rule analysis if Transform was successful
- if not matches:
- try:
- matches.extend(runner.run())
- except Exception as err: # pylint: disable=W0703
- LOGGER.error('Tried to process rules on file %s but got an error: %s', filename, str(err))
- exit(1)
- matches.sort(key=lambda x: (x.filename, x.linenumber, x.rule.id))
-
- return(matches)
diff --git a/src/cfnlint/rules/functions/RefExist.py b/src/cfnlint/rules/functions/RefExist.py
--- a/src/cfnlint/rules/functions/RefExist.py
+++ b/src/cfnlint/rules/functions/RefExist.py
@@ -18,7 +18,6 @@
import six
from cfnlint import CloudFormationLintRule
from cfnlint import RuleMatch
-from cfnlint.parser import list_node
class RefExist(CloudFormationLintRule):
@@ -77,7 +76,7 @@ def match(self, cfn):
subparams = []
if isinstance(sub, (six.text_type, six.string_types)):
parammatches = self.searchstring(sub)
- elif isinstance(subtree[-1], (list, list_node)):
+ elif isinstance(subtree[-1], (list)):
if len(sub) == 2:
parammatches = self.searchstring(sub[0])
for subparam in sub[1]:
| diff --git a/test/module/helpers/__init__.py b/test/module/core/__init__.py
similarity index 100%
rename from test/module/helpers/__init__.py
rename to test/module/core/__init__.py
diff --git a/test/module/core/test_arg_parser.py b/test/module/core/test_arg_parser.py
new file mode 100644
--- /dev/null
+++ b/test/module/core/test_arg_parser.py
@@ -0,0 +1,57 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+import logging
+import cfnlint.core # pylint: disable=E0401
+from testlib.testcase import BaseTestCase
+
+LOGGER = logging.getLogger('cfnlint')
+
+
+class TestArgsParser(BaseTestCase):
+ """Test Parser Arguments """
+ def tearDown(self):
+ """Setup"""
+ for handler in LOGGER.handlers:
+ LOGGER.removeHandler(handler)
+
+ def test_create_parser(self):
+ """Test success run"""
+
+ parser = cfnlint.core.create_parser()
+ args = parser.parse_args([
+ '--template', 'test.yaml', '--ignore-bad-template',
+ '--format', 'quiet', '--log-level', 'debug'])
+ self.assertEqual(vars(args)['template'], 'test.yaml')
+ self.assertEqual(vars(args)['ignore_bad_template'], True)
+ self.assertEqual(vars(args)['format'], 'quiet')
+ self.assertEqual(vars(args)['log_level'], 'debug')
+
+ def test_override_template_defaults(self):
+ """Test second parser"""
+ parser = cfnlint.core.create_parser()
+ defaults = {
+ 'ignore_checks': ['E0110']
+ }
+
+ # just write the defaults
+
+ cfnlint.core.append_parser(parser, defaults)
+ args = parser.parse_args([
+ '--ignore-checks', 'E0101'
+ ])
+
+ self.assertEqual(vars(args)['ignore_checks'], ['E0101'])
diff --git a/test/module/main/test_logging.py b/test/module/core/test_logging.py
similarity index 87%
rename from test/module/main/test_logging.py
rename to test/module/core/test_logging.py
--- a/test/module/main/test_logging.py
+++ b/test/module/core/test_logging.py
@@ -15,13 +15,13 @@
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
import logging
-import cfnlint.__main__ # pylint: disable=E0401
+import cfnlint.core # pylint: disable=E0401
from testlib.testcase import BaseTestCase
LOGGER = logging.getLogger('cfnlint')
-class TestDefaultArguments(BaseTestCase):
+class TestLogging(BaseTestCase):
"""Test Logging Arguments """
def tearDown(self):
"""Setup"""
@@ -31,20 +31,20 @@ def tearDown(self):
def test_logging_info(self):
"""Test success run"""
- cfnlint.__main__.configure_logging('info')
+ cfnlint.core.configure_logging('info')
self.assertEqual(logging.INFO, LOGGER.level)
self.assertEqual(len(LOGGER.handlers), 1)
def test_logging_debug(self):
"""Test debug level"""
- cfnlint.__main__.configure_logging('debug')
+ cfnlint.core.configure_logging('debug')
self.assertEqual(logging.DEBUG, LOGGER.level)
self.assertEqual(len(LOGGER.handlers), 1)
def test_logging_error(self):
"""Test debug level"""
- cfnlint.__main__.configure_logging(None)
+ cfnlint.core.configure_logging(None)
self.assertEqual(logging.ERROR, LOGGER.level)
self.assertEqual(len(LOGGER.handlers), 1)
diff --git a/test/module/helpers/test_run_checks.py b/test/module/core/test_run_checks.py
similarity index 66%
rename from test/module/helpers/test_run_checks.py
rename to test/module/core/test_run_checks.py
--- a/test/module/helpers/test_run_checks.py
+++ b/test/module/core/test_run_checks.py
@@ -14,29 +14,24 @@
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
-from cfnlint import Runner, RulesCollection, DEFAULT_RULESDIR
+from cfnlint import Runner, RulesCollection
+import cfnlint.core
import cfnlint.helpers # pylint: disable=E0401
from testlib.testcase import BaseTestCase
-class TestDefaultArguments(BaseTestCase):
+class TestRunChecks(BaseTestCase):
"""Test Run Checks """
- def setUp(self):
- """Setup"""
- self.rules = RulesCollection()
- rulesdirs = [DEFAULT_RULESDIR]
- for rulesdir in rulesdirs:
- self.rules.extend(
- RulesCollection.create_from_directory(rulesdir))
def test_good_template(self):
"""Test success run"""
filename = 'templates/good/generic.yaml'
- (_, template) = cfnlint.helpers.get_template_default_args(filename, True)
+ (args, template, rules) = cfnlint.core.get_template_args_rules([
+ '--template', filename])
- results = cfnlint.helpers.run_checks(
- filename, template, self.rules, {}, {}, ['us-east-1'])
+ results = cfnlint.core.run_checks(
+ vars(args)['template'], template, rules, {}, {}, ['us-east-1'])
assert(results == [])
@@ -44,10 +39,11 @@ def test_bad_template(self):
"""Test bad template"""
filename = 'templates/quickstart/nat-instance.json'
- (_, template) = cfnlint.helpers.get_template_default_args(filename, True)
+ (args, template, rules) = cfnlint.core.get_template_args_rules([
+ '--template', filename])
- results = cfnlint.helpers.run_checks(
- filename, template, self.rules, {}, {}, ['us-east-1'])
+ results = cfnlint.core.run_checks(
+ vars(args)['template'], template, rules, {}, {}, ['us-east-1'])
assert(results[0].rule.id == 'W2506')
assert(results[1].rule.id == 'W2001')
diff --git a/test/module/core/test_run_cli.py b/test/module/core/test_run_cli.py
new file mode 100644
--- /dev/null
+++ b/test/module/core/test_run_cli.py
@@ -0,0 +1,153 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+import logging
+import cfnlint.core # pylint: disable=E0401
+from testlib.testcase import BaseTestCase
+
+LOGGER = logging.getLogger('cfnlint')
+
+
+class TestCli(BaseTestCase):
+ """Test CLI processing """
+ def tearDown(self):
+ """Setup"""
+ for handler in LOGGER.handlers:
+ LOGGER.removeHandler(handler)
+
+ def test_template_not_found(self):
+ """Test template not found"""
+
+ filename = 'templates/good/core/not_found.yaml'
+
+ with self.assertRaises(SystemExit) as exit_code:
+ cfnlint.core.get_template_args_rules([
+ '--template', filename, '--ignore_bad_template'])
+
+ self.assertEqual(exit_code.exception.code, 1)
+
+ def test_template_invalid_yaml(self):
+ """Test template not found"""
+ filename = 'templates/bad/core/config_invalid_yaml.yaml'
+
+ with self.assertRaises(SystemExit) as exit_code:
+ cfnlint.core.get_template_args_rules([
+ '--template', filename])
+
+ self.assertEqual(exit_code.exception.code, 1)
+
+ def test_template_invalid_json(self):
+ """Test template not found"""
+ filename = 'templates/bad/core/config_invalid_json.json'
+
+ with self.assertRaises(SystemExit) as exit_code:
+ cfnlint.core.get_template_args_rules([
+ '--template', filename])
+
+ self.assertEqual(exit_code.exception.code, 1)
+
+ def test_template_invalid_yaml_ignore(self):
+ """Test template not found"""
+ filename = 'templates/bad/core/config_invalid_yaml.yaml'
+
+ (args, _, _) = cfnlint.core.get_template_args_rules([
+ '--template', filename, '--ignore-bad-template'])
+
+ self.assertEqual(vars(args), {
+ 'append_rules': [],
+ 'format': None,
+ 'ignore_bad_template': True,
+ 'ignore_checks': [],
+ 'listrules': False,
+ 'log_level': None,
+ 'override_spec': None,
+ 'regions': ['us-east-1'],
+ 'template': 'templates/bad/core/config_invalid_yaml.yaml',
+ 'update_specs': False})
+
+ def test_template_invalid_json_ignore(self):
+ """Test template not found"""
+ filename = 'templates/bad/core/config_invalid_json.json'
+ (args, _, _) = cfnlint.core.get_template_args_rules([
+ '--template', filename, '--ignore-bad-template'])
+
+ self.assertEqual(vars(args), {
+ 'append_rules': [],
+ 'format': None,
+ 'ignore_bad_template': True,
+ 'ignore_checks': [],
+ 'listrules': False,
+ 'log_level': None,
+ 'override_spec': None,
+ 'regions': ['us-east-1'],
+ 'template': 'templates/bad/core/config_invalid_json.json',
+ 'update_specs': False})
+
+ def test_template_config(self):
+ """Test template config"""
+ filename = 'templates/good/core/config_parameters.yaml'
+ (args, _, _) = cfnlint.core.get_template_args_rules([
+ '--template', filename, '--ignore-bad-template'])
+
+ self.assertEqual(vars(args), {
+ 'append_rules': [],
+ 'format': None,
+ 'ignore_bad_template': True,
+ 'ignore_checks': ['E0101'],
+ 'listrules': False,
+ 'log_level': None,
+ 'override_spec': None,
+ 'regions': ['us-east-1'],
+ 'template': 'templates/good/core/config_parameters.yaml',
+ 'update_specs': False})
+
+ def test_override_parameters(self):
+ """Test overriding parameters"""
+ filename = 'templates/good/core/config_parameters.yaml'
+ (args, _, _) = cfnlint.core.get_template_args_rules([
+ '--template', filename, '--ignore-bad-template',
+ '--ignore-checks', 'E0000'])
+
+ self.assertEqual(vars(args), {
+ 'append_rules': [],
+ 'format': None,
+ 'ignore_bad_template': True,
+ 'ignore_checks': ['E0000'],
+ 'listrules': False,
+ 'log_level': None,
+ 'override_spec': None,
+ 'regions': ['us-east-1'],
+ 'template': 'templates/good/core/config_parameters.yaml',
+ 'update_specs': False})
+
+ def test_bad_config(self):
+ """ Test bad formatting in config"""
+
+ filename = 'templates/bad/core/config_parameters.yaml'
+ (args, _, _) = cfnlint.core.get_template_args_rules([
+ '--template', filename, '--ignore-bad-template'])
+
+ self.assertEqual(vars(args), {
+ 'append_rules': [],
+ 'format': None,
+ 'ignore_bad_template': True,
+ 'ignore_checks': [],
+ 'listrules': False,
+ 'log_level': None,
+ 'override_spec': None,
+ 'regions': ['us-east-1'],
+ 'template': filename,
+ 'update_specs': False})
diff --git a/test/module/helpers/test_default_args.py b/test/module/helpers/test_default_args.py
deleted file mode 100644
--- a/test/module/helpers/test_default_args.py
+++ /dev/null
@@ -1,80 +0,0 @@
-"""
- Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
-
- Permission is hereby granted, free of charge, to any person obtaining a copy of this
- software and associated documentation files (the "Software"), to deal in the Software
- without restriction, including without limitation the rights to use, copy, modify,
- merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
- INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
- PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
- OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
- SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-"""
-import cfnlint.helpers # pylint: disable=E0401
-from testlib.testcase import BaseTestCase
-
-
-class TestDefaultArguments(BaseTestCase):
- """Test Default Arguments """
-
- def test_default_arguments(self):
- """Test success run"""
-
- filename = 'templates/good/helpers/config_cfn_lint.yaml'
- ignore_bad_template = True
-
- (defaults, _) = cfnlint.helpers.get_template_default_args(filename, ignore_bad_template)
-
- assert(defaults == {'regions': ['us-east-1', 'us-east-2'], 'ignore_checks': ['E2530']})
-
- def test_template_not_found(self):
- """Test template not found"""
- filename = 'templates/good/helpers/not_found.yaml'
- ignore_bad_template = True
-
- with self.assertRaises(SystemExit) as exit_code:
- cfnlint.helpers.get_template_default_args(filename, ignore_bad_template)
-
- self.assertEqual(exit_code.exception.code, 1)
-
- def test_template_invalid_yaml(self):
- """Test template not found"""
- filename = 'templates/bad/helpers/config_invalid_yaml.yaml'
- ignore_bad_template = False
-
- with self.assertRaises(SystemExit) as exit_code:
- cfnlint.helpers.get_template_default_args(filename, ignore_bad_template)
-
- self.assertEqual(exit_code.exception.code, 1)
-
- def test_template_invalid_json(self):
- """Test template not found"""
- filename = 'templates/bad/helpers/config_invalid_json.json'
- ignore_bad_template = False
-
- with self.assertRaises(SystemExit) as exit_code:
- cfnlint.helpers.get_template_default_args(filename, ignore_bad_template)
-
- self.assertEqual(exit_code.exception.code, 1)
-
- def test_template_invalid_yaml_ignore(self):
- """Test template not found"""
- filename = 'templates/bad/helpers/config_invalid_yaml.yaml'
- ignore_bad_template = True
-
- (defaults, _) = cfnlint.helpers.get_template_default_args(filename, ignore_bad_template)
-
- self.assertEqual(defaults, {})
-
- def test_template_invalid_json_ignore(self):
- """Test template not found"""
- filename = 'templates/bad/helpers/config_invalid_json.json'
- ignore_bad_template = True
-
- (defaults, _) = cfnlint.helpers.get_template_default_args(filename, ignore_bad_template)
-
- self.assertEqual(defaults, {})
diff --git a/test/module/main/__init__.py b/test/module/main/__init__.py
deleted file mode 100644
--- a/test/module/main/__init__.py
+++ /dev/null
@@ -1,16 +0,0 @@
-"""
- Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
-
- Permission is hereby granted, free of charge, to any person obtaining a copy of this
- software and associated documentation files (the "Software"), to deal in the Software
- without restriction, including without limitation the rights to use, copy, modify,
- merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
- INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
- PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
- OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
- SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-"""
diff --git a/test/module/test_cfn_json.py b/test/module/test_cfn_json.py
--- a/test/module/test_cfn_json.py
+++ b/test/module/test_cfn_json.py
@@ -15,7 +15,8 @@
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
import json
-from cfnlint import Template, RulesCollection, DEFAULT_RULESDIR # pylint: disable=E0401
+from cfnlint import Template, RulesCollection # pylint: disable=E0401
+from cfnlint.core import DEFAULT_RULESDIR # pylint: disable=E0401
import cfnlint.cfn_json # pylint: disable=E0401
from testlib.testcase import BaseTestCase
diff --git a/test/module/test_duplicate.py b/test/module/test_duplicate.py
--- a/test/module/test_duplicate.py
+++ b/test/module/test_duplicate.py
@@ -15,8 +15,9 @@
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
import json
-from cfnlint import Template, RulesCollection, DEFAULT_RULESDIR # pylint: disable=E0401
-import cfnlint.parser # pylint: disable=E0401
+from cfnlint import Template, RulesCollection
+from cfnlint.core import DEFAULT_RULESDIR # pylint: disable=E0401
+import cfnlint.cfn_yaml # pylint: disable=E0401
import cfnlint.cfn_json # pylint: disable=E0401
from testlib.testcase import BaseTestCase
@@ -38,10 +39,10 @@ def test_success_run(self):
try:
fp = open(filename)
- loader = cfnlint.parser.MarkedLoader(fp.read())
- loader.add_multi_constructor('!', cfnlint.parser.multi_constructor)
+ loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
+ loader.add_multi_constructor('!', cfnlint.cfn_yaml.multi_constructor)
loader.get_single_data()
- except cfnlint.parser.DuplicateError:
+ except cfnlint.cfn_yaml.DuplicateError:
assert(False)
return
@@ -70,10 +71,10 @@ def test_fail_yaml_run(self):
try:
fp = open(filename)
- loader = cfnlint.parser.MarkedLoader(fp.read())
- loader.add_multi_constructor('!', cfnlint.parser.multi_constructor)
+ loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
+ loader.add_multi_constructor('!', cfnlint.cfn_yaml.multi_constructor)
loader.get_single_data()
- except cfnlint.parser.DuplicateError:
+ except cfnlint.cfn_yaml.DuplicateError:
assert(True)
return
diff --git a/test/module/test_null_values.py b/test/module/test_null_values.py
--- a/test/module/test_null_values.py
+++ b/test/module/test_null_values.py
@@ -15,8 +15,9 @@
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
import json
-from cfnlint import RulesCollection, DEFAULT_RULESDIR # pylint: disable=E0401
-import cfnlint.parser # pylint: disable=E0401
+from cfnlint import RulesCollection # pylint: disable=E0401
+from cfnlint.core import DEFAULT_RULESDIR
+import cfnlint.cfn_yaml # pylint: disable=E0401
import cfnlint.cfn_json # pylint: disable=E0401
from testlib.testcase import BaseTestCase
@@ -38,10 +39,10 @@ def test_success_run(self):
try:
fp = open(filename)
- loader = cfnlint.parser.MarkedLoader(fp.read())
- loader.add_multi_constructor('!', cfnlint.parser.multi_constructor)
+ loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
+ loader.add_multi_constructor('!', cfnlint.cfn_yaml.multi_constructor)
loader.get_single_data()
- except cfnlint.parser.NullError:
+ except cfnlint.cfn_yaml.NullError:
assert(False)
return
@@ -70,10 +71,10 @@ def test_fail_yaml_run(self):
try:
fp = open(filename)
- loader = cfnlint.parser.MarkedLoader(fp.read())
- loader.add_multi_constructor('!', cfnlint.parser.multi_constructor)
+ loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
+ loader.add_multi_constructor('!', cfnlint.cfn_yaml.multi_constructor)
loader.get_single_data()
- except cfnlint.parser.NullError:
+ except cfnlint.cfn_yaml.NullError:
assert(True)
return
diff --git a/test/module/test_rules_collections.py b/test/module/test_rules_collections.py
--- a/test/module/test_rules_collections.py
+++ b/test/module/test_rules_collections.py
@@ -14,8 +14,9 @@
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
-from cfnlint import RulesCollection, Template, DEFAULT_RULESDIR # pylint: disable=E0401
-import cfnlint.parser # pylint: disable=E0401
+from cfnlint import RulesCollection, Template
+from cfnlint.core import DEFAULT_RULESDIR # pylint: disable=E0401
+import cfnlint.cfn_yaml # pylint: disable=E0401
from testlib.testcase import BaseTestCase
@@ -40,8 +41,8 @@ def test_success_run(self):
""" Test Run Logic"""
filename = 'templates/good/generic.yaml'
fp = open(filename)
- loader = cfnlint.parser.MarkedLoader(fp.read())
- loader.add_multi_constructor("!", cfnlint.parser.multi_constructor)
+ loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
+ loader.add_multi_constructor("!", cfnlint.cfn_yaml.multi_constructor)
template = loader.get_single_data()
cfn = Template(template, ['us-east-1'])
@@ -53,8 +54,8 @@ def test_fail_run(self):
"""Test failure run"""
filename = 'templates/bad/generic.yaml'
fp = open(filename)
- loader = cfnlint.parser.MarkedLoader(fp.read())
- loader.add_multi_constructor("!", cfnlint.parser.multi_constructor)
+ loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
+ loader.add_multi_constructor("!", cfnlint.cfn_yaml.multi_constructor)
template = loader.get_single_data()
cfn = Template(template, ['us-east-1'])
@@ -66,8 +67,8 @@ def test_fail_sub_properties_run(self):
"""Test failure run"""
filename = 'templates/bad/properties_onlyone.yaml'
fp = open(filename)
- loader = cfnlint.parser.MarkedLoader(fp.read())
- loader.add_multi_constructor("!", cfnlint.parser.multi_constructor)
+ loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
+ loader.add_multi_constructor("!", cfnlint.cfn_yaml.multi_constructor)
template = loader.get_single_data()
cfn = Template(template, ['us-east-1'])
diff --git a/test/rules/__init__.py b/test/rules/__init__.py
--- a/test/rules/__init__.py
+++ b/test/rules/__init__.py
@@ -14,7 +14,8 @@
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
-from cfnlint import Runner, RulesCollection, TransformsCollection, DEFAULT_TRANSFORMSDIR
+from cfnlint import Runner, RulesCollection, TransformsCollection
+from cfnlint.core import DEFAULT_TRANSFORMSDIR
from testlib.testcase import BaseTestCase
diff --git a/test/templates/bad/helpers/config_invalid_json.json b/test/templates/bad/core/config_invalid_json.json
similarity index 100%
rename from test/templates/bad/helpers/config_invalid_json.json
rename to test/templates/bad/core/config_invalid_json.json
diff --git a/test/templates/bad/helpers/config_invalid_yaml.yaml b/test/templates/bad/core/config_invalid_yaml.yaml
similarity index 100%
rename from test/templates/bad/helpers/config_invalid_yaml.yaml
rename to test/templates/bad/core/config_invalid_yaml.yaml
diff --git a/test/templates/bad/core/config_parameters.yaml b/test/templates/bad/core/config_parameters.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/bad/core/config_parameters.yaml
@@ -0,0 +1,7 @@
+---
+AWSTemplateFormatVersion: "2010-09-09"
+Metadata:
+ cfn-lint:
+ config:
+ ignore_checks: E0101
+Resources: {}
diff --git a/test/templates/good/helpers/config_cfn_lint.json b/test/templates/good/core/config_cfn_lint.json
similarity index 100%
rename from test/templates/good/helpers/config_cfn_lint.json
rename to test/templates/good/core/config_cfn_lint.json
diff --git a/test/templates/good/helpers/config_cfn_lint.yaml b/test/templates/good/core/config_cfn_lint.yaml
similarity index 100%
rename from test/templates/good/helpers/config_cfn_lint.yaml
rename to test/templates/good/core/config_cfn_lint.yaml
diff --git a/test/templates/good/core/config_parameters.yaml b/test/templates/good/core/config_parameters.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/good/core/config_parameters.yaml
@@ -0,0 +1,8 @@
+---
+AWSTemplateFormatVersion: "2010-09-09"
+Metadata:
+ cfn-lint:
+ config:
+ ignore_checks:
+ - E0101
+Resources: {}
diff --git a/test/testlib/testcase.py b/test/testlib/testcase.py
--- a/test/testlib/testcase.py
+++ b/test/testlib/testcase.py
@@ -15,7 +15,7 @@
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from unittest import TestCase
-from cfnlint.parser import MarkedLoader, multi_constructor
+from cfnlint.cfn_yaml import MarkedLoader, multi_constructor
class BaseTestCase(TestCase):
diff --git a/test/transforms/__init__.py b/test/transforms/__init__.py
--- a/test/transforms/__init__.py
+++ b/test/transforms/__init__.py
@@ -14,7 +14,8 @@
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
-from cfnlint import Runner, TransformsCollection, DEFAULT_TRANSFORMSDIR
+from cfnlint import Runner, TransformsCollection
+from cfnlint.core import DEFAULT_TRANSFORMSDIR
from testlib.testcase import BaseTestCase
| Test command line argument processing
Just had an issue reported that would have hopefully been caught with testing of the parameters and how they are processed.
Add testing so we can make sure we are honoring the parameters correctly.
| #72 was a start of this. Included testing reading parameters out of a template. | 2018-05-20T13:44:19Z | [] | [] |
aws-cloudformation/cfn-lint | 83 | aws-cloudformation__cfn-lint-83 | [
"42"
] | d5e243a0767fc4f7b0b9976f24268eecc068a803 | diff --git a/src/cfnlint/helpers.py b/src/cfnlint/helpers.py
--- a/src/cfnlint/helpers.py
+++ b/src/cfnlint/helpers.py
@@ -58,6 +58,11 @@
'cn-north-1a', 'cn-north-1b',
]
+FUNCTIONS = [
+ 'Fn::Base64', 'Fn::GetAtt', 'Fn::GetAZs', 'Fn::ImportValue',
+ 'Fn::Join', 'Fn::Split', 'Fn::FindInMap', 'Fn::Select', 'Ref',
+ 'Fn::If', 'Fn::Contains', 'Fn::Sub', 'Fn::Cidr']
+
LIMITS = {
'mappings': {
'number': 100,
diff --git a/src/cfnlint/rules/resources/properties/Properties.py b/src/cfnlint/rules/resources/properties/Properties.py
--- a/src/cfnlint/rules/resources/properties/Properties.py
+++ b/src/cfnlint/rules/resources/properties/Properties.py
@@ -34,7 +34,16 @@ def __init__(self):
self.parameternames = {}
def primitivetypecheck(self, value, primtype, proppath):
- """Check primitive types"""
+ """
+ Check primitive types.
+ Only check that a primitive type is actual a primitive type:
+ - If its JSON let it go
+ - If its Conditions check each sub path of the condition
+ - If its a object make sure its a valid function and function
+ - If its a list raise an error
+
+ """
+
matches = list()
if isinstance(value, dict) and primtype == 'Json':
return matches
@@ -55,33 +64,8 @@ def primitivetypecheck(self, value, primtype, proppath):
'Fn::If', 'Fn::Contains', 'Fn::Sub', 'Fn::Cidr']:
message = 'Property %s has an illegal function %s' % ('/'.join(map(str, proppath)), sub_key)
matches.append(RuleMatch(proppath, message))
- elif isinstance(value, str):
- if primtype in ['Integer', 'Double', 'Long']:
- try:
- int(value)
- except ValueError:
- # LOGGER.error('Tried to convert %s to int. %s',
- # text[prop], Exception)
- message = 'Property %s should be of type Int/Boolean' % ('/'.join(map(str, proppath)))
- matches.append(RuleMatch(proppath, message))
- elif primtype == 'Boolean':
- if value not in ['true', 'false', 'True', 'False']:
- message = 'Property %s should be of type Boolean' % ('/'.join(map(str, proppath)))
- matches.append(RuleMatch(proppath, message))
- elif primtype != 'String':
- message = 'Property %s should be of type String' % ('/'.join(map(str, proppath)))
- matches.append(RuleMatch(proppath, message))
- elif isinstance(value, bool):
- if primtype != 'Boolean' and primtype != 'String':
- message = 'Property %s should be of type %s' % ('/'.join(map(str, proppath)), primtype)
- matches.append(RuleMatch(proppath, message))
- elif isinstance(value, int):
- if primtype in ['String', 'Double', 'Long']:
- pass
- # LOGGER.info('%s is an int but should be %s for resource %s',
- # text[prop], primtype, resourcename)
- elif primtype not in ['Integer', 'Long']:
- message = 'Property %s should be of type Integer' % ('/'.join(map(str, proppath)))
+ else:
+ message = 'Property is an object instead of %s at %s' % (primtype, '/'.join(map(str, proppath)))
matches.append(RuleMatch(proppath, message))
elif isinstance(value, list):
message = 'Property should be of type %s not List at %s' % (primtype, '/'.join(map(str, proppath)))
diff --git a/src/cfnlint/rules/resources/properties/ValuePrimitiveType.py b/src/cfnlint/rules/resources/properties/ValuePrimitiveType.py
new file mode 100644
--- /dev/null
+++ b/src/cfnlint/rules/resources/properties/ValuePrimitiveType.py
@@ -0,0 +1,114 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+import sys
+import six
+from cfnlint import CloudFormationLintRule
+from cfnlint import RuleMatch
+import cfnlint.helpers
+
+
+class ValuePrimitiveType(CloudFormationLintRule):
+ """Check if Resource PrimitiveTypes are correct"""
+ id = 'E3012'
+ shortdesc = 'Check resource properties values'
+ description = 'Checks resource property values with Primitive Types for ' \
+ 'values that match those types.'
+ tags = ['base', 'resources']
+
+ def __init__(self, ):
+ """Init """
+ specs = cfnlint.helpers.RESOURCE_SPECS.get('us-east-1')
+ self.property_specs = specs.get('PropertyTypes')
+ self.resource_specs = specs.get('ResourceTypes')
+ for resource_spec in self.resource_specs:
+ self.resource_property_types.append(resource_spec)
+ for property_spec in self.property_specs:
+ self.resource_sub_property_types.append(property_spec)
+
+ def check_value(self, value, path, **kwargs):
+ """Check Value"""
+ matches = list()
+ primitive_type = kwargs.get('primitive_type', {})
+ if isinstance(value, dict) and primitive_type == 'Json':
+ return matches
+ if primitive_type in ['String']:
+ if not isinstance(value, (str, six.text_type, six.string_types)):
+ message = 'Property %s should be of type String' % ('/'.join(map(str, path)))
+ matches.append(RuleMatch(path, message))
+ elif primitive_type in ['Boolean']:
+ if not isinstance(value, (bool)):
+ message = 'Property %s should be of type Boolean' % ('/'.join(map(str, path)))
+ matches.append(RuleMatch(path, message))
+ elif primitive_type in ['Double']:
+ if not isinstance(value, (float, int)):
+ message = 'Property %s should be of type Double' % ('/'.join(map(str, path)))
+ matches.append(RuleMatch(path, message))
+ elif primitive_type in ['Integer']:
+ if not isinstance(value, (int)):
+ message = 'Property %s should be of type Integer' % ('/'.join(map(str, path)))
+ matches.append(RuleMatch(path, message))
+ elif primitive_type in ['Long']:
+ if sys.version_info < (3,):
+ integer_types = (int, long,) # pylint: disable=undefined-variable
+ else:
+ integer_types = (int,)
+ if not isinstance(value, integer_types):
+ message = 'Property %s should be of type Long' % ('/'.join(map(str, path)))
+ matches.append(RuleMatch(path, message))
+ elif isinstance(value, list):
+ message = 'Property should be of type %s at %s' % (primitive_type, '/'.join(map(str, path)))
+ matches.append(RuleMatch(path, message))
+
+ return matches
+
+ def check(self, cfn, properties, specs, path):
+ """Check itself"""
+ matches = list()
+
+ for prop in properties:
+ if prop in specs:
+ primitive_type = specs.get(prop).get('PrimitiveType')
+ if not primitive_type:
+ primitive_type = specs.get(prop).get('PrimitiveItemType')
+
+ if primitive_type:
+ matches.extend(
+ cfn.check_value(
+ properties, prop, path,
+ check_value=self.check_value,
+ primitive_type=primitive_type
+ )
+ )
+
+ return matches
+
+ def match_resource_sub_properties(self, properties, property_type, path, cfn):
+ """Match for sub properties"""
+ matches = list()
+
+ property_specs = self.property_specs.get(property_type, {}).get('Properties', {})
+ matches.extend(self.check(cfn, properties, property_specs, path))
+
+ return matches
+
+ def match_resource_properties(self, properties, resource_type, path, cfn):
+ """Check CloudFormation Properties"""
+ matches = list()
+ resource_specs = self.resource_specs.get(resource_type, {}).get('Properties', {})
+ matches.extend(self.check(cfn, properties, resource_specs, path))
+
+ return matches
| diff --git a/test/module/test_cfn_json.py b/test/module/test_cfn_json.py
--- a/test/module/test_cfn_json.py
+++ b/test/module/test_cfn_json.py
@@ -34,7 +34,7 @@ def setUp(self):
self.filenames = {
"config_rule": {
"filename": 'templates/quickstart/config-rules.json',
- "failures": 0
+ "failures": 2
},
"iam": {
"filename": 'templates/quickstart/iam.json',
@@ -46,11 +46,11 @@ def setUp(self):
},
"vpc_management": {
"filename": 'templates/quickstart/vpc-management.json',
- "failures": 16
+ "failures": 32
},
"vpc": {
"filename": 'templates/quickstart/vpc.json',
- "failures": 1
+ "failures": 42
}
}
@@ -64,7 +64,7 @@ def test_success_parse(self):
matches = list()
matches.extend(self.rules.run(filename, cfn, []))
- assert len(matches) == failures, 'Expected {} failures, got {}'.format(failures, len(matches))
+ assert len(matches) == failures, 'Expected {} failures, got {} on {}'.format(failures, len(matches), filename)
def test_fail_run(self):
"""Test failure run"""
diff --git a/test/module/test_rules_collections.py b/test/module/test_rules_collections.py
--- a/test/module/test_rules_collections.py
+++ b/test/module/test_rules_collections.py
@@ -61,7 +61,7 @@ def test_fail_run(self):
matches = list()
matches.extend(self.rules.run(filename, cfn, []))
- assert(len(matches) == 25)
+ assert len(matches) == 27, 'Expected {} failures, got {}'.format(27, len(matches))
def test_fail_sub_properties_run(self):
"""Test failure run"""
@@ -74,4 +74,4 @@ def test_fail_sub_properties_run(self):
matches = list()
matches.extend(self.rules.run(filename, cfn, []))
- assert(len(matches) == 2)
+ assert len(matches) == 3, 'Expected {} failures, got {}'.format(2, len(matches))
diff --git a/test/rules/resources/properties/test_properties.py b/test/rules/resources/properties/test_properties.py
--- a/test/rules/resources/properties/test_properties.py
+++ b/test/rules/resources/properties/test_properties.py
@@ -35,7 +35,7 @@ def test_file_positive_template(self):
def test_file_negative(self):
"""Test failure"""
- self.helper_file_negative('templates/bad/generic.yaml', 7)
+ self.helper_file_negative('templates/bad/generic.yaml', 6)
def test_file_negative_2(self):
"""Failure test"""
@@ -43,4 +43,4 @@ def test_file_negative_2(self):
def test_file_negative_3(self):
"""Failure test"""
- self.helper_file_negative('templates/bad/resource_properties.yaml', 5)
+ self.helper_file_negative('templates/bad/resource_properties.yaml', 4)
diff --git a/test/templates/good/no_value.yaml b/test/templates/good/no_value.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/good/no_value.yaml
@@ -0,0 +1,161 @@
+---
+AWSTemplateFormatVersion: '2010-09-09'
+
+Description: MyApp RDS instances
+
+Parameters:
+ pApplicationName:
+ Type: String
+ Description: Application name (typically MyApp).
+ Default: MyApp
+ pMultiAZ:
+ Type: String
+ Description: Set to true to create instances in both AZs, false for one.
+ AllowedValues:
+ - true
+ - false
+ pEnhancedMonitoring:
+ Type: String
+ Description: Set to true to enable RDS enhanced monitoring, false to disable.
+ AllowedValues:
+ - true
+ - false
+ pDBAllocatedStorage:
+ Type: String
+ Description: The amount of disk storage allocated to the database server.
+ pDBParameterGroupFamily:
+ Type: String
+ Description: The RDS parameter group family.
+ pDBInstanceClass:
+ Type: String
+ Description: The RDS instance class.
+ pDBEngine:
+ Type: String
+ Description: The RDS Engine.
+ pDBEngineVersion:
+ Type: String
+ Description: The RDS Engine version.
+ pDBMasterUsername:
+ Type: String
+ Description: The DB Master Username.
+ pDBServerPort:
+ Type: Number
+ Description: The DB engine port. Valid values are 1150-65535 except for 1434, 3389, 47001, 49152, and 49152 through 49156.
+ Default: 1433
+ pProdMonitoringInterval:
+ Type: Number
+ Description: The interval, in seconds, between points when Enhanced Monitoring metrics are collected for the DB instance when running in the Prod stage.
+ Default: 60
+ pDevMonitoringInterval:
+ Type: Number
+ Description: The interval, in seconds, between points when Enhanced Monitoring metrics are collected for the DB instance when running in the Dev stage.
+ Default: 0
+
+Resources:
+
+ rParameterGroup:
+ Type: AWS::RDS::DBParameterGroup
+ Properties:
+ Description: !Join [' ', [!Ref pApplicationName, 'RDS Parameter Group.']]
+ Family: !Ref pDBParameterGroupFamily
+ Tags:
+ - Key: app
+ Value: !Ref pApplicationName
+ - Key: env
+ Value:
+ Fn::ImportValue: !Sub "${pApplicationName}:config:env"
+
+ rDBSubnetGroup:
+ Type: AWS::RDS::DBSubnetGroup
+ Properties:
+ DBSubnetGroupDescription: !Join [' ', [!Ref pApplicationName, 'RDS Subnet Group.']]
+ SubnetIds:
+ - Fn::ImportValue: !Sub "${pApplicationName}:subnet:data:1"
+ - Fn::ImportValue: !Sub "${pApplicationName}:subnet:data:2"
+ Tags:
+ - Key: app
+ Value: !Ref pApplicationName
+ - Key: env
+ Value:
+ Fn::ImportValue: !Sub "${pApplicationName}:config:env"
+
+ rDBPassword:
+ Type: Custom::Secret
+ Properties:
+ Name: !Sub "/passwords/rds/${AWS::StackName}"
+ KeyAlias: alias/aws/ssm
+ Alphabet: abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789
+ Length: 30
+ ReturnSecret: true
+ ServiceToken:
+ Fn::Join: [ ":", [ "arn:aws:lambda", !Ref "AWS::Region", ! "Ref": "AWS::AccountId", "function:binxio-cfn-secret-provider" ] ]
+
+ rDBMonitoringRole:
+ Type: AWS::IAM::Role
+ Condition: EnhancedMonitoring
+ Properties:
+ AssumeRolePolicyDocument:
+ Statement:
+ - Effect: Allow
+ Principal:
+ Service: monitoring.rds.amazonaws.com
+ Action: sts:AssumeRole
+ Policies:
+ - PolicyName: "MyAppRDSEnhancedMonitoring"
+ PolicyDocument:
+ Version: '2012-10-17'
+ Statement:
+ - Effect: Allow
+ Action:
+ - logs:CreateLogGroup
+ - logs:PutRetentionPolicy
+ Resource:
+ - arn:aws:logs:*:*:log-group:RDS*
+ - Effect: Allow
+ Action:
+ - logs:CreateLogStream
+ - logs:PutLogEvents
+ - logs:DescribeLogStreams
+ - logs:GetLogEvents
+ Resource:
+ - arn:aws:logs:*:*:log-group:RDS*:log-stream:*
+
+ rDBServerInstance:
+ Type: AWS::RDS::DBInstance
+ Properties:
+ AllocatedStorage: !Ref pDBAllocatedStorage
+ AllowMajorVersionUpgrade: False
+ AutoMinorVersionUpgrade: True
+ BackupRetentionPeriod: 35
+ CopyTagsToSnapshot: True
+ DBInstanceClass: !Ref pDBInstanceClass
+ DBParameterGroupName: !Ref rParameterGroup
+ DBSubnetGroupName: !Ref rDBSubnetGroup
+ Engine: !Ref pDBEngine
+ EngineVersion: !Ref pDBEngineVersion
+ LicenseModel: license-included
+ MasterUserPassword: !GetAtt [ rDBPassword, "Secret" ]
+ MasterUsername: !Ref pDBMasterUsername
+ # MonitoringInterval: !If [ EnhancedMonitoring, !Ref pProdMonitoringInterval, !Ref pDevMonitoringInterval ]
+ MonitoringRoleArn:
+ Fn::If:
+ - EnhancedMonitoring
+ - !GetAtt [ rDBMonitoringRole, Arn ]
+ - !Ref AWS::NoValue
+ MultiAZ: !If [ MultiAZ, true, false ]
+ Port: !Ref pDBServerPort
+ PubliclyAccessible: False
+ StorageEncrypted: True
+ StorageType: gp2
+ Tags:
+ - Key: app
+ Value: !Ref pApplicationName
+ - Key: env
+ Value:
+ Fn::ImportValue: !Sub "${pApplicationName}:config:env"
+ VPCSecurityGroups:
+ - Fn::ImportValue: !Sub "${pApplicationName}:sg:data"
+
+Conditions:
+ MultiAZ: !Equals [ !Ref pMultiAZ, true ]
+ EnhancedMonitoring: !Equals [ !Ref pEnhancedMonitoring, true ]
diff --git a/test/templates/quickstart/test.yaml b/test/templates/quickstart/test.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/quickstart/test.yaml
@@ -0,0 +1,157 @@
+---
+AWSTemplateFormatVersion: '2010-09-09'
+
+Description: MyApp RDS instances
+
+Parameters:
+ pApplicationName:
+ Type: String
+ Description: Application name (typically MyApp).
+ Default: MyApp
+ pMultiAZ:
+ Type: String
+ Description: Set to true to create instances in both AZs, false for one.
+ AllowedValues:
+ - true
+ - false
+ pEnhancedMonitoring:
+ Type: String
+ Description: Set to true to enable RDS enhanced monitoring, false to disable.
+ AllowedValues:
+ - true
+ - false
+ pDBAllocatedStorage:
+ Type: String
+ Description: The amount of disk storage allocated to the database server.
+ pDBParameterGroupFamily:
+ Type: String
+ Description: The RDS parameter group family.
+ pDBInstanceClass:
+ Type: String
+ Description: The RDS instance class.
+ pDBEngine:
+ Type: String
+ Description: The RDS Engine.
+ pDBEngineVersion:
+ Type: String
+ Description: The RDS Engine version.
+ pDBMasterUsername:
+ Type: String
+ Description: The DB Master Username.
+ pDBServerPort:
+ Type: Number
+ Description: The DB engine port. Valid values are 1150-65535 except for 1434, 3389, 47001, 49152, and 49152 through 49156.
+ Default: 1433
+ pProdMonitoringInterval:
+ Type: Number
+ Description: The interval, in seconds, between points when Enhanced Monitoring metrics are collected for the DB instance when running in the Prod stage.
+ Default: 60
+ pDevMonitoringInterval:
+ Type: Number
+ Description: The interval, in seconds, between points when Enhanced Monitoring metrics are collected for the DB instance when running in the Dev stage.
+ Default: 0
+
+Resources:
+
+ rParameterGroup:
+ Type: AWS::RDS::DBParameterGroup
+ Properties:
+ Description: !Join [' ', [!Ref pApplicationName, 'RDS Parameter Group.']]
+ Family: !Ref pDBParameterGroupFamily
+ Tags:
+ - Key: app
+ Value: !Ref pApplicationName
+ - Key: env
+ Value:
+ Fn::ImportValue: !Sub "${pApplicationName}:config:env"
+
+ rDBSubnetGroup:
+ Type: AWS::RDS::DBSubnetGroup
+ Properties:
+ DBSubnetGroupDescription: !Join [' ', [!Ref pApplicationName, 'RDS Subnet Group.']]
+ SubnetIds:
+ - Fn::ImportValue: !Sub "${pApplicationName}:subnet:data:1"
+ - Fn::ImportValue: !Sub "${pApplicationName}:subnet:data:2"
+ Tags:
+ - Key: app
+ Value: !Ref pApplicationName
+ - Key: env
+ Value:
+ Fn::ImportValue: !Sub "${pApplicationName}:config:env"
+
+ rDBPassword:
+ Type: Custom::Secret
+ Properties:
+ Name: !Sub "/passwords/rds/${AWS::StackName}"
+ KeyAlias: alias/aws/ssm
+ Alphabet: abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789
+ Length: 30
+ ReturnSecret: true
+ ServiceToken:
+ Fn::Join: [ ":", [ "arn:aws:lambda", !Ref "AWS::Region", ! "Ref": "AWS::AccountId", "function:binxio-cfn-secret-provider" ] ]
+
+ rDBMonitoringRole:
+ Type: AWS::IAM::Role
+ Condition: EnhancedMonitoring
+ Properties:
+ AssumeRolePolicyDocument:
+ Statement:
+ - Effect: Allow
+ Principal:
+ Service: monitoring.rds.amazonaws.com
+ Action: sts:AssumeRole
+ Policies:
+ - PolicyName: "MyAppRDSEnhancedMonitoring"
+ PolicyDocument:
+ Version: '2012-10-17'
+ Statement:
+ - Effect: Allow
+ Action:
+ - logs:CreateLogGroup
+ - logs:PutRetentionPolicy
+ Resource:
+ - arn:aws:logs:*:*:log-group:RDS*
+ - Effect: Allow
+ Action:
+ - logs:CreateLogStream
+ - logs:PutLogEvents
+ - logs:DescribeLogStreams
+ - logs:GetLogEvents
+ Resource:
+ - arn:aws:logs:*:*:log-group:RDS*:log-stream:*
+
+ rDBServerInstance:
+ Type: AWS::RDS::DBInstance
+ Properties:
+ AllocatedStorage: !Ref pDBAllocatedStorage
+ AllowMajorVersionUpgrade: False
+ AutoMinorVersionUpgrade: True
+ BackupRetentionPeriod: 35
+ CopyTagsToSnapshot: True
+ DBInstanceClass: !Ref pDBInstanceClass
+ DBParameterGroupName: !Ref rParameterGroup
+ DBSubnetGroupName: !Ref rDBSubnetGroup
+ Engine: !Ref pDBEngine
+ EngineVersion: !Ref pDBEngineVersion
+ LicenseModel: license-included
+ MasterUserPassword: !GetAtt [ rDBPassword, "Secret" ]
+ MasterUsername: !Ref pDBMasterUsername
+ MonitoringInterval: !If [ EnhancedMonitoring, !Ref pProdMonitoringInterval, !Ref pDevMonitoringInterval ]
+ MonitoringRoleArn: !If [ EnhancedMonitoring, !GetAtt rDBMonitoringRole.Arn, !Ref AWS::NoValue ]
+ MultiAZ: !If [ MultiAZ, true, false ]
+ Port: !Ref pDBServerPort
+ PubliclyAccessible: False
+ StorageEncrypted: True
+ StorageType: gp2
+ Tags:
+ - Key: app
+ Value: !Ref pApplicationName
+ - Key: env
+ Value:
+ Fn::ImportValue: !Sub "${pApplicationName}:config:env"
+ VPCSecurityGroups:
+ - Fn::ImportValue: !Sub "${pApplicationName}:sg:data"
+
+Conditions:
+ MultiAZ: !Equals [ !Ref pMultiAZ, true ]
+ EnhancedMonitoring: !Equals [ !Ref pEnhancedMonitoring, true ]
| Remove try... convert of integers (E3002)
In the property Type check, when the property value should be an integer (but it's not), there is an attempt to convert it:
https://github.com/awslabs/cfn-python-lint/blob/master/src/cfnlint/rules/resources/properties/Properties.py#L56
Since both YAML and JSON just handle these types out the box, the `try..except` can in theory be removed (since the type's don't match, a string is not an integer).
Personally I like the check to be more "strict', who do other think?
Example (JSON):
https://github.com/awslabs/cfn-python-lint/blob/master/test/templates/quickstart/vpc-management.json#L816
Example (YAML):
https://github.com/awslabs/cfn-python-lint/blob/master/test/templates/good/resource_properties.yaml#L464
These values can easily be written as actual integers
```
- CidrIp:
Ref: SSHLocation
FromPort: 22
IpProtocol: tcp
ToPort: 22
```
| To make sure I understand completely. You want numbers to not be strings at all? I started that way but after hitting a few quickstarts I noticed a large number of examples of people still using strings so I added that check.
@cmmeyer what do you think? This gets into this tricky space as the template would work but wouldn't follow best practices. This seems like something that should be a Warning not an Error.
Yup, that. We have the same in almost all out stacks: a lot of numbers specified as strings.
It's annoying but the types actually don't match, so semantically it's actually "wrong", althought it works.
Just a question because it works fine "as is", but don't mind it being strict.
Perhaps create a similar rule as a `warning` that actually breaks?
I actually have the reverse - an invalid integer where a String is required by CFN itself, that cfn-lint doesn't catch. The CloudFormation Designer doesn't catch it either.
In a https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-elasticbeanstalk-configurationtemplate-configurationoptionsetting.html all properties must be Strings.
For example, an entirely reasonable-looking, but wrong use of an integer:
```json
{
"Namespace": "aws:autoscaling:asg",
"OptionName": "MinSize",
"Value": 12
},
```
Does anyone know if the same bit of code is related, or do I need to hunt for a bug in the Specification?
@finchd and this fails when you launch to the stack? I think it’s a similar issue to what is being described. I think it’s a fair request by both to say that if it’s a string it’s a string and if it’s a number it’s a number and try not to translate it. We should be capturing your issue if that stack failed to deploy because of that issue. I will need to track that down if that’s the case. I’m not sure this is a spec issue as it looks like they use that generic property for string and number based values.
Yes, it definitely fails to create the stack: "Value of property Value must be of type String"
`aws cloudformation validate-template` succeeds with no errors either.
Thanks. I’ll take a look at it tonight. We should be catching that
After chatting with @kddejong tonight, I'm in the camp of strong enforcement of types. It may trigger a lot of errors/warnings in old templates, but it's an opportunity to polish them up. It'll be like when I first added the Flake8 linter to Atom. :) | 2018-05-23T16:34:29Z | [] | [] |
aws-cloudformation/cfn-lint | 91 | aws-cloudformation__cfn-lint-91 | [
"86"
] | bdcbe910eb4768758725e5c7f2b3c8120525662a | diff --git a/src/cfnlint/__init__.py b/src/cfnlint/__init__.py
--- a/src/cfnlint/__init__.py
+++ b/src/cfnlint/__init__.py
@@ -833,3 +833,11 @@ def run(self):
if not any(match == u for u in return_matches):
return_matches.append(match)
return return_matches
+
+
+class ParseError(cfnlint.CloudFormationLintRule):
+ """Parse Lint Rule"""
+ id = 'E0000'
+ shortdesc = 'Parsing error found when parsing the template'
+ description = 'Checks for Null values and Duplicate values in resources'
+ tags = ['base']
diff --git a/src/cfnlint/__main__.py b/src/cfnlint/__main__.py
--- a/src/cfnlint/__main__.py
+++ b/src/cfnlint/__main__.py
@@ -24,13 +24,13 @@
def main():
"""Main function"""
- (args, template, rules) = cfnlint.core.get_template_args_rules(sys.argv[1:])
+ (args, template, rules, fmt, formatter) = cfnlint.core.get_template_args_rules(sys.argv[1:])
return(
cfnlint.core.run_cli(
- vars(args)['template'], template, rules, vars(args)['format'],
+ vars(args)['template'], template, rules, fmt,
vars(args)['ignore_checks'], vars(args)['regions'],
- vars(args)['override_spec']))
+ vars(args)['override_spec'], formatter))
if __name__ == '__main__':
diff --git a/src/cfnlint/cfn_json.py b/src/cfnlint/cfn_json.py
--- a/src/cfnlint/cfn_json.py
+++ b/src/cfnlint/cfn_json.py
@@ -18,12 +18,26 @@
import json
from json.decoder import WHITESPACE, WHITESPACE_STR, BACKSLASH, STRINGCHUNK
from json.scanner import NUMBER_RE
-from cfnlint.cfn_yaml import DuplicateError, NullError
+import cfnlint
LOGGER = logging.getLogger(__name__)
+class DuplicateError(Exception):
+ """
+ Error thrown when the template contains duplicates
+ """
+ pass
+
+
+class NullError(Exception):
+ """
+ Error thrown when the template contains Nulls
+ """
+ pass
+
+
def check_duplicates(ordered_pairs):
"""
Check for duplicate keys on the current level, this is not desirable
@@ -50,7 +64,7 @@ class JSONDecodeError(ValueError):
colno: The column corresponding to pos
"""
# Note that this exception is used from _json
- def __init__(self, msg, doc, pos):
+ def __init__(self, msg, doc, pos, key=' '):
lineno = doc.count('\n', 0, pos) + 1
colno = pos - doc.rfind('\n', 0, pos)
errmsg = '%s: line %d column %d (char %d)' % (msg, lineno, colno, pos)
@@ -60,6 +74,9 @@ def __init__(self, msg, doc, pos):
self.pos = pos
self.lineno = lineno
self.colno = colno
+ self.match = cfnlint.Match(
+ lineno, colno + 1, lineno,
+ colno + 1 + len(key), '', cfnlint.ParseError(), message=msg)
def __reduce__(self):
return self.__class__, (self.msg, self.doc, self.pos)
@@ -262,9 +279,9 @@ def CfnJSONObject(s_and_end, strict, scan_once, object_hook, object_pairs_hook,
try:
result = object_pairs_hook(pairs)
except DuplicateError as err:
- raise JSONDecodeError('Duplicate found {}'.format(err), s, end)
+ raise JSONDecodeError('Duplicate found {}'.format(err), s, begin, key)
except NullError as err:
- raise JSONDecodeError('Null Error {}'.format(err), s, end)
+ raise JSONDecodeError('Null Error {}'.format(err), s, begin, key)
return result, end
pairs = dict(pairs)
if object_hook is not None:
diff --git a/src/cfnlint/cfn_yaml.py b/src/cfnlint/cfn_yaml.py
--- a/src/cfnlint/cfn_yaml.py
+++ b/src/cfnlint/cfn_yaml.py
@@ -26,6 +26,7 @@
from yaml import MappingNode
from yaml.constructor import SafeConstructor
from yaml.constructor import ConstructorError
+import cfnlint
UNCONVERTED_SUFFIXES = ['Ref', 'Condition']
FN_PREFIX = 'Fn::'
@@ -33,18 +34,22 @@
LOGGER = logging.getLogger(__name__)
-class DuplicateError(ConstructorError):
+class CfnParseError(ConstructorError):
"""
- Error thrown when the template contains duplicates
+ Error thrown when the template contains Cfn Error
"""
- pass
+ def __init__(self, message, line_number, column_number, key=' '):
+ # Call the base class constructor with the parameters it needs
+ super(CfnParseError, self).__init__(message)
-class NullError(ConstructorError):
- """
- Error thrown when the template contains Nulls
- """
- pass
+ # Now for your custom code...
+ self.line_number = line_number
+ self.column_number = column_number
+ self.message = message
+ self.match = cfnlint.Match(
+ line_number + 1, column_number + 1, line_number + 1,
+ column_number + 1 + len(key), '', cfnlint.ParseError(), message=message)
def create_node_class(cls):
@@ -93,7 +98,9 @@ def construct_yaml_map(self, node):
value = self.construct_object(value_node, False)
if key in mapping:
- raise DuplicateError('"{}" (line {})'.format(key, key_node.start_mark.line + 1))
+ raise CfnParseError(
+ 'Duplicate resource found "{}" (line {})'.format(key, key_node.start_mark.line + 1),
+ key_node.start_mark.line, key_node.start_mark.column, key)
mapping[key] = value
obj, = SafeConstructor.construct_yaml_map(self, node)
@@ -110,7 +117,9 @@ def construct_yaml_str(self, node):
def construct_yaml_null_error(self, node):
"""Throw a null error"""
- raise NullError('Null value at line {0} column {1}'.format(node.start_mark.line, node.start_mark.column))
+ raise CfnParseError(
+ 'Null value at line {0} column {1}'.format(node.start_mark.line, node.start_mark.column),
+ node.start_mark.line, node.start_mark.column, ' ')
NodeConstructor.add_constructor(
diff --git a/src/cfnlint/core.py b/src/cfnlint/core.py
--- a/src/cfnlint/core.py
+++ b/src/cfnlint/core.py
@@ -18,6 +18,10 @@
import sys
import os
import json
+try:
+ from json.decoder import JSONDecodeError
+except ImportError:
+ JSONDecodeError = ValueError
import argparse
import six
from yaml.parser import ParserError, ScannerError
@@ -40,11 +44,9 @@ def error(self, message):
self.exit(32, '%s: error: %s\n' % (self.prog, message))
-def run_cli(filename, template, rules, fmt, ignore_checks, regions, override_spec):
+def run_cli(filename, template, rules, fmt, ignore_checks, regions, override_spec, formatter):
"""Process args and run"""
- formatter = get_formatter(fmt)
-
if override_spec:
cfnlint.helpers.override_specs(override_spec)
@@ -53,11 +55,7 @@ def run_cli(filename, template, rules, fmt, ignore_checks, regions, override_spe
filename, template, rules, transforms, ignore_checks,
regions)
- if fmt == 'json':
- print(json.dumps(matches, indent=4, cls=CustomEncoder))
- else:
- for match in matches:
- print(formatter.format(match))
+ print_matches(matches, fmt, formatter)
return get_exit_code(matches)
@@ -195,6 +193,9 @@ def get_template_args_rules(cli_args):
args = parser.parse_known_args(cli_args)
configure_logging(vars(args[0])['log_level'])
+ fmt = vars(args[0])['format']
+ formatter = get_formatter(fmt)
+
if vars(args[0])['template']:
filename = vars(args[0])['template']
ignore_bad_template = vars(args[0])['ignore_bad_template']
@@ -214,31 +215,40 @@ def get_template_args_rules(cli_args):
elif e.errno == 13:
LOGGER.error('Permission denied when accessing template file: %s', filename)
sys.exit(1)
- except cfnlint.cfn_yaml.DuplicateError as err:
- LOGGER.error('Template %s contains duplicates: %s', filename, err)
- sys.exit(1)
- except cfnlint.cfn_yaml.NullError as err:
- LOGGER.error('Template %s contains nulls: %s', filename, err)
- sys.exit(1)
- except (ParserError, ScannerError) as err:
- try:
- template = json.load(open(filename), cls=cfnlint.cfn_json.CfnJSONDecoder)
- except cfnlint.cfn_json.JSONDecodeError as json_err:
- if ignore_bad_template:
- LOGGER.info('Template %s is malformed: %s', filename, err.problem)
- LOGGER.error('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
- else:
- LOGGER.error('Template %s is malformed: %s', filename, err.problem)
- LOGGER.error('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
- sys.exit(1)
- except Exception as json_err: # pylint: disable=W0703
- if ignore_bad_template:
- LOGGER.info('Template %s is malformed: %s', filename, err.problem)
- LOGGER.info('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
- else:
- LOGGER.error('Template %s is malformed: %s', filename, err.problem)
- LOGGER.error('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
- sys.exit(1)
+ except cfnlint.cfn_yaml.CfnParseError as err:
+ err.match.Filename = filename
+ matches = [err.match]
+ print_matches(matches, fmt, formatter)
+ sys.exit(get_exit_code(matches))
+ except ParserError as err:
+ matches = [create_match_yaml_parser_error(err, filename)]
+ print_matches(matches, fmt, formatter)
+ sys.exit(get_exit_code(matches))
+ except ScannerError as err:
+ if err.problem == 'found character \'\\t\' that cannot start any token':
+ try:
+ template = json.load(open(filename), cls=cfnlint.cfn_json.CfnJSONDecoder)
+ except cfnlint.cfn_json.JSONDecodeError as json_err:
+ json_err.match.filename = filename
+ matches = [json_err.match]
+ print_matches(matches, fmt, formatter)
+ sys.exit(get_exit_code(matches))
+ except JSONDecodeError as json_err:
+ matches = [create_match_json_parser_error(json_err, filename)]
+ print_matches(matches, fmt, formatter)
+ sys.exit(get_exit_code(matches))
+ except Exception as json_err: # pylint: disable=W0703
+ if ignore_bad_template:
+ LOGGER.info('Template %s is malformed: %s', filename, err.problem)
+ LOGGER.info('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
+ else:
+ LOGGER.error('Template %s is malformed: %s', filename, err.problem)
+ LOGGER.error('Tried to parse %s as JSON but got error: %s', filename, str(json_err))
+ sys.exit(1)
+ else:
+ matches = [create_match_yaml_parser_error(err, filename)]
+ print_matches(matches, fmt, formatter)
+ sys.exit(get_exit_code(matches))
append_parser(parser, defaults)
args = parser.parse_args(cli_args)
@@ -257,7 +267,7 @@ def get_template_args_rules(cli_args):
parser.print_help()
exit(1)
- return(args, template, rules)
+ return(args, template, rules, fmt, formatter)
def get_default_args(template):
@@ -317,6 +327,39 @@ def run_checks(filename, template, rules, transforms, ignore_checks, regions):
return(matches)
+def print_matches(matches, fmt, formatter):
+ """Print matches"""
+ if fmt == 'json':
+ print(json.dumps(matches, indent=4, cls=CustomEncoder))
+ else:
+ for match in matches:
+ print(formatter.format(match))
+
+
+def create_match_yaml_parser_error(parser_error, filename):
+ """Create a Match for a parser error"""
+ lineno = parser_error.problem_mark.line + 1
+ colno = parser_error.problem_mark.column + 1
+ msg = parser_error.problem
+ return cfnlint.Match(
+ lineno, colno, lineno, colno + 1, filename,
+ cfnlint.ParseError(), message=msg)
+
+
+def create_match_json_parser_error(parser_error, filename):
+ """Create a Match for a parser error"""
+ if sys.version_info[0] == 3:
+ lineno = parser_error.lineno
+ colno = parser_error.colno
+ msg = parser_error.msg
+ elif sys.version_info[0] == 2:
+ lineno = 1
+ colno = 1
+ msg = parser_error.message
+ return cfnlint.Match(
+ lineno, colno, lineno, colno + 1, filename, cfnlint.ParseError(), message=msg)
+
+
class CustomEncoder(json.JSONEncoder):
"""Custom Encoding for the Match Object"""
# pylint: disable=E0202
| diff --git a/test/module/core/test_run_checks.py b/test/module/core/test_run_checks.py
--- a/test/module/core/test_run_checks.py
+++ b/test/module/core/test_run_checks.py
@@ -27,7 +27,7 @@ def test_good_template(self):
"""Test success run"""
filename = 'templates/good/generic.yaml'
- (args, template, rules) = cfnlint.core.get_template_args_rules([
+ (args, template, rules, _, _) = cfnlint.core.get_template_args_rules([
'--template', filename])
results = cfnlint.core.run_checks(
@@ -39,7 +39,7 @@ def test_bad_template(self):
"""Test bad template"""
filename = 'templates/quickstart/nat-instance.json'
- (args, template, rules) = cfnlint.core.get_template_args_rules([
+ (args, template, rules, _, _) = cfnlint.core.get_template_args_rules([
'--template', filename])
results = cfnlint.core.run_checks(
diff --git a/test/module/core/test_run_cli.py b/test/module/core/test_run_cli.py
--- a/test/module/core/test_run_cli.py
+++ b/test/module/core/test_run_cli.py
@@ -47,7 +47,7 @@ def test_template_invalid_yaml(self):
cfnlint.core.get_template_args_rules([
'--template', filename])
- self.assertEqual(exit_code.exception.code, 1)
+ self.assertEqual(exit_code.exception.code, 2)
def test_template_invalid_json(self):
"""Test template not found"""
@@ -57,49 +57,32 @@ def test_template_invalid_json(self):
cfnlint.core.get_template_args_rules([
'--template', filename])
- self.assertEqual(exit_code.exception.code, 1)
+ self.assertEqual(exit_code.exception.code, 2)
def test_template_invalid_yaml_ignore(self):
"""Test template not found"""
filename = 'templates/bad/core/config_invalid_yaml.yaml'
- (args, _, _) = cfnlint.core.get_template_args_rules([
- '--template', filename, '--ignore-bad-template'])
+ with self.assertRaises(SystemExit) as exit_code:
+ cfnlint.core.get_template_args_rules([
+ '--template', filename, '--ignore-bad-template'])
- self.assertEqual(vars(args), {
- 'append_rules': [],
- 'format': None,
- 'ignore_bad_template': True,
- 'ignore_checks': [],
- 'listrules': False,
- 'log_level': None,
- 'override_spec': None,
- 'regions': ['us-east-1'],
- 'template': 'templates/bad/core/config_invalid_yaml.yaml',
- 'update_specs': False})
+ self.assertEqual(exit_code.exception.code, 2)
def test_template_invalid_json_ignore(self):
"""Test template not found"""
filename = 'templates/bad/core/config_invalid_json.json'
- (args, _, _) = cfnlint.core.get_template_args_rules([
- '--template', filename, '--ignore-bad-template'])
- self.assertEqual(vars(args), {
- 'append_rules': [],
- 'format': None,
- 'ignore_bad_template': True,
- 'ignore_checks': [],
- 'listrules': False,
- 'log_level': None,
- 'override_spec': None,
- 'regions': ['us-east-1'],
- 'template': 'templates/bad/core/config_invalid_json.json',
- 'update_specs': False})
+ with self.assertRaises(SystemExit) as exit_code:
+ cfnlint.core.get_template_args_rules([
+ '--template', filename, '--ignore-bad-template'])
+
+ self.assertEqual(exit_code.exception.code, 2)
def test_template_config(self):
"""Test template config"""
filename = 'templates/good/core/config_parameters.yaml'
- (args, _, _) = cfnlint.core.get_template_args_rules([
+ (args, _, _, _, _) = cfnlint.core.get_template_args_rules([
'--template', filename, '--ignore-bad-template'])
self.assertEqual(vars(args), {
@@ -117,7 +100,7 @@ def test_template_config(self):
def test_override_parameters(self):
"""Test overriding parameters"""
filename = 'templates/good/core/config_parameters.yaml'
- (args, _, _) = cfnlint.core.get_template_args_rules([
+ (args, _, _, _, _) = cfnlint.core.get_template_args_rules([
'--template', filename, '--ignore-bad-template',
'--ignore-checks', 'E0000'])
@@ -137,7 +120,7 @@ def test_bad_config(self):
""" Test bad formatting in config"""
filename = 'templates/bad/core/config_parameters.yaml'
- (args, _, _) = cfnlint.core.get_template_args_rules([
+ (args, _, _, _, _) = cfnlint.core.get_template_args_rules([
'--template', filename, '--ignore-bad-template'])
self.assertEqual(vars(args), {
diff --git a/test/module/test_duplicate.py b/test/module/test_duplicate.py
--- a/test/module/test_duplicate.py
+++ b/test/module/test_duplicate.py
@@ -42,7 +42,7 @@ def test_success_run(self):
loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
loader.add_multi_constructor('!', cfnlint.cfn_yaml.multi_constructor)
loader.get_single_data()
- except cfnlint.cfn_yaml.DuplicateError:
+ except cfnlint.cfn_yaml.CfnParseError:
assert(False)
return
@@ -74,7 +74,7 @@ def test_fail_yaml_run(self):
loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
loader.add_multi_constructor('!', cfnlint.cfn_yaml.multi_constructor)
loader.get_single_data()
- except cfnlint.cfn_yaml.DuplicateError:
+ except cfnlint.cfn_yaml.CfnParseError:
assert(True)
return
diff --git a/test/module/test_null_values.py b/test/module/test_null_values.py
--- a/test/module/test_null_values.py
+++ b/test/module/test_null_values.py
@@ -42,7 +42,7 @@ def test_success_run(self):
loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
loader.add_multi_constructor('!', cfnlint.cfn_yaml.multi_constructor)
loader.get_single_data()
- except cfnlint.cfn_yaml.NullError:
+ except cfnlint.cfn_yaml.CfnParseError:
assert(False)
return
@@ -74,7 +74,7 @@ def test_fail_yaml_run(self):
loader = cfnlint.cfn_yaml.MarkedLoader(fp.read())
loader.add_multi_constructor('!', cfnlint.cfn_yaml.multi_constructor)
loader.get_single_data()
- except cfnlint.cfn_yaml.NullError:
+ except cfnlint.cfn_yaml.CfnParseError:
assert(True)
return
| AWS::NoValue without quotes causes error: "Template is malformed: found unexpected ':'"
I'm getting an error with this template, but CFN builds it fine, and the js cfn-linter claims it has no errors or warnings.
**Debug Logs:**
```
$ cfn-lint --template templates/rds.yaml --log-level debug
2018-05-24 10:54:46,166 - cfnlint - ERROR - Template templates/rds.yaml is malformed: found unexpected ':'
2018-05-24 10:54:46,166 - cfnlint - ERROR - Tried to parse templates/rds.yaml as JSON but got error: Expecting value: line 1 column 1 (char 0)
```
If I comment out the `MonitoringInterval` and `MonitoringRoleArn` in the `rDBServerInstance` resource, the error seems to go away. So it seems related to my !If statements.
These lines appear to be the issue:
```
MonitoringInterval: !If [ EnhancedMonitoring, !Ref pProdMonitoringInterval, !Ref pDevMonitoringInterval ]
MonitoringRoleArn: !If [ EnhancedMonitoring, !GetAtt [ rDBMonitoringRole, Arn ], !Ref AWS::NoValue ]
```
In fact, if I comment out just `MonitoringRoleArn` I get an entirely different failure.
**Debug Logs:**
```
cfn-lint --template templates/rds.yaml --log-level debug
2018-05-24 11:02:20,595 - cfnlint - DEBUG - Transform templates if needed
2018-05-24 11:02:20,596 - cfnlint - DEBUG - Run scan of template...
...
2018-05-24 11:02:20,606 - cfnlint - DEBUG - Starting match function for rule E3002 at 2018-05-24 11:02:20.606796
2018-05-24 11:02:20,606 - cfnlint - DEBUG - Get names of all parameters from template...
2018-05-24 11:02:20,607 - cfnlint - DEBUG - Get resources from template...
2018-05-24 11:02:20,607 - cfnlint - DEBUG - Get condition values...
2018-05-24 11:02:20,607 - cfnlint - DEBUG - Get condition values...
2018-05-24 11:02:20,607 - cfnlint - DEBUG - Complete match function for rule E3002 at 2018-05-24 11:02:20.607507. Ran in 0:00:00.000713
2018-05-24 11:02:20,607 - cfnlint - DEBUG - Results from rule E3002 are [<cfnlint.RuleMatch object at 0x10907c240>, <cfnlint.RuleMatch object at 0x108fa1f28>]:
2018-05-24 11:02:20,607 - cfnlint - DEBUG - Get location of path ['Resources', 'rDBServerInstance', 'Properties', 'MonitoringInterval', 1, 'Ref']
2018-05-24 11:02:20,607 - cfnlint - DEBUG - Get location of path ['rDBServerInstance', 'Properties', 'MonitoringInterval', 1, 'Ref']
2018-05-24 11:02:20,607 - cfnlint - DEBUG - Get location of path ['Properties', 'MonitoringInterval', 1, 'Ref']
2018-05-24 11:02:20,607 - cfnlint - DEBUG - Get location of path ['MonitoringInterval', 1, 'Ref']
2018-05-24 11:02:20,608 - cfnlint - DEBUG - Get location of path [1, 'Ref']
2018-05-24 11:02:20,608 - cfnlint - ERROR - Tried to process rules on file templates/rds.yaml but got an error: 1
```
**js cfn-lint:**
```
$ /usr/local/bin/cfn-lint validate templates/rds.yaml
0 infos
0 warn
0 crit
Template valid!
```
**Template:**
```
---
AWSTemplateFormatVersion: '2010-09-09'
Description: MyApp RDS instances
Parameters:
pApplicationName:
Type: String
Description: Application name (typically MyApp).
Default: MyApp
pMultiAZ:
Type: String
Description: Set to true to create instances in both AZs, false for one.
AllowedValues:
- true
- false
pEnhancedMonitoring:
Type: String
Description: Set to true to enable RDS enhanced monitoring, false to disable.
AllowedValues:
- true
- false
pDBAllocatedStorage:
Type: String
Description: The amount of disk storage allocated to the database server.
pDBParameterGroupFamily:
Type: String
Description: The RDS parameter group family.
pDBInstanceClass:
Type: String
Description: The RDS instance class.
pDBEngine:
Type: String
Description: The RDS Engine.
pDBEngineVersion:
Type: String
Description: The RDS Engine version.
pDBMasterUsername:
Type: String
Description: The DB Master Username.
pDBServerPort:
Type: Number
Description: The DB engine port. Valid values are 1150-65535 except for 1434, 3389, 47001, 49152, and 49152 through 49156.
Default: 1433
pProdMonitoringInterval:
Type: Number
Description: The interval, in seconds, between points when Enhanced Monitoring metrics are collected for the DB instance when running in the Prod stage.
Default: 60
pDevMonitoringInterval:
Type: Number
Description: The interval, in seconds, between points when Enhanced Monitoring metrics are collected for the DB instance when running in the Dev stage.
Default: 0
Resources:
rParameterGroup:
Type: AWS::RDS::DBParameterGroup
Properties:
Description: !Join [' ', [!Ref pApplicationName, 'RDS Parameter Group.']]
Family: !Ref pDBParameterGroupFamily
Tags:
- Key: app
Value: !Ref pApplicationName
- Key: env
Value:
Fn::ImportValue: !Sub "${pApplicationName}:config:env"
rDBSubnetGroup:
Type: AWS::RDS::DBSubnetGroup
Properties:
DBSubnetGroupDescription: !Join [' ', [!Ref pApplicationName, 'RDS Subnet Group.']]
SubnetIds:
- Fn::ImportValue: !Sub "${pApplicationName}:subnet:data:1"
- Fn::ImportValue: !Sub "${pApplicationName}:subnet:data:2"
Tags:
- Key: app
Value: !Ref pApplicationName
- Key: env
Value:
Fn::ImportValue: !Sub "${pApplicationName}:config:env"
rDBPassword:
Type: Custom::Secret
Properties:
Name: !Sub "/passwords/rds/${AWS::StackName}"
KeyAlias: alias/aws/ssm
Alphabet: abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789
Length: 30
ReturnSecret: true
ServiceToken:
Fn::Join: [ ":", [ "arn:aws:lambda", !Ref "AWS::Region", ! "Ref": "AWS::AccountId", "function:binxio-cfn-secret-provider" ] ]
rDBMonitoringRole:
Type: AWS::IAM::Role
Condition: EnhancedMonitoring
Properties:
AssumeRolePolicyDocument:
Statement:
- Effect: Allow
Principal:
Service: monitoring.rds.amazonaws.com
Action: sts:AssumeRole
Policies:
- PolicyName: "MyAppRDSEnhancedMonitoring"
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- logs:CreateLogGroup
- logs:PutRetentionPolicy
Resource:
- arn:aws:logs:*:*:log-group:RDS*
- Effect: Allow
Action:
- logs:CreateLogStream
- logs:PutLogEvents
- logs:DescribeLogStreams
- logs:GetLogEvents
Resource:
- arn:aws:logs:*:*:log-group:RDS*:log-stream:*
rDBServerInstance:
Type: AWS::RDS::DBInstance
Properties:
AllocatedStorage: !Ref pDBAllocatedStorage
AllowMajorVersionUpgrade: False
AutoMinorVersionUpgrade: True
BackupRetentionPeriod: 35
CopyTagsToSnapshot: True
DBInstanceClass: !Ref pDBInstanceClass
DBParameterGroupName: !Ref rParameterGroup
DBSubnetGroupName: !Ref rDBSubnetGroup
Engine: !Ref pDBEngine
EngineVersion: !Ref pDBEngineVersion
LicenseModel: license-included
MasterUserPassword: !GetAtt [ rDBPassword, "Secret" ]
MasterUsername: !Ref pDBMasterUsername
MonitoringInterval: !If [ EnhancedMonitoring, !Ref pProdMonitoringInterval, !Ref pDevMonitoringInterval ]
MonitoringRoleArn: !If [ EnhancedMonitoring, !GetAtt [ rDBMonitoringRole, Arn ], !Ref AWS::NoValue ]
MultiAZ: !If [ MultiAZ, true, false ]
Port: !Ref pDBServerPort
PubliclyAccessible: False
StorageEncrypted: True
StorageType: gp2
Tags:
- Key: app
Value: !Ref pApplicationName
- Key: env
Value:
Fn::ImportValue: !Sub "${pApplicationName}:config:env"
VPCSecurityGroups:
- Fn::ImportValue: !Sub "${pApplicationName}:sg:data"
Conditions:
MultiAZ: !Equals [ !Ref pMultiAZ, true ]
EnhancedMonitoring: !Equals [ !Ref pEnhancedMonitoring, true ]
```
| Ok I found two issues.
1. I'm going to have to dig a little deeper. It looks like the Python YAML parser doesn't handle `AWS::NoValue` without quotes very well. @cmmeyer says this should work but we are getting into the details of how the Python yaml parser works to figure out why this didn't work.
2. Found an issue that I'm going to submit shortly with how conditions are handled.
#87 should fix the second issue and added tests to make sure continue to cover this appropriately.
for the first one the quickest fix for you is to quote AWS::NoValue until we can do more testing and get a fix out for that.
Thanks, updated the title to reflect the fault a little better for others to find it.
@alytle and @cmmeyer I have a few updates on this... if you take this template and try to implement it (via the AWS Console) you get `Template validation error: Template format error: YAML not well-formed. (line 140, column 102)`
From what I can tell `AWS::NoValue` (without quotes) works fine as long as it isn't in short hand function that has a list behind it. So !Ref is fine but !If, !Select, etc. is not.
As an example this works for cfn-lint and CloudFormation service.
```
MonitoringRoleArn:
Fn::If:
- EnhancedMonitoring
- !GetAtt [ rDBMonitoringRole, Arn ]
- !Ref AWS::NoValue
```
This will also work for cfn-lint and CloudFormation service
```
MonitoringRoleArn: !Ref AWS::NoValue
```
So I'm actually thinking we are consistent with how CloudFormation service works but failing in showing what the parse error is. | 2018-05-25T19:01:29Z | [] | [] |
aws-cloudformation/cfn-lint | 98 | aws-cloudformation__cfn-lint-98 | [
"93"
] | 9a342f8be2630b0851827dd426a3d0b6893c03b7 | diff --git a/src/cfnlint/rules/parameters/Cidr.py b/src/cfnlint/rules/parameters/Cidr.py
--- a/src/cfnlint/rules/parameters/Cidr.py
+++ b/src/cfnlint/rules/parameters/Cidr.py
@@ -19,7 +19,7 @@
class Cidr(CloudFormationLintRule):
- """Check Availibility Zone parameter checks """
+ """Check Availability Zone parameter checks """
id = 'W2509'
shortdesc = 'CIDR Parameters have allowed values'
description = 'Check if a parameter is being used as a CIDR. ' \
@@ -49,8 +49,8 @@ def __init__(self):
'AWS::EC2::SecurityGroup.Ingress',
]
- for resoruce_type_spec in resource_type_specs:
- self.resource_property_types.append(resoruce_type_spec)
+ for resource_type_spec in resource_type_specs:
+ self.resource_property_types.append(resource_type_spec)
for property_type_spec in property_type_specs:
self.resource_sub_property_types.append(property_type_spec)
@@ -62,9 +62,10 @@ def check_cidr_ref(self, value, path, parameters, resources):
if value in parameters:
parameter = parameters.get(value, {})
allowed_pattern = parameter.get('AllowedPattern', None)
- if not allowed_pattern:
+ allowed_values = parameter.get('AllowedValues', None)
+ if not allowed_pattern and not allowed_values:
param_path = ['Parameters', value]
- message = 'AllowedPattern for Parameter should be specified at {1}. Example "{0}"'
+ message = 'AllowedPattern and/or AllowedValues for Parameter should be specified at {1}. Example for AllowedPattern "{0}"'
matches.append(RuleMatch(param_path, message.format(self.cidr_regex, ('/'.join(param_path)))))
return matches
diff --git a/src/cfnlint/rules/parameters/CidrAllowedValues.py b/src/cfnlint/rules/parameters/CidrAllowedValues.py
new file mode 100644
--- /dev/null
+++ b/src/cfnlint/rules/parameters/CidrAllowedValues.py
@@ -0,0 +1,125 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+import re
+from cfnlint import CloudFormationLintRule
+from cfnlint import RuleMatch
+
+
+class CidrAllowedValues(CloudFormationLintRule):
+ """Check Availability Zone parameter checks """
+ id = 'E2004'
+ shortdesc = 'CIDR Allowed Values should be a Cidr Range'
+ description = 'Check if a parameter is being used as a CIDR. ' \
+ 'If it is make sure allowed values are proper CIDRs'
+ tags = ['base', 'parameters', 'cidr']
+
+ # pylint: disable=C0301
+ cidr_regex = r'^(([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])\.){3}([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])(\/([0-9]|[1-2][0-9]|3[0-2]))$'
+
+ def __init__(self):
+ """Init"""
+ resource_type_specs = [
+ 'AWS::EC2::Subnet',
+ 'AWS::EC2::Vpc',
+ 'AWS::RDS::DBSecurityGroupIngress',
+ 'AWS::EC2::NetworkAclEntry',
+ 'AWS::EC2::SecurityGroupIngress',
+ 'AWS::EC2::SecurityGroupEgress',
+ 'AWS::Redshift::ClusterSecurityGroupIngress',
+ 'AWS::EC2::VPCCidrBlock',
+ ]
+
+ property_type_specs = [
+ 'AWS::RDS::DBSecurityGroup.Ingress',
+ 'AWS::EC2::SecurityGroup.Egress',
+ 'AWS::SES::ReceiptFilter.IpFilter',
+ 'AWS::EC2::SecurityGroup.Ingress',
+ ]
+
+ for resource_type_spec in resource_type_specs:
+ self.resource_property_types.append(resource_type_spec)
+ for property_type_spec in property_type_specs:
+ self.resource_sub_property_types.append(property_type_spec)
+
+ # pylint: disable=W0613
+ def check_cidr_ref(self, value, path, parameters, resources):
+ """Check ref for VPC"""
+ matches = list()
+
+ if value in parameters:
+ parameter = parameters.get(value, {})
+ allowed_values = parameter.get('AllowedValues', None)
+ if allowed_values:
+ for cidr in allowed_values:
+ pattern = re.compile(self.cidr_regex)
+ if not pattern.match(cidr):
+ cidr_path = ['Parameters', value]
+ message = 'Cidr should be a Cidr Range based string for {0}'
+ matches.append(RuleMatch(cidr_path, message.format(cidr)))
+
+ return matches
+
+ def check(self, properties, resource_type, path, cfn):
+ """Check itself"""
+ matches = list()
+
+ matches.extend(
+ cfn.check_value(
+ properties, 'CIDRIP', path,
+ check_value=None, check_ref=self.check_cidr_ref,
+ check_mapping=None, check_split=None, check_join=None
+ )
+ )
+ matches.extend(
+ cfn.check_value(
+ properties, 'Cidr', path,
+ check_value=None, check_ref=self.check_cidr_ref,
+ check_mapping=None, check_split=None, check_join=None
+ )
+ )
+ matches.extend(
+ cfn.check_value(
+ properties, 'CidrBlock', path,
+ check_value=None, check_ref=self.check_cidr_ref,
+ check_mapping=None, check_split=None, check_join=None
+ )
+ )
+ matches.extend(
+ cfn.check_value(
+ properties, 'CidrIp', path,
+ check_value=None, check_ref=self.check_cidr_ref,
+ check_mapping=None, check_split=None, check_join=None
+ )
+ )
+
+ return matches
+
+ def match_resource_sub_properties(self, properties, property_type, path, cfn):
+ """Match for sub properties"""
+ matches = list()
+
+ matches.extend(self.check(properties, property_type, path, cfn))
+
+ return matches
+
+ def match_resource_properties(self, properties, resource_type, path, cfn):
+ """Check CloudFormation Properties"""
+ matches = list()
+
+ matches.extend(self.check(properties, resource_type, path, cfn))
+
+ return matches
| diff --git a/test/rules/parameters/test_cidr_allowed_values.py b/test/rules/parameters/test_cidr_allowed_values.py
new file mode 100644
--- /dev/null
+++ b/test/rules/parameters/test_cidr_allowed_values.py
@@ -0,0 +1,38 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+from cfnlint.rules.parameters.CidrAllowedValues import CidrAllowedValues # pylint: disable=E0401
+from .. import BaseRuleTestCase
+
+
+class TestParameterCidrAllowedValues(BaseRuleTestCase):
+ """Test template parameter configurations"""
+ def setUp(self):
+ """Setup"""
+ super(TestParameterCidrAllowedValues, self).setUp()
+ self.collection.register(CidrAllowedValues())
+
+ success_templates = [
+ 'templates/good/properties_ec2_vpc.yaml',
+ ]
+
+ def test_file_positive(self):
+ """Test Positive"""
+ self.helper_file_positive()
+
+ def test_file_negative(self):
+ """Test failure"""
+ self.helper_file_negative('templates/bad/properties_ec2_network.yaml', 3)
diff --git a/test/templates/bad/properties_ec2_network.yaml b/test/templates/bad/properties_ec2_network.yaml
--- a/test/templates/bad/properties_ec2_network.yaml
+++ b/test/templates/bad/properties_ec2_network.yaml
@@ -5,6 +5,12 @@ Description: >
Parameters:
cidrBlock:
Type: Number
+ cidrBlockAllowedValues:
+ Type: String
+ AllowedValues:
+ - '127.0.0.1'
+ - '8.8.8.8'
+ - 'notacidr'
vpcTenancy:
Type: String
AllowedValues:
@@ -23,6 +29,11 @@ Resources:
Properties:
InstanceTenancy: !Ref vpcTenancy
CidrBlock: 10.0.0.3
+ myVpc3:
+ Type: AWS::EC2::VPC
+ Properties:
+ InstanceTenancy: !Ref vpcTenancy
+ CidrBlock: !Ref cidrBlockAllowedValues
mySubnet2-1:
Type: AWS::EC2::Subnet
Properties:
diff --git a/test/templates/good/properties_ec2_vpc.yaml b/test/templates/good/properties_ec2_vpc.yaml
--- a/test/templates/good/properties_ec2_vpc.yaml
+++ b/test/templates/good/properties_ec2_vpc.yaml
@@ -3,9 +3,20 @@ AWSTemplateFormatVersion: "2010-09-09"
Description: >
AWS EC2 Good Template
Parameters:
- cidrBlock:
+ cidrBlockAllowedPattern:
Type: String
AllowedPattern: '^(([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])\.){3}([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])(\/([0-9]|[1-2][0-9]|3[0-2]))$'
+ cidrBlockAllowedValues:
+ Type: String
+ AllowedValues:
+ - '127.0.0.1/32'
+ - '8.8.8.8/32'
+ cidrBlockAllowedPatternValues:
+ Type: String
+ AllowedPattern: '^(([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])\.){3}([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])(\/([0-9]|[1-2][0-9]|3[0-2]))$'
+ AllowedValues:
+ - '127.0.0.1/32'
+ - '8.8.8.8/32'
vpcTenancy:
Type: String
AllowedValues:
@@ -15,23 +26,33 @@ Resources:
myVpc1:
Type: AWS::EC2::VPC
Properties:
- CidrBlock: !Ref cidrBlock
+ CidrBlock: !Ref cidrBlockAllowedPattern
InstanceTenancy: default
myVpc2:
Type: AWS::EC2::VPC
Properties:
InstanceTenancy: !Ref vpcTenancy
- CidrBlock: !Ref cidrBlock
+ CidrBlock: !Ref cidrBlockAllowedPattern
+ myVpc3:
+ Type: AWS::EC2::VPC
+ Properties:
+ InstanceTenancy: !Ref vpcTenancy
+ CidrBlock: !Ref cidrBlockAllowedValues
+ myVpc4:
+ Type: AWS::EC2::VPC
+ Properties:
+ InstanceTenancy: !Ref vpcTenancy
+ CidrBlock: !Ref cidrBlockAllowedPatternValues
mySubnet21:
Type: AWS::EC2::Subnet
Properties:
CidrBlock:
Fn::Select:
- 0
- - !Cidr [!Ref cidrBlock, 3, 16]
+ - !Cidr [!Ref cidrBlockAllowedPattern, 3, 16]
VpcId: vpc-1234567
mySubnet22:
Type: AWS::EC2::Subnet
Properties:
- CidrBlock: !Ref cidrBlock
+ CidrBlock: !Ref cidrBlockAllowedPattern
VpcId: vpc-1234567
| Unsupported AllowedValues in parameter Cidr linter
The Paramter Cidr linter checks for an AllowedPattern, but it's also possible that a Cidr parameter is controlled with `AllowedValues`. This makes the check on the `AllowedPattern` obsolete:
https://github.com/awslabs/cfn-python-lint/blob/master/src/cfnlint/rules/parameters/Cidr.py#L65
Besides that the allowed values itself are not checked.
Example:
```
EgressOracle:
Type: "String"
AllowedValues:
- "XXX.XXX.XXX.XXX/28" # Testing
- "YYY.YYY.YYY.YYY/28" # Production
Description: "Egress (Outbound) CIDR for Oracle connectivity (port 1521)"
```
This raises the
```
AllowedPattern for Parameter should be specified at Parameters/EgressOracle. Example "^(([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])\.){3}([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])(\/([0-9]|[1-2][0-9]|3[0-2]))$"
```
While there are AllowedValues that specify it. But those aren't checked, so this would be "OK" according to the current code:
```
EgressOracle:
Type: "String"
AllowedValues:
- "XXX.XXX.XXX.XXX" # Testing
- "YYY.YYY.YYY.YYY" # Production
Description: "Egress (Outbound) CIDR for Oracle connectivity (port 1521)"
```
There should be support for `AllowedValues`:
* Don't raise the AllowedPattern Warning if there are AllowedValues
* If there are AllowedValues, check those values for valid Cidr's
| @kddejong / @cmmeyer Can I be assigned to this issue? We're working on this, so PR will be coming soon.
(Just making issues of all remaining things that we encounter in our stacks to get a clear overview)
makes sense to me. thanks @fatbasstard | 2018-05-31T12:00:53Z | [] | [] |
aws-cloudformation/cfn-lint | 100 | aws-cloudformation__cfn-lint-100 | [
"99"
] | bfa56e41ed492962d1e4dd745f2590e79900d331 | diff --git a/src/cfnlint/rules/functions/Ref.py b/src/cfnlint/rules/functions/Ref.py
--- a/src/cfnlint/rules/functions/Ref.py
+++ b/src/cfnlint/rules/functions/Ref.py
@@ -31,11 +31,11 @@ def match(self, cfn):
matches = list()
- ref_objs = cfn.search_deep_keys('Fn::Ref')
+ ref_objs = cfn.search_deep_keys('Ref')
for ref_obj in ref_objs:
value = ref_obj[-1]
- if not isinstance(value, six.string_types):
+ if not isinstance(value, (six.string_types, six.text_type)):
message = 'Ref can only be a string for {0}'
matches.append(RuleMatch(ref_obj[:-1], message.format('/'.join(map(str, ref_obj[:-1])))))
diff --git a/src/cfnlint/rules/functions/RefExist.py b/src/cfnlint/rules/functions/RefExist.py
--- a/src/cfnlint/rules/functions/RefExist.py
+++ b/src/cfnlint/rules/functions/RefExist.py
@@ -65,11 +65,12 @@ def match(self, cfn):
# start with the basic ref calls
for reftree in reftrees:
ref = reftree[-1]
- if ref not in valid_refs:
- message = 'Ref {0} not found as a resource or parameter'
- matches.append(RuleMatch(
- reftree[:-2], message.format(ref)
- ))
+ if isinstance(ref, (six.string_types, six.text_type, int)):
+ if ref not in valid_refs:
+ message = 'Ref {0} not found as a resource or parameter'
+ matches.append(RuleMatch(
+ reftree[:-2], message.format(ref)
+ ))
for subtree in subtrees:
sub = subtree[-1]
parammatches = []
diff --git a/src/cfnlint/rules/functions/RefInCondition.py b/src/cfnlint/rules/functions/RefInCondition.py
new file mode 100644
--- /dev/null
+++ b/src/cfnlint/rules/functions/RefInCondition.py
@@ -0,0 +1,45 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+import six
+from cfnlint import CloudFormationLintRule
+from cfnlint import RuleMatch
+
+
+class RefInCondition(CloudFormationLintRule):
+ """Check if Ref value is a string"""
+ id = 'E1026'
+ shortdesc = 'Cannot reference resources in the Conditions block of the template'
+ description = 'Check that any Refs in the Conditions block uses no resources'
+ tags = ['base', 'functions', 'ref']
+
+ def match(self, cfn):
+ """Check CloudFormation Ref"""
+
+ matches = list()
+
+ ref_objs = cfn.search_deep_keys('Ref')
+ resource_names = cfn.get_resource_names()
+
+ for ref_obj in ref_objs:
+ if ref_obj[0] == 'Conditions':
+ value = ref_obj[-1]
+ if isinstance(value, (six.string_types, six.text_type, int)):
+ if value in resource_names:
+ message = 'Cannot reference resource {0} in the Conditions block of the template at {1}'
+ matches.append(RuleMatch(ref_obj[:-1], message.format(value, '/'.join(map(str, ref_obj[:-1])))))
+
+ return matches
diff --git a/src/cfnlint/rules/resources/CircularDependency.py b/src/cfnlint/rules/resources/CircularDependency.py
--- a/src/cfnlint/rules/resources/CircularDependency.py
+++ b/src/cfnlint/rules/resources/CircularDependency.py
@@ -93,12 +93,13 @@ def match(self, cfn):
resources = {}
for ref_obj in ref_objs:
value = ref_obj[-1]
- ref_type, ref_name = ref_obj[:2]
- if ref_type == 'Resources':
- if cfn.template.get('Resources', {}).get(value, {}):
- if not resources.get(ref_name):
- resources[ref_name] = []
- resources[ref_name].append(value)
+ if isinstance(value, (six.text_type, six.string_types, int)):
+ ref_type, ref_name = ref_obj[:2]
+ if ref_type == 'Resources':
+ if cfn.template.get('Resources', {}).get(value, {}):
+ if not resources.get(ref_name):
+ resources[ref_name] = []
+ resources[ref_name].append(value)
getatt_objs = cfn.search_deep_keys('Fn::GetAtt')
for getatt_obj in getatt_objs:
| diff --git a/test/rules/functions/test_ref.py b/test/rules/functions/test_ref.py
new file mode 100644
--- /dev/null
+++ b/test/rules/functions/test_ref.py
@@ -0,0 +1,34 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+from cfnlint.rules.functions.Ref import Ref # pylint: disable=E0401
+from .. import BaseRuleTestCase
+
+
+class TestRulesRef(BaseRuleTestCase):
+ """Test Rules Ref exists """
+ def setUp(self):
+ """Setup"""
+ super(TestRulesRef, self).setUp()
+ self.collection.register(Ref())
+
+ def test_file_positive(self):
+ """Test Positive"""
+ self.helper_file_positive()
+
+ def test_file_negative(self):
+ """Test failure"""
+ self.helper_file_negative('templates/bad/functions/ref.yaml', 1)
diff --git a/test/rules/functions/test_ref_exist.py b/test/rules/functions/test_ref_exist.py
--- a/test/rules/functions/test_ref_exist.py
+++ b/test/rules/functions/test_ref_exist.py
@@ -31,4 +31,4 @@ def test_file_positive(self):
def test_file_negative(self):
"""Test failure"""
- self.helper_file_negative('templates/bad/functions_ref.yaml', 5)
+ self.helper_file_negative('templates/bad/functions/ref.yaml', 5)
diff --git a/test/rules/functions/test_ref_in_condition.py b/test/rules/functions/test_ref_in_condition.py
new file mode 100644
--- /dev/null
+++ b/test/rules/functions/test_ref_in_condition.py
@@ -0,0 +1,34 @@
+"""
+ Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this
+ software and associated documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to use, copy, modify,
+ merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""
+from cfnlint.rules.functions.RefInCondition import RefInCondition # pylint: disable=E0401
+from .. import BaseRuleTestCase
+
+
+class TestRulesRefInCondition(BaseRuleTestCase):
+ """Test Rules Ref exists """
+ def setUp(self):
+ """Setup"""
+ super(TestRulesRefInCondition, self).setUp()
+ self.collection.register(RefInCondition())
+
+ def test_file_positive(self):
+ """Test Positive"""
+ self.helper_file_positive()
+
+ def test_file_negative(self):
+ """Test failure"""
+ self.helper_file_negative('templates/bad/functions/ref.yaml', 1)
diff --git a/test/templates/bad/functions/ref.yaml b/test/templates/bad/functions/ref.yaml
new file mode 100644
--- /dev/null
+++ b/test/templates/bad/functions/ref.yaml
@@ -0,0 +1,71 @@
+---
+AWSTemplateFormatVersion: "2010-09-09"
+Parameters:
+ myVpcId:
+ Description: MyVpc Id
+ Type: AWS::EC2::VPC::Id
+Conditions:
+ cVpc: !Equals [!Ref mySecurityGroupVpc1, 'VpcId']
+Resources:
+ mySecurityGroupVpc1:
+ Type: AWS::EC2::SecurityGroup
+ Properties:
+ GroupDescription: !Ref [ 1 ]
+ VpcId: !Ref myVpcId
+ SecurityGroupIngress:
+ -
+ IpProtocol: 1
+ SourceSecurityGroupId: 'sg-1234567'
+ -
+ IpProtocol: 1
+ SourceSecurityGroupId: !Ref mySecurityGroupVpc2
+ mySecurityGroupVpc2:
+ Type: AWS::EC2::SecurityGroup
+ Properties:
+ GroupDescription: 'Security Group Vpc 2'
+ VpcId: !Ref myVpcId
+ SecurityGroupIngress:
+ -
+ IpProtocol: 1
+ SourceSecurityGroupId: !Ref mySecurityGroupVpc1
+ MyEC2Instance:
+ Type: "AWS::EC2::Instance"
+ Properties:
+ ImageId: "ami-2f726546"
+ InstanceType: t1.micro
+ KeyName: testkey
+ BlockDeviceMappings:
+ -
+ DeviceName: /dev/sdm
+ Ebs:
+ VolumeType: io1
+ Iops: !Ref pIops
+ DeleteOnTermination: false
+ VolumeSize: 20
+ NetworkInterfaces:
+ - DeviceIndex: "1"
+ # Package doesn't exist as parameter
+ UserData: !Sub |
+ yum install ${Package}
+ AnotherInstance:
+ Type: "AWS::EC2::Instance"
+ Properties:
+ ImageId: "ami-2f726546"
+ InstanceType: t1.micro
+ KeyName: testkey
+ BlockDeviceMappings:
+ -
+ DeviceName: /dev/sdm
+ Ebs:
+ VolumeType: io1
+ Iops: !Ref pIops
+ DeleteOnTermination: false
+ VolumeSize: 20
+ NetworkInterfaces:
+ - DeviceIndex: "1"
+ # Package doesn't exist as parameter
+ UserData:
+ Fn::Sub:
+ - "yum install ${myPackage} ${Package}"
+ -
+ myPackage: !Ref httpdPackage
| FindInMap in Conditions
```
Conditions:
cCreate:
Fn::Equals:
- !FindInMap [myMap, !Ref myInstance1, instance ]
- true
Resources:
myInstance1:
Condition: cCreate
Type: AWS::EC2::Instance
Properties:
ImageId: abc-1234567
```
should result in `Template validation error: Template format error: Unresolved dependencies [myInstance1]. Cannot reference resources in the Conditions block of the template`
New rule has alerts on any Ref in the Conditions block thats go to a Resource.
| 2018-06-01T03:03:31Z | [] | [] |
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