text: #!/usr/bin/env python3
  
  ###############################################################################
  #                                                                             #
  # RMG - Reaction Mechanism Generator                                          #
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  # Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu),           #
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  ###############################################################################
  
  import logging
  import unittest
  from copy import deepcopy
  
  from rmgpy.kinetics.arrhenius import Arrhenius
  from rmgpy.pdep.collision import SingleExponentialDown
  from rmgpy.pdep.configuration import Configuration
  from rmgpy.pdep.network import Network
  from rmgpy.reaction import Reaction
  from rmgpy.rmg.pdep import PDepNetwork
  from rmgpy.species import Species, TransitionState
  from rmgpy.statmech.conformer import Conformer
  from rmgpy.statmech.rotation import NonlinearRotor
  from rmgpy.statmech.torsion import HinderedRotor
  from rmgpy.statmech.translation import IdealGasTranslation
  from rmgpy.statmech.vibration import HarmonicOscillator
  from rmgpy.transport import TransportData
  
  
  ###################################################
  
  class TestPdep(unittest.TestCase):
  
      def setUp(self):
          """
          A method that is run before each unit test in this class.
          """
          self.nC4H10O = Species(
              label='n-C4H10O',
              conformer=Conformer(
                  E0=(-317.807, 'kJ/mol'),
                  modes=[
                      IdealGasTranslation(mass=(74.07, "g/mol")),
                      NonlinearRotor(inertia=([41.5091, 215.751, 233.258], "amu*angstrom^2"), symmetry=1),
                      HarmonicOscillator(frequencies=(
                      [240.915, 341.933, 500.066, 728.41, 809.987, 833.93, 926.308, 948.571, 1009.3, 1031.46, 1076,
                       1118.4, 1184.66, 1251.36, 1314.36, 1321.42, 1381.17, 1396.5, 1400.54, 1448.08, 1480.18, 1485.34,
                       1492.24, 1494.99, 1586.16, 2949.01, 2963.03, 2986.19, 2988.1, 2995.27, 3026.03, 3049.05, 3053.47,
                       3054.83, 3778.88], "cm^-1")),
                      HinderedRotor(inertia=(0.854054, "amu*angstrom^2"), symmetry=1, fourier=(
                      [[0.25183, -1.37378, -2.8379, 0.0305112, 0.0028088],
                       [0.458307, 0.542121, -0.599366, -0.00283925, 0.0398529]], "kJ/mol")),
                      HinderedRotor(inertia=(8.79408, "amu*angstrom^2"), symmetry=1, fourier=(
                      [[0.26871, -0.59533, -8.15002, -0.294325, -0.145357],
                       [1.1884, 0.99479, -0.940416, -0.186538, 0.0309834]], "kJ/mol")),
                      HinderedRotor(inertia=(7.88153, "amu*angstrom^2"), symmetry=1, fourier=(
                      [[-4.67373, 2.03735, -6.25993, -0.27325, -0.048748],
                       [-0.982845, 1.76637, -1.57619, 0.474364, -0.000681718]], "kJ/mol")),
                      HinderedRotor(inertia=(2.81525, "amu*angstrom^2"), symmetry=3, barrier=(2.96807, "kcal/mol")),
                  ],
                  spin_multiplicity=1,
                  optical_isomers=1,
              ),
              molecular_weight=(74.07, "g/mol"),
              transport_data=TransportData(sigma=(5.94, 'angstrom'), epsilon=(559, 'K')),
              energy_transfer_model=SingleExponentialDown(alpha0=(447.5 * 0.011962, "kJ/mol"), T0=(300, "K"), n=0.85),
          )
  
          self.nC4H10O.from_smiles('CCCCO')
  
          self.nC4H8 = Species(
              label='n-C4H8',
              conformer=Conformer(
                  E0=(-17.8832, 'kJ/mol'),
                  modes=[
                      IdealGasTranslation(mass=(56.06, "g/mol")),
                      NonlinearRotor(inertia=([22.2748, 122.4, 125.198], "amu*angstrom^2"), symmetry=1),
                      HarmonicOscillator(frequencies=(
                      [308.537, 418.67, 636.246, 788.665, 848.906, 936.762, 979.97, 1009.48, 1024.22, 1082.96, 1186.38,
                       1277.55, 1307.65, 1332.87, 1396.67, 1439.09, 1469.71, 1484.45, 1493.19, 1691.49, 2972.12, 2994.31,
                       3018.48, 3056.87, 3062.76, 3079.38, 3093.54, 3174.52], "cm^-1")),
                      HinderedRotor(inertia=(5.28338, "amu*angstrom^2"), symmetry=1, fourier=(
                      [[-0.579364, -0.28241, -4.46469, 0.143368, 0.126756],
                       [1.01804, -0.494628, -0.00318651, -0.245289, 0.193728]], "kJ/mol")),
                      HinderedRotor(inertia=(2.60818, "amu*angstrom^2"), symmetry=3, fourier=(
                      [[0.0400372, 0.0301986, -6.4787, -0.0248675, -0.0324753],
                       [0.0312541, 0.0538, -0.493785, 0.0965968, 0.125292]], "kJ/mol")),
                  ],
                  spin_multiplicity=1,
                  optical_isomers=1,
              ),
          )
  
          self.nC4H8.from_smiles('CCC=C')
  
          self.H2O = Species(
              label='H2O',
              conformer=Conformer(
                  E0=(-269.598, 'kJ/mol'),
                  modes=[
                      IdealGasTranslation(mass=(18.01, "g/mol")),
                      NonlinearRotor(inertia=([0.630578, 1.15529, 1.78586], "amu*angstrom^2"), symmetry=2),
                      HarmonicOscillator(frequencies=([1622.09, 3771.85, 3867.85], "cm^-1")),
                  ],
                  spin_multiplicity=1,
                  optical_isomers=1,
              ),
          )
  
          self.H2O.from_smiles('O')
  
          self.N2 = Species(
              label='N2',
              molecular_weight=(28.04, "g/mol"),
              transport_data=TransportData(sigma=(3.41, "angstrom"), epsilon=(124, "K")),
              energy_transfer_model=None,
          )
  
          self.N2.from_smiles('N#N')
  
          logging.error('to TS')
  
          self.TS = TransitionState(
              label='TS',
              conformer=Conformer(
                  E0=(-42.4373, "kJ/mol"),
                  modes=[
                      IdealGasTranslation(mass=(74.07, "g/mol")),
                      NonlinearRotor(inertia=([40.518, 232.666, 246.092], "u*angstrom**2"), symmetry=1, quantum=False),
                      HarmonicOscillator(frequencies=(
                      [134.289, 302.326, 351.792, 407.986, 443.419, 583.988, 699.001, 766.1, 777.969, 829.671, 949.753,
                       994.731, 1013.59, 1073.98, 1103.79, 1171.89, 1225.91, 1280.67, 1335.08, 1373.9, 1392.32, 1417.43,
                       1469.51, 1481.61, 1490.16, 1503.73, 1573.16, 2972.85, 2984.3, 3003.67, 3045.78, 3051.77, 3082.37,
                       3090.44, 3190.73, 3708.52], "kayser")),
                      HinderedRotor(inertia=(2.68206, "amu*angstrom^2"), symmetry=3, barrier=(3.35244, "kcal/mol")),
                      HinderedRotor(inertia=(9.77669, "amu*angstrom^2"), symmetry=1, fourier=(
                      [[0.208938, -1.55291, -4.05398, -0.105798, -0.104752],
                       [2.00518, -0.020767, -0.333595, 0.137791, -0.274578]], "kJ/mol")),
                  ],
                  spin_multiplicity=1,
                  optical_isomers=1,
              ),
              frequency=(-2038.34, 'cm^-1'),
          )
  
          self.reaction = Reaction(
              label='dehydration',
              reactants=[self.nC4H10O],
              products=[self.nC4H8, self.H2O],
              transition_state=self.TS,
              kinetics=Arrhenius(A=(0.0387, 'm^3/(mol*s)'), n=2.7, Ea=(2.6192e4, 'J/mol'), T0=(1, 'K'))
          )
  
          self.network = Network(
              label='n-butanol',
              isomers=[Configuration(self.nC4H10O)],
              reactants=[],
              products=[Configuration(self.nC4H8, self.H2O)],
              path_reactions=[self.reaction],
              bath_gas={self.N2: 1.0},
          )
  
          self.pdepnetwork = deepcopy(self.network)
          self.pdepnetwork.__class__ = PDepNetwork
          self.pdepnetwork.source = [self.pdepnetwork.isomers[0].species[0]]
          self.pdepnetwork.index = 1
          self.pdepnetwork.explored = []
  
      def test_energy_filter(self):
          rxns = self.pdepnetwork.get_energy_filtered_reactions(1000.0, 0.0)
          self.assertEquals(len(rxns), 1)
          self.assertEquals(rxns[0], self.pdepnetwork.path_reactions[0])
  
      def test_flux_filter(self):
          prods = self.pdepnetwork.get_rate_filtered_products(1000.0, 100000.0, 1.0)
          self.assertEquals(len(prods), 0)
  
  
  if __name__ == '__main__':
      unittest.main()
  