# -*- coding: utf-8 -*-

"""
    Pair-state basis level diagram calculations

    Calculates Rydberg spaghetti of level diagrams, as well as pertubative C6
    and similar properties. It also allows calculation of Foster resonances
    tuned by DC electric fields.

    Example:
        Calculation of the Rydberg eigenstates in pair-state basis for Rubidium
        in the vicinity of the
        :math:`|60~S_{1/2}~m_j=1/2,~60~S_{1/2}~m_j=1/2\\rangle` state. Colour
        highlights coupling strength from state :math:`6~P_{1/2}~m_j=1/2` with
        :math:`\\pi` (:math:`q=0`) polarized light.
        eigenstates::

            from arc import *
            calc1 = PairStateInteractions(Rubidium(), 60, 0, 0.5, 60, 0, 0.5,0.5, 0.5)
            calc1.defineBasis( 0., 0., 4, 5,10e9)
            # optionally we can save now results of calculation for future use
            saveCalculation(calc1,"mycalculation.pkl")
            calculation1.diagonalise(linspace(1,10.0,30),250,progressOutput = True,drivingFromState=[6,1,0.5,0.5,0])
            calc1.plotLevelDiagram()
            calc1.ax.set_xlim(1,10)
            calc1.ax.set_ylim(-2,2)
            calc1.showPlot()

"""

from __future__ import division, print_function, absolute_import

from .wigner import Wigner6j, Wigner3j, CG, WignerDmatrix
from .alkali_atom_functions import _atomLightAtomCoupling
from scipy.constants import physical_constants, pi
import gzip
import sys
import datetime
import matplotlib
from matplotlib.colors import LinearSegmentedColormap
from .calculations_atom_single import StarkMap
from .alkali_atom_functions import *
from .divalent_atom_functions import DivalentAtom
from scipy.special import factorial
from scipy import floor
from scipy.sparse.linalg import eigsh
from scipy.sparse import csr_matrix
from numpy.lib.polynomial import real
from numpy.ma import conjugate
from scipy.optimize import curve_fit
from scipy.constants import e as C_e
from scipy.constants import h as C_h
from scipy.constants import c as C_c
from scipy.constants import k as C_k
import re
import numpy as np
from math import exp, sqrt
import matplotlib.pyplot as plt
import matplotlib as mpl
mpl.rcParams['xtick.minor.visible'] = True
mpl.rcParams['ytick.minor.visible'] = True
mpl.rcParams['xtick.major.size'] = 8
mpl.rcParams['ytick.major.size'] = 8
mpl.rcParams['xtick.minor.size'] = 4
mpl.rcParams['ytick.minor.size'] = 4
mpl.rcParams['xtick.direction'] = 'in'
mpl.rcParams['ytick.direction'] = 'in'
mpl.rcParams['xtick.top'] = True
mpl.rcParams['ytick.right'] = True
mpl.rcParams['font.family'] = 'serif'


# for matrices


if sys.version_info > (2,):
    xrange = range


DPATH = os.path.join(os.path.expanduser('~'), '.arc-data')


class PairStateInteractions:
    """
        Calculates Rydberg level diagram (spaghetti) for the given pair state

        Initializes Rydberg level spaghetti calculation for the given atom
        species (or for two atoms of different species) in the vicinity
        of the given pair state. For details of calculation see
        Ref. [1]_. For a quick start point example see
        `interactions example snippet`_.
        For inter-species calculations see
        `inter-species interaction calculation snippet`_.

        .. _`interactions example snippet`:
            ./Rydberg_atoms_a_primer.html#Short-range-interactions

        .. _`inter-species interaction calculation snippet`:
           ./ARC_3_0_introduction.html#Inter-species-pair-state-calculations

        Parameters:
            atom (:obj:`arc.alkali_atom_functions.AlkaliAtom` or :obj:`arc.divalent_atom_functions.DivalentAtom`):
                = {
                :obj:`arc.alkali_atom_data.Lithium6`,
                :obj:`arc.alkali_atom_data.Lithium7`,
                :obj:`arc.alkali_atom_data.Sodium`,
                :obj:`arc.alkali_atom_data.Potassium39`,
                :obj:`arc.alkali_atom_data.Potassium40`,
                :obj:`arc.alkali_atom_data.Potassium41`,
                :obj:`arc.alkali_atom_data.Rubidium85`,
                :obj:`arc.alkali_atom_data.Rubidium87`,
                :obj:`arc.alkali_atom_data.Caesium`,
                :obj:`arc.divalent_atom_data.Strontium88`,
                :obj:`arc.divalent_atom_data.Calcium40`
                :obj:`arc.divalent_atom_data.Ytterbium174` }
                Select the alkali metal for energy level
                diagram calculation
            n (int): 
                principal quantum number for the *first* atom
            l (int):
                orbital angular momentum for the *first* atom
            j (float):
                total angular momentum for the *first* atom
            nn (int):
                principal quantum number for the *second* atom
            ll (int):
                orbital angular momentum for the *second* atom
            jj (float):
                total angular momentum for the *second* atom
            m1 (float):
                projection of the total angular momentum on z-axis
                for the *first* atom
            m2 (float):
                projection of the total angular momentum on z-axis
                for the *second* atom
            interactionsUpTo (int):
                Optional. If set to 1, includes only
                dipole-dipole interactions. If set to 2 includes interactions
                up to quadrupole-quadrupole. Default value is 1.
            s (float):
                optional, spin state of the first atom. Default value
                of 0.5 is correct for :obj:`arc.alkali_atom_functions.AlkaliAtom`
                but for :obj:`arc.divalent_atom_functions.DivalentAtom`
                it has to be explicitly set to 0 or 1 for
                singlet and triplet states respectively.
                **If `s2` is not specified, it is assumed that the second
                atom is in the same spin state.**
            s2 (float):
                optinal, spin state of the second atom. If not
                specified (left to default value None) it will assume spin
                state of the first atom.
            atom2 (:obj:`arc.alkali_atom_functions.AlkaliAtom` or :obj:`arc.divalent_atom_functions.DivalentAtom`):
                optional,
                specifies atomic species for the second atom, enabeling
                calculation of **inter-species pair-state interactions**.
                If not specified (left to default value None) it will assume
                spin state of the first atom.

        References:
            .. [1] T. G Walker, M. Saffman, PRA **77**, 032723 (2008)
                https://doi.org/10.1103/PhysRevA.77.032723

        Examples:
            **Advanced interfacing of pair-state is2=None, atom2=Nonenteractions calculations
            (PairStateInteractions class).** This
            is an advanced example intended for building up extensions to the
            existing code. If you want to directly access the pair-state
            interaction matrix, constructed by :obj:`defineBasis`,
            you can assemble it easily from diagonal part
            (stored in :obj:`matDiagonal` ) and off-diagonal matrices whose
            spatial dependence is :math:`R^{-3},R^{-4},R^{-5}` stored in that
            order in :obj:`matR`. Basis states are stored in :obj:`basisStates`
            array.

            >>> from arc import *
            >>> calc = PairStateInteractions(Rubidium(), 60,0,0.5, \
                60,0,0.5, 0.5,0.5,interactionsUpTo = 1)
            >>> # theta=0, phi = 0, range of pqn, range of l, deltaE = 25e9
            >>> calc.defineBasis(0 ,0 , 5, 5, 25e9, progressOutput=True)
            >>> # now calc stores interaction matrix and relevant basis
            >>> # we can access this directly and generate interaction matrix
            >>> # at distance rval :
            >>> rval = 4  # in mum
            >>> matrix = calc.matDiagonal
            >>> rX = (rval*1.e-6)**3
            >>> for matRX in self.matR:
            >>>     matrix = matrix + matRX/rX
            >>>     rX *= (rval*1.e-6)
            >>> # matrix variable now holds full interaction matrix for
            >>> # interacting atoms at distance rval calculated in
            >>> # pair-state basis states can be accessed as
            >>> basisStates = calc.basisStates
    """

    dataFolder = DPATH

    # =============================== Methods ===============================

    def __init__(self, atom, n, l, j, nn, ll, jj, m1, m2,
                 interactionsUpTo=1,
                 s=0.5,
                 s2=None, atom2=None):
        # alkali atom type, principal quantum number, orbital angular momentum,
        #  total angular momentum projections of the angular momentum on z axis
        self.atom1 = atom  #: the first atom type (isotope)
        if atom2 is None:
            self.atom2 = atom  #: the second atom type (isotope)
        else:
            self.atom2 = atom2  #: thge second atom type (isotope)
        self.n = n  # : pair-state definition: principal quantum number of the first atom
        self.l = l  # : pair-state definition: orbital angular momentum of the first atom
        self.j = j  # : pair-state definition: total angular momentum of the first atom
        self.nn = nn  # : pair-state definition: principal quantum number of the second atom
        self.ll = ll  # : pair-state definition: orbital angular momentum of the second atom
        self.jj = jj  # : pair-state definition: total angular momentum of the second atom
        self.m1 = m1  # : pair-state definition: projection of the total ang. momentum for the *first* atom
        self.m2 = m2  # : pair-state definition: projection of the total angular momentum for the *second* atom
        self.interactionsUpTo = interactionsUpTo
        """ Specifies up to which approximation we include in pair-state interactions.
            By default value is 1, corresponding to pair-state interactions up to
            dipole-dipole coupling. Value of 2 is also supported, corresponding
            to pair-state interactions up to quadrupole-quadrupole coupling.
        """

        if (issubclass(type(atom),DivalentAtom) and not (s == 0 or s == 1)):
            raise ValueError("total angular spin s has to be defined explicitly "
                             "for calculations, and value has to be 0 or 1 "
                             "for singlet and tripplet states respectively.")
        self.s1 = s  #: total spin angular momentum, optional (default 0.5)

        if s2 is None:
            self.s2 = s
        else:
            self.s2 = s2

        # check that values of spin states are valid for entered atomic species

        if issubclass(type(self.atom1), DivalentAtom):
            if (abs(self.s1) > 0.1 and abs(self.s1 - 1) > 0.1):
                raise ValueError("atom1 is DivalentAtom and its spin has to be "
                                 "s=0 or s=1 (for singlet and triplet states "
                                 "respectively)")
        elif (abs(self.s1 - 0.5) > 0.1):
                raise ValueError("atom1 is AlkaliAtom and its spin has to be "
                                 "s=0.5")
        if issubclass(type(self.atom2), DivalentAtom):
            if (abs(self.s2) > 0.1 and abs(self.s2 - 1) > 0.1):
                raise ValueError("atom2 is DivalentAtom and its spin has to be "
                                 "s=0 or s=1 (for singlet and triplet states "
                                 "respectively)")
        elif  (abs(self.s2 - 0.5) > 0.1):
            # we have divalent atom
            raise ValueError("atom2 is AlkaliAtom and its spin has to be "
                             "s=0.5")
        if (abs((self.s1-self.m1) % 1) > 0.1):
            raise ValueError("atom1 with spin s = %.1d cannot have m1 = %.1d"
                             % (self.s1, self.m1))
        if (abs((self.s2-self.m2) % 1) > 0.1):
            raise ValueError("atom2 with spin s = %.1d cannot have m2 = %.1d"
                             % (self.s2, self.m2))

        # ====================== J basis (not resolving mj) ===================

        self.coupling = []
        """
            List of matrices defineing coupling strengths between the states in
            J basis (not resolving :math:`m_j` ). Basis is given by
            :obj:`PairStateInteractions.channel`. Used as intermediary for full
            interaction matrix calculation by
            :obj:`PairStateInteractions.defineBasis`.
        """
        self.channel = []
        """
            states relevant for calculation, defined in J basis (not resolving
            :math:`m_j`. Used as intermediary for full interaction matrix
            calculation by :obj:`PairStateInteractions.defineBasis`.
        """

        # ======================= Full basis (resolving mj) ===================

        self.basisStates = []
        """
            List of pair-states for calculation. In the form
            [[n1,l1,j1,mj1,n2,l2,j2,mj2], ...].
            Each state is an array [n1,l1,j1,mj1,n2,l2,j2,mj2] corresponding to
            :math:`|n_1,l_1,j_1,m_{j1},n_2,l_2,j_2,m_{j2}\\rangle` state.
            Calculated by :obj:`PairStateInteractions.defineBasis`.
        """
        self.matrixElement = []
        """
            `matrixElement[i]` gives index of state in
            :obj:`PairStateInteractions.channel` basis
            (that doesn't resolve :math:`m_j` states), for the given index `i`
            of the state in :obj:`PairStateInteractions.basisStates` 
            ( :math:`m_j` resolving) basis.
        """

        # variuos parts of interaction matrix in pair-state basis
        self.matDiagonal = []
        """
            Part of interaction matrix in pair-state basis that doesn't depend
            on inter-atomic distance. E.g. diagonal elements of the interaction
            matrix, that describe energies of the pair states in unperturbed
            basis, will be stored here. Basis states are stored in
            :obj:`PairStateInteractions.basisStates`. Calculated by
            :obj:`PairStateInteractions.defineBasis`.
        """
        self.matR = []
        """
            Stores interaction matrices in pair-state basis
            that scale as :math:`1/R^3`, :math:`1/R^4` and :math:`1/R^5`
            with distance in  :obj:`matR[0]`, :obj:`matR[1]` and :obj:`matR[2]`
            respectively. These matrices correspond to dipole-dipole
            ( :math:`C_3`), dipole-quadrupole ( :math:`C_4`) and
            quadrupole-quadrupole ( :math:`C_5`) interactions
            coefficients. Basis states are stored in
            :obj:`PairStateInteractions.basisStates`.
            Calculated by :obj:`PairStateInteractions.defineBasis`.
        """
        self.originalPairStateIndex = 0
        """
            index of the original n,l,j,m1,nn,ll,jj,m2 pair-state in the
            :obj:`PairStateInteractions.basisStates` basis.
        """

        self.matE = []
        self.matB_1 = []
        self.matB_2 = []

        # ===================== Eigen states and plotting =====================

        # finding perturbed energy levels
        self.r = []    # detuning scale
        self.y = []    # energy levels
        self.highlight = []

        # pointers towards figure
        self.fig = 0
        self.ax = 0

        # for normalization of the maximum coupling later
        self.maxCoupling = 0.

        # n,l,j,mj, drive polarization q
        self.drivingFromState = [0, 0, 0, 0, 0]

        # sam = saved angular matrix metadata
        self.angularMatrixFile = "angularMatrix.npy"
        self.angularMatrixFile_meta = "angularMatrix_meta.npy"
        #self.sam = []
        self.savedAngularMatrix_matrix = []

        # intialize precalculated values for factorial term
        # in __getAngularMatrix_M
        def fcoef(l1, l2, m):
            return factorial(l1 + l2) / (factorial(l1 + m)
                                         * factorial(l1 - m)
                                         * factorial(l2 + m)
                                         * factorial(l2 - m))**0.5
        x = self.interactionsUpTo
        self.fcp = np.zeros((x + 1, x + 1, 2 * x + 1))
        for c1 in range(1, x + 1):
            for c2 in range(1, x + 1):
                for p in range(-min(c1, c2), min(c1, c2) + 1):
                    self.fcp[c1, c2, p + x] = fcoef(c1, c2, p)

        self.conn = False

    def __getAngularMatrix_M(self, l, j, ll, jj, l1, j1, l2, j2):
        # did we already calculated this matrix?
        c = self.conn.cursor()
        c.execute('''SELECT ind FROM pair_angularMatrix WHERE
             l1 = ? AND j1_x2 = ? AND
             l2 = ? AND j2_x2 = ? AND
             l3 = ? AND j3_x2 = ? AND
             l4 = ? AND j4_x2 = ?
             ''', (l, j * 2, ll, jj * 2, l1, j1 * 2, l2, j2 * 2))

        index = c.fetchone()
        if (index):
            return self.savedAngularMatrix_matrix[index[0]]

        # determine coupling
        dl = abs(l - l1)
        dj = abs(j - j1)
        c1 = 0
        if dl == 1 and (dj < 1.1):
            c1 = 1  # dipole coupling
        elif (dl == 0 or dl == 2 or dl == 1):
            c1 = 2  # quadrupole coupling
        else:
            raise ValueError("error in __getAngularMatrix_M")

        dl = abs(ll - l2)
        dj = abs(jj - j2)
        c2 = 0
        if dl == 1 and (dj < 1.1):
            c2 = 1  # dipole coupling
        elif (dl == 0 or dl == 2 or dl == 1):
            c2 = 2  # quadrupole coupling
        else:
            raise ValueError("error in __getAngularMatrix_M")

        am = np.zeros((int(round((2 * j1 + 1) * (2 * j2 + 1), 0)),
                       int(round((2 * j + 1) * (2 * jj + 1), 0))),
                      dtype=np.float64)

        if (c1 > self.interactionsUpTo) or (c2 > self.interactionsUpTo):
            return am

        j1range = np.linspace(-j1, j1, round(2 * j1) + 1)
        j2range = np.linspace(-j2, j2, round(2 * j2) + 1)
        jrange = np.linspace(-j, j, int(2 * j) + 1)
        jjrange = np.linspace(-jj, jj, int(2 * jj) + 1)

        for m1 in j1range:
            for m2 in j2range:
                # we have chosen the first index
                index1 = int(round(m1 * (2.0 * j2 + 1.0) + m2
                                   + (j1 * (2.0 * j2 + 1.0) + j2), 0))
                for m in jrange:
                    for mm in jjrange:
                        # we have chosen the second index
                        index2 = int(round(m * (2.0 * jj + 1.0)
                                           + mm + (j * (2.0 * jj + 1.0) + jj),
                                           0)
                                     )

                        # angular matrix element from Sa??mannshausen, Heiner,
                        # Merkt, Fr??d??ric, Deiglmayr, Johannes
                        # PRA 92: 032505 (2015)
                        elem = (-1.0)**(j + jj + self.s1 + self.s2 + l1 + l2) * \
                            CG(l, 0, c1, 0, l1, 0) * CG(ll, 0, c2, 0, l2, 0)
                        elem = elem * \
                            sqrt((2.0 * l + 1.0) * (2.0 * ll + 1.0)) * \
                            sqrt((2.0 * j + 1.0) * (2.0 * jj + 1.0))
                        elem = elem * \
                            Wigner6j(l, self.s1, j, j1, c1, l1) * \
                            Wigner6j(ll, self.s2, jj, j2, c2, l2)

                        sumPol = 0.0  # sum over polarisations
                        limit = min(c1, c2)
                        for p in xrange(-limit, limit + 1):
                            sumPol = sumPol + \
                                self.fcp[c1, c2, p + self.interactionsUpTo] * \
                                CG(j, m, c1, p, j1, m1) *\
                                CG(jj, mm, c2, -p, j2, m2)
                        am[index1, index2] = elem * sumPol

        index = len(self.savedAngularMatrix_matrix)

        c.execute(''' INSERT INTO pair_angularMatrix
                            VALUES (?,?, ?,?, ?,?, ?,?, ?)''',
                       (l, j * 2, ll, jj * 2, l1, j1 * 2, l2, j2 * 2, index))
        self.conn.commit()

        self.savedAngularMatrix_matrix.append(am)
        self.savedAngularMatrixChanged = True

        return am

    def __updateAngularMatrixElementsFile(self):
        if not (self.savedAngularMatrixChanged):
            return

        try:
            c = self.conn.cursor()
            c.execute('''SELECT * FROM pair_angularMatrix ''')
            data = []
            for v in c.fetchall():
                data.append(v)

            data = np.array(data, dtype=np.float32)

            data[:, 1] /= 2.  # 2 r j1 -> j1
            data[:, 3] /= 2.  # 2 r j2 -> j2
            data[:, 5] /= 2.  # 2 r j3 -> j3
            data[:, 7] /= 2.  # 2 r j4 -> j4

            fileHandle = gzip.GzipFile(
                os.path.join(self.dataFolder, self.angularMatrixFile_meta),
                'wb'
                )
            np.save(fileHandle, data)
            fileHandle.close()
        except IOError as e:
            print("Error while updating angularMatrix \
                data meta (description) File " + self.angularMatrixFile_meta)

        try:
            fileHandle = gzip.GzipFile(
                os.path.join(self.dataFolder, self.angularMatrixFile),
                'wb'
                )
            np.save(fileHandle, self.savedAngularMatrix_matrix)
            fileHandle.close()
        except IOError as e:
            print("Error while updating angularMatrix \
                    data File " + self.angularMatrixFile)
            print(e)

    def __loadAngularMatrixElementsFile(self):
        try:
            fileHandle = gzip.GzipFile(
                os.path.join(self.dataFolder, self.angularMatrixFile_meta),
                'rb'
                )
            data = np.load(fileHandle, encoding='latin1', allow_pickle=True)
            fileHandle.close()
        except Exception as ex:
            print(ex)
            print("Note: No saved angular matrix metadata files to be loaded.")
            print(sys.exc_info())
            return

        data[:, 1] *= 2  # j1 -> 2 r j1
        data[:, 3] *= 2  # j2 -> 2 r j2
        data[:, 5] *= 2  # j3 -> 2 r j3
        data[:, 7] *= 2  # j4 -> 2 r j4

        data = np.array(np.rint(data), dtype=np.int)

        try:
            c = self.conn.cursor()
            c.executemany('''INSERT INTO pair_angularMatrix
                (l1, j1_x2 ,
                 l2 , j2_x2 ,
                 l3, j3_x2,
                 l4 , j4_x2 ,
                 ind)
                      VALUES (?,?,?,?,?,?,?,?,?)''', data)

            self.conn.commit()

        except sqlite3.Error as e:
            print("Error while loading precalculated values into the database!")
            print(e)
            exit()
        if len(data) == 0:
            print("error")
            return

        try:
            fileHandle = gzip.GzipFile(
                os.path.join(self.dataFolder, self.angularMatrixFile),
                'rb'
                )
            self.savedAngularMatrix_matrix = np.load(
                fileHandle,
                encoding='latin1',
                allow_pickle=True).tolist()
            fileHandle.close()
        except Exception as ex:
            print(ex)
            print("Note: No saved angular matrix files to be loaded.")
            print(sys.exc_info())

    def __isCoupled(self, n, l, j, nn, ll, jj, n1, l1, j1, n2, l2, j2, limit):
        if ((abs(self.__getEnergyDefect(n, l, j,
                                        nn, ll, jj,
                                        n1, l1, j1,
                                        n2, l2, j2)
                 ) / C_h < limit)
            and not (n == n1 and nn == n2
                     and l == l1 and ll == l2
                     and j == j1 and jj == j2)
                and not ((abs(l1 - l) != 1
                          and( (abs(j - 0.5) < 0.1
                                and abs(j1 - 0.5) < 0.1) # j = 1/2 and j'=1/2 forbidden
                                or
                                (abs(j) < 0.1
                                and abs(j1 - 1) < 0.1)  # j = 0 and j'=1 forbidden
                                or
                                (abs(j-1) < 0.1
                                and abs(j1) < 0.1)  # j = 1 and j'=0 forbidden
                                )
                          )
                         or (abs(l2 - ll) != 1
                            and( (abs(jj - 0.5) < 0.1
                                and abs(j2 - 0.5) < 0.1) # j = 1/2 and j'=1/2 forbidden
                                or
                                (abs(jj) < 0.1
                                and abs(j2 - 1) < 0.1)  # j = 0 and j'=1 forbidden
                                or
                                (abs(jj-1) < 0.1
                                and abs(j2) < 0.1)  # j = 1 and j'=0 forbidden
                                )
                          )
                        )
                and not(abs(j)<0.1 and abs(j1)<0.1)  # j = 0 and j'=0 forbiden
                and not (abs(jj)<0.1 and abs(j2)<0.1)
                and not (abs(l)<0.1 and abs(l1)<0.1) # l = 0 and l' = 0 is forbiden
                and not (abs(ll)<0.1 and abs(l2)<0.1)
                ):
            # determine coupling
            dl = abs(l - l1)
            dj = abs(j - j1)
            c1 = 0
            if dl == 1 and (dj < 1.1):
                c1 = 1  # dipole coupling
            elif (dl == 0 or dl == 2 or dl == 1)and (dj < 2.1) and \
                    (2 <= self.interactionsUpTo):
                c1 = 2  # quadrupole coupling
            else:
                return False
            dl = abs(ll - l2)
            dj = abs(jj - j2)
            c2 = 0
            if dl == 1 and (dj < 1.1):
                c2 = 1  # dipole coupling
            elif (dl == 0 or dl == 2 or dl == 1) and (dj < 2.1) and \
                    (2 <= self.interactionsUpTo):
                c2 = 2  # quadrupole coupling
            else:
                return False
            return c1 + c2
        else:
            return False

    def __getEnergyDefect(self,
                          n, l, j,
                          nn, ll, jj,
                          n1, l1, j1,
                          n2, l2, j2):
        """
        Energy defect between |n,l,j>x|nn,ll,jj> state and |n1,l1,j1>x|n1,l1,j1>
        state of atom1 and atom2 in respective spins states s1 and s2

        Takes spin vales s1 and s2 as the one defined when defining calculation.

        Parameters:
            n (int): principal quantum number
            l (int): orbital angular momenutum
            j (float): total angular momentum
            nn (int): principal quantum number
            ll (int): orbital angular momenutum
            jj (float): total angular momentum
            n1 (int): principal quantum number
            l1 (int): orbital angular momentum
            j1 (float): total angular momentum
            n2 (int): principal quantum number
            l2 (int): orbital angular momentum
            j2 (float): total angular momentum

        Returns:
            float:  energy defect (SI units: J)
        """
        return C_e * (self.atom1.getEnergy(n1, l1, j1, s=self.s1)
                      + self.atom2.getEnergy(n2, l2, j2, s=self.s2)
                      - self.atom1.getEnergy(n, l, j, s=self.s1)
                      - self.atom2.getEnergy(nn, ll, jj, s=self.s2))

    def __makeRawMatrix2(self,
                         n, l, j,
                         nn, ll, jj,
                         k, lrange, limit, limitBasisToMj,
                         progressOutput=False, debugOutput=False):
        # limit = limit in Hz on energy defect
        # k defines range of n' = [n-k, n+k]
        dimension = 0

        # which states/channels contribute significantly in the second order perturbation?
        states = []

        # original pairstate index
        opi = 0

        # this numbers are conserved if we use only dipole-dipole interactions
        Lmod2 = ((l + ll) % 2)

        l1start = max(l - self.interactionsUpTo, 0)
        l2start = max(ll - self.interactionsUpTo, 0)

        if debugOutput:
            print("\n ======= Relevant states =======\n")

        for n1 in xrange(max(n - k, 1), n + k + 1):
            for n2 in xrange(max(nn - k, 1), nn + k + 1):
                l1max = max(l + self.interactionsUpTo, lrange) + 1
                l1max = min(l1max, n1 - 1)
                for l1 in xrange(l1start, l1max):
                    l2max = max(ll + self.interactionsUpTo, lrange) + 1
                    l2max = min(l2max, n2 - 1)
                    for l2 in xrange(l2start, l2max):
                        j1 = l1 - self.s1
                        while j1 < -0.1:
                            j1 += 2 * self.s1
                        while j1 <= l1 + self.s1 + 0.1:
                            j2 = l2 - self.s2
                            while j2 < -0.1:
                                j2 += 2 * self.s2

                            while j2 <= l2 + self.s2 + 0.1:
                                ed = self.__getEnergyDefect(n, l, j,
                                                            nn, ll, jj,
                                                            n1, l1, j1,
                                                            n2, l2, j2) / C_h
                                if (abs(ed) < limit
                                    and (not (self.interactionsUpTo == 1)
                                         or (Lmod2 == ((l1 + l2) % 2)))
                                    and ((not limitBasisToMj)
                                         or (j1 + j2 + 0.1
                                             > self.m1 + self.m2))
                                    and (n1 >= self.atom1.groundStateN
                                         or [n1, l1, j1] in self.atom1.extraLevels)
                                    and (n2 >= self.atom2.groundStateN
                                        or [n2, l2, j2] in self.atom2.extraLevels)
                                        ):

                                    if debugOutput:
                                        pairState = (
                                            "|"
                                            + printStateString(n1, l1, j1,
                                                               s=self.s1)
                                            + ","
                                            + printStateString(n2, l2, j2,
                                                               s=self.s2)
                                            + ">")
                                        print(
                                            pairState
                                            + ("\t EnergyDefect = %.3f GHz"
                                               % (ed * 1.e-9)
                                              )
                                            )

                                    states.append([n1, l1, j1, n2, l2, j2])

                                    if (n == n1 and nn == n2
                                        and l == l1 and ll == l2
                                        and j == j1 and jj == j2
                                            ):
                                        opi = dimension

                                    dimension = dimension + 1
                                j2 = j2 + 1.0
                            j1 = j1 + 1.0

        if debugOutput:
            print("\tMatrix dimension\t=\t", dimension)

        # mat_value, mat_row, mat_column for each sparce matrix describing
        # dipole-dipole, dipole-quadrupole (and quad-dipole) and quadrupole-quadrupole
        couplingMatConstructor = [[[], [], []]
                                  for i in xrange(2 * self.interactionsUpTo - 1)]

        # original pair-state (i.e. target pair state) Zeeman Shift
        opZeemanShift = (self.atom1.getZeemanEnergyShift(
            self.l, self.j, self.m1,
            self.Bz,
            s=self.s1)
            + self.atom2.getZeemanEnergyShift(
                self.ll, self.jj, self.m2,
                self.Bz,
                s=self.s2)
            ) / C_h * 1.0e-9  # in GHz

        if debugOutput:
            print("\n ======= Coupling strengths (radial part only) =======\n")

        maxCoupling = "quadrupole-quadrupole"
        if (self.interactionsUpTo == 1):
            maxCoupling = "dipole-dipole"
        if debugOutput:
            print("Calculating coupling (up to ",
                  maxCoupling, ") between the pair states")

        for i in xrange(dimension):

            ed = self.__getEnergyDefect(
                states[opi][0], states[opi][1], states[opi][2],
                states[opi][3], states[opi][4], states[opi][5],
                states[i][0], states[i][1], states[i][2],
                states[i][3], states[i][4], states[i][5]) / C_h * 1.0e-9\
                - opZeemanShift

            pairState1 = (
                "|"
                + printStateString(states[i][0], states[i][1], states[i][2],
                                   s=self.s1)
                + ","
                + printStateString(states[i][3], states[i][4], states[i][5],
                                   s=self.s2)
                + ">"
                )

            states[i].append(ed)  # energy defect of given state

            for j in xrange(i + 1, dimension):

                coupled = self.__isCoupled(
                    states[i][0], states[i][1], states[i][2],
                    states[i][3], states[i][4], states[i][5],
                    states[j][0], states[j][1], states[j][2],
                    states[j][3], states[j][4], states[j][5], limit)

                if (states[i][0] == 24 and states[j][0] == 18):
                    print("\n")
                    print(states[i])
                    print(states[j])
                    print(coupled)

                if coupled and (abs(states[i][0] - states[j][0]) <= k
                                and abs(states[i][3] - states[j][3]) <= k):
                    if debugOutput:
                        pairState2 = ("|"
                            + printStateString(states[j][0],
                                               states[j][1],
                                               states[j][2],
                                               s=self.s1)
                            + ","
                            + printStateString(states[j][3],
                                               states[j][4],
                                               states[j][5],
                                               s=self.s2)
                            + ">")
                        print(pairState1 + " <---> " + pairState2)

                    couplingStregth = _atomLightAtomCoupling(
                        states[i][0], states[i][1], states[i][2],
                        states[i][3], states[i][4], states[i][5],
                        states[j][0], states[j][1], states[j][2],
                        states[j][3], states[j][4], states[j][5],
                        self.atom1, atom2=self.atom2,
                        s=self.s1, s2=self.s2) / C_h * 1.0e-9

                    couplingMatConstructor[coupled - 2][0].append(
                        couplingStregth)
                    couplingMatConstructor[coupled - 2][1].append(i)
                    couplingMatConstructor[coupled - 2][2].append(j)

                    exponent = coupled + 1
                    if debugOutput:
                        print(("\tcoupling (C_%d/R^%d) = %.5f"
                               % (exponent, exponent,
                                  couplingStregth * (1e6)**(exponent))),
                              "/R^", exponent, " GHz  (mu m)^", exponent, "\n"
                              )

        # coupling = [1,1] dipole-dipole, [2,1]  quadrupole dipole, [2,2] quadrupole quadrupole

        couplingMatArray = [
            csr_matrix(
                (couplingMatConstructor[i][0],
                 (couplingMatConstructor[i][1], couplingMatConstructor[i][2])
                 ),
                shape=(dimension, dimension)
                )
            for i in xrange(len(couplingMatConstructor))
            ]
        return states, couplingMatArray

    def __initializeDatabaseForMemoization(self):
        # memoization of angular parts
        self.conn = sqlite3.connect(os.path.join(self.dataFolder,
                                                 "precalculated_pair.db"))
        c = self.conn.cursor()

        # ANGULAR PARTS
        c.execute('''DROP TABLE IF EXISTS pair_angularMatrix''')
        c.execute('''SELECT COUNT(*) FROM sqlite_master
                            WHERE type='table' AND name='pair_angularMatrix';''')
        if (c.fetchone()[0] == 0):
            # create table
            try:
                c.execute('''CREATE TABLE IF NOT EXISTS pair_angularMatrix
                 (l1 TINYINT UNSIGNED, j1_x2 TINYINT UNSIGNED,
                 l2 TINYINT UNSIGNED, j2_x2 TINYINT UNSIGNED,
                 l3 TINYINT UNSIGNED, j3_x2 TINYINT UNSIGNED,
                 l4 TINYINT UNSIGNED, j4_x2 TINYINT UNSIGNED,
                 ind INTEGER,
                 PRIMARY KEY (l1,j1_x2, l2,j2_x2, l3,j3_x2, l4,j4_x2)
                ) ''')
            except sqlite3.Error as e:
                print(e)
            self.conn.commit()
        self.__loadAngularMatrixElementsFile()
        self.savedAngularMatrixChanged = False

    def __closeDatabaseForMemoization(self):
        self.conn.commit()
        self.conn.close()
        self.conn = False

    def getLeRoyRadius(self):
        """
            Returns Le Roy radius for initial pair-state.

            Le Roy radius [#leroy]_ is defined as
            :math:`2(\\langle r_1^2 \\rangle^{1/2} + \\langle r_2^2 \\rangle^{1/2})`,
            where :math:`r_1` and :math:`r_2` are electron coordinates for the
            first and the second atom in the initial pair-state.
            Below this radius, calculations are not valid since electron
            wavefunctions start to overlap.

            Returns:
                float: LeRoy radius measured in :math:`\\mu m`

            References:
                .. [#leroy] R.J. Le Roy, Can. J. Phys. **52**, 246 (1974)
                    http://www.nrcresearchpress.com/doi/abs/10.1139/p74-035
        """
        step = 0.001
        r1, psi1_r1 = self.atom1.radialWavefunction(
            self.l, 0.5, self.j,
            self.atom1.getEnergy(self.n, self.l, self.j, s=self.s1) / 27.211,
            self.atom1.alphaC**(1 / 3.0),
            2.0 * self.n * (self.n + 15.0), step)

        sqrt_r1_on2 = np.trapz(np.multiply(np.multiply(psi1_r1, psi1_r1),
                                           np.multiply(r1, r1)),
                               x=r1)

        r2, psi2_r2 = self.atom2.radialWavefunction(
            self.ll, 0.5, self.jj,
            self.atom2.getEnergy(self.nn, self.ll, self.jj, s=self.s2) / 27.211,
            self.atom2.alphaC**(1 / 3.0),
            2.0 * self.nn * (self.nn + 15.0), step)

        sqrt_r2_on2 = np.trapz(np.multiply(np.multiply(psi2_r2, psi2_r2),
                                           np.multiply(r2, r2)),
                               x=r2)

        return 2. * (sqrt(sqrt_r1_on2) + sqrt(sqrt_r2_on2))\
            * (physical_constants["Bohr radius"][0] * 1.e6)


    def getC6perturbatively(self, theta, phi, nRange, energyDelta,
                            degeneratePerturbation=False):
        r"""
        Calculates :math:`C_6` from second order perturbation theory.

        Calculates
        :math:`C_6=\sum_{\rm r',r''}|\langle {\rm r',r''}|V|\
        {\rm r1,r2}\rangle|^2/\Delta_{\rm r',r''}`, where
        :math:`\Delta_{\rm r',r''}\equiv E({\rm r',r''})-E({\rm r1, r2})`
        When second order perturbation couples to multiple energy degenerate
        states, users shold use **degenerate perturbation calculations** by
        setting `degeneratePerturbation=True` .

        This calculation is faster then full diagonalization, but it is valid
        only far from the so called spaghetti region that occurs when atoms
        are close to each other. In that region multiple levels are strongly
        coupled, and one needs to use full diagonalization. In region where
        perturbative calculation is correct, energy level shift can be
        obtained as :math:`V(R)=-C_6/R^6`

        See `perturbative C6 calculations example snippet`_ and for
        degenerate perturbation calculation see
        `degenerate pertubation C6 calculation example snippet`_

        .. _`perturbative C6 calculations example snippet`:
            ./Rydberg_atoms_a_primer.html#Dispersion-Coefficients

       .. _`degenerate pertubation C6 calculation example snippet`:
           ./ARC_3_0_introduction.html#Pertubative-C6-calculation-in-the-manifold-of-degenerate-states

        Parameters:
            theta (float):
                orientation of inter-atomic axis with respect
                to quantization axis (:math:`z`) in Euler coordinates
                (measured in units of radian)
            phi (float):
                orientation of inter-atomic axis with respect
                to quantization axis (:math:`z`) in Euler coordinates
                (measured in units of radian)
            nRange (int):
                how much below and above the given principal quantum number
                of the pair state we should be looking
            energyDelta (float):
                what is maximum energy difference ( :math:`\Delta E/h` in Hz)
                between the original pair state and the other pair states that we are including in
                calculation
            degeneratePerturbation (bool):
                optional, default False. Should one
                use degenerate perturbation theory. This should be used whenever
                angle between quantisation and interatomic axis is non-zero,
                as well as when one considers non-stretched states.

        Returns:
            float: if **degeneratePerturbation=False**, returns
            :math:`C_6` measured in :math:`\text{GHz }\mu\text{m}^6`;
            if **degeneratePerturbation=True**, returns array of
            :math:`C_6` measured in :math:`\text{GHz }\mu\text{m}^6`
            AND array of corresponding eigenvectors in
            :math:`\{m_{j_1}=-j_1, \ldots, m_{j_1} = +j1\}\bigotimes \
            \{ m_{j_2}=-j_2, \ldots, m_{j_2} = +j2\}`
            basis


        Example:
            If we want to quickly calculate :math:`C_6` for two Rubidium
            atoms in state :math:`62 D_{3/2} m_j=3/2`, positioned in space
            along the shared quantization axis::

                from arc import *
                calculation = PairStateInteractions(Rubidium(), 62, 2, 1.5, 62, 2, 1.5, 1.5, 1.5)
                c6 = calculation.getC6perturbatively(0,0, 5, 25e9)
                print "C_6 = %.0f GHz (mu m)^6" % c6

            Which returns::

                C_6 = 767 GHz (mu m)^6

            Quick calculation of angular anisotropy of for Rubidium
            :math:`D_{2/5},m_j=5/2` states::

                # Rb 60 D_{2/5}, mj=2.5 , 60 D_{2/5}, mj=2.5 pair state
                calculation1 = PairStateInteractions(Rubidium(), 60, 2, 2.5, 60, 2, 2.5, 2.5, 2.5)
                # list of atom orientations
                thetaList = np.linspace(0,pi,30)
                # do calculation of C6 pertubatively for all atom orientations
                c6 = []
                for theta in thetaList:
                    value = calculation1.getC6perturbatively(theta,0,5,25e9)
                    c6.append(value)
                    print ("theta = %.2f * pi \tC6 = %.2f GHz  mum^6" % (theta/pi,value))
                # plot results
                plot(thetaList/pi,c6,"b-")
                title("Rb, pairstate  60 $D_{5/2},m_j = 5/2$, 60 $D_{5/2},m_j = 5/2$")
                xlabel(r"$\Theta /\pi$")
                ylabel(r"$C_6$ (GHz $\mu$m${}^6$")
                show()

        """
        self.__initializeDatabaseForMemoization()

        # ========= START OF THE MAIN CODE ===========

        # wigner D matrix allows calculations with arbitrary orientation of
        # the two atoms
        wgd = WignerDmatrix(theta, phi)

        # any conservation?
        # this numbers are conserved if we use only dipole-dipole interactions
        Lmod2 = ((self.l + self.ll) % 2)

        # find nearby states

        lmin1 = self.l - 1
        if lmin1 < -0.1:
            lmin1 = 1
        lmin2 = self.ll - 1
        if lmin2 < -0.1:
            lmin2 = 1

        interactionMatrix = np.zeros((int(round((2 * self.j + 1)
                                                * (2 * self.jj + 1)
                                                )
                                          ),
                                      int(round((2 * self.j + 1)
                                                * (2 * self.jj + 1)
                                                )
                                          )
                                      ),
                                     dtype=np.complex)

        for n1 in xrange(max(self.n - nRange, 1), self.n + nRange + 1):
            for n2 in xrange(max(self.nn - nRange, 1), self.nn + nRange + 1):
                lmax1 = min(self.l + 2, n1)
                for l1 in xrange(lmin1, lmax1, 2):
                    lmax2 = min(self.ll + 2, n2)
                    for l2 in xrange(lmin2, lmax2, 2):
                        if ((l1+l2) % 2 == Lmod2):
                            j1 = l1 - self.s1
                            while j1 < -0.1:
                                j1 += 2 * self.s1
                            while j1 <= l1 + self.s1 + 0.1:
                                j2 = l2 - self.s2
                                while j2 < -0.1:
                                    j2 += 2 * self.s2

                                while j2 <= l2 + self.s2 + 0.1:
                                    coupled = self.__isCoupled(
                                        self.n, self.l, self.j,
                                        self.nn, self.ll, self.jj,
                                        n1, l1, j1,
                                        n2, l2, j2,
                                        energyDelta)
                                    if (coupled
                                        and (not (self.interactionsUpTo == 1)
                                             or (Lmod2 == ((l1 + l2) % 2)))
                                        and (n1 >= self.atom1.groundStateN
                                             or [n1, l1, j1] in
                                             self.atom1.extraLevels)
                                        and (n2 >= self.atom2.groundStateN
                                             or [n2, l2, j2] in
                                             self.atom2.extraLevels)
                                            ):
                                        energyDefect = self.__getEnergyDefect(
                                            self.n, self.l, self.j,
                                            self.nn, self.ll, self.jj,
                                            n1, l1, j1,
                                            n2, l2, j2) / C_h
                                        energyDefect = energyDefect * 1.0e-9  # GHz
                                        if (abs(energyDefect) < 1e-10):
                                            raise ValueError(
                                                "The requested pair-state "
                                                "is dipole coupled resonatly "
                                                "(energy defect = 0)"
                                                "to other pair-states"
                                                "Aborting pertubative "
                                                "calculation."
                                                "(This usually happens for "
                                                "high-L states for which "
                                                "identical quantum defects give "
                                                "raise to degeneracies, making "
                                                "total L ultimately not "
                                                "conserved quantum number) ")

                                        # calculate radial part
                                        couplingStregth = (
                                            _atomLightAtomCoupling(
                                                self.n, self.l, self.j,
                                                self.nn, self.ll, self.jj,
                                                n1, l1, j1,
                                                n2, l2, j2,
                                                self.atom1, atom2=self.atom2,
                                                s=self.s1, s2=self.s2)
                                            * (1.0e-9 * (1.e6)**3 / C_h)
                                            )  # GHz / mum^3

                                        d = self.__getAngularMatrix_M(
                                            self.l, self.j,
                                            self.ll, self.jj,
                                            l1, j1,
                                            l2, j2)

                                        interactionMatrix += (
                                            d.conj().T.dot(d)
                                            * abs(couplingStregth)**2
                                            / energyDefect
                                            )

                                    j2 = j2 + 1.0
                                j1 = j1 + 1.0

        rotationMatrix = np.kron(wgd.get(self.j).toarray(),
                                 wgd.get(self.jj).toarray())

        interactionMatrix = rotationMatrix.dot(
            interactionMatrix.dot(rotationMatrix.conj().T)
            )
        # ========= END OF THE MAIN CODE ===========
        self.__closeDatabaseForMemoization()

        value, vectors = np.linalg.eigh(interactionMatrix)
        vectors = vectors.T
        stateCom = compositeState(singleAtomState(self.j, self.m1),
                           singleAtomState(self.jj, self.m2)).T

        if not degeneratePerturbation:
            for i, v in enumerate(vectors):
                if (abs(np.vdot(v, stateCom)) > 1-1e-9):
                    return value[i]
            #    else:
            #        print(np.vdot(v, stateCom))
            # if initial state is not eigen state print warning and return
            # results for eigenstates, and eigenstate composition
            """
            print("WARNING: Requested state is not eigenstate when dipole-dipole "
                  "interactions and/or relative position of atoms are "
                  "taken into account.\n"
                  "We will use degenerate pertubative theory to correctly "
                  "calculate C6.\n"
                  "Method will return values AND eigenvectors in basis \n"
                  "{mj1 = -j1, ... , mj1 = +j1} x {mj2 = -j2, ... , m2 = +j2}, "
                  "where x denotes Kronecker product\n"
                  "To not see this warning request explicitly "
                  "degeneratePerturbation=True in call of this method.\n")
            """
            #print(stateCom.conj().dot(interactionMatrix.dot(stateCom.T)))
            #print(stateCom.conj().dot(interactionMatrix.dot(stateCom.T)).shape)
            return np.real(stateCom.conj().dot(
                            interactionMatrix.dot(stateCom.T))[0][0])
        return np.real(value), vectors

    def defineBasis(self, theta, phi, nRange, lrange, energyDelta,
                    Bz=0, progressOutput=False, debugOutput=False):
        r"""
            Finds relevant states in the vicinity of the given pair-state

            Finds relevant pair-state basis and calculates interaction matrix.
            Pair-state basis is saved in :obj:`basisStates`.
            Interaction matrix is saved in parts depending on the scaling with
            distance. Diagonal elements :obj:`matDiagonal`, correponding to
            relative energy defects of the pair-states, don't change with
            interatomic separation. Off diagonal elements can depend
            on distance as :math:`R^{-3}, R^{-4}` or :math:`R^{-5}`,
            corresponding to dipole-dipole (:math:`C_3` ), dipole-qudrupole
            (:math:`C_4` ) and quadrupole-quadrupole coupling (:math:`C_5` )
            respectively. These parts of the matrix are stored in
            :obj:`PairStateInteractions.matR`
            in that order. I.e. :obj:`matR[0]`
            stores dipole-dipole coupling
            (:math:`\propto R^{-3}`),
            :obj:`matR[1]` stores dipole-quadrupole
            couplings etc.

            Parameters:
                theta (float):  relative orientation of the two atoms
                    (see figure on top of the page), range 0 to :math:`\pi`
                phi (float): relative orientation of the two atoms (see figure
                    on top of the page), range 0 to :math:`2\pi`
                nRange (int): how much below and above the given principal
                    quantum number of the pair state we should be looking?
                lrange (int): what is the maximum angular orbital momentum
                    state that we are including in calculation
                energyDelta (float): what is maximum energy difference (
                    :math:`\Delta E/h` in Hz)
                    between the original pair state and the other pair states
                    that we are including in calculation
                Bz (float): optional, magnetic field directed along z-axis in
                    units of Tesla. Calculation will be correct only for weak
                    magnetic fields, where paramagnetic term is much stronger
                    then diamagnetic term. Diamagnetic term is neglected.
                progressOutput (bool): optional, False by default. If true,
                    prints information about the progress of the calculation.
                debugOutput (bool): optional, False by default. If true,
                    similarly to progressOutput=True, this will print
                    information about the progress of calculations, but with
                    more verbose output.

            See also:
                :obj:`arc.alkali_atom_functions.saveCalculation` and
                :obj:`arc.alkali_atom_functions.loadSavedCalculation` for
                information on saving intermediate results of calculation for
                later use.
        """

        self.__initializeDatabaseForMemoization()

        # save call parameters
        self.theta = theta
        self.phi = phi
        self.nRange = nRange
        self.lrange = lrange
        self.energyDelta = energyDelta
        self.Bz = Bz

        self.basisStates = []

        # wignerDmatrix
        wgd = WignerDmatrix(theta, phi)

        limitBasisToMj = False
        if (theta < 0.001):
            limitBasisToMj = True  # Mj will be conserved in calculations

        originalMj = self.m1 + self.m2

        self.channel, self.coupling = self.__makeRawMatrix2(
            self.n, self.l, self.j,
            self.nn, self.ll, self.jj,
            nRange, lrange, energyDelta,
            limitBasisToMj,
            progressOutput=progressOutput,
            debugOutput=debugOutput)

        self.atom1.updateDipoleMatrixElementsFile()
        self.atom2.updateDipoleMatrixElementsFile()

        # generate all the states (with mj principal quantum number)

        # opi = original pairstate index
        opi = 0

        # NEW FOR SPACE MATRIX
        self.index = np.zeros(len(self.channel) + 1, dtype=np.int16)

        for i in xrange(len(self.channel)):
            self.index[i] = len(self.basisStates)

            stateCoupled = self.channel[i]

            for m1c in np.linspace(stateCoupled[2], -stateCoupled[2],
                                   round(1 + 2 * stateCoupled[2])):
                for m2c in np.linspace(stateCoupled[5], -stateCoupled[5],
                                       round(1 + 2 * stateCoupled[5])):
                    if ((not limitBasisToMj) or (abs(originalMj
                                                     - m1c - m2c) < 0.1)):
                        self.basisStates.append(
                            [stateCoupled[0], stateCoupled[1], stateCoupled[2],
                             m1c,
                             stateCoupled[3], stateCoupled[4], stateCoupled[5],
                             m2c])
                        self.matrixElement.append(i)

                        if (abs(stateCoupled[0] - self.n) < 0.1
                            and abs(stateCoupled[1] - self.l) < 0.1
                            and abs(stateCoupled[2] - self.j) < 0.1
                            and abs(m1c - self.m1) < 0.1
                            and abs(stateCoupled[3] - self.nn) < 0.1
                            and abs(stateCoupled[4] - self.ll) < 0.1
                            and abs(stateCoupled[5] - self.jj) < 0.1
                            and abs(m2c - self.m2) < 0.1):
                            opi = len(self.basisStates) - 1
            if (self.index[i] == len(self.basisStates)):
                print(stateCoupled)
        self.index[-1] = len(self.basisStates)

        if progressOutput or debugOutput:
            print("\nCalculating Hamiltonian matrix...\n")

        dimension = len(self.basisStates)
        if progressOutput or debugOutput:
            print("\n\tmatrix (dimension ", dimension, ")\n")

        # INITIALIZING MATICES
        # all (sparce) matrices will be saved in csr format
        # value, row, column
        matDiagonalConstructor = [[], [], []]

        matRConstructor = [[[], [], []]
                           for i in xrange(self.interactionsUpTo * 2 - 1)]

        matRIndex = 0
        for c in self.coupling:
            progress = 0.
            for ii in xrange(len(self.channel)):
                if progressOutput:
                    dim = len(self.channel)
                    progress += ((dim - ii) * 2 - 1)
                    sys.stdout.write(
                        "\rMatrix R%d %.1f %% (state %d of %d)"
                        % (matRIndex + 3,
                           float(progress) / float(dim**2) * 100.,
                           ii + 1,
                           len(self.channel)))
                    sys.stdout.flush()

                ed = self.channel[ii][6]

                # solves problems with exactly degenerate basisStates
                degeneracyOffset = 0.00000001

                i = self.index[ii]
                dMatrix1 = wgd.get(self.basisStates[i][2])
                dMatrix2 = wgd.get(self.basisStates[i][6])

                for i in xrange(self.index[ii], self.index[ii + 1]):
                    statePart1 = singleAtomState(
                        self.basisStates[i][2], self.basisStates[i][3])
                    statePart2 = singleAtomState(
                        self.basisStates[i][6], self.basisStates[i][7])
                    # rotate individual states

                    statePart1 = dMatrix1.T.conjugate().dot(statePart1)
                    statePart2 = dMatrix2.T.conjugate().dot(statePart2)

                    stateCom = compositeState(statePart1, statePart2)

                    if (matRIndex == 0):
                        zeemanShift = (
                            self.atom1.getZeemanEnergyShift(
                                self.basisStates[i][1],
                                self.basisStates[i][2],
                                self.basisStates[i][3],
                                self.Bz,
                                s=self.s1)
                            + self.atom2.getZeemanEnergyShift(
                                self.basisStates[i][5],
                                self.basisStates[i][6],
                                self.basisStates[i][7],
                                self.Bz,
                                s=self.s2)
                            ) / C_h * 1.0e-9   # in GHz
                        matDiagonalConstructor[0].append(ed + zeemanShift
                                                         + degeneracyOffset)
                        degeneracyOffset += 0.00000001
                        matDiagonalConstructor[1].append(i)
                        matDiagonalConstructor[2].append(i)

                    for dataIndex in xrange(c.indptr[ii], c.indptr[ii + 1]):

                        jj = c.indices[dataIndex]
                        radialPart = c.data[dataIndex]

                        j = self.index[jj]
                        dMatrix3 = wgd.get(self.basisStates[j][2])
                        dMatrix4 = wgd.get(self.basisStates[j][6])

                        if (self.index[jj] != self.index[jj + 1]):
                            d = self.__getAngularMatrix_M(
                                self.basisStates[i][1], self.basisStates[i][2],
                                self.basisStates[i][5], self.basisStates[i][6],
                                self.basisStates[j][1], self.basisStates[j][2],
                                self.basisStates[j][5], self.basisStates[j][6])
                            secondPart = d.dot(stateCom)
                        else:
                            print(" - - - ", self.channel[jj])

                        for j in xrange(self.index[jj], self.index[jj + 1]):
                            statePart1 = singleAtomState(
                                self.basisStates[j][2], self.basisStates[j][3])
                            statePart2 = singleAtomState(
                                self.basisStates[j][6], self.basisStates[j][7])
                            # rotate individual states

                            statePart1 = dMatrix3.T.conjugate().dot(statePart1)
                            statePart2 = dMatrix4.T.conjugate().dot(statePart2)
                            # composite state of two atoms
                            stateCom2 = compositeState(statePart1, statePart2)

                            angularFactor = stateCom2.T.conjugate().dot(secondPart)
                            if (abs(self.phi) < 1e-9):
                                angularFactor = angularFactor[0, 0].real
                            else:
                                angularFactor = angularFactor[0, 0]

                            if (abs(angularFactor) > 1.e-5):
                                matRConstructor[matRIndex][0].append(
                                    (radialPart * angularFactor).conj())
                                matRConstructor[matRIndex][1].append(i)
                                matRConstructor[matRIndex][2].append(j)

                                matRConstructor[matRIndex][0].append(
                                    radialPart * angularFactor)
                                matRConstructor[matRIndex][1].append(j)
                                matRConstructor[matRIndex][2].append(i)
            matRIndex += 1
            if progressOutput or debugOutput:
                print("\n")

        self.matDiagonal = csr_matrix(
            (matDiagonalConstructor[0],
             (matDiagonalConstructor[1], matDiagonalConstructor[2])),
            shape=(dimension, dimension)
            )

        self.matR = [
            csr_matrix((matRConstructor[i][0],
                        (matRConstructor[i][1], matRConstructor[i][2])),
                       shape=(dimension, dimension)
                       ) for i in xrange(self.interactionsUpTo * 2 - 1)
            ]

        self.originalPairStateIndex = opi

        self.__updateAngularMatrixElementsFile()
        self.__closeDatabaseForMemoization()

    def diagonalise(self, rangeR, noOfEigenvectors,
                    drivingFromState=[0, 0, 0, 0, 0],
                    eigenstateDetuning=0.,
                    sortEigenvectors=False,
                    progressOutput=False,
                    debugOutput=False):
        r"""
            Finds eigenstates in atom pair basis.

            ARPACK ( :obj:`scipy.sparse.linalg.eigsh`) calculation of the
            `noOfEigenvectors` eigenvectors closest to the original state. If
            `drivingFromState` is specified as `[n,l,j,mj,q]` coupling between
            the pair-states and the situation where one of the atoms in the
            pair state basis is in :math:`|n,l,j,m_j\rangle` state due to
            driving with a laser field that drives :math:`q` transition
            (+1,0,-1 for :math:`\sigma^-`, :math:`\pi` and :math:`\sigma^+`
            transitions respectively) is calculated and marked by the
            colourmaping these values on the obtained eigenvectors.

            Parameters:
                rangeR ( :obj:`array`): Array of values for distance between
                    the atoms (in :math:`\mu` m) for which we want to calculate
                    eigenstates.
                noOfEigenvectors (int): number of eigen vectors closest to the
                    energy of the original (unperturbed) pair state. Has to be
                    smaller then the total number of states.
                eigenstateDetuning (float, optional): Default is 0. This
                    specifies detuning from the initial pair-state (in Hz)
                    around which we want to find `noOfEigenvectors`
                    eigenvectors. This is useful when looking only for couple
                    of off-resonant features.
                drivingFromState ([int,int,float,float,int]): Optional. State
                    of one of the atoms from the original pair-state basis
                    from which we try to drive to the excited pair-basis
                    manifold, **assuming that the first of the two atoms is
                    already excited to the specified Rydberg state**.
                    By default, program will calculate just
                    contribution of the original pair-state in the eigenstates
                    obtained by diagonalization, and will highlight it's
                    admixure by colour mapping the obtained eigenstates plot.
                    State is specified as :math:`[n,\ell,j,mj, d]`
                    where :math:`d` is +1, 0 or
                    -1 for driving :math:`\sigma^-` , :math:`\pi`
                    and :math:`\sigma^+` transitions respectively.
                sortEigenvectors(bool): optional, False by default. Tries to
                    sort eigenvectors so that given eigen vector index
                    corresponds to adiabatically changing eigenstate, as
                    detirmined by maximising overlap between old and new
                    eigenvectors.
                progressOutput (bool): optional, False by default. If true,
                    prints information about the progress of the calculation.
                debugOutput (bool): optional, False by default. If true,
                    similarly to progressOutput=True, this will print
                    information about the progress of calculations, but with
                    more verbose output.
        """

        self.r = np.sort(rangeR)
        dimension = len(self.basisStates)

        self.noOfEigenvectors = noOfEigenvectors

        # energy of the state - to be calculated
        self.y = []
        # how much original state is contained in this eigenvector
        self.highlight = []
        # what are the dominant contributing states?
        self.composition = []

        if (noOfEigenvectors >= dimension - 1):
            noOfEigenvectors = dimension - 1
            print("Warning: Requested number of eigenvectors >=dimension-1\n \
                 ARPACK can only find up to dimension-1 eigenvectors, where\
                dimension is matrix dimension.\n")
            if noOfEigenvectors < 1:
                return

        coupling = []
        self.maxCoupling = 0.
        self.maxCoupledStateIndex = 0
        if (drivingFromState[0] != 0):
            self.drivingFromState = drivingFromState
            if progressOutput:
                print("Finding coupling strengths")
            # get first what was the state we are calculating coupling with
            state1 = drivingFromState
            n1 = int(round(state1[0]))
            l1 = int(round(state1[1]))
            j1 = state1[2]
            m1 = state1[3]
            q = state1[4]

            for i in xrange(dimension):
                thisCoupling = 0.

                if (int(abs(self.basisStates[i][5] - l1)) == 1
                    and abs(self.basisStates[i][0]
                            - self.basisStates[self.originalPairStateIndex][0])
                        < 0.1
                    and abs(self.basisStates[i][1]
                            - self.basisStates[self.originalPairStateIndex][1])
                        < 0.1
                    and abs(self.basisStates[i][2]
                            - self.basisStates[self.originalPairStateIndex][2])
                        < 0.1
                    and abs(self.basisStates[i][3]
                            - self.basisStates[self.originalPairStateIndex][3])
                    < 0.1
                        ):
                    state2 = self.basisStates[i]
                    n2 = int(state2[0 + 4])
                    l2 = int(state2[1 + 4])
                    j2 = state2[2 + 4]
                    m2 = state2[3 + 4]
                    if debugOutput:
                        print(n1, " ", l1, " ", j1, " ", m1, " ", n2,
                              " ", l2, " ", j2, " ", m2, " q=", q)
                        print(self.basisStates[i])
                    dme = self.atom2.getDipoleMatrixElement(n1, l1, j1, m1,
                                                           n2, l2, j2, m2,
                                                           q,  s=self.s2)
                    thisCoupling += dme

                thisCoupling = abs(thisCoupling)**2
                if thisCoupling > self.maxCoupling:
                    self.maxCoupling = thisCoupling
                    self.maxCoupledStateIndex = i
                if (thisCoupling > 0.000001) and debugOutput:
                    print("original pairstate index = ",
                          self.originalPairStateIndex)
                    print("this pairstate index = ", i)
                    print("state itself ", self.basisStates[i])
                    print("coupling = ", thisCoupling)
                coupling.append(thisCoupling)

            print("Maximal coupling from a state")
            print("is to a state ",
                  self.basisStates[self.maxCoupledStateIndex])
            print("is equal to %.3e a_0 e" % self.maxCoupling)

        if progressOutput:
            print("\n\nDiagonalizing interaction matrix...\n")

        rvalIndex = 0.
        previousEigenvectors = []

        for rval in self.r:
            if progressOutput:
                sys.stdout.write("\r%d%%" %
                                 (rvalIndex / len(self.r - 1) * 100.))
                sys.stdout.flush()
            rvalIndex += 1.

            # calculate interaction matrix

            m = self.matDiagonal

            rX = (rval * 1.e-6)**3
            for matRX in self.matR:
                m = m + matRX / rX
                rX *= (rval * 1.e-6)

            # uses ARPACK algorithm to find only noOfEigenvectors eigenvectors
            # sigma specifies center frequency (in GHz)
            ev, egvector = eigsh(
                m, noOfEigenvectors,
                sigma=eigenstateDetuning * 1.e-9,
                which='LM',
                tol=1E-6)

            if sortEigenvectors:
                # Find which eigenvectors overlap most with eigenvectors from
                # previous diagonalisatoin, in order to find "adiabatic"
                # continuation for the respective states

                if previousEigenvectors == []:
                    previousEigenvectors = np.copy(egvector)
                rowPicked = [False for i in range(len(ev))]
                columnPicked = [False for i in range(len(ev))]

                stateOverlap = np.zeros((len(ev), len(ev)))
                for i in range(len(ev)):
                    for j in range(len(ev)):
                        stateOverlap[i, j] = np.vdot(
                            egvector[:, i], previousEigenvectors[:, j])**2

                sortedOverlap = np.dstack(
                    np.unravel_index(
                        np.argsort(stateOverlap.ravel()),
                        (len(ev), len(ev)))
                    )[0]

                sortedEigenvaluesOrder = np.zeros(len(ev), dtype=np.int32)
                j = len(ev)**2 - 1
                for i in range(len(ev)):
                    while rowPicked[sortedOverlap[j, 0]] or \
                            columnPicked[sortedOverlap[j, 1]]:
                        j -= 1
                    rowPicked[sortedOverlap[j, 0]] = True
                    columnPicked[sortedOverlap[j, 1]] = True
                    sortedEigenvaluesOrder[sortedOverlap[j, 1]
                                           ] = sortedOverlap[j, 0]

                egvector = egvector[:, sortedEigenvaluesOrder]
                ev = ev[sortedEigenvaluesOrder]
                previousEigenvectors = np.copy(egvector)

            self.y.append(ev)

            if (drivingFromState[0] < 0.1):
                # if we've defined from which state we are driving
                sh = []
                comp = []
                for i in xrange(len(ev)):
                    sh.append(abs(egvector[self.originalPairStateIndex, i])**2)
                    comp.append(self._stateComposition(egvector[:, i]))
                self.highlight.append(sh)
                self.composition.append(comp)
            else:
                sh = []
                comp = []
                for i in xrange(len(ev)):
                    sumCoupledStates = 0.
                    for j in xrange(dimension):
                        sumCoupledStates += (
                            abs(coupling[j] / self.maxCoupling)
                            * abs(egvector[j, i])**2
                            )
                    comp.append(self._stateComposition(egvector[:, i]))
                    sh.append(sumCoupledStates)
                self.highlight.append(sh)
                self.composition.append(comp)

        # end of FOR loop over inter-atomic dinstaces

    def exportData(self, fileBase, exportFormat="csv"):
        """
            Exports PairStateInteractions calculation data.

            Only supported format (selected by default) is .csv in a
            human-readable form with a header that saves details of calculation.
            Function saves three files: 1) `filebase` _r.csv;
            2) `filebase` _energyLevels
            3) `filebase` _highlight

            For more details on the format, see header of the saved files.

            Parameters:
                filebase (string): filebase for the names of the saved files
                    without format extension. Add as a prefix a directory path
                    if necessary (e.g. saving outside the current working directory)
                exportFormat (string): optional. Format of the exported file. Currently
                    only .csv is supported but this can be extended in the future.
        """
        fmt = 'on %Y-%m-%d @ %H:%M:%S'
        ts = datetime.datetime.now().strftime(fmt)

        commonHeader = "Export from Alkali Rydberg Calculator (ARC) %s.\n" % ts
        commonHeader += ("\n *** Pair State interactions for %s %s m_j = %d/2 , %s %s m_j = %d/2 pair-state. ***\n\n" %
                         (self.atom1.elementName,
                          printStateString(self.n, self.l, self.j), int(
                              round(2. * self.m1)),
                          self.atom2.elementName,
                          printStateString(self.nn, self.ll, self.jj), int(round(2. * self.m2))))
        if (self.interactionsUpTo == 1):
            commonHeader += " - Pair-state interactions included up to dipole-dipole coupling.\n"
        elif (self.interactionsUpTo == 2):
            commonHeader += " - Pair-state interactions included up to quadrupole-quadrupole coupling.\n"
        commonHeader += (" - Pair-state interactions calculated for manifold with spin angular momentum s1 = %.1d s2 = %.1d .\n"
                         % (self.s1, self.s2))

        if hasattr(self, 'theta'):
            commonHeader += " - Atom orientation:\n"
            commonHeader += "      theta (polar angle) = %.5f x pi\n" % (
                self.theta / pi)
            commonHeader += "      phi (azimuthal angle) = %.5f x pi\n" % (
                self.phi / pi)
            commonHeader += " - Calculation basis includes:\n"
            commonHeader += "      States with principal quantum number in range [%d-%d]x[%d-%d],\n" %\
                            (self.n - self.nRange, self.n + self.nRange,
                             self.nn - self.nRange, self.nn + self.nRange)
            commonHeader += "      AND whose orbital angular momentum (l) is in range [%d-%d] (i.e. %s-%s),\n" %\
                            (0, self.lrange, printStateLetter(
                                0), printStateLetter(self.lrange))
            commonHeader += "      AND whose pair-state energy difference is at most %.3f GHz\n" %\
                (self.energyDelta / 1.e9)
            commonHeader += "      (energy difference is measured relative to original pair-state).\n"
        else:
            commonHeader += " ! Atom orientation and basis not yet set (this is set in defineBasis method).\n"

        if hasattr(self, "noOfEigenvectors"):
            commonHeader += " - Finding %d eigenvectors closest to the given pair-state\n" %\
                            self.noOfEigenvectors

            if self.drivingFromState[0] < 0.1:
                commonHeader += " - State highlighting based on the relative contribution \n" +\
                    "   of the original pair-state in the eigenstates obtained by diagonalization.\n"
            else:
                commonHeader += (" - State highlighting based on the relative driving strength \n" +
                                 "   to a given energy eigenstate (energy level) from state\n" +
                                 "   %s m_j =%d/2 with polarization q=%d.\n" %
                                 (printStateString(*self.drivingFromState[0:3]),
                                  int(round(2. * self.drivingFromState[3])),
                                     self.drivingFromState[4]))

        else:
            commonHeader += " ! Energy levels not yet found (this is done by calling diagonalise method).\n"

        if exportFormat == "csv":
            print("Exporting StarkMap calculation results as .csv ...")

            commonHeader += " - Export consists of three (3) files:\n"
            commonHeader += ("       1) %s,\n" %
                             (fileBase + "_r." + exportFormat))
            commonHeader += ("       2) %s,\n" %
                             (fileBase + "_energyLevels." + exportFormat))
            commonHeader += ("       3) %s.\n\n" %
                             (fileBase + "_highlight." + exportFormat))

            filename = fileBase + "_r." + exportFormat
            np.savetxt(filename,
                       self.r, fmt='%.18e', delimiter=', ',
                       newline='\n',
                       header=(commonHeader +
                               " - - - Interatomic distance, r (\mu m) - - -"),
                       comments='# ')
            print("   Interatomic distances (\mu m) saved in %s" % filename)

            filename = fileBase + "_energyLevels." + exportFormat
            headerDetails = " NOTE : Each row corresponds to eigenstates for a single specified interatomic distance"
            np.savetxt(filename,
                       self.y, fmt='%.18e', delimiter=', ',
                       newline='\n',
                       header=(commonHeader +
                               ' - - - Energy (GHz) - - -\n' + headerDetails),
                       comments='# ')
            print("   Lists of energies (in GHz relative to the original pair-state energy)" +
                  (" saved in %s" % filename))

            filename = fileBase + "_highlight." + exportFormat
            np.savetxt(filename,
                       self.highlight, fmt='%.18e', delimiter=', ',
                       newline='\n',
                       header=(
                           commonHeader + ' - - - Highlight value (rel.units) - - -\n' + headerDetails),
                       comments='# ')
            print("   Highlight values saved in %s" % filename)

            print("... data export finished!")
        else:
            raise ValueError("Unsupported export format (.%s)." % format)

    def _stateComposition(self, stateVector):
        contribution = np.absolute(stateVector)
        order = np.argsort(contribution, kind='heapsort')
        index = -1
        totalContribution = 0
        value = "$"
        while (index > -5) and (totalContribution < 0.95):
            i = order[index]
            if (index != -1 and
                (stateVector[i].real > 0 or abs(stateVector[i].imag) > 1e-9)):
                value += "+"
            if (abs(self.phi) < 1e-9):
                value = value + \
                    ("%.2f" % stateVector[i]) + \
                    self._addState(*self.basisStates[i])
            else:
                value = value + \
                    ("(%.2f+i%.2f)" % (stateVector[i].real, stateVector[i].imag)) + \
                    self._addState(*self.basisStates[i])
            totalContribution += contribution[i]**2
            index -= 1

        if totalContribution < 0.999:
            value += "+\\ldots"
        return value + "$"

    def _addState(self, n1, l1, j1, mj1, n2, l2, j2, mj2):
        stateString = ""
        if (abs(self.s1 - 0.5) < 0.1):
            # Alkali atom
            stateString += "|%s %d/2" %\
                (printStateStringLatex(n1, l1, j1, s=self.s1), int(2 * mj1))
        else:
            # divalent atoms
            stateString += "|%s %d" %\
                (printStateStringLatex(n1, l1, j1, s=self.s1), int(mj1))

        if (abs(self.s2 - 0.5) < 0.1):
            # Alkali atom
            stateString += ",%s %d/2\\rangle" %\
                (printStateStringLatex(n2, l2, j2, s=self.s2), int(2 * mj2))
        else:
            # divalent atom
            stateString += ",%s %d\\rangle" %\
                (printStateStringLatex(n2, l2, j2, s=self.s2), int(mj2))
        return stateString

    def plotLevelDiagram(self,  highlightColor='red',
                         highlightScale='linear',
                         units='GHz'):
        """
            Plots pair state level diagram

            Call :obj:`showPlot` if you want to display a plot afterwards.

            Parameters:
                highlightColor (string): optional, specifies the colour used
                    for state highlighting
                highlightScale (string): optional, specifies scaling of
                    state highlighting. Default is 'linear'. Use 'log-2' or
                    'log-3' for logarithmic scale going down to 1e-2 and 1e-3
                    respectively. Logarithmic scale is useful for spotting
                    weakly admixed states.
                units (:obj:`char`,optional): possible values {'*GHz*','cm','eV'};
                    [case insensitive] if value is 'GHz' (default), diagram will
                    be plotted as energy :math:`/h` in units of GHz; if the
                    string contains 'cm' diagram will be plotted in energy units
                    cm :math:`{}^{-1}`; if the value is 'eV', diagram
                    will be plotted as energy in units eV.
        """

        rvb = LinearSegmentedColormap.from_list('mymap',
                                                ['0.9', highlightColor])

        if units.lower() == 'ev':
            self.units = 'eV'
            self.scaleFactor = 1e9 * C_h / C_e
            eLabel = '';
        elif units.lower() == 'ghz':
            self.units = 'GHz'
            self.scaleFactor = 1
            eLabel = '/h'
        elif 'cm' in units.lower():
            self.units = 'cm$^{-1}$'
            self.scaleFactor = 1e9 / (C_c * 100)
            eLabel = '/(h c)'

        if highlightScale == 'linear':
            cNorm = matplotlib.colors.Normalize(vmin=0., vmax=1.)
        elif highlightScale == 'log-2':
            cNorm = matplotlib.colors.LogNorm(vmin=1e-2, vmax=1)
        elif highlightScale == 'log-3':
            cNorm = matplotlib.colors.LogNorm(vmin=1e-3, vmax=1)
        else:
            raise ValueError("Only 'linear', 'log-2' and 'log-3' are valid "
                             "inputs for highlightScale")

        print(" Now we are plotting...")
        self.fig, self.ax = plt.subplots(1, 1, figsize=(11.5, 5.0))

        self.y = np.array(self.y)
        self.highlight = np.array(self.highlight)

        colorfulX = []
        colorfulY = []
        colorfulState = []

        for i in xrange(len(self.r)):

            for j in xrange(len(self.y[i])):
                colorfulX.append(self.r[i])
                colorfulY.append(self.y[i][j])
                colorfulState.append(self.highlight[i][j])

        colorfulState = np.array(colorfulState)
        sortOrder = colorfulState.argsort(kind='heapsort')
        colorfulX = np.array(colorfulX)
        colorfulY = np.array(colorfulY)

        colorfulX = colorfulX[sortOrder]
        colorfulY = colorfulY[sortOrder]
        colorfulState = colorfulState[sortOrder]

        self.ax.scatter(colorfulX, colorfulY * self.scaleFactor,
                        s=10, c=colorfulState, linewidth=0,
                        norm=cNorm, cmap=rvb, zorder=2, picker=5)
        cax = self.fig.add_axes([0.91, 0.1, 0.02, 0.8])
        cb = matplotlib.colorbar.ColorbarBase(cax, cmap=rvb, norm=cNorm)

        if (self.drivingFromState[0] == 0):
            # colouring is based on the contribution of the original pair state here
            label = ""
            if (abs(self.s1-0.5) < 0.1):
                # Alkali atom
                label += r"$|\langle %s m_j=%d/2 " % \
                             (printStateStringLatex(self.n, self.l, self.j),
                              int(round(2. * self.m1, 0)))
            else:
                # divalent atom
                label += r"$|\langle %s m_j=%d " % \
                             (printStateStringLatex(self.n, self.l, self.j,
                                                    s=self.s1),
                              int(round(self.m1, 0)))

            if (abs(self.s2-0.5) < 0.1):
                # Alkali atom
                label += r", %s m_j=%d/2 | \mu \rangle |^2$" % \
                             (printStateStringLatex(self.nn, self.ll, self.jj),
                              int(round(2. * self.m2, 0)))
            else:
                # divalent atom
                label += r", %s m_j=%d | \mu \rangle |^2$" % \
                             (printStateStringLatex(self.nn, self.ll, self.jj,
                                                    s=self.s2),
                              int(round(self.m2, 0)))

            cb.set_label(label)
        else:
            # colouring is based on the coupling to different states
            cb.set_label(r"$(\Omega_\mu/\Omega)^2$")

        self.ax.set_xlabel(r"Interatomic distance, $R$ ($\mu$m)")
        self.ax.set_ylabel(r"Pair-state relative energy, $\Delta E %s$ (%s)"
                           % (eLabel, self.units))

    def savePlot(self, filename="PairStateInteractions.pdf"):
        """
            Saves plot made by :obj:`PairStateInteractions.plotLevelDiagram`

            Args:
                filename (:obj:`str`, optional): file location where the plot
                    should be saved
        """
        if (self.fig != 0):
            self.fig.savefig(filename, bbox_inches='tight')
        else:
            print("Error while saving a plot: nothing is plotted yet")
        return 0

    def showPlot(self, interactive=True):
        """
            Shows level diagram printed by
            :obj:`PairStateInteractions.plotLevelDiagram`

            By default, it will output interactive plot, which means that
            clicking on the state will show the composition of the clicked
            state in original basis (dominant elements)

            Args:
                interactive (bool): optional, by default it is True. If true,
                    plotted graph will be interactive, i.e. users can click
                    on the state to identify the state composition

            Note:
                interactive=True has effect if the graphs are explored in usual
                matplotlib pop-up windows. It doesn't have effect on inline
                plots in Jupyter (IPython) notebooks.


        """
        if interactive:
            self.ax.set_title("Click on state to see state composition")
            self.clickedPoint = 0
            self.fig.canvas.draw()
            self.fig.canvas.mpl_connect('pick_event', self._onPick)

        plt.show()
        return 0

    def _onPick(self, event):
        if isinstance(event.artist, matplotlib.collections.PathCollection):
            x = event.mouseevent.xdata
            y = event.mouseevent.ydata / self.scaleFactor

            i = np.searchsorted(self.r, x)
            if i == len(self.r):
                i -= 1
            if ((i > 0) and (abs(self.r[i - 1] - x) < abs(self.r[i] - x))):
                i -= 1

            j = 0
            for jj in xrange(len(self.y[i])):
                if (abs(self.y[i][jj] - y) < abs(self.y[i][j] - y)):
                    j = jj

            # now choose the most higlighted state in this area
            distance = abs(self.y[i][j] - y) * 1.5
            for jj in xrange(len(self.y[i])):
                if (abs(self.y[i][jj] - y) < distance and
                        (abs(self.highlight[i][jj]) > abs(self.highlight[i][j]))):
                    j = jj

            if (self.clickedPoint != 0):
                self.clickedPoint.remove()

            self.clickedPoint, = self.ax.plot([self.r[i]],
                                              [self.y[i][j] * self.scaleFactor], "bs",
                                              linewidth=0, zorder=3)

            self.ax.set_title("State = " + self.composition[i][j] +
                              ("   Colourbar = %.2f" % self.highlight[i][j]), fontsize=11)

            event.canvas.draw()

    def getC6fromLevelDiagram(self, rStart, rStop, showPlot=False,
                              minStateContribution=0.0):
        """
            Finds :math:`C_6` coefficient for original pair state.

            Function first finds for each distance in the range
            [ `rStart` , `rStop` ] the eigen state with highest contribution of
            the original state. One can set optional parameter
            `minStateContribution` to value in the range [0,1), so that function
            finds only states if they have contribution of the original state
            that is bigger then `minStateContribution`.

            Once original pair-state is found in the range of interatomic
            distances, from smallest `rStart` to the biggest `rStop`, function
            will try to perform fitting of the corresponding state energy
            :math:`E(R)` at distance :math:`R` to the function
            :math:`A+C_6/R^6` where :math:`A` is some offset.

            Args:
                rStart (float): smallest inter-atomic distance to be used for fitting
                rStop (float): maximum inter-atomic distance to be used for fitting
                showPlot (bool): If set to true, it will print the plot showing
                    fitted energy level and the obtained best fit. Default is
                    False
                minStateContribution (float): valid values are in the range [0,1).
                    It specifies minimum amount of the original state in the given
                    energy state necessary for the state to be considered for
                    the adiabatic continuation of the original unperturbed
                    pair state.

            Returns:
                float:
                    :math:`C_6` measured in :math:`\\text{GHz }\\mu\\text{m}^6`
                    on success; If unsuccessful returns False.

            Note:
                In order to use this functions, highlighting in
                :obj:`diagonalise` should be based on the original pair
                state contribution of the eigenvectors (that this,
                `drivingFromState` parameter should not be set, which
                corresponds to `drivingFromState` = [0,0,0,0,0]).
        """
        initialStateDetuning = []
        initialStateDetuningX = []

        fromRindex = -1
        toRindex = -1
        for br in xrange(len(self.r)):
            if (fromRindex == -1) and (self.r[br] >= rStart):
                fromRindex = br
            if (self.r[br] > rStop):
                toRindex = br - 1
                break
        if (fromRindex != -1) and (toRindex == -1):
            toRindex = len(self.r) - 1
        if (fromRindex == -1):
            print("\nERROR: could not find data for energy levels for interatomic")
            print("distances between %2.f and %.2f mu m.\n\n" % (rStart, rStop))
            return 0

        for br in xrange(fromRindex, toRindex + 1):
            index = -1
            maxPortion = minStateContribution
            for br2 in xrange(len(self.y[br])):
                if (abs(self.highlight[br][br2]) > maxPortion):
                    index = br2
                    maxPortion = abs(self.highlight[br][br2])
            if (index != -1):
                initialStateDetuning.append(abs(self.y[br][index]))
                initialStateDetuningX.append(self.r[br])

        initialStateDetuning = np.log(np.array(initialStateDetuning))
        initialStateDetuningX = np.array(initialStateDetuningX)

        def c6fit(r, c6, offset):
            return np.log(c6 / r**6 + offset)

        try:
            popt, pcov = curve_fit(c6fit,
                                   initialStateDetuningX,
                                   initialStateDetuning,
                                   [1, 0])
        except Exception as ex:
            print(ex)
            print("ERROR: unable to find a fit for C6.")
            return False
        print("c6 = ", popt[0], " GHz /R^6 (mu m)^6")
        print("offset = ", popt[1])

        y_fit = []
        for val in initialStateDetuningX:
            y_fit.append(c6fit(val, popt[0], popt[1]))
        y_fit = np.array(y_fit)

        if showPlot:
            fig, ax = plt.subplots(1, 1, figsize=(8.0, 5.0))
            ax.loglog(initialStateDetuningX, np.exp(initialStateDetuning),
                      "b-", lw=2, zorder=1)
            ax.loglog(initialStateDetuningX, np.exp(y_fit),
                      "r--", lw=2, zorder=2)

            ax.legend(("calculated energy level", "fitted model function"),
                      loc=1, fontsize=10)

            ax.set_xlim(np.min(self.r),
                        np.max(self.r))
            ymin = np.min(initialStateDetuning)
            ymax = np.max(initialStateDetuning)
            ax.set_ylim(exp(ymin), exp(ymax))

            minorLocator = mpl.ticker.MultipleLocator(1)
            minorFormatter = mpl.ticker.FormatStrFormatter('%d')
            ax.xaxis.set_minor_locator(minorLocator)
            ax.xaxis.set_minor_formatter(minorFormatter)
            ax.xaxis.set_major_formatter(plt.NullFormatter())
            ax.set_xlabel(r"Interatomic distance, $r$ ($\mu$m)")
            ax.set_ylabel(r"Pair-state energy, $|E|$ (GHz)")
            ax.set_title(r"$C_6$ fit")
            plt.show()

        self.fitX = initialStateDetuningX
        self.fitY = initialStateDetuning
        self.fittedCurveY = y_fit

        return popt[0]

    def getC3fromLevelDiagram(self, rStart, rStop, showPlot=False,
                              minStateContribution=0.0,
                              resonantBranch=+1):
        """
            Finds :math:`C_3` coefficient for original pair state.

            Function first finds for each distance in the range
            [`rStart` , `rStop`] the eigen state with highest contribution of
            the original state. One can set optional parameter
            `minStateContribution` to value in the range [0,1), so that function
            finds only states if they have contribution of the original state
            that is bigger then `minStateContribution`.

            Once original pair-state is found in the range of interatomic
            distances, from smallest `rStart` to the biggest `rStop`, function
            will try to perform fitting of the corresponding state energy
            :math:`E(R)` at distance :math:`R` to the function
            :math:`A+C_3/R^3` where :math:`A` is some offset.

            Args:
                rStart (float): smallest inter-atomic distance to be used for fitting
                rStop (float): maximum inter-atomic distance to be used for fitting
                showPlot (bool): If set to true, it will print the plot showing
                    fitted energy level and the obtained best fit. Default is
                    False
                minStateContribution (float): valid values are in the range [0,1).
                    It specifies minimum amount of the original state in the given
                    energy state necessary for the state to be considered for
                    the adiabatic continuation of the original unperturbed
                    pair state.
                resonantBranch (int): optional, default +1. For resonant
                    interactions we have two branches with identical
                    state contributions. In this case, we will select only
                    positively detuned branch (for resonantBranch = +1)
                    or negatively detuned branch (fore resonantBranch = -1)
                    depending on the value of resonantBranch optional parameter
            Returns:
                float:
                    :math:`C_3` measured in :math:`\\text{GHz }\\mu\\text{m}^6`
                    on success; If unsuccessful returns False.

            Note:
                In order to use this functions, highlighting in
                :obj:`diagonalise` should be based on the original pair
                state contribution of the eigenvectors (that this,
                `drivingFromState` parameter should not be set, which
                corresponds to `drivingFromState` = [0,0,0,0,0]).
        """

        selectBranch = False
        if (abs(self.l - self.ll) == 1):
            selectBranch = True
            resonantBranch = float(resonantBranch)

        initialStateDetuning = []
        initialStateDetuningX = []

        fromRindex = -1
        toRindex = -1
        for br in xrange(len(self.r)):
            if (fromRindex == -1) and (self.r[br] >= rStart):
                fromRindex = br
            if (self.r[br] > rStop):
                toRindex = br - 1
                break
        if (fromRindex != -1) and (toRindex == -1):
            toRindex = len(self.r) - 1
        if (fromRindex == -1):
            print("\nERROR: could not find data for energy levels for interatomic")
            print("distances between %2.f and %.2f mu m.\n\n" % (rStart, rStop))
            return False

        discontinuityDetected = False
        for br in xrange(toRindex, fromRindex - 1, -1):
            index = -1
            maxPortion = minStateContribution
            for br2 in xrange(len(self.y[br])):
                if (abs(self.highlight[br][br2]) > maxPortion) \
                        and (not selectBranch or (self.y[br][br2] * selectBranch > 0.)):
                    index = br2
                    maxPortion = abs(self.highlight[br][br2])

            if (len(initialStateDetuningX) > 2):
                slope1 = (initialStateDetuning[-1] - initialStateDetuning[-2]) /\
                    (initialStateDetuningX[-1] - initialStateDetuningX[-2])
                slope2 = (abs(self.y[br][index]) - initialStateDetuning[-1]) /\
                    (self.r[br] - initialStateDetuningX[-1])
                if abs(slope2) > 3. * abs(slope1):
                    discontinuityDetected = True
            if (index != -1)and (not discontinuityDetected):
                initialStateDetuning.append(abs(self.y[br][index]))
                initialStateDetuningX.append(self.r[br])

        initialStateDetuning = np.log(np.array(initialStateDetuning))  # *1e9
        initialStateDetuningX = np.array(initialStateDetuningX)

        def c3fit(r, c3, offset):
            return np.log(c3 / r**3 + offset)

        try:
            popt, pcov = curve_fit(c3fit,
                                   initialStateDetuningX,
                                   initialStateDetuning,
                                   [1, 0])
        except Exception as ex:
            print(ex)
            print("ERROR: unable to find a fit for C3.")
            return False
        print("c3 = ", popt[0], " GHz /R^3 (mu m)^3")
        print("offset = ", popt[1])

        y_fit = []

        for val in initialStateDetuningX:
            y_fit.append(c3fit(val, popt[0], popt[1]))
        y_fit = np.array(y_fit)

        if showPlot:
            fig, ax = plt.subplots(1, 1, figsize=(8.0, 5.0))
            ax.loglog(initialStateDetuningX, np.exp(initialStateDetuning),
                      "b-", lw=2, zorder=1)
            ax.loglog(initialStateDetuningX, np.exp(y_fit),
                      "r--", lw=2, zorder=2)

            ax.legend(("calculated energy level", "fitted model function"),
                      loc=1, fontsize=10)
            ax.set_xlim(np.min(self.r),
                        np.max(self.r))
            ymin = np.min(initialStateDetuning)
            ymax = np.max(initialStateDetuning)
            ax.set_ylim(exp(ymin), exp(ymax))

            minorLocator = mpl.ticker.MultipleLocator(1)
            minorFormatter = mpl.ticker.FormatStrFormatter('%d')
            ax.xaxis.set_minor_locator(minorLocator)
            ax.xaxis.set_minor_formatter(minorFormatter)
            ax.xaxis.set_major_formatter(plt.NullFormatter())
            ax.set_xlabel(r"Interatomic distance, $r$ ($\mu$m)")
            ax.set_ylabel(r"Pair-state energy, $|E|$ (GHz)")

            locatorStep = 1.
            while (locatorStep > (ymax - ymin)) and locatorStep > 1.e-4:
                locatorStep /= 10.

            ax.yaxis.set_major_locator(mpl.ticker.MultipleLocator(locatorStep))
            ax.yaxis.set_major_formatter(mpl.ticker.FormatStrFormatter('%.3f'))
            ax.yaxis.set_minor_locator(
                mpl.ticker.MultipleLocator(locatorStep / 10.))
            ax.yaxis.set_minor_formatter(plt.NullFormatter())
            # ax.yaxis.set_minor_formatter(mpl.ticker.FormatStrFormatter('%.3f'))

            ax.set_title(r"$C_3$ fit")

            plt.show()

        self.fitX = initialStateDetuningX
        self.fitY = initialStateDetuning
        self.fittedCurveY = y_fit

        return popt[0]

    def getVdwFromLevelDiagram(self, rStart, rStop, showPlot=False,
                               minStateContribution=0.0):
        """
            Finds :math:`r_{\\rm vdW}` coefficient for original pair state.

            Function first finds for each distance in the range [`rStart`,`rStop`]
            the eigen state with highest contribution of the original state.
            One can set optional parameter `minStateContribution` to value in
            the range [0,1), so that function finds only states if they have
            contribution of the original state that is bigger then
            `minStateContribution`.

            Once original pair-state is found in the range of interatomic
            distances, from smallest `rStart` to the biggest `rStop`, function
            will try to perform fitting of the corresponding state energy
            :math:`E(R)` at distance :math:`R` to the function
            :math:`A+B\\frac{1-\\sqrt{1+(r_{\\rm vdW}/r)^6}}{1-\\sqrt{1+r_{\\rm vdW}^6}}`
             where :math:`A` and :math:`B` are some offset.

            Args:
                rStart (float): smallest inter-atomic distance to be used for fitting
                rStop (float): maximum inter-atomic distance to be used for fitting
                showPlot (bool): If set to true, it will print the plot showing
                    fitted energy level and the obtained best fit. Default is
                    False
                minStateContribution (float): valid values are in the range [0,1).
                    It specifies minimum amount of the original state in the given
                    energy state necessary for the state to be considered for
                    the adiabatic continuation of the original unperturbed
                    pair state.
            Returns:
                float: :math:`r_{\\rm vdW}`  measured in :math:`\\mu\\text{m}`
                on success; If unsuccessful returns False.

            Note:
                In order to use this functions, highlighting in
                :obj:`diagonalise` should be based on the original pair
                state contribution of the eigenvectors (that this,
                `drivingFromState` parameter should not be set, which
                corresponds to `drivingFromState` = [0,0,0,0,0]).
        """

        initialStateDetuning = []
        initialStateDetuningX = []

        fromRindex = -1
        toRindex = -1
        for br in xrange(len(self.r)):
            if (fromRindex == -1) and (self.r[br] >= rStart):
                fromRindex = br
            if (self.r[br] > rStop):
                toRindex = br - 1
                break
        if (fromRindex != -1) and (toRindex == -1):
            toRindex = len(self.r) - 1
        if (fromRindex == -1):
            print("\nERROR: could not find data for energy levels for interatomic")
            print("distances between %2.f and %.2f mu m.\n\n" % (rStart, rStop))
            return False

        discontinuityDetected = False
        for br in xrange(toRindex, fromRindex - 1, -1):
            index = -1
            maxPortion = minStateContribution
            for br2 in xrange(len(self.y[br])):
                if (abs(self.highlight[br][br2]) > maxPortion):
                    index = br2
                    maxPortion = abs(self.highlight[br][br2])
            if (len(initialStateDetuningX) > 2):
                slope1 = (initialStateDetuning[-1] - initialStateDetuning[-2]) /\
                    (initialStateDetuningX[-1] - initialStateDetuningX[-2])
                slope2 = (abs(self.y[br][index]) - initialStateDetuning[-1]) /\
                    (self.r[br] - initialStateDetuningX[-1])
                if abs(slope2) > 3. * abs(slope1):
                    discontinuityDetected = True
            if (index != -1)and (not discontinuityDetected):
                initialStateDetuning.append(abs(self.y[br][index]))
                initialStateDetuningX.append(self.r[br])

        initialStateDetuning = np.log(abs(np.array(initialStateDetuning)))
        initialStateDetuningX = np.array(initialStateDetuningX)

        def vdwFit(r, offset, scale, vdw):
            return np.log(abs(offset
                              + scale * (1. - np.sqrt(1. + (vdw / r)**6))
                              / (1. - np.sqrt(1 + vdw**6))
                              )
                          )

        noOfPoints = len(initialStateDetuningX)
        print("Data points to fit = ", noOfPoints)

        try:
            popt, pcov = curve_fit(vdwFit,
                                   initialStateDetuningX,
                                   initialStateDetuning,
                                   [0, initialStateDetuning[noOfPoints // 2],
                                    initialStateDetuningX[noOfPoints // 2]])
        except Exception as ex:
            print(ex)
            print("ERROR: unable to find a fit for van der Waals distance.")
            return False

        if ((initialStateDetuningX[0] < popt[2])
                or (popt[2] < initialStateDetuningX[-1])):
            print("WARNING: vdw radius seems to be outside the fitting range!")
            print(
                "It's estimated to be around %.2f mu m from the current fit."
                % popt[2])

        print("Rvdw =  ", popt[2], " mu m")
        print("offset = ", popt[0], "\n scale = ", popt[1])

        y_fit = []

        for val in initialStateDetuningX:
            y_fit.append(vdwFit(val, popt[0], popt[1], popt[2]))
        y_fit = np.array(y_fit)

        if showPlot:
            fig, ax = plt.subplots(1, 1, figsize=(8.0, 5.0))
            ax.loglog(initialStateDetuningX, np.exp(initialStateDetuning),
                      "b-", lw=2, zorder=1)
            ax.loglog(initialStateDetuningX, np.exp(y_fit),
                      "r--", lw=2, zorder=2)

            ax.set_xlim(np.min(self.r),
                        np.max(self.r))
            ymin = np.min(initialStateDetuning)
            ymax = np.max(initialStateDetuning)
            ax.set_ylim(exp(ymin), exp(ymax))

            ax.axvline(x=popt[2], color="k")
            ax.text(popt[2], exp((ymin + ymax) / 2.),
                    r"$R_{vdw} = %.1f$ $\mu$m" % popt[2])

            minorLocator = mpl.ticker.MultipleLocator(1)
            minorFormatter = mpl.ticker.FormatStrFormatter('%d')
            ax.xaxis.set_minor_locator(minorLocator)
            ax.xaxis.set_minor_formatter(minorFormatter)
            ax.xaxis.set_major_formatter(plt.NullFormatter())
            ax.set_xlabel(r"Interatomic distance, $r$ ($\mu$m)")
            ax.set_ylabel(r"Pair-state energy, $|E|$ (GHz)")
            ax.legend(("calculated energy level", "fitted model function"),
                      loc=1, fontsize=10)

            plt.show()

        self.fitX = initialStateDetuningX
        self.fitY = initialStateDetuning
        self.fittedCurveY = y_fit

        return popt[2]


class StarkMapResonances:
    """
        Calculates pair state Stark maps for finding resonances

        Tool for finding conditions for Foster resonances. For a given pair
        state, in a given range of the electric fields, looks for the pair-state
        that are close in energy and coupled via dipole-dipole interactions
        to the original pair-state.

        See `Stark resonances example snippet`_.

        .. _`Stark resonances example snippet`:
                ././Rydberg_atoms_a_primer.html#Tuning-the-interaction-strength-with-electric-fields

        Parameters:
            atom1 (:obj:`arc.alkali_atom_functions.AlkaliAtom` or :obj:`arc.divalent_atom_functions.DivalentAtom`):
                ={ :obj:`arc.alkali_atom_data.Lithium6`,
                :obj:`arc.alkali_atom_data.Lithium7`,
                :obj:`arc.alkali_atom_data.Sodium`,
                :obj:`arc.alkali_atom_data.Potassium39`,
                :obj:`arc.alkali_atom_data.Potassium40`,
                :obj:`arc.alkali_atom_data.Potassium41`,
                :obj:`arc.alkali_atom_data.Rubidium85`,
                :obj:`arc.alkali_atom_data.Rubidium87`,
                :obj:`arc.alkali_atom_data.Caesium`,
                :obj:`arc.divalent_atom_data.Strontium88`,
                :obj:`arc.divalent_atom_data.Calcium40`
                :obj:`arc.divalent_atom_data.Ytterbium174` }
                 the first atom in the pair-state
            state1 ([int,int,float,float,(float)]): specification of the state
                of the first state as an array of values :math:`[n,l,j,m_j]`.
                For :obj:`arc.divalent_atom_functions.DivalentAtom` and other divalent atoms, 5th value
                should be added specifying total spin angular momentum `s`.
                Full definition of state then has format
                :math:`[n,l,j,m_j,s]`.
            atom2 (:obj:`arc.alkali_atom_functions.AlkaliAtom` or :obj:`arc.divalent_atom_functions.DivalentAtom`):
                ={ :obj:`arc.alkali_atom_data.Lithium6`,
                :obj:`arc.alkali_atom_data.Lithium7`,
                :obj:`arc.alkali_atom_data.Sodium`,
                :obj:`arc.alkali_atom_data.Potassium39`,
                :obj:`arc.alkali_atom_data.Potassium40`,
                :obj:`arc.alkali_atom_data.Potassium41`,
                :obj:`arc.alkali_atom_data.Rubidium85`,
                :obj:`arc.alkali_atom_data.Rubidium87`,
                :obj:`arc.alkali_atom_data.Caesium`,
                :obj:`arc.divalent_atom_data.Strontium88`,
                :obj:`arc.divalent_atom_data.Calcium40`
                :obj:`arc.divalent_atom_data.Ytterbium174` }
                 the second atom in the pair-state
            state2 ([int,int,float,float,(float)]): specification of the state
                of the first state as an array of values :math:`[n,l,j,m_j]`,
                For :obj:`arc.divalent_atom_functions.DivalentAtom` and other divalent atoms, 5th value
                should be added specifying total spin angular momentum `s`.
                Full definition of state then has format
                :math:`[n,l,j,m_j,s]`.

        Note:
            In checking if certain state is dipole coupled to the original
            state, only the highest contributing state is checked for dipole
            coupling. This should be fine if one is interested in resonances
            in weak fields. For stronger fields, one might want to include
            effect of coupling to other contributing base states.



    """

    def __init__(self, atom1, state1, atom2, state2):

        self.atom1 = atom1
        if (issubclass(type(self.atom1), DivalentAtom)
            and (len(state1) != 5 or (state1[4] != 0 and state1[4] != 1))
                ):
            raise ValueError("For divalent atoms state specification has to "
                             "include total spin angular momentum s as the last "
                             "number in the state specification [n,l,j,m_j,s].")
        self.state1 = state1
        # add exlicitly total spin of the state for Alkaline atoms
        if (len(self.state1) == 4): self.state1.append(0.5)

        self.atom2 = atom2
        if (issubclass(type(self.atom2), DivalentAtom)
                and (len(state1) != 5 or (state1[4] != 0 and state1[4] != 1))
                    ):
            raise ValueError("For divalent atoms state specification has to "
                             "include total spin angular momentum s as the last "
                             "numbre in the state specification [n,l,j,m_j,s].")
        self.state2 = state2
        # add exlicitly total spin of the state for Alkaline atoms
        if (len(self.state2) == 4):
            self.state2.append(0.5)

        self.pairStateEnergy = (
            atom1.getEnergy(self.state1[0],
                            self.state1[1],
                            self.state1[2],
                            s=self.state1[4])
            + atom2.getEnergy(self.state2[0],
                              self.state2[1],
                              self.state2[2],
                              s=self.state2[4])
            ) * C_e / C_h * 1e-9

    def findResonances(self, nMin, nMax, maxL, eFieldList, energyRange=[-5.e9, +5.e9],
                       Bz=0, progressOutput=False):
        """
            Finds near-resonant dipole-coupled pair-states

            For states in range of principal quantum numbers [`nMin`,`nMax`]
            and orbital angular momentum [0,`maxL`], for a range of electric fields
            given by `eFieldList` function will find near-resonant pair states.

            Only states that are in the range given by `energyRange` will be
            extracted from the pair-state Stark maps.

            Args:
                nMin (int): minimal principal quantum number of the state to be
                    included in the StarkMap calculation
                nMax (int): maximal principal quantum number of the state to be
                    included in the StarkMap calculation
                maxL (int): maximum value of orbital angular momentum for the states
                    to be included in the calculation
                eFieldList ([float]): list of the electric fields (in V/m) for
                    which to calculate level diagram (StarkMap)
                Bz (float): optional, magnetic field directed along z-axis in
                    units of Tesla. Calculation will be correct only for weak
                    magnetic fields, where paramagnetic term is much stronger
                    then diamagnetic term. Diamagnetic term is neglected.
                energyRange ([float,float]): optinal argument. Minimal and maximal
                    energy of that some dipole-coupled state should have in order
                    to keep it in the plot (in units of Hz). By default it finds
                    states that are :math:`\pm 5` GHz
                progressOutput (:obj:`bool`, optional): if True prints the
                    progress of calculation; Set to false by default.
        """

        self.eFieldList = eFieldList
        self.Bz = Bz
        eMin = energyRange[0] * 1.e-9  # in GHz
        eMax = energyRange[1] * 1.e-9

        # find where is the original pair state

        sm1 = StarkMap(self.atom1)
        sm1.defineBasis(self.state1[0], self.state1[1], self.state1[2],
                        self.state1[3], nMin, nMax, maxL, Bz=self.Bz,
                        progressOutput=progressOutput,
                        s=self.state1[4])
        sm1.diagonalise(eFieldList,  progressOutput=progressOutput)
        if ((self.atom2 is self.atom1)
            and (self.state1[0] == self.state2[0])
            and (self.state1[1] == self.state2[1])
            and (abs(self.state1[2] - self.state2[2]) < 0.1)
            and (abs(self.state1[3] - self.state2[3]) < 0.1)
            and (abs(self.state1[4] - self.state2[4]) < 0.1)
                ):
            sm2 = sm1
        else:
            sm2 = StarkMap(self.atom2)
            sm2.defineBasis(self.state2[0], self.state2[1], self.state2[2],
                            self.state2[3], nMin, nMax, maxL, Bz=self.Bz,
                            progressOutput=progressOutput,
                            s=self.state2[4])
            sm2.diagonalise(eFieldList,  progressOutput=progressOutput)

        self.originalStateY = []
        self.originalStateContribution = []
        for i in xrange(len(sm1.eFieldList)):
            jmax1 = 0
            jmax2 = 0
            for j in xrange(len(sm1.highlight[i])):
                if (sm1.highlight[i][j] > sm1.highlight[i][jmax1]):
                    jmax1 = j
            for j in xrange(len(sm2.highlight[i])):
                if (sm2.highlight[i][j] > sm2.highlight[i][jmax2]):
                    jmax2 = j

            self.originalStateY.append(sm1.y[i][jmax1] + sm2.y[i][jmax2]
                                       - self.pairStateEnergy)
            self.originalStateContribution.append((sm1.highlight[i][jmax1]
                                                   + sm2.highlight[i][jmax2]
                                                   ) / 2.)

        # M= mj1+mj2 is conserved with dipole-dipole interaction

        dmlist1 = [1, 0]
        if self.state1[3] != 0.5:
            dmlist1.append(-1)
        dmlist2 = [1, 0]
        if self.state2[3] != 0.5:
            dmlist2.append(-1)

        n1 = self.state1[0]
        l1 = self.state1[1] + 1
        j1 = self.state1[2] + 1
        mj1 = self.state1[3]

        n2 = self.state2[0]
        l2 = self.state2[1] + 1
        j2 = self.state2[2] + 1
        mj2 = self.state2[3]

        self.fig, self.ax = plt.subplots(1, 1, figsize=(9., 6))
        cm = LinearSegmentedColormap.from_list(
            'mymap', ['0.9', 'red', 'black'])
        cNorm = matplotlib.colors.Normalize(vmin=0., vmax=1.)

        self.r = []
        self.y = []
        self.composition = []

        for dm1 in dmlist1:
            sm1.defineBasis(n1, l1, j1, mj1 + dm1, nMin, nMax, maxL,
                            Bz=self.Bz,
                            progressOutput=progressOutput,
                            s=self.state1[4])
            sm1.diagonalise(eFieldList, progressOutput=progressOutput)

            for dm2 in dmlist2:
                sm2.defineBasis(n2, l2, j2, mj2 + dm2, nMin, nMax, maxL,
                                Bz=self.Bz,
                                progressOutput=progressOutput,
                                s=self.state2[4])
                sm2.diagonalise(eFieldList,  progressOutput=progressOutput)

                for i in xrange(len(sm1.eFieldList)):
                    yList = []
                    compositionList = []
                    if progressOutput:
                        sys.stdout.write("\rE=%.2f V/m " % sm1.eFieldList[i])
                        sys.stdout.flush()
                    for j in xrange(len(sm1.y[i])):
                        for jj in xrange(len(sm2.y[i])):
                            energy = sm1.y[i][j] + sm2.y[i][jj]\
                                - self.pairStateEnergy
                            statec1 = sm1.basisStates[sm1.composition[i][j][0][1]]
                            statec2 = sm2.basisStates[sm2.composition[i][jj][0][1]]
                            if (energy > eMin) and (energy < eMax) and\
                                (abs(statec1[1] - self.state1[1]) == 1) and\
                                    (abs(statec2[1] - self.state2[1]) == 1):
                                # add this to PairStateMap
                                yList.append(energy)
                                compositionList.append([
                                    sm1._stateComposition(
                                        sm1.composition[i][j]),
                                    sm2._stateComposition(
                                        sm2.composition[i][jj])
                                    ])

                    if (len(self.y) <= i):
                        self.y.append(yList)
                        self.composition.append(compositionList)
                    else:
                        self.y[i].extend(yList)
                        self.composition[i].extend(compositionList)

                if progressOutput:
                    print("\n")

        for i in xrange(len(sm1.eFieldList)):
            self.y[i] = np.array(self.y[i])
            self.composition[i] = np.array(self.composition[i])
            self.ax.scatter([sm1.eFieldList[i] / 100.] * len(self.y[i]),
                            self.y[i], c="k",
                            s=5, norm=cNorm, cmap=cm, lw=0, picker=5)
        self.ax.plot(sm1.eFieldList / 100.,
                     self.originalStateY, "r-", lw=1)
        self.ax.set_ylim(eMin, eMax)
        self.ax.set_xlim(min(self.eFieldList) / 100.,
                         max(self.eFieldList) / 100.)
        self.ax.set_xlabel("Electric field (V/cm)")
        self.ax.set_ylabel(r"Pair-state relative energy, $\Delta E/h$ (GHz)")

    def showPlot(self, interactive=True):
        """
            Plots initial state Stark map and its dipole-coupled resonances

            Args:

                interactive (optional, bool): if True (by default) points on plot
                    will be clickable so that one can find the state labels
                    and their composition (if they are heavily admixed).

            Note:
                Zero is given by the initial states of the atom given in
                initialisation of calculations, calculated **in absence of
                magnetic field B_z**. In other words, for non-zero magnetic
                field the inital states will have offset from zero even
                for zero electric field due to Zeeman shift.
        """

        if (self.fig != 0):
            if interactive:
                self.ax.set_title("Click on state to see state composition")
                self.clickedPoint = 0
                self.fig.canvas.draw()
                self.fig.canvas.mpl_connect('pick_event', self._onPick)
            plt.show()
        else:
            print("Error while showing a plot: nothing is plotted yet")

    def _onPick(self, event):
        if isinstance(event.artist, matplotlib.collections.PathCollection):

            x = event.mouseevent.xdata * 100.
            y = event.mouseevent.ydata

            i = np.searchsorted(self.eFieldList, x)
            if i == len(self.eFieldList):
                i -= 1
            if ((i > 0) and (abs(self.eFieldList[i - 1] - x) <
                             abs(self.eFieldList[i] - x))):
                i -= 1

            j = 0
            for jj in xrange(len(self.y[i])):
                if (abs(self.y[i][jj] - y) < abs(self.y[i][j] - y)):
                    j = jj

            if (self.clickedPoint != 0):
                self.clickedPoint.remove()

            self.clickedPoint, = self.ax.plot([self.eFieldList[i] / 100.],
                                              [self.y[i][j]], "bs",
                                              linewidth=0, zorder=3)

            atom1 = self.atom1.elementName
            atom2 = self.atom2.elementName
            composition1 = str(self.composition[i][j][0])
            composition2 = str(self.composition[i][j][1])
            self.ax.set_title(("[%s,%s]=[" % (atom1, atom2))
                              + composition1 + ","
                              + composition2 + "]",
                              fontsize=10)

            event.canvas.draw()

    def _onPick2(self, xdata, ydata):
        x = xdata * 100.
        y = ydata

        i = np.searchsorted(self.eFieldList, x)
        if i == len(self.eFieldList):
            i -= 1
        if ((i > 0) and (abs(self.eFieldList[i - 1] - x)
                         < abs(self.eFieldList[i] - x))):
            i -= 1

        j = 0
        for jj in xrange(len(self.y[i])):
            if (abs(self.y[i][jj] - y) < abs(self.y[i][j] - y)):
                j = jj

        if (self.clickedPoint != 0):
            self.clickedPoint.remove()

        self.clickedPoint, = self.ax.plot([self.eFieldList[i] / 100.],
                                          [self.y[i][j]], "bs",
                                          linewidth=0, zorder=3)

        atom1 = self.atom1.elementName
        atom2 = self.atom2.elementName
        composition1 = str(self.composition[i][j][0])
        composition2 = str(self.composition[i][j][1])
        self.ax.set_title(("[%s,%s]=[" % (atom1, atom2))
                          + composition1 + ","
                          + composition2 + "]",
                          fontsize=10)

matplotlib.colors.LinearSegmentedColormap.from_list matplotlib.pyplot.subplots matplotlib.ticker.MultipleLocator matplotlib.ticker.FormatStrFormatter matplotlib.pyplot.show matplotlib.colors.LogNorm matplotlib.colors.Normalize matplotlib.colorbar.ColorbarBase matplotlib.pyplot.NullFormatter