Source code for GSASIIElem

# -*- coding: utf-8 -*-
"""
*GSASIIElem: functions for element types*
-----------------------------------------

"""
# Copyright: 2008, Robert B. Von Dreele & Brian H. Toby (Argonne National Laboratory)
########### SVN repository information ###################
# $Date: 2021-04-20 02:50:52 +0000 (Tue, 20 Apr 2021) $
# $Author: toby $
# $Revision: 4887 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIElem.py $
# $Id: GSASIIElem.py 4887 2021-04-20 02:50:52Z toby $
########### SVN repository information ###################

import math
import sys
import os.path
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 4887 $")
import numpy as np
import atmdata
import GSASIImath as G2mth
import ElementTable as ET


getElSym = lambda sym: sym.split('+')[0].split('-')[0].capitalize()
[docs]def GetFormFactorCoeff(El): """Read X-ray form factor coefficients from `atomdata.py` file :param str El: element 1-2 character symbol, case irrevelant :return: `FormFactors`: list of form factor dictionaries Each X-ray form factor dictionary is: * `Symbol`: 4 character element symbol with valence (e.g. 'NI+2') * `Z`: atomic number * `fa`: 4 A coefficients * `fb`: 4 B coefficients * `fc`: C coefficient """ Els = El.capitalize().strip() valences = [ky for ky in atmdata.XrayFF.keys() if Els == getElSym(ky)] FormFactors = [atmdata.XrayFF[val] for val in valences] for Sy,FF in zip(valences,FormFactors): FF.update({'Symbol':Sy.upper()}) return FormFactors
[docs]def GetFFtable(atomTypes): ''' returns a dictionary of form factor data for atom types found in atomTypes :param list atomTypes: list of atom types :return: FFtable, dictionary of form factor data; key is atom type ''' FFtable = {} for El in atomTypes: FFs = GetFormFactorCoeff(getElSym(El)) for item in FFs: if item['Symbol'] == El.upper(): FFtable[El] = item return FFtable
[docs]def GetMFtable(atomTypes,Landeg): ''' returns a dictionary of magnetic form factor data for atom types found in atomTypes :param list atomTypes: list of atom types :param list Landeg: Lande g factors for atomTypes :return: FFtable, dictionary of form factor data; key is atom type ''' MFtable = {} for El,gfac in zip(atomTypes,Landeg): MFs = GetMagFormFacCoeff(getElSym(El)) for item in MFs: if item['Symbol'] == El.upper(): item['gfac'] = gfac MFtable[El] = item return MFtable
[docs]def GetBLtable(General): ''' returns a dictionary of neutron scattering length data for atom types & isotopes found in General :param dict General: dictionary of phase info.; includes AtomTypes & Isotopes :return: BLtable, dictionary of scattering length data; key is atom type ''' atomTypes = General['AtomTypes'] BLtable = {} isotope = General['Isotope'] for El in atomTypes: ElS = getElSym(El) if 'Nat' in isotope[El]: BLtable[El] = [isotope[El],atmdata.AtmBlens[ElS+'_']] else: BLtable[El] = [isotope[El],atmdata.AtmBlens[ElS+'_'+isotope[El]]] return BLtable
[docs]def getFFvalues(FFtables,SQ,ifList=False): 'Needs a doc string' if ifList: FFvals = [] for El in FFtables: FFvals.append(ScatFac(FFtables[El],SQ)[0]) else: FFvals = {} for El in FFtables: FFvals[El] = ScatFac(FFtables[El],SQ)[0] return FFvals
[docs]def getBLvalues(BLtables,ifList=False): 'Needs a doc string' if ifList: BLvals = [] for El in BLtables: if 'BW-LS' in El: BLvals.append(BLtables[El][1]['BW-LS'][0]) else: BLvals.append(BLtables[El][1]['SL'][0]) else: BLvals = {} for El in BLtables: if 'BW-LS' in El: BLvals[El] = BLtables[El][1]['BW-LS'][0] else: BLvals[El] = BLtables[El][1]['SL'][0] return BLvals
[docs]def getMFvalues(MFtables,SQ,ifList=False): 'Needs a doc string' if ifList: MFvals = [] for El in MFtables: MFvals.append(MagScatFac(MFtables[El],SQ)[0]) else: MFvals = {} for El in MFtables: MFvals[El] = MagScatFac(MFtables[El],SQ)[0] return MFvals
[docs]def GetFFC5(ElSym): '''Get 5 term form factor and Compton scattering data :param ElSym: str(1-2 character element symbol with proper case); :return El: dictionary with 5 term form factor & compton coefficients ''' import FormFactors as FF El = {} FF5 = FF.FFac5term[ElSym] El['fa'] = FF5[:5] El['fc'] = FF5[5] El['fb'] = FF5[6:] Cmp5 = FF.Compton[ElSym] El['cmpz'] = Cmp5[0] El['cmpa'] = Cmp5[1:6] El['cmpb'] = Cmp5[6:] return El
def GetBVS(Pair,atSeq,Valences): Els = Pair.strip().split('-') iAt = atSeq.index(Els[0]) iVal = Valences[iAt][0] if Els[1] in ['O','F','Cl']: iEls = ['O','F','Cl'].index(Els[1]) if iVal in atmdata.BVScoeff: return atmdata.BVScoeff[iVal][iEls] else: return 0.0 elif Els[1] in ['Br','I','S','Se','Te','N','P','As','H','D']: iEls = ['Br','I','S','Se','Te','N','P','As','H','D'].index(Els[1]) if Els[0] in atmdata.BVSnotOFCl: return atmdata.BVSnotOFCl[Els[0]][iEls] else: return 0.0 else: return 0.0
[docs]def CheckElement(El): '''Check if element El is in the periodic table :param str El: One or two letter element symbol, capitaliztion ignored :returns: True if the element is found ''' Elements = [] for elem in ET.ElTable: Elements.append(elem[0][0]) if El.capitalize() in Elements: return True else: return False
[docs]def FixValence(El): 'Returns the element symbol, even when a valence is present' if '+' in El[-1]: #converts An+/- to A+/-n num = El[-2] El = El.split(num)[0]+'+'+num if '+0' in El: El = El.split('+0')[0] if '-' in El[-1]: num = El[-2] El = El.split(num)[0]+'-'+num if '-0' in El: El = El.split('-0')[0] return El
[docs]def GetAtomInfo(El,ifMag=False): 'reads element information from atmdata.py' Elem = ET.ElTable if ifMag: Elem = ET.MagElTable Elements = [elem[0][0] for elem in Elem] AtomInfo = {} ElS = getElSym(El) if El not in atmdata.XrayFF and El not in atmdata.MagFF: if ElS not in atmdata.XrayFF: if ElS.endswith('0') and ElS[:-1] in atmdata.XrayFF: ElS = ElS[:-1] else: ElS = 'H' print('Atom type '+El+' not found, using '+ElS) El = ElS AtomInfo.update(dict(zip(['Drad','Arad','Vdrad','Hbrad'],atmdata.AtmSize[ElS]))) AtomInfo['Symbol'] = El AtomInfo['Color'] = ET.ElTable[Elements.index(ElS)][6] AtomInfo['Z'] = atmdata.XrayFF[ElS]['Z'] isotopes = [ky for ky in atmdata.AtmBlens.keys() if ElS == ky.split('_')[0]] isotopes.sort() AtomInfo['Mass'] = atmdata.AtmBlens[isotopes[0]]['Mass'] #default to nat. abund. AtomInfo['Isotopes'] = {} for isotope in isotopes: data = atmdata.AtmBlens[isotope] if isotope == ElS+'_': AtomInfo['Isotopes']['Nat. Abund.'] = data else: AtomInfo['Isotopes'][isotope.split('_')[1]] = data AtomInfo['Lande g'] = 2.0 return AtomInfo
def GetElInfo(El,inst): ElemSym = El.strip().capitalize() if 'X' in inst['Type'][0]: keV = 12.397639/G2mth.getWave(inst) FpMu = FPcalc(GetXsectionCoeff(ElemSym), keV) ElData = GetFormFactorCoeff(ElemSym)[0] ElData['FormulaNo'] = 0.0 ElData.update(GetAtomInfo(ElemSym)) ElData.update(dict(zip(['fp','fpp','mu'],FpMu))) ElData.update(GetFFC5(El)) else: #'N'eutron ElData = {} ElData.update(GetAtomInfo(ElemSym)) ElData['FormulaNo'] = 0.0 ElData.update({'mu':0.0,'fp':0.0,'fpp':0.0}) return ElData
[docs]def GetXsectionCoeff(El): """Read atom orbital scattering cross sections for fprime calculations via Cromer-Lieberman algorithm :param El: 2 character element symbol :return: Orbs: list of orbitals each a dictionary with detailed orbital information used by FPcalc each dictionary is: * 'OrbName': Orbital name read from file * 'IfBe' 0/2 depending on orbital * 'BindEn': binding energy * 'BB': BindEn/0.02721 * 'XSectIP': 5 cross section inflection points * 'ElEterm': energy correction term * 'SEdge': absorption edge for orbital * 'Nval': 10/11 depending on IfBe * 'LEner': 10/11 values of log(energy) * 'LXSect': 10/11 values of log(cross section) """ AU = 2.80022e+7 C1 = 0.02721 ElS = El.upper() ElS = ElS.ljust(2) filename = os.path.join(os.path.split(__file__)[0],'Xsect.dat') try: xsec = open(filename,'r') except: print ('**** ERROR - File Xsect.dat not found in directory %s'%os.path.split(filename)[0]) sys.exit() S = '1' Orbs = [] while S: S = xsec.readline() if S[:2] == ElS: S = S[:-1]+xsec.readline()[:-1]+xsec.readline() OrbName = S[9:14] S = S[14:] IfBe = int(S[0]) S = S[1:] val = S.split() BindEn = float(val[0]) BB = BindEn/C1 Orb = {'OrbName':OrbName,'IfBe':IfBe,'BindEn':BindEn,'BB':BB} Energy = [] XSect = [] for i in range(11): Energy.append(float(val[2*i+1])) XSect.append(float(val[2*i+2])) XSecIP = [] for i in range(5): XSecIP.append(XSect[i+5]/AU) Orb['XSecIP'] = XSecIP if IfBe == 0: Orb['SEdge'] = XSect[10]/AU Nval = 11 else: Orb['ElEterm'] = XSect[10] del Energy[10] del XSect[10] Nval = 10 Orb['SEdge'] = 0.0 Orb['Nval'] = Nval D = dict(zip(Energy,XSect)) Energy.sort() X = [] for key in Energy: X.append(D[key]) XSect = X LEner = [] LXSect = [] for i in range(Nval): LEner.append(math.log(Energy[i])) if XSect[i] > 0.0: LXSect.append(math.log(XSect[i])) else: LXSect.append(0.0) Orb['LEner'] = LEner Orb['LXSect'] = LXSect Orbs.append(Orb) xsec.close() return Orbs
[docs]def GetMagFormFacCoeff(El): """Read magnetic form factor data from atmdata.py :param El: 2 character element symbol :return: MagFormFactors: list of all magnetic form factors dictionaries for element El. each dictionary contains: * 'Symbol':Symbol * 'Z':Z * 'mfa': 4 MA coefficients * 'nfa': 4 NA coefficients * 'mfb': 4 MB coefficients * 'nfb': 4 NB coefficients * 'mfc': MC coefficient * 'nfc': NC coefficient """ Els = El.capitalize().strip() MagFormFactors = [] mags = [ky for ky in atmdata.MagFF.keys() if Els == getElSym(ky)] for mag in mags: magData = {} data = atmdata.MagFF[mag] magData['Symbol'] = mag.upper() magData['Z'] = atmdata.XrayFF[getElSym(mag)]['Z'] magData['mfa'] = [data['M'][i] for i in [0,2,4,6]] magData['mfb'] = [data['M'][i] for i in [1,3,5,7]] magData['mfc'] = data['M'][8] magData['nfa'] = [data['N'][i] for i in [0,2,4,6]] magData['nfb'] = [data['N'][i] for i in [1,3,5,7]] magData['nfc'] = data['N'][8] MagFormFactors.append(magData) return MagFormFactors
[docs]def ScatFac(El, SQ): """compute value of form factor :param El: element dictionary defined in GetFormFactorCoeff :param SQ: (sin-theta/lambda)**2 :return: real part of form factor """ fa = np.array(El['fa']) fb = np.array(El['fb']) t = -fb[:,np.newaxis]*SQ return np.sum(fa[:,np.newaxis]*np.exp(t)[:],axis=0)+El['fc']
[docs]def MagScatFac(El, SQ): """compute value of form factor :param El: element dictionary defined in GetFormFactorCoeff :param SQ: (sin-theta/lambda)**2 :param gfac: Lande g factor (normally = 2.0) :return: real part of form factor """ mfa = np.array(El['mfa']) mfb = np.array(El['mfb']) nfa = np.array(El['nfa']) nfb = np.array(El['nfb']) mt = -mfb[:,np.newaxis]*SQ nt = -nfb[:,np.newaxis]*SQ MMF = np.sum(mfa[:,np.newaxis]*np.exp(mt)[:],axis=0)+El['mfc'] MMF0 = np.sum(mfa)+El['mfc'] NMF = np.sum(nfa[:,np.newaxis]*np.exp(nt)[:],axis=0)+El['nfc'] NMF0 = np.sum(nfa)+El['nfc'] MF0 = MMF0+(2.0/El['gfac']-1.0)*NMF0 return (MMF+(2.0/El['gfac']-1.0)*NMF)/MF0
def BlenResCW(Els,BLtables,wave): FP = np.zeros(len(Els)) FPP = np.zeros(len(Els)) for i,El in enumerate(Els): BL = BLtables[El][1] if 'BW-LS' in BL: Re,Im,E0,gam,A,E1,B,E2 = BL['BW-LS'][1:] Emev = 81.80703/wave**2 T0 = Emev-E0 T1 = Emev-E1 T2 = Emev-E2 D0 = T0**2+gam**2 D1 = T1**2+gam**2 D2 = T2**2+gam**2 FP[i] = Re*(T0/D0+A*T1/D1+B*T2/D2)+BL['BW-LS'][0] FPP[i] = -Im*(1/D0+A/D1+B/D2) else: FPP[i] = BL['SL'][1] #for Li, B, etc. return FP,FPP def BlenResTOF(Els,BLtables,wave): FP = np.zeros((len(Els),len(wave))) FPP = np.zeros((len(Els),len(wave))) BL = [BLtables[el][1] for el in Els] for i,El in enumerate(Els): if 'BW-LS' in BL[i]: Re,Im,E0,gam,A,E1,B,E2 = BL[i]['BW-LS'][1:] Emev = 81.80703/wave**2 T0 = Emev-E0 T1 = Emev-E1 T2 = Emev-E2 D0 = T0**2+gam**2 D1 = T1**2+gam**2 D2 = T2**2+gam**2 FP[i] = Re*(T0/D0+A*T1/D1+B*T2/D2)+BL[i]['BW-LS'][0] FPP[i] = -Im*(1/D0+A/D1+B/D2) else: FPP[i] = np.ones(len(wave))*BL[i]['SL'][1] #for Li, B, etc. return FP,FPP
[docs]def ComptonFac(El,SQ): """compute Compton scattering factor :param El: element dictionary :param SQ: (sin-theta/lambda)**2 :return: compton scattering factor """ ca = np.array(El['cmpa']) cb = np.array(El['cmpb']) t = -cb[:,np.newaxis]*SQ return El['cmpz']-np.sum(ca[:,np.newaxis]*np.exp(t),axis=0)
[docs]def FPcalc(Orbs, KEv): """Compute real & imaginary resonant X-ray scattering factors :param Orbs: list of orbital dictionaries as defined in GetXsectionCoeff :param KEv: x-ray energy in keV :return: C: (f',f",mu): real, imaginary parts of resonant scattering & atomic absorption coeff. """ def Aitken(Orb, LKev): Nval = Orb['Nval'] j = Nval-1 LEner = Orb['LEner'] for i in range(Nval): if LEner[i] <= LKev: j = i if j > Nval-3: j= Nval-3 T = [0,0,0,0,0,0] LXSect = Orb['LXSect'] for i in range(3): T[i] = LXSect[i+j] T[i+3] = LEner[i+j]-LKev T[1] = (T[0]*T[4]-T[1]*T[3])/(LEner[j+1]-LEner[j]) T[2] = (T[0]*T[5]-T[2]*T[3])/(LEner[j+2]-LEner[j]) T[2] = (T[1]*T[5]-T[2]*T[4])/(LEner[j+2]-LEner[j+1]) C = T[2] return C def DGauss(Orb,CX,RX,ISig): ALG = (0.11846344252810,0.23931433524968,0.284444444444, 0.23931433524968,0.11846344252810) XLG = (0.04691007703067,0.23076534494716,0.5, 0.76923465505284,0.95308992296933) D = 0.0 B2 = Orb['BB']**2 R2 = RX**2 XSecIP = Orb['XSecIP'] for i in range(5): X = XLG[i] X2 = X**2 XS = XSecIP[i] if ISig == 0: S = BB*(XS*(B2/X2)-CX*R2)/(R2*X2-B2) elif ISig == 1: S = 0.5*BB*B2*XS/(math.sqrt(X)*(R2*X2-X*B2)) elif ISig == 2: T = X*X2*R2-B2/X S = 2.0*BB*(XS*B2/(T*X2**2)-(CX*R2/T)) else: S = BB*B2*(XS-Orb['SEdge']*X2)/(R2*X2**2-X2*B2) A = ALG[i] D += A*S return D AU = 2.80022e+7 C1 = 0.02721 C = 137.0367 FP = 0.0 FPP = 0.0 Mu = 0.0 LKev = math.log(KEv) RX = KEv/C1 if Orbs: for Orb in Orbs: CX = 0.0 BB = Orb['BB'] BindEn = Orb['BindEn'] if Orb['IfBe'] != 0: ElEterm = Orb['ElEterm'] if BindEn <= KEv: CX = math.exp(Aitken(Orb,LKev)) Mu += CX CX /= AU Corr = 0.0 if Orb['IfBe'] == 0 and BindEn >= KEv: CX = 0.0 FPI = DGauss(Orb,CX,RX,3) Corr = 0.5*Orb['SEdge']*BB**2*math.log((RX-BB)/(-RX-BB))/RX else: FPI = DGauss(Orb,CX,RX,Orb['IfBe']) if CX != 0.0: Corr = -0.5*CX*RX*math.log((RX+BB)/(RX-BB)) FPI = (FPI+Corr)*C/(2.0*math.pi**2) FPPI = C*CX*RX/(4.0*math.pi) FP += FPI FPP += FPPI FP -= ElEterm return (FP, FPP, Mu)
mapDefault = {'MapType':'','RefList':'','GridStep':0.25,'Show bonds':True, 'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
[docs]def SetupGeneral(data, dirname): '''Initialize the General sections of the Phase tree contents Called by SetupGeneral in GSASIIphsGUI and in GSASIIscriptable.SetupGeneral ''' generalData = data['General'] atomData = data['Atoms'] generalData['AtomTypes'] = [] generalData['Isotopes'] = {} # various patches if 'Isotope' not in generalData: generalData['Isotope'] = {} if 'Data plot type' not in generalData: generalData['Data plot type'] = 'Mustrain' if 'POhkl' not in generalData: generalData['POhkl'] = [0,0,1] if 'Map' not in generalData: generalData['Map'] = mapDefault.copy() if 'Flip' not in generalData: generalData['Flip'] = {'RefList':'','GridStep':0.25,'Norm element':'None', 'k-factor':0.1,'k-Max':20.,} if 'testHKL' not in generalData['Flip']: generalData['Flip']['testHKL'] = [[0,0,2],[2,0,0],[1,1,1],[0,2,0],[1,2,3]] if 'doPawley' not in generalData: generalData['doPawley'] = False #ToDo: change to '' if 'Pawley dmin' not in generalData: generalData['Pawley dmin'] = 1.0 if 'Pawley dmax' not in generalData: generalData['Pawley dmax'] = 100.0 if 'Pawley neg wt' not in generalData: generalData['Pawley neg wt'] = 0.0 if '3Dproj' not in generalData: generalData['3Dproj'] = '' if 'doDysnomia' not in generalData: generalData['doDysnomia'] = False if 'Algolrithm' in generalData.get('MCSA controls',{}) or \ 'MCSA controls' not in generalData: generalData['MCSA controls'] = {'Data source':'','Annealing':[0.7,0.1,250], 'dmin':2.8,'Algorithm':'log','fast parms':[0.8,0.6],'log slope':0.9, 'Cycles':1,'Results':[],'newDmin':True} if 'AtomPtrs' not in generalData: generalData['AtomPtrs'] = [3,1,7,9] if generalData['Type'] == 'macromolecular': generalData['AtomPtrs'] = [6,4,10,12] elif generalData['Type'] == 'magnetic': generalData['AtomPtrs'] = [3,1,10,12] if generalData['Modulated']: if 'Super' not in generalData: generalData['Super'] = 1 generalData['SuperVec'] = [[0.,0.,0.],False,1] generalData['SSGData'] = {} if '4DmapData' not in generalData: generalData['4DmapData'] = mapDefault.copy() generalData['4DmapData'].update({'MapType':'Fobs'}) atomData = data['Atoms'] for atom in atomData: # if 'SS1' not in atom: # atom += [[],[],{'SS1':{'waveType':'Fourier','Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}] if isinstance(atom[-1],dict) and 'waveType' in atom[-1]['SS1']: waveType = atom[-1]['SS1']['waveType'] for parm in ['Sfrac','Spos','Sadp','Smag']: if len(atom[-1]['SS1'][parm]): wType = 'Fourier' if parm == 'Sfrac': if 'Crenel' in waveType: wType = 'Crenel' elif parm == 'Spos': if not 'Crenel' in waveType: wType = waveType atom[-1]['SS1'][parm] = [wType,]+list(atom[-1]['SS1'][parm]) del atom[-1]['SS1']['waveType'] else: generalData['Super'] = 0 if 'Modulated' not in generalData: generalData['Modulated'] = False if 'HydIds' not in generalData: generalData['HydIds'] = {} if generalData['Type'] == 'magnetic': if 'SGGray' not in generalData['SGData']: generalData['SGData']['SGGray'] = False if 'Resolution' in generalData['Map']: generalData['Map']['GridStep'] = generalData['Map']['Resolution']/2. generalData['Flip']['GridStep'] = generalData['Flip']['Resolution']/2. del generalData['Map']['Resolution'] del generalData['Flip']['Resolution'] if 'Compare' not in generalData: generalData['Compare'] = {'Oatoms':'','Tatoms':'', 'Tilts':{'Otilts':[],'Ttilts':[]}, 'Bonds':{'Obonds':[],'Tbonds':[]},'Vects':{'Ovec':[],'Tvec':[]}, 'dVects':{'Ovec':[],'Tvec':[]},'Sampling':1.0} if 'Sampling' not in generalData['Compare']: generalData['Compare']['Sampling'] = 1.0 # end of patches cx,ct,cs,cia = generalData['AtomPtrs'] generalData['NoAtoms'] = {} generalData['BondRadii'] = [] generalData['AngleRadii'] = [] generalData['vdWRadii'] = [] generalData['AtomMass'] = [] generalData['Color'] = [] if generalData['Type'] == 'magnetic': generalData['MagDmin'] = generalData.get('MagDmin',1.0) landeg = generalData.get('Lande g',[]) generalData['Mydir'] = dirname badList = {} for iat,atom in enumerate(atomData): atom[ct] = atom[ct].lower().capitalize() #force to standard form if generalData['AtomTypes'].count(atom[ct]): generalData['NoAtoms'][atom[ct]] += atom[cx+3]*float(atom[cs+1]) elif atom[ct] != 'UNK': Info = GetAtomInfo(atom[ct]) if not Info: if atom[ct] not in badList: badList[atom[ct]] = 0 badList[atom[ct]] += 1 atom[ct] = 'UNK' continue atom[ct] = Info['Symbol'] # N.B. symbol might be changed by GetAtomInfo generalData['AtomTypes'].append(atom[ct]) generalData['Z'] = Info['Z'] generalData['Isotopes'][atom[ct]] = Info['Isotopes'] generalData['BondRadii'].append(Info['Drad']) generalData['AngleRadii'].append(Info['Arad']) generalData['vdWRadii'].append(Info['Vdrad']) if atom[ct] in generalData['Isotope']: if generalData['Isotope'][atom[ct]] not in generalData['Isotopes'][atom[ct]]: isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1] generalData['Isotope'][atom[ct]] = isotope generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]]['Mass']) else: generalData['Isotope'][atom[ct]] = 'Nat. Abund.' if 'Nat. Abund.' not in generalData['Isotopes'][atom[ct]]: isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1] generalData['Isotope'][atom[ct]] = isotope generalData['AtomMass'].append(Info['Mass']) generalData['NoAtoms'][atom[ct]] = atom[cx+3]*float(atom[cs+1]) generalData['Color'].append(Info['Color']) if generalData['Type'] == 'magnetic': if len(landeg) < len(generalData['AtomTypes']): landeg.append(2.0) if generalData['Type'] == 'magnetic': generalData['Lande g'] = landeg[:len(generalData['AtomTypes'])] F000X = 0. F000N = 0. for i,elem in enumerate(generalData['AtomTypes']): F000X += generalData['NoAtoms'][elem]*generalData['Z'] isotope = generalData['Isotope'][elem] F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope]['SL'][0] generalData['F000X'] = F000X generalData['F000N'] = F000N generalData['Mass'] = G2mth.getMass(generalData) if badList: msg = 'Warning: element symbol(s) not found:' for key in badList: msg += '\n\t' + key if badList[key] > 1: msg += ' (' + str(badList[key]) + ' times)' #wx.MessageBox(msg,caption='Element symbol error') raise ValueError("Phase error:\n" + msg)