Changeset 4659 for trunk


Ignore:
Timestamp:
Nov 21, 2020 2:15:49 PM (3 years ago)
Author:
toby
Message:

extensive Origin 1->2 updates; merge SetupGeneral? into a single routine in G2Elem; read sym ops from CIF; fix sites sym/mult after cood xform

Location:
trunk
Files:
2 added
8 edited

Legend:

Unmodified
Added
Removed

  • trunk/GSASIIElem.py

    r4629 r4659  
    543543    return (FP, FPP, Mu)
    544544   
    545 
     545mapDefault = {'MapType':'','RefList':'','GridStep':0.25,'Show bonds':True,
     546                'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
     547
     548def SetupGeneral(data, dirname):
     549    '''Initialize the General sections of the Phase tree contents
     550    Called by SetupGeneral in GSASIIphsGUI and in GSASIIscriptable.SetupGeneral
     551    '''
     552    generalData = data['General']
     553    atomData = data['Atoms']
     554    generalData['AtomTypes'] = []
     555    generalData['Isotopes'] = {}
     556# various patches
     557    if 'Isotope' not in generalData:
     558        generalData['Isotope'] = {}
     559    if 'Data plot type' not in generalData:
     560        generalData['Data plot type'] = 'Mustrain'
     561    if 'POhkl' not in generalData:
     562        generalData['POhkl'] = [0,0,1]
     563    if 'Map' not in generalData:
     564        generalData['Map'] = mapDefault.copy()
     565    if 'Flip' not in generalData:
     566        generalData['Flip'] = {'RefList':'','GridStep':0.25,'Norm element':'None',
     567            'k-factor':0.1,'k-Max':20.,}
     568    if 'testHKL' not in generalData['Flip']:
     569        generalData['Flip']['testHKL'] = [[0,0,2],[2,0,0],[1,1,1],[0,2,0],[1,2,3]]
     570    if 'doPawley' not in generalData:
     571        generalData['doPawley'] = False     #ToDo: change to ''
     572    if 'Pawley dmin' not in generalData:
     573        generalData['Pawley dmin'] = 1.0
     574    if 'Pawley dmax' not in generalData:
     575        generalData['Pawley dmax'] = 100.0
     576    if 'Pawley neg wt' not in generalData:
     577        generalData['Pawley neg wt'] = 0.0
     578    if '3Dproj' not in generalData:
     579        generalData['3Dproj'] = ''
     580    if 'doDysnomia' not in generalData:
     581        generalData['doDysnomia'] = False
     582    if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
     583        'MCSA controls' not in generalData:
     584        generalData['MCSA controls'] = {'Data source':'','Annealing':[0.7,0.1,250],
     585        'dmin':2.8,'Algorithm':'log','fast parms':[0.8,0.6],'log slope':0.9,
     586        'Cycles':1,'Results':[],'newDmin':True}
     587    if 'AtomPtrs' not in generalData:
     588        generalData['AtomPtrs'] = [3,1,7,9]
     589        if generalData['Type'] == 'macromolecular':
     590            generalData['AtomPtrs'] = [6,4,10,12]
     591        elif generalData['Type'] == 'magnetic':
     592            generalData['AtomPtrs'] = [3,1,10,12]
     593    if generalData['Modulated']:
     594        if 'Super' not in generalData:
     595            generalData['Super'] = 1
     596            generalData['SuperVec'] = [[0.,0.,0.],False,1]
     597            generalData['SSGData'] = {}
     598        if '4DmapData' not in generalData:
     599            generalData['4DmapData'] = mapDefault.copy()
     600            generalData['4DmapData'].update({'MapType':'Fobs'})
     601        atomData = data['Atoms']
     602        for atom in atomData:
     603#                if 'SS1' not in atom:
     604#                    atom += [[],[],{'SS1':{'waveType':'Fourier','Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}]
     605            if isinstance(atom[-1],dict) and 'waveType' in atom[-1]['SS1']:
     606                waveType = atom[-1]['SS1']['waveType']
     607                for parm in ['Sfrac','Spos','Sadp','Smag']:
     608                    if len(atom[-1]['SS1'][parm]):
     609                        wType = 'Fourier'
     610                        if parm == 'Sfrac':
     611                            if 'Crenel' in waveType:
     612                                wType = 'Crenel'
     613                        elif parm == 'Spos':
     614                            if not 'Crenel' in waveType:
     615                                wType = waveType
     616                        atom[-1]['SS1'][parm] = [wType,]+list(atom[-1]['SS1'][parm])
     617                del atom[-1]['SS1']['waveType']
     618    else:
     619        generalData['Super'] = 0
     620    if 'Modulated' not in generalData:
     621        generalData['Modulated'] = False
     622    if 'HydIds' not in generalData:
     623        generalData['HydIds'] = {}
     624    if generalData['Type'] == 'magnetic':
     625        if 'SGGray' not in generalData['SGData']:
     626            generalData['SGData']['SGGray'] = False
     627    if 'Resolution' in generalData['Map']:
     628        generalData['Map']['GridStep'] = generalData['Map']['Resolution']/2.
     629        generalData['Flip']['GridStep'] = generalData['Flip']['Resolution']/2.
     630        del generalData['Map']['Resolution']
     631        del generalData['Flip']['Resolution']
     632    if 'Compare' not in generalData:
     633        generalData['Compare'] = {'Oatoms':'','Tatoms':'',
     634                'Tilts':{'Otilts':[],'Ttilts':[]},
     635            'Bonds':{'Obonds':[],'Tbonds':[]},'Vects':{'Ovec':[],'Tvec':[]},
     636            'dVects':{'Ovec':[],'Tvec':[]},'Sampling':1.0}
     637    if 'Sampling' not in generalData['Compare']:
     638        generalData['Compare']['Sampling'] = 1.0
     639
     640# end of patches
     641    cx,ct,cs,cia = generalData['AtomPtrs']
     642    generalData['NoAtoms'] = {}
     643    generalData['BondRadii'] = []
     644    generalData['AngleRadii'] = []
     645    generalData['vdWRadii'] = []
     646    generalData['AtomMass'] = []
     647    generalData['Color'] = []
     648    if generalData['Type'] == 'magnetic':
     649        generalData['MagDmin'] = generalData.get('MagDmin',1.0)
     650        landeg = generalData.get('Lande g',[])
     651    generalData['Mydir'] = dirname
     652    badList = {}
     653    for iat,atom in enumerate(atomData):
     654        atom[ct] = atom[ct].lower().capitalize()              #force to standard form
     655        if generalData['AtomTypes'].count(atom[ct]):
     656            generalData['NoAtoms'][atom[ct]] += atom[cx+3]*float(atom[cs+1])
     657        elif atom[ct] != 'UNK':
     658            Info = GetAtomInfo(atom[ct])
     659            if not Info:
     660                if atom[ct] not in badList:
     661                    badList[atom[ct]] = 0
     662                badList[atom[ct]] += 1
     663                atom[ct] = 'UNK'
     664                continue
     665            atom[ct] = Info['Symbol'] # N.B. symbol might be changed by GetAtomInfo
     666            generalData['AtomTypes'].append(atom[ct])
     667            generalData['Z'] = Info['Z']
     668            generalData['Isotopes'][atom[ct]] = Info['Isotopes']
     669            generalData['BondRadii'].append(Info['Drad'])
     670            generalData['AngleRadii'].append(Info['Arad'])
     671            generalData['vdWRadii'].append(Info['Vdrad'])
     672            if atom[ct] in generalData['Isotope']:
     673                if generalData['Isotope'][atom[ct]] not in generalData['Isotopes'][atom[ct]]:
     674                    isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1]
     675                    generalData['Isotope'][atom[ct]] = isotope
     676                generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]]['Mass'])
     677            else:
     678                generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
     679                if 'Nat. Abund.' not in generalData['Isotopes'][atom[ct]]:
     680                    isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1]
     681                    generalData['Isotope'][atom[ct]] = isotope
     682                generalData['AtomMass'].append(Info['Mass'])
     683            generalData['NoAtoms'][atom[ct]] = atom[cx+3]*float(atom[cs+1])
     684            generalData['Color'].append(Info['Color'])
     685            if generalData['Type'] == 'magnetic':
     686                if len(landeg) < len(generalData['AtomTypes']):
     687                    landeg.append(2.0)
     688    if generalData['Type'] == 'magnetic':
     689        generalData['Lande g'] = landeg[:len(generalData['AtomTypes'])]
     690
     691    F000X = 0.
     692    F000N = 0.
     693    for i,elem in enumerate(generalData['AtomTypes']):
     694        F000X += generalData['NoAtoms'][elem]*generalData['Z']
     695        isotope = generalData['Isotope'][elem]
     696        F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope]['SL'][0]
     697    generalData['F000X'] = F000X
     698    generalData['F000N'] = F000N
     699    generalData['Mass'] = G2mth.getMass(generalData)
     700 
     701    if badList:
     702        msg = 'Warning: element symbol(s) not found:'
     703        for key in badList:
     704            msg += '\n\t' + key
     705            if badList[key] > 1:
     706                msg += ' (' + str(badList[key]) + ' times)'
     707        #wx.MessageBox(msg,caption='Element symbol error')
     708        raise ValueError("Phase error:\n" + msg)       

  • trunk/GSASIIctrlGUI.py

    r4654 r4659  
    169169import GSASIIobj as G2obj
    170170import GSASIIfiles as G2fil
     171import GSASIIElem as G2elem
    171172import GSASIIscriptable as G2sc
    172173import GSASIIpwd as G2pwd
    173174import GSASIIlattice as G2lat
     175import GSASIImath as G2mth
     176import GSASIIstrMain as G2stMn
    174177if sys.version_info[0] >= 3:
    175178    unicode = str
    … …  
    70097012    AutoLoadWindow = dlg # save window reference
    70107013
     7014################################################################################
     7015# Deal with Origin 1/2 ambiguities
     7016################################################################################
     7017def ChooseOrigin(G2frame,rd):   
     7018    # make copy of Phase but shift atoms Origin 1->2
     7019    O2Phase = copy.deepcopy(rd.Phase)
     7020    # make copy of atoms, shift to alternate origin
     7021    T = G2spc.spg2origins[rd.Phase['General']['SGData']['SpGrp']]
     7022    O2atoms = O2Phase['Atoms']
     7023    cx,ct,cs,cia = rd.Phase['General']['AtomPtrs']
     7024    SGData = rd.Phase['General']['SGData']
     7025    for atom in O2atoms:
     7026        for i in [0,1,2]:
     7027            atom[cx+i] += T[i]
     7028            atom[cs:cs+2] = G2spc.SytSym(atom[3:6],SGData)[0:2] # update symmetry & mult
     7029    #get density & distances
     7030    DisAglData = {}
     7031    DisAglData['SGData'] = rd.Phase['General']['SGData']
     7032    DisAglData['Cell'] = rd.Phase['General']['Cell'][1:] #+ volume
     7033    DisAglCtls = {'Factors': [0.85, 0],
     7034                 'BondRadii': [], 'AngleRadii': [], 'AtomTypes': []}
     7035    for atom in rd.Phase['Atoms']:
     7036        DisAglCtls['BondRadii'].append(1.5)
     7037        DisAglCtls['AngleRadii'].append(0)
     7038        DisAglCtls['AtomTypes'].append(atom[ct])
     7039    txt = ''
     7040    for i,phObj in enumerate([rd.Phase,O2Phase]):
     7041        if i:
     7042            txt += "\n\nWith origin shift applied\n"
     7043        else:
     7044            txt += "\nWith original origin\n"
     7045        cellContents = {}
     7046        for atom in phObj['Atoms']:
     7047            if atom[ct] in cellContents:
     7048                cellContents[atom[ct]] += atom[cs+1]
     7049            else:
     7050                cellContents[atom[ct]] = atom[cs+1]
     7051        txt += '   Unit cell Contents: '
     7052        for i,k in enumerate(cellContents):
     7053            if i: txt += ', '
     7054            txt += '{}*{}'.format(cellContents[k],k)
     7055        G2elem.SetupGeneral(phObj,G2frame.dirname)
     7056        den,_ = G2mth.getDensity(phObj['General'])
     7057        txt += "\n   Density {:.2f} g/cc\n".format(den)
     7058                   
     7059        DisAglData['OrigAtoms'] = DisAglData['TargAtoms'] = [
     7060                        [i,]+atom[ct-1:ct+1]+atom[cx:cx+3] for
     7061                        i,atom in enumerate(phObj['Atoms'])]
     7062        lbl,dis,angle = G2stMn.RetDistAngle(DisAglCtls,DisAglData)
     7063        # get unique distances
     7064        minDis = {}
     7065        for i in dis:
     7066            for j,o,s,d,e in dis[i]:
     7067                key = '-'.join(sorted([lbl[i],lbl[j]]))
     7068                if key not in minDis:
     7069                    minDis[key] = d
     7070                elif d < minDis[key]:
     7071                    minDis[key] = d
     7072        thirdShortest = sorted([minDis[k] for k in minDis])[:3][-1]
     7073        shortTxt = ''
     7074        for k in minDis:
     7075            if minDis[k] <= thirdShortest:
     7076                if shortTxt: shortTxt += ', '
     7077                shortTxt += "{}: {:.2f}".format(k,minDis[k])
     7078        txt += "   Shortest distances are "+shortTxt
     7079
     7080    # do we know if there is a center of symmetry at origin?
     7081    centro = None
     7082    if 'xyz' in rd.SymOps:
     7083        centro = False
     7084        if '-x,-y,-z' in [i.replace(' ','').lower() for i in rd.SymOps['xyz']]:
     7085            centro = True
     7086           
     7087    msg = 'Be careful here. This space group has two origin settings. GSAS-II requires the origin to be placed at a center of symmetry (Origin 2). You must choose the correct option below or all subsequent results will be *wrong*. For more info, press the help button (bottom right).\n'
     7088    if centro:
     7089        msg += '\nThere is an -x,-y,-z symmetry op in the file input, so this is likely already in Origin 2.\n'
     7090    elif centro is None:
     7091        msg += '\nNo symmetry operations read from the input file; you must decide what to do. You are recommended to review a plot of the structure to make sure the symmetry is correct.\n'
     7092    else:
     7093        msg += '\nSymmetry operations in the input file do not contain -x,-y,-z, indicating an origin shift is likely needed.\n'
     7094
     7095    msg += '\nNote that computations below, made from the coordinates, may help determine the correct origin choice:'
     7096
     7097    width = 600
     7098    dlg = wx.Dialog(G2frame,wx.ID_ANY,'Warning: Shift origin?',
     7099                pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE,
     7100                size=(width,-1))
     7101    dlg.CenterOnParent()
     7102    mainSizer = wx.BoxSizer(wx.VERTICAL)
     7103    txtbox = wx.StaticText(dlg,wx.ID_ANY,msg)
     7104    txtbox.Wrap(width-10)
     7105    mainSizer.Add(txtbox,0)
     7106    mainSizer.Add((5,5))
     7107    txtbox = wx.StaticText(dlg,wx.ID_ANY,txt)
     7108    mainSizer.Add(txtbox,0,wx.ALIGN_CENTER,1)
     7109    mainSizer.Add((10,10))
     7110
     7111    O1Btn = wx.Button(dlg,wx.ID_ANY,"Shift to Origin 2")
     7112    O1Btn.Bind(wx.EVT_BUTTON, lambda x: dlg.EndModal(wx.ID_OK))
     7113    O2Btn = wx.Button(dlg,wx.ID_ANY,"Keep current coordinates")
     7114    O2Btn.Bind(wx.EVT_BUTTON, lambda x: dlg.EndModal(wx.ID_YES))
     7115    if centro:
     7116        O2Btn.SetDefault()
     7117    elif centro is not None:
     7118        O1Btn.SetDefault()
     7119    btnSizer = wx.BoxSizer(wx.HORIZONTAL)
     7120    btnSizer.Add((20,20),1)
     7121    btnSizer.Add(O1Btn)
     7122    btnSizer.Add((10,10),0)
     7123    btnSizer.Add(O2Btn)
     7124    btnSizer.Add((20,20),1)
     7125    btnSizer.Add(HelpButton(dlg,helpIndex='Origin1'),0,wx.RIGHT,5)
     7126    mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10)
     7127    dlg.SetSizer(mainSizer)
     7128    dlg.Fit()
     7129    ans = dlg.ShowModal()
     7130    if ans == wx.ID_OK:
     7131        dlg.Destroy()
     7132        return O2Phase
     7133    elif ans == wx.ID_YES:
     7134        dlg.Destroy()
     7135        return rd.Phase
     7136    else:
     7137        dlg.Destroy()
     7138        return None
    70117139
    70127140if __name__ == '__main__':

  • trunk/GSASIIdataGUI.py

    r4658 r4659  
    11271127            rd.Phase['General']['Name'] = G2obj.MakeUniqueLabel(PhaseName,phaseNameList)
    11281128            if rd.Phase['General']['SGData']['SpGrp'] in G2spc.spg2origins:
    1129                 wx.MessageDialog(self,' The atom positions for this structure must be in the 2nd setting for the space group '+
    1130                     rd.Phase['General']['SGData']['SpGrp'],
    1131                     'Is this 2nd setting?',  wx.OK).ShowModal()
    1132                
     1129                choice = G2G.ChooseOrigin(self,rd)
     1130                if choice is None: return # dialog cancelled
     1131                rd.Phase = choice
    11331132            PhaseName = rd.Phase['General']['Name'][:]
    11341133            newPhaseList.append(PhaseName)

  • trunk/GSASIIobj.py

    r4655 r4659  
    24322432            extensionlist,strictExtension)
    24332433        self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
     2434        self.SymOps = {} # specified when symmetry ops are in file (e.g. CIF)
    24342435        self.Constraints = None
    24352436

  • trunk/GSASIIphsGUI.py

    r4654 r4659  
    8080BLACK = wx.Colour(0,0,0)
    8181WACV = wx.ALIGN_CENTER_VERTICAL
    82 mapDefault = {'MapType':'','RefList':'','GridStep':0.25,'Show bonds':True,
    83                 'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
     82mapDefault = G2elem.mapDefault
    8483TabSelectionIdDict = {}
    8584# trig functions in degrees
    … …  
    16151614
    16161615    def SetupGeneral():
    1617         generalData = data['General']
    1618         atomData = data['Atoms']
    1619         generalData['AtomTypes'] = []
    1620         generalData['Isotopes'] = {}
    1621 # various patches
    1622         if 'Isotope' not in generalData:
    1623             generalData['Isotope'] = {}
    1624         if 'Data plot type' not in generalData:
    1625             generalData['Data plot type'] = 'Mustrain'
    1626         if 'POhkl' not in generalData:
    1627             generalData['POhkl'] = [0,0,1]
    1628         if 'Map' not in generalData:
    1629             generalData['Map'] = mapDefault.copy()
    1630         if 'Flip' not in generalData:
    1631             generalData['Flip'] = {'RefList':'','GridStep':0.25,'Norm element':'None',
    1632                 'k-factor':0.1,'k-Max':20.,}
    1633         if 'testHKL' not in generalData['Flip']:
    1634             generalData['Flip']['testHKL'] = [[0,0,2],[2,0,0],[1,1,1],[0,2,0],[1,2,3]]
    1635         if 'doPawley' not in generalData:
    1636             generalData['doPawley'] = False     #ToDo: change to ''
    1637         if 'Pawley dmin' not in generalData:
    1638             generalData['Pawley dmin'] = 1.0
    1639         if 'Pawley dmax' not in generalData:
    1640             generalData['Pawley dmax'] = 100.0
    1641         if 'Pawley neg wt' not in generalData:
    1642             generalData['Pawley neg wt'] = 0.0
    1643         if '3Dproj' not in generalData:
    1644             generalData['3Dproj'] = ''
    1645         if 'doDysnomia' not in generalData:
    1646             generalData['doDysnomia'] = False
    1647         if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
    1648             'MCSA controls' not in generalData:
    1649             generalData['MCSA controls'] = {'Data source':'','Annealing':[0.7,0.1,250],
    1650             'dmin':2.8,'Algorithm':'log','fast parms':[0.8,0.6],'log slope':0.9,
    1651             'Cycles':1,'Results':[],'newDmin':True}
    1652         if 'AtomPtrs' not in generalData:
    1653             generalData['AtomPtrs'] = [3,1,7,9]
    1654             if generalData['Type'] == 'macromolecular':
    1655                 generalData['AtomPtrs'] = [6,4,10,12]
    1656             elif generalData['Type'] == 'magnetic':
    1657                 generalData['AtomPtrs'] = [3,1,10,12]
    1658         if generalData['Modulated']:
    1659             if 'Super' not in generalData:
    1660                 generalData['Super'] = 1
    1661                 generalData['SuperVec'] = [[0.,0.,0.],False,1]
    1662                 generalData['SSGData'] = {}
    1663             if '4DmapData' not in generalData:
    1664                 generalData['4DmapData'] = mapDefault.copy()
    1665                 generalData['4DmapData'].update({'MapType':'Fobs'})
    1666             atomData = data['Atoms']
    1667             for atom in atomData:
    1668 #                if 'SS1' not in atom:
    1669 #                    atom += [[],[],{'SS1':{'waveType':'Fourier','Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}]
    1670                 if isinstance(atom[-1],dict) and 'waveType' in atom[-1]['SS1']:
    1671                     waveType = atom[-1]['SS1']['waveType']
    1672                     for parm in ['Sfrac','Spos','Sadp','Smag']:
    1673                         if len(atom[-1]['SS1'][parm]):
    1674                             wType = 'Fourier'
    1675                             if parm == 'Sfrac':
    1676                                 if 'Crenel' in waveType:
    1677                                     wType = 'Crenel'
    1678                             elif parm == 'Spos':
    1679                                 if not 'Crenel' in waveType:
    1680                                     wType = waveType
    1681                             atom[-1]['SS1'][parm] = [wType,]+list(atom[-1]['SS1'][parm])
    1682                     del atom[-1]['SS1']['waveType']
    1683         else:
    1684             generalData['Super'] = 0
    1685         if 'Modulated' not in generalData:
    1686             generalData['Modulated'] = False
    1687         if 'HydIds' not in generalData:
    1688             generalData['HydIds'] = {}
    1689         if generalData['Type'] == 'magnetic':
    1690             if 'SGGray' not in generalData['SGData']:
    1691                 generalData['SGData']['SGGray'] = False
    1692         if 'Resolution' in generalData['Map']:
    1693             generalData['Map']['GridStep'] = generalData['Map']['Resolution']/2.
    1694             generalData['Flip']['GridStep'] = generalData['Flip']['Resolution']/2.
    1695             del generalData['Map']['Resolution']
    1696             del generalData['Flip']['Resolution']
    1697         if 'Compare' not in generalData:
    1698             generalData['Compare'] = {'Oatoms':'','Tatoms':'',
    1699                     'Tilts':{'Otilts':[],'Ttilts':[]},
    1700                 'Bonds':{'Obonds':[],'Tbonds':[]},'Vects':{'Ovec':[],'Tvec':[]},
    1701                 'dVects':{'Ovec':[],'Tvec':[]},'Sampling':1.0}
    1702         if 'Sampling' not in generalData['Compare']:
    1703             generalData['Compare']['Sampling'] = 1.0
    1704                
    1705 # end of patches
    1706         cx,ct,cs,cia = generalData['AtomPtrs']
    1707         generalData['NoAtoms'] = {}
    1708         generalData['BondRadii'] = []
    1709         generalData['AngleRadii'] = []
    1710         generalData['vdWRadii'] = []
    1711         generalData['AtomMass'] = []
    1712         generalData['Color'] = []
    1713         if generalData['Type'] == 'magnetic':
    1714             generalData['MagDmin'] = generalData.get('MagDmin',1.0)
    1715             landeg = generalData.get('Lande g',[])
    1716         generalData['Mydir'] = G2frame.dirname
    1717         badList = {}
    1718         for iat,atom in enumerate(atomData):
    1719             atom[ct] = atom[ct].lower().capitalize()              #force to standard form
    1720             if generalData['AtomTypes'].count(atom[ct]):
    1721                 generalData['NoAtoms'][atom[ct]] += atom[cx+3]*float(atom[cs+1])
    1722             elif atom[ct] != 'UNK':
    1723                 Info = G2elem.GetAtomInfo(atom[ct])
    1724                 if not Info:
    1725                     if atom[ct] not in badList:
    1726                         badList[atom[ct]] = 0
    1727                     badList[atom[ct]] += 1
    1728                     atom[ct] = 'UNK'
    1729                     continue
    1730                 atom[ct] = Info['Symbol'] # N.B. symbol might be changed by GetAtomInfo
    1731                 generalData['AtomTypes'].append(atom[ct])
    1732                 generalData['Z'] = Info['Z']
    1733                 generalData['Isotopes'][atom[ct]] = Info['Isotopes']
    1734                 generalData['BondRadii'].append(Info['Drad'])
    1735                 generalData['AngleRadii'].append(Info['Arad'])
    1736                 generalData['vdWRadii'].append(Info['Vdrad'])
    1737                 if atom[ct] in generalData['Isotope']:
    1738                     if generalData['Isotope'][atom[ct]] not in generalData['Isotopes'][atom[ct]]:
    1739                         isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1]
    1740                         generalData['Isotope'][atom[ct]] = isotope
    1741                     generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]]['Mass'])
    1742                 else:
    1743                     generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
    1744                     if 'Nat. Abund.' not in generalData['Isotopes'][atom[ct]]:
    1745                         isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1]
    1746                         generalData['Isotope'][atom[ct]] = isotope
    1747                     generalData['AtomMass'].append(Info['Mass'])
    1748                 generalData['NoAtoms'][atom[ct]] = atom[cx+3]*float(atom[cs+1])
    1749                 generalData['Color'].append(Info['Color'])
    1750                 if generalData['Type'] == 'magnetic':
    1751                     if len(landeg) < len(generalData['AtomTypes']):
    1752                         landeg.append(2.0)
    1753         if generalData['Type'] == 'magnetic':
    1754             generalData['Lande g'] = landeg[:len(generalData['AtomTypes'])]
    1755                        
    1756         if badList:
    1757             msg = 'Warning: element symbol(s) not found:'
    1758             for key in badList:
    1759                 msg += '\n\t' + key
    1760                 if badList[key] > 1:
    1761                     msg += ' (' + str(badList[key]) + ' times)'
     1616        try:
     1617            G2elem.SetupGeneral(data,G2frame.dirname)
     1618        except ValueError as msg:
    17621619            wx.MessageBox(msg,caption='Element symbol error')
    1763         F000X = 0.
    1764         F000N = 0.
    1765         for i,elem in enumerate(generalData['AtomTypes']):
    1766             F000X += generalData['NoAtoms'][elem]*generalData['Z']
    1767             isotope = generalData['Isotope'][elem]
    1768             F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope]['SL'][0]
    1769         generalData['F000X'] = F000X
    1770         generalData['F000N'] = F000N
    1771         generalData['Mass'] = G2mth.getMass(generalData)
    1772        
    17731620
    17741621################################################################################
    … …  
    30052852                        SGData['SGSpin'] = G2spc.GetSGSpin(SGData,SGData['MagSpGrp'])
    30062853                else:
    3007                     dlg.Destroy()
    30082854                    return
    30092855            finally:
    … …  
    30192865                    for i in [0,1,2]:
    30202866                        atom[cx+i] += T[i]
     2867                    SytSym,Mul,Nop,dupDir = G2spc.SytSym(atom[3:6],SGData) # update symmetry & mult
     2868                    atom[cs:cs+2] = SytSym,Mul
    30212869                data['Drawing'] = []
    3022                 break
     2870                #force redraw of page
     2871                sub = G2frame.GPXtree.GetSelection()
     2872                G2frame.GPXtree.SelectItem(G2frame.GPXtree.root)
     2873                wx.CallAfter(G2frame.GPXtree.SelectItem,sub)
     2874                return
    30232875            else:
    30242876                phaseName = newPhase['General']['Name']

  • trunk/GSASIIscriptable.py

    r4654 r4659  
    13941394
    13951395def SetupGeneral(data, dirname):
    1396     """Helps initialize phase data.
    1397 
    1398     From GSASIIphsGui.py, function of the same name. Minor changes for imports etc.
    1399 
    1400     Author: Jackson O'Donnell (jacksonhodonnell .at. gmail.com)
    1401     """
    1402     mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
    1403                 'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
    1404     generalData = data['General']
    1405     atomData = data['Atoms']
    1406     generalData['AtomTypes'] = []
    1407     generalData['Isotopes'] = {}
    1408 
    1409     if 'Isotope' not in generalData:
    1410         generalData['Isotope'] = {}
    1411     if 'Data plot type' not in generalData:
    1412         generalData['Data plot type'] = 'Mustrain'
    1413     if 'POhkl' not in generalData:
    1414         generalData['POhkl'] = [0,0,1]
    1415     if 'Map' not in generalData:
    1416         generalData['Map'] = mapDefault.copy()
    1417     if 'Flip' not in generalData:
    1418         generalData['Flip'] = {'RefList':'','Resolution':0.5,'Norm element':'None',
    1419             'k-factor':0.1,'k-Max':20.,}
    1420     if 'testHKL' not in generalData['Flip']:
    1421         generalData['Flip']['testHKL'] = [[0,0,2],[2,0,0],[1,1,1],[0,2,0],[1,2,3]]
    1422     if 'doPawley' not in generalData:
    1423         generalData['doPawley'] = False     #ToDo: change to ''
    1424     if 'Pawley dmin' not in generalData:
    1425         generalData['Pawley dmin'] = 1.0
    1426     if 'Pawley neg wt' not in generalData:
    1427         generalData['Pawley neg wt'] = 0.0
    1428     if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
    1429         'MCSA controls' not in generalData:
    1430         generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
    1431         'dmin':2.0,'Algorithm':'log','Jump coeff':[0.95,0.5],'boltzmann':1.0,
    1432         'fast parms':[1.0,1.0,1.0],'log slope':0.9,'Cycles':1,'Results':[],'newDmin':True}
    1433     if 'AtomPtrs' not in generalData:
    1434         generalData['AtomPtrs'] = [3,1,7,9]
    1435         if generalData['Type'] == 'macromolecular':
    1436             generalData['AtomPtrs'] = [6,4,10,12]
    1437         elif generalData['Type'] == 'magnetic':
    1438             generalData['AtomPtrs'] = [3,1,10,12]
    1439     if generalData['Modulated']:
    1440         generalData['Type'] = 'nuclear'
    1441         if 'Super' not in generalData:
    1442             generalData['Super'] = 1
    1443             generalData['SuperVec'] = [[0,0,.1],False,4]
    1444             generalData['SSGData'] = {}
    1445         if '4DmapData' not in generalData:
    1446             generalData['4DmapData'] = mapDefault.copy()
    1447             generalData['4DmapData'].update({'MapType':'Fobs'})
    1448     if 'Modulated' not in generalData:
    1449         generalData['Modulated'] = False
    1450     if 'HydIds' not in generalData:
    1451         generalData['HydIds'] = {}
    1452     cx,ct,cs,cia = generalData['AtomPtrs']
    1453     generalData['NoAtoms'] = {}
    1454     generalData['BondRadii'] = []
    1455     generalData['AngleRadii'] = []
    1456     generalData['vdWRadii'] = []
    1457     generalData['AtomMass'] = []
    1458     generalData['Color'] = []
    1459     if generalData['Type'] == 'magnetic':
    1460         generalData['MagDmin'] = generalData.get('MagDmin',1.0)
    1461         landeg = generalData.get('Lande g',[])
    1462     generalData['Mydir'] = dirname
    1463     badList = {}
    1464     for iat,atom in enumerate(atomData):
    1465         atom[ct] = atom[ct].lower().capitalize()              #force to standard form
    1466         if generalData['AtomTypes'].count(atom[ct]):
    1467             generalData['NoAtoms'][atom[ct]] += atom[cx+3]*float(atom[cs+1])
    1468         elif atom[ct] != 'UNK':
    1469             Info = G2elem.GetAtomInfo(atom[ct])
    1470             if not Info:
    1471                 if atom[ct] not in badList:
    1472                     badList[atom[ct]] = 0
    1473                 badList[atom[ct]] += 1
    1474                 atom[ct] = 'UNK'
    1475                 continue
    1476             atom[ct] = Info['Symbol'] # N.B. symbol might be changed by GetAtomInfo
    1477             generalData['AtomTypes'].append(atom[ct])
    1478             generalData['Z'] = Info['Z']
    1479             generalData['Isotopes'][atom[ct]] = Info['Isotopes']
    1480             generalData['BondRadii'].append(Info['Drad'])
    1481             generalData['AngleRadii'].append(Info['Arad'])
    1482             generalData['vdWRadii'].append(Info['Vdrad'])
    1483             if atom[ct] in generalData['Isotope']:
    1484                 if generalData['Isotope'][atom[ct]] not in generalData['Isotopes'][atom[ct]]:
    1485                     isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1]
    1486                     generalData['Isotope'][atom[ct]] = isotope
    1487                 generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]]['Mass'])
    1488             else:
    1489                 generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
    1490                 if 'Nat. Abund.' not in generalData['Isotopes'][atom[ct]]:
    1491                     isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1]
    1492                     generalData['Isotope'][atom[ct]] = isotope
    1493                 generalData['AtomMass'].append(Info['Mass'])
    1494             generalData['NoAtoms'][atom[ct]] = atom[cx+3]*float(atom[cs+1])
    1495             generalData['Color'].append(Info['Color'])
    1496             if generalData['Type'] == 'magnetic':
    1497                 if len(landeg) < len(generalData['AtomTypes']):
    1498                     landeg.append(2.0)
    1499     if generalData['Type'] == 'magnetic':
    1500         generalData['Lande g'] = landeg[:len(generalData['AtomTypes'])]
    1501 
    1502     if badList:
    1503         msg = 'Warning: element symbol(s) not found:'
    1504         for key in badList:
    1505             msg += '\n\t' + key
    1506             if badList[key] > 1:
    1507                 msg += ' (' + str(badList[key]) + ' times)'
    1508         raise G2ScriptException("Phase error:\n" + msg)
    1509         # wx.MessageBox(msg,caption='Element symbol error')
    1510     F000X = 0.
    1511     F000N = 0.
    1512     for i,elem in enumerate(generalData['AtomTypes']):
    1513         F000X += generalData['NoAtoms'][elem]*generalData['Z']
    1514         isotope = generalData['Isotope'][elem]
    1515         F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope]['SL'][0]
    1516     generalData['F000X'] = F000X
    1517     generalData['F000N'] = F000N
    1518     import GSASIImath as G2mth
    1519     generalData['Mass'] = G2mth.getMass(generalData)
    1520 
     1396    '''Initialize phase data.
     1397    '''
     1398    try:
     1399        G2elem.SetupGeneral(data,dirname)
     1400    except ValueError as msg:
     1401        raise G2ScriptException(msg)
    15211402
    15221403def make_empty_project(author=None, filename=None):

  • trunk/help/gsasII.html

    r4621 r4659  
    58235823"Times New Roman"'>This gives overall parameters describing the phase such as
    58245824the name, space group, the unit cell parameters and overall parameters for the
    5825 atom present in the phase. It also has the controls for computing Fourier maps
    5826 for this phase.<span class=MsoHyperlink><span style='color:windowtext;
     5825atom present in the phase. It also has the controls for Pawley
     5826intensity extraction and for computing Fourier maps
     5827for this phase. It can also be used to compute new structures based on
     5828the unit cell and atom poistions.
     5829<span class=MsoHyperlink><span style='color:windowtext;
    58275830text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    58285831
    … …  
    58385841</span></span></span></span><![endif]><span style='mso-fareast-font-family:
    58395842"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Compute’</b> –
    5840 The compute menu shows computations that are possible for this phase.<span
    5841 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5842 text-underline:none'><o:p></o:p></span></span></span></p>
    5843 
    5844 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5845 auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
    5846 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5847 color:windowtext;text-decoration:none;text-underline:none'><span
    5848 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5849 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5850 style='mso-fareast-font-family:"Times New Roman"'>Fourier maps</span></b><span
    5851 style='mso-fareast-font-family:"Times New Roman"'> – compute Fourier maps
    5852 according to the controls set at bottom of General page.<span
    5853 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5854 text-underline:none'><o:p></o:p></span></span></span></p>
    5855 
    5856 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5857 auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
    5858 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5859 color:windowtext;text-decoration:none;text-underline:none'><span
    5860 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5861 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5862 style='mso-fareast-font-family:"Times New Roman"'>Search maps </span></b><span
    5863 style='mso-fareast-font-family:"Times New Roman"'>– search the computed Fourier
     5843The compute menu shows computations that are possible for this phase.
     5844
     5845<DL class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5846  auto;mso-list:l2 level2 lfo27'>
     5847<DT><B>Fourier maps</B></DT>
     5848  <DD>compute Fourier maps
     5849  according to the controls set at bottom of General page.</DD>
     5850<DT><B>Search maps</B></DT>
     5851<DD>search the computed Fourier
    58645852map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this
    58655853procedure; they will be printed on the console and will be shown in the ‘<a
    5866 href="Map_peaks">Map peaks</a><span
    5867 style='mso-bookmark:Map_peaks'></span>’ page. This page will immediately be
     5854href="Map_peaks">Map peaks</a>’ page. This page will immediately be
    58685855shown and the peaks will be shown on the structure drawing for this phase as
    5869 white 3-D crosses.<span class=MsoHyperlink><span style='color:windowtext;
    5870 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    5871 
    5872 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5873 auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
    5874 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5875 color:windowtext;text-decoration:none;text-underline:none'><span
    5876 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5877 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5878 style='mso-fareast-font-family:"Times New Roman"'>Charge flipping </span></b><span
    5879 style='mso-fareast-font-family:"Times New Roman"'>– This performs a charge
     5856  white 3-D crosses.</DD>
     5857<DT><B>Charge flipping </B></DT>
     5858<DD>This performs a charge
    58805859flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution
    58815860using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You
    … …  
    58905869properly place symmetry operators (NB: depends on the quality of the resulting
    58915870phases), searched for peaks and the display shifts to <b style='mso-bidi-font-weight:
    5892 normal'>Map peaks</b> to show them.<span class=MsoHyperlink><span
    5893 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    5894 
    5895 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5896 auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
    5897 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5898 color:windowtext;text-decoration:none;text-underline:none'><span
    5899 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5900 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5901 style='mso-fareast-font-family:"Times New Roman"'>Clear map </span></b><span
    5902 style='mso-fareast-font-family:"Times New Roman"'>– This clears any
    5903 Fourier/charge flip map from memory; the Fourier map controls are also cleared.<span
     5871  normal'>Map peaks</b> to show them.</DD>
     5872<DT><B>Clear map </B></DT>
     5873<DD>This clears any
     5874Fourier/charge flip map from memory; the Fourier map controls are also
     5875  cleared.</DD>
     5876<DT><B>Transform</B></DT>
     5877<DD>This allows for a change in axes, symmetry or unit cell. It is
     5878  also used to create a magnetic phase from a chemical (nuclear)
     5879  phase. One important transformation that can be done here is for
     5880  Origin 1 settings to Origin 2 (<a href="#Origin1">described below</a>)
     5881
     5882 
     5883</DD>
     5884</DL>
     5885
     5886<span
    59045887class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    59055888text-underline:none'><o:p></o:p></span></span></span></p>
    … …  
    62816264algorithm is chosen these determine the jump components for each trial.<o:p></o:p></span></span></p>
    62826265
     6266<h5 style='margin-left:0.5in'><a name=Origin1></a>Origin 1 ->
     6267Origin 2 Transformations</h5>
     6268
     6269<p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
     6270An important transformation may be needed in certain cases when space
     6271groups that two alternate origin settings
     6272(<A
     6273href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#GSASIIspc.spg2origins">listed here</a>).
     6274These are centrosymmetric space groups where the highest symmetry
     6275point in the structure does not contain a center of symmetry. Origin 1
     6276places the origin at the highest symmetry setting while Origin 2
     6277places the origin at a center of symmetry (creating a -x,-y,-z
     6278symmetry operator, which means that reflection phases can only be 0 or π.)
     6279GSAS-II requires use of the Origin 2 settings because computations are much
     6280faster and simpler without complex structure factors.
     6281Alas, the literature contains a number of structures reported in
     6282Origin 1, where the origin choice may not be clearly communicated. (The
     6283CIF standard does not require that origin choice be indicated.)
     6284When a structure is imported that uses any of the space groups where
     6285an origin choice is possible, a message is shown in GSAS-II notifying
     6286the user that they must confirm that the origin choice is correct.
     6287</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
     6288<B>Example:</B>
     6289An
     6290example of what can go wrong is illustrated with the structure of
     6291anatase. The space group is <I>I</I> 4<sub>1</sub>/<I>a m d</I>. In
     6292Origin 1 the coordinates are:
     6293<TABLE border=2; style='margin-left:2.0in'>
     6294  <TR>
     6295    <th colspan=4>Origin 1</th>
     6296  </TR>
     6297  <TR>
     6298    <th>atom</th>
     6299    <th colspan=3>coordinates</th>
     6300  </TR>
     6301  <TR>
     6302    <TD>Ti</TD>
     6303    <TD>0</TD>
     6304    <TD>0</TD>
     6305    <TD>0</TD>
     6306  </TR>
     6307  <TR>
     6308    <TD>O</TD>
     6309    <TD>0</TD>
     6310    <TD>0</TD>
     6311    <TD>0.208</TD>
     6312  </TR>
     6313</TABLE>
     6314
     6315and in Origin 2 the coordinates are:
     6316<TABLE border=2; style='margin-left:2.0in'>
     6317  <TR>
     6318    <th colspan=4>Origin 2</th>
     6319  </TR>
     6320  <TR>
     6321    <th>atom</th>
     6322    <th colspan=3>coordinates</th>
     6323  </TR>
     6324  <TR>
     6325    <TD>Ti</TD>
     6326    <TD>0</TD>
     6327    <TD>1/4</TD>
     6328    <TD>-1/8</TD>
     6329  </TR>
     6330  <TR>
     6331    <TD>O</TD>
     6332    <TD>0</TD>
     6333    <TD>1/4</TD>
     6334    <TD>0.083</TD>
     6335  </TR>
     6336</TABLE>
     6337where the origin is shifted by (0,0.25,-0.125).
     6338</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
     6339<img src="gsasII_files/wrong.png" align="right">
     6340Since GSAS-II always the symmetry operators for Origin 2,
     6341if structure is input incorrectly with the coordinates set for Origin
     63421, there are several fairly obvious signs of problems: (1) the
     6343site symmetries and multiplicities are wrong, often giving an incorrect
     6344chemical formula, (2) the interatomic distances are incorrect, and (3)
     6345a plot of the structure is improbable.
     6346In this case incorrect multiplicities gives
     6347rise to a density of 7.9 g/cc, double the correct value.
     6348Impossible interatomic distances of 1.88&Aring for Ti-Ti, and
     63491.39&Aring; for Ti-O are seen. The unit
     6350cell contents with the wrong space group operators is shown to the
     6351right.
     6352</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
     6353With coordinates that match the space
     6354group operations, the correct Ti-O distances are 1.92&Aring; and
     63551.97&Aring; and the shortest Ti-Ti distance is 3.0&Aring;.
     6356(Note that interatomic distances can be computed in GSAS-II using the Phase Atoms
     6357tab and the Compute/"Show Distances & Angles" menu item.)
     6358
     6359</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span
     6360style='mso-fareast-font-family:"Times New Roman"'>
     6361<img src="gsasII_files/xform.png" align="right">
     6362<B>Transform Origin:</B>
     6363To transform a space group setting from Origin setting 1 to 2, use the
     6364Transform option in the Compute menu and then select the last option in the "Common
     6365transformations" pulldown menu, which will be setting 1->2 for space
     6366groups where both origins are available, as shown to the right. The
     6367transformation matrix will be set to the identity and the "V" vector
     6368will have the required origin shift loaded. Press OK. The changes can
     6369be seen by selecting the Atoms tab.
     6370
     6371</span></p>
     6372<BR CLEAR="right" />
    62836373<h4 style='margin-left:0.25in'><a name=Data></a><u>Data</u></h4>
    62846374
    … …  
    73537443<hr size=2 width="100%" align=center>
    73547444
    7355 <!-- hhmts start -->Last modified: Fri Oct 23 15:56:02 CDT 2020 <!-- hhmts end -->
     7445<!-- hhmts start -->Last modified: Sat Nov 21 12:25:40 CST 2020 <!-- hhmts end -->
    73567446
    73577447</div>

  • trunk/imports/G2phase_CIF.py

    r4635 r4659  
    250250                SGData = G2obj.P1SGData # P 1
    251251            self.Phase['General']['SGData'] = SGData
     252            # save symmetry operators, if specified (use to check for origin 1 in GSASIIdataGUI OnImportPhase)
     253            ops = blk.get("_symmetry_equiv_pos_as_xyz")   # try older name 1st
     254            if ops:
     255                self.SymOps['xyz'] = ops
     256            elif blk.get("_space_group_symop_operation_xyz"):
     257                self.SymOps['xyz'] = blk.get("_space_group_symop_operation_xyz")
     258            else:
     259                if 'xyz' in self.SymOps: del self.SymOps['xyz']
    252260            if Super:
    253261                E,SSGData = G2spc.SSpcGroup(SGData,SuperSg)
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