Changeset 4659 for trunk/GSASIIElem.py

Timestamp:

Nov 21, 2020 2:15:49 PM (2 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

File:

• trunk/GSASIIElem.py (modified) (1 diff)

trunk/GSASIIElem.py

@@ -543 +543 @@
     return (FP, FPP, Mu)
     
-
+mapDefault = {'MapType':'','RefList':'','GridStep':0.25,'Show bonds':True,
+                'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
+
+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)