Changeset 4659

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:

• GSASIIElem.py (modified) (1 diff)
• GSASIIctrlGUI.py (modified) (2 diffs)
• GSASIIdataGUI.py (modified) (1 diff)
• GSASIIobj.py (modified) (1 diff)
• GSASIIphsGUI.py (modified) (4 diffs)
• GSASIIscriptable.py (modified) (1 diff)
• help/gsasII.html (modified) (5 diffs)
• help/gsasII_files/wrong.png (added)
• help/gsasII_files/xform.png (added)
• imports/G2phase_CIF.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)        

trunk/GSASIIctrlGUI.py

@@ -169 +169 @@
 import GSASIIobj as G2obj
 import GSASIIfiles as G2fil
+import GSASIIElem as G2elem
 import GSASIIscriptable as G2sc
 import GSASIIpwd as G2pwd
 import GSASIIlattice as G2lat
+import GSASIImath as G2mth
+import GSASIIstrMain as G2stMn
 if sys.version_info[0] >= 3:
     unicode = str
@@ -7009 +7012 @@
     AutoLoadWindow = dlg # save window reference
 
+################################################################################
+# Deal with Origin 1/2 ambiguities
+################################################################################
+def ChooseOrigin(G2frame,rd):    
+    # make copy of Phase but shift atoms Origin 1->2
+    O2Phase = copy.deepcopy(rd.Phase)
+    # make copy of atoms, shift to alternate origin
+    T = G2spc.spg2origins[rd.Phase['General']['SGData']['SpGrp']]
+    O2atoms = O2Phase['Atoms']
+    cx,ct,cs,cia = rd.Phase['General']['AtomPtrs']
+    SGData = rd.Phase['General']['SGData']
+    for atom in O2atoms:
+        for i in [0,1,2]:
+            atom[cx+i] += T[i]
+            atom[cs:cs+2] = G2spc.SytSym(atom[3:6],SGData)[0:2] # update symmetry & mult
+    #get density & distances
+    DisAglData = {}
+    DisAglData['SGData'] = rd.Phase['General']['SGData']
+    DisAglData['Cell'] = rd.Phase['General']['Cell'][1:] #+ volume
+    DisAglCtls = {'Factors': [0.85, 0],
+                 'BondRadii': [], 'AngleRadii': [], 'AtomTypes': []}
+    for atom in rd.Phase['Atoms']:
+        DisAglCtls['BondRadii'].append(1.5)
+        DisAglCtls['AngleRadii'].append(0)
+        DisAglCtls['AtomTypes'].append(atom[ct])
+    txt = ''
+    for i,phObj in enumerate([rd.Phase,O2Phase]):
+        if i:
+            txt += "\n\nWith origin shift applied\n"
+        else:
+            txt += "\nWith original origin\n"
+        cellContents = {}
+        for atom in phObj['Atoms']:
+            if atom[ct] in cellContents:
+                cellContents[atom[ct]] += atom[cs+1]
+            else:
+                cellContents[atom[ct]] = atom[cs+1]
+        txt += '   Unit cell Contents: '
+        for i,k in enumerate(cellContents):
+            if i: txt += ', '
+            txt += '{}*{}'.format(cellContents[k],k)
+        G2elem.SetupGeneral(phObj,G2frame.dirname)
+        den,_ = G2mth.getDensity(phObj['General'])
+        txt += "\n   Density {:.2f} g/cc\n".format(den)
+                    
+        DisAglData['OrigAtoms'] = DisAglData['TargAtoms'] = [
+                        [i,]+atom[ct-1:ct+1]+atom[cx:cx+3] for
+                        i,atom in enumerate(phObj['Atoms'])]
+        lbl,dis,angle = G2stMn.RetDistAngle(DisAglCtls,DisAglData)
+        # get unique distances
+        minDis = {} 
+        for i in dis: 
+            for j,o,s,d,e in dis[i]: 
+                key = '-'.join(sorted([lbl[i],lbl[j]])) 
+                if key not in minDis: 
+                    minDis[key] = d 
+                elif d < minDis[key]: 
+                    minDis[key] = d
+        thirdShortest = sorted([minDis[k] for k in minDis])[:3][-1]
+        shortTxt = ''
+        for k in minDis:
+            if minDis[k] <= thirdShortest:
+                if shortTxt: shortTxt += ', '
+                shortTxt += "{}: {:.2f}".format(k,minDis[k])
+        txt += "   Shortest distances are "+shortTxt
+
+    # do we know if there is a center of symmetry at origin?
+    centro = None
+    if 'xyz' in rd.SymOps:
+        centro = False
+        if '-x,-y,-z' in [i.replace(' ','').lower() for i in rd.SymOps['xyz']]:
+            centro = True
+            
+    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'
+    if centro:
+        msg += '\nThere is an -x,-y,-z symmetry op in the file input, so this is likely already in Origin 2.\n'
+    elif centro is None:
+        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'
+    else:
+        msg += '\nSymmetry operations in the input file do not contain -x,-y,-z, indicating an origin shift is likely needed.\n'
+
+    msg += '\nNote that computations below, made from the coordinates, may help determine the correct origin choice:'
+
+    width = 600
+    dlg = wx.Dialog(G2frame,wx.ID_ANY,'Warning: Shift origin?',
+                pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE,
+                size=(width,-1))
+    dlg.CenterOnParent()
+    mainSizer = wx.BoxSizer(wx.VERTICAL)
+    txtbox = wx.StaticText(dlg,wx.ID_ANY,msg)
+    txtbox.Wrap(width-10)
+    mainSizer.Add(txtbox,0)
+    mainSizer.Add((5,5))
+    txtbox = wx.StaticText(dlg,wx.ID_ANY,txt)
+    mainSizer.Add(txtbox,0,wx.ALIGN_CENTER,1)
+    mainSizer.Add((10,10))
+
+    O1Btn = wx.Button(dlg,wx.ID_ANY,"Shift to Origin 2")
+    O1Btn.Bind(wx.EVT_BUTTON, lambda x: dlg.EndModal(wx.ID_OK))
+    O2Btn = wx.Button(dlg,wx.ID_ANY,"Keep current coordinates")
+    O2Btn.Bind(wx.EVT_BUTTON, lambda x: dlg.EndModal(wx.ID_YES))
+    if centro:
+        O2Btn.SetDefault()
+    elif centro is not None:
+        O1Btn.SetDefault()
+    btnSizer = wx.BoxSizer(wx.HORIZONTAL)
+    btnSizer.Add((20,20),1)
+    btnSizer.Add(O1Btn)
+    btnSizer.Add((10,10),0)
+    btnSizer.Add(O2Btn)
+    btnSizer.Add((20,20),1)
+    btnSizer.Add(HelpButton(dlg,helpIndex='Origin1'),0,wx.RIGHT,5)
+    mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10)
+    dlg.SetSizer(mainSizer)
+    dlg.Fit()
+    ans = dlg.ShowModal()
+    if ans == wx.ID_OK:
+        dlg.Destroy()
+        return O2Phase
+    elif ans == wx.ID_YES:
+        dlg.Destroy()
+        return rd.Phase
+    else:
+        dlg.Destroy()
+        return None
 
 if __name__ == '__main__':

trunk/GSASIIdataGUI.py

@@ -1127 +1127 @@
             rd.Phase['General']['Name'] = G2obj.MakeUniqueLabel(PhaseName,phaseNameList)
             if rd.Phase['General']['SGData']['SpGrp'] in G2spc.spg2origins:
-                wx.MessageDialog(self,' The atom positions for this structure must be in the 2nd setting for the space group '+
-                    rd.Phase['General']['SGData']['SpGrp'], 
-                    'Is this 2nd setting?',  wx.OK).ShowModal()
-                
+                choice = G2G.ChooseOrigin(self,rd)
+                if choice is None: return # dialog cancelled
+                rd.Phase = choice
             PhaseName = rd.Phase['General']['Name'][:]
             newPhaseList.append(PhaseName)

trunk/GSASIIobj.py

@@ -2432 +2432 @@
             extensionlist,strictExtension)
         self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
+        self.SymOps = {} # specified when symmetry ops are in file (e.g. CIF)
         self.Constraints = None
 

trunk/GSASIIphsGUI.py

@@ -80 +80 @@
 BLACK = wx.Colour(0,0,0)
 WACV = wx.ALIGN_CENTER_VERTICAL
-mapDefault = {'MapType':'','RefList':'','GridStep':0.25,'Show bonds':True,
-                'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
+mapDefault = G2elem.mapDefault
 TabSelectionIdDict = {}
 # trig functions in degrees
@@ -1615 +1614 @@
 
     def 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'] = G2frame.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 = G2elem.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'])]
-                        
-        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)'
+        try:
+            G2elem.SetupGeneral(data,G2frame.dirname)
+        except ValueError as msg:
             wx.MessageBox(msg,caption='Element symbol error')
-        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)
-       
 
 ################################################################################
@@ -3005 +2852 @@
                         SGData['SGSpin'] = G2spc.GetSGSpin(SGData,SGData['MagSpGrp'])
                 else:
-                    dlg.Destroy()
                     return
             finally:
@@ -3019 +2865 @@
                     for i in [0,1,2]:
                         atom[cx+i] += T[i]
+                    SytSym,Mul,Nop,dupDir = G2spc.SytSym(atom[3:6],SGData) # update symmetry & mult
+                    atom[cs:cs+2] = SytSym,Mul
                 data['Drawing'] = []
-                break
+                #force redraw of page
+                sub = G2frame.GPXtree.GetSelection()
+                G2frame.GPXtree.SelectItem(G2frame.GPXtree.root)
+                wx.CallAfter(G2frame.GPXtree.SelectItem,sub)
+                return
             else:
                 phaseName = newPhase['General']['Name']

trunk/GSASIIscriptable.py

@@ -1394 +1394 @@
 
 def SetupGeneral(data, dirname):
-    """Helps initialize phase data.
-
-    From GSASIIphsGui.py, function of the same name. Minor changes for imports etc.
-
-    Author: Jackson O'Donnell (jacksonhodonnell .at. gmail.com)
-    """
-    mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
-                'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
-    generalData = data['General']
-    atomData = data['Atoms']
-    generalData['AtomTypes'] = []
-    generalData['Isotopes'] = {}
-
-    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':'','Resolution':0.5,'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 neg wt' not in generalData:
-        generalData['Pawley neg wt'] = 0.0
-    if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
-        'MCSA controls' not in generalData:
-        generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
-        'dmin':2.0,'Algorithm':'log','Jump coeff':[0.95,0.5],'boltzmann':1.0,
-        'fast parms':[1.0,1.0,1.0],'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']:
-        generalData['Type'] = 'nuclear'
-        if 'Super' not in generalData:
-            generalData['Super'] = 1
-            generalData['SuperVec'] = [[0,0,.1],False,4]
-            generalData['SSGData'] = {}
-        if '4DmapData' not in generalData:
-            generalData['4DmapData'] = mapDefault.copy()
-            generalData['4DmapData'].update({'MapType':'Fobs'})
-    if 'Modulated' not in generalData:
-        generalData['Modulated'] = False
-    if 'HydIds' not in generalData:
-        generalData['HydIds'] = {}
-    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 = G2elem.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'])]
-
-    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)'
-        raise G2ScriptException("Phase error:\n" + msg)
-        # wx.MessageBox(msg,caption='Element symbol error')
-    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
-    import GSASIImath as G2mth
-    generalData['Mass'] = G2mth.getMass(generalData)
-
+    '''Initialize phase data.
+    '''
+    try:
+        G2elem.SetupGeneral(data,dirname)
+    except ValueError as msg:
+        raise G2ScriptException(msg)
 
 def make_empty_project(author=None, filename=None):

trunk/help/gsasII.html

@@ -5823 +5823 @@
 "Times New Roman"'>This gives overall parameters describing the phase such as
 the name, space group, the unit cell parameters and overall parameters for the
-atom present in the phase. It also has the controls for computing Fourier maps
-for this phase.<span class=MsoHyperlink><span style='color:windowtext;
+atom present in the phase. It also has the controls for Pawley
+intensity extraction and for computing Fourier maps
+for this phase. It can also be used to compute new structures based on
+the unit cell and atom poistions. 
+<span class=MsoHyperlink><span style='color:windowtext;
 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
 
@@ -5838 +5841 @@
 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
 "Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Compute’</b> –
-The compute menu shows computations that are possible for this phase.<span
-class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
-text-underline:none'><o:p></o:p></span></span></span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
-auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
-class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
-color:windowtext;text-decoration:none;text-underline:none'><span
-style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
-style='mso-fareast-font-family:"Times New Roman"'>Fourier maps</span></b><span
-style='mso-fareast-font-family:"Times New Roman"'> – compute Fourier maps
-according to the controls set at bottom of General page.<span
-class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
-text-underline:none'><o:p></o:p></span></span></span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
-auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
-class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
-color:windowtext;text-decoration:none;text-underline:none'><span
-style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
-style='mso-fareast-font-family:"Times New Roman"'>Search maps </span></b><span
-style='mso-fareast-font-family:"Times New Roman"'>– search the computed Fourier
+The compute menu shows computations that are possible for this phase.
+
+<DL class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 
+  auto;mso-list:l2 level2 lfo27'>
+<DT><B>Fourier maps</B></DT>
+  <DD>compute Fourier maps
+  according to the controls set at bottom of General page.</DD>
+<DT><B>Search maps</B></DT>
+<DD>search the computed Fourier
 map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this
 procedure; they will be printed on the console and will be shown in the ‘<a
-href="Map_peaks">Map peaks</a><span
-style='mso-bookmark:Map_peaks'></span>’ page. This page will immediately be
+href="Map_peaks">Map peaks</a>’ page. This page will immediately be
 shown and the peaks will be shown on the structure drawing for this phase as
-white 3-D crosses.<span class=MsoHyperlink><span style='color:windowtext;
-text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
-auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
-class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
-color:windowtext;text-decoration:none;text-underline:none'><span
-style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
-style='mso-fareast-font-family:"Times New Roman"'>Charge flipping </span></b><span
-style='mso-fareast-font-family:"Times New Roman"'>– This performs a charge
+  white 3-D crosses.</DD>
+<DT><B>Charge flipping </B></DT>
+<DD>This performs a charge
 flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution
 using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You
@@ -5890 +5869 @@
 properly place symmetry operators (NB: depends on the quality of the resulting
 phases), searched for peaks and the display shifts to <b style='mso-bidi-font-weight:
-normal'>Map peaks</b> to show them.<span class=MsoHyperlink><span
-style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
-auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
-class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
-color:windowtext;text-decoration:none;text-underline:none'><span
-style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
-style='mso-fareast-font-family:"Times New Roman"'>Clear map </span></b><span
-style='mso-fareast-font-family:"Times New Roman"'>– This clears any
-Fourier/charge flip map from memory; the Fourier map controls are also cleared.<span
+  normal'>Map peaks</b> to show them.</DD>
+<DT><B>Clear map </B></DT>
+<DD>This clears any
+Fourier/charge flip map from memory; the Fourier map controls are also
+  cleared.</DD>
+<DT><B>Transform</B></DT>
+<DD>This allows for a change in axes, symmetry or unit cell. It is
+  also used to create a magnetic phase from a chemical (nuclear)
+  phase. One important transformation that can be done here is for
+  Origin 1 settings to Origin 2 (<a href="#Origin1">described below</a>)
+
+  
+</DD>
+</DL>
+
+<span
 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
 text-underline:none'><o:p></o:p></span></span></span></p>
@@ -6281 +6264 @@
 algorithm is chosen these determine the jump components for each trial.<o:p></o:p></span></span></p>
 
+<h5 style='margin-left:0.5in'><a name=Origin1></a>Origin 1 ->
+Origin 2 Transformations</h5>
+
+<p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
+An important transformation may be needed in certain cases when space
+groups that two alternate origin settings
+(<A
+href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#GSASIIspc.spg2origins">listed here</a>).
+These are centrosymmetric space groups where the highest symmetry
+point in the structure does not contain a center of symmetry. Origin 1
+places the origin at the highest symmetry setting while Origin 2
+places the origin at a center of symmetry (creating a -x,-y,-z
+symmetry operator, which means that reflection phases can only be 0 or π.)
+GSAS-II requires use of the Origin 2 settings because computations are much
+faster and simpler without complex structure factors.
+Alas, the literature contains a number of structures reported in
+Origin 1, where the origin choice may not be clearly communicated. (The
+CIF standard does not require that origin choice be indicated.)
+When a structure is imported that uses any of the space groups where
+an origin choice is possible, a message is shown in GSAS-II notifying
+the user that they must confirm that the origin choice is correct. 
+</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
+<B>Example:</B>
+An
+example of what can go wrong is illustrated with the structure of
+anatase. The space group is <I>I</I> 4<sub>1</sub>/<I>a m d</I>. In
+Origin 1 the coordinates are:
+<TABLE border=2; style='margin-left:2.0in'>
+  <TR>
+    <th colspan=4>Origin 1</th>
+  </TR>
+  <TR>
+    <th>atom</th>
+    <th colspan=3>coordinates</th>
+  </TR>
+  <TR>
+    <TD>Ti</TD>
+    <TD>0</TD>
+    <TD>0</TD>
+    <TD>0</TD>
+  </TR>
+  <TR>
+    <TD>O</TD>
+    <TD>0</TD>
+    <TD>0</TD>
+    <TD>0.208</TD>
+  </TR>
+</TABLE>
+
+and in Origin 2 the coordinates are: 
+<TABLE border=2; style='margin-left:2.0in'>
+  <TR>
+    <th colspan=4>Origin 2</th>
+  </TR>
+  <TR>
+    <th>atom</th>
+    <th colspan=3>coordinates</th>
+  </TR>
+  <TR>
+    <TD>Ti</TD>
+    <TD>0</TD>
+    <TD>1/4</TD>
+    <TD>-1/8</TD>
+  </TR>
+  <TR>
+    <TD>O</TD>
+    <TD>0</TD>
+    <TD>1/4</TD>
+    <TD>0.083</TD>
+  </TR>
+</TABLE>
+where the origin is shifted by (0,0.25,-0.125).
+</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
+<img src="gsasII_files/wrong.png" align="right">
+Since GSAS-II always the symmetry operators for Origin 2,
+if structure is input incorrectly with the coordinates set for Origin
+1, there are several fairly obvious signs of problems: (1) the
+site symmetries and multiplicities are wrong, often giving an incorrect
+chemical formula, (2) the interatomic distances are incorrect, and (3)
+a plot of the structure is improbable. 
+In this case incorrect multiplicities gives
+rise to a density of 7.9 g/cc, double the correct value.
+Impossible interatomic distances of 1.88&Aring for Ti-Ti, and
+1.39&Aring; for Ti-O are seen. The unit
+cell contents with the wrong space group operators is shown to the
+right. 
+</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
+With coordinates that match the space
+group operations, the correct Ti-O distances are 1.92&Aring; and
+1.97&Aring; and the shortest Ti-Ti distance is 3.0&Aring;. 
+(Note that interatomic distances can be computed in GSAS-II using the Phase Atoms
+tab and the Compute/"Show Distances & Angles" menu item.) 
+
+</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span 
+style='mso-fareast-font-family:"Times New Roman"'>
+<img src="gsasII_files/xform.png" align="right">
+<B>Transform Origin:</B>
+To transform a space group setting from Origin setting 1 to 2, use the
+Transform option in the Compute menu and then select the last option in the "Common
+transformations" pulldown menu, which will be setting 1->2 for space
+groups where both origins are available, as shown to the right. The
+transformation matrix will be set to the identity and the "V" vector
+will have the required origin shift loaded. Press OK. The changes can
+be seen by selecting the Atoms tab. 
+
+</span></p>
+<BR CLEAR="right" />
 <h4 style='margin-left:0.25in'><a name=Data></a><u>Data</u></h4>
 
@@ -7353 +7443 @@
 <hr size=2 width="100%" align=center>
 
-<!-- hhmts start -->Last modified: Fri Oct 23 15:56:02 CDT 2020 <!-- hhmts end -->
+<!-- hhmts start -->Last modified: Sat Nov 21 12:25:40 CST 2020 <!-- hhmts end -->
 
 </div>

trunk/imports/G2phase_CIF.py

@@ -250 +250 @@
                 SGData = G2obj.P1SGData # P 1
             self.Phase['General']['SGData'] = SGData
+            # save symmetry operators, if specified (use to check for origin 1 in GSASIIdataGUI OnImportPhase)
+            ops = blk.get("_symmetry_equiv_pos_as_xyz")   # try older name 1st
+            if ops:
+                self.SymOps['xyz'] = ops
+            elif blk.get("_space_group_symop_operation_xyz"):
+                self.SymOps['xyz'] = blk.get("_space_group_symop_operation_xyz")
+            else:
+                if 'xyz' in self.SymOps: del self.SymOps['xyz']
             if Super:
                 E,SSGData = G2spc.SSpcGroup(SGData,SuperSg)