add axis choices for vector & residue RBs; needed to resolve RB placement on special positions

fix import of structure factors from Olex2 prepared cif files.

Author: vondreele

GSASII/GSASIImath.py

@@ -45,6 +45,7 @@
 acosd = lambda x: 180.*np.arccos(x)/np.pi
 atand = lambda x: 180.*np.arctan(x)/np.pi
 atan2d = lambda y,x: 180.*np.arctan2(y,x)/np.pi
+vnorm = lambda v: v/nl.norm(v)
 try:  # fails on doc build
     twopi = 2.0*np.pi
     twopisq = 2.0*np.pi**2
@@ -1355,7 +1356,7 @@ def RotateRBXYZ(Bmat,Cart,oriQ,symAxis=None):
         Q = oriQ
     else:
         a,v = Q2AV(oriQ)
-        symaxis = np.array(symAxis)
+        symaxis = vnorm(np.array(symAxis))
         vdotsym = min(1.0,max(-1.0,np.vdot(v,symaxis)))
         xformAng = np.arccos(vdotsym)
         xformVec = np.cross(symaxis,v)
@@ -1405,7 +1406,7 @@ def UpdateRBXYZ(Bmat,RBObj,RBData,RBType):
         Q = RBObj['Orient'][0]
     else:
         a,v = Q2AV(RBObj['Orient'][0])
-        symaxis = np.array(RBObj.get('symAxis'))
+        symaxis = vnorm(np.array(RBObj.get('symAxis')))
         vdotsym = min(1.0,max(-1.0,np.vdot(v,symaxis)))
         xformAng = np.arccos(vdotsym)
         xformVec = np.cross(symaxis,v)

GSASII/GSASIIphsGUI.py

@@ -9580,7 +9580,7 @@ def OnTLSRef(event):
                 thermSizer.Add(Tcheck,0,WACV)
             return thermSizer
 
-        def LocationSizer(RBObj,rbType):
+        def LocationSizer(RBObj,rbType,rbId):
 
             def OnOrigRef(event):
                 RBObj['Orig'][1] = Ocheck.GetValue()
@@ -9655,6 +9655,21 @@ def OnOrien(*args, **kwargs):
                 except ValueError:
                     pass
 
+            def OnSymRadioSet(event):
+                '''Set the polar axis for the sp. harm. as
+                RBdata['Spin'][RBId]['symAxis']. This may never be
+                set, so use RBdata['Spin'][RBId].get('symAxis') to
+                access this so the default value is [0,0,1].
+                '''
+                Obj = event.GetEventObject()
+                axis = ([1,0,0],[0,1,0],[0,0,1],[1,1,0],[1,1,1])[Obj.GetSelection()]
+                RBObj['symAxis'] = axis
+                A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
+                ApplyAV(A,V)
+                data['Drawing']['Atoms'] = []
+                UpdateDrawAtoms(G2frame,data)
+                G2plt.PlotStructure(G2frame,data)
+
             SGData = data['General']['SGData']
             rbSizer = wx.BoxSizer(wx.VERTICAL)
             topSizer = wx.FlexGridSizer(0,7,5,5)
@@ -9725,6 +9740,17 @@ def OnOrien(*args, **kwargs):
             sytsymtxt = wx.StaticText(RigidBodies,label='%s site symmetry: %s, multiplicity: %d '%(Name,Sytsym,Mult))
             rbSizer.Add(topSizer)
             rbSizer.Add(sytsymtxt)
+            choices = [' x ',' y ',' z ','x+y','x+y+z']
+            RBObj['symAxis'] = RBObj.get('symAxis',[0,0,1])   #set default as 'z'
+            try:
+                symax = dict(zip([str(x) for x in [[1,0,0],[0,1,0],[0,0,1],[1,1,0],[1,1,1]]],choices))[str(RBObj['symAxis'])]
+            except KeyError:
+                symax = ' z '
+            symRadioSet = wx.RadioBox(RigidBodies,choices=choices,label='RB polar axis is aligned along:')
+            symRadioSet.SetStringSelection(symax)
+            symRadioSet.Bind(wx.EVT_RADIOBOX, OnSymRadioSet)
+            Indx[symRadioSet.GetId()] = rbId
+            rbSizer.Add(symRadioSet)
             return rbSizer
 
         def SpnrbSizer(RBObj,spnIndx):
@@ -9747,17 +9773,6 @@ def OnDelSpnRB(event):
                 G2plt.PlotStructure(G2frame,data)
                 wx.CallAfter(FillRigidBodyGrid,True)
 
-            def OnSymRadioSet(event):
-                '''Set the polar axis for the sp. harm. as
-                RBdata['Spin'][RBId]['symAxis']. This may never be
-                set, so use RBdata['Spin'][RBId].get('symAxis') to
-                access this so the default value is [0,0,1].
-                '''
-                Obj = event.GetEventObject()
-                axis = ([1,0,0],[0,1,0],[0,0,1],[1,1,0],[1,1,1])[Obj.GetSelection()]
-                RBObj['symAxis'] = axis
-                G2plt.PlotStructure(G2frame,data)
-
             def OnAddShell(event):
                 rbNames = []
                 rbIds = {}
@@ -9965,15 +9980,7 @@ def OnSliceShell(event):
             Indx[hidesh.GetId()] = 0
             topLine.Add(hidesh,0,WACV)
             sprbSizer.Add(wx.StaticText(RigidBodies,label='Spinning RB orientation parameters for %s:'%RBObj['RBname'][0]))
-            sprbSizer.Add(LocationSizer(RBObj,'Spin'))
-            choices = [' x ',' y ',' z ','x+y','x+y+z']
-            RBObj['symAxis'] = RBObj.get('symAxis',[0,0,1])   #set default as 'z'
-            symax = dict(zip([str(x) for x in [[1,0,0],[0,1,0],[0,0,1],[1,1,0],[1,1,1]]],choices))[str(RBObj['symAxis'])]
-            symRadioSet = wx.RadioBox(RigidBodies,choices=choices,label='Sp harm polar axis is aligned along:')
-            symRadioSet.SetStringSelection(symax)
-            symRadioSet.Bind(wx.EVT_RADIOBOX, OnSymRadioSet)
-            Indx[symRadioSet.GetId()] = rbId
-            sprbSizer.Add(symRadioSet)
+            sprbSizer.Add(LocationSizer(RBObj,'Spin',rbId))
             plotLine = wx.BoxSizer(wx.HORIZONTAL)
             RBObj['useAtColor'] = RBObj.get('useAtColor',True)
             atColor = wx.CheckBox(RigidBodies,label='Use atom color?')
@@ -10073,7 +10080,7 @@ def OnDelResRB(event):
             topLine.Add(wx.StaticText(RigidBodies,-1,
                     '  (variables '+varname+')'),0,WACV)
             resrbSizer.Add(topLine)
-            resrbSizer.Add(LocationSizer(RBObj,'Residue'))
+            resrbSizer.Add(LocationSizer(RBObj,'Residue',rbId))
             if len(RBObj['Torsions']):
                 resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0)
             torSizer = wx.FlexGridSizer(0,8,5,5)
@@ -10162,7 +10169,7 @@ def OnDelVecRB(event):
             Indx[delRB.GetId()] = rbId
             topLine.Add(delRB,0,WACV)
             vecrbSizer.Add(topLine)
-            vecrbSizer.Add(LocationSizer(RBObj,'Vector'))
+            vecrbSizer.Add(LocationSizer(RBObj,'Vector',rbId))
             members = 'Rigid body members: '
             for Id in RBObj['Ids']:
                 members += data['Atoms'][AtLookUp[Id]][ct-1].strip()+', '

GSASII/imports/G2sfact_CIF.py

@@ -98,7 +98,7 @@ def Reader(self, filename, ParentFrame=None, **kwarg):
         # scan blocks for reflections
         self.errors = 'Error during scan of blocks for datasets'
         blklist = []
-        EmbeddedShelx = []
+        EmbeddedShelx = []      #as made by Olex2
         for blk in cf.keys(): # scan for reflections, F or F2 values and cell lengths.
             # Ignore blocks that do not have structure factors and a cell
             blkkeys = [k.lower() for k in cf[blk].keys()]
@@ -110,7 +110,7 @@ def Reader(self, filename, ParentFrame=None, **kwarg):
                 if hklitems[i][0] in blkkeys and hklitems[i][1] in blkkeys and hklitems[i][2] in blkkeys:
                     dnIndex = i
                     break
-            if '_shelx_hkl_file' in blkkeys:
+            if '_shelx_hkl_file' in blkkeys:    #found Olex2 reflection block from Shelx; should be h,k,l,Fo^2,sig(Fo^2)
                 blklist.append(blk)
                 EmbeddedShelx.append(blk)
                 break
@@ -190,17 +190,20 @@ def Reader(self, filename, ParentFrame=None, **kwarg):
                     self.errors = '  Error reading line '+str(line+1)
                     if not len(S.strip()): continue
                     items = S.split()
-                    h,k,l,Fo,sigFo = items[:5]
+                    h,k,l,Fo,sigFo = items[:5]      #will only be h,k,l,fo^2,sig(Fo^2)
                     h,k,l = [int(h),int(k),int(l)]
-                    if not any([h,k,l]):
+                    if not any([h,k,l]):    #end of file found
                         break
                     Fo = float(Fo)
                     sigFo = float(sigFo)
-                    self.RefDict['RefList'].append([h,k,l,1,0,Fo**2,2.*Fo*sigFo,0,Fo**2,0,0,1])
+                    self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,1])
                 self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
                 self.RefDict['Type'] = 'SXC'
                 self.RefDict['Super'] = 0
-                self.UpdateParameters(Type='SXC',Wave=None) # histogram type
+                wave = 0.70926
+                if blk.get('_diffrn_radiation_wavelength'):
+                    wave = float(blk['_diffrn_radiation_wavelength'])
+                self.UpdateParameters(Type='SXC',Wave=wave) # histogram type
                 return True
             except:
                 return False                
@@ -348,11 +351,10 @@ def Reader(self, filename, ParentFrame=None, **kwarg):
                 Type = 'SNC'
         self.RefDict['Type'] = Type
         self.RefDict['Super'] = im
+        wave = 0.70926
         if blk.get('_diffrn_radiation_wavelength'):
             wave = float(blk['_diffrn_radiation_wavelength'])
         elif blk.get('_diffrn_radiation.wavelength'):
             wave = float(blk['_diffrn_radiation.wavelength'])
-        else:
-            wave = 0.70926
         self.UpdateParameters(Type=Type,Wave=wave) # histogram type
         return True