Changeset 1956

Timestamp:

Aug 12, 2015 1:30:41 PM (7 years ago)

Author:

vondreele

Message:

fix (again) fill unit cell, dynamic SS drawing & GenAtom? issues - now all OK
fixes to get SS structure factors to compute & twins in SS data issues

Location:

trunk

Files:

• GSASII.py (modified) (2 diffs)
• GSASIImath.py (modified) (1 diff)
• GSASIIspc.py (modified) (3 diffs)
• GSASIIstrIO.py (modified) (2 diffs)
• imports/G2sfact_CIF.py (modified) (1 diff)

trunk/GSASII.py

@@ -697 +697 @@
                             H = hkl
                         ref[4+Super] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
-                        iabsnt,ref[3+Super],Uniq,phi = G2spc.GenHKLf(H,SGData)
+                        iabsnt = G2spc.GenHKLf(H,SGData)[0]
                         if iabsnt:  #flag space gp. absences
-                            ref[3+Super] = 0
+                            if Super: 
+                                if not ref[2+Super]:
+                                    ref[3+Super] = 0
+                                else:
+                                    ref[3+Super] = 1    #twin id?
+                            else:
+                                ref[3] = 0
                     UseList[histoName] = SetDefaultDData(reflData['Type'],histoName)
                 elif histoName in PWDRlist:
@@ -852 +858 @@
                     iabsnt,mul,Uniq,phi = G2spc.GenHKLf(H,SGData)
                     if iabsnt:  #flag space gp. absences
-                        ref[3+Super] = 0
+                        if Super: 
+                            if not ref[2+Super]:
+                                ref[3+Super] = 0
+                            else:
+                                ref[3+Super] = 1    #twin id?
+                        else:
+                            ref[3] = 0
         wx.EndBusyCursor()
         

trunk/GSASIImath.py

@@ -994 +994 @@
     drawAtoms = drawingData['Atoms']
     for atom in atoms:    
-        atxyz = np.array(atom[cx:cx+3])
+        atxyz = G2spc.MoveToUnitCell(np.array(atom[cx:cx+3]))[0]
         atuij = np.array(atom[cia+2:cia+8])
         waveType = atom[-1]['SS1']['waveType']

trunk/GSASIIspc.py

@@ -1110 +1110 @@
     Cell = []
     X = np.array(XYZ)
+    if Move:
+        X = MoveToUnitCell(X)[0]
     for ic,cen in enumerate(SGData['SGCen']):
         C = np.array(cen)
@@ -1123 +1125 @@
                     XT = -XT
                 XT += C
-                cell = np.zeros(3)
-                cellj = np.zeros(3)
+                cell = np.zeros(3,dtype=np.int32)
+                cellj = np.zeros(3,dtype=np.int32)
                 if Move:
                     newX,cellj = MoveToUnitCell(XT)
@@ -1779 +1781 @@
             Sdtau.append(np.sum(mst*(XYZ-SGOps[iop][1])-epsinv*SSGOps[iop][1][3]))
     SdIndx = np.argsort(np.array(Sdtau))     # just to do in sensible order
-    OpText =  [MT2text(s).replace(' ','') for s in Sop]         #debug?
-    SSOpText = [SSMT2text(ss).replace(' ','') for ss in SSop]   #debug?
-    if debug: print 'special pos super operators: ',SSOpText
+    if debug: print 'special pos super operators: ',[SSMT2text(ss).replace(' ','') for ss in SSop]
     #setup displacement arrays
     tau = np.linspace(-1,1,49,True)

trunk/GSASIIstrIO.py

@@ -1157 +1157 @@
                     AtomSS = at[-1]['SS1']
                     waveType = AtomSS['waveType']
-                    phaseDict[pfx+'waveType:'+str(i)] = waveType    
+                    phaseDict[pfx+'waveType:'+str(i)] = waveType
                     for Stype in ['Sfrac','Spos','Sadp','Smag']:
                         Waves = AtomSS[Stype]
                         for iw,wave in enumerate(Waves):
                             if not iw:
-                                CSI = G2spc.GetSSfxuinel(waveType,iw,at[cx:cx+3],SGData,SSGData)
+                                CSI = G2spc.GetSSfxuinel(waveType,iw+1,at[cx:cx+3],SGData,SSGData)
                             else:
-                                CSI = G2spc.GetSSfxuinel('Fourier',iw,at[cx:cx+3],SGData,SSGData)
+                                CSI = G2spc.GetSSfxuinel('Fourier',iw+1,at[cx:cx+3],SGData,SSGData)
                             uId,uCoef = CSI[Stype]
                             stiw = str(i)+':'+str(iw)
@@ -2188 +2188 @@
                         HKLd = G2mth.sortArray(HKLd,4,reverse=True)
                         for h,k,l,m,d in HKLd:
-                            ext,mul,uniq,phi = G2spc.GenHKLf([h,k,l],SGData)    #is this right for SS refl.??
+                            ext,mul,uniq,phi = G2spc.GenHKLf([h,k,l],SGData)
                             mul *= 2      # for powder overlap of Friedel pairs
                             if m or not ext:

trunk/imports/G2sfact_CIF.py

@@ -266 +266 @@
                     #h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,Ext
                     if im:
-                        ref = HKL+[1,0,0,0,0, 0,0,0,0,0, 0,0] 
+                        ref = HKL+[1,0,0,0,1, 0,0,0,0,0, 0,0] 
                     else:
-                        ref = HKL+[1,0,0,0,0, 0,0,0,0,0, 0] 
+                        ref = HKL+[1,0,0,1,0, 0,0,0,0,0, 0] 
                     if F2dn:
                         F2 = item[itemkeys[F2dn]]