Fixes to atom deformation stuff.

Author: vondreele

GSASII/GSASIIphsGUI.py

@@ -9094,7 +9094,7 @@ def SelDeformAtom(event):
                             #     orbDict.update(cofTerms)
                             #     orbDict.update({'Ne':[float(orbs[orb]['Ne']),False]})
                             #     data['Deformations'][Ids[indx]].append([orb,orbDict])
-                data['Deformations'][-Ids[indx]] = {'U':'X','V':'Y','UVmat':np.eye(3),
+                data['Deformations'][-Ids[indx]] = {'U':'X','V':'Y','UVmat':np.eye(3),'PtGrp':'1',
                     'MUV':"A: X'=U, Y'=(UxV)xU & Z'=UxV",'Radial':radial,'fxchoice':fxchoice}
         dlg.Destroy()
         if not len(indxes):

GSASII/GSASIIplot.py

@@ -3523,8 +3523,8 @@ def PlotDeform(G2frame,general,atName,atType,deform,UVmat,radial,neigh):
     RAP = G2mth.Cart2Polar(XYZ[0],XYZ[1],XYZ[2])
     P  = np.zeros((31,31))
     for shc in SHC:
-        p = 2.*SHC[shc][0]*SHC[shc][2]**3*G2lat.KslCalc(shc,RAP[1],RAP[2]).reshape((31,31))
-        P += p**2
+        p = 2.*SHC[shc][0]*SHC[shc][2]**3*(G2lat.KslCalc(shc,RAP[1],RAP[2])**2).reshape((31,31))
+        P += p
     if not np.any(P):
         P = np.ones((31,31))
 #    P *= P
@@ -7353,20 +7353,21 @@ def Draw(caller='',Fade=[],NPkey=False):
                         defCtrls = deformationData[-atom[ci]]
                         defParms = deformationData[atom[ci]]
                         SytSym = G2spc.SytSym(atom[cx:cx+3],SGData)[0]
+                        SGM = np.array(G2spc.GetOpFromCode(atom[cs-1],SGData)[0])
                         if defCtrls.get('showDef',False) and defCtrls['Radial'] == 'Slater':
                             useAtColor = defCtrls.get('atColor',True) 
                             atcolor = None
                             if useAtColor:
                                 atcolor = atColor*255
                             SHC = defParms[0][1]
                             SHC = {item.replace('D','C'):SHC[item] for item in SHC if item not in ['Ne','kappa']}
-                            UVMat = defCtrls['UVmat']
+                            UVMat = np.inner(SGM.T,defCtrls['UVmat'])
                             Npsi,Ngam = 90,45 
                             PSI,GAM = np.mgrid[0:Npsi,0:Ngam]   #[azm,pol]
                             PSI = PSI.flatten()*360./Npsi  #azimuth 0-360 ncl
                             GAM = GAM.flatten()*180./Ngam  #polar 0-180 incl
-                            Rp,PSIp,GAMp = G2mth.RotPolbyM(np.ones_like(PSI),PSI,GAM,UVMat)
-                            P = G2lat.SHarmcal(SytSym,SHC,PSIp,GAMp).reshape((Npsi,Ngam))
+                            Rp,PSIp,GAMp = G2mth.RotPolbyM(np.ones_like(PSI),PSI,GAM,UVMat) #TODO: needs symmetry operation for equiv. positions
+                            P = G2lat.SHarmcal(SytSym,SHC,PSIp,GAMp).reshape((Npsi,Ngam))**2
                             if np.min(P) < np.max(P):
                                 P = (P-np.min(P))/(np.max(P)-np.min(P))
                             RenderTextureSphere(x,y,z,radius,atcolor,shape=[Npsi,Ngam],Texture=P.T,ifFade=False)

GSASII/GSASIIspc.py

@@ -1459,6 +1459,26 @@ def GetOpNum(Opr,SGData):
     opNum += cent*Nops
     return opNum
 
+def GetOpFromCode(Code,SGData):
+    "takes Sym Op code from Draw Atoms table & returns space group operation details"
+    SGOps = SGData['SGOps']
+    SGCent = SGData['SGCen']
+    if '+' not in Code:
+        SymOp = Code
+        Unit = '(0,0,0)'
+    else:
+        SymOp,Unit = Code.split('+')
+    SymOp = int(SymOp)
+    opNum = abs(SymOp)%100-1
+    cent = abs(opNum)//100
+    Unit = list(eval(Unit))
+    Cent = SGCent[cent]
+    SGM,SGT = SGOps[opNum]
+    if SymOp < 0:
+        SGM *= -1
+        SGT *= -1
+    return SGM,SGT,Cent,Unit   
+
 ################################################################################
 #### Superspace group codes
 ################################################################################

GSASII/GSASIIstrMath.py

@@ -437,7 +437,7 @@ def MakeSpHarmFF(HKL,Amat,Bmat,SHCdict,Tdata,hType,FFtables,ORBtables,BLtables,F
     :param str hType: histogram type
     :param dict FFtables: x-ray form factor tables
     :param dict ORBtables: x-ray orbital form factor tables
-    :param dict BLtables: neutron scattering lenghts
+    :param dict BLtables: neutron scattering lengths
     :param array FF: form factors - will be modified by adding the spin/deformation RB spherical harmonics terms
     :param array SQ: 1/4d^2 for the HKL set
     :param bool ifDeriv: True if dFF/dcoff to be returned
@@ -580,7 +580,7 @@ def MakePolar(Orient,QB):
                     for term in orbs[orb]:
                         if 'D(' in term:
                             item = term.replace('D','C')
-                            SH = G2lat.KslCalc(item,Th,Ph)
+                            SH = G2lat.KslCalc(item,Th,Ph)**2
                             FFval += SH*orbs[orb][term]*ff
                             name = 'A%s%s:%d'%(term,orb,iAt)
                             dFFdS[name] = SH*ff
@@ -597,7 +597,7 @@ def MakePolar(Orient,QB):
                     for term in orbs[orb]:
                         if 'D(' in term:    #skip 'Ne'
                             item = term.replace('D','C')
-                            SH = G2lat.KslCalc(item,Th,Ph)
+                            SH = G2lat.KslCalc(item,Th,Ph)**2
                             FFval += SH*orbs[orb][term]*ff
                             name = 'A%s%s:%d'%(term,orb,iAt)
                             dFFdS[name] = SH*ff

GSASII/exports/G2export_PDB.py

@@ -277,7 +277,7 @@ def Exporter(self,event=None):
             A,B = G2lat.cell2AB(Cell)
             self.Write('# GSAS-II generated ORCA input file\n# Basic Mode')
             self.Write('#%Sym SymThresh 0.01 End')
-            self.Write('# after xyz is charge & multiplicity; change as needed')
+            self.Write('# after xyz is charge & multiplicity; change as needed for ions')
             self.Write('* xyz 0 1')
             fmt = '{:4s}'+3*'{:12.4f}'
             for atom in Atoms: