single crystal importers default Extc = 1 (not 0)

checks on negative Fo (not Sig) for HKLF in various places

Author: vondreele

GSASII/GSASIIdataGUI.py

@@ -8280,7 +8280,7 @@ def OnErrorAnalysis(event):
         Should be straight line of slope 1 - never is'''
         def OnPlotFoFcVsFc():
             ''' Extinction check, plots Fo-Fc & 1/ExtC vs Fo for single crystal data '''
-            test = lambda xy:(xy[iFlg+Super]>0 and (xy[iFc+Super]>0 or xy[iFo+Super]>0))
+            test = lambda xy:(xy[iFlg+Super]>0 and xy[iFo+Super]>0)
             iFlg,iFo,iSig,iFc,iFcT,iExt = 3,5,6,7,9,11
             refList = data[1]['RefList']
             wtFctr = data[0]['wtFactor']
@@ -8290,6 +8290,7 @@ def OnPlotFoFcVsFc():
             Sig = np.array([xy[iSig+Super] for xy in refList if test(xy)])/wtFctr      #sig(fo^2)/wtFactor (1/GOF)
             XE = [[xy[iFcT+Super],xy[iExt+Super]] for xy in refList if test(xy)]
             XE = np.array([[np.sqrt(xe[0]),xe[1]] for xe in XE]).T
+            XE[1] = np.where(XE[1]>0.,XE[1],1.0)
             G2plt.PlotXY(G2frame,[[FcT,2.*Fo*(Fo-Fc)/Sig],],XY2=[XE,],labelX='Fc',labelY=GkDelta+'F/sig, ExtC',newPlot=False,
                Title='Extinction check',lines=False,points2=True,names=[GkDelta+'F/sig',],names2=['ExtC',])
 

GSASII/GSASIIddataGUI.py

@@ -955,7 +955,7 @@ def OnFixVals(event):
         useData.Bind(wx.EVT_CHECKBOX, OnUseData)
         useData.SetValue(UseList[G2frame.hist]['Use'])
         useBox.Add(useData,0,WACV)
-        Htype = UseList[G2frame.hist]['Type']
+        Htype = UseList[G2frame.hist].get('Type','SXC')
         useBox.Add(wx.StaticText(DData,label=' Histogram type: '+Htype))
         if not generalData['doPawley'] and 'PWDR' in G2frame.hist[:4]:
             lbLabel = 'Start Le Bail extraction?   '

GSASII/GSASIIobj.py

@@ -652,8 +652,9 @@ def CompileVarDesc():
         'Ep$' : 'Primary extinction',
         'Es$' : 'Secondary type II extinction',
         'Eg$' : 'Secondary type I extinction',
-        'Ma$' : 'Low F dynamic scattering scale',
-        'Mb$' : 'Low F dynamic scattering exponent',
+        'Ma$' : 'microED dynamic scattering coeff A',
+        'Mb$' : 'microED dynamic scattering coeff B',
+        'Mc$' : 'microED dynamic scattering coeff C',
         'Flack' : 'Flack parameter',
         'TwinFr' : 'Twin fraction',
         'Layer Disp'  : 'Layer displacement along beam',

GSASII/GSASIIplot.py

@@ -1892,7 +1892,7 @@ def PlotDeltSig(G2frame,kind,PatternName=None):
         sumWdelt = 0.0
         Nobs = 0
         for ref in refl:
-            if ref[6+im] > 0.:
+            if ref[5+im] > 0.:
                 if ref[3+im] > 0:
                     Nobs += 1
                     w2 = 1./ref[6+im]

GSASII/GSASIIstrMath.py

@@ -2723,11 +2723,10 @@ def SStructureFactorDervTw(refDict,im,G,hfx,pfx,SGData,SSGData,calcControls,parm
     return dFdvDict
 
 def SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varyList):
-    ''' Single crystal extinction function; returns extinction & derivative
+    ''' Single crystal extinction function; returns extinction & derivatives
     '''
     extCor = 1.0
     dervDict = {}
-    dervCor = 1.0
     if 'microED' in calcControls[phfx+'EType']:
         FPone = np.sqrt(ref[9+im])
         PA = np.exp(-parmDict[phfx+'Ma']*FPone)
@@ -2737,7 +2736,7 @@ def SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varyList):
         dervDict[phfx+'Ma'] = -PA*FPone/3.
         dervDict[phfx+'Mb'] = -PB*FPone**2/3.
         dervDict[phfx+'Mc'] = -PC*FPone**3/3.
-        return extCor,dervDict,dervCor
+        return extCor,dervDict
 
     if calcControls[phfx+'EType'] != 'None':
         SQ = 1/(4.*ref[4+im]**2)
@@ -2798,7 +2797,6 @@ def SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varyList):
             extCor = np.sqrt(PF4)
             PF3 = 0.5*(CL+2.*AL*PF/(1.+BL*PF)-AL*PF**2*BL/(1.+BL*PF)**2)/(PF4*extCor)
 
-        dervCor = (1.+PF)*PF3/DScorr   #extinction corr for other derivatives
         if 'Primary' in calcControls[phfx+'EType']:
             if phfx+'Ep' in varyList:
                 dervDict[phfx+'Ep'] = -ref[7+im]*PLZ*PF3/DScorr
@@ -2808,7 +2806,7 @@ def SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varyList):
         if 'I' in calcControls[phfx+'EType'] and phfx+'Eg' in varyList:
             dervDict[phfx+'Eg'] = -ref[7+im]*PLZ*PF3*(PSIG/parmDict[phfx+'Eg'])**3*PL**2
 
-    return 1./extCor,dervDict,dervCor
+    return 1./extCor,dervDict
 
 def Dict2Values(parmdict, varylist):
     '''Use before call to leastsq to setup list of values for the parameters
@@ -4593,7 +4591,7 @@ def dervHKLF(Histogram,Phase,calcControls,varylist,parmDict,rigidbodyDict):
     if calcControls['F**2']:
         for iref,ref in enumerate(refDict['RefList']):
             if ref[6+im] > 0:
-                dervDict,dervCor = SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varylist+dependentVars)[1:]
+                dervDict = SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varylist+dependentVars)[1]
                 w = 1.0/ref[6+im]
                 if ref[3+im] > 0:
                     wdf[iref] = w*(ref[5+im]-ref[7+im])
@@ -4607,7 +4605,7 @@ def dervHKLF(Histogram,Phase,calcControls,varylist,parmDict,rigidbodyDict):
                         dMdvh[varylist.index(phfx+'Scale')][iref] = w*ref[7+im]*ref[11+im]/parmDict[phfx+'Scale']  #OK
                     elif phfx+'Scale' in dependentVars:
                         depDerivDict[phfx+'Scale'][iref] = w*ref[7+im]*ref[11+im]/parmDict[phfx+'Scale']   #OK
-                    for item in ['Ep','Es','Eg','Ma','Mb']:
+                    for item in ['Ep','Es','Eg','Ma','Mb','Mc']:
                         if phfx+item in varylist and phfx+item in dervDict:
                             dMdvh[varylist.index(phfx+item)][iref] = w*dervDict[phfx+item]/ref[11+im]  #OK
                         elif phfx+item in dependentVars and phfx+item in dervDict:
@@ -4620,7 +4618,7 @@ def dervHKLF(Histogram,Phase,calcControls,varylist,parmDict,rigidbodyDict):
     else:   #F refinement
         for iref,ref in enumerate(refDict['RefList']):
             if ref[5+im] > 0.:
-                dervDict,dervCor = SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varylist+dependentVars)[1:]
+                dervDict = SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varylist+dependentVars)[1]
                 Fo = np.sqrt(ref[5+im])
                 Fc = np.sqrt(ref[7+im])
                 w = 1.0/ref[6+im]
@@ -4636,7 +4634,7 @@ def dervHKLF(Histogram,Phase,calcControls,varylist,parmDict,rigidbodyDict):
                         dMdvh[varylist.index(phfx+'Scale')][iref] = w*ref[7+im]*ref[11+im]/parmDict[phfx+'Scale']  #OK
                     elif phfx+'Scale' in dependentVars:
                         depDerivDict[phfx+'Scale'][iref] = w*ref[7+im]*ref[11+im]/parmDict[phfx+'Scale']   #OK
-                    for item in ['Ep','Es','Eg','Ma','Mb']:   #OK!
+                    for item in ['Ep','Es','Eg','Ma','Mb','Mc']:   #OK!
                         if phfx+item in varylist and phfx+item in dervDict:
                             dMdvh[varylist.index(phfx+item)][iref] = w*dervDict[phfx+item]/ref[11+im]
                         elif phfx+item in dependentVars and phfx+item in dervDict:
@@ -4969,7 +4967,7 @@ def errRefine(values,HistoPhases,parmDict,histDict1,varylist,calcControls,pawley
             maxH = 0
             if calcControls['F**2']:
                 for i,ref in enumerate(refDict['RefList']):
-                    if ref[6+im] > 0:
+                    if ref[5+im] > 0:
                         ref[11+im] = SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varylist)[0]
                         w = wtFactor/ref[6+im]   # 1/sig(F^2)
                         ref[7+im] *= parmDict[phfx+'Scale']*ref[11+im]  #correct Fc^2 for extinction
@@ -4996,6 +4994,7 @@ def errRefine(values,HistoPhases,parmDict,histDict1,varylist,calcControls,pawley
                                 SSnobs[ind] += 1
                                 maxH = max(maxH,ind)
                         else:
+                            ref[11+im] = 1.0
                             if ref[3+im]:
                                 ref[3+im] = -abs(ref[3+im])      #mark as rejected
                                 nrej += 1
@@ -5009,7 +5008,7 @@ def errRefine(values,HistoPhases,parmDict,histDict1,varylist,calcControls,pawley
                         ref[8+im] = ref[5+im]/(parmDict[phfx+'Scale']*ref[11+im])
                         Fo = np.sqrt(ref[5+im])
                         Fc = np.sqrt(ref[7+im])
-                        w = 2.0*wtFactor*Fo/ref[6+im]    # 1/sig(F)?
+                        w = 2.0*wtFactor*Fo/ref[6+im]
                         if UserRejectHKL(ref,im,calcControls['UsrReject']) and ref[3+im]:    #skip sp.gp. absences (mul=0)
                             ref[3+im] = abs(ref[3+im])      #mark as allowed
                             sumFo += Fo
@@ -5031,6 +5030,7 @@ def errRefine(values,HistoPhases,parmDict,histDict1,varylist,calcControls,pawley
                                 SSnobs[ind] += 1
                                 maxH = max(maxH,ind)
                         else:
+                            ref[11+im] = 1.0
                             if ref[3+im]:
                                 ref[3+im] = -abs(ref[3+im])      #mark as rejected
                                 nrej += 1

GSASII/imports/G2sfact.py

@@ -62,7 +62,7 @@ def Reader(self,filename, ParentFrame=None, **unused):
                 Fo = float(Fo)
                 sigFo = float(sigFo)
                 # h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
-                self.RefDict['RefList'].append([h,k,l,1,0,Fo**2,2.*Fo*sigFo,0,Fo**2,0,0,0])
+                self.RefDict['RefList'].append([h,k,l,1,0,Fo**2,2.*Fo*sigFo,0,Fo**2,0,0,1])
             fp.close()
             self.errors = 'Error after reading reflections (unexpected!)'
             self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
@@ -106,7 +106,7 @@ def Reader(self,filename, ParentFrame=None, **unused):
                 if Fo < 1.0:
                     sigFo2 = 1.0
                # h,k,l,m,tw,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
-                self.RefDict['RefList'].append([h,k,l,m,1,0,Fo**2,sigFo2,0,Fo**2,0,0,0])
+                self.RefDict['RefList'].append([h,k,l,m,1,0,Fo**2,sigFo2,0,Fo**2,0,0,1])
             fp.close()
             self.errors = 'Error after reading reflections (unexpected!)'
             self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
@@ -158,7 +158,7 @@ def Reader(self,filename, ParentFrame=None, **unused):
                 Fo = float(Fo)
                 sigFo = float(sigFo)
                 # h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
-                self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0])
+                self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,1])
                 #self.RefDict['FF'].append({}) # now done in OnImportSfact
             fp.close()
             self.errors = 'Error after reading reflections (unexpected!)'
@@ -252,9 +252,9 @@ def Reader(self,filename, ParentFrame=None, **unused):
                     sigFo = float(sigFo)
                     # h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
                     if self.Super == 0:
-                        self.RefDict['RefList'].append([h,k,l,int(Tw),0,Fo,sigFo,0,Fo,0,0,0])
+                        self.RefDict['RefList'].append([h,k,l,int(Tw),0,Fo,sigFo,0,Fo,0,0,1])
                     elif self.Super == 1:
-                        self.RefDict['RefList'].append([h,k,l,m1,int(Tw),0,Fo,sigFo,0,Fo,0,0,0])
+                        self.RefDict['RefList'].append([h,k,l,m1,int(Tw),0,Fo,sigFo,0,Fo,0,0,1])
                 TwMax[0] = max(TwMax[0],TwId)
             fp.close()
             self.errors = 'Error after reading reflections (unexpected!)'
@@ -430,9 +430,9 @@ def Reader(self,filename,filepointer, ParentFrame=None, **unused):
                 sigFo = float(sigFo)
                 # h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
                 if self.Super == 0:
-                    self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0])
+                    self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,1])
                 elif self.Super == 1:
-                    self.RefDict['RefList'].append([h,k,l,m1,1,0,Fo,sigFo,0,Fo,0,0,0])
+                    self.RefDict['RefList'].append([h,k,l,m1,1,0,Fo,sigFo,0,Fo,0,0,1])
             fp.close()
             self.errors = 'Error after reading reflections (unexpected!)'
             self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
@@ -510,10 +510,10 @@ def Reader(self,filename, ParentFrame=None, **unused):
                 wave = float(wave)
                 tbar = float(tbar)
                 if len(self.Banks):
-                    self.Banks[int(bN)-1]['RefDict']['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0,wave,tbar])
+                    self.Banks[int(bN)-1]['RefDict']['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,1,wave,tbar])
                 else:
                 # h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
-                    self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0,wave,tbar])
+                    self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,1,wave,tbar])
             fp.close()
             if len(self.Banks):
                 self.UpdateParameters(Type='SNT',Wave=None) # histogram type
@@ -583,7 +583,7 @@ def Reader(self,filename,filepointer, ParentFrame=None, **unused):
                 wave = float(wave)
                 tbar = float(tbar)
                 if len(self.Banks):
-                    self.Banks[int(bN)-1]['RefDict']['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0,wave,tbar])
+                    self.Banks[int(bN)-1]['RefDict']['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,1,wave,tbar])
                 else:
                 # h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
                     self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0,wave,tbar])
@@ -646,7 +646,7 @@ def Reader(self,filename,filepointer, ParentFrame=None, **unused):
                 Fo = float(Fo)
                 sigFo = float(sigFo)
                 # h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
-                self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0])
+                self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,1])
             fp.close()
             self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
             self.RefDict['Type'] = 'SNC'

GSASII/imports/G2sfact_CIF.py

@@ -258,9 +258,9 @@ def Reader(self, filename, ParentFrame=None, **kwarg):
                         HKL.append('.')
                 #h,k,l,tw,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,Ext
                 if im:
-                    ref = HKL+[1,0,0,0,1, 0,0,0,0,0, 0,0]
+                    ref = HKL+[1,0,0,0,1, 0,0,0,0,0, 0,0,1]
                 else:
-                    ref = HKL+[1,0,0,1,0, 0,0,0,0,0, 0]
+                    ref = HKL+[1,0,0,1,0, 0,0,0,0,0, 0,1]
                 if F2dn:
                     F2 = item[itemkeys[F2dn]]
                     if '(' in F2: