Changeset 2727

Timestamp:

Feb 27, 2017 3:06:07 PM (6 years ago)

Author:

vondreele

Message:

fix issue with formula volume in PDF creation
block Lebail selection if DoPawley? is selected
force Flat Bkg >= 0
avoid crash if Refine done with no atoms

Location:

trunk

Files:

• GSASII.py (modified) (5 diffs)
• GSASIIddataGUI.py (modified) (1 diff)
• GSASIIimgGUI.py (modified) (2 diffs)
• GSASIIobj.py (modified) (3 diffs)
• GSASIIpwdGUI.py (modified) (2 diffs)
• GSASIIstrIO.py (modified) (1 diff)
• GSASIIstrMath.py (modified) (3 diffs)

trunk/GSASII.py

@@ -3574 +3574 @@
                     Qlimits.append([0.9*qMax,qMax])
                     ElList = {}
+                    sumnum = 1.
                     for item in Comments:           #grab chemical formula from Comments
                         if 'formula' in item[:15].lower():
@@ -3581 +3582 @@
                                 nums = formula[1::2]
                                 Formula = zip(elems,nums)
+                                sumnum = 0.
                                 for [elem,num] in Formula:
                                     ElData = G2elem.GetElInfo(elem,Parms)
                                     ElData['FormulaNo'] = float(num)
+                                    sumnum += float(num)
                                     ElList[elem] = ElData
+                                
                             except ValueError:
                                 ElData = G2elem.GetElInfo(formula[0],Parms)
@@ -3599 +3603 @@
                     for i in dlg.GetSelections():
                         PDFnames = G2gd.GetPatternTreeDataNames(self,['PDF ',])
-                        G2obj.CreatePDFitems(self,TextList[i],ElLists[i],Qlimits[i],pwdrMin,PDFnames)
+                        G2obj.CreatePDFitems(self,TextList[i],ElLists[i],Qlimits[i],sumnum,pwdrMin,PDFnames)
                 for item in self.ExportPDF: item.Enable(True)
             finally:
@@ -3867 +3871 @@
         Called from the Calculate/Refine menu.
         '''
+        self.dataFrame.userReSize = False               #avoids bad resizing based on MessageDialog
         Id = G2gd.GetPatternTreeItemId(self,self.root,'Sequential results')
         if Id:
@@ -3928 +3933 @@
         else:
             self.ErrorDialog('Refinement error',Msg)
-        self.dataFrame.userReSize = False
         
     def SaveTreeSetting(self):

trunk/GSASIIddataGUI.py

@@ -867 +867 @@
         useData.SetValue(UseList[G2frame.hist]['Use'])
         useBox.Add(useData,0,WACV)
-        lebail = wx.CheckBox(DData,wx.ID_ANY,label='Do LeBail extraction?')
-        lebail.Bind(wx.EVT_CHECKBOX, OnLeBail)
-        lebail.SetValue(UseList[G2frame.hist]['LeBail'])
-        useBox.Add(lebail,0,WACV)
+        if not generalData['doPawley']:
+            lebail = wx.CheckBox(DData,wx.ID_ANY,label='Do LeBail extraction?')
+            lebail.Bind(wx.EVT_CHECKBOX, OnLeBail)
+            lebail.SetValue(UseList[G2frame.hist]['LeBail'])
+            useBox.Add(lebail,0,WACV)
         bottomSizer.Add(useBox,0,WACV|wx.TOP|wx.BOTTOM|wx.LEFT,5)
         

trunk/GSASIIimgGUI.py

@@ -2922 +2922 @@
                     G2frame,imgId, 'Comments'))
                 ElList = {}
+                sumnum = 1.0
                 for item in Comments:           #grab chemical formula from Comments, if there
                     if 'formula' in item[:15].lower():
@@ -2928 +2929 @@
                         nums = formula[1::2]
                         formula = zip(elems,nums)
+                        sumnum = 0.
                         for [elem,num] in formula:
                             ElData = G2elem.GetElInfo(elem,Parms)
                             ElData['FormulaNo'] = float(num)
+                            sumnum += float(num)
                             ElList[elem] = ElData
                 PDFnames = G2gd.GetPatternTreeDataNames(G2frame,['PDF ',])
-                PDFid = G2obj.CreatePDFitems(G2frame,pwdr,ElList.copy(),Qlimits,pwdrMin,PDFnames)
+                PDFid = G2obj.CreatePDFitems(G2frame,pwdr,ElList.copy(),Qlimits,sumnum,pwdrMin,PDFnames)
                 if not PDFid: continue
                 PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(

trunk/GSASIIobj.py

@@ -2092 +2092 @@
         return repr(self.msg)
 
-def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,FltBkg=0,PDFnames=[]):
+def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
     '''Create and initialize a new set of PDF tree entries
 
@@ -2099 +2099 @@
     :param dict ElList: data structure with composition
     :param list Qlimits: Q limits to be used for computing the PDF
+    :param float numAtm: no. atom in chemical formula
+    :param float FltBkg: flat background value
+    :param list PDFnames: previously used PDF names
+    
     :returns: the Id of the newly created PDF entry
     '''
@@ -2112 +2116 @@
         'Container':{'Name':'','Mult':-1.0,'Refine':False},
         'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
-        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0,'Flat Bkg':FltBkg,
+        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
         'DetType':'Area detector','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':Qlimits,
         'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,

trunk/GSASIIpwdGUI.py

@@ -4802 +4802 @@
                     Cmin += CBmin*data['Container Bkg.']['Mult']
                 Smin += Cmul*Cmin
-            data['Flat Bkg'] = Smin
+            data['Flat Bkg'] = max(0,Smin)
                             
         PDFfileSizer = wx.BoxSizer(wx.VERTICAL)
@@ -4984 +4984 @@
             sqBox.Add(obliqCoeff,0)
         sqBox.Add(wx.StaticText(G2frame.dataDisplay,label=' Flat Bkg.: '),0,WACV)
-        flatBkg = G2G.ValidatedTxtCtrl(G2frame.dataDisplay,data,'Flat Bkg',nDig=(10,0),
+        flatBkg = G2G.ValidatedTxtCtrl(G2frame.dataDisplay,data,'Flat Bkg',nDig=(10,0),min=0,
                 typeHint=float,OnLeave=AfterChangeNoRefresh)
         sqBox.Add(flatBkg,0)

trunk/GSASIIstrIO.py

@@ -187 +187 @@
     Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = \
         GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
-    hapVary,hapDict,controlDict = GetHistogramPhaseData(Phases,Histograms,Print=False)
+    hapVary,hapDict,controlDict = GetHistogramPhaseData(Phases,Histograms,Print=False,resetRefList=False)
     histVary,histDict,controlDict = GetHistogramData(Histograms,Print=False)
     varyList = rbVary+phaseVary+hapVary+histVary

trunk/GSASIIstrMath.py

@@ -3079 +3079 @@
         GA,GB = G2lat.Gmat2AB(G)    #Orthogonalization matricies
         Vst = np.sqrt(nl.det(G))    #V*
-        if not Phase['General'].get('doPawley') and not parmDict[phfx+'LeBail']:
+        if not Phase['General'].get('doPawley') and not parmDict[phfx+'LeBail'] and len(refDict['FF']):
             if im:
                 SStructureFactor(refDict,G,hfx,pfx,SGData,SSGData,calcControls,parmDict)
@@ -3254 +3254 @@
         G,g = G2lat.A2Gmat(A)       #recip & real metric tensors
         GA,GB = G2lat.Gmat2AB(G)    #Orthogonalization matricies
-        if not Phase['General'].get('doPawley')  and not parmDict[phfx+'LeBail']:
+        if not Phase['General'].get('doPawley')  and not parmDict[phfx+'LeBail'] and len(refDict['FF']):
             if im:
                 dFdvDict = SStructureFactorDerv(refDict,im,G,hfx,pfx,SGData,SSGData,calcControls,parmDict)
@@ -3449 +3449 @@
                         if Ka2 and iFin2-iBeg2:
                             depDerivDict[phfx+name][iBeg2:iFin2] += parmDict[phfx+'Scale']*dFdvDict[phfx+name][iref]*dervDict2['int']/refl[9+im]                  
-            if not Phase['General'].get('doPawley')  and not parmDict[phfx+'LeBail']:
+            if not Phase['General'].get('doPawley')  and not parmDict[phfx+'LeBail'] and len(refDict['FF']):
                 #do atom derivatives -  for RB,F,X & U so far - how do I scale mixed phase constraints?
                 corr = 0.