Changeset 404 for trunk/GSASIIstruct.py

Timestamp:

Oct 28, 2011 1:59:03 PM (10 years ago)

Author:

vondreele

Message:

put error bars on seq refinement plots
add cubic elastic strain coeff
make sure results are saved from seq refinements

File:

• trunk/GSASIIstruct.py (modified) (10 diffs)

trunk/GSASIIstruct.py

@@ -201 +201 @@
     return Histograms,Phases
     
-def GPXBackup(GPXfile):
+def GPXBackup(GPXfile,makeBack=True):
     import distutils.file_util as dfu
     GPXpath,GPXname = ospath.split(GPXfile)
@@ -210 +210 @@
         name = name.split('.')
         if len(name) == 3 and name[0] == Name and 'bak' in name[1]:
-            last = max(last,int(name[1].strip('bak'))+1)
+            if makeBack:
+                last = max(last,int(name[1].strip('bak'))+1)
+            else:
+                last = max(last,int(name[1].strip('bak')))
     GPXback = ospath.join(GPXpath,ospath.splitext(GPXname)[0]+'.bak'+str(last)+'.gpx')
     dfu.copy_file(GPXfile,GPXback)
     return GPXback
         
-def SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,CovData):
+def SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,CovData,makeBack=True):
     ''' Updates gpxfile from all histograms that are found in any phase
     and any phase that used a histogram
@@ -223 +226 @@
         Phases = dictionary of phases that use histograms
         CovData = dictionary of refined variables, varyList, & covariance matrix
+        makeBack = True if new backup of .gpx file is to be made; else use the last one made
     '''
                         
-    GPXback = GPXBackup(GPXfile)
+    GPXback = GPXBackup(GPXfile,makeBack)
     print '\n',135*'-'
     print 'Read from file:',GPXback
@@ -906 +910 @@
 
     def PrintHStrain(hapData,SGData):
-        print '\n Hydrostatic strain: '
+        print '\n Hydrostatic/elastic strain: '
         Hsnames = G2spc.HStrainNames(SGData)
         ptlbls = ' names :'
@@ -1098 +1102 @@
             
     def PrintHStrainAndSig(hapData,strainSig,SGData):
-        print '\n Hydrostatic strain: '
+        print '\n Hydrostatic/elastic strain: '
         Hsnames = G2spc.HStrainNames(SGData)
         ptlbls = ' name  :'
@@ -1897 +1901 @@
     h,k,l = refl[:3]
     if laue in ['m3','m3m']:
-        Dij = parmDict[phfx+'D11']*(h**2+k**2+l**2)
+        Dij = parmDict[phfx+'D11']*(h**2+k**2+l**2)+ \
+            refl[4]**2*parmDict[phfx+'eA']*((h*k)**2+(h*l)**2+(k*l)**2)/(h**2+k**2+l**2)**2
     elif laue in ['6/m','6/mmm','3m1','31m','3']:
         Dij = parmDict[phfx+'D11']*(h**2+k**2+h*k)+parmDict[phfx+'D33']*l**2
@@ -1924 +1929 @@
     h,k,l = refl[:3]
     if laue in ['m3','m3m']:
-        dDijDict = {phfx+'D11':h**2+k**2+l**2,}
+        dDijDict = {phfx+'D11':h**2+k**2+l**2,
+            phfx+'eA':((h*k)**2+(h*l)**2+(k*l)**2)/(h**2+k**2+l**2)**2}
     elif laue in ['6/m','6/mmm','3m1','31m','3']:
         dDijDict = {phfx+'D11':h**2+k**2+h*k,phfx+'D33':l**2}
@@ -2421 +2427 @@
     GetFobsSq(Histograms,Phases,parmDict,calcControls)
     sigDict = dict(zip(varyList,sig))
-    covData = {'variables':result[0],'varyList':varyList,'covMatrix':covMatrix,
-        'title':GPXfile,'newAtomDict':newAtomDict}
+    covData = {'variables':result[0],'varyList':varyList,'sig':sig,
+        'covMatrix':covMatrix,'title':GPXfile,'newAtomDict':newAtomDict}
     SetPhaseData(parmDict,sigDict,Phases,covData)
     SetHistogramPhaseData(parmDict,sigDict,Phases,Histograms)
@@ -2468 +2474 @@
             histNames.reverse()
     SeqResult = {'histNames':histNames}
-    
+    makeBack = True
     for ihst,histogram in enumerate(histNames):
         ifPrint = False
@@ -2560 +2566 @@
         GetFobsSq(Histo,Phases,parmDict,calcControls)
         sigDict = dict(zip(varyList,sig))
-        covData = {'variables':result[0],'varyList':varyList,'covMatrix':covMatrix,
-            'title':histogram,'newAtomDict':newAtomDict}
+        covData = {'variables':result[0],'varyList':varyList,'sig':sig,
+            'covMatrix':covMatrix,'title':histogram,'newAtomDict':newAtomDict}
         SetHistogramPhaseData(parmDict,sigDict,Phases,Histo,ifPrint)
         SetHistogramData(parmDict,sigDict,Histo,ifPrint)
         SeqResult[histogram] = covData
+        SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,covData,makeBack)
+        makeBack = False
     SetSeqResult(GPXfile,Histograms,SeqResult)