Changeset 404

Timestamp:

Oct 28, 2011 1:59:03 PM (12 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

Location:

trunk

Files:

• GSASII.py (modified) (1 diff)
• GSASIIgrid.py (modified) (2 diffs)
• GSASIIphsGUI.py (modified) (1 diff)
• GSASIIplot.py (modified) (2 diffs)
• GSASIIspc.py (modified) (1 diff)
• GSASIIstruct.py (modified) (10 diffs)

trunk/GSASII.py

@@ -356 +356 @@
                     DataType = DataType.strip()[0:3]                                #just 1st 3 chars
                     wx.BeginBusyCursor()
-                    Sample = G2pdG.GetDefaultSample()
+                    Sample = G2pdG.SetDefaultSample()
+                    Sample['Temperature'] = Temperature
                     try:
                         for Item in Data:

trunk/GSASIIgrid.py

@@ -700 +700 @@
     histNames = data['histNames']
     
+    def GetSigData(parm):
+        sigData = []
+        for name in histNames:
+            sigList = data[name]['sig']
+            sigData.append(sigList[parm])
+        return sigData
+    
     def Select(event):
         cols = self.dataDisplay.GetSelectedCols()
@@ -705 +712 @@
         if cols:
             plotData = []
+            plotSig = []
             plotNames = []
             for col in cols:
                 plotData.append(self.SeqTable.GetColValues(col))
+                plotSig.append(GetSigData(col))
                 plotNames.append(self.SeqTable.GetColLabelValue(col))
             plotData = np.array(plotData)
-            G2plt.PlotSeq(self,plotData,plotNames)
+            G2plt.PlotSeq(self,plotData,plotSig,plotNames)
         elif rows:
             name = histNames[rows[0]]

trunk/GSASIIphsGUI.py

@@ -2530 +2530 @@
                 mainSizer.Add((0,5),0)
                 
-                mainSizer.Add(wx.StaticText(dataDisplay,-1,' Hydrostatic strain:'))
+                mainSizer.Add(wx.StaticText(dataDisplay,-1,' Hydrostatic/elastic strain:'))
                 mainSizer.Add(HstrainSizer())
                     

trunk/GSASIIplot.py

@@ -1446 +1446 @@
     Page.canvas.draw()
     
-def PlotSeq(self,SeqData,SeqNames):
+def PlotSeq(self,SeqData,SeqSig,SeqNames):
     
     try:
@@ -1464 +1464 @@
     if len(SeqData):    
         X = np.arange(0,len(SeqData[0]),1)
-        for Y,name in zip(SeqData,SeqNames):
-            Plot.plot(X,Y,label=name)        
+        for Y,sig,name in zip(SeqData,SeqSig,SeqNames):
+            Plot.errorbar(X,Y,yerr=sig,label=name)        
         Plot.legend(loc='best')
         Page.canvas.draw()

trunk/GSASIIspc.py

@@ -551 +551 @@
     uniq = SGData['SGUniq']
     if laue in ['m3','m3m']:
-        return ['D11']
+        return ['D11','eA']         #add cubic strain term
     elif laue in ['6/m','6/mmm','3m1','31m','3']:
         return ['D11','D33']

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)