Changeset 3068

Timestamp:

Sep 12, 2017 10:54:45 AM (6 years ago)

Author:

vondreele

Message:

fix parameter display to show nan (crashed before)
trap with error if any parameter is nan
skip postprocessing for failed refinements (IfOK=False)
fix Jacobian to use GetProfileDervMP

Location:

trunk

Files:

• GSASIIpy3.py (modified) (2 diffs)
• GSASIIstrMain.py (modified) (4 diffs)
• GSASIIstrMath.py (modified) (1 diff)

trunk/GSASIIpy3.py

@@ -142 +142 @@
             return '0.0'
     # negative numbers, leave room for a sign
-    if val < 0: maxdigits -= 1
+    if np.isnan(val):
+        return str(val)
+    if val < 0: maxdigits -= 1        
     if abs(val) < 1e-99 or abs(val) > 9.999e99:
         decimals = min(maxdigits-6,sigfigs)
@@ -156 +158 @@
         fmt = "{" + (":{:d}.{:d}g".format(maxdigits,decimals))+"}"
     elif abs(val) < 1: # small numbers, add to decimal places
-        decimals = sigfigs - int(np.log10(abs(val)))
+        decimals = sigfigs - int(np.log10(np.abs(val)))
         fmt = "{" + (":{:d}.{:d}f".format(maxdigits,decimals))+"}"
     else: # larger numbers, remove decimal places
-        decimals = sigfigs - 1 - int(np.log10(abs(val)))
+        decimals = sigfigs - 1 - int(np.log10(np.abs(val)))
         if decimals <= 0: 
             fmt = "{" + (":{:d}.0f".format(maxdigits))+"}."

trunk/GSASIIstrMain.py

@@ -54 +54 @@
         begin = time.time()
         values =  np.array(G2stMth.Dict2Values(parmDict, varyList))
+        if np.any(np.isnan(values)):
+            raise G2obj.G2Exception('ERROR - nan found in LS parameters - use Calculate/View LS parms to locate')
         # test code to compute GOF and save for external repeat
         #args = ([Histograms,Phases,restraintDict,rigidbodyDict],parmDict,varyList,calcControls,pawleyLookup,dlg)
@@ -135 +137 @@
                         del(varyList[ipvt-1])
                         break
-    G2stMth.GetFobsSq(Histograms,Phases,parmDict,calcControls)
+    if IfOK:
+        G2stMth.GetFobsSq(Histograms,Phases,parmDict,calcControls)
     return IfOK,Rvals,result,covMatrix,sig
 
@@ -212 +215 @@
         IfOK,Rvals,result,covMatrix,sig = RefineCore(Controls,Histograms,Phases,restraintDict,
             rigidbodyDict,parmDict,varyList,calcControls,pawleyLookup,ifPrint,printFile,dlg)
-        sigDict = dict(zip(varyList,sig))
-        newCellDict = G2stMth.GetNewCellParms(parmDict,varyList)
-        newAtomDict = G2stMth.ApplyXYZshifts(parmDict,varyList)
-        covData = {'variables':result[0],'varyList':varyList,'sig':sig,'Rvals':Rvals,
-                   'varyListStart':varyListStart,
-                   'covMatrix':covMatrix,'title':GPXfile,'newAtomDict':newAtomDict,
-                   'newCellDict':newCellDict,'freshCOV':True}
-        # add the uncertainties into the esd dictionary (sigDict)
-        sigDict.update(G2mv.ComputeDepESD(covMatrix,varyList,parmDict))
-        G2mv.PrintIndependentVars(parmDict,varyList,sigDict,pFile=printFile)
-        G2stMth.ApplyRBModels(parmDict,Phases,rigidbodyDict,True)
-        G2stIO.SetRigidBodyModels(parmDict,sigDict,rigidbodyDict,printFile)
-        G2stIO.SetPhaseData(parmDict,sigDict,Phases,rbIds,covData,restraintDict,printFile)
-        G2stIO.SetHistogramPhaseData(parmDict,sigDict,Phases,Histograms,calcControls['FFtables'],pFile=printFile)
-        G2stIO.SetHistogramData(parmDict,sigDict,Histograms,calcControls['FFtables'],pFile=printFile)
-        G2stIO.SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,rigidbodyDict,covData,makeBack)
-        printFile.close()
-        print ' Refinement results are in file: '+ospath.splitext(GPXfile)[0]+'.lst'
-        print ' ***** Refinement successful *****'
+        if IfOK:
+            sigDict = dict(zip(varyList,sig))
+            newCellDict = G2stMth.GetNewCellParms(parmDict,varyList)
+            newAtomDict = G2stMth.ApplyXYZshifts(parmDict,varyList)
+            covData = {'variables':result[0],'varyList':varyList,'sig':sig,'Rvals':Rvals,
+                       'varyListStart':varyListStart,
+                       'covMatrix':covMatrix,'title':GPXfile,'newAtomDict':newAtomDict,
+                       'newCellDict':newCellDict,'freshCOV':True}
+            # add the uncertainties into the esd dictionary (sigDict)
+            sigDict.update(G2mv.ComputeDepESD(covMatrix,varyList,parmDict))
+            G2mv.PrintIndependentVars(parmDict,varyList,sigDict,pFile=printFile)
+            G2stMth.ApplyRBModels(parmDict,Phases,rigidbodyDict,True)
+            G2stIO.SetRigidBodyModels(parmDict,sigDict,rigidbodyDict,printFile)
+            G2stIO.SetPhaseData(parmDict,sigDict,Phases,rbIds,covData,restraintDict,printFile)
+            G2stIO.SetHistogramPhaseData(parmDict,sigDict,Phases,Histograms,calcControls['FFtables'],pFile=printFile)
+            G2stIO.SetHistogramData(parmDict,sigDict,Histograms,calcControls['FFtables'],pFile=printFile)
+            G2stIO.SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,rigidbodyDict,covData,makeBack)
+            printFile.close()
+            print ' Refinement results are in file: '+ospath.splitext(GPXfile)[0]+'.lst'
+            print ' ***** Refinement successful *****'
+        else:
+            print '****ERROR - Refinement failed'
+            raise G2obj.G2Exception('****ERROR - Refinement failed')
     except G2obj.G2Exception,Msg:
         printFile.close()
@@ -236 +243 @@
 
 #for testing purposes!!!
-    if DEBUG:
+    if DEBUG and IfOK:
 #needs: values,HistoPhases,parmDict,varylist,calcControls,pawleyLookup
         import cPickle

trunk/GSASIIstrMath.py

@@ -4070 +4070 @@
             xB = np.searchsorted(x,Limits[0])
             xF = np.searchsorted(x,Limits[1])+1
-            dMdvh = np.sqrt(w[xB:xF])*getPowderProfileDerv(parmDict,x[xB:xF],
-                varylist,Histogram,Phases,rigidbodyDict,calcControls,pawleyLookup,dependentVars)
+            dMdvh = np.sqrt(w[xB:xF])*getPowderProfileDervMP([parmDict,x[xB:xF],
+                varylist,Histogram,Phases,rigidbodyDict,calcControls,pawleyLookup,dependentVars])
         elif 'HKLF' in histogram[:4]:
             Histogram = Histograms[histogram]