Changeset 1315

Timestamp:

May 1, 2014 3:20:21 PM (9 years ago)

Author:

vondreele

Message:

new controls parameter 'Contrast' & remove Substances from arguments list

Location:

trunk

Files:

• GSASIIpwdGUI.py (modified) (12 diffs)
• GSASIIsasd.py (modified) (12 diffs)

trunk/GSASIIpwdGUI.py

@@ -2684 +2684 @@
             data['Particle']['Levels'].append({
                 'Controls':{'FormFact':'Sphere','DistType':'LogNormal','Material':material,
-                    'FFargs':{},'SFargs':{},'NumPoints':50,'Cutoff':0.01,
+                    'FFargs':{},'SFargs':{},'NumPoints':50,'Cutoff':0.01,'Contrast':0.0,
                     'SlitSmear':[0.0,False],'StrFact':'Dilute'},    #last 2 not used - future?
                 'LogNormal':{'Volume':[0.05,False],'Mean':[1000.,False],'StdDev':[0.5,False],'MinSize':[10.,False],},
@@ -2696 +2696 @@
                     'PkSig':[10,False],'PkGam':[10,False],},        #reasonable 31A peak
                 })
-            G2sasd.ModelFxn(Profile,ProfDict,Limits,Substances,Sample,data)
+            G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
             RefreshPlots(True)
                     
@@ -2789 +2789 @@
                 ILimits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Limits'))
                 IInst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Instrument Parameters'))
-                ISubstances = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Substances'))
-                IfOK,result,varyList,sig,Rvals,covMatrix = G2sasd.ModelFit(IProfile,IProfDict,ILimits,ISubstances,ISample,IModel)
+#                ISubstances = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Substances'))
+                IfOK,result,varyList,sig,Rvals,covMatrix = G2sasd.ModelFit(IProfile,IProfDict,ILimits,ISample,IModel)
                 if not IfOK:
                     G2frame.ErrorDialog('Failed sequential refinement for data '+name,
@@ -2799 +2799 @@
                     break
                 
-                G2sasd.ModelFxn(IProfile,IProfDict,ILimits,ISubstances,ISample,IModel)
+                G2sasd.ModelFxn(IProfile,IProfDict,ILimits,ISample,IModel)
                 SeqResult[name] = {'variables':result[0],'varyList':varyList,'sig':sig,'Rvals':Rvals,
                     'covMatrix':covMatrix,'title':name}
@@ -2822 +2822 @@
                     ' Do Substances and then Sample parameters')
                 return
-            G2sasd.SizeDistribution(Profile,ProfDict,Limits,Substances,Sample,data)
+            G2sasd.SizeDistribution(Profile,ProfDict,Limits,Sample,data)
             G2plt.PlotSASDSizeDist(G2frame)
             RefreshPlots(True)
@@ -2828 +2828 @@
         elif data['Current'] == 'Particle fit':
             SaveState()
-            if not G2sasd.ModelFit(Profile,ProfDict,Limits,Substances,Sample,data)[0]:
+            if not G2sasd.ModelFit(Profile,ProfDict,Limits,Sample,data)[0]:
                 G2frame.ErrorDialog('Failed refinement',
                     'You need to rethink your selection of parameters\n'+    \
                     ' Model restored to previous version')
-            G2sasd.ModelFxn(Profile,ProfDict,Limits,Substances,Sample,data)
+            G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
             RefreshPlots(True)
             wx.CallAfter(UpdateModelsGrid,G2frame,data)
@@ -2842 +2842 @@
         G2frame.dataFrame.SasdUndo.Enable(False)
         UpdateModelsGrid(G2frame,data)
-        G2sasd.ModelFxn(Profile,ProfDict,Limits,Substances,Sample,data)
+        G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
         RefreshPlots(True)
 
@@ -3031 +3031 @@
                 sldrObj.SetRange(slMult*valMinMax[0],slMult*valMinMax[1])
                 sldrObj.SetValue(slMult*logv)
-            G2sasd.ModelFxn(Profile,ProfDict,Limits,Substances,Sample,data)
+            G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
             RefreshPlots()
             
@@ -3044 +3044 @@
                     item['SFargs'] = StructureFactors[Obj.GetValue()]
                 wx.CallAfter(UpdateModelsGrid,G2frame,data)
-                G2sasd.ModelFxn(Profile,ProfDict,Limits,Substances,Sample,data)
+                G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
                 RefreshPlots()
                 
@@ -3052 +3052 @@
             del data['Particle']['Levels'][item]
             wx.CallAfter(UpdateModelsGrid,G2frame,data)
-            G2sasd.ModelFxn(Profile,ProfDict,Limits,Substances,Sample,data)
+            G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
             RefreshPlots()
             
@@ -3065 +3065 @@
             item[key][0] = value
             pvObj.SetValue('%.3g'%(item[key][0]))
-            G2sasd.ModelFxn(Profile,ProfDict,Limits,Substances,Sample,data)
+            G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
             RefreshPlots()
             
@@ -3096 +3096 @@
                 sizeSizer.Add(matSel,0,WACV) #do neutron test here?
                 rho = Substances['Substances'][level['Controls']['Material']].get('XAnom density',0.0)
-                contrast = (rho-rhoMat)**2
+                level['Controls']['Contrast'] = contrast = (rho-rhoMat)**2                 
                 sizeSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Resonant X-ray contrast: '),0,WACV)
                 sizeSizer.Add(wx.StaticText(G2frame.dataDisplay,label='  %.2f 10%scm%s'%(contrast,Pwr20,Pwrm4)),0,WACV)

trunk/GSASIIsasd.py

@@ -1005 +1005 @@
 ###############################################################################
 
-def SizeDistribution(Profile,ProfDict,Limits,Substances,Sample,data):
+def SizeDistribution(Profile,ProfDict,Limits,Sample,data):
     shapes = {'Spheroid':[SpheroidFF,SpheroidVol],'Cylinder':[CylinderDFF,CylinderDVol],
         'Cylinder AR':[CylinderARFF,CylinderARVol],'Unified sphere':[UniSphereFF,UniSphereVol],
@@ -1053 +1053 @@
 ################################################################################
 
-def ModelFit(Profile,ProfDict,Limits,Substances,Sample,Model):
+def ModelFit(Profile,ProfDict,Limits,Sample,Model):
     shapes = {'Spheroid':[SpheroidFF,SpheroidVol],'Cylinder':[CylinderDFF,CylinderDVol],
         'Cylinder AR':[CylinderARFF,CylinderARVol],'Unified sphere':[UniSphereFF,UniSphereVol],
@@ -1081 +1081 @@
         parmDict['Back'] = Back[0]
         partData = Model['Particle']
-        parmDict['Matrix density'] = Substances['Substances'][partData['Matrix']['Name']].get('XAnom density',0.0)
         for i,level in enumerate(partData['Levels']):
             cid = str(i)+':'
@@ -1094 +1093 @@
                 parmDict[cid+'FFVolume'] = shapes[controls['FormFact']][1]
                 parmDict[cid+'StrFact'] = sfxns[controls['StrFact']]
-                parmDict[cid+'XAnom density'] = Substances['Substances'][controls['Material']].get('XAnom density',0.0)
+                parmDict[cid+'Contrast'] = controls['Contrast']
                 for item in FFparmOrder:
                     if item in controls['FFargs']:
@@ -1126 +1125 @@
             Type = controls['DistType']
             if Type in ['LogNormal','Gaussian','LSW','Schulz-Zimm','Monodisperse']:
-                print ' Component %d: Type: %s: Structure Factor: %s'%(i,Type,controls['StrFact'])                
+                print ' Component %d: Type: %s: Structure Factor: %s Contrast: %12.3f'  \
+                    %(i,Type,controls['StrFact'],controls['Contrast'])                
             else:
                 print ' Component %d: Type: %s: '%(i,Type,)
@@ -1152 +1152 @@
     def getSASD(Q,levelTypes,parmDict):
         Ic = np.zeros_like(Q)
-        rhoMat = parmDict['Matrix density']
         for i,Type in enumerate(levelTypes):
             cid = str(i)+':'
@@ -1171 +1170 @@
                     if item in parmDict:
                         distDict[item.split(':')[1]] = parmDict[item]
-                rho = parmDict[cid+'XAnom density']
-                contrast = (rho-rhoMat)**2
+                contrast = parmDict[cid+'Contrast']
                 rBins,dBins,dist = MakeDiamDist(Type,parmDict[cid+'NumPoints'],parmDict[cid+'Cutoff'],distDict)
                 Gmat = G_matrix(Q,rBins,contrast,FFfxn,Volfxn,FFargs).T
@@ -1200 +1198 @@
                     if item in parmDict: 
                         SFargs.append(parmDict[item])
-                rho = parmDict[cid+'XAnom density']
-                contrast = (rho-rhoMat)**2
+                contrast = parmDict[cid+'Contrast']
                 R = parmDict[cid+'Radius']
                 Gmat = G_matrix(Q,R,contrast,FFfxn,Volfxn,FFargs)             
@@ -1252 +1249 @@
         return False,0,0,0,0,0
     
-def ModelFxn(Profile,ProfDict,Limits,Substances,Sample,sasdData):
+def ModelFxn(Profile,ProfDict,Limits,Sample,sasdData):
     
     shapes = {'Spheroid':[SpheroidFF,SpheroidVol],'Cylinder':[CylinderDFF,CylinderDVol],
@@ -1264 +1261 @@
 #    pdb.set_trace()
     partData = sasdData['Particle']
-    rhoMat = Substances['Substances'][partData['Matrix']['Name']].get('XAnom density',0.0)
     matFrac = partData['Matrix']['VolFrac'] #[value,flag]        
     Scale = Sample['Scale']     #[value,flag]
@@ -1294 +1290 @@
                 if item in controls['FFargs']: 
                     FFargs.append(controls['FFargs'][item][0])
-            rho = Substances['Substances'][level['Controls']['Material']].get('XAnom density',0.0)
-            contrast = (rho-rhoMat)**2
+            contrast = controls['Contrast']
             distDict = {}
             for item in parmDict:
@@ -1336 +1331 @@
                 if item in controls['FFargs']: 
                     FFargs.append(controls['FFargs'][item][0])
-            rho = Substances['Substances'][level['Controls']['Material']].get('XAnom density',0.0)
-            contrast = (rho-rhoMat)**2
+            contrast = controls['Contrast']
             Gmat = G_matrix(Q[Ibeg:Ifin],R,contrast,FFfxn,Volfxn,FFargs)             
             Ic[Ibeg:Ifin] += Gmat[0]*level[distFxn]['Volume'][0]*SFfxn(Q[Ibeg:Ifin],args=SFargs)