Changeset 2170

Timestamp:

Mar 14, 2016 9:13:28 AM (7 years ago)

Author:

vondreele

Message:

fix isotope problem for atyoms with no "Nat. Abund."
add scale & background to stacking simulation - still under development

Location:

trunk

Files:

• GSASIIphsGUI.py (modified) (5 diffs)
• GSASIIpwd.py (modified) (4 diffs)

trunk/GSASIIphsGUI.py

@@ -291 +291 @@
                 generalData['vdWRadii'].append(Info['Vdrad'])
                 if atom[ct] in generalData['Isotope']:
+                    if generalData['Isotope'][atom[ct]] not in generalData['Isotopes'][atom[ct]]:
+                        isotope = generalData['Isotopes'][atom[ct]].keys()[-1]
+                        generalData['Isotope'][atom[ct]] = isotope
                     generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]]['Mass'])
                 else:
                     generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
+                    if 'Nat. Abund.' not in generalData['Isotopes'][atom[ct]]:
+                        isotope = generalData['Isotopes'][atom[ct]].keys()[-1]
+                        generalData['Isotope'][atom[ct]] = isotope
                     generalData['AtomMass'].append(Info['Mass'])
                 generalData['NoAtoms'][atom[ct]] = atom[cs-1]*float(atom[cs+1])
@@ -624 +630 @@
                 item = Indx[Obj.GetId()]
                 isotope = Obj.GetValue()
-                generalData['Isotope'][item] = isotope
+                data['General']['Isotope'][item] = isotope
                 indx = generalData['AtomTypes'].index(item)
                 data['General']['AtomMass'][indx] = generalData['Isotopes'][item][isotope]['Mass']
@@ -677 +683 @@
                 colorTxt.SetBackgroundColour(wx.Colour(R,G,B))
                 elemSizer.Add(colorTxt,0,WACV)
+            
             return elemSizer
         
@@ -2885 +2892 @@
         PWDR = data['Histograms'][HistName]
         G2frame.PatternId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,HistName)
-        
+        sample = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(
+            G2frame,G2frame.PatternId, 'Sample Parameters'))
+        scale = sample['Scale'][0]
+        background = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(
+            G2frame,G2frame.PatternId, 'Background'))        
         limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(
             G2frame,G2frame.PatternId, 'Limits'))[1]
@@ -2893 +2904 @@
             wx.MessageBox("Can't simulate neutron TOF patterns yet",caption='Data error',style=wx.ICON_EXCLAMATION)
             return            
-        profile = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)[1]
-            
-        G2pwd.StackSim(data['Layers'],HistName,limits,inst,profile)
+        profile = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)[1]            
+        G2pwd.StackSim(data['Layers'],HistName,scale,background,limits,inst,profile)
         G2plt.PlotPatterns(G2frame,plotType='PWDR')
         

trunk/GSASIIpwd.py

@@ -1737 +1737 @@
 ################################################################################
 
-def StackSim(Layers,HistName,limits,inst,profile):
+def StackSim(Layers,HistName,scale,background,limits,inst,profile):
     '''Simulate powder pattern from stacking faults using DIFFaX
     
@@ -1744 +1744 @@
                         'Layers':[],'Stacking':[],'Transitions':[]}
     param: HistName str: histogram name to simulate 'PWDR...'
+    param: scale float: scale factor
+    param: background dict: background parameters
     param: limits list: min/max 2-theta to be calculated
     param: inst dict: instrumnet parameters dictionary
@@ -1779 +1781 @@
     iBeg = np.searchsorted(x0,limits[0])
     iFin = np.searchsorted(x0,limits[1])
+    if iFin-iBeg > 20000:
+        iFin = iBeg+19999
     x = x0[iBeg:iFin]
     dx = x0[iBeg+1]-x0[iBeg]
@@ -1851 +1855 @@
     print 'DIFFaX time = %.2fs'%(time.time()-time0)
     X = np.loadtxt('GSASII-DIFFaX.spc')
-    profile[3][:len(X.T[1])] = X.T[1]
+    bakType,backDict,backVary = SetBackgroundParms(background)
+    backDict['Lam1'] = G2mth.getWave(inst)
+#    GSASIIpath.IPyBreak()
+    iB = np.searchsorted(profile[0],X.T[0])[0]
+    iF = np.searchsorted(profile[0],X.T[-1])[0]
+    if not iF:
+        iF = -1
+    profile[4][iB:iF] = getBackground('',backDict,bakType,inst['Type'][0],X.T[0])[0]    
+    profile[3][iB:iF] = X.T[1]*scale+profile[4][iB:iF]
+    if not np.any(profile[1]):                   #fill dummy data x,y,w,yc,yb,yd
+        rv = st.poisson(profile[3][iB:iF])
+        profile[1][iB:iF] = rv.rvs()
+        Z = np.ones_like(profile[3][iB:iF])
+        Z[1::2] *= -1
+        profile[1][iB:iF] = profile[3][iB:iF]+np.abs(profile[1][iB:iF]-profile[3][iB:iF])*Z
+        profile[2][iB:iF] = np.where(profile[1][iB:iF]>0.,1./profile[1][iB:iF],1.0)
+    profile[5][iB:iF] = profile[1][iB:iF]-profile[3][iB:iF]
+
+
     #cleanup files..
     os.remove('data.sfc')