Changeset 709

Timestamp:

Aug 13, 2012 12:18:20 PM (10 years ago)

Author:

vondreele

Message:

add testGSASIIstruct.py
a fix to the data window restore after Refine
make getMass & getDensity routines in GSASIImath.py
update atom mass info after Refine

Location:

trunk

Files:

• GSASII.py (modified) (1 diff)
• GSASIImath.py (modified) (1 diff)
• GSASIIphsGUI.py (modified) (4 diffs)
• GSASIIstruct.py (modified) (1 diff)
• testGSASIIstruct.py (added)

trunk/GSASII.py

@@ -2109 +2109 @@
                 if parentName:
                     parentId = G2gd.GetPatternTreeItemId(self, self.root, parentName)
-                    itemId = G2gd.GetPatternTreeItemId(self, parentId, oldName)
+                    if parentId:
+                        itemId = G2gd.GetPatternTreeItemId(self, parentId, oldName)
+                    else:
+                        itemId = G2gd.GetPatternTreeItemId(self, self.root, oldName)
                     self.PatternTree.SelectItem(itemId)
                 elif Id:

trunk/GSASIImath.py

@@ -157 +157 @@
     return vcov
 
+def getMass(generalData):
+    mass = 0.
+    for i,elem in enumerate(generalData['AtomTypes']):
+        mass += generalData['NoAtoms'][elem]*generalData['AtomMass'][i]
+    return mass    
+
+def getDensity(generalData):
+    
+    mass = getMass(generalData)
+    Volume = generalData['Cell'][7]
+    density = mass/(0.6022137*Volume)
+    return density,Volume/mass
+    
 def getRestDist(XYZ,Amat):
     return np.sqrt(np.sum(np.inner(Amat,(XYZ[1]-XYZ[0]))**2))

trunk/GSASIIphsGUI.py

@@ -409 +409 @@
         generalData['Mydir'] = G2frame.dirname
         cx,ct,cs,cia = [3,1,7,9]
-        generalData['AtomPtrs'] = [cx,ct,cs,cia]
         if generalData['Type'] =='macromolecular':
             cx,ct,cs,cia = [6,4,10,12]
-            generalData['AtomPtrs'] = [cx,ct,cs,cia]
+        generalData['AtomPtrs'] = [cx,ct,cs,cia]
         for atom in atomData:
             atom[ct] = atom[ct].lower().capitalize()              #force to standard form
@@ -620 +619 @@
                 cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7]))
                 volVal.SetValue("%.3f"%(cell[7]))
-                density,mattCoeff = getDensity()
+                density,mattCoeff = G2mth.getDensity(generalData)
                 denSizer[1].SetValue('%.3f'%(density))
                 if denSizer[2]:
@@ -664 +663 @@
                 indx = generalData['AtomTypes'].index(item)
                 data['General']['AtomMass'][indx] = generalData['Isotopes'][item][isotope][0]
-                density,mattCoeff = getDensity()
+                density,mattCoeff = G2mth.getDensity(generalData)
                 denSizer[1].SetValue('%.3f'%(density))
                 if denSizer[2]:
@@ -716 +715 @@
             return elemSizer
         
-        def getDensity():
-            
-            mass = 0.
-            for i,elem in enumerate(generalData['AtomTypes']):
-                mass += generalData['NoAtoms'][elem]*generalData['AtomMass'][i]
-            Volume = generalData['Cell'][7]
-            density = mass/(0.6022137*Volume)
-            return density,Volume/mass
-            
         def DenSizer():
             
-            density,mattCoeff = getDensity()
+            density,mattCoeff = G2mth.getDensity(generalData)
             denSizer = wx.BoxSizer(wx.HORIZONTAL)
             denSizer.Add(wx.StaticText(dataDisplay,-1,' Density: '),0,wx.ALIGN_CENTER_VERTICAL)

trunk/GSASIIstruct.py

@@ -839 +839 @@
                 11:'%8.5f',12:'%8.5f',13:'%8.5f',14:'%8.5f',15:'%8.5f',16:'%8.5f'}
             noFXsig = {3:[10*' ','%10s'],4:[10*' ','%10s'],5:[10*' ','%10s'],6:[8*' ','%8s']}
+            for atyp in General['AtomTypes']:       #zero composition
+                General['NoAtoms'][atyp] = 0.
             for i,at in enumerate(Atoms):
+                General['NoAtoms'][at[1]] += at[6]*float(at[8])     #new composition
                 name = fmt[0]%(at[0])+fmt[1]%(at[1])+':'
                 valstr = ' values:'