Changeset 1606

Timestamp:

Dec 13, 2014 10:51:53 AM (8 years ago)

Author:

vondreele

Message:

more FillAtomLookUp? errors
a few more orthorhombic SS symbols
some fixes for missing/deleted phases

Location:

trunk

Files:

• GSASII.py (modified) (1 diff)
• GSASIIobj.py (modified) (1 diff)
• GSASIIphsGUI.py (modified) (3 diffs)
• GSASIIspc.py (modified) (2 diffs)
• GSASIIstrMath.py (modified) (4 diffs)
• imports/G2phase.py (modified) (1 diff)

trunk/GSASII.py

@@ -2749 +2749 @@
                             if len(refList):
                                 for i,item in DelList:
-                                    del(refList[item])
+                                    if item in refList:
+                                        del(refList[item])
                             self.PatternTree.SetItemPyData(Id,refList)
                         item, cookie = self.PatternTree.GetNextChild(self.root, cookie)

trunk/GSASIIobj.py

@@ -1294 +1294 @@
         'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
         'constr([0-9]*)' : 'Parameter from constraint',
-        # supersymmetry parameters
+        # supersymmetry parameters  'Flen','Fcent'?
         'mV([0-2])' : 'Modulation vector component \\1',
-#        'Flen','Fcent','Fsin','Fcos'
+        'Fsin'  :   'Sin site fraction modulation',
+        'Fcos'  :   'Cos site fraction modulation',
         '[XYZ]sin'  : 'Sin position wave for \\1',
         '[XYZ]cos'  : 'Cos position wave for \\1',

trunk/GSASIIphsGUI.py

@@ -3972 +3972 @@
         if refresh:
             RigidBodies.DestroyChildren()
-        AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
         general = data['General']
-        cx = general['AtomPtrs'][0]
+        cx,ct,cs,cia = generalData['AtomPtrs']
+        AtLookUp = G2mth.FillAtomLookUp(data['Atoms'],cia+8)
         Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
         RBData = G2frame.PatternTree.GetItemPyData(   
@@ -4344 +4344 @@
         RBIds = dict(zip(RBNames,rbKeys))
         general = data['General']
+        cx,ct,cs,cia = generalData['AtomPtrs']
         Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
         Atoms = data['Atoms']
-        AtLookUp = G2mth.FillAtomLookUp(Atoms)
+        AtLookUp = G2mth.FillAtomLookUp(Atoms,cia+8)
         if 'macro' not in general['Type']:
             print '**** ERROR - this phase is not a macromolecule ****'
@@ -4429 +4430 @@
         
     def OnGlobalResRBTherm(event):
-        AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
         RBObjs = data['RBModels']['Residue']
         names = ['None','Uiso','T','TL','TLS']
         cia = data['General']['AtomPtrs'][3]
+        AtLookUp = G2mth.FillAtomLookUp(data['Atoms'],cia+8)
         dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names)
         if dlg.ShowModal() == wx.ID_OK:

trunk/GSASIIspc.py

@@ -1283 +1283 @@
     return KNsym[key]        
 
-def GetNXUPQsym(siteSym):        
-    'Needs a doc string'
+def GetNXUPQsym(siteSym):
+    '''        
+    The codes XUPQ are for lookup of symmetry constraints for position(X), thermal parm(U) & magnetic moments 
+    (P&Q-not used in GSAS-II)
+    '''
     NXUPQsym = {
         '    1   ':(28,29,28,28),'   -1   ':( 1,29,28, 0),'    2(x)':(12,18,12,25),'    m(x)':(25,18,12,25),
@@ -2061 +2064 @@
         '(00g)','(1/21/2g)0q0','(1/21/2g)q00','(a00)','(a1/21/2)00q','(b1/21/2)0q0',],
 #35        
-    'C m m 2':[],
-    'A 2 m m':[],
-    'B m 2 m':[],
+    'C m m 2':['(00g)','(00g)s0s','(00g)0ss','(00g)ss0','(10g)','(10g)s0s','(10g)0ss','(10g)ss0',
+        '(01g)','(01g)s0s','(01g)0ss','(01g)ss0','(a00)','(a00)0s0','(a01/2)','(a01/2)0s0',
+        '(0b0)','(0b0)s00','(0b1/2)','(0b1/2)s00',],
+    'A 2 m m':['(a00)','(a00)s0s','(a00)0ss','(a00)ss0','(a10)','(a10)s0s','(a10)0ss','(a10)ss0',
+        '(a01)','(a01)s0s','(a01)0ss','(a01)ss0','(0b0)','(0b0)00s','(1/2b0)','(1/2b0)00s',
+        '(00g)','(00g)0s0','(01/2g)','(01/2g)0s0',],
+    'B m 2 m':['(0b0)','(0b0)s0s','(0b0)0ss','(0b0)ss0','(1b0)','(1b0)s0s','(1b0)0ss','(1b0)ss0',
+        '(0b1)','(0b1)s0s','(0b1)0ss','(0b1)ss0','(a00)','(a00)00s','(a01/2)','(a01/2)00s',
+        '(00g)','(00g)s00','(1/20g)','(1/20g)s00',],
 #36
-    'C m c 21':[],
-    'A 21 m a':[],
-    'B m 21 b':[],
-    'B b 21 m':[],
-    'C c m 21':[],
-    'A 21 a m':[],
+    'C m c 21':['(00g)','(00g)s0s','(10g)','(10g)s0s','(a00)','(a00)0s0','(0b0)','(0b0)s00',],
+    'A 21 m a':['(a00)','(a00)ss0','(a10)','(a10)ss0','(0b0)','(0b0)00s','(00g)','(00g)0s0',],
+    'B m 21 b':['(0b0)','(0b0)ss0','(1b0)','(1b0)ss0','(a00)','(a00)00s','(00g)','(00g)s00',],
+    'B b 21 m':['(0b0)','(0b0)0ss','(0b1)','(0b1)ss0','(a00)','(a00)00s','(00g)','(00g)s00',],
+    'C c m 21':['(00g)','(00g)0ss','(01g)','(01g)0ss','(a00)','(a00)0s0','(0b0)','(0b0)s00',],
+    'A 21 a m':['(a00)','(a00)s0s','(a01)','(a01)s0s','(0b0)','(0b0)00s','(00g)','(00g)0s0',],
 #37
-    'C c c 2':[],
-    'A 2 a a':[],
-    'B b 2 b':[],
+    'C c c 2':['(00g)','(00g)s0s','(00g)0ss','(10g)','(10g)s0s','(10g)0ss','(01g)','(01g)s0s','(01g)0ss',
+        '(a00)','(a00)0s0','(0b0)','(0b0)s00',],
+    'A 2 a a':['(a00)','(a00)ss0','(a00)s0s','(a10)','(a10)ss0','(a10)ss0','(a01)','(a01)ss0','(a01)ss0',
+        '(0b0)','(0b0)00s','(00g)','(00g)0s0',],
+    'B b 2 b':['(0b0)','(0b0)0ss','(0b0)ss0','(0b1)','(0b1)0ss','(0b1)ss0','(1b0)','(1b0)0ss','(1b0)ss0',
+        '(a00)','(a00)00s','(00g)','(00g)s00',],
 #38
     'A m m 2':[],

trunk/GSASIIstrMath.py

@@ -1536 +1536 @@
             refLists = Histogram['Reflection Lists']
             for phase in refLists:
+                if phase not in Phases:     #skips deleted or renamed phases silently!
+                    continue
                 Phase = Phases[phase]
                 im = 0
@@ -1581 +1583 @@
                     sumdF += np.abs(Fo-Fc)
                     sumdFsq += (refl[8+im]-refl[9+im])**2
-                Histogram['Residuals'][phfx+'Rf'] = min(100.,(sumdF/sumFo)*100.)
-                Histogram['Residuals'][phfx+'Rf^2'] = min(100.,np.sqrt(sumdFsq/sumFosq)*100.)
+                if sumFo:
+                    Histogram['Residuals'][phfx+'Rf'] = min(100.,(sumdF/sumFo)*100.)
+                    Histogram['Residuals'][phfx+'Rf^2'] = min(100.,np.sqrt(sumdFsq/sumFosq)*100.)
+                else:
+                    Histogram['Residuals'][phfx+'Rf'] = 100.
+                    Histogram['Residuals'][phfx+'Rf^2'] = 100.
                 Histogram['Residuals'][phfx+'Nref'] = len(refDict['RefList'])
                 Histogram['Residuals']['hId'] = hId
@@ -1640 +1646 @@
     for phase in Histogram['Reflection Lists']:
         refDict = Histogram['Reflection Lists'][phase]
+        if phase not in Phases:     #skips deleted or renamed phases silently!
+            continue
         Phase = Phases[phase]
         pId = Phase['pId']
@@ -1816 +1824 @@
     for phase in Histogram['Reflection Lists']:
         refDict = Histogram['Reflection Lists'][phase]
+        if phase not in Phases:     #skips deleted or renamed phases silently!
+            continue
         Phase = Phases[phase]
         SGData = Phase['General']['SGData']

trunk/imports/G2phase.py

@@ -404 +404 @@
             elif 'spgroup' in S:
                 if 'X' in S:
-                    raise self.ImportException("Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry")            
+                    raise self.ImportException("Supersymmetry "+S+" too high; GSAS-II limited to (3+1) supersymmetry")            
                 SpGrp = S.split()[1]
                 SuperSg = ''