Changeset 1924

Timestamp:

Jul 9, 2015 5:00:23 PM (8 years ago)

Author:

vondreele

Message:

work on H-atom riding constraints
extend "short" phase names to full length - needed for riding constraint development

Location:

trunk

Files:

• GSASIIconstrGUI.py (modified) (5 diffs)
• GSASIIgrid.py (modified) (1 diff)
• GSASIIobj.py (modified) (1 diff)
• GSASIIphsGUI.py (modified) (2 diffs)
• GSASIIstrMath.py (modified) (1 diff)
• imports/G2sfact.py (modified) (1 diff)

trunk/GSASIIconstrGUI.py

@@ -30 +30 @@
 import GSASIIstrIO as G2stIO
 import GSASIImapvars as G2mv
+import GSASIImath as G2mth
+import GSASIIlattice as G2lat
 import GSASIIgrid as G2gd
 import GSASIIctrls as G2G
@@ -702 +704 @@
         legend = "Select atoms to ride (only one of the atom variables will be varied when all are set to be varied)"
         GetAddAtomVars(page,title1,title2,varList,constrDictEnt,'riding')
-        
-        
    
     def OnAddFunction(event):
@@ -759 +759 @@
         OnPageChanged(None)
                         
+    def FindNeighbors(phase,FrstName,AtNames):
+        General = phase['General']
+        cx,ct,cs,cia = General['AtomPtrs']
+        Atoms = phase['Atoms']
+        atNames = [atom[ct-1] for atom in Atoms]
+        Cell = General['Cell'][1:7]
+        Amat,Bmat = G2lat.cell2AB(Cell)
+        atTypes = General['AtomTypes']
+        Radii = np.array(General['BondRadii'])
+        AtInfo = dict(zip(atTypes,Radii)) #or General['BondRadii']
+        Orig = atNames.index(FrstName.split()[1])
+        OType = Atoms[Orig][ct]
+        XYZ = G2mth.getAtomXYZ(Atoms,cx)        
+        Neigh = []
+        Dx = np.inner(Amat,XYZ-XYZ[Orig]).T
+        dist = np.sqrt(np.sum(Dx**2,axis=1))
+        sumR = AtInfo[OType]+0.5
+        IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
+        for j in IndB[0]:
+            if j != Orig:
+                Neigh.append(AtNames[j])
+        return Neigh
+        
     def GetAddAtomVars(page,title1,title2,varList,constrDictEnt,constType):
         '''Get the atom variables to be added for OnAddAtomEquiv. Then create and 
-        check the constraints.
+        check the constraints. Riding for H atoms only.
         '''
         Atoms = {G2obj.VarDescr(i)[0]:[] for i in varList if 'Atom' in G2obj.VarDescr(i)[0]}
@@ -778 +801 @@
             sel = dlg.GetSelection()
             FrstAtom = AtNames[sel]
-            AtNames.remove(FrstAtom)
+            if 'riding' in constType:
+                phaseName = (FrstAtom.split(' in ')[1]).strip()
+                phase = Phases[phaseName]
+                AtNames = FindNeighbors(phase,FrstAtom,AtNames)
+            else:
+                AtNames.remove(FrstAtom)
         dlg.Destroy()
         if FrstAtom == '':
@@ -796 +824 @@
         for name in Atoms[FrstAtom]:
             newcons = []
-            constr = [[1.0,G2obj.G2VarObj(name)]]
+            constr = []
+            if 'riding' in constType:
+                if 'AU11' in name or 'AUiso' in name:
+                    parts = name.split('AU11').split('AUiso')
+                    constr = [[1.0,G2obj.G2VarObj(parts[0]+'AUiso'+parts[1])]]
+                elif 'AU' not in name:
+                    constr = [[1.0,G2obj.G2VarObj(name)]]
+            else:
+                constr = [[1.0,G2obj.G2VarObj(name)]]
             pref = name.rsplit(':',1)[0]
-            if 'riding' in constType and 'U' in pref:
-                continue
             for sel in Selections:
                 id = Atoms[AtNames[sel]][0].rsplit(':',1)[-1]
-                constr += [[1.0,G2obj.G2VarObj('%s:%s'%(pref,id))]]
+                if 'riding' in constType:
+                    if 'AU11' in pref or 'AUiso' in pref:
+                        constr += [[1.2,G2obj.G2VarObj('%s:%s'%(parts[0]+'AUiso',id))]]
+                    elif 'AU' not in pref:
+                        constr += [[1.0,G2obj.G2VarObj('%s:%s'%(pref,id))]]
+                else:
+                    constr += [[1.0,G2obj.G2VarObj('%s:%s'%(pref,id))]]
+            if not constr:
+                continue
             if 'frac' in pref and 'riding' not in constType:
                 newcons = [constr+[1.0,None,'c']]

trunk/GSASIIgrid.py

@@ -622 +622 @@
             help='Add equivalences between atom parameter values')
         self.ConstraintEdit.Enable(wxID_EQUIVALANCEATOMS,False)
-        self.ConstraintEdit.Append(id=wxID_ADDRIDING, kind=wx.ITEM_NORMAL,text='Add riding constraints',
-            help='Add riding constraints between atom parameter values')
+        self.ConstraintEdit.Append(id=wxID_ADDRIDING, kind=wx.ITEM_NORMAL,text='Add H riding constraints',
+            help='Add H atom riding constraints between atom parameter values')
         self.ConstraintEdit.Enable(wxID_ADDRIDING,False)
         wxID_ADDRIDING

trunk/GSASIIobj.py

@@ -996 +996 @@
         PhaseIdLookup[pId] = (ph,ranId)
         PhaseRanIdLookup[ranId] = pId
-        shortname = ph[:10]
+        shortname = ph  #[:10]
         while shortname in ShortPhaseNames.values():
             shortname = ph[:8] + ' ('+ pId + ')'

trunk/GSASIIphsGUI.py

@@ -1540 +1540 @@
         indx = Atoms.GetSelectedRows()
         if indx:
-            DisAglData['OrigIndx'] = indx
+            generalData = data['General']
             if 'DisAglCtls' in generalData:
                 DisAglCtls = generalData['DisAglCtls']
@@ -1552 +1552 @@
             generalData['DisAglCtls'] = DisAglCtls
             atomData = data['Atoms']
-            generalData = data['General']
             colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
             for ind in indx:

trunk/GSASIIstrMath.py

@@ -602 +602 @@
             if parm in parmDict:
                 keys[key][iatm] = parmDict[parm]
-    Fdata = np.where(Fdata,Fdata,1.e-8)         #avoid divide by zero in derivative calc.?
+    Fdata = np.where(Fdata,Fdata,1.e-8)         #avoid divide by zero in derivative calc.
     return Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata
     

trunk/imports/G2sfact.py

@@ -196 +196 @@
                 else:
                     if Tw != '1':  #fix reversed twin ids
+                        if first:
+                            self.warnings += '\nPrimary twin id changed to 1\nNB: multiple primary twins not working'
+                            first = False
                         Tw = '1'
                     TwId = int(Tw)-1