Changeset 2318

Timestamp:

Jun 13, 2016 9:11:36 PM (7 years ago)

Author:

vondreele

Message:

Add atom-atom distance to seq results table - needs debugging

Location:

trunk

Files:

• GSASIIgrid.py (modified) (2 diffs)
• GSASIImath.py (modified) (1 diff)
• GSASIIobj.py (modified) (1 diff)

trunk/GSASIIgrid.py

@@ -1468 +1468 @@
             help='Add a new bond distance pseudo-variable')
         self.SequentialPvars.Append(
-            id=wxADDSEQANGLE, kind=wx.ITEM_NORMAL,text='Calc Angle',
+            id=wxADDSEQANGLE, kind=wx.ITEM_NORMAL,text='Add Angle',
             help='Add a new bond angle pseudo-variable')
         self.SequentialPvars.Append(
@@ -2777 +2777 @@
                 Phase = Phases[pName]
                 General = Phase['General']
-                Cell = General['Cell'][1:7]
-                Amat = G2lat.cell2AB(Cell)[0]
+                cx,ct = General['AtomPtrs'][:2]
+                pId = Phase['pId']
+                SGData = General['SGData']
+                sB = Tatom.find('(')+1
+                symNo = 0
+                if sB:
+                    sF = Tatom.find(')')
+                    symNo = int(Tatom[sB:sF])
+                cellNo = [0,0,0]
+                cB = Tatom.find('[')
+                if cB>0:
+                    cF = Tatom.find(']')+1
+                    cellNo = eval(Tatom[cB:cF])
+                Atoms = Phase['Atoms']
+                aNames = [atom[ct-1] for atom in Atoms]
+                oId = aNames.index(Oatom)
+                tId = aNames.index(Tatom.split(' +')[0])
                 # create an expression object
                 obj = G2obj.ExpressionObj()
                 obj.expression = 'Dist(%s,%s)'%(Oatom,Tatom.split(' d=')[0].replace(' ',''))
-                obj.distance_stuff = {'Amat':Amat,}
-                obj.distance_atoms = [1,2]
+                obj.distance_dict = {'pId':pId,'SGData':SGData,'symNo':symNo,'cellNo':cellNo}
+                obj.distance_atoms = [oId,tId]
         else: 
             dlg.Destroy()

trunk/GSASIImath.py

@@ -1505 +1505 @@
 ################################################################################
 
+def CalcDist(distance_dict, distance_atoms, parmDict):
+    if not len(parmDict):
+        return 0.
+    pId = distance_dict['pId']
+    pfx = '%d::'%(pId)
+    A = [parmDict['%s::A%d'%(pId,i)] for i in range(6)]
+    Amat = G2lat.cell2AB(G2lat.A2cell(A))[0]
+    Oxyz = [parmDict['%s::A%s:%d'%(pId,x,distance_atoms[0])] for x in ['x','y','z']]
+    Txyz = [parmDict['%s::A%s:%d'%(pId,x,distance_atoms[1])] for x in ['x','y','z']]
+    inv = 1
+    symNo = distance_dict['symNo']
+    if symNo < 0:
+        inv = -1
+        symNo *= -1
+    cen = symNo/100
+    op = symNo%100-1
+    M,T = distance_dict['SGData']['SGOps'][op]
+    M *= inv
+    T *= inv
+    D = T+distance_dict['SGData']['SGCen'][cen]
+    D += distance_dict['cellNo']
+    Txyz = np.inner(M,Txyz)+D
+    dist = np.sqrt(np.sum(np.inner(Amat,(Txyz-Oxyz))**2))
+#    GSASIIpath.IPyBreak()
+    return dist    
+   
 def getSyXYZ(XYZ,ops,SGData):
     '''default doc string

trunk/GSASIIobj.py

@@ -2043 +2043 @@
         if self.eObj.expression.startswith('Dist'):
             dist = 0
-            #dist = CalcDist(self.eObj.distance_stuff, self.eObj.distance_atoms, self.parmDict)
+#            GSASIIpath.IPyBreak()
+            dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
             return dist 
         if self.compiledExpr is None: