Changeset 2328

Timestamp:

Jun 16, 2016 4:06:26 PM (9 years ago)

Author:

vondreele

Message:

seq dist table entries & plot now have sus computed from v-cov matrix

Location:

trunk

Files:

• GSASIIgrid.py (modified) (2 diffs)
• GSASIImath.py (modified) (2 diffs)

trunk/GSASIIgrid.py ¶

@@ -3461 +3461 @@
             parmDict = data[name]['parmDict']
             G2mv.GenerateConstraints(groups,parmlist,varyList,constrDict,fixedList,parmDict,SeqHist=ihst)
-            derivs = np.array(
-                [EvalPSvarDeriv(calcobj,parmDict.copy(),sampleDict[name],var,ESD)
-                 for var,ESD in zip(varyList,sigs)])
-            esdList.append(np.sqrt(
-                np.inner(derivs,np.inner(data[name]['covMatrix'],derivs.T)) ))
+            if 'Dist' in expr:
+                derivs = G2mth.CalcDistDeriv(obj.distance_dict,obj.distance_atoms, parmDict)
+                pId = obj.distance_dict['pId']
+                aId,bId = obj.distance_atoms
+                varyNames = ['%d::dA%s:%d'%(pId,ip,aId) for ip in ['x','y','z']]
+                varyNames += ['%d::dA%s:%d'%(pId,ip,bId) for ip in ['x','y','z']]
+                VCoV = G2mth.getVCov(varyNames,varyList,data[name]['covMatrix'])
+                esdList.append(np.sqrt(np.inner(derivs,np.inner(VCoV,derivs.T)) ))
+#                GSASIIpath.IPyBreak()
+            elif 'Angle' in expr:
+                derivs = G2mth.CalcAngleDeriv(obj.angle_dict,obj.angle_atoms, parmDict)
+                pId = obj.angle_dict['pId']
+                aId,bId = obj.distance_atoms
+                varyNames = ['%d::dA%s:%d'%(pId,ip,aId) for ip in ['x','y','z']]
+                varyNames += ['%d::dA%s:%d'%(pId,ip,bId[0]) for ip in ['x','y','z']]
+                varyNames += ['%d::dA%s:%d'%(pId,ip,bId[1]) for ip in ['x','y','z']]
+                VCoV = G2mth.getVCov(varyNames,varyList,data[name]['covMatrix'])
+                esdList.append(np.sqrt(np.inner(derivs,np.inner(VCoV,derivs.T)) ))
+            else:
+                derivs = np.array(
+                    [EvalPSvarDeriv(calcobj,parmDict.copy(),sampleDict[name],var,ESD)
+                     for var,ESD in zip(varyList,sigs)])
+                esdList.append(np.sqrt(
+                    np.inner(derivs,np.inner(data[name]['covMatrix'],derivs.T)) ))
             PSvarDict = parmDict.copy()
             PSvarDict.update(sampleDict[name])
@@ -3471 +3490 @@
             calcobj.UpdateDict(PSvarDict)
             valList.append(calcobj.EvalExpression())
-            if calcobj.su is not None: esdList[-1] = calcobj.su
+#            if calcobj.su is not None: esdList[-1] = calcobj.su
         if not esdList:
             esdList = None

trunk/GSASIImath.py ¶

@@ -1528 +1528 @@
 #    GSASIIpath.IPyBreak()
     return dist    
+    
+def CalcDistDeriv(distance_dict, distance_atoms, parmDict):
+    if not len(parmDict):
+        return None
+    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']
+    Tunit = distance_dict['cellNo']
+    SGData = distance_dict['SGData']    
+    deriv = getDistDerv(Oxyz,Txyz,Amat,Tunit,symNo,SGData)
+    return deriv
    
-def CalcDistSu(distance_dict, distance_atoms, parmDict,covData={}):
-    '''default doc string
-    
-    :param type name: description
-    
-    :returns: type name: description
-    
-    '''
-    sig = 0.001
-    
-    return sig
-
 def CalcAngle(angle_dict, angle_atoms, parmDict):
     if not len(parmDict):
@@ -1573 +1577 @@
     return angle
 
-def CalcAngleSu(angle_dict, angle_atoms, parmDict,covData={}):
-    '''default doc string
-    
-    :param type name: description
-    
-    :returns: type name: description
-    
-    '''
-    sig = 0.5
-    
-    return sig
+def CalcAngleDeriv(angle_dict, angle_atoms, parmDict):
+    if not len(parmDict):
+        return None
+    pId = angle_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']
+    Tunit = distance_dict['cellNo']
+    SGData = distance_dict['SGData']    
+    deriv = getDistDerv(Oxyz,Txyz,Amat,Tunit,symNo,SGData)
+    return deriv
 
 def getSyXYZ(XYZ,ops,SGData):