RB fixes

Author: vondreele

GSASII/GSASIIdataGUI.py

@@ -7684,8 +7684,8 @@ def _makemenu():     # routine to create menu when first used
                 'Locate rigid body in structure mapping to existing atoms')
             self.RigidBodiesEdit.Append(G2G.wxID_AUTOFINDRESRB,'Auto find residues',
                 'Auto find of residue RBs in macromolecule')
-            self.RigidBodiesEdit.Append(G2G.wxID_COPYRBPARMS,'Copy rigid body parms',
-                'Copy rigid body location & TLS parameters')
+            self.RigidBodiesEdit.Append(G2G.wxID_COPYRBPARMS,'Duplicate rigid body parms',
+                'Duplicate rigid body location & TLS parameters')
             self.RigidBodiesEdit.Append(G2G.wxID_GLOBALTHERM,'Global thermal motion',
                 'Global setting of residue thermal motion models')
             self.RigidBodiesEdit.Append(G2G.wxID_GLOBALRESREFINE,'Global residue refine',

GSASII/GSASIImath.py

@@ -1364,7 +1364,8 @@ def QsymAxis(Q,symAxis):
     if symAxis is None:
         return Q
     a,v = Q2AV(Q)
-    symaxis = np.array(symAxis)
+    v = vnorm(v)
+    symaxis = vnorm(np.array(symAxis))
     vdotsym = min(1.0,max(-1.0,np.vdot(v,symaxis)))
     if vdotsym in [-1.0,1.0]:   #Q, symAxis parallel/antiparallel
         return Q
@@ -1426,6 +1427,7 @@ def UpdateRBXYZ(Bmat,RBObj,RBData,RBType):
         XYZ = [np.array(RBObj['Orig'][0]),]
         return XYZ,Cart
     # if symmetry axis is defined, place symmetry axis along quaternion
+    RBRes['symAxis'] = RBRes.get('symAxis',[0,0,1])
     Q = QsymAxis(RBObj['Orient'][0],RBRes['symAxis'])
     XYZ = np.zeros_like(Cart)
     for i,xyz in enumerate(Cart):
@@ -1480,7 +1482,7 @@ def UpdateRBUIJ(Bmat,Cart,RBObj):
                 S[0]*X[1]-S[1]*X[2]+S[7]*X[0]
             Umat = G2lat.U6toUij(U)
             Umat = np.inner(np.inner(QMat,Umat),QMat)
-            beta = np.inner(np.inner(Bmat,Umat),Bmat)
+            beta = np.inner(np.inner(Bmat.T,Umat),Bmat.T)
             Uout.append(['A',0.0,]+list(G2lat.UijtoU6(beta)*gvec))
         else:
             Uout.append(['N',])

GSASII/GSASIIphsGUI.py

@@ -9665,6 +9665,8 @@ def OnThermval(invalid,value,tc):
                         data['Atoms'][AtLookUp[Id]][cia+1] = Uout[i][1]
                     else:
                         data['Atoms'][AtLookUp[Id]][cia+2:cia+8] = Uout[i][2:8]
+                data['Drawing']['Atoms'] = []
+                UpdateDrawAtoms(G2frame,data)
                 G2plt.PlotStructure(G2frame,data)
 
             def OnTLSRef(event):
@@ -9724,13 +9726,18 @@ def ApplyAV(A,V):
                 if not any(Q):
                     raise ValueError
                 RBObj['Orient'][0] = Q
-                if rbType != 'Spin':
-                    newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
+                if rbType != 'Spin':                    
+                    newXYZ,Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)
+                    Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj)
                     maxFrac = 0.0
-                    for Id in RBObj['Ids']:
+                    for i,Id in enumerate(RBObj['Ids']):
                         maxFrac = max(maxFrac,data['Atoms'][AtLookUp[Id]][cx+3])
                     for i,Id in enumerate(RBObj['Ids']):
                         data['Atoms'][AtLookUp[Id]][cx:cx+3] = newXYZ[i]
+                        if Uout[i][0] == 'I':
+                            data['Atoms'][AtLookUp[Id]][cia+1] = Uout[i][1]
+                        else:
+                            data['Atoms'][AtLookUp[Id]][cia+2:cia+8] = Uout[i][2:8]
                         data['Atoms'][AtLookUp[Id]][cx+3] = maxFrac
                     data['Atoms'] = G2lat.RBsymCheck(data['Atoms'],ct,cx,cs,AtLookUp,Amat,RBObj['Ids'],SGData)
 
@@ -10553,10 +10560,10 @@ def RepaintRBInfo(rbType,rbIndx,Scroll=0):
 
     def OnRBCopyParms(event):
         RBObjs = []
-        for rbType in ['Vector','Residue']:
+        for rbType in ['Vector',]:
             RBObjs += data['RBModels'].get(rbType,[])
         if not len(RBObjs):
-            print ('**** ERROR - no rigid bodies defined ****')
+            print ('**** ERROR - only allowed for defined Vector rigid bodies ****')
             return
         if len(RBObjs) == 1:
             print ('**** INFO - only one rigid body defined; nothing to copy to ****')
@@ -10565,19 +10572,19 @@ def OnRBCopyParms(event):
         sourceRB = {}
         for RBObj in RBObjs:
             Source.append(RBObj['RBname'])
-        dlg = wx.SingleChoiceDialog(G2frame,'Select source','Copy rigid body parameters',Source)
+        dlg = wx.SingleChoiceDialog(G2frame,'Select source','Duplicate rigid body parameters',Source)
         if dlg.ShowModal() == wx.ID_OK:
             sel = dlg.GetSelection()
             for item in ['Orig','Orient','ThermalMotion','AtomFract']:
                 sourceRB.update({item:RBObjs[sel][item],})
         dlg.Destroy()
         if not sourceRB:
             return
-        dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Copy rigid body parameters',Source)
+        dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Duplicate rigid body parameters',Source)
         if dlg.ShowModal() == wx.ID_OK:
             sel = dlg.GetSelections()
             for x in sel:
-                RBObjs[x].update(copy.copy(sourceRB))
+                RBObjs[x].update(copy.copy(sourceRB))   #NB: this duplicates the objects; not make independent copies!
         G2plt.PlotStructure(G2frame,data)
         wx.CallAfter(FillRigidBodyGrid,True)
 
@@ -11581,6 +11588,7 @@ def OnRBRemoveAll(event):
         RBData = G2frame.GPXtree.GetItemPyData(
             G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies'))
         for RBType in ['Vector','Residue','Spin']:
+            RBData[RBType] = RBData.get(RBType,[])
             for rbId in RBData[RBType]:
                 RBData[RBType][rbId]['useCount'] = 0
         FillRigidBodyGrid(True)