fix sytSym calculation in GenAtm

Author: vondreele

GSASII/GSASIIphsGUI.py

@@ -9806,6 +9806,7 @@ def OnOrigX(invalid,value,tc):
                 for i,Id in enumerate(RBObj['Ids']):
                     data['Atoms'][AtLookUp[Id]][cx:cx+3] = newXYZ[i]
                     data['Atoms'][AtLookUp[Id]][cx+3] = maxFrac
+                    data['Atoms'][AtLookUp[Id]][cs,cs+2] = G2spc.SytSym(newXYZ[i],SGData)[:2]
                 data['Atoms'] = G2lat.RBsymCheck(data['Atoms'],ct,cx,cs,AtLookUp,Amat,RBObj['Ids'],SGData)
                 data['Drawing']['Atoms'] = []
                 UpdateDrawAtoms(G2frame,data)
@@ -9824,6 +9825,7 @@ def ApplyAV(A,V):
                         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]
+                        data['Atoms'][AtLookUp[Id]][cs:cs+2] = G2spc.SytSym(newXYZ[i],SGData)[:2]
                         if Uout[i][0] == 'I':
                             data['Atoms'][AtLookUp[Id]][cia+1] = Uout[i][1]
                         else:

GSASII/GSASIIspc.py

@@ -2202,7 +2202,7 @@ def GenAtom(XYZ,SGData,All=False,Uij=[],Move=True):
         inv = 1
     SpnFlp = SGData.get('SpnFlp',[])
     spnflp = []
-    X = np.array(XYZ)
+    X = np.round(np.array(XYZ),6)
     mj = 0
     for ic,cen in enumerate(icen):
         C = np.array(cen)
@@ -2223,10 +2223,12 @@ def GenAtom(XYZ,SGData,All=False,Uij=[],Move=True):
                 else:
                     newX = XT
                 if All:
-                    if np.allclose(newX,X,atol=0.0002):     #do we want %1. here?
+                    newX = np.round(newX,6)
+#                    if np.sqrt(np.sum(np.round(newX%1.,6)**2-np.round(X%1.,6)**2)) < 1.e-6:
+                    if np.allclose(newX,X,atol=2.e-5):     #do we want %1. here?
                         idup = False
                 else:
-                    if True in [np.allclose(newX%1.,oldX%1.,atol=0.0002) for oldX in XYZEquiv]:
+                    if True in [np.allclose(newX%1.,oldX%1.,atol=2.e-5) for oldX in XYZEquiv]:
                         idup = False
                 if All or idup:
                     XYZEquiv.append(newX)