Changeset 4440

Timestamp:

May 26, 2020 10:44:15 AM (3 years ago)

Author:

vondreele

Message:

fix atom draw update problem when atoms not in unit cell2Arelated fixes for RMCProfile & fullrmc big box building routines

Location:

trunk

Files:

• GSASIIlattice.py (modified) (2 diffs)
• GSASIIpwd.py (modified) (2 diffs)
• GSASIIspc.py (modified) (2 diffs)

trunk/GSASIIlattice.py

@@ -501 +501 @@
         XYZ = np.array(atom[cx:cx+3])
         xyz = XYZ
+        cellj = np.zeros(3,dtype=np.int32)
         if Force:
-            xyz %= 1.
+            xyz,cellj = G2spc.MoveToUnitCell(xyz)
         if atom[cia] == 'A':
             Uij = atom[cia+2:cia+8]
-            result = G2spc.GenAtom(xyz,SGData,False,Uij,True)
+            result = G2spc.GenAtom(xyz,SGData,False,Uij,Force)
             for item in result:
+                item = list(item)
+                item[2] += cellj
 #                if item[0][2] >= .95: item[0][2] -= 1.
                 atom[cx:cx+3] = item[0]
@@ -519 +522 @@
                 atomData.append(atom[:cia+9])  #not SS stuff
         else:
-            result = G2spc.GenAtom(xyz,SGData,False,Move=True)
+            result = G2spc.GenAtom(xyz,SGData,False,Move=Force)
             for item in result:
-                if item[0][2] >= .95: item[0][2] -= 1.
+                item = list(item)
+                item[2] += cellj
+#                if item[0][2] >= .95: item[0][2] -= 1.
                 atom[cx:cx+3] = item[0]
                 if cm:

trunk/GSASIIpwd.py

@@ -2241 +2241 @@
     GB = G2lat.cell2Gmat( newPhase['General']['Cell'][1:7])[0]
     RMCPdict['Rmax'] = np.min(np.sqrt(np.array([1./G2lat.calc_rDsq2(H,GB) for H in [[1,0,0],[0,1,0],[0,0,1]]])))/2.
-    newPhase,Atcodes = G2lat.TransformPhase(Phase,newPhase,Trans,np.zeros(3),np.zeros(3),ifMag=False,Force=False)
+    newPhase,Atcodes = G2lat.TransformPhase(Phase,newPhase,Trans,np.zeros(3),np.zeros(3),ifMag=False,Force=True)
     Natm = np.core.defchararray.count(np.array(Atcodes),'+')    #no. atoms in original unit cell
     Natm = np.count_nonzero(Natm-1)
@@ -2787 +2787 @@
     newPhase['General']['SGData'] = G2spc.SpcGroup('P 1')[1]
     newPhase['General']['Cell'][1:] = G2lat.TransformCell(Cell,Trans.T)
-    newPhase,Atcodes = G2lat.TransformPhase(Phase,newPhase,Trans,np.zeros(3),np.zeros(3),ifMag=False,Force=False)
+    newPhase,Atcodes = G2lat.TransformPhase(Phase,newPhase,Trans,np.zeros(3),np.zeros(3),ifMag=False,Force=True)
     Atoms = newPhase['Atoms']
 

trunk/GSASIIspc.py

@@ -2026 +2026 @@
     :returns: XYZ - numpy array of new coordinates now 0 or greater and less than 1
     '''
-    XYZ = (np.array(xyz)+10.)%1.
+    XYZ = np.array(xyz)%1.
     cell = np.asarray(np.rint(XYZ-xyz),dtype=np.int32)
     return XYZ,cell
@@ -2084 +2084 @@
     mj = 0
     cell0 = np.zeros(3,dtype=np.int32)
-    if Move:
-        X,cell0 = MoveToUnitCell(X)
     for ic,cen in enumerate(icen):
         C = np.array(cen)