Changeset 4435

Timestamp:

May 25, 2020 8:57:49 PM (3 years ago)

Author:

vondreele

Message:

fix MakeRMC6f for fractional atom fracs

File:

• trunk/GSASIIpwd.py (modified) (2 diffs)

trunk/GSASIIpwd.py

@@ -2230 +2230 @@
     Dups,Fracs = findDup(Phase['Atoms'])
     Sfracs = [np.cumsum(fracs) for fracs in Fracs]
+    ifSfracs = np.any(np.array(Sfracs)-1.)
     Sample = PWDdata['Sample Parameters']
     Meta['temperature'] = Sample['Temperature']
@@ -2240 +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)
+    newPhase,Atcodes = G2lat.TransformPhase(Phase,newPhase,Trans,np.zeros(3),np.zeros(3),ifMag=False,Force=False)
     Natm = np.core.defchararray.count(np.array(Atcodes),'+')    #no. atoms in original unit cell
     Natm = np.count_nonzero(Natm-1)
     Atoms = newPhase['Atoms']
-    Satoms = G2mth.sortArray(G2mth.sortArray(G2mth.sortArray(Atoms,5),4),3)
-    Datoms = [[atom for atom in Satoms if atom[0] in dup] for dup in Dups]
-    Natoms = []
     reset = False
-    for idup,dup in enumerate(Dups):
-        ldup = len(dup)
-        datoms = Datoms[idup]
-        natm = len(datoms)
-        i = 0
-        while i < natm:
-            atoms = datoms[i:i+ldup]
-            try:
-                atom = atoms[np.searchsorted(Sfracs[idup],rand.random())]
-                Natoms.append(atom)
-            except IndexError:      #what about vacancies?
-                if 'Va' not in Atseq:
-                    reset = True
-                    Atseq.append('Va')
-                    RMCPdict['aTypes']['Va'] = 0.0
-                atom = atoms[0]
-                atom[1] = 'Va'
-                Natoms.append(atom)
-            i += ldup
+    
+    if ifSfracs:
+        Natm = np.core.defchararray.count(np.array(Atcodes),'+')    #no. atoms in original unit cell
+        Natm = np.count_nonzero(Natm-1)
+        Satoms = []
+        for i in range(len(Atoms)//Natm):
+            ind = i*Natm
+            Satoms.append(G2mth.sortArray(G2mth.sortArray(G2mth.sortArray(Atoms[ind:ind+Natm],5),4),3))
+        Natoms = []
+        for satoms in Satoms:
+            for idup,dup in enumerate(Dups):
+                ldup = len(dup)
+                natm = len(satoms)
+                i = 0
+                while i < natm:
+                    if satoms[i][0] in dup:
+                        atoms = satoms[i:i+ldup]
+                        try:
+                            atom = atoms[np.searchsorted(Sfracs[idup],rand.random())]
+                            Natoms.append(atom)
+                        except IndexError:      #what about vacancies?
+                            if 'Va' not in Atseq:
+                                reset = True
+                                Atseq.append('Va')
+                                RMCPdict['aTypes']['Va'] = 0.0
+                            atom = atoms[0]
+                            atom[1] = 'Va'
+                            Natoms.append(atom)
+                        i += ldup
+                    else:
+                       i += 1
+    else:
+        Natoms = Atoms
+    
     NAtype = np.zeros(len(Atseq))
     for atom in Natoms: