Changeset 4464 for trunk

Timestamp:

Jun 5, 2020 9:32:31 AM (3 years ago)

Author:

vondreele

Message:

reinstate the old FindCoordination? as FindCoordination2 - was used in FillCoordSphere?; new one incompatible.

File:

• trunk/GSASIIphsGUI.py (modified) (4 diffs)

trunk/GSASIIphsGUI.py

@@ -1261 +1261 @@
     return neighborArray
     
-# def FindCoordination(ind,data,cmx=0,targets=None):
-#     'Find atoms coordinating atom ind, somewhat faster version'
-#     time1 = time.time()
-#     generalData = data['General']
-#     Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
-#     atomTypes,radii = getAtomRadii(data)
-#     atomData = data['Drawing']['Atoms']
-#     numAtoms = len(atomData)
-#     cx,ct,cs,ci = data['Drawing']['atomPtrs']
-#     cij = ci+2
-#     SGData = generalData['SGData']
-#     cellArray = G2lat.CellBlock(1)
+def FindCoordination2(ind,data,cmx=0,targets=None):
+    'Find atoms coordinating atom ind, somewhat faster version'
+    time1 = time.time()
+    generalData = data['General']
+    Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
+    atomTypes,radii = getAtomRadii(data)
+    atomData = data['Drawing']['Atoms']
+    numAtoms = len(atomData)
+    cx,ct,cs,ci = data['Drawing']['atomPtrs']
+    cij = ci+2
+    SGData = generalData['SGData']
+    cellArray = G2lat.CellBlock(1)
     
-#     newAtomList = []
-#     atomA = atomData[ind]
-#     xyzA = np.array(atomA[cx:cx+3])
-#     indA = atomTypes.index(atomA[ct])
-#     for atomB in atomData:
-#         if targets and atomB[ct] not in targets:
-#             continue
-#         indB = atomTypes.index(atomB[ct])
-#         sumR = radii[indA]+radii[indB]
-#         xyzB = np.array(atomB[cx:cx+3])
-#         Uij = atomB[cs+5:cs+5+6]
-#         for item in G2spc.GenAtom(xyzB,SGData,False,Uij,True):
-#             atom = copy.copy(atomB)
-#             atom[cx:cx+3] = item[0]
-#             Opr = abs(item[2])%100
-#             M = SGData['SGOps'][Opr-1][0]
-#             if cmx:
-#                 opNum = G2spc.GetOpNum(item[2],SGData)
-#                 mom = np.array(atom[cmx:cmx+3])
-#                 if SGData['SGGray']:
-#                     atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)
-#                 else:    
-#                     atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum-1]
-#             atom[cs-1] = str(item[2])+'+'
-#             atom[cs+5:cs+5+6] = item[1]
-#             posInAllCells = cellArray+np.array(atom[cx:cx+3])
-#             dists = np.sqrt(np.sum(np.inner(Amat,posInAllCells-xyzA)**2,axis=0))
-#             bonded = np.logical_and(dists < data['Drawing']['radiusFactor']*sumR, dists !=0)
-#             for xyz in posInAllCells[bonded]:
-#                 if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]: continue
-#                 C = xyz-atom[cx:cx+3]+item[3]
-#                 newAtom = atom[:]
-#                 newAtom[cx:cx+3] = xyz
-#                 newAtom[cs-1] += str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
-#                 newAtomList.append(newAtom)
-#     print ('Search time: %.2fs'%(time.time()-time1))
-#     return newAtomList
+    newAtomList = []
+    atomA = atomData[ind]
+    xyzA = np.array(atomA[cx:cx+3])
+    indA = atomTypes.index(atomA[ct])
+    for atomB in atomData:
+        if targets and atomB[ct] not in targets:
+            continue
+        indB = atomTypes.index(atomB[ct])
+        sumR = radii[indA]+radii[indB]
+        xyzB = np.array(atomB[cx:cx+3])
+        Uij = atomB[cs+5:cs+5+6]
+        for item in G2spc.GenAtom(xyzB,SGData,False,Uij,True):
+            atom = copy.copy(atomB)
+            atom[cx:cx+3] = item[0]
+            Opr = abs(item[2])%100
+            M = SGData['SGOps'][Opr-1][0]
+            if cmx:
+                opNum = G2spc.GetOpNum(item[2],SGData)
+                mom = np.array(atom[cmx:cmx+3])
+                if SGData['SGGray']:
+                    atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)
+                else:    
+                    atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum-1]
+            atom[cs-1] = str(item[2])+'+'
+            atom[cs+5:cs+5+6] = item[1]
+            posInAllCells = cellArray+np.array(atom[cx:cx+3])
+            dists = np.sqrt(np.sum(np.inner(Amat,posInAllCells-xyzA)**2,axis=0))
+            bonded = np.logical_and(dists < data['Drawing']['radiusFactor']*sumR, dists !=0)
+            for xyz in posInAllCells[bonded]:
+                if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]: continue
+                C = xyz-atom[cx:cx+3]+item[3]
+                newAtom = atom[:]
+                newAtom[cx:cx+3] = xyz
+                newAtom[cs-1] += str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
+                newAtomList.append(newAtom)
+    print ('Search time: %.2fs'%(time.time()-time1))
+    return newAtomList
 
 def FindCoordination(ind,data,neighborArray,coordsArray,cmx=0,targets=None):
@@ -8018 +8018 @@
         if 'Mx' in colLabels:
             cmx = colLabels.index('Mx')
-        SGData = generalData['SGData']
-        cellArray = G2lat.CellBlock(1)
         neighborArray = FindCoordinationByLabel(data)
 
@@ -8036 +8034 @@
         added = 0
         targets = [item for item in atomTypes if params[item]]
+        cx,ct,cs,ci = getAtomPtrs(data,draw=True)      
         for rep in range(params['maxrep']):
             startlen = len(data['Drawing']['Atoms'])
-            coordsArray = np.array([a[cx:cx+3] for a in atomData])
+            coordsArray = np.array([a[cx:cx+3] for a in data['Drawing']['Atoms']])
             addedAtoms = []
             for Ind,ind in enumerate(indx):
@@ -8091 +8090 @@
             pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
         for Ind,ind in enumerate(indx):
-            atomData += FindCoordination(ind,data,cmx)
+            atomData += FindCoordination2(ind,data,cmx)
             GoOn = pgbar.Update(Ind,newmsg='Atoms done=%d'%(Ind))
             if not GoOn[0]: break