Changeset 4471

Timestamp:

Jun 8, 2020 10:57:13 AM (3 years ago)

Author:

vondreele

Message:

restore FillCoordSphere? from G2 version #4379

File:

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

trunk/GSASIIphsGUI.py

@@ -1261 +1261 @@
     return neighborArray
     
-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
-
 def FindCoordination(ind,data,neighborArray,coordsArray,cmx=0,targets=None):
     'Find atoms coordinating atom ind, speed-up version'
@@ -8066 +8015 @@
         
     def FillCoordSphere(event):
+        time0 = time.time()
+        generalData = data['General']
+        Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
+        radii = generalData['BondRadii']
+        atomTypes = generalData['AtomTypes']
+        try:
+            indH = atomTypes.index('H')
+            radii[indH] = 0.5
+        except:
+            pass            
+        indx = drawAtoms.GetSelectedRows()
+        if indx:
+            indx.sort()
+            atomData = data['Drawing']['Atoms']
+            numAtoms = len(atomData)
+            cx,ct,cs,ci = data['Drawing']['atomPtrs']
+            cij = ci+2
+            SGData = generalData['SGData']
+            cellArray = G2lat.CellBlock(1)
+            nind = len(indx)
+            pgbar = wx.ProgressDialog('Fill CN sphere for %d atoms'%nind,'Atoms done=',nind+1, 
+                style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT)
+            screenSize = wx.ClientDisplayRect()
+            Size = pgbar.GetSize()
+            if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0
+                pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x
+                pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
+            for Ind,ind in enumerate(indx):
+                atomA = atomData[ind]
+                xyzA = np.array(atomA[cx:cx+3])
+                indA = atomTypes.index(atomA[ct])
+                for atomB in atomData[:numAtoms]:
+                    indB = atomTypes.index(atomB[ct])
+                    sumR = radii[indA]+radii[indB]
+                    xyzB = np.array(atomB[cx:cx+3])
+                    for xyz in cellArray+xyzB:
+                        dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
+                        if 0 < dist <= data['Drawing']['radiusFactor']*sumR:
+                            if noDuplicate(xyz,atomData):
+                                oprB = atomB[cs-1]
+                                C = xyz-xyzB
+                                newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
+                                newAtom = atomB[:]
+                                newAtom[cx:cx+3] = xyz
+                                newAtom[cs-1] = G2spc.StringOpsProd(oprB,newOp,SGData)
+                                atomData.append(newAtom[:cij+9])  #not SS stuff
+                GoOn = pgbar.Update(Ind,newmsg='Atoms done=%d'%(Ind))
+                if not GoOn[0]:
+                    break
+            pgbar.Destroy()   
+            data['Drawing']['Atoms'] = atomData
+            print('search time: %.3f'%(time.time()-time0))
+            UpdateDrawAtoms()
+            drawAtoms.ClearSelection()
+            G2plt.PlotStructure(G2frame,data)
+        else:
+            G2G.G2MessageBox(G2frame,'Select atoms first')
+            
+    def FillCoordSphereNew(event):
+        time0 = time.time()
         indx = getAtomSelections(drawAtoms)
         if not indx: return
@@ -8080 +8089 @@
         cx,ct,cs,ci = data['Drawing']['atomPtrs']
         colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
+        neighborArray = FindCoordinationByLabel(data)
+        coordsArray = np.array([a[cx:cx+3] for a in data['Drawing']['Atoms']])
         cmx = 0
         if 'Mx' in colLabels:
@@ -8092 +8103 @@
             pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
         for Ind,ind in enumerate(indx):
-            atomData += FindCoordination2(ind,data,cmx)
+            atomData += FindCoordination(ind,data,neighborArray,coordsArray,cmx,atomTypes)
             GoOn = pgbar.Update(Ind,newmsg='Atoms done=%d'%(Ind))
             if not GoOn[0]: break
         pgbar.Destroy()   
         data['Drawing']['Atoms'] = atomData
+        print('search time: %.3f'%(time.time()-time0))
         UpdateDrawAtoms()
         drawAtoms.ClearSelection()