Changeset 4427

Timestamp:

May 20, 2020 7:33:57 PM (4 years ago)

Author:

vondreele

Message:

fullrmc fixes

Location:

trunk

Files:

• GSASIIphsGUI.py (modified) (13 diffs)
• GSASIIpwd.py (modified) (6 diffs)

trunk/GSASIIphsGUI.py

@@ -4366 +4366 @@
                 atSeq = RMCPdict['atSeq']
                 lenA = len(atSeq)
-                for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA)] for i in range(lenA)]:
+                for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA) if 'Va' not in atSeq[j]] for i in range(lenA) if 'Va' not in atSeq[i]]:
                     Pairs += pair
                 RMCPdict['Pairs'] = {pairs:[0.0,0.0,0.0] for pairs in Pairs}
@@ -4407 +4407 @@
                 for itype in range(nTypes):
                     atmChoice.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['Oxid'][itype],1,min=0.),0,WACV)
-            atmChoice.Add(wx.StaticText(G2frame.FRMC,label=' Set max shift: '),0,WACV)
-            for iType in range(nTypes):
-                atId = RMCPdict['atSeq'][iType]
-                atmChoice.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['aTypes'],atId,min=0.,max=1.),0,WACV)
+            if G2frame.RMCchoice == 'RMCProfile':
+                atmChoice.Add(wx.StaticText(G2frame.FRMC,label=' Set max shift: '),0,WACV)
+                for iType in range(nTypes):
+                    atId = RMCPdict['atSeq'][iType]
+                    atmChoice.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['aTypes'],atId,min=0.,max=1.),0,WACV)
             return atmChoice
         
@@ -4577 +4578 @@
                         corrChk.Bind(wx.EVT_CHECKBOX,OnCorrChk)
                         fileSizer.Add(corrChk,0,WACV)
-                        delBtn = wx.Button(G2frame.FRMC,label='Delete')
-                        delBtn.Bind(wx.EVT_BUTTON,OnDelBtn)
-                        Indx[delBtn.GetId()] = fil
-                        fileSizer.Add(delBtn,0,WACV)
+                    delBtn = wx.Button(G2frame.FRMC,label='Delete')
+                    delBtn.Bind(wx.EVT_BUTTON,OnDelBtn)
+                    Indx[delBtn.GetId()] = fil
+                    fileSizer.Add(delBtn,0,WACV)
                 else:
                     RMCPdict['files'][fil][0] = 'Select'
@@ -4630 +4631 @@
                 lenA = len(atSeq)
                 Pairs= []
-                for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA)] for i in range(lenA)]:
+                for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA) if 'Va' not in atSeq[j]] for i in range(lenA) if 'Va' not in atSeq[i]]:
                     Pairs += pair
                 Pairs = {pairs:[0.0,0.0,0.0] for pairs in Pairs}
@@ -4715 +4716 @@
                 finally:
                     dlg.Destroy()
+                wx.CallAfter(UpdateRMC)
                 
             def OnAddAngle(event):
@@ -4741 +4743 @@
                 
                 Indx = {}
-                atChoice = RMCPdict['atSeq']
+                atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm]
                 angleSizer = wx.FlexGridSizer(6,5,5)
                 fxcnLabels = [' ','Atom-A','Atom-B','Atom-C',' min angle',' max angle']
@@ -4778 +4780 @@
                 
                 Indx = {}
+                atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm]
                 torsionSizer = wx.FlexGridSizer(11,5,5)
                 fxcnLabels = [' ','Atom-A','Atom-B','Atom-C','Atom-D',' min angle1',' max angle1',' min angle2',' max angle2',' min angle3',' max angle3']
@@ -4788 +4791 @@
                     torsionSizer.Add(delBtn,0,WACV)
                     for i in [0,1,2,3]:
-                        atmSel = wx.ComboBox(G2frame.FRMC,choices=atNames,style=wx.CB_DROPDOWN|wx.TE_READONLY)
+                        atmSel = wx.ComboBox(G2frame.FRMC,choices=atChoice,style=wx.CB_DROPDOWN|wx.TE_READONLY)
                         atmSel.SetStringSelection(torsion[i])
                         atmSel.Bind(wx.EVT_COMBOBOX,OnTorsionAtSel)
@@ -4935 +4938 @@
                 lenA = len(atSeq)
                 Pairs= []
-                for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA)] for i in range(lenA)]:
+                for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA) if 'Va' not in atSeq[j]] for i in range(lenA) if 'Va' not in atSeq[i]]:
                     Pairs += pair
                 Pairs = {pairs:[0.0,0.0,0.0] for pairs in Pairs}
                 BVSpairs = []
                 if lenA > 1:
-                    for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i+1,lenA)] for i in range(lenA)]:
+                    for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i+1,lenA)] for i in range(lenA)] and 'Va' not in pair:
                         BVSpairs += pair
                 BVS = {pairs:[0.0,0.0,0.0,0.0] for pairs in BVSpairs}
@@ -5077 +5080 @@
                 
                 fxcnSizer = wx.FlexGridSizer(8,5,5)
-                atChoice = RMCPdict['atSeq']
+                atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm]
                 fxcnLabels = [' ','Atom-1','Atom-2','min dist','max dist','CN','fraction','weight']
                 for lab in fxcnLabels:
@@ -5113 +5116 @@
                                
                 avcnSizer = wx.FlexGridSizer(7,5,5)
-                atChoice = RMCPdict['atSeq']
+                atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm]
                 fxcnLabels = [' ','Atom-1','Atom-2','min dist','max dist','CN','weight']
                 for lab in fxcnLabels:
@@ -5150 +5153 @@
                     RMCPdict['ReStart'][1] = True
                 
-                atChoice = RMCPdict['atSeq']
+                atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm]
                 angleSizer = wx.FlexGridSizer(8,5,5)
                 fxcnLabels = [' ','Atom-A','Atom-B','Atom-C',' ABC angle','AB dist','BC dist','potential']
@@ -5188 +5191 @@
                     RMCPdict['ReStart'][1] = True
                 
-                atChoice = RMCPdict['atSeq']
+                atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm]
                 bondSizer = wx.FlexGridSizer(5,5,5)
                 fxcnLabels = [' ','Atom-A','Atom-B',' AB dist','potential']

trunk/GSASIIpwd.py

@@ -2509 +2509 @@
         nbrs = G2mth.FindAllNeighbors(Phase,FrstName,list(AtDict.keys()),notName=notNames,Short=True)[0]
         Atyp1 = AtDict[FrstName]
+        if 'Va' in Atyp1:
+            continue
         for nbr in nbrs:
             Atyp2 = AtDict[nbr[0]]
+            if 'Va' in Atyp2:
+                continue
             try:
                 bndData = Pairs[' %s-%s'%(Atyp1,Atyp2)][1:]
@@ -2614 +2618 @@
 # fullrmc imports (all that are potentially useful)
 import numpy as np
+import time
 from fullrmc.sincConvolution import sincConvolution
 from fullrmc.Globals import LOGGER
@@ -2635 +2640 @@
 from fullrmc.debugStuff import *
 InvokeDebugOpts()
+time0 = time.time()
 SwapGen = {}
 # engine setup\n'''
@@ -2743 +2749 @@
         rundata += '        ENGINE.run(restartPdb="%s",numberOfSteps=10000*(1.-sProb), saveFrequency=1000)\n'%restart
     rundata += 'ENGINE.close()\n'
+    rundata += 'print("ENGINE run time %.2f s"%(time.time()-time0))\n'
     rfile = open(rname,'w')
     rfile.writelines(rundata)
@@ -2755 +2762 @@
     Dups,Fracs = findDup(Phase['Atoms'])
     Sfracs = [np.cumsum(fracs) for fracs in Fracs]
+    ifSfracs = np.any(np.array(Sfracs)-1.)
     Supercell = RMCPdict['SuperCell']
     Cell = generalData['Cell'][1:7]
@@ -2764 +2772 @@
     Atoms = newPhase['Atoms']
 
-    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 = []
-    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:
-                    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:
+                                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
 
     XYZ = np.array([atom[3:6] for atom in Natoms]).T