Merge remote-tracking branch 'origin/main' into TOFgroup

Author: briantoby

.notes/.linenoteplus

@@ -0,0 +1,5 @@
+# The location of this `.linenoteplus` file determines
+# the path to store and retrieve your notes.
+
+# To relocate your notes, simply move or rename 
+# the directory that contains this `.linenoteplus` file.

GSASII/GSASIIpath.py

@@ -2160,6 +2160,15 @@ def openInNewTerm(project=None,g2script=None,pythonapp=sys.executable):
         lastver = sorted([t for t in taglist if 'v' in t])[-1]
         lastnum = sorted([t for t in taglist if 'v' not in t],key=int)[-1]
         #print('tags=',lastver,lastnum)
+        # make directory for config file if needed
+        localdir = os.path.expanduser(os.path.normpath('~/.GSASII'))
+        if not os.path.exists(localdir):
+            try:
+                os.mkdir(localdir)
+                print(f'Created directory {localdir}')
+            except Exception as msg:
+                print(f'Error trying to create directory {localdir}\n{msg}')
+                sys.exit()
         # add tag info to config file
         import configparser
         cfgfile = os.path.expanduser(os.path.normpath('~/.GSASII/config.ini'))

GSASII/GSASIIphsGUI.py

@@ -6388,8 +6388,12 @@ def RunRMCProfile(event):
             ascript_file = os.path.join(os.getcwd(), "runrmc.script")
             with open(ascript_file, 'w') as f:
                 f.write('tell application "Terminal"\n')
-                f.write(f'''  do script "echo 'Running RMCprofile'"\n''')
+                f.write('  if not (exists window 1) then\n')
+                f.write(f'    do script "bash {script_file}"\n')
+                f.write('  else\n')
                 f.write(f'  do script "bash {script_file}" in window 1\n')
+                f.write('  end if\n')
+                f.write('  activate\n')
                 f.write("end tell\n")
             subp.Popen(['osascript', ascript_file])
         elif sys.platform.startswith("linux"):
@@ -6607,8 +6611,12 @@ def OnViewRMC(event):
             generalData = data['General']
             RMCPdict = data['RMC']['RMCProfile']
             pName = generalData['Name'].replace(' ','_')
+            if sys.platform == "darwin":
+               wildcard = 'RMCProfile result csv files|' + pName + '*.csv' + '|All files|*.*'
+            else:
+               wildcard = 'RMCProfile result csv files|' + pName + '*.csv'
             dlg = wx.FileDialog(G2frame, "Choose any RMCProfile csv results file for "+pName+":",
-                defaultDir=G2frame.LastGPXdir,style=wx.FD_CHANGE_DIR,wildcard='RMCProfile result csv files|'+pName+'*.csv')
+                defaultDir=G2frame.LastGPXdir,style=wx.FD_CHANGE_DIR,wildcard=wildcard)
             if dlg.ShowModal() == wx.ID_OK:
                 path = os.path.split(dlg.GetPath())[0]
                 dlg.Destroy()
@@ -6631,8 +6639,9 @@ def OnViewRMC(event):
                       '_SQ1partials.csv':[],'_SQ2partials.csv':[],'_FQ1.csv':[],'_FT_XFQ1.csv':[],
                       '_FQ1partials.csv':[],'_bragg.csv':[],'.chi2':[]}
             for item in files:
-                if os.path.exists(os.path.join(path,pName+item)):
-                    OutFile = open(pName+item,'r')
+                fileName = os.path.join(path,pName+item)
+                if os.path.exists(fileName):
+                    OutFile = open(fileName,'r')
                     files[item] = OutFile.readlines()
                     OutFile.close()
                     print('RMCProfile file %s read'%(pName+item))
@@ -9094,7 +9103,7 @@ def SelDeformAtom(event):
                             #     orbDict.update(cofTerms)
                             #     orbDict.update({'Ne':[float(orbs[orb]['Ne']),False]})
                             #     data['Deformations'][Ids[indx]].append([orb,orbDict])
-                data['Deformations'][-Ids[indx]] = {'U':'X','V':'Y','UVmat':np.eye(3),
+                data['Deformations'][-Ids[indx]] = {'U':'X','V':'Y','UVmat':np.eye(3),'PtGrp':'1',
                     'MUV':"A: X'=U, Y'=(UxV)xU & Z'=UxV",'Radial':radial,'fxchoice':fxchoice}
         dlg.Destroy()
         if not len(indxes):

GSASII/GSASIIphsGUI2.py

@@ -314,8 +314,9 @@ def NeSizer(deformation,orbSizer,dId,orb,Indx):
         Indx[Tcheck.GetId()] = [dId,iorb,'Ne']
         orbSizer.Add(Tcheck)
 
-    def Dsizer(deformation,orbSizer,dId,orb,Indx):
-        orbSizer.Add(wx.StaticText(deformation,label=item+':'))
+    def Dsizer(deformation,orbSizer,Names,dId,orb,Indx):
+        name = Names.get(item,'') #Names only go to order = 3
+        orbSizer.Add(wx.StaticText(deformation,label=item+name+':'))
         orbSizer.Add(G2G.ValidatedTxtCtrl(deformation,orb[1][item],0,nDig=(8,5),xmin=-1.,xmax=1.))
         Tcheck = wx.CheckBox(deformation,-1,'Refine?')
         Tcheck.SetValue(orb[1][item][1])
@@ -506,6 +507,10 @@ def OnAtCol(event):
             oriSizer.Add(delHarm,0,WACV)
         mainSizer.Add(oriSizer)
         G2G.HorizontalLine(mainSizer,deformation)
+        Names = {'D(1,-1)':'px','D(1,0)':'pz','D(1,1)':'py',
+                 'D(2,-2)':'dxy','D(2,-1)':'dxz','D(2,0)':'dz2','D(2,1)':'dyz','D(2,2)':'dx2-y2',
+                 'D(3,-3)':'fy(3x2-y2)','D(3,-2)':'fz(x2-y2)','D(3,-1':'fyz2','D(3,0)':'fz3',
+                 'D(3,1)':'fxz2','D(3,2)':'fxyz','D(3,3)':'fy(3x2-y2)',}
         mainSizer.Add(wx.StaticText(deformation,label=' Deformation parameters:'))
         orbSizer = wx.FlexGridSizer(0,9,2,2)
         for iorb,orb in enumerate(deformationData[dId]):
@@ -529,7 +534,7 @@ def OnAtCol(event):
                 for item in orb[1]:
                     if 'D' in item:                            
                         nItem += 1
-                        Dsizer(deformation,orbSizer,dId,orb,Indx)
+                        Dsizer(deformation,orbSizer,Names,dId,orb,Indx)
                         if nItem in [2,4,6,8,10]:
                             for i in range(3): orbSizer.Add((5,5),0)
                 for i in range(3): orbSizer.Add((5,5),0)
@@ -551,7 +556,7 @@ def OnAtCol(event):
                             if nItems:
                                 nB = 9-nItems
                                 for i in range(nB): orbSizer.Add((5,5),0)
-                        Dsizer(deformation,orbSizer,dId,orb,Indx)
+                        Dsizer(deformation,orbSizer,Names,dId,orb,Indx)
         mainSizer.Add(orbSizer)    
 
     G2phsG.SetPhaseWindow(deformation,mainSizer)

GSASII/GSASIIplot.py

@@ -3523,8 +3523,8 @@ def PlotDeform(G2frame,general,atName,atType,deform,UVmat,radial,neigh):
     RAP = G2mth.Cart2Polar(XYZ[0],XYZ[1],XYZ[2])
     P  = np.zeros((31,31))
     for shc in SHC:
-        p = 2.*SHC[shc][0]*SHC[shc][2]**3*G2lat.KslCalc(shc,RAP[1],RAP[2]).reshape((31,31))
-        P += p**2
+        p = 2.*SHC[shc][0]*SHC[shc][2]**3*(G2lat.KslCalc(shc,RAP[1],RAP[2])**2).reshape((31,31))
+        P += p
     if not np.any(P):
         P = np.ones((31,31))
 #    P *= P
@@ -7351,22 +7351,23 @@ def Draw(caller='',Fade=[],NPkey=False):
                     #### put deformation texture on sphere here
                     if atom[ci] in deformationData:
                         defCtrls = deformationData[-atom[ci]]
-                        defParms = deformationData[atom[ci]]
-                        SytSym = G2spc.SytSym(atom[cx:cx+3],SGData)[0]
                         if defCtrls.get('showDef',False) and defCtrls['Radial'] == 'Slater':
                             useAtColor = defCtrls.get('atColor',True) 
                             atcolor = None
                             if useAtColor:
                                 atcolor = atColor*255
+                            defParms = deformationData[atom[ci]]
+                            SytSym = G2spc.SytSym(atom[cx:cx+3],SGData)[0]
+                            SGM = np.array(G2spc.GetOpFromCode(atom[cs-1],SGData)[0])
                             SHC = defParms[0][1]
                             SHC = {item.replace('D','C'):SHC[item] for item in SHC if item not in ['Ne','kappa']}
-                            UVMat = defCtrls['UVmat']
+                            UVMat = np.inner(defCtrls['UVmat'],SGM)
                             Npsi,Ngam = 90,45 
                             PSI,GAM = np.mgrid[0:Npsi,0:Ngam]   #[azm,pol]
-                            PSI = PSI.flatten()*360./Npsi  #azimuth 0-360 ncl
+                            PSI = PSI.flatten()*360./Npsi  #azimuth 0-360 incl
                             GAM = GAM.flatten()*180./Ngam  #polar 0-180 incl
-                            Rp,PSIp,GAMp = G2mth.RotPolbyM(np.ones_like(PSI),PSI,GAM,UVMat)
-                            P = G2lat.SHarmcal(SytSym,SHC,PSIp,GAMp).reshape((Npsi,Ngam))
+                            Rp,PSIp,GAMp = G2mth.RotPolbyM(np.ones_like(PSI),PSI,GAM,UVMat) #TODO: needs symmetry operation for equiv. positions
+                            P = G2lat.SHarmcal(SytSym,SHC,PSIp,GAMp).reshape((Npsi,Ngam))**2
                             if np.min(P) < np.max(P):
                                 P = (P-np.min(P))/(np.max(P)-np.min(P))
                             RenderTextureSphere(x,y,z,radius,atcolor,shape=[Npsi,Ngam],Texture=P.T,ifFade=False)

GSASII/GSASIIpwd.py

@@ -3431,7 +3431,7 @@ def MakeRMCPdat(PWDdata,Name,Phase,RMCPdict):
     dMin = refList[-1][4]
     gsasType = 'xray2'
     if 'T' in inst['Type'][1]:
-        gsasType = 'gsas3'
+        gsasType = 'gsas3_new'
     elif 'X' in inst['Type'][1]:
         XFF = G2elem.GetFFtable(Atseq)
         Xfl = open(Name+'.xray','w')

GSASII/GSASIIrmcGUI.py

@@ -226,13 +226,14 @@ def OnFileSel(event):
                 style=wx.FD_OPEN ,wildcard=fil+'(*.*)|*.*')
             if dlg.ShowModal() == wx.ID_OK:
                 fpath,fName = os.path.split(dlg.GetPath())
-                if os.path.exists(fName): # is there a file by this name in the current directory?
+                if os.path.exists(os.path.join(G2frame.LastGPXdir,fName)): # is there a file by this name in the current directory?
                     RMCPdict['files'][fil][0] = fName
                 else: # nope, copy it
                     # TODO: is G2frame.LastGPXdir the right choice here or
                     #       do I want the current working directory (same?)
                     shutil.copy(dlg.GetPath(), os.path.join(G2frame.LastGPXdir,fName))
-                if not os.path.exists(fName): # sanity check
+                    RMCPdict['files'][fil][0] = fName
+                if not os.path.exists(os.path.join(G2frame.LastGPXdir,fName)): # sanity check
                     print(f'Error: file {fName} not found in .gpx directory ({G2frame.LastGPXdir})')
                     return
                 G2frame.LastImportDir = fpath    #set so next file is found in same place
@@ -260,7 +261,10 @@ def OnFileSel(event):
         def OnFileFormat(event):
             Obj = event.GetEventObject()
             fil = Indx[Obj.GetId()]
-            RMCPdict['files'][fil][3] = Obj.GetStringSelection()
+            Fmt = Obj.GetStringSelection()
+            RMCPdict['files'][fil][3] = Fmt
+            if 'PDF' in Fmt:
+                RMCPdict['files'][fil][2] = 'G(r)P'
 
         def OnPlotBtn(event):
             Obj = event.GetEventObject()
@@ -270,7 +274,7 @@ def OnPlotBtn(event):
             XY = np.empty((1,2))
             while XY.shape[0] == 1:
                 try:
-                    XY = np.loadtxt(fileItem[0],skiprows=start)
+                    XY = np.loadtxt(os.path.join(G2frame.LastGPXdir,fileItem[0]),skiprows=start)
                 except ValueError:
                     start += 1
                     if start > 500:     #absurd number of header lines!
@@ -345,7 +349,7 @@ def OnSeqReverse(event):
             mainSizer.Add(topSizer)
             Heads = ['Name','File','type','Plot','Delete']
             fileSizer = wx.FlexGridSizer(5,5,5)
-            Formats = ['RMC','GUDRUN','STOG']
+            Formats = ['RMC','GUDRUN','STOG','PDFGET']
             for head in Heads:
                 fileSizer.Add(wx.StaticText(G2frame.FRMC,label=head),0,WACV)
             for fil in RMCPdict['files']:
@@ -411,7 +415,7 @@ def OnSeqReverse(event):
         if G2frame.RMCchoice == 'PDFfit' and RMCPdict['refinement'] == 'sequential':
 
             def OnAddPDF(event):
-                ''' Add PDF G(r)s while maintanining original sequence
+                ''' Add PDF G(r)s while maintaining original sequence
                 '''
                 usedList = RMCPdict['seqfiles']
                 PDFlist = [item[1:][0] for item in G2frame.GetFileList('PDF')]
@@ -534,7 +538,7 @@ def OnSetVal(event):
         # RMCProfile & PDFfit (Normal)
         Heads = ['Name','File','Format','Weight','Plot','Delete']
         fileSizer = wx.FlexGridSizer(6,5,5)
-        Formats = ['RMC','GUDRUN','STOG']
+        Formats = ['RMC','GUDRUN','STOG','PDFGET']
         for head in Heads:
             fileSizer.Add(wx.StaticText(G2frame.FRMC,label=head),0,WACV)
         for fil in RMCPdict['files']:
@@ -547,11 +551,13 @@ def OnSetVal(event):
             Indx[filSel.GetId()] = fil
             fileSizer.Add(filSel,0,WACV)
             nform = 3
+            if 'G(r)' in fil:
+                nform = 4
             Name = 'Ndata'
             if 'Xray' in fil:
                 nform = 1
                 Name = 'Xdata'
-            if Rfile and os.path.exists(Rfile): #incase .gpx file is moved away from G(R), F(Q), etc. files
+            if Rfile and os.path.exists(os.path.join(G2frame.LastGPXdir,Rfile)): #incase .gpx file is moved away from G(R), F(Q), etc. files
                 fileFormat = wx.ComboBox(G2frame.FRMC,choices=Formats[:nform],style=wx.CB_DROPDOWN|wx.TE_READONLY)
                 fileFormat.SetStringSelection(RMCPdict['files'][fil][3])
                 Indx[fileFormat.GetId()] = fil

GSASII/GSASIIspc.py

@@ -1459,6 +1459,26 @@ def GetOpNum(Opr,SGData):
     opNum += cent*Nops
     return opNum
 
+def GetOpFromCode(Code,SGData):
+    "takes Sym Op code from Draw Atoms table & returns space group operation details"
+    SGOps = SGData['SGOps']
+    SGCent = SGData['SGCen']
+    if '+' not in Code:
+        SymOp = Code
+        Unit = '(0,0,0)'
+    else:
+        SymOp,Unit = Code.split('+')
+    SymOp = int(SymOp)
+    opNum = abs(SymOp)%100-1
+    cent = abs(opNum)//100
+    Unit = list(eval(Unit))
+    Cent = SGCent[cent]
+    SGM,SGT = SGOps[opNum]
+    if SymOp < 0:
+        SGM *= -1
+        SGT *= -1
+    return SGM,SGT,Cent,Unit   
+
 ################################################################################
 #### Superspace group codes
 ################################################################################

GSASII/GSASIIstrMath.py

@@ -437,7 +437,7 @@ def MakeSpHarmFF(HKL,Amat,Bmat,SHCdict,Tdata,hType,FFtables,ORBtables,BLtables,F
     :param str hType: histogram type
     :param dict FFtables: x-ray form factor tables
     :param dict ORBtables: x-ray orbital form factor tables
-    :param dict BLtables: neutron scattering lenghts
+    :param dict BLtables: neutron scattering lengths
     :param array FF: form factors - will be modified by adding the spin/deformation RB spherical harmonics terms
     :param array SQ: 1/4d^2 for the HKL set
     :param bool ifDeriv: True if dFF/dcoff to be returned
@@ -580,7 +580,7 @@ def MakePolar(Orient,QB):
                     for term in orbs[orb]:
                         if 'D(' in term:
                             item = term.replace('D','C')
-                            SH = G2lat.KslCalc(item,Th,Ph)
+                            SH = G2lat.KslCalc(item,Th,Ph)**2
                             FFval += SH*orbs[orb][term]*ff
                             name = 'A%s%s:%d'%(term,orb,iAt)
                             dFFdS[name] = SH*ff
@@ -597,7 +597,7 @@ def MakePolar(Orient,QB):
                     for term in orbs[orb]:
                         if 'D(' in term:    #skip 'Ne'
                             item = term.replace('D','C')
-                            SH = G2lat.KslCalc(item,Th,Ph)
+                            SH = G2lat.KslCalc(item,Th,Ph)**2
                             FFval += SH*orbs[orb][term]*ff
                             name = 'A%s%s:%d'%(term,orb,iAt)
                             dFFdS[name] = SH*ff

GSASII/exports/G2export_PDB.py

@@ -277,7 +277,7 @@ def Exporter(self,event=None):
             A,B = G2lat.cell2AB(Cell)
             self.Write('# GSAS-II generated ORCA input file\n# Basic Mode')
             self.Write('#%Sym SymThresh 0.01 End')
-            self.Write('# after xyz is charge & multiplicity; change as needed')
+            self.Write('# after xyz is charge & multiplicity; change as needed for ions')
             self.Write('* xyz 0 1')
             fmt = '{:4s}'+3*'{:12.4f}'
             for atom in Atoms: