Changeset 5320

Timestamp:

Aug 21, 2022 10:16:38 AM (16 months ago)

Author:

toby

Message:

more fullrmc work (all but swaps done?); misc docs fixes

Location:

trunk

Files:

• GSASIIimgGUI.py (modified) (1 diff)
• GSASIImath.py (modified) (1 diff)
• GSASIIphsGUI.py (modified) (2 diffs)
• GSASIIpwd.py (modified) (6 diffs)
• GSASIIscriptable.py (modified) (9 diffs)

trunk/GSASIIimgGUI.py

@@ -75 +75 @@
 
     :param wx.Frame G2frame: main GSAS-II frame
-    :param: dict data: Image Controls dictionary
+    :param dict data: Image Controls dictionary
 
     :returns: array sumImg: corrected image for background/dark/flat back

trunk/GSASIImath.py

@@ -858 +858 @@
     
     :param dict data: GSAS-II phase data structure
-    :param: dict seqData: GSAS-II sequential refinement results structure
+    :param dict seqData: GSAS-II sequential refinement results structure
     :param bool PF2: if True then seqData is from a sequential run of PDFfit2
     

trunk/GSASIIphsGUI.py

@@ -5586 +5586 @@
                     mainSizer.Add(grpBox,0)
 
+            RMCPdict['addThermalBroadening'] = RMCPdict.get('addThermalBroadening',False)
+            mainSizer.Add((-1,5))
+            distBox = wx.BoxSizer(wx.HORIZONTAL)
+            distBox.Add(wx.StaticText(G2frame.FRMC,label=' Add thermal broadening? '),0,WACV)
+            distBox.Add(G2G.G2CheckBox(G2frame.FRMC,'',RMCPdict,'addThermalBroadening',OnChange=UpdateRMC),
+                            0,WACV)
+            if RMCPdict['addThermalBroadening']:
+                distBox.Add((15,-1))
+                distBox.Add(wx.StaticText(G2frame.FRMC,label='Uiso equiv.'),0,WACV)
+                RMCPdict['ThermalU'] = RMCPdict.get('ThermalU',{})
+                for atm in RMCPdict['aTypes']:
+                    RMCPdict['ThermalU'][atm] = RMCPdict['ThermalU'].get(atm,0.005)
+                    distBox.Add(wx.StaticText(G2frame.FRMC,label='  '+atm+':'),0,WACV)
+                    distBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['ThermalU'],atm,
+                                                xmin=0.0001,xmax=0.25,size=(50,25)),0,WACV)
+            mainSizer.Add(distBox,0)
+            if RMCPdict['addThermalBroadening']: mainSizer.Add((-1,5))
+                    
             # Torsions are difficult to implement. Need to be internal to a unit cell & named with fullrmc
             # atom labels. Leave this out, at least for now. 
@@ -6869 +6887 @@
         G2frame.GPXtree.SetItemPyData(psub,G2obj.SetNewPhase(Name=PhaseName,SGData=SGData))
         newPhase = G2frame.GPXtree.GetItemPyData(psub)
-        # add a restraint tree entry
-        subr = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints')
-        G2frame.GPXtree.GetItemPyData(subr).update({PhaseName:{}})
         # read in info from file
         pName = (G2frame.GSASprojectfile.split('.')[0] + '-'
                      + data['General']['Name'])
         pName = pName.replace(' ','_')
-        with open(pName+'-fullrmc.atoms','r') as fp:
-            cell = [float(i) for i in fp.readline().split(':')[1].split()]
-            supercell = [int(i) for i in fp.readline().split(':')[1].split()]
-            if super:
-                for i in range(3): cell[i] *= supercell[i]
-            # set cell & volume
-            newPhase['General']['Cell'][1:7] = cell
-            newPhase['General']['Cell'][7] = G2lat.calc_V(G2lat.cell2A(cell))
-            A,B = G2lat.cell2AB(cell)
-            # add atoms
-            for line in fp:
-                Name,El,ox,oy,oz = line.split()
-                oxyz = [float(i) for i in (ox,oy,oz)]
+        try:
+            with open(pName+'-fullrmc.atoms','r') as fp:
+                cell = [float(i) for i in fp.readline().split(':')[1].split()]
+                supercell = [int(i) for i in fp.readline().split(':')[1].split()]
                 if super:
-                    (x,y,z) = np.inner(B,oxyz)
-                else:
-                    (x,y,z),disp = G2spc.MoveToUnitCell(np.inner(B,oxyz))
-                atId = ran.randint(0,sys.maxsize)
-                newPhase['Atoms'].append([Name,El,'',x,y,z,1.,'1',1,'I',0.01,0,0,0,0,0,0,atId])
-
+                    for i in range(3): cell[i] *= supercell[i]
+                # set cell & volume
+                newPhase['General']['Cell'][1:7] = cell
+                newPhase['General']['Cell'][7] = G2lat.calc_V(G2lat.cell2A(cell))
+                A,B = G2lat.cell2AB(cell)
+                # add atoms
+                for line in fp:
+                    Name,El,ox,oy,oz = line.split()
+                    oxyz = [float(i) for i in (ox,oy,oz)]
+                    if super:
+                        (x,y,z) = np.inner(B,oxyz)
+                    else:
+                        (x,y,z),disp = G2spc.MoveToUnitCell(np.inner(B,oxyz))
+                    atId = ran.randint(0,sys.maxsize)
+                    newPhase['Atoms'].append([Name,El,'',x,y,z,1.,'1',1,'I',0.01,0,0,0,0,0,0,atId])
+        except:
+            G2G.G2MessageBox(G2frame,
+                    'Unable to open or read file '+pName+'-fullrmc.atoms. '
+                    'Was a fullrmc run from the current .gpx file '
+                    'and for the current phase?',
+                    'Error on read')
+            G2frame.GPXtree.Delete(psub)
+            return
+        # add a restraint tree entry for new phase
+        subr = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints')
+        G2frame.GPXtree.GetItemPyData(subr).update({PhaseName:{}})
         SetupGeneral()  # index elements
         

trunk/GSASIIpwd.py

@@ -3687 +3687 @@
     Files = RMCPdict['files']
     rundata = ''
-    rundata += '#### fullrmc %s file; edit by hand if you so choose #####\n'%scrname
+    rundata += '## fullrmc %s file ##\n## OK to edit this by hand ##\n'%scrname
     rundata += '# created in '+__file__+" v"+filversion.split()[1]
     rundata += dt.datetime.strftime(dt.datetime.now()," at %Y-%m-%dT%H:%M\n")
@@ -3719 +3719 @@
 # utility routines
 def writeHeader(ENGINE,statFP):
-    'header for stats file'
+    """header for stats file"""
     statFP.write('generated-steps, total-error, ')
     for c in ENGINE.constraints:
@@ -3728 +3728 @@
     
 def writeCurrentStatus(ENGINE,statFP,plotF):
-    'line in stats file & current constraint plots'
+    """line in stats file & current constraint plots"""
     statFP.write(str(ENGINE.generated))
     statFP.write(', ')
@@ -3749 +3749 @@
 
 def calcRmax(ENGINE):
-    'from Bachir, works for non-orthorhombic cells'
+    """from Bachir, works for non-orthorhombic cells"""
     a,b,c = ENGINE.basisVectors
     lens = []
@@ -3759 +3759 @@
     lens.extend( [ts/np.linalg.norm(a), ts/np.linalg.norm(c)] )
     return min(lens)
-
+'''
+    if RMCPdict.get('Groups',[]): rundata += '''
 def makepdb(atoms, coords, bbox=None):
-    'creates a supercell directly from atom info'
+    """creates a supercell directly from atom info"""
     # used when ENGINE.build_crystal_set_pdb is not called
     prevcell = None
@@ -3918 +3919 @@
             rundata += '    ENGINE.add_constraints([GofR])\n'
             rundata += '    GofR.set_limits((None, calcRmax(ENGINE)))\n'
+            if RMCPdict['addThermalBroadening']:
+                rundata += "    GofR.set_thermal_corrections({'defaultFactor': 0.001})\n"
+                rundata += "    GofR.thermalCorrections['factors'] = {\n"
+                RMCPdict['addThermalBroadening']
+                for atm1 in RMCPdict['aTypes']:
+                    for atm2 in RMCPdict['aTypes']:
+                        rundata += "         ('{}', '{}'): {},\n".format(
+                            atm1,atm2,
+                            (RMCPdict['ThermalU'].get(atm1,0.005)+                                           RMCPdict['ThermalU'].get(atm2,0.005))/2)
+                rundata += '    }\n'
         elif '(Q)' in File:
             rundata += '    SOQ = np.loadtxt(os.path.join(dirName,"%s")).T\n'%filDat[0]

trunk/GSASIIscriptable.py

@@ -851 +851 @@
     datadir = "/Users/toby/software/G2/Tutorials/PythonScript/data"
     PathWrap = lambda fil: os.path.join(datadir,fil)
-    gpx = G2sc.G2Project(filename='PbSO4sim.gpx') # create a project    
+    gpx = G2sc.G2Project(newgpx='PbSO4sim.gpx') # create a project    
     phase0 = gpx.add_phase(PathWrap("PbSO4-Wyckoff.cif"),
              phasename="PbSO4",fmthint='CIF') # add a phase to the project
@@ -878 +878 @@
     cifdir = "/Users/toby/software/G2/Tutorials/PythonScript/data"
     datadir = "/Users/toby/software/G2/Tutorials/TOF-CW Joint Refinement/data"
-    gpx = G2sc.G2Project(filename='/tmp/PbSO4simT.gpx') # create a project
+    gpx = G2sc.G2Project(newgpx='/tmp/PbSO4simT.gpx') # create a project
     phase0 = gpx.add_phase(os.path.join(cifdir,"PbSO4-Wyckoff.cif"),
              phasename="PbSO4",fmthint='CIF') # add a phase to the project
@@ -972 +972 @@
     PathWrap = lambda fil: os.path.join(datadir,fil)
 
-    gpx = G2sc.G2Project(filename=PathWrap('inttest.gpx'))
+    gpx = G2sc.G2Project(newgpx=PathWrap('inttest.gpx'))
     imlst = gpx.add_image(PathWrap('Si_free_dc800_1-00000.tif'),fmthint="TIF")
     imlst[0].loadControls(PathWrap('Si_free_dc800_1-00000.imctrl'))
@@ -990 +990 @@
         fil)
 
-    gpx = G2sc.G2Project(filename='/tmp/img.gpx')
+    gpx = G2sc.G2Project(newgpx='/tmp/img.gpx')
     for f in glob.glob(PathWrap('*.tif')): 
         im = gpx.add_image(f,fmthint="TIF")
@@ -1044 +1044 @@
         fil)
 
-    gpx = G2sc.G2Project(filename='/tmp/calib.gpx')
+    gpx = G2sc.G2Project(newgpx='/tmp/calib.gpx')
     for f in glob.glob(PathWrap('*.tif')): 
         im = gpx.add_image(f,fmthint="TIF")
@@ -2018 +2018 @@
     :param str newgpx: The filename the project should be saved to in
             the future. If both newgpx and gpxfile are present, the project is
-            loaded from the gpxfile, then when saved will be written to newgpx.
-    :param str filename: Name to be used to save the project. Has same function as
-            parameter newgpx (do not use both gpxfile and filename). Use of newgpx
-            is preferred over filename.
+            loaded from the file named by gpxfile and then when saved will 
+            be written to the file named by newgpx.
+    :param str filename: To be deprecated. Serves the same function as newgpx, 
+            which has a somewhat more clear name. 
+            (Do not specify both newgpx and filename). 
 
     There are two ways to initialize this object:
@@ -2061 +2062 @@
         if filename is not None and newgpx is not None:
             raise G2ScriptException('Do not use filename and newgpx together')
+        elif filename is not None:
+            G2fil.G2Print("Warning - recommending use of parameter newgpx rather than filename\n\twhen creating a G2Project")
         elif newgpx:
             filename = newgpx
@@ -5711 +5714 @@
         Example: 
 
-        >>> sclEnt = p.getHAPentryList(0,'Scale')[0]                                    >>> sclEnt
+        >>> sclEnt = p.getHAPentryList(0,'Scale')[0]
+        >>> sclEnt
         [(['PWDR test Bank 1', 'Scale'], list, [1.0, False])]
         >>> p.getHAPentryValue(sclEnt[0])
@@ -6237 +6241 @@
     Example use of G2Image:
 
-    >>> gpx = G2sc.G2Project(filename='itest.gpx')
+    >>> gpx = G2sc.G2Project(newgpx='itest.gpx')
     >>> imlst = gpx.add_image(idata,fmthint="TIF")
     >>> imlst[0].loadControls('stdSettings.imctrl')