Changeset 3246

Timestamp:

Jan 28, 2018 8:56:19 PM (5 years ago)

Author:

toby

Message:

cif export: use sig for x,x,x positions etc; column order for seq table atom positions; misc Py3 fixes

Location:

trunk

Files:

• GSASIIIO.py (modified) (4 diffs)
• GSASIIdataGUI.py (modified) (4 diffs)
• GSASIIpath.py (modified) (1 diff)
• exports/G2export_CIF.py (modified) (2 diffs)
• makeTutorial.py (modified) (1 diff)

trunk/GSASIIIO.py

@@ -1420 +1420 @@
                 return True
             elif len(self.Phases) == 1:
-                self.phasenam = self.Phases.keys()
+                self.phasenam = list(self.Phases.keys())
             elif self.multiple: 
                 choices = sorted(self.Phases.keys())
@@ -1481 +1481 @@
                 return True
             elif len(self.Histograms) == 1:
-                self.histnam = self.Histograms.keys()
+                self.histnam = list(self.Histograms.keys())
             else:
                 choices = sorted(self.Histograms.keys())
@@ -1604 +1604 @@
         else:
             varyList = list(varyList)
+        # add symmetry-generated constraints
+        rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(   
+            G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
+        rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
+        rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
+        Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
+            Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
         try:
             groups,parmlist = G2mv.GroupConstraints(constDict)
             G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
+            #print(G2mv.VarRemapShow(varyList))
         except:
             # this really should not happen
@@ -2660 +2668 @@
             l[-1] += j
     t += n + l + ['','Unused columns:']
-    usedCols = lbldict.keys()
+    usedCols = list(lbldict.keys())
     for i in keyCols.values(): usedCols += i
     for i in range(len(items)):

trunk/GSASIIdataGUI.py

@@ -24 +24 @@
 import sys
 import os
-import glob
-import imp
+#import glob
+#import imp
 import inspect
 if '2' in platform.python_version_tuple()[0]:
@@ -6675 +6675 @@
     # sort out the variables in their selected order
     varcols = 0
-    for d in posdict.itervalues():
+    for d in posdict.values():
         varcols = max(varcols,max(d.keys())+1)
     # get labels for each column
@@ -6756 +6756 @@
 
     # add atom parameters to table
-    colLabels += list(atomLookup.keys())
+    colLabels += sorted(atomLookup.keys())
     for parm in sorted(atomLookup):
         G2frame.colList += [[data[name]['newAtomDict'][atomLookup[parm]][1] for name in histNames]]
@@ -6830 +6830 @@
     # Also dicts of variables 
     # for Parametric fitting from the data table
-    parmDict = dict(zip(colLabels,zip(*G2frame.colList)[0])) # scratch dict w/all values in table
+    parmDict = dict(zip(colLabels,list(zip(*G2frame.colList))[0])) # scratch dict w/all values in table
     parmDict.update({var:val for var,val in newCellDict.values()}) #  add varied reciprocal cell terms
     del parmDict['Use']

trunk/GSASIIpath.py

@@ -630 +630 @@
     '''
     from IPython.core import ultratb
+    # IPyBreak_base() # need fix below for Python3
     if 'win' in sys.platform:
         ultratb.FormattedTB(call_pdb=False,color_scheme='NoColor')(*args)

trunk/exports/G2export_CIF.py

@@ -56 +56 @@
 import GSASIIspc as G2spc
 import GSASIIstrMain as G2stMn
+import GSASIImapvars as G2mv
 
 DEBUG = False    #True to skip printing of reflection/powder profile lists
@@ -166 +167 @@
                     val = parmDict.get(var,at[j])
                     sig = sigDict.get(dvar,sigdig)
+                    if dvar in G2mv.GetDependentVars(): # do not include an esd for dependent vars
+                        sig = -abs(sig)
                 s += PutInCol(G2mth.ValEsd(val,sig),dig)
         s += PutInCol(at[cs+1],3)

trunk/makeTutorial.py

@@ -19 +19 @@
 from __future__ import print_function
 import os
+import GSASIIpath
 
-import GSASIIpath
-GSASIIpath.SetBinaryPath()
-import GSASIIctrlGUI as G2G
-G2BaseURL = G2G.G2BaseURL
-tutorialIndex = G2G.tutorialIndex
-tutURL = G2BaseURL +'/Tutorials'
-outname = os.path.join(GSASIIpath.path2GSAS2,'help','Tutorials.html')
+if __name__ == '__main__':
+    GSASIIpath.SetBinaryPath()
+    import GSASIIctrlGUI as G2G
+    G2BaseURL = G2G.G2BaseURL
+    tutorialIndex = G2G.tutorialIndex
+    tutURL = G2BaseURL +'/Tutorials'
+    outname = os.path.join(GSASIIpath.path2GSAS2,'help','Tutorials.html')
 
-dirList = [l[0] for l in tutorialIndex if len(l) == 3]
+    dirList = [l[0] for l in tutorialIndex if len(l) == 3]
 
-# loop through directories in Tutorials repository
-dirs = [d[:-1] for d in GSASIIpath.svnList(tutURL,False).split('\n') if d and d[-1] == '/']    
-for d in dirs:
-    if d not in dirList: print(u"makeTutorial: Listed tutorial is missing: "+d)
+    # loop through directories in Tutorials repository
+    dirs = [d[:-1] for d in GSASIIpath.svnList(tutURL,False).split('\n') if d and d[-1] == '/']    
+    for d in dirs:
+        if d not in dirList: print(u"makeTutorial: Listed tutorial is missing: "+d)
 
-#import sys
-#out = sys.stdout
-out = open(outname,'w')
-print('<!-- Do not edit this file. It is created by makeTutorial.py from info in GSASIIctrlGUI.py --!>',file=out)
-print('<h2>List of GSAS-II tutorials</H2><UL>',file=out)
-print('''
-<p> A list of available tutorials appears below. Each tutorial is a
-web page that can be opened using the link below, but most tutorials also need
-to have example data files downloaded. This can also be done with links included below, 
-but it can be easier to access tutorials using 
-<b>Help/Tutorials</b> menu item.
-When this menu entry is used from inside GSAS-II (unless "browse tutorial on web" is selected),
-the data files are downloaded to a local directory and GSAS-II will start from that directory
-for most file open commands. 
-</p>''',file=out)
+    #import sys
+    #out = sys.stdout
+    out = open(outname,'w')
+    print('<!-- Do not edit this file. It is created by makeTutorial.py from info in GSASIIctrlGUI.py --!>',file=out)
+    print('<h2>List of GSAS-II tutorials</H2><UL>',file=out)
+    print('''
+    <p> A list of available tutorials appears below. Each tutorial is a
+    web page that can be opened using the link below, but most tutorials also need
+    to have example data files downloaded. This can also be done with links included below, 
+    but it can be easier to access tutorials using 
+    <b>Help/Tutorials</b> menu item.
+    When this menu entry is used from inside GSAS-II (unless "browse tutorial on web" is selected),
+    the data files are downloaded to a local directory and GSAS-II will start from that directory
+    for most file open commands. 
+    </p>''',file=out)
 
-for l in tutorialIndex:
-    if len(l) == 1:
-        print("</UL><h4>{}</H4><UL>".format(l[0]),file=out)
-    else:
-        pageURL = tutURL+'/'+l[0]+'/'+l[1]
-        dataURL = tutURL+'/'+l[0]+'/data'
-        suffix = ''
-        if l[2][0] == ' ':
-            suffix = ' <A href="#prereq">*</A>'
-        if suffix: 
-            print('<UL><LI><A href="{}">{}</A>{}'.format(pageURL,l[2].strip(),suffix),file=out)
+    for l in tutorialIndex:
+        if len(l) == 1:
+            print("</UL><h4>{}</H4><UL>".format(l[0]),file=out)
         else:
-            print('<LI><A href="{}">{}</A>'.format(pageURL,l[2].strip()),file=out)
-            
-        if GSASIIpath.svnList(dataURL,False):
-            print(' [link: <A href="{}">Exercise files</A>].'.format(dataURL),file=out)
-        else:
-            print(' [No exercise files].',file=out)
-        if suffix: print('</UL>',file=out)
-#        if l[2][0] == ' ':
-#            print(' (Note that this tutorial requires previous as prerequisite)',file=out)
+            pageURL = tutURL+'/'+l[0]+'/'+l[1]
+            dataURL = tutURL+'/'+l[0]+'/data'
+            suffix = ''
+            if l[2][0] == ' ':
+                suffix = ' <A href="#prereq">*</A>'
+            if suffix: 
+                print('<UL><LI><A href="{}">{}</A>{}'.format(pageURL,l[2].strip(),suffix),file=out)
+            else:
+                print('<LI><A href="{}">{}</A>'.format(pageURL,l[2].strip()),file=out)
 
-print('</UL>\n<A name=prereq>* Indented tutorials require the previous unindented tutorial as a prerequisite',file=out)
-out.close()
+            if GSASIIpath.svnList(dataURL,False):
+                print(' [link: <A href="{}">Exercise files</A>].'.format(dataURL),file=out)
+            else:
+                print(' [No exercise files].',file=out)
+            if suffix: print('</UL>',file=out)
+    #        if l[2][0] == ' ':
+    #            print(' (Note that this tutorial requires previous as prerequisite)',file=out)
+
+    print('</UL>\n<A name=prereq>* Indented tutorials require the previous unindented tutorial as a prerequisite',file=out)
+    out.close()