Changeset 1985

Timestamp:

Oct 5, 2015 2:05:04 PM (7 years ago)

Author:

toby

Message:

fix CIF import where ? is used for Uiso value and where iso/aniso type is inferred

Location:

trunk

Files:

• GSASII.py (modified) (1 diff)
• imports/G2phase_CIF.py (modified) (4 diffs)

trunk/GSASII.py

@@ -284 +284 @@
             except AttributeError:
                 print 'Import_'+errprefix+': Attribute Error '+str(filename)
-                pass
-            except ImportError:
-                print 'Import_'+errprefix+': Error importing file '+str(filename)
-                pass
+            #except ImportError:
+            #    print 'Import_'+errprefix+': Error importing file '+str(filename)
+            except Exception,errmsg:
+                print('\nImport_'+errprefix+': Error importing file '+str(filename))
+                print('Error message: '+str(errmsg)+'\n')
             if fp: fp.close()
 

trunk/imports/G2phase_CIF.py

@@ -178 +178 @@
                     anisoloop = blk.GetLoop('_atom_site_aniso_label')
                     anisokeys = [i.lower() for i in anisoloop.keys()]
+                    anisolabels = blk.get('_atom_site_aniso_label')
                 else:
                     anisoloop = None
                     anisokeys = []
+                    anisolabels = []
                 self.Phase['Atoms'] = []
                 G2AtomDict = {  '_atom_site_type_symbol' : 1,
@@ -204 +206 @@
                         if col >= 3:
                             atomlist[col] = cif.get_number_with_esd(val)[0]
+                            if col >= 11: atomlist[9] = 'A' # if any Aniso term is defined, set flag
                         elif col is not None:
                             atomlist[col] = val
@@ -211 +214 @@
                                 atomlist[9] = 'A'
                         elif key == '_atom_site_u_iso_or_equiv':
-                            atomlist[10] =cif.get_number_with_esd(val)[0]
+                            uisoval =cif.get_number_with_esd(val)[0]
+                            if uisoval is not None: atomlist[10] = uisoval
                     if not atomlist[1] and atomlist[0]:
                         typ = atomlist[0].rstrip('0123456789-+')
@@ -219 +223 @@
                             atomlist[1] = 'Xe'
                             self.warnings += ' Atom type '+typ+' not recognized; Xe assumed\n'
-                    ulbl = '_atom_site_aniso_label'
-                    if  atomlist[9] == 'A' and atomlist[0] in blk.get(ulbl):
-                        for val,key in zip(anisoloop.GetKeyedPacket(ulbl,atomlist[0]),
-                                           anisokeys):
+                    if atomlist[0] in anisolabels: # does this atom have aniso values in separate loop?
+                        atomlist[9] = 'A'  # set the aniso flag
+                        for val,key in zip( # load the values
+                                anisoloop.GetKeyedPacket('_atom_site_aniso_label',atomlist[0]), 
+                                anisokeys):
                             col = G2AtomDict.get(key)
                             if col: