Changeset 963 for trunk

Timestamp:

Jun 20, 2013 5:07:33 PM (12 years ago)

Author:

toby

Message:

more CIF work, more docs

Location:

trunk

Files:

• GSASIIobj.py (modified) (3 diffs)
• GSASIIspc.py (modified) (2 diffs)
• exports/G2cif.py (modified) (11 diffs)

trunk/GSASIIobj.py ¶

@@ -143 +143 @@
 ==========  ===============  ====================================================
 General         \            Overall information for the phase (dict)
-  \         AtomPtrs         ? (list)
+  \         AtomPtrs         list of four locations to use to pull info
+                             from the atom records (list)
   \         F000X            x-ray F(000) intensity (float)
   \         F000N            neutron F(000) intensity (float)
@@ -183 +184 @@
 pId             \            Phase Id number for current project (int).
 Atoms           \            Atoms in phase as a list of lists. The outer list
-                             is for each atom, the inner list contains 18
-                             items:
-                             0) atom label, 1) the atom type,
-                             2) the refinement flags, 3-6) x, y, z, frac
-                             7) site symmetry, 8) site multiplicity,
-                             9) 'I' or 'A' for iso/anisotropic,
-                             10) Uiso, 10-16) Uij, 16) unique Id #.
+                             is for each atom, the inner list contains varying
+                             items depending on the type of phase, see
+                             the :ref:`Atom Records <Atoms_table>` description.
                              (list of lists)
 Drawing         \            Display parameters (dict)
@@ -285 +282 @@
             '111' is used (P 1, and ?).
 ==========  ====================================================
+
+Atom Records
+------------
+
+.. _Atoms_table:
+
+.. index::
+   single: Atoms record description
+   single: Data object descriptions; Atoms record
+
+
+If ``phasedict`` points to the phase information in the data tree, then
+atoms are contained in a list of atom records (list) in
+``phasedict['Atoms']``. Also needed to read atom information 
+are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
+which define locations in the atom record, as shown below. 
+
+.. tabularcolumns:: |l|p{4.5in}|
+
+==============   ====================================================
+location         explanation
+==============   ====================================================
+cx,cx+1,cx+2      the x,y and z coordinates
+cx+3              fractional occupancy (also cs-1)
+ct-1              atom label
+ct                atom type
+ct+1              refinement flags
+cs                site symmetry string
+cs+1              site multiplicity
+cia               ADP flag: Isotropic ('I') or Anisotropic ('A')
+cia+1             Uiso
+cia+2...cia+6     U11, U22, U33, U12, U13, U23
+==============   ====================================================
+
+
+*Classes and routines*
+----------------------
 
 '''

trunk/GSASIIspc.py ¶

@@ -202 +202 @@
 def AllOps(SGData):
     '''
-    Returns a list of all operators for a space group, including those for centering and a center of symmetry
+    Returns a list of all operators for a space group, including those for
+    centering and a center of symmetry
     
     :param SGData: from :func:`SpcGroup`
-    :returns: list of strings of formatted symmetry operators
-    '''
-    SGText = []
+    :returns: (SGTextList,offsetList,symOpList,G2oprList) where
+
+      * SGTextList: a list of strings with formatted and normalized
+        symmetry operators.
+      * offsetList: a tuple of (dx,dy,dz) offsets that relate the GSAS-II
+        symmetry operation to the operator in SGTextList and symOpList.
+        these dx (etc.) values are added to the GSAS-II generated
+        positions to provide the positions that are generated
+        by the normalized symmetry operators.        
+      * symOpList: a list of tuples with the normalized symmetry
+        operations as (M,T) values
+        (see ``SGOps`` in the :ref:`Space Group object<SGData_table>`)
+      * G2oprList: The GSAS-II operations for each symmetry operation as
+        a tuple with (center,mult,opnum), where center is (0,0,0), (0.5,0,0),
+        (0.5,0.5,0.5),...; where mult is 1 or -1 for the center of symmetry
+        and opnum is the number for the symmetry operation, in ``SGOps``
+        (starting with 0).
+    '''
+    SGTextList = []
+    offsetList = []
+    symOpList = []
+    G2oprList = []
     onebar = (1,)
     if SGData['SGInv']:
@@ -213 +233 @@
     for cen in SGData['SGCen']:
         for mult in onebar:
-            for M,T in SGData['SGOps']:
-                OPtxt = MT2text(mult*M,(mult*T)+cen)
-                SGText.append(OPtxt.replace(' ',''))
-    return SGText
-
+            for j,(M,T) in enumerate(SGData['SGOps']):
+                offset = [0,0,0]
+                Tprime = (mult*T)+cen
+                for i in range(3):
+                    while Tprime[i] < 0:
+                        Tprime[i] += 1
+                        offset[i] += 1
+                    while Tprime[i] >= 1:
+                        Tprime[i] += -1
+                        offset[i] += -1
+                OPtxt = MT2text(mult*M,Tprime)
+                SGTextList.append(OPtxt.replace(' ',''))
+                offsetList.append(tuple(offset))
+                symOpList.append((mult*M,Tprime))
+                G2oprList.append((cen,mult,j))
+    return SGTextList,offsetList,symOpList,G2oprList
     
 def MT2text(M,T):

trunk/exports/G2cif.py ¶

@@ -6 +6 @@
 import os.path
 import GSASIIIO as G2IO
-reload(G2IO)
+#reload(G2IO)
 import GSASIIgrid as G2gd
 import GSASIIstrIO as G2stIO
@@ -13 +13 @@
 import GSASIIlattice as G2lat
 import GSASIIspc as G2spg
+reload(G2spg)
 
 def getCallerDocString(): # for development
@@ -67 +68 @@
 
         def WriteOverall():
-            '''TODO: Write out overall refinement information
+            '''Write out overall refinement information.
+
+            More could be done here, but this is a good start.
             '''
             WriteCIFitem('_pd_proc_info_datetime', self.CIFdate)
@@ -85 +88 @@
             WriteCIFitem('_refine_ls_goodness_of_fit_all',GOF)
 
+            # get restraint info
+            # restraintDict = self.OverallParms.get('Restraints',{})
+            # for i in  self.OverallParms['Constraints']:
+            #     print i
+            #     for j in self.OverallParms['Constraints'][i]:
+            #         print j
             #WriteCIFitem('_refine_ls_number_restraints',TEXT)
             
@@ -300 +309 @@
                         cia+1:'AUiso',cia+2:'AU11',cia+3:'AU22',cia+4:'AU33',
                         cia+5:'AU12',cia+6:'AU13',cia+7:'AU23'}
-            labellist = []
+            self.labellist = []
             
             pfx = str(phasedict['pId'])+'::'
@@ -306 +315 @@
             naniso = 0
             for i,at in enumerate(Atoms):
-                s = PutInCol(MakeUniqueLabel(at[ct-1],labellist),6) # label
+                s = PutInCol(MakeUniqueLabel(at[ct-1],self.labellist),6) # label
                 fval = self.parmDict.get(fpfx+str(i),at[cfrac])
                 if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
@@ -354 +363 @@
                 if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
                 if at[cia] == 'I': continue
-                s = PutInCol(labellist[i],6) # label
+                s = PutInCol(self.labellist[i],6) # label
                 for j in (2,3,4,5,6,7):
                     sigdig = -0.0009
@@ -444 +453 @@
                           G2mth.ValEsd(cellmass/Z,-0.09,True))
 
+        def WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList):
+            '''Report bond distances and angles for the CIF
+
+            Note that _geom_*_symmetry_* fields are values of form
+            n_klm where n is the symmetry operation in SymOpList (counted
+            starting with 1) and (k-5, l-5, m-5) are translations to add
+            to (x,y,z). See
+            http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Igeom_angle_site_symmetry_.html
+
+            TODO: need a method to select publication flags for distances/angles
+            '''
+            phasedict = self.Phases[phasenam] # pointer to current phase info            
+            Atoms = phasedict['Atoms']
+            cx,ct,cs,cia = phasedict['General']['AtomPtrs']
+            fpfx = str(phasedict['pId'])+'::Afrac:'        
+            cfrac = cx+3
+            # loop over interatomic distances for this phase
+            WriteCIFitem('\n# MOLECULAR GEOMETRY')
+            WriteCIFitem('loop_' + 
+                         '\n\t_geom_bond_atom_site_label_1' +
+                         '\n\t_geom_bond_atom_site_label_2' + 
+                         '\n\t_geom_bond_distance' + 
+                         '\n\t_geom_bond_site_symmetry_1' + 
+                         '\n\t_geom_bond_site_symmetry_2' + 
+                         '\n\t_geom_bond_publ_flag')
+
+            # Note that labels should be read from self.labellist to correspond
+            # to the values reported in the atoms table and zero occupancy atoms
+            # should not be included
+            fpfx = str(phasedict['pId'])+'::Afrac:'        
+            for i,at in enumerate(Atoms):
+                if self.parmDict.get(fpfx+str(i),at[cfrac]) == 0.0: continue
+                lbl = self.labellist[i]
+
+
+            # loop over interatomic angles for this phase
+            WriteCIFitem('loop_' + 
+                         '\n\t_geom_angle_atom_site_label_1' + 
+                         '\n\t_geom_angle_atom_site_label_2' + 
+                         '\n\t_geom_angle_atom_site_label_3' + 
+                         '\n\t_geom_angle' + 
+                         '\n\t_geom_angle_site_symmetry_1' +
+                         '\n\t_geom_angle_site_symmetry_2' + 
+                         '\n\t_geom_angle_site_symmetry_3' + 
+                         '\n\t_geom_angle_publ_flag')
+
+
         def WritePhaseInfo(phasenam):
-            # see writepha.for
-            print 'TODO: phase info for',phasenam,'goes here'
-            # THINK: how to select publication flags for distances/angles?
+            WriteCIFitem('\n# phase info for '+str(phasenam) + ' follows')
             phasedict = self.Phases[phasenam] # pointer to current phase info            
             WriteCIFitem('_pd_phase_name', phasenam)
@@ -478 +532 @@
 
             # generate symmetry operations including centering and center of symmetry
-            WriteCIFitem('loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz')
-            for i,op in enumerate(G2spg.AllOps(phasedict['General']['SGData']),start=1):
+            SymOpList,offsetList,symOpList,G2oprList = G2spg.AllOps(
+                phasedict['General']['SGData'])
+            WriteCIFitem('loop_ _space_group_symop_id _space_group_symop_operation_xyz')
+            for i,op in enumerate(SymOpList,start=1):
                 WriteCIFitem('   {:3d}  {:}'.format(i,op.lower()))
 
@@ -512 +568 @@
             # report cell contents
             WriteComposition(phasenam)
-#            if not self.quickmode:
-                # report distances and angles
-#                WriteDistances(phasenam)
+            if not self.quickmode:      # report distances and angles
+                WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList)
 
             #raise Exception,'Testing'
-
-            #C now loop over interatomic distances for this phase
-            WriteCIFitem('\n# MOLECULAR GEOMETRY')
-            WriteCIFitem('loop_' + 
-                         '\n\t_geom_bond_atom_site_label_1' +
-                         '\n\t_geom_bond_atom_site_label_2' + 
-                         '\n\t_geom_bond_distance' + 
-                         '\n\t_geom_bond_site_symmetry_1' + 
-                         '\n\t_geom_bond_site_symmetry_2' + 
-                         '\n\t_geom_bond_publ_flag')
-
-            #C now loop over interatomic angles for this phase
-            WriteCIFitem('loop_' + 
-                         '\n\t_geom_angle_atom_site_label_1' + 
-                         '\n\t_geom_angle_atom_site_label_2' + 
-                         '\n\t_geom_angle_atom_site_label_3' + 
-                         '\n\t_geom_angle' + 
-                         '\n\t_geom_angle_site_symmetry_1' +
-                         '\n\t_geom_angle_site_symmetry_2' + 
-                         '\n\t_geom_angle_site_symmetry_3' + 
-                         '\n\t_geom_angle_publ_flag')
 
         def WritePowderData(histlbl):
@@ -968 +1002 @@
                     WriteSingleXtalData(key1)
 
-        # TODO: how to report _pd_proc_ls_peak_cutoff?
         WriteCIFitem('#--' + 15*'eof--' + '#')