Added bsym.process function to return site coordinates from a sitelist

bsym/configuration.py

@@ -21,7 +21,6 @@ def is_in_list( self, list ):
             return False
 
     def has_equivalent_in_list( self, list, symmetry_operations ):
-        print( 'i' )
         for config in list:
             print( config.as_number, self.as_number )
             if ( self.is_equivalent_to( config, symmetry_operations ) ):

bsym/process.py

@@ -1,5 +1,6 @@
 from bsym.permutations  import unique_permutations, next_permutationS, flatten_list
 from bsym.configuration import Configuration
+import numpy as np
 
 def unique_configurations_from_sites( site_distribution, spacegroup, verbose=False ):
     number_of_sites = sum( site_distribution.values() )
@@ -33,3 +34,14 @@ def coordinate_list_from_sitelists( configs, labels, sitelists ):
             for pos in config.position( label ):
                 for sitelist in sitelists:
                     sitelist.print_site( pos )
+
+def list_of_coordinates_from_sitelists( configs, labels, sitelists ):
+    all_coords = []
+    for config in configs:
+        coords = [] 
+        for label in labels:
+            for pos in config.position( label ):
+                for sitelist in sitelists:
+                    coords.append( sitelist[ pos ] )   
+        all_coords.append( coords )
+    return np.array( all_coords )

examples/pymatgen_structure_analysis_spinel.py

@@ -25,7 +25,7 @@
     sg = spacegroup_from_structure( parent_structure )
 
     # define the site occupations
-    site_dist = { 1 : 4, 
+    site_dist = { 1 : 1, 
                   0 : 4 }
 
     # find the unique configurations