Added connectivity to molecule info

GrupEstructuraElectronicaSimetria · May 19, 2020 · 00372c1 · 00372c1
1 parent 88c35e4
commit 00372c1
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Showing 2 changed files with 14 additions and 1 deletion.
diff --git a/cosymlib/file_io/tools.py b/cosymlib/file_io/tools.py
@@ -24,7 +24,13 @@ def print_input_info(initial_geometries, output=sys.stdout):
 
         for idn, array in enumerate(geometry.get_positions()):
             output.write('{:2s}'.format(geometry.get_symbols()[idn]))
-            output.write(' {:11.7f} {:11.7f} {:11.7f}\n'.format(array[0], array[1], array[2]))
+            output.write(' {:11.7f} {:11.7f} {:11.7f}'.format(array[0], array[1], array[2]))
+
+            if geometry.get_connectivity() is not None:
+                output.write('  ' +
+                             '  '.join(['{:3}'.format(i+1) for i in range(geometry.get_n_atoms())
+                                        if [idn+1, i+1] in geometry.get_connectivity()])+
+                             '\n')
         output.write('\n')
 
 

diff --git a/cosymlib/tools/__init__.py b/cosymlib/tools/__init__.py
@@ -76,3 +76,10 @@ def generate_connectivity_from_geometry(geometry, thresh=1.1):
         return None
 
     return (np.array(np.where(relative_differences < thresh - 1)).T + 1).tolist()
+
+
+def get_connectivity_matrix(connectivity, ndim):
+    cm = np.zeros((ndim, ndim), dtype=int)
+    for pair in connectivity:
+        cm[pair[0]-1, pair[1]-1] = 1
+    return cm