Trevor's constrain issue command added

pynta/utils.py

@@ -25,19 +25,21 @@ def get_unique_sym(geoms):
 
     '''
     comparator = SymmetryEquivalenceCheck()
-
+    geoms_copy = deepcopy(geoms)
+
     good_adsorbates_atom_obj_list = []
     geos_out = []
 
-    for geom in geoms:
+    for i, geom in enumerate(geoms_copy):
         adsorbate_atom_obj = read(geom)
         adsorbate_atom_obj.pbc = True
+        adsorbate_atom_obj.set_constraint()  # Reset constraints
         comparision = comparator.compare(
             adsorbate_atom_obj, good_adsorbates_atom_obj_list)
 
         if comparision is False:
             good_adsorbates_atom_obj_list.append(adsorbate_atom_obj)
-            geos_out.append(geom)
+            geos_out.append(geoms[i])
 
     return geos_out
 
@@ -50,19 +52,20 @@ def get_unique_sym_indices(geoms):
 
     '''
     comparator = SymmetryEquivalenceCheck()
-
+    geoms_copy = deepcopy(geoms)
     good_adsorbates_atom_obj_list = []
     geos_out = []
 
-    for geom in geoms:
+    for i, geom in enumerate(geoms_copy):
         adsorbate_atom_obj = read(geom)
         adsorbate_atom_obj.pbc = True
+        adsorbate_atom_obj.set_constraint()  # Reset constraints
         comparision = comparator.compare(
             adsorbate_atom_obj, good_adsorbates_atom_obj_list)
 
         if comparision is False:
             good_adsorbates_atom_obj_list.append(adsorbate_atom_obj)
-            geos_out.append(geom)
+            geos_out.append(geoms[i])
 
     indices = [geoms.index(g) for g in geos_out]
 
@@ -87,6 +90,7 @@ def get_unique_sym_structs(geoms):
     for i,geom in enumerate(geoms_copy):
         adsorbate_atom_obj = geom
         adsorbate_atom_obj.pbc = True
+        adsorbate_atom_obj.set_constraint()  # Reset constraints
         comparision = comparator.compare(
             adsorbate_atom_obj, good_adsorbates_atom_obj_list)
 
@@ -115,6 +119,7 @@ def get_unique_sym_struct_indices(geoms):
     for i,geom in enumerate(geoms_copy):
         adsorbate_atom_obj = geom
         adsorbate_atom_obj.pbc = True
+        adsorbate_atom_obj.set_constraint()  # Reset constraints
         comparision = comparator.compare(
             adsorbate_atom_obj, good_adsorbates_atom_obj_list)
 
@@ -143,6 +148,7 @@ def get_unique_sym_struct_index_clusters(geoms):
     for i,geom in enumerate(geoms_copy):
         adsorbate_atom_obj = geom
         adsorbate_atom_obj.pbc = True
+        adsorbate_atom_obj.set_constraint()  # Reset constraints
         comparison = None
         for j,adlist in enumerate(good_adsorbates_atom_obj_list):
             comparison = comparator.compare(adsorbate_atom_obj, [adlist[0]])
@@ -168,27 +174,29 @@ def filter_nonunique_TS_guess_indices(geoms,Es):
     geoms: list of paths to .xyz or .traj files to compare
 
     '''
+    geoms_copy = deepcopy(geoms)
     comparator = SymmetryEquivalenceCheck()
 
     good_adsorbates_atom_obj_list = []
     geos_out = []
     Esout = []
 
-    for j,geom in enumerate(geoms):
+    for j,geom in enumerate(geoms_copy):
         adsorbate_atom_obj = read(geom)
         adsorbate_atom_obj.pbc = True
+        adsorbate_atom_obj.set_constraint()  # Reset constraints
         for i,good_adsorbate in enumerate(good_adsorbates_atom_obj_list):
             comparison = comparator.compare(adsorbate_atom_obj,good_adsorbate)
             if comparison and Es[j] < Esout[i]:
-                geos_out[i] = geom
+                geos_out[i] = geoms[j]
                 good_adsorbates_atom_obj_list[i] = adsorbate_atom_obj
                 Esout[i] = Es[j]
                 break
             elif comparison:
                 break
         else:
             good_adsorbates_atom_obj_list.append(adsorbate_atom_obj)
-            geos_out.append(geom)
+            geos_out.append(geoms[j])
             Esout.append(Es[j])
 
     return geos_out,Esout