From 2ac9f4e5cc76b4bd11b46f4d008d13bf0a59e119 Mon Sep 17 00:00:00 2001
From: tdprice-858 <76229513+tdprice-858@users.noreply.github.com>
Date: Fri, 15 Mar 2024 12:18:23 -0700
Subject: [PATCH] Remove constraints before comparison

Fixes a bug where leaving constraints on throws an error within the ase comparison algorithm
---
 pynta/utils.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/pynta/utils.py b/pynta/utils.py
index e901e330..56264bfd 100644
--- a/pynta/utils.py
+++ b/pynta/utils.py
@@ -31,6 +31,7 @@ def get_unique_sym(geoms):
     for geom in geoms:
         adsorbate_atom_obj = read(geom)
         adsorbate_atom_obj.pbc = True
+        adsorbate_atom_obj.set_constraint() # Reset constraints for comparison
         comparision = comparator.compare(
             adsorbate_atom_obj, good_adsorbates_atom_obj_list)
 
@@ -56,6 +57,7 @@ def get_unique_sym_indices(geoms):
     for geom in geoms:
         adsorbate_atom_obj = read(geom)
         adsorbate_atom_obj.pbc = True
+        adsorbate_atom_obj.set_constraint() # Reset constraints before comparison
         comparision = comparator.compare(
             adsorbate_atom_obj, good_adsorbates_atom_obj_list)
 
@@ -86,6 +88,7 @@ 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 before comparison
         comparision = comparator.compare(
             adsorbate_atom_obj, good_adsorbates_atom_obj_list)
 
@@ -114,6 +117,7 @@ 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 before comparison
         comparision = comparator.compare(
             adsorbate_atom_obj, good_adsorbates_atom_obj_list)
 
@@ -142,6 +146,7 @@ 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 before comparison
         comparison = None
         for j,adlist in enumerate(good_adsorbates_atom_obj_list):
             comparison = comparator.compare(adsorbate_atom_obj, [adlist[0]])
@@ -176,6 +181,7 @@ def filter_nonunique_TS_guess_indices(geoms,Es):
     for j,geom in enumerate(geoms):
         adsorbate_atom_obj = read(geom)
         adsorbate_atom_obj.pbc = True
+        adsorbate_atom_obj.set_constraint() # Reset constraints before comparison
         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]:
@@ -249,4 +255,4 @@ def construct_constraint(d):
     constraint_dict = copy.deepcopy(d)
     constructor = getattr(ase.constraints,constraint_dict["type"])
     del constraint_dict["type"]
-    return constructor(**constraint_dict)
\ No newline at end of file
+    return constructor(**constraint_dict)