Auto stash before merge of "main" and "origin/main"

Added the graph comparison functionality.

src/check_graph_iso.py

@@ -1,18 +1,105 @@
-import glob, os
+import os
 from ase.io import read
+from pymatgen.io.ase import AseAtomsAdaptor
+from pymatgen.analysis.graphs import MoleculeGraph
+from pymatgen.analysis.local_env import OpenBabelNN
+from networkx.algorithms.graph_hashing import weisfeiler_lehman_graph_hash
 
-ref_dir = '/global/cfs/cdirs/m2834/kumaranu/neb_nn_inputs'
 
-for i in range(265):
-    logdir = os.path.join(ref_dir, f'{i:03}')
-    if os.path.exists(logdir):
-        reactant_traj_file = os.path.join(logdir, 'reactant_opt.traj')
-        if os.path.exists(reactant_traj_file):
-            traj_atoms = read(reactant_traj_file, index=':', format="traj")
+def add_specie_suffix(graph):
+    """
+    Add a suffix to each node's 'specie' attribute in the graph.
+
+    Args:
+        graph (networkx.Graph): The graph.
+    """
+    for idx in graph.nodes():
+        graph.nodes()[idx]["specie"] = graph.nodes()[idx]["specie"] + str(idx)
+
+
+def get_graph_hash(graph):
+    """
+    Get the hash of the graph using the Weisfeiler-Lehman algorithm.
+
+    Args:
+        graph (networkx.Graph): The graph.
+
+    Returns:
+        str: The graph hash.
+    """
+    return weisfeiler_lehman_graph_hash(graph, node_attr='specie')
+
+
+def create_molecule_graph(molecule):
+    """
+    Create a molecule graph using the OpenBabelNN strategy.
+
+    Args:
+        molecule (pymatgen.core.structure.Molecule): The molecule.
+
+    Returns:
+        pymatgen.analysis.graphs.MoleculeGraph: The molecule graph.
+    """
+    return MoleculeGraph.with_local_env_strategy(molecule, OpenBabelNN())
+
+
+def compare_mols(molecule_1, molecule_2) -> bool:
+    """
+    Compare two molecules based on their graph structure.
+
+    Args:
+        molecule_1 (pymatgen.core.structure.Molecule): First molecule.
+        molecule_2 (pymatgen.core.structure.Molecule): Second molecule.
+
+    Returns:
+        bool: True if the molecules have the same graph structure, False otherwise.
+    """
+    molgraph_1 = create_molecule_graph(molecule_1)
+    molgraph_2 = create_molecule_graph(molecule_2)
+
+    graph_1 = molgraph_1.graph.to_undirected()
+    graph_2 = molgraph_2.graph.to_undirected()
+
+    add_specie_suffix(graph_1)
+    add_specie_suffix(graph_2)
+
+    graph_1_hash = get_graph_hash(graph_1)
+    graph_2_hash = get_graph_hash(graph_2)
+
+    return graph_1_hash == graph_2_hash
+
+
+def check_graph_iso(ref_dir):
+    for i in range(265):
+        logdir = os.path.join(ref_dir, f'{i:03}')
+        if os.path.exists(logdir):
+            reactant_traj_file = os.path.join(logdir, 'reactant_opt.traj')
+            if os.path.exists(reactant_traj_file):
+                reactant_traj_atoms = read(reactant_traj_file, index=':', format="traj")
+            else:
+                print(f"Reactant's traj file could not be found for index {i:03}")
+                continue
+            product_traj_file = os.path.join(logdir, 'product_opt.traj')
+            if os.path.exists(product_traj_file):
+                pdt_traj_atoms = read(product_traj_file, index=':', format="traj")
+            else:
+                print(f"Product's traj file could not be found for index {i:03}")
+                continue
+            traj_pymat_mol1 = AseAtomsAdaptor.get_molecule(reactant_traj_atoms[0])
+            traj_pymat_mol2 = AseAtomsAdaptor.get_molecule(reactant_traj_atoms[-1])
+            bool_reactant = compare_mols(traj_pymat_mol1, traj_pymat_mol2)
+            traj_pymat_mol1 = AseAtomsAdaptor.get_molecule(pdt_traj_atoms[0])
+            traj_pymat_mol2 = AseAtomsAdaptor.get_molecule(pdt_traj_atoms[-1])
+            bool_product = compare_mols(traj_pymat_mol1, traj_pymat_mol2)
+            if bool_reactant and bool_product:
+                continue
+            else:
+                print(f'bool_reactant: {bool_reactant}, bool_product: {bool_product} for index {i:03}')
         else:
-            print(f"Reactant's traj file could not be found for index {i:03}")
-        #for atoms in traj_atoms:
-        #    print(i, atoms)
-    else:
-        print(f'Path could not be found for index {i:03}.')
+            print(f'Path could not be found for index {i:03}.')
+
 
+if __name__ == '__main__':
+    # ref_dir = '/global/cfs/cdirs/m2834/kumaranu/neb_nn_inputs'
+    ref_dir = '/home/kumaranu/Downloads/neb_nn_inputs'
+    check_graph_iso(ref_dir)