Merge pull request #805 from ThomasWarford/preproc

Preprocessing: Save statistics.json in a way which can be loaded by ast.literal_eval
ACEsuit · Jan 27, 2025 · 5dccd81 · 5dccd81
2 parents a686631 + e157d3a
commit 5dccd81
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/mace/cli/preprocess_data.py b/mace/cli/preprocess_data.py
@@ -240,7 +240,7 @@ def run(args: argparse.Namespace):
             "avg_num_neighbors": avg_num_neighbors,
             "mean": mean,
             "std": std,
-            "atomic_numbers": str(z_table.zs),
+            "atomic_numbers": str([int(z) for z in z_table.zs]),
             "r_max": args.r_max,
         }
 

diff --git a/mace/data/utils.py b/mace/data/utils.py
@@ -269,16 +269,17 @@ def load_from_xyz(
                 len(atoms) == 1 and atoms.info.get("config_type") == "IsolatedAtom"
             )
             if isolated_atom_config:
+                atomic_number = int(atoms.get_atomic_numbers()[0])
                 if energy_key in atoms.info.keys():
-                    atomic_energies_dict[atoms.get_atomic_numbers()[0]] = atoms.info[
+                    atomic_energies_dict[atomic_number] = float(atoms.info[
                         energy_key
-                    ]
+                    ])
                 else:
                     logging.warning(
                         f"Configuration '{idx}' is marked as 'IsolatedAtom' "
                         "but does not contain an energy. Zero energy will be used."
                     )
-                    atomic_energies_dict[atoms.get_atomic_numbers()[0]] = np.zeros(1)
+                    atomic_energies_dict[atomic_number] = 0.0
             else:
                 atoms_without_iso_atoms.append(atoms)