Merge pull request #616 from ACEsuit/develop

fix swa bigger than epoch

mace/calculators/mace.py

@@ -50,9 +50,9 @@ class MACECalculator(Calculator):
 
     def __init__(
         self,
-        model_paths: Union[list, str] | None = None,
-        device: str | None = None,
-        models: Union[list[torch.nn.Module], torch.nn.Module] | None = None,
+        model_paths: Union[list, str, None] = None,
+        models: Union[list[torch.nn.Module], torch.nn.Module, None] = None,
+        device: str = "cpu",
         energy_units_to_eV: float = 1.0,
         length_units_to_A: float = 1.0,
         default_dtype="",

mace/cli/create_lammps_model.py

@@ -20,6 +20,13 @@ def parse_args():
         help="Head of the model to be converted to LAMMPS",
         default=None,
     )
+    parser.add_argument(
+        "--dtype",
+        type=str,
+        nargs="?",
+        help="Data type of the model to be converted to LAMMPS",
+        default="float64",
+    )
     return parser.parse_args()
 
 
@@ -58,7 +65,11 @@ def main():
         model_path,
         map_location=torch.device("cuda" if torch.cuda.is_available() else "cpu"),
     )
-    model = model.double().to("cpu")
+    if args.dtype == "float64":
+        model = model.double().to("cpu")
+    elif args.dtype == "float32":
+        print("Converting model to float32, this may cause loss of precision.")
+        model = model.float().to("cpu")
 
     if args.head is None:
         head = select_head(model)

mace/cli/preprocess_data.py

@@ -66,7 +66,22 @@ def pool_compute_stats(inputs: List):
         pool.join()
 
     results = [r.get() for r in tqdm.tqdm(re)]
-    return np.average(results, axis=0)
+
+    if not results:
+        raise ValueError(
+            "No results were computed. Check if the input files exist and are readable."
+        )
+
+    # Separate avg_num_neighbors, mean, and std
+    avg_num_neighbors = np.mean([r[0] for r in results])
+    means = np.array([r[1] for r in results])
+    stds = np.array([r[2] for r in results])
+
+    # Compute averages
+    mean = np.mean(means, axis=0).item()
+    std = np.mean(stds, axis=0).item()
+
+    return avg_num_neighbors, mean, std
 
 
 def split_array(a: np.ndarray, max_size: int):

mace/cli/run_train.py

@@ -245,7 +245,6 @@ def run(args: argparse.Namespace) -> None:
         args.loss = "universal"
         if (
             args.foundation_model in ["small", "medium", "large"]
-            or "mp" in args.foundation_model
             or args.pt_train_file is None
         ):
             logging.info(
@@ -344,6 +343,7 @@ def run(args: argparse.Namespace) -> None:
     atomic_energies_dict = {}
     for head_config in head_configs:
         if head_config.atomic_energies_dict is None or len(head_config.atomic_energies_dict) == 0:
+            assert head_config.E0s is not None, "Atomic energies must be provided"
             if check_path_ase_read(head_config.train_file) and head_config.E0s.lower() != "foundation":
                 atomic_energies_dict[head_config.head_name] = get_atomic_energies(
                     head_config.E0s, head_config.collections.train, head_config.z_table
@@ -403,7 +403,10 @@ def run(args: argparse.Namespace) -> None:
         # )
         atomic_energies = dict_to_array(atomic_energies_dict, heads)
         for head_config in head_configs:
-            logging.info(f"Atomic Energies used (z: eV) for head {head_config.head_name}: " + "{" + ", ".join([f"{z}: {atomic_energies_dict[head_config.head_name][z]}" for z in head_config.z_table.zs]) + "}")
+            try:
+                logging.info(f"Atomic Energies used (z: eV) for head {head_config.head_name}: " + "{" + ", ".join([f"{z}: {atomic_energies_dict[head_config.head_name][z]}" for z in head_config.z_table.zs]) + "}")
+            except KeyError as e:
+                raise KeyError(f"Atomic number {e} not found in atomic_energies_dict for head {head_config.head_name}, add E0s for this atomic number") from e
 
 
     valid_sets = {head: [] for head in heads}
@@ -627,9 +630,7 @@ def run(args: argparse.Namespace) -> None:
         stop_first_test = True
     for head_config in head_configs:
         if check_path_ase_read(head_config.train_file):
-            print(head_config.test_file)
             for name, subset in head_config.collections.tests:
-                print(name)
                 test_sets[name] = [
                     data.AtomicData.from_config(
                         config, z_table=z_table, cutoff=args.r_max, heads=heads

mace/modules/utils.py

@@ -378,6 +378,7 @@ def compute_statistics(
     forces_list = []
     num_neighbors = []
     head_list = []
+    head_batch = []
 
     for batch in data_loader:
         head = batch.head
@@ -391,21 +392,22 @@ def compute_statistics(
         )  # {[n_graphs], }
         forces_list.append(batch.forces)  # {[n_graphs*n_atoms,3], }
         head_list.append(head)  # {[n_graphs], }
-
+        head_batch.append(head[batch.batch])
         _, receivers = batch.edge_index
         _, counts = torch.unique(receivers, return_counts=True)
         num_neighbors.append(counts)
 
     atom_energies = torch.cat(atom_energy_list, dim=0)  # [total_n_graphs]
     forces = torch.cat(forces_list, dim=0)  # {[total_n_graphs*n_atoms,3], }
     head = torch.cat(head_list, dim=0)  # [total_n_graphs]
+    head_batch = torch.cat(head_batch, dim=0)  # [total_n_graphs]
 
     # mean = to_numpy(torch.mean(atom_energies)).item()
     mean = to_numpy(scatter_mean(src=atom_energies, index=head, dim=0).squeeze(-1))
-    # do the mean for each head
-    # rms = to_numpy(torch.sqrt(torch.mean(torch.square(forces)))).item()
     rms = to_numpy(
-        torch.sqrt(scatter_mean(src=torch.square(forces), index=head, dim=0))
+        torch.sqrt(
+            scatter_mean(src=torch.square(forces), index=head_batch, dim=0).mean(-1)
+        )
     )
 
     avg_num_neighbors = torch.mean(

mace/tools/scripts_utils.py

@@ -449,10 +449,11 @@ def get_swa(
     if args.start_swa is None:
         args.start_swa = max(1, args.max_num_epochs // 4 * 3)
     else:
-        if args.start_swa > args.max_num_epochs:
+        if args.start_swa >= args.max_num_epochs:
             logging.warning(
                 f"Start Stage Two must be less than max_num_epochs, got {args.start_swa} > {args.max_num_epochs}"
             )
+            swas[-1] = False
     if args.loss == "forces_only":
         raise ValueError("Can not select Stage Two with forces only loss.")
     if args.loss == "virials":