Update for reading pypolymlp MLPs from file

phono3py/api_phono3py.py

@@ -60,6 +60,7 @@ from phonopy.interface.pypolymlp import (
     PypolymlpParams,
     develop_polymlp,
     evalulate_polymlp,
+    load_polymlp,
     parse_mlp_params,
 )
 from phonopy.structure.atoms import PhonopyAtoms
@@ -2226,8 +2227,12 @@ class Phono3py:
             verbose=self._log_level - 1 > 0,
         )
 
+    def load_mlp(self, filename: str = "pypolymlp.mlp"):
+        """Load machine learning potential of pypolymlp."""
+        self._mlp = load_polymlp(filename=filename)
+
     def evaluate_mlp(self):
-        """Evaluate the machine learning potential of pypolymlp.
+        """Evaluate machine learning potential of pypolymlp.
 
         This method calculates the supercell energies and forces from the MLP
         for the displacements in self._dataset of type 2. The results are stored

phono3py/cui/create_force_constants.py

@@ -502,7 +502,8 @@ def _read_dataset_fc3(
         file_exists(e.filename, log_level=log_level)
 
     if use_pypolymlp:
-        phono3py.mlp_dataset = dataset
+        if forces_in_dataset(dataset):
+            phono3py.mlp_dataset = dataset
         run_pypolymlp_to_compute_forces(
             phono3py,
             mlp_params,
@@ -521,6 +522,7 @@ def run_pypolymlp_to_compute_forces(
     displacement_distance: Optional[float] = None,
     number_of_snapshots: Optional[int] = None,
     random_seed: Optional[int] = None,
+    mlp_filename: str = "pypolymlp.mlp",
     log_level: int = 0,
 ):
     """Run pypolymlp to compute forces."""
@@ -536,10 +538,18 @@ def run_pypolymlp_to_compute_forces(
                     print(f"  {k}: {v}")
     if log_level > 1:
         print("")
-    if log_level:
-        print("Developing MLPs by pypolymlp...", flush=True)
 
-    ph3py.develop_mlp(params=mlp_params)
+    if forces_in_dataset(ph3py.mlp_dataset):
+        if log_level:
+            print("Developing MLPs by pypolymlp...", flush=True)
+        ph3py.develop_mlp(params=mlp_params)
+    else:
+        if pathlib.Path(mlp_filename).exists():
+            if log_level:
+                print(f'Load MLPs from "{mlp_filename}".')
+            ph3py.load_mlp(mlp_filename)
+        else:
+            raise RuntimeError(f'"{mlp_filename}" is not found.')
 
     if log_level:
         print("-" * 30 + " pypolymlp end " + "-" * 31, flush=True)
@@ -577,9 +587,6 @@ def run_pypolymlp_to_compute_forces(
             flush=True,
         )
 
-    if ph3py.mlp_dataset is None:
-        msg = "mlp_dataset has to be set before calling this method."
-        raise RuntimeError(msg)
     if ph3py.supercells_with_displacements is None:
         raise RuntimeError("Displacements are not set. Run generate_displacements.")
 

phono3py/cui/load.py

@@ -416,7 +416,8 @@ def set_dataset_and_force_constants(
     )
     if not read_fc["fc3"]:
         if use_pypolymlp:
-            ph3py.mlp_dataset = dataset
+            if forces_in_dataset(dataset):
+                ph3py.mlp_dataset = dataset
         else:
             ph3py.dataset = dataset
     read_fc["fc2"], phonon_dataset = _get_dataset_phonon_dataset_or_fc2(
@@ -461,8 +462,8 @@ def compute_force_constants_from_datasets(
     """
     fc3_calculator = extract_fc2_fc3_calculators(fc_calculator, 3)
     fc2_calculator = extract_fc2_fc3_calculators(fc_calculator, 2)
-    if not read_fc["fc3"] and (ph3py.dataset or ph3py.mlp_dataset):
-        if use_pypolymlp and forces_in_dataset(ph3py.mlp_dataset):
+    if not read_fc["fc3"]:
+        if use_pypolymlp:
             run_pypolymlp_to_compute_forces(
                 ph3py,
                 mlp_params=mlp_params,

phono3py/phonon3/displacement_fc3.py

@@ -272,7 +272,7 @@ def get_bond_symmetry(
 def get_least_orbits(atom_index, cell, site_symmetry, symprec=1e-5):
     """Find least orbits for a centering atom."""
     orbits = _get_orbits(atom_index, cell, site_symmetry, symprec)
-    mapping = np.arange(cell.get_number_of_atoms())
+    mapping = np.arange(len(cell))
 
     for i, orb in enumerate(orbits):
         for num in np.unique(orb):

phono3py/phonon3/reciprocal_to_normal.py

@@ -88,7 +88,7 @@ class ReciprocalToNormal:
                 self._fc3_normal[i, j, k] = fc3_elem / fff
 
     def _sum_in_atoms(self, band_indices, eigvecs):
-        num_atom = self._primitive.get_number_of_atoms()
+        num_atom = len(self._primitive)
         (e1, e2, e3) = eigvecs
         (b1, b2, b3) = band_indices