Fix load dataset wo forces

phono3py/api_phono3py.py

@@ -846,6 +846,9 @@ def displacements(self):
         """
         dataset = self._dataset
 
+        if self._dataset is None:
+            raise RuntimeError("displacement dataset is not set.")
+
         if "first_atoms" in dataset:
             num_scells = len(dataset["first_atoms"])
             for disp1 in dataset["first_atoms"]:
@@ -1218,10 +1221,10 @@ def run_phonon_solver(self, grid_points=None):
 
     def generate_displacements(
         self,
-        distance=0.03,
-        cutoff_pair_distance=None,
-        is_plusminus="auto",
-        is_diagonal=True,
+        distance: float = 0.03,
+        cutoff_pair_distance: Optional[float] = None,
+        is_plusminus: Union[bool, str] = "auto",
+        is_diagonal: bool = True,
         number_of_snapshots: Optional[int] = None,
         random_seed: Optional[int] = None,
         is_random_distance: bool = False,
@@ -1410,7 +1413,7 @@ def produce_fc3(
         self,
         symmetrize_fc3r: bool = False,
         is_compact_fc: bool = False,
-        fc_calculator: Optional[str] = None,
+        fc_calculator: Optional[Union[str, dict]] = None,
         fc_calculator_options: Optional[Union[str, dict]] = None,
     ):
         """Calculate fc3 from displacements and forces.
@@ -2150,7 +2153,9 @@ def run_thermal_conductivity(
                 log_level=_log_level,
             )
 
-    def save(self, filename="phono3py_params.yaml", settings=None):
+    def save(
+        self, filename: str = "phono3py_params.yaml", settings: Optional[dict] = None
+    ):
         """Save parameters in Phono3py instants into file.
 
         Parameters

phono3py/cui/create_force_constants.py

@@ -95,8 +95,6 @@ def create_phono3py_force_constants(
     symmetrize_fc3r = settings.is_symmetrize_fc3_r or settings.fc_symmetry
     symmetrize_fc2 = settings.is_symmetrize_fc2 or settings.fc_symmetry
 
-    (fc_calculator, fc_calculator_options) = get_fc_calculator_params(settings)
-
     if log_level:
         show_phono3py_force_constants_settings(settings)
 
@@ -113,6 +111,9 @@ def create_phono3py_force_constants(
     ):
         pass
     else:
+        (fc_calculator, fc_calculator_options) = get_fc_calculator_params(
+            settings, log_level=(not settings.read_fc3) * 1
+        )
         if settings.read_fc3:
             _read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename, log_level)
         else:  # fc3 from FORCES_FC3 or ph3py_yaml
@@ -292,10 +293,17 @@ def parse_forces(
     # Type-1 FORCES_FC*.
     # dataset comes either from disp_fc*.yaml or phono3py*.yaml.
     if not forces_in_dataset(dataset):
-        if fc_type == "phonon_fc2":
-            parse_FORCES_FC2(dataset, filename=force_filename)
-        else:
-            parse_FORCES_FC3(dataset, filename=force_filename)
+        if force_filename is not None:
+            if fc_type == "phonon_fc2":
+                parse_FORCES_FC2(dataset, filename=force_filename)
+            else:
+                parse_FORCES_FC3(dataset, filename=force_filename)
+
+            if log_level:
+                print(
+                    f'Sets of supercell forces were read from "{force_filename}".',
+                    flush=True,
+                )
 
         # Unit of displacements is already converted.
         # Therefore, only unit of forces is converted.
@@ -305,15 +313,13 @@ def parse_forces(
                 force_to_eVperA=physical_units["force_to_eVperA"],
             )
 
-        if log_level:
-            print('Sets of supercell forces were read from "%s".' % force_filename)
-            sys.stdout.flush()
-
     return dataset
 
 
 def forces_in_dataset(dataset: dict) -> bool:
     """Return whether forces in dataset or not."""
+    if dataset is None:
+        return False
     return "forces" in dataset or (
         "first_atoms" in dataset and "forces" in dataset["first_atoms"][0]
     )
@@ -326,7 +332,7 @@ def displacements_in_dataset(dataset: Optional[dict]) -> bool:
     return "displacements" in dataset or "first_atoms" in dataset
 
 
-def get_fc_calculator_params(settings):
+def get_fc_calculator_params(settings, log_level=0):
     """Return fc_calculator and fc_calculator_params from settings."""
     fc_calculator = None
     fc_calculator_list = []
@@ -339,13 +345,49 @@ def get_fc_calculator_params(settings):
         if fc_calculator_list:
             fc_calculator = "|".join(fc_calculator_list)
 
-    fc_calculator_options = None
-    if settings.fc_calculator_options is not None:
-        fc_calculator_options = settings.fc_calculator_options
+    fc_calculator_options = settings.fc_calculator_options
+    if settings.cutoff_pair_distance:
+        if fc_calculator_list and fc_calculator_list[-1] in ("alm", "symfc"):
+            if fc_calculator_list[-1] == "alm":
+                cutoff_str = f"-1 {settings.cutoff_pair_distance}"
+            if fc_calculator_list[-1] == "symfc":
+                cutoff_str = f"{settings.cutoff_pair_distance}"
+            fc_calculator_options = _set_cutoff_in_fc_calculator_options(
+                fc_calculator_options,
+                cutoff_str,
+                log_level,
+            )
 
     return fc_calculator, fc_calculator_options
 
 
+def _set_cutoff_in_fc_calculator_options(
+    fc_calculator_options: Optional[str],
+    cutoff_str: str,
+    log_level: int,
+):
+    str_appended = f"cutoff={cutoff_str}"
+    calc_opts = fc_calculator_options
+    if calc_opts is None:
+        calc_opts = "|"
+    if "|" in calc_opts:
+        calc_opts_fc2, calc_opts_fc3 = [v.strip() for v in calc_opts.split("|")][:2]
+    else:
+        calc_opts_fc2 = calc_opts
+        calc_opts_fc3 = calc_opts
+
+    if calc_opts_fc3 == "":
+        calc_opts_fc3 += f"{str_appended}"
+        if log_level:
+            print(f'Set "{str_appended}" to fc_calculator_options for fc3.')
+    elif "cutoff" not in calc_opts_fc3:
+        calc_opts_fc3 += f", {str_appended}"
+        if log_level:
+            print(f'Appended "{str_appended}" to fc_calculator_options for fc3.')
+
+    return f"{calc_opts_fc2}|{calc_opts_fc3}"
+
+
 def _read_phono3py_fc3(phono3py: Phono3py, symmetrize_fc3r, input_filename, log_level):
     if input_filename is None:
         filename = "fc3.hdf5"
@@ -417,7 +459,7 @@ def _read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level):
 
 def read_type2_dataset(natom, filename="FORCES_FC3", log_level=0) -> Optional[dict]:
     """Read type-2 FORCES_FC3."""
-    if not pathlib.Path(filename).exists():
+    if filename is None or not pathlib.Path(filename).exists():
         return None
 
     with open(filename, "r") as f:

phono3py/cui/load.py

@@ -453,7 +453,7 @@ 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 ph3py.mlp_dataset and use_pypolymlp:
+        if use_pypolymlp and forces_in_dataset(ph3py.mlp_dataset):
             run_pypolymlp_to_compute_forces(
                 ph3py,
                 mlp_params=mlp_params,
@@ -462,17 +462,22 @@ def compute_force_constants_from_datasets(
                 random_seed=random_seed,
                 log_level=log_level,
             )
-        ph3py.produce_fc3(
-            symmetrize_fc3r=symmetrize_fc,
-            is_compact_fc=is_compact_fc,
-            fc_calculator=fc3_calculator,
-            fc_calculator_options=extract_fc2_fc3_calculators(fc_calculator_options, 3),
-        )
+        if forces_in_dataset(ph3py.dataset):
+            ph3py.produce_fc3(
+                symmetrize_fc3r=symmetrize_fc,
+                is_compact_fc=is_compact_fc,
+                fc_calculator=fc3_calculator,
+                fc_calculator_options=extract_fc2_fc3_calculators(
+                    fc_calculator_options, 3
+                ),
+            )
 
-        if log_level and symmetrize_fc and fc_calculator is None:
-            print("fc3 was symmetrized.")
+            if log_level and symmetrize_fc and fc_calculator is None:
+                print("fc3 was symmetrized.")
 
-    if not read_fc["fc2"] and (ph3py.dataset or ph3py.phonon_dataset):
+    if not read_fc["fc2"] and (
+        forces_in_dataset(ph3py.dataset) or forces_in_dataset(ph3py.phonon_dataset)
+    ):
         ph3py.produce_fc2(
             symmetrize_fc2=symmetrize_fc,
             is_compact_fc=is_compact_fc,
@@ -495,6 +500,7 @@ def _get_dataset_or_fc3(
     p2s_map = ph3py.primitive.p2s_map
     read_fc3 = False
     dataset = None
+
     if fc3_filename is not None or pathlib.Path("fc3.hdf5").exists():
         if fc3_filename is None:
             _fc3_filename = "fc3.hdf5"
@@ -532,8 +538,17 @@ def _get_dataset_or_fc3(
             cutoff_pair_distance,
             log_level,
         )
-        if not forces_in_dataset(dataset):
-            dataset = None
+    elif ph3py_yaml is not None and ph3py_yaml.dataset is not None:
+        # not forces_in_dataset(ph3py_yaml.dataset)
+        # but want to read displacement dataset.
+        dataset = _get_dataset_for_fc3(
+            ph3py,
+            ph3py_yaml,
+            None,
+            phono3py_yaml_filename,
+            cutoff_pair_distance,
+            log_level,
+        )
 
     return read_fc3, dataset
 
@@ -585,8 +600,16 @@ def _get_dataset_phonon_dataset_or_fc2(
             "phonon_fc2",
             log_level,
         )
-        if not forces_in_dataset(phonon_dataset):
-            phonon_dataset = None
+    elif ph3py_yaml is not None and ph3py_yaml.phonon_dataset is not None:
+        # not forces_in_dataset(ph3py_yaml.dataset)
+        # but want to read displacement dataset.
+        phonon_dataset = _get_dataset_for_fc2(
+            ph3py,
+            ph3py_yaml,
+            None,
+            "phonon_fc2",
+            log_level,
+        )
 
     return read_fc2, phonon_dataset
 

phono3py/cui/phono3py_script.py

@@ -528,8 +528,6 @@ def store_force_constants(
         if log_level:
             print("-" * 29 + " Force constants " + "-" * 30)
 
-        (fc_calculator, fc_calculator_options) = get_fc_calculator_params(settings)
-
         read_fc = set_dataset_and_force_constants(
             phono3py,
             ph3py_yaml=ph3py_yaml,
@@ -538,6 +536,9 @@ def store_force_constants(
             use_pypolymlp=settings.use_pypolymlp,
             log_level=log_level,
         )
+        (fc_calculator, fc_calculator_options) = get_fc_calculator_params(
+            settings, log_level=(not read_fc["fc3"]) * 1
+        )
         try:
             compute_force_constants_from_datasets(
                 phono3py,