Merge branch 'develop' into publish-gh-pages

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Jun-7-2024: Version 3.1.0
+
+- Change to write forces in phono3py-yaml as default.
+
 ## Jun-7-2024: Version 3.0.4
 
 - Bug fix when handling different supercell size of fc2 than that of fc3.

doc/conf.py

@@ -60,7 +60,7 @@
 # The short X.Y version.
 version = "3.0"
 # The full version, including alpha/beta/rc tags.
-release = "3.0.4"
+release = "3.1.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

phono3py/api_phono3py.py

@@ -44,6 +44,7 @@
     directions_to_displacement_dataset,
     get_least_displacements,
 )
+from phonopy.harmonic.dynamical_matrix import DynamicalMatrix
 from phonopy.harmonic.force_constants import get_fc2 as get_phonopy_fc2
 from phonopy.harmonic.force_constants import (
     set_permutation_symmetry,
@@ -179,7 +180,7 @@ def __init__(
             Supercell matrix used for fc2. In phono3py, supercell matrix for fc3
             and fc2 can be different to support longer range interaction of fc2
             than that of fc3. Unless setting this, supercell_matrix is used.
-            This is only valide when unitcell or unitcell_filename is given.
+            This is only valid when unitcell or unitcell_filename is given.
             Default is None.
         cutoff_frequency : float, optional
             Phonon frequency below this value is ignored when the cutoff is
@@ -297,7 +298,7 @@ def __init__(
         self._set_band_indices()
 
     @property
-    def version(self):
+    def version(self) -> str:
         """Return phono3py release version number.
 
         str
@@ -317,7 +318,7 @@ def calculator(self) -> Optional[str]:
         return self._calculator
 
     @property
-    def fc3(self):
+    def fc3(self) -> Optional[np.ndarray]:
         """Setter and getter of third order force constants (fc3).
 
         ndarray
@@ -334,7 +335,7 @@ def fc3(self, fc3):
         self._fc3 = fc3
 
     @property
-    def fc2(self):
+    def fc2(self) -> Optional[np.ndarray]:
         """Setter and getter of second order force constants (fc2).
 
         ndarray
@@ -351,12 +352,12 @@ def fc2(self, fc2):
         self._fc2 = fc2
 
     @property
-    def force_constants(self):
+    def force_constants(self) -> Optional[np.ndarray]:
         """Return fc2. This is same as the getter attribute `fc2`."""
         return self.fc2
 
     @property
-    def sigmas(self):
+    def sigmas(self) -> list:
         """Setter and getter of smearing widths.
 
         list
@@ -386,7 +387,7 @@ def sigmas(self, sigmas):
                     self._sigmas.append(None)
 
     @property
-    def sigma_cutoff(self):
+    def sigma_cutoff(self) -> Optional[float]:
         """Setter and getter of Smearing cutoff width.
 
         This is given as a multiple of the standard deviation.
@@ -403,7 +404,7 @@ def sigma_cutoff(self, sigma_cutoff):
         self._sigma_cutoff = sigma_cutoff
 
     @property
-    def nac_params(self):
+    def nac_params(self) -> Optional[dict]:
         """Setter and getter of parameters for non-analytical term correction.
 
         dict
@@ -427,7 +428,7 @@ def nac_params(self, nac_params):
             self._init_dynamical_matrix()
 
     @property
-    def dynamical_matrix(self):
+    def dynamical_matrix(self) -> Optional[DynamicalMatrix]:
         """Return DynamicalMatrix instance.
 
         This is not dynamical matrices but the instance of DynamicalMatrix
@@ -522,7 +523,7 @@ def phonon_supercell_symmetry(self) -> Symmetry:
         return self._phonon_supercell_symmetry
 
     @property
-    def supercell_matrix(self):
+    def supercell_matrix(self) -> np.ndarray:
         """Return transformation matrix to supercell cell from unit cell.
 
         ndarray
@@ -533,7 +534,7 @@ def supercell_matrix(self):
         return self._supercell_matrix
 
     @property
-    def phonon_supercell_matrix(self):
+    def phonon_supercell_matrix(self) -> Optional[np.ndarray]:
         """Return transformation matrix to phonon supercell from unit cell.
 
         ndarray
@@ -544,7 +545,7 @@ def phonon_supercell_matrix(self):
         return self._phonon_supercell_matrix
 
     @property
-    def primitive_matrix(self):
+    def primitive_matrix(self) -> np.ndarray:
         """Return transformation matrix to primitive cell from unit cell.
 
         ndarray
@@ -555,7 +556,7 @@ def primitive_matrix(self):
         return self._primitive_matrix
 
     @property
-    def unit_conversion_factor(self):
+    def unit_conversion_factor(self) -> float:
         """Return phonon frequency unit conversion factor.
 
         float
@@ -567,7 +568,7 @@ def unit_conversion_factor(self):
         return self._frequency_factor_to_THz
 
     @property
-    def dataset(self):
+    def dataset(self) -> Optional[dict]:
         """Setter and getter of displacement-force dataset.
 
         dict
@@ -629,7 +630,7 @@ def dataset(self, dataset):
         self._phonon_supercells_with_displacements = None
 
     @property
-    def phonon_dataset(self):
+    def phonon_dataset(self) -> Optional[dict]:
         """Setter and getter of displacement-force dataset for fc2.
 
         dict
@@ -674,10 +675,10 @@ def phonon_dataset(self, dataset):
         self._phonon_supercells_with_displacements = None
 
     @property
-    def band_indices(self):
+    def band_indices(self) -> list[np.ndarray]:
         """Setter and getter of band indices.
 
-        array_like
+        list[np.ndarray]
             List of band indices specified to select specific bands
             to computer ph-ph interaction related properties.
 
@@ -693,11 +694,11 @@ def _set_band_indices(self, band_indices=None):
             num_band = len(self._primitive) * 3
             self._band_indices = [np.arange(num_band, dtype="int_")]
         else:
-            self._band_indices = band_indices
+            self._band_indices = [np.array(bi, dtype="int_") for bi in band_indices]
         self._band_indices_flatten = np.hstack(self._band_indices).astype("int_")
 
     @property
-    def masses(self):
+    def masses(self) -> np.ndarray:
         """Setter and getter of atomic masses of primitive cell."""
         return self._primitive.masses
 
@@ -719,7 +720,7 @@ def masses(self, masses):
         self._phonon_supercell.masses = s_masses
 
     @property
-    def supercells_with_displacements(self):
+    def supercells_with_displacements(self) -> list[PhonopyAtoms]:
         """Return supercells with displacements.
 
         list of PhonopyAtoms
@@ -2038,7 +2039,7 @@ def save(self, filename="phono3py_params.yaml", settings=None):
             the settings expected to be updated from the following
             default settings are needed to be set in the dictionary.
             The possible parameters and their default settings are:
-                {'force_sets': False,
+                {'force_sets': True,
                  'displacements': True,
                  'force_constants': False,
                  'born_effective_charge': True,

phono3py/cui/create_force_constants.py

@@ -34,8 +34,11 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
+from __future__ import annotations
+
 import copy
 import os
+import pathlib
 import sys
 from typing import Optional
 
@@ -247,7 +250,7 @@ def parse_forces(
     # None is returned unless type-2.
     # can emit FileNotFoundError.
     if dataset is None or dataset is not None and not forces_in_dataset(dataset):
-        _dataset = _get_type2_dataset(
+        _dataset = read_type2_dataset(
             natom, filename=force_filename, log_level=log_level
         )
         # Do not overwrite dataset when _dataset is None.
@@ -311,13 +314,18 @@ def parse_forces(
     return dataset
 
 
-def forces_in_dataset(dataset):
+def forces_in_dataset(dataset: dict) -> bool:
     """Return whether forces in dataset or not."""
     return "forces" in dataset or (
         "first_atoms" in dataset and "forces" in dataset["first_atoms"][0]
     )
 
 
+def displacements_in_dataset(dataset: dict) -> bool:
+    """Return whether displacements in dataset or not."""
+    return "displacements" in dataset or "first_atoms" in dataset
+
+
 def get_fc_calculator_params(settings):
     """Return fc_calculator and fc_calculator_params from settings."""
     fc_calculator = None
@@ -338,7 +346,7 @@ def get_fc_calculator_params(settings):
     return fc_calculator, fc_calculator_options
 
 
-def _read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename, log_level):
+def _read_phono3py_fc3(phono3py: Phono3py, symmetrize_fc3r, input_filename, log_level):
     if input_filename is None:
         filename = "fc3.hdf5"
     else:
@@ -357,7 +365,7 @@ def _read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename, log_level):
         if log_level:
             print_error()
         sys.exit(1)
-    num_atom = phono3py.supercell.get_number_of_atoms()
+    num_atom = len(phono3py.supercell)
     if fc3.shape[1] != num_atom:
         print("Matrix shape of fc3 doesn't agree with supercell size.")
         if log_level:
@@ -407,8 +415,9 @@ def _read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level):
     phono3py.fc2 = phonon_fc2
 
 
-def _get_type2_dataset(natom, filename="FORCES_FC3", log_level=0):
-    if not os.path.isfile(filename):
+def read_type2_dataset(natom, filename="FORCES_FC3", log_level=0) -> Optional[dict]:
+    """Read type-2 FORCES_FC3."""
+    if not pathlib.Path(filename).exists():
         return None
 
     with open(filename, "r") as f:

phono3py/cui/load.py

@@ -48,7 +48,12 @@
 from phonopy.structure.cells import determinant
 
 from phono3py import Phono3py
-from phono3py.cui.create_force_constants import forces_in_dataset, parse_forces
+from phono3py.cui.create_force_constants import (
+    displacements_in_dataset,
+    forces_in_dataset,
+    parse_forces,
+    read_type2_dataset,
+)
 from phono3py.file_IO import read_fc2_from_hdf5, read_fc3_from_hdf5
 from phono3py.interface.phono3py_yaml import Phono3pyYaml
 from phono3py.phonon3.fc3 import show_drift_fc3
@@ -494,28 +499,31 @@ def _set_dataset_or_fc3(
         read_fc3 = True
         if log_level:
             print('fc3 was read from "fc3.hdf5".')
-    elif pathlib.Path("FORCES_FC3").exists():
-        _set_dataset_for_fc3(
-            ph3py,
-            ph3py_yaml,
-            "FORCES_FC3",
-            phono3py_yaml_filename,
-            cutoff_pair_distance,
-            log_level,
-        )
-    elif (
-        ph3py_yaml is not None
-        and ph3py_yaml.dataset is not None
-        and forces_in_dataset(ph3py_yaml.dataset)
-    ):
-        _set_dataset_for_fc3(
-            ph3py,
-            ph3py_yaml,
-            None,
-            phono3py_yaml_filename,
-            cutoff_pair_distance,
-            log_level,
-        )
+    elif dataset := read_type2_dataset(
+        len(ph3py.supercell), "FORCES_FC3", log_level=log_level
+    ):  # := Assignment Expressions (Python>=3.8)
+        ph3py.dataset = dataset
+    elif ph3py_yaml is not None and ph3py_yaml.dataset is not None:
+        if pathlib.Path("FORCES_FC3").exists() and displacements_in_dataset(
+            ph3py_yaml.dataset
+        ):
+            _set_dataset_for_fc3(
+                ph3py,
+                ph3py_yaml,
+                "FORCES_FC3",
+                phono3py_yaml_filename,
+                cutoff_pair_distance,
+                log_level,
+            )
+        if forces_in_dataset(ph3py_yaml.dataset):
+            _set_dataset_for_fc3(
+                ph3py,
+                ph3py_yaml,
+                None,
+                phono3py_yaml_filename,
+                cutoff_pair_distance,
+                log_level,
+            )
     return read_fc3
 
 

phono3py/cui/phono3py_script.py

@@ -541,14 +541,7 @@ def store_force_constants(
                 log_level=log_level,
             )
         except ForceCalculatorRequiredError:
-            if log_level:
-                print("")
-                print(
-                    "Built-in force constants calculator doesn't support the "
-                    "dispalcements-forces dataset. "
-                    "An external force calculator, e.g., ALM (--alm), has to be used "
-                    "to compute force constants."
-                )
+            _show_fc_calculator_not_found(log_level)
 
         if log_level:
             if phono3py.fc3 is None:
@@ -592,15 +585,31 @@ def store_force_constants(
             if log_level:
                 print('fc2 was written into "fc2.hdf5".')
     else:
-        create_phono3py_force_constants(
-            phono3py,
-            settings,
-            ph3py_yaml=ph3py_yaml,
-            phono3py_yaml_filename=phono3py_yaml_filename,
-            input_filename=input_filename,
-            output_filename=output_filename,
-            log_level=log_level,
+        try:
+            create_phono3py_force_constants(
+                phono3py,
+                settings,
+                ph3py_yaml=ph3py_yaml,
+                phono3py_yaml_filename=phono3py_yaml_filename,
+                input_filename=input_filename,
+                output_filename=output_filename,
+                log_level=log_level,
+            )
+        except ForceCalculatorRequiredError:
+            _show_fc_calculator_not_found(log_level)
+
+
+def _show_fc_calculator_not_found(log_level):
+    if log_level:
+        print("")
+        print(
+            "Built-in force constants calculator doesn't support the "
+            "dispalcements-forces dataset. "
+            "An external force calculator, e.g., ALM (--alm), has to be used "
+            "to compute force constants."
         )
+        print_error()
+    sys.exit(1)
 
 
 def run_gruneisen_then_exit(phono3py, settings, output_filename, log_level):