phonopy 3.2.1__tar.gz → 3.3.0__tar.gz

{phonopy-3.2.1 → phonopy-3.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phonopy
-Version: 3.2.1
+Version: 3.3.0
 Summary: This is the phonopy module.
 Author-Email: Atsushi Togo <atz.togo@gmail.com>
 License-Expression: BSD-3-Clause

phonopy-3.3.0/phonopy/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '3.3.0'
+__version_tuple__ = version_tuple = (3, 3, 0)
+
+__commit_id__ = commit_id = 'g9532062a8'

{phonopy-3.2.1 → phonopy-3.3.0}/phonopy/harmonic/displacement.py

@@ -78,7 +78,7 @@ class FirstAtomDisplacement(TypedDict):
     """Displacement information of one displaced atom."""
 
     number: int
-    displacement: list[float]
+    displacement: NDArray[np.double]
 
 
 class FirstAtomDisplacementWithForces(FirstAtomDisplacement, total=False):

{phonopy-3.2.1 → phonopy-3.3.0}/phonopy/interface/phonopy_yaml.py

@@ -651,17 +651,11 @@ class PhonopyYamlDumperBase(ABC):
         dataset: DisplacementDataset | None,
         with_forces: bool = False,
         key_prefix: str = "",
-        v223_mode: bool = False,
     ) -> list[str]:
         """Choose yaml writer depending on the dataset type.
 
         See type1 and type2 at Phonopy.dataset.
 
-        Parameters
-        ----------
-        v223_mode : bool
-            When True, old dataset yaml format is generated. Default is False.
-
         """
         if dataset is not None:
             if "first_atoms" in dataset:
@@ -669,24 +663,25 @@ class PhonopyYamlDumperBase(ABC):
                     dataset, with_forces=with_forces, key_prefix=key_prefix
                 )
             elif "displacements" in dataset:
-                if v223_mode:
-                    return self._displacements_yaml_lines_type2_v223(
-                        dataset, with_forces=with_forces, key_prefix=key_prefix
-                    )
-                else:
-                    return self._displacements_yaml_lines_type2(
-                        dataset, with_forces=with_forces, key_prefix=key_prefix
-                    )
+                return self._displacements_yaml_lines_type2(
+                    dataset, with_forces=with_forces, key_prefix=key_prefix
+                )
         return []
 
-    @abstractmethod
     def _displacements_yaml_lines_type1(
         self,
         dataset: Type1DisplacementDataset,
         with_forces: bool = False,
         key_prefix: str = "",
     ) -> list[str]:
-        pass
+        """Return type1 dataset in yaml.
+
+        See data structure at Phonopy.dataset.
+
+        """
+        return _displacements_yaml_lines_type1(
+            dataset, with_forces=with_forces, key_prefix=key_prefix
+        )
 
     def _displacements_yaml_lines_type2(
         self,
@@ -725,47 +720,6 @@ class PhonopyYamlDumperBase(ABC):
 
         return lines
 
-    def _displacements_yaml_lines_type2_v223(
-        self,
-        dataset: Type2DisplacementDataset,
-        with_forces: bool = False,
-        key_prefix: str = "",
-    ) -> list[str]:
-        """Return type2 dataset in old stype yaml.
-
-        This is the format < v2.24.
-
-        See data structure at Phonopy.dataset.
-
-        """
-        if "random_seed" in dataset:
-            lines = [
-                "random_seed: %d" % dataset["random_seed"],
-                f"{key_prefix}displacements:",
-            ]
-        else:
-            lines = [
-                f"{key_prefix}displacements:",
-            ]
-        for i, dset in enumerate(dataset["displacements"]):
-            lines.append(f"- # {i + 1}")
-            for j, d in enumerate(dset):
-                lines.append(f"  - displacement: # {j + 1}")
-                lines.append("      [ %20.16f,%20.16f,%20.16f ]" % tuple(d))
-                if with_forces and "forces" in dataset:
-                    f = dataset["forces"][i][j]
-                    lines.append("    force:")
-                    lines.append("      [ %20.16f,%20.16f,%20.16f ]" % tuple(f))
-        lines.append("")
-
-        if "supercell_energies" in dataset:
-            lines.append(f"{key_prefix}supercell_energies:")
-            for i, energy in enumerate(dataset["supercell_energies"]):
-                lines.append(f"- {energy:.8f} # {i + 1}")
-            lines.append("")
-
-        return lines
-
     def _force_constants_yaml_lines(self) -> list[str]:
         lines = []
         if (
@@ -809,18 +763,6 @@ class PhonopyYamlDumper(PhonopyYamlDumperBase):
             symbols = self._data.primitive.symbols
         return self._nac_yaml_lines_given_symbols(symbols)
 
-    def _displacements_yaml_lines_type1(
-        self, dataset: dict, with_forces: bool = False, key_prefix: str = ""
-    ) -> list[str]:
-        """Return type1 dataset in yaml.
-
-        See data structure at Phonopy.dataset.
-
-        """
-        return _displacements_yaml_lines_type1(
-            dataset, with_forces=with_forces, key_prefix=key_prefix
-        )
-
 
 class PhonopyYaml:
     """PhonopyYaml is a container of phonopy setting.
@@ -1224,7 +1166,7 @@ def load_yaml(fp: str | os.PathLike | typing.IO) -> dict:
 
 
 def _displacements_yaml_lines_type1(
-    dataset: dict, with_forces: bool = False, key_prefix: str = ""
+    dataset: Type1DisplacementDataset, with_forces: bool = False, key_prefix: str = ""
 ) -> list:
     """Return type1 dataset in yaml.
 

{phonopy-3.2.1 → phonopy-3.3.0}/phonopy/phonon/group_velocity.py

@@ -81,7 +81,7 @@ class GroupVelocity:
 
     def __init__(
         self,
-        dynamical_matrix: DynamicalMatrix | DynamicalMatrixNAC,
+        dynamical_matrix: DynamicalMatrix,
         q_length: float | None = None,
         symmetry: Symmetry | None = None,
         frequency_factor_to_THz: float | None = None,
@@ -89,7 +89,7 @@ class GroupVelocity:
     ) -> None:
         """Init method.
 
-        dynamical_matrix : DynamicalMatrix or DynamicalMatrixNAC
+        dynamical_matrix : DynamicalMatrix
             Dynamical matrix class instance.
         q_length : float
             This is used such as D(q + q_length) - D(q - q_length) for
@@ -107,7 +107,9 @@ class GroupVelocity:
         self._dynmat = dynamical_matrix
         primitive = dynamical_matrix.primitive
         self._reciprocal_lattice_inv = primitive.cell
-        self._reciprocal_lattice = np.linalg.inv(self._reciprocal_lattice_inv)
+        self._reciprocal_lattice: NDArray[np.double] = np.linalg.inv(
+            self._reciprocal_lattice_inv
+        )  # type: ignore
         self._q_length = q_length
         if isinstance(self._dynmat, DynamicalMatrixGL):
             if self._q_length is None:

{phonopy-3.2.1 → phonopy-3.3.0}/phonopy/version.py

@@ -34,4 +34,4 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-__version__ = "3.2.1"
+__version__ = "3.3.0"

phonopy-3.2.1/phonopy/_version.py

@@ -1,34 +0,0 @@
-# file generated by setuptools-scm
-# don't change, don't track in version control
-
-__all__ = [
-    "__version__",
-    "__version_tuple__",
-    "version",
-    "version_tuple",
-    "__commit_id__",
-    "commit_id",
-]
-
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple
-    from typing import Union
-
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-    COMMIT_ID = Union[str, None]
-else:
-    VERSION_TUPLE = object
-    COMMIT_ID = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-commit_id: COMMIT_ID
-__commit_id__: COMMIT_ID
-
-__version__ = version = '3.2.1'
-__version_tuple__ = version_tuple = (3, 2, 1)
-
-__commit_id__ = commit_id = 'gbc7b2c188'