Adds PhonopyAtomsAdaptor

Bridges between ASE and Phonopy Atoms objects, similarly
to how we have used AseAtomsAdaptor from Pymatgen.

Author: harveydevereux

janus_core/calculations/phonons.py

@@ -27,6 +27,7 @@
     PathLike,
     PhononCalcs,
 )
+from janus_core.helpers.struct_io import PhonopyAtomsAdaptor
 from janus_core.helpers.utils import (
     build_file_dir,
     none_to_dict,
@@ -498,7 +499,7 @@ def calc_force_constants(
 
         self._set_info_units()
 
-        cell = self._ASE_to_PhonopyAtoms(self.struct)
+        cell = PhonopyAtomsAdaptor.get_phonopy_atoms(self.struct)
 
         if len(self.supercell) == 3:
             supercell_matrix = (
@@ -988,53 +989,6 @@ def write_pdos(
             build_file_dir(self.pdos_plot_file)
             bplt.savefig(self.pdos_plot_file)
 
-    # No magnetic moments considered
-    # Disable invalid-function-name
-    def _Phonopy_to_ASEAtoms(self, struct: PhonopyAtoms) -> Atoms:  # noqa: N802
-        """
-        Convert Phonopy Atoms structure to ASE Atoms structure.
-
-        Parameters
-        ----------
-        struct
-            PhonopyAtoms structure to be converted.
-
-        Returns
-        -------
-        Atoms
-            Converted ASE Atoms structure.
-        """
-        return Atoms(
-            symbols=struct.symbols,
-            scaled_positions=struct.scaled_positions,
-            cell=struct.cell,
-            masses=struct.masses,
-            pbc=True,
-            calculator=self.calc,
-        )
-
-    # Disable invalid-function-name
-    def _ASE_to_PhonopyAtoms(self, struct: Atoms) -> PhonopyAtoms:  # noqa: N802
-        """
-        Convert ASE Atoms structure to Phonopy Atoms structure.
-
-        Parameters
-        ----------
-        struct
-            ASE Atoms structure to be converted.
-
-        Returns
-        -------
-        PhonopyAtoms
-            Converted PhonopyAtoms structure.
-        """
-        return PhonopyAtoms(
-            symbols=struct.get_chemical_symbols(),
-            cell=struct.cell.array,
-            scaled_positions=struct.get_scaled_positions(),
-            masses=struct.get_masses(),
-        )
-
     def _calc_forces(self, struct: PhonopyAtoms) -> ndarray:
         """
         Calculate forces on PhonopyAtoms structure.
@@ -1049,8 +1003,7 @@ def _calc_forces(self, struct: PhonopyAtoms) -> ndarray:
         ndarray
             Forces on the structure.
         """
-        atoms = self._Phonopy_to_ASEAtoms(struct)
-        return atoms.get_forces()
+        return PhonopyAtomsAdaptor.get_atoms(struct).get_forces()
 
     def run(self) -> None:
         """Run phonon calculations."""

janus_core/helpers/struct_io.py

@@ -9,9 +9,11 @@
 from typing import Any, get_args
 
 from ase import Atoms
+from ase.calculators.calculator import Calculator
 from ase.calculators.singlepoint import SinglePointCalculator
 from ase.io import read, write
 from ase.io.formats import filetype
+from phonopy.structure.atoms import PhonopyAtoms
 
 from janus_core.helpers.janus_types import (
     Architectures,
@@ -321,3 +323,56 @@ def output_structs(
 
         build_file_dir(write_kwargs["filename"])
         write(images=images, **write_kwargs)
+
+
+class PhonopyAtomsAdaptor:
+    """Adaptor to bridge between ASE and pymatgen atoms."""
+
+    # No magnetic moments considered
+    @staticmethod
+    def get_atoms(struct: PhonopyAtoms, calc: Calculator | None = None) -> Atoms:
+        """
+        Convert Phonopy Atoms structure to ASE Atoms structure.
+
+        Parameters
+        ----------
+        struct
+            PhonopyAtoms structure to be converted.
+        calc
+            Optional calculator to attach.
+
+        Returns
+        -------
+        Atoms
+            Converted ASE Atoms structure.
+        """
+        return Atoms(
+            symbols=struct.symbols,
+            scaled_positions=struct.scaled_positions,
+            cell=struct.cell,
+            masses=struct.masses,
+            pbc=True,
+            calculator=calc,
+        )
+
+    @staticmethod
+    def get_phonopy_atoms(struct: Atoms) -> PhonopyAtoms:
+        """
+        Convert ASE Atoms structure to Phonopy Atoms structure.
+
+        Parameters
+        ----------
+        struct
+            ASE Atoms structure to be converted.
+
+        Returns
+        -------
+        PhonopyAtoms
+            Converted PhonopyAtoms structure.
+        """
+        return PhonopyAtoms(
+            symbols=struct.get_chemical_symbols(),
+            cell=struct.cell.array,
+            scaled_positions=struct.get_scaled_positions(),
+            masses=struct.get_masses(),
+        )

tests/test_struct_io.py

@@ -0,0 +1,27 @@
+"""Test utility functions."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+from ase.calculators.lj import LennardJones
+from ase.io import read
+
+from janus_core.helpers.struct_io import PhonopyAtomsAdaptor
+
+DATA_PATH = Path(__file__).parent / "data"
+
+
+def test_phonopyadaptor():
+    """Test Phonopy atoms to ASE atoms adpator."""
+    struct = read(DATA_PATH / "NaCl.cif")
+    phonopy_struct = PhonopyAtomsAdaptor.get_phonopy_atoms(struct)
+    assert struct == PhonopyAtomsAdaptor.get_atoms(phonopy_struct)
+
+    struct.calc = LennardJones()
+    phonopy_struct = PhonopyAtomsAdaptor.get_phonopy_atoms(struct)
+
+    assert PhonopyAtomsAdaptor.get_atoms(phonopy_struct).calc is None
+    assert (
+        PhonopyAtomsAdaptor.get_atoms(phonopy_struct, struct.calc).calc == struct.calc
+    )