Calculate thermal conductivity with phono3py

atomistics/workflows/conductivity.py

@@ -0,0 +1,154 @@
+from typing import Optional
+
+import numpy as np
+import structuretoolkit
+from ase.atoms import Atoms
+from phono3py import Phono3py
+from phonopy.units import VaspToTHz
+
+from atomistics.workflows.interface import Workflow
+
+
+def generate_structures_helper(
+    structure: Atoms,
+    supercell_matrix: Optional[list] = None,
+    primitive_matrix: Optional[list] = None,
+    phonon_supercell_matrix: Optional[list] = None,
+    mesh_numbers: Optional[list] = None,
+    cutoff_frequency: float = 0.0001,
+    frequency_factor_to_THz: float = VaspToTHz,
+    is_symmetry: bool = True,
+    is_mesh_symmetry: bool = True,
+    use_grg: bool = False,
+    SNF_coordinates: str = "reciprocal",
+    make_r0_average: bool = True,
+    symprec: float = 1e-05,
+    log_level: int = 0,
+):
+    if primitive_matrix is None:
+        primitive_matrix = (
+            structuretoolkit.analyse.get_primitive_cell(structure).cell.array
+            / np.diag(structure.cell.array).mean()
+        )
+    if supercell_matrix is None:
+        supercell_matrix = [2, 2, 2]
+    if phonon_supercell_matrix is None:
+        phonon_supercell_matrix = [4, 4, 4]
+    if mesh_numbers is None:
+        mesh_numbers = [11, 11, 11]
+    phono = Phono3py(
+        unitcell=structuretoolkit.common.atoms_to_phonopy(structure),
+        supercell_matrix=supercell_matrix,
+        primitive_matrix=primitive_matrix,
+        phonon_supercell_matrix=phonon_supercell_matrix,
+        cutoff_frequency=cutoff_frequency,
+        frequency_factor_to_THz=frequency_factor_to_THz,
+        is_symmetry=is_symmetry,
+        is_mesh_symmetry=is_mesh_symmetry,
+        use_grg=use_grg,
+        SNF_coordinates=SNF_coordinates,
+        make_r0_average=make_r0_average,
+        symprec=symprec,
+        calculator=None,
+        log_level=log_level,
+    )
+    phono.mesh_numbers = mesh_numbers
+    phono.generate_displacements()
+    phono.generate_fc2_displacements()
+    task_dict_lst = [
+        {"calc_forces": structuretoolkit.common.phonopy_to_atoms(s)}
+        for s in phono.supercells_with_displacements
+    ]
+    task_dict_phono_lst = [
+        {"calc_forces": structuretoolkit.common.phonopy_to_atoms(s)}
+        for s in phono.phonon_supercells_with_displacements
+    ]
+    supercell_count = len(task_dict_lst)
+    phonocell_count = len(task_dict_phono_lst)
+    return task_dict_lst + task_dict_phono_lst, supercell_count, phonocell_count, phono
+
+
+def analyse_structures_helper(
+    phono: Phono3py,
+    forces_lst: list,
+    supercell_count: int,
+):
+    phono.forces = np.array(forces_lst[:supercell_count])
+    phono.phonon_forces = np.array(forces_lst[supercell_count:])
+    phono.produce_fc2()
+    phono.produce_fc3()
+    phono.init_phph_interaction()
+    phono.run_phonon_solver()
+    phono.run_thermal_conductivity()
+    return {
+        "temperature": phono.thermal_conductivity.get_temperatures(),
+        "kappa": phono.thermal_conductivity.kappa[0],
+    }
+
+
+class ConductivityWorkflow(Workflow):
+    def __init__(
+        self,
+        structure: Atoms,
+        supercell_matrix: Optional[list] = None,
+        primitive_matrix: Optional[list] = None,
+        phonon_supercell_matrix: Optional[list] = None,
+        mesh_numbers: Optional[list] = None,
+        cutoff_frequency: float = 0.0001,
+        frequency_factor_to_THz: float = VaspToTHz,
+        is_symmetry: bool = True,
+        is_mesh_symmetry: bool = True,
+        use_grg: bool = False,
+        SNF_coordinates: str = "reciprocal",
+        make_r0_average: bool = True,
+        symprec: float = 1e-05,
+        log_level: int = 0,
+    ):
+        self._structure = structure
+        self._supercell_matrix = supercell_matrix
+        self._primitive_matrix = primitive_matrix
+        self._phonon_supercell_matrix = phonon_supercell_matrix
+        self._mesh_numbers = mesh_numbers
+        self._cutoff_frequency = cutoff_frequency
+        self._frequency_factor_to_THz = frequency_factor_to_THz
+        self._is_symmetry = is_symmetry
+        self._is_mesh_symmetry = is_mesh_symmetry
+        self._use_grg = use_grg
+        self._SNF_coordinates = SNF_coordinates
+        self._make_r0_average = make_r0_average
+        self._symprec = symprec
+        self._log_level = log_level
+        self._supercell_count = None
+        self._phonocell_count = None
+        self._phono = None
+
+    def generate_structures(self) -> dict:
+        task_dict_lst, supercell_count, phonocell_count, phono = (
+            generate_structures_helper(
+                structure=self._structure,
+                supercell_matrix=self._supercell_matrix,
+                primitive_matrix=self._primitive_matrix,
+                phonon_supercell_matrix=self._phonon_supercell_matrix,
+                mesh_numbers=self._mesh_numbers,
+                cutoff_frequency=self._cutoff_frequency,
+                frequency_factor_to_THz=self._frequency_factor_to_THz,
+                is_symmetry=self._is_symmetry,
+                is_mesh_symmetry=self._is_mesh_symmetry,
+                use_grg=self._use_grg,
+                SNF_coordinates=self._SNF_coordinates,
+                make_r0_average=self._make_r0_average,
+                symprec=self._symprec,
+                log_level=self._log_level,
+            )
+        )
+        self._supercell_count = supercell_count
+        self._phonocell_count = phonocell_count
+        self._phono = phono
+        return task_dict_lst
+
+    def analyse_structures(self, forces_lst: list) -> dict:
+        return analyse_structures_helper(
+            phono=self._phono,
+            forces_lst=forces_lst,
+            supercell_count=self._supercell_count,
+        )