mirror of https://github.com/phonopy/phono3py.git
210 lines
7.0 KiB
Python
210 lines
7.0 KiB
Python
"""Tests of Phono3py API."""
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from __future__ import annotations
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from pathlib import Path
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import numpy as np
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import pytest
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from phonopy.interface.pypolymlp import PypolymlpParams
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from phono3py import Phono3py
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cwd = Path(__file__).parent
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def test_displacements_setter_NaCl(nacl_pbe: Phono3py):
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"""Test Phono3py.displacements setter.
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Just check no error.
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"""
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ph3_in = nacl_pbe
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displacements = ph3_in.displacements
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ph3 = Phono3py(
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ph3_in.unitcell,
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supercell_matrix=ph3_in.supercell_matrix,
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primitive_matrix=ph3_in.primitive_matrix,
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)
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ph3.displacements = displacements
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def test_displacements_setter_Si(si_pbesol_111_222_fd: Phono3py):
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"""Test Phono3py.displacements setter and Phono3py.phonon_displacements setter.
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Just check no error.
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"""
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ph3_in = si_pbesol_111_222_fd
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displacements = ph3_in.displacements
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phonon_displacements = ph3_in.phonon_displacements
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ph3 = Phono3py(
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ph3_in.unitcell,
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supercell_matrix=ph3_in.supercell_matrix,
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phonon_supercell_matrix=ph3_in.phonon_supercell_matrix,
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primitive_matrix=ph3_in.primitive_matrix,
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)
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ph3.displacements = displacements
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ph3.phonon_displacements = phonon_displacements
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def test_type1_forces_energies_setter_Si(si_111_222_fd: Phono3py):
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"""Test type1 supercell_energies, phonon_supercell_energies attributes."""
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ph3_in = si_111_222_fd
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ref_ph_supercell_energies = [-346.85204143]
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ref_supercell_energies = [
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-43.3509760,
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-43.33608775,
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-43.35352904,
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-43.34370672,
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-43.34590849,
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-43.34540162,
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-43.34421408,
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-43.34481089,
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-43.34703607,
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-43.34241924,
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-43.34786243,
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-43.34168203,
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-43.34274245,
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-43.34703607,
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-43.34786243,
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-43.34184454,
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]
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np.testing.assert_allclose(ph3_in.supercell_energies, ref_supercell_energies)
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np.testing.assert_allclose(
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ph3_in.phonon_supercell_energies, ref_ph_supercell_energies
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)
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ref_force00 = [-0.4109520800000000, 0.0000000100000000, 0.0000000300000000]
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ref_force_last = [0.1521426300000000, 0.0715600600000000, -0.0715600700000000]
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ref_ph_force00 = [-0.4027479600000000, 0.0000000200000000, 0.0000001000000000]
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np.testing.assert_allclose(ph3_in.forces[0, 0], ref_force00)
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np.testing.assert_allclose(ph3_in.forces[-1, -1], ref_force_last)
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np.testing.assert_allclose(ph3_in.phonon_forces[0, 0], ref_ph_force00)
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ph3 = Phono3py(
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ph3_in.unitcell,
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supercell_matrix=ph3_in.supercell_matrix,
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phonon_supercell_matrix=ph3_in.phonon_supercell_matrix,
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primitive_matrix=ph3_in.primitive_matrix,
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)
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ph3.dataset = ph3_in.dataset
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ph3.phonon_dataset = ph3_in.phonon_dataset
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ph3.supercell_energies = ph3_in.supercell_energies + 1
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ph3.phonon_supercell_energies = ph3_in.phonon_supercell_energies + 1
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np.testing.assert_allclose(ph3_in.supercell_energies + 1, ph3.supercell_energies)
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np.testing.assert_allclose(
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ph3_in.phonon_supercell_energies + 1, ph3.phonon_supercell_energies
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)
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ph3.forces = ph3_in.forces + 1
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ph3.phonon_forces = ph3_in.phonon_forces + 1
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np.testing.assert_allclose(ph3_in.forces + 1, ph3.forces)
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np.testing.assert_allclose(ph3_in.phonon_forces + 1, ph3.phonon_forces)
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def test_type2_forces_energies_setter_Si(si_111_222_rd: Phono3py):
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"""Test type2 supercell_energies, phonon_supercell_energies attributes."""
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ph3_in = si_111_222_rd
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ref_ph_supercell_energies = [
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-346.81061270, # 1
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-346.81263617, # 2
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]
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ref_supercell_energies = [
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-43.35270268, # 1
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-43.35211687, # 2
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-43.35122776, # 3
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-43.35226673, # 4
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-43.35146358, # 5
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-43.35133209, # 6
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-43.35042212, # 7
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-43.35008442, # 8
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-43.34968796, # 9
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-43.35348999, # 10
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-43.35134937, # 11
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-43.35335251, # 12
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-43.35160892, # 13
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-43.35009115, # 14
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-43.35202797, # 15
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-43.35076370, # 16
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-43.35174477, # 17
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-43.35107001, # 18
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-43.35037949, # 19
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-43.35126123, # 20
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]
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np.testing.assert_allclose(ph3_in.supercell_energies, ref_supercell_energies)
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np.testing.assert_allclose(
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ph3_in.phonon_supercell_energies, ref_ph_supercell_energies
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)
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ref_force00 = [0.0445647800000000, 0.1702929900000000, 0.0913398200000000]
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ref_force_last = [-0.1749668700000000, 0.0146997300000000, -0.1336066300000000]
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ref_ph_force00 = [-0.0161598900000000, -0.1161657500000000, 0.1399128100000000]
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ref_ph_force_last = [0.1049486700000000, 0.0795870900000000, 0.1062164600000000]
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np.testing.assert_allclose(ph3_in.forces[0, 0], ref_force00)
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np.testing.assert_allclose(ph3_in.forces[-1, -1], ref_force_last)
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np.testing.assert_allclose(ph3_in.phonon_forces[0, 0], ref_ph_force00)
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np.testing.assert_allclose(ph3_in.phonon_forces[-1, -1], ref_ph_force_last)
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ph3 = Phono3py(
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ph3_in.unitcell,
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supercell_matrix=ph3_in.supercell_matrix,
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phonon_supercell_matrix=ph3_in.phonon_supercell_matrix,
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primitive_matrix=ph3_in.primitive_matrix,
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)
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ph3.dataset = ph3_in.dataset
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ph3.phonon_dataset = ph3_in.phonon_dataset
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ph3.supercell_energies = ph3_in.supercell_energies + 1
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ph3.phonon_supercell_energies = ph3_in.phonon_supercell_energies + 1
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np.testing.assert_allclose(ph3_in.supercell_energies + 1, ph3.supercell_energies)
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np.testing.assert_allclose(
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ph3_in.phonon_supercell_energies + 1, ph3.phonon_supercell_energies
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)
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ph3.forces = ph3_in.forces + 1
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ph3.phonon_forces = ph3_in.phonon_forces + 1
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np.testing.assert_allclose(ph3_in.forces + 1, ph3.forces)
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np.testing.assert_allclose(ph3_in.phonon_forces + 1, ph3.phonon_forces)
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def test_use_pypolymlp_mgo(mgo_222rd_444rd: Phono3py):
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"""Test use_pypolymlp in produce_fc3."""
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pytest.importorskip("pypolymlp")
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pytest.importorskip("symfc")
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ph3_in = mgo_222rd_444rd
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ph3 = Phono3py(
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ph3_in.unitcell,
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supercell_matrix=ph3_in.supercell_matrix,
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phonon_supercell_matrix=ph3_in.phonon_supercell_matrix,
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primitive_matrix=ph3_in.primitive_matrix,
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log_level=2,
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)
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ph3.mlp_dataset = {
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"displacements": ph3_in.displacements[:10],
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"forces": ph3_in.forces[:10],
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"supercell_energies": ph3_in.supercell_energies[:10],
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}
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ph3.phonon_dataset = ph3_in.phonon_dataset
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ph3.nac_params = ph3_in.nac_params
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ph3.displacements = ph3_in.displacements[:100]
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atom_energies = {"Mg": -0.00896717, "O": -0.95743902}
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params = PypolymlpParams(gtinv_maxl=(4, 4), atom_energies=atom_energies)
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ph3.generate_displacements(distance=0.001, is_plusminus=True)
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ph3.develop_mlp(params=params)
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ph3.evaluate_mlp()
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ph3.produce_fc3(fc_calculator="symfc")
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ph3.produce_fc2(fc_calculator="symfc")
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ph3.mesh_numbers = 30
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ph3.init_phph_interaction()
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ph3.run_thermal_conductivity(temperatures=[300])
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assert (
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pytest.approx(63.0018546, abs=1e-1) == ph3.thermal_conductivity.kappa[0, 0, 0]
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)
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