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|
"""Tests of Phonopy API."""
import copy
from pathlib import Path
import numpy as np
import pytest
import phonopy
from phonopy import Phonopy
from phonopy.interface.pypolymlp import PypolymlpParams
from phonopy.structure.dataset import get_displacements_and_forces
cwd = Path(__file__).parent
def test_displacements_setter_NaCl(ph_nacl: Phonopy):
"""Test Phonopy.displacements setter and getter."""
ph_in = ph_nacl
assert ph_in.dataset is not None
displacements, _ = get_displacements_and_forces(ph_in.dataset)
ph = Phonopy(
ph_in.unitcell,
supercell_matrix=ph_in.supercell_matrix,
primitive_matrix=ph_in.primitive_matrix,
)
ph.displacements = displacements
np.testing.assert_allclose(displacements, ph.displacements)
def test_displacements_masses_setter_NaCl(ph_nacl: Phonopy):
"""Test Phonopy.masses setter and getter."""
ph_in = ph_nacl
ph = Phonopy(
ph_in.unitcell,
supercell_matrix=ph_in.supercell_matrix,
primitive_matrix=ph_in.primitive_matrix,
)
ph.masses = ph_in.masses * 2
np.testing.assert_allclose(ph.primitive.masses, ph_in.primitive.masses * 2)
np.testing.assert_allclose(ph.unitcell.masses, ph_in.unitcell.masses * 2)
np.testing.assert_allclose(ph.supercell.masses, ph_in.supercell.masses * 2)
def test_forces_setter_NaCl_type1(ph_nacl: Phonopy):
"""Test Phonopy.forces setter and getter (type1 dataset)."""
ph_in = ph_nacl
forces = ph_in.forces
ph = Phonopy(
ph_in.unitcell,
supercell_matrix=ph_in.supercell_matrix,
primitive_matrix=ph_in.primitive_matrix,
)
ph.dataset = ph_in.dataset
ph.forces = forces
np.testing.assert_allclose(ph.forces, forces)
def test_forces_setter_NaCl_type2(ph_nacl: Phonopy):
"""Test Phonopy.forces setter and getter (type2 dataset)."""
ph_in = ph_nacl
assert ph_in.dataset is not None
displacements, forces = get_displacements_and_forces(ph_in.dataset)
ph = Phonopy(
ph_in.unitcell,
supercell_matrix=ph_in.supercell_matrix,
primitive_matrix=ph_in.primitive_matrix,
)
ph.displacements = displacements
assert forces is not None
ph.forces = forces
np.testing.assert_allclose(ph.forces, forces)
def test_energies_setter_NaCl_type1(ph_nacl_fd: Phonopy):
"""Test Phonopy.energies setter and getter (type1 dataset)."""
ph_in = ph_nacl_fd
energies = ph_in.supercell_energies
ref_supercell_energies = [-216.82820693, -216.82817843]
np.testing.assert_allclose(energies, ref_supercell_energies)
ph = Phonopy(
ph_in.unitcell,
supercell_matrix=ph_in.supercell_matrix,
primitive_matrix=ph_in.primitive_matrix,
)
ph.dataset = ph_in.dataset
np.testing.assert_allclose(energies, ph.supercell_energies)
ph.supercell_energies = ph_in.supercell_energies + 1
np.testing.assert_allclose(ph.supercell_energies, ph_in.supercell_energies + 1)
def test_energies_setter_NaCl_type2(ph_nacl_rd: Phonopy):
"""Test Phonopy.energies setter and getter (type2 dataset)."""
ph_in = ph_nacl_rd
energies = ph_in.supercell_energies
ref_supercell_energies = [
-216.84472784,
-216.84225045,
-216.84473283,
-216.84431749,
-216.84276813,
-216.84204234,
-216.84150156,
-216.84438529,
-216.84339285,
-216.84005085,
]
np.testing.assert_allclose(energies, ref_supercell_energies)
ph = Phonopy(
ph_in.unitcell,
supercell_matrix=ph_in.supercell_matrix,
primitive_matrix=ph_in.primitive_matrix,
)
ph.dataset = ph_in.dataset
np.testing.assert_allclose(energies, ph.supercell_energies)
ph.supercell_energies = ph_in.supercell_energies + 1
np.testing.assert_allclose(ph.supercell_energies, ph_in.supercell_energies + 1)
def test_mlp_NaCl_type2(ph_nacl_rd: Phonopy):
"""Test MLP features in Phonopy."""
pytest.importorskip("pypolymlp", minversion="0.10.0")
pytest.importorskip("symfc")
atom_energies = {"Cl": -0.31144759, "Na": -0.24580545}
params = PypolymlpParams(gtinv_maxl=(4, 4), atom_energies=atom_energies)
ph_in = ph_nacl_rd
ph = Phonopy(
ph_in.unitcell,
supercell_matrix=ph_in.supercell_matrix,
primitive_matrix=ph_in.primitive_matrix,
log_level=2,
)
ph.nac_params = ph_in.nac_params
assert ph_in.dataset is not None
ph.mlp_dataset = copy.copy(ph_in.dataset)
ph.develop_mlp(params=params)
# ph.generate_displacements(distance=0.001, number_of_snapshots=2, random_seed=1)
displacements = [
[0.000180268321, -0.000453658023, 0.000872752961],
[0.000536302753, 0.000050282117, -0.000842526596],
[0.000330618905, 0.000445286170, -0.000832112593],
[-0.000977576278, -0.000171846132, -0.000121710833],
[0.000607898748, -0.000579136579, 0.000543194196],
[0.000555067463, 0.000770704299, 0.000312913718],
[-0.000270591925, -0.000887099147, 0.000373945335],
[0.000364662102, -0.000646885856, -0.000669746400],
[0.000359734499, 0.000038998419, 0.000932239354],
[0.000195533352, -0.000904804839, 0.000378278881],
[0.000017818877, 0.000017550564, -0.000999687184],
[0.000334379657, -0.000033555286, 0.000941840904],
[-0.000286551811, 0.000349696633, 0.000891964307],
[-0.000135098844, -0.000758622299, -0.000637369995],
[-0.000608721346, -0.000790266333, 0.000070266958],
[0.000384760855, 0.000214070436, 0.000897849059],
[0.000013841826, -0.000856378711, -0.000516162676],
[-0.000079142622, 0.000838911994, -0.000538482229],
[-0.000468826199, -0.000418905515, -0.000777637554],
[-0.000268087282, -0.000760751939, -0.000591088569],
[0.000007848629, 0.000830081071, -0.000557587494],
[-0.000412491332, -0.000059615806, 0.000909008722],
[0.000583819791, -0.000802793210, 0.000121150786],
[0.000585221724, 0.000364440907, -0.000724360656],
[-0.000935217657, 0.000295063265, 0.000195718173],
[-0.000699970508, -0.000166726794, 0.000694437517],
[-0.000140708283, -0.000226715275, 0.000963743412],
[-0.000357234776, 0.000411213978, 0.000838621714],
[0.000228795432, -0.000973234658, 0.000021609030],
[0.000197815347, 0.000399039275, 0.000895341692],
[0.000906486344, 0.000085304595, -0.000413528275],
[-0.000740336533, -0.000449341675, 0.000499993877],
[-0.000261310807, -0.000963364513, -0.000060377788],
[0.000870822149, -0.000096174508, 0.000482098795],
[0.000546221585, -0.000739403615, 0.000393604210],
[0.000408838031, 0.000617459207, -0.000672008625],
[-0.000936345792, 0.000262474817, 0.000233159879],
[-0.000751311446, 0.000356530493, 0.000555353148],
[0.000145685606, 0.000117114073, -0.000982374673],
[0.000173753618, 0.000419028597, -0.000891192861],
[-0.000745516709, -0.000475608261, -0.000466906435],
[-0.000384951997, 0.000376399525, -0.000842695293],
[-0.000035517628, 0.000879858577, 0.000473906513],
[-0.000574194999, -0.000188219889, 0.000796789418],
[-0.000098215583, -0.000592446474, 0.000799600447],
[0.000313320598, -0.000517929638, 0.000795976817],
[0.000073314590, -0.000991531263, -0.000107194801],
[-0.000564042854, -0.000781494973, 0.000266685705],
[0.000623511496, 0.000145121020, -0.000768227378],
[0.000688006698, -0.000224596761, 0.000690074690],
[0.000177528488, 0.000796142755, 0.000578481072],
[-0.000659533276, 0.000000162534, 0.000751675350],
[0.000761914593, 0.000337309495, -0.000552909086],
[-0.000464787706, 0.000882434676, 0.000072673446],
[0.000931458075, -0.000318646515, -0.000175642402],
[-0.000423266534, 0.000567390964, 0.000706337692],
[0.000811828321, -0.000561681248, 0.000159527280],
[-0.000009794644, -0.000394612095, -0.000918795603],
[-0.000917520322, -0.000269115301, 0.000292802689],
[-0.000164198626, -0.000060007868, 0.000984600359],
[0.000034663251, -0.000897822527, 0.000438991082],
[0.000296035060, -0.000038085104, 0.000954417502],
[-0.000507436256, -0.000861487867, 0.000018630641],
[-0.000417040087, 0.000524283593, -0.000742431330],
[0.000109479743, -0.000044429923, -0.000992995553],
[-0.000315952423, -0.000434554398, -0.000843407696],
[0.000248711151, -0.000959271491, -0.000133943908],
[0.000838362745, -0.000424336937, 0.000342178420],
[-0.000915490715, -0.000123865082, 0.000382797848],
[0.000225588394, -0.000926260058, -0.000301914194],
[0.000678113565, -0.000509310476, 0.000529872468],
[-0.000662290126, -0.000416648648, -0.000622716383],
[-0.000679239662, -0.000436273575, -0.000590168492],
[0.000510270225, 0.000637097261, 0.000577694883],
[0.000171060563, 0.000767991408, -0.000617193229],
[0.000311891939, 0.000005577608, -0.000950101210],
[-0.000285022166, 0.000391020374, -0.000875137379],
[-0.000742080749, -0.000668649865, 0.000047154221],
[-0.000034953305, 0.000202524320, -0.000978653241],
[-0.000779346397, -0.000053462565, -0.000624308375],
[0.000797012992, 0.000498226591, -0.000341380366],
[0.000089955695, 0.000743474829, -0.000662686315],
[-0.000514184744, -0.000719123655, -0.000467413326],
[-0.000913862571, 0.000199529903, -0.000353614224],
[0.000584220150, -0.000726561971, -0.000361655248],
[0.000438770705, 0.000382247620, 0.000813244751],
[-0.000424456131, -0.000870675074, 0.000248519432],
[-0.000000633079, -0.000299034961, -0.000954241946],
[0.000452396031, 0.000205837949, -0.000867737616],
[0.000448029552, 0.000586822782, 0.000674469082],
[0.000419253562, 0.000035786554, 0.000907163587],
[0.000279226575, -0.000863126212, 0.000420767944],
[-0.000147749171, -0.000862441833, 0.000484111833],
[-0.000124657458, 0.000425963710, 0.000896111285],
[0.000999755946, -0.000005207967, -0.000021469160],
[-0.000795940478, -0.000595425502, -0.000109303373],
[-0.000083944712, 0.000510770307, -0.000855609128],
[0.000049889341, 0.000629281721, -0.000775574348],
[-0.000519037986, 0.000318052532, 0.000793373907],
[0.000222101337, -0.000224646491, -0.000948791310],
[-0.000618130873, 0.000786003433, 0.000010622050],
[0.000439368229, -0.000540554267, -0.000717465431],
[-0.000210145069, 0.000953743624, 0.000214970116],
[0.000550756193, -0.000403614562, 0.000730590789],
[0.000861918314, 0.000476875033, -0.000172299227],
[0.000294442568, 0.000773260802, 0.000561579297],
[-0.000647672986, -0.000544329599, 0.000533127556],
[-0.000958579939, -0.000032428810, 0.000282971504],
[0.000714544090, 0.000015874900, 0.000699410274],
[-0.000078029664, 0.000834102940, 0.000546061953],
[-0.000665035019, 0.000686276604, -0.000294538361],
[0.000102753664, -0.000868485814, -0.000484947498],
[-0.000195298729, 0.000466901888, -0.000862473787],
[0.000693979808, 0.000606796409, 0.000387543732],
[0.000015790804, 0.000988458582, -0.000150666125],
[0.000004290865, -0.000524016021, 0.000851697598],
[-0.000348973828, -0.000261934267, 0.000899782033],
[0.000328409977, 0.000932542909, -0.000150035366],
[-0.000595572294, -0.000780605767, -0.000189600315],
[0.000305891510, -0.000550999592, 0.000776421171],
[0.000615171274, 0.000208731729, -0.000760260067],
[-0.000807433341, 0.000539322252, -0.000239129481],
[-0.000904567307, -0.000245259646, 0.000348720080],
[0.000502975931, 0.000440396051, -0.000743684430],
[0.000981936098, 0.000045073472, -0.000183765833],
[-0.000540310857, 0.000819838365, -0.000189550079],
[-0.000884174313, -0.000001073455, 0.000467155897],
[0.000507583278, 0.000853411695, 0.000118522969],
]
ph.displacements = np.reshape(displacements, (2, -1, 3))
ph.evaluate_mlp()
ph.produce_force_constants(fc_calculator="symfc")
ph.run_mesh([2, 2, 2])
freqs = ph.get_mesh_dict()["frequencies"]
print(freqs.ravel().tolist())
freqs_ref = [
1.9479582873751362,
1.9479582873751387,
3.201448818645571,
4.3184184471176446,
4.318418447117647,
6.962692062451476,
2.7407481459662795,
3.55742972698832,
3.921702373852099,
4.487456193539974,
4.894982489029413,
5.46152086052448,
]
np.testing.assert_allclose(freqs.ravel(), freqs_ref, atol=1e-5)
def test_load_mlp_pypolymlp(ph_kcl: Phonopy):
"""Test load_mlp."""
pytest.importorskip("pypolymlp", minversion="0.9.2")
ph_kcl.load_mlp(cwd / ".." / "polymlp_KCL-120.yaml")
ph_kcl.load_mlp(cwd / ".." / "polymlp_KCL-120.yaml.xz")
def test_Phonopy_calculator():
"""Test phonopy_load with phonopy_params.yaml."""
ph_orig = phonopy.load(
cwd / ".." / "phonopy_params_NaCl-fd.yaml.xz", produce_fc=False, log_level=2
)
ph = Phonopy(
unitcell=ph_orig.unitcell,
supercell_matrix=ph_orig.supercell_matrix,
primitive_matrix=ph_orig.primitive_matrix,
)
assert ph.calculator is None
assert ph.unit_conversion_factor == pytest.approx(15.6333023)
with pytest.warns(DeprecationWarning):
ph = Phonopy(
unitcell=ph_orig.unitcell,
supercell_matrix=ph_orig.supercell_matrix,
primitive_matrix=ph_orig.primitive_matrix,
factor=100,
)
assert ph.unit_conversion_factor == pytest.approx(100)
def test_Phonopy_calculator_QE():
"""Test phonopy_load with phonopy_params.yaml for QE."""
ph_orig = phonopy.load(
cwd / ".." / "phonopy_params_NaCl-QE.yaml.xz", produce_fc=False, log_level=2
)
ph = Phonopy(
unitcell=ph_orig.unitcell,
supercell_matrix=ph_orig.supercell_matrix,
primitive_matrix=ph_orig.primitive_matrix,
calculator="qe",
set_factor_by_calculator=False,
)
assert ph.calculator == "qe"
assert ph.unit_conversion_factor == pytest.approx(15.6333023)
ph = Phonopy(
unitcell=ph_orig.unitcell,
supercell_matrix=ph_orig.supercell_matrix,
primitive_matrix=ph_orig.primitive_matrix,
calculator="qe",
set_factor_by_calculator=True,
)
assert ph.unit_conversion_factor == pytest.approx(108.9707718)
|
