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"""Tests of PhonopyYaml."""
import io
from pathlib import Path
import numpy as np
import yaml
import phonopy
from phonopy import Phonopy
from phonopy.interface.phonopy_yaml import (
PhonopyYaml,
PhonopyYamlLoader,
load_phonopy_yaml,
read_cell_yaml,
read_phonopy_yaml,
)
from phonopy.interface.vasp import read_vasp
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.structure.cells import get_primitive
from phonopy.structure.dataset import get_displacements_and_forces
cwd = Path(__file__).parent
def test_read_poscar_yaml(helper_methods):
"""Test to parse PhonopyAtoms.__str__ output."""
filename = cwd / "NaCl-vasp.yaml"
cell = _get_unitcell(filename)
_compare_NaCl_convcell(cell, helper_methods.compare_cells_with_order)
def test_read_phonopy_yaml(helper_methods):
"""Test to parse phonopy.yaml like file."""
filename = cwd / "phonopy.yaml"
cell = read_phonopy_yaml(filename).unitcell
_compare_NaCl_convcell(cell, helper_methods.compare_cells_with_order)
def test_read_phonopy_yaml_with_stream(helper_methods):
"""Test to parse phonopy.yaml like file stream."""
filename = cwd / "phonopy.yaml"
with open(filename) as fp:
cell = read_phonopy_yaml(fp).unitcell
_compare_NaCl_convcell(cell, helper_methods.compare_cells_with_order)
def test_PhonopyYaml_read(helper_methods):
"""Test to parse phonopy.yaml like file using PhonopyYaml.read()."""
filename = cwd / "phonopy.yaml"
cell = _get_unitcell(filename)
_compare_NaCl_convcell(cell, helper_methods.compare_cells_with_order)
def test_PhonopyYaml_read_with_stream(helper_methods):
"""Test to parse phonopy.yaml like file stream using PhonopyYaml.read()."""
filename = cwd / "phonopy.yaml"
with open(filename) as fp:
cell = _get_unitcell(fp)
_compare_NaCl_convcell(cell, helper_methods.compare_cells_with_order)
def test_read_cell_yaml(helper_methods):
"""Test to parse phonopy_symcells.yaml like file."""
filename = cwd / "phonopy_symcells_NaCl.yaml"
cell = read_cell_yaml(filename)
_compare_NaCl_convcell(cell, helper_methods.compare_cells)
pcell = read_cell_yaml(filename, cell_type="primitive")
helper_methods.compare_cells(pcell, get_primitive(cell, "F"))
def test_read_cell_yaml_with_stream(helper_methods):
"""Test to parse phonopy_symcells.yaml like file."""
filename = cwd / "phonopy_symcells_NaCl.yaml"
with open(filename) as fp:
cell = _get_unitcell(fp)
_compare_NaCl_convcell(cell, helper_methods.compare_cells)
fp.seek(0)
pcell = read_cell_yaml(fp, cell_type="primitive")
helper_methods.compare_cells(pcell, get_primitive(cell, "F"))
def test_write_phonopy_yaml(ph_nacl_nofcsym: Phonopy, helper_methods):
"""Test PhonopyYaml.set_phonon_info, __str__, yaml_data, parse."""
phonon = ph_nacl_nofcsym
phpy_yaml = PhonopyYaml(calculator="vasp")
phpy_yaml.set_phonon_info(phonon)
phpy_yaml_test = PhonopyYaml()
phpy_yaml_test._data = load_phonopy_yaml(
yaml.safe_load(io.StringIO(str(phpy_yaml))), calculator=phpy_yaml.calculator
)
helper_methods.compare_cells_with_order(
phpy_yaml.primitive, phpy_yaml_test.primitive
)
helper_methods.compare_cells_with_order(phpy_yaml.unitcell, phpy_yaml_test.unitcell)
helper_methods.compare_cells_with_order(
phpy_yaml.supercell, phpy_yaml_test.supercell
)
assert phpy_yaml.version == phpy_yaml_test.version
np.testing.assert_allclose(
phpy_yaml.supercell_matrix, phpy_yaml_test.supercell_matrix, atol=1e-8
)
np.testing.assert_allclose(
phpy_yaml.primitive_matrix, phpy_yaml_test.primitive_matrix, atol=1e-8
)
def test_write_phonopy_yaml_extra(ph_nacl_nofcsym: Phonopy):
"""Test PhonopyYaml.set_phonon_info, __str__, yaml_data, parse.
settings parameter controls amount of yaml output. In this test,
more data than the default are dumped and those are tested.
"""
phonon = ph_nacl_nofcsym
settings = {
"force_sets": True,
"displacements": True,
"force_constants": True,
"born_effective_charge": True,
"dielectric_constant": True,
}
phpy_yaml = PhonopyYaml(calculator="vasp", settings=settings)
phpy_yaml.set_phonon_info(phonon)
phpy_yaml_test = PhonopyYaml()
phpy_yaml_test._data = load_phonopy_yaml(
yaml.safe_load(io.StringIO(str(phpy_yaml))), calculator=phpy_yaml.calculator
)
np.testing.assert_allclose(
phpy_yaml.force_constants, phpy_yaml_test.force_constants, atol=1e-8
)
np.testing.assert_allclose(
phpy_yaml.nac_params["born"], phpy_yaml_test.nac_params["born"], atol=1e-8
)
np.testing.assert_allclose(
phpy_yaml.nac_params["dielectric"],
phpy_yaml_test.nac_params["dielectric"],
atol=1e-8,
)
np.testing.assert_allclose(
phpy_yaml.nac_params["factor"],
phpy_yaml_test.nac_params["factor"],
atol=1e-8,
)
disps, forces = get_displacements_and_forces(phpy_yaml.dataset)
disps_test, forces_test = get_displacements_and_forces(phpy_yaml_test.dataset)
np.testing.assert_allclose(forces, forces_test, atol=1e-8)
np.testing.assert_allclose(disps, disps_test, atol=1e-8)
def test_load_nac_yaml():
"""Test to read NAC params using PhonopyYamlLoader."""
pyl = PhonopyYamlLoader(yaml.safe_load(open(cwd / "nac.yaml"))).parse()
assert pyl.data.nac_params
for key in (
"dielectric",
"born",
"factor",
"method",
):
assert key in pyl.data.nac_params
assert pyl.data.nac_params["dielectric"].shape == (3, 3)
assert pyl.data.nac_params["born"].shape == (2, 3, 3)
assert isinstance(pyl.data.nac_params["factor"], float)
assert isinstance(pyl.data.nac_params["method"], str)
def test_phonopy_yaml_extended_symbol(nacl_unitcell_order1: PhonopyAtoms):
"""Test of PhonopyYaml with extended symbol."""
unitcell = nacl_unitcell_order1
symbols = unitcell.symbols
symbols[-1] = "Cl1"
cell = PhonopyAtoms(
cell=unitcell.cell,
symbols=symbols,
scaled_positions=unitcell.scaled_positions,
masses=unitcell.masses,
)
ph = Phonopy(cell, supercell_matrix=[2, 2, 2])
assert ph.primitive.symbols[:4] == ["Na"] * 4
assert ph.primitive.symbols[4:7] == ["Cl"] * 3
assert ph.primitive.symbols[-1] == "Cl1"
assert ph.unitcell.symbols[:4] == ["Na"] * 4
assert ph.unitcell.symbols[4:7] == ["Cl"] * 3
assert ph.unitcell.symbols[-1] == "Cl1"
assert ph.supercell.symbols[:32] == ["Na"] * 32
assert ph.supercell.symbols[-32:-8] == ["Cl"] * 24
assert ph.supercell.symbols[-8:] == ["Cl1"] * 8
ph_load = phonopy.load(io.StringIO(str(PhonopyYaml().set_phonon_info(ph))))
assert ph_load.primitive.symbols[:4] == ["Na"] * 4
assert ph_load.primitive.symbols[4:7] == ["Cl"] * 3
assert ph_load.primitive.symbols[-1] == "Cl1"
assert ph_load.unitcell.symbols[:4] == ["Na"] * 4
assert ph_load.unitcell.symbols[4:7] == ["Cl"] * 3
assert ph_load.unitcell.symbols[-1] == "Cl1"
assert ph_load.supercell.symbols[:32] == ["Na"] * 32
assert ph_load.supercell.symbols[-32:-8] == ["Cl"] * 24
assert ph_load.supercell.symbols[-8:] == ["Cl1"] * 8
def _compare_NaCl_convcell(cell, compare_cells):
cell_ref = read_vasp(cwd / ".." / "POSCAR_NaCl")
compare_cells(cell, cell_ref)
def _get_unitcell(filename):
phpy_yaml = PhonopyYaml().read(filename)
return phpy_yaml.unitcell
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