def test_write_phonopy_yaml_extra(self):
phonopy = self._get_phonon()
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(phonopy)
def get_phonopy_yaml_txt(structure,
settings,
supercell_matrix=None,
primitive_matrix=None,
calculator=None):
unitcell = phonopy_atoms_from_structure(structure)
ph = Phonopy(unitcell,
supercell_matrix=settings['supercell_matrix'],
primitive_matrix='auto',
calculator=calculator)
phpy_yaml = PhonopyYaml()
phpy_yaml.set_phonon_info(ph)
return str(phpy_yaml)
def run_task(self, fw_spec):
unitcell = read_vasp("POSCAR-unitcell")
phonon = phonopy.Phonopy(unitcell, self.get("supercell"))
supercell = phonon.get_supercell()
phonon.generate_displacements()
supercells = phonon.supercells_with_displacements
ids = np.arange(len(supercells)) + 1
write_supercells_with_displacements(supercell, supercells, ids)
units = get_default_physical_units("vasp")
phpy_yaml = PhonopyYaml(physical_units=units,
settings={
'force_sets': False,
'born_effective_charge': False,
'dielectric_constant': False,
'displacements': True
})
phpy_yaml.set_phonon_info(phonon)
with open("phonopy_disp.yaml", 'w') as w:
w.write(str(phpy_yaml))
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.yaml_data = yaml.safe_load(StringIO(str(phpy_yaml)))
phpy_yaml_test.parse()
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_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.yaml_data = yaml.safe_load(StringIO(str(phpy_yaml)))
phpy_yaml_test.parse()
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)
import phonopy
from phonopy.interface.phonopy_yaml import PhonopyYaml
phonon = phonopy.load(supercell_matrix=[[2, 0, 0], [0, 2, 0], [0, 0, 2]],
primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5],
[0.5, 0.5, 0]],
unitcell_filename="POSCAR-unitcell",
force_sets_filename="FORCE_SETS",
born_filename="BORN")
phpy_yaml = PhonopyYaml(calculator='vasp', settings={'force_constants': True})
phpy_yaml.set_phonon_info(phonon)
print(phpy_yaml)
def test_write_phonopy_yaml(self):
phonopy = self._get_phonon()
phpy_yaml = PhonopyYaml(calculator='vasp')
phpy_yaml.set_phonon_info(phonopy)
from phonopy import Phonopy
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS, parse_BORN
from phonopy.interface.phonopy_yaml import PhonopyYaml
unitcell = read_vasp("POSCAR")
phonon = Phonopy(unitcell,
[[2, 0, 0],
[0, 2, 0],
[0, 0, 2]],
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]])
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, filename="BORN")
phonon.set_nac_params(nac_params)
phpy_yaml = PhonopyYaml(calculator='vasp',
show_force_constants=True)
phpy_yaml.set_phonon_info(phonon)
print(phpy_yaml)
def test_write_phonopy_yaml(self):
phonopy = self._get_phonon()
phpy_yaml = PhonopyYaml(calculator='vasp')
phpy_yaml.set_phonon_info(phonopy)