def setUp(self):
with open(os.path.join(test_dir, "NaCl_ph_dos.json"), "r") as f:
self.dos = PhononDos.from_dict(json.load(f))
with open(os.path.join(test_dir, "NaCl_complete_ph_dos.json"),
"r") as f:
self.structure = CompletePhononDos.from_dict(
json.load(f)).structure
def phdos(self):
"""
Returns: PhononDos object
"""
return PhononDos(self.tdos.frequency_points, self.tdos.dos)
def setUp(self):
with open(os.path.join(PymatgenTest.TEST_FILES_DIR,
"NaCl_ph_dos.json")) as f:
self.dos = PhononDos.from_dict(json.load(f))
with open(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"NaCl_complete_ph_dos.json")) as f:
self.structure = CompletePhononDos.from_dict(
json.load(f)).structure
def get_ph_dos(total_dos_path):
"""
Creates a pymatgen PhononDos from a total_dos.dat file.
Args:
total_dos_path: path to the total_dos.dat file.
"""
a = np.loadtxt(total_dos_path)
return PhononDos(a[:, 0], a[:, 1])
def get_phonon_dos_from_fc(
structure: Structure,
supercell_matrix: np.ndarray,
force_constants: np.ndarray,
mesh_density: float = 100.0,
num_dos_steps: int = 200,
**kwargs,
) -> CompletePhononDos:
"""
Get a projected phonon density of states from phonopy force constants.
Args:
structure: A structure.
supercell_matrix: The supercell matrix used to generate the force
constants.
force_constants: The force constants in phonopy format.
mesh_density: The density of the q-point mesh. See the docstring
for the ``mesh`` argument in Phonopy.init_mesh() for more details.
num_dos_steps: Number of frequency steps in the energy grid.
**kwargs: Additional kwargs passed to the Phonopy constructor.
Returns:
The density of states.
"""
structure_phonopy = get_phonopy_structure(structure)
phonon = Phonopy(structure_phonopy,
supercell_matrix=supercell_matrix,
**kwargs)
phonon.set_force_constants(force_constants)
phonon.run_mesh(
mesh_density,
is_mesh_symmetry=False,
with_eigenvectors=True,
is_gamma_center=True,
)
# get min, max, step frequency
frequencies = phonon.get_mesh_dict()["frequencies"]
freq_min = frequencies.min()
freq_max = frequencies.max()
freq_pitch = (freq_max - freq_min) / num_dos_steps
phonon.run_projected_dos(freq_min=freq_min,
freq_max=freq_max,
freq_pitch=freq_pitch)
dos_raw = phonon.projected_dos.get_partial_dos()
pdoss = dict(zip(structure, dos_raw[1]))
total_dos = PhononDos(dos_raw[0], dos_raw[1].sum(axis=0))
return CompletePhononDos(structure, total_dos, pdoss)
def get_complete_ph_dos(partial_dos_path, phonopy_yaml_path):
"""
Creates a pymatgen CompletePhononDos from a partial_dos.dat and phonopy.yaml files.
The second is produced when generating a Dos and is needed to extract
the structure.
Args:
partial_dos_path: path to the partial_dos.dat file.
phonopy_yaml_path: path to the phonopy.yaml file.
"""
a = np.loadtxt(partial_dos_path).transpose()
d = loadfn(phonopy_yaml_path)
structure = get_structure_from_dict(d['primitive_cell'])
total_dos = PhononDos(a[0], a[1:].sum(axis=0))
pdoss = {}
for site, pdos in zip(structure, a[1:]):
pdoss[site] = pdos.tolist()
return CompletePhononDos(structure, total_dos, pdoss)
def setUp(self):
with open(os.path.join(test_dir, "NaCl_ph_dos.json"), "r") as f:
self.dos = PhononDos.from_dict(json.load(f))
with open(os.path.join(test_dir, "NaCl_complete_ph_dos.json"), "r") as f:
self.structure = CompletePhononDos.from_dict(json.load(f)).structure
def setUp(self):
with open(os.path.join(test_dir, "NaCl_ph_dos.json"), "r") as f:
self.dos = PhononDos.from_dict(json.load(f))
def setUp(self):
with open(os.path.join(test_dir, "NaCl_ph_dos.json"), "r") as f:
self.dos = PhononDos.from_dict(json.load(f))