def get_properties_from_phonopy(structure, phonopy_input, force_constants):
"""
Calculate DOS and thermal properties using phonopy (locally)
:param structure: Aiida StructureData Object
:param phonopy_input: Aiida Parametersdata object containing a dictionary with the data needed to run phonopy:
supercells matrix, primitive matrix and q-points mesh.
:param force_constants:
:return:
"""
from phonopy.structure.atoms import Atoms as PhonopyAtoms
from phonopy import Phonopy
# Generate phonopy phonon object
bulk = PhonopyAtoms(symbols=[site.kind_name for site in structure.sites],
positions=[site.position for site in structure.sites],
cell=structure.cell)
phonopy_input = phonopy_input.get_dict()
force_constants = force_constants.get_array('force_constants')
phonon = Phonopy(bulk,
phonopy_input['supercell'],
primitive_matrix=phonopy_input['primitive'])
phonon.set_force_constants(force_constants)
#Normalization factor primitive to unit cell
normalization_factor = phonon.unitcell.get_number_of_atoms(
) / phonon.primitive.get_number_of_atoms()
phonon.set_mesh(phonopy_input['mesh'],
is_eigenvectors=True,
is_mesh_symmetry=False)
phonon.set_total_DOS()
phonon.set_partial_DOS()
# get DOS (normalized to unit cell)
total_dos = phonon.get_total_DOS() * normalization_factor
partial_dos = phonon.get_partial_DOS() * normalization_factor
# Stores DOS data in DB as a workflow result
dos = ArrayData()
dos.set_array('frequency', total_dos[0])
dos.set_array('total_dos', total_dos[1])
dos.set_array('partial_dos', partial_dos[1])
#THERMAL PROPERTIES (per primtive cell)
phonon.set_thermal_properties()
t, free_energy, entropy, cv = phonon.get_thermal_properties()
# Stores thermal properties (per unit cell) data in DB as a workflow result
thermal_properties = ArrayData()
thermal_properties.set_array('temperature', t)
thermal_properties.set_array('free_energy',
free_energy * normalization_factor)
thermal_properties.set_array('entropy', entropy * normalization_factor)
thermal_properties.set_array('cv', cv * normalization_factor)
return {'thermal_properties': thermal_properties, 'dos': dos}
def phonopy_calculation_inline(**kwargs):
from phonopy.structure.atoms import Atoms as PhonopyAtoms
from phonopy import Phonopy
structure = kwargs.pop('structure')
phonopy_input = kwargs.pop('phonopy_input').get_dict()
force_constants = kwargs.pop('force_constants').get_array(
'force_constants')
# Generate phonopy phonon object
bulk = PhonopyAtoms(symbols=[site.kind_name for site in structure.sites],
positions=[site.position for site in structure.sites],
cell=structure.cell)
phonon = Phonopy(bulk,
phonopy_input['supercell'],
primitive_matrix=phonopy_input['primitive'],
distance=phonopy_input['distance'])
phonon.set_force_constants(force_constants)
# Normalization factor primitive to unit cell
normalization_factor = phonon.unitcell.get_number_of_atoms(
) / phonon.primitive.get_number_of_atoms()
phonon.set_mesh(phonopy_input['mesh'],
is_eigenvectors=True,
is_mesh_symmetry=False)
phonon.set_total_DOS()
phonon.set_partial_DOS()
# get DOS (normalized to unit cell)
total_dos = phonon.get_total_DOS() * normalization_factor
partial_dos = phonon.get_partial_DOS() * normalization_factor
# Stores DOS data in DB as a workflow result
dos = ArrayData()
dos.set_array('frequency', total_dos[0])
dos.set_array('total_dos', total_dos[1])
dos.set_array('partial_dos', partial_dos[1])
# THERMAL PROPERTIES (per primtive cell)
phonon.set_thermal_properties()
t, free_energy, entropy, cv = phonon.get_thermal_properties()
# Stores thermal properties (per unit cell) data in DB as a workflow result
thermal_properties = ArrayData()
thermal_properties.set_array('temperature', t)
thermal_properties.set_array('free_energy',
free_energy * normalization_factor)
thermal_properties.set_array('entropy', entropy * normalization_factor)
thermal_properties.set_array('cv', cv * normalization_factor)
return {'thermal_properties': thermal_properties, 'dos': dos}
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.5, 0.5])
phonon.set_band_structure(bands)
q_points, distances, frequencies, eigvecs = phonon.get_band_structure()
for q, d, freq in zip(q_points, distances, frequencies):
print q, d, freq
phonon.plot_band_structure().show()
# Mesh sampling 20x20x20
phonon.set_mesh([20, 20, 20])
phonon.set_thermal_properties(t_step=10,
t_max=1000,
t_min=0)
# DOS
phonon.set_total_DOS(sigma=0.1)
for omega, dos in np.array(phonon.get_total_DOS()).T:
print "%15.7f%15.7f" % (omega, dos)
phonon.plot_total_DOS().show()
# Thermal properties
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
print ("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv )
phonon.plot_thermal_properties().show()
# PDOS
phonon.set_mesh([10, 10, 10],
is_mesh_symmetry=False,
is_eigenvectors=True)
phonon.set_partial_DOS(tetrahedron_method=True)
omegas, pdos = phonon.get_partial_DOS()
pdos_indices = [[0], [1]]
append_band(bands, [0.5, 0.0, 0.0], [0.5, 0.5, 0.0])
append_band(bands, [0.5, 0.5, 0.0], [0.0, 0.0, 0.0])
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.5, 0.5])
phonon.set_band_structure(bands)
q_points, distances, frequencies, eigvecs = phonon.get_band_structure()
for q, d, freq in zip(q_points, distances, frequencies):
print q, d, freq
phonon.plot_band_structure().show()
# Mesh sampling 20x20x20
phonon.set_mesh([20, 20, 20])
phonon.set_thermal_properties(t_step=10, t_max=1000, t_min=0)
# DOS
phonon.set_total_DOS(sigma=0.1)
for omega, dos in np.array(phonon.get_total_DOS()).T:
print "%15.7f%15.7f" % (omega, dos)
phonon.plot_total_DOS().show()
# Thermal properties
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
print("%12.3f " + "%15.7f" * 3) % (t, free_energy, entropy, cv)
phonon.plot_thermal_properties().show()
# PDOS
phonon.set_mesh([10, 10, 10], is_mesh_symmetry=False, is_eigenvectors=True)
phonon.set_partial_DOS(tetrahedron_method=True)
omegas, pdos = phonon.get_partial_DOS()
pdos_indices = [[0], [1]]
phonon.plot_partial_DOS(pdos_indices=pdos_indices, legend=pdos_indices).show()
def phonopy_calculation_inline(**kwargs):
from phonopy.structure.atoms import Atoms as PhonopyAtoms
from phonopy import Phonopy
structure = kwargs.pop('structure')
phonopy_input = kwargs.pop('phonopy_input').get_dict()
force_constants = kwargs.pop('force_constants').get_array(
'force_constants')
bands = get_path_using_seekpath(structure)
# Generate phonopy phonon object
bulk = PhonopyAtoms(symbols=[site.kind_name for site in structure.sites],
positions=[site.position for site in structure.sites],
cell=structure.cell)
phonon = Phonopy(bulk,
phonopy_input['supercell'],
primitive_matrix=phonopy_input['primitive'],
symprec=phonopy_input['symmetry_precision'])
phonon.set_force_constants(force_constants)
try:
print('trying born')
nac_data = kwargs.pop('nac_data')
born = nac_data.get_array('born_charges')
epsilon = nac_data.get_array('epsilon')
phonon.set_nac_params(get_born_parameters(phonon, born, epsilon))
print('born succeed')
except:
pass
# Normalization factor primitive to unit cell
norm_primitive_to_unitcell = phonon.unitcell.get_number_of_atoms(
) / phonon.primitive.get_number_of_atoms()
phonon.set_band_structure(bands['ranges'])
phonon.set_mesh(phonopy_input['mesh'],
is_eigenvectors=True,
is_mesh_symmetry=False)
phonon.set_total_DOS(tetrahedron_method=True)
phonon.set_partial_DOS(tetrahedron_method=True)
# get band structure
band_structure_phonopy = phonon.get_band_structure()
q_points = np.array(band_structure_phonopy[0])
q_path = np.array(band_structure_phonopy[1])
frequencies = np.array(band_structure_phonopy[2])
band_labels = np.array(bands['labels'])
# stores band structure
band_structure = ArrayData()
band_structure.set_array('q_points', q_points)
band_structure.set_array('q_path', q_path)
band_structure.set_array('frequencies', frequencies)
band_structure.set_array('labels', band_labels)
# get DOS (normalized to unit cell)
total_dos = phonon.get_total_DOS() * norm_primitive_to_unitcell
partial_dos = phonon.get_partial_DOS() * norm_primitive_to_unitcell
# Stores DOS data in DB as a workflow result
dos = ArrayData()
dos.set_array('frequency', total_dos[0])
dos.set_array('total_dos', total_dos[1] * norm_primitive_to_unitcell)
dos.set_array('partial_dos', partial_dos[1] * norm_primitive_to_unitcell)
dos.set_array('partial_symbols', np.array(phonon.primitive.symbols))
# THERMAL PROPERTIES (per primtive cell)
phonon.set_thermal_properties()
t, free_energy, entropy, cv = phonon.get_thermal_properties()
# Stores thermal properties (per mol) data in DB as a workflow result
thermal_properties = ArrayData()
thermal_properties.set_array('temperature', t)
thermal_properties.set_array('free_energy',
free_energy * norm_primitive_to_unitcell)
thermal_properties.set_array('entropy',
entropy * norm_primitive_to_unitcell)
thermal_properties.set_array('cv', cv * norm_primitive_to_unitcell)
return {
'thermal_properties': thermal_properties,
'dos': dos,
'band_structure': band_structure
}
class PhonopyJob(AtomisticParallelMaster):
"""
Args:
project:
job_name:
"""
def __init__(self, project, job_name):
super(PhonopyJob, self).__init__(project, job_name)
self.__name__ = "PhonopyJob"
self.__version__ = "0.0.1"
self.input["interaction_range"] = (10.0,
"Minimal size of supercell, Ang")
self.input["factor"] = (
VaspToTHz,
"Frequency unit conversion factor (default for VASP)",
)
self.input["displacement"] = (0.01, "atoms displacement, Ang")
self.input["dos_mesh"] = (20, "mesh size for DOS calculation")
self.phonopy = None
self._job_generator = PhonopyJobGenerator(self)
self._disable_phonopy_pickle = False
s.publication_add(phonopy_publication())
@property
def phonopy_pickling_disabled(self):
return self._disable_phonopy_pickle
@phonopy_pickling_disabled.setter
def phonopy_pickling_disabled(self, disable):
self._disable_phonopy_pickle = disable
@property
def _phonopy_unit_cell(self):
if self.structure is not None:
return atoms_to_phonopy(self.structure)
else:
return None
def _enable_phonopy(self):
if self.phonopy is None:
if self.structure is not None:
self.phonopy = Phonopy(
unitcell=self._phonopy_unit_cell,
supercell_matrix=self._phonopy_supercell_matrix(),
factor=self.input["factor"],
)
self.phonopy.generate_displacements(
distance=self.input["displacement"])
self.to_hdf()
else:
raise ValueError(
"No reference job/ No reference structure found.")
def list_structures(self):
if self.structure is not None:
self._enable_phonopy()
return [struct for _, struct in self._job_generator.parameter_list]
else:
return []
def _phonopy_supercell_matrix(self):
if self.structure is not None:
supercell_range = np.ceil(
self.input["interaction_range"] / np.array([
np.linalg.norm(vec)
for vec in self._phonopy_unit_cell.get_cell()
]))
return np.eye(3) * supercell_range
else:
return np.eye(3)
def run_static(self):
# Initialise the phonopy object before starting the first calculation.
self._enable_phonopy()
super(PhonopyJob, self).run_static()
def run_if_interactive(self):
self._enable_phonopy()
super(PhonopyJob, self).run_if_interactive()
def to_hdf(self, hdf=None, group_name=None):
"""
Store the PhonopyJob in an HDF5 file
Args:
hdf (ProjectHDFio): HDF5 group object - optional
group_name (str): HDF5 subgroup name - optional
"""
super(PhonopyJob, self).to_hdf(hdf=hdf, group_name=group_name)
if self.phonopy is not None and not self._disable_phonopy_pickle:
with self.project_hdf5.open("output") as hdf5_output:
hdf5_output["phonopy_pickeled"] = codecs.encode(
pickle.dumps(self.phonopy), "base64").decode()
def from_hdf(self, hdf=None, group_name=None):
"""
Restore the PhonopyJob from an HDF5 file
Args:
hdf (ProjectHDFio): HDF5 group object - optional
group_name (str): HDF5 subgroup name - optional
"""
super(PhonopyJob, self).from_hdf(hdf=hdf, group_name=group_name)
with self.project_hdf5.open("output") as hdf5_output:
if "phonopy_pickeled" in hdf5_output.list_nodes():
self.phonopy = pickle.loads(
codecs.decode(hdf5_output["phonopy_pickeled"].encode(),
"base64"))
if "dos_total" in hdf5_output.list_nodes():
self._dos_total = hdf5_output["dos_total"]
if "dos_energies" in hdf5_output.list_nodes():
self._dos_energies = hdf5_output["dos_energies"]
def collect_output(self):
"""
Returns:
"""
if self.server.run_mode.interactive:
forces_lst = self.project_hdf5.inspect(
self.child_ids[0])["output/generic/forces"]
else:
forces_lst = [
self.project_hdf5.inspect(job_id)["output/generic/forces"][-1]
for job_id in self._get_jobs_sorted()
]
self.phonopy.set_forces(forces_lst)
self.phonopy.produce_force_constants()
self.phonopy.set_mesh(mesh=[self.input["dos_mesh"]] * 3)
qpoints, weights, frequencies, eigvecs = self.phonopy.get_mesh()
self.phonopy.set_total_DOS()
erg, dos = self.phonopy.get_total_DOS()
self.to_hdf()
with self.project_hdf5.open("output") as hdf5_out:
hdf5_out["dos_total"] = dos
hdf5_out["dos_energies"] = erg
hdf5_out["qpoints"] = qpoints
hdf5_out["supercell_matrix"] = self._phonopy_supercell_matrix()
hdf5_out[
"displacement_dataset"] = self.phonopy.get_displacement_dataset(
)
hdf5_out[
"dynamical_matrix"] = self.phonopy.dynamical_matrix.get_dynamical_matrix(
)
hdf5_out["force_constants"] = self.phonopy.force_constants
def write_phonopy_force_constants(self,
file_name="FORCE_CONSTANTS",
cwd=None):
"""
Args:
file_name:
cwd:
Returns:
"""
if cwd is not None:
file_name = posixpath.join(cwd, file_name)
write_FORCE_CONSTANTS(force_constants=self.phonopy.force_constants,
filename=file_name)
def get_hesse_matrix(self):
"""
Returns:
"""
unit_conversion = (
scipy.constants.physical_constants["Hartree energy in eV"][0] /
scipy.constants.physical_constants["Bohr radius"][0]**2 *
scipy.constants.angstrom**2)
force_shape = np.shape(self.phonopy.force_constants)
force_reshape = force_shape[0] * force_shape[2]
return (np.transpose(self.phonopy.force_constants,
(0, 2, 1, 3)).reshape(
(force_reshape, force_reshape)) /
unit_conversion)
def get_thermal_properties(self,
t_min=1,
t_max=1500,
t_step=50,
temperatures=None):
"""
Args:
t_min:
t_max:
t_step:
temperatures:
Returns:
"""
self.phonopy.set_thermal_properties(t_step=t_step,
t_max=t_max,
t_min=t_min,
temperatures=temperatures)
return thermal(*self.phonopy.get_thermal_properties())
@property
def dos_total(self):
"""
Returns:
"""
return self["output/dos_total"]
@property
def dos_energies(self):
"""
Returns:
"""
return self["output/dos_energies"]
@property
def dynamical_matrix(self):
"""
Returns:
"""
return np.real_if_close(
self.phonopy.get_dynamical_matrix().get_dynamical_matrix())
def dynamical_matrix_at_q(self, q):
"""
Args:
q:
Returns:
"""
return np.real_if_close(self.phonopy.get_dynamical_matrix_at_q(q))
def plot_dos(self, ax=None, *args, **qwargs):
"""
Args:
*args:
ax:
**qwargs:
Returns:
"""
try:
import pylab as plt
except ImportError:
import matplotlib.pyplot as plt
if ax is None:
fig, ax = plt.subplots(1, 1)
ax.plot(self["output/dos_energies"], self["output/dos_total"], *args,
**qwargs)
ax.set_xlabel("Frequency [THz]")
ax.set_ylabel("DOS")
ax.set_title("Phonon DOS vs Energy")
return ax
cell = aseAtoms(symbols=sc.get_chemical_symbols(), scaled_positions=sc.get_scaled_positions(),
cell=sc.get_cell(), pbc=(1,1,1))
cell = Atoms(cell)
cell.set_calculator(pot)
forces.append(cell.get_forces())
phonon.set_forces(forces)
phonon.produce_force_constants()
mesh = [nqx, nqy, nqz]
phonon.set_mesh(mesh, is_eigenvectors=True)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
#SHOW DOS STRUCTURE
phonon.set_total_DOS(freq_min=0.0, freq_max=12.0, tetrahedron_method=False)
phonon.get_total_DOS()
phonon.write_total_DOS()
phonon.plot_total_DOS().show()
#BAND STRUCTURE
phonon.set_band_structure(paths, is_eigenvectors=False, is_band_connection=True)
phonon.get_band_structure()
ph_plot = phonon.plot_band_structure(labels=["G", "N", "P"])
ph_plot.show()
#WRITE ANIMATION MODE
phonon.write_animation()
#TEMPERATURE
phonon.set_thermal_properties(t_step=10, t_max=1000, t_min=0)
temp_plot = open('temp_plot.dat', 'w')
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
print >> temp_plot, ("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv )
def get_properties_from_phonopy(**kwargs):
"""
Calculate DOS and thermal properties using phonopy (locally)
:param structure: StructureData Object
:param ph_settings: Parametersdata object containing a dictionary with the data needed to run phonopy:
supercells matrix, primitive matrix and q-points mesh.
:param force_constants: (optional)ForceConstantsData object containing the 2nd order force constants
:param force_sets: (optional) ForceSetsData object containing the phonopy force sets
:param nac: (optional) ArrayData object from a single point calculation data containing dielectric tensor and Born charges
:return: phonon band structure, force constants, thermal properties and DOS
"""
structure = kwargs.pop('structure')
ph_settings = kwargs.pop('ph_settings')
bands = kwargs.pop('bands')
from phonopy import Phonopy
phonon = Phonopy(phonopy_bulk_from_structure(structure),
supercell_matrix=ph_settings.dict.supercell,
primitive_matrix=ph_settings.dict.primitive,
symprec=ph_settings.dict.symmetry_precision)
if 'force_constants' in kwargs:
force_constants = kwargs.pop('force_constants')
phonon.set_force_constants(force_constants.get_data())
else:
force_sets = kwargs.pop('force_sets')
phonon.set_displacement_dataset(force_sets.get_force_sets())
phonon.produce_force_constants()
force_constants = ForceConstantsData(data=phonon.get_force_constants())
if 'nac_data' in kwargs:
print('use born charges')
nac_data = kwargs.pop('nac_data')
primitive = phonon.get_primitive()
nac_parameters = nac_data.get_born_parameters_phonopy(
primitive_cell=primitive.get_cell())
phonon.set_nac_params(nac_parameters)
# Normalization factor primitive to unit cell
normalization_factor = phonon.unitcell.get_number_of_atoms(
) / phonon.primitive.get_number_of_atoms()
# DOS
phonon.set_mesh(ph_settings.dict.mesh,
is_eigenvectors=True,
is_mesh_symmetry=False)
phonon.set_total_DOS(tetrahedron_method=True)
phonon.set_partial_DOS(tetrahedron_method=True)
total_dos = phonon.get_total_DOS()
partial_dos = phonon.get_partial_DOS()
dos = PhononDosData(
frequencies=total_dos[0],
dos=total_dos[1] * normalization_factor,
partial_dos=np.array(partial_dos[1]) * normalization_factor,
atom_labels=np.array(phonon.primitive.get_chemical_symbols()))
# THERMAL PROPERTIES (per primtive cell)
phonon.set_thermal_properties()
t, free_energy, entropy, cv = phonon.get_thermal_properties()
# Stores thermal properties (per unit cell) data in DB as a workflow result
thermal_properties = ArrayData()
thermal_properties.set_array('temperature', t)
thermal_properties.set_array('free_energy',
free_energy * normalization_factor)
thermal_properties.set_array('entropy', entropy * normalization_factor)
thermal_properties.set_array('heat_capacity', cv * normalization_factor)
# BAND STRUCTURE
phonon.set_band_structure(bands.get_bands())
band_structure = BandStructureData(bands=bands.get_bands(),
labels=bands.get_labels(),
unitcell=bands.get_unitcell())
band_structure.set_band_structure_phonopy(phonon.get_band_structure())
return {
'thermal_properties': thermal_properties,
'dos': dos,
'band_structure': band_structure,
'force_constants': force_constants
}
