def phonons(model, bulk, supercell, dx, mesh=None, points=None, n_points=50):
import model
unitcell = PhonopyAtoms(symbols=bulk.get_chemical_symbols(),
cell=bulk.get_cell(),
scaled_positions=bulk.get_scaled_positions())
phonon = Phonopy(unitcell, supercell)
phonon.generate_displacements(distance=dx)
sets_of_forces = []
for s in phonon.get_supercells_with_displacements():
at = Atoms(cell=s.get_cell(),
symbols=s.get_chemical_symbols(),
scaled_positions=s.get_scaled_positions(),
pbc=3 * [True])
at.set_calculator(model.calculator)
sets_of_forces.append(at.get_forces())
phonon.set_forces(sets_of_forces=sets_of_forces)
phonon.produce_force_constants()
properties = {}
if mesh is not None:
phonon.set_mesh(mesh, is_gamma_center=True)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
properties["frequencies"] = frequencies.tolist()
properties["weights"] = weights.tolist()
if points is not None:
bands = []
for i in range(len(points) - 1):
band = []
for r in np.linspace(0, 1, n_points):
band.append(points[i] + (points[i + 1] - points[i]) * r)
bands.append(band)
phonon.set_band_structure(bands,
is_eigenvectors=True,
is_band_connection=False)
band_q_points, band_distances, band_frequencies, band_eigvecs = phonon.get_band_structure(
)
band_distance_max = np.max(band_distances)
band_distances = [(_b / band_distance_max).tolist()
for _b in band_distances]
band_frequencies = [_b.tolist() for _b in band_frequencies]
properties["band_q_points"] = band_q_points
properties["band_distances"] = band_distances
properties["band_frequencies"] = band_frequencies
properties["band_eigvecs"] = band_eigvecs
properties["phonopy"] = phonon
return properties
import phonopy.interface.vasp as vasp
import numpy as np
import lxml.etree as etree
from phonopy import Phonopy
from phonopy.structure.atoms import Atoms as PhonopyAtoms
vasprun = etree.iterparse('vasprun.xml', tag='varray')
fc = vasp.get_force_constants_vasprun_xml(vasprun)
primitive = vasp.get_atoms_from_poscar(open('POSCAR-p'),'W')
superc = vasp.get_atoms_from_poscar(open('POSCAR'),'W')
print superc.get_scaled_positions()
a = 5.404
bulk = PhonopyAtoms(symbols=['W'] * 216,
positions=superc.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,[[1,0,0],[0,1,0],[0,0,1]],primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]])
phonon.set_force_constants(fc)
mesh = [3, 3, 3]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
phonon.set_total_DOS()
phonon.plot_total_DOS().show()
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
#We need to get the forces on these atoms...
forces = []
print 'There are', len(supercells), 'displacement patterns'
for sc in supercells:
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
def __init__(self, numbatom=125, supercell=5):
#species = 'WRe_0.25_conv'
species = 'WRe_0.00'
#species = 'Re'
###read force constants from vasprun.xml###
vasprun = etree.iterparse('vasprun.xml', tag='varray')
#fc = vasp.get_force_constants_vasprun_xml(vasprun,1) #pass xml input and species atomic weight.
###########################################
########### read positionsl ###############
primitive = vasp.get_atoms_from_poscar(open('POSCAR-p'),'W')
superc = vasp.get_atoms_from_poscar(open('POSCAR'),'W')
###########################################
numbatom = superc.get_number_of_atoms()
#print primitive.get_cell()
#print primitive.get_scaled_positions()
#print superc.get_scaled_positions()
print numbatom, species, os.getcwd()
if species=='W':
#Tungsten
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,0,64)
s = 4.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species=='W_conv_2x2x2':
#Tungsten
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,2)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W','W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species=='W_conv':
#Tungsten
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,2)
s = 4.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W','W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species=='WRe_0.25_conv':
#Tungsten
fc = vasp.get_force_constants_vasprun_xml(vasprun,8,2,64)
s = 4.
a = superc.get_cell()[0][0]*2.
print a, primitive.get_scaled_positions()
bulk = PhonopyAtoms(symbols=['W','W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
#print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_B2':
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,1)
s = 5.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W','Re'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.00':
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,0,numbatom)
s = supercell
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [200, 200, 200]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.03':
fc = vasp.get_force_constants_vasprun_xml(vasprun,2,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.06':
fc = vasp.get_force_constants_vasprun_xml(vasprun,3,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.09':
fc = vasp.get_force_constants_vasprun_xml(vasprun,4,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.12':
fc = vasp.get_force_constants_vasprun_xml(vasprun,5,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.18':
fc = vasp.get_force_constants_vasprun_xml(vasprun,6,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.25':
fc = vasp.get_force_constants_vasprun_xml(vasprun,7,0)
s = 2.
a = primitive.get_cell()[0][0]*2.
print a, primitive.get_scaled_positions()
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
#phonon.set_partial_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.50':
fc = vasp.get_force_constants_vasprun_xml(vasprun,8,0)
s = 2.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
#print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
#print frequencies
phonon.set_total_DOS()
#phonon.set_partial_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'Au':
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,0)
#Gold
s = 5.
a = superc.get_cell()[0][0]
bulk = PhonopyAtoms(symbols=['Au'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[0.5, 0.5, 0.0],[0.0, 0.5, 0.5],[0.5, 0.0, 0.5]],
distance=0.01, factor=15.633302)
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_partial_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=1300,
t_min=0)
elif species == 'Mo':
fc = vasp.get_force_constants_vasprun_xml(vasprun,10,0)
s = 5.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['Mo'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=2500,
t_min=0)
elif species == 'Re':
fc = vasp.get_force_constants_vasprun_xml(vasprun,9,0)
s = 5.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['Re'] * 1,
scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
[[s,0.,0.],[0.,s,0.],[0.,0.,s]],
primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
distance=0.01, factor=15.633302)
print fc
phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=2500,
t_min=0)
f = open('F_TV','w')
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
#print t, cv
#print ("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv )
f.write(("%12.3f " + "%15.7f" + "\n") % ( t, free_energy))
f.close()
fc = open('thermal_properties','w')
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
fc.write(("%12.3f " + "%15.7f" *3 + "\n") % ( t, free_energy, entropy, cv ))
fc.close()
#phonon.plot_thermal_properties().show()
#phonon.plot_total_DOS().show()
phonon.write_total_DOS()
#phonon.write_partial_DOS()
phonon.write_yaml_thermal_properties()
bands = []
#### PRIMITIVE
q_start = np.array([0.0, 0.0, 0.0])
#q_start = np.array([0.5, 0.5, 0.0])
q_end = np.array([-0.5, 0.5, 0.5])
#q_end = np.array([0., 0., 0.])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
band = []
q_start = np.array([-0.5, 0.5, 0.5])
#q_start = np.array([0., 0., 0.])
q_end = np.array([0.25, 0.25, 0.25])
#q_end = np.array([1., 0., 0.])
for i in range(101):
#band.append([-0.5+3*1/400*i, 0.5-1/400*i, 0.5-1/400*i])
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
#print band
q_start = np.array([0.25, 0.25, 0.25])
q_end = np.array([0., 0., 0.])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([0., 0., 0.])
q_end = np.array([0.0, 0., 0.5])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
#q_start = np.array([0.0, 0.0, 0.0])
#q_end = np.array([0.5, 0.5, 0.5])
#band = []
#for i in range(101):
# band.append(q_start + (q_end - q_start) / 100 * i)
#bands.append(band)
"""
###### CONVENTIONAL CELL ######
q_start = np.array([0.0, 0.0, 0.0])
q_end = np.array([-0.5, 0.5, 0.5])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([-0.5, 0.5, 0.5])
q_end = np.array([1./4., 1./4., 1./4.])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([1./4., 1./4., 1./4.])
q_end = np.array([0.0, 0.0, 0.0])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([0.0, 0.0, 0.0])
q_end = np.array([0.5, 0.0, 0.0])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
"""
phonon.set_band_structure(bands)
#phonon.plot_band_structure().show()
q_points, distances, frequencies, eigvecs = phonon.get_band_structure()
disp = {'q':q_points, 'distances':distances, 'frequencies':frequencies, 'eigvecs':eigvecs}
f = open('ph_dispersion.pkl','w')
pickle.dump(disp, f)
f.close()
import numpy as np
from phonopy import Phonopy
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS, parse_BORN
import matplotlib.pyplot as plt
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)
phonon.set_group_velocity()
phonon.set_mesh([31, 31, 31])
qpoints, weights, frequencies, _ = phonon.get_mesh()
group_velocity = phonon.get_group_velocity()
gv_norm = np.sqrt((group_velocity**2).sum(axis=2))
for i, (f, g) in enumerate(zip(frequencies.T, gv_norm.T)):
plt.plot(f, g, 'o', label=('band%d' % (i + 1)))
plt.legend()
plt.xlabel("Frequency (THz)")
plt.ylabel("|group-velocity| (THz.A)")
plt.show()
class thermal_conductivity():
def __init__(self, primitive_cell, super_cell):
self.primitive_cell = primitive_cell
self.super_cell = super_cell
def input_files(self, path_POSCAR, path_FORCECONSTANT):
bulk = read_vasp(path_POSCAR)
self.phonon = Phonopy(bulk,
self.super_cell,
primitive_matrix=self.primitive_cell)
force_constants = file_IO.parse_FORCE_CONSTANTS(path_FORCECONSTANT)
self.phonon.set_force_constants(force_constants)
return self.phonon
def set_mesh(self, mesh):
self.phonon.set_mesh(mesh, is_eigenvectors=True)
def set_point_defect_parameter(self, fi, defect_mass, defect_fc_ratio):
self.mass = self.phonon.get_primitive().get_masses().sum(
) / self.phonon.get_primitive().get_number_of_atoms()
self.cellvol = self.phonon.get_primitive().get_volume()
self.mass_fc_factor = self.cellvol * 10**-30 / 2.0 / 4 / np.pi * (
fi *
((self.mass - defect_mass) / self.mass + 2 * defect_fc_ratio)**2)
def kappa_separate(self, gamma, thetaD, T, P=1, m=3, n=1):
"""
nkpts: number of phonon k-points
frequencies: list of eigenvalue-arrays as output by phonopy
vgroup: group velocities
T: temperature in K
following parameters from Eq (70) in Tritt book, p.14
P: proportionality factor of Umklapp scattering rate, defualt 1
mass: mass in amu (average mass of unitcell)
gamma: Gruneisen parameter, unitless
thetaD: Debye temperature of relevance (acoustic modes) 283K for Mo3Sb7
m = 3 by default
n = 1 by default
cellvol: unit cell volume in A^3
"""
T = float(T)
#self.phonon.set_mesh(mesh, is_eigenvectors=True)
#self.mass = self.phonon.get_primitive().get_masses().sum()/self.phonon.get_primitive().get_number_of_atoms()
self.cellvol = self.phonon.get_primitive().get_volume()
self.qpoints, self.weigths, self.frequencies, self.eigvecs = self.phonon.get_mesh(
)
nkpts = self.frequencies.shape[0]
numbranches = self.frequencies.shape[1]
self.group_velocity = np.zeros((nkpts, numbranches, 3))
for i in range(len(self.qpoints)):
self.group_velocity[i, :, :] = self.phonon.get_group_velocity_at_q(
self.qpoints[i])
inv_nor_Um = np.zeros((nkpts, numbranches))
inv_point_defect_mass_fc = np.zeros((nkpts, numbranches))
inv_tau_total = np.zeros((nkpts, numbranches))
kappa_Um = np.zeros((nkpts, numbranches))
kappa_point_defect_mass_fc = np.zeros((nkpts, numbranches))
kappa_total = np.zeros((nkpts, numbranches))
self.kappaten = np.zeros((nkpts, numbranches, 3, 3))
v_group = np.zeros((nkpts, numbranches))
capacity = np.zeros((nkpts, numbranches))
for i in range(nkpts):
for j in range(numbranches):
nu = self.frequencies[i][
j] # frequency (in Thz) of current mode
velocity = self.group_velocity[
i, j, :] # cartesian vector of group velocity
v_group = (velocity[0]**2 + velocity[1]**2 +
velocity[2]**2)**(0.5) * THztoA
capacity[i, j] = mode_cv(
T, nu * THzToEv) * eV2Joule / (self.cellvol * Ang2meter**3)
# tau inverse phonon-phonon, inverse lifetime
inv_nor_Um[i, j] = P * hbar * gamma**2 / (
self.mass * amu) / v_group**2 * (T**n) / thetaD * (
2 * np.pi * THz * nu)**2 * np.exp(
(-1.0) * thetaD / m / T)
# tau inverse point defect, inverse lifetime
inv_point_defect_mass_fc[i, j] = (self.mass_fc_factor) * (
2 * np.pi * THz * nu)**4 / v_group**3
# tau inverst, inverse lifetime
inv_tau_total[
i, j] = inv_nor_Um[i, j] + inv_point_defect_mass_fc[i, j]
kappa_total[
i,
j] = (1.0 / 3.0) * self.weigths[i] * v_group**2 * capacity[
i,
j] / inv_tau_total[i,
j] # 1/3 is for isotropic condition
kappa_Um[
i,
j] = (1.0 / 3.0) * self.weigths[i] * v_group**2 * capacity[
i, j] / inv_nor_Um[i,
j] # 1/3 is for isotropic condition
kappa_point_defect_mass_fc[
i,
j] = (1.0 / 3.0) * self.weigths[i] * v_group**2 * capacity[
i, j] / inv_point_defect_mass_fc[
i, j] # 1/3 is for isotropic condition
self.kappaten[i, j, :, :] = self.weigths[i] * np.outer(
velocity,
velocity) * THztoA**2 * capacity[i, j] / inv_tau_total[i,
j]
#print(np.sum(inv_nor_Um, axis =1))
#print(np.sum(inv_point_defect_mass_fc, axis =1))
#print(np.sum(inv_tau_total, axis =1))
self.tau = np.concatenate(
(inv_nor_Um, inv_point_defect_mass_fc, inv_tau_total), axis=1)
self.kappa = [
kappa_Um.sum() / self.weigths.sum(),
kappa_point_defect_mass_fc.sum() / self.weigths.sum(),
kappa_total.sum() / self.weigths.sum()
]
return self.tau, self.kappa, self.kappaten
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS, parse_BORN
import matplotlib.pyplot as plt
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)
phonon.set_group_velocity()
phonon.set_mesh([31, 31, 31])
qpoints, weights, frequencies, _ = phonon.get_mesh()
group_velocity = phonon.get_group_velocity()
gv_norm = np.sqrt((group_velocity ** 2).sum(axis=2))
for i, (f, g) in enumerate(zip(frequencies.T, gv_norm.T)):
plt.plot(f, g, 'o', label=('band%d' % (i + 1)))
plt.legend()
plt.xlabel("Frequency (THz)")
plt.ylabel("|group-velocity| (THz.A)")
plt.show()
