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
def obtain_phonon_dispersion_spectra(structure, bands_ranges, NAC=False, band_resolution=30):
print("Calculating phonon dispersion spectra...")
bulk = PhonopyAtoms(
symbols=structure.get_atomic_types(),
scaled_positions=structure.get_scaled_positions(),
cell=structure.get_cell().T,
)
phonon = Phonopy(
bulk,
structure.get_super_cell_phonon(),
primitive_matrix=structure.get_primitive_matrix(),
is_auto_displacements=False,
)
if NAC:
print("Phonopy warning: Using Non Analitical Corrections")
print("BORN file is needed to do this")
get_is_symmetry = True # sfrom phonopy: settings.get_is_symmetry()
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, get_is_symmetry)
phonon.set_nac_params(nac_params=nac_params)
phonon.set_displacement_dataset(copy.deepcopy(structure.get_force_set()))
phonon.produce_force_constants()
bands = []
for q_start, q_end in bands_ranges:
band = []
for i in range(band_resolution + 1):
band.append(np.array(q_start) + (np.array(q_end) - np.array(q_start)) / band_resolution * i)
bands.append(band)
phonon.set_band_structure(bands)
return phonon.get_band_structure()
# [0, 2.43533967, 0],
# [0, 0, 2.43533967]]
# factors = 14.400
# nac_params = {'born': born,
# 'factor': factors,
# 'dielectric': epsilon}
phonon.set_nac_params(nac_params)
# BAND = 0.0 0.0 0.0 0.5 0.0 0.0 0.5 0.5 0.0 0.0 0.0 0.0 0.5 0.5 0.5
bands = []
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.0, 0.0])
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()
# [0, 2.43533967, 0],
# [0, 0, 2.43533967]]
# factors = 14.400
# nac_params = {'born': born,
# 'factor': factors,
# 'dielectric': epsilon}
phonon.set_nac_params(nac_params)
# BAND = 0.0 0.0 0.0 0.5 0.0 0.0 0.5 0.5 0.0 0.0 0.0 0.0 0.5 0.5 0.5
bands = []
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.0, 0.0])
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
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
}
q_start = np.array([0, 0, 0])
q_end = np.array([1./3, 1./3, 1./2])
band = []
for i in range(51):
band.append(q_start + ( q_end - q_start ) / 50 * i)
bands.append(band)
#*********************
# Matplotlib required
#*********************
print "\nPhonon dispersion:"
phonon.set_band_structure(bands,
is_eigenvectors=True)
phonon.plot_band_structure(["X", "$\Gamma$", "L"]).show()
bands = phonon.get_band_structure()
distances = bands[1]
frequencies = bands[2]
qpoints = bands[0]
for (qs_at_segments,
dists_at_segments,
freqs_at_segments) in zip(qpoints, distances, frequencies):
for q, d, f in zip(qs_at_segments,
dists_at_segments,
freqs_at_segments):
print "# %f %f %f" % tuple(q)
print d, ("%f " * len(f)) % tuple(f)
# If you just want to plot along q-points of all band segments, the
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 )
phonon.plot_thermal_properties().show()
#Finally write parametrs of calculation i.e. supercell size for force_constant
#and qpoint mesh
with open('subgb.json','w') as f:
gb_dict = {}
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()
class PhononFromModel(object):
"""
This class uses frozen phonon method to calculate the phonon dispersion curves and thermodynamic
properties of a structure.
The steps are as follows:
1. Displaced structures are obtained from pristine structure via phonopy.
2. The forces of each displaced structures are calculated by model
3. The forces are passed to phonopy object and the force constant are produced
4. Phonon is calculated once the force constant matrix is available.
Args:
model (model object): a model object that has a method "calculate_forces" that takes in a list of
structures and return a list of N*3 forces, where N are the number of atoms in each structures
structure (pymatgen structure): a pristine pymatgen structure
atom_disp (float): small displacements in Angstrom
"""
def __init__(self, model=None, structure=None, atom_disp=0.015, **kwargs):
self.model = model
self.structure = structure
self.atom_disp = atom_disp
self.qpoints, self.vertices = get_qpoints_and_vertices(self.structure)
is_plusminus = kwargs.get('is_plusminus', True)
is_diagonal = kwargs.get('is_diagonal', True)
is_trigonal = kwargs.get('is_diagonal', False)
supercell_matrix = kwargs.get('is_diagonal', None)
ph_structure = get_phonopy_structure(self.structure)
if supercell_matrix is None:
supercell_matrix = np.eye(3) * np.array((1, 1, 1))
self.phonon = Phonopy(unitcell=ph_structure, supercell_matrix=supercell_matrix)
self.phonon.generate_displacements(distance=self.atom_disp,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal)
disp_supercells = self.phonon.get_supercells_with_displacements()
# Perfect supercell structure
init_supercell = self.phonon.get_supercell()
# Structure list to be returned
self.structure_list = [get_pmg_structure(init_supercell)]
for c in disp_supercells:
if c is not None:
self.structure_list.append(get_pmg_structure(c))
forces = self.model.calculate_forces(self.structure_list)
self.phonon.set_forces(forces[1:])
self.phonon.produce_force_constants()
logging.info("Force constant produced")
def get_thermo_properties(self, mesh=[8, 8, 8], t_step=10, t_max=3000, t_min=0):
self.phonon.set_mesh(mesh=mesh)
self.phonon.set_thermal_properties(t_step=t_step,
t_max=t_max,
t_min=t_min)
plt = self.phonon.plot_thermal_properties()
return plt
def get_bs_plot(self, points_per_line=50, figsize=(6, 4), ylim=[-1, 5]):
bands = []
bands = append_bands(bands, self.qpoints, points_per_line)
self.phonon.set_band_structure(bands)
q_points, self.distances, self.frequencies, eigvecs = self.phonon.get_band_structure()
special_points = self.phonon._band_structure._special_points
distance = self.phonon._band_structure._distance
plt.figure(figsize=figsize)
for j, (d, f) in enumerate(zip(self.distances, self.frequencies)):
for i, freqs in enumerate(f.T):
if i == 0 and j == 0:
plt.plot(d, freqs, "b-", lw=1)
else:
plt.plot(d, freqs, "b-", lw=1)
for sp in special_points:
plt.axvline(x=sp, linestyle=':', linewidth=1, color='k')
plt.axhline(y=0, linestyle=':', linewidth=1, color='k')
plt.xticks(special_points, ["$\mathrm{%s}$" % i for i in self.vertices])
plt.xlabel("Wave vector")
plt.ylabel("Frequency (THz)")
plt.xlim(0, distance)
plt.ylim(ylim)
plt.yticks(list(range(ylim[0], ylim[-1]+1)))
plt.tight_layout()
return plt
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
}
