def _get_phonon(self, spgtype, dim, pmat):
cell = read_vasp("POSCAR_%s" % spgtype)
phonon = Phonopy(cell, np.diag(dim), primitive_matrix=pmat)
force_sets = parse_FORCE_SETS(filename="FORCE_SETS_%s" % spgtype)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
print(phonon.get_symmetry().get_pointgroup())
return phonon
def _get_phonon(self, spgtype, dim, pmat):
cell = read_vasp(os.path.join(data_dir,"POSCAR_%s" % spgtype))
phonon = Phonopy(cell,
np.diag(dim),
primitive_matrix=pmat)
force_sets = parse_FORCE_SETS(filename=os.path.join(data_dir,"FORCE_SETS_%s" % spgtype))
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
print(phonon.get_symmetry().get_pointgroup())
return phonon
def get_spacegroup_string(self, symprec=0.001):
"""
Returns string of spacegroup information like Imma (74).
symprec controls the symmetry tolerance for atomic positions (in Angstroms)
"""
unit_cell_phonopy_structure = self.convert_structure_to_phonopy_atoms()
supercell_dimensions_matrix = np.diag([1, 1, 1])
phonon = Phonopy(unitcell=unit_cell_phonopy_structure,
supercell_matrix=supercell_dimensions_matrix,
symprec=symprec)
symmetry = phonon.get_symmetry()
return str(symmetry.get_international_table())
# [0.5, 0, 0.5],
# [0.5, 0.5, 0],
# [0.5, 0.5, 0.5],
# [0.5, 0, 0],
# [0, 0.5, 0],
# [0, 0, 0.5]])
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]])
symmetry = phonon.get_symmetry()
print "Space group:", symmetry.get_international_table()
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
primitive = phonon.get_primitive()
# Born effective charges and dielectric constants are read from BORN file.
nac_params = parse_BORN(primitive, filename="BORN")
# Or it can be of course given by hand as follows:
# born = [[[1.08703, 0, 0],
# [0, 1.08703, 0],
# [0, 0, 1.08703]],
# [[-1.08672, 0, 0],
# [0, -1.08672, 0],
from phonopy import Phonopy
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS, parse_BORN
import numpy as np
cell = read_vasp("POSCAR")
# Initialize phonon. Supercell matrix has to have the shape of (3, 3)
phonon = Phonopy(cell, np.diag([3, 3, 2]))
symmetry = phonon.get_symmetry()
print "Space group:", symmetry.get_international_table()
# Read forces and displacements
force_sets = parse_FORCE_SETS()
# Sets of forces have to be set before phonon.set_post_process or
# at phonon.set_post_process(..., sets_of_forces=sets_of_forces, ...).
phonon.set_force_sets(force_sets)
phonon.set_post_process()
# Character table
phonon.set_irreps([1./3, 1./3, 0], 1e-4)
ct = phonon.get_irreps()
band_indices = ct.get_band_indices()
characters = np.rint(ct.get_characters()).real
for bi, cts in zip(band_indices, characters):
print np.array(bi) + 1, cts
# phonon.show_character_table()
def calculate_phonon(atoms,
calc=None,
forces_set_file=None,
ndim=np.eye(3),
primitive_matrix=np.eye(3),
distance=0.01,
factor=VaspToTHz,
is_plusminus='auto',
is_symmetry=True,
symprec=1e-5,
func=None,
prepare_initial_wavecar=False,
skip=None,
restart=True,
parallel=True,
sc_mag=None,
**func_args):
"""
"""
if 'magmoms' in atoms.arrays or 'initial_magmoms' in atoms.arrays:
is_mag = True
else:
is_mag = False
print("is_mag: ", is_mag)
# 1. get displacements and supercells
if calc is not None:
atoms.set_calculator(calc)
# bulk = PhonopyAtoms(atoms=atoms)
if is_mag:
bulk = PhonopyAtoms(
symbols=atoms.get_chemical_symbols(),
scaled_positions=atoms.get_scaled_positions(),
cell=atoms.get_cell(),
magmoms=atoms.arrays['initial_magmoms'],
)
else:
bulk = PhonopyAtoms(symbols=atoms.get_chemical_symbols(),
scaled_positions=atoms.get_scaled_positions(),
cell=atoms.get_cell())
phonon = Phonopy(bulk,
ndim,
primitive_matrix=primitive_matrix,
factor=factor,
symprec=symprec)
phonon.generate_displacements(distance=distance, is_plusminus=is_plusminus)
disps = phonon.get_displacements()
for d in disps:
print(("[phonopy] %d %s" % (d[0], d[1:])))
supercell0 = phonon.get_supercell()
supercells = phonon.get_supercells_with_displacements()
#write_supercells_with_displacements(supercell0, supercells)
write_disp_yaml(disps, supercell0)
# 2. calculated forces.
if forces_set_file is not None:
symmetry = phonon.get_symmetry()
set_of_forces = parse_FORCE_SETS(
is_translational_invariance=False,
filename=forces_set_file) # ['first_atoms']
# set_of_forces=np.array(set_of_forces)
#set_of_forces=[np.asarray(f) for f in set_of_forces]
phonon.set_displacement_dataset(set_of_forces)
phonon.produce_force_constants()
else:
# initialize set of forces
if restart and os.path.exists('forces_set.pickle'):
try:
with open("forces_set.pickle", 'rb') as myfile:
set_of_forces = pickle.load(myfile)
iskip = len(set_of_forces) - 1
except:
set_of_forces = []
iskip = -1
else:
set_of_forces = []
iskip = -1
if prepare_initial_wavecar and skip is None:
scell = supercell0
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
if is_mag:
cell.set_initial_magnetic_moments(sc_mag)
write('Supercell.cif', cell)
mcalc = copy.deepcopy(calc)
mcalc.set(lwave=True, lcharg=True)
cell.set_calculator(mcalc)
dir_name = "SUPERCELL0"
cur_dir = os.getcwd()
if not os.path.exists(dir_name):
os.mkdir(dir_name)
os.chdir(dir_name)
mcalc.scf_calculation(cell)
os.chdir(cur_dir)
def calc_force(iscell):
scell = supercells[iscell]
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
if is_mag:
cell.set_initial_magnetic_moments(sc_mag)
cell.set_calculator(copy.deepcopy(calc))
dir_name = "PHON_CELL%s" % iscell
cur_dir = os.getcwd()
if not os.path.exists(dir_name):
os.mkdir(dir_name)
if prepare_initial_wavecar:
os.system('ln -s %s %s' %
(os.path.abspath("SUPERCELL0/WAVECAR"),
os.path.join(dir_name, 'WAVECAR')))
os.chdir(dir_name)
forces = cell.get_forces()
print("[Phonopy] Forces: %s" % forces)
# Do something other than calculating the forces with func.
# func: func(atoms, calc, func_args)
if func is not None:
func(cell, calc, **func_args)
os.chdir(cur_dir)
drift_force = forces.sum(axis=0)
print("[Phonopy] Drift force:", "%11.5f" * 3 % tuple(drift_force))
# Simple translational invariance
for force in forces:
force -= drift_force / forces.shape[0]
return forces
if parallel:
p = Pool()
set_of_forces = p.map(calc_force,
list(range(iskip, len(supercells))))
else:
for iscell, scell in enumerate(supercells):
if iscell > iskip:
fs = calc_force(iscell)
set_of_forces.append(fs)
with open("forces_set.pickle", 'wb') as myfile:
pickle.dump(set_of_forces, myfile)
phonon.produce_force_constants(forces=np.array(set_of_forces))
force_constants = phonon.get_force_constants()
write_FORCE_CONSTANTS(force_constants, filename='FORCE_CONSTANTS')
#print("[Phonopy] Phonon frequencies at Gamma:")
# for i, freq in enumerate(phonon.get_frequencies((0, 0, 0))):
# print(("[Phonopy] %3d: %10.5f THz" % (i + 1, freq))) # THz
# print(("[Phonopy] %3d: %10.5f cm-1" % (i + 1, freq * 33.35))) #cm-1
with open('phonon.pickle', 'wb') as myfile:
pickle.dump(phonon, myfile)
phonon.save(settings={'force_constants': True})
return phonon
# initial settings
#
cell = read_vasp_from_strings(poscar_str)
phonon = Phonopy(cell, np.diag([2, 2, 2]))
force_sets = parse_FORCE_SETS_from_strings(force_sets_str,
cell.get_number_of_atoms() * 8)
phonon.set_force_sets(force_sets)
phonon.set_post_process(primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]],
is_nac=True)
born_params = parse_BORN_from_strings(born_str,
phonon.get_primitive())
phonon.set_nac_params(born_params)
print phonon.get_symmetry().get_international_table()
primitive = phonon.get_primitive()
reclat = np.linalg.inv(primitive.get_cell())
print reclat
ndiv = 100
band = get_band([0.0, 0.0, 0.0], [0.5, 0.5, 0.0], ndiv)
bands = [band]
phonon.set_band_structure(bands)
#
# Run1
#
band_index = 2
vg = GroupVelocity(phonon.get_dynamical_matrix(), phonon.get_primitive(), q_length=1e-5)
q_points = band
