def run_task(self, fw_spec):
unitcell = read_vasp("POSCAR-unitcell")
phonon = phonopy.Phonopy(unitcell, self.get("supercell"))
supercell = phonon.get_supercell()
phonon.generate_displacements()
supercells = phonon.supercells_with_displacements
ids = np.arange(len(supercells)) + 1
write_supercells_with_displacements(supercell, supercells, ids)
units = get_default_physical_units("vasp")
phpy_yaml = PhonopyYaml(physical_units=units,
settings={
'force_sets': False,
'born_effective_charge': False,
'dielectric_constant': False,
'displacements': True
})
phpy_yaml.set_phonon_info(phonon)
with open("phonopy_disp.yaml", 'w') as w:
w.write(str(phpy_yaml))
def write_supercells_with_displacements(interface_mode, supercell,
cells_with_disps,
num_unitcells_in_supercell,
optional_structure_info):
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import write_supercells_with_displacements
write_supercells_with_displacements(supercell, cells_with_disps)
elif interface_mode is 'abinit':
from phonopy.interface.abinit import (
write_supercells_with_displacements)
write_supercells_with_displacements(supercell, cells_with_disps)
elif interface_mode is 'qe':
from phonopy.interface.qe import write_supercells_with_displacements
write_supercells_with_displacements(supercell, cells_with_disps,
optional_structure_info[1])
elif interface_mode == 'wien2k':
from phonopy.interface.wien2k import (
write_supercells_with_displacements)
unitcell_filename, npts, r0s, rmts = optional_structure_info
write_supercells_with_displacements(supercell,
cells_with_disps,
npts,
r0s,
rmts,
num_unitcells_in_supercell,
filename=unitcell_filename)
elif interface_mode == 'elk':
from phonopy.interface.elk import write_supercells_with_displacements
write_supercells_with_displacements(supercell, cells_with_disps,
optional_structure_info[1])
elif interface_mode == 'siesta':
from phonopy.interface.siesta import (
write_supercells_with_displacements)
write_supercells_with_displacements(supercell, cells_with_disps,
optional_structure_info[1])
elif interface_mode == 'cp2k':
from phonopy.interface.cp2k import write_supercells_with_displacements
write_supercells_with_displacements(supercell, cells_with_disps)
elif interface_mode == 'crystal':
from phonopy.interface.crystal import (
write_supercells_with_displacements)
write_supercells_with_displacements(supercell,
cells_with_disps,
optional_structure_info[1],
num_unitcells_in_supercell,
template_file="TEMPLATE")
elif interface_mode == 'dftbp':
from phonopy.interface.dftbp import (
write_supercells_with_displacements)
write_supercells_with_displacements(supercell, cells_with_disps)
elif interface_mode == 'turbomole':
from phonopy.interface.turbomole import (
write_supercells_with_displacements)
write_supercells_with_displacements(supercell, cells_with_disps)
else:
raise RuntimeError("No calculator interface was found.")
def write_supercells_with_displacements(interface_mode,
supercell,
cells_with_disps,
optional_structure_info,
displacement_ids=None,
zfill_width=3,
additional_info=None):
"""Utility method to write out supercell structures with displacements
interface_mode : str
Calculator interface such as 'vasp', 'qe', ...
supercell : Supercell
Supercell.
cells_with_disps : list of PhonopyAtoms
Supercells with displacements.
optional_structure_info : tuple
Information returned by the method ``read_crystal_structure``.
See the docstring.
displacements_ids : array_like or None, optional
Integer 1d array with the length of cells_with_disps, containing
numbers to be assigned to the supercells with displacements.
Default is None, which gives [1, 2, 3, ...].
zfill_width : int, optional
Supercell numbers are filled by zeros from the left with the digits
as given, which results in 001, 002, ..., when zfill_width=3.
additional_info : dict or None, optional
Any information expected to be given to writers of calculators.
Default is None.
"""
if displacement_ids is None:
ids = np.arange(len(cells_with_disps), dtype=int) + 1
else:
ids = displacement_ids
args = (supercell, cells_with_disps, ids)
kwargs = {'width': zfill_width}
if 'pre_filename' in additional_info:
kwargs['pre_filename'] = additional_info['pre_filename']
if interface_mode is None or interface_mode == 'vasp':
import phonopy.interface.vasp as vasp
vasp.write_supercells_with_displacements(*args, **kwargs)
write_magnetic_moments(supercell, sort_by_elements=True)
elif interface_mode == 'abinit':
import phonopy.interface.abinit as abinit
abinit.write_supercells_with_displacements(*args, **kwargs)
elif interface_mode == 'qe':
import phonopy.interface.qe as qe
pp_filenames = optional_structure_info[1]
qe_args = args + (pp_filenames, )
qe.write_supercells_with_displacements(*qe_args, **kwargs)
write_magnetic_moments(supercell, sort_by_elements=False)
elif interface_mode == 'wien2k':
import phonopy.interface.wien2k as wien2k
unitcell_filename, npts, r0s, rmts = optional_structure_info
N = abs(determinant(additional_info['supercell_matrix']))
w2k_args = args + (npts, r0s, rmts, N)
if 'pre_filename' not in kwargs:
kwargs['pre_filename'] = unitcell_filename
wien2k.write_supercells_with_displacements(*w2k_args, **kwargs)
elif interface_mode == 'elk':
import phonopy.interface.elk as elk
sp_filenames = optional_structure_info[1]
elk_args = args + (sp_filenames, )
elk.write_supercells_with_displacements(*elk_args, **kwargs)
elif interface_mode == 'siesta':
import phonopy.interface.siesta as siesta
atypes = optional_structure_info[1]
sst_args = args + (atypes, )
siesta.write_supercells_with_displacements(*sst_args, **kwargs)
elif interface_mode == 'cp2k':
import phonopy.interface.cp2k as cp2k
cp2k_args = args + (optional_structure_info, )
cp2k.write_supercells_with_displacements(*cp2k_args, **kwargs)
elif interface_mode == 'crystal':
import phonopy.interface.crystal as crystal
if additional_info is None:
kwargs['template_file'] = "TEMPLATE"
else:
kwargs['template_file'] = additional_info.get(
'template_file', "TEMPLATE")
conv_numbers = optional_structure_info[1]
N = abs(determinant(additional_info['supercell_matrix']))
cst_args = args + (conv_numbers, N)
crystal.write_supercells_with_displacements(*cst_args, **kwargs)
elif interface_mode == 'dftbp':
import phonopy.interface.dftbp as dftbp
dftbp.write_supercells_with_displacements(*args, **kwargs)
elif interface_mode == 'turbomole':
import phonopy.interface.turbomole as turbomole
turbomole.write_supercells_with_displacements(*args, **kwargs)
elif interface_mode == 'aims':
import phonopy.interface.aims as aims
aims.write_supercells_with_displacements(*args, **kwargs)
else:
raise RuntimeError("No calculator interface was found.")
def calculate_phonon(atoms,
calc,
ndim=np.eye(3),
primitive_matrix=np.eye(3),
distance=0.01,
factor=VaspToTHz,
is_symmetry=True,
symprec=1e-5,
func=None,
**func_args):
"""
"""
if 'magmoms' in atoms.arrays:
is_mag = True
else:
is_mag = False
# 1. get displacements and supercells
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['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)
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.
set_of_forces = []
for iscell, scell in enumerate(supercells):
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(
atoms.get_initial_magnetic_moments())
cell.set_calculator(calc)
dir_name = "PHON_CELL%s" % iscell
cur_dir = os.getcwd()
if not os.path.exists(dir_name):
os.mkdir(dir_name)
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]
set_of_forces.append(forces)
# Phonopy post-process
phonon.produce_force_constants(forces=set_of_forces)
force_constants = phonon.get_force_constants()
write_FORCE_CONSTANTS(force_constants, filename='FORCE_CONSTANTS')
print('')
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
return phonon
NNN,
# primitive_matrix = [[0.5,0.5,0],[0,0.5,0.5],[0.5,0,0.5]],
primitive_matrix=primitive_matrix,
nac_params=nac_params,
factor=factor,
is_symmetry=is_symmetry,
)
phonon.generate_displacements(
distance=delta,
is_plusminus=is_plusminus,
)
pho_disp = phonon.get_supercells_with_displacements()
vasp.write_supercells_with_displacements(
phonon.get_supercell(),
pho_disp,
)
######### get new phonon object ##########
#
import ss_phonopy as ssp
phonon = ssp.calc_phonon(
calc,
phonon,
acoustic_sum_rule=acou_sum_rule,
rot_sum_rule=rot_sum_rule,
r_cut=r_cut,
# F_0_correction=True,
# verbose=True,
# ase_calc=ase_calc,
cp_files=cp_files,
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,
parallel=True,
**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:
set_of_forces = []
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(
atoms.get_initial_magnetic_moments())
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()
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(
atoms.get_initial_magnetic_moments())
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
#with ProcessPoolExecutor() as executor:
# if skip is not None:
# skip=0
# set_of_forces=executor.map(calc_force,list(range(skip,len(supercells))))
if skip is None:
iskip = 0
else:
iskip = skip
if parallel:
p = Pool()
set_of_forces = p.map(calc_force,
list(range(iskip, len(supercells))))
else:
set_of_forces = []
for iscell, scell in enumerate(supercells[iskip:]):
set_of_forces.append(calc_force(iscell))
#phonon.set_displacement_dataset(set_of_forces)
phonon.produce_force_constants(forces=np.array(set_of_forces))
# Phonopy post-process
print('==============')
print(phonon._displacement_dataset['first_atoms'])
#phonon.produce_force_constants(forces=np.array(set_of_forces))
#phonon.produce_force_constants()
force_constants = phonon.get_force_constants()
#print(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)
return phonon
def write_supercells_with_displacements(interface_mode,
supercell,
cells_with_disps,
num_unitcells_in_supercell,
optional_structure_info):
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import write_supercells_with_displacements
write_supercells_with_displacements(supercell, cells_with_disps)
elif interface_mode is 'abinit':
from phonopy.interface.abinit import write_supercells_with_displacements
write_supercells_with_displacements(supercell, cells_with_disps)
elif interface_mode is 'qe':
from phonopy.interface.qe import write_supercells_with_displacements
write_supercells_with_displacements(supercell,
cells_with_disps,
optional_structure_info[1])
elif interface_mode == 'wien2k':
from phonopy.interface.wien2k import write_supercells_with_displacements
unitcell_filename, npts, r0s, rmts = optional_structure_info
write_supercells_with_displacements(
supercell,
cells_with_disps,
npts,
r0s,
rmts,
num_unitcells_in_supercell,
filename=unitcell_filename)
elif interface_mode == 'elk':
from phonopy.interface.elk import write_supercells_with_displacements
write_supercells_with_displacements(supercell,
cells_with_disps,
optional_structure_info[1])
elif interface_mode == 'siesta':
from phonopy.interface.siesta import write_supercells_with_displacements
write_supercells_with_displacements(supercell,
cells_with_disps,
optional_structure_info[1])
elif interface_mode == 'cp2k':
from phonopy.interface.cp2k import write_supercells_with_displacements
write_supercells_with_displacements(supercell, cells_with_disps)
elif interface_mode == 'crystal':
from phonopy.interface.crystal import write_supercells_with_displacements
write_supercells_with_displacements(supercell,
cells_with_disps,
optional_structure_info[1],
num_unitcells_in_supercell,
template_file="TEMPLATE")
def get_phonon_distrib_alist(
prim_cell,
NNN,
T,
seed_range,
calc,
cp_files=None,
plus_minus=True,
delta=0.01,
):
"""
prim_cell (str)
ASE readable primitive unitcell structure file.
NNN (list of int, shape: (3,3))
Supercell matrix used to calculate force constants.
T (float)
Temperature in Kelvin unit.
seed_range (range or list of int)
Seeds for random number generation.
calc (str, choices: ('lmp', 'vasp'))
Calculator for force calculation.
cp_files (list of str)
List of input files for force calculation.
plus_minus (bool)
Option handed to ASE function.
delta (float)
Displacement in Angstrom for finite displacement method.
"""
# Main
from ase.io import read, write
atoms = read(prim_cell)
from phonopy import Phonopy
phonon = Phonopy(
atoms,
NNN,
)
phonon.generate_displacements(
delta,
)
pho_super = phonon.get_supercell()
pho_disp = phonon.get_supercells_with_displacements()
from phonopy.interface import vasp
vasp.write_supercells_with_displacements(
pho_super,
pho_disp,
)
import ss_phonopy as ssp
phonon = ssp.calc_phonon(
calc,
phonon,
cp_files=cp_files,
)
masses = pho_super.masses
job_name = 'eig_x{}{}{}_d{:5.3f}_sym{}'.format(NNN[0][0], NNN[1][1], NNN[2][2], delta, phonon._is_symmetry)
try:
e_s = np.load('{}.npz'.format(job_name))
except:
print('Failed to load {}.npz file. Start to solve eigen problem.'.format(job_name))
eigen_set = get_eigen_set(
phonon.get_force_constants(),
masses,
)
np.savez('{}.npz'.format(job_name), w2=eigen_set[0], D=eigen_set[1])
else:
print('Successfully loaded {}.npz file!'.format(job_name))
eigen_set = (e_s['w2'], e_s['D'])
from ase.md.velocitydistribution import phonon_harmonics
from ase import Atoms, units
alist = []
for i in seed_range:
d_ac, v_ac = phonon_harmonics(
None,
masses,
T *units.kB,
eigen_set=eigen_set,
# rng=np.random.rand,
seed=i,
quantum=True,
plus_minus=plus_minus,
# return_eigensolution=False,
# failfast=True,
)
new_super = Atoms(
cell = pho_super.get_cell(),
symbols = pho_super.get_chemical_symbols(),
positions = pho_super.get_positions() + d_ac,
velocities = v_ac,
pbc = True,
)
alist.append(new_super)
return(alist)
