def get_frequency(poscar_filename, force_sets_filename):
bulk = read_vasp(poscar_filename)
volume = bulk.get_volume()
phonon = Phonopy(bulk, [[2, 0, 0], [0, 2, 0], [0, 0, 2]],
is_auto_displacements=False)
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_force_sets(force_sets)
phonon.set_post_process([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
return phonon.get_frequencies([0.5, 0.5, 0]), volume
def get_frequency(poscar_filename, force_sets_filename):
bulk = read_vasp(poscar_filename)
volume = bulk.get_volume()
phonon = Phonopy(bulk, [[2, 0, 0], [0, 2, 0], [0, 0, 2]],
is_auto_displacements=False)
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_force_sets(force_sets)
phonon.set_post_process([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
return phonon.get_frequencies([0.5, 0.5, 0]), volume
def get_frequency(poscar_filename, force_sets_filename):
unitcell = read_vasp(poscar_filename)
volume = unitcell.get_volume()
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(filename=force_sets_filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon.get_frequencies([0.5, 0.5, 0]), volume
def do_phonons(strt=None,parameters=None):
p= get_phonopy_atoms(mat=strt)
bulk =p
c_size=parameters['phon_size']
dim1=int((float(c_size)/float( max(abs(strt.lattice.matrix[0])))))+1
dim2=int(float(c_size)/float( max(abs(strt.lattice.matrix[1]))))+1
dim3=int(float(c_size)/float( max(abs(strt.lattice.matrix[2]))))+1
Poscar(strt).write_file("POSCAR")
tmp=strt.copy()
tmp.make_supercell([dim1,dim2,dim3])
Poscar(tmp).write_file("POSCAR-Super.vasp")
print ('supercells',dim1,dim2,dim3)
phonon = Phonopy(bulk,[[dim1,0,0],[0,dim2,0],[0,0,dim3]])
print ("[Phonopy] Atomic displacements:")
disps = phonon.get_displacements()
for d in disps:
print ("[Phonopy]", d[0], d[1:])
supercells = phonon.get_supercells_with_displacements()
# Force calculations by calculator
set_of_forces = []
disp=0
for scell in supercells:
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
disp=disp+1
mat = Poscar(AseAtomsAdaptor().get_structure(cell))
mat.comment=str("disp-")+str(disp)
parameters['min']='skip'
parameters['control_file']= parameters['phonon_control_file'] #'/users/knc6/in.phonon'
#a,b,forces=run_job(mat=mat,parameters={'min':'skip','pair_coeff': '/data/knc6/JARVIS-FF-NEW/ALLOY4/Mishin-Ni-Al-2009.eam.alloy', 'control_file': '/users/knc6/in.phonon', 'pair_style': 'eam/alloy', 'atom_style': 'charge'})
a,b,forces=run_job(mat=mat,parameters=parameters)
#print "forces=",forces
drift_force = forces.sum(axis=0)
#print "drift forces=",drift_force
#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)
phonon.produce_force_constants(forces=set_of_forces)
write_FORCE_CONSTANTS(phonon.get_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
def get_frequency(poscar_filename, force_sets):
"""Calculate phonons and return frequencies."""
unitcell = read_vasp(poscar_filename)
volume = unitcell.volume
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]],
)
disps = np.zeros_like(force_sets)
disps[0] = [0.01, 0, 0]
phonon.dataset = {
"natom":
len(force_sets),
"first_atoms": [{
"number": 0,
"displacement": [0.01, 0, 0],
"forces": force_sets
}],
}
phonon.produce_force_constants()
return phonon.get_frequencies([0.5, 0.5, 0]), volume
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
print "[Phonopy] Atomic displacements:"
disps = phonon.get_displacements()
for d in disps:
print "[Phonopy]", d[0], d[1:]
supercells = phonon.get_supercells_with_displacements()
# Force calculations by calculator
set_of_forces = []
for scell in supercells:
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
cell.set_calculator(calc)
forces = cell.get_forces()
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)
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
0]],
distance=0.01)
print "[Phonopy] Atomic displacements:"
disps = phonon.get_displacements()
for d in disps:
print "[Phonopy]", d[0], d[1:]
supercells = phonon.get_supercells_with_displacements()
# Force calculations by calculator
set_of_forces = []
for scell in supercells:
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
cell.set_calculator(calc)
forces = cell.get_forces()
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)
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
