def _get_dos_calc(self, phonon, structure, kpoint_density):
tempfilename = tempfile.gettempprefix() + '.yaml'
kpoint = Kpoints.automatic_density(structure=structure,
kppa=kpoint_density,
force_gamma=True)
phonon.run_mesh(kpoint.kpts[0])
phonon.run_total_dos()
phonon.write_total_dos(filename=tempfilename)
dos = get_ph_dos(tempfilename)
os.remove(tempfilename)
return dos
def _get_phono3pyobject_phono3py(self, structure, potential,
kpoint_density,
displacementdistancephono3py,
max_distance_third_order):
cell = get_phonopy_structure(structure)
kpoint = Kpoints.automatic_density(structure=structure,
kppa=kpoint_density,
force_gamma=True)
mesh = kpoint.kpts[0]
phono3py = Phono3py(cell,
self.smat,
primitive_matrix=[[1, 0., 0.], [0., 1, 0.],
[0., 0., 1]],
mesh=mesh,
log_level=1)
phono3py.generate_displacements(
distance=displacementdistancephono3py,
cutoff_pair_distance=max_distance_third_order)
scells_with_disps = phono3py.get_supercells_with_displacements()
disp_dataset = phono3py.get_displacement_dataset()
numatoms = len(scells_with_disps[0].get_scaled_positions())
dummy_force = np.zeros((numatoms, 3))
set_of_forces = []
for scell in scells_with_disps:
if scell is not None:
# this part is adapted from: https://web.archive.org/web/20200610084959/https://github.com/phonopy/phonopy/blob/develop/example/ase/8Si-phonon.py
# Copyright by Atsushi Togo
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
cell.set_calculator(potential)
forces = cell.get_forces()
drift_force = forces.sum(axis=0)
print(("[Phonopy] Drift force:" + "%11.5f" * 3) %
tuple(drift_force))
for force in forces:
force -= drift_force / forces.shape[0]
set_of_forces.append(forces)
else:
set_of_forces.append(dummy_force)
phono3py.produce_fc3(set_of_forces,
displacement_dataset=disp_dataset,
symmetrize_fc3r=True)
fc3 = phono3py.get_fc3()
show_drift_fc3(fc3)
return phono3py
def from_structure(cls,
structure: Structure,
reciprocal_density: Optional[int] = 50000,
**kwargs):
"""
Get a ShengBTE control object from a structure.
Args:
structure: A structure object.
reciprocal_density: If not None, the q-point grid ("ngrid") will be
set using this density.
kwargs: Additional options to be passed to the Control constructor.
See the docstring of the __init__ method for more details
Returns:
A ShengBTE control object.
"""
elements = list(map(str, structure.composition.elements))
unique_nums = np.unique(structure.atomic_numbers)
types_dict = dict(zip(unique_nums, range(len(unique_nums))))
types = [types_dict[i] + 1 for i in structure.atomic_numbers]
control_dict = {
"nelements": structure.ntypesp,
"natoms": structure.num_sites,
"norientations": 0,
"lfactor": 0.1,
"lattvec": structure.lattice.matrix.tolist(),
"elements": elements,
"types": types,
"positions": structure.frac_coords.tolist(),
}
if reciprocal_density:
kpoints = Kpoints.automatic_density(structure, reciprocal_density)
control_dict["ngrid"] = kpoints.kpts[0]
control_dict.update(**kwargs)
return Control(**control_dict)
def vac_antisite_def_struct_gen(args):
mpid = args.mpid
mapi_key = args.mapi_key
cellmax = args.cellmax
if not mpid:
print ("============\nERROR: Provide an mpid\n============")
return
if not mapi_key:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
else:
with MPRester(mapi_key) as mp:
struct = mp.get_structure_by_material_id(mpid)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites/prim_struct_sites)
sc_scale = get_sc_scale(struct,cellmax)
mpvis = MPRelaxSet(struct, user_incar_settings={"LDAU": False})
# Begin defaults: All default settings.
blk_vasp_incar_param = {'IBRION':-1,'EDIFF':1e-4,'EDIFFG':0.001,'NSW':0,}
def_vasp_incar_param = {'ISIF':2,'NELM':99,'IBRION':2,'EDIFF':1e-6,
'EDIFFG':0.001,'NSW':40,}
kpoint_den = 6000
# End defaults
ptcr_flag = True
try:
potcar = mpvis.potcar
except:
print ("VASP POTCAR folder not detected.\n" \
"Only INCAR, POSCAR, KPOINTS are generated.\n" \
"If you have VASP installed on this system, \n" \
"refer to pymatgen documentation for configuring the settings.")
ptcr_flag = False
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
site_no = scs[0].num_sites
if site_no > cellmax:
max_sc_dim = max(sc_scale)
i = sc_scale.index(max_sc_dim)
sc_scale[i] -= 1
scs = vac.make_supercells_with_defects(sc_scale)
for i in range(len(scs)):
sc = scs[i]
mpvis = MPRelaxSet(sc, user_incar_settings={"LDAU": False})
poscar = mpvis.poscar
kpoints = Kpoints.automatic_density(sc,kpoint_den)
incar = mpvis.incar
if ptcr_flag:
potcar = mpvis.potcar
interdir = mpid
if not i:
fin_dir = os.path.join(interdir,'bulk')
try:
os.makedirs(fin_dir)
except:
pass
incar.update(blk_vasp_incar_param)
incar.write_file(os.path.join(fin_dir,'INCAR'))
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(vac.get_defectsite_multiplicity(i-1)/conv_prim_rat)
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir ='vacancy_{}_mult-{}_sitespecie-{}'.format(str(i),
site_mult, vac_symbol)
fin_dir = os.path.join(interdir,vac_dir)
try:
os.makedirs(fin_dir)
except:
pass
incar.update(def_vasp_incar_param)
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
incar.write_file(os.path.join(fin_dir,'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
# Antisite generation at all vacancy sites
struct_species = scs[0].types_of_specie
for specie in set(struct_species)-set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
mpvis = MPRelaxSet(anti_struct, user_incar_settings={"LDAU": False})
poscar = mpvis.poscar
incar = mpvis.incar
incar.update(def_vasp_incar_param)
as_dir ='antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir,as_dir)
try:
os.makedirs(fin_dir)
except:
pass
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
incar.write_file(os.path.join(fin_dir,'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
def vac_antisite_def_struct_gen(args):
mpid = args.mpid
mapi_key = args.mapi_key
cellmax = args.cellmax
if not mpid:
print("============\nERROR: Provide an mpid\n============")
return
if not mapi_key:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
else:
with MPRester(mapi_key) as mp:
struct = mp.get_structure_by_material_id(mpid)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites / prim_struct_sites)
sc_scale = get_sc_scale(struct, cellmax)
mpvis = MPRelaxSet(struct, user_incar_settings={"LDAU": False})
# Begin defaults: All default settings.
blk_vasp_incar_param = {
'IBRION': -1,
'EDIFF': 1e-4,
'EDIFFG': 0.001,
'NSW': 0,
}
def_vasp_incar_param = {
'ISIF': 2,
'NELM': 99,
'IBRION': 2,
'EDIFF': 1e-6,
'EDIFFG': 0.001,
'NSW': 40,
}
kpoint_den = 6000
# End defaults
ptcr_flag = True
try:
potcar = mpvis.potcar
except:
print ("VASP POTCAR folder not detected.\n" \
"Only INCAR, POSCAR, KPOINTS are generated.\n" \
"If you have VASP installed on this system, \n" \
"refer to pymatgen documentation for configuring the settings.")
ptcr_flag = False
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
site_no = scs[0].num_sites
if site_no > cellmax:
max_sc_dim = max(sc_scale)
i = sc_scale.index(max_sc_dim)
sc_scale[i] -= 1
scs = vac.make_supercells_with_defects(sc_scale)
for i in range(len(scs)):
sc = scs[i]
mpvis = MPRelaxSet(sc, user_incar_settings={"LDAU": False})
poscar = mpvis.poscar
kpoints = Kpoints.automatic_density(sc, kpoint_den)
incar = mpvis.incar
if ptcr_flag:
potcar = mpvis.potcar
interdir = mpid
if not i:
fin_dir = os.path.join(interdir, 'bulk')
try:
os.makedirs(fin_dir)
except:
pass
incar.update(blk_vasp_incar_param)
incar.write_file(os.path.join(fin_dir, 'INCAR'))
poscar.write_file(os.path.join(fin_dir, 'POSCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(
vac.get_defectsite_multiplicity(i - 1) / conv_prim_rat)
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir = 'vacancy_{}_mult-{}_sitespecie-{}'.format(
str(i), site_mult, vac_symbol)
fin_dir = os.path.join(interdir, vac_dir)
try:
os.makedirs(fin_dir)
except:
pass
incar.update(def_vasp_incar_param)
poscar.write_file(os.path.join(fin_dir, 'POSCAR'))
incar.write_file(os.path.join(fin_dir, 'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
# Antisite generation at all vacancy sites
struct_species = scs[0].types_of_specie
for specie in set(struct_species) - set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
mpvis = MPRelaxSet(anti_struct,
user_incar_settings={"LDAU": False})
poscar = mpvis.poscar
incar = mpvis.incar
incar.update(def_vasp_incar_param)
as_dir = 'antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir, as_dir)
try:
os.makedirs(fin_dir)
except:
pass
poscar.write_file(os.path.join(fin_dir, 'POSCAR'))
incar.write_file(os.path.join(fin_dir, 'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
