def test_to_dict_from_dict(self):
k = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
d = k.to_dict
k2 = Kpoints.from_dict(d)
self.assertEqual(k.kpts, k2.kpts)
self.assertEqual(k.style, k2.style)
self.assertEqual(k.kpts_shift, k2.kpts_shift)
def test_to_dict_from_dict(self):
k = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
d = k.to_dict
k2 = Kpoints.from_dict(d)
self.assertEqual(k.kpts, k2.kpts)
self.assertEqual(k.style, k2.style)
self.assertEqual(k.kpts_shift, k2.kpts_shift)
def test_kpt_bands_to_dict_from_dict(self):
file_name = os.path.join(test_dir, 'KPOINTS.band')
k = Kpoints.from_file(file_name)
d = k.to_dict
import json
json.dumps(d)
#This doesn't work
k2 = Kpoints.from_dict(d)
self.assertEqual(k.kpts, k2.kpts)
self.assertEqual(k.style, k2.style)
self.assertEqual(k.kpts_shift, k2.kpts_shift)
self.assertEqual(k.num_kpts, k2.num_kpts)
def test_kpt_bands_to_dict_from_dict(self):
file_name = os.path.join(test_dir, 'KPOINTS.band')
k = Kpoints.from_file(file_name)
d = k.to_dict
import json
json.dumps(d)
#This doesn't work
k2 = Kpoints.from_dict(d)
self.assertEqual(k.kpts, k2.kpts)
self.assertEqual(k.style, k2.style)
self.assertEqual(k.kpts_shift, k2.kpts_shift)
self.assertEqual(k.num_kpts, k2.num_kpts)
def get_kpoints(self, structure):
"""
Writes out a KPOINTS file using the automated gamma grid method.
VASP crashes GW calculations on none gamma centered meshes.
"""
if self.sort_structure:
structure = structure.get_sorted_structure()
dens = int(self.kpoints_settings['grid_density'])
if dens == 1:
return Kpoints.gamma_automatic()
else:
return Kpoints.automatic_gamma_density(structure, dens)
def get_kpoints(self, structure):
"""
Writes out a KPOINTS file using the automated gamma grid method.
VASP crashes GW calculations on none gamma centered meshes.
"""
if self.sort_structure:
structure = structure.get_sorted_structure()
dens = int(self.kpoints_settings['grid_density'])
if dens == 1:
return Kpoints.gamma_automatic()
else:
return Kpoints.automatic_gamma_density(structure, dens)
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, "Gamma")
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, "Monkhorst")
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, "Automatic")
self.assertEqual(kpoints.kpts, [[100]])
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 3, 4]])
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, "Gamma")
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, "Monkhorst")
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, "Automatic")
self.assertEqual(kpoints.kpts, [[100]])
filepath = os.path.join(test_dir, "POSCAR")
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 3, 4]])
def get_kpoints(self, structure):
"""
Get a KPOINTS file for NonSCF calculation. In "Line" mode, kpoints are
generated along high symmetry lines. In "Uniform" mode, kpoints are
Gamma-centered mesh grid. Kpoints are written explicitly in both cases.
Args:
structure (Structure/IStructure): structure to get Kpoints
"""
if self.mode == "Line":
kpath = HighSymmKpath(structure)
cart_k_points, k_points_labels = kpath.get_kpoints()
frac_k_points = [kpath._prim_rec.get_fractional_coords(k)
for k in cart_k_points]
return Kpoints(comment="Non SCF run along symmetry lines",
style="Reciprocal", num_kpts=len(frac_k_points),
kpts=frac_k_points, labels=k_points_labels,
kpts_weights=[1] * len(cart_k_points))
else:
num_kpoints = self.kpoints_settings["kpoints_density"] * \
structure.lattice.reciprocal_lattice.volume
kpoints = Kpoints.automatic_density(
structure, num_kpoints * structure.num_sites)
mesh = kpoints.kpts[0]
ir_kpts = SymmetryFinder(structure, symprec=self.sym_prec) \
.get_ir_reciprocal_mesh(mesh)
kpts = []
weights = []
for k in ir_kpts:
kpts.append(k[0])
weights.append(int(k[1]))
return Kpoints(comment="Non SCF run on uniform grid",
style="Reciprocal", num_kpts=len(ir_kpts),
kpts=kpts, kpts_weights=weights)
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, "Gamma")
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, "Monkhorst")
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, "Automatic")
self.assertEqual(kpoints.kpts, [[100]])
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 4, 4]])
self.assertEqual(kpoints.style, "Monkhorst")
kpoints = Kpoints.automatic_density(poscar.structure, 500, True)
self.assertEqual(kpoints.style, "Gamma")
kpoints = Kpoints.automatic_density_by_vol(poscar.structure, 1000)
self.assertEqual(kpoints.kpts, [[6, 11, 13]])
self.assertEqual(kpoints.style, "Gamma")
s = poscar.structure
s.make_supercell(3)
kpoints = Kpoints.automatic_density(s, 500)
self.assertEqual(kpoints.kpts, [[1, 1, 1]])
self.assertEqual(kpoints.style, "Gamma")
def get_kpoints(self, structure, kpoints_density=1000):
"""
Get a KPOINTS file for NonSCF calculation. In "Line" mode, kpoints are
generated along high symmetry lines. In "Uniform" mode, kpoints are
Gamma-centered mesh grid. Kpoints are written explicitly in both cases.
Args:
kpoints_density:
kpoints density for the reciprocal cell of structure.
Suggest to use a large kpoints_density.
Might need to increase the default value when calculating
metallic materials.
"""
if self.mode == "Line":
kpath = HighSymmKpath(structure)
cart_k_points, k_points_labels = kpath.get_kpoints()
frac_k_points = [
kpath._prim_rec.get_fractional_coords(k) for k in cart_k_points
]
return Kpoints(comment="Non SCF run along symmetry lines",
style="Reciprocal",
num_kpts=len(frac_k_points),
kpts=frac_k_points,
labels=k_points_labels,
kpts_weights=[1] * len(cart_k_points))
else:
num_kpoints = kpoints_density * \
structure.lattice.reciprocal_lattice.volume
kpoints = Kpoints.automatic_density(
structure, num_kpoints * structure.num_sites)
mesh = kpoints.kpts[0]
ir_kpts = SymmetryFinder(structure, symprec=0.01)\
.get_ir_reciprocal_mesh(mesh)
kpts = []
weights = []
for k in ir_kpts:
kpts.append(k[0])
weights.append(int(k[1]))
return Kpoints(comment="Non SCF run on uniform grid",
style="Reciprocal",
num_kpts=len(ir_kpts),
kpts=kpts,
kpts_weights=weights)
def get_kpoints(self, structure):
"""
Writes out a KPOINTS file using the fully automated grid method. Uses
Gamma centered meshes for hexagonal cells and Monk grids otherwise.
Algorithm:
Uses a simple approach scaling the number of divisions along each
reciprocal lattice vector proportional to its length.
"""
dens = int(self.kpoints_settings['grid_density'])
return Kpoints.automatic_density(structure, dens)
def get_kpoints(self, structure):
"""
Writes out a KPOINTS file using the fully automated grid method. Uses
Gamma centered meshes for hexagonal cells and Monk grids otherwise.
Algorithm:
Uses a simple approach scaling the number of divisions along each
reciprocal lattice vector proportional to its length.
"""
dens = int(self.kpoints_settings['grid_density'])
return Kpoints.automatic_density(structure, dens)
def get_kpoints(self, structure):
"""
Get a KPOINTS file for NonSCF calculation. kpoints are
Gamma-centered mesh grid.
Args:
structure (Structure/IStructure): structure to get Kpoints
"""
kppa = self.kpoints_settings["kpoints_density"]
kpoints = Kpoints.automatic_gamma_density(structure, kppa)
return kpoints
def test_init(self):
filepath = os.path.join(test_dir, 'KPOINTS.auto')
kpoints = Kpoints.from_file(filepath)
self.assertEqual(kpoints.kpts, [[10]], "Wrong kpoint lattice read")
filepath = os.path.join(test_dir, 'KPOINTS.cartesian')
kpoints = Kpoints.from_file(filepath)
self.assertEqual(kpoints.kpts,
[[0.25, 0, 0], [0, 0.25, 0], [0, 0, 0.25]],
"Wrong kpoint lattice read")
self.assertEqual(kpoints.kpts_shift, [0.5, 0.5, 0.5],
"Wrong kpoint shift read")
filepath = os.path.join(test_dir, 'KPOINTS')
kpoints = Kpoints.from_file(filepath)
self.assertEqual(kpoints.kpts, [[2, 4, 6]])
filepath = os.path.join(test_dir, 'KPOINTS.band')
kpoints = Kpoints.from_file(filepath)
self.assertIsNotNone(kpoints.labels)
self.assertEqual(kpoints.style, "Line_mode")
filepath = os.path.join(test_dir, 'KPOINTS.explicit')
kpoints = Kpoints.from_file(filepath)
self.assertIsNotNone(kpoints.kpts_weights)
filepath = os.path.join(test_dir, 'KPOINTS.explicit_tet')
kpoints = Kpoints.from_file(filepath)
self.assertEqual(kpoints.tet_connections, [(6, [1, 2, 3, 4])])
def test_init(self):
filepath = os.path.join(test_dir, "KPOINTS.auto")
kpoints = Kpoints.from_file(filepath)
self.assertEqual(kpoints.kpts, [[10]], "Wrong kpoint lattice read")
filepath = os.path.join(test_dir, "KPOINTS.cartesian")
kpoints = Kpoints.from_file(filepath)
self.assertEqual(kpoints.kpts, [[0.25, 0, 0], [0, 0.25, 0], [0, 0, 0.25]], "Wrong kpoint lattice read")
self.assertEqual(kpoints.kpts_shift, [0.5, 0.5, 0.5], "Wrong kpoint shift read")
filepath = os.path.join(test_dir, "KPOINTS")
kpoints = Kpoints.from_file(filepath)
self.assertEqual(kpoints.kpts, [[2, 4, 6]])
filepath = os.path.join(test_dir, "KPOINTS.band")
kpoints = Kpoints.from_file(filepath)
self.assertIsNotNone(kpoints.labels)
self.assertEqual(kpoints.style, "Line_mode")
filepath = os.path.join(test_dir, "KPOINTS.explicit")
kpoints = Kpoints.from_file(filepath)
self.assertIsNotNone(kpoints.kpts_weights)
filepath = os.path.join(test_dir, "KPOINTS.explicit_tet")
kpoints = Kpoints.from_file(filepath)
self.assertEqual(kpoints.tet_connections, [(6, [1, 2, 3, 4])])
def setUp(self):
filepath = os.path.join(test_dir, "INCAR")
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, "POSCAR")
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..", "test_files")
)
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, "POTCAR")
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, "KPOINTS.auto")
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def setUp(self):
filepath = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
"test_files"))
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, 'POTCAR')
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, 'KPOINTS.auto')
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def get_kpoints(self, structure, kpoints_density=1000):
"""
Get a KPOINTS file for NonSCF calculation. In "Line" mode, kpoints are
generated along high symmetry lines. In "Uniform" mode, kpoints are
Gamma-centered mesh grid. Kpoints are written explicitly in both cases.
Args:
kpoints_density:
kpoints density for the reciprocal cell of structure.
Suggest to use a large kpoints_density.
Might need to increase the default value when calculating
metallic materials.
"""
if self.mode == "Line":
kpath = HighSymmKpath(structure)
cart_k_points, k_points_labels = kpath.get_kpoints()
frac_k_points = [kpath._prim_rec.get_fractional_coords(k)
for k in cart_k_points]
return Kpoints(comment="Non SCF run along symmetry lines",
style="Reciprocal", num_kpts=len(frac_k_points),
kpts=frac_k_points, labels=k_points_labels,
kpts_weights=[1]*len(cart_k_points))
else:
num_kpoints = kpoints_density * \
structure.lattice.reciprocal_lattice.volume
kpoints = Kpoints.automatic_density(
structure, num_kpoints * structure.num_sites)
mesh = kpoints.kpts[0]
ir_kpts = SymmetryFinder(structure, symprec=0.01)\
.get_ir_reciprocal_mesh(mesh)
kpts = []
weights = []
for k in ir_kpts:
kpts.append(k[0])
weights.append(int(k[1]))
return Kpoints(comment="Non SCF run on uniform grid",
style="Reciprocal", num_kpts=len(ir_kpts),
kpts=kpts, kpts_weights=weights)
def substitute_def_struct_gen(mpid, solute, mapi_key, cellmax):
print(mpid, solute, mapi_key, cellmax)
if not mpid:
print("============\nERROR: Provide an mpid\n============")
return
if not solute:
print("============\nERROR: Provide solute atom\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)
print(struct.formula)
mpvis = MPGGAVaspInputSet()
# 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
# Check if POTCAR file can be geneated
ptcr_flag = True
try:
potcar = mpvis.get_potcar(struct)
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
print(ptcr_flag)
vac = Vacancy(struct, {}, {})
sc_scale = get_sc_scale(struct, cellmax)
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)
print len(scs)
interdir = mpid
blk_str_sites = set(scs[0].sites)
for i in range(1, len(scs)):
sc = scs[i]
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = vac.get_defectsite_multiplicity(i - 1)
vac_site_specie = vac_site.specie
vac_specie = vac_site.specie.symbol
# Solute substitution defect generation at all vacancy sites
struct_species = scs[0].types_of_specie
solute_struct = sc.copy()
solute_struct.append(solute, vac_site.frac_coords)
incar = mpvis.get_incar(solute_struct)
incar.update(def_vasp_incar_param)
poscar = mpvis.get_poscar(solute_struct)
kpoints = Kpoints.automatic_density(solute_struct, kpoint_den)
if ptcr_flag:
potcar = mpvis.get_potcar(solute_struct)
sub_def_dir = 'solute_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_specie, solute)
fin_dir = os.path.join(interdir, sub_def_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'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))
def test_kpt_bands_to_dict_from_dict(self):
file_name = os.path.join(test_dir, 'KPOINTS.band')
k = Kpoints.from_file(file_name)
d = k.to_dict
def run_task(self, fw_spec):
Incar.from_dict(fw_spec['vasp']['incar']).write_file('INCAR')
Poscar.from_dict(fw_spec['vasp']['poscar']).write_file('POSCAR')
Potcar.from_dict(fw_spec['vasp']['potcar']).write_file('POTCAR')
Kpoints.from_dict(fw_spec['vasp']['kpoints']).write_file('KPOINTS')
def get_calibration_task(structure, phase="CalibrateBulk", \
slab_interface_params={'hkl':[1,0,0], 'ligand': None},\
turn_knobs={}, incar_params={}, other_params={}):
"""
returns general calibration task for a structure
Args:
structure : pymatgen structure to be calibrated (can be a bulk, ligand, slab
or interface)
phase : calibration type, viz. CalibrateBulk, CalibrateMolecule,
CalibrateSlab, CalibrateInterface
hkl : in case of Slab and Interface miller indices of facet
turn_knobs : specifies the parameters to be calibrated
incar_params : dictionary of additional incar parameters, refer defined
incar_dict for defaults
other_params : other parameters for calibration, viz. job_dir, is_matrix, etc.
described in the calibrate module
"""
#structure definition
poscar = Poscar(structure)
incar_dict = { 'SYSTEM': 'slab',
'ENCUT': 500,
'ISIF': 2,
'IBRION': 2,
'ISMEAR': 1,
'EDIFF': 1e-05,
'NPAR': 4,
'SIGMA': 0.1,
'PREC': 'Accurate'
}
if incar_params:
incar_dict.update(incar_params)
incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts=(8, 8, 1))
que = { 'nnodes':1,
'nprocs':16,
'walltime':'48:00:00',
'job_bin': '/home/km468/Software/VASP/vaspsol_kappa.5.3.5/vasp'
}
# calibration task: relax hkl
calparams = {}
calparams['calibrate'] = phase
calparams['incar'] = incar.as_dict()
calparams['poscar'] = poscar.as_dict()
calparams['kpoints'] = kpoints.as_dict()
calparams['que_params'] = que
calparams['turn_knobs'] = turn_knobs
if phase == 'CalibrateSlab':
calparams['system'] = {'hkl':slab_interface_params['hkl'],
'ligand':slab_interface_params['ligand']
}
elif phase == 'CalibrateInterface':
calparams['system'] = {'hkl':hkl,
'ligand':structure.ligand.reduced_formula
}
calparams['other_params'] = {
'is_matrix':False,
'from_ase':True,
'Grid_type':'M'
}
if other_params:
calparams['other_params'].update(other_params)
return MPINTCalibrateTask(calparams)
def vac_antisite_def_struct_gen(mpid, mapi_key, 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 = MPGGAVaspInputSet()
# 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.get_potcar(struct)
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]
poscar = mpvis.get_poscar(sc)
kpoints = Kpoints.automatic_density(sc,kpoint_den)
incar = mpvis.get_incar(sc)
if ptcr_flag:
potcar = mpvis.get_potcar(sc)
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)
poscar = mpvis.get_poscar(anti_struct)
incar = mpvis.get_incar(anti_struct)
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'))
# read structure
if os.path.exists(fstruct):
struct = mg.read_structure(fstruct)
else:
print("File %s does not exist" % fstruct)
exit(1)
# symmetry information
struct_sym = SymmetryFinder(struct)
print("lattice type : {0}".format(struct_sym.get_lattice_type()))
print("space group : {0} ({1})".format(struct_sym.get_spacegroup_symbol(),
struct_sym.get_spacegroup_number()))
# Compute first brillouin zone
ibz = HighSymmKpath(struct)
ibz.get_kpath_plot(savefig="path.png")
print("ibz type : {0}".format(ibz.name))
# print specific kpoints in the first brillouin zone
for key, val in ibz.kpath["kpoints"].items():
print("%8s %s" % (key, str(val)))
# suggested path for the band structure
print("paths in first brillouin zone :")
for path in ibz.kpath["path"]:
print(path)
# write the KPOINTS file
Kpoints.automatic_linemode(ndiv, ibz).write_file("KPOINTS")
def get_kpoints(self, structure):
return Kpoints.gamma_automatic()
def get_VASP_inputs(structure, workdir, job_name, nproc=64, kppa=500, extra_incar_dict = None):
if os.path.exists(workdir):
print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB'
return -1
poscar = Poscar(structure)
list_potcar_singles, potcar= get_POTCAR(poscar)
kpoints = Kpoints.automatic_density(structure, kppa=kppa)
# Default values
incar_dict = dict( SYSTEM = structure.formula, # Name of job
LREAL = 'Auto', # Should projections be done in real space? Let VASP decide
ENCUT = 520., # 520. eV, just like Ceder
IBRION = 2, # Controls ionic relataxion: 1-> DISS, 2 -> CG, 3-> MD
EDIFF = 1E-7, # criterion to stop SCF loop, in eV
EDIFFG = -1E-3, # criterion to stop ionic relaxations. Negative means FORCES < |EDIFFG|
PREC = 'HIGH', # level of precision
AMIX = 0.2,
AMIX_MAG= 0.8,
BMIX = 0.001,
BMIX_MAG= 0.001,
NSW = 150, # Maximum number of ionic steps
ISMEAR = 0, # smearing scheme. Use 0 for insulators, as suggested by VASPWIKI
ISPIN = 2, # spin polarized
NPAR = 8, # VASPWIKI recommends sqrt(ncore)
LSCALU = False, # Don't use scalapack. Probably a can of worms.
ALGO = 'NORMAL', # what ionic relaxation scheme to use?
LORBIT = 11, # 11 prints out the DOS
ISIF = 3, # Controls the computation of stress tensor. 3 computes everything
NSIM = 4, # how many bands to treat in parallel? Default is 4, probably fine.
SIGMA = 0.025, # smearing in eV
LMAXMIX = 4, # Description: LMAXMIX controls up to which l-quantum number the one-center PAW charge densities are passed through the charge density mixer. MaterialsProject uses 4.
LCHARG = False, # Write charge densities?
LWAVE = False, # write out the wavefunctions?
LPLANE = True, # Plane distribution of FFT coefficients. Reduces communications in FFT.
NELM = 100, # maximum number of SCF cycles.
NELMDL = -10, # since initial orbitals may be random, fixes hamiltonian for |NELM| SCF cycles to give wf a chance to simmer down.
ISTART = 0, # begin from scratch!
ISYM = 2) # use symmetry
if extra_incar_dict != None:
incar_dict.update( extra_incar_dict )
incar = Incar.from_dict(incar_dict )
incar.write_file(workdir+'INCAR')
poscar.write_file(workdir+'POSCAR', vasp4_compatible = True)
kpoints.write_file(workdir+'KPOINTS')
potcar.write_file(workdir+'POTCAR')
potcar.sort()
hack_potcar_file(workdir,list_potcar_singles)
with open(workdir+'job.sh','w') as f:
f.write(submit_template.format(job_name,nproc))
with open(workdir+'clean.sh','w') as f:
f.write(clean_template)
return 0
def from_previous_vasp_run(previous_vasp_dir, output_dir='.',
user_incar_settings=None,
make_dir_if_not_present=True):
"""
Generate a set of Vasp input files for static calculations from a
directory of previous Vasp run.
Args:
previous_vasp_dir:
The directory contains the outputs(vasprun.xml and OUTCAR) of
previous vasp run.
output_dir:
The directory to write the VASP input files for the static
calculations. Default to write in the current directory.
make_dir_if_not_present:
Set to True if you want the directory (and the whole path) to
be created if it is not present.
"""
try:
vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
parse_dos=False, parse_eigen=None)
outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
previous_incar = Incar.from_file(os.path.join(previous_vasp_dir,
"INCAR"))
kpoints = Kpoints.from_file(os.path.join(previous_vasp_dir,
"KPOINTS"))
except:
traceback.format_exc()
raise RuntimeError("Can't get valid results from previous run")
structure = MPStaticVaspInputSet.get_structure(
vasp_run, outcar)
mpsvip = MPStaticVaspInputSet()
mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
new_incar = Incar.from_file(os.path.join(output_dir, "INCAR"))
# Use previous run INCAR and override necessary parameters
previous_incar.update({"IBRION": -1, "ISMEAR": -5, "LAECHG": True,
"LCHARG": True, "LORBIT": 11, "LVHAR": True,
"LWAVE": False, "NSW": 0, "ICHARG": 0})
# Compare ediff between previous and staticinputset values,
# choose the tigher ediff
previous_incar.update({"EDIFF": min(previous_incar["EDIFF"],
new_incar["EDIFF"])})
# add user settings
if user_incar_settings:
previous_incar.update(user_incar_settings)
previous_incar.write_file(os.path.join(output_dir, "INCAR"))
# Prefer to use k-point scheme from previous run
kpoints_out = Kpoints.from_file(os.path.join(output_dir, "KPOINTS"))
if kpoints.style != kpoints_out.style and \
SymmetryFinder(structure, 0.01).get_lattice_type() != \
"hexagonal":
k_div = (kp + 1 if kp % 2 == 1 else kp
for kp in kpoints_out.kpts[0])
Kpoints.monkhorst_automatic(k_div).write_file(
os.path.join(output_dir, "KPOINTS"))
def get_kpoints(self, structure):
return Kpoints.gamma_automatic()
def from_previous_vasp_run(previous_vasp_dir, output_dir='.',
user_incar_settings=None,
make_dir_if_not_present=True,
kpoints_density=90, sym_prec=0.1):
"""
Generate a set of Vasp input files for static calculations from a
directory of previous Vasp run.
Args:
previous_vasp_dir (str): Directory containing the outputs(
vasprun.xml and OUTCAR) of previous vasp run.
output_dir (str): Directory to write the VASP input files for
the static calculations. Defaults to current directory.
make_dir_if_not_present (bool): Set to True if you want the
directory (and the whole path) to be created if it is not
present.
kpoints_density (int): kpoints density for the reciprocal cell
of structure. Might need to increase the default value when
calculating metallic materials.
sym_prec (float): Tolerance for symmetry finding
"""
# Read input and output from previous run
try:
vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
parse_dos=False, parse_eigen=None)
outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
previous_incar = vasp_run.incar
previous_kpoints = vasp_run.kpoints
except:
traceback.format_exc()
raise RuntimeError("Can't get valid results from previous run")
mpsvip = MPStaticVaspInputSet(kpoints_density=kpoints_density,
sym_prec=sym_prec)
structure = mpsvip.get_structure(vasp_run, outcar)
mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
new_incar = mpsvip.get_incar(structure)
# Use previous run INCAR and override necessary parameters
previous_incar.update({"IBRION": -1, "ISMEAR": -5, "LAECHG": True,
"LCHARG": True, "LORBIT": 11, "LVHAR": True,
"LWAVE": False, "NSW": 0, "ICHARG": 0})
for incar_key in ["MAGMOM", "NUPDOWN"]:
if new_incar.get(incar_key, None):
previous_incar.update({incar_key: new_incar[incar_key]})
else:
previous_incar.pop(incar_key, None)
# use new LDAUU when possible b/c the Poscar might have changed
# representation
if previous_incar.get('LDAU'):
u = previous_incar.get('LDAUU', [])
j = previous_incar.get('LDAUJ', [])
if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
previous_incar.update({tag: new_incar[tag]})
# ensure to have LMAXMIX for GGA+U static run
if "LMAXMIX" not in previous_incar:
previous_incar.update({"LMAXMIX": new_incar["LMAXMIX"]})
# Compare ediff between previous and staticinputset values,
# choose the tighter ediff
previous_incar.update({"EDIFF": min(previous_incar.get("EDIFF", 1),
new_incar["EDIFF"])})
# add user settings
if user_incar_settings:
previous_incar.update(user_incar_settings)
previous_incar.write_file(os.path.join(output_dir, "INCAR"))
# Perform checking on INCAR parameters
if any([previous_incar.get("NSW", 0) != 0, previous_incar["IBRION"] != -1,
previous_incar["LCHARG"] != True,
any([sum(previous_incar["LDAUU"])<=0, previous_incar["LMAXMIX"]<4])
if previous_incar.get("LDAU") else False]):
raise ValueError("Incompatible INCAR parameters!")
# Prefer to use k-point scheme from previous run
new_kpoints = mpsvip.get_kpoints(structure)
if previous_kpoints.style[0] != new_kpoints.style[0]:
if previous_kpoints.style[0] == "M" and \
SymmetryFinder(structure, 0.1).get_lattice_type() != \
"hexagonal":
k_div = (kp + 1 if kp % 2 == 1 else kp
for kp in new_kpoints.kpts[0])
Kpoints.monkhorst_automatic(k_div). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
Kpoints.gamma_automatic(new_kpoints.kpts[0]). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
new_kpoints.write_file(os.path.join(output_dir, "KPOINTS"))
def substitute_def_struct_gen(mpid, solute, mapi_key, cellmax):
print (mpid, solute, mapi_key, cellmax)
if not mpid:
print ("============\nERROR: Provide an mpid\n============")
return
if not solute:
print ("============\nERROR: Provide solute atom\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)
print (struct.formula)
mpvis = MPGGAVaspInputSet()
# 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
# Check if POTCAR file can be geneated
ptcr_flag = True
try:
potcar = mpvis.get_potcar(struct)
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
print (ptcr_flag)
vac = Vacancy(struct, {}, {})
sc_scale = get_sc_scale(struct,cellmax)
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)
print len(scs)
interdir = mpid
blk_str_sites = set(scs[0].sites)
for i in range(1,len(scs)):
sc = scs[i]
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = vac.get_defectsite_multiplicity(i-1)
vac_site_specie = vac_site.specie
vac_specie = vac_site.specie.symbol
# Solute substitution defect generation at all vacancy sites
struct_species = scs[0].types_of_specie
solute_struct = sc.copy()
solute_struct.append(solute, vac_site.frac_coords)
incar = mpvis.get_incar(solute_struct)
incar.update(def_vasp_incar_param)
poscar = mpvis.get_poscar(solute_struct)
kpoints = Kpoints.automatic_density(solute_struct,kpoint_den)
if ptcr_flag:
potcar = mpvis.get_potcar(solute_struct)
sub_def_dir ='solute_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_specie, solute)
fin_dir = os.path.join(interdir,sub_def_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'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
slab_potcar.write_file("./Slab_with_vdw/POTCAR")
#set the common INCAR file and KPOINTS
incar_dict = {
'SYSTEM': 'ligand_PbS',
'ENCUT': 600,
'ISIF': 2,
'IBRION': 2,
'ALGO': 'Normal',
'ISMEAR': 1,
'ISPIN': 1,
'EDIFF': 1e-06,
'EDIFFG': -0.005,
'NPAR': 8,
'SIGMA': 0.1,
'PREC': 'Accurate',
'IVDW': 2,
'NSW': 1000
}
incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts= (8, 8, 1), shift= (0, 0, 0))
#write the files in appropriate directory
incar.write_file("./Interface_with_vdw/INCAR")
incar.write_file("./Slab_with_vdw/INCAR")
kpoints.write_file("./Interface_with_vdw/KPOINTS")
kpoints.write_file("./Slab_with_vdw/KPOINTS")
shu.copy("./submit_job", "./Interface_with_vdw/")
shu.copy("./submit_job", "./Slab_with_vdw")
def vac_antisite_def_struct_gen(mpid, mapi_key, 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 = MPGGAVaspInputSet()
# 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.get_potcar(struct)
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]
poscar = mpvis.get_poscar(sc)
kpoints = Kpoints.automatic_density(sc, kpoint_den)
incar = mpvis.get_incar(sc)
if ptcr_flag:
potcar = mpvis.get_potcar(sc)
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)
poscar = mpvis.get_poscar(anti_struct)
incar = mpvis.get_incar(anti_struct)
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 test_kpt_bands_to_dict_from_dict(self):
file_name = os.path.join(test_dir, "KPOINTS.band")
k = Kpoints.from_file(file_name)
d = k.to_dict
def run_task(self, fw_spec):
Incar.from_dict(fw_spec['vasp']['incar']).write_file('INCAR')
Poscar.from_dict(fw_spec['vasp']['poscar']).write_file('POSCAR')
Potcar.from_dict(fw_spec['vasp']['potcar']).write_file('POTCAR')
Kpoints.from_dict(fw_spec['vasp']['kpoints']).write_file('KPOINTS')
for line in id_expgap:
words=line.split()
print words
id_line=words[0]
os.mkdir(id_line)
os.chdir(id_line)
s = mpr.get_structure_by_material_id(id_line)
# obtain structural information from Materials Project database
#print json.dumps(s.to_dict)
# convert structural infomation into a dictionary and then dump to a json file
user_incar_settings={"ALGO":'Normal',"EDIFF":1E-8,"ENCUT":500,"NSW":0,"LWAVE":True}
mpvis = MPVaspInputSet(user_incar_settings=user_incar_settings)
mpvis.get_incar(s).write_file('INCAR')
# from the GW input set, get the incar parameters, generate INCAR
print mpvis.get_incar(s)
#
kp_density = mpvis.get_kpoints(s).kpts[0]
# from the GW input set, get the k-point density
kpoints = Kpoints.gamma_automatic(kp_density)
# generate Gamma centered k-point mesh
kpoints.write_file('KPOINTS')
# generate KPOINTS file
mpvis.get_poscar(s).write_file('POSCAR')
# generate POSCAR file
mpvis.get_potcar(s).write_file('POTCAR')
# generate POTCAR file
os.chdir('..')
id_expgap.close()
def from_previous_vasp_run(previous_vasp_dir, output_dir='.',
user_incar_settings=None,
make_dir_if_not_present=True):
"""
Generate a set of Vasp input files for static calculations from a
directory of previous Vasp run.
Args:
previous_vasp_dir:
The directory contains the outputs(vasprun.xml and OUTCAR) of
previous vasp run.
output_dir:
The directory to write the VASP input files for the static
calculations. Default to write in the current directory.
make_dir_if_not_present:
Set to True if you want the directory (and the whole path) to
be created if it is not present.
"""
try:
vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
parse_dos=False, parse_eigen=None)
outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
previous_incar = vasp_run.incar
previous_kpoints = vasp_run.kpoints
previous_final_structure = vasp_run.final_structure
except:
traceback.format_exc()
raise RuntimeError("Can't get valid results from previous run")
structure = MPStaticVaspInputSet.get_structure(vasp_run, outcar)
mpsvip = MPStaticVaspInputSet()
mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
#new_incar = Incar.from_file(os.path.join(output_dir, "INCAR"))
new_incar = mpsvip.get_incar(structure)
# Use previous run INCAR and override necessary parameters
previous_incar.update({"IBRION": -1, "ISMEAR": -5, "LAECHG": True,
"LCHARG": True, "LORBIT": 11, "LVHAR": True,
"LWAVE": False, "NSW": 0, "ICHARG": 0})
for incar_key in ["MAGMOM", "NUPDOWN"]:
if new_incar.get(incar_key, None):
previous_incar.update({incar_key: new_incar[incar_key]})
else:
previous_incar.pop(incar_key, None)
# use new LDAUU when possible b/c the Poscar might have changed
# representation
if previous_incar.get('LDAU'):
u = previous_incar.get('LDAUU', [])
j = previous_incar.get('LDAUJ', [])
if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
previous_incar.update({tag: new_incar[tag]})
# Compare ediff between previous and staticinputset values,
# choose the tighter ediff
previous_incar.update({"EDIFF": min(previous_incar.get("EDIFF", 1),
new_incar["EDIFF"])})
# add user settings
if user_incar_settings:
previous_incar.update(user_incar_settings)
previous_incar.write_file(os.path.join(output_dir, "INCAR"))
# Prefer to use k-point scheme from previous run
previous_kpoints_density = np.prod(previous_kpoints.kpts[0]) / \
previous_final_structure.lattice.reciprocal_lattice.volume
new_kpoints_density = max(previous_kpoints_density, 90)
new_kpoints = mpsvip.get_kpoints(structure,
kpoints_density=new_kpoints_density)
if previous_kpoints.style[0] != new_kpoints.style[0]:
if previous_kpoints.style[0] == "M" and \
SymmetryFinder(structure, 0.01).get_lattice_type() != \
"hexagonal":
k_div = (kp + 1 if kp % 2 == 1 else kp
for kp in new_kpoints.kpts[0])
Kpoints.monkhorst_automatic(k_div). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
Kpoints.gamma_automatic(new_kpoints.kpts[0]). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
new_kpoints.write_file(os.path.join(output_dir, "KPOINTS"))