def write_band_structure_kpoints(structure,
n_kpts=20,
dim=2,
ibzkpt_path="../"):
"""
Writes a KPOINTS file for band structure calculations. Does
not use the typical linemode syntax for NSCF calculations,
but uses the IBZKPT + high-symmetry path syntax described in
http://cms.mpi.univie.ac.at/wiki/index.php/Si_bandstructure
so that SCF calculations can be performed. This is more
reliable than re-using the CHGCAR from a previous run, which
often results in "dimensions on the CHGCAR are different"
errors in VASP.
Args:
structure (Structure): structure for determining k-path
n_kpts (int): number of divisions along high-symmetry lines
dim (int): 2 for a 2D material, 3 for a 3D material.
ibzkpt_path (str): location of IBZKPT file. Defaults to one
directory up.
"""
ibz_lines = open(os.path.join(ibzkpt_path, "IBZKPT")).readlines()
n_ibz_kpts = int(ibz_lines[1].split()[0])
kpath = HighSymmKpath(structure)
Kpoints.automatic_linemode(n_kpts, kpath).write_file('KPOINTS')
if dim == 2:
remove_z_kpoints()
linemode_lines = open('KPOINTS').readlines()
abs_path = []
i = 4
while i < len(linemode_lines):
start_kpt = linemode_lines[i].split()
end_kpt = linemode_lines[i + 1].split()
increments = [(float(end_kpt[0]) - float(start_kpt[0])) / 20,
(float(end_kpt[1]) - float(start_kpt[1])) / 20,
(float(end_kpt[2]) - float(start_kpt[2])) / 20]
abs_path.append(start_kpt[:3] + ['0', start_kpt[4]])
for n in range(1, 20):
abs_path.append([
str(float(start_kpt[0]) + increments[0] * n),
str(float(start_kpt[1]) + increments[1] * n),
str(float(start_kpt[2]) + increments[2] * n), '0'
])
abs_path.append(end_kpt[:3] + ['0', end_kpt[4]])
i += 3
n_linemode_kpts = len(abs_path)
with open('KPOINTS', 'w') as kpts:
kpts.write('Automatically generated mesh\n')
kpts.write('{}\n'.format(n_ibz_kpts + n_linemode_kpts))
kpts.write('Reciprocal Lattice\n')
for line in ibz_lines[3:]:
kpts.write(line)
for point in abs_path:
kpts.write('{}\n'.format(' '.join(point)))
def get_kpoints_wannier(structure, n_kpts=1, dim=2):
kpath = HighSymmKpath(structure)
os.system('mv KPOINTS K_temp')
Kpoints.automatic_linemode(n_kpts, kpath).write_file('KPOINTS')
if dim == 2:
remove_z_kpoints()
path = find_kpath(f='KPOINTS')
os.system('rm KPOINTS')
os.system('mv K_temp KPOINTS')
return path
def run_pbe_calculation(dim=2, submit=True, force_overwrite=False):
"""
Setup and submit a normal PBE calculation for band structure along
high symmetry k-paths.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
"""
PBE_INCAR_DICT = {
'EDIFF': 1e-6,
'IBRION': 2,
'ISIF': 3,
'ISMEAR': 1,
'NSW': 0,
'LVTOT': True,
'LVHAR': True,
'LORBIT': 1,
'LREAL': 'Auto',
'NPAR': 4,
'PREC': 'Accurate',
'LWAVE': True,
'SIGMA': 0.1,
'ENCUT': 500,
'ISPIN': 2
}
directory = os.path.basename(os.getcwd())
if not os.path.isdir('pbe_bands'):
os.mkdir('pbe_bands')
if force_overwrite or not is_converged('pbe_bands'):
shutil.copy("CONTCAR", "pbe_bands/POSCAR")
if os.path.isfile('POTCAR'):
shutil.copy("POTCAR", "pbe_bands")
PBE_INCAR_DICT.update(
{'MAGMOM': get_magmom_string(Structure.from_file('POSCAR'))})
Incar.from_dict(PBE_INCAR_DICT).write_file('pbe_bands/INCAR')
structure = Structure.from_file('POSCAR')
kpath = HighSymmKpath(structure)
Kpoints.automatic_linemode(20, kpath).write_file('pbe_bands/KPOINTS')
os.chdir('pbe_bands')
if dim == 2:
remove_z_kpoints()
if QUEUE_SYSTEM == 'pbs':
write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00',
VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
write_slurm_runjob(directory, 16, '800mb', '6:00:00', VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
_ = subprocess.check_output(submission_command.split())
os.chdir('../')
def run_hse_calculation(dim=2,
submit=True,
force_overwrite=False,
destroy_prep_directory=False):
"""
Setup/submit an HSE06 calculation to get an accurate band structure.
Requires a previous IBZKPT from a standard DFT run. See
http://cms.mpi.univie.ac.at/wiki/index.php/Si_bandstructure for more
details.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
destroy_prep_directory (bool): whether or not to remove
(rm -r) the hse_prep directory, if it exists. This
can help to automatically clean up and save space.
"""
HSE_INCAR_DICT = {
'LHFCALC': True,
'HFSCREEN': 0.2,
'AEXX': 0.25,
'ALGO': 'D',
'TIME': 0.4,
'NSW': 0,
'LVTOT': True,
'LVHAR': True,
'LORBIT': 11,
'LWAVE': True,
'NPAR': 8,
'PREC': 'Accurate',
'EDIFF': 1e-4,
'ENCUT': 450,
'ICHARG': 2,
'ISMEAR': 1,
'SIGMA': 0.1,
'IBRION': 2,
'ISIF': 3,
'ISPIN': 2
}
if not os.path.isdir('hse_bands'):
os.mkdir('hse_bands')
if force_overwrite or not is_converged('hse_bands'):
os.chdir('hse_bands')
os.system('cp ../CONTCAR ./POSCAR')
if os.path.isfile('../POTCAR'):
os.system('cp ../POTCAR .')
HSE_INCAR_DICT.update(
{'MAGMOM': get_magmom_string(Structure.from_file('POSCAR'))})
Incar.from_dict(HSE_INCAR_DICT).write_file('INCAR')
# Re-use the irreducible brillouin zone KPOINTS from a
# previous standard DFT run.
if os.path.isdir('../hse_prep'):
ibz_lines = open('../hse_prep/IBZKPT').readlines()
if destroy_prep_directory:
os.system('rm -r ../hse_prep')
else:
ibz_lines = open('../IBZKPT').readlines()
n_ibz_kpts = int(ibz_lines[1].split()[0])
kpath = HighSymmKpath(Structure.from_file('POSCAR'))
Kpoints.automatic_linemode(20, kpath).write_file('KPOINTS')
if dim == 2:
remove_z_kpoints()
linemode_lines = open('KPOINTS').readlines()
abs_path = []
i = 4
while i < len(linemode_lines):
start_kpt = linemode_lines[i].split()
end_kpt = linemode_lines[i + 1].split()
increments = [(float(end_kpt[0]) - float(start_kpt[0])) / 20,
(float(end_kpt[1]) - float(start_kpt[1])) / 20,
(float(end_kpt[2]) - float(start_kpt[2])) / 20]
abs_path.append(start_kpt[:3] + ['0', start_kpt[4]])
for n in range(1, 20):
abs_path.append([
str(float(start_kpt[0]) + increments[0] * n),
str(float(start_kpt[1]) + increments[1] * n),
str(float(start_kpt[2]) + increments[2] * n), '0'
])
abs_path.append(end_kpt[:3] + ['0', end_kpt[4]])
i += 3
n_linemode_kpts = len(abs_path)
with open('KPOINTS', 'w') as kpts:
kpts.write('Automatically generated mesh\n')
kpts.write('{}\n'.format(n_ibz_kpts + n_linemode_kpts))
kpts.write('Reciprocal Lattice\n')
for line in ibz_lines[3:]:
kpts.write(line)
for point in abs_path:
kpts.write('{}\n'.format(' '.join(point)))
if QUEUE_SYSTEM == 'pbs':
write_pbs_runjob('{}_hsebands'.format(os.getcwd().split('/')[-2]),
2, 64, '1800mb', '50:00:00', VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
write_slurm_runjob(
'{}_hsebands'.format(os.getcwd().split('/')[-2]), 64, '1800mb',
'50:00:00', VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
_ = subprocess.check_output(submission_command.split())
os.chdir('../')