def run_hse_prep_calculation(dim=2, submit=True):
"""
Submits a quick static calculation to calculate the IBZKPT
file using a smaller number of k-points (200/atom instead of
1000/atom). The other outputs from this calculation are
essentially useless.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
"""
if not os.path.isdir('hse_prep'):
os.mkdir('hse_prep')
os.chdir('hse_prep')
os.system('cp ../CONTCAR ./POSCAR')
if os.path.isfile('../POTCAR'):
os.system('cp POTCAR .')
relax(dim=2, submit=False)
incar_dict = Incar.from_file('INCAR').as_dict()
incar_dict.update({'NSW': 0, 'NELM': 1, 'LWAVE': False, 'LCHARG': False,
'LAECHG': False})
Incar.from_dict(incar_dict).write_file('INCAR')
Kpoints.automatic_density(
Structure.from_file('POSCAR'), 200
).write_file('KPOINTS')
if dim == 2:
kpts_lines = open('KPOINTS').readlines()
with open('KPOINTS', 'w') as kpts:
for line in kpts_lines[:3]:
kpts.write(line)
kpts.write(kpts_lines[3].split()[0] + ' '
+ kpts_lines[3].split()[1] + ' 1')
if QUEUE == 'pbs':
write_pbs_runjob('{}_prep'.format(
os.getcwd().split('/')[-2]), 1, 16, '800mb', '6:00:00', VASP)
submission_command = 'qsub runjob'
elif QUEUE == 'slurm':
write_slurm_runjob('{}_prep'.format(
os.getcwd().split('/')[-2]), 16, '800mb', '6:00:00', VASP)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
os.chdir('../')
INTERVAL = 360 # Seconds between convergence checks
directories = [
dir for dir in os.listdir(os.getcwd())
if os.path.isdir(dir) and dir not in ['all_competitors']
]
if __name__ == '__main__':
competing_species = get_competing_species(directories)
relax_competing_species(competing_species)
for directory in directories:
os.chdir(directory)
relax()
os.chdir('../')
loop = True
while loop:
print('>> Checking convergence')
finished_2d, finished_3d = [], []
for directory in directories:
if is_converged(directory):
finished_2d.append(directory)
for directory in competing_species:
if is_converged('all_competitors/{}'.format(directory[0])):
finished_3d.append(directory[0])
if len(finished_2d + finished_3d) == len(directories +
plot_hull_distances)
INTERVAL = 360 # Seconds between convergence checks
directories = [dir for dir in os.listdir(os.getcwd()) if os.path.isdir(dir)
and dir not in ['all_competitors']]
if __name__ == '__main__':
competing_species = get_competing_species(directories)
relax_competing_species(competing_species)
for directory in directories:
os.chdir(directory)
relax()
os.chdir('../')
loop = True
while loop:
print('>> Checking convergence')
finished_2d, finished_3d = [], []
for directory in directories:
if is_converged(directory):
finished_2d.append(directory)
for directory in competing_species:
if is_converged('all_competitors/{}'.format(directory[0])):
finished_3d.append(directory[0])
if len(finished_2d + finished_3d) == len(
