# os.path.join(
# vasp_simulation.simulation_directory,
# 'KPOINTS'))
vasp_simulation.kpoints.write(os.path.join(sim_dir, "KPOINTS"))
# write slurm script
# slurm.write_vasp_batch_script(
# filename=os.path.join(\
# vasp_simulation.simulation_directory,
# "runjob_hpg.slurm"),
# job_name=slurm_job_name,
# email=slurm_email,
# qos=slurm_qos,
# ntasks=slurm_ntasks,
# time=slurm_time)
slurm.write_vasp_batch_script(filename=os.path.join(
sim_dir, "runjob_hpg.slurm"),
job_name=slurm_job_name,
email=slurm_email,
qos=slurm_qos,
ntasks=slurm_ntasks,
time=slurm_time)
# submit job
init_dir = os.getcwd()
# os.chdir(vasp_simulation.simulation_directory)
os.chdir(sim_dir)
print('running in {}'.format(os.getcwd()))
os.system('sbatch runjob_hpg.slurm')
os.chdir(init_dir)
vasp_simulation.incar.ispin = 2 # spin-polarized calculations
vasp_simulation.incar.magmom = "{}*{}".format(
vasp_simulation.poscar.n_atoms, magmom_init)
vasp_simulation.incar.ibrion = 2 # conjugate gradient method
vasp_simulation.incar.isif = 3 # relax everything
vasp_simulation.incar.potim = 0.5 # dampening parameter
vasp_simulation.incar.ediffg = -0.001 # ev/Ang
vasp_simulation.poscar.write(
os.path.join(vasp_simulation.simulation_directory, "POSCAR"))
vasp_simulation.incar.write(
os.path.join(vasp_simulation.simulation_directory, "INCAR"))
vasp_simulation.kpoints.write(
os.path.join(vasp_simulation.simulation_directory, "KPOINTS"))
slurm.write_vasp_batch_script(filename=os.path.join(
vasp_simulation.simulation_directory, "runjob_hpg.slurm"),
job_name=job_name,
email=email,
qos=qos,
ntasks=ntasks,
time=time)
# submit job
init_dir = os.getcwd()
os.chdir(vasp_simulation.simulation_directory)
print('running in {}'.format(os.getcwd()))
os.system('sbatch runjob_hpg.slurm')
os.chdir(init_dir)
def minimize_init():
if __name__ == "__main__":
ase_symbol = 'Ni'
ase_sg = 'bcc'
ase_a = 3.508
ase_shape = 'cubic'
system_name = '{}_{}_{}'.format(ase_symbol,ase_sg,ase_a,ase_shape)
init_dir = os.path.join(os.getcwd(),system_name)
if os.path.exists(init_dir):
# simulation has already been started
else:
os.mkdir(init_dir)
minimize_init_task_name = 'minimize_init'
minimize_init_slurm_job_name = "{}_{}_min_0".format(symbol,sg)
minimize_init_slurm_email = "*****@*****.**"
minimize_init_slurm_qos="phillpot"
minimize_init_slurm_ntasks=16
minimize_init_slurm_time="1:00:00"
task_dir = os.path.join(os.getcwd(),task_name)
vasp_simulation = vasp.VaspSimulation()
vasp_simulation.simulation_directory = task_dir
vasp_simulation.poscar = vasp.Poscar(\
ase.build.bulk(symbol,sg,a,cubic=True))
vasp_simulation.incar = vasp.Incar()
vasp_simulation.potcar = vasp.Potcar()
vasp_simulation.kpoints = vasp.Kpoints()
# create directory
# create vasp simulation directory and files
# delete the directory and the contents if it exists
if os.path.exists(vasp_simulation.simulation_directory):
shutil.rmtree(vasp_simulation.simulation_directory)
os.mkdir(vasp_simulation.simulation_directory)
# configure potcar file
print('confguring potcar file...')
vasp_simulation.xc = 'GGA'
vasp_simulation.symbols = vasp_simulation.poscar.symbols
vasp_simulation.potcar.symbols = vasp_simulation.symbols
vasp_simulation.potcar.xc = vasp_simulation.xc
# get information from potcar
vasp_simulation.potcar.write(
os.path.join(vasp_simulation.simulation_directory,"POTCAR"))
vasp_simulation.potcar.read(
os.path.join(vasp_simulation.simulation_directory,"POTCAR"))
# stuff to put into tests
# use the largest enmax of all a
# print('symbols:{}'.format(','.join(vasp_simulation.potcar.symbols)))
# print('recommended encut range: {}-{}'.format(
# min(vasp_simulation.potcar.encut_min)
# max(vasp_simulation.potcar.encut_max)
# vasp_simulation.encut_min,
# vasp_simulation.encut_max))
# print('n_atoms:{}'.format(vasp_simulation.poscar.n_atoms))
# print('n_atomic_basis:{}'.format(len(vasp_simulation.poscar.atomic_basis)))
# print('n_interstitials:{}'.format(len(vasp_simulation.poscar.interstitials)))
# configure incar file
vasp_simulation.encut = max(vasp_simulation.potcar.encut_max)
vasp_simulation.natoms = vasp_simulation.poscar.n_atoms
vasp_simulation.incar.encut = vasp_simulation.encut
magmom_init = 1.0
vasp_simulation.incar.ismear = 1 # methfessel paxton order 1
vasp_simulation.incar.sigma = 0.20 # smearing parameter
vasp_simulation.incar.ispin = 2 # spin-polarized calculations
vasp_simulation.incar.magmom = "{}*{}".format(
vasp_simulation.poscar.n_atoms,magmom_init)
vasp_simulation.incar.ibrion = 2 # conjugate gradient method
vasp_simulation.incar.isif = 3 # relax everything
vasp_simulation.incar.potim = 0.5 # dampening parameter
vasp_simulation.incar.ediffg = -0.001 # ev/Ang
vasp_simulation.poscar.write(
os.path.join(vasp_simulation.simulation_directory,"POSCAR"))
vasp_simulation.incar.write(
os.path.join(vasp_simulation.simulation_directory,"INCAR"))
vasp_simulation.kpoints.write(
os.path.join(vasp_simulation.simulation_directory,"KPOINTS"))
slurm.write_vasp_batch_script(
filename=os.path.join(vasp_simulation.simulation_directory,"runjob_hpg.slurm"),
job_name=job_name,
email=email,
qos=qos,
ntasks=ntasks,
time=time)
# submit job
init_dir = os.getcwd()
os.chdir(vasp_simulation.simulation_directory)
print('running in {}'.format(os.getcwd()))
os.system('sbatch runjob_hpg.slurm')
os.chdir(init_dir)