def test_change_encut(self):
incar1 = vasp.Incar()
incar1.encut = 123
incar1.write('INCAR.encuttest')
incar2 = vasp.Incar(2)
incar2.read('INCAR.encuttest')
assert incar2.encut == incar1.encut
def __init__(self,task_name,task_directory,restart=True):
Task.__init__(self,task_name,task_directory,restart)
self.poscar = vasp.Poscar()
self.incar = vasp.Incar()
self.potcar = vasp.Potcar()
self.kpoints = vasp.Kpoints()
self.contcar = vasp.Contcar()
def vasp_structural_minimization(structure, task_name):
assert isinstance(structure, pypospack.crystal.SimulationCell)
assert isinstance(task_name, str)
vasp_simulation = vasp.VaspSimulation()
vasp_simulation.simulation_directory = task_dir
vasp_simulation.poscar = vasp.Poscar(structure)
vasp_simulation.incar = vasp.Incar()
vasp_simulation.potcar = vasp.Potcar()
vasp_simulation.kpoints = vasp.Kpoints()
def read_incar(self,incar='None'):
if incar is None:
if os.path.exists(os.path.join(self.task_directory,'INCAR')):
self.incar = vasp.Incar()
self.incar.read(os.path.join(self.task_directory,'INCAR'))
else:
self.incar = vasp.Incar()
elif isinstance(incar,str):
self.incar = vasp.Incar()
self.incar.read(incar)
elif isinstance(incar,dict):
# check to see if the incar already exists, and read it in
if os.path.exists(os.path.join(self.task_directory,'INCAR')):
self.incar = vasp.Incar()
self.incar.read(os.path.join(self.task_directory,'INCAR'))
# otherwise, we're just going to use the default configuarion
else:
self.incar = vasp.Incar()
# now update based upon what is dictionary
for k,v in incar.items():
setattr(self.incar,k,v)
else:
raise VaspSimulationError
def create_simulation(self):
# initialize input files
self.vs = vasp.VaspSimulation()
self.vs.poscar = vasp.Poscar(obj_structure)
self.vs.incar = vasp.Incar()
self.vs.potcar = vasp.Potcar()
self.vs.kpoints = vasp.Kpoints()
self.vs.xc = self.xc
self.vs.simulation_directory = self.sim_dir
self.vs.symbols = self.vs.poscar.symbols
# configure potcar file
self.vs.potcar.symbols = self.vs.symbols
self.vs.potcar.xc = self.vs.xc
fn_potcar = os.path.join(self.vs.simulation_directory, 'POTCAR')
self.vs.potcar.write(fn_potcar)
self.vs.potcar.read(fn_potcar)
self.vs.encut = max(self.vs.potcar.encut_max)
self.vs.natoms = self.vs.poscar.n_atoms
# configure incar file
magmom_0 = 1.0
self.vs.incar.ismear = 1
self.vs.incar.sigma = 0.20
self.vs.incar.ispin = 2
self.vs.incar.magmom = "{}*{}".format(self.vs.natoms, magmom_0)
self.vs.incar.ibrion = 2
self.vs.incar.isif = 3
self.vs.incar.potim = 0.5
self.vs.incar.ediffg = -0.001
self.vs.poscar.write(os.path.join(\
self.vs.simulation_directory,"POSCAR"))
self.vs.incar.write(os.path.join(\
self.vs.simulation_directory,"INCAR"))
self.vs.kpoints.write(os.path.join(\
self.vs.simulation_directory,"KPOINTS"))
a = 3.508
task_name = 'minimize_init'
job_name = "{}_{}_min1".format(symbol, sg)
email = "*****@*****.**"
qos = "phillpot"
ntasks = 16
time = "1:00:00"
init_directory = os.getcwd()
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
def test_write(self):
incar = vasp.Incar()
incar.write('INCAR.std')
def test_init(self):
incar = vasp.Incar()
def test_write_w_ibrion_2(self):
incar = vasp.Incar()
incar.ibrion = 2
incar.isif = 3
incar.write('INCAR.ibrion2')
def test_read(self):
incar = vasp.Incar()
incar.read('INCAR.std')
def test_read(self):
incar = vasp.Incar()
incar.read('INCAR.std')
def test_write_w_ibrion_2(self):
incar = vasp.Incar()
incar.ibrion = 2
incar.isif = 3
incar.write('INCAR.ibrion2')
def test_change_encut(self):
incar1 = vasp.Incar()
incar1.encut = 123
incar1.write('INCAR.encuttest')
incar2 = vasp.Incar(2)
incar2.read('INCAR.encuttest')
assert incar2.encut == incar1.encut
if __name__ == "__main__":
filename = 'INCAR.std'
incar = vasp.Incar()
incar.write(filename)
filename = 'INCAR.ibrion2'
incar = vasp.Incar()
incar.ibrion = 2
incar.write(filename)
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)
