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 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"))
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
vasp_simulation.potcar.xc = vasp_simulation.xc
import pypospack.io.vasp as vasp
if __name__ == '__main__':
symbols = ['Mg', 'O']
filename = 'POTCAR'
# let's try to read
potcar = vasp.Potcar(symbols=symbols)
potcar.write('POTCAR')
# now let's try to write
potcar = vasp.Potcar(symbols=symbols)
potcar.write('POTCAR')
potcar.read('POTCAR')
print('symbols', potcar.symbols)
print('encut_min', potcar.encut_min)
print('encut_max', potcar.encut_max)
print('lexch', potcar.xc)
print('models', potcar.models)
def __init__(self,
structure='POSCAR',
xc='GGA',
encut_min=None,
encut_max=None,
encut_step=25,
incar_dict=None,
slurm_dict=None,
full_auto=True):
# check argument 'structure'
if isinstance(structure, crystal.SimulationCell):
self.structure_filename = 'POSCAR'
self.poscar = vasp.Poscar(structure)
self.poscar.write(structure_filename)
elif isinstance(structure, str):
self.structure_filename = structure
self.poscar = vasp.Poscar()
self.poscar.read(structure)
else:
msg_err = "structure must either be an instance of "
msg_err += "pypospack.crystal.SimulationCell or a string"
raise ValueError(msg_err)
self.xc = xc
# determine energy cutoff
if any([encut_min is None, encut_max is None]):
# create a potcar containing the information contained in the
# potcar files
potcar = vasp.Potcar()
potcar.symbols = self.poscar.symbols
potcar.xc = xc
# this is kind of clunky because I have to write the potcar file
# before i read it.
# TODO: what I should actually do is read the POTCARS for each
# individual symbol and collect the information I need
potcar.write('POTCAR.tmp')
potcar.read('POTCAR.tmp')
os.remove('POTCAR.tmp')
# set encut min
if any([isinstance(encut_min, float), isinstance(encut_min, int)]):
self.encut_min = encut_min
else:
self.encut_min = max(potcar.encut_min)
# set encut max
if any([isinstance(encut_max, float), isinstance(encut_max, int)]):
self.encut_max = encut_max
else:
self.encut_max = 1.5 * max(potcar.encut_max)
else:
self.encut_min = encut_min
self.encut_max = encut_max
self.encut_step = encut_step
# set incut_dict
if isinstance(incar_dict, dict):
self.incar_dict = copy.deepcopy(incar_dict)
# set slurm_dict
if isinstance(slurm_dict, dict):
self.slurm_dict = copy.deepcopy(slurm_dict)
# additional attributes which aren't parameters
self.tasks = {}
self.task_results = {}
if full_auto is True:
self.do_full_auto()
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)
def __init__(self,directory=None,structure='POSCAR',xc='GGA',
encut_min=None,encut_max=None,encut_step=25,
incar_dict=None,kpoints_dict=None,slurm_dict=None,full_auto=True):
self.orig_directory = os.getcwd()
self.filename_results = 'converg.encut.results'
self.manifest_filename = 'pypospack.manifest.yaml'
# --- PROCESS ARGUMENTS ---
# process the dictionary attribute
if directory is not None:
if os.path.isabs(directory):
self.directory = directory
else:
self.directory = os.path.join(
self.orig_directory,
directory)
if not os.path.exists(self.directory):
os.makedirs(self.directory)
# change the location of the result output file
self.filename_results = os.path.join(
self.directory,
self.filename_results)
self.manifest_filename = os.path.join(
self.directory,
self.manifest_filename)
# check argument 'structure'
if isinstance(structure,crystal.SimulationCell):
self.structure_filename = 'POSCAR'
self.poscar = vasp.Poscar(structure)
self.poscar.write(structure_filename)
elif isinstance(structure,str):
if os.path.isabs(structure):
self.structure_filename = structure
else:
# convert to absolute path
self.structure_filename = os.path.join(
self.orig_directory,
structure)
self.structure_filename = os.path.normpath(
self.structure_filename)
# read the poscar file
self.poscar = vasp.Poscar()
self.poscar.read(self.structure_filename)
else:
msg_err = "structure must either be an instance of "
msg_err += "pypospack.crystal.SimulationCell or a string"
raise ValueError(msg_err)
# self exchange correlation functional
self.xc = xc
# determine energy cutoff
if any([encut_min is None, encut_max is None]):
# create a potcar containing the information contained in the
# potcar files
potcar = vasp.Potcar()
potcar.symbols = self.poscar.symbols
potcar.xc = xc
# this is kind of clunky because I have to write the potcar file
# before i read it.
# TODO: what I should actually do is read the POTCARS for each
# individual symbol and collect the information I need
potcar.write('POTCAR.tmp')
potcar.read('POTCAR.tmp')
os.remove('POTCAR.tmp')
# set encut min
if any([isinstance(encut_min,float),
isinstance(encut_min,int)]):
self.encut_min = encut_min
else:
self.encut_min = max(potcar.encut_min)
# set encut max
if any([isinstance(encut_max,float),
isinstance(encut_max,int)]):
self.encut_max = encut_max
else:
self.encut_max = 1.5 * max (potcar.encut_max)
else:
self.encut_min = encut_min
self.encut_max = encut_max
self.encut_min = (self.encut_min//encut_step)*encut_step
self.encut_max = ((self.encut_max//encut_step)+1)*encut_step
self.encut_step = encut_step
# set incut_dict
if isinstance(incar_dict, dict):
self.incar_dict = copy.deepcopy(incar_dict)
# set kpoints_dict
self.kpoints_dict = None
if isinstance(kpoints_dict, dict):
self.kpoints_dict = copy.deepcopy(kpoints_dict)
# set slurm_dict
if isinstance(slurm_dict, dict):
self.slurm_dict = copy.deepcopy(slurm_dict)
# additional attributes which aren't parameters
self.tasks = {}
self.task_results = {}
if full_auto is True:
self.do_full_auto()
import pypospack.io.vasp as vasp
# an array of symbols
symbols = ['Mg', 'O']
xc = 'GGA'
potcar = vasp.Potcar(symbols=symbols, xc='GGA')
potcar.write('POTCAR')
symbols = ['Ni']
xc = 'GGA'
potcar = vasp.Potcar(symbols=symbols, xc=xc)
potcar.write('POTCAR')
