def setUp(self):
lattice = [[10, 0, 0], [-5, 8.660254, 0], [0, 0, 5]]
self.hexagonal = Structure(lattice=lattice,
species=["H"],
coords=[[0, 0, 0]])
self.kpoints_g = Kpoints.gamma_automatic(kpts=(2, 2, 2))
lattice2 = [[1, 0, 0], [0, 2, 0], [0, 0, 3]]
self.ortho = Structure(lattice=lattice2,
species=["H"],
coords=[[0, 0, 0]])
self.kpoints_mp = Kpoints.monkhorst_automatic(kpts=(2, 2, 2))
self.kpoints_reciprocal = \
Kpoints(style=Kpoints.supported_modes.Reciprocal,
num_kpts=2,
kpts=((0, 0, 0), (0.5, 0.5, 0.5)),
kpts_weights=[1, 1])
def get_jobs(args):
# Returns a generator of jobs. Allows of "infinite" jobs.
vasp_command = args.command.split()
# save initial INCAR for rampU runs
n_ramp_u = args.jobs.count('rampU')
ramps = 0
if n_ramp_u:
incar = Incar.from_file('INCAR')
ldauu = incar['LDAUU']
ldauj = incar['LDAUJ']
njobs = len(args.jobs)
post_settings = [
] # append to this list to have settings applied on next job
for i, job in enumerate(args.jobs):
final = False if i != njobs - 1 else True
if any(c.isdigit() for c in job):
suffix = "." + job
else:
suffix = ".{}{}".format(job, i + 1)
settings = post_settings
post_settings = []
backup = True if i == 0 else False
copy_magmom = False
vinput = VaspInput.from_directory(".")
if i > 0:
settings.append({
"file": "CONTCAR",
"action": {
"_file_copy": {
"dest": "POSCAR"
}
}
})
job_type = job.lower()
auto_npar = True
if args.no_auto_npar:
auto_npar = False
if job_type.startswith("static_derived"):
from pymatgen.io.vasp.sets import MPStaticSet
vis = MPStaticSet.from_prev_calc(".",
user_incar_settings={
"LWAVE": True,
"EDIFF": 1e-6
},
ediff_per_atom=False)
settings.extend([{
"dict": "INCAR",
"action": {
"_set": dict(vis.incar)
}
}, {
'dict': 'KPOINTS',
'action': {
'_set': vis.kpoints.as_dict()
}
}])
if job_type.startswith("static_dielectric_derived"):
from pymatgen.io.vasp.sets import MPStaticSet, MPStaticDielectricDFPTVaspInputSet
# vis = MPStaticSet.from_prev_calc(
# ".", user_incar_settings={"EDIFF": 1e-6, "IBRION": 8,
# "LEPSILON": True, 'LREAL':False,
# "LPEAD": True, "ISMEAR": 0,
# "SIGMA": 0.01},
# ediff_per_atom=False)
vis = MPStaticDielectricDFPTVaspInputSet()
incar = vis.get_incar(vinput["POSCAR"].structure)
unset = {}
for k in [
"NPAR", "KPOINT_BSE", "LAECHG", "LCHARG", "LVHAR", "NSW"
]:
incar.pop(k, None)
if k in vinput["INCAR"]:
unset[k] = 1
kpoints = vis.get_kpoints(vinput["POSCAR"].structure)
settings.extend([{
"dict": "INCAR",
"action": {
"_set": dict(incar),
"_unset": unset
}
}, {
'dict': 'KPOINTS',
'action': {
'_set': kpoints.as_dict()
}
}])
auto_npar = False
elif job_type.startswith("static"):
m = [i * args.static_kpoint for i in vinput["KPOINTS"].kpts[0]]
settings.extend([{
"dict": "INCAR",
"action": {
"_set": {
"NSW": 0
}
}
}, {
'dict': 'KPOINTS',
'action': {
'_set': {
'kpoints': [m]
}
}
}])
elif job_type.startswith("nonscf_derived"):
from pymatgen.io.vasp.sets import MPNonSCFSet
vis = MPNonSCFSet.from_prev_calc(
".", copy_chgcar=False, user_incar_settings={"LWAVE": True})
settings.extend([{
"dict": "INCAR",
"action": {
"_set": dict(vis.incar)
}
}, {
'dict': 'KPOINTS',
'action': {
'_set': vis.kpoints.as_dict()
}
}])
elif job_type.startswith("optics_derived"):
from pymatgen.io.vasp.sets import MPNonSCFSet
vis = MPNonSCFSet.from_prev_calc(".",
optics=True,
copy_chgcar=False,
nedos=2001,
mode="uniform",
nbands_factor=5,
user_incar_settings={
"LWAVE": True,
"ALGO": "Exact",
"SIGMA": 0.01,
"EDIFF": 1e-6
},
ediff_per_atom=False)
settings.extend([{
"dict": "INCAR",
"action": {
"_set": dict(vis.incar)
}
}, {
'dict': 'KPOINTS',
'action': {
'_set': vis.kpoints.as_dict()
}
}])
elif job_type.startswith("rampu"):
f = ramps / (n_ramp_u - 1)
settings.append({
"dict": "INCAR",
"action": {
"_set": {
"LDAUJ": [j * f for j in ldauj],
"LDAUU": [u * f for u in ldauu]
}
}
})
copy_magmom = True
ramps += 1
elif job_type.startswith("quick_relax") or job_type.startswith(\
"quickrelax"):
kpoints = vinput["KPOINTS"]
incar = vinput["INCAR"]
structure = vinput["POSCAR"].structure
if "ISMEAR" in incar:
post_settings.append({
"dict": "INCAR",
"action": {
"_set": {
"ISMEAR": incar["ISMEAR"]
}
}
})
else:
post_settings.append({
"dict": "INCAR",
"action": {
"_unset": {
"ISMEAR": 1
}
}
})
post_settings.append({
"dict": "KPOINTS",
"action": {
"_set": kpoints.as_dict()
}
})
# lattice vectors with length < 9 will get >1 KPOINT
low_kpoints = Kpoints.gamma_automatic(
[max(int(18 / l), 1) for l in structure.lattice.abc])
settings.extend([{
"dict": "INCAR",
"action": {
"_set": {
"ISMEAR": 0
}
}
}, {
'dict': 'KPOINTS',
'action': {
'_set': low_kpoints.as_dict()
}
}])
# let vasp determine encut (will be lower than
# needed for compatibility with other runs)
if "ENCUT" in incar:
post_settings.append({
"dict": "INCAR",
"action": {
"_set": {
"ENCUT": incar["ENCUT"]
}
}
})
settings.append({
"dict": "INCAR",
"action": {
"_unset": {
"ENCUT": 1
}
}
})
elif job_type.startswith("relax"):
pass
elif job_type.startswith("full_relax"):
for j in VaspJob.full_opt_run(vasp_command):
yield j
else:
print("Unsupported job type: {}".format(job))
sys.exit(-1)
if not job_type.startswith("full_relax"):
yield VaspJob(vasp_command,
final=final,
suffix=suffix,
backup=backup,
settings_override=settings,
copy_magmom=copy_magmom,
auto_npar=auto_npar)
def get_jobs(args):
# Returns a generator of jobs. Allows of "infinite" jobs.
vasp_command = args.command.split()
# save initial INCAR for rampU runs
n_ramp_u = args.jobs.count('rampU')
ramps = 0
if n_ramp_u:
incar = Incar.from_file('INCAR')
ldauu = incar['LDAUU']
ldauj = incar['LDAUJ']
njobs = len(args.jobs)
post_settings = [] # append to this list to have settings applied on next job
for i, job in enumerate(args.jobs):
final = False if i != njobs - 1 else True
if any(c.isdigit() for c in job):
suffix = "." + job
else:
suffix = ".{}{}".format(job, i + 1)
settings = post_settings
post_settings = []
backup = True if i == 0 else False
copy_magmom = False
vinput = VaspInput.from_directory(".")
if i > 0:
settings.append(
{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}})
job_type = job.lower()
auto_npar = True
if args.no_auto_npar:
auto_npar = False
if job_type.startswith("static_derived"):
from pymatgen.io.vasp.sets import MPStaticSet
vis = MPStaticSet.from_prev_calc(
".", user_incar_settings={"LWAVE": True, "EDIFF": 1e-6},
ediff_per_atom=False)
settings.extend([
{"dict" : "INCAR",
"action": {"_set": dict(vis.incar)}},
{'dict': 'KPOINTS',
'action': {'_set': vis.kpoints.as_dict()}}])
if job_type.startswith("static_dielectric_derived"):
from pymatgen.io.vasp.sets import MPStaticSet, MPStaticDielectricDFPTVaspInputSet
# vis = MPStaticSet.from_prev_calc(
# ".", user_incar_settings={"EDIFF": 1e-6, "IBRION": 8,
# "LEPSILON": True, 'LREAL':False,
# "LPEAD": True, "ISMEAR": 0,
# "SIGMA": 0.01},
# ediff_per_atom=False)
vis = MPStaticDielectricDFPTVaspInputSet()
incar = vis.get_incar(vinput["POSCAR"].structure)
unset = {}
for k in ["NPAR", "KPOINT_BSE", "LAECHG", "LCHARG", "LVHAR",
"NSW"]:
incar.pop(k, None)
if k in vinput["INCAR"]:
unset[k] = 1
kpoints = vis.get_kpoints(vinput["POSCAR"].structure)
settings.extend([
{"dict": "INCAR",
"action": {"_set": dict(incar),
"_unset": unset}},
{'dict': 'KPOINTS',
'action': {'_set': kpoints.as_dict()}}])
auto_npar = False
elif job_type.startswith("static"):
m = [i * args.static_kpoint for i in vinput["KPOINTS"].kpts[0]]
settings.extend([
{"dict": "INCAR",
"action": {"_set": {"NSW": 0}}},
{'dict': 'KPOINTS',
'action': {'_set': {'kpoints': [m]}}}])
elif job_type.startswith("nonscf_derived"):
from pymatgen.io.vasp.sets import MPNonSCFSet
vis = MPNonSCFSet.from_prev_calc(".", copy_chgcar=False,
user_incar_settings={"LWAVE": True})
settings.extend([
{"dict": "INCAR",
"action": {"_set": dict(vis.incar)}},
{'dict': 'KPOINTS',
'action': {'_set': vis.kpoints.as_dict()}}])
elif job_type.startswith("optics_derived"):
from pymatgen.io.vasp.sets import MPNonSCFSet
vis = MPNonSCFSet.from_prev_calc(
".", optics=True, copy_chgcar=False,
nedos=2001, mode="uniform", nbands_factor=5,
user_incar_settings={"LWAVE": True, "ALGO": "Exact", "SIGMA": 0.01, "EDIFF": 1e-6},
ediff_per_atom=False)
settings.extend([
{"dict": "INCAR",
"action": {"_set": dict(vis.incar)}},
{'dict': 'KPOINTS',
'action': {'_set': vis.kpoints.as_dict()}}])
elif job_type.startswith("rampu"):
f = ramps / (n_ramp_u - 1)
settings.append(
{"dict": "INCAR",
"action": {"_set": {"LDAUJ": [j * f for j in ldauj],
"LDAUU": [u * f for u in ldauu]}}})
copy_magmom = True
ramps += 1
elif job_type.startswith("quick_relax") or job_type.startswith(\
"quickrelax"):
kpoints = vinput["KPOINTS"]
incar = vinput["INCAR"]
structure = vinput["POSCAR"].structure
if "ISMEAR" in incar:
post_settings.append(
{"dict": "INCAR",
"action": {"_set": {"ISMEAR": incar["ISMEAR"]}}})
else:
post_settings.append(
{"dict": "INCAR",
"action": {"_unset": {"ISMEAR": 1}}})
post_settings.append({"dict": "KPOINTS",
"action": {"_set": kpoints.as_dict()}})
# lattice vectors with length < 9 will get >1 KPOINT
low_kpoints = Kpoints.gamma_automatic(
[max(int(18/l), 1) for l in structure.lattice.abc])
settings.extend([
{"dict": "INCAR",
"action": {"_set": {"ISMEAR": 0}}},
{'dict': 'KPOINTS',
'action': {'_set': low_kpoints.as_dict()}}])
# let vasp determine encut (will be lower than
# needed for compatibility with other runs)
if "ENCUT" in incar:
post_settings.append(
{"dict": "INCAR",
"action": {"_set": {"ENCUT": incar["ENCUT"]}}})
settings.append(
{"dict": "INCAR",
"action": {"_unset": {"ENCUT": 1}}})
elif job_type.startswith("relax"):
pass
elif job_type.startswith("full_relax"):
for j in VaspJob.full_opt_run(
vasp_command):
yield j
else:
print("Unsupported job type: {}".format(job))
sys.exit(-1)
if not job_type.startswith("full_relax"):
yield VaspJob(vasp_command, final=final, suffix=suffix,
backup=backup, settings_override=settings,
copy_magmom=copy_magmom, auto_npar=auto_npar)
