def generate_old_polarization_folders(structures):
"""
Generate the polarization calculations (old format) from the completed scf calculation
"""
for name in structures:
for i in range(3):
# compute the Berry phase along the x-i, y- and z-directions (IGPAR = 1,2,3)
# Note: calculations usualy are very sensetive to the choice of "NPPSTR" parameter. You might consider to reduce it.
MPStaticSet.from_prev_calc(
name,
user_incar_settings={
"LBERRY": True,
"IGPAR": i + 1,
"ICHARG": 2,
"NPAR": 2,
"ALGO": "Fast",
"NPPSTR": 6,
"LAECHG": False,
"LVHAR": False,
"ISIF": 2
},
user_kpoints_settings={
"reciprocal_density": 500
}).write_input(os.path.join(name, 'Berry_' + str(i + 1)))
shutil.copy(os.path.join(name, 'CHGCAR'),
os.path.join(name, 'Berry_' + str(i + 1)))
def run_task(self, fw_spec):
lepsilon = self.get("lepsilon")
default_reciprocal_density = 200 if lepsilon else 100 # more k-points for dielectric calc.
other_params = self.get("other_params", {})
user_incar_settings = other_params.get("user_incar_settings", {})
# for lepsilon runs, set EDIFF to 1E-5 unless user says otherwise
if lepsilon and "EDIFF" not in user_incar_settings and \
"EDIFF_PER_ATOM" not in user_incar_settings:
if "user_incar_settings" not in other_params:
other_params["user_incar_settings"] = {}
other_params["user_incar_settings"]["EDIFF"] = 1E-5
vis = MPStaticSet.from_prev_calc(
prev_calc_dir=self.get("prev_calc_dir", "."),
reciprocal_density=self.get("reciprocal_density",
default_reciprocal_density),
small_gap_multiply=self.get("small_gap_multiply", None),
standardize=self.get("standardize", False),
sym_prec=self.get("sym_prec", 0.1),
international_monoclinic=self.get("international_monoclinic",
True),
lepsilon=lepsilon,
**other_params)
vis.write_input(".")
def Static (self):
from pymatgen.io.vasp.sets import MPStaticSet
import shutil
import os
filePath=self.dire
for dirpath, dirnames, filenames in os.walk(filePath):
# print(dirpath)
for name in dirnames:
if 'static' not in str(name):
path = os.path.join(filePath, name)
custom_settings = {"NELM": 60,'NPAR':4} # user custom incar settings
static = MPStaticSet.from_prev_calc(path, standardize=True,
user_incar_settings=custom_settings)
diree = os.chdir(self.dire)
static.write_input("static_"+str(name))
pat = os.path.join(self.dire, "static_"+str(name))
os.chdir(pat)
#定义一个更改当前目录的变量
dire2 = './vaspstd_sub'
#确立脚本名称
shutil.copy(r"C:\Users\41958\.spyder-py3\vaspstd_sub", dire2 )
def run_task(self, fw_spec):
lepsilon = self.get("lepsilon")
default_reciprocal_density = 100 if not lepsilon else 200
other_params = self.get("other_params", {})
# for lepsilon runs, set EDIFF to 1E-5 unless user says otherwise
user_incar_settings = self.get("other_params", {}).get("user_incar_settings", {})
if lepsilon and "EDIFF" not in user_incar_settings and "EDIFF_PER_ATOM" not in user_incar_settings:
if "user_incar_settings" not in other_params:
other_params["user_incar_settings"] = {}
other_params["user_incar_settings"]["EDIFF"] = 1e-5
vis = MPStaticSet.from_prev_calc(
prev_calc_dir=self["prev_calc_dir"],
reciprocal_density=self.get("reciprocal_density", default_reciprocal_density),
small_gap_multiply=self.get("small_gap_multiply", None),
standardize=self.get("standardize", False),
sym_prec=self.get("sym_prec", 0.1),
international_monoclinic=self.get("international_monoclinic", True),
lepsilon=lepsilon,
**other_params
)
vis.write_input(".")
def generate_new_polarization_folders(structures):
"""
Generate the polarization calculations (new format) from the completed scf calculation
"""
for name in structures:
MPStaticSet.from_prev_calc(name,
user_incar_settings={
"LCALCPOL": True,
"LAECHG": False,
"LVHAR": False,
"ISIF": 2
},
user_kpoints_settings={
"reciprocal_density": 500
}).write_input(
os.path.join(name, 'Berry_new'))
shutil.copy(os.path.join(name, 'CHGCAR'),
os.path.join(name, 'Berry_new'))
def run_task(self, fw_spec):
material_id = self["material_id"]
dest_root = fw_spec["_fw_en"]["run_dest_root"]
dest = "{}/{}/bs/{}/relax".format(dest_root, os.environ["USER"],
material_id)
user_incar_settings = fw_spec.get("user_incar_settings", {})
vasp_input_set = MPStaticSet.from_prev_calc(
prev_calc_dir=dest,
standardize=1e-3,
user_incar_settings=user_incar_settings)
dec = MontyDecoder()
vis = dec.process_decoded(vasp_input_set.as_dict())
vis.write_input(".")
def run_task(self, fw_spec):
self.user_incar_settings.update({"NPAR": 2})
# Get kpoint density per vol
vol = Poscar.from_file("POSCAR").structure.volume
kppra_vol = self.kpoints_density / vol
new_set = MPStaticSet.from_prev_calc(
os.getcwd(),
user_incar_settings=self.user_incar_settings,
reciprocal_density=kppra_vol)
new_set.write_input('.')
structure = new_set.structure
sga = SpacegroupAnalyzer(structure, 0.1)
return FWAction(stored_data={
'refined_structure': sga.get_refined_structure().as_dict(),
'conventional_standard_structure': sga.get_conventional_standard_structure().as_dict(),
'symmetry_dataset': sga.get_symmetry_dataset(),
'symmetry_operations': [x.as_dict() for x in sga.get_symmetry_operations()]})
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)