def run_task(self, fw_spec):
user_incar_settings = {"NCORE": 8}
# vol = Poscar.from_file("POSCAR").structure.volume
# kppra_vol = self.kpoints_density / vol
if self.line:
MPNonSCFSet.from_prev_calc(
os.getcwd(),
mode="Line",
copy_chgcar=False,
user_incar_settings=user_incar_settings,
kpoints_line_density=self.kpoints_line_density).write_input(
'.')
kpath = HighSymmKpath(Poscar.from_file("POSCAR").structure)
return FWAction(stored_data={
"kpath": kpath.kpath,
"kpath_name": kpath.name
})
else:
MPNonSCFSet.from_prev_calc(
os.getcwd(),
mode="Uniform",
copy_chgcar=False,
user_incar_settings=user_incar_settings,
reciprocal_density=self.kpoints_density).write_input('.')
return FWAction()
def Write_NONSCF_KPOINTS(self,
mode="line",
nedos=601,
reciprocal_density=100,
sym_prec=0.1,
kpoints_line_density=20,
optics=False,
**kwargs):
"""
generate KPOINTS for DOS (mode="uniform") or band struture (mode="line") by pymatgen.io.vasp.set.MPNonSCFSet
input arguments:
-mode (str): 'line' or 'uniform'
-nedos (int): default 601. Only valid at mode='uniform'
-reciprocal_density (int): default 100. Only valid at mode='uniform'
-sym_prec (float): default 0.1
-kpoints_line_density (int): default 20. Only valid at mode='line'
-optics (bool)
"""
vis = MPNonSCFSet(structure=self.structure,
mode=mode,
nedos=nedos,
reciprocal_density=reciprocal_density,
sym_prec=sym_prec,
kpoints_line_density=kpoints_line_density,
optics=optics)
vis.kpoints.write_file(os.path.join(self.cal_loc, "KPOINTS"))
def Write_NONSCF_KPOINTS(structure_filename="./POSCAR",
mode='line',
nedos=601,
reciprocal_density=100,
sym_prec=0.1,
kpoints_line_density=20,
optics=False,
**kwargs):
"""
generate KPOINTS for DOS (mode="uniform") or band struture (mode="line") by pymatgen.io.vasp.set.MPNonSCFSet
input arguments:
-structure_filename (str): a file that can be understood by pymatgen.Structure.from_file.
-mode (str): 'line' or 'uniform'
-nedos (int): default 601. Only valid at mode='uniform'
-reciprocal_density (int): default 100. Only valid at mode='uniform'
-sym_prec (float): default 0.1
-kpoints_line_density (int): default 20. Only valid at mode='line'
-optics (bool)
"""
#print(os.getcwd())
#print(os.listdir())
#print(structure_filename)
struct = Structure.from_file(structure_filename)
vis = MPNonSCFSet(structure=struct,
mode=mode,
nedos=nedos,
reciprocal_density=reciprocal_density,
sym_prec=sym_prec,
kpoints_line_density=kpoints_line_density,
optics=optics)
folder = os.path.split(structure_filename)[0]
vis.kpoints.write_file(os.path.join(folder, "KPOINTS"))
def write_vasp(self, k0_rlv, scfdir, destdir):
'''Generate VASP nscf input files
'''
r = Vasprun(join(scfdir, 'vasprun.xml'))
rlv = r.lattice_rec.matrix
is_k_spin = True
try:
len(k0_rlv[0])
except:
is_k_spin = False
k0_up = k0_rlv
k0_dn = None
if is_k_spin:
k0_up, k0_dn = k0_rlv[0], k0_rlv[1]
list_k = self.kpoints(rlv, k0_up)
if r.is_spin and is_k_spin:
list_k = np.concatenate((list_k, self.kpoints(rlv, k0_dn)))
nscf = MPNonSCFSet.from_prev_calc(scfdir,
user_incar_settings={
"NCORE": 4,
"EDIFF": "1E-7"
})
nscf.write_input(destdir)
mode = Kpoints.supported_modes.Reciprocal
kpt = Kpoints(style=mode,
kpts=list_k,
num_kpts=len(list_k),
kpts_weights=[1.0] * len(list_k),
comment="5-point stencil h:{}".format(self.h))
kpt.write_file(join(destdir, 'KPOINTS'))
def setUp(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = [
[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603],
]
structure = Structure(lattice, ["Si", "Si"], coords)
input_sets = {
"GGA Structure Optimization": MPRelaxSet(structure),
"GGA Static": MPStaticSet(structure),
"GGA NSCF Line": MPNonSCFSet(structure, mode="line"),
"GGA NSCF Uniform": MPNonSCFSet(structure, mode="uniform"),
}
tasks = []
t_id = 1
for task_type, input_set in input_sets.items():
doc = {
"true_task_type": task_type,
"last_updated": datetime.now(),
"task_id": t_id,
"state": "successful",
"orig_inputs": {
"incar": input_set.incar.as_dict(),
"kpoints": input_set.kpoints.as_dict(),
},
"output": {
"structure": structure.as_dict()
},
}
t_id += 1
tasks.append(doc)
self.test_tasks = MemoryStore("tasks")
self.task_types = MemoryStore("task_types")
self.test_tasks.connect()
self.task_types.connect()
self.test_tasks.update(tasks)
def run_task(self, fw_spec):
material_id = self["material_id"]
mode = self["mode"]
dest_root = fw_spec["_fw_env"]["run_dest_root"]
dest = "{}/{}/bs/{}/static".format(dest_root, os.environ["USER"],
material_id)
user_incar_settings = fw_spec.get("user_incar_settings", {})
if mode.lower() == "line":
vasp_input_set = MPNonSCFSet.from_prev_calc(
dest,
standardize=1e-3,
user_incar_settings=user_incar_settings,
mode=mode)
dec = MontyDecoder()
vis = dec.process_decoded(vasp_input_set.as_dict())
vis.write_input(".")
elif mode.lower() == "uniform":
vasp_input_set = MPNonSCFSet.from_prev_calc(
dest, user_incar_settings=user_incar_settings, mode=mode)
dec = MontyDecoder()
vis = dec.process_decoded(vasp_input_set.as_dict())
vis.write_input(".")
def run_task(self, fw_spec):
vis = MPNonSCFSet.from_prev_calc(
prev_calc_dir=self.get("prev_calc_dir", "."),
copy_chgcar=self.get("copy_chgcar", False),
user_incar_settings=self.get("user_incar_settings", {}),
nbands_factor=self.get("nbands_factor", 2),
reciprocal_density=self.get("reciprocal_density", 100),
kpoints_line_density=self.get("kpoints_line_density", 30),
small_gap_multiply=self.get("small_gap_multiply", None),
standardize=self.get("standardize", False),
sym_prec=self.get("sym_prec", 0.1),
mode=self.get("mode", "line"),
**self.get("other_params", {}))
vis.write_input(".")
def run_task(self, fw_spec):
vis = MPNonSCFSet.from_prev_calc(
prev_calc_dir=self["prev_calc_dir"],
copy_chgcar=self.get("copy_chgcar", False),
nbands_factor=self.get("nbands_factor", 1.2),
reciprocal_density=self.get("reciprocal_density", 100),
kpoints_line_density=self.get("kpoints_line_density", 20),
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),
mode=self.get("mode", "uniform"),
nedos=self.get("nedos", 601),
optics=self.get("optics", False),
**self.get("other_params", {}))
vis.write_input(".")
def run_task(self, fw_spec):
vis = MPNonSCFSet.from_prev_calc(
prev_calc_dir=self.get("prev_calc_dir", "."),
copy_chgcar=self.get("copy_chgcar", False),
nbands_factor=self.get("nbands_factor", 1.2),
reciprocal_density=self.get("reciprocal_density", 100),
kpoints_line_density=self.get("kpoints_line_density", 20),
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),
mode=self.get("mode", "uniform"),
nedos=self.get("nedos", 601),
optics=self.get("optics", False),
**self.get("other_params", {}))
vis.write_input(".")
def Scf (self):
from pymatgen.io.vasp.sets import MPNonSCFSet
import shutil
import os
filePath=self.dire
for dirpath, dirnames, filenames in os.walk(filePath):
# print(dirpath)
for name in dirnames:
if 'dos' not in str(name):
path = os.path.join(filePath, name)
custom_settings = {"LAECHG": "False", "LVHAR": "False",'NPAR':4} # user custom incar settings
dos = MPNonSCFSet.from_prev_calc(path, mode="line",reciprocal_density=200,
user_incar_settings=custom_settings)
os.chdir(self.dire)
dos.write_input("dos_"+str(name))
pat = os.path.join(self.dire, "dos_"+str(name))
diree = 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 )
shutil.copy(os.path.join(path,'WAVECAR'), os.path.join(pat,'WAVECAR') )
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)
'NELM': 60,
"LVHAR": "False",
# "LWAVE": "True",
"ISMEAR": 1,
"SYMPREC": 1e-8,
# "LELF": "True",
}
static = MPStaticSet(struc, user_incar_settings=myset)
static.write_input(static_dir)
run_vasp(cmd, static_dir)
os.system('cp ' + static_dir + '/vasprun.xml ./static-vasprun.xml')
# 2nd run to obtain dos
dos = MPNonSCFSet.from_prev_calc(static_dir,
mode="uniform",
reciprocal_density=200,
user_incar_settings=myset)
dos.write_input(dos_dir)
run_vasp(cmd, dos_dir)
os.system('cp ' + dos_dir + '/vasprun.xml ./dos-vasprun.xml')
# 3rd run to obtain Band structure
band = MPNonSCFSet.from_prev_calc(static_dir,
mode="line",
standardize=True,
user_incar_settings=myset)
band.write_input(band_dir)
run_vasp(cmd, band_dir)
os.system('cp ' + band_dir + '/vasprun.xml ./band-vasprun.xml')
os.system('cp ' + band_dir + '/KPOINTS ./')
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)