def test_from_directory(self):
vi = VaspInput.from_directory(test_dir, optional_files={"CONTCAR.Li2O": Poscar})
self.assertEqual(vi["INCAR"]["ALGO"], "Damped")
self.assertIn("CONTCAR.Li2O", vi)
d = vi.to_dict
vinput = VaspInput.from_dict(d)
self.assertIn("CONTCAR.Li2O", vinput)
def test_from_directory(self):
vi = VaspInput.from_directory(test_dir,
optional_files={"CONTCAR.Li2O": Poscar})
self.assertEqual(vi["INCAR"]["ALGO"], "Damped")
self.assertIn("CONTCAR.Li2O", vi)
d = vi.to_dict
vinput = VaspInput.from_dict(d)
self.assertIn("CONTCAR.Li2O", vinput)
def setup(self):
files = os.listdir(".")
num_structures = 0
if not set(files).issuperset(VASP_INPUT_FILES):
for f in files:
try:
struct = read_structure(f)
num_structures += 1
except:
pass
if num_structures != 1:
raise RuntimeError("{} structures found. Unable to continue."
.format(num_structures))
else:
self.default_vis.write_input(struct, ".")
if self.backup:
for f in VASP_INPUT_FILES:
shutil.copy(f, "{}.orig".format(f))
if self.auto_npar:
try:
vi = VaspInput.from_directory(".")
incar = vi["INCAR"]
#Only optimized NPAR for non-HF and non-RPA calculations.
if (not incar.get("LHFCALC")) and (not incar.get("LRPA")):
import multiprocessing
ncores = multiprocessing.cpu_count()
for npar in range(int(round(math.sqrt(ncores))), ncores):
if ncores % npar == 0:
incar["NPAR"] = npar
break
incar.write_file("INCAR")
except:
pass
if self.settings_override is not None:
vi = VaspInput.from_directory(".")
m = Modder([FileActions, DictActions])
modified = []
for a in self.settings_override:
if "dict" in a:
modified.append(a["dict"])
vi[a["dict"]] = m.modify_object(a["action"],
vi[a["dict"]])
elif "filename" in a:
m.modify(a["action"], a["filename"])
for f in modified:
vi[f].write_file(f)
def setUp(self):
filepath = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
"test_files"))
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, 'POTCAR')
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, 'KPOINTS.auto')
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
class VaspInputTest(unittest.TestCase):
def setUp(self):
filepath = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
"test_files"))
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, 'POTCAR')
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, 'KPOINTS.auto')
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def test_to_from_dict(self):
d = self.vinput.as_dict()
vinput = VaspInput.from_dict(d)
comp = vinput["POSCAR"].structure.composition
self.assertEqual(comp, Composition("Fe4P4O16"))
def test_from_directory(self):
vi = VaspInput.from_directory(test_dir,
optional_files={"CONTCAR.Li2O": Poscar})
self.assertEqual(vi["INCAR"]["ALGO"], "Damped")
self.assertIn("CONTCAR.Li2O", vi)
d = vi.as_dict()
vinput = VaspInput.from_dict(d)
self.assertIn("CONTCAR.Li2O", vinput)
class VaspInputTest(unittest.TestCase):
def setUp(self):
filepath = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
"test_files"))
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, 'POTCAR')
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, 'KPOINTS.auto')
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def test_to_from_dict(self):
d = self.vinput.as_dict()
vinput = VaspInput.from_dict(d)
comp = vinput["POSCAR"].structure.composition
self.assertEqual(comp, Composition("Fe4P4O16"))
def test_from_directory(self):
vi = VaspInput.from_directory(test_dir,
optional_files={"CONTCAR.Li2O": Poscar})
self.assertEqual(vi["INCAR"]["ALGO"], "Damped")
self.assertIn("CONTCAR.Li2O", vi)
d = vi.as_dict()
vinput = VaspInput.from_dict(d)
self.assertIn("CONTCAR.Li2O", vinput)
def check(self):
vi = VaspInput.from_directory(".")
nelm = vi["INCAR"].get("NELM", 60)
try:
oszicar = Oszicar(self.output_filename)
esteps = oszicar.ionic_steps
if len(esteps) > 10:
return all([len(e) == nelm for e in esteps[-11:-1]])
except:
pass
return False
def correct(self):
backup(["INCAR", "KPOINTS", "POSCAR", "OUTCAR",
self.output_filename, "vasp.out"])
vi = VaspInput.from_directory(".")
ediff = float(vi["INCAR"].get("EDIFF", 1e-4))
actions = [{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}},
{"dict": "INCAR",
"action": {"_set": {"EDIFF": ediff*0.75}}}]
VaspModder(vi=vi).apply_actions(actions)
return {"errors": ["MaxForce"], "actions": actions}
def correct(self):
backup([self.output_filename, "INCAR", "KPOINTS", "POSCAR", "OUTCAR",
"vasprun.xml"])
vi = VaspInput.from_directory(".")
m = reduce(operator.mul, vi["KPOINTS"].kpts[0])
m = max(int(round(m ** (1 / 3))), 1)
if vi["KPOINTS"].style.lower().startswith("m"):
m += m % 2
actions = [{"dict": "KPOINTS",
"action": {"_set": {"kpoints": [[m] * 3]}}}]
VaspModder(vi=vi).apply_actions(actions)
return {"errors": ["mesh_symmetry"], "actions": actions}
def correct(self):
backup([self.output_filename, "INCAR", "KPOINTS", "POSCAR", "OUTCAR",
"vasprun.xml"])
vi = VaspInput.from_directory('.')
actions = []
if vi["INCAR"].get("ALGO", "Normal") == "Fast":
actions.append({"dict": "INCAR",
"action": {"_set": {"ALGO": "Normal"}}})
VaspModder(vi=vi).apply_actions(actions)
return {"errors": ["Frozen job"], "actions": actions}
def correct(self):
# change ALGO = Fast to Normal if ALGO is !Normal
vi = VaspInput.from_directory(".")
algo = vi["INCAR"].get("ALGO", "Normal")
if algo.lower() not in ['normal', 'n']:
backup(["INCAR", "KPOINTS", "POSCAR", "OUTCAR", "vasprun.xml"])
actions = [{"dict": "INCAR",
"action": {"_set": {"ALGO": "Normal"}}}]
VaspModder(vi=vi).apply_actions(actions)
return {"errors": ["Positive energy"], "actions": actions}
#Unfixable error. Just return None for actions.
else:
return {"errors": ["Positive energy"], "actions": None}
def run(self):
cmd = list(self.vasp_cmd)
if self.auto_gamma:
vi = VaspInput.from_directory(".")
kpts = vi["KPOINTS"]
if kpts.style == "Gamma" and tuple(kpts.kpts[0]) == (1, 1, 1):
if self.gamma_vasp_cmd is not None and os.path.exists(
self.gamma_vasp_cmd[-1]):
cmd = self.gamma_vasp_cmd
elif os.path.exists(cmd[-1] + ".gamma"):
cmd[-1] += ".gamma"
with open(self.output_file, 'w') as f:
return subprocess.Popen(cmd, stdout=f)
def correct(self):
backup()
vi = VaspInput.from_directory(".")
potim = float(vi["INCAR"].get("POTIM", 0.5)) * 0.5
actions = [{"dict": "INCAR",
"action": {"_set": {"POTIM": potim}}}]
m = Modder()
modified = []
for a in actions:
modified.append(a["dict"])
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
for f in modified:
vi[f].write_file(f)
return {"errors": ["POTIM"], "actions": actions}
def setUp(self):
filepath = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
"test_files"))
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, 'POTCAR')
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, 'KPOINTS.auto')
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def correct(self):
backup(["INCAR", "KPOINTS", "POSCAR", "OUTCAR",
"vasprun.xml"])
vi = VaspInput.from_directory(".")
potim = float(vi["INCAR"].get("POTIM", 0.5))
ibrion = int(vi["INCAR"].get("IBRION", 0))
if potim < 0.2 and ibrion != 3:
actions = [{"dict": "INCAR",
"action": {"_set": {"IBRION": 3,
"SMASS": 0.75}}}]
else:
actions = [{"dict": "INCAR",
"action": {"_set": {"POTIM": potim * 0.5}}}]
VaspModder(vi=vi).apply_actions(actions)
return {"errors": ["POTIM"], "actions": actions}
def correct(self):
backup(self.output_filename)
p = Poscar.from_file("POSCAR")
s = p.structure
trans = PerturbStructureTransformation(0.05)
new_s = trans.apply_transformation(s)
actions = [{"dict": "POSCAR",
"action": {"_set": {"structure": new_s.to_dict}},
"transformation": trans.to_dict}]
m = Modder()
vi = VaspInput.from_directory(".")
for a in actions:
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
vi["POSCAR"].write_file("POSCAR")
return {"errors": ["Frozen job"], "actions": actions}
def correct(self):
backup(self.output_filename)
vi = VaspInput.from_directory(".")
m = reduce(operator.mul, vi["KPOINTS"].kpts[0])
m = max(int(round(m ** (1 / 3))), 1)
if vi["KPOINTS"].style.lower().startswith("m"):
m += m % 2
actions = [{"dict": "KPOINTS",
"action": {"_set": {"kpoints": [[m] * 3]}}}]
m = Modder()
modified = []
for a in actions:
modified.append(a["dict"])
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
for f in modified:
vi[f].write_file(f)
return {"errors": ["mesh_symmetry"], "actions": actions}
def run_task(self, fw_spec):
chgcar_start = False
vi = VaspInput.from_directory(".") # read the VaspInput from the previous run
# figure out what GGA+U values to use and override them
mpvis = MPVaspInputSet()
incar = mpvis.get_incar(vi['POSCAR'].structure).to_dict
incar_updates = {k: incar[k] for k in incar.keys() if 'LDAU' in k} # LDAU values to use
vi['INCAR'].update(incar_updates) # override the +U keys
# start from the CHGCAR of previous run
if os.path.exists('CHGCAR'):
vi['INCAR']['ICHARG'] = 1
chgcar_start = True
vi['INCAR'].write_file('INCAR') # write back the new INCAR to the current directory
return FWAction(stored_data={'chgcar_start': chgcar_start})
def check(self):
msg = "Reciprocal lattice and k-lattice belong to different class of" \
" lattices."
try:
v = Vasprun(self.output_vasprun)
vi = VaspInput.from_directory('.')
# According to VASP admins, you can disregard this error
# if symmetry is off
#Also disregard if automatic KPOINT generation is used
if v.converged or (not v.incar.get('ISYM', True)) or\
vi["KPOINTS"].style == Kpoints.supported_modes.Automatic:
return False
except:
pass
with open(self.output_filename, "r") as f:
for line in f:
l = line.strip()
if l.find(msg) != -1:
return True
return False
def run_task(self, fw_spec):
chgcar_start = False
# read the VaspInput from the previous run
vi = VaspInput.from_directory(".")
# figure out what GGA+U values to use and override them
# LDAU values to use
mpvis = MPVaspInputSet()
incar = mpvis.get_incar(vi['POSCAR'].structure).to_dict
incar_updates = {k: incar[k] for k in incar.keys() if 'LDAU' in k}
vi['INCAR'].update(incar_updates) # override the +U keys
# start from the CHGCAR of previous run
if os.path.exists('CHGCAR'):
vi['INCAR']['ICHARG'] = 1
chgcar_start = True
# write back the new INCAR to the current directory
vi['INCAR'].write_file('INCAR')
return FWAction(stored_data={'chgcar_start': chgcar_start})
def run(self):
"""
Perform the actual VASP run.
Returns:
(subprocess.Popen) Used for monitoring.
"""
cmd = list(self.vasp_cmd)
if self.auto_gamma:
vi = VaspInput.from_directory(".")
kpts = vi["KPOINTS"]
if kpts.style == "Gamma" and tuple(kpts.kpts[0]) == (1, 1, 1):
if self.gamma_vasp_cmd is not None and which(
self.gamma_vasp_cmd[-1]):
cmd = self.gamma_vasp_cmd
elif which(cmd[-1] + ".gamma"):
cmd[-1] += ".gamma"
logging.info("Running {}".format(" ".join(cmd)))
with open(self.output_file, 'w') as f:
p = subprocess.Popen(cmd, stdout=f)
return p
def correct(self):
backup()
actions = [{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}},
{"dict": "INCAR",
"action": {"_set": {"ISTART": 1,
"ALGO": "Normal",
"NELMDL": 6,
"BMIX": 0.001,
"AMIX_MAG": 0.8,
"BMIX_MAG": 0.001}}}]
vi = VaspInput.from_directory(".")
m = Modder(actions=[DictActions, FileActions])
for a in actions:
if "dict" in a:
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
elif "file" in a:
m.modify(a["action"], a["file"])
vi["INCAR"].write_file("INCAR")
return {"errors": ["Unconverged"], "actions": actions}
def correct(self):
# if change_algo is True, change ALGO = Fast to Normal if ALGO is
# Fast. If still not converging, following Kresse's
# recommendation, we will try two iterations of different mixing
# parameters. If this error is caught again, then kil the job
vi = VaspInput.from_directory(".")
algo = vi["INCAR"].get("ALGO", "Normal")
amix = vi["INCAR"].get("AMIX", 0.4)
bmix = vi["INCAR"].get("BMIX", 1.0)
amin = vi["INCAR"].get("AMIN", 0.1)
actions = []
if self.change_algo:
if algo == "Fast":
backup(["INCAR", "KPOINTS", "POSCAR", "OUTCAR", "vasprun.xml"])
actions.append({"dict": "INCAR",
"action": {"_set": {"ALGO": "Normal"}}})
elif amix > 0.1 and bmix > 0.01:
#try linear mixing
backup(["INCAR", "KPOINTS", "POSCAR", "OUTCAR", "vasprun.xml"])
actions.append({"dict": "INCAR",
"action": {"_set": {"AMIX": 0.1, "BMIX": 0.01,
"ICHARG": 2}}})
elif bmix < 3.0 and amin > 0.01:
#Try increasing bmix
backup(["INCAR", "KPOINTS", "POSCAR", "OUTCAR", "vasprun.xml"])
actions.append({"dict": "INCAR",
"action": {"_set": {"AMIN": 0.01, "BMIX": 3.0,
"ICHARG": 2}}})
if actions:
VaspModder(vi=vi).apply_actions(actions)
return {"errors": ["Non-converging job"], "actions": actions}
#Unfixable error. Just return None for actions.
else:
return {"errors": ["Non-converging job"], "actions": None}
def correct(self): #pylint: disable=R0915,R0912,R0914
"""
"brmix"にてINCARにADDGRIDを追加する
"""
backup([self.output_filename, "INCAR", "KPOINTS", "POSCAR", "OUTCAR",
"vasprun.xml"])
actions = []
vi = VaspInput.from_directory(".")
if "tet" in self.errors or "dentet" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISMEAR": 0}}})
if "inv_rot_mat" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"SYMPREC": 1e-8}}})
if "brmix" in self.errors and "NELECT" in vi["INCAR"]:
#brmix error always shows up after DAV steps if NELECT is specified
self.errors.remove("brmix")
if "brmix" in self.errors or "zpotrf" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISYM": 0}}})
#140814 add
actions.append({"dict": "INCAR",
"action": {"_set": {"ADDGRID": True}}})
# Based on VASP forum's recommendation, you should delete the
# CHGCAR and WAVECAR when dealing with these errors.
actions.append({"file": "CHGCAR",
"action": {"_file_delete": {'mode': "actual"}}})
actions.append({"file": "WAVECAR",
"action": {"_file_delete": {'mode': "actual"}}})
if "subspacematrix" in self.errors or "rspher" in self.errors or \
"real_optlay" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"LREAL": False}}})
if "tetirr" in self.errors or "incorrect_shift" in self.errors or \
"rot_matrix" in self.errors:
actions.append({"dict": "KPOINTS",
"action": {"_set": {"generation_style": "Gamma"}}})
if "amin" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"AMIN": "0.01"}}})
if "triple_product" in self.errors:
s = vi["POSCAR"].structure
trans = SupercellTransformation(((1, 0, 0), (0, 0, 1), (0, 1, 0)))
new_s = trans.apply_transformation(s)
actions.append({"dict": "POSCAR",
"action": {"_set": {"structure": new_s.to_dict}},
"transformation": trans.to_dict})
if "pricel" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"SYMPREC": 1e-8, "ISYM": 0}}})
if "brions" in self.errors:
potim = float(vi["INCAR"].get("POTIM", 0.5)) + 0.1
actions.append({"dict": "INCAR",
"action": {"_set": {"POTIM": potim}}})
if "zbrent" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"IBRION": 1}}})
if "too_few_bands" in self.errors:
if "NBANDS" in vi["INCAR"]:
nbands = int(vi["INCAR"]["NBANDS"])
else:
with open("OUTCAR") as f:
for line in f:
if "NBANDS" in line:
try:
d = line.split("=")
nbands = int(d[-1].strip())
break
except (IndexError, ValueError):
pass
actions.append({"dict": "INCAR",
"action": {"_set": {"NBANDS": int(1.1 * nbands)}}})
if "aliasing" in self.errors:
with open("OUTCAR") as f:
grid_adjusted = False
changes_dict = {}
for line in f:
if "aliasing errors" in line:
try:
grid_vector = line.split(" NG", 1)[1]
value = [int(s) for s in grid_vector.split(" ")
if s.isdigit()][0]
changes_dict["NG" + grid_vector[0]] = value
grid_adjusted = True
except (IndexError, ValueError):
pass
#Ensure that all NGX, NGY, NGZ have been checked
if grid_adjusted and 'NGZ' in line:
actions.append({"dict": "INCAR",
"action": {"_set": changes_dict}})
break
m = Modder(actions=[DictActions, FileActions])
modified = []
for a in actions:
if "dict" in a:
modified.append(a["dict"])
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
elif "file" in a:
m.modify(a["action"], a["file"])
for f in modified:
vi[f].write_file(f)
return {"errors": list(self.errors), "actions": actions}
def test_to_from_dict(self):
d = self.vinput.to_dict
vinput = VaspInput.from_dict(d)
comp = vinput["POSCAR"].structure.composition
self.assertEqual(comp, Composition.from_formula("Fe4P4O16"))
def correct(self):
backup(self.output_filename)
actions = []
vi = VaspInput.from_directory(".")
if "tet" in self.errors or "dentet" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISMEAR": 0}}})
if "inv_rot_mat" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"SYMPREC": 1e-8}}})
if "brmix" in self.errors or "zpotrf" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISYM": 0}}})
if "subspacematrix" in self.errors or "rspher" in self.errors or \
"real_optlay" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"LREAL": False}}})
if "tetirr" in self.errors or "incorrect_shift" in self.errors:
actions.append({"dict": "KPOINTS",
"action": {"_set": {"generation_style": "Gamma"}}})
if "amin" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"AMIN": "0.01"}}})
if "too_few_bands" in self.errors:
if "NBANDS" in vi["INCAR"]:
nbands = int(vi["INCAR"]["NBANDS"])
else:
with open("OUTCAR") as f:
for line in f:
if "NBANDS" in line:
try:
d = line.split("=")
nbands = int(d[-1].strip())
break
except (IndexError, ValueError):
pass
actions.append({"dict": "INCAR",
"action": {"_set": {"NBANDS": int(1.1 * nbands)}}})
if "triple_product" in self.errors:
s = vi["POSCAR"].structure
trans = SupercellTransformation(((1, 0, 0), (0, 0, 1), (0, 1, 0)))
new_s = trans.apply_transformation(s)
actions.append({"dict": "POSCAR",
"action": {"_set": {"structure": new_s.to_dict}},
"transformation": trans.to_dict})
if "rot_matrix" in self.errors or "pricel" in self.errors:
s = vi["POSCAR"].structure
trans = PerturbStructureTransformation(0.05)
new_s = trans.apply_transformation(s)
actions.append({"dict": "POSCAR",
"action": {"_set": {"structure": new_s.to_dict}},
"transformation": trans.to_dict})
actions.append({"dict": "INCAR",
"action": {"_set": {"SYMPREC": 1e-8}}})
if "brions" in self.errors:
potim = float(vi["INCAR"].get("POTIM", 0.5)) + 0.1
actions.append({"dict": "INCAR",
"action": {"_set": {"POTIM": potim}}})
m = Modder()
modified = []
for a in actions:
modified.append(a["dict"])
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
for f in modified:
vi[f].write_file(f)
return {"errors": list(self.errors), "actions": actions}
def test_to_from_dict(self):
d = self.vinput.to_dict
vinput = VaspInput.from_dict(d)
comp = vinput["POSCAR"].structure.composition
self.assertEqual(comp, Composition.from_formula("Fe4P4O16"))
__author__ = 'Qimin'
from pymatgen.io.vaspio.vasp_output import Vasprun
from pymatgen.io.vaspio.vasp_input import VaspInput
from pymatgen.io.vaspio_set import MPNonSCFVaspInputSet
import os
vasp_dir = os.path.dirname(os.path.abspath(__file__))
vasp_run = Vasprun(os.path.join(vasp_dir, "vasprun.xml")).to_dict
nband = int(vasp_run['input']['parameters']['NBANDS'])
prec = str(vasp_run['input']['incar']['PREC'])
encut = int(vasp_run['input']['incar']['ENCUT'])
user_incar_settings={"PREC":prec,"ENCUT":encut,"EDIFF":1E-4,"NBANDS":nband,"NSW":0}
#user_incar_settings={"EDIFF":1E-4,"NBANDS":nband,"NSW":0}
mpvis = MPNonSCFVaspInputSet(user_incar_settings=user_incar_settings)
vi = VaspInput.from_directory(".") # read the VaspInput from the previous run
mpvis.get_kpoints(vi['POSCAR'].structure).write_file('KPOINTS')
mpvis.get_incar(vi['POSCAR'].structure).write_file('INCAR')
def correct(self):
backup([self.output_filename, "INCAR", "KPOINTS", "POSCAR", "OUTCAR",
"OSZICAR", "vasprun.xml"])
actions = []
vi = VaspInput.from_directory(".")
if self.errors.intersection(["tet", "dentet"]):
actions.append({"dict": "INCAR",
"action": {"_set": {"ISMEAR": 0}}})
if "inv_rot_mat" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"SYMPREC": 1e-8}}})
if "brmix" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISYM": 0}}})
if vi["KPOINTS"].style == Kpoints.supported_modes.Monkhorst:
actions.append({"dict": "KPOINTS",
"action": {"_set": {"generation_style": "Gamma"}}})
# Based on VASP forum's recommendation, you should delete the
# CHGCAR and WAVECAR when dealing with this error.
actions.append({"file": "CHGCAR",
"action": {"_file_delete": {'mode': "actual"}}})
actions.append({"file": "WAVECAR",
"action": {"_file_delete": {'mode': "actual"}}})
if "zpotrf" in self.errors:
# Usually caused by short bond distances. If on the first step,
# volume needs to be increased. Otherwise, it was due to a step
# being too big and POTIM should be decreased.
try:
oszicar = Oszicar("OSZICAR")
nsteps = len(oszicar.ionic_steps)
except:
nsteps = 0
if nsteps >= 1:
potim = float(vi["INCAR"].get("POTIM", 0.5)) / 2.0
actions.append(
{"dict": "INCAR",
"action": {"_set": {"ISYM": 0, "POTIM": potim}}})
else:
s = vi["POSCAR"].structure
s.apply_strain(0.2)
actions.append({"dict": "POSCAR",
"action": {"_set": {"structure": s.as_dict()}}})
# Based on VASP forum's recommendation, you should delete the
# CHGCAR and WAVECAR when dealing with this error.
actions.append({"file": "CHGCAR",
"action": {"_file_delete": {'mode': "actual"}}})
actions.append({"file": "WAVECAR",
"action": {"_file_delete": {'mode': "actual"}}})
if self.errors.intersection(["subspacematrix", "rspher",
"real_optlay"]):
actions.append({"dict": "INCAR",
"action": {"_set": {"LREAL": False}}})
if self.errors.intersection(["tetirr", "incorrect_shift"]):
if vi["KPOINTS"].style == Kpoints.supported_modes.Monkhorst:
actions.append({"dict": "KPOINTS",
"action": {"_set": {"generation_style": "Gamma"}}})
if "rot_matrix" in self.errors:
if vi["KPOINTS"].style == Kpoints.supported_modes.Monkhorst:
actions.append({"dict": "KPOINTS",
"action": {"_set": {"generation_style": "Gamma"}}})
else:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISYM": 0}}})
if "amin" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"AMIN": "0.01"}}})
if "triple_product" in self.errors:
s = vi["POSCAR"].structure
trans = SupercellTransformation(((1, 0, 0), (0, 0, 1), (0, 1, 0)))
new_s = trans.apply_transformation(s)
actions.append({"dict": "POSCAR",
"action": {"_set": {"structure": new_s.as_dict()}},
"transformation": trans.as_dict()})
if "pricel" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"SYMPREC": 1e-8, "ISYM": 0}}})
if "brions" in self.errors:
potim = float(vi["INCAR"].get("POTIM", 0.5)) + 0.1
actions.append({"dict": "INCAR",
"action": {"_set": {"POTIM": potim}}})
if "zbrent" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"IBRION": 1}}})
if "too_few_bands" in self.errors:
if "NBANDS" in vi["INCAR"]:
nbands = int(vi["INCAR"]["NBANDS"])
else:
with open("OUTCAR") as f:
for line in f:
if "NBANDS" in line:
try:
d = line.split("=")
nbands = int(d[-1].strip())
break
except (IndexError, ValueError):
pass
actions.append({"dict": "INCAR",
"action": {"_set": {"NBANDS": int(1.1 * nbands)}}})
if "aliasing" in self.errors:
with open("OUTCAR") as f:
grid_adjusted = False
changes_dict = {}
r = re.compile(".+aliasing errors.*(NG.)\s*to\s*(\d+)")
for line in f:
m = r.match(line)
if m:
changes_dict[m.group(1)] = int(m.group(2))
grid_adjusted = True
#Ensure that all NGX, NGY, NGZ have been checked
if grid_adjusted and 'NGZ' in line:
actions.extend(
[{"dict": "INCAR",
"action": {"_set": changes_dict}},
{"file": "CHGCAR",
"action": {"_file_delete": {'mode': "actual"}}},
{"file": "WAVECAR",
"action": {"_file_delete": {'mode': "actual"}}}])
break
if "aliasing_incar" in self.errors:
#vasp seems to give different warnings depending on whether the
#aliasing error was caused by user supplied inputs
d = {k: 1 for k in ['NGX', 'NGY', 'NGZ'] if k in vi['INCAR'].keys()}
actions.extend([{"dict": "INCAR", "action": {"_unset": d}},
{"file": "CHGCAR",
"action": {"_file_delete": {'mode': "actual"}}},
{"file": "WAVECAR",
"action": {"_file_delete": {'mode': "actual"}}}])
if "pssyevx" in self.errors:
actions.append({"dict": "INCAR", "action":
{"_set": {"ALGO": "Normal"}}})
if "eddrmm" in self.errors:
#RMM algorithm is not stable for this calculation
if vi["INCAR"].get("ALGO", "Normal") in ["Fast", "VeryFast"]:
actions.append({"dict": "INCAR", "action":
{"_set": {"ALGO": "Normal"}}})
else:
potim = float(vi["INCAR"].get("POTIM", 0.5)) / 2.0
actions.append({"dict": "INCAR",
"action": {"_set": {"POTIM": potim}}})
actions.append({"file": "CHGCAR",
"action": {"_file_delete": {'mode': "actual"}}})
actions.append({"file": "WAVECAR",
"action": {"_file_delete": {'mode': "actual"}}})
VaspModder(vi=vi).apply_actions(actions)
return {"errors": list(self.errors), "actions": actions}
