class PRLRelaxSet(DictSet):
"""
Set for performing relaxations.
The smearing must be set to give the correct forces.
The default is tuned for metal relaxations.
Kpoints have a 6000 kpoints per reciprocal atom default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
# we never are comparing relaxations, only using them for optimizing structures.
CONFIG['INCAR'].pop('ENCUT') # use the ENCUT set by PREC
CONFIG['KPOINTS'].update({
'grid_density': 6000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].update({
'EDIFF_PER_ATOM': 1e-4,
'ISMEAR': 1,
'SIGMA': 0.2,
'LREAL': False,
'PREC': 'HIGH',
'ALGO': 'NORMAL',
})
# now we reset the potentials
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, **kwargs):
self.kwargs = kwargs
super(PRLRelaxSet, self).__init__(structure, PRLRelaxSet.CONFIG,
**kwargs)
class StaticSet(DictSet):
"""Set tuned for metal relaxations (correct smearing).
Add `isif` parameter to the set to easily allow for overriding ISIF setting.
Kpoints have a 6000 reciprocal density default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
CONFIG['KPOINTS'].update({
'grid_density': 8000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].update({
'EDIFF_PER_ATOM': 1e-6,
'ENCUT': 520, # MP compatibility
'ISMEAR': -5,
"NSW": 0,
"IBRION": -1,
'LREAL': False,
'ALGO': 'NORMAL',
# other settings from MPStaticSet
"LAECHG": True,
"LCHARG": True,
"LWAVE": False,
"LORBIT": 11,
"LVHAR": True,
"ICHARG": 2,
"NEDOS": 5001,
})
# now we reset the potentials
CONFIG['POTCAR_FUNCTIONAL'] = 'PBE'
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, isif=2, **kwargs):
# pop the old kwargs, backwards compatibility from the complex StaticSet
self.isif = isif
old_kwargs = [
'prev_incar', 'prev_kpoints', 'grid_density', 'lepsilon',
'lcalcpol'
]
for k in old_kwargs:
try:
kwargs.pop(k)
except KeyError:
pass
self.kwargs = kwargs
uis = copy.deepcopy(kwargs.get('user_incar_settings', {}))
uis['ISIF'] = isif
if 'ISPIN' not in uis:
if magnetic_check(structure):
uis.update({'ISPIN': 2})
else:
uis.update({'ISPIN': 1})
StaticSet.CONFIG['INCAR'].update(uis)
super(StaticSet, self).__init__(structure,
StaticSet.CONFIG,
sort_structure=False,
**kwargs)
class RelaxSet(DictSet):
"""
Set for performing relaxations.
The smearing must be set to give the correct forces.
The default is tuned for metal relaxations.
Kpoints have a 8000 kpoints per reciprocal atom default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
# we never are comparing relaxations, only using them for optimizing structures.
CONFIG['INCAR'].pop('ENCUT') # use the ENCUT set by PREC
CONFIG['KPOINTS'].update({
'grid_density': 8000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].update({
'EDIFF_PER_ATOM': 1e-5,
'ISMEAR': 1,
'SIGMA': 0.2,
'LREAL': False,
'PREC': 'Accurate',
'ALGO': 'NORMAL',
'LWAVE': False,
'LCHARG': False,
'ISIF': 3,
"ICHARG": 2,
'ENCUT': 520,
})
# now we reset the potentials
CONFIG['POTCAR_FUNCTIONAL'] = 'PBE'
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, volume_relax=False, isif=None, **kwargs):
"""If volume relax is True, will do volume only, ISIF 7"""
self.kwargs = kwargs
self.volume_relax = volume_relax
self.isif = isif
uis = copy.deepcopy(kwargs.get('user_incar_settings', {}))
if self.volume_relax and self.isif is not None:
raise ValueError(
"isif cannot have a value while volume_relax is True.")
if self.volume_relax:
uis.update({'ISIF': 7})
#uis['ISIF'] = 7
if self.isif is not None:
uis.update({'ISIF': self.isif})
if 'ISPIN' not in uis:
if magnetic_check(structure):
uis.update({'ISPIN': 2})
else:
uis.update({'ISPIN': 1})
RelaxSet.CONFIG['INCAR'].update(uis)
super(RelaxSet, self).__init__(structure,
RelaxSet.CONFIG,
sort_structure=False,
**kwargs)
class ForceConstantsSet(DictSet):
"""
Set for calculating force constants calculations.
Force constants are calculated by the finite difference method with symmetry considered.
The smearing must be set to give the correct forces.
The default is tuned for metals.
Kpoints have a 8000 kpoints per reciprocal atom default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
# we never are comparing relaxations, only using them for optimizing structures.
CONFIG['KPOINTS'].update({
'grid_density': 8000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].pop('ENCUT') # use the ENCUT set by PREC
CONFIG['INCAR'].update({
'EDIFF_PER_ATOM': 1e-6,
'ISMEAR': 1,
'SIGMA': 0.2,
'LREAL': False,
'ISIF': 0, # only calculate the forces, stress tensor is not needed
'IBRION':
6, # calculate force constants by finite differences with symmetry
'POTIM': 0.015, # displacement distance
'NFREE': 2, # how many displacments to do. 2 gives +POTIM and -POTIM
'NSW': 1, # backwards compatibility setting
'PREC': 'Accurate',
'ALGO': 'NORMAL',
'SYMPREC':
1e-4, # some supercells seem to have issues with primcel VASP algorithm
"ICHARG": 2,
})
# now we reset the potentials
CONFIG['POTCAR_FUNCTIONAL'] = 'PBE'
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, **kwargs):
self.kwargs = kwargs
uis = copy.deepcopy(kwargs.get('user_incar_settings', {}))
if 'ISPIN' not in uis:
if magnetic_check(structure):
uis.update({'ISPIN': 2})
else:
uis.update({'ISPIN': 1})
ForceConstantsSet.CONFIG['INCAR'].update(uis)
super(ForceConstantsSet, self).__init__(structure,
ForceConstantsSet.CONFIG,
sort_structure=False,
**kwargs)
class ForcesSet(DictSet):
"""Set tuned for generic force calculations (Gaussian smearing).
"""
CONFIG = _load_yaml_config("MPRelaxSet")
CONFIG['KPOINTS'].update({
'grid_density': 8000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].pop('ENCUT', None)
CONFIG['INCAR'].update({
'EDIFF_PER_ATOM': 1e-8,
'ISMEAR': 0,
'SIGMA': 0.05,
"NSW": 0,
"IBRION": -1,
'LREAL': False,
'ALGO': 'NORMAL',
# other settings from MPStaticSet
"LCHARG": False,
"LORBIT": 11,
"LVHAR": True,
"LWAVE": False,
"ICHARG": 2,
"NEDOS": 5001,
})
# now we reset the potentials
CONFIG['POTCAR_FUNCTIONAL'] = 'PBE'
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, **kwargs):
# pop the old kwargs, backwards compatibility from the complex StaticSet
old_kwargs = [
'prev_incar', 'prev_kpoints', 'grid_density', 'lepsilon',
'lcalcpol'
]
for k in old_kwargs:
try:
kwargs.pop(k)
except KeyError:
pass
self.kwargs = kwargs
super(ForcesSet, self).__init__(structure,
ForcesSet.CONFIG,
sort_structure=False,
**kwargs)
class RelaxSet(DictSet):
"""
Set for performing relaxations.
The smearing must be set to give the correct forces.
The default is tuned for metal relaxations.
Kpoints have a 8000 kpoints per reciprocal atom default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
# we never are comparing relaxations, only using them for optimizing structures.
CONFIG['INCAR'].pop('ENCUT') # use the ENCUT set by PREC
CONFIG['KPOINTS'].update({
'grid_density': 8000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].update({
'EDIFF_PER_ATOM': 1e-5,
'ISMEAR': 1,
'SIGMA': 0.2,
'LREAL': False,
'PREC': 'Accurate',
'ALGO': 'NORMAL',
'LWAVE': False,
'LCHARG': False,
'ISIF': 3,
"ICHARG": 2,
'ENCUT': 520,
})
# now we reset the potentials
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, volume_relax=False, **kwargs):
"""If volume relax is True, will do volume only, ISIF 7"""
self.kwargs = kwargs
self.volume_relax = volume_relax
super(RelaxSet, self).__init__(structure, RelaxSet.CONFIG, **kwargs)
if self.volume_relax:
self.incar.update({'ISIF': 7})
class PRLRelaxSet(DictSet):
"""Set tuned for metal relaxations (correct smearing).
Add `isif` parameter to the set to easily allow for overriding ISIF setting.
Kpoints have a 6000 reciprocal density default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
CONFIG['INCAR'].pop('ENCUT')
CONFIG['KPOINTS'].update({
'grid_density': 6000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].update({
'ISMEAR': 1,
'SIGMA': 0.2,
'LREAL': False,
'PREC': 'HIGH',
'ALGO': 'NORMAL'
})
def __init__(self, structure, **kwargs):
self.kwargs = kwargs
super(PRLRelaxSet, self).__init__(structure, PRLRelaxSet.CONFIG,
**kwargs)
from pymatgen import MPRester
from pymatgen.analysis.phase_diagram import PhaseDiagram
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.analysis.structure_matcher import ElementComparator
from pymatgen.core import Composition
from pymatgen.entries.compatibility import MaterialsProjectCompatibility
from pymatgen.entries.computed_entries import ComputedEntry
from pymatgen.io.vasp.sets import _load_yaml_config
from garnetdnn.formation_energy import get_descriptor, get_form_e, get_tote
from garnetdnn.util import load_model_and_scaler, spe2form
import itertools
CONFIG = _load_yaml_config("MPRelaxSet")
LDAUU = CONFIG["INCAR"]['LDAUU']['O']
m = MPRester("xNebFpxTfLhTnnIH")
STD_FORMULA = {
'garnet': Composition("C3A2D3O12"),
"perovskite": Composition("A2B2O6")
}
SITES = {
'garnet': ['c', 'a', 'd'],
'perovskite': ['a', 'b']
} # use list to preserve order
SITE_INFO = {
'garnet': {
'c': {
"num_atoms": 3,
class PRLStaticSet(DictSet):
"""Set tuned for metal relaxations (correct smearing).
Add `isif` parameter to the set to easily allow for overriding ISIF setting.
Kpoints have a 6000 reciprocal density default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
CONFIG['KPOINTS'].update({
'grid_density': 8000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].update({
'EDIFF_PER_ATOM': 1e-6,
'ENCUT': 520, # MP compatibility
'ISMEAR': -5,
"NSW": 0,
"IBRION": -1,
'LREAL': False,
'ALGO': 'NORMAL',
# other settings from MPStaticSet
"LAECHG": True,
"LCHARG": True,
"LORBIT": 11,
"LVHAR": True,
"LWAVE": False,
"ICHARG": 0,
"NEDOS": 5001,
})
# now we reset the potentials
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self,
structure,
prev_incar=None,
prev_kpoints=None,
lepsilon=False,
lcalcpol=False,
grid_density=8000,
**kwargs):
super(PRLStaticSet, self).__init__(structure, PRLStaticSet.CONFIG,
**kwargs)
if isinstance(prev_incar, six.string_types):
prev_incar = Incar.from_file(prev_incar)
if isinstance(prev_kpoints, six.string_types):
prev_kpoints = Kpoints.from_file(prev_kpoints)
self.prev_incar = prev_incar
self.prev_kpoints = prev_kpoints
self.grid_density = grid_density
self.structure = structure
self.kwargs = kwargs
self.lepsilon = lepsilon
self.lcalcpol = lcalcpol
@property
def incar(self):
parent_incar = super(PRLStaticSet, self).incar
incar = Incar(self.prev_incar) if self.prev_incar is not None else \
Incar(parent_incar)
incar.update({
"IBRION": -1,
"ISMEAR": -5,
"LAECHG": True,
"LCHARG": True,
"LORBIT": 11,
"LVHAR": True,
"LWAVE": False,
"NSW": 0,
"ICHARG": 0,
"ALGO": "Normal"
})
for k in ["MAGMOM", "NUPDOWN"] + list(
self.kwargs.get("user_incar_settings", {}).keys()):
# For these parameters as well as user specified settings, override
# the incar settings.
if parent_incar.get(k, None) is not None:
incar[k] = parent_incar[k]
else:
incar.pop(k, None)
# use new LDAUU when possible b/c the Poscar might have changed
# representation
if incar.get('LDAU'):
u = incar.get('LDAUU', [])
j = incar.get('LDAUJ', [])
if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
incar.update({tag: parent_incar[tag]})
# ensure to have LMAXMIX for GGA+U static run
if "LMAXMIX" not in incar:
incar.update({"LMAXMIX": parent_incar["LMAXMIX"]})
# Compare ediff between previous and staticinputset values,
# choose the tighter ediff
incar["EDIFF"] = min(incar.get("EDIFF", 1), parent_incar["EDIFF"])
return incar
@property
def kpoints(self):
self._config_dict["KPOINTS"]["grid_density"] = self.grid_density
kpoints = super(PRLStaticSet, self).kpoints
# Prefer to use k-point scheme from previous run
if self.prev_kpoints and self.prev_kpoints.style != kpoints.style:
if self.prev_kpoints.style == Kpoints.supported_modes.Monkhorst:
k_div = [
kp + 1 if kp % 2 == 1 else kp for kp in kpoints.kpts[0]
]
kpoints = Kpoints.monkhorst_automatic(k_div)
else:
kpoints = Kpoints.gamma_automatic(kpoints.kpts[0])
return kpoints
@classmethod
def from_prev_calc(cls,
prev_calc_dir,
standardize=False,
sym_prec=0.1,
international_monoclinic=True,
grid_density=8000,
small_gap_multiply=None,
**kwargs):
"""
Generate a set of Vasp input files for static calculations from a
directory of previous Vasp run.
Args:
prev_calc_dir (str): Directory containing the outputs(
vasprun.xml and OUTCAR) of previous vasp run.
standardize (float): Whether to standardize to a primitive
standard cell. Defaults to False.
sym_prec (float): Tolerance for symmetry finding. If not 0,
the final structure from the previous run will be symmetrized
to get a primitive standard cell. Set to 0 if you don't want
that.
international_monoclinic (bool): Whether to use international
convention (vs Curtarolo) for monoclinic. Defaults True.
grid_density (int): density of k-mesh by reciprocal atom (defaults to 8000)
small_gap_multiply ([float, float]): If the gap is less than
1st index, multiply the default reciprocal_density by the 2nd
index.
\\*\\*kwargs: All kwargs supported by MPStaticSet,
other than prev_incar and prev_structure and prev_kpoints which
are determined from the prev_calc_dir.
"""
vasprun, outcar = get_vasprun_outcar(prev_calc_dir)
prev_incar = vasprun.incar
prev_kpoints = vasprun.kpoints
# We will make a standard structure for the given symprec.
prev_structure = get_structure_from_prev_run(
vasprun,
outcar,
sym_prec=standardize and sym_prec,
international_monoclinic=international_monoclinic)
# multiply the reciprocal density if needed:
if small_gap_multiply:
gap = vasprun.eigenvalue_band_properties[0]
if gap <= small_gap_multiply[0]:
grid_density = grid_density * small_gap_multiply[1]
return PRLStaticSet(structure=prev_structure,
prev_incar=prev_incar,
prev_kpoints=prev_kpoints,
grid_density=grid_density,
**kwargs)
class ElasticSet(DictSet):
"""Set tuned for metal relaxations (correct smearing).
Add `isif` parameter to the set to easily allow for overriding ISIF setting.
Kpoints have a 6000 reciprocal density default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
# 'EDIFF_PER_ATOM': 1e-6,
CONFIG['INCAR'] = {
'EDIFF': 1e-6,
'ENCUT': 520, # MP compatibility
'ISMEAR': -5,
"IBRION": 2,
'LREAL': False,
'ALGO': 'NORMAL',
# other settings from MPStaticSet
"LAECHG": True,
"LCHARG": True,
"LWAVE": False,
#"LORBIT": 11,
"LVHAR": True,
"ICHARG": 0,
"NSW": 99,
"MAGMOM": CONFIG['INCAR']['MAGMOM'],
"ISPIN": 2,
"ISIF": 2,
"PREC": "High"
}
# now we reset the potentials
CONFIG['POTCAR_FUNCTIONAL'] = 'PBE'
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, **kwargs):
# pop the old kwargs, backwards compatibility from the complex StaticSet
uis = copy.deepcopy(kwargs.get('user_incar_settings', {}))
"""
old_kwargs = ['prev_incar', 'prev_kpoints', 'grid_density', 'lepsilon', 'lcalcpol', \
'user_potcar_functional', 'user_incar_settings']
"""
old_kwargs = [
'prev_incar', 'prev_kpoints', 'grid_density', 'lepsilon',
'lcalcpol'
]
for k in old_kwargs:
try:
kwargs.pop(k)
except KeyError:
pass
self.kwargs = kwargs
if 'ISPIN' not in uis:
if magnetic_check(structure):
uis.update({'ISPIN': 2})
else:
uis.update({'ISPIN': 1})
if uis['ISPIN'] == 1:
if 'MAGMON' in uis.keys():
uis.pop['MAGMOM']
for key in uis.keys():
if key not in ElasticSet.CONFIG['INCAR']:
if key in {'NELM', 'EDIFF', 'NEDOS', 'KPOINT_BSE'}: continue
ElasticSet.CONFIG['INCAR'][key] = uis[key]
elif key == 'ISPIN':
ElasticSet.CONFIG['INCAR'][key] = uis[key]
elif key == 'ISMEAR':
ElasticSet.CONFIG['INCAR'][key] = uis[key]
elif key == 'SIGMA':
ElasticSet.CONFIG['INCAR'][key] = uis[key]
if 'ISPIN' in ElasticSet.CONFIG['INCAR']:
if ElasticSet.CONFIG['INCAR']['ISPIN'] == 1:
if 'MAGMOM' in ElasticSet.CONFIG['INCAR']:
ElasticSet.CONFIG['INCAR'].pop('MAGMOM')
if 'SIGMA' in ElasticSet.CONFIG[
'INCAR'] and 'ISMEAR' in ElasticSet.CONFIG['INCAR']:
if ElasticSet.CONFIG['INCAR']['ISMEAR'] == -5:
ElasticSet.CONFIG['INCAR'].pop('SIGMA')
from pymatgen.io.vasp.inputs import Kpoints
if metal_check(structure):
grid_density = 15625
#ElasticSet.CONFIG['INCAR']['ISMEAR'] = 1
#ElasticSet.CONFIG['INCAR']['SIGMA'] = 0.2
else:
grid_density = 8000
kpoints = Kpoints.automatic_gamma_density(structure, grid_density)
ElasticSet.CONFIG['KPOINTS'] = kpoints
pot = kwargs.get('user_potcar_functional', None)
if pot:
ElasticSet.CONFIG['POTCAR_FUNCTIONAL'] = pot
kwargs.update(
{'user_potcar_functional': ElasticSet.CONFIG['POTCAR_FUNCTIONAL']})
kwargs.update({'user_incar_settings': ElasticSet.CONFIG['INCAR']})
super(ElasticSet, self).__init__(structure,
ElasticSet.CONFIG,
sort_structure=False,
**kwargs)
class BornChargeSet(DictSet):
"""Set tuned for metal relaxations (correct smearing).
Add `isif` parameter to the set to easily allow for overriding ISIF setting.
Kpoints have a 6000 reciprocal density default.
Provide by Yi Wang, Aug. 24, 2020
"""
CONFIG = _load_yaml_config("MPRelaxSet")
CONFIG['KPOINTS'].update({
'grid_density': 8000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].update({
"LEPSILON": True, #For Born Effective Charge
"NCORE": 1,
#"NPAR": 1,
#"LCALCEPS": True, #For Born Effective Charge
"LRPA": False,
'EDIFF_PER_ATOM': 1e-6,
'ENCUT': 520, # MP compatibility
'ISMEAR': 0,
"NSW": 0,
"IBRION": -1,
'LREAL': False,
'ALGO': 'NORMAL',
# other settings from MPStaticSet
"LCHARG": False,
"LWAVE": False,
"ICHARG": 2,
})
CONFIG['POTCAR_FUNCTIONAL'] = 'PBE'
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, isif=2, **kwargs):
# pop the old kwargs, backwards compatibility from the complex StaticSet
self.isif = isif
uis = copy.deepcopy(kwargs.get('user_incar_settings', {}))
"""
old_kwargs = ['prev_incar', 'prev_kpoints', 'grid_density', 'lepsilon', 'lcalcpol', \
'user_potcar_functional', 'user_incar_settings']
"""
old_kwargs = [
'prev_incar', 'prev_kpoints', 'grid_density', 'lepsilon',
'lcalcpol'
]
for k in old_kwargs:
try:
kwargs.pop(k)
except KeyError:
pass
self.kwargs = kwargs
if 'ISPIN' not in uis:
if magnetic_check(structure):
uis.update({'ISPIN': 2})
else:
uis.update({'ISPIN': 1})
else:
if uis['ISPIN'] == 1:
if 'MAGMON' in uis.keys():
uis.pop['MAGMOM']
for key in uis.keys():
if key not in BornChargeSet.CONFIG['INCAR']:
if key in {'NELM', 'EDIFF', 'NEDOS', 'KPOINT_BSE'}: continue
BornChargeSet.CONFIG['INCAR'][key] = uis[key]
elif key == 'ISPIN':
BornChargeSet.CONFIG['INCAR'][key] = uis[key]
elif key == 'ISMEAR':
BornChargeSet.CONFIG['INCAR'][key] = uis[key]
elif key == 'SIGMA':
BornChargeSet.CONFIG['INCAR'][key] = uis[key]
if 'ISPIN' in BornChargeSet.CONFIG['INCAR']:
if BornChargeSet.CONFIG['INCAR']['ISPIN'] == 1:
if 'MAGMOM' in BornChargeSet.CONFIG['INCAR']:
BornChargeSet.CONFIG['INCAR'].pop('MAGMOM')
if 'SIGMA' in BornChargeSet.CONFIG[
'INCAR'] and 'ISMEAR' in BornChargeSet.CONFIG['INCAR']:
if BornChargeSet.CONFIG['INCAR']['ISMEAR'] == -5:
BornChargeSet.CONFIG['INCAR'].pop('SIGMA')
pot = kwargs.get('user_potcar_functional', None)
if pot:
BornChargeSet.CONFIG['POTCAR_FUNCTIONAL'] = pot
kwargs.update({
'user_potcar_functional':
BornChargeSet.CONFIG['POTCAR_FUNCTIONAL']
})
kwargs.update({'user_incar_settings': BornChargeSet.CONFIG['INCAR']})
super(BornChargeSet, self).__init__(structure,
BornChargeSet.CONFIG,
sort_structure=False,
**kwargs)
class RelaxSet(DictSet):
"""
Set for performing relaxations.
The smearing must be set to give the correct forces.
The default is tuned for metal relaxations.
Kpoints have a 8000 kpoints per reciprocal atom default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
# we never are comparing relaxations, only using them for optimizing structures.
CONFIG['INCAR'].pop('ENCUT') # use the ENCUT set by PREC
CONFIG['KPOINTS'].update({
'grid_density': 8000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].update({
'EDIFF_PER_ATOM': 1e-7,
'ISMEAR': 1,
'SIGMA': 0.2,
'LREAL': False,
'PREC': 'Accurate',
'ALGO': 'NORMAL',
"LORBIT": 11,
'LWAVE': False,
'LCHARG': False,
'ISIF': 3,
"ICHARG": 2,
'ENCUT': 520,
})
# now we reset the potentials
CONFIG['POTCAR_FUNCTIONAL'] = 'PBE'
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self,
structure,
volume_relax=False,
isif=None,
a_kwargs={},
**kwargs):
"""If volume relax is True, will do volume only, ISIF 7"""
self.kwargs = copy.deepcopy(kwargs)
self.volume_relax = volume_relax
self.isif = isif
self.a_kwargs = a_kwargs
uis = copy.deepcopy(self.kwargs.get('user_incar_settings', {}))
new_config = copy.deepcopy(RelaxSet.CONFIG)
if self.volume_relax and self.isif is not None:
raise ValueError(
"isif cannot have a value while volume_relax is True.")
if self.volume_relax:
uis.update({'ISIF': 7})
#uis['ISIF'] = 7
if self.isif is not None:
uis.update({'ISIF': self.isif})
if 'ISPIN' not in uis:
if magnetic_check(structure):
uis.update({'ISPIN': 2})
else:
uis.update({'ISPIN': 1})
if 'magmom' in uis:
if 'MAGMOM' in new_config['INCAR']:
new_config['INCAR'].pop('MAGMOM')
elif uis['ISPIN'] == 1:
if 'MAGMON' in uis.keys(): uis.pop['MAGMOM']
if 'MAGMON' in new_config['INCAR']:
new_config['INCAR'].pop['MAGMOM']
settings = self.a_kwargs.get('settings', {})
new_vasp_settings = settings.get('Relax_settings', None) or uis.get(
'Relax_settings', None)
if new_vasp_settings:
for ff in new_vasp_settings:
if ff.lower() == 'prec':
if 'ENCUT' in new_config['INCAR']:
new_config['INCAR'].pop('ENCUT')
new_config['INCAR'].update({ff: new_vasp_settings.get(ff)})
elif ff == 'grid_density':
new_config['KPOINTS'].update(
{ff: new_vasp_settings.get(ff)})
elif ff == 'k_mesh':
kpoints = Kpoints(kpts=new_vasp_settings.get(ff))
new_config['KPOINTS'] = kpoints
else:
new_config['INCAR'].update({ff: new_vasp_settings.get(ff)})
new_config['INCAR'].update(uis)
pot = self.kwargs.get('user_potcar_functional', None)
if pot:
new_config['POTCAR_FUNCTIONAL'] = pot
super(RelaxSet, self).__init__(structure,
new_config,
sort_structure=False,
**self.kwargs)
class ElasticSet(DictSet):
"""Set tuned for metal relaxations (correct smearing).
Add `isif` parameter to the set to easily allow for overriding ISIF setting.
Kpoints have a 6000 reciprocal density default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
# 'EDIFF_PER_ATOM': 1e-6,
CONFIG['INCAR'] = {
'EDIFF': 1e-6,
#'ENCUT': 520, # MP compatibility
'ISMEAR': -5,
"IBRION": 2,
'LREAL': False,
'ALGO': 'NORMAL',
# other settings from MPStaticSet
"LAECHG": True,
"LCHARG": True,
"LWAVE": False,
"LORBIT": 11,
"LVHAR": True,
"ICHARG": 0,
"NSW": 99,
#"MAGMOM": CONFIG['INCAR']['MAGMOM'],
"ISPIN": 2,
"ISIF": 2,
"PREC": "High"
}
# now we reset the potentials
CONFIG['POTCAR_FUNCTIONAL'] = 'PBE'
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, a_kwargs={}, **kwargs):
# pop the old kwargs, backwards compatibility from the complex StaticSet
self.a_kwargs = a_kwargs
uis = copy.deepcopy(kwargs.get('user_incar_settings', {}))
new_config = copy.deepcopy(ElasticSet.CONFIG)
if metal_check(structure): grid_density = 15625
else: grid_density = 8000
user_kpoints_settings = kwargs.get('user_kpoints_settings', {})
grid_density = user_kpoints_settings.get(
'grid_density') or grid_density
old_kwargs = ['prev_incar', 'prev_kpoints', 'grid_density', 'lepsilon', 'lcalcpol', \
'user_incar_settings', 'user_kpoints_settings']
for k in old_kwargs:
try:
kwargs.pop(k)
except KeyError:
pass
self.kwargs = copy.deepcopy(kwargs)
if 'ISPIN' not in uis:
if magnetic_check(structure):
uis.update({'ISPIN': 2})
else:
uis.update({'ISPIN': 1})
if 'magmom' in uis:
if 'MAGMOM' in new_config['INCAR']:
new_config['INCAR'].pop('MAGMOM')
elif uis['ISPIN'] == 1:
if 'MAGMON' in uis.keys(): uis.pop['MAGMOM']
if 'MAGMON' in new_config['INCAR']:
new_config['INCAR'].pop['MAGMOM']
for key in uis.keys():
if key == 'ENCUT': continue
if key not in new_config['INCAR']:
if key in {'NELM', 'EDIFF', 'NEDOS', 'KPOINT_BSE'}: continue
new_config['INCAR'][key] = uis[key]
elif key == 'ISPIN':
new_config['INCAR'][key] = uis[key]
elif key == 'ISMEAR':
new_config['INCAR'][key] = uis[key]
elif key == 'SIGMA':
new_config['INCAR'][key] = uis[key]
#avoid conflict betwwen HIHG and ENCUT
"""
for key in uis.keys():
if key == 'PREC':
new_config['INCAR'][key] = uis[key]
if 'ENCUT' in new_config['INCAR'] : new_config['INCAR'].pop('ENCUT')
"""
if 'SIGMA' in new_config['INCAR'] and 'ISMEAR' in new_config['INCAR']:
if new_config['INCAR']['ISMEAR'] == -5:
new_config['INCAR'].pop('SIGMA')
from pymatgen.io.vasp.inputs import Kpoints
kpoints = Kpoints(kpts=[
[31, 31, 31],
])
new_config['KPOINTS'] = kpoints
from pymatgen.io.vasp.inputs import Kpoints
settings = self.a_kwargs.get('settings', {})
new_vasp_settings = settings.get('Elastic_settings', None) or uis.get(
'Elastic_settings', None)
if new_vasp_settings:
for ff in new_vasp_settings:
if ff.lower() == 'prec':
if 'ENCUT' in new_config['INCAR']:
new_config['INCAR'].pop('ENCUT')
new_config['INCAR'].update({ff: new_vasp_settings.get(ff)})
elif ff == 'grid_density':
new_config['KPOINTS'].update(
{ff: new_vasp_settings.get(ff)})
elif ff == 'k_mesh':
kpoints = Kpoints(kpts=new_vasp_settings.get(ff))
new_config['KPOINTS'] = kpoints
else:
new_config['INCAR'].update({ff: new_vasp_settings.get(ff)})
pot = self.kwargs.get('user_potcar_functional', None)
if pot:
new_config['POTCAR_FUNCTIONAL'] = pot
super(ElasticSet, self).__init__(structure,
new_config,
sort_structure=False,
**self.kwargs)
self.config = new_config
class BornChargeSet(DictSet):
"""Set tuned for metal relaxations (correct smearing).
Add `isif` parameter to the set to easily allow for overriding ISIF setting.
Kpoints have a 6000 reciprocal density default.
Provide by Yi Wang, Aug. 24, 2020
"""
CONFIG = _load_yaml_config("MPRelaxSet")
CONFIG['KPOINTS'].update({
'grid_density': 8000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].update({
"LEPSILON": True, #For Born Effective Charge
"NCORE": 1,
#"NPAR": 1,
#"LCALCEPS": True, #For Born Effective Charge
"LRPA": False,
'EDIFF_PER_ATOM': 1e-6,
#'ENCUT': 520, # MP compatibility
'ISMEAR': 0,
"NSW": 0,
"LORBIT": 11,
"IBRION": -1,
'LREAL': False,
'ALGO': 'NORMAL',
# other settings from MPStaticSet
"LCHARG": False,
"LWAVE": False,
"ICHARG": 2,
"PREC": "High"
})
CONFIG['POTCAR_FUNCTIONAL'] = 'PBE'
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, isif=2, a_kwargs={}, **kwargs):
# pop the old kwargs, backwards compatibility from the complex StaticSet
self.a_kwargs = a_kwargs
self.isif = isif
uis = copy.deepcopy(kwargs.get('user_incar_settings', {}))
new_config = copy.deepcopy(BornChargeSet.CONFIG)
"""
old_kwargs = ['prev_incar', 'prev_kpoints', 'grid_density', 'lepsilon', 'lcalcpol', \
'user_potcar_functional', 'user_incar_settings']
"""
old_kwargs = [
'prev_incar', 'prev_kpoints', 'grid_density', 'lepsilon',
'lcalcpol'
]
for k in old_kwargs:
try:
kwargs.pop(k)
except KeyError:
pass
self.kwargs = copy.deepcopy(kwargs)
if 'LCALCEPS' in uis:
if 'LEPSILON' in new_config['INCAR']:
new_config['INCAR'].pop('LEPSILON')
if 'ISPIN' not in uis:
if magnetic_check(structure):
uis.update({'ISPIN': 2})
else:
uis.update({'ISPIN': 1})
if 'magmom' in uis:
if 'MAGMOM' in new_config['INCAR']:
new_config['INCAR'].pop('MAGMOM')
elif uis['ISPIN'] == 1:
if 'MAGMON' in uis.keys(): uis.pop['MAGMOM']
if 'MAGMON' in new_config['INCAR']:
new_config['INCAR'].pop['MAGMOM']
for key in uis.keys():
if key == 'ENCUT': continue
if key not in new_config['INCAR']:
if key in {'NELM', 'EDIFF', 'NEDOS', 'KPOINT_BSE'}: continue
new_config['INCAR'][key] = uis[key]
elif key == 'ISPIN':
new_config['INCAR'][key] = uis[key]
elif key == 'ISMEAR':
new_config['INCAR'][key] = uis[key]
elif key == 'SIGMA':
new_config['INCAR'][key] = uis[key]
if 'SIGMA' in new_config['INCAR'] and 'ISMEAR' in new_config['INCAR']:
if new_config['INCAR']['ISMEAR'] == -5:
new_config['INCAR'].pop('SIGMA')
from pymatgen.io.vasp.inputs import Kpoints
settings = self.a_kwargs.get('settings', {})
new_vasp_settings = settings.get('Born_settings', None) or uis.get(
'Born_settings', None)
if new_vasp_settings:
for ff in new_vasp_settings:
if ff.lower() == 'prec':
if 'ENCUT' in new_config['INCAR']:
new_config['INCAR'].pop('ENCUT')
new_config['INCAR'].update({ff: new_vasp_settings.get(ff)})
elif ff == 'grid_density':
new_config['KPOINTS'].update(
{ff: new_vasp_settings.get(ff)})
elif ff == 'k_mesh':
kpoints = Kpoints(kpts=new_vasp_settings.get(ff))
new_config['KPOINTS'] = kpoints
else:
new_config['INCAR'].update({ff: new_vasp_settings.get(ff)})
pot = self.kwargs.get('user_potcar_functional', None)
if pot:
new_config['POTCAR_FUNCTIONAL'] = pot
super(BornChargeSet, self).__init__(structure,
new_config,
sort_structure=False,
**self.kwargs)
class StaticSet(DictSet):
"""Set tuned for metal relaxations (correct smearing).
Add `isif` parameter to the set to easily allow for overriding ISIF setting.
Kpoints have a 6000 reciprocal density default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
CONFIG['KPOINTS'].update({
'grid_density': 8000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].update({
'EDIFF_PER_ATOM': 1e-6,
'ENCUT': 520, # MP compatibility
'ISMEAR': -5,
"NSW": 0,
"IBRION": -1,
'LREAL': False,
'ALGO': 'NORMAL',
# other settings from MPStaticSet
"LAECHG": True,
"LCHARG": True,
"LWAVE": False,
"LORBIT": 11,
"LVHAR": True,
"ICHARG": 2,
"NEDOS": 5001,
})
# now we reset the potentials
CONFIG['POTCAR_FUNCTIONAL'] = 'PBE'
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, isif=2, a_kwargs={}, **kwargs):
# pop the old kwargs, backwards compatibility from the complex StaticSet
self.isif = isif
self.a_kwargs = a_kwargs
old_kwargs = [
'prev_incar', 'prev_kpoints', 'grid_density', 'lepsilon',
'lcalcpol'
]
for k in old_kwargs:
try:
kwargs.pop(k)
except KeyError:
pass
self.kwargs = copy.deepcopy(kwargs)
uis = copy.deepcopy(self.kwargs.get('user_incar_settings', {}))
uis['ISIF'] = isif
new_config = copy.deepcopy(StaticSet.CONFIG)
if 'ISPIN' not in uis:
if magnetic_check(structure):
uis.update({'ISPIN': 2})
else:
uis.update({'ISPIN': 1})
if 'magmom' in uis:
if 'MAGMOM' in new_config['INCAR']:
new_config['INCAR'].pop('MAGMOM')
elif uis['ISPIN'] == 1:
if 'MAGMON' in uis.keys(): uis.pop['MAGMOM']
if 'MAGMON' in new_config['INCAR']:
new_config['INCAR'].pop['MAGMOM']
settings = self.a_kwargs.get('settings', {})
new_vasp_settings = settings.get('Static_settings', None) or uis.get(
'Static_settings', None)
if new_vasp_settings:
for ff in new_vasp_settings:
if ff.lower() == 'prec':
if 'ENCUT' in new_config['INCAR']:
new_config['INCAR'].pop('ENCUT')
new_config['INCAR'].update({ff: new_vasp_settings.get(ff)})
elif ff == 'grid_density':
new_config['KPOINTS'].update(
{ff: new_vasp_settings.get(ff)})
elif ff == 'k_mesh':
kpoints = Kpoints(kpts=new_vasp_settings.get(ff))
new_config['KPOINTS'] = kpoints
else:
new_config['INCAR'].update({ff: new_vasp_settings.get(ff)})
new_config['INCAR'].update(uis)
pot = self.kwargs.get('user_potcar_functional', None)
if pot:
new_config['POTCAR_FUNCTIONAL'] = pot
super(StaticSet, self).__init__(structure,
new_config,
sort_structure=False,
**self.kwargs)
self.config = new_config
class ForceConstantsSet(DictSet):
"""
Set for calculating force constants calculations.
Force constants are calculated by the finite difference method with symmetry considered.
The smearing must be set to give the correct forces.
The default is tuned for metals.
Kpoints have a 8000 kpoints per reciprocal atom default.
"""
CONFIG = _load_yaml_config("MPRelaxSet")
# we never are comparing relaxations, only using them for optimizing structures.
CONFIG['KPOINTS'].update({
'grid_density': 8000,
})
CONFIG['KPOINTS'].pop('reciprocal_density') # to be explicit
CONFIG['INCAR'].pop('ENCUT') # use the ENCUT set by PREC
CONFIG['INCAR'].update({
'EDIFF': 5e-7,
'ISMEAR': 1,
'SIGMA': 0.2,
'LREAL': False,
"LORBIT": 11,
'ISIF': 2, # only calculate the forces, stress tensor is not needed
'IBRION':
6, # calculate force constants by finite differences with symmetry
'POTIM': 0.015, # displacement distance
'NFREE': 2, # how many displacments to do. 2 gives +POTIM and -POTIM
'NSW': 1, # backwards compatibility setting
'PREC': 'Accurate',
'ALGO': 'Fast',
'SYMPREC':
1e-4, # some supercells seem to have issues with primcel VASP algorithm
"ICHARG": 2,
})
# now we reset the potentials
CONFIG['POTCAR_FUNCTIONAL'] = 'PBE'
CONFIG['POTCAR'].update(POTCAR_UPDATES)
def __init__(self, structure, a_kwargs={}, **kwargs):
self.kwargs = copy.deepcopy(kwargs)
self.a_kwargs = a_kwargs
uis = copy.deepcopy(self.kwargs.get('user_incar_settings', {}))
new_config = copy.deepcopy(ForceConstantsSet.CONFIG)
if 'ISPIN' not in uis:
if magnetic_check(structure):
uis.update({'ISPIN': 2})
else:
uis.update({'ISPIN': 1})
if 'magmom' in uis:
if 'MAGMOM' in new_config['INCAR']:
new_config['INCAR'].pop('MAGMOM')
elif uis['ISPIN'] == 1:
if 'MAGMON' in uis.keys(): uis.pop['MAGMOM']
if 'MAGMON' in new_config['INCAR']:
new_config['INCAR'].pop['MAGMOM']
new_config['INCAR'].update(uis)
from pymatgen.io.vasp.inputs import Kpoints
"""
user_kpoints_settings = kwargs.get('user_kpoints_settings', {})
grid_density = user_kpoints_settings.get('grid_density') or None
if grid_density is not None:
#new_config['KPOINTS'].update({'grid_density': grid_density})
new_config['INCAR'].update({'PREC': 'High'})
kpoints = Kpoints.automatic_gamma_density(structure, grid_density)
new_config['KPOINTS'] = kpoints
"""
settings = self.a_kwargs.get('settings', {})
new_vasp_settings = settings.get('Forceconstant_settings',
None) or uis.get(
'Forceconstant_settings', None)
if new_vasp_settings:
for ff in new_vasp_settings:
if ff.lower() == 'prec':
if 'ENCUT' in new_config['INCAR']:
new_config['INCAR'].pop('ENCUT')
new_config['INCAR'].update({ff: new_vasp_settings.get(ff)})
elif ff == 'grid_density':
new_config['KPOINTS'].update(
{ff: new_vasp_settings.get(ff)})
elif ff == 'k_mesh':
kpoints = Kpoints(kpts=new_vasp_settings.get(ff))
new_config['KPOINTS'] = kpoints
else:
new_config['INCAR'].update({ff: new_vasp_settings.get(ff)})
else:
kpoints = Kpoints(kpts=[
[3, 3, 3],
])
new_config['KPOINTS'] = kpoints
pot = self.kwargs.get('user_potcar_functional', None)
if pot:
new_config['POTCAR_FUNCTIONAL'] = pot
super(ForceConstantsSet, self).__init__(structure,
new_config,
sort_structure=False,
force_gamma=True,
**self.kwargs)
