def __init__(self,
structure,
parents,
name="hse gap",
vasp_cmd="vasp",
db_file=None,
**kwargs):
"""
For getting a more accurate band gap with HSE - requires previous
calculation that gives VBM/CBM info. Note that this method is not
intended for energies, etc. due to sparse k-mesh.
Args:
structure (Structure): Input structure.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
name (str): Name for the Firework.
vasp_cmd (str): Command to run vasp.
db_file (str): Path to file specifying db credentials.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
t.append(CopyVaspOutputs(calc_loc=True, additional_files=["CHGCAR"]))
t.append(WriteVaspHSEBSFromPrev(prev_calc_dir='.'))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDbTask(db_file=db_file,
additional_fields={"task_label": name}))
super(HSEBSFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
structure,
name="boltztrap",
db_file=None,
parents=None,
**kwargs):
"""
Run Boltztrap
Args:
structure: (Structure) - only used for setting name of FW
name: (str) name of this FW
parents (Firework): Parents of this particular Firework. FW or list of FWS.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True))
t.append(RunBoltztrap())
t.append(BoltztrapToDBTask(db_file=db_file))
t.append(PassCalcLocs(name=name))
super(BoltztrapFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
structure,
name="nscf",
mode="uniform",
vasp_cmd="vasp",
copy_vasp_outputs=True,
db_file=None,
parents=None,
**kwargs):
"""
Standard NonSCF Calculation Firework supporting both
uniform and line modes.
Args:
structure (Structure): Input structure.
name (str): Name for the Firework.
mode (str): uniform or line mode.
vasp_cmd (str): Command to run vasp.
copy_vasp_outputs (bool): Whether to copy outputs from previous
run. Defaults to True.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
if copy_vasp_outputs:
t.append(
CopyVaspOutputs(calc_loc=True, additional_files=["CHGCAR"]))
mode = mode.lower()
if mode == "uniform":
t.append(
WriteVaspNSCFFromPrev(prev_calc_dir=".",
mode="uniform",
reciprocal_density=1000))
else:
t.append(
WriteVaspNSCFFromPrev(prev_calc_dir=".",
mode="line",
reciprocal_density=20))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd,
auto_npar=">>auto_npar<<"))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDbTask(db_file=db_file,
additional_fields={"task_label": name + " " + mode},
parse_dos=(mode == "uniform"),
bandstructure_mode=mode))
super(NonSCFFW, self).__init__(
t,
parents=parents,
name="%s-%s %s" %
(structure.composition.reduced_formula, name, mode),
**kwargs)
def __init__(self,
structure,
magmom,
name="spinorbit coupling",
saxis=(0, 0, 1),
vasp_cmd="vasp_ncl",
copy_vasp_outputs=True,
db_file=None,
parents=None,
**kwargs):
"""
Firework for spin orbit coupling calculation.
Args:
structure (Structure): Input structure.
name (str): Name for the Firework.
vasp_cmd (str): Command to run vasp.
copy_vasp_outputs (bool): Whether to copy outputs from previous
run. Defaults to True.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
if parents:
if copy_vasp_outputs:
t.append(
CopyVaspOutputs(calc_loc=True,
additional_files=["CHGCAR"],
contcar_to_poscar=True))
t.append(
WriteVaspSOCFromPrev(prev_calc_dir=".",
magmom=magmom,
saxis=saxis))
else:
vasp_input_set = MPSOCSet(structure)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.extend([
RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<"),
PassCalcLocs(name=name),
VaspToDbTask(db_file=db_file,
additional_fields={"task_label": name})
])
super(SOCFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
**kwargs)
def __init__(self,
structure,
name="structure optimization",
vasp_input_set=None,
vasp_cmd="vasp",
override_default_vasp_params=None,
ediffg=None,
db_file=None,
parents=None,
**kwargs):
"""
Standard structure optimization Firework.
Args:
structure (Structure): Input structure.
name (str): Name for the Firework.
vasp_input_set (VaspInputSet): input set to use.
Defaults to MPRelaxSet() if None.
override_default_vasp_params (dict): If this is not None,
these params are passed to the default vasp_input_set, i.e.,
MPRelaxSet. This allows one to easily override some
settings, e.g., user_incar_settings, etc.
vasp_cmd (str): Command to run vasp.
ediffg (float): Shortcut to set ediffg in certain jobs
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or MPRelaxSet(
structure, force_gamma=True, **override_default_vasp_params)
t = []
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
job_type="double_relaxation_run",
max_force_threshold=0.25,
ediffg=ediffg,
auto_npar=">>auto_npar<<"))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDbTask(db_file=db_file,
additional_fields={"task_label": name}))
super(OptimizeFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def test_passcalclocs(self):
fw1 = Firework([PassCalcLocs(name="fw1")], name="fw1")
fw2 = Firework([PassCalcLocs(name="fw2")], name="fw2", parents=fw1)
fw3 = Firework([PassCalcLocs(name="fw3")], name="fw3", parents=fw2)
wf = Workflow([fw1, fw2, fw3])
self.lp.add_wf(wf)
rapidfire(self.lp)
fw2 = self.lp.get_fw_by_id(self.lp.get_fw_ids({"name": "fw2"})[0])
fw3 = self.lp.get_fw_by_id(self.lp.get_fw_ids({"name": "fw3"})[0])
self.assertEqual(len(fw2.spec["calc_locs"]), 1)
self.assertEqual(len(fw3.spec["calc_locs"]), 2)
self.assertEqual(fw3.spec["calc_locs"][0]["name"], "fw1")
self.assertEqual(fw3.spec["calc_locs"][1]["name"], "fw2")
self.assertNotEqual(fw3.spec["calc_locs"][0]["path"],
fw3.spec["calc_locs"][1]["path"])
calc_locs = fw3.spec["calc_locs"]
self.assertEqual(get_calc_loc("fw1", calc_locs), calc_locs[0])
self.assertEqual(get_calc_loc("fw2", calc_locs), calc_locs[1])
self.assertEqual(get_calc_loc(True, calc_locs), calc_locs[1])
def __init__(self,
structure,
name="static",
vasp_input_set=None,
vasp_cmd="vasp",
copy_vasp_outputs=True,
db_file=None,
parents=None,
**kwargs):
"""
Standard static calculation Firework.
Args:
structure (Structure): Input structure.
name (str): Name for the Firework.
vasp_input_set (VaspInputSet): input set to use (for jobs w/no parents)
Defaults to MPStaticSet() if None.
vasp_cmd (str): Command to run vasp.
copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
if parents:
if copy_vasp_outputs:
t.append(CopyVaspOutputs(calc_loc=True,
contcar_to_poscar=True))
t.append(WriteVaspStaticFromPrev(prev_calc_dir='.'))
else:
vasp_input_set = MPStaticSet(structure) or vasp_input_set
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd,
auto_npar=">>auto_npar<<"))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDbTask(db_file=db_file,
additional_fields={"task_label": name}))
super(StaticFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
structure,
start_temp,
end_temp,
nsteps,
name="molecular dynamics run",
vasp_input_set=None,
vasp_cmd="vasp",
override_default_vasp_params=None,
wall_time=19200,
db_file=None,
parents=None,
copy_vasp_outputs=True,
**kwargs):
"""
Standard firework for a single MD run.
Args:
structure (Structure): Input structure.
start_temp (float): Start temperature of MD run.
end_temp (float): End temperature of MD run.
nsteps (int): Number of MD steps
name (string): Name for the Firework.
vasp_input_set (string): string name for the VASP input set (e.g.,
"MITMDVaspInputSet").
vasp_cmd (string): Command to run vasp.
override_default_vasp_params (dict): If this is not None,
these params are passed to the default vasp_input_set, i.e.,
MITMDSet. This allows one to easily override some
settings, e.g., user_incar_settings, etc. Particular to MD,
one can control time_step and all other settings of the input set.
wall_time (int): Total wall time in seconds.
copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True.
db_file (string): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or MITMDSet(
structure,
start_temp=start_temp,
end_temp=end_temp,
nsteps=nsteps,
**override_default_vasp_params)
t = []
if parents:
if copy_vasp_outputs:
t.append(
CopyVaspOutputs(calc_loc=True,
additional_files=["CHGCAR"],
contcar_to_poscar=True))
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
gamma_vasp_cmd=">>gamma_vasp_cmd<<",
handler_group="md",
wall_time=wall_time))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDbTask(db_file=db_file,
additional_fields={"task_label": name},
defuse_unsuccessful=False))
super(MDFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
**kwargs)
def __init__(self,
structure,
transformations,
transformation_params=None,
vasp_input_set=None,
name="structure transmuter",
vasp_cmd="vasp",
copy_vasp_outputs=True,
db_file=None,
parents=None,
override_default_vasp_params=None,
**kwargs):
"""
Apply the transformations to the input structure, write the input set corresponding
to the transformed structure and run vasp on them.
Args:
structure (Structure): Input structure.
transformations (list): list of names of transformation classes as defined in
the modules in pymatgen.transformations.
eg: transformations=['DeformStructureTransformation', 'SupercellTransformation']
transformation_params (list): list of dicts where each dict specify the input parameters to
instantiate the transformation class in the transformations list.
vasp_input_set (VaspInputSet): VASP input set, used to write the input set for the
transmuted structure.
name (string): Name for the Firework.
vasp_cmd (string): Command to run vasp.
copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True.
db_file (string): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
override_default_vasp_params (dict): additional user input settings for vasp_input_set.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
vasp_input_set = vasp_input_set or MPStaticSet(
structure, force_gamma=True, **override_default_vasp_params)
if parents:
if copy_vasp_outputs:
t.append(CopyVaspOutputs(calc_loc=True,
contcar_to_poscar=True))
t.append(
WriteTransmutedStructureIOSet(
structure=structure,
transformations=transformations,
transformation_params=transformation_params,
vasp_input_set=vasp_input_set,
override_default_vasp_params=override_default_vasp_params,
prev_calc_dir="."))
else:
t.append(
WriteTransmutedStructureIOSet(
structure=structure,
transformations=transformations,
transformation_params=transformation_params,
vasp_input_set=vasp_input_set,
override_default_vasp_params=override_default_vasp_params))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDbTask(db_file=db_file,
additional_fields={
"task_label": name,
"transmuter": {
"transformations": transformations,
"transformation_params": transformation_params
}
}))
super(TransmuterFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
structure,
name="static dielectric",
vasp_cmd="vasp",
copy_vasp_outputs=True,
db_file=None,
parents=None,
phonon=False,
mode=None,
displacement=None,
**kwargs):
"""
Standard static calculation Firework for dielectric constants using DFPT.
Args:
structure (Structure): Input structure.
name (str): Name for the Firework.
vasp_cmd (str): Command to run vasp.
copy_vasp_outputs (bool): Whether to copy outputs from previous
run. Defaults to True.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
phonon (bool): Whether or not to extract normal modes and pass it. This argument along
with the mode and displacement arguments must be set for the calculation of
dielectric constant in the Raman tensor workflow.
mode (int): normal mode index.
displacement (float): displacement along the normal mode in Angstroms.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
if parents:
if copy_vasp_outputs:
t.append(
CopyVaspOutputs(calc_loc=True,
additional_files=["CHGCAR"],
contcar_to_poscar=True))
t.append(
WriteVaspStaticFromPrev(prev_calc_dir=".", lepsilon=True))
else:
vasp_input_set = MPStaticSet(structure, lepsilon=True)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if phonon:
if mode is None and displacement is None:
name = "{} {}".format("phonon", name)
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
else:
name = "raman_{}_{} {}".format(str(mode), str(displacement),
name)
t.extend([
WriteNormalmodeDisplacedPoscar(mode=mode,
displacement=displacement),
RunVaspCustodian(vasp_cmd=vasp_cmd),
PassEpsilonTask(mode=mode, displacement=displacement)
])
t.append(PassNormalmodesTask())
else:
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
t.extend([
PassCalcLocs(name=name),
VaspToDbTask(db_file=db_file,
additional_fields={"task_label": name})
])
super(LepsFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
**kwargs)