def test_ioset_explicit(self):
ft = WriteVaspFromIOSet(
dict(structure=self.struct_si,
vasp_input_set=MPRelaxSet(self.struct_si, force_gamma=True)))
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files()
def test_ioset_explicit(self):
ft = WriteVaspFromIOSet(
dict(structure=self.struct_si, vasp_input_set=MPRelaxSet(self.struct_si, force_gamma=True))
)
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files()
def test_potcar_spec(self):
ft = WriteVaspFromIOSet(
structure=self.struct_si,
vasp_input_set="MPRelaxSet",
potcar_spec=True,
)
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files(potcar_spec=True)
def test_ioset_params(self):
ft = WriteVaspFromIOSet(
dict(structure=self.struct_si, vasp_input_set="MPRelaxSet",
vasp_input_params={"user_incar_settings": {"ISMEAR": 1000}}))
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
incar = Incar.from_file("INCAR")
self.assertEqual(incar["ISMEAR"], 1000) # make sure override works
incar['ISMEAR'] = -5 # switch back to default
incar.write_file("INCAR")
self._verify_files(skip_kpoints=True)
def test_ioset_params(self):
ft = WriteVaspFromIOSet(
dict(structure=self.struct_si, vasp_input_set="MPRelaxSet",
vasp_input_params={"user_incar_settings": {"ISMEAR": 1000}}))
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
incar = Incar.from_file("INCAR")
self.assertEqual(incar["ISMEAR"], 1000) # make sure override works
incar['ISMEAR'] = -5 # switch back to default
incar.write_file("INCAR")
self._verify_files(skip_kpoints=True)
def __init__(self,
structure,
name="structure optimization",
vasp_input_set=None,
vasp_cmd=VASP_CMD,
override_default_vasp_params=None,
ediffg=None,
db_file=DB_FILE,
force_gamma=True,
job_type="double_relaxation_run",
max_force_threshold=RELAX_MAX_FORCE,
auto_npar=">>auto_npar<<",
half_kpts_first_relax=HALF_KPOINTS_FIRST_RELAX,
parents=None,
**kwargs):
"""
Optimize the given structure.
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 to place output parsing.
force_gamma (bool): Force gamma centered kpoint generation
job_type (str): custodian job type (default "double_relaxation_run")
max_force_threshold (float): max force on a site allowed at end; otherwise, reject job
auto_npar (bool or str): whether to set auto_npar. defaults to env_chk: ">>auto_npar<<"
half_kpts_first_relax (bool): whether to use half the kpoints for the first relaxation
parents ([Firework]): Parents of this particular Firework.
\*\*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=force_gamma, **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=job_type,
max_force_threshold=max_force_threshold,
ediffg=ediffg,
auto_npar=auto_npar,
half_kpts_first_relax=half_kpts_first_relax))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(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 __init__(self, structure=None, prev_calc_dir=None, name="static dielectric", vasp_cmd=VASP_CMD,
copy_vasp_outputs=True, lepsilon=True,
db_file=DB_FILE, parents=None, user_incar_settings=None,
pass_nm_results=False, **kwargs):
"""
Static DFPT calculation Firework
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
name (str): Name for the Firework.
lepsilon (bool): Turn on LEPSILON to calculate polar properties
vasp_cmd (str): Command to run vasp.
copy_vasp_outputs (str or bool): Whether to copy outputs from previous
run. Defaults to True.
prev_calc_dir (str): Path to a previous calculation to copy from
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
user_incar_settings (dict): Parameters in INCAR to override
pass_nm_results (bool): if true the normal mode eigen vals and vecs are passed so that
next firework can use it.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
name = "static dielectric" if lepsilon else "phonon"
fw_name = "{}-{}".format(structure.composition.reduced_formula if structure else "unknown", name)
user_incar_settings = user_incar_settings or {}
t = []
if prev_calc_dir:
t.append(CopyVaspOutputs(calc_dir=prev_calc_dir, contcar_to_poscar=True))
t.append(WriteVaspStaticFromPrev(lepsilon=lepsilon, other_params={
'user_incar_settings': user_incar_settings, 'force_gamma': True}))
elif parents and copy_vasp_outputs:
t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True))
t.append(WriteVaspStaticFromPrev(lepsilon=lepsilon, other_params={
'user_incar_settings': user_incar_settings, 'force_gamma': True}))
elif structure:
vasp_input_set = MPStaticSet(structure, lepsilon=lepsilon, force_gamma=True,
user_incar_settings=user_incar_settings)
t.append(WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
else:
raise ValueError("Must specify structure or previous calculation")
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
if pass_nm_results:
t.append(pass_vasp_result({"structure": "a>>final_structure",
"eigenvals": "a>>normalmode_eigenvals",
"eigenvecs": "a>>normalmode_eigenvecs"},
parse_eigen=True,
mod_spec_key="normalmodes"))
t.append(PassCalcLocs(name=name))
t.append(VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
super(DFPTFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
def __init__(self,
structure,
name="static",
vasp_input_set=None,
vasp_cmd="vasp",
prev_calc_loc=True,
db_file=None,
parents=None,
**kwargs):
"""
Standard static calculation Firework - either from a previous location or from a structure.
Args:
structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
is only used to set the name of the FW and any structure with the same composition
can be used.
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.
prev_calc_loc (bool or str): If true (default), copies outputs from previous calc. If
a str value, grabs a previous calculation output by name. If False/None, will create
new static calculation using the provided structure.
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__.
"""
# TODO: @computron - I really don't like how you need to set the structure even for
# prev_calc_loc jobs. Sometimes it makes appending new FWs to an existing workflow
# difficult. Maybe think about how to remove this need? -computron
t = []
if parents:
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(WriteVaspStaticFromPrev())
else:
vasp_input_set = vasp_input_set or MPStaticSet(structure)
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(
VaspToDb(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,
scale_lattice=None,
name="static",
vasp_input_set=None,
vasp_cmd="vasp",
metadata=None,
prev_calc_loc=True,
db_file=None,
parents=None,
**kwargs):
# TODO: @computron - I really don't like how you need to set the structure even for
# prev_calc_loc jobs. Sometimes it makes appending new FWs to an existing workflow
# difficult. Maybe think about how to remove this need? -computron
metadata = metadata or {}
vasp_input_set = vasp_input_set or StaticSet(structure)
site_properties = deepcopy(structure).site_properties
t = []
if parents:
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspFromIOSetPrevStructure(
vasp_input_set=vasp_input_set,
site_properties=site_properties))
else:
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if scale_lattice is not None:
t.append(ScaleVolumeTransformation(scale_factor=scale_lattice))
t.append(ModifyIncar(incar_update=">>incar_update<<"))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
auto_npar=">>auto_npar<<",
gzip_output=False))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(
db_file=db_file,
parse_dos=True,
additional_fields={
"task_label": name,
"metadata": metadata
},
))
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",
vasp_input_set=None, vasp_cmd=VASP_CMD,
override_default_vasp_params=None,
wall_time=19200, db_file=DB_FILE, 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 before writing STOPCAR.
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 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(VaspToDb(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,
name="structure optimization",
vasp_input_set=None,
job_type="normal",
vasp_cmd="vasp",
isif=None,
metadata=None,
override_default_vasp_params=None,
db_file=None,
force_gamma=True,
parents=None,
**kwargs):
"""
Optimize the given structure.
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.
isif : int
Shortcut to override the ISIF parameter. Defaults to None.
Will take precedent over override_default_vasp_params
vasp_cmd (str): Command to run vasp.
db_file (str): Path to file specifying db credentials to place output parsing.
force_gamma (bool): Force gamma centered kpoint generation
parents ([Firework]): Parents of this particular Firework.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
metadata = metadata or {}
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or PRLRelaxSet(
structure, force_gamma=force_gamma, **override_default_vasp_params)
t = []
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if isif:
t.append(ModifyIncar(incar_update={'ISIF': isif}))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, job_type=job_type))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(db_file=db_file,
additional_fields={
"task_label": name,
"metadata": metadata
}))
super(OptimizeFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self, structure=None, name="static", vasp_input_set=None, vasp_input_set_params=None,
vasp_cmd=VASP_CMD, prev_calc_loc=True, prev_calc_dir=None, db_file=DB_FILE, vasptodb_kwargs=None,
parents=None, **kwargs):
"""
Standard static calculation Firework - either from a previous location or from a structure.
Args:
structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
is only used to set the name of the FW and any structure with the same composition
can be used.
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_input_set_params (dict): Dict of vasp_input_set kwargs.
vasp_cmd (str): Command to run vasp.
prev_calc_loc (bool or str): If true (default), copies outputs from previous calc. If
a str value, retrieves a previous calculation output by name. If False/None, will create
new static calculation using the provided structure.
prev_calc_dir (str): Path to a previous calculation to copy from
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
vasptodb_kwargs (dict): kwargs to pass to VaspToDb
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
vasp_input_set_params = vasp_input_set_params or {}
vasptodb_kwargs = vasptodb_kwargs or {}
if "additional_fields" not in vasptodb_kwargs:
vasptodb_kwargs["additional_fields"] = {}
vasptodb_kwargs["additional_fields"]["task_label"] = name
fw_name = "{}-{}".format(structure.composition.reduced_formula if structure else "unknown", name)
if prev_calc_dir:
t.append(CopyVaspOutputs(calc_dir=prev_calc_dir, contcar_to_poscar=True))
t.append(WriteVaspStaticFromPrev(other_params=vasp_input_set_params))
elif parents:
if prev_calc_loc:
t.append(CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(WriteVaspStaticFromPrev(other_params=vasp_input_set_params))
elif structure:
vasp_input_set = vasp_input_set or MPStaticSet(structure, **vasp_input_set_params)
t.append(WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
else:
raise ValueError("Must specify structure or previous calculation")
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<"))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(db_file=db_file, **vasptodb_kwargs))
super(StaticFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
def __init__(self,
structure,
magmom,
name="spin-orbit 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. If copy_vasp_outputs, used only to set the
name of the FW.
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 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),
VaspToDb(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="static",
previous_structure=False,
vasp_input_set=None,
vasp_cmd="vasp",
db_file=None,
parents=None,
override_default_vasp_params=None,
pass_structure=True,
prev_calc_loc=False,
**kwargs):
"""
This Firework is modified from atomate.vasp.fireworks.core.StaticFW to fit the needs of mpmorph
Standard static calculation Firework - either from a previous location or from a structure.
Args:
structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
is only used to set the name of the FW and any structure with the same composition
can be used.
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.
prev_calc_loc (bool or str): If true (default), copies outputs from previous calc. If
a str value, grabs a previous calculation output by name. If False/None, will create
new static calculation using the provided structure.
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 = []
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or MPStaticSet(
structure, **override_default_vasp_params)
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if previous_structure:
t.append(PreviousStructureTask())
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd,
auto_npar=">>auto_npar<<"))
t.append(SaveStructureTask())
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
name = f'{structure.composition.reduced_formula}-{name}'
super(StaticFW, self).__init__(t, parents=parents, name=name, **kwargs)
def __init__(self, spec, label, user_incar_settings=None,
user_kpoints_settings=None,
additional_cust_args=None, **kwargs):
"""
Args:
spec (dict): Specification of the job to run.
label (str): "parent", "ep0" or "ep1"
vasp_input_set (VaspInputSet): Input set to use.
user_kpoints_settings (dict): Additional KPOINTS settings.
additional_cust_args (dict): Other kwargs that are passed to RunVaspCustodian.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
# Get structure from spec
assert label in ["parent", "ep0", "ep1"]
structure_dict = spec[label]
structure = Structure.from_dict(structure_dict)
user_incar_settings = user_incar_settings or {}
user_kpoints_settings = user_kpoints_settings or {}
additional_cust_args = additional_cust_args or {}
# Task 1: Write input sets
if label == 'parent':
vasp_input_set = MITRelaxSet(structure,
user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings)
else: # label == "ep0" or "ep1"
from pymatgen_diffusion.neb.io import MVLCINEBEndPointSet
vasp_input_set = MVLCINEBEndPointSet(structure,
user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings)
write_ep_task = WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set)
# Task 2: Run VASP using Custodian
cust_args = {"job_type": "normal", "gzip_output": False,
"handler_group": "no_handler"}
cust_args.update(additional_cust_args)
run_vasp = RunVaspCustodian(vasp_cmd=">>vasp_cmd<<",
gamma_vasp_cmd=">>gamma_vasp_cmd<<",
**cust_args)
# Task 3, 4: Transfer and PassCalLocs
tasks = [write_ep_task, run_vasp, TransferNEBTask(label=label),
PassCalcLocs(name=label)]
super(NEBRelaxationFW, self).__init__(tasks, spec=spec, name=label,
**kwargs)
def __init__(self,
structure,
name="structure optimization",
vasp_input_set=None,
job_type="normal",
vasp_cmd="vasp",
metadata=None,
override_default_vasp_params=None,
db_file=None,
force_gamma=True,
prev_calc_loc=True,
parents=None,
db_insert=False,
**kwargs):
metadata = metadata or {}
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or PRLRelaxSet(
structure, force_gamma=force_gamma, **override_default_vasp_params)
t = []
if parents:
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set))
else:
vasp_input_set = vasp_input_set or PRLRelaxSet(structure)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
job_type=job_type,
gzip_output=False))
t.append(PassCalcLocs(name=name))
if db_insert:
t.append(
VaspToDb(db_file=db_file,
additional_fields={
"task_label": name,
"metadata": metadata
}))
super(PRLOptimizeFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
structure,
approx_neb_wf_uuid,
db_file=DB_FILE,
vasp_input_set=None,
vasp_cmd=VASP_CMD,
override_default_vasp_params=None,
job_type="double_relaxation_run",
additional_fields=None,
tags=None,
**kwargs):
"""
Launches a VASP calculation for the provided empty host structure
and adds task doc fields for approx_neb workflow record keeping.
Initializes a doc in the approx_neb collection and stores relevant
outputs from the host.
Args:
structure (Structure): structure of empty host
approx_neb_wf_uuid (str): unique id for approx neb
workflow record keeping
db_file (str): path to file containing the database
credentials.
vasp_input_set (VaspInputSet class): can use to
define VASP input parameters.
See pymatgen.io.vasp.sets module for more
information. MPRelaxSet() and
override_default_vasp_params are used if
vasp_input_set = None.
vasp_cmd (str): the name of the full executable for running
VASP.
override_default_vasp_params (dict): if provided,
vasp_input_set is disregarded and the Vasp Input
Set is created by passing
override_default_vasp_params to MPRelaxSet().
Allows for easy modification of MPRelaxSet().
For example, to set ISIF=2 in the INCAR use:
{"user_incar_settings":{"ISIF":2}}
job_type (str): custodian job type
additional_fields (dict): specifies more information
to be stored in the approx_neb collection to
assist user record keeping.
tags (list): list of strings to be stored in the
approx_neb collection under the "tags" field to
assist user record keeping.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
parents ([Firework]): Parents of this particular Firework.
"""
# set additional_fields to be added to task doc by VaspToDb
# initiates the information stored in the tasks collection to aid record keeping
fw_name = "{} {}".format(structure.composition.reduced_formula, "host")
fw_spec = {
"tags": ["approx_neb", approx_neb_wf_uuid, "host", "relaxation"]
}
task_doc_additional_fields = {
"approx_neb": {
"wf_uuids": [],
"_source_wf_uuid": approx_neb_wf_uuid,
"calc_type": "host",
"task_label": "relaxation",
}
}
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or MPRelaxSet(
structure, **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=job_type))
t.append(PassCalcLocs(name="host"))
t.append(
VaspToDb(
db_file=db_file,
additional_fields=task_doc_additional_fields,
parse_chgcar=True,
task_fields_to_push={"host_task_id": "task_id"},
))
t.append(
HostToDb(
db_file=db_file,
approx_neb_wf_uuid=approx_neb_wf_uuid,
additional_fields=additional_fields,
tags=tags,
))
super().__init__(tasks=t, spec=fw_spec, name=fw_name, **kwargs)
def __init__(self,
structure,
scale_lattice=None,
symmetry_tolerance=None,
name="structure optimization",
vasp_input_set=None,
job_type="normal",
vasp_cmd="vasp",
metadata=None,
override_default_vasp_params=None,
db_file=None,
record_path=False,
modify_incar=None,
force_gamma=True,
prev_calc_loc=True,
parents=None,
db_insert=False,
Pos_Shape_relax=False,
modify_incar_params={},
modify_kpoints_params={},
**kwargs):
metadata = metadata or {}
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or RelaxSet(
structure, force_gamma=force_gamma, **override_default_vasp_params)
site_properties = deepcopy(structure).site_properties
t = []
# Avoids delivery (prev_calc_loc == '' (instead by True))
if type(prev_calc_loc) == str:
t.append(
CopyVaspOutputs(calc_dir=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspFromIOSetPrevStructure(
vasp_input_set=vasp_input_set,
site_properties=site_properties))
elif parents:
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspFromIOSetPrevStructure(
vasp_input_set=vasp_input_set,
site_properties=site_properties))
else:
# vasp_input_set = vasp_input_set or RelaxSet(structure) # ??
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if scale_lattice is not None:
t.append(ScaleVolumeTransformation(scale_factor=scale_lattice))
t.append(ModifyIncar(incar_update=">>incar_update<<"))
if modify_incar != None:
t.append(ModifyIncar(incar_update=modify_incar))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
job_type=job_type,
gzip_output=False))
t.append(PassCalcLocs(name=name))
if record_path:
t.append(
Record_relax_running_path(db_file=db_file,
metadata=metadata,
Pos_Shape_relax=Pos_Shape_relax))
if db_insert:
t.append(
VaspToDb(db_file=db_file,
additional_fields={
"task_label": name,
"metadata": metadata
}))
# This has to happen at the end because dynamically adding Fireworks if the symmetry breaks skips the rest of the tasks in the Firework.
if symmetry_tolerance is not None:
t.append(
CheckSymmetry(tolerance=symmetry_tolerance,
vasp_cmd=vasp_cmd,
db_file=db_file,
structure=structure,
metadata=metadata,
name=name,
modify_incar_params=modify_incar_params,
modify_kpoints_params=modify_kpoints_params,
Pos_Shape_relax=Pos_Shape_relax))
super(OptimizeFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def test_ioset_implicit(self):
ft = WriteVaspFromIOSet(dict(structure=self.struct_si, vasp_input_set="MPRelaxSet"))
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files(skip_kpoints=True)
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,
user_incar_settings=None,
**kwargs):
"""
Standard static calculation Firework for dielectric constants using DFPT.
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
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.
user_incar_settings (dict): Parameters in INCAR to override
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
user_incar_settings = user_incar_settings or {}
t = []
if copy_vasp_outputs:
t.append(
CopyVaspOutputs(calc_loc=True,
additional_files=["CHGCAR"],
contcar_to_poscar=True))
t.append(
WriteVaspStaticFromPrev(
lepsilon=True,
other_params={'user_incar_settings': user_incar_settings}))
else:
vasp_input_set = MPStaticSet(
structure,
lepsilon=True,
user_incar_settings=user_incar_settings)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if phonon:
if mode is None and displacement is None:
# TODO: @matk86 - I really don't understand the point of setting phonon=True w/o
# the mode or displacement. It seems to simply be running a regular static run and
# doing nothing else than changing the name of the Firework and perhaps passing
# normal modes data (but it's unclear how that data is generated. Why would anyone
# want to do this? -computron
name = "{} {}".format("phonon", name)
# TODO: @matk86 - not sure why this line is here. I understand you are trying to
# keep the code short but the logic is very confusing. The RunVaspCustodian is
# common to all 3 situations (phonon=F, phonon=T/mode=F, phonon=T/mode=T) yet is
# duplicated in each place. Instead, for better clarity construct the Firework
# sequentially (write inputs, run vasp, parse output data, pass output data) and
# add if/else for phonons where it is needed. Any name overrides can go near the
# top of the Firework. -computron
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
t.append(
pass_vasp_result(
{
"structure": "a>>final_structure",
"eigenvals": "a>>normalmode_eigenvals",
"eigenvecs": "a>>normalmode_eigenvecs"
},
parse_eigen=True,
mod_spec_key="normalmodes"))
else:
# TODO: @matk86 - Why is this second calculation being tacked on to the first one?
# It looks like it will overwrite INCAR/CHGCAR/etc of the first calculation and
# thus completely remove access to the original output files. Shouldn't this be a
# new Firework rather than a second calculation in the same Firework? -computron
name = "raman_{}_{} {}".format(str(mode), str(displacement),
name)
key = "{}_{}".format(mode, displacement).replace('-',
'm').replace(
'.', 'd')
pass_fw = pass_vasp_result(pass_dict={
"mode": mode,
"displacement": displacement,
"epsilon": "a>>epsilon_static"
},
mod_spec_key="raman_epsilon->" +
key,
parse_eigen=True)
t.extend([
WriteNormalmodeDisplacedPoscar(mode=mode,
displacement=displacement),
RunVaspCustodian(vasp_cmd=vasp_cmd), pass_fw
])
else:
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
t.extend([
PassCalcLocs(name=name),
VaspToDb(db_file=db_file, additional_fields={"task_label": name})
])
super(LepsFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
**kwargs)
def __init__(self,
structure,
isif=4,
name="structure optimization",
override_symmetry_tolerances=None,
job_type="normal",
vasp_cmd="vasp_std",
metadata=None,
override_default_vasp_params=None,
db_file=None,
prev_calc_loc=True,
parents=None,
db_insert=False,
tag=None,
**kwargs):
metadata = metadata or {}
metadata = metadata or {}
tag = tag or metadata.get('tag')
# generate a tag with a warning
if tag is None:
tag = str(uuid4())
metadata['tag'] = tag
override_default_vasp_params = override_default_vasp_params or {}
override_symmetry_tolerances = override_symmetry_tolerances or {}
vasp_input_set = RelaxSet(structure,
isif=isif,
**override_default_vasp_params)
site_properties = deepcopy(structure).site_properties
t = []
if parents:
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspFromIOSetPrevStructure(
vasp_input_set=vasp_input_set,
site_properties=site_properties))
else:
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(ModifyIncar(incar_update=">>incar_update<<"))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
job_type=job_type,
gzip_output=False))
t.append(PassCalcLocs(name=name))
if db_insert:
t.append(
VaspToDb(db_file=db_file,
additional_fields={
"task_label": name,
"metadata": metadata
}))
common_kwargs = {
'vasp_cmd': vasp_cmd,
'db_file': db_file,
"metadata": metadata,
"tag": tag
}
relax_kwargs = {}
static_kwargs = {}
t.append(
CheckRelaxation(db_file=db_file,
metadata=metadata,
tag=tag,
common_kwargs=common_kwargs,
relax_kwargs=relax_kwargs,
static_kwargs=static_kwargs,
**override_symmetry_tolerances))
super().__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
structure,
start_temp,
end_temp,
nsteps,
name="molecular dynamics",
vasp_input_set=None,
vasp_cmd="vasp",
override_default_vasp_params=None,
wall_time=None,
db_file=None,
parents=None,
copy_vasp_outputs=False,
previous_structure=False,
insert_db=False,
save_structure=True,
**kwargs):
"""
This Firework is modified from atomate.vasp.fireworks.core.MDFW to fit the needs of mpmorph
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 before writing STOPCAR.
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 MPMDSet(
structure,
start_temp=start_temp,
end_temp=end_temp,
nsteps=nsteps,
**override_default_vasp_params)
t = []
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if previous_structure:
t.append(PreviousStructureTask())
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))
if save_structure:
t.append(SaveStructureTask())
name = f'{structure.composition.reduced_formula}-{name}'
if insert_db:
t.append(
VaspMDToDb(db_file=db_file,
additional_fields={"task_label": name},
defuse_unsuccessful=False,
md_structures=True))
super(MDFW, self).__init__(t, parents=parents, name=name, **kwargs)
def __init__(self,
structure=None,
mode="cs",
isotopes=None,
name="nmr tensor",
prev_calc_dir=None,
vasp_cmd="vasp",
copy_vasp_outputs=True,
db_file=None,
parents=None,
**kwargs):
"""
Firework for NMR tensor calculations
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
mode (str): the NMR calculation type: cs or efg, default is cs
isotopes (list): list of isotopes to include, default is to include the
lowest mass quadrupolar isotope for all applicable elements
name (str): Name for the Firework.
prev_calc_dir (str): Path to a previous calculation to copy from
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__.
"""
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown",
name)
isotopes = isotopes.split() if isinstance(isotopes, str) else isotopes
t = []
if prev_calc_dir:
t.append(
CopyVaspOutputs(calc_dir=prev_calc_dir,
contcar_to_poscar=True))
t.append(
WriteVaspNMRFromPrev(prev_calc_dir=".",
mode=mode,
isotopes=isotopes))
elif parents and copy_vasp_outputs:
t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True))
t.append(
WriteVaspNMRFromPrev(prev_calc_dir=".",
mode=mode,
isotopes=isotopes))
elif structure:
vasp_input_set = MPNMRSet(structure, mode=mode, isotopes=isotopes)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
else:
raise ValueError("Must specify structure or previous calculation.")
t.extend([
RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<"),
PassCalcLocs(name=name),
VaspToDb(db_file=db_file, additional_fields={"task_label": name})
])
super(NMRFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
def __init__(self,
structure,
name="structure optimization",
vasp_input_set=None,
insert_db=True,
vasp_cmd="vasp",
override_default_vasp_params=None,
ediffg=None,
db_file=None,
force_gamma=True,
job_type="double_relaxation_run",
max_force_threshold=None,
previous_structure=False,
auto_npar=">>auto_npar<<",
half_kpts_first_relax=False,
parents=None,
handler_group="default",
prev_calc_loc=False,
**kwargs):
"""
Optimize the given structure.
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 to place output parsing.
force_gamma (bool): Force gamma centered kpoint generation
job_type (str): custodian job type (default "double_relaxation_run")
max_force_threshold (float): max force on a site allowed at end; otherwise, reject job
auto_npar (bool or str): whether to set auto_npar. defaults to env_chk: ">>auto_npar<<"
half_kpts_first_relax (bool): whether to use half the kpoints for the first relaxation
parents ([Firework]): Parents of this particular Firework.
\*\*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=force_gamma, **override_default_vasp_params)
t = []
if prev_calc_loc:
additional_files = kwargs.get("additional_files", [])
if "additional_files" in kwargs.keys():
del kwargs["additional_files"]
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True,
additional_files=additional_files))
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if previous_structure:
t.append(PreviousStructureTask())
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
job_type=job_type,
max_force_threshold=max_force_threshold,
ediffg=ediffg,
auto_npar=auto_npar,
half_kpts_first_relax=half_kpts_first_relax,
handler_group=handler_group))
t.append(PassCalcLocs(name=name))
t.append(SaveStructureTask())
if insert_db:
t.append(
VaspToDb(db_file=db_file,
additional_fields={"task_label": name}))
name = f'{structure.composition.reduced_formula}-{name}'
super(OptimizeFW, self).__init__(t,
parents=parents,
name=name,
**kwargs)
def test_ioset_implicit(self):
ft = WriteVaspFromIOSet(structure=self.struct_si,
vasp_input_set="MPRelaxSet")
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files(skip_kpoints=True)
def __init__(self,
structure,
name="static dielectric",
vasp_cmd="vasp",
copy_vasp_outputs=True,
db_file=None,
parents=None,
user_incar_settings=None,
pass_nm_results=False,
**kwargs):
"""
Static DFPT calculation Firework
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
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.
user_incar_settings (dict): Parameters in INCAR to override
pass_nm_results (bool): if true the normal mode eigen vals and vecs are passed so that
next firework can use it.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
name = "{} {}".format("phonon", name)
user_incar_settings = user_incar_settings or {}
t = []
if copy_vasp_outputs:
t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True))
t.append(
WriteVaspStaticFromPrev(lepsilon=True,
other_params={
'user_incar_settings':
user_incar_settings,
'force_gamma': True
}))
else:
vasp_input_set = MPStaticSet(
structure,
lepsilon=True,
force_gamma=True,
user_incar_settings=user_incar_settings)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
if pass_nm_results:
t.append(
pass_vasp_result(
{
"structure": "a>>final_structure",
"eigenvals": "a>>normalmode_eigenvals",
"eigenvecs": "a>>normalmode_eigenvecs"
},
parse_eigen=True,
mod_spec_key="normalmodes"))
t.append(
VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
spec = kwargs.pop("spec", {})
spec.update({
"_files_out": {
"POSCAR": "CONTCAR",
"OUTCAR": "OUTCAR*",
'vasprunxml': "vasprun.xml*"
}
})
super(DFPTFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
spec=spec,
**kwargs)
def __init__(
self,
structure=None,
name="SCAN structure optimization",
vasp_input_set=None,
vasp_input_set_params=None,
vasp_cmd=VASP_CMD,
vdw_kernel_dir=VDW_KERNEL_DIR,
prev_calc_loc=None,
prev_calc_dir=None,
db_file=DB_FILE,
vasptodb_kwargs=None,
parents=None,
**kwargs,
):
"""
Structure optimization using the SCAN metaGGA functional. If this Firework is
initialized with no parents, it will perform a GGA optimization of the provided
structure using the PBESol functional. This GGA-relaxed structure is intended
to be passed to a second instance of this Firework for optimization with SCAN.
(see workflow definition in SCAN_optimization.yaml)
Args:
structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
is only used to set the name of the FW and any structure with the same composition
can be used.
name (str): Name for the Firework.
vasp_input_set (VaspInputSet): input set to use (for jobs w/no parents)
Defaults to MpScanRelaxSet() if None.
vasp_input_set_params (dict): Dict of vasp_input_set kwargs.
vasp_cmd (str): Command to run vasp.
vdw_kernel_dir (str): Directory containing the pre-compiled VdW
kernel. Supports env_chk.
prev_calc_loc (bool or str): If true (default), copies outputs from previous calc. If
a str value, retrieves a previous calculation output by name. If False/None, will create
new SCAN calculation using the provided structure.
prev_calc_dir (str): Path to a previous calculation to copy from
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework. FW or list of FWs.
vasptodb_kwargs (dict): kwargs to pass to VaspToDb
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
vasp_input_set_params = vasp_input_set_params or {}
vasptodb_kwargs = vasptodb_kwargs or {}
if "additional_fields" not in vasptodb_kwargs:
vasptodb_kwargs["additional_fields"] = {}
vasptodb_kwargs["additional_fields"]["task_label"] = name
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown",
name)
has_previous_calc = False
# Raise a warning if the InputSet is not MPScanRelaxSet, because the
# kspacing calculation from bandgap is only supported in MPScanRelaxSet.
if vasp_input_set and not isinstance(vasp_input_set, MPScanRelaxSet):
raise UserWarning("You have specified a vasp_input_set other than \
MPScanRelaxSet. Automatic adjustment of kspacing\
is not supported by this InputSet.")
if prev_calc_dir:
has_previous_calc = True
# Copy the CHGCAR from previous calc directory (usually PBE)
t.append(
CopyVaspOutputs(
calc_dir=prev_calc_dir,
contcar_to_poscar=True,
additional_files=["CHGCAR"],
))
elif parents:
if prev_calc_loc:
has_previous_calc = True
# Copy the CHGCAR from previous calc location (usually PBE)
t.append(
CopyVaspOutputs(
calc_loc=prev_calc_loc,
contcar_to_poscar=True,
additional_files=["CHGCAR"],
))
else:
raise UserWarning(
"You specified parent Firework but did not provide its location. Set "
"prev_calc_dir or prev_calc_loc and try again.")
elif prev_calc_loc:
raise UserWarning(
"You specified prev_calc_loc but did not provide a parent Firework. Set "
"parents and try again.")
if has_previous_calc:
# Update the InputSet with the bandgap from the previous calc
t.append(
WriteScanRelaxFromPrev(
vasp_input_set_params=vasp_input_set_params))
# Set ICHARG to 1 to utilize the pre-existing CHGCAR
settings = {"_set": {"ICHARG": 1}}
if vasp_input_set_params.get("vdw"):
# Copy the pre-compiled VdW kernel for VASP
t.append(
CopyFiles(files_to_copy=["vdw_kernel.bindat"],
from_dir=vdw_kernel_dir))
# Enable vdW for the SCAN step
settings["_set"]["LUSE_VDW"] = True
settings["_set"]["BPARAM"] = 15.7
t.append(ModifyIncar(incar_dictmod=settings))
# use the 'scan' custodian handler group
handler_group = "scan"
elif structure:
vasp_input_set = vasp_input_set or MPScanRelaxSet(
structure, **vasp_input_set_params)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
# Update the INCAR for the PBESol GGA preconditioning step
pre_opt_settings = {
"_set": {
"GGA": "Ps",
"METAGGA": None,
"EDIFFG": -0.05
}
}
# Disable vdW for the precondition step
if vasp_input_set_params.get("vdw"):
pre_opt_settings.update(
{"_unset": {
"LUSE_VDW": True,
"BPARAM": 15.7
}})
t.append(ModifyIncar(incar_dictmod=pre_opt_settings))
# use the 'default' custodian handler group
handler_group = "default"
else:
raise ValueError("Must specify structure or previous calculation")
# Run VASP
t.append(
RunVaspCustodian(
vasp_cmd=vasp_cmd,
auto_npar=">>auto_npar<<",
handler_group=handler_group,
gzip_output=False,
))
t.append(PassCalcLocs(name=name))
# Parse
t.append(VaspToDb(db_file=db_file, **vasptodb_kwargs))
# Delete the VdW kernel
t.append(DeleteFiles(files=["vdw_kernel.bindat"]))
# zip the output (don't rely on custodian to do it)
t.append(GzipDir())
super().__init__(t, parents=parents, name=fw_name, **kwargs)
def __init__(self,
structure,
supercell_matrix,
t_min=5,
t_max=2000,
t_step=5,
name="phonon",
vasp_input_set=None,
vasp_cmd="vasp",
metadata=None,
tag=None,
prev_calc_loc=True,
db_file=None,
parents=None,
**kwargs):
metadata = metadata or {}
tag = tag or metadata.get('tag')
# generate a tag with a warning
if tag is None:
tag = str(uuid4())
warnings.warn(
'No ``tag`` was passed explicitly or in ``metadata`` to PRLPhononFW. In order to find this Firework later, you should assign one. This was assigned: {}'
.format(tag))
metadata['tag'] = tag
vasp_input_set = vasp_input_set or PRLForceConstantsSet(structure)
t = []
# We need to get the POSCAR from the previous run or from the passed Structure
# so it can be transformed to a supercell in the next step
if parents:
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
else:
# write the input set first, just to get the POSCAR file in the directory
# the other inputs will get overridden by WriteVaspFromIOSetPrevStructure
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(SupercellTransformation(supercell_matrix=supercell_matrix))
t.append(
WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
auto_npar=">>auto_npar<<",
gzip_output=False))
t.append(PassCalcLocs(name=name))
t.append(
CalculatePhononThermalProperties(supercell_matrix=supercell_matrix,
t_min=t_min,
t_max=t_max,
t_step=t_step,
db_file=db_file,
tag=tag,
metadata=metadata))
super(PRLPhononFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
structure,
symmetry_tolerance=None,
name="structure optimization",
vasp_input_set=None,
job_type="normal",
vasp_cmd="vasp",
metadata=None,
override_default_vasp_params=None,
db_file=None,
force_gamma=True,
prev_calc_loc=True,
parents=None,
db_insert=False,
**kwargs):
metadata = metadata or {}
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or RelaxSet(
structure, force_gamma=force_gamma, **override_default_vasp_params)
site_properties = deepcopy(structure).site_properties
t = []
if parents:
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspFromIOSetPrevStructure(
vasp_input_set=vasp_input_set,
site_properties=site_properties))
else:
vasp_input_set = vasp_input_set or RelaxSet(structure)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(ModifyIncar(incar_update=">>incar_update<<"))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
job_type=job_type,
gzip_output=False))
t.append(PassCalcLocs(name=name))
if db_insert:
t.append(
VaspToDb(db_file=db_file,
additional_fields={
"task_label": name,
"metadata": metadata
}))
# This has to happen at the end because dynamically adding Fireworks if the symmetry breaks skips the rest of the tasks in the Firework.
if symmetry_tolerance is not None:
t.append(
CheckSymmetry(tolerance=symmetry_tolerance,
vasp_cmd=vasp_cmd,
db_file=db_file,
structure=structure,
metadata=metadata,
name=name))
super(OptimizeFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
structure=None,
prev_calc_dir=None,
name="phonon band",
vasp_cmd=VASP_CMD,
prev_calc_loc=True,
db_file=DB_FILE,
parents=None,
user_incar_settings=None,
user_kpoints_settings=None,
supercell=None,
**kwargs):
"""
Phonon calculation Firework using finite difference method
Args:
structure (Structure): Input structure. If prev_calc_loc, used only to set the
name of the FW.
name (str): Name for the Firework.
vasp_cmd (str): Command to run vasp.
prev_calc_loc (str or bool): Whether to copy outputs from previous run. Defaults to True.
prev_calc_dir (str): Path to a previous calculation to copy from
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
user_incar_settings (dict): Parameters in INCAR to override
user_kpoints_settings (Kpoint): Kpoint set to use.
supercell (list) size of supercell:
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown",
name)
t = []
if prev_calc_dir:
t.append(
CopyVaspOutputs(calc_dir=prev_calc_dir,
contcar_to_poscar=True))
t.append(
WriteVaspStaticFromPrev(
user_incar_settings=user_incar_settings,
standardize=False,
supercell=supercell))
elif parents and prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspStaticFromPrev(
user_incar_settings=user_incar_settings,
standardize=False,
supercell=supercell))
elif structure:
vasp_input_set = MPStaticSet(
structure,
user_kpoints_settings=user_kpoints_settings,
user_incar_settings=user_incar_settings)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
else:
raise ValueError("Must specify structure or previous calculation")
t.append(WriteSupercellWithDisp(supercell=supercell))
t.append(PassCalcLocs(name=name))
super(MyPhononFiniteDiffFW, self).__init__(t,
parents=parents,
name=fw_name,
**kwargs)
def __init__(self,
structure,
name="static dielectric",
vasp_cmd=VASP_CMD,
copy_vasp_outputs=True,
db_file=DB_FILE,
parents=None,
phonon=False,
mode=None,
displacement=None,
user_incar_settings=None,
**kwargs):
"""
Standard static calculation Firework for dielectric constants using DFPT.
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
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.
user_incar_settings (dict): Parameters in INCAR to override
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
warnings.warn(
"This firework will be removed soon. Use DFPTFW and/or RamanFW fireworks."
)
user_incar_settings = user_incar_settings or {}
t = []
if copy_vasp_outputs:
t.append(
CopyVaspOutputs(calc_loc=True,
additional_files=["CHGCAR"],
contcar_to_poscar=True))
t.append(
WriteVaspStaticFromPrev(
lepsilon=True,
other_params={'user_incar_settings': user_incar_settings}))
else:
vasp_input_set = MPStaticSet(
structure,
lepsilon=True,
user_incar_settings=user_incar_settings)
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))
t.append(
pass_vasp_result(
{
"structure": "a>>final_structure",
"eigenvals": "a>>normalmode_eigenvals",
"eigenvecs": "a>>normalmode_eigenvecs"
},
parse_eigen=True,
mod_spec_key="normalmodes"))
else:
name = "raman_{}_{} {}".format(str(mode), str(displacement),
name)
key = "{}_{}".format(mode, displacement).replace('-',
'm').replace(
'.', 'd')
pass_fw = pass_vasp_result(pass_dict={
"mode": mode,
"displacement": displacement,
"epsilon": "a>>epsilon_static"
},
mod_spec_key="raman_epsilon->" +
key,
parse_eigen=True)
t.extend([
WriteNormalmodeDisplacedPoscar(mode=mode,
displacement=displacement),
RunVaspCustodian(vasp_cmd=vasp_cmd), pass_fw
])
else:
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
t.extend([
PassCalcLocs(name=name),
VaspToDb(db_file=db_file, additional_fields={"task_label": name})
])
super(LepsFW, 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_input_set_params=None,
count=1,
vasp_cmd=VASP_CMD,
ediffg=None,
db_file=DB_FILE,
prev_calc_loc=False,
strain=0.0,
force_gamma=True,
job_type="normal",
max_force_threshold=RELAX_MAX_FORCE,
auto_npar=">>auto_npar<<",
half_kpts_first_relax=HALF_KPOINTS_FIRST_RELAX,
parents=None,
**kwargs):
"""
Optimize the given structure.
Args:
structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
is only used to set the name of the FW and any structure with the same composition
can be used.
name (str): Name for the Firework.
vasp_input_set (VaspInputSet): input set to use. Defaults to MPRelaxSet() if None.
vasp_input_set_params (dict): Parameters in INCAR to override.
count (int): A counter to record round of structure optimization.
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 to place output parsing.
prev_calc_loc (bool or str): If true, copies outputs from previous calc. If
a str value, retrieves a previous calculation output by name. If False/None, will create
new static calculation using the provided structure.
strain (float): strain executed on structure in each direction of lattice.
force_gamma (bool): Force gamma centered kpoint generation
job_type (str): custodian job type (default "double_relaxation_run")
max_force_threshold (float): max force on a site allowed at end; otherwise, reject job
auto_npar (bool or str): whether to set auto_npar. defaults to env_chk: ">>auto_npar<<"
half_kpts_first_relax (bool): whether to use half the kpoints for the first relaxation
parents ([Firework]): Parents of this particular Firework.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
if parents and prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspForDeformedCrystal(
strain=strain, user_incar_settings=vasp_input_set_params))
else:
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
job_type=job_type,
auto_npar=auto_npar,
gzip_output=False))
t.append(
CheckOptimization(vasp_input_set=vasp_input_set,
vasp_input_set_params=vasp_input_set_params,
vasp_cmd=vasp_cmd,
db_file=db_file,
name=name,
count=count,
kwargs=kwargs))
super(MyOptimizeFW,
self).__init__(t,
parents=parents,
name="{}-{}-{}".format(
structure.composition.reduced_formula, name,
str(count)),
**kwargs)