def test_modifyincar(self):
# create an INCAR
incar = self.ref_incar
incar.write_file(os.path.join(module_dir, "INCAR"))
# modify and test
ft = ModifyIncar({
"incar_update": {
"ISMEAR": 1000
},
"incar_multiply": {
"ENCUT": 1.5
},
"incar_dictmod": {
"_inc": {
"ISPIN": -1
}
}
})
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
incar_mod = Incar.from_file("INCAR")
self.assertEqual(incar_mod['ISMEAR'], 1000)
self.assertEqual(incar_mod['ENCUT'], 780)
self.assertEqual(incar_mod['ISPIN'], 1)
def __init__(self, structure, isif=2, scale_lattice=None, name="static", vasp_input_set=None,
vasp_cmd="vasp", metadata=None, prev_calc_loc=True, Prestatic=False, modify_incar=None,
db_file=None, parents=None, tag=None, override_default_vasp_params=None,
store_volumetric_data=False, **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 {}
tag = tag or metadata.get('tag')
# generate a tag with a warning
if tag is None:
tag = str(uuid4())
metadata['tag'] = tag
if isinstance(store_volumetric_data, (list, tuple)):
store_volumetric_data = store_volumetric_data
elif isinstance(store_volumetric_data, bool):
if store_volumetric_data:
store_volumetric_data = STORE_VOLUMETRIC_DATA
else:
store_volumetric_data = ()
else:
raise ValueError('The store_volumetric_data should be list or bool')
override_default_vasp_params = override_default_vasp_params or {}
self.override_default_vasp_params = override_default_vasp_params
vasp_input_set = vasp_input_set or StaticSet(structure, isif=isif, **override_default_vasp_params)
site_properties = deepcopy(structure).site_properties
# Avoids delivery (prev_calc_loc == '' (instead by True))
t = []
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:
t.append(WriteVaspFromIOSetPrevStructure(structure=structure, vasp_input_set=vasp_input_set, site_properties=site_properties))
if (scale_lattice is not None) and not Prestatic:
t.append(ScaleVolumeTransformation(scale_factor=scale_lattice, structure=structure))
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, auto_npar=">>auto_npar<<", gzip_output=False))
t.append(PassCalcLocs(name=name))
if Prestatic:
t.append(Record_PreStatic_result(db_file = ">>db_file<<", metadata = metadata, structure = structure, scale_lattice = scale_lattice))
else:
t.append(VaspToDb(db_file=">>db_file<<", parse_dos=True, additional_fields={"task_label": name, "metadata": metadata,
"version_atomate": atomate_ver, "version_dfttk": dfttk_ver, "adopted": True, "tag": tag},
store_volumetric_data=store_volumetric_data))
run_task_ext(t,vasp_cmd,">>db_file<<",structure,tag,self.override_default_vasp_params)
t.append(CheckSymmetryToDb(db_file=">>db_file<<", tag=tag, site_properties=site_properties))
super(StaticFW, self).__init__(t, parents=parents, name="{}-{}".format(
structure.composition.reduced_formula, name), **kwargs)
def __init__(self, structure, scale_lattice=None, isif=4, override_symmetry_tolerances=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,
prev_calc_loc=True, parents=None, db_insert=False, tag=None,
run_isif2=False, pass_isif4=False, force_gamma=True, store_volumetric_data=False,
modify_incar=None, modify_incar_params={}, modify_kpoints_params={}, **kwargs):
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
metadata.update({'tag': tag})
if isinstance(store_volumetric_data, (list, tuple)):
store_volumetric_data = store_volumetric_data
elif isinstance(store_volumetric_data, bool):
if store_volumetric_data:
store_volumetric_data = STORE_VOLUMETRIC_DATA
else:
store_volumetric_data = ()
else:
raise ValueError('The store_volumetric_data should be list or bool')
override_default_vasp_params = override_default_vasp_params or {}
override_symmetry_tolerances = override_symmetry_tolerances or {}
vasp_input_set = vasp_input_set or RelaxSet(structure, isif=isif, 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(WriteVaspFromIOSetPrevStructure(structure=structure, vasp_input_set=vasp_input_set, site_properties=site_properties))
if scale_lattice is not None:
t.append(ScaleVolumeTransformation(scale_factor=scale_lattice, structure=structure))
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, run_isif2=run_isif2, pass_isif4=pass_isif4))
if db_insert:
t.append(VaspToDb(db_file=db_file, additional_fields={"task_label": name, "metadata": metadata}, store_volumetric_data=store_volumetric_data))
t.append(CheckSymmetryToDb(db_file=db_file, tag=tag, override_symmetry_tolerances=override_symmetry_tolerances, site_properties=site_properties))
super(OptimizeFW, self).__init__(t, parents=parents, name="{}-{}".format(structure.composition.reduced_formula, name), **kwargs)
def add_modify_incar(original_wf,
modify_incar_params=None,
fw_name_constraint=None):
"""
Every FireWork that runs VASP has a ModifyIncar task just beforehand. For example, allows
you to modify the INCAR based on the Worker using env_chk or using hard-coded changes.
Args:
original_wf (Workflow)
modify_incar_params (dict) - dict of parameters for ModifyIncar.
fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.
Returns:
Workflow
"""
modify_incar_params = modify_incar_params or {
"incar_update": ">>incar_update<<"
}
for idx_fw, idx_t in get_fws_and_tasks(
original_wf,
fw_name_constraint=fw_name_constraint,
task_name_constraint="RunVasp"):
original_wf.fws[idx_fw].tasks.insert(
idx_t, ModifyIncar(**modify_incar_params))
return original_wf
def test_modify_incar(self):
# create an INCAR
incar = self.ref_incar
incar.write_file("INCAR")
# modify and test
ft = ModifyIncar(
{"incar_update": {"ISMEAR": 1000}, "incar_multiply": {"ENCUT": 1.5},
"incar_dictmod": {"_inc": {"ISPIN": -1}}})
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
incar_mod = Incar.from_file("INCAR")
self.assertEqual(incar_mod['ISMEAR'], 1000)
self.assertEqual(incar_mod['ENCUT'], 780)
self.assertEqual(incar_mod['ISPIN'], 1)
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 run_task(self, fw_spec):
prev_checkpoint_dirs = fw_spec.get(
"checkpoint_dirs",
[]) # If this is the first spawn, have no prev dirs
prev_checkpoint_dirs.append(os.getcwd(
)) # add the current directory to the list of checkpoints
vasp_cmd = self["vasp_cmd"]
wall_time = self["wall_time"]
db_file = self.get("db_file", None)
spawn_count = self["spawn_count"]
production = self['production']
num_checkpoints = production.get('num_checkpoints', 1)
incar_update = production.get('incar_update', None)
if spawn_count > num_checkpoints:
logger.info(
"LOGGER: Production run completed. Took {} spawns total".
format(spawn_count))
return FWAction(stored_data={'production_run_completed': True})
else:
name = ("ProductionRun" + str(abs(spawn_count)))
logger.info("LOGGER: Starting spawn {} of production run".format(
spawn_count))
t = []
t.append(
CopyVaspOutputs(calc_dir=os.getcwd(), contcar_to_poscar=True))
if incar_update:
t.append(ModifyIncar(incar_update=incar_update))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
gamma_vasp_cmd=">>vasp_gam<<",
handler_group="md",
wall_time=wall_time))
t.append(
ProductionSpawnTask(wall_time=wall_time,
vasp_cmd=vasp_cmd,
db_file=db_file,
spawn_count=spawn_count + 1,
production=production))
new_fw = Firework(t,
name=name,
spec={'checkpoint_dirs': prev_checkpoint_dirs})
return FWAction(
stored_data={'production_run_completed': False},
update_spec={'checkpoint_dirs': prev_checkpoint_dirs},
detours=[new_fw])
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 test_modify_incar(self):
# create an INCAR
incar = self.ref_incar
incar.write_file("INCAR")
# modify and test
ft = ModifyIncar(
incar_update={"ISMEAR": 1000},
incar_multiply={"ENCUT": 1.5},
incar_dictmod={"_inc": {
"ISPIN": -1
}},
)
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
incar_mod = Incar.from_file("INCAR")
self.assertEqual(incar_mod["ISMEAR"], 1000)
self.assertEqual(incar_mod["ENCUT"], 780)
self.assertEqual(incar_mod["ISPIN"], 1)
def __init__(self, structure, isif=7, name="structure optimization", isif4=False, level=1,
override_symmetry_tolerances=None, job_type="normal", vasp_input_set=None,
vasp_cmd="vasp", metadata=None, override_default_vasp_params=None, db_file=None,
prev_calc_loc=True, parents=None, db_insert=False, tag=None, modify_incar_params={},
modify_kpoints_params={}, energy_with_isif={}, store_volumetric_data=False,
**kwargs):
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
if isinstance(store_volumetric_data, (list, tuple)):
store_volumetric_data = store_volumetric_data
elif isinstance(store_volumetric_data, bool):
if store_volumetric_data:
store_volumetric_data = STORE_VOLUMETRIC_DATA
else:
store_volumetric_data = ()
else:
raise ValueError('The store_volumetric_data should be list or bool')
override_default_vasp_params = override_default_vasp_params or {}
override_symmetry_tolerances = override_symmetry_tolerances or {}
vasp_input_set = vasp_input_set or 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(WriteVaspFromIOSetPrevStructure(structure=structure, vasp_input_set=vasp_input_set, site_properties=site_properties))
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}, store_volumetric_data=store_volumetric_data))
t.append(CheckSymmetryToDb(db_file=">>db_file<<", tag=tag, site_properties=site_properties))
common_kwargs = {'vasp_cmd': vasp_cmd, 'db_file': ">>db_file<<", "metadata": metadata, "tag": tag,
'override_default_vasp_params': override_default_vasp_params}
static_kwargs = {}
relax_kwargs = {}
t.append(CheckRelaxation(db_file=">>db_file<<", metadata=metadata, tag=tag, isif4=isif4, level=level, energy_with_isif=energy_with_isif,
common_kwargs=common_kwargs, relax_kwargs=relax_kwargs, static_kwargs=static_kwargs, site_properties=site_properties,
store_volumetric_data=store_volumetric_data,
**override_symmetry_tolerances))
super().__init__(t, parents=parents, name="{}-{}".format(structure.composition.reduced_formula, name), **kwargs)
def modify_to_soc(original_wf, nbands, structure=None, modify_incar_params=None, fw_name_constraint=None):
"""
Takes a regular workflow and transforms its VASP fireworkers that are specified with
fw_name_constraints to non-collinear calculations taking spin orbit coupling into account.
Args:
original_wf (Workflow)
nbands (int): number of bands selected by the user (for now)
structure (Structure)
modify_incar_params ({}): a dictionary containing the setting for modyfining the INCAR (e.g. {"ICHARG": 11})
fw_name_constraint (string): name of the fireworks to be modified (all if None is passed)
Returns:
Workflow: modified with SOC
"""
if structure is None:
try:
sid = get_fws_and_tasks(original_wf, fw_name_constraint="structure optimization",
task_name_constraint="WriteVasp")
fw_id = sid[0][0]
task_id = sid[0][1]
structure = original_wf.fws[fw_id].tasks[task_id]["vasp_input_set"].structure
except:
raise ValueError("modify_to_soc powerup requires the structure in vasp_input_set")
magmom = ""
for _ in structure:
magmom += "0 0 0.6 "
# TODO: add saxis as an input parameter with default being (0 0 1)
modify_incar_params = modify_incar_params or {"incar_update": {"LSORBIT": "T", "NBANDS":
nbands, "MAGMOM": magmom, "ISPIN": 1, "LMAXMIX": 4, "ISYM": 0}}
for idx_fw, idx_t in get_fws_and_tasks(original_wf, fw_name_constraint=fw_name_constraint,
task_name_constraint="RunVasp"):
original_wf.fws[idx_fw].tasks[idx_t]["vasp_cmd"] = ">>vasp_ncl<<"
original_wf.fws[idx_fw].tasks.insert(idx_t, ModifyIncar(**modify_incar_params))
original_wf.fws[idx_fw].name += " soc"
for idx_fw, idx_t in get_fws_and_tasks(original_wf, fw_name_constraint=fw_name_constraint,
task_name_constraint="RunBoltztrap"):
original_wf.fws[idx_fw].name += " soc"
return original_wf
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,
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 __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,
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)