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,
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, 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 __init__(self, structure, isif=2, scale_lattice=None, name="born charge", vasp_input_set=None,
vasp_cmd="vasp", metadata=None, override_default_vasp_params=None, tag=None,
prev_calc_loc=True, modify_incar=None, 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())
metadata['tag'] = tag
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or BornChargeSet(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):
t.append(ScaleVolumeTransformation(scale_factor=scale_lattice, structure=structure))
#the following statement may not correct to Born effective charge calculation, so be commented.
"""
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(RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=False, gzip_output=False))
t.append(PassCalcLocs(name=name))
t.append(BornChargeToDb(db_file=">>db_file<<", tag=tag))
#t.append(CheckSymmetryToDb(db_file=db_file, tag=tag))
super(BornChargeFW, 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)