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 __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)