def get_wf(
self, scan=False, perform_bader=True, num_orderings_hard_limit=16, c=None
):
"""
Retrieve the FireWorks workflow.
Args:
scan: if True, use the SCAN functional instead of GGA+U, since
the SCAN functional has shown to have improved performance for
magnetic systems in some cases
perform_bader: if True, make sure the "bader" binary is in your
path, will use Bader analysis to calculate atom-projected magnetic
moments
num_orderings_hard_limit: will make sure total number of magnetic
orderings does not exceed this number even if there are extra orderings
of equivalent symmetry
c: additional config dict (as used elsewhere in atomate)
Returns: FireWorks Workflow
"""
c = c or {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
fws = []
analysis_parents = []
# trim total number of orderings (useful in high-throughput context)
# this is somewhat course, better to reduce num_orderings kwarg and/or
# change enumeration strategies
ordered_structures = self.ordered_structures
ordered_structure_origins = self.ordered_structure_origins
def _add_metadata(structure):
"""
For book-keeping, store useful metadata with the Structure
object for later database ingestion including workflow
version and a UUID for easier querying of all tasks generated
from the workflow.
Args:
structure: Structure
Returns: TransformedStructure
"""
# this could be further improved by storing full transformation
# history, but would require an improved transformation pipeline
return TransformedStructure(
structure, other_parameters={"wf_meta": self.wf_meta}
)
ordered_structures = [_add_metadata(struct) for struct in ordered_structures]
if (
num_orderings_hard_limit
and len(self.ordered_structures) > num_orderings_hard_limit
):
ordered_structures = self.ordered_structures[0:num_orderings_hard_limit]
ordered_structure_origins = self.ordered_structure_origins[
0:num_orderings_hard_limit
]
logger.warning(
"Number of ordered structures exceeds hard limit, "
"removing last {} structures.".format(
len(self.ordered_structures) - len(ordered_structures)
)
)
# always make sure input structure is included
if self.input_index and self.input_index > num_orderings_hard_limit:
ordered_structures.append(self.ordered_structures[self.input_index])
ordered_structure_origins.append(
self.ordered_structure_origins[self.input_index]
)
# default incar settings
user_incar_settings = {"ISYM": 0, "LASPH": True, "EDIFFG": -0.05}
if scan:
# currently, using SCAN relaxation as a static calculation also
# since it is typically high quality enough, but want to make
# sure we are also writing the AECCAR* files
user_incar_settings.update({"LAECHG": True})
user_incar_settings.update(c.get("user_incar_settings", {}))
c["user_incar_settings"] = user_incar_settings
for idx, ordered_structure in enumerate(ordered_structures):
analyzer = CollinearMagneticStructureAnalyzer(ordered_structure)
name = " ordering {} {} -".format(idx, analyzer.ordering.value)
if not scan:
vis = MPRelaxSet(
ordered_structure, user_incar_settings=user_incar_settings
)
# relax
fws.append(
OptimizeFW(
ordered_structure,
vasp_input_set=vis,
vasp_cmd=c["VASP_CMD"],
db_file=c["DB_FILE"],
max_force_threshold=0.05,
half_kpts_first_relax=False,
name=name + " optimize",
)
)
# static
fws.append(
StaticFW(
ordered_structure,
vasp_cmd=c["VASP_CMD"],
db_file=c["DB_FILE"],
name=name + " static",
prev_calc_loc=True,
parents=fws[-1],
)
)
else:
# wf_scan_opt is just a single FireWork so can append it directly
scan_fws = wf_scan_opt(ordered_structure, c=c).fws
# change name for consistency with non-SCAN
new_name = scan_fws[0].name.replace(
"structure optimization", name + " optimize"
)
scan_fws[0].name = new_name
scan_fws[0].tasks[-1]["additional_fields"]["task_label"] = new_name
fws += scan_fws
analysis_parents.append(fws[-1])
fw_analysis = Firework(
MagneticOrderingsToDB(
db_file=c["DB_FILE"],
wf_uuid=self.uuid,
auto_generated=False,
name="MagneticOrderingsToDB",
parent_structure=self.sanitized_structure,
origins=ordered_structure_origins,
input_index=self.input_index,
perform_bader=perform_bader,
scan=scan,
),
name="Magnetic Orderings Analysis",
parents=analysis_parents,
spec={"_allow_fizzled_parents": True},
)
fws.append(fw_analysis)
formula = self.sanitized_structure.composition.reduced_formula
wf_name = "{} - magnetic orderings".format(formula)
if scan:
wf_name += " - SCAN"
wf = Workflow(fws, name=wf_name)
wf = add_additional_fields_to_taskdocs(wf, {"wf_meta": self.wf_meta})
tag = "magnetic_orderings group: >>{}<<".format(self.uuid)
wf = add_tags(wf, [tag, ordered_structure_origins])
return wf
def get_wf(self,
scan=False,
perform_bader=True,
num_orderings_hard_limit=16,
c=None):
"""
Retrieve the FireWorks workflow.
Args:
scan (bool): if True, use the SCAN functional instead of GGA+U,
since the SCAN functional has shown to have improved
performance for magnetic systems in some cases
perform_bader (bool): if True, make sure the "bader" binary is in
your path, will use Bader analysis to calculate
atom-projected magnetic moments
num_orderings_hard_limit (int): will make sure total number of
magnetic orderings does not exceed this number even if there
are extra orderings of equivalent symmetry
c (dict): additional config dict (as used elsewhere in atomate)
Returns: FireWorks Workflow
"""
c_defaults = {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
additional_fields = {"relax": not self.static}
c = c or {}
for k, v in c_defaults.items():
if k not in c:
c[k] = v
fws = []
analysis_parents = []
# trim total number of orderings (useful in high-throughput context)
# this is somewhat course, better to reduce num_orderings kwarg and/or
# change enumeration strategies
ordered_structures = self.ordered_structures
ordered_structure_origins = self.ordered_structure_origins
def _add_metadata(structure):
"""
For book-keeping, store useful metadata with the Structure
object for later database ingestion including workflow
version and a UUID for easier querying of all tasks generated
from the workflow.
Args:
structure: Structure
Returns: TransformedStructure
"""
# this could be further improved by storing full transformation
# history, but would require an improved transformation pipeline
return TransformedStructure(
structure, other_parameters={"wf_meta": self.wf_meta})
ordered_structures = [
_add_metadata(struct) for struct in ordered_structures
]
if (num_orderings_hard_limit
and len(self.ordered_structures) > num_orderings_hard_limit):
ordered_structures = self.ordered_structures[
0:num_orderings_hard_limit]
ordered_structure_origins = self.ordered_structure_origins[
0:num_orderings_hard_limit]
logger.warning("Number of ordered structures exceeds hard limit, "
"removing last {} structures.".format(
len(self.ordered_structures) -
len(ordered_structures)))
# always make sure input structure is included
if self.input_index and self.input_index > num_orderings_hard_limit:
ordered_structures.append(
self.ordered_structures[self.input_index])
ordered_structure_origins.append(
self.ordered_structure_origins[self.input_index])
# default incar settings
user_incar_settings = {"ISYM": 0, "LASPH": True, "EDIFFG": -0.05}
if scan:
# currently, using SCAN relaxation as a static calculation also
# since it is typically high quality enough, but want to make
# sure we are also writing the AECCAR* files
user_incar_settings.update({"LAECHG": True})
user_incar_settings.update(c.get("user_incar_settings", {}))
c["user_incar_settings"] = user_incar_settings
for idx, ordered_structure in enumerate(ordered_structures):
analyzer = CollinearMagneticStructureAnalyzer(ordered_structure)
name = f" ordering {idx} {analyzer.ordering.value} -"
if not scan:
vis = MPRelaxSet(ordered_structure,
user_incar_settings=user_incar_settings)
if not self.static:
# relax
fws.append(
OptimizeFW(
ordered_structure,
vasp_input_set=vis,
vasp_cmd=c["VASP_CMD"],
db_file=c["DB_FILE"],
max_force_threshold=0.05,
half_kpts_first_relax=False,
name=name + " optimize",
))
# static
fws.append(
StaticFW(
ordered_structure,
vasp_cmd=c["VASP_CMD"],
db_file=c["DB_FILE"],
name=name + " static",
prev_calc_loc=True,
parents=fws[-1],
vasptodb_kwargs={
"parse_chgcar": True,
"parse_aeccar": True
},
))
if not self.static:
# so a failed optimize doesn't crash workflow
fws[-1].spec["_allow_fizzled_parents"] = True
elif scan:
# wf_scan_opt is just a single FireWork so can append it directly
scan_fws = wf_scan_opt(ordered_structure, c=c).fws
# change name for consistency with non-SCAN
new_name = scan_fws[0].name.replace("structure optimization",
name + " optimize")
scan_fws[0].name = new_name
scan_fws[0].tasks[-1]["additional_fields"][
"task_label"] = new_name
fws += scan_fws
analysis_parents.append(fws[-1])
fw_analysis = Firework(
MagneticOrderingsToDb(
db_file=c["DB_FILE"],
wf_uuid=self.uuid,
parent_structure=self.sanitized_structure,
origins=ordered_structure_origins,
input_index=self.input_index,
perform_bader=perform_bader,
scan=scan,
additional_fields=additional_fields,
),
name="Magnetic Orderings Analysis",
parents=analysis_parents,
spec={"_allow_fizzled_parents": True},
)
fws.append(fw_analysis)
formula = self.sanitized_structure.composition.reduced_formula
wf_name = f"{formula} - magnetic orderings"
if scan:
wf_name += " - SCAN"
wf = Workflow(fws, name=wf_name)
wf = add_additional_fields_to_taskdocs(wf, {"wf_meta": self.wf_meta})
tag = f"magnetic_orderings group: >>{self.uuid}<<"
wf = add_tags(wf, [tag, ordered_structure_origins])
return wf