def get_relax_static_wf(structures,
vasp_cmd=">>vasp_cmd<<",
db_file=">>db_file<<",
name="regular_relax",
**kwargs):
"""
:param structures:
:param vasp_cmd:
:param db_file:
:param name:
:param kwargs:
:return:
"""
wfs = []
for s in structures:
fw1 = OptimizeFW(s,
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=[],
**kwargs)
fw2 = StaticFW(s, vasp_cmd=vasp_cmd, db_file=db_file, parents=[fw1])
wfs.append(
Workflow([fw1, fw2],
name=name + str(s.composition.reduced_formula)))
return wfs
def get_wf_structure_sampler(xdatcar_file,
n=10,
steps_skip_first=1000,
vasp_cmd=">>vasp_cmd<<",
db_file=">>db_file<<",
name="structure_sampler",
**kwargs):
"""
:param xdatcar_file:
:param n:
:param steps_skip_first:
:param vasp_cmd:
:param db_file:
:param name:
:param kwargs:
:return:
"""
structures = get_sample_structures(xdatcar_path=xdatcar_file,
n=n,
steps_skip_first=steps_skip_first)
wfs = []
for s in structures:
fw1 = OptimizeFW(s,
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=[],
**kwargs)
fw2 = StaticFW(s, vasp_cmd=vasp_cmd, db_file=db_file, parents=[fw1])
wfs.append(
Workflow([fw1, fw2],
name=name + str(s.composition.reduced_formula)))
return wfs
def run_task(self, fw_spec):
#create structure from CONTCAR
struct = Poscar.from_file('CONTCAR').structure
#repeat layers of bulk to create supercell
struct.make_supercell([1, 1, self.get("num_layers", 2)])
#add vacuum to create slab
struct = add_vacuum(struct, self.get("vacuum", 15))
#add selective dynamics
selective_dynamics = []
"""
min_bulk = self.get("surf_layers_to_relax",3)/(self.get("atomic_thickness")*self.get("num_layers",2)) * max([site.z for site in struct.sites])
max_bulk = (self.get("atomic_thickness")*self.get("num_layers",2) - self.get("surf_layers_to_relax",3))/(self.get("atomic_thickness")*self.get("num_layers",2)) * max([site.z for site in struct.sites])
for site in struct.sites:
if site.z > min_bulk and site.z <= max_bulk:
selective_dynamics.append([False, False, False])
else:
selective_dynamics.append([True, True, True])
struct.add_site_property("selective_dynamics", selective_dynamics)
"""
#create optimize and static fireworks using the newly created slab
slab_optimize = OptimizeFW(struct,
name=name + '_slab_optimization' + time,
vasp_cmd=">>vasp_cmd<<",
db_file=">>db_file<<",
parents=[bulk_optimize])
slab_optimize = Workflow(slab_optimize)
optimize_incar_settings = {"ISIF": 2}
optimize_update = {"incar_update": optimize_incar_settings}
slab_optimize = add_modify_incar(slab_optimize,
modify_incar_params=optimize_update,
fw_name_constraint='optimization')
slab_static = StaticFW(struct,
name=name + '_slab_static_' + time,
parents=[slab_optimize],
prev_calc_loc=True,
vasp_cmd=">>vasp_cmd<<",
db_file=">>db_file<<")
#slab_static.tasks.append(Slab_energy_and_SA())
#surface_energy_calc_fw = Firework(Surface_energy_calc(), parents = [bulk_static, slab_static])
#return FWAction(additions = [slab_optimize, slab_static, surface_energy_calc_fw])
return FWAction(additions=[slab_optimize, slab_static])
def testLobsterFW(self):
static_fw = StaticFW(structure=self.structure).name
self.assertEqual(
LobsterFW(structure=self.structure, parents=static_fw).name,
"Si-lobster_calculation",
)
lobster_fw = LobsterFW(prev_calc_dir="/",
delete_wavecar=True,
delete_wavecar_previous_fw=True)
self.assertEqual(lobster_fw.name, "unknown-lobster_calculation")
self.assertEqual(lobster_fw.tasks[0]["calc_dir"], "/")
self.assertEqual(len(lobster_fw.tasks), 7)
lobster_fw = LobsterFW(prev_calc_dir="/",
delete_wavecar=False,
delete_wavecar_previous_fw=False)
self.assertEqual(len(lobster_fw.tasks), 5)
# check for ValueError when no parent or calc_dir are provided
with self.assertRaises(ValueError):
LobsterFW()
def run_task(self, fw_spec):
inserted_structure = fw_spec.get("optimal_structure")
working_ion = fw_spec.get("working_ion")
vasptodb_kwargs = fw_spec.get("vasptodb_kwargs")
staticfw_kwargs = fw_spec.get("staticfw_kwargs", {})
fw1 = StaticFW(
inserted_structure,
vasptodb_kwargs=vasptodb_kwargs,
db_file=DB_FILE,
**staticfw_kwargs,
)
n_ion = int(
inserted_structure.composition.element_composition[working_ion])
fw2 = Firework(
[AnalyzeChgcar(), GetInsertionCalcs()],
name=f"Charge Density Analysis-{n_ion}",
parents=fw1,
)
wf = Workflow([fw1, fw2], name=f"Obtain inserted sites-{n_ion}")
wf = get_powerup_wf(wf, fw_spec)
update_wf_keys(wf, fw_spec)
return FWAction(additions=[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
def get_wf(self, c=None):
"""
Get the workflow.
Returns:
Workflow
"""
c = c or {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
nsites = len(self.structure.sites)
vis = MPRelaxSet(self.structure, potcar_functional="PBE_54", force_gamma=True)
opt_fw = OptimizeFW(
self.structure,
vasp_input_set=vis,
vasp_cmd=c["VASP_CMD"],
db_file=c["DB_FILE"],
)
vis = MPStaticSet(self.structure, potcar_functional="PBE_54", force_gamma=True)
static_fw = StaticFW(
self.structure,
vasp_input_set=vis,
vasp_cmd=c["VASP_CMD"],
db_file=c["DB_FILE"],
parents=[opt_fw],
)
# Separate FW for each BZ surface calc
# Run Z2Pack on unique TRIM planes in the BZ
surfaces = ["kx_0", "kx_1"]
equiv_planes = self.get_equiv_planes()
# Only run calcs on inequivalent BZ surfaces
if self.symmetry_reduction:
for add_surface in equiv_planes.keys():
mark = True
for surface in surfaces:
if surface in equiv_planes[add_surface]:
mark = False
if mark and add_surface not in surfaces:
surfaces.append(add_surface)
else: # 4 TRI surfaces define Z2 in 3D
surfaces = ["kx_1", "ky_1", "kz_0", "kz_1"]
z2pack_fws = []
for surface in surfaces:
z2pack_fw = Z2PackFW(
parents=[static_fw],
structure=self.structure,
surface=surface,
uuid=self.uuid,
name="z2pack",
vasp_cmd=c["VASP_CMD"],
db_file=c["DB_FILE"],
)
z2pack_fws.append(z2pack_fw)
analysis_fw = InvariantFW(
parents=z2pack_fws,
structure=self.structure,
symmetry_reduction=self.symmetry_reduction,
equiv_planes=equiv_planes,
uuid=self.uuid,
name="invariant",
db_file=c["DB_FILE"],
)
fws = [opt_fw, static_fw] + z2pack_fws + [analysis_fw]
wf = Workflow(fws)
wf = add_additional_fields_to_taskdocs(wf, {"wf_meta": self.wf_meta})
# Add vdW corrections if structure is layered
dim_data = StructureDimensionality(self.structure)
if np.any(
[
dim == 2
for dim in [dim_data.larsen_dim, dim_data.cheon_dim, dim_data.gorai_dim]
]
):
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {
"IVDW": 11,
"EDIFFG": 0.005,
"IBRION": 2,
"NSW": 100,
}
},
fw_name_constraint="structure optimization",
)
wf = add_modify_incar(
wf,
modify_incar_params={"incar_update": {"IVDW": 11}},
fw_name_constraint="static",
)
wf = add_modify_incar(
wf,
modify_incar_params={"incar_update": {"IVDW": 11}},
fw_name_constraint="z2pack",
)
else:
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {"EDIFFG": 0.005, "IBRION": 2, "NSW": 100}
},
fw_name_constraint="structure optimization",
)
# Helpful vasp settings and no parallelization
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {
"ADDGRID": ".TRUE.",
"LASPH": ".TRUE.",
"GGA": "PS",
"NCORE": 1,
}
},
)
# Generate inputs for Z2Pack with a static calc
wf = add_modify_incar(
wf,
modify_incar_params={"incar_update": {"PREC": "Accurate"}},
fw_name_constraint="static",
)
wf = add_common_powerups(wf, c)
wf.name = "{} {}".format(self.structure.composition.reduced_formula, "Z2Pack")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf, fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, self.structure)
tag = "z2pack: {}".format(self.uuid)
wf = add_tags(wf, [tag])
return wf
tilt_count = 15
temp_structs = copy.deepcopy(tilts_and_orders)
comp_tag = composition[0] + composition[1] + 'N' + 'O' + str(
composition[2])
struct_tag = 'tetra'
for structure in temp_structs:
if composition[2] == 1:
structure.replace_species({'O': 'N', 'N': 'O'})
structure.replace_species({
default_B: composition[1]
}) #this will break if B-site is default_a but that shouldn't happen
structure.replace_species({default_A: composition[0]})
poscar_key = tetra_dict[tilt_count]
opt = OptimizeFW(structure, vasp_cmd='ibrun tacc_affinity vasp_std')
stat = StaticFW(parents=opt, vasp_cmd='ibrun tacc_affinity vasp_std')
wf = Workflow([opt, stat])
wf = add_modify_incar(wf,
modify_incar_params={
'incar_update': {
'KPAR': 2,
'NCORE': 4,
'NSIM': 8,
'EDIFF': 0.000002,
'LMAXMIX': 6,
'LSCALAPACK': '.FALSE.',
'ALGO': 'All'
}
})
wf = add_modify_incar(wf,
modify_incar_params={