"""
FWs for wflows.
"""
from fireworks import Firework
from atomate.common.firetasks.glue_tasks import PassCalcLocs
from atomate.vasp.firetasks.glue_tasks import CopyVaspOutputs
from pytopomat.workflows.firetasks import (
RunIrrep,
IrrepToDb,
RunIRVSP,
IRVSPToDb,
Vasp2TraceToDb,
RunVasp2Trace,
RunVasp2TraceMagnetic,
Z2PackToDb,
SetUpZ2Pack,
RunZ2Pack,
WriteWannier90Win,
InvariantsToDB,
StandardizeCell,
)
[docs]class IrrepFW(Firework):
def __init__(
self,
parents=None,
structure=None,
name="irrep",
wf_uuid=None,
db_file=None,
prev_calc_dir=None,
irrep_out=None,
vasp_cmd=None,
**kwargs
):
"""
Run irrep and parse the output data. Assumes you have a previous FW with the
calc_locs passed into the current FW.
Args:
structure (Structure): - only used for setting name of FW
name (str): name of this FW
wf_uuid (str): unique wf id
db_file (str): path to the db file
parents (Firework): Parents of this particular Firework. FW or list of FWS.
prev_calc_dir (str): Path to a previous calculation to copy from
\\*\\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown", name
)
t = []
if prev_calc_dir:
t.append(
CopyVaspOutputs(
calc_dir=prev_calc_dir,
additional_files=["CHGCAR", "WAVECAR", "POSCAR"],
contcar_to_poscar=True,
)
)
elif parents:
t.append(
CopyVaspOutputs(
calc_loc=True,
additional_files=["CHGCAR", "WAVECAR", "POSCAR"],
contcar_to_poscar=True,
)
)
else:
raise ValueError("Must specify structure or previous calculation")
t.extend(
[
RunIrrep(),
PassCalcLocs(name=name),
IrrepToDb(db_file=db_file, wf_uuid=wf_uuid, irrep_out=irrep_out),
]
)
super(IrrepFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
[docs]class IrvspFW(Firework):
def __init__(
self,
parents=None,
structure=None,
name="irvsp",
wf_uuid=None,
db_file=None,
prev_calc_dir=None,
irvsp_out=None,
vasp_cmd=None,
**kwargs
):
"""
Run IRVSP and parse the output data. Assumes you have a previous FW with the
calc_locs passed into the current FW.
Args:
structure (Structure): - only used for setting name of FW
name (str): name of this FW
wf_uuid (str): unique wf id
db_file (str): path to the db file
parents (Firework): Parents of this particular Firework. FW or list of FWS.
prev_calc_dir (str): Path to a previous calculation to copy from
\\*\\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown", name
)
t = []
if prev_calc_dir:
t.append(
CopyVaspOutputs(
calc_dir=prev_calc_dir,
additional_files=["CHGCAR", "WAVECAR"],
contcar_to_poscar=True,
)
)
elif parents:
t.append(
CopyVaspOutputs(
calc_loc=True,
additional_files=["CHGCAR", "WAVECAR"],
contcar_to_poscar=True,
)
)
else:
raise ValueError("Must specify structure or previous calculation")
t.extend(
[
RunIRVSP(),
PassCalcLocs(name=name),
IRVSPToDb(db_file=db_file, wf_uuid=wf_uuid, irvsp_out=irvsp_out),
]
)
super(IrvspFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
[docs]class StandardizeFW(Firework):
def __init__(
self,
parents=None,
structure=None,
name="standardize",
db_file=None,
prev_calc_dir=None,
vasp_cmd=None,
**kwargs
):
"""
Standardize the structure with spglib. Output is the primitive standard.
Args:
structure (Structure): pmg structure.
name (str): name of this FW
db_file (str): path to the db file
parents (Firework): Parents of this particular Firework. FW or list of FWS.
prev_calc_dir (str): Path to a previous calculation to copy from
\\*\\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown", name
)
t = []
if prev_calc_dir:
t.append(CopyVaspOutputs(calc_dir=prev_calc_dir, contcar_to_poscar=True,))
elif parents:
t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True,))
else:
raise ValueError("Must specify structure or previous calculation")
t.extend(
[StandardizeCell(), PassCalcLocs(name=name),]
)
super(StandardizeFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
[docs]class Vasp2TraceFW(Firework):
def __init__(
self,
parents=None,
structure=None,
name="vasp2trace",
db_file=None,
prev_calc_dir=None,
vasp2trace_out=None,
vasp_cmd=None,
**kwargs
):
"""
Run Vasp2Trace and parse the output data. Assumes you have a previous FW with the
calc_locs passed into the current FW.
Args:
structure (Structure): - only used for setting name of FW
name (str): name of this FW
db_file (str): path to the db file
parents (Firework): Parents of this particular Firework. FW or list of FWS.
prev_calc_dir (str): Path to a previous calculation to copy from
\\*\\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown", name
)
t = []
if prev_calc_dir:
t.append(
CopyVaspOutputs(
calc_dir=prev_calc_dir,
additional_files=["CHGCAR", "WAVECAR", "PROCAR"],
contcar_to_poscar=True,
)
)
elif parents:
t.append(
CopyVaspOutputs(
calc_loc=True,
additional_files=["CHGCAR", "WAVECAR", "PROCAR"],
contcar_to_poscar=True,
)
)
else:
raise ValueError("Must specify structure or previous calculation")
t.extend(
[
RunVasp2Trace(),
PassCalcLocs(name=name),
Vasp2TraceToDb(db_file=db_file, vasp2trace_out=vasp2trace_out),
]
)
super(Vasp2TraceFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
[docs]class Vasp2TraceMagneticFW(Firework):
def __init__(
self,
parents=None,
structure=None,
name="vasp2trace",
db_file=None,
prev_calc_dir=None,
vasp2trace_out=None,
vasp_cmd=None,
**kwargs
):
"""
Run Vasp2Trace on a spin-polarized calculation and parse the output data.
Assumes you have a previous FW with the calc_locs passed into the current FW.
Args:
structure (Structure): - only used for setting name of FW
name (str): name of this FW
db_file (str): path to the db file
parents (Firework): Parents of this particular Firework. FW or list of FWS.
prev_calc_dir (str): Path to a previous calculation to copy from
\\*\\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown", name
)
t = []
if prev_calc_dir:
t.append(
CopyVaspOutputs(
calc_dir=prev_calc_dir,
additional_files=["CHGCAR", "WAVECAR", "PROCAR"],
contcar_to_poscar=True,
)
)
elif parents:
t.append(
CopyVaspOutputs(
calc_loc=True,
additional_files=["CHGCAR", "WAVECAR", "PROCAR"],
contcar_to_poscar=True,
)
)
else:
raise ValueError("Must specify structure or previous calculation")
t.extend(
[
RunVasp2TraceMagnetic(),
PassCalcLocs(name=name),
Vasp2TraceToDb(db_file=db_file, vasp2trace_out=vasp2trace_out),
]
)
super(Vasp2TraceMagneticFW, self).__init__(
t, parents=parents, name=fw_name, **kwargs
)
[docs]class Z2PackFW(Firework):
def __init__(
self,
parents=None,
structure=None,
surface=None,
uuid=None,
name="z2pack",
db_file=None,
prev_calc_dir=None,
z2pack_out=None,
vasp_cmd=None,
**kwargs
):
"""
Run Z2Pack and parse the output data.
Assumes you have a previous FW with the calc_locs passed into the current FW.
Args:
structure (Structure): Structure object.
surface (str): Like "kx_0", "kx_1", "ky_0", etc. that indicates TRIM surface in BZ.
uuid (str): Unique wf identifier.
name (str): name of this FW
db_file (str): path to the db file
parents (Firework): Parents of this particular Firework. FW or list of FWS.
prev_calc_dir (str): Path to a previous calculation to copy from
\\*\\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
self.structure = structure
nsites = len(self.structure.sites)
# Check for magmoms
if "magmom" in self.structure.site_properties:
l = [[0.0, 0.0, m] for m in self.structure.site_properties["magmom"]]
ncl_magmoms = [elem for ll in l for elem in ll]
else:
ncl_magmoms = 3 * nsites * [0.0]
ncl_magmoms = [str(m) for m in ncl_magmoms]
ncl_magmoms = " ".join(ncl_magmoms)
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown", surface
)
t = []
if prev_calc_dir:
t.append(
CopyVaspOutputs(
calc_dir=prev_calc_dir,
additional_files=["CHGCAR"],
contcar_to_poscar=True,
)
)
elif parents:
t.append(
CopyVaspOutputs(
calc_loc=True, additional_files=["CHGCAR"], contcar_to_poscar=True
)
)
else:
raise ValueError("Must specify structure or previous calculation")
t.append(WriteWannier90Win(wf_uuid=uuid, db_file=db_file))
# Copy files to a folder called 'input' for z2pack
t.append(SetUpZ2Pack(ncl_magmoms=ncl_magmoms, wf_uuid=uuid, db_file=db_file))
t.append(RunZ2Pack(surface=surface))
t.extend([PassCalcLocs(name=name), Z2PackToDb(db_file=db_file, wf_uuid=uuid)])
super().__init__(t, parents=parents, name=fw_name, **kwargs)
[docs]class InvariantFW(Firework):
def __init__(
self,
parents=None,
structure=None,
symmetry_reduction=None,
equiv_planes=None,
uuid=None,
name="invariant",
db_file=None,
**kwargs
):
"""
Process Z2Pack outputs, e.g. calculate Z2=(v0; v1, v2, v3).
Args:
parents (list): Parent FWs.
structure (Structure): Structure object.
symmetry_reduction (bool): Set to False to disable symmetry reduction and
include all 6 BZ surfaces (for magnetic systems).
equiv_planes (list): Like "kx_0", "kx_1", "ky_0", etc. that indicates TRIM surface in BZ.
uuid (str): Unique wf identifier.
name (str): name of this FW
db_file (str): path to the db file
parents (Firework): Parents of this particular Firework. FW or list of FWS.
\\*\\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown",
"invariant",
)
t = []
# Create a dictionary of TRIM surface: Z2 invariant, Chern number
t.append(
InvariantsToDB(
wf_uuid=uuid,
db_file=db_file,
structure=structure,
symmetry_reduction=symmetry_reduction,
equiv_planes=equiv_planes,
)
)
super().__init__(t, parents=parents, name=fw_name, **kwargs)
