def test_cleanupfiles_calc_loc(self):
# will test deleting files from previous folder
fw1 = Firework(
[
CreateFolder(folder_name="to_remove.relax0"),
CreateFolder(folder_name="to_remove.relax1"),
CreateFolder(folder_name="dont_remove.relax0"),
CreateFolder(folder_name="shouldnt_touch"),
PassCalcLocs(name="fw1"),
],
name="fw1",
)
fw2 = Firework(
[
DeleteFilesPrevFolder(files=["to_remove*", "dont_remove"],
calc_loc=True),
PassCalcLocs(name="fw2"),
],
name="fw2",
parents=fw1,
)
wf = Workflow([fw1, fw2])
self.lp.add_wf(wf)
rapidfire(self.lp)
fw2 = self.lp.get_fw_by_id(self.lp.get_fw_ids({"name": "fw2"})[0])
calc_locs = fw2.spec["calc_locs"]
self.assertTrue(
os.path.exists(
os.path.join(
get_calc_loc("fw1", calc_locs)["path"],
"dont_remove.relax0")))
self.assertTrue(
os.path.exists(
os.path.join(
get_calc_loc("fw1", calc_locs)["path"], "shouldnt_touch")))
self.assertFalse(
os.path.exists(
os.path.join(
get_calc_loc("fw1", calc_locs)["path"],
"to_remove.relax0")))
self.assertFalse(
os.path.exists(
os.path.join(
get_calc_loc("fw1", calc_locs)["path"],
"to_remove.relax1")))
def test_createfolder(self):
folder_name = "test_folder"
fw1 = Firework([
CreateFolder(folder_name=folder_name, change_dir=False),
PassCalcLocs(name="fw1")
],
name="fw3")
fw2 = Firework([PassCalcLocs(name="fw2")], name="fw2", parents=fw1)
wf = Workflow([fw1, fw2])
self.lp.add_wf(wf)
rapidfire(self.lp)
fw2 = self.lp.get_fw_by_id(self.lp.get_fw_ids({"name": "fw2"})[0])
calc_locs = fw2.spec["calc_locs"]
self.assertTrue(
os.path.exists(
get_calc_loc("fw1", calc_locs)["path"] + "/" + folder_name))
def __init__(
self,
structure,
name="static dipole moment",
static_name="static",
vasp_cmd="vasp",
vasp_input_set=None,
vasp_input_set_params=None,
db_file=None,
parents=None,
gap_threshold=0.010,
interpolate=False,
start=None,
end=None,
this_image=0,
nimages=5,
**kwargs,
):
"""
Static Firework that calculates the dipole moment of structure or a
single interpolated image of structures output by two calculations
specified by PassCalcLoc names start and end.
This Firework uses three steps to calculate the dipole moment.
1. A StaticFW or StaticInterpolatFW calculation is performed to compute
the band gap of the structure.
2. Because VASP cannot compute the dipole moment of metallic structures,
CheckBandgap checks that the structure has a band gap greater than
gap_threshold. If the structure has a band gap less than
gap_threshold, the Firework defuses. Otherwise,
3. a polarization calculation (LCALCPOL=TRUE) is performed to calculate
the dipole moment.
If interpolate is equal to True, the keywords start and end are
PassCalcLoc names used to locate the output structures (CONTCAR) of two
previous calculations. These two structures must have the same number
and type of atoms given in identical order in the structures. These
structures are used to create nimages structures interpolations.
this_image specifies which of the interpolated structures to use in this
Firework. For example in the ferroelectric workflow, two structures that
can be distorted into one another (a high-symmetry nonpolar structure
and a low-symmetry polar structure) are relaxed using OptimizeFW. Then
the dipole moment is calculated for nimages intermediate structures
generated by interpolating between these two relaxed structures.
Args:
structure (Structure): Input structure. For an interpolation, this
is a dummy structure. See interpolate arg description.
name (str): Name for the polarization FireWork.
static_name (str): Name for the SCF run to be used in PassCalcLoc
if copy_vasp_outputs != True.
vasp_cmd (str): Command to run vasp.
vasp_input_set (str): string name for the VASP input set (e.g.,
"MITMDVaspInputSet").
vasp_input_set_params (dict): Dict of vasp_input_set_kwargs.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework. FW or list
of FWS.
gap_threshold: Band gap cutoff for determining whether polarization
calculation will proceed from SCF band gap.
interpolate (bool): use structure created by interpolating CONTCAR
structure from calculations indicated by start and end
PassCalcLoc names. If interpolate is False, start and end do
not need to be set.
start (str): PassCalcLoc name of StaticFW or RelaxFW run of starting
structure
end (str): PassCalcLoc name of StaticFW or RelaxFW run of ending
structure
this_image (int): which interpolation to use for this run of the
nimage interpolations.
nimages (int): number of interpolations between CONTCAR structures
from calculations indicated by start and end args.
"""
t = []
# Ensure that LWAVE is set to true so we can use WAVECAR for
# polarization calculation.
vasp_input_set_params = vasp_input_set_params or {}
vasp_input_set_params = vasp_input_set_params.copy()
if not vasp_input_set_params.get("user_incar_settings", None):
vasp_input_set_params.update({"user_incar_settings": {}})
vasp_input_set_params["user_incar_settings"].update({"LWAVE": True})
vasp_input_set = vasp_input_set or "MPStaticSet"
if interpolate:
static = StaticInterpolateFW(
structure,
start,
end,
name=static_name,
vasp_input_set=vasp_input_set,
vasp_input_set_params=vasp_input_set_params,
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=parents,
this_image=this_image,
nimages=nimages,
**kwargs,
)
else:
vasp_input_set = MPStaticSet(structure, **vasp_input_set_params)
static = StaticFW(
structure,
name=static_name,
vasp_input_set=vasp_input_set,
vasp_input_set_params=vasp_input_set_params,
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=parents,
**kwargs,
)
t.extend(static.tasks)
# Defuse workflow if bandgap is less than gap_threshold.
t.append(CheckBandgap(min_gap=gap_threshold))
# Create new directory and move to that directory to perform
# polarization calculation
t.append(CreateFolder(folder_name="polarization", change_dir=True))
# Copy VASP Outputs from static calculation
t.extend([
CopyVaspOutputs(
calc_loc=static_name,
additional_files=["CHGCAR", "WAVECAR"],
contcar_to_poscar=True,
),
ModifyIncar(incar_update={"lcalcpol": True}),
RunVaspCustodian(vasp_cmd=vasp_cmd),
PassCalcLocs(name=name),
VaspToDb(db_file=db_file, additional_fields={"task_label": name}),
])
# Note, Outcar must have read_lcalcpol method for polarization
# information to be processed. ...assuming VaspDrone will automatically
# assimilate all properties of the Outcar.
super().__init__(
t,
parents=parents,
name=f"{structure.composition.reduced_formula}-{name}",
**kwargs,
)