def get_wf_deformations(structure,
deformations,
name="deformation",
vasp_input_set=None,
vasp_cmd="vasp",
db_file=None,
tag="",
copy_vasp_outputs=True,
metadata=None):
"""
Returns a structure deformation workflow.
Firework 1 : structural relaxation
Firework 2 - len(deformations): Deform the optimized structure and run static calculations.
Args:
structure (Structure): input structure to be optimized and run
deformations (list of 3x3 array-likes): list of deformations
name (str): some appropriate name for the transmuter fireworks.
vasp_input_set (DictVaspInputSet): vasp input set for static deformed structure calculation.
vasp_cmd (str): command to run
db_file (str): path to file containing the database credentials.
tag (str): some unique string that will be appended to the names of the fireworks so that
the data from those tagged fireworks can be queried later during the analysis.
copy_vasp_outputs (bool): whether or not copy the outputs from the previous calc(usually
structure optimization) before the transmuter fireworks.
metadata (dict): meta data
Returns:
Workflow
"""
fws, parents = [], []
vasp_input_set = vasp_input_set or MPStaticSet(structure, force_gamma=True)
# Deformation fireworks with the task to extract and pass stress-strain appended to it.
for n, deformation in enumerate(deformations):
fw = TransmuterFW(name="{} {} {}".format(tag, name, n),
structure=structure,
transformations=['DeformStructureTransformation'],
transformation_params=[{
"deformation":
deformation.tolist()
}],
vasp_input_set=vasp_input_set,
copy_vasp_outputs=copy_vasp_outputs,
parents=parents,
vasp_cmd=vasp_cmd,
db_file=db_file)
fws.append(fw)
wfname = "{}:{}".format(structure.composition.reduced_formula, name)
return Workflow(fws, name=wfname, metadata=metadata)
def get_wf_deformations(
structure,
deformations,
name="deformation",
vasp_input_set=None,
vasp_cmd="vasp",
db_file=None,
tag="",
copy_vasp_outputs=True,
metadata=None,
):
"""
Returns a structure deformation workflow.
Worfklow consists of: len(deformations) in which the structure is deformed followed
by a static calculation.
Args:
structure (Structure): input structure to be optimized and run
deformations (list of 3x3 array-likes): list of deformations
name (str): some appropriate name for the transmuter fireworks.
vasp_input_set (DictVaspInputSet): vasp input set for static deformed structure
calculation.
vasp_cmd (str): command to run
db_file (str): path to file containing the database credentials.
tag (str): some unique string that will be appended to the names of the
fireworks so that the data from those tagged fireworks can be queried later
during the analysis.
copy_vasp_outputs (bool): whether or not copy the outputs from the previous calc
(usually structure optimization) before the transmuter fireworks.
metadata (dict): meta data
Returns:
Workflow
"""
vasp_input_set = vasp_input_set or MPStaticSet(structure, force_gamma=True)
fws = []
for n, deformation in enumerate(deformations):
fw = TransmuterFW(
name=f"{tag} {name} {n}",
structure=structure,
transformations=["DeformStructureTransformation"],
transformation_params=[{
"deformation": deformation.tolist()
}],
vasp_input_set=vasp_input_set,
copy_vasp_outputs=copy_vasp_outputs,
vasp_cmd=vasp_cmd,
db_file=db_file,
)
fws.append(fw)
wfname = f"{structure.composition.reduced_formula}:{name}"
return Workflow(fws, name=wfname, metadata=metadata)
def get_slab_fw(slab,
transmuter=False,
db_file=None,
vasp_input_set=None,
parents=None,
vasp_cmd="vasp",
name="",
add_slab_metadata=True,
user_incar_settings=None):
"""
Function to generate a a slab firework. Returns a TransmuterFW if
bulk_structure is specified, constructing the necessary transformations
from the slab and slab generator parameters, or an OptimizeFW if only a
slab is specified.
Args:
slab (Slab or Structure): structure or slab corresponding
to the slab to be calculated
transmuter (bool): whether or not to use a TransmuterFW based
on slab params, if this option is selected, input slab must
be a Slab object (as opposed to Structure)
vasp_input_set (VaspInputSet): vasp_input_set corresponding to
the slab calculation
parents (Fireworks or list of ints): parent FWs
db_file (string): path to database file
vasp_cmd (string): vasp command
name (string): name of firework
add_slab_metadata (bool): whether to add slab metadata to task doc
Returns:
Firework corresponding to slab calculation
"""
vasp_input_set = vasp_input_set or MPSurfaceSet(
slab, user_incar_settings=user_incar_settings)
# If a bulk_structure is specified, generate the set of transformations,
# else just create an optimize FW with the slab
if transmuter:
if not isinstance(slab, Slab):
raise ValueError(
"transmuter mode requires slab to be a Slab object")
# Get transformation from oriented bulk and slab
oriented_bulk = slab.oriented_unit_cell
slab_trans_params = get_slab_trans_params(slab)
trans_struct = SlabTransformation(**slab_trans_params)
slab_from_bulk = trans_struct.apply_transformation(oriented_bulk)
# Ensures supercell construction
supercell_trans = SupercellTransformation.from_scaling_factors(
round(slab.lattice.a / slab_from_bulk.lattice.a),
round(slab.lattice.b / slab_from_bulk.lattice.b))
# Get site properties, set velocities to zero if not set to avoid
# custodian issue
site_props = slab.site_properties
if 'velocities' not in site_props:
site_props['velocities'] = [0. for s in slab]
# Get adsorbates for InsertSitesTransformation
if "adsorbate" in slab.site_properties.get("surface_properties", ""):
ads_sites = [
site for site in slab
if site.properties["surface_properties"] == "adsorbate"
]
else:
ads_sites = []
transformations = [
"SlabTransformation", "SupercellTransformation",
"InsertSitesTransformation", "AddSitePropertyTransformation"
]
trans_params = [
slab_trans_params, {
"scaling_matrix": supercell_trans.scaling_matrix
}, {
"species": [site.species_string for site in ads_sites],
"coords": [site.frac_coords for site in ads_sites]
}, {
"site_properties": site_props
}
]
fw = TransmuterFW(name=name,
structure=oriented_bulk,
transformations=transformations,
transformation_params=trans_params,
copy_vasp_outputs=True,
db_file=db_file,
vasp_cmd=vasp_cmd,
parents=parents,
vasp_input_set=vasp_input_set)
else:
fw = OptimizeFW(name=name,
structure=slab,
vasp_input_set=vasp_input_set,
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=parents,
job_type="normal")
# Add slab metadata
if add_slab_metadata:
parent_structure_metadata = get_meta_from_structure(
slab.oriented_unit_cell)
fw.tasks[-1]["additional_fields"].update({
"slab":
slab,
"parent_structure":
slab.oriented_unit_cell,
"parent_structure_metadata":
parent_structure_metadata
})
return fw
def get_slab_fw(slab,
bulk_structure=None,
slab_gen_params={},
db_file=None,
vasp_input_set=None,
parents=None,
vasp_cmd="vasp",
name=""):
"""
Function to generate a a slab firework. Returns a TransmuterFW if bulk_structure is specified,
constructing the necessary transformations from the slab and slab generator parameters,
or an OptimizeFW if only a slab is specified.
Args:
slab (Slab or Structure): structure or slab corresponding
to the slab to be calculated
bulk_structure (Structure): bulk structure corresponding to slab, if
provided, slab firework is constructed as a TransmuterFW using
the necessary transformations to get the slab from the bulk
slab_gen_params (dict): dictionary of slab generation parameters
used to generate the slab, necessary to get the slab
that corresponds to the bulk structure
vasp_input_set (VaspInputSet): vasp_input_set corresponding to
the slab calculation
parents (Fireworks or list of ints): parent FWs
db_file (string): path to database file
vasp_cmd (string): vasp command
Returns:
Firework
"""
vasp_input_set = vasp_input_set or MVLSlabSet(slab)
# If a bulk_structure is specified, generate the set of transformations, else
# just create an optimize FW with the slab
if bulk_structure:
if not isinstance(slab, Slab):
raise ValueError(
"structure input to get_slab_fw requires slab to be a slab object!"
)
slab_trans_params = {
"miller_index": slab.miller_index,
"shift": slab.shift
}
slab_trans_params.update(slab_gen_params)
# Get supercell parameters
trans_struct = SlabTransformation(**slab_trans_params)
slab_from_bulk = trans_struct.apply_transformation(bulk_structure)
supercell_trans = SupercellTransformation.from_scaling_factors(
round(slab.lattice.a / slab_from_bulk.lattice.a),
round(slab.lattice.b / slab_from_bulk.lattice.b))
# Get adsorbates for InsertSitesTransformation
if "adsorbate" in slab.site_properties.get("surface_properties",
[None]):
ads_sites = [
site for site in slab
if site.properties["surface_properties"] == "adsorbate"
]
else:
ads_sites = []
transformations = [
"SlabTransformation", "SupercellTransformation",
"InsertSitesTransformation", "AddSitePropertyTransformation"
]
trans_params = [
slab_trans_params, {
"scaling_matrix": supercell_trans.scaling_matrix
}, {
"species": [site.species_string for site in ads_sites],
"coords": [site.frac_coords for site in ads_sites]
}, {
"site_properties": slab.site_properties
}
]
return TransmuterFW(name=name,
structure=bulk_structure,
transformations=transformations,
transformation_params=trans_params,
copy_vasp_outputs=True,
db_file=db_file,
vasp_cmd=vasp_cmd,
parents=parents,
vasp_input_set=vasp_input_set)
else:
return OptimizeFW(name=name,
structure=slab,
vasp_input_set=vasp_input_set,
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=parents,
job_type="normal")