def get_wf_eels(absorbing_atom, structure=None, spectrum_type="ELNES", edge="K", radius=10.,
beam_energy=100, beam_direction=None, collection_angle=1, convergence_angle=1,
user_eels_settings=None, user_tag_settings=None, feff_cmd="feff", db_file=None,
metadata=None, use_primitive=False, feff_input_set=None):
"""
Returns FEFF ELNES/EXELFS spectroscopy workflow.
Args:
absorbing_atom (str): absorbing atom symbol
structure (Structure): input structure. If None and mp_id is provided, the corresponding
structure will be fetched from the Materials Project db.
spectrum_type (str): ELNES or EXELFS
edge (str): absorption edge. K, L1, L2, L3
radius (float): cluster radius in angstroms. Ignored for reciprocal space calculations
beam_energy (float): the incident beam energy in keV
beam_direction (list): incident beam direction. Default is none ==> the spectrum will be
averaged over all directions.
collection_angle (float): collection angle in mrad
convergence_angle (float): convergence angle in mrad
user_eels_settings (dict): override default eels settings.
user_tag_settings (dict): override other general feff default tag settings.
feff_cmd (str): path to the feff binary
db_file (str): path to the db file.
metadata (dict): meta data
use_primitive (bool): convert the structure to primitive form. This helps to
reduce the number of fireworks in the workflow if the absorbing atoms is
specified by its atomic symbol.
feff_input_set (FeffDictSet)
Returns:
Workflow
"""
if use_primitive:
structure = structure.get_primitive_structure()
# get the absorbing atom site index/indices
ab_atom_indices = get_all_absorbing_atoms(absorbing_atom, structure)
override_default_feff_params = {"user_tag_settings": user_tag_settings}
# add firework for each absorbing atom site index
fws = []
for ab_idx in ab_atom_indices:
fw_metadata = dict(metadata) if metadata else {}
fw_metadata["absorbing_atom_index"] = ab_idx
fw_name = "{}-{}-{}".format(spectrum_type, edge, ab_idx)
fws.append(EELSFW(ab_idx, structure, spectrum_type, edge=edge, radius=radius,
beam_energy=beam_energy, beam_direction=beam_direction,
collection_angle=collection_angle, convergence_angle=convergence_angle,
user_eels_settings=user_eels_settings, feff_cmd=feff_cmd, db_file=db_file,
metadata=fw_metadata, name=fw_name, feff_input_set=feff_input_set,
override_default_feff_params=override_default_feff_params))
wfname = "{}:{}:{} edge".format(structure.composition.reduced_formula,
"{} spectroscopy".format(spectrum_type), edge)
wf_metadata = dict(metadata) if metadata else {}
wf_metadata["absorbing_atom_indices"] = list(ab_atom_indices)
return Workflow(fws, name=wfname, metadata=wf_metadata)
def get_wf_xas(absorbing_atom, structure, spectrum_type="XANES", edge="K", radius=10.0,
feff_input_set=None, feff_cmd="feff", db_file=None, metadata=None,
user_tag_settings=None, use_primitive=False):
"""
Returns FEFF XANES/EXAFS spectroscopy workflow.
Args:
absorbing_atom (str/int): absorbing atom symbol or site index. If the symbol is given,
then the returned workflow will have fireworks for each absorbing site with the
same symbol.
structure (Structure): input structure
spectrum_type (str): XANES or EXAFS
edge (str): absorption edge. Example: K, L1, L2, L3
radius (float): cluster radius in angstroms. Ignored for K space calculations
feff_input_set (FeffDictSet): the input set for the FEFF run
feff_cmd (str): path to the feff binary
db_file (str): path to the db file.
metadata (dict): meta data
user_tag_settings (dict): override feff default tag settings
use_primitive (bool): convert the structure to primitive form. This helps to
reduce the number of fireworks in the workflow if the absorbing atom is
specified by its atomic symbol.
Returns:
Workflow
"""
if use_primitive:
structure = structure.get_primitive_structure()
# get the absorbing atom site index/indices
ab_atom_indices = get_all_absorbing_atoms(absorbing_atom, structure)
override_default_feff_params = {"user_tag_settings": user_tag_settings}
# add firework for each absorbing atom site index
fws = []
for ab_idx in ab_atom_indices:
fw_metadata = dict(metadata) if metadata else {}
fw_metadata["absorbing_atom_index"] = ab_idx
fw_name = "{}-{}-{}".format(spectrum_type, edge, ab_idx)
fws.append(XASFW(ab_idx, structure, spectrum_type, edge=edge, radius=radius,
feff_input_set=feff_input_set, feff_cmd=feff_cmd, db_file=db_file,
metadata=fw_metadata, name=fw_name,
override_default_feff_params=override_default_feff_params))
wf_metadata = dict(metadata) if metadata else {}
wf_metadata["absorbing_atom_indices"] = list(ab_atom_indices)
wfname = "{}:{}:{} edge".format(structure.composition.reduced_formula,
"{} spectroscopy".format(spectrum_type), edge)
return Workflow(fws, name=wfname, metadata=metadata)