pymatgen.io.feff.sets module

This module defines the FeffInputSet abstract base class and a concrete implementation for the Materials Project. The basic concept behind an input set is to specify a scheme to generate a consistent set of Feff inputs from a structure without further user intervention. This ensures comparability across runs.

class AbstractFeffInputSet[source]

Bases: MSONable

Abstract base class representing a set of Feff input parameters. The idea is that using a FeffInputSet, a complete set of input files (feffPOT, feffXANES, feffEXAFS, ATOMS, feff.inp)set_ can be generated in an automated fashion for any structure.

all_input()[source]

Returns all input files as a dict of {filename: feffio object}

abstract property atoms[source]

Returns Atoms string from a structure that goes in feff.inp file.

Returns:

Atoms object.

abstract header()[source]

Returns header to be used in feff.inp file from a pymatgen structure

abstract property potential[source]

Returns POTENTIAL section used in feff.inp from a structure.

abstract property tags[source]

Returns standard calculation parameters.

write_input(output_dir='.', make_dir_if_not_present=True)[source]

Writes a set of FEFF input to a directory.

Parameters:

  • output_dir – Directory to output the FEFF input files

  • make_dir_if_not_present – Set to True if you want the directory ( and the whole path) to be created if it is not present.

class FEFFDictSet(absorbing_atom: str | int, structure: Structure | Molecule, radius: float, config_dict: dict, edge: str = 'K', spectrum: str = 'EXAFS', nkpts=1000, user_tag_settings: dict | None = None, spacegroup_analyzer_settings: dict | None = None)[source]

Bases: AbstractFeffInputSet

Standard implementation of FeffInputSet, which can be extended by specific implementations.

Parameters:

  • absorbing_atom (str/int) – absorbing atom symbol or site index

  • structure – Structure or Molecule object. If a Structure, SpaceGroupAnalyzer is used to determine symmetrically-equivalent sites. If a Molecule, there is no symmetry checking.

  • radius (float) – cluster radius

  • config_dict (dict) – control tag settings dict

  • edge (str) – absorption edge

  • spectrum (str) – type of spectrum to calculate, available options : EXAFS, XANES, DANES, XMCD, ELNES, EXELFS, FPRIME, NRIXS, XES. The default is EXAFS.

  • nkpts (int) – Total number of kpoints in the brillouin zone. Used only when feff is run in the reciprocal space mode.

  • user_tag_settings (dict) –

    override default tag settings. To delete tags, set the key ‘_del’ in the user_tag_settings. eg: user_tag_settings={“_del”: [“COREHOLE”, “EXCHANGE”]} To specify a net charge on the structure, pass an “IONS” tag containing a list

    of tuples where the first element is the unique potential value (ipot value) and the second element is the charge to be applied to atoms associated with that potential, e.g. {“IONS”: [(0, 0.1), (1, 0.1), (2, 0.1)]} will result in

    ION 0 0.1 ION 1 0.1 ION 2 0.1

    being written to the input file.

  • spacegroup_analyzer_settings (dict) – parameters passed to SpacegroupAnalyzer. E.g., {“symprec”: 0.01, “angle_tolerance”: 4}

property atoms: Atoms[source]

absorber + the rest

Returns:

Atoms

static from_directory(input_dir)[source]

Read in a set of FEFF input files from a directory, which is useful when existing FEFF input needs some adjustment.

header(source: str = '', comment: str = '')[source]

Creates header string from structure object

Parameters:

  • source – Source identifier used to create structure, can be defined however user wants to organize structures, calculations, etc. example would be Materials Project material ID number.

  • comment – comment to include in header

Returns:

Header

property potential: Potential[source]

FEFF potential

Returns:

Potential

property tags: Tags[source]

FEFF job parameters.

Returns:

Tags

class MPEELSDictSet(absorbing_atom, structure, edge, spectrum, radius, beam_energy, beam_direction, collection_angle, convergence_angle, config_dict, user_eels_settings=None, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]

Bases: FEFFDictSet

FeffDictSet for ELNES spectroscopy.

Parameters:

  • absorbing_atom (str/int) – absorbing atom symbol or site index

  • structure (Structure) – input structure

  • edge (str) – absorption edge

  • spectrum (str) – ELNES or EXELFS

  • radius (float) – cluster radius in Angstroms.

  • beam_energy (float) – Incident beam energy in keV

  • beam_direction (list) – Incident beam direction. If None, the cross section will be averaged.

  • collection_angle (float) – Detector collection angle in mrad.

  • convergence_angle (float) – Beam convergence angle in mrad.

  • user_eels_settings (dict) – override default EELS config. See MPELNESSet.yaml for supported keys.

  • nkpts (int) – Total number of kpoints in the brillouin zone. Used only when feff is run in the reciprocal space mode.

  • user_tag_settings (dict) – override default tag settings

  • **kwargs – Passthrough to FEFFDictSet

class MPELNESSet(absorbing_atom, structure, edge: str = 'K', radius: float = 10.0, beam_energy: float = 100, beam_direction=None, collection_angle: float = 1, convergence_angle: float = 1, user_eels_settings=None, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]

Bases: MPEELSDictSet

FeffDictSet for ELNES spectroscopy.

Parameters:

  • absorbing_atom (str/int) – absorbing atom symbol or site index

  • structure (Structure) – input structure

  • edge (str) – absorption edge

  • radius (float) – cluster radius in Angstroms.

  • beam_energy (float) – Incident beam energy in keV

  • beam_direction (list) – Incident beam direction. If None, the cross section will be averaged.

  • collection_angle (float) – Detector collection angle in mrad.

  • convergence_angle (float) – Beam convergence angle in mrad.

  • user_eels_settings (dict) – override default EELS config. See MPELNESSet.yaml for supported keys.

  • nkpts (int) – Total number of kpoints in the brillouin zone. Used only when feff is run in the reciprocal space mode.

  • user_tag_settings (dict) – override default tag settings

  • **kwargs – Passthrough to FEFFDictSet

CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'ELNES': {'ANGLES': '1 1', 'BEAM_DIRECTION': '0 1 0', 'BEAM_ENERGY': '100 0 1 1', 'ENERGY': '4 0.04 0.1', 'MESH': '50 1', 'POSITION': '0.0 0.0'}, 'EXCHANGE': '0 0.0 0.0 2', 'FMS': '7.5 0', 'LDOS': '-20.0 20.0 0.1', 'PRINT': '1 0 0 0 0 0', 'S02': 0.0, 'SCF': '6.0 0 30 0.2 1'}[source]
class MPEXAFSSet(absorbing_atom, structure, edge: str = 'K', radius: float = 10.0, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]

Bases: FEFFDictSet

FeffDictSet for EXAFS spectroscopy.

Parameters:

  • absorbing_atom (str/int) – absorbing atom symbol or site index

  • structure (Structure) – input structure

  • edge (str) – absorption edge

  • radius (float) – cluster radius in Angstroms.

  • nkpts (int) – Total number of kpoints in the brillouin zone. Used only when feff is run in the reciprocal space mode.

  • user_tag_settings (dict) – override default tag settings

  • **kwargs – Passthrough to FEFFDictSet

CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXAFS': 20, 'PRINT': '1 0 0 0 0 0', 'RPATH': 10, 'S02': 0.0, 'SCF': '4.5 0 30 .2 1'}[source]
class MPEXELFSSet(absorbing_atom, structure, edge='K', radius: float = 10.0, beam_energy: float = 100, beam_direction=None, collection_angle: float = 1, convergence_angle: float = 1, user_eels_settings=None, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]

Bases: MPEELSDictSet

FeffDictSet for EXELFS spectroscopy.

Parameters:

  • absorbing_atom (str/int) – absorbing atom symbol or site index

  • structure (Structure) – input structure

  • edge (str) – absorption edge

  • radius (float) – cluster radius in Angstroms.

  • beam_energy (float) – Incident beam energy in keV

  • beam_direction (list) – Incident beam direction. If None, the cross section will be averaged.

  • collection_angle (float) – Detector collection angle in mrad.

  • convergence_angle (float) – Beam convergence angle in mrad.

  • user_eels_settings (dict) – override default EELS config. See MPEXELFSSet.yaml for supported keys.

  • nkpts (int) – Total number of kpoints in the brillouin zone. Used only when feff is run in the reciprocal space mode.

  • user_tag_settings (dict) – override default tag settings

  • **kwargs – Passthrough to FEFFDictSet

CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXCHANGE': '0 0.0 0.0 2', 'EXELFS': {'ANGLES': '1 1', 'BEAM_DIRECTION': '0 1 0', 'BEAM_ENERGY': '100 0 1 1', 'ENERGY': 20, 'MESH': '50 1', 'POSITION': '0.0 0.0'}, 'PRINT': '1 0 0 0 0 0', 'RPATH': 10, 'S02': 0.0, 'SCF': '5.0 0 30 0.2 1'}[source]
class MPXANESSet(absorbing_atom, structure, edge: str = 'K', radius: float = 10.0, nkpts: int = 1000, user_tag_settings: dict | None = None, **kwargs)[source]

Bases: FEFFDictSet

FeffDictSet for XANES spectroscopy.

Parameters:

  • absorbing_atom (str/int) – absorbing atom symbol or site index

  • structure (Structure) – input

  • edge (str) – absorption edge

  • radius (float) – cluster radius in Angstroms.

  • nkpts (int) – Total number of kpoints in the brillouin zone. Used only when feff is run in the reciprocal space mode.

  • user_tag_settings (dict) – override default tag settings

  • **kwargs – Passthrough to FEFFDictSet

CONFIG = {'CONTROL': '1 1 1 1 1 1', 'COREHOLE': 'FSR', 'EDGE': 'K', 'EXCHANGE': '0 0.0 0.0 2', 'FMS': '7.5 0', 'LDOS': '-30. 15. .1', 'PRINT': '1 0 0 0 0 0', 'S02': 0.0, 'SCF': '4.5 0 30 .2 1', 'XANES': '3.7 .04 .1'}[source]