LobsterGraph

LobsterGraph#

class lobsterpy.structuregraph.graph.LobsterGraph(path_to_poscar, path_to_charge, path_to_cohpcar, path_to_icohplist, path_to_madelung, add_additional_data_sg=True, path_to_icooplist=None, path_to_icobilist=None, which_bonds='all', cutoff_icohp=0.1, noise_cutoff=0.1, start=None)[source]#

Bases: object

Class to generate structure graph objects with bonding data from Lobster.

Mode of automatic bonding analysis can be cation-anion or all bonds. The strongest bond is determined based on the ICOHPs. The coordination environments are determined based on cutoff_icohp * ICOHPs values. If the path of ICOBILIST (ICOOPLIST) is provided, the ICOBI (ICOOP) values corresponding to relevant bond labels obtained from the ICOHPLIST are also added as edge properties to the structure graph objects. The Mulliken and Loewdin charges are added as node properties to the structure graph objects.

Variables:

sg – return structure_graph object

Parameters:

  • path_to_poscar (str | Path) – path to POSCAR (e.g., “POSCAR”).

  • path_to_charge (str | Path) – path to CHARGE.lobster (e.g., “CHARGE.lobster”).

  • path_to_cohpcar (str | Path) – path to COHPCAR.lobster (e.g., “COHPCAR.lobster”).

  • path_to_icohplist (str | Path) – path to ICOHPLIST.lobster (e.g., “ICOHPLIST.lobster”).

  • path_to_icooplist (str | Path | None) – path to ICOOPLIST.lobster (e.g., “ICOOPLIST.lobster”).

  • path_to_icobilist (str | Path | None) – path to ICOBILIST.lobster (e.g., “ICOBILIST.lobster”).

  • path_to_madelung (str | Path) – path to MadelungEnergies.lobster (e.g., “MadelungEnergies.lobster”)

  • cutoff_icohp (float) – only bonds that are stronger than cutoff_icohp * strongest ICOHP will be considered.

  • noise_cutoff (float) – if provided hardcodes the lower limit of icohps considered.

  • add_additional_data_sg (bool) – if True will add the information from ICOOPLIST.lobster and ICOBILIST.lobster based on ICOHPLIST.lobster relevant bond.

  • which_bonds (str) – selects which kind of bonds are analyzed. “all” is the default.

  • start (float | None) – start energy for bonding antibonding percent integration.

get_decorated_sg()[source]#

Create a graph object decorated with bonding data from LobsterPy.

Returns:

structure graph object