vaspparser.vasp.vasprun.Vasprun

class vaspparser.vasp.vasprun.Vasprun

Bases: object

This module is used to parse vasprun.xml files and store the data consistent with the pyiron input/output storage formats.

vasprun_dict

Dictionary containing all information from the calculation parsed from the vasprun.xml

file. If you consider a simulation with N atoms and M ionic steps

‘positions’ (numpy.ndarray): MxNx3 array containing all the relative positions ‘cell’ (numpy.ndarray): Mx3x3 array containing all the size and shape of cells at every iteration point ‘forces’ (numpy.ndarray): MxNx3 array containing all the forces in eV/A ‘total_energies’ (numpy.ndarray): 1xM array containing all the total energies in eV

Type:

dict

__init__()

Methods

__init__()
from_file([filename])	Parsing vasprun.xml from the working directory
get_electronic_structure([es_class])	Construct an ElectronicStructure object from the parsed vasprun.xml data.
get_final_structure()	Gets the final structure from the simulation
get_initial_structure()	Gets the initial structure from the simulation
get_potentiostat_output()	Gets the input from the vasp potentiostat output and stores it using intuitive names
get_valence_electrons_per_atom()	Gets the number of valence electrons for each atom in the final structure
parse_atom_information_to_dict(node, d)	Parses atom information from a node to a dictionary
parse_calc_to_dict(node, d)	Parses ionic step data from a node to a dictionary
parse_cce_to_dict(node, d)	Parse constrained-charge-equilibration (CCE) output from a vasprun.xml node.
parse_eigenvalues_to_dict(node, d)	Parses eigenvalue and occupancy data from a node to a dictionary
parse_fermi_level_to_dict(node, d)	Parses fermi level from a node to a dictionary
parse_item_to_dict(node, d)	Parses values from an item to a dictionary
parse_kpoints_to_dict(node, d)	Parses k-points data from a node to a dictionary
parse_parameters(node, d)	Parses parameter data from a node to a dictionary
parse_partial_dos_to_dict(node, d)	Parses partial dos data from a node to a dictionary
parse_projected_dos_to_dict(node, d)	Parses partial dos data from a node to a dictionary
parse_recursively(node, d[, key_name])	Parses recursively from a node to a dictionary
parse_root_to_dict(filename)	Parse the vasprun.xml file and populate vasprun_dict with all data.
parse_scf(node)	Parses the total energy and dipole moments for a VASP calculation
parse_structure_to_dict(node, d)	Parses structure from a node to a dictionary
parse_total_dos_to_dict(node, d)	Parses total dos data from a node to a dictionary

from_file(filename: str = 'vasprun.xml')

Parsing vasprun.xml from the working directory

Parameters:

filename (str) – Path to the vasprun file

get_electronic_structure(es_class=<class 'vaspparser.dft.waves.electronic.ElectronicStructure'>)

Construct an ElectronicStructure object from the parsed vasprun.xml data.

Transfers k-point list, k-point weights, eigenvalue matrix, occupancy matrix, Fermi level, total DOS (if available), atom-resolved DOS (if LORBIT >= 10), and projected DOS (if LORBIT = 11) into the returned object.

Parameters:

es_class – Class to instantiate for the electronic structure; defaults to ElectronicStructure.

Returns:

Populated electronic structure object

Return type:

ElectronicStructure

get_final_structure()

Gets the final structure from the simulation

Returns:

The final structure

Return type:

pyiron.atomistics.structure.atoms.Atoms

get_initial_structure()

Gets the initial structure from the simulation

Returns:

The initial structure

Return type:

pyiron.atomistics.structure.atoms.Atoms

get_potentiostat_output()

Gets the input from the vasp potentiostat output and stores it using intuitive names

Returns:

Dictionary with potentiostat output

Return type:

dict/None

get_valence_electrons_per_atom()

Gets the number of valence electrons for each atom in the final structure

Returns:

Array of valence charges

Return type:

numpy.ndarray

parse_atom_information_to_dict(node, d)

Parses atom information from a node to a dictionary

Parameters:

• node (xml.etree.Element instance) – The node to parse

• d (dict) – The dictionary to which data is to be parsed

parse_calc_to_dict(node, d)

Parses ionic step data from a node to a dictionary

Parameters:

• node (xml.etree.Element instance) – The node to parse

• d (dict) – The dictionary to which data is to be parsed

static parse_cce_to_dict(node, d: dict)

Parse constrained-charge-equilibration (CCE) output from a vasprun.xml node.

Parameters:

• node (xml.etree.Element) – The CCE node to parse

• d (dict) – Dictionary to which the parsed values are appended

parse_eigenvalues_to_dict(node, d)

Parses eigenvalue and occupancy data from a node to a dictionary

Parameters:

• node (xml.etree.Element instance) – The node to parse

• d (dict) – The dictionary to which data is to be parsed

parse_fermi_level_to_dict(node, d)

Parses fermi level from a node to a dictionary

Parameters:

• node (xml.etree.Element instance) – The node to parse

• d (dict) – The dictionary to which data is to be parsed

static parse_item_to_dict(node, d)

Parses values from an item to a dictionary

Parameters:

• node (etree.Element instance) – Node to be parsed

• d (dict) – The dictionary to which data is to be parsed

Returns:

d (dictionary)

parse_kpoints_to_dict(node, d: dict)

Parses k-points data from a node to a dictionary

Parameters:

• node (xml.etree.Element instance) – The node to parse

• d (dict) – The dictionary to which data is to be parsed

parse_parameters(node, d)

Parses parameter data from a node to a dictionary

Parameters:

• node (xml.etree.Element instance) – The node to parse

• d (dict) – The dictionary to which data is to be parsed

parse_partial_dos_to_dict(node, d)

Parses partial dos data from a node to a dictionary

Parameters:

• node (xml.etree.Element instance) – The node to parse

• d (dict) – The dictionary to which data is to be parsed

parse_projected_dos_to_dict(node, d)

Parses partial dos data from a node to a dictionary

Parameters:

• node (xml.etree.Element instance) – The node to parse

• d (dict) – The dictionary to which data is to be parsed

parse_recursively(node, d, key_name=None)

Parses recursively from a node to a dictionary

Parameters:

• node (xml.etree.Element instance) – The node to parse

• d (dict) – The dictionary to which data is to be parsed

• key_name (str) – Forcefully assign a key name in case it is not present in the xml file

parse_root_to_dict(filename: str)

Parse the vasprun.xml file and populate vasprun_dict with all data.

This method iterates over the XML tree using iterparse and dispatches each recognized top-level element (generator, incar, kpoints, atominfo, structure, calculation, parameters) to the appropriate sub-parser. After parsing, positions are converted to fractional coordinates if they appear to be in Cartesian, and all lists are converted to numpy arrays.

Parameters:

filename (str) – Path to the vasprun.xml file

parse_scf(node)

Parses the total energy and dipole moments for a VASP calculation

Parameters:

node – (xml.etree.Element instance): The node to parse

Returns:

Dictionary to containing parsed data

Return type:

d (dict)

parse_structure_to_dict(node, d)

Parses structure from a node to a dictionary

Parameters:

• node (xml.etree.Element instance) – The node to parse

• d (dict) – The dictionary to which data is to be parsed

parse_total_dos_to_dict(node, d)

Parses total dos data from a node to a dictionary

Parameters:

• node (xml.etree.Element instance) – The node to parse

• d (dict) – The dictionary to which data is to be parsed