pymatgen.io.pwmat package

This package implements modules for input and output to and from PWmat.

Submodules

pymatgen.io.pwmat.inputs module

class ACExtractor(file_path: PathLike)[source]

Bases: ACExtractorBase

Extract information contained in atom.config : number of atoms, lattice, types, frac_coords, magmoms

Initialization function

Args: file_path (str): The absolute path of atom.config file.

get_coords() → ndarray[source]

Return the fractional coordinates in structure.

Returns:: Fractional coordinates.
Return type:: np.ndarray

get_lattice() → ndarray[source]

Return the lattice of structure.

Returns:: np.ndarray, shape = (9,)
Return type:: lattice

get_magmoms() → ndarray[source]

Return the magenetic moments of atoms in structure.

Returns:: The magnetic moments of individual atoms.
Return type:: np.ndarray

get_n_atoms() → int[source]: Return the number of atoms in the structure.

get_types() → ndarray[source]

Return the atomic number of atoms in structure.

Returns:: Atomic numbers in order corresponding to sites
Return type:: np.ndarray

class ACExtractorBase[source]

Bases: ABC

A parent class of ACExtractor and ACstrExtractor, ensuring that they are as consistent as possible

abstract get_coords() → ndarray[source]: Get fractional coordinates of atoms in structure defined by atom.config file

abstract get_lattice() → ndarray[source]: Get the lattice of structure defined by atom.config file

abstract get_magmoms() → ndarray[source]: Get atomic magmoms of atoms in structure defined by atom.config file

abstract get_n_atoms() → int[source]: Get the number of atoms in structure defined by atom.config file.

abstract get_types() → ndarray[source]: Get atomic number of atoms in structure defined by atom.config file

class ACstrExtractor(atom_config_str: str)[source]

Bases: ACExtractorBase

Extract information from atom.config file. You can get str by slicing the MOVEMENT.

Initialization function.

Parameters:: atom_config_str (str) – A string describing the structure in atom.config file.

get_atom_energies() → ndarray | None[source]

Return the energies of individual atoms in material system.

Returns:: The energies of individual atoms within the material system.
Return type:: np.ndarray | None

Description:: When turn on ENERGY DEPOSITION, PWmat will output energy per atom.

get_atom_forces() → ndarray[source]

Return the force on atoms in material system.

Returns:: Forces acting on individual atoms of shape=(num_atoms*3,)
Return type:: np.ndarray

get_coords() → ndarray[source]

Return the fractional coordinate of atoms in structure.

Returns:: Fractional coordinates of atoms of shape=(num_atoms*3,)
Return type:: np.ndarray

get_e_tot() → ndarray[source]

Return the total energy of structure.

Returns:: The total energy of the material system.
Return type:: np.ndarray

get_lattice() → ndarray[source]

Return the lattice of structure.

Returns:: Lattice basis vectors of shape=(9,)
Return type:: np.ndarray

get_magmoms() → ndarray[source]

Return the magnetic moments of atoms in structure.

Returns:: Atomic magnetic moments.
Return type:: np.ndarray

get_n_atoms() → int[source]

Return the number of atoms in structure.

Returns:: The number of atoms
Return type:: int

get_types() → ndarray[source]

Return the atomic number of atoms in structure.

Returns:: Types of elements.
Return type:: np.ndarray

get_virial() → ndarray | None[source]

Return the virial tensor of material system.

Returns:: Virial tensor of shape=(9,)
Return type:: np.ndarray | None

class AtomConfig(structure: Structure, sort_structure: bool = False)[source]

Bases: MSONable

Object for representing the data in a atom.config or final.config file.

Initialization function.

Parameters:

structure (Structure) – Structure object
sort_structure (bool, optional) – Whether to sort the structure. Useful if species are not grouped properly together. Defaults to False.

as_dict()[source]

Returns:: dict

classmethod from_dict(dct: dict) → AtomConfig[source]

Returns a AtomConfig object from a dictionary.

Parameters:: dct – dict containing atom.config data
Returns:: AtomConfig object.

classmethod from_file(filename: PathLike, mag: bool = False) → AtomConfig[source]

Returns a AtomConfig from a file

Parameters:

filename (PathLike) – File name containing AtomConfig data
mag (bool, optional) – Whether to read magnetic moments. Defaults to True.

Returns:

AtomConfig object.

classmethod from_str(data: str, mag: bool = False) → AtomConfig[source]

Reads a atom.config from a string.

Parameters:

data (str) – string containing atom.config data
mag (bool, optional) – Whether to read magnetic moment information.

Returns:

AtomConfig object

get_str() → str[source]

Return a string describing the structure in atom.config format.

Returns:: String representation of atom.config
Return type:: str

write_file(filename: PathLike, **kwargs)[source]: Writes AtomConfig to a file.

class GenKpt(reciprocal_lattice: ndarray, kpoints: dict[str, ndarray], path: list[list[str]], density: float = 0.01)[source]

Bases: MSONable

GenKpt object for reading and writing gen.kpt. This file just generate line-mode kpoints.

Initialization function.

Parameters:

reciprocal_lattice (np.array) – Reciprocal lattice with factor of 2*pi.
kpoints (dict[str, np.array]) – Kpoints and their corresponding fractional coordinates.
kpath (list[list[str]]) – All kpaths, with each list representing one kpath.
density (float) – The density of kpoints mesh with factor of 2*pi.

static from_structure(structure: Structure, dim: int, density: float = 0.01) → GenKpt[source]

Obtain a AtomConfig object from Structure object.

Parameters:

strutcure (Structure) – A structure object.
dim (int) – The dimension of the material system (2 or 3).
density (float) – Kpoints mesh without factor with 2*pi. Program will automatically convert it with 2*pi.

get_str()[source]: Returns a string to be written as a gen.kpt file.

write_file(filename: PathLike)[source]

Writes gen.kpt to a file.

Parameters:: filename (PathLike) – The absolute path of file to be written.

class HighSymmetryPoint(reciprocal_lattice: ndarray, kpts: dict[str, list], path: list[list[str]], density: float)[source]

Bases: MSONable

HighSymmetryPoint object for reading and writing HIGH_SYMMETRY_POINTS file which generate line-mode kpoints.

Initialization function.

Parameters:

reciprocal_lattice (np.array) – Reciprocal lattice.
kpts (dict[str, list[float]]) – Kpoints and their corresponding fractional coordinates.
path (list[list[str]]) – All k-paths, with each list representing one k-path.
density (float) – Density of kpoints mesh with factor of 2*pi.

static from_structure(structure: Structure, dim: int, density: float = 0.01) → HighSymmetryPoint[source]

Obtain HighSymmetry object from Structure object.

Parameters:

structure (Structure) – A structure object.
dim (int) – Dimension of the material system (2 or 3).
density (float, optional) – Density of kpoints mesh without factor of 2*pi. Defaults to 0.01. The program will automatically convert it to with factor of 2*pi.

get_str() → str[source]: Returns a string describing high symmetry points in HIGH_SYMMETRY_POINTS format.

write_file(filename: PathLike)[source]: Write HighSymmetryPoint to a file.

class LineLocator[source]

Bases: MSONable

Find the line indices (starts from 1) of a certain paragraph of text from the file.

static locate_all_lines(file_path: PathLike, content: str) → list[int][source]

Locate the line in file where a certain paragraph of text is located (return all indices)

Parameters:

file_path (PathLike) – Absolute path to file.
content (str) – Certain paragraph of text that needs to be located.

class ListLocator[source]

Bases: MSONable

Find the element indices (starts from 0) of a certain paragraph of text from the list.

static locate_all_lines(strs_lst: list[str], content: str) → list[int][source]

Locate the elements in list where a certain paragraph of text is located (return all indices)

Parameters:

strs_lst (list[str]) – List of strings.
content (str) – Certain paragraph of text that needs to be located.

pymatgen.io.pwmat.outputs module

class DosSpin(filename: PathLike)[source]

Bases: MSONable

Extract information of DOS from DOS_SPIN file: - DOS.totalspin, DOS.totalspin_projected - DOS.spinup, DOS.spinup_projected - DOS.spindown, DOS.spindown_projected

property dos: ndarray[source]: Returns value of density of state.

get_partial_dos(part: str) → ndarray[source]

Get partial dos for give element or orbital.

Parameters:

part (str) –

The name of partial dos. e.g. ‘Energy’, ‘Total’, ‘Cr-3S’, ‘Cr-3P’,

’Cr-4S’, ‘Cr-3D’, ‘I-4D’, ‘I-5S’, ‘I-5P’, ‘Cr-3S’, ‘Cr-3Pz’, ‘Cr-3Px’, ‘Cr-3Py’, ‘Cr-4S’, ‘Cr-3Dz2’,’Cr-3Dxz’, ‘Cr-3Dyz’, ‘Cr-3D(x^2-y^2)’, ‘Cr-3Dxy’, ‘I-4Dz2’, ‘I-4Dxz’, ‘I-4Dyz’, ‘I-4D(x^2-y^2)’, ‘I-4Dxy’, ‘I-5S’, ‘I-5Pz’, ‘I-5Px’, ‘I-5Py’

Returns:

np.array

Return type:

partial_dos

property labels: list[str][source]: Returns the name of the partial density of states

class Movement(filename: PathLike, ionic_step_skip: int | None = None, ionic_step_offset: int | None = None)[source]

Bases: MSONable

Parser for data in MOVEMENT which records trajectory during MD.

Initialization function.

Parameters:

filename (PathLike) – The path of MOVEMENT
ionic_step_skip (int | None, optional) – If ionic_step_skip is a number > 1, only every ionic_step_skip ionic steps will be read for structure and energies. This is very useful if you are parsing very large MOVEMENT files. Defaults to None.
ionic_step_offset (int | None, optional) – Used together with ionic_step_skip. If set, the first ionic step read will be offset by the amount of ionic_step_offset. Defaults to None.

property atom_configs: list[Structure][source]

Returns AtomConfig object for structures contained in MOVEMENT.

Returns:: List of Structure objects for the structure at each ionic step.
Return type:: list[Structure]

property atom_forces: ndarray[source]

Returns forces on atoms in each structures contained in MOVEMENT.

Returns:

The forces on atoms of each ionic step structure,: with shape of (n_ionic_steps, n_atoms, 3).

Return type:

np.ndarray

property e_atoms: ndarray[source]

Returns individual energies of atoms in each ionic step structures contained in MOVEMENT.

Returns:

The individual energy of atoms in each ionic step structure,: with shape of (n_ionic_steps, n_atoms).

Return type:

np.ndarray

property e_tots: ndarray[source]

Returns total energies of each ionic step structures contained in MOVEMENT.

Returns:

Total energy of of each ionic step structure,: with shape of (n_ionic_steps,).

Return type:

np.ndarray

property virials: ndarray[source]

Returns virial tensor of each ionic step structure contained in MOVEMENT.

Returns:

The virial tensor of each ionic step structure,: with shape of (n_ionic_steps, 3, 3)

Return type:

np.ndarray

class OutFermi(filename: PathLike)[source]

Bases: MSONable

Extract fermi energy (eV) from OUT.FERMI

Initialization function

Parameters:: filename (PathLike) – The absolute path of OUT.FERMI file.

property e_fermi: float[source]

Returns the fermi energy level.

Returns:: Fermi energy level.
Return type:: float

class Report(filename: PathLike)[source]

Bases: MSONable

Extract information of spin, kpoints, bands, eigenvalues from REPORT file.

Initialization function.

Parameters:: filename (PathLike) – The absolute path of REPORT file.

property eigenvalues: ndarray[source]

Returns the eigenvalues.

Returns:

The first index represents spin, the second index: represents kpoint, the third index represents band.

Return type:

np.ndarray

property hsps: dict[str, ndarray][source]

Return the high symmetry points.

Returns:

The label and fractional coordinate of: high symmetry points. Return empty dict when task is not line-mode kpath.

Return type:

dict[str, np.ndarray]

property kpoints: ndarray[source]: Returns the fractional coordinates of kpoints.

property kpoints_weight: ndarray[source]: Returns the weight of kpoints.

property n_bands: int[source]: Returns the number of bands.

property n_kpoints: int[source]: Returns the number of k-points.

property spin: int[source]

Return the spin switches.

Returns:: Spin switches. 1 represents turn on spin, 2 represents turn down spin.
Return type:: int