tepkit.io.vasp.Poscar

class tepkit.io.vasp.Poscar

Bases: tepkit.io.StructuredTextFile

See: https://www.vasp.at/wiki/index.php/POSCAR

Attributes

Attribute	Default Value	Description
default_file_name	'POSCAR'	The default name of file when use from_dir() .
comment	'POSCAR'	The first line of POSCAR.
scaling_factor	1.0
has_species_names	True
species_names	['Unknown']
ions_per_species	[1]
ion_coordinates_mode	None
has_selective_dynamics	False
selective_dynamics	None
has_lattice_velocities	False
lattice_velocities	None
has_ion_velocities	False
ion_velocities	None
md_extra	None

Properties

unscale_lattice
ion_positions
lattice
reciprocal_lattice
n_ions
species_index_per_ion	Returns a list of species indexes for each ion.
species_name_per_ion	Returns a list of species names for each ion.
thickness_info	Returns thickness-related data.

Methods

from_string(→ tepkit.utils.typing_tools.Self)	Parse the string to structured data.
__str__()
get_lattice(...)
get_reciprocal_lattice(...)
get_shengbte_types(→ list[int])	Returns a list of integers for ShengBTE-CONTROL-crystal-types.
get_cartesian_ion_positions(...)	Return the Cartesian coordinates of ions.
get_fractional_ion_positions(...)	Return the fractional coordinates of ions.
get_volume(→ float)
get_high_symmetry_points_2d(decimal[, with_2pi])	Get the absolute and relative coordinates of all possible high symmetry points of a 2D material.
get_interatomic_distances(...)	Return the distances between ions.
get_neighbor_distances(→ list[float])	Return the distances of the n-th neighbors.
get_atomic_numbers(→ list[int])
get_pymatgen_poscar()
to_supercell(→ tepkit.utils.typing_tools.Self)

All Members

default_file_name = 'POSCAR'

The default name of file when use from_dir() .

comment: str = 'POSCAR'

The first line of POSCAR.

scaling_factor: float | list[float] = 1.0

has_species_names: bool = True

species_names: list[str] = ['Unknown']

ions_per_species: list[int] = [1]

ion_coordinates_mode: VaspCoordinatesMode

has_selective_dynamics: bool = False

selective_dynamics: NumpyArrayNx3[bool] | None = None

has_lattice_velocities: bool = False

lattice_velocities: NumpyArrayNx3[float] | None = None

has_ion_velocities: bool = False

ion_velocities: NumpyArrayNx3[float] | None = None

md_extra: str | None = None

property unscale_lattice: NumpyArray3x3[float]

property ion_positions: NumpyArrayNx3[float]

classmethod from_string(string: str) → Self

Parse the string to structured data.

__str__()

get_lattice() → NumpyArray3x3[float]

get_reciprocal_lattice(with_2pi=True) → NumpyArray3x3[float]

Parameters:

with_2pi – VASP Cartesian KPOINTS use with_2pi=False

Returns:

property lattice: NumpyArray3x3[float]

property reciprocal_lattice: NumpyArray3x3[float]

property n_ions: int

property species_index_per_ion: list[int]

Returns a list of species indexes for each ion. e.g. [0, 0, 1, 1, 2] from Bi2Se2Te

get_shengbte_types() → list[int]

Returns a list of integers for ShengBTE-CONTROL-crystal-types. e.g. [1, 1, 2, 2, 3] from Bi2Se2Te

property species_name_per_ion: list[str]

Returns a list of species names for each ion. e.g. [“Bi”, “Bi”, “Se”, “Se”, “Te”] from Bi2Se2Te

property thickness_info: dict

Returns thickness-related data. Such as effective thickness, van der Waals radius of edge atoms, etc.

get_cartesian_ion_positions(*, threshold: float | None = None) → NumpyArrayNx3[float]

Return the Cartesian coordinates of ions.

Parameters:

threshold – The absolute values smaller than this value will be set to zero. (Recommended value: 1e-13)

get_fractional_ion_positions() → NumpyArrayNx3[float]

Return the fractional coordinates of ions.

get_volume(unit: str = 'Angstrom^3') → float

get_high_symmetry_points_2d(decimal, with_2pi=True)

Get the absolute and relative coordinates of all possible high symmetry points of a 2D material.

Parameters:

• decimal

• with_2pi – VASP Cartesian KPOINTS use with_2pi=False

Returns:

get_interatomic_distances() → NumpyArrayNxN[float]

Return the distances between ions.

get_neighbor_distances(max_nth=100) → list[float]

Return the distances of the n-th neighbors.

get_atomic_numbers(per_ion=False) → list[int]

>>> poscar = Poscar.from_file("Bi2Te3.poscar")
>>> poscar.get_atomic_numbers() # noinspection PyDocstringTypes
[83, 52]
>>> poscar.get_atomic_numbers(per_ion=True)
[83, 83, 52, 52, 52]

get_pymatgen_poscar()

to_supercell(na: int, nb: int, nc: int) → Self