General Classes

The classes under the conquest module are used across the library, and are often required to be initialised and passed as arguments to other classes.

class conquest2a.conquest.Atom(species: int, coords: ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy.float64]], can_move: ~collections.abc.Sequence[str], number: int, label: str = '', forces: ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy.float64]] = <factory>, spins: ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy.float64]] = <factory>)

Class which holds Atom data.

Parameters:

  • species (int) – The integer referring to the species as defined in the Conquest_input file.

  • coords (REAL ARRAY) – Fractional coordinates of the atom in the interval \([0,1)\). Numbers outside this range are wrapped back into the range.

  • can_move (Sequence[str] - list of ‘T’ or ‘F’.) – Whether the atom is allowed to move in each Cartesian axis.

  • number (int) – The atom number, i.e. its position in the coordinates file.

  • label (str) – The atom element

  • cart_coords (REAL ARRAY) – Cartesian coordinates of the atom.

  • forces (REAL ARRAY) – Force vector of the atom, defaults to np.array([0.0, 0.0, 0.0]).

  • spins (REAL ARRAY) – Spin moment on the atom, defaults to np.array([0.0, 0.0, 0.0]).

to_ase() → Atom

Method to return an equivalent ASE `Atom <https://ase-lib.org/ase/atom.html>`__. The spins field is set to the Atom.magmom whilst the forces field is set to Atom.momentum.

Returns:

ase.Atom: Equivalent ASE Atom object.

Return type:

ase.Atom

class conquest2a.conquest.atom_charge(coordinates: conquest_coordinates, atom_charge_path: str)

Class to process AtomCharge.dat from CONQUEST output files.

It is assumed each row of AtomCharge.dat is arranged such that it is equivalent to the same CONQUEST input coordinates file.

In particular, make use of the conquest_coordinates class to contain the list of Atoms

Parameters:
assign_atom_charge() → None

Assign each Atom its spin values from the AtomCharge.dat file: up - down

open_file() → None

Reads in the AtomCharge.dat Format of the file is 3 columns: total, spin up spin down CONQUEST only deals with collinear spins

class conquest2a.conquest.block_processor

Generic class to process CONQUEST output files which are split into blocks via &

Sometimes these blocks are categorised by spins and have comments # at the start of the section

process_block(line: str) → None

Extracts blocks, which are separated by & on its own newline, for data processing.

process_headers(line: str) → None

This function can be overridden by subclasses to process header lines starting with # Bandstructure and DOS/pDOS files have slightly different headers.

read_file(filename: str) → None

Generic method which calls process_headers() and process_block().

Parameters:

filename (str) – Path to file

class conquest2a.conquest.conquest_coordinates(conquest_input: conquest_input)

Class which holds data about the system, including the Atom s in the system.

Parameters:

conquest_input (conquest_input) – conquest_input instance.

assign_atom_labels() → None

Assign each Atom its label. If the conquest_input does not define labels for all species, these species labels will be silently skipped.

get_cartesian_positions() → ndarray[tuple[Any, ...], dtype[float64]]

Returns the Cartesian position of all the atoms in the system and attaches to its Atom field.

Returns:

The 3D vector of the Cartesian position.

Return type:

REAL ARRAY

index_to_atom_map() → None

Form a dictionary with keys an element label, and values a list of all the Atom s with that label. External file formats, such as .vasp, require a count of the number of atoms per element.

number_of_elements() → dict[str, int]

Function to get the number of atoms of each element.

Returns:

Returns a dictionary of the number of atoms per element

Return type:

dict[str, int]

class conquest2a.conquest.conquest_coordinates_processor(path: str, conquest_input: conquest_input)

Class which extracts data from a CONQUEST coordinates file and populates a conquest_coordinates instance.

Parameters:

  • path (str) – Path of the CONQUEST coordinates file to read.

  • conquest_input (conquest_input) – conquest_input instance.

open_file() → None

This method reads a CONQUEST coordinate file.

CONQUEST coords file split into 3 main chunks:

  • first 3 lines are lattice vectors

  • fourth line is the total number of atoms in the unit cell

  • the following lines describe each atom and look like

    <double> <double> <double> <int> <char> <char> <char>