File conversion

File conversion from the CONQUEST coordinates file is handled by the writers module.

class conquest2a.writers.conquest_writer(dest: str, coords: conquest_coordinates, encoding: str = 'utf-8', precision: int = 10)

Class to write a CONQUEST coordinates file given a conquest_coordinates instance.

Parameters:

  • dest (str) – Path to write the new coordinates file.

  • coords (conquest_coordinates) – conquest_coordinates instance to write.

  • encoding (str, optional) – File encoding, defaults to “utf-8”

  • precision (int, optional) – Float precision, defaults to 10

Raises:

ValueError – If the float precision is not at least 1.

class conquest2a.writers.extxyz_writer(dest: str, data: conquest_coordinates, encoding: str = 'utf-8', time: float = 0.0)

Class to write a .extxyz for a basic XYZ file given a conquest_coordinates instance.

The main advantage of .extxyz is the ability to specify columns and the time, which is very useful for animations. I recommend just using CONQUEST’s ability to output .extxyz files at different timesteps.

Parameters:

  • dest (str) – Path to write the new coordinates file.

  • data (conquest_coordinates) – conquest_coordinates instance to write.

  • encoding (str, optional) – File encoding, defaults to “utf-8”.

  • time (float, optional) – The instance of time of the cell, defaults to 0.0.

create_comment_line() → str

Creates the .extxyz comment line: specifies columns, formats and time.

Returns:

The file’s comment line.

Return type:

str

class conquest2a.writers.file_writer(dest: str, mode: str = 'w', encoding: str = 'utf-8', is_angstrom: bool = False)

Generic parent class to define file operations and variables.

Parameters:

  • dest (str) – _description_

  • mode (str, optional) – _description_, defaults to “w”

  • encoding (str, optional) – _description_, defaults to “utf-8”

  • is_angstrom (bool, optional) – _description_, defaults to False

class conquest2a.writers.vasp_writer(dest: str, data: conquest_coordinates, encoding: str = 'utf-8', is_angstrom: bool = False)

Class to write a VASP file given a conquest_coordinates instance.

Parameters:

  • dest (str) – Path to write the new coordinates file.

  • data (conquest_coordinates) – conquest_coordinates instance to write.

  • encoding (str, optional) – File encoding, defaults to “utf-8”

  • is_angstrom (bool, optional) – Whether the data in conquest_coordinates is already in angstroms instead of Bohrs, defaults to False.

class conquest2a.writers.xsf_writer(dest: str, data: conquest_coordinates, write_extra: Literal['spin', 'force'] = 'spin', encoding: str = 'utf-8')

Class to write .xsf files given a conquest_coordinates instance.

XSF files support an extra 3 columns alongside the 3 columns used for position. These columns specify a vector associated with each atom. In CONQUEST, the relevant vectors are forces and spins. Note that CONQUEST only supports collinear spin (up and down), so the spin vector is visualised along the \(c\)-axis of the simulation cell.

Parameters:

  • dest (str) – Path to write the new coordinates file.

  • data (conquest_coordinates) – conquest_coordinates instance to write.

  • encoding (str, optional) – File encoding, defaults to “utf-8”.

  • write_extra (Literal["spin", "force"], optional) – Whether to extract the force vector or spin vector of atoms, defaults to “spin”.

class conquest2a.writers.xsf_writer_spins(dest: str, charges: atom_charge, xsf_file: str, encoding: str = 'utf-8')

XSF writer class that includes spin information from the AtomCharge.dat file, by editing an existing XSF file generated by PostProcessCQ.

Parameters:

  • dest (str) – Path to write the new coordinates file.

  • data (conquest_coordinates) – conquest_coordinates instance to write.

  • encoding (str, optional) – File encoding, defaults to “utf-8”.

  • charges (atom_charge :param xsf_file: XSF file to modify.) – atom_charge instance to read spin data from.

process_xsf_file() → None

Process an existing XSF file to include spin information.

class conquest2a.writers.xyz_writer(dest: str, data: conquest_coordinates, encoding: str = 'utf-8', comment_line: str = 'comment line')

Class to write a .xyz for a basic XYZ file given a conquest_coordinates instance.

Parameters:

  • dest (str) – Path to write the new coordinates file.

  • data (conquest_coordinates) – conquest_coordinates instance to write.

  • encoding (str, optional) – File encoding, defaults to “utf-8”

  • comment_line (str, optional) – What string to write as the comment line

create_atoms_str() → tuple[str, str]

Creates a line for an atom, for the XYZ file.

Returns:

Components of the line to write: the element and the numbers

Return type:

tuple[str, str]

write() → None

XYZ format expects cells in Cartesian coordinates. Since CONQUEST only deals with orthorhombic unit cells, we can just multiply the non-zero coordinates of the lattice vectors with the fractional coordinates