kliff.dataset.extxyz

kliff.dataset.extxyz.read_extxyz(filename)

Read atomic configuration stored in extended xyz file_format.

Parameters:

filename (Path) – filename to the extended xyz file

Returns:

3x3 array, supercell lattice vectors species: species of atoms coords: Nx3 array, coordinates of atoms PBC: periodic boundary conditions energy: potential energy of the configuration; None if not provided in file forces: Nx3 array, forces on atoms; None if not provided in file stress: 1D array of size 6, stress on the cell in Voigt notation; None if not

provided in file

Return type:

cell

kliff.dataset.extxyz.write_extxyz(filename, cell, species, coords, PBC, energy=None, forces=None, stress=None, bool_as_str=False)

Write configuration info to a file in extended xyz file_format.

Parameters:

• filename (Path) – filename to the extended xyz file

• cell (ndarray) – 3x3 array, supercell lattice vectors

• species (List[str]) – species of atoms

• coords (ndarray) – Nx3 array, coordinates of atoms

• PBC (List[bool]) – periodic boundary conditions

• energy (Optional[float]) – potential energy of the configuration; If None, not write to file

• forces (Optional[ndarray]) – Nx3 array, forces on atoms; If None, not write to file

• stress (Optional[List[float]]) – 1D array of size 6, stress on the cell in Voigt notation; If None, not write to file

• bool_as_str (bool) – If True, write PBC as “T” or “F”; otherwise, write PBC as 1 or 0.