PAOFLOW.writers.write2xsf#

Functions#

write2xsf(data_controller, filename[, data])

Write crystal structure and optional 3-D volumetric data in XSF format.

Module Contents#

PAOFLOW.writers.write2xsf.write2xsf(data_controller, filename, data=None)[source]#

Write crystal structure and optional 3-D volumetric data in XSF format.

Parameters:

  • data_controller (DataController) – Object providing data_arrays and data_attributes. Required arrays: atoms (list of element symbols), a_vectors (shape (3, 3) in units of alat), tau (shape (natoms, 3) in Bohr radii). Required attribute: alat (lattice constant in Bohr radii).

  • filename (str) – Absolute or relative path of the XSF output file.

  • data (Optional[np.ndarray]) – Volumetric scalar field on a real-space grid of shape (nr1, nr2, nr2). If None, only the crystal structure block is written. Complex arrays are converted to \(|\psi|^2\) before writing.

Returns:

Creates (or overwrites) the file at filename.

Return type:

None

Notes

The file is written in the XCrySDen Structure Format (XSF), which is supported by XCrySDen and VESTA for structure and charge-density visualisation. The structure block includes primitive cell vectors (in Bohr radii) and atomic positions with atomic numbers obtained from the mendeleev library.

When data is provided, a BEGIN_BLOCK_DATAGRID_3D section is appended. The grid is extended by one point in each direction (periodic boundary) to satisfy XSF convention, i.e. the grid size written is (nr1+1, nr2+1, nr3+1).