Creating sketches of a surface slab and adsorption complexes

Sketches of adsorption complexes and a surface slab should be provided as Extended XYZ files with the following additional parameters specified in comments seciton:

  1. Lattice - cell vectors in a standart format of nine numbers.

  2. size - 2-dimensional integer size of the slab

For example:

Lattice="8.585559375 0.054762105 0.0 4.340198118 7.5174013785 0.0 0.0 0.0 20.0" Properties=species:S:1:pos:R:3 size="3 3"

Files with adsorption complex sketches should provide information for distinguishing adsorbate (surface) and adsorbent atoms. There are several ways to do it

  • With a parameter specified as a key-value pairs in comments section of XYZ file. The following parameters are accepted by SuSMoST:

    1. surface_zlevel - value of z-coordinate that separates adsorbate atoms (above) and adsorbent atoms (bellow). Important: surface_zlevel is meassured from ac_origin. It means that if ac_origin="0 0 3" and surface_zlevel=5, then all atoms with z-coordinate less than 3 + 5 = 8 are considered as surface atoms.

    2. adsorbate_indices - list of integers that enumerate indices of adsorbate atoms in an XYZ file.

    3. adsorbate_elements - list of chemical symbols of adsorbate atoms. Can be used only if sets of adsorbate and adsorbent elements do not intersect.

  • With additional atom-wise parameter adsorption. Atom-wise parameters should be specified for each atom. All atoms with adsorption parameter equal to s are considered as surface atoms. Important: Structure of atom-wise parameters in Extended XYZ format is specified as key-value pair Parameters in a a comments section of XYZ file.