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:
Lattice- cell vectors in a standart format of nine numbers.
size- 2-dimensional integer size of the slab
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:
surface_zlevel- value of z-coordinate that separates adsorbate atoms (above) and adsorbent atoms (bellow). Important:
surface_zlevelis 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.
adsorbate_indices- list of integers that enumerate indices of adsorbate atoms in an XYZ file.
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
adsorptionparameter equal to
sare considered as surface atoms. Important: Structure of atom-wise parameters in Extended XYZ format is specified as key-value pair
Parametersin a a comments section of XYZ file.