ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
ontop hollow fcc hcp bridge shortbridge longbridge
Adding new utility functions If you need other surfaces than the ones above, the easiest is to look in the source
file surface.py, and adapt one of the existing functions. Please contribute any such function that you make either
by cheking it into SVN or by mailing it to the developers.
Adding adsorbates
After a slab has been created, a vacuum layer can be added. It is also possible to add one or more adsorbates.
ase.lattice.surface.add_adsorbate(slab, adsorbate, height, position=(0, 0), offset=None,
mol_index=0)
Add an adsorbate to a surface.
This function adds an adsorbate to a slab. If the slab is produced by one of the utility functions in
ase.lattice.surface, it is possible to specify the position of the adsorbate by a keyword (the supported keywords
depend on which function was used to create the slab).
If the adsorbate is a molecule, the atom indexed by the mol_index optional argument is positioned on top
of the adsorption position on the surface, and it is the responsibility of the user to orient the adsorbate in a
sensible way.
This function can be called multiple times to add more than one adsorbate.
Parameters:
slab: The surface onto which the adsorbate should be added.
adsorbate: The adsorbate. Must be one of the following three types: A string containing the chemical
symbol for a single atom. An atom object. An atoms object (for a molecular adsorbate).
height: Height above the surface.
position: The x-y position of the adsorbate, either as a tuple of two numbers or as a keyword (if the surface
is produced by one of the functions in ase.lattice.surfaces).
offset (default: None): Offsets the adsorbate by a number of unit cells. Mostly useful when adding
more than one adsorbate.
mol_index (default: 0): If the adsorbate is a molecule, index of the atom to be positioned above the location
specified by the position argument.
Note position is given in absolute xy coordinates (or as a keyword), whereas offset is specified in unit cells.
This can be used to give the positions in units of the unit cell by using offset instead.
Create specific non-common surfaces
New in version 3.5.2. In addition to the most normal surfaces, a function has been constructed to create more
uncommon surfaces that one could be interested in. It is constructed upon the Miller Indices defining the surface
and can be used for both fcc, bcc and hcp structures. The theory behind the implementation can be found here:
general_surface.pdf.
Example
To setup a Au(211) surface with 9 layers and 10 Å of vacuum:
from ase.lattice.surface import surface
s1 = surface(’Au’, (2, 1, 1), 9)
s1.center(vacuum=10, axis=2)
90 Chapter 7. Documentation for modules in ASE