The Site/Coordinate Syntax

In the atomistic kMC simulations pursued here one defines processes in terms of sites on some more or less fixed lattice. This reflects the physical observation that molecules on surfaces adsorb on very specific locations above a solid.

To represent this in a computer program, we first need to make a small but crucial differentiation: namely the difference between the sites of a (surface) structure and the coordinates of a process. The difference is that a given structure contains each site defined exactly once, whereas a process may use the same site several times however in a different unit cell. So this differentation owes to the fact that we commonly simulate highly periodic structures.

Ok, having this out of the way you start to define and use sites and coordinates. The minimum constructor for a site is

site = Site(name='site_name')

where site_name can be a string without spaces and all names should be unique within one layer. Usually it is reasonable to add a position in relative coordinates right-away like so

site = Site(name='hollow', pos='0.5 0.5 0.0')

which would place the site at the bottom center of the cell. A direct benefit is that you can measure distances between coordinates later on to, e.g. select all nearest neighbor or next-nearest neighbor sites.

A site can have some more attributes. Some of them are only needed in conjunction with GUI use. It is worth to know that each site can have one or more tags. This way one create types of site and conveniently select all sites with a one more tags. The syntax here is as follows

site = Site(name='hollow', pos='0.5 0.5 0.0', tags='tag1 tag2 ...')

The second part is to generate the coordinates that are used in the process description.

Manual generation

To quickly generate single coordinates you can generate it from a Project like so


Let’s look at the generation string. The general syntax is


The site_name and the layer_name must have been defined before. The offset is a tuple of three integer numbers (0, 0, 1) and specifies the relative unit cell of this coordinate. Of course this only becomes meaningful as soon as you use more than one coordinate in a process.

Missing values will be filled in from the back using default values, such that

site -> site.(0,0,0) -> site.(0,0,0).default_layer

Advanced Coordinate Techniques

Generating large process lists with a lot of similar or even degenerate processes is a very boring task. So we should try to use programming logic as much as possible. Here I will outline a couple of idioms you can use here.

Often times it is handier (less typing) to generate a larger set of coordinates at first and then select different subsets from it in a process definition. For this purpose you can use

pset = pt.lattice.generate_coord_set(size=[x,y,z], layer_name='layer_name')

This collects all sites from the given layer and generates all coordinates in the first unit cell (offset=(1,1,1)) and all x, y, and z unit cells in the respective direction.

To select subsets in a readable way I suggest you use list comprehensions, like so

[ x for x in pset if not x.offset.any() ]

which again selects all sites in the first unit cell. Or to select all site tagged with foo you could use

[ x for x in pset if 'foo' in x.tags.split() ]

or having defined a unit cell size and a site position your can measure real-space distances between coordinate like so


Or of course you can use any combination of the above.

Taking it home

  • sites belong to a structure while coordinates belong to a process
  • coordinates are generated from sites
  • coordinate sets can be selected and chopped using list comprehensions and tags