reax/c/species question

This question is directed towards Ray, but may be of general use to the lammps community.

Hi Ray,

I’ve been playing with the reax/c/species fix. In my system I have a slab of atoms that interact with various molecules. Under certain conditions the molecules crack/decompose on the surface. I basically want to track this decomposition. In the fix the entire slab is treated as a single molecule (of course). When one of the molecules sticks to the slab, the species fix detects this and reports it as a new molecule. Now if the molecule cracks on the surface into two new molecules (as confirmed by visualization) the species fix does not detect this because the number of atoms on the surface doesn’t actually change. Similar complications arise if additional molecules alight on the slab. I am thinking one solution might be to set a very large bond order cutoff between atoms in the molecules and slab atoms so the fix effectively ignores slab-molecule interactions. This info could be combined with output from reax/c/bonds. where I’d look for atoms belonging molecules bonded to slab atoms. I am wondering if you might have any other good ideas as to how to handle this problem?



In your described scenario where a molecule originally bonded to a substrate breaks into two, it is definite that fix reax/c/species is not going to detect this. This is because when the substrate-bonded molecule A breaks into molecules B and C, B and C are still bonded to the substrate, and the whole “substrate+B+C” is still going to be identified as one big molecule, which is the same molecule as “substrate+A”

Your proposed method of assigning a large BO cutoff between substrate and incident atoms is one solution. An alternative is to just apply the fix to a group that excludes the substrate atoms.