[lammps-users] Delete high energy atoms instantly


Thanks for your answer!

In my simulation, atom displacements occur by knock-on collisions of highly energetic electrons in the specimen. If the transferred energy is higher than the threshold, the nuclei of the atoms would be sublimated and knocked out or vanish.

I read lammps manual and could’t find any fix commands to check kinetic energy information of each atom. But I found “compute ke/atom” to define a computation that calculates the per−atom translational kinetic energy for each atom. I looped all atoms evey 1000 steps as below:


This is what as I was suggesting “in spirit”,
but the syntax needs to be corrected in more than one place,
which is well described in the corresponding doc pages…
Few egs. Referencing a variable requires ${} when it is greater than a single character in length;
group of type id adds the atom to a group if it already exists,
in your case you need to initialize the del group;
reference to the compute value is not correct, you also probably need to first save the value in a variable…

as Steve says, a better way to do it would be to write a fix,
…this is a round about way to do it, based on the capabilities available in the present version.


Don't try to loop over all your atoms in
an input script. Just write a fix to compute
the KE of an atom (or whatever condition),
then delete it if needed.


2010/1/23 Mario Pinto <[email protected]>: