[SPAM] using input coordinates as reference sites

Dear lammps-users,
I want to use the coordinates from an xyz file to define some reference sites or some reference zones during my simulation, so that I can detect if atoms are in the cutoff distance from these sites.

To achieve this,I tried to first create “reference” atoms from the xyz file and then create “real” atoms for my simulation so that I can use “compute cluster/atom” to see whether “real” atoms’ cluster-IDs are smaller than the greatest “reference” atoms’ ID or not. But before that I have to exclude the reference atoms from neighbor lists to avoid the interactions with the real ones, which makes my plan invalid.

Can lammps do this directly or indirectly?

Thanks in advance.

Philip

Dear lammps-users,
I want to use the coordinates from an xyz file to define some reference
sites or some reference zones during my simulation, so that I can detect if
atoms are in the cutoff distance from these sites.

To achieve this,I tried to first create "reference" atoms from the xyz file
and then create "real" atoms for my simulation so that I can use "compute
cluster/atom" to see whether "real" atoms' cluster-IDs are smaller than the
greatest "reference" atoms' ID or not. But before that I have to exclude the
reference atoms from neighbor lists to avoid the interactions with the real
ones, which makes my plan invalid.

Can lammps do this directly or indirectly?

please have a look at fix store/state. you can then reference that
data via atom style variables and compute displacements
correspondingly without having to define actual particles for that.

axel.