Hi All,
Thank you in advance for your help!
My system is made up of many rigid bodies (determined by molecule ID) that contain ellipsoids with one ellipsoid acting as a ‘core-atom’ at the center of each rigid body. There are only non-bonded interactions in my system.
I want to calculate the number of free monomers in my simulation box throughout a single LAMMPS run and the best method I can think of for doing this is to use cluster/atom on the group of ‘core’ atoms with some constraint that says two monomers are bound if their core sites are within some distance. If I then count the number of cluster IDs in that list that only occur once I should have the number of free monomers.
The second step has been quite difficult…
My first thought was to use a python variable function (this calculation is very easy in post-processing using Python) but there doesn’t seem to be a way to use data types other than string, float, int or SELF. So inputting the per-atom vector as a list for example is not possible.
My current method is to modify the compute cluster/atom so that it does the calculation for me. Which I am working on.
My question is if any of the LAMMPS developers can think of a better way to do this calculation that I can’t see?
Thank you,
Andrew