dump molecules with atomic potential energy larger than a specific value

Dear all lammps users

I am trying to dump molecules whose atoms have atomic potential energy larger than a predefined magnitude. Are there any ways that I can do this directly in lammps? I know how to dump a group of atoms with atomic potential energy larger than certain magnitudes; however, how can I dump the whole molecules with atomic potential energies larger than a predefined magnitude?



I don’t know if it’s possible currently, but to
use dump_modify thresh the way you

can for individual atoms, you would

have to create a per-atom variable

that is the value for the entire molecule
that atom is in. To do that, a first
step would be to use compute atom/molecule
to sum up the “energy” of a molecule
based on the per-atom energies of its atoms.

That would give you a vector of length # of
molecules. There would then need to
be some way to have each atom extract
the right value from that vector for

its new per-atom “value”.



How difficult would it be to use the methodology of the ‘compute cluster/atom’ command?

For this application, the cluster would be identified with the molecule, but if the compute was extended so that a ‘per atom’ variable was averaged across the atoms within the cluster/molecule, then that averaged value could be associated with every atom in the cluster or molecule.


Something like that might work, but a compute
like atom/molecule cannot produce both
a global and peratom value. I need to think
about some way to do it.