Compute pe/atom with custom fix wall graphite

Dear LAMMPS users,

I need to calculate the per atom potential energy (PE) for a system with Polyethelene between two graphite walls (custom fix wall graphite from Mansfield-Theodorou).

It seems like the potential energy of the system from thermo-output is correct, while the potential energy calculated from the pe/atom command does not include the interactions of the polymer with the graphite walls, as it was expected [http://lammps.sandia.gov/doc/compute_pe_atom.html].

Is there a way to include the PE of the graphite wall in the computation as with the case with the “compute stress/atom” where its possible to add a fix in the keywords?

Thanks!

Aris Sgouros

Dear LAMMPS users,

I need to calculate the per atom potential energy (PE) for a system with
Polyethelene between two graphite walls (custom fix wall graphite from
Mansfield-Theodorou).

It seems like the potential energy of the system from thermo-output is
correct, while the potential energy calculated from the pe/atom command does
not include the interactions of the polymer with the graphite walls, as it
was expected [http://lammps.sandia.gov/doc/compute_pe_atom.html].

Is there a way to include the PE of the graphite wall in the computation as
with the case with the "compute stress/atom" where its possible to add a fix
in the keywords?

this would require some C++ programming. in fixes, there currently
only a general infrastructure to tally contributions to the per-atom
virial. that would have to be duplicated/expanded for per-atom
energies.

a less invasive change would be to have the fix wall fix provide a
per-atom compute with the energy contribution and then you could use
an atom style variable to combine it with the existing per-atom energy
contributions.

axel.

Thanks Axel,
I think ill try the second (less invasive) option.

Cheers!

Aris Sgouros