I simulated uni-axial tension test on a polymer system containing 80 molecules.
I have the result on the individual chain deformation during external loading, and I want to get the stress information on the individual molecule.
My question is : is there a way to output the intrachain stress and interchain stress for each molecule? So that I can relate the molecule deformation to the interchain stress?
P.S. The intrachain stress is composed of the stress due to covalent bonds , the stress due to the valence-angle interaction ,
the stress due to both the proper and improper-torsion interactions , and the stress due to intrachain LJ interactions .
The interchain stress is from the interchain LJ interactions.
The compute pressure command has options to only include the
virial for different componets, e.g. pair, bond, etc.
If you used the rerun command on your dump file configs,
you could also turn on/off various pairwise interactions (e.g. inter-
vs intra-chain) and thus use compute pressure to extract different
values.
Incidentally, there is a variation of the "lj/charmm/coul/charmm"
pair style which allows you to specify different inter-molecular and
intra-molecular uncharged Lennard-Jones pair forces. (I know I
promote this code a lot these days. It's nothing terribly exiting.)
If your molecules are neutral, then can use this to turn off intra or
inter-molecular interactions for example. It might be useful to use
this combination with the "rerun" command Steve mentioned. If you use
Lennard-Jones pair forces with a single cutoff, you can approximate
this behavior by setting the inner and outer cutoffs equal to each
other (or very close to each other). This should work well enough if
you only care about computing the forces (stresses) accurately. The
documentation for this new pair style is currently here: http://www.moltemplate.org/lammps_code/pair_lj_charmm_coul_charmm_inter.html
but hopefully it will be added to the main LAMMPS documentation soon.
(This is my fault. My apologies Steve for not reformatting the
documentation yet. I'll do it soon.)