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Re: [lammps-users] Compute rdf commad g(r)
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Re: [lammps-users] Compute rdf commad g(r)


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 11 Apr 2018 14:41:23 -0400

On Wed, Apr 11, 2018 at 1:44 PM, Chuanxing Zhan via lammps-users
<lammps-users@lists.sourceforge.net> wrote:
> Dear lammps User,
>
> Hello, everyone! I have some understanding problem about compute rdf in
> lammps, I read the instruction in lammps website,  instruction doesn't
> mention any  detail for how to compute the atoms rdf between two molecules.
> My question is,  when we compute  atomes rdf g(r), how the lammps command
> work? For example, if I have a CO2, and I want to compute the O-O rdf, but
> there are two Oxygen atoms in the specific molecule (the molecule we chose
> as center to calculate the rdf), does the lammps calculate the O-O rdf in
> the specific molecule?

g(r) is an entity that is only defined for (point) particles, or
rather pairs of point particles. so molecules are in principle
irrelevant for this.

however, the compute rdf function uses the pairwise neighbor lists for
that. and while it does not *care* whether a pair is inter- or
intra-molecular,
depending on your choice of force field, intramolecular interactions
may be excluded as special 1-2, 1-3, or 1-4 pairs (this will happen
when the special_bonds setting is lj/coul 0.0 0.0 0.0).
so for CO2 (if you define bonds between C and O and exclude 1-3
neighbors completely), they will not show up in the output of compute
rdf. on the other hand, if you use 1.0e-20 instead of 0.0, those pairs
would be included. which is the preferred of the two options depends
strongly on what kind of analysis you need the resulting g(r)s for. in
some cases you need the intra-molecular peak, in some it is easier to
leave them out.

axel.


>
> Any explantion would be appreciate.
>
> Thanks,
> Kerwin
>
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.