Lammps users:
Is there a way to alias an atom type for fix_rdf?
I have two different carbonyl carbon types in my system, but for the RDF, I’d like them to be looked at as the same atom type. In other other words, I don’t want an ester-ester RDF, a acid-acid RDF, and a ester-acid RDF, I just want a carbonyl-carbonyl RDF.
Can lammps do that? I have a code to write out RDFs from dump files, but it is brute force and slow. Rather let lammps do it for me.
If there isn’t, thanks anyways.
Kevin
Lammps users:
Is there a way to alias an atom type for fix_rdf?
I have two different carbonyl carbon types in my system, but for the RDF,
I’d like them to be looked at as the same atom type. In other other words,
I don’t want an ester-ester RDF, a acid-acid RDF, and a ester-acid RDF, I
just want a carbonyl-carbonyl RDF.Can lammps do that? I have a code to write out RDFs from dump files, but it
is brute force and slow. Rather let lammps do it for me.
how large is your data set?
have you tried the RDF code in VMD?
it allows you to pick atoms in very flexible ways,
and is multi-threaded on the CPU and supports
(multiple) GPUs, too, if you have them.
http://dx.doi.org/10.1016/j.jcp.2011.01.048
cheers,
axel.
The doc page for compute rdf explains that you can use a wildcard
notation for specifying the atom type. E.g. if you carbonyl C
are types 1 and 2, you can ask for the rdf of 1*2 with 1*2.
I the types are 10 and 15, then you're out of luck.
Steve