How can finds the index number of particular atoms after equilibration

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1

Dear All

I want to calculate MSD of some atoms in a group with same atom type. For example, I have tree types of atoms like, nitrogen, carbon, oxygen. Now after equilibration, I calculate the RDF and found that the first neighbor distance from nitrogen to carbon 0.31nm and from oxygen 0.37nm. Since, all ate in a mixture, I want to calculate the carbons those have 0.31nm distance from nitrogen. Therefore, I thinking If I can, find the index of those carbons then I can make a group and calculate the MSD.

It will be very helpful if someone help how can I do it in LAMMPS

Thank you very much

Anderson
Houston University

2

Since nobody else replied yet, ...

Take a look at the "compute cluster/atom" command:
http://lammps.sandia.gov/doc/compute_cluster_atom.html

It does not do exactly what you want, but perhaps it points you in a
good direction.

More generally, you could write your own code to compute the RDFs you need.

The DUMP files created by the LAMMPS' dump command have a simple,
easy-to-parse syntax.

Usually you can write a short program which can read an ordinary DUMP
file (trajectory file) created by LAMMPS, and calculate the quantities
you are interested in. The best way to learn the file format is to
create a DUMP file using the LAMMPS' dump command:
http://lammps.sandia.gov/doc/dump.html

Cheers

Andrew

Also, check out pizza.py:
http://pizza.sandia.gov/doc/Manual.html

3

Dear All

I want to calculate MSD of some atoms in a group with same atom type. For
example, I have tree types of atoms like, nitrogen, carbon, oxygen. Now
after equilibration, I calculate the RDF and found that the first neighbor
distance from nitrogen to carbon 0.31nm and from oxygen 0.37nm. Since, all
ate in a mixture, I want to calculate the carbons those have 0.31nm
distance from nitrogen. Therefore, I thinking If I can, find the index of
those carbons then I can make a group and calculate the MSD.

​this may be possible using compute coord/atom. please check out the
documentation.

axel.​

4

I like Axel’s suggestion:

a) use compute coord/atom to give a non-zero count for atoms of a certain type

that are within a cutoff distance of aother type(s)

b) use the group variable command to put atoms in a group

that have a non-zero count, with an atom-style variable that is count != 0 or the like

c) use that group in your compute msd command

Steve