Hi, all, does anyone try this command fix_renum/mol before? I cannot find the cpp code inside the src folder and I tried to use it in lammps version 2011 but the error like ERROR: Invalid fix style.
Since I found this syntax in documentation, I think it should be able to apply for any case, am I right?
Best,
Haoxiang
Hi, all, does anyone try this command fix_renum/mol before? I cannot find the cpp code inside the src folder and I tried to use it in lammps version 2011 but the error like ERROR: Invalid fix style.
fix renum/mol was never part of LAMMPS and i don't see any reference
to it in the documentation.
Since I found this syntax in documentation, I think it should be able to apply for any case, am I right?
no.
It isn’t a part of the official LAMMPS distribution. More information about it (with a link for downloading necessary files): http://lammps.sandia.gov/threads/msg54025.html
There is a compute cluster/atom command which
will generate a unique ID for all the atoms in individual
clusters, defined by a geometric length separation.
If you define an atom-style variable that uses the output
of that compute, then the set command can be used
to set the molecule ID for each atom to the value
of the variable, i.e. the cluster ID.
Steve
Thanks Steve and Michal
Dear Haoxiang
If you can accomplish what you are trying to do using Steve's
suggestion, do it that way. That seems like a more elegant way to
solve this problem. If not, the code is at
http://www.moltemplate.org/lammps_code/downloads/
The problem is that fix renum/mol works in serial mode only. (I
think I know why it fails in parallel, but I don't have time to fix
it.) I never intended it to be publicly available.
When I have a chance to post the next moltemplate update, I'll try
to remember to take down (or at least add a HUGE warning message) to
the fix renum/mol documentation and code. I'm sorry that this keeps
getting posted to the mailing list.
Andrew
P.S.
fix renum/mol has some other features, but it's not clear that
these are useful. (Such as clustering pairs of atoms which are
connected by bonds, but usually the bond-lengths are shorter than the
distance cutoff you would use. The atom type-qualifiers and "either"
"nucleate" features might be possible to accomplish in lammps using
the "variable" command with logic operators ( < > || ). (I have not
tried this however.)
Thank you guys' suggestion, that helps me a lot, Andrew, I will take a look at your code to see how it works. I appreciate for your answer.
Best,
Haoxiang