[lammps-users] basic problems with data file creation

Hello,

I want to create a data file with a bundle of aligned Carbon nanotubes and with molecules on both ends, in order to simulate diffusion through the bundle.

Can anybody tell me which program to use to create SWCNT, make a bundle and then add molecules to the system? Is it possible with the pizza tool kit?

Also: Is a methane molecule simplified as a single atom when running LAMMPS with lj potential forces?

Many thanks in advance

Thomas

Hello,

thomas,

I want to create a data file with a bundle of aligned Carbon nanotubes
and with molecules on both ends, in order to simulate diffusion
through the bundle.

Can anybody tell me which program to use to create SWCNT, make a
bundle and then add molecules to the system? Is it possible with the
pizza tool kit?

i cannot comment on pizza.py, but i'm certain that steve is able to.

my preferred tool for operations like that is VMD, and with the very
latest beta version there is an integrated plugin (with GUI) that
can create SWCNTs, and a bunch of scripts/plugins, that allow to
replicate and merge them, as well as adding molecules to it.
however, this is all very new and - obviously - not fully automated.
so you would have to do some tcl scripting in VMD, but at least the
hard tasks (including writing the resulting combined system topology
to a lammps format data file) have already been programmed.

Also: Is a methane molecule simplified as a single atom when running
LAMMPS with lj potential forces?

lammps does not come with a hardcoded force field. so it is you
choice. as far as i know, a united atom approach for methane is
usually considered a good approximation.

cheers,
    axel.

Pizza.py does not have any builder tool for CNTs. If VMD does,
I would use that.

Steve

Hello users,

I have some trouble starting a batch mode of lammps.
The programm works fine if I start it interactively with mpirun...
However when starting a batch job with job_submit ... the connection is
lost and the lammps log file is empty except for the date.

Any comments?

I use the latest version of lamps, compiled with a modified intel
makefile and HP MPI 2.2.1

Best regards

Thomas

Hello users,

hello thomas,

I have some trouble starting a batch mode of lammps.
The programm works fine if I start it interactively with mpirun...
However when starting a batch job with job_submit ... the connection is
lost and the lammps log file is empty except for the date.

Any comments?

looks like an MPI problem. perhaps your mpirun wrapper code
has problems redirecting stdin/stdout/stderr.

have you tried running LAMMPS with the -in <input> -log <output> flags?

then you can just append: < /dev/null >& /dev/null

cheers,
   axel.