Gay-Berne fluid

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1

I guess there are two questions:

   1) How to create LAMMPS input files (input-script, data-file) so
that you can run a LAMMPS simulation.
As Axel pointed out, the examples/ellipse subdirectory contains a file
"in.ellipse.gayberne" (see attachment) which can be used to run a
LAMMPS simulation (if you have compiled LAMMPS with the "asphere"
package enabled.)
       One way to place atoms in a LAMMPS simulation is to use the
"lattice" and "region" and "create_atoms" commands. That is the
method used in the "ellipse" example ("in.ellipse.gayberne" file).
These commands work great if you want to place particles (ellipsoids)
uniformly at points on a lattice. However if instead you want to
manually control the placement (and orientation) of all of the
ellipsoids, then you need to create a "data" file. Axel was saying
that one way to do this is to add the "write_data" command somewhere
before the "run" command, (and optionally comment out the run
commands, since you are only trying to create a data file). The
advantage of this approach (over writing one from scratch) is that it
will create a working data file which you know LAMMPS will accept.
Then you can customize this file.

   2) How to modify a LAMMPS input script so that you can view the
simulation trajectory results in OVITO:

To do that, see:
http://www.ovito.org/manual/howto.aspherical_particles.html

I attached the original "in.ellipse.gayberne" and a modified version
which includes these two changes. (But I have not tested the modified
version.)

Andrew

P.S. Note: if you are using the simple, commonly used force-fields
supported by the LAMMPS developers, it is probably okay if you want to
put force-field parameters in the data file (which is what
"write_data" does by default). Otherwise, you should leave the
"coeff" commands in the input script (by using "write_data" with the
"nocoeff" option).

in.ellipse.gayberne (1.54 KB)

in.ellipse.gayberne.modified (2.44 KB)

2

> Thank you very much for your answer. In order to clarify: I want to run
the
> molecular graphics program Ovito, which can read output files from
Lammps.
> Therefore I need to know the format of those files.

I guess there are two questions:

​...and one glaring omission:

the format of dump files is explained in the dump command documentation and
the format of data files is documented with the read_data command. in both
cases the documentation is very detailed and complete. having an example
file can help, but will rarely tell the whole story. reading the
documentation does. in short: "there ain't no escape from the blues"​, or
in other words. it is imperative to always study the documentation well.
people that ask questions revealing that they have not invested any effort
into reading the documentation will quickly end up being ignored. people
write documentation so the don't have to explain things over and over
again. it is often painful enough for a developer to write good and
detailed documentation, it multiplies the pain to see it ignored.

axel.