This directory used to contain utility scripts for using VMD to
visualize and analyze LAMMPS trajectories. As of April 2010 all of the
scripts and many additional features have been merged into the
topotools plugin that is shipped with VMD. Please see
http://www.ks.uiuc.edu/Research/vmd/plugins/topotools and
http://sites.google.com/site/akohlmey/software/topotools for more
details about the latest version of VMD.

The scripts within VMD are maintained by Axel Kohlmeyer
<akohlmey@gmail.com>; please contact him through the LAMMPS mailing
list in case of problems.

Below are a few comment on support for LAMMPS in VMD.

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1. File formats and VMD limitations

VMD currently supports reading several but not all file formats
that LAMMPS can generate. Supported are: atom (text mode), custom
(text mode, only some fields are directly supported, please see
below for more details), dcd, xyz and xtc. Cfg and binary native
dump files are not supported (04/2010).

VMD requires all frames of a file to have the same number of
atoms. If the number of atoms changes between two frames, the file
reader will stop. The topotools plugin has a special scripted file
reader for .xyz files that can generate the necessary padding so
that the file can still be read into VMD. Whether an atom is real
or "invisible" is then flagged in the "user" field. For efficiency
reasons this script will not preserve atom identity between frames.

2. Topology files, a.k.a. as "data" files

The topotools plugin also contains a read and write option for
LAMMPS data files. This reader will try to preserve as much
information as possible and will also store useful information as
comments upon writing. It does not store or read coefficient data
and it cannot handle class2 force fields. In combination with
other functionality in topotools complete topologies for rather
complicated systems can be build.

3. Reading custom data fields into VMD

At this moment VMD only supports reading coordinates and velocities
(if present) as per timestep data. Everthing else is just taken
from the first frame or whatever file was used to generate this
structure information. Through setting the environment variable
LAMMPSREMAPFIELDS, custom properties can be mapped to the x, y, z,
vx, vy, vz data fields and then accessed from within VMD. For
example to store radius and charge of a particle in the vx and vy
fields, respectively set this variable to "vx=radius,vy=q". Future
versions of VMD will allow more flexibility.

4. Recovering information about elements

Colorization in VMD is by default based on atom names, yet LAMMPS
requires identification of atoms by consecutive numbers starting at
1. With the option of reading a LAMMPS data file, additional
information is provided that can help to recover some of this
data. 'topo guessatom element mass' will guess the atom's element
name from it mass (with fuzz, where possible).

5. Reading files from the command line

Converting a LAMMPS data file to a .psf file can be very convenient
for loading trajectories from the command line. This conversion is
done with

topo readlammpsdata data.rhodo full
animate write psf rhodo.psf

In the future you can now load this PSF file first and then the
LAMMPS dump file(s) (or a more compact and faster loading DCD or
XTC file) with:

vmd micelle.psf -lammpstrj dump.micelle

Note how the -lammpstrj flag will tell VMD that dump.micelle is a
lammps trajectory file.