Homec4science
Diffusion lammps (lammm-master) Browse

lammps/tools/lmp2vmd/README.txt
11533ea7590elammm-master

Last Change
Raw File

README.txt
View Options

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 bundled with VMD. Updates between VMD releases are here:
http://sites.google.com/site/akohlmey/software/topotools
This page also contains detailed documentation and some tutorials.
These scripts within VMD and the plugin for native LAMMPS dump files are
are maintained by Axel Kohlmeyer <akohlmey@gmail.com>; please contact
him through the LAMMPS mailing list in case of problems.
Below are a few comments on support for LAMMPS in VMD.
-------------------------
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 (06/2012). The new molfile dump style
in addition allows to use VMD molfile plugins to write dumps in
any format that is supported by VMD.
However 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. In combination
with other functionality in topotools complete topologies for rather
complicated systems for LAMMPS can be build with VMD scripting.
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.
c4science · Help