git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3997 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/lmp2vmd/README.txt

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+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.
+
+-------------------------
+
+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.