forked from lijiext/lammps
81 lines
3.7 KiB
Plaintext
81 lines
3.7 KiB
Plaintext
This directory used to contain utility scripts for using VMD to
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visualize and analyze LAMMPS trajectories. As of April 2010 all of the
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scripts and many additional features have been merged into the topotools
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plugin that is bundled with VMD. Updates between VMD releases are here:
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http://sites.google.com/site/akohlmey/software/topotools
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This page also contains detailed documentation and some tutorials.
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These scripts within VMD and the plugin for native LAMMPS dump files are
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are maintained by Axel Kohlmeyer <akohlmey@gmail.com>; please contact
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him through the LAMMPS mailing list in case of problems.
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Below are a few comments on support for LAMMPS in VMD.
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1. File formats and VMD limitations
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VMD currently supports reading several but not all file formats
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that LAMMPS can generate. Supported are: atom (text mode), custom
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(text mode, only some fields are directly supported, please see
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below for more details), dcd, xyz and xtc. Cfg and binary native
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dump files are not supported (06/2012). The new molfile dump style
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in addition allows to use VMD molfile plugins to write dumps in
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any format that is supported by VMD.
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However VMD requires all frames of a file to have the same number of
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atoms. If the number of atoms changes between two frames, the file
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reader will stop. The topotools plugin has a special scripted file
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reader for .xyz files that can generate the necessary padding so that
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the file can still be read into VMD. Whether an atom is real or
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"invisible" is then flagged in the "user" field. For efficiency
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reasons this script will not preserve atom identity between frames.
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2. Topology files, a.k.a. as "data" files
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The topotools plugin also contains a read and write option for LAMMPS
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data files. This reader will try to preserve as much information as
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possible and will also store useful information as comments upon
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writing. It does not store or read coefficient data. In combination
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with other functionality in topotools complete topologies for rather
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complicated systems for LAMMPS can be build with VMD scripting.
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3. Reading custom data fields into VMD
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At this moment VMD only supports reading coordinates and velocities
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(if present) as per timestep data. Everthing else is just taken
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from the first frame or whatever file was used to generate this
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structure information. Through setting the environment variable
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LAMMPSREMAPFIELDS, custom properties can be mapped to the x, y, z,
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vx, vy, vz data fields and then accessed from within VMD. For
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example to store radius and charge of a particle in the vx and vy
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fields, respectively set this variable to "vx=radius,vy=q". Future
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versions of VMD will allow more flexibility.
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4. Recovering information about elements
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Colorization in VMD is by default based on atom names, yet LAMMPS
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requires identification of atoms by consecutive numbers starting at
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1. With the option of reading a LAMMPS data file, additional
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information is provided that can help to recover some of this
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data. 'topo guessatom element mass' will guess the atom's element
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name from it mass (with fuzz, where possible).
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5. Reading files from the command line
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Converting a LAMMPS data file to a .psf file can be very convenient
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for loading trajectories from the command line. This conversion is
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done with
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topo readlammpsdata data.rhodo full
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animate write psf rhodo.psf
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In the future you can now load this PSF file first and then the
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LAMMPS dump file(s) (or a more compact and faster loading DCD or
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XTC file) with:
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vmd micelle.psf -lammpstrj dump.micelle
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Note how the -lammpstrj flag will tell VMD that dump.micelle is a
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lammps trajectory file.
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