From 1db5834b99d07ddb9225d67ab55fdcfdd85e6f41 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer <akohlmey@gmail.com> Date: Wed, 22 Mar 2017 15:12:49 -0400 Subject: [PATCH] Revert "Cleanup of a few more references to obsoleted and removed tools like xmovie" This reverts commit 127597023df5a081bbe854ec8e633a0111d2b7a9. --- doc/src/Section_howto.txt | 51 +++++++++++++++++++++++++++------------ 1 file changed, 35 insertions(+), 16 deletions(-) diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index 682646d5d7..aedc2fc64f 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -751,33 +751,52 @@ simulations can be visualized (and analyzed) in a variety of ways. LAMMPS snapshots are created by the "dump"_dump.html command which can create files in several formats. The native LAMMPS dump format is a -text file (see "dump atom" or "dump custom") which can be read by -several popular visualization tools. +text file (see "dump atom" or "dump custom") which can be visualized +by the "xmovie"_Section_tools.html#xmovie program, included with the +LAMMPS package. This produces simple, fast 2d projections of 3d +systems, and can be useful for rapid debugging of simulation geometry +and atom trajectories. Several programs included with LAMMPS as auxiliary tools can convert native LAMMPS dump files to other formats. See the -"Section 9"_Section_tools.html doc page for details. +"Section 9"_Section_tools.html doc page for details. The first is +the "ch2lmp tool"_Section_tools.html#charmm, which contains a +lammps2pdb Perl script which converts LAMMPS dump files into PDB +files. The second is the "lmp2arc tool"_Section_tools.html#arc which +converts LAMMPS dump files into Accelrys' Insight MD program files. +The third is the "lmp2cfg tool"_Section_tools.html#cfg which converts +LAMMPS dump files into CFG files which can be read into the +"AtomEye"_atomeye visualizer. A Python-based toolkit distributed by our group can read native LAMMPS dump files, including custom dump files with additional columns of user-specified atom information, and convert them to various formats or pipe them into visualization software directly. See the "Pizza.py -WWW site"_pizza for details. - -LAMMPS can create a selection of file formats natively (via "dump"_dump.html) -and also supports "VMD molfile plugins"_vmd. Lists of possible -"visualization programs"_http://lammps.sandia.gov/viz.html and -"pre-/post-processing tools"_http://lammps.sandia.gov/prepost.html -are maintained on the LAMMPS homepage. - -In addition LAMMPS also includes a small render library to create -visualization snapshot images directly during a simulation -(via "dump image"_dump_image.html) or automatically convert -them to movies by piping the images to an external FFmpeg -executable (via "dump movie"_dump_image.html). +WWW site"_pizza for details. Specifically, Pizza.py can convert +LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats. +Pizza.py can pipe LAMMPS dump files directly into the Raster3d and +RasMol visualization programs. Pizza.py has tools that do interactive +3d OpenGL visualization and one that creates SVG images of dump file +snapshots. + +LAMMPS can create XYZ files directly (via "dump xyz") which is a +simple text-based file format used by many visualization programs +including "VMD"_vmd. + +LAMMPS can create DCD files directly (via "dump dcd") which can be +read by "VMD"_vmd in conjunction with a CHARMM PSF file. Using this +form of output avoids the need to convert LAMMPS snapshots to PDB +files. See the "dump"_dump.html command for more information on DCD +files. + +LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS +file format which can also be read by "VMD"_vmd for visualization. +See the "dump"_dump.html command for more information on XTC files. :link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) :link(vmd,http://www.ks.uiuc.edu/Research/vmd) +:link(ensight,http://www.ensight.com) +:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) :line -- GitLab