From 61e7595a94bf2c9a0dca2f2adbb7862cc65c5360 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer <akohlmey@gmail.com> Date: Mon, 27 Mar 2017 14:59:58 -0400 Subject: [PATCH] remove references to xmovie, streamline dump and viz descriptions --- doc/src/Section_howto.txt | 36 ++++++------------------------------ doc/src/Section_intro.txt | 8 +++----- 2 files changed, 9 insertions(+), 35 deletions(-) diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index a378d8d088..3ca9c3d199 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -759,23 +759,14 @@ LAMMPS itself does not do visualization, but snapshots from LAMMPS 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 +create files in several formats. The native LAMMPS dump format is a 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. - +by several popular visualization tools. The "dump image"_dump_image.html +and "dump movie"_dump_image.html styles can output internally rendered +images and convert a sequence of them to a movie during the MD run. 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. 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. +between LAMMPS format files and other formats. +See the "Section 9"_Section_tools.html doc page for details. A Python-based toolkit distributed by our group can read native LAMMPS dump files, including custom dump files with additional columns of @@ -788,22 +779,7 @@ 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) diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt index ab7091d2e7..33c3cf395f 100644 --- a/doc/src/Section_intro.txt +++ b/doc/src/Section_intro.txt @@ -338,15 +338,13 @@ dynamics timestepping, particularly if the computations are not parallel, so it is often better to leave such analysis to post-processing codes. -A very simple (yet fast) visualizer is provided with the LAMMPS -package - see the "xmovie"_Section_tools.html#xmovie tool in "this -section"_Section_tools.html. It creates xyz projection views of -atomic coordinates and animates them. We find it very useful for -debugging purposes. For high-quality visualization we recommend the +For high-quality visualization we recommend the following packages: "VMD"_http://www.ks.uiuc.edu/Research/vmd "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A +"OVITO"_http://www.ovito.org/ +"ParaView"_http://www.paraview.org/ "PyMol"_http://www.pymol.org "Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html "RasMol"_http://www.openrasmol.org :ul -- GitLab