forked from lijiext/lammps
remove references to deleted tools. update/clarify section on restart2data
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@ -12,9 +12,12 @@ Section"_Section_modify.html :c
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LAMMPS is designed to be a computational kernel for performing
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molecular dynamics computations. Additional pre- and post-processing
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steps are often necessary to setup and analyze a simulation. A few
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additional tools are provided with the LAMMPS distribution and are
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described in this section.
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steps are often necessary to setup and analyze a simulation. A
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list of such tools can be found on the LAMMPS home page
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at "http://lammps.sandia.gov/prepost.html"_http://lammps.sandia.gov/prepost.html
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A few additional tools are provided with the LAMMPS distribution
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and are described in this section.
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Our group has also written and released a separate toolkit called
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"Pizza.py"_pizza which provides tools for doing setup, analysis,
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@ -45,7 +48,6 @@ own sub-directories with their own Makefiles.
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"chain"_#chain
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"colvars"_#colvars
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"createatoms"_#create
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"data2xmovie"_#data
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"eam database"_#eamdb
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"eam generate"_#eamgn
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"eff"_#eff
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@ -56,7 +58,6 @@ own sub-directories with their own Makefiles.
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"kate"_#kate
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"lmp2arc"_#arc
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"lmp2cfg"_#cfg
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"lmp2vmd"_#vmd
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"matlab"_#matlab
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"micelle2d"_#micelle
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"moltemplate"_#moltemplate
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@ -69,7 +70,6 @@ own sub-directories with their own Makefiles.
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"restart2data"_#restart
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"vim"_#vim
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"xmgrace"_#xmgrace
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"xmovie"_#xmovie :ul
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:line
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@ -171,19 +171,6 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
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:line
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data2xmovie tool :h4,link(data)
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The file data2xmovie.c converts a LAMMPS data file into a snapshot
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suitable for visualizing with the "xmovie"_#xmovie tool, as if it had
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been output with a dump command from LAMMPS itself. The syntax for
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running the tool is
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data2xmovie \[options\] < infile > outfile :pre
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See the top of the data2xmovie.c file for a discussion of the options.
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:line
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eam database tool :h4,link(eamdb)
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The tools/eam_database directory contains a Fortran program that will
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@ -317,18 +304,6 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
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:line
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lmp2vmd tool :h4,link(vmd)
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The lmp2vmd sub-directory contains a README.txt file that describes
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details of scripts and plugin support within the "VMD
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package"_http://www.ks.uiuc.edu/Research/vmd for visualizing LAMMPS
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dump files.
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The VMD plugins and other supporting scripts were written by Axel
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Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
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:line
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matlab tool :h4,link(matlab)
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The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
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@ -381,16 +356,14 @@ supports it. It has its own WWW page at
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msi2lmp tool :h4,link(msi)
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The msi2lmp sub-directory contains a tool for creating LAMMPS input
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data files from Accelrys' Insight MD code (formerly MSI/Biosym and
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its Discover MD code). See the README file for more information.
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data files from BIOVIA's Materias Studio files (formerly Accelrys'
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Insight MD code, formerly MSI/Biosym and its Discover MD code).
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This tool was written by John Carpenter (Cray), Michael Peachey
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(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
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(jec at mayo.edu), but still fields questions about the tool.
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(Cray), and Steve Lustig (Dupont). Several people contributed changes
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to remove bugs and adapt its output to changes in LAMMPS.
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This tool may be out-of-date with respect to the current LAMMPS and
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Insight versions. Since we don't use it at Sandia, you'll need to
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experiment with it yourself.
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See the README file for more information.
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:line
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@ -484,32 +457,13 @@ read_restart restartfile
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write_data datafile
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which will produce the same data file that the restart2data tool used
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to create. The following information is included in case you have an
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older version of LAMMPS which still includes the restart2data tool.
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to create.
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The file restart2data.cpp converts a binary LAMMPS restart file into
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an ASCII data file. The syntax for running the tool is
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restart2data restart-file data-file (input-file) :pre
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Input-file is optional and if specified will contain LAMMPS input
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commands for the masses and force field parameters, instead of putting
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those in the data-file. Only a few force field styles currently
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support this option.
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This tool must be compiled on a platform that can read the binary file
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created by a LAMMPS run, since binary files are not compatible across
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all platforms.
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Note that a text data file has less precision than a binary restart
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file. Hence, continuing a run from a converted data file will
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typically not conform as closely to a previous run as will restarting
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from a binary restart file.
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If a "%" appears in the specified restart-file, the tool expects a set
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of multiple files to exist. See the "restart"_restart.html and
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"write_restart"_write_restart.html commands for info on how such sets
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of files are written by LAMMPS, and how the files are named.
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IMPORTANT NOTE: LAMMPS' binary restart files are generally not portable
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between platforms, compiler settings and LAMMPS versions. Changes in
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the format itself are rare, but no effort is made to maintain backward
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compatibility. Data files are mostly backward and forward portable,
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if no features are used that exist in only one LAMMPS version.
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:line
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@ -537,32 +491,3 @@ See the README file for details.
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These files were provided by Vikas Varshney (vv0210 at gmail.com)
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:line
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xmovie tool :h4,link(xmovie)
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The xmovie tool is an X-based visualization package that can read
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LAMMPS dump files and animate them. It is in its own sub-directory
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with the tools directory. You may need to modify its Makefile so that
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it can find the appropriate X libraries to link against.
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The syntax for running xmovie is
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xmovie \[options\] dump.file1 dump.file2 ... :pre
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If you just type "xmovie" you will see a list of options. Note that
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by default, LAMMPS dump files are in scaled coordinates, so you
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typically need to use the -scale option with xmovie. When xmovie runs
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it opens a visualization window and a control window. The control
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options are straightforward to use.
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Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he
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spent a summer at Sandia. It displays 2d projections of a 3d domain.
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While simple in design, it is an amazingly fast program that can
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render large numbers of atoms very quickly. It's a useful tool for
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debugging LAMMPS input and output and making sure your simulation is
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doing what you think it should. The animations on the Examples page
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of the "LAMMPS WWW site"_lws were created with xmovie.
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I've lost contact with Mike, so I hope he's comfortable with us
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distributing his great tool!
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