remove references to deleted tools. update/clarify section on restart2data

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Axel Kohlmeyer 2017-03-20 18:57:30 -04:00
parent 0c9cd11b4e
commit 6482df6c2f
1 changed files with 17 additions and 92 deletions

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