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Merge pull request #1014 from lammps/doc-reorg2

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Doc Reorganization - Tools Section
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Steve Plimpton
2018-07-25 08:37:38 -06:00
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commit bf83e55cfa
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4
doc/src/Manual.txt
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@ -116,7 +116,7 @@ it gives quick access to documentation for all LAMMPS commands.
Section_howto
Section_example
Section_perf
Section_tools
Tools
Section_modify
Section_python
Section_errors
@ -210,7 +210,7 @@ END_RST -->
6.27 "Drude induced dipoles"_howto_27 :ule,b
"Example problems"_Section_example.html :l
"Performance & scalability"_Section_perf.html :l
"Additional tools"_Section_tools.html :l
"Auxiliary tools"_Tools.html :l
"Modifying & extending LAMMPS"_Section_modify.html :l
10.1 "Atom styles"_mod_1 :ulb,b
10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b

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doc/src/Section_howto.txt
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@ -188,9 +188,9 @@ used in the CHARMM, AMBER, and DREIDING force fields. Setting
coefficients is done in the input data file via the
"read_data"_read_data.html command or in the input script with
commands like "pair_coeff"_pair_coeff.html or
"bond_coeff"_bond_coeff.html. See "Section 9"_Section_tools.html
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.
"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for
additional tools that can use CHARMM or AMBER to assign force field
coefficients and convert their output into LAMMPS input.
See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force
@ -762,12 +762,12 @@ 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 visualized
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
between LAMMPS format files and other formats.
See the "Section 9"_Section_tools.html doc page for details.
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 between LAMMPS format files and other
formats. See the "Tools"_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

18
doc/src/Section_intro.txt
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@ -234,8 +234,8 @@ Multi-replica models :h4
Pre- and post-processing :h4
Various pre- and post-processing serial tools are packaged
with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l
Various pre- and post-processing serial tools are packaged with
LAMMPS; see the "Tools"_Tools.html doc page for details. :ulb,l
Our group has also written and released a separate toolkit called
"Pizza.py"_pizza which provides tools for doing setup, analysis,
@ -296,9 +296,9 @@ visualize your MD simulation
plot your output data :ul
A few tools for pre- and post-processing tasks are provided as part of
the LAMMPS package; they are described in "this
section"_Section_tools.html. However, many people use other codes or
write their own tools for these tasks.
the LAMMPS package; they are described on the "Tools"_Tools.html doc
page. However, many people use other codes or write their own tools
for these tasks.
As noted above, our group has also written and released a separate
toolkit called "Pizza.py"_pizza which addresses some of the listed
@ -327,8 +327,8 @@ topology information and hundreds of force-field coefficients must
typically be specified. We suggest you use a program like
"CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup
such problems and dump its information to a file. You can then
reformat the file as LAMMPS input. Some of the tools in "this
section"_Section_tools.html can assist in this process.
reformat the file as LAMMPS input. Some of the tools described on the
"Tools"_Tools.html doc page can assist in this process.
Similarly, LAMMPS creates output files in a simple format. Most users
post-process these files with their own analysis tools or re-format
@ -442,8 +442,8 @@ directory. :l
The tools sub-directory of the LAMMPS distribution has various
stand-alone codes for pre- and post-processing of LAMMPS data. More
details are given in "Section 9"_Section_tools.html. If you write
a new tool that users will find useful, it can be added to the LAMMPS
details are given on the "Tools"_Tools.html doc page. If you write a
new tool that users will find useful, it can be added to the LAMMPS
distribution. :l
LAMMPS is designed to be easy to extend with new code for features

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doc/src/Section_modify.txt
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@ -1,5 +1,5 @@
"Previous Section"_Section_tools.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
"Previous Section"_Tools.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_python.html :c
:link(lws,http://lammps.sandia.gov)

4
doc/src/Section_perf.txt
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@ -1,4 +1,6 @@
"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_tools.html :c
"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Tools.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)

101
doc/src/Section_tools.txt → doc/src/Tools.txt
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@ -2,39 +2,46 @@
Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_modify.html :c
<!-- future sequence of sections:
"Previous Section"_Python.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Modify.html :c
-->
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
9. Additional tools :h2
Auxiliary tools :h3
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
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
steps are often necessary to setup and analyze a simulation. A list
of such tools can be found on the "LAMMPS webpage"_lws at these links:
A few additional tools are provided with the LAMMPS distribution
and are described in this section.
"Pre/Post processing"_http://lammps.sandia.gov/prepost.html
"Offsite LAMMPS packages & tools"_http://lammps.sandia.gov/offsite.html
"Pizza.py toolkit"_pizza :ul
Our group has also written and released a separate toolkit called
"Pizza.py"_pizza which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in "Python"_python and is available for download from "the
Pizza.py WWW site"_pizza.
The last link for "Pizza.py"_pizza is a Python-based tool developed at
Sandia which provides tools for doing setup, analysis, plotting, and
visualization for LAMMPS simulations.
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(pizza,http://pizza.sandia.gov)
:link(python,http://www.python.org)
Additional tools included in the LAMMPS distribution are described on
this page.
Note that many users write their own setup or analysis tools or use
other existing codes and convert their output to a LAMMPS input format
or vice versa. The tools listed here are included in the LAMMPS
distribution as examples of auxiliary tools. Some of them are not
actively supported by Sandia, as they were contributed by LAMMPS
users. If you have problems using them, we can direct you to the
authors.
actively supported by the LAMMPS developers, as they were contributed
by LAMMPS users. If you have problems using them, we can direct you
to the authors.
The source code for each of these codes is in the tools sub-directory
of the LAMMPS distribution. There is a Makefile (which you may need
@ -71,11 +78,12 @@ own sub-directories with their own Makefiles and/or README files.
"reax"_#reax_tool
"smd"_#smd
"vim"_#vim
"xmgrace"_#xmgrace
"xmgrace"_#xmgrace :ul
:line
:line
amber2lmp tool :h3,link(amber)
amber2lmp tool :h4,link(amber)
The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
@ -90,7 +98,7 @@ necessary modifications yourself.
:line
binary2txt tool :h3,link(binary)
binary2txt tool :h4,link(binary)
The file binary2txt.cpp converts one or more binary LAMMPS dump file
into ASCII text files. The syntax for running the tool is
@ -103,7 +111,7 @@ since binary files are not compatible across all platforms.
:line
ch2lmp tool :h3,link(charmm)
ch2lmp tool :h4,link(charmm)
The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS.
@ -128,7 +136,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
:line
chain tool :h3,link(chain)
chain tool :h4,link(chain)
The file chain.f creates a LAMMPS data file containing bead-spring
polymer chains and/or monomer solvent atoms. It uses a text file
@ -145,7 +153,7 @@ system for the "chain benchmark"_Section_perf.html.
:line
colvars tools :h3,link(colvars)
colvars tools :h4,link(colvars)
The colvars directory contains a collection of tools for postprocessing
data produced by the colvars collective variable library.
@ -167,7 +175,7 @@ gmail.com) at ICTP, Italy.
:line
createatoms tool :h3,link(createatoms)
createatoms tool :h4,link(createatoms)
The tools/createatoms directory contains a Fortran program called
createAtoms.f which can generate a variety of interesting crystal
@ -180,7 +188,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
:line
doxygen tool :h3,link(doxygen)
doxygen tool :h4,link(doxygen)
The tools/doxygen directory contains a shell script called
doxygen.sh which can generate a call graph and API lists using
@ -192,7 +200,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
:line
drude tool :h3,link(drude)
drude tool :h4,link(drude)
The tools/drude directory contains a Python script called
polarizer.py which can add Drude oscillators to a LAMMPS
@ -205,7 +213,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
:line
eam database tool :h3,link(eamdb)
eam database tool :h4,link(eamdb)
The tools/eam_database directory contains a Fortran program that will
generate EAM alloy setfl potential files for any combination of 16
@ -221,7 +229,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
:line
eam generate tool :h3,link(eamgn)
eam generate tool :h4,link(eamgn)
The tools/eam_generate directory contains several one-file C programs
that convert an analytic formula into a tabulated "embedded atom
@ -234,7 +242,7 @@ The source files and potentials were provided by Gerolf Ziegenhain
:line
eff tool :h3,link(eff)
eff tool :h4,link(eff)
The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
@ -245,7 +253,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
:line
emacs tool :h3,link(emacs)
emacs tool :h4,link(emacs)
The tools/emacs directory contains a Lips add-on file for Emacs that
enables a lammps-mode for editing of input scripts when using Emacs,
@ -256,7 +264,7 @@ These tools were provided by Aidan Thompson at Sandia
:line
fep tool :h3,link(fep)
fep tool :h4,link(fep)
The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
@ -269,7 +277,7 @@ See README file in the tools/fep directory.
:line
i-pi tool :h3,link(ipi)
i-pi tool :h4,link(ipi)
The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
@ -286,7 +294,7 @@ calculations with LAMMPS.
:line
ipp tool :h3,link(ipp)
ipp tool :h4,link(ipp)
The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input
@ -300,7 +308,7 @@ tools/createatoms tool's input file.
:line
kate tool :h3,link(kate)
kate tool :h4,link(kate)
The file in the tools/kate directory is an add-on to the Kate editor
in the KDE suite that allow syntax highlighting of LAMMPS input
@ -311,7 +319,7 @@ The file was provided by Alessandro Luigi Sellerio
:line
lmp2arc tool :h3,link(arc)
lmp2arc tool :h4,link(arc)
The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys' Insight MD code (formerly
@ -327,7 +335,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
:line
lmp2cfg tool :h3,link(cfg)
lmp2cfg tool :h4,link(cfg)
The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of *.cfg files which can be read into the
@ -338,7 +346,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
:line
matlab tool :h3,link(matlab)
matlab tool :h4,link(matlab)
The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
post-processing LAMMPS output. The scripts include readers for log
@ -356,7 +364,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
:line
micelle2d tool :h3,link(micelle)
micelle2d tool :h4,link(micelle)
The file micelle2d.f creates a LAMMPS data file containing short lipid
chains in a monomer solution. It uses a text file containing lipid
@ -373,7 +381,7 @@ definition file. This tool was used to create the system for the
:line
moltemplate tool :h3,link(moltemplate)
moltemplate tool :h4,link(moltemplate)
The moltemplate sub-directory contains a Python-based tool for
building molecular systems based on a text-file description, and
@ -387,7 +395,7 @@ supports it. It has its own WWW page at
:line
msi2lmp tool :h3,link(msi)
msi2lmp tool :h4,link(msi)
The msi2lmp sub-directory contains a tool for creating LAMMPS template
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
@ -404,7 +412,7 @@ See the README file in the tools/msi2lmp folder for more information.
:line
phonon tool :h3,link(phonon)
phonon tool :h4,link(phonon)
The phonon sub-directory contains a post-processing tool useful for
analyzing the output of the "fix phonon"_fix_phonon.html command in
@ -419,7 +427,7 @@ University.
:line
polybond tool :h3,link(polybond)
polybond tool :h4,link(polybond)
The polybond sub-directory contains a Python-based tool useful for
performing "programmable polymer bonding". The Python file
@ -433,7 +441,7 @@ This tool was written by Zachary Kraus at Georgia Tech.
:line
pymol_asphere tool :h3,link(pymol)
pymol_asphere tool :h4,link(pymol)
The pymol_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
@ -451,7 +459,7 @@ This tool was written by Mike Brown at Sandia.
:line
python tool :h3,link(pythontools)
python tool :h4,link(pythontools)
The python sub-directory contains several Python scripts
that perform common LAMMPS post-processing tasks, such as:
@ -467,7 +475,7 @@ README for more info on Pizza.py and how to use these scripts.
:line
reax tool :h3,link(reax_tool)
reax tool :h4,link(reax_tool)
The reax sub-directory contains stand-alond codes that can
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
@ -478,7 +486,7 @@ These tools were written by Aidan Thompson at Sandia.
:line
smd tool :h3,link(smd)
smd tool :h4,link(smd)
The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
Makefile which can be compiled and used to convert triangle output
@ -494,7 +502,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
:line
vim tool :h3,link(vim)
vim tool :h4,link(vim)
The files in the tools/vim directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the README.txt
@ -505,7 +513,7 @@ ziegenhain.com)
:line
xmgrace tool :h3,link(xmgrace)
xmgrace tool :h4,link(xmgrace)
The files in the tools/xmgrace directory can be used to plot the
thermodynamic data in LAMMPS log files via the xmgrace plotting
@ -517,4 +525,3 @@ simulation.
See the README file for details.
These files were provided by Vikas Varshney (vv0210 at gmail.com)

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doc/src/dump.txt
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@ -1,4 +1,4 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -184,10 +184,10 @@ file and in what format. Settings made via the
individual values and the file itself.
The {atom}, {local}, and {custom} styles create files in a simple text
format that is self-explanatory when viewing a dump file. Many of the
LAMMPS "post-processing tools"_Section_tools.html, including
"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with this
format, as does the "rerun"_rerun.html command.
format that is self-explanatory when viewing a dump file. Some of the
LAMMPS post-processing tools described on the "Tools"_Tools.html doc
page, including "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html,
work with this format, as does the "rerun"_rerun.html command.
For post-processing purposes the {atom}, {local}, and {custom} text
files are self-describing in the following sense.
@ -413,10 +413,10 @@ If the filename ends with ".bin", the dump file (or files, if "*" or
will be about the same size as a text version, but will typically
write out much faster. Of course, when post-processing, you will need
to convert it back to text format (see the "binary2txt
tool"_Section_tools.html#binary) or write your own code to read the
binary file. The format of the binary file can be understood by
looking at the tools/binary2txt.cpp file. This option is only
available for the {atom} and {custom} styles.
tool"_Tools.html#binary) or write your own code to read the binary
file. The format of the binary file can be understood by looking at
the tools/binary2txt.cpp file. This option is only available for the
{atom} and {custom} styles.
If the filename ends with ".gz", the dump file (or files, if "*" or "%"
is also used) is written in gzipped format. A gzipped dump file will

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doc/src/lammps.book
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@ -14,7 +14,7 @@ accelerate_opt.html
Section_howto.html
Section_example.html
Section_perf.html
Section_tools.html
Tools.html
Section_modify.html
Section_python.html
Section_errors.html