Unverified Commit 2c190797 authored by Steve Plimpton's avatar Steve Plimpton Committed by GitHub
Browse files

Merge pull request #1062 from lammps/doc-reformat

change format of Howto and Tools doc pages
parents 21c33235 f8faf4df
......@@ -8,27 +8,44 @@ Section"_Examples.html :c
:line
How to discussions :h2
Howto discussions :h2
These doc pages describe how to perform various tasks with LAMMPS,
both for users and developers. The
"glossary"_http://lammps.sandia.gov website page also lists MD
terminology with links to corresponding LAMMPS manual pages.
The example input scripts included in the examples dir of the LAMMPS
terminology with links to corresponding LAMMPS manual pages. The
example input scripts included in the examples dir of the LAMMPS
distribution and highlighted on the "Examples"_Examples.html doc page
also show how to setup and run various kinds of simulations.
Tutorials howto :h3
<!-- RST
.. toctree::
:name: tutorials
:maxdepth: 1
Howto_github
Howto_pylammps
Howto_bash
END_RST -->
<!-- HTML_ONLY -->
"Using GitHub with LAMMPS"_Howto_github.html
"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
<!-- END_HTML_ONLY -->
General howto :h3
<!-- RST
.. toctree::
:name: general
:maxdepth: 1
Howto_restart
......@@ -38,35 +55,86 @@ also show how to setup and run various kinds of simulations.
Howto_library
Howto_couple
.. toctree::
:maxdepth: 1
END_RST -->
Howto_output
Howto_chunk
<!-- HTML_ONLY -->
"Restart a simulation"_Howto_restart.html
"Visualize LAMMPS snapshots"_Howto_viz.html
"Run multiple simulations from one input script"_Howto_multiple.html
"Multi-replica simulations"_Howto_replica.html
"Library interface to LAMMPS"_Howto_library.html
"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
<!-- END_HTML_ONLY -->
Settings howto :h3
<!-- RST
.. toctree::
:name: settings
:maxdepth: 1
Howto_2d
Howto_triclinic
Howto_thermostat
Howto_barostat
Howto_walls
Howto_nemd
Howto_granular
Howto_spherical
Howto_dispersion
END_RST -->
<!-- HTML_ONLY -->
"2d simulations"_Howto_2d.html
"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
"Thermostats"_Howto_thermostat.html
"Barostats"_Howto_barostat.html
"Walls"_Howto_walls.html
"NEMD simulations"_Howto_nemd.html
"Long-range dispersion settings"_Howto_dispersion.html :all(b)
<!-- END_HTML_ONLY -->
Analysis howto :h3
<!-- RST
.. toctree::
:name: analysis
:maxdepth: 1
Howto_output
Howto_chunk
Howto_temperature
Howto_thermostat
Howto_barostat
Howto_elastic
Howto_kappa
Howto_viscosity
Howto_diffusion
END_RST -->
<!-- HTML_ONLY -->
"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
"Calculate temperature"_Howto_temperature.html
"Calculate elastic constants"_Howto_elastic.html
"Calculate thermal conductivity"_Howto_kappa.html
"Calculate viscosity"_Howto_viscosity.html
"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
<!-- END_HTML_ONLY -->
Force fields howto :h3
<!-- RST
.. toctree::
:name: force
:maxdepth: 1
Howto_bioFF
......@@ -74,9 +142,27 @@ also show how to setup and run various kinds of simulations.
Howto_tip4p
Howto_spc
END_RST -->
<!-- HTML_ONLY -->
"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
"TIP3P water model"_Howto_tip3p.html
"TIP4P water model"_Howto_tip4p.html
"SPC water model"_Howto_spc.html :all(b)
<!-- END_HTML_ONLY -->
Packages howto :h3
<!-- RST
.. toctree::
:name: packages
:maxdepth: 1
Howto_spherical
Howto_granular
Howto_body
Howto_polarizable
Howto_coreshell
......@@ -87,43 +173,11 @@ also show how to setup and run various kinds of simulations.
END_RST -->
<!-- HTML_ONLY -->
"Using GitHub with LAMMPS"_Howto_github.html
"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
"Restart a simulation"_Howto_restart.html
"Visualize LAMMPS snapshots"_Howto_viz.html
"Run multiple simulations from one input script"_Howto_multiple.html
"Multi-replica simulations"_Howto_replica.html
"Library interface to LAMMPS"_Howto_library.html
"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
<!-- HTML_ONLY -->
"2d simulations"_Howto_2d.html
"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
"Walls"_Howto_walls.html
"NEMD simulations"_Howto_nemd.html
"Granular models"_Howto_granular.html
"Finite-size spherical and aspherical particles"_Howto_spherical.html
"Long-range dispersion settings"_Howto_dispersion.html :all(b)
"Calculate temperature"_Howto_temperature.html
"Thermostats"_Howto_thermostat.html
"Barostats"_Howto_barostat.html
"Calculate elastic constants"_Howto_elastic.html
"Calculate thermal conductivity"_Howto_kappa.html
"Calculate viscosity"_Howto_viscosity.html
"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
"TIP3P water model"_Howto_tip3p.html
"TIP4P water model"_Howto_tip4p.html
"SPC water model"_Howto_spc.html :all(b)
"Granular models"_Howto_granular.html
"Body style particles"_Howto_body.html
"Polarizable models"_Howto_polarizable.html
"Adiabatic core/shell model"_Howto_coreshell.html
......
......@@ -66,7 +66,7 @@ every LAMMPS command.
.. toctree::
:maxdepth: 2
:numbered:
:numbered: 3
:caption: User Documentation
:name: userdoc
:includehidden:
......
......@@ -43,40 +43,55 @@ to edit for your platform) which will build several of the tools which
reside in that directory. Most of them are larger packages in their
own sub-directories with their own Makefiles and/or README files.
"amber2lmp"_#amber
"binary2txt"_#binary
"ch2lmp"_#charmm
"chain"_#chain
"colvars"_#colvars
"createatoms"_#createatoms
"doxygen"_#doxygen
"drude"_#drude
"eam database"_#eamdb
"eam generate"_#eamgn
"eff"_#eff
"emacs"_#emacs
"fep"_#fep
"i-pi"_#ipi
"ipp"_#ipp
"kate"_#kate
"lmp2arc"_#arc
"lmp2cfg"_#cfg
"matlab"_#matlab
"micelle2d"_#micelle
"moltemplate"_#moltemplate
"msi2lmp"_#msi
"phonon"_#phonon
"polybond"_#polybond
"pymol_asphere"_#pymol
"python"_#pythontools
"reax"_#reax_tool
"smd"_#smd
"vim"_#vim
"xmgrace"_#xmgrace :ul
:line
amber2lmp tool :h3,link(amber)
:line
Pre-processing tools :h3
"amber2lmp"_#amber,
"ch2lmp"_#charmm,
"chain"_#chain,
"createatoms"_#createatoms,
"drude"_#drude,
"eam database"_#eamdb,
"eam generate"_#eamgn,
"eff"_#eff,
"ipp"_#ipp,
"micelle2d"_#micelle,
"moltemplate"_#moltemplate,
"msi2lmp"_#msi,
"polybond"_#polybond :tb(c=6,ea=c,a=l)
Post-processing tools :h3
"amber2lmp"_#amber,
"binary2txt"_#binary,
"ch2lmp"_#charmm,
"colvars"_#colvars,
"eff"_#eff,
"fep"_#fep,
"lmp2arc"_#arc,
"lmp2cfg"_#cfg,
"matlab"_#matlab,
"phonon"_#phonon,
"pymol_asphere"_#pymol,
"python"_#pythontools,
"reax"_#reax_tool,
"smd"_#smd,
"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
Miscellaneous tools :h3
"doxygen"_#doxygen,
"emacs"_#emacs,
"i-pi"_#ipi,
"kate"_#kate,
"vim"_#vim :tb(c=5,ea=c,a=l)
:line
Tool descriptions :h3
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
......@@ -91,7 +106,7 @@ 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
......@@ -104,7 +119,7 @@ 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.
......@@ -129,7 +144,7 @@ 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
......@@ -146,7 +161,7 @@ for the "chain benchmark"_Speed_bench.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.
......@@ -168,7 +183,7 @@ 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
......@@ -181,7 +196,7 @@ 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
......@@ -193,7 +208,7 @@ 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
......@@ -206,7 +221,7 @@ 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
......@@ -222,7 +237,7 @@ 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
......@@ -235,7 +250,7 @@ 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
......@@ -246,7 +261,7 @@ 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 an Emacs Lisp add-on file for GNU Emacs
that enables a lammps-mode for editing input scripts when using GNU Emacs,
......@@ -257,7 +272,7 @@ 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
......@@ -270,7 +285,7 @@ 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
......@@ -287,7 +302,7 @@ 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
......@@ -301,7 +316,7 @@ 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
......@@ -312,7 +327,7 @@ 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
......@@ -328,7 +343,7 @@ 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
......@@ -339,7 +354,7 @@ 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
......@@ -357,7 +372,7 @@ 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
......@@ -374,7 +389,7 @@ 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
......@@ -388,7 +403,7 @@ 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'
......@@ -405,7 +420,7 @@ 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
......@@ -420,7 +435,7 @@ 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
......@@ -434,7 +449,7 @@ 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
......@@ -452,7 +467,7 @@ 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:
......@@ -468,7 +483,7 @@ 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
......@@ -479,7 +494,7 @@ 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
......@@ -495,7 +510,7 @@ 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
......@@ -506,7 +521,7 @@ 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
......
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