change format of Howto and Tools doc pages

This commit is contained in:
Steven J. Plimpton 2018-08-17 09:20:44 -06:00
parent 6c5d339a94
commit 5436169c20
2 changed files with 149 additions and 139 deletions

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@ -19,80 +19,14 @@ 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.
<!-- RST
.. toctree::
:maxdepth: 1
Howto_github
Howto_pylammps
Howto_bash
.. toctree::
:maxdepth: 1
Howto_restart
Howto_viz
Howto_multiple
Howto_replica
Howto_library
Howto_couple
.. toctree::
:maxdepth: 1
Howto_output
Howto_chunk
.. toctree::
:maxdepth: 1
Howto_2d
Howto_triclinic
Howto_walls
Howto_nemd
Howto_granular
Howto_spherical
Howto_dispersion
.. toctree::
:maxdepth: 1
Howto_temperature
Howto_thermostat
Howto_barostat
Howto_elastic
Howto_kappa
Howto_viscosity
Howto_diffusion
.. toctree::
:maxdepth: 1
Howto_bioFF
Howto_tip3p
Howto_tip4p
Howto_spc
.. toctree::
:maxdepth: 1
Howto_body
Howto_polarizable
Howto_coreshell
Howto_drude
Howto_drude2
Howto_manifold
Howto_spins
END_RST -->
<!-- HTML_ONLY -->
Tutorials howto :h3
"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)
General howto :h3
"Restart a simulation"_Howto_restart.html
"Visualize LAMMPS snapshots"_Howto_viz.html
"Run multiple simulations from one input script"_Howto_multiple.html
@ -100,30 +34,93 @@ END_RST -->
"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)
Settings howto :h3
"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
"Walls"_Howto_walls.html
"NEMD simulations"_Howto_nemd.html
"Long-range dispersion settings"_Howto_dispersion.html :all(b)
Analysis howto :h3
"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
"Use chunks to calculate system properties"_Howto_chunk.html
"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)
"Calculate diffusion coefficients"_Howto_diffusion.html :all(b)
Force fields howto :h3
"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)
Packages howto :h3
"Finite-size spherical and aspherical particles"_Howto_spherical.html
"Granular models"_Howto_granular.html
"Body style particles"_Howto_body.html
"Polarizable models"_Howto_polarizable.html
"Adiabatic core/shell model"_Howto_coreshell.html
"Drude induced dipoles"_Howto_drude.html
"Drude induced dipoles (extended)"_Howto_drude2.html
"Manifolds (surfaces)"_Howto_manifold.html
"Magnetic spins"_Howto_spins.html :all(b)
<!-- HTML_ONLY -->
External howto :h3
"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)
General howto :h3
"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)
Settings howto :h3
"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)
Analysis howto :h3
"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)
Force fields howto :h3
"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)
Packages howto :h3
"Finite-size spherical and aspherical particles"_Howto_spherical.html
"Granular models"_Howto_granular.html
"Body style particles"_Howto_body.html
"Polarizable models"_Howto_polarizable.html
"Adiabatic core/shell model"_Howto_coreshell.html

View File

@ -43,40 +43,53 @@ 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
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
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
@ -91,7 +104,7 @@ 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 +117,7 @@ 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 +142,7 @@ 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 +159,7 @@ 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 +181,7 @@ 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 +194,7 @@ 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 +206,7 @@ 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 +219,7 @@ 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 +235,7 @@ 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 +248,7 @@ 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 +259,7 @@ 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 +270,7 @@ 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 +283,7 @@ 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 +300,7 @@ 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 +314,7 @@ 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 +325,7 @@ 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 +341,7 @@ 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 +352,7 @@ 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 +370,7 @@ 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 +387,7 @@ 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 +401,7 @@ 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 +418,7 @@ 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 +433,7 @@ 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 +447,7 @@ 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 +465,7 @@ 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 +481,7 @@ 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 +492,7 @@ 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 +508,7 @@ 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 +519,7 @@ 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