From 5436169c205438a54d250c7e05689a7503edbf51 Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov> Date: Fri, 17 Aug 2018 09:20:44 -0600 Subject: [PATCH] change format of Howto and Tools doc pages --- doc/src/Howto.txt | 143 +++++++++++++++++++++++----------------------- doc/src/Tools.txt | 139 ++++++++++++++++++++++++-------------------- 2 files changed, 146 insertions(+), 136 deletions(-) diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt index fc7329aad5..bcfae46579 100644 --- a/doc/src/Howto.txt +++ b/doc/src/Howto.txt @@ -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 +"Thermostats"_Howto_thermostat.html +"Barostats"_Howto_barostat.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) +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 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 diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt index 8b4e779cbe..5e02e00715 100644 --- a/doc/src/Tools.txt +++ b/doc/src/Tools.txt @@ -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 - -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 + +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 -- GitLab