diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt index 85ee531cfd905371ebef6f17db26713c2a496d6c..aa4adb7dc1a89c909388b0b50879884f202f61c0 100644 --- a/doc/src/Tools.txt +++ b/doc/src/Tools.txt @@ -77,7 +77,7 @@ own sub-directories with their own Makefiles and/or README files. :line :line -amber2lmp tool :h4,link(amber) +amber2lmp tool :h3,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 @@ -92,7 +92,7 @@ necessary modifications yourself. :line -binary2txt tool :h4,link(binary) +binary2txt tool :h3,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 @@ -105,7 +105,7 @@ since binary files are not compatible across all platforms. :line -ch2lmp tool :h4,link(charmm) +ch2lmp tool :h3,link(charmm) The ch2lmp sub-directory contains tools for converting files back-and-forth between the CHARMM MD code and LAMMPS. @@ -130,7 +130,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London. :line -chain tool :h4,link(chain) +chain tool :h3,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 @@ -147,7 +147,7 @@ for the "chain benchmark"_Speed_bench.html. :line -colvars tools :h4,link(colvars) +colvars tools :h3,link(colvars) The colvars directory contains a collection of tools for postprocessing data produced by the colvars collective variable library. @@ -169,7 +169,7 @@ gmail.com) at ICTP, Italy. :line -createatoms tool :h4,link(createatoms) +createatoms tool :h3,link(createatoms) The tools/createatoms directory contains a Fortran program called createAtoms.f which can generate a variety of interesting crystal @@ -182,7 +182,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov. :line -doxygen tool :h4,link(doxygen) +doxygen tool :h3,link(doxygen) The tools/doxygen directory contains a shell script called doxygen.sh which can generate a call graph and API lists using @@ -194,7 +194,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com. :line -drude tool :h4,link(drude) +drude tool :h3,link(drude) The tools/drude directory contains a Python script called polarizer.py which can add Drude oscillators to a LAMMPS @@ -207,7 +207,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr :line -eam database tool :h4,link(eamdb) +eam database tool :h3,link(eamdb) The tools/eam_database directory contains a Fortran program that will generate EAM alloy setfl potential files for any combination of 16 @@ -223,7 +223,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, :line -eam generate tool :h4,link(eamgn) +eam generate tool :h3,link(eamgn) The tools/eam_generate directory contains several one-file C programs that convert an analytic formula into a tabulated "embedded atom @@ -236,7 +236,7 @@ The source files and potentials were provided by Gerolf Ziegenhain :line -eff tool :h4,link(eff) +eff tool :h3,link(eff) The tools/eff directory contains various scripts for generating structures and post-processing output for simulations using the @@ -247,7 +247,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech :line -emacs tool :h4,link(emacs) +emacs tool :h3,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, @@ -258,7 +258,7 @@ These tools were provided by Aidan Thompson at Sandia :line -fep tool :h4,link(fep) +fep tool :h3,link(fep) The tools/fep directory contains Python scripts useful for post-processing results from performing free-energy perturbation @@ -271,7 +271,7 @@ See README file in the tools/fep directory. :line -i-pi tool :h4,link(ipi) +i-pi tool :h3,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 @@ -288,7 +288,7 @@ calculations with LAMMPS. :line -ipp tool :h4,link(ipp) +ipp tool :h3,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 @@ -302,7 +302,7 @@ tools/createatoms tool's input file. :line -kate tool :h4,link(kate) +kate tool :h3,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 @@ -313,7 +313,7 @@ The file was provided by Alessandro Luigi Sellerio :line -lmp2arc tool :h4,link(arc) +lmp2arc tool :h3,link(arc) The lmp2arc sub-directory contains a tool for converting LAMMPS output files to the format for Accelrys' Insight MD code (formerly @@ -329,7 +329,7 @@ Greathouse at Sandia (jagreat at sandia.gov). :line -lmp2cfg tool :h4,link(cfg) +lmp2cfg tool :h3,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 @@ -340,7 +340,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). :line -matlab tool :h4,link(matlab) +matlab tool :h3,link(matlab) The matlab sub-directory contains several "MATLAB"_matlabhome scripts for post-processing LAMMPS output. The scripts include readers for log @@ -358,7 +358,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ :line -micelle2d tool :h4,link(micelle) +micelle2d tool :h3,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 @@ -375,7 +375,7 @@ definition file. This tool was used to create the system for the :line -moltemplate tool :h4,link(moltemplate) +moltemplate tool :h3,link(moltemplate) The moltemplate sub-directory contains a Python-based tool for building molecular systems based on a text-file description, and @@ -389,7 +389,7 @@ supports it. It has its own WWW page at :line -msi2lmp tool :h4,link(msi) +msi2lmp tool :h3,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' @@ -406,7 +406,7 @@ See the README file in the tools/msi2lmp folder for more information. :line -phonon tool :h4,link(phonon) +phonon tool :h3,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 @@ -421,7 +421,7 @@ University. :line -polybond tool :h4,link(polybond) +polybond tool :h3,link(polybond) The polybond sub-directory contains a Python-based tool useful for performing "programmable polymer bonding". The Python file @@ -435,7 +435,7 @@ This tool was written by Zachary Kraus at Georgia Tech. :line -pymol_asphere tool :h4,link(pymol) +pymol_asphere tool :h3,link(pymol) The pymol_asphere sub-directory contains a tool for converting a LAMMPS dump file that contains orientation info for ellipsoidal @@ -453,7 +453,7 @@ This tool was written by Mike Brown at Sandia. :line -python tool :h4,link(pythontools) +python tool :h3,link(pythontools) The python sub-directory contains several Python scripts that perform common LAMMPS post-processing tasks, such as: @@ -469,7 +469,7 @@ README for more info on Pizza.py and how to use these scripts. :line -reax tool :h4,link(reax_tool) +reax tool :h3,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 @@ -480,7 +480,7 @@ These tools were written by Aidan Thompson at Sandia. :line -smd tool :h4,link(smd) +smd tool :h3,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 @@ -496,7 +496,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). :line -vim tool :h4,link(vim) +vim tool :h3,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 @@ -507,7 +507,7 @@ ziegenhain.com) :line -xmgrace tool :h4,link(xmgrace) +xmgrace tool :h3,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