Loading doc/src/Tools.txt +30 −30 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading @@ -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. Loading @@ -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 Loading @@ -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. Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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, Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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' Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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: Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading Loading
doc/src/Tools.txt +30 −30 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading @@ -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. Loading @@ -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 Loading @@ -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. Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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, Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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' Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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: Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading
