Loading doc/src/Howto.txt +70 −73 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading doc/src/Tools.txt +76 −63 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading @@ -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. Loading @@ -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 Loading @@ -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. Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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, Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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' Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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: Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading Loading
doc/src/Howto.txt +70 −73 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading
doc/src/Tools.txt +76 −63 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading @@ -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. Loading @@ -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 Loading @@ -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. Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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, Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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' Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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: Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading
