Loading doc/src/Howto.txt +100 −46 Original line number Diff line number Diff line Loading @@ -13,22 +13,39 @@ How to discussions :h2 These doc pages describe how to perform various tasks with LAMMPS, both for users and developers. The "glossary"_http://lammps.sandia.gov website page also lists MD terminology with links to corresponding LAMMPS manual pages. The example input scripts included in the examples dir of the LAMMPS terminology with links to corresponding LAMMPS manual pages. 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. Tutorials howto :h3 <!-- RST .. toctree:: :name: tutorials :maxdepth: 1 Howto_github Howto_pylammps Howto_bash END_RST --> <!-- HTML_ONLY --> "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) <!-- END_HTML_ONLY --> General howto :h3 <!-- RST .. toctree:: :name: general :maxdepth: 1 Howto_restart Loading @@ -38,35 +55,86 @@ also show how to setup and run various kinds of simulations. Howto_library Howto_couple .. toctree:: :maxdepth: 1 END_RST --> Howto_output Howto_chunk <!-- HTML_ONLY --> "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) <!-- END_HTML_ONLY --> Settings howto :h3 <!-- RST .. toctree:: :name: settings :maxdepth: 1 Howto_2d Howto_triclinic Howto_thermostat Howto_barostat Howto_walls Howto_nemd Howto_granular Howto_spherical Howto_dispersion END_RST --> <!-- HTML_ONLY --> "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) <!-- END_HTML_ONLY --> Analysis howto :h3 <!-- RST .. toctree:: :name: analysis :maxdepth: 1 Howto_output Howto_chunk Howto_temperature Howto_thermostat Howto_barostat Howto_elastic Howto_kappa Howto_viscosity Howto_diffusion END_RST --> <!-- HTML_ONLY --> "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) <!-- END_HTML_ONLY --> Force fields howto :h3 <!-- RST .. toctree:: :name: force :maxdepth: 1 Howto_bioFF Loading @@ -74,9 +142,27 @@ also show how to setup and run various kinds of simulations. Howto_tip4p Howto_spc END_RST --> <!-- HTML_ONLY --> "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) <!-- END_HTML_ONLY --> Packages howto :h3 <!-- RST .. toctree:: :name: packages :maxdepth: 1 Howto_spherical Howto_granular Howto_body Howto_polarizable Howto_coreshell Loading @@ -87,43 +173,11 @@ also show how to setup and run various kinds of simulations. END_RST --> <!-- HTML_ONLY --> "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) "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) "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html "Use chunks to calculate system properties"_Howto_chunk.html :all(b) <!-- HTML_ONLY --> "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 "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) "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) "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/Manual.txt +1 −1 Original line number Diff line number Diff line Loading @@ -66,7 +66,7 @@ every LAMMPS command. .. toctree:: :maxdepth: 2 :numbered: :numbered: 3 :caption: User Documentation :name: userdoc :includehidden: Loading doc/src/Tools.txt +78 −63 Original line number Diff line number Diff line Loading @@ -43,40 +43,55 @@ 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 Tool descriptions :h3 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 +106,7 @@ 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 +119,7 @@ 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 +144,7 @@ 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 +161,7 @@ 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 +183,7 @@ 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 +196,7 @@ 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 +208,7 @@ 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 +221,7 @@ 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 +237,7 @@ 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 +250,7 @@ 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 +261,7 @@ 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 +272,7 @@ 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 +285,7 @@ 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 +302,7 @@ 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 +316,7 @@ 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 +327,7 @@ 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 +343,7 @@ 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 +354,7 @@ 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 +372,7 @@ 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 +389,7 @@ 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 +403,7 @@ 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 +420,7 @@ 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 +435,7 @@ 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 +449,7 @@ 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 +467,7 @@ 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 +483,7 @@ 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 +494,7 @@ 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 +510,7 @@ 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 +521,7 @@ 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 +100 −46 Original line number Diff line number Diff line Loading @@ -13,22 +13,39 @@ How to discussions :h2 These doc pages describe how to perform various tasks with LAMMPS, both for users and developers. The "glossary"_http://lammps.sandia.gov website page also lists MD terminology with links to corresponding LAMMPS manual pages. The example input scripts included in the examples dir of the LAMMPS terminology with links to corresponding LAMMPS manual pages. 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. Tutorials howto :h3 <!-- RST .. toctree:: :name: tutorials :maxdepth: 1 Howto_github Howto_pylammps Howto_bash END_RST --> <!-- HTML_ONLY --> "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) <!-- END_HTML_ONLY --> General howto :h3 <!-- RST .. toctree:: :name: general :maxdepth: 1 Howto_restart Loading @@ -38,35 +55,86 @@ also show how to setup and run various kinds of simulations. Howto_library Howto_couple .. toctree:: :maxdepth: 1 END_RST --> Howto_output Howto_chunk <!-- HTML_ONLY --> "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) <!-- END_HTML_ONLY --> Settings howto :h3 <!-- RST .. toctree:: :name: settings :maxdepth: 1 Howto_2d Howto_triclinic Howto_thermostat Howto_barostat Howto_walls Howto_nemd Howto_granular Howto_spherical Howto_dispersion END_RST --> <!-- HTML_ONLY --> "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) <!-- END_HTML_ONLY --> Analysis howto :h3 <!-- RST .. toctree:: :name: analysis :maxdepth: 1 Howto_output Howto_chunk Howto_temperature Howto_thermostat Howto_barostat Howto_elastic Howto_kappa Howto_viscosity Howto_diffusion END_RST --> <!-- HTML_ONLY --> "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) <!-- END_HTML_ONLY --> Force fields howto :h3 <!-- RST .. toctree:: :name: force :maxdepth: 1 Howto_bioFF Loading @@ -74,9 +142,27 @@ also show how to setup and run various kinds of simulations. Howto_tip4p Howto_spc END_RST --> <!-- HTML_ONLY --> "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) <!-- END_HTML_ONLY --> Packages howto :h3 <!-- RST .. toctree:: :name: packages :maxdepth: 1 Howto_spherical Howto_granular Howto_body Howto_polarizable Howto_coreshell Loading @@ -87,43 +173,11 @@ also show how to setup and run various kinds of simulations. END_RST --> <!-- HTML_ONLY --> "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) "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) "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html "Use chunks to calculate system properties"_Howto_chunk.html :all(b) <!-- HTML_ONLY --> "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 "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) "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) "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/Manual.txt +1 −1 Original line number Diff line number Diff line Loading @@ -66,7 +66,7 @@ every LAMMPS command. .. toctree:: :maxdepth: 2 :numbered: :numbered: 3 :caption: User Documentation :name: userdoc :includehidden: Loading
doc/src/Tools.txt +78 −63 Original line number Diff line number Diff line Loading @@ -43,40 +43,55 @@ 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 Tool descriptions :h3 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 +106,7 @@ 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 +119,7 @@ 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 +144,7 @@ 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 +161,7 @@ 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 +183,7 @@ 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 +196,7 @@ 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 +208,7 @@ 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 +221,7 @@ 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 +237,7 @@ 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 +250,7 @@ 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 +261,7 @@ 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 +272,7 @@ 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 +285,7 @@ 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 +302,7 @@ 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 +316,7 @@ 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 +327,7 @@ 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 +343,7 @@ 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 +354,7 @@ 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 +372,7 @@ 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 +389,7 @@ 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 +403,7 @@ 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 +420,7 @@ 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 +435,7 @@ 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 +449,7 @@ 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 +467,7 @@ 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 +483,7 @@ 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 +494,7 @@ 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 +510,7 @@ 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 +521,7 @@ 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
