From da1be29278a7a9e623fdd76478cd572a789f77f5 Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Tue, 24 Jul 2018 14:31:55 -0600 Subject: [PATCH 1/6] 2nd try at incremental doc page reorg, Section_tools --- doc/src/Manual.txt | 4 +- doc/src/Tools.txt | 527 +++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 529 insertions(+), 2 deletions(-) create mode 100644 doc/src/Tools.txt diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index e69797d9ec..d6d46570c1 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -116,7 +116,7 @@ it gives quick access to documentation for all LAMMPS commands. Section_howto Section_example Section_perf - Section_tools + Tools Section_modify Section_python Section_errors @@ -210,7 +210,7 @@ END_RST --> 6.27 "Drude induced dipoles"_howto_27 :ule,b "Example problems"_Section_example.html :l "Performance & scalability"_Section_perf.html :l -"Additional tools"_Section_tools.html :l +"Auxiliary tools"_Tools.html :l "Modifying & extending LAMMPS"_Section_modify.html :l 10.1 "Atom styles"_mod_1 :ulb,b 10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt new file mode 100644 index 0000000000..8fc371c4ef --- /dev/null +++ b/doc/src/Tools.txt @@ -0,0 +1,527 @@ +"Previous Section"_Section_perf.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Section_modify.html :c + + + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html#comm) + +:line + +Auxiliary tools :h3 + +LAMMPS is designed to be a computational kernel for performing +molecular dynamics computations. Additional pre- and post-processing +steps are often necessary to setup and analyze a simulation. A list +of such tools can be found on the "LAMMPS webpage"_lws at these links: + +"Pre/Post processing"_http://lammps.sandia.gov/prepost.html +"Offsite LAMMPS packages & tools"_http://lammps.sandia.gov/offsite.html +"Pizza.py toolkit"_pizza :ul + +The last link for "Pizza.py"_pizza is a Python-based tool developed at +Sandia which provides tools for doing setup, analysis, plotting, and +visualization for LAMMPS simulations. + +"link(pizza,http://pizza.sandia.gov) +:link(python,http://www.python.org) + +Additional tools included in the LAMMPS distribution are described on +this page. + +Note that many users write their own setup or analysis tools or use +other existing codes and convert their output to a LAMMPS input format +or vice versa. The tools listed here are included in the LAMMPS +distribution as examples of auxiliary tools. Some of them are not +actively supported by the LAMMPS developers, as they were contributed +by LAMMPS users. If you have problems using them, we can direct you +to the authors. + +The source code for each of these codes is in the tools sub-directory +of the LAMMPS distribution. There is a Makefile (which you may need +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 +: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 +README file in amber2lmp for more information. + +These tools were written by Keir Novik while he was at Queen Mary +University of London. Keir is no longer there and cannot support +these tools which are out-of-date with respect to the current LAMMPS +version (and maybe with respect to AMBER as well). Since we don't use +these tools at Sandia, you'll need to experiment with them and make +necessary modifications yourself. + +:line + +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 + +binary2txt file1 file2 ... :pre + +which creates file1.txt, file2.txt, etc. This tool must be compiled +on a platform that can read the binary file created by a LAMMPS run, +since binary files are not compatible across all platforms. + +:line + +ch2lmp tool :h4,link(charmm) + +The ch2lmp sub-directory contains tools for converting files +back-and-forth between the CHARMM MD code and LAMMPS. + +They are intended to make it easy to use CHARMM as a builder and as a +post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a +PDB file with associated CHARMM info, including CHARMM force field +data, into its LAMMPS equivalent. Support for the CMAP correction of +CHARMM22 and later is available as an option. This tool can also add +solvent water molecules and Na+ or Cl- ions to the system. +Using lammps2pdb.pl you can convert LAMMPS atom dumps into PDB files. + +See the README file in the ch2lmp sub-directory for more information. + +These tools were created by Pieter in't Veld (pjintve at sandia.gov) +and Paul Crozier (pscrozi at sandia.gov) at Sandia. + +CMAP support added and tested by Xiaohu Hu (hux2 at ornl.gov) and +Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and +Tigran Abramyan, (Clemson University) and +Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London. + +:line + +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 +containing chain definition parameters as an input. The created +chains and solvent atoms can strongly overlap, so LAMMPS needs to run +the system initially with a "soft" pair potential to un-overlap it. +The syntax for running the tool is + +chain < def.chain > data.file :pre + +See the def.chain or def.chain.ab files in the tools directory for +examples of definition files. This tool was used to create the +system for the "chain benchmark"_Section_perf.html. + +:line + +colvars tools :h4,link(colvars) + +The colvars directory contains a collection of tools for postprocessing +data produced by the colvars collective variable library. +To compile the tools, edit the makefile for your system and run "make". + +Please report problems and issues the colvars library and its tools +at: https://github.com/colvars/colvars/issues + +abf_integrate: + +MC-based integration of multidimensional free energy gradient +Version 20110511 + +Syntax: ./abf_integrate < filename > \[-n < nsteps >\] \[-t < temp >\] \[-m \[0|1\] (metadynamics)\] \[-h < hill_height >\] \[-f < variable_hill_factor >\] :pre + +The LAMMPS interface to the colvars collective variable library, as +well as these tools, were created by Axel Kohlmeyer (akohlmey at +gmail.com) at ICTP, Italy. + +:line + +createatoms tool :h4,link(createatoms) + +The tools/createatoms directory contains a Fortran program called +createAtoms.f which can generate a variety of interesting crystal +structures and geometries and output the resulting list of atom +coordinates in LAMMPS or other formats. + +See the included Manual.pdf for details. + +The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov. + +:line + +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 +the "Doxygen software"_http://doxygen.org. + +See the included README file for details. + +The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com. + +:line + +drude tool :h4,link(drude) + +The tools/drude directory contains a Python script called +polarizer.py which can add Drude oscillators to a LAMMPS +data file in the required format. + +See the header of the polarizer.py file for details. + +The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua +at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr + +:line + +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 +elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, +Zr. The files can then be used with the "pair_style +eam/alloy"_pair_eam.html command. + +The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov, +and is based on his paper: + +X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, +144113 (2004). + +:line + +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 +method (EAM)"_pair_eam.html setfl potential file. The potentials they +produce are in the potentials directory, and can be used with the +"pair_style eam/alloy"_pair_eam.html command. + +The source files and potentials were provided by Gerolf Ziegenhain +(gerolf at ziegenhain.com). + +:line + +eff tool :h4,link(eff) + +The tools/eff directory contains various scripts for generating +structures and post-processing output for simulations using the +electron force field (eFF). + +These tools were provided by Andres Jaramillo-Botero at CalTech +(ajaramil at wag.caltech.edu). + +:line + +emacs tool :h4,link(emacs) + +The tools/emacs directory contains a Lips add-on file for Emacs that +enables a lammps-mode for editing of input scripts when using Emacs, +with various highlighting options setup. + +These tools were provided by Aidan Thompson at Sandia +(athomps at sandia.gov). + +:line + +fep tool :h4,link(fep) + +The tools/fep directory contains Python scripts useful for +post-processing results from performing free-energy perturbation +simulations using the USER-FEP package. + +The scripts were contributed by Agilio Padua (Universite Blaise +Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr. + +See README file in the tools/fep directory. + +:line + +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 +be used with the "fix ipi"_fix_ipi.html command to perform +path-integral molecular dynamics (PIMD). + +The i-PI package was created and is maintained by Michele Ceriotti, +michele.ceriotti at gmail.com, to interface to a variety of molecular +dynamics codes. + +See the tools/i-pi/manual.pdf file for an overview of i-PI, and the +"fix ipi"_fix_ipi.html doc page for further details on running PIMD +calculations with LAMMPS. + +:line + +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 +script or tools/createatoms input file) using a template file. + +ipp was created and is maintained by Reese Jones (Sandia), rjones at +sandia.gov. + +See two examples in the tools/ipp directory. One of them is for the +tools/createatoms tool's input file. + +:line + +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 +scripts. See the README.txt file for details. + +The file was provided by Alessandro Luigi Sellerio +(alessandro.sellerio at ieni.cnr.it). + +:line + +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 +MSI/Biosym and its Discover MD code). See the README file for more +information. + +This tool was written by John Carpenter (Cray), Michael Peachey +(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic +(jec at mayo.edu), but still fields questions about the tool. + +This tool was updated for the current LAMMPS C++ version by Jeff +Greathouse at Sandia (jagreat at sandia.gov). + +:line + +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 +"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualizer. See +the README file for more information. + +This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). + +:line + +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 +and dump files, a reader for EAM potential files, and a converter that +reads LAMMPS dump files and produces CFG files that can be visualized +with the "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A +visualizer. + +See the README.pdf file for more information. + +These scripts were written by Arun Subramaniyan at Purdue Univ +(asubrama at purdue.edu). + +:link(matlabhome,http://www.mathworks.com) + +:line + +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 +definition parameters as an input. The created molecules and solvent +atoms can strongly overlap, so LAMMPS needs to run the system +initially with a "soft" pair potential to un-overlap it. The syntax +for running the tool is + +micelle2d < def.micelle2d > data.file :pre + +See the def.micelle2d file in the tools directory for an example of a +definition file. This tool was used to create the system for the +"micelle example"_Section_example.html. + +:line + +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 +creating LAMMPS data files that encode their molecular topology as +lists of bonds, angles, dihedrals, etc. See the README.TXT file for +more information. + +This tool was written by Andrew Jewett (jewett.aij at gmail.com), who +supports it. It has its own WWW page at +"http://moltemplate.org"_http://moltemplate.org. + +:line + +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' +Insight MD code, formerly MSI/Biosym and its Discover MD code). + +This tool was written by John Carpenter (Cray), Michael Peachey +(Cray), and Steve Lustig (Dupont). Several people contributed changes +to remove bugs and adapt its output to changes in LAMMPS. + +This tool has several known limitations and is no longer under active +development, so there are no changes except for the occasional bugfix. + +See the README file in the tools/msi2lmp folder for more information. + +:line + +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 +the USER-PHONON package. + +See the README file for instruction on building the tool and what +library it needs. And see the examples/USER/phonon directory +for example problems that can be post-processed with this tool. + +This tool was written by Ling-Ti Kong at Shanghai Jiao Tong +University. + +:line + +polybond tool :h4,link(polybond) + +The polybond sub-directory contains a Python-based tool useful for +performing "programmable polymer bonding". The Python file +lmpsdata.py provides a "Lmpsdata" class with various methods which can +be invoked by a user-written Python script to create data files with +complex bonding topologies. + +See the Manual.pdf for details and example scripts. + +This tool was written by Zachary Kraus at Georgia Tech. + +:line + +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 +particles into an input file for the "PyMol visualization +package"_pymolhome or its "open source variant"_pymolopen. + +:link(pymolhome,http://www.pymol.org) +:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) + +Specifically, the tool triangulates the ellipsoids so they can be +viewed as true ellipsoidal particles within PyMol. See the README and +examples directory within pymol_asphere for more information. + +This tool was written by Mike Brown at Sandia. + +:line + +python tool :h4,link(pythontools) + +The python sub-directory contains several Python scripts +that perform common LAMMPS post-processing tasks, such as: + +extract thermodynamic info from a log file as columns of numbers +plot two columns of thermodynamic info from a log file using GnuPlot +sort the snapshots in a dump file by atom ID +convert multiple "NEB"_neb.html dump files into one dump file for viz +convert dump files into XYZ, CFG, or PDB format for viz by other packages :ul + +These are simple scripts built on "Pizza.py"_pizza modules. See the +README for more info on Pizza.py and how to use these scripts. + +:line + +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 +command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See +the README.txt file for more info. + +These tools were written by Aidan Thompson at Sandia. + +:line + +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 +files created by the Smooth-Mach Dynamics (USER-SMD) package into a +VTK-compatible unstructured grid file. It could then be read in and +visualized by VTK. + +See the header of dump2vtk.cpp for more details. + +This tool was written by the USER-SMD package author, Georg +Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, +Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). + +:line + +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 +file for details. + +These files were provided by Gerolf Ziegenhain (gerolf at +ziegenhain.com) + +:line + +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 +package. There are several tools in the directory that can be used in +post-processing mode. The lammpsplot.cpp file can be compiled and +used to create plots from the current state of a running LAMMPS +simulation. + +See the README file for details. + +These files were provided by Vikas Varshney (vv0210 at gmail.com) From d83d05088fa284a0608d8cace4f7ac0be6d1482b Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Tue, 24 Jul 2018 14:33:27 -0600 Subject: [PATCH 2/6] remove replaced file --- doc/src/Section_tools.txt | 520 -------------------------------------- 1 file changed, 520 deletions(-) delete mode 100644 doc/src/Section_tools.txt diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt deleted file mode 100644 index 7cc07cbec5..0000000000 --- a/doc/src/Section_tools.txt +++ /dev/null @@ -1,520 +0,0 @@ -"Previous Section"_Section_perf.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_modify.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -9. Additional tools :h2 - -LAMMPS is designed to be a computational kernel for performing -molecular dynamics computations. Additional pre- and post-processing -steps are often necessary to setup and analyze a simulation. A -list of such tools can be found on the LAMMPS home page -at "http://lammps.sandia.gov/prepost.html"_http://lammps.sandia.gov/prepost.html - -A few additional tools are provided with the LAMMPS distribution -and are described in this section. - -Our group has also written and released a separate toolkit called -"Pizza.py"_pizza which provides tools for doing setup, analysis, -plotting, and visualization for LAMMPS simulations. Pizza.py is -written in "Python"_python and is available for download from "the -Pizza.py WWW site"_pizza. - -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) -:link(python,http://www.python.org) - -Note that many users write their own setup or analysis tools or use -other existing codes and convert their output to a LAMMPS input format -or vice versa. The tools listed here are included in the LAMMPS -distribution as examples of auxiliary tools. Some of them are not -actively supported by Sandia, as they were contributed by LAMMPS -users. If you have problems using them, we can direct you to the -authors. - -The source code for each of these codes is in the tools sub-directory -of the LAMMPS distribution. There is a Makefile (which you may need -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 - -:line - -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 -README file in amber2lmp for more information. - -These tools were written by Keir Novik while he was at Queen Mary -University of London. Keir is no longer there and cannot support -these tools which are out-of-date with respect to the current LAMMPS -version (and maybe with respect to AMBER as well). Since we don't use -these tools at Sandia, you'll need to experiment with them and make -necessary modifications yourself. - -:line - -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 - -binary2txt file1 file2 ... :pre - -which creates file1.txt, file2.txt, etc. This tool must be compiled -on a platform that can read the binary file created by a LAMMPS run, -since binary files are not compatible across all platforms. - -:line - -ch2lmp tool :h3,link(charmm) - -The ch2lmp sub-directory contains tools for converting files -back-and-forth between the CHARMM MD code and LAMMPS. - -They are intended to make it easy to use CHARMM as a builder and as a -post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a -PDB file with associated CHARMM info, including CHARMM force field -data, into its LAMMPS equivalent. Support for the CMAP correction of -CHARMM22 and later is available as an option. This tool can also add -solvent water molecules and Na+ or Cl- ions to the system. -Using lammps2pdb.pl you can convert LAMMPS atom dumps into PDB files. - -See the README file in the ch2lmp sub-directory for more information. - -These tools were created by Pieter in't Veld (pjintve at sandia.gov) -and Paul Crozier (pscrozi at sandia.gov) at Sandia. - -CMAP support added and tested by Xiaohu Hu (hux2 at ornl.gov) and -Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and -Tigran Abramyan, (Clemson University) and -Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London. - -:line - -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 -containing chain definition parameters as an input. The created -chains and solvent atoms can strongly overlap, so LAMMPS needs to run -the system initially with a "soft" pair potential to un-overlap it. -The syntax for running the tool is - -chain < def.chain > data.file :pre - -See the def.chain or def.chain.ab files in the tools directory for -examples of definition files. This tool was used to create the -system for the "chain benchmark"_Section_perf.html. - -:line - -colvars tools :h3,link(colvars) - -The colvars directory contains a collection of tools for postprocessing -data produced by the colvars collective variable library. -To compile the tools, edit the makefile for your system and run "make". - -Please report problems and issues the colvars library and its tools -at: https://github.com/colvars/colvars/issues - -abf_integrate: - -MC-based integration of multidimensional free energy gradient -Version 20110511 - -Syntax: ./abf_integrate < filename > \[-n < nsteps >\] \[-t < temp >\] \[-m \[0|1\] (metadynamics)\] \[-h < hill_height >\] \[-f < variable_hill_factor >\] :pre - -The LAMMPS interface to the colvars collective variable library, as -well as these tools, were created by Axel Kohlmeyer (akohlmey at -gmail.com) at ICTP, Italy. - -:line - -createatoms tool :h3,link(createatoms) - -The tools/createatoms directory contains a Fortran program called -createAtoms.f which can generate a variety of interesting crystal -structures and geometries and output the resulting list of atom -coordinates in LAMMPS or other formats. - -See the included Manual.pdf for details. - -The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov. - -:line - -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 -the "Doxygen software"_http://doxygen.org. - -See the included README file for details. - -The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com. - -:line - -drude tool :h3,link(drude) - -The tools/drude directory contains a Python script called -polarizer.py which can add Drude oscillators to a LAMMPS -data file in the required format. - -See the header of the polarizer.py file for details. - -The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua -at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr - -:line - -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 -elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, -Zr. The files can then be used with the "pair_style -eam/alloy"_pair_eam.html command. - -The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov, -and is based on his paper: - -X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, -144113 (2004). - -:line - -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 -method (EAM)"_pair_eam.html setfl potential file. The potentials they -produce are in the potentials directory, and can be used with the -"pair_style eam/alloy"_pair_eam.html command. - -The source files and potentials were provided by Gerolf Ziegenhain -(gerolf at ziegenhain.com). - -:line - -eff tool :h3,link(eff) - -The tools/eff directory contains various scripts for generating -structures and post-processing output for simulations using the -electron force field (eFF). - -These tools were provided by Andres Jaramillo-Botero at CalTech -(ajaramil at wag.caltech.edu). - -:line - -emacs tool :h3,link(emacs) - -The tools/emacs directory contains a Lips add-on file for Emacs that -enables a lammps-mode for editing of input scripts when using Emacs, -with various highlighting options setup. - -These tools were provided by Aidan Thompson at Sandia -(athomps at sandia.gov). - -:line - -fep tool :h3,link(fep) - -The tools/fep directory contains Python scripts useful for -post-processing results from performing free-energy perturbation -simulations using the USER-FEP package. - -The scripts were contributed by Agilio Padua (Universite Blaise -Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr. - -See README file in the tools/fep directory. - -:line - -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 -be used with the "fix ipi"_fix_ipi.html command to perform -path-integral molecular dynamics (PIMD). - -The i-PI package was created and is maintained by Michele Ceriotti, -michele.ceriotti at gmail.com, to interface to a variety of molecular -dynamics codes. - -See the tools/i-pi/manual.pdf file for an overview of i-PI, and the -"fix ipi"_fix_ipi.html doc page for further details on running PIMD -calculations with LAMMPS. - -:line - -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 -script or tools/createatoms input file) using a template file. - -ipp was created and is maintained by Reese Jones (Sandia), rjones at -sandia.gov. - -See two examples in the tools/ipp directory. One of them is for the -tools/createatoms tool's input file. - -:line - -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 -scripts. See the README.txt file for details. - -The file was provided by Alessandro Luigi Sellerio -(alessandro.sellerio at ieni.cnr.it). - -:line - -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 -MSI/Biosym and its Discover MD code). See the README file for more -information. - -This tool was written by John Carpenter (Cray), Michael Peachey -(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic -(jec at mayo.edu), but still fields questions about the tool. - -This tool was updated for the current LAMMPS C++ version by Jeff -Greathouse at Sandia (jagreat at sandia.gov). - -:line - -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 -"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualizer. See -the README file for more information. - -This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). - -:line - -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 -and dump files, a reader for EAM potential files, and a converter that -reads LAMMPS dump files and produces CFG files that can be visualized -with the "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A -visualizer. - -See the README.pdf file for more information. - -These scripts were written by Arun Subramaniyan at Purdue Univ -(asubrama at purdue.edu). - -:link(matlabhome,http://www.mathworks.com) - -:line - -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 -definition parameters as an input. The created molecules and solvent -atoms can strongly overlap, so LAMMPS needs to run the system -initially with a "soft" pair potential to un-overlap it. The syntax -for running the tool is - -micelle2d < def.micelle2d > data.file :pre - -See the def.micelle2d file in the tools directory for an example of a -definition file. This tool was used to create the system for the -"micelle example"_Section_example.html. - -:line - -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 -creating LAMMPS data files that encode their molecular topology as -lists of bonds, angles, dihedrals, etc. See the README.TXT file for -more information. - -This tool was written by Andrew Jewett (jewett.aij at gmail.com), who -supports it. It has its own WWW page at -"http://moltemplate.org"_http://moltemplate.org. - -:line - -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' -Insight MD code, formerly MSI/Biosym and its Discover MD code). - -This tool was written by John Carpenter (Cray), Michael Peachey -(Cray), and Steve Lustig (Dupont). Several people contributed changes -to remove bugs and adapt its output to changes in LAMMPS. - -This tool has several known limitations and is no longer under active -development, so there are no changes except for the occasional bugfix. - -See the README file in the tools/msi2lmp folder for more information. - -:line - -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 -the USER-PHONON package. - -See the README file for instruction on building the tool and what -library it needs. And see the examples/USER/phonon directory -for example problems that can be post-processed with this tool. - -This tool was written by Ling-Ti Kong at Shanghai Jiao Tong -University. - -:line - -polybond tool :h3,link(polybond) - -The polybond sub-directory contains a Python-based tool useful for -performing "programmable polymer bonding". The Python file -lmpsdata.py provides a "Lmpsdata" class with various methods which can -be invoked by a user-written Python script to create data files with -complex bonding topologies. - -See the Manual.pdf for details and example scripts. - -This tool was written by Zachary Kraus at Georgia Tech. - -:line - -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 -particles into an input file for the "PyMol visualization -package"_pymolhome or its "open source variant"_pymolopen. - -:link(pymolhome,http://www.pymol.org) -:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) - -Specifically, the tool triangulates the ellipsoids so they can be -viewed as true ellipsoidal particles within PyMol. See the README and -examples directory within pymol_asphere for more information. - -This tool was written by Mike Brown at Sandia. - -:line - -python tool :h3,link(pythontools) - -The python sub-directory contains several Python scripts -that perform common LAMMPS post-processing tasks, such as: - -extract thermodynamic info from a log file as columns of numbers -plot two columns of thermodynamic info from a log file using GnuPlot -sort the snapshots in a dump file by atom ID -convert multiple "NEB"_neb.html dump files into one dump file for viz -convert dump files into XYZ, CFG, or PDB format for viz by other packages :ul - -These are simple scripts built on "Pizza.py"_pizza modules. See the -README for more info on Pizza.py and how to use these scripts. - -:line - -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 -command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See -the README.txt file for more info. - -These tools were written by Aidan Thompson at Sandia. - -:line - -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 -files created by the Smooth-Mach Dynamics (USER-SMD) package into a -VTK-compatible unstructured grid file. It could then be read in and -visualized by VTK. - -See the header of dump2vtk.cpp for more details. - -This tool was written by the USER-SMD package author, Georg -Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, -Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). - -:line - -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 -file for details. - -These files were provided by Gerolf Ziegenhain (gerolf at -ziegenhain.com) - -:line - -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 -package. There are several tools in the directory that can be used in -post-processing mode. The lammpsplot.cpp file can be compiled and -used to create plots from the current state of a running LAMMPS -simulation. - -See the README file for details. - -These files were provided by Vikas Varshney (vv0210 at gmail.com) - From 8385f5666bef66882a3d5d7aebd41593db0e6900 Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Tue, 24 Jul 2018 14:43:48 -0600 Subject: [PATCH 3/6] link changes for new Tools.html --- doc/src/Section_howto.txt | 18 +++++++++--------- doc/src/Section_intro.txt | 18 +++++++++--------- doc/src/Section_modify.txt | 4 ++-- doc/src/Section_perf.txt | 4 +++- doc/src/dump.txt | 18 +++++++++--------- 5 files changed, 32 insertions(+), 30 deletions(-) diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index 2784858f02..a46b29c73b 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -188,9 +188,9 @@ used in the CHARMM, AMBER, and DREIDING force fields. Setting coefficients is done in the input data file via the "read_data"_read_data.html command or in the input script with commands like "pair_coeff"_pair_coeff.html or -"bond_coeff"_bond_coeff.html. See "Section 9"_Section_tools.html -for additional tools that can use CHARMM or AMBER to assign force -field coefficients and convert their output into LAMMPS input. +"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for +additional tools that can use CHARMM or AMBER to assign force field +coefficients and convert their output into LAMMPS input. See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force @@ -762,12 +762,12 @@ simulations can be visualized (and analyzed) in a variety of ways. LAMMPS snapshots are created by the "dump"_dump.html command which can create files in several formats. The native LAMMPS dump format is a text file (see "dump atom" or "dump custom") which can be visualized -by several popular visualization tools. The "dump image"_dump_image.html -and "dump movie"_dump_image.html styles can output internally rendered -images and convert a sequence of them to a movie during the MD run. -Several programs included with LAMMPS as auxiliary tools can convert -between LAMMPS format files and other formats. -See the "Section 9"_Section_tools.html doc page for details. +by several popular visualization tools. The "dump +image"_dump_image.html and "dump movie"_dump_image.html styles can +output internally rendered images and convert a sequence of them to a +movie during the MD run. Several programs included with LAMMPS as +auxiliary tools can convert between LAMMPS format files and other +formats. See the "Tools"_Tools.html doc page for details. A Python-based toolkit distributed by our group can read native LAMMPS dump files, including custom dump files with additional columns of diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt index 67293b2ee3..fd1d702d0b 100644 --- a/doc/src/Section_intro.txt +++ b/doc/src/Section_intro.txt @@ -234,8 +234,8 @@ Multi-replica models :h4 Pre- and post-processing :h4 -Various pre- and post-processing serial tools are packaged -with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l +Various pre- and post-processing serial tools are packaged with +LAMMPS; see the "Tools"_Tools.html doc page for details. :ulb,l Our group has also written and released a separate toolkit called "Pizza.py"_pizza which provides tools for doing setup, analysis, @@ -296,9 +296,9 @@ visualize your MD simulation plot your output data :ul A few tools for pre- and post-processing tasks are provided as part of -the LAMMPS package; they are described in "this -section"_Section_tools.html. However, many people use other codes or -write their own tools for these tasks. +the LAMMPS package; they are described on the "Tools"_Tools.html doc +page. However, many people use other codes or write their own tools +for these tasks. As noted above, our group has also written and released a separate toolkit called "Pizza.py"_pizza which addresses some of the listed @@ -327,8 +327,8 @@ topology information and hundreds of force-field coefficients must typically be specified. We suggest you use a program like "CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup such problems and dump its information to a file. You can then -reformat the file as LAMMPS input. Some of the tools in "this -section"_Section_tools.html can assist in this process. +reformat the file as LAMMPS input. Some of the tools described on the +"Tools"_Tools.html doc page can assist in this process. Similarly, LAMMPS creates output files in a simple format. Most users post-process these files with their own analysis tools or re-format @@ -442,8 +442,8 @@ directory. :l The tools sub-directory of the LAMMPS distribution has various stand-alone codes for pre- and post-processing of LAMMPS data. More -details are given in "Section 9"_Section_tools.html. If you write -a new tool that users will find useful, it can be added to the LAMMPS +details are given on the "Tools"_Tools.html doc page. If you write a +new tool that users will find useful, it can be added to the LAMMPS distribution. :l LAMMPS is designed to be easy to extend with new code for features diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt index f1d55758c8..6948ac062a 100644 --- a/doc/src/Section_modify.txt +++ b/doc/src/Section_modify.txt @@ -1,5 +1,5 @@ - "Previous Section"_Section_tools.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next + "Previous Section"_Tools.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_python.html :c :link(lws,http://lammps.sandia.gov) diff --git a/doc/src/Section_perf.txt b/doc/src/Section_perf.txt index 9998cb0d9a..56b1d7dd04 100644 --- a/doc/src/Section_perf.txt +++ b/doc/src/Section_perf.txt @@ -1,4 +1,6 @@ -"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_tools.html :c +"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Tools.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) diff --git a/doc/src/dump.txt b/doc/src/dump.txt index 438ff1d4e0..d130846519 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -1,4 +1,4 @@ - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -184,10 +184,10 @@ file and in what format. Settings made via the individual values and the file itself. The {atom}, {local}, and {custom} styles create files in a simple text -format that is self-explanatory when viewing a dump file. Many of the -LAMMPS "post-processing tools"_Section_tools.html, including -"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with this -format, as does the "rerun"_rerun.html command. +format that is self-explanatory when viewing a dump file. Some of the +LAMMPS post-processing tools described on the "Tools"_Tools.html doc +page, including "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, +work with this format, as does the "rerun"_rerun.html command. For post-processing purposes the {atom}, {local}, and {custom} text files are self-describing in the following sense. @@ -413,10 +413,10 @@ If the filename ends with ".bin", the dump file (or files, if "*" or will be about the same size as a text version, but will typically write out much faster. Of course, when post-processing, you will need to convert it back to text format (see the "binary2txt -tool"_Section_tools.html#binary) or write your own code to read the -binary file. The format of the binary file can be understood by -looking at the tools/binary2txt.cpp file. This option is only -available for the {atom} and {custom} styles. +tool"_Tools.html#binary) or write your own code to read the binary +file. The format of the binary file can be understood by looking at +the tools/binary2txt.cpp file. This option is only available for the +{atom} and {custom} styles. If the filename ends with ".gz", the dump file (or files, if "*" or "%" is also used) is written in gzipped format. A gzipped dump file will From 678df2498acbf439d1eee9a02070f9a2956f49c9 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 25 Jul 2018 09:32:02 -0400 Subject: [PATCH 4/6] Updated lammps.book --- doc/src/lammps.book | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 06f4bf3718..fe8eb13161 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -14,7 +14,7 @@ accelerate_opt.html Section_howto.html Section_example.html Section_perf.html -Section_tools.html +Tools.html Section_modify.html Section_python.html Section_errors.html From 7ac3f08eec6c17c5666bbaa0083a0c8f7569e6ab Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 25 Jul 2018 09:39:18 -0400 Subject: [PATCH 5/6] Fix typo --- doc/src/Tools.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt index 8fc371c4ef..859bb9d50c 100644 --- a/doc/src/Tools.txt +++ b/doc/src/Tools.txt @@ -29,7 +29,7 @@ The last link for "Pizza.py"_pizza is a Python-based tool developed at Sandia which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. -"link(pizza,http://pizza.sandia.gov) +:link(pizza,http://pizza.sandia.gov) :link(python,http://www.python.org) Additional tools included in the LAMMPS distribution are described on From 80d85841af82b105ea2b6bd5afe35b765dee7df3 Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Wed, 25 Jul 2018 08:15:25 -0600 Subject: [PATCH 6/6] one more tweak on a link --- doc/src/Tools.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt index 859bb9d50c..0674e3cfcc 100644 --- a/doc/src/Tools.txt +++ b/doc/src/Tools.txt @@ -10,7 +10,7 @@ Section"_Modify.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Commands.html#comm) +:link(lc,Section_commands.html#comm) :line