diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt deleted file mode 100644 index 7cc07cbec55a5e7c4f3545c623875be8cc6919cc..0000000000000000000000000000000000000000 --- 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) -