diff --git a/README b/README index 784b1cb13ea9abfc852cf790b1ed40c579305619..680986bf6146b9ddc77a092e6dcc6d4c09dd6b8e 100644 --- a/README +++ b/README @@ -36,7 +36,14 @@ tools pre- and post-processing tools Point your browser at any of these files to get started: -doc/Manual.html the LAMMPS manual -doc/Section_intro.html hi-level introduction to LAMMPS -doc/Section_start.html how to build and use LAMMPS -doc/Developer.pdf LAMMPS developer guide +http://lammps.sandia.gov/doc/Manual.html the LAMMPS manual +http://lammps.sandia.gov/doc/Intro.html hi-level introduction +http://lammps.sandia.gov/doc/Build.html how to build LAMMPS +http://lammps.sandia.gov/doc/Run_head.html how to run LAMMPS +http://lammps.sandia.gov/doc/Developer.pdf LAMMPS developer guide + +You can also create these doc pages locally: + +% cd doc +% make html # creates HTML pages in doc/html +% make pdf # creates Manual.pdf and Developer.pdf diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index c42bb21c7e129d2bca820515331f3c80f0bbbe5b..08c1c72180a417b259078753dd1245d4f93cc6ce 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -13,12 +13,10 @@ This page is a short summary of how to use CMake to build LAMMPS. Details on CMake variables that enable specific LAMMPS build options are given on the pages linked to from the "Build"_Build.html doc page. -Richard Berger (Temple U) has also written a more comprehensive guide +Richard Berger (Temple U) has also written a "more comprehensive +guide"_https://github.com/lammps/lammps/blob/master/cmake/README.md for how to use CMake to build LAMMPS. If you are new to CMake it is a -good place to start: - -"Bulding LAMMPS using -CMake"_https://github.com/lammps/lammps/blob/master/cmake/README.md +good place to start. :line @@ -81,8 +79,9 @@ directory to un-install all packages. The purge removes all the *.h files auto-generated by make. You must have CMake version 2.8 or later on your system to build -LAMMPS. If you include the GPU or KOKKOS packages, CMake version 3.2 -or later is required. Installation instructions for CMake are below. +LAMMPS. A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a +later version. CMake will print a message telling you if a later +version is required. Installation instructions for CMake are below. After the initial build, if you edit LAMMPS source files, or add your own new files to the source directory, you can just re-type make from diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 6bbf504496006b30daf8652f5275f419686e26ab..5c33a0a4d44f97545e8d94819161e2bce9fad78e 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -48,7 +48,7 @@ This is the list of packages that may require additional steps. "USER-QMMM"_#user-qmmm, "USER-QUIP"_#user-quip, "USER-SMD"_#user-smd, -"USER-VTK"_#user-vtk :tb(c=6,ea=c) +"USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l) :line @@ -175,8 +175,15 @@ package?" page. [CMake build]: -D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes --D KIM_LIBRARY=path # path to KIM shared library (only needed if a custom location) --D KIM_INCLUDE_DIR=path # path to KIM include directory (only needed if a custom location) :pre +-D KIM_LIBRARY=path # KIM library file (only needed if a custom location) +-D KIM_INCLUDE_DIR=path # KIM include directory (only needed if a custom location) :pre + +If DOWNLOAD_KIM is set, the KIM library will be downloaded and built +inside the CMake build directory. If the KIM library is already on +your system (in a location CMake cannot find it), KIM_LIBRARY is the +filename (plus path) of the KIM library file, not the directory the +library file is in. KIM_INCLUDE_DIR is the directory the KIM include +file is in. [Traditional make]: @@ -296,7 +303,13 @@ library. [CMake build]: -D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes --D LATTE_LIBRARY=path # path to LATTE shared library (only needed if a custom location) :pre +-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location) :pre + +If DOWNLOAD_LATTE is set, the LATTE library will be downloaded and +built inside the CMake build directory. If the LATTE library is +already on your system (in a location CMake cannot find it), +LATTE_LIBRARY is the filename (plus path) of the LATTE library file, +not the directory the library file is in. [Traditional make]: @@ -371,8 +384,15 @@ lib/mscg/README and MSCG/Install files for more details. [CMake build]: -D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes --D MSCG_LIBRARY=path # path to MSCG shared library (only needed if a custom location) --D MSCG_INCLUDE_DIR=path # path to MSCG include directory (only needed if a custom location) :pre +-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location) +-D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location) :pre + +If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built +inside the CMake build directory. If the MSCG library is already on +your system (in a location CMake cannot find it), MSCG_LIBRARY is the +filename (plus path) of the MSCG library file, not the directory the +library file is in. MSCG_INCLUDE_DIR is the directory the MSCG +include file is in. [Traditional make]: @@ -515,8 +535,15 @@ library"_voro_home. [CMake build]: -D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes --D VORO_LIBRARY=path # (only needed if at custom location) path to VORO shared library --D VORO_INCLUDE_DIR=path # (only needed if at custom location) path to VORO include directory :pre +-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location) +-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) :pre + +If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and +built inside the CMake build directory. If the Voro++ library is +already on your system (in a location CMake cannot find it), +VORO_LIBRARY is the filename (plus path) of the Voro++ library file, +not the directory the library file is in. VORO_INCLUDE_DIR is the +directory the Voro++ include file is in. [Traditional make]: @@ -877,7 +904,10 @@ Eigen3 is a template library, so you do not need to build it. -D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes -D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) :pre -Set EIGEN3_INCLUDE_DIR if CMake cannot find the Eigen3 library. +If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and +inside the CMake build directory. If the Eig3n3 library is already on +your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR +is the directory the Eigen3++ include file is in. [Traditional make]: diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt index 0c7d1917de3085452f3a933cef39967adca5c6ea..4f71e9eb18067d4ef3210aada08a8722e38e8687 100644 --- a/doc/src/Build_package.txt +++ b/doc/src/Build_package.txt @@ -59,7 +59,7 @@ packages: "USER-QMMM"_Build_extras.html#user-qmmm, "USER-QUIP"_Build_extras.html#user-quip, "USER-SMD"_Build_extras.html#user-smd, -"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c) +"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l) The mechanism for including packages is simple but different for CMake versus make. diff --git a/doc/src/Howto_diffusion.txt b/doc/src/Howto_diffusion.txt index 401c1e359c05ee83ef37ecbae44073cdd4ecfacf..6c920c9bc3da9463589362805d5e46592996ffe4 100644 --- a/doc/src/Howto_diffusion.txt +++ b/doc/src/Howto_diffusion.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -Calculate a diffusion coefficient :h3 +Calculate diffusion coefficients :h3 The diffusion coefficient D of a material can be measured in at least 2 ways using various options in LAMMPS. See the examples/DIFFUSE diff --git a/doc/src/Howto_dispersion.txt b/doc/src/Howto_dispersion.txt index 4ea286258e11a38aa07e6e93df4c3e22cb0aca0a..8a5953d84dbf692bddb7be8b58a86a2680aea526 100644 --- a/doc/src/Howto_dispersion.txt +++ b/doc/src/Howto_dispersion.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -Long-raage dispersion settings :h3 +Long-range dispersion settings :h3 The PPPM method computes interactions by splitting the pair potential into two parts, one of which is computed in a normal pairwise fashion, diff --git a/doc/src/Howto_temperature.txt b/doc/src/Howto_temperature.txt index 8a9e262da1b071abde5ab8b6957addba8444b718..896cc96a403a2555b9aceb1cb7da90793d9a909a 100644 --- a/doc/src/Howto_temperature.txt +++ b/doc/src/Howto_temperature.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -Calcalate temperature :h3 +Calculate temperature :h3 Temperature is computed as kinetic energy divided by some number of degrees of freedom (and the Boltzmann constant). Since kinetic energy diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt index 5d9efb30775e4d5d510a6e633a9f62a12adea409..b909265a3eebc70abdcbbb8a439fa319589a8346 100644 --- a/doc/src/Intro_authors.txt +++ b/doc/src/Intro_authors.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -LAMMPS authors :h3 +Authors of LAMMPS :h3 The primary LAMMPS developers are at Sandia National Labs and Temple University: @@ -15,7 +15,8 @@ University: "Steve Plimpton"_sjp, sjplimp at sandia.gov Aidan Thompson, athomps at sandia.gov Stan Moore, stamoor at sandia.gov -Axel Kohlmeyer, akohlmey at gmail.com :ul +Axel Kohlmeyer, akohlmey at gmail.com +Richard Berger, richard.berger at temple.edu :ul :link(sjp,http://www.cs.sandia.gov/~sjplimp) @@ -24,26 +25,31 @@ and Ray Shan, now at Materials Design. :line -The following folks are responsible for significant contributions to -the code, or other aspects of the LAMMPS development effort. Many of -the packages they have written are somewhat unique to LAMMPS and the -code would not be as general-purpose as it is without their expertise -and efforts. +The "Authors page"_http://lammps.sandia.gov/authors.html of the +"LAMMPS website"_lws has a comprehensive list of all the individuals +who have contributed code for a new feature or command or tool to +LAMMPS. -Richard Berger (Temple U), Python interface, GitHub site, Sphinx doc pages +:line + +The following folks deserve special recognition. Many of the packages +they have written are unique for an MD code and LAMMPS would not be as +general-purpose as it is without their expertise and efforts. + +Metin Aktulga (MSU), USER-REAXC package for C version of ReaxFF +Mike Brown (Intel), GPU and USER-INTEL packages +Colin Denniston (U Western Ontario), USER-LB package +Georg Ganzenmuller (EMI), USER-SMD and USER-SPH packages +Andres Jaramillo-Botero (Caltech), USER-EFF package for electron force field +Reese Jones (Sandia) and colleagues, USER-ATC package for atom/continuum coupling +Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS +Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion +Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages +Mike Parks (Sandia), PERI package for Peridynamics Roy Pollock (LLNL), Ewald and PPPM solvers -Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages -Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential -Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics -Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion -Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling -Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD -Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages -Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field -Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling -Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF -Georg Gunzenmueller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages -Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul +Christian Trott (Sandia), USER-CUDA and KOKKOS packages +Ilya Valuev (JIHT), USER-AWPMD package for wave-packet MD +Greg Wagner (Northwestern U), MEAM package for MEAM potential :ul :line @@ -58,322 +64,3 @@ Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb) Steve Lustig (Dupont) Jim Belak and Roy Pollock (LLNL) :ul -:line - -Here is a timeline for when various individuals contributed to a new -feature or command or tool added to LAMMPS: - -Aug18 : CMake build option for LAMMPS : Christoph Junghans (LANL), Richard Berger, and Axel Kohlmeyer (Temple U) -Jul18 : DEM polygonal and polyhedron particles : Trung Nguyen (Northwestern U) -Jun18 : SPIN package : Julien Tranchida (Sandia and CEA) -Jun18 : compute entropy/atom : Pablo Piaggi (EPLF, Switzerland) -May18 : fix bond/react : Jake Gissinger (CU Boulder) -Apr18 : USER-BOCS package : Nicholas Dunn and Michael DeLyser (Penn State U) -Mar18: pair coul/shield, kolmogorov/crespi/full, ilp/graphene/hbn : Wengen Ouyang (Tel Aviv U) -Feb18 : pair lj/cut/coul/wolf : Vishal Boddu (U of Erlangen-Nuremberg) -Feb18 : USER-MOFFF package : Hendrik Heenen (Technical U of Munich) and Rochus Schmid (Ruhr-University Bochum) -Feb18 : pair ufm : Rodolfo Paula Leite and Maurice de Koning (Unicamp/Brazil) -Dec17 : fix python/move : Richard Berger (Temple U) -Nov17 : pair extep : Jaap Kroes (Radboud U) -Oct17 : USER-UEF package : David Nicholson (MIT) -Oct17 : fix rhok : Ulf Pederson (Roskilde U) -Oct17 : bond gromos : Axel Kohlmeyer (Temple U) -Oct17 : pair born/coul/wolf/cs and coul/wolf/cs : Vishal Boddu -Sep17 : fix latte : Christian Negre (LANL) -Sep17 : temper_npt : Amulya Pervaje and Cody Addington (NCSU) -Aug17 : USER-MESO package : Zhen Li (Brown University) -Aug17 : compute aggregate/atom & fragment/atom : Axel Kohlmeyer (Temple U) -Jul17 : pair meam/c : Sebastian Hutter (Otto-von-Guericke University) -Jun17 : pair reaxc/omp : Metin Aktulga (MSU) and Axel Kohlmeyer (Temple U) -Jun17 : pair vashishita/gpu : Anders Hafreager (UiO) -Jun17 : kspace pppm/disp/intel and pair lj/long/coul/long/intel : Mike Brown (Intel) and William McDoniel (RWTH Aachen U) -Jun17 : compute cnp/atom : Paulo Branicio (USC) -May17 : fix python and pair python : Richard Berger (Temple U) -May17 : pair edip/multi : Chao Jiang (U Wisconsin) -May17 : pair gw and gw/zbl : German Samolyuk (ORNL) -Mar17 : pair charmm fsw and fsh : Robert Meissner & Lucio Colombi Ciacchi (Bremen U), Robert Latour (Clemson U) -Mar17 : pair momb : Ya Zhou, Kristen Fichthorn, and Tonnam Balankura (PSU) -Mar17 : fix filter/corotate : Lukas Fath (KIT) -Mar17 : pair kolmogorov/crespi/z : Jaap Kroes (Radboud Universiteit) -Feb17 : Kokkos versions of the class2 bond/angle/dihedral/improper : Ray Shan (Materials Design) -Jan17 : USER-CGDNA package : Oliver Henrich (U Edinburgh) -Jan17 : fix mscg : Lauren Abbott (Sandia) -Nov16 : temper/grem and fix grem : David Stelter (BU), Edyta Malolepsza (Broad Institute), Tom Keyes (BU) -Nov16 : pair agni : Axel Kohlmeyer (Temple U) and Venkatesh Botu -Nov16 : pair tersoff/mod.c : Ganga P Purja Pun (George Mason University) -Nov16 : pair born/coul/dsf and pair born/coul/dsf/cs : Ariel Lozano -Nov16 : fix reaxc/species/kk & fix reaxc/bonds/kk : Stan Moore (Sandia) -Oct16 : fix wall/gran/region : Dan Bolintineanu (Sandia) -Sep16 : weight options for balance & fix balance : Axel Kohlmeyer (Temple U) & Iain Bethune (EPCC) -Sep16 : fix cmap : Xiaohu Hu (ORNL), David Hyde-Volpe & Tigran Abramyan & Robert Latour (Clemson U), Chris Lorenz (Kings College, London) -Sep16 : pair vashishta/table : Anders Hafreager (U Oslo) -Sep16 : kspace pppm/kk : Stan Moore (Sandia) -Aug16 : fix flow/gauss : Steve Strong and Joel Eaves (U Colorado) -Aug16 : fix controller : Aidan Thompson (Sandia) -Jul16 : dipole integration by DLM method : Iain Bethune (EPCC) -Jul16 : dihedral spherical : Andrew Jewett -Jun16 : pair reax/c/kk : Ray Shan (Materials Design), Stan Moore (Sandia) -Jun16 : fix orient/bcc : Tegar Wicaksono (UBC) -Jun16 : fix ehex : Peter Wirnsberger (University of Cambridge) -Jun16 : reactive DPD extensions to USER-DPD : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL), Christopher Stone (Computational Science & Engineering, LLC) -May16 : USER-MANIFOLD package : Stefan Paquay (Eindhoven U of Tech, The Netherlands) -Apr16 : write_coeff : Axel Kohlmeyer (Temple U) -Apr16 : pair morse/soft : Stefan Paquay (Eindhoven U of Tech, The Netherlands) -Apr16 : compute dipole/chunk : Axel Kohlmeyer (Temple U) -Apr16 : bond write : Axel Kohlmeyer (Temple U) -Mar16 : pair morse/smooth/linear : Stefan Paquay (Eindhoven U of Tech, The Netherlands) -Feb16 : pair/bond/angle/dihedral/improper zero : Carsten Svaneborg (SDU) -Feb16 : dump custom/vtk : Richard Berger (JKU) and Daniel Queteschiner (DCS Computing) -Feb16 : fix (nvt/npt/nph)/body and compute temp/body : Trung Nguyen -Feb16 : USER-DPD package : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL) -Dec15 : fix qeq/fire : Ray Shan (Sandia) -Dec15 : pair lj/mdf, pair lennard/mdf, pair buck/mdf, improper distance : Paolo Raiteri (Curtin University) -Nov15 : compute orientorder/atom : Aidan Thompson (Sandia) and Axel Kohlmeyer (U Temple) -Nov15 : compute hexorder/atom : Aidan Thompson (Sandia) -Oct15 : displace_atoms variable option : Reese Jones (Sandia) -Oct15 : pair mgpt & USER-MGPT package : Tomas Oppelstrup and John Moriarty (LLNL) -Oct15 : pair smtbq & USER-SMTBQ package : Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS) -Oct15 : fix ave/correlate/long command : Jorge Ramirez (UPM) and Alexei Likhtman (U Reading) -Oct15 : pair vashishta command : Aidan Thompson (Sandia) and Yongnan Xiong (HNU) -Aug15 : USER-TALLY package : Axel Kohlmeyer (Temple U) -Aug15 : timer command : Axel Kohlmeyer (Temple U) -Aug15 : USER-H5MD package : Pierre de Buyl (KU Leuven) -Aug15 : COMPRESS package : Axel Kohlmeyer (Temple U) -Aug15 : USER-SMD package : Georg Gunzenmueller (EMI) -Jul15 : new HTML format for "doc pages"_Manual.html with search option : Richard Berger (JKU) -Jul15 : rRESPA with pair hybrid : Sam Genheden (U of Southampton) -Jul15 : pair_modify special : Axel Kohlmeyer (Temple U) -Jul15 : pair polymorphic : Xiaowang Zhou and Reese Jones (Sandia) -Jul15 : USER-DRUDE package : Alain Dequidt and Agilio Padua (U Blaise Pascal Clermont-Ferrand) and Julien Devemy (CNRS) -Jul15 : USER-QTB package : Yuan Shen, Tingting Qi, and Evan Reed (Stanford U) -Jul15 : USER-DIFFRACTION package : Shawn Coleman (ARL) -Mar15 : fix temp/csld : Axel Kohlmeyer (Temple U) -Mar15 : CORESHELL package : Hendrik Heenen (Technical University of Munich) -Feb15 : pair quip for GAP and other potentials : Albert Bartok-Partay (U Cambridge) -Feb15 : pair coul/streitz for Streitz-Mintmire potential : Ray Shan (Sandia) -Feb15 : fix tfmc : Kristof Bal (U of Antwerp) -Feb15 : fix ttm/mod : Sergey Starikov and Vasily Pisarev (JIHT of RAS) -Jan15 : fix atom/swap for MC swaps of atom types/charge : Paul Crozier (Sandia) -Nov14 : fix pimd for path-integral MD : Chris Knight and Yuxing Peng (U Chicago) -Nov14 : fix gle and fix ipi for path-integral MD : Michele Ceriotti (EPFL) -Nov14 : pair style srp : Tim Sirk (ARL) and Pieter in 't Veld (BASF) -Nov14 : fix ave/spatial/sphere : Niall Jackson (Imperial College) -Sep14 : QEQ package and several fix qeq/variant styles : Ray Shan (Sandia) -Sep14 : SNAP package and pair style : Aidan Thompson (Sandia) and collaborators -Aug14 : USER-INTEL package : Mike Brown (Intel) -May14 : KOKKOS pacakge : Christian Trott and Carter Edwards (Sandia) -May14 : USER-FEP pacakge : Agilio Padua (U Blaise Pascal Clermont-Ferrand) -Apr14 : fix rigid/small NVE/NVT/NPH/NPT : Trung Nguyen (ORNL) -Apr14 : fix qmmm for QM/MM coupling : Axel Kohlmeyer (Temple U) -Mar14 : kspace_modify collective for faster FFTs on BG/Q : Paul Coffman (IBM) -Mar14 : fix temp/csvr and fix oneway : Axel Kohlmeyer (Temple U) -Feb14 : pair peri/eps, compute dilatation/atom, compute plasticity/atom : Rezwanur Rahman and John Foster (UTSA) -Jan14 : MPI-IO options for dump and restart files : Paul Coffman (IBM) -Nov13 : USER-LB package for Lattice Boltzmann : Francis Mackay and Colin Denniston (U Western Ontario) -Nov13 : fix ti/rs and ti/spring : Rodrigo Freitas (UC Berkeley) -Nov13 : pair comb3 : Ray Shan (Sandia), Tao Liang and Dundar Yilmaz (U Florida) -Nov13 : write_dump and dump movie : Axel Kohlmeyer (Temple U) -Sep13 : xmgrace tool : Vikas Varshney -Sep13 : pair zbl : Aidan Thompson and Stephen Foiles (Sandia) -Aug13 : pair nm and variants : Julien Devemy (ICCF) -Aug13 : fix wall/lj1043 : Jonathan Lee (Sandia) -Jul13 : pair peri/ves : Rezwan Rahman, JT Foster (U Texas San Antonio) -Jul13 : pair tersoff/mod : Vitaly Dozhdikov (JIHT of RAS) -Jul13 : compute basal/atom : Christopher Barrett,(Mississippi State) -Jul13 : polybond tool : Zachary Kraus (Georgia Tech) -Jul13 : fix gld : Stephen Bond and Andrew Baczewski (Sandia) -Jun13 : pair nb3b/harmonic : Todd Zeitler (Sandia) -Jun13 : kspace_style pppm/stagger : Stan Moore (Sandia) -Jun13 : fix tune/kspace : Paul Crozier (Sandia) -Jun13 : long-range point dipoles : Stan Moore (Sandia) and Pieter in 't Veld (BASF) -May13 : compute msd/nongauss : Rob Hoy -May13 : pair list : Axel Kohlmeyer (Temple U) -May13 : triclinic support for long-range solvers : Stan Moore (Sandia) -Apr13 : dump_modify nfile and fileper : Christopher Knight -Mar13 : fix phonon : Ling-Ti Kong (Shanghai Jiao Tong University) -Mar13 : pair_style lj/cut/tip4p/cut : Pavel Elkind (Gothenburg University) -Feb13 : immediate variables in input script : Daniel Moller (Autonomous University of Barcelona) -Feb13 : fix species : Ray Shan (Sandia) -Jan13 : compute voronoi/atom : Daniel Schwen -Nov12 : pair_style mie/cut : Cassiano Aimoli Petrobras (U Notre Dame) -Oct12 : pair_style meam/sw/spline : Robert Rudd (LLNL) -Oct12 : angle_style fourier and fourier/simple and quartic : Loukas Peristeras (Scienomics) -Oct12 : dihedral_style fourier and nharmonic and quadratic : Loukas Peristeras (Scienomics) -Oct12 : improper_style fourier : Loukas Peristeras (Scienomics) -Oct12 : kspace_style pppm/disp for 1/r^6 : Rolf Isele-Holder (Aachen University) -Oct12 : moltemplate molecular builder tool : Andrew Jewett (UCSB) -Sep12 : pair_style lj/cut/coul/dsf and coul/dsf : Trung Nguyen (ORNL) -Sep12 : multi-level summation long-range solver : Stan Moore, Stephen Bond, and Paul Crozier (Sandia) -Aug12 : fix rigid/npt and fix rigid/nph : Trung Nguyen (ORNL) -Aug12 : Fortran wrapper on lib interface : Karl Hammond (UT, Knoxville) -Aug12 : kspace_modify diff for 2-FFT PPPM : Rolf Isele-Holder (Aachen University), Stan Moore (BYU), Paul Crozier (Sandia) -Jun12 : pair_style bop : Don Ward and Xiaowang Zhou (Sandia) -Jun12 : USER-MOLFILE package : Axel Kohlmeyer (U Temple) -Jun12 : USER-COLVARS package : Axel Kohlmeyer (U Temple) -May12 : read_dump : Tim Sirk (ARL) -May12 : improper_style cossq and ring : Georgios Vogiatzis (CoMSE, NTU Athens) -May12 : pair_style lcbop : Dominik Wojt (Wroclaw University of Technology) -Feb12 : PPPM per-atom energy/virial : Stan Moore (BYU) -Feb12 : Ewald per-atom energy/virial : German Samolyuk (ORNL), Stan Moore (BYU) -Feb12 : minimize forcezero linesearch : Asad Hasan (CMU) -Feb12 : pair_style beck : Jon Zimmerman (Sandia) -Feb12 : pair_style meam/spline : Alex Stukowski (LLNL) -Jan12 : pair_style kim : Valeriu Smirichinski, Ryan Elliott, Ellad Tadmor (U Minn) -Jan12 : dihedral_style table : Andrew Jewett (UCSB) -Jan12 : angle_style dipole : Mario Orsi -Jan12 : pair_style lj/smooth/linear : Jon Zimmerman (Sandia) -Jan12 : fix reax/c/bond : Tzu-Ray Shan (Sandia) -Dec11 : pair_style coul/wolf : Yongfeng Zhang (INL) -Dec11 : run_style verlet/split : Yuxing Peng and Chris Knight (U Chicago) -Dec11 : pair_style tersoff/table : Luca Ferraro (CASPUR) -Nov11 : per-atom energy/stress for reax/c : Tzu-Ray Shan (Sandia) -Oct11 : Fast Lubrication Dynamics (FLD) package: Amit Kumar, Michael Bybee, Jonathan Higdon (UIUC) -Oct11 : USER-OMP package : Axel Kohlmeyer (Temple U) -Sep11 : pair_style edip : Luca Ferraro (CASPUR) -Aug11 : USER-SPH package : Georg Ganzenmuller (FIHSD, EMI, Germany) -Aug11 : fix restrain : Craig Tenney (Sandia) -Aug11 : USER-CUDA package : Christian Trott (U Tech Ilmenau) -Aug11 : pair_style lj/sf : Laurent Joly (U Lyon) -Aug11 : bond_style harmonic/shift and harmonic/shift/cut : Carsten Svaneborg -Aug11 : angle_style cosine/shift and cosine/shift/exp : Carsten Svaneborg -Aug11 : dihedral_style cosine/shift/exp : Carsten Svaneborg -Aug11 : pair_style dipole/sf : Mario Orsi -Aug11 : fix addtorque and compute temp/rotate : Laurent Joly (U Lyon) -Aug11 : FFT support via FFTW3, MKL, ACML, KISS FFT libraries : \ - Axel Kohlmeyer (Temple U) -Jun11 : pair_style adp : Chris Weinberger (Sandia), Stephen Foiles (Sandia), \ - Chandra Veer Singh (Cornell) -Jun11 : Windows build option via Microsoft Visual Studio : \ - Ilya Valuev (JIHT, Moscow, Russia) -Jun11 : antisymmetrized wave packet MD : Ilya Valuev (JIHT, Moscow, Russia) -Jun11 : dump image : Nathan Fabian (Sandia) -May11 : pppm GPU single and double : Mike Brown (ORNL) -May11 : pair_style lj/expand/gpu : Inderaj Bains (NVIDIA) -2010 : pair_style reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL) -- : DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (Caltech) -- : fix adapt and compute ti for thermodynamic integration for \ - free energies : Sai Jayaraman (Sandia) -- : pair_style born and gauss : Sai Jayaraman (Sandia) -- : stochastic rotation dynamics (SRD) via fix srd : \ - Jeremy Lechman (Sandia) and Pieter in 't Veld (BASF) -- : ipp Perl script tool : Reese Jones (Sandia) -- : eam_database and createatoms tools : Xiaowang Zhou (Sandia) -- : electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech) -- : embedded ion method (EIM) potential : Xiaowang Zhou (Sandia) -- : COMB potential with charge equilibration : Tzu-Ray Shan (U Florida) -- : fix ave/correlate : Benoit Leblanc, Dave Rigby, \ - Paul Saxe (Materials Design) and Reese Jones (Sandia) -- : pair_style peri/lps : Mike Parks (Sandia) -- : fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford) -- : thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U) -- : fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan) -- : public SVN & Git repositories for LAMMPS : \ - Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia) -- : compute heat/flux : German Samolyuk (ORNL) and \ - Mario Pinto (Computational Research Lab, Pune, India) -- : pair_style yukawa/colloid : Randy Schunk (Sandia) -- : fix wall/colloid : Jeremy Lechman (Sandia) -2009 : fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ) -- : concentration-dependent EAM potential : \ - Alexander Stukowski (Technical University of Darmstadt) -- : parallel replica dymamics (PRD) : Mike Brown (Sandia) -- : min_style hftn : Todd Plantenga (Sandia) -- : fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia) -- : dump cfg : Liang Wan (Chinese Academy of Sciences) -- : fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland) -- : pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia) -- : pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo -- : fix langevin tally : Carolyn Phillips (U Michigan) -- : compute heat/flux for Green-Kubo : Reese Jones (Sandia), \ - Philip Howell (Siemens), Vikas Varsney (AFRL) -- : region cone : Pim Schravendijk -- : pair_style born/coul/long : Ahmed Ismail (Sandia) -- : fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan) -- : fix box/relax : Aidan Thompson and David Olmsted (Sandia) -- : ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT) -- : compute cna/atom : Liang Wan (Chinese Academy of Sciences) -2008 : Tersoff/ZBL potential : Dave Farrell (Northwestern U) -- : peridynamics : Mike Parks (Sandia) -- : fix smd for steered MD : Axel Kohlmeyer (U Penn) -- : GROMACS pair potentials : Mark Stevens (Sandia) -- : lmp2vmd tool : Axel Kohlmeyer (U Penn) -- : compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U) -- : USER-CG-CMM package for coarse-graining : Axel Kohlmeyer (U Penn) -- : cosine/delta angle potential : Axel Kohlmeyer (U Penn) -- : VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain -- : pair_style lubricate : Randy Schunk (Sandia) -- : compute ackland/atom : Gerolf Ziegenhain -- : kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \ - Pieter in 't Veld (Sandia) -- : AI-REBO bond-order potential : Ase Henry (MIT) -- : making LAMMPS a true "object" that can be instantiated \ - multiple times, e.g. as a library : Ben FrantzDale (RPI) -- : pymol_asphere viz tool : Mike Brown (Sandia) -2007 : NEMD SLLOD integration : Pieter in 't Veld (Sandia) -- : tensile and shear deformations : Pieter in 't Veld (Sandia) -- : GayBerne potential : Mike Brown (Sandia) -- : ellipsoidal particles : Mike Brown (Sandia) -- : colloid potentials : Pieter in 't Veld (Sandia) -- : fix heat : Paul Crozier and Ed Webb (Sandia) -- : neighbor multi and communicate multi : Pieter in 't Veld (Sandia) -- : MATLAB post-processing scripts : Arun Subramaniyan (Purdue) -- : triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia) -- : thermo_extract tool: Vikas Varshney (Wright Patterson AFB) -- : fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia) -- : MEAM potential : Greg Wagner (Sandia) -- : optimized pair potentials for lj/cut, charmm/long, eam, morse : \ - James Fischer (High Performance Technologies), \ - David Richie and Vincent Natoli (Stone Ridge Technologies) -2006 : fix wall/lj126 : Mark Stevens (Sandia) -- : Stillinger-Weber and Tersoff potentials : \ - Aidan Thompson and Xiaowang Zhou (Sandia) -- : region prism : Pieter in 't Veld (Sandia) -- : fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U) -- : multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U) -- : OPLS dihedral potential: Mark Stevens (Sandia) -- : POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI) -- : faster pair hybrid potential: James Fischer \ - (High Performance Technologies, Inc), Vincent Natoli and \ - David Richie (Stone Ridge Technology) -- : breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia) -- : DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U) -- : grain boundary orientation fix : Koenraad Janssens and \ - David Olmsted (Sandia) -- : pair_style lj/smooth potential : Craig Maloney (UCSB) -- : radius-of-gyration spring fix : Naveen Michaud-Agrawal \ - (Johns Hopkins U) and Paul Crozier (Sandia) -- : self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U) -- : EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea) -- : cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U) -- : helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \ - Mark Stevens (Sandia) -- : Finnis/Sinclair EAM: Tim Lau (MIT) -- : dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \ - Frank van Swol (Sandia) -- : TIP4P potential (4-site water): Ahmed Ismail and \ - Amalie Frischknecht (Sandia) -2005 : uniaxial strain fix: Carsten Svaneborg (Max Planck Institute) -- : compressed dump files: Erik Luijten (U Illinois) -- : cylindrical indenter fix: Ravi Agrawal (Northwestern U) -- : electric field fix: Christina Payne (Vanderbilt U) -- : AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \ - Vikas Varshney (U Akron) -- : CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia) -- : Morse bond potential: Jeff Greathouse (Sandia) -- : radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia) -- : force tables for long-range Coulombics: Paul Crozier (Sandia) -2004 : targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \ - Christian Burisch (Bochum University, Germany) -- : FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech) -- : lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \ - Andrey Kalinichev (Sandia) -- : parallel tempering: Mark Sears (Sandia) -earlier : granular force fields and BC: Leo Silbert & Gary Grest (Sandia) -- : multi-harmonic dihedral potential: Mathias Putz (Sandia) -- : embedded atom method (EAM) potential: Stephen Foiles (Sandia) -- : msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray) -- : HTFN energy minimizer: Todd Plantenga (Sandia) -- : class 2 force fields: Eric Simon (Cray) -- : NVT/NPT integrators: Mark Stevens (Sandia) -- : rRESPA: Mark Stevens & Paul Crozier (Sandia) -- : Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:,ca1=c)