From d43381d50cea9781047a43f4cf24613eebff5120 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 1 Sep 2011 14:51:33 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6904 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_history.html | 70 +++++++-------- doc/Section_history.txt | 70 +++++++-------- doc/Section_intro.html | 184 +++++++++---------------------------- doc/Section_intro.txt | 190 +++++++++------------------------------ 4 files changed, 146 insertions(+), 368 deletions(-) diff --git a/doc/Section_history.html b/doc/Section_history.html index e84bb721ed..522e4e1220 100644 --- a/doc/Section_history.html +++ b/doc/Section_history.html @@ -24,56 +24,46 @@ molecular dynamics codes I've distributed.

13.1 Coming attractions

-

The current version of LAMMPS incorporates nearly all the features -from previous parallel MD codes developed at Sandia. These include -earlier versions of LAMMPS itself, Warp and ParaDyn for metals, and -GranFlow for granular materials. +

The Wish list link on the +LAMMPS WWW page gives a list of features we are hoping to add to +LAMMPS in the future, including contact names of individuals you can +email if you are interested in contributing to the developement or +would be a future user of that feature.

-

These are new features we'd like to eventually add to LAMMPS. Some -are being worked on; some haven't been implemented because of lack of -time or interest; others are just a lot of work! See this -page on the LAMMPS WWW site for more details. +

You can also send email to the +developers if you want to add +your wish to the list.

- - -

13.2 Past versions

LAMMPS development began in the mid 1990s under a cooperative research & development agreement (CRADA) between two DOE labs (Sandia and LLNL) -and 3 companies (Cray, Bristol Myers Squibb, and Dupont). Soon after -the CRADA ended, a final F77 version of the code, LAMMPS 99, was -released. As development of LAMMPS continued at Sandia, the memory -management in the code was converted to F90; a final F90 version was -released as LAMMPS 2001. +and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was +to develop a large-scale parallel classical MD code; the coding effort +was led by Steve Plimpton at Sandia. +

+

After the CRADA ended, a final F77 version, LAMMPS 99, was +released. As development of LAMMPS continued at Sandia, its memory +management was converted to F90; a final F90 version was released as +LAMMPS 2001.

The current LAMMPS is a rewrite in C++ and was first publicly released -in 2004. It includes many new features, including features from other -parallel molecular dynamics codes written at Sandia, namely ParaDyn, -Warp, and GranFlow. ParaDyn is a parallel implementation of the -popular serial DYNAMO code developed by Stephen Foiles and Murray Daw -for their embedded atom method (EAM) metal potentials. ParaDyn uses -atom- and force-decomposition algorithms to run in parallel. Warp is -also a parallel implementation of the EAM potentials designed for -large problems, with boundary conditions specific to shearing solids -in varying geometries. GranFlow is a granular materials code with -potentials and boundary conditions peculiar to granular systems. All -of these codes (except ParaDyn) use spatial-decomposition techniques -for their parallelism. +as an open source code in 2004. It includes many new features beyond +those in LAMMPS 99 or 2001. It also includes features from older +parallel MD codes written at Sandia, namely ParaDyn, Warp, and +GranFlow (see below). +

+

In late 2006 we began merging new capabilities into LAMMPS that were +developed by Aidan Thompson at Sandia for his MD code GRASP, which has +a parallel framework similar to LAMMPS. Most notably, these have +included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF - +and the associated charge-equilibration routines needed for ReaxFF. +

+

The History link on the +LAMMPS WWW page gives a timeline of features added to the +C++ open-source version of LAMMPS over the last several years.

These older codes are available for download from the LAMMPS WWW site, except for Warp & GranFlow which were primarily used diff --git a/doc/Section_history.txt b/doc/Section_history.txt index de84ffb2bf..92600b7e22 100644 --- a/doc/Section_history.txt +++ b/doc/Section_history.txt @@ -21,30 +21,15 @@ molecular dynamics codes I've distributed. 13.1 Coming attractions :h4,link(hist_1) -The current version of LAMMPS incorporates nearly all the features -from previous parallel MD codes developed at Sandia. These include -earlier versions of LAMMPS itself, Warp and ParaDyn for metals, and -GranFlow for granular materials. +The "Wish list link"_http://lammps.sandia.gov/future.html on the +LAMMPS WWW page gives a list of features we are hoping to add to +LAMMPS in the future, including contact names of individuals you can +email if you are interested in contributing to the developement or +would be a future user of that feature. -These are new features we'd like to eventually add to LAMMPS. Some -are being worked on; some haven't been implemented because of lack of -time or interest; others are just a lot of work! See "this -page"_lwsfuture on the LAMMPS WWW site for more details. - -:link(lwsfuture,http://lammps.sandia.gov/future.html) - -Coupling to finite elements for streess-strain -New ReaxFF implementation -Nudged elastic band -Temperature accelerated dynamics -Triangulated particles -Stochastic rotation dynamics -Stokesian dynamics via fast lubrication dynamics -Long-range point-dipole solver -Per-atom energy and stress for long-range Coulombics -Long-range Coulombics via Ewald and PPPM for triclinic boxes -Metadynamics -Direct Simulation Monte Carlo - DSMC :ul +You can also send "email to the +developers"_http://lammps.sandia.gov/authors.html if you want to add +your wish to the list. :line @@ -52,25 +37,30 @@ Direct Simulation Monte Carlo - DSMC :ul LAMMPS development began in the mid 1990s under a cooperative research & development agreement (CRADA) between two DOE labs (Sandia and LLNL) -and 3 companies (Cray, Bristol Myers Squibb, and Dupont). Soon after -the CRADA ended, a final F77 version of the code, LAMMPS 99, was -released. As development of LAMMPS continued at Sandia, the memory -management in the code was converted to F90; a final F90 version was -released as LAMMPS 2001. +and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was +to develop a large-scale parallel classical MD code; the coding effort +was led by Steve Plimpton at Sandia. + +After the CRADA ended, a final F77 version, LAMMPS 99, was +released. As development of LAMMPS continued at Sandia, its memory +management was converted to F90; a final F90 version was released as +LAMMPS 2001. The current LAMMPS is a rewrite in C++ and was first publicly released -in 2004. It includes many new features, including features from other -parallel molecular dynamics codes written at Sandia, namely ParaDyn, -Warp, and GranFlow. ParaDyn is a parallel implementation of the -popular serial DYNAMO code developed by Stephen Foiles and Murray Daw -for their embedded atom method (EAM) metal potentials. ParaDyn uses -atom- and force-decomposition algorithms to run in parallel. Warp is -also a parallel implementation of the EAM potentials designed for -large problems, with boundary conditions specific to shearing solids -in varying geometries. GranFlow is a granular materials code with -potentials and boundary conditions peculiar to granular systems. All -of these codes (except ParaDyn) use spatial-decomposition techniques -for their parallelism. +as an open source code in 2004. It includes many new features beyond +those in LAMMPS 99 or 2001. It also includes features from older +parallel MD codes written at Sandia, namely ParaDyn, Warp, and +GranFlow (see below). + +In late 2006 we began merging new capabilities into LAMMPS that were +developed by Aidan Thompson at Sandia for his MD code GRASP, which has +a parallel framework similar to LAMMPS. Most notably, these have +included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF - +and the associated charge-equilibration routines needed for ReaxFF. + +The "History link"_http://lammps.sandia.gov/history.html on the +LAMMPS WWW page gives a timeline of features added to the +C++ open-source version of LAMMPS over the last several years. These older codes are available for download from the "LAMMPS WWW site"_lws, except for Warp & GranFlow which were primarily used diff --git a/doc/Section_intro.html b/doc/Section_intro.html index b77261945d..afc3c5d040 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -477,154 +477,58 @@ Hierarchical Modeling". -

The following papers describe the parallel algorithms used in LAMMPS. +

The following paper describe the basic parallel algorithms used in +LAMMPS. If you use LAMMPS results in your published work, please cite +this paper and include a pointer to the LAMMPS WWW Site +(http://lammps.sandia.gov):

S. J. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995).

-

S. J. Plimpton, R. Pollock, M. Stevens, Particle-Mesh Ewald and -rRESPA for Parallel Molecular Dynamics Simulations, in Proc of the -Eighth SIAM Conference on Parallel Processing for Scientific -Computing, Minneapolis, MN (March 1997). +

Other papers describing specific algorithms used in LAMMPS are listed +under the Citing LAMMPS link of +the LAMMPS WWW page.

-

If you use LAMMPS results in your published work, please cite the J -Comp Phys reference and include a pointer to the LAMMPS WWW Site -(http://lammps.sandia.gov). +

The Publications link on the +LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is +not listed there for some reason, feel free to send us the info. If +the simulations in your paper produced cool pictures or animations, +we'll be pleased to add them to the +Pictures or +Movies pages of the LAMMPS WWW +site.

-

If you send is information about your publication, we'll be pleased to -add it to the Publications page of the LAMMPS WWW Site. Ditto -for a picture or movie for the Pictures or Movies pages. +

The core group of LAMMPS developers is at Sandia National Labs:

-

The core group of LAMMPS developers is at Sandia National Labs. They -include Steve Plimpton, Paul Crozier, and Aidan Thompson and can -be contacted via email: sjplimp, pscrozi, athomps at sandia.gov. +

+

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.

-

Here are various folks who have made significant contributions to -features in LAMMPS. The most recent contributions are at the top of -the list. -

- - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
pppm GPU single and double Mike Brown (ORNL)
pair_style lj/cut/expand Inderaj Bains (NVIDIA)
temperature accelerated dynamics (TAD) Aidan Thompson (Sandia)
pair 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 integreation for free energies Sai Jayaraman (Sandia)
pair born and pair gauss Sai Jayaraman (Sandia)
stochastic rotation dynamics (SRD) via fix srd Jemery 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)
fix nvt, fix nph, fix npt, Parinello/Rahman dynamics, fix box/relax Aidan Thompson (Sandia)
compute heat/flux German Samolyuk (ORNL) and Mario Pinto (Computational Research Lab, Pune, India)
pair yukawa/colloid Randy Schunk (Sandia)
fix wall/colloid Jeremy Lechman (Sandia)
pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling Paul Crozier (Sandia)
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
fix reax/bonds Aidan Thompson (Sandia)
pair 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 Wan Liang (Chinese Academy of Sciences)
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 lubricate Randy Schunk (Sandia)
compute ackland/atom Gerolf Zeigenhain
kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul Pieter in 't Veld (Sandia)
AIREBO 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)
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)
fix wall/lj126 Mark Stevens (Sandia)
Stillinger-Weber and Tersoff potentials Aidan Thompson and Xiaowang Zhou (Sandia)
region prism Pieter in 't Veld (Sandia)
LJ tail corrections for energy/pressure Paul Crozier (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)
lj/smooth pair 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)
uniaxial strain fix Carsten Svaneborg (Max Planck Institute)
thermodynamics enhanced by fix quantities Aidan Thompson (Sandia)
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)
targeted molecular dynamics (TMD) Paul Crozier (Sandia) and Christian Burisch (Bochum University, Germany)
FFT support for SGI SCSL (Altix) Jim Shepherd (Ga Tech)
lmp2cfg and lmp2traj tools Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia)
parallel tempering Mark Sears (Sandia)
embedded atom method (EAM) potential Stephen Foiles (Sandia)
multi-harmonic dihedral potential Mathias Puetz (Sandia)
granular force fields and BC Leo Silbert & Gary Grest (Sandia)
2d Ewald/PPPM Paul Crozier (Sandia)
CHARMM force fields Paul Crozier (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) -
- -

Other CRADA partners involved in the design and testing of LAMMPS were +

+

As discussed in this section, LAMMPS originated +as a cooperative project between DOE labs and industrial +partners. Folks involved in the design and testing of the original +version of LAMMPS were the following: