forked from lijiext/lammps
more mods to Intro section
This commit is contained in:
Steven J. Plimpton
parent
90897f570e
commit
c105e21a73
|
|
@ -1,6 +1,6 @@
|
|||
"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws -
|
||||
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
|
||||
Section"_Section_start.html :c
|
||||
Section"_Install.html :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
|
|
@ -10,34 +10,28 @@ Section"_Section_start.html :c
|
|||
|
||||
Introduction :h2
|
||||
|
||||
The "LAMMPS website"_lws is the best introduction to LAMMPS.
|
||||
These pages provide a brief introduction to LAMMPS.
|
||||
|
||||
Here is a list of webpages you can browse:
|
||||
<!-- RST
|
||||
|
||||
"Brief intro and significant recent features"_lws
|
||||
"List of features"_http://lammps.sandia.gov/features.html
|
||||
"List of non-features"_http://lammps.sandia.gov/non_features.html
|
||||
"Recent bug fixes and new features"_http://lammps.sandia.gov/bug.html :ul
|
||||
.. toctree::
|
||||
|
||||
"Download info"_http://lammps.sandia.gov/download.html
|
||||
"GitHub site"_https://github.com/lammps/lammps
|
||||
"SourceForge site"_https://sourceforge.net/projects/lammps
|
||||
"Open source and licensing info"_http://lammps.sandia.gov/open_source.html :ul
|
||||
Intro_overview
|
||||
Intro_features
|
||||
Intro_nonfeatures
|
||||
Intro_opensource
|
||||
Intro_authors
|
||||
Intro_website
|
||||
|
||||
"Glossary of MD terms relevant to LAMMPS"_http://lammps.sandia.gov/glossary.html
|
||||
"LAMMPS highlights with images"_http://lammps.sandia.gov/pictures.html
|
||||
"LAMMPS highlights with movies"_http://lammps.sandia.gov/movies.html
|
||||
"Mail list"_http://lammps.sandia.gov/mail.html
|
||||
"Workshops"_http://lammps.sandia.gov/workshops.html
|
||||
"Tutorials"_http://lammps.sandia.gov/tutorials.html
|
||||
"Developer guide"_http://lammps.sandia.gov/Developer.pdf :ul
|
||||
END_RST -->
|
||||
|
||||
"Pre- and post-processing tools for LAMMPS"_http://lammps.sandia.gov/prepost.html
|
||||
"Other software usable with LAMMPS"_http://lammps.sandia.gov/offsite.html
|
||||
"Viz tools usable with LAMMPS"_http://lammps.sandia.gov/viz.html :ul
|
||||
<!-- HTML_ONLY -->
|
||||
|
||||
"Benchmark performance"_http://lammps.sandia.gov/bench.html
|
||||
"Publications that have cited LAMMPS"_http://lammps.sandia.gov/papers.html
|
||||
"Authors of the LAMMPS code"_http://lammps.sandia.gov/authors.html
|
||||
"History of LAMMPS development"_http://lammps.sandia.gov/history.html
|
||||
"Funding for LAMMPS"_http://lammps.sandia.gov/funding.html :ul
|
||||
"Overview of LAMMPS"_Intro_overview.html
|
||||
"LAMMPS features"_Intro_features.html
|
||||
"LAMMPS non-features"_Intro_nonfeatures.html
|
||||
"LAMMPS open-source license"_Intro_license.html
|
||||
"LAMMPS authors"_Intro_authors.html
|
||||
"Additional website links"_Intro_website.html :all(b)
|
||||
|
||||
<!-- END_HTML_ONLY -->
|
||||
|
|
|
|||
|
|
@ -0,0 +1,379 @@
|
|||
"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
LAMMPS authors :h3
|
||||
|
||||
The primary LAMMPS developers are at Sandia National Labs and Temple
|
||||
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
|
||||
|
||||
:link(sjp,http://www.cs.sandia.gov/~sjplimp)
|
||||
|
||||
Past developers include Paul Crozier and Mark Stevens, both at Sandia,
|
||||
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.
|
||||
|
||||
Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM packages
|
||||
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
|
||||
|
||||
:line
|
||||
|
||||
As discussed on the "History
|
||||
page"_http://lammps.sandia.gov/history.html of the website, 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:
|
||||
|
||||
John Carpenter (Mayo Clinic, formerly at Cray Research)
|
||||
Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
|
||||
Steve Lustig (Dupont)
|
||||
Jim Belak and Roy Pollock (LLNL) :ul
|
||||
|
||||
:line
|
||||
:line
|
||||
|
||||
Here is a timeline for when various individuals contributed to a new
|
||||
feature or command or tool added to LAMMPS:
|
||||
|
||||
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"_doc/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, KISSFFT 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)
|
||||
|
|
@ -0,0 +1,202 @@
|
|||
"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
LAMMPS features :h3
|
||||
|
||||
LAMMPS is a classical molecular dynamics (MD) code with these general
|
||||
classes of functionality:
|
||||
|
||||
"General features"_#general
|
||||
"Particle and model types"_#particle
|
||||
"Interatomic potentials (force fields)"_#ff
|
||||
"Atom creation"_#create
|
||||
"Ensembles, constraints, and boundary conditions"_#ensemble
|
||||
"Integrators"_#integrate
|
||||
"Diagnostics"_#diag
|
||||
"Output"_#output
|
||||
"Multi-replica models"_#replica
|
||||
"Pre- and post-processing"_#prepost
|
||||
"Specialized features (beyond MD itself)"_#special :ul
|
||||
|
||||
:line
|
||||
|
||||
General features :h4,link(general)
|
||||
|
||||
runs on a single processor or in parallel
|
||||
distributed-memory message-passing parallelism (MPI)
|
||||
spatial-decomposition of simulation domain for parallelism
|
||||
open-source distribution
|
||||
highly portable C++
|
||||
optional libraries used: MPI and single-processor FFT
|
||||
GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features
|
||||
easy to extend with new features and functionality
|
||||
runs from an input script
|
||||
syntax for defining and using variables and formulas
|
||||
syntax for looping over runs and breaking out of loops
|
||||
run one or multiple simulations simultaneously (in parallel) from one script
|
||||
build as library, invoke LAMMPS thru library interface or provided Python wrapper
|
||||
couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
|
||||
|
||||
Particle and model types :h4,link(particle)
|
||||
("atom style"_atom_style.html command)
|
||||
|
||||
atoms
|
||||
coarse-grained particles (e.g. bead-spring polymers)
|
||||
united-atom polymers or organic molecules
|
||||
all-atom polymers, organic molecules, proteins, DNA
|
||||
metals
|
||||
granular materials
|
||||
coarse-grained mesoscale models
|
||||
finite-size spherical and ellipsoidal particles
|
||||
finite-size line segment (2d) and triangle (3d) particles
|
||||
point dipole particles
|
||||
rigid collections of particles
|
||||
hybrid combinations of these :ul
|
||||
|
||||
Interatomic potentials (force fields) :h4,link(ff)
|
||||
("pair style"_pair_style.html, "bond style"_bond_style.html,
|
||||
"angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
|
||||
"improper style"_improper_style.html, "kspace style"_kspace_style.html
|
||||
commands)
|
||||
|
||||
pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
|
||||
Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
|
||||
charged pairwise potentials: Coulombic, point-dipole
|
||||
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
|
||||
embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
|
||||
REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
|
||||
long-range interactions for charge, point-dipoles, and LJ dispersion: \
|
||||
Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
|
||||
polarization models: "QEq"_fix_qeq.html, \
|
||||
"core/shell model"_Section_howto.html#howto_26, \
|
||||
"Drude dipole model"_Section_howto.html#howto_27
|
||||
charge equilibration (QEq via dynamic, point, shielded, Slater methods)
|
||||
coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
|
||||
mesoscopic potentials: granular, Peridynamics, SPH
|
||||
electron force field (eFF, AWPMD)
|
||||
bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
|
||||
quartic (breakable)
|
||||
angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \
|
||||
class 2 (COMPASS)
|
||||
dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
|
||||
class 2 (COMPASS), OPLS
|
||||
improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
|
||||
polymer potentials: all-atom, united-atom, bead-spring, breakable
|
||||
water potentials: TIP3P, TIP4P, SPC
|
||||
implicit solvent potentials: hydrodynamic lubrication, Debye
|
||||
force-field compatibility with common CHARMM, AMBER, DREIDING, \
|
||||
OPLS, GROMACS, COMPASS options
|
||||
access to "KIM archive"_http://openkim.org of potentials via \
|
||||
"pair kim"_pair_kim.html
|
||||
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
|
||||
potentials can be used in one simulation
|
||||
overlaid potentials: superposition of multiple pair potentials :ul
|
||||
|
||||
Atom creation :h4,link(create)
|
||||
("read_data"_read_data.html, "lattice"_lattice.html,
|
||||
"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
|
||||
"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
|
||||
|
||||
read in atom coords from files
|
||||
create atoms on one or more lattices (e.g. grain boundaries)
|
||||
delete geometric or logical groups of atoms (e.g. voids)
|
||||
replicate existing atoms multiple times
|
||||
displace atoms :ul
|
||||
|
||||
Ensembles, constraints, and boundary conditions :h4,link(ensemble)
|
||||
("fix"_fix.html command)
|
||||
|
||||
2d or 3d systems
|
||||
orthogonal or non-orthogonal (triclinic symmetry) simulation domains
|
||||
constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
|
||||
thermostatting options for groups and geometric regions of atoms
|
||||
pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
|
||||
simulation box deformation (tensile and shear)
|
||||
harmonic (umbrella) constraint forces
|
||||
rigid body constraints
|
||||
SHAKE bond and angle constraints
|
||||
Monte Carlo bond breaking, formation, swapping
|
||||
atom/molecule insertion and deletion
|
||||
walls of various kinds
|
||||
non-equilibrium molecular dynamics (NEMD)
|
||||
variety of additional boundary conditions and constraints :ul
|
||||
|
||||
Integrators :h4,link(integrate)
|
||||
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
|
||||
|
||||
velocity-Verlet integrator
|
||||
Brownian dynamics
|
||||
rigid body integration
|
||||
energy minimization via conjugate gradient or steepest descent relaxation
|
||||
rRESPA hierarchical timestepping
|
||||
rerun command for post-processing of dump files :ul
|
||||
|
||||
Diagnostics :h4,link(diag)
|
||||
|
||||
see various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
|
||||
|
||||
Output :h4,link(output)
|
||||
("dump"_dump.html, "restart"_restart.html commands)
|
||||
|
||||
log file of thermodynamic info
|
||||
text dump files of atom coords, velocities, other per-atom quantities
|
||||
binary restart files
|
||||
parallel I/O of dump and restart files
|
||||
per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
|
||||
user-defined system-wide (log file) or per-atom (dump file) calculations
|
||||
spatial and time averaging of per-atom quantities
|
||||
time averaging of system-wide quantities
|
||||
atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
|
||||
|
||||
Multi-replica models :h4,link(replica)
|
||||
|
||||
"nudged elastic band"_neb.html
|
||||
"parallel replica dynamics"_prd.html
|
||||
"temperature accelerated dynamics"_tad.html
|
||||
"parallel tempering"_temper.html :ul
|
||||
|
||||
Pre- and post-processing :h4,link(prepost)
|
||||
|
||||
A handful of pre- and post-processing tools are packaged with LAMMPS,
|
||||
some of which can convert input and output files to/from formats used
|
||||
by other codes; see the "Toos"_Tools.html doc page. :ulb,l
|
||||
|
||||
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. :l,ule
|
||||
|
||||
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
|
||||
:link(python,http://www.python.org)
|
||||
|
||||
Specialized features :h4,link(special)
|
||||
|
||||
LAMMPS can be built with optional packages which implement a variety
|
||||
of additional capabilities. See the "Packages"_Packages.html doc
|
||||
page for details.
|
||||
|
||||
These are LAMMPS capabilities which you may not think of as typical
|
||||
classical MD options:
|
||||
|
||||
"static"_balance.html and "dynamic load-balancing"_fix_balance.html
|
||||
"generalized aspherical particles"_body.html
|
||||
"stochastic rotation dynamics (SRD)"_fix_srd.html
|
||||
"real-time visualization and interactive MD"_fix_imd.html
|
||||
calculate "virtual diffraction patterns"_compute_xrd.html
|
||||
"atom-to-continuum coupling"_fix_atc.html with finite elements
|
||||
coupled rigid body integration via the "POEMS"_fix_poems.html library
|
||||
"QM/MM coupling"_fix_qmmm.html
|
||||
Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_swap.html
|
||||
"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
|
||||
"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
|
||||
"Peridynamics mesoscale modeling"_pair_peri.html
|
||||
"Lattice Boltzmann fluid"_fix_lb_fluid.html
|
||||
"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
|
||||
"two-temperature electron model"_fix_ttm.html :ul
|
||||
|
|
@ -0,0 +1,83 @@
|
|||
"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
LAMMPS non-features :h3
|
||||
|
||||
LAMMPS is designed to be a fast, parallel engine for molecular
|
||||
dynamics (MD) simulations. It provides only a modest amount of
|
||||
functionality for setting up simulations and analyzing their output.
|
||||
|
||||
Specifically, LAMMPS does not:
|
||||
|
||||
run thru a GUI
|
||||
build molecular systems
|
||||
assign force-field coefficients automagically
|
||||
perform sophisticated analyses of your MD simulation
|
||||
visualize your MD simulation interactively
|
||||
plot your output data :ul
|
||||
|
||||
Here are suggestions on how to perform these tasks:
|
||||
|
||||
GUI: LAMMPS can be built as a library and a Python wrapper that wraps
|
||||
the library interface is provided. Thus, GUI interfaces can be
|
||||
written in Python (or C or C++ if desired) that run LAMMPS and
|
||||
visualize or plot its output. Examples of this are provided in the
|
||||
python directory and described on the "Python"_Python.html doc
|
||||
page. :ulb,l
|
||||
|
||||
Builder: Several pre-processing tools are packaged with LAMMPS. Some
|
||||
of them convert input files in formats produced by other MD codes such
|
||||
as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them
|
||||
are simple programs that will build simple molecular systems, such as
|
||||
linear bead-spring polymer chains. The moltemplate program is a true
|
||||
molecular builder that will generate complex molecular models. See
|
||||
the "Tools"_Tools.html doc page for details on tools packaged with
|
||||
LAMMPS. The "Pre/post processing
|
||||
page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
|
||||
describes a variety of 3rd party tools for this task. :l
|
||||
|
||||
Force-field assignment: The conversion tools described in the previous
|
||||
bullet for CHARMM, AMBER, and Insight will also assign force field
|
||||
coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
|
||||
or Accelerys force field files. :l
|
||||
|
||||
Simulation analyses: If you want to perform analyses on-the-fly as
|
||||
your simulation runs, see the "compute"_compute.html and
|
||||
"fix"_fix.html doc pages, which list commands that can be used in a
|
||||
LAMMPS input script. Also see the "Modify"_Modify.html doc page for
|
||||
info on how to add your own analysis code or algorithms to LAMMPS.
|
||||
For post-processing, LAMMPS output such as "dump file
|
||||
snapshots"_dump.html can be converted into formats used by other MD or
|
||||
post-processing codes. Some post-processing tools packaged with
|
||||
LAMMPS will do these conversions. Scripts provided with the {python}
|
||||
tool in the tools directory can extract and massage data in dump files
|
||||
to make it easier to import into other programs. See the
|
||||
"Tools"_Tools.html doc page for details on these various options. :l
|
||||
|
||||
Visualization: LAMMPS can produce JPG or PNG snapshot images
|
||||
on-the-fly via its "dump image"_dump_image.html command. For
|
||||
high-quality, interactive visualization there are many excellent and
|
||||
free tools available. See the "Other Codes
|
||||
page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
|
||||
visualization packages that can use LAMMPS output data. :l
|
||||
|
||||
Plotting: See the next bullet about Pizza.py as well as the
|
||||
"Python"_Python.html doc page for examples of plotting LAMMPS output.
|
||||
Scripts provided with the {python} tool in the tools directory will
|
||||
extract and massage data in log and dump files to make it easier to
|
||||
analyze and plot. See the "Tools"_Tools.html doc page for more
|
||||
discussion of the various tools. :l
|
||||
|
||||
Pizza.py: Our group has also written a separate toolkit called
|
||||
"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
|
||||
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
|
||||
simulations. It thus provides some functionality for several of the
|
||||
above bullets. Pizza.py is written in "Python"_http://www.python.org
|
||||
and is available for download from "this
|
||||
page"_http://www.cs.sandia.gov/~sjplimp/download.html. :l,ule
|
||||
|
|
@ -0,0 +1,44 @@
|
|||
"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
LAMMPS open-source license :h3
|
||||
|
||||
LAMMPS is a freely-available open-source code, distributed under the
|
||||
terms of the "GNU Public License"_gnu, which means you can use or
|
||||
modify the code however you wish.
|
||||
|
||||
LAMMPS comes with no warranty of any kind. As each source file states
|
||||
in its header, it is a copyrighted code that is distributed free-of-
|
||||
charge, under the terms of the "GNU Public License"_gnu (GPL). This
|
||||
is often referred to as open-source distribution - see
|
||||
"www.gnu.org"_gnuorg or "www.opensource.org"_opensource. The legal
|
||||
text of the GPL is in the LICENSE file included in the LAMMPS
|
||||
distribution.
|
||||
|
||||
:link(gnu,http://www.gnu.org/copyleft/gpl.html)
|
||||
:link(gnuorg,http://www.gnu.org)
|
||||
:link(opensource,http://www.opensource.org)
|
||||
|
||||
Here is a summary of what the GPL means for LAMMPS users:
|
||||
|
||||
(1) Anyone is free to use, modify, or extend LAMMPS in any way they
|
||||
choose, including for commercial purposes.
|
||||
|
||||
(2) If you distribute a modified version of LAMMPS, it must remain
|
||||
open-source, meaning you distribute it under the terms of the GPL.
|
||||
You should clearly annotate such a code as a derivative version of
|
||||
LAMMPS.
|
||||
|
||||
(3) If you release any code that includes LAMMPS source code, then it
|
||||
must also be open-sourced, meaning you distribute it under the terms
|
||||
of the GPL.
|
||||
|
||||
(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
|
||||
source file headers (including the copyright and GPL notices) should
|
||||
remain part of the code.
|
||||
|
|
@ -0,0 +1,59 @@
|
|||
"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
Overview of LAMMPS :h3
|
||||
|
||||
LAMMPS is a classical molecular dynamics (MD) code that models
|
||||
ensembles of particles in a liquid, solid, or gaseous state. It can
|
||||
model atomic, polymeric, biological, solid-state (metals, ceramics,
|
||||
oxides), granular, coarse-grained, or macroscopic systems using a
|
||||
variety of interatomic potentials (force fields) and boundary
|
||||
conditions. The majority of these models are for materials of various
|
||||
kinds. It can model 2d or 3d systems with only a few particles up to
|
||||
millions or billions.
|
||||
|
||||
LAMMPS can be built and run on a laptop or destop machine, but is
|
||||
designed for parallel computers. It will run on any parallel machine
|
||||
that supports the "MPI"_mpi message-passing library. This includes
|
||||
shared-memory boxes and distributed-memory clusters and
|
||||
supercomputers.
|
||||
|
||||
:link(mpi,http://www-unix.mcs.anl.gov/mpi)
|
||||
|
||||
LAMMPS is written in C++. Earlier versions were written in F77 and
|
||||
F90. See the "History page"_http://lammps.sandia.gov/history.html of
|
||||
the website for details. All versions can be downloaded from the
|
||||
"LAMMPS website"_lws.
|
||||
|
||||
LAMMPS is designed to be easy to modify or extend with new
|
||||
capabilities, such as new force fields, atom types, boundary
|
||||
conditions, or diagnostics. See the "Modify"_Modify.html doc page for
|
||||
more details.
|
||||
|
||||
In the most general sense, LAMMPS integrates Newton's equations of
|
||||
motion for a collection of interacting particles. A single particle
|
||||
can be an atom or molecule or electron, a coarse-grained cluster of
|
||||
atoms, or a mesoscopic or macroscopic clump of material. The
|
||||
interaction models that LAMMPS includes are mostly short-range in
|
||||
nature; some long-range models are included as well.
|
||||
|
||||
LAMMPS uses neighbor lists to keep track of nearby particles. The
|
||||
lists are optimized for systems with particles that are repulsive at
|
||||
short distances, so that the local density of particles never becomes
|
||||
too large. This is in contrast to methods used for modeling plasmas
|
||||
or gravitational bodies (e.g. galaxy formation).
|
||||
|
||||
On parallel machines, LAMMPS uses spatial-decomposition techniques to
|
||||
partition the simulation domain into small sub-domains of equal
|
||||
computational cost, one of which is assigned to each processor.
|
||||
Processors communicate and store "ghost" atom information for atoms
|
||||
that border their sub-domain.
|
||||
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,42 @@
|
|||
"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
Additional website links :h3
|
||||
|
||||
The "LAMMPS website"_lws has a variety of additional info about
|
||||
LAMMPS, beyond what is in this manual. Some of the other pages in
|
||||
this Intr are included in this list.
|
||||
|
||||
"Brief intro and recently added significant features"_lws
|
||||
"List of features"_http://lammps.sandia.gov/features.html
|
||||
"List of non-features"_http://lammps.sandia.gov/non_features.html
|
||||
"Recent bug fixes and new features"_http://lammps.sandia.gov/bug.html :ul
|
||||
|
||||
"Download info"_http://lammps.sandia.gov/download.html
|
||||
"GitHub site"_https://github.com/lammps/lammps
|
||||
"SourceForge site"_https://sourceforge.net/projects/lammps
|
||||
"LAMMPS open-source license"_http://lammps.sandia.gov/open_source.html :ul
|
||||
|
||||
"Glossary of MD terms relevant to LAMMPS"_http://lammps.sandia.gov/glossary.html
|
||||
"LAMMPS highlights with images"_http://lammps.sandia.gov/pictures.html
|
||||
"LAMMPS highlights with movies"_http://lammps.sandia.gov/movies.html
|
||||
"Mail list"_http://lammps.sandia.gov/mail.html
|
||||
"Workshops"_http://lammps.sandia.gov/workshops.html
|
||||
"Tutorials"_http://lammps.sandia.gov/tutorials.html
|
||||
"Developer guide"_http://lammps.sandia.gov/Developer.pdf :ul
|
||||
|
||||
"Pre- and post-processing tools for LAMMPS"_http://lammps.sandia.gov/prepost.html
|
||||
"Other software usable with LAMMPS"_http://lammps.sandia.gov/offsite.html
|
||||
"Viz tools usable with LAMMPS"_http://lammps.sandia.gov/viz.html :ul
|
||||
|
||||
"Benchmark performance"_http://lammps.sandia.gov/bench.html
|
||||
"Publications that have cited LAMMPS"_http://lammps.sandia.gov/papers.html
|
||||
"Authors of LAMMPS"_http://lammps.sandia.gov/authors.html
|
||||
"History of LAMMPS development"_http://lammps.sandia.gov/history.html
|
||||
"Funding for LAMMPS"_http://lammps.sandia.gov/funding.html :ul
|
||||
|
|
@ -21,7 +21,7 @@
|
|||
<H1></H1>
|
||||
|
||||
LAMMPS Documentation :c,h1
|
||||
16 Mar 2018 version :c,h2
|
||||
16 Jul 2018 version :c,h2
|
||||
|
||||
"What is a LAMMPS version?"_Manual_version.html
|
||||
|
||||
|
|
@ -29,15 +29,18 @@ LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
|
|||
Simulator.
|
||||
|
||||
LAMMPS is a classical molecular dynamics simulation code designed to
|
||||
run efficiently on parallel computers. It was developed originally at
|
||||
Sandia National Laboratories, a US Department of Energy facility, with
|
||||
funding from the DOE. It is an open-source code, distributed freely
|
||||
under the terms of the GNU Public License (GPL).
|
||||
run efficiently on parallel computers. It is primarily used for
|
||||
materials modeling of various kinds. It was developed originally at
|
||||
Sandia National Laboratories, a US Department of Energy facility. The
|
||||
majority of funding for LAMMPS has come from the US Department of
|
||||
Energy (DOE). LAMMPS is an open-source code, distributed freely under
|
||||
the terms of the GNU Public License (GPL).
|
||||
|
||||
The "LAMMPS website"_lws has information about the code authors, a
|
||||
"mail list"_http://lammps.sandia.gov where users can post questions,
|
||||
and a "GitHub site"https://github.com/lammps/lammps where all LAMMPS
|
||||
development is coordinated.
|
||||
The "LAMMPS website"_lws has a variety of information about the code.
|
||||
It includes links to an on-line version of this manual, a "mail
|
||||
list"_http://lammps.sandia.gov/mail.html where users can post
|
||||
questions, and a "GitHub site"https://github.com/lammps/lammps where
|
||||
all LAMMPS development is coordinated.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue