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			"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_start.html :c

			:link(lws,http://lammps.sandia.gov)
			:link(ld,Manual.html)
			:link(lc,Section_commands.html#comm)

			:line

			1. Introduction :h3

			These sections provide an overview of what LAMMPS can and can't do,
			describe what it means for LAMMPS to be an open-source code, and
			acknowledge the funding and people who have contributed to LAMMPS over
			the years.

			1.1 "What is LAMMPS"_#1_1
			1.2 "LAMMPS features"_#1_2
			1.3 "LAMMPS non-features"_#1_3
			1.4 "Open source distribution"_#1_4
			1.5 "Acknowledgments and citations"_#1_5 :all(b)

			:line

			1.1 What is LAMMPS :link(1_1),h4

			LAMMPS is a classical molecular dynamics code that models an ensemble
			of particles in a liquid, solid, or gaseous state. It can model
			atomic, polymeric, biological, metallic, granular, and coarse-grained
			systems using a variety of force fields and boundary conditions.

			For examples of LAMMPS simulations, see the Publications page of the
			"LAMMPS WWW Site"_lws.

			LAMMPS runs efficiently on single-processor desktop or laptop
			machines, but is designed for parallel computers. It will run on any
			parallel machine that compiles C++ and supports the "MPI"_mpi
			message-passing library. This includes distributed- or shared-memory
			parallel machines and Beowulf-style clusters.

			:link(mpi,http://www-unix.mcs.anl.gov/mpi)

			LAMMPS can model systems with only a few particles up to millions or
			billions. See "this section"_Section_perf.html for information on LAMMPS
			performance and scalability, or the Benchmarks section of the "LAMMPS
			WWW Site"_lws.

			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. See "this section"_#1_4 for a brief
			discussion of the open-source philosophy.

			:link(gnu,http://www.gnu.org/copyleft/gpl.html)

			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 "this section"_Section_modify.html for
			more details.

			The current version of LAMMPS is written in C++. Earlier versions
			were written in F77 and F90. See "this section"_Section_history.html
			for more information on different versions. All versions can be
			downloaded from the "LAMMPS WWW Site"_lws.

			LAMMPS was originally developed under a US Department of Energy CRADA
			(Cooperative Research and Development Agreement) between two DOE labs
			and 3 companies. It is distributed by "Sandia National Labs"_snl.
			See "this section"_#1_5 for more information on LAMMPS funding and
			individuals who have contributed to LAMMPS.

			:link(snl,http://www.sandia.gov)

			In the most general sense, LAMMPS integrates Newton's equations of
			motion for collections of atoms, molecules, or macroscopic particles
			that interact via short- or long-range forces with a variety of
			initial and/or boundary conditions. For computational efficiency
			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. On parallel machines, LAMMPS uses spatial-decomposition
			techniques to partition the simulation domain into small 3d
			sub-domains, one of which is assigned to each processor. Processors
			communicate and store "ghost" atom information for atoms that border
			their sub-domain. LAMMPS is most efficient (in a parallel sense) for
			systems whose particles fill a 3d rectangular box with roughly uniform
			density. Papers with technical details of the algorithms used in
			LAMMPS are listed in "this section"_#1_5.

			:line

			1.2 LAMMPS features :link(1_2),h4

			This section highlights LAMMPS features, with pointers to specific
			commands which give more details. If LAMMPS doesn't have your
			favorite interatomic potential, boundary condition, or atom type, see
			"this section"_Section_modify.html, which describes how you can add it to
			LAMMPS.

			Kinds of systems LAMMPS can simulate: :h4
			("atom style"_atom_style.html command)

			atomic (e.g. box of Lennard-Jonesium)
			bead-spring polymers
			united-atom polymers or organic molecules
			all-atom polymers, organic molecules, proteins, DNA
			metals
			granular materials
			coarse-grained mesoscale models
			ellipsoidal particles
			point dipolar particles
			hybrid systems :ul

			Force fields: :h4
			("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, \
			Yukawa, soft, class 2 (COMPASS), tabulated
			charged pairwise potentials: Coulombic, point-dipole
			manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
			Stillinger-Weber, Tersoff, AI-REBO
			coarse-grain potentials: granular, DPD, GayBerne, REsquared, colloidal
			bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
			quartic (breakable)
			angle potentials: harmonic, CHARMM, cosine, cosine/squared, \
			class 2 (COMPASS)
			dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
			class 2 (COMPASS), OPLS
			improper potentials: harmonic, cvff, class 2 (COMPASS)
			hybrid potentials: multiple pair, bond, angle, dihedral, improper \
			potentials can be used in one simulation
			overlaid potentials: superposition of multiple pair potentials
			polymer potentials: all-atom, united-atom, bead-spring, breakable
			water potentials: TIP3P, TIP4P, SPC
			implicit solvent potentials: hydrodynamic lubrication, Debye
			long-range Coulombics and dispersion: Ewald, \
			PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones
			CHARMM, AMBER, OPLS, GROMACS, force-field compatibility :ul

			Creation of atoms: :h4
			("read_data"_read_data.html, "lattice"_lattice.html,
			"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
			"displace_atoms"_displace_atoms.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)
			displace atoms :ul

			Ensembles, constraints, and boundary conditions: :h4
			("fix"_fix.html command)

			2d or 3d systems
			orthogonal or non-orthogonal (triclinic symmetry) simulation domains
			constant NVE, NVT, NPT, NPH 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
			independent or coupled rigid body integration
			SHAKE bond and angle constraints
			walls of various kinds
			targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints
			non-equilibrium molecular dynamics (NEMD)
			variety of additional boundary conditions and constraints :ul

			Integrators: :h4
			("run"_run.html, "run_style"_run_style.html, "temper"_temper.html commands)

			velocity-Verlet integrator
			Brownian dynamics
			energy minimization via conjugate gradient relaxation
			rRESPA hierarchical timestepping
			parallel tempering (replica exchange)
			run multiple independent simulations simultaneously :ul

			Output: :h4
			("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
			per-atom quantities (energy, stress, centro-symmetry parameter, 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 formats :ul

			Pre- and post-processing: :h4

			Our group has also written and released a separate toolkit called
			"Pizza.py"_pizza which provides tools for doing setup, analysis,
			plotting, and visualization for LAMMPS simulations. Pizza.py is
			written in "Python"_python and is available for download from "the
			Pizza.py WWW site"_pizza.

			:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)
			:link(python,http://www.python.org)

			:line

			1.3 LAMMPS non-features :link(1_3),h4

			LAMMPS is designed to efficiently compute Newton's equations of motion
			for a system of interacting particles. Many of the tools needed to
			pre- and post-process the data for such simulations are not included
			in the LAMMPS kernel for several reasons:

			the desire to keep LAMMPS simple
			they are not parallel operations
			other codes already do them
			limited development resources :ul

			Specifically, LAMMPS itself 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
			plot your output data :ul

			A few tools for pre- and post-processing tasks are provided as part of
			the LAMMPS package; they are described in "this
			section"_Section_tools.html. However, many people use other codes or
			write their own tools for these tasks.

			As noted above, our group has also written and released a separate
			toolkit called "Pizza.py"_pizza which addresses some of the listed
			bullets. It 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.

			LAMMPS requires as input a list of initial atom coordinates and types,
			molecular topology information, and force-field coefficients assigned
			to all atoms and bonds. LAMMPS will not build molecular systems and
			assign force-field parameters for you.

			For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html
			command which places atoms on solid-state lattices (fcc, bcc,
			user-defined, etc). Assigning small numbers of force field
			coefficients can be done via the "pair coeff"_pair_coeff.html, "bond
			coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, etc commands.
			For molecular systems or more complicated simulation geometries, users
			typically use another code as a builder and convert its output to
			LAMMPS input format, or write their own code to generate atom
			coordinate and molecular topology for LAMMPS to read in.

			For complicated molecular systems (e.g. a protein), a multitude of
			topology information and hundreds of force-field coefficients must
			typically be specified. We suggest you use a program like
			"CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup
			such problems and dump its information to a file. You can then
			reformat the file as LAMMPS input. Some of the tools in "this
			section"_Section_tools.html can assist in this process.

			Similarly, LAMMPS creates output files in a simple format. Most users
			post-process these files with their own analysis tools or re-format
			them for input into other programs, including visualization packages.
			If you are convinced you need to compute something on-the-fly as
			LAMMPS runs, see "this section"_Section_modify.html for a discussion
			of how you can use the "dump"_dump.html and "compute"_compute.html and
			"fix"_fix.html commands to print out data of your choosing. Keep in
			mind that complicated computations can slow down the molecular
			dynamics timestepping, particularly if the computations are not
			parallel, so it is often better to leave such analysis to
			post-processing codes.

			A very simple (yet fast) visualizer is provided with the LAMMPS
			package - see the "xmovie"_Section_tools.html#xmovie tool in "this
			section"_Section_tools.html. It creates xyz projection views of
			atomic coordinates and animates them. We find it very useful for
			debugging purposes. For high-quality visualization we recommend the
			following packages:

			"VMD"_http://www.ks.uiuc.edu/Research/vmd
			"AtomEye"_http://164.107.79.177/Archive/Graphics/A
			"PyMol"_http://pymol.sourceforge.net
			"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
			"RasMol"_http://www.openrasmol.org :ul

			Other features that LAMMPS does not yet (and may never) support are
			discussed in "this section"_Section_history.html.

			Finally, these are freely-available molecular dynamics codes, most of
			them parallel, which may be well-suited to the problems you want to
			model. They can also be used in conjunction with LAMMPS to perform
			complementary modeling tasks.

			"CHARMM"_charmm
			"AMBER"_amber
			"NAMD"_namd
			"NWCHEM"_nwchem
			"DL_POLY"_dlpoly
			"Tinker"_tinker :ul

			:link(charmm,http://www.scripps.edu/brooks)
			:link(amber,http://amber.scripps.edu)
			:link(namd,http://www.ks.uiuc.edu/Research/namd/)
			:link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
			:link(dlpoly,http://www.cse.clrc.ac.uk/msi/software/DL_POLY)
			:link(tinker,http://dasher.wustl.edu/tinker)

			CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
			modeling biological molecules. CHARMM and AMBER use
			atom-decomposition (replicated-data) strategies for parallelism; NAMD
			and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
			Tinker is a serial code. DL_POLY includes potentials for a variety of
			biological and non-biological materials; both a replicated-data and
			spatial-decomposition version exist.

			:line

			1.4 Open source distribution :link(1_4),h4

			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 for more
			details. The legal text of the GPL is in the LICENSE file that is
			included in the LAMMPS distribution.

			: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.

			In the spirit of an open-source code, these are various ways you can
			contribute to making LAMMPS better. You can send email to the
			"developers"_http://lammps.sandia.gov/authors.html on any of these
			items.

			Point prospective users to the "LAMMPS WWW Site"_lws. Mention it in
			talks or link to it from your WWW site. :ulb,l

			If you find an error or omission in this manual or on the "LAMMPS WWW
			Site"_lws, or have a suggestion for something to clarify or include,
			send an email to the
			"developers"_http://lammps.sandia.gov/authors.html. :l

			If you find a bug, "this section"_Section_errors.html#9_2 describes
			how to report it. :l

			If you publish a paper using LAMMPS results, send the citation (and
			any cool pictures or movies if you like) to add to the Publications,
			Pictures, and Movies pages of the "LAMMPS WWW Site"_lws, with links
			and attributions back to you. :l

			Create a new Makefile.machine that can be added to the src/MAKE
			directory. :l

			The tools sub-directory of the LAMMPS distribution has various
			stand-alone codes for pre- and post-processing of LAMMPS data. More
			details are given in "this section"_Section_tools.html. If you write
			a new tool that users will find useful, it can be added to the LAMMPS
			distribution. :l

			LAMMPS is designed to be easy to extend with new code for features
			like potentials, boundary conditions, diagnostic computations, etc.
			"This section"_Section_modify.html gives details. If you add a
			feature of general interest, it can be added to the LAMMPS
			distribution. :l

			The Benchmark page of the "LAMMPS WWW Site"_lws lists LAMMPS
			performance on various platforms. The files needed to run the
			benchmarks are part of the LAMMPS distribution. If your machine is
			sufficiently different from those listed, your timing data can be
			added to the page. :l

			You can send feedback for the User Comments page of the "LAMMPS WWW
			Site"_lws. It might be added to the page. No promises. :l

			Cash. Small denominations, unmarked bills preferred. Paper sack OK.
			Leave on desk. VISA also accepted. Chocolate chip cookies
			encouraged. :ule,l

			:line

			1.5 Acknowledgments and citations :h4,link(1_5)

			LAMMPS development has been funded by the "US Department of
			Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
			programs and its "OASCR"_oascr and "OBER"_ober offices.

			Specifically, work on the latest version was funded in part by the US
			Department of Energy's Genomics:GTL program
			("www.doegenomestolife.org"_gtl) under the "project"_ourgtl, "Carbon
			Sequestration in Synechococcus Sp.: From Molecular Machines to
			Hierarchical Modeling".

			:link(doe,http://www.doe.gov)
			:link(gtl,http://www.doegenomestolife.org)
			:link(ourgtl,http://www.genomes2life.org)
			:link(oascr,http://www.sc.doe.gov/ascr/home.html)
			:link(ober,http://www.er.doe.gov/production/ober/ober_top.html)

			The following papers describe the parallel algorithms used in LAMMPS.

			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).

			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"_lws
			(http://lammps.sandia.gov).

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

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

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

			:link(sjp,http://www.cs.sandia.gov/~sjplimp)

			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)
			CG-CMM user 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)
			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)
			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) : :tb(s=:)

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

			John Carpenter (Mayo Clinic, formerly at Cray Research)
			Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
			Steve Lustig (Dupont)
			Jim Belak (LLNL) :ul

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