lammps/doc/Section_intro.txt

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

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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