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

This section provides an overview of what LAMMPS can and can't do,
describes what it means for LAMMPS to be an open-source code, and
acknowledges the funding and people who have contributed to LAMMPS
over the years.

1.1 "What is LAMMPS"_#intro_1
1.2 "LAMMPS features"_#intro_2
1.3 "LAMMPS non-features"_#intro_3
1.4 "Open source distribution"_#intro_4
1.5 "Acknowledgments and citations"_#intro_5 :all(b)

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1.1 What is LAMMPS :link(intro_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 "Section_perf"_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"_#intro_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 "Section_modify"_Section_modify.html
for more details.

The current version of LAMMPS is written in C++.  Earlier versions
were written in F77 and F90.  See
"Section_history"_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"_#intro_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"_#intro_5.

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1.2 LAMMPS features :link(intro_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
"Section_modify"_Section_modify.html, which describes how you can add
it to LAMMPS.

General features :h5

  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(R) Xeon Phi(TM) coprocessors, 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 :h5
("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

Force fields :h5
("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 :h5
("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 :h5
("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 :h5
("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 :h5

  see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul

Output :h5
("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 :h5

"nudged elastic band"_neb.html
"parallel replica dynamics"_prd.html
"temperature accelerated dynamics"_tad.html
"parallel tempering"_temper.html

Pre- and post-processing :h5

Various pre- and post-processing serial tools are packaged
with LAMMPS; see these "doc pages"_Section_tools.html. :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 :h5

These are LAMMPS capabilities which you may not think of as typical
molecular dynamics 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
"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_swap.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

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1.3 LAMMPS non-features :link(intro_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 "Section_modify"_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://mt.seas.upenn.edu/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 "Section_history"_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(intro_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, "Section_errors 2"_Section_errors.html#err_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 "Section_tools"_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

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1.5 Acknowledgments and citations :h4,link(intro_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 paper describe the basic parallel algorithms used in
LAMMPS.  If you use LAMMPS results in your published work, please cite
this paper and include a pointer to the "LAMMPS WWW Site"_lws
(http://lammps.sandia.gov):

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

Other papers describing specific algorithms used in LAMMPS are listed
under the "Citing LAMMPS link"_http://lammps.sandia.gov/cite.html of
the LAMMPS WWW page.

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

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

Steve Plimpton, sjplimp at sandia.gov
Aidan Thompson, athomps at sandia.gov
Paul Crozier, pscrozi at sandia.gov :ul

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 and USER-OMP packages
Roy Pollock (LLNL), Ewald and PPPM solvers
Mike Brown (ORNL), brownw at ornl.gov, GPU package
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 package
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 Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package :ul

As discussed in "Section_history"_Section_history.html, 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 (LLNL) :ul