"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,Commands_all.html)

: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"_#replica1
"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 through 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
  many-body 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"_Howto_coreshell.html, \
    "Drude dipole model"_Howto_drude.html
  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 the "OpenKIM Repository"_http://openkim.org of potentials via \
    "kim_init, kim_interactions, and kim_query"_kim_commands.html commands
  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, Parrinello/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(replica1)

"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"_Howto_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_atom_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
