LAMMPS 9Jan09

Portable Large-scale Atomic/Molecular Massively Parallel Simulator
LAMMPS is a classical molecular dynamics (MD) code. As the name implies, it's designed to run well on parallel machines, but it also runs fine on single-processor desktop machines.

LAMMPS is very portable. It should build on any platform with a C++ compiler. The GNU g++ compiler or commercial compilers work fine. LAMMPS has been built for several parallel and desktop machines, that run Mac OS X, Unix or Linux variants.

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grain systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the mesoscale or continuum levels.

LAMMPS runs on single-processor machines or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

Main features of LAMMPS:

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 needed: MPI and single-processor FFT

in parallel, run one or multiple simulations simultaneously

easy to extend with new features and functionality

atoms, polymers, molecules, metals, granular particles, coarse-grained particles, ellipsoids, point-dipoles, or hybrid combinations of these

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, 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

overlayed 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 force-field compatibility

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 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) constraints

non-equilibrium molecular dynamics (NEMD)

variety of additional boundary conditions and constraints

velocity-Verlet integrator

Brownian dynamics

energy minimization via conjugate-gradient relaxation

rRESPA hierarchical timestepping

parallel tempering (replica exchange)

run multiple independent simulations simultaneously

log file of thermodynanmic 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


What's New in This Release:

New release of LAMMPS (C++ version). 138,720 lines of code in src dir with all packages included (but no library source files).

IMPORTANT: The syntax of the following commands has changed: pair_style gran/hooke, pair_style gran/hooke/history, pair_style gran/hertz/history, and special_bonds. The keyword "tag" in the dump custom command has been changed to "id". The default for specifying layer thicknesses in the fix ave/spatial command has been changed from box units to lattice units.