LAMMPS Portable Large-scale Atomic/Molecular Massively Parallel Simulator
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simulate model modeller atom modeller particle simulator molecular simulator

LAMMPS Description

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. Here are some key 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.

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