www.freechemical.info

338 Database entries



LAMMPS


Ratings:    9  votes
Please vote:   

OS: Linux

License: Freeware, GPL

Methods: MM, MD



LAMMPS is a classical molecular dynamics code with the following functionality:

General features
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
easy to extend with new features and functionality
in parallel, run one or multiple simulations simultaneously
runs from an input script
syntax for defining and using variables and formulas
syntax for looping over runs and breaking out of loops
run a series of simluations from one script Kinds of systems LAMMPS can simulate

Kinds of systems LAMMPS can simulate
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 combinations of these

Force fields
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, ReaxFF
coarse-grain potentials: DPD, GayBerne, REsquared, colloidal
mesoscopic potentials: granular, Peridynamics
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
force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options
handful of GPU-enabled pair styles

Creation of atoms
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

Ensembles, constraints, and boundary conditions
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
rigid body integration
SHAKE bond and angle constraints
bond breaking, formation, swapping
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

Integrators
velocity-Verlet integrator
Brownian dynamics
energy minimization via conjugate gradient or steepest descent relaxation
rRESPA hierarchical timestepping
parallel tempering (replica exchange)
parallel replica dyanmics (accelerated dynamics)

Diagnostics
see the various flavors of the fix and compute commands

Output
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, 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

Specialized features
atom-to-continuum coupling with finite elements
coupled rigid body integratin via the POEMS library

http://lammps.sandia.gov/



webmaster@freechemical.info