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About

The Etomica molecular modeling framework enables object-oriented molecular simulations to be constructed using classes written in Java. It has been under development since 1997. The framework is formed from more than 1000 such classes, enabling a wide variety of simulations to be constructed. Key capabilities include the following.

Molecular Dynamics​

  • Velocity Verlet
  • Collision-based
  • Thermostats, barostats

Monte Carlo​

  • Atom moves: molecule translation, rotation,...
  • Ensembles: NVT, NVE, isobaric, grand-canonical, semigrand,...
  • Biasing methods

Potential-energy functions​

  • Soft: Lennard-Jones, Exp-6, Yukawa, WCA,...
  • Hard: Spheres, square well, tether,...
  • Electrostatics: Coulomb, point multipole, Ewald sum
  • Multibody: MEAM, Axilrod-Teller, polarizable,...
  • Intramolecular: Stretch, bending, torsion,...
  • Various realistic molecular models (e.g., GCPM water)
  • Hard or soft walls
  • Energies, forces, torques, Hessian
  • Neighbor listing

Space and Boxes​

  • 3-, 2-, or 1-dimensional systems
  • Single box for conventional simulations
  • Multiple boxes for Gibbs ensemble, parallel tempering
  • Period boundaries in all, some, or no coordinate directions
  • Deformable boundaries

Properties​

  • First- and second-derivative thermodynamic
  • Transport coefficients
  • Free energy
  • Structure
  • Uncertainty estimates for all calculations

Mode of Operation​

  • GUI-based, for interactive exploration of behavior
  • Batch, for reproducible, scripted production runs
  • Inputs and outputs may be specified in arbitrary units

Virial Coefficients​

  • Mayer-sampling Monte Carlo
  • Wheatley recursion
  • Temperature derivatives
  • Multibody potentials
  • Flexible correction
  • Nuclear quantum effects: semiclassical or path integral