1. Features and release notes

1.1. Features

The main features of Yaff are:

  • Error-free implementations of the force-field energy (and forces).
  • Full control over the convergence of long-range interactions.
  • Readable code.
  • Flexible definition of the force field through an extensible parameter file format.
  • Control of the program through a Python scripting interface.
  • Efficient evaluation of the energy, forces and virial in low-level C routines.
  • Robust geometry and cell optimization
  • Molecular dynamics (NVE, NVT and annealing).
  • Elastic constants (0K) and Hessians by taking finite differences of analytical first-order derivatives.
  • HDF5-based trajectory format.
  • Integrated atom-typing language.
  • Integrated trajectory analysis.
  • Integrated force-field parameter tuning.
  • Extensively tested code through a unit-testing framework.

Missing features (work in progress) include:

  • Parallel force evaluaton.
  • Parallel sampling schemes.

1.2. Release notes

  • Version 1.4.2 August 30, 2017
    • Numerically more stable computation of error on the conserved quantity.
  • Version 1.4.1 August 30, 2017
    • Fix corner case when writing out HDF files for the system.
    • Fix typo in install docs.
  • Version 1.4.0 August 11, 2017
    • Conda packages for Windows, Linux and OSX.
    • Fix some consistency issues with cross terms.
    • Less pedantic warnings for missing energy terms.
  • Version 1.3.0 August 5, 2017
    • Python 3 support
  • Version 1.2.0
    • Installable with pip.
    • Installable with conda.
    • Automatic deployment of new releases.
    • Fix parallel unit testing issues.
  • Version 1.1.3
    • Correct anharmonic covalent MM3 terms.
  • Version 1.1.2
    • Removed flush option from HDF5Writer.
  • Version 1.1.1
    • Fixed a few bugs in System.iter_matches.