Topic outline

  • General

  • Siesta

    SIESTA is both a method to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA's efficiency stems from the use of strictly localized basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems.

    SIESTA require an input file in fdf format.  Some examples and a batch submission script are provided below.

  • GARFfield

    GARFfield is a multi-platform, multi-objective parallel hybrid genetic algorithm (GA) / conjugate-gradient (CG) based force field optimization framework.  It utilizes LAMMPS for calculating the MD part.

    GARFfield requires atleast four files as input;

    • params file - Describes the parameter set you'd like to optimize.
    • forcefield file - The force field you which to optimize.
    • training_set file - Computaional or experimental data you which to optimize against.
    • geo file - Geometry file which describes the molecular system.
  • Quantum Espresso

    Quantum Espresso s an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

  • ASE - Atomic Simulation Environment

    ASE is an Atomistic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations.