Jumos: customisable molecular simulation package

Jumos is a package for molecular simulations written using the Julia language. It provides a set of customisable blocks for running molecular simulations, and developing novel algorithm for each part of a simulation. Every algorithm (potential computation, long range interactions, pair lists computing, outputs, etc.) can easily be customised.

Note

This package is in a very alpha stage, and still in heavy developement. Breaking changes can occurs in the API without any notice at any time.

This documentation is divided in two parts: first come the user manual, starting by some explanation about usal algorithms in simulations and an example of how we can use Jumos to run a molecular dynamic simulation. The second part is the developer documentation, exposing the internal of Jumos, and how we can use them to programm new algorithms.

Installation

Jumos uses the 0.4 prerelease version of Julia, and can be installed at julia prompt with the Pkg.add("Jumos") command. You also can run the unit tests with the Pkg.test("Jumos") command.

User manual

• Package overview
  • Simulation flow
  • Simulation example
  • Main types
• Universes
  • UnitCell
  • Topology
  • Frame
  • Interactions
  • Potentials
  • Universe type
  • Loading initial configurations from files
• Simulations
  • Molecular Dynamics
  • Computing values of interest
  • Exporting values of interest
• Propagator
  • Simulation type
• Utilities
  • Internal units
  • Interaction with others units systems
  • Periodic boundary conditions and distances computations
  • Trajectories
  • Array3D

Extending Jumos

• Extending Jumos
  • Defining a new potential
  • Algorithms for all simulations
  • Algorithms for molecular dynamics