Welcome to Jumos’s documentation!

Jumos is a package for molecular simulations using the Julia language. It aims at being as flexible as possible, and allowing the easy use and development of novel algorithm for each part of a simulation. Every algorithm, from potential computation, long range interactions, pair lists computing, outputs, etc. can be customised.

Jumos also includes code for trajectory analysis, either during the simulation run or by reading frames in a file.

Warning

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.

User manual

• Simulations
  • Usage example
  • Usual simulation steps
  • Creating simulations
  • Potentials
  • Exporting values of interest
  • Computing values of interest
  • Selecting the algorithms
  • Functions for algorithms selection
• Trajectories
  • Reading and writing trajectories
  • Readind and writing topologies
• Analysis
  • Base Histogram type
  • Radial distribution function
  • Density profile
• Internal units

Developer documentation

• Developer documentation
  • Atoms
  • Universe
  • Periodic boundary conditions and distances computations
  • Interaction with others units systems
  • Developping new algorithms

Installation

To install, simply run Pkg.clone(https://github.com/Luthaf/Jumos.jl) at julia prompt. You may also want to run Pkg.test("Jumos") to run the tests.

Only 0.4 julia prerelease version is supported, because Jumos makes use of features from the 0.4 version.