example.rst

Simulation example

In |Jumos|, one run simulations by writting specials Julia scripts. A primer intoduction to the Julia language can be found here, if needed.

Lennard-Jones fluid

Here is a simple simulation script for running a simulation of a Lennard-Jones fluid at 300K.

.. literalinclude:: /../examples/lennard-jones.jl
   :language: julia
   :linenos:

Each simulation script should start by the using Jumos directive. This imports the module and the exported names in the current scope.

Then, in this script, we create two main objects: a :ref:`simulation <Type-Simulation>`, and an :ref:`universe <Type-Universe>`. The topology and the original positions for the universe are read from the same file, as an :file:`.xyz` file contains topological information (mainly the atomics names) and coordinates. The velocities are then initialized from a Boltzmann distribution at 300K.

The only interaction — a :ref:`Lennard-Jones <lennard-jones-potential>` interaction — is also added to the universe before the run. The next lines add some outputs to the simulation, namely a :ref:`trajectory <type-TrajectoryOutput>` and an :ref:`energy <type-EnergyOutput>` output. Finally, the simulation runs for 5000 steps.

Other example

Some other examples scripts can be found in the example folder in Jumos' source tree. To go there, use the julia prompt:

julia> Pkg.dir("Jumos")
"~/.julia/v0.4/Jumos"

julia>; cd $ans/examples
~/.julia/v0.4/Jumos/examples