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The only interaction — a Lennard-Jones (page 10) interaction — is also added to the universe before the run. The
next lines add some outputs to the simulation, namely a trajectory and an energy 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
Main types
Jumos is organised around two main types: the Universe hold data about the system we are simulating; and the
Simulation type hold data about the algorithms we should use for the simulation.
Universe
The Universe type contains data. It is built around four other basic types:
• The Topology (page 8) contains data about the atomic organisation, i.e. the particles, bonds, angles and
dihedral angles in the system;
• The UnitCell (page 5) contains data about the bounding box of the simulation;
• The Interactions (page 9) type contains data about the potentials (page 9) to use for the atoms in the system;
• The Frame (page 8) type contains raw data about the positions and maybe velocities of the particles in the
system;
Simulation
The Simulation type contains algorithms. The progagator (page 12) algorithm is the one responsible for
propagating the Universe along the simulation. It also contains some analysis algorithms (called compute
(page 15) in Jumos); and some output (page 17) algorithms, to save data during the simulation run.
2.2 Universes
UnitCell
A simulation cell (UnitCell type) is the virtual container in which all the particles of a simulation move. The
UnitCell type is parametrized by the celltype. There are three different types of simulation cells:
• Infinite cells (InfiniteCell) do not have any boundaries. Any move is allowed inside these cells;
• Orthorombic cells (OrthorombicCell) have up to three independent lenghts; all the angles of the cell
are set to 90° (𝜋/2 radians)
• Triclinic cells (TriclinicCell) have 6 independent parameters: 3 lenghts and 3 angles.