ExTinyMD

ExTinyMD.jl for Extremely Tiny Molecular Dynamic is a simple package written in Julia, which provide a simple software for MD simulations.

Getting Started

You can simple type ] to enter the package in Julia REPL and type

pkg> add ExTinyMD

to install the package.

Here is an example, which simulate a 3D LJ fluid and plot its rdf:

using ExTinyMD, Plots

begin
    # create the atoms and the box
    n_atoms = 1000
    n_atoms = Int64(round(n_atoms))
    L = 100.0
    boundary = CubicBoundary(L)

    atoms = create_atoms([(n_atoms, Atom(type = 1, mass = 1.0, charge = 0.0))])

    # random init, position and velocity
    info = SimulationInfo(n_atoms, atoms, (0.0, L, 0.0, L, 0.0, L), boundary; min_r = 0.1, temp = 1.0)

    # set up the interaction needed, here only LJ, neighbors by cell_list
    interactions = [(LennardJones(), CellList3D(info, 4.5, boundary, 100))]

    # loggers, will store the data during simulations
    loggers = [TemperatureLogger(100, output = false), TrajectoryLogger(step = 1000, output = false)]

    # simulator and thermostat
    simulator = VerletProcess(dt = 0.001, thermostat = AndersenThermoStat(1.0, 0.05))

    # create MDSys
    sys = MDSys(
        n_atoms = n_atoms,
        atoms = atoms,
        boundary = boundary,
        interactions = interactions,
        loggers = loggers,
        simulator = simulator
    )

    # run 1e6 steps
    simulate!(simulator, sys, info, 1000000)

    # sample 2e6 steps to get rdf
    N = 20000
    bin_num = 100

    hist, volume, r, dr = hist_init(N, bin_num, 4.6)

    for i in 1:N
        simulate!(simulator, sys, info, 100)
        distance_hist!(hist, sys.interactions[1][2].neighbor_list, dr)
    end

    rdf = hist ./ (N .* volume)
    plot(r, 2 .* rdf, xlim = (0.0, 4.0), ylim = (0.0, 3.0))
    savefig("rdf_LJ_fluid.png")
end

How to Contribute

If you find any bug or have any suggestion, please open an issue.

If you want to add some new features, such as force or loggers, you can simply define something in your own package as

function ExTinyMD.update_acceleration!(
    interaction::YourForce, 
    neighborfinder::YourFinder, 
    sys::MDSys{T}, 
    info::SimulationInfo{T}) where {T<:Number}

    update_finder!(neighborfinder, info)
    YourForce!(interaction, neighborfinder, sys.atoms, sys.boundary, info)

    return nothing
end

and run them together. The package QuasiEwald.jl can be an example.