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 a minimal simulation — a Lennard-Jones fluid, thermostatted, run for a few thousand steps:

using ExTinyMD

n_atoms  = 1000
L        = 100.0
boundary = CubicBoundary(L)
atoms    = create_atoms([(n_atoms, Atom(type = 1, mass = 1.0, charge = 0.0))])

info = SimulationInfo(n_atoms, atoms, (0.0, L, 0.0, L, 0.0, L), boundary;
                      min_r = 0.1, temp = 1.0)

sys = MDSys(
    n_atoms      = n_atoms,
    atoms        = atoms,
    boundary     = boundary,
    interactions = [(LennardJones(), CellList3D(info, 4.5, boundary, 100))],
    loggers      = [TemperatureLogger(100)],
    simulator    = VerletProcess(dt = 0.001,
                                 thermostat = AndersenThermoStat(1.0, 0.05)),
)

simulate!(sys.simulator, sys, info, 10_000)

The documentation carries the full version of this walkthrough, including how to accumulate a radial distribution function from the run, along with reference pages for the simulators, thermostats, loggers and neighbour finders.

Electrostatics

ExTinyMD also includes a small electrostatics standard library: Ewald summation and the image-charge method for dielectrically confined slabs, usable either standalone (a plan object plus plain arrays) or as an ordinary MDSys interaction. Six methods are available:

• Ewald3D — triply periodic Ewald summation.
• PME3D — particle-mesh Ewald for the same triply periodic system, computing the identical sum as Ewald3D in O(N log N) instead of O(N·K). Requires using FINUFFT (a weak dependency, loaded via a package extension).
• Ewald2D — exact Ewald summation for a slab periodic in x, y and free in z.
• ICMEwald2D — Ewald2D plus the image-charge method, for a slab confined between two dielectric walls.
• ICMEwald3D — the image-charge method combined with Ewald3D and an electrostatic layer correction, for the same confined slab at lower cost.
• ICMPME3D — the image-charge method combined with PME3D and the same layer correction, the O(N log N) counterpart of ICMEwald3D. Also requires using FINUFFT.

See the Electrostatics page of the documentation for a full guide, including how to choose α/s and the image-charge parameters.

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 — ExTinyMD will call it like any built-in interaction. The electrostatics library under src/interactions/electrostatics/ is a worked example of the same contract, and the Interactions page documents it.

(The companion packages QuasiEwald.jl, SoEwald2D.jl and FastSpecSoG.jl implement this interface too, but currently pin ExTinyMD = "0.2" and do not yet resolve against the current release.)