Support for Molly.jl

KIM_API provides out of the box extensions compatible with Molly.jl, a molecular dynamics simulation package in Julia. To use KIM models in Molly.jl, you can create a KIMCalculator and pass it to the general_inters field of a System. Here is an example of how to set up and run a molecular dynamics simulation of silicon using the Stillinger-Weber potential from the KIM repository with Molly.jl:

using Molly
using KIM_API
using StaticArrays
using Unitful: Å, ustrip
using UnitfulAtomic

# Conventional lattice constant for Si (L in Å)
a0 = 5.431u"Å"
repeats = (2, 2, 2)            # 2×2×2 supercell → 8 × 8 = 64 atoms

# Fractional coordinates for diamond cubic conventional cell
diamond_basis = SVector.([
    (0.0, 0.0, 0.0),
    (0.5, 0.5, 0.0),
    (0.5, 0.0, 0.5),
    (0.0, 0.5, 0.5),
    (0.25, 0.25, 0.25),
    (0.75, 0.75, 0.25),
    (0.75, 0.25, 0.75),
    (0.25, 0.75, 0.75),
])

atoms = Atom[]
coords_ = SVector{3, typeof(1.0u"Å")}[]  # stores SVector{3} with Å units
a0_val = ustrip(Å, a0)                  # lattice constant as plain Float64

for (ix, iy, iz) in Iterators.product(0:repeats[1]-1, 0:repeats[2]-1, 0:repeats[3]-1)
    shift = SVector(ix, iy, iz)
    for bf in diamond_basis
        push!(atoms, Atom(atom_type="Si", mass=28.0855u"u"))
        cart = SVector((bf .+ shift) .* a0_val) * Å  # convert to Å
        push!(coords_, cart)
    end
end

velocities = zero(coords_) .* (1.0u"ps"^-1)
boundary = CubicBoundary(repeats[1] * a0)  # 2a0 along each axis

calc = KIM_API.KIMCalculator(
    "SW_StillingerWeber_1985_Si__MO_405512056662_006";
    units = :metal,
)
ggers=(
      temp=TemperatureLogger(10),
      coords=CoordinatesLogger(10),
  )
sys = System(
    atoms = atoms,
    coords = coords_,
    boundary = boundary,
    velocities = velocities,
    general_inters = (kim = calc,),
    force_units = u"eV/Å",
    energy_units = u"eV",
    loggers = loggers,
)

temp = 298.0u"K"
simulator = VelocityVerlet(
    dt = 0.002u"ps",
    coupling = AndersenThermostat(temp, 1.0u"ps"),
)

simulate!(sys, simulator, 10000)

# Optional: visualize the trajectory
using GLMakie
visualize(sys.loggers.coords, boundary, "sim5x5x5.mp4")

Please consult OpenKIM and Molly.jl documentation for more details on available models and simulation options.