Load Ar dataset with energies computed by Lennard-Jones and postprocess

Setup experiment

Load packages.

using Unitful, UnitfulAtomic
using AtomsBase, InteratomicPotentials, PotentialLearning
using LinearAlgebra, Plots, DisplayAs

Define paths.

base_path = haskey(ENV, "BASE_PATH") ? ENV["BASE_PATH"] : "../../"
ds_path   = "$base_path/examples/data/LJ-AR/lj-ar.yaml";

Load datasets

ds, thermo = load_data(ds_path, YAML(:Ar, u"eV", u"Å"))
ds = @views ds[2:end] # Filter first configuration (zero energy)

DataSet{num_configs = 10000} 
	 Configuration{S, Energy, AtomsBase.FlexibleSystem{3, AtomsBase.Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(a₀, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}}, Forces}
	 Configuration{S, Energy, AtomsBase.FlexibleSystem{3, AtomsBase.Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(a₀, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}}, Forces}
	 ⋮
	 Configuration{S, Energy, AtomsBase.FlexibleSystem{3, AtomsBase.Atom{3, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Unitful.Quantity{Float64, 𝐋 𝐓^-1, Unitful.FreeUnits{(a₀, s^-1), 𝐋 𝐓^-1, nothing}}, Unitful.Quantity{Float64, 𝐌, Unitful.FreeUnits{(u,), 𝐌, nothing}}}, Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}}, Forces}

Compute distances, energies, and time range.

Get atom positions and compute distance from origin.

systems = get_system.(ds)
n_atoms = length(first(systems)) # Note: in this dataset all systems contain the same no. of atoms
positions = position.(systems)
dists_origin = map(x->ustrip.(norm.(x)), positions);

Extract LJ energies from dataset.

energies = get_values.(get_energy.(ds));

Define time range.

time_range = 0.5:0.5:5000;

Post-process results

Plot distance from origin vs time.

p = plot(xlabel = "τ | ps",
         ylabel = "Distance from origin | Å",
         dpi = 300, fontsize = 12)
for i = 1:n_atoms
    plot!(time_range, map(x->x[i], dists_origin), label="")
end
DisplayAs.PNG(p)

Plot LJ energies vs time.

p = plot(time_range, energies,
         xlabel = "τ | ps",
         ylabel = "Lennard Jones energy | eV",
         dpi = 300, fontsize = 12)
DisplayAs.PNG(p)

This page was generated using Literate.jl.