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feat: enable Lennard-Jones as a model #56

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Merged
romainljsimon merged 3 commits into from
Jan 15, 2026
+15 −9
Merged

feat: enable Lennard-Jones as a model #56

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0c0c5be
feat: shifting LJ potentials is now optional
Jan 15, 2026
4574b08
feat: handle shift potential boolean in IO
Jan 15, 2026
d2380ce
feat: export LennardJones as a model
Jan 15, 2026
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14 changes: 8 additions & 6 deletions src/IO/IO.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ module IO
using ..ParticlesMC: Particles, Atoms, Molecules, System
using ..ParticlesMC: fold_back, volume_sphere
using ..ParticlesMC: EmptyList, LinkedList, CellList
using ..ParticlesMC: Model, GeneralKG, JBB, BHHP, SoftSpheres, KobAndersen, Trimer
using ..ParticlesMC: Model, GeneralKG, JBB, BHHP, SoftSpheres, KobAndersen, Trimer, LennardJones
using Arianna
using Distributions, LinearAlgebra, StaticArrays, Printf
using DataStructures: OrderedDict
Expand Down Expand Up @@ -131,7 +131,7 @@ function get_model(data, i::Int, j::Int)
m = data[key]
if m["name"] == "GeneralKG"
rcut = get(m, "rcut", nothing)

return GeneralKG(m["epsilon"], m["sigma"], m["k"], m["r0"];
filter_kwargs(
:rcut => get(m, "rcut", nothing),
Expand All @@ -146,7 +146,9 @@ function get_model(data, i::Int, j::Int)
elseif m["name"] == "LennardJones"
return LennardJones(m["epsilon"], m["sigma"];
filter_kwargs(
:rcut => get(m, "rcut", nothing))...)
:rcut => get(m, "rcut", nothing),
:shift_potential => get(m, "shift_potential", true),
)...)
else
error("Model $(m["name"]) is not implemented")
return nothing
Expand All @@ -156,7 +158,7 @@ end
function read_bonds(data, N, format::Arianna.Format)
selrow = get_selrow(format, N, 1)
bonds_data = data[N+selrow:end]

if length(bonds_data) == 0
error("No bonds found in the file")
else
Expand Down Expand Up @@ -306,7 +308,7 @@ function formatted_string(num::Real, digits::Integer)
end

function write_position(io, position, digits::Int)
for position_i in position
for position_i in position
formatted_position_i = formatted_string(position_i, digits)
print(io, " ")
print(io, formatted_position_i)
Expand Down Expand Up @@ -360,4 +362,4 @@ function Arianna.store_lastframe(io, system::Molecules, t, format::Arianna.Forma
return nothing
end

end # module IO
end # module IO
10 changes: 7 additions & 3 deletions src/models.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -107,10 +107,14 @@ struct LennardJones{T<:AbstractFloat} <: DiscreteModel
shift::T
end

function LennardJones(ϵ, σ; rcut=2.5*σ, name="LennardJones")
function LennardJones(ϵ, σ; rcut=2.5*σ, name="LennardJones", shift_potential=true)
σ2 = σ ^ 2
rcut2 = rcut ^ 2
shift = lennard_jones(rcut2, 4ϵ, σ2)
if shift_potential
shift = lennard_jones(rcut2, 4ϵ, σ2)
else
shift = 0.0
end
return LennardJones(name, ϵ, 4ϵ, σ, σ2, rcut, rcut2, shift)
end

Expand Down Expand Up @@ -237,4 +241,4 @@ function Trimer()
KG_33 = GeneralKG(ϵ[3,3], σ[3,3], k[3,3], r0[3,3])
return SMatrix{3, 3, typeof(KG_11), 9}([KG_11 KG_12 KG_13; KG_12 KG_22 KG_23; KG_13 KG_23 KG_33])
end
###############################################################################
###############################################################################