commit de99d1360cf24862401092f7746ad4365385d981
Author: Niki Laptop <2212719@stud.hs-mannheim.de>
Date:   Wed May 21 12:26:24 2025 +0200

    initial commit with project structure

diff --git a/Manifest.toml b/Manifest.toml
new file mode 100644
index 0000000..9797664
--- /dev/null
+++ b/Manifest.toml
@@ -0,0 +1,2863 @@
+# This file is machine-generated - editing it directly is not advised
+
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+    ADTypesConstructionBaseExt = "ConstructionBase"
+    ADTypesEnzymeCoreExt = "EnzymeCore"
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+[[deps.AbstractFFTs]]
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+    AbstractFFTsTestExt = "Test"
+
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+git-tree-sha1 = "7ed9347888fac59a618302ee38216dd0379c480d"
+uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa"
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+
+[[deps.Xorg_libxcb_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXau_jll", "Xorg_libXdmcp_jll"]
+git-tree-sha1 = "bfcaf7ec088eaba362093393fe11aa141fa15422"
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+
+[[deps.Xorg_libxkbfile_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"]
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+version = "1.1.3+0"
+
+[[deps.Xorg_xkbcomp_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"]
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+uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4"
+version = "1.4.7+0"
+
+[[deps.Xorg_xkeyboard_config_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"]
+git-tree-sha1 = "00af7ebdc563c9217ecc67776d1bbf037dbcebf4"
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+version = "2.44.0+0"
+
+[[deps.Xorg_xtrans_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "a63799ff68005991f9d9491b6e95bd3478d783cb"
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+
+[[deps.Zlib_jll]]
+deps = ["Libdl"]
+uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+version = "1.2.13+1"
+
+[[deps.Zstd_jll]]
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+
+[[deps.isoband_jll]]
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+
+[[deps.libaom_jll]]
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+
+[[deps.libass_jll]]
+deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"]
+git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e"
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+
+[[deps.libblastrampoline_jll]]
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+
+[[deps.libdecor_jll]]
+deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"]
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+
+[[deps.libfdk_aac_jll]]
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+
+[[deps.libpng_jll]]
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+
+[[deps.libsixel_jll]]
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+
+[[deps.libvorbis_jll]]
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+
+[[deps.libwebp_jll]]
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+[[deps.nghttp2_jll]]
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+[[deps.oneTBB_jll]]
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+[[deps.p7zip_jll]]
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+[[deps.x264_jll]]
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+[[deps.x265_jll]]
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+
+[[deps.xkbcommon_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"]
+git-tree-sha1 = "c950ae0a3577aec97bfccf3381f66666bc416729"
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diff --git a/Project.toml b/Project.toml
new file mode 100644
index 0000000..9337038
--- /dev/null
+++ b/Project.toml
@@ -0,0 +1,3 @@
+[deps]
+DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
diff --git a/model_fhn.jl b/model_fhn.jl
new file mode 100644
index 0000000..7722318
--- /dev/null
+++ b/model_fhn.jl
@@ -0,0 +1,14 @@
+function fhn!(du, u, p::FHNParams, t)
+    N, dx = p.N, p.dx
+
+    u_mat = reshape(u[1:N^2], N, N)
+    v_mat = reshape(u[N^2+1:end], N, N)
+
+    Δu = laplacian(u_mat) / dx^2
+    Δv = laplacian(v_mat) / dx^2
+
+    fu = p.Du * Δu .+ u_mat .- u_mat .^ 3 ./ 3 .- v_mat
+    fv = p.Dv * Δv .+ p.ε * (u_mat .+ p.a .- p.b .* v_mat)
+
+    du .= vcat(vec(fu), vec(fv))
+end
diff --git a/scripts/run_simulation.jl b/scripts/run_simulation.jl
new file mode 100644
index 0000000..842a71a
--- /dev/null
+++ b/scripts/run_simulation.jl
@@ -0,0 +1,13 @@
+include("../src/AnimalFurFHN.jl")  # this loads the module code
+using .AnimalFurFHN
+# include optional visualizer only if needed:
+include("../src/visualization.jl")
+using .Visualization
+
+N = 100
+tspan = (0.0, 100.0)
+
+sol = run_simulation(N, tspan)
+
+
+Visualization.step_through_solution(sol, N)
\ No newline at end of file
diff --git a/scripts/show_frame.jl b/scripts/show_frame.jl
new file mode 100644
index 0000000..e645396
--- /dev/null
+++ b/scripts/show_frame.jl
@@ -0,0 +1,21 @@
+using GLMakie
+include("../src/AnimalFurFHN.jl")
+using .AnimalFurFHN
+
+# === Parameters ===
+N = 100
+tspan = (0.0, 100.0)
+frame_index = 1  # final time step
+
+# === Run simulation ===
+sol = run_simulation(N, tspan)
+
+# === Extract activator u ===
+u = sol.u[frame_index][1:N^2]
+u_mat = reshape(u, N, N)
+
+# === Plot ===
+fig = Figure()
+ax = Axis(fig[1, 1])
+heatmap!(ax, u_mat, colormap=:viridis)
+fig
diff --git a/src/AnimalFurFHN.jl b/src/AnimalFurFHN.jl
new file mode 100644
index 0000000..fafd5d6
--- /dev/null
+++ b/src/AnimalFurFHN.jl
@@ -0,0 +1,11 @@
+# src/AnimalFurFHN.jl
+module AnimalFurFHN
+
+include("constants.jl")
+include("initial_conditions.jl")
+include("laplacian.jl")
+include("model_fhn.jl")
+include("solver.jl")
+
+export run_simulation   # Make sure this is here!
+end
diff --git a/src/constants.jl b/src/constants.jl
new file mode 100644
index 0000000..d2f2bbd
--- /dev/null
+++ b/src/constants.jl
@@ -0,0 +1,9 @@
+struct FHNParams
+    N::Int
+    dx::Float64
+    Du::Float64
+    Dv::Float64
+    ε::Float64
+    a::Float64
+    b::Float64
+end
diff --git a/src/initial_conditions.jl b/src/initial_conditions.jl
new file mode 100644
index 0000000..44f5b4b
--- /dev/null
+++ b/src/initial_conditions.jl
@@ -0,0 +1,6 @@
+function initial_conditions(N)
+    Random.seed!(1234)
+    u = 0.1 .+ 0.01 .* rand(N, N)
+    v = 0.1 .+ 0.01 .* rand(N, N)
+    return vec(u), vec(v)
+end
diff --git a/src/laplacian.jl b/src/laplacian.jl
new file mode 100644
index 0000000..9d80986
--- /dev/null
+++ b/src/laplacian.jl
@@ -0,0 +1,6 @@
+function laplacian(u, N, h)
+    U = reshape(u, N, N)
+    padded = circshift(U, (-1, 0)) .+ circshift(U, (1, 0)) .+
+             circshift(U, (0, -1)) .+ circshift(U, (0, 1)) .- 4 .* U
+    return vec(padded) ./ h^2
+end
diff --git a/src/model_fhn.jl b/src/model_fhn.jl
new file mode 100644
index 0000000..7722318
--- /dev/null
+++ b/src/model_fhn.jl
@@ -0,0 +1,14 @@
+function fhn!(du, u, p::FHNParams, t)
+    N, dx = p.N, p.dx
+
+    u_mat = reshape(u[1:N^2], N, N)
+    v_mat = reshape(u[N^2+1:end], N, N)
+
+    Δu = laplacian(u_mat) / dx^2
+    Δv = laplacian(v_mat) / dx^2
+
+    fu = p.Du * Δu .+ u_mat .- u_mat .^ 3 ./ 3 .- v_mat
+    fv = p.Dv * Δv .+ p.ε * (u_mat .+ p.a .- p.b .* v_mat)
+
+    du .= vcat(vec(fu), vec(fv))
+end
diff --git a/src/solver.jl b/src/solver.jl
new file mode 100644
index 0000000..49e3e7c
--- /dev/null
+++ b/src/solver.jl
@@ -0,0 +1,34 @@
+function run_simulation(N::Int, tspan::Tuple{Float64,Float64})
+    # ✅ Turing pattern parameters — promotes stable spots
+    a = 0.1
+    b = 0.5
+    ϵ = 0.01
+    Du = 1e-5   # activator diffusion
+    Dv = 1e-3   # inhibitor diffusion (>> Du)
+
+    # Laplacian setup (assumes ∆x = 1)
+    dx = 1.0
+    L = laplacian_matrix(N, dx)
+
+    # ✅ Local random noise around a constant for initial conditions
+    u0, v0 = initial_conditions(N)  # Should include a seeded RNG
+    y0 = vcat(u0, v0)
+
+    # ODE system for Reaction-Diffusion with FitzHugh-Nagumo dynamics
+    function f!(du, u, p, t)
+        U = u[1:N^2]
+        V = u[N^2+1:end]
+
+        ΔU = Du .* (L * U)
+        ΔV = Dv .* (L * V)
+
+        du[1:N^2] = ΔU .+ (U .- (U .^ 3) ./ 3 .- V) ./ ϵ
+        du[N^2+1:end] = ΔV .+ ϵ .* (U .+ a .- b .* V)
+    end
+
+    # ✅ Use stiff solver for stability
+    prob = ODEProblem(f!, y0, tspan)
+    sol = solve(prob, Rosenbrock23(), saveat=1.0, reltol=1e-6, abstol=1e-6)
+
+    return sol
+end
diff --git a/src/visualization.jl b/src/visualization.jl
new file mode 100644
index 0000000..fb19860
--- /dev/null
+++ b/src/visualization.jl
@@ -0,0 +1,24 @@
+module Visualization
+
+using GLMakie
+
+function step_through_solution(sol, N)
+    fig = Figure(resolution=(600, 600))
+    ax = Axis(fig[1, 1])
+    slider = Slider(fig[2, 1], range=1:length(sol), startvalue=1)
+
+    # Initialize heatmap with first time step
+    u0 = reshape(sol[1][1:N^2], N, N)
+    heat_obs = Observable(u0)
+    hmap = heatmap!(ax, heat_obs, colormap=:magma)
+
+    # Update heatmap on slider movement
+    on(slider.value) do i
+        u = reshape(sol[i][1:N^2], N, N)
+        heat_obs[] = u
+    end
+
+    display(fig)
+end
+
+end