diff --git a/docs/make.jl b/docs/make.jl index dece0f7a..bd4dfa85 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -38,6 +38,8 @@ makedocs(; linkcheck=true, modules=[ CriticalTransitions, + # CriticalTransitions.StochasticDiffEq, + CriticalTransitions.DiffEqNoiseProcess, Base.get_extension(CriticalTransitions, :ChaosToolsExt), Base.get_extension(CriticalTransitions, :CoupledSDEsBaisin), ], diff --git a/docs/pages.jl b/docs/pages.jl index 8e174cbe..c2feb779 100644 --- a/docs/pages.jl +++ b/docs/pages.jl @@ -11,7 +11,7 @@ pages = [ "Large deviation theory" => "man/largedeviations.md", "Utilities" => "man/utils.md", ], - "Predefined systems" => "man/systems.md", - "Development stage" => "man/dev.md", + # "Predefined systems" => "man/systems.md", + # "Development stage" => "man/dev.md", ] #! format: on diff --git a/src/CoupledSDEs.jl b/src/CoupledSDEs.jl index f1e035bc..2a0c1178 100644 --- a/src/CoupledSDEs.jl +++ b/src/CoupledSDEs.jl @@ -52,7 +52,9 @@ If you want to specify a solver, do so by using the keyword `alg`, e.g.: `diffeq = (alg = Tsit5(), reltol = 1e-6)`. This requires you to have been first `using OrdinaryDiffEq` to access the solvers. The default `diffeq` is: +```julia $(DynamicalSystemsBase.DEFAULT_DIFFEQ) +``` `diffeq` keywords can also include `callback` for [event handling ](http://docs.juliadiffeq.org/latest/features/callback_functions.html). diff --git a/src/largedeviations/action.jl b/src/largedeviations/action.jl index 84d76243..a4289c8a 100644 --- a/src/largedeviations/action.jl +++ b/src/largedeviations/action.jl @@ -13,7 +13,7 @@ Returns a single number, which is the value of the action functional where ``\\phi_t`` denotes the path in state space, ``b`` the drift field, and ``T`` the total time of the path. The subscript ``Q`` refers to the -generalized norm ``||a||_Q^2 := \\langle a, Q^{-1} b \\rangle`` (see [`anorm`](@ref)). Here +generalized norm ``||a||_Q^2 := \\langle a, Q^{-1} b \\rangle`` (see `anorm``). Here ``Q`` is the noise covariance matrix `sys.Σ`. ## Keyword arguments @@ -53,7 +53,7 @@ Returns a single number, which is the value of the action functional where ``\\phi_t`` denotes the path in state space, ``b`` the drift field, ``T`` the total time of the path, and ``\\sigma`` the noise strength. The subscript ``Q`` refers to the -generalized norm ``||a||_Q^2 := \\langle a, Q^{-1} b \\rangle`` (see [`anorm`](@ref)). Here +generalized norm ``||a||_Q^2 := \\langle a, Q^{-1} b \\rangle`` (see `anorm``). Here ``Q`` is the noise covariance matrix. ## Keyword arguments @@ -112,7 +112,7 @@ by the integral where ``s`` is the arclength coordinate, ``L`` the arclength, ``b`` the drift field, and the subscript ``Q`` refers to the generalized dot product ``\\langle a, b \\rangle_Q := a^{\\top} -\\cdot Q^{-1} b`` (see [`anorm`](@ref)). Here ``Q`` is the noise covariance matrix `sys.Σ`. +\\cdot Q^{-1} b`` (see `anorm``). Here ``Q`` is the noise covariance matrix `sys.Σ`. ## Keyword arguments * `cov_inv = nothing`: Inverse of the covariance matrix ``\\Sigma``. diff --git a/src/utils.jl b/src/utils.jl index d683dd8f..5346da8f 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -65,52 +65,50 @@ function intervals_to_box(bmin::Vector, bmax::Vector) return box end; -function additive_idx!(du, u, p, t, idx) - du[idx] = 1.0 - return nothing -end; +# function additive_idx!(du, u, p, t, idx) +# du[idx] = 1.0 +# return nothing +# end; -function additive_idx(u, p, t, idx) - du = zeros(length(u)) - du[idx] = 1.0 - return SVector{length(u)}(du) -end; +# function additive_idx(u, p, t, idx) +# du = zeros(length(u)) +# du[idx] = 1.0 +# return SVector{length(u)}(du) +# end; -function multiplicative_idx!(du, u, p, t, idx) - return du[idx] = u[idx] -end; +# function multiplicative_idx!(du, u, p, t, idx) +# return du[idx] = u[idx] +# end; -function multiplicative_idx(u, p, t, idx) - du = zeros(length(u)) - du[idx] = u[idx] - return SVector{length(u)}(du) -end +# function multiplicative_idx(u, p, t, idx) +# du = zeros(length(u)) +# du[idx] = u[idx] +# return SVector{length(u)}(du) +# end -function multiplicative_first!(du, u, p, t) - return du[1] = u[1] -end; +# function multiplicative_first!(du, u, p, t) +# return du[1] = u[1] +# end; -function multiplicative_first(u, p, t) - du = zeros(length(u)) - du[1] = u[1] +# function multiplicative_first(u, p, t) +# du = zeros(length(u)) +# du[1] = u[1] - return SVector{length(u)}(du) -end; +# return SVector{length(u)}(du) +# end; -function additive_first!(du, u, p, t) - return du[1] = 1 -end; +# function additive_first!(du, u, p, t) +# return du[1] = 1 +# end; -function additive_first(u, p, t) - du = zeros(length(u)) - du[1] = 1 +# function additive_first(u, p, t) +# du = zeros(length(u)) +# du[1] = 1 - return SVector{length(u)}(du) -end; +# return SVector{length(u)}(du) +# end; """ -$(TYPEDSIGNATURES) - Calculates the generalized ``A``-norm of the vector `vec`, ``||v||_A := \\sqrt(v^\\top \\cdot A \\cdot v)``, where `A` is a square matrix of dimension `(length(vec) x length(vec))`.