changes functions finite_differences

improve allocations in computing

src/Utils.jl

@@ -84,25 +84,6 @@ function finite_differences(F, x::AbstractVector; δ = 1e-9)
     N = length(x)
     Nf = length(F(x))
     J = zeros(eltype(x), Nf, N)
-    finite_differences!(F, J, x; δ)
-    return J
-end
-
-function finite_differences(F, x::AbstractVector, p; δ = 1e-9)
-    N = length(x)
-    Nf = length(F(x, p))
-    J = zeros(eltype(x), Nf, N)
-    finite_differences!(F, J, x, p; δ = δ)
-    return J
-end
-
-"""
-$(SIGNATURES)
-
-Compute a Jacobian by Finite Differences, update J. Use the centered formula (f(x+δ)-f(x-δ))/2δ.
-"""
-function finite_differences!(F, J, x::AbstractVector; δ = 1e-9)
-    f = F(x)
     x1 = copy(x)
     @inbounds for i in eachindex(x)
         x1[i] += δ
@@ -115,15 +96,19 @@ function finite_differences!(F, J, x::AbstractVector; δ = 1e-9)
     return J
 end
 
-function finite_differences!(F, J, x::AbstractVector, p; δ = 1e-9)
-    f = F(x,p)
+"""
+$(SIGNATURES)
+
+Same as finite_differences but with inplace `F`
+"""
+@views function finite_differences!(F, J, x::AbstractVector; δ = 1e-9, tmp = copy(x))
     x1 = copy(x)
     @inbounds for i in eachindex(x)
         x1[i] += δ
-        J[:, i] .= F(x1,p)
+        F(J[:, i], x1)
         x1[i] -= 2δ
-        J[:, i] .-= F(x1,p)
-        J[:, i] ./= 2δ
+        F(tmp, x1)
+        J[:, i] .= @. (J[:, i] - tmp) / (2δ)
         x1[i] += δ
     end
     return J

src/periodicorbit/Floquet.jl

@@ -420,7 +420,7 @@ end
     vals = values[indvalid]
     # these are the Floquet multipliers
     μ = @. Complex(1 / (1 + vals))
-    vp0 = minimum(abs∘log, μ)
+    vp0 = minimum(abs ∘ log, μ)
     if vp0 > 1e-8
         @warn "The precision on the Floquet multipliers is $vp0. Either decrease `tol_stability` in the option ContinuationPar or use a different method than `FloquetCollGEV`"
     end
@@ -455,7 +455,7 @@ end
     _eig_floquet_col(J, n, m, Ntst, nev)
 end
 
-function _eig_floquet_col(J::AbstractMatrix{𝒯}, n, m, Ntst, nev) where 𝒯
+@views function _eig_floquet_col(J::AbstractMatrix{𝒯}, n, m, Ntst, nev) where 𝒯
     nbcoll = n * m
     N = n
     In = LinearAlgebra.I(N)
@@ -478,7 +478,7 @@ function _eig_floquet_col(J::AbstractMatrix{𝒯}, n, m, Ntst, nev) where 𝒯
 
     Jcop = copy(J)
     Jcop[end-N:end-1,end-N:end-1] .= In
-    Jcop[end-N:end-1,1:N] .= -In
+    Jcop[end-N:end-1,1:N] .= (-1) .* In
     Jcop[end, end] = J[end,end]
     Lₜ = LowerTriangular(copy(blockⱼ))
     for 𝐢 in 1:Ntst
@@ -532,7 +532,7 @@ function _eig_floquet_col(J::AbstractMatrix{𝒯}, n, m, Ntst, nev) where 𝒯
     # give indications on the precision on the Floquet coefficients
     vp0 = minimum(abs, σ)
     if vp0 > 1e-9
-        @warn "The precision on the Floquet multipliers is $vp0.\n It may be not enough to allow for precise bifurcation detection.\n Either decrease `tol_stability` in the option ContinuationPar or use a different method than `FloquetColl` for computing Floquet coefficients."
+        @debug "The precision on the Floquet multipliers is $vp0.\n It may be not enough to allow for precise bifurcation detection.\n Either decrease `tol_stability` in the option ContinuationPar or use a different method than `FloquetColl` for computing Floquet coefficients."
     end
     return σ, Complex.(vecs[I, :]), true, 1
 end

test/problems.jl

@@ -31,4 +31,4 @@ BK.re_make(prob, J = (x,p)->zeros(2,2), Jᵗ = (x,p)->zeros(2,2), d2F=(x,p,dx1,d
 ######################################################################
 # test finite differences
 BK.finite_differences(identity, zeros(2))
-BK.finite_differences((x,p)->x, zeros(2), nothing)
+BK.finite_differences!((o,x)->o.=x, zeros(2, 2), zeros(2))

test/simple_continuation.jl

@@ -130,7 +130,7 @@ br0 = @time continuation(prob,
 ###############
 br0 = @time continuation(prob, PALC(), opts; callback_newton = BK.cbMaxNormAndΔp(10,10)) #(6.20 k allocations: 409.469 KiB)
 try
-    continuation(prob, PALC(), opts; callback_newton = BK.cbMaxNormAndΔp(10,10), bla = 1)
+    continuation(prob, PALC(), opts; callback_newton = BK.cbMaxNormAndΔp(10,10))
 catch
 end