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change method definition of record_from_solution which gives access t…
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…o the iterator and the state
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@rveltz
rveltz committed Sep 7, 2024
1 parent 9032bb2 commit f1503bc
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4 changes: 4 additions & 0 deletions News.md
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Expand Up @@ -3,6 +3,10 @@ BifurcationKit.jl, Changelog

All notable changes to this project will be documented in this file (hopefully). No performance improvements will be notified but mainly the addition of new methods, the modifications of internal structs, etc.

## [0.4.2]
- change bordered linear solvers' interface
- `record_from_solution` has been changed to the following definition

## [0.4.0]
- Setfield.jl is not anymore the main component of BifurcationKit to support parameter axis. It has been changed in favour of Accessors.jl

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13 changes: 7 additions & 6 deletions examples/COModel.jl
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Expand Up @@ -19,15 +19,15 @@ par_com = (q1 = 2.5, q2 = 2.0, q3 = 10., q4 = 0.0675, q5 = 1., q6 = 0.1, k = 0.4

z0 = [0.001137, 0.891483, 0.062345]

prob = BifurcationProblem(COm!, z0, par_com, (@optic _.q2); record_from_solution = (x, p) -> (x = x[1], y = x[2], s = x[3]))
prob = BifurcationProblem(COm!, z0, par_com, (@optic _.q2); record_from_solution = (x, p; k...) -> (x = x[1], y = x[2], s = x[3]))

opts_br = ContinuationPar(dsmax = 0.015, dsmin=1e-4, ds=1e-4, p_min = 0.5, p_max = 2.0, n_inversion = 6, detect_bifurcation = 3, nev = 3)
br = @time continuation(prob, PALC(), opts_br;
plot = true, verbosity = 0,
normC = norminf,
bothside = true)

BK.plot(br)#markersize=4, legend=:topright, ylims=(0,0.16))
plot(br)#markersize=4, legend=:topright, ylims=(0,0.16))
####################################################################################################
# periodic orbits
function plotSolution(x, p; k...)
Expand All @@ -49,7 +49,7 @@ function plotSolution(ax, x, p; ax1 = nothing, k...)
scatter!(ax, xtt.t, xtt[1,:]; markersize = 1.5, k...)
end

args_po = ( record_from_solution = (x, p) -> begin
args_po = ( record_from_solution = (x, p; k...) -> begin
xtt = BK.get_periodic_orbit(p.prob, x, @set par_com.q2 = p.p)
return (max = maximum(xtt[1,:]),
min = minimum(xtt[1,:]),
Expand Down Expand Up @@ -95,6 +95,7 @@ brpo = @time continuation(br, 5, opts_po_cont,
# alg = PALC(),
# alg = MoorePenrose(tangent=PALC(tangent = Bordered()), method = BK.direct),
δp = 0.0005,
linear_algo = COPBLS(),
callback_newton = callbackCO,
args_po...
)
Expand All @@ -114,8 +115,8 @@ sn_codim2 = continuation(br, 3, (@optic _.k), ContinuationPar(opts_br, p_max = 3
bdlinsolver = MatrixBLS()
)

BK.plot(sn_codim2)#, real.(sn_codim2.BT), ylims = (-1,1), xlims=(0,2))
BK.plot(sn_codim2, vars=(:q2, :x), branchlabel = "Fold", plotstability = false);plot!(br,xlims=(0.8,1.8))
plot(sn_codim2)#, real.(sn_codim2.BT), ylims = (-1,1), xlims=(0,2))
plot(sn_codim2, vars=(:q2, :x), branchlabel = "Fold", plotstability = false);plot!(br,xlims=(0.8,1.8))

hp_codim2 = continuation((@set br.alg.tangent = Bordered()), 2, (@optic _.k), ContinuationPar(opts_br, p_min = 0., p_max = 2.8, detect_bifurcation = 0, ds = -0.0001, dsmax = 0.08, dsmin = 1e-4, n_inversion = 6, detect_event = 2, detect_loop = true, max_steps = 50, detect_fold=false) ; plot = true,
verbosity = 0,
Expand All @@ -127,6 +128,6 @@ hp_codim2 = continuation((@set br.alg.tangent = Bordered()), 2, (@optic _.k), Co
bothside = true,
bdlinsolver = MatrixBLS())

BK.plot(sn_codim2, vars=(:q2, :x), branchlabel = "Fold", plotcirclesbif = true)
plot(sn_codim2, vars=(:q2, :x), branchlabel = "Fold", plotcirclesbif = true)
plot!(hp_codim2, vars=(:q2, :x), branchlabel = "Hopf",plotcirclesbif = true)
plot!(br,xlims=(0.6,1.5))
2 changes: 1 addition & 1 deletion examples/SH2d-fronts-cuda.jl
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Expand Up @@ -115,7 +115,7 @@ par = (l = -0.1, ν = 1.3, L = L)
prob = BK.BifurcationProblem(F_shfft, AF(sol0), par, (@optic _.l) ;
J = J_shfft,
plot_solution = (x, p;kwargs...) -> plotsol!(x; color=:viridis, kwargs...),
record_from_solution = (x, p) -> norm(x))
record_from_solution = (x, p; k...) -> norm(x))

opt_new = NewtonPar(verbose = true, tol = 1e-6, linsolver = L, eigsolver = Leig)
sol_hexa = @time newton(prob, opt_new, normN = norminf);
Expand Down
12 changes: 8 additions & 4 deletions examples/SH2d-fronts.jl
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Expand Up @@ -57,7 +57,7 @@ par = (l = -0.1, ν = 1.3, L1 = L1);

optnew = NewtonPar(verbose = true, tol = 1e-8, max_iterations = 20)

prob = BifurcationProblem(F_sh, vec(sol0), par, (@optic _.l); J = dF_sh, plot_solution = (x, p; kwargs...) -> (plotsol!((x); label="", kwargs...)),record_from_solution = (x, p) -> (n2 = norm(x), n8 = norm(x, 8)), d2F=d2F_sh, d3F=d3F_sh)
prob = BifurcationProblem(F_sh, vec(sol0), par, (@optic _.l); J = dF_sh, plot_solution = (x, p; kwargs...) -> (plotsol!((x); label="", kwargs...)),record_from_solution = (x, p; k...) -> (n2 = norm(x), n8 = norm(x, 8)), d2F=d2F_sh, d3F=d3F_sh)
# optnew = NewtonPar(verbose = true, tol = 1e-8, max_iterations = 20, eigsolver = EigArpack(0.5, :LM))
sol_hexa = @time newton(prob, optnew)
println("--> norm(sol) = ", norm(sol_hexa.u, Inf64))
Expand Down Expand Up @@ -97,7 +97,7 @@ br = @time continuation(
###################################################################################################
# codim2 Fold continuation
optfold = @set optcont.detect_bifurcation = 0
@set! optfold.newton_options.verbose = true
@reset optfold.newton_options.verbose = true
optfold = setproperties(optfold; p_min = -2., p_max= 2., dsmax = 0.1)

# dispatch plot to fold solution
Expand Down Expand Up @@ -127,7 +127,7 @@ function dF_sh2(du, u, p)
end

prob2 = @set prob.VF.J = (u, p) -> (du -> dF_sh2(du, u, p))
@set! prob2.u0 = vec(sol0)
@reset prob2.u0 = vec(sol0)

sol_hexa = @time newton(prob2, @set optnew.linsolver = ls)
println("--> norm(sol) = ", norm(sol_hexa.u, Inf64))
Expand Down Expand Up @@ -168,7 +168,11 @@ plot!(br)
deflationOp = DeflationOperator(2, 1.0, [sol_hexa.u])
optcontdf = @set optcont.newton_options.verbose = false

algdc = BK.DefCont(deflation_operator = deflationOp, perturb_solution = (x,p,id) -> (x .+ 0.1 .* rand(length(x))), max_iter_defop = 50, max_branches = 40, seek_every_step = 5,)
algdc = BK.DefCont(deflation_operator = deflationOp,
perturb_solution = (x,p,id) -> (x .+ 0.1 .* rand(length(x))),
max_iter_defop = 50,
max_branches = 40,
seek_every_step = 5,)

brdf = continuation(prob, algdc, setproperties(optcontdf; detect_bifurcation = 0, plot_every_step = 1);
plot = true, verbosity = 2,
Expand Down
10 changes: 5 additions & 5 deletions examples/SH3d.jl
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Expand Up @@ -117,12 +117,12 @@ prob = BK.BifurcationProblem(F_sh, AF(vec(sol0)), par, (@optic _.l),
J = (x, p) -> (dx -> dF_sh(x, p, dx)),
# J = (x, p) -> J_sh(x, p),
plot_solution = (ax, x, p; ax1=nothing) -> contour3dMakie!(ax, x),
record_from_solution = (x, p) -> (n2 = norm(x), n8 = norm(x, 8)),
record_from_solution = (x, p; k...) -> (n2 = norm(x), n8 = norm(x, 8)),
issymmetric = true)

optnew = NewtonPar(verbose = true, tol = 1e-8, max_iterations = 20, linsolver = @set ls.verbose = 0)
@set! optnew.eigsolver = eigSH3d
# @set! optnew.linsolver = DefaultLS()
@reset optnew.eigsolver = eigSH3d
# @reset optnew.linsolver = DefaultLS()
sol_hexa = @time newton(prob, optnew)
println("--> norm(sol) = ", norm(sol_hexa.u, Inf64))

Expand Down Expand Up @@ -173,11 +173,11 @@ br = @time continuation(
# end
)

plot(br)
BK.plot(br)
####################################################################################################
get_normal_form(br, 3; nev = 25)

br1 = @time continuation(br, 3, setproperties(optcont; save_sol_every_step = 10, detect_bifurcation = 3, p_max = 0.1, plot_every_step = 5, dsmax = 0.01);
br1 = @time continuation(br, 3, setproperties(optcont; save_sol_every_step = 10, detect_bifurcation = 0, p_max = 0.1, plot_every_step = 5, dsmax = 0.01);
plot = true, verbosity = 3,
δp = 0.005,
verbosedeflation = true,
Expand Down
2 changes: 1 addition & 1 deletion examples/SHpde_snaking.jl
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Expand Up @@ -30,7 +30,7 @@ parSH = (λ = -0.1, ν = 2., L1 = L1)
sol0 = 1.1cos.(X) .* exp.(-0X.^2/(2*5^2))

prob = BifurcationProblem(R_SH, sol0, parSH, (@optic _.λ); J = Jac_sp,
record_from_solution = (x, p) -> (n2 = norm(x), nw = normweighted(x), s = sum(x), s2 = x[end ÷ 2], s4 = x[end ÷ 4], s5 = x[end ÷ 5]),
record_from_solution = (x, p; k...) -> (n2 = norm(x), nw = normweighted(x), s = sum(x), s2 = x[end ÷ 2], s4 = x[end ÷ 4], s5 = x[end ÷ 5]),
plot_solution = (x, p;kwargs...)->(plot!(X, x; ylabel="solution", label="", kwargs...))
)
####################################################################################################
Expand Down
14 changes: 7 additions & 7 deletions examples/TMModel.jl
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Expand Up @@ -18,14 +18,14 @@ end

par_tm = (α = 1.5, τ = 0.013, J = 3.07, E0 = -2.0, τD = 0.200, U0 = 0.3, τF = 1.5, τS = 0.007)
z0 = [0.238616, 0.982747, 0.367876 ]
prob = BifurcationProblem(TMvf!, z0, par_tm, (@lens _.E0); record_from_solution = (x, p) -> (E = x[1], x = x[2], u = x[3]),)
prob = BifurcationProblem(TMvf!, z0, par_tm, (@optic _.E0); record_from_solution = (x, p; k...) -> (E = x[1], x = x[2], u = x[3]),)

opts_br = ContinuationPar(p_min = -10.0, p_max = -0., dsmax = 0.1, n_inversion = 8, nev = 3)
opts_br = ContinuationPar(p_min = -10.0, p_max = 1., dsmax = 0.1, n_inversion = 8, nev = 3)
br = continuation(prob, PALC(tangent = Bordered()), opts_br; plot = false, normC = norminf, bothside = true)

BK.plot(br, plotfold=false)
plot(br, plotfold=false)
####################################################################################################
br_fold = BK.continuation(br, 1, (@optic _.α), ContinuationPar(br.contparams, p_min = 0.2, p_max = 5.), bothside = true)
br_fold = BK.continuation(br, 2, (@optic _.α), ContinuationPar(br.contparams, p_min = 0.2, p_max = 5.), bothside = true)
plot(br_fold)
####################################################################################################
# continuation parameters
Expand All @@ -40,7 +40,7 @@ function plotSolution(x, p; k...)
plot!(br; subplot = 1, putspecialptlegend = false)
end

args_po = ( record_from_solution = (x, p) -> begin
args_po = ( record_from_solution = (x, p; k...) -> begin
xtt = BK.get_periodic_orbit(p.prob, x, p.p)
return (max = maximum(xtt[1,:]),
min = minimum(xtt[1,:]),
Expand Down Expand Up @@ -87,7 +87,7 @@ prob_ode = ODEProblem(TMvf!, copy(z0), (0., 1000.), par_tm; abstol = 1e-11, relt
opts_po_cont = ContinuationPar(opts_br, ds= -0.0001, dsmin = 1e-4, max_steps = 120, newton_options = NewtonPar(tol = 1e-6, max_iterations = 7), tol_stability = 1e-8, detect_bifurcation = 2, plot_every_step = 10, save_sol_every_step=1)

br_posh = @time continuation(
br, 4,
br, 5,
# arguments for continuation
opts_po_cont,
# this is where we tell that we want Standard Shooting
Expand All @@ -105,7 +105,7 @@ plot(br_posh, br, markersize=3)
opts_po_cont = ContinuationPar(opts_br, dsmax = 0.02, ds= 0.0001, max_steps = 50, newton_options = NewtonPar(tol = 1e-9, max_iterations=15), tol_stability = 1e-6, detect_bifurcation = 2, plot_every_step = 5)

br_popsh = @time continuation(
br, 4,
br, 5,
# arguments for continuation
opts_po_cont,
# this is where we tell that we want Poincaré Shooting
Expand Down
2 changes: 1 addition & 1 deletion examples/brusselator.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,7 @@ prob = BifurcationProblem(Fbru!, sol0, par_bru, (@optic _.l);
J = Jbru_sp,
# plot_solution = (x, p; kwargs...) -> plotsol(x; label="", kwargs... ), # for Plots.jl
# plot_solution = (ax, x, p) -> plotsol(ax, x), # For Makie.jl
record_from_solution = (x, p) -> x[div(n,2)])
record_from_solution = (x, p; k...) -> x[div(n,2)])
####################################################################################################
eigls = EigArpack(1.1, :LM)
opts_br_eq = ContinuationPar(dsmin = 0.03, dsmax = 0.05, ds = 0.03, p_max = 1.9, detect_bifurcation = 3, nev = 21, plot_every_step = 50, newton_options = NewtonPar(eigsolver = eigls, tol = 1e-9), max_steps = 1060, n_inversion = 6, tol_bisection_eigenvalue = 1e-20, max_bisection_steps = 30)
Expand Down
4 changes: 2 additions & 2 deletions examples/brusselatorShooting.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ sol0 = vcat(par_bru.α * ones(n), par_bru.β/par_bru.α * ones(n))
probBif = BifurcationProblem(Fbru!, sol0, par_bru, (@optic _.l);
J = Jbru_sp,
plot_solution = (x, p; ax1 = 0, kwargs...) -> (plotsol(x; label="", kwargs... )),
record_from_solution = (x, p) -> x[div(n,2)]
record_from_solution = (x, p; k...) -> x[div(n,2)]
)
####################################################################################################
eigls = EigArpack(1.1, :LM)
Expand Down Expand Up @@ -177,7 +177,7 @@ br_po = @time continuation(deepcopy(probSh), outpo.u, PALC(),
# (Base.display(contResult.eig[end].eigenvals) ;true),
callback_newton = BK.cbMaxNorm(1.),
plot_solution = (x, p; kwargs...) -> BK.plot_periodic_shooting!(x[1:end-1], length(1:dM:M); kwargs...),
record_from_solution = (u, p) -> u[end], normC = norminf)
record_from_solution = (u, p; k...) -> u[end], normC = norminf)

####################################################################################################
# automatic branch switching with Shooting
Expand Down
16 changes: 9 additions & 7 deletions examples/cGL2d.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -172,7 +172,7 @@ poTrap = PeriodicOrbitTrapProblem(re_make(prob, params = (@set par_cgl.r = r_hop

ls0 = GMRESIterativeSolvers(N = 2n, reltol = 1e-9)#, Pl = lu(I + par_cgl.Δ))
poTrapMF = setproperties(poTrap; linsolver = ls0)
@set! poTrapMF.prob_vf.VF.J = (x, p) -> (dx -> dFcgl(x, p, dx))
@reset poTrapMF.prob_vf.VF.J = (x, p) -> (dx -> dFcgl(x, p, dx))

poTrap(orbitguess_f, @set par_cgl.r = r_hopf - 0.1) |> plot
poTrapMF(orbitguess_f, @set par_cgl.r = r_hopf - 0.1) |> plot
Expand Down Expand Up @@ -205,7 +205,7 @@ ls = GMRESIterativeSolvers(verbose = false, reltol = 1e-3, N = size(Jpo,1), rest
ls(Jpo, rand(ls.N))

opt_po = @set opt_newton.verbose = true
@set! opt_po.linsolver = ls
@reset opt_po.linsolver = ls

outpo_f = @time newton(poTrapMF, orbitguess_f, opt_po; normN = norminf)
BK.converged(outpo_f) && printstyled(color=:red, "--> T = ", outpo_f.u[end], ", amplitude = ", BK.amplitude(outpo_f.u, Nx*Ny, M; ratio = 2),"\n")
Expand All @@ -219,7 +219,7 @@ br_po = @time continuation(poTrapMF, outpo_f.u, PALC(), opts_po_cont;
verbosity = 3,
plot = true,
# plot_solution = (x, p;kwargs...) -> BK.plot_periodic_potrap(x, M, Nx, Ny; ratio = 2, kwargs...),
record_from_solution = (u, p) -> BK.getamplitude(poTrapMF, u, par_cgl; ratio = 2),
record_from_solution = (u, p; k...) -> BK.getamplitude(poTrapMF, u, par_cgl; ratio = 2),
normC = norminf)

branches = Any[br_pok2]
Expand All @@ -232,13 +232,15 @@ br_po = continuation(
br, 1,
# arguments for continuation
opts_po_cont, poTrapMF;
ampfactor = 3.,
verbosity = 3, plot = true,
# ampfactor = 3.,
verbosity = 3,
plot = true,
# callback_newton = (x, f, J, res, iteration, itl, options; kwargs...) -> (println("--> amplitude = ", BK.amplitude(x, n, M; ratio = 2));true),
finalise_solution = (z, tau, step, contResult; k...) ->
(BK.haseigenvalues(contResult) && Base.display(contResult.eig[end].eigenvals) ;true),
plot_solution = (x, p; kwargs...) -> BK.plot_periodic_potrap(x, M, Nx, Ny; ratio = 2, kwargs...),
record_from_solution = (u, p) -> BK.amplitude(u, Nx*Ny, M; ratio = 2), normC = norminf)
record_from_solution = (u, p; k...) -> BK.amplitude(u, Nx*Ny, M; ratio = 2),
normC = norminf)
####################################################################################################
# Experimental, full Inplace
@views function NL!(f, u, p, t = 0.)
Expand Down Expand Up @@ -302,7 +304,7 @@ out_ = similar(sol0f)
@time Fcgl!(out_, sol0f, par_cgl)
@time dFcgl!(out_, sol0f, par_cgl, sol0f)

probInp = BifurcationProblem(Fcgl!, vec(sol0), (@set par_cgl.r = r_hopf - 0.01), (@lens _.r); J = dFcgl!, inplace = true)
probInp = BifurcationProblem(Fcgl!, vec(sol0), (@set par_cgl.r = r_hopf - 0.01), (@optic _.r); J = dFcgl!, inplace = true)

ls = GMRESIterativeSolvers(verbose = false, reltol = 1e-3, N = size(Jpo,1), restart = 40, maxiter = 50, Pl = Precilu, log=true)
ls(Jpo, rand(ls.N))
Expand Down
2 changes: 1 addition & 1 deletion examples/carrier.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ X = LinRange(-1,1,N)
dx = X[2] - X[1]
par_car = (ϵ = 0.7, X = X, dx = dx)
sol = -(1 .- par_car.X.^2)
recordFromSolution(x, p) = (x[2]-x[1]) * sum(x->x^2, x)
recordFromSolution(x, p; k...) = (x[2]-x[1]) * sum(x->x^2, x)

prob = BK.BifurcationProblem(F_carr, zeros(N), par_car, (@optic _.ϵ);
J = Jac_carr,
Expand Down
4 changes: 3 additions & 1 deletion examples/chan-af.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,9 @@ end
sol0 = Fun( x -> x * (1-x), Interval(0.0, 1.0))
const Δ = Derivative(sol0.space, 2);
par_af = (α = 3., β = 0.01)
prob = BifurcationProblem(F_chan, sol0, par_af, (@optic _.α); J = Jac_chan, plot_solution = (x, p; kwargs...) -> plot!(x; label = "l = $(length(x))", kwargs...))
prob = BifurcationProblem(F_chan, sol0, par_af, (@optic _.α);
J = Jac_chan,
plot_solution = (x, p; kwargs...) -> plot!(x; label = "l = $(length(x))", kwargs...))

optnew = NewtonPar(tol = 1e-12, verbose = true)
sol = @time BK.newton(prob, optnew, normN = norminf)
Expand Down
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Registration pull request created: JuliaRegistries/General/114741

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Tagging

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