`BifurcationKit.BifDetectEvent`

— Constant``BifDetectEvent``

This event implements the detection of bifurcations points along a continuation curve. The detection is based on monitoring the number of unstable eigenvalues. More details are given at Detection of bifurcation points of Equilibria.

`BifurcationKit.FoldDetectEvent`

— Constant``FoldDetectEvent``

This event implements the detection of Fold points based on the p-component of the tangent vector to the continuation curve. It is designed to work with `PALC(tangent=Bordered())`

as continuation algorithm. To use it, pass `event = FoldDetectEvent`

to `continuation`

.

`LinearAlgebra.I`

— Method```
I(coll, u, par)
```

Compute the identity matrix associated with the collocation problem.

`BifurcationKit.AutoDiff`

— TypeSingleton type to trigger the computation of the jacobian Matrix using ForwardDiff.jl. It can be used for example in newton or in deflated newton.

`BifurcationKit.AutoDiffMF`

— TypeSingleton type to trigger the computation of the jacobian vector product (jvp) using ForwardDiff.jl. It can be used for example in newton or in deflated newton.

`BifurcationKit.BTMAProblem`

— Type`struct BTMAProblem{Tprob, Tjac, Tu0, Tp, Tl<:Union{Nothing, Lens}, Tplot, Trecord} <: BifurcationKit.AbstractMABifurcationProblem{Tprob}`

Problem wrap of a functional. It is not meant to be used directly albeit perhaps by advanced users.

`prob::Any`

`jacobian::Any`

`u0::Any`

`params::Any`

`lens::Union{Nothing, Lens}`

`plotSolution::Any`

`recordFromSolution::Any`

`BifurcationKit.BTProblemMinimallyAugmented`

— Type`mutable struct BTProblemMinimallyAugmented{Tprob<:BifurcationKit.AbstractBifurcationProblem, vectype, S<:BifurcationKit.AbstractLinearSolver, Sa<:BifurcationKit.AbstractLinearSolver, Sbd<:BifurcationKit.AbstractBorderedLinearSolver, Sbda<:BifurcationKit.AbstractBorderedLinearSolver, Sbdblock<:BifurcationKit.AbstractBorderedLinearSolver, Tlens<:Lens} <: BifurcationKit.AbstractProblemMinimallyAugmented{Tprob<:BifurcationKit.AbstractBifurcationProblem}`

Structure to encode Bogdanov-Takens functional based on a Minimally Augmented formulation.

**Fields**

`prob_vf`

: Functional F(x, p) - vector field - with all derivatives`a`

: close to null vector of Jᵗ`b`

: close to null vector of J`zero`

: vector zero, to avoid allocating it many times`linsolver`

: linear solver. Used to invert the jacobian of MA functional`linsolverAdjoint`

: linear solver for the jacobian adjoint`linbdsolver`

: bordered linear solver`linbdsolverAdjoint`

: linear bordered solver for the jacobian adjoint`linbdsolverBlock`

: bordered linear solver for blocks`lens2`

: second parameter axis`usehessian`

: whether to use the hessian of prob_vf

`BifurcationKit.Bautin`

— Type`mutable struct Bautin{Tv, Tpar, Tlens, Tevr, Tevl, Tnf} <: BifurcationKit.AbstractBifurcationPoint`

`x0::Any`

: Bifurcation point`params::Any`

: Parameters used by the vector field.`lens::Any`

: Parameter axis used to compute the branch on which this cusp point was detected.`ζ::Any`

: Right eigenvector`ζ★::Any`

: Left eigenvector`nf::Any`

: Normal form coefficients`type::Symbol`

: Type of bifurcation

`BifurcationKit.BifDiagNode`

— TypeStructure to hold a connected component of a bifurcation diagram.

**Fields**

`level::Int64`

: current recursion level`code::Int64`

: code for finding the current node in the tree, this is the index of the bifurcation point from which γ branches off`γ::Any`

: branch associated to the current node`child::Any`

: children of current node. These are the different branches off the bifurcation point in γ

**Methods**

`hasbranch(diagram)`

`from(diagram)`

`diagram[code]`

For example`diagram[1,2,3]`

returns`diagram.child[1].child[2].child[3]`

`BifurcationKit.BifFunction`

— Type`struct BifFunction{Tf, Tdf, Tdfad, Tj, Tjad, Td2f, Td2fc, Td3f, Td3fc, Tsym, Tδ} <: BifurcationKit.AbstractBifurcationFunction`

Structure to hold the vector field and its derivatives. It should rarely be called directly. Also, in essence, it is very close to `SciMLBase.ODEFunction`

.

**Fields**

`F::Any`

: Vector field. Function of type out-of-place`result = f(x, p)`

or inplace`f(result, x, p)`

. For type stability, the types of`x`

and`result`

should match`dF::Any`

: Differential of`F`

with respect to`x`

, signature`dF(x,p,dx)`

`dFad::Any`

: Adjoint of the Differential of`F`

with respect to`x`

, signature`dFad(x,p,dx)`

`J::Any`

: Jacobian of`F`

at`(x, p)`

. It can assume three forms. 1. Either`J`

is a function and`J(x, p)`

returns a`::AbstractMatrix`

. In this case, the default arguments of`contparams::ContinuationPar`

will make`continuation`

work. 2. Or`J`

is a function and`J(x, p)`

returns a function taking one argument`dx`

and returning`dr`

of the same type as`dx`

. In our notation,`dr = J * dx`

. In this case, the default parameters of`contparams::ContinuationPar`

will not work and you have to use a Matrix Free linear solver, for example`GMRESIterativeSolvers`

, 3. Or`J`

is a function and`J(x, p)`

returns a variable`j`

which can assume any type. Then, you must implement a linear solver`ls`

as a composite type, subtype of`AbstractLinearSolver`

which is called like`ls(j, rhs)`

and which returns the solution of the jacobian linear system. See for example`examples/SH2d-fronts-cuda.jl`

. This linear solver is passed to`NewtonPar(linsolver = ls)`

which itself passed to`ContinuationPar`

. Similarly, you have to implement an eigensolver`eig`

as a composite type, subtype of`AbstractEigenSolver`

.`Jᵗ::Any`

: jacobian adjoint, it should be implemented in an efficient manner. For matrix-free methods,`transpose`

is not readily available and the user must provide a dedicated method. In the case of sparse based jacobian,`Jᵗ`

should not be passed as it is computed internally more efficiently, i.e. it avoids recomputing the jacobian as it would be if you pass`Jᵗ = (x, p) -> transpose(dF(x, p))`

.`d2F::Any`

: Second Differential of`F`

with respect to`x`

, signature`d2F(x,p,dx1,dx2)`

`d3F::Any`

: Third Differential of`F`

with respect to`x`

, signature`d3F(x,p,dx1,dx2,dx3)`

`d2Fc::Any`

: [internal] Second Differential of`F`

with respect to`x`

which accept complex vectors dxi`d3Fc::Any`

: [internal] Third Differential of`F`

with respect to`x`

which accept complex vectors dxi`isSymmetric::Any`

: Whether the jacobian is auto-adjoint.`δ::Any`

: used internally to compute derivatives (with finite differences), for example for normal form computation and codim 2 continuation.`inplace::Bool`

: optionally sets whether the function is inplace or not

**Methods**

`residual(pb::BifFunction, x, p)`

calls`pb.F(x,p)`

`jacobian(pb::BifFunction, x, p)`

calls`pb.J(x, p)`

`dF(pb::BifFunction, x, p, dx)`

calls`pb.dF(x,p,dx)`

- etc

`BifurcationKit.BifurcationProblem`

— Type`struct BifurcationProblem{Tvf, Tu, Tp, Tl<:Lens, Tplot, Trec} <: BifurcationKit.AbstractAllJetBifProblem`

Structure to hold the bifurcation problem.

**Fields**

`VF::Any`

: Vector field, typically a`BifFunction`

`u0::Any`

: Initial guess`params::Any`

: parameters`lens::Lens`

: Typically a`Setfield.Lens`

. It specifies which parameter axis among`params`

is used for continuation. For example, if`par = (α = 1.0, β = 1)`

, we can perform continuation w.r.t.`α`

by using`lens = (@lens _.α)`

. If you have an array`par = [ 1.0, 2.0]`

and want to perform continuation w.r.t. the first variable, you can use`lens = (@lens _[1])`

. For more information, we refer to`SetField.jl`

.`plotSolution::Any`

: user function to plot solutions during continuation. Signature:`plot_solution(x, p; kwargs...)`

for Plot.jl and`plot_solution(ax, x, p; kwargs...)`

for the Makie package(s).`recordFromSolution::Any`

:`record_from_solution = (x, p) -> norm(x)`

function used record a few indicators about the solution. It could be`norm`

or`(x, p) -> x[1]`

. This is also useful when saving several huge vectors is not possible for memory reasons (for example on GPU). This function can return pretty much everything but you should keep it small. For example, you can do`(x, p) -> (x1 = x[1], x2 = x[2], nrm = norm(x))`

or simply`(x, p) -> (sum(x), 1)`

. This will be stored in`contres.branch`

where`contres::ContResult`

is the continuation curve of the bifurcation problem. Finally, the first component is used for plotting in the continuation curve.

**Methods**

`re_make(pb; kwargs...)`

modify a bifurcation problem`getu0(pb)`

calls`pb.u0`

`getparams(pb)`

calls`pb.params`

`getlens(pb)`

calls`pb.lens`

`getparam(pb)`

calls`get(pb.params, pb.lens)`

`setparam(pb, p0)`

calls`set(pb.params, pb.lens, p0)`

`record_from_solution(pb)`

calls`pb.recordFromSolution`

`plot_solution(pb)`

calls`pb.plotSolution`

`is_symmetric(pb)`

calls`is_symmetric(pb.prob)`

**Constructors**

`BifurcationProblem(F, u0, params, lens)`

all derivatives are computed using ForwardDiff.`BifurcationProblem(F, u0, params, lens; J, Jᵗ, d2F, d3F, kwargs...)`

and`kwargs`

are the fields above. You can pass your own jacobian with`J`

(see`BifFunction`

for description of the jacobian function) and jacobian adjoint with`Jᵗ`

. For example, this can be used to provide finite differences based jacobian using`BifurcationKit.finiteDifferences`

.

`BifurcationKit.BilinearMap`

— Type`struct BilinearMap{Tm}`

This structure wraps a bilinear map to allow evaluation on Complex arguments. This is especially useful when these maps are produced by ForwardDiff.jl.

`BifurcationKit.BogdanovTakens`

— Type`mutable struct BogdanovTakens{Tv, Tpar, Tlens, Tevr, Tevl, Tnf, Tnf2} <: BifurcationKit.AbstractBifurcationPoint`

`x0::Any`

: Bogdanov-Takens point`params::Any`

: Parameters used by the vector field.`lens::Any`

: Parameter axis used to compute the branch on which this BT point was detected.`ζ::Any`

: Right eigenvectors`ζ★::Any`

: Left eigenvectors`nf::Any`

: Normal form coefficients (basic)`nfsupp::Any`

: Normal form coefficients (detailed)`type::Symbol`

: Type of bifurcation

`BifurcationKit.Bordered`

— Type`Bordered Tangent predictor`

`BifurcationKit.BorderedArray`

— Type`mutable struct BorderedArray{vectype1, vectype2}`

This defines an array (although not `<: AbstractArray`

) to hold two arrays or an array and a scalar. This is useful when one wants to add constraints (phase, ...) to a functional for example. It is used throughout the package for the Pseudo Arc Length Continuation, for the continuation of Fold / Hopf points, for periodic orbits... It is also used to define periodic orbits as (orbit, period). As such, it is a convenient alternative to `cat`

, `vcat`

and friends. We chose not to make it a subtype of AbstractArray as we wish to apply the current package to general "arrays", see Requested methods for Custom State. Finally, it proves useful for the GPU where the operation `x[end]`

can be slow.

`BifurcationKit.BorderingBLS`

— Type`struct BorderingBLS{S<:Union{Nothing, BifurcationKit.AbstractLinearSolver}, Ttol} <: BifurcationKit.AbstractBorderedLinearSolver`

This struct is used to provide the bordered linear solver based on the Bordering Method. Using the options, you can trigger a sequence of Bordering reductions to meet a precision.

**Reference**

This is the solver BEC + k in Govaerts, W. “Stable Solvers and Block Elimination for Bordered Systems.” SIAM Journal on Matrix Analysis and Applications 12, no. 3 (July 1, 1991): 469–83. https://doi.org/10.1137/0612034.

`solver::Union{Nothing, BifurcationKit.AbstractLinearSolver}`

: Linear solver for the Bordering method. Default: nothing`tol::Any`

: Tolerance for checking precision Default: 1.0e-12`check_precision::Bool`

: Check precision of the linear solve? Default: true`k::Int64`

: Number of recursions to achieve tolerance Default: 1

**Constructors**

- there is a simple constructor
`BorderingBLS(ls)`

where`ls`

is a linear solver, for example`ls = DefaultLS()`

- you can use keyword argument to create such solver, for example
`BorderingBLS(solver = DefaultLS(), tol = 1e-4)`

`BifurcationKit.Branch`

— Type`struct Branch{Tkind, Tprob, T<:Union{ContResult, Vector{ContResult}}, Tbp} <: BifurcationKit.AbstractResult{Tkind, Tprob}`

A Branch is a structure which encapsulates the result of the computation of a branch bifurcating from a bifurcation point.

`γ::Union{ContResult, Vector{ContResult}}`

: Set of branches branching off the bifurcation point`bp`

`bp::Any`

: Bifurcation point. It is thought as the root of the branches in γ

`BifurcationKit.BranchPoint`

— Type`mutable struct BranchPoint{Tv, Tτ, T, Tpar, Tlens<:Lens, Tevl, Tevr, Tnf} <: BifurcationKit.AbstractSimpleBranchPoint`

`x0::Any`

: Bifurcation point.`τ::Any`

: Tangent of the curve at the bifurcation point.`p::Any`

: Parameter value at the bifurcation point.`params::Any`

: Parameters used by the vector field.`lens::Lens`

: Parameter axis used to compute the branch on which this bifurcation point was detected.`ζ::Any`

: Right eigenvector(s).`ζ★::Any`

: Left eigenvector(s).`nf::Any`

: Normal form coefficients.`type::Symbol`

: Type of bifurcation point

**Predictor**

You can call `predictor(bp, ds; kwargs...)`

on such bifurcation point `bp`

to find the zeros of the normal form polynomials.

`BifurcationKit.BranchPointMap`

— Type`mutable struct BranchPointMap{Tv, Tτ, T, Tpar, Tlens<:Lens, Tevl, Tevr, Tnf} <: BifurcationKit.AbstractSimpleBranchPointForMaps`

`x0::Any`

: Bifurcation point.`τ::Any`

: Tangent of the curve at the bifurcation point.`p::Any`

: Parameter value at the bifurcation point.`params::Any`

: Parameters used by the vector field.`lens::Lens`

: Parameter axis used to compute the branch on which this bifurcation point was detected.`ζ::Any`

: Right eigenvector(s).`ζ★::Any`

: Left eigenvector(s).`nf::Any`

: Normal form coefficients.`type::Symbol`

: Type of bifurcation point

**Predictor**

You can call `predictor(bp, ds; kwargs...)`

on such bifurcation point `bp`

to find the zeros of the normal form polynomials.

`BifurcationKit.BranchPointPO`

— Type`mutable struct BranchPointPO{Tprob, Tv, T, Tevr, Tevl, Tnf} <: BifurcationKit.AbstractSimpleBifurcationPointPO`

`po::Any`

: Bifurcation point (periodic orbit)`T::Any`

: Period`ζ::Any`

: Right eigenvector(s)`ζ★::Any`

: Left eigenvector(s)`nf::Any`

: Normal form`prob::Any`

: Periodic orbit problem`prm::Bool`

: Normal form computed using Poincaré return map

**Associated methods**

**Predictor**

You can call `predictor(bp, ds; kwargs...)`

on such bifurcation point `bp`

to find the zeros of the normal form polynomials.

`BifurcationKit.ContIterable`

— Type`struct ContIterable{Tkind<:BifurcationKit.AbstractContinuationKind, Tprob, Talg, T, S, E, TnormC, Tfinalisesolution, TcallbackN, Tevent} <: BifurcationKit.AbstractContinuationIterable{Tkind<:BifurcationKit.AbstractContinuationKind}`

Define a continuation iterator. This allows for example to do

```
iter = ContIterable(prob, alg, opts; kwargs...)
for state in iter
println("Continuation step = ", state.step)
end
```

More information is available on the website

**Useful functions**

`setparam(iter, p)`

set parameter with lens`iter.prob.lens`

to`p`

`is_event_active(iter)`

whether the event detection is active`compute_eigenelements(iter)`

whether to compute eigen elements`save_eigenvectors(iter)`

whether to save eigen vectors`getparams(iter)`

get full list of continuation parameters`isindomain(iter, p)`

whether`p`

in is domain [p*min, p*max]. (See`ContinuationPar`

)`is_on_boundary(iter, p)`

whether`p`

in is {p*min, p*max}

`BifurcationKit.ContResult`

— Type`struct ContResult{Tkind<:BifurcationKit.AbstractContinuationKind, Tbr, Teigvals, Teigvec, Biftype, Tsol, Tparc, Tprob, Talg} <: BifurcationKit.AbstractResult{Tkind<:BifurcationKit.AbstractContinuationKind, Tprob}`

Structure which holds the results after a call to `continuation`

.

You can see the propertynames of a result `br`

by using `propertynames(br)`

or `propertynames(br.branch)`

.

**Fields**

`branch::StructArrays.StructArray`

: holds the low-dimensional information about the branch. More precisely,`branch[i+1]`

contains the following information`(record_from_solution(u, param), param, itnewton, itlinear, ds, θ, n_unstable, n_imag, stable, step)`

for each continuation step`i`

.`itnewton`

number of Newton iterations`itlinear`

total number of linear iterations during newton (corrector)`n_unstable`

number of eigenvalues with positive real part for each continuation step (to detect stationary bifurcation)`n_imag`

number of eigenvalues with positive real part and non zero imaginary part at current continuation step (useful to detect Hopf bifurcation).`stable`

stability of the computed solution for each continuation step. Hence,`stable`

should match`eig[step]`

which corresponds to`branch[k]`

for a given`k`

.`step`

continuation step (here equal`i`

)

`eig::Array{@NamedTuple{eigenvals::Teigvals, eigenvecs::Teigvec, converged::Bool, step::Int64}, 1} where {Teigvals, Teigvec}`

: A vector with eigen-elements at each continuation step.`sol::Any`

: Vector of solutions sampled along the branch. This is set by the argument`save_sol_every_step::Int64`

(default 0) in`ContinuationPar`

.`contparams::Any`

: The parameters used for the call to`continuation`

which produced this branch. Must be a`ContinuationPar`

`kind::BifurcationKit.AbstractContinuationKind`

: Type of solutions computed in this branch. Default: EquilibriumCont()`prob::Any`

: Bifurcation problem used to compute the branch, useful for branch switching. For example, when computing periodic orbits, the functional`PeriodicOrbitTrapProblem`

,`ShootingProblem`

... will be saved here. Default: nothing`specialpoint::Vector`

: A vector holding the set of detected bifurcation points. See`SpecialPoint`

for a list of special points.`alg::Any`

: Continuation algorithm used for the computation of the branch

**Associated methods**

`length(br)`

number of the continuation steps`show(br)`

display information about the branch`eigenvals(br, ind)`

returns the eigenvalues for the ind-th continuation step`eigenvec(br, ind, indev)`

returns the indev-th eigenvector for the ind-th continuation step`get_normal_form(br, ind)`

compute the normal form of the ind-th points in`br.specialpoint`

`getlens(br)`

return the parameter axis used for the branch`getlenses(br)`

return the parameter two axis used for the branch when 2 parameters continuation is used (Fold, Hopf, NS, PD)`br[k+1]`

gives information about the k-th step. A typical run yields the following

```
julia> br[1]
(x = 0.0, param = 0.1, itnewton = 0, itlinear = 0, ds = -0.01, θ = 0.5, n_unstable = 2, n_imag = 2, stable = false, step = 0, eigenvals = ComplexF64[0.1 - 1.0im, 0.1 + 1.0im], eigenvecs = ComplexF64[0.7071067811865475 - 0.0im 0.7071067811865475 + 0.0im; 0.0 + 0.7071067811865475im 0.0 - 0.7071067811865475im])
```

which provides the value `param`

of the parameter of the current point, its stability, information on the newton iterations, etc. The fields can be retrieved using `propertynames(br.branch)`

. This information is stored in `br.branch`

which is a `StructArray`

. You can thus extract the vector of parameters along the branch as

```
julia> br.param
10-element Vector{Float64}:
0.1
0.08585786437626905
0.06464466094067263
0.03282485578727799
-1.2623798512809007e-5
-0.07160718539365075
-0.17899902778635765
-0.3204203840236672
-0.4618417402609767
-0.5
```

`get_solx(br, k)`

returns the k-th solution on the branch`get_solp(br, k)`

returns the parameter value associated with k-th solution on the branch`getparams(br)`

Parameters passed to continuation and used in the equation`F(x, par) = 0`

.`setparam(br, p0)`

set the parameter value`p0`

according to`::Lens`

for the parameters of the problem`br.prob`

`getlens(br)`

get the lens used for the computation of the branch`continuation(br, ind)`

performs automatic branch switching (aBS) from ind-th bifurcation point. Typically branching from equilibrium to equilibrium, or periodic orbit to periodic orbit.`continuation(br, ind, lens2)`

performs two parameters`(getLens(br), lens2)`

continuation of the ind-th bifurcation point.`continuation(br, ind, probPO::AbstractPeriodicOrbitProblem)`

performs aBS from ind-th bifurcation point (which must be a Hopf bifurcation point) to branch of periodic orbits.

`BifurcationKit.ContState`

— Type`mutable struct ContState{Tv, T, Teigvals, Teigvec, Tcb} <: BifurcationKit.AbstractContinuationState{Tv}`

Structure containing the state of the continuation procedure. The fields are meant to change during the continuation procedure.

If you mutate these fields yourself, you can break the continuation procedure. Use the methods below to access the fields knowing that they do not yield copies.

**Arguments**

`z_pred`

current solution on the branch`converged`

Boolean for newton correction`τ`

tangent predictor`z`

previous solution`itnewton`

Number of newton iteration (in corrector)`step`

current continuation step`ds`

step size`stopcontinuation`

Boolean to stop continuation

**Useful functions**

`copy(state)`

returns a copy of`state`

`copyto!(dest, state)`

copy`state`

into`dest`

`getsolution(state)`

returns the current solution (x, p)`gettangent(state)`

return the tangent at the current solution`getpredictor(state)`

return the predictor at the current solution`getx(state)`

returns the x component of the current solution`getp(state)`

returns the p component of the current solution`get_previous_solution(state)`

returns the previous solution (x, p)`getpreviousx(state)`

returns the x component of the previous solution`getpreviousp(state)`

returns the p component of the previous solution`is_stable(state)`

whether the current state is stable

`BifurcationKit.ContinuationPar`

— Type`options = ContinuationPar(dsmin = 1e-4,...)`

Returns a variable containing parameters to affect the `continuation`

algorithm used to solve `F(x, p) = 0`

.

**Arguments**

`dsmin, dsmax`

are the minimum, maximum arclength allowed value. It controls the density of points in the computed branch of solutions.`ds = 0.01`

is the initial arclength.`p_min, p_max`

allowed parameter range for`p`

`max_steps = 100`

maximum number of continuation steps`newton_options::NewtonPar`

: options for the Newton algorithm`save_to_file = false`

: save to file. A name is automatically generated or can be defined in`continuation`

. This requires`using JLD2`

.`save_sol_every_step::Int64 = 0`

at which continuation steps do we save the current solution`plot_every_step = 10`

at which continuation steps do we plot the current solution

**Handling eigen elements, their computation is triggered by the argument detect_bifurcation (see below)**

`nev = 3`

number of eigenvalues to be computed. It is automatically increased to have at least`nev`

unstable eigenvalues. To be set for proper bifurcation detection. See Detection of bifurcation points of Equilibria for more informations.`save_eig_every_step = 1`

record eigen vectors every specified steps.**Important**for memory limited resource,*e.g.*GPU.`save_eigenvectors = true`

**Important**for memory limited resource,*e.g.*GPU.

**Handling bifurcation detection**

`tol_stability = 1e-10`

lower bound on the real part of the eigenvalues to test for stability of equilibria and periodic orbits`detect_fold = true`

detect Fold bifurcations? It is a useful option although the detection of Fold is cheap. Indeed, it may happen that there is a lot of Fold points and this can saturate the memory in memory limited devices (e.g. on GPU)`detect_bifurcation::Int`

∈ {0, 1, 2, 3} If set to 0, nothing is done. If set to 1, the eigen-elements are computed. If set to 2, the bifurcations points are detected during the continuation run, but not located precisely. If set to 3, a bisection algorithm is used to locate the bifurcations points (slower). The possibility to switch off detection is a useful option. Indeed, it may happen that there are a lot of bifurcation points and this can saturate the memory of memory limited devices (e.g. on GPU)`dsmin_bisection = 1e-16`

dsmin for the bisection algorithm for locating bifurcation points`n_inversion = 2`

number of sign inversions in bisection algorithm`max_bisection_steps = 15`

maximum number of bisection steps`tol_bisection_eigenvalue = 1e-16`

tolerance on real part of eigenvalue to detect bifurcation points in the bisection steps

**Handling ds adaptation (see continuation for more information)**

`a = 0.5`

aggressiveness factor. It is used to adapt`ds`

in order to have a number of newton iterations per continuation step roughly constant. The higher`a`

is, the larger the step size`ds`

is changed at each continuation step.

**Handling event detection**

`detect_event::Int`

∈ {0, 1, 2} If set to 0, nothing is done. If set to 1, the event locations are sought during the continuation run, but not located precisely. If set to 2, a bisection algorithm is used to locate the event (slower).`tol_param_bisection_event = 1e-16`

tolerance on parameter to locate event

**Misc**

`η = 150.`

parameter to estimate tangent at first point with parameter p₀ + ds / η`detect_loop`

[WORK IN PROGRESS] detect loops in the branch and stop the continuation

For performance reasons, we decided to use an immutable structure to hold the parameters. One can use the package `Setfield.jl`

to drastically simplify the mutation of different fields. See tutorials for more examples.

`BifurcationKit.ContinuousEvent`

— Type`struct ContinuousEvent{Tcb, Tl, T} <: BifurcationKit.AbstractContinuousEvent`

Structure to pass a ContinuousEvent function to the continuation algorithm. A continuous call back returns a **tuple/scalar** value and we seek its zeros.

`nb::Int64`

: number of events, ie the length of the result returned by the callback function`condition::Any`

: ,`(iter, state) -> NTuple{nb, T}`

callback function which, at each continuation state, returns a tuple. For example, to detect crossing 1.0 and -2.0, you can pass`(iter, state) -> (getp(state)+2, getx(state)[1]-1)),`

. Note that the type`T`

should match the one of the parameter specified by the`::Lens`

in`continuation`

.`computeEigenElements::Bool`

: whether the event requires to compute eigen elements`labels::Any`

: Labels used to display information. For example`labels[1]`

is used to qualify an event of the type`(0, 1.3213, 3.434)`

. You can use`labels = ("hopf",)`

or`labels = ("hopf", "fold")`

. You must have`labels::Union{Nothing, NTuple{N, String}}`

.`tol::Any`

: Tolerance on event value to declare it as true event.

`BifurcationKit.Cusp`

— Type`mutable struct Cusp{Tv, Tpar, Tlens, Tevr, Tevl, Tnf} <: BifurcationKit.AbstractBifurcationPoint`

`x0::Any`

: Bifurcation point`params::Any`

: Parameters used by the vector field.`lens::Any`

: Parameter axis used to compute the branch on which this cusp point was detected.`ζ::Any`

: Right eigenvector`ζ★::Any`

: Left eigenvector`nf::Any`

: Normal form coefficients`type::Symbol`

: Type of bifurcation

`BifurcationKit.CustomDist`

— TypeWrapper for a distance. You need to pass a function `d(u, v)`

.

`BifurcationKit.DCResult`

— Type`struct DCResult{Tprob, Tbr, Tit, Tsol, Talg} <: BifurcationKit.AbstractBranchResult`

Structure holding the result from deflated continuation.

`prob::Any`

: Bifurcation problem`branches::Any`

: Branches of solution`iter::Any`

: Continuation iterator`sol::Any`

: Solutions`alg::Any`

: Algorithm

`BifurcationKit.DefCont`

— Type`struct DefCont{Tdo, Talg, Tps, Tas, Tud, Tk} <: BifurcationKit.AbstractContinuationAlgorithm`

Structure which holds the parameters specific to Deflated continuation.

**Fields**

`deflation_operator::Any`

: Deflation operator,`::DeflationOperator`

Default: nothing`alg::Any`

: Used as a predictor,`::AbstractContinuationAlgorithm`

. For example`PALC()`

,`Natural()`

,... Default: PALC()`max_branches::Int64`

: maximum number of (active) branches to be computed Default: 100`seek_every_step::Int64`

: whether to seek new (deflated) solution at every step Default: 1`max_iter_defop::Int64`

: maximum number of deflated Newton iterations Default: 5`perturb_solution::Any`

: perturb function Default: _perturbSolution`accept_solution::Any`

: accept (solution) function Default: _acceptSolution`update_deflation_op::Any`

: function to update the deflation operator, ie pushing new solutions Default: _updateDeflationOp`jacobian::Any`

: jacobian for deflated newton. Can be`DeflatedProblemCustomLS()`

, or`Val(:autodiff)`

,`Val(:fullIterative)`

Default: DeflatedProblemCustomLS()

`BifurcationKit.DefProbFullIterativeLinearSolver`

— Type`struct DefProbFullIterativeLinearSolver{T} <: BifurcationKit.AbstractLinearSolverForDeflation`

Full iterative linear solver for deflated problem.

`BifurcationKit.DefaultEig`

— TypeThe struct `Default`

is used to provide the backslash operator to our Package

`BifurcationKit.DefaultGEig`

— TypeThe struct `Default`

is used to provide the backslash operator to our Package

`BifurcationKit.DefaultLS`

— Type`struct DefaultLS <: BifurcationKit.AbstractDirectLinearSolver`

This struct is used to provide the backslash operator. Can be used to solve `(a₀ * I + a₁ * J) * x = rhs`

.

`useFactorization::Bool`

: Whether to catch a factorization for multiple solves. Some operators may not support LU (like ApproxFun.jl) or QR factorization so it is best to let the user decides. Some matrices do not have`factorize`

like`StaticArrays.MMatrix`

. Default: true

`BifurcationKit.DefaultPILS`

— Type`struct DefaultPILS <: BifurcationKit.AbstractIterativeLinearSolver`

Mainly for debugging!! This is defined as an iterative pseudo-inverse linear solver This struct is used to test Moore-Penrose continuation. Used to solve `J * x = rhs`

.

`useFactorization::Bool`

: Whether to catch a factorization for multiple solves. Some operators may not support LU (like ApproxFun.jl) or QR factorization so it is best to let the user decides. Some matrices do not have`factorize`

like`StaticArrays.MMatrix`

. Default: true

`BifurcationKit.DeflatedProblem`

— Type`pb = DeflatedProblem(prob, M::DeflationOperator, jactype)`

Create a `DeflatedProblem`

.

This creates a deflated functional (problem) $M(u) \cdot F(u) = 0$ where `M`

is a `DeflationOperator`

which encodes the penalization term. `prob`

is an `AbstractBifurcationProblem`

which encodes the functional. It is not meant not be used directly albeit by advanced users.

`BifurcationKit.DeflatedProblem`

— MethodReturn the deflated function M(u) * F(u) where M(u) ∈ R

`BifurcationKit.DeflatedProblem`

— MethodReturn the jacobian of the deflated function M(u) * F(u) where M(u) ∈ R

`BifurcationKit.DeflatedProblemCustomLS`

— Type`struct DeflatedProblemCustomLS{T} <: BifurcationKit.AbstractLinearSolverForDeflation`

Custom linear solver for deflated problem, very close to the Sherman-Morrison formula.

`BifurcationKit.DeflatedProblemCustomLS`

— MethodImplement the custom linear solver for the deflated problem.

`BifurcationKit.DeflationOperator`

— Type`struct DeflationOperator{Tp<:Real, Tdot, T<:Real, vectype} <: BifurcationKit.AbstractDeflationFactor`

Structure for defining a custom distance.

This operator allows to handle the following situation. Assume you want to solve `F(x)=0`

with a Newton algorithm but you want to avoid the process to return some already known solutions $roots_i$. The deflation operator penalizes these roots. You can create a `DeflationOperator`

to define a scalar function `M(u)`

used to find, with Newton iterations, the zeros of the following function $F(u) \cdot Π_i(\|u - root_i\|^{-2p} + \alpha) := F(u) \cdot M(u)$ where $\|u\|^2 = dot(u, u)$. The fields of the struct `DeflationOperator`

are as follows:

`power::Real`

: power`p`

. You can use an`Int`

for example`dot::Any`

: function, this function has to be bilinear and symmetric for the linear solver to work well`α::Real`

: shift`roots::Vector`

: roots`tmp::Any`

`autodiff::Bool`

`δ::Real`

Given `defOp::DeflationOperator`

, one can access its roots via `defOp[n]`

as a shortcut for `defOp.roots[n]`

. Note that you can also use `defOp[end]`

.

Also, one can add (resp. remove) a new root by using `push!(defOp, newroot)`

(resp. `pop!(defOp)`

). Finally `length(defOp)`

is a shortcut for `length(defOp.roots)`

**Constructors**

`DeflationOperator(p::Real, α::Real, roots::Vector{vectype}; autodiff = false)`

`DeflationOperator(p::Real, dt, α::Real, roots::Vector{vectype}; autodiff = false)`

`DeflationOperator(p::Real, α::Real, roots::Vector{vectype}, v::vectype; autodiff = false)`

The option `autodiff`

triggers the use of automatic differentiation for the computation of the gradient of the scalar function `M`

. This works only on `AbstractVector`

for now.

**Custom distance**

You are asked to pass a scalar product like `dot`

to build a `DeflationOperator`

. However, in some cases, you may want to pass a custom distance `dist(u, v)`

. You can do this using

``DeflationOperator(p, CustomDist(dist), α, roots)``

Note that passing `CustomDist(dist, true)`

will trigger the use of automatic differentiation for the gradient of `M`

.

**Linear solvers**

When used with newton, you have access to the following linear solvers

- custom solver
`DeflatedProblemCustomLS()`

which requires solving two linear systems`J⋅x = rhs`

. - For other linear solvers
`<: AbstractLinearSolver`

, a matrix free method is used for the deflated functional. - if passed
`Val(:autodiff)`

, then`ForwardDiff.jl`

is used to compute the jacobian Matrix of the deflated problem - if passed
`Val(:fullIterative)`

, then a full matrix free method is used for the deflated problem.

`BifurcationKit.DiscreteEvent`

— Type`struct DiscreteEvent{Tcb, Tl} <: BifurcationKit.AbstractDiscreteEvent`

Structure to pass a DiscreteEvent function to the continuation algorithm. A discrete call back returns a discrete value and we seek when it changes.

`nb::Int64`

: number of events, ie the length of the result returned by the callback function`condition::Any`

: =`(iter, state) -> NTuple{nb, Int64}`

callback function which at each continuation state, returns a tuple. For example, to detect a value change.`computeEigenElements::Bool`

: whether the event requires to compute eigen elements`labels::Any`

: Labels used to display information. For example`labels[1]`

is used to qualify an event occurring in the first component. You can use`labels = ("hopf",)`

or`labels = ("hopf", "fold")`

. You must have`labels::Union{Nothing, NTuple{N, String}}`

.

`BifurcationKit.DotTheta`

— Type`struct DotTheta{Tdot, Ta}`

`dot::Any`

: dot product used in pseudo-arclength constraint`apply!::Any`

: Linear operator associated with dot product, i.e. dot(x, y) = <x, Ay>, where <,> is the standard dot product on R^N. You must provide an inplace function which evaluates A. For example`x -> rmul!(x, 1/length(x))`

.

This parametric type allows to define a new dot product from the one saved in `dt::dot`

. More precisely:

`dt(u1, u2, p1::T, p2::T, theta::T) where {T <: Real}`

computes, the weighted dot product $\langle (u_1,p_1), (u_2,p_2)\rangle_\theta = \theta \Re \langle u_1,u_2\rangle +(1-\theta)p_1p_2$ where $u_i\in\mathbb R^N$. The $\Re$ factor is put to ensure a real valued result despite possible complex valued arguments.

This is used in the pseudo-arclength constraint with the dot product $\frac{1}{N} \langle u_1, u_2\rangle,\quad u_i\in\mathbb R^N$

`BifurcationKit.EigArnoldiMethod`

— Type`struct EigArnoldiMethod{T, Tby, Tw, Tkw, vectype} <: BifurcationKit.AbstractIterativeEigenSolver`

`sigma::Any`

: Shift for Shift-Invert method`which::Any`

: Which eigen-element to extract LR(), LM(), ...`by::Any`

: how do we sort the computed eigenvalues, defaults to real`kwargs::Any`

: Key words arguments passed to EigArpack`x₀::Any`

: Example of vector used for Krylov iterations

More information is available at ArnoldiMethod.jl. For example, you can pass the parameters `tol, mindim, maxdim, restarts`

.

**Constructor**

`EigArnoldiMethod(;sigma = nothing, which = ArnoldiMethod.LR(), x₀ = nothing, kwargs...)`

`BifurcationKit.EigArpack`

— Type`struct EigArpack{T, Tby, Tw} <: BifurcationKit.AbstractIterativeEigenSolver`

`sigma::Any`

: Shift for Shift-Invert method with `(J - sigma⋅I)`which::Symbol`

: Which eigen-element to extract :LR, :LM, ...`by::Any`

: Sorting function, default to real`kwargs::Any`

: Keyword arguments passed to EigArpack

More information is available at Arpack.jl. You can pass the following parameters `tol=0.0, maxiter=300, ritzvec=true, v0=zeros((0,))`

.

**Constructor**

`EigArpack(sigma = nothing, which = :LR; kwargs...)`

`BifurcationKit.EigKrylovKit`

— Type`struct EigKrylovKit{T, vectype} <: BifurcationKit.AbstractMFEigenSolver`

`dim::Int64`

: Krylov Dimension Default: KrylovDefaults.krylovdim`tol::Any`

: Tolerance Default: 0.0001`restart::Int64`

: Number of restarts Default: 200`maxiter::Int64`

: Maximum number of iterations Default: KrylovDefaults.maxiter`verbose::Int64`

: Verbosity ∈ {0, 1, 2} Default: 0`which::Symbol`

: Which eigenvalues are looked for :LR (largest real), :LM, ... Default: :LR`issymmetric::Bool`

: If the linear map is symmetric, only meaningful if T<:Real Default: false`ishermitian::Bool`

: If the linear map is hermitian Default: false`x₀::Any`

: Example of vector to usen for Krylov iterations Default: nothing

`BifurcationKit.Finaliser`

— Type`struct Finaliser{Tp, Tf}`

Structure to hold a specific finaliser and simplify dispatch on it. It is mainly used for periodic orbits computation and adaption of mesh and section. It is meant to be called like a callable struct.

`BifurcationKit.FiniteDifferences`

— TypeSingleton type to trigger the computation of the jacobian using finite differences. It can be used for example in newton or in deflated newton.

`BifurcationKit.FiniteDifferencesMF`

— TypeSingleton type to trigger the computation of the jacobian vector product (jvp) using finite differences. It can be used for example in newton or in deflated newton.

`BifurcationKit.FloquetColl`

— Type`eigfloquet = BifurcationKit.FloquetColl()`

Computation of Floquet coefficients for the orthogonal collocation method. The method is based on the condensation of parameters described in [1] and used in Auto07p with a twist from [2] in which we form the monodromy matrix with a product of `Ntst`

matrices.

This is much faster than `FloquetCollGEV`

but less precise. The best version uses a Periodic Schur decomposition instead of the product of `Ntst`

matrices. This is provided in the package `PeriodicSchurBifurcationKit.jl`

.

**References**

[1] Doedel, Eusebius, Herbert B. Keller, et Jean Pierre Kernevez. «NUMERICAL ANALYSIS AND CONTROL OF BIFURCATION PROBLEMS (II): BIFURCATION IN INFINITE DIMENSIONS». International Journal of Bifurcation and Chaos 01, nᵒ 04 (décembre 1991): 745‑72. https://doi.org/10.1142/S0218127491000555.

[2] Lust, Kurt. «Improved Numerical Floquet Multipliers». International Journal of Bifurcation and Chaos 11, nᵒ 09 (septembre 2001): 2389‑2410. https://doi.org/10.1142/S0218127401003486.

`BifurcationKit.FloquetCollGEV`

— TypeComputation of Floquet coefficients for the orthogonal collocation method. The method is based on a formulation through a generalised eigenvalue problem (GEV). Relatively slow but quite precise.

This is a simplified version of [1].

**Arguments**

`eigls`

an eigensolver`ntot`

total number of unknowns (without counting the period), ie`length(::PeriodicOrbitOCollProblem)`

`n`

space dimension

**Example**

You can create such solver like this (here `n=2`

):

`eigfloquet = BifurcationKit.FloquetCollGEV(DefaultEig(), (30*4+1)*2, 2))`

**References**

[1] Fairgrieve, Thomas F., and Allan D. Jepson. “O. K. Floquet Multipliers.” SIAM Journal on Numerical Analysis 28, no. 5 (October 1991): 1446–62. https://doi.org/10.1137/0728075.

`BifurcationKit.FloquetQaD`

— Type`floquet = FloquetQaD(eigsolver::AbstractEigenSolver)`

This composite type implements the computation of the eigenvalues of the monodromy matrix in the case of periodic orbits problems (based on the Shooting method or Finite Differences (Trapeze method)), also called the Floquet multipliers. The method, dubbed Quick and Dirty (QaD), is not numerically very precise for large / small Floquet exponents when the number of time sections is large because of many matrix products. It allows, nevertheless, to detect bifurcations. The arguments are as follows:

`eigsolver::AbstractEigenSolver`

solver used to compute the eigenvalues.

If `eigsolver == DefaultEig()`

, then the monodromy matrix is formed and its eigenvalues are computed. Otherwise, a Matrix-Free version of the monodromy is used.

The computation of Floquet multipliers is necessary for the detection of bifurcations of periodic orbits (which is done by analyzing the Floquet exponents obtained from the Floquet multipliers). Hence, the eigensolver `eigsolver`

needs to compute the eigenvalues with largest modulus (and not with largest real part which is their default behavior). This can be done by changing the option `which = :LM`

of `eigsolver`

. Nevertheless, note that for most implemented eigensolvers in the current Package, the proper option is set.

`BifurcationKit.FloquetWrapper`

— Type`mutable struct FloquetWrapper{Tpb, Tjacpb, Torbitguess, Tp}`

Define a structure to interface the jacobian of the periodic orbits functional with the Floquet computation methods. If we use the same code as for `newton`

(see below) but in `continuation`

, it is difficult to tell the eigensolver that it should not use the jacobian but the monodromy matrix instead.

`pb::Any`

`jacpb::Any`

`x::Any`

`par::Any`

`BifurcationKit.Flow`

— Type`struct Flow{TF, Tf, Tts, Tff, Td, Tad, Tse, Tprob, TprobMono, Tfs, Tcb, Tδ} <: BifurcationKit.AbstractFlow`

`F::Any`

: The vector field`(x, p) -> F(x, p)`

associated to a Cauchy problem. Used for the differential of the shooting problem. Default: nothing`flow::Any`

: The flow (or semigroup)`(x, p, t) -> flow(x, p, t)`

associated to the Cauchy problem. Only the last time point must be returned in the form (u = ...) Default: nothing`flowTimeSol::Any`

: Flow which returns the tuple (t, u(t)). Optional, mainly used for plotting on the user side. Default: nothing`flowFull::Any`

: [Optional] The flow (or semigroup) associated to the Cauchy problem`(x, p, t) -> flow(x, p, t)`

. The whole solution on the time interval [0,t] must be returned. It is not strictly necessary to provide this, it is mainly used for plotting on the user side. Please use`nothing`

as default. Default: nothing`jvp::Any`

: The differential`dflow`

of the flow*w.r.t.*`x`

,`(x, p, dx, t) -> dflow(x, p, dx, t)`

. One important thing is that we require`dflow(x, dx, t)`

to return a Named Tuple:`(t = t, u = flow(x, p, t), du = dflow(x, p, dx, t))`

, the last component being the value of the derivative of the flow. Default: nothing`vjp::Any`

: The adjoint differential`vjpflow`

of the flow*w.r.t.*`x`

,`(x, p, dx, t) -> vjpflow(x, p, dx, t)`

. One important thing is that we require`vjpflow(x, p, dx, t)`

to return a Named Tuple:`(t = t, u = flow(x, p, t), du = vjpflow(x, p, dx, t))`

, the last component being the value of the derivative of the flow. Default: nothing`jvpSerial::Any`

: [Optional] Serial version of dflow. Used internally when using parallel multiple shooting. Please use`nothing`

as default. Default: nothing`prob::Any`

: [Internal] store the ODEProblem associated to the flow of the Cauchy problem Default: nothing`probMono::Any`

: [Internal] store the ODEProblem associated to the flow of the variational problem Default: nothing`flowSerial::Any`

: [Internal] Serial version of the flow Default: nothing`callback::Any`

: [Internal] Store possible callback Default: nothing`delta::Any`

: [Internal] Default: 1.0e-8

**Simplified constructor(s)**

We provide a simple constructor where you only pass the vector field `F`

, the flow `ϕ`

and its differential `dϕ`

:

`fl = Flow(F, ϕ, dϕ)`

**Simplified constructors for DifferentialEquations.jl**

These are some simple constructors for which you only have to pass a `prob::ODEProblem`

or `prob::EnsembleProblem`

(for parallel computation) from `DifferentialEquations.jl`

and an ODE time stepper like `Tsit5()`

. Hence, you can do for example

`fl = Flow(prob, Tsit5(); kwargs...)`

where `kwargs`

is passed to `SciMLBase::solve`

. If your vector field depends on parameters `p`

, you can define a `Flow`

using

`fl = Flow(prob, Tsit5(); kwargs...)`

Finally, you can pass two `ODEProblem`

where the second one is used to compute the variational equation:

`fl = Flow(prob1::ODEProblem, alg1, prob2::ODEProblem, alg2; kwargs...)`

`BifurcationKit.Fold`

— Type`mutable struct Fold{Tv, Tτ, T, Tpar, Tlens<:Lens, Tevl, Tevr, Tnf} <: BifurcationKit.AbstractSimpleBranchPoint`

`x0::Any`

: Bifurcation point.`τ::Any`

: Tangent of the curve at the bifurcation point.`p::Any`

: Parameter value at the bifurcation point.`params::Any`

: Parameters used by the vector field.`lens::Lens`

: Parameter axis used to compute the branch on which this bifurcation point was detected.`ζ::Any`

: Right eigenvector(s).`ζ★::Any`

: Left eigenvector(s).`nf::Any`

: Normal form coefficients.`type::Symbol`

: Type of bifurcation point

**Predictor**

`predictor(bp, ds; kwargs...)`

on such bifurcation point `bp`

to find the zeros of the normal form polynomials.

`BifurcationKit.FoldMAProblem`

— Type`struct FoldMAProblem{Tprob, Tjac, Tu0, Tp, Tl<:Union{Nothing, Lens}, Tplot, Trecord} <: BifurcationKit.AbstractMABifurcationProblem{Tprob}`

Problem wrap of a functional. It is not meant to be used directly albeit perhaps by advanced users.

`prob::Any`

`jacobian::Any`

`u0::Any`

`params::Any`

`lens::Union{Nothing, Lens}`

`plotSolution::Any`

`recordFromSolution::Any`

`BifurcationKit.FoldProblemMinimallyAugmented`

— Type`mutable struct FoldProblemMinimallyAugmented{Tprob<:BifurcationKit.AbstractBifurcationProblem, vectype, T<:Real, S<:BifurcationKit.AbstractLinearSolver, Sa<:BifurcationKit.AbstractLinearSolver, Sbd<:BifurcationKit.AbstractBorderedLinearSolver, Sbda<:BifurcationKit.AbstractBorderedLinearSolver, Tmass} <: BifurcationKit.AbstractProblemMinimallyAugmented{Tprob<:BifurcationKit.AbstractBifurcationProblem}`

Structure to encode Fold / Hopf functional based on a Minimally Augmented formulation.

**Fields**

`prob_vf`

: Functional F(x, p) - vector field - with all derivatives`a`

: close to null vector of Jᵗ`b`

: close to null vector of J`zero`

: vector zero, to avoid allocating it many times`l1`

: Lyapunov coefficient`CP`

: Cusp test value`BT`

: Bogdanov-Takens test value`GH`

: Bautin test values`ZH`

: Zero-Hopf test values`linsolver`

: linear solver. Used to invert the jacobian of MA functional`linsolverAdjoint`

: linear solver for the jacobian adjoint`linbdsolver`

: bordered linear solver`linbdsolverAdjoint`

: linear bordered solver for the jacobian adjoint`usehessian`

: whether to use the hessian of prob_vf`massmatrix`

: whether to use a mass matrix M for studying M⋅∂ₜu = F(u), default = I

`BifurcationKit.GEigArpack`

— Type`struct GEigArpack{T, Tby, Tw, Tb} <: BifurcationKit.AbstractGEigenSolver`

`sigma::Any`

: Shift for Shift-Invert method with `(J - sigma⋅I)`which::Symbol`

: Which eigen-element to extract :LR, :LM, ...`by::Any`

: Sorting function, default to real`kwargs::Any`

: Keyword arguments passed to EigArpack`B::Any`

: Mass matrix

More information is available at Arpack.jl. You can pass the following parameters `tol=0.0, maxiter=300, ritzvec=true, v0=zeros((0,))`

.

**Constructor**

`EigArpack(sigma = nothing, which = :LR; kwargs...)`

`BifurcationKit.GMRESIterativeSolvers`

— Type`mutable struct GMRESIterativeSolvers{T, Tl, Tr} <: BifurcationKit.AbstractIterativeLinearSolver`

Linear solver based on gmres from `IterativeSolvers.jl`

. Can be used to solve `(a₀ * I + a₁ * J) * x = rhs`

.

`abstol::Any`

: Absolute tolerance for solver Default: 0.0`reltol::Any`

: Relative tolerance for solver Default: 1.0e-8`restart::Int64`

: Number of restarts Default: 200`maxiter::Int64`

: Maximum number of iterations Default: 100`N::Int64`

: Dimension of the problem Default: 0`verbose::Bool`

: Display information during iterations Default: false`log::Bool`

: Record information Default: true`initially_zero::Bool`

: Start with zero guess Default: true`Pl::Any`

: Left preconditioner Default: IterativeSolvers.Identity()`Pr::Any`

: Right preconditioner Default: IterativeSolvers.Identity()`ismutating::Bool`

: Whether the linear operator is written inplace Default: false

`BifurcationKit.GMRESKrylovKit`

— Type`mutable struct GMRESKrylovKit{T, Tl} <: BifurcationKit.AbstractIterativeLinearSolver`

Create a linear solver based on GMRES from `KrylovKit.jl`

. Can be used to solve `(a₀ * I + a₁ * J) * x = rhs`

.

`dim::Int64`

: Krylov Dimension Default: KrylovDefaults.krylovdim`atol::Any`

: Absolute tolerance for solver Default: KrylovDefaults.tol`rtol::Any`

: Relative tolerance for solver Default: KrylovDefaults.tol`maxiter::Int64`

: Maximum number of iterations Default: KrylovDefaults.maxiter`verbose::Int64`

: Verbosity ∈ {0,1,2} Default: 0`issymmetric::Bool`

: If the linear map is symmetric, only meaningful if T<:Real Default: false`ishermitian::Bool`

: If the linear map is hermitian Default: false`isposdef::Bool`

: If the linear map is positive definite Default: false`Pl::Any`

: Left preconditioner Default: nothing

By tuning the options, you can select CG, GMRES... see here

`BifurcationKit.Hopf`

— Type`mutable struct Hopf{Tv, Tτ, T, Tω, Tpar, Tlens<:Lens, Tevr, Tevl, Tnf} <: BifurcationKit.AbstractSimpleBranchPoint`

`x0::Any`

: Hopf point`τ::Any`

: Tangent of the curve at the bifurcation point.`p::Any`

: Parameter value at the Hopf point`ω::Any`

: Frequency at the Hopf point`params::Any`

: Parameters used by the vector field.`lens::Lens`

: Parameter axis used to compute the branch on which this Hopf point was detected.`ζ::Any`

: Right eigenvector`ζ★::Any`

: Left eigenvector`nf::Any`

: Normal form coefficient ex: (a = 0., b = 1 + 1im)`type::Symbol`

: Type of Hopf bifurcation

**Associated methods**

**Predictor**

You can call `predictor(bp::Hopf, ds)`

on such bifurcation point `bp`

to get the guess for the periodic orbit.

`BifurcationKit.HopfHopf`

— Type`mutable struct HopfHopf{Tv, Tpar, Tlens, Tevr, Tevl, Tnf} <: BifurcationKit.AbstractBifurcationPoint`

`x0::Any`

: Bifurcation point`params::Any`

: Parameters used by the vector field.`lens::Any`

: Parameter axis used to compute the branch on which this cusp point was detected.`ζ::Any`

: Right eigenvector`ζ★::Any`

: Left eigenvector`nf::Any`

: Normal form coefficients`type::Symbol`

: Type of bifurcation

`BifurcationKit.HopfMAProblem`

— Type`struct HopfMAProblem{Tprob, Tjac, Tu0, Tp, Tl<:Union{Nothing, Lens}, Tplot, Trecord} <: BifurcationKit.AbstractMABifurcationProblem{Tprob}`

Problem wrap of a functional. It is not meant to be used directly albeit perhaps by advanced users.

`prob::Any`

`jacobian::Any`

`u0::Any`

`params::Any`

`lens::Union{Nothing, Lens}`

`plotSolution::Any`

`recordFromSolution::Any`

`BifurcationKit.HopfProblemMinimallyAugmented`

— Type`mutable struct HopfProblemMinimallyAugmented{Tprob<:BifurcationKit.AbstractBifurcationProblem, vectype, T<:Real, S<:BifurcationKit.AbstractLinearSolver, Sa<:BifurcationKit.AbstractLinearSolver, Sbd<:BifurcationKit.AbstractBorderedLinearSolver, Sbda<:BifurcationKit.AbstractBorderedLinearSolver, Tmass} <: BifurcationKit.AbstractProblemMinimallyAugmented{Tprob<:BifurcationKit.AbstractBifurcationProblem}`

Structure to encode Fold / Hopf functional based on a Minimally Augmented formulation.

**Fields**

`prob_vf`

: Functional F(x, p) - vector field - with all derivatives`a`

: close to null vector of Jᵗ`b`

: close to null vector of J`zero`

: vector zero, to avoid allocating it many times`l1`

: Lyapunov coefficient`CP`

: Cusp test value`BT`

: Bogdanov-Takens test value`GH`

: Bautin test values`ZH`

: Zero-Hopf test values`linsolver`

: linear solver. Used to invert the jacobian of MA functional`linsolverAdjoint`

: linear solver for the jacobian adjoint`linbdsolver`

: bordered linear solver`linbdsolverAdjoint`

: linear bordered solver for the jacobian adjoint`usehessian`

: whether to use the hessian of prob_vf`massmatrix`

: whether to use a mass matrix M for studying M⋅∂ₜu = F(u), default = I

`BifurcationKit.LSFromBLS`

— Type`struct LSFromBLS{Ts} <: BifurcationKit.AbstractLinearSolver`

This structure is used to provide the following linear solver. To solve (1) J⋅x = rhs, one decomposes J using Matrix by blocks and then use a bordering strategy to solve (1).

`solver::Any`

: Linear solver used to solve the smaller linear systems.

The solver only works for `AbstractMatrix`

`BifurcationKit.MatrixBLS`

— Type`struct MatrixBLS{S<:Union{Nothing, BifurcationKit.AbstractLinearSolver}} <: BifurcationKit.AbstractBorderedLinearSolver`

This struct is used to provide the bordered linear solver based on inverting the full matrix.

`solver::Union{Nothing, BifurcationKit.AbstractLinearSolver}`

: Linear solver used to invert the full matrix.

`BifurcationKit.MatrixFreeBLS`

— Type`struct MatrixFreeBLS{S<:Union{Nothing, BifurcationKit.AbstractLinearSolver}} <: BifurcationKit.AbstractBorderedLinearSolver`

This struct is used to provide the bordered linear solver based a matrix free operator for the full system in `(x, p)`

.

**Constructor**

`MatrixFreeBLS(solver, ::Bool)`

**Fields**

`solver::Union{Nothing, BifurcationKit.AbstractLinearSolver}`

: Linear solver for solving the extended linear system`use_bordered_array::Bool`

: What is the structure used to hold`(x, p)`

. If`true`

, this is achieved using`BorderedArray`

. If`false`

, a`Vector`

is used.

`BifurcationKit.MeshCollocationCache`

— Type`cache = MeshCollocationCache(Ntst::Int, m::Int, Ty = Float64)`

Structure to hold the cache for the collocation method. More precisely, it starts from a partition of [0,1] based on the mesh points:

`0 = τ₁ < τ₂ < ... < τₙₜₛₜ₊₁ = 1`

On each mesh interval [τⱼ, τⱼ₊₁] mapped to [-1,1], a Legendre polynomial of degree m is formed.

`Ntst::Int64`

: Coarse mesh size`degree::Int64`

: Collocation degree, usually called m`lagrange_vals::Matrix`

: Lagrange matrix`lagrange_∂::Matrix`

: Lagrange matrix for derivative`gauss_nodes::Vector`

: Gauss nodes`gauss_weight::Vector`

: Gauss weights`τs::Vector`

: Values of the coarse mesh, call τj. This can be adapted.`σs::LinRange`

: Values of collocation points, call σj. These are fixed.`full_mesh::Vector`

: Full mesh containing both the coarse mesh and the collocation points.

**Constructor**

`MeshCollocationCache(Ntst::Int, m::Int, Ty = Float64)`

`Ntst`

number of time steps`m`

degree of the collocation polynomials`Ty`

type of the time variable

`BifurcationKit.MoorePenrose`

— Type`Moore-Penrose predictor / corrector`

Moore-Penrose continuation algorithm.

Additional information is available on the website.

**Constructors**

`alg = MoorePenrose()`

`alg = MoorePenrose(tangent = PALC())`

**Fields**

`tangent::Any`

: Tangent predictor, for example`PALC()`

`method::MoorePenroseLS`

: Moore Penrose linear solver. Can be BifurcationKit.direct, BifurcationKit.pInv or BifurcationKit.iterative`ls::BifurcationKit.AbstractLinearSolver`

: (Bordered) linear solver

`BifurcationKit.MoorePenrose`

— Method```
MoorePenrose(; tangent, method, ls)
```

`BifurcationKit.Multiple`

— Type`Multiple Tangent continuation algorithm.`

`alg::PALC`

: Tangent predictor used Default: PALC()`τ::Any`

: Save the current tangent`α::Real`

: Damping in Newton iterations, 0 < α < 1`nb::Int64`

: Number of predictors`currentind::Int64`

: Index of the largest converged predictor Default: 0`pmimax::Int64`

: Index for lookup in residual history Default: 1`imax::Int64`

: Maximum index for lookup in residual history Default: 4`dsfact::Real`

: Factor to increase ds upon successful step Default: 1.5

**Constructor(s)**

```
Multiple(alg, x0, α, n)
Multiple(pred, x0, α, n)
Multiple(x0, α, n)
```

`BifurcationKit.NSMAProblem`

— Type`struct NSMAProblem{Tprob, Tjac, Tu0, Tp, Tl<:Union{Nothing, Lens}, Tplot, Trecord} <: BifurcationKit.AbstractMABifurcationProblem{Tprob}`

Problem wrap of a functional. It is not meant to be used directly albeit perhaps by advanced users.

`prob::Any`

`jacobian::Any`

`u0::Any`

`params::Any`

`lens::Union{Nothing, Lens}`

`plotSolution::Any`

`recordFromSolution::Any`

`BifurcationKit.Natural`

— Type`Natural continuation algorithm. The predictor is the constant predictor and the parameter is incremented by `ContinuationPar().ds` at each continuation step.`

`BifurcationKit.NdBranchPoint`

— TypeThis is a type which holds information for the bifurcation points of equilibria with dim(Ker)>1.

`mutable struct NdBranchPoint{Tv, Tτ, T, Tpar, Tlens<:Lens, Tevl, Tevr, Tnf} <: BifurcationKit.AbstractBranchPoint`

`x0::Any`

: Bifurcation point`τ::Any`

: Tangent of the curve at the bifurcation point.`p::Any`

: Parameter value at the bifurcation point`params::Any`

: Parameters used by the vector field.`lens::Lens`

: Parameter axis used to compute the branch on which this bifurcation point was detected.`ζ::Any`

: Right eigenvectors`ζ★::Any`

: Left eigenvectors`nf::Any`

: Normal form coefficients`type::Symbol`

: Type of bifurcation point

**Associated methods**

You can call `type(bp::NdBranchPoint), length(bp::NdBranchPoint)`

.

**Predictor**

You can call `predictor(bp, ds)`

on such bifurcation point `bp`

to find the zeros of the normal form polynomials.

**Manipulating the normal form**

You can use

`bp(Val(:reducedForm), x, p)`

to evaluate the normal form polynomials on the vector`x`

for (scalar) parameter`p`

.You can use

`bp(x, δp::Real)`

to get the (large dimensional guess) associated to the low dimensional vector`x`

. Note that we must have`length(x) == length(bp)`

.You can use

`BifurcationKit.nf(bp; kwargs...)`

to pretty print the normal form with a string.

`BifurcationKit.NeimarkSacker`

— Type`mutable struct NeimarkSacker{Tv, Tτ, T, Tω, Tpar, Tlens<:Lens, Tevr, Tevl, Tnf} <: BifurcationKit.AbstractSimpleBranchPointForMaps`

`x0::Any`

: Neimark-Sacker point`τ::Any`

: Tangent of the curve at the bifurcation point.`p::Any`

: Parameter value at the Neimark-Sacker point`ω::Any`

: Frequency at the Neimark-Sacker point`params::Any`

: Parameters used by the vector field.`lens::Lens`

: Parameter axis used to compute the branch on which this Neimark-Sacker point was detected.`ζ::Any`

: Right eigenvector`ζ★::Any`

: Left eigenvector`nf::Any`

: Normal form coefficient ex: (a = 0., b = 1 + 1im)`type::Symbol`

: Type of Hopf bifurcation

**Associated methods**

**Predictor**

You can call `predictor(bp::NeimarkSacker, ds)`

on such bifurcation point `bp`

to get the guess for the periodic orbit.

`BifurcationKit.NeimarkSackerPO`

— Type`mutable struct NeimarkSackerPO{Tprob, Tv, T, Tω, Tevr, Tevl, Tnf} <: BifurcationKit.AbstractSimpleBifurcationPointPO`

`po::Any`

: Bifurcation point (periodic orbit)`T::Any`

: Period`p::Any`

: Parameter value at the Neimark-Sacker point`ω::Any`

: Frequency of the Neimark-Sacker point`ζ::Any`

: Right eigenvector(s).`ζ★::Any`

: Left eigenvector(s).`nf::Any`

: Normal form`prob::Any`

: Periodic orbit problem`prm::Bool`

: Normal form computed using Poincaré return map

**Associated methods**

**Predictor**

You can call `predictor(bp::NeimarkSackerPO, ds)`

on such bifurcation point `bp`

to get the guess for the periodic orbit.

`BifurcationKit.NeimarkSackerProblemMinimallyAugmented`

— Type`mutable struct NeimarkSackerProblemMinimallyAugmented{Tprob<:BifurcationKit.AbstractBifurcationProblem, vectype, T<:Real, S<:BifurcationKit.AbstractLinearSolver, Sa<:BifurcationKit.AbstractLinearSolver, Sbd<:BifurcationKit.AbstractBorderedLinearSolver, Sbda<:BifurcationKit.AbstractBorderedLinearSolver, Tmass} <: BifurcationKit.AbstractProblemMinimallyAugmented{Tprob<:BifurcationKit.AbstractBifurcationProblem}`

Structure to encode the functional based on a Minimally Augmented formulation.

**Fields**

`prob_vf`

: Functional F(x, p) - vector field - with all derivatives`a`

: close to null vector of Jᵗ`b`

: close to null vector of J`zero`

: vector zero, to avoid allocating it many times`l1`

: Lyapunov coefficient`CP`

: Cusp test value`FOLDNS`

: Fold-Neimark Sacker test value`GPD`

: Generalised period douling test value`FLIPNS`

: Fold-NS test values`R1`

: Resonance 1`R2`

: Resonance 2`R3`

: Resonance 3`R4`

: Resonance 4`linsolver`

: linear solver. Used to invert the jacobian of MA functional`linsolverAdjoint`

: linear solver for the jacobian adjoint`linbdsolver`

: bordered linear solver`linbdsolverAdjoint`

: linear bordered solver for the jacobian adjoint`usehessian`

: wether to use the hessian of prob_vf`massmatrix`

: wether to use a mass matrix M for studying M⋅∂tu = F(u), default = I

`BifurcationKit.NewtonPar`

— Type`struct NewtonPar{T, L<:BifurcationKit.AbstractLinearSolver, E<:AbstractEigenSolver}`

Returns a variable containing parameters to affect the `newton`

algorithm when solving `F(x) = 0`

.

**Arguments (with default values):**

`tol::Any`

: absolute tolerance for`F(x)`

Default: 1.0e-12`max_iterations::Int64`

: number of Newton iterations Default: 25`verbose::Bool`

: display Newton iterations? Default: false`linsolver::BifurcationKit.AbstractLinearSolver`

: linear solver, must be`<: AbstractLinearSolver`

Default: DefaultLS()`eigsolver::AbstractEigenSolver`

: eigen solver, must be`<: AbstractEigenSolver`

Default: DefaultEig()`linesearch::Bool`

: Default: false`α::Any`

: Default: convert(typeof(tol), 1.0)`αmin::Any`

: Default: convert(typeof(tol), 0.001)

**Arguments for line search (Armijo)**

`linesearch = false`

: use line search algorithm (i.e. Newton with Armijo's rule)`α = 1.0`

: initial value of α (damping) parameter for line search algorithm`αmin = 0.001`

: minimal value of the damping`alpha`

For performance reasons, we decided to use an immutable structure to hold the parameters. One can use the package `Setfield.jl`

to drastically simplify the mutation of different fields. See the tutorials for examples.

`BifurcationKit.NonLinearSolution`

— TypeStructure which holds the solution from application of Newton-Krylov algorithm to a nonlinear problem.

For example

`sol = newton(prob, NewtonPar())`

**Fields**

`u::Any`

: solution`prob::Any`

: nonlinear problem, typically a`BifurcationProblem`

`residuals::Any`

: sequence of residuals`converged::Bool`

: has algorithm converged?`itnewton::Int64`

: number of newton steps`itlineartot::Any`

: total number of linear iterations

**methods**

`converged(sol)`

return whether the solution has converged.

`BifurcationKit.ODEBifProblem`

— Type`struct ODEBifProblem{Tvf, Tu, Tp, Tl<:Lens, Tplot, Trec} <: BifurcationKit.AbstractAllJetBifProblem`

Structure to hold the bifurcation problem.

**Fields**

`VF::Any`

: Vector field, typically a`BifFunction`

`u0::Any`

: Initial guess`params::Any`

: parameters`lens::Lens`

: Typically a`Setfield.Lens`

. It specifies which parameter axis among`params`

is used for continuation. For example, if`par = (α = 1.0, β = 1)`

, we can perform continuation w.r.t.`α`

by using`lens = (@lens _.α)`

. If you have an array`par = [ 1.0, 2.0]`

and want to perform continuation w.r.t. the first variable, you can use`lens = (@lens _[1])`

. For more information, we refer to`SetField.jl`

.`plotSolution::Any`

: user function to plot solutions during continuation. Signature:`plot_solution(x, p; kwargs...)`

for Plot.jl and`plot_solution(ax, x, p; kwargs...)`

for the Makie package(s).`recordFromSolution::Any`

:`record_from_solution = (x, p) -> norm(x)`

function used record a few indicators about the solution. It could be`norm`

or`(x, p) -> x[1]`

. This is also useful when saving several huge vectors is not possible for memory reasons (for example on GPU). This function can return pretty much everything but you should keep it small. For example, you can do`(x, p) -> (x1 = x[1], x2 = x[2], nrm = norm(x))`

or simply`(x, p) -> (sum(x), 1)`

. This will be stored in`contres.branch`

where`contres::ContResult`

is the continuation curve of the bifurcation problem. Finally, the first component is used for plotting in the continuation curve.

**Methods**

`re_make(pb; kwargs...)`

modify a bifurcation problem`getu0(pb)`

calls`pb.u0`

`getparams(pb)`

calls`pb.params`

`getlens(pb)`

calls`pb.lens`

`getparam(pb)`

calls`get(pb.params, pb.lens)`

`setparam(pb, p0)`

calls`set(pb.params, pb.lens, p0)`

`record_from_solution(pb)`

calls`pb.recordFromSolution`

`plot_solution(pb)`

calls`pb.plotSolution`

`is_symmetric(pb)`

calls`is_symmetric(pb.prob)`

**Constructors**

`BifurcationProblem(F, u0, params, lens)`

all derivatives are computed using ForwardDiff.`BifurcationProblem(F, u0, params, lens; J, Jᵗ, d2F, d3F, kwargs...)`

and`kwargs`

are the fields above. You can pass your own jacobian with`J`

(see`BifFunction`

for description of the jacobian function) and jacobian adjoint with`Jᵗ`

. For example, this can be used to provide finite differences based jacobian using`BifurcationKit.finiteDifferences`

.

`BifurcationKit.PALC`

— Type`struct PALC{Ttang<:BifurcationKit.AbstractTangentComputation, Tbls<:BifurcationKit.AbstractLinearSolver, T, Tdot} <: BifurcationKit.AbstractContinuationAlgorithm`

Pseudo-arclength continuation algorithm.

Additional information is available on the website.

**Fields**

`tangent::BifurcationKit.AbstractTangentComputation`

: Tangent predictor, must be a subtype of`AbstractTangentComputation`

. For example`Secant()`

or`Bordered()`

, Default: Secant()`θ::Any`

:`θ`

is a parameter in the arclength constraint. It is very**important**to tune it. It should be tuned for the continuation to work properly especially in the case of large problems where the < x - x*0, dx*0 > component in the constraint equation might be favoured too much. Also, large thetas favour p as the corresponding term in N involves the term 1-theta. Default: 0.5`_bothside::Bool`

: [internal], Default: false`bls::BifurcationKit.AbstractLinearSolver`

: Bordered linear solver used to invert the jacobian of the newton bordered problem. It is also used to compute the tangent for the predictor`Bordered()`

, Default: MatrixBLS()`dotθ::Any`

:`dotθ = DotTheta()`

, this sets up a dot product`(x, y) -> dot(x, y) / length(x)`

used to define the weighted dot product (resp. norm) $\|(x, p)\|^2_\theta$ in the constraint $N(x, p)$ (see online docs on PALC). This argument can be used to remove the factor`1/length(x)`

for example in problems where the dimension of the state space changes (mesh adaptation, ...) Default: DotTheta()

`BifurcationKit.PDEBifProblem`

— Type`struct PDEBifProblem{Tvf, Tu, Tp, Tl<:Lens, Tplot, Trec} <: BifurcationKit.AbstractAllJetBifProblem`

Structure to hold the bifurcation problem.

**Fields**

`VF::Any`

: Vector field, typically a`BifFunction`

`u0::Any`

: Initial guess`params::Any`

: parameters`lens::Lens`

: Typically a`Setfield.Lens`

. It specifies which parameter axis among`params`

is used for continuation. For example, if`par = (α = 1.0, β = 1)`

, we can perform continuation w.r.t.`α`

by using`lens = (@lens _.α)`

. If you have an array`par = [ 1.0, 2.0]`

and want to perform continuation w.r.t. the first variable, you can use`lens = (@lens _[1])`

. For more information, we refer to`SetField.jl`

.`plotSolution::Any`

: user function to plot solutions during continuation. Signature:`plot_solution(x, p; kwargs...)`

for Plot.jl and`plot_solution(ax, x, p; kwargs...)`

for the Makie package(s).`recordFromSolution::Any`

:`record_from_solution = (x, p) -> norm(x)`

function used record a few indicators about the solution. It could be`norm`

or`(x, p) -> x[1]`

. This is also useful when saving several huge vectors is not possible for memory reasons (for example on GPU). This function can return pretty much everything but you should keep it small. For example, you can do`(x, p) -> (x1 = x[1], x2 = x[2], nrm = norm(x))`

or simply`(x, p) -> (sum(x), 1)`

. This will be stored in`contres.branch`

where`contres::ContResult`

is the continuation curve of the bifurcation problem. Finally, the first component is used for plotting in the continuation curve.

**Methods**

`re_make(pb; kwargs...)`

modify a bifurcation problem`getu0(pb)`

calls`pb.u0`

`getparams(pb)`

calls`pb.params`

`getlens(pb)`

calls`pb.lens`

`getparam(pb)`

calls`get(pb.params, pb.lens)`

`setparam(pb, p0)`

calls`set(pb.params, pb.lens, p0)`

`record_from_solution(pb)`

calls`pb.recordFromSolution`

`plot_solution(pb)`

calls`pb.plotSolution`

`is_symmetric(pb)`

calls`is_symmetric(pb.prob)`

**Constructors**

`BifurcationProblem(F, u0, params, lens)`

all derivatives are computed using ForwardDiff.`BifurcationProblem(F, u0, params, lens; J, Jᵗ, d2F, d3F, kwargs...)`

and`kwargs`

are the fields above. You can pass your own jacobian with`J`

(see`BifFunction`

for description of the jacobian function) and jacobian adjoint with`Jᵗ`

. For example, this can be used to provide finite differences based jacobian using`BifurcationKit.finiteDifferences`

.

`BifurcationKit.PDMAProblem`

— Type`struct PDMAProblem{Tprob, Tjac, Tu0, Tp, Tl<:Union{Nothing, Lens}, Tplot, Trecord} <: BifurcationKit.AbstractMABifurcationProblem{Tprob}`

Problem wrap of a functional. It is not meant to be used directly albeit perhaps by advanced users.

`prob::Any`

`jacobian::Any`

`u0::Any`

`params::Any`

`lens::Union{Nothing, Lens}`

`plotSolution::Any`

`recordFromSolution::Any`

`BifurcationKit.POCollCache`

— Typecache to remove allocations from PeriodicOrbitOCollProblem

`BifurcationKit.POSolution`

— TypeStructure to encode the solution associated to a functional like `::PeriodicOrbitOCollProblem`

or `::ShootingProblem`

. In the particular case of `::PeriodicOrbitOCollProblem`

, this allows to use the collocation polynomials to interpolate the solution. Hence, if `sol::POSolution`

, one can call

```
sol = BifurcationKit.POSolution(prob_coll, x)
sol(t)
```

on any time `t`

.

`BifurcationKit.PairOfEvents`

— Type`struct PairOfEvents{Tc<:BifurcationKit.AbstractContinuousEvent, Td<:BifurcationKit.AbstractDiscreteEvent} <: BifurcationKit.AbstractEvent`

Structure to pass a PairOfEvents function to the continuation algorithm. It is composed of a pair ContinuousEvent / DiscreteEvent. A `PairOfEvents`

is constructed by passing to the constructor a `ContinuousEvent`

and a `DiscreteEvent`

:

`PairOfEvents(contEvent, discreteEvent)`

**Fields**

`eventC::BifurcationKit.AbstractContinuousEvent`

: Continuous event`eventD::BifurcationKit.AbstractDiscreteEvent`

: Discrete event

`BifurcationKit.PeriodDoubling`

— Type`mutable struct PeriodDoubling{Tv, Tτ, T, Tpar, Tlens<:Lens, Tevl, Tevr, Tnf} <: BifurcationKit.AbstractSimpleBranchPointForMaps`

`x0::Any`

: Bifurcation point.`τ::Any`

: Tangent of the curve at the bifurcation point.`p::Any`

: Parameter value at the bifurcation point.`params::Any`

: Parameters used by the vector field.`lens::Lens`

: Parameter axis used to compute the branch on which this bifurcation point was detected.`ζ::Any`

: Right eigenvector(s).`ζ★::Any`

: Left eigenvector(s).`nf::Any`

: Normal form coefficients.`type::Symbol`

: Type of bifurcation point

**Predictor**

`predictor(bp, ds; kwargs...)`

on such bifurcation point `bp`

to find the zeros of the normal form polynomials.

`BifurcationKit.PeriodDoublingPO`

— Type`mutable struct PeriodDoublingPO{Tprob, Tv, T, Tevr, Tevl, Tnf} <: BifurcationKit.AbstractSimpleBifurcationPointPO`

`po::Any`

: Bifurcation point (periodic orbit)`T::Any`

: Period`ζ::Any`

: Right eigenvector(s)`ζ★::Any`

: Left eigenvector(s)`nf::Any`

: Normal form`prob::Any`

: Periodic orbit problem`prm::Bool`

: Normal form computed using Poincaré return map

**Associated methods**

**Predictor**

`predictor(bp, ds; kwargs...)`

on such bifurcation point `bp`

to find the zeros of the normal form polynomials.

`BifurcationKit.PeriodDoublingProblemMinimallyAugmented`

— Type`mutable struct PeriodDoublingProblemMinimallyAugmented{Tprob<:BifurcationKit.AbstractBifurcationProblem, vectype, T<:Real, S<:BifurcationKit.AbstractLinearSolver, Sa<:BifurcationKit.AbstractLinearSolver, Sbd<:BifurcationKit.AbstractBorderedLinearSolver, Sbda<:BifurcationKit.AbstractBorderedLinearSolver, Tmass} <: BifurcationKit.AbstractProblemMinimallyAugmented{Tprob<:BifurcationKit.AbstractBifurcationProblem}`

Structure to encode the functional based on a Minimally Augmented formulation.

**Fields**

`prob_vf`

: Functional F(x, p) - vector field - with all derivatives`a`

: close to null vector of Jᵗ`b`

: close to null vector of J`zero`

: vector zero, to avoid allocating it many times`l1`

: Lyapunov coefficient`CP`

: Cusp test value`FOLDNS`

: Fold-Neimark Sacker test value`GPD`

: Generalised period douling test value`FLIPNS`

: Fold-NS test values`R1`

: Resonance 1`R2`

: Resonance 2`R3`

: Resonance 3`R4`

: Resonance 4`linsolver`

: linear solver. Used to invert the jacobian of MA functional`linsolverAdjoint`

: linear solver for the jacobian adjoint`linbdsolver`

: bordered linear solver`linbdsolverAdjoint`

: linear bordered solver for the jacobian adjoint`usehessian`

: wether to use the hessian of prob_vf`massmatrix`

: wether to use a mass matrix M for studying M⋅∂tu = F(u), default = I

`BifurcationKit.PeriodicOrbitOCollProblem`

— Type`pb = PeriodicOrbitOCollProblem(kwargs...)`

This composite type implements an orthogonal collocation (at Gauss points) method of piecewise polynomials to locate periodic orbits. More details (maths, notations, linear systems) can be found here.

**Arguments**

`prob`

a bifurcation problem`ϕ::AbstractVector`

used to set a section for the phase constraint equation`xπ::AbstractVector`

used in the section for the phase constraint equation`N::Int`

dimension of the state space`mesh_cache::MeshCollocationCache`

cache for collocation. See docs of`MeshCollocationCache`

`update_section_every_step`

updates the section every`update_section_every_step`

step during continuation`jacobian = DenseAnalytical()`

describes the type of jacobian used in Newton iterations. Can only be`AutoDiffDense(), DenseAnalytical(), FullSparse(), FullSparseInplace()`

.`meshadapt::Bool = false`

whether to use mesh adaptation`verbose_mesh_adapt::Bool = true`

verbose mesh adaptation information`K::Float64 = 500`

parameter for mesh adaptation, control new mesh step size. More precisely, we set max(hᵢ) / min(hᵢ) ≤ K if hᵢ denotes the time steps.

**Methods**

Here are some useful methods you can apply to `pb`

`length(pb)`

gives the total number of unknowns`size(pb)`

returns the triplet`(N, m, Ntst)`

`getmesh(pb)`

returns the mesh`0 = τ0 < ... < τNtst+1 = 1`

. This is useful because this mesh is born to vary during automatic mesh adaptation`get_mesh_coll(pb)`

returns the (static) mesh`0 = σ0 < ... < σm+1 = 1`

`get_times(pb)`

returns the vector of times (length`1 + m * Ntst`

) at the which the collocation is applied.`generate_solution(pb, orbit, period)`

generate a guess from a function`t -> orbit(t)`

which approximates the periodic orbit.`POSolution(pb, x)`

return a function interpolating the solution`x`

using a piecewise polynomials function

**Orbit guess**

You can evaluate the residual of the functional (and other things) by calling `pb(orbitguess, p)`

on an orbit guess `orbitguess`

. Note that `orbitguess`

must be of size 1 + N * (1 + m * Ntst) where N is the number of unknowns in the state space and `orbitguess[end]`

is an estimate of the period $T$ of the limit cycle.

**Constructors**

`PeriodicOrbitOCollProblem(Ntst::Int, m::Int; kwargs)`

creates an empty functional with`Ntst`

and`m`

.

Note that you can generate this guess from a function using `generate_solution`

.

**Functional**

A functional, hereby called `G`

, encodes this problem. The following methods are available

`pb(orbitguess, p)`

evaluates the functional G on`orbitguess`

`BifurcationKit.PeriodicOrbitTrapProblem`

— TypeThis composite type implements Finite Differences based on a Trapezoidal rule (Order 2 in time) to locate periodic orbits. More details (maths, notations, linear systems) can be found here.

**Fields**

`prob`

a bifurcation problem`M::Int`

number of time slices`ϕ`

used to set a section for the phase constraint equation, of size N*M`xπ`

used in the section for the phase constraint equation, of size N*M`linsolver: = DefaultLS()`

linear solver for each time slice, i.e. to solve`J⋅sol = rhs`

. This is only needed for the computation of the Floquet multipliers in a full matrix-free setting.`ongpu::Bool`

whether the computation takes place on the gpu (Experimental)`massmatrix`

a mass matrix. You can pass for example a sparse matrix. Default: identity matrix.`update_section_every_step`

updates the section every`update_section_every_step`

step during continuation`jacobian::Symbol`

symbol which describes the type of jacobian used in Newton iterations (see below).

The scheme is as follows. We first consider a partition of $[0,1]$ given by $0<s_0<\cdots<s_m=1$ and one looks for `T = x[end]`

such that

$M_a\cdot\left(x_{i} - x_{i-1}\right) - \frac{T\cdot h_i}{2} \left(F(x_{i}) + F(x_{i-1})\right) = 0,\ i=1,\cdots,m-1$

with $u_{0} := u_{m-1}$ and the periodicity condition $u_{m} - u_{1} = 0$ and

where $h_1 = s_i-s_{i-1}$. $M_a$ is a mass matrix. Finally, the phase of the periodic orbit is constrained by using a section (but you could use your own)

$\sum_i\langle x_{i} - x_{\pi,i}, \phi_{i}\rangle=0.$

**Constructors**

The structure can be created by calling `PeriodicOrbitTrapProblem(;kwargs...)`

. For example, you can declare such a problem without vector field by doing

`PeriodicOrbitTrapProblem(M = 100)`

**Orbit guess**

You will see below that you can evaluate the residual of the functional (and other things) by calling `pb(orbitguess, p)`

on an orbit guess `orbitguess`

. Note that `orbitguess`

must be a vector of size M * N + 1 where N is the number of unknowns in the state space and `orbitguess[M*N+1]`

is an estimate of the period $T$ of the limit cycle. More precisely, using the above notations, `orbitguess`

must be $orbitguess = [x_{1},x_{2},\cdots,x_{M}, T]$.

Note that you can generate this guess from a function solution using `generateSolution`

.

**Functional**

A functional, hereby called `G`

, encodes this problem. The following methods are available

`pb(orbitguess, p)`

evaluates the functional G on`orbitguess`

`pb(orbitguess, p, du)`

evaluates the jacobian`dG(orbitguess).du`

functional at`orbitguess`

on`du`

`pb(Val(:JacFullSparse), orbitguess, p)`

return the sparse matrix of the jacobian`dG(orbitguess)`

at`orbitguess`

without the constraints. It is called`A_γ`

in the docs.`pb(Val(:JacFullSparseInplace), J, orbitguess, p)`

. Same as`pb(Val(:JacFullSparse), orbitguess, p)`

but overwrites`J`

inplace. Note that the sparsity pattern must be the same independently of the values of the parameters or of`orbitguess`

. In this case, this is significantly faster than`pb(Val(:JacFullSparse), orbitguess, p)`

.`pb(Val(:JacCyclicSparse), orbitguess, p)`

return the sparse cyclic matrix Jc (see the docs) of the jacobian`dG(orbitguess)`

at`orbitguess`

`pb(Val(:BlockDiagSparse), orbitguess, p)`

return the diagonal of the sparse matrix of the jacobian`dG(orbitguess)`

at`orbitguess`

. This allows to design Jacobi preconditioner. Use`blockdiag`

.

**Jacobian**

Specify the choice of the jacobian (and linear algorithm), `jacobian`

must belong to `[:FullLU, :FullSparseInplace, :Dense, :DenseAD, :BorderedLU, :BorderedSparseInplace, :FullMatrixFree, :BorderedMatrixFree, :FullMatrixFreeAD]`

. This is used to select a way of inverting the jacobian `dG`

of the functional G.

- For
`jacobian = :FullLU`

, we use the default linear solver based on a sparse matrix representation of`dG`

. This matrix is assembled at each newton iteration. This is the default algorithm. - For
`jacobian = :FullSparseInplace`

, this is the same as for`:FullLU`

but the sparse matrix`dG`

is updated inplace. This method allocates much less. In some cases, this is significantly faster than using`:FullLU`

. Note that this method can only be used if the sparsity pattern of the jacobian is always the same. - For
`jacobian = :Dense`

, same as above but the matrix`dG`

is dense. It is also updated inplace. This option is useful to study ODE of small dimension. - For
`jacobian = :DenseAD`

, evaluate the jacobian using ForwardDiff - For
`jacobian = :BorderedLU`

, we take advantage of the bordered shape of the linear solver and use a LU decomposition to invert`dG`

using a bordered linear solver. - For
`jacobian = :BorderedSparseInplace`

, this is the same as for`:BorderedLU`

but the cyclic matrix`dG`

is updated inplace. This method allocates much less. In some cases, this is significantly faster than using`:BorderedLU`

. Note that this method can only be used if the sparsity pattern of the jacobian is always the same. - For
`jacobian = :FullMatrixFree`

, a matrix free linear solver is used for`dG`

: note that a preconditioner is very likely required here because of the cyclic shape of`dG`

which affects negatively the convergence properties of GMRES. - For
`jacobian = :BorderedMatrixFree`

, a matrix free linear solver is used but for`Jc`

only (see docs): it means that`options.linsolver`

is used to invert`Jc`

. These two Matrix-Free options thus expose different part of the jacobian`dG`

in order to use specific preconditioners. For example, an ILU preconditioner on`Jc`

could remove the constraints in`dG`

and lead to poor convergence. Of course, for these last two methods, a preconditioner is likely to be required. - For
`jacobian = :FullMatrixFreeAD`

, the evaluation map of the differential is derived using automatic differentiation. Thus, unlike the previous two cases, the user does not need to pass a Matrix-Free differential.

For these methods to work on the GPU, for example with `CuArrays`

in mode `allowscalar(false)`

, we face the issue that the function `extract_period_fdtrap`

won't be well defined because it is a scalar operation. Note that you must pass the option `ongpu = true`

for the functional to be evaluated efficiently on the gpu.

`BifurcationKit.PeriodicOrbitTrapProblem`

— MethodThis method returns the jacobian of the functional G encoded in PeriodicOrbitTrapProblem using a Sparse representation.

`BifurcationKit.PeriodicOrbitTrapProblem`

— MethodThis method returns the jacobian of the functional G encoded in PeriodicOrbitTrapProblem using an inplace update. In case where the passed matrix J0 is a sparse one, it updates J0 inplace assuming that the sparsity pattern of J0 and dG(orbitguess0) are the same.

`BifurcationKit.Pitchfork`

— Type`mutable struct Pitchfork{Tv, Tτ, T, Tpar, Tlens<:Lens, Tevl, Tevr, Tnf} <: BifurcationKit.AbstractSimpleBranchPoint`

`x0::Any`

: Bifurcation point.`τ::Any`

: Tangent of the curve at the bifurcation point.`p::Any`

: Parameter value at the bifurcation point.`params::Any`

: Parameters used by the vector field.`lens::Lens`

: Parameter axis used to compute the branch on which this bifurcation point was detected.`ζ::Any`

: Right eigenvector(s).`ζ★::Any`

: Left eigenvector(s).`nf::Any`

: Normal form coefficients.`type::Symbol`

: Type of bifurcation point

**Predictor**

`predictor(bp, ds; kwargs...)`

on such bifurcation point `bp`

to find the zeros of the normal form polynomials.

`BifurcationKit.PitchforkMap`

— Type`mutable struct PitchforkMap{Tv, Tτ, T, Tpar, Tlens<:Lens, Tevl, Tevr, Tnf} <: BifurcationKit.AbstractSimpleBranchPointForMaps`

`x0::Any`

: Bifurcation point.`τ::Any`

: Tangent of the curve at the bifurcation point.`p::Any`

: Parameter value at the bifurcation point.`params::Any`

: Parameters used by the vector field.`lens::Lens`

: Parameter axis used to compute the branch on which this bifurcation point was detected.`ζ::Any`

: Right eigenvector(s).`ζ★::Any`

: Left eigenvector(s).`nf::Any`

: Normal form coefficients.`type::Symbol`

: Type of bifurcation point

**Predictor**

`predictor(bp, ds; kwargs...)`

on such bifurcation point `bp`

to find the zeros of the normal form polynomials.

`BifurcationKit.PoincareShootingProblem`

— Type`pb = PoincareShootingProblem(flow::Flow, M, sections; δ = 1e-8, interp_points = 50, parallel = false)`

This composite type implements the Poincaré Shooting method to locate periodic orbits by relying on Poincaré return maps. More details (maths, notations, linear systems) can be found here. The arguments are as follows

`flow::Flow`

: implements the flow of the Cauchy problem though the structure`Flow`

.`M`

: the number of Poincaré sections. If`M == 1`

, then the simple shooting is implemented and the multiple one otherwise.`sections`

: function or callable struct which implements a Poincaré section condition. The evaluation`sections(x)`

must return a scalar number when`M == 1`

. Otherwise, one must implement a function`section(out, x)`

which populates`out`

with the`M`

sections. See`SectionPS`

for type of section defined as a hyperplane.`δ = 1e-8`

used to compute the jacobian of the functional by finite differences. If set to`0`

, an analytical expression of the jacobian is used instead.`interp_points = 50`

number of interpolation point used to define the callback (to compute the hitting of the hyperplane section)`parallel = false`

whether the shooting are computed in parallel (threading). Only available through the use of Flows defined by`EnsembleProblem`

.`par`

parameters of the model`lens`

parameter axis`update_section_every_step`

updates the section every`update_section_every_step`

step during continuation`jacobian::Symbol`

symbol which describes the type of jacobian used in Newton iterations (see below).

**Jacobian**

`jacobian`

Specify the choice of the linear algorithm, which must belong to`[AutoDiffMF(), MatrixFree(), AutodiffDense(), AutoDiffDenseAnalytical(), FiniteDifferences(), FiniteDifferencesMF()]`

. This is used to select a way of inverting the jacobian dG- For
`MatrixFree()`

, matrix free jacobian, the jacobian is specified by the user in`prob`

. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutoDiffMF()`

, we use Automatic Differentiation (AD) to compute the (matrix-free) derivative of`x -> prob(x, p)`

using a directional derivative. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutodiffDense()`

. Same as for`AutoDiffMF`

but the jacobian is formed as a dense Matrix. You can use a direct solver or an iterative one. - For
`FiniteDifferences()`

, same as for`AutoDiffDense`

but we use Finite Differences to compute the jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument. - For
`AutoDiffDenseAnalytical()`

. Same as for`AutoDiffDense`

but the jacobian is formed using a mix of AD and analytical formula. - For
`FiniteDifferencesMF()`

, use Finite Differences to compute the matrix-free jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument.

- For

**Simplified constructors**

The first important constructor is the following which is used for branching to periodic orbits from Hopf bifurcation points pb = PoincareShootingProblem(M::Int, prob::Union{ODEProblem, EnsembleProblem}, alg; kwargs...)

A convenient way is to create a functional is

`pb = PoincareShootingProblem(prob::ODEProblem, alg, section; kwargs...)`

for simple shooting or

`pb = PoincareShootingProblem(prob::Union{ODEProblem, EnsembleProblem}, alg, M::Int, section; kwargs...)`

for multiple shooting . Here `prob`

is an `Union{ODEProblem, EnsembleProblem}`

which is used to create a flow using the ODE solver `alg`

(for example `Tsit5()`

). Finally, the arguments `kwargs`

are passed to the ODE solver defining the flow. We refer to `DifferentialEquations.jl`

for more information.

- Another convenient call is

`pb = PoincareShootingProblem(prob::Union{ODEProblem, EnsembleProblem}, alg, normals::AbstractVector, centers::AbstractVector; δ = 1e-8, kwargs...)`

where `normals`

(resp. `centers`

) is a list of normals (resp. centers) which defines a list of hyperplanes $\Sigma_i$. These hyperplanes are used to define partial Poincaré return maps.

**Computing the functionals**

A functional, hereby called `G`

encodes this shooting problem. You can then call `pb(orbitguess, par)`

to apply the functional to a guess. Note that `orbitguess::AbstractVector`

must be of size M * N where N is the number of unknowns in the state space and `M`

is the number of Poincaré maps. Another accepted `guess`

is such that `guess[i]`

is the state of the orbit on the `i`

th section. This last form allows for non-vector state space which can be convenient for 2d problems for example.

Note that you can generate this guess from a function solution using `generate_solution`

.

`pb(orbitguess, par)`

evaluates the functional G on`orbitguess`

`pb(orbitguess, par, du)`

evaluates the jacobian`dG(orbitguess).du`

functional at`orbitguess`

on`du`

`pb`

(Val(:JacobianMatrixInplace), J, x, par)` compute the jacobian of the functional analytically. This is based on ForwardDiff.jl. Useful mainly for ODEs.`pb(Val(:JacobianMatrix), x, par)`

same as above but out-of-place.

You can use the function `getperiod(pb, sol, par)`

to get the period of the solution `sol`

for the problem with parameters `par`

.

`BifurcationKit.PoincaréMap`

— TypeConstruct a Poincaré return map `Π`

to an hyperplane `Σ`

from a `AbstractPeriodicOrbitProblem`

. If the state space is of size `Nₓ x N𝕪`

, then we can evaluate the map as `Π(xₛ, par)`

where `xₛ ∈ Σ`

is of size `Nₓ x N𝕪`

.

`BifurcationKit.Polynomial`

— Type`Polynomial Tangent predictor`

`n::Int64`

: Order of the polynomial`k::Int64`

: Length of the last solutions vector used for the polynomial fit`A::Matrix{T} where T<:Real`

: Matrix for the interpolation`tangent::BifurcationKit.AbstractTangentComputation`

: Algo for tangent when polynomial predictor is not possible`solutions::DataStructures.CircularBuffer`

: Vector of solutions`parameters::DataStructures.CircularBuffer{T} where T<:Real`

: Vector of parameters`arclengths::DataStructures.CircularBuffer{T} where T<:Real`

: Vector of arclengths`coeffsSol::Vector`

: Coefficients for the polynomials for the solution`coeffsPar::Vector{T} where T<:Real`

: Coefficients for the polynomials for the parameter`update::Bool`

: Update the predictor by adding the last point (x, p)? This can be disabled in order to just use the polynomial prediction. It is useful when the predictor is called mutiple times during bifurcation detection using bisection.

**Constructor(s)**

```
Polynomial(pred, n, k, v0)
Polynomial(n, k, v0)
```

`n`

order of the polynomial`k`

length of the last solutions vector used for the polynomial fit`v0`

example of solution to be stored. It is only used to get the`eltype`

of the tangent.

Can be used like

`PALC(tangent = Polynomial(Bordered(), 2, 6, rand(1)))`

`BifurcationKit.Secant`

— Type`Secant Tangent predictor`

`BifurcationKit.SectionPS`

— Type`struct SectionPS{Tn, Tc, Tnb, Tcb, Tr} <: BifurcationKit.AbstractSection`

This composite type (named for SectionPoincaréShooting) encodes a type of Poincaré sections implemented by hyperplanes. It can be used in conjunction with `PoincareShootingProblem`

. Each hyperplane is defined par a point (one example in `centers`

) and a normal (one example in `normals`

).

`M::Int64`

`normals::Any`

`centers::Any`

`indices::Vector{Int64}`

`normals_bar::Any`

`centers_bar::Any`

`radius::Any`

**Constructor(s)**

`SectionPS(normals::Vector{Tv}, centers::Vector{Tv})`

`BifurcationKit.SectionSS`

— Type`struct SectionSS{Tn, Tc} <: BifurcationKit.AbstractSection`

This composite type (named for Section Standard Shooting) encodes a type of section implemented by a single hyperplane. It can be used in conjunction with `ShootingProblem`

. The hyperplane is defined by a point `center`

and a `normal`

.

`normal::Any`

: Normal to define hyperplane`center::Any`

: Representative point on hyperplane

`BifurcationKit.SetOfEvents`

— Type`struct SetOfEvents{Tc<:Tuple, Td<:Tuple} <: BifurcationKit.AbstractEvent`

Multiple events can be chained together to form a `SetOfEvents`

. A `SetOfEvents`

is constructed by passing to the constructor `ContinuousEvent`

, `DiscreteEvent`

or other `SetOfEvents`

instances:

`SetOfEvents(cb1, cb2, cb3)`

**Example**

` BifurcationKit.SetOfEvents(BK.FoldDetectCB, BK.BifDetectCB)`

You can pass as many events as you like.

`eventC::Tuple`

: Continuous event`eventD::Tuple`

: Discrete event

`BifurcationKit.ShootingProblem`

— Type`pb = ShootingProblem(flow::Flow, ds, section; parallel = false)`

Create a problem to implement the Simple / Parallel Multiple Standard Shooting method to locate periodic orbits. More details (maths, notations, linear systems) can be found here. The arguments are as follows

`flow::Flow`

: implements the flow of the Cauchy problem though the structure`Flow`

.`ds`

: vector of time differences for each shooting. Its length is written`M`

. If`M == 1`

, then the simple shooting is implemented and the multiple one otherwise.`section`

: implements a phase condition. The evaluation`section(x, T)`

must return a scalar number where`x`

is a guess for**one point**on the periodic orbit and`T`

is the period of the guess. Also, the method`section(x, T, dx, dT)`

must be available and which returns the differential of`section`

. The type of`x`

depends on what is passed to the newton solver. See`SectionSS`

for a type of section defined as a hyperplane.`parallel`

whether the shooting is computed in parallel (threading). Available through the use of Flows defined by`EnsembleProblem`

(this is automatically set up for you).`par`

parameters of the model`lens`

parameter axis`update_section_every_step`

updates the section every`update_section_every_step`

step during continuation`jacobian::Symbol`

symbol which describes the type of jacobian used in Newton iterations (see below).

A functional, hereby called `G`

, encodes the shooting problem. For example, the following methods are available:

`pb(orbitguess, par)`

evaluates the functional G on`orbitguess`

`pb(orbitguess, par, du)`

evaluates the jacobian`dG(orbitguess)⋅du`

functional at`orbitguess`

on`du`

.`pb`

(Val(:JacobianMatrixInplace), J, x, par)` compute the jacobian of the functional analytically. This is based on ForwardDiff.jl. Useful mainly for ODEs.`pb(Val(:JacobianMatrix), x, par)`

same as above but out-of-place.

You can then call `pb(orbitguess, par)`

to apply the functional to a guess. Note that `orbitguess::AbstractVector`

must be of size `M * N + 1`

where N is the number of unknowns of the state space and `orbitguess[M * N + 1]`

is an estimate of the period `T`

of the limit cycle. This form of guess is convenient for the use of the linear solvers in `IterativeSolvers.jl`

(for example) which only accept `AbstractVector`

s. Another accepted guess is of the form `BorderedArray(guess, T)`

where `guess[i]`

is the state of the orbit at the `i`

th time slice. This last form allows for non-vector state space which can be convenient for 2d problems for example, use `GMRESKrylovKit`

for the linear solver in this case.

Note that you can generate this guess from a function solution using `generate_solution`

.

**Jacobian**

`jacobian`

Specify the choice of the linear algorithm, which must belong to`[AutoDiffMF(), MatrixFree(), AutodiffDense(), AutoDiffDenseAnalytical(), FiniteDifferences(), FiniteDifferencesMF()]`

. This is used to select a way of inverting the jacobian dG- For
`MatrixFree()`

, matrix free jacobian, the jacobian is specified by the user in`prob`

. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutoDiffMF()`

, we use Automatic Differentiation (AD) to compute the (matrix-free) derivative of`x -> prob(x, p)`

using a directional derivative. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutodiffDense()`

. Same as for`AutoDiffMF`

but the jacobian is formed as a dense Matrix. You can use a direct solver or an iterative one. - For
`FiniteDifferences()`

, same as for`AutoDiffDense`

but we use Finite Differences to compute the jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument. - For
`AutoDiffDenseAnalytical()`

. Same as for`AutoDiffDense`

but the jacobian is formed using a mix of AD and analytical formula. - For
`FiniteDifferencesMF()`

, use Finite Differences to compute the matrix-free jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument.

- For

**Simplified constructors**

- The first important constructor is the following which is used for branching to periodic orbits from Hopf bifurcation points:

`pb = ShootingProblem(M::Int, prob::Union{ODEProblem, EnsembleProblem}, alg; kwargs...)`

- A convenient way to build the functional is to use:

`pb = ShootingProblem(prob::Union{ODEProblem, EnsembleProblem}, alg, centers::AbstractVector; kwargs...)`

where `prob`

is an `ODEProblem`

(resp. `EnsembleProblem`

) which is used to create a flow using the ODE solver `alg`

(for example `Tsit5()`

). `centers`

is list of `M`

points close to the periodic orbit, they will be used to build a constraint for the phase. `parallel = false`

is an option to use Parallel simulations (Threading) to simulate the multiple trajectories in the case of multiple shooting. This is efficient when the trajectories are relatively long to compute. Finally, the arguments `kwargs`

are passed to the ODE solver defining the flow. Look at `DifferentialEquations.jl`

for more information. Note that, in this case, the derivative of the flow is computed internally using Finite Differences.

- Another way to create a Shooting problem with more options is the following where in particular, one can provide its own scalar constraint
`section(x)::Number`

for the phase:

`pb = ShootingProblem(prob::Union{ODEProblem, EnsembleProblem}, alg, M::Int, section; parallel = false, kwargs...)`

or

`pb = ShootingProblem(prob::Union{ODEProblem, EnsembleProblem}, alg, ds, section; parallel = false, kwargs...)`

- The next way is an elaboration of the previous one

`pb = ShootingProblem(prob1::Union{ODEProblem, EnsembleProblem}, alg1, prob2::Union{ODEProblem, EnsembleProblem}, alg2, M::Int, section; parallel = false, kwargs...)`

or

`pb = ShootingProblem(prob1::Union{ODEProblem, EnsembleProblem}, alg1, prob2::Union{ODEProblem, EnsembleProblem}, alg2, ds, section; parallel = false, kwargs...)`

where we supply now two `ODEProblem`

s. The first one `prob1`

, is used to define the flow associated to `F`

while the second one is a problem associated to the derivative of the flow. Hence, `prob2`

must implement the following vector field $\tilde F(x,y,p) = (F(x,p), dF(x,p)\cdot y)$.

`BifurcationKit.SpecialPoint`

— Type`struct SpecialPoint{T, Tp, Tv, Tvτ} <: BifurcationKit.AbstractBifurcationPoint`

Structure to record special points on a curve. There are two types of special points that are recorded in this structure: bifurcation points and events (see https://bifurcationkit.github.io/BifurcationKitDocs.jl/dev/EventCallback/).

`type::Symbol`

: Description of the special points. In case of Events, this field records the user passed named to the event, or the default`:userD`

,`:userC`

. In case of bifurcation points, it can be one of the following:`- :bp Bifurcation point, simple eigenvalue crossing the imaginary axis - :fold Fold point - :hopf Hopf point - :nd not documented bifurcation point. Detected by multiple eigenvalues crossing. Generally occurs in problems with symmetries or in cases where the continuation step size is too large and merge two different bifurcation points. - :cusp Cusp point - :gh Generalized Hopf point (also called Bautin point) - :bt Bogdanov-Takens point - :zh Zero-Hopf point - :hh Hopf-Hopf point - :ns Neimark-Sacker point - :pd Period-doubling point - :R1 Strong resonance 1:1 of periodic orbits - :R2 Strong resonance 1:2 of periodic orbits - :R3 Strong resonance 1:3 of periodic orbits - :R4 Strong resonance 1:4 of periodic orbits - :foldFlip Fold / Flip of periodic orbits - :foldNS Fold / Neimark-Sacker of periodic orbits - :pdNS Period-Doubling / Neimark-Sacker of periodic orbits - :gpd Generalized Period-Doubling of periodic orbits - :nsns Double Neimark-Sacker of periodic orbits - :ch Chenciner bifurcation of periodic orbits Default: :none`

`idx::Int64`

: Index in`br.branch`

or`br.eig`

(see`ContResult`

) for which the bifurcation occurs. Default: 0`param::Any`

: Parameter value at the special point (this is an estimate). Default: 0.0`norm::Any`

: Norm of the equilibrium at the special point Default: 0.0`printsol::Any`

:`printsol = record_from_solution(x, param)`

where`record_from_solution`

is one of the arguments to`continuation`

Default: 0.0`x::Any`

: Equilibrium at the special point Default: Vector{T}(undef, 0)`τ::BorderedArray{Tvτ, T} where {T, Tvτ}`

: Tangent along the branch at the special point Default: BorderedArray(x, T(0))`ind_ev::Int64`

: Eigenvalue index responsible for detecting the special point (if applicable) Default: 0`step::Int64`

: Continuation step at which the special occurs Default: 0`status::Symbol`

:`status ∈ {:converged, :guess, :guessL}`

indicates whether the bisection algorithm was successful in detecting the special (bifurcation) point. If`status == :guess`

, the bissection algorithm failed to meet the requirements given in`::ContinuationPar`

. Same for`status == :guessL`

but the bissection algorithm stopped on the left of the bifurcation point. Default: :guess`δ::Tuple{Int64, Int64}`

:`δ = (δr, δi)`

where δr indicates the change in the number of unstable eigenvalues and δi indicates the change in the number of unstable eigenvalues with nonzero imaginary part.`abs(δr)`

is thus an estimate of the dimension of the kernel of the Jacobian at the special (bifurcation) point. Default: (0, 0)`precision::Any`

: Precision in the location of the special point Default: -1`interval::Tuple{T, T} where T`

: Interval parameter containing the special point Default: (0, 0)

`BifurcationKit.TWProblem`

— TypeTWProblem(prob, ∂::Tuple, u₀; DAE = 0, jacobian::Symbol = :AutoDiff)

This composite type implements a functional for freezing symmetries in order, for example, to compute travelling waves (TW). Note that you can freeze many symmetries, not just one, by passing many Lie generators. When you call `pb(x, par)`

, it computes:

```
┌ ┐
│ f(x, par) - s⋅∂⋅x │
│ <x - u₀, ∂⋅u₀> │
└ ┘
```

**Arguments**

`prob`

bifurcation problem with continuous symmetries`∂::Tuple = (T1, T2, ⋯)`

tuple of Lie generators. In effect, each of these is an (differential) operator which can be specified as a (sparse) matrix or as an operator implementing`LinearAlgebra.mul!`

.`u₀`

reference solution

**Additional Constructor(s)**

`pb = TWProblem(prob, ∂, u₀; kw...)`

This simplified call handles the case where a single symmetry needs to be frozen.

**Useful function**

`updatesection!(pb::TWProblem, u0)`

updates the reference solution of the problem using`u0`

.`nb_constraints(::TWProblem)`

number of constraints (or Lie generators)

`BifurcationKit.Transcritical`

— Type`mutable struct Transcritical{Tv, Tτ, T, Tpar, Tlens<:Lens, Tevl, Tevr, Tnf} <: BifurcationKit.AbstractSimpleBranchPoint`

`x0::Any`

: Bifurcation point.`τ::Any`

: Tangent of the curve at the bifurcation point.`p::Any`

: Parameter value at the bifurcation point.`params::Any`

: Parameters used by the vector field.`lens::Lens`

: Parameter axis used to compute the branch on which this bifurcation point was detected.`ζ::Any`

: Right eigenvector(s).`ζ★::Any`

: Left eigenvector(s).`nf::Any`

: Normal form coefficients.`type::Symbol`

: Type of bifurcation point

**Predictor**

`predictor(bp, ds; kwargs...)`

on such bifurcation point `bp`

to find the zeros of the normal form polynomials.

`BifurcationKit.TranscriticalMap`

— Type`mutable struct TranscriticalMap{Tv, Tτ, T, Tpar, Tlens<:Lens, Tevl, Tevr, Tnf} <: BifurcationKit.AbstractSimpleBranchPointForMaps`

`x0::Any`

: Bifurcation point.`τ::Any`

: Tangent of the curve at the bifurcation point.`p::Any`

: Parameter value at the bifurcation point.`params::Any`

: Parameters used by the vector field.`lens::Lens`

: Parameter axis used to compute the branch on which this bifurcation point was detected.`ζ::Any`

: Right eigenvector(s).`ζ★::Any`

: Left eigenvector(s).`nf::Any`

: Normal form coefficients.`type::Symbol`

: Type of bifurcation point

**Predictor**

`predictor(bp, ds; kwargs...)`

on such bifurcation point `bp`

to find the zeros of the normal form polynomials.

`BifurcationKit.TrilinearMap`

— Type`struct TrilinearMap{Tm}`

This structure wraps a trilinear map to allow evaluation on Complex arguments. This is especially useful when these maps are produced by ForwardDiff.jl.

`BifurcationKit.WrapPOColl`

— Type`struct WrapPOColl{Tprob, Tjac, Tu0, Tp, Tl<:Union{Nothing, Lens}, Tplot, Trecord} <: BifurcationKit.AbstractBifurcationProblem`

Problem wrap of a functional. It is not meant to be used directly albeit perhaps by advanced users.

`prob::Any`

`jacobian::Any`

`u0::Any`

`params::Any`

`lens::Union{Nothing, Lens}`

`plotSolution::Any`

`recordFromSolution::Any`

`BifurcationKit.WrapPOSh`

— Type`struct WrapPOSh{Tprob, Tjac, Tu0, Tp, Tl<:Union{Nothing, Lens}, Tplot, Trecord} <: BifurcationKit.AbstractBifurcationProblem`

Problem wrap of a functional. It is not meant to be used directly albeit perhaps by advanced users.

`prob::Any`

`jacobian::Any`

`u0::Any`

`params::Any`

`lens::Union{Nothing, Lens}`

`plotSolution::Any`

`recordFromSolution::Any`

`BifurcationKit.WrapPOTrap`

— Type`struct WrapPOTrap{Tprob, Tjac, Tu0, Tp, Tl<:Union{Nothing, Lens}, Tplot, Trecord} <: BifurcationKit.AbstractBifurcationProblem`

Problem wrap of a functional. It is not meant to be used directly albeit perhaps by advanced users.

`prob::Any`

`jacobian::Any`

`u0::Any`

`params::Any`

`lens::Union{Nothing, Lens}`

`plotSolution::Any`

`recordFromSolution::Any`

`BifurcationKit.WrapTW`

— Type`struct WrapTW{Tprob, Tjac, Tu0, Tp, Tl<:Union{Nothing, Lens}, Tplot, Trecord} <: BifurcationKit.AbstractBifurcationProblem`

Problem wrap of a functional. It is not meant to be used directly albeit perhaps by advanced users.

`prob::Any`

`jacobian::Any`

`u0::Any`

`params::Any`

`lens::Union{Nothing, Lens}`

`plotSolution::Any`

`recordFromSolution::Any`

`BifurcationKit.ZeroHopf`

— Type`mutable struct ZeroHopf{Tv, Tpar, Tlens, Tevr, Tevl, Tnf} <: BifurcationKit.AbstractBifurcationPoint`

`x0::Any`

: Bifurcation point`params::Any`

: Parameters used by the vector field.`lens::Any`

: Parameter axis used to compute the branch on which this cusp point was detected.`ζ::Any`

: Right eigenvector`ζ★::Any`

: Left eigenvector`nf::Any`

: Normal form coefficients`type::Symbol`

: Type of bifurcation

`BifurcationKit.cbMaxNorm`

— Type`cb = cbMaxNorm(maxres)`

Create a callback used to reject residuals larger than `cb.maxres`

in the Newton iterations. See docs for `newton`

.

`Base.size`

— Function```
size(tree)
size(tree, code)
```

Return the size of the bifurcation diagram. The argument `code`

is the same as in `get_branch`

.

`Base.size`

— MethodThe method `size`

returns (n, m, Ntst) when applied to a `PeriodicOrbitOCollProblem`

`BifurcationKit.Aγ!`

— MethodFunction to compute the Matrix-Free version of Aγ, see docs for its expression.

`BifurcationKit.HopfPoint`

— MethodFor an initial guess from the index of a Hopf bifurcation point located in ContResult.specialpoint, returns a point which can be refined using `newton_hopf`

.

`BifurcationKit.Jc`

— MethodFunction to compute the Matrix-Free version of the cyclic matrix Jc, see docs for its expression.

`BifurcationKit.PoincareMap`

— Method```
PoincareMap(wrap, po, par, optn)
```

Constructor for the Poincaré return map. Return a `PoincaréMap`

`BifurcationKit.PoincareMap`

— Method```
PoincareMap(wrap, po, par, optn)
```

Constructor for the Poincaré return map. Return a `PoincaréMap`

`BifurcationKit.PrecPartialSchurArnoldiMethod`

— Function`PrecPartialSchurArnoldiMethod(J, N, nev, which = LM(); tol = 1e-9, kwargs...)`

Builds a preconditioner based on deflation of `nev`

eigenvalues chosen according to `which`

. A partial Schur decomposition is computed (Matrix-Free), using the package `ArnoldiMethod.jl`

, from which a projection is built. See the package `ArnoldiMethod.jl`

for how to pass the proper options.

`BifurcationKit.PrecPartialSchurKrylovKit`

— Function`PrecPartialSchurKrylovKit(J, x0, nev, which = :LM; krylovdim = max(2nev, 20), verbosity = 0)`

Builds a preconditioner based on deflation of `nev`

eigenvalues chosen according to `which`

. A partial Schur decomposition is computed (Matrix-Free), using the package `KrylovKit.jl`

, from which a projection is built. The options are similar to the ones of `EigKrylovKit()`

.

`BifurcationKit.SaveAtEvent`

— Method``SaveAtEvent(positions::Tuple)``

This event implements the detection of when the parameter values, used during continuation, equals one of the values in `positions`

. This state is then saved in the branch.

For example, you can use it like `continuation(args...; event = SaveAtEvent((1., 2., -3.)))`

`BifurcationKit._axpy`

— MethodThis function returns a₀ * I + a₁ * J and ensures that we don't perform unnecessary computations like 0*I + 1*J.

`BifurcationKit._axpy_op`

— MethodThis function implements the operator a₀ * I + a₁ * J and ensures that we don't perform unnecessary computations like 0*I + 1*J.

`BifurcationKit._cat!`

— Method```
_cat!(br, br2)
```

Merge two `ContResult`

s and put the result in `br`

.

`BifurcationKit._contresult`

— Method```
_contresult(
prob,
alg,
printsol,
br,
x0,
τ,
eiginfo,
contParams,
computeEigElements,
kind
)
```

Function is used to initialize the composite type `ContResult`

according to the options contained in `contParams`

**Arguments**

`br`

result from`get_state_summary`

`par`

: parameters`lens`

: lens to specify the continuation parameter`eiginfo`

: eigen-elements (eigvals, eigvecs)

`BifurcationKit._isinplace`

— MethodDetermine if the vector field is of the form `f!(out,z,p)`

.

`BifurcationKit._keep_opts_cont`

— MethodInternal function to select the keys out of nt that are valid for the continuation function below. Can be used like `foo(kw...) = _keep_opts_cont(values(nt))`

`BifurcationKit._merge`

— MethodSame as _cat! but determine the ordering so that the branches merge properly

`BifurcationKit.analytical_jacobian!`

— Method```
analytical_jacobian!(
J,
coll,
u,
pars;
_transpose,
ρD,
ρF,
ρI
)
```

Compute the jacobian of the problem defining the periodic orbits by orthogonal collocation using an analytical formula. More precisely, it discretises

ρD * D - T*(ρF * F + ρI * I)

`BifurcationKit.applyD`

— Method`ss`

tuple of speeds`D`

tuple of Lie generators

`BifurcationKit.bifurcation_points`

— Method```
bifurcation_points(br)
```

Return the list of bifurcation points on a branch. It essentially filters the field `specialpoint`

.

`BifurcationKit.bifurcationdiagram!`

— Method```
bifurcationdiagram!(
prob,
node,
maxlevel,
options;
code,
halfbranch,
verbosediagram,
kwargs...
)
```

Similar to `bifurcationdiagram`

but you pass a previously computed `node`

from which you want to further compute the bifurcated branches. It is usually used with `node = get_branch(diagram, code)`

from a previously computed bifurcation `diagram`

.

**Arguments**

`node::BifDiagNode`

a node in the bifurcation diagram`maxlevel = 1`

required maximal level of recursion.`options = (x, p, level) -> contparams`

this function allows to change the`continuation`

options depending on the branching`level`

. The argument`x, p`

denotes the current solution to`F(x, p)=0`

.

**Optional arguments**

`code = "0"`

code used to display iterations`usedeflation = false`

`halfbranch = false`

for Pitchfork / Transcritical bifurcations, compute only half of the branch. Can be useful when there are symmetries.`verbosediagram`

verbose specific to bifurcation diagram. Print information about the branches as they are being computed.`kwargs`

optional arguments as for`continuation`

but also for the different versions listed in Continuation.

`BifurcationKit.bifurcationdiagram`

— Method```
bifurcationdiagram(
prob,
alg,
level,
options;
linear_algo,
kwargs...
)
```

Compute the bifurcation diagram associated with the problem `F(x, p) = 0`

recursively.

**Arguments**

`prob::AbstractBifurcationProblem`

bifurcation problem`alg`

continuation algorithm`level`

maximum branching (or recursion) level for computing the bifurcation diagram`options = (x, p, level) -> contparams`

this function allows to change the`continuation`

options depending on the branching`level`

. The argument`x, p`

denotes the current solution to`F(x, p)=0`

.`kwargs`

optional arguments. Look at`bifurcationdiagram!`

for more details.

**Simplified call:**

We also provide the method

`bifurcationdiagram(prob, br::ContResult, level::Int, options; kwargs...)`

where `br`

is a branch computed after a call to `continuation`

from which we want to compute the bifurcating branches recursively.

`BifurcationKit.biorthogonalise`

— Method```
biorthogonalise(ζs, ζ★s, verbose; _dot)
```

Bi-orthogonalise the two sets of vectors.

**Optional argument**

`_dot = dot`

specify your own dot product

`BifurcationKit.bogdanov_takens_normal_form`

— Method```
bogdanov_takens_normal_form(
prob_ma,
L,
pt;
δ,
verbose,
detailed,
autodiff,
bls,
bls_block
)
```

Compute the Bogdanov-Takens normal form.

**Arguments**

`prob_ma`

a`FoldProblemMinimallyAugmented`

or`HopfProblemMinimallyAugmented`

`pt::BogdanovTakens`

BogdanovTakens bifurcation point`ls`

linear solver

**Optional arguments**

`δ = 1e-8`

used for finite differences`verbose`

bool to print information`autodiff = true`

only for Bogdanov-Takens point. Whether to use ForwardDiff for the many differentiations that are required to compute the normal form.`detailed = true`

only for Bogdanov-Takens point. Whether to compute only a simplified normal form.

`BifurcationKit.bogdanov_takens_normal_form`

— Method```
bogdanov_takens_normal_form(
_prob,
br,
ind_bif;
δ,
nev,
verbose,
ζs,
ζs_ad,
lens,
Teigvec,
scaleζ,
bls,
bls_adjoint,
bls_block,
detailed,
autodiff
)
```

Compute the Bogdanov-Takens normal form.

**Arguments**

`prob`

bifurcation problem, typically`br.prob`

`br`

branch result from a call to`continuation`

`ind_bif`

index of the bifurcation point in`br`

`options`

options for the Newton solver

**Optional arguments**

`δ = 1e-8`

used for finite differences with respect to parameters`nev = 5`

number of eigenvalues to compute to estimate the spectral projector`verbose`

bool to print information`autodiff = true`

Whether to use ForwardDiff for the many differentiations that are required to compute the normal form.`detailed = true`

Whether to compute only a simplified normal form where not all coefficients are computed.`ζs`

list of vectors spanning the kernel of`dF`

at the bifurcation point. Useful to enforce the basis for the normal form.`ζs_ad`

list of vectors spanning the kernel of`transpose(dF)`

at the bifurcation point. Useful to enforce the basis for the normal form. The vectors must be listed so that the corresponding eigenvalues are equals to the ones associated to each vector in ζs.`scaleζ`

function to normalise the kernel basis. Indeed, when used with large vectors and`norm`

, it results in ζs and the normal form coefficient being super small.`bls`

specify Bordered linear solver for dF.`bls_adjoint`

specify Bordered linear solver for transpose(dF).

`BifurcationKit.branch_normal_form`

— Method[WIP] Note that the computation of this normal form is not implemented yet.

`BifurcationKit.bt_point`

— MethodFor an initial guess from the index of a BT bifurcation point located in ContResult.specialpoint, returns a point which will be refined using `newtonBT`

.

`BifurcationKit.compute_error!`

— Method```
compute_error!(coll, x; normE, verbosity, K, par, kw...)
```

Perform mesh adaptation of the periodic orbit problem. Modify `pb`

and `x`

inplace if the adaptation is successfull.

See page 367 of [1] and also [2].

References: [1] Ascher, Uri M., Robert M. M. Mattheij, and Robert D. Russell. Numerical Solution of Boundary Value Problems for Ordinary Differential Equations. Society for Industrial and Applied Mathematics, 1995. https://doi.org/10.1137/1.9781611971231.

[2] R. D. Russell and J. Christiansen, “Adaptive Mesh Selection Strategies for Solving Boundary Value Problems,” SIAM Journal on Numerical Analysis 15, no. 1 (February 1978): 59–80, https://doi.org/10.1137/0715004.

`BifurcationKit.continuation`

— Function```
continuation(br, ind_bif, lens2; ...)
continuation(
br,
ind_bif,
lens2,
options_cont;
prob,
start_with_eigen,
detect_codim2_bifurcation,
update_minaug_every_step,
kwargs...
)
```

Codimension 2 continuation of Fold / Hopf points. This function turns an initial guess for a Fold / Hopf point into a curve of Fold / Hopf points based on a Minimally Augmented formulation. The arguments are as follows

`br`

results returned after a call to continuation`ind_bif`

bifurcation index in`br`

`lens2`

second parameter used for the continuation, the first one is the one used to compute`br`

, e.g.`getlens(br)`

`options_cont = br.contparams`

arguments to be passed to the regular continuation

**Optional arguments:**

`bdlinsolver`

bordered linear solver for the constraint equation`update_minaug_every_step`

update vectors`a, b`

in Minimally Formulation every`update_minaug_every_step`

steps`start_with_eigen = false`

whether to start the Minimally Augmented problem with information from eigen elements`detect_codim2_bifurcation ∈ {0,1,2}`

whether to detect Bogdanov-Takens, Bautin and Cusp. If equals`1`

non precise detection is used. If equals`2`

, a bisection method is used to locate the bifurcations.`kwargs`

keywords arguments to be passed to the regular continuation

where the parameters are as above except that you have to pass the branch `br`

from the result of a call to `continuation`

with detection of bifurcations enabled and `index`

is the index of Hopf point in `br`

you want to refine.

For ODE problems, it is more efficient to use the Matrix based Bordered Linear Solver passing the option `bdlinsolver = MatrixBLS()`

It is recommended that you use the option `start_with_eigen = true`

`BifurcationKit.continuation`

— Method```
continuation(
probPO,
orbitguess,
alg,
contParams,
linear_algo;
δ,
eigsolver,
record_from_solution,
plot_solution,
kwargs...
)
```

This is the continuation method for computing a periodic orbit using a (Standard / Poincaré) Shooting method.

**Arguments**

Similar to `continuation`

except that `probPO`

is either a `ShootingProblem`

or a `PoincareShootingProblem`

. By default, it prints the period of the periodic orbit.

**Optional arguments**

`eigsolver`

specify an eigen solver for the computation of the Floquet exponents, defaults to`FloquetQaD`

`jacobian`

Specify the choice of the linear algorithm, which must belong to`[AutoDiffMF(), MatrixFree(), AutodiffDense(), AutoDiffDenseAnalytical(), FiniteDifferences(), FiniteDifferencesMF()]`

. This is used to select a way of inverting the jacobian dG- For
`MatrixFree()`

, matrix free jacobian, the jacobian is specified by the user in`prob`

. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutoDiffMF()`

, we use Automatic Differentiation (AD) to compute the (matrix-free) derivative of`x -> prob(x, p)`

using a directional derivative. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutodiffDense()`

. Same as for`AutoDiffMF`

but the jacobian is formed as a dense Matrix. You can use a direct solver or an iterative one. - For
`FiniteDifferences()`

, same as for`AutoDiffDense`

but we use Finite Differences to compute the jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument. - For
`AutoDiffDenseAnalytical()`

. Same as for`AutoDiffDense`

but the jacobian is formed using a mix of AD and analytical formula. - For
`FiniteDifferencesMF()`

, use Finite Differences to compute the matrix-free jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument.

- For

`BifurcationKit.continuation`

— Method```
continuation(
prob,
alg,
contparams;
linear_algo,
bothside,
kwargs...
)
```

Compute the continuation curve associated to the functional `F`

which is stored in the bifurcation problem `prob`

. General information is available in Continuation methods: introduction.

**Arguments:**

`prob::AbstractBifurcationFunction`

a`::AbstractBifurcationProblem`

, typically a`BifurcationProblem`

which holds the vector field and its jacobian. We also refer to`BifFunction`

for more details.`alg`

continuation algorithm, for example`Natural(), PALC(), Multiple(),...`

. See algos`contparams::ContinuationPar`

parameters for continuation. See`ContinuationPar`

**Optional Arguments:**

`plot = false`

whether to plot the solution/branch/spectrum while computing the branch`bothside = true`

compute the branches on the two sides of the initial parameter value`p0`

, merge them and return it.`normC = norm`

norm used in the nonlinear solves`filename`

to save the computed branch during continuation. The identifier .jld2 will be appended to this filename. This requires`using JLD2`

.`callback_newton`

callback for newton iterations. See docs of`newton`

. For example, it can be used to change the preconditioners.`finalise_solution = (z, tau, step, contResult; kwargs...) -> true`

Function called at the end of each continuation step. Can be used to alter the continuation procedure (stop it by returning`false`

), save personal data, plot... The notations are`z = BorderedArray(x, p)`

where`x`

(resp.`p`

) is the current solution (resp. parameter value),`tau::BorderedArray`

is the tangent at`z`

,`step::Int`

is the index of the current continuation step and`contResult`

is the current branch. For advanced use:- the state
`state::ContState`

of the continuation iterator is passed in`kwargs`

. This can be used for testing whether this is called from bisection for locating bifurcation points / events:`in_bisection(state)`

for example. This allows to escape some personal code in this case.

- the iterator
`iter::ContIterable`

of the continuation is passed in`kwargs`

.

- the state
`verbosity::Int = 0`

controls the amount of information printed during the continuation process. Must belong to`{0,1,2,3}`

. In case`contparams.newton_options.verbose = false`

, the following is valid (otherwise the newton iterations are shown). Each case prints more information than the previous one:- case 0: print nothing
- case 1: print basic information about the continuation: used predictor, step size and parameter values
- case 2: print newton iterations number, stability of solution, detected bifurcations / events
- case 3: print information during bisection to locate bifurcations / events

`linear_algo`

set the linear solver for the continuation algorithm`alg.`

For example,`PALC`

needs a linear solver for an enlarged problem (size`n+1`

instead of`n`

) and one thus needs to tune the one passed in`contparams.newton_options.linsolver`

. This is a convenient argument to thus change the`alg`

linear solver and is used mostly internally. The proper way is to pass directly to`alg`

the correct linear solver.`kind::AbstractContinuationKind`

[Internal] flag to describe continuation kind (equilibrium, codim 2, ...). Default =`EquilibriumCont()`

**Output:**

`contres::ContResult`

composite type which contains the computed branch. See`ContResult`

for more information.

Just change the sign of `ds`

in `ContinuationPar`

.

Use debug mode to access more irformation about the progression of the continuation run, like iterative solvers convergence, problem update, ...

`BifurcationKit.continuation`

— Method```
continuation(
prob,
algdc,
contParams;
verbosity,
plot,
linear_algo,
dot_palc,
callback_newton,
filename,
normC,
kwcont...
)
```

This function computes the set of curves of solutions `γ(s) = (x(s), p(s))`

to the equation `F(x,p) = 0`

based on the algorithm of **deflated continuation** as described in Farrell, Patrick E., Casper H. L. Beentjes, and Ásgeir Birkisson. “The Computation of Disconnected Bifurcation Diagrams.” ArXiv:1603.00809 [Math], March 2, 2016. http://arxiv.org/abs/1603.00809.

Depending on the options in `contParams`

, it can locate the bifurcation points on each branch. Note that you can specify different predictors using `alg`

.

**Arguments:**

`prob::AbstractBifurcationProblem`

bifurcation problem`alg::DefCont`

, deflated continuation algorithm, see`DefCont`

`contParams`

parameters for continuation. See`ContinuationPar`

for more information about the options

**Optional Arguments:**

`plot = false`

whether to plot the solution while computing,`callback_newton`

callback for newton iterations. see docs for`newton`

. Can be used to change preconditioners or affect the newton iterations. In the deflation part of the algorithm, when seeking for new branches, the callback is passed the keyword argument`fromDeflatedNewton = true`

to tell the user can it is not in the continuation part (regular newton) of the algorithm,`verbosity::Int`

controls the amount of information printed during the continuation process. Must belong to`{0,⋯,5}`

,`normC = norm`

norm used in the Newton solves,`dot_palc = (x, y) -> dot(x, y) / length(x)`

, dot product used to define the weighted dot product (resp. norm) $\|(x, p)\|^2_\theta$ in the constraint $N(x, p)$ (see online docs on PALC). This argument can be used to remove the factor`1/length(x)`

for example in problems where the dimension of the state space changes (mesh adaptation, ...),

**Outputs:**

`contres::DCResult`

composite type which contains the computed branches. See`ContResult`

for more information,

`BifurcationKit.continuation`

— Method```
continuation(
br,
ind_bif,
_contParams,
pbPO;
prob_vf,
alg,
δp,
ampfactor,
usedeflation,
nev,
kwargs...
)
```

Perform automatic branch switching from a Hopf bifurcation point labelled `ind_bif`

in the list of the bifurcated points of a previously computed branch `br::ContResult`

. It first computes a Hopf normal form.

**Arguments**

`br`

branch result from a call to`continuation`

`ind_hopf`

index of the bifurcation point in`br`

`contParams`

parameters for the call to`continuation`

`probPO`

problem used to specify the way the periodic orbit is computed. It can be`PeriodicOrbitTrapProblem`

,`ShootingProblem`

or`PoincareShootingProblem`

.

**Optional arguments**

`alg = br.alg`

continuation algorithm`δp`

used to specify a particular guess for the parameter on the bifurcated branch which is otherwise determined by`contParams.ds`

. This allows to use a step larger than`contParams.dsmax`

.`ampfactor = 1`

factor to alter the amplitude of the bifurcated solution. Useful to magnify the bifurcated solution when the bifurcated branch is very steep.`usedeflation = true`

whether to use nonlinear deflation (see Deflated problems) to help finding the guess on the bifurcated branch`nev`

number of eigenvalues to be computed to get the right eigenvector- all
`kwargs`

from`continuation`

A modified version of `prob`

is passed to `plot_solution`

and `finalise_solution`

.

You have to be careful about the options `contParams.newton_options.linsolver`

. In the case of Matrix-Free solver, you have to pass the right number of unknowns `N * M + 1`

. Note that the options for the preconditioner are not accessible yet.

`BifurcationKit.continuation`

— Method```
continuation(
prob,
orbitguess,
alg,
_contParams;
linear_algo,
kwargs...
)
```

This is the continuation routine for computing a periodic orbit using a (Standard / Poincaré) Shooting method.

**Arguments**

Similar to `continuation`

except that `prob`

is either a `ShootingProblem`

or a `PoincareShootingProblem`

. By default, it prints the period of the periodic orbit.

**Optional argument**

`linear_algo::AbstractBorderedLinearSolver`

`jacobian`

Specify the choice of the linear algorithm, which must belong to- For
`MatrixFree()`

, matrix free jacobian, the jacobian is specified by the user in`prob`

. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutoDiffMF()`

, we use Automatic Differentiation (AD) to compute the (matrix-free) derivative of`x -> prob(x, p)`

using a directional derivative. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutodiffDense()`

. Same as for`AutoDiffMF`

but the jacobian is formed as a dense Matrix. You can use a direct solver or an iterative one. - For
`FiniteDifferences()`

, same as for`AutoDiffDense`

but we use Finite Differences to compute the jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument. - For
`AutoDiffDenseAnalytical()`

. Same as for`AutoDiffDense`

but the jacobian is formed using a mix of AD and analytical formula. - For
`FiniteDifferencesMF()`

, use Finite Differences to compute the matrix-free jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument.

- For

`BifurcationKit.continuation`

— Method```
continuation(
probPO,
orbitguess,
alg,
_contParams,
linear_algo;
δ,
eigsolver,
record_from_solution,
plot_solution,
kwargs...
)
```

This is the continuation method for computing a periodic orbit using an orthogonal collocation method.

**Arguments**

Similar to `continuation`

except that `prob`

is a `PeriodicOrbitOCollProblem`

. By default, it prints the period of the periodic orbit.

**Keywords arguments**

`eigsolver`

specify an eigen solver for the computation of the Floquet exponents, defaults to`FloquetQaD`

`BifurcationKit.continuation`

— Method```
continuation(
prob,
orbitguess,
alg,
_contParams;
record_from_solution,
linear_algo,
kwargs...
)
```

This is the continuation routine for computing a periodic orbit using a functional G based on Finite Differences and a Trapezoidal rule.

**Arguments**

`prob::PeriodicOrbitTrapProblem`

encodes the functional G`orbitguess`

a guess for the periodic orbit where`orbitguess[end]`

is an estimate of the period of the orbit. It could be a vector of size`N * M + 1`

where`M`

is the number of time slices,`N`

is the dimension of the phase space. This must be compatible with the numbers`N, M`

in`prob`

.`alg`

continuation algorithm`contParams`

same as for the regular`continuation`

method

**Keyword arguments**

`linear_algo`

same as in`continuation`

Specify the choice of the jacobian (and linear algorithm), `jacobian`

must belong to `[:FullLU, :FullSparseInplace, :Dense, :DenseAD, :BorderedLU, :BorderedSparseInplace, :FullMatrixFree, :BorderedMatrixFree, :FullMatrixFreeAD]`

. This is used to select a way of inverting the jacobian `dG`

of the functional G.

- For
`jacobian = :FullLU`

, we use the default linear solver based on a sparse matrix representation of`dG`

. This matrix is assembled at each newton iteration. This is the default algorithm. - For
`jacobian = :FullSparseInplace`

, this is the same as for`:FullLU`

but the sparse matrix`dG`

is updated inplace. This method allocates much less. In some cases, this is significantly faster than using`:FullLU`

. Note that this method can only be used if the sparsity pattern of the jacobian is always the same. - For
`jacobian = :Dense`

, same as above but the matrix`dG`

is dense. It is also updated inplace. This option is useful to study ODE of small dimension. - For
`jacobian = :DenseAD`

, evaluate the jacobian using ForwardDiff - For
`jacobian = :BorderedLU`

, we take advantage of the bordered shape of the linear solver and use a LU decomposition to invert`dG`

using a bordered linear solver. - For
`jacobian = :BorderedSparseInplace`

, this is the same as for`:BorderedLU`

but the cyclic matrix`dG`

is updated inplace. This method allocates much less. In some cases, this is significantly faster than using`:BorderedLU`

. Note that this method can only be used if the sparsity pattern of the jacobian is always the same. - For
`jacobian = :FullMatrixFree`

, a matrix free linear solver is used for`dG`

: note that a preconditioner is very likely required here because of the cyclic shape of`dG`

which affects negatively the convergence properties of GMRES. - For
`jacobian = :BorderedMatrixFree`

, a matrix free linear solver is used but for`Jc`

only (see docs): it means that`options.linsolver`

is used to invert`Jc`

. These two Matrix-Free options thus expose different part of the jacobian`dG`

in order to use specific preconditioners. For example, an ILU preconditioner on`Jc`

could remove the constraints in`dG`

and lead to poor convergence. Of course, for these last two methods, a preconditioner is likely to be required. - For
`jacobian = :FullMatrixFreeAD`

, the evaluation map of the differential is derived using automatic differentiation. Thus, unlike the previous two cases, the user does not need to pass a Matrix-Free differential.

Note that by default, the method prints the period of the periodic orbit as function of the parameter. This can be changed by providing your `record_from_solution`

argument.

`BifurcationKit.continuation`

— Method```
continuation(br, ind_bif; ...)
continuation(
br,
ind_bif,
options_cont;
alg,
δp,
ampfactor,
nev,
usedeflation,
verbosedeflation,
max_iter_deflation,
perturb,
plot_solution,
Teigvec,
scaleζ,
tol_fold,
kwargs_deflated_newton,
kwargs...
)
```

Automatic branch switching at branch points based on a computation of the normal form. More information is provided in Branch switching. An example of use is provided in 2d generalized Bratu–Gelfand problem.

**Arguments**

`br`

branch result from a call to`continuation`

`ind_bif`

index of the bifurcation point in`br`

from which you want to branch from`options_cont`

options for the call to`continuation`

**Optional arguments**

`alg = br.alg`

continuation algorithm to be used, default value:`br.alg`

`δp`

used to specify a specific value for the parameter on the bifurcated branch which is otherwise determined by`options_cont.ds`

. This allows to use a step larger than`options_cont.dsmax`

.`ampfactor = 1`

factor to alter the amplitude of the bifurcated solution. Useful to magnify the bifurcated solution when the bifurcated branch is very steep.`nev`

number of eigenvalues to be computed to get the right eigenvector`usedeflation = false`

whether to use nonlinear deflation (see Deflated problems) to help finding the guess on the bifurcated`verbosedeflation`

print deflated newton iterations`max_iter_deflation`

number of newton steps in deflated newton`perturb = identity`

which perturbation function to use during deflated newton`Teigvec = _getvectortype(br)`

type of the eigenvector. Useful when`br`

was loaded from a file and this information was lost`scaleζ = norm`

pass a norm to normalize vectors during normal form computation`plot_solution`

change plot solution method in the problem`br.prob`

`kwargs`

optional arguments to be passed to`continuation`

, the regular`continuation`

one and to`get_normal_form`

.

In the case of a very large model and use of special hardware (GPU, cluster), we suggest to discouple the computation of the reduced equation, the predictor and the bifurcated branches. Have a look at `methods(BifurcationKit.multicontinuation)`

to see how to call these versions. These methods has been tested on GPU with very high memory pressure.

`BifurcationKit.continuation`

— Method```
continuation(
br,
ind_bif,
_contParams;
alg,
δp,
ampfactor,
usedeflation,
linear_algo,
detailed,
prm,
override,
kwargs...
)
```

Branch switching at a bifurcation point on a branch of periodic orbits (PO) specified by a `br::AbstractBranchResult`

. The functional used to compute the PO is `br.prob`

. A deflated Newton-Krylov solver can be used to improve the branch switching capabilities.

**Arguments**

`br`

branch of periodic orbits computed with a`PeriodicOrbitTrapProblem`

`ind_bif`

index of the branch point`_contParams`

parameters to be used by a regular`continuation`

**Optional arguments**

`δp = 0.1`

used to specify a particular guess for the parameter in the branch which is otherwise determined by`contParams.ds`

. This allows to use a step larger than`contParams.dsmax`

.`ampfactor = 1`

factor which alters the amplitude of the bifurcated solution. Useful to magnify the bifurcated solution when the bifurcated branch is very steep.`detailed = false`

whether to fully compute the normal form.`usedeflation = true`

whether to use nonlinear deflation (see Deflated problems) to help finding the guess on the bifurcated branch`record_from_solution = (u, p) -> u[end]`

, record method used in the bifurcation diagram, by default this records the period of the periodic orbit.`linear_algo = BorderingBLS()`

, same as for`continuation`

`kwargs`

keywords arguments used for a call to the regular`continuation`

and the ones specific to periodic orbits (POs).

`BifurcationKit.continuation`

— Method```
continuation(
prob,
x0,
par0,
x1,
p1,
alg,
lens,
contParams;
bothside,
kwargs...
)
```

[Internal] This function is not meant to be called directly.

This function is the analog of `continuation`

when the first two points on the branch are passed (instead of a single one). Hence `x0`

is the first point on the branch (with palc `s=0`

) with parameter `par0`

and `x1`

is the second point with parameter `set(par0, lens, p1)`

.

`BifurcationKit.continuation_coll_fold`

— Method```
continuation_coll_fold(br, ind_bif, lens2; ...)
continuation_coll_fold(
br,
ind_bif,
lens2,
options_cont;
start_with_eigen,
bdlinsolver,
kwargs...
)
```

Continuation of curve of fold bifurcations of periodic orbits computed using collocation method.

**Arguments**

`br`

branch of periodic orbits computed with a`PeriodicOrbitTrapProblem`

`ind_bif`

index of the fold point`lens2::Lens`

second parameter axis`options_cont`

parameters to be used by a regular`continuation`

`BifurcationKit.continuation_coll_ns`

— Method```
continuation_coll_ns(br, ind_bif, lens2; ...)
continuation_coll_ns(
br,
ind_bif,
lens2,
options_cont;
alg,
start_with_eigen,
bdlinsolver,
prm,
kwargs...
)
```

Continuation of curve of Neimark-Sacker bifurcations of periodic orbits computed using collocation method.

**Arguments**

`br`

branch of periodic orbits computed with a`PeriodicOrbitTrapProblem`

`ind_bif`

index of the NS point`lens2::Lens`

second parameter axis`options_cont`

parameters to be used by a regular`continuation`

`BifurcationKit.continuation_coll_pd`

— Method```
continuation_coll_pd(br, ind_bif, lens2; ...)
continuation_coll_pd(
br,
ind_bif,
lens2,
options_cont;
alg,
start_with_eigen,
bdlinsolver,
prm,
kwargs...
)
```

Continuation of curve of period-doubling bifurcations of periodic orbits computed using collocation method.

**Arguments**

`br`

branch of periodic orbits computed with a`PeriodicOrbitTrapProblem`

`ind_bif`

index of the PD point`lens2::Lens`

second parameter axis`options_cont`

parameters to be used by a regular`continuation`

`BifurcationKit.continuation_fold`

— Method```
continuation_fold(
prob,
alg,
foldpointguess,
par,
lens1,
lens2,
eigenvec,
eigenvec_ad,
options_cont;
update_minaug_every_step,
normC,
bdlinsolver,
bdlinsolver_adjoint,
jacobian_ma,
compute_eigen_elements,
usehessian,
kind,
record_from_solution,
kwargs...
)
```

Codim 2 continuation of Fold points. This function turns an initial guess for a Fold point into a curve of Fold points based on a Minimally Augmented formulation. The arguments are as follows

`prob::AbstractBifurcationFunction`

`foldpointguess`

initial guess (x*0, p1*0) for the Fold point. It should be a`BorderedArray`

as returned by the function`foldpoint`

`par`

set of parameters`lens1`

parameter axis for parameter 1`lens2`

parameter axis for parameter 2`eigenvec`

guess for the right null vector`eigenvec_ad`

guess for the left null vector`options_cont`

arguments to be passed to the regular`continuation`

**Optional arguments:**

`jacobian_ma::Symbol = :autodiff`

, how the linear system of the Fold problem is solved. Can be`:autodiff, :finiteDifferencesMF, :finiteDifferences, :minaug`

`bdlinsolver`

bordered linear solver for the constraint equation with top-left block J. Required in the linear solver for the Minimally Augmented Fold functional. This option can be used to pass a dedicated linear solver for example with specific preconditioner.`bdlinsolver_adjoint`

bordered linear solver for the constraint equation with top-left block J^*. Required in the linear solver for the Minimally Augmented Fold functional. This option can be used to pass a dedicated linear solver for example with specific preconditioner.`update_minaug_every_step`

update vectors`a, b`

in Minimally Formulation every`update_minaug_every_step`

steps`compute_eigen_elements = false`

whether to compute eigenelements. If`options_cont.detect_event>0`

, it allows the detection of ZH points.`kwargs`

keywords arguments to be passed to the regular`continuation`

**Simplified call**

`continuation_fold(br::AbstractBranchResult, ind_fold::Int64, lens2::Lens, options_cont::ContinuationPar ; kwargs...)`

where the parameters are as above except that you have to pass the branch `br`

from the result of a call to `continuation`

with detection of bifurcations enabled and `index`

is the index of Fold point in `br`

that you want to continue.

The adjoint of the jacobian `J`

is computed internally when `Jᵗ = nothing`

by using `transpose(J)`

which works fine when `J`

is an `AbstractArray`

. In this case, do not pass the jacobian adjoint like `Jᵗ = (x, p) -> transpose(d_xF(x, p))`

otherwise the jacobian would be computed twice!

For ODE problems, it is more efficient to use the Matrix based Bordered Linear Solver passing the option `bdlinsolver = MatrixBLS()`

. This is the default setting.

In order to trigger the detection, pass `detect_event = 1 or 2`

in `options_cont`

.

`BifurcationKit.continuation_hopf`

— Method```
continuation_hopf(
prob_vf,
alg,
hopfpointguess,
par,
lens1,
lens2,
eigenvec,
eigenvec_ad,
options_cont;
update_minaug_every_step,
normC,
linsolve_adjoint,
bdlinsolver,
bdlinsolver_adjoint,
jacobian_ma,
compute_eigen_elements,
usehessian,
kind,
massmatrix,
record_from_solution,
kwargs...
)
```

codim 2 continuation of Hopf points. This function turns an initial guess for a Hopf point into a curve of Hopf points based on a Minimally Augmented formulation. The arguments are as follows

`prob::AbstractBifurcationProblem`

`hopfpointguess`

initial guess (x*0, p1*0) for the Hopf point. It should be a`Vector`

or a`BorderedArray`

`par`

set of parameters`lens1`

parameter axis for parameter 1`lens2`

parameter axis for parameter 2`eigenvec`

guess for the iω eigenvector at p1_0`eigenvec_ad`

guess for the -iω eigenvector at p1_0`options_cont`

keywords arguments to be passed to the regular`continuation`

**Optional arguments:**

`jacobian_ma::Symbol = :autodiff`

, how the linear system of the Fold problem is solved. Can be`:autodiff, :finiteDifferencesMF, :finiteDifferences, :minaug`

`linsolve_adjoint`

solver for (J+iω)^* ⋅sol = rhs`bdlinsolver`

bordered linear solver for the constraint equation with top-left block (J-iω). Required in the linear solver for the Minimally Augmented Hopf functional. This option can be used to pass a dedicated linear solver for example with specific preconditioner.`bdlinsolver_adjoint`

bordered linear solver for the constraint equation with top-left block (J-iω)^*. Required in the linear solver for the Minimally Augmented Hopf functional. This option can be used to pass a dedicated linear solver for example with specific preconditioner.`update_minaug_every_step`

update vectors`a,b`

in Minimally Formulation every`update_minaug_every_step`

steps`compute_eigen_elements = false`

whether to compute eigenelements. If`options_cont.detect_event>0`

, it allows the detection of ZH, HH points.`kwargs`

keywords arguments to be passed to the regular`continuation`

**Simplified call:**

`continuation_hopf(br::AbstractBranchResult, ind_hopf::Int, lens2::Lens, options_cont::ContinuationPar ; kwargs...)`

where the parameters are as above except that you have to pass the branch `br`

from the result of a call to `continuation`

with detection of bifurcations enabled and `index`

is the index of Hopf point in `br`

that you want to refine.

For ODE problems, it is more efficient to use the Matrix based Bordered Linear Solver passing the option `bdlinsolver = MatrixBLS()`

. This is the default setting.

The adjoint of the jacobian `J`

is computed internally when `Jᵗ = nothing`

by using `transpose(J)`

which works fine when `J`

is an `AbstractArray`

. In this case, do not pass the jacobian adjoint like `Jᵗ = (x, p) -> transpose(d_xF(x, p))`

otherwise the jacobian would be computed twice!

In order to trigger the detection, pass `detect_event = 1,2`

in `options_cont`

. Note that you need to provide `d3F`

in `prob`

.

`BifurcationKit.continuation_potrap`

— Method```
continuation_potrap(
prob,
orbitguess,
alg,
contParams,
linear_algo;
eigsolver,
record_from_solution,
plot_solution,
kwargs...
)
```

This is the continuation routine for computing a periodic orbit using a functional G based on Finite Differences and a Trapezoidal rule.

**Arguments**

`prob::PeriodicOrbitTrapProblem`

encodes the functional G`orbitguess`

a guess for the periodic orbit where`orbitguess[end]`

is an estimate of the period of the orbit. It could be a vector of size`N * M + 1`

where`M`

is the number of time slices,`N`

is the dimension of the phase space. This must be compatible with the numbers`N, M`

in`prob`

.`alg`

continuation algorithm`contParams`

same as for the regular`continuation`

method`linear_algo`

same as in`continuation`

**Keywords arguments**

`eigsolver`

specify an eigen solver for the computation of the Floquet exponents, defaults to`FloquetQaD`

Specify the choice of the jacobian (and linear algorithm), `jacobian`

must belong to `[:FullLU, :FullSparseInplace, :Dense, :DenseAD, :BorderedLU, :BorderedSparseInplace, :FullMatrixFree, :BorderedMatrixFree, :FullMatrixFreeAD]`

. This is used to select a way of inverting the jacobian `dG`

of the functional G.

- For
`jacobian = :FullLU`

, we use the default linear solver based on a sparse matrix representation of`dG`

. This matrix is assembled at each newton iteration. This is the default algorithm. - For
`jacobian = :FullSparseInplace`

, this is the same as for`:FullLU`

but the sparse matrix`dG`

is updated inplace. This method allocates much less. In some cases, this is significantly faster than using`:FullLU`

. Note that this method can only be used if the sparsity pattern of the jacobian is always the same. - For
`jacobian = :Dense`

, same as above but the matrix`dG`

is dense. It is also updated inplace. This option is useful to study ODE of small dimension. - For
`jacobian = :DenseAD`

, evaluate the jacobian using ForwardDiff - For
`jacobian = :BorderedLU`

, we take advantage of the bordered shape of the linear solver and use a LU decomposition to invert`dG`

using a bordered linear solver. - For
`jacobian = :BorderedSparseInplace`

, this is the same as for`:BorderedLU`

but the cyclic matrix`dG`

is updated inplace. This method allocates much less. In some cases, this is significantly faster than using`:BorderedLU`

. Note that this method can only be used if the sparsity pattern of the jacobian is always the same. - For
`jacobian = :FullMatrixFree`

, a matrix free linear solver is used for`dG`

: note that a preconditioner is very likely required here because of the cyclic shape of`dG`

which affects negatively the convergence properties of GMRES. - For
`jacobian = :BorderedMatrixFree`

, a matrix free linear solver is used but for`Jc`

only (see docs): it means that`options.linsolver`

is used to invert`Jc`

. These two Matrix-Free options thus expose different part of the jacobian`dG`

in order to use specific preconditioners. For example, an ILU preconditioner on`Jc`

could remove the constraints in`dG`

and lead to poor convergence. Of course, for these last two methods, a preconditioner is likely to be required. - For
`jacobian = :FullMatrixFreeAD`

, the evaluation map of the differential is derived using automatic differentiation. Thus, unlike the previous two cases, the user does not need to pass a Matrix-Free differential.

Note that by default, the method prints the period of the periodic orbit as function of the parameter. This can be changed by providing your `record_from_solution`

argument.

`BifurcationKit.continuation_sh_fold`

— Method```
continuation_sh_fold(br, ind_bif, lens2; ...)
continuation_sh_fold(
br,
ind_bif,
lens2,
options_cont;
start_with_eigen,
bdlinsolver,
Jᵗ,
kwargs...
)
```

Continuation of curve of fold bifurcations of periodic orbits computed using shooting method.

**Arguments**

`br`

branch of periodic orbits computed with a`PeriodicOrbitTrapProblem`

`ind_bif`

index of the fold point`lens2::Lens`

second parameter axis`options_cont`

parameters to be used by a regular`continuation`

`BifurcationKit.continuation_sh_ns`

— Method```
continuation_sh_ns(br, ind_bif, lens2; ...)
continuation_sh_ns(
br,
ind_bif,
lens2,
options_cont;
alg,
start_with_eigen,
bdlinsolver,
kwargs...
)
```

Continuation of curve of Neimark-Sacker bifurcations of periodic orbits computed using shooting method.

**Arguments**

`br`

branch of periodic orbits computed with a`PeriodicOrbitTrapProblem`

`ind_bif`

index of the NS point`lens2::Lens`

second parameter axis`options_cont`

parameters to be used by a regular`continuation`

`BifurcationKit.continuation_sh_pd`

— Method```
continuation_sh_pd(br, ind_bif, lens2; ...)
continuation_sh_pd(
br,
ind_bif,
lens2,
options_cont;
alg,
start_with_eigen,
Jᵗ,
kwargs...
)
```

Continuation of curve of period-doubling bifurcations of periodic orbits computed using shooting method.

**Arguments**

`br`

branch of periodic orbits computed with a`PeriodicOrbitTrapProblem`

`ind_bif`

index of the PD point`lens2::Lens`

second parameter axis`options_cont`

parameters to be used by a regular`continuation`

`BifurcationKit.correct_bifurcation`

— Method```
correct_bifurcation(contres)
```

This function uses information in the branch to detect codim 2 bifurcations like BT, ZH and Cusp.

`BifurcationKit.cusp_normal_form`

— Method```
cusp_normal_form(
_prob,
br,
ind_bif;
δ,
nev,
verbose,
ζs,
lens,
Teigvec,
scaleζ
)
```

Compute the Cusp normal form.

**Arguments**

`prob`

bifurcation problem`pt::Cusp`

Cusp bifurcation point`ls`

linear solver

**Optional arguments**

`δ = 1e-8`

used for finite differences`verbose`

bool to print information

`BifurcationKit.cylic_potrap_block!`

— MethodThis function populates Jc with the cyclic matrix using the different Jacobians

`BifurcationKit.detect_loop`

— Method```
detect_loop(br, x, p; rtol, verbose)
```

Function to detect continuation branches which loop on themselves.

`BifurcationKit.diff_poincare_map`

— MethodThis function computes the derivative of the Poincare return map Π(x) = ϕ(t(x),x) where t(x) is the return time of x to the section.

`BifurcationKit.eigenvals`

— Function```
eigenvals(br, ind)
eigenvals(br, ind, verbose)
```

Return the eigenvalues of the ind-th continuation step. `verbose`

is used to tell the number of unstable eigen elements.

Note that `ind = 0`

is allowed.

`BifurcationKit.eigenvalsfrombif`

— Method```
eigenvalsfrombif(br, ind)
```

Return the eigenvalues of the ind-th bifurcation point.

`BifurcationKit.eigenvec`

— Method```
eigenvec(br, ind, indev)
```

Return the indev-th eigenvectors of the ind-th continuation step.

`BifurcationKit.finite_differences!`

— Method```
finite_differences!(F, J, x; δ)
```

Compute a Jacobian by Finite Differences, update J. Use the centered formula (f(x+δ)-f(x-δ))/2δ.

`BifurcationKit.finite_differences`

— Method```
finite_differences(F, x; δ)
```

Compute a Jacobian by Finite Differences. Use the centered formula (f(x+δ)-f(x-δ))/2δ.

`BifurcationKit.foldpoint`

— Method```
foldpoint(br, index)
```

For an initial guess from the index of a Fold bifurcation point located in ContResult.specialpoint, returns a point which will can refined using `newtonFold`

.

`BifurcationKit.from`

— Method```
from(br)
```

Return the bifurcation point of a `::Branch`

.

`BifurcationKit.generate_ci_problem`

— Method```
generate_ci_problem(pb, bifprob, sol, period)
```

Generate a periodic orbit problem from a solution.

**Arguments**

`pb`

a`PeriodicOrbitOCollProblem`

which provides basic information, like the number of time slices`M`

`bifprob`

a bifurcation problem to provide the vector field`sol`

basically, and `ODEProblem`period`

estimate of the period of the periodic orbit

**Output**

- returns a
`PeriodicOrbitOCollProblem`

and an initial guess.

`BifurcationKit.generate_ci_problem`

— Method```
generate_ci_problem(pb, bifprob, sol, tspan; ktrap...)
```

Generate a periodic orbit problem from a solution.

**Arguments**

`pb`

a`PeriodicOrbitTrapProblem`

which provides basic information, like the number of time slices`M`

`bifprob`

a bifurcation problem to provide the vector field`sol`

basically, and `ODEProblem`tspan = (0,1.)`

estimate of the time span (period) of the periodic orbit

**Output**

- returns a
`PeriodicOrbitTrapProblem`

and an initial guess.

`BifurcationKit.generate_ci_problem`

— Method```
generate_ci_problem(
pb,
bifprob,
prob_de,
sol,
tspan;
alg,
ksh...
)
```

Generate a periodic orbit problem from a solution.

**Arguments**

`pb`

a`PoincareShootingProblem`

which provides basic information, like the number of time slices`M`

`bifprob`

a bifurcation problem to provide the vector field`prob_de::ODEProblem`

associated to`sol`

`sol`

basically, and `ODEProblem`period`

estimate of the period of the periodic orbit`k`

kwargs arguments passed to the constructor of`ShootingProblem`

**Output**

- returns a
`ShootingProblem`

and an initial guess.

`BifurcationKit.generate_ci_problem`

— Method```
generate_ci_problem(
pb,
bifprob,
prob_de,
sol,
tspan;
prob_mono,
alg,
alg_mono,
use_bordered_array,
ksh...
)
```

Generate a periodic orbit problem from a solution.

**Arguments**

`pb`

a`ShootingProblem`

which provides basic information, like the number of time slices`M`

`bifprob`

a bifurcation problem to provide the vector field`prob_de::ODEProblem`

associated to`sol`

`sol`

basically, and `ODEProblem`tspan::Tuple`

estimate of the period of the periodic orbit`alg`

algorithm for solving the Cauchy problem`prob_mono`

problem for monodromy`alg_mono`

algorithm for solving the monodromy Cauchy problem`k`

kwargs arguments passed to the constructor of`ShootingProblem`

**Output**

- returns a
`ShootingProblem`

and an initial guess.

`BifurcationKit.generate_solution`

— Method```
generate_solution(pb, orbit, period)
```

This function generates an initial guess for the solution of the problem `pb`

based on the orbit `t -> orbit(t)`

for t ∈ [0,2π] and the period `period`

.

`BifurcationKit.generate_solution`

— Method```
generate_solution(pb, orbit, period)
```

This function generates an initial guess for the solution of the problem `pb`

based on the orbit `t -> orbit(t * period)`

for t ∈ [0,1] and the `period`

.

`BifurcationKit.get_Ls`

— Method`L, ∂L = get_Ls(pb)`

Return the collocation matrices for evaluation and derivation.

`BifurcationKit.get_adjoint_basis`

— Method```
get_adjoint_basis(L★, λ, eigsolver; nev, verbose)
```

Return a left eigenvector for an eigenvalue closest to λ. `nev`

indicates how many eigenvalues must be computed by the eigensolver. Indeed, for iterative solvers, it may be needed to compute more eigenvalues than necessary.

`BifurcationKit.get_bifurcation_type`

— MethodFunction for coarse detection of bifurcation points.

`BifurcationKit.get_blocks`

— Method```
get_blocks(coll, Jac)
```

This function extracts the indices of the blocks composing the matrix J which is a M x M Block matrix where each block N x N has the same sparsity.

`BifurcationKit.get_blocks`

— Method```
get_blocks(A, N, M)
```

This function extracts the indices of the blocks composing the matrix A which is a M x M Block matrix where each block N x N has the same sparsity.

`BifurcationKit.get_branch`

— Method```
get_branch(diagram, code)
```

Return the part of the diagram (bifurcation diagram) by recursively descending down the diagram using the `Int`

valued tuple `code`

. For example `get_branch(diagram, (1,2,3,))`

returns `diagram.child[1].child[2].child[3]`

.

`BifurcationKit.get_branches_from_BP`

— Method```
get_branches_from_BP(diagram, indbif)
```

Return the part of the diagram corresponding to the indbif-th bifurcation point on the root branch.

`BifurcationKit.get_first_points_on_branch`

— Function```
get_first_points_on_branch(br, bpnf, solfromRE; ...)
get_first_points_on_branch(
br,
bpnf,
solfromRE,
options_cont;
δp,
Teigvec,
usedeflation,
verbosedeflation,
max_iter_deflation,
lsdefop,
perturb_guess,
kwargs...
)
```

Function to transform predictors `solfromRE`

in the normal form coordinates of `bpnf`

into solutions. Note that `solfromRE = (before = Vector{vectype}, after = Vector{vectype})`

.

`BifurcationKit.get_normal_form`

— Method```
get_normal_form(
prob,
br,
id_bif;
nev,
verbose,
ζs,
ζs_ad,
lens,
Teigvec,
scaleζ,
detailed,
autodiff,
bls,
bls_adjoint,
bls_block
)
```

Compute the normal form of the bifurcation point located at `br.specialpoint[ind_bif]`

.

**Arguments**

`prob::AbstractBifurcationProblem`

`br`

result from a call to`continuation`

`ind_bif`

index of the bifurcation point in`br.specialpoint`

**Optional arguments**

`nev`

number of eigenvalues used to compute the spectral projection. This number has to be adjusted when used with iterative methods.`verbose`

whether to display information`ζs`

list of vectors spanning the kernel of`dF`

at the bifurcation point. Useful to enforce the basis for the normal form.`lens::Lens`

specify which parameter to take the partial derivative ∂pF`scaleζ`

function to normalise the kernel basis. Indeed, when used with large vectors and`norm`

, it results in ζs and the normal form coefficient being super small.`autodiff = true`

whether to use ForwardDiff for the differentiations w.r.t the parameters that are required to compute the normal form. Used for example for Bogdanov-Takens point. You can set to`autodiff = false`

if you wish.`detailed = true`

whether to compute only a simplified normal form. Used for example for Bogdanov-Takens point.`bls = MatrixBLS()`

specify Bordered linear solver. Used for example for Bogdanov-Takens point.

**Available method**

You can directly call

`get_normal_form(br, ind_bif ; kwargs...)`

which is a shortcut for `get_normal_form(getprob(br), br, ind_bif ; kwargs...)`

.

Once the normal form `nf`

has been computed, you can call `predictor(nf, δp)`

to obtain an estimate of the bifurcating branch.

`BifurcationKit.get_normal_form`

— Method```
get_normal_form(
prob,
br,
id_bif;
nev,
verbose,
ζs,
lens,
Teigvec,
scaleζ,
prm,
autodiff,
detailed,
δ
)
```

Compute the normal form of periodic orbits. We detail the additional keyword arguments specific to periodic orbits

**Optional arguments**

`prm = true`

compute the normal form using Poincaré return map (PRM). If false, use the Iooss normal form.

`BifurcationKit.get_normal_form1d`

— Method```
get_normal_form1d(
prob,
br,
ind_bif;
nev,
verbose,
lens,
Teigvec,
tol_fold,
scaleζ,
autodiff
)
```

Compute a normal form based on Golubitsky, Martin, David G Schaeffer, and Ian Stewart. Singularities and Groups in Bifurcation Theory. New York: Springer-Verlag, 1985, VI.1.d page 295.

`BifurcationKit.get_normal_form1d_maps`

— Method```
get_normal_form1d_maps(
prob,
bp,
ls;
bls,
verbose,
tol_fold,
scaleζ,
autodiff
)
```

Compute a normal form based on Golubitsky, Martin, David G Schaeffer, and Ian Stewart. Singularities and Groups in Bifurcation Theory. New York: Springer-Verlag, 1985, VI.1.d page 295.

**Note**

We could have copied the implementation of `get_normal_form1d`

but we would have to redefine the jacobian which for shooting problem might sound a bit hacky. Nevertheless, it amounts to applying the same result to G(x) ≡ F(x) - x. Hence, we only chnage the linear solvers below.

`BifurcationKit.get_periodic_orbit`

— Method```
get_periodic_orbit(prob, u, p)
```

Compute the full periodic orbit associated to `x`

. Mainly for plotting purposes.

`BifurcationKit.get_periodic_orbit`

— Method```
get_periodic_orbit(prob, u, p)
```

Compute the full periodic orbit associated to `x`

. Mainly for plotting purposes.

`BifurcationKit.get_periodic_orbit`

— Method```
get_periodic_orbit(prob, x_bar, p)
```

Compute the full periodic orbit associated to `x`

. Mainly for plotting purposes.

`BifurcationKit.get_periodic_orbit`

— Method```
get_periodic_orbit(prob, x, par; kode...)
```

Compute the full periodic orbit associated to `x`

. Mainly for plotting purposes.

`BifurcationKit.get_solp`

— Method```
get_solp(br, ind)
```

Return the parameter for the ind-th point stored in br.sol

`BifurcationKit.get_solx`

— Method```
get_solx(br, ind)
```

Return the solution for the ind-th point stored in br.sol

`BifurcationKit.get_time_diff`

— Method```
get_time_diff(pb, u)
```

Compute `norm(du/dt)`

`BifurcationKit.get_times`

— Method```
get_times(cache)
```

Return all the times at which the problem is evaluated.

`BifurcationKit.getamplitude`

— Method```
getamplitude(prob, x, p; ratio)
```

Compute the amplitude of the periodic orbit associated to `x`

. The keyword argument `ratio = 1`

is used as follows. If `length(x) = ratio * n`

, the call returns the amplitude over `x[1:n]`

.

`BifurcationKit.getamplitude`

— Method```
getamplitude(prob, x, p; ratio)
```

Compute the amplitude of the periodic orbit associated to `x`

. The keyword argument `ratio = 1`

is used as follows. If `length(x) = 1 + ratio * n`

, the call returns the amplitude over `x[1:n]`

.

`BifurcationKit.getmaximum`

— Method```
getmaximum(prob, x, p; ratio)
```

Compute the maximum of the periodic orbit associated to `x`

. The keyword argument `ratio = 1`

is used as follows. If `length(x) = ratio * n`

, the call returns the amplitude over `x[1:n]`

.

`BifurcationKit.getmaximum`

— Method```
getmaximum(prob, x, p)
```

Compute the maximum of the periodic orbit associated to `x`

.

`BifurcationKit.getmaximum`

— Method```
getmaximum(prob, x, p; ratio)
```

Compute the maximum of the periodic orbit associated to `x`

. The keyword argument `ratio = 1`

is used as follows. If `length(x) = 1 + ratio * n`

, the call returns the amplitude over `x[1:n]`

.

`BifurcationKit.getmesh`

— MethodReturns the vector of size m+1, 0 = τ₁ < τ₂ < ... < τₘ < τₘ₊₁ = 1

`BifurcationKit.getparams`

— MethodReturn the parameters of the bifurcation problem.

`BifurcationKit.getparams`

— MethodReturn the parameters of the bifurcation problem of the branch.

`BifurcationKit.getperiod`

— Function```
getperiod(, x)
getperiod(, x, par)
```

Compute the period of the periodic orbit associated to `x`

.

`BifurcationKit.getperiod`

— Method```
getperiod(prob, x, p)
```

Compute the period of the periodic orbit associated to `x`

.

`BifurcationKit.getperiod`

— Method```
getperiod(psh, x_bar, par)
```

Compute the period of the periodic orbit associated to `x_bar`

.

`BifurcationKit.guess_from_hopf`

— Method```
guess_from_hopf(
br,
ind_hopf,
eigsolver,
M,
amplitude;
phase
)
```

This function returns several useful quantities regarding a Hopf bifurcation point. More precisely, it returns:

- the parameter value at which a Hopf bifurcation occurs
- the period of the bifurcated periodic orbit
- a guess for the bifurcated periodic orbit
- the equilibrium at the Hopf bifurcation point
- the eigenvector at the Hopf bifurcation point.

The arguments are

`br`

: the continuation branch which lists the Hopf bifurcation points`ind_hopf`

: index of the bifurcation branch, as in`br.specialpoint`

`eigsolver`

: the eigen solver used to find the eigenvectors`M`

number of time slices in the periodic orbit guess`amplitude`

: amplitude of the periodic orbit guess

`BifurcationKit.hopfMALinearSolver`

— MethodThis function solves the linear problem associated with a linearization of the minimally augmented formulation of the Hopf bifurcation point. The keyword `debugArray`

is used to debug the routine by returning several key quantities.

`BifurcationKit.hopf_normal_form`

— Method```
hopf_normal_form(
prob,
br,
ind_hopf;
nev,
verbose,
lens,
Teigvec,
detailed,
scaleζ
)
```

Compute the Hopf normal form.

**Arguments**

`prob::AbstractBifurcationProblem`

bifurcation problem`br`

branch result from a call to`continuation`

`ind_hopf`

index of the bifurcation point in`br`

`options`

options for the Newton solver

**Optional arguments**

`nev = 5`

number of eigenvalues to compute to estimate the spectral projector`verbose`

bool to print information

**Available method**

Once the normal form `hopfnf`

has been computed, you can call `predictor(hopfnf, ds)`

to obtain an estimate of the bifurcating periodic orbit.

`BifurcationKit.hopf_normal_form`

— Method```
hopf_normal_form(prob, pt, ls; verbose, L)
```

Compute the Hopf normal form.

**Arguments**

`prob::AbstractBifurcationProblem`

bifurcation problem`pt::Hopf`

Hopf bifurcation point`ls`

linear solver

**Optional arguments**

`verbose`

bool to print information

`BifurcationKit.is_stable`

— MethodThis function checks whether the solution with eigenvalues `eigvalues`

is stable and also compute the number of unstable eigenvalues with nonzero imaginary part

`BifurcationKit.jacobian_potrap_block`

— MethodMatrix by blocks expression of the Jacobian for the PO functional computed at the space-time guess: `u0`

`BifurcationKit.kernel_dimension`

— Method```
kernel_dimension(bp)
```

Return the dimension of the kernel of the special point.

`BifurcationKit.locate_bifurcation!`

— FunctionFunction to locate precisely bifurcation points using a bisection algorithm. We make sure that at the end of the algorithm, the state is just after the bifurcation point (in the s coordinate).

`BifurcationKit.mod_counter`

— Method```
mod_counter(step, everyN)
```

This function implements a counter. If `everyN == 0`

, it returns false. Otherwise, it returns `true`

when `step`

is a multiple of `everyN`

`BifurcationKit.multicontinuation`

— Function```
multicontinuation(br, ind_bif; ...)
multicontinuation(
br,
ind_bif,
options_cont;
δp,
ampfactor,
nev,
Teigvec,
ζs,
verbosedeflation,
scaleζ,
perturb_guess,
plot_solution,
kwargs...
)
```

Automatic branch switching at branch points based on a computation of the normal form. More information is provided in Branch switching. An example of use is provided in 2d generalized Bratu–Gelfand problem.

**Arguments**

`br`

branch result from a call to`continuation`

`ind_bif`

index of the bifurcation point in`br`

from which you want to branch from`options_cont`

options for the call to`continuation`

**Optional arguments**

`alg = br.alg`

continuation algorithm to be used, default value:`br.alg`

`δp`

used to specify a particular guess for the parameter on the bifurcated branch which is otherwise determined by`options_cont.ds`

. This allows to use a step larger than`options_cont.dsmax`

.`ampfactor = 1`

factor which alters the amplitude of the bifurcated solution. Useful to magnify the bifurcated solution when the bifurcated branch is very steep.`nev`

number of eigenvalues to be computed to get the right eigenvector`verbosedeflation = true`

whether to display the nonlinear deflation iterations (see Deflated problems) to help finding the guess on the bifurcated branch`scaleζ`

norm used to normalize eigenbasis when computing the reduced equation`Teigvec`

type of the eigenvector. Useful when`br`

was loaded from a file and this information was lost`ζs`

basis of the kernel`perturb_guess = identity`

perturb the guess from the predictor just before the deflated-newton correction`kwargs`

optional arguments to be passed to`continuation`

, the regular`continuation`

one.

In the case of a very large model and use of special hardware (GPU, cluster), we suggest to discouple the computation of the reduced equation, the predictor and the bifurcated branches. Have a look at `methods(BifurcationKit.multicontinuation)`

to see how to call these versions. These methods has been tested on GPU with very high memory pressure.

`BifurcationKit.multicontinuation`

— Function```
multicontinuation(br, bpnf, defOpm, defOpp; ...)
multicontinuation(
br,
bpnf,
defOpm,
defOpp,
options_cont;
alg,
δp,
Teigvec,
verbosedeflation,
max_iter_deflation,
lsdefop,
plot_solution,
kwargs...
)
```

Automatic branch switching at branch points based on a computation of the normal form. More information is provided in Branch switching. An example of use is provided in 2d generalized Bratu–Gelfand problem.

**Arguments**

`br`

branch result from a call to`continuation`

`bpnf`

normal form`defOpm::DeflationOperator, defOpp::DeflationOperator`

to specify converged points on nonn-trivial branches before/after the bifurcation points.

The rest is as the regular `multicontinuation`

function.

`BifurcationKit.neimark_sacker_normal_form`

— Method```
neimark_sacker_normal_form(
prob,
br,
ind_ns;
nev,
verbose,
lens,
Teigvec,
detailed,
scaleζ
)
```

Compute the Neimark-Sacker normal form.

**Arguments**

`prob::AbstractBifurcationProblem`

bifurcation problem`br`

branch result from a call to`continuation`

`ind_ns`

index of the bifurcation point in`br`

`options`

options for the Newton solver

**Optional arguments**

`nev = 5`

number of eigenvalues to compute to estimate the spectral projector`verbose`

bool to print information`detailed = false`

compute the coefficient a in the normal form

`BifurcationKit.neimark_sacker_normal_form`

— Method```
neimark_sacker_normal_form(prob, pt, ls; detailed, verbose)
```

Compute the Neimark-Sacker normal form.

**Arguments**

`prob::AbstractBifurcationProblem`

bifurcation problem`pt::NeimarkSacker`

Neimark-Sacker bifurcation point`ls`

linear solver

**Optional arguments**

`verbose`

bool to print information

`BifurcationKit.newton`

— Method```
newton(prob, orbitguess, options; lens, δ, kwargs...)
```

This is the Newton-Krylov Solver for computing a periodic orbit using the (Standard / Poincaré) Shooting method. Note that the linear solver has to be appropriately set up in `options`

.

**Arguments**

Similar to `newton`

except that `prob`

is either a `ShootingProblem`

or a `PoincareShootingProblem`

. These two problems have specific options to be tuned, we refer to their link for more information and to the tutorials.

`prob`

a problem of type`<: AbstractShootingProblem`

encoding the shooting functional G.`orbitguess`

a guess for the periodic orbit. See`ShootingProblem`

and See`PoincareShootingProblem`

for information regarding the shape of`orbitguess`

.`par`

parameters to be passed to the functional`options`

same as for the regular`newton`

method.

**Optional argument**

`jacobian`

Specify the choice of the linear algorithm, which must belong to- For
`MatrixFree()`

, matrix free jacobian, the jacobian is specified by the user in`prob`

. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutoDiffMF()`

, we use Automatic Differentiation (AD) to compute the (matrix-free) derivative of`x -> prob(x, p)`

using a directional derivative. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutodiffDense()`

. Same as for`AutoDiffMF`

but the jacobian is formed as a dense Matrix. You can use a direct solver or an iterative one. - For
`FiniteDifferences()`

, same as for`AutoDiffDense`

but we use Finite Differences to compute the jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument. - For
`AutoDiffDenseAnalytical()`

. Same as for`AutoDiffDense`

but the jacobian is formed using a mix of AD and analytical formula. - For
`FiniteDifferencesMF()`

, use Finite Differences to compute the matrix-free jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument.

- For

`BifurcationKit.newton`

— Method` newton(prob::AbstractBifurcationProblem, options::NewtonPar; normN = norm, callback = (;x, fx, J, residual, step, itlinear, options, x0, residuals; kwargs...) -> true, kwargs...)`

This is the Newton-Krylov Solver for `F(x, p0) = 0`

with Jacobian w.r.t. `x`

written `J(x, p0)`

and initial guess `x0`

. It is important to set the linear solver `options.linsolver`

properly depending on your problem. This linear solver is used to solve $J(x, p_0)u = -F(x, p_0)$ in the Newton step. You can for example use `linsolver = DefaultLS()`

which is the operator backslash: it works well for Sparse / Dense matrices. See Linear solvers (LS) for more informations.

**Arguments**

`prob`

a`::AbstractBifurcationProblem`

, typically a`BifurcationProblem`

which holds the vector field and its jacobian. We also refer to`BifFunction`

for more details.`options::NewtonPar`

variable holding the internal parameters used by the`newton`

method

**Optional Arguments**

`normN = norm`

specifies a norm for the convergence criteria`callback`

function passed by the user which is called at the end of each iteration. The default one is the following`cb_default((x, fx, J, residual, step, itlinear, options, x0, residuals); k...) = true`

. Can be used to update a preconditionner for example. You can use for example`cbMaxNorm`

to limit the residuals norms. If yo want to specify your own, the arguments passed to the callback are as follows`x`

current solution`fx`

current residual`J`

current jacobian`residual`

current norm of the residual`step`

current newton step`itlinear`

number of iterations to solve the linear system`options`

a copy of the argument`options`

passed to`newton`

`residuals`

the history of residuals`kwargs`

kwargs arguments, contain your initial guess`x0`

`kwargs`

arguments passed to the callback. Useful when`newton`

is called from`continuation`

**Output:**

`solution::NonLinearSolution`

, we refer to`NonLinearSolution`

for more information.

Make sure that the linear solver (Matrix-Free...) corresponds to your jacobian (Matrix-Free vs. Matrix based).

`BifurcationKit.newton`

— Method```
newton(
br,
ind_bif;
normN,
options,
start_with_eigen,
lens2,
kwargs...
)
```

This function turns an initial guess for a Fold / Hopf point into a solution to the Fold / Hopf problem based on a Minimally Augmented formulation.

**Arguments**

`br`

results returned after a call to continuation`ind_bif`

bifurcation index in`br`

**Optional arguments:**

`options::NewtonPar`

, default value`br.contparams.newton_options`

`normN = norm`

`options`

You can pass newton parameters different from the ones stored in`br`

by using this argument`options`

.`bdlinsolver`

bordered linear solver for the constraint equation`start_with_eigen = false`

whether to start the Minimally Augmented problem with information from eigen elements.`kwargs`

keywords arguments to be passed to the regular Newton-Krylov solver

For ODE problems, it is more efficient to use the Matrix based Bordered Linear Solver passing the option `bdlinsolver = MatrixBLS()`

It is recommended that you use the option `start_with_eigen=true`

`BifurcationKit.newton`

— Method```
newton(probPO, orbitguess, defOp, options; kwargs...)
```

This function is similar to `newton(probPO, orbitguess, options, jacobianPO; kwargs...)`

except that it uses deflation in order to find periodic orbits different from the ones stored in `defOp`

. We refer to the mentioned method for a full description of the arguments. The current method can be used in the vicinity of a Hopf bifurcation to prevent the Newton-Krylov algorithm from converging to the equilibrium point.

`BifurcationKit.newton`

— Method```
newton(probPO, orbitguess, options; kwargs...)
```

This is the Newton Solver for computing a periodic orbit using orthogonal collocation method. Note that the linear solver has to be apropriately set up in `options`

.

**Arguments**

Similar to `newton`

except that `prob`

is a `PeriodicOrbitOCollProblem`

.

`prob`

a problem of type`<: PeriodicOrbitOCollProblem`

encoding the shooting functional G.`orbitguess`

a guess for the periodic orbit.`options`

same as for the regular`newton`

method.

**Optional argument**

`jacobian`

Specify the choice of the linear algorithm, which must belong to`(AutoDiffDense(), )`

. This is used to select a way of inverting the jacobian dG- For
`AutoDiffDense()`

. The jacobian is formed as a dense Matrix. You can use a direct solver or an iterative one using`options`

. The jacobian is formed inplace. - For
`DenseAnalytical()`

Same as for`AutoDiffDense`

but the jacobian is formed using a mix of AD and analytical formula.

- For

`BifurcationKit.newton`

— Method```
newton(probPO, orbitguess, options; kwargs...)
```

This is the Krylov-Newton Solver for computing a periodic orbit using a functional G based on Finite Differences and a Trapezoidal rule.

**Arguments:**

`prob`

a problem of type`PeriodicOrbitTrapProblem`

encoding the functional G`orbitguess`

a guess for the periodic orbit where`orbitguess[end]`

is an estimate of the period of the orbit. It should be a vector of size`N * M + 1`

where`M`

is the number of time slices,`N`

is the dimension of the phase space. This must be compatible with the numbers`N, M`

in`prob`

.`par`

parameters to be passed to the functional`options`

same as for the regular`newton`

method

`jacobian`

must belong to `dG`

of the functional G.

- For
`jacobian = :FullLU`

, we use the default linear solver based on a sparse matrix representation of`dG`

. This matrix is assembled at each newton iteration. This is the default algorithm. - For
`jacobian = :FullSparseInplace`

, this is the same as for`:FullLU`

but the sparse matrix`dG`

is updated inplace. This method allocates much less. In some cases, this is significantly faster than using`:FullLU`

. Note that this method can only be used if the sparsity pattern of the jacobian is always the same. - For
`jacobian = :Dense`

, same as above but the matrix`dG`

is dense. It is also updated inplace. This option is useful to study ODE of small dimension. - For
`jacobian = :DenseAD`

, evaluate the jacobian using ForwardDiff - For
`jacobian = :BorderedLU`

, we take advantage of the bordered shape of the linear solver and use a LU decomposition to invert`dG`

using a bordered linear solver. - For
`jacobian = :BorderedSparseInplace`

, this is the same as for`:BorderedLU`

but the cyclic matrix`dG`

is updated inplace. This method allocates much less. In some cases, this is significantly faster than using`:BorderedLU`

. Note that this method can only be used if the sparsity pattern of the jacobian is always the same. - For
`jacobian = :FullMatrixFree`

, a matrix free linear solver is used for`dG`

: note that a preconditioner is very likely required here because of the cyclic shape of`dG`

which affects negatively the convergence properties of GMRES. - For
`jacobian = :BorderedMatrixFree`

, a matrix free linear solver is used but for`Jc`

only (see docs): it means that`options.linsolver`

is used to invert`Jc`

. These two Matrix-Free options thus expose different part of the jacobian`dG`

in order to use specific preconditioners. For example, an ILU preconditioner on`Jc`

could remove the constraints in`dG`

and lead to poor convergence. Of course, for these last two methods, a preconditioner is likely to be required. - For
`jacobian = :FullMatrixFreeAD`

, the evaluation map of the differential is derived using automatic differentiation. Thus, unlike the previous two cases, the user does not need to pass a Matrix-Free differential.

`BifurcationKit.newton`

— MethodThis specific Newton-Krylov method first tries to converge to a solution `sol0`

close the guess `x0`

. It then attempts to converge from the guess `x1`

while avoiding the previous converged solution close to `sol0`

. This is very handy for branch switching. The method is based on a deflated Newton-Krylov solver.

**Arguments**

Compared to `newton`

, the only different arguments are

`defOp::DeflationOperator`

deflation operator`linsolver`

linear solver used to invert the Jacobian of the deflated functional.- custom solver
`DeflatedProblemCustomLS()`

which requires solving two linear systems`J⋅x = rhs`

. - For other linear solvers
`<: AbstractLinearSolver`

, a matrix free method is used for the deflated functional. - if passed
`Val(:autodiff)`

, then`ForwardDiff.jl`

is used to compute the jacobian Matrix of the deflated problem - if passed
`Val(:fullIterative)`

, then a full matrix free method is used for the deflated problem.

- custom solver

`BifurcationKit.newton`

— Method```
newton(prob, orbitguess, defOp, options; lens, kwargs...)
```

This is the deflated Newton-Krylov Solver for computing a periodic orbit using a (Standard / Poincaré) Shooting method.

**Arguments**

Similar to `newton`

except that `prob`

is either a `ShootingProblem`

or a `PoincareShootingProblem`

.

**Optional argument**

`jacobian`

Specify the choice of the linear algorithm, which must belong to- For
`MatrixFree()`

, matrix free jacobian, the jacobian is specified by the user in`prob`

. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutoDiffMF()`

, we use Automatic Differentiation (AD) to compute the (matrix-free) derivative of`x -> prob(x, p)`

using a directional derivative. This is to be used with an iterative solver (e.g. GMRES) to solve the linear system - For
`AutodiffDense()`

. Same as for`AutoDiffMF`

but the jacobian is formed as a dense Matrix. You can use a direct solver or an iterative one. - For
`FiniteDifferences()`

, same as for`AutoDiffDense`

but we use Finite Differences to compute the jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument. - For
`AutoDiffDenseAnalytical()`

. Same as for`AutoDiffDense`

but the jacobian is formed using a mix of AD and analytical formula. - For
`FiniteDifferencesMF()`

, use Finite Differences to compute the matrix-free jacobian of`x -> prob(x, p)`

using the`δ = 1e-8`

which can be passed as an argument.

- For

**Output:**

- solution::NonLinearSolution, see
`NonLinearSolution`

`BifurcationKit.newton`

— Method```
newton(prob, defOp, options; ...)
newton(prob, defOp, options, _linsolver; kwargs...)
```

This is the deflated version of the Krylov-Newton Solver for `F(x, p0) = 0`

.

We refer to the regular `newton`

for more information. It penalises the roots saved in `defOp.roots`

. The other arguments are as for `newton`

. See `DeflationOperator`

for more information on `defOp`

.

**Arguments**

Compared to `newton`

, the only different arguments are

`defOp::DeflationOperator`

deflation operator`linsolver`

linear solver used to invert the Jacobian of the deflated functional.- custom solver
`DeflatedProblemCustomLS()`

which requires solving two linear systems`J⋅x = rhs`

. - For other linear solvers
`<: AbstractLinearSolver`

, a matrix free method is used for the deflated functional. - if passed
`Val(:autodiff)`

, then`ForwardDiff.jl`

is used to compute the jacobian Matrix of the deflated problem - if passed
`Val(:fullIterative)`

, then a full matrix free method is used for the deflated problem.

- custom solver

`BifurcationKit.newton`

— Method```
newton(probPO, orbitguess, defOp, options; kwargs...)
```

This function is similar to `newton(probPO, orbitguess, options, jacobianPO; kwargs...)`

except that it uses deflation in order to find periodic orbits different from the ones stored in `defOp`

. We refer to the mentioned method for a full description of the arguments. The current method can be used in the vicinity of a Hopf bifurcation to prevent the Newton-Krylov algorithm from converging to the equilibrium point.

`BifurcationKit.newton_bt`

— Method```
newton_bt(
prob,
btpointguess,
par,
lens2,
eigenvec,
eigenvec_ad,
options;
normN,
jacobian_ma,
usehessian,
bdlinsolver,
bdlinsolver_adjoint,
bdlinsolver_block,
kwargs...
)
```

This function turns an initial guess for a BT point into a solution to the BT problem based on a Minimally Augmented formulation. The arguments are as follows

`prob::AbstractBifurcationFunction`

`btpointguess`

initial guess (x*0, p*0) for the BT point. It should be a`BorderedArray`

as returned by the function`BTPoint`

`par`

parameters used for the vector field`eigenvec`

guess for the 0 eigenvector`eigenvec_ad`

guess for the 0 adjoint eigenvector`options::NewtonPar`

options for the Newton-Krylov algorithm, see`NewtonPar`

.

**Optional arguments:**

`normN = norm`

`bdlinsolver`

bordered linear solver for the constraint equation`jacobian_ma::Symbol = true`

specify the way the (newton) linear system is solved. Can be (:autodiff, :finitedifferences, :minaug)`kwargs`

keywords arguments to be passed to the regular Newton-Krylov solver

**Simplified call**

Simplified call to refine an initial guess for a BT point. More precisely, the call is as follows

`newton(br::AbstractBranchResult, ind_bt::Int; options = br.contparams.newton_options, kwargs...)`

The parameters / options are as usual except that you have to pass the branch `br`

from the result of a call to `continuation`

with detection of bifurcations enabled and `index`

is the index of bifurcation point in `br`

you want to refine. You can pass newton parameters different from the ones stored in `br`

by using the argument `options`

.

The adjoint of the jacobian `J`

is computed internally when `Jᵗ = nothing`

by using `transpose(J)`

which works fine when `J`

is an `AbstractArray`

. In this case, do not pass the jacobian adjoint like `Jᵗ = (x, p) -> transpose(d_xF(x, p))`

otherwise the jacobian will be computed twice!

For ODE problems, it is more efficient to pass the option `jacobian_ma = :autodiff`

`BifurcationKit.newton_bt`

— Method```
newton_bt(
br,
ind_bt;
probvf,
normN,
options,
nev,
start_with_eigen,
bdlinsolver,
bdlinsolver_adjoint,
kwargs...
)
```

This function turns an initial guess for a Bogdanov-Takens point into a solution to the Bogdanov-Takens problem based on a Minimally Augmented formulation.

**Arguments**

`br`

results returned after a call to continuation`ind_bif`

bifurcation index in`br`

**Optional arguments:**

`options::NewtonPar`

, default value`br.contparams.newton_options`

`normN = norm`

`options`

You can pass newton parameters different from the ones stored in`br`

by using this argument`options`

.`jacobian_ma::Symbol = true`

specify the way the (newton) linear system is solved. Can be (:autodiff, :finitedifferences, :minaug)`bdlinsolver`

bordered linear solver for the constraint equation`start_with_eigen = false`

whether to start the Minimally Augmented problem with information from eigen elements.`kwargs`

keywords arguments to be passed to the regular Newton-Krylov solver

For ODE problems, it is more efficient to pass the option `jacobian = :autodiff`

For ODE problems, it is more efficient to pass the option `start_with_eigen = true`

`BifurcationKit.newton_fold`

— Method```
newton_fold(
prob,
foldpointguess,
par,
eigenvec,
eigenvec_ad,
options;
normN,
bdlinsolver,
usehessian,
kwargs...
)
```

This function turns an initial guess for a Fold point into a solution to the Fold problem based on a Minimally Augmented formulation. The arguments are as follows

`prob::AbstractBifurcationFunction`

`foldpointguess`

initial guess (x*0, p*0) for the Fold point. It should be a`BorderedArray`

as returned by the function`foldpoint`

`par`

parameters used for the vector field`eigenvec`

guess for the right null vector`eigenvec_ad`

guess for the left null vector`options::NewtonPar`

options for the Newton-Krylov algorithm, see`NewtonPar`

.

**Optional arguments:**

`normN = norm`

`bdlinsolver`

bordered linear solver for the constraint equation`kwargs`

keywords arguments to be passed to the regular Newton-Krylov solver

**Simplified call**

Simplified call to refine an initial guess for a Fold point. More precisely, the call is as follows

`newtonFold(br::AbstractBranchResult, ind_fold::Int; options = br.contparams.newton_options, kwargs...)`

The parameters / options are as usual except that you have to pass the branch `br`

from the result of a call to `continuation`

with detection of bifurcations enabled and `index`

is the index of bifurcation point in `br`

you want to refine. You can pass newton parameters different from the ones stored in `br`

by using the argument `options`

.

The adjoint of the jacobian `J`

is computed internally when `Jᵗ = nothing`

by using `transpose(J)`

which works fine when `J`

is an `AbstractArray`

. In this case, do not pass the jacobian adjoint like `Jᵗ = (x, p) -> transpose(d_xF(x, p))`

otherwise the jacobian will be computed twice!

For ODE problems, it is more efficient to pass the Bordered Linear Solver using the option `bdlinsolver = MatrixBLS()`

`BifurcationKit.newton_hopf`

— Method```
newton_hopf(
prob,
hopfpointguess,
par,
eigenvec,
eigenvec_ad,
options;
normN,
bdlinsolver,
usehessian,
kwargs...
)
```

This function turns an initial guess for a Hopf point into a solution to the Hopf problem based on a Minimally Augmented formulation. The arguments are as follows

`prob::AbstractBifurcationProblem`

where`p`

is a set of parameters.`hopfpointguess`

initial guess (x*0, p*0) for the Hopf point. It should a`BorderedArray`

as returned by the function`HopfPoint`

.`par`

parameters used for the vector field`eigenvec`

guess for the iω eigenvector`eigenvec_ad`

guess for the -iω eigenvector`options::NewtonPar`

options for the Newton-Krylov algorithm, see`NewtonPar`

.

**Optional arguments:**

`normN = norm`

`bdlinsolver`

bordered linear solver for the constraint equation`kwargs`

keywords arguments to be passed to the regular Newton-Krylov solver

**Simplified call:**

Simplified call to refine an initial guess for a Hopf point. More precisely, the call is as follows

`newton_hopf(br::AbstractBranchResult, ind_hopf::Int; normN = norm, options = br.contparams.newton_options, kwargs...)`

The parameters / options are as usual except that you have to pass the branch `br`

from the result of a call to `continuation`

with detection of bifurcations enabled and `index`

is the index of bifurcation point in `br`

you want to refine. You can pass newton parameters different from the ones stored in `br`

by using the argument `options`

.

The adjoint of the jacobian `J`

is computed internally when `Jᵗ = nothing`

by using `transpose(J)`

which works fine when `J`

is an `AbstractArray`

. In this case, do not pass the jacobian adjoint like `Jᵗ = (x, p) -> transpose(d_xF(x, p))`

otherwise the jacobian will be computed twice!

For ODE problems, it is more efficient to use the Matrix based Bordered Linear Solver passing the option `bdlinsolver = MatrixBLS()`

`BifurcationKit.newton_palc`

— FunctionThis is the classical Newton-Krylov solver for `F(x, p) = 0`

together with the scalar condition `n(x, p) ≡ θ ⋅ <x - x0, τx> + (1-θ) ⋅ (p - p0) * τp - n0 = 0`

. This makes a problem of dimension N + 1.

The initial guess for the newton method is located in `state.z_pred`

`BifurcationKit.newton_pd`

— Method```
newton_pd(
prob,
pdpointguess,
par,
eigenvec,
eigenvec_ad,
options;
normN,
bdlinsolver,
usehessian,
kwargs...
)
```

This function turns an initial guess for a PD point into a solution to the PD problem based on a Minimally Augmented formulation. The arguments are as follows

`prob::AbstractBifurcationFunction`

`pdpointguess`

initial guess (x*0, p*0) for the PD point. It should be a`BorderedArray`

as returned by the function`PDPoint`

`par`

parameters used for the vector field`eigenvec`

guess for the 0 eigenvector`eigenvec_ad`

guess for the 0 adjoint eigenvector`options::NewtonPar`

options for the Newton-Krylov algorithm, see`NewtonPar`

.

**Optional arguments:**

`normN = norm`

`bdlinsolver`

bordered linear solver for the constraint equation`kwargs`

keywords arguments to be passed to the regular Newton-Krylov solver

**Simplified call**

Simplified call to refine an initial guess for a PD point. More precisely, the call is as follows

`newton_pd(br::AbstractBranchResult, ind_pd::Int; options = br.contparams.newton_options, kwargs...)`

`br`

from the result of a call to `continuation`

with detection of bifurcations enabled and `index`

is the index of bifurcation point in `br`

you want to refine. You can pass newton parameters different from the ones stored in `br`

by using the argument `options`

.

`J`

is computed internally when `Jᵗ = nothing`

by using `transpose(J)`

which works fine when `J`

is an `AbstractArray`

. In this case, do not pass the jacobian adjoint like `Jᵗ = (x, p) -> transpose(d_xF(x, p))`

otherwise the jacobian will be computed twice!

For ODE problems, it is more efficient to pass the Bordered Linear Solver using the option `bdlinsolver = MatrixBLS()`

`BifurcationKit.nf`

— Method```
nf(bp; tol, digits)
```

Print the normal form `bp`

with a nice string.

`BifurcationKit.ns_point`

— Method```
ns_point(br, index)
```

For an initial guess from the index of a NS bifurcation point located in ContResult.specialpoint, returns a point which will be refined using `newtonFold`

.

`BifurcationKit.pd_point`

— Method```
pd_point(br, index)
```

For an initial guess from the index of a PD bifurcation point located in ContResult.specialpoint, returns a point which will be refined using `newton_fold`

.

`BifurcationKit.phase_condition`

— Method```
phase_condition(pb, uc, , period)
```

[INTERNAL] Implementation of phase condition ∫_0^T < u(t), ∂ϕ(t) > dt. Note that it works for non uniform mesh.

**Arguments**

- uj n x (m + 1)
- guj n x m

`BifurcationKit.potrap_functional!`

— MethodThis function implements the functional for finding periodic orbits based on finite differences using the Trapezoidal rule. It works for inplace / out of place vector fields `pb.F`

`BifurcationKit.potrap_functional_jac!`

— MethodMatrix free expression of the Jacobian of the problem for computing periodic obits when evaluated at `u`

and applied to `du`

.

`BifurcationKit.predictor`

— Method```
predictor(nf, δp, ampfactor; override)
```

Compute the predictor for the simple branch point of periodic orbit.

`BifurcationKit.predictor`

— Method```
predictor(hp, ds; verbose, ampfactor)
```

This function provides prediction for the periodic orbits branching off the Hopf bifurcation point.

**Arguments**

`bp::Hopf`

the bifurcation point`ds`

at with distance relative to the bifurcation point do you want the prediction. Can be negative. Basically the new parameter is`p = bp.p + ds`

.

**Optional arguments**

`verbose`

display information`ampfactor = 1`

factor multiplied to the amplitude of the periodic orbit.

**Returned values**

`t -> orbit(t)`

2π periodic function guess for the bifurcated orbit.`amp`

amplitude of the guess of the bifurcated periodic orbits.`ω`

frequency of the periodic orbit (corrected with normal form coefficients)`period`

of the periodic orbit (corrected with normal form coefficients)`p`

new parameter value`dsfactor`

factor which has been multiplied to`abs(ds)`

in order to select the correct side of the bifurcation point where the bifurcated branch exists.

`BifurcationKit.predictor`

— Method```
predictor(nf, δp, ampfactor; override)
```

Compute the predictor for the period bifurcation of periodic orbit.

`BifurcationKit.predictor`

— Method```
predictor(gh, , ϵ; verbose, ampfactor)
```

Compute the predictor for the curve of Folds of periodic orbits near the Bautin bifurcation point.

**Reference**

Kuznetsov, Yu A., H. G. E. Meijer, W. Govaerts, and B. Sautois. “Switching to Nonhyperbolic Cycles from Codim 2 Bifurcations of Equilibria in ODEs.” Physica D: Nonlinear Phenomena 237, no. 23 (December 2008): 3061–68. https://doi.org/10.1016/j.physd.2008.06.006.

`BifurcationKit.predictor`

— Method```
predictor(bt, , ds; verbose, ampfactor)
```

Compute the predictor for the Fold curve near the Bogdanov-Takens point.

`BifurcationKit.predictor`

— Method```
predictor(bt, , ds; verbose, ampfactor)
```

Compute the predictor for the curve of homoclinic orbits near the Bogdanov-Takens point.

**Reference**

Al-Hdaibat, B., W. Govaerts, Yu. A. Kuznetsov, and H. G. E. Meijer. “Initialization of Homoclinic Solutions near Bogdanov–Takens Points: Lindstedt–Poincaré Compared with Regular Perturbation Method.” SIAM Journal on Applied Dynamical Systems 15, no. 2 (January 2016): 952–80. https://doi.org/10.1137/15M1017491.

`BifurcationKit.predictor`

— Method```
predictor(bt, , ds; verbose, ampfactor)
```

Compute the predictor for the Hopf curve near the Bogdanov-Takens point.

`BifurcationKit.predictor`

— Method```
predictor(hh, , ds; verbose, ampfactor)
```

Compute the predictor for the Hopf curve near the Hopf-Hopf bifurcation point.

`BifurcationKit.predictor`

— Method```
predictor(hh, , ϵ; verbose, ampfactor)
```

Compute the predictor for the curve of Neimark-Sacker points near the Hopf-Hopf bifurcation point.

**Reference**

Kuznetsov, Yu A., H. G. E. Meijer, W. Govaerts, and B. Sautois. “Switching to Nonhyperbolic Cycles from Codim 2 Bifurcations of Equilibria in ODEs.” Physica D: Nonlinear Phenomena 237, no. 23 (December 2008): 3061–68. https://doi.org/10.1016/j.physd.2008.06.006.

`BifurcationKit.predictor`

— Method```
predictor(
bp,
δp;
verbose,
ampfactor,
nbfailures,
maxiter,
perturb,
J,
normN,
optn
)
```

This function provides prediction for what the zeros of the reduced equation / normal form should be for the parameter value `δp`

. The algorithm for finding these zeros is based on deflated newton.

**Optional arguments**

`J`

jacobian of the normal form. It is evaluated with ForwardDiff otherwise.`perturb`

perturb function used in Deflated newton`normN`

norm used for newton.

`BifurcationKit.predictor`

— Method```
predictor(
bp,
,
δp;
verbose,
ampfactor,
nbfailures,
maxiter,
perturb,
J,
igs,
normN,
optn
)
```

This function provides prediction for what the zeros of the reduced equation / normal form should be should be for the parameter value `δp`

. The algorithm for finding these zeros is based on deflated newton. The initial guesses are the vertices of the hypercube.

**Optional arguments**

`J`

jacobian of the normal form. It is evaluated with ForwardDiff otherwise.`perturb`

perturb function used in Deflated newton`normN`

norm used for newton.`igs`

vector of initial guesses. If not passed, these are the vertices of the hypercube.

`BifurcationKit.predictor`

— Method```
predictor(zh, , ds; verbose, ampfactor)
```

Compute the predictor for the curve of Fold bifurcations near the Zero-Hopf bifurcation point.

`BifurcationKit.predictor`

— Method```
predictor(zh, , ds; verbose, ampfactor)
```

Compute the predictor for the curve of Hopf bifurcations near the Zero-Hopf bifurcation point.

`BifurcationKit.predictor`

— Method```
predictor(zh, , ϵ; verbose, ampfactor)
```

Compute the predictor for the curve of Neimark-Sacker bifurcations near the Zero-Hopf bifurcation point.

**Reference**

Kuznetsov, Yu A., H. G. E. Meijer, W. Govaerts, and B. Sautois. “Switching to Nonhyperbolic Cycles from Codim 2 Bifurcations of Equilibria in ODEs.” Physica D: Nonlinear Phenomena 237, no. 23 (December 2008): 3061–68. https://doi.org/10.1016/j.physd.2008.06.006.

`BifurcationKit.predictor`

— Method```
predictor(bp, ds; verbose, ampfactor)
```

This function provides prediction for the zeros of the Pitchfork bifurcation point.

**Arguments**

`bp::Pitchfork`

the bifurcation point`ds`

at with distance relative to the bifurcation point do you want the prediction. Based on the criticality of the Picthfork, its sign is enforced no matter what you pass. Basically the parameter is`bp.p + abs(ds) * dsfactor`

where`dsfactor = ±1`

depending on the criticality.

**Optional arguments**

`verbose`

display information`ampfactor = 1`

factor multiplying prediction

**Returned values**

`x0`

trivial solution (which bifurcates)`x1`

non trivial guess`p`

new parameter value`dsfactor`

factor which has been multiplied to`abs(ds)`

in order to select the correct side of the bifurcation point where the bifurcated branch exists.`amp`

non trivial zero of the normal form

`BifurcationKit.predictor`

— Method```
predictor(bp, ds; verbose, ampfactor)
```

This function provides prediction for the zeros of the Transcritical bifurcation point.

**Arguments**

`bp::Transcritical`

the bifurcation point`ds`

distance to the bifurcation point for the prediction. Can be negative. Basically the parameter is`p = bp.p + ds`

**Optional arguments**

`verbose`

display information`ampfactor = 1`

factor multiplying prediction

**Returned values**

`x0`

trivial solution (which bifurcates)`x1`

non trivial guess, corrected with Lyapunov-Schmidt expansion`p`

new parameter value`amp`

non trivial zero of the normal form (not corrected)`xm1`

non trivial guess for the parameter`pm1`

`pm1`

parameter value`bp.p - ds`

`BifurcationKit.projection`

— Method```
projection(psh, x)
```

Compute the projection of each vector (`x[i, :]`

is a `Vector`

) on the Poincaré section.

`BifurcationKit.projection`

— Method```
projection(psh, x)
```

Compute the projection of each vector (`x[i]`

is a `Vector`

) on the Poincaré section.

`BifurcationKit.re_make`

— Method```
re_make(
prob;
u0,
params,
lens,
record_from_solution,
plot_solution,
J,
Jᵗ,
d2F,
d3F
)
```

This function changes the fields of a problem `::AbstractBifurcationProblem`

. For example, you can change the initial condition by doing

`re_make(prob; u0 = new_u0)`

`BifurcationKit.set_collocation_size`

— Method```
set_collocation_size(pb, Ntst, m)
```

This function change the parameters `Ntst, m`

for the collocation problem `pb`

and return a new problem.

`BifurcationKit.setparam`

— Method`setparam(br, p0)`

Set the parameter value `p0`

according to the `::Lens`

stored in `br`

for the parameters of the problem `br.prob`

.

`BifurcationKit.split_events`

— Method`split_events(cs, ds, args...)`

Split comma separated callbacks into sets of continuous and discrete callbacks. Inspired by DiffEqBase.

`BifurcationKit.update!`

— Method`update!(hyp::SectionPS, normals, centers)`

Update the hyperplanes saved in `hyp`

.

`BifurcationKit.updatesection!`

— Method```
updatesection!(pb, centers_bar, par; _norm)
```

This function updates the normals and centers of the hyperplanes defining the Poincaré sections.

`BifurcationKit.∫`

— Function```
∫(pb, uc, vc)
∫(pb, uc, vc, T)
```

[INTERNAL] Implementation of ∫_0^T < u(t), v(t) > dt.

`∫(pb, uc, vc, T = 1)`

**Arguments**

- uj n x (m + 1)
- vj n x (m + 1)