API

Finding Tikhonov-Fenichel Parameter Values

TikhonovFenichelReductions.system_components — Method

system_components(
    problem::ReductionProblem
) -> Vector{Nemo.QQMPolyRingElem}

Convenience function to get components of ODE system from instance of ReductionProblem.

source

TikhonovFenichelReductions.system_parameters — Method

system_parameters(
    problem::ReductionProblem
) -> Vector{Nemo.QQMPolyRingElem}

Convenience function to get parameters of ODE system from instance of ReductionProblem.

source

TikhonovFenichelReductions.tfpvs_and_varieties — Method

tfpvs_and_varieties(
    problem::ReductionProblem;
    preset
) -> Tuple{Vector{Vector{Bool}}, Vector{Vector{Variety}}}

Find all slow-fast separations π⁺ that are TFPVs by using the necessary conditions

the affine variety V(f0) contains an irreducible component Y of dimension s
the s-th coefficient of the characteristic polynomial of D₁f(x,π⁺) is non-zero for x∈Y

preset can be used to restrict the search for TFPVs to slow-fast separations of rates with predefined slow/fast rates, e.g. for preset=(α=0, β=1) only TFPVs with α ∈ O(ε) and β ∈ O(1) are considered.

Description

The irreducible components are obtained by computing a minimal primary decomposition. The Jacobian at a point in an irreducible component Y is constructed symbolically by computing normal forms with respect to a Gröbner basis G, s.t. G generates the vanishing ideal of Y. To obtain all general TFPVs and not just slow-fast separations, one can use the function tfpvs_groebner.

source

TikhonovFenichelReductions.tfpvs_groebner — Method

tfpvs_groebner(
    problem::ReductionProblem
) -> Vector{Nemo.QQMPolyRingElem}

Use the necessary conditions imposed by the RHS of the polynomial ODE System and its Jacobian to filter out TFPV candidates. All TFPVs must result in the vanishing of the returned set of polynomials.

Description

If π⁺ is a TFPV yielding a reduction onto an s-dimensional slow manifold, there exist a point x₀, such that

f(x₀,π⁺)=0
for any k>s the determinants of all k×k minors of D₁f(x₀,π⁺) vanish

These properties can be used to filter out possible TFPV candidates.

We are interested in partial solutions of the system of polynomials defined by the conditions above. In particular, we only consider conditions on the parameters, since there might be multiple slow manifolds and reductions. Thus, we eliminate the state variables from the ideal generated by the polynomial conditions above. This function computes a generating set for this elimination ideal and all TFPVs lie in its vanishing set.

Computing a Tikhonov-Fenichel Reduction

TikhonovFenichelReductions.compute_reduction! — Method

compute_reduction!(reduction::Reduction) -> Bool

Compute the reduced system after the slow manifold, non-singular point and product decomposition have been set successfully.

The function returns true if the reduced system was computed successfully. The reduction in raw form, i.e. before substituting the variables x according to the slow manifold is set reduction.g_raw while the s-dimensional reduction on the slow manifold is given by reduction.g. A safe getter function for this is get_reduced_system(reduction::Reduction).

source

TikhonovFenichelReductions.get_explicit_manifold — Method

get_explicit_manifold(
    problem::ReductionProblem,
    variety::Variety
) -> Tuple{Any, Any}

Heuristic approach to get an explicit (i.e. parameterized) representation of the slow manifold from a variety. If succesfull, the function returns the (attempted) explicit manifold together with a boolean value indicating whether the manifold could be computed automatically.

source

TikhonovFenichelReductions.get_varieties — Method

get_varieties(
    problem::ReductionProblem,
    sf_separation::Vector{Bool}
) -> Tuple{Bool, Vector{Oscar.MPolyIdeal{AbstractAlgebra.Generic.MPoly{AbstractAlgebra.Generic.RationalFunctionFieldElem{Nemo.QQFieldElem, Nemo.QQMPolyRingElem}}}}, Union{Vector{Any}, Vector{Int64}, Vector{Nemo.NegInf}}}

Compute the irreducible components of V(f0) and their dimensions for a given TFPV candidate. If there exist a reduction, the corresponding slow manifold must be contained in one of these components.

Arguments

problem: Reduction problem type holding information on system and dimension of reduction.
sf_separation: Boolean index indicating slow-fast separation of rates (0: small, 1: large).

Description

This function can be used if one wants to check whether a particular slow-fast separation of rates yields a reduction for any dimension. If the dimension of an irreducible component of V(f0) differs from what was defined with ReductionProblem, the constructor Reduction can be called with the additional argument s specifying the dimension.

See also: Reduction, set_manifold!

source

TikhonovFenichelReductions.set_decomposition! — Method

set_decomposition!(
    reduction::Reduction,
    P::Union{AbstractAlgebra.Generic.MatSpaceElem, VecOrMat},
    Psi::Union{AbstractAlgebra.Generic.MatSpaceElem, Vector{Nemo.QQMPolyRingElem}}
) -> Bool

Set product decomposition f0=P⋅Psi locally satisfying V(f0)=V(Psi), where P is a matrix of rational functions and Psi is a vector of polynomials.

source

TikhonovFenichelReductions.set_decomposition! — Method

set_decomposition!(
    reduction::Reduction,
    Psi::Union{Variety, Vector{Nemo.QQMPolyRingElem}}
) -> Bool

Try to automatically compute matrix of rational functions P from given vector of polynomials Psi, such that f0=P⋅Psi and V(f0)=V(Psi) holds locally.

NOTE: This always works if the drop in dimension r=n-s=1, but may fail for r>1 (if the number of generators for the irreducible component of V(f0) is greater than r).

Description

Psi can be chosen from r algebraically independent entries of f0. Practically, one can use the generators of the ideals defining the irreducible components of V(f0) as entries for Psi (possibly rewriting the rational equations as polynomials by multiplying appropriately with parameters occurring in a denominator).

source

TikhonovFenichelReductions.set_manifold! — Method

set_manifold!(
    reduction::Reduction,
    M::AbstractVector
) -> Bool

Set the slow manifold by defining the values of the components of the system. Note that M must be defined as a vector with the same length as the system's components, i.e. reduction.problem.x.

source

TikhonovFenichelReductions.set_point! — Method

set_point!(reduction::Reduction, x0::AbstractVector) -> Bool

Set non-singular point on irreducible component of V(f0) corresponding to the slow manifold. Typically, this can be done automatically by setting the slow manifold.

source

TikhonovFenichelReductions.Reduction — Type

Type that holds all information to compute a Tikhonov-Fenichel reduction for a given slow-fast separation of rates.

Fields

problem::ReductionProblem: information on input system
sf_separation::Vector{Bool}: slow-fast separation (0: slow, 1: fast)
_p::Vector{Nemo.QQMPolyRingElem}: Parameters of the system where small ones are set to 0
f0::Vector{Nemo.QQMPolyRingElem}: RHS of system as vector with elements of ring R
f1::Vector{Nemo.QQMPolyRingElem}: Slow part of the system
higher_order_terms::Vector{Nemo.QQMPolyRingElem}: Second order terms in ε
Df0::AbstractAlgebra.Generic.MatSpaceElem{Nemo.QQMPolyRingElem}: Jacobian of f0
Df0_at_x0::AbstractAlgebra.Generic.MatSpaceElem{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}: Jacobian of f0 at the non-singular point x0
T::AbstractAlgebra.Generic.PolyRing{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}: Polynomial ring Q(p,x)[λ] for characteristic polynomial of Df0
chi::AbstractAlgebra.Generic.Poly{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}: Characteristic polynomial of Df0
M::Vector{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}: Components of the system on slow manifold
x0::Vector{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}: Non-singular point in the irreducible component of V(f0) containing the slow manifold
P::AbstractAlgebra.Generic.MatSpaceElem{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}: Matrix with rational functions, such that f0=P⋅Psi
Psi::AbstractAlgebra.Generic.MatSpaceElem{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}: Vector with polynomials, such that f0=P⋅Psi
DPsi::AbstractAlgebra.Generic.MatSpaceElem{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}: Jacobian of Psi
success::Vector{Bool}: Indicates whether slow manifold M, non-singular point x0 and product decomposition f0=P⋅Psi have been set successfully to allow the computation of the reduced system
idx_components::Vector{Bool}: Boolean indices of components that determine the flow on the slow manifold
g_raw::Vector{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}: Reduced system in general form (before substituting variables according to the slow manifold)
g::Vector{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}: Reduced system on the slow manifold
reduction_cached::Vector{Bool}: Whether g and g_raw are already computed

source

TikhonovFenichelReductions.Reduction — Method

Reduction(
    problem::ReductionProblem,
    sf_separation::Vector{Bool},
    V::Union{Variety, Vector{Nemo.QQMPolyRingElem}},
    M::Vector{<:AbstractAlgebra.RingElem};
    s
) -> Reduction

Convenience function that constructs an object of type Reduction and calls set_manifold! and set_decomposition!.

Arguments

problem: Reduction problem type holding information on system and dimension of reduction.
sf_separation: Boolean index indicating slow-fast separation of rates (0: small, 1: large).
V: Generators of affine variety corresponding to the the slow manifold
M: Slow manifold in explicit form
s::Int: (optional) Dimension of slow manifold. Can be specified if a reduction corresponding to a TFPV for dimension different from problem.s should be considered (e.g. for manually computing a reduction for a given slow-fast separation that is not necessarily obtained via tfpvs_and_varieties).

source

TikhonovFenichelReductions.Reduction — Method

Reduction(
    problem::ReductionProblem,
    sf_separation::Vector{Bool};
    s
) -> Reduction

Constructor for Reduction Type.

Arguments

problem: Reduction problem type holding information on system and dimension of reduction.
sf_separation: Boolean index indicating slow-fast separation of rates (0: small, 1: large).
s::Int: (optional) Dimension of slow manifold. Can be specified if a reduction corresponding to a TFPV for dimension different from problem.s should be considered (e.g. for manually computing a reduction for a given slow-fast separation that is not necessarily obtained via tfpvs_and_varieties).

source

Computing Multiple Tikhonov-Fenichel Reductions Simultaneously

TikhonovFenichelReductions.compute_all_reductions — Method

compute_all_reductions(
    problem::ReductionProblem,
    sf_separations::Vector{Vector{Bool}},
    varieties::Vector{Vector{Variety}},
    M::Union{Vector{Vector{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}}, Vector{Vector{Nemo.QQMPolyRingElem}}};
    print
) -> Tuple{Vector{Vector{Reduction}}, Vector{Vector{Tuple{Int64, Int64}}}}

Compute reductions for TFPVs sf_separations onto each of the explicitly given slow manifolds in M. Returns the reductions R in the same format as varieties and indices idx such that M[k] corresponds to varieties[i][j] and R[i][j] for each (i,j) in idx[k].

Description

All possible choices of slow manifolds can be obtained with unique_varieties. For each of these (that one is interested in), a parameterized form, i.e. the slow manifold in phase space defined by the remaining components of the system, must be provided. In most cases this can be obtained with get_explicit_manifold. The backwards step, i.e. finding all manifolds for which this is an explicit description, is then done automatically with find_varieties.

source

TikhonovFenichelReductions.find_varieties — Method

find_varieties(
    problem::ReductionProblem,
    varieties::Vector{Vector{Variety}},
    M::Union{Vector{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}, Vector{Nemo.QQMPolyRingElem}}
) -> Vector{Tuple{Int64, Int64}}

Find all varieties as returned by tfpvs_and_varieties for a given explicit manifold, i.e. a parametric description as a vector with the same size as problem.x.

Output

TikhonovFenichelReductions.print_system — Function

print_system([io::IO,] problem::ReductionProblem; latex::Bool=false)

Print input ODE system.

source

TikhonovFenichelReductions.print_results — Function

print_results(
  [io::IO,]
  problem::ReductionProblem,
  sf_separations::Vector{Vector{Bool}},
  V::Vector{Vector{Variety}};
  idx::Union{AbstractVector{Int}, Vector{Bool}}=1:length(V)
)

Print slow-fast separations that are TFPVs and generators for the corresponding irreducible components of V(f0) together with their Krull dimension as stored in Variety object.

Arguments

problem: ReductionProblem
sf_separations: Boolean indices defining all TFPVs π⁺ that are slow-fast separations (0: slow, 1: fast).
V: Generators for the irreducible component of the affine varietiy V(f(⋅,π⁺)) for each slow-fast separation and their respective dimension.
idx: (optional) index vector to include only certain TFPVs (boolean or numeric)

source

TikhonovFenichelReductions.print_tfpvs — Function

print_tfpvs(
  [io::IO,] 
  problem::ReductionProblem,
  sf_separations::Vector{Vector{Bool}}; 
  latex::Bool=false,
  idx::Union{AbstractVector{Int}, Vector{Bool}}=1:length(sf_separations)
)

Print slow-fast separations to terminal or use latex=true to print LaTeX instead. Optionally only print subset defined by (boolean or numeric) index set idx.

source

TikhonovFenichelReductions.print_varieties — Function

print_varieties(
  [io::IO,]
  V::Vector{Vector{Variety}};
  latex::Bool=false,
  idx::Union{AbstractVector{Int}, Vector{Bool}}=1:length(V)
)

Print generators of ideals corresponding to the irreducible components of varieties V(f0) for TFPV candidates and their dimension as returned by tfpvs_and_varieties (these are wrapped in the type Variety). Use keyword argument latex=true to print LaTeX code instead.

source

TikhonovFenichelReductions.print_reduced_system — Function

print_reduced_system(
  [io::IO,] 
  reduction::Reduction; 
  rewrite::Bool=true,
  factor::Bool=false, 
  latex::Bool=false,
  local_coordinates::Bool=true
)

Print the reduced system (after compute_reduction! has been called successfully on the Reduction object). If the slow manifold was successfully specified, this returns the system on the slow manifold. If local_coordinates=true, the reduced system is only given in s-dimensions (i.e. the local coordinates on the slow manifold). If the reduction could be computed but the slow manifold was not set successfully, the reduced system is shown in the original phase space.

Arguments

reduction: Reduction holding the reduced system
rewrite: Whether the RHS should be decomposed into polynomial and rational part (default is true), see rewrite_rational
factor: Whether the polynomial parts should be factorized
latex: Whether to print latex string
local_coordinates: Whether to present reduced system in local coordinates on slow manifold (i.e. as s dimensional ODE system)

source

TikhonovFenichelReductions.print_slow_fast — Function

print_slow_fast([io::IO,] reduction::Reduction; latex::Bool=false)

Print slow and fast parameters.

source

TikhonovFenichelReductions.rewrite_rational — Function

rewrite_rational(
    term::AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem};
    factor
) -> Tuple{Nemo.QQMPolyRingElem, Nemo.QQMPolyRingElem, Nemo.QQMPolyRingElem}

Decompose a rational function f = p/q into polynomial and rational part, i.e. return f = h + r/q, where p,q,h,r are polynomials.

Arguments

factor: Whether all polynomials should be factorized (default is false)