Bifurcation kit extension #2300

TorkelE · 2023-10-04T16:46:10Z

This extension creates dispatches for BifurcationKit.jl's BifurcationProblem when used on NonlinearSystem or ODESystems.

This should work now:

using ModelingToolkit
using BifurcationKit

# Define ODEFunction
begin
    @variables t x(t) y(t)
    @parameters μ α
    eqs = [0 ~ μ*x - x^3 + α*y,
           0 ~ -y]
    @named nsys = NonlinearSystem(eqs, [x, y], [μ, α])
end

# Define other bifurcation inputs
begin
    p_span = (-4.0, 6.0)
    bif_par = μ
    plot_var = x
    p_start = [μ => -1.0, α => 1.0]
    u0_guess = [x => 1.0, y => 1.0]
end

# Creates a BifurcationProblem.
# This dispatch is what is implemented here, then it is BK stuff all the way.
bprob = BifurcationProblem(nsys, u0_guess, p_start, bif_par; plot_var=plot_var, jac=false)

# Sets bifurcation parameters
opt_newton = NewtonPar(tol = 1e-9, max_iterations = 20)
opts_br = ContinuationPar(dsmin = 0.001, dsmax = 0.05, ds = 0.01,
	max_steps = 100, nev = 2, newton_options = opt_newton,
	p_max = p_span[2], p_min = p_span[1],
	detect_bifurcation = 3, n_inversion = 4, tol_bisection_eigenvalue = 1e-8, dsmin_bisection = 1e-9)

# Creates the bifurcation diagram.
bf = bifurcationdiagram(bprob, PALC(), 2, (args...) -> opts_br; bothside=true)

# You can plot the diagram like
using Plots
plot(bf; putspecialptlegend=false, markersize=2, plotfold=false, title = "#branches = $(size(bf))")

Tests and docs not added yet, will do if people think this approach looks good.

Co-authored-by: Fredrik Bagge Carlson <[email protected]>

Support heterogeneous parameters for linearize and remake

ChrisRackauckas · 2023-10-06T01:15:11Z

ext/MTKBifurcationKitExt.jl

+# When input is a NonlinearSystem.
+function BifurcationKit.BifurcationProblem(nsys::NonlinearSystem, u0_guess, p_start, bif_par, args...; plot_var=nothing, record_from_solution=BifurcationKit.record_sol_default, kwargs...)
+    # Creates F and J functions.
+    ofun = NonlinearFunction(nsys; jac=true)


is the jac required? The user should request it if it's not.

I will make it optional.

ChrisRackauckas · 2023-10-06T01:16:02Z

This looks like a great idea. Just needs tests and docs.

TorkelE · 2023-10-06T01:37:35Z

Sounds good, there is a bug in this for for systems with more species/parameters that I need to fix. I might also drop the p_span input (will discuss it with Romain). Once I'm sure of this I will make an updated version, and test+docs (and then make an extension in Catalyst that builds on this one).

@time

The recursive structure of SystemStructure was giving precompilation an issue so I removed that module. Then I setup precompilation on the basic interface. Test case: ```julia @time using ModelingToolkit @time using DifferentialEquations @time using Plots @time begin @variables t x(t) D = Differential(t) @nAmed sys = ODESystem([D(x) ~ -x]) end; @time prob = ODEProblem(structural_simplify(sys), [x => 30.0], (0, 100), [], jac = true); @time sol = solve(prob); @time plot(sol, idxs=[x]); ``` Before: ``` 11.082586 seconds (19.32 M allocations: 1.098 GiB, 4.09% gc time, 0.71% compilation time: 87% of which was recompilation) 0.639738 seconds (661.39 k allocations: 101.321 MiB, 4.33% gc time, 6.46% compilation time) 3.703724 seconds (5.71 M allocations: 322.840 MiB, 5.22% gc time, 9.92% compilation time: 86% of which was recompilation) 7.795297 seconds (8.25 M allocations: 483.041 MiB, 2.50% gc time, 99.88% compilation time) 21.719376 seconds (44.11 M allocations: 2.485 GiB, 5.68% gc time, 99.48% compilation time) 2.602250 seconds (4.04 M allocations: 253.058 MiB, 4.60% gc time, 99.90% compilation time) 2.450509 seconds (5.17 M allocations: 332.101 MiB, 5.89% gc time, 99.41% compilation time: 30% of which was recompilation) ``` After: ``` 9.129141 seconds (22.77 M allocations: 1.291 GiB, 4.65% gc time, 0.62% compilation time: 87% of which was recompilation) 0.784464 seconds (667.59 k allocations: 101.524 MiB, 3.95% gc time, 4.16% compilation time) 3.111142 seconds (5.42 M allocations: 305.594 MiB, 3.82% gc time, 6.39% compilation time: 82% of which was recompilation) 0.105567 seconds (157.39 k allocations: 10.522 MiB, 8.81% gc time, 95.49% compilation time: 74% of which was recompilation) 1.993642 seconds (4.03 M allocations: 218.310 MiB, 2.69% gc time, 96.95% compilation time: 82% of which was recompilation) 1.806758 seconds (4.06 M allocations: 254.371 MiB, 4.44% gc time, 99.91% compilation time) 1.694666 seconds (5.27 M allocations: 339.088 MiB, 6.18% gc time, 99.39% compilation time: 31% of which was recompilation) ``` And that's on v1.9, so v1.10 should be even better. 20 seconds off hehe.

Fix recursive structure and setup precompilation

…model`

- All sections, except building hierarchal models, use `@mtkmodel`. - "Non-DSL way of defining an ODESystem" section is added.

Remove ODAEProblem from acausal tutorial

one more tutorial simplification

Support implicit name unpack in `at extend`

Simplify `at extend`

update docs for new extension syntax

non canon docstrings

TorkelE · 2023-10-14T15:19:08Z

Added some docs and a test. If things seems to work out I could add a couple of more tests.

ChrisRackauckas · 2023-10-16T08:07:46Z

ext/MTKBifurcationKitExt.jl

@@ -0,0 +1,40 @@
+module MTKBifurcationKitExt


fix the naming.

what should I name it?

ChrisRackauckas · 2023-10-16T08:08:03Z

Tests fail because the Project.toml needs to be updated.

…ifurcationKitExtension

ChrisRackauckas · 2023-10-17T10:41:02Z

That rebase did not go well

TorkelE · 2023-10-17T18:02:46Z

Yeah, no idea what happened. Just tried putting it back at master.

ChrisRackauckas · 2023-10-17T18:24:28Z

Well I think it may be ready to go if it's cleaned up.

TorkelE · 2023-10-17T18:50:24Z

I will probably just make a new PR, easier that way.

TorkelE · 2023-10-17T20:27:43Z

Replaced by: #2321

Brad Carman and others added 21 commits September 25, 2023 10:18

split parameters linearize bug

e56de20

added old MatrixGain definition for comparison

cee69ed

new promote_to_concrete

b4f821e

improvements to protmote_to_concrete

e62e3ee

remake issue

ee4deb9

Suppose heterogeneous parameters for linearize and remake

a9c56b6

Fix zero_dummy_der

1a96915

Co-authored-by: Fredrik Bagge Carlson <[email protected]>

Relax tests

023e024

Don't use SciMLBase 2

119cb27

Merge branch 'master' into bgc/split_params_bug

6bb0b2e

Fix eq ordering

29aec7b

Change bounds back

addf335

Format

2e4c1bb

Be careful with string sorting

2a553a7

Update LaTeXify ref tests

f9ea3a6

init

c2f92f1

makefunction

b05bc5f

1.6 has a different term ordering

f2d80b0

Fix DiscreteProblem construction

ae05041

Merge pull request #2283 from SciML/bgc/split_params_bug

2309f9f

Support heterogeneous parameters for linearize and remake

Update Project.toml

fb7c3af

ChrisRackauckas reviewed Oct 6, 2023

View reviewed changes

ChrisRackauckas and others added 6 commits October 6, 2023 12:03

Merge pull request #2301 from SciML/precompile_workload

7949761

Fix recursive structure and setup precompilation

docs(refactor): update acausal components tutorial with @mtkmodel

c5bd821

docs(refactor): update structural identifiability tutorial with `@mtk…

6ac545d

…model`

docs(fix): set a u0 within the constraint for the optimization problem

278698b

docs(refactor): refactor "Getting Started" section with @mtkmodel

94fb749

- All sections, except building hierarchal models, use `@mtkmodel`. - "Non-DSL way of defining an ODESystem" section is added.

YingboMa and others added 16 commits October 8, 2023 18:16

Stop using at testset macro

73f9e0a

Remove ODAEProblem from acausal tutorial

718ae81

Merge pull request #2308 from SciML/odaeproblem

0bcdee8

Remove ODAEProblem from acausal tutorial

Merge pull request #2307 from SciML/tuts

379161f

one more tutorial simplification

Merge pull request #2306 from SciML/myb/extend

314bb1d

Support implicit name unpack in `at extend`

patch system names

298a9a5

Simplify at extend

bdc45d1

update docs for new extension syntax

1152f30

fix for simplified extend

9e45fee

Merge pull request #2310 from SciML/myb/extend

563f04f

Simplify `at extend`

Merge pull request #2309 from SciML/extend

2c17d63

update docs for new extension syntax

Update Project.toml

d4239a7

non canonical docstrings

bc93796

update contributing docs

b54b05b

Merge pull request #2315 from ArnoStrouwen/docs

0ef0bb4

non canon docstrings

updates

2c86306

ChrisRackauckas reviewed Oct 16, 2023

View reviewed changes

TorkelE added 4 commits October 16, 2023 22:26

init

3249aeb

makefunction

7f5d8be

updates

c4a1a20

Merge remote-tracking branch 'TorkelE/BifurcationKitExtension' into B…

918f5e6

…ifurcationKitExtension

TorkelE mentioned this pull request Oct 17, 2023

BifurcationKit Extension (take 2) #2321

Merged

TorkelE closed this Oct 17, 2023

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Bifurcation kit extension #2300

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Bifurcation kit extension #2300

Bifurcation kit extension #2300

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