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[v14 ready] New stability computation #739

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merged 28 commits into from
May 23, 2024
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@TorkelE TorkelE commented Dec 4, 2023

New version of: #730 (rebasing was a mess)

Enables computation of stability of steady states. Conservation laws should be accounted for.

Simple example:

using Catalyst
import HomotopyContinuation

rs = @reaction_network begin
    (v/10.0 + hill(X, v, K, n), d), 0 <--> X
end
p = [:v => 2.0, :K => 1.0, :n => 3, :d => 1.0]
steady_states = hc_steady_states(rs, p)

steady_state_stability(steady_states[1], rs, p) # true
steady_state_stability(steady_states[2], rs, p) # false
steady_state_stability(steady_states[3], rs, p) # true

steady_state_stability(steady_states, rs, p) # [1, 0, 1]

ss_jac = steady_state_jac(rs) # [1, 0, 1]
steady_state_stability(steady_states, rs, p; ss_jac=ss_jac) # [1, 0, 1]

Also add a function is_autnomous that checks whether a system is autonomous. Add this as an error check when creating BifurcationProblems, NonlinearSystems, and computing steady states using hc_steady_states.

@TorkelE TorkelE mentioned this pull request Dec 4, 2023
@TorkelE TorkelE changed the title New stability computation [v14 ready] New stability computation Feb 2, 2024
@TorkelE TorkelE changed the base branch from master to Catalyst_version_14 February 2, 2024 15:34
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TorkelE commented Feb 2, 2024

Remove autonomy check for NonlinearSystems for now, however, it is probably something we will have to think about at some point (at least the user will get an error quite soon right now anyway).

Base automatically changed from Catalyst_version_14 to master May 15, 2024 17:37
@TorkelE TorkelE force-pushed the new_stability_computation branch from 7836e03 to e29711a Compare May 20, 2024 19:00
@TorkelE TorkelE force-pushed the new_stability_computation branch from 9cc116b to 9cc5f9c Compare May 21, 2024 17:29
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TorkelE and others added 5 commits May 23, 2024 15:16
…putation.md

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
@TorkelE TorkelE merged commit 3abba83 into master May 23, 2024
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@TorkelE TorkelE deleted the new_stability_computation branch May 23, 2024 20:33
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2 participants