Steady state sensitivity modes #1727
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| Original file line number | Diff line number | Diff line change |
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@@ -94,16 +94,22 @@ void SteadystateProblem::workSteadyStateBackwardProblem( | |
| void SteadystateProblem::findSteadyState(const Solver &solver, Model &model, | ||
| int it) { | ||
| steady_state_status_.resize(3, SteadyStateStatus::not_run); | ||
| bool turnOffNewton = model.getSteadyStateSensitivityMode() == | ||
| SteadyStateSensitivityMode::integrationOnly && | ||
| ((it == -1 && solver.getSensitivityMethodPreequilibration() == | ||
| SensitivityMethod::forward) || solver.getSensitivityMethod() == | ||
| SensitivityMethod::forward); | ||
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| /* First, try to run the Newton solver */ | ||
| if (!turnOffNewton) | ||
| findSteadyStateByNewtonsMethod(model, false); | ||
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| /* Newton solver didn't work, so try to simulate to steady state */ | ||
| if (!checkSteadyStateSuccess()) | ||
| findSteadyStateBySimulation(solver, model, it); | ||
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| /* Simulation didn't work, retry the Newton solver from last sim state. */ | ||
| if (!turnOffNewton && !checkSteadyStateSuccess()) | ||
| findSteadyStateByNewtonsMethod(model, true); | ||
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| /* Nothing worked, throw an as informative error as possible */ | ||
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@@ -243,11 +249,17 @@ void SteadystateProblem::computeSteadyStateQuadrature(const Solver &solver, | |
| We therefore compute the integral over xB first and then do a | ||
| matrix-vector multiplication */ | ||
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| auto sensitivityMode = model.getSteadyStateSensitivityMode(); | ||
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| /* Try to compute the analytical solution for quadrature algebraically */ | ||
| if (sensitivityMode == SteadyStateSensitivityMode::newtonOnly | ||
| || sensitivityMode == SteadyStateSensitivityMode::integrateIfNewtonFails) | ||
| getQuadratureByLinSolve(model); | ||
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| /* Perform simulation */ | ||
| if (sensitivityMode == SteadyStateSensitivityMode::integrationOnly || | ||
| (sensitivityMode == SteadyStateSensitivityMode::integrateIfNewtonFails | ||
| && !hasQuadrature())) | ||
| getQuadratureBySimulation(solver, model); | ||
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| /* If analytic solution and integration did not work, throw an Exception */ | ||
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@@ -366,8 +378,10 @@ bool SteadystateProblem::getSensitivityFlag(const Model &model, | |
| bool forwardSensisAlreadyComputed = | ||
| solver.getSensitivityOrder() >= SensitivityOrder::first && | ||
| steady_state_status_[1] == SteadyStateStatus::success && | ||
| (model.getSteadyStateSensitivityMode() == | ||
| SteadyStateSensitivityMode::integrationOnly || | ||
| model.getSteadyStateSensitivityMode() == | ||
| SteadyStateSensitivityMode::integrateIfNewtonFails); | ||
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| bool simulationStartedInSteadystate = | ||
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There was a problem hiding this comment. I think this code requires some updates as the newton solver can't check if we started in a steadystate if it is turned off. There was a problem hiding this comment. When is this an issue? There was a problem hiding this comment. For models that start in steady-state (e.g., computed outside of amici or extracted from other simulations), we don't want to be forced to deactivate the newton solver. See #1422. There was a problem hiding this comment. But thinking about it more carefully, we will only have misleading values if the newton solver is deactivated. In that case we will simply rextract sensitvities from the solver, which should be fine (but we probably perform a single, unnecessary simulaton step with sensitivities, which might be expensive). |
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| steady_state_status_[0] == SteadyStateStatus::success && | ||
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@@ -392,9 +406,13 @@ bool SteadystateProblem::getSensitivityFlag(const Model &model, | |
| !simulationStartedInSteadystate; | ||
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| /* When we're creating a new solver object */ | ||
| bool needForwardSensiAtCreation = | ||
| needForwardSensisPreeq && | ||
| (model.getSteadyStateSensitivityMode() == | ||
| SteadyStateSensitivityMode::integrationOnly || | ||
| model.getSteadyStateSensitivityMode() == | ||
| SteadyStateSensitivityMode::integrateIfNewtonFails | ||
| ); | ||
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| /* Check if we need to store sensis */ | ||
| switch (context) { | ||
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I think we need some documentation of the behavior for the different values, for example in the function
Model::setSteadyStateSensitivityMode(). https://github.com/AMICI-dev/AMICI/blob/master/python/examples/example_constant_species/ExampleEquilibrationLogic.ipynb also needs to be updated.There was a problem hiding this comment.
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Yeah, this notebook definitely needs to be updated.