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Ability to setup and solve as a well-mixed system #3

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justinlaughlin opened this issue Oct 28, 2019 · 1 comment
Open

Ability to setup and solve as a well-mixed system #3

justinlaughlin opened this issue Oct 28, 2019 · 1 comment
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enhancement: non-critical A nice enhancement to have but not critical to the alpha release

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@justinlaughlin
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Currently models can only be setup in 3d with 2d boundary conditions. The ability to setup the system in 0d (i.e. well-mixed) and solve via e.g. sympy solve_ivp would allow quicker testing of model parameters

@justinlaughlin justinlaughlin added the enhancement: non-critical A nice enhancement to have but not critical to the alpha release label Oct 28, 2019
@Rabona17
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Benefits:
Allows faster flux value computation using Scipy, instead of assembling into dolphin object.

Use cases:

  1. Typically if one is using third-party PDE solvers, setting up the system and configuration will be time consuming. This feature allows significantly faster solves in non-spatial (0d) models. This is particularly useful when the sensitivity analysis and stability analysis require a lot of model runs.

Sub issues:

  1. The units and magnitudes should be converted to be consistent between different species before solving.
  2. The user should specify the initial values for species, and those values should satisfy expected values if the system is in equilibrium.

@justinlaughlin justinlaughlin added enhancement: critical An enhancement that is critical to the alpha release and removed enhancement: non-critical A nice enhancement to have but not critical to the alpha release labels Feb 27, 2020
@justinlaughlin justinlaughlin added enhancement: non-critical A nice enhancement to have but not critical to the alpha release and removed enhancement: critical An enhancement that is critical to the alpha release labels Jan 4, 2022
finsberg pushed a commit that referenced this issue Mar 3, 2023
Updated examples 2-4, changed details of sphere mesh generation in common, and implemented a check and fix for negative solutions in model.monolithic_solve
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Labels
enhancement: non-critical A nice enhancement to have but not critical to the alpha release
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