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RangamaniLabUCSD / smart

Spatial Modeling Algorithms for Reactions and Transport
https://rangamanilabucsd.github.io/smart/
GNU Lesser General Public License v3.0
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Ability to setup and solve as a well-mixed system #3

Open justinlaughlin opened 5 years ago

justinlaughlin commented 5 years ago

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

Rabona17 commented 4 years ago

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.