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Add pseudo-spectral discretisation and use Catalyst's spatial reaction interface.#61

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Homo-carbonis wants to merge 158 commits intohiscocklab:masterfrom
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Add pseudo-spectral discretisation and use Catalyst's spatial reaction interface.#61
Homo-carbonis wants to merge 158 commits intohiscocklab:masterfrom
Homo-carbonis:master

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This has all the new code needed to use the new pseudo-spectral solver and the Catalyst interface for diffusion parameters. I've also refactored the code slightly to make it a bit easier to extend and updated the documentation.

Major Changes

  • When running simulate you can choose either discretisation=:pseudospectral (the default) or discretisation=:finitedifference to use the finite difference method provided by Catalyst.
  • Diffusion is represented by Catalyst .SpatialReaction objects which associate diffusion parameters with reactants.
  • The input provided by the user is a Model object which contains a complete description of the system apart from the parameter values.
  • Parameters for reaction and diffusion are supplied together as a dictionary or collection of pairs e.g. (:a => [0.3], :b => range(0.0,3.0,4) :Dᵥ => [50.0])

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