Starting to add diffusion - #331

Merged

gustavdelius merged 49 commits into

diffusion_gemini

Apr 9, 2026

Commits on Feb 16, 2026

Add vignette to document numerical scheme
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feat: Implement a semi-implicit upwind finite volume scheme with diffusion using the Thomas algorithm for projecting species abundance.
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test: Add analytical test for transport equation solver with corresponding vignette and test file.
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b575811
Avoid warnings in tests
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a165dea
feat: Implement diffusion in steady state calculation
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c1846ec
feat: Account for diffusion in the `get_required_reproduction` calculation at the minimum size.
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feat: Add diffusion support to `get_steady_state_n` and refactor steady-state calculations to use it.
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Refactor project_n to use thomas_solve
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Keep fast projection code if no diffusion
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feat: Add new vignette demonstrating cohort dynamics and the effect of diffusion in a single-species size-spectrum model.
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Choose better parameters for vignette on cohort dynamics
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Removing some build problems
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1647aa6

Commits on Feb 17, 2026

docs: Adjust diffusion coefficients in the cohort dynamics vignette.
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Add alt text to all images
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Add discussion of numerical diffusion to vignettes
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Adding discussion of numerical diffusion arising from implicit time stepping.
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feat: Migrate `project_n`'s tridiagonal solver to C++ for improved performance.
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Remove unwanted arguments from `get_transport_coefs()`
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Fix vignette title
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138a6ce
Add vignette explaining use of FFT
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e1f32ba

Commits on Feb 18, 2026

Small change to argument list of a helper function
gustavdelius
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d75bdd6

Commits on Feb 19, 2026

Commits on Feb 20, 2026

Commits on Feb 22, 2026

Commits on Feb 23, 2026

Don't issue warning if growth rate becomes zero only after maturity size.
gustavdelius
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19ec442

Commits on Feb 26, 2026

Commits on Mar 11, 2026

Thanks to Jess for catching this. C++ is not as clever as R!
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0e24210

Commits on Mar 18, 2026

Instruction file for Claude Code
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090f7ff

Commits on Mar 23, 2026

Update .*ignore
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f183733

Commits on Apr 9, 2026

merged master
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Merge branch 'master' into diffusion_gemini
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Update NEWS.md
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NEWS.md now updated also with changes on the master branch.
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Spelling corrections
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