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Created with Raphaël 2.2.07Feb4128Jan27223217Dec5Nov22Aug14Jun10765323May221686528Apr25242319171682127Mar2312Feb730Nov13223Sep227Aug26Nov17Aug8543224Jul2119141312111098764230Jun292523151325May20829Apr282721151187654131Mar302928252423222117161514832122Feb212015Jan24Nov26Oct2019141314Sep31Aug271091Apr30Mar231914922Feb201413108754330Jan24191816158Dec227Nov18171611943229Oct2623222120191413729Sep2825242221181716159875331Aug302726252418121065431Jul30292221201918171614131279Jun22May2015121110328Apr272220161412118762127Mar26252423201917151412109625Feb241716141312111031Jan2015146330Dec1918328Nov2726251918Comparison with Julia works quite well for all cases with new mesh.mastermasterFix bug in initial condition.Mesh can now be fine inside, really fine at the boundary, coarse outside.Adding to previous commit. Forgot to stage jupyter notebook.Putting solver and mesh generation in for loop. Mesh now takes geometry input.Add numerical error.Comparison with Julia, seems to work in principle, but not extensively tried.Trying different search strategies.Work on fitting, currently for 50mM, also works for 200mM sample.Chamber height is now an input to gmsh from Jupyter. Also expanding finepossibly fixed close-file error?Starting error calculations.Prototyping optimization for low top geometry using fenics / scipy.Adding mesh for low top.Ramp outside in principal works.Clean up commit.Trying out 200mM data with low top geometry. Works in principle.Streamline mesh creation.Fixed typo in gradient, which fixes problem with volume fraction aboveGradient analytical not working, see note in bioRxiv submission Appendix.Refactor for efficient storage of effective droplet modelCorrect and stratify plot_sim.Diffusion movie for Tony.Starting work on checking steady state.Swapping A and B, for consistency with reaction-terms in the draft.This is the case that should be close to what Stefano wants.Switching to Backwards Euler scheme for stability. This case here is specialCorrect typo in sign of omega, double check!Profiles for chemical reaction paper seems to work well. Both symmetricsystem seems to work, but is spookeyly symmetric.Chemical reactions work, but flat steady-state.Source/sink now works without reactions, but with phase separation.WIP: this has an interesting intermediate state, but crashes later.Clean up.For Tony/Frank meeting. Works with and without reaction.Streamlined SourceSinkExpression, changed parameters, this now works withThis seems to be close to a real steady state!Also seems to work with corrected concentration terms.Incorporate 1D mesh into 'working' chemical reaction case.Introduce 1D case (via GPT4o), I've found a steady-state with: