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Created with Raphaël 2.2.022Sep7Aug26Nov17Aug8543224Jul2119141312111098764230Jun292523151325May20829Apr282721151187654131Mar302928252423222117161514832122Feb212015Jan24Nov26Oct2019141314Sep31Aug271091Apr30Mar231914922Feb201413108754330Jan24191816158Dec227Nov18171611943229Oct2623222120191413729Sep2825242221181716159875331Aug302726252418121065431Jul30292221201918171614131279Jun22May2015121110328Apr272220161412118762127Mar26252423201917151412109625Feb241716141312111031Jan2015146330Dec1918328Nov2726251918Update line thickness.Checking mass conservation.Add code for ROPP review. Figure showing model accuracy (client-binding).Allow for interpolated initial conditions outside.Introduce edge case k=0 and k==NaN.Cosmetics.A_in is not an output anymore.Delete adaptive time stepping remnants.Revert accidental changes.Merge remote-tracking branch 'origin/master'Add extrapolation to boundary condition.Experimental initial condition now possible.BC working (preliminary, partly hard-coded).Replace geometry with geomUpdate gitignore.Trying scaling error with t. No major improvement in efficiency.added further constraint in adapt_delta_t, gain scaling more gradually, no major improvement in efficiencyincreasing size of x_b domain and reducing r in adapt_delta_t gets rid of oscillations and allows for higher gain. Efficiency increased of 12%. But gain and r depend on initial conditions. Introduce a check for oscillations?Oscillations reduced to minimum (?). Need to introduce a check for stabilityFor small enough gain, stable in the inside, unstable outside. NEXT:trying different gains at different points in the simulationThe gain parameter is dependent on t dimensions. For longer simulations higher gain is needed BUT it results in oscillatory behaviour.Modified effective_t and u size cutting zeros. Working with gain=0 but not for non 0 gainNow completed adaptive time stepping with new effective_t. Runs.Comment out plotting.Function computing optimal delta-t at each cycle.Added gradients for each step and the next.Fix typo in case with no interface resistance.Interface resistance works as expected.Faster simulation without too much worse results.Introduce a third compartment with larger step size outside. Works well.Update ML comparison.Works well for realistic parameters.Keeping alpha outside close to one allows 1000fold difference.Still works extremely well for 100fold difference in D.Comparison with Matlab works for small differences in diffusion.Fixing bug in x outside (x out started at 0, no R).Comment out adaptive time stepping.Fix layout to <= 80 characters per line.Merge remote-tracking branch 'origin/3D-two-matrices'Revert parallel for loop. Too complicated, not enough promise for speed-