Don Elbert

I will try this with a fresh install on a new machine that I will be getting. It might soon or it might take some time. I'm confident that this...

The MPI.Accumulate! could also be done in one shot: MPI.Accumulate!(matches, root,0,MPI.SUM, win_accumulate).

Yes, indeed, and thank you for your work on this interesting project and your talk at JuliaCon. The equations and states are promoted 'as requested'. The parameters are not. It...

The abstol and reltol are inside DynamicSS, not attached to solve. Moving them outside of DynamicSS into solve makes the termination much worse, as expected. But these are definitely inside...

Corrected in edit: xxx[Okay, I think the root issues are the aggressive time step growth and the reltol = 1e-6 is too large. The delta t is growing fast and...

It appears to be exactly the same, but I'm only 99% sure of my implementation of TerminationCondition: ``` using FiniteDiff using ForwardDiff using Optimization using OptimizationOptimJL using NonlinearSolve using DifferentialEquations...

I'll point out that if you have changing compartment volumes and the state variables are concentrations, you need to apply the quotient rule as d(amount/V)/dt = (V d(amount)/dt - amount...

> This is a very good point, and something for example importers like SBMLImporter deals with. But I also think it should, given that each specie has a unit, should...

> One questions whether there should be a special "compartment" tag for a `ReactionSystem`, in which case one might be able to define some additional properties, but also disallow some...

> Do you have a link to how Antimony does it? Antimony is just a text file or string that Tellurium converts to SBML before solving the SBML model with...