previously I had neglected to actually call the heuristic removing weak reaclib reactions. This is now called properly. Therefore it is this commit which actually prevents weak reaclib reactions from getting registered
reaclib provides a small number of weak reactions which allow for things like closing the CNO cycle. Howevever, they are not of the same quality as the WRL reactions. Therefore we ignore them during network construction through a simple heuristic (is the mass number the same on both sides and is there exactly 1 product and reactant (ignoring the beta +/- particle). This is one of the final steps before actually enabling weak reactions since withouty turning these off we would be double counting weak reactions.
previousl the sparsity calculations for the jacobian matrix were completly broken. The method subgraph_sparsity was returning that all derivities were only depenednt on temperature and density. It should have been reporting that they also depended on some of the abundances. This was resolved by switching to a different structural sparsity engine (for_jac_sparsity). This bug had turned the solver into a fixed point iteration solver which failed for the stiff system we have. Now that it is resolved the solver can once again evolved over Gyr timescales.
Previously, due to a indexing issue, reverse rates were sometimes included in the forward rates for strong reactions. This lead to erroneously high molar reaction flows for some reactions. This has been resolved so now each logical reaction set is guareteed to include only either forward reactions or reverse reactions (not both)
previously recordADTape was duplicating a lot of work which recordEpsTape also needed to do. Now all derivs are being recorded into m_rhsADFun so that only one tape recording phase is needed per network build stage.
essentially all callers can now inform the graph engine about which species they hold active and graph engine then uses those to define a sparsity pattern and only calculate the jacobian along that sparsity pattern
All jacobian calculations were broken because the indexing used to record the AD tape was broken (see not parallel to) the indexing used by the composition object. A fix for this was to sort the network species by mass. However, more generally we should introduce a mechanism to ensure these two indexed sets always remain parallel
This fourdst version bump brings the libcomposition v1.9.0 which brings the abstract base class CompositionAbstract. This will allow us to impliment overrides which return specific molarAbundances skirting around Composition internal checks. This is for the purpose of allowing unrestricted molar flow when ccalculating the destruction rate constant for particular species.
bigs were introduced by the interface change from accepting raw molar abundance vectors to using the composition vector. This commit resolves many of these, including preformant ways to report that a species is not present in the composition and unified index lookups using composition object tooling.
BREAKING CHANGE:
Major weak rate progress which includes: A refactor of many of the public interfaces for GridFire Engines to use composition objects as opposed to raw abundance vectors. This helps prevent index mismatch errors. Further, the weak reaction class has been expanded with the majority of an implimentation, including an atomic_base derived class to allow for proper auto diff tracking of the interpolated table results. Some additional changes are that the version of fourdst and libcomposition have been bumped to versions with smarter caching of intermediate vectors and a few bug fixes.
