Added new ways to select exactly what types of reactions (strong, beta+, beta-, electron capture, positron capture, or any combination thereof) can be turned on at network construction time. There are a few quality of life masks added as well such as weak which addes all weak type reactions, and all which adds weak + strong reactions. The default is to just add strong reactions for now.
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)
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
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.
