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.
