Previously QSE solving was done using Eigen. While this worked we were
limited in the ability to use previous iterations to speed up later
steps. We have switched to KINSOL, from SUNDIALS, for linear solving.
This has drastically speed up the process of solving for QSE abundances,
primarily because the jacobian matrix does not need to be generated
every single time time a QSE abundance is requested.
FOr QSE solving the Jacobian does not change meaninfully between steps.
We have introduced caching so that it does not need to be reevaluated
every step
We added one new check to the partitioning stage for
MultiscalePartitioningEngine view which, after group validation, prunes
any species only connected by reactions with a log(flow/mean involved
species abundance) less than -30. Currently this is a magic number and
will need to be adjusted. These pruned groups succsessfully prevent
light elements getting vacumed up into QSE groups due to their overall
weak couplings to the entire network. This is important else the
conditioning of the QSE systems falls apart.
There are times when the jacobian matrix has infinities or nans. If
these cases correspond to species (rows or columns) which have
effectivley zero abundance (i.e. if Y(Cl-32) ~ 1e-310 and
(dY(H-2)/dt)/dY(Cl-32) is inf) then it is safe to regularize these
entries to 0. If this is not done then the solver will end up finding
NaN values for the molar abundances on subsequent steps. This has been
implimented through a small regularization function in the
CVODE_solver_strategy file.
Previously Jacobians were stored by engines and accessed through engine
accessors (e.g getJacobianMatrixEntry); however, this resulted in
desynced jacobian states. We have changed to a pattern of Engine creates
a jacobian and returns it to the caller. The caller can then do what
they will with it. Because of this the getJacobianMatrixEntry method has
been removed.
BREAKING CHANGE:
- There is no longer any getJacobianMatrixEntry method on
DynamicEngine classes
- the generateJacobian method signature has changed to return a
NetworkJacobian object. Internally this uses an Eigen Sparse Matrix to
store its data.
one major issue was that QSE solving was only running at each partition. This was creating effectivley infinite sources of partitioned species. Now we partition when engine updates are triggered, however, solveQSEAbundance is called every timestep. This has major performance implications and so has required a lot of optimization to make it even somewhat viable. For now construction is much slower. Time per iteration is still slower than it was before; however, it is tractable. There is also currently too much stiffness in the network. This is likeley a bug that was introduced in this refactoring which will be addressed soon.
This entailed a major rewrite of the composition handling from each engine and engine view along with the solver and primer. The intent here is to let Compositions be constructed from the same extensive property which the solver tracks internally. This addressed C0 discontinuity issues in the tracked molar abundances of species which were introduced by repeadidly swaping from molar abundance space to mass fraction space and back. This also allowed for a simplification of the primeNetwork method. Specifically the mass borrowing system was dramatically simplified as molar abundances are extensive.
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.
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
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.
