GridFire can now support unity builds. This is useful for python
bindings. The main limitation is that openssl (a dependency of
libplugin) does not support unity builds. Therefore when building in a
unity build libplugin must be disabled. This is done with the
-Dunity-safe=ture flag at setup time
GridFire failed to compile on gcc and gnu stdlibc++ this has been
resolved. Further, the boost dependency has been removed since we no
longer use boost at all. This should dramatically simplify installation.
Finally we have added some build system checks to ensure that the
correct version of a C++ and fortran compiler are present on the system
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.
Fized stoichiometry matrix initialization, added penames to reablib reactions, began work on LogicalReaction to sum the contributions of different fitting functions provided by reaclib
we need an autodiff library at some point (or we need to roll our own but I do not think that makes sense). CppAD is well tested and header only and easy to include. It is also Liscene compatible with GPL v3.0. Here we bring it in as a dependency
