This enables incremental mechanism construction for gas phase kinetics. For
surface kinetics, adding new species changes the kinetics species index of
existing species in other phases, so this feature is disabled.
All reaction-sized arrays are now allocated as reactions are added, which means
that the finalize() method is unnecessary and reactions can be continuously
added, even after the Kinetics object has been used for rate calculations.
This ensures that deprecated methods aren't being called anywhere in the test
suite, without having to manually scan the test output for warning messages.
Increasing the density of grid points is more likely to lead to a non-extinct
solution, but takes longer to solve. To give good average-case performance,
first try solving on a grid with few points, then increase the number of points
until a reacting solution is found, if possible.
Throwing an exception when a state variable is being set to NaN transforms some
reactor network integration errors from unrecoverable errors into recoverable
errors.
If any of the reaction orders differ from the corresponding stoichiometric
coefficients, the reaction needs to be handled as the general case, instead of
just when the orders are non-integral.
This also modifies the test to explicitly test each of the equilibrium solvers,
so that failures in any one solver aren't hidden by the fact that a different
solver works for a particular initial condition.
The old version of this test didn't actually check any meaninful results. The
ChemEquil and VCS solvers are both able to solve this problem, but the
MultiPhase solver currently fails. Also, the BasisOptimize function may fail
depending on the order that the elements are specified in the input file.
XML_Node::build will make that node the root node (i.e. the 'ctml' node)
of the tree, instead of giving that node a child node containing the actual
root node.
Since the Species object now stores its SpeciesThermoInterpType contents as a
shared_ptr, it is undesirable to have the Species constructor take this as a raw
pointer argument.
