This function is called after any change in composition, and can be used by
phases to update quantities that are affected by the composition change, instead
of needing to overload all of the different functions which update the
composition.
Can't be constructed from ThermoFactory, and constructor from file is not
implemented. Also, the getChemPotentials method uses the m_work array, which is
never initialized because the private method initLengths() is never called.
See #267
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.
Where possible, extend arrays as species are added rather than requiring a
later call to initThermo(). For phases that do not require any data except
that which is included in the Species objects themselves (notably, this
includes IdealGasPhase), species can now be added dynamically without
affecting the phase state.
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 can be used to invalidate cached data after a change to underlying data
such as species thermo coefficients or reaction rate coefficients. Needs to be
user-accessible so that dependent objects can be updated manually.
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.
For most problems, these new default tolerances for both time stepping and
steady state solves are more likely to converge than tighter tolerances, but
still give well-resolved results. Tighter tolerances are required in some cases,
e.g. when evaluating sensitivity coefficients by finite difference.
The existing functions for getting tolerances are difficult to use because
they return the tolerances based on the steady/unsteady mode of the solver
which the user shouldn't have to care about (and can't easily set).
Previously, the first species was always used, which could cause problems with
negative mass fractions in cases where the first species has a mass fraction
near zero.
