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.
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.
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.
Replace the O(k) implementation of Phase::speciesIndex with one that is
O(log(k)). This function is called frequently as part of Kinetics object
initialization. Optimize for the more common case where the species name is not
qualified with a phase name.
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.
Phase::addElements(string name, ...) is the single entry point for adding
elements. It always perform the uniqueness check, and can do the extra
additional work required to add elements to a phase that already has species,
removing the need for "freezing" the phase's elements. Parsing the XML tree for
elements is now handled in "installElements". The variant element-adding methods
are deprecated.
This makes it easier to set the composition of a phase based on the composition
of another phase with a different set of species. The threshold argument allows
species with negligible concentrations to be skipped.
Deprecate the unused getMoleFractionsByName function that didn't return a
value.
There are a series of activity coefficients for published battery models
which actually overflows. Cantera was treating this as a nonerror and changing
the return results without comment. This is not correct. Made the behavior a
user controlled capability.
Now the complete XML file is storred within the ThermPhase object starting with the root node.
This is needed for later processing of kinetics and transport mechanisms when the ThermoPhase
file is duplicated and the original file is deleted.
xml() is now a const function, and still returns the same pointer.
setXMLdata() is a new function will stores the xml data.
