The order now matches the order in which the corresponding sensitivity reactions
are added to the ReactorNet, regardless of the order in which Reactors and Walls
are added to the network.
Sensitivity parameter names can be accessed using the "sensitivityParameterName"
method of ReactorNet, and the "sensParamID" methods of Reactor and Wall have
been removed as they no longer meaningful.
Sensitivity analysis requires that the system responds appropriately to small
perturbations in the solution, a condition which is not satisfied when using the
default iterative method implemented by ThermoPhase::setState_UV. Instead, we
now use Newton's method to calculate the mixture temperature to within a small
multiple of machine precision.
Removed the optional argument to ReactorNet::initialize so that setInitialTime
is the only interface for setting the integrator start time, and made initialize
protected to make it clear that it does not need to be explicitly called by the
user.
These changes make it unnecessary to copy header files around during
the build process, which tends to confuse IDEs and debuggers. The
headers which comprise Cantera's external C++ interface are now in
the 'include' directory.
All of the samples and demos are now in the 'samples' subdirectory.
