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.
The lack of space between adjacent fields would cause test failures when
comparing output files when using some versions of MinGW (due to 3-digit
exponents).
If multiple processes tried to read the same input file simultaneously,
get_modified_time would fail. With this change, get_modified_time
does not need to actually open the file in order to read the metadata.
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.
These values were selected for optimal performance across a large set of flames
in each configuration and using mechanisms of various sizes to give good average
performance. It should not generally be necessary for users to change these
values.
The solver could previously get left in transient mode if an exception occurred
during time stepping, making it impossible to make a new attempt at solving the
steady-state problem.
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.
Preserve the sign of elements of the solution vector when perturbing them in
order to avoid triggering discontinuous behavior as the cross zero (which is
caused by the way rate evaluation is handled for negative species
concentrations).
The transient mask should only be zeroed when doing a full evaluation of the
residual function, since the partial evaluations done while evaluating the
Jacobian will not fill in all elements of the mask. This error was causing
Jacobian update in MultiNewton::solve to always effectively generate the
steady-state Jacobian, even when in time-stepping mode.
