The structure of this calculation previously led to an apparent increase in
pressure along the length of the reactor. This is a good example of when to use
a PressureController.
The classes implementing specific flame geometries don't directly interact with
any of the underlying C++ implementation, so they can be moved out of the
compiled Cython extension. This reduces the size of the compiled extension, and
makes it easier to implement additional flame types in Python.
In C++, these are the reactantString() and productString() methods. In Python,
these are the 'reactants' and 'products' properties.
Resolves Issue 110.
Adds ReactorNet::reinitialize, which skips all one-time initialization and
re-uses the same CVODES integrator. The Reactor::syncState() method is
introduced for applying new initial conditions for individual Reactor objects.
This approach increases efficiency when solving many similar problems with short
integration times, for example when being used as the chemistry term integrator
in an operator-split CFD code.
This reflects how the function is usually used. The old signature is now
deprecated, as is the extra argument for transfering "ownership" to the
ReactorNet object.
The threshold for printing species is a new, optional parameter to the
'report' function. If any species are excluded, the total number of
minor species and their aggregate mass and mole fraction are printed.
These tests are based on the 'plasma_equilibrium.py' example, and include
a fairly large number of phases, some of which are only present for certain
temperature ranges.
Some calls to the print function weren't being converted to print statements
correctly by 3to2, so now we use the alternative fix, which is to use the
backported print function.
Fixes Issue 216.
Since stdout may be used for writing the actual output file, direct all error
and debug messages to stderr, so that they can be shown to the user when
ctml_writer is invoked via ct2ctml_string.
When using Python 3, using -1 as the dummy value for density and site_density
causes probems, because the (ordered) comparison between a density specified
with units (as a tuple) and 0 is not allowed. Instead, use None as the
placeholder value.
