Fix examples #905

When loading reactions from a YAML file, an instance of a Kinetics object is required so that the species associated with the reactions are available. The required object is now constructed from the already loaded species definitions. Fixes Cantera#821, problem introduced in 1866e35

This change reworks the abortion criteria for the diffusion flame extinction example. Previously, the loop was only aborted when the flame temperature was above the inlet temperature, the difference of the flame temperature in the prior two iterations was less than the threshold, AND the change in strain rate parameter was less than the threshold. However, I found that this combination of conditions was never reached, because the only way to change the strain rate delta was to have an extinguished flame, and eventually the flame remains extinguished even if the delta_alpha is reduced. This leads to an infinite loop, since the abortion criteria check are only done if the flame is burning. This change moves the abortion criteria check into the case where the flame is not burning. In addition, the flame temperature check is modified to use np.isclose(). I found that on the last burning iteration, the maximum flame temperature was only just barely above the oxidizer inlet temperature. Thus, the result printed to the screen was not very useful. The change to np.isclose() produces a more useful result for the final burning iteration before extinction. The last non-burning iteration is also saved to the output file(s) for reference. Fixes Cantera#872

The set_boundary_emissivities method is deprecated and will be removed after Cantera 2.5.0. This change switches one example to use the new property. The property was also missing from the FlameBase class.

This allows the script to be run from the installed location, or from the root of the source tree.

argon.yaml is deprecated, use air.yaml and specify the composition instead.

The calculation for the production of gas phase species from surface reactions assumed that the gas phase species were stored at the beginning of the rate-of-production array. This is only the case when the gas ThermoPhase instance is the first phase in the Kinetics thermo vector, which is not guaranteed to be the case. It happens that XML input usually forced the gas phase to be the first phase in the thermo vector, so everything worked out fine. This was because the associated phase(s) for a surface phase had to be listed in an XML file, and the XML initializer reads that list to fill the Kinetics thermo vector. In the YAML format, the associated phase does not need to be explicitly listed. Instead, instances of the appropriate phases are passed to the constructor when the InterfaceKinetics is created. The gas phase can then come before or after the surface phase, meaning there is no guarantee of the order of species. This change checks for the starting index of the gas phase species in the InterfaceKinetics species-length arrays to make sure that the appropriate rates of production are added for the gas phase species. Fixes Cantera#902, Cantera#877, Cantera#873

Adds a getter function for the coverage_enabled property on the ReactingSurface1D Python class, and the corresponding C++ method.

The switch to the YAML input file revealed that the calculation of the anode and cathode currents in sofc.py relied on a particular order of the phases. This change corrects that by finding the index of the electron "species" in the anode and cathode phases.

Matplotlib issues a UserWarning if the xticklabels are explicitly set but the xticks are not explicitly set. We choose to set ticks every 360 degrees of crank angle, which corresponds to every 0.02 seconds in the simulation.

One of the Fortran samples needs to include the extra_inc_dirs variable so that system header files in non-standard locations will be found.

Use pathlib to write the text content to a file in write_dot. This automatically closes the file handle after the text is written. Also modify the reaction_path.py example to use pathlib and subprocess. These are available since at least Python 3.5 and represent modern best-practices in Python scripts.

The multiprocess.Pool object must be closed properly, or the process can hang according to the Python docs. The recommended method for short code blocks is to use the context manager. The format of the arguments to Pool is chosen to allow the last line to be de-dented to remove ambiguity about the definition of the context manager and the content.

pandas v1.1.0 issues a FutureWarning when plotting single columns from a DataFrame using the Matplotlib pyplot API. This can be avoided by using the pandas plotting API instead.

The content of ch4_ion.yaml now matches ch4_ion.cti (the file was re-created using cti2yaml)

A reduction of domain size makes the example more stable.

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Fix examples #905

Fix examples #905

Commits on Aug 20, 2020