surfchem - modified ck,py, production.py, utilities.py and converter.py

[jAnirudh]

Reworked the CEPTR modules generating mechanism.cpp to work with heterogeneous reaction mechanisms.

• Methods changed/added in:
  1. ck.py: ckncf, cksyme_str, cksyms_str, ckkfkr
  2. production.py: progress_rate_fr
  3. utilities.py: Added get_function_prefix, get_phase, def get_element_id, get_atomic_weight, get_element_names methods
• Added a NUM_QSS_GAS_SPECIES preprocessor directive to converter.py along with changes corresponding to above additions/modifications
• Regenerated all non-qss mechanisms

[marchdf]

@jAnirudh can you rebase your branch on the latest? Once this looks good, I can update the qss chems as well.

[baperry2]

Just a thought: as this work will be implemented over a series of PRs, maybe it would be helpful to open an issue to track the progress and plans, similar to what we did here: #446

[jAnirudh]

Just a thought: as this work will be implemented over a series of PRs, maybe it would be helpful to open an issue to track the progress and plans, similar to what we did here: #446

@baperry2 Sure, I'll put together a plan and open an issue.

Meanwhile, @marchdf could you please regenerate the qss mechanisms for me? The qss files are still somehow changing on my linux box.

[marchdf]

@nickwimer and @jAnirudh Does this diff look right for the QSS mech? I am a little confused by the numbers. Actually maybe it's ok. Though I would want a second pair of eyes on this. I pushed the changes if you want to see them all.

[jAnirudh]

@nickwimer and @jAnirudh Does this diff look right for the QSS mech? I am a little confused by the numbers. Actually maybe it's ok. Though I would want a second pair of eyes on this. I pushed the changes if you want to see them all.

I had introduced NUM_QSSA_GAS_SPECIES without realizing that the QSS species are a subset of NUM_GAS_SPECIES. Here I roll back the definition of NUM_QSSA_GAS_SPECIES to NUM_GAS_SPECIES and add NUM_QSS_SPECIES with the intent that hard coded calls, if any, coming from species_info.n_qssa_species can be replaced by NUM_QSS_SPECIES down the line.

[marchdf]

@jAnirudh and @nickwimer I regenerated the QSS mechs with the latest. Feels like we need to confirm that all is well.

[jAnirudh]

Hi @marchdf @baperry2 @nickwimer could you please share your comments on this PR for review/merge? Also tagging @ndeak here. Thanks.