search

AtChem / AtChem2

Atmospheric chemistry box-model for the MCM
MIT License
59 stars 22 forks source link

DILUTE Error with Latest Stoichiometry Update #515

Closed AlfredMayhew closed 6 months ago

AlfredMayhew commented 6 months ago

I have noticed that all AtChem2 models now fail if DILUTE is not set to NOTUSED, following the changes in #514 . This is because the added dilution reactions in the mechanism.reac file don't have defined stoichiometric coefficients. I have fixed this by adding a coefficient of 1.

codecov[bot] commented 6 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (27ede44) 52.05% compared to head (0840c46) 52.05%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #515 +/- ## ======================================= Coverage 52.05% 52.05% ======================================= Files 17 17 Lines 2096 2096 Branches 166 166 ======================================= Hits 1091 1091 Misses 933 933 Partials 72 72 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

rs028 commented 6 months ago

One question, does the stoichiometric coeff need to be a real number or does this work even if the user set it to an integer?

PS: you should be able to merge this, after you accept the invite to be member (I think!)

AlfredMayhew commented 6 months ago

The accepted formats in the mechanism file should be either a integer or decimal number, with or without a space. i.e. all of the following should be accepted:

This is then read by python and converted to a float in the separate_stoichiometry function. This means it's always written out to mechanism.reac and mechanism.prod as a decimal (real?). I haven't actually tried manually editing these files to change the 1.0 to an integer of 1. I suspect that would cause a FORTRAN error because it would be the wrong type, but I'm not sure.

One thing that has come to mind that I will test is I'm not sure how the .kpp conversion script will handle this change either, so I'll try and test that at some point!

I can't seem to merge the request, so feel free to do that.

AlfredMayhew commented 6 months ago

Ok, looking at the kpp conversion script it seems like it treats the reaction lines as a 'rate section' and a 'reaction section' and just swaps them, without digging into what the individual species are. This means it should carry any stoichiometry through. I think the kpp test would have failed too if there was an issue, but I will double check when I have some time.