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It says here that the units should be photons/cm^2/s

but IntegrateJ.m really wants it in spectral actinic flux units, photons/cm^2/s/nm

Hi Glenn,

Just wanted to let you know there's a typo in the Troe formulation of K_PRPE_OH in GEOSCHEM_K.m that must have been carried over from earlier versions of the CB mechanisms. It's at line 113, and the 2 here should be positive, not negative:

krx(:,i) = (LPL./(1+LPL./HPL)).*0.5.^(1./(1+(log10(LPL./HPL)).^2));

I think this is the only reaction affected in the GEOS-Chem mechanism.

Best,
Maggie

User on F0AM forum noted that title function is not properly removing radical exchange reactions, e.g. using CH3O and CH3O2 as input, it retains the CH3O2 + NO -> CH3O + NO2 reaction. I think the code for identifying these reactions needs to be reworked to use S.Chem.f instead of string comparison.

Noticed that some CS/QY parameterizations may still assume that P is in Torr instead of mbar. Need to comb through photolysis code and make sure all units are correct.

The model makes some assumptions about Met variables that start with J. This needs to be documented in the code and user manual. Alternatively, those assumptions could be eradicated.

Hello
I have run the MCM_Chamber.m (modified according to ExampleSetup_Chamber.m) for the simulation of atmospheric photochemical reaction process with no constrains. When using different chemical mechanisms, the number of the same species concentration output are different (e.g. when using MCM, S.Conc.HNO3: 241×1 double, when using CB05, S.Conc.HNO3: 194×1 double). I was wondering whether the number of S.Conc.xx can be modified.
In F0AM paper "The Framework for 0-D Atmospheric Modeling (F0AM) v3.1", it says In the second paragraph of part “2 Model description” that “MATLAB is a higher-level language than FORTRAN and can be less computationally efficient; however, it is easier to learn for researchers with little programming experience and is used extensively by the experimental community”. But it took 24 seconds to run a 3-hours simulation by runing MCM_Chamber.m, while it takes 15 hours to run a 3-hours simulation by AtChem(FORTRAN) on HPC. Speed of F0AM is so fast! I was wondering what causes the large difference in simulation speed between F0AM and AtChem.
Thank you very much for your kind consideration. Not sure what I am doing wrong, any assistance would be appreciated, or just fyi.

There have been some bug fixes since 4.0, might be nice to do a bug fix release (maybe 4.0.2?), just so anyone who comes here can quickly tell.

When specifying options in PlotRates (and probably other plot functions), if a user gives the name of the option but not the value, no error is returned. This could be fixed with more rigorous input checking in ParsePairs.m.

The averaging routine is unweighted, meaning that runs with lots of points in the beginning get weighted towards those points when taking the average. It would be much better to integrate over time using trapz.