Add New Biogenic Emissions Feature

[drnimbusrain]

Based on the LES chemistry simulations of Clifton et al. (2022), and after issue #21 - #28 are completed, we can add simplified submodules representing biogenic emissions, chemical reactions, dry deposition/CRFsoilnox as new features to the canopy-app.

[drnimbusrain]

@zmoon Started initial branch for a parameterized canopy biogenic isoprene emissions model for broadleaf leaves. This is based on MEGANv3 and a combination of Clifton et al. (2022) and Silva et al. (2020).

It is not fully implemented yet, but initial tests create what seem to be a reasonable isoprene biogenic emissions profile (compared to Silva et al. 2020) for the canopy. Once issue #41 is addressed to enhance the example txt/ncf input files, I can fully integrate as a new option and test fully.
Z/Hc= 0.0000000000000000 ISOP_EMI (umol/m2 hr) = 1.9335550856135315E-002
Z/Hc= 2.6315789473684209E-002 ISOP_EMI= 1.8967588519345848E-002
Z/Hc= 5.2631578947368418E-002 ISOP_EMI= 1.8615665753298358E-002
Z/Hc= 7.8947368421052627E-002 ISOP_EMI= 1.8280842367729203E-002
Z/Hc= 0.10526315789473684 ISOP_EMI= 1.7964992408099862E-002
Z/Hc= 0.13157894736842105 ISOP_EMI= 1.7671080710774414E-002
Z/Hc= 0.15789473684210525 ISOP_EMI= 1.7403519451140052E-002
Z/Hc= 0.18421052631578946 ISOP_EMI= 1.7168622302706556E-002
Z/Hc= 0.21052631578947367 ISOP_EMI= 1.6975180671047349E-002
Z/Hc= 0.23684210526315788 ISOP_EMI= 1.6835199830554117E-002
Z/Hc= 0.26315789473684209 ISOP_EMI= 1.6764857679851648E-002
Z/Hc= 0.28947368421052633 ISOP_EMI= 1.6785792852173641E-002
Z/Hc= 0.31578947368421051 ISOP_EMI= 1.6926903600960479E-002
Z/Hc= 0.34210526315789475 ISOP_EMI= 1.7226962276376444E-002
Z/Hc= 0.36842105263157893 ISOP_EMI= 1.7738552144808177E-002
Z/Hc= 0.39473684210526316 ISOP_EMI= 1.8534165810999169E-002
Z/Hc= 0.42105263157894735 ISOP_EMI= 1.9715861737364559E-002
Z/Hc= 0.44736842105263158 ISOP_EMI= 2.1430830808078595E-002
Z/Hc= 0.47368421052631576 ISOP_EMI= 2.3896900190555171E-002
Z/Hc= 0.50000000000000000 ISOP_EMI= 2.7444993579065012E-002
Z/Hc= 0.52631578947368418 ISOP_EMI= 3.2151179169661703E-002
Z/Hc= 0.55263157894736847 ISOP_EMI= 3.9095793250497946E-002
Z/Hc= 0.57894736842105265 ISOP_EMI= 4.9489728025963117E-002
Z/Hc= 0.60526315789473684 ISOP_EMI= 6.5342216456981128E-002
Z/Hc= 0.63157894736842102 ISOP_EMI= 9.0044863884275142E-002
Z/Hc= 0.65789473684210531 ISOP_EMI= 0.12939548311259880
Z/Hc= 0.68421052631578949 ISOP_EMI= 0.19336407155357199
Z/Hc= 0.71052631578947367 ISOP_EMI= 0.29902810315839790
Z/Hc= 0.73684210526315785 ISOP_EMI= 0.47509928274218638
Z/Hc= 0.76315789473684215 ISOP_EMI= 0.76785332506737347
Z/Hc= 0.78947368421052633 ISOP_EMI= 1.2456831943223998
Z/Hc= 0.81578947368421051 ISOP_EMI= 1.9911922367630281
Z/Hc= 0.84210526315789469 ISOP_EMI= 3.0460112306294205
Z/Hc= 0.86842105263157898 ISOP_EMI= 4.1979421377338868
Z/Hc= 0.89473684210526316 ISOP_EMI= 4.6800622361241304
Z/Hc= 0.92105263157894735 ISOP_EMI= 3.6895014089219917
Z/Hc= 0.94736842105263153 ISOP_EMI= 1.9189336295028030
Z/Hc= 0.97368421052631582 ISOP_EMI= 0.87116445900409967

I think eventually after refining these isoprene-only biogenic emissions profile for broadleaf leaves, we could later extend this module/option and make it more flexible for other BVOC species across of course other plant functional/vegetation types using the different "emission capacities/factors" and "emission activities" from MEGANv2 and v3. Maybe we can look into the MEGANv3 codes to pull those out and integrate into canopy-app in the best way. But, isoprene is the dominant biogenic emissions so its good to start here.

[drnimbusrain]

@zmoon Following PR #50 discussion, I think we should bring in some aspect of canopy layer and ground energy balance models into Canopy-App following other applications of MEGANv3 (see Hopper codes: /groups/ESS/pcampbe8/MEGAN/MEGANv3.2_Dec_2021/src/MEGCAN/megcan.f) , Bonan's many works, or other applications of canopy parameterizations in gridded models, like WRF MCANOPY who followed Bonan's work. This will allow us to do more sophisticated parameterizations of biogenics, deposition, soil fluxes, and things like biogeochemical fluxes of carbon etc.

Indeed essential components of canopy models will have some aspect of canopy layer energy balance model, but I have since neglected it so far for simplicity and efficiency purposes. I think we have the components to calculate the canopy layer energy balance since we have things like our photolysis attenuation and, momentum drag (in-canopy winds), etc.

Just some food for thought in the future...

[drnimbusrain]

@zmoon I think to better track I changed the name of this issue to isolate the initial biogenic emissions feature, and we can make new issues for other new features and feature improvements as they come along. Since initial biogenic have been been merged I am closing this issue.