Setting up a BGCM + SAV growth model involves many steps. So here are notes to setup the case and do read the summary of notes in the end. I will keep refining these notes.

Initial file

SAV growth model, these are initialized using standard values following empirical relations (no need for source data)

  1. AGB
  2. BGB
  3. EPB
  4. Plant density, diameter, thickness, height
  5. Dinsed

More inputs for Biogeochem model->

  1. LdetritusC - Large fraction carbon detritus concentration
  2. LdetritusN
  3. NH4
  4. NO3
  5. SdetritusC - Small fraction carbon detritus concentration
  6. SdetritusN
  7. TIC - Total inorganic Carbon
  8. Talk - Total alkanity
  9. Chlorophyll
  10. Oxygen
  11. Phytoplankton
  12. Zooplankton
  13. salt
  14. temp

Boundary forcing It could be any direction. North, South, West, East

  1. temperature
  2. salinity
  3. Oxygen

Climatological Boundary forcing

  1. Uwind
  2. Vwind
  3. Pair
  4. Tair
  5. Qair
  6. rain
  7. Swrad
  8. Lwrad
  9. cloud

River forcing (if any) In West Falmouth Harbor Additional bc forcing came from river inputs In West Falmouth setup, only NO3 was non-zero

  1. temperature
  2. salt
  3. nutrient
  4. NO3
  5. NH4
  6. DON
  7. PON
  8. Detritus
  9. SDeN
  10. SDeC
  11. TIC
  12. Alkanity
  13. Oxygen

Analytical inputs Other inputs and notes (Not to add confusion) ana_biology.h ana_clouds.h ana_tobc.h -> Had oxygen temperture and salt coming from western bc. dont know why it was not done in bc file. Taran notes: I think I am going to keep them same as WFH

ana_srflx- solar shortwave radiation- In idealized case, I have an input in ana file but in WFH I don’t. Because I think WFH already has a bulk forcing file that contains the inputs to get srflx within the model Taran notes: May be not do it for CH Bay

**Taran summary notes**: For initial conditions: I don’t know how one can get all of the initial tracers. Some inputs are almost constant in WFH so can assume no geospatial variation Below are inputs that had REAL geospatial variation in initial file for WFH On the other hand none of these inputs were specified in the idealized case. So biology model works without all this too.

  1. LdetritusC - Large fraction carbon detritus concentration
  2. LdetritusN
  3. NH4
  4. NO3
  5. TIC
  6. Cholorphyll
  7. Oxygen
  8. phytoplankton
  9. Zooplankton

For boundary condition: only temp, salt, oxygen, and climatology is required –> In WFH NO3 was input

  1. We adapted the bgcm equations of fennel in this modified file https://github.com/DOI-USGS/COAWST/blob/main/ROMS/Nonlinear/Biology/estuarybgc.h

  2. This is where we added the SAV biomass calculations I would refer you to study the two pieces of code that are responsible for this model https://github.com/DOI-USGS/COAWST/blob/main/ROMS/Nonlinear/Biology/sav_biomass.h

  3. As always, start with the distributed test case in COAWST which will help in understanding the model.

  4. Is it possible to set Epiphyte growth to zero? Response: You can set scl(epb) in inputs to 0. I think that should lead to epiphyte growth to zero

-2 How was Dissolved Inorganic Nitrogen in the sediment (DINsed) calculated?

Response: Dinsed gets passed as Dinsed_loc in sav_biomass.h Dinsed is based on below ground biomass respiration and mortality:

See this: https://github.com/DOI-USGS/COAWST/blob/main/ROMS/Nonlinear/Biology/sav_biomass.h#L467

-3. Does plant mortality put nutrients back to water column and soil?

Response: When it comes to the water column, the equations alter the water column nutrient loading through SAV mortality. The soil in theory gets impacted but we don’t work with sediment chemistry in this model. In other words, sediment chemistry is currently not modified. Sediment properties through their physical characteristics only modify the SAV growth.