Hi community,
I think we may have a problem with the physical-biological coupling in terms of light. Please correct me if I'm wrong.
When SOLAR_SOURCE is defined, short wave radiation penetrates the water column and contributes to T. The decay penetration function is based on Jerlov's water type, which considers 2 radiation bands and has 2 absorption coefficients.
When including Fasham biology (I haven't checked other ecosystem models yet) shortwave is attenuated by water and chlorophyll, and the absorption coefficients are given as input in biofasham.in.
I believe that this brings mainly 2 problems:
1) attenuation is different for T and for P
2) light absorption by P doesn't feedback to the water column
I'm not sure whether this problem makes a big difference in the model results. I'll appreciate your opinions/ideas!
Thanks,
Laura
Light issues when Biology is defined
Ups, I missed something 
: The 2 radiation bands also represent the distinction between photosynthetically available and not available radiation for P (i.e, PAR or not PAR).
So the 1st problem that I mentioned above should be re-phrased:
1) The attenuation for T and P is the same if we are careful to set:
* PARfrac = (1 - lmd_r1), where lmd_r1 is the fraction of total radiance for wavelength in band 1, and PARfrac is the fraction of shortwave that is PAR
* AttSW= 1/lmd_mu2, where lmd_mu2 is the reciprocal absorption coeff for band 2, and AttSW is the light attenuation of seawater used in the biological code
Note: lmd_r1 and lmd_mu2 are given in mod_scalars, while PARfrac and AttSW are given as input in BioFasham.in
As far as I understand it, issue 2) remains the same.
Best,
Laura
: The 2 radiation bands also represent the distinction between photosynthetically available and not available radiation for P (i.e, PAR or not PAR).So the 1st problem that I mentioned above should be re-phrased:
1) The attenuation for T and P is the same if we are careful to set:
* PARfrac = (1 - lmd_r1), where lmd_r1 is the fraction of total radiance for wavelength in band 1, and PARfrac is the fraction of shortwave that is PAR
* AttSW= 1/lmd_mu2, where lmd_mu2 is the reciprocal absorption coeff for band 2, and AttSW is the light attenuation of seawater used in the biological code
Note: lmd_r1 and lmd_mu2 are given in mod_scalars, while PARfrac and AttSW are given as input in BioFasham.in
As far as I understand it, issue 2) remains the same.
Best,
Laura
"light absorption by P doesn't feedback to the water co
It's mostly in a visible band when P absorbs light. For the T's sake, we care mostly non-visible band, most likely IR band, which is far beyond 700 nm in wave spectrum. So, it may not much matter for heating-up of water temperature with or without a feedback of P on light extinction (of visible band).
Light issues ....
Laura,
You are right about point 2). Currently there is no mechanism in place to feedback attenuation of light by organic material in biological models back into water column physics in ROMS.
As for point 1) this is also an issue in EcoSim where attenuation of light for photosynthesis is prescribed by an analytical radiative transfer model (see ana_specir.h in Functionals and ecosim.h in Nonlinear), independent of attenuation of shortwave radiation for temperature in ROMS.
We have been experimenting with variable attenuation coefficients and simple feedbacks using the EcoSim model with ROMS in coastal waters influenced by turbid plumes. We found that there are important feedback mechanisms between the attenuation of light and the resulting impact on the mixed layer depth. High concentrations of chlorophyll, detritus and colored dissolved organic matter in the upper water column as a result of enhanced stratification increased the attenuation of light and modified the buoyancy driven circulation in our simulations. This further impacted the growth of phytoplankton in the model and subsequently modified the vertical profile of the attenuation coefficient, which in turn fed back into the overall heat budget. We used a simple proxy for variable attenuation in our experiments (submitted GRL), but are now working on implementing a direct feedback loop between spectral attenuation of light by organic biomass in EcoSim and the heat budget in ROMS. Will post more progress on this as things develop, in the meantime, if you are working in coastal waters, in particular, it becomes very important to resolve these feedbacks.
- Bronwyn
You are right about point 2). Currently there is no mechanism in place to feedback attenuation of light by organic material in biological models back into water column physics in ROMS.
As for point 1) this is also an issue in EcoSim where attenuation of light for photosynthesis is prescribed by an analytical radiative transfer model (see ana_specir.h in Functionals and ecosim.h in Nonlinear), independent of attenuation of shortwave radiation for temperature in ROMS.
We have been experimenting with variable attenuation coefficients and simple feedbacks using the EcoSim model with ROMS in coastal waters influenced by turbid plumes. We found that there are important feedback mechanisms between the attenuation of light and the resulting impact on the mixed layer depth. High concentrations of chlorophyll, detritus and colored dissolved organic matter in the upper water column as a result of enhanced stratification increased the attenuation of light and modified the buoyancy driven circulation in our simulations. This further impacted the growth of phytoplankton in the model and subsequently modified the vertical profile of the attenuation coefficient, which in turn fed back into the overall heat budget. We used a simple proxy for variable attenuation in our experiments (submitted GRL), but are now working on implementing a direct feedback loop between spectral attenuation of light by organic biomass in EcoSim and the heat budget in ROMS. Will post more progress on this as things develop, in the meantime, if you are working in coastal waters, in particular, it becomes very important to resolve these feedbacks.
- Bronwyn