Hi,
I am new in ROMS so I apologize in advance if my questions seem to naive. I am interested in using the BESTNPZ biogeochemical model coupled with a 3D circulation-ice ROMS Pan-Arctic implementation. I have chosen BESTNPZ because it includes ice algae. I tried to find some literature about it and I have the impression that the lower trophic components of this model are the same of the GOANPZ described in Hinckley et al Deep-Sea Research II56(2009)2520–2536. However, I found no description for ice algae dynamics. Therefore, my first question is if anyone knows about some reference I may use to learn more about the BESTNPZ model. The next questions are more technical and have to do with PAR light intensity and the feedback from the light extinction that results from the presence of chlorophyll in the water and in the ice towards the physical processes in ROMS. To start with I found this piece of code in bextnpz.h that calculates PAR for the surface layer:
PAR(i,N(ng)) = PARfrac(ng) * cff2 &
& * exp( k_ext + k_chl*(Bio(i,N(ng),iPhS)/ccr + &
& Bio(i,N(ng),iPhL)/ccrPhL)**0.428 &
& * ( z_r(i,j,N(ng)) - z_w(i,j,N(ng)) ) )
According to this code it seems that the light path defined by ( z_r(i,j,N(ng)) - z_w(i,j,N(ng)) ) is not being multiplied by K_ext and I think it should. Can someone confirm this?
In fact, for the layers below, the contribution of water to light extinction is calculated as:
cff1 = k_ext * ( z_r(i,j,k) - z_r(i,j,k+1) )
Taking into account the light path.
Now, independently of some possible problems here, I would like to know if the light extinctions calculated in biogeochemical models feedback light fluxes in the circulation model. I think I saw some discussion in this forum about this but I could not find it again. The same question applies to ice thermodynamics and the light extinction by ice algae. I suppose this may be quite relevant both for water and ice physics. Now, I wonder if and how this is or may be taken into account in ROMS to guarantee two way feedback between physics and biology.
Thanks in advance for any help.
Photosynthetically Active Radiation and feedbacks
Re: Photosynthetically Active Radiation and feedbacks
That code comes from Georgina Gibson and is several years out of date compared to what she is running - I asked her to look at this thread. I believe the ice algae comes from Mei-Bing Jin and the people putting ice algae into CICE.
Re: Photosynthetically Active Radiation and feedbacks
Hi,
Yes, Kate is right. This is a VERY old version of the code - I actually even forgot it was in her main distribution - and the light attenuation code went through a few itterations. Kate and I are going to work to re-sync an up-to-date version of the BEST-NPZ code with her branch of ROMS. It will likely take us a couple fo weeks to get all the updates in and adequately test but hang tight.
Georgina.
Yes, Kate is right. This is a VERY old version of the code - I actually even forgot it was in her main distribution - and the light attenuation code went through a few itterations. Kate and I are going to work to re-sync an up-to-date version of the BEST-NPZ code with her branch of ROMS. It will likely take us a couple fo weeks to get all the updates in and adequately test but hang tight.
Georgina.
Re: Photosynthetically Active Radiation and feedbacks
...and to actually answer your other questions... yes there is feedback between the light attenuation by the phytoplankton and the physics (attenuation of shortwave) we do this in the bulk flux files where ice phytoplankton attenuates the surface flux of shortwave radiation and in pre_step3d where the watercolumn phytoplanton concentration is used to attenuate the shortwave radiation penetrating the watercolumn. A reasonably comprehensive model description is in Gibson and Spitz 2011 (http://www.sciencedirect.com/science/ar ... 6311000972) - let me know if you need help with access -, although some of the formulations have changed a bit since then.
Re: Photosynthetically Active Radiation and feedbacks
Hi,
Thank you both for your prompt replies. I already saw the paper by Gibson and Spitz 2011 and yesterday, while I was going through the code, I realized that the ice algal model was taken from Meibing but it was nice to have your confirmation on that. I also saw in the Gibson and Spitz paper that the ice algal model was changed a bit regarding silicate limitation and grazing. It is good to know that the phytoplankton-light feedback is accounted for in the physics. I wonder if this is also the case for the light extinction in the ice due to ice algae.
It is good to know that you are considering update the BEST-NPZ code. I am looking forward to work with it. Meanwhile, I think I will try to compile and run the version I have just as a learning exercise.
With my best regards
Thank you both for your prompt replies. I already saw the paper by Gibson and Spitz 2011 and yesterday, while I was going through the code, I realized that the ice algal model was taken from Meibing but it was nice to have your confirmation on that. I also saw in the Gibson and Spitz paper that the ice algal model was changed a bit regarding silicate limitation and grazing. It is good to know that the phytoplankton-light feedback is accounted for in the physics. I wonder if this is also the case for the light extinction in the ice due to ice algae.
It is good to know that you are considering update the BEST-NPZ code. I am looking forward to work with it. Meanwhile, I think I will try to compile and run the version I have just as a learning exercise.
With my best regards