hi all,

I have a question regarding the chlorophyll code in Fennel model,

Bio(i,k,iChlo)=Bio(i,k,iChlo)+ &

& (dtdays*t_PPmax*t_PPmax*LTOT*LTOT* &

& Chl2C_m(ng)*Bio(i,k,iChlo))/ &

& (PhyIS(ng)*MAX(Chl2C,eps)*PAR+eps)

This is following Geider et al. (1997), which (in my notations) states,

dChl/dt=G=r*g*C

where C is phytoplankton biomass in carbon unit, g is the phytoplankton photosynthesis rate (t_PPmax) multiplied by the nutrient limiting factor (LTOT). In ROMS notations,

g = t_PPmax*LTOT

And

r = Chl2C_max*g/(theta*par*Chl2C)

Where theta is the initial P-I slope (PhyIS). In ROMS notations,

r = Chl2C_m*t_PPmax*LTOT/(PhyIS*PAR*Chl2C)

Therefore,

G = r*g*C

= [Chl2C_m*t_PPmax*LTOT/(PhyIS*PAR*Chl2C)] * [t_PPmax*LTOT] * [Bio(i,k,iPhyt)*C2N(ng)]

= Chl2C_m*t_PPmax*t_PPmax*LTOT*LTOT/(PhyIS*PAR*Chl2C) *Bio(i,k,iPhyt)*C2N(ng)

If this is correct, the original Bio(i,k,iChlo) should be replaced with Bio(i,k,iPhyt) * C2N(ng).

Am I right? Thanks.

Mingshun

## a question about the chlorophyll growth term in fennel.h

### Re: a question about the chlorophyll growth term in fennel.h

ok, I realized the error in my post. The PhyIS(ng) is the code is not chlorophyll-specific. So,

Bio(i,k,iChlo)=Bio(i,k,iChlo)+ &

& (dtdays*t_PPmax*t_PPmax*LTOT*LTOT* &

& Chl2C_m(ng)*Bio(i,k,iChlo))/ &

& (PhyIS(ng)*MAX(Chl2C,eps)*PAR+eps)

can be rewritten as,

Bio(i,k,iChlo)=Bio(i,k,iChlo)+ &

& (dtdays*t_PPmax*t_PPmax*LTOT*LTOT* &

& Chl2C_m(ng)*Bio(i,k,iChlo))/ &

& (PhyIS_chl(ng)*Chl2C*MAX(Chl2C,eps)*PAR+eps)

where PhyIS_chl(ng) is Chlorophyll-specific initial P_I slope. And,

Bio(i,k,iChlo)/Chl2C = C

Bio(i,k,iChlo)=Bio(i,k,iChlo)+ &

& (dtdays*t_PPmax*t_PPmax*LTOT*LTOT* &

& Chl2C_m(ng)*Bio(i,k,iChlo))/ &

& (PhyIS(ng)*MAX(Chl2C,eps)*PAR+eps)

can be rewritten as,

Bio(i,k,iChlo)=Bio(i,k,iChlo)+ &

& (dtdays*t_PPmax*t_PPmax*LTOT*LTOT* &

& Chl2C_m(ng)*Bio(i,k,iChlo))/ &

& (PhyIS_chl(ng)*Chl2C*MAX(Chl2C,eps)*PAR+eps)

where PhyIS_chl(ng) is Chlorophyll-specific initial P_I slope. And,

Bio(i,k,iChlo)/Chl2C = C

### Re: a question about the chlorophyll growth term in fennel.h

Dear Mingshun,

I was about to answer to your post, but you beat me to it. You are correct that there is a discrepancy in notation with the Geider et al. (1997) paper.

Geider et al. (1997) describe the factor rho_chl, i.e. the factor that determines synthesis of chlorophyll in viable phytoplankton cells, as the ratio between achieved phytosynthesis and maximum potential photosynthesis. In Fennel and Boss (2003) in equation 10 and in Fennel et al. (2006) in equation 8, I calculate maximum potential photosynthesis as alpha x I x Chl, because the amount of pigment that can absorb photons determines maximum photosynthetic potential. I believe this is the correct implementation of the intention of the Geider model, i.e. regulating chlorophyll synthesis by the ratio of achieved-to-maximum potential photosynthesis.

Hence I would discourage the substitution you proposed. Before doing so you could explore the ramifications in a simple test case like the steady-state model in Fennel and Boss (2003).

Fennel & Boss (2003): http://aslo.org/lo/toc/vol_48/issue_4/1521.pdf

Fennel et al. (2006): http://memg.ocean.dal.ca/memg/pubs/Fenn ... GBC_06.pdf

Best, Katja

I was about to answer to your post, but you beat me to it. You are correct that there is a discrepancy in notation with the Geider et al. (1997) paper.

Geider et al. (1997) describe the factor rho_chl, i.e. the factor that determines synthesis of chlorophyll in viable phytoplankton cells, as the ratio between achieved phytosynthesis and maximum potential photosynthesis. In Fennel and Boss (2003) in equation 10 and in Fennel et al. (2006) in equation 8, I calculate maximum potential photosynthesis as alpha x I x Chl, because the amount of pigment that can absorb photons determines maximum photosynthetic potential. I believe this is the correct implementation of the intention of the Geider model, i.e. regulating chlorophyll synthesis by the ratio of achieved-to-maximum potential photosynthesis.

Hence I would discourage the substitution you proposed. Before doing so you could explore the ramifications in a simple test case like the steady-state model in Fennel and Boss (2003).

Fennel & Boss (2003): http://aslo.org/lo/toc/vol_48/issue_4/1521.pdf

Fennel et al. (2006): http://memg.ocean.dal.ca/memg/pubs/Fenn ... GBC_06.pdf

Best, Katja