Light attenuation models

Nearly all BGC models require some model of the attenuation of PAR through the water. Usually this depends on the concentration of chlorophyll in the water (in phytoplankton), and may depend on the concentration of coloured dissolved organic matter or particulates.

We currently have two models of light attenuation, a two band model by Karleskind et al. (2011) and the more widely used three band model by Morel (1988). As the light level is diagnostic of the phytoplankton concentration these models are implemented with the light level as various auxiliary fields which are updated with callbacks within the biogeochemical model.

Models requiring light attenuation models will set these up automatically, for example LOBSTER sets light_attenuation_model = TwoBandPhotosyntheticallyActiveRadiation(). You may choose others. Additionally, you can pass the surface PAR as a function of horizontal position and time. The default for LOBSTER is (x, y, t) -> 100*max(0.0, cos(t*π/(12hours))).

Model equations (for the two band model)

Light attenuation is calculated by integrating attenuation (from the surface). The $PAR$ is considered as two components attenuated at different rates. At depth $z$ the total $PAR$ is given by:

\[PAR = \frac{PAR_0}{2} \left[\exp\left(k_rz + \chi_r\int_{z=0}^z Chl_r dz\right) + \exp\left(k_bz + \chi_b\int_{z=0}^z Chl_b dz\right)\right],\]

where $PAR_0$ is the surface value, $k_r$ and $k_b$ are the red and blue attenuation coefficients of water, $\chi_r$ and $\chi_b$ are the red and blue chlorophyll attenuation coefficients, and $Chl_r$ and $Chl_b$ are the red and blue chlorophyll pigment concentrations. The chlorophyll pigment concentration is derived from the phytoplankton concentration where it is assumed that the pigment concentration is given by:

\[Chl = PR_{Chl:P},\]

where the ratio is constant and found in Parameters. The red and blue pigment concentrations are then found as $Chl_r = \left(\frac{Chl}{r_\text{pig}}\right)^{e_r}$ and $Chl_b = \left(\frac{Chl}{r_\text{pig}}\right)^{e_b}$.

Parameter variable names