Ligth formulation in ROMS biology models

[arango]

Warning: This is an important upgrade to ROMS biology models.

The light attenuation formulation for photosynthesis (PAR) in couple of biology models in ROMS were revisited. We are now using the averaged (finite volume) value of PAR at the center of the grid cell instead of the median value. It turns out that the old fomulation understimates primary productivity. See the following forum ​post for details. I only correted BIO_FENNEL and NPZD_POWELL. I still need to fix this problem in the NEMURO model, which has in addition a photoinhibition (Platt et al., 1980) formulation.

Many thanks to Mark Baird for bringing this problem to our attention and to Bronwying Cahill for testing this upgrade.

I am also releasing a new NPZD model with iron limitation (Fiechter et al., 2009). This model is similar to the Powell et al. (2006) formulation but it includes iron limitation on phytoplankton growth. This new model is activated with the NPZD_IRON option. To activate the iron limitation on phytoplankton growth, use in addition IRON_LIMIT option. In addition, use IRON_RELAX to similatate the sources of dissolved iron in coastal areas where the bathymetry h(i,j) <= FeHmin (See input script npzd_iron.in for details).

This new NPZD model (npzd_iron.h) also has a tangent linear, representer, and adjoint model version which we are still testing. Many thanks to Jerome Fiechter and Andy Moore for their help on developing this nee model.