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Date last modified:Aug 27, 2019
Contributors: Nicole Jeffery

1. Requirement: Add remineralization and nitrification fluxes to sea ice biogeochemical reactions.

The improved formulation of the reaction equations for NH4, DON, algal nitrogen (N) and NO3 are described in NitrogenCycleMPAS_SI.pdf

The v1 code does not include DON_remin in equation (3) and the fraction of grazing contributing to DON in equation (4) has been modified from f_don fgs  to (1-f_gs + f_ng f_gs) to close the grazing pathway.  In addition, Algal mortality is now a source of DON.

2. Requirement: Add adsorption of nitrate produced from nitrification

The sea ice vertical bgc subroutine follows the algorithm: 1) compute the new mobile and stationary fractions based on the sea ice area tracer, f_mobile, and evolution timescales; 2) solve the vertical transport equation for the mobile fraction; 3) evolve the stationary fraction based on sea ice boundary changes (melt and growth); 4)  solve the reaction equation for the total brine concentration of the tracer; and 5) combine to evaluate the new bulk tracer concentration. 

In order to add adsorption of nitrate from nitrification, we need to first modify (1) to allow transformation from stationary to mobile for nitrate but not mobile to transformation. The change in the mobile fraction for tracer C,  dmobile(m), is currently:

dmobile = mobile_C* ([C]_mobile * (exp(-dt * tau_ret)-1) + [C]_stationary* (1-exp(-dt * tau_rel))

where mobile_C is 1 for tracers that move between phases and 0 for purely mobile tracers like nitrate.  If we now use

dmobile = mobile_C* ([C]_mobile * (exp(-dt * tau_ret)-1) + [C]_stationary* (1-exp(-dt * tau_rel)) + (1-mobile_C )* [C]_stationary* (1-exp(-dt * tau_rel))

then tracers with mobile_C = 0  (nitrate and silicate) will have transformations in one direction only, stationary to mobile.  Although we are not adding silicate remineralization, it would now be a simple matter include this improvement if later warranted.

For each requirement, there is a design solution that is intended to meet that requirement. Design solutions can include detailed technical discussions of PDEs, algorithms, solvers and similar, as well as technical discussion of performance issues. In general, this section should steer away from a detailed discussion of low-level software issues such as variable declarations, interfaces and sequencing.

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