Contact:  Eric Galbraith ,  Anand Gnanandesikan
Reviewers:  Rick Slater
Change History: WebCVS Log

* Inorganic nutrients are incorporated into organic matter in the presence * * of light. Once in the organic pool, the nutrient elements are recycled * * between organisms and labile reservoirs as long as light is present in * * sufficient abundance to fuel continued growth. In the absence of light, * * inorganic nutrients gradually accumulate once again. The ideal nutrient * * tracers are intended to capture the fundamental dynamics of these * * light-dependent inorganic-organic transitions, but in a very simple, * * transparent way that depends only on the physical circulation and the * * availability of PAR. Thus, they ignore the complexities of ecosystems, * * in terms of uptake dynamics and remineralization pathways. Although this * * will certainly decrease their ability to reproduce the observed * * distributions of nutrients in the ocean, they are computationally * * inexpensive and easy to interpret, features which will hopefully give * * them some utility. * * The simplest ideal nutrient tracer, ideal_n, is non-conservative, * * designed to quickly approach equilibrium (order 10 years), avoiding the * * need for long integrations. The slightly less straightforward, * * conservative tracers are remineralized through the water column and * * therefore approach steady state on much longer, multi-centennial * * timescales. * * * The core behaviour of the ideal nutrients are given by the exponential, * * exp(-IRR/IRRk). IRR is the available light (average SW radiation, in * * W/m2, within the grid cell) and IRRk (in W/m2) determines the light * * level at which the phytoplankton growth rate approaches saturation. * * Thus, this term is 1 when IRR is 0, and approaches 0 as IRR increases. A * * larger value for IRRk causes the exponential to approach 0 more slowly, * * ie. to saturate at a higher light level. * * * Uptake is determined by the product of the 1 minus the exponential term, * * a maximum uptake velocity (Vmax, in s-1), and limitation caused by the * * concentration of the ideal nutrient itself, N (in mol kg-1): * * * * -Vmax * (1 - exp( -IRR / IRRk )) * (N / N + k) * * * * The last term causes nutrient uptake to slow as the nutrient * * concentration approaches 0, according to Michaelis-Menten dynamics. * * * * In ideal_n, regeneration is simply a constant rate, R. * * * Starting from this simple foundation, biogeochemical functionality is * * added by creating a macronutrient (iPO4) with identical uptake to * * ideal_n, but for which mass is conserved within the ocean. This is * * achieved by separating the uptake into dissolved and particulate * * organic matter, the latter of which is instantaneously remineralized * * throughout the water column below according to a variant of the OCMPIP2 * * protocol. This calculates the remineralization rate at each level as a * * function of the temperature, base remineralization rate, and sinking * * rate (itself a function of depth). Any flux reaching the bottom box is * * instantly remineralized there to conserve mass within the ocean. * * Meanwhile, Dissolved Organic Phosphorus (iDOP) is transported within the * * ocean, decaying to PO4 at a temperature-dependent rate. * * * Given the apparent importance of iron (Fe) as a limiting micronutrient * * in the oceans, it seemed interesting to try making another PO4 tracer, * * limited by Fe, in addition to the basic limitations given above: this is * * called iPO4f. The iron input is highly idealized, and the scavenging * * function very simple, but iron-limitation develops and modulates * * growth rate through iron-light colimitation in a way that may not be * * totally unlike the real ocean. The Fe-limited PO4 cycle is completely * * independent of the non-Fe-limited PO4, and they can be run on their own * * or in parallel for comparison. * * A full biogeochemical simulation can then be made by selecting one of * * the iPO4s as the central bgc variable (default is iPO4). Biological * * consumption and production of other quantities, including a number of * * gases and idealized gas tracers, are then determined from the generally * * reliable Redfield stoichiometries. * * * Isotopic fractionations are simulated by multiplying the uptake rate of * * the chemical species by the isotopic rate ratio, alpha. The tracer * * concentrations of the heavy isotope species are actually * * equal to the true concentration divided by the isotopic ratio of the * * standard, e.g. 15NO3 = [15NO3] * [14Nair] / [15Nair]. The true value in * * permil is given by (15NO3 / NO3 - 1.) * 1000. * * * Dissolved gases are handled according to the OCMIP2 protocol. The air- * * sea exchange code was taken from the ocmip2_abiotic and ocmip2_biotic * * modules, with negligible modification. Note that the 14C implementation * * differs from that of abiotic, in that biological uptake and remineraliz- * * ation of carbon impact the distribution of 14C, analagous to 15N. * * * Chlorophyll is estimated diagnostically from the net bgc iPO4 (or iPO4f) * * uptake rate, with an adjustment for photoadaptation.

A general note on nomenclature Variables starting with 'j' are source/sink terms; jprod_x is the biological production term for the quantity 'x'; jremin_x is the remineralization rate of the quantity 'x'. Variables starting with 'fp' are sinking particulate flux terms. Most of the 'i's stand for idealized, as in iBGC, and help to avoid duplication of arrays and tracer names used by TOPAZ and BLING, so that ibgc can be run in parallel with these other models. Most of the 'p's stand for particulate, though a lot of them stand for phosphorus. So, for example, jprod_pip is the production rate of particulate idealized phosphorus through the uptake of iPO4.

Tracer units are generally in mol kg-1, with some exceptions (suntan, ideal_n, Fe).

A general note on parameter values: Pretty much all of the parameter values were selected ad hoc, from very loose principles. They were not particularly well 'tuned' to match any given circulation model, though they gave reasonable results with the 3-degree ocean model, om1p7. As such, the user should feel free to make changes to the default values given here. Exceptions to this are: gas exchange parameters, radiocarbon decay, nutrient stoichiometry, fractionation factors.

        diag_manager_mod
       field_manager_mod
                 mpp_mod
                 fms_mod
              fms_io_mod
        time_manager_mod
time_interp_external_mod
         mpp_domains_mod
           constants_mod
      ocean_tpm_util_mod
             fm_util_mod
         ocean_types_mod
      ocmip2_co2calc_mod
       coupler_types_mod
  atmos_ocean_fluxes_mod

allocate_arrays:

ocean_ibgc_bbc:

ocean_ibgc_end:

ocean_ibgc_restart:

ocean_ibgc_sbc:

ocean_ibgc_flux_init:

ocean_ibgc_init:

ocean_ibgc_init_sfc:

ocean_ibgc_sum_sfc:

ocean_ibgc_zero_sfc:

ocean_ibgc_avg_sfc:

ocean_ibgc_sfc_end:

ocean_ibgc_source:

ocean_ibgc_start:

ocean_ibgc_tracer:

None.

&ocean_ibgc_nml

None.

None.

1. The basic nutrient uptake equations will be described in an upcoming paper by Galbraith et al. (in prep.). The remainder of the biogeochemistry module may be documented more officially elsewhere. All are welcome to use ibgc model output for the purposes of publication; however, please contact Eric Galbraith (Eric.Galbraith@mcgill.ca) for the appropriate reference.

None.

None.

None.

None.

None.

None.

None.

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