AED

Documentation

Science manual:

The current manual contains an overview of the AED science basis, mathematical expressions and parameter values. This document is generic for both FABM-AED and AED² code versions. A brief summary is also listed below.

• PDF: Science Manual (Final version pending)

Modules available:

The AED modules support the following, and they are presented here in order of hierarchical dependence, which is important in setting the order of module configuration in the fabm.nml control file:

aed_oxygen:

• Surface/bottom exchange
• Photosynthesis / respiration
• OM mineralisation

aed_silica:

• benthic flux
• phyto uptake

aed_phosphorus:

• benthic flux of PO4
• phytoplankton uptake
• organic matter mineralisation
• adsorption to inorganic particles

aed_nitrogen:

• benthic flux of NO3 and NH4
• phytoplankton uptake
• denitrification/nitrification
• organic matter mineralisation

aed_organicmatter:

• POM and DOM for C, N, and P
• Decomposition and hydrolysis of detrital material, and mineralisation
• Benthic flux of dissolved organic material
• phytoplankton production through excretion, exudation and mortality
• Multiple “pools” can be configured (eg. labile/refractory)

aed_chla:

• generic bulk phytoplankton module for simulating growth of chl-a

aed_phytoplankton:

• Multiple groups, support flexible setting of interactions and configuration (eg. N uptake of NH4, NO3, DON, N2 possible)
• defined a comprehensive aed_phyto_database.nml which stores many pre-configured parameter sets that users can choose from. general library of temp, light, nutrient environmental dependencies
• Light functions from Baklouti et al (2006) and CAEDYM are included
• Variable IN:IP (droop) or fixed N:P (static) allowed

aed_zooplankton:

• Multiple groups can be configures to represent species/functional groups or size classes within species/functional groups.
• Physiological parameters set by user in name list aed_zoop_params.nml.
• Choice of food set in name list from phytoplankton, bacteria and particulate organic matter

aed_pathogens:

• Multiple groups can be configures to represent species/functional groups
• Processes for mortality and inactivation depending on environmental conditions, and optional growth term also included.
• Physiological parameters set by user in name list aed_pathogen_pars.nml.

aed_geochemistry: (not currently in the public release)

• Aqueous geochemical model for simulating major ions, metals, pH, acidity/alkalinity and mineral precipitaiton/dissolution.

aed_seddiagenesis: (not currently in the public release)

• Vertically resolved sediment diagenesis model for simulation of vertical profiles of sediment geochemical conditions and associated fluxes to the water column.

aed_totals:

• A general model that links to above modules for provind the user with TN, TP, TOC and TSS, as required.

The commonly used state variables that can be simulated in the AED modules are listed in Table 1. Although there are numerous state variables in total, many are not compulsory and depend on the modules selected and how the interactions between modules are configured. For a simple water quality simulation the variables there is a minimum configuration of DO, DOM, POM, PO4, NH4 and NO3, and phytoplankton/chlorophyll-a are available. However, these are not compulsory if the user simply wishes to model pathogens or suspended sediment for example. They are configured via options outlined in the fabm.nml file.

Each of the variables listed below can also be specified as an output via the NetCDF output. They are generally available as a suffix to the module name, aed_module_varname, for example, to view oxygen search for the aed_oxygen_oxy. The keywords for most of the simulated variables are also used to specify the inflow boundary conditions in relevant inflow files (depending on the hydrodynamic driver).

Table 1 - AED variable list (note this is the shortened version, numerous other modules and diagnostic output are also available)

FAQ's & Troubleshooting

An active user forum is also available which is hosted on the AEMON website. Please consult this forum for FAQ’s and to ask questions and for support.