AED

Aquatic EcoDynamics Modelling Library

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Downloading

The AED models are available already coupled via FABM (FABM-AED) to GLM with pre-compiled executables for windows and linux operating systems available and several test-cases . Click button to the right to download GLM-FABM-AED for Windows.

Source code and compilation instructions for FABM are available here . This includes last public release of FABM-AED (2 April 2014) - note this code may be behind the AED2 and could be ~6-12 months old.

For the latest AED2 source code and compilation instructions visit our GIT repository ...here... (note, currently under construction, contact us for more info)

Installation

Refer to installation details for the driver models (e.g., GLM, GOTM etc). No specific installation is required for AED other than the presence of the configuration nml file.

Model Operation

Once an AED model configuration is designed and the approapriate setup is prepared for fabm.nml (see below) then the operation of the model is largely controlled by the physical model which is driving the FABM-AED or AED2 library.
For use with GLM, then click here.
Click here for an example TUFLOWFV control file (fvc) with AED enabled and example AED configuration file.

Configuration of the AED modules: fabm.nml

AED modules are engaged by including them as indivdual models in the &models section of fabm.nml (note the ! indicates a commented line to disable a module):

&fabm_nml
   models = 'aed_oxygen',
            'aed_carbon',
            'aed_nitrogen',
            'aed_phosphorus',
            'aed_organic_matter',
            'aed_phytoplankton',
            !'aed_zooplankton'
            !'aed_pathogens'
/

For AED2, the main fabm model configuraiton interface is not used, and therefore users specify in aed2.nml:

&aed
   models = 'aed2_oxygen',
            'aed2_carbon',
            'aed2_nitrogen',
            'aed2_phosphorus',
            'aed2_organic_matter',
            'aed2_phytoplankton',
            !'aed2_zooplankton'
            !'aed2_pathogens'
            !'aed2_seddiagenesis'
            'aed2_totals'
/

Variables are identified 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). 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. This configuration is done via options outlined in the fabm.nml file (or aed.nml if FABM is not being used). For example, setting the target for excretion would be done by setting the variable:

n_excretion_target_variable = “aed_organic_matter_don” 

An example fabm.nml file configured to run a simple AED model setup is available below:


Note that some of the more complex AED modules require extra nml files for parameters to be read in (click to download examples as txt, then be sure rename to name as listed here):

Also refer to the provided GLM-FABM-AED tutorial found here.