Support / Getting Started
Downloading
If you do not wish to compile the code, then download the latest pre-compiled files for the relevant simulation type from here.
Compilation
For the latest AED2 source code and compilation instructions visit our GIT repository here and the developer page.
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 in the simulation directory.
Model Operation
Once an AED model configuration is designed and the appropriate setup is prepared within the aed2.nml or fabm.nml control files (see below), then the operation of the model is largely controlled by the physical model which is driving the FABM-AED or AED2 library.
Configuration of the AED library coupler
Under Construction
Under Construction
Configuration of the AED modules via the namelist (nml) file
Individual AED/AED2 modules are engaged by including them in the model list in the &models section of the respective namelist file (note the ! indicates a commented line to disable a module). Refer to the specific tab below for the appropriate nml file templates. After the intiial model list declaration, the library then expects a sequence of nml blocks for each module in the order listed; example nml blocks for each module are included in the module descriptions.
For AED2, the main fabm model configuraiton interface is not used, and therefore users specify in aed2.nml:
&aed2
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 - MOD_varname - for example, to view oxygen search for the OXY_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 aed2.nml file.
For example, setting the target for excretion would be done by setting the variable:
n_excretion_target_variable = “OGM_don” Example aed2.nml files configured to run a AED2 model setups with varying complexity are available below, and in the examples.
- AED2 configuration -> aed2.nml (English version, please rename to aed2.nml before use).
&fabm_nml
models = 'aed_oxygen',
'aed_carbon',
'aed_nitrogen',
'aed_phosphorus',
'aed_organic_matter',
'aed_phytoplankton',
!'aed_zooplankton'
!'aed_pathogens'
/
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.
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:
- AED configuration for FABM -> fabm_english.nml (English version, please rename to fabm.nml for use).
- AED configuration for FABM -> fabm_espanol.nml (Español version, please rename to fabm.nml for use).
Note that some of the more complex AED/AED2 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):
- Phytoplankton parameter library ->
aed_phyto_pars.nml. - Zooplankton parameter library ->
aed_zoop_pars.nml. - Pathogens parameter library ->
aed_pathogen_pars.nml. - Geochemistry parameter library ->
aed_geochem_pars.dat.
Refer to the linked science modules for details of the parameter database files. Also refer to the provided GLM-AED tutorial(s) found here for new users..
