Support / Setup of an AED2 Model Configuration Template
Configuration of the AED library "coupler"
Aside from the setup of the modules to be simulated (described below), several configuration options must first be defined for AED2 to manage its operation and interaction with the host model. Note this is different for GLM vs TUFLOW-FV.
For TUFLOW-FV users, an extra settings block is required at the beginning of aed2.nml. An example is shown below:
&aed2_bio
!-- AED2 configuration settings
solution_method = 1
display_minmax = .false.
do_limiter = .true.
do_2d_atm_flux = .true.
do_particle_bgc = .false.
do_zone_averaging = .false.
glob_min = -1e38
glob_max = 1e38
min_water_depth =0.0401
n_equil_substep = 12
!-- Linkages with host model: PHYSICS
link_bottom_drag = .false.
link_surface_drag = .false.
link_water_density = .false.
!-- Linkages with host model: LIGHT
link_ext_par = .false.
link_water_clarity = .false.
base_par_extinction = 0.2
ext_tss_extinction = .false.
tss_par_extinction = 0.02
!-- Linkages with host model: RIPARIAN
link_solar_shade = .false.
link_rain_loss = .false.
!-- Benthic variable initialisation
init_values_file = ''
route_table_file = '../External/AED2/Routing_Tbl.csv'
/
An up to date example compatible with the latest model version is provided here. Note that in addition to this information, for a TUFLOW-FV simulation to enable AED2, then the user must specify the wq model input file in the *.fvc file as described here.
For GLM users, the water quality model is configured via an optional block in the glm2.nml file. An example is shown below:
&wq_setup
!-- Choose 'aed2' or 'fabm' (aed2 is the default)
wq_lib = 'aed2'
wq_nml_file = 'aed2.nml'
ode_method = 1
split_factor = 1
bioshade_feedback = .true.
repair_state = .true.
mobility_off = .false.
benthic_mode = 1
n_zones = 3
zone_heights = 10, 20, 40
/
Selection of the AED modules to simulate, via the namelist (nml) file
Individual AED/AED2/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, as explained in the next section.
For AED2, users must specify the chosen modules in aed2.nml as a list, with unwanted modules commented out using !, for example:
&aed2_models
models =
!--> NUTRIENT/CHEMISTRY modules <--!
'aed2_sedflux', !core module
'aed2_tracer', !core module
'aed2_oxygen', !core module
'aed2_carbon', !core module
'aed2_silica', !core module
'aed2_nitrogen', !core module
'aed2_phosphorus', !core module
'aed2_organic_matter', !core module
!off 'aed2_seddiagenesis', !plus module
!--> BIOLOGY modules <--!
'aed2_phytoplankton', !core module
'aed2_zooplankton', !core module
'aed2_macrophyte', !plus module
!off 'aed2_macroalgae', !plus module
!off 'aed2_bivalve', !plus module
!off 'aed2_pathogens', !plus module
!--> RIPARIAN modules <--!
!off 'aed2_geochemistry', !plus module
!off 'aed2_land', !plus module
!off 'aed2_soilbgc', !plus module
!off 'aed2_vegetation', !plus module
!off 'aed2_ass', !plus module
!--> SUMMARY modules <--!
'aed2_totals', !core module
'aed2_habitat' !plus module
/
Note that the chosen module list must consider the order of dependencies (i.e., linked modules) and appear in the correct order for the dependencies to be met. As a guide start with the order in the above example.
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).
For users wishing to use (legacy) AED modules via the FABM library, the chosen modules are specified via the main fabm.nml configuration file:
&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).
Inclusion of &module parameter "blocks" for each chosen module
Following the block that chooses the selected modules (described above), each module then requires a specific namelist block outlining the module specific parameters and options. These must appear in the order outlined in the model selection block. Refer to the specific modules for examples and details of block specification here.
Selection of supporting parameter files
Some of the more complex models rely on an associated "database" file of parameters.
Examples are linked here (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. A online database and file creation utility is also available via the following button.
Goto AED2 Online Parameter DatabaseSetup of supporting "benthic map" initialisation files
Several AED2+ modules support spatially variable benthic and/or sediment properties. In GLM this relates to different "Sediment Zones" (when benthic_mode=2), and for TUFLOW-FV this relates to the "Material ID" specified for each cell when creating the mesh. These are read in via *.csv files specified in the "coupler" section above. Section pending updates soon...
Checking and reviewing an AED2 setup
As the model initialises, it will configure the relevant variables from the selected modules, based on the options and flags that were set in aed2.nml. Users can review how a simulation is configured by viewing the list of initialised variables that are output to the screen and/or log file at the beginning of a simulation as per the example below. Refer to specific modules for variable descriptions and their units.
TO BE UPDATED
AED2 var name( 1 ) : OXY_oxy
AED2 var name( 2 ) : CAR_dic
AED2 var name( 3 ) : CAR_pH
AED2 var name( 4 ) : CAR_ch4
AED2 var name( 5 ) : SIL_rsi
AED2 var name( 6 ) : NIT_amm
AED2 var name( 7 ) : NIT_nit
AED2 var name( 8 ) : PHS_frp
AED2 var name( 9 ) : OGM_doc
AED2 var name( 10 ) : OGM_poc
AED2 var name( 11 ) : OGM_don
AED2 var name( 12 ) : OGM_pon
AED2 var name( 13 ) : OGM_dop
AED2 var name( 14 ) : OGM_pop
AED2 var name( 15 ) : PHY_green
AED2 var name( 16 ) : PHY_green_IN
AED2 var name( 17 ) : PHY_green_IP
AED2 var name( 18 ) : PHY_diatom
AED2 var name( 19 ) : PHY_diatom_IN
AED2 var name( 20 ) : PHY_diatom_IP
AED2 var name( 21 ) : PHY_crypto
AED2 var name( 22 ) : PHY_crypto_IN
AED2 var name( 23 ) : PHY_crypto_IP
AED2 var name( 24 ) : ZOO_zoo01
AED2 var name( 25 ) : ZOO_zoo02
AED2 var name( 26 ) : BIV_filtfrac
AED2 var name( 27 ) : TRC_ss1
AED2 var name( 28 ) : TRC_ret
AED2 var name( 29 ) : TST_pel
AED2 var name( 30 ) : TST_pel_bflux
AED2 var_ben name( 1 ) : BIV_zebra
AED2 var_ben name( 2 ) : BIV_quagga
AED2 var_ben name( 3 ) : TST_ben
