This dataset contains most parameters within the glm3.nml and the aed.nml
file. This includes 452 GLM parameters across 24 namelist blocks (e.g.,
&glm_setup, &mixing, &morphometry, &meteorology,
&inflow, &outflow) and 452 AED parameters across 24 modules
(e.g., aed_oxygen, aed_nitrogen, aed_phosphorus,
aed_silica, aed_phytoplankton, aed_sedflux,
aed_seddiagenesis), for a combined total of 452 rows.
Format
A data frame with 452 rows and 9 variables:
- module
Character. The configuration block (GLM) or module (AED) the parameter belongs to. GLM modules correspond to Fortran namelist blocks in glm3.nml (e.g.,
"glm_setup","mixing","morphometry","time","output","init_profiles","light","bird_model","sediment","snowice","meteorology","inflow","outflow","wq_setup"). AED modules correspond to namelist blocks in aed.nml (e.g.,"aed_oxygen","aed_nitrogen","aed_phosphorus","aed_silica","aed_phytoplankton","aed_sedflux","aed_seddiagenesis").- group
Character. An optional sub-category grouping related parameters by process or function within a module. For example,
"nitrification","denitrification", and"sediment_flux"within theaed_nitrogenmodule; or"radiation","wind", and"rainfall"within themeteorologymodule. Empty string ("") where no sub-grouping applies.- parameter
Character. The parameter name as used in the configuration file (e.g.,
"max_layers","Fsed_oxy","R_nitrif").- label
Character. A short, human-readable label for the parameter (e.g.,
"Layers","Sediment O2 flux","Nitrification rate").- symbol
Character. The mathematical symbol used in the model documentation and equations, rendered as plain text (e.g.,
"N_MAX","F_sed^oxy","theta_nitrif"). Empty string where no symbol is defined.- description
Character. A description of the parameter, its role in the model, and any relevant context.
- units
Character. The units of the parameter. Uses
"-"for dimensionless quantities,"string"for text parameters, and"boolean"for logical switches. Physical units follow standard abbreviations (e.g.,"m","mmol O2/m3","mmol N/m2/d","/d").- default
Character. The default value of the parameter as documented, or an empty string (
"") where no default is specified in the source documentation.- source
Character. URL of the documentation page from which the parameter information was extracted. GLM parameters are sourced from https://aquatic.science.uwa.edu.au/research/models/GLM/configuration.html and AED parameters from individual chapter pages of the AED Science Manual at https://aquaticecodynamics.github.io/aed-science/.
Source
GLM configuration reference: https://aquatic.science.uwa.edu.au/research/models/GLM/configuration.html
AED Science Manual: https://aquaticecodynamics.github.io/aed-science/
Hipsey, M.R., Bruce, L.C., Boon, C., Busch, B., Carey, C.C., Hamilton, D.P., Hanson, P.C., Read, J.S., de Sousa, E., Weber, M. and Winslow, L.A. (2019). A General Lake Model (GLM 3.0) for linking with high-frequency sensor data from the Global Lake Ecological Observatory Network (GLEON). Geoscientific Model Development, 12, 473–523. doi:10.5194/gmd-12-473-2019
Hipsey, M.R. (Ed.) (2022). Modelling Aquatic Eco-Dynamics: Overview of the AED modular simulation platform. Zenodo. doi:10.5281/zenodo.6516222
Details
Parameters are organised by module (the namelist block or AED module
they belong to) and optionally by group (a sub-category describing
the process context, such as "nitrification",
"sediment_flux", or "radiation").
The GLM (General Lake Model) parameters configure the hydrodynamic model, including layer structure, mixing, morphometry, meteorological forcing, boundary conditions (inflows and outflows), light penetration, ice/snow dynamics, and sediment heat exchange.
The AED (Aquatic EcoDynamics) parameters configure the water quality and
biogeochemical modules that couple to GLM. The modules included in this
dataset cover dissolved oxygen, inorganic nitrogen (ammonium, nitrate,
nitrification, denitrification), inorganic phosphorus (phosphate,
adsorption), silica, phytoplankton (growth, light, nutrient uptake,
respiration, mortality, settling), and sediment biogeochemistry (static
sediment fluxes via aed_sedflux and dynamic diagenesis via
aed_seddiagenesis).
Note that aed_phytoplankton parameters listed under groups such as
"growth", "light", "nitrogen", "phosphorus",
and "silica" are per-phytoplankton-group parameters typically
specified in a separate phyto_data namelist file rather than
directly in aed.nml.
Examples
# Load the parameter library
data(glm_aed_parameter_library)
# View the structure
str(glm_aed_parameter_library)
#> tibble [452 × 9] (S3: tbl_df/tbl/data.frame)
#> $ module : chr [1:452] "glm_setup" "glm_setup" "glm_setup" "glm_setup" ...
#> $ group : chr [1:452] NA NA NA NA ...
#> $ parameter : chr [1:452] "sim_name" "max_layers" "min_layer_vol" "min_layer_thick" ...
#> $ label : chr [1:452] "Run name" "Layers" "Min layer volume" "Min layer thickness" ...
#> $ symbol : chr [1:452] NA "N_MAX" "Delta_V_min" "Delta_z_min" ...
#> $ description: chr [1:452] "Title of simulation" "Maximum number of layers" "Minimum layer volume" "Minimum thickness of a layer" ...
#> $ units : chr [1:452] "string" "-" "m3" "m" ...
#> $ default : chr [1:452] "lake" "500" NA NA ...
#> $ source : chr [1:452] "https://aquatic.science.uwa.edu.au/research/models/GLM/configuration.html" "https://aquatic.science.uwa.edu.au/research/models/GLM/configuration.html" "https://aquatic.science.uwa.edu.au/research/models/GLM/configuration.html" "https://aquatic.science.uwa.edu.au/research/models/GLM/configuration.html" ...
# List all unique modules
unique(glm_aed_parameter_library$module)
#> [1] "glm_setup" "mixing" "wq_setup"
#> [4] "morphometry" "time" "output"
#> [7] "init_profiles" "light" "bird_model"
#> [10] "sediment" "snowice" "meteorology"
#> [13] "inflow" "outflow" "aed_oxygen"
#> [16] "aed_nitrogen" "aed_phosphorus" "aed_silica"
#> [19] "aed_phytoplankton" "aed_sedflux" "aed_seddiagenesis"
#> [22] "aed_organic_matter" "aed_zooplankton" "aed_macrophyte"
# Filter to a specific module
glm_aed_parameter_library[glm_aed_parameter_library$module == "aed_oxygen", ]
#> # A tibble: 9 × 9
#> module group parameter label symbol description units default source
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 aed_oxygen initialisa… oxy_init… Init… O2|t=0 Initial di… mmol… NA https…
#> 2 aed_oxygen initialisa… oxy_min Min … O2_min Minimum di… mmol… 0 https…
#> 3 aed_oxygen initialisa… oxy_max Max … O2_max Maximum di… mmol… 600 https…
#> 4 aed_oxygen sediment_f… fsed_oxy Sedi… F_sed… Sediment O… mmol… NA https…
#> 5 aed_oxygen sediment_f… ksed_oxy Half… K_sod… Half-satur… mmol… NA https…
#> 6 aed_oxygen sediment_f… theta_se… Thet… theta… Arrhenius … - NA https…
#> 7 aed_oxygen sediment_f… fsed_oxy… Sed … NA Variable n… stri… SDF_Fs… https…
#> 8 aed_oxygen atmospheri… oxy_pist… Pist… Theta… Selection … - NA https…
#> 9 aed_oxygen atmospheri… altitude Alti… H Altitude o… m 0 https…
# Get all phytoplankton growth parameters
glm_aed_parameter_library[glm_aed_parameter_library$module == "aed_phytoplankton" &
glm_aed_parameter_library$group == "growth", ]
#> # A tibble: 12 × 9
#> module group parameter label symbol description units default source
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 aed_phytoplank… grow… R_growth Max … R_gro… Maximum ph… /d NA https…
#> 2 aed_phytoplank… grow… fT_Method Temp… Theta… Method for… - 1 https…
#> 3 aed_phytoplank… grow… theta_gr… Thet… theta… Arrhenius … - 1.06 https…
#> 4 aed_phytoplank… grow… T_std Stan… T_std Standard t… degC 20 https…
#> 5 aed_phytoplank… grow… T_opt Opti… T_opt Optimum te… degC 25 https…
#> 6 aed_phytoplank… grow… T_max Maxi… T_max Maximum te… degC 35 https…
#> 7 aed_phytoplank… grow… R_growth Max … R_{gr… Phyto max … /day NA https…
#> 8 aed_phytoplank… grow… fT_Method Temp… NA Specifies … - NA https…
#> 9 aed_phytoplank… grow… theta_gr… Grow… theta… Arrhenius … - NA https…
#> 10 aed_phytoplank… grow… T_std Stan… T_{st… Standard t… deg C NA https…
#> 11 aed_phytoplank… grow… T_opt Opti… T_{op… Optimum te… deg C NA https…
#> 12 aed_phytoplank… grow… T_max Maxi… T_{ma… Maximum te… deg C NA https…
# Count parameters per module
table(glm_aed_parameter_library$module)
#>
#> aed_macrophyte aed_nitrogen aed_organic_matter aed_oxygen
#> 27 27 60 9
#> aed_phosphorus aed_phytoplankton aed_seddiagenesis aed_sedflux
#> 15 95 18 7
#> aed_silica aed_zooplankton bird_model glm_setup
#> 7 31 6 7
#> inflow init_profiles light meteorology
#> 12 8 7 28
#> mixing morphometry outflow output
#> 9 10 28 15
#> sediment snowice time wq_setup
#> 10 3 6 7