The lake hydrodynamic model GLM simulates:

The lake water balance (all water input and output volumes)

The lake heat balance (all surface heat fluxes and heat inputs associated with inflows)

Lake stratification and mixing (based on light attenuation and several mixing processes)
This hydrodynamic model can also be used to “drive” the biogeochemical model FABM, which simulates:

Transport and mixing of chemical and biological variables (eg. inflows and dilution of nutrients)

Cycling of material between simulated chemical/ ecological variables (eg. nutrient uptake)

Fluxes of chemicals across the sediment-water interface (eg. oxygen and nutrient release)

Deposition of particulate material (eg. settling of algae into the sediment)
Refer to the provided user manuals for further technical details ofthe models.
GETTING STARTED WITH GLM
First, download a precompiled version of GLM off LMS. Save it to the drive named after your student number, not
the one named “studentdata”. This contains the model program (“exe”) and two sets of example files. Unzip using
7-zip” by right clicking on the zip file (sometimes the windows unzipper doesn’t extract things fully, hence 7-zip is
better). Note, you also may download directly off the GLM website, however this may be a more advanced release:
http:[zaed.see.uwa.edu.au[research[models[GLMz
The examples folder file has two example simulations (“warmlake” and “coldlake”) and you can run these with the
appropriate model executables (exe files that are either 32 and 64-bit for Windows or Linux operating systems).
The simulations include both GLM (hydrodynamics) and FABM (water quality) modules running together. For this
exercise we will focus on warmlake and first look at the hydrodynamic model and then secondly explore in more
detail the biogeochemistry part of the simulation. The FABM library includes numerous types of water quality
models, and this tutorial introduces two of them: NPZD and AED.
On Windows, the model can be run via the command prompt by calling glm.exe form the main folder where your
simulation files are (use either the 32 or 64 bit version depending on your operating system). However – we can
automatically call the model “exe” (executable) using a batch-file – “glm32 . bat” is provided in the download and
you double-click it to run the model simulation.
The file is already setup to work, but you can right-click and edit this file to make sure it is setup correctly and
points to the appropriate “bin” folder where the glm.exe file is located for your system.
The bat file will contain a command such as:
bin\glm32\glm.exe
or
bin\glm32\glm.exe -xdisp
This works for the example but can be customized depending on your own specific directory names. The “..\” refers
to “parent directory”. Once correct, double-click on “glm32 . bat” to run the model.
Note that if you include the -xdisp option when you call the exe file, then you can get automatic plots to show
the model results while the model is running. However, you must make sure the in-built GLM plotting configuration
file, plots . nml, is available in the same directory as glm. nml. (i.e., where you are running the simulation). Three
preconfigured plot files of focusing on different aspects are provided in this example that can be used. If the plotting
option is selected a plot window will open and update as the model is running.
EXERCISE A: LAKE HYDRODYNAMIC SIMULATION USING GLM
The simulation in the “\warmlake” directory is an example 40 m deep, monomictic lake that is used to
supply drinking water and supports an active fishery. Monomictic means that it seasonally stratifies and
destratifies, once per year.
Before running the model, open the file glm. nml (or glm2 . nml ‘ 7
depending on your version) in a text editor of choice and inspect the _ ., . I
model setup. This file is the main configuration file that drives the ‘ ‘7
model. For editing text files we recommend jEdit or Notepad++
(https://notepad-plus-plus.org), but Wordpad will suffice (don’t use MS
Word). The file glm. nml has several key sections in it related to the
model domain and parameters, the sources of boundary condition data,
and details of outputs. Scan the parameter, eg number of layers, light
extinction coefficient, mixing coefficient etc. Refer to Table 1 in the User i 7
Manual to understand what the parameters refer to. ., 7’
Identify and open the boundary condition input files – these are csv files ‘ f”
containing time-series of meteorological information, and inflow and ” ‘_ ~ 3,; . .3?”-
outflow volumes. These files can be opened in Excel or a text-editor. ‘ J – 7-335 3″
Find where these files are called from within glm. nml. ‘ ‘ ‘1 -.x ‘ {4,14 {f‘
1. Draw a schematic picture of the lake, the relevant boundary conditions (inflow and outflow water
volumes, and the meteorological inputs affecting the surface]. Refer to Page 7-9 ofthe manual.
Once the model has run, you can inspect the results. There are three ways to look at output:
0 general information on the daily water and energy balance is in the output file lake . csv; and
0 Via the time vs depth contour plots that appear during the run (configured Via plots . nml);
0 time series values of selected state variables (eg. temp, salinity etc) can be requested for a
specific depth (depth above bottom)- this is setup in &outputs (eg. WQ_17 . csv).

Once you are comfortable with the model operation, analyze the predictions:
2. Plot the lake water balance – volume, water level andfluxes including inflows, outflows, rainfall and
evaporation (refer to columns in lake . csv and definitions in Table 7 ofthe manual].
3. Plot the surface heat fluxes such as shortwave, longwave, sensible heat latent heat ( refer to columns
in lake . csv].
4. Goto the &output section of glm. nml and customize the configuration to make two outputfiles,
1 at 5m from the bottom (ie. in the lake hypolimnion] and one at 35m from the bottom (ie. in the
lake epilimnion]. Plot the temperate of the two layers in excel.
5. Also, plot how the degree of stratification changes over the year ( this is the temp difference between
top and bottom]. Explain what variables determine the seasonal change in lake stratification.
6. Calculate the mean average error (MAE) in the simulation using the provided temperature data
Observed TempData.xlsx, assume the provided temperature data is from the surface layer].
7. Calculate the sensitivity of the modelled temperature to changes in water clarity ( the light
extinction coefficient, Kw] and wind speed (wind_factor]. These can be found in glm. nml.
EXERCISE B: ADDING IN NUTRIENTS AND PLAN KTON
The “warmlake” model simulation ran above has the ecological model FABM enabled (refer to lecture!). It
has been pre-configured to run two different ecological model setups: the default NPZD (nutrient-
phytoplankton-zooplankton-detritus) module and the customisable AED modules. These are separate
models, but have been setup to run side-by-side. They are configured using the text file fabm . nml.
Open the file fabm.nml in a text editor (not MS Word) and inspect the model setup in the &models
section at the top. This lists the models to be run. For now ignore the aed modules that are listed.
1. Refer to the sketch and Burchard et al. (2006]. Summarise: a] thefour variables and their units, and
b] the material fluxes that are connecting them (eg. photosynthesis, grazing etc].
Before running this model we must update the file that lists the
plots being produced (plots . nml) to include the 4 NPZD 2
variables. A pre-configured plot file is already made (in
alt_files) and you must rename it from
plots_npzd . nml to plots . nml. Note the four variables of
this FABM model (nut, phy, zoo, det) are named with a
“gotm_npzd_” prefix, so the variable names to plot from the
output file are written as: “gotm_npzd_nut”.
Lets also add these variables to the specific depth output files.
To do so we must edit the output section of the glm. nml
I I I See: Burchard, 1-1., Boldlng, K.,Kuhn, W., Melster,A., Neumann, T.
file, by addlng the Varlables gOtm_and_th EtC as extra Umlauf, L. 2006. Description ofa flexible and extendable physical-
bio eochemical models stem for the water column. journalo
columns into the csv file that was configured above. Maine System 61: 180_y2 1 1. f
Now run the model as above by double clicking the
glm.bat.
Once you are comfortable with the model operation, analyze the predictions:
2. Review and describe the change in N, P, Z and D over the depth ofthe lake and over time – why do
thefour variables change seasonally and why do they look difi‘erent in the top and bottom?
3. Create a ”stacked area graph” of the surface concentration of the 4 variables to show their relative
contribution over time.
4. What happens to phytoplankton ifwe change the water clarity?
(HINT: you must change the extinction coefi‘icient in glm. nml file].
EXERCISE C: CAPTURING MORE DETAIL USING THE “AED” WATER
QUALITY MODEL
The AED model is similar to the NPZD model, but it has multiple “P” groups and more detailed resolution
of the nitrogen and phosphorus nutrient pools (see below diagram). It also has oxygen, which can impact
on nutrient cycling processes.
Re-run the model, but this time use plot s_aed . nml as your plots . nml file. This one is
preconfigured to plot AED specific variables. Refer to the AED manual for more details on the individual
models parameter names.
Once you can see the AED variables being plotted, analyze the predictions: