Reference no: EM132411929

Modelling Natural Systems

LAKE WATER QUALITY MODELLING

In this module, we take a look at modelling aquatic systems. Aquatic systems require a range of modelling specialties, from hydrodynamics to chemistry and ecology. We are going to explore the use of "complex dynamic models" and in particular we are looking at the theory of coupled hydrodynamic-biogeochemical models.

In the first session we will focus on terminology and run a practical modelling the water and heat balance, and turbulent mixing processes within a stratified lake. In the afternoon, we extend this to look at variables relevant to water quality and undertake several simulations to explore aquatic ecosystem interactions.

GETTING STARTED WITH GLM

First, download and extract a compiled version of GLM from LMS (under Module 4: Water Quality -> GLM Model Download). Save it to a drive that has enough space - at least 1 GB - to save the outputs from each simulation. If you run it from a thumb drive or external hard drive, it will run slowly. The zipped folder you download contains winGLM and mac GLM (the model program files written in binary) and a simulation (Kinneret97). The simulations include both GLM (hydrodynamics) and aed2 (water quality) modules running together. For this exercise we will first look at the hydrodynamic model and then secondly explore in more detail the biogeochemistry.

A: Lake Stratification with the General Lake Model (GLM)

Exercises:
Draw a schematic picture of the lake, the relevant boundary conditions (both related to water fluxes and energy fluxes).
Identify and open the boundary condition input files - these are csv files containing time-series of meteorological information, and inflow and outflow volumes. These files can be opened in Excel or a text-editor. Find where these files are called from within glm.nml.
Plot the lake water balance - volume, water level and fluxes including inflows, outflows, rainfall and evaporation (refer to columns in lake.csv, and copy the appropriate data into your own excel spreadsheet).
Plot the surface heat fluxes such as shortwave, longwave, sensible heat latent heat (refer to columns in lake.csv).
Go to the &output section of glm3.nml and customize the configuration to make two output files, one at 5 m from the bottom (ie. in the lake hypolimnion) and one at 35 m from the bottom (ie. in the lake epilimnion). Plot the temperate of the two layers in excel.
Assess how the degree of stratification changes as the initial water level of the lake is reduced by 20 m. To do this change the initial starting lake depth and profile (&init_profiles) and sediment details in glm3.nml. You will also need to update the output depth of your surface output file.

B: The ecosystem model

Exercise:

Add these variables to the specific depth output files. Edit the &output section of the glm3.nml file, by adding the variables as extra columns to the csv file that were configured above. Once they are there, make sure that the number of variables is large enough to include them all.

Also add them to the plots.nml file. You will have to create titles for them (see the manual or the website, or an example in plots_aed2.nml), and set the upper and lower limits of the colourbar. This may take a bit of trial and error until you get a nice contrast.
Create a well formatted, interesting graph of variables of your choice (for example, you may like to consider all of the phytoplankton groups, all of the nitrogen variables, or create sums of these to generate a NPZD model) to see how they interact and change over time. If any variables are much bigger or smaller than the others, then use two y axes or multiple plots.
How would these concentrations change if the air temperature increased by 2 °C?
(You will need to edit the met_hourly.csv file). Date format is also hourly (YYYY-MM-DD hh:mm)
What happens if we change the water clarity? Increase and decrease from the original value to see the response
(HINT: you must change the light extinction coefficient Kw (0-1) in the glm.nml file).

C: ASSESSING ERROR & SENSITIVITY

Calculate the mean absolute error in the simulation using the provided temperature data

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. Try increasing and decreasing the default parameter value by 20% and see how much the output changes.

D: GLMr and the graphical user interface
Software assessment:
How do you compare using a text editor and Excel versus using RStudio for running GLM? What are the strengths and weaknesses of each approach?
How do you compare using Excel versus using RStudio for making figures? What are the strengths and weaknesses of each approach?
What would you like to see added to the GLMr package?

Software assessment:
How do you compare the first two approaches versus using the GUI?
What are the main bugs of the GUI at the moment? Which bugs were you able to solve by altering the code? Which need to be solved by the developers?

Attachment:- Workshop - Modelling natural Systems.rar