Tutorial

About this tutorial

This tutorial is designed to guide you through the initial set-up of the BETR Global model, and to illustrate how to perform and visualize results of a steady-state and a dynamic model calculation. In order to successfully complete the tutorial you will need a Windows PC running Excel 2007.

In the tutorial you will conduct steady state and dynamic (unsteady state) global fate and transport calculations for decamethylcyclopentasiloxane (D5). You can find some information about D5 and see its structure here. The physico-chemical property data and emission estimates for D5 used in this tutorial are based on values reported in the recent UK risk assessment report. This tutorial is inspired by the work of McLachlan et al. (2010), and the results you obtain here can be directly compared to results in their paper.

Part 1: Set-up and steady state calculation

1. Start by downloading the BETR Global model and saving the zip file somewhere on your hard drive.

2. Download and install the Panoply data viewer provided by NASA as described on their website.

3. Locate the file "BETRGlobal2.0.zip" that you downloaded. Extract the two files in the zip archive to a temporary folder, then copy the folder "BETR" to C:\ so that the two files that were in the zip archive are located in "C:\BETR\".

4. Launch the BETR Global model by double clicking the file "BETR Global V2.0.xlsm". This should automatically start Excel 2007. At start-up you may receive some warnings that the file contains Visual Basic macros. You must enable macros in Excel in order to run the BETR Global model. Instructions to do this can be found here.

5. If the model opened successfully you should reach the BETR Global V2.0 main page:

(Click on any screenshot in the tutorial to enlarge it)

On the main page you can:

1. Specify whether you want to run a steady-state calculation or a dynamic (unsteady-state) calculation,

2. Set conditions for an unsteady-state calculation,

3. Use the tabs at the bottom to navigate to input data for chemical properties and emissions,

4. Show or hide additional spreadsheet tabs with model parameters, and,

5. Execute a BETR Global calculation for the current model set-up.

6. Our first goal in this tutorial is to perform a steady-state model calculation. In a steady-state calculation we assume a constant emission rate of chemical and average environmental conditions, and calculate the concentrations chemical in the environment under the condition that the emissions are balanced by removals of the chemical by degradation and irreversible sequestration. This type of calculation is also called a Level III fugacity calculation. To set-up a steady-state calculation, make sure that the radio button marked "Level III - Steady State Calculation" is selected.

7. Navigate to the Chemical Properties sheet by selecting the "Chemical" tab at the bottom of the Excel window.

8. You should now see the Chemical Properties sheet:

Here, you can select a chemical from the chemical database, or enter physico-chemical properties for a new substance of interest. Chemicals can be added or deleted from the database using the controls provided. Note that double clicking the database does not automatically select a chemical. You must use the "Select" button. You may also set some options for how the degradation half-life in air is specified, and you may estimate internal energies of phase change for the specified chemical using the methodology recommended by MacLeod et al. (2007).

Select D5 from the chemical database.

9. Navigate to the Level III Emissions sheet by selecting the "EmissionsLevelIII" tab at the bottom of the Excel window.

10. You should now see the worksheet for entering a Level III constant emission scenario:

On this tab you should enter region- and compartment-specific emission rates for the chemical, in kg/year. Compartments are listed across the top, and are upper air (or free troposphere), lower air (tropospheric boundary layer), vegetation, fresh water, coastal water, soil and sediment. The BETR Global regions are referred to in this sheet by their numerical index, and a key to that index is provided in the world map on the right-hand side of the sheet. Often, estimating emission rates is one of the most challenging tasks in assembling a global mass budget for a chemical. The version of the model that you downloaded should already have emission estimates for D5 to the lower air compartment of the model specified. These emission estimates total 20,000 tonnes of D5 per year, which is based on the estimate of emissions from consumer products in the UK risk assessment document. This total has been allocated geographically according to the proportion of total night-time light emissions from different parts of the world (see examples on the NASA website). This geographical distribution was selected for this illustrative case study to weight emissions toward industrialized countries where D5 emissions are likely higher.

11. Navigate to the BETR Global main page by clicking the BETR tab at the bottom of the Excel window.

12. Double check that you have selected the "Level III" radio button under the heading "Select Calculation Type". Then, start the Level III calculation by pressing the button labeled "Execute BETR Global Calculation. You should see a progress bar that will go through four stages: 1) Initializing, 2) Populating Matrices, 3) Calculation Progress and 4) Finalizing.

The entire calculation should take about 1 minute to complete.

13. When the calculation is complete the results are written to a new Excel workbook. You can activate this workbook by selecting it from the Windows taskbar at the bottom of the screen. If this is the first calculation you have done, the workbook will be called "Book1" by default. When you select the workbook with the model results you should see this:

14. You can see details of the steady-state mass balance in any of the 288 regions of the model by selecting a region from the drop-down menu. When you do this the output workbook supplies details of values from the fugacity calculation for the selected region, and produces a mass balance diagram for the region that can be viewed by scrolling down. You will also notice a set of tabs along the bottom that lead to detailed outputs of the model. As an illustration, select Region 79 from the drop down menu, which is located on the east coast of North America:

You should find that more than 77% of D5 in Region 79 is found in the atmosphere (ie, the sum of percentages in upper and lower air), and that almost all of the rest of the inventory is in soil (23%). You can also inspect the mass balance diagram to identify the dominant removal processes for D5 from the region. These are advection in air to neighboring regions, and degradation in air.

15. If you decide to save the output workbook, be sure you save it as a macro-enabled workbook.

16. By scrolling slightly to the right, you will find a box where you can generate a NetCDF file to visualize the steady state model output:

If desired you can change the name of the NetCDF file by clicking on Cell P6 in the spreadsheet. If you don't assign a unique name, then any existing file with the same name in the same target directory will be overwritten. For the purposes of this tutorial, leave the name as the default, and press the "Generate NetCDF File" button.

17. Creating the NetCDF file should only take a few seconds. When it is complete, launch Panoply and use the File -> Open File menu option to open your NetCDF file.

18. In the Panoply window you should now see a list of "Plottable Variables" on the left hand side. Right-click on "Log(Concentration) and select "Create Standard Plot":

19. Panoply will prompt you to specify what type of plot it should create. Select "Lon-Lat" to create a map:

20. You should now have a map of log concentrations that can be edited in a multitude of ways using Panoply. Note that there is only one "Model time" in this steady-state example. Also note that you can plot concentrations in any of the seven model compartments by making a selection on the "Array(s)" tab of the Panoply plot window. The compartments are: 1 - Upper air, 2 - Lower air, 3 - Vegetation, 4 - Fresh water, 5 - Coastal water, 6 - Soil and 7 - Fresh water sediments. By adjusting some settings in Panoply you should be able to produce a plot similar to the one below for concentration (on a log scale) of D5 in the lower atmosphere compartment from your steady-state model results:

Part 2: Dynamic (unsteady-state) calculation

When you are done playing with your steady-state results in Panoply you will be ready to try a dynamic (unsteady-state) calculation. In this tutorial you will perform a 2-year long simulation for constant emissions of D5, starting with initial conditions from the steady-state calculation. The results of this calculation will illustrate the effect of variable environmental factors (especially, the variable concentration of OH radicals in the atmosphere) during the course of a year on the concentrations of D5 in the atmosphere.

21. Return to the BETR Global model and select the main page. Change the calculation type to "Level IV - Unsteady State Calculation". When you do this, you will notice that one of the tabs at the bottom changes. Now, you have a new tab called "EmissionsLevelIV", instead of the the "EmissionsLevelIII" tab. This is necessary because the dynamic calculation requires information about how emissions change in time.

22. On the left hand side of the main page, click the check box next to "Environment is contaminated at t=0 (set initial conditions)". This will add another tab at the bottom of the window called "InitialConditions".

23. Change the values in Cells E10 and E11 to so that the "Total simulation time" is 2 years and model results are printed to output every 1 month. Your screen should now look like this:

23. If you like, click the "Chemical" tab and confirm that the property data for D5 are still selected.

24. Click on the "EmissionsLevelIV" tab. Scroll down in the bottom section until you reach the section where emissions to the Lower air compartment are specified. You should see something like this:

For an unsteady-state calculation you must enter emission estimates (in kg/y) for each compartment during the whole time period of the model calculation. This can be done in the columns starting with Column Q of the spreadsheet, with emissions for each year specified in sequential columns. In some cases, emissions might be known to take place during a specific time of the year. For example, pesticides might be released to soil and air only in the spring time. If this is the case, monthly emission factors in Columns C to N can be specified. These monthly emission factors should total to 12. To force all yearly emission to occur in April, you would enter a zero in all of the columns except the one for April, where you would enter "12". In the special case where emissions are from diffusive sources, you can estimate the monthly emission factors to lower air as a function of temperature in each region by pressing the appropriate button.

In the version of BETR Global you have downloaded, the emission estimates for D5 to the lower atmosphere are already entered in the appropriate cells, and should look like the screenshot above. Note that we assume that emissions of D5 are equal during each month of the year.

25. Select the "InitialConditions" tab at the bottom of the Excel window. You should see something like this:

Here, you can set the concentrations of chemical that are present in each environmental compartment of the model at the beginning of the dynamic model calculation. In this tutorial example, we will set the initial conditions to be the same as the concentrations calculated in our earlier steady-state model run.

26. Make sure that your steady-state results file is open in Excel. If you have not saved it with a new name, it will be called "Book1". If you have renamed the file, make sure to include the extension when you enter the name, for example, "SteadyStateResults.xlsm". Enter the name of the steady-state results file in Cell H4, and press the button labeled "Import steady state results from file". If the import is successful, you should see a confirmation message, and data should have populated the cells beginning in D9.

27. Navigate to the main page by selecting the "BETR" tab at the bottom of the Excel window.

28. You are now ready to perform the calculation. Press the "Execute BETR Global Calculation" button. The calculation will take approximately 30 minutes, depending on the speed and amount of RAM in your computer. You will again see the "Calculation Progress" bar during the calculation.

29. When the calculation is finished you will again see a new workbook in the Windows taskbar that contains the dynamic output. Select this new workbook and you should see something like this:

By selecting the tabs at the bottom of the Excel window you can view various model outputs and see how they vary as a function of time in the calculation.

30. Create a NetCDF file to visualize the results of your calculation by specifying a name for the file in Cell H11 and pressing the "Generate NetCDF file" button. Because the dynamic model output includes more data than the steady state, generating the NetCDF file may take several seconds.

31. As before, open Panoply and then open your new NetCDF file with the dynamic model results.

32. Right click on the "Log(Concentration)" variable and select "Lat-Lon" to produce a map.

33. Now, you will find that there are 24 options for "Model time in months" that correspond to the 2 years of model simulation that you ran. The "Comp." setting again refers to the 7 environmental compartments as above. With some adjustments of the Panoply settings you should be able to produce a plot of concentrations of D5 in lower air in month 13 (January of the 2nd year) of the simulation that looks similar to the one below:

Note that concentrations of D5 in Lower Air in the Northern Hemisphere are markedly higher in this figure than in the steady-state result illustrated above. This is because concentrations of OH radicals in the Northern Hemisphere are lower during the winter than on average. Since degradation by OH is the primary sink for D5 in the atmosphere, concentrations are higher when OH radical concentrations are low.

34. By experimenting with Panoply and a tool for creating animated GIF files (such as UnFREEZe), you should be able to produce animated maps of the changes in concentrations with time. The example below shows concentrations of D5 in the lower air compartment of the Northern Hemisphere during the second year of the dynamic simulation carried out in this tutorial on a continuous loop.