The Master Chemical Mechanism
Isopleth plots are useful tools for designing chamber experiments to be carried out under different tropospheric conditions. They are used to choose initial conditions for which maximum ozone can be produced and enables the evaluation of the model under both NOx and VOC limited conditions.
The following exercise involves the construction of a simple propene photo-smog experiment isopleth plot.
In order to construct an isopleth plot we must run many simulations under a variety of NOx and VOC conditions. Each simulation is run for the duration of the experiment and the maximum ozone formed for the given initial NOx/VOC ratio is extracted. This can involve running hundreds of full simulations.
The model, propiso_test.fac, is set up to take a set of 10 initial pairs of propene and NO concentrations, to constrain the model to them and to run an 11 hour simulation for each set of conditions (10 model runs).
Open propiso_test.fac and add the propene mechanism from the MCM website.
propiso_test.fac is set up to run 10 different subsequent model runs and is constrained to data contained in propno_test.in.
propno_test.in contains 10 identical pairs of initial VOC and NOx concentrations (20 species in total). This will be used to test the model for errors before we run the full model, which will involve 100 subsequent model runs of 11 hours each (total of about 49 days!).
If you look through propiso_test.fac you can see that the model is set up to run (starting at 07:00) for the initial 11 hour model run and then for the second, restart the photolysis calculations from the start time and reset initial conditions for all species (see DATAIN).
Time control is set to 1.80E+03*220 which allows for 10 new sets of initial conditions, each running for 39600 s (11 hours). Note the model is set up to output every 30 minutes.
Run propiso_test.fac (constraining it with propno_test.in) from the location "C:\mcmtutorial\ISOPLETH\" .
Look at then plot the output for C3H6 and O3 in a spreadsheet. Note what the maximum concentration of ozone is for each of the model runs. They should all be identical (except for the initial run).
Open Origin; Origin can be customised to read data from your *.007 output file and to extract the maximum ozone concentration from each of the model runs. In order to do this you will need to download the following files by right clicking on the links below.custom.OGS
NOTE: The scripts assume that the model is running from the file path "C:\mcmtutorial\isopleth" if you are running the model from a different location you will need to edit the scripts. The scripts and templates also all need to be saved in the location "C:\mcmtutorial\isopleth" except for the custom script which needs to replace the exisiting custom script associated with origin this is typically found at the location "C:\Program Files\OriginLab\Origin7".
Press run the "custom routine" button. Look at the "results" sheet. This should give the initial VOC in column X, the initial NO in column Y and the maximum O3 in column Z. Again, if the max O3 concentrations are all equal then we can proceed to the full model.
Open propiso2.fac. This model is essentially the same as propiso_test.fac except it is set up to read in 100 pairs of initial NOx and VOC concentrations from propno1.in and hence run 100 consecutive 11 hour simulations (starting at 07:00).
Time control this time is set to 1.8E+03*2200 which allows for 100 new sets of initial conditions, each running for 39600 s (11 hours).
Run propiso2.fac from the run location, constraining it to propno1.in. (NOTE: on some of the computers this may take several minutes!)
Open Origin on the desktop and run the "custom routine"
Check the output in the "results" sheet (initial VOC (X), initial NO (Y), max O3 (Z)).
In order to form the matrix for the isopleth plot:
In order to plot the matrix as a contour plot go to "plot" and click on "contour"
You now should have an isopleth plot for maximum ozone from the propene model.
You can adjust the number of contours on your plot by clicking on one of the contours and going to the "colour map/contour" section. Click on "level" to change the number of contours.
If you have time then add one of the MCM mechanisms from any of the models you have been using over the past few days to the propiso2.fac and construct a new isopleth plot.Section 5 checklist