Methane isotopologues with SD-WACCM

[ebuzan@odu_edu]

Hello,
I am trying to run SD-WACCM under CESM 1.0.5 with the methane isotopolugues 13CH4 and CH3D so I can do comparisons with satellite isotope fractionation data. I've added the two species and a few corresponding reactions to a preprocessor input file and the model runs fine. However, it pus out junk data for these species since I asusme no initial data exists for them. What I would like to do is specify an isotope ratio for the initial data and sources of methane. Is this possible, or is there another way of keeping track of the isotopologues separately?

 

[mmills]

Your approach of adding your isotope species to the IC and source files would be the only way to do this. In the case of CH4, the source is the lower boundary condition file (lbc_file), which is listed in the namelist (atm_in):

 flbc_file              = '/glade/p/cesm/cseg//inputdata/atm/waccm/lb/LBC_1765-2500_1.9x2.5_CMIP5_RCP45_za_c120204.nc'

 flbc_list              = 'CCL4', 'CF2CLBR', 'CF3BR', 'CFC11', 'CFC113', 'CFC12', 'CH3BR', 'CH3CCL3', 'CH3CL', 'CH4', 'CO2', 'H2', 'HCFC22', 'N2O', 'OCS'

 flbc_type              = 'SERIAL'

You would copy this file, and add your isotope species to it, then add it to the flbc_list.

 

[ebuzan@odu_edu]

It looks like I also forgot to add photolysis reactions which are screwing up things in the upper atmosphere. I'm trying to follow along with the source code but I'm getting lost. What I want to do is duplicate the following reactions from mozart:

<span style="font-family: courier new,courier;"> [jch4_a]    CH4 + hv -> H + CH3O2</span><br /><span style="font-family: courier new,courier;"> [jch4_b]    CH4 + hv -> 1.44*H2 + .18*CH2O + .18*O + .66*OH + .44*CO2 + .38*CO + .05*H2O</span><br /><br />for CH3D and 13CH4 with the same rate constant. <br /><br />

 

[mmills]

This should be easy to do with a chemistry pre-processor input file. Are you using one? You should not have to put the reactions and species directly into the source code. There are a number of tutorials that can show you how to do this on our WACCM Working Group Tutorials and Lectures page. For example, see:http://www.cesm.ucar.edu/working_groups/WACCM/Tutorials/2012_08_CESM_Tutorial/WACCM_CAMChem_Practical.pdfSee the section, "Changing a reaction rate". First you will need the chemistry preprocessor input file used in your previous run, which is in your $CASEROOT/CaseDocs/chem_mech.in, or in the source code under the chemistry package you are using for that compset. For example the standard WACCM stratospheric chemistry is in:$srcdir/models/atm/cam/src/chemistry/pp_waccm_mozartThe input file in there is called chem_mech.in. Copy this file to somewhere else (such as your case directory), and add your species and reactions. Then follow the tutorial slide "Building the model with new chemistry", which tells you point the model to your new chemistry input file.The tutorial was written for CESM1.0, and some things have changed in more recent versions. For example, in CESM1.0 you edit env_conf.xml, while in CESM1.2 you edit env_build.xml. In either case you want to edit the line for CAM_CONFIG_OPTS to add a flag "-usr_mech_infile" followed by the path to your new input file.

 

[ebuzan@odu_edu]

I have a pre-processor input file set up already. However, the two reactions I want to modify are "user-specified" which point to the file mo_usrrxt.F90 according to the tutorial. I looked through that file and didn't see anything about those two reactions.

 

[mmills]

Sorry for the confusion; I see you mentioned the pre-processor input in your original question.Those two reactions are photolytic, which are not user-specified reactions. If you wish to use the same photolysis rates (J-values) as the major methane isotopologue  you can use the same rate specifiers, [jch4_a] and [jch4_b].I suspect, however, that you wish to introduce new modified photolysis rates for your new isotopologues. In this case, you need to add new species and cross sections to the input files specified in your namelist: xs_short_file (121-199 nm) and xs_long_file (201-725 nm). Modifying this file may require our assistance, so let me know if you need to do that.

 

[ebuzan@odu_edu]

I tried using the the same rate speficiers and I get an error when I configure the run. I do want to use different rates, so for now I created variables for the new reactions in xs_short_list and just copied over the regular CH4 data. The model is running with just the modified xs_short_file, so does the model just assume a cross section of 0 for the longer wavelengths since they are not specified? I think I can figure out how to add my own rates for the isotopes... xs_short_file has cross sections as a function of wavelength, and xs_long_file has cross sections as a function of wavelength, temperature, and pressure?

 

[mmills]

I have spoken with Doug Kinnison, who creates our photolysis input files. He will have to create a new file for you. Please send the cross-sections you would like to him at dkin@ucar.edu. He will have to run some code to interpolate them to our wavelength bins and generate the look-up table file.