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Next: 3.18 Global Ocean State Up: 3.17 Biogeochemistry Tutorial Previous: 3.17.3 Code configuration   Contents

3.17.4 Running the example

You will first need to download the MITgcm code. Instructions for downloading the code can be found in section 3.2.

  1. go to the build directory in verification/dic_example:
    cd verification/dic_example/build
  2. create the Makefile:
    ../../../tools/genmake2 -mods=code
  3. create all the links:
    make depend
  4. compile (the executable will be called mitgcmuv):
    make
  5. move the executable to the directory with all the inputs:
    mv mitgcmuv ../input/
  6. go to the input directory and run the model:
    cd ../input
    ./mitgcmuv
As the model is set up to run in the verification experiment, it only runs for 4 timestep (2 days) and outputs data at the end of this short run. For a more informative run, you will need to run longer. As set up, this model starts from a pre-spun up state and initializes physical fields and the biogeochemical tracers from the pickup files.

Physical data (e.g. S,T, velocities etc) will be output as for any regular ocean run. The biogeochemical output are:

  • tracer snap shots: either netcdf, or older-style binary (depending on how data.mnc is set up). Look in data.ptracers to see which number matches which type of tracer (e.g. ptracer01 is DIC).
  • tracer time averages: either netcdf, or older-style binary (depending on how data.mnc is set up)
  • specific DIC diagnostics: these are averaged over taveFreq (set in data) and are specific to the dic package, and currently are only available in binary format:
    • DIC_Biotave: 3-D biological community productivity (mol P m$ ^{-3}$ s$ ^{-1}$ )
    • DIC_Cartave: 3-D tendencies due to calcium carbonate cycle (mol C m$ ^{-3}$ s$ ^{-1}$ )
    • DIC_fluxCO2ave: 2-D air-sea flux of CO$ _2$ (mol C m$ ^{-2}$ s$ ^{-1}$ )
    • DIC_pCO2tave: 2-D partial pressure of CO$ _2$ in surface layer
    • DIC_pHtave: 2-D pH in surface layer
    • DIC_SurOtave: 2-D tendency due to air-sea flux of O$ _2$ (mol O m$ ^{-3}$ s$ ^{-1}$ )
    • DIC_Surtave: 2-D surface tendency of DIC due to air-sea flux and virtual flux (mol C m$ ^{-3}$ s$ ^{-1}$ )

next up previous contents
Next: 3.18 Global Ocean State Up: 3.17 Biogeochemistry Tutorial Previous: 3.17.3 Code configuration   Contents
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