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The model has been designed to be very user-friendly, however some modifications must be done to fit with your machine. So, please read the following steps to correctly start the model.


  • Ensure first that gfortran is installed on your machine.
  • Ensure that the NETCDF FORTRAN libraries are installed on your machine.
  • Change the path for the NETCDF FORTRAN module and libraries in the makefile.
  • Compile the source codes using the command make. The executable will be created in the parent directory.
  • You can also delete all object file and the executable by using the command make mrproper.

Use the model

  • The model use namelists in nml/ allowing to change some parameter values without recompiling the source code.
  • Outputs will be generated in the directory output/.

Use the model with GOTM

  • The model can call GOTM to produce a diffusivity profile. If you want to use this feature you have to change the value of the parameter mix_state in the namelist model_parameter.
  • Before doing this, ensure that GOTM is installed on your machine and copy all the GOTM namelists you need in the directory gotm/. You should also create a symbolic link of the executable in the directory gotm/.

Use the batch mode

  • You can also run the model in batch mode. To do this, you must change the batch_bio_pbs.sh.

Have fun!

For question, please contact me at baudryjeremy@gmail.com.

Last edited by Dany Dumont