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Welcome to Phlag, the Phytoplankton Lagrangian Model! 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.

1. Compile 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.

2. 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/.

3. 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/.

4. Use the model in the batch mode

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

Have fun!

If you have questions, please contact me at

5. References

Baudry, J., D. Dumont, I.R. Schloss (2018) Turbulent mixing and phytoplankton life history: A Lagrangian versus Eulerian model comparison, Mar. Ecol. Prog. Ser., 600, 55-70, doi:10.3354/meps12634.