This 1D model was built by Jérémy Baudry to study phytoplankton dynamics in a Lagrangian framework, taking into account life history of cell clusters. It is designed to facilitate the comparison with the Eulerian formulation in various conditions. – README.md

README.md

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
    file batch_bio_pbs.sh.

Have fun!

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