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