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 parametermix_state
in the namelistmodel_parameter
. - Before doing this, ensure that GOTM is installed on your machine and copy
all the GOTM namelists you need in the directorygotm/
. You should also
create a symbolic link of the executable in the directorygotm/
.
4. Use the model in the batch mode
- You can also run the model in batch mode. To do this, you must change the
filebatch_bio_pbs.sh
.
Have fun!
For question, please contact me at baudryjeremy@gmail.com