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README.md

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Welcome to the Phytoplankton Lagrangian Model 2014!
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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.

# 1) COMPILATION:

+ 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 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