README.md 1.77 KB
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Welcome to Phlag, the Phytoplankton Lagrangian Model! The model has been  
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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.
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#### 1. Compile the model
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+ 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`.
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#### 2. Use the model
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+ 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/`.
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#### 3. Use the model with GOTM
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+ 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/`.
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#### 4. Use the model in the batch mode
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+ You can also run the model in batch mode. To do this, you must change the  
   file `batch_bio_pbs.sh`.
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 Have fun!
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 If you have questions, please contact me at baudryjeremy@gmail.com

#### 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.
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