Commit 34525fb8457af6c70c17d20192a4d61801f947be

Authored by Dany Dumont
1 parent d9de79a3
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README.md
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3 3 ----------------------------------------------------
4 4 Welcome to the Phytoplankton Lagrangian Model 2014!
5 5 ----------------------------------------------------
6 6  
7   -
8 7 The model has been designed to be very user-friendly, however some modifications
9   - must be done to fit with your machine.
10   - So, please read the following steps to correctly start the model.
11   -
12   -
13   - # 1) COMPILATION:
14   -
15   - + Ensure first that gfortran is installed on your machine.
16   - + Ensure that the NETCDF FORTRAN libraries are installed on your machine.
17   - + Change the path for the NETCDF FORTRAN module and libraries in the makefile
18   -
19   - + compile the source codes using the command «make». The executable will be
20   - created in the parent directory.
21   - + you can also delete all object file and the executable by using the command «make mrproper»
  8 + must be done to fit with your machine. So, please read the following steps to
  9 + correctly start the model.
22 10  
23   - 2) USE THE MODEL
  11 +# 1) COMPILATION:
24 12  
25   - - The model use namelists in nml/ allowing to change some parameter values without recompiling
26   - the source code
27   - - outputs will be generated in the directory output/
  13 ++ Ensure first that `gfortran` is installed on your machine.
  14 ++ Ensure that the NETCDF FORTRAN libraries are installed on your machine.
  15 ++ Change the path for the NETCDF FORTRAN module and libraries in the makefile.
  16 ++ Compile the source codes using the command `make`. The executable will be
  17 + created in the parent directory.
  18 ++ You can also delete all object file and the executable by using the command
  19 + `make mrproper`.
28 20  
29   - 3) USE THE MODEL WITH GOTM
  21 +# 2) USE THE MODEL
30 22  
31   - - The model can call GOTM to produce a diffusivity profile. If you want to use this feature
32   - you have to change the value of the parameter «mix_state» in the namelist model_parameter
33   - - Before doing this, ensure that GOTM is installed on your machine and copy all the GOTM namelists
34   - you need in the directory gotm/. You should also create a symbolic link of the executable in the
35   - directory gotm/
  23 ++ The model use namelists in `nml/` allowing to change some parameter values
  24 + without recompiling the source code.
  25 ++ outputs will be generated in the directory `output/`.
36 26  
37   - 4) USE BATCH MODE
  27 +# 3) USE THE MODEL WITH GOTM
38 28  
39   - - you can also run the model in batch mode. To do this, you must change the file
40   - batch_bio_pbs.sh
  29 ++ The model can call GOTM to produce a diffusivity profile. If you want to use
  30 + this feature you have to change the value of the parameter `mix_state`
  31 + in the namelist `model_parameter`.
  32 ++ Before doing this, ensure that GOTM is installed on your machine and copy
  33 + all the GOTM namelists you need in the directory `gotm/`. You should also
  34 + create a symbolic link of the executable in the directory `gotm/`.
41 35  
  36 +# 4) USE BATCH MODE
42 37  
43   - have fun
  38 ++ You can also run the model in batch mode. To do this, you must change the
  39 + file `batch_bio_pbs.sh`.
44 40  
  41 + Have fun!
45 42  
46   - for question, please contact me at baudryjeremy@gmail.com
  43 + For question, please contact me at mailto:baudryjeremy@gmail.com
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