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README
V0.1 - 2012/02/27. JBG.

- The structure has been created in that way: code/{exe,mkfile,{model,model_build}/{src,inc}} .
- genmakefilel and compile_complex.sh have been written and tested in several configurations, but needs some additional tests.
- psom (versionfrom JBW) has been fitted into the structure.
- a lot to do:
   - improve the portability
   - add pgf95
   - add comments
   - improve the user-friendlyness.

Additional interesting readings:
  * src/README : all about the modifications of psom itself.
  * the scripts in tools are commented (or will soon be).
  * optfile is also roughly commented.
***********************************************************************************

Here is the directory where the code is hosted and from where the model can be ran.

1. To get started:

* Please edit the ./optfile to set the options that fit your environment. Be careful with the syntax ! 
* When this file is correctly set, you can type this command:
   ##############################
   #  sh tools/compile_complex.sh
   ##############################
  It will create the makefile in ./mkfile.
  
* Please edit the ./namelist file (not commented...).
* When this file is correctly set, you can type this command:
   ##############################
   # ./exe/nh < ./namelist
   ##############################
  It will start and run the model.
  By default, the output will appear on the screen and the output files will go to ../output/.



2. Further use:

* If nothing is put in model_build, then the compilation is a classical one. 
* BUT, this directory comes with a structure (model / model_build) that may make the development easier. You can use it this way:
    Instead of replacing files in ./model, you can copy (from ./model and then make modifications or from your own versions) .f90 files in ./model_build.
    When using tools/compile_complex.sh, these new files will overtake those from ./model. The executable will be created based on a combination of old and new .f90 files.   

* If you do not want to use that possibility, you still can use tools/compile_complex.sh, which will then be equivalent to :
   ##############################
   # sh tools/genmakefilel
   # sh tools/compile_simple.sh
   ##############################


3. Additional indications:

* To clean up a bit the mkfile directory, you can type:
   ##############################
   # make -Cmkfile/ clean 
   ##############################
   Use cleanmore instead of clean to also remove the executable file. 



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