A quick run-through of our new setup
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The Top-level region directory
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The setup is now strictly oriented around the grids. Each of the model main 
directories may have just one file which is common to all experiments; the file
regional.grid.[ab]. If you create a new regional.grid file, you should create a new
main dir (ex NATa1.00). You will also need a file REGION.src in the top-level
region directory which contains (among other things) the name of the region in
the environment variable ``R''. 

The files regional.grid.[ab] and grid.info should be placed in the topo/
subdirectory.

The Experiment directories
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Experiment directories contain a few key files such as blkdat.input infile.in
and so on. You should have an example in the directory "expt_01.0". You can call
the next one expt_01.1, for instance.  Also, to ease the setup, I have created a
file in the experiment directory called "EXPT.src". The key elements of that
file is the experiment number X (example 01.0) and E (which is X without the
period, ex 010).

Another key parameter is topography version which can be different for different
experiments (for instance one experiment can run with nesting into TOPAZ3,
another one with nesting into another model).  Topography version starts from 01
and upwards, always use two digits.

Set the input files in the experiment directory to proper values before
proceeding with creating input data. blkdat.input is used frequently in the
setup process, so make sure it is ok.

Creating input data
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No more details here, but the steps are:

1 ) Set up topography and partitioning in the directory topo
2 ) Set up relaxation/initial climatology in directory relax 
3 ) Set up forcing climatology in directory force
4 ) Set up river and other forcing in directory force 
5 ) Set up tides in tide_nersc and nesting in nest_nersc (if needed)


Final steps
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6 ) Compile model - this uses primarily the partitioning set up in the topo
7 ) Set up data and scratch dirs in experiment directory, set up job scripts and
    run the model


Useful scripts
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The script bin/newRegion.sh under the region directory can be used to set up a
new region based on a old region.

The script bin/newExpt.sh under the region directory can be used to set up a
new experiment directory based on a old directory.