LAT-LON-Polar-Cap setup
-----------------------
ed@eh3.com, cnh@mit.edu, heimbach@mit.edu

Setup code/, input/
-------------------
Note that the *.mitgrid files must be named using the following pattern
or they will not be read correctly by MITgcm:

  cd run
  for i in 1 2 3 4 5 6; do 
    ln -s ../input/llc_p90_${i}.mitgrid tile00${i}.mitgrid
  done

Change topology:
 
cd MITgcm/utils/exch2/matlab-topology-generator/
 
modify matlab script driver.m
line
nr = 360; ng = 90; nb = 90; tnx=90;tny=90;
to (e.g.)
nr = 360; ng = 90; nb = 90; tnx=45;tny=45;
for compact format, set 
mapIO=1
make sure blanklist.txt is correct 
(or empty, if no tiles to be omitted)
then run driver.m
 
This generates routine and header
w2_e2setup.F
W2_EXCH2_TOPOLOGY.h
which need to go in code/

Accordingly, bathy.0??.0??.data need changing.

N.B. Domain decomposition nPy not active with exch2, i.e.
possible decomps are (for orig. with 17 tiles):
sNx = 90 30 90  30
sNy = 90 30 90  30
nSx = 17 17  1   1
nSy =  1  1  1   1
nPx =  1  9 17 153
nPy =  1  1  1   1

I've generated artificial tile #18 with all zeros
blanklist.txt needs to be generated by hand.

Setup code_15lev/, input_15lev/
-------------------------------

* Real bathymetry, 15 vertical levels,
* monthly climatological forcing via exf package, uses
  4x4 deg. fields with on-the-fly interpolation
* Bathymetry is generated via script ... in ...
* Initial conditions for T, S are generated via script ... in ...

All input fields can be downloaded using script input_15lev/prepare_run
(which also contains link pattern to standard tile00${i}.mitgrid fields),
then link to run directory.

Setup code_50lev/, input_50lev/
-------------------------------

* Based on ETOPO2 bathy, 
* 50 vertical level exactly matching high_res_cube (ECCO2), incl. partial cell params.
* forced by 6-hourly NCEP atmos. state, uses original reduced Gaussian grid
  and exf interpolation on-the-fly
* initial conditions generated via scripts in 
  MITgcm_contrib/eh3/llc/ecco-godae/climatology/
  resulting fields are
  llc90x90x360_50lev_ptemp.bin, llc90x90x360_50lev_salt.bin
  these fields are run are run with a diffusion/conv.adj. setup of MITgcm
  for 10 days to remove some instabilities
* input fields can be obtained at
  http://channel.mit.edu/datasets/MITgcm_input_files/MITgcm_contrib/eh3/llc/ecco-godae/data_50lev/

Required input to generate bathy & initial conditions:
(1)
(in directory input/ )
llc_p90_1.nc
llc_p90_2.nc
llc_p90_3.nc
llc_p90_4.nc
llc_p90_5.nc
llc_p90_6.nc
(2)
ETOPO2.raw.bin
(3)
directory CLIMannual/

Generation steps:

1) run script "gen_bathy"
   Input:
   -----
llc_p90_1.nc
llc_p90_2.nc
llc_p90_3.nc
llc_p90_4.nc
llc_p90_5.nc
llc_p90_6.nc
   Output:
   -----
llc_p90_bathy.f001.nc
llc_p90_bathy.f002.nc
llc_p90_bathy.f003.nc
llc_p90_bathy.f004.nc
llc_p90_bathy.f005.nc

2) run script "gen_initial_cond_50_lev"
   Input:
   -----
(a) above llc_p90_*.nc
(b) orig. climatology fields in CLIMannual/
   Output:
   -----

3) run script "t18_to_global_inputs.m"

4) run script "fill_shallow_regions_and_isolated_basins.m"