--- MITgcm_contrib/eh3/llc/ecco-godae/README	2006/08/25 16:42:57	1.1
+++ MITgcm_contrib/eh3/llc/ecco-godae/README	2007/03/28 18:29:45	1.5
@@ -1,9 +1,123 @@
 
+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 ; do 
+  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"
+