topo/README.topo:

Illustrates how to convert bathymetry from MICOM to HYCOM grid orientation.  

An alternative is to initially generate the bathymetry on the HYCOM grid.
This can be done using hycom/ALL/topo/src/bathy_05min and the 5-minute 
TerrainBase dataset configured for bathy_05min available at:
ftp://obelix.rsmas.miami.edu/awall/hycom/tbase_for_hycom.tar.gz
See README/README.topo.new and hycom/ATLb2.00/topo_IASb0.50.

README.topo		this file

depth.51x56		MICOM bathymetry file (Atlantic, 2-deg.)
depth_ATLb2.00_01.[ab]	HYCOM bathymetry file
depth_ATLb2.00_01.com	script to create depth_ATLb2.00_01.[ab]
depth_ATLb2.00_01.log	From csh depth_ATLb2.00_01.com >& depth_ATLb2.00_01.log

depth_ATLb2.00_02.com	script to create depth_ATLb2.00_02.[ab] (smoothed 01)

depth_ATLb2.00_03.com	script to create depth_ATLb2.00_03.[ab] (flat bottom)

new_topo.com		script to customize scripts for a new region

regional.grid.[ab]	HYCOM grid location file
regional.grid.com	script to create regional.grid.[ab]
regional.grid.log	From csh regional.grid.com >& regional.grid.log

The source code is domain-independent (and therefore in ../../ALL/topo).
All programs read regional.grid.b at run-time to get idm and jdm for the 
particular region being processed.  So regional.grid.com must be run
first to generate regional.grid.[ab].

The depth file includes the region name (ATLb2.00) so that files from
several regions can be collected in one directory.  The ending "_01"
indicates version 01 of the bathymetry, and this convention allows for 
up to 99 distinct bathymetries for the same region and resolution.
In this case, depth_ATLb2.00_02 and depth_ATLb2.00_03 have the same 
land/sea boundary as depth_ATLb2.00_01 but 02 applies a 9-point smoother
to the 01 depths and 03 has a flat bottom at 5000m.  

Since filenames include the region name, new_topo.com is provided to
copy scripts from one region to another.

Additional smoothing, as in depth_ATLb2.00_02, may not be necessary at
2 degree resolution but one or two smoothing passes might be appropriate
when using higher resolution.

See ../doc/meshmap_hycom.* and ../doc/meshmap_micom.* for details of 
the grid layouts.

Since both files leave out the last row and column (which are always
outside the region), the translation is simple (HYCOM idm,jdm):

      do j= 1,jdm-1
        do i= 1,idm-1
          dh(i,j) = dm(jdm-j,i)
        enddo
      enddo

Some MICOM bathymetry files use an alternative "pakk" encoding.  If the
HYCOM bathymetery from topo_m2h does not look right, try topo_malt2h
which links in pakk_micom.f instead of pakk_hycom.f.  The only differences 
between these files are six lines in subroutine unpakk (lines 107-112).