Back   Home

Setting-up Modeling Domains in HOPS

The setting-up of modeling domains with the HOPS software is accomplished with three separate packages.

  1. GRIDS: a package to perform the basic definition functions.
  2. PE_mask: a package to define land masks for the domains.
  3. Cond_Topo: a MATLAB® package to conditions the domain topography for improved Primitive Equation performance.

HOPS Horizontal Grid


The GRIDS package enables the user to design a model domain for the Harvard Ocean Prediction System (HOPS). In particular, the GRIDS package allows the user to

The GRIDS package, itself, is split-up into three programs:

The workhorse program. It performs most of the described operations.
Input: netCDF topography
ASCII parameter input file
Output: netCDF domain descriptor (GRIDS file)
GMETA plot file
Run Time: A few minutes
A utility to help design collocated nested sub-domains.
Input: GRIDS file
ASCII parameter input file
Output: ASCII text
Run Time:
A utility to align topographic & masking data between one GRIDS file and a nested sub-domain GRIDS file.
Input: 2 GRIDS files
Terminal input
Output: Overwrites one of the GRIDS files
Run Time:

A more complete description of the GRIDS package in contained in the GRIDS User's Guide. A gzipped PostScript version of the guide ( is distributed with the GRIDS package.

HOPS Masking  (MATLAB version)


The program PE_MASK appends/modifies the Land/Sea mask data to an existing GRIDS NetCDF file. The Land/Sea data is first computed from the raw bathymetry contained in the GRIDS NetCDF by specifying a transition isobath (said zero meters) between Land and Sea. The user then modifies the mask to remove problem spots (isolated ocean points, channels too narrow, etc).

The PE_MASK package is an interactive one. It includes several FORTRAN routines and MATLAB M-files; both the FORTRAN and MATLAB routines perform the same task. The MATLAB routines have the advantage that the mask data can be determined graphically and it is faster and not so tedious as the FORTRAN program. In addition, the MATLAB routines have had several niceties added to reduce the work involved. These features have not yet been ported to the FORTRAN version

If MATLAB is available, the MATLAB version of PE_mask is highly recommended over the FORTRAN version.


COND_TOPO is a series of MATLAB executable scripts designed to reduce the slope of the topography for use in the HOPS Primitive Equation model. These scripts are designed to modify only the topography in areas where the slope exceeds a user-specified value according a user-specified measure.

Raw Western North Atlantic Topography Conditioned Western North Atlantic Topography
Raw, Western North Atlantic Topography Conditioned, Western North Atlantic Topography

Currently, COND_TOPO exists only in MATLAB form. This is due to a couple of reasons. The first is convenience. MATLAB was an easy environment to work in while we were still developing this utility. The second reason is that, on occasion, the conditioning can get really "lost". This means that the user must carefully inspect the results of conditioning before accepting them. MATLAB provides many tools for this.

A more complete description of COND_TOPO is provided in a couple of gzipped PostScript files:

HOPS Domains Software

Directory Files Date
Size Compressed
Size Uncompressed
Grids/ Readme.grids 01/16/2001 14103 01/16/2001 2422796 11270708
grids_7.2.tar.Z 01/16/2001 212641 995840
Ex_grids_7.2.tar.gz 01/16/2001 1064737 2673664
PE_mask/ Readme.mask 08/03/2000 16111
pemask_4.1.tar.Z 08/03/2000 103411 423424
Ex_mat_pemask_4.1.tar.gz 08/03/2000 544669 1881088
Ex_for_pemask_4.1.tar.gz 08/03/2000 464043 3356672
Cond_Topo/ Readme.cond_topo 08/14/2001 5360
cond_topo_3.5.tar.Z 08/14/2001 48648 179712 08/14/2001 71007 188461 08/14/2001 162004 736342
Ex_cond_topo_3.5.tar.gz 08/14/2001 386641 1577984

HOPS Compatible Topography Datasets

Directory Files Date
Size Compressed
Size Uncompressed
Atlas/ Readme.atlas 11/18/1997 1631 07/31/1995 11372838 18697556 11/13/1997 2779740 6372740