Domain Tools

Code and tools to edit and manipulate ocean model grids and topographies.

Below is a list of included tools and short documentation for each.

topogtools (Russ' Fortran tools)

usage: topogtools [--help] <command> [<args>]

Collection of tools to edit and manipulate ocean model topographies. See topogtools --help <command> to read about a specific subcommand.

Available commands:

• gen_topo - Generate a new topography file from a bathymetry
• deseas - Remove enclosed seas
• min_max_depth - Set minimum and maximum depth
• check_nonadvective - Check for non-advective cells
• fix_nonadvective - Fix non-advective cells
• mask - Generate mask

gen_topo

usage: topogtools gen_topo --input <input_file> --output <output_file>
                           --hgrid <grid> [<options>]

Generate a new topography from <input_file> on the tracer points of <grid> and writes the result to <output_file>. Note that <grid> must be a super-grid.

Options

• --tripolar set this option if the horizontal grid is a tripolar grid
• --longitude-offset <value> offset (in degrees) between the central longitude of the ocean horizontal grid and of the bathymetry grid (default '0.0')

deseas

usage: topogtools deseas --input <input_file> --output <output_file>

Remove enclosed seas from <input_file> and writes the result to <output_file>.

min_max_depth

usage: topogtools min_max_depth --input <input_file> --output <output_file>
                                --level <level> [--vgrid <vgrid>]

Set minimum depth to the depth at a specified level and set maximum depth to deepest in <vgrid>. <level> is the minimum number of depth levels (e.g. 4). Can produce non-advective cells.

Options

• --vgrid <vgrid> vertical grid (default 'ocean_vgrid.nc')

fill_fraction

usage: topogtools fill_fraction --input <input_file> --output <output_file>
                                --fraction <frac>

Cells with a fraction of sea area smaller than will have their depth set to zero. Can produce non-advective cells and/or new seas.

check_nonadvective

usage: topogtools check_nonadvective --input <input_file>
                                     [--vgrid <vgrid> --potholes --coastal-cells]

Check for non-advective cells. There are two types of checks available: potholes and non-advective coastal cells. Checking for non-advective coastal cells should only be needed when using a B-grid.

Options

• --vgrid <vgrid> vertical grid (default 'ocean_vgrid.nc')
• --potholes check for potholes
• --coastal-cells check for non-advective coastal cells

fix_nonadvective

usage: topogtools fix_nonadvective --input <input_file> --output <output_file>
                                   [--vgrid <vgrid> --potholes --coastal-cells]

Fix non-advective cells. There are two types of fixes available: potholes and non-advective coastal cells. Fixes to non-advective coastal cells should only be needed when using a B-grid.

Options

• --vgrid <vgrid> vertical grid (default 'ocean_vgrid.nc')
• --potholes fix potholes
• --coastal-cells fix non-advective coastal cells

mask

usage: topogtools mask  --input <input_file> --output <output_file>
                        [--fraction <frac>]

Creates a land mask from a topography.

Options

• --fraction <frac> cells with a fraction of sea area smaller than <frac> will be set as land (default '0.0')

float_vgrid

usage: float_vgrid [--vgrid <vgrid>]

Alter values in ocean vertical grid so they can be used with both single- and double-precision topography file.

Options

• --vgrid <vgrid> vertical grid (default 'ocean_vgrid.nc')

Building and Installation

General Instructions

Prerequisites

To compile these tools one needs:

• Fortran compiler
• netCDF-Fortran
• CMake

Step-by-step instructions

domain-tools uses CMake for building and installation. Therefore the procedure to build the sources and install the executables is fairly standard:

git clone https://github.com/COSIMA/domain-tools.git
cd domain-tools
cmake -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build
cmake --install build --prefix=<directory where to install the tools>

Gadi

An installation of these tools is available on Gadi. To use it, you need to be a member of group ik11 and load the corresponding module:

module use /g/data/ik11/spack/modules
module load domain-tools

If instead you wish to build and install the tools from the sources, you can follow a slighly modified version of above step-be-step instructions:

module load intel-compiler netcdf
export NetCDF_ROOT=$(nc-config --prefix)
git clone https://github.com/COSIMA/domain-tools.git
cd domain-tools
cmake -B build -DCMAKE_BUILD_TYPE=Release -DNetCDF_Fortran_LIBRARY=$NetCDF_ROOT/lib/Intel/libnetcdff.so -DNetCDF_C_LIBRARY=$NetCDF_ROOT/lib/libnetcdf.so -DNetCDF_Fortran_INCLUDE_DIRS=$NetCDF_ROOT/include/Intel
cmake --build build
cmake --install build --prefix=<directory where to install the tools>