mesh-topo v3.2.3¶

Mercurial revision 5786:5c8b45563631 | 2026-08-04

Description¶

Interpolates bathymetry and its gradient onto a given finite element (FE) mesh. This tool is designed for ocean modeling applications, allowing for the integration of bathymetric data into unstructured grids.

Usage¶

mesh-topo [OPTIONS] -m <mesh_file> -b <bathymetry_file> -p <paire>

Options¶

Option	Description
`-h,--help`	Print this help message.
`-m <mesh_file>`	Input mesh file (`.nei` format). Use `mesh-format` to convert from other formats (e.g., GMSH).
`-b <bathymetry_file>`	Bathymetry file (netCDF or `.grd` format).
`-v <variable>`	Variable name in the bathymetry file (e.g., `z`, `bathymetry`). If not specified, the tool attempts common names.
`-o <output_file>`	Output file name (optional). If not specified, files are auto-generated.
`-p <paire>`	Computational element pair. Required. Valid options: `LGP0xLGP1`, `DGP1xLGP2`, `DNP1xLGP2`, `Q1xQ0`, `CQP1xCQP0`. Determines how topography and its gradient are computed and saved.
`--rootname <name>`	Root name for output files (e.g., `output-topo-LGP1-0.s2r`).
`--smoothed <iterations>`	Number of smoothing iterations to apply to the bathymetry (default: 0).
`--change-sign=<yes\|no>`	Change the sign of bathymetry values (default: `yes`). Models typically expect positive depths.
`-missing <value>`	Missing value threshold (default: `99999.9`).
`-nomask`	Replace masked values in the bathymetry file with zero.
`-debug`	Enable debug mode for verbose output.
`-z <zone>`	Deprecated: Zone identifier (optional).
`-d <discretisation>`	Deprecated: Discretisation type. Use `-p` instead.

Examples¶

Basic Usage¶

Interpolate bathymetry onto a mesh using the LGP0xLGP1 pair:

mesh-topo -m mesh.nei -b bathymetry.nc -p LGP0xLGP1

Smoothing Bathymetry¶

Apply 5 smoothing iterations to the bathymetry:

mesh-topo -m mesh.nei -b bathymetry.nc -p LGP0xLGP1 --smoothed 5

Custom Output Root Name¶

Specify a root name for output files:

mesh-topo -m mesh.nei -b bathymetry.nc -p LGP0xLGP1 --rootname my_output

Disable Sign Change¶

Disable the automatic sign change for bathymetry values:

mesh-topo -m mesh.nei -b bathymetry.nc -p LGP0xLGP1 --change-sign=no

Multiple Bathymetry Files¶

Use multiple bathymetry files (prioritized in order):

mesh-topo -m mesh.nei -b bathymetry1.nc -b bathymetry2.grd -p LGP0xLGP1

Environment Variables¶

None.

Notes¶

Sign Convention: By default, mesh-topo converts negative depths (common in databases) to positive depths (expected by most ocean models). Use --change-sign=no to disable this.
Masked Values: Masked values in the bathymetry file are replaced with the --missing threshold. Use -nomask to replace them with zero.
Discretisation Pairs: The -p option determines the computational pair for topography and its gradient. For example:
- LGP0xLGP1: Topography on elevation nodes, gradient on velocity nodes.
- DGP1xLGP2: Higher-order discretisation for complex geometries.
Output Files: If -o is not specified, output files are auto-generated with names like topo-{discretisation}-0.s2r (raw interpolation) or topo-{discretisation}-1.s2r (optimal estimate).