# mesh-estuary v3.2.3

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

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## Description

`mesh-estuary` interpolates a **bathymetry** and its **gradient** onto a given **finite element (FE) mesh**.

- The bathymetry (topography) values are saved on **elevation nodes**.
- The gradients are saved on **velocity nodes**.

> **Note:** The mesh file must be in `.nei` format. If needed, use `mesh-format` to convert from other formats (e.g., GMSH).

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## Usage

```bash
mesh-estuary -m MESH_FILE -b BATHYMETRY_FILE
```

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## Options


| Option         | Description                                                                       |
| -------------- | --------------------------------------------------------------------------------- |
| `-h`, `--help` | Print this help and exit.                                                         |
| `-m <file>`    | Path to the **mesh file** (`.nei` format) on which to interpolate the bathymetry. |
| `-b <file>`    | Path to the **bathymetry file** (NetCDF or `.grd` format).                        |
| `--debug`      | Enable debug mode.                                                                |


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## Deprecated Options

> ⚠️ **Warning:** These options are **no longer supported** and may be removed in future versions.


| Option            | Description                                                                                      |
| ----------------- | ------------------------------------------------------------------------------------------------ |
| `--smoothed <n>`  | Number of smoothing iterations (deprecated).                                                     |
| `-f <file>`       | Boundary file (deprecated).                                                                      |
| `-p <file>`       | Polygon file to limit the working area (deprecated).                                             |
| `-o <file>`       | Output file name (deprecated).                                                                   |
| `-d <descriptor>` | Discretization element pair (e.g., `LGP0xLGP1`, `DGP1xLGP2`, `DNP1xLGP2`, `Q1xQ0`) (deprecated). |
| `-z <zone>`       | Zone file (deprecated).                                                                          |
| `-s <meshsize>`   | Mesh size (deprecated).                                                                          |


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## Examples

### **Basic Usage**

Interpolate bathymetry onto a mesh:

```bash
mesh-estuary -m mesh.nei -b bathymetry.nc
```

### **Debug Mode**

Enable debug mode for troubleshooting:

```bash
mesh-estuary --debug -m mesh.nei -b bathymetry.grd
```

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## Environment Variables

None.

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## Notes

1. **Input Files:**
  - The **mesh file** must be in `.nei` format. Use `mesh-format` to convert from other formats if necessary.
  - The **bathymetry file** must be in **NetCDF** or `.grd` format.
2. **Output:**
  - The interpolated bathymetry is saved on **elevation nodes** of the mesh.
  - The gradients are saved on **velocity nodes** of the mesh.
3. **Debugging:**
  - Use `--debug` to print additional information during execution.
4. **Deprecated Options:**
  - Avoid using deprecated options, as they may not be supported in future versions.

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## See Also

- [`mesh-format`](https://www.comodo-ocean.fr/) (for converting mesh files to `.nei` format)
- [NetCDF Format](https://www.unidata.ucar.edu/software/netcdf/) (for bathymetry file requirements)