Resolving Gmsh Tag Error in Python

[tkoyama010]

Describe the feature you would like to be added.

The tag error in Gmsh is typically caused by duplicated or invalid tags (IDs) for entities or elements. To resolve this issue, you can consider the following steps:

1. Avoid Duplicate Tags

Gmsh requires unique IDs for geometry and mesh elements. In your code, you're assigning point IDs with id_ = i + 1, but it's possible that these IDs are conflicting with others. You need to ensure that the IDs for points, curves, and surfaces are unique across all entities.

For example, you can manage the tags using offset variables to avoid overlap between different entities:

point_id_offset = 1
curve_id_offset = len(points) + 1
surface_id_offset = curve_id_offset + len(faces)

# Add points
for i, (point, target_size) in enumerate(zip(points, target_sizes)):
    gmsh.model.geo.add_point(point[0], point[1], point[2], target_size, point_id_offset + i)

# Add curves and surfaces
for i, face in enumerate(faces):
    curve_tags = []
    for j, _ in enumerate(face):
        start_tag = face[j - 1] + point_id_offset
        end_tag = face[j] + point_id_offset
        curve_tag = gmsh.model.geo.add_line(start_tag, end_tag, curve_id_offset + len(curve_tags))
        curve_tags.append(curve_tag)
    gmsh.model.geo.add_curve_loop(curve_tags, surface_id_offset + i)
    gmsh.model.geo.add_plane_surface([surface_id_offset + i], surface_id_offset + i)

2. Timing of remove_all_duplicates

The gmsh.model.geo.remove_all_duplicates() function is used to remove duplicates, but it should be called at the appropriate time. Generally, this should be done after defining all geometry and before the final synchronize().

Example:

# After defining all geometry
gmsh.model.geo.remove_all_duplicates()
gmsh.model.geo.synchronize()

3. Timing of synchronize Calls

Frequent calls to synchronize can cause inconsistencies within Gmsh's internal state. It's best to define all geometry first and then call synchronize once, rather than multiple times throughout the code.

Example:

# Call synchronize only once after all geometry definitions
gmsh.model.geo.synchronize()

4. Check the Error Message

Understanding the specific error message can help diagnose the problem. You can set gmsh.option.set_number("General.Verbosity", 5) right after gmsh.initialize() to get more detailed error messages, which can provide more insight into what's going wrong.

5. General Workflow in Gmsh

Ensure you follow the typical workflow in Gmsh:

1. Define all geometry.
2. Remove duplicates.
3. Synchronize.
4. Generate the mesh.

By following these steps, you should be able to resolve the tag error in your Gmsh script.

Links to Gmsh Documentation, Examples, or Class Definitions.

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Pseudocode or Screenshots

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[tkoyama010]

import pygmsh
import pyvista as pv

def delaunay_3d_pygmsh(
    edge_source: pv.PolyData,
    target_sizes: float | list[float] | None = None,
) -> pv.UnstructuredGrid | None:
    """
    Delaunay 3D mesh algorithm using pygmsh.

    Parameters
    ----------
    edge_source : pyvista.PolyData
        Source object specifying constrained edges and loops. If set,
        and lines/polygons are defined, a constrained triangulation is created.
        The lines/polygons are assumed to reference points in the input point
        set (i.e., point ids are identical in the input and source).

    target_sizes : float | list[float]
        Target mesh size close to the points.

    Returns
    -------
    pyvista.UnstructuredGrid
        Mesh from the 3D Delaunay generation.

    Notes
    -----
    .. versionadded:: 0.2.0

    """
    points = edge_source.points
    faces = edge_source.faces.reshape(-1, 4)[:, 1:]  # Assuming triangular faces

    with pygmsh.geo.Geometry() as geom:
        # Add points to the geometry
        point_tags = []
        for i, point in enumerate(points):
            if isinstance(target_sizes, float):
                target_size = target_sizes
            elif isinstance(target_sizes, list):
                target_size = target_sizes[i]
            else:
                target_size = None
            point_tags.append(geom.add_point(point, lcar=target_size))

        # Add lines and surfaces
        surface_loop = []
        for face in faces:
            line_tags = []
            for j in range(3):
                start_point = point_tags[face[j - 1]]
                end_point = point_tags[face[j]]
                line_tags.append(geom.add_line(start_point, end_point))
            line_loop = geom.add_curve_loop(line_tags)
            surface_loop.append(geom.add_plane_surface(line_loop))

        # Create the volume
        geom.add_surface_loop(surface_loop)
        volume = geom.add_volume([surface_loop])

        # Generate the mesh
        mesh = geom.generate_mesh()

    # Convert the mesh to PyVista format
    cells = mesh.cells_dict['tetra']
    cell_types = [pv.CellType.TETRA] * len(cells)
    pv_mesh = pv.UnstructuredGrid(mesh.points, cells.ravel(), cell_types)
    
    return pv_mesh