Other GMSH Examples

Other GMSH Examples#

This directory contains other examples of mesh generated with GMSH:

  • a sphere from a stl file,

  • a breast-like phantom as well as a tire-like geometry from Lavigne et al. 2023b

The GMSH tagged meshes can be converted to meshes with fenics legacy compatibility considering the following:

def create_mesh(mesh, cell_type, prune_z=False):
    import meshio
    cells = mesh.get_cells_type(cell_type)
    cell_data = mesh.get_cell_data("gmsh:physical", cell_type)
    points = mesh.points[:, :2] if prune_z else mesh.points
    out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}, cell_data={
                           "name_to_read": [cell_data]})
    return out_mesh

3D meshes:#

import meshio
msh = meshio.read("mesh.msh")
# BCs
surface_mesh = create_mesh(msh, "triangle", prune_z=False)
meshio.write("facet_tags.xdmf", surface_mesh)
# Mesh
tetra_mesh = create_mesh(msh, "tetra", prune_z=False)
meshio.write("mesh.xdmf", tetra_mesh)

2D meshes#

import meshio
msh = meshio.read("Mesh_refine.msh")
# BCs
line_mesh = create_mesh(msh, "line", prune_z=True)
meshio.write("facet_mesh_refine.xdmf", line_mesh)
# Mesh
triangle_mesh = create_mesh(msh, "triangle", prune_z=True)
meshio.write("mesh_refine.xdmf", triangle_mesh)

Tomography to conform mutlipart meshes from several STL files#

Python tutorials#

Contents (from Gitlab GMSH):

  • t1: Geometry basics, elementary entities, physical groups

  • t2: Transformations, extruded geometries, volumes

  • t3: Extruded meshes, parameters, options

  • t4: Built-in functions, holes in surfaces, annotations, entity colors

  • t5: Mesh sizes, loops, holes in volumes

  • t6: Transfinite meshes, deleting entities

  • t7: Background meshes

  • t8: Post-processing, image export and animations

  • t9: Plugins

  • t10: Mesh size fields

  • t11: Unstructured quadrangular meshes

  • t12: Cross-patch meshing with compounds

  • t13: Remeshing an STL file without an underlying CAD model

  • t14: Homology and cohomology computation

  • t15: Embedded points, lines and surfaces

  • t16: Constructive Solid Geometry, OpenCASCADE geometry kernel

  • t17: Anisotropic background mesh

  • t18: Periodic meshes

  • t19: Thrusections, fillets, pipes, mesh size from curvature

  • t20: STEP import and manipulation, geometry partitioning

  • t21: Mesh partitioning

Extended tutorials (API only):

  • x1: Geometry and mesh data

  • x2: Mesh import, discrete entities, hybrid models, terrain meshing

  • x3: Post-processing data import: list-based

  • x4: Post-processing data import: model-based

  • x5: Additional geometrical data: parametrizations, normals, curvatures

  • x6: Additional mesh data: integration points, Jacobians and basis functions

  • x7: Additional mesh data: internal edges and faces

Contents