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Python interface to tetgen

Project description

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This Python library is an interface to Hang Si’s TetGen C++ software. This module combines speed of C++ with the portability and ease of installation of Python along with integration to PyVista for 3D visualization and analysis. See the TetGen GitHub page for more details on the original creator.

This Python library uses the C++ source from TetGen (version 1.6.0, released on August 31, 2020) hosted at libigl/tetgen.

Brief description from Weierstrass Institute Software:

TetGen is a program to generate tetrahedral meshes of any 3D polyhedral domains. TetGen generates exact constrained Delaunay tetrahedralization, boundary conforming Delaunay meshes, and Voronoi partitions.

TetGen provides various features to generate good quality and adaptive tetrahedral meshes suitable for numerical methods, such as finite element or finite volume methods. For more information of TetGen, please take a look at a list of features.

License (AGPL)

The original TetGen software is under AGPL (see LICENSE) and thus this Python wrapper package must adopt that license as well.

Please look into the terms of this license before creating a dynamic link to this software in your downstream package and understand commercial use limitations. We are not lawyers and cannot provide any guidance on the terms of this license.

Please see https://www.gnu.org/licenses/agpl-3.0.en.html

Installation

From PyPI

pip install tetgen

From source at GitHub

git clone https://github.com/pyvista/tetgen
cd tetgen
pip install .

Basic Example

The features of the C++ TetGen software implemented in this module are primarily focused on the tetrahedralization a manifold triangular surface. This basic example demonstrates how to tetrahedralize a manifold surface and plot part of the mesh.

import pyvista as pv
import tetgen
import numpy as np
pv.set_plot_theme('document')

sphere = pv.Sphere()
tet = tetgen.TetGen(sphere)
tet.tetrahedralize(order=1, mindihedral=20, minratio=1.5)
grid = tet.grid
grid.plot(show_edges=True)
https://github.com/pyvista/tetgen/raw/master/doc/images/sphere.png

Tetrahedralized Sphere

Extract a portion of the sphere’s tetrahedral mesh below the xy plane and plot the mesh quality.

# get cell centroids
cells = grid.cells.reshape(-1, 5)[:, 1:]
cell_center = grid.points[cells].mean(1)

# extract cells below the 0 xy plane
mask = cell_center[:, 2] < 0
cell_ind = mask.nonzero()[0]
subgrid = grid.extract_cells(cell_ind)

# advanced plotting
plotter = pv.Plotter()
plotter.add_mesh(subgrid, 'lightgrey', lighting=True, show_edges=True)
plotter.add_mesh(sphere, 'r', 'wireframe')
plotter.add_legend([[' Input Mesh ', 'r'],
                    [' Tessellated Mesh ', 'black']])
plotter.show()
https://github.com/pyvista/tetgen/raw/master/doc/images/sphere_subgrid.png

Here is the cell quality as computed according to the minimum scaled jacobian.

Compute cell quality

>>> cell_qual = subgrid.compute_cell_quality()['CellQuality']

Plot quality

>>> subgrid.plot(scalars=cell_qual, stitle='Quality', cmap='bwr', clim=[0, 1],
...              flip_scalars=True, show_edges=True)
https://github.com/pyvista/tetgen/raw/master/doc/images/sphere_qual.png

Acknowledgments

Software was originally created by Hang Si based on work published in TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator.

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