scikit-fem 3.1.0

Simple finite element assemblers

scikit-fem is a lightweight Python 3.7+ library for performing finite element assembly. Its main purpose is the transformation of bilinear forms into sparse matrices and linear forms into vectors. The library supports triangular, quadrilateral, tetrahedral and hexahedral meshes as well as one-dimensional problems.

The library fills a gap in the spectrum of finite element codes. The library is lightweight and has minimal dependencies. It contains no compiled code meaning that it's easy to install and use on all platforms that support NumPy. Despite being fully interpreted, the code has a reasonable performance.

Installation

The most recent release can be installed simply by

pip install scikit-fem

or

conda install -c conda-forge scikit-fem

Examples

Solve the Poisson problem (see also ex01.py):

from skfem import *
from skfem.helpers import dot, grad

# create the mesh
m = MeshTri().refined(4)
# or, with your own points and cells:
# m = MeshTri(points, cells)

e = ElementTriP1()
basis = InteriorBasis(m, e)

# this method could also be imported from skfem.models.laplace
@BilinearForm
def laplace(u, v, _):
    return dot(grad(u), grad(v))


# this method could also be imported from skfem.models.unit_load
@LinearForm
def rhs(v, _):
    return 1.0 * v

A = asm(laplace, basis)
b = asm(rhs, basis)
# or:
# A = laplace.assemble(basis)
# b = rhs.assemble(basis)

# enforce Dirichlet boundary conditions
A, b = enforce(A, b, D=m.boundary_nodes())

# solve -- can be anything that takes a sparse matrix and a right-hand side
x = solve(A, b)

# plot the solution
from skfem.visuals.matplotlib import plot, savefig
plot(m, x, shading='gouraud', colorbar=True)
savefig('solution.png')

Meshes can be initialized manually, loaded from external files using meshio, or created with the help of special constructors:

import numpy as np
from skfem import MeshLine, MeshTri, MeshTet

mesh = MeshLine(np.array([0., .5, 1.]))
mesh = MeshTri(
    np.array([[0., 0.],
              [1., 0.],
              [0., 1.]]).T,
    np.array([[0, 1, 2]]).T,
)
mesh = MeshTri.load("docs/examples/meshes/square.msh")
mesh = MeshTet.init_tensor(*((np.linspace(0, 1, 60),) * 3))

We support many common finite elements. Below the stiffness matrix is assembled using second-order tetrahedra:

from skfem import InteriorBasis, ElementTetP2

basis = InteriorBasis(mesh, ElementTetP2())  # quadratic tetrahedron
A = laplace.assemble(basis)  # type: scipy.sparse.csr_matrix

More examples can be found in the gallery.

Benchmark

The following benchmark (docs/examples/performance.py) demonstrates the time spent on finite element assembly in comparison to the time spent on linear solve. The given numbers were calculated using a ThinkPad X1 Carbon laptop (7th gen). Note that the timings are only illustrative as they depend on, e.g., the type of element used, the number of quadrature points used, the type of linear solver, and the complexity of the forms. This benchmark solves the Laplace equation using linear tetrahedral elements and the default direct sparse solver of scipy.sparse.linalg.spsolve.

Degrees-of-freedom	Assembly (s)	Linear solve (s)
4096	0.04805	0.04241
8000	0.09804	0.16269
15625	0.20347	0.87741
32768	0.46399	5.98163
64000	1.00143	36.47855
125000	2.05274	nan
262144	4.48825	nan
512000	8.82814	nan
1030301	18.25461	nan

Documentation

The project is documented using Sphinx under docs/. Built version can be found from Read the Docs. Here are direct links to additional resources:

• Examples from our test suite
• Examples from the FEniCS tutorial

Getting help

If you encounter an issue and cannot find help from the documentation, you can use the Github issue tracker to ask questions using the question label. Try to provide a snippet of code which fails and include also the version of the library you are using. The version can be found as follows:

python -c "import pkg_resources; print(pkg_resources.get_distribution('scikit-fem').version)"

Dependencies

The minimal dependencies for installing scikit-fem are numpy, scipy and meshio. In addition, many examples use matplotlib for visualization. Some examples demonstrate the use of other external packages; see requirements.txt for a list of test dependencies.

Testing

The tests are run by Github Actions. The Makefile in the repository root has targets for running the testing container locally using docker. For example, make test_py38 runs the tests using py38 branch from kinnala/scikit-fem-docker-action. The releases are tested in kinnala/scikit-fem-release-tests.

Licensing

The contents of skfem/ and the PyPI package scikit-fem are licensed under the 3-clause BSD license. Some examples under docs/examples/ have a different license, see LICENSE.md for more information.

Acknowledgements

This project was started while working under a grant from the Finnish Cultural Foundation. Versions 2.0.0+ were prepared while working in a project funded by the Academy of Finland. The approach used in the finite element assembly has been inspired by the work of A. Hannukainen and M. Juntunen.

Contributing

We are happy to welcome any contributions to the library. Reasonable projects for first timers include:

• Reporting a bug
• Writing an example
• Improving the tests
• Finding typos in the documentation.

By contributing code to scikit-fem, you are agreeing to release it under BSD-3-Clause, see LICENSE.md.

Citing the library

You may use the following BibTeX entry:

@article{skfem2020,
  doi = {10.21105/joss.02369},
  url = {https://doi.org/10.21105/joss.02369},
  year = {2020},
  publisher = {The Open Journal},
  volume = {5},
  number = {52},
  pages = {2369},
  author = {Tom Gustafsson and G. D. McBain},
  title = {scikit-fem: A Python package for finite element assembly},
  journal = {Journal of Open Source Software}
}

Use the Zenodo DOIs only if you want to cite a specific version, e.g., to ensure reproducibility.

In literature

The library has been used in the preparation of the following scientific works. Feel free to add your publication to the list.

• Gustafsson, T. (2020). A simple technique for unstructured mesh generation via adaptive finite elements. arXiv preprint arXiv:2011.07919.
• Huang, X., Shi, Y., & Wang, W. (2020). A Morley-Wang-Xu element method for a fourth order elliptic singular perturbation problem. arXiv preprint arXiv:2011.14064.
• Gustafsson, T., Stenberg, R., & Videman, J. (2020). Nitsche's method for Kirchhoff plates. arXiv preprint arXiv:2007.00403.
• Aquino, A., Mallinson, S., McBain, G. D., Horrocks, G., & Barber, T. (2020). Two-dimensional numerical simulation of inkjet print-zone flows. 22nd Australasian Fluid Mechanics Conference AFMC2020. Open access.
• Gustafsson, T., & McBain, G. D. (2020). scikit-fem: A Python package for finite element assembly. Journal of Open Source Software, 52(5). Open access.
• Gustafsson, T., Stenberg, R., & Videman, J. (2020). On Nitsche's method for elastic contact problems. SIAM Journal on Scientific Computing, 42(2), B425–B446. arXiv preprint arXiv:1902.09312.
• Gustafsson, T., Stenberg, R., & Videman, J. (2019). Nitsche's Master-Slave Method for Elastic Contact Problems. arXiv:1912.08279.
• McBain, G. D., Mallinson, S. G., Brown, B. R., Gustafsson, T. (2019). Three ways to compute multiport inertance. The ANZIAM Journal, 60, C140–C155. Open access.
• Gustafsson, T., Stenberg, R., & Videman, J. (2019). Error analysis of Nitsche's mortar method. Numerische Mathematik, 142(4), 973–994. Open access.
• Gustafsson, T., Stenberg, R., & Videman, J. (2019). Nitsche's method for unilateral contact problems. Port. Math. 75, 189–204. arXiv preprint arXiv:1805.04283.
• Gustafsson, T., Stenberg, R. & Videman, J. (2018). A posteriori estimates for conforming Kirchhoff plate elements. SIAM Journal on Scientific Computing, 40(3), A1386–A1407. arXiv preprint arXiv:1707.08396.
• Gustafsson, T., Rajagopal, K. R., Stenberg, R., & Videman, J. (2018). An adaptive finite element method for the inequality-constrained Reynolds equation. Computer Methods in Applied Mechanics and Engineering, 336, 156–170. arXiv preprint arXiv:1711.04274.
• Gustafsson, T., Stenberg, R., & Videman, J. (2018). A stabilised finite element method for the plate obstacle problem. BIT Numerical Mathematics, 59(1), 97–124. arXiv preprint arXiv:1711.04166.
• Gustafsson, T., Stenberg, R., & Videman, J. (2017). Nitsche’s Method for the Obstacle Problem of Clamped Kirchhoff Plates. In European Conference on Numerical Mathematics and Advanced Applications, 407–415. Springer.
• Gustafsson, T., Stenberg, R., & Videman, J. (2017). A posteriori analysis of classical plate elements. Rakenteiden Mekaniikka, 50(3), 141–145. Open access.

Changelog

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning with respect to documented and/or tested features.

Unreleased

[3.1.0] - 2021-06-18

• Added: Basis, a shorthand for CellBasis
• Added: CellBasis, a new preferred name for InteriorBasis
• Added: BoundaryFacetBasis, a new preferred name for ExteriorFacetBasis
• Added: utils.penalize, an alternative to condense and enforce for essential boundary conditions
• Added: InteriorBasis.point_source, with ex38
• Added: ElementTetDG, similar to ElementTriDG for tetrahedral meshes
• Fixed: MeshLine1.element_finder

[3.0.0] - 2021-04-19

• Added: Completely rewritten Mesh base class which is "immutable" and uses Element classes to define the ordering of nodes; better support for high-order and other more general mesh types in the future
• Added: New quadratic mesh types: MeshTri2, MeshQuad2, MeshTet2 and MeshHex2
• Added: InteriorBasis.probes; like InteriorBasis.interpolator but returns a matrix that operates on solution vectors to interpolate them at the given points
• Added: More overloads for DiscreteField, e.g., multiplication, summation and subtraction are now explicitly supported inside the form definitions
• Added: MeshHex.to_meshtet for splitting hexahedra into tetrahedra
• Added: MeshHex.element_finder for interpolating finite element solutions on hexahedral meshes via InteriorBasis.interpolator
• Added: Mesh.with_boundaries, a functional replacement to Mesh.define_boundary, i.e. defining boundaries via Boolean lambda function
• Added: Mesh.with_subdomains for defining subdomains via Boolean lambda function
• Added: skfem.utils.projection, a replacement of skfem.utils.project with a different, more intuitive order of arguments
• Added: skfem.utils.enforce for setting essential boundary conditions by changing matrix rows to zero and diagonals to one.
• Deprecated: skfem.utils.project in favor of skfem.utils.projection
• Deprecated: Mesh.define_boundary in favor of Mesh.with_boundaries
• Removed: Mesh.{refine,scale,translate}; the replacements are Mesh.{refined,scaled,translated}
• Removed: skfem.models.helpers; available as skfem.helpers
• Removed: DiscreteField.{f,df,ddf,hod}; available as DiscreteField.{value,grad,hess,grad3,...}
• Removed: Python 3.6 support
• Changed: Mesh.refined no more attempts to fix the indexing of Mesh.boundaries after refine
• Changed: skfem.utils.solve now uses scipy.sparse.eigs instead of scipy.sparse.eigsh by default; the old behavior can be retained by explicitly passing solver=solver_scipy_eigs_sym()
• Fixed: High memory usage and other small fixes in skfem.visuals.matplotlib related to 1D plotting

[2.5.0] - 2021-02-13

• Deprecated: side keyword argument to FacetBasis in favor of the more explicit InteriorFacetBasis and MortarFacetBasis.
• Added: InteriorFacetBasis for integrating over the interior facets, e.g., evaluating error estimators with jumps and implementing DG methods.
• Added: MortarFacetBasis for integrating over the mortar mesh.
• Added: InteriorBasis.with_element for reinitializing an equivalent basis that uses a different element.
• Added: Form.partial for applying functools.partial to the form function wrapped by Form.
• Fixed: Include explicit Python 3.9 support.

[2.4.0] - 2021-01-20

• Deprecated: List and tuple keyword argument types to asm.
• Deprecated: Mesh2D.mirror in favor of the more general Mesh.mirrored.
• Deprecated: Mesh.refine, Mesh.scale and Mesh.translate in favor of Mesh.refined, Mesh.scaled and Mesh.translated.
• Added: Mesh.refined, Mesh.scaled, and Mesh.translated. The new methods return a copy instead of modifying self.
• Added: Mesh.mirrored for mirroring a mesh using a normal and a point.
• Added: Functional now supports forms that evaluate to vectors or other tensors.
• Added: ElementHex0, piecewise constant element for hexahedral meshes.
• Added: FacetBasis.trace for restricting existing solutions to lower dimensional meshes on boundaries or interfaces.
• Fixed: MeshLine.refined now correctly performs adaptive refinement of one-dimensional meshes.

[2.3.0] - 2020-11-24

• Added: ElementLineP0, one-dimensional piecewise constant element.
• Added: skfem.helpers.curl now calculates the rotated gradient for two-dimensional elements.
• Added: MeshTet.init_ball for meshing a ball.
• Fixed: ElementQuad0 was not compatible with FacetBasis.

[2.2.3] - 2020-10-16

• Fixed: Remove an unnecessary dependency.

[2.2.2] - 2020-10-15

• Fixed: Make the preconditioner in TestEx32 more robust.

[2.2.1] - 2020-10-15

• Fixed: Remove tests from the PyPI distribution.

[2.2.0] - 2020-10-14

• Deprecated: L2_projection will be replaced by project.
• Deprecated: derivative will be replaced by project.
• Added: MeshTet.element_finder and MeshLine.element_finder for using InteriorBasis.interpolator.
• Added: ElementTriCR, the nonconforming Crouzeix-Raviart element for Stokes flow.
• Added: ElementTetCR, tetrahedral nonconforming Crouzeix-Raviart element.
• Added: ElementTriHermite, an extension of ElementLineHermite to triangular meshes.
• Fixed: Fix Mesh.validate for unsigned Mesh.t.

[2.1.1] - 2020-10-01

• Fixed: Further optimizations to Mesh3D.boundary_edges: tested to run on a laptop with over 10 million elements.

[2.1.0] - 2020-09-30

• Added: ElementHex2, a triquadratic hexahedral element.
• Added: MeshTri.init_circle, constructor for a circle mesh.
• Fixed: Mesh3D.boundary_edges (and, consequently, Basis.find_dofs) was slow and used lots of memory due to an exhaustive search of all edges.

[2.0.0] - 2020-08-21

• Deprecated: project will only support functions like lambda x: x[0] instead of lambda x, y, z: x in the future.
• Added: Support for complex-valued forms: BilinearForm and LinearForm now take an optional argument dtype which defaults to np.float64 but can be also np.complex64.
• Added: Dofs.__or__ and Dofs.__add__, for merging degree-of-freedom sets (i.e. Dofs objects) using | and + operators.
• Added: Dofs.drop and Dofs.keep, for further filtering the degree-of-freedom sets
• Removed: Support for old-style decorators bilinear_form, linear_form, and functional (deprecated since 1.0.0).
• Fixed: FacetBasis did not initialize with ElementQuadP.

[1.2.0] - 2020-07-07

• Added: MeshQuad._splitquads aliased as MeshQuad.to_meshtri.
• Added: Mesh.__add__, for merging meshes using + operator: duplicated nodes are joined.
• Added: ElementHexS2, a 20-node quadratic hexahedral serendipity element.
• Added: ElementLineMini, MINI-element for one-dimensional mesh.
• Fixed: Mesh3D.boundary_edges was broken in case of hexahedral meshes.
• Fixed: skfem.utils.project did not work for ElementGlobal.

[1.1.0] - 2020-05-18

• Added: ElementTetMini, MINI-element for tetrahedral mesh.
• Fixed: Mesh3D.boundary_edges incorrectly returned all edges where both nodes are on the boundary.

[1.0.0] - 2020-04-22

• Deprecated: Old-style form constructors bilinear_form, linear_form, and functional.
• Changed: Basis.interpolate returns DiscreteField objects instead of ndarray tuples.
• Changed: Basis.interpolate works now properly for vectorial and high-order elements by interpolating all components and higher order derivatives.
• Changed: Form.assemble accepts now any keyword arguments (with type DiscreteField) that are passed over to the forms.
• Changed: Renamed skfem.importers to skfem.io.
• Changed: Renamed skfem.models.helpers to skfem.helpers.
• Changed: skfem.utils.solve will now expand also the solutions of eigenvalue problems.
• Added: New-style form constructors BilinearForm, LinearForm, and Functional.
• Added: skfem.io.json for serialization of meshes to/from json-files.
• Added: ElementLinePp, p-th order one-dimensional elements.
• Added: ElementQuadP, p-th order quadrilateral elements.
• Added: ElementQuadDG for transforming quadrilateral H1 elements to DG elements.
• Added: ElementQuadBFS, Bogner-Fox-Schmit element for biharmonic problems.
• Added: ElementTriMini, MINI-element for Stokes problems.
• Added: ElementComposite for using multiple elements in one bilinear form.
• Added: ElementQuadS2, quadratic Serendipity element.
• Added: ElementLineHermite, cubic Hermite element for Euler-Bernoulli beams.
• Added: Mesh.define_boundary for defining named boundaries.
• Added: Basis.find_dofs for finding degree-of-freedom indices.
• Added: Mesh.from_basis for defining high-order meshes.
• Added: Basis.split for splitting multicomponent solutions.
• Added: MortarMapping with basic support for mortar methods in 2D.
• Added: Basis constructors now accept quadrature keyword argument for specifying a custom quadrature rule.