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Simple finite element assemblers

Project description

scikit-fem

scikit-fem is a pure 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.

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The library

  • has minimal dependencies
  • contains no compiled code
  • supports one-dimensional, triangular, quadrilateral, tetrahedral and hexahedral finite elements
  • includes special elements such as Raviart-Thomas, Nédélec, MINI, Crouzeix-Raviart, Argyris, ...

If you use the library in your research, you can cite the following article:

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

Installation

The most recent release can be installed simply by

pip install scikit-fem[all]

Remove [all] to not install the optional dependencies meshio for mesh input/output, and matplotlib for creating simple visualizations. The minimal dependencies are numpy and scipy. You can also try the library in browser through Google Colab.

Examples

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

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

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

basis = Basis(mesh, ElementTriP1())

@BilinearForm
def laplace(u, v, _):
    return dot(grad(u), grad(v))

@LinearForm
def rhs(v, _):
    return 1. * v

A = laplace.assemble(basis)
b = rhs.assemble(basis)

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

# solve the linear system
x = solve(A, b)

# plot using matplotlib
mesh.plot(x, shading='gouraud', colorbar=True).show()
# or, save to external file:
# mesh.save('output.vtk', point_data={'solution': x})

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")  # requires meshio
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 Basis, ElementTetP2

basis = Basis(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:

Getting help

If you encounter an issue you can use GitHub issue tracker. If you cannot find help from the documentation, you can use the GitHub Discussions to ask questions. 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:

import skfem; print(skfem.__version__)

Dependencies

The minimal dependencies for installing scikit-fem are numpy and scipy. In addition, many examples use matplotlib for visualization and meshio for loading/saving different mesh file formats. 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/ or snippets in the documentation may have a different license.

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 Academy of Finland (decisions nr. 324611 and 338341). 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.

Changelog

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

[7.0.1] - 2022-08-03

  • Fixed: Updated changelog was missing.

[7.0.0] - 2022-08-03

  • Changed: Removed the optimization of using DiscreteField.is_zero in the helpers to skip the evaluation of zero components in ElementComposite to improve type stability with respect to the size of the underlying numpy arrays; this is technically a backwards incompatible change and might affect self-created helper functions
  • Deprecated: FacetBasis.trace in favor of Basis.interpolator and Basis.project
  • Added: Output of Basis.interpolator supports trailing axes; can be now passed to Basis.project for (inexact) interpolation between meshes
  • Added: Renamed ElementTriRT0 to ElementTriRT1 and added alias for backwards compatibility
  • Added: Renamed ElementTetRT0 to ElementTetRT1 and added alias for backwards compatibility
  • Added: Renamed ElementQuadRT0 to ElementQuadRT1 and added alias for backwards compatibility
  • Added: ElementTriRT2, the second order Raviart-Thomas element
  • Added: ElementHexRT1, the first order Raviart-Thomas element for hexahedral meshes
  • Added: Basis.project now better supports ElementComposite[6.0.0] - 2022-03-15
  • Added: solver_iter_cg, a simple pure Python conjugate gradient solver for environments that do not have sparse solver libraries (e.g., Pyodide)
  • Added: ElementTriP2B and ElementTriP1B, new aliases for ElementTriMini and ElementTriCCR
  • Added: ElementTriP1G and ElementTriP2G, variants of ElementTriP1 and ElementTriP2 using ElementGlobal so that second derivatives are available (useful, e.g., for stabilized methods and the Stokes problem)
  • Added: Basis.plot3, a wrapper to skfem.visuals.*.plot3
  • Fixed: Calculation of size in Basis.__repr__ was slow and incorrect
  • Fixed: Subclasses of ElementHdiv did not work together with FacetBasis

[6.0.0] - 2022-03-15

  • Changed: DiscreteField is now a subclass of ndarray instead of NamedTuple and, consequently, the components of DiscreteField cannot no more be indexed inside forms like u[1] (use u.grad instead)
  • Changed: Writing w['u'] and w.u inside the form definition is now equivalent (previously w.u == w['u'].value)
  • Changed: Mesh.draw now uses matplotlib by default, calling Mesh.draw("vedo") uses vedo
  • Changed: skfem.visuals.matplotlib now uses jet as the default colormap
  • Changed: BoundaryFacetBasis is now an alias of FacetBasis instead of other way around
  • Deprecated: DiscreteField.value remains for backwards-compatibility but is now deprecated and can be dropped
  • Added: Mesh.plot, a wrapper to skfem.visuals.*.plot
  • Added: Basis.plot, a wrapper to skfem.visuals.*.plot
  • Added: Basis.refinterp now supports vectorial fields
  • Added: skfem.visuals.matplotlib.plot now has a basic quiver plot for vector fields
  • Added: Mesh.facets_around which constructs a set of facets around a subdomain
  • Added: Mesh.save and load now preserve the orientation of boundaries and interfaces
  • Added: OrientedBoundary which is a subclass of ndarray for facet index arrays with the orientation information (0 or 1 per facet) available as OrientedBoundary.ori
  • Added: FacetBasis will use the facet orientations (if present) to calculate traces and normal vectors
  • Added: skfem.visuals.matplotlib.draw will visualize the orientations if boundaries=True is given
  • Added: Mesh.facets_satisfying allows specifying the keyword argument normal for orienting the resulting interface
  • Added: FacetBasis constructor now has the keyword argument side which allows changing the side of the facet used to calculate the basis function values and gradients
  • Added: Basis.boundary method to quickly initialize the corresponding FacetBasis
  • Fixed: Improvements to backwards compatibility in asm/assemble keyword arguments
  • Fixed: Save format issue with meshio 5.3.0+
  • Fixed: CellBasis did not properly support elements argument
  • Fixed: Basis.interpolate did not properly interpolate all components of ElementComposite

[5.2.0] - 2021-12-27

  • Added: Basis.project, a more general and easy to use alternative for projection
  • Added: Basis and FacetBasis kwargs elements and facets can now be a string refering to subdomain and boundary tags
  • Added: ElementQuadRT0, lowest-order quadrilateral Raviart-Thomas element
  • Fixed: Functional returned only the first component for forms with non-scalar output

[5.1.0] - 2021-11-30

  • Added: skfem.helpers.mul for matrix multiplication
  • Added: Basis.split will now also split ElementVector into its components
  • Fixed: ElementDG was not included in the wildcard import
  • Fixed: Automatic visualization of MeshTri2 and MeshQuad2 in Jupyter notebooks raised exception

[5.0.0] - 2021-11-21

  • Changed: meshio is now an optional dependency
  • Changed: ElementComposite uses DiscreteField() to represent zero
  • Added: Support more argument types in Basis.get_dofs
  • Added: Version information in skfem.__version__
  • Added: Preserve Mesh.boundaries during uniform refinement of MeshLine1, MeshTri1 and MeshQuad1
  • Fixed: Refinement of quadratic meshes will now fall back to the refinement algorithm of first-order meshes instead of crashing
  • Fixed: Edge cases in the adaptive refine of MeshTet1 that failed to produce a valid mesh
  • Deprecated: Basis.find_dofs in favor of Basis.get_dofs
  • Deprecated: Merging DofsView objects via + and | because of surprising behavior in some edge cases

[4.0.1] - 2021-10-15

  • Fixed: MappingIsoparametric can now be pickled

[4.0.0] - 2021-09-27

  • Added: Mesh.save/Mesh.load now exports/imports Mesh.subdomains and Mesh.boundaries
  • Added: Mesh.load now optionally writes any mesh data to a list passed via the keyword argument out, e.g., out=data where data = ['point_data']
  • Added: Mesh.load (and skfem.io.meshio.from_file) now supports the additional keyword argument force_meshio_type for loading mesh files that have multiple element types written in the same file, one element type at a time
  • Added: asm will now accept a list of bases, assemble the same form using all of the bases and sum the result (useful for jump terms and mixed meshes, see Example 41)
  • Added: Mesh.with_boundaries now allows the definition of internal boundaries/interfaces via the flag boundaries_only=False
  • Added: MeshTri1DG, MeshQuad1DG, MeshHex1DG, MeshLine1DG; new mesh types for describing meshes with a discontinuous topology, e.g., periodic meshes (see Example 42)
  • Added: ElementHexDG for transforming hexahedral H1 elements to DG/L2 elements.
  • Added: ElementTriP1DG, ElementQuad1DG, ElementHex1DG, ElementLineP1DG; shorthands for ElementTriDG(ElementTriP1()) etc.
  • Added: ElementTriSkeletonP0 and ElementTriSkeletonP1 for defining Lagrange multipliers on the skeleton mesh (see Example 40)
  • Added: TrilinearForm for assembling a sparse 3-tensor, e.g., when dealing with unknown material data
  • Added: MeshTri.oriented for CCW oriented triangular meshes which can be useful for debugging or interfacing to external tools
  • Added: partial support for MeshWedge1 and ElementWedge1, the lowest order wedge mesh and element
  • Added: ElementTriP3, cubic triangular Lagrange element
  • Added: ElementTriP4, quartic triangular Lagrange element
  • Added: ElementTri15ParamPlate, 15-parameter nonconforming triangular element for plates
  • Added: ElementTriBDM1, the lowest order Brezzi-Douglas-Marini element
  • Added: Mesh.draw().show() will now visualize any mesh interactively (requires vedo)
  • Added: Adaptive refinement for MeshTet1
  • Fixed: MappingIsoparametric is now about 2x faster for large meshes thanks to additional caching
  • Fixed: MeshHex2.save did not work properly
  • Fixed: Mesh.load ignores unparseable cell_sets inserted by meshio in MSH 4.1
  • Changed: Mesh string representation is now more informative
  • Changed: Form.assemble no more allows keyword arguments with list or dict type: from now on only DiscreteField or 1d/2d ndarray objects are allowed and 1d ndarray is passed automatically to Basis.interpolate for convenience
  • Changed: MeshLine is now a function which initializes MeshLine1 and not an alias to MeshLine1
  • Changed: FacetBasis is now a shorthand for BoundaryFacetBasis and no longer initializes InteriorFacetBasis or MortarFacetBasis if the keyword argument side is passed to the constructor
  • Removed: the deprecated Mesh.define_boundary method

[3.2.0] - 2021-08-02

  • Added: ElementTriCCR and ElementTetCCR, conforming Crouzeix-Raviart finite elements
  • Fixed: Mesh.mirrored returned a wrong mesh when a point other than the origin was used
  • Fixed: MeshLine constructor accepted only numpy arrays and not plain Python lists
  • Fixed: Mesh.element_finder (and CellBasis.probes, CellBasis.interpolator) was not working properly for a small number of elements (<5) or a large number of input points (>1000)
  • Fixed: MeshTet and MeshTri.element_finder are now more robust against degenerate elements
  • Fixed: Mesh.element_finder (and CellBasis.probes, CellBasis.interpolator) raises exception if the query point is outside of the domain

[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
  • Removed: skfem.utils.L2_projection
  • Removed: skfem.utils.derivative
  • 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 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.

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