355 lines
19 KiB
HTML
355 lines
19 KiB
HTML
<h1 id="awesome-scientific-computing-awesome">Awesome Scientific
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Computing <a href="https://awesome.re"><img
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src="https://awesome.re/badge.svg" alt="Awesome" /></a></h1>
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<p><a
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href="#readme"><img src="https://nschloe.github.io/awesome-scientific-computing/sunglasses.svg" align="right" width="30%"></a></p>
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<blockquote>
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<p>Useful resources for scientific computing and numerical analysis.</p>
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</blockquote>
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<p>Scientific computing and numerical analysis are research fields that
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aim to provide methods for solving large-scale problems from various
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areas of science with the help of computers. Typical problems are
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ordinary and partial differential equations (ODEs, PDEs), their
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discretizations, and the solution of linear algebra problems arising
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from them.</p>
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<h2 id="contents">Contents</h2>
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<ul>
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<li><a href="#basic-linear-algebra">Basic linear algebra</a></li>
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<li><a href="#multi-purpose-toolkits">Multi-purpose toolkits</a></li>
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<li><a href="#finite-elements">Finite Elements</a></li>
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<li><a href="#meshing">Meshing</a></li>
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<li><a href="#data-formats">Data formats</a></li>
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<li><a href="#sparse-linear-solvers">Sparse linear solvers</a></li>
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<li><a href="#visualization">Visualization</a></li>
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<li><a href="#other-libraries-and-tools">Other libraries and
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tools</a></li>
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<li><a href="#community">Community</a></li>
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</ul>
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<h2 id="basic-linear-algebra">Basic linear algebra</h2>
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<ul>
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<li><a href="https://netlib.org/blas/">BLAS</a> - Standard building
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blocks for performing basic vector and matrix operations. (Fortran,
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public domain, <a
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href="https://github.com/Reference-LAPACK/lapack/tree/master/BLAS">GitHub</a>)</li>
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<li><a href="https://www.openblas.net">OpenBLAS</a> - Optimized BLAS
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library based on GotoBLAS2. (C and Assembly, BSD, <a
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href="https://github.com/OpenMathLib/OpenBLAS">GitHub</a>)</li>
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<li><a href="https://github.com/flame/blis">BLIS</a> - High-performance
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BLAS-like dense linear algebra libraries. (C, BSD, GitHub)</li>
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<li><a href="https://netlib.org/lapack/">LAPACK</a> - Routines for
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solving systems of linear equations, linear least-squares, eigenvalue
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problems, etc. (Fortran, BSD, <a
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href="https://github.com/Reference-LAPACK/lapack">GitHub</a>)</li>
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<li><a
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href="https://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen</a> -
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C++ template library for linear algebra. (C++, MPL 2, <a
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href="https://gitlab.com/libeigen/eigen">GitLab</a>)</li>
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<li><a href="https://ginkgo-project.github.io/">Ginkgo</a> -
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High-performance manycore linear algebra library, focus on sparse
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systems. (C++, BSD, <a
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href="https://github.com/ginkgo-project/ginkgo">GitHub</a>)</li>
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<li><a href="https://bitbucket.org/blaze-lib/blaze">blaze</a> -
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High-performance C++ math library for dense and sparse arithmetic. (C++,
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BSD, Bitbucket)</li>
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</ul>
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<h2 id="multi-purpose-toolkits">Multi-purpose toolkits</h2>
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<ul>
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<li><a href="https://www.mcs.anl.gov/petsc/">PETSc</a> - Parallel
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solution of scientific applications modeled by PDEs. (C, 2-clause BSD,
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<a href="https://gitlab.com/petsc/petsc">GitLab</a>)</li>
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<li><a href="https://www.dune-project.org">DUNE Numerics</a> - Toolbox
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for solving PDEs with grid-based methods. (C++, GPL 2, <a
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href="https://gitlab.dune-project.org/core/">GitLab</a>)</li>
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<li><a href="https://scipy.org">SciPy</a> - Python modules for
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statistics, optimization, integration, linear algebra, etc. (Python,
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mostly BSD, <a href="https://github.com/scipy/scipy/">GitHub</a>)</li>
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<li><a href="https://numpy.org/">NumPy</a> - Fundamental package needed
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for scientific computing with Python. (Python, BSD, <a
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href="https://github.com/numpy/numpy">GitHub</a>)</li>
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<li><a href="https://diffeq.sciml.ai/">DifferentialEquations.jl</a> -
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Toolbox for solving different types of differential equations
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numerically. (Julia, MIT, <a
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href="https://github.com/SciML/DifferentialEquations.jl">GitHub</a>)</li>
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</ul>
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<h2 id="finite-elements">Finite Elements</h2>
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<ul>
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<li><a href="https://fenicsproject.org">FEniCS</a> - Computing platform
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for solving PDEs in Python and C++. (C++/Python, LGPL 3, <a
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href="https://github.com/FEniCS">GitHub</a>/<a
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href="https://bitbucket.org/fenics-project/">Bitbucket</a>)</li>
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<li><a href="https://libmesh.github.io">libMesh</a> - Framework for the
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numerical simulation of PDEs using unstructured discretizations. (C++,
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LGPL 2.1, <a href="https://github.com/libMesh/libmesh">GitHub</a>)</li>
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<li><a href="https://dealii.org">deal.II</a> - Software library
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supporting the creation of finite element codes. (C++, LGPL 2.1, <a
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href="https://github.com/dealii/dealii">GitHub</a>)</li>
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<li><a href="https://ngsolve.org">Netgen/NGSolve</a> - High performance
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multiphysics finite element software. (C++, LGPL 2.1, <a
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href="https://github.com/NGSolve/netgen">GitHub</a>)</li>
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<li><a href="https://www.firedrakeproject.org">Firedrake</a> - Automated
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system for the solution of PDEs using the finite element method.
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(Python, LGPL 3, <a
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href="https://github.com/firedrakeproject/firedrake">GitHub</a>)</li>
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<li><a href="https://mooseframework.inl.gov/">MOOSE</a> - Multiphysics
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Object Oriented Simulation Environment. (C++, LGPL 2.1, <a
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href="https://github.com/idaholab/moose">GitHub</a>)</li>
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<li><a href="https://mfem.org">MFEM</a> - Free, lightweight, scalable
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C++ library for finite element methods. (C++, BSD-3-Clause, <a
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href="https://github.com/mfem/mfem">GitHub</a>)</li>
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<li><a href="https://sfepy.org">SfePy</a> - Simple Finite Elements in
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Python. (Python, BSD, <a
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href="https://github.com/sfepy/sfepy">GitHub</a>)</li>
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<li><a href="https://freefem.org">FreeFEM</a> - High level
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multiphysics-multimesh finite element language. (C++, LGPL, <a
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href="https://github.com/FreeFem">GitHub</a>)</li>
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<li><a
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href="https://libceed.readthedocs.io/en/latest/index.html">libceed</a> -
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Code for Efficient Extensible Discretizations. (C, 2-clause BSD, <a
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href="https://github.com/CEED/libCEED">GitHub</a>)</li>
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<li><a href="https://github.com/kinnala/scikit-fem">scikit-fem</a> -
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Simple finite element assemblers. (Python, BSD/GPL, GitHub)</li>
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</ul>
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<h2 id="meshing">Meshing</h2>
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<h3 id="triangular-and-tetrahedral-meshing">Triangular and tetrahedral
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meshing</h3>
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<ul>
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<li><a href="https://gmsh.info">Gmsh</a> - Three-dimensional finite
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element mesh generator with pre- and post-processing facilities. (C++,
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GPL, <a href="https://gitlab.onelab.info/gmsh/gmsh">GitLab</a>)</li>
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<li><a href="https://github.com/nschloe/pygmsh">pygmsh</a> - Python
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interface for Gmsh. (Python, GPL 3, GitHub)</li>
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<li><a href="https://mathema.tician.de/software/meshpy/">MeshPy</a> -
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Quality triangular and tetrahedral mesh generation. (Python, MIT, <a
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href="https://github.com/inducer/meshpy">GitHub</a>)</li>
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<li><a href="https://www.cgal.org">CGAL</a> - Algorithms for
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computational geometry. (C++, mixed LGPL/GPL, <a
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href="https://github.com/CGAL/cgal">GitHub</a>)</li>
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<li><a href="https://github.com/meshpro/pygalmesh">pygalmesh</a> -
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Python interface for CGAL’s 3D meshing capabilities. (Python, GPL 3,
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GitHub)</li>
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<li><a
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href="https://www.wias-berlin.de/software/index.jsp?id=TetGen">TetGen</a>
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- Quality tetrahedral mesh generator and 3D Delaunay triangulator. (C++,
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AGPLv3)</li>
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<li><a href="https://www.cs.cmu.edu/~quake/triangle.html">Triangle</a> -
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Two-dimensional quality mesh generator and Delaunay triangulator. (C,
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<em>nonfree software</em>)</li>
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<li><a href="http://persson.berkeley.edu/distmesh/">distmesh</a> -
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Simple generator for unstructured triangular and tetrahedral meshes.
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(MATLAB, GPL 3)</li>
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<li><a href="https://trimesh.org">trimesh</a> - Loading and using
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triangular meshes with an emphasis on watertight surfaces. (Python, MIT,
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<a href="https://github.com/mikedh/trimesh">GitHub</a>)</li>
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<li><a href="https://github.com/meshpro/dmsh">dmsh</a> - Simple
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generator for unstructured triangular meshes, inspired by distmesh.
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(Python, proprietary, GitHub)</li>
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<li><a href="https://yixin-hu.github.io/tetwild.pdf">TetWild</a> -
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Generate tetrahedral meshes for triangular surface meshes. (C++, GPL 3,
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<a href="https://github.com/Yixin-Hu/TetWild">GitHub</a>)</li>
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<li><a
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href="https://cims.nyu.edu/gcl/papers/2019-TriWild.pdf">TriWild</a> -
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Robust triangulation with curve constraints. (C++, MPL 2, <a
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href="https://github.com/wildmeshing/TriWild">GitHub</a>)</li>
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<li><a href="https://arxiv.org/abs/1908.03581">fTetWild</a> - Same as
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TetWild, but faster. (C++, MPL 2, <a
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href="https://github.com/wildmeshing/fTetWild">GitHub</a>)</li>
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<li><a href="https://github.com/krober10nd/SeismicMesh">SeismicMesh</a>
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- Parallel 2D/3D triangle/tetrahedral mesh generation with sliver
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removal. (Python and C++, GPL 3, GitHub)</li>
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</ul>
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<h3 id="quadrilateral-and-hexahedral-meshing">Quadrilateral and
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hexahedral meshing</h3>
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<ul>
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<li><a
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href="https://stanford.edu/~jingweih/papers/quadriflow/">QuadriFlow</a>
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- Scalable and robust quadrangulation from triangulation. (C++, BSD, <a
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href="https://github.com/hjwdzh/QuadriFlow">GitHub</a>)</li>
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</ul>
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<h3 id="mesh-tools">Mesh tools</h3>
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<ul>
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<li><a href="https://github.com/nschloe/meshio">meshio</a> - I/O for
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various mesh formats, file conversion. (Python, MIT, GitHub)</li>
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<li><a href="https://sigma.mcs.anl.gov/moab-library/">MOAB</a> -
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Representing and evaluating mesh data. (C++, mostly LGPL 3, <a
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href="https://bitbucket.org/fathomteam/moab/">Bitbucket</a>)</li>
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<li><a href="https://github.com/meshpro/optimesh">optimesh</a> -
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Triangular mesh smoothing. (Python, proprietary, GitHub)</li>
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<li><a href="https://www.pmp-library.org/">pmp-library</a> - Polygon
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mesh processing library. (C++, MIT with Employer Disclaimer, <a
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href="https://github.com/pmp-library/pmp-library/">GitHub</a>)</li>
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<li><a href="https://www.mmgtools.org/">Mmg</a> - Robust, open-source
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& multidisciplinary software for remeshing. (C, LGPL 3, <a
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href="https://github.com/MmgTools/mmg">GitHub</a>)</li>
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<li><a href="https://github.com/meshpro/meshplex">meshplex</a> - Fast
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tools for simplex meshes. (Python, proprietary, GitHub)</li>
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</ul>
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<h2 id="data-formats">Data formats</h2>
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<ul>
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<li><a href="https://www.unidata.ucar.edu/software/netcdf/">NetCDF</a> -
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Software libraries and data formats for array-oriented scientific data.
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(C/C++/Fortran/Java/Python, <a
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href="https://www.unidata.ucar.edu/software/netcdf/copyright.html">custom
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open-source license</a>, <a
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href="https://github.com/Unidata/netcdf-c/">GitHub</a>)</li>
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<li><a href="https://www.hdfgroup.org/solutions/hdf5/">HDF5</a> - Data
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model, library, and file format for storing and managing data.
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(C/Fortran, BSD, <a
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href="https://github.com/HDFGroup/hdf5">GitHub</a>)</li>
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<li><a href="https://xdmf.org/index.php/Main_Page">XDMF</a> - eXtensible
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Data Model and Format for data from High Performance Computing codes.
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(C++, <a href="https://gitlab.kitware.com/xdmf/xdmf">GitLab</a>)</li>
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<li><a href="https://zarr.readthedocs.io/en/stable/">Zarr</a> - Format
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for the storage of chunked, compressed, N-dimensional arrays. (Python,
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MIT, <a
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href="https://github.com/zarr-developers/zarr-python">GitHub</a>)</li>
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</ul>
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<h2 id="sparse-linear-solvers">Sparse linear solvers</h2>
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<ul>
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<li><a
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href="https://portal.nersc.gov/project/sparse/superlu/">SuperLU</a> -
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Direct solution of large, sparse, nonsymmetric systems of linear
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equations. (C, mostly BSD, <a
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href="https://github.com/xiaoyeli/superlu">GitHub</a>)</li>
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<li><a href="https://pyamg.readthedocs.io/en/latest/">PyAMG</a> -
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Algebraic Multigrid Solvers in Python. (Python, MIT, <a
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href="https://github.com/pyamg/pyamg">GitHub</a>)</li>
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<li><a
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href="https://computing.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods">hypre</a>
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- Library of high-performance preconditioners and solvers. (C, Apache
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2.0/MIT, <a href="https://github.com/hypre-space/hypre">GitHub</a>)</li>
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</ul>
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<h2 id="visualization">Visualization</h2>
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<ul>
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<li><a href="https://www.paraview.org">ParaView</a> - Multi-platform
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data analysis and visualization application based on VTK. (C++, BSD, <a
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href="https://gitlab.kitware.com/paraview/paraview">GitLab</a>)</li>
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<li><a href="https://vtk.org/">VTK</a> - Process images and create 3D
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computer graphics. (C++, BSD, <a
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href="https://gitlab.kitware.com/vtk/vtk">GitLab</a>)</li>
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<li><a href="https://docs.enthought.com/mayavi/mayavi/">Mayavi</a> - 3D
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scientific data visualization and plotting in Python. (Python, BSD, <a
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href="https://github.com/enthought/mayavi">GitHub</a>)</li>
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<li><a href="https://polyscope.run/">Polyscope</a> - Viewer and user
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interface for 3D geometry processing. (C++, MIT, <a
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href="https://github.com/nmwsharp/polyscope">GitHub</a>)</li>
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<li><a href="https://docs.pyvista.org/">PyVista</a> - 3D plotting and
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mesh analysis through a streamlined interface for VTK. (Python, MIT, <a
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href="https://github.com/pyvista/pyvista">GitHub</a>)</li>
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<li><a href="https://vedo.embl.es">vedo</a> - Library for scientific
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analysis and visualization of 3D objects based on VTK. (Python, MIT, <a
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href="https://github.com/marcomusy/vedo">GitHub</a>)</li>
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<li><a href="https://yt-project.org/">yt</a> - Toolkit for analysis and
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visualization of volumetric data. (Python, BSD, <a
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href="https://github.com/yt-project/yt">GitHub</a>)</li>
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<li><a href="https://f3d.app/">F3D</a> - Cross-platform, fast, and
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minimalist 3D viewer with scientific visualization tools. (C++, BSD, <a
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href="https://github.com/f3d-app/f3d">GitHub</a>)</li>
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<li><a href="https://topology-tool-kit.github.io/">TTK</a> - Topological
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data analysis and visualization. (C++/Python, BSD, <a
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href="https://github.com/topology-tool-kit/ttk">GitHub</a>)</li>
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<li><a
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href="https://github.com/ABRG-Models/morphologica">morphologica</a> -
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Header-only, modern OpenGL code to visualize numerical simulations at
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runtime. (C++, Apache 2.0, GitHub)</li>
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</ul>
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<h2 id="other-libraries-and-tools">Other libraries and tools</h2>
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<ul>
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<li><a href="http://www.fftw.org">FFTW</a> - Discrete Fourier transforms
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in one or more dimensions, of arbitrary input size, real and complex.
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(C, GPL2, <a href="https://github.com/FFTW/fftw3">GitHub</a>)</li>
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<li><a href="http://www.qhull.org">Qhull</a> - Convex hull, Delaunay
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triangulation, Voronoi diagram, halfspace intersection about a point,
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etc. (C/C++, <a href="http://www.qhull.org/COPYING.txt">custom open
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source license</a>, <a
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href="https://github.com/qhull/qhull/">GitHub</a>)</li>
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<li><a href="https://www.gnu.org/software/gsl/">GSL</a> - Random number
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generators, special functions, and least-squares fitting etc. (C/C++,
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GPL 3, <a
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href="https://savannah.gnu.org/projects/gsl">Savannah</a>)</li>
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<li><a href="https://www.openfoam.com">OpenFOAM</a> - Free, open source
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CFD (computational fluid dynamics) software. (C++, GPL 3, <a
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href="https://github.com/OpenFOAM/OpenFOAM-dev">GitHub</a>)</li>
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<li><a href="https://github.com/sigma-py/quadpy">quadpy</a> - Numerical
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integration (quadrature, cubature) in Python. (Python, proprietary,
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GitHub)</li>
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<li><a href="https://www.ctcms.nist.gov/fipy/">FiPy</a> - Finite-volume
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PDE solver. (Python, <a
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href="https://www.nist.gov/open/copyright-fair-use-and-licensing-statements-srd-data-software-and-technical-series-publications">custom
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open-source license</a>, <a
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href="https://github.com/usnistgov/fipy">GitHub</a>)</li>
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<li><a href="https://github.com/sigma-py/accupy">accupy</a> - Accurate
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sums and dot products for Python. (Python, GPL 3, GitHub)</li>
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<li><a href="https://slepc.upv.es">SLEPc</a> - Scalable Library for
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Eigenvalue Problem Computations. (C, 2-clause BSD, <a
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href="https://gitlab.com/slepc/slepc">GitLab</a>)</li>
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<li><a href="https://www.chebfun.org/">Chebfun</a> - Computing with
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functions to about 15-digit accuracy. (MATLAB, BSD, <a
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href="https://github.com/chebfun/chebfun">GitHub</a>)</li>
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<li><a href="https://pymor.org/">pyMOR</a> - Model Order Reduction with
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Python. (Python, 2-clause BSD, <a
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href="https://github.com/pymor/pymor/">GitHub</a>)</li>
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<li><a href="https://www.cvxpy.org/">cvxpy</a> - Modeling language for
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convex optimization problems. (Python, Apache 2.0, <a
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href="https://github.com/cvxpy/cvxpy">GitHub</a>)</li>
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<li><a
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href="https://pywavelets.readthedocs.io/en/latest/">PyWavelets</a> -
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Wavelet transforms in Python. (Python, MIT, <a
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href="https://github.com/PyWavelets/pywt">GitHub</a>)</li>
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<li><a href="https://www-user.tu-chemnitz.de/~potts/nfft/">NFFT</a> -
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Nonequispaced fast Fourier transform. (C/MATLAB, GPL 2, <a
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href="https://github.com/NFFT/nfft">GitHub</a>)</li>
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<li><a href="https://precice.org/">preCICE</a> - Coupling library for
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partitioned multi-physics simulations (FSI, CHT, and more). (C++, LGPL
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3, <a href="https://github.com/precice/">GitHub</a>)</li>
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<li><a href="https://github.com/sigma-py/orthopy">orthopy</a> - Compute
|
||
orthogonal polynomials efficiently. (Python, proprietary, GitHub)</li>
|
||
<li><a href="https://pygam.readthedocs.io/en/latest/">pyGAM</a> -
|
||
Generalized Additive Models in Python. (Python, Apache 2.0, <a
|
||
href="https://github.com/dswah/pyGAM">GitHub</a>)</li>
|
||
<li><a href="https://dedalus-project.org/">Dedalus</a> - Solve partial
|
||
differential equations with spectral methods. (Python, GPL 3, <a
|
||
href="https://github.com/DedalusProject/dedalus">GitHub</a>)</li>
|
||
<li><a href="https://esa.github.io/pygmo/">PyGMO</a> - Massively
|
||
parallel optimization. (Python/C++, MPL 2, <a
|
||
href="https://github.com/esa/pygmo2">GitHub</a>)</li>
|
||
<li><a href="https://shenfun.readthedocs.io/en/latest/">shenfun</a> -
|
||
High-performance Python library for the spectral Galerkin method.
|
||
(Python, BSD-2, <a
|
||
href="https://github.com/spectralDNS/shenfun">GitHub</a>)</li>
|
||
<li><a href="https://github.com/mathLab/PyDMD">PyDMD</a> - Dynamic Mode
|
||
Decomposition (DMD) in Python. (Python, MIT, GitHub)</li>
|
||
<li><a href="https://github.com/hpddm/hpddm">HPDDM</a> -
|
||
High-performance unified framework for domain decomposition methods.
|
||
(C++, LGPL 3, GitHub)</li>
|
||
</ul>
|
||
<h2 id="community">Community</h2>
|
||
<ul>
|
||
<li><a href="https://scicomp.stackexchange.com/">SciComp
|
||
StackExchange</a> - Computational Science on the StackExchange
|
||
network.</li>
|
||
<li><a
|
||
href="https://www.math.colostate.edu/~bangerth/videos.html">Wolfgang
|
||
Bangerth’s video class</a> - MATH 676: Finite element methods in
|
||
scientific computing.</li>
|
||
<li><a href="https://nhigham.com/">Nick Higham’s blog</a> - Mostly on
|
||
MATLAB, general computing advice.</li>
|
||
<li><a href="https://people.maths.ox.ac.uk/trefethen/videos.html">Nick
|
||
Trefethen’s Video Lectures</a> - 36 video lectures on approximation
|
||
theory/practice and scientific computing.</li>
|
||
<li><a href="https://www.johndcook.com/blog/">John D. Cook’s blog</a> -
|
||
Feats of scientific computing.</li>
|
||
<li><a href="https://netlib.org/utk/people/JackDongarra/la-sw.html">Jack
|
||
Dongarra’s software list</a> - List of freely available software for the
|
||
solution of linear algebra problems.</li>
|
||
<li><a href="https://netlib.org/na-digest-html/">NA Digest</a> -
|
||
Collection of articles on topics related to numerical analysis and those
|
||
who practice it.</li>
|
||
<li><a href="https://bsky.app/profile/gabrielpeyre.bsky.social">Gabriel
|
||
Peyré on Bluesky</a> - One post a day on computational mathematics.</li>
|
||
<li><a href="https://discord.com/invite/hnTJ5MRX2Y">Discord: Numerical
|
||
Software</a> - Discord messaging server on numerical software.</li>
|
||
</ul>
|
||
<p><a
|
||
href="https://github.com/nschloe/awesome-scientific-computing">scientificcomputing.md
|
||
Github</a></p>
|