Software Bookmarks

Location: http://people.sc.fsu.edu/~jburkardt/html/software_bookmarks.html

  1. AUTO, software by Eusebius Doedel for continuation and bifurcation problems in ordinary differential equations: http://indy.cs.concordia.ca/auto/
  2. CFD Python, "Twelve Steps to Navier Stokes", a collection of iPython notebooks by Lorena Barba that teach a beginner how to use Python to solve a series of increasingly involved problems in computational fluid dynamics: http://lorenabarba.com/blog/cfd-python-12-steps-to-navier-stokes/
  3. CFD Python, "ME702: Computational Fluid Dynamics", a set of 28 lectures by Lorena Barba, hosted on YouTube, which offer the theoretical background for the CFD Python notebooks: https://www.youtube.com/playlist?list=PL30F4C5ABCE62CB61
  4. CMCL: Courant Mathematics and Computing Laboratory Software. http://www.cims.nyu.edu/cmcl/software.html .
  5. MATLAB Cody Coursework, https://www.mathworks.com/academia/cody-coursework.html .
  6. CSPARSE sparse matrix software by Timothy Davis: http://www.cise.ufl.edu/research/sparse/CSparse
  7. CSPARSE videos by Timothy Davis: http://www.youtube.com/playlist?list=PL5EvFKC69QIyRLFuxWRnH6hIw6e1-bBXB ;
  8. DEAL.II, a finite element library, using quadrilaterals in 2D and hexahedrons in 3D: https://www.dealii.org/ ;
  9. DEAL.II videos (and finite elements and more) by Wolfgang Bangerth: http://www.math.tamu.edu/~bangerth/videos.html ;
  10. DIR3, Delaunay Incremental Refinement in 3D, a 3D meshing tool: http://www.math.cmu.edu/~arand/DIR3/ ;
  11. DISLIN, a plotting library: http://www.mps.mpg.de/dislin/ ;
  12. Featflow, a Computational Fluid Dynamics (CFD) Benchmarking Project: http://www.featflow.de/en/benchmarks.html ;
  13. FENICS, a collection of software for the automatic solution of differential equations using the finite element method: http://fenicsproject.org/ ;
  14. FREEFEM++, a PDE solver for multiphysics nonlinear systems in 2D and 3D, using the finite element method, with triangular or tetrahedral elements: http://www.freefem.org/ ;
  15. Globus: http://www.globus.org,
  16. GMSH, a 3D finite element mesh generator: http://geuz.org/gmsh/ ;
  17. GSL, the Gnu Scientific Library: http://www.gnu.org/software/gsl/ ;
  18. GSOC, the Google Summer of Code: https://developers.google.com/open-source/gsoc/
  19. HSL, the Harwell Subroutine Library: http://www.hsl.rl.ac.uk/ ;
  20. IFISS, a MATLAB toolbox for solving Poisson, convection-diffusion, Stokes, and Navier-Stokes PDE's: http://www.cs.umd.edu/~elman/ifiss/index.html ;
  21. ImageJ, a very useful image manipulation package: http://rsbweb.nih.gov/ij/ ;
  22. Insight, the home page for "Insight Through Computing", by Charles Van Loan and Daisy Fan, http://www.cs.cornell.edu/insight ;
  23. Intrepid, part of the Trilinos package, a library for compatible discretization of Partial Differential Equations: http://trilinos.org/packages/intrepid/ ;
  24. Kaggle, the home of data science competitions: https://www.kaggle.com/ ;
  25. LAMMPS, a molecular dynamics code: http://lammps.sandia.gov/ ;
  26. LIBMESH, a library for the numerical simulation of partial differential equations on arbitrary unstructured meshes in 1/2/3D with a variety of finite element types: http://libmesh.sourceforge.net/ ;
  27. LIS, a library of linear iterative solvers, with preconditioning, multiple precision, C/Fortran interface, OpenMP/MPI interface: http://www.ssisc.org/lis/index.en.html;
  28. MEDIT, an OpenGL-based scientific visualization tool, by Pascal Frey: http://www.ann.jussieu.fr/frey/software.html;
  29. MESH2D, Automatic 2D Mesh Generation in MATLAB: http://www.mathworks.com/matlabcentral/fileexchange/25555-mesh2d-automatic-mesh-generation ;
  30. Mesh and grid generation web page of Robert Schneiders: http://www.robertschneiders.de/meshgeneration/meshgeneration.html ;
  31. MeshLab, software for processing and editing unstructured 3D triangular surface meshes: http://meshlab.sourceforge.net/ ;
  32. MFEM, a scalable C++ library for finite element methods: http://mfem.org/ ;
  33. NaSt3DGP, a parallel 3D flow solver, using finite differences, from the Michael Griebel group at the University of Bonn: http://wissrech.iam.uni-bonn.de/research/projects/NaSt3DGP/index.htm ;
  34. nbviewer, which can display Jupyter notebooks through a browser: https://nbviewer.jupyter.org/ ;
  35. NetCDF software for dataset storage: http://www.unidata.ucar.edu/software/netcdf/ ;
  36. NETGEN, an automatic 3D mesh generator: http://www.hpfem.jku.at/netgen/ ;
  37. NETLIB: http://www.netlib.org,
  38. Ngram Viewer: http://ngrams.googlelabs.com ;
  39. NS2D, a MATLAB 2D flow solver, using triangular finite elements, from Jeff Borggaard at Virginia Tech: http://jborggaard.github.io/ns2d/ ;
  40. Octave, a Gnu program that is a numerical computing environment: https://www.gnu.org/software/octave/ ;
  41. OpenACC: http://www.openacc.org,
  42. OpenFOAM, an open source computational fluid dynamics toolbox for 3D flow including heat transfer, chemical reactions and turbulence: http://www.openfoam.com ;
  43. Paraview, a 3D graphics program: http://www.paraview.org/ ;
  44. Pencil, an easy-to-use drawing code: http://pencilcode.net/edit/myprogram ;
  45. Plot.ly, a system for creating plots online: https://plot.ly/plot ;
  46. PLTMG, (Piecewise Linear Triangle MultiGrid solver for Finite Elements), by Randolph Bank, http://ccom.ucsd.edu/~reb/ ;
  47. SciLab, a numerical computing environment: http://www.scilab.org/ ;
  48. SciPy, a numerical computing environment: http://www.scipy.org/ ;
  49. Scratch, a programming language. https://scratch.mit.edu/ ;
  50. Slatec, a numerical library: http://www.netlib.org/slatec/index.html ;
  51. SLURM: https://slurm.schedmd.com/,
  52. Socrative: www.socrative.com ;
  53. the SuiteSparse libraries by Timothy Davis of University of Florida: http://www.cise.ufl.edu/research/sparse/ ;
  54. SuperLU, a direct solver for large sparse linear systems of equations, including sequential, shared memory, and distributed memory versions: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ ;
  55. TASMANIAN, libraries for high dimensional integration, interpolation, and calibration, including a sparse grid library: http://tasmanian.ornl.gov/ ;
  56. Tensorflow, an open-source software library for machine intelligence: https://www.tensorflow.org ;
  57. TETGEN, a quality 3D mesh generator and Delaunay triangulator: http://wias-berlin.de/software/tetgen/ ;
  58. TOPCODER, a site that offers coding challenges and cash rewards: https://www.topcoder.com/ ;
  59. Trilinos, an ensemble of solvers for large scale multi-physics problems: http://trilinos.sandia.gov/ ;
  60. TSPLIB, the traveling salesman problem library: http://comopt.ifi.uni-heidelberg.de/software/TSPLIB95/ ;
  61. VirtualBox allows you to run a "guest operating system". In particular, a Windows user can set up a Linux environment: https://www.virtualbox.org/ ;
  62. VisIt, visualization tool: https://wci.llnl.gov/codes/visit/ ;
  63. VisItUsers, the VisIt user community web site: www.visitusers.org/ ;
  64. Wolfram demonstrations project: http://demonstrations.wolfram.com/
  65. XSEDE training slides https://www.psc.edu/index.php/xsede-hpc-series-all-workshops

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Last revised on 27 January 2017.