tag:joss.theoj.org,2005:/papers/tagged/FEniCSJournal of Open Source Software2024-02-02T16:32:04ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/45712024-02-02T16:32:04Z2024-02-03T00:00:40ZFEniCS-arclength: A numerical continuation package in FEniCS for nonlinear problems in solid mechanicsacceptedv0.1.02023-06-29 15:19:07 UTC942024-02-02 16:32:04 UTC920245727PeerasaitPrachasereeDepartment of Mechanical Engineering, Boston University, Massachusetts, the United States of America0009-0000-3325-1410SaeedMohammadzadehDepartment of Systems Engineering, Boston University, Massachusetts, the United States of America0000-0001-9879-044XBerkinDortdivanliogluDepartment of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, the United States of America, Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, the United States of America0000-0001-7105-1452EmmaLejeuneDepartment of Mechanical Engineering, Boston University, Massachusetts, the United States of America0000-0001-8099-346810.21105/joss.05727https://doi.org/10.5281/zenodo.10563095Pythonhttps://joss.theoj.org/papers/10.21105/joss.05727.pdfFEniCS, Finite Element Analysis, Solid Mechanicstag:joss.theoj.org,2005:Paper/45862024-01-16T15:49:05Z2024-01-19T17:33:56ZAmbit – A FEniCS-based cardiovascular multi-physics solveraccepteddevelopment2023-07-07 14:32:49 UTC932024-01-16 15:49:05 UTC920245744MarcHirschvogelDepartment of Biomedical Engineering, School of Biomedical Engineering & Imaging Sciences, King's College London, London, United Kingdom, MOX, Dipartimento di Matematica, Politecnico di Milano, Milan, Italy0000-0002-4575-912010.21105/joss.05744https://doi.org/10.5281/zenodo.10501275Python, Gnuplothttps://joss.theoj.org/papers/10.21105/joss.05744.pdfcardiovascular mechanics, finite strain solid mechanics, nonlinear elastodynamics, fluid dynamics, 0D lumped models, fluid-solid interaction, fsi, multi-physics couplingtag:joss.theoj.org,2005:Paper/45362023-10-19T10:06:55Z2023-10-24T01:50:14ZSMART: Spatial Modeling Algorithms for Reactions and Transportacceptedv2.1.12023-06-09 16:19:04 UTC902023-10-19 10:06:55 UTC820235580JustinG.LaughlinDepartment of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, United States of America0000-0001-8229-9760JørgenS.DokkenDepartment of Numerical Analysis and Scientific Computing, Simula Research Laboratory, Oslo, Norway0000-0001-6489-8858HenrikN.t.FinsbergDepartment of Computational Physiology, Simula Research Laboratory, Oslo, Norway0000-0003-3766-2393EmmetA.FrancisDepartment of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, United States of America0000-0001-6070-805XChristopherT.LeeDepartment of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, United States of America0000-0002-0670-2308MarieE.RognesDepartment of Numerical Analysis and Scientific Computing, Simula Research Laboratory, Oslo, Norway0000-0002-6872-3710PadminiRangamaniDepartment of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, United States of America0000-0001-5953-434710.21105/joss.05580https://doi.org/10.5281/zenodo.10019519Pythonhttps://joss.theoj.org/papers/10.21105/joss.05580.pdfFEniCS, reactions, transport, biophysics, cellular processestag:joss.theoj.org,2005:Paper/38562023-01-09T15:28:55Z2023-01-10T00:01:03Zsimcardems: A FEniCS-based cardiac electro-mechanics solveracceptedv2022.3.02022-09-07 12:28:58 UTC812023-01-09 15:28:55 UTC820234753HenrikNicolay TopnesFinsbergSimula Research Laboratory, Oslo, Norway0000-0003-3766-2393IlsbethGerarda Mariavan HerckSimula Research Laboratory, Oslo, Norway0000-0003-0728-3958CécileDaversin-CattySimula Research Laboratory, Oslo, NorwayHermenegildArevaloSimula Research Laboratory, Oslo, NorwaySamuelWallSimula Research Laboratory, Oslo, Norway10.21105/joss.04753https://doi.org/10.5281/zenodo.7503468Pythonhttps://joss.theoj.org/papers/10.21105/joss.04753.pdfFEniCS, Cardiac Electro-Mechanics, Finite Element Method, Computational Biologytag:joss.theoj.org,2005:Paper/21352021-03-21T07:05:59Z2021-03-22T05:32:38ZBVPy: A FEniCS-based Python package to ease the expression and study of boundary value problems in Biology.acceptedv1.0.02020-10-28 15:59:22 UTC592021-03-21 07:05:59 UTC620212831FlorianGaconLaboratoire Reproduction et Développement des Plantes, Université de Lyon, Ecole Normale Supérieure de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA; 46, allée d'Italie, 69364 LYON Cedex 07, France.0000-0002-1873-5246ChristopheGodinLaboratoire Reproduction et Développement des Plantes, Université de Lyon, Ecole Normale Supérieure de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA; 46, allée d'Italie, 69364 LYON Cedex 07, France.0000-0002-1202-8460OlivierAliLaboratoire Reproduction et Développement des Plantes, Université de Lyon, Ecole Normale Supérieure de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA; 46, allée d'Italie, 69364 LYON Cedex 07, France.0000-0001-7671-722510.21105/joss.02831https://doi.org/10.5281/zenodo.4590758Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.02831.pdfBiomechanics, Finite Element Method, Boundary Value Problem, FEniCS, Condatag:joss.theoj.org,2005:Paper/14722020-06-16T11:18:37Z2021-02-15T11:31:02ZturtleFSI: A Robust and Monolithic FEniCS-based Fluid-Structure Interaction Solveracceptedv1.32020-02-06 12:12:13 UTC502020-06-16 11:18:37 UTC520202089AslakW.BergersenDepartment of Computational Physiology, Simula Research Laboratory, Fornebu, Norway0000-0001-5063-3680AndreasSlyngstadDepartment of Computational Physiology, Simula Research Laboratory, Fornebu, NorwaySebastianGjertsenDepartment of Computational Physiology, Simula Research Laboratory, Fornebu, NorwayAlbanSoucheDepartment of Computational Physiology, Simula Research Laboratory, Fornebu, Norway0000-0001-7547-7979KristianValen-SendstadDepartment of Computational Physiology, Simula Research Laboratory, Fornebu, Norway0000-0002-2907-017110.21105/joss.02089https://doi.org/10.5281/zenodo.3895443Pythonhttps://joss.theoj.org/papers/10.21105/joss.02089.pdffluid-structure interaction, FEniCS, finite-elements, numerical methodstag:joss.theoj.org,2005:Paper/10132019-09-24T16:43:16Z2021-02-15T11:32:09Zpulse: A python package based on FEniCS for solving problems in cardiac mechanicsaccepted0.1.12019-05-25 04:39:00 UTC412019-09-24 16:43:16 UTC420191539HenrikNicolay TopnesFinsbergSimula Research Laboratory, Oslo, Norway0000-0003-3766-239310.21105/joss.01539https://doi.org/10.5281/zenodo.3376811Pythonhttps://joss.theoj.org/papers/10.21105/joss.01539.pdfFEniCS, Cardiac Mechanics, Finite Element Method, Continuum Mechanicstag:joss.theoj.org,2005:Paper/7662019-06-18T11:45:46Z2021-02-15T11:32:42Zdolfin-adjoint 2018.1: automated adjoints for FEniCS and Firedrakeaccepted2018.12018-12-31 16:39:19 UTC382019-06-18 11:45:46 UTC420191292SebastianK.MituschSimula Research Laboratory0000-0002-8888-6568SimonW.FunkeSimula Research Laboratory0000-0003-4709-8415JørgenS.DokkenSimula Research Laboratory0000-0001-6489-885810.21105/joss.01292https://doi.org/10.5281/zenodo.3247690Python, GLSLhttps://joss.theoj.org/papers/10.21105/joss.01292.pdffinite element method, optimization, adjoint, gradients, partial differential equationstag:joss.theoj.org,2005:Paper/8482019-03-27T18:15:23Z2021-02-15T11:32:33ZOcellaris: a DG FEM solver for free-surface flowsaccepted2019.0.12019-02-06 20:15:41 UTC352019-03-27 18:15:23 UTC420191239TormodLandetDepartment of Mathematics, University of Oslo0000-0001-5070-805610.21105/joss.01239https://doi.org/10.5281/zenodo.2601988Python, GLSL, C++https://joss.theoj.org/papers/10.21105/joss.01239.pdfDG FEM, Navier--Stokes, free-surface flow, multi-phase flow, incompressible, FEniCStag:joss.theoj.org,2005:Paper/7142018-12-18T16:22:52Z2021-02-15T11:32:50ZArtery.FE: An implementation of the 1D blood flow equations in FEniCSacceptedv1.02018-11-01 15:03:05 UTC322018-12-18 16:22:52 UTC320181107SyverD.AgdesteinDepartment of Computational Physiology, Simula Research Laboratory0000-0002-1589-2916KristianValen-SendstadDepartment of Computational Physiology, Simula Research LaboratoryAlexandraK.DiemDepartment of Computational Physiology, Simula Research Laboratory0000-0003-1719-194210.21105/joss.01107https://doi.org/10.5281/zenodo.2383815Pythonhttps://joss.theoj.org/papers/10.21105/joss.01107.pdfpython, fenics, blood flow, pde, finite element