tag:joss.theoj.org,2005:/papers/tagged/SimulationJournal of Open Source Software2024-03-05T10:10:26ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/44002024-03-05T10:10:26Z2024-03-06T00:00:49ZWorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Modelsacceptedv0.4.22023-04-13 20:15:11 UTC952024-03-05 10:10:26 UTC920245772PierluigiCrescenziGran Sasso Science Institute, L’Aquila, Italy, COATI, INRIA d’Université Côte d’Azur, Sophia Antipolis, France0000-0001-8789-3195EmanueleNataleCOATI, INRIA d’Université Côte d’Azur, Sophia Antipolis, France0000-0002-8755-3892AuroraRossiCOATI, INRIA d’Université Côte d’Azur, Sophia Antipolis, France0009-0001-3302-0468PauloBrunoSerafimGran Sasso Science Institute, L’Aquila, Italy0000-0002-5980-814910.21105/joss.05772https://doi.org/10.5281/zenodo.10684579Juliahttps://joss.theoj.org/papers/10.21105/joss.05772.pdfIntegrated Assessment Model, Modeling and Simulation, Scientific Computingtag:joss.theoj.org,2005:Paper/46922024-03-01T08:15:12Z2024-03-05T12:14:06ZΦ-ML: Intuitive Scientific Computing with Dimension Types for Jax, PyTorch, TensorFlow & NumPyacceptedv1.0.02023-08-11 11:05:07 UTC952024-03-01 08:15:12 UTC920246171PhilippHollSchool of Computation, Information and Technology, Technical University of Munich, Germany0000-0001-9246-5195NilsThuereySchool of Computation, Information and Technology, Technical University of Munich, Germany0000-0001-6647-891010.21105/joss.06171https://doi.org/10.6084/m9.figshare.25282300Python, C++https://joss.theoj.org/papers/10.21105/joss.06171.pdfMachine Learning, Jax, TensorFlow, PyTorch, NumPy, Differentiable simulations, Sparse linear systems, Preconditionerstag:joss.theoj.org,2005:Paper/51272024-02-29T21:34:54Z2024-03-01T00:00:22ZCoSApp: a Python library to create, simulate and design complex systems.acceptedv0.15.32024-01-23 12:22:22 UTC942024-02-29 21:34:54 UTC920246292ÉtienneLacSafran Tech, Digital Sciences & Technologies Department, France0000-0002-6964-0044GuySpiegeleertwiinIT, France0009-0005-9828-0550AdrienDelsalletwiinIT, France0009-0001-8126-4045FrédéricCollonvalWebScIT, France0009-0000-3579-3424Duc-TrungLêQuantStack, France0009-0000-0415-8399MathiasMalandainInria centre at Rennes University, France0000-0001-9740-491410.21105/joss.06292https://doi.org/10.5281/zenodo.10722403Python, C#, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.06292.pdfMultidisciplinary Design Analysis and Optimization, System designtag:joss.theoj.org,2005:Paper/48402024-02-28T01:15:09Z2024-02-29T00:01:19Zscida: scalable analysis for scientific big dataacceptedv0.2.32023-10-09 11:11:58 UTC942024-02-28 01:15:09 UTC920246064ChrisByrohlHeidelberg University, Institute for Theoretical Astronomy, Albert-Ueberle-Str. 2, 69120 Heideberg, Germany0000-0002-0885-8090DylanNelsonHeidelberg University, Institute for Theoretical Astronomy, Albert-Ueberle-Str. 2, 69120 Heideberg, Germany0000-0001-8421-589010.21105/joss.06064https://doi.org/10.5281/zenodo.10681463Pythonhttps://joss.theoj.org/papers/10.21105/joss.06064.pdfsimulations, i/o, point cloudstag:joss.theoj.org,2005:Paper/42702024-02-22T16:46:16Z2024-02-23T00:01:10ZAkantu: an HPC finite-element library for contact and dynamic fracture simulationsacceptedv4.0.12023-02-28 19:10:56 UTC942024-02-22 16:46:16 UTC920245253NicolasRichartCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland0000-0002-1463-4405GuillaumeAnciauxCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland0000-0002-9624-5621EmilGallyamovCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland0000-0002-2970-0890LucasFrérotCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland, Department of Microsystems Engineering, University of Freiburg, Germany, Institut Jean le Rond d'Alembert, CNRS UMR 7190, Sorbonne Université, France0000-0002-4138-1052DavidKammerCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland, Institute for Building Materials, ETH Zurich, Switzerland0000-0003-3782-9368MohitPundirCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland, Institute for Building Materials, ETH Zurich, Switzerland0000-0001-7244-7416MarcoVocialtaCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, SwitzerlandAureliaCubaRamosCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, SwitzerlandMauroCorradoCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland, Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, ItalyPhilipMüllerInstitute for Building Materials, ETH Zurich, SwitzerlandFabianBarrasCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland, The Njord Centre Department of Physics, Department of Geosciences, University of Oslo, Norway0000-0003-1109-0200ShenghanZhangCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland, The Hong Kong University of Science and Technology, Department of Civil and Environmental Engineering0000-0002-4327-9115RoxaneFerryCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland0000-0003-1881-6596ShadDurusselCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland0009-0001-6036-168XJean-FrançoisMolinariCivil Engineering Institute, École Polytechnique Fédérale de Lausanne, Switzerland0000-0002-1728-184410.21105/joss.05253https://doi.org/10.5281/zenodo.10668768C, C++, Pythonhttps://joss.theoj.org/papers/10.21105/joss.05253.pdfcohesive element, contact, fracture, pythontag:joss.theoj.org,2005:Paper/47052024-02-19T16:19:20Z2024-02-20T13:50:07Zkinisi: Bayesian analysis of mass transport from molecular dynamics simulationsaccepted0.7.02023-08-16 15:02:57 UTC942024-02-19 16:19:20 UTC920245984AndrewR.McCluskeyCentre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom, European Spallation Source ERIC, Ole Maaløes vej 3, 2200 København N, Denmark0000-0003-3381-5911AlexanderG.SquiresSchool of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, The Faraday Institution, Quad One, Harwell Science and Innovation Campus, Didcot, OX11 0RA, United Kingdom0000-0001-6967-3690JoshDunnCentre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom0000-0003-2659-0806SamuelW.ColesDepartment of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom, The Faraday Institution, Quad One, Harwell Science and Innovation Campus, Didcot, OX11 0RA, United Kingdom0000-0001-9722-5676BenjaminJ.MorganDepartment of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom, The Faraday Institution, Quad One, Harwell Science and Innovation Campus, Didcot, OX11 0RA, United Kingdom0000-0002-3056-823310.21105/joss.05984https://doi.org/10.5281/zenodo.10651128Pythonhttps://joss.theoj.org/papers/10.21105/joss.05984.pdfmolecular dynamics, diffusion, covariance matrix, Bayesian regressiontag:joss.theoj.org,2005:Paper/48972024-02-14T14:57:13Z2024-02-19T16:23:56ZPyTASER: Simulating transient absorption spectroscopy (TAS) for crystals from first principlesacceptedv2.2.02023-10-24 15:23:57 UTC942024-02-14 14:57:13 UTC920245999SavyasanchiAggarwalThomas Young Centre and Department of Materials, Imperial College London, London, United Kingdom, Thomas Young Centre and Department of Chemistry, University College London, London, United Kingdom0009-0007-7128-3465SeánR.KavanaghThomas Young Centre and Department of Materials, Imperial College London, London, United Kingdom, Thomas Young Centre and Department of Chemistry, University College London, London, United Kingdom0000-0003-4577-9647YoungWonWooThomas Young Centre and Department of Materials, Imperial College London, London, United Kingdom, Department of Materials Science and Engineering, Yonsei University, Seoul, KoreaLucasG.VergaThomas Young Centre and Department of Materials, Imperial College London, London, United Kingdom0000-0002-7453-238XAlexM.GanoseDepartment of Chemistry, Imperial College London, London, United Kingdom0000-0002-4486-3321AronWalshThomas Young Centre and Department of Materials, Imperial College London, London, United Kingdom0000-0001-5460-703310.21105/joss.05999https://doi.org/10.5281/zenodo.10634762Pythonhttps://joss.theoj.org/papers/10.21105/joss.05999.pdfmaterials science, first-principles, optics, differential-absorption, spectroscopy, density functional theorytag:joss.theoj.org,2005:Paper/47172024-02-07T21:21:42Z2024-02-14T14:53:20ZCLEAVING: a LAMMPS package to compute surface free energiesacceptedv1.0.02023-08-24 09:40:12 UTC942024-02-07 21:21:42 UTC920245886NicodemoDi PasqualeDepartment of Chemical Engineering, Brunel University London, United Kingdom, (Current affiliation) Department of Industrial Chemistry, University of Bologna, Italy0000-0001-5676-8527RuslanDavidchackDepartment of Mathematics, University of Leicester, United Kingdom0000-0001-9418-5322LorenzoRovigattiDepartment of Physics, Sapienza University of Rome, Italy, CNR-ISC UoS Sapienza, Rome, Italy0000-0001-5017-282910.21105/joss.05886https://doi.org/10.5281/zenodo.10567702C++, Python, Fortranhttps://joss.theoj.org/papers/10.21105/joss.05886.pdfLAMMPS, Molecular simulations, Phase Transitionstag:joss.theoj.org,2005:Paper/42112024-01-29T16:38:15Z2024-01-30T08:20:19ZChitin Builder: a VMD tool for the generation of structures of chitin molecular crystals for atomistic simulationsaccepted1.02023-02-15 16:12:05 UTC932024-01-29 16:38:15 UTC920245771DavidMalaspinaInstitut de Ciencia de Materials de Barcelona (ICMAB-CSIC),Campus UAB Bellaterra, Barcelona, Spain0000-0002-5420-9534JordiFaraudoInstitut de Ciencia de Materials de Barcelona (ICMAB-CSIC),Campus UAB Bellaterra, Barcelona, Spain0000-0002-6315-499310.21105/joss.05771https://doi.org/10.5281/zenodo.3274725Tcl, Rich Text Formathttps://joss.theoj.org/papers/10.21105/joss.05771.pdfVMD, chitin polymer structure, molecular dynamics, tcltag:joss.theoj.org,2005:Paper/45912024-01-28T18:34:03Z2024-01-29T08:05:01Zmatscipy: materials science at the atomic scale with Pythonaccepted0.8.02023-07-10 11:58:56 UTC932024-01-28 18:34:03 UTC920245668PetrGrigorevAix-Marseille Université, CNRS, CINaM UMR 7325, Campus de Luminy, 13288 Marseille, France0000-0002-6409-9092LucasFrérotDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany0000-0002-4138-1052FraserBirksWarwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom0009-0008-9117-0393AdrienGolaDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany, Institute for Applied Materials, Karlsruhe Institute of Technology, Engelbert-Arnold-Straße 4, 76131 Karlsruhe, Germany0000-0002-5102-1931JacekGolebiowskiDepartment of Materials, Imperial College London, London SW7 2AZ, United Kingdom0000-0001-8053-8318JanGrießerDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany0000-0003-2149-6730JohannesL.HörmannDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany, Cluster of Excellence livMatS, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany0000-0001-5867-695XAndreasKlemenzFraunhofer IWM, MikroTribologie Centrum µTC, Wöhlerstraße 11, 79108 Freiburg, Germany0000-0001-5677-5639GianpietroMorasFraunhofer IWM, MikroTribologie Centrum µTC, Wöhlerstraße 11, 79108 Freiburg, Germany0000-0002-4623-2881WolframG.NöhringDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany0000-0003-4203-755XJonasA.OldenstaedtDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany0000-0002-7475-3019PunitPatelWarwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United KingdomThomasReichenbachFraunhofer IWM, MikroTribologie Centrum µTC, Wöhlerstraße 11, 79108 Freiburg, Germany0000-0001-7477-6248ThomasRockeWarwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom0000-0002-4612-9112LakshmiShenoyWarwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom0000-0001-5760-3345MichaelWalterCluster of Excellence livMatS, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany0000-0001-6679-2491SimonWengertFritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany0000-0002-8008-1482LeiZhangEngineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands0000-0003-4414-7111JamesR.KermodeWarwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom0000-0001-6755-6271LarsPastewkaDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany, Cluster of Excellence livMatS, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany0000-0001-8351-733610.21105/joss.05668https://doi.org/10.5281/zenodo.10564956C++, C, Meson, Python, Rubyhttps://joss.theoj.org/papers/10.21105/joss.05668.pdfMaterial Science, Atomistic simulations