tag:joss.theoj.org,2005:/papers/tagged/SimulatorJournal of Open Source Software2024-03-28T11:28:09ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/45762024-03-28T11:28:09Z2024-03-29T00:01:23ZsimChef: High-quality data science simulations in Racceptedv0.0.32023-07-03 18:14:27 UTC952024-03-28 11:28:09 UTC920246156JamesDuncanGraduate Group in Biostatistics, University of California, Berkeley, United States of America0000-0003-3297-681XTiffanyTangDepartment of Statistics, University of California, Berkeley, United States of America0000-0002-8079-6867CorrineF.ElliottDepartment of Statistics, University of California, Berkeley, United States of America0000-0001-7935-9945PhilippeBoileauGraduate Group in Biostatistics, University of California, Berkeley, United States of America0000-0002-4850-2507BinYuGraduate Group in Biostatistics, University of California, Berkeley, United States of America, Department of Statistics, University of California, Berkeley, United States of America, Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, United States of America, Center for Computational Biology, University of California, Berkeley, United States of America0000-0002-8888-406010.21105/joss.06156https://doi.org/10.5281/zenodo.10845638R, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.06156.pdfsimulations, data sciencetag:joss.theoj.org,2005:Paper/48572024-03-26T15:54:37Z2024-03-27T00:01:22ZMold: a LAMMPS package to compute interfacial free energies and nucleation ratesacceptedLAMMPS 20232023-10-20 08:11:09 UTC952024-03-26 15:54:37 UTC920246083AndresR.TejedorYusuf Hamied Department of Chemistry, University of Cambridge, United Kingdom, Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0002-9437-6169IgnacioSanchez-BurgosCavendish Laboratory, Department of Physics, University of Cambridge, United Kingdom0000-0002-1160-3945EduardoSanzDepartamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0001-6474-5835CarlosVegaDepartamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0002-2417-9645FelipeJ.BlasLaboratorio de Simulacion Molecular y Quimica Computacional, CIQSO-Centro de Investigacion en Quimica Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, Spain0000-0001-9030-040XRuslanL.DavidchackSchool of Computing and Mathematical Sciences, University of Leicester, United Kingdom0000-0001-9418-5322NicodemoDi PasqualeDepartment of Chemical Engineering, Brunel University London, United Kingdom, Dipartimento di Chimica Industriale, Università di Bologna, Italy0000-0001-5676-8527JorgeRamirezDepartment of Chemical Engineering, Universidad Politécnica de Madrid, Spain0000-0002-8946-3786JorgeR.EspinosaDepartamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0001-9530-265810.21105/joss.06083https://doi.org/10.5281/zenodo.10843863C++https://joss.theoj.org/papers/10.21105/joss.06083.pdfLAMMPS, Molecular simulations, Phase Transitions, Nucleation theorytag:joss.theoj.org,2005:Paper/48192024-03-22T13:55:40Z2024-03-23T00:01:17Zcheckpoint_schedules: schedules for incremental checkpointing of adjoint simulationsacceptedv1.0.02023-09-28 08:06:01 UTC952024-03-22 13:55:40 UTC920246148DaianeI.DolciDepartment of Mathematics, Imperial College London, London, United Kingdom.0000-0002-1435-9538JamesR.MaddisonSchool of Mathematics and Maxwell Institute for Mathematical Sciences, The University of Edinburgh, United Kingdom.0000-0001-5742-4363DavidA.HamDepartment of Mathematics, Imperial College London, London, United Kingdom.0000-0001-9545-9110GuillaumePallezInria, University of Rennes, Rennes, France.0000-0001-8862-3277JulienHerrmannCNRS, IRIT, Université de Toulouse, Toulouse, France.0000-0003-4935-236810.21105/joss.06148https://doi.org/10.5281/zenodo.10817312Pythonhttps://joss.theoj.org/papers/10.21105/joss.06148.pdfCheckpointing methods, Adjoint-based gradienttag: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 theory