Acknowledgements#
Zoomy builds on open-source software and on published numerical methods. We
thank their authors. The list below is rendered from
references/third_party.bib,
the one place where every component Zoomy uses is recorded with its citation.
If you publish results computed with Zoomy, please also cite the components
your run used. If we missed one, please
open an issue or add it to the file.
Nina Aguillon, Sophie Hörnschemeyer, and Jacques Sainte-Marie. Barotropic-baroclinic splitting for multilayer shallow water models with exchanges. 2026. Preprint, HAL hal-05483700. arXiv:2601.16709, doi:10.48550/arXiv.2601.16709.
James Ahrens, Berk Geveci, and Charles Law. ParaView: an end-user tool for large-data visualization. In Visualization Handbook, pages 717–731. Elsevier, 2005. URL: Kitware/ParaView, doi:10.1016/B978-012387582-2/50038-1.
Martin S. Alnæs, Anders Logg, Kristian B. Ølgaard, Marie E. Rognes, and Garth N. Wells. Unified form language: a domain-specific language for weak formulations of partial differential equations. ACM Transactions on Mathematical Software, 40(2):9:1–9:37, 2014. URL: FEniCS/ufl, doi:10.1145/2566630.
Uri M. Ascher, Steven J. Ruuth, and Raymond J. Spiteri. Implicit-explicit Runge-Kutta methods for time-dependent partial differential equations. Applied Numerical Mathematics, 25(2–3):151–167, 1997. doi:10.1016/S0168-9274(97)00056-1.
Emmanuel Audusse, François Bouchut, Marie-Odile Bristeau, Rupert Klein, and Benoît Perthame. A fast and stable well-balanced scheme with hydrostatic reconstruction for shallow water flows. SIAM Journal on Scientific Computing, 25(6):2050–2065, 2004. doi:10.1137/S1064827503431090.
Emmanuel Audusse and Marie-Odile Bristeau. A well-balanced positivity preserving “second-order” scheme for shallow water flows on unstructured meshes. Journal of Computational Physics, 206(1):311–333, 2005. doi:10.1016/j.jcp.2004.12.016.
Satish Balay, Shrirang Abhyankar, Mark F. Adams, Steven Benson, Jed Brown, Peter Brune, Kris Buschelman, Emil Constantinescu, Lisandro Dalcin, Alp Dener, Victor Eijkhout, Jacob Faibussowitsch, William D. Gropp, Václav Hapla, Tobin Isaac, Pierre Jolivet, Dmitry Karpeev, Dinesh Kaushik, Matthew G. Knepley, Fande Kong, Scott Kruger, Dave A. May, Lois Curfman McInnes, Richard Tran Mills, Lawrence Mitchell, Todd Munson, Jose E. Roman, Karl Rupp, Patrick Sanan, Jason Sarich, Barry F. Smith, Hansol Suh, Stefano Zampini, Hong Zhang, Hong Zhang, and Junchao Zhang. PETSc/TAO users manual. Technical Report ANL-21/39 - Revision 3.24, Argonne National Laboratory, 2025. URL: petsc/petsc, doi:10.2172/2998643.
Igor A. Baratta, Joseph P. Dean, Jørgen S. Dokken, Michal Habera, Jack S. Hale, Chris N. Richardson, Marie E. Rognes, Matthew W. Scroggs, Nathan Sime, and Garth N. Wells. DOLFINx: the next generation FEniCS problem solving environment. Preprint, Zenodo, 2023. URL: FEniCS/dolfinx, doi:10.5281/zenodo.10447666.
Timothy Barth and Dennis Jespersen. The design and application of upwind schemes on unstructured meshes. In 27th Aerospace Sciences Meeting. American Institute of Aeronautics and Astronautics, 1989. AIAA Paper 89-0366. doi:10.2514/6.1989-366.
Nathan Bell, Luke N. Olson, and Jacob Schroder. PyAMG: algebraic multigrid solvers in Python. Journal of Open Source Software, 7(72):4142, 2022. URL: pyamg/pyamg, doi:10.21105/joss.04142.
James Bradbury, Roy Frostig, Peter Hawkins, Matthew James Johnson, Yash Katariya, Chris Leary, Dougal Maclaurin, George Necula, Adam Paszke, Jake VanderPlas, Skye Wanderman-Milne, and Qiao Zhang. JAX: composable transformations of Python+NumPy programs. 2018. URL: jax-ml/jax.
Alexandre Joel Chorin. Numerical solution of the Navier-Stokes equations. Mathematics of Computation, 22(104):745–762, 1968. doi:10.1090/S0025-5718-1968-0242392-2.
Gerasimos Chourdakis, Kyle Davis, Benjamin Rodenberg, Miriam Schulte, Frédéric Simonis, Benjamin Uekermann, Georg Abrams, Hans-Joachim Bungartz, Lucia Cheung Yau, Ishaan Desai, Konrad Eder, Richard Hertrich, Florian Lindner, Alexander Rusch, Dmytro Sashko, David Schneider, Amin Totounferoush, Dominik Volland, Peter Vollmer, and Oguz Ziya Koseomur. preCICE v2: a sustainable and user-friendly coupling library [version 2; peer review: 2 approved]. Open Research Europe, 2022. URL: precice/precice, doi:10.12688/openreseurope.14445.2.
S. Clain, S. Diot, and R. Loubère. A high-order finite volume method for systems of conservation laws—Multi-dimensional Optimal Order Detection (MOOD). Journal of Computational Physics, 230(10):4028–4050, 2011. doi:10.1016/j.jcp.2011.02.026.
Laurent Courty. Pyswashes: Python wrapper for SWASHES. lrntct/pyswashes, 2026. URL: lrntct/pyswashes (visited on 2026-10-09).
Casper da Costa-Luis, Stephen Karl Larroque, Kyle Altendorf, and others. Tqdm: a fast, extensible progress bar for Python and CLI. 2026. URL: tqdm/tqdm, doi:10.5281/zenodo.595120.
Gianni Dal Maso, Philippe G. LeFloch, and François Murat. Definition and weak stability of nonconservative products. Journal de Mathématiques Pures et Appliquées, 74(6):483–548, 1995.
Lisandro Dalcin and Yao-Lung L. Fang. Mpi4py: status update after 12 years of development. Computing in Science & Engineering, 23(4):47–54, 2021. URL: mpi4py/mpi4py, doi:10.1109/MCSE.2021.3083216.
Lisandro D. Dalcin, Rodrigo R. Paz, Pablo A. Kler, and Alejandro Cosimo. Parallel distributed computing using Python. Advances in Water Resources, 34(9):1124–1139, 2011. URL: petsc/petsc, doi:10.1016/j.advwatres.2011.04.013.
S. F. Davis. Simplified second-order Godunov-type methods. SIAM Journal on Scientific and Statistical Computing, 9(3):445–473, 1988. doi:10.1137/0909030.
DeepMind, Igor Babuschkin, Kate Baumli, Alison Bell, Surya Bhupatiraju, Jake Bruce, Peter Buchlovsky, David Budden, Trevor Cai, Aidan Clark, Ivo Danihelka, Antoine Dedieu, Claudio Fantacci, Jonathan Godwin, Chris Jones, Ross Hemsley, Tom Hennigan, Matteo Hessel, Shaobo Hou, Steven Kapturowski, Thomas Keck, Iurii Kemaev, Michael King, Markus Kunesch, Lena Martens, Hamza Merzic, Vladimir Mikulik, Tamara Norman, George Papamakarios, John Quan, Roman Ring, Francisco Ruiz, Alvaro Sanchez, Laurent Sartran, Rosalia Schneider, Eren Sezener, Stephen Spencer, Srivatsan Srinivasan, Miloš Stanojević, Wojciech Stokowiec, Luyu Wang, Guangyao Zhou, and Fabio Viola. The DeepMind JAX Ecosystem. 2020. Requested citation for Optax, google-deepmind/optax. URL: google-deepmind.
Olivier Delestre, Carine Lucas, Pierre-Antoine Ksinant, Frédéric Darboux, Christian Laguerre, T.-N.-Tuoi Vo, François James, and Stéphane Cordier. SWASHES: a compilation of shallow water analytic solutions for hydraulic and environmental studies. International Journal for Numerical Methods in Fluids, 72(3):269–300, 2013. URL: https://sourcesup.renater.fr/projects/swashes/, doi:10.1002/fld.3741.
Delgan. Loguru: Python logging made (stupidly) simple. Delgan/loguru, 2026. URL: Delgan/loguru (visited on 2026-10-09).
The Pyodide development team. Pyodide/pyodide. August 2021. URL: pyodide/pyodide, doi:10.5281/zenodo.5156931.
J. W. Elder. The dispersion of marked fluid in turbulent shear flow. Journal of Fluid Mechanics, 5(4):544–560, 1959. doi:10.1017/S0022112059000374.
C. Escalante, E. D. Fernández-Nieto, T. Morales de Luna, and M. J. Castro. An efficient two-layer non-hydrostatic approach for dispersive water waves. Journal of Scientific Computing, 79(1):273–320, 2019. doi:10.1007/s10915-018-0849-9.
C. Escalante, T. Morales de Luna, F. Cantero-Chinchilla, and O. Castro-Orgaz. Vertically averaged and moment equations: new derivation, efficient numerical solution and comparison with other physical approximations for modeling non-hydrostatic free surface flows. Journal of Computational Physics, 504:112882, 2024. doi:10.1016/j.jcp.2024.112882.
Robert D. Falgout and Ulrike Meier Yang. Hypre: a library of high performance preconditioners. In Computational Science – ICCS 2002, volume 2331 of Lecture Notes in Computer Science, 632–641. Springer, 2002. URL: hypre-space/hypre, doi:10.1007/3-540-47789-6_66.
Enrique D. Fernández-Nieto, Martin Parisot, Yohan Penel, and Jacques Sainte-Marie. A hierarchy of dispersive layer-averaged approximations of Euler equations for free surface flows. Communications in Mathematical Sciences, 16(5):1169–1202, 2018. doi:10.4310/CMS.2018.v16.n5.a1.
John I. Finnie and Roland W. Jeppson. Solving turbulent flows using finite elements. Journal of Hydraulic Engineering, 117(11):1513–1530, 1991. doi:10.1061/(ASCE)0733-9429(1991)117:11(1513).
Edgar Gabriel, Graham E. Fagg, George Bosilca, Thara Angskun, Jack J. Dongarra, Jeffrey M. Squyres, Vishal Sahay, Prabhanjan Kambadur, Brian Barrett, Andrew Lumsdaine, Ralph H. Castain, David J. Daniel, Richard L. Graham, and Timothy S. Woodall. Open MPI: goals, concept, and design of a next generation MPI implementation. In Recent Advances in Parallel Virtual Machine and Message Passing Interface, volume 3241 of Lecture Notes in Computer Science, 97–104. Springer, 2004. URL: open-mpi/ompi, doi:10.1007/978-3-540-30218-6_19.
Christophe Geuzaine and Jean-François Remacle. Gmsh: a 3-D finite element mesh generator with built-in pre- and post-processing facilities. International Journal for Numerical Methods in Engineering, 79(11):1309–1331, 2009. URL: https://gitlab.onelab.info/gmsh/gmsh, doi:10.1002/nme.2579.
Jonathan Godwin, Thomas Keck, Peter Battaglia, Victor Bapst, Thomas Kipf, Yujia Li, Kimberly Stachenfeld, Petar Veličković, and Alvaro Sanchez-Gonzalez. Jraph: A library for graph neural networks in jax. 2020. URL: deepmind/jraph.
Gaël Guennebaud, Benoît Jacob, and others. Eigen v3. https://eigen.tuxfamily.org, 2010. URL: libeigen/eigen.
David A. Ham, Paul H. J. Kelly, Lawrence Mitchell, Colin J. Cotter, Robert C. Kirby, Koki Sagiyama, Nacime Bouziani, Sophia Vorderwuelbecke, Thomas J. Gregory, Jack Betteridge, Daniel R. Shapero, Reuben W. Nixon-Hill, Connor J. Ward, Patrick E. Farrell, Pablo D. Brubeck, India Marsden, Thomas H. Gibson, Miklós Homolya, Tianjiao Sun, Andrew T. T. McRae, Fabio Luporini, Alastair Gregory, Michael Lange, Simon W. Funke, Florian Rathgeber, Gheorghe-Teodor Bercea, and Graham R. Markall. Firedrake User Manual. Imperial College London and University of Oxford and Baylor University and University of Washington, first edition edition, 5 2023. URL: firedrakeproject/firedrake, doi:10.25561/104839.
Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, Julian Taylor, Sebastian Berg, Nathaniel J. Smith, Robert Kern, Matti Picus, Stephan Hoyer, Marten H. van Kerkwijk, Matthew Brett, Allan Haldane, Jaime Fernández del Río, Mark Wiebe, Pearu Peterson, Pierre Gérard-Marchant, Kevin Sheppard, Tyler Reddy, Warren Weckesser, Hameer Abbasi, Christoph Gohlke, and Travis E. Oliphant. Array programming with NumPy. Nature, 585(7825):357–362, 2020. URL: numpy/numpy, doi:10.1038/s41586-020-2649-2.
Amiram Harten, Peter D. Lax, and Bram van Leer. On upstream differencing and Godunov-type schemes for hyperbolic conservation laws. SIAM Review, 25(1):35–61, 1983. doi:10.1137/1025002.
Van Emden Henson and Ulrike Meier Yang. BoomerAMG: a parallel algebraic multigrid solver and preconditioner. Applied Numerical Mathematics, 41(1):155–177, 2002. doi:10.1016/S0168-9274(01)00115-5.
John D. Hunter. Matplotlib: a 2D graphics environment. Computing in Science & Engineering, 9(3):90–95, 2007. URL: matplotlib/matplotlib, doi:10.1109/MCSE.2007.55.
Dion Häfner and Filippo Vicentini. Mpi4jax: zero-copy MPI communication of JAX arrays. Journal of Open Source Software, 6(65):3419, 2021. URL: mpi4jax/mpi4jax, doi:10.21105/joss.03419.
George Karypis and Vipin Kumar. A fast and high quality multilevel scheme for partitioning irregular graphs. SIAM Journal on Scientific Computing, 20(1):359–392, 1998. URL: KarypisLab/METIS, doi:10.1137/S1064827595287997.
Patrick Kidger and Cristian Garcia. Equinox: neural networks in JAX via callable PyTrees and filtered transformations. Differentiable Programming workshop at Neural Information Processing Systems 2021, 2021. URL: patrick-kidger/equinox, arXiv:2111.00254, doi:10.48550/arXiv.2111.00254.
Thomas Kluyver, Benjamin Ragan-Kelley, Fernando Pérez, Brian Granger, Matthias Bussonnier, Jonathan Frederic, Kyle Kelley, Jessica Hamrick, Jason Grout, Sylvain Corlay, Paul Ivanov, Damián Avila, Safia Abdalla, Carol Willing, and Jupyter Development Team. Jupyter notebooks – a publishing format for reproducible computational workflows. In Positioning and Power in Academic Publishing: Players, Agents and Agendas, 87–90. IOS Press, 2016. URL: jupyter/notebook, doi:10.3233/978-1-61499-649-1-87.
Andreas Klöckner. PyMetis: a Python wrapper for METIS. inducer/pymetis, 2026. URL: inducer/pymetis (visited on 2026-10-09).
Matthew G. Knepley and Dmitry A. Karpeev. Mesh algorithms for PDE with Sieve I: mesh distribution. Scientific Programming, 17(3):215–230, 2009. doi:10.1155/2009/948613.
Stuart Knightley. JSZip: create, read and edit .zip files with JavaScript. Stuk/jszip, 2026. URL: Stuk/jszip (visited on 2026-10-09).
Julian Koellermeier and Marvin Rominger. Analysis and numerical simulation of hyperbolic shallow water moment equations. Communications in Computational Physics, 28(3):1038–1084, 2020. doi:10.4208/cicp.OA-2019-0065.
Julia Kowalski and Manuel Torrilhon. Moment approximations and model cascades for shallow flow. Communications in Computational Physics, 25(3):669–702, 2019. doi:10.4208/cicp.OA-2017-0263.
Nicolas Kruchten, Andrew Seier, and Chris Parmer. An interactive, open-source, and browser-based graphing library for Python. 2024. URL: plotly/plotly.py, doi:10.5281/zenodo.14503524.
Alexander Kurganov and Guergana Petrova. A second-order well-balanced positivity preserving central-upwind scheme for the Saint-Venant system. Communications in Mathematical Sciences, 5(1):133–160, 2007. doi:10.4310/CMS.2007.v5.n1.a6.
Gregory M. Kurtzer, Vanessa Sochat, and Michael W. Bauer. Singularity: scientific containers for mobility of compute. PLOS ONE, 12(5):e0177459, 2017. URL: apptainer/apptainer, doi:10.1371/journal.pone.0177459.
Michael Lange, Lawrence Mitchell, Matthew G. Knepley, and Gerard J. Gorman. Efficient mesh management in Firedrake using PETSc-DMPlex. SIAM Journal on Scientific Computing, 38(5):S143–S155, 2016. doi:10.1137/15M1026092.
Randall J. LeVeque. Finite Volume Methods for Hyperbolic Problems. Cambridge University Press, 2002. doi:10.1017/CBO9780511791253.
Yi Liu, Xiantao Fan, and Jian-Xun Wang. JAX-AMG: a GPU-accelerated differentiable sparse linear solver library for JAX. SoftwareX, 35:102966, 2026. URL: jx-wang-s-group/JAX-AMG, doi:10.1016/j.softx.2026.102966.
Niels Lohmann. JSON for modern C++. nlohmann/json, 2025. Vendored in Zoomy as library/zoomy_dmplex/nlohmann/json.hpp (MIT licence). URL: nlohmann/json.
Stephen McDowell. Exhale: automatic C++ library API documentation generator using Doxygen, Sphinx, and Breathe. svenevs/exhale, 2026. URL: svenevs/exhale (visited on 2026-10-09).
Aaron Meurer, Christopher P. Smith, Mateusz Paprocki, Ondřej Čertík, Sergey B. Kirpichev, Matthew Rocklin, AMiT Kumar, Sergiu Ivanov, Jason K. Moore, Sartaj Singh, Thilina Rathnayake, Sean Vig, Brian E. Granger, Richard P. Muller, Francesco Bonazzi, Harsh Gupta, Shivam Vats, Fredrik Johansson, Fabian Pedregosa, Matthew J. Curry, Andy R. Terrel, Štěpán Roučka, Ashutosh Saboo, Isuru Fernando, Sumith Kulal, Robert Cimrman, and Anthony Scopatz. SymPy: symbolic computing in Python. PeerJ Computer Science, 3:e103, 2017. URL: sympy/sympy, doi:10.7717/peerj-cs.103.
Maxim Naumov, Marat Arsaev, Patrice Castonguay, Jonathan Cohen, Julien Demouth, Joe Eaton, Simon Layton, Nikolay Markovskiy, István Reguly, Nikolai Sakharnykh, Vijay Sellappan, and Robert Strzodka. AmgX: a library for GPU accelerated algebraic multigrid and preconditioned iterative methods. SIAM Journal on Scientific Computing, 37(5):S602–S626, 2015. URL: NVIDIA/AMGX, doi:10.1137/140980260.
Carlos Parés. Numerical methods for nonconservative hyperbolic systems: a theoretical framework. SIAM Journal on Numerical Analysis, 44(1):300–321, 2006. doi:10.1137/050628052.
Carlos Parés and Manuel Castro. On the well-balance property of Roe's method for nonconservative hyperbolic systems. applications to shallow-water systems. ESAIM: Mathematical Modelling and Numerical Analysis, 38(5):821–852, 2004. doi:10.1051/m2an:2004041.
Stéphane Popinet and others. Basilisk. http://basilisk.fr, 2026. URL: http://basilisk.fr (visited on 2026-10-09).
Sebastián Ramírez. FastAPI. fastapi/fastapi, 2026. URL: fastapi/fastapi (visited on 2026-10-09).
Ashok K. Rastogi and Wolfgang Rodi. Predictions of heat and mass transfer in open channels. Journal of the Hydraulics Division, 104(3):397–420, 1978. doi:10.1061/JYCEAJ.0004962.
P. L. Roe. Approximate Riemann solvers, parameter vectors, and difference schemes. Journal of Computational Physics, 43(2):357–372, 1981. doi:10.1016/0021-9991(81)90128-5.
V. V. Rusanov. The calculation of the interaction of non-stationary shock waves and obstacles. USSR Computational Mathematics and Mathematical Physics, 1(2):304–320, 1962. doi:10.1016/0041-5553(62)90062-9.
Youcef Saad. A flexible inner-outer preconditioned GMRES algorithm. SIAM Journal on Scientific Computing, 14(2):461–469, 1993. doi:10.1137/0914028.
Youcef Saad and Martin H. Schultz. GMRES: a generalized minimal residual algorithm for solving nonsymmetric linear systems. SIAM Journal on Scientific and Statistical Computing, 7(3):856–869, 1986. doi:10.1137/0907058.
Nico Schlömer. Meshio: tools for mesh files. 2024. URL: nschloe/meshio, doi:10.5281/zenodo.1173115.
Will Schroeder, Ken Martin, and Bill Lorensen. The Visualization Toolkit. Kitware, 4th edition, 2006. ISBN 978-1-930934-19-1. URL: Kitware/VTK.
Matthew W. Scroggs, Igor A. Baratta, Chris N. Richardson, and Garth N. Wells. Basix: a runtime finite element basis evaluation library. Journal of Open Source Software, 7(73):3982, 2022. URL: FEniCS/basix, doi:10.21105/joss.03982.
Matthew W. Scroggs, Jørgen S. Dokken, Chris N. Richardson, and Garth N. Wells. Construction of arbitrary order finite element degree-of-freedom maps on polygonal and polyhedral cell meshes. ACM Transactions on Mathematical Software, 48(2):18:1–18:23, 2022. doi:10.1145/3524456.
Chi-Wang Shu and Stanley Osher. Efficient implementation of essentially non-oscillatory shock-capturing schemes. Journal of Computational Physics, 77(2):439–471, 1988. doi:10.1016/0021-9991(88)90177-5.
Gilbert Strang. On the construction and comparison of difference schemes. SIAM Journal on Numerical Analysis, 5(3):506–517, 1968. doi:10.1137/0705041.
C. Bane Sullivan and Alexander Kaszynski. PyVista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK). Journal of Open Source Software, 4(37):1450, 2019. URL: pyvista/pyvista, doi:10.21105/joss.01450.
Paul Tol. Tol-colors: Paul Tol's colour schemes for Python. Descanonge/tol_colors, 2026. URL: Descanonge/tol_colors (visited on 2026-10-09).
E. F. Toro, M. Spruce, and W. Speares. Restoration of the contact surface in the HLL-Riemann solver. Shock Waves, 4(1):25–34, 1994. doi:10.1007/BF01414629.
Dimitri van Heesch. Doxygen. doxygen/doxygen, 2026. URL: doxygen/doxygen (visited on 2026-10-09).
Bram van Leer. Towards the ultimate conservative difference scheme. V. A second-order sequel to Godunov's method. Journal of Computational Physics, 32(1):101–136, 1979. doi:10.1016/0021-9991(79)90145-1.
V. Venkatakrishnan. Convergence to steady state solutions of the Euler equations on unstructured grids with limiters. Journal of Computational Physics, 118(1):120–130, 1995. doi:10.1006/jcph.1995.1084.
Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, Stéfan J. van der Walt, Matthew Brett, Joshua Wilson, K. Jarrod Millman, Nikolay Mayorov, Andrew R. J. Nelson, Eric Jones, Robert Kern, Eric Larson, C J Carey, İlhan Polat, Yu Feng, Eric W. Moore, Jake VanderPlas, Denis Laxalde, Josef Perktold, Robert Cimrman, Ian Henriksen, E. A. Quintero, Charles R. Harris, Anne M. Archibald, Antônio H. Ribeiro, Fabian Pedregosa, Paul van Mulbregt, and SciPy 1.0 Contributors. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nature Methods, 17:261–272, 2020. URL: scipy/scipy, doi:10.1038/s41592-019-0686-2.
Joseph G. Wallwork, Davor Dundovic, Eleda Johnson, and Stephan C. Kramer. Animate: anisotropic mesh adaptation toolkit for Firedrake. mesh-adaptation/animate, 2024. Vendored in Zoomy as library/firedrake_animate (MIT licence). URL: mesh-adaptation/animate.
Michael L. Waskom. Seaborn: statistical data visualization. Journal of Open Source Software, 6(60):3021, 2021. URL: mwaskom/seaborn, doi:10.21105/joss.03021.
H. G. Weller, G. Tabor, H. Jasak, and C. Fureby. A tensorial approach to computational continuum mechanics using object-oriented techniques. Computers in Physics, 12(6):620–631, 1998. doi:10.1063/1.168744.
Marc Wouts. Jupytext: Jupyter notebooks as Markdown documents, Julia, Python or R scripts. mwouts/jupytext, 2026. URL: mwouts/jupytext (visited on 2026-10-09).
Yulong Xing and Xiangxiong Zhang. Positivity-preserving well-balanced discontinuous Galerkin methods for the shallow water equations on unstructured triangular meshes. Journal of Scientific Computing, 57(1):19–41, 2013. doi:10.1007/s10915-013-9695-y.
Yulong Xing, Xiangxiong Zhang, and Chi-Wang Shu. Positivity-preserving high order well-balanced discontinuous Galerkin methods for the shallow water equations. Advances in Water Resources, 33(12):1476–1493, 2010. doi:10.1016/j.advwatres.2010.08.005.
W. Zhang, A. Myers, K. Gott, A. Almgren, and J. Bell. AMReX: Block-structured adaptive mesh refinement for multiphysics applications. The International Journal of High Performance Computing Applications, 35(6):508–526, 2021. doi:10.1177/10943420211022811.
Weiqun Zhang, Ann Almgren, Vince Beckner, John Bell, Johannes Blaschke, Cy Chan, Marcus Day, Brian Friesen, Kevin Gott, Daniel Graves, Max Katz, Andrew Myers, Tan Nguyen, Andrew Nonaka, Michele Rosso, Samuel Williams, and Michael Zingale. AMReX: a framework for block-structured adaptive mesh refinement. Journal of Open Source Software, 4(37):1370, 2019. URL: AMReX-Codes/amrex, doi:10.21105/joss.01370.
Docker, Inc. Docker. docker/cli, 2026. URL: docker/cli (visited on 2026-10-09).
Eclipse Foundation. Eclipse Theia. eclipse-theia/theia, 2026. URL: eclipse-theia/theia (visited on 2026-10-09).
Encode. Uvicorn: an ASGI web server for Python. encode/uvicorn, 2026. URL: encode/uvicorn (visited on 2026-10-09).
Executable Books Community. Jupyter book. 2020. URL: jupyter-book/jupyter-book, doi:10.5281/zenodo.2561065.
Executable Books Community. Sphinx-book-theme. executablebooks/sphinx-book-theme, 2026. URL: executablebooks/sphinx-book-theme (visited on 2026-10-09).
Executable Books Community. MyST-Parser: an extended commonmark compliant parser, with bridges to docutils and Sphinx. executablebooks/MyST-Parser, 2026. URL: executablebooks/MyST-Parser (visited on 2026-10-09).
HoloViz developers. Param: declarative parameters for robust Python code. holoviz/param, 2026. URL: holoviz/param (visited on 2026-10-09).
The attrs developers. Attrs: Python classes without boilerplate. python-attrs/attrs, 2026. URL: python-attrs/attrs (visited on 2026-10-09).
The Breathe developers. Breathe: Sphinx extension for Doxygen output. breathe-doc/breathe, 2026. URL: breathe-doc/breathe (visited on 2026-10-09).
The h5py developers. H5py: HDF5 for Python. h5py/h5py, 2026. URL: h5py/h5py (visited on 2026-10-09).
The HDF Group. Hierarchical data format, version 5. HDFGroup/hdf5, 2026. URL: HDFGroup/hdf5 (visited on 2026-10-09).
The imageio developers. Imageio: Python library for reading and writing image data. imageio/imageio, 2026. URL: imageio/imageio (visited on 2026-10-09).
The JupyterLite developers. JupyterLite: Jupyter running in the browser. jupyterlite/jupyterlite, 2026. URL: jupyterlite/jupyterlite (visited on 2026-10-09).
The KaTeX developers. KaTeX: fast math typesetting for the web. KaTeX/KaTeX, 2026. URL: KaTeX/KaTeX (visited on 2026-10-09).
The marked developers. Marked: a markdown parser and compiler. markedjs/marked, 2026. URL: markedjs/marked (visited on 2026-10-09).
The OpenFOAM Foundation. OpenFOAM 13. OpenFOAM/OpenFOAM-13, 2026. URL: https://openfoam.org (visited on 2026-10-09).
The preCICE developers. Pyprecice: Python language bindings for the preCICE coupling library. precice/python-bindings, 2026. URL: precice/python-bindings (visited on 2026-10-09).
The Pydantic developers. Pydantic: data validation using Python type hints. pydantic/pydantic, 2026. URL: pydantic/pydantic (visited on 2026-10-09).
The Rasterio developers. Rasterio: geospatial raster I/O for Python programmers. rasterio/rasterio, 2026. URL: rasterio/rasterio (visited on 2026-10-09).
The Sphinx developers. Sphinx: Python documentation generator. sphinx-doc/sphinx, 2026. URL: sphinx-doc/sphinx (visited on 2026-10-09).
The TELEMAC-MASCARET Consortium. TELEMAC-MASCARET. https://gitlab.pam-retd.fr/otm/telemac-mascaret, 2026. URL: https://gitlab.pam-retd.fr/otm/telemac-mascaret (visited on 2026-10-09).