Create a JOSS paper for Musubi

.github/workflows/draft-pdf.yml

@@ -0,0 +1,24 @@
+name: Draft PDF
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper.pdf

paper.bib

@@ -0,0 +1,322 @@
+@Book{Ierusalimschy:2016,
+  author    = {Ierusalimschy, Roberto},
+  publisher = {Lua.org},
+  title     = {Programming in Lua},
+  year      = {2016},
+  address   = {Rio de Janeiro},
+  edition   = {Fourth edition},
+  isbn      = {9788590379867},
+  pagetotal = {369},
+  ppn_gvk   = {870069926},
+}
+
+
+@article{Klimach:2012vi,
+    author = {Klimach, Harald and Hasert, Manuel and Zudrop, Jens and Roller, Sabine},
+    title = {{Distributed Octree Mesh Infrastructure for Flow Simulations}},
+    journal = {European Congress on Computational Methods in Applied Sciences and Engineering},
+    year = {2012},
+    pages = {1--15}
+}
+
+@InProceedings{Harlacher:2012,
+    author="Harlacher, Daniel F.
+    and Hasert, Manuel
+    and Klimach, Harald
+    and Zimny, Simon
+    and Roller, Sabine",
+    doi = {10.1007/978-3-642-22244-3_6},
+    editor="Resch, Michael
+    and Wang, Xin
+    and Bez, Wolfgang
+    and Focht, Erich
+    and Kobayashi, Hiroaki
+    and Roller, Sabine",
+    title="Tree Based Voxelization of STL Data",
+    booktitle="High Performance Computing on Vector Systems 2011",
+    year="2012",
+    publisher="Springer Berlin Heidelberg",
+    address="Berlin, Heidelberg",
+    pages="81--92",
+    isbn="978-3-642-22244-3"
+}
+
+@article{hasert:2013jc,
+	author = {Hasert, Manuel and Masilamani, Kannan and Zimny, Simon and Klimach, Harald and Qi, Jiaxing and Bernsdorf, J{\"o}rg and Roller, Sabine},
+	doi = {10.1016/j.jocs.2013.11.001},
+	issn = {1877-7503},
+	journal = {Journal of Computational Science},
+	month = {sep},
+	number = {5},
+	pages = {784--794},
+	title = {Complex fluid simulations with the parallel tree-based {Lattice} {Boltzmann} solver {Musubi}},
+	volume = {5},
+	year = {2014}
+}
+
+@phdthesis{Hasert:2013,
+	Annote = {Supervisor: Roller, Sabine},
+	Author = {Hasert, Manuel},
+	School = {RWTH Aachen University},
+	Title = {Multi-Scale Lattice Boltzmann Simulations on Distributed Octrees},
+	Year = {2013}
+}
+
+@article{Zimny:2013,
+	author = {Zimny, Simon and Chopard, Bastien and Malaspinas, Orestis and Lorenz, Eric and Jain, Kartik and Roller, Sabine and Bernsdorf, J{\"o}rg},
+	doi = {10.1016/j.procs.2013.05.266},
+	issn = {1877-0509},
+	journal = {Procedia Computer Science},
+	keywords = {Multiscale Simulation, Lattice Boltzmann Method, Scale Separation Map, Thrombus, Intracranial Aneurysms},
+	note = {2013 International Conference on Computational Science},
+	pages = {1006--1015},
+	title = {A Multiscale Approach for the Coupled Simulation of Blood Flow and Thrombus Formation in Intracranial Aneurysms},
+	volume = {18},
+	year = {2013},
+}
+
+
+@inproceedings{Klimach:2014,
+	address = {Munich, Germany},
+	doi = {10.3233/978-1-61499-381-0-703},
+	author = {Klimach, Harald and Jain, Kartik and Roller, Sabine},
+	booktitle = {Parallel Computing: Accelerating Computational Science and Engineering (CSE)},
+	date-added = {2014-03-05 14:36:31 +0100},
+	date-modified = {2016-04-21 07:20:21 +0000},
+	editor = {Bader, Michael and Bode, Arndt and Bungartz, Hans-Joachim and Gerndt, Michael and Joubert, Gerhard R. and Peters, Frans},
+	month = {sep},
+	pages = {703--711},
+	publisher = {IOS Press},
+	series = {Advances in Parallel Computing},
+	title = {End-to-end parallel simulations with APES},
+	volume = {25},
+	year = {2014}
+}
+
+
+@phdthesis{Zimny:2015,
+	Annote = {Supervisor: Roller, Sabine},
+	Author = {Zimny, Simon},
+	School = {RWTH Aachen University},
+	Title = {Hemodynamic Flow Simulation in Patient Specific Cerebral Aneurysms},
+	Year = {2015}
+}
+
+@phdthesis{Zudrop:2015,
+	Annote = {Supervisor: Roller, Sabine},
+	Author = {Zudrop, Jens},
+	School = {RWTH Aachen University},
+	Title = {Efficient Numerical Methods for Fluid- and Electrodynamics on Massively Parallel Systems},
+	Year = {2015}
+}
+
+@inproceedings{Qi:2015,
+	author = {Qi, Jiaxing and Hasert, Manuel and Klimach, Harald and Roller, Sabine},
+	booktitle = {Sustained Simulation Performance 2015},
+	doi = {10.1007/978-3-319-20340-9_16},
+	editor = {Resch, Michael and Bez, Wolfgang and Focht, Erich and Kobayashi, Hiroaki and Qi, Jiaxing and Roller, Sabine},
+	pages = {195--204},
+	publisher = {Springer International Publishing},
+	title = {Aeroacoustic Simulation of Flow Through Porous Media Based on Lattice Boltzmann Method},
+	year = {2015}
+}
+
+
+@article{Johannink:2015,
+title = {Predictive pressure drop models for membrane channels with non-woven and woven spacers},
+journal = {Desalination},
+volume = {376},
+pages = {41-54},
+year = {2015},
+issn = {0011-9164},
+doi = {10.1016/j.desal.2015.07.024},
+url = {https://www.sciencedirect.com/science/article/pii/S0011916415300321},
+author = {Matthias Johannink and Kannan Masilamani and Adel Mhamdi and Sabine Roller and Wolfgang Marquardt},
+keywords = {Membrane processes, Spacer, Pressure drop, Modeling},
+}
+
+@article{JainCaF:2016,
+	annote = {Journal Papers},
+	author = {Jain, Kartik and Roller, Sabine and Mardal, Kent-Andr{\'e}},
+	doi = {doi:10.1016/j.compfluid.2015.12.011},
+	journal = {Computers \& Fluids},
+	month = {mar},
+	pages = {36--46},
+	publisher = {Pergamon},
+	title = {Transitional flow in intracranial aneurysms--a space and time refinement study below the Kolmogorov scales using Lattice Boltzmann Method},
+	volume = {127},
+	year = {2016}
+}
+
+@phdthesis{Jain:2016,
+	Annote = {Supervisor: Roller, Sabine},
+	Author = {Jain, Kartik},
+	School = {Universit{\"a}t Siegen},
+	Title = {Transition to Turbulence in Physiological Flows: Direct Numerical Simulation of Hemodynamics in Intracranial Aneurysms and Cerebrospinal Fluid Hydrodynamics in the Spinal Canal},
+	isbn = {978-3-936533-83-5},
+	Year = {2016}
+}
+
+@inproceedings{Qi:2016,
+	author = {Qi, Jiaxing and Jain, Kartik and Klimach, Harald and Roller, Sabine},
+	booktitle = {Parallel Computing: On the Road to Exascale},
+	editor = {Gerhard R. Joubert and Hugh Leather and Mark Parsons and Frans Peters and Mark Sawyer},
+	pages = {807--816},
+    doi = {10.3233/978-1-61499-621-7-807},
+	series = {Advances in Parallel Computing},
+	title = {Performance Evaluation of the LBM Solver Musubi on Various HPC Architectures},
+	volume = {27},
+	year = {2016}
+}
+
+@article{Masilamani:2017,
+	annote = {Journal Papers},
+	author = {Zudrop, Jens and Masilamani, Kannan and Roller, Sabine, and Asinari, Pietro},
+	doi = {10.1016/j.compfluid.2017.04.021},
+	issn = {0045-7930},
+	journal = {Computers and Fluids},
+	keywords = {Lattice Boltzmann; Multicomponent flow; Maxwell--Stefan diffusion; High performance computing; Massively parallel simulations; Octree},
+	pages = {20-33},
+	publisher = {Elsevier},
+	title = {A robust lattice Boltzmann method for parallel simulations of multicomponent flows in complex geometries},
+	url = {http://www.sciencedirect.com/science/article/pii/S0045793017301482},
+	volume = {153},
+	year = {2017},
+}
+
+
+@phdthesis{Qi:2017,
+	Annote = {Supervisor: Roller, Sabine},
+	Author = {Qi, Jiaxing},
+	School = {RWTH Aachen University},
+	Title = {Efficient Lattice Boltzmann Simulations on Large Scale High Performance Computing Systems},
+    doi = {10.18154/RWTH-2017-04121},
+	Year = {2017}
+}
+
+@phdthesis{Masilamani:2020,
+	Annote = {Supervisor: Roller, Sabine},
+	Author = {Masilamani, Kannan},
+	School = {RWTH Aachen University},
+	Title = {Framework for Coupled Simulation of Electrodialysis Processes},
+    doi = {10.18154/RWTH-2021-02437},
+	Year = {2020}
+}
+
+@article{Hebbink:2022,
+  title = {Computational analysis of human upper airway aerodynamics},
+  volume = {61},
+  ISSN = {1741-0444},
+  url = {http://dx.doi.org/10.1007/s11517-022-02716-8},
+  DOI = {10.1007/s11517-022-02716-8},
+  number = {2},
+  journal = {Medical & Biological Engineering & Computing},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Hebbink,  Rutger H.J. and Wessels,  Bas J. and Hagmeijer,  Rob and Jain,  Kartik},
+  year = {2022},
+  month = dec,
+  pages = {541–553}
+}
+
+@phdthesis{Vlogman:2025,
+    title = "Coupled Lattice Boltzmann and discrete element method simulations with applications to liver radioembolization",
+    author = "Tristan Vlogman",
+    year = "2025",
+    month = jul,
+    day = "11",
+    doi = "10.3990/1.9789036567046",
+    isbn = "978-90-365-6703-9",
+    publisher = "University of Twente",
+    address = "Netherlands",
+    type = "PhD Thesis - Research UT, graduation UT",
+    school = "University of Twente"
+}
+
+
+@article{Palabos2020,
+    title = "Palabos: Parallel Lattice Boltzmann Solver",
+    journal = "Computers & Mathematics with Applications",
+    year = "2020",
+    issn = "0898-1221",
+    doi = "10.1016/j.camwa.2020.03.022",
+    author = "Jonas Latt and Orestis Malaspinas and Dimitrios Kontaxakis and Andrea Parmigiani and Daniel Lagrava and Federico Brogi and Mohamed Ben Belgacem and Yann Thorimbert and Sébastien Leclaire and Sha Li and Francesco Marson and Jonathan Lemus and Christos Kotsalos and Raphaël Conradin and Christophe Coreixas and Rémy Petkantchin and Franck Raynaud and Joël Beny and Bastien Chopard",
+}
+
+@article{olbPaper2021,
+  author   = {Krause, M.J. and Kummerl\"ander, A. and Avis, S.J. and Kusumaatmaja, H. and Dapelo, D. and Klemens, F. and Gaedtke, M. and Hafen, N. and Mink, A. and Trunk, R. and Marquardt, J.E. and Maier, M.L. and Haussmann, M. and Simonis, S.},
+  title    = {{OpenLB--Open source lattice Boltzmann code}},
+  doi      = {10.1016/j.camwa.2020.04.033},
+  issn     = {0898-1221},
+  pages    = {258--288},
+  url      = {http://www.sciencedirect.com/science/article/pii/S0898122120301875},
+  volume   = {81},
+  journal  = {Computers \& Mathematics with Applications},
+  keywords = {Numerical simulation, Lattice Boltzmann methods, Partial differential equations, Computational fluid dynamics, Transport problems, OpenLB},
+  year     = {2021}
+}
+
+@article{BAUER2021478,
+    title = {waLBerla: A block-structured high-performance framework for multiphysics simulations},
+    journal = {Computers & Mathematics with Applications},
+    volume = {81},
+    pages = {478-501},
+    year = {2021},
+    issn = {0898-1221},
+    doi = {10.1016/j.camwa.2020.01.007},
+    url = {https://www.sciencedirect.com/science/article/pii/S0898122120300146},
+    author = {Martin Bauer and Sebastian Eibl and Christian Godenschwager and Nils Kohl and Michael Kuron and Christoph Rettinger and Florian Schornbaum and Christoph Schwarzmeier and Dominik Thönnes and Harald Köstler and Ulrich Rüde},
+    keywords = {High-performance computing, Multiphysics, Lattice Boltzmann, Rigid particle dynamics, Adaptive mesh refinement, Code generation}
+}
+
+@article{Spinelli:2023,
+    title = {HPC performance study of different collision models using the Lattice Boltzmann solver Musubi},
+    journal = {Computers & Fluids},
+    volume = {255},
+    pages = {105833},
+    year = {2023},
+    issn = {0045-7930},
+    doi = {10.1016/j.compfluid.2023.105833},
+    url = {https://www.sciencedirect.com/science/article/pii/S0045793023000580},
+    author = {Gregorio Gerardo Spinelli and Tobias Horstmann and Kannan Masilamani and Malav Mukesh Soni and Harald Klimach and Arthur Stück and Sabine Roller},
+    keywords = {Lattice Boltzmann method, Hybrid recursive regularized BGK, Cumulant, Turbulence modeling, Musubi}
+}
+
+@articleInfo{Spinelli:2024,
+    title = {Key ingredients for wall-modeled LES with the Lattice Boltzmann method: Systematic comparison of collision schemes, SGS models, and wall functions on simulation accuracy and efficiency for turbulent channel flow},
+    journal = {Discrete and Continuous Dynamical Systems - S},
+    volume = {17},
+    number = {11},
+    pages = {3224-3251},
+    year = {2024},
+    issn = {1937-1632},
+    doi = {10.3934/dcdss.2023212},
+    url = {https://www.aimsciences.org/article/id/6578251d4aaea52710702d59},
+    author = {Gregorio Gerardo Spinelli and Jana Gericke and Kannan Masilamani and Harald Günther Klimach},
+    keywords = {Lattice Boltzmann method, Hybrid recursive regularized BGK, Cumulant, turbulence modeling, Musubi, wall functions}
+}
+
+@ARTICLE{Blanken:2025,
+  author={Blanken, Nathan and Heiles, Baptiste and Kuliesh, Alina and Versluis, Michel and Jain, Kartik and Maresca, David and Lajoinie, Guillaume},
+  journal={IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control},
+  title={PROTEUS: A Physically Realistic Contrast-Enhanced Ultrasound Simulator—Part I: Numerical Methods},
+  year={2025},
+  volume={72},
+  number={7},
+  pages={848-865},
+  keywords={Ultrasonic imaging;Acoustics;Imaging;Frequency control;Transducers;Propagation;Trajectory;Blood flow measurement;multiphysics simulation;nonlinear wave propagation;open-source software;ultrasound contrast agents (UCAs);ultrasound imaging},
+  doi={10.1109/TUFFC.2024.3427850}
+}
+
+
+@article{Geier:2025,
+    title = {VirtualFluids – open source parallel LBM solver},
+    journal = {Computer Physics Communications},
+    volume = {317},
+    pages = {109810},
+    year = {2025},
+    issn = {0010-4655},
+    doi = {10.1016/j.cpc.2025.109810},
+    url = {https://www.sciencedirect.com/science/article/pii/S0010465525003121},
+    author = {Martin Geier and Konstantin Kutscher and Martin Schönherr and Anna Wellmann and Sören Peters and Hussein Alihussein and Jan Linxweiler and Manfred Krafczyk},
+    keywords = {Open source, Lattice Boltzmann method, Cumulant LBM, Grid refinement, Research software engineering, FAIR, HPC, CPU, GPU}
+}