diff --git a/joss.05744/10.21105.joss.05744.crossref.xml b/joss.05744/10.21105.joss.05744.crossref.xml index de097320bc..5da4516d79 100644 --- a/joss.05744/10.21105.joss.05744.crossref.xml +++ b/joss.05744/10.21105.joss.05744.crossref.xml @@ -6,8 +6,8 @@ version="5.3.1" xsi:schemaLocation="http://www.crossref.org/schema/5.3.1 http://www.crossref.org/schemas/crossref5.3.1.xsd"> - 20240119T173053-5c56efb2ae82adbfd1388a0f546d19631a4e9d42 - 20240119173053 + 20240701090541-5c56efb2ae82adbfd1388a0f546d19631a4e9d42 + 20240701090541 JOSS Admin admin@theoj.org @@ -413,15 +413,16 @@ https://doi.org/10.1146/annurev-publhealth-112810-151726 FEBio: Finite elements for biomechanics - S. A. Maas + Maas J Biomech Eng 1 134 10.1115/1.4005694 2012 - S. A. Maas, G. A. A., B. J. Ellis. -(2012). FEBio: Finite elements for biomechanics. J Biomech Eng, 134(1), -011005. https://doi.org/10.1115/1.4005694 + Maas, S. A., Ellis, B. J., Ateshian, +G. A., & Weiss, J. A. (2012). FEBio: Finite elements for +biomechanics. J Biomech Eng, 134(1), 011005. +https://doi.org/10.1115/1.4005694 Fluid-solid coupling for the investigation of diff --git a/joss.05744/10.21105.joss.05744.pdf b/joss.05744/10.21105.joss.05744.pdf index 18532f7b32..49e6a99f40 100644 Binary files a/joss.05744/10.21105.joss.05744.pdf and b/joss.05744/10.21105.joss.05744.pdf differ diff --git a/joss.05744/paper.jats/10.21105.joss.05744.jats b/joss.05744/paper.jats/10.21105.joss.05744.jats new file mode 100644 index 0000000000..f5af395793 --- /dev/null +++ b/joss.05744/paper.jats/10.21105.joss.05744.jats @@ -0,0 +1,892 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +5744 +10.21105/joss.05744 + +Ambit – A FEniCS-based cardiovascular multi-physics +solver + + + +https://orcid.org/0000-0002-4575-9120 + +Hirschvogel +Marc + + + + + + +Department of Biomedical Engineering, School of Biomedical +Engineering & Imaging Sciences, King’s College London, London, +United Kingdom + + + + +MOX, Dipartimento di Matematica, Politecnico di Milano, +Milan, Italy + + + + +7 +7 +2023 + +9 +93 +5744 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2022 +The article authors + +Authors of papers retain copyright and release the work under +a Creative Commons Attribution 4.0 International License (CC BY +4.0) + + + +Python +cardiovascular mechanics +finite strain solid mechanics +nonlinear elastodynamics +fluid dynamics +0D lumped models +fluid-solid interaction +fsi +multi-physics coupling + + + + + + Summary +

Ambit is an open-source multi-physics finite element solver written + in Python, supporting solid and fluid mechanics, fluid-structure + interaction (FSI), and lumped-parameter models. It is tailored towards + solving problems in cardiac mechanics, but may also be used for more + general nonlinear finite element analysis. The code encompasses + re-implementations and generalizations of methods developed by the + author for his PhD thesis + (Hirschvogel, + 2019) and beyond. Ambit makes use of the open-source finite + element library + FEniCS/dolfinx + (Logg + et al., 2012) along with the linear algebra package + PETSc + (Balay + et al., 2022), hence guaranteeing a state-of-the-art finite + element and linear algebra backend. It is constantly updated to ensure + compatibility with a recent dolfinx development version. I/O routines + are designed such that the user only needs to provide input files that + define parameters through Python dictionaries, hence no programming or + in-depth knowledge of any library-specific syntax is required.

+

Ambit provides general nonlinear (compressible or incompressible) + finite strain solid dynamics + (Holzapfel, + 2000), implementing a range of hyperelastic, viscous, and + active material models. Specifically, the well-known anisotropic + Holzapfel-Ogden + (Holzapfel + & Ogden, 2009) and Guccione models + (Guccione + et al., 1995) for structural description of the myocardium are + provided, along with a bunch of other models. It further implements + strain- and stress-mediated volumetric growth models + (Göktepe + et al., 2010) that allow to model (maladaptive) ventricular + shape and size changes. Inverse mechanics approaches to imprint loads + into a reference state are implemented using the so-called + prestressing method + (Gee et + al., 2010) in displacement formulation + (Schein + & Gee, 2021).

+

Furthermore, fluid dynamics in terms of incompressible + Navier-Stokes/Stokes equations – either in Eulerian or Arbitrary + Lagrangian-Eulerian (ALE) reference frames – are implemented. + Taylor-Hood elements or equal-order approximations with SUPG/PSPG + stabilization + (Tezduyar + & Osawa, 2000) can be used.

+

A variety of reduced 0D lumped models targeted at blood circulation + modeling are implemented, including 3- and 4-element Windkessel models + (Westerhof + et al., 2009) as well as closed-loop full circulation + (Hirschvogel + et al., 2017) and coronary flow models + (Arthurs + et al., 2016).

+

Monolithic fluid-solid interaction (FSI) + (Nordsletten + et al., 2011) in ALE formulation using a Lagrange multiplier + field is supported, along with coupling of 3D and 0D models (solid or + fluid with 0D lumped circulation systems) such that cardiovascular + simulations with realistic boundary conditions can be performed.

+

Implementations for a recently proposed novel physics- and + projection-based model reduction for FSI, denoted as + fluid-reduced-solid interaction (FrSI) + (Hirschvogel + et al., 2022), are provided, along with POD-based Galerkin + model reduction techniques + (Farhat + et al., 2014) using full or boundary subspaces.

+

The nonlinear (single- or multi-field) problems are solved with a + customized Newton solver with PTC + (Gee et + al., 2009) adaptivity in case of divergence, providing + robustness for numerically challenging problems. Linear solvers and + preconditioners can be chosen from the PETSc repertoire, and specific + block preconditioners are made available for coupled problems.

+

Avenues for future functionality include cardiac electrophysiology, + scalar transport, or finite strain plasticity.

+ + + Statement of need +

Cardiovascular disease entities are the most prevalent ones in the + industrialized world + (Dimmeler, + 2011; + Luepker, + 2011) and a leading cause of death worldwide. Therefore, models + that promote a better understanding of cardiac diseases and their + progression represent a valuable tool to guide or assist therapy + planning, support device dimensioning and design + (Hirschvogel + et al., 2019), or help predict intervention planning + (Bonini + et al., 2022; + Taylor + et al., 2013).

+

Software packages that are tailored towards cardiac modeling have + been provided to the open source community. Amongst them are the + cardiovascular FSI solver svFSI + (Zhu + et al., 2022) along with SimVascular + (Updegrove + et al., 2017), providing a full medical image-to-model + pipeline, as well as FEBio + (Maas + et al., 2012), focusing on advanced structural mechanics of + soft tissue. FEniCS-based open-source solvers are pulse + (Finsberg, + 2019) for cardiac solid mechanics and cbcbeat + (Rognes + et al., 2017) for cardiac electrophysiology, both fused to a + combined toolkit for cardiac electro-mechanics named simcardems + (Finsberg + et al., 2023). Another framework for simulating cardiac + electrophysiology is openCARP + (Plank + et al., 2021), and CRIMSON + (Arthurs + et al., 2021) provides a modeling suite for 3D and + reduced-dimensional hemodynamics in arteries. A general purpose + library that provides the building blocks for cardiac modeling is + lifex + (Africa, + 2022), and a FEniCS-based monolithic FSI solver for general + applications is turtleFSI + (Bergersen + et al., 2020).

+

Ambit represents a complete open-source code for simulating cardiac + mechanics, encompassing advanced structural mechanics of the + myocardium, ventricular fluid dynamics, reduced-dimensional blood + flow, and multi-physics coupling. Therefore, a wide range of + mechanical problems can be simulated, and the code structure allows + easy and straightforward extensibility (e.g. implementations of new + constitutive models) without the need for low-level library-specific + syntax or advanced programming. Due to its simple design in terms of + clearly organized input files, Ambit is easy to use and hence + represents a valuable tool for novices or advanced researchers who + want to address cardiovascular mechanics problems.

+ + + Basic code structure +

[fig:codedesign] + represents a basic sketch of the main building blocks of Ambit. + Depending on the physics of interest, the respective problem class is + instantiated along with all the necessary input parameters, including + boundary conditions (Dirichlet, Neumann, Robin), load curves, + specification of coupling interfaces, etc. Single-physics problems + like nonlinear elastodynamics (problem type + solid) or fluid mechanics (problem type + fluid) as well as 0D blood flow (problem type + flow0d) can be solved as standalone problems. + Additionally, FSI (problem type fsi) and 3D-0D + coupling for 0D flow to 3D solid or fluid domains is supported + (problem types solid_flow0d and + fluid_flow0d), as well as fluid mechanics in + ALE description (problem type fluid_ale), plus + coupling to 0D models (problem types + fluid_ale_flow0d and + fsi_flow0d).

+

The (coupled) problem object then is passed to a solver class, + which calls the main routine to solve the nonlinear problem. This + routine implements a time stepping scheme and a monolithic Newton + solver which solves the (coupled multi-physics or single-field) + problem and updates all variables simultaneously.

+ +

Basic sketch of Ambit code structure: Problem class, + solver class, and main code execution flow. Single-physics problems + that can be solved encompass solid mechanics + (solid), fluid mechanics + (fluid), or 0D models + (flow0d). Two-physics problems like 3D-0D + coupling (solid_flow0d, + fluid_flow0d), as well as fluid in ALE + description (fluid_ale) are defined by + instantiating the respective single-physics problems. Three-physics + problems arise for coupling of ALE fluid to 0D models + (fluid_ale_flow0d) or for fluid-solid + interaction (fsi), whereas four-physics + problems would encompass FSI linked to 0D models + (fsi_flow0d). Note that the single-physics + problem ale just mimics a dummy linear + elastic solid and would be irrelevant as a standalone + problem.

+ + + + + + + + + + + AfricaP. C. + + lifex: A flexible, high performance library for the numerical solution of complex finite element problems + SoftwareX + 2022 + + + 10.1016/j.softx.2022.101252 + 101252 + + + + + + + ArthursC. J. + LauK. D. + AsrressK. N. + RedwoodS. R. + FigueroaC. A. + + A mathematical model of coronary blood flow control: Simulation of patient-specific three-dimensional hemodynamics during exercise + Am J Physiol Heart Circ Physiol + 2016 + 310 + 9 + 10.1152/ajpheart.00517.2015 + H1242 + H1258 + + + + + + ArthursC. J. + KhlebnikovR. + MelvilleA. + MarčanM. + GomezA. + Dillon-MurphyD. + CuomoF. + 1M. Silva Vieira + SchollenbergerJ. + LynchS. R. + Tossas-BetancourtC. + IyerK. + HopperS. + LivingstonE. + YoussefiP. + 1A. Noorani + AhmedS. Ben + NautaF. J. H. + BakelT. M. J. van + AhmedY. + BakelP. A. J. van + MynardJ. + AchilleP. Di + GharahiH. + LauK. D. + FilonovaV. + AguirreM. + NamaN. + XiaoN. + BaekS. + GarikipatiK. + SahniO. + NordslettenD. + FigueroaC. A. + + CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation + PLoS Comput Biol + 2021 + 17 + 5 + 10.1371/journal.pcbi.1008881 + e1008881 + + + + + + + BalayS. + AbhyankarS. + AdamsM. F. + BensonS. + BrownJ. + BruneP. + BuschelmanK. + ConstantinescuE. + DalcinL. + DenerA. + EijkhoutV. + GroppW. D. + HaplaV. + IsaacT. + JolivetP. + KarpeevD. + KaushikD. + KnepleyM. G. + KongF. + KrugerS. + MayD. A. + McInnesL. C. + MillsR. T. + MitchellL. + MunsonT. + RomanJ. E. + RuppK. + SananP. + SarichJ. + SmithB. F. + ZampiniS. + ZhangH. + ZhangH. + ZhangJ. + + PETSc/TAO users manual + Argonne National Laboratory + 2022 + + + + + + BergersenAslak W. + SlyngstadA. + GjertsenS. + SoucheA. + Valen-SendstadK. + + turtleFSI: A robust and monolithic FEniCS-based fluid-structure interaction solver + The Journal of Open Source Software + 2020 + 5 + 50 + 10.21105/joss.02089 + 2089 + + + + + + + BoniniM. + HirschvogelM. + AhmedY. + XuH. + YoungA. + TangP. C. + NordslettenD. + + Hemodynamic modeling for mitral regurgitation + The Journal of Heart and Lung Transplantation + 2022 + 41 + 4 (Supplement) + 10.1016/j.healun.2022.01.1685 + S218 + S219 + + + + + + DimmelerS. + + Cardiovascular disease review series + EMBO Mol Med + 2011 + 3 + 12 + 10.1002/emmm.201100182 + 697 + + + + + + + FarhatC. + AveryP. + ChapmanT. + CortialJ. + + Dimensional reduction of nonlinear finite element dynamic models with finite rotations and energy-based mesh sampling and weighting for computational efficiency + International Journal for Numerical Methods in Engineering + 2014 + 98 + 9 + 10.1002/nme.4668 + 625 + 662 + + + + + + FinsbergH. N. T. + + pulse: A python package based on FEniCS for solving problems in cardiac mechanics + The Journal of Open Source Software + 2019 + 4 + 41 + 10.21105/joss.01539 + 1539 + + + + + + + FinsbergH. N. T. + HerckI. G. M. van + Daversin-CattyC. + ArevaloH. + WallS. + + simcardems: A FEniCS-based cardiac electro-mechanics solver + The Journal of Open Source Software + 2023 + 8 + 81 + 10.21105/joss.04753 + 4753 + + + + + + + GeeM. W. + KelleyC. T. + LehoucqR. B. + + Pseudo-transient continuation for nonlinear transient elasticity + International Journal for Numerical Methods in Engineering + 2009 + 78 + 10 + 10.1002/nme.2527 + 1209 + 1219 + + + + + + GeeM. W. + FörsterCh. + WallW. A. + + A computational strategy for prestressing patient-specific biomechanical problems under finite deformation + International Journal for Numerical Methods in Biomedical Engineering + 2010 + 26 + 1 + 10.1002/cnm.1236 + 52 + 72 + + + + + + GöktepeS. + AbilezO. J. + ParkerK. K. + KuhlE. + + A multiscale model for eccentric and concentric cardiac growth through sarcomerogenesis + J Theor Biol + 2010 + 265 + 3 + 10.1016/j.jtbi.2010.04.023 + 433 + 442 + + + + + + GuccioneJ. M. + CostaK. D. + McCullochA. D. + + Finite element stress analysis of left ventricular mechanics in the beating dog heart + J Biomech + 1995 + 28 + 10 + 10.1016/0021-9290(94)00174-3 + 1167 + 1177 + + + + + + HirschvogelM. + BassiliousM. + JagschiesL. + WildhirtS. M. + GeeM. W. + + A monolithic 3D-0D coupled closed-loop model of the heart and the vascular system: Experiment-based parameter estimation for patient-specific cardiac mechanics + Int J Numer Method Biomed Eng + 2017 + 33 + 8 + 10.1002/cnm.2842 + e2842 + + + + + + + HirschvogelM. + + Computational modeling of patient-specific cardiac mechanics with model reduction-based parameter estimation and applications to novel heart assist technologies + Verlag Dr. Hut, MediaTUM + 2019 + 1 + https://mediatum.ub.tum.de/1445317 + + + + + + HirschvogelM. + JagschiesL. + MaierA. + WildhirtS. M. + GeeM. W. + + An in-silico twin for epicardial augmentation of the failing heart + Int J Numer Method Biomed Eng + 2019 + 35 + 10 + 10.1002/cnm.3233 + e3233 + + + + + + + HirschvogelM. + BalmusM. + BoniniM. + NordslettenD. + + Fluid-reduced-solid interaction (FrSI): Physics- and projection-based model reduction for cardiovascular applications + Preprint, submitted to Elsevier + 2022 + + + https://ssrn.com/abstract=4281317 + 10.2139/ssrn.4281317 + + + + + + + + HolzapfelG. A. + + Nonlinear solid mechanics – A continuum approach for engineering + Wiley Press Chichester + 2000 + + + + + + HolzapfelG. A. + OgdenR. W. + + Constitutive modelling of passive myocardium: A structurally based framework for material characterization + Phil Trans R Soc A + 2009 + 367 + 1902 + 10.1098/rsta.2009.0091 + 3445 + 3475 + + + + + Automated solution of differential equations by the finite element method – the FEniCS book + + LoggA. + MardalK.-A. + WellsG. N. + + Springer + 2012 + 978-3-642-23098-1 + 10.1007/978-3-642-23099-8 + + + + + + LuepkerR. V. + + Cardiovascular disease: Rise, fall, and future prospects + Annual Review of Public Health + 2011 + 32 + 12 + 10.1146/annurev-publhealth-112810-151726 + 1 + 3 + + + + + + MaasS. A. + EllisB. J. + AteshianG. A. + WeissJ. A. + + FEBio: Finite elements for biomechanics + J Biomech Eng + 2012 + 134 + 1 + 10.1115/1.4005694 + 011005 + + + + + + + NordslettenD. A. + McCormickM. + KilnerP. J. + HunterP. + KayD. + SmithN. P. + + Fluid-solid coupling for the investigation of diastolic and systolic human left ventricular function + International Journal for Numerical Methods in Biomedical Engineering + 2011 + 27 + 7 + 10.1002/cnm.1405 + 1017 + 1039 + + + + + + PlankG. + LoeweA. + NeicA. + AugustinC. + HuangY.-L. + GsellM. A. F. + KarabelasE. + NothsteinM. + PrasslA. J. + SánchezJ. + SeemannG. + VigmondE. J. + + The openCARP simulation environment for cardiac electrophysiology + Computer Methods and Programs in Biomedicine + 2021 + 208 + + 10.1016/j.cmpb.2021.106223 + 106223 + + + + + + + RognesM. E. + FarrellP. E. + FunkeS. W. + HakeJ. E. + MaleckarM. M. C. + + cbcbeat: An adjoint-enabled framework for computational cardiac electrophysiology + The Journal of Open Source Software + 2017 + 2 + 13 + 10.21105/joss.00224 + 224 + + + + + + + ScheinA. + GeeM. W. + + Greedy maximin distance sampling based model order reduction of prestressed and parametrized abdominal aortic aneurysms + Advanced Modeling and Simulation in Engineering Sciences + 2021 + 8 + 18 + 10.1186/s40323-021-00203-7 + + + + + + + + TaylorC. A. + FonteT. A. + MinJ. K. + + Computational fluid dynamics applied to cardiac computed tomography for noninvasive quantification of fractional flow reserve + JACC + 2013 + 61 + 22 + 10.1016/j.jacc.2012.11.083 + 2233 + 2241 + + + + + + TezduyarT. E. + OsawaY. + + Finite element stabilization parameters computed from element matrices and vectors + Computer Methods in Applied Mechanics and Engineering + 2000 + 190 + 3–4 + 10.1016/S0045-7825(00)00211-5 + 411 + 430 + + + + + + UpdegroveA. + WilsonN. M. + MerkowJ. + LanH. + MarsdenA. L. + ShaddenS. C. + + SimVascular: An open source pipeline for cardiovascular simulation + Ann Biomed Eng + 2017 + 45 + 3 + 10.1007/s10439-016-1762-8 + 525 + 541 + + + + + + WesterhofN. + LankhaarJ.-W. + WesterhofB. E. + + The arterial Windkessel + Med Biol Eng Comput + 2009 + 47 + 2 + 10.1007/s11517-008-0359-2 + H81 + H88 + + + + + + ZhuC. + VedulaV. + ParkerD. + WilsonN. + ShaddenS. + MarsdenA. + + svFSI: A multiphysics package for integrated cardiac modeling + The Journal of Open Source Software + 2022 + 7 + 78 + 10.21105/joss.04118 + 4118 + + + + + +