diff --git a/Class.png b/Class.png deleted file mode 100644 index 7350e61d..00000000 Binary files a/Class.png and /dev/null differ diff --git a/Mesh.png b/Mesh.png deleted file mode 100644 index e64d9f91..00000000 Binary files a/Mesh.png and /dev/null differ diff --git a/README.md b/README.md index cf309994..7576f8d7 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,3 @@ -## NOTE - -This branch is created from master on Jan 4, 2022 and will be referenced in the manuscript to be submitted for the Journal of Open Source Software (JOSS). - ## Introduction `svFSI` is a multi-physics finite element solver designed for computational modeling of the cardiovascular system. It is a major component of the ongoing SimVascular [**SimCardio**](http://simvascular.github.io/docsSimCardio.html) project that aims to provide the complete pipeline for cardiac modeling, from image segmentation to computational modeling. diff --git a/README_JOSS.md b/README_JOSS.md deleted file mode 100644 index 9f966677..00000000 --- a/README_JOSS.md +++ /dev/null @@ -1,17 +0,0 @@ -- There are two ways to generate pdf file: - -1. GitHub Action - - GitHub will automatically compile the paper each time the repository is updated. The pdf is available via the Actions tab in the project and click on the latest workflow run. - -2. Docker -``` -docker run --rm \ - --volume $PWD:/data \ - --user $(id -u):$(id -g) \ - --env JOURNAL=joss \ - openjournals/paperdraft -``` - -- [Official documentation](https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain) on what should be included in the paper. - diff --git a/paper.bib b/paper.bib deleted file mode 100644 index 4926c10c..00000000 --- a/paper.bib +++ /dev/null @@ -1,225 +0,0 @@ -@article{Xu2020, - author={Xu, JQ and Murphy, SL and Kochanek, KD and Arias, E}, - title={{Mortality in the United States, 2018}}, - journal={NCHS Data Brief No. 355}, - year={2020}, - publisher={National Center for Health Statistics}, - url = {https://www.cdc.gov/nchs/products/databriefs/db355.htm} -} - -@article{Mittal2015, - author = {Mittal, Rajat and Seo, Jung Hee and Vedula, Vijay and Choi, Young J. and Liu, Hang and Huang, H. Howie and Jain, Saurabh and Younes, Laurent and Abraham, Theodore and George, Richard T.}, - doi = {10.1016/j.jcp.2015.11.022}, - issn = {00219991}, - journal = {Journal of Computational Physics}, - pages = {1065--1082}, - publisher = {Elsevier Inc.}, - title = {{Computational modeling of cardiac hemodynamics: Current status and future outlook}}, - url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999115007627}, - volume = {305}, - year = {2015} -} - -@article{Trayanova2011, -author = {Trayanova, Natalia A.}, -doi = {10.1161/CIRCRESAHA.110.223610}, -issn = {00097330}, -journal = {Circulation Research}, -keywords = {Cardiac disease,Electromechanical modeling,Electrophysiological modeling,Simulation,Whole-heart model}, -number = {1}, -pages = {113--128}, -pmid = {21212393}, -title = {{Whole-heart modeling : Applications to cardiac electrophysiology and electromechanics}}, -volume = {108}, -year = {2011} -} - - -@article{Updegrove2017, - author = {Updegrove, Adam and Wilson, Nathan M. and Merkow, Jameson and Lan, Hongzhi and Marsden, Alison L. and Shadden, Shawn C.}, - doi = {10.1007/s10439-016-1762-8}, - issn = {15739686}, - journal = {Annals of Biomedical Engineering}, - keywords = {Hemodynamics,Image-based CFD,Open-source,Patient-specific modeling}, - number = {3}, - pages = {525--541}, - pmid = {27933407}, - title = {{SimVascular: An Open Source Pipeline for Cardiovascular Simulation}}, - volume = {45}, - year = {2017} -} - -@article{Maas2012, - title={FEBio: finite elements for biomechanics}, - author={Maas, Steve A and Ellis, Benjamin J and Ateshian, Gerard A and Weiss, Jeffrey A}, - journal={Journal of biomechanical engineering}, - volume={134}, - number={1}, - year={2012}, - doi={10.1115/1.4005694}, - publisher={American Society of Mechanical Engineers Digital Collection} -} - -@article{Plank2021, -title = {The openCARP simulation environment for cardiac electrophysiology}, -journal = {Computer Methods and Programs in Biomedicine}, -volume = {208}, -pages = {106223}, -year = {2021}, -issn = {0169-2607}, -doi = {https://doi.org/10.1016/j.cmpb.2021.106223}, -url = {https://www.sciencedirect.com/science/article/pii/S0169260721002972}, -author = {Gernot Plank and Axel Loewe and Aurel Neic and Christoph Augustin and Yung-Lin Huang and Matthias A.F. Gsell and Elias Karabelas and Mark Nothstein and Anton J. Prassl and Jorge Sánchez and Gunnar Seemann and Edward J. Vigmond}, -} - -@article{Bertagna2017, - title={The LifeV library: engineering mathematics beyond the proof of concept}, - author={Bertagna, Luca and Deparis, Simone and Formaggia, Luca and Forti, Davide and Veneziani, Alessandro}, - journal={arXiv preprint}, - year={2017}, - url={https://arxiv.org/abs/1710.06596} -} - -@book{Logg2012, - title = {Automated Solution of Differential Equations by the Finite Element Method}, - author = {Anders Logg and Kent-Andre Mardal and Garth N. Wells and others}, - year = {2012}, - publisher = {Springer}, - doi = {10.1007/978-3-642-23099-8}, - isbn = {978-3-642-23098-1}, -} - -@article{Vedula2017, - title={A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling}, - author={Vedula, Vijay and Lee, Juhyun and Xu, Hao and Kuo, C-C Jay and Hsiai, Tzung K and Marsden, Alison L}, - journal={PLoS computational biology}, - volume={13}, - number={10}, - pages={e1005828}, - year={2017}, - doi={10.1371/journal.pcbi.1005828}, - publisher={Public Library of Science San Francisco, CA USA} -} - -@article{Grande2021, - title={Computational modeling of blood component transport related to coronary artery thrombosis in Kawasaki disease}, - author={Grande Guti{\'e}rrez, Noelia and Alber, Mark and Kahn, Andrew M and Burns, Jane C and Mathew, Mathew and McCrindle, Brian W and Marsden, Alison L}, - journal={PLOS Computational Biology}, - volume={17}, - number={9}, - pages={e1009331}, - year={2021}, - doi={10.1371/journal.pcbi.1009331}, - publisher={Public Library of Science San Francisco, CA USA} -} - -@article{Arzani2018, -title = {Wall shear stress fixed points in cardiovascular fluid mechanics}, -journal = {Journal of Biomechanics}, -volume = {73}, -pages = {145-152}, -year = {2018}, -issn = {0021-9290}, -doi = {10.1016/j.jbiomech.2018.03.034}, -url = {https://www.sciencedirect.com/science/article/pii/S0021929018302239}, -author = {Amirhossein Arzani and Shawn C. Shadden}, -keywords = {Blood flow, Hemodynamics, Mass transport, Endothelial cells}, -} - -@article{Seo2020a, - title={The effects of clinically-derived parametric data uncertainty in patient-specific coronary simulations with deformable walls}, - author={Seo, Jongmin and Schiavazzi, Daniele E and Kahn, Andrew M and Marsden, Alison L}, - journal={International journal for numerical methods in biomedical engineering}, - volume={36}, - number={8}, - pages={e3351}, - year={2020}, - doi={10.1002/cnm.3351}, - publisher={Wiley Online Library} -} - -@article{Seo2020b, - title={Multifidelity estimators for coronary circulation models under clinically informed data uncertainty}, - author={Seo, Jongmin and Fleeter, Casey and Kahn, Andrew M and Marsden, Alison L and Schiavazzi, Daniele E}, - journal={International Journal for Uncertainty Quantification}, - volume={10}, - number={5}, - year={2020}, - doi={10.1615/Int.J.UncertaintyQuantification.2020033068}, - publisher={Begel House Inc.} -} - -@article{Baumler2020, - title={Fluid--structure interaction simulations of patient-specific aortic dissection}, - author={B{\"a}umler, Kathrin and Vedula, Vijay and Sailer, Anna M and Seo, Jongmin and Chiu, Peter and Mistelbauer, Gabriel and Chan, Frandics P and Fischbein, Michael P and Marsden, Alison L and Fleischmann, Dominik}, - journal={Biomechanics and modeling in mechanobiology}, - volume={19}, - number={5}, - pages={1607--1628}, - year={2020}, - doi={10.1007/s10237-020-01294-8}, - publisher={Springer} -} - -@article{Kong2020, - author = {Kong, Fanwei and Shadden, Shawn C.}, - title = "{Automating Model Generation for Image-Based Cardiac Flow Simulation}", - journal = {Journal of Biomechanical Engineering}, - volume = {142}, - number = {11}, - year = {2020}, - month = {09}, - issn = {0148-0731}, - doi = {10.1115/1.4048032}, - url = {https://doi.org/10.1115/1.4048032}, - note = {111011}, - eprint = {https://asmedigitalcollection.asme.org/biomechanical/article-pdf/142/11/111011/6565541/bio\_142\_11\_111011.pdf}, -} - -@article{heroux2005, - title={An overview of the Trilinos project}, - author={Heroux, Michael A and Bartlett, Roscoe A and Howle, Vicki E and Hoekstra, Robert J and Hu, Jonathan J and Kolda, Tamara G and Lehoucq, Richard B and Long, Kevin R and Pawlowski, Roger P and Phipps, Eric T and others}, - journal={ACM Transactions on Mathematical Software (TOMS)}, - volume={31}, - number={3}, - pages={397--423}, - year={2005}, - publisher={ACM New York, NY, USA}, - url={https://doi.org/10.1145/1089014.1089021} -} - -@article{quateroni_a, - doi = {10.48550/ARXIV.2201.03303}, - - url = {https://arxiv.org/abs/2201.03303}, - - author = {Africa, Pasquale C. and Piersanti, Roberto and Fedele, Marco and Dede', Luca and Quarteroni, Alfio}, - - keywords = {Mathematical Software (cs.MS), Distributed, Parallel, and Cluster Computing (cs.DC), Numerical Analysis (math.NA), FOS: Computer and information sciences, FOS: Computer and information sciences, FOS: Mathematics, FOS: Mathematics, G.4; G.1; J.3, 68-04, 68N30 (Primary), 35-04, 65-04, 65M60, 65N30, 65Y05, 92-04, 92C50 (Secondary)}, - - title = {life$^x$ - heart module: a high-performance simulator for the cardiac function. Package 1: Fiber generation}, - - publisher = {arXiv}, - - year = {2022}, - - copyright = {Creative Commons Attribution Non Commercial Share Alike 4.0 International} -} - - -@article{quateroni_b, - doi = {10.48550/ARXIV.2207.12460}, - url = {https://arxiv.org/abs/2207.12460}, - - author = {Fedele, Marco and Piersanti, Roberto and Regazzoni, Francesco and Salvador, Matteo and Africa, Pasquale Claudio and Bucelli, Michele and Zingaro, Alberto and Dede', Luca and Quarteroni, Alfio}, - - keywords = {Numerical Analysis (math.NA), Computational Engineering, Finance, and Science (cs.CE), Distributed, Parallel, and Cluster Computing (cs.DC), Medical Physics (physics.med-ph), FOS: Mathematics, FOS: Mathematics, FOS: Computer and information sciences, FOS: Computer and information sciences, FOS: Physical sciences, FOS: Physical sciences}, - - title = {A comprehensive and biophysically detailed computational model of the whole human heart electromechanics}, - - publisher = {arXiv}, - - year = {2022}, - - copyright = {Creative Commons Attribution Non Commercial No Derivatives 4.0 International} -} diff --git a/paper.md b/paper.md deleted file mode 100755 index 57db291f..00000000 --- a/paper.md +++ /dev/null @@ -1,94 +0,0 @@ ---- -title: '`svFSI`: A Multiphysics Package for Integrated Cardiac Modeling' -tags: - - fortran - - cardiac modeling - - active contraction - - fluid-structure interaction - - finite element method -authors: - - name: Chi Zhu - orcid: 0000-0002-1099-8893 - equal-contrib: true - affiliation: "1, 2" - - name: Vijay Vedula - affiliation: 3 - equal-contrib: true - - name: Dave Parker - affiliation: 4 - - name: Nathan Wilson - affiliation: 5 - - name: Shawn Shadden - affiliation: 1 - corresponding: true - - name: Alison Marsden - affiliation: 4 - corresponding: true -affiliations: - - name: University of California, Berkeley, United States of America - index: 1 - - name: Peking University, Beijing, People's Republic of China - index: 2 - - name: Columbia University, New York City, United States of America - index: 3 - - name: Stanford University, Stanford, United States of America - index: 4 - - name: University of California, Los Angeles, United States of America - index: 5 -date: 20 January 2021 -bibliography: paper.bib - -# Optional fields if submitting to a AAS journal too, see this blog post: -# # https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing -# aas-doi: 10.3847/xxxxx <- update this with the DOI from AAS once you know it. -# aas-journal: Astrophysical Journal <- The name of the AAS journal. ---- - -# Summary - -Heart disease is the number one cause of death in the US [@Xu2020]. Many efforts have been devoted to studying its progression, diagnosis, and treatment. During the past decade, computational modeling has made significant inroads into the research of heart disease. The heart is inherently a multiphysics system that includes electrophysiology, tissue mechanics, and blood dynamics. Its normal function starts with the propagation of electrical signals that trigger the active contraction of the heart muscle to pump blood into the circulatory system. Rooted in fundamental laws of physics such as the balance of mass, momentum, and energy, computational modeling has been instrumental in studying cardiac physiology such as left ventricular function [@Mittal2015], cardiac arrhythmia [@Trayanova2011], and blood flow in the cardiovascular system [@Arzani2018;@Grande2021]. `svFSI` is the first open source software that specializes in enabling coupled electro-mechano-hemodynamic simulations of the heart. - -# Statement of need - -Accompanying the growing popularity of studying cardiac physiology with computational modeling, many open source software tools that specialize in modeling one or two aspects of the multiphysics process in the heart have been developed. For example, `SimVascular` [@Updegrove2017] enables patient-specific blood flow modeling by providing a complete pipeline from medical image segmentation to simulation results. `FEBio` [@Maas2012] specializes in modeling large-deformation structure mechanics in biophysics with fluid-structure interaction (FSI) capability as well. `openCARP` [@Plank2021] focuses on modeling cardiac electrophysiology. There are other general-purpose open source software such as `LifeV` [@Bertagna2017] and `FEniCS` [@Logg2012], that can be flexibly adapted to simulate different physics in the heart, but significant development effort may be required for this purpose. Recently, Quarteroni et al. have also been developing an open source simulator for the cardiac function, and the fiber generation module [@quateroni_a] and electromechanics [@quateroni_b] have been announced so far. - -`svFSI` is a new multiphysics finite element solver designed specifically for computational modeling of integrative heart dynamics. As the next generation finite element solver for the `SimVascular` software, `svFSI` is capable of modeling hemodynamics, performing large-deformation FSI to capture the motion of cardiac chambers and their interaction with the blood flow, and simulating the complex excitation-contraction coupling between the intracellular ion-exchange processes and tissue contraction. To suit the diverse needs of users, our team has implemented non-Newtonian blood viscosity models, fiber-reinforced nonlinear hyperelastic material models, and both phenomenological and biophysics-based cellular activation models. `svFSI` is also capable of resolving the inherent multi-scale phenomena in cardiac physiology such as the interaction between Purkinje fibers and cardiac muscle, and setting up closed-loop multi-scale hemodynamic simulations with physiological boundary conditions. Moreover, it is worth emphasizing that `svFSI` is fully compatibility with `SimVascular`, and thus can take advantage of the existing pipeline for medical image segmentation, anatomic model construction, meshing, boundary condition prescription, etc. `svFSI` is written in Fortran, taking advantage of the object-oriented programming features of Fortran 2003. It is capable of parallel simulation using MPI. It also provides several built-in iterative linear solvers and preconditioners, along with many other options through Trilinos[@heroux2005]. The code is highly modularized for ease of interoperability and extension. We acknowledge the limited open source compiler support for Fortran on Windows systems, and there is an ongoing effort to convert `svFSI` into pure C++ software. - -# Software architecture - -![Illustration of a multi-mesh, multi-domain simulation configuration.\label{fig:mesh}](Mesh.png){ width=80% } - -The `svFSI` solver defines a modeling task through three key components (objects): mesh, domain, and equation. A mesh defines a spatial discretization of the physical regions such as the Purkinje network, myocardium, or the blood volume. It can be divided into non-overlapping domains through unique domain IDs. Different physical equations, such as the Navier-Stokes (fluid) equation and the structural mechanics (struct) equation are solved on each domain with domain-specific material properties. \autoref{fig:mesh} illustrates how these three objects are utilized in the multiphysics modeling of cardiac mechanics. The whole computational model is composed of two meshes. Mesh 1 represents the ventricular myocardium, where both electrophysiology and nonlinear solid mechanics equations are solved. Given the material heterogeneity of the myocardium, mesh 1 can be further divided into multiple domains so that domain-specific material properties, such as electrical conductivity and material elasticity, can be assigned. Mesh 2 is the fluid region where only the Navier-Stokes equations are solved. - -![Class hierarchy that constitutes a simulation. Description of each class is provided in \autoref{tab:class}. \label{fig:class}](Class.png){ width=80% } - -This highly flexible, multi-mesh, and multi-domain modeling capability is realized in `svFSI` through the class hierarchy depicted in \autoref{fig:class}. The three key components, i.e. mesh, domain, and equation, correspond to classes mshType, dmnType and eqType, respectively. The material heterogeneity for electrophysiology, tissue mechanics or hemodynamics within each domain is defined through cepModelType, stModelType or viscModelType (see \autoref{tab:class}). Two other important classes, bcType and lsType, are also shown in \autoref{fig:class}. They define the boundary conditions and settings for the linear solver that are essential to generating a well-posed simulation configuration. - -\begin{table}[H] - \centering - \begin{tabular}{|l|p{8cm}|} - \hline - \textbf{Class name} & \textbf{Description} \\ \hline - mshType & Defines properties of the mesh, such as the element type, number of nodes per element, and coordinates. \\ \hline - eqType & Defines properties of the equation, such as the physics (fluid/struct/electrophysiology), domains, linear solvers, and boundary conditions. \\ \hline - dmnType & Defines properties of the domain, such as the physics (fluid/structure/electrophysiology), material properties, stabilization parameters, etc. \\ \hline - bcType & Defines properties of the boundary conditions, such as Dirichlet or Neumann, time dependence, spatial profile, etc. \\ \hline - lsType & Defines properties of linear solvers. \\ \hline - cepModelType & Defines properties of the electrophysiology model \\ \hline - stModelType & Defines properties of the structure material model \\ \hline - viscModelType & Defines properties of the viscosity model for fluids \\ \hline - \end{tabular} - \caption{Main classes defined in svFSI.} - \label{tab:class} -\end{table} - -Full documentation for `svFSI` functionality is available from the `SimVascular` website at http://simvascular.github.io. - -# Conclusion -`svFSI` is a multiphysics finite-element solver focusing on whole heart modeling and consists of modules that can efficiently simulate hemodynamics, cardiac mechanics, cardiac electrophysiology as well as the multiphysical interactions among them. `svFSI` has been used to generate several publications [@Vedula2017;@Seo2020a;@Seo2020b;@Baumler2020;@Kong2020] and is employed in several active projects. We will continue to support and develop the software. New features such as methods to simulate heart valves, vascular growth and remodeling are currently under development. The software is envisioned to be applicable to a wide range of research questions in both pediatric and adult cardiovascular disease. - -# Acknowledgments - -This work was supported by the National Science Foundation SI2-SSI 1663671 and 1663747. C.Z. also acknowledges funding from the American Heart Association award 20POST35200253. Previous contribution to the software by Dr. Mahdi Esmaily-Moghadam and Dr. Justin Tran is also acknowledged. - -# References diff --git a/paper.pdf b/paper.pdf deleted file mode 100644 index b735431b..00000000 Binary files a/paper.pdf and /dev/null differ