diff --git a/joss.06531/10.21105.joss.06531.crossref.xml b/joss.06531/10.21105.joss.06531.crossref.xml new file mode 100644 index 0000000000..9d94922bd2 --- /dev/null +++ b/joss.06531/10.21105.joss.06531.crossref.xml @@ -0,0 +1,414 @@ + + + + 20240531220818-c74dbe332ce7b89e74e955f1a1f57292dea7ab12 + 20240531220818 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Software + JOSS + 2475-9066 + + 10.21105/joss + https://joss.theoj.org + + + + + 05 + 2024 + + + 9 + + 97 + + + + EchemFEM: A Firedrake-based Python package for +electrochemical transport + + + + Thomas + Roy + https://orcid.org/0000-0002-4286-4507 + + + Julian + Andrej + https://orcid.org/0000-0001-7661-4840 + + + Aymeric + Antimes + + + Victor A. + Beck + https://orcid.org/0000-0002-0625-9545 + + + Victoria + Ehlinger + https://orcid.org/0000-0001-7333-1271 + + + Florian + Euzenat + + + Nitish + Govindarajan + https://orcid.org/0000-0003-3227-5183 + + + Jack + Guo + https://orcid.org/0000-0003-4090-9289 + + + Tiras Y. + Lin + https://orcid.org/0000-0002-3377-9933 + + + Thomas + Moore + https://orcid.org/0000-0003-0802-5547 + + + + 05 + 31 + 2024 + + + 6531 + + + 10.21105/joss.06531 + + + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + + + + Software archive + 10.5281/zenodo.11403579 + + + GitHub review issue + https://github.com/openjournals/joss-reviews/issues/6531 + + + + 10.21105/joss.06531 + https://joss.theoj.org/papers/10.21105/joss.06531 + + + https://joss.theoj.org/papers/10.21105/joss.06531.pdf + + + + + + OpenFOAM + 2024 + OpenFOAM. (2024). +www.openfoam.org + + + Gmsh: A 3-d finite element mesh generator +with built-in pre-and post-processing facilities + Geuzaine + International journal for numerical methods +in engineering + 11 + 79 + 10.1002/nme.2579 + 2009 + Geuzaine, C., & Remacle, J.-F. +(2009). 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. +https://doi.org/10.1002/nme.2579 + + + A scalable DG solver for the electroneutral +Nernst-Planck equations + Roy + Journal of Computational +Physics + 475 + 10.1016/j.jcp.2022.111859 + 2023 + Roy, T., Andrej, J., & Beck, V. +A. (2023). A scalable DG solver for the electroneutral Nernst-Planck +equations. Journal of Computational Physics, 475, 111859. +https://doi.org/10.1016/j.jcp.2022.111859 + + + Coupling microkinetics with continuum +transport models to understand electrochemical CO_2 reduction in flow +reactors + Govindarajan + PRX Energy + 3 + 2 + 10.1103/PRXEnergy.2.033010 + 2023 + Govindarajan, N., Lin, T. Y., Roy, +T., Hahn, C., & Varley, J. B. (2023). Coupling microkinetics with +continuum transport models to understand electrochemical CO_2 reduction +in flow reactors. PRX Energy, 2(3), 033010. +https://doi.org/10.1103/PRXEnergy.2.033010 + + + Firedrake user manual + Ham + 10.25561/104839 + 2023 + Ham, D. A., Kelly, P. H. J., +Mitchell, L., Cotter, C. J., Kirby, R. C., Sagiyama, K., Bouziani, N., +Vorderwuelbecke, S., Gregory, T. J., Betteridge, J., Shapero, D. R., +Nixon-Hill, R. W., Ward, C. J., Farrell, P. E., Brubeck, P. D., Marsden, +I., Gibson, T. H., Homolya, M., Sun, T., … Markall, G. R. (2023). +Firedrake user manual (First edition). Imperial College London; +University of Oxford; Baylor University; University of Washington. +https://doi.org/10.25561/104839 + + + PETSc/TAO users manual + Balay + 10.2172/1968587 + 2023 + Balay, S., Abhyankar, S., Adams, M. +F., Benson, S., Brown, J., Brune, P., Buschelman, K., Constantinescu, +E., Dalcin, L., Dener, A., Eijkhout, V., Faibussowitsch, J., Gropp, W. +D., Hapla, V., Isaac, T., Jolivet, P., Karpeev, D., Kaushik, D., +Knepley, M. G., … Zhang, J. (2023). PETSc/TAO users manual (ANL-21/39 - +Revision 3.20). Argonne National Laboratory. +https://doi.org/10.2172/1968587 + + + PETSc Web page + Balay + 2023 + Balay, S., Abhyankar, S., Adams, M. +F., Benson, S., Brown, J., Brune, P., Buschelman, K., Constantinescu, E. +M., Dalcin, L., Dener, A., Eijkhout, V., Faibussowitsch, J., Gropp, W. +D., Hapla, V., Isaac, T., Jolivet, P., Karpeev, D., Kaushik, D., +Knepley, M. G., … Zhang, J. (2023). PETSc Web page. https://petsc.org/. +https://petsc.org/ + + + CatMAP: A software package for +descriptor-based microkinetic mapping of catalytic +trends + Medford + Catal. Lett. + 3 + 145 + 10.1007/s10562-015-1495-6 + 2015 + Medford, A. J., Shi, C., Hoffmann, M. +J., Lausche, A. C., Fitzgibbon, S. R., Bligaard, T., & Nørskov, J. +K. (2015). CatMAP: A software package for descriptor-based microkinetic +mapping of catalytic trends. Catal. Lett., 145(3), 794–807. +https://doi.org/10.1007/s10562-015-1495-6 + + + Simulations of cyclic voltammetry for +electric double layers in asymmetric electrolytes: A generalized +modified Poisson–Nernst–Planck model + Wang + The Journal of Physical Chemistry +C + 36 + 117 + 10.1021/jp402181e + 2013 + Wang, H., Thiele, A., & Pilon, L. +(2013). Simulations of cyclic voltammetry for electric double layers in +asymmetric electrolytes: A generalized modified Poisson–Nernst–Planck +model. The Journal of Physical Chemistry C, 117(36), 18286–18297. +https://doi.org/10.1021/jp402181e + + + Python for electrochemistry: A free and +all-in-one toolset + Zheng + ECS Advances + 4 + 2 + 10.1149/2754-2734/acff0b + 2023 + Zheng, W. (2023). Python for +electrochemistry: A free and all-in-one toolset. ECS Advances, 2(4), +040502. https://doi.org/10.1149/2754-2734/acff0b + + + Python battery mathematical modelling +(PyBaMM) + Sulzer + Journal of Open Research +Software + 1 + 9 + 10.5334/jors.309 + 2021 + Sulzer, V., Marquis, S. G., Timms, +R., Robinson, M., & Chapman, S. J. (2021). Python battery +mathematical modelling (PyBaMM). Journal of Open Research Software, +9(1). https://doi.org/10.5334/jors.309 + + + Dolfin-adjoint 2018.1: Automated adjoints for +FEniCS and Firedrake + Mitusch + Journal of Open Source +Software + 38 + 4 + 10.21105/joss.01292 + 2019 + Mitusch, S. K., Funke, S. W., & +Dokken, J. S. (2019). Dolfin-adjoint 2018.1: Automated adjoints for +FEniCS and Firedrake. Journal of Open Source Software, 4(38), 1292. +https://doi.org/10.21105/joss.01292 + + + Topology optimization for the design of +porous electrodes + Roy + Structural and Multidisciplinary +Optimization + 6 + 65 + 10.1007/s00158-022-03249-2 + 2022 + Roy, T., Salazar de Troya, M. A., +Worsley, M. A., & Beck, V. A. (2022). Topology optimization for the +design of porous electrodes. Structural and Multidisciplinary +Optimization, 65(6), 171. +https://doi.org/10.1007/s00158-022-03249-2 + + + Design and additive manufacturing of +optimized electrodes for energy storage applications + Reale Batista + Carbon + 205 + 10.1016/j.carbon.2023.01.044 + 2023 + Reale Batista, M. D., Chandrasekaran, +S., Moran, B. D., Salazar de Troya, M., Pinongcos, A., Wang, Z., +Hensleigh, R., Carleton, A., Zeng, M., Roy, T., Lin, D., Xue, X., Beck, +V. A., Tortorelli, D. A., Stadermann, M., Zheng, R., Li, Y., & +Worsley, M. A. (2023). Design and additive manufacturing of optimized +electrodes for energy storage applications. Carbon, 205, 262–269. +https://doi.org/10.1016/j.carbon.2023.01.044 + + + Unified form language: A domain-specific +language for weak formulations of partial differential +equations + Alnæs + ACM Transactions on Mathematical Software +(TOMS) + 2 + 40 + 10.1145/2566630 + 2014 + Alnæs, M. S., Logg, A., Ølgaard, K. +B., Rognes, M. E., & Wells, G. N. (2014). Unified form language: A +domain-specific language for weak formulations of partial differential +equations. ACM Transactions on Mathematical Software (TOMS), 40(2), +1–37. https://doi.org/10.1145/2566630 + + + Automated solution of differential equations +by the finite element method: The FEniCS book + Logg + 84 + 10.1007/978-3-642-23099-8 + 2012 + Logg, A., Mardal, K.-A., & Wells, +G. (2012). Automated solution of differential equations by the finite +element method: The FEniCS book (Vol. 84). Springer Science & +Business Media. +https://doi.org/10.1007/978-3-642-23099-8 + + + DOLFINx: The next generation FEniCS problem +solving environment + Barrata + 10.5281/zenodo.10447666 + 2023 + Barrata, I. A., Dean, J. P., Dokken, +J. S., HABERA, M., HALE, J., Richardson, C., Rognes, M. E., Scroggs, M. +W., Sime, N., & Wells, G. N. (2023). DOLFINx: The next generation +FEniCS problem solving environment. +https://doi.org/10.5281/zenodo.10447666 + + + Topology optimization for the full-cell +design of porous electrodes in electrochemical energy storage +devices + Li + arXiv preprint +arXiv:2403.18184 + 10.48550/arXiv.2403.18184 + 2024 + Li, H., Bucci, G., Brady, N. W., +Cross, N. R., Ehlinger, V. M., Lin, T. Y., Salazar de Troya, M., +Tortorelli, D., Worsley, M. A., & Roy, T. (2024). Topology +optimization for the full-cell design of porous electrodes in +electrochemical energy storage devices. arXiv Preprint arXiv:2403.18184. +https://doi.org/10.48550/arXiv.2403.18184 + + + cideMOD: An open source tool for battery cell +inhomogeneous performance understanding + Aylagas + Journal of The Electrochemical +Society + 9 + 169 + 10.1149/1945-7111/ac91fb + 2022 + Aylagas, R. C., Ganuza, C., Parra, +R., Yañez, M., & Ayerbe, E. (2022). cideMOD: An open source tool for +battery cell inhomogeneous performance understanding. Journal of The +Electrochemical Society, 169(9), 090528. +https://doi.org/10.1149/1945-7111/ac91fb + + + + + + diff --git a/joss.06531/10.21105.joss.06531.pdf b/joss.06531/10.21105.joss.06531.pdf new file mode 100644 index 0000000000..196356376f Binary files /dev/null and b/joss.06531/10.21105.joss.06531.pdf differ diff --git a/joss.06531/paper.jats/10.21105.joss.06531.jats b/joss.06531/paper.jats/10.21105.joss.06531.jats new file mode 100644 index 0000000000..3cf7be56fb --- /dev/null +++ b/joss.06531/paper.jats/10.21105.joss.06531.jats @@ -0,0 +1,785 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +6531 +10.21105/joss.06531 + +EchemFEM: A Firedrake-based Python package for +electrochemical transport + + + +https://orcid.org/0000-0002-4286-4507 + +Roy +Thomas + + +* + + +https://orcid.org/0000-0001-7661-4840 + +Andrej +Julian + + + + + +Antimes +Aymeric + + + + +https://orcid.org/0000-0002-0625-9545 + +Beck +Victor A. + + + + +https://orcid.org/0000-0001-7333-1271 + +Ehlinger +Victoria + + + + + +Euzenat +Florian + + + + +https://orcid.org/0000-0003-3227-5183 + +Govindarajan +Nitish + + + + +https://orcid.org/0000-0003-4090-9289 + +Guo +Jack + + + + +https://orcid.org/0000-0002-3377-9933 + +Lin +Tiras Y. + + + + +https://orcid.org/0000-0003-0802-5547 + +Moore +Thomas + + + + + +Lawrence Livermore National Laboratory, CA, United States +of America + + + + +TotalEnergies OneTech, France + + + + +Queensland University of Technology, +Australia + + + + +* E-mail: + + +8 +2 +2024 + +9 +97 +6531 + +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 +Firedrake +Finite Element Method +electrochemistry + + + + + + Summary +

The transition from fossil fuels to renewable energy has brought + about a rapid increase in the availability of clean electricity. + However, electricity generated from sources such as wind and solar are + limited to intermittent operation due to daily and seasonal variation. + One solution is to utilize electrochemical devices in energy storage + and electrochemical manufacturing applications, where they can harness + surplus energy and decarbonize chemical industries traditionally + reliant on petrochemical feedstocks. Managing the growing prevalence + of renewable energy underscores the importance of developing and + scaling up these technologies, which can in turn facilitate the + achievement of carbon emission reduction commitments of companies and + developed economies. Likewise, the electrification of transport + creates an increasing need for energy-dense electrochemical energy + storage devices such as batteries and supercapacitors. Naturally, + simulation tools are required to assist in the design of efficient and + industrial-scale electrochemical devices.

+

Modeling and simulation are used extensively to describe the + physics of the electrochemical and transport mechanisms in + electrochemical devices. These devices have many applications, from + miniaturized lithium-ion batteries for medical devices up to + industrial-scale hydrogen fuel cells for backup power generation. + Energy storage devices include batteries and supercapacitors, as well + as flow batteries, which utilize a flowing electrolyte instead of a + stationary liquid or polymer electrolyte. Electrolyzers are devices + that use electrical energy to perform electrochemical reactions. Some + current industrial applications for electrolysis include the + chlor-alkali process for the production of chlorine gas and the + Hall-Héroult process for aluminum production. Active areas of research + include the development of electrolyzers that transform carbon dioxide + into useful chemicals such as base molecules for sustainable aviation + fuels or the chemical industry, as well as electrolyzers that create + hydrogen from water. In the reverse process, fuel cells use fuels such + as hydrogen to generate electricity. While electrochemical devices + span many scales and industries, the governing equations and + underlying physical phenomena remain similar.

+

The transport of charged chemical species in a fluid is often + modeled using the Nernst-Planck equation, which includes the usual + advection and diffusion transport as well as + electromigration, where charged species are + transported by an electric field. Often, these species are also + undergoing reactions either in the bulk fluid or on the + boundaries.

+

EchemFEM provides a high-level user interface for a finite element + implementation of the Nernst-Planck equation. The user is simply + required to provide physical parameters as well as functions + describing the chemical reactions (charge-transfer or bulk reactions). + The mesh can be defined using either built-in functions for simple + geometries, or imported from external packages, such as Gmsh + (Geuzaine + & Remacle, 2009), for more complex geometries. Then, the + desired transport physics are selected using keyword arguments. Ionic + charge can be modeled using either the Poisson equation or the + electroneutrality approximation. The simulated devices can have + resolved electrolyte-electrode interfaces or homogenized porous + electrodes, in which case electron conduction is also modeled. + Additionally, finite size effects are available, which includes models + such as Generalized Modified Poisson-Nernst-Planck (GMPNP) + (Wang + et al., 2013). Lastly, a fluid flow solver for the + incompressible Navier-Stokes and Navier-Stokes-Brinkman equations is + provided.

+

EchemFEM is based on Firedrake + (Ham + et al., 2023), an open-source finite element package similar to + FEniCS + (Logg + et al., 2012) and FEniCSx + (Barrata + et al., 2023), enabling straightforward implementation of the + governing equations in Python through the Unified Form Language (UFL) + (Alnæs + et al., 2014). Firedake has access to scalable, customizable, + solvers through its interface with PETSc + (Balay + et al., 2023b, + 2023a), + allowing for parallelization and scalability on computing clusters. + This balance between usability and scalability permits a seamless + transition from prototyping to large-scale simulation. EchemFEM + leverages Firedrake’s capabilities while further increasing the + ease-of-use. Indeed, since the governing equations are already + implemented, little to no knowledge of Firedrake and the finite + element method is required to use EchemFEM. Firedrake is preferred + over FEniCS and FEniCSx for several reasons: it offers a custom + preconditioning interface + (Mitusch + et al., 2019), Firedrake continues to be actively developed + unlike FEniCS, and unlike FEniCSx, it already includes automatic + adjoint capabilities.

+

The repository includes several examples of electrochemical devices + such as flow reactors, flow batteries, and CO2 electrolyzers.

+
+ + Statement of need +

Electrochemical phenomena are highly complex, making + characterization of electrochemical devices through in-operando + experiments challenging. Simulation is an important tool for + predicting the performance of electrochemical devices, as well as + assisting in their design. As technologies get scaled up from the + laboratory scale to industrial scale, experiments become less + tractable and therefore simulation increasingly important. Naturally, + the scalability of simulators is crucial. Furthermore, many existing + models and codes are just one dimensional. To capture the effects of + fluid flow and non-monolithic, architected electrodes, + higher-dimensional effects do matter. For three-dimensional systems, + iterative methods and appropriate preconditioners are required to + maintain scalability.

+

Currently, commercial software are the most commonly used codes for + electrochemistry simulations. COMSOL Multiphysics®, with its detailed + electrochemistry module, is the most popular, while Simcenter™ + STAR-CCM+™ is also used commonly for flowing systems. These programs + provide simple graphical user interfaces (GUI), which allow users to + quickly set up new simulations. Additionally, other physics modules + such as fluid dynamics are available and can usually be coupled with + the electrochemistry simulation. However, there are several drawbacks + to using such commercial software. For instance, license fees can be + prohibitively expensive, therefore limiting collaboration. + Furthermore, the closed nature of the source code limits the + flexibility of the software. Indeed, it is not possible to implement + new discretization schemes and preconditioning approaches that may be + required for numerical stability or scalability, respectively. + Finally, since everything needs to be set up through the GUI, + scripting and coupling to other software are difficult tasks.

+

There is a growing number of open-source software for + electrochemistry, especially Python-based packages + (Zheng, + 2023), many of which are specialized for specific applications, + notably batteries. One such package, PyBaMM + (Sulzer + et al., 2021), is a battery modelling code with a flexible + implementation, allowing for new models and numerical methods to be + tested. Similarly, cideMOD + (Aylagas + et al., 2022) leverages FEniCSx in a manner analogous to how + EchemFEM employs Firedrake, thus enabling the simulation of 2D and 3D + battery cell geometries. OpenFOAM + (OpenFOAM, + 2024) is a popular tool that is mainly used for computational + fluid dynamics, but implementation of custom transport mechanisms, + such as those from electrochemistry, can have a steep learning + curve.

+

EchemFEM provides a general framework for simulating + electrochemical transport: it is not specific to an application. Since + it is based on Firedrake, any additional physics that can be + implemented in a finite element framework can be coupled to EchemFEM. + In one of the demos, the incompressible Navier-Stokes equations are + solved in a reactor with an irregular surface, providing a velocity + field for the transport equations. Similarly, in a flow battery + example, the Navier-Stokes-Brinkman equations are solved.

+

In some cases, for example for fast flows, stabilization schemes + that are not offered in other software may be required. For continuous + Galerkin (CG) elements, a streamline-upwind Petrov-Galerkin (SUPG) + method for the Nernst-Planck equation is provided. For discontinuous + Galerkin (DG), a custom upwind scheme for the Nernst-Planck equation + is used + (Roy + et al., 2023). In both cases, the upwinding considers the + combined advection-migration ``velocity’’.

+

As opposed to commercial software, custom scalable solvers are + available in Firedrake. A plethora of solver options are available + through simple PETSc keywords and custom operators for preconditioning + can be defined using Firedrake + (Mitusch + et al., 2019). In Roy et al. + (2023), + scalable block preconditioners were developed for the electroneutral + Nernst-Planck equations with DG and implemented in EchemFEM.

+

Combining EchemFEM with other Python packages is rather simple. In + Govindarajan et al. + (2023), + multi-scale simulations for CO2 reduction in flow reactors are + performed by coupling a microkinetics model from CatMAP + (Medford + et al., 2015) with the GMPNP transport model from EchemFEM. The + simulations are two orders of magnitude faster than a previous + implementation where the transport is done in COMSOL Multiphysics®, + due to the tedious interface between the commercial software and + CatMAP.

+

Firedrake’s automatic adjoint capabilities facilitate the + straightforward solution of PDE-constrained optimization problems + (Mitusch + et al., 2019), already employed in electrochemical applications + (Li + et al., 2024; + Reale + Batista et al., 2023; + Roy + et al., 2022). We are currently investigating optimization + problems using EchemFEM.

+
+ + Acknowledgements +

This work was performed under the auspices of the U.S. Department + of Energy by Lawrence Livermore National Laboratory (LLNL) under + Contract DE-AC52-07NA27344, and was partially supported by a + Cooperative Research and Development Agreement (CRADA) between LLNL + and TotalEnergies American Services, Inc. (affiliate of TotalEnergies + SE) under agreement number TC02307 and Laboratory Directed Research + and Development (LDRD) funding under projects 19-ERD-035 and + 22-SI-006. LLNL Release Number LLNL-JRNL-860653.

+
+ + + + + + OpenFOAM + 2024 + www.openfoam.org + + + + + + GeuzaineChristophe + RemacleJean-François + + Gmsh: A 3-d finite element mesh generator with built-in pre-and post-processing facilities + International journal for numerical methods in engineering + Wiley Online Library + 2009 + 79 + 11 + 10.1002/nme.2579 + 1309 + 1331 + + + + + + RoyThomas + AndrejJulian + BeckVictor A + + A scalable DG solver for the electroneutral Nernst-Planck equations + Journal of Computational Physics + Elsevier + 2023 + 475 + 10.1016/j.jcp.2022.111859 + 111859 + + + + + + + GovindarajanNitish + LinTiras Y + RoyThomas + HahnChristopher + VarleyJoel B + + Coupling microkinetics with continuum transport models to understand electrochemical CO_2 reduction in flow reactors + PRX Energy + APS + 2023 + 2 + 3 + 10.1103/PRXEnergy.2.033010 + 033010 + + + + + + + HamDavid A. + KellyPaul H. J. + MitchellLawrence + CotterColin J. + KirbyRobert C. + SagiyamaKoki + BouzianiNacime + VorderwuelbeckeSophia + GregoryThomas J. + BetteridgeJack + ShaperoDaniel R. + Nixon-HillReuben W. + WardConnor J. + FarrellPatrick E. + BrubeckPablo D. + MarsdenIndia + GibsonThomas H. + HomolyaMiklós + SunTianjiao + McRaeAndrew T. 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