diff --git a/joss.07244/10.21105.joss.07244.crossref.xml b/joss.07244/10.21105.joss.07244.crossref.xml new file mode 100644 index 000000000..8ce38703c --- /dev/null +++ b/joss.07244/10.21105.joss.07244.crossref.xml @@ -0,0 +1,266 @@ + + + + 20241217083246-dee07d7649bec92603cda195631ac3575ef9e248 + 20241217083246 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Software + JOSS + 2475-9066 + + 10.21105/joss + https://joss.theoj.org + + + + + 12 + 2024 + + + 9 + + 104 + + + + RNMC: kinetic Monte Carlo implementations for complex reaction networks + + + + Laura + Zichi + + Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America 94720 + Department of Physics, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America 48109 + + https://orcid.org/0000-0003-3897-3097 + + + Daniel + Barter + + Energy Storage and Distributed Resources, Lawrence Berkeley National Laboratory, Berkeley, CA United States of America 94720 + + https://orcid.org/0000-0002-6408-1255 + + + Eric + Sivonxay + + Energy Storage and Distributed Resources, Lawrence Berkeley National Laboratory, Berkeley, CA United States of America 94720 + + https://orcid.org/0000-0002-6408-1255 + + + Evan Walter Clark + Spotte-Smith + + Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America 94720 + Department of Materials Science and Engineering, University of California - Berkeley, CA, United States of America 94720 + + https://orcid.org/0000-0003-1554-197X + + + Rohith Srinivaas + Mohanakrishnan + + Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America 94720 + Department of Materials Science and Engineering, University of California - Berkeley, CA, United States of America 94720 + + + + Emory M. + Chan + + Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America 94720 + + + + Kristin Aslaug + Persson + + Department of Materials Science and Engineering, University of California - Berkeley, CA, United States of America 94720 + Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America 94720 + + + + Samuel M. + Blau + + Energy Storage and Distributed Resources, Lawrence Berkeley National Laboratory, Berkeley, CA United States of America 94720 + + + + + 12 + 17 + 2024 + + + 7244 + + + 10.21105/joss.07244 + + + 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.14360064 + + + GitHub review issue + https://github.com/openjournals/joss-reviews/issues/7244 + + + + 10.21105/joss.07244 + https://joss.theoj.org/papers/10.21105/joss.07244 + + + https://joss.theoj.org/papers/10.21105/joss.07244.pdf + + + + + + On the theory of electron-transfer reactions. VI. Unified treatment for homogeneous and electrode reactions + Marcus + The Journal of Chemical Physics + 2 + 43 + 10.1063/1.1696792 + 1965 + Marcus, R. A. (1965). On the theory of electron-transfer reactions. VI. Unified treatment for homogeneous and electrode reactions. The Journal of Chemical Physics, 43(2), 679–701. https://doi.org/10.1063/1.1696792 + + + Exact stochastic simulation of coupled chemical reactions + Gillespie + The Journal of Physical Chemistry + 25 + 81 + 1977 + Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry, 81(25), 2340–2361. + + + Crossing the mesoscale no-mans land via parallel kinetic monte carlo + Garcia Cardona + 2009 + Garcia Cardona, C., Wagner, G. J., Tikare, V., Holm, E. A., Plimpton, S. J., Thompson, A. P., Slepoy, A., Zhou, X. W., Battaile, C. C., & Chandross, M. E. (2009). Crossing the mesoscale no-mans land via parallel kinetic monte carlo. Sandia National Laboratories (SNL), Albuquerque, NM,; Livermore, CA. + + + Kmos: A lattice kinetic monte carlo framework + Hoffmann + Computer Physics Communications + 7 + 185 + 10.1016/j.cpc.2014.04.003 + 2014 + Hoffmann, M. J., Matera, S., & Reuter, K. (2014). Kmos: A lattice kinetic monte carlo framework. Computer Physics Communications, 185(7), 2138–2150. https://doi.org/10.1016/j.cpc.2014.04.003 + + + Electrochemical systems + Newman + 2021 + Newman, J., & Balsara, N. P. (2021). Electrochemical systems. John Wiley & Sons. + + + Toward a mechanistic model of solid–electrolyte interphase formation and evolution in lithium-ion batteries + Spotte-Smith + ACS Energy Letters + 4 + 7 + 10.1021/acsenergylett.2c00517 + 2022 + Spotte-Smith, E. W. C., Kam, R. L., Barter, D., Xie, X., Hou, T., Dwaraknath, S., Blau, S. M., & Persson, K. A. (2022). Toward a mechanistic model of solid–electrolyte interphase formation and evolution in lithium-ion batteries. ACS Energy Letters, 7(4), 1446–1453. https://doi.org/10.1021/acsenergylett.2c00517 + + + Predictive stochastic analysis of massive filter-based electrochemical reaction networks + Barter + Digital Discovery + 1 + 2 + 10.1039/D2DD00117A + 2023 + Barter, D., Spotte-Smith, E. W. C., Redkar, N. S., Khanwale, A., Dwaraknath, S., Persson, K. A., & Blau, S. M. (2023). Predictive stochastic analysis of massive filter-based electrochemical reaction networks. Digital Discovery, 2(1), 123–137. https://doi.org/10.1039/D2DD00117A + + + Chemical reaction networks explain gas evolution mechanisms in Mg-ion batteries + Spotte-Smith + Journal of the American Chemical Society + 22 + 145 + 10.1021/jacs.3c02222 + 2023 + Spotte-Smith, E. W. C., Blau, S. M., Barter, D., Leon, N. J., Hahn, N. T., Redkar, N. S., Zavadil, K. R., Liao, C., & Persson, K. A. (2023). Chemical reaction networks explain gas evolution mechanisms in Mg-ion batteries. Journal of the American Chemical Society, 145(22), 12181–12192. https://doi.org/10.1021/jacs.3c02222 + + + Accelerating the design of multishell upconverting nanoparticles through bayesian optimization + Xia + Nano Letters + 23 + 23 + 10.1021/acs.nanolett.3c03568 + 2023 + Xia, X., Sivonxay, E., Helms, B. A., Blau, S. M., & Chan, E. M. (2023). Accelerating the design of multishell upconverting nanoparticles through bayesian optimization. Nano Letters, 23(23), 11129–11136. https://doi.org/10.1021/acs.nanolett.3c03568 + + + Combinatorial approaches for developing upconverting nanomaterials: High-throughput screening, modeling, and applications + Chan + Chemical Society Reviews + 6 + 44 + 10.1039/C4CS00205A + 2015 + Chan, E. M. (2015). Combinatorial approaches for developing upconverting nanomaterials: High-throughput screening, modeling, and applications. Chemical Society Reviews, 44(6), 1653–1679. https://doi.org/10.1039/C4CS00205A + + + A generalized approach to photon avalanche upconversion in luminescent nanocrystals + Skripka + Nano Letters + 15 + 23 + 10.1021/acs.nanolett.3c01955 + 2023 + Skripka, A., Lee, M., Qi, X., Pan, J.-A., Yang, H., Lee, C., Schuck, P. J., Cohen, B. E., Jaque, D., & Chan, E. M. (2023). A generalized approach to photon avalanche upconversion in luminescent nanocrystals. Nano Letters, 23(15), 7100–7106. https://doi.org/10.1021/acs.nanolett.3c01955 + + + Energy transfer networks within upconverting nanoparticles are complex systems with collective, robust, and history-dependent dynamics + Teitelboim + The Journal of Physical Chemistry C + 4 + 123 + 10.1021/acs.jpcc.9b00161 + 2019 + Teitelboim, A., Tian, B., Garfield, D. J., Fernandez-Bravo, A., Gotlin, A. C., Schuck, P. J., Cohen, B. E., & Chan, E. M. (2019). Energy transfer networks within upconverting nanoparticles are complex systems with collective, robust, and history-dependent dynamics. The Journal of Physical Chemistry C, 123(4), 2678–2689. https://doi.org/10.1021/acs.jpcc.9b00161 + + + + + + diff --git a/joss.07244/10.21105.joss.07244.pdf b/joss.07244/10.21105.joss.07244.pdf new file mode 100644 index 000000000..381eb86aa Binary files /dev/null and b/joss.07244/10.21105.joss.07244.pdf differ diff --git a/joss.07244/paper.jats/10.21105.joss.07244.jats b/joss.07244/paper.jats/10.21105.joss.07244.jats new file mode 100644 index 000000000..5110cdced --- /dev/null +++ b/joss.07244/paper.jats/10.21105.joss.07244.jats @@ -0,0 +1,528 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +7244 +10.21105/joss.07244 + +RNMC: kinetic Monte Carlo implementations for complex +reaction networks + + + +https://orcid.org/0000-0003-3897-3097 + +Zichi +Laura + + + + + +https://orcid.org/0000-0002-6408-1255 + +Barter +Daniel + + + + +https://orcid.org/0000-0002-6408-1255 + +Sivonxay +Eric + + + + +https://orcid.org/0000-0003-1554-197X + +Spotte-Smith +Evan Walter Clark + + + + + + +Mohanakrishnan +Rohith Srinivaas + + + + + + +Chan +Emory M. + + + + + +Persson +Kristin Aslaug + + + +* + + + +Blau +Samuel M. + + +* + + + +Materials Science Division, Lawrence Berkeley National +Laboratory, Berkeley, CA, United States of America 94720 + + + + +Department of Physics, University of Michigan - Ann Arbor, +Ann Arbor, MI, United States of America 48109 + + + + +Energy Storage and Distributed Resources, Lawrence Berkeley +National Laboratory, Berkeley, CA United States of America +94720 + + + + +Department of Materials Science and Engineering, University +of California - Berkeley, CA, United States of America +94720 + + + + +Molecular Foundry, Lawrence Berkeley National Laboratory, +Berkeley, CA, United States of America 94720 + + + + +* E-mail: +* E-mail: + + +14 +8 +2024 + +9 +104 +7244 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2024 +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) + + + +C++ +chemical dynamics +kinetic Monte Carlo +nanoparticle +electrochemistry +Gillespie + + + + + + Summary +

Macroscopic chemical and physical phenomena are driven by + microscopic interactions at the atomic and molecular scales. In order + to capture complex processes with high fidelity, simulation methods + that bridge disparate time and length scales are needed. While + techniques like molecular dynamics and ab initio + simulations capture dynamics and reactivity at high resolution, they + cannot be used beyond relatively small length (hundreds to thousands + of atoms) and time scales (picoseconds to microseconds). Kinetic Monte + Carlo (kMC) approaches overcome these limitations to bridge length and + time scales across several orders of magnitude while retaining + relevant microscopic resolution, making it a powerful and flexible + tool.

+

Here, we present Reaction Network Monte Carlo + (RNMC), an easy-to-use, modular, + high-performance kMC simulation framework that enables modeling of + complex systems. RNMC consists of a core module + defining the common features of kMC algorithms, including an + implementation of the Gillespie algorithm + (Gillespie, + 1977), input/output operations leveraging SQLite databases, + random number sampling, threading logic for parallel execution, and + dependency graphs for efficient event propensity updates. In addition, + there are currently three modules defining kMC implementations for + different types of applications. The GMC + (Gillespie Monte Carlo) module enables simulations of reaction + networks in a homogeneous (well-mixed) environment. + GMC is a basic tool that is appropriate for + general simulations of solution-phase chemistry. The + NPMC (NanoParticle Monte Carlo) module enables + simulation of dynamics in nanoparticles with 3D statistical field + theory and supports one- and two-site interactions. Finally, the + LGMC (Lattice Gillespie Monte Carlo) module is + designed for simulations of multi-phase systems (especially at + solid-fluid interfaces) where chemical and electrochemical reactions + can occur between a lattice region and a homogeneous region. We have + designed RNMC to be easily extensible, enabling + users to add additional kMC modules for other diverse chemical and + physical systems.

+ + + Statement of need +

There are many existing kMC implementations, including several open + source examples (e.g. the Stochastic Parallel PARticle Kinetic + Simulator or SPPARKS + (Garcia + Cardona et al., 2009) and kmos + (Hoffmann + et al., 2014)). RNMC began as a fork of + SPPARKS but differs in several important ways. First, because + RNMC uses the widely supported SQLite database + engine for simulation inputs and outputs, it facilitates the + automation of simulations. Second, RNMC has a + focus on modularity. All simulators leverage the small core library, + which serves as a common interface through the use of templating. As + long as they can operate through this shared core, different + simulation implementations are totally independent. This means that + new developers need only read and understand the core library to be + able to add new capabilities to RNMC, lowering + the barrier to entry, and further reduces the likelihood that new + additions will adversely affect pre-existing code.

+

The simulation modules already implemented in + RNMC provide unique capabilities that are not + widely available in other open source codes. + NPMC is specifically designed for 3D + simulations of the complex photophysical interaction networks in + nanocrystals + (Teitelboim + et al., 2019), particularly multi-domain heterostructures whose + optical properties cannot be calculated deterministically + (Skripka + et al., 2023). NPMC can be used to + simulate energy transfer interactions between dopants in + nanoparticles, their radiative transitions, and nonlinear processes + such as upconversion + (Chan, + 2015) and photon avalanching + (Skripka + et al., 2023). LGMC is also somewhat + unique in that it can simulate multi-phase systems and electrochemical + processes. Simulations using LGMC can include a + lattice region and a homogeneous solution region which can interact + via interfacial reactions. Electrochemical reactions + can be treated using Marcus theory + (Marcus, + 1965) or Butler-Volmer kinetics + (Newman + & Balsara, 2021). Because it allows for a dynamic lattice + region, LGMC is also appropriate for + simulations of nucleation and growth, dissolution, precipitation, and + related phenomena.

+

We have already used the GMC module in a + number of prior works in applications related to Li-ion and Mg-ion + batteries + (Barter + et al., 2023; + Spotte-Smith + et al., 2022, + 2023). + We note that these simulations included tens of millions of reactions, + demonstrating that RNMC is able to scale to + large and complex reaction networks. In addition, we have used + NPMC to perform Bayesian optimization of + upconverting nanoparticles + (Xia + et al., 2023).

+ + + Acknowledgements +

This project was intellectually led by the Laboratory Directed + Research and Development Program of Lawrence Berkeley National + Laboratory under U.S. Department of Energy Contract + No. DE-AC02-05CH11231. L.Z. was supported in part by the U.S. + Department of Energy, Office of Science, Office of Workforce + Development for Teachers and Scientists (WDTS) under the Science + Undergraduate Laboratory Internships Program (SULI). E.W.C.S.-S. was + supported by the Kavli Energy NanoScience Institute Philomathia + Graduate Student Fellowship. Work at the Molecular Foundry (E.M.C., + K.A.P) was supported by the Office of Science, Office of Basic Energy + Sciences, of the U.S. Department of Energy under Contract + No. DE-AC02-05CH11231. Additional support came from the Joint Center + for Energy Storage Research (JCESR), an Energy Innovation Hub funded + by the U.S. Department of Energy, Office of Science, Basic Energy + Sciences. This code was developed and tested using computational + resources provided by the National Energy Research Scientific + Computing Center (NERSC), a U.S. Department of Energy Office of + Science User Facility under Contract No. DE-AC02-05CH11231, the Eagle + and Swift HPC systems at the National Renewable Energy Laboratory + (NREL), and the Lawrencium HPC cluster at Lawrence Berkeley National + Laboratory.

+ + + + + + + + + MarcusRudolph A + + On the theory of electron-transfer reactions. VI. Unified treatment for homogeneous and electrode reactions + The Journal of Chemical Physics + American Institute of Physics + 1965 + 43 + 2 + 10.1063/1.1696792 + 679 + 701 + + + + + + GillespieDaniel T + + Exact stochastic simulation of coupled chemical reactions + The Journal of Physical Chemistry + ACS Publications + 1977 + 81 + 25 + 2340 + 2361 + + + + + + Garcia CardonaCristina + WagnerGregory John + TikareVeena + HolmElizabeth Ann + PlimptonSteven James + ThompsonAidan Patrick + SlepoyAlexander + ZhouXiao Wang + BattaileCorbett Chandler + ChandrossMichael Evan + + Crossing the mesoscale no-mans land via parallel kinetic monte carlo + Sandia National Laboratories (SNL), Albuquerque, NM,; Livermore, CA + 2009 + + + + + + HoffmannMax J + MateraSebastian + ReuterKarsten + + Kmos: A lattice kinetic monte carlo framework + Computer Physics Communications + Elsevier + 2014 + 185 + 7 + 10.1016/j.cpc.2014.04.003 + 2138 + 2150 + + + + + + NewmanJohn + BalsaraNitash P + + Electrochemical systems + John Wiley & Sons + 2021 + + + + + + Spotte-SmithEvan Walter Clark + KamRonald L + BarterDaniel + XieXiaowei + HouTingzheng + DwaraknathShyam + BlauSamuel M + PerssonKristin A + + Toward a mechanistic model of solid–electrolyte interphase formation and evolution in lithium-ion batteries + ACS Energy Letters + ACS Publications + 2022 + 7 + 4 + 10.1021/acsenergylett.2c00517 + 1446 + 1453 + + + + + + BarterDaniel + Spotte-SmithEvan Walter Clark + RedkarNikita S + KhanwaleAniruddh + DwaraknathShyam + PerssonKristin A + BlauSamuel M + + Predictive stochastic analysis of massive filter-based electrochemical reaction networks + Digital Discovery + Royal Society of Chemistry + 2023 + 2 + 1 + 10.1039/D2DD00117A + 123 + 137 + + + + + + Spotte-SmithEvan Walter Clark + BlauSamuel M + BarterDaniel + LeonNoel J + HahnNathan T + RedkarNikita S + ZavadilKevin R + LiaoChen + PerssonKristin A + + Chemical reaction networks explain gas evolution mechanisms in Mg-ion batteries + Journal of the American Chemical Society + ACS Publications + 2023 + 145 + 22 + 10.1021/jacs.3c02222 + 12181 + 12192 + + + + + + XiaXiaojing + SivonxayEric + HelmsBrett A + BlauSamuel M + ChanEmory M + + Accelerating the design of multishell upconverting nanoparticles through bayesian optimization + Nano Letters + ACS Publications + 2023 + 23 + 23 + 10.1021/acs.nanolett.3c03568 + 11129 + 11136 + + + + + + ChanEmory M + + Combinatorial approaches for developing upconverting nanomaterials: High-throughput screening, modeling, and applications + Chemical Society Reviews + Royal Society of Chemistry + 2015 + 44 + 6 + 10.1039/C4CS00205A + 1653 + 1679 + + + + + + SkripkaArtiom + LeeMinji + QiXiao + PanJia-Ahn + YangHaoran + LeeChanghwan + SchuckP. James + CohenBruce E. + JaqueDaniel + ChanEmory M. + + A generalized approach to photon avalanche upconversion in luminescent nanocrystals + Nano Letters + 2023 + 23 + 15 + 10.1021/acs.nanolett.3c01955 + 7100 + 7106 + + + + + + TeitelboimAyelet + TianBining + GarfieldDavid J + Fernandez-BravoAngel + GotlinAdam C + SchuckP James + CohenBruce E + ChanEmory M + + Energy transfer networks within upconverting nanoparticles are complex systems with collective, robust, and history-dependent dynamics + The Journal of Physical Chemistry C + ACS Publications + 2019 + 123 + 4 + 10.1021/acs.jpcc.9b00161 + 2678 + 2689 + + + + +