diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml index 623b369..5eec5d3 100644 --- a/.github/workflows/draft-pdf.yml +++ b/.github/workflows/draft-pdf.yml @@ -1,3 +1,4 @@ +name: Draft PDF on: [push] jobs: @@ -14,7 +15,7 @@ jobs: # This should be the path to the paper within your repo. paper-path: paper.md - name: Upload - uses: actions/upload-artifact@v1 + uses: actions/upload-artifact@v4 with: name: paper # This is the output path where Pandoc will write the compiled diff --git a/README.md b/README.md index b7add64..8ab2c45 100644 --- a/README.md +++ b/README.md @@ -18,4 +18,14 @@ The complete documentation for `RNMC` can be found [here](https://blaugroup.gith ## Dependencies -RNMC depends on [GSL](https://www.gnu.org/software/gsl/) for pseudo random number generation and [sqlite](https://www.sqlite.org/index.html) for the database interfaces. \ No newline at end of file +RNMC depends on [GSL](https://www.gnu.org/software/gsl/) for pseudo random number generation and [sqlite](https://www.sqlite.org/index.html) for the database interfaces. + +## Contributing/Support + +We welcome community contributions to RNMC! Please submit code contributions as [pull requests (PRs)](https://github.com/BlauGroup/RNMC/pulls). Work-in-progress PRs are encouraged; just include "\[WIP\]" in the title of your PR. + +If you don't know where to start, you can check out the open [issues](https://github.com/BlauGroup/RNMC/issues) or reach out to [Sam Blau](mailto:smblau@lbl.gov) and describe what ideas you may have in mind. + +Have a problem installing or running RNMC, or have an idea for how the code could be better? Need support in using RNMC? Please open a new issue, and label the issue (with *e.g.*, “bug”, “enhancement”, or “question”) so that we can triage appropriately. Issues are preferred over e-mails or other private communications because multiple users might encounter the same problem. + +A more complete guide to contributing can be found in our [online documentation](https://blaugroup.github.io/RNMC/Contributors.html). \ No newline at end of file diff --git a/paper.bib b/paper.bib index 2fd1822..2c5aeca 100644 --- a/paper.bib +++ b/paper.bib @@ -6,7 +6,8 @@ @article{marcus1965theory number={2}, pages={679--701}, year={1965}, - publisher={American Institute of Physics} + publisher={American Institute of Physics}, + doi={10.1063/1.1696792} } @article{gillespie1977exact, @@ -17,7 +18,7 @@ @article{gillespie1977exact number={25}, pages={2340--2361}, year={1977}, - publisher={ACS Publications} + publisher={ACS Publications}, } @techreport{garcia2009crossing, @@ -35,7 +36,8 @@ @article{hoffmann2014kmos number={7}, pages={2138--2150}, year={2014}, - publisher={Elsevier} + publisher={Elsevier}, + doi={10.1016/j.cpc.2014.04.003} } @book{newman2021electrochemical, @@ -53,7 +55,8 @@ @article{spotte2022toward number={4}, pages={1446--1453}, year={2022}, - publisher={ACS Publications} + publisher={ACS Publications}, + doi={10.1021/acsenergylett.2c00517} } @article{barter2023predictive, @@ -64,18 +67,20 @@ @article{barter2023predictive number={1}, pages={123--137}, year={2023}, - publisher={Royal Society of Chemistry} + publisher={Royal Society of Chemistry}, + doi={10.1039/D2DD00117A} } @article{spotte2023chemical, - title={Chemical reaction networks explain gas evolution mechanisms in mg-ion batteries}, + title={Chemical reaction networks explain gas evolution mechanisms in {Mg}-ion batteries}, author={Spotte-Smith, Evan Walter Clark and Blau, Samuel M and Barter, Daniel and Leon, Noel J and Hahn, Nathan T and Redkar, Nikita S and Zavadil, Kevin R and Liao, Chen and Persson, Kristin A}, journal={Journal of the American Chemical Society}, volume={145}, number={22}, pages={12181--12192}, year={2023}, - publisher={ACS Publications} + publisher={ACS Publications}, + doi={10.1021/jacs.3c02222} } @article{xia2023accelerating, @@ -86,7 +91,8 @@ @article{xia2023accelerating number={23}, pages={11129--11136}, year={2023}, - publisher={ACS Publications} + publisher={ACS Publications}, + doi={10.1021/acs.nanolett.3c03568} } @article{chan2015combinatorial, @@ -97,7 +103,8 @@ @article{chan2015combinatorial number={6}, pages={1653--1679}, year={2015}, - publisher={Royal Society of Chemistry} + publisher={Royal Society of Chemistry}, + doi={10.1039/C4CS00205A} } @article{skripka2023NL, @@ -109,8 +116,6 @@ @article{skripka2023NL pages = {7100-7106}, year = {2023}, doi = {10.1021/acs.nanolett.3c01955}, - URL = {https://doi.org/10.1021/acs.nanolett.3c01955}, - eprint = {https://doi.org/10.1021/acs.nanolett.3c01955}, } @article{teitelboim2019energy, @@ -121,5 +126,6 @@ @article{teitelboim2019energy number={4}, pages={2678--2689}, year={2019}, - publisher={ACS Publications} + publisher={ACS Publications}, + doi={10.1021/acs.jpcc.9b00161} } diff --git a/paper.md b/paper.md index 523a6db..3ccb3a8 100644 --- a/paper.md +++ b/paper.md @@ -51,7 +51,7 @@ affiliations: index: 4 - name: Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA 94720 index: 5 -date: 2024-08-14 +date: 14 August 2024 bibliography: paper.bib --- @@ -73,20 +73,20 @@ We have designed `RNMC` to be easily extensible, enabling users to add additiona # Statement of need -Three are many existing kMC implementations, including several open source examples (e.g. the Stochastic Parallel PARticle Kinetic Simulator or `SPPARKS`[@garcia2009crossing] and `kmos`).[@hoffmann2014kmos] +Three are many existing kMC implementations, including several open source examples (e.g. the Stochastic Parallel PARticle Kinetic Simulator or `SPPARKS` [@garcia2009crossing] and `kmos` [@hoffmann2014kmos]). `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; it is designed such that users can quickly develop new types of kMC simulations using a common core library. 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,[@teitelboim2019energy] particularly multi-domain heterostructures whose optical properties cannot be calculated deterministically.[@skripka2023NL] -`NPMC` can be used to simulate energy transfer interactions between dopants in nanoparticles, their radiative transitions, and nonlinear processes such as upconversion [@chan2015combinatorial] and photon avalanching.[@skripka2023NL] +`NPMC` is specifically designed for 3D simulations of the complex photophysical interaction networks in nanocrystals [@teitelboim2019energy], particularly multi-domain heterostructures whose optical properties cannot be calculated deterministically [@skripka2023NL]. +`NPMC` can be used to simulate energy transfer interactions between dopants in nanoparticles, their radiative transitions, and nonlinear processes such as upconversion [@chan2015combinatorial] and photon avalanching [@skripka2023NL]. `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. -Electrochemcial reactions can be treated using Marcus theory[@marcus1965theory] or Butler-Volmer kinetics.[@newman2021electrochemical] +Electrochemcial reactions can be treated using Marcus theory [@marcus1965theory] or Butler-Volmer kinetics [@newman2021electrochemical]. 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.[@spotte2022toward; @barter2023predictive; @spotte2023chemical] 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.[@xia2023accelerating] +We have already used the `GMC` module in a number of prior works in applications related to Li-ion and Mg-ion batteries [@spotte2022toward; @barter2023predictive; @spotte2023chemical]. 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 [@xia2023accelerating]. # Acknowledgements diff --git a/paper.pdf b/paper.pdf index 068fb9d..dd4880b 100644 Binary files a/paper.pdf and b/paper.pdf differ