Merge branch 'main' of https://github.com/BlauGroup/RNMC

merge

.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

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.
+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:[email protected]) 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).

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}
 }

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