Merge pull request #83 from orionarcher/paper

Add JOSS paper draft.

.github/workflows/draft-pdf.yml

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+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: joss_paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: joss_paper/paper.pdf

joss_paper/paper.bib

@@ -0,0 +1,153 @@
+@article{Michaud-Agrawal:2014,
+title = {MDAnalysis: A toolkit for the analysis of molecular dynamics simulations},
+author = {Michaud‐Agrawal, Naveen and Denning, Elizabeth J. and Woolf, Thomas B. and Beckstein, Oliver},
+year = 2011,
+month = 04,
+journal = {Journal of Computational Chemistry},
+issn = {0192-8651},
+pmid = {21500218},
+pmcid = {PMC3144279},
+pages = {2319 - 2327},
+number = {10},
+volume = {32},
+doi = {10.1002/jcc.21787},
+}
+
+@InProceedings{Gowers:2016,
+author = { Gowers, Richard and Linke, Max and Barnoud, Jonathan and Reddy,
+           Tyler and Melo, Manuel and Seyler, Sean and Domański, Jan and Dotson,
+           David and Buchoux, Sébastien and Kenney, Ian and Beckstein, Oliver },
+title = { MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations },
+url = {https://conference.scipy.org/proceedings/scipy2016/oliver\_beckstein.html},
+pages = {98 - 105},
+year = 2016,
+doi = {10.25080/majora-629e541a-00e},
+}
+
+@online{plotly:2015,
+author = {Plotly},
+title = {Collaborative data science},
+publisher = {Plotly Technologies Inc.},
+address = {Montreal, QC},
+year = 2015,
+url = {https://plot.ly},
+}
+
+@article{scipy:2020,
+author  = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and
+        Haberland, Matt and Reddy, Tyler and Cournapeau, David and
+        Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and
+        Bright, Jonathan and {van der Walt}, St{\'e}fan J. and
+        Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and
+        Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and
+        Kern, Robert and Larson, Eric and Carey, C J and
+        Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and
+        {VanderPlas}, Jake and Laxalde, Denis and Perktold, Josef and
+        Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and
+        Harris, Charles R. and Archibald, Anne M. and
+        Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and
+        {van Mulbregt}, Paul and {SciPy 1.0 Contributors}},
+title   = {{SciPy} 1.0: Fundamental Algorithms for Scientific
+           Computing in Python},
+journal = {Nature Methods},
+year    = {2020},
+volume  = {17},
+pages   = {261--272},
+adsurl  = {https://rdcu.be/b08Wh},
+doi     = {10.1038/s41592-019-0686-2},
+}
+
+@article{matplotlib:2007,
+Author    = {Hunter, J. D.},
+Title     = {Matplotlib: A 2D graphics environment},
+Journal   = {Computing in Science \& Engineering},
+Volume    = {9},
+Number    = {3},
+Pages     = {90--95},
+abstract  = {Matplotlib is a 2D graphics package used for Python for
+application development, interactive scripting, and publication-quality
+image generation across user interfaces and operating systems.},
+publisher = {IEEE COMPUTER SOC},
+doi       = {10.1109/MCSE.2007.55},
+year      = 2007,
+}
+
+@article{numpy:2020,
+author  = {Harris, Charles R. and Millman, K. Jarrod and van der Walt,
+Stéfan J and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David
+and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith,
+Nathaniel J. and Kern, Robert and Picus, Matti and Hoyer, Stephan and van
+Kerkwijk, Marten H. and Brett, Matthew and Haldane, Allan and Fernández
+del Río, Jaime and Wiebe, Mark and Peterson, Pearu and Gérard-Marchant,
+Pierre and Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren
+and Abbasi, Hameer and Gohlke, Christoph and Oliphant, Travis E.},
+title   = {Array programming with {NumPy}},
+journal = {Nature},
+year    = {2020},
+volume  = {585},
+number  = {7825},
+pages   = {357--362},
+pages   = {357–362},
+doi     = {10.1038/s41586-020-2649-2},
+}
+
+@software{pandas:2020,
+author       = {DevTeam},
+title        = {pandas-dev/pandas: Pandas},
+month        = 02,
+year         = 2020,
+publisher    = {Zenodo},
+version      = {latest},
+doi          = {10.5281/zenodo.3509134},
+url          = {https://doi.org/10.5281/zenodo.3509134},
+}
+
+@article{Hou:2019,
+title = {The influence of FEC on the solvation structure and reduction reaction of LiPF6/EC electrolytes and its implication for solid electrolyte interphase formation},
+author = {Hou, Tingzheng and Yang, Guang and Rajput, Nav Nidhi and Self, Julian and Park, Sang-Won and Nanda, Jagjit and Persson, Kristin A.},
+journal = {Nano Energy},
+issn = {22112855},
+url = {https://linkinghub.elsevier.com/retrieve/pii/S2211285519305877},
+year = {2019},
+pages = {103881},
+volume = {64},
+month = {10},
+doi = {10.1016/j.nanoen.2019.103881},
+}
+
+
+@article{Dong-Joo:2022,
+author = {Yoo, Dong-Joo and Liu, Qian and Cohen, Orion and Kim, Minkyu and Persson, Kristin A. and Zhang, Zhengcheng},
+title = {Understanding the Role of SEI Layer in Low-Temperature Performance of Lithium-Ion Batteries},
+journal = {ACS Applied Materials \& Interfaces},
+volume = {14},
+number = {9},
+pages = {11910-11918},
+year = {2022},
+doi = {10.1021/acsami.1c23934},
+}
+
+@article{Self:2019,
+year = {2019},
+title = {Transport in Superconcentrated LiPF6 and LiBF4/Propylene Carbonate Electrolytes},
+author = {Self, Julian and Fong, Kara D. and Persson, Kristin A.},
+journal = {ACS Energy Letters},
+issn = {2380-8195},
+doi = {10.1021/acsenergylett.9b02118},
+pages = {2843--2849},
+number = {12},
+volume = {4},
+}
+
+
+@article{Xie:2023,
+year = {2023},
+title = {{Spatially resolved structural order in low-temperature liquid electrolyte}},
+author = {Xie, Yujun and Wang, Jingyang and Savitzky, Benjamin H. and Chen, Zheng and Wang, Yu and Betzler, Sophia and Bustillo, Karen and Persson, Kristin and Cui, Yi and Wang, Lin-Wang and Ophus, Colin and Ercius, Peter and Zheng, Haimei},
+journal = {Science Advances},
+doi = {10.1126/sciadv.adc9721},
+pmid = {36638171},
+pages = {eadc9721},
+number = {2},
+volume = {9}
+}

joss_paper/paper.md

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+---
+title: 'SolvationAnalysis: A Python toolkit for understanding liquid solvation structure in classical molecular dynamics simulations'
+tags:
+ - python
+ - chemistry
+ - electrolytes
+ - molecular dynamics
+ - solvation structure
+authors:
+ - name: Orion Archer Cohen
+   orcid: 0000-0003-3940-2456
+   affiliation: 1
+ - name: Hugo Macdermott-Opeskin
+   orcid: 0000-0002-7393-7457
+   affiliation: 2
+ - name: Lauren Lee
+   affiliation: 1
+ - name: Tingzheng Hou
+   orcid: 0000-0002-7163-2561
+   affiliation: 3
+ - name: Kara D. Fong
+   orcid: 0000-0002-0711-097X
+   affiliation: 1
+ - name: Ryan Kingsbury
+   orcid: 0000-0002-7168-3967
+   affiliation: 4
+ - name: Jingyang Wang
+   orcid: 0000-0003-3307-5132
+   affiliation: 1
+ - name: Kristin A. Persson
+   orcid: 0000-0003-2495-5509
+   affiliation: "5,6"
+affiliations:
+ - name: Materials Science Division, Lawrence Berkeley National Laboratory, USA
+   index: 1
+ - name: Australian National University, Australia
+   index: 2
+ - name: Institute of Materials Research, Shenzhen International Graduate School, Tsinghua University, China
+   index: 3
+ - name: Energy Storage & Distributed Resources Division, Lawrence Berkeley National Laboratory, USA
+   index: 4
+ - name: Department of Materials Science, University of California, USA
+   index: 5
+ - name: Molecular Foundry, Lawrence Berkeley National Laboratory, USA
+   index: 6
+date: 12 January 2023
+bibliography: paper.bib
+---
+
+# Summary
+
+The macroscopic behavior of matter is determined by the microscopic
+arrangement of atoms, but this arrangement is often
+difficult or impossible to observe experimentally. Instead, researchers use
+simulation techniques like molecular dynamics to probe the microscopic
+structure and dynamics of everything from proteins to battery electrolytes.
+SolvationAnalysis extracts solvation information from completed
+molecular dynamics simulations, letting researchers access key solvation
+structure statistics with minimal effort and accelerating scientific research.
+
+# Statement of need
+
+Molecular dynamics studies of liquid solvation structures often replicate
+established analyses on novel systems. In electrolyte systems, it is common
+to calculate coordination numbers, radial distribution functions, solute
+dissociation, and cluster speciation [@Hou:2019]. In principle, these analyses are highly
+similar across a diversity of systems. In practice, many specialized bespoke
+tools have sprung up to address the same underlying problem. Enter `SolvationAnalysis`, 
+an easy-to-use Python package with an interactive interface for
+computing a wide variety of solvation properties. Building on `MDAnalysis` and
+`pandas` [@Michaud-Agrawal:2014] [@Gowers:2016] [@pandas:2020], it efficiently
+processes output from a wide variety of Molecular Dynamics simulation packages.
+
+`SolvationAnalysis` was designed to free researchers from laboriously
+implementing and validating common analyses. In addition to routine properties like
+coordination numbers, solute-solvent pairing, and solute speciation,
+SolvationAnalysis uses tools from the SciPy ecosystem [@numpy:2020] [@scipy:2020]
+to implement analyses of network formation [@Xie:2023] and residence
+times [@Self:2019], summarized in \autoref{fig:summary}. To make visualization fast, 
+the package includes a robust set of plotting tools built
+on top of `Matplotlib` and `Plotly` [@matplotlib:2007] [@plotly:2015].
+A full set of tutorials based on state-of-the-art battery electrolytes 
+[@Hou:2019] [@Dong-Joo:2022] are also included to familiarize new researchers
+with solvation structure analysis. Together, these features allow for
+rapid interactive or programmatic calculation of solvation properties.
+
+# Figures
+
+![A visual summary of SolvationAnalysis capabilities. \label{fig:summary}](summary_figure.jpg)
+
+# Acknowledgements
+
+Thank you to Oliver Beckstein, Richard Gowers, Irfan Alibay, and Lily Wang for
+technical advice about MDAnalysis and Python development. Thank you to Google 
+Summer of Code, the NSF GRFP Fellowship, and the US Department of Energy for 
+funding.
+
+# References