First draft for GMSO paper (#797)

* add first draft for GMSO paper * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add the paper dir to code coverage ignore * add in PIs * add Brad and Chris J comments/edits, revised some paragraph * remove LLC from Atomfold * add in more edits from Brad * add my orcid * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add missing citations * more edits --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: chrisjonesBSU <[email protected]>
mosdef-hub · Jan 24, 2024 · 85dc0d8 · 85dc0d8
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diff --git a/codecov.yml b/codecov.yml
@@ -1,5 +1,6 @@
 ignore:
   - "gmso/examples"
   - "gmso/tests"
+  - "gmso/paper"
   - "gmso/formats/networkx.py"
   - "gmso/external/convert_foyer_xml.py"
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -0,0 +1,334 @@
+# mBuild paper
+@article{klein2016hierarchical,
+  title={A hierarchical, component based approach to screening properties of soft matter},
+  author={Klein, Christoph and Sallai, J{\'a}nos and Jones, Trevor J and Iacovella, Christopher R and McCabe, Clare and Cummings, Peter T},
+  journal={Foundations of molecular modeling and simulation: Select papers from FOMMS 2015},
+  pages={79--92},
+  year={2016},
+  publisher={Springer}
+}
+
+# Foyer paper
+@article{klein2019formalizing,
+  title={Formalizing atom-typing and the dissemination of force fields with foyer},
+  author={Klein, Christoph and Summers, Andrew Z and Thompson, Matthew W and Gilmer, Justin B and McCabe, Clare and Cummings, Peter T and Sallai, Janos and Iacovella, Christopher R},
+  journal={Comput. Mater. Sci.},
+  volume={167},
+  pages={215--227},
+  year={2019},
+  publisher={Elsevier}
+}
+
+# TRUE
+@article{thompson2020towards,
+  title = {Towards molecular simulations that are transparent,  reproducible,  usable by others,  and extensible (TRUE)},
+  volume = {118},
+  ISSN = {1362-3028},
+  url = {http://dx.doi.org/10.1080/00268976.2020.1742938},
+  DOI = {10.1080/00268976.2020.1742938},
+  number = {9–10},
+  journal = {Molecular Physics},
+  publisher = {Informa UK Limited},
+  author = {Thompson,  Matthew W. and Gilmer,  Justin B. and Matsumoto,  Ray A. and Quach,  Co D. and Shamaprasad,  Parashara and Yang,  Alexander H. and Iacovella,  Christopher R. and McCabe,  Clare and Cummings,  Peter T.},
+  year = {2020},
+  month = apr,
+  pages = {e1742938}
+}
+
+# MoSDeF
+@article{cummings2021opena,
+  title={Open{\^a}€ source molecular modeling software in chemical engineering focusing on the Molecular Simulation Design Framework},
+  author={Cummings, Peter T and MCabe, Clare and Iacovella, Christopher R and Ledeczi, Akos and Jankowski, Eric and Jayaraman, Arthi and Palmer, Jeremy C and Maginn, Edward J and Glotzer, Sharon C and Anderson, Joshua A and others},
+  journal={AIChE J.},
+  volume={67},
+  number={3},
+  year={2021}
+}
+
+# Reproducibility issue
+@article{baker2016reproducibility,
+  title={Reproducibility crisis},
+  author={Baker, Monya},
+  journal={Nature},
+  volume={533},
+  number={26},
+  pages={353--66},
+  year={2016}
+}
+
+# Ovito
+@article{stukowski2009visualization,
+  title = {Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool},
+  volume = {18},
+  ISSN = {1361-651X},
+  url = {http://dx.doi.org/10.1088/0965-0393/18/1/015012},
+  DOI = {10.1088/0965-0393/18/1/015012},
+  number = {1},
+  journal = {Modelling and Simulation in Materials Science and Engineering},
+  publisher = {IOP Publishing},
+  author = {Stukowski,  Alexander},
+  year = {2009},
+  month = dec,
+  pages = {015012}
+}
+
+# VMD
+@article{humphrey1996vmd,
+  author={William Humphrey and Andrew Dalke and Klaus Schulten},
+  title={{VMD} -- {V}isual {M}olecular {D}ynamics},
+  journal={Journal of Molecular Graphics},
+  year=1996,
+  volume=14,
+  pages={33-38},
+  note={},
+  tbstatus={Published.},
+  techrep={},
+  tbreference={222}
+}
+
+# GROMACS
+@article{abraham2015gromacs,
+  title={GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers},
+  author={Abraham, Mark James and Murtola, Teemu and Schulz, Roland and P{\'a}ll, Szil{\'a}rd and Smith, Jeremy C and Hess, Berk and Lindahl, Erik},
+  journal={SoftwareX},
+  volume={1},
+  pages={19--25},
+  year={2015},
+  publisher={Elsevier}
+}
+
+# LAMMPS
+@article{thompson2022lammps,
+author = {Thompson, Aidan P and Aktulga, H Metin and Berger, Richard and Bolintineanu, Dan S and Brown, W Michael and Crozier, Paul S and {in 't Veld}, Pieter J and Kohlmeyer, Axel and Moore, Stan G and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J and Tranchida, Julien and Trott, Christian and Plimpton, Steven J},
+doi = {https://doi.org/10.1016/j.cpc.2021.108171},
+issn = {0010-4655},
+journal = {Comput. Phys. Commun.},
+keywords = {LAMMPS,Materials modeling,Molecular dynamics,Parallel algorithms},
+mendeley-groups = {QE-Paper},
+pages = {108171},
+title = {{LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales}},
+url = {https://www.sciencedirect.com/science/article/pii/S0010465521002836},
+volume = {271},
+year = {2022}
+}
+
+# HOOMD-Blue
+@article{anderson2010hoomd,
+  title = {HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations},
+  volume = {173},
+  ISSN = {0927-0256},
+  url = {http://dx.doi.org/10.1016/j.commatsci.2019.109363},
+  DOI = {10.1016/j.commatsci.2019.109363},
+  journal = {Computational Materials Science},
+  publisher = {Elsevier BV},
+  author = {Anderson,  Joshua A. and Glaser,  Jens and Glotzer,  Sharon C.},
+  year = {2020},
+  month = feb,
+  pages = {109363}
+}
+
+# Cassandra
+@article{shah2017cassandra,
+  title = {Cassandra: An open source Monte Carlo package for molecular simulation},
+  volume = {38},
+  ISSN = {1096-987X},
+  url = {http://dx.doi.org/10.1002/jcc.24807},
+  DOI = {10.1002/jcc.24807},
+  number = {19},
+  journal = {Journal of Computational Chemistry},
+  publisher = {Wiley},
+  author = {Shah,  Jindal K. and Marin‐Rimoldi,  Eliseo and Mullen,  Ryan Gotchy and Keene,  Brian P. and Khan,  Sandip and Paluch,  Andrew S. and Rai,  Neeraj and Romanielo,  Lucienne L. and Rosch,  Thomas W. and Yoo,  Brian and Maginn,  Edward J.},
+  year = {2017},
+  month = apr,
+  pages = {1727–1739}
+}
+
+# GOMC
+@article{nejahi2021update,
+  title={Update 2.70 to “GOMC: GPU Optimized Monte Carlo for the Simulation of Phase Equilibria and Physical Properties of Complex Fluids”},
+  author={Nejahi, Younes and Barhaghi, Mohammad Soroush and Schwing, Gregory and Schwiebert, Loren and Potoff, Jeffrey},
+  journal={SoftwareX},
+  volume={13},
+  pages={100627},
+  year={2021},
+  publisher={Elsevier}
+}
+
+# MoSDeF-Cassandra
+@article{defever2021mosdef,
+  title = {MoSDeF Cassandra: A complete Python interface for the Cassandra Monte Carlo software},
+  volume = {42},
+  ISSN = {1096-987X},
+  url = {http://dx.doi.org/10.1002/jcc.26544},
+  DOI = {10.1002/jcc.26544},
+  number = {18},
+  journal = {Journal of Computational Chemistry},
+  publisher = {Wiley},
+  author = {DeFever,  Ryan S. and Matsumoto,  Ray A. and Dowling,  Alexander W. and Cummings,  Peter T. and Maginn,  Edward J.},
+  year = {2021},
+  month = apr,
+  pages = {1321–1331}
+}
+
+# MoSDeF-GOMC
+@article{crawford2023mosdefgomc,
+    author = {Crawford, Brad and Timalsina, Umesh and Quach, Co D. and Craven, Nicholas C. and Gilmer, Justin B. and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey J.},
+    title = {MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC},
+    journal = {Journal of Chemical Information and Modeling},
+    volume = {63},
+    number = {4},
+    pages = {1218-1228},
+    year = {2023},
+    doi = {10.1021/acs.jcim.2c01498},
+    note ={PMID: 36791286},
+
+    url = {
+    https://doi.org/10.1021/acs.jcim.2c01498
+
+    },
+    }
+
+# Studies using mbuild
+@article{albooyeh2023flowermd,
+    doi = {10.21105/joss.05989},
+    url = {https://doi.org/10.21105/joss.05989},
+    year = {2023},
+    publisher = {The Open Journal},
+    volume = {8},
+    number = {92},
+    pages = {5989},
+    author = {Marjan Albooyeh and Chris Jones and Rainier Barrett and Eric Jankowski},
+    title = {FlowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics},
+    journal = {Journal of Open Source Software}
+}
+
+@ar{summers2020mosdef,
+  title     = "{MoSDeF}, a Python framework enabling large-scale computational
+               screening of soft matter: Application to chemistry-property
+               relationships in lubricating monolayer films",
+  author    = "Summers, Andrew Z and Gilmer, Justin B and Iacovella,
+               Christopher R and Cummings, Peter T and McCabe, Clare",
+  journal   = "J. Chem. Theory Comput.",
+  publisher = "American Chemical Society (ACS)",
+  volume    =  16,
+  number    =  3,
+  pages     = "1779--1793",
+  month     =  mar,
+  year      =  2020,
+  language  = "en"
+}
+
+@article{quach2022high,
+  doi = {10.1063/5.0080838},
+  url = {https://doi.org/10.1063/5.0080838},
+  year = {2022},
+  month = apr,
+  publisher = {{AIP} Publishing},
+  volume = {156},
+  number = {15},
+  pages = {154902},
+  author = {Co D. Quach and Justin B. Gilmer and Daniel Pert and Akanke Mason-Hogans and Christopher R. Iacovella and Peter T. Cummings and Clare McCabe},
+  title = {High-throughput screening of tribological properties of monolayer films using molecular dynamics and machine learning},
+  journal = {J. Chem. Phys.}
+}
+
+@article{ma2022dynamics,
+    title = {Molecular dynamics simulation of the competitive adsorption behavior of effluent organic matters by heated aluminum oxide particles (HAOPs)},
+    journal = {Separation and Purification Technology},
+    volume = {292},
+    pages = {120961},
+    year = {2022},
+    issn = {1383-5866},
+    doi = {https://doi.org/10.1016/j.seppur.2022.120961},
+    url = {https://www.sciencedirect.com/science/article/pii/S1383586622005184},
+    author = {Yunqiao Ma and Tao Hua and Thien An Trinh and Rong Wang and Jia Wei Chew},
+    keywords = {Dynamic membrane, Heated aluminum oxide particles (HAOPs), Molecular dynamics simulation, Effluent organic matter (EfOM), Membrane fouling},
+}
+
+# ParmEd
+@article{shirts2016lessons,
+  title = {Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset},
+  volume = {31},
+  ISSN = {1573-4951},
+  url = {http://dx.doi.org/10.1007/s10822-016-9977-1},
+  DOI = {10.1007/s10822-016-9977-1},
+  number = {1},
+  journal = {Journal of Computer-Aided Molecular Design},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Shirts,  Michael R. and Klein,  Christoph and Swails,  Jason M. and Yin,  Jian and Gilson,  Michael K. and Mobley,  David L. and Case,  David A. and Zhong,  Ellen D.},
+  year = {2016},
+  month = oct,
+  pages = {147–161}
+}
+
+# OpenMM
+@article{eastman2017openmm,
+  title = {OpenMM 7: Rapid development of high performance algorithms for molecular dynamics},
+  volume = {13},
+  ISSN = {1553-7358},
+  url = {http://dx.doi.org/10.1371/journal.pcbi.1005659},
+  DOI = {10.1371/journal.pcbi.1005659},
+  number = {7},
+  journal = {PLOS Computational Biology},
+  publisher = {Public Library of Science (PLoS)},
+  author = {Eastman,  Peter and Swails,  Jason and Chodera,  John D. and McGibbon,  Robert T. and Zhao,  Yutong and Beauchamp,  Kyle A. and Wang,  Lee-Ping and Simmonett,  Andrew C. and Harrigan,  Matthew P. and Stern,  Chaya D. and Wiewiora,  Rafal P. and Brooks,  Bernard R. and Pande,  Vijay S.},
+  editor = {Gentleman,  Robert},
+  year = {2017},
+  month = jul,
+  pages = {e1005659}
+}
+# Sympy
+@article{meurer2017sympy,
+    title = {SymPy: symbolic computing in Python},
+    author = {Meurer, Aaron and Smith, Christopher P. and Paprocki, Mateusz and \v{C}ert\'{i}k, Ond\v{r}ej and Kirpichev, Sergey B. and Rocklin, Matthew and Kumar, AMiT and Ivanov, Sergiu and Moore, Jason K. and Singh, Sartaj and Rathnayake, Thilina and Vig, Sean and Granger, Brian E. and Muller, Richard P. and Bonazzi, Francesco and Gupta, Harsh and Vats, Shivam and Johansson, Fredrik and Pedregosa, Fabian and Curry, Matthew J. and Terrel, Andy R. and Rou\v{c}ka, \v{S}t\v{e}p\'{a}n and Saboo, Ashutosh and Fernando, Isuru and Kulal, Sumith and Cimrman, Robert and Scopatz, Anthony},
+    year = 2017,
+    month = jan,
+    keywords = {Python, Computer algebra system, Symbolics},
+    volume = 3,
+    pages = {e103},
+    journal = {PeerJ Computer Science},
+    issn = {2376-5992},
+    url = {https://doi.org/10.7717/peerj-cs.103},
+    doi = {10.7717/peerj-cs.103}
+}
+
+# Unyt
+@article{goldbaum2018unyt,
+  doi = {10.21105/joss.00809},
+  url = {https://doi.org/10.21105/joss.00809},
+  year  = {2018},
+  month = {aug},
+  publisher = {The Open Journal},
+  volume = {3},
+  number = {28},
+  pages = {809},
+  author = {Nathan J. Goldbaum and John A. ZuHone and Matthew J. Turk and Kacper Kowalik and Anna L. Rosen},
+  title = {unyt: Handle,  manipulate,  and convert data with units in Python},
+  journal = {Journal of Open Source Software}
+}
+
+# Signac
+@article{adorf2018simple,
+  title={Simple data and workflow management with the signac framework},
+  author={Adorf, Carl S and Dodd, Paul M and Ramasubramani, Vyas and Glotzer, Sharon C},
+  journal={	Comput. Mater. Sci.},
+  volume={146},
+  pages={220--229},
+  year={2018},
+  publisher={Elsevier}
+}
+
+# Example of high-throughput with MoSDeF
+@article{thompson2019scalable,
+  doi = {10.1021/acs.jpcb.8b11527},
+  url = {https://doi.org/10.1021/acs.jpcb.8b11527},
+  year = {2019},
+  month = jan,
+  publisher = {American Chemical Society ({ACS})},
+  volume = {123},
+  number = {6},
+  pages = {1340--1347},
+  author = {Matthew W. Thompson and Ray Matsumoto and Robert L. Sacci and Nicolette C. Sanders and Peter T. Cummings},
+  title = {Scalable Screening of Soft Matter: A Case Study of Mixtures of Ionic Liquids and Organic Solvents},
+  journal = {J. Phys. Chem. B}
+}