Add list of selected scientific papers using signac (#142)

* Merge requirements files.

* Update pre-commit hooks to process bibtex files.

* Add papers using signac.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Skip formats setting.

* Add Google Scholar link.

* Update bibliography style.

* Sort papers by publication date, from newest to oldest.

* Update signac.bib link.

Co-authored-by: Carl Simon Adorf <carl.simon.adorf@gmail.com>

* Remove extra comma.

Co-authored-by: Corwin Kerr <cbkerr@umich.edu>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Carl Simon Adorf <carl.simon.adorf@gmail.com>
Co-authored-by: Corwin Kerr <cbkerr@umich.edu>

.pre-commit-config.yaml

@@ -37,3 +37,20 @@ repos:
     hooks:
       - id: nbqa-black
       - id: nbqa-pyupgrade
+  - repo: https://github.com/FlamingTempura/bibtex-tidy
+    rev: '3559fc3b264d67441cbfcaec53500cbd66cefc7e'
+    hooks:
+      - id: bibtex-tidy
+        args:
+          - --omit=abstract,keywords,archiveprefix,mendeley-tags,pmid,eprint,arxivid
+          - --curly
+          - --numeric
+          - --space=2
+          - --align=0
+          - --sort=key,type,author,-year
+          - --duplicates=key,doi,citation
+          - --strip-enclosing-braces
+          - --drop-all-caps
+          - --sort-fields=title,shorttitle,author,year,month,day,journal,booktitle,location,on,publisher,address,series,volume,number,pages,doi,isbn,issn,url,urldate,copyright,category,note,metadata
+          - --remove-empty-fields
+          - --no-remove-dupe-fields

.readthedocs.yaml

@@ -1,7 +1,5 @@
 version: 2
 
-formats: all
-
 python:
   version: 3
   install:

docs/requirements.txt

@@ -5,4 +5,4 @@ nbconvert
 nbsphinx
 sphinx
 sphinx_rtd_theme>=0.5.2
-sphinxcontrib-bibtex
+sphinxcontrib-bibtex>=2.2.0

docs/source/conf.py

@@ -48,8 +48,12 @@
     "sphinx.ext.autosummary",
     "nbsphinx",
     "jupyter_sphinx",
+    "sphinxcontrib.bibtex",
 ]
 
+# For sphinxcontrib.bibtex.
+bibtex_bibfiles = ["signac.bib"]
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 

docs/source/index.rst

@@ -8,6 +8,7 @@ Welcome to the signac framework documentation!
 
 The **signac** framework supports researchers in managing project-related data with a well-defined indexable storage layout for data and metadata.
 This streamlines post-processing and analysis and makes data collectively accessible.
+The **signac** framework aims to help make computational research projects *Transparent*, *Reproducible*, *Usable by others*, and *Extensible* (TRUE) :cite:`Thompson2020`, a set of principles put forth by the MoSDeF Collaboration :cite:`Cummings2021`.
 
 This is the overall **framework documentation**.
 It provides a comprehensive overview on what you can do with packages that are part of the **signac** framework.
@@ -58,10 +59,12 @@ If you are new to **signac**, the best place to start is to read the :ref:`intro
    :caption: Reference
 
    community
+   scientific_papers
    GitHub <https://github.com/glotzerlab/signac>
    Twitter <https://twitter.com/signacdata>
    license
    acknowledge
+   zreferences
 
 Indices and tables
 ==================

docs/source/scientific_papers.rst

@@ -0,0 +1,85 @@
+.. _scientific-papers:
+
+=================
+Scientific Papers
+=================
+
+The **signac** framework has been cited over 50 times and has been used in a range of research fields with various types of computational workflows.
+Here, we showcase a few examples of scientific papers that have used **signac**.
+To find additional papers using **signac**, please refer to citations of the articles mentioned in :ref:`acknowledge` or this list of `citing works on Google Scholar <https://scholar.google.com/scholar?cites=14270565839129827405,11696507121891896813>`__.
+
+We encourage users to add publications citing **signac** to this list via a pull request.
+To add a paper, put citation information in `signac.bib <https://github.com/glotzerlab/signac-docs/edit/master/docs/source/signac.bib>`__ and follow the formatting of this page.
+Papers are sorted by publication date, from newest to oldest.
+
+--------
+
+.. bibliography::
+    :filter: False
+
+    Cersonsky2021
+
+Identifies photonic band gaps over a space of 151,593 crystal structures. Simulations performed using MIT Photonic Bands (MPB).
+
+--------
+
+.. bibliography::
+    :filter: False
+
+    Musil2021
+
+Benchmarking atom-density representations for use in machine learning. Data generated using librascal.
+
+--------
+
+.. bibliography::
+    :filter: False
+
+    Harper2020
+
+Electromagnetic simulations of silicon cylinders on a SiO\ :sub:`2` substrate are performed using RCWA and managed via **signac**. The resulting data is used in a machine learning model using TensorFlow to predict optical properties.
+
+--------
+
+.. bibliography::
+    :filter: False
+
+    Howard2019
+
+Simulating fluid flow in polymer solutions as a function of chain length :math:`M`, polymer concentration :math:`\phi_p`, body force :math:`f_x`, and droplet viscosity :math:`\mu_d`. Simulations performed using HOOMD-blue.
+
+--------
+
+.. bibliography::
+    :filter: False
+
+    Thompson2019
+
+Molecular dynamics simulations of room-temperature ionic liquids spanning 396 state points: 18 compositions by mass fraction and 22 unique solvents from five chemical families (nitriles, alcohols, halocarbons, carbonyls, and glymes). Simulations performed using GROMACS.
+
+--------
+
+.. bibliography::
+    :filter: False
+
+    Adorf2018
+
+Uses relative entropy minimization in Fourier space to identify isotropic particle interaction potentials that result in self-assembly of various crystal structures. Simulations performed using HOOMD-blue.
+
+--------
+
+.. bibliography::
+    :filter: False
+
+    Thomas2018
+
+4,480 molecular dynamics simulations of epoxy curing, each containing millions of particles. Simulations performed using HOOMD-blue.
+
+--------
+
+.. bibliography::
+    :filter: False
+
+    Govoni2018
+
+Validation study using five different codes to compute the vertical ionization potential and electron affinities of 100 molecules with the :math:`G_0W_0` approximation. Simulations performed using BerkeleyGW, FHI-aims, TURBOMOLE, VASP, and WEST.

docs/source/signac.bib

@@ -0,0 +1,118 @@
+@article{Adorf2018,
+  title = {Inverse design of simple pair potentials for the self-assembly of complex structures},
+  author = {Adorf, Carl S. and Antonaglia, James and Dshemuchadse, Julia and Glotzer, Sharon C.},
+  year = 2018,
+  month = nov,
+  journal = {The Journal of Chemical Physics},
+  volume = 149,
+  number = 20,
+  pages = {204102--204102},
+  doi = {10.1063/1.5063802}
+}
+@article{Cersonsky2021,
+  title = {The diversity of three-dimensional photonic crystals},
+  author = {Cersonsky, Rose K. and Antonaglia, James and Dice, Bradley D. and Glotzer, Sharon C.},
+  year = 2021,
+  month = may,
+  journal = {Nature Communications},
+  volume = 12,
+  number = 1,
+  pages = 2543,
+  doi = {10.1038/s41467-021-22809-6},
+  issn = {2041-1723}
+}
+@article{Cummings2021,
+  title = {Open-source molecular modeling software in chemical engineering focusing on the {Molecular} {Simulation} {Design} {Framework}},
+  author = {Cummings, Peter T. and McCabe, 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 Siepmann, J. Ilja and Potoff, Jeffrey and Matsumoto, Ray A. and Gilmer, Justin B. and DeFever, Ryan S. and Singh, Ramanish and Crawford, Brad},
+  year = 2021,
+  month = jan,
+  journal = {AIChE Journal},
+  volume = 67,
+  number = 3,
+  pages = {e17206},
+  doi = {10.1002/aic.17206},
+  issn = {1547-5905}
+}
+@article{Govoni2018,
+  title = {{GW100}: Comparison of Methods and Accuracy of Results Obtained with the {WEST} Code},
+  author = {Govoni, Marco and Galli, Giulia},
+  year = 2018,
+  month = feb,
+  journal = {Journal of Chemical Theory and Computation},
+  volume = 14,
+  number = 4,
+  pages = {1895--1909},
+  doi = {10.1021/acs.jctc.7b00952}
+}
+@article{Harper2020,
+  title = {Inverse design of broadband highly reflective metasurfaces using neural networks},
+  author = {Harper, Eric S. and Coyle, Eleanor J. and Vernon, Jonathan P. and Mills, Matthew S.},
+  year = 2020,
+  month = may,
+  journal = {Physical Review B},
+  volume = 101,
+  number = 19,
+  pages = 195104,
+  doi = {10.1103/PhysRevB.101.195104}
+}
+@article{Howard2019,
+  title = {Cross-stream migration of a {Brownian} droplet in a polymer solution under {Poiseuille} flow},
+  author = {P. Howard, Michael and M. Truskett, Thomas and Nikoubashman, Arash},
+  year = 2019,
+  month = mar,
+  journal = {Soft Matter},
+  volume = 15,
+  number = 15,
+  pages = {3168--3178},
+  doi = {10.1039/c8sm02552e}
+}
+@article{Musil2021,
+  title = {Efficient implementation of atom-density representations},
+  author = {Musil, F\'{e}lix and Veit, Max and Goscinski, Alexander and Fraux, Guillaume and Willatt, Michael J. and Stricker, Markus and Junge, Till and Ceriotti, Michele},
+  year = 2021,
+  month = mar,
+  journal = {The Journal of Chemical Physics},
+  volume = 154,
+  number = 11,
+  pages = 114109,
+  doi = {10.1063/5.0044689},
+  issn = {0021-9606}
+}
+@article{Thomas2018,
+  title = {Routine million-particle simulations of epoxy curing with dissipative particle dynamics},
+  author = {Thomas, Stephen and Alberts, Monet and Henry, Michael M and Estridge, Carla E and Jankowski, Eric},
+  year = 2018,
+  month = may,
+  journal = {Journal of Theoretical and Computational Chemistry},
+  volume = 17,
+  number = {03},
+  pages = 1840005,
+  doi = {10.1142/s0219633618400059},
+  issn = {0219-6336}
+}
+@article{Thompson2019,
+  title = {Scalable {{Screening}} of {{Soft Matter}}: {{A Case Study}} of {{Mixtures}} of {{Ionic Liquids}} and {{Organic Solvents}}},
+  shorttitle = {Scalable {{Screening}} of {{Soft Matter}}},
+  author = {Thompson, Matthew W. and Matsumoto, Ray and Sacci, Robert L. and Sanders, Nicolette C. and Cummings, Peter T.},
+  year = 2019,
+  month = jan,
+  journal = {J. Phys. Chem. B},
+  publisher = {American Chemical Society},
+  volume = 123,
+  number = 6,
+  pages = {1340--1347},
+  doi = {10.1021/acs.jpcb.8b11527},
+  issn = {1520-6106}
+}
+@article{Thompson2020,
+  title = {Towards molecular simulations that are transparent, reproducible, usable by others, and extensible ({TRUE})},
+  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,
+  journal = {Molecular Physics},
+  volume = 118,
+  number = {9-10},
+  pages = {e1742938},
+  doi = {10.1080/00268976.2020.1742938},
+  issn = {0026-8976}
+}

docs/source/zreferences.rst

@@ -0,0 +1,10 @@
+==========
+References
+==========
+
+.. It's necessary to have a file that creates the bibliography that is
+   processed by Sphinx AFTER all of the :cite: commands have been parsed. To
+   fix this, we name this file "zreferences.rst" so that it comes as late as
+   possible and import the bibliography here.
+
+.. bibliography:: signac.bib