Merge branch 'paper'

.github/workflows/draft-pdf.yml

@@ -0,0 +1,25 @@
+name: paper
+
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - 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: 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: paper/paper.pdf

docs/background.rst

@@ -75,7 +75,7 @@ the value of :math:`r_{\text{cut}}`.
     fingerprint is going to be determined. Based on the cutoff distance, this
     atom has six neighbors as indicated by the circles. (2) For these
     neighbors, an adjacency matrix is constructed. For each off-diagonal
-    element in this matrix a value of one is assigned if the distance the
+    element in this matrix a value of one is assigned if the distance of the
     corresponding two neighbors is less than the cutoff distance. If not, the
     element has a value of zero.  (3) For each node in the adjacency matrix,
     a triplet of CNA indices is determined corresponding to (i) the number of

paper/.gitignore

@@ -0,0 +1,5 @@
+paper.jats
+paper.pdf
+!img/*.png
+!img/*.jpg
+!img/*.jpeg

paper/compile.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# Perform Docker compilation under Windows using Git BASH
+
+# provide the path to the location where the paper is stored; note that under
+# Windows Git Bash, two slashes need to be used instead of one
+
+if [ -d "/c/PROGRAMMING/CPP/bramble/paper" ]
+then
+    PAPERPATH="//c//PROGRAMMING//CPP//bramble//paper"
+elif [ -d "/d/PROGRAMMING/CPP/bramble/paper" ]
+then
+    PAPERPATH="//d//PROGRAMMING//CPP//bramble//paper"
+else
+    echo "Cannot find compilation path"
+    exit -1
+fi
+
+docker run --rm \
+--volume $PAPERPATH:/data \
+--user $(id -u):$(id -g) \
+--env JOURNAL=joss \
+openjournals/inara

paper/paper.bib

@@ -0,0 +1,163 @@
+@inbook{vansanten:2017,
+    publisher = {John Wiley & Sons, Ltd},
+    author = {van Santen, R.A.},
+    isbn = {9783527810253},
+    title = {Heterogeneous Catalysis},
+    booktitle = {Modern Heterogeneous Catalysis},
+    doi = {10.1002/9783527810253.ch1},
+    year = {2017},
+    keywords = {Berzelius definition, Ostwald rate definition of catalysis, Sabatier principle},
+}
+
+@article{faken:1994,
+    title = {Systematic analysis of local atomic structure combined with 3D computer graphics},
+    journal = {Computational Materials Science},
+    volume = {2},
+    number = {2},
+    pages = {279-286},
+    year = {1994},
+    doi = {10.1016/0927-0256(94)90109-0},
+    author = {Faken, D. and Jónsson, H.}
+}
+
+@article{stukowski:2012,
+    doi = {10.1088/0965-0393/20/4/045021},
+    url = {https://dx.doi.org/10.1088/0965-0393/20/4/045021},
+    year = {2012},
+    publisher = {IOP Publishing},
+    volume = {20},
+    number = {4},
+    pages = {045021},
+    author = {Stukowski, Alexander},
+    title = {Structure identification methods for atomistic simulations of crystalline materials},
+    journal = {Modelling and Simulation in Materials Science and Engineering}
+}
+
+@article{vanetten:2021,
+    author = {van Etten, Michel P. C. and Zijlstra, Bart and Hensen, Emiel J. M. and Filot, Ivo A. W.},
+    title = {Enumerating Active Sites on Metal Nanoparticles: Understanding the Size Dependence of Cobalt Particles for CO Dissociation},
+    journal = {ACS Catalysis},
+    volume = {11},
+    number = {14},
+    pages = {8484-8492},
+    year = {2021},
+    doi = {10.1021/acscatal.1c00651},
+}
+
+@article{sterk:2022,
+    author = {Sterk, Ellen B. and Nieuwelink, Anne-Eva and Monai, Matteo and Louwen, Jaap N. and Vogt, Eelco T. C. and Filot, Ivo A. W. and Weckhuysen, Bert M.},
+    title = {Structure Sensitivity of CO2 Conversion over Nickel Metal Nanoparticles Explained by Micro-Kinetics Simulations},
+    journal = {JACS Au},
+    volume = {2},
+    number = {12},
+    pages = {2714-2730},
+    year = {2022},
+    doi = {10.1021/jacsau.2c00430}
+}
+
+@article{reinhart:2017,
+    author = {Reinhart, Wesley F. and Long, Andrew W. and Howard, Michael P. and Ferguson, Andrew L. and Panagiotopoulos, Athanassios Z.},
+    title  = {Machine learning for autonomous crystal structure identification},
+    journal = {Soft Matter},
+    year = {2017},
+    volume = {13},
+    issue = {27},
+    pages = {4733-4745},
+    publisher = {The Royal Society of Chemistry},
+    doi = {10.1039/C7SM00957G},
+}
+
+
+@article{hafner:2008,
+    author = {Hafner, Jürgen},
+    title = {Ab-initio simulations of materials using VASP: Density-functional theory and beyond},
+    journal = {Journal of Computational Chemistry},
+    volume = {29},
+    number = {13},
+    pages = {2044-2078},
+    doi = {10.1002/jcc.21057},
+    year = {2008}
+}
+
+@article{momma:2011,
+    author = "Momma, Koichi and Izumi, Fujio",
+    title = "{{\it VESTA3} for three-dimensional visualization of crystal, volumetric and morphology data}",
+    journal = "{Journal of Applied Crystallography}",
+    year = "2011",
+    volume = "44",
+    number = "6",
+    pages = "1272-1276",
+    month = "Dec",
+    doi = {10.1107/S0021889811038970},
+}
+
+@MISC{eigenweb,
+    author = {Ga\"{e}l Guennebaud and Beno\^{i}t Jacob and others},
+    title = {Eigen v3},
+    howpublished = {http://eigen.tuxfamily.org},
+    year = {2010}
+}
+
+@article{Ovito,
+    Author = {Stukowski, Alexander},
+    Title = {Visualization and analysis of atomistic simulation data with OVITO-the
+       Open Visualization Tool},
+    Journal = {Modelling and Simulation in Materials Science and Engineering},
+    Year = {2010},
+    Volume = {18},
+    Number = {1},
+    DOI = {10.1088/0965-0393/18/1/015012},
+    Article-Number = {015012},
+}
+
+@article{Pyscal,
+    doi = {10.21105/joss.01824},
+    year = {2019},
+    volume = {4},
+    number = {43},
+    pages = {1824},
+    author = {Sarath Menon and Grisell Díaz Leines and Jutta Rogal},
+    title = {pyscal: A python module for structural analysis of atomic environments},
+    journal = {Journal of Open Source Software}
+}
+
+@Inbook{BoostLibrary,
+    author="Koranne, Sandeep",
+    title="Boost C++ Libraries",
+    bookTitle="Handbook of Open Source Tools",
+    year="2011",
+    publisher="Springer US",
+    address="Boston, MA",
+    pages="127--143",
+    isbn = "978-1-4419-7719-9",
+    doi= " 10.1007/978-1-4419-7719-9_6",
+    url = "https://doi.org/10.1007/978-1-4419-7719-9_6"
+}
+
+@misc{TclapLibrary,
+    author = {Michael E. Smoot and Daniel Aarno and others},
+    year   = {2009},
+    title  = {Templatized C++ Command Line Parser Library},
+    howpublished = "{https://tclap.sourceforge.net/}",
+}
+
+@Article{hunter: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.},
+  doi       = {10.1109/MCSE.2007.55},
+  year      = {2007}
+}
+
+@misc{cuda,
+  author={NVIDIA and Vingelmann, Péter and Fitzek, Frank H.P.},
+  title={CUDA, release: 10.2.89},
+  year={2020},
+  url={https://developer.nvidia.com/cuda-toolkit},
+}