Adding citations

paper/.gitignore

@@ -3,3 +3,4 @@ paper.pdf
 !img/*.png
 !img/*.jpg
 !img/*.jpeg
+media/*

paper/compile.sh

@@ -5,19 +5,8 @@
 # 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/den2obj/paper" ]
-then
-    PAPERPATH="//c//PROGRAMMING//CPP//den2obj//paper"
-elif [ -d "/d/PROGRAMMING/CPP/den2obj/paper" ]
-then
-    PAPERPATH="//d//PROGRAMMING//CPP//den2obj//paper"
-else
-    echo "Cannot find compilation path"
-    exit -1
-fi
-
 docker run --rm \
---volume $PAPERPATH:/data \
+--volume `pwd`:/data \
 --user $(id -u):$(id -g) \
 --env JOURNAL=joss \
 openjournals/inara

paper/paper.bib

@@ -1,84 +1,3 @@
-@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{vanetten:2023,
-    author = {van Etten, Michel P. C. and De Laat, M.E. and Hensen, Emiel J. M. and Filot, Ivo A. W.},
-    title = {Unraveling the Role of Metal–Support Interactions on the Structure Sensitivity of Fischer–Tropsch Synthesis},
-    journal = {J. Phys. Chem. C},
-    volume = {127},
-    number = {31},
-    pages = {15148-15156},
-    year = {2023},
-    doi = {10.1021/acs.jpcc.3c02240},
-}
-
-@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},
@@ -109,6 +28,27 @@ @MISC{eigenweb
     year = {2010}
 }
 
+@misc{bzip2web,
+    author = {Mark Wielaard and Federico Mena and Micah Snyder},
+    title = {bzip2},
+    howpublished = {https://sourceware.org/bzip2/},
+    year = {1996}
+}
+
+@misc{gzipweb,
+    author = {Jean-loup Gailly and Mark Adler},
+    title = {gzip},
+    howpublished = {https://www.gnu.org/software/gzip/},
+    year = {1992}
+}
+
+@misc{lzmaweb,
+    author = {Igor Pavlov},
+    title = {lzma},
+    howpublished = {https://www.7-zip.org/},
+    year = {1996}
+}
+
 @article{Ovito,
     Author = {Stukowski, Alexander},
     Title = {Visualization and analysis of atomistic simulation data with OVITO-the
@@ -175,3 +115,144 @@ @book{cuda
     address = {San Francisco, CA, USA},
     edition = {1st}
 }
+
+@misc{gaussian,
+author={M. J. Frisch and G. W. Trucks and H. B. Schlegel and G. E. Scuseria and M. A. Robb and J. R. Cheeseman and G. Scalmani and V. Barone and G. A. Petersson and H. Nakatsuji and X. Li and M. Caricato and A. V. Marenich and J. Bloino and B. G. Janesko and R. Gomperts and B. Mennucci and H. P. Hratchian and J. V. Ortiz and A. F. Izmaylov and J. L. Sonnenberg and D. Williams-Young and F. Ding and F. Lipparini and F. Egidi and J. Goings and B. Peng and A. Petrone and T. Henderson and D. Ranasinghe and V. G. Zakrzewski and J. Gao and N. Rega and G. Zheng and W. Liang and M. Hada and M. Ehara and K. Toyota and R. Fukuda and J. Hasegawa and M. Ishida and T. Nakajima and Y. Honda and O. Kitao and H. Nakai and T. Vreven and K. Throssell and Montgomery, {Jr.}, J. A. and J. E. Peralta and F. Ogliaro and M. J. Bearpark and J. J. Heyd and E. N. Brothers and K. N. Kudin and V. N. Staroverov and T. A. Keith and R. Kobayashi and J. Normand and K. Raghavachari and A. P. Rendell and J. C. Burant and S. S. Iyengar and J. Tomasi and M. Cossi and J. M. Millam and M. Klene and C. Adamo and R. Cammi and J. W. Ochterski and R. L. Martin and K. Morokuma and O. Farkas and J. B. Foresman and D. J. Fox},
+title={Gaussian16 {R}evision {C}.01},
+year={2016},
+note={Gaussian Inc. Wallingford CT}
+}
+
+@book{martin:2004,
+    place={Cambridge},
+    title={Electronic Structure: Basic Theory and Practical Methods},
+    DOI={10.1017/CBO9780511805769},
+    publisher={Cambridge University Press},
+    author={Martin, Richard M.},
+    year={2004}
+}
+
+@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}
+}
+
+@misc{ParaView,
+    title = {ParaView: An End-User Tool for Large-Data Visualization},
+    editor = {Charles D. Hansen and Chris R. Johnson},
+    booktitle = {Visualization Handbook},
+    publisher = {Butterworth-Heinemann},
+    address = {Burlington},
+    pages = {717-731},
+    year = {2005},
+    isbn = {978-0-12-387582-2},
+    doi = {10.1016/B978-012387582-2/50038-1},
+    author    = {James Ahrens and Berk Geveci and Charles Law},
+}
+
+@book{OpenDX,
+  title     = "OpenDX Paths to Visualization",
+  author    = "David L. Thompson and Jeff A. Braun and Ray Ford",
+  year      = 2004,
+  publisher = "Visualization and Imagery Solutions Inc.",
+  address   = "Missoula"
+}
+
+
+@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{papior:2023,
+  author = {Papior, Nick},
+  title  = {sisl: v0.13.0},
+  year   = {2023},
+  doi    = {10.5281/zenodo.597181},
+  url    = {https://doi.org/10.5281/zenodo.597181}
+}
+
+@misc{MATLAB,
+    year = {2022},
+    author = {{The MathWorks Inc.}},
+    title = {MATLAB version: 9.13.0 (R2022b)},
+    publisher = {The MathWorks Inc.},
+    address = {Natick, Massachusetts, United States},
+    url = {https://www.mathworks.com}
+}
+
+@article{museth:2013,
+    author = {Museth, Ken},
+    title = {VDB: High-resolution sparse volumes with dynamic topology},
+    year = {2013},
+    journal = {ACM Trans. Graph.},
+    volume = {32},
+    number = {3},
+    issn = {0730-0301},
+    url = {https://doi.org/10.1145/2487228.2487235},
+    doi = {10.1145/2487228.2487235},
+}
+
+@article{lorensen:1987,
+    author = {Lorensen, William E. and Cline, Harvey E.},
+    title = {Marching cubes: A high resolution 3D surface construction algorithm},
+    year = {1987},
+    volume = {21},
+    number = {4},
+    url = {https://doi.org/10.1145/37402.37422},
+    doi = {10.1145/37402.37422},
+    journal = {SIGGRAPH Comput. Graph.},
+    pages = {163–169},
+}
+
+@misc{burke:1994,
+    year = {1994},
+    author = {Paul Burke},
+    title = {Polygonising a scalar field},
+    url = {https://paulbourke.net/geometry/polygonise/}
+}
+
+@article{filot:2016,
+    title = {A quantum-chemical DFT study of CO dissociation on Fe-promoted stepped Rh surfaces},
+    journal = {Catalysis Today},
+    volume = {275},
+    pages = {111-118},
+    year = {2016},
+    doi = {https://doi.org/10.1016/j.cattod.2015.10.009},
+    author = {Ivo A.W. Filot and Farid Fariduddin and Robin J.P. Broos and Bart Zijlstra and Emiel J.M. Hensen},
+}
+
+@article{su:2016,
+    author = {Su, Ya-Qiong and Filot, Ivo A. W. and Liu, Jin-Xun and Tranca, Ionut and Hensen, Emiel J. M.},
+    title = {Charge Transport over the Defective CeO2(111) Surface},
+    journal = {Chemistry of Materials},
+    volume = {28},
+    number = {16},
+    pages = {5652-5658},
+    year = {2016},
+    doi = {10.1021/acs.chemmater.6b01548}
+}
+
+@article{su:2018,
+    author = {Su, Ya-Qiong and Filot, Ivo A. W. and Liu, Jin-Xun and Hensen, Emiel J. M.},
+    title = {Stable Pd-Doped Ceria Structures for CH4 Activation and CO Oxidation},
+    journal = {ACS Catalysis},
+    volume = {8},
+    number = {1},
+    pages = {75-80},
+    year = {2018},
+    doi = {10.1021/acscatal.7b03295},
+}