Merge pull request #16 from jstse/Solid-Surfinpy-Josh

Solid surfinpy josh

README.md

@@ -106,7 +106,7 @@ To build the documentation from scratch
 
 ### Contact
 
-If you have questions regarding any aspect of the software then please get in touch with the developer Adam Symington via email - [email protected]. 
+If you have questions regarding any aspect of the software then please get in touch with the development team via email Adam Symington ([email protected]), Joshua Tse ([email protected]). 
 Alternatively you can create an issue on the [Issue Tracker](https://github.com/symmy596/SurfinPy/issues) or you can discuss your questions on our [gitter channel](https://gitter.im/Surfinpy/Lobby).
 
 ### Bugs
@@ -130,7 +130,7 @@ workflow while core developers use branches in the main repository:
       project. A more detailed discussion can take place there before
       the changes are accepted.
 
-For further information please contact Adam Symington, [email protected]
+For further information please contact Adam Symington - [email protected], Joshua Tse - [email protected]
 
 ## Research
 
@@ -142,8 +142,9 @@ For further information please contact Adam Symington, [email protected]
 ## Author
 
 * Adam R.Symington
-
+* Joshua Tse (Uniersity of Huddersfield)  
+
 ## Acknowledgements
 
 * [Prof Stephen C.Parker](http://people.bath.ac.uk/chsscp/) - (Bath University)
-* Joshua Tse (Huddersfield Uniersity)
+

paper/paper.bib

@@ -1,55 +1,52 @@
 @article{Symington2019,
-author = {Symington, Adam and Tse, Joshua and Molinari, Marco and Marmier, Arnaud and Parker, Stephen},
-doi = {10.21105/joss.01210},
-issn = {2475-9066},
-journal = {Journal of Open Source Software},
-month = {feb},
-number = {34},
-pages = {1210},
-publisher = {The Open Journal},
-title = {{surfinpy: A Surface Phase Diagram Generator}},
-url = {http://joss.theoj.org/papers/10.21105/joss.01210},
-volume = {4},
-year = {2019}
+  doi = {10.21105/joss.01210},
+  url = {https://doi.org/10.21105/joss.01210},
+  year = {2019},
+  publisher = {The Open Journal},
+  volume = {4},
+  number = {34},
+  pages = {1210},
+  author = {Adam R. Symington and Joshua Tse and Marco Molinari and Arnaud Marmier and Stephen C. Parker},
+  title = {surfinpy: A Surface Phase Diagram Generator},
+  journal = {Journal of Open Source Software}
 }
 
+
 @article{Symington2020a,
-abstract = {Licence: CC BY-NC-ND 4.0 Citation information: Symington, Adam; Harker, Robert M.; Storr, Mark T.; Molinari, Marco; Parker, Stephen Charles (2020): Thermodynamic Evolution of Cerium Oxide Nanoparticle Morphology using Carbon Dioxide.. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.11522565.v3 Many nanoparticles show enhanced catalytic activity on particular surfaces. Hence, a key challenge is to identify strategies to control the expression of such surfaces and to avoid their disappearance over time. Here, we use density functional theory to explore the adsorption of carbon dioxide on the surfaces of Cerium oxide (CeO 2), and its relationship with the resulting nanoparticle morphology under conditions of pressure and temperature. CeO 2 is an important solid electrolyte in fuel cells, a catalyst, and enzyme mimetic agent in biomedicine, and has been shown to interact strongly with CO 2. We demonstrate that the adsorption of CO 2 as a carbonate ion is energetically favorable on the {\{}111{\}}, {\{}110{\}} and {\{}100{\}} surfaces of CeO 2 , and that the strength of this interaction is morphology and surface stoichiometry dependent. By predicting the surface stability as a function of temperature and pressure, we built surface phase diagrams and predict the surface dependent desorption temperatures of CO 2. These temperatures of desorption follow the order {\{}100{\}} {\textgreater} {\{}110{\}} {\textgreater} {\{}111{\}} and are higher for surfaces containing oxygen vacancies compared to stoichiometric surfaces, indicating that surface oxidation processes can reduce the stability of surface carbonate groups. Finally, we propose a thermodynamic strategy to predict the evolution of nanoparticle morphology in the presence of CO 2 as the external conditions of temperature and pressure change. We show that there is a thermodynamic driving force dependent on CO 2 adsorption that should be considered when selecting nanoparticle morphologies in catalytic applications. File list (2) download file view on ChemRxiv Manuscript.pdf (1.37 MiB) download file view on ChemRxiv Manuscript.docx (3.36 MiB)},
-author = {Symington, Adam and Harker, Robert M and Storr, Mark T and Molinari, Marco and Parker, Stephen Charles},
-doi = {10.26434/chemrxiv.11522565.v3},
-title = {{Thermodynamic Evolution of Cerium Oxide Nanoparticle Mor-phology using Carbon Dioxide}},
-url = {https://doi.org/10.26434/chemrxiv.11522565.v3}
+author = {Symington, Adam R. and Harker, Robert M. and Storr, Mark T. and Molinari, Marco and Parker, Stephen C.},
+title = {Thermodynamic Evolution of Cerium Oxide Nanoparticle Morphology Using Carbon Dioxide},
+journal = {The Journal of Physical Chemistry C},
+volume = {124},
+number = {42},
+pages = {23210-23220},
+year = {2020},
+doi = {10.1021/acs.jpcc.0c07437},
+URL = {https://doi.org/10.1021/acs.jpcc.0c07437},
+eprint = {https://doi.org/10.1021/acs.jpcc.0c07437}
 }
 
-@article{Moxon2020,
-abstract = {Radiolytic corrosion of actinide materials represent an issue for the long term storage and disposal of nuclear materials. Molecular species adsorbed at the surface of the actinides may impact the rate of radiolysis, and as the surfaces corrode, the soluble toxic and radioactive species leach into groundwater. It is therefore critical to characterise the surface composition of actinides. Here, we employ ab initio modelling to determine the surface composition of PuO2 with respect to adsorbed CO2. We found that CO2 interacts strongly with the surface forming carbonate species. By mapping the energetics of this interaction, we then calculate the temperature of desorption, finding that surface morphology has a strong impact on the adsorption of CO2, with the {\{}100{\}} being the most and the {\{}111{\}} the least affected by carbonation. Finally, we predict the effect of carbonation on the morphology of PuO2 nanoparticles as a function of temperature and pressure, finding that truncated octahedral is the preferred morphology. This modelling strategy helps characterise surface compensition and nanoparticle morphology, and we discuss the implication for radiolytically driven dispersal of material into the environment.},
-author = {Moxon, Samuel and Symington, Adam R. and Tse, Joshua S. and Dawson, James and Flitcroft, Joseph M. and Parker, Stephen C. and Cooke, David J. and Harker, Robert M. and Molinari, Marco},
-doi = {10.1039/d0cp00021c},
-issn = {14639076},
-journal = {Physical Chemistry Chemical Physics},
-month = {apr},
-number = {15},
-pages = {7728--7737},
-pmid = {32191781},
-publisher = {Royal Society of Chemistry},
-title = {{The energetics of carbonated PuO2 surfaces affects nanoparticle morphology: A DFT+: U study}},
-url = {https://pubs.rsc.org/en/content/articlehtml/2020/cp/d0cp00021c https://pubs.rsc.org/en/content/articlelanding/2020/cp/d0cp00021c},
-volume = {22},
-year = {2020}
+@Article{Moxon2020,
+author ="Moxon, Samuel and Symington, Adam R. and Tse, Joshua S. and Dawson, James and Flitcroft, Joseph M. and Parker, Stephen C. and Cooke, David J. and Harker, Robert M. and Molinari, Marco",
+title  ="The energetics of carbonated PuO2 surfaces affects nanoparticle morphology: a DFT+U study",
+journal  ="Phys. Chem. Chem. Phys.",
+year  ="2020",
+volume  ="22",
+issue  ="15",
+pages  ="7728-7737",
+publisher  ="The Royal Society of Chemistry",
+doi  ="10.1039/D0CP00021C",
+url  ="http://dx.doi.org/10.1039/D0CP00021C",
 }
 
 @article{Symington2020c,
-abstract = {The surface structure and composition of functional materials are well known to be critically important factors controlling the surface reactivity. However, when doped the surface composition will change and the challenge is to identify its impact on important surface processes and nanoparticle morphologies. We have begun to address this by using a combination of density functional theory and potential-based methods to investigate the effect of surface dopants on water adsorption and morphology of the technologically important material, CeO2, which finds application as electrolyte in SOFCs, catalyst in soot combustion, and enzyme mimetic agent in biomedicine. We show that by mapping CeO2 surface phase diagrams we can predict nanoparticle morphologies as a function of dopant, temperature and water partial pressure. Our results show that a low temperature, un-doped CeO2 nanocubes with active {\{}100{\}} surface sites are thermodynamically stable. But at the typical high temperature operating},
 author = {Symington, Adam R. and Molinari, Marco and Moxon, Samuel and Flitcroft, Joseph M. and Sayle, Dean C. and Parker, Stephen C.},
-doi = {10.1021/acs.jpcc.9b09046},
-issn = {1932-7447},
+title = {Strongly Bound Surface Water Affects the Shape Evolution of Cerium Oxide Nanoparticles},
 journal = {The Journal of Physical Chemistry C},
-month = {feb},
-number = {6},
-pages = {3577--3588},
-publisher = {American Chemical Society (ACS)},
-title = {{Strongly Bound Surface Water Affects the Shape Evolution of Cerium Oxide Nanoparticles}},
-url = {https://dx.doi.org/10.1021/acs.jpcc.9b09046},
 volume = {124},
-year = {2020}
+number = {6},
+pages = {3577-3588},
+year = {2020},
+doi = {10.1021/acs.jpcc.9b09046},
+URL = {https://doi.org/10.1021/acs.jpcc.9b09046},
+eprint = {https://doi.org/10.1021/acs.jpcc.9b09046}
 }

paper/paper.md

@@ -10,22 +10,22 @@ tags:
 authors:
 - name: Joshua S. Tse
   orcid: 0000-0002-1320-557X
-  affiliation: 2
+  affiliation: 1
 - name: Marco Molinari
   orcid: 0000-0001-7144-6075
-  affiliation: 2
+  affiliation: 1
 - name: Stephen C. Parker
   orcid: 0000-0003-3804-0975
-  affiliation: 1
+  affiliation: 2
 - name: Adam R. Symington
   orcid: 0000-0001-6059-497X
-  affiliation: "1"
+  affiliation: "2"
 affiliations:
-- name: Department of Chemistry, University of Bath
-  index: 1
 - name: Department of Chemistry, University of Huddersfield
+  index: 1
+- name: Department of Chemistry, University of Bath
   index: 2
-date: 30 September 2020
+date: 08 December 2020
 bibliography: paper.bib
 ---
 
@@ -72,4 +72,4 @@ With this release SurfinPy is no longer limited to the surface chemistry, but ex
 
 The authors acknowledge the EPSRC (EP/K025597/1 and EP/R010366/1), and the Royal Society (Newton Advanced Fellowship NA150190).
 
-# References
+# References