Merge pull request #38 from lucaskorol21/version_paper

Added contributing, doi, license, and updated readme file

CONTRIBUTING.md

@@ -0,0 +1,21 @@
+# Contributing to GO-RXR
+
+Thank you for considering contributing to GO-RXR! This document outlines the guidelines for contributing to this project. Please take a moment to review these guidelines before making contributions.
+
+## How to Contribute
+
+We welcome contributions from all members of the community. Here are a few ways you can contribute to GO-RXR:
+
+1.  **Bug Reports**: If you've come across some behavior that you think is a bug or a missing feature, the first step is to check if it's already known. For this, take a look at the [repository issues page](https://github.com/lucaskorol21/GO-RXR/issues). If you can't find anything related there, you're welcome to open a new issue.
+2.  **Feature Requests**: If you have ideas for new features or enhancements, feel free to [open a new issue](https://github.com/lucaskorol21/GO-RXR/issues) to discuss them.
+3.  **Code Contributions:** If you're interested in contributing code, please fork the repository, make your changes, and submit a pull request. Make sure to follow our coding style as possible.
+4. ****Documentation**: Improving documentation is always appreciated! If you notice any gaps or errors in the code documentation, tutorials, or user guide, please submit a pull request with your proposed changes.
+
+And if you find the project valuable but don't have the time to contribute directly, there are still ways to support us and show your appreciation:
+
+-   **Star the Project**: Show your support by starring the project on GitHub.
+-   **Spread the Word**: Share about GO-RXR on social media platforms or in relevant online communities.
+-   **Include in Your Project's README**: Consider mentioning GO-RXR in your project's README to help others discover it.
+-   **Recommend at Meetups**: If you attend local meetups or conferences, recommending GO-RXR to your peers can help increase its visibility and adoption.
+
+We appreciate any contributions you make to improve GO-RXR and make it even more valuable for the community. Thank you for your support!

PAPER/paper.bib

@@ -1,60 +1,64 @@
 @article{keimer_moore_NPh_2017,
-  title={The physics of quantum materials},
-  author={Keimer, Bernhard and Moore, Joel},
-  journal={Nature Phys},
-  volume={13},
-  pages={1045--1055},
-  year={2017},
-  doi={10.1038/nphys4302},
-  url={https://doi.org/10.1038/nphys4302}
+    title={The physics of quantum materials},
+    author={Keimer, Bernhard and Moore, Joel},
+    journal={Nature Phys},
+    volume={13},
+    pages={1045--1055},
+    year={2017},
+    doi={10.1038/nphys4302},
+    url={https://doi.org/10.1038/nphys4302}
 }
 
 @article{green-etal_SRN_2020,
-  title={Resonant Soft X-ray Reflectometry and Diffraction Studies of Emergent Phenomena in Oxide Heterostructures},
-  author={Green, R. J. and Sutarto, R. and He, F. and Hepting, M. and Hawthorn, D. G. and Sawatzky, G. A.},
-  journal={Synchrotron Radiation News},
-  volume={33},
-  number={2},
-  pages={20--24},
-  year={2020},
-  doi={10.1080/08940886.2020.1725797}
+    title={Resonant Soft X-ray Reflectometry and Diffraction Studies of Emergent Phenomena in Oxide Heterostructures},
+    author={Green, R. J. and Sutarto, R. and He, F. and Hepting, M. and Hawthorn, D. G. and Sawatzky, G. A.},
+    journal={Synchrotron Radiation News},
+    volume={33},
+    number={2},
+    pages={20--24},
+    year={2020},
+    doi={10.1080/08940886.2020.1725797},
+    url={https://doi.org/10.1080/08940886.2020.1725797}
 }
 
 @masterthesis{korol_MSc_2023,
-  title={Global optimization of resonant x-ray reflectometry models: Analysis of perovskite oxide heterostructures},
-  author={Korol, Lucas},
-  school={University of Saskatchewan},
-  year={2023},
-  address={Saskatoon},
-  month={August},
-  type={Master's thesis}
+    title={Global optimization of resonant x-ray reflectometry models: Analysis of perovskite oxide heterostructures},
+    author={Korol, Lucas},
+    school={University of Saskatchewan},
+    year={2023},
+    address={Saskatoon},
+    month={August},
+    type={Master's thesis}
 }
 
 @article{vanderMinne_etal_2023,
     author = {{van der Minne}, Emma and Korol, Lucas and Krakers, Lidewij M. A. and Verhage, Michael and Rosário, Carlos M. M. and Roskamp, Thijs J. and Spiteri, Raymond J. and Biz, Chiara and Fianchini, Mauro and Boukamp, Bernard A. and Rijnders, Guus and Flipse, Kees and Gracia, Jose and Mul, Guido and Hilgenkamp, Hans and Green, Robert J. and Koster, Gertjan and Baeumer, Christoph},
-    title = "{The effect of intrinsic magnetic order on electrochemical water splitting}",
+    title = {The effect of intrinsic magnetic order on electrochemical water splitting},
     journal = {Applied Physics Reviews},
     volume = {11},
     number = {1},
     pages = {011420},
     year = {2024},
     issn = {1931-9401},
     doi = {10.1063/5.0174662},
+    url = {https://doi.org/10.1063/5.0174662}
 }
 
 @article{verhage_etal_2023,
-  title={A complementary experimental study of epitaxial La0. 67Sr0. 33MnO3 to identify morphological and chemical disorder},
-  author={Verhage, Michael and van der Minne, Emma and Kiens, Ellen M and Korol, Lucas and Spiteri, Raymond J and Koster, Gertjan and Green, Robert J and Baeumer, Christoph and Flipse, Kees},
-  journal={arXiv preprint arXiv:2311.00504},
-  year={2023}
+    title={A complementary experimental study of epitaxial La0. 67Sr0. 33MnO3 to identify morphological and chemical disorder},
+    author={Verhage, Michael and van der Minne, Emma and Kiens, Ellen M and Korol, Lucas and Spiteri, Raymond J and Koster, Gertjan and Green, Robert J and Baeumer, Christoph and Flipse, Kees},
+    journal={arXiv},
+    doi={10.48550/arXiv.2311.00504},
+    year={2023},
+    url={https://doi.org/10.48550/arXiv.2311.00504}
 }
 
 @misc{pythonreflectivity,
-  author = {Zwiebler, M.},
-  title = {PyXMRTool: Python Package for the analysis of X-Ray Magnetic Reflectivity data measured on heterostructures},
-  year = {2018},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  howpublished = {\url{https://github.com/malaclypseII/PyXMRTool/tree/master}},
-  commit = {30d1ed552cf807d3635d2e274dd89151c2a83090}
+    author = {Zwiebler, M.},
+    title = {PyXMRTool: Python Package for the analysis of X-Ray Magnetic Reflectivity data measured on heterostructures},
+    year = {2018},
+    publisher = {GitHub},
+    journal = {GitHub repository},
+    howpublished = {\url{https://github.com/malaclypseII/PyXMRTool/tree/master}},
+    commit = {30d1ed552cf807d3635d2e274dd89151c2a83090}
 }

PAPER/paper.md

@@ -29,10 +29,14 @@ date: 2 April 2024
 bibliography: paper.bib
 ---
 
-# Summary and Statement of Need
+# Summary
 
 Resonant x-ray reflectometry (RXR) is a cutting-edge synchrotron technique used to characterize the depth-dependent structure of quantum materials [@keimer_moore_NPh_2017; @green-etal_SRN_2020]. However, the main challenge impeding the success of RXR data analysis lies in its extreme complexity, driven by complicated model construction and the fitting of numerous independent variables. This complexity results in prolonged analysis periods that demand significant engagement from researchers. In response to these challenges, the Global Optimization of Resonant X-ray Reflectometry (GO-RXR) software emerged from rigorous development efforts as a main contribution from the work by [@korol_MSc_2023]. GO-RXR streamlines data analysis, enhances visualization, and reduces the expertise required, offering researchers a more efficient means to analyze RXR data. 
 
+This paper presents an overview of GO-RXR, highlighting its functionality, example use-cases, and impact in materials science research. Through its comprehensive approach and user-friendly design, GO-RXR offers researchers an efficient tool for analyzing RXR data, facilitating breakthroughs in understanding complex material systems. Additionally, publications and ongoing research utilizing GO-RXR underscore its versatility and impact in advancing scientific exploration.
+
+# Statement of Need
+
 One of the challenges addressed by [@korol_MSc_2023] included the analysis of LaMnO<sub>3</sub>/SrTiO<sub>3</sub> thin-film heterostructures. The data for these samples were collected at the resonant elastic and inelastic x-ray scattering beamline (REIXS) at the Candian Light Source (CLS) in 2017. Although the initial data collection took only three days, attempts to analyze it with the tools available in 2021 yielded little success. In 2023, use of the GO-RXR tool led to a successful analysis, highlighting the efficacy of the software in overcoming longstanding analysis barriers.
 
 The analysis of RXR presents multifaceted challenges, extending beyond computational aspects to encompass expertise in materials and the physics of light-matter interactions. This expertise is pivotal because it provides intuition about parameter adjustments and guides the direction of data analysis to achieve desired outcomes. In addressing this challenge, GO-RXR integrates global optimization algorithms, thereby lowering the expertise threshold necessary for effective data analysis. Through the extensive development of GO-RXR, diverse global optimization algorithms and unique objective functions were thoroughly explored. The software's capability to capture features in experimental data without exhaustive parameter understanding significantly reduces the expertise required. GO-RXR serves as a valuable scientific tool for material scientists, offering advanced capabilities to streamline data analysis and reduce the expertise barrier, ultimately facilitating breakthrough discoveries in the field of materials science.

README.md

@@ -151,25 +151,12 @@ Contribution made by:
 GO-RXR would have not been possible without the University of Saskatchewan and the funding provided by the U of S Physics and Engineering Physics Department, the NSERC-CREATE to INSPIRE fellowship, and the NSERC CGS M.
 
 ## License
-Copyright © 2023 QMaX and Numerical Simulations Lab
 
-GO-RXR has been developed at in the Department of Physics and Engineering Physics at the University of Saskatchewan and is copyrighted by the QMaX and Numerical Simulation Lab. All rights are reserved by the authors, QMaX Research Group, and the Numerical Simulations Research Lab. 
+GO-RXR has been developed by the QMaX and Numerical Simulation Lab at the Department of Physics and Engineering Physics, University of Saskatchewan. The distribution of GO-RXR is subject to the terms and conditions of the [BSD 3-Clause License](LICENSE). For specific details, please refer to the LICENSE file included with this distribution.
 
-GO-RXR is a a free software: you can redistribute it and/or modify it under the terms an conditions of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.
+## Contributing
 
-This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
-
-ANY WORK USING THE SOFTWARE OR ANY RESULTS OBTAINED WITH THE HELP OF THIS SOFTWARE HAS TO CITE GO-RXR AND THE AUTHORS PROPERLY.
-
-**Disclaimer of Warranty**
-
-THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
-**Disclaimer of Liability**
-
-IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
-
-END OF TERMS AND CONDITIONS
+We welcome contributions from the community! If you're interested in contributing to GO-RXR, please read our [Contribution Guidelines](CONTRIBUTING.md) for more information.
 
 ## Publications