diff --git a/JOSSpaper/JOSSpaper.md b/JOSSpaper/JOSSpaper.md new file mode 100644 index 0000000..3ef2cd8 --- /dev/null +++ b/JOSSpaper/JOSSpaper.md @@ -0,0 +1,98 @@ +--- +title: 'MacroDensity: Understanding The Electrostatic Potential and Electron Density Landscapes within Systems of Quantum Mechanical Simulations' +tags: + - Python + - Density Functional Theory + - DFT + - electrostatic potentials + - electron density + - ab initio + - vasp +authors: + - name: Calysta A. Tesiman + orcid: 0009-0008-7784-4320 + equal-contrib: true + affiliation: "1, 2" # (Multiple affiliations must be quoted) + - name: Author Without ORCID + equal-contrib: true # (This is how you can denote equal contributions between multiple authors) + affiliation: 2 + - name: Author with no affiliation + corresponding: true # (This is how to denote the corresponding author) + affiliation: 3 + - given-names: Ludwig + dropping-particle: van + surname: Beethoven + affiliation: 3 +affiliations: + - name: Lyman Spitzer, Jr. Fellow, Princeton University, USA + index: 1 + - name: Institution Name, Country + index: 2 + - name: Independent Researcher, Country + index: 3 +date: 13 August 2017 +bibliography: paper.bib + +--- + +# Summary + +Summary + +# Statement of need + +When assessing the potential utility of novel semiconducting devices (p-n juntions, +heterostructures, surface terminations) through simulation, an understanding of the +variation in the electrostatic potential and electron density across the system is key. +However, extraction and useful presentation of this data from the raw output of the +simulation can prove cumbersome and often requires the use of visualisation software followed +by manual data extraction. This can result in bottlenecks in high throughput screening projects, +where the same data extraction procedure is repeatedly applied to large databases of candidate structures. + +To address this, ``MacroDensity`` was developed to simplify the data extraction and visualisation processes. +By using the landscape of electrostatic potentials and electronic density within a system seperated by grid points, +it becomes trivial to produce meaningful analysis and plots for visualisation. + +# MacroDensity + +MacroDensity is a set of Python modules developed to read and analyse electrostatic potentials and electron +density data from electronic structure calculations derived from Density Functional Theory (DFT). The package +allows users to read from VASP LOCPOT [@vasp], CHGCAR files, FHI-AIMS [@fhi_aims] , *.cube file, and GULP *.out +file and format the data into physically meaningful quantities, which can then be plotted for user interpretation. + +(MOVE ME TO ANOTHER SECTION) +#The code has been used to rapidly generate data for these publications: 1,2, amongst others.# + +The package formats datasets containing information about a system's lattice parameters electron density, and +electrostatic potentials. ``MacroDensity`` contains some high-level tools and functions to calculate +the planar and macroscopic average (as defined in Jackson's Electrodynamics [@Jackson:1999]), the spherical average +around a user-defined point, and calculates band energy offsets, deformation potential, and volume changes of a system. +``MacroDensity`` can also calculate the localised potential around a certain atomic nucleus of a system. The approach +to calculating this on site (Hartree) potential is similar to calculating the Madelung potential. this is useful for +electron energy level predictions [@aron:2014]. + +# Citations + +Citations to entries in paper.bib should be in +[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html) +format. + +If you want to cite a software repository URL (e.g. something on GitHub without a preferred +citation) then you can do it with the example BibTeX entry below for @fidgit. + +For a quick reference, the following citation commands can be used: +- `@author:2001` -> "Author et al. (2001)" +- `[@author:2001]` -> "(Author et al., 2001)" +- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)" + +# Figures + +Figures can be included like this: +![Caption for example figure.\label{fig:example}](figure.png) +and referenced from text using \autoref{fig:example}. + +Figure sizes can be customized by adding an optional second parameter: +![Caption for example figure.](figure.png){ width=20% } + +# Acknowledgements +