added JOSSpaper folder for organisation

JOSSpaper/JOSSpaper.md

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+---
+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
+