Merge pull request #20 from ifilot/develop

Improving documentation and paper per reviewer suggestions
ifilot · May 1, 2023 · 1c0608b · 1c0608b
2 parents 9b8369a + 5edc05b
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diff --git a/docs/community_guidelines.rst b/docs/community_guidelines.rst
@@ -0,0 +1,14 @@
+.. _community_guidelines:
+.. index:: Community Guidelines
+
+Community guidelines
+********************
+
+* Contributions to :program:`EDP` are always welcome and appreciated. Before doing
+  so, please first read the `CONTRIBUTING <https://github.com/ifilot/edp/blob/master/CONTRIBUTING.md>`_
+  guide.
+* For reporting issues or problems with the software, you are kindly invited to
+  `to open a new issue on Github with the bug tag <https://github.com/ifilot/edp/issues/new?labels=bug>`_.
+* If you seek support in using :program:`EDP`, please
+  `open an issue with the question tag <https://github.com/ifilot/edp/issues/new?labels=question>`_.
+* If you wish to contact the developers, please send an e-mail to i.a.w.filot@tue.nl.
diff --git a/docs/examples.rst b/docs/examples.rst
@@ -93,6 +93,13 @@ between 0-15, inclusive.
 Special features
 ================
 
+.. note::
+   In the subsections below, a list of special features of :program:`EDP` is given.
+   To visualize the results, we have made use of `NumPy <https://numpy.org/doc/stable/index.html>`_
+   and `Matplotlib <https://matplotlib.org/>`_.
+   These programs are typically readily available on Linux operating systems. The
+   scripts used below can be found `in the examples folder on Github <https://github.com/ifilot/edp/tree/master/examples>`_.
+
 Z-averaging
 -----------
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -40,6 +40,7 @@ requests are ideally submitted via the `github issue tracker
    examples
    user_interface
    publications
+   community_guidelines
 
 Indices and tables
 ------------------

diff --git a/docs/user_interface.rst b/docs/user_interface.rst
@@ -165,7 +165,7 @@ to `line_extraction.txt`.
 
 Calculate the average electron density (or electrostatic potential) at a
 radius :math:`r \in 0,R` from an atom with 0.01 Å increments. The sampling
-points are based on the coordinates of the 23<sup>rd</sup> order Lebedev
+points are based on the coordinates of the 23\ :sup:`rd` order Lebedev
 quadrature. The result is written to `spherical_average.txt`.
 
 *Example*: ``-r 1,1.5``
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -169,9 +169,9 @@ @Article{hunter:2007
 
 @software{MATLAB,
     year = {2022},
-    author = {The MathWorks Inc.},
+    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}
-}
+}
diff --git a/paper/paper.md b/paper/paper.md
@@ -24,7 +24,7 @@ The electron density is a scalar field, which means that it is a function that a
 
 # Statement of need
 
-The visualization of scalar fields using contour plots or heat maps is ubiquitous in science and engineering and plenty of general purpose programs such as `Open Data Explorer` [@OpenDX] and `ParaView` [@ParaView] readily accomodate this task. There exist also programs that specifically cater to `VASP`, such as `Vesta` [@momma:2011] and `sisl` [@papior:2023]. These programs are typically designed for interactive use , `sisl` being a notable exception, and utilize a graphical user interface of some sort. In contrast, `EDP` is a C++ based command line tool that carries out the projection of the electron density scalar field as stored in `VASP` CHGCAR or PARCHG file onto a plane. This plane is then rendered onto a canvas using a color map and stored as a PNG file. `EDP` uses a minimal set of dependencies, i.e. Boost[@BoostLibrary], Cairo[@CairoLibrary], `TCLAP`[@TclapLibrary], Eigen3[@eigenweb], which are all readily available on modern Linux based operating systems.
+The visualization of scalar fields using contour plots or heat maps is ubiquitous in science and engineering and plenty of general purpose programs such as `Open Data Explorer` [@OpenDX] and `ParaView` [@ParaView] readily accomodate this task. There exist also programs that specifically cater to `VASP`, such as `Vesta` [@momma:2011] and `sisl` [@papior:2023]. These programs are typically designed for interactive use , `sisl` being a notable exception, and utilize a graphical user interface of some sort. In contrast, `EDP` is a C++ based command line tool that carries out the projection of the electron density scalar field as stored in `VASP`[@hafner:2008] CHGCAR or PARCHG file onto a plane. This plane is then rendered onto a canvas using a color map and stored as a PNG file. `EDP` uses a minimal set of dependencies, i.e. Boost[@BoostLibrary], Cairo[@CairoLibrary], `TCLAP`[@TclapLibrary], Eigen3[@eigenweb], which are all readily available on modern Linux based operating systems.
 
 `EDP` was designed to be used by researchers and students working in computational materials modelling using the VASP software. It has already been used in a number of scientific publications[@zijlstra:2019; @vogt:2019; @filot:2016]. `EDP` is designed with ease of use in mind. The projection planes can be defined with respect to the atomic coordinates, which are available in the structure block of CHGCAR and PARCHG files. This allows for users to efficiently define projection plane intersecting one or more atoms of interest. This feature is especially relevant to chemists who study the electron density to understand bonding patterns and explain chemical reactivity.