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Fixing file extension
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ifilot committed Apr 17, 2024
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6 changes: 3 additions & 3 deletions docs/tutorial.rst
Original file line number Diff line number Diff line change
Expand Up @@ -103,15 +103,15 @@ the drop-down menu as follows::
Select the file and click on ``Import PLY``. You should now see something
similar as to the image below.

.. figure:: _static/img/tutorials/genus2_blender_01.JPG
.. figure:: _static/img/tutorials/genus2_blender_01.jpg
:alt: The imported Genus 2 isosurface in Blender.

Finally, we assign a material to the object, tune the camera to bring the
object fully into view, set the color of the background to black, add
two sun-type light sources and set the film to transparent. For the material,
we have used the settings as can be seen in the figure below.

.. figure:: _static/img/tutorials/genus2_blender_02.JPG
.. figure:: _static/img/tutorials/genus2_blender_02.jpg
:alt: The imported Genus 2 isosurface in Blender.

The only step that remains is to render the image, which will give the image
Expand Down Expand Up @@ -259,4 +259,4 @@ looks as seen in the image below.
Finally, we can render the scene to create a nice picture of the molecular orbital.

.. figure:: _static/img/tutorials/benzene_homo_result.png
:alt: Benzene highest occupied molecular orbital
:alt: Benzene highest occupied molecular orbital
85 changes: 85 additions & 0 deletions paper/paper.jats
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@@ -0,0 +1,85 @@
<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.2 20190208//EN"
"JATS-publishing1.dtd">
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
<front>
<journal-meta>
<journal-id></journal-id>
<journal-title-group>
<journal-title>Journal of Open Source Software</journal-title>
<abbrev-journal-title>JOSS</abbrev-journal-title>
</journal-title-group>
<issn publication-format="electronic">2475-9066</issn>
<publisher>
<publisher-name>Open Journals</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">0</article-id>
<article-id pub-id-type="doi">N/A</article-id>
<title-group>
<article-title>Den2Obj: A command line program for producing isosurfaces
from density files</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" corresp="yes">
<contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-1403-8379</contrib-id>
<name>
<surname>Filot</surname>
<given-names>I. A. W.</given-names>
</name>
<xref ref-type="aff" rid="aff-1"/>
<xref ref-type="corresp" rid="cor-1"><sup>*</sup></xref>
</contrib>
<aff id="aff-1">
<institution-wrap>
<institution>Inorganic Materials and Catalysis, Department of Chemical
Engineering and Chemistry, Eindhoven University of Technology,
Eindhoven, The Netherlands</institution>
</institution-wrap>
</aff>
</contrib-group>
<author-notes>
<corresp id="cor-1">* E-mail: <email></email></corresp>
</author-notes>
<pub-date date-type="pub" publication-format="electronic" iso-8601-date="2024-04-10">
<day>10</day>
<month>4</month>
<year>2024</year>
</pub-date>
<volume>¿VOL?</volume>
<issue>¿ISSUE?</issue>
<fpage>¿PAGE?</fpage>
<permissions>
<copyright-statement>Authors of papers retain copyright and release the
work under a Creative Commons Attribution 4.0 International License (CC
BY 4.0)</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>The article authors</copyright-holder>
<license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by/4.0/">
<license-p>Authors of papers retain copyright and release the work under
a Creative Commons Attribution 4.0 International License (CC BY
4.0)</license-p>
</license>
</permissions>
</article-meta>
</front>
<body>
<sec id="summary">
<title>Summary</title>
</sec>
<sec id="statement-of-need">
<title>Statement of need</title>
</sec>
<sec id="acknowledgements">
<title>Acknowledgements</title>
<p>This work was supported by the Netherlands Center for Multiscale
Catalytic Energy Conversion, and NWO Gravitation program funded by the
Ministry of Education, Culture and Science of the government of the
Netherlands. The Netherlands Organization for Scientific Research is
acknowledged for providing access to computational resources.</p>
</sec>
</body>
<back>
</back>
</article>
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