Merging

.github/workflows/docs.yml

@@ -2,35 +2,60 @@ name: docs
 
 on:
   push:
-    branches: [ "master"]
+    branches: [ "docs" ]
   pull_request:
-    branches: [ "master"]
+    branches: [ "docs" ]
 
 jobs:
   build-docs:
     runs-on: ubuntu-latest
+    container: ghcr.io/ifilot/sphinx:v0.9.0
     steps:
     - uses: actions/checkout@v3
-    - name: Install packages
-      run: sudo apt update && sudo apt install -y git build-essential curl wget python3 python3-pip texlive texlive-pictures texlive-latex-extra pdf2svg poppler-utils netpbm imagemagick ghostscript
-    - name: Install Python packages
-      run: sudo pip install sphinx sphinx-rtd-theme sphinxcontrib-tikz
     - name: Build documentation
       run: cd docs && make html
-    - name: Upload math result for job 1
+    - name: Upload documentation as artifact
       uses: actions/upload-artifact@v3
       with:
         name: html-docs
         path: ./docs/_build/html
 
   deploy:
-    runs-on: [self-hosted, linux, x64]
+    runs-on: ubuntu-latest
     needs: build-docs
+    permissions:
+      contents: read
+      packages: write
+
     steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
     - name: Download docs
       uses: actions/download-artifact@v3
       with:
         name: html-docs
         path: html-docs
-    - name: Deploy
-      run: touch ${{ secrets.DEPLOY_PATH }}/html && rm -r ${{ secrets.DEPLOY_PATH }}/html/* && cp -rv html-docs/* ${{ secrets.DEPLOY_PATH }}/html
+
+    - name: Extract metadata (tags, labels) for Docker
+      id: meta
+      uses: docker/metadata-action@v4
+      with:
+        images: |
+          ghcr.io/ifilot/den2obj-docs-nginx
+
+    - name: Log in to the Container registry
+      uses: docker/login-action@v2
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Build and push Docker images
+      uses: docker/build-push-action@v4
+      with:
+        context: .
+        file: doc.Dockerfile
+        push: true
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}

doc.Dockerfile

@@ -0,0 +1,2 @@
+FROM nginx:latest
+COPY html-docs/ /usr/share/nginx/html/

docs/installation.rst

@@ -48,7 +48,7 @@ looks as follows::
     cmake ../src
     make -j9
 
-To install :program:`EDP`, you can in addition run::
+To install :program:`Den2Obj`, you can in addition run::
 
     sudo make install
 

docs/tutorial.rst

@@ -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
@@ -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

paper/paper.jats

@@ -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>

scripts/genus2.py

@@ -1,3 +1,67 @@
+<<<<<<< HEAD
+# -*- coding: utf-8 -*-
+
+#
+# Generate the "genus-2" scalar field. The function has
+# been taken from: https://doi.org/10.1109/3DV.2015.36
+#
+
+import numpy as np
+import gzip
+
+def main():
+    dim = 2
+    grid = generate_grid(dim = dim)
+    store_d2o(grid,dim)
+
+def store_d2o(grid, dim):
+    """
+    Store Genus2 scalar field as a d2o file. See
+    https://den2obj.imc-tue.nl/d2o_fileformat.html
+    for the specifications of the d2o file type.
+    """
+    f = open('genus2.d2o', 'wb')  
+
+    # write header
+    f.write('D2O'.encode('utf-8'))
+
+    # write protocol identifier
+    f.write(np.uint32(1).tobytes())
+
+    # write unit cell matrix
+    unitcell = np.diag(np.ones(3, dtype=np.float32) * dim * 2)
+    f.write(unitcell.flatten().tobytes())
+
+    # write grid dimensions
+    f.write(np.array(grid.shape, dtype=np.uint32).tobytes())
+
+    # write floating point bytesize
+    f.write(np.uint8(4).tobytes())
+
+    # write data stream
+    compressed_data = gzip.compress(np.array(grid.flatten(), dtype=np.float32).tobytes(),
+                                    compresslevel=9)
+    f.write(np.uint64(len(compressed_data)).tobytes())
+    f.write(compressed_data)
+
+    f.close()
+
+def generate_grid(dim = 2, npts = 100):
+    x = np.linspace(-dim, dim, npts)
+    y = np.linspace(-dim, dim, npts)
+    z = np.linspace(-dim, dim, npts)
+
+    xx, yy, zz = np.meshgrid(x, y, z, indexing='ij')
+
+    return genus2(xx,yy,zz)
+
+def genus2(x,y,z):
+    F = 2*y*(y**2 - 3*x**2) * (1 - z**2) + \
+        (x**2 + y**2)**2 - (9*z**2 - 1) * (1 - z**2)
+    return F
+
+if __name__ == '__main__':
+=======
 # -*- coding: utf-8 -*-
 
 #
@@ -60,4 +124,5 @@ def genus2(x,y,z):
     return F
 
 if __name__ == '__main__':
+>>>>>>> master
     main()

src/test/CMakeLists.txt

@@ -21,7 +21,7 @@
 add_library(unittest STATIC unittest.cpp)
 
 # set executables
-SET(EXECUTABLES TestIsosurface TestScalarField TestD2OFileFormat)
+SET(EXECUTABLES TestIsosurface TestScalarField TestD2OFileFormat TestGenerator)
 
 # only add this test when not using GCOV
 if(NOT USE_GCOV)
@@ -39,6 +39,7 @@ endif()
 add_executable(TestIsosurface test_isosurface.cpp)
 add_executable(TestScalarField test_scalarfield.cpp)
 add_executable(TestD2OFileFormat test_d2o_fileformat.cpp)
+add_executable(TestGenerator test_generator.cpp)
 
 # only add this test when not using GCOV
 if(NOT USE_GCOV)

src/test/test_d2o_fileformat.h

@@ -37,6 +37,7 @@ class TestD2OFileFormat : public CppUnit::TestFixture
 
 public:
   void setUp();
+
   void tearDown();
 
   void test_gzip_compression();