some new figures!

Signed-off-by: Philipp Pracht <[email protected]>

README.md

@@ -4,3 +4,14 @@ This project contains a documentation for CREST to be hosted on github-pages.
 The site was created with [Jekyll](https://jekyllrb.com/) 
 and uses the [Just-the-Docs theme](https://github.com/just-the-docs/just-the-docs) 
 
+
+---
+
+It is possible to build the page locally for testing.
+See [this help page on GitHub](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/testing-your-github-pages-site-locally-with-jekyll).
+
+Very briefly:
+
+1. Install [Jekyll](https://jekyllrb.com/docs/installation/), [Ruby](https://www.ruby-lang.org/en/documentation/installation/), and [bundler](https://bundler.io/)
+2. Run `bundle install` in this repository
+3. Run `bundle exec jekyll serve`

_config.yml

@@ -88,7 +88,7 @@ back_to_top: true
 back_to_top_text: "Back to top <i class='fa-solid fa-circle-up'></i>"
 
 footer_content: >
-  Copyright &copy; 2022-2023 Philipp Pracht.
+  Copyright &copy; 2022-2024 Philipp Pracht.
   <br><br>
   CREST is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of

_includes/twitter.html

@@ -1,7 +1,9 @@
 
 
 <div class="row">
+<!--
 <blockquote class="twitter-tweet" data-width="400" data-height="400"><p lang="en" dir="ltr">[ASAP] Fast Screening of Minimum Energy Crossing Points with Semiempirical Tight-Binding Methods <a href="https://t.co/lyOmdpjoX7">https://t.co/lyOmdpjoX7</a></p>&mdash; JCTC Papers (@jctc_papers) <a href="https://twitter.com/jctc_papers/status/1572293038533115904?ref_src=twsrc%5Etfw">September 20, 2022</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script> 
+-->
 <a class="twitter-timeline"  data-width="400" data-height="500" data-theme="light" href="https://twitter.com/GrimmeLab?ref_src=twsrc%5Etfw">Tweets by GrimmeLab</a> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script> 
 </div>
 

index.md

@@ -10,7 +10,7 @@ permalink: /
 
 Welcome to the documentation site of {% include tooltip.html tool="CREST" tip=site.data.glossary.crest %}.
 
-{% include image.html file="crest.png" alt="CREST" max-width=250 %}
+{% include image.html file="newtoc.png" alt="CREST" max-width=800 %}
 
 
 ## Introduction

page/examples/msreact-example_1.md

@@ -698,7 +698,7 @@ CREGEN> running RMSDs ... done.
 {% endcapture %}
 {% include codecell.html content=output_file style="text-align:justify" %}
 </div>
-{% include defaulttab.html %}
+{% include defaulttab.html id="open-1" %}
 
 CREST produces 25 unique products and writes them sorted according to their relative energy to the file `crest_msreact_products.xyz`. Additionally, isomers are written to `isomers.xyz`, fragmentpairs to `fragmentpairs.xyz`.
-{: .text-justify }
+{: .text-justify }

page/examples/msreact-example_2.md

@@ -4979,9 +4979,9 @@ p318              isomer      199.86063132
 {% endcapture %}
 {% include codecell.html content=output_file  style="text-align:justify" %}
 </div>
-{% include defaulttab.html %}
+{% include defaulttab.html id="open-1" %}
 
 {% include image.html file="benzisos.png" alt="Isomers of benzene" caption="Selected generated isomers of benzene, the numbering corresponds to their ordering according to the relative energy of all obtained isomers." max-width=800 %}
 
 In total, we obtain 318 unique isomers, including the important valence isomers benzvalene (**2**), bicyclopropenyl (**117**), Dewar benzene (**5**) and the well-known compounds fulvene (**1**) and hexa-1,3-dien-5-yne (**12**).
-{: .text-justify }
+{: .text-justify }

page/overview/workflows.md

@@ -82,7 +82,7 @@ All CREs that are found within the iterations are included in the conformer/rota
 The iMTD-GC worflow is outlined graphically in the figure below.
 {: .text-justify }
 
-{% include image.html file="imtd-gc.png" alt="iMTD-GC Workflow" caption="Flowchart for the iMTD-GC workflow." %}
+{% include image.html file="imtdgc-new.png" alt="iMTD-GC Workflow" caption="Flowchart for the iMTD-GC workflow." %}
 
 
 
@@ -102,7 +102,7 @@ After each sMTD iteration, new bias structures for the potential are identified
 The iMTD-sMTD workflow is outlined in the figure below.
 {: .text-justify }
 
-{% include image.html file="imtd-smtd.png" alt="iMTD-sMTD Workflow" caption="Flowchart for the iMTD-sMTD workflow." %}
+{% include image.html file="imtdsmtd-new.png" alt="iMTD-sMTD Workflow" caption="Flowchart for the iMTD-sMTD workflow." %}
 
 
 This algorithm can be used not only for ensemble generation, but also provides the capability to determine a
@@ -172,6 +172,7 @@ action products.
 
 [Go to the MSREACT keyword documentation <i class="fa-solid fa-book"></i>]({{site.baseurl}}/page/documentation/msreact.html){: .btn .btn-blue }
 
+---
 
 ## Quantum Cluster Growth (QCG)