Replication Code for: Implementation Pitfalls for Carbonate Mineral Dissolution – a Technical Note

<p>This dataset contains a Docker image that provides a complete computational environment for reproducing the numerical calculations presented in our manuscript. The image includes pre-built installations of DuMuX and Reaktoro, configured to run our specific simulation cases.</p>

<h4>Contents</h4>
<ul>
<li><code>docker_image_paper_reviewer.tar</code> (8.8 GB): Docker image containing the full computational environment</li>
</ul>

<h4>Running Simulations and Data Transfer</h4>
<ol>
<li>Create and prepare the output directory:
<pre><code>mkdir output</code></pre>
<pre><code>chmod 777 output</code></pre>
</li>
<li>Load the image into Docker:
<pre><code>docker load < docker_image_paper_reviewer.tar</code></pre>
</li>
<li>Run the container with mounted output directory:
<pre><code>docker run -itv ./output:/home/reviewer/output reviewer_docker_new</code></pre>
</li>
<li>To detach from the container without stopping it:
<br>Press <code>Ctrl+P</code> followed by <code>Ctrl+Q</code>
</li>
<li>To reenter a detached container:
<pre><code>docker ps</code></pre>
Find your container ID, then:
<pre><code>docker attach CONTAINER_ID</code></pre>
</li>
<li>Inside the container, run the DuMuX simulation:
<pre><code>cd ${DUMUX_BATCH_DIR}/build-cmake/test/reaction_rate/</code></pre>
<pre><code>./test_ReactionRate</code></pre>
</li>
<li>Run the Reaktoro simulations:
<pre><code>cd ${REAKTORO_BATCH_DIR}/build</code></pre>
<pre><code>./calcite_dissolution_corrected</code></pre>
<pre><code>./calcite_dissolution_palandri_kharaka</code></pre>
</li>
<li>Copy results to the mounted output directory:
<pre><code>cd ${DUMUX_BATCH_DIR}/build-cmake/test/reaction_rate/</code></pre>
<pre><code>cp dumux-corrected.csv ${OUTPUT_DIR}/</code></pre>
<pre><code>cd ${REAKTORO_BATCH_DIR}/build</code></pre>
<pre><code>cp reaktoro-palandri-kharaka.csv ${OUTPUT_DIR}/</code></pre>
<pre><code>cp reaktoro-corrected.csv ${OUTPUT_DIR}/</code></pre>
</li>
<li>Exit the container:
<br>Type <code>exit</code> or press <code>Ctrl+D</code>
</li>
<li>The results are now available in your local './output' directory</li>
</ol>

<h4>Security Notice</h4>
<p>This Docker container requires elevated privileges to run. While we ensure no malicious content is included, as with any third-party software requiring elevated privileges, users should exercise appropriate caution. For maximum security, users can alternatively build the environment themselves using our publicly available Dockerfile and installation instructions at: <a href="https://git.iws.uni-stuttgart.de/dumux-pub/weis2024a">Git Repository</a></p>

<h4>Alternative Installation</h4>
<p>For users who prefer to build the environment manually or cannot use the provided Docker image, please refer to our <a href="https://git.iws.uni-stuttgart.de/dumux-pub/weis2024a">Git Repository</a> which contains:</p>
<ul>
<li>Source Code of Simulations</li>
<li>Complete Dockerfile</li>
<li>Manual installation instructions</li>
<li>All necessary source code and configuration files</li>
</ul>