DOI: 10.18419/darus-4716
title: Replication Code for: Implementation Pitfalls for Carbonate Mineral Dissolution – a Technical Note

description: &lt;p&gt;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.&lt;/p&gt;

&lt;h4&gt;Contents&lt;/h4&gt;
&lt;ul&gt;
 &lt;li&gt;&lt;code&gt;docker_image_paper_reviewer.tar&lt;/code&gt; (8.8 GB): Docker image containing the full computational environment&lt;/li&gt;
&lt;/ul&gt;


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

&lt;h4&gt;Security Notice&lt;/h4&gt;
&lt;p&gt;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: &lt;a href="https://git.iws.uni-stuttgart.de/dumux-pub/weis2024a"&gt;Git Repository&lt;/a&gt;&lt;/p&gt;

&lt;h4&gt;Alternative Installation&lt;/h4&gt;
&lt;p&gt;For users who prefer to build the environment manually or cannot use the provided Docker image, please refer to our &lt;a href="https://git.iws.uni-stuttgart.de/dumux-pub/weis2024a"&gt;Git Repository&lt;/a&gt; which contains:&lt;/p&gt;
&lt;ul&gt;
 &lt;li&gt;Source Code of Simulations&lt;/li&gt;
 &lt;li&gt;Complete Dockerfile&lt;/li&gt;
 &lt;li&gt;Manual installation instructions&lt;/li&gt;
 &lt;li&gt;All necessary source code and configuration files&lt;/li&gt;
&lt;/ul&gt;
description: Use persistent identifiers from Software Heritage (
 
) to cite individual files or even lines of the source code.
description: DUNE, 2.9
description: DuMuX, 3.9
description: Reaktoro, 2.12.5