DOI: 10.18419/darus-3276
title: Code for: Seasonal Dynamics of Gaseous CO2 Concentrations in a Karst Cave Correspond With Aqueous Concentrations in a Stagnant Water Column

description: This dataset contains the DuMux code for the simulations in &lt;br&gt;
 &lt;a href="https://doi.org/10.3390/geosciences13020051"&gt;https://doi.org/10.3390/geosciences13020051&lt;/a&gt; &lt;br&gt;
For the detailed list of software used, please have a look at the file &lt;b&gt;install_class2023.sh&lt;/b&gt;.&lt;br&gt;
To run the simulations at your own computer, please conduct the following steps:
&lt;ol&gt;
&lt;li&gt; Install docker &lt;a href="https://docs.docker.com/engine/install/ubuntu/"&gt;for example in ubuntu&lt;/a&gt; .&lt;/li&gt;
&lt;li&gt; Make sure you can run docker &lt;a href="https://docs.docker.com/engine/install/linux-postinstall/"&gt;without sudo&lt;/a&gt;.&lt;/li&gt;
&lt;li&gt; build the docker image: &lt;pre&gt;&lt;samp&gt;docker build -t class2023 --build-arg UID=$(id -u) --build-arg GID=$(id -g) . 
&lt;/samp&gt;&lt;/pre&gt; This makes sure that your container has the right user and group id to avoid permission issues. &lt;/li&gt;
&lt;li&gt; Run the container.&lt;pre&gt;&lt;samp&gt; ./docker_class2023.sh open &lt;/pre&gt;&lt;/samp&gt;&lt;/li&gt;
&lt;li&gt; To exit the container type: &lt;pre&gt;&lt;samp&gt; exit&lt;/pre&gt;&lt;/samp&gt;&lt;/li&gt;
&lt;li&gt; To re enter the container type: &lt;pre&gt;&lt;samp&gt; docker restart [container-id]&lt;/pre&gt;&lt;/samp&gt; 
&lt;pre&gt;&lt;samp&gt; docker exec -it [container-id] bash&lt;/pre&gt;&lt;/samp&gt;&lt;/li&gt;
&lt;/ol&gt;
When you are inside the running container you can run the following simulations: 
&lt;ol&gt;
&lt;li&gt; Simulations of the real world scenario: &lt;pre&gt;&lt;samp&gt;cd class2023a/build-cmake/appl/isothermal/column/
&lt;/pre&gt;&lt;/samp&gt; 
Select the scenario by entering the folder (for example the normal case)
&lt;pre&gt;&lt;samp&gt; cd normal&lt;/pre&gt;&lt;/samp&gt; 
Run the simulation
&lt;pre&gt;&lt;samp&gt;./../column_isothermal ./../params.input&lt;/pre&gt;&lt;/samp&gt;
For other scenarios enter a different directory and type either:
&lt;pre&gt;&lt;samp&gt;./../column_isothermal_pulses ./../params.input&lt;/pre&gt;&lt;/samp&gt;
&lt;pre&gt;&lt;samp&gt;./../column_isothermal_superdiffusion ./../params.input&lt;/pre&gt;&lt;/samp&gt;
&lt;/li&gt;
&lt;li&gt;Grid studies:
 &lt;pre&gt;&lt;samp&gt;cd class2023a/build-cmake/test/isothermal/columntop_constant/results/&lt;/pre&gt;&lt;/samp&gt; 
or : 
&lt;pre&gt;&lt;samp&gt;cd class2023a/build-cmake/test/isothermal/columntop_usedata/results/&lt;/pre&gt;&lt;/samp&gt;
Run the prepare simulation script: 
&lt;pre&gt;&lt;samp&gt; python3 prepare_simulations.py &lt;/pre&gt;&lt;samp&gt; 
Go in the directory of interest and run the simulation: 
&lt;pre&gt;&lt;samp&gt;./../../columntop_constant params.input &lt;/pre&gt;&lt;/samp&gt;
Or:
&lt;pre&gt;&lt;samp&gt;./../../columntop_usedata params.input &lt;/pre&gt;&lt;/samp&gt;
&lt;/li&gt;
&lt;li&gt; 2D and 3D comparison:
First the 2D simulation:
&lt;pre&gt;&lt;samp&gt;cd class2023a/build-cmake/test/isothermal/smallcolumn/results/ &lt;/pre&gt;&lt;/samp&gt; 
Then run the simulation
&lt;pre&gt;&lt;samp&gt; ./../smallcolumn_isothermal ./../params.input &lt;/pre&gt;&lt;/samp&gt;
3D simulation: 
&lt;pre&gt;&lt;samp&gt;cd class2023a/build-cmake/test/isothermal/smallcolumn3D/results/ &lt;/pre&gt;&lt;/samp&gt; 
Then run the simulation 
&lt;pre&gt;&lt;samp&gt; ./../smallcolumn3D_isothermal ./../params.input &lt;/pre&gt;&lt;/samp&gt;
&lt;/li&gt;
&lt;/ol&gt;
All the results of the simulation will be available on your host-machine in the corresponding folder.