Data for: Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog

<p>This dataset contains laboratory‑experiment data and simulation data for the publication
<strong>Validating a Numerical Model for Calco‑Carbonic Reactive Flow in a Laboratory Scale Fracture Analog.</strong>
For missing details see the attached README.md</p>

<p>To create the graphs in the publication, download <strong>fracture_analog.tar.xz</strong>.
Make sure that you have the dependencies shown in <strong>requirements_paper_2025.txt</strong>.
The scripts can recreate the graphs directly with Python.</p>

<p>The structure of the dataset in <strong>fracture_analog.tar.xz</strong> is as follows:</p>

<ul>
<li><strong>experimentalDataset</strong> – contains the relevant experimental data set.</li>
<li><strong>ftb</strong> – contains the simulation data organized in folders for each case.</li>
<li><strong>python</strong> – contains Python scripts that allow reproducing the publication graphs. Data created with the scripts are also saved in dedicated folders.</li>
<li><strong>stg</strong> – contains the initializers for the simulations in <strong>ftb</strong>.</li>
</ul>

<h1>Create Figures</h1>

<p>To reproduce the plots and figures in the paper, go into the folder containing the Python scripts:</p>

<pre>
<kbd>cd fracture_analog/python</kbd>
</pre>

<p>Typical usage (run from the <code>python</code> folder):</p>

<pre>
<kbd>python plot.py # shows help</kbd>
<kbd>python plot.py time --show --save</kbd>
<kbd>python plot.py da --save --out-dir ./my_figures</kbd>
<kbd>python plot.py sherwood</kbd>
</pre>

<p>If neither <code>--save</code> nor <code>--show</code> is supplied, the script defaults to both actions.</p>

<h1>Python scripts (folder <code>python</code>)</h1>

<p>The main entry point is <strong>plot.py</strong>. It provides three sub‑commands:</p>

<ul>
<li><code>time</code> – concentration vs. time.</li>
<li><code>da</code> – Damköhler‑number curves.</li>
<li><code>sherwood</code> – Sherwood‑number curves.</li>
</ul>

<p>Common options (apply before the sub‑command):</p>

<ul>
<li><code>--save</code> – write each figure to a PDF (default folder: <code>fracture_analog/python/figures</code>).</li>
<li><code>--show</code> – display the interactive Matplotlib window.</li>
<li><code>--out-dir DIR</code> – destination directory for saved PDFs (used with <code>--save</code>).</li>
</ul>

<p>Additional plotting scripts:</p>

<ul>
<li><strong>plot_outlet_contours.py</strong> – generates Figure D2.</li>
<li><strong>plot_plug_flow_contours.py</strong> – generates Figure D3.</li>
</ul>

<h1>Reproducing the VTK files</h1>

<p>The raw simulation outputs have the extension “.dumux” (e.g., <code>t_u_list-00000.dumux</code>).
If you are interested in inspecting the VTK contour plots we recommend the following strategy:</p>

<ol>
<li>Clone the repository:
<a href="https://git.iws.uni-stuttgart.de/dumux-pub/wendel2025a">https://git.iws.uni-stuttgart.de/dumux-pub/wendel2025a</a>
into a folder that contains only the code.</li>
<li>Enter the cloned folder (<code>wendel2025a</code>) and execute the install script:
<pre>./installscript.sh</pre>
This will clone, configure, and build the main parts.</li>
<li>Build the VTK reconstruction binary:
<pre>
cd ~/wendel2025a/build-cmake/appl/forcedtoptobottom/ftb2Dyz/
make Reconstructvtk_forcedflow_toptobottom_2DYZ
</pre>
</li>
<li>Run the binary on a case folder, supplying the full path:
<pre>
/full/path/to/Reconstructvtk_forcedflow_toptobottom_2DYZ -i params.input -o output.vtk
</pre>
</li>
</ol>

<p>You can customize the VTK output granularity via the <code>SteppingStride</code> parameter. Edit <code>params.input</code> or pass the option directly, e.g.:</p>

<pre>
cd fracture_analog/ftb/examplecase
/full/path/to/Reconstructvtk_forcedflow_toptobottom_2DYZ -BinarySolutionLoad.SteppingStride 10
</pre>

<p>Because DuMux is not installed system‑wide, always use the full path to guarantee the correct binary is executed.</p>

<h2>Helper scripts</h2>

<ul>
<li><strong>calculate_Sherwood_theory_numbers.py</strong> – computes the data shown in Tables 3 and 4; saves CSV files in <code>fracture_analog/python/sherwood_calculations</code>.</li>
<li><strong>compare_experiment_simulation.py</strong> – conducts an error analysis comparing experimental and simulation outcomes; saves
<code>comparison_results_transient.csv</code> (Table C1) and <code>comparison_results.csv</code> (stationary outlet concentrations).</li>
<li><strong>get_preexperimental_inlet_fluid_pH.py</strong> – estimates the pH of the process fluid (appears in Table 1, column <code>pH_in</code>); prints to console.</li>
<li><strong>get_surface_retreat.py</strong> – estimates the surface retreat expected in the experiments; prints to console.</li>
<li><strong>interpolate_co2_diffusion_coefficients.py</strong> – fits CO₂‑diffusion coefficients and prints the parameters.</li>
<li><strong>investigate_recirculation.py</strong> – performs various analyses and produces CSV or console output useful for supplementary tables; creates <code>recirculation_table.csv</code> containing Richardson numbers (Table D2).</li>
</ul>

<h1>Folder‑structure summary</h1>

<p>Inside the <code>stp</code> folder are the initialization simulation raw data sets; the <code>ftb</code> folders then contain the setups where the pump has been switched on in the experiment.
Both folders use the pattern <code>groupName__caseLabel</code> (e.g., <code>dwIniClo__a6mm_pC1.0_T22</code>).</p>

<p>The <code>caseLabel</code> encodes the main characteristics of the simulation:</p>

<ul>
<li><code>aXmm</code> – aperture in mm (X mm).</li>
<li><code>pCY.YY</code> – CO₂ partial pressure in bar (Y.YY bar).</li>
<li><code>TZZ</code> – temperature in °C (ZZ °C).</li>
<li><code>tAAmin</code> – residence time in minutes (AA min).
Note that a stagnant simulation setup does not need a mean residence time, so this attribute is omitted.</li>
</ul>

<p>For the stagnant‑prior (<code>stg</code>) cases, the recommended binary is:</p>

<pre>
build-cmake/appl/stagnant/stg2Dyz/ReconstructVtk_stagnant_2DYZ
</pre>

<h2>Detailed explanation: Data structure of the <code>ftb</code> data sets</h2>

<p>Each case folder under <code>ftb</code> contains the following files:</p>

<ul>
<li><strong>params.input</strong> – parameter file used to run the simulation in DuMux.</li>
<li><strong>integralQuantities.csv</strong> – processing information on the outflowing fluid and total mass/moles inside the model domain.</li>
<li><strong>recirculation.csv</strong> – time series of the upper and lower bounds of recirculation patterns; an absent row means no recirculation at that time.</li>
<li><strong>sherwood.csv</strong> – processing information for the Sherwood number study (section 3.4.4).</li>
<li><strong>systemcharacteristicnumbers.txt</strong> – a‑priori characteristic system information.</li>
</ul>