DOI: 10.18419/darus-4814
title: Data used in and produced during calibration and validation of the model for bioconcrete production

description: Data used in and produced during calibration and validation of the &lt;a href ="https://doi.org/10.18419/DARUS-4813"&gt;model for bioconcrete production&lt;/a&gt; in the paper "A numerical 1D reactive flow and transport model for cementation processes in bio-concrete production".
Experimental data is derived from &lt;a href ="https://doi.org/10.1038/s44296-023-00004-6"&gt;Smirnova et al. 2023&lt;/a&gt;.
The experiment TR1-2 was used to calibrate the developed model for bioconcrete production using &lt;a href ="http://www.pesthomepage.org/"&gt;PEST&lt;/a&gt;. Other experimental setups (TR3-1, TR5-3, TR5-6, and TR7-2) were used for validation of the model. The experimental data used are the injection rates over time, the average sample porosities over time, and the final porosity distribution along the sample length.

&lt;br&gt;&lt;br&gt;
Content of this data set:
&lt;br&gt;
&lt;ul&gt;
&lt;li&gt;The subfolder "pestFiles" contains files used by and generated by &lt;a href ="http://www.pesthomepage.org/"&gt;PEST&lt;/a&gt; for the calibration of the bioconcrete production model. The files are:
&lt;ul&gt;
&lt;li&gt;"Biocement.pst" is the pest control file where all parameters for the calibration are set and the observation data is defined.&lt;/li&gt;
&lt;li&gt;"Biocement_inj.ins": a PEST instruction file for the injection data.&lt;/li&gt;
&lt;li&gt;"Biocement_poro.ins": a PEST instruction file for the porosity data.&lt;/li&gt;
&lt;li&gt;"Biocement.tpl": a template of the bioconcrete production model's input file into which PEST inserts the parameter values it determined to be evaluated in the bioconcrete production model. &lt;/li&gt;
&lt;li&gt;"Biocement.rec": the log file of the model calibration by PEST, containing e.g. the updated calibration-parameter estimates, parameter updates, parameter standard deviations and more. &lt;/li&gt;
&lt;li&gt;"Biocement.isen": a PEST output file giving the model sensitivities to the calibration parameters for each iteration. &lt;/li&gt;
&lt;li&gt;"Biocement.post.cov": a PEST output file giving the calibration parameter's covariances after the calibration.&lt;/li&gt;
&lt;li&gt;"coVars.txt": the covariances from "Biocement.post.cov" normalized using the script "normalizeCovariances.py"&lt;/li&gt;
&lt;li&gt;"normalizeCovariances.py": the script used to normalize the covariances&lt;/li&gt;
&lt;li&gt;"contributionsPorosity.txt": the contributions of the porosity values to the objective function as calculated by PEST&lt;/li&gt;
&lt;li&gt;"contributionsInjections.txt": the contributions of the injection values to the objective function as calculated by PEST&lt;/li&gt;
&lt;li&gt;"Asw.txt": the values of the fitted parameter Asw (initial surface area) extracted from "Biocement.rec" for each iteration&lt;/li&gt;
&lt;li&gt;"Expo.txt": the values of the fitted parameter E (exponent of the porosity-permeability relation) extracted from "Biocement.rec" for each iteration&lt;/li&gt;
&lt;li&gt;"kpowder.txt": the values of the fitted parameter kpowder (the maximum reaction rate constant of the ureolysis rate equation at room temperature) extracted from "Biocement.rec" for each iteration&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;li&gt;Subfolders in the format "trx-y" for each experimental setup which contains the experimental and model data used in the paper "A numerical 1D reactive flow and transport model for cementation processes in bio-concrete production".
Those are named "tr1-2", "tr3-1", "tr5-3", "tr5-6", and "tr7-2", based on the names for the experimental setups in &lt;a href ="https://doi.org/10.1038/s44296-023-00004-6"&gt;Smirnova et al. 2023&lt;/a&gt;.
Each folder contains: 
&lt;ul&gt;
&lt;li&gt;"avgporoexperiment.txt": the average porosity of the setup determined experimentally for each injection cycle.&lt;/li&gt;
&lt;li&gt;"avgporoovertime.txt": the average porosity of the setup based on the model results for every time step of the simulation.&lt;/li&gt;
&lt;li&gt;"finalporosities.txt": the final porosity distribution over the length of the sample as predicted by the model.&lt;/li&gt;
&lt;li&gt;"injectionovertime.txt": the injection rates over time as predicted by the model.&lt;/li&gt;
&lt;li&gt;"refinjectionrates.txt": the experimentally measured injection rates for each injection cycle.&lt;/li&gt;
&lt;li&gt;"trx-y.input": the input file used for the model for the given setup.&lt;/li&gt;
&lt;li&gt;The folder "tr1-2" additionally contains a subfolder "initialGuess" that contains the model results and input file for the initial-guess values of the calibration parameters, but no experimental data (only "avgporoovertime.txt", "finalporosities.txt", "injectionovertime.txt", and "tr1-2.input").&lt;/li&gt;
&lt;li&gt;The folder "tr1-2" additionally contains the data file "finalporosities_experiment.txt" with the final porosity distribution along the column measured in the experiment&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;li&gt; the python script "plots.py" that reads in the experimental and model data from the folders and files discussed above and plots them.&lt;/li&gt;
&lt;li&gt;"finalAveragePorosities.csv" contains a table of all final average porosities measured in the experiment and predicted by the model as well as the error in the model prediction calculated based on the given values.&lt;/li&gt;
&lt;/ul&gt;
description: DUMUX, 3.8
description: PEST, pestpp-glm 5.2.10