Data used in and produced during calibration and validation of the model for bioconcrete production

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• The subfolder "pestFiles" contains files used by and generated by PEST for the calibration of the bioconcrete production model. The files are:
  • "Biocement.pst" is the pest control file where all parameters for the calibration are set and the observation data is defined.
  • "Biocement_inj.ins": a PEST instruction file for the injection data.
  • "Biocement_poro.ins": a PEST instruction file for the porosity data.
  • "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.
  • "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.
  • "Biocement.isen": a PEST output file giving the model sensitivities to the calibration parameters for each iteration.
  • "Biocement.post.cov": a PEST output file giving the calibration parameter's covariances after the calibration.
  • "coVars.txt": the covariances from "Biocement.post.cov" normalized using the script "normalizeCovariances.py"
  • "normalizeCovariances.py": the script used to normalize the covariances
  • "contributionsPorosity.txt": the contributions of the porosity values to the objective function as calculated by PEST
  • "contributionsInjections.txt": the contributions of the injection values to the objective function as calculated by PEST
  • "Asw.txt": the values of the fitted parameter Asw (initial surface area) extracted from "Biocement.rec" for each iteration
  • "Expo.txt": the values of the fitted parameter E (exponent of the porosity-permeability relation) extracted from "Biocement.rec" for each iteration
  • "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
• 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 Smirnova et al. 2023. Each folder contains:
  • "avgporoexperiment.txt": the average porosity of the setup determined experimentally for each injection cycle.
  • "avgporoovertime.txt": the average porosity of the setup based on the model results for every time step of the simulation.
  • "finalporosities.txt": the final porosity distribution over the length of the sample as predicted by the model.
  • "injectionovertime.txt": the injection rates over time as predicted by the model.
  • "refinjectionrates.txt": the experimentally measured injection rates for each injection cycle.
  • "trx-y.input": the input file used for the model for the given setup.
  • 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").
  • The folder "tr1-2" additionally contains the data file "finalporosities_experiment.txt" with the final porosity distribution along the column measured in the experiment
• the python script "plots.py" that reads in the experimental and model data from the folders and files discussed above and plots them.
• "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.