DOI: 10.18419/darus-1713
title: Enzymatically induced carbonate precipitation and its effect on capillary pressure-saturation relations of porous media - column samples

description: This data set includes processed image data from three experiments on enzymatically induced carbonate precipitation ( further named low-, medium-, and high-mineralization or column 10, column 3, and column 4, respectively). Related data sets with the CT data this data set is based on are:

&lt;ul&gt;
&lt;li&gt;low-mineralization sample: column 10, &lt;a href="http://doi.org/10.18419/darus-2908"&gt;http://doi.org/10.18419/darus-2908&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;medium-mineralization sample: column 3, &lt;a href="http://doi.org/10.18419/darus-2906"&gt;http://doi.org/10.18419/darus-2906&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;high-mineralization sample: column 4, &lt;a href="http://doi.org/10.18419/darus-2907"&gt;http://doi.org/10.18419/darus-2907&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

The experimental procedure for mineralization is described in those related data sets, this data set is only concerned about the evaluation and assessment of the experimental image data with respect to the effects of enzymatically induced carbonate precipitation on capillary pressure-saturation relations. The workflow was to use 13 sections of 100 images from each of the segmented images "&lt;b&gt;segmentedPNGs.tar.gz&lt;/b&gt;" to extract pore networks "&lt;b&gt;poreNetworks.tar.gz&lt;/b&gt;" of all the columns of the initial (segmentedPNGs/columnN/precip_plus_void) and the mineralized pore geometry (segmentedPNGs/columnN/green_void) using python scripts utilizing PoreSpy "&lt;b&gt;PNGtoPN.py&lt;/b&gt;". Using the python script "&lt;b&gt;PN2GridFormat.py&lt;/b&gt;", the extracted pore networks were converted into DUMUX-readable grid files (dgf files) for the pore network simulations "&lt;b&gt;poreNetworkModeling.tar.gz&lt;/b&gt;". In the subfolders (poreNetworkModeling/initial_column&lt;i&gt;N&lt;/i&gt;_&lt;i&gt;X&lt;/i&gt; for the initial geometries and poreNetworkModeling/mineralized_column&lt;i&gt;N&lt;/i&gt;_&lt;i&gt;X&lt;/i&gt; for the mineralized geometries). Then numerical primary-drainage experiments were conducted using the pore network model of DUMUX, using the convenience python script "&lt;b&gt;Mass_dumux.py&lt;/b&gt;". Reproducing the results can also be achieved using the docker container based on the image "&lt;b&gt;gehring2022a.tar&lt;/b&gt;". &lt;br&gt;
The script "&lt;b&gt;docker_gehring2022a&lt;/b&gt;" can be used to run the docker container. Alternatively the code is published at: &lt;a href="https://git.iws.uni-stuttgart.de/dumux-pub/gehring2022a"&gt;https://git.iws.uni-stuttgart.de/dumux-pub/gehring2022a&lt;/a&gt;.&lt;br&gt;
The simulations will result in 101 vtp files (&lt;b&gt;test_pnm_2p_static-00&lt;i&gt;P&lt;/i&gt;.vtp&lt;/b&gt;) as a result for the 100 steps in capillary pressure (&lt;i&gt;P&lt;/i&gt; = pressure steps, 0-100) of the numerical primary-drainage experiments as well as the determined capillary pressure-saturation curves in (&lt;b&gt;test_pnm_2p_static_pc-s-curve.txt&lt;/b&gt;) and the simulation input file (&lt;b&gt;test_pnm_2p_static.input&lt;/b&gt;). The capillary pressure-saturation curves are then used to fit the parameters of both the Brooks-Corey (&lt;b&gt;fitting_pcSwBrooksCorey.m&lt;/b&gt;) and the Van Genuchten (&lt;b&gt;fitting_pcSwVanGenuchten.m&lt;/b&gt;) capillary pressure-saturation relations. The fitted paramters are provided in the Tables "&lt;b&gt;parametersBrookCorey.csv&lt;/b&gt;" and "&lt;b&gt;parametersVanGenuchten.csv&lt;/b&gt;". "&lt;b&gt;supportingData.tar.gz&lt;/b&gt;" provides evaluations of the volume fractions of the samples along their length.&lt;br&gt;&lt;br&gt;

This data set contains:

 &lt;ul&gt;

 &lt;li&gt;"&lt;b&gt;segmentedPNGs.tar.gz&lt;/b&gt;" with a subfolder (column&lt;i&gt;N&lt;/i&gt;) for each column (&lt;i&gt;N&lt;/i&gt; = 3, 4, 10) containing in subsubfolders the binarized stacks of images of each of the phases from the CT data of the related data sets in which white signifies the presence of the respective phase at the location and black absence of the respective phase:
 &lt;ul&gt;
 &lt;li&gt;glass beads ("&lt;b&gt;column&lt;i&gt;N&lt;/i&gt;/red_sand&lt;/b&gt;"), &lt;/li&gt;
 &lt;li&gt;precipitated calcium carbonate ("&lt;b&gt;column&lt;i&gt;N&lt;/i&gt;/blue_precip&lt;/b&gt;"), &lt;/li&gt;
 &lt;li&gt;pore space ("&lt;b&gt;column&lt;i&gt;N&lt;/i&gt;/green_void&lt;/b&gt;"), &lt;/li&gt;
 &lt;li&gt;as well as precipitate and pore space representing the initial, unmineralized pore space, ("&lt;b&gt;column&lt;i&gt;N&lt;/i&gt;/precip_plus_void&lt;/b&gt;"). &lt;/li&gt;
 &lt;/ul&gt;
 &lt;/li&gt;

 &lt;li&gt;"&lt;b&gt;poreNetworks.tar.gz&lt;/b&gt;" with the extracted pore networks as a csv file "&lt;b&gt;column&lt;i&gt;N&lt;/i&gt;_&lt;i&gt;STAGE&lt;/i&gt;_outputfile&lt;i&gt;X&lt;/i&gt;.csv&lt;/b&gt;" for further processing as well as a vtp file "&lt;b&gt;column&lt;i&gt;N&lt;/i&gt;_&lt;i&gt;STAGE&lt;/i&gt;_outputfile&lt;i&gt;X&lt;/i&gt;.vtp&lt;/b&gt;" for visualization of the extracted pore network, with &lt;i&gt;X&lt;/i&gt; being the number of the section the pore network represents and &lt;i&gt;STAGE&lt;/i&gt; being the stage at which the pore network extracted: &lt;i&gt;STAGE&lt;/i&gt;=void standing for the mineralized sample's pore geometry and &lt;i&gt;STAGE&lt;/i&gt;=void+precip standing for the initial, unmineralized sample's pore geometry.
 &lt;/li&gt;

 &lt;li&gt;"&lt;b&gt;poreNetworkModeling.tar.gz&lt;/b&gt;" with the subfolders:
 &lt;ul&gt;
 &lt;li&gt; "&lt;b&gt;initial_column&lt;i&gt;N&lt;/i&gt;_&lt;i&gt;X&lt;/i&gt;&lt;/b&gt;" for the initial geometries, (&lt;i&gt;N&lt;/i&gt; = 3, 4, 10; &lt;i&gt;X&lt;/i&gt; = Sections 1-13)&lt;/li&gt;
 &lt;li&gt; and "&lt;b&gt;mineralized_column&lt;i&gt;N&lt;/i&gt;_&lt;i&gt;X&lt;/i&gt;&lt;/b&gt;" for the mineralized geometries, (&lt;i&gt;N&lt;/i&gt; = 3, 4, 10; &lt;i&gt;X&lt;/i&gt; = Sections 1-13)&lt;/li&gt;
 &lt;/ul&gt;
 101 vtp files "&lt;b&gt;test_pnm_2p_static-00&lt;i&gt;P&lt;/i&gt;.vtp&lt;/b&gt;", one for the initial and each of the 100 steps in capillary pressure (&lt;i&gt;P&lt;/i&gt; = pressure steps, 0-100) of the numerical primary-drainage experiments as well as the determined capillary pressure-saturation curves in "&lt;b&gt;test_pnm_2p_static_pc-s-curve.txt&lt;/b&gt;" and the simulation input file used "&lt;b&gt;test_pnm_2p_static.input&lt;/b&gt;"
 &lt;/li&gt;

 &lt;li&gt;"&lt;b&gt;supportingData.tar.gz&lt;/b&gt;" provides evaluations of the volume fractions of the samples along their length, a matlab script "&lt;b&gt;plotVolumeFractions.m&lt;/b&gt;" for evaluating and plotting the volume fractions, the resulting plots for the three columns "&lt;b&gt;column3MediumMineralizationVolumefractions.eps&lt;/b&gt;", "&lt;b&gt;column4HighMineralizationVolumefractions.eps&lt;/b&gt;", and "&lt;b&gt;column10LowMineralizationVolumefractions.eps&lt;/b&gt;", and the determined overall initial and mineralized porosities and porosity reductions in the Table "&lt;b&gt;porosities.csv&lt;/b&gt;"
 &lt;/li&gt;

&lt;li&gt;"&lt;b&gt;3DpcSw_BC.eps&lt;/b&gt;" resulting plot of the capillary pressure-saturation curves from "&lt;b&gt;poreNetworks.tar.gz&lt;/b&gt;" as well as the sample-averaged fitted Brooks-Corey capillary pressure-saturation relations as fitted and plotted by the matlab script "&lt;b&gt;fitting_pcSwBrooksCorey.m&lt;/b&gt;" &lt;/li&gt;

&lt;li&gt;"&lt;b&gt;3DpcSw_VG.eps&lt;/b&gt;" resulting plot of the capillary pressure-saturation curves from "&lt;b&gt;poreNetworks.tar.gz&lt;/b&gt;" as well as the sample-averaged fitted Van Genuchten capillary pressure-saturation relations as fitted and plotted by the matlab script "&lt;b&gt;fitting_pcSwVanGenuchten.m&lt;/b&gt;"&lt;/li&gt;

&lt;li&gt;"&lt;b&gt;fitting_pcSwBrooksCorey.m&lt;/b&gt;" matlab script to fit the parameters of the Brooks-Corey capillary pressure-saturation relations to the capillary pressure-saturation curves from "&lt;b&gt;poreNetworkModeling.tar.gz&lt;/b&gt;" as well as plot all for visual comparison. &lt;/li&gt;

&lt;li&gt;"&lt;b&gt;fitting_pcSwVanGenuchten.m&lt;/b&gt;" matlab script to fit the parameters of the Van Genuchten capillary pressure-saturation relations to the capillary pressure-saturation curves from "&lt;b&gt;poreNetworkModeling.tar.gz&lt;/b&gt;" as well as plot all for visual comparison.&lt;/li&gt;

&lt;li&gt;"&lt;b&gt;Mass_dumux.py&lt;/b&gt;" convenience script to run all DUMUX pore network-model simulations&lt;/li&gt;

&lt;li&gt;"&lt;b&gt;parametersBrookCorey.csv&lt;/b&gt;" parameters of the Brooks-Corey capillary pressure-saturation relations as fitted by the matlab script "&lt;b&gt;fitting_pcSwBrooksCorey.m&lt;/b&gt;"&lt;/li&gt;

&lt;li&gt;"&lt;b&gt;parametersVanGenuchten.csv&lt;/b&gt;" parameters of the Van Genuchten capillary pressure-saturation relations as fitted by the matlab script "&lt;b&gt;fitting_pcSwVanGenuchten.m&lt;/b&gt;"&lt;/li&gt;

&lt;li&gt;"&lt;b&gt;PN2GridFormat.py&lt;/b&gt;" python script to generate DUMUX-readable grid files from the pore networks extracted by "&lt;b&gt;PNGtoPN.py&lt;/b&gt;" from the segmented images in "&lt;b&gt;segmentedPNGs.tar.gz&lt;/b&gt;"&lt;/li&gt;

&lt;li&gt;"&lt;b&gt;PNGtoPN.py&lt;/b&gt;" python script to extract pore networks from the segmented images in "&lt;b&gt;segmentedPNGs.tar.gz&lt;/b&gt;"&lt;/li&gt;

&lt;/ul&gt;
description: PoreSpy, 2.0.2
description: MATLAB, 2019b
description: DuMuX, 3.4 + special files (https://git.iws.uni-stuttgart.de/dumux-pub/gehring2022a)