This HydroShare resource provides supporting information for a series of reactive transport laboratory experiments reported in Cook, T.J. (2024). Experimental Study of the Relationship between Porous Media Clogging and Dynamic Permeability: Assessment of Calcite Precipitation Reaction, Pore-Scale Clogging, and Flow Rate in a Quasi-2D Flow Cell. Master's Report, Department of Civil Engineering, University of Colorado Denver, Denver, Colorado, USA.

Folder Contents

01_Media_Recordings
02_Data
03_Analysis
04_Final_Deliverables

Summary of Folder Contents

01_Media Recordings

Photos and videos by date and/or experiment. Folders contain images of materials, preliminary testing, and experimental images. Folders contain videos of experimental operations. Real time videos were recorded from the front (observation side) of the quasi-2D flow cell apparatus and timelapse videos were recorded from the back (piezometer side). Folder names with dates only represent preliminary 2-D flow cell testing images and videos. These media were used to document updates to the flow cell, leak tests, and preferential flow tests. Pressure head data were collected for the preferential flow test completed on Saturday February 2, 2024. These data were included in the 2024_02_03 folder, which contains Images and WPD_Excel folders. The Images folder stores the extracted raw data images for each time step, while the WPD_Excel folder contains the output comma-separated values files from the Web Plot Digitizer. These data were collected to test the applicability and workflow for the Web Plot Digitizer used by this study. File names containing "Experiment..." contain experimental videos and photos. In each of these experiment folders, there are timelapse videos (.MOV) and standard speed videos (.MP4) for the piezometer and observation sides of the flow cell apparatus, respectively. Timelapse videos were recorded using Apple iPhone 15 Pro timelapse camera function, while real time videos were recorded using a Sony Cyber-Shot DSC-HX400.

02_Data

This folder contains the raw data from each experiment (1-5). Raw data images were extracted from the timelapse videos in 02_Media_Recordings and saved as JPEG files in 03_Data. Also included in 03_Data are the raw data comma-separated values (CSV) files. These files were created using the referenced raw data images and WebPlotDigitizer (https://automeris.io/WebPlotDigitizer.html). Piezometer photos are labeled according to date of experiment and experimental time of measurement. This same naming convention is carried over for the CSV files exported from WebPlotDigitizer. CSV files from the WebPlotDigitizer are named in "Date_TimeStamp" format, while the Matlab output CSV files are named in "Date_Head" format. The Matlab output "Head" CSV files are combined raw data spreadsheets, which are organized by Time (Column 1:n) and Piezometer (Row 1:N). The Matlab script that is included within each "_Spreadsheet_Data" folder has been used to convert the series of WebPlotDigitizer output CSV files into a single Head.CSV file. When the Matlab script is to be used for a new experiment, the date and timestep strings must be updated to find the appropriate CSV files and to output a complete raw data spreadsheet. Failure to update the date and timestep strings may result in an error.

03_Analysis

This folder contains Excel workbooks used for (1) calculations, (2) dynamic plotters for analysis and comparison of experimental data, and (3) Matlab scripts for each experiment. Each of these will be discussed in turn.

(1) Excel_Calcs

This subfolder contains Excel workbooks with tabular calculations and plots from experimental data. Raw data from 03_Data have been copied into these workbooks where Darcy's law and intrinsic permeability calculations have been carried out. Generally, the raw data have been pasted into the first sheet of each workbook and labeled according to its experiment number. From left to right, the variables for the referenced calculations are computed and labeled according to experiment number. Subsequent sheets of the Excel workbooks contain plots of permeability versus time, among other comparative computations (also labeled). 

(2) Excel_Plotters_Analysis

This subfolder contains a series of Excel workbooks containing dynamic plots for the experiments of this study. Exp_1-4_Head_Plotter.xlsx plots the raw head measurements for each column and row for experiments 1-4. The plots provide a comparison with the average head computed for each column and row during the initial DI water flush and calcium chloride stages of the experiments. Exp_All_DH_Plotter contains a series of plots comparing the vertical and horizontal pressure head gradients versus time for each experiment. Exp_All_k_Plotter contains a series of plots of average permeability (k) versus time, using a coarse ad hoc assumption of uniform flow through each column, which is only very approximately correct, and therefore generates a highly uncertain estimate of permeability. Specifically, the permeability has been computed on a per column basis and represents the average permeability assuming each column conveys flows at rate equal to 20 percent of the total experimental flow rate. 

(3) Matlab_By_Experiment

This subfolder contains Matlab scripts for heatmap plotting of hydraulic head measurements. Head.CSV files for each experiment have been copied into each experiment folder and re-indexed using the macro included within the XLSX workbooks. The macro may be accessed by going into the XLSX files>Developer Tab>Macros. Copying, pasting, and running this macro into any unaltered Head.CSV file will re-index the sheet so that it will plot appropriately using the Matlab script. Each copy of the Matlab script has been updated for the times, number of timesteps, and range of head values for each experiment. Future experiments will need to update these values accordingly. PDF copies of output hydraulic head heatmap plots have also been included for each experiment. These PDF documents were generated using the print preview interface in Matlab. This interface allows the user to maximize the figure on the page before printing to PDF.

04_Final_Deliverables

This folder contains materials from Tylere Cooks master report presentation on 1 May 2024, as well as the final report Cook-MS-2024.pdf, the latter of which should be referenced for experimental conditions when accessing the folders above.

Defense

This subfolder contains the slide deck, presentation notes, transcript, and video recording of Tylere Cooks master report presentation on 1 May 2024