This folder contains code that can be used to reproduce the data and results from the paper "Modelling the influence of rhizodeposits on root water uptake"

Code contents

1. "dataconverteryglobalmesh_generator.py" A Python script that converts the CRootBox output data for each root system into a format from which density functions for surface area and root length can be generated. The script also generates the finite element mesh for the domain within which all simulations are carried out.

2. "rlsadensityconstructor3D.py" A Python/FEniCS script that generates root length and surface area density functions of 3-dimensional space for all ages of root systems considered.

3. "rlsadensity_1D.py" A Python/FEniCS script that converts the 3-dimensional root length and surface area density functions to 1D density functions so that they can be used in the 1D models for water transport.

4. "contactanglemodel_fitter.py" A Python script that fits a function to the data of Zickenrott et al. (2016), for the relationship between water-soil contact angle and wheat rhizodeposit concentration, and saves out the parameter values.

5. "surfacetensionmodel_fitter.py" A Python script that fits a function to the data of Read et al. (2003), for the relationship between soil water surface tension and wheat rhizodeposit concentration, and saves out the parameter values.

6. "model_simulator.py" The Python/FEniCS script that is used to simulate the model shown in the paper and obtain the data presented in Figures 3 to 7 and Tables 2 and 3.

7. "datavisualisationfig36tab2_3.py" The Python script that can be used to plot the Figures 3 to 6 of the paper and generate the calculate the total uptakes shown in Tables 2 and 3.

8. "datavisualisationfigure_7.py" The Python script that can be used to plot Figure 7 of the paper.

9. Folder named "rhizodeposits-image" Image file for installing FEniCS, see FEniCS_setup.txt.
   No need to edit this file in anyway. Do not open with Notepad.

Data contents

All found within the "data" folder.

1. Folder named "calibratedparametervalues" Contains the calibrated values of the parameters beta, kappad, and kappaw of the model system in the paper. These were established in the work of Gomez et al. (2025).

2. xml.gz files: File for the finite element mesh defined over the soil domain.

3. H5 Files: Files involved in storing data for root density functions, and profiles of water content, pressure head, water flux, inverse air entry pressure head, hydraulic conductivity, dried rhizodeposit concentration, and solubilised rhizodeposit concentration
   so that they can be read into finite element scripts or visualised in Paraview.

4. txt files

   • Fitted parameter values in functions for surface tension and contact angle
     against rhizodeposit concentration.
   • CRootBox data for the architecture of each root system
   • Architecture data for each root system after formatting by script "dataconverteryglobalmesh_generator.py".
   • Data for evaporation rates, uptake rates and deep percolation rates etc that are generated by the code "model_simulator.py" and then picked up by the data visualisation scripts.

5. XDMF files:

   • Data for visualising root density functions, and profiles of water content, pressure head, water flux, inverse air entry pressure head, hydraulic conductivity, dried rhizodeposit concentration, and solubilised rhizodeposit concentration.

Figures

1. All generated figures end up in the "figures" folder.

Implementation instructions

1. One .txt file for guidance on FEniCS setup
2. One .txt file describing the required implementation procedure of the codes above, in order to obtain the results of the paper.

DOI