PFOS fate and transport model using HYDRUS1D and MODFLOW6 Python libraries
Since recent years both MODFLOW/MT3D and HYDRUS1D have their own respective Python libraries. This allows parametrization, execution, and result interpretation while scripting, providing higher flexibility in the way models are built.
Phydrus is the Python library written by R.A. Collenteur, G. Brunetti and M. Vremec (Collenteur et al., 2021) that runs HYDRUS-1D unsaturated zone model developed by Šimůnek, J., M. Th. van Genuchten, and M. Šejna. FloPy is the Python package that allows to create, run and post-process MODFLOW-based models (Bakker et al., 2024, Hughes et al., 2023; Bakker et al., 2016, Langevin et al., 2017). Using both models allows to consider PFAS transport from its release point at the soil surface, travelling towards the unsaturated and saturated zones towards an exfiltration surface water body.
In this example, linear absorption has been assumed the main process driving PFAS transport in the subsoil. Moreover, the groundwater level is assumed to be static; thus, effect of drying and rewatering in PFAS transport is neglected. Since these are strong simplifications of the PFAS behaviour in the subsurface, this approach may only be used for a first approximation of the PFAS fate and transport, especially useful when the data available is limited.
Both models are executed concatenated, meaning that the output leakage generated by the unsaturated zone 1D model (Phydrus), is injected into the fully saturated 2D model (FloPy) as a recharge flux at the location where pollution is expected to occur.
General information and examples of FloPy package can the be obtained from the developers website: https://flopy.readthedocs.io/en/stable/index.html. FloPy can be installed using conda or pip Python functions. Additionally, MODFLOW-based model executables are freely available at USGS website : https://www.usgs.gov/software/modflow-6-usgs-modular-hydrologic-model. The library needs to be imported at the begining of the code: import flopy as fp
Information on how to install Phydrus can be found at the developers website : https://phydrus.readthedocs.io/en/latest/index.html. Phydrus package can be installed using pip, while HYDRUS-1D executable needs to be compiled, or downloaded together with the HYDRUS-1D user interface from the developers website : https://www.pc-progress.com/en/Default.aspx?Downloads. The library needs to be imported at the begining of the code: import phydrus as ps
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import datetime as dt
import os
import shutil
H1D_Input_Atmos.csv, .csv file with precipitation and estimated evapotranspiration for Atmospheric BC of HYDRUS 1D.
MF6_Input_Geometry.xlsx, array with top and bottom elevation of saturated zone model layers.
MF6_Input_Heads.xlsx, time dependent heads at the inland boundary conditions for MF6.
Collenteur, R., G. Brunetti, and M. Vremec. Phydrus: Python implementation of the hydrus-1d unsaturated zone model. Phydrus Documentation. Release 0.2.0. 2021
Šimůnek, J., M. Th. van Genuchten, and M. Šejna. The HYDRUS-1D Software Package for Simulating the Movement of Water, Heat, and Multiple Solutes in Variably Saturated Media, Version 3.0. HYDRUS. Software Series 1, Department of Environmental Sciences, University of California Riverside, Riverside, California, USA, 2005
Bakker, Mark, Post, Vincent, Hughes, J. D., Langevin, C. D., White, J. T., Leaf, A. T., Paulinski, S. R., Bellino, J. C., Morway, E. D., Toews, M. W., Larsen, J. D., Fienen, M. N., Starn, J. J., Brakenhoff, D. A., and Bonelli, W. P., 2024, FloPy v3.10.0.dev1: U.S. Geological Survey Software Release, 20 December 2024, https://doi.org/10.5066/F7BK19FH
Hughes, J.D., Langevin, C.D., Paulinski, S.R., Larsen, J.D. and Brakenhoff, D. (2023), FloPy Workflows for Creating Structured and Unstructured MODFLOW Models. Groundwater. https://doi.org/10.1111/gwat.13327
Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, https://doi:10.1111/gwat.12413
Langevin, C.D., Hughes, J.D., Banta, E.R., Provost, A.M., Niswonger, R.G., and Panday, Sorab, 2017, MODFLOW 6 Modular Hydrologic Model: U.S. Geological Survey Software, https://doi.org/10.5066/F76Q1VQV