PFAS - a package for semi-analytical modeling of PFAS transport in the vadose zone

A Python package for modeling the transport of per- and polyfluoroalkyl substances (PFAS) through the unsaturated zone.

Overview

PFAS is a toolkit for simulating the movement and fate of PFAS contaminants in the unsaturated zone. It provides a flexible, modular framework for constructing transport models with configurable preprocessing steps and analytical solvers. The package is designed for researchers and engineers studying PFAS contamination and remediation.

Features

• Modular Architecture: Build complex transport models using pluggable preprocessors and solvers.
• Flexible Configuration: Define simulations using intuitive TOML configuration files or directly in code.
• Sorption Modeling: Support for linear and non-linear sorption processes to soil particles and Air-Water Interface, in combination with flexible approaches for defining these processes.
• Vadose Zone Transport: Simulate PFAS movement through the unsaturated zone under steady-state flow conditions.
• Embedded PFAS data: The package contains modules with sorption data for Air-Water interface computation, Air-Water interfacial sorption coefficients and solid phase sorption coefficients.
• Grid Generation: Automatic mesh generation for spatial domains
• Boundary Condition Management: Flexible handling of domain boundaries

Requirements

• Python >= 3.9
• NumPy >= 2
• SciPy
• Matplotlib
• Pydantic
• Marimo (for tutorials)

Installation

From PyPI

pip install pfas

From Source

git clone https://github.com/UU-PFAS-Living-Lab/pfas.git
cd pfas
pip install -e .

For Development

Install with additional testing, documentation, and example dependencies:

pip install -e ".[dev]"

Or install individual extras:

pip install -e ".[test]"      # For testing
pip install -e ".[docs]"      # For building documentation
pip install -e ".[examples]"  # For running examples

Quick Start

Here's a minimal example to get started:

from pfas.component import (
    BoundaryPreprocessor,
    EquilibriumSolver,
    GridGenerator,
    LinearSPsorption,
    Retardation,
    SWCsorption,
    WaterPreprocessor,
)
from pfas.model import Model

model = Model()

model.compute(
    GridGenerator,
    domain_length=60,
    spatial_resolution=1.0,
    time_resolution=100,
    time_total=10000,
)
model.compute(
    WaterPreprocessor,
    average_infiltration_rate=1.5,
    hydraulic_conductivity=6,
    porosity=0.34,
    dispersivity=1.5,
    van_genuchten_n=1.31,
    residual_water_content=0.04,
)
model.compute(BoundaryPreprocessor, C_list=[10.0, 0], T_list=[0, 2000])
model.compute(
    LinearSPsorption,
    sorption_solid={
        "kinetic_sorption": True,
        "sorption_isotherm": "linear",
        "linear": {"Kd_method": "direct_input", "Kd": 5.0},
    },
)
model.compute(
    SWCsorption,
    sigma0=71,
    scaling_factor_awi=1.0,
    van_genuchten_alpha=0.019,
)
model.compute(Retardation, Kaw=0.5, bulk_density=1.6)
model.compute(EquilibriumSolver)

# Access results
grid = model.grid
concentration = model.C_tot

Documentation

Full documentation is available at Read the Docs.

Examples

Several example scripts are provided in the examples/ directory, demonstrating:

• data_structure.py - Data structure handling
• initial_value_problem.py - Setting up initial value problems
• Kd_sorption_component.py - Linear and component-based sorption modeling
• gen_example.py - Basic PFAS transport simulation
• kin_vs_eq.py - Kinetic versus equilibrium sorption
• mass_balance.py - Mass-balance checking
• RunningModelDifferentSoils.py - Running models for different soils
• loop_for_Staring_soils_and_PFASs.py - Looping over soils and PFAS compounds

To run these examples, you need Marimo.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use PFAS in your research, please cite:

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

Contact

For questions and support, please contact: Valerie de Rijk (v.derijk@uu.nl)

Acknowledgments

This package was developed at Utrecht University as part of the PFAS Living Lab.