pfas 0.1.0

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

PFAS Transport Modeling Package

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 soil and groundwater systems. 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
• Vadose Zone Transport: Simulate PFAS movement through the unsaturated zone
• Soil-Water Content Effects: Account for soil-water characteristic curves in moisture dynamics
• 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 interactive documentation)

Installation

From PyPI (coming soon)

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.configuration import read_toml
from pfas.preprocessing import (
    WaterPreprocessor,
    BoundaryPreprocessor,
    GridGenerator,
    SpRetardationPreprocessor,
    SWCAdsorptionPreprocessor,
    SorptionKawiDirectInput,
    SimulationRunner
)
from pfas.model import Model

# Load configuration from file
config = read_toml("examples/data/config.toml")

# Create and configure the model
model = (Model(config)
    .add(WaterPreprocessor, porosity=0.4)
    .add(BoundaryPreprocessor)
    .add(GridGenerator)
    .add(SpRetardationPreprocessor)
    .add(SWCAdsorptionPreprocessor)
    .add(SorptionKawiDirectInput)
    .add(SimulationRunner)
)

# Access results
data = model.generated_data
C_tot = data["C_tot"]  # Total PFAS concentration
grid = data["grid"]    # Grid information

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.py - Linear sorption (Kd) modeling
• factory.py - Factory patterns for model creation
• gen_example.py - Configuration generation

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:

Acknowledgments

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