MODFLOW 6 and PHREEQC Reactive Transport Modeling

Main branch:

Develop branch:

Platforms

Benchmarks

Benchmark comparing model results against PHT3D are in benchmark/. Each folder contains a Jupyter notebook to write and execute an MF6RTM model via the MUP3D class. Additionally, PHT3D files are provided in the corresponding pht3d directory for each example.

Considerations

The current version is intended to work with structured grids (dis object in MF6), unstructured grids (disv) and one MF6 simulation that includes the flow and transport solutions. No support is currently provided for a 'flow then transport scheme,' meaning that advanced packages cannot be incorporated yet.

On the PHREEQC side, the following have been included:

Solution
Equilibrium phases
Cation Exchange
Surface Complexation
Kinetic Phases

Most options for each phreeqc block can be passed by adding list with options. However, not all options had been tested, so please create an issue if any option is not working or crashing the model.

Software requirements

All dependencies and executables are included in this repo. This package extensively uses modflowapi and phreeqcrm

Installation

Quick Start with pip

The package can be installed via pip:

pip install mf6rtm

Installing MODFLOW 6 executables

After installing mf6rtm, install the MODFLOW 6 executables:

pip install modflow-devtools
get-modflow --subset mf6,libmf6,gridgen :python

Once installed, the executables in envs/[env-name]/bin will be automatically invoked whenever mf6rtm runs within the environment.

Custom MODFLOW Versions

If you need custom or older versions of mf6 (e.g., for running PESTPP on an HPC cluster), place them in a separate directory and use the provided utility to bring them to the model working directory:

from mf6rtm import utils

utils.prep_bins(model_dir, src_path=path_to_bins)

Running the benchmark notebooks

We have provided some benchmarks in the form of Jupyter notebooks. We have also included the executables needed to run them out of the box. Nevertheless, they can also be run using the executables downloaded with modflow-devtools.

Developing

With Pixi

For development, we use pixi for fast, reproducible environments:

# Fork and clone the repository
git clone https://github.com/YOUR-USERNAME/mf6rtm.git
cd mf6rtm

# Install development environment with all dependencies
pixi install

# Run tests
pixi run test

# Run tests with coverage
pixi run test-cov

# Run linting
pixi run lint

# Test with specific Python version
pixi run -e py311 test

Documentation

The documentation is available in mf6rtm - read the docs

Funding

The developing of mf6rtm was kindly supported by INTERA, Inc.

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