bdfqmmm 0.1.3

BDF QM/MM toolkit

BDF QM/MM Toolkit

bdfqmmm is a Python toolkit for building BDF-based QM/MM workflows.

The Python package name is bdfqmmm; the command line entry point is:

bdf-qmmm

Development

Install the project in editable mode:

python3 -m pip install -e .

Check the command line interface:

bdf-qmmm --help

Pip Installation

Install from a source checkout:

python3 -m pip install .

By default this builds the bundled pDynamo runtime with CMake and installs it into the wheel alongside bdfqmmm. The build uses the bundled BLAS/LAPACK code and disables OpenMP by default to keep source installs portable.

Extra CMake options can be passed with:

BDFQMMM_PDYNAMO_CMAKE_ARGS="-DPDYNAMO_USE_OPENMP=ON" python3 -m pip install .

For a quick Python-only install during documentation or CLI development:

BDFQMMM_SKIP_PDYNAMO_BUILD=1 python3 -m pip install .

This mode does not install pDynamo and should not be used for production QM/MM workflows.

BDF Configuration

After installing bdfqmmm, record the bdfrc file generated by the BDF installation:

bdf-qmmm config set-bdfrc /path/to/bdfrc

Show the resolved BDF runtime configuration:

bdf-qmmm config show

Validate the configured paths:

bdf-qmmm config check

The default user configuration file is:

~/.config/bdfqmmm/config.toml

Configuration priority is:

environment variables > bdfqmmm config file > bdfrc values

Supported environment variables are BDFHOME, BDF_TMPDIR, BDF_MPIRUN, BDF_MPIROOT, BDFRC, and BDFQMMM_CONFIG.

Project Layout

bdfqmmm/
├── src/
│   └── bdfqmmm/        # BDF QM/MM toolkit source code
├── external/
│   └── pdynamo2/       # Vendored pDynamo2 runtime source and parameters
├── tests/              # Lightweight package tests only
├── docs/
└── pyproject.toml

Third-party packages that are checked into this repository should live under external/. Project-owned Python code should stay under src/bdfqmmm/.

Large QM/MM examples, BDF examples, functional tests, benchmarks, trajectories, and reference outputs should live in a separate repository such as bdfqmmm-tests.

License

Project-owned bdfqmmm code is licensed under the MIT License.

This source distribution also bundles third-party pDynamo2 code under external/pdynamo2, which remains under its original license terms, including CeCILL v2 and LGPL-3.0-or-later notices in selected bundled sources. See LICENSE, THIRD_PARTY_NOTICES.md, and external/pdynamo2/Licence_CeCILL_V2-en.txt.