v1.0.3

Mdapy 1.0.3 (March 28, 2026)

🛠️ Other Improvements

• Added explained_variance_ratio for PCA.
• For these analysis methods (CNA, PTM, and IDS), simulation boxes with a thickness below 15 Å are automatically treated as small boxes.
• The optimized elastic constant workflow can be validated using pymatgen.
• Improved the calculator setup behavior for the System.
• Fixed a bug in the minimize class.
• Updated parts of the documentation.

v1.0.2

Mdapy 1.0.2 (March 4, 2026)

🛠️ Other Improvements

• Reduced the size of the published source distribution (sdist).

• Added support for writing bec, stress, and virial fields in the comment line when using write_xyz.

• Improved LammpsPotential handling of general simulation boxes; it can now correctly compute stress, forces, and energy for such structures.

• Added newest version of NEPCPU for fixing a bug in qNEP.

v1.0.1

Mdapy 1.0.1 (March 2, 2026)

🏆 New Features

• Added support for converting VASP OUTCAR files to XYZ format for GPUMD.
  This supports single-point calculations, structure minimization,
  and AIMD multi-frame trajectories.

• Added functionality to identify chemical species based on vdW-radius
  connectivity between atoms.

🛠️ Other Improvements

• Fixed a bug in the HEA model builder.

• Optimized the cfg2xyz conversion tool.

• Added a neighbor-search benchmark to the documentation.

• Improved the energy minimization workflow.

• Optimized stress computation in LammpsPotential and added corresponding tests.

• Added support for saving BEC information in XYZTraj.

• Added tests for qNEP.

• Removed warnings in test_void by introducing an explicit implode cast method.

🚀 Build System

• Binary wheels are now built separately for each Python version,
  instead of using the stable ABI (> Python 3.12). This change ensures
  compatibility with Python 3.13, where the stable ABI is not supported.

v1.0.0

Mdapy 1.0.0 (January 3, 2026)

🚀 Summary

This is a milestone update for mdapy, featuring a near-complete rewrite of the core architecture. A primary driver for this transition was the limitations of our previous JIT dependency, Taichi; its development pace constrained our support for newer Python versions.

To ensure long-term sustainability, we have reconstructed mdapy by migrating computationally intensive kernels to C++ using the modern nanobind wrapper. As a result, mdapy now depends solely on NumPy and Polars, making it exceptionally lightweight and compatible with all modern Python environments.

Key changes include:

• Engine Shift: With the removal of Taichi, mdapy now focuses on high-performance CPU computation.
• GUI & Tools: Experimental Polyscope support has been removed to focus on core stability. However, a lightweight Jupyter-based GUI remains available as an optional dependency.
• Modern Build System: We have transitioned from setup.py to pyproject.toml.
• Reliability: Extensive test suites have been added to ensure the correctness of all algorithms.

This is a brand-new foundation for the project, and we strongly recommend all users to upgrade.

🏆 New features

• qNEP Integration: Support for evaluating energy, force, virial, charge, and BEC properties.
• Structural Analysis: Added Static Structure Factors and the Wigner-Seitz method for point defect detection.
• Mechanical Properties: Support for calculating elastic constants.
• I/O Enhancements: Added XYZ trajectory loading and introduced the MP file format (Parquet-based), providing high-speed I/O and efficient storage.
• Minimization: Improved FIRE2 method for energy minimization with cell optimization.
• GPUMD Ecosystem: A series of new features compatible with the GPUMD economy.

🛠️ Other improvements

• Compatibility: Full support for Python >= 3.9.
• Reliability: Significantly expanded test case coverage.
• Efficiency: Optimized import overhead; import mdapy is now significantly faster.

⚠️ Limitations

• Documentation: The documentation is currently being updated and is not yet complete. We are actively working on this and welcome any community contributions or feedback.

v0.11.5

🏆 Highlights

• Add feature to calculate local WCP parameter, fix #8
• Remove NEP model output.

v0.11.4

🏆 Highlights

• Add feature to Minimizer class for optimizing the box.
• Add many options for calculating SteinhardtBondOrientation, including the Voronoi neighbor, weighted by Voronoi face area and average version, fix #7 .

🐞 Bug fixes

• Fix a bug for reading xyz format with multi space.

Mdapy 0.11.3

🛠️ Other improvements

• Upgrade the minimum polars to the latest version 1.8.0, so many code changes have been done.
• Update doc.

Mdapy 0.11.2

🏆 Highlights

• Add a new feature to calculate the distribution of bond length and bond angle.

🐞 Bug fixes

• Fix a typo bug for LammpsPotential.

🛠️ Other improvements

• Add test script for lammps interface.

Mdapy 0.11.1

🏆 Highlights

• Refactor the visualization code in Jupyter, make it more beautiful and convinient.
• Add minimizer engine with FIRE method.
• Add a new feature to calculate the atomic shear strain.
• Add OrthogonalBox module to change triclinic box to rectangular box.
• Add adaptive common neighbor analysis method.
• Add IdentifyDiamondStructure method.

🚀 Performance improvements

• Improve the performance for split_dump and split_xyz method.

✨ Enhancements

• Add an example to compute Vacancy Formation energy.
• Make CreatePolycrystalline module can accept any files as matrix.
• Let the max type in LammpsPotential module is determined by given elemental list, enabling more flexible usage.

🐞 Bug fixes

• Fix a bug for cell_opt class.
• Fix a bug for neighbor class.
• Fix a bug for RDF with partial interaction in multi-elemental system.
• Fix a bug for reading cp2k output file with OT method.
• Let GUI model compatible with latest polars.

🛠️ Other improvements

• Update NEP interface to V1.3, compatible with GPUMD 3.9.5.
• Updated some documentations.

v0.11.0

• Fix a bug for create_polycrystalline module.
• Fix a bug for reading xyz.