Change log

v2026.11.12

Python >= 3.11 is required. DGL is no longer a dependency; matgl>=3.0.3 (PyTorch backend) is required.
MatGL describers (MatGLStructure, MatGLSite) and DIRECTSampler default to M3GNet-Eform-MP-2019.4.1. The previous default, M3GNet-Eform-MP-2018.6.1, has been removed from Hugging Face. (#731)
MTPotential defaults to MLIP-3 (version="mlip-3"). MLIP-2 and mlip-dev remain available via version. (#728)
ElementStats weighted std, skewness, kurtosis and moment:k (k >= 2) change for compositions with unequal element fractions, after a fix to the weighted root moment. Retrain models built on these features. (#723)

MatGLStructure and MatGLSite describers for MatGL foundation models.
MTPotential supports MLIP-3 for train() and evaluate(). MLIP-3’s LAMMPS interface is not yet supported. (#728)
MTPotential.train() with MLIP-3 writes atomic numbers as atom types, so the fitted potential records its elements. MTPotential.from_config() reads them from the file and elements becomes optional. (#618)
MTPotential.from_config() validates elements against species_count, rejects duplicates and warns when the order differs from the electronegativity order used in training. default_element_ordering=True reorders. (#618)
BirchClustering uses fastcluster for the Ward step when n is set, cutting memory from O(M^2) to O(M·d) for large DIRECT samples. use_fastcluster=False restores the scikit-learn step. (#732)

MTP: min_dist is computed in Python instead of mlp mindist (#601), and a diverged fit raises a clear error instead of JSONDecodeError (#702). (#728)
GAP: dft_virial is quoted in extended XYZ files, so gap_fit trains with stresses and evaluate() reads quip output. gap_fit/quip failures report the program’s own error. (#729, #677)
Describers: n_jobs and memory work for model-backed describers (M3GNet, MatGL). (#730, #637)
n2p2: NaN-padded columns are filtered when parsing elements and global_nodes_short in load_input.
42 bugs found while raising test coverage: maml.apps.pes (15), core modules (9), symbolic (7), describers (5), bowsr (5) and gbe (GBBond break-bond ratio). (#722-#727)

Test coverage raised to ~99% for most modules, with mocked binaries for the PES apps and a real MLIP-3 binary in CI.
README rewritten; notebooks and docs updated.

Set up namespace package architecture for maml.apps. The RFXAS package is now available as a separate package maml-apps.rfxas. Usage remains similar.