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@aalexmmaldonado aalexmmaldonado released this 12 Dec 18:03
· 23 commits to main since this release
v0.0.4
e034607

Added

  • mbgdml.descriptors.Criteria class for setting up structure descriptors and cutoffs for models.
  • Model analysis with Matérn covariance function.
  • mbe_contrib tests.
  • Radial distribution function analysis
  • Periodic many-body expansions with the minimum image convention.
  • Many-body alchemical parameter.

Changed

  • Unified use of Z, z, R, and r.
  • dataSet to DataSet
  • Switch to qcelemental for atom properties.
  • Do not restrict sigma_bounds for Bayesian optimization after initial grid search.
  • mbgdml.criteria is now mbgdml.descriptors with a modular handling of descriptors and cutoffs.
  • Provide changeable Z, R, E, and F keys for loading npz data sets.
  • Modularize the error and loss calculations.
  • Reduce regularization strength to 1e-10 instead of 1e-15.
  • Split predict module into models and predictors.
  • Install bayesian-optimization from git until scipy bug is fixed.
  • Merged sGDML changes up to v0.5.4 (124de3dd8d46a0622bd10c3b4ab033a00dbd3c27).
  • Predict times are logged at debug level.
  • Ray must be initialized outside of mbePredict class.
  • Use n_workers instead of n_cores in mbePredict.

Fixed

  • mbe_worker with heterogeneous n-body structures (e.g., solute+solvent).
  • Custom todict method for ASE calculator.
    Fixes attached ASE trajectory in reading entity_ids.
  • Store ASE Atoms object to avoid recalculating energies and forces in ASE calculator.
  • Doc references to respective SchNet functions.

Removed

  • Dependency on natsort.
  • mbgdml.data.mbModel was adsorbed into mbgdml.models.gdmlModel.
  • structureSets and sampling for data sets are no longer supported and subsequently removed.
    This functionality was incorporated into reptar.
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