Changelog

• 2.0.1:

  • Fixes:

    • Fix precision issue in Fortran for values of \(l\) larger than 10 in all bond-orientational descriptors.

    • Set an upper limit \(l_\mathrm{max}=16\) for all bond-orientational descriptors.

• 2.0.0:

  • New features:

    • Add new structural descriptors:

      • TetrahedralDescriptor (tutorial).

      • SmoothedBondAngleDescriptor (tutorial).

      • SmoothedBondOrientationalDescriptor (tutorial).

      • RadialBondOrientationalDescriptor (tutorial).

      • CompactnessDescriptor (tutorial).

      • CoordinationDescriptor (tutorial).

    • Add radical Voronoi tessellation to identify nearest neighbors in Trajectory.compute_nearest_neighbors() using method="voronoi".

    • Add Voronoi tessellation to compute particles’ Voronoi signatures in Trajectory.compute_voronoi_signatures().

    • List-type additional_fields (e.g. lists of neighbors) can now be read and written by Trajectory.

    • Nearest neighbors can be read from the input trajectory file using the additional_fields parameter.

    • Add a verbose attribute to descriptors to show warnings, messages and progress bars (using tqdm) for the computation of the descriptors.

    • Add an accept_nans property and a discard_nans() method to descriptors to filter out (or keep) NaN elements in the features array when some feature vectors cannot be computed (e.g. due to a lack of neighbors).

    • Trajectory.write() now handles particle aliases.

    • A few new particle aliases (e.g. for neighbors and Voronoi signatures).

    • Improved docstrings and documentation.

  • Non backward-compatible changes:

    • Subpackage partycls.descriptor renamed partycls.descriptors.

    • Deletion of abstract class AngularStructuralDescriptor.

    • Nearest neighbors and their cutoffs are now computed in Trajectory and System with the compute_nearest_neighbors() and compute_nearest_neighbors_cutoffs() methods.

    • No more unique index as Particle.index attribute in Particle.

    • Rename a few attributes and methods.

  • Fixes:

    • Major increase in performance for the computation of nearest neighbors and for the computation of most descriptors.

    • Fix the computation of partial correlations in descriptors when group=1 is not trivial.

    • Fix the setup of bounds in RadialDescriptor.

    • Minor fixes throughout the code.