Changelog

  • 2.1.1:
    • Added:

      • Better validation of the input system, including checks and possible normalization of positions, cell, atomic numbers and periodic boundary conditions.

    • Fixed:

      • Issue with ACSF G5 calculation. See issue #138.

  • 2.1.0:
    • Added:

      • New compression option for SOAP courtesy of jlparkI.

    • Removed:

      • The crossover parameter from SOAP, now available under the compression parameter.

  • 2.0.1:
    • Added:

      • Wheel distributions for Linux, MacOS and Windows.

    • Fixed:

      • Issue with exception not being raised when analytical derivatives were requested for SOAP with weighting turned on. See issue #113.

  • 2.0.0:
    • Added:

      • Added numerical derivatives for SineMatrix, EwaldSumMatrix, ACSF, MBTR, LMBTR and ValleOganov.

      • attach=True is now supported when getting analytical SOAP derivatives.

      • periodic=True is now supported when getting numerical SOAP derivatives.

      • Added analytical derivatives for MBTR when using the smooth_cutoff weighting and/or valle_oganov normalization.

      • Added new tutorial on using descriptors for visualization

    • Fixed:

      • Fixed issue in all atoms not being taken into account when using the smooth_cutoff weighting of MBTR.

    • Changed:

      • Renamed the positions argument of local descriptors to centers.

      • The MBTR, LMBTR and ValleOganov interfaces has been simplified so that only one term can be calculated at once.

    • Removed:

      • “unflattened” outputs from MBTR, LMBTR, CoulombMatrix, EwaldSumMatrix and SineMatrix.

      • The rcut, nmax, and lmax options for SOAP, use r_cut, n_max and l_max instead.

      • The rcut and gcut options for EwaldSumMatrix, use r_cut and g_max instead.

  • 1.2.3:
    • Added:

      • Analytical derivatives for MBTR, thanks to jarnlaak. Note that not all normalization options and geometry functions are supported.

      • Tutorial on how to create visualizations by employing a mapping from descriptor feature space into colors.

  • 1.2.2:
    • Fixed:

      • An issue with CoulombMatrix ordering using sorted_l2 that was introduced in version 1.2.0. See issue #89.

    • Deprecated:

      • The rcut, nmax, and lmax options for SOAP, use r_cut, n_max and l_max instead.

      • The rcut and gcut options for EwaldSumMatrix, use r_cut and g_max instead.

  • 1.2.0:
  • 1.1.0:
    • Added:

      • Support for l_max <= 20 for the SOAP GTO basis.

      • Support for weighting the gaussians contributing to the atomic density. For more details see the updated SOAP tutorial (and issues #20, #58).

      • attach-argument for the derivatives-function (see issue #63).

  • 1.0.0:
    • Added:

      • Possibility to calculate the derivatives of the SOAP descriptor with respect to atom positions. For now, only non-periodic structures are supported. Supports numerical derivatives for any SOAP configuration, and analytical derivatives when using the GTO radial basis.

    • Changed:

      • The periodic attribute now instructs the code to take into account the periodicity of the system as defined by the pbc-attribute the ase.Atoms. So in addition to setting periodic=True in the descriptor, also make your system periodic in the wanted directions through the pbc attribute.

      • The sparse output now uses the sparse matrices from the sparse library-library. This change is motivated by the need for n-dimensional sparse arrays in various places. See more at the documentation page for sparse output.

      • The output shapes have been made more consistent across different descriptors: global descriptors now produce 1D flattened output and local descriptors produce 2D flattened output for a single system. Whenever multiple systems are given, an additional dimension is added that runs across the different systems: for systems with the same number of atoms the output becomes a five-dimensional array, otherwise the output becomes a list of four-dimensional arrays.

  • 0.4.0:
    • Added:

      • Support for different averaging modes in SOAP. See issue #44.

    • Fixed:

      • An issue with the layout of the SOAP descriptor. The output size was incorrectly missing elements. See issue #48.

    • Changed:

      • Migrated completely from Cython to pybind11.

  • 0.3.5:
    • Added:

      • Support for Python 3.8. See issue #40.

  • 0.3.2:
    • Changed:

      • Improved performance for SOAP in combination with very large systems. See issue #31.

  • 0.2.8:
    • Removed:

      • Support for Python 2.