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CHANGELOG.rst

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0.0.1

Improvements:

  • new "glue-on" method for damping coulomb energies locally
  • Improve compatibility with ASE functions such as mixing calculators and trajectory saving.

0.0.1b4

New Features:

  • Added an interface to LAMMPS using the LAMMPS MLIAP UNIFIED pair style. see /examples/lammps/ and the documentation for more information.

Improvements:

  • Add a setting to create plots with transparent backgrounds
  • Improvements to documentation display
  • Add an example for training to the Ani-1x dataset directly from the h5 file.
  • ASE Calculator is now compatible with more ASE functions including mixing with other calculators.
  • Cross-device restarting is now properly handled. Corresponding documentation has been added.

Bug Fixes:

  • Fixed a bug which expected files saved in a .pkl format, when in fact they are saved as .pt (pytorch) files.
  • Fixed a bug in parsing of local settings file.
  • Fixed a bug in parsing of settings through environmental variables.
  • Fixed a false low distance warning when sensitivity functions are plotted.

0.0.1b3

New Features:

  • Cupy based interaction kernels are now available (GPU only). These kernels are typically higher performance than numba-based kernels, although overall gains will depend on many factors. To activate the kernels, install cupy.

Improvements:

  • Sorted values of pair-lists handled by custom kernels are now cached. This drastically improves the ease of saturating the GPU by reducing the need for pair synchronization
  • Numba GPU kernel overhead has been reduced by speeding up the time to convert between the torch and numba GPU array types.
  • Misc. other improvements to reduce CPU/GPU synchronization needs.
  • PyAnitools database is now more flexible and can read additional properties, for example parsing the COMP6 test set.

Bug Fixes:

  • small bugs in database loading

0.0.1b1

New features:

  • PeriodicPairIndexer can now handle arbitrary cells sizes with arbitrary boundary conditions, and is suitable for use in general training sets. As a result, it is no longer necessary to use DynamicPeriodicPairs, and caching pairs is less likely to bring performance improvements.

Improvements

  • The throughput of DynamicPeriodicPairs has been dramatically increased.
  • If numba fails to find a GPU, a better error message is displayed.
  • Loss broadcasting debugging can be changed with a new setting variable.

Bug fixes:

  • Fixed a bug where _DispatchNeighbors module incorrectly indexed atoms in the case where blank atoms did not appear after real ones.
  • Fixed a bug where an ASE calculator couldn't be created when the training PairFinder is a subclass of _DispatchNeighbors
  • Fixed a bug where an ASE calculator couldn't be created when the encoder and species indexer were generated using a python list for species.
  • Fixed a bug with the ASE calculator failing in open boundary conditions.
  • Fixed an incompatibility between our API and the pytorch API that prevented loading pytorch schedulers from a checkpoint.

0.0.1a2

New features:

  • New Pair test format, PaddedNeighborNode:
    • This node can convert pair-style lists into a flat array of neighbors for each atom in the batch.
    • The output indices will be padded with index values of [-1] so that the array is rectangular, and the output difference vectors padded with vectors of 0.
  • New function calculate_min_dists, node MinDistNode
    • This node can compute the minimum distance from atoms to other atoms, and aggregate this information over systems.
    • The primary utility is encapsulated in hippynn.pretraining.calculate_min_dists. This function computers the minimum distance between any pair of atoms for each molecule in the dataset. This information can be useful for identifying data which is physically problematic or for setting the initial parameters for distance sensitivity in a network.

Improvements:

  • Pyanitools database improvements
    • Can now specify the key value to use as the species array.
    • Species array can be either string valued, i.e. ['C','H','H','H'], or integer valued, i.e. [6,1,1,1]. Previously only strings were accepted.

Bug fixes:

  • DynamicPeriodicPairs would find pairs in the wrong images in some cases, fixed.
  • Scalar broadcasting of a node with a scalar, e.g. in algebraic operations, was broken, this is fixed.
  • allow_unfound argument for databases was not working for some database formats.
  • Anitools Databases were not filtering arrays, this is fixed.

0.0.1a

Initial public release.