- 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.
- 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.
- 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.
- 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 Pair test format,
- New function
calculate_min_dists, nodeMinDistNode - 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.
- New function
- 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.
- 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_unfoundargument for databases was not working for some database formats.- Anitools Databases were not filtering arrays, this is fixed.
Initial public release.