Adding some preprocessing tools to the transform module, including descriptors computation and tools.
NB-1 Transform object are supposed not to have trainable parameters.
NB-2 Position-dependent descriptors are implemented only for cubic/orthorhombic cells.
The structure of the module is:
Tools
Normalization
Switching functions (new)
Continuous Histogram (new, derivable histogram using KDE)
Descriptors, acting on positions
Multiple descriptors (new, wrapper class to compute multiple descriptors on the same set of positions)
Pairwise distances (new, computes ALL pairwise distances from a set of positions)
Torsional angle (new, computes the torsional angle from a set of positions + index of 4 involved atoms)
Coordination number (new, computes from a set of positions coordination numbers of elements of group A wrt group B)
Eigs adjacency matrix (new, computes adjacency matrix eigenvalues. Could be moved to a tutorial)
Already implemented but likely to be kept out of this PR:
Radius graph (compute graph inputs in the format: edge sources, edge destinations and edge distances)
Radial distribution function (compute RDF from a set of position and optionally the integral of a peak)
codecov[bot]
commented
5 months ago
Description
Adding some preprocessing tools to the transform module, including descriptors computation and tools.
NB-1 Transform object are supposed not to have trainable parameters. NB-2 Position-dependent descriptors are implemented only for cubic/orthorhombic cells.
The structure of the module is:
Tools
Descriptors, acting on positions
Already implemented but likely to be kept out of this PR:
Status