Bond-related Descriptors

This module computes relatively simple descriptors based on nearest-neighbor bonds, with few additional transformations.

pythia.bonds.neighborhood_angle_singvals(box, positions, neighbors, rmax_guess=2.0)[source]

Construct a matrix of pairwise angles between (rk - ri) and (rj - ri) for all neighbors j and k(==j) of each particle i, for a particular number of neighbors. Returns the singular values of this matrix to fix permutation invariance.

This function uses the following citations:

@misc{freud2016,
        title = {freud},
        url = {https://doi.org/10.5281/zenodo.166564},
        abstract = {First official open-source release, includes a zenodo DOI for citations.},
        author = {Harper, Eric S and Spellings, Matthew and Anderson, Joshua A and Glotzer, Sharon C},
        month = nov,
        year = {2016},
        doi = {10.5281/zenodo.166564},
}
pythia.bonds.neighborhood_angle_sorted(box, positions, neighbors, rmax_guess=2.0)[source]

Construct a matrix of pairwise angles between (rk - ri) and (rj - ri) for all neighbors j and k(==j) of each particle i, for a particular number of neighbors. Returns the sorted values of this matrix to fix permutation invariance.

This function uses the following citations:

@misc{freud2016,
        title = {freud},
        url = {https://doi.org/10.5281/zenodo.166564},
        abstract = {First official open-source release, includes a zenodo DOI for citations.},
        author = {Harper, Eric S and Spellings, Matthew and Anderson, Joshua A and Glotzer, Sharon C},
        month = nov,
        year = {2016},
        doi = {10.5281/zenodo.166564},
}
pythia.bonds.neighborhood_distance_singvals(box, positions, neighbors, rmax_guess=2.0)[source]

Construct a matrix of pairwise distances filled with |r_k - r_j| for all neighbors j and k(==j) of each particle i. Returns the singular values of this matrix to fix permutation invariance.

This function uses the following citations:

@misc{freud2016,
        title = {freud},
        url = {https://doi.org/10.5281/zenodo.166564},
        abstract = {First official open-source release, includes a zenodo DOI for citations.},
        author = {Harper, Eric S and Spellings, Matthew and Anderson, Joshua A and Glotzer, Sharon C},
        month = nov,
        year = {2016},
        doi = {10.5281/zenodo.166564},
}
pythia.bonds.neighborhood_distance_sorted(box, positions, neighbors, rmax_guess=2.0)[source]

Construct a matrix of pairwise distances filled with |r_k - r_j| for all neighbors j and k(==j) of each particle i. Returns the sorted contents of this matrix to fix permutation invariance.

This function uses the following citations:

@misc{freud2016,
        title = {freud},
        url = {https://doi.org/10.5281/zenodo.166564},
        abstract = {First official open-source release, includes a zenodo DOI for citations.},
        author = {Harper, Eric S and Spellings, Matthew and Anderson, Joshua A and Glotzer, Sharon C},
        month = nov,
        year = {2016},
        doi = {10.5281/zenodo.166564},
}
pythia.bonds.neighborhood_range_angle_singvals(box, positions, neigh_min, neigh_max, rmax_guess=2.0)[source]

Construct a matrix of pairwise angles between (rk - ri) and (rj - ri) for all neighbors j and k(==j) of each particle i, for a range of neighborhood sizes from neigh_min to neigh_max (inclusive). Returns the singular values of this matrix to fix permutation invariance.

This function uses the following citations:

@misc{freud2016,
        title = {freud},
        url = {https://doi.org/10.5281/zenodo.166564},
        abstract = {First official open-source release, includes a zenodo DOI for citations.},
        author = {Harper, Eric S and Spellings, Matthew and Anderson, Joshua A and Glotzer, Sharon C},
        month = nov,
        year = {2016},
        doi = {10.5281/zenodo.166564},
}
pythia.bonds.neighborhood_range_distance_singvals(box, positions, neigh_min, neigh_max, rmax_guess=2.0)[source]

Construct a matrix of pairwise distances filled with |r_k - r_j| for all neighbors j and k(==j) of each particle i, for a range of neighborhood sizes from neigh_min to neigh_max (inclusive). Returns the singular values of this matrix to fix permutation invariance.

This function uses the following citations:

@misc{freud2016,
        title = {freud},
        url = {https://doi.org/10.5281/zenodo.166564},
        abstract = {First official open-source release, includes a zenodo DOI for citations.},
        author = {Harper, Eric S and Spellings, Matthew and Anderson, Joshua A and Glotzer, Sharon C},
        month = nov,
        year = {2016},
        doi = {10.5281/zenodo.166564},
}
pythia.bonds.normalized_radial_distance(box, positions, neighbors, rmax_guess=2.0)[source]

Returns the ratio of the euclidean distance of each near-neighbor to that of the nearest neighbor for each particle.

This function uses the following citations:

@misc{freud2016,
        title = {freud},
        url = {https://doi.org/10.5281/zenodo.166564},
        abstract = {First official open-source release, includes a zenodo DOI for citations.},
        author = {Harper, Eric S and Spellings, Matthew and Anderson, Joshua A and Glotzer, Sharon C},
        month = nov,
        year = {2016},
        doi = {10.5281/zenodo.166564},
}