Bond-related Descriptors¶
This module computes relatively simple descriptors based on nearest-neighbor bonds, with few additional transformations.
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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}, }
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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}, }
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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}, }
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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}, }
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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}, }
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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}, }
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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}, }