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Update snap_molecule_indices or use function from cmeutils? #33
Description
morphct/morphct/mobility_kmc.py
Line 502 in 31ddf26
I changed this code to the code below to deal with an indexing artifact of how the xml was converted to gsd . Is this worth updating in morph? Or is this redundant with this cmeutils PR cmelab/cmeutils#20
system = freud.AABBQuery.from_system(snap)
bonds = snap.bonds.group
bonds = bonds[np.lexsort((bonds[:,1],bonds[:,0]))]
snap.bonds.group = bonds
n_query_pts = n_pts = snap.bonds.N
query_pt_inds = snap.bonds.group[:,0]
pt_inds = snap.bonds.group[:, 1]
distances = system.box.compute_distances(
system.points[query_pt_inds], system.points[pt_inds]
)
nlist = freud.NeighborList.from_arrays(
n_query_pts, n_pts, query_pt_inds, pt_inds, distances
)
cluster = freud.cluster.Cluster()
cluster.compute(system=system, neighbors=nlist)
return cluster.cluster_idx
Activity
jennyfothergill commentedon Jan 25, 2022
If we switch to using snap_molecule_indices from cmeutils, then yes. Probably that should be done.
[-]Should this be changed?[/-][+]Update `snap_molecule_indices` or use function from cmeutils?[/+]