Open JimmyRushing opened 2 years ago
https://github.com/cmelab/morphct/blob/31ddf263979b7200b7015fa16eb4d6af3ea01fca/morphct/mobility_kmc.py#L502
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 https://github.com/cmelab/cmeutils/pull/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
If we switch to using snap_molecule_indices from cmeutils, then yes. Probably that should be done.
https://github.com/cmelab/morphct/blob/31ddf263979b7200b7015fa16eb4d6af3ea01fca/morphct/mobility_kmc.py#L502
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 https://github.com/cmelab/cmeutils/pull/20