Skip to content

Around keyword can use KDTree for periodic boundary conditions #2022

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
richardjgowers merged 3 commits into from
Aug 5, 2018
Merged

Around keyword can use KDTree for periodic boundary conditions #2022

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
100a666
kdtree now works with pbc, modified _apply_kdtree method in pointsele…
ayushsuhane Aug 4, 2018
1761ff4
CHANGELOG
ayushsuhane Aug 4, 2018
cae0704
Merge branch 'develop' into selections
richardjgowers Aug 5, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion package/CHANGELOG
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,8 @@ The rules for this file:

Enhancements


* Modified around selections to work with KDTree and periodic boundary
conditions. Should reduce memory usage (#974 PR #2022)
* Modified topology.guessers.guess_bonds to automatically select the
fastest method for guessing bonds using
lib.distance.self_capped_distance (PR # 2006)
Expand Down
16 changes: 9 additions & 7 deletions package/MDAnalysis/core/selection.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -243,9 +243,6 @@ def __init__(self):
self.apply = self._apply_distmat

self.periodic = flags['use_periodic_selections']
# KDTree doesn't support periodic
if self.periodic:
self.apply = self._apply_distmat

def validate_dimensions(self, dimensions):
r"""Check if the system is periodic in all three-dimensions.
Expand Down Expand Up @@ -282,6 +279,9 @@ def _apply_KDTree(self, group):
# All atoms in group that aren't in sel
sys = group[~np.in1d(group.indices, sel.indices)]

if not sys:
return sys[[]]

box = self.validate_dimensions(group.dimensions)

cut = self.cutoff if box is not None else None
Expand Down Expand Up @@ -321,7 +321,8 @@ def _apply_KDTree(self, group):
"""
sel = self.sel.apply(group)
box = self.validate_dimensions(group.dimensions)
ref = sel.center_of_geometry(pbc=self.periodic)
periodic = box is not None
ref = sel.center_of_geometry(pbc=periodic)
kdtree = PeriodicKDTree(box=box)

cutoff = self.exRadius if box is not None else None
Expand Down Expand Up @@ -363,7 +364,8 @@ def _apply_KDTree(self, group):
"""
sel = self.sel.apply(group)
box = self.validate_dimensions(group.dimensions)
ref = sel.center_of_geometry(pbc=self.periodic)
periodic = box is not None
ref = sel.center_of_geometry(pbc=periodic)

cut = self.cutoff if box is not None else None
kdtree = PeriodicKDTree(box=box)
Expand Down Expand Up @@ -483,7 +485,7 @@ def __init__(self, parser, tokens):
self.cutoff = float(tokens.popleft())

def _apply_KDTree(self, group):
box = group.dimensions if self.periodic else None
box = self.validate_dimensions(group.dimensions)
kdtree = PeriodicKDTree(box=box)
cut = self.cutoff if box is not None else None
kdtree.set_coords(group.positions, cutoff=cut)
Expand All @@ -496,7 +498,7 @@ def _apply_distmat(self, group):
ref_coor = self.ref[np.newaxis, ...]

ref_coor = np.asarray(ref_coor, dtype=np.float32)
box = group.dimensions if self.periodic else None
box = self.validate_dimensions(group.dimensions)

dist = distances.distance_array(group.positions, ref_coor, box)
mask = (dist <= self.cutoff).any(axis=1)
Expand Down