Skip to content

Fix non-PBC fake-cell sizing in get_neighborhood #1501

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

Closed
keceli wants to merge 1 commit into from
Closed

Fix non-PBC fake-cell sizing in get_neighborhood #1501

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
21 changes: 14 additions & 7 deletions mace/data/neighborhood.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,16 +24,23 @@ def get_neighborhood(
pbc_y = pbc[1]
pbc_z = pbc[2]
identity = np.identity(3, dtype=float)
max_positions = np.max(np.absolute(positions)) + 1
# Extend cell in non-periodic directions
# For models with more than 5 layers, the multiplicative constant needs to be increased.
# temp_cell = np.copy(cell)
# Extend cell in non-periodic directions so an atom's receptive field cannot
# reach its periodic image. Use molecular extent (translation-invariant) plus
# an additive safety margin equal to receptive-field × cutoff; the additive
# form prevents the matscipy linked-cell grid from exploding when
# the molecule is far from the origin. Bump the safety
# multiplier if the model uses more than 5 message-passing layers.
if positions.size:
extent = positions.max(axis=0) - positions.min(axis=0)
else:
extent = np.zeros(3, dtype=float)
safety = 5 * cutoff
if not pbc_x:
cell[0, :] = max_positions * 5 * cutoff * identity[0, :]
cell[0, :] = (extent[0] + safety) * identity[0, :]
if not pbc_y:
cell[1, :] = max_positions * 5 * cutoff * identity[1, :]
cell[1, :] = (extent[1] + safety) * identity[1, :]
if not pbc_z:
cell[2, :] = max_positions * 5 * cutoff * identity[2, :]
cell[2, :] = (extent[2] + safety) * identity[2, :]

sender, receiver, unit_shifts = neighbour_list(
quantities="ijS",
Expand Down
Loading