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Fix non-periodic cell inflation causing PolarMACE k-space OOM #1473

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Fix non-periodic cell inflation causing PolarMACE k-space OOM #1473

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22 changes: 15 additions & 7 deletions mace/data/neighborhood.py
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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 using the actual extent of
# the atoms plus cutoff padding. The previous formula used
# ``max(abs(positions)) * 5 * cutoff`` which (a) depended on the
# absolute coordinate origin rather than the molecular extent, and
# (b) created unnecessarily large cells that caused PolarMACE's
# k-space electrostatics to OOM on GPUs. The extent-based cell
# gives identical neighbour lists and identical PolarMACE energies /
# forces (verified to float32 precision).
if not pbc_x:
cell[0, :] = max_positions * 5 * cutoff * identity[0, :]
extent_x = positions[:, 0].max() - positions[:, 0].min()
cell[0, :] = (extent_x + 2 * cutoff + 1) * identity[0, :]
if not pbc_y:
cell[1, :] = max_positions * 5 * cutoff * identity[1, :]
extent_y = positions[:, 1].max() - positions[:, 1].min()
cell[1, :] = (extent_y + 2 * cutoff + 1) * identity[1, :]
if not pbc_z:
cell[2, :] = max_positions * 5 * cutoff * identity[2, :]
extent_z = positions[:, 2].max() - positions[:, 2].min()
cell[2, :] = (extent_z + 2 * cutoff + 1) * identity[2, :]

sender, receiver, unit_shifts = neighbour_list(
quantities="ijS",
Expand Down Expand Up @@ -64,3 +71,4 @@ def get_neighborhood(
shifts = np.dot(unit_shifts, cell) # [n_edges, 3]

return edge_index, shifts, unit_shifts, cell

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