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Cache some charge increment calculations #1126

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merged 5 commits into from
Jan 23, 2025
Merged

Cache some charge increment calculations #1126

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e6f9f88
PERF: Cache some charge increment calculations
mattwthompson Dec 11, 2024
7a931c2
Merge remote-tracking branch 'upstream/main' into fix-charge-summing
mattwthompson Jan 15, 2025
f3037f0
Fix
mattwthompson Jan 15, 2025
6fc864c
Merge remote-tracking branch 'upstream/main' into fix-charge-summing
mattwthompson Jan 17, 2025
fe8f88f
Merge remote-tracking branch 'upstream/main' into fix-charge-summing
mattwthompson Jan 21, 2025
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23 changes: 18 additions & 5 deletions openff/interchange/smirnoff/_nonbonded.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@
LibraryChargeHandler,
]

_ZERO_CHARGE = Quantity(0.0, unit.elementary_charge)
_ZERO_CHARGE = Quantity(0.0, "elementary_charge")


@functools.lru_cache(None)
Expand Down Expand Up @@ -352,7 +352,10 @@ def _get_charges(
for i, increment in enumerate(parameter_value):
orientation_atom_index = topology_key.orientation_atom_indices[i]

charges[orientation_atom_index] = charges.get(orientation_atom_index, 0.0) + increment.m
charges[orientation_atom_index] = _add_charges(
charges.get(orientation_atom_index, _ZERO_CHARGE).m,
increment.m,
)

elif parameter_key == "charge":
assert len(topology_key.atom_indices) == 1
Expand All @@ -365,15 +368,22 @@ def _get_charges(
"molecules_with_preset_charges",
"ExternalSource",
):
charges[atom_index] = charges.get(atom_index, 0.0) + parameter_value.m
charges[atom_index] = _add_charges(
charges.get(atom_index, _ZERO_CHARGE).m,
parameter_value.m,
)

elif potential_key.associated_handler in ( # type: ignore[operator]
"ChargeIncrementModelHandler"
):
# the "charge" and "charge_increment" keys may not appear in that order, so
# we "add" the charge whether or not the increment was already applied.
# There should be a better way to do this.
charges[atom_index] = charges.get(atom_index, 0.0) + parameter_value.m

charges[atom_index] = _add_charges(
charges.get(atom_index, _ZERO_CHARGE).m,
parameter_value.m,
)

else:
raise RuntimeError(
Expand All @@ -385,7 +395,10 @@ def _get_charges(

atom_index = topology_key.atom_indices[0]

charges[atom_index] = charges.get(atom_index, 0.0) + parameter_value.m
charges[atom_index] = _add_charges(
charges.get(atom_index, _ZERO_CHARGE).m,
parameter_value.m,
)

logger.info(
"Charge section ChargeIncrementModel, applying charge increment from atom " # type: ignore[union-attr]
Expand Down
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