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Backport fix from PR #33 #34

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Merged
lohedges merged 1 commit into from
Jul 28, 2026
Merged

Backport fix from PR #33 #34

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12 changes: 8 additions & 4 deletions src/loch/_sampler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2397,6 +2397,12 @@ def _initialise_gpu_memory(self):
"Could not find the GhostNonGhostNonbondedForce in the system"
)

# Resolve the unit conversions once. Doing this per atom, by
# formatting and re-parsing a string, dominates the setup time for
# large systems.
nm_to_angstrom = _sr.u("1 nm").to("angstrom")
kj_per_mol_to_kcal_per_mol = _sr.u("1 kJ/mol").to("kcal/mol")

# Get the parameters for the GhostNonGhostNonbondedForce.
charges = _np.zeros(self._num_atoms, dtype=_np.float32)
sigmas = _np.zeros(self._num_atoms, dtype=_np.float32)
Expand All @@ -2410,10 +2416,8 @@ def _initialise_gpu_memory(self):
# Charge in |e|, sigma in nm, epsilon in kJ/mol.
charges[i] = q
# Rescale and convert units.
sigmas[i] = _sr.u(f"{2.0 * half_sigma} nm").to("angstrom")
epsilons[i] = _sr.u(f"{(0.5 * two_sqrt_epsilon) ** 2} kJ/mol").to(
"kcal/mol"
)
sigmas[i] = 2.0 * half_sigma * nm_to_angstrom
epsilons[i] = (0.5 * two_sqrt_epsilon) ** 2 * kj_per_mol_to_kcal_per_mol
# Store the softening parameter.
alphas[i] = alpha

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