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Fix issue #32 #33

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Merged
lohedges merged 1 commit into from
Jul 28, 2026
+9 −5
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Fix issue #32 #33

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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -6,7 +6,8 @@ Changelog

* Please add an item to this CHANGELOG for any new features or bug fixes when creating a PR.
* Restrict PME energy calculation to required force groups [#29](https://github.com/OpenBioSim/loch/pull/29).
* Add `set_lambda` and `_precompute_lambdas` so that a sampler can be re-used across lambda values without rebuilding an OpenMM context.
* Add `set_lambda` and `_precompute_lambdas` so that a sampler can be re-used across lambda values without rebuilding an OpenMM context [#30](https://github.com/OpenBioSim/loch/pull/30).
* Resolve unit conversions once when extracting the lambda dependent non-bonded parameters, rather than per atom, which dominated sampler setup [#33](https://github.com/OpenBioSim/loch/pull/33).

[2026.1.0](https://github.com/openbiosim/loch/compare/2025.2.0...2026.1.0) - Jun 2026
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11 changes: 7 additions & 4 deletions src/loch/_sampler.py
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Expand Up @@ -2529,6 +2529,11 @@ def _precompute_lambdas(

num_particles = gng_force.getNumParticles()

# 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")

for lambda_value, rest2_scale in wanted:
d.set_lambda(lambda_value, rest2_scale=rest2_scale)

Expand All @@ -2545,10 +2550,8 @@ def _precompute_lambdas(
# 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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