Merge pull request #34 from OpenBioSim/backport_33

Author: lohedges

src/loch/_sampler.py

@@ -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)
@@ -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