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perf: cache LJ probe-framework mixing constants #14

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perf: cache LJ probe-framework mixing constants #14

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8 changes: 5 additions & 3 deletions src/moxel/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -191,6 +191,9 @@ def calculate(
self._lj_params = np.array(
[lj_params[atom.species_string] for atom in self._simulation_box]
)
# Cache mixed constants for the probe-framework LJ interactions.
self._lj_sigma_mix = 0.5 * (self._lj_params[:, 1] + self.sigma)
self._lj_epsilon_mix4 = 4 * np.sqrt(self._lj_params[:, 0] * self.epsilon)

# Cache fractional coordinates since this is a slow function in pymatgen.
self._frac_coords = self._simulation_box.frac_coords
Expand Down Expand Up @@ -238,9 +241,8 @@ def lj_potential(self, coords):
if np.any(r_ij < 1e-3): # Close contact, infinite energy.
return np.inf

es_j = self._lj_params[indices]
x = (0.5 * (es_j[:, 1] + self.sigma)) / r_ij
e = 4 * np.sqrt(es_j[:, 0] * self.epsilon)
x = self._lj_sigma_mix[indices] / r_ij
e = self._lj_epsilon_mix4[indices]

return np.sum(e * (x**12 - x**6))

Expand Down