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Optimizes construction of attraction strength CVs #99

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May 8, 2024
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Optimizes construction of attraction strength CVs #99

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10 changes: 7 additions & 3 deletions cvpack/attraction_strength.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@

import typing as t

import numpy as np
import openmm
from openmm import unit as mmunit

Expand Down Expand Up @@ -205,11 +206,14 @@ def __init__( # pylint: disable=too-many-locals
self.setCutoffDistance(cutoff)
for parameter in ("charge", "sigma", "epsilon") + ("sign",) * contrasting:
self.addPerParticleParameter(parameter)
for atom in range(nonbondedForce.getNumParticles()):
contrast_atoms = np.zeros(nonbondedForce.getNumParticles(), dtype=bool)
if contrasting:
contrast_atoms[contrastGroup] = True
for atom, in_group in enumerate(contrast_atoms):
charge, sigma, epsilon = nonbondedForce.getParticleParameters(atom)
if contrasting:
sign = -1 if atom in contrastGroup else 1
scale = contrastScaling if atom in contrastGroup else 1
sign = -1 if in_group else 1
scale = contrastScaling if in_group else 1
self.addParticle([charge * scale, sigma, epsilon * scale**2, sign])
else:
self.addParticle([charge, sigma, epsilon])
Expand Down
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