def test_gb(self):
k_1 = 1.2
k_2 = 2.4
mu = 2.
nu = 5.
sigma_0 = 1.2
epsilon_0 = 0.8
cut = 3.3
self.system.part[:].pos = ((1, 2, 3), (2.2, 2.1, 2.9))
self.system.non_bonded_inter[0, 0].gay_berne.set_params(
sig=sigma_0, cut=cut, eps=epsilon_0, k1=k_1, k2=k_2, mu=mu, nu=nu)
p1 = self.system.part[0]
p2 = self.system.part[1]
p1.rotate(axis=(1, 2, 3), angle=0.3)
p1.rotate(axis=(1, -2, -4), angle=1.2)
r = self.system.distance_vec(p1, p2)
r_cut = r * cut / numpy.linalg.norm(r)
self.assertAlmostEqual(
self.system.analysis.energy()["non_bonded"],
tests_common.gay_berne_potential(r, p1.director, p2.director, epsilon_0, sigma_0, mu, nu, k_1, k_2) -
tests_common.gay_berne_potential(
r_cut, p1.director, p2.director, epsilon_0, sigma_0, mu, nu,
k_1, k_2),
delta=1E-14)
self.system.integrator.run(0)
self.system.non_bonded_inter[0, 0].gay_berne.set_params(
sig=sigma_0, cut=0, eps=0, k1=k_1, k2=k_2, mu=mu, nu=nu)
self.system.integrator.run(0)
self.assertEqual(self.system.analysis.energy()["non_bonded"], 0.0)
def get_reference_energy(gb_params, r, director1, director2):
k_1, k_2, mu, nu, sigma_0, epsilon_0, cut = gb_params
r_cut = r * cut / np.linalg.norm(r)
E_ref = tests_common.gay_berne_potential(
r, director1, director2, epsilon_0, sigma_0, mu, nu, k_1, k_2)
E_ref -= tests_common.gay_berne_potential(
r_cut, director1, director2, epsilon_0, sigma_0, mu, nu,
k_1, k_2)
return E_ref