def test_fene(self):
fene_k = 23.15
fene_d_r_max = 3.355
fene_r_0 = 1.1
fene = espressomd.interactions.FeneBond(
k=fene_k, d_r_max=fene_d_r_max, r_0=fene_r_0)
self.run_test(fene,
lambda r: tests_common.fene_force(
scalar_r=r, k=fene_k, d_r_max=fene_d_r_max, r_0=fene_r_0),
lambda r: tests_common.fene_potential(
scalar_r=r, k=fene_k, d_r_max=fene_d_r_max, r_0=fene_r_0),
0.01, fene_r_0 + fene_d_r_max, True)
def test_fene(self):
fene_k = 23.15
fene_d_r_max = 3.355
fene_r_0 = 1.1
fene = espressomd.interactions.FeneBond(k=fene_k,
d_r_max=fene_d_r_max,
r_0=fene_r_0)
self.system.bonded_inter.add(fene)
self.system.part[0].add_bond((fene, 1))
for i in range(445):
self.system.part[1].pos = self.system.part[1].pos + self.step
self.system.integrator.run(recalc_forces=True, steps=0)
# Calculate energies
E_sim = self.system.analysis.energy()["bonded"]
E_ref = tests_common.fene_potential(scalar_r=(i + 1) *
self.step_width,
k=fene_k,
d_r_max=fene_d_r_max,
r_0=fene_r_0)
# Calculate forces
f0_sim = self.system.part[0].f
f1_sim = self.system.part[1].f
f1_ref = self.axis * \
tests_common.fene_force(scalar_r=(i + 1) * self.step_width,
k=fene_k, d_r_max=fene_d_r_max, r_0=fene_r_0)
# Check that energies match, ...
np.testing.assert_almost_equal(E_sim, E_ref)
# force equals minus the counter-force ...
self.assertTrue((f0_sim == -f1_sim).all())
# and has correct value.
f1_sim_copy = np.copy(f1_sim)
np.testing.assert_almost_equal(f1_sim_copy, f1_ref, decimal=5)
# Check that bond breaks when distance > r_cut
self.system.part[1].pos = self.system.part[1].pos + self.step
with self.assertRaisesRegexp(Exception,
"Encoutered errors during integrate"):
self.system.integrator.run(recalc_forces=True, steps=0)