def test_harmonic(self):
hb_k = 5
hb_r_0 = 1.5
hb_r_cut = 3.355
hb = espressomd.interactions.HarmonicBond(k=hb_k,
r_0=hb_r_0,
r_cut=hb_r_cut)
self.run_test(
hb, lambda r: tests_common.harmonic_force(
scalar_r=r, k=hb_k, r_0=hb_r_0),
lambda r: tests_common.harmonic_potential(
scalar_r=r, k=hb_k, r_0=hb_r_0), 0.01, hb_r_cut, True)
def test_harmonic(self):
hb_k = 5
hb_r_0 = 1.5
hb_r_cut = 3.355
hb = espressomd.interactions.HarmonicBond(k=hb_k,
r_0=hb_r_0,
r_cut=hb_r_cut)
self.system.bonded_inter.add(hb)
self.system.part[0].add_bond((hb, 1))
for i in range(335):
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.harmonic_potential(scalar_r=(i + 1) *
self.step_width,
k=hb_k,
r_0=hb_r_0,
r_cut=hb_r_cut)
# Calculate forces
f0_sim = self.system.part[0].f
f1_sim = self.system.part[1].f
f1_ref = self.axis * \
tests_common.harmonic_force(scalar_r=(i + 1) * self.step_width,
k=hb_k, r_0=hb_r_0, r_cut=hb_r_cut)
# 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)
# 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)