def test_wca(self):
wca_eps = 2.12
wca_sig = 1.37
wca_cutoff = wca_sig * 2.**(1. / 6.)
wca_shift = -((wca_sig / wca_cutoff)**12 - (wca_sig / wca_cutoff)**6)
self.system.non_bonded_inter[0, 0].wca.set_params(epsilon=wca_eps,
sigma=wca_sig)
E_ref = tests_common.lj_generic_potential(
r=np.arange(1, 232) * self.step_width, eps=wca_eps, sig=wca_sig,
cutoff=wca_cutoff, shift=4. * wca_shift)
for i in range(231):
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()["non_bonded"]
# Calculate forces
f0_sim = self.system.part[0].f
f1_sim = self.system.part[1].f
f1_ref = self.axis * tests_common.lj_generic_force(
espressomd, r=(i + 1) * self.step_width, eps=wca_eps,
sig=wca_sig, cutoff=wca_cutoff)
# Check that energies match, ...
self.assertFractionAlmostEqual(E_sim, E_ref[i])
# force equals minus the counter-force ...
self.assertTrue((f0_sim == -f1_sim).all())
# and has correct value.
self.assertItemsFractionAlmostEqual(f1_sim, f1_ref)
self.system.non_bonded_inter[0, 0].wca.set_params(epsilon=0., sigma=1.)
def test_wca(self):
wca_eps = 2.12
wca_sig = 1.37
wca_cutoff = wca_sig * 2.**(1. / 6.)
wca_shift = -((wca_sig / wca_cutoff)**12 - (wca_sig / wca_cutoff)**6)
self.run_test("wca",
{"epsilon": wca_eps,
"sigma": wca_sig},
force_kernel=lambda espressomd, r, epsilon, sigma: tests_common.lj_generic_force(
espressomd, r, epsilon=epsilon, sigma=sigma, cutoff=wca_cutoff),
energy_kernel=lambda r, epsilon, sigma: tests_common.lj_generic_potential(
r, epsilon=epsilon, sigma=sigma, cutoff=wca_cutoff, shift=4. * wca_shift),
n_steps=231,
force_kernel_needs_espressomd=True)
def test_lj_generic_softcore(self):
lj_eps = 2.12
lj_sig = 1.37
lj_cut = 2.125
lj_off = 0.182
lj_b1 = 6.22
lj_b2 = 3.63
lj_e1 = 13.32
lj_e2 = 3.74
lj_shift = 0.13
lj_delta = 0.1
lj_lam = 0.34
self.system.non_bonded_inter[0, 0].generic_lennard_jones.set_params(
epsilon=lj_eps, sigma=lj_sig, cutoff=lj_cut, offset=lj_off,
b1=lj_b1, b2=lj_b2, e1=lj_e1, e2=lj_e2, shift=lj_shift,
delta=lj_delta, lam=lj_lam)
for i in range(231):
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()["non_bonded"]
E_ref = tests_common.lj_generic_potential(
r=(i + 1) * self.step_width, eps=lj_eps, sig=lj_sig,
cutoff=lj_cut, offset=lj_off, b1=lj_b1, b2=lj_b2, e1=lj_e1,
e2=lj_e2, shift=lj_shift, delta=lj_delta, lam=lj_lam)
# Calculate forces
f0_sim = self.system.part[0].f
f1_sim = self.system.part[1].f
f1_ref = self.axis * tests_common.lj_generic_force(
espressomd, r=(i + 1) * self.step_width, eps=lj_eps, sig=lj_sig,
cutoff=lj_cut, offset=lj_off, b1=lj_b1, b2=lj_b2, e1=lj_e1,
e2=lj_e2, delta=lj_delta, lam=lj_lam)
# Check that energies match, ...
self.assertFractionAlmostEqual(E_sim, E_ref)
# force equals minus the counter-force ...
self.assertTrue((f0_sim == -f1_sim).all())
# and has correct value.
self.assertItemsFractionAlmostEqual(f1_sim, f1_ref)
self.system.non_bonded_inter[0, 0].generic_lennard_jones.set_params(
epsilon=0.)
def test_lj_generic(self):
lj_eps = 2.12
lj_sig = 1.37
lj_cut = 2.122
lj_off = 0.185
lj_b1 = 4.22
lj_b2 = 3.63
lj_e1 = 10.32
lj_e2 = 5.81
lj_shift = -0.13
self.system.non_bonded_inter[0, 0].generic_lennard_jones.set_params(
epsilon=lj_eps, sigma=lj_sig, cutoff=lj_cut, offset=lj_off,
b1=lj_b1, b2=lj_b2, e1=lj_e1, e2=lj_e2, shift=lj_shift)
E_ref = tests_common.lj_generic_potential(
r=np.arange(1, 232) * self.step_width, eps=lj_eps, sig=lj_sig,
cutoff=lj_cut, offset=lj_off, b1=lj_b1, b2=lj_b2, e1=lj_e1,
e2=lj_e2, shift=lj_shift)
for i in range(231):
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()["non_bonded"]
# Calculate forces
f0_sim = np.copy(self.system.part[0].f)
f1_sim = np.copy(self.system.part[1].f)
f1_ref = self.axis * tests_common.lj_generic_force(
espressomd, r=(i + 1) * self.step_width, eps=lj_eps, sig=lj_sig,
cutoff=lj_cut, offset=lj_off, b1=lj_b1, b2=lj_b2, e1=lj_e1,
e2=lj_e2)
# Check that energies match, ...
self.assertFractionAlmostEqual(E_sim, E_ref[i])
# force equals minus the counter-force ...
np.testing.assert_array_equal(f0_sim, -f1_sim)
# and has correct value.
self.assertItemsFractionAlmostEqual(f1_sim, f1_ref)
self.system.non_bonded_inter[0, 0].generic_lennard_jones.set_params(
epsilon=0.)
