def test_galilei_transform(self):
g = GalileiTransform()
g.galilei_transform()
np.testing.assert_allclose(np.copy(g.system_CMS_velocity()),
np.zeros((3, )),
atol=1e-15)
def test_cms_velocity(self):
parts = self.system.part[:]
g = GalileiTransform()
total_mass = np.sum(parts.mass)
com_v = np.sum(np.multiply(parts.mass.reshape((-1, 1)), parts.v),
axis=0) / total_mass
np.testing.assert_allclose(np.copy(g.system_CMS_velocity()), com_v)
def test_cms(self):
parts = self.system.part[:]
g = GalileiTransform()
total_mass = np.sum(parts.mass)
com = np.sum(np.multiply(parts.mass.reshape((N_PART, 1)), parts.pos),
axis=0) / total_mass
np.testing.assert_allclose(np.copy(g.system_CMS()), com)
def test_galilei_transform(self):
g = GalileiTransform()
no_virtual = self.system.part.select(virtual=False)
# Center of mass
np.testing.assert_allclose(
np.copy(g.system_CMS()),
np.average(no_virtual.pos, weights=no_virtual.mass, axis=0))
# Center of mass velocity
np.testing.assert_allclose(
np.copy(g.system_CMS_velocity()),
np.average(no_virtual.v, weights=no_virtual.mass, axis=0))
def test_kill_particle_forces(self):
g = GalileiTransform()
g.kill_particle_forces()
np.testing.assert_array_equal(np.copy(self.system.part[:].f), 0)
if espressomd.has_features("ROTATION"):
np.testing.assert_array_less(
np.copy(self.system.part[:].torque_lab), 0)
g.kill_particle_forces(torque=True)
np.testing.assert_array_equal(
np.copy(self.system.part[:].torque_lab), 0)
def test_kill_particle_motion(self):
g = GalileiTransform()
g.kill_particle_motion()
np.testing.assert_array_equal(np.copy(self.system.part[:].v), 0)
if espressomd.has_features("ROTATION"):
np.testing.assert_array_less(
np.copy(self.system.part[:].omega_lab), 0)
g.kill_particle_motion(rotation=True)
np.testing.assert_array_equal(
np.copy(self.system.part[:].omega_lab), 0)
def test_kill_particle_forces(self):
g = GalileiTransform()
g.kill_particle_forces()
np.testing.assert_array_equal(np.copy(self.system.part[:].f), 0)
def test_kill_particle_motion(self):
g = GalileiTransform()
g.kill_particle_motion()
np.testing.assert_array_equal(np.copy(self.system.part[:].v),
np.zeros((N_PART, 3)))
# Set up the DPD friction interaction
system.non_bonded_inter[0, 0].dpd.set_params(weight_function=1,
gamma=gamma,
r_cut=r_cut,
trans_weight_function=0,
trans_gamma=0,
trans_r_cut=0)
# Set up the repulsive interaction
system.non_bonded_inter[0, 0].hat.set_params(F_max=F_max, cutoff=r_cut)
# Warm up and equilibration
system.integrator.run(1000000)
# Reset COM movement
g = GalileiTransform()
g.galilei_transform()
# Set up of correlators to obtain stress autocorrelation functions
dso = espressomd.observables.DPDStress()
plain_old_stress = espressomd.observables.StressTensor()
c_dpd = Correlator(obs1=dso,
tau_lin=tau_lin,
tau_max=tau_max,
delta_N=1,
corr_operation="componentwise_product",
compress1="discard1")
c_old = Correlator(obs1=plain_old_stress,
tau_lin=tau_lin,
tau_max=tau_max,