def test_single_wall_mobility_zero_at_wall(self):
'''
Test that single wall mobility from Swan Brady paper is zero for very small
particles at the wall.
'''
a = 0.0001
r_vectors = [np.array([0., 0., a]), np.array([1., 1., 8.])]
mobility = mb.single_wall_fluid_mobility(r_vectors, 1., a)
for j in range(3):
for k in range(3):
self.assertAlmostEqual(mobility[j, 3 + k], 0.0, places=6)
def test_single_wall_mobility_zero_at_wall(self):
'''
Test that single wall mobility from Swan Brady paper is zero for very small
particles at the wall.
'''
a = 0.0001
r_vectors = [np.array([0., 0., a]),
np.array([1., 1., 8.])]
mobility = mb.single_wall_fluid_mobility(r_vectors, 1., a)
for j in range(3):
for k in range(3):
self.assertAlmostEqual(mobility[j, 3 + k], 0.0, places=6)
def test_finite_size_limit(self):
''' Test that the finite size mobility goes to the oseen for small a.'''
n_particles = 4
a = 0.000001
# Random configuration, all above wall.
r_vectors = [np.random.normal(5., 1., 3) for _ in range(n_particles)]
mobility_finite = mb.single_wall_fluid_mobility(r_vectors, 1., a)
mobility_point = mb.image_singular_stokeslet(r_vectors, 1.0, a)
for j in range(3*n_particles):
for k in range(3*n_particles):
# We multiply by a to get reasonable numbers for mobility.
self.assertAlmostEqual(a*mobility_finite[j,k], a*mobility_point[j,k])
def test_finite_size_limit(self):
''' Test that the finite size mobility goes to the oseen for small a.'''
n_particles = 4
a = 0.000001
# Random configuration, all above wall.
r_vectors = [np.random.normal(5., 1., 3) for _ in range(n_particles)]
mobility_finite = mb.single_wall_fluid_mobility(r_vectors, 1., a)
mobility_point = mb.image_singular_stokeslet(r_vectors, 1.0, a)
for j in range(3 * n_particles):
for k in range(3 * n_particles):
# We multiply by a to get reasonable numbers for mobility.
self.assertAlmostEqual(a * mobility_finite[j, k],
a * mobility_point[j, k])
def test_boosted_v_python_agreement(self):
'''
Test that for random R vectors, the boosted and python
versions of mobility agree.'''
location = [np.random.normal(10., 3., 3) for _ in range(4)]
eta = 1.0
a = 0.25
fluid_mobility = mb.single_wall_fluid_mobility(location, eta, a)
fluid_mobility_boost = mb.boosted_single_wall_fluid_mobility(
location, eta, a)
for i in range(len(fluid_mobility)):
for j in range(len(fluid_mobility[0])):
self.assertAlmostEqual(fluid_mobility[i, j],
fluid_mobility_boost[i, j])
def test_boosted_v_python_agreement(self):
'''
Test that for random R vectors, the boosted and python
versions of mobility agree.'''
location = [np.random.normal(10., 3., 3) for _ in range(4)]
eta = 1.0
a = 0.25
fluid_mobility = mb.single_wall_fluid_mobility(location, eta, a)
fluid_mobility_boost = mb.boosted_single_wall_fluid_mobility(
location, eta, a)
for i in range(len(fluid_mobility)):
for j in range(len(fluid_mobility[0])):
self.assertAlmostEqual(fluid_mobility[i, j], fluid_mobility_boost[i, j])
def test_single_wall_mobility_spd(self):
''' Test that single wall mobility from Swan Brady paper is SPD. '''
# Number of particles
n_particles = 5
height = 10.
def is_pos_def(x):
return np.all(np.linalg.eigvals(x) > 0)
# Random configuration.
r_vectors = [np.random.normal(height, 1., 3) for _ in range(n_particles)]
mobility = mb.single_wall_fluid_mobility(r_vectors, 1., 1.)
self.assertTrue(is_pos_def(mobility))
for j in range(3*n_particles):
for k in range(j+1, 3*n_particles):
self.assertAlmostEqual(mobility[j, k], mobility[k, j])
def test_single_wall_mobility_spd(self):
''' Test that single wall mobility from Swan Brady paper is SPD. '''
# Number of particles
n_particles = 5
height = 10.
def is_pos_def(x):
return np.all(np.linalg.eigvals(x) > 0)
# Random configuration.
r_vectors = [
np.random.normal(height, 1., 3) for _ in range(n_particles)
]
mobility = mb.single_wall_fluid_mobility(r_vectors, 1., 1.)
self.assertTrue(is_pos_def(mobility))
for j in range(3 * n_particles):
for k in range(j + 1, 3 * n_particles):
self.assertAlmostEqual(mobility[j, k], mobility[k, j])
u_no_wall_pycuda = mob.no_wall_mobility_trans_times_force_pycuda(r_vectors, force, eta, a)
timer('zz_no_wall_pycuda')
u_no_wall_pycuda = mob.no_wall_mobility_trans_times_force_pycuda(r_vectors, force, eta, a)
timer('zz_no_wall_pycuda')
# ================================================================
# WALL TESTS
# ================================================================
timer('python_loops')
mobility_loops = mob.single_wall_fluid_mobility_loops(r_vectors, eta, a)
u_loops = np.dot(mobility_loops, force.flatten())
timer('python_loops')
timer('python')
mobility = mob.single_wall_fluid_mobility(r_vectors, eta, a)
u = np.dot(mobility, force.flatten())
timer('python')
u_numba = mob.single_wall_mobility_trans_times_force_numba(r_vectors, force, eta, a)
timer('numba')
u_numba = mob.single_wall_mobility_trans_times_force_numba(r_vectors, force, eta, a, periodic_length = L)
timer('numba')
if found_pycuda:
u_gpu = mob.single_wall_mobility_trans_times_force_pycuda(r_vectors, force, eta, a)
timer('pycuda')
u_gpu = mob.single_wall_mobility_trans_times_force_pycuda(r_vectors, force, eta, a, periodic_length = L)
timer('pycuda')
if found_cpp:
u_no_wall_pycuda = mob.no_wall_mobility_trans_times_force_pycuda(r_vectors, force, eta, a)
timer('zz_no_wall_pycuda')
u_no_wall_pycuda = mob.no_wall_mobility_trans_times_force_pycuda(r_vectors, force, eta, a)
timer('zz_no_wall_pycuda')
# ================================================================
# WALL TESTS
# ================================================================
timer('python_loops')
mobility_loops = mob.single_wall_fluid_mobility_loops(r_vectors, eta, a)
u_loops = np.dot(mobility_loops, force.flatten())
timer('python_loops')
timer('python')
mobility = mob.single_wall_fluid_mobility(r_vectors, eta, a)
u = np.dot(mobility, force.flatten())
timer('python')
if found_boost:
timer('boost_full_matrix')
mobility_boost = mob.boosted_single_wall_fluid_mobility(r_vectors, eta, a)
u_boost_full = np.dot(mobility_boost, force.flatten())
timer('boost_full_matrix')
timer('boost')
force_hstack=np.hstack(force)
u_boost = mob.boosted_mobility_vector_product(r_vectors, force_hstack, eta, a, periodic_length = L)
timer('boost')