def test_force(self):
"""Ensure forces are in the correct direction using a minimal model."""
r0 = np.array([
[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
[1.0, 1.0, 0.0],
])
horizon = 1.01
elastic_modulus = 0.05
bond_stiffness = 18.0 * elastic_modulus / (np.pi * horizon**4)
volume = np.full(3, 0.16666667)
nl, n_neigh = create_neighbour_list(r0, horizon, 3)
# Displace particles, but do not update neighbour list
r = r0 + np.array([[0.0, 0.0, 0.0], [0.05, 0.0, 0.0],
[0.05, 0.05, 0.0]])
actual_force = bond_force(r, r0, nl, n_neigh, volume, bond_stiffness)
# Ensure force array is correct
force_value = 0.00229417
expected_force = np.array([[force_value, 0., 0.],
[-force_value, force_value, 0.],
[0., -force_value, 0.]])
assert np.allclose(actual_force, expected_force)
def test_create_crack():
"""Test crack creations function."""
r = np.array([
[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[2.0, 0.0, 0.0],
[0.0, 0.0, 1.0],
])
horizon = 1.1
nl, n_neigh = create_neighbour_list(r, horizon, 3)
nl_expected = np.array([[1, 2, 4], [0, 3, 0], [0, 0, 0], [1, 0, 0],
[0, 0, 0]])
n_neigh_expected = np.array([3, 2, 1, 1, 1])
assert np.all(nl == nl_expected)
assert np.all(n_neigh == n_neigh_expected)
crack = np.array([(0, 2), (1, 3)], dtype=np.int32)
create_crack(crack, nl, n_neigh)
nl_expected = np.array([[1, 4, 4], [0, 3, 0], [0, 0, 0], [1, 0, 0],
[0, 0, 0]])
n_neigh_expected = np.array([2, 1, 0, 0, 1])
assert np.all(nl == nl_expected)
assert np.all(n_neigh == n_neigh_expected)
def test_break_bonds():
"""Test neighbour list function."""
r0 = np.array([
[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[2.0, 0.0, 0.0],
[0.0, 0.0, 1.0],
])
horizon = 1.1
nl, n_neigh = create_neighbour_list(r0, horizon, 3)
nl_expected = np.array([[1, 2, 4], [0, 3, 0], [0, 0, 0], [1, 0, 0],
[0, 0, 0]])
n_neigh_expected = np.array([3, 2, 1, 1, 1])
assert np.all(nl == nl_expected)
assert np.all(n_neigh == n_neigh_expected)
r = np.array([
[0.0, 0.0, 0.0],
[2.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[3.0, 0.0, 0.0],
[0.0, 0.0, 2.0],
])
critical_strain = 1.0
break_bonds(r, r0, nl, n_neigh, critical_strain)
nl_expected = np.array([[2, 2, 4], [3, 3, 0], [0, 0, 0], [1, 0, 0],
[0, 0, 0]])
n_neigh_expected = np.array([1, 1, 1, 1, 0])
assert np.all(nl == nl_expected)
assert np.all(n_neigh == n_neigh_expected)
def test_neighbour_list():
"""Test neighbour list function."""
r = np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[2.0, 0.0, 0.0]])
nl, n_neigh = create_neighbour_list(r, 1.1, 3)
nl_expected = np.array([[1, 2, 0], [0, 3, 0], [0, 0, 0], [1, 0, 0]])
n_neigh_expected = np.array([2, 2, 1, 1])
assert np.all(nl == nl_expected)
assert np.all(n_neigh == n_neigh_expected)
def test_break_bonds(context, queue, program):
"""Test neighbour list function."""
r0 = np.array([
[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[2.0, 0.0, 0.0],
[0.0, 0.0, 1.0],
])
horizon = 1.1
max_neigh = 3
nl, n_neigh = create_neighbour_list(r0, horizon, max_neigh)
nl_expected = np.array([[1, 2, 4], [0, 3, 0], [0, 0, 0], [1, 0, 0],
[0, 0, 0]])
n_neigh_expected = np.array([3, 2, 1, 1, 1])
assert np.all(nl == nl_expected)
assert np.all(n_neigh == n_neigh_expected)
r = np.array([
[0.0, 0.0, 0.0],
[2.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[3.0, 0.0, 0.0],
[0.0, 0.0, 2.0],
])
critical_strain = 1.0
# Create buffers
r_d = cl.Buffer(context, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf=r)
r0_d = cl.Buffer(context, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf=r0)
nlist_d = cl.Buffer(context, mf.READ_WRITE | mf.COPY_HOST_PTR, hostbuf=nl)
n_neigh_d = cl.Buffer(context,
mf.READ_WRITE | mf.COPY_HOST_PTR,
hostbuf=n_neigh)
# Call kernel
break_bonds = program.break_bonds
break_bonds(queue, n_neigh.shape, None, r_d, r0_d, nlist_d, n_neigh_d,
np.int32(max_neigh), np.float64(critical_strain))
cl.enqueue_copy(queue, nl, nlist_d)
cl.enqueue_copy(queue, n_neigh, n_neigh_d)
nl_expected = np.array([[2, 2, 4], [3, 3, 0], [0, 0, 0], [1, 0, 0],
[0, 0, 0]])
n_neigh_expected = np.array([1, 1, 1, 1, 0])
assert np.all(nl == nl_expected)
assert np.all(n_neigh == n_neigh_expected)
def test_force(self, context, queue, program):
"""Ensure forces are in the correct direction using a minimal model."""
r0 = np.array([
[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
[1.0, 1.0, 0.0],
],
dtype=np.float64)
horizon = 1.01
elastic_modulus = 0.05
bond_stiffness = 18.0 * elastic_modulus / (np.pi * horizon**4)
max_neigh = 3
volume = np.full(3, 0.16666667, dtype=np.float64)
nlist, n_neigh = create_neighbour_list(r0, horizon, max_neigh)
# Displace particles, but do not update neighbour list
r = r0 + np.array(
[[0.0, 0.0, 0.0], [0.05, 0.0, 0.0], [0.05, 0.05, 0.0]],
dtype=np.float64)
force_value = 0.00229417
force_expected = np.array([[force_value, 0., 0.],
[-force_value, force_value, 0.],
[0., -force_value, 0.]])
force_actual = np.empty_like(force_expected)
# Create buffers
r_d = cl.Buffer(context, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf=r)
r0_d = cl.Buffer(context, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf=r0)
nlist_d = cl.Buffer(context,
mf.READ_ONLY | mf.COPY_HOST_PTR,
hostbuf=nlist)
n_neigh_d = cl.Buffer(context,
mf.READ_ONLY | mf.COPY_HOST_PTR,
hostbuf=n_neigh)
volume_d = cl.Buffer(context,
mf.READ_ONLY | mf.COPY_HOST_PTR,
hostbuf=volume)
force_d = cl.Buffer(context, mf.WRITE_ONLY, force_expected.nbytes)
# Call kernel
bond_force = program.bond_force
bond_force(queue, n_neigh.shape, None, r_d, r0_d, nlist_d, n_neigh_d,
np.int32(max_neigh), volume_d, np.float64(bond_stiffness),
force_d)
cl.enqueue_copy(queue, force_actual, force_d)
assert np.allclose(force_actual, force_expected)
def test_initial_force(self):
"""Ensure forces are zero when there is no displacement."""
r0 = np.array([
[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[2.0, 0.0, 0.0],
[0.0, 0.0, 1.0],
])
horizon = 1.1
volume = np.ones(5)
bond_stiffness = 1.0
nl, n_neigh = create_neighbour_list(r0, horizon, 3)
force_expected = np.zeros((5, 3))
force_actual = bond_force(r0, r0, nl, n_neigh, volume, bond_stiffness)
assert np.allclose(force_actual, force_expected)
def test_initial_force(self, context, queue, program):
"""Ensure forces are zero when there is no displacement."""
r0 = np.array([
[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[2.0, 0.0, 0.0],
[0.0, 0.0, 1.0],
],
dtype=np.float64)
horizon = 1.1
volume = np.ones(5, dtype=np.float64)
bond_stiffness = 1.0
max_neigh = 3
nlist, n_neigh = create_neighbour_list(r0, horizon, max_neigh)
force_expected = np.zeros((5, 3), dtype=np.float64)
force_actual = np.empty_like(force_expected)
# Create buffers
r_d = cl.Buffer(context, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf=r0)
r0_d = cl.Buffer(context, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf=r0)
nlist_d = cl.Buffer(context,
mf.READ_ONLY | mf.COPY_HOST_PTR,
hostbuf=nlist)
n_neigh_d = cl.Buffer(context,
mf.READ_ONLY | mf.COPY_HOST_PTR,
hostbuf=n_neigh)
volume_d = cl.Buffer(context,
mf.READ_ONLY | mf.COPY_HOST_PTR,
hostbuf=volume)
force_d = cl.Buffer(context, mf.WRITE_ONLY, force_expected.nbytes)
# Call kernel
bond_force = program.bond_force
bond_force(queue, n_neigh.shape, None, r_d, r0_d, nlist_d, n_neigh_d,
np.int32(max_neigh), volume_d, np.float64(bond_stiffness),
force_d)
cl.enqueue_copy(queue, force_actual, force_d)
assert np.allclose(force_actual, force_expected)