def test_init_invalid_dimension(self):
if self.dim == 2:
mat = material.create(1.0, 0.3, 3)
cls = material._GreenOperatorForStrains2D
elif self.dim == 3:
mat = material.create(1.0, 0.3, 2)
cls = material._GreenOperatorForStrains3D
else:
raise ValueError()
with pytest.raises(ValueError):
cls(mat)
def test_apply(self, path_to_ref, rtol, flag):
npz_file = np.load(path_to_ref)
x = npz_file['x']
expected = npz_file['y']
# This is a workaround to avoid
# ResourceWarning: unclosed file <_io.BufferedReader name='xxx.npz'>
# self.zip.close()
npz_file.zip.fp.close()
n = x.shape[:-1]
transform = fft.create_real(n)
green = self.greend(material.create(MU, NU, len(n)).green_operator(),
n,
1.,
transform=transform)
if flag == 0:
actual = green.apply(x)
elif flag == 1:
actual = green.apply(x, x)
elif flag == 2:
base = np.zeros(transform.ishape + (green.oshape[-1], ),
np.float64)
actual = green.apply(x, base)
else:
raise ValueError()
assert_allclose(actual, expected, rtol, 10 * ULP)
def test_apply_by_freq(self, n, x, flag):
"""flag allows the specification of various calling sequences:
- flag = 0: apply_by_freq(x)
- flag = 1: apply_by_freq(x, x)
- flag = 2: apply_by_freq(x, y)
"""
dim = len(n)
green = self.greend(material.create(MU, NU, dim).green_operator(),
n, 1.)
for b in multi_indices(n):
green.set_frequency(b)
g = np.asarray(green.to_memoryview())
expected = np.dot(g, x)
if flag == 0:
base = None
elif flag == 1:
base = x
elif flag == 2:
base = np.empty_like(expected)
else:
raise(ValueError)
actual = green.apply_by_freq(x, base)
if flag != 0:
#assert get_base(actual) is base
assert actual.base is base
assert_allclose(actual, expected, ULP, ULP)
def test_apply_by_freq(self, n, x, flag):
"""flag allows the specification of various calling sequences:
- flag = 0: apply_by_freq(x)
- flag = 1: apply_by_freq(x, x)
- flag = 2: apply_by_freq(x, y)
"""
dim = len(n)
green = self.greend(
material.create(MU, NU, dim).green_operator(), n, 1.)
for b in multi_indices(n):
green.set_frequency(b)
g = np.asarray(green.to_memoryview())
expected = np.dot(g, x)
if flag == 0:
base = None
elif flag == 1:
base = x
elif flag == 2:
base = np.empty_like(expected)
else:
raise (ValueError)
actual = green.apply_by_freq(x, base)
if flag != 0:
#assert get_base(actual) is base
assert actual.base is base
assert_allclose(actual, expected, ULP, ULP)
def test_apply(self, path_to_ref, rtol, flag):
comm = MPI.COMM_WORLD
root = 0
rank = comm.rank
# Load reference data
n = None
expected = None
if rank == root:
npz_file = np.load(path_to_ref)
x = npz_file['x']
expected = npz_file['y']
n = x.shape[:-1]
# Broadcast global size of grid
n = comm.bcast(n, root)
# Create local FFT object, and send local grid-size to root process
transform = fft.create_real(n, comm, flags=FFTW_ESTIMATE)
n_locs = comm.gather((transform.ishape[0], transform.offset0), root)
green = self.greend(material.create(0.75, 0.3, len(n))
.green_operator(),
n, 1., transform)
# Scatter x
x_locs = None
if rank == root:
x_locs = [x[offset0:offset0 + n0] for n0, offset0 in n_locs]
x_loc = comm.scatter(x_locs, root)
# if flag == 0:
# y_loc = green.apply(x_loc)
# elif flag == 1:
# y_loc = green.apply(x_loc, x_loc)
# elif flag == 2:
# base = np.empty(transform.ishape + (green.oshape[-1],),
# dtype=np.float64)
# y_loc = green.apply(x_loc, base)
# else:
# raise ValueError()
y_loc = np.empty(transform.ishape + (green.oshape[-1],),
dtype=np.float64)
green.apply(x_loc, y_loc)
# Gather y
y_locs = comm.gather(y_loc, root)
if rank == root:
actual = np.empty_like(expected)
for y_loc, (n0, offset0) in zip(y_locs, n_locs):
actual[offset0:offset0 + n0] = y_loc
assert_allclose(actual, expected, rtol, 10 * ULP)
def test_apply(self, path_to_ref, rtol, flag):
comm = MPI.COMM_WORLD
root = 0
rank = comm.rank
# Load reference data
n = None
expected = None
if rank == root:
npz_file = np.load(path_to_ref)
x = npz_file['x']
expected = npz_file['y']
n = x.shape[:-1]
# Broadcast global size of grid
n = comm.bcast(n, root)
# Create local FFT object, and send local grid-size to root process
transform = fft.create_real(n, comm, flags=FFTW_ESTIMATE)
n_locs = comm.gather((transform.ishape[0], transform.offset0), root)
green = self.greend(
material.create(0.75, 0.3, len(n)).green_operator(), n, 1.,
transform)
# Scatter x
x_locs = None
if rank == root:
x_locs = [x[offset0:offset0 + n0] for n0, offset0 in n_locs]
x_loc = comm.scatter(x_locs, root)
# if flag == 0:
# y_loc = green.apply(x_loc)
# elif flag == 1:
# y_loc = green.apply(x_loc, x_loc)
# elif flag == 2:
# base = np.empty(transform.ishape + (green.oshape[-1],),
# dtype=np.float64)
# y_loc = green.apply(x_loc, base)
# else:
# raise ValueError()
y_loc = np.empty(transform.ishape + (green.oshape[-1], ),
dtype=np.float64)
green.apply(x_loc, y_loc)
# Gather y
y_locs = comm.gather(y_loc, root)
if rank == root:
actual = np.empty_like(expected)
for y_loc, (n0, offset0) in zip(y_locs, n_locs):
actual[offset0:offset0 + n0] = y_loc
assert_allclose(actual, expected, rtol, 10 * ULP)
def test_to_memoryview(self, n, flag):
dim = len(n)
greenc = material.create(MU, NU, dim).green_operator()
greend = self.greend(greenc, n, 1.0)
k = np.empty((dim, ), dtype=np.float64)
for b in multi_indices(n):
expected = self.to_memoryview_expected(greenc, n, b)
greend.set_frequency(b)
if flag == 0:
actual = greend.to_memoryview()
elif flag == 1:
base = np.empty_like(expected)
actual = greend.to_memoryview(base)
assert actual.base is base
else:
raise ValueError
assert_allclose(actual, expected, ULP, ULP)
def test_to_memoryview(self, n, flag):
dim = len(n)
greenc = material.create(MU, NU, dim).green_operator()
greend = self.greend(greenc, n, 1.0)
k = np.empty((dim,), dtype=np.float64)
for b in multi_indices(n):
expected = self.to_memoryview_expected(greenc, n, b)
greend.set_frequency(b)
if flag == 0:
actual = greend.to_memoryview()
elif flag == 1:
base = np.empty_like(expected)
actual = greend.to_memoryview(base)
assert actual.base is base
else:
raise ValueError
assert_allclose(actual, expected, ULP, ULP)
def test_apply(self, path_to_ref, rtol, flag):
npz_file = np.load(path_to_ref)
x = npz_file['x']
expected = npz_file['y']
# This is a workaround to avoid
# ResourceWarning: unclosed file <_io.BufferedReader name='xxx.npz'>
# self.zip.close()
npz_file.zip.fp.close()
n = x.shape[:-1]
transform = fft.create_real(n)
green = self.greend(material.create(MU, NU, len(n)).green_operator(),
n, 1., transform=transform)
if flag == 0:
actual = green.apply(x)
elif flag == 1:
actual = green.apply(x, x)
elif flag == 2:
base = np.zeros(transform.ishape + (green.oshape[-1],), np.float64)
actual = green.apply(x, base)
else:
raise ValueError()
assert_allclose(actual, expected, rtol, 10 * ULP)
def test_poisson_from_bulk_and_shear_moduli(g, nu, dim):
mat = material.create(g, nu, dim)
k = mat.k
assert material.poisson_from_bulk_and_shear_moduli(k, g, dim) == nu
# End: apply
# Begin: params
if __name__ == "__main__":
dim = 2 # Spatial dimension
sym = (dim * (dim + 1)) // 2 # Dim. of space of second rank, symmetric tensors
n = 256 # Number of cells along each side of the grid
mu_i, nu_i = 100, 0.2 # Shear modulus and Poisson ratio of inclusion
mu_m, nu_m = 1, 0.3 # Shear modulus and Poisson ratio of matrix
mu_0, nu_0 = 50, 0.3 # Shear modulus and Poisson ratio of ref. mat.
num_cells = n ** dim # Total number of cells
# End: params
# Begin: instantiate example
example = Example(
mat_i=material.create(mu_i, nu_i, dim),
mat_m=material.create(mu_m, nu_m, dim),
mat_0=material.create(mu_0, nu_0, dim),
n=n,
dim=dim,
)
# End: instantiate example
# Begin: define strains
avg_eps = np.zeros((sym,), dtype=np.float64)
avg_eps[-1] = 1.0
eps = np.empty(example.green.ishape, dtype=np.float64)
new_eps = np.empty_like(eps)
# End: define strains
# Begin: iterate
num_iter = 400
def material(self):
return material.create(self.mu, self.nu, self.dim)
self.green.apply(out, out)
# End: apply
# Begin: params
if __name__ == '__main__':
dim = 2 # Spatial dimension
sym = (dim*(dim+1))//2 # Dim. of space of second rank, symmetric tensors
n = 256 # Number of cells along each side of the grid
mu_i, nu_i = 100, 0.2 # Shear modulus and Poisson ratio of inclusion
mu_m, nu_m = 1, 0.3 # Shear modulus and Poisson ratio of matrix
mu_0, nu_0 = 50, 0.3 # Shear modulus and Poisson ratio of ref. mat.
num_cells = n**dim # Total number of cells
# End: params
# Begin: instantiate example
example = Example(mat_i=material.create(mu_i, nu_i, dim),
mat_m=material.create(mu_m, nu_m, dim),
mat_0=material.create(mu_0, nu_0, dim),
n=n,
dim=dim)
# End: instantiate example
# Begin: define strains
avg_eps = np.zeros((sym,), dtype=np.float64)
avg_eps[-1] = 1.0
eps = np.empty(example.green.ishape, dtype=np.float64)
new_eps = np.empty_like(eps)
# End: define strains
# Begin: iterate
num_iter = 400
res = np.empty((num_iter,), dtype=np.float64)
def pytest_generate_tests(self, metafunc):
if metafunc.function.__name__ == 'test_init_invalid_params':
g2 = material.create(MU, NU, 2).green_operator()
g3 = material.create(MU, NU, 3).green_operator()
params = [(g3, (9, 9), 1., None),
(g2, (-1, 9), 1., None),
(g2, (9, -1), 1., None),
(g2, (9, 9), -1., None),
(g2, (9, 9), 1., fft.create_real((8, 9))),
(g2, (9, 9), 1., fft.create_real((9, 8))),
(g2, (9, 9, 9), 1., None),
(g3, (-1, 9, 9), 1., None),
(g3, (9, -1, 9), 1., None),
(g3, (9, 9, -1), 1., None),
(g3, (9, 9, 9), -1., None)]
metafunc.parametrize('greenc, n, h, transform', params)
elif metafunc.function.__name__ == 'test_to_memoryview':
params = [(n, flag) for n in GRID_SIZES for flag in [0, 1]]
metafunc.parametrize('n, flag', params)
elif metafunc.function.__name__ == 'test_to_memoryview_invalid_params':
g2 = self.greend(material.create(MU, NU, 2).green_operator(),
(8, 16), 1.0)
g3 = self.greend(material.create(MU, NU, 3).green_operator(),
(8, 16, 32), 1.0)
params = [(g2, (g2.oshape[-1], g2.ishape[-1] + 1)),
(g2, (g2.oshape[-1] + 1, g2.ishape[-1])),
(g3, (g3.oshape[-1], g3.ishape[-1] + 1)),
(g3, (g3.oshape[-1] + 1, g3.ishape[-1])),]
metafunc.parametrize('greend, out_shape', params)
elif metafunc.function.__name__ == 'test_apply_by_freq':
x = [np.array([0.3, -0.4, 0.5]),
np.array([0.1, -0.2, 0.3, -0.4, 0.5, -0.6])]
params = [(n, x[len(n) - 2], flag) for n in GRID_SIZES
for flag in range(3)]
metafunc.parametrize('n, x, flag', params)
elif metafunc.function.__name__ == 'test_apply_by_freq_invalid_params':
g2 = self.greend(material.create(MU, NU, 2).green_operator(),
(8, 16), 1.0)
g3 = self.greend(material.create(MU, NU, 3).green_operator(),
(8, 16, 32), 1.0)
params = [(g2, g2.ishape[-1], g2.oshape[-1] + 1),
(g2, g2.ishape[-1] + 1, g2.oshape[-1]),
(g3, g3.ishape[-1], g3.oshape[-1] + 1),
(g3, g3.ishape[-1] + 1, g3.oshape[-1]),]
metafunc.parametrize('greend, x_size, y_size', params)
elif metafunc.function.__name__ == 'test_apply':
if self.operates_in_place:
flags = [0, 1, 2]
else:
flags = [0, 2]
params = [i + (j,) for i in self.params_test_apply() for j in flags]
metafunc.parametrize('path_to_ref, rtol, flag', params)
elif metafunc.function.__name__ == 'test_apply_invalid_params':
g = self.greend(material.create(MU, NU, 2).green_operator(),
(8, 16), 1.0)
i0, i1, i2 = g.ishape
o0, o1, o2 = g.oshape
params2 = [(g, (i0 + 1, i1, i2), (o0, o1, o2)),
(g, (i0, i1 + 1, i2), (o0, o1, o2)),
(g, (i0, i1, i2 + 1), (o0, o1, o2)),
(g, (i0, i1, i2), (o0 + 1, o1, o2)),
(g, (i0, i1, i2), (o0, o1 + 1, o2)),
(g, (i0, i1, i2), (o0, o1, o2 + 1))]
g = self.greend(material.create(MU, NU, 3).green_operator(),
(8, 16, 32), 1.0)
i0, i1, i2, i3 = g.ishape
o0, o1, o2, o3 = g.oshape
params3 = [(g, (i0 + 1, i1, i2, i3), (o0, o1, o2, o3)),
(g, (i0, i1 + 1, i2, i3), (o0, o1, o2, o3)),
(g, (i0, i1, i2 + 1, i3), (o0, o1, o2, o3)),
(g, (i0, i1, i2, i3 + 1), (o0, o1, o2, o3)),
(g, (i0, i1, i2, i3), (o0 + 1, o1, o2, o3)),
(g, (i0, i1, i2, i3), (o0, o1 + 1, o2, o3)),
(g, (i0, i1, i2, i3), (o0, o1, o2 + 1, o3)),
(g, (i0, i1, i2, i3), (o0, o1, o2, o3 + 1))]
metafunc.parametrize('greend, x_shape, y_shape', params2 + params3)
def test_read_only_attribute(self, name, value):
mat = material.create(1.0, 0.3, 3)
with pytest.raises(AttributeError):
setattr(mat, name, value)
def test_init_invalid_params(self, g, nu, dim):
with pytest.raises(ValueError):
mat = material.create(g, nu, dim)
def test_init(self, g, k, nu, dim):
mat = material.create(g, nu, dim)
assert mat.g == g
assert mat.k == k
assert mat.nu == nu
def pytest_generate_tests(self, metafunc):
if metafunc.function.__name__ == 'test_init_invalid_params':
g2 = material.create(MU, NU, 2).green_operator()
g3 = material.create(MU, NU, 3).green_operator()
params = [(g3, (9, 9), 1., None), (g2, (-1, 9), 1., None),
(g2, (9, -1), 1., None), (g2, (9, 9), -1., None),
(g2, (9, 9), 1., fft.create_real((8, 9))),
(g2, (9, 9), 1., fft.create_real((9, 8))),
(g2, (9, 9, 9), 1., None), (g3, (-1, 9, 9), 1., None),
(g3, (9, -1, 9), 1., None), (g3, (9, 9, -1), 1., None),
(g3, (9, 9, 9), -1., None)]
metafunc.parametrize('greenc, n, h, transform', params)
elif metafunc.function.__name__ == 'test_to_memoryview':
params = [(n, flag) for n in GRID_SIZES for flag in [0, 1]]
metafunc.parametrize('n, flag', params)
elif metafunc.function.__name__ == 'test_to_memoryview_invalid_params':
g2 = self.greend(
material.create(MU, NU, 2).green_operator(), (8, 16), 1.0)
g3 = self.greend(
material.create(MU, NU, 3).green_operator(), (8, 16, 32), 1.0)
params = [
(g2, (g2.oshape[-1], g2.ishape[-1] + 1)),
(g2, (g2.oshape[-1] + 1, g2.ishape[-1])),
(g3, (g3.oshape[-1], g3.ishape[-1] + 1)),
(g3, (g3.oshape[-1] + 1, g3.ishape[-1])),
]
metafunc.parametrize('greend, out_shape', params)
elif metafunc.function.__name__ == 'test_apply_by_freq':
x = [
np.array([0.3, -0.4, 0.5]),
np.array([0.1, -0.2, 0.3, -0.4, 0.5, -0.6])
]
params = [(n, x[len(n) - 2], flag) for n in GRID_SIZES
for flag in range(3)]
metafunc.parametrize('n, x, flag', params)
elif metafunc.function.__name__ == 'test_apply_by_freq_invalid_params':
g2 = self.greend(
material.create(MU, NU, 2).green_operator(), (8, 16), 1.0)
g3 = self.greend(
material.create(MU, NU, 3).green_operator(), (8, 16, 32), 1.0)
params = [
(g2, g2.ishape[-1], g2.oshape[-1] + 1),
(g2, g2.ishape[-1] + 1, g2.oshape[-1]),
(g3, g3.ishape[-1], g3.oshape[-1] + 1),
(g3, g3.ishape[-1] + 1, g3.oshape[-1]),
]
metafunc.parametrize('greend, x_size, y_size', params)
elif metafunc.function.__name__ == 'test_apply':
if self.operates_in_place:
flags = [0, 1, 2]
else:
flags = [0, 2]
params = [
i + (j, ) for i in self.params_test_apply() for j in flags
]
metafunc.parametrize('path_to_ref, rtol, flag', params)
elif metafunc.function.__name__ == 'test_apply_invalid_params':
g = self.greend(
material.create(MU, NU, 2).green_operator(), (8, 16), 1.0)
i0, i1, i2 = g.ishape
o0, o1, o2 = g.oshape
params2 = [(g, (i0 + 1, i1, i2), (o0, o1, o2)),
(g, (i0, i1 + 1, i2), (o0, o1, o2)),
(g, (i0, i1, i2 + 1), (o0, o1, o2)),
(g, (i0, i1, i2), (o0 + 1, o1, o2)),
(g, (i0, i1, i2), (o0, o1 + 1, o2)),
(g, (i0, i1, i2), (o0, o1, o2 + 1))]
g = self.greend(
material.create(MU, NU, 3).green_operator(), (8, 16, 32), 1.0)
i0, i1, i2, i3 = g.ishape
o0, o1, o2, o3 = g.oshape
params3 = [(g, (i0 + 1, i1, i2, i3), (o0, o1, o2, o3)),
(g, (i0, i1 + 1, i2, i3), (o0, o1, o2, o3)),
(g, (i0, i1, i2 + 1, i3), (o0, o1, o2, o3)),
(g, (i0, i1, i2, i3 + 1), (o0, o1, o2, o3)),
(g, (i0, i1, i2, i3), (o0 + 1, o1, o2, o3)),
(g, (i0, i1, i2, i3), (o0, o1 + 1, o2, o3)),
(g, (i0, i1, i2, i3), (o0, o1, o2 + 1, o3)),
(g, (i0, i1, i2, i3), (o0, o1, o2, o3 + 1))]
metafunc.parametrize('greend, x_shape, y_shape', params2 + params3)
def truncated_factory():
return truncated(material.create(1.0, 0.3, 2).green_operator(),
(128, 128),
1.)
self.tau2eps = operators.BlockDiagonalOperator2D(ops)
def create_vector(self):
return PETSc.Vec().createMPI(size=(self.n1 * self.n1 * 3),
bsize=(self.n0 * self.n1 * 3))
def mult(self, mat, x, y):
x_arr = x.array.reshape((self.n0, self.n1, 3))
y_arr = y.array.reshape((self.n0, self.n1, 3))
self.green.apply(x_arr, y_arr)
y_arr += np.asarray(self.tau2eps.apply(x_arr))
if __name__ == '__main__':
comm = MPI.COMM_WORLD
mat_i = material.create(10.0, 0.2, dim=2)
mat_m = material.create(1.0, 0.3, dim=2)
mat_0 = material.create(0.9, 0.3, dim=2)
a = 0.5
n = 256
example = SquareInclusion(a, mat_i, mat_m, mat_0, n)
local_shape = (example.n0, example.n1, 3)
x = example.create_vector()
y = example.create_vector()
b = example.create_vector()
x_arr = x.array.reshape(local_shape)
y_arr = y.array.reshape(local_shape)
import sys
sys.path.append('..')
import numpy as np
import skimage.io
skimage.io.use_plugin('freeimage', 'imread')
skimage.io.use_plugin('freeimage', 'imsave')
import janus.green as green
import janus.material.elastic.linear.isotropic as material
mat = material.create(1.0, 0.3, 2)
n0 = 256
n1 = 256
n = (n0, n1)
greenc = mat.green_operator()
greend = green.FilteredGreenOperator2D(greenc, n, 1.)
g = np.empty((n0, n1), dtype=np.float64)
b = np.empty((2,), dtype=np.intc)
tau = np.array([0., 0., 1.])
eta = np.empty_like(tau)
for b0 in range(n0):
b[0] = b0
for b1 in range(n1):
b[1] = b1