def test_pCoordinates(self):
NWorld = np.array([5])
xp = util.pCoordinates(NWorld)
self.assertTrue(np.allclose(xp.T - np.array([0., 1., 2., 3., 4., 5.])/5, 0))
NWorld = np.array([9, 9, 9, 9])
xp = util.pCoordinates(NWorld)
ind = util.convertpCoordinateToIndex(NWorld, [7, 3, 6, 0])
self.assertTrue(np.allclose(xp[ind] - np.array([7., 3., 6., 0.])/9., 0))
def invert_cq1_mapping(N, mapping):
"""Invert a y = psi(x) CQ1 mapping using the iterative method "A
simple fixed-point approach to invert a deformation field", Chen
et al 2008.
"""
coords = util.pCoordinates(N)
displace = mapping - coords
inv_displace = np.zeros_like(displace)
max_iter = 100
iter = 0
tolerance = 1e-7
error = 1
while iter < max_iter and error > tolerance:
inv_displace_previous = inv_displace
points = np.maximum(0, np.minimum(1.0, coords + inv_displace))
inv_displace = -func.evaluateCQ1(N, displace, points)
iter += 1
error = np.max(np.abs(inv_displace - inv_displace_previous))
return inv_displace + coords
def create(self):
NFine = self.world.NWorldFine
fine = NFine[0]
x = util.pCoordinates(NFine)
num_dots = self.num_dots
epsilon = 0.4
frequency = 2 * np.pi * num_dots
displacement_unscaled = 1. / (frequency) * np.column_stack([
0.5 * (np.sin(0.5 * frequency * x[:, 0]) + 1) *
np.sin(frequency * x[:, 0]), 0.5 *
(np.sin(0.5 * frequency * x[:, 1]) + 1) *
np.sin(frequency * x[:, 1])
])
point_tile_index = np.array(np.minimum(np.floor(num_dots * x),
num_dots - 1),
dtype=int)
tile_scaling = epsilon * 2 * np.random.rand(num_dots, num_dots)**2
point_scaling = tile_scaling[point_tile_index[:, 0],
point_tile_index[:, 1]]
displacement = displacement_unscaled * point_scaling[..., None]
self.psi = discrete_mapping.MappingCQ1(NFine, x + displacement)
def d3plotter(N, s, String='FinescaleSolution', boundary=None, Blues=None, zmax=None, zmin=None, fig=None, ax=None):
if fig is None:
fig = plt.figure(String)
if ax is None:
ax = fig.add_subplot(111, projection='3d')
xp = util.pCoordinates(N)
X = xp[0:,1:].flatten()
Y = xp[0:,:1].flatten()
X = np.unique(X)
Y = np.unique(Y)
X, Y = np.meshgrid(X, Y)
uLodFine = s.reshape(N+1)
# Plot the surface.
if zmin is not None:
surf = ax.plot_surface(X, Y, uLodFine, cmap=cm.coolwarm, vmin=zmin, vmax=zmax)
if boundary is not None:
surf = ax.plot_surface(X, Y, uLodFine, cmap=cm.coolwarm, vmin=boundary[0], vmax=boundary[1])
ax.set_zlim(boundary[0], boundary[1])
ax.zaxis.set_major_locator(LinearLocator(10))
if zmin is not None:
ax.set_zlim(zmin,zmax)
ax.axis('off')
ax.grid(False)
fig.subplots_adjust(left=0.00,bottom=0.00,right=1,top=1,wspace=0.2,hspace=0.2)
def d3sol(N, s, String='FinescaleSolution'):
'''
3d solution
'''
fig = plt.figure(String)
ax = fig.add_subplot(111, projection='3d')
xp = util.pCoordinates(N)
X = xp[0:,1:].flatten()
Y = xp[0:,:1].flatten()
X = np.unique(X)
Y = np.unique(Y)
X, Y = np.meshgrid(X, Y)
uLodFine = s.reshape(N+1)
# Plot the surface.
surf = ax.plot_surface(X, Y, uLodFine, cmap=cm.coolwarm)
ymin, ymax = ax.set_zlim()
ax.set_zticks((ymin,ymax))
ax.set_zlabel('$z$')
ax.set_xlabel('$x$')
ax.set_ylabel('$y$')
ax.zaxis.set_major_locator(LinearLocator(10))
ax.axis('off')
def d3sol(N, s, String='FinescaleSolution'):
'''
3d solution
'''
fig = plt.figure(String)
ax = fig.add_subplot(111, projection='3d')
xp = util.pCoordinates(N)
X = xp[0:, 1:].flatten()
Y = xp[0:, :1].flatten()
X = np.unique(X)
Y = np.unique(Y)
X, Y = np.meshgrid(X, Y)
uLodFine = s.reshape(N + 1)
# Plot the surface.
ymin, ymax = ax.set_zlim([0, 0.021])
ax.set_zticks((ymin, ymax))
ax.zaxis.set_major_formatter(FormatStrFormatter('%.3f'))
ax.set_zlabel('$z$', size=16)
ax.set_xlabel('$x$', size=16)
ax.set_ylabel('$y$', size=16)
# ax.view_init(50, 35)
ax.zaxis.set_major_locator(LinearLocator(4))
ax.tick_params(labelsize=12)
#ax.axis('off')
# Add a color bar which maps values to colors.
surf = ax.plot_surface(X, Y, uLodFine, cmap=cm.hot, vmin=0, vmax=0.021)
def test_stiffnessMatrixForConstantFullA(self):
N = np.array([3, 4, 5], dtype='int64')
AConstant = np.array([[3.0, 0.2, 0.1], [0.2, 2.0, 0.3],
[0.1, 0.3, 1.0]])
aPatch = np.tile(AConstant, [3 * 4 * 5, 1, 1])
ALocTensor = fem.localStiffnessTensorMatrixCoefficient(N)
A = fem.assemblePatchMatrix(N, ALocTensor, aPatch)
# Create the functions x1, x2 and x3
pc = util.pCoordinates(N)
x1 = pc[:, 0]
x2 = pc[:, 1]
x3 = pc[:, 2]
# Check diagonal elements
self.assertTrue(np.isclose(np.dot(x1, A * x1), 3.0))
self.assertTrue(np.isclose(np.dot(x2, A * x2), 2.0))
self.assertTrue(np.isclose(np.dot(x3, A * x3), 1.0))
# Check off-diagonal elements
self.assertTrue(np.isclose(np.dot(x1, A * x2), 0.2))
self.assertTrue(np.isclose(np.dot(x2, A * x1), 0.2))
self.assertTrue(np.isclose(np.dot(x1, A * x3), 0.1))
self.assertTrue(np.isclose(np.dot(x3, A * x1), 0.1))
self.assertTrue(np.isclose(np.dot(x2, A * x3), 0.3))
self.assertTrue(np.isclose(np.dot(x3, A * x2), 0.3))
def evaluateSolution(self, u):
NFine = self.world.NWorldFine
xpFine = util.pCoordinates(NFine)
xpFine_ref = self.psi.inverse_evaluate(xpFine)
return func.evaluateCQ1(NFine, u, xpFine_ref)
def test_boundaryNormalDerivativeMatrixProperties(self):
# BoundaryNormalDerivative bilinear form should map constants to 0
NPatch = np.array([3, 4, 5])
CLocGetter = fem.localBoundaryNormalDerivativeMatrixGetter(NPatch)
C = fem.assemblePatchBoundaryMatrix(NPatch, CLocGetter)
constant = np.ones(np.prod(NPatch + 1))
self.assertTrue(np.isclose(np.linalg.norm(C * constant), 0))
# BoundaryNormalDerivative bilinear form (a=constant) should map planes to 0
NPatch = np.array([3, 4, 5, 6])
CLocGetter = fem.localBoundaryNormalDerivativeMatrixGetter(NPatch)
C = fem.assemblePatchBoundaryMatrix(NPatch, CLocGetter)
p = util.pCoordinates(NPatch)
pSum = np.sum(p, axis=1)
ones = np.ones(np.prod(NPatch + 1))
self.assertTrue(np.isclose(np.linalg.norm(np.dot(ones, C * pSum)), 0))
# A function f with df/dx_k = 1 at x_k = 0 and df/dx_k = 0 at
# x_k = 1 should give 1'*C*f = -d
NPatch = np.array([5, 4, 3, 7])
CLocGetter = fem.localBoundaryNormalDerivativeMatrixGetter(NPatch)
C = fem.assemblePatchBoundaryMatrix(NPatch, CLocGetter)
p = util.pCoordinates(NPatch)
p = np.minimum(p, 0.5)
pSum = np.sum(p, axis=1)
ones = np.ones(np.prod(NPatch + 1))
self.assertTrue(np.isclose(np.dot(ones, C * pSum), -4))
# Same test as above, but with a coefficient a
NPatch = np.array([5, 4, 3, 7])
CLocGetter = fem.localBoundaryNormalDerivativeMatrixGetter(NPatch)
p = util.pCoordinates(NPatch)
p0 = p[:, 0]
pElement = util.pCoordinates(NPatch, NPatch=NPatch - 1)
pElement0 = pElement[:, 0]
aPatch = 1. * (pElement0 < 0.5) + 10. * (pElement0 >= 0.5)
C = fem.assemblePatchBoundaryMatrix(NPatch, CLocGetter, aPatch)
ones = np.ones(np.prod(NPatch + 1))
self.assertTrue(np.isclose(np.dot(ones, C * p0), 10 - 1))
def test_computeElementFaceFlux_2d(self):
NPatchCoarse = np.array([4, 6])
NCoarseElement = np.array([10, 20])
NPatchFine = NPatchCoarse*NCoarseElement
NtFine = np.prod(NPatchFine)
NpFine = np.prod(NPatchFine+1)
aPatch = np.ones(NtFine)
uPatch = np.ones(NpFine)
fluxTF = transport.computeElementFaceFlux(NPatchCoarse, NPatchCoarse, NCoarseElement, aPatch, uPatch)
self.assertTrue(np.all(fluxTF.shape == (24, 4)))
self.assertTrue(np.all(fluxTF == 0))
x = util.pCoordinates(NPatchFine)[:,0]
y = util.pCoordinates(NPatchFine)[:,1]
uPatch = x
xFaceArea = 1./NPatchCoarse[1]
fluxTF = transport.computeElementFaceFlux(NPatchCoarse, NPatchCoarse, NCoarseElement, aPatch, uPatch)
self.assertTrue(np.allclose(fluxTF[:,0], xFaceArea) and np.allclose(fluxTF[:,1], -xFaceArea))
uPatch = x+y
xFaceArea = 1./NPatchCoarse[1]
yFaceArea = 1./NPatchCoarse[0]
fluxTF = transport.computeElementFaceFlux(NPatchCoarse, NPatchCoarse, NCoarseElement, aPatch, uPatch)
self.assertTrue(np.allclose(fluxTF[:,0], xFaceArea) and np.allclose(fluxTF[:,1], -xFaceArea))
self.assertTrue(np.allclose(fluxTF[:,2], yFaceArea) and np.allclose(fluxTF[:,3], -yFaceArea))
aPatch = 10*aPatch
fluxTF = transport.computeElementFaceFlux(NPatchCoarse, NPatchCoarse, NCoarseElement, aPatch, uPatch)
self.assertTrue(np.allclose(fluxTF[:,0], 10*xFaceArea) and np.allclose(fluxTF[:,1], -10*xFaceArea))
self.assertTrue(np.allclose(fluxTF[:,2], 10*yFaceArea) and np.allclose(fluxTF[:,3], -10*yFaceArea))
aPatch = np.ones(NtFine)
NWorldCoarse = np.array(NPatchCoarse)
NWorldCoarse[0] = 10*NWorldCoarse[0]
fluxTF = transport.computeElementFaceFlux(NWorldCoarse, NPatchCoarse, NCoarseElement, aPatch, uPatch)
self.assertTrue(np.allclose(fluxTF[:,0], 10*xFaceArea) and np.allclose(fluxTF[:,1], -10*xFaceArea))
self.assertTrue(np.allclose(fluxTF[:,2], 0.1*yFaceArea) and np.allclose(fluxTF[:,3], -0.1*yFaceArea))
def test_smooth_1d(self):
N = np.array([1000])
x = util.pCoordinates(N)
e = np.exp(1)
mapping = (np.exp(x)-1)/(e-1)
inv_mapping = discrete_mapping.invert_cq1_mapping(N, mapping)
inv_mapping_should_be = np.log((e-1)*x+1)
self.assertTrue(np.allclose(inv_mapping, inv_mapping_should_be, atol=1e-3))
def create(self):
NFine = self.world.NWorldFine
fine = NFine[0]
xpFine = util.pCoordinates(NFine)
forward_mapping = np.stack([xpFine[:, 0], xpFine[:, 1]], axis=1)
xpFine_shaped = xpFine.reshape(fine + 1, fine + 1, 2)
for i in [1, 3]:
middle = int((fine + 1) * (i / 4))
intervall = int((fine + 1) / 8)
left_2 = middle - int(intervall)
right_2 = middle + int(intervall)
left, right = left_2, right_2
# print(fine + 1, left, right)
part_x = xpFine_shaped[left:right, left_2:right_2, 0]
part_y = xpFine_shaped[left:right, left_2:right_2, 1]
left_margin_x = np.min(part_x)
right_margin_x = np.max(part_x)
left_margin_y = np.min(part_y)
right_margin_y = np.max(part_y)
# print(left_margin_x, right_margin_x, left_margin_y, right_margin_y)
epsilon = self.bending_factor / (
right_margin_y - left_margin_y
) # why does this have to be so large???
forward_mapping_partial = np.stack([
xpFine_shaped[left:right, left_2:right_2, 0] + epsilon *
(xpFine_shaped[left:right, left_2:right_2, 0] - left_margin_x)
* (right_margin_x -
xpFine_shaped[left:right, left_2:right_2, 0]) *
(xpFine_shaped[left:right, left_2:right_2, 1] - left_margin_y)
* (right_margin_y -
xpFine_shaped[left:right, left_2:right_2, 1]),
xpFine_shaped[left:right, left_2:right_2, 1]
],
axis=2)
forward_mapping_shaped = forward_mapping.reshape(
fine + 1, fine + 1, 2)
forward_mapping_shaped[left:right,
left_2:right_2, :] = forward_mapping_partial
forward_mapping = forward_mapping_shaped.reshape((fine + 1)**2, 2)
self.psi = discrete_mapping.MappingCQ1(NFine, forward_mapping)
def test_smooth_2d(self):
N = np.array([100, 100])
x = util.pCoordinates(N)
e = np.exp(1)
mapping = (np.exp([x[:,0] + 0.1*x[:,0]*(1-x[:,0])*x[:,1]*(1-x[:,1]),
x[:,1] + 0.1*x[:,1]*(1-x[:,1])*x[:,0]*(1-x[:,0])])-1)/(e-1)
mapping = np.transpose(mapping)
inv_mapping = discrete_mapping.invert_cq1_mapping(N, mapping)
inv_inv_mapping = discrete_mapping.invert_cq1_mapping(N, inv_mapping)
self.assertTrue(np.allclose(mapping, inv_inv_mapping, atol=1e-4))
def create(self):
NFine = self.world.NWorldFine
fine = NFine[0]
xpFine = util.pCoordinates(NFine)
forward_mapping = np.stack([xpFine[:, 0], xpFine[:, 1]], axis=1)
xpFine_shaped = xpFine.reshape(fine + 1, fine + 1, 2)
left = int((fine + 1) * self.area[0])
right = int((fine + 1) * self.area[1])
# TODO: enable other left_2 and right_2
left_2, right_2 = left, right
print('left_right ', left, right)
part_x = xpFine_shaped[left:right, left_2:right_2, 0]
part_y = xpFine_shaped[left:right, left_2:right_2, 1]
left_margin_x = np.min(part_x)
right_margin_x = np.max(part_x)
left_margin_y = np.min(part_y)
right_margin_y = np.max(part_y)
print(left_margin_x, right_margin_x, left_margin_y, right_margin_y)
epsilon = self.bending_factor / (
right_margin_y - left_margin_y
) # why does this have to be so large???
forward_mapping_partial = np.stack([
xpFine_shaped[left:right, left_2:right_2, 0] + epsilon *
(xpFine_shaped[left:right, left_2:right_2, 0] - left_margin_x) *
(right_margin_x - xpFine_shaped[left:right, left_2:right_2, 0]) *
(xpFine_shaped[left:right, left_2:right_2, 1] - left_margin_y) *
(right_margin_y - xpFine_shaped[left:right, left_2:right_2, 1]),
xpFine_shaped[left:right, left_2:right_2, 1]
],
axis=2)
forward_mapping_shaped = forward_mapping.reshape(fine + 1, fine + 1, 2)
forward_mapping_shaped[left:right,
left_2:right_2, :] = forward_mapping_partial
forward_mapping = forward_mapping_shaped.reshape((fine + 1)**2, 2)
self.psi = discrete_mapping.MappingCQ1(NFine, forward_mapping)
def test_boundarypIndexMap(self):
N = np.array([3,4,5])
Np = np.prod(N+1)
shouldBe = np.setdiff1d(np.arange(Np), util.interiorpIndexMap(N))
self.assertTrue(np.all(util.boundarypIndexMapLarge(N) == shouldBe))
boundaryMap = np.array([[True, False],
[True, True],
[True, True]])
shouldBe = np.setdiff1d(np.arange(Np), util.interiorpIndexMap(N))
coords = util.pCoordinates(N)
shouldBe = np.setdiff1d(shouldBe, np.where(np.logical_and(coords[:,0] == 1,
np.logical_and(coords[:,1] != 0,
np.logical_and(coords[:,1] != 1,
np.logical_and(coords[:,2] != 0,
coords[:,2] != 1)))))[0])
self.assertTrue(np.all(util.boundarypIndexMapLarge(N, boundaryMap) == shouldBe))
boundaryMap = np.array([[True, True],
[False, True],
[True, True]])
shouldBe = np.setdiff1d(np.arange(Np), util.interiorpIndexMap(N))
shouldBe = np.setdiff1d(shouldBe, np.where(np.logical_and(coords[:,0] != 0,
np.logical_and(coords[:,0] != 1,
np.logical_and(coords[:,1] == 0,
np.logical_and(coords[:,2] != 0,
coords[:,2] != 1)))))[0])
self.assertTrue(np.all(util.boundarypIndexMapLarge(N, boundaryMap) == shouldBe))
boundaryMap = np.array([[True, True],
[False, False],
[True, True]])
shouldBe = np.setdiff1d(np.arange(Np), util.interiorpIndexMap(N))
shouldBe = np.setdiff1d(shouldBe, np.where(np.logical_and(coords[:,0] != 0,
np.logical_and(coords[:,0] != 1,
np.logical_and(coords[:,1] == 0,
np.logical_and(coords[:,2] != 0,
coords[:,2] != 1)))))[0])
shouldBe = np.setdiff1d(shouldBe, np.where(np.logical_and(coords[:,0] != 0,
np.logical_and(coords[:,0] != 1,
np.logical_and(coords[:,1] == 1,
np.logical_and(coords[:,2] != 0,
coords[:,2] != 1)))))[0])
self.assertTrue(np.all(util.boundarypIndexMapLarge(N, boundaryMap) == shouldBe))
def create(self):
NFine = self.world.NWorldFine
fine = NFine[0]
x = util.pCoordinates(NFine)
x0 = np.array([0.5, 0.5])
r = np.linalg.norm((x - x0), axis=1)
r_min = self.r_min
r_bounded = np.maximum(r, r_min) / r_min
tapering = np.prod(np.sin(np.pi * x), axis=1)
displacement = np.column_stack([
tapering * self.displacement_factor * (r_bounded)**-2,
tapering * self.displacement_factor * (r_bounded)**-2
])
self.psi = discrete_mapping.MappingCQ1(NFine, x + displacement)
def test_stiffnessMatrixForVaryingDiagonalA(self):
N = np.array([3, 4, 5], dtype='int64')
AConstant1 = np.array([[1.0, 0, 0], [0, 2.0, 0], [0, 0, 1.0]])
AConstant2 = np.array([[1.0, 0, 0], [0, 7.0, 0], [0, 0, 1.0]])
aPatchCube = np.tile(AConstant1, [3, 4, 5, 1, 1])
aPatchCube[:, :2, :, :, :] = AConstant2
aPatch = np.reshape(aPatchCube, [3 * 4 * 5, 3, 3])
ALocTensor = fem.localStiffnessTensorMatrixCoefficient(N)
A = fem.assemblePatchMatrix(N, ALocTensor, aPatch)
# Create the functions x1, x2 and x3
pc = util.pCoordinates(N)
x1 = pc[:, 0]
x2 = pc[:, 1]
x3 = pc[:, 2]
self.assertTrue(np.isclose(np.dot(x1, A * x1), 1.0))
self.assertTrue(np.isclose(np.dot(x2, A * x2), 0.5 * (2. + 7.)))
self.assertTrue(np.isclose(np.dot(x3, A * x3), 1.0))
def computeTransformation(self, aFine, f_ref):
assert (len(aFine) == np.prod(self.world.NWorldFine))
assert (len(f_ref) == np.prod(self.world.NWorldFine + 1))
assert (self.psi)
psi = self.psi
NFine = self.world.NWorldFine
xtFine = util.tCoordinates(NFine)
a_trans = np.einsum('tij, t, tkj, t -> tik', psi.Jinv(xtFine), aFine,
psi.Jinv(xtFine), psi.detJ(xtFine))
xpFine = util.pCoordinates(NFine)
xpFine_pert = self.psi.evaluate(xpFine)
f_trans = func.evaluateCQ1(NFine, f_ref, xpFine_pert)
f_trans = np.einsum('t, t -> t', f_trans, psi.detJ(xpFine_pert))
return a_trans, f_trans
def computePerturbation(self, aFine, f_ref):
assert (self.psi)
assert (len(aFine) == np.prod(self.world.NWorldFine))
NFine = self.world.NWorldFine
# Elements
xtFine = util.tCoordinates(NFine)
xtFine_ref = self.psi.inverse_evaluate(xtFine)
xtFine_pert = self.psi.evaluate(xtFine_ref)
# Nodes
xpFine = util.pCoordinates(NFine)
xpFine_ref = self.psi.inverse_evaluate(xpFine)
xpFine_pert = self.psi.evaluate(xpFine_ref)
self.checkInvertible(xpFine_pert, xpFine)
aFine_pert = func.evaluateDQ0(NFine, aFine, xtFine_ref)
# f_pert = func.evaluateCQ1(NFine, f_ref, xpFine_ref)
return aFine_pert, f_ref
def d3solextra(N, s, fig, ax, ymin, ymax):
'''
function for 2d fem example
'''
xp = util.pCoordinates(N)
X = xp[0:, 1:].flatten()
Y = xp[0:, :1].flatten()
X = np.unique(X)
Y = np.unique(Y)
X, Y = np.meshgrid(X, Y)
uLodFine = s.reshape(N + 1)
# Plot the surface.
surf = ax.plot_surface(X, Y, uLodFine, cmap=cm.jet)
ymin, ymax = ax.set_zlim()
ax.set_zlim(ymin, ymax)
ax.set_zlabel('$z$')
ax.set_xlabel('$x$')
ax.set_ylabel('$y$')
ax.zaxis.set_major_locator(LinearLocator(10))
ax.axis('off')
import matplotlib.pyplot as plt from gridlod import util, fem, coef, interp from gridlod.world import World import lod_wave # fine mesh parameters fine = 1024 NFine = np.array([fine]) NpFine = np.prod(NFine + 1) boundaryConditions = np.array([[0, 0]]) world = World(NFine, NFine // NFine, boundaryConditions) NWorldFine = world.NWorldCoarse * world.NCoarseElement # fine grid elements and nodes xt = util.tCoordinates(NFine).flatten() xp = util.pCoordinates(NFine).flatten() # time step parameters tau = 0.1 numTimeSteps = 10 # ms coefficients epsA = 2 ** (-4) epsB = 2 ** (-6) aFine = (2 - np.sin(2 * np.pi * xt / epsA)) ** (-1) bFine = (2 - np.cos(2 * np.pi * xt / epsB)) ** (-1) k_0 = np.inf k_1 = k_0 N = 16
def test_1d(self):
# Example from Peterseim, Variational Multiscale Stabilization and the Exponential Decay of correctors, p. 2
# Two modifications: A with minus and u(here) = 1/4*u(paper).
NFine = np.array([3200])
NpFine = np.prod(NFine + 1)
NList = [10, 20, 40, 80, 160]
epsilon = 1024. / NFine
epsilon = 1. / 320
k = 2
pi = np.pi
xt = util.tCoordinates(NFine).flatten()
xp = util.pCoordinates(NFine).flatten()
#aFine = (2 + np.cos(2*pi*xt/epsilon))**(-1)
aFine = (2 - np.cos(2 * pi * xt / epsilon))**(-1)
uSol = 4 * (xp - xp**2) - 4 * epsilon * (
1 / (4 * pi) * np.sin(2 * pi * xp / epsilon) - 1 /
(2 * pi) * xp * np.sin(2 * pi * xp / epsilon) - epsilon /
(4 * pi**2) * np.cos(2 * pi * xp / epsilon) + epsilon /
(4 * pi**2))
uSol = uSol / 4
previousErrorCoarse = np.inf
previousErrorFine = np.inf
for N in NList:
NWorldCoarse = np.array([N])
NCoarseElement = NFine / NWorldCoarse
boundaryConditions = np.array([[0, 0]])
world = World(NWorldCoarse, NCoarseElement, boundaryConditions)
xpCoarse = util.pCoordinates(NWorldCoarse).flatten()
NpCoarse = np.prod(NWorldCoarse + 1)
IPatchGenerator = lambda i, N: interp.L2ProjectionPatchMatrix(
i, N, NWorldCoarse, NCoarseElement, boundaryConditions)
aCoef = coef.coefficientFine(NWorldCoarse, NCoarseElement, aFine)
pglod = pg.PetrovGalerkinLOD(world, k, IPatchGenerator, 0)
pglod.updateCorrectors(aCoef, clearFineQuantities=False)
KFull = pglod.assembleMsStiffnessMatrix()
MFull = fem.assemblePatchMatrix(NWorldCoarse, world.MLocCoarse)
free = util.interiorpIndexMap(NWorldCoarse)
f = np.ones(NpCoarse)
bFull = MFull * f
KFree = KFull[free][:, free]
bFree = bFull[free]
xFree = sparse.linalg.spsolve(KFree, bFree)
basis = fem.assembleProlongationMatrix(NWorldCoarse,
NCoarseElement)
basisCorrectors = pglod.assembleBasisCorrectors()
modifiedBasis = basis - basisCorrectors
xFull = np.zeros(NpCoarse)
xFull[free] = xFree
uLodCoarse = basis * xFull
uLodFine = modifiedBasis * xFull
AFine = fem.assemblePatchMatrix(NFine, world.ALocFine, aFine)
MFine = fem.assemblePatchMatrix(NFine, world.MLocFine)
newErrorCoarse = np.sqrt(
np.dot(uSol - uLodCoarse, MFine * (uSol - uLodCoarse)))
newErrorFine = np.sqrt(
np.dot(uSol - uLodFine, AFine * (uSol - uLodFine)))
self.assertTrue(newErrorCoarse < previousErrorCoarse)
self.assertTrue(newErrorFine < previousErrorFine)
def computeFunctions():
pc = util.pCoordinates(NFine)
x1 = pc[:,0]
x2 = pc[:,1]
return [x1, 2*x2]
aFine_ref_shaped = CoefClass.SpecificMove(Number=np.arange(0, 10),
steps=4,
Right=1)
aFine_ref = aFine_ref_shaped.flatten()
number_of_channels = len(CoefClass.ShapeRemember)
# Discrete mapping
Nmapping = np.array([int(fine), int(fine)])
size_of_an_element = 1. / fine
walk_with_perturbation = size_of_an_element
channels_position_from_zero = space
channels_end_from_zero = channels_position_from_zero + thick
xpFine = util.pCoordinates(NFine)
xtFine = util.tCoordinates(NFine)
NWorldCoarse = np.array([N, N])
boundaryConditions = np.array([[0, 0], [0, 0]])
NCoarseElement = NFine // NWorldCoarse
world = World(NWorldCoarse, NCoarseElement, boundaryConditions)
every_psi_was_valid = []
k = 3
#I want to know the exact places of the channels
ref_array = aFine_ref_shaped[0]
def create_psi_function():
def computeFunctions():
pc = util.pCoordinates(world.NWorldFine)
x1 = pc[:,0]
x2 = pc[:,1]
return [x1]
def test_pgtransport(self):
NWorldCoarse = np.array([16, 16])
NCoarseElement = np.array([8, 8])
NWorldFine = NWorldCoarse * NCoarseElement
boundaryConditions = np.array([[1, 1], [0, 0]])
d = 2
world = World(NWorldCoarse, NCoarseElement, boundaryConditions)
# Load coefficient
aLogBase = np.loadtxt(
os.path.dirname(os.path.realpath(__file__)) +
'/data/randomfield64x64')
#aBase = np.loadtxt(os.path.dirname(os.path.realpath(__file__)) + '/data/upperness_x.txt')
#aBase = aBase[:60*220]
#aLogBase = np.random.rand(128*128)
aBase = np.exp(3 * aLogBase)
drawCoefficient(NWorldFine, aBase)
plt.title('a')
# Compute coordinates
coordsFine = util.pCoordinates(NWorldFine)
xFine = coordsFine[:, 0]
yFine = coordsFine[:, 1]
# Compute fixed and free dofs
allDofs = np.arange(world.NpFine)
fixed = util.boundarypIndexMap(NWorldFine, boundaryConditions == 0)
free = np.setdiff1d(allDofs, fixed)
# Compute matrices
AFull = fem.assemblePatchMatrix(NWorldFine, world.ALocFine, aBase)
A = AFull[free][:, free]
# Compute rhs
gFine = 1 - yFine
bFull = -AFull * gFine
b = bFull[free]
# Solve fine system
u0Free = sparse.linalg.spsolve(A, b)
u0Full = np.zeros(world.NpFine)
u0Full[free] = u0Free
uFull = u0Full + gFine
## First, compute flux on fine mesh
def computeAvgVelocitiesTF(NFluxElement):
fluxWorld = World(NWorldFine / NFluxElement, NFluxElement,
boundaryConditions)
if True:
avgFluxTF = transport.computeHarmonicMeanFaceFlux(
fluxWorld.NWorldCoarse, fluxWorld.NWorldCoarse,
NFluxElement, aBase, uFull)
avgFluxTF = transport.computeAverageFaceFlux(
fluxWorld.NWorldCoarse, avgFluxTF)
conservativeFluxTF = transport.computeConservativeFlux(
fluxWorld, avgFluxTF)
if False:
avgFluxTF = transport.computeElementFaceFlux(
fluxWorld.NWorldCoarse, fluxWorld.NWorldCoarse,
NFluxElement, aBase, uFull)
avgFluxTF = transport.computeAverageFaceFlux(
fluxWorld.NWorldCoarse, avgFluxTF)
return avgFluxTF, conservativeFluxTF
avgFluxTF, conservativeFluxTF = computeAvgVelocitiesTF(NCoarseElement)
avgFluxtf, conservativeFluxtf = computeAvgVelocitiesTF(
np.ones_like(NCoarseElement))
def fractionalFlow(s):
return s**3
boundarys = np.array([[0, 0], [1, 0]])
sT = np.zeros(world.NtCoarse)
st = np.zeros(world.NtFine)
nTime = 1e5
endTime = 1
dTime = endTime / float(nTime)
volt = np.prod(1. / world.NWorldFine)
volT = np.prod(1. / world.NWorldCoarse)
plt.figure()
h1 = plt.gcf().number
plt.figure()
h2 = plt.gcf().number
plt.figure()
h3 = plt.gcf().number
for timeStep in np.arange(nTime):
def computeElementNetFluxT(NFluxElement, avgFluxTF, sT):
fluxWorld = World(NWorldFine / NFluxElement, NFluxElement,
boundaryConditions)
netFluxT = transport.computeElementNetFlux(
fluxWorld, avgFluxTF, sT, boundarys, fractionalFlow)
return netFluxT
netFluxT = computeElementNetFluxT(NCoarseElement,
conservativeFluxTF, sT)
netFluxt = computeElementNetFluxT(np.ones_like(NCoarseElement),
conservativeFluxtf, st)
sT = sT + dTime / volT * netFluxT
#sT[sT > 1] = 1.
#sT[sT < 0] = 0.
st = st + dTime / volt * netFluxt
#st[st > 1] = 1.
#st[st < 0] = 0.
if timeStep % 1000 == 0 or timeStep == nTime - 1:
plt.figure(h1)
drawSaturation(NWorldCoarse, sT)
plt.title('sT')
plt.gcf().canvas.draw()
plt.figure(h2)
drawSaturation(NWorldFine, st)
plt.title('st')
plt.gcf().canvas.draw()
plt.figure(h3)
stProjected = projectSaturation(NWorldCoarse, NCoarseElement,
st)
drawSaturation(NWorldCoarse, stProjected)
plt.title('st projected')
plt.gcf().canvas.draw()
print np.sqrt(np.mean((stProjected - sT)**2))
plt.pause(0.0001)
plt.show()
def create(self):
NFine = self.world.NWorldFine
fine = NFine[0]
xpFine = util.pCoordinates(NFine)
epsilonT = []
forward_mapping = np.stack([xpFine[:, 0], xpFine[:, 1]], axis=1)
xpFine_shaped = xpFine.reshape(fine + 1, fine + 1, 2)
left, right = 0, fine + 1
for c in range(self.number_of_channels):
count = 0
for i in range(np.size(self.ref_array)):
if self.ref_array[i] == 1:
count += 1
if count == (c + 1) * self.thick:
begin = i + 1 - self.space // 2
end = i + 1 + self.thick + self.space // 2
break
print(begin, end)
left_2, right_2 = begin, end
if c == 3:
epsilon = 25
# elif c == 4:
# epsilon = -25
# elif c % 2 == 0:
# epsilon = 0
else:
epsilon = np.random.uniform(-10, 10)
part_x = xpFine_shaped[left:right, left_2:right_2, 0]
part_y = xpFine_shaped[left:right, left_2:right_2, 1]
left_margin_x = np.min(part_x)
right_margin_x = np.max(part_x)
left_margin_y = np.min(part_y)
right_margin_y = np.max(part_y)
print(left_margin_x, right_margin_x, left_margin_y, right_margin_y)
forward_mapping_partial = np.stack([
xpFine_shaped[left:right, left_2:right_2, 0] + epsilon *
(xpFine_shaped[left:right, left_2:right_2, 0] - left_margin_x)
* (right_margin_x -
xpFine_shaped[left:right, left_2:right_2, 0]) *
(xpFine_shaped[left:right, left_2:right_2, 1] - left_margin_y)
* (right_margin_y -
xpFine_shaped[left:right, left_2:right_2, 1]),
xpFine_shaped[left:right, left_2:right_2, 1]
],
axis=2)
forward_mapping_shaped = forward_mapping.reshape(
fine + 1, fine + 1, 2)
forward_mapping_shaped[left:right,
left_2:right_2, :] = forward_mapping_partial
epsilonT.append(epsilon)
forward_mapping = forward_mapping_shaped.reshape((fine + 1)**2, 2)
print('Those are the results of the shift epsilon', epsilonT)
self.psi = discrete_mapping.MappingCQ1(NFine, forward_mapping)
def create(self):
NFine = self.world.NWorldFine
fine = NFine[0]
xpFine = util.pCoordinates(NFine)
Nmapping = np.array([int(fine), int(fine)])
size_of_an_element = 1. / fine
print('the size of a fine element is {}'.format(size_of_an_element))
walk_with_perturbation = size_of_an_element
epsilonT = []
cq1 = np.zeros((int(fine) + 1, int(fine) + 1))
random.seed(20)
cs = np.random.randint(0, 2, self.number_of_channels)
cs = [c * random.sample([-1, 1], 1)[0] for c in cs]
## or manually
cs[2] = 0
cs[3] = -1
cs[4] = 0
cs[5] = 0
print(cs)
last_value = 0
for i, c in enumerate(cs):
platform = self.space // 2 + 2 * self.thick
begin = platform // 2 + i * (self.space + self.thick)
end = begin + self.space - platform + self.thick
epsilon = c * walk_with_perturbation
epsilonT.append(epsilon)
walk = epsilon - last_value
constant_length = platform + self.thick
increasing_length = end - begin
for i in range(increasing_length):
cq1[:, begin +
i] = last_value + (i + 1) / increasing_length * walk
for i in range(constant_length):
cq1[:, begin + increasing_length + i] = epsilon
last_value = epsilon
# ending
begin += self.space + self.thick
end = begin + self.space - platform + self.thick
epsilon = 0
walk = epsilon - last_value
increasing_length = end - begin
for i in range(increasing_length):
cq1[:, begin + i] = last_value + (i + 1) / increasing_length * walk
if self.plot_mapping:
plt.plot(np.arange(0, fine + 1),
cq1[self.space, :],
label='$id(x) - \psi(x)$')
plt.title('Domain mapping')
plt.legend()
plt.show()
print('These are the results of the shift epsilon', epsilonT)
cq1 = cq1.flatten()
alpha = 1.
for_mapping = np.stack(
(xpFine[:, 0] + alpha * func.evaluateCQ1(Nmapping, cq1, xpFine),
xpFine[:, 1]),
axis=1)
self.psi = discrete_mapping.MappingCQ1(NFine, for_mapping)
#two examples of the offline coeffs
Nepsilon = np.array([64, 64])
NFine = np.array([256, 256])
NCoarse = np.array([32, 32])
k = 2
alpha = 0.1
beta = 1.
incl_bl = np.array([0.25, 0.25])
incl_tr = np.array([0.75, 0.75])
NCoarseElement = NFine // NCoarse
world = World(NCoarse, NCoarseElement, None)
middle = world.NWorldCoarse[1] // 2 * world.NWorldCoarse[
0] + world.NWorldCoarse[0] // 2
patch = lod_periodic.PatchPeriodic(world, k, middle)
xpFine = util.pCoordinates(world.NWorldCoarse, patch.iPatchWorldCoarse,
patch.NPatchCoarse)
aRefList_rand = build_coefficient.build_checkerboardbasis(
patch.NPatchCoarse, Nepsilon // NCoarse, world.NCoarseElement, alpha, beta)
fig = plt.figure()
for ii in range(4):
ax = fig.add_subplot(2, 2, ii + 1)
apertGrid = aRefList_rand[-1 + ii].reshape(patch.NPatchFine, order='C')
im = ax.imshow(apertGrid,
origin='lower_left',
extent=(xpFine[:, 0].min(), xpFine[:, 0].max(),
xpFine[:, 1].min(), xpFine[:, 1].max()),
cmap='Greys')
plt.show()
def create(self):
NFine = self.world.NWorldFine
fine = NFine[0]
xpFine = util.pCoordinates(NFine)
number_of_perturbed_channels = 4
now = 0
count = 0
for i in range(np.size(self.ref_array)):
if self.ref_array[i] == 1:
count += 1
if count == 8 * self.thick: # at the 8ths shape (which is the last dot in one line, the cq starts)
begin = i + 1
break
count = 0
for i in range(np.size(self.ref_array)):
if self.ref_array[i] == 1:
count += 1
if count == 13 * self.thick - 3: # it ends after the last channel
end = i
break
# Discrete mapping
Nmapping = np.array([int(fine), int(fine)])
cq1 = np.zeros((int(fine) + 1, int(fine) + 1))
# I only want to perturb on the fine mesh.
size_of_an_element = 1. / fine
walk_with_perturbation = size_of_an_element
channels_position_from_zero = self.space
channels_end_from_zero = channels_position_from_zero + self.thick
# The next only have the purpose to make the psi invertible.
increasing_length = (end - begin) // (number_of_perturbed_channels +
1) - self.thick - 2
constant_length = (end - begin) - increasing_length * 2
maximum_walk = (increasing_length - 6) * walk_with_perturbation
walk_with_perturbation = maximum_walk
for i in range(increasing_length):
cq1[:, begin + 1 +
i] = (i + 1) / increasing_length * walk_with_perturbation
cq1[:, begin + increasing_length + i +
constant_length] = walk_with_perturbation - (
i + 1) / increasing_length * walk_with_perturbation
for i in range(constant_length):
cq1[:, begin + increasing_length + i] = walk_with_perturbation
# Check what purtubation I have
if self.plot_mapping:
plt.figure('DomainMapping')
plt.plot(np.arange(0, fine + 1),
cq1[self.space, :],
label='$id(x) - \psi(x)$')
plt.title('Domain mapping')
plt.legend()
cq1 = cq1.flatten()
xpFine = util.pCoordinates(NFine)
alpha = 1.
for_mapping = np.stack(
(xpFine[:, 0] + alpha * func.evaluateCQ1(Nmapping, cq1, xpFine),
xpFine[:, 1]),
axis=1)
self.psi = discrete_mapping.MappingCQ1(NFine, for_mapping)
