def test_rectangle():
points, cells = meshzoo.rectangle(nx=11, ny=11, zigzag=False)
assert len(points) == 121
assert _near_equal(numpy.sum(points, axis=0), [60.5, 60.5, 0.0])
assert len(cells) == 200
points, cells = meshzoo.rectangle(nx=11, ny=11, zigzag=True)
assert len(points) == 121
assert _near_equal(numpy.sum(points, axis=0), [60.5, 60.5, 0.0])
assert len(cells) == 200
points, cells = meshzoo.rectangle(nx=2, ny=2, zigzag=True)
assert len(points) == 4
assert _near_equal(numpy.sum(points, axis=0), [2.0, 2.0, 0.0])
assert len(cells) == 2
points, cells = meshzoo.rectangle(nx=3, ny=2, zigzag=False)
assert len(points) == 6
assert _near_equal(numpy.sum(points, axis=0), [3.0, 3.0, 0.0])
assert len(cells) == 4
assert set(cells[0]) == set([0, 1, 4])
assert set(cells[2]) == set([0, 3, 4])
points, cells = meshzoo.rectangle(nx=3, ny=2, zigzag=True)
assert len(points) == 6
assert _near_equal(numpy.sum(points, axis=0), [3.0, 3.0, 0.0])
assert len(cells) == 4
assert set(cells[0]) == set([0, 1, 4])
assert set(cells[2]) == set([0, 3, 4])
return
def test_rectangle():
points, cells = meshzoo.rectangle(nx=11, ny=11, variant="up")
assert len(points) == 121
assert _near_equal(numpy.sum(points, axis=0), [60.5, 60.5])
assert len(cells) == 200
points, cells = meshzoo.rectangle(nx=11, ny=11, variant="zigzag")
assert len(points) == 121
assert _near_equal(numpy.sum(points, axis=0), [60.5, 60.5])
assert len(cells) == 200
points, cells = meshzoo.rectangle(nx=2, ny=2, variant="zigzag")
assert len(points) == 4
assert _near_equal(numpy.sum(points, axis=0), [2.0, 2.0])
assert len(cells) == 2
points, cells = meshzoo.rectangle(nx=3, ny=2, variant="up")
assert len(points) == 6
assert _near_equal(numpy.sum(points, axis=0), [3.0, 3.0])
assert len(cells) == 4
assert set(cells[0]) == {0, 1, 4}
assert set(cells[2]) == {0, 3, 4}
points, cells = meshzoo.rectangle(nx=3, ny=2, variant="zigzag")
assert len(points) == 6
assert _near_equal(numpy.sum(points, axis=0), [3.0, 3.0])
assert len(cells) == 4
assert set(cells[0]) == {0, 1, 4}
assert set(cells[2]) == {0, 3, 4}
def test_rectangle():
points, cells = meshzoo.rectangle(nx=11, ny=11, zigzag=False)
assert len(points) == 121
assert _near_equal(numpy.sum(points, axis=0), [60.5, 60.5, 0.0])
assert len(cells) == 200
points, cells = meshzoo.rectangle(nx=11, ny=11, zigzag=True)
assert len(points) == 121
assert _near_equal(numpy.sum(points, axis=0), [60.5, 60.5, 0.0])
assert len(cells) == 200
points, cells = meshzoo.rectangle(nx=2, ny=2, zigzag=True)
assert len(points) == 4
assert _near_equal(numpy.sum(points, axis=0), [2.0, 2.0, 0.0])
assert len(cells) == 2
points, cells = meshzoo.rectangle(nx=3, ny=2, zigzag=False)
assert len(points) == 6
assert _near_equal(numpy.sum(points, axis=0), [3.0, 3.0, 0.0])
assert len(cells) == 4
assert set(cells[0]) == set([0, 1, 4])
assert set(cells[2]) == set([0, 3, 4])
points, cells = meshzoo.rectangle(nx=3, ny=2, zigzag=True)
assert len(points) == 6
assert _near_equal(numpy.sum(points, axis=0), [3.0, 3.0, 0.0])
assert len(cells) == 4
assert set(cells[0]) == set([0, 1, 4])
assert set(cells[2]) == set([0, 3, 4])
return
def test():
class EnergyEdgeKernel(object):
def __init__(self):
self.subdomains = [None]
return
def eval(self, mesh, cell_mask):
edge_ce_ratio = mesh.ce_ratios[..., cell_mask]
beta = 1.0
return numpy.array(
[
[edge_ce_ratio, -edge_ce_ratio * numpy.exp(1j * beta)],
[-edge_ce_ratio * numpy.exp(-1j * beta), edge_ce_ratio],
]
)
vertices, cells = meshzoo.rectangle(0.0, 2.0, 0.0, 1.0, 101, 51)
mesh = meshplex.MeshTri(vertices, cells)
matrix = pyfvm.get_fvm_matrix(mesh, [EnergyEdgeKernel()], [], [], [])
rhs = mesh.control_volumes.copy()
sa = pyamg.smoothed_aggregation_solver(matrix, smooth="energy")
u = sa.solve(rhs, tol=1e-10)
# Cannot write complex data ot VTU; split real and imaginary parts first.
# <http://stackoverflow.com/a/38902227/353337>
mesh.write("out.vtk", point_data={"u": u.view("(2,)float")})
return
def test():
class Bratu:
def apply(self, u):
return integrate(lambda x: -n_dot_grad(u(x)), dS) - integrate(
lambda x: 2.0 * exp(u(x)), dV)
def dirichlet(self, u):
return [(u, Boundary())]
vertices, cells = meshzoo.rectangle(0.0, 2.0, 0.0, 1.0, 101, 51)
mesh = meshplex.MeshTri(vertices, cells)
f, jac_u = pyfvm.discretize(Bratu(), mesh)
def jacobian_solver(u0, rhs):
from scipy.sparse import linalg
jac = jac_u.get_linear_operator(u0)
return linalg.spsolve(jac, rhs)
u0 = numpy.zeros(len(vertices))
u = pyfvm.newton(lambda u: f.eval(u), jacobian_solver, u0)
# import scipy.optimize
# u = scipy.optimize.newton_krylov(f_eval, u0)
mesh.write("out.vtk", point_data={"u": u})
return
def plot_tree_2d(n,
*args,
res=100,
colorbar=True,
cmap="RdBu_r",
clim=None,
**kwargs):
import dufte
import meshzoo
from matplotlib import pyplot as plt
plt.style.use(dufte.style)
points, cells = meshzoo.rectangle(-1.0, 1.0, -1.0, 1.0, res, res)
evaluator = Eval(points.T, *args, **kwargs)
plt.set_cmap(cmap)
plt.gca().set_aspect("equal")
plt.axis("off")
for k, values in enumerate(itertools.islice(evaluator, n + 1)):
for r, z in enumerate(values):
offset = [2.8 * (r - k / 2), -2.6 * k]
pts = points + offset
plt.tripcolor(pts[:, 0], pts[:, 1], cells, z, shading="flat")
plt.clim(clim)
# rectangle outlines
corners = numpy.array([[-1, 1, 1, -1, -1], [-1, -1, 1, 1, -1]])
corners = (corners.T + offset).T
plt.plot(corners[0], corners[1], "-k")
if colorbar:
plt.colorbar()
def test_jacobian():
from test_ginzburg_landau import GinzburgLandau
a = 10.0
n = 10
points, cells = meshzoo.rectangle(-a / 2, a / 2, -a / 2, a / 2, n, n)
mesh = meshplex.MeshTri(points, cells)
gl = GinzburgLandau(mesh)
glr = GinzburgLandauReal(mesh)
n = points.shape[0]
numpy.random.seed(123)
for _ in range(10):
psi = numpy.random.rand(n) + 1j * numpy.random.rand(n)
mu = numpy.random.rand(1)[0]
jac0 = gl.jacobian(psi, mu)
jac1 = glr.jacobian(to_real(psi), mu)
for _ in range(10):
phi = numpy.random.rand(n) + 1j * numpy.random.rand(n)
out0 = (jac0 * phi) * mesh.control_volumes
out1 = to_complex(jac1 * to_real(phi))
assert numpy.all(numpy.abs(out0 - out1) < 1.0e-12)
def test():
class Bratu(object):
def apply(self, u):
return integrate(lambda x: -n_dot_grad(u(x)), dS) - integrate(
lambda x: 2.0 * exp(u(x)), dV
)
def dirichlet(self, u):
return [(u, Boundary())]
vertices, cells = meshzoo.rectangle(0.0, 2.0, 0.0, 1.0, 101, 51)
mesh = meshplex.MeshTri(vertices, cells)
f, jac_u = pyfvm.discretize(Bratu(), mesh)
def jacobian_solver(u0, rhs):
from scipy.sparse import linalg
jac = jac_u.get_linear_operator(u0)
return linalg.spsolve(jac, rhs)
u0 = numpy.zeros(len(vertices))
u = pyfvm.newton(lambda u: f.eval(u), jacobian_solver, u0)
# import scipy.optimize
# u = scipy.optimize.newton_krylov(f_eval, u0)
mesh.write("out.vtk", point_data={"u": u})
return
def test():
class D1(Subdomain):
def is_inside(self, x):
return x[1] < 0.5
is_boundary_only = True
class Poisson(object):
def apply(self, u):
return (
integrate(lambda x: -n_dot_grad(u(x)), dS)
+ integrate(lambda x: 3.0, dGamma)
- integrate(lambda x: 1.0, dV)
)
def dirichlet(self, u):
return [(u, D1())]
vertices, cells = meshzoo.rectangle(0.0, 1.0, 0.0, 1.0, 51, 51)
mesh = meshplex.MeshTri(vertices, cells)
matrix, rhs = pyfvm.discretize_linear(Poisson(), mesh)
u = linalg.spsolve(matrix, rhs)
mesh.write("out.vtk", point_data={"u": u})
return
def test():
class EnergyEdgeKernel:
def __init__(self):
self.subdomains = [None]
return
def eval(self, mesh, cell_mask):
edge_ce_ratio = mesh.ce_ratios[..., cell_mask]
beta = 1.0
return numpy.array([
[edge_ce_ratio, -edge_ce_ratio * numpy.exp(1j * beta)],
[-edge_ce_ratio * numpy.exp(-1j * beta), edge_ce_ratio],
])
vertices, cells = meshzoo.rectangle(0.0, 2.0, 0.0, 1.0, 101, 51)
mesh = meshplex.MeshTri(vertices, cells)
matrix = pyfvm.get_fvm_matrix(mesh, [EnergyEdgeKernel()], [], [], [])
rhs = mesh.control_volumes.copy()
sa = pyamg.smoothed_aggregation_solver(matrix, smooth="energy")
u = sa.solve(rhs, tol=1e-10)
# Cannot write complex data ot VTU; split real and imaginary parts first.
# <http://stackoverflow.com/a/38902227/353337>
mesh.write("out.vtk", point_data={"u": u.view("(2,)float")})
return
def test_2d(solver, write_file=False):
n = 200
np.random.seed(123)
x0 = np.random.rand(n, 2) - 0.5
# y0 = np.ones(n)
# y0 = x0[:, 0]
# y0 = x0[:, 0]**2
# y0 = np.cos(np.pi*x0.T[0])
# y0 = np.cos(np.pi*x0.T[0]) * np.cos(np.pi*x0.T[1])
y0 = np.cos(np.pi * np.sqrt(x0.T[0]**2 + x0.T[1]**2))
import meshzoo
points, cells = meshzoo.rectangle(-1.0, 1.0, -1.0, 1.0, 32, 32)
# import pygmsh
# geom = pygmsh.built_in.Geometry()
# geom.add_circle([0.0, 0.0, 0.0], 1.0, 0.1)
# points, cells, _, _, _ = pygmsh.generate_mesh(geom)
# cells = cells['triangle']
u = smoothfit.fit(x0, y0, points, cells, lmbda=1.0e-5, solver=solver)
# ref = 4.411_214_155_799_310_5
# val = assemble(u * u * dx)
# assert abs(val - ref) < 1.0e-10 * ref
if write_file:
from dolfin import XDMFFile
xdmf = XDMFFile("temp.xdmf")
xdmf.write(u)
def test():
class D1(Subdomain):
def is_inside(self, x):
return x[1] < 0.5
is_boundary_only = True
class Poisson:
def apply(self, u):
return (integrate(lambda x: -n_dot_grad(u(x)), dS) +
integrate(lambda x: 3.0, dGamma) -
integrate(lambda x: 1.0, dV))
def dirichlet(self, u):
return [(u, D1())]
vertices, cells = meshzoo.rectangle(0.0, 1.0, 0.0, 1.0, 51, 51)
mesh = meshplex.MeshTri(vertices, cells)
matrix, rhs = pyfvm.discretize_linear(Poisson(), mesh)
u = linalg.spsolve(matrix, rhs)
mesh.write("out.vtk", point_data={"u": u})
return
def get_mesh(self, k):
n = 2**(k + 1)
vertices, cells = meshzoo.rectangle(0.0,
1.0,
0.0,
1.0,
n + 1,
n + 1,
zigzag=True)
return meshplex.MeshTri(vertices, cells)
def __init__(self):
points, cells = meshzoo.rectangle(0.0, 1.0, 0.0, 1.0, 30, 30)
self.mesh = meshplex.MeshTri(points, cells)
# This matrix self.A is negative semidefinite
self.A, _ = pyfvm.discretize_linear(Poisson(), self.mesh)
tol = 1.0e-12
self.idx_left = numpy.where(self.mesh.node_coords[:, 0] < tol)[0]
self.idx_right = numpy.where(self.mesh.node_coords[:, 0] > 1.0 - tol)[0]
self.idx_bottom = numpy.where(self.mesh.node_coords[:, 1] < tol)[0]
self.idx_top = numpy.where(self.mesh.node_coords[:, 1] > 1.0 - tol)[0]
def test_ginzburg_landau(max_steps=5, n=20):
a = 10.0
points, cells = meshzoo.rectangle(-a / 2, a / 2, -a / 2, a / 2, n, n)
mesh = meshplex.MeshTri(points, cells)
problem = GinzburgLandau(mesh)
n = problem.mesh.control_volumes.shape[0]
u0 = numpy.ones(n, dtype=complex)
mu0 = 0.0
mu_list = []
filename = "sol.xdmf"
with meshio.xdmf.TimeSeriesWriter(filename) as writer:
writer.write_points_cells(problem.mesh.node_coords,
{"triangle": problem.mesh.cells["nodes"]})
def callback(k, mu, sol):
mu_list.append(mu)
# Store the solution
psi = numpy.array([numpy.real(sol), numpy.imag(sol)]).T
writer.write_data(k, point_data={"psi": psi})
with open("data.yml", "w") as fh:
yaml.dump(
{
"filename": filename,
"mu": [float(m) for m in mu_list]
}, fh)
# pacopy.natural(
# problem,
# u0,
# mu0,
# callback,
# max_steps=1000,
# lambda_stepsize0=1.0e-2,
# newton_max_steps=5,
# newton_tol=1.0e-10,
# )
pacopy.euler_newton(
problem,
u0,
mu0,
callback,
max_steps=max_steps,
stepsize0=1.0e-2,
stepsize_max=1.0,
newton_tol=1.0e-10,
)
def __init__(self):
a = 24.0
points, cells = meshzoo.rectangle(-a / 2, a / 2, -a / 2, a / 2, 50, 50)
self.mesh = meshplex.MeshTri(points, cells)
x, y, z = self.mesh.node_coords.T
assert numpy.all(numpy.abs(z) < 1.0e-15)
self.omega = 0.2
self.V = 0.5 * self.omega**2 * (x**2 + y**2)
# For the preconditioner
assert numpy.all(self.V >= 0)
self.A, _ = pyfvm.discretize_linear(Poisson(), self.mesh)
def __init__(self):
a = 20.0
points, cells = meshzoo.rectangle(-a / 2, a / 2, -a / 2, a / 2, 40, 40)
self.mesh = meshplex.MeshTri(points, cells)
self.A, _ = pyfvm.get_fvm_matrix(self.mesh, [Poisson()])
# k = 1
# ka = 4.5
# DD = 8
# nu = np.sqrt(1 / DD)
# kbcrit = np.sqrt(1 + ka * nu)
self.a = 4.0
self.d1 = 1.0
self.d2 = 2.0
def test_f_i_psi():
"""Assert that <f(psi), i psi> == 0.
"""
points, cells = meshzoo.rectangle(-5.0, 5.0, -5.0, 5.0, 30, 30)
mesh = meshplex.MeshTri(points, cells)
problem = GinzburgLandau(mesh)
n = problem.mesh.control_volumes.shape[0]
numpy.random.seed(0)
for _ in range(100):
mu = numpy.random.rand(1)
psi = numpy.random.rand(n) + 1j * numpy.random.rand(n)
f = problem.f(psi, mu)
assert abs(problem.inner(1j * psi, f)) < 1.0e-13
def test_self_adjointness():
a = 10.0
n = 10
points, cells = meshzoo.rectangle(-a / 2, a / 2, -a / 2, a / 2, n, n)
mesh = meshplex.MeshTri(points, cells)
problem = GinzburgLandauReal(mesh)
n = problem.mesh.control_volumes.shape[0]
psi = numpy.random.rand(2 * n)
jac = problem.jacobian(psi, 0.1)
for _ in range(1000):
u = numpy.random.rand(2 * n)
v = numpy.random.rand(2 * n)
a0 = problem.inner(u, jac * v)
a1 = problem.inner(jac * u, v)
assert abs(a0 - a1) < 1.0e-12
def test_io_2d():
vertices, cells = meshzoo.rectangle(0.0, 1.0, 0.0, 1.0, 2, 2)
mesh = meshplex.MeshTri(vertices, cells)
# mesh = meshplex.read('pacman.vtu')
assert mesh.num_delaunay_violations() == 0
# mesh.show(show_axes=False, boundary_edge_color="g")
# mesh.show_vertex(0)
_, fname = tempfile.mkstemp(suffix=".vtk")
mesh.write(fname)
mesh2 = meshplex.read(fname)
for k in range(len(mesh.cells["nodes"])):
assert tuple(mesh.cells["nodes"][k]) == tuple(mesh2.cells["nodes"][k])
def test():
class Singular:
def apply(self, u):
return (integrate(lambda x: -1.0e-2 * n_dot_grad(u(x)), dS) +
integrate(u, dV) - integrate(lambda x: 1.0, dV))
def dirichlet(self, u):
return [(u, Boundary())]
vertices, cells = meshzoo.rectangle(0.0, 1.0, 0.0, 1.0, 51, 51)
mesh = meshplex.MeshTri(vertices, cells)
matrix, rhs = pyfvm.discretize_linear(Singular(), mesh)
u = linalg.spsolve(matrix, rhs)
mesh.write("out.vtk", point_data={"u": u})
return
def test_io_2d():
vertices, cells = meshzoo.rectangle(0.0, 1.0, 0.0, 1.0, 2, 2, zigzag=True)
mesh = voropy.mesh_tri.MeshTri(vertices, cells)
# mesh, _, _, _ = voropy.read('pacman.vtu')
assert mesh.num_delaunay_violations() == 0
mesh.show(show_axes=False, boundary_edge_color='g')
mesh.show_vertex(0)
_, fname = tempfile.mkstemp(suffix='.msh')
mesh.write(fname)
mesh2, _, _, _ = voropy.read(fname)
for k in range(len(mesh.cells['nodes'])):
assert tuple(mesh.cells['nodes'][k]) == tuple(mesh2.cells['nodes'][k])
return
def generate_2D_mesh(H, W):
_, faces = meshzoo.rectangle(xmin=-1.,
xmax=1.,
ymin=-1.,
ymax=1.,
nx=W,
ny=H,
zigzag=True)
x = torch.arange(0, W, 1).float().cuda()
y = torch.arange(0, H, 1).float().cuda()
xx = x.repeat(H, 1)
yy = y.view(H, 1).repeat(1, W)
grid = torch.stack([xx, yy], dim=0)
return grid, faces
def test():
class DC(object):
def apply(self, u):
a = numpy.array([2, 1, 0])
return integrate(lambda x: -n_dot_grad(u(x)) + n_dot(a) * u(x),
dS) - integrate(lambda x: 1.0, dV)
def dirichlet(self, u):
return [(u, Boundary())]
vertices, cells = meshzoo.rectangle(0.0, 1.0, 0.0, 1.0, 51, 51)
mesh = meshplex.MeshTri(vertices, cells)
matrix, rhs = pyfvm.discretize_linear(DC(), mesh)
u = linalg.spsolve(matrix, rhs)
mesh.write("out.vtk", point_data={"u": u})
return
def test_df_dlmbda():
points, cells = meshzoo.rectangle(-5.0, 5.0, -5.0, 5.0, 30, 30)
mesh = meshplex.MeshTri(points, cells)
problem = GinzburgLandau(mesh)
n = problem.mesh.control_volumes.shape[0]
numpy.random.seed(0)
for _ in range(100):
mu = numpy.random.rand(1)
psi = numpy.random.rand(n) + 1j * numpy.random.rand(n)
out = problem.df_dlmbda(psi, mu)
# finite difference
eps = 1.0e-5
diff = (problem.f(psi, mu + eps) - problem.f(psi, mu - eps)) / (2 *
eps)
nrm = numpy.dot((out - diff).conj(), out - diff).real
assert nrm < 1.0e-12
def test():
class DC(object):
def apply(self, u):
a = numpy.array([2, 1, 0])
return integrate(
lambda x: -n_dot_grad(u(x)) + n_dot(a) * u(x), dS
) - integrate(lambda x: 1.0, dV)
def dirichlet(self, u):
return [(u, Boundary())]
vertices, cells = meshzoo.rectangle(0.0, 1.0, 0.0, 1.0, 51, 51)
mesh = meshplex.MeshTri(vertices, cells)
matrix, rhs = pyfvm.discretize_linear(DC(), mesh)
u = linalg.spsolve(matrix, rhs)
mesh.write("out.vtk", point_data={"u": u})
return
def test_readme_images():
from dolfin import (
MeshEditor, Mesh, FunctionSpace, assemble, EigenMatrix, dot, grad, dx,
TrialFunction, TestFunction
)
import meshzoo
points, cells = meshzoo.rectangle(-1.0, 1.0, -1.0, 1.0, 20, 20)
# Convert points, cells to dolfin mesh
editor = MeshEditor()
mesh = Mesh()
# topological and geometrical dimension 2
editor.open(mesh, 'triangle', 2, 2, 1)
editor.init_vertices(len(points))
editor.init_cells(len(cells))
for k, point in enumerate(points):
editor.add_vertex(k, point[:2])
for k, cell in enumerate(cells.astype(numpy.uintp)):
editor.add_cell(k, cell)
editor.close()
V = FunctionSpace(mesh, 'CG', 1)
u = TrialFunction(V)
v = TestFunction(V)
L = EigenMatrix()
assemble(dot(grad(u), grad(v)) * dx, tensor=L)
A = L.sparray()
# M = A.T.dot(A)
M = A
with tempfile.TemporaryDirectory() as temp_dir:
filepath = os.path.join(temp_dir, 'test.png')
betterspy.write_png(filepath, M, border_width=2)
# betterspy.write_png(
# 'ATA.png', M, border_width=2,
# colormap='viridis'
# )
return
def test_df_dlmbda():
from test_ginzburg_landau import GinzburgLandau
a = 10.0
n = 10
points, cells = meshzoo.rectangle(-a / 2, a / 2, -a / 2, a / 2, n, n)
mesh = meshplex.MeshTri(points, cells)
gl = GinzburgLandau(mesh)
glr = GinzburgLandauReal(mesh)
n = points.shape[0]
numpy.random.seed(123)
for _ in range(10):
psi = numpy.random.rand(n) + 1j * numpy.random.rand(n)
mu = numpy.random.rand(1)[0]
out = gl.df_dlmbda(psi, mu) * mesh.control_volumes
out2 = glr.df_dlmbda(to_real(psi), mu)
assert numpy.all(numpy.abs(out - to_complex(out2)) < 1.0e-12)
def test():
class Singular(object):
def apply(self, u):
return (
integrate(lambda x: -1.0e-2 * n_dot_grad(u(x)), dS)
+ integrate(u, dV)
- integrate(lambda x: 1.0, dV)
)
def dirichlet(self, u):
return [(u, Boundary())]
vertices, cells = meshzoo.rectangle(0.0, 1.0, 0.0, 1.0, 51, 51)
mesh = meshplex.MeshTri(vertices, cells)
matrix, rhs = pyfvm.discretize_linear(Singular(), mesh)
u = linalg.spsolve(matrix, rhs)
mesh.write("out.vtk", point_data={"u": u})
return
def test_2d(solver):
n = 200
numpy.random.seed(123)
x0 = numpy.random.rand(n, 2) - 0.5
# y0 = numpy.ones(n)
# y0 = x0[:, 0]
# y0 = x0[:, 0]**2
# y0 = numpy.cos(numpy.pi*x0.T[0])
# y0 = numpy.cos(numpy.pi*x0.T[0]) * numpy.cos(numpy.pi*x0.T[1])
y0 = numpy.cos(numpy.pi * numpy.sqrt(x0.T[0]**2 + x0.T[1]**2))
import meshzoo
points, cells = meshzoo.rectangle(-1.0, 1.0, -1.0, 1.0, 20, 20)
# import pygmsh
# geom = pygmsh.built_in.Geometry()
# geom.add_circle([0.0, 0.0, 0.0], 1.0, 0.1)
# points, cells, _, _, _ = pygmsh.generate_mesh(geom)
# cells = cells['triangle']
u = smoothfit.fit2d(x0,
y0,
points,
cells,
eps=1.0e-0,
verbose=True,
solver=solver)
ref = 2.277266345700909
val = assemble(u * u * dx)
assert abs(val - ref) < 1.0e-10 * ref
# from dolfin import XDMFFile
# xdmf = XDMFFile('temp.xdmf')
# xdmf.write(u)
return
def generate_mesh():
"""Generates a fairly large mesh.
"""
points, cells = meshzoo.rectangle(nx=300, ny=300)
return meshio.Mesh(points, {"triangle": cells})
def test_center():
points, cells = meshzoo.rectangle(nx=11, ny=9, variant="center")
meshzoo.show2d(points, cells)
assert len(points) == 99
assert len(cells) == 160
def __init__(self,
delta,
n,
ufunc=None,
coarseMesh=None,
dim=2,
outdim=1,
ansatz="CG",
boundaryConditionType="Dirichlet",
is_constructAdjaciencyGraph=True,
zigzag=False):
### TEST 27.07.2020
#self.Zeta = np.arange(12, dtype=np.int).reshape(4, 3)
#####
self.n = n
self.dim = dim
self.delta = delta
self.sqdelta = delta**2
# Construct Meshgrid -------------------------------------------------------------
if self.dim == 2:
self.h = 12 / n / 10
points, cells = meshzoo.rectangle(xmin=-self.delta,
xmax=1.0 + self.delta,
ymin=-self.delta,
ymax=1.0 + self.delta,
nx=n + 1,
ny=n + 1,
variant="up")
self.vertices = np.array(points[:, :2])
# Set up Delaunay Triangulation --------------------------------------------------
# Construct and Sort Vertices ----------------------------------------------------
self.vertexLabels = np.array(
[self.get_vertexLabel(v) for v in self.vertices])
self.argsort_labels = np.argsort(-self.vertexLabels)
self.vertices = self.vertices[self.argsort_labels]
self.vertexLabels = self.vertexLabels[self.argsort_labels]
# Get Number of Vertices in Omega ------------------------------------------------
self.omega = np.where(self.vertexLabels > 0)[0]
self.nV = self.vertices.shape[0]
self.nV_Omega = self.omega.shape[0]
# Set up Delaunay Triangulation --------------------------------------------------
self.elements = np.array(cells, dtype=np.int)
self.remapElements()
# Get Triangle Labels ------------------------------------------------------------
self.nE = self.elements.shape[0]
self.elementLabels = np.zeros(self.nE, dtype=np.int)
for k, E in enumerate(self.elements):
self.elementLabels[k] = self.get_elementLabel(E)
self.nE_Omega = np.sum(self.elementLabels > 0)
order = np.argsort(-self.elementLabels)
self.elements = self.elements[order]
self.elementLabels = self.elementLabels[order]
# Read adjaciency list
if is_constructAdjaciencyGraph:
self.neighbours = constructAdjaciencyGraph(self.elements)
self.nNeighbours = self.neighbours.shape[1]
else:
self.neighbours = None
# Set Matrix Dimensions ----------------------------------------------------------
# In case of Neumann conditions we assemble a Maitrx over Omega + OmegaI.
# In order to achieve that we "redefine" Omega := Omega + OmegaI
# This is rather a shortcut to make things work quickly.
self.is_NeumannBoundary = False
if boundaryConditionType == "Neumann":
self.nE_Omega = self.nE
self.nV_Omega = self.nV
self.is_NeumannBoundary = True
self.outdim = outdim
if ansatz == "DG":
self.K = self.nE * 3 * self.outdim
self.K_Omega = self.nE_Omega * 3 * self.outdim
self.is_DiscontinuousGalerkin = True
else:
self.K = self.nV * self.outdim
self.K_Omega = self.nV_Omega * self.outdim
self.is_DiscontinuousGalerkin = False
# Set Mesh Data if provided ------------------------------------------------------
self.u_exact = None
self.ud = None
self.diam = self.h * np.sqrt(2)
if ufunc is not None:
if hasattr(ufunc, '__call__'):
self.set_u_exact(ufunc)
if coarseMesh is not None:
if coarseMesh.is_DiscontinuousGalerkin:
coarseDGverts = np.zeros(
((coarseMesh.K // coarseMesh.outdim), coarseMesh.dim))
for i, E in enumerate(coarseMesh.elements):
for ii, vdx in enumerate(E):
vert = coarseMesh.vertices[vdx]
coarseDGverts[3 * i + ii] = vert
self.interpolator = LinearNDInterpolator(
coarseDGverts, coarseMesh.ud)
ud_aux = self.interpolator(self.vertices)
self.ud = np.zeros(((self.K // self.outdim), self.outdim))
for i, E in enumerate(self.elements):
for ii, vdx in enumerate(E):
self.ud[3 * i + ii] = ud_aux[vdx]
pass
else:
self.interpolator = LinearNDInterpolator(
coarseMesh.vertices, coarseMesh.ud)
self.ud = self.interpolator(self.vertices)
def test():
mu = 5.0e-2
V = -1.0
g = 1.0
class Energy(object):
"""Specification of the kinetic energy operator.
"""
def __init__(self):
self.magnetic_field = mu * numpy.array([0.0, 0.0, 1.0])
self.subdomains = [None]
return
def eval(self, mesh, cell_mask):
nec = mesh.idx_hierarchy[..., cell_mask]
X = mesh.node_coords[nec]
edge_midpoint = 0.5 * (X[0] + X[1])
edge = X[1] - X[0]
edge_ce_ratio = mesh.ce_ratios[..., cell_mask]
# project the magnetic potential on the edge at the midpoint
magnetic_potential = 0.5 * numpy.cross(self.magnetic_field, edge_midpoint)
# The dot product <magnetic_potential, edge>, executed for many
# points at once; cf. <http://stackoverflow.com/a/26168677/353337>.
beta = numpy.einsum("...k,...k->...", magnetic_potential, edge)
return numpy.array(
[
[edge_ce_ratio, -edge_ce_ratio * numpy.exp(-1j * beta)],
[-edge_ce_ratio * numpy.exp(1j * beta), edge_ce_ratio],
]
)
vertices, cells = meshzoo.rectangle(-5.0, 5.0, -5.0, 5.0, 51, 51)
mesh = meshplex.MeshTri(vertices, cells)
keo = pyfvm.get_fvm_matrix(mesh, edge_kernels=[Energy()])
def f(psi):
cv = mesh.control_volumes
return keo * psi + cv * psi * (V + g * abs(psi) ** 2)
def jacobian(psi):
def _apply_jacobian(phi):
cv = mesh.control_volumes
y = keo * phi + cv * alpha * phi + cv * gPsi0Squared * phi.conj()
return y
alpha = V + g * 2.0 * (psi.real ** 2 + psi.imag ** 2)
gPsi0Squared = g * psi ** 2
num_unknowns = len(mesh.node_coords)
return pykry.LinearOperator(
(num_unknowns, num_unknowns),
complex,
dot=_apply_jacobian,
dot_adj=_apply_jacobian,
)
def jacobian_solver(psi0, rhs):
jac = jacobian(psi0)
out = pykry.gmres(
A=jac,
b=rhs,
inner_product=lambda a, b: numpy.dot(a.T.conj(), b).real,
maxiter=1000,
tol=1.0e-10,
)
return out.xk
u0 = numpy.ones(len(vertices), dtype=complex)
u = pyfvm.newton(f, jacobian_solver, u0)
mesh.write("out.vtk", point_data={"u": u.view("(2,)float")})
return
def test_continuation(max_steps=5):
a = 10.0
n = 20
points, cells = meshzoo.rectangle(-a / 2, a / 2, -a / 2, a / 2, n, n)
mesh = meshplex.MeshTri(points, cells)
problem = GinzburgLandauReal(mesh)
num_unknowns = 2 * problem.mesh.control_volumes.shape[0]
u0 = numpy.ones(num_unknowns)
u0[1::2] = 0.0
mu0 = 0.0
# plt.ion()
# fig = plt.figure()
# ax = fig.add_subplot(111)
# plt.axis("square")
# plt.xlabel("$\\mu$")
# plt.ylabel("$||\\psi||_2$")
# plt.grid()
# b_list = []
# values_list = []
# line1, = ax.plot(b_list, values_list, "-", color="#1f77f4")
mu_list = []
filename = "sol.xdmf"
with meshio.xdmf.TimeSeriesWriter(filename) as writer:
writer.write_points_cells(problem.mesh.node_coords,
{"triangle": problem.mesh.cells["nodes"]})
def callback(k, mu, sol):
mu_list.append(mu)
# Store the solution
psi = numpy.array([sol[0::2], sol[1::2]]).T
writer.write_data(k, point_data={"psi": psi})
with open("data.yml", "w") as fh:
yaml.dump(
{
"filename": filename,
"mu": [float(m) for m in mu_list]
}, fh)
# pacopy.natural(
# problem,
# u0,
# b0,
# callback,
# max_steps=1,
# lambda_stepsize0=1.0e-2,
# newton_max_steps=5,
# newton_tol=1.0e-10,
# )
pacopy.euler_newton(
problem,
u0,
mu0,
callback,
max_steps=max_steps,
stepsize0=1.0e-2,
stepsize_max=1.0,
newton_tol=1.0e-10,
)
def get_mesh(self, k):
n = 2 ** (k + 1)
vertices, cells = meshzoo.rectangle(
0.0, 1.0, 0.0, 1.0, n + 1, n + 1, zigzag=True
)
return meshplex.MeshTri(vertices, cells)
def __init__(self, delta, n,
ufunc=None,
coarseMesh=None,
dim=2, outdim=1,
n_start=12,
ansatz="CG",
is_constructAdjaciencyGraph=True,
variant="up"):
### TEST 27.07.2020
#self.Zeta = np.arange(12, dtype=np.int).reshape(4, 3)
#####
deltaK = int(np.round(delta * 10))
if not deltaK:
raise ValueError("Delta has to be of the form delta = deltaK/10. for deltaK in N.")
n_start = 10 + 2*deltaK
self.n = n
self.dim = dim
self.delta = delta
self.sqdelta = delta**2
# Construct Meshgrid -------------------------------------------------------------
if self.dim == 2:
self.h = n_start/n/10.
points, cells = meshzoo.rectangle(
xmin=-self.delta, xmax=1.0+self.delta,
ymin=-self.delta, ymax=1.0+self.delta,
nx=n+1, ny=n+1,
variant=variant
)
self.vertices = np.array(points[:, :2])
# Set up Delaunay Triangulation --------------------------------------------------
# Construct and Sort Vertices ----------------------------------------------------
self.vertexLabels = np.array([self.get_vertexLabel(v) for v in self.vertices])
# Get Number of Vertices in Omega ------------------------------------------------
self.nV = self.vertices.shape[0]
self.nV_Omega = np.sum(self.vertexLabels > 0)
# Set up Delaunay Triangulation --------------------------------------------------
self.elements = np.array(cells, dtype=np.int)
# Get Triangle Labels ------------------------------------------------------------
self.nE = self.elements.shape[0]
self.elementLabels = np.zeros(self.nE, dtype=np.int)
for k, E in enumerate(self.elements):
self.elementLabels[k] = self.get_elementLabel(E)
self.nE_Omega = np.sum(self.elementLabels > 0)
# Read adjaciency list -----------------------------------------------------------
if is_constructAdjaciencyGraph:
self.neighbours = constructAdjaciencyGraph(self.elements)
self.nNeighbours = self.neighbours.shape[1]
else:
self.neighbours = None
# Set Matrix Dimensions ----------------------------------------------------------
self.is_NeumannBoundary = False
# This option is deprecated. It is sufficient to simply not
self.outdim = outdim
if ansatz == "DG":
self.K = self.nE*(self.dim+1)*self.outdim
self.K_Omega = self.nE_Omega*(self.dim+1)*self.outdim
self.nodeLabels = np.repeat(self.elementLabels, (self.dim+1)*self.outdim)
self.is_DiscontinuousGalerkin = True
else:
self.K = self.nV*self.outdim
self.K_Omega = self.nV_Omega*self.outdim
self.nodeLabels = np.repeat(self.vertexLabels, self.outdim)
self.is_DiscontinuousGalerkin = False
# Set Mesh Data if provided ------------------------------------------------------
self.u_exact = None
self.ud = None
self.diam = self.h*np.sqrt(2)
if ufunc is not None:
if hasattr(ufunc, '__call__'):
self.set_u_exact(ufunc)
if coarseMesh is not None:
if coarseMesh.is_DiscontinuousGalerkin:
coarseDGverts = np.zeros(((coarseMesh.K // coarseMesh.outdim), coarseMesh.dim))
for i, E in enumerate(coarseMesh.elements):
for ii, vdx in enumerate(E):
vert = coarseMesh.vertices[vdx]
coarseDGverts[(self.dim+1)*i + ii] = vert
self.interpolator = LinearNDInterpolator(coarseDGverts, coarseMesh.ud)
ud_aux = self.interpolator(self.vertices)
self.ud = np.zeros(((self.K // self.outdim), self.outdim))
for i, E in enumerate(self.elements):
for ii, vdx in enumerate(E):
self.ud[(self.dim + 1)*i + ii] = ud_aux[vdx]
pass
else:
self.interpolator = LinearNDInterpolator(coarseMesh.vertices, coarseMesh.ud)
self.ud = self.interpolator(self.vertices)
