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 poisson(self, mesh, alpha, beta):
from scipy.sparse import linalg
# Define the problem
class Poisson(LinearFvmProblem):
def apply(self, u):
return integrate(lambda x: - n_dot_grad(u(x)), dS) \
- integrate(lambda x: 1.0, dV)
def dirichlet(self, u):
return [(u, 'boundary')]
linear_system = pyfvm.discretize(Poisson(), mesh)
x = linalg.spsolve(linear_system.matrix, linear_system.rhs)
k0 = -1
for k, coord in enumerate(mesh.node_coords):
# print(coord - [0.5, 0.5, 0.0])
if numpy.linalg.norm(coord - [0.5, 0.5, 0.0]) < 1.0e-5:
k0 = k
break
self.assertNotEqual(k0, -1)
self.assertAlmostEqual(x[k0], alpha, delta=1.0e-7)
x_dot_x = numpy.dot(x, mesh.control_volumes * x)
self.assertAlmostEqual(x_dot_x, beta, delta=1.0e-7)
return
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_boundaries(self):
import meshzoo
from scipy.sparse import linalg
class Gamma0(Subdomain):
def is_inside(self, x): return x[1] < 0.5
is_boundary_only = True
class Gamma1(Subdomain):
def is_inside(self, x): return x[1] >= 0.5
is_boundary_only = True
# Define the problem
class Poisson(LinearFvmProblem):
def apply(self, u):
return integrate(lambda x: -n_dot_grad(u(x)), dS) \
- integrate(lambda x: 1.0, dV)
def dirichlet(self, u):
return [
(lambda x: u(x) - 0.0, Gamma0()),
(lambda x: u(x) - 1.0, Gamma1())
]
# Create mesh using meshzoo
vertices, cells = meshzoo.rectangle.create_mesh(
0.0, 1.0, 0.0, 1.0,
21, 21,
zigzag=True
)
mesh = pyfvm.meshTri.meshTri(vertices, cells)
linear_system = pyfvm.discretize(Poisson(), mesh)
x = linalg.spsolve(linear_system.matrix, linear_system.rhs)
import meshio
meshio.write('test.vtu', mesh.node_coords, {'triangle':
mesh.cells['nodes']}, point_data={'x': x})
k0 = -1
for k, coord in enumerate(mesh.node_coords):
# print(coord - [0.5, 0.5, 0.0])
if numpy.linalg.norm(coord - [0.5, 0.5, 0.0]) < 1.0e-5:
k0 = k
break
self.assertNotEqual(k0, -1)
self.assertAlmostEqual(x[k0], 0.59455184740329481, delta=1.0e-7)
x_dot_x = numpy.dot(x, mesh.control_volumes * x)
self.assertAlmostEqual(x_dot_x, 0.42881926935620163, delta=1.0e-7)
return
def solver(mesh):
f, jacobian = pyfvm.discretize(problem, mesh)
def jacobian_solver(u0, rhs):
from scipy.sparse import linalg
jac = jacobian.get_linear_operator(u0)
return linalg.spsolve(jac, rhs)
u0 = numpy.zeros(len(mesh.node_coords))
u = pyfvm.newton(f.eval, jacobian_solver, u0, verbose=False)
return u
def solver(mesh):
f, jacobian = pyfvm.discretize(problem, mesh)
def jacobian_solver(u0, rhs):
from scipy.sparse import linalg
jac = jacobian.get_linear_operator(u0)
return linalg.spsolve(jac, rhs)
u0 = numpy.zeros(len(mesh.node_coords))
u = pyfvm.newton(f.eval, jacobian_solver, u0, verbose=False)
return u
def test_neumann(self):
import meshzoo
from scipy.sparse import linalg
class D1(Subdomain):
def is_inside(self, x): return x[1] < 0.5
is_boundary_only = True
# Define the problem
class Poisson(LinearFvmProblem):
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())]
# Create mesh using meshzoo
vertices, cells = meshzoo.rectangle.create_mesh(
0.0, 1.0, 0.0, 1.0,
21, 21,
zigzag=True
)
mesh = pyfvm.meshTri.meshTri(vertices, cells)
linear_system = pyfvm.discretize(Poisson(), mesh)
x = linalg.spsolve(linear_system.matrix, linear_system.rhs)
k0 = -1
for k, coord in enumerate(mesh.node_coords):
# print(coord - [0.5, 0.5, 0.0])
if numpy.linalg.norm(coord - [0.5, 0.5, 0.0]) < 1.0e-5:
k0 = k
break
self.assertNotEqual(k0, -1)
self.assertAlmostEqual(x[k0], -1.3249459366260112, delta=1.0e-7)
x_dot_x = numpy.dot(x, mesh.control_volumes * x)
self.assertAlmostEqual(x_dot_x, 3.1844205150779601, delta=1.0e-7)
return
def test_singular_perturbation(self):
import meshzoo
from scipy.sparse import linalg
# Define the problem
class Poisson(LinearFvmProblem):
def apply(self, u):
return integrate(lambda x: - 1.0e-2 * n_dot_grad(u(x)), dS) \
+ integrate(lambda x: u(x), dV) \
- integrate(lambda x: 1.0, dV)
def dirichlet(self, u):
return [(u, 'boundary')]
# Create mesh using meshzoo
vertices, cells = meshzoo.rectangle.create_mesh(
0.0, 1.0, 0.0, 1.0,
21, 21,
zigzag=True
)
mesh = pyfvm.meshTri.meshTri(vertices, cells)
linear_system = pyfvm.discretize(Poisson(), mesh)
x = linalg.spsolve(linear_system.matrix, linear_system.rhs)
k0 = -1
for k, coord in enumerate(mesh.node_coords):
# print(coord - [0.5, 0.5, 0.0])
if numpy.linalg.norm(coord - [0.5, 0.5, 0.0]) < 1.0e-5:
k0 = k
break
self.assertNotEqual(k0, -1)
self.assertAlmostEqual(x[k0], 0.97335485230869123, delta=1.0e-7)
x_dot_x = numpy.dot(x, mesh.control_volumes * x)
self.assertAlmostEqual(x_dot_x, 0.49724636865618776, delta=1.0e-7)
return
def test_convection(self):
import meshzoo
from scipy.sparse import linalg
# Define the problem
class Poisson(LinearFvmProblem):
def apply(self, u):
a = sympy.Matrix([2, 1, 0])
return integrate(lambda x: - n_dot_grad(u(x)) + dot(a.T, n) * u(x), dS) - \
integrate(lambda x: 1.0, dV)
def dirichlet(self, u):
return [(u, 'boundary')]
# Create mesh using meshzoo
vertices, cells = meshzoo.rectangle.create_mesh(
0.0, 1.0, 0.0, 1.0,
21, 21,
zigzag=True
)
mesh = pyfvm.meshTri.meshTri(vertices, cells)
linear_system = pyfvm.discretize(Poisson(), mesh)
x = linalg.spsolve(linear_system.matrix, linear_system.rhs)
k0 = -1
for k, coord in enumerate(mesh.node_coords):
if numpy.linalg.norm(coord - [0.5, 0.5, 0.0]) < 1.0e-5:
k0 = k
break
self.assertNotEqual(k0, -1)
self.assertAlmostEqual(x[k0], 0.07041709172659899, delta=1.0e-7)
x_dot_x = numpy.dot(x, mesh.control_volumes * x)
self.assertAlmostEqual(x_dot_x, 0.0016076431631658172, delta=1.0e-7)
return
# 25, 25, 25
# )
# mesh = pyfvm.meshTetra.meshTetra(vertices, cells)
# vertices, cells = meshzoo.rectangle.create_mesh(
# 0.0, 2.0,
# 0.0, 1.0,
# 401, 201,
# zigzag=True
# )
# mesh = pyfvm.meshTri.meshTri(vertices, cells)
import mshr
import dolfin
h = 2.5e-2
# cell_size = 2 * pi / num_boundary_points
c = mshr.Circle(dolfin.Point(0., 0., 0.), 1, int(2*pi / h))
# cell_size = 2 * bounding_box_radius / res
m = mshr.generate_mesh(c, 2.0 / h)
coords = m.coordinates()
coords = numpy.c_[coords, numpy.zeros(len(coords))]
mesh = pyfvm.meshTri.meshTri(coords, m.cells())
linear_system = pyfvm.discretize(Poisson(), mesh)
ml = pyamg.ruge_stuben_solver(linear_system.matrix)
x = ml.solve(linear_system.rhs, tol=1e-10)
# from scipy.sparse import linalg
# x = linalg.spsolve(linear_system.matrix, linear_system.rhs)
mesh.write('out.vtu', point_data={'x': x})
def perform_convergence_tests(
problem, exact_sol, get_mesh, rng, verbose=False
):
n = len(rng)
H = numpy.empty(n)
error_norm_1 = numpy.empty(n)
order_1 = numpy.empty(n-1)
error_norm_inf = numpy.empty(n)
order_inf = numpy.empty(n-1)
if verbose:
print(79 * '-')
print('k' + 5*' ' + 'num verts' + 4*' ' + 'max edge length' + 4*' ' +
'||error||_1' + 8*' ' + '||error||_inf'
)
print(38*' ' + '(order)' + 12*' ' + '(order)')
print(79 * '-')
# Add "zero" to all entities. This later gets translated into
# np.zeros with the appropriate length, making sure that scalar
# terms in the lambda expression correctly return np.arrays.
zero = sympy.Symbol('zero')
x = sympy.DeferredVector('x')
# See <http://docs.sympy.org/dev/modules/utilities/lambdify.html>.
array2array = [{'ImmutableMatrix': numpy.array}, 'numpy']
exact_eval = sympy.lambdify((x, zero), exact_sol(x), modules=array2array)
for k in rng:
mesh = get_mesh(k)
H[k] = max(mesh.edge_lengths)
linear_system = pyfvm.discretize(problem, mesh)
# x = linalg.spsolve(linear_system.matrix, linear_system.rhs)
ml = pyamg.ruge_stuben_solver(linear_system.matrix)
x = ml.solve(linear_system.rhs, tol=1e-10)
zero = numpy.zeros(len(mesh.node_coords))
error = x - exact_eval(mesh.node_coords.T, zero)
# import meshio
# meshio.write(
# 'sol%d.vtu' % k,
# mesh.node_coords, {'triangle': mesh.cells['nodes']},
# point_data={'x': x, 'error': error},
# )
error_norm_1[k] = numpy.sum(abs(mesh.control_volumes * error))
error_norm_inf[k] = max(abs(error))
# numerical orders of convergence
if k > 0:
order_1[k-1] = \
numpy.log(error_norm_1[k-1] / error_norm_1[k]) / \
numpy.log(H[k-1] / H[k])
order_inf[k-1] = \
numpy.log(error_norm_inf[k-1] / error_norm_inf[k]) / \
numpy.log(H[k-1] / H[k])
if verbose:
print
print((38*' ' + '%0.5f' + 12*' ' + '%0.5f') %
(order_1[k-1], order_inf[k-1])
)
print
if verbose:
num_nodes = len(mesh.control_volumes)
print('%2d %5.3e %0.10e %0.10e %0.10e' %
(k, num_nodes, H[k], error_norm_1[k], error_norm_inf[k])
)
return H, error_norm_1, error_norm_inf, order_1, order_inf
import pyfvm
from pyfvm.form_language import *
import meshzoo
from scipy.sparse import linalg
class DC(LinearFvmProblem):
def apply(self, u):
a = sympy.Matrix([2, 1, 0])
return \
integrate(lambda x: -n_dot_grad(u(x)) + dot(a.T, n) * u(x), dS) - \
integrate(lambda x: 1.0, dV)
def dirichlet(self, u):
return [(u, 'boundary')]
vertices, cells = meshzoo.rectangle.create_mesh(
0.0, 1.0,
0.0, 1.0,
51, 51,
zigzag=True
)
mesh = pyfvm.meshTri.meshTri(vertices, cells)
linear_system = pyfvm.discretize(DC(), mesh)
x = linalg.spsolve(linear_system.matrix, linear_system.rhs)
mesh.write('out.vtu', point_data={'x': x})
#
import meshzoo
import pyfvm
from pyfvm.form_language import *
from scipy.sparse import linalg
class Singular(LinearFvmProblem):
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')]
# Create mesh using meshzoo
vertices, cells = meshzoo.rectangle.create_mesh(
0.0, 1.0,
0.0, 1.0,
51, 51,
zigzag=True
)
mesh = pyfvm.meshTri.meshTri(vertices, cells)
linear_system = pyfvm.discretize(Singular(), mesh)
x = linalg.spsolve(linear_system.matrix, linear_system.rhs)
mesh.write('out.vtu', point_data={'x': x})