vx = Explicit(f=lambda x: -x[:, 1], dim=2)
vy = Explicit(f=lambda x: x[:, 0], dim=2)
uB = Explicit(f=lambda x: np.cos(2 * np.pi * (x[:, 1] + 0.25)), dim=2)
problem = [
Form(epsilon, trial=ux, test=ux),
Form(epsilon, trial=uy, test=uy),
Form(vx, trial=ux, test=u),
Form(vy, trial=uy, test=u),
Form(0, test=u)
]
print('assembling', end=' ')
assembler = Assembler(problem, mesh)
assembler.assemble()
print('done')
print('solving', end=' ')
A = assembler.get_matrix()
b = np.zeros(u.n_dofs())
system = LS(u, A=A, b=b)
system.add_dirichlet_constraint('B', uB)
system.add_dirichlet_constraint('perimeter', 0)
system.solve_system()
ua = system.get_solution()
print('done')
plot = Plot()
plot.wire(ua)
#
# Problems
#
problems = [[a_qe,L], [a_one]]
#
# Assembly
#
assembler = Assembler(problems, mesh)
assembler.assemble()
# =============================================================================
# Linear system for generating observations
# =============================================================================
system = LinearSystem(assembler,0)
f = system.get_rhs()
#
# Incorporate constraints
#
system.add_dirichlet_constraint('left',0)
system.add_dirichlet_constraint('right',0)
#
# Compute model output
#
system.solve_system()
ue = system.get_solution(as_function=True)
ue_x = ue.derivative((1,0))
def test08_1d_sampled_rhs(self):
#
# Mesh
#
mesh = Mesh1D(resolution=(1, ))
mesh.mark_region('left', lambda x: np.abs(x) < 1e-9, on_boundary=True)
mesh.mark_region('right',
lambda x: np.abs(1 - x) < 1e-9,
on_boundary=True)
#
# Elements
#
Q3 = QuadFE(1, 'Q3')
dofhandler = DofHandler(mesh, Q3)
dofhandler.distribute_dofs()
#
# Basis
#
v = Basis(dofhandler, 'u')
vx = Basis(dofhandler, 'ux')
#
# Define sampled right hand side and exact solution
#
xv = dofhandler.get_dof_vertices()
n_points = dofhandler.n_dofs()
n_samples = 6
a = np.arange(n_samples)
f = lambda x, a: a * x
u = lambda x, a: a / 6 * (x - x**3) + x
fdata = np.zeros((n_points, n_samples))
udata = np.zeros((n_points, n_samples))
for i in range(n_samples):
fdata[:, i] = f(xv, a[i]).ravel()
udata[:, i] = u(xv, a[i]).ravel()
# Define sampled function
fn = Nodal(data=fdata, basis=v)
ue = Nodal(data=udata, basis=v)
#
# Forms
#
one = Constant(1)
a = Form(Kernel(one), test=vx, trial=vx)
L = Form(Kernel(fn), test=v)
problem = [a, L]
#
# Assembler
#
assembler = Assembler(problem, mesh)
assembler.assemble()
A = assembler.get_matrix()
b = assembler.get_vector()
#
# Linear System
#
system = LinearSystem(v, A=A, b=b)
# Set constraints
system.add_dirichlet_constraint('left', 0)
system.add_dirichlet_constraint('right', 1)
#system.set_constraint_relation()
#system.incorporate_constraints()
# Solve and resolve constraints
system.solve_system()
#system.resolve_constraints()
# Extract finite element solution
ua = system.get_solution(as_function=True)
# Check that the solution is close
print(ue.data()[:, [0]])
print(ua.data())
self.assertTrue(np.allclose(ue.data()[:, [0]], ua.data()))
def test09_1d_inverse(self):
"""
Compute the inverse of a matrix and apply it to a vector/matrix.
"""
#
# Mesh
#
mesh = Mesh1D(resolution=(1, ))
mesh.mark_region('left', lambda x: np.abs(x) < 1e-9, on_boundary=True)
mesh.mark_region('right',
lambda x: np.abs(1 - x) < 1e-9,
on_boundary=True)
#
# Elements
#
Q3 = QuadFE(1, 'Q3')
dofhandler = DofHandler(mesh, Q3)
dofhandler.distribute_dofs()
#
# Basis
#
u = Basis(dofhandler, 'u')
ux = Basis(dofhandler, 'ux')
#
# Define sampled right hand side and exact solution
#
xv = dofhandler.get_dof_vertices()
n_points = dofhandler.n_dofs()
n_samples = 6
a = np.arange(n_samples)
ffn = lambda x, a: a * x
ufn = lambda x, a: a / 6 * (x - x**3) + x
fdata = np.zeros((n_points, n_samples))
udata = np.zeros((n_points, n_samples))
for i in range(n_samples):
fdata[:, i] = ffn(xv, a[i]).ravel()
udata[:, i] = ufn(xv, a[i]).ravel()
# Define sampled function
fn = Nodal(data=fdata, basis=u)
ue = Nodal(data=udata, basis=u)
#
# Forms
#
one = Constant(1)
a = Form(Kernel(one), test=ux, trial=ux)
L = Form(Kernel(fn), test=u)
problem = [[a], [L]]
#
# Assembler
#
assembler = Assembler(problem, mesh)
assembler.assemble()
A = assembler.get_matrix()
b = assembler.get_vector(i_problem=1)
#
# Linear System
#
system = LinearSystem(u, A=A)
# Set constraints
system.add_dirichlet_constraint('left', 0)
system.add_dirichlet_constraint('right', 1)
system.solve_system(b)
# Extract finite element solution
ua = system.get_solution(as_function=True)
system2 = LinearSystem(u, A=A, b=b)
# Set constraints
system2.add_dirichlet_constraint('left', 0)
system2.add_dirichlet_constraint('right', 1)
system2.solve_system()
u2 = system2.get_solution(as_function=True)
# Check that the solution is close
self.assertTrue(np.allclose(ue.data()[:, 0], ua.data()[:, 0]))
self.assertTrue(np.allclose(ue.data()[:, [0]], u2.data()))
def test01_1d_dirichlet_linear(self):
"""
Solve one dimensional boundary value problem with dirichlet
conditions on left and right
"""
#
# Define mesh
#
mesh = Mesh1D(resolution=(10, ))
for etype in ['Q1', 'Q2', 'Q3']:
element = QuadFE(1, etype)
dofhandler = DofHandler(mesh, element)
dofhandler.distribute_dofs()
phi = Basis(dofhandler)
#
# Exact solution
#
ue = Nodal(f=lambda x: x, basis=phi)
#
# Define Basis functions
#
u = Basis(dofhandler, 'u')
ux = Basis(dofhandler, 'ux')
#
# Define bilinear form
#
one = Constant(1)
zero = Constant(0)
a = Form(kernel=Kernel(one), trial=ux, test=ux)
L = Form(kernel=Kernel(zero), test=u)
problem = [a, L]
#
# Assemble
#
assembler = Assembler(problem, mesh)
assembler.assemble()
#
# Form linear system
#
A = assembler.get_matrix()
b = assembler.get_vector()
system = LinearSystem(u, A=A, b=b)
#
# Dirichlet conditions
#
# Boundary functions
bm_left = lambda x: np.abs(x) < 1e-9
bm_rght = lambda x: np.abs(x - 1) < 1e-9
# Mark boundary regions
mesh.mark_region('left', bm_left, on_boundary=True)
mesh.mark_region('right', bm_rght, on_boundary=True)
# Add Dirichlet constraints
system.add_dirichlet_constraint('left', ue)
system.add_dirichlet_constraint('right', ue)
#
# Solve system
#
#system.solve_system()
system.solve_system()
#
# Get solution
#
#ua = system.get_solution(as_function=True)
uaa = system.get_solution(as_function=True)
#uaa = uaa.data().ravel()
# Compare with exact solution
#self.assertTrue(np.allclose(ua.data(), ue.data()))
self.assertTrue(np.allclose(uaa.data(), ue.data()))
def test05_2d_dirichlet(self):
"""
Two dimensional Dirichlet problem with hanging nodes
"""
#
# Define mesh
#
mesh = QuadMesh(resolution=(1, 2))
mesh.cells.get_child(1).mark(1)
mesh.cells.refine(refinement_flag=1)
mesh.cells.refine()
#
# Mark left and right boundaries
#
bm_left = lambda x, dummy: np.abs(x) < 1e-9
bm_right = lambda x, dummy: np.abs(1 - x) < 1e-9
mesh.mark_region('left', bm_left, entity_type='half_edge')
mesh.mark_region('right', bm_right, entity_type='half_edge')
for etype in ['Q1', 'Q2', 'Q3']:
#
# Element
#
element = QuadFE(2, etype)
dofhandler = DofHandler(mesh, element)
dofhandler.distribute_dofs()
#
# Basis
#
u = Basis(dofhandler, 'u')
ux = Basis(dofhandler, 'ux')
uy = Basis(dofhandler, 'uy')
#
# Construct forms
#
ue = Nodal(f=lambda x: x[:, 0], basis=u)
ax = Form(kernel=Kernel(Constant(1)), trial=ux, test=ux)
ay = Form(kernel=Kernel(Constant(1)), trial=uy, test=uy)
L = Form(kernel=Kernel(Constant(0)), test=u)
problem = [ax, ay, L]
#
# Assemble
#
assembler = Assembler(problem, mesh)
assembler.assemble()
#
# Get system matrices
#
A = assembler.get_matrix()
b = assembler.get_vector()
#
# Linear System
#
system = LinearSystem(u, A=A, b=b)
#
# Constraints
#
# Add dirichlet conditions
system.add_dirichlet_constraint('left', ue)
system.add_dirichlet_constraint('right', ue)
#
# Solve
#
system.solve_system()
#system.resolve_constraints()
#
# Check solution
#
ua = system.get_solution(as_function=True)
self.assertTrue(np.allclose(ua.data(), ue.data()))
def test04_1d_periodic(self):
#
# Dirichlet Problem on a Periodic Mesh
#
# Define mesh, element
mesh = Mesh1D(resolution=(100, ), periodic=True)
element = QuadFE(1, 'Q3')
dofhandler = DofHandler(mesh, element)
dofhandler.distribute_dofs()
# Basis functions
u = Basis(dofhandler, 'u')
ux = Basis(dofhandler, 'ux')
# Exact solution
ue = Nodal(f=lambda x: np.sin(2 * np.pi * x), basis=u)
#
# Mark dirichlet regions
#
bnd_left = lambda x: np.abs(x) < 1e-9
mesh.mark_region('left', bnd_left, entity_type='vertex')
#
# Set up forms
#
# Bilinear form
a = Form(kernel=Kernel(Constant(1)), trial=ux, test=ux)
# Linear form
f = Explicit(lambda x: 4 * np.pi**2 * np.sin(2 * np.pi * x), dim=1)
L = Form(kernel=Kernel(f), test=u)
#
# Assemble
#
problem = [a, L]
assembler = Assembler(problem, mesh)
assembler.assemble()
A = assembler.get_matrix()
b = assembler.get_vector()
#
# Linear System
#
system = LinearSystem(u, A=A, b=b)
# Add dirichlet constraint
system.add_dirichlet_constraint('left', 0, on_boundary=False)
# Assemble constraints
#system.set_constraint_relation()
#system.incorporate_constraints()
system.solve_system()
#system.resolve_constraints()
# Compare with interpolant of exact solution
ua = system.get_solution(as_function=True)
#plot = Plot(2)
#plot.line(ua)
#plot.line(ue)
self.assertTrue(np.allclose(ua.data(), ue.data()))
def test02_1d_dirichlet_higher_order(self):
mesh = Mesh1D()
for etype in ['Q2', 'Q3']:
element = QuadFE(1, etype)
dofhandler = DofHandler(mesh, element)
dofhandler.distribute_dofs()
# Basis functions
ux = Basis(dofhandler, 'ux')
u = Basis(dofhandler, 'u')
# Exact solution
ue = Nodal(f=lambda x: x * (1 - x), basis=u)
# Define coefficient functions
one = Constant(1)
two = Constant(2)
# Define forms
a = Form(kernel=Kernel(one), trial=ux, test=ux)
L = Form(kernel=Kernel(two), test=u)
problem = [a, L]
# Assemble problem
assembler = Assembler(problem, mesh)
assembler.assemble()
A = assembler.get_matrix()
b = assembler.get_vector()
# Set up linear system
system = LinearSystem(u, A=A, b=b)
# Boundary functions
bnd_left = lambda x: np.abs(x) < 1e-9
bnd_right = lambda x: np.abs(1 - x) < 1e-9
# Mark mesh
mesh.mark_region('left', bnd_left, entity_type='vertex')
mesh.mark_region('right', bnd_right, entity_type='vertex')
# Add Dirichlet constraints to system
system.add_dirichlet_constraint('left', 0)
system.add_dirichlet_constraint('right', 0)
# Solve system
system.solve_system()
system.resolve_constraints()
# Compare solution with the exact solution
ua = system.get_solution(as_function=True)
self.assertTrue(np.allclose(ua.data(), ue.data()))
#
# Problems
#
problems = [[a_qe,L], [a_one], [m]]
#
# Assembly
#
assembler = Assembler(problems, mesh)
assembler.assemble()
# =============================================================================
# Linear system for generating observations
# =============================================================================
system = LinearSystem(assembler,0)
b = system.get_rhs()
#
# Incorporate constraints
#
system.add_dirichlet_constraint('left',0)
system.add_dirichlet_constraint('right',0)
#
# Compute model output
#
system.solve_system()
ue = system.get_solution(as_function=True)
ue_data = ue.fn()
n_points = ue_data.shape[0]
]
problem = [
Form(eps, test=ux, trial=ux),
Form(1, trial=ux, test=u),
Form(0, test=u),
Form(k_eps, trial=uxx, test=ux),
Form(k_a, trial=ux, test=ux)
]
# Assemble forms
assembler = Assembler(problem, mesh)
assembler.assemble()
A = assembler.af[0]['bilinear'].get_matrix()
b = assembler.af[0]['linear'].get_matrix()
# Define linear system
system = LinearSystem(u)
system.set_matrix(A)
system.set_rhs(b)
# Add Dirichlet constraints
system.add_dirichlet_constraint('left', 0)
system.add_dirichlet_constraint('right', 1)
system.set_constraint_relation()
system.solve_system()
u = system.get_solution()
plot = Plot()
plot.line(u)
# =============================================================================
# Generate Snapshot Set
# =============================================================================
phi = Basis(dofhandler, 'u')
phi_x = Basis(dofhandler, 'ux')
problems = [[Form(kernel=qfn, trial=phi_x, test=phi_x),
Form(1, test=phi)], [Form(1, test=phi, trial=phi)]]
assembler = Assembler(problems, mesh)
assembler.assemble()
A = assembler.af[0]['bilinear'].get_matrix()
b = assembler.af[0]['linear'].get_matrix()
linsys = LinearSystem(phi)
linsys.add_dirichlet_constraint('left', 1)
linsys.add_dirichlet_constraint('right', 0)
y_snap = Nodal(dofhandler=dofhandler, data=np.empty((n, n_samples)))
y_data = np.empty((n, n_samples))
for i in range(n_samples):
linsys.set_matrix(A[i].copy())
linsys.set_rhs(b.copy())
linsys.solve_system()
y_data[:, [i]] = linsys.get_solution(as_function=False)
y_snap.set_data(y_data)
plot = Plot()
plot.line(y_snap, i_sample=np.arange(n_samples))
# =============================================================================