def sample_qoi(q, dofhandler):
"""
Sample total energy of output for a given sample of q's
"""
#
# Set up weak form
#
# Basis
phi = Basis(dofhandler, 'v')
phi_x = Basis(dofhandler, 'vx')
# Elliptic problem
problems = [[Form(q, test=phi_x, trial=phi_x), Form(1, test=phi)],
[Form(1, test=phi, trial=phi)]]
# Assemble
assembler = Assembler(problems, mesh)
assembler.assemble()
# System matrices
A = assembler.af[0]['bilinear'].get_matrix()
b = assembler.af[0]['linear'].get_matrix()
M = assembler.af[1]['bilinear'].get_matrix()
# Define linear system
system = LS(phi)
system.add_dirichlet_constraint('left',1)
system.add_dirichlet_constraint('right',0)
n_samples = q.n_samples()
y_smpl = []
QoI_smpl = []
for i in range(n_samples):
# Sample system
if n_samples > 1:
Ai = A[i]
else:
Ai = A
system.set_matrix(Ai)
system.set_rhs(b.copy())
# Solve system
system.solve_system()
# Record solution and qoi
y = system.get_solution(as_function=False)
y_smpl.append(y)
QoI_smpl.append(y.T.dot(M.dot(y)))
# Convert to numpy array
y_smpl = np.concatenate(y_smpl,axis=1)
QoI = np.concatenate(QoI_smpl, axis=1).ravel()
return y_smpl, QoI
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()))
def test01_solve_2d(self):
"""
Solve a simple 2D problem with no hanging nodes
"""
mesh = QuadMesh(resolution=(5, 5))
# Mark dirichlet boundaries
mesh.mark_region('left',
lambda x, dummy: np.abs(x) < 1e-9,
entity_type='half_edge')
mesh.mark_region('right',
lambda x, dummy: np.abs(x - 1) < 1e-9,
entity_type='half_edge')
Q1 = QuadFE(mesh.dim(), 'Q1')
dQ1 = DofHandler(mesh, Q1)
dQ1.distribute_dofs()
phi = Basis(dQ1, 'u')
phi_x = Basis(dQ1, 'ux')
phi_y = Basis(dQ1, 'uy')
problem = [
Form(1, test=phi_x, trial=phi_x),
Form(1, test=phi_y, trial=phi_y),
Form(0, test=phi)
]
assembler = Assembler(problem, mesh)
assembler.add_dirichlet('left', dir_fn=0)
assembler.add_dirichlet('right', dir_fn=1)
assembler.assemble()
# Get matrix dirichlet correction and right hand side
A = assembler.get_matrix().toarray()
x0 = assembler.assembled_bnd()
b = assembler.get_vector()
ua = np.zeros((phi.n_dofs(), 1))
int_dofs = assembler.get_dofs('interior')
ua[int_dofs, 0] = np.linalg.solve(A, b - x0)
dir_bc = assembler.get_dirichlet()
dir_vals = np.array([dir_bc[dof] for dof in dir_bc])
dir_dofs = [dof for dof in dir_bc]
ua[dir_dofs] = dir_vals
ue_fn = Nodal(f=lambda x: x[:, 0], basis=phi)
ue = ue_fn.data()
self.assertTrue(np.allclose(ue, ua))
self.assertTrue(np.allclose(x0 + A.dot(ua[int_dofs, 0]), b))
def experiment01():
"""
Compute the quantity of interest, it's expectation and variance
"""
#
# FE Discretization
#
# Computational mesh
mesh = Mesh1D(resolution=(64, ))
# Element
element = QuadFE(mesh.dim(), 'DQ0')
dofhandler = DofHandler(mesh, element)
dofhandler.distribute_dofs()
# Linear Functional
mesh.mark_region('integrate',
lambda x: x > 0.75,
entity_type='cell',
strict_containment=False)
phi = Basis(dofhandler)
assembler = Assembler(Form(1, test=phi, flag='integrate'))
assembler.assemble()
L = assembler.get_vector()
def sampling_error():
"""
Test the sampling error by comparing the accuracy of the quantities of
interest q1 = E[|y|] and q2 = E[y(0.5)]
"""
c = Verbose()
mesh = Mesh1D(resolution=(1026,))
mesh.mark_region('left', lambda x:np.abs(x)<1e-10)
mesh.mark_region('right', lambda x:np.abs(x-1)<1e-10)
element = QuadFE(1,'Q1')
dofhandler = DofHandler(mesh, element)
dofhandler.distribute_dofs()
dofhandler.set_dof_vertices()
phi = Basis(dofhandler,'u')
phi_x = Basis(dofhandler,'ux')
ns_ref = 10000
z = get_points(n_samples=ns_ref)
q = set_diffusion(dofhandler,z)
problems = [[Form(q, test=phi_x, trial=phi_x), Form(1, test=phi)],
[Form(1, test=phi, trial=phi)]]
c.tic('assembling')
assembler = Assembler(problems, mesh)
assembler.assemble()
c.toc()
A = assembler.af[0]['bilinear'].get_matrix()
b = assembler.af[0]['linear'].get_matrix()
M = assembler.af[0]['bilinear'].get_matrix()
system = LS(phi)
system.add_dirichlet_constraint('left')
system.add_dirichlet_constraint('right')
c.tic('solving')
for n in range(ns_ref):
system.set_matrix(A[n])
system.set_rhs(b.copy())
system.solve_system()
c.toc()
def test01_solve_1d(self):
"""
Test solving 1D systems
"""
mesh = Mesh1D(resolution=(20, ))
mesh.mark_region('left', lambda x: np.abs(x) < 1e-9)
mesh.mark_region('right', lambda x: np.abs(x - 1) < 1e-9)
Q1 = QuadFE(1, 'Q1')
dQ1 = DofHandler(mesh, Q1)
dQ1.distribute_dofs()
phi = Basis(dQ1, 'u')
phi_x = Basis(dQ1, 'ux')
problem = [Form(1, test=phi_x, trial=phi_x), Form(0, test=phi)]
assembler = Assembler(problem, mesh)
assembler.add_dirichlet('left', dir_fn=0)
assembler.add_dirichlet('right', dir_fn=1)
assembler.assemble()
# Get matrix dirichlet correction and right hand side
A = assembler.get_matrix().toarray()
x0 = assembler.assembled_bnd()
b = assembler.get_vector()
ua = np.zeros((phi.n_dofs(), 1))
int_dofs = assembler.get_dofs('interior')
ua[int_dofs, 0] = np.linalg.solve(A, b - x0)
dir_bc = assembler.get_dirichlet()
dir_vals = np.array([dir_bc[dof] for dof in dir_bc])
dir_dofs = [dof for dof in dir_bc]
ua[dir_dofs] = dir_vals
ue_fn = Nodal(f=lambda x: x[:, 0], basis=phi)
ue = ue_fn.data()
self.assertTrue(np.allclose(ue, ua))
self.assertTrue(np.allclose(x0 + A.dot(ua[int_dofs, 0]), b))
def sensitivity_sample_qoi(exp_q, dofhandler):
"""
Sample QoI by means of Taylor expansion
J(q+dq) ~= J(q) + dJdq(q)dq
"""
# Basis
phi = Basis(dofhandler, 'v')
phi_x = Basis(dofhandler, 'vx')
# Define problem
exp_q_fn = Nodal(data=exp_q, basis=phi)
primal = [Form(exp_q_fn, test=phi_x, trial=phi_x), Form(1, test=phi)]
adjoint = [Form(exp_q_fn, test=phi_x, trial=phi_x), Form(0, test=phi)]
qoi = [Form(exp_q_fn, test=phi_x)]
problems = [primal, adjoint, qoi]
# Define assembler
assembler = Assembler(problems)
#
# Dirichlet conditions for primal problem
#
assembler.add_dirichlet('left', 0, i_problem=0)
assembler.add_dirichlet('right', 1, i_problem=0)
# Dirichlet conditions for adjoint problem
assembler.add_dirichlet('left', 0, i_problem=1)
assembler.add_dirichlet('right', -1, i_problem=1)
# Assemble system
assembler.assemble()
# Compute solution and qoi at q (primal)
u = assembler.solve(i_problem=0)
# Compute solution of the adjoint problem
v = assembler.solve(i_problem=1)
# Evaluate J
J = u.dot(assembler.get_vector(2))
#
# Assemble gradient
#
ux_fn = Nodal(data=u, basis=phi_x)
vx_fn = Nodal(data=v, basis=phi_x)
k_int = Kernel(f=[exp_q_fn, ux_fn, vx_fn],
F=lambda exp_q, ux, vx: exp_q * ux * vx)
problem = [Form(k_int, test=phi)]
assembler = Assembler(problem)
assembler.assemble()
dJ = -assembler.get_vector()
return dJ
def test_edge_integrals(self):
"""
Test computing
"""
mesh = QuadMesh(resolution=(1, 1))
Q = QuadFE(2, 'Q1')
dQ = DofHandler(mesh, Q)
dQ.distribute_dofs()
phi = Basis(dQ, 'u')
f = Nodal(data=np.ones((phi.n_dofs(), 1)), basis=phi)
kernel = Kernel(f)
form = Form(kernel, dmu='ds')
assembler = Assembler(form, mesh)
cell = mesh.cells.get_leaves()[0]
shape_info = assembler.shape_info(cell)
xg, wg, phi, dofs = assembler.shape_eval(cell)
def test02_variance():
"""
Compute the variance of J(q) for different mesh refinement levels
and compare with MC estimates.
"""
l_max = 8
for i_res in np.arange(2, l_max):
# Computational mesh
mesh = Mesh1D(resolution=(2**i_res, ))
# Element
element = QuadFE(mesh.dim(), 'DQ0')
dofhandler = DofHandler(mesh, element)
dofhandler.distribute_dofs()
# Linear Functional
mesh.mark_region('integrate',
lambda x: x >= 0.75,
entity_type='cell',
strict_containment=False)
phi = Basis(dofhandler)
assembler = Assembler(Form(4, test=phi, flag='integrate'))
assembler.assemble()
L = assembler.get_vector()
# Define Gaussian random field
C = Covariance(dofhandler, name='gaussian', parameters={'l': 0.05})
C.compute_eig_decomp()
eta = GaussianField(dofhandler.n_dofs(), K=C)
eta.update_support()
n_samples = 100000
J_paths = L.dot(eta.sample(n_samples=n_samples))
var_mc = np.var(J_paths)
lmd, V = C.get_eig_decomp()
LV = L.dot(V)
var_an = LV.dot(np.diag(lmd).dot(LV.transpose()))
print(var_mc, var_an)
def sample_state(mesh,dQ,z,mflag,reference=False):
"""
Compute the sample output corresponding to a given input
"""
n_samples = z.shape[0]
q = set_diffusion(dQ,z)
phi = Basis(dQ,'u', mflag)
phi_x = Basis(dQ, 'ux', mflag)
if reference:
problems = [[Form(q,test=phi_x,trial=phi_x), Form(1,test=phi)],
[Form(1,test=phi, trial=phi)],
[Form(1,test=phi_x, trial=phi_x)]]
else:
problems = [[Form(q,test=phi_x,trial=phi_x), Form(1,test=phi)]]
assembler = Assembler(problems, mesh, subforest_flag=mflag)
assembler.assemble()
A = assembler.af[0]['bilinear'].get_matrix()
b = assembler.af[0]['linear'].get_matrix()
if reference:
M = assembler.af[1]['bilinear'].get_matrix()
K = assembler.af[2]['bilinear'].get_matrix()
system = LS(phi)
system.add_dirichlet_constraint('left')
system.add_dirichlet_constraint('right')
n_dofs = dQ.n_dofs(subforest_flag=mflag)
y = np.empty((n_dofs,n_samples))
for n in range(n_samples):
system.set_matrix(A[n])
system.set_rhs(b.copy())
system.solve_system()
y[:,n] = system.get_solution(as_function=False)[:,0]
y_fn = Nodal(dofhandler=dQ,subforest_flag=mflag,data=y)
if reference:
return y_fn, M, K
else:
return y_fn
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 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()))
#
# Random diffusion coefficient
#
n_samples = 200
cov = Covariance(dh_y, name='gaussian', parameters={'l':0.1})
k = GaussianField(ny, K=cov)
k.update_support()
kfn = Nodal(dofhandler=dh_y, data=k.sample(n_samples=n_samples))
# =============================================================================
# Assembly
# =============================================================================
K = Kernel(kfn, F=lambda f:np.exp(f)) # diffusivity
problems = [[Form(K, test=phi_x, trial=phi_x)],
[Form(test=phi, trial=phi)]]
assembler = Assembler(problems, mesh)
assembler.assemble()
# Mass matrix (for control)
M = assembler.af[1]['bilinear'].get_matrix()
# =============================================================================
# Define State and Adjoint Systems
# =============================================================================
state = LS(phi)
adjoint = LS(phi)
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 reference_solution():
"""
Use sparse grid method to compute a benchmark solution
"""
mesh = QuadMesh(resolution=(10,10))
mesh.mark_region('boundary', lambda x,y:True,
entity_type='half_edge', on_boundary=True)
element = QuadFE(mesh.dim(), 'Q1')
dofhandler = DofHandler(mesh, element)
dofhandler.distribute_dofs()
n = dofhandler.n_dofs()
phi = Basis(dofhandler, 'u')
phi_x = Basis(dofhandler, 'ux')
phi_y = Basis(dofhandler, 'uy')
yd_fn = Explicit(lambda x: np.sin(2*np.pi*x[:,0])*np.sin(2*np.pi*x[:,1]),dim=2)
g = np.ones((n,1))
#
# Random diffusion coefficient
#
# Sparse grid
tasmanian_library="/home/hans-werner/bin/TASMANIAN-6.0/libtasmaniansparsegrid.so"
grid = TasmanianSG.TasmanianSparseGrid(tasmanian_library=tasmanian_library)
dimensions = 4
outputs = 1
depth = 4
type = 'tensor'
rule = 'gauss-legendre'
grid.makeGlobalGrid(dimensions, outputs, depth, type, rule)
Y = grid.getPoints()
w = grid.getQuadratureWeights()
n_samples = grid.getNumPoints()
x = dofhandler.get_dof_vertices()
a_nodal = 1 + 0.1*(np.outer(np.cos(np.pi*x[:,1]),Y[:,0])+\
np.outer(np.cos(np.pi*x[:,0]),Y[:,1])+\
np.outer(np.sin(2*np.pi*x[:,1]),Y[:,2])+\
np.outer(np.sin(2*np.pi*x[:,0]),Y[:,3]))
a = Nodal(data=a_nodal, dofhandler=dofhandler)
yd_vec = yd_fn.eval(x)
problems = [[Form(a, test=phi_x, trial=phi_x),
Form(a, test=phi_y, trial=phi_y)],
[Form(1, test=phi, trial=phi)]]
assembler = Assembler(problems, mesh)
assembler.assemble()
A = assembler.af[0]['bilinear'].get_matrix()
M = assembler.af[1]['bilinear'].get_matrix()
state = LS(phi)
state.add_dirichlet_constraint('boundary')
adjoint = LS(phi)
adjoint.add_dirichlet_constraint('boundary')
tau = 10
k_max = 20
alpha = 0.1
u = np.zeros((n,1))
norm_dJ_iter = []
J_iter = []
u_iter = []
for k in range(k_max):
print('iteration', k)
#
# Compute average cost and gradient
#
dJ = np.zeros((n,1))
J = 0
print('sampling')
for n in range(n_samples):
print(n)
yn, pn, Jn, dJn = cost_gradient(state,adjoint,A[n],M,
g,u,yd_vec,alpha)
J += w[n]*Jn
dJ += w[n]*dJn
print('')
norm_dJ = np.sqrt(dJ.T.dot(M.dot(dJ)))
#
# Store current iterates
#
norm_dJ_iter.append(norm_dJ)
J_iter.append(J)
u_iter.append(u)
#
# Check for convergence
#
if norm_dJ<1e-8:
break
#
# Update iterate
#
u -= tau*dJ
cov.compute_eig_decomp()
q = GaussianField(dQ0.n_dofs(), K=cov)
# Sample Random field
n_samples = 100
eq = Nodal(basis=phi_0, data=np.exp(q.sample(n_samples)))
plot.contour(eq, n_sample=25)
#
# Compute state
#
# Define weak form
state = [[
Form(eq, test=phix_1, trial=phix_1),
Form(eq, test=phiy_1, trial=phiy_1),
Form(1, test=phi_1)
], [Form(1, test=phi_1, flag='dmn')]]
# Assemble system
assembler = Assembler(state)
assembler.add_dirichlet('bnd')
assembler.assemble()
J = assembler.get_vector(1)
# Solve system
u_vec = assembler.solve()
u = Nodal(basis=phi_1, data=u_vec)
n_samples = n_batches * n_samples_per_batch
f_mc = []
g_mc = []
for n_batch in tqdm(range(n_batches)):
#
# Generate random sample
#
z = np.random.normal(size=(r, n_samples_per_batch))
q_smpl = Vr.dot(np.diag(np.sqrt(lr)).dot(z))
q.set_data(q_smpl)
expq = Kernel(q, F=lambda f: np.exp(f))
#
# Assemble system
#
problems = [[Form(expq, test=phi_x, trial=phi_x)],
[Form(test=phi, trial=phi)]]
assembler = Assembler(problems, mesh)
assembler.assemble()
M = assembler.af[0]['bilinear'].get_matrix()[0]
for n in range(n_samples_per_batch):
A = assembler.af[0]['bilinear'].get_matrix()[n]
fn, gn, yn, pn = sample_cost_gradient(state, adjoint, A, M, u, y_data,
gamma)
f_mc.append(fn)
g_mc.append(gn)
f_mc = np.concatenate(f_mc, axis=1)
g_mc = np.concatenate(g_mc, axis=1)
np.save('f_mc', f_mc)
# =============================================================================
Q1 = QuadFE(2, 'Q1')
dofhandler = DofHandler(mesh, Q1)
dofhandler.distribute_dofs()
u = Basis(dofhandler, 'u')
ux = Basis(dofhandler, 'ux')
uy = Basis(dofhandler, 'uy')
epsilon = 1e-6
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)
def plot_heuristics(f, tht, basis, region, condition):
"""
Parameters
----------
f : lambda,
Function of θ to be integrated.
n : int,
Sample size for Monte Carlo sample
"""
tht.update_support()
#
# Plot samples of the random field
#
n = 10000
tht_sample = tht.sample(n)
tht_fn = Nodal(data=tht_sample, basis=basis)
#
# Compute the quantity of interest
#
# Define the kernel
kf = Kernel(tht_fn, F=f)
# Assemble over the mesh
problems = [[Form(kernel=kf, flag=region)], [Form(flag=region)]]
assembler = Assembler(problems, basis.mesh())
assembler.assemble()
# Extract sample
dx = assembler.get_scalar(i_problem=1)
q_sample = assembler.get_scalar(i_sample=None) / dx
#
# Compute correlation coefficients of q with spatial data
#
plot = Plot(quickview=False)
fig, ax = plt.subplots()
plt_args = {'linewidth': 0.5, 'color': 'k'}
ax = plot.line(tht_fn,
axis=ax,
i_sample=list(range(100)),
plot_kwargs=plt_args)
fig.savefig('ex01_sample_paths.eps')
fig, ax = plt.subplots()
ftht = Nodal(data=f(tht_sample), basis=basis)
ax = plot.line(ftht,
axis=ax,
i_sample=list(range(100)),
plot_kwargs=plt_args)
fig.savefig('ex01_integrand.eps')
fig, ax = plt.subplots(1, 1)
plt.hist(q_sample, bins=50, density=True)
ax.set_title(r'Histogram $Q(\theta)$')
fig.savefig('ex01_histogram.eps')
plt.close('all')
dh = basis.dofhandler()
n_dofs = dh.n_dofs()
# Extract the region on which we condition
cnd_dofs = dh.get_region_dofs(entity_flag=condition)
I = np.eye(n_dofs)
I = I[cnd_dofs, :]
# Measured tht
tht_msr = tht_sample[cnd_dofs, 0][:, None]
n_cnd = 30
cnd_tht = tht.condition(I, tht_msr, n_samples=n_cnd)
#cnd_tht_data = np.array([tht_sample[:,0] for dummy in range(n_cnd)])
#cnd_tht_data[cnd_dofs,:] = cnd_tht
cnd_tht_fn = Nodal(data=f(cnd_tht), basis=basis)
fig, ax = plt.subplots()
ax = plot.line(cnd_tht_fn,
axis=ax,
i_sample=np.arange(n_cnd),
plot_kwargs=plt_args)
fig.tight_layout()
plt.show()
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()))
""" Task: Modify the kernel class to allow for the computation of forms involving (i) normal derivatives or (ii) jumps across cell edges. i.e. I n.A*grad(u) ds or """ # # Define mesh # mesh = QuadMesh(resolution=(20, 20)) element = QuadFE(2, 'DQ1') u = Nodal(f=lambda x: -1 + x[:, 0]**5 + x[:, 1]**8, mesh=mesh, element=element) print(u.data()) plot = Plot(3) plot.wire(u) kernel = JumpKernel(u, dfdx='fx') form = Form(kernel=kernel, dmu='ds') assembler = Assembler(form, mesh) assembler.assemble() cf = assembler.af[0]['constant'] print(cf.get_matrix())
eta_trunc_sg = V[:, :k].dot(np.diag(np.sqrt(D[:k])).dot(z.T))
# Generate a Monte Carlo sample on top of sparse grid
n_mc = 20
zz = np.random.randn(n_dofs - k, n_mc)
eta_tail_mc = V[:, k:].dot(np.diag(np.sqrt(D[k:]))).dot(zz)
# -----------------------------------------------------------------------------
# Sample and Integrate
# -----------------------------------------------------------------------------
# Samples of random field
theta_trunc = Nodal(data=eta_trunc_sg[:, [50]] + eta_tail_mc, basis=phi_1)
# Assembler
k = Kernel(theta_trunc, F=lambda tht: tht**2)
problem = Form(flag='integration', kernel=k)
assembler = Assembler(problem, mesh)
assembler.assemble()
v = assembler.get_scalar(i_sample=3)
#plot = Plot(quickview=False)
#fig, ax = plt.subplots()
#plot.mesh(mesh,regions=[('region','cell')])
"""
ax = plot.line(theta_trunc, axis=ax, i_sample=np.arange(n_mc),
plot_kwargs={'linewidth':0.2,
'color':'k'})
"""
#plt.show()
y) < 1e-6 or abs(1 - y) < 1e-6
mesh.mark_region('bnd', bnd_fn, entity_type='half_edge', on_boundary=True)
# Mark averaging region
dmn_fn = lambda x, y: x >= 0.75 and x <= 1 and y >= 0.75 and y <= 1
mesh.mark_region('dmn',
dmn_fn,
entity_type='cell',
strict_containment=True,
on_boundary=False)
#cells = mesh.get_region(flag='dmn', entity_type='cell', on_boundary=False, subforest_flag=None)
#plot.mesh(mesh, regions=[('bnd','edge'),('dmn','cell')])
# Define Elements
Q0 = QuadFE(mesh.dim(), 'DQ0')
dQ0 = DofHandler(mesh, Q0)
dQ0.distribute_dofs()
phi = Basis(dQ0)
q = Nodal(
f=lambda x: np.sin(2 * np.pi * x[:, 0]) * np.sin(2 * np.pi * x[:, 1]),
dim=2,
basis=phi)
problem = Form(q)
mesh.cells.refine(new_label='fine_mesh')
assembler = Assembler(problem, mesh, subforest_flag='fine_mesh')
assembler.assemble()
def reference_qoi(f, tht, basis, region, n=1000000, verbose=True):
"""
Parameters
----------
f : lambda function,
Function of θ to be integrated.
tht : GaussianField,
Random field θ defined on mesh in terms of its mean and covariance
basis : Basis,
Basis function defining the nodal interpolant. It incorporates the
mesh, the dofhandler, and the derivative.
region : meshflag,
Flag indicating the region of integration
n : int, default=1000000
Sample size
Returns
-------
Q_ref : double,
Reference quantity of interest
err : double,
Expected RMSE given by var(Q)/n.
"""
#
# Assemble integral
#
batch_size = 100000
n_batches = n // batch_size + (0 if (n % batch_size) == 0 else 1)
if verbose:
print('Computing Reference Quantity of Interest')
print('========================================')
print('Sample size: ', n)
print('Batch size: ', batch_size)
print('Number of batches: ', n_batches)
Q_smpl = np.empty(n)
for k in range(n_batches):
# Determine sample sizes for each batch
if k < n_batches - 1:
n_sample = batch_size
else:
# Last sample may be smaller than batch_size
n_sample = n - k * batch_size
if verbose:
print(' - Batch Number ', k)
print(' - Sample Size: ', n_sample)
print(' - Sampling random field')
# Sample from field
tht_smpl = tht.sample(n_sample)
# Define kernel
tht_n = Nodal(data=tht_smpl, basis=basis)
kf = Kernel(tht_n, F=f)
# Define forms
if k == 0:
problems = [[Form(kernel=kf, flag=region)], [Form(flag=region)]]
else:
problems = [Form(kernel=kf, flag=region)]
if verbose:
print(' - Assembling.')
# Compute the integral
assembler = Assembler(problems, basis.mesh())
assembler.assemble()
#
# Compute statistic
#
# Get samples
if k == 0:
dx = assembler.get_scalar(i_problem=1)
if verbose:
print(' - Updating samples \n')
batch_sample = assembler.get_scalar(i_problem=0, i_sample=None)
Q_smpl[k * batch_size:k * batch_size + n_sample] = batch_sample / dx
# Compute mean and MSE
Q_ref = np.mean(Q_smpl)
err = np.var(Q_smpl) / n
# Return reference
return Q_ref, err
Q,R = linalg.qr(A, mode='economic')
r = np.diag(R)
print(len(r[np.abs(r)>1e-13]))
print(Q,'\n',R)
'''
print("TasmanianSG version: {0:s}".format(TasmanianSG.__version__))
print("TasmanianSG license: {0:s}".format(TasmanianSG.__license__))
mesh = Mesh1D(resolution=(2, ))
element = QuadFE(mesh.dim(), 'Q1')
dofhandler = DofHandler(mesh, element)
phi_x = Basis(dofhandler, 'ux')
problems = [Form(1, test=phi_x, trial=phi_x)]
assembler = Assembler(problems, mesh)
assembler.assemble()
A = assembler.af[0]['bilinear'].get_matrix()
n = dofhandler.n_dofs()
b = np.ones((n, 1))
mesh.mark_region('left', lambda x: np.abs(x) < 1e-9)
mesh.mark_region('right', lambda x: np.abs(1 - x) < 1e-9)
print('A before constraint', A.toarray())
system = LS(phi_x)
system.add_dirichlet_constraint('left', 1)
system.add_dirichlet_constraint('right', 0)
# Define element
#
element = QuadFE(2, etype)
dofhandler = DofHandler(mesh, element)
dofhandler.distribute_dofs()
#
# Define Basis Functions
#
u = Basis(dofhandler, 'u')
ux = Basis(dofhandler, 'ux')
uy = Basis(dofhandler, 'uy')
#
# Define weak form
#
a_diff_x = Form(eps, trial=ux, test=ux)
a_diff_y = Form(eps, trial=uy, test=uy)
a_adv_x = Form(vx, trial=ux, test=u)
a_adv_y = Form(vy, trial=uy, test=u)
b = Form(f, test=u)
problem = [a_diff_x, a_diff_y, a_adv_x, a_adv_y, b]
#
# Assembler system
#
assembler = Assembler([problem], mesh)
assembler.add_dirichlet(None, ue)
assembler.assemble()
#
# Sample from field
tht_fn = Nodal(data=tht.sample(n_samples=3), basis=phi)
plot = Plot()
plot.contour(tht_fn)
#
# Advection
#
v = [0.1, -0.1]
plot.mesh(mesh, regions=[('in', 'edge'), ('out', 'edge'), ('reg', 'cell')])
k = Kernel(tht_fn, F=lambda tht: np.exp(tht))
adv_diff = [
Form(k, trial=phi_x, test=phi_x),
Form(k, trial=phi_y, test=phi_y),
Form(0, test=phi),
Form(v[0], trial=phi_x, test=phi),
Form(v[1], trial=phi_y, test=phi)
]
average = [Form(1, test=phi, flag='reg'), Form(1, flag='reg')]
assembler = Assembler([adv_diff, average], mesh)
assembler.add_dirichlet('out', dir_fn=0)
assembler.add_dirichlet('in', dir_fn=10)
assembler.assemble()
u_vec = assembler.solve(i_problem=0, i_matrix=0, i_vector=0)
plot.contour(Nodal(data=u_vec, basis=phi))
one = Function(1, 'constant') k1 = 1e-9 k2 = 1000 # # Basis functions # u = Basis(Q1, 'u') ux = Basis(Q1, 'ux') q = Basis(Q1, 'q') # # Forms # a_qe = Form(kernel=Kernel(qe), trial=ux, test=ux) a_one = Form(kernel=Kernel(one), trial=ux, test=ux) L = Form(kernel=Kernel(one), test=u) # # Problems # problems = [[a_qe,L], [a_one]] # # Assembly # assembler = Assembler(problems, mesh) assembler.assemble()
Q1 = QuadFE(1, 'Q1') qe = Function(qfn, 'explicit', dim=1) one = Function(1, 'constant') # # Basis functions # u = Basis(Q1, 'u') ux = Basis(Q1, 'ux') q = Basis(Q0, 'q') # # Forms # a_qe = Form(kernel=Kernel(qe), trial=ux, test=ux) a_one = Form(kernel=Kernel(one), trial=ux, test=ux) m = Form(kernel=Kernel(one), trial=u, test=u) L = Form(kernel=Kernel(one), test=u) # # Problems # problems = [[a_qe,L], [a_one], [m]] # # Assembly # assembler = Assembler(problems, mesh) assembler.assemble()
