def check_ass_penaro(bcsd=None, bcssfuns=None, V=None, plot=False):
mesh = V.mesh()
bcone = bcsd[1]
contshfunone = bcssfuns[1]
Gammaone = bcone()
bparts = dolfin.MeshFunction('size_t', mesh, mesh.topology().dim() - 1)
Gammaone.mark(bparts, 0)
u = dolfin.TrialFunction(V)
v = dolfin.TestFunction(V)
# Robin boundary form
arob = dolfin.inner(u, v) * dolfin.ds(0)
brob = dolfin.inner(v, contshfunone) * dolfin.ds(0)
amatrob = dolfin.assemble(arob, exterior_facet_domains=bparts)
bmatrob = dolfin.assemble(brob, exterior_facet_domains=bparts)
amatrob = dts.mat_dolfin2sparse(amatrob)
amatrob.eliminate_zeros()
print 'Number of nonzeros in amatrob:', amatrob.nnz
bmatrob = bmatrob.array() # [ININDS]
if plot:
plt.figure(2)
plt.spy(amatrob)
if plot:
plt.figure(1)
for x in contshfunone.xs:
plt.plot(x[0], x[1], 'bo')
plt.show()
def check_ass_penaro(bcsd=None, bcssfuns=None, V=None, plot=False):
mesh = V.mesh()
bcone = bcsd[1]
contshfunone = bcssfuns[1]
Gammaone = bcone()
bparts = dolfin.MeshFunction('size_t', mesh, mesh.topology().dim() - 1)
Gammaone.mark(bparts, 0)
u = dolfin.TrialFunction(V)
v = dolfin.TestFunction(V)
# Robin boundary form
arob = dolfin.inner(u, v) * dolfin.ds(0)
brob = dolfin.inner(v, contshfunone) * dolfin.ds(0)
amatrob = dolfin.assemble(arob, exterior_facet_domains=bparts)
bmatrob = dolfin.assemble(brob, exterior_facet_domains=bparts)
amatrob = dts.mat_dolfin2sparse(amatrob)
amatrob.eliminate_zeros()
print('Number of nonzeros in amatrob:', amatrob.nnz)
bmatrob = bmatrob.array() # [ININDS]
if plot:
plt.figure(2)
plt.spy(amatrob)
if plot:
plt.figure(1)
for x in contshfunone.xs:
plt.plot(x[0], x[1], 'bo')
plt.show()
def __init__(self, V, u, v, b,
kappa, rho, cp,
source,
dirichlet_bcs=[],
neumann_bcs={},
robin_bcs={},
dx=dx,
ds=ds
):
super(HeatCylindrical, self).__init__()
self.dirichlet_bcs = dirichlet_bcs
r = Expression('x[0]', degree=1, domain=V.mesh())
self.V = V
self.dx_multiplier = 2*pi*r
self.F0 = kappa * r * dot(grad(u), grad(v / (rho * cp))) \
* 2*pi * dx
#F -= dot(b, grad(u)) * v * 2*pi*r * dx_workpiece(0)
if b:
self.F0 += (b[0] * u.dx(0) + b[1] * u.dx(1)) * v * 2*pi*r * dx
# Joule heat
self.F0 -= 1.0 / (rho * cp) * source * v * 2*pi*r * dx
# Neumann boundary conditions
for k, nGradT in neumann_bcs.iteritems():
self.F0 -= r * kappa * nGradT * v / (rho * cp) \
* 2 * pi * ds(k)
# Robin boundary conditions
for k, value in robin_bcs.iteritems():
alpha, u0 = value
self.F0 -= r * kappa * alpha * (u - u0) * v / (rho * cp) \
* 2 * pi * ds(k)
return
def solve(self, dt):
self.u = Function(self.V0)
self.w = TestFunction(self.V0)
self.du = TrialFunction(self.V0)
x = SpatialCoordinate(self.mesh0)
L = inner( self.S(), self.eps(self.w) )*dx(degree=4)\
- inner( self.b, self.w )*dx(degree=4)\
- inner( self.h, self.w )*ds(degree=4)\
+ inner( 1e-6*self.u, self.w )*ds(degree=4)\
- inner( min_value(x[2]+self.ut[2]+self.u[2], 0) * Constant((0,0,-1.0)), self.w )*ds(degree=4)
a = derivative(L, self.u, self.du)
problem = NonlinearVariationalProblem(L, self.u, bcs=[], J=a)
solver = NonlinearVariationalSolver(problem)
solver.solve()
self.ut.vector()[:] = self.ut.vector()[:] + self.u.vector()[:]
ALE.move(self.mesh, Function(self.V, self.u.vector()))
self.v.vector()[:] = self.u.vector()[:] / dt
self.n = FacetNormal(self.mesh)
def QoI_FEM(x0,y0,lam1,lam2,gridx,gridy,p):
mesh = fn.UnitSquareMesh(gridx, gridy)
V = fn.FunctionSpace(mesh, "Lagrange", p)
# Define diffusion tensor (here, just a scalar function) and parameters
A = fn.Expression((('exp(lam1)','a'),
('a','exp(lam2)')), a = fn.Constant(0.0), lam1 = lam1, lam2 = lam2, degree=3)
u_exact = fn.Expression("sin(lam1*pi*x[0])*cos(lam2*pi*x[1])", lam1 = lam1, lam2 = lam2, degree=2+p)
# Define the mix of Neumann and Dirichlet BCs
class LeftBoundary(fn.SubDomain):
def inside(self, x, on_boundary):
return (x[0] < fn.DOLFIN_EPS)
class RightBoundary(fn.SubDomain):
def inside(self, x, on_boundary):
return (x[0] > 1.0 - fn.DOLFIN_EPS)
class TopBoundary(fn.SubDomain):
def inside(self, x, on_boundary):
return (x[1] > 1.0 - fn.DOLFIN_EPS)
class BottomBoundary(fn.SubDomain):
def inside(self, x, on_boundary):
return (x[1] < fn.DOLFIN_EPS)
# Create a mesh function (mf) assigning an unsigned integer ('uint')
# to each edge (which is a "Facet" in 2D)
mf = fn.MeshFunction('size_t', mesh, 1)
mf.set_all(0) # initialize the function to be zero
# Setup the boundary classes that use Neumann boundary conditions
NTB = TopBoundary() # instatiate
NTB.mark(mf, 1) # set all values of the mf to be 1 on this boundary
NBB = BottomBoundary()
NBB.mark(mf, 2) # set all values of the mf to be 2 on this boundary
NRB = RightBoundary()
NRB.mark(mf, 3)
# Define Dirichlet boundary conditions
Gamma_0 = fn.DirichletBC(V, u_exact, LeftBoundary())
bcs = [Gamma_0]
# Define data necessary to approximate exact solution
f = ( fn.exp(lam1)*(lam1*fn.pi)**2 + fn.exp(lam2)*(lam2*fn.pi)**2 ) * u_exact
g1 = fn.Expression("-exp(lam2)*lam2*pi*sin(lam1*pi*x[0])*sin(lam2*pi*x[1])", lam1=lam1, lam2=lam2, degree=2+p) #pointing outward unit normal vector, pointing upaward (0,1)
g2 = fn.Expression("exp(lam2)*lam2*pi*sin(lam1*pi*x[0])*sin(lam2*pi*x[1])", lam1=lam1, lam2=lam2, degree=2+p) #pointing downward (0,1)
g3 = fn.Expression("exp(lam1)*lam1*pi*cos(lam1*pi*x[0])*cos(lam2*pi*x[1])", lam1=lam1, lam2=lam2, degree=2+p)
fn.ds = fn.ds(subdomain_data=mf)
# Define variational problem
u = fn.TrialFunction(V)
v = fn.TestFunction(V)
a = fn.inner(A*fn.grad(u), fn.grad(v))*fn.dx
L = f*v*fn.dx + g1*v*fn.ds(1) + g2*v*fn.ds(2) + g3*v*fn.ds(3) #note the 1, 2 and 3 correspond to the mf
# Compute solution
u = fn.Function(V)
fn.solve(a == L, u, bcs)
return u(x0,y0)
def conj_coef_fun(derJ, derJ_old, hol_cyl, boundary_faces, mark_in, mark_ex,
time_v, cut_end, method, itera, path_to_do):
'''
Conjugation coefficient.
method = 'PR' (Polak-Ribière) or 'FR' (Fletcher-Reeves).
'''
num_v = np.zeros(np.shape(time_v))
den_v = np.zeros(np.shape(time_v))
for count_t_i, t_i in enumerate(time_v):
if method == 'PR':
#Polak-Ribière method
#scalar
num_v[count_t_i] = do.assemble(
derJ[count_t_i] * (derJ[count_t_i] - derJ_old[count_t_i]) *
do.ds(mark_in, domain=hol_cyl, subdomain_data=boundary_faces))
elif method == 'FR':
#Fletcher-Reeves method
#scalar
num_v[count_t_i] = do.assemble(
pow(derJ[count_t_i], 2.) *
do.ds(mark_in, domain=hol_cyl, subdomain_data=boundary_faces))
#scalar
den_v[count_t_i] = do.assemble(
pow(derJ_old[count_t_i], 2.) *
do.ds(mark_in, domain=hol_cyl, subdomain_data=boundary_faces))
fig_inf = plt.figure(figsize=(20, 10))
ax_inf = fig_inf.add_subplot(211)
ax_inf.plot(num_v, 'r.', label='num1')
ax_inf.plot(den_v, 'b.', label='den1')
ax_inf.legend()
ax_inf = fig_inf.add_subplot(223)
ax_inf.plot(num_v[:10], 'r.', label='num1')
ax_inf.plot(den_v[:10], 'b.', label='den1')
ax_inf.legend()
ax_inf = fig_inf.add_subplot(224)
ax_inf.plot(num_v[-10:], 'r.', label='num1')
ax_inf.plot(den_v[-10:], 'b.', label='den1')
ax_inf.legend()
nam_inf = os.path.join(path_to_do,
'gamma_CG_{}_{}.pdf'.format(itera, method))
fig_inf.savefig(nam_inf, dpi=150)
#integration
num_gamma_CG = np.trapz(num_v[:cut_end], x=time_v[:cut_end])
den_gamma_CG = np.trapz(den_v[:cut_end], x=time_v[:cut_end])
#https://en.wikipedia.org/wiki/Nonlinear_conjugate_gradient_method
gamma_CG = max(0., num_gamma_CG / den_gamma_CG)
return gamma_CG
def create_bc(self):
#Input
G_rhs_inner, G_rhs_outer = self.inhomogeneity()
local_bc = 0.0
df.ds = self.my_mesh_cls.ds #<---- Important
local_bc += (-0.5 * df.inner(self.v,((self.BC1_rhs-self.BC2_rhs) \
* G_rhs_inner)) ) * df.ds(3000) #RHS-2
local_bc += (-0.5 * df.inner(self.v,((self.BC1_rhs-self.BC2_rhs)\
* G_rhs_outer)) ) * df.ds(3100) #RHS-2
return local_bc
def assemble_lui_stiffness(self, g, f, mesh, robin_boundary):
V = FunctionSpace(mesh, "Lagrange", self.p)
u = TrialFunction(V)
v = TestFunction(V)
n = FacetNormal(mesh)
robin = MeshFunction('size_t', mesh, mesh.topology().dim() - 1)
robin_boundary.mark(robin, 1)
ds = Measure('ds', subdomain_data=robin)
a = inner(grad(u), grad(v)) * dx
b = (1 - g) * (inner(grad(u), n)) * v * ds(1)
c = f * u * v * ds(1)
k = lhs(a + b - c)
K = PETScMatrix()
assemble(k, tensor=K)
return K, V
def V0constrainedE(self,inverse=False): mesh = self.parameters["mesh"] u = self.parameters["displacement_variable"] ds = dolfin.ds(subdomain_data=self.parameters["facetboundaries"]) dsendo = ds(self.parameters["endoid"], domain = self.parameters["mesh"], subdomain_data = self.parameters["facetboundaries"]) pendo = self.parameters["volconst_variable"] V0= self.parameters["constrained_vol"] X = SpatialCoordinate(mesh) x = u + X F = self.Fmat() N = self.parameters["facet_normal"] n = cofac(F)*N area = assemble(Constant(1.0) * dsendo) if inverse: V_u = - Constant(0.0/3.0) * inner(x, n) Wvol = (Constant(0.0/area) * pendo * V0 * dsendo) - (pendo * V_u *dsendo) else: V_u = - Constant(1.0/3.0) * inner(x, n) Wvol = (Constant(1.0/area) * pendo * V0 * dsendo) - (pendo * V_u *dsendo) return Wvol
def __init__(self, U_m, mesh):
"""Function spaces and BCs"""
V = VectorFunctionSpace(mesh, 'P', 2)
Q = FunctionSpace(mesh, 'P', 1)
self.mesh = mesh
self.vu, self.vp = TestFunction(V), TestFunction(Q) # for integration
self.u_, self.p_ = Function(V), Function(Q) # for the solution
self.u_1, self.p_1 = Function(V), Function(Q) # for the prev. solution
self.u_k, self.p_k = Function(V), Function(Q) # for the prev. solution
self.u, self.p = TrialFunction(V), TrialFunction(Q) # unknown!
U0_str = "4.*U_m*x[1]*(.41-x[1])/(.41*.41)"
x = [0,
.41 / 2] # evaluate the Expression at the center of the channel
self.U_mean = np.mean(2 / 3 * eval(U0_str))
U0 = Expression((U0_str, "0"), U_m=U_m, degree=2)
bc0 = DirichletBC(V, Constant((0, 0)), cylinderwall)
bc1 = DirichletBC(V, Constant((0, 0)), topandbottom)
bc2 = DirichletBC(V, U0, inlet)
bc3 = DirichletBC(Q, Constant(0), outlet)
self.bcu = [bc0, bc1, bc2]
self.bcp = [bc3]
# ds is needed to compute drag and lift.
ASD1 = AutoSubDomain(topandbottom)
ASD2 = AutoSubDomain(cylinderwall)
mf = MeshFunction("size_t", mesh, 1)
mf.set_all(0)
ASD1.mark(mf, 1)
ASD2.mark(mf, 2)
self.ds_ = ds(subdomain_data=mf, domain=mesh)
return
def main():
fsr = FunctionSubspaceRegistry()
deg = 2
mesh = dolfin.UnitSquareMesh(100, 3)
muc = mesh.ufl_cell()
el_w = dolfin.FiniteElement('DG', muc, deg - 1)
el_j = dolfin.FiniteElement('BDM', muc, deg)
el_DG0 = dolfin.FiniteElement('DG', muc, 0)
el = dolfin.MixedElement([el_w, el_j])
space = dolfin.FunctionSpace(mesh, el)
DG0 = dolfin.FunctionSpace(mesh, el_DG0)
fsr.register(space)
facet_normal = dolfin.FacetNormal(mesh)
xyz = dolfin.SpatialCoordinate(mesh)
trial = dolfin.Function(space)
test = dolfin.TestFunction(space)
w, c = dolfin.split(trial)
v, phi = dolfin.split(test)
sympy_exprs = derive_exprs()
exprs = {
k: sympy_dolfin_printer.to_ufl(sympy_exprs['R'], mesh, v)
for k, v in sympy_exprs['quantities'].items()
}
f = exprs['f']
w0 = dolfin.project(dolfin.conditional(dolfin.gt(xyz[0], 0.5), 1.0, 0.3),
DG0)
w_BC = exprs['w']
dx = dolfin.dx()
form = (+v * dolfin.div(c) * dx - v * f * dx +
dolfin.exp(w + w0) * dolfin.dot(phi, c) * dx +
dolfin.div(phi) * w * dx -
(w_BC - w0) * dolfin.dot(phi, facet_normal) * dolfin.ds() -
(w0('-') - w0('+')) * dolfin.dot(phi('+'), facet_normal('+')) *
dolfin.dS())
solver = NewtonSolver(form,
trial, [],
parameters=dict(relaxation_parameter=1.0,
maximum_iterations=15,
extra_iterations=10,
relative_tolerance=1e-6,
absolute_tolerance=1e-7))
solver.solve()
with closing(XdmfPlot("out/qflop_test.xdmf", fsr)) as X:
CG1 = dolfin.FunctionSpace(mesh, dolfin.FiniteElement('CG', muc, 1))
X.add('w0', 1, w0, CG1)
X.add('w_c', 1, w + w0, CG1)
X.add('w_e', 1, exprs['w'], CG1)
X.add('f', 1, f, CG1)
X.add('cx_c', 1, c[0], CG1)
X.add('cx_e', 1, exprs['c'][0], CG1)
def test_store_mesh(casedir):
pp = PostProcessor(dict(casedir=casedir))
from dolfin import (UnitSquareMesh, CellFunction, FacetFunction,
AutoSubDomain, Mesh, HDF5File, assemble, Expression,
ds, dx)
# Store mesh
mesh = UnitSquareMesh(6, 6)
celldomains = CellFunction("size_t", mesh)
celldomains.set_all(0)
AutoSubDomain(lambda x: x[0] < 0.5).mark(celldomains, 1)
facetdomains = FacetFunction("size_t", mesh)
AutoSubDomain(lambda x, on_boundary: x[0] < 0.5 and on_boundary).mark(
facetdomains, 1)
pp.store_mesh(mesh, celldomains, facetdomains)
# Read mesh back
mesh2 = Mesh()
f = HDF5File(mpi_comm_world(), os.path.join(pp.get_casedir(), "mesh.hdf5"),
'r')
f.read(mesh2, "Mesh", False)
celldomains2 = CellFunction("size_t", mesh2)
f.read(celldomains2, "CellDomains")
facetdomains2 = FacetFunction("size_t", mesh2)
f.read(facetdomains2, "FacetDomains")
e = Expression("1+x[1]", degree=1)
dx1 = dx(1, domain=mesh, subdomain_data=celldomains)
dx2 = dx(1, domain=mesh2, subdomain_data=celldomains2)
C1 = assemble(e * dx1)
C2 = assemble(e * dx2)
assert abs(C1 - C2) < 1e-10
ds1 = ds(1, domain=mesh, subdomain_data=facetdomains)
ds2 = ds(1, domain=mesh2, subdomain_data=facetdomains2)
F1 = assemble(e * ds1)
F2 = assemble(e * ds2)
assert abs(F1 - F2) < 1e-10
def navier_stokes_IPCS(mesh, dt, parameter):
"""
fenics code: weak form of the problem.
"""
mu, rho, nu = parameter
V = VectorFunctionSpace(mesh, 'P', 2)
Q = FunctionSpace(mesh, 'P', 1)
bc0 = DirichletBC(V, Constant((0, 0)), cylinderwall)
bc1 = DirichletBC(V, Constant((0, 0)), topandbottom)
bc2 = DirichletBC(V, U0, inlet)
bc3 = DirichletBC(Q, Constant(1), outlet)
bcs = [bc0, bc1, bc2, bc3]
# ds is needed to compute drag and lift. Not used here.
ASD1 = AutoSubDomain(topandbottom)
ASD2 = AutoSubDomain(cylinderwall)
mf = MeshFunction("size_t", mesh, 1)
mf.set_all(0)
ASD1.mark(mf, 1)
ASD2.mark(mf, 2)
ds_ = ds(subdomain_data=mf, domain=mesh)
vu, vp = TestFunction(V), TestFunction(Q) # for integration
u_, p_ = Function(V), Function(Q) # for the solution
u_1, p_1 = Function(V), Function(Q) # for the prev. solution
u, p = TrialFunction(V), TrialFunction(Q) # unknown!
bcu = [bcs[0], bcs[1], bcs[2]]
bcp = [bcs[3]]
n = FacetNormal(mesh)
u_mid = (u + u_1) / 2.0
F1 = rho*dot((u - u_1) / dt, vu)*dx \
+ rho*dot(dot(u_1, nabla_grad(u_1)), vu)*dx \
+ inner(sigma(u_mid, p_1, mu), epsilon(vu))*dx \
+ dot(p_1*n, vu)*ds - dot(mu*nabla_grad(u_mid)*n, vu)*ds
a1 = lhs(F1)
L1 = rhs(F1)
# Define variational problem for step 2
a2 = dot(nabla_grad(p), nabla_grad(vp)) * dx
L2 = dot(nabla_grad(p_1), nabla_grad(vp)) * dx - (
rho / dt) * div(u_) * vp * dx # rho missing in FEniCS tutorial
# Define variational problem for step 3
a3 = dot(u, vu) * dx
L3 = dot(u_, vu) * dx - dt * dot(nabla_grad(p_ - p_1), vu) * dx
# Assemble matrices
A1 = assemble(a1)
A2 = assemble(a2)
A3 = assemble(a3)
# Apply boundary conditions to matrices
[bc.apply(A1) for bc in bcu]
[bc.apply(A2) for bc in bcp]
return u_, p_, u_1, p_1, L1, A1, L2, A2, L3, A3, bcu, bcp
def cavityvol(self): u = self.parameters["displacement_variable"] N = self.parameters["facet_normal"] mesh = self.parameters["mesh"] X = SpatialCoordinate(mesh) ds = dolfin.ds(subdomain_data=self.parameters["facetboundaries"]) F = self.Fmat() vol_form = -Constant(1.0/3.0) * inner(det(F)*dot(inv(F).T, N), X + u)*ds(self.parameters["endoid"]) return assemble(vol_form)
def set_FEM(self):
"""
Define finite element space of elliptic PDE.
"""
self.mesh = df.UnitSquareMesh(self.nx, self.ny)
self.mpi_comm = self.mesh.mpi_comm()
# boundaries
self.boundaries = df.FacetFunction("size_t", self.mesh, 0)
self.ds = df.ds(subdomain_data=self.boundaries)
# 2. Define the finite element spaces and build mixed space
try:
V_fe = df.FiniteElement("CG", self.mesh.ufl_cell(), 2)
L_fe = df.FiniteElement("CG", self.mesh.ufl_cell(), 2)
self.V = df.FunctionSpace(self.mesh, V_fe)
self.W = df.FunctionSpace(self.mesh, V_fe * L_fe)
except TypeError:
print('Warning: '
'MixedFunctionSpace'
' has been deprecated in DOLFIN version 1.7.0.')
print('It will be removed from version 2.0.0.')
self.V = df.FunctionSpace(self.mesh, 'CG', 2)
L = df.FunctionSpace(self.mesh, 'CG', 2)
self.W = self.V * L
# 3. Define boundary conditions
bc_lagrange = df.DirichletBC(
self.W.sub(1), df.Constant(0.0),
"fabs(x[0])>2.0*DOLFIN_EPS & fabs(x[0]-1.0)>2.0*DOLFIN_EPS & fabs(x[1])>2.0*DOLFIN_EPS & fabs(x[1]-1.0)>2.0*DOLFIN_EPS"
)
self.ess_bc = [bc_lagrange]
# Create adjoint boundary conditions (homogenized forward BCs)
def homogenize(bc):
bc_copy = df.DirichletBC(bc)
bc_copy.homogenize()
return bc_copy
self.adj_bcs = [homogenize(bc) for bc in self.ess_bc]
def compute(self, get):
u = get("Velocity")
mu = get("DynamicViscosity")
if isinstance(mu, (float, int)):
mu = Constant(mu)
n = self._n
T = -mu*dot((grad(u) + grad(u).T), n)
Tn = dot(T, n)
Tt = T - Tn*n
tau_form = dot(self.v, Tt)*ds()
assemble(tau_form, tensor=self.tau.vector())
#self.b[self._keys] = self.tau.vector()[self._values] # FIXME: This is not safe!!!
get_set_vector(self.b, self._keys, self.tau.vector(), self._values, self._temp_array)
# Ensure proper scaling
self.solver.solve(self.tau_boundary.vector(), self.b)
return self.tau_boundary
def compute(self, get):
u = get("Velocity")
mu = get("DynamicViscosity")
if isinstance(mu, (float, int)):
mu = Constant(mu)
n = self._n
T = -mu * dot((grad(u) + grad(u).T), n)
Tn = dot(T, n)
Tt = T - Tn * n
tau_form = dot(self.v, Tt) * ds()
assemble(tau_form, tensor=self.tau.vector())
#self.b[self._keys] = self.tau.vector()[self._values] # FIXME: This is not safe!!!
get_set_vector(self.b, self._keys, self.tau.vector(), self._values,
self._temp_array)
# Ensure proper scaling
self.solver.solve(self.tau_boundary.vector(), self.b)
return self.tau_boundary
def setup_problem(mesh, U0, coupled=True):
# Build function space
V = VectorFunctionSpace(mesh, 'P', 2)
Q = FunctionSpace(mesh, 'P', 1)
L = FunctionSpace(mesh, 'P', 1)
VQL = (V, Q, L)
# bc0 = DirichletBC(V, Constant((0, 0)), cylinderwall)
bc1 = DirichletBC(V, Constant((0, 0)), topandbottom)
bc2 = DirichletBC(V, U0, inlet)
bc3 = DirichletBC(Q, Constant(1), outlet)
# bcs = [bc0, bc1, bc2, bc3]
bcs = [bc1, bc2, bc3]
warnings.warn("no no-slip for cyl-wall!")
ASD1 = AutoSubDomain(topandbottom)
ASD2 = AutoSubDomain(cylinderwall)
mf = MeshFunction("size_t", mesh, 1)
mf.set_all(0)
ASD1.mark(mf, 1)
ASD2.mark(mf, 2)
ds_ = ds(subdomain_data=mf, domain=mesh)
return VQL, bcs, ds_
def ds(self):
"""Return the surface measure of exterior facets using
self.mesh as domain and self.ffun as subdomain_data
"""
return dolfin.ds(domain=self.mesh, subdomain_data=self.ffun)
def solve(self):
""" Find eigenvalues for transformed mesh. """
self.progress("Building mesh.")
# build transformed mesh
mesh = self.refineMesh()
# dim = mesh.topology().dim()
if self.bcLast:
mesh = transform_mesh(mesh, self.transformList)
Robin, Steklov, shift, bcs = get_bc_parts(mesh, self.bcList)
else:
Robin, Steklov, shift, bcs = get_bc_parts(mesh, self.bcList)
mesh = transform_mesh(mesh, self.transformList)
# boundary conditions computed on non-transformed mesh
# copy the values to transformed mesh
fun = FacetFunction("size_t", mesh, shift)
fun.array()[:] = bcs.array()[:]
bcs = fun
ds = Measure('ds', domain=mesh, subdomain_data=bcs)
V = FunctionSpace(mesh, self.method, self.deg)
u = TrialFunction(V)
v = TestFunction(V)
self.progress("Assembling matrices.")
wTop = Expression(self.wTop, degree=self.deg)
wBottom = Expression(self.wBottom, degree=self.deg)
#
# build stiffness matrix form
#
s = dot(grad(u), grad(v))*wTop*dx
# add Robin parts
for bc in Robin:
s += Constant(bc.parValue)*u*v*wTop*ds(bc.value+shift)
#
# build mass matrix form
#
if len(Steklov) > 0:
m = 0
for bc in Steklov:
m += Constant(bc.parValue)*u*v*wBottom*ds(bc.value+shift)
else:
m = u*v*wBottom*dx
# assemble
# if USE_EIGEN:
# S, M = EigenMatrix(), EigenMatrix()
# tempv = EigenVector()
# else:
S, M = PETScMatrix(), PETScMatrix()
# tempv = PETScVector()
if not np.any(bcs.array() == shift+1):
# no Dirichlet parts
assemble(s, tensor=S)
assemble(m, tensor=M)
else:
#
# with EIGEN we could
# apply Dirichlet condition symmetrically
# completely remove rows and columns
#
# Dirichlet parts are marked with shift+1
#
# temp = Constant(0)*v*dx
bc = DirichletBC(V, Constant(0.0), bcs, shift+1)
# assemble_system(s, temp, bc, A_tensor=S, b_tensor=tempv)
# assemble_system(m, temp, bc, A_tensor=M, b_tensor=tempv)
assemble(s, tensor=S)
bc.apply(S)
assemble(m, tensor=M)
# bc.zero(M)
# if USE_EIGEN:
# M = M.sparray()
# M.eliminate_zeros()
# print M.shape
# indices = M.indptr[:-1] - M.indptr[1:] < 0
# M = M[indices, :].tocsc()[:, indices]
# S = S.sparray()[indices, :].tocsc()[:, indices]
# print M.shape
#
# solve the eigenvalue problem
#
self.progress("Solving eigenvalue problem.")
eigensolver = SLEPcEigenSolver(S, M)
eigensolver.parameters["problem_type"] = "gen_hermitian"
eigensolver.parameters["solver"] = "krylov-schur"
if self.target is not None:
eigensolver.parameters["spectrum"] = "target real"
eigensolver.parameters["spectral_shift"] = self.target
else:
eigensolver.parameters["spectrum"] = "smallest magnitude"
eigensolver.parameters["spectral_shift"] = -0.01
eigensolver.parameters["spectral_transform"] = "shift-and-invert"
eigensolver.solve(self.number)
self.progress("Generating eigenfunctions.")
if eigensolver.get_number_converged() == 0:
return None
eigf = []
eigv = []
if self.deg > 1:
mesh = refine(mesh)
W = FunctionSpace(mesh, 'CG', 1)
for i in range(eigensolver.get_number_converged()):
pair = eigensolver.get_eigenpair(i)[::2]
eigv.append(pair[0])
u = Function(V)
u.vector()[:] = pair[1]
eigf.append(interpolate(u, W))
return eigv, eigf
def main():
L = 10.0
H = 10.0
mesh = df.UnitSquare(10,10,'left')
mesh.coordinates()[:,0] *= L
mesh.coordinates()[:,1] *= H
U = df.VectorFunctionSpace(mesh, "Lagrange", 1, dim=2)
U_x, U_y = U.split()
u = df.TrialFunction(U)
v = df.TestFunction(U)
E = 2.0E11
nu = 0.3
lmbda = nu*E/((1.0 + nu)*(1.0 - 2.0*nu))
mu = E/(2.0*(1.0 + nu))
# Elastic Modulus
C_numpy = np.array([[lmbda + 2.0*mu, lmbda, 0.0],
[lmbda, lmbda + 2.0*mu, 0.0],
[0.0, 0.0, mu ]])
C = df.as_matrix(C_numpy)
from dolfin import dot, dx, grad, inner, ds
def eps(u):
""" Returns a vector of strains of size (3,1) in the Voigt notation
layout {eps_xx, eps_yy, gamma_xy} where gamma_xy = 2*eps_xy"""
return df.as_vector([u[i].dx(i) for i in range(2)] +
[u[i].dx(j) + u[j].dx(i) for (i,j) in [(0,1)]])
a = inner(eps(v), C*eps(u))*dx
A = a
# Dirichlet BC
class LeftBoundary(df.SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and np.abs(x[0]) < tol
class RightBoundary(df.SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and np.abs(x[0] - self.L) < tol
class BottomBoundary(df.SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and np.abs(x[1]) < tol
left_boundary = LeftBoundary()
right_boundary = RightBoundary()
right_boundary.L = L
bottom_boundary = BottomBoundary()
zero = df.Constant(0.0)
bc_left_Ux = df.DirichletBC(U_x, zero, left_boundary)
bc_bottom_Uy = df.DirichletBC(U_y, zero, bottom_boundary)
bcs = [bc_left_Ux, bc_bottom_Uy]
# Neumann BCs
t = df.Constant(10000.0)
boundary_parts = df.EdgeFunction("uint", mesh, 1)
right_boundary.mark(boundary_parts, 0)
l = inner(t,v[0])*ds(0)
u_h = df.Function(U)
problem = df.LinearVariationalProblem(A, l, u_h, bcs=bcs)
solver = df.LinearVariationalSolver(problem)
solver.parameters["linear_solver"] = "direct"
solver.solve()
u_x, u_y = u_h.split()
stress = df.project(C*eps(u_h), df.VectorFunctionSpace(mesh, "Lagrange", 1, dim=3))
df.plot(u_x)
df.plot(u_y)
df.plot(stress[0])
df.interactive()
def ds(self):
"""Returns the mesh surface measure using `self.ffun` as `subdomain_data`
"""
return df.ds(domain=self.mesh, subdomain_data=self.ffun)
def gamma_fun(
v,
hol_cyl,
T_step_d, #from direct pbm
boundary_faces,
mark_in,
mark_ex,
T_ex_d,
g_d,
gamma_reg0, #the old gamma_reg
omegac, #contraction factor
muc,
itera_div,
unitNormal,
time_v,
cut_end,
itera,
path_to_do):
'''
Returns the optimal regularization parameter.
T_step from direct problem.
'''
num1_v = np.zeros((len(T_step_d), ))
num2_v = np.zeros((len(T_step_d), ))
num3_v = np.zeros((len(T_step_d), ))
den1_v = np.zeros((len(T_step_d), ))
for count_it in sorted(T_step_d):
#scalar
num1_v[count_it] = do.assemble(
pow(T_step_d[count_it] - T_ex_d[count_it], 2.) *
do.ds(mark_ex, domain=hol_cyl, subdomain_data=boundary_faces))
num2_v[count_it] = do.assemble(
pow(T_step_d[count_it], 2.) *
do.ds(mark_ex, domain=hol_cyl, subdomain_data=boundary_faces))
num3_v[count_it] = do.assemble(
pow(T_ex_d[count_it], 2.) *
do.ds(mark_ex, domain=hol_cyl, subdomain_data=boundary_faces))
#scalar
den1_v[count_it] = do.assemble(
pow(g_d[count_it], 2.) *
do.ds(mark_in, domain=hol_cyl, subdomain_data=boundary_faces))
print 'gamma: count_t = {}, num1 = {}'.format(count_it,
num1_v[count_it])
print 'gamma: count_t = {}, den1 = {}'.format(count_it,
den1_v[count_it]), '\n'
fig_inf = plt.figure(figsize=(20, 10))
for i_fig in xrange(12):
vari = 1. * num1_v * (i_fig / 3 == 0) + \
1. * num2_v * (i_fig / 3 == 1) + \
1. * num3_v * (i_fig / 3 == 2) + \
1. * den1_v * (i_fig / 3 == 3)
ytag = 'num1' * (i_fig / 3 == 0) + \
'num2' * (i_fig / 3 == 1) + \
'num3' * (i_fig / 3 == 2) + \
'den1' * (i_fig / 3 == 3)
stai = 0 * (i_fig % 3 == 0) + \
0 * (i_fig % 3 == 1) + \
-50 * (i_fig % 3 == 2)
endi = len(vari) * (i_fig % 3 == 0) + \
50 * (i_fig % 3 == 1) + \
len(vari) * (i_fig % 3 == 2)
ax_inf = fig_inf.add_subplot(4, 3, i_fig + 1)
ax_inf.plot(vari[stai:endi])
ax_inf.set_ylabel(ytag)
ax_inf.grid()
nam_inf = os.path.join(path_to_do, 'gamma_{}.pdf'.format(itera))
fig_inf.savefig(nam_inf, dpi=150)
#num1_avg = np.trapz(num1_v[5 : -5], x = time_v[5 : -5])
#den1_avg = np.trapz(den1_v[5 : -5], x = time_v[5 : -5])
num1_avg = np.trapz(num1_v[:cut_end], x=time_v[:cut_end])
num2_avg = np.trapz(num2_v[:cut_end], x=time_v[:cut_end])
num3_avg = np.trapz(num3_v[:cut_end], x=time_v[:cut_end])
den1_avg = np.trapz(den1_v[:cut_end], x=time_v[:cut_end])
if itera > itera_div:
#divisions are allowed
C_avg = -1. / den1_avg * (num2_avg + gamma_reg0 * den1_avg)**2.
T_avg = num2_avg / den1_avg
#Eq. (2.10) in Heng's paper
aH = 2. * muc * num3_avg
bH = +(2. + 4. * muc) * C_avg
cH = -(2. + 2. * muc) * C_avg * T_avg
x10 = (-bH + (bH**2. - 4. * aH * cH)**.5) / (2. * aH)
x20 = (-bH - (bH**2. - 4. * aH * cH)**.5) / (2. * aH)
x11 = x10 - T_avg
x21 = x20 - T_avg
if x11 > 1e-14 and x21 > 1e-14:
#Two positive roots
#take the smaller one
gamma_reg = min(x11, x21)
else:
#Remark 3.8 in Heng's paper
#restart
gamma_reg = -omegac * (T_avg + cH / bH + aH / bH *
(T_avg + gamma_reg0)**2.)
gamma_reg_unused = 2. * num1_avg / den1_avg
else:
#divisions are not allowed
gamma_reg = 1. * gamma_reg0
gamma_reg_unused = 1. * gamma_reg0
return gamma_reg, gamma_reg_unused, \
num1_avg, num2_avg, num3_avg, den1_avg
def nablau_fun(
V,
v,
hol_cyl,
A,
boundary_faces,
mark_in,
dg_d, #S_in
k_mesh_old,
cp_mesh_old,
rho_mesh_old,
dt,
time_v,
theta,
itera):
'''
Sensitivity problem.
Solves A u = L.
A = dt * theta * k_mesh * do.dot(do.grad(T), do.grad(v)) * do.dx(domain = hol_cyl) + \
rho_mesh * cp_mesh * T * v * do.dx(domain = hol_cyl)
Solved after setting dg_in = p^k.
'''
#solver parameters
#linear solvers from
#list_linear_solver_methods()
#preconditioners from
#do.list_krylov_solver_preconditioners()
solver = do.KrylovSolver('gmres', 'ilu')
do.info(solver.parameters, False) #prints default values
solver.parameters['relative_tolerance'] = 1e-13
solver.parameters['maximum_iterations'] = 200000
solver.parameters['monitor_convergence'] = True #on the screen
#http://fenicsproject.org/qa/1124/
#is-there-a-way-to-set-the-inital-guess-in-the-krylov-solver
'''solver.parameters['nonzero_initial_guess'] = True'''
#solver.parameters['absolute_tolerance'] = 1e-15
#uses whatever in q_v as my initial condition
#starts from 0
#u_stept = do.TrialFunction(V)
u_step3 = do.Function(V)
#starts from 0
u_old = do.Function(V)
u_step3_d = {}
theta = do.Constant(theta)
dt = do.Constant(dt)
#A = dt / 2. * k_mesh_old * do.dot(do.grad(u_stept), do.grad(v)) * do.dx(domain = hol_cyl) + \
# rho_mesh_old * cp_mesh_old * u_stept * v * do.dx(domain = hol_cyl)
for count_t_i, t_i in enumerate(time_v[1:]):
#storage
u_step3_d[count_t_i] = do.Function(V)
u_step3_d[count_t_i].vector()[:] = u_step3.vector().array()
#int_fluxT_ex = 0
int_fluxT_in = dg_d[count_t_i + 1] * v * do.ds(
mark_in, domain=hol_cyl, subdomain_data=boundary_faces)
int_fluxT_in_old = dg_d[count_t_i] * v * do.ds(
mark_in, domain=hol_cyl, subdomain_data=boundary_faces)
#L -= (int_fluxT_in + int_fluxT_ex)
L_old = -dt * (1. - theta) * k_mesh_old * do.dot(do.grad(u_old), do.grad(v)) * \
do.dx(domain = hol_cyl) + \
rho_mesh_old * cp_mesh_old * u_old * v * do.dx(domain = hol_cyl)
L = L_old + (dt * theta * int_fluxT_in + dt *
(1. - theta) * int_fluxT_in_old)
do.solve(A == L, u_step3)
print 'u: count_t = {}, min(dg) = {}'.format(
count_t_i, min(dg_d[count_t_i].vector().array()))
print 'u: count_t = {}, max(dg) = {}'.format(
count_t_i, max(dg_d[count_t_i].vector().array()))
print 'u: count_t = {}, min(int_fluxT_in) = {}'.format(
count_t_i, min(do.assemble(int_fluxT_in).array()))
print 'u: count_t = {}, max(int_fluxT_in) = {}'.format(
count_t_i, max(do.assemble(int_fluxT_in).array()))
print 'u: count_t = {}, min(L) = {}'.format(
count_t_i, min(do.assemble(L).array()))
print 'u: count_t = {}, max(L) = {}'.format(
count_t_i, max(do.assemble(L).array()))
print 'u: count_t = {}, min(u) = {}'.format(
count_t_i, min(u_step3.vector().array()))
print 'u: count_t = {}, max(u) = {}'.format(
count_t_i, max(u_step3.vector().array())), '\n'
u_old.assign(u_step3)
count_t_i += 1
#storage
u_step3_d[count_t_i] = do.Function(V)
u_step3_d[count_t_i].vector()[:] = u_step3.vector().array()
return u_step3_d
def transport_linear(integrator_type, mesh, subdomains, boundaries, t_start, dt, T, solution0, \
alpha_0, K_0, mu_l_0, lmbda_l_0, Ks_0, \
alpha_1, K_1, mu_l_1, lmbda_l_1, Ks_1, \
alpha, K, mu_l, lmbda_l, Ks, \
cf_0, phi_0, rho_0, mu_0, k_0,\
cf_1, phi_1, rho_1, mu_1, k_1,\
cf, phi, rho, mu, k, \
d_0, d_1, d_t,
vel_c, p_con, A_0, Temp, c_extrapolate):
# Create mesh and define function space
parameters["ghost_mode"] = "shared_facet" # required by dS
dx = Measure('dx', domain=mesh, subdomain_data=subdomains)
ds = Measure('ds', domain=mesh, subdomain_data=boundaries)
dS = Measure('dS', domain=mesh, subdomain_data=boundaries)
C_cg = FiniteElement("CG", mesh.ufl_cell(), 1)
C_dg = FiniteElement("DG", mesh.ufl_cell(), 0)
mini = C_cg + C_dg
C = FunctionSpace(mesh, mini)
C = BlockFunctionSpace([C])
TM = TensorFunctionSpace(mesh, 'DG', 0)
PM = FunctionSpace(mesh, 'DG', 0)
n = FacetNormal(mesh)
vc = CellVolume(mesh)
fc = FacetArea(mesh)
h = vc / fc
h_avg = (vc('+') + vc('-')) / (2 * avg(fc))
penalty1 = Constant(1.0)
tau = Function(PM)
tau = tau_cal(tau, phi, -0.5)
tuning_para = 0.25
vel_norm = (dot(vel_c, n) + abs(dot(vel_c, n))) / 2.0
cell_size = CellDiameter(mesh)
vnorm = sqrt(dot(vel_c, vel_c))
I = Identity(mesh.topology().dim())
d_eff = Function(TM)
d_eff = diff_coeff_cal_rev(d_eff, d_0, tau,
phi) + tuning_para * cell_size * vnorm * I
monitor_dt = dt
# Define variational problem
dc, = BlockTrialFunction(C)
dc_dot, = BlockTrialFunction(C)
psic, = BlockTestFunction(C)
block_c = BlockFunction(C)
c, = block_split(block_c)
block_c_dot = BlockFunction(C)
c_dot, = block_split(block_c_dot)
theta = -1.0
a_time = phi * rho * inner(c_dot, psic) * dx
a_dif = dot(rho*d_eff*grad(c),grad(psic))*dx \
- dot(avg_w(rho*d_eff*grad(c),weight_e(rho*d_eff,n)), jump(psic, n))*dS \
+ theta*dot(avg_w(rho*d_eff*grad(psic),weight_e(rho*d_eff,n)), jump(c, n))*dS \
+ penalty1/h_avg*k_e(rho*d_eff,n)*dot(jump(c, n), jump(psic, n))*dS
a_adv = -dot(rho*vel_c*c,grad(psic))*dx \
+ dot(jump(psic), rho('+')*vel_norm('+')*c('+') - rho('-')*vel_norm('-')*c('-') )*dS \
+ dot(psic, rho*vel_norm*c)*ds(3)
R_c = R_c_cal(c_extrapolate, p_con, Temp)
c_D1 = Constant(0.5)
rhs_c = R_c * A_s_cal(phi, phi_0, A_0) * psic * dx - dot(
rho * phi * vel_c, n) * c_D1 * psic * ds(1)
r_u = [a_dif + a_adv]
j_u = block_derivative(r_u, [c], [dc])
r_u_dot = [a_time]
j_u_dot = block_derivative(r_u_dot, [c_dot], [dc_dot])
r = [r_u_dot[0] + r_u[0] - rhs_c]
# this part is not applied.
exact_solution_expression1 = Expression("1.0",
t=0,
element=C[0].ufl_element())
def bc(t):
p5 = DirichletBC(C.sub(0),
exact_solution_expression1,
boundaries,
1,
method="geometric")
return BlockDirichletBC([p5])
# Define problem wrapper
class ProblemWrapper(object):
def set_time(self, t):
pass
# Residual and jacobian functions
def residual_eval(self, t, solution, solution_dot):
return r
def jacobian_eval(self, t, solution, solution_dot,
solution_dot_coefficient):
return [[
Constant(solution_dot_coefficient) * j_u_dot[0, 0] + j_u[0, 0]
]]
# Define boundary condition
def bc_eval(self, t):
pass
# Define initial condition
def ic_eval(self):
return solution0
# Define custom monitor to plot the solution
def monitor(self, t, solution, solution_dot):
pass
problem_wrapper = ProblemWrapper()
(solution, solution_dot) = (block_c, block_c_dot)
solver = TimeStepping(problem_wrapper, solution, solution_dot)
solver.set_parameters({
"initial_time": t_start,
"time_step_size": dt,
"monitor": {
"time_step_size": monitor_dt,
},
"final_time": T,
"exact_final_time": "stepover",
"integrator_type": integrator_type,
"problem_type": "linear",
"linear_solver": "mumps",
"report": True
})
export_solution = solver.solve()
return export_solution, T
def __ufl_forms(self, nu, f):
(w, q, wbar, qbar) = self.__test_functions()
(u, p, ubar, pbar) = self.__trial_functions()
# Infer geometric dimension
zero_vec = np.zeros(self.gdim)
ds = self.ds
n = self.n
he = self.he
alpha = self.alpha
h_d = self.h_d
beta_stab = self.beta_stab
facet_integral = self.facet_integral
pI = p * Identity(
self.mixedL.sub(1).ufl_cell().topological_dimension())
pbI = pbar * \
Identity(self.mixedL.sub(1).ufl_cell().topological_dimension())
# Upper left block
# Contribution comes from local momentum balance
AB = inner(2*nu*sym(grad(u)), grad(w))*dx \
+ facet_integral(dot(-2*nu*sym(grad(u))*n
+ (2*nu*alpha/he)*u, w)) \
+ facet_integral(dot(-2*nu*u, sym(grad(w))*n)) \
- inner(pI, grad(w))*dx
# Contribution comes from local mass balance
BtF = -dot(q, div(u))*dx - \
facet_integral(beta_stab*he/(nu+1)*dot(p, q))
A_S = AB + BtF
# Upper right block
# Contribution from local momentum
CD = facet_integral(-alpha/he*2*nu*inner(ubar, w)) \
+ facet_integral(2*nu*inner(ubar, sym(grad(w))*n)) \
+ facet_integral(dot(pbI*n, w))
H = facet_integral(beta_stab * he / (nu + 1) * dot(pbar, q))
G_S = CD + H
# Transpose block
CDT = facet_integral(- alpha/he*2*nu*inner(wbar, u)) \
+ facet_integral(2*nu*inner(wbar, sym(grad(u))*n)) \
+ facet_integral(qbar * dot(u, n))
HT = facet_integral(beta_stab * he / (nu + 1) * dot(p, qbar))
G_ST = CDT + HT
# Lower right block, penalty on ds(98) approximates free-slip
KL = facet_integral(alpha/he * 2 * nu*dot(ubar, wbar)) \
- facet_integral(dot(pbar*n, wbar)) \
+ Constant(1E12)/he * inner(outer(ubar, wbar), outer(n, n)) * ds(98)
LtP = - facet_integral(dot(ubar, n)*qbar) \
- facet_integral(beta_stab*he/(nu+1) * pbar * qbar)
B_S = KL + LtP
# Righthandside
Q_S = dot(f, w) * dx
S_S = facet_integral(dot(Constant(zero_vec), wbar))
S_S += dot(h_d[0], wbar) * ds(99) + dot(h_d[1], wbar) * ds(
100) #Neumann BC
return {
'A_S': A_S,
'G_S': G_S,
'G_ST': G_ST,
'B_S': B_S,
'Q_S': Q_S,
'S_S': S_S
}
boundary_markers = dolfin.MeshFunction('size_t', mesh, boundary_dim)
boundary_markers.set_all(0) # Assign all elements the default value
id_subdomain_fix = 1 # Fixed boundary id
id_subdomain_msr = 2 # Loaded boundary id
id_subdomains_dic = 3 # displacement field measurement boundary id
boundary_fix.mark(boundary_markers, id_subdomain_fix)
boundary_msr.mark(boundary_markers, id_subdomain_msr)
boundary_dic.mark(boundary_markers, id_subdomains_dic)
### Integration measures
dx = dolfin.dx(domain=mesh) # for the whole domain
ds = dolfin.ds(domain=mesh) # for the entire boundary
ds_msr_T = dolfin.Measure('ds',
mesh,
subdomain_id=id_subdomain_msr,
subdomain_data=boundary_markers)
ds_msr_u = dolfin.Measure('ds',
mesh,
subdomain_id=id_subdomains_dic,
subdomain_data=boundary_markers)
### Finite element function spaces
V = dolfin.VectorFunctionSpace(mesh, 'CG', FINITE_ELEMENT_DEGREE)
dolfin.lt((x[0] - 0.5)**2, 0.35**2), 1.0, 0.0)
bcs = [dolfin.DirichletBC(space, lower_boundary_value, lower_boundary)]
if not no_side_bc:
def _side_bc(subdomain):
bcs.append(dolfin.DirichletBC(space, dolfin.Constant(0.0), subdomain))
if theta < np.pi / 2:
_side_bc(left_boundary)
else:
_side_bc(right_boundary)
# alpha = dolfin.Constant(1.0)
alpha = dolfin.conditional(
dolfin.lt((x[0] - 0.5)**2 + (x[1] - 0.5)**2, 0.2**2), 6.0, 1.0)
# alpha = dolfin.conditional(dolfin.And(dolfin.gt(x[0], 0.5), dolfin.gt(x[1], 0.5)), 4.0, 1.0)
alpha = dolfin.project(alpha, space) # needs to be continuous
S = dolfin.Constant(0.0) * x[0]
dsf, dxf = make_form(I=u, v=test_function, omega=omega, beta=alpha, S=S)
form = dsf * dolfin.ds() + dxf * dolfin.dx()
solver = NewtonSolver(form, u, bcs)
solver.solve()
# dolfin.plot(u)
# dolfin.plot(alpha)
MPI.barrier(mpicomm)
t0 = time()
KV = assemble(weak_V)
MPI.barrier(mpicomm)
t1 = time()
if mpirank == 0: print 'Time to assemble KV = {}'.format(t1-t0)
elif myrun == 2:
class LeftRight(SubDomain):
def inside(self, x, on_boundary):
return (x[0] < 1e-16 or x[0] > 1.0 - 1e-16) \
and on_boundary
class_bc_abc = LeftRight()
abc_boundaryparts = FacetFunction("size_t", mesh)
class_bc_abc.mark(abc_boundaryparts, 1)
ds = Measure("ds")[abc_boundaryparts]
weak_1 = inner(sqrt(lam1*rho1)*nabla_grad(trial), nabla_grad(test))*ds(1)
weak_2 = inner(sqrt(lam2*rho2)*nabla_grad(trial), nabla_grad(test))*ds(1)
lam1.vector()[:] = 1.0
rho1.vector()[:] = 1.0
print 'Start assembling K2'
t0 = time()
K2 = assemble(weak_2)
t1 = time()
print 'Time to assemble K2 = {}'.format(t1-t0)
lam2.vector()[:] = 1.0
rho2.vector()[:] = 1.0
print 'Start assembling K1'
t0 = time()
K1 = assemble(weak_1)
def nablaT_fun(
V,
v,
hol_cyl,
A,
boundary_faces,
mark_in,
mark_ex,
T_old_v,
g_d, #S_in
T_sol_d,
T_ex, #S_ex
unitNormal,
k_mesh_old,
cp_mesh_old,
rho_mesh_old,
dt,
time_v,
theta,
itera,
mesh_name,
savings_do):
'''
Direct problem.
Solves A T = L.
A = dt * theta * k_mesh * do.dot(do.grad(T), do.grad(v)) * do.dx(domain = hol_cyl) + \
rho_mesh * cp_mesh * T * v * do.dx(domain = hol_cyl)
int_fluxT_ex = -k_mesh * do.dot(unitNormal, do.grad(T_sol)) * v * \
do.ds(mark_ex,
domain = hol_cyl,
subdomain_data = boundary_faces)
no T_ex on outer boundary.
'''
#solver parameters
#linear solvers from
#list_linear_solver_methods()
#preconditioners from
#do.list_krylov_solver_preconditioners()
solver = do.KrylovSolver('gmres', 'ilu')
do.info(solver.parameters, False) #prints default values
solver.parameters['relative_tolerance'] = 1e-13
solver.parameters['maximum_iterations'] = 2000000
solver.parameters['monitor_convergence'] = True #on the screen
#http://fenicsproject.org/qa/1124/
#is-there-a-way-to-set-the-inital-guess-in-the-krylov-solver
solver.parameters['nonzero_initial_guess'] = True
#solver.parameters['absolute_tolerance'] = 1e-15
#T_stept = do.TrialFunction(V)
T_step1 = do.Function(V)
T_old = do.Function(V)
#T_old_v is a scalar
T_step1.vector()[:] = T_old_v
T_old.vector()[:] = T_old_v
T_step1_d = {}
print 'T: min(g_d[0]) = ', min(g_d[0].vector().array())
print 'T: max(g_d[0]) = ', max(g_d[0].vector().array())
theta = do.Constant(theta)
dt = do.Constant(dt)
T_step1_f = do.File(os.path.join(savings_do, str(itera), 'dir_IHCP.pvd'))
#A = dt / 2. * k_mesh_old * do.dot(do.grad(T_stept), do.grad(v)) * do.dx(domain = hol_cyl) + \
# rho_mesh_old * cp_mesh_old * T_stept * v * do.dx(domain = hol_cyl)
for count_t_i, t_i in enumerate(time_v[1:]):
#storage
T_step1_d[count_t_i] = do.Function(V)
T_step1_d[count_t_i].vector()[:] = T_step1.vector().array()
#g is a k * dot(grad(T), n)
int_fluxT_in = g_d[count_t_i + 1] * v * do.ds(
mark_in, domain=hol_cyl, subdomain_data=boundary_faces)
int_fluxT_in_old = g_d[count_t_i] * v * do.ds(
mark_in, domain=hol_cyl, subdomain_data=boundary_faces)
int_fluxT_ex = + k_mesh_old * do.dot(unitNormal, do.grad(T_sol_d[count_t_i + 1])) * \
v * do.ds(mark_ex,
domain = hol_cyl,
subdomain_data = boundary_faces)
int_fluxT_ex_old = + k_mesh_old * do.dot(unitNormal, do.grad(T_sol_d[count_t_i])) * \
v * do.ds(mark_ex,
domain = hol_cyl,
subdomain_data = boundary_faces)
#print 'T: type(int_fluxT_in) = ', type(int_fluxT_in)
#print 'T: type(int_fluxT_in_old) = ', type(int_fluxT_in_old)
#print 'T: min(int_fluxT_in) = ', min(do.assemble(int_fluxT_in))
#L -= (int_fluxT_in + int_fluxT_ex)
L_old = -dt * (1. - theta) * k_mesh_old * do.dot(do.grad(T_old), do.grad(v)) * \
do.dx(domain = hol_cyl) + \
rho_mesh_old * cp_mesh_old * T_old * v * do.dx(domain = hol_cyl)
L = L_old + (dt * theta * int_fluxT_in + dt *
(1. - theta) * int_fluxT_in_old +
dt * theta * int_fluxT_ex + dt *
(1. - theta) * int_fluxT_ex_old)
do.solve(A == L, T_step1) #, bc_ex)
print 'T: count_t = {}, avg(g) = {}'.format(
count_t_i, np.mean(g_d[count_t_i + 1].vector().array()))
print 'T: count_t = {}, min(L) = {}'.format(
count_t_i, min(do.assemble(L).array()))
print 'T: count_t = {}, max(L) = {}'.format(
count_t_i, max(do.assemble(L).array()))
print 'T: count_t = {}, min(T) = {}'.format(
count_t_i, min(T_step1.vector().array()))
print 'T: count_t = {}, max(T) = {}'.format(
count_t_i, max(T_step1.vector().array()))
print 'T: count_t = {}, min(T_DHCP) = {}'.format(
count_t_i, min(T_sol_d[count_t_i].vector().array()))
print 'T: count_t = {}, max(T_DHCP) = {}'.format(
count_t_i, max(T_sol_d[count_t_i].vector().array())), '\n'
T_old.assign(T_step1)
#rename
T_step1.rename('IHCP_T', 'temperature from IHCP')
T_step1_f << (T_step1, t_i)
count_t_i += 1
#storage
T_step1_d[count_t_i] = do.Function(V)
T_step1_d[count_t_i].vector()[:] = T_step1.vector().array()
return T_step1_d
g_v = dolfin.Constant(-2.0) # In[164]: g_h = dolfin.Constant(1.0) # In[165]: L = f * v * dolfin.dx(domain=mesh, subdomain_data=boundary_parts) # In[166]: L += g_v * v * dolfin.ds(0, domain=mesh, subdomain_data=boundary_parts) # In[167]: L += g_h * v * dolfin.ds(1, domain=mesh, subdomain_data=boundary_parts) # In[168]: u_sol = dolfin.Function(V) # In[169]: dolfin.solve(a == L, u_sol, bc)
def nablap_fun(
V,
v,
hol_cyl,
A,
boundary_faces,
mark_ex,
T_step_d,
T_exp_d, #S_ex
k_mesh_oldp,
cp_mesh_oldp,
rho_mesh_oldp,
dt,
time_v,
theta,
itera,
mesh_name,
savings_do):
'''
Adjoint problem.
Solves A p = L.
A = dt * theta * k_mesh * do.dot(do.grad(p), do.grad(v)) * do.dx(domain = hol_cyl) + \
rho_mesh * cp_mesh * p * v * do.dx(domain = hol_cyl)
T_stepp: from T_step flipped.
T_exp : from T_ex flipped.
'''
#solver parameters
#linear solvers from
#list_linear_solver_methods()
#preconditioners from
#do.list_krylov_solver_preconditioners()
solver = do.KrylovSolver('gmres', 'ilu')
do.info(solver.parameters, False) #prints default values
solver.parameters['relative_tolerance'] = 1e-13
solver.parameters['maximum_iterations'] = 2000000
solver.parameters['monitor_convergence'] = True #on the screen
#http://fenicsproject.org/qa/1124/
#is-there-a-way-to-set-the-inital-guess-in-the-krylov-solver
'''solver.parameters['nonzero_initial_guess'] = True'''
#solver.parameters['absolute_tolerance'] = 1e-15
#uses whatever in q_v as my initial condition
#p_stept = do.TrialFunction(V)
p_step2 = do.Function(V)
#starts from 0
p_old = do.Function(V)
p_step2_d = {}
#e.g., e.g., count_t_i = 100
#storage
p_step2_d[len(time_v) - 1] = do.Function(V)
p_step2_d[len(time_v) - 1].vector()[:] = p_old.vector().array()
theta = do.Constant(theta)
dt = do.Constant(dt)
p_step2_f = do.File(os.path.join(savings_do, str(itera), 'adj_IHCP.pvd'))
#A = dt / 2. * k_mesh_oldp * do.dot(do.grad(p_stept), do.grad(v)) * do.dx(domain = hol_cyl) + \
# rho_mesh_oldp * cp_mesh_oldp * p_stept * v * do.dx(domain = hol_cyl)
#runs backwards in time
for count_t_i, t_i in reversed(list(enumerate(time_v[:-1]))):
#int_fluxT_in = 0
#e.g., count_t_i = 99
int_fluxT_ex = (T_step_d[count_t_i] - T_exp_d[count_t_i]) * v * \
do.ds(mark_ex,
domain = hol_cyl,
subdomain_data = boundary_faces)
#'old' = old tau = new time; e.g., count_t_i + 1 = 100
int_fluxT_ex_old = (T_step_d[count_t_i + 1] - T_exp_d[count_t_i + 1]) * v * \
do.ds(mark_ex,
domain = hol_cyl,
subdomain_data = boundary_faces)
L_oldp = -dt * (1. - theta) * k_mesh_oldp * do.dot(do.grad(p_old), do.grad(v)) * \
do.dx(domain = hol_cyl) + \
rho_mesh_oldp * cp_mesh_oldp * p_old * v * do.dx(domain = hol_cyl)
#before:
#L = L_oldp - (dt * theta * int_fluxT_ex + dt * (1. - theta) * int_fluxT_ex_old)
L = L_oldp + (dt * theta * int_fluxT_ex + dt *
(1. - theta) * int_fluxT_ex_old)
do.solve(A == L, p_step2)
print 'p: count_t = {}, min(T_step_d) = {}'.format(
count_t_i, min(T_step_d[count_t_i].vector().array()))
print 'p: count_t = {}, max(T_step_d) = {}'.format(
count_t_i, max(T_step_d[count_t_i].vector().array()))
print 'p: count_t = {}, min(int_fluxT_ex) = {}'.format(
count_t_i, min(do.assemble(int_fluxT_ex).array()))
print 'p: count_t = {}, max(int_fluxT_ex) = {}'.format(
count_t_i, max(do.assemble(int_fluxT_ex).array()))
print 'p: count_t = {}, min(L) = {}'.format(
count_t_i, min(do.assemble(L).array()))
print 'p: count_t = {}, max(L) = {}'.format(
count_t_i, max(do.assemble(L).array()))
print 'p: count_t = {}, min(p) = {}'.format(count_t_i,
min(p_step2.vector()))
print 'p: count_t = {}, max(p) = {}'.format(
count_t_i, max(p_step2.vector())), '\n'
p_old.assign(p_step2)
p_step2.rename('dual_T', 'dual temperature')
#storage
p_step2_d[count_t_i] = do.Function(V)
p_step2_d[count_t_i].vector()[:] = p_step2.vector().array()
p_step2_f << (p_step2, t_i)
return p_step2_d
print 'err: len(keys in T_sol_d2) = ', len(T_sol_d2.keys())
print 'err: len(keys in T_step_d2) = ', len(T_step_d2.keys())
#update variables
for count_t_i1, t_i1 in enumerate(time_v1):
#heat flux
g_d2[count_t_i1].vector()[:] = g_d2[count_t_i1].vector().array() + \
alpha_step2 * p_step_d2[count_t_i1].vector().array()
#adjoint variable
derJ_step_old_d2[count_t_i1].vector(
)[:] = derJ_step_d2[count_t_i1].vector().array()
#exit criterion
exit_crit_v[count_t_i1] = do.assemble(
pow(alpha_step2 * p_step_d2[count_t_i1], 2.) * do.ds(
mark_in2, domain=hol_cyl2, subdomain_data=boundary_faces2))
#do.File(os.path.join(savings_dol1,
#'{}__T_from_IHCP.pvd'.format(mesh_name1.split('.')[0]))) << T_step11
print 'err: count_t_i1 = ', count_t_i1
#T_sol_d3 instead of T_sol_d2
e11_v[count_t_i1], e21_v[count_t_i1] = err_est_fun(
mesh_name2, hol_cyl2, T_sol_d3[count_t_i1],
T_step_d2[count_t_i1], deg_choice1, hol_cyl2, count_t_i1)
#functional
J2 = .5 * obj_f1 + .5 * gamma_reg2 * obj_f2
#store the error
err_d2.append(
[gamma_reg2_old,
def eta_fun(
v,
hol_cyl,
#k, #conductivity
gamma, #regularization
T_step_d, #from direct pbm
p_step_d, #from adjoint pbm and gamma_CG1
u_step_d, #from sensitivity pbm
boundary_faces,
mark_in,
mark_ex,
g_d,
dg_d,
T_ex_d,
unitNormal,
time_v,
cut_end,
itera,
path_to_do):
'''
Returns the optimal step size.
T_step from direct problem.
p_step from adjoint problem.
u_step from sensitivity problem.
'''
num1_v = np.zeros((len(T_step_d), ))
num2_v = np.zeros((len(T_step_d), ))
den1_v = np.zeros((len(T_step_d), ))
den2_v = np.zeros((len(T_step_d), ))
for count_it in sorted(T_step_d):
#scalar
'''
num1_v[count_it] = do.assemble(dg_d[count_it] * p_step_d[count_it] *
do.ds(mark_in,
domain = hol_cyl,
subdomain_data = boundary_faces))
'''
num1_v[count_it] = do.assemble(
(T_step_d[count_it] - T_ex_d[count_it]) * u_step_d[count_it] *
do.ds(mark_ex, domain=hol_cyl, subdomain_data=boundary_faces))
#scalar
num2_v[count_it] = do.assemble(
p_step_d[count_it] * g_d[count_it] *
do.ds(mark_in, domain=hol_cyl, subdomain_data=boundary_faces))
#scalar
den1_v[count_it] = do.assemble(
pow(u_step_d[count_it], 2.) *
do.ds(mark_ex, domain=hol_cyl, subdomain_data=boundary_faces))
#scalar
den2_v[count_it] = do.assemble(
pow(p_step_d[count_it], 2.) *
do.ds(mark_in, domain=hol_cyl, subdomain_data=boundary_faces))
print 'eta: count_t = {}, num1 = {}'.format(count_it, num1_v[count_it])
print 'eta: count_t = {}, num2 = {}'.format(count_it, num2_v[count_it])
print 'eta: count_t = {}, den1 = {}'.format(count_it, den1_v[count_it])
print 'eta: count_t = {}, den2 = {}'.format(count_it,
den2_v[count_it]), '\n'
fig_inf = plt.figure(figsize=(20, 10))
for i_fig in xrange(12):
vari = 1. * num1_v * (i_fig / 3 == 0) + \
1. * num2_v * (i_fig / 3 == 1) + \
1. * den1_v * (i_fig / 3 == 2) + \
1. * den2_v * (i_fig / 3 == 3)
ytag = 'num1' * (i_fig / 3 == 0) + \
'num2' * (i_fig / 3 == 1) + \
'den1' * (i_fig / 3 == 2) + \
'den2' * (i_fig / 3 == 3)
stai = 0 * (i_fig % 3 == 0) + \
0 * (i_fig % 3 == 1) + \
-50 * (i_fig % 3 == 2)
endi = len(vari) * (i_fig % 3 == 0) + \
50 * (i_fig % 3 == 1) + \
len(vari) * (i_fig % 3 == 2)
ax_inf = fig_inf.add_subplot(4, 3, i_fig + 1)
ax_inf.plot(vari[stai:endi])
ax_inf.set_ylabel(ytag)
ax_inf.grid()
nam_inf = os.path.join(path_to_do, 'eta_{}.pdf'.format(itera))
fig_inf.savefig(nam_inf, dpi=150)
num1_avg = np.trapz(num1_v[:cut_end], x=time_v[:cut_end])
num2_avg = np.trapz(num2_v[:cut_end], x=time_v[:cut_end])
den1_avg = np.trapz(den1_v[:cut_end], x=time_v[:cut_end])
den2_avg = np.trapz(den2_v[:cut_end], x=time_v[:cut_end])
return -(num1_avg + gamma * num2_avg) / (den1_avg + gamma * den2_avg)
import dolfin
mesh = dolfin.UnitSquareMesh(50, 20)
el = dolfin.FiniteElement("BDM", mesh.ufl_cell(), 1)
x = dolfin.SpatialCoordinate(mesh)
expr = dolfin.as_vector((dolfin.sin(1 / x[0] + x[1]), 2 * x[1]))
W = dolfin.FunctionSpace(mesh, el)
w = dolfin.project(expr, W)
example_testfunc = dolfin.TestFunction(W)
example_form = dolfin.dot(w,
example_testfunc) * dolfin.dx() + w[0] * dolfin.ds()
def solve_tr_dir__const_rheo(mesh_name, hol_cyl, deg_choice, T_in_expr,
T_inf_expr, HTC, T_old_v, k_mesh, cp_mesh,
rho_mesh, k_mesh_old, cp_mesh_old, rho_mesh_old,
dt, time_v, theta, bool_plot, bool_solv,
savings_do, logger_f):
'''
mesh_name: a proper XML file.
bool_plot: plots if bool_plot = 1.
Solves a direct, steady-state heat conduction problem, and
returns A_np, b_np, D_np, T_np, bool_ex, bool_in.
A_np: stiffness matrix, ordered by vertices.
b_np: integrated volumetric heat sources and surface heat fluxes, ordered by vertices.
The surface heat fluxes come from the solution to the direct problem;
hence, these terms will not be there in a real IHCP.
D_np: integrated Laplacian of T, ordered by vertices.
Option 2.
The Laplacian of q is properly assembled from D_np.
If do.dx(domain = hol_cyl) -> do.Measure('ds')[boundary_faces] and
do.Measure('ds')[boundary_faces] -> something representative of Gamma,
I would get option 1.
T_np: solution to the direct heat conduction problem, ordered by vertices.
bool_ex: boolean array declaring which vertices lie on the outer boundary.
bool_in: boolean array indicating which vertices lie on the inner boundary.
T_sol: solution to the direct heat conduction problem.
deg_choice: degree in FunctionSpace.
hol_cyl: mesh.
'''
#comm1 = MPI.COMM_WORLD
#current proc
#rank1 = comm1.Get_rank()
V = do.FunctionSpace(hol_cyl, 'CG', deg_choice)
if 'hollow' in mesh_name and 'cyl' in mesh_name:
from hollow_cyl_inv_mesh import geo_fun as geo_fun_hollow_cyl
geo_params_d = geo_fun_hollow_cyl()[1]
#x_c is a scalar here
#y_c is a scalar here
elif 'four' in mesh_name and 'cyl' in mesh_name:
from four_hole_cyl_inv_mesh import geo_fun as geo_fun_four_hole_cyl
geo_params_d = geo_fun_four_hole_cyl()[1]
#x_c is an array here
#y_c is an array here
x_c_l = [geo_params_d['x_0_{}'.format(itera)] for itera in xrange(4)]
y_c_l = [geo_params_d['y_0_{}'.format(itera)] for itera in xrange(4)]
elif 'one_hole_cir' in mesh_name:
from one_hole_cir_adj_mesh import geo_fun as geo_fun_one_hole_cir
geo_params_d = geo_fun_one_hole_cir()[1]
#x_c is an array here
#y_c is an array here
x_c_l = [geo_params_d['x_0']]
y_c_l = [geo_params_d['y_0']]
elif 'reinh_cir' in mesh_name:
from reinh_cir_adj_mesh import geo_fun as geo_fun_one_hole_cir
geo_params_d = geo_fun_one_hole_cir()[1]
#x_c is an array here
#y_c is an array here
x_c_l = [geo_params_d['x_0']]
y_c_l = [geo_params_d['y_0']]
elif 'small_circle' in mesh_name:
from four_hole_small_cir_adj_mesh import geo_fun as geo_fun_four_hole_cir
geo_params_d = geo_fun_four_hole_cir()[1]
#x_c is an array here
#y_c is an array here
x_c_l = [geo_params_d['x_0_{}'.format(itera)] for itera in xrange(4)]
y_c_l = [geo_params_d['y_0_{}'.format(itera)] for itera in xrange(4)]
#center of the cylinder base
x_c = geo_params_d['x_0']
y_c = geo_params_d['y_0']
R_in = geo_params_d['R_in']
R_ex = geo_params_d['R_ex']
#define variational problem
T = do.TrialFunction(V)
g = do.Function(V)
v = do.TestFunction(V)
T_old = do.Function(V)
T_inf = do.Function(V)
#scalar
T_old.vector()[:] = T_old_v
T_inf.vector()[:] = T_inf_expr
#solution
T_sol = do.Function(V)
#scalar
T_sol.vector()[:] = T_old_v
# Create boundary markers
mark_all = 3
mark_in = 4
mark_ex = 5
#x_c is an array here
#y_c is an array here
g_in = g_in_mesh(mesh_name, x_c_l, y_c_l, R_in)
g_ex = g_ex_mesh(mesh_name, x_c, y_c, R_ex)
in_boundary = do.AutoSubDomain(g_in)
ex_boundary = do.AutoSubDomain(g_ex)
#normal
unitNormal = do.FacetNormal(hol_cyl)
boundary_faces = do.MeshFunction('size_t', hol_cyl,
hol_cyl.topology().dim() - 1)
boundary_faces.set_all(mark_all)
in_boundary.mark(boundary_faces, mark_in)
ex_boundary.mark(boundary_faces, mark_ex)
bc_in = do.DirichletBC(V, T_in_expr, boundary_faces, mark_in)
#bc_ex = do.DirichletBC(V, T_ex_expr, boundary_faces, mark_ex)
bcs = [bc_in]
#k = do.Function(V) #W/m/K
#k.vector()[:] = k_mesh
#A0 = k * do.dot(do.grad(T), do.grad(v)) * do.dx(domain = hol_cyl)
A = dt / 2. * k_mesh * do.dot(do.grad(T), do.grad(v)) * do.dx(domain = hol_cyl) + \
rho_mesh * cp_mesh * T * v * do.dx(domain = hol_cyl)
A_full = A + dt / 2. * HTC * T * v * do.ds(
mark_ex, domain=hol_cyl, subdomain_data=boundary_faces)
L = -dt / 2. * k_mesh_old * do.dot(do.grad(T_old), do.grad(v)) * \
do.dx(domain = hol_cyl) + \
rho_mesh_old * cp_mesh_old * T_old * v * do.dx(domain = hol_cyl) - \
dt / 2. * HTC * (T_old) * v * do.ds(mark_ex,
domain = hol_cyl,
subdomain_data = boundary_faces) + \
dt * HTC * T_inf * v * do.ds(mark_ex,
domain = hol_cyl,
subdomain_data = boundary_faces)
#numpy version of A, T, and (L + int_fluxT)
#A_np__not_v2d = do.assemble(A).array() #before applying BCs - needs v2d
#L_np__not_v2d = do.assemble(L).array() #before applying BCs - needs v2d
#Laplacian of T, without any -1/k int_S q*n*v dS
'''
Approximated integral of the Laplacian of T.
Option 2.
The Laplacian of q is properly assembled from D_np.
If do.dx(domain = hol_cyl) -> do.Measure('ds')[boundary_faces] and
do.Measure('ds')[boundary_faces] -> something representative of Gamma,
I would get option 1.
'''
#D_np__not_v2d = do.assemble(-do.dot(do.grad(T), do.grad(v)) * do.dx(domain = hol_cyl) +
# do.dot(unitNormal, do.grad(T)) * v *
# do.Measure('ds')[boundary_faces]).array()
#print np.max(D_np__not_v2d)#, np.max(A_np__not_v2d)
#logger_f.warning('shape of D_np = {}, {}'.format(D_np__not_v2d.shape[0],
#D_np__not_v2d.shape[1]))
#nonzero_entries = []
#for row in D_np__not_v2d:
# nonzero_entries += [len(np.where(abs(row) > 1e-16)[0])]
#logger_f.warning('max, min, and mean of nonzero_entries = {}, {}, {}'.format(
# max(nonzero_entries), min(nonzero_entries), np.mean(nonzero_entries)))
#solver parameters
#linear solvers from
#list_linear_solver_methods()
#preconditioners from
#do.list_krylov_solver_preconditioners()
solver = do.KrylovSolver('gmres', 'ilu')
do.info(solver.parameters, True) #prints default values
solver.parameters['relative_tolerance'] = 1e-16
solver.parameters['maximum_iterations'] = 20000000
solver.parameters['monitor_convergence'] = True #on the screen
#http://fenicsproject.org/qa/1124/is-there-a-way-to-set-the-inital-guess-in-the-krylov-solver
'''solver.parameters['nonzero_initial_guess'] = True'''
solver.parameters['absolute_tolerance'] = 1e-15
#uses whatever in q_v as my initial condition
#the next lines are used for CHECK 3 only
#A_sys, b_sys = do.assemble_system(A, L, bcs)
do.File(
os.path.join(savings_do, '{}__markers.pvd'.format(
mesh_name.split('.')[0]))) << boundary_faces
if bool_plot:
do.plot(boundary_faces, '3D mesh', title='boundary markers')
#storage
T_sol_d = {}
g_d = {}
if bool_solv == 1:
xdmf_DHCP_T = do.File(os.path.join(savings_do, 'DHCP', 'T.pvd'))
xdmf_DHCP_q = do.File(os.path.join(savings_do, 'DHCP', 'q.pvd'))
for count_t_i, t_i in enumerate(time_v[1:]):
#T_in_expr.ts = t_i
#T_ex_expr.ts = t_i
#storage
T_sol_d[count_t_i] = do.Function(V)
T_sol_d[count_t_i].vector()[:] = T_sol.vector().array()
do.solve(A_full == L, T_sol, bcs)
'''
TO BE UPDATED:
rheology is not updated
'''
#updates L
T_old.assign(T_sol)
T_sol.rename('DHCP_T', 'temperature from DHCP')
#write solution to file
#paraview format
xdmf_DHCP_T << (T_sol, t_i)
#plot solution
if bool_plot:
do.plot(T_sol, title='T') #, interactive = True)
logger_f.warning('len(T) = {}'.format(len(T_sol.vector().array())))
print 'T: count_t = {}, min(T_DHCP) = {}'.format(
count_t_i, min(T_sol_d[count_t_i].vector().array()))
print 'T: count_t = {}, max(T_DHCP) = {}'.format(
count_t_i, max(T_sol_d[count_t_i].vector().array())), '\n'
#save flux - required for solving IHCP
#same result if do.ds(mark_ex, subdomain_data = boundary_faces)
#instead of do.Measure('ds')[boundary_faces]
#Langtangen, p. 37:
#either do.dot(do.nabla_grad(T), unitNormal)
#or do.dot(unitNormal, do.grad(T))
#int_fluxT = do.assemble(-k * do.dot(unitNormal, do.grad(T_sol)) * v *
# do.Measure('ds')[boundary_faces])
fluxT = do.project(
-k_mesh * do.grad(T_sol),
do.VectorFunctionSpace(hol_cyl, 'CG', deg_choice, dim=2))
if bool_plot:
do.plot(fluxT,
title='flux at iteration = {}'.format(count_t_i))
fluxT.rename('DHCP_flux', 'flux from DHCP')
xdmf_DHCP_q << (fluxT, t_i)
print 'DHCP: iteration = {}'.format(count_t_i)
####################################################
#full solution
#T_sol_full = do.Vector()
#T_sol.vector().gather(T_sol_full, np.array(range(V.dim()), 'intc'))
####################################################
count_t_i += 1
#copy previous lines
#storage
T_sol_d[count_t_i] = do.Function(V)
T_sol_d[count_t_i].vector()[:] = T_sol.vector().array()
for count_t_i, t_i in enumerate(time_v):
#storage
g_d[count_t_i] = do.Function(V)
g_d[count_t_i].vector()[:] = g.vector().array()
gdim = hol_cyl.geometry().dim()
dofmap = V.dofmap()
dofs = dofmap.dofs()
#Get coordinates as len(dofs) x gdim array
dofs_x = V.tabulate_dof_coordinates().reshape((-1, gdim))
#booleans corresponding to the outer boundary -> ints since they are sent to root = 0
bool_ex = 1. * np.array([g_ex(dof_x) for dof_x in dofs_x])
#booleans corresponding to the inner boundary -> ints since they are sent to root = 0
bool_in = 1. * np.array([g_in(dof_x) for dof_x in dofs_x])
T_np_ex = []
T_np_in = []
for i_coor, coor in enumerate(dofs_x):
if g_ex(coor):
T_np_ex += [T_sol.vector().array()[i_coor]]
if g_in(coor):
T_np_in += [T_sol.vector().array()[i_coor]]
print 'CHECK: mean(T) on the outer boundary = ', np.mean(np.array(T_np_ex))
print 'CHECK: mean(T) on the inner boundary = ', np.mean(np.array(T_np_in))
print 'CHECK: mean(HTC) = ', np.mean(do.project(HTC, V).vector().array())
#v2d = do.vertex_to_dof_map(V) #orders by hol_cyl.coordinates()
if deg_choice == 1:
print 'len(dof_to_vertex_map) = ', len(do.dof_to_vertex_map(V))
print 'min(dofs) = ', min(dofs), ', max(dofs) = ', max(dofs)
print 'len(bool ex) = ', len(bool_ex)
print 'len(bool in) = ', len(bool_in)
print 'bool ex[:10] = ', repr(bool_ex[:10])
print 'type(T) = ', type(T_sol.vector().array())
#first global results, then local results
return A, L, g_d, \
V, v, k_mesh, \
mark_in, mark_ex, \
boundary_faces, bool_ex, \
R_in, R_ex, T_sol_d, deg_choice, hol_cyl, \
unitNormal, dofs_x
def femsolve():
''' Bilineaarinen muoto:
a(u,v) = L(v)
a(u,v) = (inner(grad(u), grad(v)) + u*v)*dx
L(v) = f*v*dx - g*v*ds
g(x) = -du/dx = -u1, x = x1
u(x0) = u0
Omega = {xeR|x0<=x<=x1}
'''
from dolfin import UnitInterval, FunctionSpace, DirichletBC, TrialFunction
from dolfin import TestFunction, grad, Constant, Function, solve, inner, dx, ds
from dolfin import MeshFunction, assemble
import dolfin
# from dolfin import set_log_level, PROCESS
# Create mesh and define function space
mesh = UnitInterval(30)
V = FunctionSpace(mesh, 'Lagrange', 2)
boundaries = MeshFunction('uint', mesh, mesh.topology().dim()-1)
boundaries.set_all(0)
class Left(dolfin.SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14 # tolerance for coordinate comparisons
return on_boundary and abs(x[0]) < tol
class Right(dolfin.SubDomain):
def inside(self, x, on_boundary):
return dolfin.near(x[0], 1.0)
left = Left()
right = Right()
left.mark(boundaries, 1)
right.mark(boundaries, 2)
# def u0_boundary(x):
# return abs(x[0]) < tol
#
# bc = DirichletBC(V, Constant(u0), lambda x: abs(x[0]) < tol)
bcs = [DirichletBC(V, Constant(u0), boundaries, 1)]
# Define variational problem
u = TrialFunction(V)
v = TestFunction(V)
a = (inner(grad(u), grad(v)) + u*v)*dx
g = Constant(-u1)
L = Constant(f)*v*dx - g*v*ds(2)
# set_log_level(PROCESS)
# Compute solution
A = assemble(a, exterior_facet_domains=boundaries)
b = assemble(L, exterior_facet_domains=boundaries)
for bc in bcs:
bc.apply(A, b)
u = Function(V)
solve(A, u.vector(), b, 'lu')
coor = mesh.coordinates()
u_array = u.vector().array()
a = []
b = []
for i in range(mesh.num_vertices()):
a.append(coor[i])
b.append(u_array[i])
print('u(%3.2f) = %0.14E'%(coor[i],u_array[i]))
import numpy as np
np.savez('fem',a,b)