Fem-fenics

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Package for solving Partial Differential Equations based on Fenics.

Tutorials

Poisson Equation

Here is a first example for the solution of the Poisson equation. The equation being solved is

Code: Define Poisson problem
 
pkg load fem-fenics msh
import_ufl_Problem ('Poisson')

# Create mesh and define function space
x = y = linspace (0, 1, 33);
mesh = Mesh(msh2m_structured_mesh (x, y, 1, 1:4));

# File Poisson.ufl
# element = FiniteElement("Lagrange", triangle, 1)
V = FunctionSpace('Poisson', mesh);





# Define boundary condition

bc = DirichletBC(V, @(x, y) 0.0, [2;4]);

# Define variational problem
# File Poisson.ufl
# u = TrialFunction(element)
# v = TestFunction(element)
# f = Coefficient(element)
# g = Coefficient(element)

f = Expression ('f', 
                 @(x,y) 10*exp(-((x - 0.5)^2 + (y - 0.5)^2) / 0.02));
g = Expression ('g', @(x,y) sin (5.0 * x));

# File Poisson.ufl
# a = inner(grad(u), grad(v))*dx
# L = f*v*dx + g*v*ds

a = BilinearForm ('Poisson', V);
L = LinearForm ('Poisson', V, f, g);

# Compute solution

[A, b] = assemble_system (a, L, bc);
sol = A \ b;
u = Function ('u', V, sol);

# Save solution in VTK format

save (u, 'poisson')

# Plot solution
plot (u);
Code: Define Poisson problem
 
from dolfin import *


# Create mesh and define function space

mesh = UnitSquareMesh(32, 32)



V = FunctionSpace(mesh, "Lagrange", 1)

# Define Dirichlet boundary (x = 0 or x = 1)
def boundary(x):
    return x[0] < DOLFIN_EPS or x[0] > 1.0 - DOLFIN_EPS

# Define boundary condition
u0 = Constant(0.0)
bc = DirichletBC(V, u0, boundary)

# Define variational problem

u = TrialFunction(V)
v = TestFunction(V)



f = Expression("10*exp(-(pow(x[0] - 0.5, 2) + pow(x[1] - 0.5, 2)) / 0.02)")

g = Expression("sin(5*x[0])")





a = inner(grad(u), grad(v))*dx
L = f*v*dx + g*v*ds

# Compute solution
u = Function(V)
(A, b) = assemble_system (a, L, bc);
solve(A, u.vector(), b, "gmres", "default")


# Save solution in VTK format
file = File("poisson.pvd")
file << u

# Plot solution
plot(u, interactive=True)


Mixed Formulation for Poisson Equation

Code: Define Poisson problem
 
pkg load fem-fenics msh
import_ufl_Problem ('MixedPoisson')

# Create mesh
x = y = linspace (0, 1, 33);
mesh = Mesh(msh2m_structured_mesh (x, y, 1, 1:4));

# File MixedPoisson.ufl
#  BDM = FiniteElement("BDM", triangle, 1)
#  DG  = FiniteElement("DG", triangle, 0)
#  W = BDM * DG
V = FunctionSpace('MixedPoisson', mesh);

# Define trial and test function
# File MixedPoisson.ufl
#  (sigma, u) = TrialFunctions(W)
#  (tau, v)   = TestFunctions(W)
#  CG = FiniteElement("CG", triangle, 1)
#  f = Coefficient(CG)
f = Expression ('f', 
                 @(x,y) 10*exp(-((x - 0.5)^2 + (y - 0.5)^2) / 0.02));

# Define variational form
# File MixedPoisson.ufl
#  a = (dot(sigma, tau) + div(tau)*u + div(sigma)*v)*dx
#  L = - f*v*dx
a = BilinearForm ('MixedPoisson', V);
L = LinearForm ('MixedPoisson', V, f);
















# Define essential boundary


bc1 = DirichletBC (SubSpace (V, 1), @(x,y) [0; -sin(5.0*x)], 1);
bc2 = DirichletBC (SubSpace (V, 1), @(x,y) [0;  sin(5.0*x)], 3);

# Compute solution
[A, b] = assemble_system (a, L, bc1, bc2);
sol = A \ b;
func = Function ('func', V, sol);

sigma = Function ('sigma', func, 1);
u = Function ('u', func, 2);

# Plot solution
plot (sigma);
plot (u);
Code: Define Poisson problem
 
from dolfin import *


# Create mesh
mesh = UnitSquareMesh(32, 32)

# Define function spaces and mixed (product) space
BDM = FunctionSpace(mesh, "BDM", 1)
DG = FunctionSpace(mesh, "DG", 0)
W = BDM * DG



# Define trial and test functions
(sigma, u) = TrialFunctions(W)
(tau, v) = TestFunctions(W)



f = Expression
    ("10*exp(-(pow(x[0] - 0.5, 2) + pow(x[1] - 0.5, 2)) / 0.02)")

# Define variational form

a = (dot(sigma, tau) + div(tau)*u + div(sigma)*v)*dx
L = - f*v*dx



# Define function G such that G \cdot n = g
class BoundarySource(Expression):
    def __init__(self, mesh):
        self.mesh = mesh
    def eval_cell(self, values, x, ufc_cell):
        cell = Cell(self.mesh, ufc_cell.index)
        n = cell.normal(ufc_cell.local_facet)
        g = sin(5*x[0])
        values[0] = g*n[0]
        values[1] = g*n[1]
    def value_shape(self):
        return (2,)

G = BoundarySource(mesh)

# Define essential boundary
def boundary(x):
    return x[1] < DOLFIN_EPS or x[1] > 1.0 - DOLFIN_EPS

bc = DirichletBC(W.sub(0), G, boundary)

# Compute solution
w = Function(W)
solve(a == L, w, bc)


(sigma, u) = w.split()


# Plot sigma and u
plot(sigma)
plot(u)
interactive()

Mixed Formulation for Poisson Equation

This time we compare the code with the c++ version of DOLFIN.

Code: HyperElasticity Problem: the ufl file
 
# Function spaces
element = VectorElement("Lagrange", tetrahedron, 1)

# Trial and test functions
du = TrialFunction(element)     # Incremental displacement
v  = TestFunction(element)      # Test function

# Functions
u = Coefficient(element)        # Displacement from previous iteration
B = Coefficient(element)        # Body force per unit volume
T = Coefficient(element)        # Traction force on the boundary

# Kinematics
I = Identity(element.cell().d)  # Identity tensor
F = I + grad(u)                 # Deformation gradient
C = F.T*F                       # Right Cauchy-Green tensor

# Invariants of deformation tensors
Ic = tr(C)
J  = det(F)

# Elasticity parameters
mu    = Constant(tetrahedron)
lmbda = Constant(tetrahedron)

# Stored strain energy density (compressible neo-Hookean model)
psi = (mu/2)*(Ic - 3) - mu*ln(J) + (lmbda/2)*(ln(J))**2

# Total potential energy
Pi = psi*dx - inner(B, u)*dx - inner(T, u)*ds

# First variation of Pi (directional derivative about u in the direction of v)
F = derivative(Pi, u, v)

# Compute Jacobian of F
J = derivative(F, u, du)
Code: Define Poisson problem
Code: Define Poisson problem