coupling_boundary = CouplingBoundary()
remaining_boundary = OuterBoundary()
bcs = [DirichletBC(V, u_D, remaining_boundary)]
# Define initial value
u_n = interpolate(u_D, V)
u_n.rename("Temperature", "")
precice = Adapter(adapter_config_filename,
interpolation_strategy=interpolation_strategy)
if problem is ProblemType.DIRICHLET:
precice_dt = precice.initialize(coupling_subdomain=coupling_boundary,
mesh=mesh,
read_field=u_D_function,
write_field=f_N_function,
u_n=u_n)
elif problem is ProblemType.NEUMANN:
precice_dt = precice.initialize(coupling_subdomain=coupling_boundary,
mesh=mesh,
read_field=f_N_function,
write_field=u_D_function,
u_n=u_n)
dt = Constant(0)
dt.assign(np.min([fenics_dt, precice_dt]))
# Define variational problem
u = TrialFunction(V)
v = TestFunction(V)
class Fluid(object):
def __init__(self, mesh, coupling_boundary, complementary_boundary, bndry, dt, theta, v_max,
mu_f, rho_f, result, *args, **kwargs):
# initialize meshes and boundaries
self.mesh = mesh
self.coupling_boundary = coupling_boundary
self.complementary_boundary = complementary_boundary
bnd_mesh = BoundaryMesh(mesh, 'exterior')
self.bndry = bndry # boundary-marking function for integration
self.fenics_dt = float(dt)
self.dt = Constant(dt)
self.theta = theta
self.t = 0.0
self.v_max = v_max
self.mu_f = mu_f
self.rho_f = rho_f
# bounding box tree
self.bb = BoundingBoxTree()
self.bb.build(self.mesh)
# Define finite elements
eV = VectorElement("CG", mesh.ufl_cell(), 2) # velocity element
eU = VectorElement("CG", mesh.ufl_cell(), 2) # displacement element
eP = FiniteElement("CG", mesh.ufl_cell(), 1) # pressure element
eW = MixedElement([eV, eU, eP]) # mixed element
W = FunctionSpace(self.mesh, eW) # function space for ALE fluid equation
self.W = W
self.U = FunctionSpace(self.mesh, eU) # function space for projected functions
self.W_boundary = VectorFunctionSpace(bnd_mesh, 'CG', 2) # boundary function space
self.fun4forces = Function(self.W) # function for Variational formulation
# Set boundary conditions
self.v_in = Expression(("t<2.0? 0.5*(1.0 - cos(0.5*pi*t))*v_max*4/(gW*gW)*(x[1]*(gW - x[1])): \
v_max*4/(gW*gW)*(x[1]*(gW - x[1]))", "0.0"),
degree = 2, v_max = Constant(self.v_max), gW = Constant(gW), t = self.t)
#info("Expression set.")
bc_v_in = DirichletBC(self.W.sub(0), self.v_in, bndry, _INFLOW)
bc_v_walls = DirichletBC(self.W.sub(0), Constant((0.0, 0.0)), bndry, _WALLS)
bc_v_circle = DirichletBC(self.W.sub(0), Constant((0.0, 0.0)), bndry, _FLUID_CYLINDER)
bc_u_in = DirichletBC(self.W.sub(1), Constant((0.0, 0.0)), bndry, _INFLOW)
bc_u_walls = DirichletBC(self.W.sub(1).sub(1), Constant(0.0), bndry, _WALLS)
bc_u_circle = DirichletBC(self.W.sub(1), Constant((0.0, 0.0)), bndry, _FLUID_CYLINDER)
bc_u_out = DirichletBC(self.W.sub(1), Constant((0.0, 0.0)), bndry, _OUTFLOW)
self.bcs = [bc_v_in, bc_v_walls, bc_v_circle, bc_u_in, bc_u_walls, bc_u_circle, bc_u_out]
#info("Normal and Circumradius.")
self.n = FacetNormal(self.mesh)
I = Identity(self.W.mesh().geometry().dim())
# Define functions
self.w = Function(self.W)
self.w0 = Function(self.W)
(v_, u_, p_) = TestFunctions(self.W)
(self.v, self.u, self.p) = split(self.w)
(self.v0, self.u0, self.p0) = split(self.w0)
# define coupling BCs
self.u_D = Constant((0.0, 0.0)) # Dirichlet BC (for Fluid)
self.u_D_function = interpolate(self.u_D, self.U) # Dirichlet BC as function
self.f_N = Constant((0.0, 0.0)) # Neumann BC (for Solid)
self.f_N_function = interpolate(self.f_N, self.U) # Neumann BC as function
# start preCICE adapter
info('Initialize Adapter.')
self.precice = Adapter()
# read forces(Neumann condition for solid) and write displacement(Dirichlet condition for fluid)
info('Call precice.initialize(...).')
self.precice_dt = self.precice.initialize(
coupling_subdomain=self.coupling_boundary, mesh=self.mesh,
read_field=self.u_D_function, write_field=self.f_N_function, u_n=self.w,#u_n,
coupling_marker=self.bndry)
# TODO: need to set DirichletBC for displacement AND velocity
# functions for displacement BC
self.u_bc = self.precice.create_coupling_dirichlet_boundary_condition(self.U)
self.u_bc0 = self.u_bc
dt = self.dt.values()[0]
self.v_bc = self.u_bc # wrong condition, but code runs
#self.v_bc = (1.0/self.dt)*(self.u_bc - self.u_bc0) # I need to do this, but raises error
bc_u_FSI = DirichletBC(self.W.sub(1), self.u_bc, coupling_boundary)
bc_v_FSI = DirichletBC(self.W.sub(0), self.v_bc, coupling_boundary)
self.bcs.append(bc_u_FSI)
self.bcs.append(bc_v_FSI)
# define deformation gradient, Jacobian
self.FF = I + grad(self.u)
self.FF0 = I + grad(self.u0)
self.JJ = det(self.FF)
self.JJ0 = det(self.FF0)
# mesh-moving eqaution (pseudoelasticity)
self.gamma = 9.0/8.0
h = CellVolume(self.mesh)**(self.gamma) # makes mesh stiffer when mesh finer
# (our mesh is finer by the FSI -moving- interface)
E = Constant(1.0)
E_mesh = E/h # Young Modulus
nu_mesh = Constant(-0.02) # Poisson ratio
mu_mesh = E_mesh/(2*(1.0+nu_mesh)) # Lame 1
lambda_mesh = (nu_mesh*E_mesh)/((1+nu_mesh)*(1-2*nu_mesh)) # Lame 2
# variational formulation for mesh motion
F_mesh = inner(mu_mesh*2*sym(grad(self.u)), grad(u_))*dx(0) \
+ lambda_mesh*inner(div(self.u), div(u_))*dx(0)
# define referential Grad and Div shortcuts
def Grad(f, F): return dot( grad(f), inv(F) )
def Div(f, F): return tr( Grad(f, F) )
# approximate time derivatives
du = (1.0/self.dt)*(self.u - self.u0)
dv = (1.0/self.dt)*(self.v - self.v0)
# compute velocuty part of Cauchy stress tensor for fluid
self.T_f = -self.p*I + 2*self.mu_f*sym(Grad(self.v, self.FF))
self.T_f0 = -self.p*I + 2*self.mu_f*sym(Grad(self.v0, self.FF0))
# compute 1st Piola-Kirchhoff tensor for fluid
self.S_f = self.JJ *( -self.p*I + self.T_f )*inv(self.FF).T
self.S_f0 = -self.JJ*self.p*I*inv(self.FF).T \
+ self.JJ0*self.T_f0*inv(self.FF0).T
# write equations for fluid
a_fluid = inner(self.S_f , Grad(v_, self.FF))*self.JJ*dx \
+ inner(self.rho_f*Grad(self.v, self.FF )*(self.v - du), v_)*self.JJ*dx
a_fluid0 = inner(self.S_f0, Grad(v_, self.FF0))*self.JJ0*dx \
+ inner(self.rho_f*Grad(self.v0, self.FF0)*(self.v0 - du), v_)*self.JJ0*dx
b_fluid = inner(Div( self.v, self.FF ), p_)*self.JJ*dx
b_fluid0 = inner(Div( self.v, self.FF ), p_)*self.JJ*dx
# final variationl formulation
self.F_fluid = (self.theta*self.JJ+(1.0 - self.theta)*self.JJ0)*self.rho_f*inner(dv, v_)*dx\
+ self.theta*(a_fluid + b_fluid) + (1.0 - self.theta)*(a_fluid0 + b_fluid0) \
+ F_mesh
# differentiate w.r.t. unknown
dF_fluid = derivative(self.F_fluid, self.w)
# define problem and its solver
self.problem = NonlinearVariationalProblem(self.F_fluid, self.w, bcs=self.bcs, J=dF_fluid)
self.solver = NonlinearVariationalSolver(self.problem)
# Variational problem for extracting forces
(v, u, p) = TrialFunctions(self.W)
self.traction = self.F_fluid - inner(v, v_)*ds(_FSI)
self.hBC = DirichletBC(self.W.sub(0), Constant((0.0, 0.0)), self.complementary_boundary)
# configure solver parameters
self.solver.parameters['newton_solver']['relative_tolerance'] = 1e-6
self.solver.parameters['newton_solver']['absolute_tolerance'] = 1e-10
self.solver.parameters['newton_solver']['maximum_iterations'] = 50
self.solver.parameters['newton_solver']['linear_solver'] = 'mumps'
# create files for saving
if my_rank == 0:
if not os.path.exists(result):
os.makedirs(result)
self.vfile = XDMFFile("%s/velocity.xdmf" % result)
self.ufile = XDMFFile("%s/displacement.xdmf" % result)
self.pfile = XDMFFile("%s/pressure.xdmf" % result)
self.sfile = XDMFFile("%s/stress.xdmf" % result)
self.vfile.parameters["flush_output"] = True
self.ufile.parameters["flush_output"] = True
self.pfile.parameters["flush_output"] = True
self.sfile.parameters["flush_output"] = True
with open(result+'/data.csv', 'w') as data_file:
writer = csv.writer(data_file, delimiter=';', lineterminator='\n')
writer.writerow(['time',
'x-coordinate of end of beam', 'y-coordinate of end of beam',
'drag', 'lift'])
#info("Fluid __init__ done")
def solve(self, t, n):
self.t = t
self.v_in.t = t
self.dt.assign(np.min([self.fenics_dt, self.precice_dt]))
# solve fluid equations
self.solver.solve()
# force-extracting procedure
ABdry = assemble(lhs(self.traction),keep_diagonal=True)
bBdry = assemble(rhs(self.traction))
self.hBC.apply(ABdry, bBdry)
solve(ABdry, self.fun4forces.vector(), bBdry)
self.fun4forces.set_allow_extrapolation(True)
(self.forces, _, _) = split(self.fun4forces)
self.forces = project(self.forces, self.U)
forces_for_solid = interpolate(self.forces, self.W_boundary)
# precice coupling step
t, n, precice_timestep_complete, self.precice_dt \
= self.precice.advance(forces_for_solid, self.w, self.w0, t, self.dt.values()[0], n)
return t, n, precice_timestep_complete
def save(self, t):
(v, u, p) = self.w.split()
# save functions to files
v.rename("v", "velocity")
u.rename("u", "displacement")
p.rename("p", "pressure")
self.vfile.write(v, t)
self.ufile.write(u, t)
self.pfile.write(p, t)
# Compute drag and lift
w_ = Function(self.W)
Fbc1 = DirichletBC(self.W.sub(0), Constant((1.0, 0.0)), self.bndry, _FLUID_CYLINDER)
Fbc2 = DirichletBC(self.W.sub(0), Constant((1.0, 0.0)), self.bndry, _FSI)
Fbc1.apply(w_.vector())
Fbc2.apply(w_.vector())
drag = -assemble(action(self.F_fluid,w_))
w_ = Function(self.W)
Fbc1 = DirichletBC(self.W.sub(0), Constant((0.0, 1.0)), self.bndry, _FLUID_CYLINDER)
Fbc2 = DirichletBC(self.W.sub(0), Constant((0.0, 1.0)), self.bndry, _FSI)
Fbc1.apply(w_.vector())
Fbc2.apply(w_.vector())
lift = -assemble(action(self.F_fluid,w_))
# MPI trick to extract beam displacement
self.w.set_allow_extrapolation(True)
Ax_loc = self.u[0]((A.x(), A.y()))
Ay_loc = self.u[1]((A.x(), A.y()))
self.w.set_allow_extrapolation(False)
pi = 0
if self.bb.compute_first_collision(A) < 4294967295:
pi = 1
else:
Ax_loc = 0.0
Ay_loc = 0.0
Ax = MPI.sum(comm, Ax_loc) / MPI.sum(comm, pi)
Ay = MPI.sum(comm, Ay_loc) / MPI.sum(comm, pi)
pi = 0
if self.bb.compute_first_collision(B) < 4294967295:
pi = 1
else:
pB_loc = 0.0
pB = MPI.sum(comm, pB_loc) / MPI.sum(comm, pi)
p_diff = pB - pA
# write data to data file
if my_rank == 0:
with open(result+'/data.csv', 'a') as data_file:
writer = csv.writer(data_file, delimiter=';', lineterminator='\n')
writer.writerow([t, Ax, Ay, drag, lift])
class Solid(object):
"""
Solid is defined as a object for which the subroutines solve() and save() are called externally in the time loop.
"""
def __init__(self, mesh, coupling_boundary, complementary_boundary, bndry,
dt, theta, lambda_s, mu_s, rho_s, result, *args, **kwargs):
self.mesh = mesh
self.coupling_boundary = coupling_boundary
self.complementary_boundary = complementary_boundary
self.fenics_dt = dt
self.dt = Constant(dt)
self.theta = theta
self.lambda_s = lambda_s
self.mu_s = mu_s
self.rho_s = rho_s
self.bndry = bndry
# bounding box tree - in parallel computations takes care about proper parallelization
self.bb = BoundingBoxTree()
self.bb.build(self.mesh)
# Define finite elements
eV = VectorElement("CG", mesh.ufl_cell(), 2) # velocity space
eU = VectorElement("CG", mesh.ufl_cell(), 2) # displacement space
eW = MixedElement([eV, eU]) # function space
W = FunctionSpace(self.mesh, eW)
self.W = W
self.U = FunctionSpace(self.mesh,
eU) # function space for exchanging BCs
# define Dirichlet boundary conditions
bc_u = DirichletBC(self.W.sub(1), Constant((0.0, 0.0)),
self.complementary_boundary)
bc_v = DirichletBC(self.W.sub(0), Constant((0.0, 0.0)),
self.complementary_boundary)
self.bcs = [bc_v, bc_u]
# define normal
self.n = FacetNormal(self.mesh)
# define Identity
I = Identity(self.W.mesh().geometry().dim())
# Define functions
self.w = Function(self.W) # solution in current time step
self.w0 = Function(self.W) # solution from previous time step
(v_, u_) = TestFunctions(self.W) # test functions
# split mixed functions into velocity (v) and displacement part (u)
(self.v, self.u) = split(self.w)
(self.v0, self.u0) = split(self.w0)
# define coupling BCs
self.u_D = Constant((0.0, 0.0)) # Dirichlet BC (for Fluid)
self.u_D_function = interpolate(self.u_D,
self.U) # Dirichlet BC as function
self.f_N = Constant((0.0, 0.0)) # Neumann BC (for Solid)
self.f_N_function = interpolate(self.f_N,
self.U) # Neumann BC as function
# initial value of Dirichlet BC
self.u_n = interpolate(self.u_D, self.U)
# create self.displacement function for exchanging BCs
self.displacement = Function(self.U)
self.displacement.assign(project(self.u, self.U))
self.displacement.rename("Displacement", "")
# start preCICE adapter
info('Initialize Adapter.')
self.precice = Adapter()
# read forces(Neumann condition for solid) and write displacement(Dirichlet condition for fluid)
info('Call precice.initialize(...).')
self.precice_dt = self.precice.initialize(
coupling_subdomain=self.coupling_boundary,
mesh=self.mesh,
read_field=self.f_N_function,
write_field=self.u_D_function,
u_n=self.w, #u_n,
coupling_marker=self.bndry)
# choose time step
self.dt.assign(np.min([self.precice_dt, self.fenics_dt]))
# define deformation gradient
self.FF = I + grad(self.u)
self.FF0 = I + grad(self.u0)
# approximate time derivatives
du = (1.0 / self.dt) * (self.u - self.u0)
dv = (1.0 / self.dt) * (self.v - self.v0)
# write Green-St. Venant strain tensor
E_s = 0.5 * (self.FF.T * self.FF - I)
E_s0 = 0.5 * (self.FF0.T * self.FF0 - I)
# compute 1st Piola-Kirchhoff tensor for solid (St. Venant - Kirchhoff model)
S_s = self.FF * (self.lambda_s * tr(E_s) * I + 2.0 * self.mu_s * (E_s))
S_s0 = self.FF0 * (self.lambda_s * tr(E_s0) * I + 2.0 * self.mu_s *
(E_s0))
#delta_W = 0.01
alpha = Constant(1.0) # Constant(1.0/delta_W) # Constant(1000)
# get surface forces from precice
self.f_surface = alpha * self.precice.create_coupling_neumann_boundary_condition(
v_, 1, self.U)
#self.f_surface = Function(self.U)
# write equation for solid
self.F_solid = rho_s*inner(dv, v_)*dx \
+ self.theta*inner(S_s , grad(v_))*dx \
+ (1.0 - self.theta)*inner(S_s0, grad(v_))*dx \
+ inner(du - (self.theta*self.v + (1.0 - self.theta)*self.v0), u_)*dx \
- inner(self.f_surface, v_)*dss(1)
# apply Neumann boundary condition on coupling interface
#self.F_solid += self.precice.create_coupling_neumann_boundary_condition(v_, 1, self.U)
# differentiate equation for solid for the Newton scheme
self.dF_solid = derivative(self.F_solid, self.w)
# define Nonlinear Variational problem and Newton solver
self.problem = NonlinearVariationalProblem(self.F_solid,
self.w,
bcs=self.bcs,
J=self.dF_solid)
self.solver = NonlinearVariationalSolver(self.problem)
# configure solver parameters
self.solver.parameters['newton_solver']['relative_tolerance'] = 1e-6
self.solver.parameters['newton_solver']['absolute_tolerance'] = 1e-10
self.solver.parameters['newton_solver']['maximum_iterations'] = 50
self.solver.parameters['newton_solver']['linear_solver'] = 'mumps'
# create files for saving
if not os.path.exists(result):
os.makedirs(result)
self.vfile = XDMFFile("%s/velocity.xdmf" % result)
self.ufile = XDMFFile("%s/displacement.xdmf" % result)
self.sfile = XDMFFile("%s/stress.xdmf" % result)
#self.ffile = XDMFFile("%s/forces.xdmf" % result)
self.vfile.parameters["flush_output"] = True
self.ufile.parameters["flush_output"] = True
self.sfile.parameters["flush_output"] = True
#self.ffile.parameters["flush_output"] = True
with open(result + '/data.csv', 'w') as data_file:
writer = csv.writer(data_file, delimiter=';', lineterminator='\n')
writer.writerow(
['time', 'Ax_displacement', 'Ay_displacement', 'lift', 'drag'])
info("Solid __init__ done")
def solve(self, t, n):
self.t = t
self.dt.assign(np.min([self.fenics_dt, self.precice_dt]))
# solve problem
self.solver.solve()
# extract velocity v and displacement u from mixed vector w
(v, u) = self.w.split()
# update displacement (Dirichlet BC for fluid)
self.displacement.assign(project(u, self.U))
#self.displacement0.assign(self.displacement)
#self.displacement.assign(project(self.u, self.U))
# precice coupling step
t, n, precice_timestep_complete, self.precice_dt \
= self.precice.advance(self.displacement, self.w, self.w0,#self.displacement, self.displacement0,
t, self.dt.values()[0], n)
return t, n, precice_timestep_complete
def save(self, t):
(v, u) = self.w.split()
# save velocity and displacement
v.rename("v", "velocity")
u.rename("u", "displacement")
self.vfile.write(v, t)
self.ufile.write(u, t)
#self.ffile.write(self.f_surface, t)
# extract values of displacament in point A = (0.6, 0.2)
self.w.set_allow_extrapolation(True)
Ax_loc = self.u[0]((A.x(), A.y()))
Ay_loc = self.u[1]((A.x(), A.y()))
self.w.set_allow_extrapolation(False)
# MPI trick to extract nodal values in case of more processes
pi = 0
if self.bb.compute_first_collision(A) < 4294967295:
pi = 1
else:
Ax_loc = 0.0
Ay_loc = 0.0
Ax = MPI.sum(comm, Ax_loc) / MPI.sum(comm, pi)
Ay = MPI.sum(comm, Ay_loc) / MPI.sum(comm, pi)
# evaluate forces exerted by the fluid (lift and drag)
drag = -assemble(self.f_surface[0] * dss(1))
lift = -assemble(self.f_surface[1] * dss(1))
# write displacement and forces to file
with open(result + '/data.csv', 'a') as data_file:
writer = csv.writer(data_file, delimiter=';', lineterminator='\n')
writer.writerow([t, Ax, Ay, lift, drag])
info(' Ax: {}\n Ay: {} \n lift: {} \n drag: {}'.format(
Ax, Ay, lift, drag))
u_D_function = interpolate(u_D, V)
# Define flux in x direction on coupling interface (grad(u_D) in normal direction)
f_N = Constant('0')
f_N_function = interpolate(f_N, V)
coupling_boundary = TopBoundary()
bottom_boundary = BottomBoundary()
# Define initial value
u_n = interpolate(u_D, V)
u_n.rename("T", "")
# Adapter definition and initialization
precice = Adapter(adapter_config_filename="precice-adapter-config.json")
precice_dt = precice.initialize(coupling_boundary, mesh, V)
# Create a FEniCS Expression to define and control the coupling boundary values
coupling_expression = precice.create_coupling_expression()
# Assigning appropriate dt
dt = Constant(0)
dt.assign(np.min([fenics_dt, precice_dt]))
# Define variational problem
u = TrialFunction(V)
v = TestFunction(V)
F = u * v / dt * dx + alpha * dot(grad(u), grad(v)) * dx - u_n * v / dt * dx
# apply constant Dirichlet boundary condition at bottom edge
# apply Dirichlet boundary condition on coupling interface
# get the adapter ready
# read fenics-adapter json-config-file)
adapter_config_filename = "precice-adapter-config-fsi-s.json"
# create Adapter
precice = Adapter(adapter_config_filename)
# create subdomains used by the adapter
clamped_boundary_domain = AutoSubDomain(left_boundary)
force_boundary = AutoSubDomain(remaining_boundary)
precice_dt = precice.initialize(coupling_subdomain=coupling_boundary,
mesh=mesh,
read_field=f_N_function,
write_field=u_function,
u_n=u_n,
dimension=dim,
dirichlet_boundary=clamped_boundary_domain)
fenics_dt = precice_dt # if fenics_dt == precice_dt, no subcycling is applied
#fenics_dt = 0.02 # if fenics_dt < precice_dt, subcycling is applied
dt = Constant(np.min([precice_dt, fenics_dt]))
# generalized alpha method (time stepping) parameters
alpha_m = Constant(0.2)
alpha_f = Constant(0.4)
gamma = Constant(0.5 + alpha_f - alpha_m)
beta = Constant((gamma + 0.5)**2 * 0.25)
# clamp (u == 0) the beam at the left
# Function to calculate displacement Deltas
u_delta = Function(V)
u_ref = Function(V)
f_N_function = interpolate(Expression(("1", "0"), degree=1), V)
u_function = interpolate(Expression(("0", "0"), degree=1), V)
coupling_boundary = AutoSubDomain(neumann_boundary)
fixed_boundary = AutoSubDomain(clamped_boundary)
precice = Adapter(adapter_config_filename="precice-adapter-config-fsi-s.json")
# Initialize the coupling interface
precice_dt = precice.initialize(coupling_boundary,
read_function_space=V,
write_object=V,
fixed_boundary=fixed_boundary)
fenics_dt = precice_dt # if fenics_dt == precice_dt, no subcycling is applied
# fenics_dt = 0.02 # if fenics_dt < precice_dt, subcycling is applied
dt = Constant(np.min([precice_dt, fenics_dt]))
# clamp the beam at the bottom
bc = DirichletBC(V, Constant((0, 0)), fixed_boundary)
# alpha method parameters
alpha_m = Constant(0.2)
alpha_f = Constant(0.4)
gamma = Constant(0.5 + alpha_f - alpha_m)
beta = Constant((gamma + 0.5)**2 / 4.)