def solve(self, parameters=default_parameters()):
"Solve and return computed solution (u_F, p_F, U_S, P_S, U_M, P_M)"
# Create submeshes and mappings (only first time)
if self.Omega is None:
# Refine original mesh
mesh = self._original_mesh
for i in range(parameters["num_initial_refinements"]):
mesh = refine(mesh)
# Initialize meshes
self.init_meshes(mesh, parameters)
# Create solver
solver = FSISolver(self)
# Solve
return solver.solve(parameters)
class FixedPointFSI(CBCProblem):
"""Basic problem class for fixedpoint FSI """
def __init__(self, mesh):
"Create FSI problem"
if dolfin.__version__ > 1:
print "CBC Swing has not been updated beyond dolfin version 1.0.0, use at your own risk. Press any key to continue"
foo = raw_input()
# Initialize base class
CBCProblem.__init__(self)
# Store original mesh
self._original_mesh = mesh
self.Omega = None
def solve(self, parameters=default_parameters()):
"Solve and return computed solution (u_F, p_F, U_S, P_S, U_M, P_M)"
# Store parameters
store_parameters(parameters)
# Create submeshes and mappings (only first time)
if self.Omega is None:
# Refine original mesh
mesh = self._original_mesh
for i in range(parameters["num_initial_refinements"]):
mesh = refine(mesh)
# Initialize meshes
self.init_meshes(mesh, parameters)
# Create solver
self.solver = FSISolver(self)
# Solve
return self.solver.solve(parameters)
def init_meshes(self, Omega, parameters):
"Create mappings between submeshes"
info("Extracting fluid and structure submeshes")
# Set global mesh
self.Omega = Omega
# Create cell markers (0 = fluid, 1 = structure)
D = Omega.topology().dim()
cell_domains = MeshFunction("uint", self.Omega, D)
cell_domains.set_all(0)
structure = self.structure()
structure.mark(cell_domains, 1)
# Extract submeshes for fluid and structure
Omega_F = SubMesh(self.Omega, cell_domains, 0)
Omega_S = SubMesh(self.Omega, cell_domains, 1)
info("Computing mappings between submeshes")
# Extract matching indices for fluid and structure
fluid_to_structure_v = compute_vertex_map(Omega_F, Omega_S)
fluid_to_structure_e = compute_edge_map(Omega_F, Omega_S)
# Extract matching vertex indices for fluid and structure
v_F = array([i for i in fluid_to_structure_v.iterkeys()])
v_S = array([i for i in fluid_to_structure_v.itervalues()])
# Extract matching edge indices for fluid and structure
e_F = array([i for i in fluid_to_structure_e.iterkeys()])
e_S = array([i for i in fluid_to_structure_e.itervalues()])
# Extract matching dofs for fluid and structure
structure_element_degree = parameters["structure_element_degree"]
Nv_F = Omega_F.num_vertices()
Nv_S = Omega_S.num_vertices()
Ne_F = Omega_F.num_edges()
Ne_S = Omega_S.num_edges()
if structure_element_degree == 1:
fdofs = append(v_F, v_F + Nv_F)
sdofs = append(v_S, v_S + Nv_S)
elif structure_element_degree == 2:
fdofs = append(append(v_F, Nv_F + e_F), append((Nv_F + Ne_F) + v_F, (Nv_F + Ne_F + Nv_F) + e_F))
sdofs = append(append(v_S, Nv_S + e_S), append((Nv_S + Ne_S) + v_S, (Nv_S + Ne_S + Nv_S) + e_S))
else:
error("Only know how to map dofs for P1 and P2 elements.")
# Extract map from vertices in Omega to vertices in Omega_F
vertex_map_to_fluid = {}
vertex_map_from_fluid = Omega_F.data().mesh_function("parent_vertex_indices")
for i in range(vertex_map_from_fluid.size()):
vertex_map_to_fluid[vertex_map_from_fluid[i]] = i
# Extract map from vertices in Omega to vertices in Omega_S
vertex_map_to_structure = {}
vertex_map_from_structure = Omega_S.data().mesh_function("parent_vertex_indices")
for i in range(vertex_map_from_structure.size()):
vertex_map_to_structure[vertex_map_from_structure[i]] = i
info("Computing FSI boundary and orientation markers")
# Initialize FSI boundary and orientation markers on Omega
Omega.init(D - 1, D)
fsi_boundary = FacetFunction("uint", Omega, D - 1)
fsi_boundary.set_all(0)
fsi_orientation = Omega.data().create_mesh_function("facet_orientation", D - 1)
fsi_orientation.set_all(0)
# Initialize FSI boundary on Omega_F
Omega_F.init(D - 1, D)
Omega_F.init(0, 1)
fsi_boundary_F = MeshFunction("uint", Omega_F, D - 1)
fsi_boundary_F.set_all(0)
# Initialize FSI boundary on Omega_S
Omega_S.init(D - 1, D)
Omega_S.init(0, 1)
fsi_boundary_S = MeshFunction("uint", Omega_S, D - 1)
fsi_boundary_S.set_all(0)
# Compute FSI boundary and orientation markers on Omega
for facet in facets(Omega):
# Handle facets on the boundary
cells = facet.entities(D)
if len(cells) == 1:
# Create cell and midpoint
c = cells[0]
cell = Cell(Omega, c)
p = cell.midpoint()
# Check whether point is inside structure domain
facet_index = facet.index()
if structure.inside(p0, True):
# On structure boundary
fsi_boundary[facet_index] = 1
fsi_orientation[facet_index] = c
else:
# On fluid boundary
fsi_boundary[facet_index] = 0
fsi_orientation[facet_index] = c
continue
# Sanity check
if len(cells) != 2:
error("Strange, expecting one or two facets!")
# Create the two cells
c0, c1 = cells
cell0 = Cell(Omega, c0)
cell1 = Cell(Omega, c1)
# Get the two midpoints
p0 = cell0.midpoint()
p1 = cell1.midpoint()
# Check if the points are inside
p0_inside = structure.inside(p0, False)
p1_inside = structure.inside(p1, False)
# Just set c0, will be set only for FSI facets below
fsi_orientation[facet.index()] = c0
# Markers:
#
# 0 = fluid
# 1 = structure
# 2 = FSI boundary
# Look for points where exactly one is inside the structure
facet_index = facet.index()
if p0_inside and not p1_inside:
# On FSI boundary
fsi_boundary[facet_index] = 2
fsi_orientation[facet_index] = c1
fsi_boundary_F[_map_to_facet(facet_index, Omega, Omega_F, vertex_map_to_fluid)] = 2
fsi_boundary_S[_map_to_facet(facet_index, Omega, Omega_S, vertex_map_to_structure)] = 2
elif p1_inside and not p0_inside:
# On FSI boundary
fsi_boundary[facet_index] = 2
fsi_orientation[facet_index] = c0
fsi_boundary_F[_map_to_facet(facet_index, Omega, Omega_F, vertex_map_to_fluid)] = 2
fsi_boundary_S[_map_to_facet(facet_index, Omega, Omega_S, vertex_map_to_structure)] = 2
elif p0_inside and p1_inside:
# Inside structure domain
fsi_boundary[facet_index] = 1
else:
# Inside fluid domain
fsi_boundary[facet_index] = 0
# Initialize global edge indices (used in read_primal_data)
init_parent_edge_indices(Omega_F, Omega)
init_parent_edge_indices(Omega_S, Omega)
# Store data
self.Omega_F = Omega_F
self.Omega_S = Omega_S
self.cell_domains = cell_domains
self.fdofs = fdofs
self.sdofs = sdofs
self.fsi_boundary = fsi_boundary
self.fsi_orientation = fsi_orientation
self.fsi_boundary_F = fsi_boundary_F
self.fsi_boundary_S = fsi_boundary_S
def mesh(self):
"Return mesh for full domain"
return self.Omega
def fluid_mesh(self):
"Return mesh for fluid domain"
return self.Omega_F
def structure_mesh(self):
"Return mesh for structure domain"
return self.Omega_S
def add_f2s(self, xs, xf):
"Compute xs += xf for corresponding indices"
xs_array = xs.array()
xf_array = xf.array()
xs_array[self.sdofs] += xf_array[self.fdofs]
xs[:] = xs_array
def add_s2f(self, xf, xs):
"Compute xf += xs for corresponding indices"
xf_array = xf.array()
xs_array = xs.array()
xf_array[self.fdofs] += xs_array[self.sdofs]
xf[:] = xf_array
#--- Optional functions ---
def update(self, t0, t1, dt):
return []
def fluid_body_force(self):
return []
def structure_body_force(self):
return []
def structure_boundary_traction_extra(self):
return Constant((0, 0))
def mesh_right_hand_side(self):
return Constant((0, 0))
def exact_solution(self):
return None
#Goal Functional
def evaluate_functional(self, u_F, p_F, U_S, P_S, U_M, dx_F, dx_S, dx_M):
return inner(u_F,u_F)*dx
class FixedPointFSI(CBCProblem):
"""Basic problem class for fixedpoint FSI """
def __init__(self, mesh):
"Create FSI problem"
if dolfin.__version__ > 1:
print "CBC Swing has not been updated beyond dolfin version 1.0.0, use at your own risk. Press any key to continue"
foo = raw_input()
# Initialize base class
CBCProblem.__init__(self)
# Store original mesh
self._original_mesh = mesh
self.Omega = None
def solve(self, parameters=default_parameters()):
"Solve and return computed solution (u_F, p_F, U_S, P_S, U_M, P_M)"
# Store parameters
store_parameters(parameters)
# Create submeshes and mappings (only first time)
if self.Omega is None:
# Refine original mesh
mesh = self._original_mesh
for i in range(parameters["num_initial_refinements"]):
mesh = refine(mesh)
# Initialize meshes
self.init_meshes(mesh, parameters)
# Create solver
self.solver = FSISolver(self)
# Solve
return self.solver.solve(parameters)
def init_meshes(self, Omega, parameters):
"Create mappings between submeshes"
info("Extracting fluid and structure submeshes")
# Set global mesh
self.Omega = Omega
# Create cell markers (0 = fluid, 1 = structure)
D = Omega.topology().dim()
cell_domains = MeshFunction("uint", self.Omega, D)
cell_domains.set_all(0)
structure = self.structure()
structure.mark(cell_domains, 1)
# Extract submeshes for fluid and structure
Omega_F = SubMesh(self.Omega, cell_domains, 0)
Omega_S = SubMesh(self.Omega, cell_domains, 1)
info("Computing mappings between submeshes")
# Extract matching indices for fluid and structure
fluid_to_structure_v = compute_vertex_map(Omega_F, Omega_S)
fluid_to_structure_e = compute_edge_map(Omega_F, Omega_S)
# Extract matching vertex indices for fluid and structure
v_F = array([i for i in fluid_to_structure_v.iterkeys()])
v_S = array([i for i in fluid_to_structure_v.itervalues()])
# Extract matching edge indices for fluid and structure
e_F = array([i for i in fluid_to_structure_e.iterkeys()])
e_S = array([i for i in fluid_to_structure_e.itervalues()])
# Extract matching dofs for fluid and structure
structure_element_degree = parameters["structure_element_degree"]
Nv_F = Omega_F.num_vertices()
Nv_S = Omega_S.num_vertices()
Ne_F = Omega_F.num_edges()
Ne_S = Omega_S.num_edges()
if structure_element_degree == 1:
fdofs = append(v_F, v_F + Nv_F)
sdofs = append(v_S, v_S + Nv_S)
elif structure_element_degree == 2:
fdofs = append(
append(v_F, Nv_F + e_F),
append((Nv_F + Ne_F) + v_F, (Nv_F + Ne_F + Nv_F) + e_F))
sdofs = append(
append(v_S, Nv_S + e_S),
append((Nv_S + Ne_S) + v_S, (Nv_S + Ne_S + Nv_S) + e_S))
else:
error("Only know how to map dofs for P1 and P2 elements.")
# Extract map from vertices in Omega to vertices in Omega_F
vertex_map_to_fluid = {}
vertex_map_from_fluid = Omega_F.data().mesh_function(
"parent_vertex_indices")
for i in range(vertex_map_from_fluid.size()):
vertex_map_to_fluid[vertex_map_from_fluid[i]] = i
# Extract map from vertices in Omega to vertices in Omega_S
vertex_map_to_structure = {}
vertex_map_from_structure = Omega_S.data().mesh_function(
"parent_vertex_indices")
for i in range(vertex_map_from_structure.size()):
vertex_map_to_structure[vertex_map_from_structure[i]] = i
info("Computing FSI boundary and orientation markers")
# Initialize FSI boundary and orientation markers on Omega
Omega.init(D - 1, D)
fsi_boundary = FacetFunction("uint", Omega, D - 1)
fsi_boundary.set_all(0)
fsi_orientation = Omega.data().create_mesh_function(
"facet_orientation", D - 1)
fsi_orientation.set_all(0)
# Initialize FSI boundary on Omega_F
Omega_F.init(D - 1, D)
Omega_F.init(0, 1)
fsi_boundary_F = MeshFunction("uint", Omega_F, D - 1)
fsi_boundary_F.set_all(0)
# Initialize FSI boundary on Omega_S
Omega_S.init(D - 1, D)
Omega_S.init(0, 1)
fsi_boundary_S = MeshFunction("uint", Omega_S, D - 1)
fsi_boundary_S.set_all(0)
# Compute FSI boundary and orientation markers on Omega
for facet in facets(Omega):
# Handle facets on the boundary
cells = facet.entities(D)
if len(cells) == 1:
# Create cell and midpoint
c = cells[0]
cell = Cell(Omega, c)
p = cell.midpoint()
# Check whether point is inside structure domain
facet_index = facet.index()
if structure.inside(p0, True):
# On structure boundary
fsi_boundary[facet_index] = 1
fsi_orientation[facet_index] = c
else:
# On fluid boundary
fsi_boundary[facet_index] = 0
fsi_orientation[facet_index] = c
continue
# Sanity check
if len(cells) != 2:
error("Strange, expecting one or two facets!")
# Create the two cells
c0, c1 = cells
cell0 = Cell(Omega, c0)
cell1 = Cell(Omega, c1)
# Get the two midpoints
p0 = cell0.midpoint()
p1 = cell1.midpoint()
# Check if the points are inside
p0_inside = structure.inside(p0, False)
p1_inside = structure.inside(p1, False)
# Just set c0, will be set only for FSI facets below
fsi_orientation[facet.index()] = c0
# Markers:
#
# 0 = fluid
# 1 = structure
# 2 = FSI boundary
# Look for points where exactly one is inside the structure
facet_index = facet.index()
if p0_inside and not p1_inside:
# On FSI boundary
fsi_boundary[facet_index] = 2
fsi_orientation[facet_index] = c1
fsi_boundary_F[_map_to_facet(facet_index, Omega, Omega_F,
vertex_map_to_fluid)] = 2
fsi_boundary_S[_map_to_facet(facet_index, Omega, Omega_S,
vertex_map_to_structure)] = 2
elif p1_inside and not p0_inside:
# On FSI boundary
fsi_boundary[facet_index] = 2
fsi_orientation[facet_index] = c0
fsi_boundary_F[_map_to_facet(facet_index, Omega, Omega_F,
vertex_map_to_fluid)] = 2
fsi_boundary_S[_map_to_facet(facet_index, Omega, Omega_S,
vertex_map_to_structure)] = 2
elif p0_inside and p1_inside:
# Inside structure domain
fsi_boundary[facet_index] = 1
else:
# Inside fluid domain
fsi_boundary[facet_index] = 0
# Initialize global edge indices (used in read_primal_data)
init_parent_edge_indices(Omega_F, Omega)
init_parent_edge_indices(Omega_S, Omega)
# Store data
self.Omega_F = Omega_F
self.Omega_S = Omega_S
self.cell_domains = cell_domains
self.fdofs = fdofs
self.sdofs = sdofs
self.fsi_boundary = fsi_boundary
self.fsi_orientation = fsi_orientation
self.fsi_boundary_F = fsi_boundary_F
self.fsi_boundary_S = fsi_boundary_S
def mesh(self):
"Return mesh for full domain"
return self.Omega
def fluid_mesh(self):
"Return mesh for fluid domain"
return self.Omega_F
def structure_mesh(self):
"Return mesh for structure domain"
return self.Omega_S
def add_f2s(self, xs, xf):
"Compute xs += xf for corresponding indices"
xs_array = xs.array()
xf_array = xf.array()
xs_array[self.sdofs] += xf_array[self.fdofs]
xs[:] = xs_array
def add_s2f(self, xf, xs):
"Compute xf += xs for corresponding indices"
xf_array = xf.array()
xs_array = xs.array()
xf_array[self.fdofs] += xs_array[self.sdofs]
xf[:] = xf_array
#--- Optional functions ---
def update(self, t0, t1, dt):
return []
def fluid_body_force(self):
return []
def structure_body_force(self):
return []
def structure_boundary_traction_extra(self):
return Constant((0, 0))
def mesh_right_hand_side(self):
return Constant((0, 0))
def exact_solution(self):
return None
#Goal Functional
def evaluate_functional(self, u_F, p_F, U_S, P_S, U_M, dx_F, dx_S, dx_M):
return inner(u_F, u_F) * dx