def linear_solve(self):
"""
Solve Ax = b with numpy and also with removal of uneccesary rows
using the spaces object
"""
timings.startnext("Numpy linear solve")
info("Numpy Linear Solve")
dofs = self.problem.spaces.usefuldofs
#Original np array
b = -self.F.array()
#New np array
b_np = b[dofs]
#Solve the system
x_np = np.linalg.solve(self.J_np, b_np)
#map the solution back to the bigger space
x = np.zeros(len(b))
x[dofs] = x_np
## #Create a Vector
x_vec = Vector(len(x))
x_vec[:] = x
##
self.inc.vector()[:] = x
timings.stop("Numpy linear solve")
def linear_solve(self):
"""
Solve Ax = b with numpy and also with removal of uneccesary rows
using the spaces object
"""
timings.startnext("Numpy linear solve")
info("Numpy Linear Solve")
dofs = self.problem.spaces.usefuldofs
#Original np array
b = -self.F.array()
#New np array
b_np = b[dofs]
#Solve the system
x_np = np.linalg.solve(self.J_np,b_np)
#map the solution back to the bigger space
x = np.zeros(len(b))
x[dofs] = x_np
## #Create a Vector
x_vec = Vector(len(x))
x_vec[:] = x
##
self.inc.vector()[:] = x
timings.stop("Numpy linear solve")
def build_residual(self):
"""Assemble Residual"""
timings.startnext("Residual assembly")
info("Residual Assembly")
self.F = assemble(self.problem.f, tensor = self.F,
cell_domains = self.problem.cell_domains,
interior_facet_domains = self.problem.interior_facet_domains,
exterior_facet_domains = self.problem.exterior_facet_domains)
[bc.apply(self.F) for bc in self.problem.bc]
timings.stop("Residual assembly")
def assemble_J_buff(self):
"""Assembles the buffered jacobian"""
info("Assembling Buffered Jacobian")
timings.startnext("Buffered Jacobian assembly")
J_buff = assemble(self.j_buff,
cell_domains = self.problem.meshfunctions["cell"],
interior_facet_domains = self.problem.meshfunctions["interiorfacet"],
exterior_facet_domains = self.problem.meshfunctions["exteriorfacet"] )
timings.stop("Buffered Jacobian assembly")
return J_buff
def assemble_J_buff(self):
"""Assembles the buffered jacobian"""
info("Assembling Buffered Jacobian")
timings.startnext("Buffered Jacobian assembly")
J_buff = assemble(self.j_buff,
cell_domains = self.problem.cellfunc,
interior_facet_domains = self.problem.fsiboundfunc,
exterior_facet_domains = self.problem.extboundfunc)
timings.stop("Buffered Jacobian assembly")
return J_buff
def build_residual(self):
"""Assemble Residual"""
timings.startnext("Residual assembly")
info("Residual Assembly")
self.F = assemble(
self.problem.f,
tensor=self.F,
cell_domains=self.problem.cell_domains,
interior_facet_domains=self.problem.interior_facet_domains,
exterior_facet_domains=self.problem.exterior_facet_domains)
[bc.apply(self.F) for bc in self.problem.bc]
timings.stop("Residual assembly")
def __init__(self,problem,params = fsinewton_params):
timings.startnext("Fsi Newton Solver init")
info_blue("Initializing FSI Newton Solver")
info("Using params \n" + str(params) )
#Initialize base class
ccom.CBCSolver.__init__(self)
self.problem = problem
self.params = params
#Define the various helper objects of the fsinewton solver
self.spaces = FSISpaces(problem,params)
self.fsibc = FSIBC(problem,self.spaces)
#Define mixed Functions
self.U0 = self.__initial_state()
self.U1 = Function(self.spaces.fsispace)
#Define Subfunction references to the mixed functions
(self.U1_F,self.P1_F,self.L1_U,self.D1_S,self.U1_S,self.D1_F,self.L1_D) = self.U1.split()
(self.U0_F,self.P0_F,self.L0_U,self.D0_S,self.U0_S,self.D0_F,self.L0_D) = self.U0.split()
#Define list tensor references to the mixed funtions
self.U1list = self.spaces.unpack_function(self.U1)
self.U0list = self.spaces.unpack_function(self.U0)
#Define Mixed Trial and Test Functions
self.IU = TrialFunctions(self.spaces.fsispace)
self.V = TestFunctions(self.spaces.fsispace)
#Define time relevant variables
self.dt = self.problem.initial_step()
self.kn = Constant(self.dt)
self.t = 0.0
#Define Time Descretized Functions
self.Umid,self.Udot = self.time_discreteU(self.U1list,self.U0list,self.kn)
self.IUmid,self.IUdot = self.time_discreteI(self.IU,self.kn)
#Initialize any Body forces if present
self.__init_forces()
#Define Forms and buffered part of the jacobian matrix.
self.r,self.j,self.j_buff = self.create_forms()
self.runtimedata = FsiRunTimeData(self)
timings.stop("Fsi Newton Solver init")
def build_jacobian(self):
"""Assemble Jacobian"""
info("Assembling Jacobian")
#If buffered matrix add the variable part to the buffered part.
if self.problem.J_buff is not None:
timings.startnext("Copy Buffered Jacobian")
self.J = self.problem.J_buff.copy()
timings.startnext("Jacobian Assembly")
self.J = assemble(self.problem.j, tensor = self.J,
cell_domains = self.problem.cell_domains,
interior_facet_domains = self.problem.interior_facet_domains,
exterior_facet_domains = self.problem.exterior_facet_domains,
reset_sparsity = False,
add_values = True,
form_compiler_parameters = self.ffc_opt)
timings.stop("Jacobian Assembly")
else:
#No buffering just assemble
timings.startnext("Jacobian Assembly")
self.J = assemble(self.problem.j, tensor = self.J,
cell_domains = self.problem.cell_domains,
interior_facet_domains = self.problem.interior_facet_domains,
exterior_facet_domains = self.problem.exterior_facet_domains,
form_compiler_parameters = self.ffc_opt)
timings.stop("Jacobian Assembly")
#Give the Jacobian it's BC.
self.apply_ident_bc()
#Create an LU Solver
# Create linear solver and factorize matrix
self.linsolver = LUSolver(self.J)
self.linsolver.parameters["reuse_factorization"] = True
def build_jacobian(self):
"""Assemble Jacobian"""
info("Assembling Jacobian")
#If buffered matrix add the variable part to the buffered part.
if self.problem.J_buff is not None:
timings.startnext("Copy Buffered Jacobian")
self.J = self.problem.J_buff.copy()
timings.startnext("Jacobian Assembly")
self.J = assemble(
self.problem.j,
tensor=self.J,
cell_domains=self.problem.cell_domains,
interior_facet_domains=self.problem.interior_facet_domains,
exterior_facet_domains=self.problem.exterior_facet_domains,
reset_sparsity=False,
add_values=True,
form_compiler_parameters=self.ffc_opt)
timings.stop("Jacobian Assembly")
else:
#No buffering just assemble
timings.startnext("Jacobian Assembly")
self.J = assemble(
self.problem.j,
tensor=self.J,
cell_domains=self.problem.cell_domains,
interior_facet_domains=self.problem.interior_facet_domains,
exterior_facet_domains=self.problem.exterior_facet_domains,
form_compiler_parameters=self.ffc_opt)
timings.stop("Jacobian Assembly")
#Give the Jacobian it's BC.
self.apply_ident_bc()
#Create an LU Solver
# Create linear solver and factorize matrix
self.linsolver = LUSolver(self.J)
self.linsolver.parameters["reuse_factorization"] = True
def linear_solve(self):
"""Dolfin/PETSc linear solve"""
timings.startnext("PETSc linear solve")
info("PETSc Linear Solve")
self.linsolver.solve(self.inc.vector(),-self.F)
timings.stop("PETSc linear solve")
def linear_solve(self):
"""Dolfin/PETSc linear solve"""
timings.startnext("PETSc linear solve")
info("PETSc Linear Solve")
self.linsolver.solve(self.inc.vector(), -self.F)
timings.stop("PETSc linear solve")
def solve_primal(self, problem, parameters):
"Solve primal FSI problem"
#def __init__()
# Get parameters
T = problem.end_time()
dt = initial_timestep(problem, parameters)
TOL = parameters["tolerance"]
w_k = parameters["w_k"]
w_c = parameters["w_c"]
save_solution = parameters["save_solution"]
uniform_timestep = parameters["uniform_timestep"]
plot_solution = parameters["plot_solution"]
# Create files for saving to VTK
level = refinement_level()
if save_solution:
files = (File("%s/pvd/level_%d/u_F.pvd" %
(parameters["output_directory"], level)),
File("%s/pvd/level_%d/p_F.pvd" %
(parameters["output_directory"], level)),
File("%s/pvd/level_%d/U_S.pvd" %
(parameters["output_directory"], level)),
File("%s/pvd/level_%d/P_S.pvd" %
(parameters["output_directory"], level)),
File("%s/pvd/level_%d/U_M.pvd" %
(parameters["output_directory"], level)))
# Create time series for storing solution
primal_series = create_primal_series(parameters)
# Create time series for dual solution
if level > 0:
dual_series = create_dual_series(parameters)
else:
dual_series = None
# Record CPU time
cpu_time = python_time()
# Record number of time steps
timestep_counter = 0
# Update of user problem at t = 0 (important for initial conditions)
problem.update(0.0, 0.0, dt)
# Define the three subproblems
F = FluidProblem(problem, solver_type=parameters["fluid_solver"])
S = StructureProblem(problem, parameters)
M = MeshProblem(problem, parameters)
# Get solution values
u_F0, u_F1, p_F0, p_F1 = F.solution_values()
U_M0, U_M1 = M.solution_values()
# Extract number of dofs
num_dofs_FSM = extract_num_dofs(F, S, M)
info("FSI problem has %d dofs (%d + %d + %d)" % \
(num_dofs_FSM, F.num_dofs, S.num_dofs, M.num_dofs))
# Get initial structure displacement (used for plotting and checking convergence)
structure_element_degree = parameters["structure_element_degree"]
V_S = VectorFunctionSpace(problem.structure_mesh(), "CG",
structure_element_degree)
U_S0 = Function(V_S)
# Save initial solution to file and series
U = extract_solution(F, S, M)
if save_solution:
_save_solution(U, files)
write_primal_data(U, 0, primal_series)
# Initialize adaptive data
init_adaptive_data(problem, parameters)
# Initialize time-stepping
t0 = 0.0
t1 = dt
at_end = abs(t1 - T) / T < 100.0 * DOLFIN_EPS
# Initialize integration of goal functional (assuming M(u) = 0 at t = 0)
integrated_goal_functional = 0.0
old_goal_functional = 0.0
# Get reference value of goal functional
if hasattr(problem, "reference_value"):
reference_value = problem.reference_value()
else:
reference_value = None
if parameters["primal_solver"] == "Newton":
#If no initial_step function try to generate one
if not hasattr(problem, "initial_step"):
problem.initial_step = lambda: parameters["initial_timestep"]
# Initialize an FSINewtonSolver Object
fsinewtonsolver = FSINewtonSolver(problem,\
params = parameters["FSINewtonSolver"].to_dict())
#initialize the solve settings
fsinewtonsolver.prepare_solve()
#def solve_primal()
while True:
# Display progress
info("")
info("-" * 80)
begin("* Starting new time step")
info_blue(" * t = %g (T = %g, dt = %g)" % (t1, T, dt))
# Update of user problem
problem.update(t0, t1, dt)
# Compute tolerance for FSI iterations
itertol = compute_itertol(problem, w_c, TOL, dt, t1, parameters)
if parameters["primal_solver"] == "Newton":
#Newtonsolver has it's own timings
assert save_solution, "Parameter save_solution must be true to use the Newton Solver"
U_S1, U_S0, P_S1, increment, numiter = newton_solve(
F, S, M, U_S0, dt, parameters, itertol, problem,
fsinewtonsolver)
elif parameters["primal_solver"] == "fixpoint":
timings.startnext("FixpointSolve")
U_S0, U_S1, P_S1, increment, numiter = fixpoint_solve(
F, S, U_S0, M, dt, t1, parameters, itertol, problem)
timings.stop("FixpointSolve")
else:
raise Exception(
"Only 'fixpoint' and 'Newton' are possible values \
for the parameter 'primal_solver'")
self.g_numiter = numiter
#####################################################
#The primal solve worked so now go to post processing
#####################################################
#def postprocessing():
# Plot solution
if plot_solution:
_plot_solution(u_F1, p_F1, U_S0, U_M1)
if problem.exact_solution() is not None:
update_exactsol(u_F1, p_F1, U_S1, U_M1, F, problem, t1)
info("")
info_green(
"Increment = %g (tolerance = %g), converged after %d iterations"
% (increment, itertol, numiter + 1))
info("")
end()
# Saving number of FSI iterations
save_no_FSI_iter(t1, numiter + 1, parameters)
# Evaluate user goal functional
goal_functional = assemble(
problem.evaluate_functional(u_F1, p_F1, U_S1, P_S1, U_M1, dx,
dx, dx))
# Integrate goal functional
integrated_goal_functional += 0.5 * dt * (old_goal_functional +
goal_functional)
old_goal_functional = goal_functional
# Save goal functional
save_goal_functional(t1, goal_functional,
integrated_goal_functional, parameters)
# Save solution and time series to file
U = extract_solution(F, S, M)
if save_solution:
_save_solution(U, files)
write_primal_data(U, t1, primal_series)
# Move to next time step
F.update(t1)
S.update()
M.update(t1)
# Update time step counter
timestep_counter += 1
# FIXME: This should be done automatically by the solver
F.update_extra()
# Check if we have reached the end time
if at_end:
info("")
info_green("Finished time-stepping")
save_dofs(num_dofs_FSM, timestep_counter, parameters)
end()
break
# Use constant time step
if uniform_timestep:
t0 = t1
t1 = min(t1 + dt, T)
dt = t1 - t0
at_end = abs(t1 - T) / T < 100.0 * DOLFIN_EPS
# Compute new adaptive time step
else:
Rk = compute_time_residual(primal_series, dual_series, t0, t1,
problem, parameters)
(dt, at_end) = compute_time_step(problem, Rk, TOL, dt, t1, T,
w_k, parameters)
t0 = t1
t1 = t1 + dt
#End of Time loop
#Call post processing for the Newton Solver if necessary.
if parameters["primal_solver"] == "Newton":
fsinewtonsolver.post_processing()
# Save final value of goal functional
save_goal_functional_final(goal_functional, integrated_goal_functional,
reference_value, parameters)
# Report elapsed time
info_blue("Primal solution computed in %g seconds." %
(python_time() - cpu_time))
info("")
# Return solution
info(timings.report_str())
return (goal_functional, integrated_goal_functional)
def solve_primal(self,problem, parameters):
"Solve primal FSI problem"
#def __init__()
# Get parameters
T = problem.end_time()
dt = initial_timestep(problem, parameters)
TOL = parameters["tolerance"]
w_k = parameters["w_k"]
w_c = parameters["w_c"]
save_solution = parameters["save_solution"]
uniform_timestep = parameters["uniform_timestep"]
plot_solution = parameters["plot_solution"]
# Create files for saving to VTK
level = refinement_level()
if save_solution:
files = (File("%s/pvd/level_%d/u_F.pvd" % (parameters["output_directory"], level)),
File("%s/pvd/level_%d/p_F.pvd" % (parameters["output_directory"], level)),
File("%s/pvd/level_%d/U_S.pvd" % (parameters["output_directory"], level)),
File("%s/pvd/level_%d/P_S.pvd" % (parameters["output_directory"], level)),
File("%s/pvd/level_%d/U_M.pvd" % (parameters["output_directory"], level)))
# Create time series for storing solution
primal_series = create_primal_series(parameters)
# Create time series for dual solution
if level > 0:
dual_series = create_dual_series(parameters)
else:
dual_series = None
# Record CPU time
cpu_time = python_time()
# Record number of time steps
timestep_counter = 0
# Update of user problem at t = 0 (important for initial conditions)
problem.update(0.0, 0.0, dt)
# Define the three subproblems
F = FluidProblem(problem, solver_type=parameters["fluid_solver"])
S = StructureProblem(problem, parameters)
M = MeshProblem(problem, parameters)
# Get solution values
u_F0, u_F1, p_F0, p_F1 = F.solution_values()
U_M0, U_M1 = M.solution_values()
# Extract number of dofs
num_dofs_FSM = extract_num_dofs(F, S, M)
info("FSI problem has %d dofs (%d + %d + %d)" % \
(num_dofs_FSM, F.num_dofs, S.num_dofs, M.num_dofs))
# Get initial structure displacement (used for plotting and checking convergence)
structure_element_degree = parameters["structure_element_degree"]
V_S = VectorFunctionSpace(problem.structure_mesh(), "CG", structure_element_degree)
U_S0 = Function(V_S)
# Save initial solution to file and series
U = extract_solution(F, S, M)
if save_solution:
_save_solution(U, files)
write_primal_data(U, 0, primal_series)
# Initialize adaptive data
init_adaptive_data(problem, parameters)
# Initialize time-stepping
t0 = 0.0
t1 = dt
at_end = abs(t1 - T) / T < 100.0*DOLFIN_EPS
# Initialize integration of goal functional (assuming M(u) = 0 at t = 0)
integrated_goal_functional = 0.0
old_goal_functional = 0.0
# Get reference value of goal functional
if hasattr(problem, "reference_value"):
reference_value = problem.reference_value()
else:
reference_value = None
if parameters["primal_solver"] == "Newton":
#If no initial_step function try to generate one
if not hasattr(problem,"initial_step"):
problem.initial_step = lambda :parameters["initial_timestep"]
# Initialize an FSINewtonSolver Object
fsinewtonsolver = FSINewtonSolver(problem,\
params = parameters["FSINewtonSolver"].to_dict())
#initialize the solve settings
fsinewtonsolver.prepare_solve()
#def solve_primal()
while True:
# Display progress
info("")
info("-"*80)
begin("* Starting new time step")
info_blue(" * t = %g (T = %g, dt = %g)" % (t1, T, dt))
# Update of user problem
problem.update(t0, t1, dt)
# Compute tolerance for FSI iterations
itertol = compute_itertol(problem, w_c, TOL, dt, t1, parameters)
if parameters["primal_solver"] == "Newton":
#Newtonsolver has it's own timings
assert save_solution,"Parameter save_solution must be true to use the Newton Solver"
U_S1,U_S0,P_S1,increment,numiter = newton_solve(F,S,M,U_S0,dt,parameters,itertol,problem,fsinewtonsolver)
elif parameters["primal_solver"] == "fixpoint":
timings.startnext("FixpointSolve")
U_S0,U_S1,P_S1,increment,numiter = fixpoint_solve(F,S,U_S0,M,dt,t1,parameters,itertol,problem)
timings.stop("FixpointSolve")
else:
raise Exception("Only 'fixpoint' and 'Newton' are possible values \
for the parameter 'primal_solver'")
self.g_numiter = numiter
#####################################################
#The primal solve worked so now go to post processing
#####################################################
#def postprocessing():
# Plot solution
if plot_solution:
_plot_solution(u_F1, p_F1, U_S0, U_M1)
if problem.exact_solution() is not None:
update_exactsol(u_F1,p_F1,U_S1,U_M1,F,problem,t1)
info("")
info_green("Increment = %g (tolerance = %g), converged after %d iterations" % (increment, itertol, numiter + 1))
info("")
end()
# Saving number of FSI iterations
save_no_FSI_iter(t1, numiter + 1, parameters)
# Evaluate user goal functional
goal_functional = assemble(problem.evaluate_functional(u_F1, p_F1, U_S1, P_S1, U_M1, dx, dx, dx))
# Integrate goal functional
integrated_goal_functional += 0.5 * dt * (old_goal_functional + goal_functional)
old_goal_functional = goal_functional
# Save goal functional
save_goal_functional(t1, goal_functional, integrated_goal_functional, parameters)
# Save solution and time series to file
U = extract_solution(F, S, M)
if save_solution:
_save_solution(U, files)
write_primal_data(U, t1, primal_series)
# Move to next time step
F.update(t1)
S.update()
M.update(t1)
# Update time step counter
timestep_counter += 1
# FIXME: This should be done automatically by the solver
F.update_extra()
# Check if we have reached the end time
if at_end:
info("")
info_green("Finished time-stepping")
save_dofs(num_dofs_FSM, timestep_counter, parameters)
end()
break
# Use constant time step
if uniform_timestep:
t0 = t1
t1 = min(t1 + dt, T)
dt = t1 - t0
at_end = abs(t1 - T) / T < 100.0*DOLFIN_EPS
# Compute new adaptive time step
else:
Rk = compute_time_residual(primal_series, dual_series, t0, t1, problem, parameters)
(dt, at_end) = compute_time_step(problem, Rk, TOL, dt, t1, T, w_k, parameters)
t0 = t1
t1 = t1 + dt
#End of Time loop
#Call post processing for the Newton Solver if necessary.
if parameters["primal_solver"] == "Newton":
fsinewtonsolver.post_processing()
# Save final value of goal functional
save_goal_functional_final(goal_functional, integrated_goal_functional, reference_value, parameters)
# Report elapsed time
info_blue("Primal solution computed in %g seconds." % (python_time() - cpu_time))
info("")
# Return solution
info(timings.report_str())
return (goal_functional, integrated_goal_functional)