// The main program.
int main (int argc, char** argv)
{
// Initialize libMesh.
LibMeshInit init (argc, argv);
// Parse the input file
GetPot infile("fem_system_ex3.in");
// Read in parameters from the input file
const bool transient = infile("transient", true);
const Real deltat = infile("deltat", 0.25);
unsigned int n_timesteps = infile("n_timesteps", 25);
#ifdef LIBMESH_HAVE_EXODUS_API
const unsigned int write_interval = infile("write_interval", 1);
#endif
// Initialize the cantilever mesh
const unsigned int dim = 3;
// Make sure libMesh was compiled for 3D
libmesh_example_requires(dim == LIBMESH_DIM, "3D support");
// Create a 3D mesh distributed across the default MPI communicator.
Mesh mesh(init.comm(), dim);
MeshTools::Generation::build_cube (mesh,
40,
10,
5,
0., 1.*x_scaling,
0., 0.3,
0., 0.1,
HEX8);
// Print information about the mesh to the screen.
mesh.print_info();
// Let's add some node and edge boundary conditions
MeshBase::const_element_iterator el = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end_el = mesh.active_local_elements_end();
for ( ; el != end_el; ++el)
{
const Elem* elem = *el;
unsigned int side_max_x = 0, side_min_y = 0,
side_max_y = 0, side_max_z = 0;
bool found_side_max_x = false, found_side_max_y = false,
found_side_min_y = false, found_side_max_z = false;
for(unsigned int side=0; side<elem->n_sides(); side++)
{
if( mesh.get_boundary_info().has_boundary_id(elem, side, BOUNDARY_ID_MAX_X))
{
side_max_x = side;
found_side_max_x = true;
}
if( mesh.get_boundary_info().has_boundary_id(elem, side, BOUNDARY_ID_MIN_Y))
{
side_min_y = side;
found_side_min_y = true;
}
if( mesh.get_boundary_info().has_boundary_id(elem, side, BOUNDARY_ID_MAX_Y))
{
side_max_y = side;
found_side_max_y = true;
}
if( mesh.get_boundary_info().has_boundary_id(elem, side, BOUNDARY_ID_MAX_Z))
{
side_max_z = side;
found_side_max_z = true;
}
}
// If elem has sides on boundaries
// BOUNDARY_ID_MAX_X, BOUNDARY_ID_MAX_Y, BOUNDARY_ID_MAX_Z
// then let's set a node boundary condition
if(found_side_max_x && found_side_max_y && found_side_max_z)
{
for(unsigned int n=0; n<elem->n_nodes(); n++)
{
if (elem->is_node_on_side(n, side_max_x) &&
elem->is_node_on_side(n, side_max_y) &&
elem->is_node_on_side(n, side_max_z) )
{
mesh.get_boundary_info().add_node(elem->get_node(n), NODE_BOUNDARY_ID);
}
}
}
// If elem has sides on boundaries
// BOUNDARY_ID_MAX_X and BOUNDARY_ID_MIN_Y
// then let's set an edge boundary condition
if(found_side_max_x && found_side_min_y)
{
for(unsigned int e=0; e<elem->n_edges(); e++)
{
if (elem->is_edge_on_side(e, side_max_x) &&
elem->is_edge_on_side(e, side_min_y) )
{
mesh.get_boundary_info().add_edge(elem, e, EDGE_BOUNDARY_ID);
}
}
}
}
// Create an equation systems object.
EquationSystems equation_systems (mesh);
// Declare the system "Navier-Stokes" and its variables.
ElasticitySystem & system =
equation_systems.add_system<ElasticitySystem> ("Linear Elasticity");
// Create ExplicitSystem to help output velocity
ExplicitSystem & v_system =
equation_systems.add_system<ExplicitSystem> ("Velocity");
v_system.add_variable("u_vel", FIRST, LAGRANGE);
v_system.add_variable("v_vel", FIRST, LAGRANGE);
v_system.add_variable("w_vel", FIRST, LAGRANGE);
// Create ExplicitSystem to help output acceleration
ExplicitSystem & a_system =
equation_systems.add_system<ExplicitSystem> ("Acceleration");
a_system.add_variable("u_accel", FIRST, LAGRANGE);
a_system.add_variable("v_accel", FIRST, LAGRANGE);
a_system.add_variable("w_accel", FIRST, LAGRANGE);
// Solve this as a time-dependent or steady system
if (transient)
system.time_solver =
UniquePtr<NewmarkSolver>(new NewmarkSolver(system));
else
{
system.time_solver =
UniquePtr<TimeSolver>(new SteadySolver(system));
libmesh_assert_equal_to (n_timesteps, 1);
}
// Initialize the system
equation_systems.init ();
// Set the time stepping options
system.deltat = deltat;
// And the nonlinear solver options
DiffSolver &solver = *(system.time_solver->diff_solver().get());
solver.quiet = infile("solver_quiet", true);
solver.verbose = !solver.quiet;
solver.max_nonlinear_iterations =
infile("max_nonlinear_iterations", 15);
solver.relative_step_tolerance =
infile("relative_step_tolerance", 1.e-3);
solver.relative_residual_tolerance =
infile("relative_residual_tolerance", 0.0);
solver.absolute_residual_tolerance =
infile("absolute_residual_tolerance", 0.0);
// And the linear solver options
solver.max_linear_iterations =
infile("max_linear_iterations", 50000);
solver.initial_linear_tolerance =
infile("initial_linear_tolerance", 1.e-3);
// Print information about the system to the screen.
equation_systems.print_info();
NewmarkSolver* newmark = cast_ptr<NewmarkSolver*>(system.time_solver.get());
newmark->compute_initial_accel();
// Copy over initial velocity and acceleration for output.
// Note we can do this because of the matching variables/FE spaces
(*v_system.solution) = system.get_vector("_old_solution_rate");
(*a_system.solution) = system.get_vector("_old_solution_accel");
#ifdef LIBMESH_HAVE_EXODUS_API
// Output initial state
{
std::ostringstream file_name;
// We write the file in the ExodusII format.
file_name << "out.e-s."
<< std::setw(3)
<< std::setfill('0')
<< std::right
<< 0;
ExodusII_IO(mesh).write_timestep(file_name.str(),
equation_systems,
1, /* This number indicates how many time steps
are being written to the file */
system.time);
}
#endif // #ifdef LIBMESH_HAVE_EXODUS_API
// Now we begin the timestep loop to compute the time-accurate
// solution of the equations.
for (unsigned int t_step=0; t_step != n_timesteps; ++t_step)
{
// A pretty update message
std::cout << "\n\nSolving time step " << t_step << ", time = "
<< system.time << std::endl;
system.solve();
// Advance to the next timestep in a transient problem
system.time_solver->advance_timestep();
// Copy over updated velocity and acceleration for output.
// Note we can do this because of the matching variables/FE spaces
(*v_system.solution) = system.get_vector("_old_solution_rate");
(*a_system.solution) = system.get_vector("_old_solution_accel");
#ifdef LIBMESH_HAVE_EXODUS_API
// Write out this timestep if we're requested to
if ((t_step+1)%write_interval == 0)
{
std::ostringstream file_name;
// We write the file in the ExodusII format.
file_name << "out.e-s."
<< std::setw(3)
<< std::setfill('0')
<< std::right
<< t_step+1;
ExodusII_IO(mesh).write_timestep(file_name.str(),
equation_systems,
1, /* This number indicates how many time steps
are being written to the file */
system.time);
}
#endif // #ifdef LIBMESH_HAVE_EXODUS_API
}
// All done.
return 0;
}
// The main program.
int main (int argc, char ** argv)
{
// Initialize libMesh.
LibMeshInit init (argc, argv);
// This example requires a linear solver package.
libmesh_example_requires(libMesh::default_solver_package() != INVALID_SOLVER_PACKAGE,
"--enable-petsc, --enable-trilinos, or --enable-eigen");
// Parse the input file
GetPot infile("fem_system_ex3.in");
// Override input file arguments from the command line
infile.parse_command_line(argc, argv);
// Read in parameters from the input file
const Real deltat = infile("deltat", 0.25);
unsigned int n_timesteps = infile("n_timesteps", 1);
#ifdef LIBMESH_HAVE_EXODUS_API
const unsigned int write_interval = infile("write_interval", 1);
#endif
// Initialize the cantilever mesh
const unsigned int dim = 3;
// Make sure libMesh was compiled for 3D
libmesh_example_requires(dim == LIBMESH_DIM, "3D support");
// Create a 3D mesh distributed across the default MPI communicator.
Mesh mesh(init.comm(), dim);
MeshTools::Generation::build_cube (mesh,
32,
8,
4,
0., 1.*x_scaling,
0., 0.3,
0., 0.1,
HEX8);
// Print information about the mesh to the screen.
mesh.print_info();
// Let's add some node and edge boundary conditions.
// Each processor should know about each boundary condition it can
// see, so we loop over all elements, not just local elements.
for (const auto & elem : mesh.element_ptr_range())
{
unsigned int
side_max_x = 0, side_min_y = 0,
side_max_y = 0, side_max_z = 0;
bool
found_side_max_x = false, found_side_max_y = false,
found_side_min_y = false, found_side_max_z = false;
for (auto side : elem->side_index_range())
{
if (mesh.get_boundary_info().has_boundary_id(elem, side, BOUNDARY_ID_MAX_X))
{
side_max_x = side;
found_side_max_x = true;
}
if (mesh.get_boundary_info().has_boundary_id(elem, side, BOUNDARY_ID_MIN_Y))
{
side_min_y = side;
found_side_min_y = true;
}
if (mesh.get_boundary_info().has_boundary_id(elem, side, BOUNDARY_ID_MAX_Y))
{
side_max_y = side;
found_side_max_y = true;
}
if (mesh.get_boundary_info().has_boundary_id(elem, side, BOUNDARY_ID_MAX_Z))
{
side_max_z = side;
found_side_max_z = true;
}
}
// If elem has sides on boundaries
// BOUNDARY_ID_MAX_X, BOUNDARY_ID_MAX_Y, BOUNDARY_ID_MAX_Z
// then let's set a node boundary condition
if (found_side_max_x && found_side_max_y && found_side_max_z)
for (auto n : elem->node_index_range())
if (elem->is_node_on_side(n, side_max_x) &&
elem->is_node_on_side(n, side_max_y) &&
elem->is_node_on_side(n, side_max_z))
mesh.get_boundary_info().add_node(elem->node_ptr(n), NODE_BOUNDARY_ID);
// If elem has sides on boundaries
// BOUNDARY_ID_MAX_X and BOUNDARY_ID_MIN_Y
// then let's set an edge boundary condition
if (found_side_max_x && found_side_min_y)
for (auto e : elem->edge_index_range())
if (elem->is_edge_on_side(e, side_max_x) &&
elem->is_edge_on_side(e, side_min_y))
mesh.get_boundary_info().add_edge(elem, e, EDGE_BOUNDARY_ID);
}
// Create an equation systems object.
EquationSystems equation_systems (mesh);
// Declare the system "Navier-Stokes" and its variables.
ElasticitySystem & system =
equation_systems.add_system<ElasticitySystem> ("Linear Elasticity");
// Solve this as a time-dependent or steady system
std::string time_solver = infile("time_solver","DIE!");
ExplicitSystem * v_system;
ExplicitSystem * a_system;
if( time_solver == std::string("newmark") )
{
// Create ExplicitSystem to help output velocity
v_system = &equation_systems.add_system<ExplicitSystem> ("Velocity");
v_system->add_variable("u_vel", FIRST, LAGRANGE);
v_system->add_variable("v_vel", FIRST, LAGRANGE);
v_system->add_variable("w_vel", FIRST, LAGRANGE);
// Create ExplicitSystem to help output acceleration
a_system = &equation_systems.add_system<ExplicitSystem> ("Acceleration");
a_system->add_variable("u_accel", FIRST, LAGRANGE);
a_system->add_variable("v_accel", FIRST, LAGRANGE);
a_system->add_variable("w_accel", FIRST, LAGRANGE);
}
if( time_solver == std::string("newmark"))
system.time_solver.reset(new NewmarkSolver(system));
else if( time_solver == std::string("euler") )
{
system.time_solver.reset(new EulerSolver(system));
EulerSolver & euler_solver = cast_ref<EulerSolver &>(*(system.time_solver.get()));
euler_solver.theta = infile("theta", 1.0);
}
else if( time_solver == std::string("euler2") )
{
system.time_solver.reset(new Euler2Solver(system));
Euler2Solver & euler_solver = cast_ref<Euler2Solver &>(*(system.time_solver.get()));
euler_solver.theta = infile("theta", 1.0);
}
else if( time_solver == std::string("steady"))
{
system.time_solver.reset(new SteadySolver(system));
libmesh_assert_equal_to (n_timesteps, 1);
}
else
libmesh_error_msg(std::string("ERROR: invalid time_solver ")+time_solver);
// Initialize the system
equation_systems.init ();
// Set the time stepping options
system.deltat = deltat;
// And the nonlinear solver options
DiffSolver & solver = *(system.time_solver->diff_solver().get());
solver.quiet = infile("solver_quiet", true);
solver.verbose = !solver.quiet;
solver.max_nonlinear_iterations = infile("max_nonlinear_iterations", 15);
solver.relative_step_tolerance = infile("relative_step_tolerance", 1.e-3);
solver.relative_residual_tolerance = infile("relative_residual_tolerance", 0.0);
solver.absolute_residual_tolerance = infile("absolute_residual_tolerance", 0.0);
// And the linear solver options
solver.max_linear_iterations = infile("max_linear_iterations", 50000);
solver.initial_linear_tolerance = infile("initial_linear_tolerance", 1.e-3);
// Print information about the system to the screen.
equation_systems.print_info();
// If we're using EulerSolver or Euler2Solver, and we're using EigenSparseLinearSolver,
// then we need to reset the EigenSparseLinearSolver to use SPARSELU because BICGSTAB
// chokes on the Jacobian matrix we give it and Eigen's GMRES currently doesn't work.
NewtonSolver * newton_solver = dynamic_cast<NewtonSolver *>( &solver );
if( newton_solver &&
(time_solver == std::string("euler") || time_solver == std::string("euler2") ) )
{
LinearSolver<Number> & linear_solver = newton_solver->get_linear_solver();
#ifdef LIBMESH_HAVE_EIGEN_SPARSE
EigenSparseLinearSolver<Number> * eigen_linear_solver =
dynamic_cast<EigenSparseLinearSolver<Number> *>(&linear_solver);
if( eigen_linear_solver )
eigen_linear_solver->set_solver_type(SPARSELU);
#endif
}
if( time_solver == std::string("newmark") )
{
NewmarkSolver * newmark = cast_ptr<NewmarkSolver*>(system.time_solver.get());
newmark->compute_initial_accel();
// Copy over initial velocity and acceleration for output.
// Note we can do this because of the matching variables/FE spaces
*(v_system->solution) = system.get_vector("_old_solution_rate");
*(a_system->solution) = system.get_vector("_old_solution_accel");
}
#ifdef LIBMESH_HAVE_EXODUS_API
// Output initial state
{
std::ostringstream file_name;
// We write the file in the ExodusII format.
file_name << std::string("out.")+time_solver+std::string(".e-s.")
<< std::setw(3)
<< std::setfill('0')
<< std::right
<< 0;
ExodusII_IO(mesh).write_timestep(file_name.str(),
equation_systems,
1, // This number indicates how many time steps
// are being written to the file
system.time);
}
#endif // #ifdef LIBMESH_HAVE_EXODUS_API
// Now we begin the timestep loop to compute the time-accurate
// solution of the equations.
for (unsigned int t_step=0; t_step != n_timesteps; ++t_step)
{
// A pretty update message
libMesh::out << "\n\nSolving time step "
<< t_step
<< ", time = "
<< system.time
<< std::endl;
system.solve();
// Advance to the next timestep in a transient problem
system.time_solver->advance_timestep();
// Copy over updated velocity and acceleration for output.
// Note we can do this because of the matching variables/FE spaces
if( time_solver == std::string("newmark") )
{
*(v_system->solution) = system.get_vector("_old_solution_rate");
*(a_system->solution) = system.get_vector("_old_solution_accel");
}
#ifdef LIBMESH_HAVE_EXODUS_API
// Write out this timestep if we're requested to
if ((t_step+1)%write_interval == 0)
{
std::ostringstream file_name;
// We write the file in the ExodusII format.
file_name << std::string("out.")+time_solver+std::string(".e-s.")
<< std::setw(3)
<< std::setfill('0')
<< std::right
<< t_step+1;
ExodusII_IO(mesh).write_timestep(file_name.str(),
equation_systems,
1, // This number indicates how many time steps
// are being written to the file
system.time);
}
#endif // #ifdef LIBMESH_HAVE_EXODUS_API
}
// All done.
return 0;
}
