void run_timestepping(EquationSystems& systems, GetPot& args)
{
TransientExplicitSystem& aux_system = systems.get_system<TransientExplicitSystem>("auxiliary");
SolidSystem& solid_system = systems.get_system<SolidSystem>("solid");
AutoPtr<VTKIO> io = AutoPtr<VTKIO>(new VTKIO(systems.get_mesh()));
Real duration = args("duration", 1.0);
for (unsigned int t_step = 0; t_step < duration/solid_system.deltat; t_step++) {
// Progress in current phase [0..1]
Real progress = t_step * solid_system.deltat / duration;
systems.parameters.set<Real>("progress") = progress;
systems.parameters.set<unsigned int>("step") = t_step;
// Update message
out << "===== Time Step " << std::setw(4) << t_step;
out << " (" << std::fixed << std::setprecision(2) << std::setw(6) << (progress*100.) << "%)";
out << ", time = " << std::setw(7) << solid_system.time;
out << " =====" << std::endl;
// Advance timestep in auxiliary system
aux_system.current_local_solution->close();
aux_system.old_local_solution->close();
*aux_system.older_local_solution = *aux_system.old_local_solution;
*aux_system.old_local_solution = *aux_system.current_local_solution;
out << "Solving Solid" << std::endl;
solid_system.solve();
aux_system.reinit();
// Carry out the adaptive mesh refinement/coarsening
out << "Doing a reinit of the equation systems" << std::endl;
systems.reinit();
if (t_step % args("output/frequency", 1) == 0) {
std::stringstream file_name;
file_name << args("results_directory", "./") << "fem_";
file_name << std::setw(6) << std::setfill('0') << t_step;
file_name << ".pvtu";
io->write_equation_systems(file_name.str(), systems);
}
// Advance to the next timestep in a transient problem
out << "Advancing to next step" << std::endl;
solid_system.time_solver->advance_timestep();
}
}
void setUp()
{
this->build_mesh();
// libMesh *should* renumber now, or a ParallelMesh might not have
// contiguous ids, which is a requirement to write xda files.
_mesh->allow_renumbering(true);
_es = new EquationSystems(*_mesh);
_sys = &_es->add_system<System> ("SimpleSystem");
_sys->add_variable("u", FIRST);
_es->init();
SlitFunc slitfunc;
_sys->project_solution(&slitfunc);
#ifdef LIBMESH_ENABLE_AMR
MeshRefinement(*_mesh).uniformly_refine(1);
_es->reinit();
MeshRefinement(*_mesh).uniformly_refine(1);
_es->reinit();
#endif
}
int main (int argc, char** argv)
{
LibMeshInit init(argc, argv);
if (argc < 4)
libMesh::out << "Usage: ./prog -d DIM filename" << std::endl;
// Variables to get us started
const unsigned int dim = atoi(argv[2]);
std::string meshname (argv[3]);
// declare a mesh...
Mesh mesh(init.comm(), dim);
// Read a mesh
mesh.read(meshname);
GMVIO(mesh).write ("out_0.gmv");
mesh.elem(0)->set_refinement_flag (Elem::REFINE);
MeshRefinement mesh_refinement (mesh);
mesh_refinement.refine_and_coarsen_elements ();
mesh_refinement.uniformly_refine (2);
mesh.print_info();
// Set up the equation system(s)
EquationSystems es (mesh);
LinearImplicitSystem& primary =
es.add_system<LinearImplicitSystem>("primary");
primary.add_variable ("U", FIRST);
primary.add_variable ("V", FIRST);
primary.get_dof_map()._dof_coupling->resize(2);
(*primary.get_dof_map()._dof_coupling)(0,0) = 1;
(*primary.get_dof_map()._dof_coupling)(1,1) = 1;
primary.attach_assemble_function(assemble);
es.init ();
es.print_info ();
primary.get_dof_map().print_dof_constraints ();
// call the solver.
primary.solve ();
GMVIO(mesh).write_equation_systems ("out_1.gmv",
es);
// Refine uniformly
mesh_refinement.uniformly_refine (1);
es.reinit ();
// Write out the projected solution
GMVIO(mesh).write_equation_systems ("out_2.gmv",
es);
// Solve again. Output the refined solution
primary.solve ();
GMVIO(mesh).write_equation_systems ("out_3.gmv",
es);
return 0;
}
void assemble_and_solve(MeshBase & mesh,
EquationSystems & equation_systems)
{
mesh.print_info();
LinearImplicitSystem & system =
equation_systems.add_system<LinearImplicitSystem> ("Poisson");
unsigned int u_var = system.add_variable("u", FIRST, LAGRANGE);
system.attach_assemble_function (assemble_poisson);
// the cube has boundaries IDs 0, 1, 2, 3, 4 and 5
std::set<boundary_id_type> boundary_ids;
for (int j = 0; j<6; ++j)
boundary_ids.insert(j);
// Create a vector storing the variable numbers which the BC applies to
std::vector<unsigned int> variables(1);
variables[0] = u_var;
ZeroFunction<> zf;
DirichletBoundary dirichlet_bc(boundary_ids,
variables,
&zf);
system.get_dof_map().add_dirichlet_boundary(dirichlet_bc);
equation_systems.init();
equation_systems.print_info();
#ifdef LIBMESH_ENABLE_AMR
MeshRefinement mesh_refinement(mesh);
mesh_refinement.refine_fraction() = 0.7;
mesh_refinement.coarsen_fraction() = 0.3;
mesh_refinement.max_h_level() = 5;
const unsigned int max_r_steps = 2;
for (unsigned int r_step=0; r_step<=max_r_steps; r_step++)
{
system.solve();
if (r_step != max_r_steps)
{
ErrorVector error;
KellyErrorEstimator error_estimator;
error_estimator.estimate_error(system, error);
libMesh::out << "Error estimate\nl2 norm = "
<< error.l2_norm()
<< "\nmaximum = "
<< error.maximum()
<< std::endl;
mesh_refinement.flag_elements_by_error_fraction (error);
mesh_refinement.refine_and_coarsen_elements();
equation_systems.reinit();
}
}
#else
system.solve();
#endif
}