void assemble_poisson(EquationSystems & es,
const std::string & system_name)
{
libmesh_assert_equal_to (system_name, "Poisson");
const MeshBase & mesh = es.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
LinearImplicitSystem & system = es.get_system<LinearImplicitSystem>("Poisson");
const DofMap & dof_map = system.get_dof_map();
FEType fe_type = dof_map.variable_type(0);
UniquePtr<FEBase> fe (FEBase::build(dim, fe_type));
QGauss qrule (dim, FIFTH);
fe->attach_quadrature_rule (&qrule);
UniquePtr<FEBase> fe_face (FEBase::build(dim, fe_type));
QGauss qface(dim-1, FIFTH);
fe_face->attach_quadrature_rule (&qface);
const std::vector<Real> & JxW = fe->get_JxW();
const std::vector<std::vector<Real> > & phi = fe->get_phi();
const std::vector<std::vector<RealGradient> > & dphi = fe->get_dphi();
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
std::vector<dof_id_type> dof_indices;
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;
dof_map.dof_indices (elem, dof_indices);
fe->reinit (elem);
Ke.resize (dof_indices.size(),
dof_indices.size());
Fe.resize (dof_indices.size());
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
for (unsigned int i=0; i<phi.size(); i++)
{
Fe(i) += JxW[qp]*phi[i][qp];
for (unsigned int j=0; j<phi.size(); j++)
Ke(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
}
}
dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
system.matrix->add_matrix (Ke, dof_indices);
system.rhs->add_vector (Fe, dof_indices);
}
}
void transform_mesh_and_plot(EquationSystems & es,
Real curvature,
const std::string & filename)
{
// Loop over the mesh nodes and move them!
MeshBase & mesh = es.get_mesh();
MeshBase::node_iterator node_it = mesh.nodes_begin();
const MeshBase::node_iterator node_end = mesh.nodes_end();
for ( ; node_it != node_end; node_it++)
{
Node * node = *node_it;
Real x = (*node)(0);
Real z = (*node)(2);
(*node)(0) = -1./curvature + (1./curvature + x)*cos(curvature*z);
(*node)(2) = (1./curvature + x)*sin(curvature*z);
}
#ifdef LIBMESH_HAVE_EXODUS_API
ExodusII_IO(mesh).write_equation_systems(filename, es);
#endif
}
void write_output_solvedata(EquationSystems & es,
unsigned int a_step,
unsigned int newton_steps,
unsigned int krylov_steps,
unsigned int tv_sec,
unsigned int tv_usec)
{
MeshBase & mesh = es.get_mesh();
unsigned int n_active_elem = mesh.n_active_elem();
unsigned int n_active_dofs = es.n_active_dofs();
if (mesh.processor_id() == 0)
{
// Write out the number of elements/dofs used
std::ofstream activemesh ("out_activemesh.m",
std::ios_base::app | std::ios_base::out);
activemesh.precision(17);
activemesh << (a_step + 1) << ' '
<< n_active_elem << ' '
<< n_active_dofs << std::endl;
// Write out the number of solver steps used
std::ofstream solvesteps ("out_solvesteps.m",
std::ios_base::app | std::ios_base::out);
solvesteps.precision(17);
solvesteps << newton_steps << ' '
<< krylov_steps << std::endl;
// Write out the clock time
std::ofstream clocktime ("out_clocktime.m",
std::ios_base::app | std::ios_base::out);
clocktime.precision(17);
clocktime << tv_sec << '.' << tv_usec << std::endl;
}
}
void MeshOutput<MT>::write_equation_systems (const std::string & fname,
const EquationSystems & es,
const std::set<std::string> * system_names)
{
START_LOG("write_equation_systems()", "MeshOutput");
// We may need to gather and/or renumber a ParallelMesh to output
// it, making that const qualifier in our constructor a dirty lie
MT & my_mesh = const_cast<MT &>(*_obj);
// If we're asked to write data that's associated with a different
// mesh, output files full of garbage are the result.
libmesh_assert_equal_to(&es.get_mesh(), _obj);
// A non-renumbered mesh may not have a contiguous numbering, and
// that needs to be fixed before we can build a solution vector.
if (my_mesh.max_elem_id() != my_mesh.n_elem() ||
my_mesh.max_node_id() != my_mesh.n_nodes())
{
// If we were allowed to renumber then we should have already
// been properly renumbered...
libmesh_assert(!my_mesh.allow_renumbering());
libmesh_do_once(libMesh::out <<
"Warning: This MeshOutput subclass only supports meshes which are contiguously renumbered!"
<< std::endl;);
void scale_mesh_and_plot(EquationSystems & es,
const RBParameters & mu,
const std::string & filename)
{
// Loop over the mesh nodes and move them!
MeshBase & mesh = es.get_mesh();
MeshBase::node_iterator node_it = mesh.nodes_begin();
const MeshBase::node_iterator node_end = mesh.nodes_end();
for ( ; node_it != node_end; node_it++)
{
Node * node = *node_it;
(*node)(0) *= mu.get_value("x_scaling");
}
// Post-process the solution to compute the stresses
compute_stresses(es);
#ifdef LIBMESH_HAVE_EXODUS_API
ExodusII_IO (mesh).write_equation_systems (filename, es);
#endif
// Loop over the mesh nodes and move them!
node_it = mesh.nodes_begin();
for ( ; node_it != node_end; node_it++)
{
Node * node = *node_it;
(*node)(0) /= mu.get_value("x_scaling");
}
}
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();
}
}
/*
* FIXME: This is known to write nonsense on AMR meshes
* and it strips the imaginary parts of complex Numbers
*/
void VTKIO::system_vectors_to_vtk(const EquationSystems& es, vtkUnstructuredGrid*& grid)
{
if (MeshOutput<MeshBase>::mesh().processor_id() == 0)
{
std::map<std::string, std::vector<Number> > vecs;
for (unsigned int i=0; i<es.n_systems(); ++i)
{
const System& sys = es.get_system(i);
System::const_vectors_iterator v_end = sys.vectors_end();
System::const_vectors_iterator it = sys.vectors_begin();
for (; it!= v_end; ++it)
{
// for all vectors on this system
std::vector<Number> values;
// libMesh::out<<"it "<<it->first<<std::endl;
it->second->localize_to_one(values, 0);
// libMesh::out<<"finish localize"<<std::endl;
vecs[it->first] = values;
}
}
std::map<std::string, std::vector<Number> >::iterator it = vecs.begin();
for (; it!=vecs.end(); ++it)
{
vtkDoubleArray *data = vtkDoubleArray::New();
data->SetName(it->first.c_str());
libmesh_assert_equal_to (it->second.size(), es.get_mesh().n_nodes());
data->SetNumberOfValues(it->second.size());
for (unsigned int i=0; i<it->second.size(); ++i)
{
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
libmesh_do_once (libMesh::err << "Only writing the real part for complex numbers!\n"
<< "if you need this support contact " << LIBMESH_PACKAGE_BUGREPORT
<< std::endl);
data->SetValue(i, it->second[i].real());
#else
data->SetValue(i, it->second[i]);
#endif
}
grid->GetPointData()->AddArray(data);
data->Delete();
}
}
}
void write_output(EquationSystems &es,
unsigned int a_step, // The adaptive step count
std::string solution_type) // primal or adjoint solve
{
MeshBase &mesh = es.get_mesh();
#ifdef LIBMESH_HAVE_GMV
OStringStream file_name_gmv;
file_name_gmv << solution_type << ".out.gmv.";
OSSRealzeroright(file_name_gmv,2,0,a_step);
GMVIO(mesh).write_equation_systems
(file_name_gmv.str(), es);
#endif
}
void write_output(EquationSystems &es,
unsigned int a_step, // The adaptive step count
std::string solution_type) // primal or adjoint solve
{
#ifdef LIBMESH_HAVE_GMV
MeshBase &mesh = es.get_mesh();
std::ostringstream file_name_gmv;
file_name_gmv << solution_type
<< ".out.gmv."
<< std::setw(2)
<< std::setfill('0')
<< std::right
<< a_step;
GMVIO(mesh).write_equation_systems
(file_name_gmv.str(), es);
#endif
}
void assemble_stokes (EquationSystems& es,
const std::string& system_name)
{
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Stokes");
// Get a constant reference to the mesh object.
const MeshBase& mesh = es.get_mesh();
// The dimension that we are running
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to the Convection-Diffusion system object.
LinearImplicitSystem & system =
es.get_system<LinearImplicitSystem> ("Stokes");
// Numeric ids corresponding to each variable in the system
const unsigned int u_var = system.variable_number ("u");
const unsigned int v_var = system.variable_number ("v");
const unsigned int p_var = system.variable_number ("p");
// Get the Finite Element type for "u". Note this will be
// the same as the type for "v".
FEType fe_vel_type = system.variable_type(u_var);
// Get the Finite Element type for "p".
FEType fe_pres_type = system.variable_type(p_var);
// Build a Finite Element object of the specified type for
// the velocity variables.
UniquePtr<FEBase> fe_vel (FEBase::build(dim, fe_vel_type));
// Build a Finite Element object of the specified type for
// the pressure variables.
UniquePtr<FEBase> fe_pres (FEBase::build(dim, fe_pres_type));
// A Gauss quadrature rule for numerical integration.
// Let the \p FEType object decide what order rule is appropriate.
QGauss qrule (dim, fe_vel_type.default_quadrature_order());
// Tell the finite element objects to use our quadrature rule.
fe_vel->attach_quadrature_rule (&qrule);
fe_pres->attach_quadrature_rule (&qrule);
// Here we define some references to cell-specific data that
// will be used to assemble the linear system.
//
// The element Jacobian * quadrature weight at each integration point.
const std::vector<Real>& JxW = fe_vel->get_JxW();
// The element shape function gradients for the velocity
// variables evaluated at the quadrature points.
const std::vector<std::vector<RealGradient> >& dphi = fe_vel->get_dphi();
// The element shape functions for the pressure variable
// evaluated at the quadrature points.
const std::vector<std::vector<Real> >& psi = fe_pres->get_phi();
// A reference to the \p DofMap object for this system. The \p DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers. We will talk more about the \p DofMap
// in future examples.
const DofMap & dof_map = system.get_dof_map();
// Define data structures to contain the element matrix
// and right-hand-side vector contribution. Following
// basic finite element terminology we will denote these
// "Ke" and "Fe".
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
DenseSubMatrix<Number>
Kuu(Ke), Kuv(Ke), Kup(Ke),
Kvu(Ke), Kvv(Ke), Kvp(Ke),
Kpu(Ke), Kpv(Ke), Kpp(Ke);
DenseSubVector<Number>
Fu(Fe),
Fv(Fe),
Fp(Fe);
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<dof_id_type> dof_indices;
std::vector<dof_id_type> dof_indices_u;
std::vector<dof_id_type> dof_indices_v;
std::vector<dof_id_type> dof_indices_p;
// Now we will loop over all the elements in the mesh that
// live on the local processor. We will compute the element
// matrix and right-hand-side contribution. In case users later
// modify this program to include refinement, we will be safe and
// will only consider the active elements; hence we use a variant of
// the \p active_elem_iterator.
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)
{
// Store a pointer to the element we are currently
// working on. This allows for nicer syntax later.
const Elem* elem = *el;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
dof_map.dof_indices (elem, dof_indices_u, u_var);
dof_map.dof_indices (elem, dof_indices_v, v_var);
dof_map.dof_indices (elem, dof_indices_p, p_var);
const unsigned int n_dofs = dof_indices.size();
const unsigned int n_u_dofs = dof_indices_u.size();
const unsigned int n_v_dofs = dof_indices_v.size();
const unsigned int n_p_dofs = dof_indices_p.size();
// Compute the element-specific data for the current
// element. This involves computing the location of the
// quadrature points (q_point) and the shape functions
// (phi, dphi) for the current element.
fe_vel->reinit (elem);
fe_pres->reinit (elem);
// Zero the element matrix and right-hand side before
// summing them. We use the resize member here because
// the number of degrees of freedom might have changed from
// the last element. Note that this will be the case if the
// element type is different (i.e. the last element was a
// triangle, now we are on a quadrilateral).
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
// Reposition the submatrices... The idea is this:
//
// - - - -
// | Kuu Kuv Kup | | Fu |
// Ke = | Kvu Kvv Kvp |; Fe = | Fv |
// | Kpu Kpv Kpp | | Fp |
// - - - -
//
// The \p DenseSubMatrix.repostition () member takes the
// (row_offset, column_offset, row_size, column_size).
//
// Similarly, the \p DenseSubVector.reposition () member
// takes the (row_offset, row_size)
Kuu.reposition (u_var*n_u_dofs, u_var*n_u_dofs, n_u_dofs, n_u_dofs);
Kuv.reposition (u_var*n_u_dofs, v_var*n_u_dofs, n_u_dofs, n_v_dofs);
Kup.reposition (u_var*n_u_dofs, p_var*n_u_dofs, n_u_dofs, n_p_dofs);
Kvu.reposition (v_var*n_v_dofs, u_var*n_v_dofs, n_v_dofs, n_u_dofs);
Kvv.reposition (v_var*n_v_dofs, v_var*n_v_dofs, n_v_dofs, n_v_dofs);
Kvp.reposition (v_var*n_v_dofs, p_var*n_v_dofs, n_v_dofs, n_p_dofs);
Kpu.reposition (p_var*n_u_dofs, u_var*n_u_dofs, n_p_dofs, n_u_dofs);
Kpv.reposition (p_var*n_u_dofs, v_var*n_u_dofs, n_p_dofs, n_v_dofs);
Kpp.reposition (p_var*n_u_dofs, p_var*n_u_dofs, n_p_dofs, n_p_dofs);
Fu.reposition (u_var*n_u_dofs, n_u_dofs);
Fv.reposition (v_var*n_u_dofs, n_v_dofs);
Fp.reposition (p_var*n_u_dofs, n_p_dofs);
// Now we will build the element matrix.
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
// Assemble the u-velocity row
// uu coupling
for (unsigned int i=0; i<n_u_dofs; i++)
for (unsigned int j=0; j<n_u_dofs; j++)
Kuu(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
// up coupling
for (unsigned int i=0; i<n_u_dofs; i++)
for (unsigned int j=0; j<n_p_dofs; j++)
Kup(i,j) += -JxW[qp]*psi[j][qp]*dphi[i][qp](0);
// Assemble the v-velocity row
// vv coupling
for (unsigned int i=0; i<n_v_dofs; i++)
for (unsigned int j=0; j<n_v_dofs; j++)
Kvv(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
// vp coupling
for (unsigned int i=0; i<n_v_dofs; i++)
for (unsigned int j=0; j<n_p_dofs; j++)
Kvp(i,j) += -JxW[qp]*psi[j][qp]*dphi[i][qp](1);
// Assemble the pressure row
// pu coupling
for (unsigned int i=0; i<n_p_dofs; i++)
for (unsigned int j=0; j<n_u_dofs; j++)
Kpu(i,j) += -JxW[qp]*psi[i][qp]*dphi[j][qp](0);
// pv coupling
for (unsigned int i=0; i<n_p_dofs; i++)
for (unsigned int j=0; j<n_v_dofs; j++)
Kpv(i,j) += -JxW[qp]*psi[i][qp]*dphi[j][qp](1);
} // end of the quadrature point qp-loop
// At this point the interior element integration has
// been completed. However, we have not yet addressed
// boundary conditions. For this example we will only
// consider simple Dirichlet boundary conditions imposed
// via the penalty method. The penalty method used here
// is equivalent (for Lagrange basis functions) to lumping
// the matrix resulting from the L2 projection penalty
// approach introduced in example 3.
{
// The following loops over the sides of the element.
// If the element has no neighbor on a side then that
// side MUST live on a boundary of the domain.
for (unsigned int s=0; s<elem->n_sides(); s++)
if (elem->neighbor(s) == NULL)
{
UniquePtr<Elem> side (elem->build_side(s));
// Loop over the nodes on the side.
for (unsigned int ns=0; ns<side->n_nodes(); ns++)
{
// The location on the boundary of the current
// node.
// const Real xf = side->point(ns)(0);
const Real yf = side->point(ns)(1);
// The penalty value. \f$ \frac{1}{\epsilon \f$
const Real penalty = 1.e10;
// The boundary values.
// Set u = 1 on the top boundary, 0 everywhere else
const Real u_value = (yf > .99) ? 1. : 0.;
// Set v = 0 everywhere
const Real v_value = 0.;
// Find the node on the element matching this node on
// the side. That defined where in the element matrix
// the boundary condition will be applied.
for (unsigned int n=0; n<elem->n_nodes(); n++)
if (elem->node(n) == side->node(ns))
{
// Matrix contribution.
Kuu(n,n) += penalty;
Kvv(n,n) += penalty;
// Right-hand-side contribution.
Fu(n) += penalty*u_value;
Fv(n) += penalty*v_value;
}
} // end face node loop
} // end if (elem->neighbor(side) == NULL)
} // end boundary condition section
// If this assembly program were to be used on an adaptive mesh,
// we would have to apply any hanging node constraint equations.
dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
// The element matrix and right-hand-side are now built
// for this element. Add them to the global matrix and
// right-hand-side vector. The \p NumericMatrix::add_matrix()
// and \p NumericVector::add_vector() members do this for us.
system.matrix->add_matrix (Ke, dof_indices);
system.rhs->add_vector (Fe, dof_indices);
} // end of element loop
// That's it.
return;
}
void
MultiAppProjectionTransfer::assembleL2From(EquationSystems & es, const std::string & system_name)
{
unsigned int n_apps = _multi_app->numGlobalApps();
std::vector<NumericVector<Number> *> from_slns(n_apps, NULL);
std::vector<MeshFunction *> from_fns(n_apps, NULL);
std::vector<MeshTools::BoundingBox *> from_bbs(n_apps, NULL);
// get bounding box, mesh function and solution for each subapp
for (unsigned int i = 0; i < n_apps; i++)
{
if (!_multi_app->hasLocalApp(i))
continue;
MPI_Comm swapped = Moose::swapLibMeshComm(_multi_app->comm());
FEProblem & from_problem = *_multi_app->appProblem(i);
EquationSystems & from_es = from_problem.es();
MeshBase & from_mesh = from_es.get_mesh();
MeshTools::BoundingBox * app_box = new MeshTools::BoundingBox(MeshTools::processor_bounding_box(from_mesh, from_mesh.processor_id()));
from_bbs[i] = app_box;
MooseVariable & from_var = from_problem.getVariable(0, _from_var_name);
System & from_sys = from_var.sys().system();
unsigned int from_var_num = from_sys.variable_number(from_var.name());
NumericVector<Number> * serialized_from_solution = NumericVector<Number>::build(from_sys.comm()).release();
serialized_from_solution->init(from_sys.n_dofs(), false, SERIAL);
// Need to pull down a full copy of this vector on every processor so we can get values in parallel
from_sys.solution->localize(*serialized_from_solution);
from_slns[i] = serialized_from_solution;
MeshFunction * from_func = new MeshFunction(from_es, *serialized_from_solution, from_sys.get_dof_map(), from_var_num);
from_func->init(Trees::ELEMENTS);
from_func->enable_out_of_mesh_mode(NOTFOUND);
from_fns[i] = from_func;
Moose::swapLibMeshComm(swapped);
}
const MeshBase& mesh = es.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
LinearImplicitSystem & system = es.get_system<LinearImplicitSystem>(system_name);
FEType fe_type = system.variable_type(0);
AutoPtr<FEBase> fe(FEBase::build(dim, fe_type));
QGauss qrule(dim, fe_type.default_quadrature_order());
fe->attach_quadrature_rule(&qrule);
const std::vector<Real> & JxW = fe->get_JxW();
const std::vector<std::vector<Real> > & phi = fe->get_phi();
const std::vector<Point> & xyz = fe->get_xyz();
const DofMap& dof_map = system.get_dof_map();
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
std::vector<dof_id_type> dof_indices;
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;
fe->reinit (elem);
dof_map.dof_indices (elem, dof_indices);
Ke.resize (dof_indices.size(), dof_indices.size());
Fe.resize (dof_indices.size());
for (unsigned int qp = 0; qp < qrule.n_points(); qp++)
{
Point qpt = xyz[qp];
Real f = 0.;
for (unsigned int app = 0; app < n_apps; app++)
{
Point pt = qpt - _multi_app->position(app);
if (from_bbs[app] != NULL && from_bbs[app]->contains_point(pt))
{
MPI_Comm swapped = Moose::swapLibMeshComm(_multi_app->comm());
f = (*from_fns[app])(pt);
Moose::swapLibMeshComm(swapped);
break;
}
}
// Now compute the element matrix and RHS contributions.
for (unsigned int i=0; i<phi.size(); i++)
{
// RHS
Fe(i) += JxW[qp] * (f * phi[i][qp]);
if (_compute_matrix)
for (unsigned int j = 0; j < phi.size(); j++)
{
// The matrix contribution
Ke(i,j) += JxW[qp] * (phi[i][qp] * phi[j][qp]);
}
}
dof_map.constrain_element_matrix_and_vector(Ke, Fe, dof_indices);
if (_compute_matrix)
system.matrix->add_matrix(Ke, dof_indices);
system.rhs->add_vector(Fe, dof_indices);
}
}
for (unsigned int i = 0; i < n_apps; i++)
{
delete from_fns[i];
delete from_bbs[i];
delete from_slns[i];
}
}
void
MultiAppProjectionTransfer::assembleL2To(EquationSystems & es, const std::string & system_name)
{
unsigned int app = es.parameters.get<unsigned int>("app");
FEProblem & from_problem = *_multi_app->problem();
EquationSystems & from_es = from_problem.es();
MooseVariable & from_var = from_problem.getVariable(0, _from_var_name);
System & from_sys = from_var.sys().system();
unsigned int from_var_num = from_sys.variable_number(from_var.name());
NumericVector<Number> * serialized_from_solution = NumericVector<Number>::build(from_sys.comm()).release();
serialized_from_solution->init(from_sys.n_dofs(), false, SERIAL);
// Need to pull down a full copy of this vector on every processor so we can get values in parallel
from_sys.solution->localize(*serialized_from_solution);
MeshFunction from_func(from_es, *serialized_from_solution, from_sys.get_dof_map(), from_var_num);
from_func.init(Trees::ELEMENTS);
from_func.enable_out_of_mesh_mode(0.);
const MeshBase& mesh = es.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
LinearImplicitSystem & system = es.get_system<LinearImplicitSystem>(system_name);
FEType fe_type = system.variable_type(0);
AutoPtr<FEBase> fe(FEBase::build(dim, fe_type));
QGauss qrule(dim, fe_type.default_quadrature_order());
fe->attach_quadrature_rule(&qrule);
const std::vector<Real> & JxW = fe->get_JxW();
const std::vector<std::vector<Real> > & phi = fe->get_phi();
const std::vector<Point> & xyz = fe->get_xyz();
const DofMap& dof_map = system.get_dof_map();
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
std::vector<dof_id_type> dof_indices;
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;
fe->reinit (elem);
dof_map.dof_indices (elem, dof_indices);
Ke.resize (dof_indices.size(), dof_indices.size());
Fe.resize (dof_indices.size());
for (unsigned int qp = 0; qp < qrule.n_points(); qp++)
{
Point qpt = xyz[qp];
Point pt = qpt + _multi_app->position(app);
Real f = from_func(pt);
// Now compute the element matrix and RHS contributions.
for (unsigned int i=0; i<phi.size(); i++)
{
// RHS
Fe(i) += JxW[qp] * (f * phi[i][qp]);
if (_compute_matrix)
for (unsigned int j = 0; j < phi.size(); j++)
{
// The matrix contribution
Ke(i,j) += JxW[qp] * (phi[i][qp] * phi[j][qp]);
}
}
dof_map.constrain_element_matrix_and_vector(Ke, Fe, dof_indices);
if (_compute_matrix)
system.matrix->add_matrix(Ke, dof_indices);
system.rhs->add_vector(Fe, dof_indices);
}
}
}
// We now define the matrix assembly function for the
// Poisson system. We need to first compute element
// matrices and right-hand sides, and then take into
// account the boundary conditions.
void assemble_poisson(EquationSystems& es,
const std::string& system_name)
{
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Poisson");
// Declare a performance log. Give it a descriptive
// string to identify what part of the code we are
// logging, since there may be many PerfLogs in an
// application.
PerfLog perf_log ("Matrix Assembly");
// Get a constant reference to the mesh object.
const MeshBase& mesh = es.get_mesh();
// The dimension that we are running
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to the LinearImplicitSystem we are solving
LinearImplicitSystem& system = es.get_system<LinearImplicitSystem>("Poisson");
// A reference to the \p DofMap object for this system. The \p DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers. We will talk more about the \p DofMap
// in future examples.
const DofMap& dof_map = system.get_dof_map();
// Get a constant reference to the Finite Element type
// for the first (and only) variable in the system.
FEType fe_type = dof_map.variable_type(0);
// Build a Finite Element object of the specified type. Since the
// \p FEBase::build() member dynamically creates memory we will
// store the object as an \p UniquePtr<FEBase>. This can be thought
// of as a pointer that will clean up after itself.
UniquePtr<FEBase> fe (FEBase::build(dim, fe_type));
// A 5th order Gauss quadrature rule for numerical integration.
QGauss qrule (dim, FIFTH);
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (&qrule);
// Declare a special finite element object for
// boundary integration.
UniquePtr<FEBase> fe_face (FEBase::build(dim, fe_type));
// Boundary integration requires one quadraure rule,
// with dimensionality one less than the dimensionality
// of the element.
QGauss qface(dim-1, FIFTH);
// Tell the finte element object to use our
// quadrature rule.
fe_face->attach_quadrature_rule (&qface);
// Here we define some references to cell-specific data that
// will be used to assemble the linear system.
// We begin with the element Jacobian * quadrature weight at each
// integration point.
const std::vector<Real>& JxW = fe->get_JxW();
// The physical XY locations of the quadrature points on the element.
// These might be useful for evaluating spatially varying material
// properties at the quadrature points.
const std::vector<Point>& q_point = fe->get_xyz();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> >& phi = fe->get_phi();
// The element shape function gradients evaluated at the quadrature
// points.
const std::vector<std::vector<RealGradient> >& dphi = fe->get_dphi();
// Define data structures to contain the element matrix
// and right-hand-side vector contribution. Following
// basic finite element terminology we will denote these
// "Ke" and "Fe". More detail is in example 3.
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<dof_id_type> dof_indices;
// Now we will loop over all the elements in the mesh.
// We will compute the element matrix and right-hand-side
// contribution. See example 3 for a discussion of the
// element iterators.
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)
{
// Start logging the shape function initialization.
// This is done through a simple function call with
// the name of the event to log.
perf_log.push("elem init");
// Store a pointer to the element we are currently
// working on. This allows for nicer syntax later.
const Elem* elem = *el;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
// Compute the element-specific data for the current
// element. This involves computing the location of the
// quadrature points (q_point) and the shape functions
// (phi, dphi) for the current element.
fe->reinit (elem);
// Zero the element matrix and right-hand side before
// summing them. We use the resize member here because
// the number of degrees of freedom might have changed from
// the last element. Note that this will be the case if the
// element type is different (i.e. the last element was a
// triangle, now we are on a quadrilateral).
Ke.resize (dof_indices.size(),
dof_indices.size());
Fe.resize (dof_indices.size());
// Stop logging the shape function initialization.
// If you forget to stop logging an event the PerfLog
// object will probably catch the error and abort.
perf_log.pop("elem init");
// Now we will build the element matrix. This involves
// a double loop to integrate the test funcions (i) against
// the trial functions (j).
//
// We have split the numeric integration into two loops
// so that we can log the matrix and right-hand-side
// computation seperately.
//
// Now start logging the element matrix computation
perf_log.push ("Ke");
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
for (unsigned int i=0; i<phi.size(); i++)
for (unsigned int j=0; j<phi.size(); j++)
Ke(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
// Stop logging the matrix computation
perf_log.pop ("Ke");
// Now we build the element right-hand-side contribution.
// This involves a single loop in which we integrate the
// "forcing function" in the PDE against the test functions.
//
// Start logging the right-hand-side computation
perf_log.push ("Fe");
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
// fxy is the forcing function for the Poisson equation.
// In this case we set fxy to be a finite difference
// Laplacian approximation to the (known) exact solution.
//
// We will use the second-order accurate FD Laplacian
// approximation, which in 2D on a structured grid is
//
// u_xx + u_yy = (u(i-1,j) + u(i+1,j) +
// u(i,j-1) + u(i,j+1) +
// -4*u(i,j))/h^2
//
// Since the value of the forcing function depends only
// on the location of the quadrature point (q_point[qp])
// we will compute it here, outside of the i-loop
const Real x = q_point[qp](0);
#if LIBMESH_DIM > 1
const Real y = q_point[qp](1);
#else
const Real y = 0.;
#endif
#if LIBMESH_DIM > 2
const Real z = q_point[qp](2);
#else
const Real z = 0.;
#endif
const Real eps = 1.e-3;
const Real uxx = (exact_solution(x-eps,y,z) +
exact_solution(x+eps,y,z) +
-2.*exact_solution(x,y,z))/eps/eps;
const Real uyy = (exact_solution(x,y-eps,z) +
exact_solution(x,y+eps,z) +
-2.*exact_solution(x,y,z))/eps/eps;
const Real uzz = (exact_solution(x,y,z-eps) +
exact_solution(x,y,z+eps) +
-2.*exact_solution(x,y,z))/eps/eps;
Real fxy;
if(dim==1)
{
// In 1D, compute the rhs by differentiating the
// exact solution twice.
const Real pi = libMesh::pi;
fxy = (0.25*pi*pi)*sin(.5*pi*x);
}
else
{
fxy = - (uxx + uyy + ((dim==2) ? 0. : uzz));
}
// Add the RHS contribution
for (unsigned int i=0; i<phi.size(); i++)
Fe(i) += JxW[qp]*fxy*phi[i][qp];
}
// Stop logging the right-hand-side computation
perf_log.pop ("Fe");
// If this assembly program were to be used on an adaptive mesh,
// we would have to apply any hanging node constraint equations
// Also, note that here we call heterogenously_constrain_element_matrix_and_vector
// to impose a inhomogeneous Dirichlet boundary conditions.
dof_map.heterogenously_constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
// The element matrix and right-hand-side are now built
// for this element. Add them to the global matrix and
// right-hand-side vector. The \p SparseMatrix::add_matrix()
// and \p NumericVector::add_vector() members do this for us.
// Start logging the insertion of the local (element)
// matrix and vector into the global matrix and vector
perf_log.push ("matrix insertion");
system.matrix->add_matrix (Ke, dof_indices);
system.rhs->add_vector (Fe, dof_indices);
// Start logging the insertion of the local (element)
// matrix and vector into the global matrix and vector
perf_log.pop ("matrix insertion");
}
// That's it. We don't need to do anything else to the
// PerfLog. When it goes out of scope (at this function return)
// it will print its log to the screen. Pretty easy, huh?
}
void
MultiAppProjectionTransfer::assembleL2(EquationSystems & es, const std::string & system_name)
{
// Get the system and mesh from the input arguments.
LinearImplicitSystem & system = es.get_system<LinearImplicitSystem>(system_name);
MeshBase & to_mesh = es.get_mesh();
// Get the meshfunction evaluations and the map that was stashed in the es.
std::vector<Real> & final_evals = * es.parameters.get<std::vector<Real>*>("final_evals");
std::map<unsigned int, unsigned int> & element_map = * es.parameters.get<std::map<unsigned int, unsigned int>*>("element_map");
// Setup system vectors and matrices.
FEType fe_type = system.variable_type(0);
std::unique_ptr<FEBase> fe(FEBase::build(to_mesh.mesh_dimension(), fe_type));
QGauss qrule(to_mesh.mesh_dimension(), fe_type.default_quadrature_order());
fe->attach_quadrature_rule(&qrule);
const DofMap& dof_map = system.get_dof_map();
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
std::vector<dof_id_type> dof_indices;
const std::vector<Real> & JxW = fe->get_JxW();
const std::vector<std::vector<Real> > & phi = fe->get_phi();
const MeshBase::const_element_iterator end_el = to_mesh.active_local_elements_end();
for (MeshBase::const_element_iterator el = to_mesh.active_local_elements_begin(); el != end_el; ++el)
{
const Elem* elem = *el;
fe->reinit (elem);
dof_map.dof_indices (elem, dof_indices);
Ke.resize (dof_indices.size(), dof_indices.size());
Fe.resize (dof_indices.size());
for (unsigned int qp = 0; qp < qrule.n_points(); qp++)
{
Real meshfun_eval = 0.;
if (element_map.find(elem->id()) != element_map.end())
{
// We have evaluations for this element.
meshfun_eval = final_evals[element_map[elem->id()] + qp];
}
// Now compute the element matrix and RHS contributions.
for (unsigned int i=0; i<phi.size(); i++)
{
// RHS
Fe(i) += JxW[qp] * (meshfun_eval * phi[i][qp]);
if (_compute_matrix)
for (unsigned int j = 0; j < phi.size(); j++)
{
// The matrix contribution
Ke(i,j) += JxW[qp] * (phi[i][qp] * phi[j][qp]);
}
}
dof_map.constrain_element_matrix_and_vector(Ke, Fe, dof_indices);
if (_compute_matrix)
system.matrix->add_matrix(Ke, dof_indices);
system.rhs->add_vector(Fe, dof_indices);
}
}
}
void assemble_matrices(EquationSystems & es,
const std::string & libmesh_dbg_var(system_name))
{
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Eigensystem");
#ifdef LIBMESH_HAVE_SLEPC
// Get a constant reference to the mesh object.
const MeshBase & mesh = es.get_mesh();
// The dimension that we are running.
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to our system.
EigenSystem & eigen_system = es.get_system<EigenSystem> ("Eigensystem");
// Get a constant reference to the Finite Element type
// for the first (and only) variable in the system.
FEType fe_type = eigen_system.get_dof_map().variable_type(0);
// A reference to the two system matrices
SparseMatrix<Number> & matrix_A = *eigen_system.matrix_A;
SparseMatrix<Number> & matrix_B = *eigen_system.matrix_B;
// Build a Finite Element object of the specified type. Since the
// FEBase::build() member dynamically creates memory we will
// store the object as a std::unique_ptr<FEBase>. This can be thought
// of as a pointer that will clean up after itself.
std::unique_ptr<FEBase> fe (FEBase::build(dim, fe_type));
// A Gauss quadrature rule for numerical integration.
// Use the default quadrature order.
QGauss qrule (dim, fe_type.default_quadrature_order());
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (&qrule);
// The element Jacobian * quadrature weight at each integration point.
const std::vector<Real> & JxW = fe->get_JxW();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real>> & phi = fe->get_phi();
// The element shape function gradients evaluated at the quadrature
// points.
const std::vector<std::vector<RealGradient>> & dphi = fe->get_dphi();
// A reference to the DofMap object for this system. The DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers.
const DofMap & dof_map = eigen_system.get_dof_map();
// The element mass and stiffness matrices.
DenseMatrix<Number> Me;
DenseMatrix<Number> Ke;
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<dof_id_type> dof_indices;
// Now we will loop over all the elements in the mesh that
// live on the local processor. We will compute the element
// matrix and right-hand-side contribution. In case users
// later modify this program to include refinement, we will
// be safe and will only consider the active elements;
// hence we use a variant of the active_elem_iterator.
for (const auto & elem : mesh.active_local_element_ptr_range())
{
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
// Compute the element-specific data for the current
// element. This involves computing the location of the
// quadrature points (q_point) and the shape functions
// (phi, dphi) for the current element.
fe->reinit (elem);
// Zero the element matrices before
// summing them. We use the resize member here because
// the number of degrees of freedom might have changed from
// the last element. Note that this will be the case if the
// element type is different (i.e. the last element was a
// triangle, now we are on a quadrilateral).
const unsigned int n_dofs =
cast_int<unsigned int>(dof_indices.size());
Ke.resize (n_dofs, n_dofs);
Me.resize (n_dofs, n_dofs);
// Now loop over the quadrature points. This handles
// the numeric integration.
//
// We will build the element matrix. This involves
// a double loop to integrate the test functions (i) against
// the trial functions (j).
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
for (unsigned int i=0; i<n_dofs; i++)
for (unsigned int j=0; j<n_dofs; j++)
{
Me(i,j) += JxW[qp]*phi[i][qp]*phi[j][qp];
Ke(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
}
// The calls to constrain_element_matrix below have no effect in
// the current example. However, if users modify this example to
// include hanging nodes due to mesh refinement, for example,
// then it is essential to call constrain_element_matrix.
// As a result we include constrain_element_matrix here to
// ensure this example is ready to be used with hanging nodes.
// (Note that constrained rows/cols will be eliminated from
// the eigenproblem by the CondensedEigenSystem.)
dof_map.constrain_element_matrix(Ke, dof_indices, false);
dof_map.constrain_element_matrix(Me, dof_indices, false);
// Finally, simply add the element contribution to the
// overall matrices A and B.
matrix_A.add_matrix (Ke, dof_indices);
matrix_B.add_matrix (Me, dof_indices);
} // end of element loop
#else
// Avoid compiler warnings
libmesh_ignore(es);
#endif // LIBMESH_HAVE_SLEPC
}
DTKInterpolationAdapter::DTKInterpolationAdapter(Teuchos::RCP<const Teuchos::MpiComm<int> > in_comm, EquationSystems & in_es, const Point & offset, unsigned int from_dim):
comm(in_comm),
es(in_es),
_offset(offset),
mesh(in_es.get_mesh()),
dim(mesh.mesh_dimension())
{
MPI_Comm old_comm = Moose::swapLibMeshComm(*comm->getRawMpiComm());
std::set<GlobalOrdinal> semi_local_nodes;
get_semi_local_nodes(semi_local_nodes);
num_local_nodes = semi_local_nodes.size();
vertices.resize(num_local_nodes);
Teuchos::ArrayRCP<double> coordinates(num_local_nodes * dim);
Teuchos::ArrayRCP<double> target_coordinates(num_local_nodes * from_dim);
// Fill in the vertices and coordinates
{
GlobalOrdinal i = 0;
for (std::set<GlobalOrdinal>::iterator it = semi_local_nodes.begin();
it != semi_local_nodes.end();
++it)
{
const Node & node = mesh.node(*it);
vertices[i] = node.id();
for (GlobalOrdinal j=0; j<dim; j++)
coordinates[(j*num_local_nodes) + i] = node(j) + offset(j);
for (GlobalOrdinal j=0; j<from_dim; j++)
target_coordinates[(j*num_local_nodes) + i] = node(j) + offset(j);
i++;
}
}
// Currently assuming all elements are the same!
DataTransferKit::DTK_ElementTopology element_topology = get_element_topology(mesh.elem(0));
GlobalOrdinal n_nodes_per_elem = mesh.elem(0)->n_nodes();
GlobalOrdinal n_local_elem = mesh.n_local_elem();
elements.resize(n_local_elem);
Teuchos::ArrayRCP<GlobalOrdinal> connectivity(n_nodes_per_elem*n_local_elem);
Teuchos::ArrayRCP<double> elem_centroid_coordinates(n_local_elem*from_dim);
// Fill in the elements and connectivity
{
GlobalOrdinal i = 0;
MeshBase::const_element_iterator end = mesh.local_elements_end();
for (MeshBase::const_element_iterator it = mesh.local_elements_begin();
it != end;
++it)
{
const Elem & elem = *(*it);
elements[i] = elem.id();
for (GlobalOrdinal j=0; j<n_nodes_per_elem; j++)
connectivity[(j*n_local_elem)+i] = elem.node(j);
{
Point centroid = elem.centroid();
for (GlobalOrdinal j=0; j<from_dim; j++)
elem_centroid_coordinates[(j*n_local_elem) + i] = centroid(j) + offset(j);
}
i++;
}
}
Teuchos::ArrayRCP<int> permutation_list(n_nodes_per_elem);
for (GlobalOrdinal i = 0; i < n_nodes_per_elem; ++i )
permutation_list[i] = i;
/*
Moose::out<<"n_nodes_per_elem: "<<n_nodes_per_elem<<std::endl;
Moose::out<<"Dim: "<<dim<<std::endl;
Moose::err<<"Vertices size: "<<vertices.size()<<std::endl;
{
Moose::err<<libMesh::processor_id()<<" Vertices: ";
for (unsigned int i=0; i<vertices.size(); i++)
Moose::err<<vertices[i]<<" ";
Moose::err<<std::endl;
}
Moose::err<<"Coordinates size: "<<coordinates.size()<<std::endl;
{
Moose::err<<libMesh::processor_id()<<" Coordinates: ";
for (unsigned int i=0; i<coordinates.size(); i++)
Moose::err<<coordinates[i]<<" ";
Moose::err<<std::endl;
}
Moose::err<<"Connectivity size: "<<connectivity.size()<<std::endl;
{
Moose::err<<libMesh::processor_id()<<" Connectivity: ";
for (unsigned int i=0; i<connectivity.size(); i++)
Moose::err<<connectivity[i]<<" ";
Moose::err<<std::endl;
}
Moose::err<<"Permutation_List size: "<<permutation_list.size()<<std::endl;
{
Moose::err<<libMesh::processor_id()<<" Permutation_List: ";
for (unsigned int i=0; i<permutation_list.size(); i++)
Moose::err<<permutation_list[i]<<" ";
Moose::err<<std::endl;
}
*/
Teuchos::RCP<MeshContainerType> mesh_container = Teuchos::rcp(
new MeshContainerType(dim, vertices, coordinates,
element_topology, n_nodes_per_elem,
elements, connectivity, permutation_list) );
// We only have 1 element topology in this grid so we make just one mesh block
Teuchos::ArrayRCP<Teuchos::RCP<MeshContainerType> > mesh_blocks(1);
mesh_blocks[0] = mesh_container;
// Create the MeshManager
mesh_manager = Teuchos::rcp(new DataTransferKit::MeshManager<MeshContainerType>(mesh_blocks, comm, dim) );
// Pack the coordinates into a field, this will be the positions we'll ask for other systems fields at
if (from_dim == dim)
target_coords = Teuchos::rcp(new DataTransferKit::FieldManager<MeshContainerType>(mesh_container, comm));
else
{
Teuchos::ArrayRCP<GlobalOrdinal> empty_elements(0);
Teuchos::ArrayRCP<GlobalOrdinal> empty_connectivity(0);
Teuchos::RCP<MeshContainerType> coords_only_mesh_container = Teuchos::rcp(
new MeshContainerType(from_dim, vertices, target_coordinates,
element_topology, n_nodes_per_elem,
empty_elements, empty_connectivity, permutation_list) );
target_coords = Teuchos::rcp(new DataTransferKit::FieldManager<MeshContainerType>(coords_only_mesh_container, comm));
}
{
Teuchos::ArrayRCP<GlobalOrdinal> empty_elements(0);
Teuchos::ArrayRCP<GlobalOrdinal> empty_connectivity(0);
Teuchos::RCP<MeshContainerType> centroid_coords_only_mesh_container = Teuchos::rcp(
new MeshContainerType(from_dim, elements, elem_centroid_coordinates,
element_topology, n_nodes_per_elem,
empty_elements, empty_connectivity, permutation_list) );
elem_centroid_coords = Teuchos::rcp(new DataTransferKit::FieldManager<MeshContainerType>(centroid_coords_only_mesh_container, comm));
}
// Swap back
Moose::swapLibMeshComm(old_comm);
}
void assemble_matrices(EquationSystems& es,
const std::string& system_name)
{
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Eigensystem");
#ifdef LIBMESH_HAVE_SLEPC
// Get a constant reference to the mesh object.
const MeshBase& mesh = es.get_mesh();
// The dimension that we are running.
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to our system.
EigenSystem & eigen_system = es.get_system<EigenSystem> (system_name);
// Get a constant reference to the Finite Element type
// for the first (and only) variable in the system.
FEType fe_type = eigen_system.get_dof_map().variable_type(0);
// A reference to the two system matrices
SparseMatrix<Number>& matrix_A = *eigen_system.matrix_A;
SparseMatrix<Number>& matrix_B = *eigen_system.matrix_B;
// Build a Finite Element object of the specified type. Since the
// \p FEBase::build() member dynamically creates memory we will
// store the object as an \p AutoPtr<FEBase>. This can be thought
// of as a pointer that will clean up after itself.
AutoPtr<FEBase> fe (FEBase::build(dim, fe_type));
// A Gauss quadrature rule for numerical integration.
// Use the default quadrature order.
QGauss qrule (dim, fe_type.default_quadrature_order());
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (&qrule);
// The element Jacobian * quadrature weight at each integration point.
const std::vector<Real>& JxW = fe->get_JxW();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> >& phi = fe->get_phi();
// The element shape function gradients evaluated at the quadrature
// points.
const std::vector<std::vector<RealGradient> >& dphi = fe->get_dphi();
// A reference to the \p DofMap object for this system. The \p DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers.
const DofMap& dof_map = eigen_system.get_dof_map();
// The element mass and stiffness matrices.
DenseMatrix<Number> Me;
DenseMatrix<Number> Ke;
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<unsigned int> dof_indices;
// Now we will loop over all the elements in the mesh that
// live on the local processor. We will compute the element
// matrix and right-hand-side contribution. In case users
// later modify this program to include refinement, we will
// be safe and will only consider the active elements;
// hence we use a variant of the \p active_elem_iterator.
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)
{
// Store a pointer to the element we are currently
// working on. This allows for nicer syntax later.
const Elem* elem = *el;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
// Compute the element-specific data for the current
// element. This involves computing the location of the
// quadrature points (q_point) and the shape functions
// (phi, dphi) for the current element.
fe->reinit (elem);
// Zero the element matrices before
// summing them. We use the resize member here because
// the number of degrees of freedom might have changed from
// the last element. Note that this will be the case if the
// element type is different (i.e. the last element was a
// triangle, now we are on a quadrilateral).
Ke.resize (dof_indices.size(), dof_indices.size());
Me.resize (dof_indices.size(), dof_indices.size());
// Now loop over the quadrature points. This handles
// the numeric integration.
//
// We will build the element matrix. This involves
// a double loop to integrate the test funcions (i) against
// the trial functions (j).
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
for (unsigned int i=0; i<phi.size(); i++)
for (unsigned int j=0; j<phi.size(); j++)
{
Me(i,j) += JxW[qp]*phi[i][qp]*phi[j][qp];
Ke(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
}
// On an unrefined mesh, constrain_element_matrix does
// nothing. If this assembly function is ever repurposed to
// run on a refined mesh, getting the hanging node constraints
// right will be important. Note that, even with
// asymmetric_constraint_rows = false, the constrained dof
// diagonals still exist in the matrix, with diagonal entries
// that are there to ensure non-singular matrices for linear
// solves but which would generate positive non-physical
// eigenvalues for eigensolves.
// dof_map.constrain_element_matrix(Ke, dof_indices, false);
// dof_map.constrain_element_matrix(Me, dof_indices, false);
// Finally, simply add the element contribution to the
// overall matrices A and B.
matrix_A.add_matrix (Ke, dof_indices);
matrix_B.add_matrix (Me, dof_indices);
} // end of element loop
#endif // LIBMESH_HAVE_SLEPC
/**
* All done!
*/
return;
}
void assemble_elasticity(EquationSystems & es,
const std::string & libmesh_dbg_var(system_name))
{
libmesh_assert_equal_to (system_name, "Elasticity");
const MeshBase & mesh = es.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
LinearImplicitSystem & system = es.get_system<LinearImplicitSystem>("Elasticity");
const unsigned int u_var = system.variable_number ("u");
const unsigned int v_var = system.variable_number ("v");
const DofMap & dof_map = system.get_dof_map();
FEType fe_type = dof_map.variable_type(0);
UniquePtr<FEBase> fe (FEBase::build(dim, fe_type));
QGauss qrule (dim, fe_type.default_quadrature_order());
fe->attach_quadrature_rule (&qrule);
UniquePtr<FEBase> fe_face (FEBase::build(dim, fe_type));
QGauss qface(dim-1, fe_type.default_quadrature_order());
fe_face->attach_quadrature_rule (&qface);
const std::vector<Real> & JxW = fe->get_JxW();
const std::vector<std::vector<RealGradient> > & dphi = fe->get_dphi();
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
DenseSubMatrix<Number>
Kuu(Ke), Kuv(Ke),
Kvu(Ke), Kvv(Ke);
DenseSubVector<Number>
Fu(Fe),
Fv(Fe);
std::vector<dof_id_type> dof_indices;
std::vector<dof_id_type> dof_indices_u;
std::vector<dof_id_type> dof_indices_v;
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;
dof_map.dof_indices (elem, dof_indices);
dof_map.dof_indices (elem, dof_indices_u, u_var);
dof_map.dof_indices (elem, dof_indices_v, v_var);
const unsigned int n_dofs = dof_indices.size();
const unsigned int n_u_dofs = dof_indices_u.size();
const unsigned int n_v_dofs = dof_indices_v.size();
fe->reinit (elem);
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
Kuu.reposition (u_var*n_u_dofs, u_var*n_u_dofs, n_u_dofs, n_u_dofs);
Kuv.reposition (u_var*n_u_dofs, v_var*n_u_dofs, n_u_dofs, n_v_dofs);
Kvu.reposition (v_var*n_v_dofs, u_var*n_v_dofs, n_v_dofs, n_u_dofs);
Kvv.reposition (v_var*n_v_dofs, v_var*n_v_dofs, n_v_dofs, n_v_dofs);
Fu.reposition (u_var*n_u_dofs, n_u_dofs);
Fv.reposition (v_var*n_u_dofs, n_v_dofs);
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
for (unsigned int i=0; i<n_u_dofs; i++)
for (unsigned int j=0; j<n_u_dofs; j++)
{
// Tensor indices
unsigned int C_i, C_j, C_k, C_l;
C_i=0, C_k=0;
C_j=0, C_l=0;
Kuu(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=1, C_l=0;
Kuu(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=0, C_l=1;
Kuu(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=1, C_l=1;
Kuu(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
}
for (unsigned int i=0; i<n_u_dofs; i++)
for (unsigned int j=0; j<n_v_dofs; j++)
{
// Tensor indices
unsigned int C_i, C_j, C_k, C_l;
C_i=0, C_k=1;
C_j=0, C_l=0;
Kuv(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=1, C_l=0;
Kuv(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=0, C_l=1;
Kuv(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=1, C_l=1;
Kuv(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
}
for (unsigned int i=0; i<n_v_dofs; i++)
for (unsigned int j=0; j<n_u_dofs; j++)
{
// Tensor indices
unsigned int C_i, C_j, C_k, C_l;
C_i=1, C_k=0;
C_j=0, C_l=0;
Kvu(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=1, C_l=0;
Kvu(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=0, C_l=1;
Kvu(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=1, C_l=1;
Kvu(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
}
for (unsigned int i=0; i<n_v_dofs; i++)
for (unsigned int j=0; j<n_v_dofs; j++)
{
// Tensor indices
unsigned int C_i, C_j, C_k, C_l;
C_i=1, C_k=1;
C_j=0, C_l=0;
Kvv(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=1, C_l=0;
Kvv(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=0, C_l=1;
Kvv(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
C_j=1, C_l=1;
Kvv(i,j) += JxW[qp]*(eval_elasticity_tensor(C_i, C_j, C_k, C_l) * dphi[i][qp](C_j)*dphi[j][qp](C_l));
}
}
{
for (unsigned int side=0; side<elem->n_sides(); side++)
if (elem->neighbor_ptr(side) == libmesh_nullptr)
{
const std::vector<std::vector<Real> > & phi_face = fe_face->get_phi();
const std::vector<Real> & JxW_face = fe_face->get_JxW();
fe_face->reinit(elem, side);
if (mesh.get_boundary_info().has_boundary_id (elem, side, 1)) // Apply a traction on the right side
{
for (unsigned int qp=0; qp<qface.n_points(); qp++)
for (unsigned int i=0; i<n_v_dofs; i++)
Fv(i) += JxW_face[qp] * (-1.) * phi_face[i][qp];
}
}
}
dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
system.matrix->add_matrix (Ke, dof_indices);
system.rhs->add_vector (Fe, dof_indices);
}
}
void assemble_structure (EquationSystems& es,
const std::string& system_name)
{
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Structure");
// Get a constant reference to the mesh object.
const MeshBase& mesh = es.get_mesh();
// The dimension that we are running
const uint dim = mesh.mesh_dimension();
// Get a reference to the Convection-Diffusion system object.
LinearImplicitSystem & system =
es.get_system<LinearImplicitSystem> ("Structure");
// Numeric ids corresponding to each variable in the system
const uint dx_var = system.variable_number ("dx");
const uint dy_var = system.variable_number ("dy");
const uint dz_var = system.variable_number ("dz");
// Get the Finite Element type for "u". Note this will be
// the same as the type for "v".
FEType fe_d_type = system.variable_type(dx_var);
// Build a Finite Element object of the specified type for
// the velocity variables.
AutoPtr<FEBase> fe_d (FEBase::build(dim, fe_d_type));
// A Gauss quadrature rule for numerical integration.
// Let the \p FEType object decide what order rule is appropriate.
QGauss qrule (dim, fe_d_type.default_quadrature_order());
// Tell the finite element objects to use our quadrature rule.
fe_d->attach_quadrature_rule (&qrule);
// Here we define some references to cell-specific data that
// will be used to assemble the linear system.
//
// The element Jacobian * quadrature weight at each integration point.
const std::vector<Real>& JxW = fe_d->get_JxW();
// The element shape function gradients for the velocity
// variables evaluated at the quadrature points.
const std::vector<std::vector<Real> >& phi = fe_d->get_phi();
const std::vector<std::vector<RealGradient> >& dphi = fe_d->get_dphi();
// A reference to the \p DofMap object for this system. The \p DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers. We will talk more about the \p DofMap
// in future examples.
const DofMap & dof_map = system.get_dof_map();
// Define data structures to contain the element matrix
// and right-hand-side vector contribution. Following
// basic finite element terminology we will denote these
// "Ke" and "Fe".
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
DenseSubMatrix<Number>
Kdxdx(Ke), Kdxdy(Ke), Kdxdz(Ke),
Kdydx(Ke), Kdydy(Ke), Kdydz(Ke),
Kdzdx(Ke), Kdzdy(Ke), Kdzdz(Ke);
DenseSubVector<Number>
Fdx(Fe),
Fdy(Fe),
Fdz(Fe);
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<dof_id_type> dof_indices;
std::vector<dof_id_type> dof_indices_dx;
std::vector<dof_id_type> dof_indices_dy;
std::vector<dof_id_type> dof_indices_dz;
// Now we will loop over all the elements in the mesh that
// live on the local processor. We will compute the element
// matrix and right-hand-side contribution. In case users later
// modify this program to include refinement, we will be safe and
// will only consider the active elements; hence we use a variant of
// the \p active_elem_iterator.
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)
{
// Store a pointer to the element we are currently
// working on. This allows for nicer syntax later.
const Elem* elem = *el;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
dof_map.dof_indices (elem, dof_indices_dx, dx_var);
dof_map.dof_indices (elem, dof_indices_dy, dy_var);
dof_map.dof_indices (elem, dof_indices_dz, dz_var);
const uint n_dofs = dof_indices.size();
const uint n_dx_dofs = dof_indices_dx.size();
const uint n_dy_dofs = dof_indices_dy.size();
const uint n_dz_dofs = dof_indices_dz.size();
// Compute the element-specific data for the current
// element. This involves computing the location of the
// quadrature points (q_point) and the shape functions
// (phi, dphi) for the current element.
fe_d->reinit (elem);
// Zero the element matrix and right-hand side before
// summing them. We use the resize member here because
// the number of degrees of freedom might have changed from
// the last element. Note that this will be the case if the
// element type is different (i.e. the last element was a
// triangle, now we are on a quadrilateral).
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
// Reposition the submatrices... The idea is this:
//
// - - - -
// | Kuu Kuv Kup | | Fu |
// Ke = | Kvu Kvv Kvp |; Fe = | Fv |
// | Kpu Kpv Kpp | | Fp |
// - - - -
//
// The \p DenseSubMatrix.repostition () member takes the
// (row_offset, column_offset, row_size, column_size).
//
// Similarly, the \p DenseSubVector.reposition () member
// takes the (row_offset, row_size)
Kdxdx.reposition (dx_var*n_dx_dofs, dx_var*n_dx_dofs, n_dx_dofs, n_dx_dofs);
Kdxdy.reposition (dx_var*n_dx_dofs, dy_var*n_dx_dofs, n_dx_dofs, n_dy_dofs);
Kdxdz.reposition (dx_var*n_dx_dofs, dz_var*n_dx_dofs, n_dx_dofs, n_dz_dofs);
Kdydx.reposition (dy_var*n_dy_dofs, dx_var*n_dy_dofs, n_dy_dofs, n_dx_dofs);
Kdydy.reposition (dy_var*n_dy_dofs, dy_var*n_dy_dofs, n_dy_dofs, n_dy_dofs);
Kdydz.reposition (dy_var*n_dy_dofs, dz_var*n_dy_dofs, n_dy_dofs, n_dz_dofs);
Kdzdx.reposition (dz_var*n_dy_dofs, dx_var*n_dz_dofs, n_dz_dofs, n_dx_dofs);
Kdzdy.reposition (dz_var*n_dy_dofs, dy_var*n_dz_dofs, n_dz_dofs, n_dy_dofs);
Kdzdz.reposition (dz_var*n_dy_dofs, dz_var*n_dz_dofs, n_dz_dofs, n_dz_dofs);
Fdx.reposition (dx_var*n_dx_dofs, n_dx_dofs);
Fdy.reposition (dy_var*n_dx_dofs, n_dy_dofs);
Fdz.reposition (dz_var*n_dx_dofs, n_dz_dofs);
// Now we will build the element matrix.
for (uint qp=0; qp<qrule.n_points(); qp++)
{
for (uint i=0; i<n_dx_dofs; i++)
{
Fdx(i) += JxW[qp]*f_x*phi[i][qp];
for (uint j=0; j<n_dx_dofs; j++)
{
Kdxdx(i,j) += JxW[qp]*(
mu*( 2.*dphi[i][qp](0)*dphi[j][qp](0)
+ dphi[i][qp](1)*dphi[j][qp](1)
+ dphi[i][qp](2)*dphi[j][qp](2) )
+ lmbda*dphi[i][qp](0)*dphi[j][qp](0)
);
}
for (uint j=0; j<n_dy_dofs; j++)
{
Kdxdy(i,j) += JxW[qp]*(
mu*dphi[i][qp](1)*dphi[j][qp](0)
+ lmbda*dphi[i][qp](0)*dphi[j][qp](1)
);
}
for (uint j=0; j<n_dz_dofs; j++)
{
Kdxdz(i,j) += JxW[qp]*(
mu*dphi[i][qp](2)*dphi[j][qp](0)
+ lmbda*dphi[i][qp](0)*dphi[j][qp](2)
);
}
}
for (uint i=0; i<n_dy_dofs; i++)
{
Fdy(i) += JxW[qp]*f_y*phi[i][qp];
for (uint j=0; j<n_dx_dofs; j++)
{
Kdydx(i,j) += JxW[qp]*(
mu*dphi[i][qp](0)*dphi[j][qp](1)
+ lmbda*dphi[i][qp](1)*dphi[j][qp](0)
);
}
for (uint j=0; j<n_dy_dofs; j++)
{
Kdydy(i,j) += JxW[qp]*(
mu*( dphi[i][qp](0)*dphi[j][qp](0)
+ 2.*dphi[i][qp](1)*dphi[j][qp](1)
+ dphi[i][qp](2)*dphi[j][qp](2) )
+ lmbda*dphi[i][qp](1)*dphi[j][qp](1)
);
}
for (uint j=0; j<n_dz_dofs; j++)
{
Kdydz(i,j) += JxW[qp]*(
mu*dphi[i][qp](2)*dphi[j][qp](1)
+ lmbda*dphi[i][qp](1)*dphi[j][qp](2)
);
}
}
for (uint i=0; i<n_dz_dofs; i++)
{
Fdz(i) += JxW[qp]*f_z*phi[i][qp];
for (uint j=0; j<n_dx_dofs; j++)
{
Kdzdx(i,j) += JxW[qp]*(
mu*dphi[i][qp](0)*dphi[j][qp](2)
+ lmbda*dphi[i][qp](2)*dphi[j][qp](0)
);
}
for (uint j=0; j<n_dy_dofs; j++)
{
Kdzdy(i,j) += JxW[qp]*(
mu*dphi[i][qp](1)*dphi[j][qp](2)
+ lmbda*dphi[i][qp](2)*dphi[j][qp](1)
);
}
for (uint j=0; j<n_dz_dofs; j++)
{
Kdzdz(i,j) += JxW[qp]*(
mu*( dphi[i][qp](0)*dphi[j][qp](0)
+ dphi[i][qp](1)*dphi[j][qp](1)
+ 2.*dphi[i][qp](2)*dphi[j][qp](2) )
+ lmbda*dphi[i][qp](2)*dphi[j][qp](2)
);
}
}
} // end of the quadrature point qp-loop
// If this assembly program were to be used on an adaptive mesh,
// we would have to apply any hanging node constraint equations.
dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
// The element matrix and right-hand-side are now built
// for this element. Add them to the global matrix and
// right-hand-side vector. The \p NumericMatrix::add_matrix()
// and \p NumericVector::add_vector() members do this for us.
system.matrix->add_matrix (Ke, dof_indices);
system.rhs->add_vector (Fe, dof_indices);
} // end of element loop
// system.matrix->close();
// system.matrix->print();
// system.rhs->close();
// system.rhs->print();
// That's it.
return;
}
// We now define the matrix and rhs vector assembly function
// for the shell system. This function implements the
// linear Kirchhoff-Love theory for thin shells. At the
// end we also take into account the boundary conditions
// here, using the penalty method.
void assemble_shell (EquationSystems & es,
const std::string & libmesh_dbg_var(system_name))
{
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Shell");
// Get a constant reference to the mesh object.
const MeshBase & mesh = es.get_mesh();
// Get a reference to the shell system object.
LinearImplicitSystem & system = es.get_system<LinearImplicitSystem> ("Shell");
// Get the shell parameters that we need during assembly.
const Real h = es.parameters.get<Real> ("thickness");
const Real E = es.parameters.get<Real> ("young's modulus");
const Real nu = es.parameters.get<Real> ("poisson ratio");
const Real q = es.parameters.get<Real> ("uniform load");
// Compute the membrane stiffness K and the bending
// rigidity D from these parameters.
const Real K = E * h / (1-nu*nu);
const Real D = E * h*h*h / (12*(1-nu*nu));
// Numeric ids corresponding to each variable in the system.
const unsigned int u_var = system.variable_number ("u");
const unsigned int v_var = system.variable_number ("v");
const unsigned int w_var = system.variable_number ("w");
// Get the Finite Element type for "u". Note this will be
// the same as the type for "v" and "w".
FEType fe_type = system.variable_type (u_var);
// Build a Finite Element object of the specified type.
std::unique_ptr<FEBase> fe (FEBase::build(2, fe_type));
// A Gauss quadrature rule for numerical integration.
// For subdivision shell elements, a single Gauss point per
// element is sufficient, hence we use extraorder = 0.
const int extraorder = 0;
std::unique_ptr<QBase> qrule (fe_type.default_quadrature_rule (2, extraorder));
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (qrule.get());
// The element Jacobian * quadrature weight at each integration point.
const std::vector<Real> & JxW = fe->get_JxW();
// The surface tangents in both directions at the quadrature points.
const std::vector<RealGradient> & dxyzdxi = fe->get_dxyzdxi();
const std::vector<RealGradient> & dxyzdeta = fe->get_dxyzdeta();
// The second partial derivatives at the quadrature points.
const std::vector<RealGradient> & d2xyzdxi2 = fe->get_d2xyzdxi2();
const std::vector<RealGradient> & d2xyzdeta2 = fe->get_d2xyzdeta2();
const std::vector<RealGradient> & d2xyzdxideta = fe->get_d2xyzdxideta();
// The element shape function and its derivatives evaluated at the
// quadrature points.
const std::vector<std::vector<Real>> & phi = fe->get_phi();
const std::vector<std::vector<RealGradient>> & dphi = fe->get_dphi();
const std::vector<std::vector<RealTensor>> & d2phi = fe->get_d2phi();
// A reference to the DofMap object for this system. The DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers.
const DofMap & dof_map = system.get_dof_map();
// Define data structures to contain the element stiffness matrix
// and right-hand-side vector contribution. Following
// basic finite element terminology we will denote these
// "Ke" and "Fe".
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
DenseSubMatrix<Number>
Kuu(Ke), Kuv(Ke), Kuw(Ke),
Kvu(Ke), Kvv(Ke), Kvw(Ke),
Kwu(Ke), Kwv(Ke), Kww(Ke);
DenseSubVector<Number>
Fu(Fe),
Fv(Fe),
Fw(Fe);
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<dof_id_type> dof_indices;
std::vector<dof_id_type> dof_indices_u;
std::vector<dof_id_type> dof_indices_v;
std::vector<dof_id_type> dof_indices_w;
// Now we will loop over all the elements in the mesh. We will
// compute the element matrix and right-hand-side contribution.
for (const auto & elem : mesh.active_local_element_ptr_range())
{
// The ghost elements at the boundaries need to be excluded
// here, as they don't belong to the physical shell,
// but serve for a proper boundary treatment only.
libmesh_assert_equal_to (elem->type(), TRI3SUBDIVISION);
const Tri3Subdivision * sd_elem = static_cast<const Tri3Subdivision *> (elem);
if (sd_elem->is_ghost())
continue;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
dof_map.dof_indices (elem, dof_indices_u, u_var);
dof_map.dof_indices (elem, dof_indices_v, v_var);
dof_map.dof_indices (elem, dof_indices_w, w_var);
const std::size_t n_dofs = dof_indices.size();
const std::size_t n_u_dofs = dof_indices_u.size();
const std::size_t n_v_dofs = dof_indices_v.size();
const std::size_t n_w_dofs = dof_indices_w.size();
// Compute the element-specific data for the current
// element. This involves computing the location of the
// quadrature points and the shape functions
// (phi, dphi, d2phi) for the current element.
fe->reinit (elem);
// Zero the element matrix and right-hand side before
// summing them. We use the resize member here because
// the number of degrees of freedom might have changed from
// the last element.
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
// Reposition the submatrices... The idea is this:
//
// - - - -
// | Kuu Kuv Kuw | | Fu |
// Ke = | Kvu Kvv Kvw |; Fe = | Fv |
// | Kwu Kwv Kww | | Fw |
// - - - -
//
// The DenseSubMatrix.reposition () member takes the
// (row_offset, column_offset, row_size, column_size).
//
// Similarly, the DenseSubVector.reposition () member
// takes the (row_offset, row_size)
Kuu.reposition (u_var*n_u_dofs, u_var*n_u_dofs, n_u_dofs, n_u_dofs);
Kuv.reposition (u_var*n_u_dofs, v_var*n_u_dofs, n_u_dofs, n_v_dofs);
Kuw.reposition (u_var*n_u_dofs, w_var*n_u_dofs, n_u_dofs, n_w_dofs);
Kvu.reposition (v_var*n_v_dofs, u_var*n_v_dofs, n_v_dofs, n_u_dofs);
Kvv.reposition (v_var*n_v_dofs, v_var*n_v_dofs, n_v_dofs, n_v_dofs);
Kvw.reposition (v_var*n_v_dofs, w_var*n_v_dofs, n_v_dofs, n_w_dofs);
Kwu.reposition (w_var*n_w_dofs, u_var*n_w_dofs, n_w_dofs, n_u_dofs);
Kwv.reposition (w_var*n_w_dofs, v_var*n_w_dofs, n_w_dofs, n_v_dofs);
Kww.reposition (w_var*n_w_dofs, w_var*n_w_dofs, n_w_dofs, n_w_dofs);
Fu.reposition (u_var*n_u_dofs, n_u_dofs);
Fv.reposition (v_var*n_u_dofs, n_v_dofs);
Fw.reposition (w_var*n_u_dofs, n_w_dofs);
// Now we will build the element matrix and right-hand-side.
for (unsigned int qp=0; qp<qrule->n_points(); ++qp)
{
// First, we compute the external force resulting
// from a load q distributed uniformly across the plate.
// Since the load is supposed to be transverse to the plate,
// it affects the z-direction, i.e. the "w" variable.
for (unsigned int i=0; i<n_u_dofs; ++i)
Fw(i) += JxW[qp] * phi[i][qp] * q;
// Next, we assemble the stiffness matrix. This is only valid
// for the linear theory, i.e., for small deformations, where
// reference and deformed surface metrics are indistinguishable.
// Get the three surface basis vectors.
const RealVectorValue & a1 = dxyzdxi[qp];
const RealVectorValue & a2 = dxyzdeta[qp];
RealVectorValue a3 = a1.cross(a2);
const Real jac = a3.norm(); // the surface Jacobian
libmesh_assert_greater (jac, 0);
a3 /= jac; // the shell director a3 is normalized to unit length
// Get the derivatives of the surface tangents.
const RealVectorValue & a11 = d2xyzdxi2[qp];
const RealVectorValue & a22 = d2xyzdeta2[qp];
const RealVectorValue & a12 = d2xyzdxideta[qp];
// Compute the three covariant components of the first
// fundamental form of the surface.
const RealVectorValue a(a1*a1, a2*a2, a1*a2);
// The elastic H matrix in Voigt's notation, computed from the
// covariant components of the first fundamental form rather
// than the contravariant components, exploiting that the
// contravariant first fundamental form is the inverse of the
// covariant first fundamental form (hence the determinant etc.).
RealTensorValue H;
H(0,0) = a(1) * a(1);
H(0,1) = H(1,0) = nu * a(1) * a(0) + (1-nu) * a(2) * a(2);
H(0,2) = H(2,0) = -a(1) * a(2);
H(1,1) = a(0) * a(0);
H(1,2) = H(2,1) = -a(0) * a(2);
H(2,2) = 0.5 * ((1-nu) * a(1) * a(0) + (1+nu) * a(2) * a(2));
const Real det = a(0) * a(1) - a(2) * a(2);
libmesh_assert_not_equal_to (det * det, 0);
H /= det * det;
// Precompute come cross products for the bending part below.
const RealVectorValue a11xa2 = a11.cross(a2);
const RealVectorValue a22xa2 = a22.cross(a2);
const RealVectorValue a12xa2 = a12.cross(a2);
const RealVectorValue a1xa11 = a1.cross(a11);
const RealVectorValue a1xa22 = a1.cross(a22);
const RealVectorValue a1xa12 = a1.cross(a12);
const RealVectorValue a2xa3 = a2.cross(a3);
const RealVectorValue a3xa1 = a3.cross(a1);
// Loop over all pairs of nodes I,J.
for (unsigned int i=0; i<n_u_dofs; ++i)
{
for (unsigned int j=0; j<n_u_dofs; ++j)
{
// The membrane strain matrices in Voigt's notation.
RealTensorValue MI, MJ;
for (unsigned int k=0; k<3; ++k)
{
MI(0,k) = dphi[i][qp](0) * a1(k);
MI(1,k) = dphi[i][qp](1) * a2(k);
MI(2,k) = dphi[i][qp](1) * a1(k)
+ dphi[i][qp](0) * a2(k);
MJ(0,k) = dphi[j][qp](0) * a1(k);
MJ(1,k) = dphi[j][qp](1) * a2(k);
MJ(2,k) = dphi[j][qp](1) * a1(k)
+ dphi[j][qp](0) * a2(k);
}
// The bending strain matrices in Voigt's notation.
RealTensorValue BI, BJ;
for (unsigned int k=0; k<3; ++k)
{
const Real term_ik = dphi[i][qp](0) * a2xa3(k)
+ dphi[i][qp](1) * a3xa1(k);
BI(0,k) = -d2phi[i][qp](0,0) * a3(k)
+(dphi[i][qp](0) * a11xa2(k)
+ dphi[i][qp](1) * a1xa11(k)
+ (a3*a11) * term_ik) / jac;
BI(1,k) = -d2phi[i][qp](1,1) * a3(k)
+(dphi[i][qp](0) * a22xa2(k)
+ dphi[i][qp](1) * a1xa22(k)
+ (a3*a22) * term_ik) / jac;
BI(2,k) = 2 * (-d2phi[i][qp](0,1) * a3(k)
+(dphi[i][qp](0) * a12xa2(k)
+ dphi[i][qp](1) * a1xa12(k)
+ (a3*a12) * term_ik) / jac);
const Real term_jk = dphi[j][qp](0) * a2xa3(k)
+ dphi[j][qp](1) * a3xa1(k);
BJ(0,k) = -d2phi[j][qp](0,0) * a3(k)
+(dphi[j][qp](0) * a11xa2(k)
+ dphi[j][qp](1) * a1xa11(k)
+ (a3*a11) * term_jk) / jac;
BJ(1,k) = -d2phi[j][qp](1,1) * a3(k)
+(dphi[j][qp](0) * a22xa2(k)
+ dphi[j][qp](1) * a1xa22(k)
+ (a3*a22) * term_jk) / jac;
BJ(2,k) = 2 * (-d2phi[j][qp](0,1) * a3(k)
+(dphi[j][qp](0) * a12xa2(k)
+ dphi[j][qp](1) * a1xa12(k)
+ (a3*a12) * term_jk) / jac);
}
// The total stiffness matrix coupling the nodes
// I and J is a sum of membrane and bending
// contributions according to the following formula.
const RealTensorValue KIJ = JxW[qp] * K * MI.transpose() * H * MJ
+ JxW[qp] * D * BI.transpose() * H * BJ;
// Insert the components of the coupling stiffness
// matrix KIJ into the corresponding directional
// submatrices.
Kuu(i,j) += KIJ(0,0);
Kuv(i,j) += KIJ(0,1);
Kuw(i,j) += KIJ(0,2);
Kvu(i,j) += KIJ(1,0);
Kvv(i,j) += KIJ(1,1);
Kvw(i,j) += KIJ(1,2);
Kwu(i,j) += KIJ(2,0);
Kwv(i,j) += KIJ(2,1);
Kww(i,j) += KIJ(2,2);
}
}
} // end of the quadrature point qp-loop
// The element matrix and right-hand-side are now built
// for this element. Add them to the global matrix and
// right-hand-side vector. The NumericMatrix::add_matrix()
// and NumericVector::add_vector() members do this for us.
system.matrix->add_matrix (Ke, dof_indices);
system.rhs->add_vector (Fe, dof_indices);
} // end of non-ghost element loop
// Next, we apply the boundary conditions. In this case,
// all boundaries are clamped by the penalty method, using
// the special "ghost" nodes along the boundaries. Note
// that there are better ways to implement boundary conditions
// for subdivision shells. We use the simplest way here,
// which is known to be overly restrictive and will lead to
// a slightly too small deformation of the plate.
for (const auto & elem : mesh.active_local_element_ptr_range())
{
// For the boundary conditions, we only need to loop over
// the ghost elements.
libmesh_assert_equal_to (elem->type(), TRI3SUBDIVISION);
const Tri3Subdivision * gh_elem = static_cast<const Tri3Subdivision *> (elem);
if (!gh_elem->is_ghost())
continue;
// Find the side which is part of the physical plate boundary,
// that is, the boundary of the original mesh without ghosts.
for (auto s : elem->side_index_range())
{
const Tri3Subdivision * nb_elem = static_cast<const Tri3Subdivision *> (elem->neighbor_ptr(s));
if (nb_elem == libmesh_nullptr || nb_elem->is_ghost())
continue;
/*
* Determine the four nodes involved in the boundary
* condition treatment of this side. The MeshTools::Subdiv
* namespace provides lookup tables next and prev
* for an efficient determination of the next and previous
* nodes of an element, respectively.
*
* n4
* / \
* / gh \
* n2 ---- n3
* \ nb /
* \ /
* n1
*/
const Node * nodes [4]; // n1, n2, n3, n4
nodes[1] = gh_elem->node_ptr(s); // n2
nodes[2] = gh_elem->node_ptr(MeshTools::Subdivision::next[s]); // n3
nodes[3] = gh_elem->node_ptr(MeshTools::Subdivision::prev[s]); // n4
// The node in the interior of the domain, n1, is the
// hardest to find. Walk along the edges of element nb until
// we have identified it.
unsigned int n_int = 0;
nodes[0] = nb_elem->node_ptr(0);
while (nodes[0]->id() == nodes[1]->id() || nodes[0]->id() == nodes[2]->id())
nodes[0] = nb_elem->node_ptr(++n_int);
// The penalty value. \f$ \frac{1}{\epsilon} \f$
const Real penalty = 1.e10;
// With this simple method, clamped boundary conditions are
// obtained by penalizing the displacements of all four nodes.
// This ensures that the displacement field vanishes on the
// boundary side s.
for (unsigned int n=0; n<4; ++n)
{
const dof_id_type u_dof = nodes[n]->dof_number (system.number(), u_var, 0);
const dof_id_type v_dof = nodes[n]->dof_number (system.number(), v_var, 0);
const dof_id_type w_dof = nodes[n]->dof_number (system.number(), w_var, 0);
system.matrix->add (u_dof, u_dof, penalty);
system.matrix->add (v_dof, v_dof, penalty);
system.matrix->add (w_dof, w_dof, penalty);
}
}
} // end of ghost element loop
}
void assemble(EquationSystems& es,
const std::string& libmesh_dbg_var(system_name))
{
libmesh_assert_equal_to (system_name, "primary");
const MeshBase& mesh = es.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
// Also use a 3x3x3 quadrature rule (3D). Then tell the FE
// about the geometry of the problem and the quadrature rule
FEType fe_type (FIRST);
UniquePtr<FEBase> fe(FEBase::build(dim, fe_type));
QGauss qrule(dim, FIFTH);
fe->attach_quadrature_rule (&qrule);
UniquePtr<FEBase> fe_face(FEBase::build(dim, fe_type));
QGauss qface(dim-1, FIFTH);
fe_face->attach_quadrature_rule(&qface);
LinearImplicitSystem& system =
es.get_system<LinearImplicitSystem>("primary");
// These are references to cell-specific data
const std::vector<Real>& JxW_face = fe_face->get_JxW();
const std::vector<Real>& JxW = fe->get_JxW();
const std::vector<Point>& q_point = fe->get_xyz();
const std::vector<std::vector<Real> >& phi = fe->get_phi();
const std::vector<std::vector<RealGradient> >& dphi = fe->get_dphi();
std::vector<unsigned int> dof_indices_U;
std::vector<unsigned int> dof_indices_V;
const DofMap& dof_map = system.get_dof_map();
DenseMatrix<Number> Kuu;
DenseMatrix<Number> Kvv;
DenseVector<Number> Fu;
DenseVector<Number> Fv;
Real vol=0., area=0.;
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;
// recompute the element-specific data for the current element
fe->reinit (elem);
//fe->print_info();
dof_map.dof_indices(elem, dof_indices_U, 0);
dof_map.dof_indices(elem, dof_indices_V, 1);
// zero the element matrix and vector
Kuu.resize (phi.size(),
phi.size());
Kvv.resize (phi.size(),
phi.size());
Fu.resize (phi.size());
Fv.resize (phi.size());
// standard stuff... like in code 1.
for (unsigned int gp=0; gp<qrule.n_points(); gp++)
{
for (unsigned int i=0; i<phi.size(); ++i)
{
// this is tricky. ig is the _global_ dof index corresponding
// to the _global_ vertex number elem->node(i). Note that
// in general these numbers will not be the same (except for
// the case of one unknown per node on one subdomain) so
// we need to go through the dof_map
const Real f = q_point[gp]*q_point[gp];
// const Real f = (q_point[gp](0) +
// q_point[gp](1) +
// q_point[gp](2));
// add jac*weight*f*phi to the RHS in position ig
Fu(i) += JxW[gp]*f*phi[i][gp];
Fv(i) += JxW[gp]*f*phi[i][gp];
for (unsigned int j=0; j<phi.size(); ++j)
{
Kuu(i,j) += JxW[gp]*((phi[i][gp])*(phi[j][gp]));
Kvv(i,j) += JxW[gp]*((phi[i][gp])*(phi[j][gp]) +
1.*((dphi[i][gp])*(dphi[j][gp])));
};
};
vol += JxW[gp];
};
// You can't compute "area" (perimeter) if you are in 2D
if (dim == 3)
{
for (unsigned int side=0; side<elem->n_sides(); side++)
if (elem->neighbor(side) == NULL)
{
fe_face->reinit (elem, side);
//fe_face->print_info();
for (unsigned int gp=0; gp<JxW_face.size(); gp++)
area += JxW_face[gp];
}
}
// Constrain the DOF indices.
dof_map.constrain_element_matrix_and_vector(Kuu, Fu, dof_indices_U);
dof_map.constrain_element_matrix_and_vector(Kvv, Fv, dof_indices_V);
system.rhs->add_vector(Fu, dof_indices_U);
system.rhs->add_vector(Fv, dof_indices_V);
system.matrix->add_matrix(Kuu, dof_indices_U);
system.matrix->add_matrix(Kvv, dof_indices_V);
}
libMesh::out << "Vol=" << vol << std::endl;
if (dim == 3)
libMesh::out << "Area=" << area << std::endl;
}
// This function assembles the system matrix and right-hand-side
// for the discrete form of our wave equation.
void assemble_wave(EquationSystems & es,
const std::string & system_name)
{
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Wave");
#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
// Get a constant reference to the mesh object.
const MeshBase & mesh = es.get_mesh();
// Get a reference to the system we are solving.
LinearImplicitSystem & system = es.get_system<LinearImplicitSystem>("Wave");
// A reference to the \p DofMap object for this system. The \p DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers.
const DofMap & dof_map = system.get_dof_map();
// The dimension that we are running.
const unsigned int dim = mesh.mesh_dimension();
// Copy the speed of sound to a local variable.
const Real speed = es.parameters.get<Real>("speed");
// Get a constant reference to the Finite Element type
// for the first (and only) variable in the system.
const FEType & fe_type = dof_map.variable_type(0);
// Build a Finite Element object of the specified type. Since the
// \p FEBase::build() member dynamically creates memory we will
// store the object as an \p UniquePtr<FEBase>. Check ex5 for details.
UniquePtr<FEBase> fe (FEBase::build(dim, fe_type));
// Do the same for an infinite element.
UniquePtr<FEBase> inf_fe (FEBase::build_InfFE(dim, fe_type));
// A 2nd order Gauss quadrature rule for numerical integration.
QGauss qrule (dim, SECOND);
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (&qrule);
// Due to its internal structure, the infinite element handles
// quadrature rules differently. It takes the quadrature
// rule which has been initialized for the FE object, but
// creates suitable quadrature rules by @e itself. The user
// need not worry about this.
inf_fe->attach_quadrature_rule (&qrule);
// Define data structures to contain the element matrix
// and right-hand-side vector contribution. Following
// basic finite element terminology we will denote these
// "Ke", "Ce", "Me", and "Fe" for the stiffness, damping
// and mass matrices, and the load vector. Note that in
// Acoustics, these descriptors though do @e not match the
// true physical meaning of the projectors. The final
// overall system, however, resembles the conventional
// notation again.
DenseMatrix<Number> Ke;
DenseMatrix<Number> Ce;
DenseMatrix<Number> Me;
DenseVector<Number> Fe;
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<dof_id_type> dof_indices;
// Now we will loop over all the elements in the mesh.
// We will compute the element matrix and right-hand-side
// contribution.
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)
{
// Store a pointer to the element we are currently
// working on. This allows for nicer syntax later.
const Elem * elem = *el;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
// The mesh contains both finite and infinite elements. These
// elements are handled through different classes, namely
// \p FE and \p InfFE, respectively. However, since both
// are derived from \p FEBase, they share the same interface,
// and overall burden of coding is @e greatly reduced through
// using a pointer, which is adjusted appropriately to the
// current element type.
FEBase * cfe = libmesh_nullptr;
// This here is almost the only place where we need to
// distinguish between finite and infinite elements.
// For faster computation, however, different approaches
// may be feasible.
//
// Up to now, we do not know what kind of element we
// have. Aske the element of what type it is:
if (elem->infinite())
{
// We have an infinite element. Let \p cfe point
// to our \p InfFE object. This is handled through
// an UniquePtr. Through the \p UniquePtr::get() we "borrow"
// the pointer, while the \p UniquePtr \p inf_fe is
// still in charge of memory management.
cfe = inf_fe.get();
}
else
{
// This is a conventional finite element. Let \p fe handle it.
cfe = fe.get();
// Boundary conditions.
// Here we just zero the rhs-vector. For natural boundary
// conditions check e.g. previous examples.
{
// Zero the RHS for this element.
Fe.resize (dof_indices.size());
system.rhs->add_vector (Fe, dof_indices);
} // end boundary condition section
} // else if (elem->infinite())
// This is slightly different from the Poisson solver:
// Since the finite element object may change, we have to
// initialize the constant references to the data fields
// each time again, when a new element is processed.
//
// The element Jacobian * quadrature weight at each integration point.
const std::vector<Real> & JxW = cfe->get_JxW();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> > & phi = cfe->get_phi();
// The element shape function gradients evaluated at the quadrature
// points.
const std::vector<std::vector<RealGradient> > & dphi = cfe->get_dphi();
// The infinite elements need more data fields than conventional FE.
// These are the gradients of the phase term \p dphase, an additional
// radial weight for the test functions \p Sobolev_weight, and its
// gradient.
//
// Note that these data fields are also initialized appropriately by
// the \p FE method, so that the weak form (below) is valid for @e both
// finite and infinite elements.
const std::vector<RealGradient> & dphase = cfe->get_dphase();
const std::vector<Real> & weight = cfe->get_Sobolev_weight();
const std::vector<RealGradient> & dweight = cfe->get_Sobolev_dweight();
// Now this is all independent of whether we use an \p FE
// or an \p InfFE. Nice, hm? ;-)
//
// Compute the element-specific data, as described
// in previous examples.
cfe->reinit (elem);
// Zero the element matrices. Boundary conditions were already
// processed in the \p FE-only section, see above.
Ke.resize (dof_indices.size(), dof_indices.size());
Ce.resize (dof_indices.size(), dof_indices.size());
Me.resize (dof_indices.size(), dof_indices.size());
// The total number of quadrature points for infinite elements
// @e has to be determined in a different way, compared to
// conventional finite elements. This type of access is also
// valid for finite elements, so this can safely be used
// anytime, instead of asking the quadrature rule, as
// seen in previous examples.
unsigned int max_qp = cfe->n_quadrature_points();
// Loop over the quadrature points.
for (unsigned int qp=0; qp<max_qp; qp++)
{
// Similar to the modified access to the number of quadrature
// points, the number of shape functions may also be obtained
// in a different manner. This offers the great advantage
// of being valid for both finite and infinite elements.
const unsigned int n_sf = cfe->n_shape_functions();
// Now we will build the element matrices. Since the infinite
// elements are based on a Petrov-Galerkin scheme, the
// resulting system matrices are non-symmetric. The additional
// weight, described before, is part of the trial space.
//
// For the finite elements, though, these matrices are symmetric
// just as we know them, since the additional fields \p dphase,
// \p weight, and \p dweight are initialized appropriately.
//
// test functions: weight[qp]*phi[i][qp]
// trial functions: phi[j][qp]
// phase term: phase[qp]
//
// derivatives are similar, but note that these are of type
// Point, not of type Real.
for (unsigned int i=0; i<n_sf; i++)
for (unsigned int j=0; j<n_sf; j++)
{
// (ndt*Ht + nHt*d) * nH
Ke(i,j) +=
(
(dweight[qp] * phi[i][qp] // Point * Real = Point
+ // +
dphi[i][qp] * weight[qp] // Point * Real = Point
) * dphi[j][qp]
) * JxW[qp];
// (d*Ht*nmut*nH - ndt*nmu*Ht*H - d*nHt*nmu*H)
Ce(i,j) +=
(
(dphase[qp] * dphi[j][qp]) // (Point * Point) = Real
* weight[qp] * phi[i][qp] // * Real * Real = Real
- // -
(dweight[qp] * dphase[qp]) // (Point * Point) = Real
* phi[i][qp] * phi[j][qp] // * Real * Real = Real
- // -
(dphi[i][qp] * dphase[qp]) // (Point * Point) = Real
* weight[qp] * phi[j][qp] // * Real * Real = Real
) * JxW[qp];
// (d*Ht*H * (1 - nmut*nmu))
Me(i,j) +=
(
(1. - (dphase[qp] * dphase[qp])) // (Real - (Point * Point)) = Real
* phi[i][qp] * phi[j][qp] * weight[qp] // * Real * Real * Real = Real
) * JxW[qp];
} // end of the matrix summation loop
} // end of quadrature point loop
// The element matrices are now built for this element.
// Collect them in Ke, and then add them to the global matrix.
// The \p SparseMatrix::add_matrix() member does this for us.
Ke.add(1./speed , Ce);
Ke.add(1./(speed*speed), Me);
// If this assembly program were to be used on an adaptive mesh,
// we would have to apply any hanging node constraint equations
dof_map.constrain_element_matrix(Ke, dof_indices);
system.matrix->add_matrix (Ke, dof_indices);
} // end of element loop
// Note that we have not applied any boundary conditions so far.
// Here we apply a unit load at the node located at (0,0,0).
{
// Iterate over local nodes
MeshBase::const_node_iterator nd = mesh.local_nodes_begin();
const MeshBase::const_node_iterator nd_end = mesh.local_nodes_end();
for (; nd != nd_end; ++nd)
{
// Get a reference to the current node.
const Node & node = **nd;
// Check the location of the current node.
if (std::abs(node(0)) < TOLERANCE &&
std::abs(node(1)) < TOLERANCE &&
std::abs(node(2)) < TOLERANCE)
{
// The global number of the respective degree of freedom.
unsigned int dn = node.dof_number(0,0,0);
system.rhs->add (dn, 1.);
}
}
}
#else
// dummy assert
libmesh_assert_not_equal_to (es.get_mesh().mesh_dimension(), 1);
#endif //ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
}
// Here we define the matrix assembly routine for
// the Helmholtz system. This function will be
// called to form the stiffness matrix and right-hand side.
void assemble_helmholtz(EquationSystems & es,
const std::string & system_name)
{
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Helmholtz");
// Get a constant reference to the mesh object.
const MeshBase & mesh = es.get_mesh();
// The dimension that we are in
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to our system, as before
FrequencySystem & f_system =
es.get_system<FrequencySystem> (system_name);
// A const reference to the DofMap object for this system. The DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers.
const DofMap & dof_map = f_system.get_dof_map();
// Get a constant reference to the Finite Element type
// for the first (and only) variable in the system.
const FEType & fe_type = dof_map.variable_type(0);
// For the admittance boundary condition,
// get the fluid density
const Real rho = es.parameters.get<Real>("rho");
// In here, we will add the element matrices to the
// <i>additional</i> matrices "stiffness_mass", "damping",
// and the additional vector "rhs", not to the members
// "matrix" and "rhs". Therefore, get writable
// references to them
SparseMatrix<Number> & stiffness = f_system.get_matrix("stiffness");
SparseMatrix<Number> & damping = f_system.get_matrix("damping");
SparseMatrix<Number> & mass = f_system.get_matrix("mass");
NumericVector<Number> & freq_indep_rhs = f_system.get_vector("rhs");
// Some solver packages (PETSc) are especially picky about
// allocating sparsity structure and truly assigning values
// to this structure. Namely, matrix additions, as performed
// later, exhibit acceptable performance only for identical
// sparsity structures. Therefore, explicitly zero the
// values in the collective matrix, so that matrix additions
// encounter identical sparsity structures.
SparseMatrix<Number> & matrix = *f_system.matrix;
// ------------------------------------------------------------------
// Finite Element related stuff
//
// Build a Finite Element object of the specified type. Since the
// FEBase::build() member dynamically creates memory we will
// store the object as a UniquePtr<FEBase>. This can be thought
// of as a pointer that will clean up after itself.
UniquePtr<FEBase> fe (FEBase::build(dim, fe_type));
// A 5th order Gauss quadrature rule for numerical integration.
QGauss qrule (dim, FIFTH);
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (&qrule);
// The element Jacobian// quadrature weight at each integration point.
const std::vector<Real> & JxW = fe->get_JxW();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> > & phi = fe->get_phi();
// The element shape function gradients evaluated at the quadrature
// points.
const std::vector<std::vector<RealGradient> > & dphi = fe->get_dphi();
// Now this is slightly different from example 4.
// We will not add directly to the global matrix,
// but to the additional matrices "stiffness_mass" and "damping".
// The same holds for the right-hand-side vector Fe, which we will
// later on store in the additional vector "rhs".
// The zero_matrix is used to explicitly induce the same sparsity
// structure in the overall matrix.
// see later on. (At least) the mass, and stiffness matrices, however,
// are inherently real. Therefore, store these as one complex
// matrix. This will definitely save memory.
DenseMatrix<Number> Ke, Ce, Me, zero_matrix;
DenseVector<Number> Fe;
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<dof_id_type> dof_indices;
// Now we will loop over all the elements in the mesh.
// We will compute the element matrix and right-hand-side
// contribution.
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)
{
// Start logging the element initialization.
START_LOG("elem init", "assemble_helmholtz");
// Store a pointer to the element we are currently
// working on. This allows for nicer syntax later.
const Elem * elem = *el;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
// Compute the element-specific data for the current
// element. This involves computing the location of the
// quadrature points (q_point) and the shape functions
// (phi, dphi) for the current element.
fe->reinit (elem);
// Zero & resize the element matrix and right-hand side before
// summing them, with different element types in the mesh this
// is quite necessary.
{
const unsigned int n_dof_indices = dof_indices.size();
Ke.resize (n_dof_indices, n_dof_indices);
Ce.resize (n_dof_indices, n_dof_indices);
Me.resize (n_dof_indices, n_dof_indices);
zero_matrix.resize (n_dof_indices, n_dof_indices);
Fe.resize (n_dof_indices);
}
// Stop logging the element initialization.
STOP_LOG("elem init", "assemble_helmholtz");
// Now loop over the quadrature points. This handles
// the numeric integration.
START_LOG("stiffness & mass", "assemble_helmholtz");
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
// Now we will build the element matrix. This involves
// a double loop to integrate the test funcions (i) against
// the trial functions (j). Note the braces on the rhs
// of Ke(i,j): these are quite necessary to finally compute
// Real*(Point*Point) = Real, and not something else...
for (unsigned int i=0; i<phi.size(); i++)
for (unsigned int j=0; j<phi.size(); j++)
{
Ke(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
Me(i,j) += JxW[qp]*(phi[i][qp]*phi[j][qp]);
}
}
STOP_LOG("stiffness & mass", "assemble_helmholtz");
// Now compute the contribution to the element matrix
// (due to mixed boundary conditions) if the current
// element lies on the boundary.
//
// The following loops over the sides of the element.
// If the element has no neighbor on a side then that
// side MUST live on a boundary of the domain.
for (unsigned int side=0; side<elem->n_sides(); side++)
if (elem->neighbor(side) == libmesh_nullptr)
{
LOG_SCOPE("damping", "assemble_helmholtz");
// Declare a special finite element object for
// boundary integration.
UniquePtr<FEBase> fe_face (FEBase::build(dim, fe_type));
// Boundary integration requires one quadraure rule,
// with dimensionality one less than the dimensionality
// of the element.
QGauss qface(dim-1, SECOND);
// Tell the finte element object to use our
// quadrature rule.
fe_face->attach_quadrature_rule (&qface);
// The value of the shape functions at the quadrature
// points.
const std::vector<std::vector<Real> > & phi_face =
fe_face->get_phi();
// The Jacobian// Quadrature Weight at the quadrature
// points on the face.
const std::vector<Real> & JxW_face = fe_face->get_JxW();
// Compute the shape function values on the element
// face.
fe_face->reinit(elem, side);
// For the Robin BCs consider a normal admittance an=1
// at some parts of the bounfdary
const Real an_value = 1.;
// Loop over the face quadrature points for integration.
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
// Element matrix contributrion due to precribed
// admittance boundary conditions.
for (unsigned int i=0; i<phi_face.size(); i++)
for (unsigned int j=0; j<phi_face.size(); j++)
Ce(i,j) += rho*an_value*JxW_face[qp]*phi_face[i][qp]*phi_face[j][qp];
}
}
// If this assembly program were to be used on an adaptive mesh,
// we would have to apply any hanging node constraint equations
// by uncommenting the following lines:
// std::vector<unsigned int> dof_indicesC = dof_indices;
// std::vector<unsigned int> dof_indicesM = dof_indices;
// dof_map.constrain_element_matrix (Ke, dof_indices);
// dof_map.constrain_element_matrix (Ce, dof_indicesC);
// dof_map.constrain_element_matrix (Me, dof_indicesM);
// Finally, simply add the contributions to the additional
// matrices and vector.
stiffness.add_matrix (Ke, dof_indices);
damping.add_matrix (Ce, dof_indices);
mass.add_matrix (Me, dof_indices);
// For the overall matrix, explicitly zero the entries where
// we added values in the other ones, so that we have
// identical sparsity footprints.
matrix.add_matrix(zero_matrix, dof_indices);
} // loop el
// It now remains to compute the rhs. Here, we simply
// get the normal velocities values on the boundary from the
// mesh data.
{
LOG_SCOPE("rhs", "assemble_helmholtz");
// get a reference to the mesh data.
const MeshData & mesh_data = es.get_mesh_data();
// We will now loop over all nodes. In case nodal data
// for a certain node is available in the MeshData, we simply
// adopt the corresponding value for the rhs vector.
// Note that normal data was given in the mesh data file,
// i.e. one value per node
libmesh_assert_equal_to (mesh_data.n_val_per_node(), 1);
MeshBase::const_node_iterator node_it = mesh.nodes_begin();
const MeshBase::const_node_iterator node_end = mesh.nodes_end();
for ( ; node_it != node_end; ++node_it)
{
// the current node pointer
const Node * node = *node_it;
// check if the mesh data has data for the current node
// and do for all components
if (mesh_data.has_data(node))
for (unsigned int comp=0; comp<node->n_comp(0, 0); comp++)
{
// the dof number
unsigned int dn = node->dof_number(0, 0, comp);
// set the nodal value
freq_indep_rhs.set(dn, mesh_data.get_data(node)[0]);
}
}
}
// All done!
}
void compute_stresses(EquationSystems & es)
{
LOG_SCOPE("compute_stresses()", "main");
const MeshBase & mesh = es.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
ElasticityRBConstruction & system = es.get_system<ElasticityRBConstruction>("RBElasticity");
unsigned int displacement_vars[3];
displacement_vars[0] = system.variable_number ("u");
displacement_vars[1] = system.variable_number ("v");
displacement_vars[2] = system.variable_number ("w");
const unsigned int u_var = system.variable_number ("u");
const DofMap & dof_map = system.get_dof_map();
FEType fe_type = dof_map.variable_type(u_var);
UniquePtr<FEBase> fe (FEBase::build(dim, fe_type));
QGauss qrule (dim, fe_type.default_quadrature_order());
fe->attach_quadrature_rule (&qrule);
const std::vector<Real> & JxW = fe->get_JxW();
const std::vector<std::vector<RealGradient> > & dphi = fe->get_dphi();
// Also, get a reference to the ExplicitSystem
ExplicitSystem & stress_system = es.get_system<ExplicitSystem>("StressSystem");
const DofMap & stress_dof_map = stress_system.get_dof_map();
unsigned int sigma_vars[3][3];
sigma_vars[0][0] = stress_system.variable_number ("sigma_00");
sigma_vars[0][1] = stress_system.variable_number ("sigma_01");
sigma_vars[0][2] = stress_system.variable_number ("sigma_02");
sigma_vars[1][0] = stress_system.variable_number ("sigma_10");
sigma_vars[1][1] = stress_system.variable_number ("sigma_11");
sigma_vars[1][2] = stress_system.variable_number ("sigma_12");
sigma_vars[2][0] = stress_system.variable_number ("sigma_20");
sigma_vars[2][1] = stress_system.variable_number ("sigma_21");
sigma_vars[2][2] = stress_system.variable_number ("sigma_22");
unsigned int vonMises_var = stress_system.variable_number ("vonMises");
// Storage for the stress dof indices on each element
std::vector<std::vector<dof_id_type> > dof_indices_var(system.n_vars());
std::vector<dof_id_type> stress_dof_indices_var;
// To store the stress tensor on each element
DenseMatrix<Number> elem_sigma;
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;
for (unsigned int var=0; var<3; var++)
dof_map.dof_indices (elem, dof_indices_var[var], displacement_vars[var]);
fe->reinit (elem);
elem_sigma.resize(3, 3);
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
for (unsigned int C_i=0; C_i<3; C_i++)
for (unsigned int C_j=0; C_j<3; C_j++)
for (unsigned int C_k=0; C_k<3; C_k++)
{
const unsigned int n_var_dofs = dof_indices_var[C_k].size();
// Get the gradient at this quadrature point
Gradient displacement_gradient;
for (unsigned int l=0; l<n_var_dofs; l++)
displacement_gradient.add_scaled(dphi[l][qp], system.current_solution(dof_indices_var[C_k][l]));
for (unsigned int C_l=0; C_l<3; C_l++)
elem_sigma(C_i,C_j) += JxW[qp] * (elasticity_tensor(C_i, C_j, C_k, C_l) * displacement_gradient(C_l));
}
// Get the average stresses by dividing by the element volume
elem_sigma.scale(1./elem->volume());
// load elem_sigma data into stress_system
for (unsigned int i=0; i<3; i++)
for (unsigned int j=0; j<3; j++)
{
stress_dof_map.dof_indices (elem, stress_dof_indices_var, sigma_vars[i][j]);
// We are using CONSTANT MONOMIAL basis functions, hence we only need to get
// one dof index per variable
dof_id_type dof_index = stress_dof_indices_var[0];
if ((stress_system.solution->first_local_index() <= dof_index) &&
(dof_index < stress_system.solution->last_local_index()))
{
stress_system.solution->set(dof_index, elem_sigma(i,j));
}
}
// Also, the von Mises stress
Number vonMises_value = std::sqrt(0.5*(pow(elem_sigma(0,0) - elem_sigma(1,1),2.) +
pow(elem_sigma(1,1) - elem_sigma(2,2),2.) +
pow(elem_sigma(2,2) - elem_sigma(0,0),2.) +
6.*(pow(elem_sigma(0,1),2.) + pow(elem_sigma(1,2),2.) + pow(elem_sigma(2,0),2.))
));
stress_dof_map.dof_indices (elem, stress_dof_indices_var, vonMises_var);
dof_id_type dof_index = stress_dof_indices_var[0];
if ((stress_system.solution->first_local_index() <= dof_index) &&
(dof_index < stress_system.solution->last_local_index()))
{
stress_system.solution->set(dof_index, vonMises_value);
}
}
// Should call close and update when we set vector entries directly
stress_system.solution->close();
stress_system.update();
}
void get_dirichlet_dofs(EquationSystems& es,
const std::string& system_name,
std::set<unsigned int>& dirichlet_dof_ids)
{
#ifdef LIBMESH_HAVE_SLEPC
dirichlet_dof_ids.clear();
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Eigensystem");
// Get a constant reference to the mesh object.
const MeshBase& mesh = es.get_mesh();
// The dimension that we are running.
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to our system.
EigenSystem & eigen_system = es.get_system<EigenSystem> (system_name);
// Get a constant reference to the Finite Element type
// for the first (and only) variable in the system.
FEType fe_type = eigen_system.get_dof_map().variable_type(0);
const DofMap& dof_map = eigen_system.get_dof_map();
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<unsigned int> dof_indices;
// Now we will loop over all the elements in the mesh that
// live on the local processor. We will compute the element
// matrix and right-hand-side contribution. In case users
// later modify this program to include refinement, we will
// be safe and will only consider the active elements;
// hence we use a variant of the \p active_elem_iterator.
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)
{
// Store a pointer to the element we are currently
// working on. This allows for nicer syntax later.
const Elem* elem = *el;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
{
// All boundary dofs are Dirichlet dofs in this case
for (unsigned int s=0; s<elem->n_sides(); s++)
if (elem->neighbor(s) == NULL)
{
std::vector<unsigned int> side_dofs;
FEInterface::dofs_on_side(elem, dim, fe_type,
s, side_dofs);
for(unsigned int ii=0; ii<side_dofs.size(); ii++)
dirichlet_dof_ids.insert(dof_indices[side_dofs[ii]]);
}
}
} // end of element loop
#endif // LIBMESH_HAVE_SLEPC
/**
* All done!
*/
return;
}
DTKAdapter::DTKAdapter(Teuchos::RCP<const Teuchos::Comm<int> > in_comm, EquationSystems & in_es):
comm(in_comm),
es(in_es),
mesh(in_es.get_mesh()),
dim(mesh.mesh_dimension())
{
std::set<unsigned int> semi_local_nodes;
get_semi_local_nodes(semi_local_nodes);
num_local_nodes = semi_local_nodes.size();
vertices.resize(num_local_nodes);
Teuchos::ArrayRCP<double> coordinates(num_local_nodes * dim);
// Fill in the vertices and coordinates
{
unsigned int i = 0;
for(std::set<unsigned int>::iterator it = semi_local_nodes.begin();
it != semi_local_nodes.end();
++it)
{
const Node & node = mesh.node(*it);
vertices[i] = node.id();
for(unsigned int j=0; j<dim; j++)
coordinates[(j*num_local_nodes) + i] = node(j);
i++;
}
}
// Currently assuming all elements are the same!
DataTransferKit::DTK_ElementTopology element_topology = get_element_topology(mesh.elem(0));
unsigned int n_nodes_per_elem = mesh.elem(0)->n_nodes();
unsigned int n_local_elem = mesh.n_local_elem();
Teuchos::ArrayRCP<int> elements(n_local_elem);
Teuchos::ArrayRCP<int> connectivity(n_nodes_per_elem*n_local_elem);
// Fill in the elements and connectivity
{
unsigned int i = 0;
MeshBase::const_element_iterator end = mesh.local_elements_end();
for(MeshBase::const_element_iterator it = mesh.local_elements_begin();
it != end;
++it)
{
const Elem & elem = *(*it);
elements[i] = elem.id();
for(unsigned int j=0; j<n_nodes_per_elem; j++)
connectivity[(j*n_local_elem)+i] = elem.node(j);
i++;
}
}
Teuchos::ArrayRCP<int> permutation_list(n_nodes_per_elem);
for (unsigned int i = 0; i < n_nodes_per_elem; ++i )
permutation_list[i] = i;
/*
if(this->processor_id() == 1)
sleep(1);
libMesh::out<<"n_nodes_per_elem: "<<n_nodes_per_elem<<std::endl;
libMesh::out<<"Dim: "<<dim<<std::endl;
libMesh::err<<"Vertices size: "<<vertices.size()<<std::endl;
{
libMesh::err<<this->processor_id()<<" Vertices: ";
for(unsigned int i=0; i<vertices.size(); i++)
libMesh::err<<vertices[i]<<" ";
libMesh::err<<std::endl;
}
libMesh::err<<"Coordinates size: "<<coordinates.size()<<std::endl;
{
libMesh::err<<this->processor_id()<<" Coordinates: ";
for(unsigned int i=0; i<coordinates.size(); i++)
libMesh::err<<coordinates[i]<<" ";
libMesh::err<<std::endl;
}
libMesh::err<<"Connectivity size: "<<connectivity.size()<<std::endl;
{
libMesh::err<<this->processor_id()<<" Connectivity: ";
for(unsigned int i=0; i<connectivity.size(); i++)
libMesh::err<<connectivity[i]<<" ";
libMesh::err<<std::endl;
}
libMesh::err<<"Permutation_List size: "<<permutation_list.size()<<std::endl;
{
libMesh::err<<this->processor_id()<<" Permutation_List: ";
for(unsigned int i=0; i<permutation_list.size(); i++)
libMesh::err<<permutation_list[i]<<" ";
libMesh::err<<std::endl;
}
*/
Teuchos::RCP<MeshContainerType> mesh_container = Teuchos::rcp(
new MeshContainerType(dim, vertices, coordinates,
element_topology, n_nodes_per_elem,
elements, connectivity, permutation_list) );
// We only have 1 element topology in this grid so we make just one mesh block
Teuchos::ArrayRCP<Teuchos::RCP<MeshContainerType> > mesh_blocks(1);
mesh_blocks[0] = mesh_container;
// Create the MeshManager
mesh_manager = Teuchos::rcp(new DataTransferKit::MeshManager<MeshContainerType>(mesh_blocks, comm, dim) );
// Pack the coordinates into a field, this will be the positions we'll ask for other systems fields at
target_coords = Teuchos::rcp(new DataTransferKit::FieldManager<MeshContainerType>(mesh_container, comm));
}
// Define the matrix assembly function for the 1D PDE we are solving
void assemble_1D(EquationSystems& es, const std::string& system_name)
{
#ifdef LIBMESH_ENABLE_AMR
// It is a good idea to check we are solving the correct system
libmesh_assert_equal_to (system_name, "1D");
// Get a reference to the mesh object
const MeshBase& mesh = es.get_mesh();
// The dimension we are using, i.e. dim==1
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to the system we are solving
LinearImplicitSystem& system = es.get_system<LinearImplicitSystem>("1D");
// Get a reference to the DofMap object for this system. The DofMap object
// handles the index translation from node and element numbers to degree of
// freedom numbers. DofMap's are discussed in more detail in future examples.
const DofMap& dof_map = system.get_dof_map();
// Get a constant reference to the Finite Element type for the first
// (and only) variable in the system.
FEType fe_type = dof_map.variable_type(0);
// Build a finite element object of the specified type. The build
// function dynamically allocates memory so we use an UniquePtr in this case.
// An UniquePtr is a pointer that cleans up after itself. See examples 3 and 4
// for more details on UniquePtr.
UniquePtr<FEBase> fe(FEBase::build(dim, fe_type));
// Tell the finite element object to use fifth order Gaussian quadrature
QGauss qrule(dim,FIFTH);
fe->attach_quadrature_rule(&qrule);
// Here we define some references to cell-specific data that will be used to
// assemble the linear system.
// The element Jacobian * quadrature weight at each integration point.
const std::vector<Real>& JxW = fe->get_JxW();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> >& phi = fe->get_phi();
// The element shape function gradients evaluated at the quadrature points.
const std::vector<std::vector<RealGradient> >& dphi = fe->get_dphi();
// Declare a dense matrix and dense vector to hold the element matrix
// and right-hand-side contribution
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
// This vector will hold the degree of freedom indices for the element.
// These define where in the global system the element degrees of freedom
// get mapped.
std::vector<dof_id_type> dof_indices;
// We now loop over all the active elements in the mesh in order to calculate
// the matrix and right-hand-side contribution from each element. Use a
// const_element_iterator to loop over the elements. We make
// el_end const as it is used only for the stopping condition of the loop.
MeshBase::const_element_iterator el = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator el_end = mesh.active_local_elements_end();
// Note that ++el is preferred to el++ when using loops with iterators
for( ; el != el_end; ++el)
{
// It is convenient to store a pointer to the current element
const Elem* elem = *el;
// Get the degree of freedom indices for the current element.
// These define where in the global matrix and right-hand-side this
// element will contribute to.
dof_map.dof_indices(elem, dof_indices);
// Compute the element-specific data for the current element. This
// involves computing the location of the quadrature points (q_point)
// and the shape functions (phi, dphi) for the current element.
fe->reinit(elem);
// Store the number of local degrees of freedom contained in this element
const int n_dofs = dof_indices.size();
// We resize and zero out Ke and Fe (resize() also clears the matrix and
// vector). In this example, all elements in the mesh are EDGE3's, so
// Ke will always be 3x3, and Fe will always be 3x1. If the mesh contained
// different element types, then the size of Ke and Fe would change.
Ke.resize(n_dofs, n_dofs);
Fe.resize(n_dofs);
// Now loop over quadrature points to handle numerical integration
for(unsigned int qp=0; qp<qrule.n_points(); qp++)
{
// Now build the element matrix and right-hand-side using loops to
// integrate the test functions (i) against the trial functions (j).
for(unsigned int i=0; i<phi.size(); i++)
{
Fe(i) += JxW[qp]*phi[i][qp];
for(unsigned int j=0; j<phi.size(); j++)
{
Ke(i,j) += JxW[qp]*(1.e-3*dphi[i][qp]*dphi[j][qp] +
phi[i][qp]*phi[j][qp]);
}
}
}
// At this point we have completed the matrix and RHS summation. The
// final step is to apply boundary conditions, which in this case are
// simple Dirichlet conditions with u(0) = u(1) = 0.
// Define the penalty parameter used to enforce the BC's
double penalty = 1.e10;
// Loop over the sides of this element. For a 1D element, the "sides"
// are defined as the nodes on each edge of the element, i.e. 1D elements
// have 2 sides.
for(unsigned int s=0; s<elem->n_sides(); s++)
{
// If this element has a NULL neighbor, then it is on the edge of the
// mesh and we need to enforce a boundary condition using the penalty
// method.
if(elem->neighbor(s) == NULL)
{
Ke(s,s) += penalty;
Fe(s) += 0*penalty;
}
}
// This is a function call that is necessary when using adaptive
// mesh refinement. See Adaptivity Example 2 for more details.
dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
// Add Ke and Fe to the global matrix and right-hand-side.
system.matrix->add_matrix(Ke, dof_indices);
system.rhs->add_vector(Fe, dof_indices);
}
#endif // #ifdef LIBMESH_ENABLE_AMR
}
// We now define the matrix assembly function for the
// Poisson system. We need to first compute element
// matrices and right-hand sides, and then take into
// account the boundary conditions, which will be handled
// via a penalty method.
void assemble_poisson(EquationSystems& es,
const std::string& system_name)
{
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert (system_name == "Poisson");
// Get a constant reference to the mesh object.
const MeshBase& mesh = es.get_mesh();
// The dimension that we are running
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to the LinearImplicitSystem we are solving
LinearImplicitSystem& system = es.get_system<LinearImplicitSystem> ("Poisson");
// A reference to the DofMap object for this system. The DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers. We will talk more about the DofMap
// in future examples.
const DofMap& dof_map = system.get_dof_map();
// Get a constant reference to the Finite Element type
// for the first (and only) variable in the system.
FEType fe_type = dof_map.variable_type(0);
// Build a Finite Element object of the specified type. Since the
// FEBase::build() member dynamically creates memory we will
// store the object as an AutoPtr<FEBase>. This can be thought
// of as a pointer that will clean up after itself. Example 4
// describes some advantages of AutoPtr's in the context of
// quadrature rules.
AutoPtr<FEBase> fe (FEBase::build(dim, fe_type));
// A 5th order Gauss quadrature rule for numerical integration.
QGauss qrule (dim, FIFTH);
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (&qrule);
// Declare a special finite element object for
// boundary integration.
AutoPtr<FEBase> fe_face (FEBase::build(dim, fe_type));
// Boundary integration requires one quadraure rule,
// with dimensionality one less than the dimensionality
// of the element.
QGauss qface(dim-1, FIFTH);
// Tell the finite element object to use our
// quadrature rule.
fe_face->attach_quadrature_rule (&qface);
// Here we define some references to cell-specific data that
// will be used to assemble the linear system.
//
// The element Jacobian * quadrature weight at each integration point.
const std::vector<Real>& JxW = fe->get_JxW();
// The physical XY locations of the quadrature points on the element.
// These might be useful for evaluating spatially varying material
// properties at the quadrature points.
const std::vector<Point>& q_point = fe->get_xyz();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> >& phi = fe->get_phi();
// The element shape function gradients evaluated at the quadrature
// points.
const std::vector<std::vector<RealGradient> >& dphi = fe->get_dphi();
// Define data structures to contain the element matrix
// and right-hand-side vector contribution. Following
// basic finite element terminology we will denote these
// "Ke" and "Fe". These datatypes are templated on
// Number, which allows the same code to work for real
// or complex numbers.
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<unsigned int> dof_indices;
// Now we will loop over all the elements in the mesh.
// We will compute the element matrix and right-hand-side
// contribution.
//
// Element iterators are a nice way to iterate through all the
// elements, or all the elements that have some property. The
// iterator el will iterate from the first to the last element on
// the local processor. The iterator end_el tells us when to stop.
// It is smart to make this one const so that we don't accidentally
// mess it up! In case users later modify this program to include
// refinement, we will be safe and will only consider the active
// elements; hence we use a variant of the \p active_elem_iterator.
MeshBase::const_element_iterator el = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end_el = mesh.active_local_elements_end();
// Loop over the elements. Note that ++el is preferred to
// el++ since the latter requires an unnecessary temporary
// object.
for ( ; el != end_el ; ++el)
{
// Store a pointer to the element we are currently
// working on. This allows for nicer syntax later.
const Elem* elem = *el;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
// Compute the element-specific data for the current
// element. This involves computing the location of the
// quadrature points (q_point) and the shape functions
// (phi, dphi) for the current element.
fe->reinit (elem);
// Zero the element matrix and right-hand side before
// summing them. We use the resize member here because
// the number of degrees of freedom might have changed from
// the last element. Note that this will be the case if the
// element type is different (i.e. the last element was a
// triangle, now we are on a quadrilateral).
// The DenseMatrix::resize() and the DenseVector::resize()
// members will automatically zero out the matrix and vector.
Ke.resize (dof_indices.size(),
dof_indices.size());
Fe.resize (dof_indices.size());
// Now loop over the quadrature points. This handles
// the numeric integration.
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
// Now we will build the element matrix. This involves
// a double loop to integrate the test funcions (i) against
// the trial functions (j).
for (unsigned int i=0; i<phi.size(); i++)
for (unsigned int j=0; j<phi.size(); j++)
{
Ke(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
}
// This is the end of the matrix summation loop
// Now we build the element right-hand-side contribution.
// This involves a single loop in which we integrate the
// "forcing function" in the PDE against the test functions.
{
const Real x = q_point[qp](0);
const Real y = q_point[qp](1);
const Real eps = 1.e-3;
// "fxy" is the forcing function for the Poisson equation.
// In this case we set fxy to be a finite difference
// Laplacian approximation to the (known) exact solution.
//
// We will use the second-order accurate FD Laplacian
// approximation, which in 2D is
//
// u_xx + u_yy = (u(i,j-1) + u(i,j+1) +
// u(i-1,j) + u(i+1,j) +
// -4*u(i,j))/h^2
//
// Since the value of the forcing function depends only
// on the location of the quadrature point (q_point[qp])
// we will compute it here, outside of the i-loop
const Real fxy = -(exact_solution(x,y-eps) +
exact_solution(x,y+eps) +
exact_solution(x-eps,y) +
exact_solution(x+eps,y) -
4.*exact_solution(x,y))/eps/eps;
for (unsigned int i=0; i<phi.size(); i++)
Fe(i) += JxW[qp]*fxy*phi[i][qp];
}
}
// We have now reached the end of the RHS summation,
// and the end of quadrature point loop, so
// the interior element integration has
// been completed. However, we have not yet addressed
// boundary conditions. For this example we will only
// consider simple Dirichlet boundary conditions.
//
// There are several ways Dirichlet boundary conditions
// can be imposed. A simple approach, which works for
// interpolary bases like the standard Lagrange polynomials,
// is to assign function values to the
// degrees of freedom living on the domain boundary. This
// works well for interpolary bases, but is more difficult
// when non-interpolary (e.g Legendre or Hierarchic) bases
// are used.
//
// Dirichlet boundary conditions can also be imposed with a
// "penalty" method. In this case essentially the L2 projection
// of the boundary values are added to the matrix. The
// projection is multiplied by some large factor so that, in
// floating point arithmetic, the existing (smaller) entries
// in the matrix and right-hand-side are effectively ignored.
//
// This amounts to adding a term of the form (in latex notation)
//
// \frac{1}{\epsilon} \int_{\delta \Omega} \phi_i \phi_j = \frac{1}{\epsilon} \int_{\delta \Omega} u \phi_i
//
// where
//
// \frac{1}{\epsilon} is the penalty parameter, defined such that \epsilon << 1
{
// The following loop is over the sides of the element.
// If the element has no neighbor on a side then that
// side MUST live on a boundary of the domain.
for (unsigned int side=0; side<elem->n_sides(); side++)
if (elem->neighbor(side) == NULL)
{
// The value of the shape functions at the quadrature
// points.
const std::vector<std::vector<Real> >& phi_face = fe_face->get_phi();
// The Jacobian * Quadrature Weight at the quadrature
// points on the face.
const std::vector<Real>& JxW_face = fe_face->get_JxW();
// The XYZ locations (in physical space) of the
// quadrature points on the face. This is where
// we will interpolate the boundary value function.
const std::vector<Point >& qface_point = fe_face->get_xyz();
// Compute the shape function values on the element
// face.
fe_face->reinit(elem, side);
// Loop over the face quadrature points for integration.
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
// The location on the boundary of the current
// face quadrature point.
const Real xf = qface_point[qp](0);
const Real yf = qface_point[qp](1);
// The penalty value. \frac{1}{\epsilon}
// in the discussion above.
const Real penalty = 1.e10;
// The boundary value.
const Real value = exact_solution(xf, yf);
// Matrix contribution of the L2 projection.
for (unsigned int i=0; i<phi_face.size(); i++)
for (unsigned int j=0; j<phi_face.size(); j++)
Ke(i,j) += JxW_face[qp]*penalty*phi_face[i][qp]*phi_face[j][qp];
// Right-hand-side contribution of the L2
// projection.
for (unsigned int i=0; i<phi_face.size(); i++)
Fe(i) += JxW_face[qp]*penalty*value*phi_face[i][qp];
}
}
}
// We have now finished the quadrature point loop,
// and have therefore applied all the boundary conditions.
// If this assembly program were to be used on an adaptive mesh,
// we would have to apply any hanging node constraint equations
dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
// The element matrix and right-hand-side are now built
// for this element. Add them to the global matrix and
// right-hand-side vector. The SparseMatrix::add_matrix()
// and NumericVector::add_vector() members do this for us.
system.matrix->add_matrix (Ke, dof_indices);
system.rhs->add_vector (Fe, dof_indices);
}
// All done!
}
// The matrix assembly function to be called at each time step to
// prepare for the linear solve.
void assemble_stokes (EquationSystems & es,
const std::string & system_name)
{
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Navier-Stokes");
// Get a constant reference to the mesh object.
const MeshBase & mesh = es.get_mesh();
// The dimension that we are running
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to the Stokes system object.
TransientLinearImplicitSystem & navier_stokes_system =
es.get_system<TransientLinearImplicitSystem> ("Navier-Stokes");
// Numeric ids corresponding to each variable in the system
const unsigned int u_var = navier_stokes_system.variable_number ("u");
const unsigned int v_var = navier_stokes_system.variable_number ("v");
const unsigned int p_var = navier_stokes_system.variable_number ("p");
const unsigned int alpha_var = navier_stokes_system.variable_number ("alpha");
// Get the Finite Element type for "u". Note this will be
// the same as the type for "v".
FEType fe_vel_type = navier_stokes_system.variable_type(u_var);
// Get the Finite Element type for "p".
FEType fe_pres_type = navier_stokes_system.variable_type(p_var);
// Build a Finite Element object of the specified type for
// the velocity variables.
UniquePtr<FEBase> fe_vel (FEBase::build(dim, fe_vel_type));
// Build a Finite Element object of the specified type for
// the pressure variables.
UniquePtr<FEBase> fe_pres (FEBase::build(dim, fe_pres_type));
// A Gauss quadrature rule for numerical integration.
// Let the FEType object decide what order rule is appropriate.
QGauss qrule (dim, fe_vel_type.default_quadrature_order());
// Tell the finite element objects to use our quadrature rule.
fe_vel->attach_quadrature_rule (&qrule);
fe_pres->attach_quadrature_rule (&qrule);
// Here we define some references to cell-specific data that
// will be used to assemble the linear system.
//
// The element Jacobian * quadrature weight at each integration point.
const std::vector<Real> & JxW = fe_vel->get_JxW();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> > & phi = fe_vel->get_phi();
// The element shape function gradients for the velocity
// variables evaluated at the quadrature points.
const std::vector<std::vector<RealGradient> > & dphi = fe_vel->get_dphi();
// The element shape functions for the pressure variable
// evaluated at the quadrature points.
const std::vector<std::vector<Real> > & psi = fe_pres->get_phi();
// The value of the linear shape function gradients at the quadrature points
// const std::vector<std::vector<RealGradient> > & dpsi = fe_pres->get_dphi();
// A reference to the DofMap object for this system. The DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers. We will talk more about the DofMap
// in future examples.
const DofMap & dof_map = navier_stokes_system.get_dof_map();
// Define data structures to contain the element matrix
// and right-hand-side vector contribution. Following
// basic finite element terminology we will denote these
// "Ke" and "Fe".
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
DenseSubMatrix<Number>
Kuu(Ke), Kuv(Ke), Kup(Ke),
Kvu(Ke), Kvv(Ke), Kvp(Ke),
Kpu(Ke), Kpv(Ke), Kpp(Ke);
DenseSubMatrix<Number> Kalpha_p(Ke), Kp_alpha(Ke);
DenseSubVector<Number>
Fu(Fe),
Fv(Fe),
Fp(Fe);
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<dof_id_type> dof_indices;
std::vector<dof_id_type> dof_indices_u;
std::vector<dof_id_type> dof_indices_v;
std::vector<dof_id_type> dof_indices_p;
std::vector<dof_id_type> dof_indices_alpha;
// Find out what the timestep size parameter is from the system, and
// the value of theta for the theta method. We use implicit Euler (theta=1)
// for this simulation even though it is only first-order accurate in time.
// The reason for this decision is that the second-order Crank-Nicolson
// method is notoriously oscillatory for problems with discontinuous
// initial data such as the lid-driven cavity. Therefore,
// we sacrifice accuracy in time for stability, but since the solution
// reaches steady state relatively quickly we can afford to take small
// timesteps. If you monitor the initial nonlinear residual for this
// simulation, you should see that it is monotonically decreasing in time.
const Real dt = es.parameters.get<Real>("dt");
// const Real time = es.parameters.get<Real>("time");
const Real theta = 1.;
// Now we will loop over all the elements in the mesh that
// live on the local processor. We will compute the element
// matrix and right-hand-side contribution. Since the mesh
// will be refined we want to only consider the ACTIVE elements,
// hence we use a variant of the active_elem_iterator.
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)
{
// Store a pointer to the element we are currently
// working on. This allows for nicer syntax later.
const Elem * elem = *el;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
dof_map.dof_indices (elem, dof_indices_u, u_var);
dof_map.dof_indices (elem, dof_indices_v, v_var);
dof_map.dof_indices (elem, dof_indices_p, p_var);
dof_map.dof_indices (elem, dof_indices_alpha, alpha_var);
const unsigned int n_dofs = dof_indices.size();
const unsigned int n_u_dofs = dof_indices_u.size();
const unsigned int n_v_dofs = dof_indices_v.size();
const unsigned int n_p_dofs = dof_indices_p.size();
// Compute the element-specific data for the current
// element. This involves computing the location of the
// quadrature points (q_point) and the shape functions
// (phi, dphi) for the current element.
fe_vel->reinit (elem);
fe_pres->reinit (elem);
// Zero the element matrix and right-hand side before
// summing them. We use the resize member here because
// the number of degrees of freedom might have changed from
// the last element. Note that this will be the case if the
// element type is different (i.e. the last element was a
// triangle, now we are on a quadrilateral).
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
// Reposition the submatrices... The idea is this:
//
// - - - -
// | Kuu Kuv Kup | | Fu |
// Ke = | Kvu Kvv Kvp |; Fe = | Fv |
// | Kpu Kpv Kpp | | Fp |
// - - - -
//
// The DenseSubMatrix.repostition () member takes the
// (row_offset, column_offset, row_size, column_size).
//
// Similarly, the DenseSubVector.reposition () member
// takes the (row_offset, row_size)
Kuu.reposition (u_var*n_u_dofs, u_var*n_u_dofs, n_u_dofs, n_u_dofs);
Kuv.reposition (u_var*n_u_dofs, v_var*n_u_dofs, n_u_dofs, n_v_dofs);
Kup.reposition (u_var*n_u_dofs, p_var*n_u_dofs, n_u_dofs, n_p_dofs);
Kvu.reposition (v_var*n_v_dofs, u_var*n_v_dofs, n_v_dofs, n_u_dofs);
Kvv.reposition (v_var*n_v_dofs, v_var*n_v_dofs, n_v_dofs, n_v_dofs);
Kvp.reposition (v_var*n_v_dofs, p_var*n_v_dofs, n_v_dofs, n_p_dofs);
Kpu.reposition (p_var*n_u_dofs, u_var*n_u_dofs, n_p_dofs, n_u_dofs);
Kpv.reposition (p_var*n_u_dofs, v_var*n_u_dofs, n_p_dofs, n_v_dofs);
Kpp.reposition (p_var*n_u_dofs, p_var*n_u_dofs, n_p_dofs, n_p_dofs);
// Also, add a row and a column to constrain the pressure
Kp_alpha.reposition (p_var*n_u_dofs, p_var*n_u_dofs+n_p_dofs, n_p_dofs, 1);
Kalpha_p.reposition (p_var*n_u_dofs+n_p_dofs, p_var*n_u_dofs, 1, n_p_dofs);
Fu.reposition (u_var*n_u_dofs, n_u_dofs);
Fv.reposition (v_var*n_u_dofs, n_v_dofs);
Fp.reposition (p_var*n_u_dofs, n_p_dofs);
// Now we will build the element matrix and right-hand-side.
// Constructing the RHS requires the solution and its
// gradient from the previous timestep. This must be
// calculated at each quadrature point by summing the
// solution degree-of-freedom values by the appropriate
// weight functions.
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
// Values to hold the solution & its gradient at the previous timestep.
Number u = 0., u_old = 0.;
Number v = 0., v_old = 0.;
Number p_old = 0.;
Gradient grad_u, grad_u_old;
Gradient grad_v, grad_v_old;
// Compute the velocity & its gradient from the previous timestep
// and the old Newton iterate.
for (unsigned int l=0; l<n_u_dofs; l++)
{
// From the old timestep:
u_old += phi[l][qp]*navier_stokes_system.old_solution (dof_indices_u[l]);
v_old += phi[l][qp]*navier_stokes_system.old_solution (dof_indices_v[l]);
grad_u_old.add_scaled (dphi[l][qp], navier_stokes_system.old_solution (dof_indices_u[l]));
grad_v_old.add_scaled (dphi[l][qp], navier_stokes_system.old_solution (dof_indices_v[l]));
// From the previous Newton iterate:
u += phi[l][qp]*navier_stokes_system.current_solution (dof_indices_u[l]);
v += phi[l][qp]*navier_stokes_system.current_solution (dof_indices_v[l]);
grad_u.add_scaled (dphi[l][qp], navier_stokes_system.current_solution (dof_indices_u[l]));
grad_v.add_scaled (dphi[l][qp], navier_stokes_system.current_solution (dof_indices_v[l]));
}
// Compute the old pressure value at this quadrature point.
for (unsigned int l=0; l<n_p_dofs; l++)
p_old += psi[l][qp]*navier_stokes_system.old_solution (dof_indices_p[l]);
// Definitions for convenience. It is sometimes simpler to do a
// dot product if you have the full vector at your disposal.
const NumberVectorValue U_old (u_old, v_old);
const NumberVectorValue U (u, v);
const Number u_x = grad_u(0);
const Number u_y = grad_u(1);
const Number v_x = grad_v(0);
const Number v_y = grad_v(1);
// First, an i-loop over the velocity degrees of freedom.
// We know that n_u_dofs == n_v_dofs so we can compute contributions
// for both at the same time.
for (unsigned int i=0; i<n_u_dofs; i++)
{
Fu(i) += JxW[qp]*(u_old*phi[i][qp] - // mass-matrix term
(1.-theta)*dt*(U_old*grad_u_old)*phi[i][qp] + // convection term
(1.-theta)*dt*p_old*dphi[i][qp](0) - // pressure term on rhs
(1.-theta)*dt*(grad_u_old*dphi[i][qp]) + // diffusion term on rhs
theta*dt*(U*grad_u)*phi[i][qp]); // Newton term
Fv(i) += JxW[qp]*(v_old*phi[i][qp] - // mass-matrix term
(1.-theta)*dt*(U_old*grad_v_old)*phi[i][qp] + // convection term
(1.-theta)*dt*p_old*dphi[i][qp](1) - // pressure term on rhs
(1.-theta)*dt*(grad_v_old*dphi[i][qp]) + // diffusion term on rhs
theta*dt*(U*grad_v)*phi[i][qp]); // Newton term
// Note that the Fp block is identically zero unless we are using
// some kind of artificial compressibility scheme...
// Matrix contributions for the uu and vv couplings.
for (unsigned int j=0; j<n_u_dofs; j++)
{
Kuu(i,j) += JxW[qp]*(phi[i][qp]*phi[j][qp] + // mass matrix term
theta*dt*(dphi[i][qp]*dphi[j][qp]) + // diffusion term
theta*dt*(U*dphi[j][qp])*phi[i][qp] + // convection term
theta*dt*u_x*phi[i][qp]*phi[j][qp]); // Newton term
Kuv(i,j) += JxW[qp]*theta*dt*u_y*phi[i][qp]*phi[j][qp]; // Newton term
Kvv(i,j) += JxW[qp]*(phi[i][qp]*phi[j][qp] + // mass matrix term
theta*dt*(dphi[i][qp]*dphi[j][qp]) + // diffusion term
theta*dt*(U*dphi[j][qp])*phi[i][qp] + // convection term
theta*dt*v_y*phi[i][qp]*phi[j][qp]); // Newton term
Kvu(i,j) += JxW[qp]*theta*dt*v_x*phi[i][qp]*phi[j][qp]; // Newton term
}
// Matrix contributions for the up and vp couplings.
for (unsigned int j=0; j<n_p_dofs; j++)
{
Kup(i,j) += JxW[qp]*(-theta*dt*psi[j][qp]*dphi[i][qp](0));
Kvp(i,j) += JxW[qp]*(-theta*dt*psi[j][qp]*dphi[i][qp](1));
}
}
// Now an i-loop over the pressure degrees of freedom. This code computes
// the matrix entries due to the continuity equation. Note: To maintain a
// symmetric matrix, we may (or may not) multiply the continuity equation by
// negative one. Here we do not.
for (unsigned int i=0; i<n_p_dofs; i++)
{
Kp_alpha(i,0) += JxW[qp]*psi[i][qp];
Kalpha_p(0,i) += JxW[qp]*psi[i][qp];
for (unsigned int j=0; j<n_u_dofs; j++)
{
Kpu(i,j) += JxW[qp]*psi[i][qp]*dphi[j][qp](0);
Kpv(i,j) += JxW[qp]*psi[i][qp]*dphi[j][qp](1);
}
}
} // end of the quadrature point qp-loop
// At this point the interior element integration has
// been completed. However, we have not yet addressed
// boundary conditions. For this example we will only
// consider simple Dirichlet boundary conditions imposed
// via the penalty method. The penalty method used here
// is equivalent (for Lagrange basis functions) to lumping
// the matrix resulting from the L2 projection penalty
// approach introduced in example 3.
{
// The penalty value. \f$ \frac{1}{\epsilon} \f$
const Real penalty = 1.e10;
// The following loops over the sides of the element.
// If the element has no neighbor on a side then that
// side MUST live on a boundary of the domain.
for (unsigned int s=0; s<elem->n_sides(); s++)
if (elem->neighbor(s) == libmesh_nullptr)
{
UniquePtr<Elem> side (elem->build_side(s));
// Loop over the nodes on the side.
for (unsigned int ns=0; ns<side->n_nodes(); ns++)
{
// Boundary ids are set internally by
// build_square().
// 0=bottom
// 1=right
// 2=top
// 3=left
// Set u = 1 on the top boundary, 0 everywhere else
const Real u_value =
(mesh.get_boundary_info().has_boundary_id(elem, s, 2))
? 1. : 0.;
// Set v = 0 everywhere
const Real v_value = 0.;
// Find the node on the element matching this node on
// the side. That defined where in the element matrix
// the boundary condition will be applied.
for (unsigned int n=0; n<elem->n_nodes(); n++)
if (elem->node_id(n) == side->node_id(ns))
{
// Matrix contribution.
Kuu(n,n) += penalty;
Kvv(n,n) += penalty;
// Right-hand-side contribution.
Fu(n) += penalty*u_value;
Fv(n) += penalty*v_value;
}
} // end face node loop
} // end if (elem->neighbor(side) == libmesh_nullptr)
} // end boundary condition section
// If this assembly program were to be used on an adaptive mesh,
// we would have to apply any hanging node constraint equations
dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
// The element matrix and right-hand-side are now built
// for this element. Add them to the global matrix and
// right-hand-side vector. The SparseMatrix::add_matrix()
// and NumericVector::add_vector() members do this for us.
navier_stokes_system.matrix->add_matrix (Ke, dof_indices);
navier_stokes_system.rhs->add_vector (Fe, dof_indices);
} // end of element loop
// We can set the mean of the pressure by setting Falpha
navier_stokes_system.rhs->add(navier_stokes_system.rhs->size()-1, 10.);
}
// We now define the matrix assembly function for the
// Laplace system. We need to first compute element volume
// matrices, and then take into account the boundary
// conditions and the flux integrals, which will be handled
// via an interior penalty method.
void assemble_ellipticdg(EquationSystems& es, const std::string& system_name)
{
std::cout<<" assembling elliptic dg system... ";
std::cout.flush();
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "EllipticDG");
// Get a constant reference to the mesh object.
const MeshBase& mesh = es.get_mesh();
// The dimension that we are running
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to the LinearImplicitSystem we are solving
LinearImplicitSystem & ellipticdg_system = es.get_system<LinearImplicitSystem> ("EllipticDG");
// Get some parameters that we need during assembly
const Real penalty = es.parameters.get<Real> ("penalty");
std::string refinement_type = es.parameters.get<std::string> ("refinement");
// A reference to the \p DofMap object for this system. The \p DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers. We will talk more about the \p DofMap
const DofMap & dof_map = ellipticdg_system.get_dof_map();
// Get a constant reference to the Finite Element type
// for the first (and only) variable in the system.
FEType fe_type = ellipticdg_system.variable_type(0);
// Build a Finite Element object of the specified type. Since the
// \p FEBase::build() member dynamically creates memory we will
// store the object as an \p AutoPtr<FEBase>. This can be thought
// of as a pointer that will clean up after itself.
AutoPtr<FEBase> fe (FEBase::build(dim, fe_type));
AutoPtr<FEBase> fe_elem_face(FEBase::build(dim, fe_type));
AutoPtr<FEBase> fe_neighbor_face(FEBase::build(dim, fe_type));
// Quadrature rules for numerical integration.
#ifdef QORDER
QGauss qrule (dim, QORDER);
#else
QGauss qrule (dim, fe_type.default_quadrature_order());
#endif
fe->attach_quadrature_rule (&qrule);
#ifdef QORDER
QGauss qface(dim-1, QORDER);
#else
QGauss qface(dim-1, fe_type.default_quadrature_order());
#endif
// Tell the finite element object to use our quadrature rule.
fe_elem_face->attach_quadrature_rule(&qface);
fe_neighbor_face->attach_quadrature_rule(&qface);
// Here we define some references to cell-specific data that
// will be used to assemble the linear system.
// Data for interior volume integrals
const std::vector<Real>& JxW = fe->get_JxW();
const std::vector<std::vector<RealGradient> >& dphi = fe->get_dphi();
// Data for surface integrals on the element boundary
const std::vector<std::vector<Real> >& phi_face = fe_elem_face->get_phi();
const std::vector<std::vector<RealGradient> >& dphi_face = fe_elem_face->get_dphi();
const std::vector<Real>& JxW_face = fe_elem_face->get_JxW();
const std::vector<Point>& qface_normals = fe_elem_face->get_normals();
const std::vector<Point>& qface_points = fe_elem_face->get_xyz();
// Data for surface integrals on the neighbor boundary
const std::vector<std::vector<Real> >& phi_neighbor_face = fe_neighbor_face->get_phi();
const std::vector<std::vector<RealGradient> >& dphi_neighbor_face = fe_neighbor_face->get_dphi();
// Define data structures to contain the element interior matrix
// and right-hand-side vector contribution. Following
// basic finite element terminology we will denote these
// "Ke" and "Fe".
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
// Data structures to contain the element and neighbor boundary matrix
// contribution. This matrices will do the coupling beetwen the dofs of
// the element and those of his neighbors.
// Ken: matrix coupling elem and neighbor dofs
DenseMatrix<Number> Kne;
DenseMatrix<Number> Ken;
DenseMatrix<Number> Kee;
DenseMatrix<Number> Knn;
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<dof_id_type> dof_indices;
// Now we will loop over all the elements in the mesh. We will
// compute first the element interior matrix and right-hand-side contribution
// and then the element and neighbors boundary matrix contributions.
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)
{
// Store a pointer to the element we are currently
// working on. This allows for nicer syntax later.
const Elem* elem = *el;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
const unsigned int n_dofs = dof_indices.size();
// Compute the element-specific data for the current
// element. This involves computing the location of the
// quadrature points (q_point) and the shape functions
// (phi, dphi) for the current element.
fe->reinit (elem);
// Zero the element matrix and right-hand side before
// summing them. We use the resize member here because
// the number of degrees of freedom might have changed from
// the last element.
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
// Now we will build the element interior matrix. This involves
// a double loop to integrate the test funcions (i) against
// the trial functions (j).
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
for (unsigned int i=0; i<n_dofs; i++)
{
for (unsigned int j=0; j<n_dofs; j++)
{
Ke(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
}
}
}
// Now we adress boundary conditions.
// We consider Dirichlet bc imposed via the interior penalty method
// The following loops over the sides of the element.
// If the element has no neighbor on a side then that
// side MUST live on a boundary of the domain.
for (unsigned int side=0; side<elem->n_sides(); side++)
{
if (elem->neighbor(side) == NULL)
{
// Pointer to the element face
fe_elem_face->reinit(elem, side);
AutoPtr<Elem> elem_side (elem->build_side(side));
// h elemet dimension to compute the interior penalty penalty parameter
const unsigned int elem_b_order = static_cast<unsigned int> (fe_elem_face->get_order());
const double h_elem = elem->volume()/elem_side->volume() * 1./pow(elem_b_order, 2.);
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
Number bc_value = exact_solution(qface_points[qp], es.parameters,"null","void");
for (unsigned int i=0; i<n_dofs; i++)
{
// Matrix contribution
for (unsigned int j=0; j<n_dofs; j++)
{
Ke(i,j) += JxW_face[qp] * penalty/h_elem * phi_face[i][qp] * phi_face[j][qp]; // stability
Ke(i,j) -= JxW_face[qp] * (phi_face[i][qp] * (dphi_face[j][qp]*qface_normals[qp]) + phi_face[j][qp] * (dphi_face[i][qp]*qface_normals[qp])); // consistency
}
// RHS contribution
Fe(i) += JxW_face[qp] * bc_value * penalty/h_elem * phi_face[i][qp]; // stability
Fe(i) -= JxW_face[qp] * dphi_face[i][qp] * (bc_value*qface_normals[qp]); // consistency
}
}
}
// If the element is not on a boundary of the domain
// we loop over his neighbors to compute the element
// and neighbor boundary matrix contributions
else
{
// Store a pointer to the neighbor we are currently
// working on.
const Elem* neighbor = elem->neighbor(side);
// Get the global id of the element and the neighbor
const unsigned int elem_id = elem->id();
const unsigned int neighbor_id = neighbor->id();
// If the neighbor has the same h level and is active
// perform integration only if our global id is bigger than our neighbor id.
// We don't want to compute twice the same contributions.
// If the neighbor has a different h level perform integration
// only if the neighbor is at a lower level.
if ((neighbor->active() && (neighbor->level() == elem->level()) && (elem_id < neighbor_id)) || (neighbor->level() < elem->level()))
{
// Pointer to the element side
AutoPtr<Elem> elem_side (elem->build_side(side));
// h dimension to compute the interior penalty penalty parameter
const unsigned int elem_b_order = static_cast<unsigned int>(fe_elem_face->get_order());
const unsigned int neighbor_b_order = static_cast<unsigned int>(fe_neighbor_face->get_order());
const double side_order = (elem_b_order + neighbor_b_order)/2.;
const double h_elem = (elem->volume()/elem_side->volume()) * 1./pow(side_order,2.);
// The quadrature point locations on the neighbor side
std::vector<Point> qface_neighbor_point;
// The quadrature point locations on the element side
std::vector<Point > qface_point;
// Reinitialize shape functions on the element side
fe_elem_face->reinit(elem, side);
// Get the physical locations of the element quadrature points
qface_point = fe_elem_face->get_xyz();
// Find their locations on the neighbor
unsigned int side_neighbor = neighbor->which_neighbor_am_i(elem);
if (refinement_type == "p")
fe_neighbor_face->side_map (neighbor, elem_side.get(), side_neighbor, qface.get_points(), qface_neighbor_point);
else
FEInterface::inverse_map (elem->dim(), fe->get_fe_type(), neighbor, qface_point, qface_neighbor_point);
// Calculate the neighbor element shape functions at those locations
fe_neighbor_face->reinit(neighbor, &qface_neighbor_point);
// Get the degree of freedom indices for the
// neighbor. These define where in the global
// matrix this neighbor will contribute to.
std::vector<dof_id_type> neighbor_dof_indices;
dof_map.dof_indices (neighbor, neighbor_dof_indices);
const unsigned int n_neighbor_dofs = neighbor_dof_indices.size();
// Zero the element and neighbor side matrix before
// summing them. We use the resize member here because
// the number of degrees of freedom might have changed from
// the last element or neighbor.
// Note that Kne and Ken are not square matrices if neighbor
// and element have a different p level
Kne.resize (n_neighbor_dofs, n_dofs);
Ken.resize (n_dofs, n_neighbor_dofs);
Kee.resize (n_dofs, n_dofs);
Knn.resize (n_neighbor_dofs, n_neighbor_dofs);
// Now we will build the element and neighbor
// boundary matrices. This involves
// a double loop to integrate the test funcions
// (i) against the trial functions (j).
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
// Kee Matrix. Integrate the element test function i
// against the element test function j
for (unsigned int i=0; i<n_dofs; i++)
{
for (unsigned int j=0; j<n_dofs; j++)
{
Kee(i,j) -= 0.5 * JxW_face[qp] * (phi_face[j][qp]*(qface_normals[qp]*dphi_face[i][qp]) + phi_face[i][qp]*(qface_normals[qp]*dphi_face[j][qp])); // consistency
Kee(i,j) += JxW_face[qp] * penalty/h_elem * phi_face[j][qp]*phi_face[i][qp]; // stability
}
}
// Knn Matrix. Integrate the neighbor test function i
// against the neighbor test function j
for (unsigned int i=0; i<n_neighbor_dofs; i++)
{
for (unsigned int j=0; j<n_neighbor_dofs; j++)
{
Knn(i,j) += 0.5 * JxW_face[qp] * (phi_neighbor_face[j][qp]*(qface_normals[qp]*dphi_neighbor_face[i][qp]) + phi_neighbor_face[i][qp]*(qface_normals[qp]*dphi_neighbor_face[j][qp])); // consistency
Knn(i,j) += JxW_face[qp] * penalty/h_elem * phi_neighbor_face[j][qp]*phi_neighbor_face[i][qp]; // stability
}
}
// Kne Matrix. Integrate the neighbor test function i
// against the element test function j
for (unsigned int i=0; i<n_neighbor_dofs; i++)
{
for (unsigned int j=0; j<n_dofs; j++)
{
Kne(i,j) += 0.5 * JxW_face[qp] * (phi_neighbor_face[i][qp]*(qface_normals[qp]*dphi_face[j][qp]) - phi_face[j][qp]*(qface_normals[qp]*dphi_neighbor_face[i][qp])); // consistency
Kne(i,j) -= JxW_face[qp] * penalty/h_elem * phi_face[j][qp]*phi_neighbor_face[i][qp]; // stability
}
}
// Ken Matrix. Integrate the element test function i
// against the neighbor test function j
for (unsigned int i=0; i<n_dofs; i++)
{
for (unsigned int j=0; j<n_neighbor_dofs; j++)
{
Ken(i,j) += 0.5 * JxW_face[qp] * (phi_neighbor_face[j][qp]*(qface_normals[qp]*dphi_face[i][qp]) - phi_face[i][qp]*(qface_normals[qp]*dphi_neighbor_face[j][qp])); // consistency
Ken(i,j) -= JxW_face[qp] * penalty/h_elem * phi_face[i][qp]*phi_neighbor_face[j][qp]; // stability
}
}
}
// The element and neighbor boundary matrix are now built
// for this side. Add them to the global matrix
// The \p SparseMatrix::add_matrix() members do this for us.
ellipticdg_system.matrix->add_matrix(Kne,neighbor_dof_indices,dof_indices);
ellipticdg_system.matrix->add_matrix(Ken,dof_indices,neighbor_dof_indices);
ellipticdg_system.matrix->add_matrix(Kee,dof_indices);
ellipticdg_system.matrix->add_matrix(Knn,neighbor_dof_indices);
}
}
}
// The element interior matrix and right-hand-side are now built
// for this element. Add them to the global matrix and
// right-hand-side vector. The \p SparseMatrix::add_matrix()
// and \p NumericVector::add_vector() members do this for us.
ellipticdg_system.matrix->add_matrix(Ke, dof_indices);
ellipticdg_system.rhs->add_vector(Fe, dof_indices);
}
std::cout << "done" << std::endl;
}