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 AssembleOptimization::assemble_A_and_F()
{
A_matrix->zero();
F_vector->zero();
const MeshBase & mesh = _sys.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
const unsigned int u_var = _sys.variable_number ("u");
const DofMap & dof_map = _sys.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<Real> > & phi = fe->get_phi();
const std::vector<std::vector<RealGradient> > & dphi = fe->get_dphi();
std::vector<dof_id_type> dof_indices;
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
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);
const unsigned int n_dofs = dof_indices.size();
fe->reinit (elem);
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
for (unsigned int dof_i=0; dof_i<n_dofs; dof_i++)
{
for (unsigned int dof_j=0; dof_j<n_dofs; dof_j++)
{
Ke(dof_i, dof_j) += JxW[qp] * (dphi[dof_j][qp]* dphi[dof_i][qp]);
}
Fe(dof_i) += JxW[qp] * phi[dof_i][qp];
}
}
A_matrix->add_matrix (Ke, dof_indices);
F_vector->add_vector (Fe, dof_indices);
}
A_matrix->close();
F_vector->close();
}
void
MaxQpsThread::operator() (const ConstElemRange & range)
{
ParallelUniqueId puid;
_tid = puid.id;
// For short circuiting reinit
std::set<ElemType> seen_it;
for (ConstElemRange::const_iterator elem_it = range.begin() ; elem_it != range.end(); ++elem_it)
{
const Elem * elem = *elem_it;
// Only reinit if the element type has not previously been seen
if (seen_it.insert(elem->type()).second)
{
FEType fe_type(FIRST, LAGRANGE);
unsigned int dim = elem->dim();
unsigned int side = 0; // we assume that any element will have at least one side ;)
// We cannot mess with the FE objects in Assembly, because we might need to request second derivatives
// later on. If we used them, we'd call reinit on them, thus making the call to request second
// derivatives harmful (i.e. leading to segfaults/asserts). Thus, we have to use a locally allocated object here.
UniquePtr<FEBase> fe (FEBase::build(dim, fe_type));
// figure out the number of qps for volume
UniquePtr<QBase> qrule (QBase::build(_qtype, dim, _order));
fe->attach_quadrature_rule(qrule.get());
fe->reinit(elem);
if (qrule->n_points() > _max)
_max = qrule->n_points();
unsigned int n_shape_funcs = fe->n_shape_functions();
if (n_shape_funcs > _max_shape_funcs)
_max_shape_funcs = n_shape_funcs;
// figure out the number of qps for the face
// NOTE: user might specify higher order rule for faces, thus possibly ending up with more qps than in the volume
UniquePtr<QBase> qrule_face (QBase::build(_qtype, dim - 1, _face_order));
fe->attach_quadrature_rule(qrule_face.get());
fe->reinit(elem, side);
if (qrule_face->n_points() > _max)
_max = qrule_face->n_points();
}
}
}
// 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& 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 \p K and the bending
// rigidity \p 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.
UniquePtr<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;
UniquePtr<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 \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();
// 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.
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;
// 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 \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);
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.size(); // 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
// covatiant 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 \p 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 \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 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.
el = mesh.active_local_elements_begin();
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;
// 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 (unsigned int s=0; s<elem->n_sides(); ++s)
{
const Tri3Subdivision* nb_elem = static_cast<const Tri3Subdivision*> (elem->neighbor(s));
if (nb_elem == NULL || nb_elem->is_ghost())
continue;
/*
* Determine the four nodes involved in the boundary
* condition treatment of this side. The \p MeshTools::Subdiv
* namespace provides lookup tables \p next and \p prev
* for an efficient determination of the next and previous
* nodes of an element, respectively.
*
* n4
* / \
* / gh \
* n2 ---- n3
* \ nb /
* \ /
* n1
*/
Node* nodes [4]; // n1, n2, n3, n4
nodes[1] = gh_elem->get_node(s); // n2
nodes[2] = gh_elem->get_node(MeshTools::Subdivision::next[s]); // n3
nodes[3] = gh_elem->get_node(MeshTools::Subdivision::prev[s]); // n4
// The node in the interior of the domain, \p n1, is the
// hardest to find. Walk along the edges of element \p nb until
// we have identified it.
unsigned int n_int = 0;
nodes[0] = nb_elem->get_node(0);
while (nodes[0]->id() == nodes[1]->id() || nodes[0]->id() == nodes[2]->id())
nodes[0] = nb_elem->get_node(++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 \p 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_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 LinearElasticityWithContact::compute_stresses()
{
EquationSystems & es = _sys.get_equation_systems();
const Real young_modulus = es.parameters.get<Real>("young_modulus");
const Real poisson_ratio = es.parameters.get<Real>("poisson_ratio");
const MeshBase & mesh = _sys.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
unsigned int displacement_vars[3];
displacement_vars[0] = _sys.variable_number ("u");
displacement_vars[1] = _sys.variable_number ("v");
displacement_vars[2] = _sys.variable_number ("w");
const unsigned int u_var = _sys.variable_number ("u");
const DofMap & dof_map = _sys.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[6];
sigma_vars[0] = stress_system.variable_number ("sigma_00");
sigma_vars[1] = stress_system.variable_number ("sigma_01");
sigma_vars[2] = stress_system.variable_number ("sigma_02");
sigma_vars[3] = stress_system.variable_number ("sigma_11");
sigma_vars[4] = stress_system.variable_number ("sigma_12");
sigma_vars[5] = 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(_sys.n_vars());
std::vector<dof_id_type> stress_dof_indices_var;
// To store the stress tensor on each element
DenseMatrix<Number> elem_avg_stress_tensor(3, 3);
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]);
const unsigned int n_var_dofs = dof_indices_var[0].size();
fe->reinit (elem);
// clear the stress tensor
elem_avg_stress_tensor.resize(3, 3);
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
// Row is variable u1, u2, or u3, column is x, y, or z
DenseMatrix<Number> grad_u(3, 3);
for (unsigned int var_i=0; var_i<3; var_i++)
for (unsigned int var_j=0; var_j<3; var_j++)
for (unsigned int j=0; j<n_var_dofs; j++)
grad_u(var_i, var_j) +=
dphi[j][qp](var_j) * _sys.current_solution(dof_indices_var[var_i][j]);
DenseMatrix<Number> stress_tensor(3, 3);
for (unsigned int i=0; i<3; i++)
for (unsigned int j=0; j<3; j++)
for (unsigned int k=0; k<3; k++)
for (unsigned int l=0; l<3; l++)
stress_tensor(i,j) +=
elasticity_tensor(young_modulus, poisson_ratio, i, j, k, l) * grad_u(k,l);
// We want to plot the average stress on each element, hence
// we integrate stress_tensor
elem_avg_stress_tensor.add(JxW[qp], stress_tensor);
}
// Get the average stress per element by dividing by volume
elem_avg_stress_tensor.scale(1./elem->volume());
// load elem_sigma data into stress_system
unsigned int stress_var_index = 0;
for (unsigned int i=0; i<3; i++)
for (unsigned int j=i; j<3; j++)
{
stress_dof_map.dof_indices (elem, stress_dof_indices_var, sigma_vars[stress_var_index]);
// 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_avg_stress_tensor(i,j));
stress_var_index++;
}
// Also, the von Mises stress
Number vonMises_value = std::sqrt(0.5*(pow(elem_avg_stress_tensor(0,0) - elem_avg_stress_tensor(1,1), 2.) +
pow(elem_avg_stress_tensor(1,1) - elem_avg_stress_tensor(2,2), 2.) +
pow(elem_avg_stress_tensor(2,2) - elem_avg_stress_tensor(0,0), 2.) +
6.*(pow(elem_avg_stress_tensor(0,1), 2.) +
pow(elem_avg_stress_tensor(1,2), 2.) +
pow(elem_avg_stress_tensor(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();
}
// 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
}
void assemble_poisson(EquationSystems & es,
const ElementIdMap & lower_to_upper)
{
const MeshBase & mesh = es.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
Real R = es.parameters.get<Real>("R");
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));
UniquePtr<FEBase> fe_elem_face (FEBase::build(dim, fe_type));
UniquePtr<FEBase> fe_neighbor_face (FEBase::build(dim, fe_type));
QGauss qrule (dim, fe_type.default_quadrature_order());
QGauss qface(dim-1, fe_type.default_quadrature_order());
fe->attach_quadrature_rule (&qrule);
fe_elem_face->attach_quadrature_rule (&qface);
fe_neighbor_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();
const std::vector<Real> & JxW_face = fe_elem_face->get_JxW();
const std::vector<Point> & qface_points = fe_elem_face->get_xyz();
const std::vector<std::vector<Real> > & phi_face = fe_elem_face->get_phi();
const std::vector<std::vector<Real> > & phi_neighbor_face = fe_neighbor_face->get_phi();
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
DenseMatrix<Number> Kne;
DenseMatrix<Number> Ken;
DenseMatrix<Number> Kee;
DenseMatrix<Number> Knn;
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);
const unsigned int n_dofs = dof_indices.size();
fe->reinit (elem);
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
// Assemble element interior terms for the matrix
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]);
// Boundary flux provides forcing in this example
{
for (unsigned int side=0; side<elem->n_sides(); side++)
if (elem->neighbor(side) == NULL)
{
if (mesh.get_boundary_info().has_boundary_id (elem, side, MIN_Z_BOUNDARY))
{
fe_elem_face->reinit(elem, side);
for (unsigned int qp=0; qp<qface.n_points(); qp++)
for (unsigned int i=0; i<phi.size(); i++)
Fe(i) += JxW_face[qp] * phi_face[i][qp];
}
}
}
// Add boundary terms on the crack
{
for (unsigned int side=0; side<elem->n_sides(); side++)
if (elem->neighbor(side) == NULL)
{
// Found the lower side of the crack. Assemble terms due to lower and upper in here.
if (mesh.get_boundary_info().has_boundary_id (elem, side, CRACK_BOUNDARY_LOWER))
{
fe_elem_face->reinit(elem, side);
ElementIdMap::const_iterator ltu_it =
lower_to_upper.find(std::make_pair(elem->id(), side));
dof_id_type upper_elem_id = ltu_it->second;
const Elem * neighbor = mesh.elem(upper_elem_id);
std::vector<Point> qface_neighbor_points;
FEInterface::inverse_map (elem->dim(), fe->get_fe_type(),
neighbor, qface_points, qface_neighbor_points);
fe_neighbor_face->reinit(neighbor, &qface_neighbor_points);
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();
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);
// Lower-to-lower coupling term
for (unsigned int qp=0; qp<qface.n_points(); qp++)
for (unsigned int i=0; i<n_dofs; i++)
for (unsigned int j=0; j<n_dofs; j++)
Kee(i,j) -= JxW_face[qp] * (1./R)*(phi_face[i][qp] * phi_face[j][qp]);
// Lower-to-upper coupling term
for (unsigned int qp=0; qp<qface.n_points(); qp++)
for (unsigned int i=0; i<n_dofs; i++)
for (unsigned int j=0; j<n_neighbor_dofs; j++)
Ken(i,j) += JxW_face[qp] * (1./R)*(phi_face[i][qp] * phi_neighbor_face[j][qp]);
// Upper-to-upper coupling term
for (unsigned int qp=0; qp<qface.n_points(); qp++)
for (unsigned int i=0; i<n_neighbor_dofs; i++)
for (unsigned int j=0; j<n_neighbor_dofs; j++)
Knn(i,j) -= JxW_face[qp] * (1./R)*(phi_neighbor_face[i][qp] * phi_neighbor_face[j][qp]);
// Upper-to-lower coupling term
for (unsigned int qp=0; qp<qface.n_points(); qp++)
for (unsigned int i=0; i<n_neighbor_dofs; i++)
for (unsigned int j=0; j<n_dofs; j++)
Kne(i,j) += JxW_face[qp] * (1./R)*(phi_neighbor_face[i][qp] * phi_face[j][qp]);
system.matrix->add_matrix(Kne, neighbor_dof_indices, dof_indices);
system.matrix->add_matrix(Ken, dof_indices, neighbor_dof_indices);
system.matrix->add_matrix(Kee, dof_indices);
system.matrix->add_matrix(Knn, neighbor_dof_indices);
}
}
}
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 ExactErrorEstimator::estimate_error (const System & system,
ErrorVector & error_per_cell,
const NumericVector<Number> * solution_vector,
bool estimate_parent_error)
{
// Ignore the fact that this variable is unused when !LIBMESH_ENABLE_AMR
libmesh_ignore(estimate_parent_error);
// The current mesh
const MeshBase & mesh = system.get_mesh();
// The dimensionality of the mesh
const unsigned int dim = mesh.mesh_dimension();
// The number of variables in the system
const unsigned int n_vars = system.n_vars();
// The DofMap for this system
const DofMap & dof_map = system.get_dof_map();
// Resize the error_per_cell vector to be
// the number of elements, initialize it to 0.
error_per_cell.resize (mesh.max_elem_id());
std::fill (error_per_cell.begin(), error_per_cell.end(), 0.);
// Prepare current_local_solution to localize a non-standard
// solution vector if necessary
if (solution_vector && solution_vector != system.solution.get())
{
NumericVector<Number> * newsol =
const_cast<NumericVector<Number> *>(solution_vector);
System & sys = const_cast<System &>(system);
newsol->swap(*sys.solution);
sys.update();
}
// Loop over all the variables in the system
for (unsigned int var=0; var<n_vars; var++)
{
// Possibly skip this variable
if (error_norm.weight(var) == 0.0) continue;
// The (string) name of this variable
const std::string & var_name = system.variable_name(var);
// The type of finite element to use for this variable
const FEType & fe_type = dof_map.variable_type (var);
UniquePtr<FEBase> fe (FEBase::build (dim, fe_type));
// Build an appropriate Gaussian quadrature rule
UniquePtr<QBase> qrule =
fe_type.default_quadrature_rule (dim,
_extra_order);
fe->attach_quadrature_rule (qrule.get());
// Prepare a global solution and a MeshFunction of the fine system if we need one
UniquePtr<MeshFunction> fine_values;
UniquePtr<NumericVector<Number> > fine_soln = NumericVector<Number>::build(system.comm());
if (_equation_systems_fine)
{
const System & fine_system = _equation_systems_fine->get_system(system.name());
std::vector<Number> global_soln;
// FIXME - we're assuming that the fine system solution gets
// used even when a different vector is used for the coarse
// system
fine_system.update_global_solution(global_soln);
fine_soln->init
(cast_int<numeric_index_type>(global_soln.size()), true,
SERIAL);
(*fine_soln) = global_soln;
fine_values = UniquePtr<MeshFunction>
(new MeshFunction(*_equation_systems_fine,
*fine_soln,
fine_system.get_dof_map(),
fine_system.variable_number(var_name)));
fine_values->init();
} else {
// Initialize functors if we're using them
for (unsigned int i=0; i != _exact_values.size(); ++i)
if (_exact_values[i])
_exact_values[i]->init();
for (unsigned int i=0; i != _exact_derivs.size(); ++i)
if (_exact_derivs[i])
_exact_derivs[i]->init();
for (unsigned int i=0; i != _exact_hessians.size(); ++i)
if (_exact_hessians[i])
_exact_hessians[i]->init();
}
// Request the data we'll need to compute with
fe->get_JxW();
fe->get_phi();
fe->get_dphi();
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
fe->get_d2phi();
#endif
fe->get_xyz();
#ifdef LIBMESH_ENABLE_AMR
// If we compute on parent elements, we'll want to do so only
// once on each, so we need to keep track of which we've done.
std::vector<bool> computed_var_on_parent;
if (estimate_parent_error)
computed_var_on_parent.resize(error_per_cell.size(), false);
#endif
// TODO: this ought to be threaded (and using subordinate
// MeshFunction objects in each thread rather than a single
// master)
// Iterate over all the active elements in the mesh
// that live on this processor.
MeshBase::const_element_iterator
elem_it = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator
elem_end = mesh.active_local_elements_end();
for (;elem_it != elem_end; ++elem_it)
{
// e is necessarily an active element on the local processor
const Elem * elem = *elem_it;
const dof_id_type e_id = elem->id();
#ifdef LIBMESH_ENABLE_AMR
// See if the parent of element e has been examined yet;
// if not, we may want to compute the estimator on it
const Elem * parent = elem->parent();
// We only can compute and only need to compute on
// parents with all active children
bool compute_on_parent = true;
if (!parent || !estimate_parent_error)
compute_on_parent = false;
else
for (unsigned int c=0; c != parent->n_children(); ++c)
if (!parent->child_ptr(c)->active())
compute_on_parent = false;
if (compute_on_parent &&
!computed_var_on_parent[parent->id()])
{
computed_var_on_parent[parent->id()] = true;
// Compute a projection onto the parent
DenseVector<Number> Uparent;
FEBase::coarsened_dof_values(*(system.current_local_solution),
dof_map, parent, Uparent,
var, false);
error_per_cell[parent->id()] +=
static_cast<ErrorVectorReal>
(find_squared_element_error(system, var_name,
parent, Uparent,
fe.get(),
fine_values.get()));
}
#endif
// Get the local to global degree of freedom maps
std::vector<dof_id_type> dof_indices;
dof_map.dof_indices (elem, dof_indices, var);
const unsigned int n_dofs =
cast_int<unsigned int>(dof_indices.size());
DenseVector<Number> Uelem(n_dofs);
for (unsigned int i=0; i != n_dofs; ++i)
Uelem(i) = system.current_solution(dof_indices[i]);
error_per_cell[e_id] +=
static_cast<ErrorVectorReal>
(find_squared_element_error(system, var_name, elem,
Uelem, fe.get(),
fine_values.get()));
} // End loop over active local elements
} // End loop over variables
// Each processor has now computed the error contribuions
// for its local elements. We need to sum the vector
// and then take the square-root of each component. Note
// that we only need to sum if we are running on multiple
// processors, and we only need to take the square-root
// if the value is nonzero. There will in general be many
// zeros for the inactive elements.
// First sum the vector of estimated error values
this->reduce_error(error_per_cell, system.comm());
// Compute the square-root of each component.
{
LOG_SCOPE("std::sqrt()", "ExactErrorEstimator");
for (dof_id_type i=0; i<error_per_cell.size(); i++)
if (error_per_cell[i] != 0.)
{
libmesh_assert_greater (error_per_cell[i], 0.);
error_per_cell[i] = std::sqrt(error_per_cell[i]);
}
}
// If we used a non-standard solution before, now is the time to fix
// the current_local_solution
if (solution_vector && solution_vector != system.solution.get())
{
NumericVector<Number> * newsol =
const_cast<NumericVector<Number> *>(solution_vector);
System & sys = const_cast<System &>(system);
newsol->swap(*sys.solution);
sys.update();
}
}
int main(int argc, char ** argv)
{
LibMeshInit init(argc, argv);
GetPot cl(argc, argv);
unsigned char dim = -1;
if (!cl.search("--dim"))
{
libMesh::err << "No --dim argument found!" << std::endl;
usage_error(argv[0]);
}
dim = cl.next(dim);
Mesh mesh(init.comm(), dim);
if(!cl.search("--input"))
{
libMesh::err << "No --input argument found!" << std::endl;
usage_error(argv[0]);
}
const char * meshname = cl.next("mesh.xda");
mesh.read(meshname);
libMesh::out << "Loaded mesh " << meshname << std::endl;
if(!cl.search("--newbcid"))
{
libMesh::err << "No --bcid argument found!" << std::endl;
usage_error(argv[0]);
}
boundary_id_type bcid = 0;
bcid = cl.next(bcid);
Point minnormal(-std::numeric_limits<Real>::max(),
-std::numeric_limits<Real>::max(),
-std::numeric_limits<Real>::max());
Point maxnormal(std::numeric_limits<Real>::max(),
std::numeric_limits<Real>::max(),
std::numeric_limits<Real>::max());
Point minpoint(-std::numeric_limits<Real>::max(),
-std::numeric_limits<Real>::max(),
-std::numeric_limits<Real>::max());
Point maxpoint(std::numeric_limits<Real>::max(),
std::numeric_limits<Real>::max(),
std::numeric_limits<Real>::max());
if (cl.search("--minnormalx"))
minnormal(0) = cl.next(minnormal(0));
if (cl.search("--minnormalx"))
minnormal(0) = cl.next(minnormal(0));
if (cl.search("--maxnormalx"))
maxnormal(0) = cl.next(maxnormal(0));
if (cl.search("--minnormaly"))
minnormal(1) = cl.next(minnormal(1));
if (cl.search("--maxnormaly"))
maxnormal(1) = cl.next(maxnormal(1));
if (cl.search("--minnormalz"))
minnormal(2) = cl.next(minnormal(2));
if (cl.search("--maxnormalz"))
maxnormal(2) = cl.next(maxnormal(2));
if (cl.search("--minpointx"))
minpoint(0) = cl.next(minpoint(0));
if (cl.search("--maxpointx"))
maxpoint(0) = cl.next(maxpoint(0));
if (cl.search("--minpointy"))
minpoint(1) = cl.next(minpoint(1));
if (cl.search("--maxpointy"))
maxpoint(1) = cl.next(maxpoint(1));
if (cl.search("--minpointz"))
minpoint(2) = cl.next(minpoint(2));
if (cl.search("--maxpointz"))
maxpoint(2) = cl.next(maxpoint(2));
libMesh::out << "min point = " << minpoint << std::endl;
libMesh::out << "max point = " << maxpoint << std::endl;
libMesh::out << "min normal = " << minnormal << std::endl;
libMesh::out << "max normal = " << maxnormal << std::endl;
bool matcholdbcid = false;
boundary_id_type oldbcid = 0;
if (cl.search("--oldbcid"))
{
matcholdbcid = true;
oldbcid = cl.next(oldbcid);
if (oldbcid < 0)
oldbcid = BoundaryInfo::invalid_id;
}
UniquePtr<FEBase> fe = FEBase::build(dim, FEType(FIRST,LAGRANGE));
QGauss qface(dim-1, CONSTANT);
fe->attach_quadrature_rule(&qface);
const std::vector<Point> & face_points = fe->get_xyz();
const std::vector<Point> & face_normals = fe->get_normals();
MeshBase::element_iterator el = mesh.elements_begin();
const MeshBase::element_iterator end_el = mesh.elements_end();
for (; el != end_el; ++el)
{
Elem * elem = *el;
unsigned int n_sides = elem->n_sides();
// Container to catch ids handed back from BoundaryInfo
std::vector<boundary_id_type> ids;
for (unsigned short s=0; s != n_sides; ++s)
{
if (elem->neighbor_ptr(s))
continue;
fe->reinit(elem,s);
const Point & p = face_points[0];
const Point & n = face_normals[0];
//libMesh::out << "elem = " << elem->id() << std::endl;
//libMesh::out << "centroid = " << elem->centroid() << std::endl;
//libMesh::out << "p = " << p << std::endl;
//libMesh::out << "n = " << n << std::endl;
if (p(0) > minpoint(0) && p(0) < maxpoint(0) &&
p(1) > minpoint(1) && p(1) < maxpoint(1) &&
p(2) > minpoint(2) && p(2) < maxpoint(2) &&
n(0) > minnormal(0) && n(0) < maxnormal(0) &&
n(1) > minnormal(1) && n(1) < maxnormal(1) &&
n(2) > minnormal(2) && n(2) < maxnormal(2))
{
// Get the list of boundary ids for this side
mesh.get_boundary_info().boundary_ids(elem, s, ids);
// There should be at most one value present, otherwise the
// logic here won't work.
libmesh_assert(ids.size() <= 1);
// A convenient name for the side's ID.
boundary_id_type b_id = ids.empty() ? BoundaryInfo::invalid_id : ids[0];
if (matcholdbcid && b_id != oldbcid)
continue;
mesh.get_boundary_info().remove_side(elem, s);
mesh.get_boundary_info().add_side(elem, s, bcid);
//libMesh::out << "Set element " << elem->id() << " side " << s <<
// " to boundary " << bcid << std::endl;
}
}
}
std::string outputname;
if(cl.search("--output"))
{
outputname = cl.next("mesh.xda");
}
else
{
outputname = "new.";
outputname += meshname;
}
mesh.write(outputname.c_str());
libMesh::out << "Wrote mesh " << outputname << std::endl;
return 0;
}
// We now define the matrix assembly function for the
// Laplace 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_laplace(EquationSystems& es,
const std::string& system_name)
{
#ifdef LIBMESH_ENABLE_AMR
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Laplace");
// 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",false);
// Get a constant reference to the mesh object.
const MeshBase& mesh = es.get_mesh();
// The dimension that we are running
const unsigned int mesh_dim = mesh.mesh_dimension();
// Get a reference to the LinearImplicitSystem we are solving
LinearImplicitSystem& system = es.get_system<LinearImplicitSystem>("Laplace");
// 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(mesh_dim, fe_type));
UniquePtr<FEBase> fe_face (FEBase::build(mesh_dim, fe_type));
// Quadrature rules for numerical integration.
UniquePtr<QBase> qrule(fe_type.default_quadrature_rule(mesh_dim));
UniquePtr<QBase> qface(fe_type.default_quadrature_rule(mesh_dim-1));
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (qrule.get());
fe_face->attach_quadrature_rule (qface.get());
// 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();
const std::vector<Real>& JxW_face = fe_face->get_JxW();
// The physical XY locations of the quadrature points on the element.
// These might be useful for evaluating spatially varying material
// properties or forcing functions at the quadrature points.
const std::vector<Point>& q_point = fe->get_xyz();
// The element shape functions evaluated at the quadrature points.
// For this simple problem we usually only need them on element
// boundaries.
const std::vector<std::vector<Real> >& phi = fe->get_phi();
const std::vector<std::vector<Real> >& psi = fe_face->get_phi();
// The element shape function gradients evaluated at the quadrature
// points.
const std::vector<std::vector<RealGradient> >& dphi = fe->get_dphi();
// The XY locations of the quadrature points used for face integration
const std::vector<Point>& qface_points = fe_face->get_xyz();
// 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. Here we use
// the \p const_active_local_elem_iterator to indicate we only want
// to loop over elements that are assigned to the local processor
// which are "active" in the sense of AMR. This allows each
// processor to compute its components of the global matrix for
// active elements while ignoring parent elements which have been
// refined.
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).
//
// 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<dphi.size(); i++)
for (unsigned int j=0; j<dphi.size(); j++)
Ke(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
// We need a forcing function to make the 1D case interesting
if (mesh_dim == 1)
for (unsigned int qp=0; qp<qrule->n_points(); qp++)
{
Real x = q_point[qp](0);
Real f = singularity ? sqrt(3.)/9.*pow(-x, -4./3.) :
cos(x);
for (unsigned int i=0; i<dphi.size(); ++i)
Fe(i) += JxW[qp]*phi[i][qp]*f;
}
// Stop logging the matrix computation
perf_log.pop ("Ke");
// 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.
//
// This approach adds the L2 projection of the boundary
// data in penalty form to the weak statement. This is
// a more generic approach for applying Dirichlet BCs
// which is applicable to non-Lagrange finite element
// discretizations.
{
// Start logging the boundary condition computation
perf_log.push ("BCs");
// The penalty value.
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) == NULL)
{
fe_face->reinit(elem,s);
for (unsigned int qp=0; qp<qface->n_points(); qp++)
{
const Number value = exact_solution (qface_points[qp],
es.parameters,
"null",
"void");
// RHS contribution
for (unsigned int i=0; i<psi.size(); i++)
Fe(i) += penalty*JxW_face[qp]*value*psi[i][qp];
// Matrix contribution
for (unsigned int i=0; i<psi.size(); i++)
for (unsigned int j=0; j<psi.size(); j++)
Ke(i,j) += penalty*JxW_face[qp]*psi[i][qp]*psi[j][qp];
}
}
// Stop logging the boundary condition computation
perf_log.pop ("BCs");
}
// 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");
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);
// 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?
#endif // #ifdef LIBMESH_ENABLE_AMR
}
// Jacobian assembly function for the Laplace-Young system
void LaplaceYoung::jacobian (const NumericVector<Number>& soln,
SparseMatrix<Number>& jacobian,
NonlinearImplicitSystem& sys)
{
// Get a reference to the equation system.
EquationSystems &es = sys.get_equation_systems();
// 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 NonlinearImplicitSystem we are solving
NonlinearImplicitSystem& system =
es.get_system<NonlinearImplicitSystem>("Laplace-Young");
// 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);
// 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 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 Jacobian element matrix.
// Following basic finite element terminology we will denote these
// "Ke". More detail is in example 3.
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 active elements in the mesh which
// are local to this processor.
// We will compute the element Jacobian 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);
// 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 Jacobian 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());
// Now we will build the element Jacobian. This involves
// a double loop to integrate the test funcions (i) against
// the trial functions (j). Note that the Jacobian depends
// on the current solution x, which we access using the soln
// vector.
//
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
Gradient grad_u;
for (unsigned int i=0; i<phi.size(); i++)
grad_u += dphi[i][qp]*soln(dof_indices[i]);
const Number
sa = 1. + grad_u*grad_u,
K = 1. / std::sqrt(sa),
dK = -K / sa;
for (unsigned int i=0; i<phi.size(); i++)
for (unsigned int j=0; j<phi.size(); j++)
Ke(i,j) += JxW[qp]*(
K * (dphi[i][qp]*dphi[j][qp]) +
dK * (grad_u*dphi[j][qp]) * (grad_u*dphi[i][qp]) +
_kappa * phi[i][qp] * phi[j][qp]
);
}
dof_map.constrain_element_matrix (Ke, dof_indices);
// Add the element matrix to the system Jacobian.
jacobian.add_matrix (Ke, dof_indices);
}
// That's it.
}
// Residual assembly function for the Laplace-Young system
void LaplaceYoung::residual (const NumericVector<Number>& soln,
NumericVector<Number>& residual,
NonlinearImplicitSystem& sys)
{
EquationSystems &es = sys.get_equation_systems();
// 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();
libmesh_assert_equal_to (dim, 2);
// Get a reference to the NonlinearImplicitSystem we are solving
NonlinearImplicitSystem& system =
es.get_system<NonlinearImplicitSystem>("Laplace-Young");
// 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 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 resdual contributions
DenseVector<Number> Re;
// 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 active elements in the mesh which
// are local to this processor.
// We will compute the element residual.
residual.zero();
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);
// 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).
Re.resize (dof_indices.size());
// Now we will build the residual. This involves
// the construction of the matrix K and multiplication of it
// with the current solution x. We rearrange this into two loops:
// In the first, we calculate only the contribution of
// K_ij*x_j which is independent of the row i. In the second loops,
// we multiply with the row-dependent part and add it to the element
// residual.
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
Number u = 0;
Gradient grad_u;
for (unsigned int j=0; j<phi.size(); j++)
{
u += phi[j][qp]*soln(dof_indices[j]);
grad_u += dphi[j][qp]*soln(dof_indices[j]);
}
const Number K = 1./std::sqrt(1. + grad_u*grad_u);
for (unsigned int i=0; i<phi.size(); i++)
Re(i) += JxW[qp]*(
K*(dphi[i][qp]*grad_u) +
_kappa*phi[i][qp]*u
);
}
// At this point the interior element integration has
// been completed. However, we have not yet addressed
// boundary conditions.
// 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)
{
// 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);
// Loop over the face quadrature points for integration.
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
// This is the right-hand-side contribution (f),
// which has to be subtracted from the current residual
for (unsigned int i=0; i<phi_face.size(); i++)
Re(i) -= JxW_face[qp]*_sigma*phi_face[i][qp];
}
}
dof_map.constrain_element_vector (Re, dof_indices);
residual.add_vector (Re, dof_indices);
}
// That's it.
}
/**
* Assemble the system matrix and right-hand side vector.
*/
void assemble()
{
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 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);
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<Real> >& phi = fe->get_phi();
const std::vector<std::vector<RealGradient> >& dphi = fe->get_dphi();
DenseMatrix<Number> Ke;
DenseSubMatrix<Number> Ke_var[3][3] =
{
{DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke)},
{DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke)},
{DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke)}
};
DenseVector<Number> Fe;
DenseSubVector<Number> Fe_var[3] =
{DenseSubVector<Number>(Fe), DenseSubVector<Number>(Fe), DenseSubVector<Number>(Fe)};
std::vector<dof_id_type> dof_indices;
std::vector< std::vector<dof_id_type> > dof_indices_var(3);
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);
for(unsigned int var=0; var<3; var++)
{
dof_map.dof_indices (elem, dof_indices_var[var], var);
}
const unsigned int n_dofs = dof_indices.size();
const unsigned int n_var_dofs = dof_indices_var[0].size();
fe->reinit (elem);
Ke.resize (n_dofs,n_dofs);
for(unsigned int var_i=0; var_i<3; var_i++)
for(unsigned int var_j=0; var_j<3; var_j++)
{
Ke_var[var_i][var_j].reposition (var_i*n_var_dofs, var_j*n_var_dofs, n_var_dofs, n_var_dofs);
}
Fe.resize (n_dofs);
for(unsigned int var=0; var<3; var++)
{
Fe_var[var].reposition (var*n_var_dofs, n_var_dofs);
}
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
// assemble \int_Omega C_ijkl u_k,l v_i,j \dx
for (unsigned int dof_i=0; dof_i<n_var_dofs; dof_i++)
for (unsigned int dof_j=0; dof_j<n_var_dofs; dof_j++)
{
for(unsigned int i=0; i<3; i++)
for(unsigned int j=0; j<3; j++)
for(unsigned int k=0; k<3; k++)
for(unsigned int l=0; l<3; l++)
{
Ke_var[i][k](dof_i,dof_j) += JxW[qp] *
elasticity_tensor(i,j,k,l) *
dphi[dof_j][qp](l) *
dphi[dof_i][qp](j);
}
}
// assemble \int_Omega f_i v_i \dx
DenseVector<Number> f_vec(3);
f_vec(0) = 0.;
f_vec(1) = 0.;
f_vec(2) = -1.;
for (unsigned int dof_i=0; dof_i<n_var_dofs; dof_i++)
{
for(unsigned int i=0; i<3; i++)
{
Fe_var[i](dof_i) += JxW[qp] *
( f_vec(i) * phi[dof_i][qp] );
}
}
}
// assemble \int_\Gamma g_i v_i \ds
DenseVector<Number> g_vec(3);
g_vec(0) = 0.;
g_vec(1) = 0.;
g_vec(2) = -1.;
{
for (unsigned int side=0; side<elem->n_sides(); side++)
if (elem->neighbor(side) == NULL)
{
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);
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
// Apply a traction
if( mesh.get_boundary_info().has_boundary_id
(elem, side, BOUNDARY_ID_MAX_X)
)
{
for (unsigned int dof_i=0; dof_i<n_var_dofs; dof_i++)
{
for(unsigned int i=0; i<3; i++)
{
Fe_var[i](dof_i) += JxW_face[qp] *
( g_vec(i) * phi_face[dof_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);
}
}
// 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_equal_to (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 a UniquePtr<FEBase>. This can be thought
// of as a pointer that will clean up after itself. Introduction Example 4
// describes some advantages of UniquePtr's in the context of
// quadrature rules.
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 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<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.
//
// 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 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_ptr(side) == libmesh_nullptr)
{
// 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!
}
void
InitialCondition::compute()
{
// -- NOTE ----
// The following code is a copy from libMesh project_vector.C plus it adds some features, so we can couple variable values
// and we also do not call any callbacks, but we use our initial condition system directly.
// ------------
// The element matrix and RHS for projections.
// Note that Ke is always real-valued, whereas Fe may be complex valued if complex number support is enabled
DenseMatrix<Real> Ke;
DenseVector<Number> Fe;
// The new element coefficients
DenseVector<Number> Ue;
const FEType & fe_type = _var.feType();
// The dimension of the current element
const unsigned int dim = _current_elem->dim();
// The element type
const ElemType elem_type = _current_elem->type();
// The number of nodes on the new element
const unsigned int n_nodes = _current_elem->n_nodes();
// The global DOF indices
std::vector<dof_id_type> dof_indices;
// Side/edge DOF indices
std::vector<unsigned int> side_dofs;
// Get FE objects of the appropriate type
// We cannot use the FE object in Assembly, since the following code is messing with the quadrature rules
// for projections and would screw it up. However, if we implement projections from one mesh to another,
// this code should use that implementation.
UniquePtr<FEBase> fe (FEBase::build(dim, fe_type));
// Prepare variables for projection
UniquePtr<QBase> qrule (fe_type.default_quadrature_rule(dim));
UniquePtr<QBase> qedgerule (fe_type.default_quadrature_rule(1));
UniquePtr<QBase> qsiderule (fe_type.default_quadrature_rule(dim-1));
// The values of the shape functions at the quadrature points
const std::vector<std::vector<Real> > & phi = fe->get_phi();
// The gradients of the shape functions at the quadrature points on the child element.
const std::vector<std::vector<RealGradient> > * dphi = NULL;
const FEContinuity cont = fe->get_continuity();
if (cont == C_ONE)
{
const std::vector<std::vector<RealGradient> > & ref_dphi = fe->get_dphi();
dphi = &ref_dphi;
}
// The Jacobian * quadrature weight at the quadrature points
const std::vector<Real> & JxW = fe->get_JxW();
// The XYZ locations of the quadrature points
const std::vector<Point>& xyz_values = fe->get_xyz();
// Update the DOF indices for this element based on the current mesh
_var.prepareIC();
dof_indices = _var.dofIndices();
// The number of DOFs on the element
const unsigned int n_dofs = dof_indices.size();
if (n_dofs == 0)
return;
// Fixed vs. free DoFs on edge/face projections
std::vector<char> dof_is_fixed(n_dofs, false); // bools
std::vector<int> free_dof(n_dofs, 0);
// Zero the interpolated values
Ue.resize (n_dofs);
Ue.zero();
// In general, we need a series of
// projections to ensure a unique and continuous
// solution. We start by interpolating nodes, then
// hold those fixed and project edges, then
// hold those fixed and project faces, then
// hold those fixed and project interiors
_fe_problem.sizeZeroes(n_nodes, _tid);
// Interpolate node values first
unsigned int current_dof = 0;
for (unsigned int n = 0; n != n_nodes; ++n)
{
// FIXME: this should go through the DofMap,
// not duplicate dof_indices code badly!
const unsigned int nc = FEInterface::n_dofs_at_node (dim, fe_type, elem_type, n);
if (!_current_elem->is_vertex(n))
{
current_dof += nc;
continue;
}
if (cont == DISCONTINUOUS)
{
libmesh_assert(nc == 0);
}
// Assume that C_ZERO elements have a single nodal
// value shape function
else if (cont == C_ZERO)
{
libmesh_assert(nc == 1);
_qp = n;
_current_node = _current_elem->get_node(n);
Ue(current_dof) = value(*_current_node);
dof_is_fixed[current_dof] = true;
current_dof++;
}
// The hermite element vertex shape functions are weird
else if (fe_type.family == HERMITE)
{
_qp = n;
_current_node = _current_elem->get_node(n);
Ue(current_dof) = value(*_current_node);
dof_is_fixed[current_dof] = true;
current_dof++;
Gradient grad = gradient(*_current_node);
// x derivative
Ue(current_dof) = grad(0);
dof_is_fixed[current_dof] = true;
current_dof++;
if (dim > 1)
{
// We'll finite difference mixed derivatives
Point nxminus = _current_elem->point(n),
nxplus = _current_elem->point(n);
nxminus(0) -= TOLERANCE;
nxplus(0) += TOLERANCE;
Gradient gxminus = gradient(nxminus);
Gradient gxplus = gradient(nxplus);
// y derivative
Ue(current_dof) = grad(1);
dof_is_fixed[current_dof] = true;
current_dof++;
// xy derivative
Ue(current_dof) = (gxplus(1) - gxminus(1)) / 2. / TOLERANCE;
dof_is_fixed[current_dof] = true;
current_dof++;
if (dim > 2)
{
// z derivative
Ue(current_dof) = grad(2);
dof_is_fixed[current_dof] = true;
current_dof++;
// xz derivative
Ue(current_dof) = (gxplus(2) - gxminus(2)) / 2. / TOLERANCE;
dof_is_fixed[current_dof] = true;
current_dof++;
// We need new points for yz
Point nyminus = _current_elem->point(n),
nyplus = _current_elem->point(n);
nyminus(1) -= TOLERANCE;
nyplus(1) += TOLERANCE;
Gradient gyminus = gradient(nyminus);
Gradient gyplus = gradient(nyplus);
// xz derivative
Ue(current_dof) = (gyplus(2) - gyminus(2)) / 2. / TOLERANCE;
dof_is_fixed[current_dof] = true;
current_dof++;
// Getting a 2nd order xyz is more tedious
Point nxmym = _current_elem->point(n),
nxmyp = _current_elem->point(n),
nxpym = _current_elem->point(n),
nxpyp = _current_elem->point(n);
nxmym(0) -= TOLERANCE;
nxmym(1) -= TOLERANCE;
nxmyp(0) -= TOLERANCE;
nxmyp(1) += TOLERANCE;
nxpym(0) += TOLERANCE;
nxpym(1) -= TOLERANCE;
nxpyp(0) += TOLERANCE;
nxpyp(1) += TOLERANCE;
Gradient gxmym = gradient(nxmym);
Gradient gxmyp = gradient(nxmyp);
Gradient gxpym = gradient(nxpym);
Gradient gxpyp = gradient(nxpyp);
Number gxzplus = (gxpyp(2) - gxmyp(2)) / 2. / TOLERANCE;
Number gxzminus = (gxpym(2) - gxmym(2)) / 2. / TOLERANCE;
// xyz derivative
Ue(current_dof) = (gxzplus - gxzminus) / 2. / TOLERANCE;
dof_is_fixed[current_dof] = true;
current_dof++;
}
}
}
// Assume that other C_ONE elements have a single nodal
// value shape function and nodal gradient component
// shape functions
else if (cont == C_ONE)
{
libmesh_assert(nc == 1 + dim);
_current_node = _current_elem->get_node(n);
Ue(current_dof) = value(*_current_node);
dof_is_fixed[current_dof] = true;
current_dof++;
Gradient grad = gradient(*_current_node);
for (unsigned int i=0; i != dim; ++i)
{
Ue(current_dof) = grad(i);
dof_is_fixed[current_dof] = true;
current_dof++;
}
}
else
libmesh_error();
} // loop over nodes
// From here on out we won't be sampling at nodes anymore
_current_node = NULL;
// In 3D, project any edge values next
if (dim > 2 && cont != DISCONTINUOUS)
for (unsigned int e=0; e != _current_elem->n_edges(); ++e)
{
FEInterface::dofs_on_edge(_current_elem, dim, fe_type, e, side_dofs);
// Some edge dofs are on nodes and already
// fixed, others are free to calculate
unsigned int free_dofs = 0;
for (unsigned int i=0; i != side_dofs.size(); ++i)
if (!dof_is_fixed[side_dofs[i]])
free_dof[free_dofs++] = i;
// There may be nothing to project
if (!free_dofs)
continue;
Ke.resize (free_dofs, free_dofs); Ke.zero();
Fe.resize (free_dofs); Fe.zero();
// The new edge coefficients
DenseVector<Number> Uedge(free_dofs);
// Initialize FE data on the edge
fe->attach_quadrature_rule (qedgerule.get());
fe->edge_reinit (_current_elem, e);
const unsigned int n_qp = qedgerule->n_points();
_fe_problem.sizeZeroes(n_qp, _tid);
// Loop over the quadrature points
for (unsigned int qp = 0; qp < n_qp; qp++)
{
// solution at the quadrature point
Number fineval = value(xyz_values[qp]);
// solution grad at the quadrature point
Gradient finegrad;
if (cont == C_ONE)
finegrad = gradient(xyz_values[qp]);
// Form edge projection matrix
for (unsigned int sidei = 0, freei = 0; sidei != side_dofs.size(); ++sidei)
{
unsigned int i = side_dofs[sidei];
// fixed DoFs aren't test functions
if (dof_is_fixed[i])
continue;
for (unsigned int sidej = 0, freej = 0; sidej != side_dofs.size(); ++sidej)
{
unsigned int j = side_dofs[sidej];
if (dof_is_fixed[j])
Fe(freei) -= phi[i][qp] * phi[j][qp] * JxW[qp] * Ue(j);
else
Ke(freei,freej) += phi[i][qp] * phi[j][qp] * JxW[qp];
if (cont == C_ONE)
{
if (dof_is_fixed[j])
Fe(freei) -= ((*dphi)[i][qp] * (*dphi)[j][qp]) * JxW[qp] * Ue(j);
else
Ke(freei,freej) += ((*dphi)[i][qp] * (*dphi)[j][qp]) * JxW[qp];
}
if (!dof_is_fixed[j])
freej++;
}
Fe(freei) += phi[i][qp] * fineval * JxW[qp];
if (cont == C_ONE)
Fe(freei) += (finegrad * (*dphi)[i][qp]) * JxW[qp];
freei++;
}
}
Ke.cholesky_solve(Fe, Uedge);
// Transfer new edge solutions to element
for (unsigned int i=0; i != free_dofs; ++i)
{
Number &ui = Ue(side_dofs[free_dof[i]]);
libmesh_assert(std::abs(ui) < TOLERANCE || std::abs(ui - Uedge(i)) < TOLERANCE);
ui = Uedge(i);
dof_is_fixed[side_dofs[free_dof[i]]] = true;
}
}
// Project any side values (edges in 2D, faces in 3D)
if (dim > 1 && cont != DISCONTINUOUS)
for (unsigned int s=0; s != _current_elem->n_sides(); ++s)
{
FEInterface::dofs_on_side(_current_elem, dim, fe_type, s, side_dofs);
// Some side dofs are on nodes/edges and already
// fixed, others are free to calculate
unsigned int free_dofs = 0;
for (unsigned int i=0; i != side_dofs.size(); ++i)
if (!dof_is_fixed[side_dofs[i]])
free_dof[free_dofs++] = i;
// There may be nothing to project
if (!free_dofs)
continue;
Ke.resize (free_dofs, free_dofs); Ke.zero();
Fe.resize (free_dofs); Fe.zero();
// The new side coefficients
DenseVector<Number> Uside(free_dofs);
// Initialize FE data on the side
fe->attach_quadrature_rule (qsiderule.get());
fe->reinit (_current_elem, s);
const unsigned int n_qp = qsiderule->n_points();
_fe_problem.sizeZeroes(n_qp, _tid);
// Loop over the quadrature points
for (unsigned int qp = 0; qp < n_qp; qp++)
{
// solution at the quadrature point
Number fineval = value(xyz_values[qp]);
// solution grad at the quadrature point
Gradient finegrad;
if (cont == C_ONE)
finegrad = gradient(xyz_values[qp]);
// Form side projection matrix
for (unsigned int sidei = 0, freei = 0; sidei != side_dofs.size(); ++sidei)
{
unsigned int i = side_dofs[sidei];
// fixed DoFs aren't test functions
if (dof_is_fixed[i])
continue;
for (unsigned int sidej = 0, freej = 0; sidej != side_dofs.size(); ++sidej)
{
unsigned int j = side_dofs[sidej];
if (dof_is_fixed[j])
Fe(freei) -= phi[i][qp] * phi[j][qp] * JxW[qp] * Ue(j);
else
Ke(freei,freej) += phi[i][qp] * phi[j][qp] * JxW[qp];
if (cont == C_ONE)
{
if (dof_is_fixed[j])
Fe(freei) -= ((*dphi)[i][qp] * (*dphi)[j][qp]) * JxW[qp] * Ue(j);
else
Ke(freei,freej) += ((*dphi)[i][qp] * (*dphi)[j][qp]) * JxW[qp];
}
if (!dof_is_fixed[j])
freej++;
}
Fe(freei) += (fineval * phi[i][qp]) * JxW[qp];
if (cont == C_ONE)
Fe(freei) += (finegrad * (*dphi)[i][qp]) * JxW[qp];
freei++;
}
}
Ke.cholesky_solve(Fe, Uside);
// Transfer new side solutions to element
for (unsigned int i=0; i != free_dofs; ++i)
{
Number &ui = Ue(side_dofs[free_dof[i]]);
libmesh_assert(std::abs(ui) < TOLERANCE || std::abs(ui - Uside(i)) < TOLERANCE);
ui = Uside(i);
dof_is_fixed[side_dofs[free_dof[i]]] = true;
}
}
// Project the interior values, finally
// Some interior dofs are on nodes/edges/sides and
// already fixed, others are free to calculate
unsigned int free_dofs = 0;
for (unsigned int i=0; i != n_dofs; ++i)
if (!dof_is_fixed[i])
free_dof[free_dofs++] = i;
// There may be nothing to project
if (free_dofs)
{
Ke.resize (free_dofs, free_dofs); Ke.zero();
Fe.resize (free_dofs); Fe.zero();
// The new interior coefficients
DenseVector<Number> Uint(free_dofs);
// Initialize FE data
fe->attach_quadrature_rule (qrule.get());
fe->reinit (_current_elem);
const unsigned int n_qp = qrule->n_points();
_fe_problem.sizeZeroes(n_qp, _tid);
// Loop over the quadrature points
for (unsigned int qp=0; qp<n_qp; qp++)
{
// solution at the quadrature point
Number fineval = value(xyz_values[qp]);
// solution grad at the quadrature point
Gradient finegrad;
if (cont == C_ONE)
finegrad = gradient(xyz_values[qp]);
// Form interior projection matrix
for (unsigned int i=0, freei=0; i != n_dofs; ++i)
{
// fixed DoFs aren't test functions
if (dof_is_fixed[i])
continue;
for (unsigned int j=0, freej=0; j != n_dofs; ++j)
{
if (dof_is_fixed[j])
Fe(freei) -= phi[i][qp] * phi[j][qp] * JxW[qp] * Ue(j);
else
Ke(freei,freej) += phi[i][qp] * phi[j][qp] * JxW[qp];
if (cont == C_ONE)
{
if (dof_is_fixed[j])
Fe(freei) -= ((*dphi)[i][qp] * (*dphi)[j][qp]) * JxW[qp] * Ue(j);
else
Ke(freei,freej) += ((*dphi)[i][qp] * (*dphi)[j][qp]) * JxW[qp];
}
if (!dof_is_fixed[j])
freej++;
}
Fe(freei) += phi[i][qp] * fineval * JxW[qp];
if (cont == C_ONE)
Fe(freei) += (finegrad * (*dphi)[i][qp]) * JxW[qp];
freei++;
}
}
Ke.cholesky_solve(Fe, Uint);
// Transfer new interior solutions to element
for (unsigned int i=0; i != free_dofs; ++i)
{
Number &ui = Ue(free_dof[i]);
libmesh_assert(std::abs(ui) < TOLERANCE || std::abs(ui - Uint(i)) < TOLERANCE);
ui = Uint(i);
dof_is_fixed[free_dof[i]] = true;
}
} // if there are free interior dofs
// Make sure every DoF got reached!
for (unsigned int i=0; i != n_dofs; ++i)
libmesh_assert(dof_is_fixed[i]);
NumericVector<Number> & solution = _var.sys().solution();
// 'first' and 'last' are no longer used, see note about subdomain-restricted variables below
// const dof_id_type
// first = solution.first_local_index(),
// last = solution.last_local_index();
// Lock the new_vector since it is shared among threads.
{
Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
for (unsigned int i = 0; i < n_dofs; i++)
// We may be projecting a new zero value onto
// an old nonzero approximation - RHS
// if (Ue(i) != 0.)
// This is commented out because of subdomain restricted variables.
// It can be the case that if a subdomain restricted variable's boundary
// aligns perfectly with a processor boundary that the variable will get
// no value. To counteract this we're going to let every processor set a
// value at every node and then let PETSc figure it out.
// Later we can choose to do something different / better.
// if ((dof_indices[i] >= first) && (dof_indices[i] < last))
{
solution.set(dof_indices[i], Ue(i));
if (cont == C_ZERO)
_var.setNodalValue(Ue(i), i);
}
}
}
// 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)
{
libMesh::out << " assembling elliptic dg system... ";
libMesh::out.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 UniquePtr<FEBase>. This can be thought
// of as a pointer that will clean up after itself.
UniquePtr<FEBase> fe (FEBase::build(dim, fe_type));
UniquePtr<FEBase> fe_elem_face(FEBase::build(dim, fe_type));
UniquePtr<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) == libmesh_nullptr)
{
// Pointer to the element face
fe_elem_face->reinit(elem, side);
UniquePtr<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++)
{
// stability
Ke(i,j) += JxW_face[qp] * penalty/h_elem * phi_face[i][qp] * phi_face[j][qp];
// consistency
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]));
}
// RHS contributions
// stability
Fe(i) += JxW_face[qp] * bc_value * penalty/h_elem * phi_face[i][qp];
// consistency
Fe(i) -= JxW_face[qp] * dphi_face[i][qp] * (bc_value*qface_normals[qp]);
}
}
}
// 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
UniquePtr<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++)
{
// consistency
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]));
// stability
Kee(i,j) += JxW_face[qp] * penalty/h_elem * phi_face[j][qp]*phi_face[i][qp];
}
}
// 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++)
{
// consistency
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]));
// stability
Knn(i,j) +=
JxW_face[qp] * penalty/h_elem * phi_neighbor_face[j][qp]*phi_neighbor_face[i][qp];
}
}
// 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++)
{
// consistency
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]));
// stability
Kne(i,j) -= JxW_face[qp] * penalty/h_elem * phi_face[j][qp]*phi_neighbor_face[i][qp];
}
}
// 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++)
{
// consistency
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]));
// stability
Ken(i,j) -= JxW_face[qp] * penalty/h_elem * phi_face[i][qp]*phi_neighbor_face[j][qp];
}
}
}
// 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);
}
libMesh::out << "done" << std::endl;
}
void assemble_elasticity(EquationSystems & es,
const std::string & system_name)
{
libmesh_assert_equal_to (system_name, "Elasticity");
const MeshBase & mesh = es.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
Real pival = libMesh::pi;
Real sigma = 1000.0;
Real omega = 2.0*pival*27e6;
Real Mu0 = 4e-7*pival;
char *filename = "coordinates_custom.dat";
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<Real>> & phi = fe->get_phi();
const std::vector<std::vector<RealGradient> > & dphi = fe->get_dphi();
const std::vector<Point> & q_point = fe->get_xyz();
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);
const Real eps = 1.e-3;
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
const Real x = q_point[qp](0);
const Real y = q_point[qp](1);
Real fxyz = 0.0;
Real fxy = 0.0;
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] + phi[i][qp]*phi[j][qp]/x/x)*x ;
}
if ( x<=0.3 && y>=0.0 && y<=1.0 )
{
Real Kfactor = Mu0*sigma*omega;
for (unsigned int i=0; i<n_u_dofs; i++)
for (unsigned int j=0; j<n_v_dofs; j++)
{
Kuv(i,j) += (-1.0)*(JxW[qp]*(phi[i][qp]*phi[j][qp])*Kfactor*x);
}
for (unsigned int i=0; i<n_v_dofs; i++)
for (unsigned int j=0; j<n_u_dofs; j++)
{
Kvu(i,j) += JxW[qp]*(phi[i][qp]*phi[j][qp])*Kfactor*x ;
}
fxyz = -Kfactor*solev(x,y,filename)*Mu0*omega/2.0/pival;
}
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] + phi[i][qp]*phi[j][qp]/x/x )*x ;
}
// Real fxyz = exact_solution(x,y)*pival*pival/2.0 + pival*0.5*sin(0.5*pival*x)*sin(0.5*pival*y)/x + exact_solution(x,y)/x/x + Kfactor*exact_solution2(x,y);
// Real fxy = exact_solution2(x,y)*pival*pival/2.0 - pival*0.5*cos(0.5*pival*x)*cos(0.5*pival*y)/x + exact_solution2(x,y)/x/x + Kfactor*exact_solution(x,y);
for (unsigned int i=0; i<n_u_dofs; i++)
Fu(i) += JxW[qp]*fxyz*phi[i][qp]*x;
for (unsigned int i = 0;i<n_v_dofs;i++)
Fv(i) += JxW[qp]*fxy*phi[i][qp]*x;
}
for (unsigned int s=0; s<elem->n_sides(); s++)
if (elem->neighbor(s) == libmesh_nullptr)
{
const std::vector<std::vector<Real> > & phi_face = fe_face->get_phi();
const std::vector<Real> & JxW_face = fe_face->get_JxW();
const std::vector<Point> & qface_point = fe_face->get_xyz();
const std::vector<Point>& qface_normals = fe_face->get_normals();
fe_face->reinit(elem, s);
UniquePtr<Elem> side (elem->build_side(s));
/* 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]*xf;
// 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]*xf;
}*/
double check = 0;
{
for (unsigned int ns=0; ns<side->n_nodes(); ns++)
{ const Real penalty = 1.e10;
for (unsigned int n=0; n<elem->n_nodes(); n++)
if (elem->node(n) == side->node(ns))
{
Node *node = elem->get_node(n);
Point poi = *node;
const Real xf = poi(0);
const Real yf = poi(1);
for(unsigned int j=0; j<n_u_dofs; ++j)
Kuu(n,j) = 0.;
for(unsigned int j=0; j<n_v_dofs; ++j)
Kvv(n,j) = 0.;
Kuu(n,n) = 1.;
Kvv(n,n) = 1.;
Fu(n) = 0.0;
Fv(n) = 0.0;
// Fu(n) = exact_solution(xf,yf);
// Fv(n) = exact_solution2(xf,yf);
}
}
}
}
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);
}
}
// We now define the matrix assembly function for the
// Biharmonic 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_biharmonic(EquationSystems& es,
const std::string& system_name)
{
#ifdef LIBMESH_ENABLE_AMR
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Biharmonic");
// 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",false);
// 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>("Biharmonic");
// 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));
// Quadrature rule for numerical integration.
// With 2D triangles, the Clough quadrature rule puts a Gaussian
// quadrature rule on each of the 3 subelements
UniquePtr<QBase> qrule(fe_type.default_quadrature_rule(dim));
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (qrule.get());
// Declare a special finite element object for
// boundary integration.
UniquePtr<FEBase> fe_face (FEBase::build(dim, fe_type));
// Boundary integration requires another quadraure rule,
// with dimensionality one less than the dimensionality
// of the element.
// In 1D, the Clough and Gauss quadrature rules are identical.
UniquePtr<QBase> qface(fe_type.default_quadrature_rule(dim-1));
// Tell the finte element object to use our
// quadrature rule.
fe_face->attach_quadrature_rule (qface.get());
// 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 second derivatives evaluated at the
// quadrature points. Note that for the simple biharmonic, shape
// function first derivatives are unnecessary.
const std::vector<std::vector<RealTensor> >& d2phi = fe->get_d2phi();
// For efficiency we will compute shape function laplacians n times,
// not n^2
std::vector<Real> shape_laplacian;
// 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.
Ke.resize (dof_indices.size(),
dof_indices.size());
Fe.resize (dof_indices.size());
// Make sure there is enough room in this cache
shape_laplacian.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 laplacians of the test funcions
// (i) against laplacians of the trial functions (j).
//
// This step is why we need the Clough-Tocher elements -
// these C1 differentiable elements have square-integrable
// second derivatives.
//
// 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++)
{
shape_laplacian[i] = d2phi[i][qp](0,0)+d2phi[i][qp](1,1);
if (dim == 3)
shape_laplacian[i] += d2phi[i][qp](2,2);
}
for (unsigned int i=0; i<phi.size(); i++)
for (unsigned int j=0; j<phi.size(); j++)
Ke(i,j) += JxW[qp]*
shape_laplacian[i]*shape_laplacian[j];
}
// Stop logging the matrix computation
perf_log.pop ("Ke");
// 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. Note that this is a fourth-order
// problem: Dirichlet boundary conditions include *both*
// boundary values and boundary normal fluxes.
{
// Start logging the boundary condition computation
perf_log.push ("BCs");
// The penalty values, for solution boundary trace and flux.
const Real penalty = 1e10;
const Real penalty2 = 1e10;
// 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)
{
// The value of the shape functions at the quadrature
// points.
const std::vector<std::vector<Real> >& phi_face =
fe_face->get_phi();
// The value of the shape function derivatives at the
// quadrature points.
const std::vector<std::vector<RealGradient> >& dphi_face =
fe_face->get_dphi();
// 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();
const std::vector<Point>& face_normals =
fe_face->get_normals();
// Compute the shape function values on the element
// face.
fe_face->reinit(elem, s);
// Loop over the face quagrature points for integration.
for (unsigned int qp=0; qp<qface->n_points(); qp++)
{
// The boundary value.
Number value = exact_solution(qface_point[qp],
es.parameters, "null",
"void");
Gradient flux = exact_2D_derivative(qface_point[qp],
es.parameters,
"null", "void");
// Matrix contribution of the L2 projection.
// Note that the basis function values are
// integrated against test function values while
// basis fluxes are integrated against test function
// fluxes.
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] + penalty2
* (dphi_face[i][qp] *
face_normals[qp]) *
(dphi_face[j][qp] *
face_normals[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]
+ penalty2 *
(flux * face_normals[qp])
* (dphi_face[i][qp]
* face_normals[qp]));
}
}
// Stop logging the boundary condition computation
perf_log.pop ("BCs");
}
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]*forcing_function(q_point[qp]);
// 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");
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);
// Stop 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?
#else
#endif // #ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
#endif // #ifdef LIBMESH_ENABLE_AMR
}
void LinearElasticityWithContact::residual_and_jacobian (
const NumericVector<Number>& soln,
NumericVector<Number>* residual,
SparseMatrix<Number>* jacobian,
NonlinearImplicitSystem& /*sys*/)
{
EquationSystems& es = _sys.get_equation_systems();
const Real young_modulus = es.parameters.get<Real>("young_modulus");
const Real poisson_ratio = es.parameters.get<Real>("poisson_ratio");
const Real forcing_magnitude = es.parameters.get<Real>("forcing_magnitude");
const MeshBase& mesh = _sys.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
const unsigned int u_var = _sys.variable_number ("u");
DofMap& dof_map = _sys.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);
UniquePtr<FEBase> fe_face (FEBase::build(dim, fe_type));
QGauss qface (dim-1, fe_type.default_quadrature_order());
fe_face->attach_quadrature_rule (&qface);
UniquePtr<FEBase> fe_neighbor_face (FEBase::build(dim, fe_type));
fe_neighbor_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();
const std::vector<Real>& JxW_face = fe_face->get_JxW();
const std::vector<std::vector<Real> >& phi_face = fe_face->get_phi();
const std::vector<Point>& face_normals = fe_face->get_normals();
const std::vector<Point>& face_xyz = fe_face->get_xyz();
const std::vector<std::vector<Real> >& phi_neighbor_face = fe_neighbor_face->get_phi();
// 1. Move mesh_clone based on soln.
// 2. Compute and store all contact forces.
// 3. Augment the sparsity pattern.
{
UniquePtr<MeshBase> mesh_clone = mesh.clone();
move_mesh(*mesh_clone, soln);
_augment_sparsity.clear_contact_element_map();
clear_contact_data();
MeshBase::const_element_iterator el = mesh_clone->active_elements_begin();
const MeshBase::const_element_iterator end_el = mesh_clone->active_elements_end();
for ( ; el != end_el; ++el)
{
const Elem* elem = *el;
for (unsigned int side=0; side<elem->n_sides(); side++)
{
if (elem->neighbor(side) == NULL)
{
bool on_lower_contact_surface =
mesh_clone->get_boundary_info().has_boundary_id
(elem, side, CONTACT_BOUNDARY_LOWER);
bool on_upper_contact_surface =
mesh_clone->get_boundary_info().has_boundary_id
(elem, side, CONTACT_BOUNDARY_UPPER);
if( on_lower_contact_surface && on_upper_contact_surface )
{
libmesh_error_msg("Should not be on both surfaces at the same time");
}
if( on_lower_contact_surface || on_upper_contact_surface )
{
fe_face->reinit(elem, side);
// Let's stash xyz and normals because we reinit on other_elem below
std::vector<Point> face_normals_stashed = fe_face->get_normals();
std::vector<Point> face_xyz_stashed = fe_face->get_xyz();
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
Point line_point = face_xyz_stashed[qp];
Point line_direction = face_normals_stashed[qp];
// find an element which the line intersects, based on the plane
// defined by the normal at the centroid of the other element
bool found_other_elem = false;
// Note that here we loop over all elements (not just local elements)
// to be sure we find the appropriate other element.
MeshBase::const_element_iterator other_el = mesh_clone->active_elements_begin();
const MeshBase::const_element_iterator other_end_el = mesh_clone->active_elements_end();
for ( ; other_el != other_end_el; ++other_el)
{
const Elem* other_elem = *other_el;
if( other_elem->close_to_point(line_point, _contact_proximity_tol) )
{
for (unsigned int other_side=0; other_side<other_elem->n_sides(); other_side++)
if (other_elem->neighbor(other_side) == NULL)
{
boundary_id_type other_surface_id =
on_lower_contact_surface ?
CONTACT_BOUNDARY_UPPER : CONTACT_BOUNDARY_LOWER;
if( mesh_clone->get_boundary_info().has_boundary_id
(other_elem, other_side, other_surface_id) )
{
UniquePtr<Elem> other_side_elem = other_elem->build_side(other_side);
// Define a plane based on the normal at the centroid of other_side_elem
// and check where line_point + s * line_direction (s \in R) intersects
// this plane.
const Point reference_centroid (
FEInterface::inverse_map (
other_elem->dim(),
_sys.get_dof_map().variable_type(0),
other_elem,
other_side_elem->centroid()));
std::vector<Point> reference_centroid_vector;
reference_centroid_vector.push_back(reference_centroid);
fe_face->reinit(
other_elem,
other_side,
TOLERANCE,
&reference_centroid_vector);
Point plane_normal = face_normals[0];
Point plane_point = face_xyz[0];
// line_direction.dot(plane_normal) == 0.0 if the line and plane are
// parallel. Ignore this case since it should give zero contact force.
if( (line_direction * plane_normal) != 0. )
{
// The signed distance between the line and the plane
Real signed_distance =
( (plane_point - line_point) * plane_normal) /
(line_direction * plane_normal);
Point intersection_point = line_point + signed_distance * line_direction;
// Note that signed_distance = (intersection_point - line_point) dot line_direction
// since line_direction is a unit vector.
if(other_side_elem->close_to_point(intersection_point, _contains_point_tol))
{
// If the signed distance is negative then we have overlapping elements
// i.e. we have detected contact.
if(signed_distance < 0.0)
{
// We need to store the intersection point, and the element/side
// that it belongs to. We can use this to calculate the contact
// force later on.
std::vector<Point> intersection_point_vec;
intersection_point_vec.push_back(intersection_point);
std::vector<Point> inverse_intersection_point_vec;
FEInterface::inverse_map(
other_elem->dim(),
fe->get_fe_type(),
other_elem,
intersection_point_vec,
inverse_intersection_point_vec);
IntersectionPointData contact_intersection_pt_data(
other_elem->id(),
other_side,
intersection_point,
inverse_intersection_point_vec[0],
line_point,
line_direction);
set_contact_data(
elem->id(),
side,
qp,
contact_intersection_pt_data);
// We also need to keep track of which elements
// are coupled in order to augment the sparsity pattern
// appropriately later on.
_augment_sparsity.add_contact_element(
elem->id(),
other_elem->id());
}
// If we've found an element that contains
// intersection_point then we're done for
// the current quadrature point hence break
// out to the next qp.
found_other_elem = true;
break;
}
}
}
}
}
if(found_other_elem)
{
break;
}
} // end for other_el
} // end for qp
} // end if on_contact_surface
} // end if nieghbor(side_) != NULL
} // end for side
} // end for el
}
// Clear the Jacobian matrix and reinitialize it so that
// we get the updated sparsity pattern
if(jacobian)
{
dof_map.clear_sparsity();
dof_map.compute_sparsity(mesh);
#ifdef LIBMESH_HAVE_PETSC
PetscMatrix<Number>* petsc_jacobian = cast_ptr<PetscMatrix<Number>*>(jacobian);
petsc_jacobian->update_preallocation_and_zero();
#else
libmesh_error();
#endif
}
if(residual)
{
residual->zero();
}
// Do jacobian and residual assembly, including contact forces
DenseVector<Number> Re;
DenseSubVector<Number> Re_var[3] =
{DenseSubVector<Number>(Re), DenseSubVector<Number>(Re), DenseSubVector<Number>(Re)};
DenseMatrix<Number> Ke;
DenseSubMatrix<Number> Ke_var[3][3] =
{
{DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke)},
{DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke)},
{DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke)}
};
DenseMatrix<Number> Ke_en;
DenseSubMatrix<Number> Ke_var_en[3][3] =
{
{DenseSubMatrix<Number>(Ke_en), DenseSubMatrix<Number>(Ke_en), DenseSubMatrix<Number>(Ke_en)},
{DenseSubMatrix<Number>(Ke_en), DenseSubMatrix<Number>(Ke_en), DenseSubMatrix<Number>(Ke_en)},
{DenseSubMatrix<Number>(Ke_en), DenseSubMatrix<Number>(Ke_en), DenseSubMatrix<Number>(Ke_en)}
};
std::vector<dof_id_type> dof_indices;
std::vector< std::vector<dof_id_type> > dof_indices_var(3);
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);
for(unsigned int var=0; var<3; var++)
{
dof_map.dof_indices (elem, dof_indices_var[var], var);
}
const unsigned int n_dofs = dof_indices.size();
const unsigned int n_var_dofs = dof_indices_var[0].size();
fe->reinit (elem);
Re.resize (n_dofs);
for(unsigned int var=0; var<3; var++)
{
Re_var[var].reposition (var*n_var_dofs, n_var_dofs);
}
Ke.resize (n_dofs,n_dofs);
for(unsigned int var_i=0; var_i<3; var_i++)
for(unsigned int var_j=0; var_j<3; var_j++)
{
Ke_var[var_i][var_j].reposition (var_i*n_var_dofs, var_j*n_var_dofs, n_var_dofs, n_var_dofs);
}
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
DenseMatrix<Number> grad_u(3,3);
for(unsigned int var_i=0; var_i<3; var_i++)
{
for(unsigned int var_j=0; var_j<3; var_j++)
{
for (unsigned int j=0; j<n_var_dofs; j++)
{
// Row is variable u, v, or w column is x, y, or z
grad_u(var_i,var_j) += dphi[j][qp](var_j)*soln(dof_indices_var[var_i][j]);
}
}
}
// - C_ijkl u_k,l v_i,j
for (unsigned int dof_i=0; dof_i<n_var_dofs; dof_i++)
{
for(unsigned int i=0; i<3; i++)
for(unsigned int j=0; j<3; j++)
for(unsigned int k=0; k<3; k++)
for(unsigned int l=0; l<3; l++)
{
Re_var[i](dof_i) -= JxW[qp] *
elasticity_tensor(young_modulus,poisson_ratio,i,j,k,l) *
grad_u(k,l) * dphi[dof_i][qp](j);
}
}
if( (elem->subdomain_id() == TOP_SUBDOMAIN) )
{
// assemble \int_Omega f_i v_i \dx
DenseVector<Number> f_vec(3);
f_vec(0) = forcing_magnitude/10.;
f_vec(1) = 0.0;
f_vec(2) = -forcing_magnitude;
for (unsigned int dof_i=0; dof_i<n_var_dofs; dof_i++)
{
for(unsigned int i=0; i<3; i++)
{
Re_var[i](dof_i) += JxW[qp] *
( f_vec(i) * phi[dof_i][qp] );
}
}
}
// assemble \int_Omega C_ijkl u_k,l v_i,j \dx
for (unsigned int dof_i=0; dof_i<n_var_dofs; dof_i++)
for (unsigned int dof_j=0; dof_j<n_var_dofs; dof_j++)
{
for(unsigned int i=0; i<3; i++)
for(unsigned int j=0; j<3; j++)
for(unsigned int k=0; k<3; k++)
for(unsigned int l=0; l<3; l++)
{
Ke_var[i][k](dof_i,dof_j) -= JxW[qp] *
elasticity_tensor(young_modulus,poisson_ratio,i,j,k,l) *
dphi[dof_j][qp](l) *
dphi[dof_i][qp](j);
}
}
}
// Add contribution due to contact penalty forces
for (unsigned int side=0; side<elem->n_sides(); side++)
if (elem->neighbor(side) == NULL)
{
bool on_lower_contact_surface =
mesh.get_boundary_info().has_boundary_id
(elem, side, CONTACT_BOUNDARY_LOWER);
bool on_upper_contact_surface =
mesh.get_boundary_info().has_boundary_id
(elem, side, CONTACT_BOUNDARY_UPPER);
if( on_lower_contact_surface && on_upper_contact_surface )
{
libmesh_error_msg("Should not be on both surfaces at the same time");
}
if( on_lower_contact_surface || on_upper_contact_surface )
{
fe_face->reinit(elem, side);
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
bool contact_detected =
is_contact_detected(
elem->id(),
side,
qp);
if(contact_detected)
{
IntersectionPointData intersection_pt_data =
get_contact_data(
elem->id(),
side,
qp);
Point intersection_point = intersection_pt_data._intersection_point;
Point line_point = intersection_pt_data._line_point;
Point line_direction = intersection_pt_data._line_direction;
// signed_distance = (intersection_point - line_point) dot line_direction,
// hence we use this to get the contact force
Real contact_force =
get_contact_penalty() *
( (intersection_point - line_point) * line_direction );
for (unsigned int dof_i=0; dof_i<n_var_dofs; dof_i++)
{
for(unsigned int i=0; i<3; i++)
{
Re_var[i](dof_i) += JxW_face[qp] *
( contact_force * face_normals[qp](i) * phi_face[dof_i][qp] );
}
}
// Differentiate contact_force wrt solution coefficients to get
// the Jacobian entries.
//
// Note that intersection_point and line_point
// are linear functions of the solution.
//
// Also, line_direction is a function of the solution, but let's
// neglect that for now to make it easier to get the Jacobian.
// This is probably fine anyway, since this approximation will
// have negligible effect as we approach convergence.
// dofs local to this element, due to differentiating line_point
for (unsigned int dof_i=0; dof_i<n_var_dofs; dof_i++)
for (unsigned int dof_j=0; dof_j<n_var_dofs; dof_j++)
{
for(unsigned int i=0; i<3; i++)
for(unsigned int j=0; j<3; j++)
{
Ke_var[i][j](dof_i,dof_j) += JxW_face[qp] *
( get_contact_penalty() * (-phi_face[dof_j][qp] * line_direction(j)) *
face_normals[qp](i) * phi_face[dof_i][qp] );
}
}
// contribution due to dofs on the remote element, due to
// differentiating intersection_point
{
dof_id_type neighbor_elem_id = intersection_pt_data._neighbor_element_id;
const Elem* contact_neighbor = mesh.elem(neighbor_elem_id);
unsigned char neighbor_side_index = intersection_pt_data._neighbor_side_index;
std::vector<Point> inverse_intersection_point_vec;
inverse_intersection_point_vec.push_back(
intersection_pt_data._inverse_mapped_intersection_point);
fe_neighbor_face->reinit(
contact_neighbor,
neighbor_side_index,
TOLERANCE,
&inverse_intersection_point_vec);
std::vector<dof_id_type> neighbor_dof_indices;
std::vector< std::vector<unsigned int> > neighbor_dof_indices_var(3);
dof_map.dof_indices (contact_neighbor, neighbor_dof_indices);
for(unsigned int var=0; var<3; var++)
{
dof_map.dof_indices (contact_neighbor, neighbor_dof_indices_var[var], var);
}
const unsigned int n_neighbor_dofs = neighbor_dof_indices.size();
const unsigned int n_neighbor_var_dofs = neighbor_dof_indices_var[0].size();
Ke_en.resize (n_dofs,n_neighbor_dofs);
for(unsigned int var_i=0; var_i<3; var_i++)
for(unsigned int var_j=0; var_j<3; var_j++)
{
Ke_var_en[var_i][var_j].reposition(
var_i*n_var_dofs,
var_j*n_neighbor_var_dofs,
n_var_dofs,
n_neighbor_var_dofs);
}
for (unsigned int dof_i=0; dof_i<n_var_dofs; dof_i++)
for (unsigned int dof_j=0; dof_j<n_neighbor_var_dofs; dof_j++)
{
for(unsigned int i=0; i<3; i++)
for(unsigned int j=0; j<3; j++)
{
Ke_var_en[i][j](dof_i,dof_j) += JxW_face[qp] *
( get_contact_penalty() * (phi_neighbor_face[dof_j][0] * line_direction(j)) *
face_normals[qp](i) * phi_face[dof_i][qp] );
}
}
if(jacobian)
{
jacobian->add_matrix(Ke_en,dof_indices,neighbor_dof_indices);
}
}
}
}
}
}
dof_map.constrain_element_matrix_and_vector (Ke, Re, dof_indices);
if(jacobian)
{
jacobian->add_matrix (Ke, dof_indices);
}
if(residual)
{
residual->add_vector (Re, dof_indices);
}
}
}
void assemble_mass(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
// 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 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.
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
#else
// Avoid compiler warnings
libmesh_ignore(es);
#endif // LIBMESH_HAVE_SLEPC
}
// This function assembles the system matrix and right-hand-side
// for 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");
// 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();
// Copy the speed of sound and fluid density
// to a local variable.
const Real speed = es.parameters.get<Real>("speed");
const Real rho = es.parameters.get<Real>("fluid density");
// Get a reference to our system, as before.
NewmarkSystem & t_system = es.get_system<NewmarkSystem> (system_name);
// Get a constant reference to the Finite Element type
// for the first (and only) variable in the system.
FEType fe_type = t_system.get_dof_map().variable_type(0);
// In here, we will add the element matrices to the
// @e additional matrices "stiffness_mass" and "damping"
// and the additional vector "force", not to the members
// "matrix" and "rhs". Therefore, get writable
// references to them.
SparseMatrix<Number> & stiffness = t_system.get_matrix("stiffness");
SparseMatrix<Number> & damping = t_system.get_matrix("damping");
SparseMatrix<Number> & mass = t_system.get_matrix("mass");
NumericVector<Number> & force = t_system.get_vector("force");
// 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 = *t_system.matrix;
DenseMatrix<Number> zero_matrix;
// 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 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);
// 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 = t_system.get_dof_map();
// The element mass, damping and stiffness matrices
// and the element contribution to the rhs.
DenseMatrix<Number> Ke, Ce, 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);
// 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 and rhs 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 HEX8
// and now have a PRISM6).
{
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);
}
// 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]);
Me(i,j) += JxW[qp]*phi[i][qp]*phi[j][qp]
*1./(speed*speed);
} // end of the matrix summation loop
} // end of quadrature point loop
// Now compute the contribution to the element matrix and the
// right-hand-side vector if the current element lies on the
// boundary.
{
// In this example no natural boundary conditions will
// be considered. The code is left here so it can easily
// be extended.
//
// don't do this for any side
for (unsigned int side=0; side<elem->n_sides(); side++)
if (!true)
// if (elem->neighbor(side) == libmesh_nullptr)
{
// 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);
// Here we consider a normal acceleration acc_n=1 applied to
// the whole boundary of our mesh.
const Real acc_n_value = 1.0;
// Loop over the face quadrature points for integration.
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
// Right-hand-side contribution due to prescribed
// normal acceleration.
for (unsigned int i=0; i<phi_face.size(); i++)
{
Fe(i) += acc_n_value*rho
*phi_face[i][qp]*JxW_face[qp];
}
} // end face quadrature point loop
} // end if (elem->neighbor(side) == libmesh_nullptr)
// In this example the Dirichlet boundary conditions will be
// imposed via panalty method after the
// system is assembled.
} // 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
// 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_and_vector (Ke, Fe, 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);
force.add_vector (Fe, 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);
} // end of element loop
}
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();
}
// This function defines the assembly routine which
// will be called at each time step. It is responsible
// for computing the proper matrix entries for the
// element stiffness matrices and right-hand sides.
void assemble_cd (EquationSystems & es,
const std::string & system_name)
{
#ifdef LIBMESH_ENABLE_AMR
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "Convection-Diffusion");
// 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.
TransientLinearImplicitSystem & system =
es.get_system<TransientLinearImplicitSystem> ("Convection-Diffusion");
// Get the Finite Element type for the first (and only)
// variable in the system.
FEType fe_type = 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 UniquePtr<FEBase>. This can be thought
// of as a pointer that will clean up after itself.
UniquePtr<FEBase> fe (FEBase::build(dim, fe_type));
UniquePtr<FEBase> fe_face (FEBase::build(dim, fe_type));
// A Gauss quadrature rule for numerical integration.
// Let the \p FEType object decide what order rule is appropriate.
QGauss qrule (dim, fe_type.default_quadrature_order());
QGauss qface (dim-1, fe_type.default_quadrature_order());
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (&qrule);
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 will start
// with the element Jacobian * quadrature weight at each integration point.
const std::vector<Real> & JxW = fe->get_JxW();
const std::vector<Real> & JxW_face = fe_face->get_JxW();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> > & phi = fe->get_phi();
const std::vector<std::vector<Real> > & psi = fe_face->get_phi();
// The element shape function gradients evaluated at the quadrature
// points.
const std::vector<std::vector<RealGradient> > & dphi = fe->get_dphi();
// The XY locations of the quadrature points used for face integration
const std::vector<Point> & qface_points = fe_face->get_xyz();
// 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;
// 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;
// Here we extract the velocity & parameters that we put in the
// EquationSystems object.
const RealVectorValue velocity =
es.parameters.get<RealVectorValue> ("velocity");
const Real diffusivity =
es.parameters.get<Real> ("diffusivity");
const Real dt = es.parameters.get<Real> ("dt");
// 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 \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 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());
// 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 myst 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 old solution & its gradient.
Number u_old = 0.;
Gradient grad_u_old;
// Compute the old solution & its gradient.
for (unsigned int l=0; l<phi.size(); l++)
{
u_old += phi[l][qp]*system.old_solution (dof_indices[l]);
// This will work,
// grad_u_old += dphi[l][qp]*system.old_solution (dof_indices[l]);
// but we can do it without creating a temporary like this:
grad_u_old.add_scaled (dphi[l][qp], system.old_solution (dof_indices[l]));
}
// Now compute the element matrix and RHS contributions.
for (unsigned int i=0; i<phi.size(); i++)
{
// The RHS contribution
Fe(i) += JxW[qp]*(
// Mass matrix term
u_old*phi[i][qp] +
-.5*dt*(
// Convection term
// (grad_u_old may be complex, so the
// order here is important!)
(grad_u_old*velocity)*phi[i][qp] +
// Diffusion term
diffusivity*(grad_u_old*dphi[i][qp]))
);
for (unsigned int j=0; j<phi.size(); j++)
{
// The matrix contribution
Ke(i,j) += JxW[qp]*(
// Mass-matrix
phi[i][qp]*phi[j][qp] +
.5*dt*(
// Convection term
(velocity*dphi[j][qp])*phi[i][qp] +
// Diffusion term
diffusivity*(dphi[i][qp]*dphi[j][qp]))
);
}
}
}
// 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 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.
{
// The penalty value.
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) == NULL)
{
fe_face->reinit(elem, s);
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
const Number value = exact_solution (qface_points[qp](0),
qface_points[qp](1),
system.time);
// RHS contribution
for (unsigned int i=0; i<psi.size(); i++)
Fe(i) += penalty*JxW_face[qp]*value*psi[i][qp];
// Matrix contribution
for (unsigned int i=0; i<psi.size(); i++)
for (unsigned int j=0; j<psi.size(); j++)
Ke(i,j) += penalty*JxW_face[qp]*psi[i][qp]*psi[j][qp];
}
}
}
// We have now built the element matrix and RHS vector in terms
// of the element degrees of freedom. However, it is possible
// that some of the element DOFs are constrained to enforce
// solution continuity, i.e. they are not really "free". We need
// to constrain those DOFs in terms of non-constrained DOFs to
// ensure a continuous solution. The
// \p DofMap::constrain_element_matrix_and_vector() method does
// just that.
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 SparseMatrix::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);
}
// Finished computing the sytem matrix and right-hand side.
#endif // #ifdef LIBMESH_ENABLE_AMR
}
void LinearElasticityWithContact::residual_and_jacobian (const NumericVector<Number> & soln,
NumericVector<Number> * residual,
SparseMatrix<Number> * jacobian,
NonlinearImplicitSystem & /*sys*/)
{
EquationSystems & es = _sys.get_equation_systems();
const Real young_modulus = es.parameters.get<Real>("young_modulus");
const Real poisson_ratio = es.parameters.get<Real>("poisson_ratio");
const MeshBase & mesh = _sys.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
const unsigned int u_var = _sys.variable_number ("u");
DofMap & dof_map = _sys.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);
UniquePtr<FEBase> fe_face (FEBase::build(dim, fe_type));
QGauss qface (dim-1, fe_type.default_quadrature_order());
fe_face->attach_quadrature_rule (&qface);
UniquePtr<FEBase> fe_neighbor_face (FEBase::build(dim, fe_type));
fe_neighbor_face->attach_quadrature_rule (&qface);
const std::vector<Real> & JxW = fe->get_JxW();
const std::vector<std::vector<RealGradient> > & dphi = fe->get_dphi();
if (jacobian)
jacobian->zero();
if (residual)
residual->zero();
// Do jacobian and residual assembly, including contact forces
DenseVector<Number> Re;
DenseSubVector<Number> Re_var[3] =
{DenseSubVector<Number>(Re),
DenseSubVector<Number>(Re),
DenseSubVector<Number>(Re)};
DenseMatrix<Number> Ke;
DenseSubMatrix<Number> Ke_var[3][3] =
{
{DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke)},
{DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke)},
{DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke), DenseSubMatrix<Number>(Ke)}
};
std::vector<dof_id_type> dof_indices;
std::vector< std::vector<dof_id_type> > dof_indices_var(3);
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);
for (unsigned int var=0; var<3; var++)
dof_map.dof_indices (elem, dof_indices_var[var], var);
const unsigned int n_dofs = dof_indices.size();
const unsigned int n_var_dofs = dof_indices_var[0].size();
fe->reinit (elem);
Re.resize (n_dofs);
for (unsigned int var=0; var<3; var++)
Re_var[var].reposition (var*n_var_dofs, n_var_dofs);
Ke.resize (n_dofs, n_dofs);
for (unsigned int var_i=0; var_i<3; var_i++)
for (unsigned int var_j=0; var_j<3; var_j++)
Ke_var[var_i][var_j].reposition (var_i*n_var_dofs, var_j*n_var_dofs, n_var_dofs, n_var_dofs);
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
// Row is variable u, v, or w column is x, y, or z
DenseMatrix<Number> grad_u(3, 3);
for (unsigned int var_i=0; var_i<3; var_i++)
for (unsigned int var_j=0; var_j<3; var_j++)
for (unsigned int j=0; j<n_var_dofs; j++)
grad_u(var_i, var_j) += dphi[j][qp](var_j)*soln(dof_indices_var[var_i][j]);
// - C_ijkl u_k,l v_i,j
for (unsigned int dof_i=0; dof_i<n_var_dofs; dof_i++)
for (unsigned int i=0; i<3; i++)
for (unsigned int j=0; j<3; j++)
for (unsigned int k=0; k<3; k++)
for (unsigned int l=0; l<3; l++)
Re_var[i](dof_i) -= JxW[qp] *
elasticity_tensor(young_modulus, poisson_ratio, i, j, k, l) * grad_u(k,l) * dphi[dof_i][qp](j);
// assemble \int_Omega C_ijkl u_k,l v_i,j \dx
for (unsigned int dof_i=0; dof_i<n_var_dofs; dof_i++)
for (unsigned int dof_j=0; dof_j<n_var_dofs; dof_j++)
for (unsigned int i=0; i<3; i++)
for (unsigned int j=0; j<3; j++)
for (unsigned int k=0; k<3; k++)
for (unsigned int l=0; l<3; l++)
Ke_var[i][k](dof_i, dof_j) -= JxW[qp] *
elasticity_tensor(young_modulus, poisson_ratio, i, j, k, l) * dphi[dof_j][qp](l) * dphi[dof_i][qp](j);
}
dof_map.constrain_element_matrix_and_vector (Ke, Re, dof_indices);
if (jacobian)
jacobian->add_matrix (Ke, dof_indices);
if (residual)
residual->add_vector (Re, dof_indices);
}
// Move a copy of the mesh based on the solution. This is used to get
// the contact forces.
UniquePtr<MeshBase> mesh_clone = mesh.clone();
move_mesh(*mesh_clone, soln);
// Add contributions due to contact penalty forces. Only need to do this on
// one processor.
_lambda_plus_penalty_values.clear();
LIBMESH_BEST_UNORDERED_MAP<dof_id_type, dof_id_type>::iterator it =
_augment_sparsity._contact_node_map.begin();
LIBMESH_BEST_UNORDERED_MAP<dof_id_type, dof_id_type>::iterator it_end =
_augment_sparsity._contact_node_map.end();
for ( ; it != it_end; ++it)
{
dof_id_type lower_point_id = it->first;
dof_id_type upper_point_id = it->second;
Point upper_to_lower;
{
Point lower_node_moved = mesh_clone->point(lower_point_id);
Point upper_node_moved = mesh_clone->point(upper_point_id);
upper_to_lower = (lower_node_moved - upper_node_moved);
}
// Set the contact force direction. Usually this would be calculated
// separately on each master node, but here we just set it to (0, 0, 1)
// everywhere.
Point contact_force_direction(0., 0., 1.);
// gap_function > 0. means that contact has been detected
// gap_function < 0. means that we have a gap
// This sign convention matches Simo & Laursen (1992).
Real gap_function = upper_to_lower * contact_force_direction;
// We use the sign of lambda_plus_penalty to determine whether or
// not we need to impose a contact force.
Real lambda_plus_penalty =
(_lambdas[upper_point_id] + gap_function * _contact_penalty);
if (lambda_plus_penalty < 0.)
lambda_plus_penalty = 0.;
// Store lambda_plus_penalty, we'll need to use it later to update _lambdas
_lambda_plus_penalty_values[upper_point_id] = lambda_plus_penalty;
const Node & lower_node = mesh.node_ref(lower_point_id);
const Node & upper_node = mesh.node_ref(upper_point_id);
std::vector<dof_id_type> dof_indices_on_lower_node(3);
std::vector<dof_id_type> dof_indices_on_upper_node(3);
DenseVector<Number> lower_contact_force_vec(3);
DenseVector<Number> upper_contact_force_vec(3);
for (unsigned int var=0; var<3; var++)
{
dof_indices_on_lower_node[var] = lower_node.dof_number(_sys.number(), var, 0);
lower_contact_force_vec(var) = -lambda_plus_penalty * contact_force_direction(var);
dof_indices_on_upper_node[var] = upper_node.dof_number(_sys.number(), var, 0);
upper_contact_force_vec(var) = lambda_plus_penalty * contact_force_direction(var);
}
if (lambda_plus_penalty > 0.)
{
if (residual && (_sys.comm().rank() == 0))
{
residual->add_vector (lower_contact_force_vec, dof_indices_on_lower_node);
residual->add_vector (upper_contact_force_vec, dof_indices_on_upper_node);
}
// Add the Jacobian terms due to the contact forces. The lambda contribution
// is not relevant here because it doesn't depend on the solution.
if (jacobian && (_sys.comm().rank() == 0))
for (unsigned int var=0; var<3; var++)
for (unsigned int j=0; j<3; j++)
{
jacobian->add(dof_indices_on_lower_node[var],
dof_indices_on_upper_node[j],
_contact_penalty * contact_force_direction(j) * contact_force_direction(var));
jacobian->add(dof_indices_on_lower_node[var],
dof_indices_on_lower_node[j],
-_contact_penalty * contact_force_direction(j) * contact_force_direction(var));
jacobian->add(dof_indices_on_upper_node[var],
dof_indices_on_lower_node[j],
_contact_penalty * contact_force_direction(j) * contact_force_direction(var));
jacobian->add(dof_indices_on_upper_node[var],
dof_indices_on_upper_node[j],
-_contact_penalty * contact_force_direction(j) * contact_force_direction(var));
}
}
else
{
// We add zeros to the matrix even when lambda_plus_penalty = 0.
// We do this because some linear algebra libraries (e.g. PETSc)
// will condense out any unused entries from the sparsity pattern,
// so adding these zeros in ensures that these entries are not
// condensed out.
if (jacobian && (_sys.comm().rank() == 0))
for (unsigned int var=0; var<3; var++)
for (unsigned int j=0; j<3; j++)
{
jacobian->add(dof_indices_on_lower_node[var],
dof_indices_on_upper_node[j],
0.);
jacobian->add(dof_indices_on_lower_node[var],
dof_indices_on_lower_node[j],
0.);
jacobian->add(dof_indices_on_upper_node[var],
dof_indices_on_lower_node[j],
0.);
jacobian->add(dof_indices_on_upper_node[var],
dof_indices_on_upper_node[j],
0.);
}
}
}
}
void Biharmonic::JR::residual_and_jacobian(const NumericVector<Number> & u,
NumericVector<Number> * R,
SparseMatrix<Number> * J,
NonlinearImplicitSystem &)
{
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
if (!R && !J)
return;
// 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 ("Biharmonic Residual and Jacobian", false);
// 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 = 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 a UniquePtr<FEBase>. This can be thought
// of as a pointer that will clean up after itself.
UniquePtr<FEBase> fe (FEBase::build(_biharmonic._dim, fe_type));
// Quadrature rule for numerical integration.
// With 2D triangles, the Clough quadrature rule puts a Gaussian
// quadrature rule on each of the 3 subelements
UniquePtr<QBase> qrule(fe_type.default_quadrature_rule(_biharmonic._dim));
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (qrule.get());
// Here we define some references to element-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 element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> > & phi = fe->get_phi();
// The element shape functions' derivatives evaluated at the quadrature points.
const std::vector<std::vector<RealGradient> > & dphi = fe->get_dphi();
// The element shape functions' second derivatives evaluated at the quadrature points.
const std::vector<std::vector<RealTensor> > & d2phi = fe->get_d2phi();
// For efficiency we will compute shape function laplacians n times,
// not n^2
std::vector<Real> Laplacian_phi_qp;
// Define data structures to contain the element matrix
// and right-hand-side vector contribution. Following
// basic finite element terminology we will denote these
// "Je" and "Re". More detail is in example 3.
DenseMatrix<Number> Je;
DenseVector<Number> Re;
// 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;
// Old solution
const NumericVector<Number> & u_old = *old_local_solution;
// 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 = _biharmonic._mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end_el = _biharmonic._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 function
// values/derivatives (phi, dphi, d2phi) for the current element.
fe->reinit (elem);
// Zero the element matrix, the right-hand side and the Laplacian matrix
// before summing them.
if (J)
Je.resize(dof_indices.size(), dof_indices.size());
if (R)
Re.resize(dof_indices.size());
Laplacian_phi_qp.resize(dof_indices.size());
for (unsigned int qp=0; qp<qrule->n_points(); qp++)
{
// AUXILIARY QUANTITIES:
// Residual and Jacobian share a few calculations:
// at the very least, in the case of interfacial energy only with a constant mobility,
// both calculations use Laplacian_phi_qp; more is shared the case of a concentration-dependent
// mobility and bulk potentials.
Number
u_qp = 0.0,
u_old_qp = 0.0,
Laplacian_u_qp = 0.0,
Laplacian_u_old_qp = 0.0;
Gradient
grad_u_qp(0.0, 0.0, 0.0),
grad_u_old_qp(0.0, 0.0, 0.0);
Number
M_qp = 1.0,
M_old_qp = 1.0,
M_prime_qp = 0.0,
M_prime_old_qp = 0.0;
for (unsigned int i=0; i<phi.size(); i++)
{
Laplacian_phi_qp[i] = d2phi[i][qp](0, 0);
grad_u_qp(0) += u(dof_indices[i])*dphi[i][qp](0);
grad_u_old_qp(0) += u_old(dof_indices[i])*dphi[i][qp](0);
if (_biharmonic._dim > 1)
{
Laplacian_phi_qp[i] += d2phi[i][qp](1, 1);
grad_u_qp(1) += u(dof_indices[i])*dphi[i][qp](1);
grad_u_old_qp(1) += u_old(dof_indices[i])*dphi[i][qp](1);
}
if (_biharmonic._dim > 2)
{
Laplacian_phi_qp[i] += d2phi[i][qp](2, 2);
grad_u_qp(2) += u(dof_indices[i])*dphi[i][qp](2);
grad_u_old_qp(2) += u_old(dof_indices[i])*dphi[i][qp](2);
}
u_qp += phi[i][qp]*u(dof_indices[i]);
u_old_qp += phi[i][qp]*u_old(dof_indices[i]);
Laplacian_u_qp += Laplacian_phi_qp[i]*u(dof_indices[i]);
Laplacian_u_old_qp += Laplacian_phi_qp[i]*u_old(dof_indices[i]);
} // for i
if (_biharmonic._degenerate)
{
M_qp = 1.0 - u_qp*u_qp;
M_old_qp = 1.0 - u_old_qp*u_old_qp;
M_prime_qp = -2.0*u_qp;
M_prime_old_qp = -2.0*u_old_qp;
}
// ELEMENT RESIDUAL AND JACOBIAN
for (unsigned int i=0; i<phi.size(); i++)
{
// RESIDUAL
if (R)
{
Number ri = 0.0, ri_old = 0.0;
ri -= Laplacian_phi_qp[i]*M_qp*_biharmonic._kappa*Laplacian_u_qp;
ri_old -= Laplacian_phi_qp[i]*M_old_qp*_biharmonic._kappa*Laplacian_u_old_qp;
if (_biharmonic._degenerate)
{
ri -= (dphi[i][qp]*grad_u_qp)*M_prime_qp*(_biharmonic._kappa*Laplacian_u_qp);
ri_old -= (dphi[i][qp]*grad_u_old_qp)*M_prime_old_qp*(_biharmonic._kappa*Laplacian_u_old_qp);
}
if (_biharmonic._cahn_hillard)
{
if (_biharmonic._energy == DOUBLE_WELL || _biharmonic._energy == LOG_DOUBLE_WELL)
{
ri += Laplacian_phi_qp[i]*M_qp*_biharmonic._theta_c*(u_qp*u_qp - 1.0)*u_qp;
ri_old += Laplacian_phi_qp[i]*M_old_qp*_biharmonic._theta_c*(u_old_qp*u_old_qp - 1.0)*u_old_qp;
if (_biharmonic._degenerate)
{
ri += (dphi[i][qp]*grad_u_qp)*M_prime_qp*_biharmonic._theta_c*(u_qp*u_qp - 1.0)*u_qp;
ri_old += (dphi[i][qp]*grad_u_old_qp)*M_prime_old_qp*_biharmonic._theta_c*(u_old_qp*u_old_qp - 1.0)*u_old_qp;
}
}// if (_biharmonic._energy == DOUBLE_WELL || _biharmonic._energy == LOG_DOUBLE_WELL)
if (_biharmonic._energy == DOUBLE_OBSTACLE || _biharmonic._energy == LOG_DOUBLE_OBSTACLE)
{
ri -= Laplacian_phi_qp[i]*M_qp*_biharmonic._theta_c*u_qp;
ri_old -= Laplacian_phi_qp[i]*M_old_qp*_biharmonic._theta_c*u_old_qp;
if (_biharmonic._degenerate)
{
ri -= (dphi[i][qp]*grad_u_qp)*M_prime_qp*_biharmonic._theta_c*u_qp;
ri_old -= (dphi[i][qp]*grad_u_old_qp)*M_prime_old_qp*_biharmonic._theta_c*u_old_qp;
}
} // if (_biharmonic._energy == DOUBLE_OBSTACLE || _biharmonic._energy == LOG_DOUBLE_OBSTACLE)
if (_biharmonic._energy == LOG_DOUBLE_WELL || _biharmonic._energy == LOG_DOUBLE_OBSTACLE)
{
switch(_biharmonic._log_truncation)
{
case 2:
break;
case 3:
break;
default:
break;
}// switch(_biharmonic._log_truncation)
}// if (_biharmonic._energy == LOG_DOUBLE_WELL || _biharmonic._energy == LOG_DOUBLE_OBSTACLE)
}// if (_biharmonic._cahn_hillard)
Re(i) += JxW[qp]*((u_qp-u_old_qp)*phi[i][qp]-_biharmonic._dt*0.5*((2.0-_biharmonic._cnWeight)*ri + _biharmonic._cnWeight*ri_old));
} // if (R)
// JACOBIAN
if (J)
{
Number M_prime_prime_qp = 0.0;
if (_biharmonic._degenerate) M_prime_prime_qp = -2.0;
for (unsigned int j=0; j<phi.size(); j++)
{
Number ri_j = 0.0;
ri_j -= Laplacian_phi_qp[i]*M_qp*_biharmonic._kappa*Laplacian_phi_qp[j];
if (_biharmonic._degenerate)
{
ri_j -=
Laplacian_phi_qp[i]*M_prime_qp*phi[j][qp]*_biharmonic._kappa*Laplacian_u_qp +
(dphi[i][qp]*dphi[j][qp])*M_prime_qp*(_biharmonic._kappa*Laplacian_u_qp) +
(dphi[i][qp]*grad_u_qp)*(M_prime_prime_qp*phi[j][qp])*(_biharmonic._kappa*Laplacian_u_qp) +
(dphi[i][qp]*grad_u_qp)*(M_prime_qp)*(_biharmonic._kappa*Laplacian_phi_qp[j]);
}
if (_biharmonic._cahn_hillard)
{
if (_biharmonic._energy == DOUBLE_WELL || _biharmonic._energy == LOG_DOUBLE_WELL)
{
ri_j +=
Laplacian_phi_qp[i]*M_prime_qp*phi[j][qp]*_biharmonic._theta_c*(u_qp*u_qp - 1.0)*u_qp +
Laplacian_phi_qp[i]*M_qp*_biharmonic._theta_c*(3.0*u_qp*u_qp - 1.0)*phi[j][qp] +
(dphi[i][qp]*dphi[j][qp])*M_prime_qp*_biharmonic._theta_c*(u_qp*u_qp - 1.0)*u_qp +
(dphi[i][qp]*grad_u_qp)*M_prime_prime_qp*_biharmonic._theta_c*(u_qp*u_qp - 1.0)*u_qp +
(dphi[i][qp]*grad_u_qp)*M_prime_qp*_biharmonic._theta_c*(3.0*u_qp*u_qp - 1.0)*phi[j][qp];
}// if (_biharmonic._energy == DOUBLE_WELL || _biharmonic._energy == LOG_DOUBLE_WELL)
if (_biharmonic._energy == DOUBLE_OBSTACLE || _biharmonic._energy == LOG_DOUBLE_OBSTACLE)
{
ri_j -=
Laplacian_phi_qp[i]*M_prime_qp*phi[j][qp]*_biharmonic._theta_c*u_qp +
Laplacian_phi_qp[i]*M_qp*_biharmonic._theta_c*phi[j][qp] +
(dphi[i][qp]*dphi[j][qp])*M_prime_qp*_biharmonic._theta_c*u_qp +
(dphi[i][qp]*grad_u_qp)*M_prime_prime_qp*_biharmonic._theta_c*u_qp +
(dphi[i][qp]*grad_u_qp)*M_prime_qp*_biharmonic._theta_c*phi[j][qp];
} // if (_biharmonic._energy == DOUBLE_OBSTACLE || _biharmonic._energy == LOG_DOUBLE_OBSTACLE)
if (_biharmonic._energy == LOG_DOUBLE_WELL || _biharmonic._energy == LOG_DOUBLE_OBSTACLE)
{
switch(_biharmonic._log_truncation)
{
case 2:
break;
case 3:
break;
default:
break;
}// switch(_biharmonic._log_truncation)
}// if (_biharmonic._energy == LOG_DOUBLE_WELL || _biharmonic._energy == LOG_DOUBLE_OBSTACLE)
}// if (_biharmonic._cahn_hillard)
Je(i,j) += JxW[qp]*(phi[i][qp]*phi[j][qp] - 0.5*_biharmonic._dt*(2.0-_biharmonic._cnWeight)*ri_j);
} // for j
} // if (J)
} // for i
} // for qp
// 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.
// Start logging the insertion of the local (element)
// matrix and vector into the global matrix and vector
if (R)
{
// If the mesh has hanging nodes (e.g., as a result of refinement), those need to be constrained.
dof_map.constrain_element_vector(Re, dof_indices);
R->add_vector(Re, dof_indices);
}
if (J)
{
// If the mesh has hanging nodes (e.g., as a result of refinement), those need to be constrained.
dof_map.constrain_element_matrix(Je, dof_indices);
J->add_matrix(Je, dof_indices);
}
} // for el
#endif // LIBMESH_ENABLE_SECOND_DERIVATIVES
}
// 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 AssembleOptimization::assemble_A_and_F()
{
A_matrix->zero();
F_vector->zero();
const MeshBase & mesh = _sys.get_mesh();
const unsigned int dim = mesh.mesh_dimension();
const unsigned int u_var = _sys.variable_number ("u");
const DofMap & dof_map = _sys.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<Real> > & phi = fe->get_phi();
const std::vector<std::vector<RealGradient> > & dphi = fe->get_dphi();
std::vector<dof_id_type> dof_indices;
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
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);
const unsigned int n_dofs = dof_indices.size();
fe->reinit (elem);
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
for (unsigned int dof_i=0; dof_i<n_dofs; dof_i++)
{
for (unsigned int dof_j=0; dof_j<n_dofs; dof_j++)
{
Ke(dof_i, dof_j) += JxW[qp] * (dphi[dof_j][qp]* dphi[dof_i][qp]);
}
Fe(dof_i) += JxW[qp] * phi[dof_i][qp];
}
}
// This will zero off-diagonal entries of Ke corresponding to
// Dirichlet dofs.
dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
// We want the diagonal of constrained dofs to be zero too
for (unsigned int local_dof_index=0; local_dof_index<n_dofs; local_dof_index++)
{
dof_id_type global_dof_index = dof_indices[local_dof_index];
if (dof_map.is_constrained_dof(global_dof_index))
{
Ke(local_dof_index, local_dof_index) = 0.;
}
}
A_matrix->add_matrix (Ke, dof_indices);
F_vector->add_vector (Fe, dof_indices);
}
A_matrix->close();
F_vector->close();
}
// 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!
}
// This function defines the assembly routine. It is responsible for
// computing the proper matrix entries for the element stiffness
// matrices and right-hand sides.
void assemble (EquationSystems & es,
const std::string & system_name)
{
#ifdef LIBMESH_ENABLE_AMR
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "System");
// 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> ("System");
// Get the Finite Element type for the first (and only)
// variable in the system.
FEType fe_type = system.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 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));
UniquePtr<FEBase> fe_face (FEBase::build(dim, fe_type));
// A Gauss quadrature rule for numerical integration.
// Let the FEType object decide what order rule is appropriate.
QGauss qrule (dim, fe_type.default_quadrature_order());
QGauss qface (dim-1, fe_type.default_quadrature_order());
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (&qrule);
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 will start
// with the element Jacobian * quadrature weight at each integration point.
const std::vector<Real> & JxW = fe->get_JxW();
const std::vector<Real> & JxW_face = fe_face->get_JxW();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> > & phi = fe->get_phi();
const std::vector<std::vector<Real> > & psi = fe_face->get_phi();
// The element shape function gradients evaluated at the quadrature
// points.
const std::vector<std::vector<RealGradient> > & dphi = fe->get_dphi();
// The XY locations of the quadrature points used for face integration
//const std::vector<Point>& qface_points = fe_face->get_xyz();
// 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();
// 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;
// Analogous data structures for thw two vectors v and w that form
// the tensor shell matrix.
DenseVector<Number> Ve;
DenseVector<Number> We;
// 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. 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);
// 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());
Ve.resize (dof_indices.size());
We.resize (dof_indices.size());
// 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 myst 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++)
{
// Now compute the element matrix and RHS contributions.
for (unsigned int i=0; i<phi.size(); i++)
{
// The RHS contribution
Fe(i) += JxW[qp]*phi[i][qp];
for (unsigned int j=0; j<phi.size(); j++)
{
// The matrix contribution
Ke(i,j) += JxW[qp]*(
// Stiffness matrix
(dphi[i][qp]*dphi[j][qp])
);
}
// V and W are the same for this example.
Ve(i) += JxW[qp]*phi[i][qp];
We(i) += JxW[qp]*phi[i][qp];
}
}
// 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 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.
{
// The penalty value.
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)
{
fe_face->reinit(elem, s);
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
// Matrix contribution
for (unsigned int i=0; i<psi.size(); i++)
for (unsigned int j=0; j<psi.size(); j++)
Ke(i,j) += penalty*JxW_face[qp]*psi[i][qp]*psi[j][qp];
}
}
}
// We have now built the element matrix and RHS vector in terms
// of the element degrees of freedom. However, it is possible
// that some of the element DOFs are constrained to enforce
// solution continuity, i.e. they are not really "free". We need
// to constrain those DOFs in terms of non-constrained DOFs to
// ensure a continuous solution. The
// DofMap::constrain_element_matrix_and_vector() method does
// just that.
// However, constraining both the sparse matrix (and right hand
// side) plus the rank 1 matrix is tricky. The dof_indices
// vector has to be backuped for that because the constraining
// functions modify it.
std::vector<dof_id_type> dof_indices_backup(dof_indices);
dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
dof_indices = dof_indices_backup;
dof_map.constrain_element_dyad_matrix(Ve, We, 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.get_matrix("Preconditioner").add_matrix (Ke, dof_indices);
system.rhs->add_vector (Fe, dof_indices);
system.get_vector("v").add_vector(Ve, dof_indices);
system.get_vector("w").add_vector(We, dof_indices);
}
// Finished computing the sytem matrix and right-hand side.
// Matrices and vectors must be closed manually. This is necessary
// because the matrix is not directly used as the system matrix (in
// which case the solver closes it) but as a part of a shell matrix.
system.matrix->close();
system.get_matrix("Preconditioner").close();
system.rhs->close();
system.get_vector("v").close();
system.get_vector("w").close();
#endif // #ifdef LIBMESH_ENABLE_AMR
}