std::pair<Real, Real> Tri3::min_and_max_angle() const
{
Point v10 ( this->point(1) - this->point(0) );
Point v20 ( this->point(2) - this->point(0) );
Point v21 ( this->point(2) - this->point(1) );
const Real
len_10=v10.size(),
len_20=v20.size(),
len_21=v21.size()
;
const Real
theta0=std::acos(( v10*v20)/len_10/len_20),
theta1=std::acos((-v10*v21)/len_10/len_21),
theta2=libMesh::pi - theta0 - theta1
;
libmesh_assert_greater (theta0, 0.);
libmesh_assert_greater (theta1, 0.);
libmesh_assert_greater (theta2, 0.);
return std::make_pair(std::min(theta0, std::min(theta1,theta2)),
std::max(theta0, std::max(theta1,theta2)));
}
void QBase::scale(std::pair<Real, Real> old_range,
std::pair<Real, Real> new_range)
{
// Make sure we are in 1D
libmesh_assert_equal_to (_dim, 1);
Real
h_new = new_range.second - new_range.first,
h_old = old_range.second - old_range.first;
// Make sure that we have sane ranges
libmesh_assert_greater (h_new, 0.);
libmesh_assert_greater (h_old, 0.);
// Make sure there are some points
libmesh_assert_greater (_points.size(), 0);
// Compute the scale factor
Real scfact = h_new/h_old;
// We're mapping from old_range -> new_range
for (unsigned int i=0; i<_points.size(); i++)
{
_points[i](0) = new_range.first +
(_points[i](0) - old_range.first) * scfact;
// Scale the weights
_weights[i] *= scfact;
}
}
void QBase::scale(std::pair<Real, Real> old_range,
std::pair<Real, Real> new_range)
{
// Make sure we are in 1D
libmesh_assert_equal_to (_dim, 1);
// Make sure that we have sane ranges
libmesh_assert_greater (new_range.second, new_range.first);
libmesh_assert_greater (old_range.second, old_range.first);
// Make sure there are some points
libmesh_assert_greater (_points.size(), 0);
// We're mapping from old_range -> new_range
for (unsigned int i=0; i<_points.size(); i++)
{
_points[i](0) =
(_points[i](0) - old_range.first) *
(new_range.second - new_range.first) /
(old_range.second - old_range.first) +
new_range.first;
}
// Compute the scale factor and scale the weights
const Real scfact = (new_range.second - new_range.first) /
(old_range.second - old_range.first);
for (unsigned int i=0; i<_points.size(); i++)
_weights[i] *= scfact;
}
Real Sphere::distance (const Sphere & other_sphere) const
{
libmesh_assert_greater ( this->radius(), 0. );
libmesh_assert_greater ( other_sphere.radius(), 0. );
const Real the_distance = (this->center() - other_sphere.center()).norm();
return the_distance - (this->radius() + other_sphere.radius());
}
void
MAST::Examples::ThermalJacobianScaling::set_acceleration_factor(Real f) {
libmesh_assert_greater(f, 0.);
_accel_factor = f;
}
void SubdomainPartitioner::_do_partition (MeshBase & mesh,
const unsigned int n)
{
libmesh_assert_greater (n, 0);
// Check for an easy return. If the user has not specified any
// entries in the chunks vector, we just do a single partitioning.
if ((n == 1) || chunks.empty())
{
this->single_partition (mesh);
return;
}
// Now actually do the partitioning.
LOG_SCOPE ("_do_partition()", "SubdomainPartitioner");
// For each chunk, construct an iterator range for the set of
// subdomains in question, and pass it to the internal Partitioner.
for (std::size_t c=0; c<chunks.size(); ++c)
{
MeshBase::element_iterator
it = mesh.active_subdomain_set_elements_begin(chunks[c]),
end = mesh.active_subdomain_set_elements_end(chunks[c]);
_internal_partitioner->partition_range(mesh, it, end, n);
}
}
void MeshRefinement::flag_elements_by_error_tolerance (const ErrorVector & error_per_cell_in)
{
parallel_object_only();
libmesh_assert_greater (_coarsen_threshold, 0);
// Check for valid fractions..
// The fraction values must be in [0,1]
libmesh_assert_greater_equal (_refine_fraction, 0);
libmesh_assert_less_equal (_refine_fraction, 1);
libmesh_assert_greater_equal (_coarsen_fraction, 0);
libmesh_assert_less_equal (_coarsen_fraction, 1);
// How much error per cell will we tolerate?
const Real local_refinement_tolerance =
_absolute_global_tolerance / std::sqrt(static_cast<Real>(_mesh.n_active_elem()));
const Real local_coarsening_tolerance =
local_refinement_tolerance * _coarsen_threshold;
// Prepare another error vector if we need to sum parent errors
ErrorVector error_per_parent;
if (_coarsen_by_parents)
{
Real parent_error_min, parent_error_max;
create_parent_error_vector(error_per_cell_in,
error_per_parent,
parent_error_min,
parent_error_max);
}
for (auto & elem : _mesh.active_element_ptr_range())
{
Elem * parent = elem->parent();
const dof_id_type elem_number = elem->id();
const ErrorVectorReal elem_error = error_per_cell_in[elem_number];
if (elem_error > local_refinement_tolerance &&
elem->level() < _max_h_level)
elem->set_refinement_flag(Elem::REFINE);
if (!_coarsen_by_parents && elem_error <
local_coarsening_tolerance)
elem->set_refinement_flag(Elem::COARSEN);
if (_coarsen_by_parents && parent)
{
ErrorVectorReal parent_error = error_per_parent[parent->id()];
if (parent_error >= 0.)
{
const Real parent_coarsening_tolerance =
std::sqrt(parent->n_children() *
local_coarsening_tolerance *
local_coarsening_tolerance);
if (parent_error < parent_coarsening_tolerance)
elem->set_refinement_flag(Elem::COARSEN);
}
}
}
}
Sphere::Sphere (const Point & c,
const Real r)
{
libmesh_assert_greater (r, 0.);
this->create_from_center_radius (c, r);
}
void Sphere::create_from_center_radius (const Point & c, const Real r)
{
this->center() = c;
this->radius() = r;
libmesh_assert_greater (this->radius(), 0.);
}
void EpetraVector<T>::localize (const numeric_index_type first_local_idx,
const numeric_index_type last_local_idx,
const std::vector<numeric_index_type> & send_list)
{
// Only good for serial vectors.
libmesh_assert_equal_to (this->size(), this->local_size());
libmesh_assert_greater (last_local_idx, first_local_idx);
libmesh_assert_less_equal (send_list.size(), this->size());
libmesh_assert_less (last_local_idx, this->size());
const unsigned int my_size = this->size();
const unsigned int my_local_size = (last_local_idx - first_local_idx + 1);
// Don't bother for serial cases
if ((first_local_idx == 0) &&
(my_local_size == my_size))
return;
// Build a parallel vector, initialize it with the local
// parts of (*this)
EpetraVector<T> parallel_vec(this->comm(), PARALLEL);
parallel_vec.init (my_size, my_local_size, true, PARALLEL);
// Copy part of *this into the parallel_vec
for (numeric_index_type i=first_local_idx; i<=last_local_idx; i++)
parallel_vec.set(i,this->el(i));
// localize like normal
parallel_vec.close();
parallel_vec.localize (*this, send_list);
this->close();
}
Point Sphere::unit_normal (const Point & p) const
{
libmesh_assert_greater (this->radius(), 0.);
libmesh_assert_not_equal_to (p, this->center());
// Create a vector from the center to the point
Point n = p - this->center();
return n.unit();
}
bool Sphere::above_surface (const Point & p) const
{
libmesh_assert_greater (this->radius(), 0.);
// create a vector from the center to the point.
const Point w = p - this->center();
if (w.norm() > this->radius())
return true;
return false;
}
void MeshFunction::init (const Trees::BuildType /*point_locator_build_type*/)
{
// are indices of the desired variable(s) provided?
libmesh_assert_greater (this->_system_vars.size(), 0);
// Don't do twice...
if (this->_initialized)
{
libmesh_assert(this->_point_locator);
return;
}
/*
* set up the PointLocator: either someone else
* is the master (go and get the address of his
* point locator) or this object is the master
* (build the point locator on our own).
*/
if (this->_master != NULL)
{
// we aren't the master
const MeshFunction* master =
cast_ptr<const MeshFunction*>(this->_master);
if (master->_point_locator == NULL)
libmesh_error_msg("ERROR: When the master-servant concept is used, the master has to be initialized first!");
else
{
this->_point_locator = master->_point_locator;
}
}
else
{
// we are the master: build the point locator
// constant reference to the other mesh
const MeshBase& mesh = this->_eqn_systems.get_mesh();
// build the point locator. Only \p TREE version available
//UniquePtr<PointLocatorBase> ap (PointLocatorBase::build (TREE, mesh));
//this->_point_locator = ap.release();
// this->_point_locator = new PointLocatorTree (mesh, point_locator_build_type);
this->_point_locator = mesh.sub_point_locator().release();
// Point locator no longer needs to be initialized.
// this->_point_locator->init();
}
// ready for use
this->_initialized = true;
}
void
MAST::GCMMAOptimizationInterface::set_integer_parameter(const std::string &nm, int val) {
if (nm == "max_inner_iters") {
libmesh_assert_greater(val, 0);
_max_inner_iters = val;
}
else
libMesh::out
<< "Unrecognized integer parameter: " << nm << std::endl;
}
void
MAST::GCMMAOptimizationInterface::set_real_parameter(const std::string &nm, Real val) {
if (nm == "constraint_penalty") {
libmesh_assert_greater(val, 0.);
_constr_penalty = val;
}
else
libMesh::out
<< "Unrecognized real parameter: " << nm << std::endl;
}
Point Sphere::closest_point (const Point & p) const
{
libmesh_assert_greater (this->radius(), 0.);
// get the normal from the surface in the direction
// of p
Point normal = this->unit_normal (p);
// The closest point on the sphere is in the direction
// of the normal a distance r from the center.
const Point cp = this->center() + normal*this->radius();
return cp;
}
bool Sphere::on_surface (const Point & p) const
{
libmesh_assert_greater (this->radius(), 0.);
// Create a vector from the center to the point.
const Point w = p - this->center();
// if the size of that vector is the same as the radius() then
// the point is on the surface.
if (std::abs(w.norm() - this->radius()) < 1.e-10)
return true;
return false;
}
void MeshTools::Subdivision::prepare_subdivision_mesh(MeshBase & mesh, bool ghosted)
{
mesh.prepare_for_use();
// convert all mesh elements to subdivision elements
all_subdivision(mesh);
if (!ghosted)
{
// add the ghost elements for the boundaries
add_boundary_ghosts(mesh);
}
else
{
// This assumes that the mesh already has the ghosts. Only tagging them is required here.
tag_boundary_ghosts(mesh);
}
mesh.prepare_for_use();
std::vector<std::vector<const Elem *> > nodes_to_elem_map;
MeshTools::build_nodes_to_elem_map(mesh, nodes_to_elem_map);
// compute the node valences
MeshBase::const_node_iterator nd = mesh.nodes_begin();
const MeshBase::const_node_iterator end_nd = mesh.nodes_end();
for (; nd != end_nd; ++nd)
{
Node * node = *nd;
std::vector<const Node *> neighbors;
MeshTools::find_nodal_neighbors(mesh, *node, nodes_to_elem_map, neighbors);
const unsigned int valence =
cast_int<unsigned int>(neighbors.size());
libmesh_assert_greater(valence, 1);
node->set_valence(valence);
}
MeshBase::const_element_iterator el = mesh.elements_begin();
const MeshBase::const_element_iterator end_el = mesh.elements_end();
for (; el != end_el; ++el)
{
Tri3Subdivision * elem = dynamic_cast<Tri3Subdivision *>(*el);
libmesh_assert(elem);
if (!elem->is_ghost())
elem->prepare_subdivision_properties();
}
}
// ------------------------------------------------------------
// LinearPartitioner implementation
void LinearPartitioner::_do_partition (MeshBase& mesh,
const unsigned int n)
{
libmesh_assert_greater (n, 0);
// Check for an easy return
if (n == 1)
{
this->single_partition (mesh);
return;
}
// Create a simple linear partitioning
{
START_LOG ("partition()", "LinearPartitioner");
const dof_id_type n_active_elem = mesh.n_active_elem();
const dof_id_type blksize = n_active_elem/n;
dof_id_type e = 0;
MeshBase::element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = mesh.active_elements_end();
for ( ; elem_it != elem_end; ++elem_it)
{
if ((e/blksize) < n)
{
Elem *elem = *elem_it;
elem->processor_id() =
libmesh_cast_int<processor_id_type>(e/blksize);
}
else
{
Elem *elem = *elem_it;
elem->processor_id() = 0;
elem = elem->parent();
}
e++;
}
STOP_LOG ("partition()", "LinearPartitioner");
}
}
void LaspackMatrix<T>::init (const numeric_index_type libmesh_dbg_var(m_in),
const numeric_index_type libmesh_dbg_var(n_in),
const numeric_index_type libmesh_dbg_var(m_l),
const numeric_index_type libmesh_dbg_var(n_l),
const numeric_index_type libmesh_dbg_var(nnz),
const numeric_index_type,
const numeric_index_type)
{
// noz ignored... only used for multiple processors!
libmesh_assert_equal_to (m_in, m_l);
libmesh_assert_equal_to (n_in, n_l);
libmesh_assert_equal_to (m_in, n_in);
libmesh_assert_greater (nnz, 0);
libmesh_error_msg("ERROR: Only the init() member that uses the DofMap is implemented for Laspack matrices!");
this->_is_initialized = true;
}
void EigenSparseMatrix<T>::init (const numeric_index_type m_in,
const numeric_index_type n_in,
const numeric_index_type libmesh_dbg_var(m_l),
const numeric_index_type libmesh_dbg_var(n_l),
const numeric_index_type nnz,
const numeric_index_type,
const numeric_index_type)
{
// noz ignored... only used for multiple processors!
libmesh_assert_equal_to (m_in, m_l);
libmesh_assert_equal_to (n_in, n_l);
libmesh_assert_equal_to (m_in, n_in);
libmesh_assert_greater (nnz, 0);
_mat.resize(m_in, n_in);
_mat.reserve(Eigen::Matrix<numeric_index_type, Eigen::Dynamic, 1>::Constant(m_in,nnz));
this->_is_initialized = true;
}
void LaspackMatrix<T>::init (const unsigned int libmesh_dbg_var(m),
const unsigned int libmesh_dbg_var(n),
const unsigned int libmesh_dbg_var(m_l),
const unsigned int libmesh_dbg_var(n_l),
const unsigned int libmesh_dbg_var(nnz),
const unsigned int)
{
// noz ignored... only used for multiple processors!
libmesh_assert_equal_to (m, m_l);
libmesh_assert_equal_to (n, n_l);
libmesh_assert_equal_to (m, n);
libmesh_assert_greater (nnz, 0);
libMesh::err << "ERROR: Only the init() member that uses the" << std::endl
<< "DofMap is implemented for Laspack matrices!" << std::endl;
libmesh_error();
this->_is_initialized = true;
}
Sphere::Sphere(const Point & pa,
const Point & pb,
const Point & pc,
const Point & pd)
{
Point pad = pa - pd;
Point pbd = pb - pd;
Point pcd = pc - pd;
TensorValue<Real> T(pad,pbd,pcd);
Real D = T.det();
// The points had better not be coplanar
libmesh_assert_greater (std::abs(D), 1e-12);
Real e = 0.5*(pa.norm_sq() - pd.norm_sq());
Real f = 0.5*(pb.norm_sq() - pd.norm_sq());
Real g = 0.5*(pc.norm_sq() - pd.norm_sq());
TensorValue<Real> T1(e,pad(1),pad(2),
f,pbd(1),pbd(2),
g,pcd(1),pcd(2));
Real sx = T1.det()/D;
TensorValue<Real> T2(pad(0),e,pad(2),
pbd(0),f,pbd(2),
pcd(0),g,pcd(2));
Real sy = T2.det()/D;
TensorValue<Real> T3(pad(0),pad(1),e,
pbd(0),pbd(1),f,
pcd(0),pcd(1),g);
Real sz = T3.det()/D;
Point c(sx,sy,sz);
Real r = (c-pa).norm();
this->create_from_center_radius(c,r);
}
void NonlinearNeoHookeCurrentConfig::init_for_qp(VectorValue<Gradient> & grad_u, unsigned int qp) {
this->current_qp = qp;
F.zero();
S.zero();
{
RealTensor invF;
invF.zero();
for (unsigned int i = 0; i < 3; ++i)
for (unsigned int j = 0; j < 3; ++j) {
invF(i, j) += libmesh_real(grad_u(i)(j));
}
F.add(inv(invF));
libmesh_assert_greater (F.det(), -TOLERANCE);
}
if (this->calculate_linearized_stiffness) {
this->calculate_tangent();
}
this->calculate_stress();
}
void FEXYZMap::compute_face_map(int dim, const std::vector<Real>& qw, const Elem* side)
{
libmesh_assert(side);
START_LOG("compute_face_map()", "FEXYZMap");
// The number of quadrature points.
const unsigned int n_qp = libmesh_cast_int<unsigned int>(qw.size());
switch(dim)
{
case 2:
{
// Resize the vectors to hold data at the quadrature points
{
this->xyz.resize(n_qp);
this->dxyzdxi_map.resize(n_qp);
this->d2xyzdxi2_map.resize(n_qp);
this->tangents.resize(n_qp);
this->normals.resize(n_qp);
this->curvatures.resize(n_qp);
this->JxW.resize(n_qp);
}
// Clear the entities that will be summed
// Compute the tangent & normal at the quadrature point
for (unsigned int p=0; p<n_qp; p++)
{
this->tangents[p].resize(LIBMESH_DIM-1); // 1 Tangent in 2D, 2 in 3D
this->xyz[p].zero();
this->dxyzdxi_map[p].zero();
this->d2xyzdxi2_map[p].zero();
}
// compute x, dxdxi at the quadrature points
for (unsigned int i=0; i<this->psi_map.size(); i++) // sum over the nodes
{
const Point& side_point = side->point(i);
for (unsigned int p=0; p<n_qp; p++) // for each quadrature point...
{
this->xyz[p].add_scaled (side_point, this->psi_map[i][p]);
this->dxyzdxi_map[p].add_scaled (side_point, this->dpsidxi_map[i][p]);
this->d2xyzdxi2_map[p].add_scaled(side_point, this->d2psidxi2_map[i][p]);
}
}
// Compute the tangent & normal at the quadrature point
for (unsigned int p=0; p<n_qp; p++)
{
const Point n(this->dxyzdxi_map[p](1), -this->dxyzdxi_map[p](0), 0.);
this->normals[p] = n.unit();
this->tangents[p][0] = this->dxyzdxi_map[p].unit();
#if LIBMESH_DIM == 3 // Only good in 3D space
this->tangents[p][1] = this->dxyzdxi_map[p].cross(n).unit();
#endif
// The curvature is computed via the familiar Frenet formula:
// curvature = [d^2(x) / d (xi)^2] dot [normal]
// For a reference, see:
// F.S. Merritt, Mathematics Manual, 1962, McGraw-Hill, p. 310
//
// Note: The sign convention here is different from the
// 3D case. Concave-upward curves (smiles) have a positive
// curvature. Concave-downward curves (frowns) have a
// negative curvature. Be sure to take that into account!
const Real numerator = this->d2xyzdxi2_map[p] * this->normals[p];
const Real denominator = this->dxyzdxi_map[p].size_sq();
libmesh_assert_not_equal_to (denominator, 0);
this->curvatures[p] = numerator / denominator;
}
// compute the jacobian at the quadrature points
for (unsigned int p=0; p<n_qp; p++)
{
const Real the_jac = std::sqrt(this->dxdxi_map(p)*this->dxdxi_map(p) +
this->dydxi_map(p)*this->dydxi_map(p));
libmesh_assert_greater (the_jac, 0.);
this->JxW[p] = the_jac*qw[p];
}
break;
}
case 3:
{
// Resize the vectors to hold data at the quadrature points
{
this->xyz.resize(n_qp);
this->dxyzdxi_map.resize(n_qp);
this->dxyzdeta_map.resize(n_qp);
this->d2xyzdxi2_map.resize(n_qp);
this->d2xyzdxideta_map.resize(n_qp);
this->d2xyzdeta2_map.resize(n_qp);
this->tangents.resize(n_qp);
this->normals.resize(n_qp);
this->curvatures.resize(n_qp);
this->JxW.resize(n_qp);
}
// Clear the entities that will be summed
for (unsigned int p=0; p<n_qp; p++)
{
this->tangents[p].resize(LIBMESH_DIM-1); // 1 Tangent in 2D, 2 in 3D
this->xyz[p].zero();
this->dxyzdxi_map[p].zero();
this->dxyzdeta_map[p].zero();
this->d2xyzdxi2_map[p].zero();
this->d2xyzdxideta_map[p].zero();
this->d2xyzdeta2_map[p].zero();
}
// compute x, dxdxi at the quadrature points
for (unsigned int i=0; i<this->psi_map.size(); i++) // sum over the nodes
{
const Point& side_point = side->point(i);
for (unsigned int p=0; p<n_qp; p++) // for each quadrature point...
{
this->xyz[p].add_scaled (side_point, this->psi_map[i][p]);
this->dxyzdxi_map[p].add_scaled (side_point, this->dpsidxi_map[i][p]);
this->dxyzdeta_map[p].add_scaled (side_point, this->dpsideta_map[i][p]);
this->d2xyzdxi2_map[p].add_scaled (side_point, this->d2psidxi2_map[i][p]);
this->d2xyzdxideta_map[p].add_scaled(side_point, this->d2psidxideta_map[i][p]);
this->d2xyzdeta2_map[p].add_scaled (side_point, this->d2psideta2_map[i][p]);
}
}
// Compute the tangents, normal, and curvature at the quadrature point
for (unsigned int p=0; p<n_qp; p++)
{
const Point n = this->dxyzdxi_map[p].cross(this->dxyzdeta_map[p]);
this->normals[p] = n.unit();
this->tangents[p][0] = this->dxyzdxi_map[p].unit();
this->tangents[p][1] = n.cross(this->dxyzdxi_map[p]).unit();
// Compute curvature using the typical nomenclature
// of the first and second fundamental forms.
// For reference, see:
// 1) http://mathworld.wolfram.com/MeanCurvature.html
// (note -- they are using inward normal)
// 2) F.S. Merritt, Mathematics Manual, 1962, McGraw-Hill
const Real L = -this->d2xyzdxi2_map[p] * this->normals[p];
const Real M = -this->d2xyzdxideta_map[p] * this->normals[p];
const Real N = -this->d2xyzdeta2_map[p] * this->normals[p];
const Real E = this->dxyzdxi_map[p].size_sq();
const Real F = this->dxyzdxi_map[p] * this->dxyzdeta_map[p];
const Real G = this->dxyzdeta_map[p].size_sq();
const Real numerator = E*N -2.*F*M + G*L;
const Real denominator = E*G - F*F;
libmesh_assert_not_equal_to (denominator, 0.);
this->curvatures[p] = 0.5*numerator/denominator;
}
// compute the jacobian at the quadrature points, see
// http://sp81.msi.umn.edu:999/fluent/fidap/help/theory/thtoc.htm
for (unsigned int p=0; p<n_qp; p++)
{
const Real g11 = (this->dxdxi_map(p)*this->dxdxi_map(p) +
this->dydxi_map(p)*this->dydxi_map(p) +
this->dzdxi_map(p)*this->dzdxi_map(p));
const Real g12 = (this->dxdxi_map(p)*this->dxdeta_map(p) +
this->dydxi_map(p)*this->dydeta_map(p) +
this->dzdxi_map(p)*this->dzdeta_map(p));
const Real g21 = g12;
const Real g22 = (this->dxdeta_map(p)*this->dxdeta_map(p) +
this->dydeta_map(p)*this->dydeta_map(p) +
this->dzdeta_map(p)*this->dzdeta_map(p));
const Real the_jac = std::sqrt(g11*g22 - g12*g21);
libmesh_assert_greater (the_jac, 0.);
this->JxW[p] = the_jac*qw[p];
}
break;
}
default:
libmesh_error_msg("Invalid dim = " << dim);
} // switch(dim)
STOP_LOG("compute_face_map()", "FEXYZMap");
return;
}
// ------------------------------------------------------------
// SFCPartitioner implementation
void SFCPartitioner::_do_partition (MeshBase & mesh,
const unsigned int n)
{
libmesh_assert_greater (n, 0);
// Check for an easy return
if (n == 1)
{
this->single_partition (mesh);
return;
}
// What to do if the sfcurves library IS NOT present
#ifndef LIBMESH_HAVE_SFCURVES
libmesh_here();
libMesh::err << "ERROR: The library has been built without" << std::endl
<< "Space Filling Curve support. Using a linear" << std::endl
<< "partitioner instead!" << std::endl;
LinearPartitioner lp;
lp.partition (mesh, n);
// What to do if the sfcurves library IS present
#else
LOG_SCOPE("sfc_partition()", "SFCPartitioner");
const dof_id_type n_active_elem = mesh.n_active_elem();
const dof_id_type n_elem = mesh.n_elem();
// the forward_map maps the active element id
// into a contiguous block of indices
std::vector<dof_id_type>
forward_map (n_elem, DofObject::invalid_id);
// the reverse_map maps the contiguous ids back
// to active elements
std::vector<Elem *> reverse_map (n_active_elem, libmesh_nullptr);
int size = static_cast<int>(n_active_elem);
std::vector<double> x (size);
std::vector<double> y (size);
std::vector<double> z (size);
std::vector<int> table (size);
// We need to map the active element ids into a
// contiguous range.
{
MeshBase::element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = mesh.active_elements_end();
dof_id_type el_num = 0;
for (; elem_it != elem_end; ++elem_it)
{
libmesh_assert_less ((*elem_it)->id(), forward_map.size());
libmesh_assert_less (el_num, reverse_map.size());
forward_map[(*elem_it)->id()] = el_num;
reverse_map[el_num] = *elem_it;
el_num++;
}
libmesh_assert_equal_to (el_num, n_active_elem);
}
// Get the centroid for each active element
{
// const_active_elem_iterator elem_it (mesh.const_elements_begin());
// const const_active_elem_iterator elem_end(mesh.const_elements_end());
MeshBase::element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem * elem = *elem_it;
libmesh_assert_less (elem->id(), forward_map.size());
const Point p = elem->centroid();
x[forward_map[elem->id()]] = p(0);
y[forward_map[elem->id()]] = p(1);
z[forward_map[elem->id()]] = p(2);
}
}
// build the space-filling curve
if (_sfc_type == "Hilbert")
Sfc::hilbert (&x[0], &y[0], &z[0], &size, &table[0]);
else if (_sfc_type == "Morton")
Sfc::morton (&x[0], &y[0], &z[0], &size, &table[0]);
else
{
libmesh_here();
libMesh::err << "ERROR: Unknown type: " << _sfc_type << std::endl
<< " Valid types are" << std::endl
<< " \"Hilbert\"" << std::endl
<< " \"Morton\"" << std::endl
<< " " << std::endl
<< "Proceeding with a Hilbert curve." << std::endl;
Sfc::hilbert (&x[0], &y[0], &z[0], &size, &table[0]);
}
// Assign the partitioning to the active elements
{
// {
// std::ofstream out ("sfc.dat");
// out << "variables=x,y,z" << std::endl;
// out << "zone f=point" << std::endl;
// for (unsigned int i=0; i<n_active_elem; i++)
// out << x[i] << " "
// << y[i] << " "
// << z[i] << std::endl;
// }
const dof_id_type blksize = (n_active_elem+n-1)/n;
for (dof_id_type i=0; i<n_active_elem; i++)
{
libmesh_assert_less (static_cast<unsigned int>(table[i]-1), reverse_map.size());
Elem * elem = reverse_map[table[i]-1];
elem->processor_id() = cast_int<processor_id_type>
(i/blksize);
}
}
#endif
}
Real FE<2,HIERARCHIC>::shape(const Elem* elem,
const Order order,
const unsigned int i,
const Point& p)
{
libmesh_assert(elem);
const Order totalorder = static_cast<Order>(order+elem->p_level());
libmesh_assert_greater (totalorder, 0);
switch (elem->type())
{
case TRI3:
case TRI6:
{
const Real zeta1 = p(0);
const Real zeta2 = p(1);
const Real zeta0 = 1. - zeta1 - zeta2;
libmesh_assert_less (i, (totalorder+1u)*(totalorder+2u)/2);
libmesh_assert (elem->type() == TRI6 || totalorder < 2);
// Vertex DoFs
if (i == 0)
return zeta0;
else if (i == 1)
return zeta1;
else if (i == 2)
return zeta2;
// Edge DoFs
else if (i < totalorder + 2u)
{
// Avoid returning NaN on vertices!
if (zeta0 + zeta1 == 0.)
return 0.;
const unsigned int basisorder = i - 1;
// Get factors to account for edge-flipping
Real f0 = 1;
if (basisorder%2 && (elem->point(0) > elem->point(1)))
f0 = -1.;
Real edgeval = (zeta1 - zeta0) / (zeta1 + zeta0);
Real crossfunc = zeta0 + zeta1;
for (unsigned int n=1; n != basisorder; ++n)
crossfunc *= (zeta0 + zeta1);
return f0 * crossfunc *
FE<1,HIERARCHIC>::shape(EDGE3, totalorder,
basisorder, edgeval);
}
else if (i < 2u*totalorder + 1)
{
// Avoid returning NaN on vertices!
if (zeta1 + zeta2 == 0.)
return 0.;
const unsigned int basisorder = i - totalorder;
// Get factors to account for edge-flipping
Real f1 = 1;
if (basisorder%2 && (elem->point(1) > elem->point(2)))
f1 = -1.;
Real edgeval = (zeta2 - zeta1) / (zeta2 + zeta1);
Real crossfunc = zeta2 + zeta1;
for (unsigned int n=1; n != basisorder; ++n)
crossfunc *= (zeta2 + zeta1);
return f1 * crossfunc *
FE<1,HIERARCHIC>::shape(EDGE3, totalorder,
basisorder, edgeval);
}
else if (i < 3u*totalorder)
{
// Avoid returning NaN on vertices!
if (zeta0 + zeta2 == 0.)
return 0.;
const unsigned int basisorder = i - (2u*totalorder) + 1;
// Get factors to account for edge-flipping
Real f2 = 1;
if (basisorder%2 && (elem->point(2) > elem->point(0)))
f2 = -1.;
Real edgeval = (zeta0 - zeta2) / (zeta0 + zeta2);
Real crossfunc = zeta0 + zeta2;
for (unsigned int n=1; n != basisorder; ++n)
crossfunc *= (zeta0 + zeta2);
return f2 * crossfunc *
FE<1,HIERARCHIC>::shape(EDGE3, totalorder,
basisorder, edgeval);
}
// Interior DoFs
else
{
const unsigned int basisnum = i - (3u*totalorder);
unsigned int exp0 = triangular_number_column[basisnum] + 1;
unsigned int exp1 = triangular_number_row[basisnum] + 1 -
triangular_number_column[basisnum];
Real returnval = 1;
for (unsigned int n = 0; n != exp0; ++n)
returnval *= zeta0;
for (unsigned int n = 0; n != exp1; ++n)
returnval *= zeta1;
returnval *= zeta2;
return returnval;
}
}
// Hierarchic shape functions on the quadrilateral.
case QUAD4:
libmesh_assert_less (totalorder, 2);
case QUAD8:
case QUAD9:
{
// Compute quad shape functions as a tensor-product
const Real xi = p(0);
const Real eta = p(1);
libmesh_assert_less (i, (totalorder+1u)*(totalorder+1u));
// Example i, i0, i1 values for totalorder = 5:
// 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
// static const unsigned int i0[] = {0, 1, 1, 0, 2, 3, 4, 5, 1, 1, 1, 1, 2, 3, 4, 5, 0, 0, 0, 0, 2, 3, 3, 2, 4, 4, 4, 3, 2, 5, 5, 5, 5, 4, 3, 2};
// static const unsigned int i1[] = {0, 0, 1, 1, 0, 0, 0, 0, 2, 3, 4, 5, 1, 1, 1, 1, 2, 3, 4, 5, 2, 2, 3, 3, 2, 3, 4, 4, 4, 2, 3, 4, 5, 5, 5, 5};
unsigned int i0, i1;
// Vertex DoFs
if (i == 0)
{ i0 = 0; i1 = 0; }
else if (i == 1)
{ i0 = 1; i1 = 0; }
else if (i == 2)
{ i0 = 1; i1 = 1; }
else if (i == 3)
{ i0 = 0; i1 = 1; }
// Edge DoFs
else if (i < totalorder + 3u)
{ i0 = i - 2; i1 = 0; }
else if (i < 2u*totalorder + 2)
{ i0 = 1; i1 = i - totalorder - 1; }
else if (i < 3u*totalorder + 1)
{ i0 = i - 2u*totalorder; i1 = 1; }
else if (i < 4u*totalorder)
{ i0 = 0; i1 = i - 3u*totalorder + 1; }
// Interior DoFs
else
{
unsigned int basisnum = i - 4*totalorder;
i0 = square_number_column[basisnum] + 2;
i1 = square_number_row[basisnum] + 2;
}
// Flip odd degree of freedom values if necessary
// to keep continuity on sides
Real f = 1.;
if ((i0%2) && (i0 > 2) && (i1 == 0))
f = (elem->point(0) > elem->point(1))?-1.:1.;
else if ((i0%2) && (i0>2) && (i1 == 1))
f = (elem->point(3) > elem->point(2))?-1.:1.;
else if ((i0 == 0) && (i1%2) && (i1>2))
f = (elem->point(0) > elem->point(3))?-1.:1.;
else if ((i0 == 1) && (i1%2) && (i1>2))
f = (elem->point(1) > elem->point(2))?-1.:1.;
return f*(FE<1,HIERARCHIC>::shape(EDGE3, totalorder, i0, xi)*
FE<1,HIERARCHIC>::shape(EDGE3, totalorder, i1, eta));
}
default:
libMesh::err << "ERROR: Unsupported element type!" << std::endl;
libmesh_error();
}
return 0.;
}
Real FE<2,HIERARCHIC>::shape_deriv(const Elem* elem,
const Order order,
const unsigned int i,
const unsigned int j,
const Point& p)
{
libmesh_assert(elem);
const ElemType type = elem->type();
const Order totalorder = static_cast<Order>(order+elem->p_level());
libmesh_assert_greater (totalorder, 0);
switch (type)
{
// 1st & 2nd-order Hierarchics.
case TRI3:
case TRI6:
{
const Real eps = 1.e-6;
libmesh_assert_less (j, 2);
switch (j)
{
// d()/dxi
case 0:
{
const Point pp(p(0)+eps, p(1));
const Point pm(p(0)-eps, p(1));
return (FE<2,HIERARCHIC>::shape(elem, order, i, pp) -
FE<2,HIERARCHIC>::shape(elem, order, i, pm))/2./eps;
}
// d()/deta
case 1:
{
const Point pp(p(0), p(1)+eps);
const Point pm(p(0), p(1)-eps);
return (FE<2,HIERARCHIC>::shape(elem, order, i, pp) -
FE<2,HIERARCHIC>::shape(elem, order, i, pm))/2./eps;
}
default:
libmesh_error();
}
}
case QUAD4:
libmesh_assert_less (totalorder, 2);
case QUAD8:
case QUAD9:
{
// Compute quad shape functions as a tensor-product
const Real xi = p(0);
const Real eta = p(1);
libmesh_assert_less (i, (totalorder+1u)*(totalorder+1u));
// Example i, i0, i1 values for totalorder = 5:
// 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
// static const unsigned int i0[] = {0, 1, 1, 0, 2, 3, 4, 5, 1, 1, 1, 1, 2, 3, 4, 5, 0, 0, 0, 0, 2, 3, 4, 5, 2, 3, 4, 5, 2, 3, 4, 5, 2, 3, 4, 5};
// static const unsigned int i1[] = {0, 0, 1, 1, 0, 0, 0, 0, 2, 3, 4, 5, 1, 1, 1, 1, 2, 3, 4, 5, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5};
unsigned int i0, i1;
// Vertex DoFs
if (i == 0)
{ i0 = 0; i1 = 0; }
else if (i == 1)
{ i0 = 1; i1 = 0; }
else if (i == 2)
{ i0 = 1; i1 = 1; }
else if (i == 3)
{ i0 = 0; i1 = 1; }
// Edge DoFs
else if (i < totalorder + 3u)
{ i0 = i - 2; i1 = 0; }
else if (i < 2u*totalorder + 2)
{ i0 = 1; i1 = i - totalorder - 1; }
else if (i < 3u*totalorder + 1u)
{ i0 = i - 2u*totalorder; i1 = 1; }
else if (i < 4u*totalorder)
{ i0 = 0; i1 = i - 3u*totalorder + 1; }
// Interior DoFs
else
{
unsigned int basisnum = i - 4*totalorder;
i0 = square_number_column[basisnum] + 2;
i1 = square_number_row[basisnum] + 2;
}
// Flip odd degree of freedom values if necessary
// to keep continuity on sides
Real f = 1.;
if ((i0%2) && (i0 > 2) && (i1 == 0))
f = (elem->point(0) > elem->point(1))?-1.:1.;
else if ((i0%2) && (i0>2) && (i1 == 1))
f = (elem->point(3) > elem->point(2))?-1.:1.;
else if ((i0 == 0) && (i1%2) && (i1>2))
f = (elem->point(0) > elem->point(3))?-1.:1.;
else if ((i0 == 1) && (i1%2) && (i1>2))
f = (elem->point(1) > elem->point(2))?-1.:1.;
switch (j)
{
// d()/dxi
case 0:
return f*(FE<1,HIERARCHIC>::shape_deriv(EDGE3, totalorder, i0, 0, xi)*
FE<1,HIERARCHIC>::shape (EDGE3, totalorder, i1, eta));
// d()/deta
case 1:
return f*(FE<1,HIERARCHIC>::shape (EDGE3, totalorder, i0, xi)*
FE<1,HIERARCHIC>::shape_deriv(EDGE3, totalorder, i1, 0, eta));
default:
libmesh_error();
}
}
default:
libMesh::err << "ERROR: Unsupported element type!" << std::endl;
libmesh_error();
}
return 0.;
}
// The main program
int main(int argc, char** argv)
{
// Initialize libMesh
LibMeshInit init(argc, argv);
// Parameters
GetPot infile("fem_system_params.in");
const Real global_tolerance = infile("global_tolerance", 0.);
const unsigned int nelem_target = infile("n_elements", 400);
const bool transient = infile("transient", true);
const Real deltat = infile("deltat", 0.005);
unsigned int n_timesteps = infile("n_timesteps", 1);
//const unsigned int coarsegridsize = infile("coarsegridsize", 1);
const unsigned int coarserefinements = infile("coarserefinements", 0);
const unsigned int max_adaptivesteps = infile("max_adaptivesteps", 10);
//const unsigned int dim = 2;
#ifdef LIBMESH_HAVE_EXODUS_API
const unsigned int write_interval = infile("write_interval", 5);
#endif
// Create a mesh, with dimension to be overridden later, distributed
// across the default MPI communicator.
Mesh mesh(init.comm());
GetPot infileForMesh("convdiff_mprime.in");
std::string find_mesh_here = infileForMesh("mesh","psiLF_mesh.xda");
mesh.read(find_mesh_here);
std::cout << "Read in mesh from: " << find_mesh_here << "\n\n";
// And an object to refine it
MeshRefinement mesh_refinement(mesh);
mesh_refinement.coarsen_by_parents() = true;
mesh_refinement.absolute_global_tolerance() = global_tolerance;
mesh_refinement.nelem_target() = nelem_target;
mesh_refinement.refine_fraction() = 0.3;
mesh_refinement.coarsen_fraction() = 0.3;
mesh_refinement.coarsen_threshold() = 0.1;
//mesh_refinement.uniformly_refine(coarserefinements);
// Print information about the mesh to the screen.
mesh.print_info();
// Create an equation systems object.
EquationSystems equation_systems (mesh);
// Name system
ConvDiff_MprimeSys & system =
equation_systems.add_system<ConvDiff_MprimeSys>("Diff_ConvDiff_MprimeSys");
// Steady-state problem
system.time_solver =
AutoPtr<TimeSolver>(new SteadySolver(system));
// Sanity check that we are indeed solving a steady problem
libmesh_assert_equal_to (n_timesteps, 1);
// Read in all the equation systems data from the LF solve (system, solutions, rhs, etc)
std::string find_psiLF_here = infileForMesh("psiLF_file","psiLF.xda");
std::cout << "Looking for psiLF at: " << find_psiLF_here << "\n\n";
equation_systems.read(find_psiLF_here, READ,
EquationSystems::READ_HEADER |
EquationSystems::READ_DATA |
EquationSystems::READ_ADDITIONAL_DATA);
// Check that the norm of the solution read in is what we expect it to be
Real readin_L2 = system.calculate_norm(*system.solution, 0, L2);
std::cout << "Read in solution norm: "<< readin_L2 << std::endl << std::endl;
//DEBUG
//equation_systems.write("right_back_out.xda", WRITE, EquationSystems::WRITE_DATA |
// EquationSystems::WRITE_ADDITIONAL_DATA);
#ifdef LIBMESH_HAVE_GMV
//GMVIO(equation_systems.get_mesh()).write_equation_systems(std::string("right_back_out.gmv"), equation_systems);
#endif
// Initialize the system
//equation_systems.init (); //already initialized by read-in
// And the nonlinear solver options
NewtonSolver *solver = new NewtonSolver(system);
system.time_solver->diff_solver() = AutoPtr<DiffSolver>(solver);
solver->quiet = infile("solver_quiet", true);
solver->verbose = !solver->quiet;
solver->max_nonlinear_iterations =
infile("max_nonlinear_iterations", 15);
solver->relative_step_tolerance =
infile("relative_step_tolerance", 1.e-3);
solver->relative_residual_tolerance =
infile("relative_residual_tolerance", 0.0);
solver->absolute_residual_tolerance =
infile("absolute_residual_tolerance", 0.0);
// And the linear solver options
solver->max_linear_iterations =
infile("max_linear_iterations", 50000);
solver->initial_linear_tolerance =
infile("initial_linear_tolerance", 1.e-3);
// Print information about the system to the screen.
equation_systems.print_info();
// Now we begin the timestep loop to compute the time-accurate
// solution of the equations...not that this is transient, but eh, why not...
for (unsigned int t_step=0; t_step != n_timesteps; ++t_step)
{
// A pretty update message
std::cout << "\n\nSolving time step " << t_step << ", time = "
<< system.time << std::endl;
// Adaptively solve the timestep
unsigned int a_step = 0;
for (; a_step != max_adaptivesteps; ++a_step)
{ // VESTIGIAL for now ('vestigial' eh ? ;) )
std::cout << "\n\n I should be skipped what are you doing here lalalalalalala *!**!*!*!*!*!* \n\n";
system.solve();
system.postprocess();
ErrorVector error;
AutoPtr<ErrorEstimator> error_estimator;
// To solve to a tolerance in this problem we
// need a better estimator than Kelly
if (global_tolerance != 0.)
{
// We can't adapt to both a tolerance and a mesh
// size at once
libmesh_assert_equal_to (nelem_target, 0);
UniformRefinementEstimator *u =
new UniformRefinementEstimator;
// The lid-driven cavity problem isn't in H1, so
// lets estimate L2 error
u->error_norm = L2;
error_estimator.reset(u);
}
else
{
// If we aren't adapting to a tolerance we need a
// target mesh size
libmesh_assert_greater (nelem_target, 0);
// Kelly is a lousy estimator to use for a problem
// not in H1 - if we were doing more than a few
// timesteps we'd need to turn off or limit the
// maximum level of our adaptivity eventually
error_estimator.reset(new KellyErrorEstimator);
}
// Calculate error
std::vector<Real> weights(9,1.0); // based on u, v, p, c, their adjoints, and source parameter
// Keep the same default norm type.
std::vector<FEMNormType>
norms(1, error_estimator->error_norm.type(0));
error_estimator->error_norm = SystemNorm(norms, weights);
error_estimator->estimate_error(system, error);
// Print out status at each adaptive step.
Real global_error = error.l2_norm();
std::cout << "Adaptive step " << a_step << ": " << std::endl;
if (global_tolerance != 0.)
std::cout << "Global_error = " << global_error
<< std::endl;
if (global_tolerance != 0.)
std::cout << "Worst element error = " << error.maximum()
<< ", mean = " << error.mean() << std::endl;
if (global_tolerance != 0.)
{
// If we've reached our desired tolerance, we
// don't need any more adaptive steps
if (global_error < global_tolerance)
break;
mesh_refinement.flag_elements_by_error_tolerance(error);
}
else
{
// If flag_elements_by_nelem_target returns true, this
// should be our last adaptive step.
if (mesh_refinement.flag_elements_by_nelem_target(error))
{
mesh_refinement.refine_and_coarsen_elements();
equation_systems.reinit();
a_step = max_adaptivesteps;
break;
}
}
// Carry out the adaptive mesh refinement/coarsening
mesh_refinement.refine_and_coarsen_elements();
equation_systems.reinit();
std::cout << "Refined mesh to "
<< mesh.n_active_elem()
<< " active elements and "
<< equation_systems.n_active_dofs()
<< " active dofs." << std::endl;
} // End loop over adaptive steps
// Do one last solve if necessary
if (a_step == max_adaptivesteps)
{
QoISet qois;
std::vector<unsigned int> qoi_indices;
qoi_indices.push_back(0);
qois.add_indices(qoi_indices);
qois.set_weight(0, 1.0);
system.assemble_qoi_sides = true; //QoI doesn't involve sides
std::cout << "\n~*~*~*~*~*~*~*~*~ adjoint solve start ~*~*~*~*~*~*~*~*~\n" << std::endl;
std::pair<unsigned int, Real> adjsolve = system.adjoint_solve();
std::cout << "number of iterations to solve adjoint: " << adjsolve.first << std::endl;
std::cout << "final residual of adjoint solve: " << adjsolve.second << std::endl;
std::cout << "\n~*~*~*~*~*~*~*~*~ adjoint solve end ~*~*~*~*~*~*~*~*~" << std::endl;
NumericVector<Number> &dual_solution = system.get_adjoint_solution(0);
NumericVector<Number> &primal_solution = *system.solution;
primal_solution.swap(dual_solution);
ExodusII_IO(mesh).write_timestep("super_adjoint.exo",
equation_systems,
1, /* This number indicates how many time steps
are being written to the file */
system.time);
primal_solution.swap(dual_solution);
system.assemble(); //overwrite residual read in from psiLF solve
// The total error estimate
system.postprocess(); //to compute M_HF(psiLF) and M_LF(psiLF) terms
Real QoI_error_estimate = (-0.5*(system.rhs)->dot(dual_solution)) + system.get_MHF_psiLF() - system.get_MLF_psiLF();
std::cout << "\n\n 0.5*M'_HF(psiLF)(superadj): " << std::setprecision(17) << 0.5*(system.rhs)->dot(dual_solution) << "\n";
std::cout << " M_HF(psiLF): " << std::setprecision(17) << system.get_MHF_psiLF() << "\n";
std::cout << " M_LF(psiLF): " << std::setprecision(17) << system.get_MLF_psiLF() << "\n";
std::cout << "\n\n Residual L2 norm: " << system.calculate_norm(*system.rhs, L2) << "\n";
std::cout << " Residual discrete L2 norm: " << system.calculate_norm(*system.rhs, DISCRETE_L2) << "\n";
std::cout << " Super-adjoint L2 norm: " << system.calculate_norm(dual_solution, L2) << "\n";
std::cout << " Super-adjoint discrete L2 norm: " << system.calculate_norm(dual_solution, DISCRETE_L2) << "\n";
std::cout << "\n\n QoI error estimate: " << std::setprecision(17) << QoI_error_estimate << "\n\n";
//DEBUG
std::cout << "\n------------ herp derp ------------" << std::endl;
//libMesh::out.precision(16);
//dual_solution.print();
//system.get_adjoint_rhs().print();
AutoPtr<NumericVector<Number> > adjresid = system.solution->clone();
(system.matrix)->vector_mult(*adjresid,system.get_adjoint_solution(0));
SparseMatrix<Number>& adjmat = *system.matrix;
(system.matrix)->get_transpose(adjmat);
adjmat.vector_mult(*adjresid,system.get_adjoint_solution(0));
//std::cout << "******************** matrix-superadj product (libmesh) ************************" << std::endl;
//adjresid->print();
adjresid->add(-1.0, system.get_adjoint_rhs(0));
//std::cout << "******************** superadjoint system residual (libmesh) ***********************" << std::endl;
//adjresid->print();
std::cout << "\n\nadjoint system residual (discrete L2): " << system.calculate_norm(*adjresid,DISCRETE_L2) << std::endl;
std::cout << "adjoint system residual (L2, all): " << system.calculate_norm(*adjresid,L2) << std::endl;
std::cout << "adjoint system residual (L2, 0): " << system.calculate_norm(*adjresid,0,L2) << std::endl;
std::cout << "adjoint system residual (L2, 1): " << system.calculate_norm(*adjresid,1,L2) << std::endl;
std::cout << "adjoint system residual (L2, 2): " << system.calculate_norm(*adjresid,2,L2) << std::endl;
std::cout << "adjoint system residual (L2, 3): " << system.calculate_norm(*adjresid,3,L2) << std::endl;
std::cout << "adjoint system residual (L2, 4): " << system.calculate_norm(*adjresid,4,L2) << std::endl;
std::cout << "adjoint system residual (L2, 5): " << system.calculate_norm(*adjresid,5,L2) << std::endl;
/*
AutoPtr<NumericVector<Number> > sadj_matlab = system.solution->clone();
AutoPtr<NumericVector<Number> > adjresid_matlab = system.solution->clone();
if(FILE *fp=fopen("superadj_matlab.txt","r")){
Real value;
int counter = 0;
int flag = 1;
while(flag != -1){
flag = fscanf(fp,"%lf",&value);
if(flag != -1){
sadj_matlab->set(counter, value);
counter += 1;
}
}
fclose(fp);
}
(system.matrix)->vector_mult(*adjresid_matlab,*sadj_matlab);
//std::cout << "******************** matrix-superadj product (matlab) ***********************" << std::endl;
//adjresid_matlab->print();
adjresid_matlab->add(-1.0, system.get_adjoint_rhs(0));
//std::cout << "******************** superadjoint system residual (matlab) ***********************" << std::endl;
//adjresid_matlab->print();
std::cout << "\n\nmatlab import adjoint system residual (discrete L2): " << system.calculate_norm(*adjresid_matlab,DISCRETE_L2) << "\n" << std::endl;
*/
/*
AutoPtr<NumericVector<Number> > sadj_fwd_hack = system.solution->clone();
AutoPtr<NumericVector<Number> > adjresid_fwd_hack = system.solution->clone();
if(FILE *fp=fopen("superadj_forward_hack.txt","r")){
Real value;
int counter = 0;
int flag = 1;
while(flag != -1){
flag = fscanf(fp,"%lf",&value);
if(flag != -1){
sadj_fwd_hack->set(counter, value);
counter += 1;
}
}
fclose(fp);
}
(system.matrix)->vector_mult(*adjresid_fwd_hack,*sadj_fwd_hack);
//std::cout << "******************** matrix-superadj product (fwd_hack) ***********************" << std::endl;
//adjresid_fwd_hack->print();
adjresid_fwd_hack->add(-1.0, system.get_adjoint_rhs(0));
//std::cout << "******************** superadjoint system residual (fwd_hack) ***********************" << std::endl;
//adjresid_fwd_hack->print();
std::cout << "\n\nfwd_hack import adjoint system residual (discrete L2): " << system.calculate_norm(*adjresid_fwd_hack,DISCRETE_L2) << "\n" << std::endl;
std::cout << "fwd_hack adjoint system residual (L2, 0): " << system.calculate_norm(*adjresid_fwd_hack,0,L2) << std::endl;
std::cout << "fwd_hack adjoint system residual (L2, 1): " << system.calculate_norm(*adjresid_fwd_hack,1,L2) << std::endl;
std::cout << "fwd_hack adjoint system residual (L2, 2): " << system.calculate_norm(*adjresid_fwd_hack,2,L2) << std::endl;
std::cout << "fwd_hack adjoint system residual (L2, 3): " << system.calculate_norm(*adjresid_fwd_hack,3,L2) << std::endl;
std::cout << "fwd_hack adjoint system residual (L2, 4): " << system.calculate_norm(*adjresid_fwd_hack,4,L2) << std::endl;
std::cout << "fwd_hack adjoint system residual (L2, 5): " << system.calculate_norm(*adjresid_fwd_hack,5,L2) << std::endl;
*/
//std::cout << "************************ system.matrix ***********************" << std::endl;
//system.matrix->print();
std::cout << "\n------------ herp derp ------------" << std::endl;
// The cell wise breakdown
ErrorVector cell_wise_error;
cell_wise_error.resize((system.rhs)->size());
for(unsigned int i = 0; i < (system.rhs)->size() ; i++)
{
if(i < system.get_mesh().n_elem())
cell_wise_error[i] = fabs(-0.5*((system.rhs)->el(i) * dual_solution(i))
+ system.get_MHF_psiLF(i) - system.get_MLF_psiLF(i));
else
cell_wise_error[i] = fabs(-0.5*((system.rhs)->el(i) * dual_solution(i)));
/*csv from 'save data' from gmv output gives a few values at each node point (value
for every element that shares that node), yet paraview display only seems to show one
of them -> the value in an element is given at each of the nodes that it has, hence the
repetition; what is displayed in paraview is each element's value; even though MHF_psiLF
and MLF_psiLF are stored by element this seems to give elemental contributions that
agree with if we had taken the superadj-residual dot product by integrating over elements*/
/*at higher mesh resolutions and lower k, weird-looking artifacts start to appear and
it no longer agrees with output from manual integration of superadj-residual...*/
}
// Plot it
std::ostringstream error_gmv;
error_gmv << "error.gmv";
cell_wise_error.plot_error(error_gmv.str(), equation_systems.get_mesh());
//alternate element-wise breakdown, outputed as values matched to element centroids; for matlab plotz
primal_solution.swap(dual_solution);
system.postprocess(1);
primal_solution.swap(dual_solution);
system.postprocess(2);
std::cout << "\n\n -0.5*M'_HF(psiLF)(superadj): " << std::setprecision(17) << system.get_half_adj_weighted_resid() << "\n";
primal_solution.swap(dual_solution);
std::string write_error_here = infileForMesh("error_est_output_file", "error_est_breakdown.dat");
std::ofstream output(write_error_here);
for(unsigned int i = 0 ; i < system.get_mesh().n_elem(); i++) {
Point elem_cent = system.get_mesh().elem(i)->centroid();
if(output.is_open()) {
output << elem_cent(0) << " " << elem_cent(1) << " "
<< fabs(system.get_half_adj_weighted_resid(i) + system.get_MHF_psiLF(i) - system.get_MLF_psiLF(i)) << "\n";
}
}
output.close();
} // End if at max adaptive steps
#ifdef LIBMESH_HAVE_EXODUS_API
// Write out this timestep if we're requested to
if ((t_step+1)%write_interval == 0)
{
std::ostringstream file_name;
/*
// We write the file in the ExodusII format.
file_name << "out_"
<< std::setw(3)
<< std::setfill('0')
<< std::right
<< t_step+1
<< ".e";
//this should write out the primal which should be the same as what's read in...
ExodusII_IO(mesh).write_timestep(file_name.str(),
equation_systems,
1, //number of time steps written to file
system.time);
*/
}
#endif // #ifdef LIBMESH_HAVE_EXODUS_API
}
// All done.
return 0;
} //end main
LibMeshInit::LibMeshInit (int argc, const char* const* argv,
MPI_Comm COMM_WORLD_IN)
#endif
{
// should _not_ be initialized already.
libmesh_assert (!libMesh::initialized());
// Build a command-line parser.
command_line.reset (new GetPot (argc, argv));
// Disable performance logging upon request
{
if (libMesh::on_command_line ("--disable-perflog"))
libMesh::perflog.disable_logging();
}
// Build a task scheduler
{
// Get the requested number of threads, defaults to 1 to avoid MPI and
// multithreading competition. If you would like to use MPI and multithreading
// at the same time then (n_mpi_processes_per_node)x(n_threads) should be the
// number of processing cores per node.
std::vector<std::string> n_threads(2);
n_threads[0] = "--n_threads";
n_threads[1] = "--n-threads";
libMesh::libMeshPrivateData::_n_threads =
libMesh::command_line_value (n_threads, 1);
// Set the number of OpenMP threads to the same as the number of threads libMesh is going to use
#ifdef LIBMESH_HAVE_OPENMP
omp_set_num_threads(libMesh::libMeshPrivateData::_n_threads);
#endif
task_scheduler.reset (new Threads::task_scheduler_init(libMesh::n_threads()));
}
// Construct singletons who may be at risk of the
// "static initialization order fiasco"
Singleton::setup();
// Make sure the construction worked
libmesh_assert(remote_elem);
#if defined(LIBMESH_HAVE_MPI)
// Allow the user to bypass MPI initialization
if (!libMesh::on_command_line ("--disable-mpi"))
{
// Check whether the calling program has already initialized
// MPI, and avoid duplicate Init/Finalize
int flag;
MPI_Initialized (&flag);
if (!flag)
{
#if MPI_VERSION > 1
int mpi_thread_provided;
const int mpi_thread_requested = libMesh::n_threads() > 1 ?
MPI_THREAD_FUNNELED :
MPI_THREAD_SINGLE;
MPI_Init_thread (&argc, const_cast<char***>(&argv),
mpi_thread_requested, &mpi_thread_provided);
if ((libMesh::n_threads() > 1) &&
(mpi_thread_provided < MPI_THREAD_FUNNELED))
{
libmesh_warning("Warning: MPI failed to guarantee MPI_THREAD_FUNNELED\n" <<
"for a threaded run.\n" <<
"Be sure your library is funneled-thread-safe..." <<
std::endl);
// Ideally, if an MPI stack tells us it's unsafe for us
// to use threads, we shouldn't use threads.
// In practice, we've encountered one MPI stack (an
// mvapich2 configuration) that returned
// MPI_THREAD_SINGLE as a proper warning, two stacks
// that handle MPI_THREAD_FUNNELED properly, and two
// current stacks plus a couple old stacks that return
// MPI_THREAD_SINGLE but support libMesh threaded runs
// anyway.
// libMesh::libMeshPrivateData::_n_threads = 1;
// task_scheduler.reset (new Threads::task_scheduler_init(libMesh::n_threads()));
}
#else
if (libMesh::libMeshPrivateData::_n_threads > 1)
{
libmesh_warning("Warning: using MPI1 for threaded code.\n" <<
"Be sure your library is funneled-thread-safe..." <<
std::endl);
}
MPI_Init (&argc, const_cast<char***>(&argv));
#endif
libmesh_initialized_mpi = true;
}
// Duplicate the input communicator for internal use
// And get a Parallel::Communicator copy too, to use
// as a default for that API
this->_comm = COMM_WORLD_IN;
libMesh::GLOBAL_COMM_WORLD = COMM_WORLD_IN;
#ifndef LIBMESH_DISABLE_COMMWORLD
libMesh::COMM_WORLD = COMM_WORLD_IN;
Parallel::Communicator_World = COMM_WORLD_IN;
#endif
//MPI_Comm_set_name not supported in at least SGI MPT's MPI implementation
//MPI_Comm_set_name (libMesh::COMM_WORLD, "libMesh::COMM_WORLD");
libMeshPrivateData::_processor_id =
libmesh_cast_int<processor_id_type>(this->comm().rank());
libMeshPrivateData::_n_processors =
libmesh_cast_int<processor_id_type>(this->comm().size());
// Set up an MPI error handler if requested. This helps us get
// into a debugger with a proper stack when an MPI error occurs.
if (libMesh::on_command_line ("--handle-mpi-errors"))
{
#if MPI_VERSION > 1
MPI_Comm_create_errhandler(libMesh_MPI_Handler, &libmesh_errhandler);
MPI_Comm_set_errhandler(libMesh::GLOBAL_COMM_WORLD, libmesh_errhandler);
MPI_Comm_set_errhandler(MPI_COMM_WORLD, libmesh_errhandler);
#else
MPI_Errhandler_create(libMesh_MPI_Handler, &libmesh_errhandler);
MPI_Errhandler_set(libMesh::GLOBAL_COMM_WORLD, libmesh_errhandler);
MPI_Errhandler_set(MPI_COMM_WORLD, libmesh_errhandler);
#endif // #if MPI_VERSION > 1
}
}
// Could we have gotten bad values from the above calls?
libmesh_assert_greater (libMeshPrivateData::_n_processors, 0);
// The libmesh_cast_int already tested _processor_id>=0
// libmesh_assert_greater_equal (libMeshPrivateData::_processor_id, 0);
// Let's be sure we properly initialize on every processor at once:
libmesh_parallel_only(this->comm());
#endif
#if defined(LIBMESH_HAVE_PETSC)
// Allow the user to bypass PETSc initialization
if (!libMesh::on_command_line ("--disable-petsc")
#if defined(LIBMESH_HAVE_MPI)
// If the user bypassed MPI, we'd better be safe and assume that
// PETSc was built to require it; otherwise PETSc initialization
// dies.
&& !libMesh::on_command_line ("--disable-mpi")
#endif
)
{
int ierr=0;
PETSC_COMM_WORLD = libMesh::GLOBAL_COMM_WORLD;
// Check whether the calling program has already initialized
// PETSc, and avoid duplicate Initialize/Finalize
PetscBool petsc_already_initialized;
ierr = PetscInitialized(&petsc_already_initialized);
CHKERRABORT(libMesh::GLOBAL_COMM_WORLD,ierr);
if (petsc_already_initialized != PETSC_TRUE)
libmesh_initialized_petsc = true;
# if defined(LIBMESH_HAVE_SLEPC)
// If SLEPc allows us to check whether the calling program
// has already initialized it, we do that, and avoid
// duplicate Initialize/Finalize.
// We assume that SLEPc will handle PETSc appropriately,
// which it does in the versions we've checked.
# if !SLEPC_VERSION_LESS_THAN(2,3,3)
if (!SlepcInitializeCalled)
# endif
{
ierr = SlepcInitialize (&argc, const_cast<char***>(&argv), NULL, NULL);
CHKERRABORT(libMesh::GLOBAL_COMM_WORLD,ierr);
libmesh_initialized_slepc = true;
}
# else
if (libmesh_initialized_petsc)
{
ierr = PetscInitialize (&argc, const_cast<char***>(&argv), NULL, NULL);
CHKERRABORT(libMesh::GLOBAL_COMM_WORLD,ierr);
}
# endif
}
#endif
// Re-parse the command-line arguments. Note that PETSc and MPI
// initialization above may have removed command line arguments
// that are not relevant to this application in the above calls.
// We don't want a false-positive by detecting those arguments.
command_line->parse_command_line (argc, argv);
// The following line is an optimization when simultaneous
// C and C++ style access to output streams is not required.
// The amount of benefit which occurs is probably implementation
// defined, and may be nothing. On the other hand, I have seen
// some IO tests where IO peformance improves by a factor of two.
if (!libMesh::on_command_line ("--sync-with-stdio"))
std::ios::sync_with_stdio(false);
// Honor the --separate-libmeshout command-line option.
// When this is specified, the library uses an independent ostream
// for libMesh::out/libMesh::err messages, and
// std::cout and std::cerr are untouched by any other options
if (libMesh::on_command_line ("--separate-libmeshout"))
{
// Redirect. We'll share streambufs with cout/cerr for now, but
// presumably anyone using this option will want to replace the
// bufs later.
std::ostream* newout = new std::ostream(std::cout.rdbuf());
libMesh::out = *newout;
std::ostream* newerr = new std::ostream(std::cerr.rdbuf());
libMesh::err = *newerr;
}
// Honor the --redirect-stdout command-line option.
// When this is specified each processor sends
// libMesh::out/libMesh::err messages to
// stdout.processor.####
if (libMesh::on_command_line ("--redirect-stdout"))
{
std::ostringstream filename;
filename << "stdout.processor." << libMesh::global_processor_id();
_ofstream.reset (new std::ofstream (filename.str().c_str()));
// Redirect, saving the original streambufs!
out_buf = libMesh::out.rdbuf (_ofstream->rdbuf());
err_buf = libMesh::err.rdbuf (_ofstream->rdbuf());
}
// redirect libMesh::out to nothing on all
// other processors unless explicitly told
// not to via the --keep-cout command-line argument.
if (libMesh::global_processor_id() != 0)
if (!libMesh::on_command_line ("--keep-cout"))
libMesh::out.rdbuf (NULL);
// Check command line to override printing
// of reference count information.
if(libMesh::on_command_line("--disable-refcount-printing") )
ReferenceCounter::disable_print_counter_info();
#ifdef LIBMESH_ENABLE_EXCEPTIONS
// Set our terminate handler to write stack traces in the event of a
// crash
old_terminate_handler = std::set_terminate(libmesh_terminate_handler);
#endif
if (libMesh::on_command_line("--enable-fpe"))
libMesh::enableFPE(true);
// The library is now ready for use
libMeshPrivateData::_is_initialized = true;
// Make sure these work. Library methods
// depend on these being implemented properly,
// so this is a good time to test them!
libmesh_assert (libMesh::initialized());
libmesh_assert (!libMesh::closed());
}