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);
}
}
}
}
int main (int argc, char** argv){
LibMeshInit init (argc, argv); //initialize libmesh library
std::cout << "Running " << argv[0];
for (int i=1; i<argc; i++)
std::cout << " " << argv[i];
std::cout << std::endl << std::endl;
Mesh mesh(init.comm());
mesh.read("channel_long.exo");
std::string stash_assign = "divvy.txt";
std::ofstream output(stash_assign.c_str());
MeshBase::element_iterator elem_it = mesh.elements_begin();
const MeshBase::element_iterator elem_end = mesh.elements_end();
for (; elem_it != elem_end; ++elem_it){
Elem* elem = *elem_it;
if(output.is_open()){
output << elem->id() << " " << elem->subdomain_id() << "\n";
}
}
output.close();
return 0;
}
void
GrainTracker::calculateBubbleVolumes()
{
Moose::perf_log.push("calculateBubbleVolumes()", "GrainTracker");
// The size of the bubble array will be sized to the max index of the unique grains map
unsigned int max_id = _unique_grains.size() ? _unique_grains.rbegin()->first + 1: 0;
_all_feature_volumes.resize(max_id, 0);
const MeshBase::const_element_iterator el_end = _mesh.getMesh().active_local_elements_end();
for (MeshBase::const_element_iterator el = _mesh.getMesh().active_local_elements_begin(); el != el_end; ++el)
{
Elem * elem = *el;
unsigned int elem_n_nodes = elem->n_nodes();
Real curr_volume = elem->volume();
for (std::map<unsigned int, MooseSharedPointer<FeatureData> >::iterator it = _unique_grains.begin(); it != _unique_grains.end(); ++it)
{
if (it->second->_status == INACTIVE)
continue;
if (_is_elemental)
{
dof_id_type elem_id = elem->id();
if (it->second->_local_ids.find(elem_id) != it->second->_local_ids.end())
{
mooseAssert(it->first < _all_feature_volumes.size(), "_all_feature_volumes access out of bounds");
_all_feature_volumes[it->first] += curr_volume;
break;
}
}
else
{
// Count the number of nodes on this element which are flooded.
unsigned int flooded_nodes = 0;
for (unsigned int node = 0; node < elem_n_nodes; ++node)
{
dof_id_type node_id = elem->node(node);
if (it->second->_local_ids.find(node_id) != it->second->_local_ids.end())
++flooded_nodes;
}
// If a majority of the nodes for this element are flooded,
// assign its volume to the current bubble_counter entry.
if (flooded_nodes >= elem_n_nodes / 2)
_all_feature_volumes[it->first] += curr_volume;
}
}
}
// do all the sums!
_communicator.sum(_all_feature_volumes);
Moose::perf_log.pop("calculateBubbleVolumes()", "GrainTracker");
}
Elem* SerialMesh::insert_elem (Elem* e)
{
unsigned int eid = e->id();
libmesh_assert(eid < _elements.size());
Elem *oldelem = _elements[eid];
if (oldelem)
{
libmesh_assert(oldelem->id() == eid);
this->delete_elem(oldelem);
}
_elements[e->id()] = e;
return e;
}
void MeshRefinement::flag_elements_by_mean_stddev (const ErrorVector& error_per_cell,
const Real refine_frac,
const Real coarsen_frac,
const unsigned int max_l)
{
// The function arguments are currently just there for
// backwards_compatibility
if (!_use_member_parameters)
{
// If the user used non-default parameters, lets warn
// that they're deprecated
if (refine_frac != 0.3 ||
coarsen_frac != 0.0 ||
max_l != libMesh::invalid_uint)
libmesh_deprecated();
_refine_fraction = refine_frac;
_coarsen_fraction = coarsen_frac;
_max_h_level = max_l;
}
// Get the mean value from the error vector
const Real mean = error_per_cell.mean();
// Get the standard deviation. This equals the
// square-root of the variance
const Real stddev = std::sqrt (error_per_cell.variance());
// Check for valid fractions
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);
// The refine and coarsen cutoff
const Real refine_cutoff = mean + _refine_fraction * stddev;
const Real coarsen_cutoff = std::max(mean - _coarsen_fraction * stddev, 0.);
// Loop over the elements and flag them for coarsening or
// refinement based on the element error
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)
{
Elem* elem = *elem_it;
const unsigned int id = elem->id();
libmesh_assert_less (id, error_per_cell.size());
const float elem_error = error_per_cell[id];
// Possibly flag the element for coarsening ...
if (elem_error <= coarsen_cutoff)
elem->set_refinement_flag(Elem::COARSEN);
// ... or refinement
if ((elem_error >= refine_cutoff) && (elem->level() < _max_h_level))
elem->set_refinement_flag(Elem::REFINE);
}
}
//-----------------------------------------------------------------
// Mesh refinement methods
void MeshRefinement::flag_elements_by_error_fraction (const ErrorVector& error_per_cell,
const Real refine_frac,
const Real coarsen_frac,
const unsigned int max_l)
{
parallel_only();
// The function arguments are currently just there for
// backwards_compatibility
if (!_use_member_parameters)
{
// If the user used non-default parameters, lets warn
// that they're deprecated
if (refine_frac != 0.3 ||
coarsen_frac != 0.0 ||
max_l != libMesh::invalid_uint)
libmesh_deprecated();
_refine_fraction = refine_frac;
_coarsen_fraction = coarsen_frac;
_max_h_level = max_l;
}
// 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);
// Clean up the refinement flags. These could be left
// over from previous refinement steps.
this->clean_refinement_flags();
// We're getting the minimum and maximum error values
// for the ACTIVE elements
Real error_min = 1.e30;
Real error_max = 0.;
// And, if necessary, for their parents
Real parent_error_min = 1.e30;
Real parent_error_max = 0.;
// Prepare another error vector if we need to sum parent errors
ErrorVector error_per_parent;
if (_coarsen_by_parents)
{
create_parent_error_vector(error_per_cell,
error_per_parent,
parent_error_min,
parent_error_max);
}
// We need to loop over all active elements to find the minimum
MeshBase::element_iterator el_it =
_mesh.active_local_elements_begin();
const MeshBase::element_iterator el_end =
_mesh.active_local_elements_end();
for (; el_it != el_end; ++el_it)
{
const unsigned int id = (*el_it)->id();
libmesh_assert_less (id, error_per_cell.size());
error_max = std::max (error_max, error_per_cell[id]);
error_min = std::min (error_min, error_per_cell[id]);
}
CommWorld.max(error_max);
CommWorld.min(error_min);
// Compute the cutoff values for coarsening and refinement
const Real error_delta = (error_max - error_min);
const Real parent_error_delta = parent_error_max - parent_error_min;
const Real refine_cutoff = (1.- _refine_fraction)*error_max;
const Real coarsen_cutoff = _coarsen_fraction*error_delta + error_min;
const Real parent_cutoff = _coarsen_fraction*parent_error_delta + error_min;
// // Print information about the error
// libMesh::out << " Error Information:" << std::endl
// << " ------------------" << std::endl
// << " min: " << error_min << std::endl
// << " max: " << error_max << std::endl
// << " delta: " << error_delta << std::endl
// << " refine_cutoff: " << refine_cutoff << std::endl
// << " coarsen_cutoff: " << coarsen_cutoff << std::endl;
// Loop over the elements and flag them for coarsening or
// refinement based on the element error
MeshBase::element_iterator e_it =
_mesh.active_elements_begin();
const MeshBase::element_iterator e_end =
_mesh.active_elements_end();
for (; e_it != e_end; ++e_it)
{
Elem* elem = *e_it;
const unsigned int id = elem->id();
libmesh_assert_less (id, error_per_cell.size());
const float elem_error = error_per_cell[id];
if (_coarsen_by_parents)
{
Elem* parent = elem->parent();
if (parent)
{
const unsigned int parentid = parent->id();
if (error_per_parent[parentid] >= 0. &&
error_per_parent[parentid] <= parent_cutoff)
elem->set_refinement_flag(Elem::COARSEN);
}
}
// Flag the element for coarsening if its error
// is <= coarsen_fraction*delta + error_min
else if (elem_error <= coarsen_cutoff)
{
elem->set_refinement_flag(Elem::COARSEN);
}
// Flag the element for refinement if its error
// is >= refinement_cutoff.
if (elem_error >= refine_cutoff)
if (elem->level() < _max_h_level)
elem->set_refinement_flag(Elem::REFINE);
}
}
void MeshRefinement::flag_elements_by_elem_fraction (const ErrorVector& error_per_cell,
const Real refine_frac,
const Real coarsen_frac,
const unsigned int max_l)
{
parallel_only();
// The function arguments are currently just there for
// backwards_compatibility
if (!_use_member_parameters)
{
// If the user used non-default parameters, lets warn
// that they're deprecated
if (refine_frac != 0.3 ||
coarsen_frac != 0.0 ||
max_l != libMesh::invalid_uint)
libmesh_deprecated();
_refine_fraction = refine_frac;
_coarsen_fraction = coarsen_frac;
_max_h_level = max_l;
}
// 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);
// The number of active elements in the mesh
const unsigned int n_active_elem = _mesh.n_elem();
// The number of elements to flag for coarsening
const unsigned int n_elem_coarsen =
static_cast<unsigned int>(_coarsen_fraction * n_active_elem);
// The number of elements to flag for refinement
const unsigned int n_elem_refine =
static_cast<unsigned int>(_refine_fraction * n_active_elem);
// Clean up the refinement flags. These could be left
// over from previous refinement steps.
this->clean_refinement_flags();
// This vector stores the error and element number for all the
// active elements. It will be sorted and the top & bottom
// elements will then be flagged for coarsening & refinement
std::vector<float> sorted_error;
sorted_error.reserve (n_active_elem);
// Loop over the active elements and create the entry
// in the sorted_error vector
MeshBase::element_iterator elem_it = _mesh.active_local_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_local_elements_end();
for (; elem_it != elem_end; ++elem_it)
sorted_error.push_back (error_per_cell[(*elem_it)->id()]);
CommWorld.allgather(sorted_error);
// Now sort the sorted_error vector
std::sort (sorted_error.begin(), sorted_error.end());
// If we're coarsening by parents:
// Create a sorted error vector with coarsenable parent elements
// only, sorted by lowest errors first
ErrorVector error_per_parent, sorted_parent_error;
if (_coarsen_by_parents)
{
Real parent_error_min, parent_error_max;
create_parent_error_vector(error_per_cell,
error_per_parent,
parent_error_min,
parent_error_max);
sorted_parent_error = error_per_parent;
std::sort (sorted_parent_error.begin(), sorted_parent_error.end());
// All the other error values will be 0., so get rid of them.
sorted_parent_error.erase (std::remove(sorted_parent_error.begin(),
sorted_parent_error.end(), 0.),
sorted_parent_error.end());
}
float top_error= 0., bottom_error = 0.;
// Get the maximum error value corresponding to the
// bottom n_elem_coarsen elements
if (_coarsen_by_parents && n_elem_coarsen)
{
const unsigned int dim = _mesh.mesh_dimension();
unsigned int twotodim = 1;
for (unsigned int i=0; i!=dim; ++i)
twotodim *= 2;
unsigned int n_parent_coarsen = n_elem_coarsen / (twotodim - 1);
if (n_parent_coarsen)
bottom_error = sorted_parent_error[n_parent_coarsen - 1];
}
else if (n_elem_coarsen)
{
bottom_error = sorted_error[n_elem_coarsen - 1];
}
if (n_elem_refine)
top_error = sorted_error[sorted_error.size() - n_elem_refine];
// Finally, let's do the element flagging
elem_it = _mesh.active_elements_begin();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
Elem* parent = elem->parent();
if (_coarsen_by_parents && parent && n_elem_coarsen &&
error_per_parent[parent->id()] <= bottom_error)
elem->set_refinement_flag(Elem::COARSEN);
if (!_coarsen_by_parents && n_elem_coarsen &&
error_per_cell[elem->id()] <= bottom_error)
elem->set_refinement_flag(Elem::COARSEN);
if (n_elem_refine &&
elem->level() < _max_h_level &&
error_per_cell[elem->id()] >= top_error)
elem->set_refinement_flag(Elem::REFINE);
}
}
void HPCoarsenTest::select_refinement (System & system)
{
START_LOG("select_refinement()", "HPCoarsenTest");
// The current mesh
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();
// The system number (for doing bad hackery)
const unsigned int sys_num = system.number();
// Check for a valid component_scale
if (!component_scale.empty())
{
if (component_scale.size() != n_vars)
libmesh_error_msg("ERROR: component_scale is the wrong size:\n" \
<< " component_scale.size()=" \
<< component_scale.size() \
<< "\n n_vars=" \
<< n_vars);
}
else
{
// No specified scaling. Scale all variables by one.
component_scale.resize (n_vars, 1.0);
}
// Resize the error_per_cell vectors to handle
// the number of elements, initialize them to 0.
std::vector<ErrorVectorReal> h_error_per_cell(mesh.max_elem_id(), 0.);
std::vector<ErrorVectorReal> p_error_per_cell(mesh.max_elem_id(), 0.);
// Loop over all the variables in the system
for (unsigned int var=0; var<n_vars; var++)
{
// Possibly skip this variable
if (!component_scale.empty())
if (component_scale[var] == 0.0) continue;
// The type of finite element to use for this variable
const FEType & fe_type = dof_map.variable_type (var);
// Finite element objects for a fine (and probably a coarse)
// element will be needed
fe = FEBase::build (dim, fe_type);
fe_coarse = FEBase::build (dim, fe_type);
// Any cached coarse element results have expired
coarse = libmesh_nullptr;
unsigned int cached_coarse_p_level = 0;
const FEContinuity cont = fe->get_continuity();
libmesh_assert (cont == DISCONTINUOUS || cont == C_ZERO ||
cont == C_ONE);
// Build an appropriate quadrature rule
qrule = fe_type.default_quadrature_rule(dim);
// Tell the refined finite element about the quadrature
// rule. The coarse finite element need not know about it
fe->attach_quadrature_rule (qrule.get());
// We will always do the integration
// on the fine elements. Get their Jacobian values, etc..
JxW = &(fe->get_JxW());
xyz_values = &(fe->get_xyz());
// The shape functions
phi = &(fe->get_phi());
phi_coarse = &(fe_coarse->get_phi());
// The shape function derivatives
if (cont == C_ZERO || cont == C_ONE)
{
dphi = &(fe->get_dphi());
dphi_coarse = &(fe_coarse->get_dphi());
}
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
// The shape function second derivatives
if (cont == C_ONE)
{
d2phi = &(fe->get_d2phi());
d2phi_coarse = &(fe_coarse->get_d2phi());
}
#endif // defined (LIBMESH_ENABLE_SECOND_DERIVATIVES)
// 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)
{
const Elem * elem = *elem_it;
// We're only checking elements that are already flagged for h
// refinement
if (elem->refinement_flag() != Elem::REFINE)
continue;
const dof_id_type e_id = elem->id();
// Find the projection onto the parent element,
// if necessary
if (elem->parent() &&
(coarse != elem->parent() ||
cached_coarse_p_level != elem->p_level()))
{
Uc.resize(0);
coarse = elem->parent();
cached_coarse_p_level = elem->p_level();
unsigned int old_parent_level = coarse->p_level();
(const_cast<Elem *>(coarse))->hack_p_level(elem->p_level());
this->add_projection(system, coarse, var);
(const_cast<Elem *>(coarse))->hack_p_level(old_parent_level);
// Solve the h-coarsening projection problem
Ke.cholesky_solve(Fe, Uc);
}
fe->reinit(elem);
// Get the DOF indices for the fine element
dof_map.dof_indices (elem, dof_indices, var);
// The number of quadrature points
const unsigned int n_qp = qrule->n_points();
// The number of DOFS on the fine element
const unsigned int n_dofs =
cast_int<unsigned int>(dof_indices.size());
// The number of nodes on the fine element
const unsigned int n_nodes = elem->n_nodes();
// The average element value (used as an ugly hack
// when we have nothing p-coarsened to compare to)
// Real average_val = 0.;
Number average_val = 0.;
// Calculate this variable's contribution to the p
// refinement error
if (elem->p_level() == 0)
{
unsigned int n_vertices = 0;
for (unsigned int n = 0; n != n_nodes; ++n)
if (elem->is_vertex(n))
{
n_vertices++;
const Node * const node = elem->get_node(n);
average_val += system.current_solution
(node->dof_number(sys_num,var,0));
}
average_val /= n_vertices;
}
else
{
unsigned int old_elem_level = elem->p_level();
(const_cast<Elem *>(elem))->hack_p_level(old_elem_level - 1);
fe_coarse->reinit(elem, &(qrule->get_points()));
const unsigned int n_coarse_dofs =
cast_int<unsigned int>(phi_coarse->size());
(const_cast<Elem *>(elem))->hack_p_level(old_elem_level);
Ke.resize(n_coarse_dofs, n_coarse_dofs);
Ke.zero();
Fe.resize(n_coarse_dofs);
Fe.zero();
// Loop over the quadrature points
for (unsigned int qp=0; qp<qrule->n_points(); qp++)
{
// The solution value at the quadrature point
Number val = libMesh::zero;
Gradient grad;
Tensor hess;
for (unsigned int i=0; i != n_dofs; i++)
{
dof_id_type dof_num = dof_indices[i];
val += (*phi)[i][qp] *
system.current_solution(dof_num);
if (cont == C_ZERO || cont == C_ONE)
grad.add_scaled((*dphi)[i][qp], system.current_solution(dof_num));
// grad += (*dphi)[i][qp] *
// system.current_solution(dof_num);
if (cont == C_ONE)
hess.add_scaled((*d2phi)[i][qp], system.current_solution(dof_num));
// hess += (*d2phi)[i][qp] *
// system.current_solution(dof_num);
}
// The projection matrix and vector
for (unsigned int i=0; i != Fe.size(); ++i)
{
Fe(i) += (*JxW)[qp] *
(*phi_coarse)[i][qp]*val;
if (cont == C_ZERO || cont == C_ONE)
Fe(i) += (*JxW)[qp] *
grad * (*dphi_coarse)[i][qp];
if (cont == C_ONE)
Fe(i) += (*JxW)[qp] *
hess.contract((*d2phi_coarse)[i][qp]);
for (unsigned int j=0; j != Fe.size(); ++j)
{
Ke(i,j) += (*JxW)[qp] *
(*phi_coarse)[i][qp]*(*phi_coarse)[j][qp];
if (cont == C_ZERO || cont == C_ONE)
Ke(i,j) += (*JxW)[qp] *
(*dphi_coarse)[i][qp]*(*dphi_coarse)[j][qp];
if (cont == C_ONE)
Ke(i,j) += (*JxW)[qp] *
((*d2phi_coarse)[i][qp].contract((*d2phi_coarse)[j][qp]));
}
}
}
// Solve the p-coarsening projection problem
Ke.cholesky_solve(Fe, Up);
}
// loop over the integration points on the fine element
for (unsigned int qp=0; qp<n_qp; qp++)
{
Number value_error = 0.;
Gradient grad_error;
Tensor hessian_error;
for (unsigned int i=0; i<n_dofs; i++)
{
const dof_id_type dof_num = dof_indices[i];
value_error += (*phi)[i][qp] *
system.current_solution(dof_num);
if (cont == C_ZERO || cont == C_ONE)
grad_error.add_scaled((*dphi)[i][qp], system.current_solution(dof_num));
// grad_error += (*dphi)[i][qp] *
// system.current_solution(dof_num);
if (cont == C_ONE)
hessian_error.add_scaled((*d2phi)[i][qp], system.current_solution(dof_num));
// hessian_error += (*d2phi)[i][qp] *
// system.current_solution(dof_num);
}
if (elem->p_level() == 0)
{
value_error -= average_val;
}
else
{
for (unsigned int i=0; i<Up.size(); i++)
{
value_error -= (*phi_coarse)[i][qp] * Up(i);
if (cont == C_ZERO || cont == C_ONE)
grad_error.subtract_scaled((*dphi_coarse)[i][qp], Up(i));
// grad_error -= (*dphi_coarse)[i][qp] * Up(i);
if (cont == C_ONE)
hessian_error.subtract_scaled((*d2phi_coarse)[i][qp], Up(i));
// hessian_error -= (*d2phi_coarse)[i][qp] * Up(i);
}
}
p_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * TensorTools::norm_sq(value_error));
if (cont == C_ZERO || cont == C_ONE)
p_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * grad_error.norm_sq());
if (cont == C_ONE)
p_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * hessian_error.norm_sq());
}
// Calculate this variable's contribution to the h
// refinement error
if (!elem->parent())
{
// For now, we'll always start with an h refinement
h_error_per_cell[e_id] =
std::numeric_limits<ErrorVectorReal>::max() / 2;
}
else
{
FEInterface::inverse_map (dim, fe_type, coarse,
*xyz_values, coarse_qpoints);
unsigned int old_parent_level = coarse->p_level();
(const_cast<Elem *>(coarse))->hack_p_level(elem->p_level());
fe_coarse->reinit(coarse, &coarse_qpoints);
(const_cast<Elem *>(coarse))->hack_p_level(old_parent_level);
// The number of DOFS on the coarse element
unsigned int n_coarse_dofs =
cast_int<unsigned int>(phi_coarse->size());
// Loop over the quadrature points
for (unsigned int qp=0; qp<n_qp; qp++)
{
// The solution difference at the quadrature point
Number value_error = libMesh::zero;
Gradient grad_error;
Tensor hessian_error;
for (unsigned int i=0; i != n_dofs; ++i)
{
const dof_id_type dof_num = dof_indices[i];
value_error += (*phi)[i][qp] *
system.current_solution(dof_num);
if (cont == C_ZERO || cont == C_ONE)
grad_error.add_scaled((*dphi)[i][qp], system.current_solution(dof_num));
// grad_error += (*dphi)[i][qp] *
// system.current_solution(dof_num);
if (cont == C_ONE)
hessian_error.add_scaled((*d2phi)[i][qp], system.current_solution(dof_num));
// hessian_error += (*d2phi)[i][qp] *
// system.current_solution(dof_num);
}
for (unsigned int i=0; i != n_coarse_dofs; ++i)
{
value_error -= (*phi_coarse)[i][qp] * Uc(i);
if (cont == C_ZERO || cont == C_ONE)
// grad_error -= (*dphi_coarse)[i][qp] * Uc(i);
grad_error.subtract_scaled((*dphi_coarse)[i][qp], Uc(i));
if (cont == C_ONE)
hessian_error.subtract_scaled((*d2phi_coarse)[i][qp], Uc(i));
// hessian_error -= (*d2phi_coarse)[i][qp] * Uc(i);
}
h_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * TensorTools::norm_sq(value_error));
if (cont == C_ZERO || cont == C_ONE)
h_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * grad_error.norm_sq());
if (cont == C_ONE)
h_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * hessian_error.norm_sq());
}
}
}
}
// Now that we've got our approximations for p_error and h_error, let's see
// if we want to switch any h refinement flags to p refinement
// Iterate over all the active elements in the mesh
// that live on this processor.
MeshBase::element_iterator elem_it =
mesh.active_local_elements_begin();
const MeshBase::element_iterator elem_end =
mesh.active_local_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem * elem = *elem_it;
// We're only checking elements that are already flagged for h
// refinement
if (elem->refinement_flag() != Elem::REFINE)
continue;
const dof_id_type e_id = elem->id();
unsigned int dofs_per_elem = 0, dofs_per_p_elem = 0;
// Loop over all the variables in the system
for (unsigned int var=0; var<n_vars; var++)
{
// The type of finite element to use for this variable
const FEType & fe_type = dof_map.variable_type (var);
// FIXME: we're overestimating the number of DOFs added by h
// refinement
FEType elem_fe_type = fe_type;
elem_fe_type.order =
static_cast<Order>(fe_type.order + elem->p_level());
dofs_per_elem +=
FEInterface::n_dofs(dim, elem_fe_type, elem->type());
elem_fe_type.order =
static_cast<Order>(fe_type.order + elem->p_level() + 1);
dofs_per_p_elem +=
FEInterface::n_dofs(dim, elem_fe_type, elem->type());
}
const unsigned int new_h_dofs = dofs_per_elem *
(elem->n_children() - 1);
const unsigned int new_p_dofs = dofs_per_p_elem -
dofs_per_elem;
/*
libMesh::err << "Cell " << e_id << ": h = " << elem->hmax()
<< ", p = " << elem->p_level() + 1 << "," << std::endl
<< " h_error = " << h_error_per_cell[e_id]
<< ", p_error = " << p_error_per_cell[e_id] << std::endl
<< " new_h_dofs = " << new_h_dofs
<< ", new_p_dofs = " << new_p_dofs << std::endl;
*/
const Real p_value =
std::sqrt(p_error_per_cell[e_id]) * p_weight / new_p_dofs;
const Real h_value =
std::sqrt(h_error_per_cell[e_id]) /
static_cast<Real>(new_h_dofs);
if (p_value > h_value)
{
elem->set_p_refinement_flag(Elem::REFINE);
elem->set_refinement_flag(Elem::DO_NOTHING);
}
}
STOP_LOG("select_refinement()", "HPCoarsenTest");
}
std::unique_ptr<MeshBase>
SpiralAnnularMeshGenerator::generate()
{
std::unique_ptr<ReplicatedMesh> mesh = libmesh_make_unique<ReplicatedMesh>(comm(), 2);
{
// Compute the radial bias given:
// .) the inner radius
// .) the outer radius
// .) the initial_delta_r
// .) the desired number of intervals
// Note: the exponent n used in the formula is one less than the
// number of rings the user requests.
Real alpha = 1.1;
int n = _num_rings - 1;
// lambda used to compute the residual and Jacobian for the Newton iterations.
// We capture parameters which don't need to change from the current scope at
// the time this lambda is declared. The values are not updated later, so we
// can't use this for e.g. f, df, and alpha.
auto newton = [this, n](Real & f, Real & df, const Real & alpha) {
f = (1. - std::pow(alpha, n + 1)) / (1. - alpha) -
(_outer_radius - _inner_radius) / _initial_delta_r;
df = (-(n + 1) * (1 - alpha) * std::pow(alpha, n) + (1. - std::pow(alpha, n + 1))) /
(1. - alpha) / (1. - alpha);
};
Real f, df;
int num_iter = 1;
newton(f, df, alpha);
while (std::abs(f) > 1.e-9 && num_iter <= 25)
{
// Compute and apply update.
Real dx = -f / df;
alpha += dx;
newton(f, df, alpha);
num_iter++;
}
// In case the Newton iteration fails to converge.
if (num_iter > 25)
mooseError("Newton iteration failed to converge (more than 25 iterations).");
// Set radial basis to the value of alpha that we computed with Newton.
_radial_bias = alpha;
}
// The number of rings specified by the user does not include the ring at
// the surface of the cylinder itself, so we increment it by one now.
_num_rings += 1;
// Data structure that holds pointers to the Nodes of each ring.
std::vector<std::vector<Node *>> ring_nodes(_num_rings);
// Initialize radius and delta_r variables.
Real radius = _inner_radius;
Real delta_r = _initial_delta_r;
// Node id counter.
unsigned int current_node_id = 0;
for (std::size_t r = 0; r < _num_rings; ++r)
{
ring_nodes[r].resize(_nodes_per_ring);
// Add nodes starting from either theta=0 or theta=pi/nodes_per_ring
Real theta = r % 2 == 0 ? 0 : (libMesh::pi / _nodes_per_ring);
for (std::size_t n = 0; n < _nodes_per_ring; ++n)
{
ring_nodes[r][n] = mesh->add_point(Point(radius * std::cos(theta), radius * std::sin(theta)),
current_node_id++);
// Update angle
theta += 2 * libMesh::pi / _nodes_per_ring;
}
// Go to next ring
radius += delta_r;
delta_r *= _radial_bias;
}
// Add elements
for (std::size_t r = 0; r < _num_rings - 1; ++r)
{
// even -> odd ring
if (r % 2 == 0)
{
// Inner ring (n, n*, n+1)
// Starred indices refer to nodes on the "outer" ring of this pair.
for (std::size_t n = 0; n < _nodes_per_ring; ++n)
{
// Wrap around
unsigned int np1 = (n == _nodes_per_ring - 1) ? 0 : n + 1;
Elem * elem = mesh->add_elem(new Tri3);
elem->set_node(0) = ring_nodes[r][n];
elem->set_node(1) = ring_nodes[r + 1][n];
elem->set_node(2) = ring_nodes[r][np1];
// Add interior faces to 'cylinder' sideset if we are on ring 0.
if (r == 0)
mesh->boundary_info->add_side(elem->id(), /*side=*/2, _cylinder_bid);
}
// Outer ring (n*, n+1*, n+1)
for (std::size_t n = 0; n < _nodes_per_ring; ++n)
{
// Wrap around
unsigned int np1 = (n == _nodes_per_ring - 1) ? 0 : n + 1;
Elem * elem = mesh->add_elem(new Tri3);
elem->set_node(0) = ring_nodes[r + 1][n];
elem->set_node(1) = ring_nodes[r + 1][np1];
elem->set_node(2) = ring_nodes[r][np1];
// Add exterior faces to 'exterior' sideset if we're on the last ring.
// Note: this code appears in two places since we could end on either an even or odd ring.
if (r == _num_rings - 2)
mesh->boundary_info->add_side(elem->id(), /*side=*/0, _exterior_bid);
}
}
else
{
// odd -> even ring
// Inner ring (n, n+1*, n+1)
for (std::size_t n = 0; n < _nodes_per_ring; ++n)
{
// Wrap around
unsigned int np1 = (n == _nodes_per_ring - 1) ? 0 : n + 1;
Elem * elem = mesh->add_elem(new Tri3);
elem->set_node(0) = ring_nodes[r][n];
elem->set_node(1) = ring_nodes[r + 1][np1];
elem->set_node(2) = ring_nodes[r][np1];
}
// Outer ring (n*, n+1*, n)
for (std::size_t n = 0; n < _nodes_per_ring; ++n)
{
// Wrap around
unsigned int np1 = (n == _nodes_per_ring - 1) ? 0 : n + 1;
Elem * elem = mesh->add_elem(new Tri3);
elem->set_node(0) = ring_nodes[r + 1][n];
elem->set_node(1) = ring_nodes[r + 1][np1];
elem->set_node(2) = ring_nodes[r][n];
// Add exterior faces to 'exterior' sideset if we're on the last ring.
if (r == _num_rings - 2)
mesh->boundary_info->add_side(elem->id(), /*side=*/0, _exterior_bid);
}
}
}
// Sanity check: make sure all elements have positive area. Note: we
// can't use elem->volume() for this, as that always returns a
// positive area regardless of the node ordering.
// We compute (p1-p0) \cross (p2-p0) and check that the z-component is positive.
for (const auto & elem : mesh->element_ptr_range())
{
Point cp = (elem->point(1) - elem->point(0)).cross(elem->point(2) - elem->point(0));
if (cp(2) < 0.)
mooseError("Invalid elem found with negative area");
}
// Create sideset names.
mesh->boundary_info->sideset_name(_cylinder_bid) = "cylinder";
mesh->boundary_info->sideset_name(_exterior_bid) = "exterior";
// Find neighbors, etc.
mesh->prepare_for_use();
if (_use_tri6)
{
mesh->all_second_order(/*full_ordered=*/true);
std::vector<unsigned int> nos;
// Loop over the elements, moving mid-edge nodes onto the
// nearest radius as applicable. For each element, exactly one
// edge should lie on the same radius, so we move only that
// mid-edge node.
for (const auto & elem : mesh->element_ptr_range())
{
// Make sure we are dealing only with triangles
libmesh_assert(elem->n_vertices() == 3);
// Compute vertex radii
Real radii[3] = {elem->point(0).norm(), elem->point(1).norm(), elem->point(2).norm()};
// Compute absolute differences between radii so we can determine which two are on the same
// circular arc.
Real dr[3] = {std::abs(radii[0] - radii[1]),
std::abs(radii[1] - radii[2]),
std::abs(radii[2] - radii[0])};
// Compute index of minimum dr.
auto index = std::distance(std::begin(dr), std::min_element(std::begin(dr), std::end(dr)));
// Make sure that the minimum found is also (almost) zero.
if (dr[index] > TOLERANCE)
mooseError("Error: element had no sides with nodes on same radius.");
// Get list of all local node ids on this side. The first
// two entries in nos correspond to the vertices, the last
// entry corresponds to the mid-edge node.
nos = elem->nodes_on_side(index);
// Compute the angles associated with nodes nos[0] and nos[1].
Real theta0 = std::atan2(elem->point(nos[0])(1), elem->point(nos[0])(0)),
theta1 = std::atan2(elem->point(nos[1])(1), elem->point(nos[1])(0));
// atan2 returns values in the range (-pi, pi). If theta0
// and theta1 have the same sign, we can simply average them
// to get half of the acute angle between them. On the other
// hand, if theta0 and theta1 are of opposite sign _and_ both
// are larger than pi/2, we need to add 2*pi when averaging,
// otherwise we will get half of the _obtuse_ angle between
// them, and the point will flip to the other side of the
// circle (see below).
Real new_theta = 0.5 * (theta0 + theta1);
// It should not be possible for both:
// 1.) |theta0| > pi/2, and
// 2.) |theta1| < pi/2
// as this would not be a well-formed element.
if ((theta0 * theta1 < 0) && (std::abs(theta0) > 0.5 * libMesh::pi) &&
(std::abs(theta1) > 0.5 * libMesh::pi))
new_theta = 0.5 * (theta0 + theta1 + 2 * libMesh::pi);
// The new radius will be the radius of point nos[0] or nos[1] (they are the same!).
Real new_r = elem->point(nos[0]).norm();
// Finally, move the point to its new location.
elem->point(nos[2]) = Point(new_r * std::cos(new_theta), new_r * std::sin(new_theta), 0.);
}
}
return dynamic_pointer_cast<MeshBase>(mesh);
}
void MetisPartitioner::partition_range(MeshBase & mesh,
MeshBase::element_iterator beg,
MeshBase::element_iterator end,
unsigned int n_pieces)
{
libmesh_assert_greater (n_pieces, 0);
// We don't yet support distributed meshes with this Partitioner
if (!mesh.is_serial())
libmesh_not_implemented();
// Check for an easy return
if (n_pieces == 1)
{
this->single_partition_range (beg, end);
return;
}
// What to do if the Metis library IS NOT present
#ifndef LIBMESH_HAVE_METIS
libmesh_here();
libMesh::err << "ERROR: The library has been built without" << std::endl
<< "Metis support. Using a space-filling curve" << std::endl
<< "partitioner instead!" << std::endl;
SFCPartitioner sfcp;
sfcp.partition_range (mesh, beg, end, n_pieces);
// What to do if the Metis library IS present
#else
LOG_SCOPE("partition_range()", "MetisPartitioner");
const dof_id_type n_range_elem = std::distance(beg, end);
// Metis will only consider the elements in the range.
// We need to map the range element ids into a
// contiguous range. Further, we want the unique range indexing to be
// independent of the element ordering, otherwise a circular dependency
// can result in which the partitioning depends on the ordering which
// depends on the partitioning...
vectormap<dof_id_type, dof_id_type> global_index_map;
global_index_map.reserve (n_range_elem);
{
std::vector<dof_id_type> global_index;
MeshCommunication().find_global_indices (mesh.comm(),
MeshTools::create_bounding_box(mesh),
beg, end, global_index);
libmesh_assert_equal_to (global_index.size(), n_range_elem);
MeshBase::element_iterator it = beg;
for (std::size_t cnt=0; it != end; ++it)
{
const Elem * elem = *it;
global_index_map.insert (std::make_pair(elem->id(), global_index[cnt++]));
}
libmesh_assert_equal_to (global_index_map.size(), n_range_elem);
}
// If we have boundary elements in this mesh, we want to account for
// the connectivity between them and interior elements. We can find
// interior elements from boundary elements, but we need to build up
// a lookup map to do the reverse.
typedef std::unordered_multimap<const Elem *, const Elem *> map_type;
map_type interior_to_boundary_map;
{
MeshBase::element_iterator it = beg;
for (; it != end; ++it)
{
const Elem * elem = *it;
// If we don't have an interior_parent then there's nothing
// to look us up.
if ((elem->dim() >= LIBMESH_DIM) ||
!elem->interior_parent())
continue;
// get all relevant interior elements
std::set<const Elem *> neighbor_set;
elem->find_interior_neighbors(neighbor_set);
std::set<const Elem *>::iterator n_it = neighbor_set.begin();
for (; n_it != neighbor_set.end(); ++n_it)
{
// FIXME - non-const versions of the std::set<const Elem
// *> returning methods would be nice
Elem * neighbor = const_cast<Elem *>(*n_it);
#if defined(LIBMESH_HAVE_UNORDERED_MULTIMAP) || \
defined(LIBMESH_HAVE_TR1_UNORDERED_MULTIMAP) || \
defined(LIBMESH_HAVE_HASH_MULTIMAP) || \
defined(LIBMESH_HAVE_EXT_HASH_MULTIMAP)
interior_to_boundary_map.insert(std::make_pair(neighbor, elem));
#else
interior_to_boundary_map.insert(interior_to_boundary_map.begin(),
std::make_pair(neighbor, elem));
#endif
}
}
}
// Data structure that Metis will fill up on processor 0 and broadcast.
std::vector<Metis::idx_t> part(n_range_elem);
// Invoke METIS, but only on processor 0.
// Then broadcast the resulting decomposition
if (mesh.processor_id() == 0)
{
// Data structures and parameters needed only on processor 0 by Metis.
// std::vector<Metis::idx_t> options(5);
std::vector<Metis::idx_t> vwgt(n_range_elem);
Metis::idx_t
n = static_cast<Metis::idx_t>(n_range_elem), // number of "nodes" (elements) in the graph
// wgtflag = 2, // weights on vertices only, none on edges
// numflag = 0, // C-style 0-based numbering
nparts = static_cast<Metis::idx_t>(n_pieces), // number of subdomains to create
edgecut = 0; // the numbers of edges cut by the resulting partition
// Set the options
// options[0] = 0; // use default options
// build the graph
METIS_CSR_Graph<Metis::idx_t> csr_graph;
csr_graph.offsets.resize(n_range_elem + 1, 0);
// Local scope for these
{
// build the graph in CSR format. Note that
// the edges in the graph will correspond to
// face neighbors
#ifdef LIBMESH_ENABLE_AMR
std::vector<const Elem *> neighbors_offspring;
#endif
#ifndef NDEBUG
std::size_t graph_size=0;
#endif
// (1) first pass - get the row sizes for each element by counting the number
// of face neighbors. Also populate the vwght array if necessary
MeshBase::element_iterator it = beg;
for (; it != end; ++it)
{
const Elem * elem = *it;
const dof_id_type elem_global_index =
global_index_map[elem->id()];
libmesh_assert_less (elem_global_index, vwgt.size());
// maybe there is a better weight?
// The weight is used to define what a balanced graph is
if (!_weights)
vwgt[elem_global_index] = elem->n_nodes();
else
vwgt[elem_global_index] = static_cast<Metis::idx_t>((*_weights)[elem->id()]);
unsigned int num_neighbors = 0;
// Loop over the element's neighbors. An element
// adjacency corresponds to a face neighbor
for (auto neighbor : elem->neighbor_ptr_range())
{
if (neighbor != libmesh_nullptr)
{
// If the neighbor is active, but is not in the
// range of elements being partitioned, treat it
// as a NULL neighbor.
if (neighbor->active() && !global_index_map.count(neighbor->id()))
continue;
// If the neighbor is active treat it
// as a connection
if (neighbor->active())
num_neighbors++;
#ifdef LIBMESH_ENABLE_AMR
// Otherwise we need to find all of the
// neighbor's children that are connected to
// us and add them
else
{
// The side of the neighbor to which
// we are connected
const unsigned int ns =
neighbor->which_neighbor_am_i (elem);
libmesh_assert_less (ns, neighbor->n_neighbors());
// Get all the active children (& grandchildren, etc...)
// of the neighbor.
// FIXME - this is the wrong thing, since we
// should be getting the active family tree on
// our side only. But adding too many graph
// links may cause hanging nodes to tend to be
// on partition interiors, which would reduce
// communication overhead for constraint
// equations, so we'll leave it.
neighbor->active_family_tree (neighbors_offspring);
// Get all the neighbor's children that
// live on that side and are thus connected
// to us
for (std::size_t nc=0; nc<neighbors_offspring.size(); nc++)
{
const Elem * child =
neighbors_offspring[nc];
// Skip neighbor offspring which are not in the range of elements being partitioned.
if (!global_index_map.count(child->id()))
continue;
// This does not assume a level-1 mesh.
// Note that since children have sides numbered
// coincident with the parent then this is a sufficient test.
if (child->neighbor_ptr(ns) == elem)
{
libmesh_assert (child->active());
num_neighbors++;
}
}
}
#endif /* ifdef LIBMESH_ENABLE_AMR */
}
}
// Check for any interior neighbors
if ((elem->dim() < LIBMESH_DIM) && elem->interior_parent())
{
// get all relevant interior elements
std::set<const Elem *> neighbor_set;
elem->find_interior_neighbors(neighbor_set);
num_neighbors += neighbor_set.size();
}
// Check for any boundary neighbors
typedef map_type::iterator map_it_type;
std::pair<map_it_type, map_it_type>
bounds = interior_to_boundary_map.equal_range(elem);
num_neighbors += std::distance(bounds.first, bounds.second);
csr_graph.prep_n_nonzeros(elem_global_index, num_neighbors);
#ifndef NDEBUG
graph_size += num_neighbors;
#endif
}
csr_graph.prepare_for_use();
// (2) second pass - fill the compressed adjacency array
it = beg;
for (; it != end; ++it)
{
const Elem * elem = *it;
const dof_id_type elem_global_index =
global_index_map[elem->id()];
unsigned int connection=0;
// Loop over the element's neighbors. An element
// adjacency corresponds to a face neighbor
for (auto neighbor : elem->neighbor_ptr_range())
{
if (neighbor != libmesh_nullptr)
{
// If the neighbor is active, but is not in the
// range of elements being partitioned, treat it
// as a NULL neighbor.
if (neighbor->active() && !global_index_map.count(neighbor->id()))
continue;
// If the neighbor is active treat it
// as a connection
if (neighbor->active())
csr_graph(elem_global_index, connection++) = global_index_map[neighbor->id()];
#ifdef LIBMESH_ENABLE_AMR
// Otherwise we need to find all of the
// neighbor's children that are connected to
// us and add them
else
{
// The side of the neighbor to which
// we are connected
const unsigned int ns =
neighbor->which_neighbor_am_i (elem);
libmesh_assert_less (ns, neighbor->n_neighbors());
// Get all the active children (& grandchildren, etc...)
// of the neighbor.
neighbor->active_family_tree (neighbors_offspring);
// Get all the neighbor's children that
// live on that side and are thus connected
// to us
for (std::size_t nc=0; nc<neighbors_offspring.size(); nc++)
{
const Elem * child =
neighbors_offspring[nc];
// Skip neighbor offspring which are not in the range of elements being partitioned.
if (!global_index_map.count(child->id()))
continue;
// This does not assume a level-1 mesh.
// Note that since children have sides numbered
// coincident with the parent then this is a sufficient test.
if (child->neighbor_ptr(ns) == elem)
{
libmesh_assert (child->active());
csr_graph(elem_global_index, connection++) = global_index_map[child->id()];
}
}
}
#endif /* ifdef LIBMESH_ENABLE_AMR */
}
}
if ((elem->dim() < LIBMESH_DIM) &&
elem->interior_parent())
{
// get all relevant interior elements
std::set<const Elem *> neighbor_set;
elem->find_interior_neighbors(neighbor_set);
std::set<const Elem *>::iterator n_it = neighbor_set.begin();
for (; n_it != neighbor_set.end(); ++n_it)
{
const Elem * neighbor = *n_it;
// Not all interior neighbors are necessarily in
// the same Mesh (hence not in the global_index_map).
// This will be the case when partitioning a
// BoundaryMesh, whose elements all have
// interior_parents() that belong to some other
// Mesh.
const Elem * queried_elem = mesh.query_elem_ptr(neighbor->id());
// Compare the neighbor and the queried_elem
// pointers, make sure they are the same.
if (queried_elem && queried_elem == neighbor)
{
vectormap<dof_id_type, dof_id_type>::iterator global_index_map_it =
global_index_map.find(neighbor->id());
// If the interior_neighbor is in the Mesh but
// not in the global_index_map, we have other issues.
if (global_index_map_it == global_index_map.end())
libmesh_error_msg("Interior neighbor with id " << neighbor->id() << " not found in global_index_map.");
else
csr_graph(elem_global_index, connection++) = global_index_map_it->second;
}
}
}
// Check for any boundary neighbors
for (const auto & pr : as_range(interior_to_boundary_map.equal_range(elem)))
{
const Elem * neighbor = pr.second;
csr_graph(elem_global_index, connection++) =
global_index_map[neighbor->id()];
}
}
// We create a non-empty vals for a disconnected graph, to
// work around a segfault from METIS.
libmesh_assert_equal_to (csr_graph.vals.size(),
std::max(graph_size, std::size_t(1)));
} // done building the graph
Metis::idx_t ncon = 1;
// Select which type of partitioning to create
// Use recursive if the number of partitions is less than or equal to 8
if (n_pieces <= 8)
Metis::METIS_PartGraphRecursive(&n,
&ncon,
&csr_graph.offsets[0],
&csr_graph.vals[0],
&vwgt[0],
libmesh_nullptr,
libmesh_nullptr,
&nparts,
libmesh_nullptr,
libmesh_nullptr,
libmesh_nullptr,
&edgecut,
&part[0]);
// Otherwise use kway
else
Metis::METIS_PartGraphKway(&n,
&ncon,
&csr_graph.offsets[0],
&csr_graph.vals[0],
&vwgt[0],
libmesh_nullptr,
libmesh_nullptr,
&nparts,
libmesh_nullptr,
libmesh_nullptr,
libmesh_nullptr,
&edgecut,
&part[0]);
} // end processor 0 part
// Broadcast the resulting partition
mesh.comm().broadcast(part);
// Assign the returned processor ids. The part array contains
// the processor id for each active element, but in terms of
// the contiguous indexing we defined above
{
MeshBase::element_iterator it = beg;
for (; it!=end; ++it)
{
Elem * elem = *it;
libmesh_assert (global_index_map.count(elem->id()));
const dof_id_type elem_global_index =
global_index_map[elem->id()];
libmesh_assert_less (elem_global_index, part.size());
const processor_id_type elem_procid =
static_cast<processor_id_type>(part[elem_global_index]);
elem->processor_id() = elem_procid;
}
}
#endif
}
// StoreMaterialSystem/StressSystem/
bool CMaterialInfo::StoreMaterialInfo()
{
cout<<STRING_WRITE_BEGIN << "store material info" << endl;
MeshBase& mesh = d_es->get_mesh();
Mesh::element_iterator it_el = mesh.active_local_elements_begin();//mesh.elements_begin();
const Mesh::element_iterator it_last_el = mesh.active_local_elements_end();//mesh.elements_end();
// part 1: we store the Material Info
ExplicitSystem& material_system = d_es->get_system<ExplicitSystem>("MaterialSystem");
const DofMap& material_dof_map = material_system.get_dof_map();
// need to put values from the file
vector<double> mat_values;
mat_values.resize(d_mat_paras_num);
//std::vector< std::vector<unsigned int> > dof_indices_var(system.n_vars());
std::vector<unsigned int> mat_dof_indices_var;
string var_pre = "Mat";
for ( ; it_el != it_last_el ; ++it_el)
{
Elem* elem = *it_el;
int domain_id= elem->subdomain_id();
const vector<double> & mat_values = d_material_info[domain_id].mat_paras;
for (int it_para = 0; it_para < d_mat_paras_num; it_para ++)
{ stringstream ss;
ss << it_para;
string Name_para = var_pre + ss.str();//to_string(it_para);
unsigned int mat_vars = material_system.variable_number (Name_para);
material_dof_map.dof_indices (elem, mat_dof_indices_var, mat_vars);
unsigned int dof_index = mat_dof_indices_var[0];
if( (material_system.solution->first_local_index() <= dof_index) &&
(dof_index < material_system.solution->last_local_index()) )
{
material_system.solution->set(dof_index, mat_values[it_para]);
}
}
}
material_system.solution->close();
material_system.update();
Xdr my_mat_io("material.xdr",libMeshEnums::WRITE);
material_system.write_serialized_data(my_mat_io,false);
// part 2: we store the Fiber info
if (d_have_fibers)
{
if (d_have_fiber_file)
{ DenseMatrix<Number> Fiber_data;
// part 1) have fiber file for store info
cout << STRING_CHECK_IMPORTANT << "fiber info is from file: " << endl;
if (!ReadFile2Matrix(Fiber_data,d_fiber_file) || Fiber_data.m() < d_Elem_num)
{ cout << STRING_ERROR << "check fiber file: element num < rows" << d_fiber_file << endl;
return false;
}
else if (Fiber_data.n() < d_fiber_para_num * d_fiber_types)
{
cout << STRING_ERROR << "check fiber file: fiber total paras < cols" << d_fiber_file << endl;
return false;
}
ExplicitSystem& Fiber_system = d_es->get_system<ExplicitSystem>("FiberSystem");
const DofMap& Fiber_dof_map = Fiber_system.get_dof_map();
it_el = mesh.active_local_elements_begin();
var_pre = "Fiber";
string var_middle = "Para";
vector<string> fiber_vars;
fiber_vars.resize(d_fiber_para_num * d_fiber_types);
int it_id = -1;
for (int it_fiber =0 ; it_fiber < d_fiber_types; it_fiber ++)
{
for (int it_para = 0; it_para < d_fiber_para_num; it_para ++ )
{
// each fiber: a0, a1, a2, C, alpha
it_id ++;
stringstream ss;
ss << it_para;
stringstream ss1;
ss1 << it_fiber;
fiber_vars[ it_id]= var_pre + ss1.str() + var_middle
+ ss.str();
}
}
//std::vector< std::vector<unsigned int> > dof_indices_var(system.n_vars());
std::vector<unsigned int> fiber_dof_indices_var;
for ( ; it_el != it_last_el ; ++it_el)
{
Elem* elem = *it_el;
int domain_id= elem->subdomain_id();
// mat_values =
int global_id =elem->id();
for (int it_para = 0; it_para < d_fiber_para_num * d_fiber_types; it_para ++)
{
unsigned int vars = Fiber_system.variable_number (fiber_vars[it_para]);
Fiber_dof_map.dof_indices (elem, fiber_dof_indices_var, vars);
unsigned int dof_index = fiber_dof_indices_var[0];
if( (Fiber_system.solution->first_local_index() <= dof_index) &&
(dof_index < Fiber_system.solution->last_local_index()) )
{
Fiber_system.solution->set(dof_index, Fiber_data(global_id,it_para));
}
}
}
Fiber_system.solution->close();
Fiber_system.update();
}
else
// part 2) we use parameters: currently, we use tube geometry
{
cout << STRING_CHECK_IMPORTANT <<"use parameters based on tube geometry only"
<< "; orientation based on the element center" << endl;
d_fiber_types = d_fiberPara_info[0].num_fiber_family;
d_fiber_para_num = d_fiberPara_info[0].num_para_per_fiber;
ExplicitSystem& Fiber_system = d_es->get_system<ExplicitSystem>("FiberSystem");
const DofMap& Fiber_dof_map = Fiber_system.get_dof_map();
it_el = mesh.active_local_elements_begin();
var_pre = "Fiber";
string var_middle = "Para";
vector<string> fiber_vars;
fiber_vars.resize(d_fiber_para_num * d_fiber_types);
int it_id = -1;
for (int it_fiber =0 ; it_fiber < d_fiber_types; it_fiber ++)
{
for (int it_para = 0; it_para < d_fiber_para_num; it_para ++ )
{ stringstream ss;
ss << it_fiber;
stringstream ss1;
ss1 << it_para;
// each fiber: a0, a1, a2, C, alpha
it_id ++;
fiber_vars[ it_id]= var_pre + ss.str() + var_middle
+ ss1.str();//::to_string(it_para);
}
}
//std::vector< std::vector<unsigned int> > dof_indices_var(system.n_vars());
std::vector<unsigned int> fiber_dof_indices_var;
for ( ; it_el != it_last_el ; ++it_el)
{
Elem* elem = *it_el;
int domain_id= elem->subdomain_id();
Fiber_info a_fiber_info = d_fiberPara_info[domain_id];
FiberPara2Data(a_fiber_info, elem->centroid());
// mat_values =
//int global_id =elem->id();
for (int it_para = 0; it_para < d_fiber_para_num * d_fiber_types; it_para ++)
{
unsigned int vars = Fiber_system.variable_number (fiber_vars[it_para]);
Fiber_dof_map.dof_indices (elem, fiber_dof_indices_var, vars);
unsigned int dof_index = fiber_dof_indices_var[0];
if( (Fiber_system.solution->first_local_index() <= dof_index) &&
(dof_index < Fiber_system.solution->last_local_index()) )
{
Fiber_system.solution->
set(dof_index,a_fiber_info.fiber_paras[it_para] );
//Fiber_data(global_id)(it_para));
}
}
}
Fiber_system.solution->close();
Fiber_system.update();
Xdr my_io("fiber.xdr",libMeshEnums::WRITE);
Fiber_system.write_serialized_data(my_io,false);
}
}
// part 3: we store auxiliary info
if (d_have_other)
{
DenseMatrix<Number> other_data;
if (!ReadFile2Matrix(other_data,d_other_file) || other_data.m() < d_Elem_num);
{ cout << STRING_ERROR << "check other file:" << d_other_file << endl;
return false;
}
d_other_para_num = other_data.n();
ExplicitSystem& other_system = d_es->get_system<ExplicitSystem>("OtherSystem");
const DofMap& other_dof_map = other_system.get_dof_map();
it_el = mesh.active_local_elements_begin();
std::vector<unsigned int> other_dof_indices_var;
var_pre = "Other";
for ( ; it_el != it_last_el ; ++it_el)
{
Elem* elem = *it_el;
int domain_id= elem->subdomain_id();
// mat_values =
for (int it_para = 0; it_para < d_other_para_num; it_para ++)
{ stringstream ss;
ss << it_para;
string Name_para = var_pre + ss.str();//to_string(it_para);
unsigned int other_vars = other_system.variable_number (Name_para);
other_dof_map.dof_indices (elem, other_dof_indices_var, other_vars);
unsigned int dof_index = other_dof_indices_var[0];
if( (other_system.solution->first_local_index() <= dof_index) &&
(dof_index < other_system.solution->last_local_index()) )
{
other_system.solution->set(dof_index, other_data(elem->id(),it_para));
}
}
}
other_system.solution->close();
other_system.update();
}
cout<<STRING_WRITE_END << "store material info" << endl;
return true;
} // StoreMaterialInfo
Elem *
Packing<Elem *>::unpack (std::vector<largest_id_type>::const_iterator in,
MeshBase * mesh)
{
#ifndef NDEBUG
const std::vector<largest_id_type>::const_iterator original_in = in;
const largest_id_type incoming_header = *in++;
libmesh_assert_equal_to (incoming_header, elem_magic_header);
#endif
// int 0: level
const unsigned int level =
cast_int<unsigned int>(*in++);
#ifdef LIBMESH_ENABLE_AMR
// int 1: p level
const unsigned int p_level =
cast_int<unsigned int>(*in++);
// int 2: refinement flag and encoded has_children
const int rflag = cast_int<int>(*in++);
const int invalid_rflag =
cast_int<int>(Elem::INVALID_REFINEMENTSTATE);
libmesh_assert_greater_equal (rflag, 0);
libmesh_assert_less (rflag, invalid_rflag*2+1);
const bool has_children = (rflag > invalid_rflag);
const Elem::RefinementState refinement_flag = has_children ?
cast_int<Elem::RefinementState>(rflag - invalid_rflag - 1) :
cast_int<Elem::RefinementState>(rflag);
// int 3: p refinement flag
const int pflag = cast_int<int>(*in++);
libmesh_assert_greater_equal (pflag, 0);
libmesh_assert_less (pflag, Elem::INVALID_REFINEMENTSTATE);
const Elem::RefinementState p_refinement_flag =
cast_int<Elem::RefinementState>(pflag);
#else
in += 3;
#endif // LIBMESH_ENABLE_AMR
// int 4: element type
const int typeint = cast_int<int>(*in++);
libmesh_assert_greater_equal (typeint, 0);
libmesh_assert_less (typeint, INVALID_ELEM);
const ElemType type =
cast_int<ElemType>(typeint);
const unsigned int n_nodes =
Elem::type_to_n_nodes_map[type];
// int 5: processor id
const processor_id_type processor_id =
cast_int<processor_id_type>(*in++);
libmesh_assert (processor_id < mesh->n_processors() ||
processor_id == DofObject::invalid_processor_id);
// int 6: subdomain id
const subdomain_id_type subdomain_id =
cast_int<subdomain_id_type>(*in++);
// int 7: dof object id
const dof_id_type id =
cast_int<dof_id_type>(*in++);
libmesh_assert_not_equal_to (id, DofObject::invalid_id);
#ifdef LIBMESH_ENABLE_UNIQUE_ID
// int 8: dof object unique id
const unique_id_type unique_id =
cast_int<unique_id_type>(*in++);
#endif
#ifdef LIBMESH_ENABLE_AMR
// int 9: parent dof object id.
// Note: If level==0, then (*in) == invalid_id. In
// this case, the equality check in cast_int<unsigned>(*in) will
// never succeed. Therefore, we should only attempt the more
// rigorous cast verification in cases where level != 0.
const dof_id_type parent_id =
(level == 0)
? static_cast<dof_id_type>(*in++)
: cast_int<dof_id_type>(*in++);
libmesh_assert (level == 0 || parent_id != DofObject::invalid_id);
libmesh_assert (level != 0 || parent_id == DofObject::invalid_id);
// int 10: local child id
// Note: If level==0, then which_child_am_i is not valid, so don't
// do the more rigorous cast verification.
const unsigned int which_child_am_i =
(level == 0)
? static_cast<unsigned int>(*in++)
: cast_int<unsigned int>(*in++);
#else
in += 2;
#endif // LIBMESH_ENABLE_AMR
const dof_id_type interior_parent_id =
static_cast<dof_id_type>(*in++);
// Make sure we don't miscount above when adding the "magic" header
// plus the real data header
libmesh_assert_equal_to (in - original_in, header_size + 1);
Elem * elem = mesh->query_elem_ptr(id);
// if we already have this element, make sure its
// properties match, and update any missing neighbor
// links, but then go on
if (elem)
{
libmesh_assert_equal_to (elem->level(), level);
libmesh_assert_equal_to (elem->id(), id);
//#ifdef LIBMESH_ENABLE_UNIQUE_ID
// No check for unique id sanity
//#endif
libmesh_assert_equal_to (elem->processor_id(), processor_id);
libmesh_assert_equal_to (elem->subdomain_id(), subdomain_id);
libmesh_assert_equal_to (elem->type(), type);
libmesh_assert_equal_to (elem->n_nodes(), n_nodes);
#ifndef NDEBUG
// All our nodes should be correct
for (unsigned int i=0; i != n_nodes; ++i)
libmesh_assert(elem->node_id(i) ==
cast_int<dof_id_type>(*in++));
#else
in += n_nodes;
#endif
#ifdef LIBMESH_ENABLE_AMR
libmesh_assert_equal_to (elem->refinement_flag(), refinement_flag);
libmesh_assert_equal_to (elem->has_children(), has_children);
#ifdef DEBUG
if (elem->active())
{
libmesh_assert_equal_to (elem->p_level(), p_level);
libmesh_assert_equal_to (elem->p_refinement_flag(), p_refinement_flag);
}
#endif
libmesh_assert (!level || elem->parent() != libmesh_nullptr);
libmesh_assert (!level || elem->parent()->id() == parent_id);
libmesh_assert (!level || elem->parent()->child_ptr(which_child_am_i) == elem);
#endif
// Our interior_parent link should be "close to" correct - we
// may have to update it, but we can check for some
// inconsistencies.
{
// If the sending processor sees no interior_parent here, we'd
// better agree.
if (interior_parent_id == DofObject::invalid_id)
{
if (elem->dim() < LIBMESH_DIM)
libmesh_assert (!(elem->interior_parent()));
}
// If the sending processor has a remote_elem interior_parent,
// then all we know is that we'd better have *some*
// interior_parent
else if (interior_parent_id == remote_elem->id())
{
libmesh_assert(elem->interior_parent());
}
else
{
Elem * ip = mesh->query_elem_ptr(interior_parent_id);
// The sending processor sees an interior parent here, so
// if we don't have that interior element, then we'd
// better have a remote_elem signifying that fact.
if (!ip)
libmesh_assert_equal_to (elem->interior_parent(), remote_elem);
else
{
// The sending processor has an interior_parent here,
// and we have that element, but that does *NOT* mean
// we're already linking to it. Perhaps we initially
// received elem from a processor on which the
// interior_parent link was remote?
libmesh_assert(elem->interior_parent() == ip ||
elem->interior_parent() == remote_elem);
// If the link was originally remote, update it
if (elem->interior_parent() == remote_elem)
{
elem->set_interior_parent(ip);
}
}
}
}
// Our neighbor links should be "close to" correct - we may have
// to update a remote_elem link, and we can check for possible
// inconsistencies along the way.
//
// For subactive elements, we don't bother keeping neighbor
// links in good shape, so there's nothing we need to set or can
// safely assert here.
if (!elem->subactive())
for (auto n : elem->side_index_range())
{
const dof_id_type neighbor_id =
cast_int<dof_id_type>(*in++);
// If the sending processor sees a domain boundary here,
// we'd better agree.
if (neighbor_id == DofObject::invalid_id)
{
libmesh_assert (!(elem->neighbor_ptr(n)));
continue;
}
// If the sending processor has a remote_elem neighbor here,
// then all we know is that we'd better *not* have a domain
// boundary.
if (neighbor_id == remote_elem->id())
{
libmesh_assert(elem->neighbor_ptr(n));
continue;
}
Elem * neigh = mesh->query_elem_ptr(neighbor_id);
// The sending processor sees a neighbor here, so if we
// don't have that neighboring element, then we'd better
// have a remote_elem signifying that fact.
if (!neigh)
{
libmesh_assert_equal_to (elem->neighbor_ptr(n), remote_elem);
continue;
}
// The sending processor has a neighbor here, and we have
// that element, but that does *NOT* mean we're already
// linking to it. Perhaps we initially received both elem
// and neigh from processors on which their mutual link was
// remote?
libmesh_assert(elem->neighbor_ptr(n) == neigh ||
elem->neighbor_ptr(n) == remote_elem);
// If the link was originally remote, we should update it,
// and make sure the appropriate parts of its family link
// back to us.
if (elem->neighbor_ptr(n) == remote_elem)
{
elem->set_neighbor(n, neigh);
elem->make_links_to_me_local(n);
}
}
// Our p level and refinement flags should be "close to" correct
// if we're not an active element - we might have a p level
// increased or decreased by changes in remote_elem children.
//
// But if we have remote_elem children, then we shouldn't be
// doing a projection on this inactive element on this
// processor, so we won't need correct p settings. Couldn't
// hurt to update, though.
#ifdef LIBMESH_ENABLE_AMR
if (elem->processor_id() != mesh->processor_id())
{
elem->hack_p_level(p_level);
elem->set_p_refinement_flag(p_refinement_flag);
}
#endif // LIBMESH_ENABLE_AMR
// FIXME: We should add some debug mode tests to ensure that the
// encoded indexing and boundary conditions are consistent.
}
else
{
// We don't already have the element, so we need to create it.
// Find the parent if necessary
Elem * parent = libmesh_nullptr;
#ifdef LIBMESH_ENABLE_AMR
// Find a child element's parent
if (level > 0)
{
// Note that we must be very careful to construct the send
// connectivity so that parents are encountered before
// children. If we get here and can't find the parent that
// is a fatal error.
parent = mesh->elem_ptr(parent_id);
}
// Or assert that the sending processor sees no parent
else
libmesh_assert_equal_to (parent_id, DofObject::invalid_id);
#else
// No non-level-0 elements without AMR
libmesh_assert_equal_to (level, 0);
#endif
elem = Elem::build(type,parent).release();
libmesh_assert (elem);
#ifdef LIBMESH_ENABLE_AMR
if (level != 0)
{
// Since this is a newly created element, the parent must
// have previously thought of this child as a remote element.
libmesh_assert_equal_to (parent->child_ptr(which_child_am_i), remote_elem);
parent->add_child(elem, which_child_am_i);
}
// Assign the refinement flags and levels
elem->set_p_level(p_level);
elem->set_refinement_flag(refinement_flag);
elem->set_p_refinement_flag(p_refinement_flag);
libmesh_assert_equal_to (elem->level(), level);
// If this element should have children, assign remote_elem to
// all of them for now, for consistency. Later unpacked
// elements may overwrite that.
if (has_children)
{
const unsigned int nc = elem->n_children();
for (unsigned int c=0; c != nc; ++c)
elem->add_child(const_cast<RemoteElem *>(remote_elem), c);
}
#endif // LIBMESH_ENABLE_AMR
// Assign the IDs
elem->subdomain_id() = subdomain_id;
elem->processor_id() = processor_id;
elem->set_id() = id;
#ifdef LIBMESH_ENABLE_UNIQUE_ID
elem->set_unique_id() = unique_id;
#endif
// Assign the connectivity
libmesh_assert_equal_to (elem->n_nodes(), n_nodes);
for (unsigned int n=0; n != n_nodes; n++)
elem->set_node(n) =
mesh->node_ptr
(cast_int<dof_id_type>(*in++));
// Set interior_parent if found
{
// We may be unpacking an element that was a ghost element on the
// sender, in which case the element's interior_parent may not be
// known by the packed element. We'll have to set such
// interior_parents to remote_elem ourselves and wait for a
// later packed element to give us better information.
if (interior_parent_id == remote_elem->id())
{
elem->set_interior_parent
(const_cast<RemoteElem *>(remote_elem));
}
else if (interior_parent_id != DofObject::invalid_id)
{
// If we don't have the interior parent element, then it's
// a remote_elem until we get it.
Elem * ip = mesh->query_elem_ptr(interior_parent_id);
if (!ip )
elem->set_interior_parent
(const_cast<RemoteElem *>(remote_elem));
else
elem->set_interior_parent(ip);
}
}
for (auto n : elem->side_index_range())
{
const dof_id_type neighbor_id =
cast_int<dof_id_type>(*in++);
if (neighbor_id == DofObject::invalid_id)
continue;
// We may be unpacking an element that was a ghost element on the
// sender, in which case the element's neighbors may not all be
// known by the packed element. We'll have to set such
// neighbors to remote_elem ourselves and wait for a later
// packed element to give us better information.
if (neighbor_id == remote_elem->id())
{
elem->set_neighbor(n, const_cast<RemoteElem *>(remote_elem));
continue;
}
// If we don't have the neighbor element, then it's a
// remote_elem until we get it.
Elem * neigh = mesh->query_elem_ptr(neighbor_id);
if (!neigh)
{
elem->set_neighbor(n, const_cast<RemoteElem *>(remote_elem));
continue;
}
// If we have the neighbor element, then link to it, and
// make sure the appropriate parts of its family link back
// to us.
elem->set_neighbor(n, neigh);
elem->make_links_to_me_local(n);
}
elem->unpack_indexing(in);
}
in += elem->packed_indexing_size();
// If this is a coarse element,
// add any element side or edge boundary condition ids
if (level == 0)
{
for (auto s : elem->side_index_range())
{
const boundary_id_type num_bcs =
cast_int<boundary_id_type>(*in++);
for (boundary_id_type bc_it=0; bc_it < num_bcs; bc_it++)
mesh->get_boundary_info().add_side
(elem, s, cast_int<boundary_id_type>(*in++));
}
for (auto e : elem->edge_index_range())
{
const boundary_id_type num_bcs =
cast_int<boundary_id_type>(*in++);
for (boundary_id_type bc_it=0; bc_it < num_bcs; bc_it++)
mesh->get_boundary_info().add_edge
(elem, e, cast_int<boundary_id_type>(*in++));
}
for (unsigned short sf=0; sf != 2; ++sf)
{
const boundary_id_type num_bcs =
cast_int<boundary_id_type>(*in++);
for (boundary_id_type bc_it=0; bc_it < num_bcs; bc_it++)
mesh->get_boundary_info().add_shellface
(elem, sf, cast_int<boundary_id_type>(*in++));
}
}
// Return the new element
return elem;
}
void ExodusII_IO::read (const std::string& fname)
{
// This is a serial-only process for now;
// the Mesh should be read on processor 0 and
// broadcast later
// libmesh_assert_equal_to (libMesh::processor_id(), 0);
#ifndef LIBMESH_HAVE_EXODUS_API
libMesh::err << "ERROR, ExodusII API is not defined.\n"
<< "Input file " << fname << " cannot be read"
<< std::endl;
libmesh_error();
#else
// Get a reference to the mesh we are reading
MeshBase& mesh = MeshInput<MeshBase>::mesh();
// Clear any existing mesh data
mesh.clear();
// Keep track of what kinds of elements this file contains
elems_of_dimension.clear();
elems_of_dimension.resize(4, false);
#ifdef DEBUG
this->verbose(true);
#endif
ExodusII_IO_Helper::ElementMaps em; // Instantiate the ElementMaps interface
exio_helper->open(fname.c_str()); // Open the exodus file, if possible
exio_helper->read_header(); // Get header information from exodus file
exio_helper->print_header(); // Print header information
//assertion fails due to inconsistent mesh dimension
// libmesh_assert_equal_to (static_cast<unsigned int>(exio_helper->get_num_dim()), mesh.mesh_dimension()); // Be sure number of dimensions
// is equal to the number of
// dimensions in the mesh supplied.
exio_helper->read_nodes(); // Read nodes from the exodus file
mesh.reserve_nodes(exio_helper->get_num_nodes()); // Reserve space for the nodes.
// Loop over the nodes, create Nodes with local processor_id 0.
for (int i=0; i<exio_helper->get_num_nodes(); i++)
mesh.add_point (Point(exio_helper->get_x(i),
exio_helper->get_y(i),
exio_helper->get_z(i)), i);
libmesh_assert_equal_to (static_cast<unsigned int>(exio_helper->get_num_nodes()), mesh.n_nodes());
exio_helper->read_block_info(); // Get information about all the blocks
mesh.reserve_elem(exio_helper->get_num_elem()); // Reserve space for the elements
// Read in the element connectivity for each block.
int nelem_last_block = 0;
std::map<int, unsigned int> exodus_id_to_mesh_id;
// Loop over all the blocks
for (int i=0; i<exio_helper->get_num_elem_blk(); i++)
{
// Read the information for block i
exio_helper->read_elem_in_block (i);
int subdomain_id = exio_helper->get_block_id(i);
// populate the map of names
mesh.subdomain_name(static_cast<subdomain_id_type>(subdomain_id)) =
exio_helper->get_block_name(i);
// Set any relevant node/edge maps for this element
const std::string type_str (exio_helper->get_elem_type());
const ExodusII_IO_Helper::Conversion conv = em.assign_conversion(type_str);
//if (_verbose)
//libMesh::out << "Reading a block of " << type_str << " elements." << std::endl;
// Loop over all the faces in this block
int jmax = nelem_last_block+exio_helper->get_num_elem_this_blk();
for (int j=nelem_last_block; j<jmax; j++)
{
Elem* elem = Elem::build (conv.get_canonical_type()).release();
libmesh_assert (elem);
elem->subdomain_id() = static_cast<subdomain_id_type>(subdomain_id) ;
//elem->set_id(j);// Don't try to second guess the Element ID setting scheme!
elems_of_dimension[elem->dim()] = true;
elem = mesh.add_elem (elem); // Catch the Elem pointer that the Mesh throws back
exodus_id_to_mesh_id[j+1] = elem->id();
// Set all the nodes for this element
for (int k=0; k<exio_helper->get_num_nodes_per_elem(); k++)
{
int gi = (j-nelem_last_block)*exio_helper->get_num_nodes_per_elem() + conv.get_node_map(k); // global index
int node_number = exio_helper->get_connect(gi); // Global node number (1-based)
elem->set_node(k) = mesh.node_ptr((node_number-1)); // Set node number
// Subtract 1 since
// exodus is internally 1-based
}
}
// running sum of # of elements per block,
// (should equal total number of elements in the end)
nelem_last_block += exio_helper->get_num_elem_this_blk();
}
libmesh_assert_equal_to (static_cast<unsigned int>(nelem_last_block), mesh.n_elem());
// Set the mesh dimension to the largest encountered for an element
for (unsigned int i=0; i!=4; ++i)
if (elems_of_dimension[i])
mesh.set_mesh_dimension(i);
// Read in sideset information -- this is useful for applying boundary conditions
{
exio_helper->read_sideset_info(); // Get basic information about ALL sidesets
int offset=0;
for (int i=0; i<exio_helper->get_num_side_sets(); i++)
{
offset += (i > 0 ? exio_helper->get_num_sides_per_set(i-1) : 0); // Compute new offset
exio_helper->read_sideset (i, offset);
mesh.boundary_info->sideset_name(exio_helper->get_side_set_id(i)) =
exio_helper->get_side_set_name(i);
}
const std::vector<int>& elem_list = exio_helper->get_elem_list();
const std::vector<int>& side_list = exio_helper->get_side_list();
const std::vector<int>& id_list = exio_helper->get_id_list();
for (unsigned int e=0; e<elem_list.size(); e++)
{
// Set any relevant node/edge maps for this element
Elem * elem = mesh.elem(exodus_id_to_mesh_id[elem_list[e]]);
const ExodusII_IO_Helper::Conversion conv =
em.assign_conversion(elem->type());
mesh.boundary_info->add_side (exodus_id_to_mesh_id[elem_list[e]],
conv.get_side_map(side_list[e]-1),
id_list[e]);
}
}
// Read nodeset info
{
exio_helper->read_nodeset_info();
for (int nodeset=0; nodeset<exio_helper->get_num_node_sets(); nodeset++)
{
int nodeset_id = exio_helper->get_nodeset_id(nodeset);
mesh.boundary_info->nodeset_name(nodeset_id) =
exio_helper->get_node_set_name(nodeset);
exio_helper->read_nodeset(nodeset);
const std::vector<int>& node_list = exio_helper->get_node_list();
for(unsigned int node=0; node<node_list.size(); node++)
mesh.boundary_info->add_node(node_list[node]-1, nodeset_id);
}
}
#if LIBMESH_DIM < 3
if (mesh.mesh_dimension() > LIBMESH_DIM)
{
libMesh::err << "Cannot open dimension " <<
mesh.mesh_dimension() <<
" mesh file when configured without " <<
mesh.mesh_dimension() << "D support." <<
std::endl;
libmesh_error();
}
#endif
#endif
}
// The actual implementation of building elements.
void InfElemBuilder::build_inf_elem(const Point& origin,
const bool x_sym,
const bool y_sym,
const bool z_sym,
const bool be_verbose,
std::set< std::pair<dof_id_type,
unsigned int> >* inner_faces)
{
if (be_verbose)
{
#ifdef DEBUG
libMesh::out << " Building Infinite Elements:" << std::endl;
libMesh::out << " updating element neighbor tables..." << std::endl;
#else
libMesh::out << " Verbose mode disabled in non-debug mode." << std::endl;
#endif
}
// update element neighbors
this->_mesh.find_neighbors();
START_LOG("build_inf_elem()", "InfElemBuilder");
// A set for storing element number, side number pairs.
// pair.first == element number, pair.second == side number
std::set< std::pair<dof_id_type,unsigned int> > faces;
std::set< std::pair<dof_id_type,unsigned int> > ofaces;
// A set for storing node numbers on the outer faces.
std::set<dof_id_type> onodes;
// The distance to the farthest point in the mesh from the origin
Real max_r=0.;
// The index of the farthest point in the mesh from the origin
int max_r_node = -1;
#ifdef DEBUG
if (be_verbose)
{
libMesh::out << " collecting boundary sides";
if (x_sym || y_sym || z_sym)
libMesh::out << ", skipping sides in symmetry planes..." << std::endl;
else
libMesh::out << "..." << std::endl;
}
#endif
// Iterate through all elements and sides, collect indices of all active
// boundary sides in the faces set. Skip sides which lie in symmetry planes.
// Later, sides of the inner boundary will be sorted out.
{
MeshBase::element_iterator it = this->_mesh.active_elements_begin();
const MeshBase::element_iterator end = this->_mesh.active_elements_end();
for(; it != end; ++it)
{
Elem* elem = *it;
for (unsigned int s=0; s<elem->n_neighbors(); s++)
{
// check if elem(e) is on the boundary
if (elem->neighbor(s) == NULL)
{
// note that it is safe to use the Elem::side() method,
// which gives a non-full-ordered element
AutoPtr<Elem> side(elem->build_side(s));
// bool flags for symmetry detection
bool sym_side=false;
bool on_x_sym=true;
bool on_y_sym=true;
bool on_z_sym=true;
// Loop over the nodes to check whether they are on the symmetry planes,
// and therefore sufficient to use a non-full-ordered side element
for(unsigned int n=0; n<side->n_nodes(); n++)
{
const Point dist_from_origin = this->_mesh.point(side->node(n)) - origin;
if(x_sym)
if( std::abs(dist_from_origin(0)) > 1.e-3 )
on_x_sym=false;
if(y_sym)
if( std::abs(dist_from_origin(1)) > 1.e-3 )
on_y_sym=false;
if(z_sym)
if( std::abs(dist_from_origin(2)) > 1.e-3 )
on_z_sym=false;
// if(x_sym)
// if( std::abs(dist_from_origin(0)) > 1.e-6 )
// on_x_sym=false;
// if(y_sym)
// if( std::abs(dist_from_origin(1)) > 1.e-6 )
// on_y_sym=false;
// if(z_sym)
// if( std::abs(dist_from_origin(2)) > 1.e-6 )
// on_z_sym=false;
//find the node most distant from origin
Real r = dist_from_origin.size();
if (r > max_r)
{
max_r = r;
max_r_node=side->node(n);
}
}
sym_side = (x_sym && on_x_sym) || (y_sym && on_y_sym) || (z_sym && on_z_sym);
if (!sym_side)
faces.insert( std::make_pair(elem->id(), s) );
} // neighbor(s) == NULL
} // sides
} // elems
}
// If a boundary side has one node on the outer boundary,
// all points of this side are on the outer boundary.
// Start with the node most distant from origin, which has
// to be on the outer boundary, then recursively find all
// sides and nodes connected to it. Found sides are moved
// from faces to ofaces, nodes are collected in onodes.
// Here, the search is done iteratively, because, depending on
// the mesh, a very high level of recursion might be necessary.
if (max_r_node > 0)
onodes.insert(max_r_node);
{
std::set< std::pair<dof_id_type,unsigned int> >::iterator face_it = faces.begin();
unsigned int facesfound=0;
while (face_it != faces.end()) {
std::pair<dof_id_type, unsigned int> p;
p = *face_it;
// This has to be a full-ordered side element,
// since we need the correct n_nodes,
AutoPtr<Elem> side(this->_mesh.elem(p.first)->build_side(p.second));
bool found=false;
for(unsigned int sn=0; sn<side->n_nodes(); sn++)
if(onodes.count(side->node(sn)))
{
found=true;
break;
}
// If a new oface is found, include its nodes in onodes
if(found)
{
for(unsigned int sn=0; sn<side->n_nodes(); sn++)
onodes.insert(side->node(sn));
ofaces.insert(p);
face_it++; // iteration is done here
faces.erase(p);
facesfound++;
}
else
face_it++; // iteration is done here
// If at least one new oface was found in this cycle,
// do another search cycle.
if(facesfound>0 && face_it == faces.end())
{
facesfound = 0;
face_it = faces.begin();
}
}
}
#ifdef DEBUG
if (be_verbose)
libMesh::out << " found "
<< faces.size()
<< " inner and "
<< ofaces.size()
<< " outer boundary faces"
<< std::endl;
#endif
// When the user provided a non-null pointer to
// inner_faces, that implies he wants to have
// this std::set. For now, simply copy the data.
if (inner_faces != NULL)
*inner_faces = faces;
// free memory, clear our local variable, no need
// for it any more.
faces.clear();
// outer_nodes maps onodes to their duplicates
std::map<dof_id_type, Node *> outer_nodes;
// We may need to pick our own object ids in parallel
dof_id_type old_max_node_id = _mesh.max_node_id();
dof_id_type old_max_elem_id = _mesh.max_elem_id();
// for each boundary node, add an outer_node with
// double distance from origin.
std::set<dof_id_type>::iterator on_it = onodes.begin();
for( ; on_it != onodes.end(); ++on_it)
{
Point p = (Point(this->_mesh.point(*on_it)) * 2) - origin;
if (_mesh.is_serial())
{
// Add with a default id in serial
outer_nodes[*on_it]=this->_mesh.add_point(p);
}
else
{
// Pick a unique id in parallel
Node &bnode = _mesh.node(*on_it);
dof_id_type new_id = bnode.id() + old_max_node_id;
outer_nodes[*on_it] =
this->_mesh.add_point(p, new_id,
bnode.processor_id());
}
}
#ifdef DEBUG
// for verbose, remember n_elem
dof_id_type n_conventional_elem = this->_mesh.n_elem();
#endif
// build Elems based on boundary side type
std::set< std::pair<dof_id_type,unsigned int> >::iterator face_it = ofaces.begin();
for( ; face_it != ofaces.end(); ++face_it)
{
// Shortcut to the pair being iterated over
std::pair<dof_id_type,unsigned int> p = *face_it;
// build a full-ordered side element to get the base nodes
AutoPtr<Elem> side(this->_mesh.elem(p.first)->build_side(p.second));
// create cell depending on side type, assign nodes,
// use braces to force scope.
bool is_higher_order_elem = false;
{
Elem* el;
switch(side->type())
{
// 3D infinite elements
// TRIs
case TRI3:
el=new InfPrism6;
break;
case TRI6:
el=new InfPrism12;
is_higher_order_elem = true;
break;
// QUADs
case QUAD4:
el=new InfHex8;
break;
case QUAD8:
el=new InfHex16;
is_higher_order_elem = true;
break;
case QUAD9:
el=new InfHex18;
// the method of assigning nodes (which follows below)
// omits in the case of QUAD9 the bubble node; therefore
// we assign these first by hand here.
el->set_node(16) = side->get_node(8);
el->set_node(17) = outer_nodes[side->node(8)];
is_higher_order_elem=true;
break;
// 2D infinite elements
case EDGE2:
el=new InfQuad4;
break;
case EDGE3:
el=new InfQuad6;
el->set_node(4) = side->get_node(2);
break;
// 1D infinite elements not supported
default:
libMesh::out << "InfElemBuilder::build_inf_elem(Point, bool, bool, bool, bool): "
<< "invalid face element "
<< std::endl;
continue;
}
// In parallel, assign unique ids to the new element
if (!_mesh.is_serial())
{
Elem *belem = _mesh.elem(p.first);
el->processor_id() = belem->processor_id();
// We'd better not have elements with more than 6 sides
el->set_id (belem->id() * 6 + p.second + old_max_elem_id);
}
// assign vertices to the new infinite element
const unsigned int n_base_vertices = side->n_vertices();
for(unsigned int i=0; i<n_base_vertices; i++)
{
el->set_node(i ) = side->get_node(i);
el->set_node(i+n_base_vertices) = outer_nodes[side->node(i)];
}
// when this is a higher order element,
// assign also the nodes in between
if (is_higher_order_elem)
{
// n_safe_base_nodes is the number of nodes in \p side
// that may be safely assigned using below for loop.
// Actually, n_safe_base_nodes is _identical_ with el->n_vertices(),
// since for QUAD9, the 9th node was already assigned above
const unsigned int n_safe_base_nodes = el->n_vertices();
for(unsigned int i=n_base_vertices; i<n_safe_base_nodes; i++)
{
el->set_node(i+n_base_vertices) = side->get_node(i);
el->set_node(i+n_safe_base_nodes) = outer_nodes[side->node(i)];
}
}
// add infinite element to mesh
this->_mesh.add_elem(el);
} // el goes out of scope
} // for
#ifdef DEBUG
_mesh.libmesh_assert_valid_parallel_ids();
if (be_verbose)
libMesh::out << " added "
<< this->_mesh.n_elem() - n_conventional_elem
<< " infinite elements and "
<< onodes.size()
<< " nodes to the mesh"
<< std::endl
<< std::endl;
#endif
STOP_LOG("build_inf_elem()", "InfElemBuilder");
}
void ExodusII_IO::read (const std::string & fname)
{
// Get a reference to the mesh we are reading
MeshBase & mesh = MeshInput<MeshBase>::mesh();
// Clear any existing mesh data
mesh.clear();
// Keep track of what kinds of elements this file contains
elems_of_dimension.clear();
elems_of_dimension.resize(4, false);
#ifdef DEBUG
this->verbose(true);
#endif
// Instantiate the ElementMaps interface
ExodusII_IO_Helper::ElementMaps em(*exio_helper);
// Open the exodus file in EX_READ mode
exio_helper->open(fname.c_str(), /*read_only=*/true);
// Get header information from exodus file
exio_helper->read_header();
// Read the QA records
exio_helper->read_qa_records();
// Print header information
exio_helper->print_header();
// Read nodes from the exodus file
exio_helper->read_nodes();
// Reserve space for the nodes.
mesh.reserve_nodes(exio_helper->num_nodes);
// Read the node number map from the Exodus file. This is
// required if we want to preserve the numbering of nodes as it
// exists in the Exodus file. If the Exodus file does not contain
// a node_num_map, the identity map is returned by this call.
exio_helper->read_node_num_map();
// Loop over the nodes, create Nodes with local processor_id 0.
for (int i=0; i<exio_helper->num_nodes; i++)
{
// Use the node_num_map to get the correct ID for Exodus
int exodus_id = exio_helper->node_num_map[i];
// Catch the node that was added to the mesh
Node * added_node = mesh.add_point (Point(exio_helper->x[i], exio_helper->y[i], exio_helper->z[i]), exodus_id-1);
// If the Mesh assigned an ID different from what is in the
// Exodus file, we should probably error.
if (added_node->id() != static_cast<unsigned>(exodus_id-1))
libmesh_error_msg("Error! Mesh assigned node ID " \
<< added_node->id() \
<< " which is different from the (zero-based) Exodus ID " \
<< exodus_id-1 \
<< "!");
}
// This assert is no longer valid if the nodes are not numbered
// sequentially starting from 1 in the Exodus file.
// libmesh_assert_equal_to (static_cast<unsigned int>(exio_helper->num_nodes), mesh.n_nodes());
// Get information about all the blocks
exio_helper->read_block_info();
// Reserve space for the elements
mesh.reserve_elem(exio_helper->num_elem);
// Read the element number map from the Exodus file. This is
// required if we want to preserve the numbering of elements as it
// exists in the Exodus file. If the Exodus file does not contain
// an elem_num_map, the identity map is returned by this call.
exio_helper->read_elem_num_map();
// Read in the element connectivity for each block.
int nelem_last_block = 0;
// Loop over all the blocks
for (int i=0; i<exio_helper->num_elem_blk; i++)
{
// Read the information for block i
exio_helper->read_elem_in_block (i);
int subdomain_id = exio_helper->get_block_id(i);
// populate the map of names
std::string subdomain_name = exio_helper->get_block_name(i);
if (!subdomain_name.empty())
mesh.subdomain_name(static_cast<subdomain_id_type>(subdomain_id)) = subdomain_name;
// Set any relevant node/edge maps for this element
const std::string type_str (exio_helper->get_elem_type());
const ExodusII_IO_Helper::Conversion conv = em.assign_conversion(type_str);
// Loop over all the faces in this block
int jmax = nelem_last_block+exio_helper->num_elem_this_blk;
for (int j=nelem_last_block; j<jmax; j++)
{
Elem * elem = Elem::build (conv.get_canonical_type()).release();
libmesh_assert (elem);
elem->subdomain_id() = static_cast<subdomain_id_type>(subdomain_id) ;
// Use the elem_num_map to obtain the ID of this element in the Exodus file
int exodus_id = exio_helper->elem_num_map[j];
// Assign this element the same ID it had in the Exodus
// file, but make it zero-based by subtracting 1. Note:
// some day we could use 1-based numbering in libmesh and
// thus match the Exodus numbering exactly, but at the
// moment libmesh is zero-based.
elem->set_id(exodus_id-1);
// Record that we have seen an element of dimension elem->dim()
elems_of_dimension[elem->dim()] = true;
// Catch the Elem pointer that the Mesh throws back
elem = mesh.add_elem (elem);
// If the Mesh assigned an ID different from what is in the
// Exodus file, we should probably error.
if (elem->id() != static_cast<unsigned>(exodus_id-1))
libmesh_error_msg("Error! Mesh assigned ID " \
<< elem->id() \
<< " which is different from the (zero-based) Exodus ID " \
<< exodus_id-1 \
<< "!");
// Set all the nodes for this element
for (int k=0; k<exio_helper->num_nodes_per_elem; k++)
{
// global index
int gi = (j-nelem_last_block)*exio_helper->num_nodes_per_elem + conv.get_node_map(k);
// The entries in 'connect' are actually (1-based)
// indices into the node_num_map, so to get the right
// node ID we:
// 1.) Subtract 1 from connect[gi]
// 2.) Pass it through node_num_map to get the corresponding Exodus ID
// 3.) Subtract 1 from that, since libmesh node numbering is "zero"-based,
// even when the Exodus node numbering doesn't start with 1.
int libmesh_node_id = exio_helper->node_num_map[exio_helper->connect[gi] - 1] - 1;
// Set the node pointer in the Elem
elem->set_node(k) = mesh.node_ptr(libmesh_node_id);
}
}
// running sum of # of elements per block,
// (should equal total number of elements in the end)
nelem_last_block += exio_helper->num_elem_this_blk;
}
// This assert isn't valid if the Exodus file's numbering doesn't
// start with 1! For example, if Exodus's elem_num_map is 21, 22,
// 23, 24, 25, 26, 27, 28, 29, 30, ... 84, then by the time you are
// done with the loop above, mesh.n_elem() will report 84 and
// nelem_last_block will be 64.
// libmesh_assert_equal_to (static_cast<unsigned>(nelem_last_block), mesh.n_elem());
// Set the mesh dimension to the largest encountered for an element
for (unsigned char i=0; i!=4; ++i)
if (elems_of_dimension[i])
mesh.set_mesh_dimension(i);
// Read in sideset information -- this is useful for applying boundary conditions
{
// Get basic information about all sidesets
exio_helper->read_sideset_info();
int offset=0;
for (int i=0; i<exio_helper->num_side_sets; i++)
{
// Compute new offset
offset += (i > 0 ? exio_helper->num_sides_per_set[i-1] : 0);
exio_helper->read_sideset (i, offset);
std::string sideset_name = exio_helper->get_side_set_name(i);
if (!sideset_name.empty())
mesh.get_boundary_info().sideset_name
(cast_int<boundary_id_type>(exio_helper->get_side_set_id(i)))
= sideset_name;
}
for (unsigned int e=0; e<exio_helper->elem_list.size(); e++)
{
// The numbers in the Exodus file sidesets should be thought
// of as (1-based) indices into the elem_num_map array. So,
// to get the right element ID we have to:
// 1.) Subtract 1 from elem_list[e] (to get a zero-based index)
// 2.) Pass it through elem_num_map (to get the corresponding Exodus ID)
// 3.) Subtract 1 from that, since libmesh is "zero"-based,
// even when the Exodus numbering doesn't start with 1.
dof_id_type libmesh_elem_id =
cast_int<dof_id_type>(exio_helper->elem_num_map[exio_helper->elem_list[e] - 1] - 1);
// Set any relevant node/edge maps for this element
Elem * elem = mesh.elem(libmesh_elem_id);
const ExodusII_IO_Helper::Conversion conv = em.assign_conversion(elem->type());
// Map the zero-based Exodus side numbering to the libmesh side numbering
int mapped_side = conv.get_side_map(exio_helper->side_list[e]-1);
// Check for errors
if (mapped_side == ExodusII_IO_Helper::Conversion::invalid_id)
libmesh_error_msg("Invalid 1-based side id: " \
<< exio_helper->side_list[e] \
<< " detected for " \
<< Utility::enum_to_string(elem->type()));
// Add this (elem,side,id) triplet to the BoundaryInfo object.
mesh.get_boundary_info().add_side (libmesh_elem_id,
cast_int<unsigned short>(mapped_side),
cast_int<boundary_id_type>(exio_helper->id_list[e]));
}
}
// Read nodeset info
{
exio_helper->read_nodeset_info();
for (int nodeset=0; nodeset<exio_helper->num_node_sets; nodeset++)
{
boundary_id_type nodeset_id =
cast_int<boundary_id_type>(exio_helper->nodeset_ids[nodeset]);
std::string nodeset_name = exio_helper->get_node_set_name(nodeset);
if (!nodeset_name.empty())
mesh.get_boundary_info().nodeset_name(nodeset_id) = nodeset_name;
exio_helper->read_nodeset(nodeset);
for (unsigned int node=0; node<exio_helper->node_list.size(); node++)
{
// As before, the entries in 'node_list' are 1-based
// indcies into the node_num_map array, so we have to map
// them. See comment above.
int libmesh_node_id = exio_helper->node_num_map[exio_helper->node_list[node] - 1] - 1;
mesh.get_boundary_info().add_node(cast_int<dof_id_type>(libmesh_node_id),
nodeset_id);
}
}
}
#if LIBMESH_DIM < 3
if (mesh.mesh_dimension() > LIBMESH_DIM)
libmesh_error_msg("Cannot open dimension " \
<< mesh.mesh_dimension() \
<< " mesh file when configured without " \
<< mesh.mesh_dimension() \
<< "D support.");
#endif
}
// The main program
int main(int argc, char** argv)
{
//for record-keeping
std::cout << "Running: " << argv[0];
for (int i=1; i<argc; i++)
std::cout << " " << argv[i];
std::cout << std::endl << std::endl;
clock_t begin = std::clock();
// Initialize libMesh
LibMeshInit init(argc, argv);
// Parameters
GetPot solverInfile("fem_system_params.in");
const bool transient = solverInfile("transient", false);
unsigned int n_timesteps = solverInfile("n_timesteps", 1);
const int nx = solverInfile("nx",100);
const int ny = solverInfile("ny",100);
const int nz = solverInfile("nz",100);
GetPot infile("contamTrans.in");
//std::string find_mesh_here = infile("initial_mesh","mesh.exo");
bool doContinuation = infile("do_continuation",false);
bool splitSuperAdj = infile("split_super_adjoint",true); //solve as single adjoint or two forwards
int maxIter = infile("max_model_refinements",0); //maximum number of model refinements
double refStep = infile("refinement_step",0.1); //additional proportion of domain refined per step
//this refers to additional basis functions...number of elements will be more...
double qoiErrorTol = infile("relative_error_tolerance",0.01); //stopping criterion
//bool doDivvyMatlab = infile("do_divvy_in_Matlab",false); //output files to determine next refinement in Matlab
bool avoid_sides = infile("avoid_sides",false); //DEBUG, whether to avoid sides while refining
if(refStep*maxIter > 1)
maxIter = round(ceil(1./refStep));
Mesh mesh(init.comm());
Mesh mesh2(init.comm());
//create mesh
unsigned int dim;
if(nz == 0){ //to check if oscillations happen in 2D as well...
dim = 2;
MeshTools::Generation::build_square(mesh, nx, ny, 0., 2300., 0., 1650., QUAD9);
MeshTools::Generation::build_square(mesh2, nx, ny, 0., 2300., 0., 1650., QUAD9);
}else{
dim = 3;
MeshTools::Generation::build_cube(mesh, nx, ny, nz, 0., 2300., 0., 1650., 0., 100., HEX27);
MeshTools::Generation::build_cube(mesh2, nx, ny, nz, 0., 2300., 0., 1650., 0., 100., HEX27);
}
mesh.print_info(); //DEBUG
// Create an equation systems object.
EquationSystems equation_systems (mesh);
EquationSystems equation_systems_mix(mesh2);
//name system
ConvDiff_PrimarySys & system_primary =
equation_systems.add_system<ConvDiff_PrimarySys>("ConvDiff_PrimarySys"); //for primary variables
ConvDiff_AuxSys & system_aux =
equation_systems.add_system<ConvDiff_AuxSys>("ConvDiff_AuxSys"); //for auxiliary variables
ConvDiff_MprimeSys & system_mix =
equation_systems_mix.add_system<ConvDiff_MprimeSys>("Diff_ConvDiff_MprimeSys"); //for superadj
ConvDiff_PrimarySadjSys & system_sadj_primary =
equation_systems.add_system<ConvDiff_PrimarySadjSys>("ConvDiff_PrimarySadjSys"); //for split superadj
ConvDiff_AuxSadjSys & system_sadj_aux =
equation_systems.add_system<ConvDiff_AuxSadjSys>("ConvDiff_AuxSadjSys"); //for split superadj
//steady-state problem
system_primary.time_solver =
AutoPtr<TimeSolver>(new SteadySolver(system_primary));
system_aux.time_solver =
AutoPtr<TimeSolver>(new SteadySolver(system_aux));
system_mix.time_solver =
AutoPtr<TimeSolver>(new SteadySolver(system_mix));
system_sadj_primary.time_solver =
AutoPtr<TimeSolver>(new SteadySolver(system_sadj_primary));
system_sadj_aux.time_solver =
AutoPtr<TimeSolver>(new SteadySolver(system_sadj_aux));
libmesh_assert_equal_to (n_timesteps, 1);
// Initialize the system
equation_systems.init ();
equation_systems_mix.init();
//initial guess for primary state
read_initial_parameters();
system_primary.project_solution(initial_value, initial_grad,
equation_systems.parameters);
finish_initialization();
//nonlinear solver options
NewtonSolver *solver_sadj_primary = new NewtonSolver(system_sadj_primary);
system_sadj_primary.time_solver->diff_solver() = AutoPtr<DiffSolver>(solver_sadj_primary);
solver_sadj_primary->quiet = solverInfile("solver_quiet", true);
solver_sadj_primary->verbose = !solver_sadj_primary->quiet;
solver_sadj_primary->max_nonlinear_iterations =
solverInfile("max_nonlinear_iterations", 15);
solver_sadj_primary->relative_step_tolerance =
solverInfile("relative_step_tolerance", 1.e-3);
solver_sadj_primary->relative_residual_tolerance =
solverInfile("relative_residual_tolerance", 0.0);
solver_sadj_primary->absolute_residual_tolerance =
solverInfile("absolute_residual_tolerance", 0.0);
NewtonSolver *solver_sadj_aux = new NewtonSolver(system_sadj_aux);
system_sadj_aux.time_solver->diff_solver() = AutoPtr<DiffSolver>(solver_sadj_aux);
solver_sadj_aux->quiet = solverInfile("solver_quiet", true);
solver_sadj_aux->verbose = !solver_sadj_aux->quiet;
solver_sadj_aux->max_nonlinear_iterations =
solverInfile("max_nonlinear_iterations", 15);
solver_sadj_aux->relative_step_tolerance =
solverInfile("relative_step_tolerance", 1.e-3);
solver_sadj_aux->relative_residual_tolerance =
solverInfile("relative_residual_tolerance", 0.0);
solver_sadj_aux->absolute_residual_tolerance =
solverInfile("absolute_residual_tolerance", 0.0);
NewtonSolver *solver_primary = new NewtonSolver(system_primary);
system_primary.time_solver->diff_solver() = AutoPtr<DiffSolver>(solver_primary);
solver_primary->quiet = solverInfile("solver_quiet", true);
solver_primary->verbose = !solver_primary->quiet;
solver_primary->max_nonlinear_iterations =
solverInfile("max_nonlinear_iterations", 15);
solver_primary->relative_step_tolerance =
solverInfile("relative_step_tolerance", 1.e-3);
solver_primary->relative_residual_tolerance =
solverInfile("relative_residual_tolerance", 0.0);
solver_primary->absolute_residual_tolerance =
solverInfile("absolute_residual_tolerance", 0.0);
NewtonSolver *solver_aux = new NewtonSolver(system_aux);
system_aux.time_solver->diff_solver() = AutoPtr<DiffSolver>(solver_aux);
solver_aux->quiet = solverInfile("solver_quiet", true);
solver_aux->verbose = !solver_aux->quiet;
solver_aux->max_nonlinear_iterations =
solverInfile("max_nonlinear_iterations", 15);
solver_aux->relative_step_tolerance =
solverInfile("relative_step_tolerance", 1.e-3);
solver_aux->relative_residual_tolerance =
solverInfile("relative_residual_tolerance", 0.0);
solver_aux->absolute_residual_tolerance =
solverInfile("absolute_residual_tolerance", 0.0);
solver_primary->require_residual_reduction = solverInfile("require_residual_reduction",true);
solver_sadj_primary->require_residual_reduction = solverInfile("require_residual_reduction",true);
solver_aux->require_residual_reduction = solverInfile("require_residual_reduction",true);
solver_sadj_aux->require_residual_reduction = solverInfile("require_residual_reduction",true);
//linear solver options
solver_primary->max_linear_iterations = solverInfile("max_linear_iterations",10000);
solver_primary->initial_linear_tolerance = solverInfile("initial_linear_tolerance",1.e-13);
solver_primary->minimum_linear_tolerance = solverInfile("minimum_linear_tolerance",1.e-13);
solver_primary->linear_tolerance_multiplier = solverInfile("linear_tolerance_multiplier",1.e-3);
solver_aux->max_linear_iterations = solverInfile("max_linear_iterations",10000);
solver_aux->initial_linear_tolerance = solverInfile("initial_linear_tolerance",1.e-13);
solver_aux->minimum_linear_tolerance = solverInfile("minimum_linear_tolerance",1.e-13);
solver_aux->linear_tolerance_multiplier = solverInfile("linear_tolerance_multiplier",1.e-3);
solver_sadj_primary->max_linear_iterations = solverInfile("max_linear_iterations",10000);
solver_sadj_primary->initial_linear_tolerance = solverInfile("initial_linear_tolerance",1.e-13);
solver_sadj_primary->minimum_linear_tolerance = solverInfile("minimum_linear_tolerance",1.e-13);
solver_sadj_primary->linear_tolerance_multiplier = solverInfile("linear_tolerance_multiplier",1.e-3);
solver_sadj_aux->max_linear_iterations = solverInfile("max_linear_iterations",10000);
solver_sadj_aux->initial_linear_tolerance = solverInfile("initial_linear_tolerance",1.e-13);
solver_sadj_aux->minimum_linear_tolerance = solverInfile("minimum_linear_tolerance",1.e-13);
solver_sadj_aux->linear_tolerance_multiplier = solverInfile("linear_tolerance_multiplier",1.e-3);
/*if(doDivvyMatlab){
//DOF maps and such to help visualize
std::ofstream output_global_dof("global_dof_map.dat");
for(unsigned int i = 0 ; i < system_mix.get_mesh().n_elem(); i++){
std::vector< dof_id_type > di;
system_mix.get_dof_map().dof_indices(system_mix.get_mesh().elem(i), di);
if(output_global_dof.is_open()){
output_global_dof << i << " ";
for(unsigned int j = 0; j < di.size(); j++)
output_global_dof << di[j] << " ";
output_global_dof << "\n";
}
}
output_global_dof.close();
std::ofstream output_elem_cent("elem_centroids.dat");
for(unsigned int i = 0 ; i < system_mix.get_mesh().n_elem(); i++){
Point elem_cent = system_mix.get_mesh().elem(i)->centroid();
if(output_elem_cent.is_open()){
output_elem_cent << elem_cent(0) << " " << elem_cent(1) << "\n";
}
}
output_elem_cent.close();
}*/
//inverse dof map (elements in support of each node, assuming every 6 dofs belong to same node)
std::vector<std::set<dof_id_type> > node_to_elem;
node_to_elem.resize(round(system_mix.n_dofs()/6.));
for(unsigned int i = 0 ; i < system_mix.get_mesh().n_elem(); i++){
std::vector< dof_id_type > di;
system_mix.get_dof_map().dof_indices(system_mix.get_mesh().elem(i), di);
for(unsigned int j = 0; j < di.size(); j++)
node_to_elem[round(floor(di[j]/6.))].insert(i);
}
int refIter = 0;
double relError = 2.*qoiErrorTol;
while(refIter <= maxIter && relError > qoiErrorTol){
if(!doContinuation){ //clear out previous solutions
system_primary.solution->zero();
system_aux.solution->zero();
system_sadj_primary.solution->zero();
system_sadj_aux.solution->zero();
}
system_mix.solution->zero();
clock_t begin_inv = std::clock();
system_primary.solve();
system_primary.clearQoI();
clock_t end_inv = std::clock();
clock_t begin_err_est = std::clock();
std::cout << "\n End primary solve, begin auxiliary solve..." << std::endl;
system_aux.solve();
std::cout << "\n End auxiliary solve..." << std::endl;
clock_t end_aux = std::clock();
system_primary.postprocess();
system_aux.postprocess();
system_sadj_primary.set_c_vals(system_primary.get_c_vals());
system_sadj_aux.set_auxc_vals(system_aux.get_auxc_vals());
equation_systems_mix.reinit();
//combine primary and auxiliary variables into psi
DirectSolutionTransfer sol_transfer(init.comm());
sol_transfer.transfer(system_aux.variable(system_aux.variable_number("aux_c")),
system_mix.variable(system_mix.variable_number("aux_c")));
sol_transfer.transfer(system_aux.variable(system_aux.variable_number("aux_zc")),
system_mix.variable(system_mix.variable_number("aux_zc")));
sol_transfer.transfer(system_aux.variable(system_aux.variable_number("aux_fc")),
system_mix.variable(system_mix.variable_number("aux_fc")));
AutoPtr<NumericVector<Number> > just_aux = system_mix.solution->clone();
sol_transfer.transfer(system_primary.variable(system_primary.variable_number("c")),
system_mix.variable(system_mix.variable_number("c")));
sol_transfer.transfer(system_primary.variable(system_primary.variable_number("zc")),
system_mix.variable(system_mix.variable_number("zc")));
sol_transfer.transfer(system_primary.variable(system_primary.variable_number("fc")),
system_mix.variable(system_mix.variable_number("fc")));
if(!splitSuperAdj){ //solve super-adjoint as single adjoint
system_mix.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_mix.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_sol = system_mix.get_adjoint_solution(0); //DEBUG
system_mix.assemble(); //calculate residual to correspond to solution
//std::cout << "\n sadj norm: " << system_mix.calculate_norm(dual_sol, L2) << std::endl; //DEBUG
//std::cout << system_mix.calculate_norm(dual_sol, 0, L2) << std::endl; //DEBUG
//std::cout << system_mix.calculate_norm(dual_sol, 1, L2) << std::endl; //DEBUG
//std::cout << system_mix.calculate_norm(dual_sol, 2, L2) << std::endl; //DEBUG
//std::cout << system_mix.calculate_norm(dual_sol, 3, L2) << std::endl; //DEBUG
//std::cout << system_mix.calculate_norm(dual_sol, 4, L2) << std::endl; //DEBUG
//std::cout << system_mix.calculate_norm(dual_sol, 5, L2) << std::endl; //DEBUG
}else{ //solve super-adjoint as
system_mix.assemble(); //calculate residual to correspond to solution
std::cout << "\n Begin primary super-adjoint solve...\n" << std::endl;
system_sadj_primary.solve();
std::cout << "\n End primary super-adjoint solve, begin auxiliary super-adjoint solve...\n" << std::endl;
system_sadj_aux.solve();
std::cout << "\n End auxiliary super-adjoint solve...\n" << std::endl;
const std::string & adjoint_solution0_name = "adjoint_solution0";
system_mix.add_vector(adjoint_solution0_name, false, GHOSTED);
system_mix.set_vector_as_adjoint(adjoint_solution0_name,0);
NumericVector<Number> &eep = system_mix.add_adjoint_rhs(0);
system_mix.set_adjoint_already_solved(true);
NumericVector<Number> &dual_sol = system_mix.get_adjoint_solution(0);
NumericVector<Number> &primal_sol = *system_mix.solution;
dual_sol.swap(primal_sol);
sol_transfer.transfer(system_sadj_aux.variable(system_sadj_aux.variable_number("sadj_aux_c")),
system_mix.variable(system_mix.variable_number("aux_c")));
sol_transfer.transfer(system_sadj_aux.variable(system_sadj_aux.variable_number("sadj_aux_zc")),
system_mix.variable(system_mix.variable_number("aux_zc")));
sol_transfer.transfer(system_sadj_aux.variable(system_sadj_aux.variable_number("sadj_aux_fc")),
system_mix.variable(system_mix.variable_number("aux_fc")));
sol_transfer.transfer(system_sadj_primary.variable(system_sadj_primary.variable_number("sadj_c")),
system_mix.variable(system_mix.variable_number("c")));
sol_transfer.transfer(system_sadj_primary.variable(system_sadj_primary.variable_number("sadj_zc")),
system_mix.variable(system_mix.variable_number("zc")));
sol_transfer.transfer(system_sadj_primary.variable(system_sadj_primary.variable_number("sadj_fc")),
system_mix.variable(system_mix.variable_number("fc")));
//std::cout << "\n sadj norm: " << system_mix.calculate_norm(primal_sol, L2) << std::endl; //DEBUG
dual_sol.swap(primal_sol);
//std::cout << "\n sadj norm: " << system_mix.calculate_norm(primal_sol, L2) << std::endl; //DEBUG
//std::cout << system_sadj_primary.calculate_norm(*system_sadj_primary.solution, 0, L2) << std::endl; //DEBUG
//std::cout << system_sadj_primary.calculate_norm(*system_sadj_primary.solution, 1, L2) << std::endl; //DEBUG
//std::cout << system_sadj_primary.calculate_norm(*system_sadj_primary.solution, 2, L2) << std::endl; //DEBUG
//std::cout << system_sadj_aux.calculate_norm(*system_sadj_aux.solution, 0, L2) << std::endl; //DEBUG
//std::cout << system_sadj_aux.calculate_norm(*system_sadj_aux.solution, 1, L2) << std::endl; //DEBUG
//std::cout << system_sadj_aux.calculate_norm(*system_sadj_aux.solution, 2, L2) << std::endl; //DEBUG
}
NumericVector<Number> &dual_solution = system_mix.get_adjoint_solution(0);
/*
NumericVector<Number> &primal_solution = *system_mix.solution; //DEBUG
primal_solution.swap(dual_solution); //DEBUG
ExodusII_IO(mesh).write_timestep("super_adjoint.exo",
equation_systems,
1, / his number indicates how many time steps are being written to the file
system_mix.time); //DEBUG
primal_solution.swap(dual_solution); //DEBUG
*/
//adjoint-weighted residual
AutoPtr<NumericVector<Number> > adjresid = system_mix.solution->zero_clone();
adjresid->pointwise_mult(*system_mix.rhs,dual_solution);
adjresid->scale(-0.5);
std::cout << "\n -0.5*M'_HF(psiLF)(superadj): " << adjresid->sum() << std::endl; //DEBUG
//LprimeHF(psiLF)
AutoPtr<NumericVector<Number> > LprimeHF_psiLF = system_mix.solution->zero_clone();
LprimeHF_psiLF->pointwise_mult(*system_mix.rhs,*just_aux);
std::cout << " L'_HF(psiLF): " << LprimeHF_psiLF->sum() << std::endl; //DEBUG
//QoI and error estimate
std::cout << "QoI: " << std::setprecision(17) << system_primary.getQoI() << std::endl;
std::cout << "QoI Error estimate: " << std::setprecision(17)
<< adjresid->sum()+LprimeHF_psiLF->sum() << std::endl;
relError = fabs((adjresid->sum()+LprimeHF_psiLF->sum())/system_primary.getQoI());
//print out information
std::cout << "Estimated absolute relative qoi error: " << relError << std::endl << std::endl;
std::cout << "Estimated HF QoI: " << std::setprecision(17) << system_primary.getQoI()+adjresid->sum()+LprimeHF_psiLF->sum() << std::endl;
clock_t end = clock();
std::cout << "Time so far: " << double(end-begin)/CLOCKS_PER_SEC << " seconds..." << std::endl;
std::cout << "Time for inverse problem: " << double(end_inv-begin_inv)/CLOCKS_PER_SEC << " seconds..." << std::endl;
std::cout << "Time for extra error estimate bits: " << double(end-begin_err_est)/CLOCKS_PER_SEC << " seconds..." << std::endl;
std::cout << " Time to get auxiliary problems: " << double(end_aux-begin_err_est)/CLOCKS_PER_SEC << " seconds..." << std::endl;
std::cout << " Time to get superadjoint: " << double(end-end_aux)/CLOCKS_PER_SEC << " seconds...\n" << std::endl;
//proportion of domain refined at this iteration
MeshBase::element_iterator elem_it = mesh.elements_begin();
const MeshBase::element_iterator elem_end = mesh.elements_end();
double numMarked = 0.;
for (; elem_it != elem_end; ++elem_it){
Elem* elem = *elem_it;
numMarked += elem->subdomain_id();
}
std::cout << "Refinement fraction: " << numMarked/system_mix.get_mesh().n_elem() << std::endl << std::endl;
//output at each iteration
std::stringstream ss;
ss << refIter;
std::string str = ss.str();
std::string write_error_basis_blame =
(infile("error_est_output_file_basis_blame", "error_est_breakdown_basis_blame")) + str + ".dat";
std::ofstream output2(write_error_basis_blame);
for(unsigned int i = 0 ; i < adjresid->size(); i++){
if(output2.is_open())
output2 << (*adjresid)(i) + (*LprimeHF_psiLF)(i) << "\n";
}
output2.close();
if(refIter < maxIter && relError > qoiErrorTol){ //if further refinement needed
//collapse error contributions into nodes
std::vector<std::pair<Number,dof_id_type> > node_errs(round(system_mix.n_dofs()/6.));
for(unsigned int node_num = 0; node_num < node_errs.size(); node_num++){
node_errs[node_num] = std::pair<Number,dof_id_type>
(fabs((*adjresid)(6*node_num) + (*LprimeHF_psiLF)(6*node_num)
+ (*adjresid)(6*node_num+1) + (*LprimeHF_psiLF)(6*node_num+1)
+ (*adjresid)(6*node_num+2) + (*LprimeHF_psiLF)(6*node_num+2)
+ (*adjresid)(6*node_num+3) + (*LprimeHF_psiLF)(6*node_num+3)
+ (*adjresid)(6*node_num+4) + (*LprimeHF_psiLF)(6*node_num+4)
+ (*adjresid)(6*node_num+5) + (*LprimeHF_psiLF)(6*node_num+5)), node_num);
}
//find nodes contributing the most
//double refPcnt = std::min((refIter+1)*refStep,1.);
double refPcnt = std::min(refStep,1.); //additional refinement (compared to previous iteration)
int cutoffLoc = round(node_errs.size()*refPcnt);
std::sort(node_errs.begin(), node_errs.end());
std::reverse(node_errs.begin(), node_errs.end());
//find elements in support of worst offenders
std::vector<dof_id_type> markMe;
markMe.reserve(cutoffLoc*8);
for(int i = 0; i < cutoffLoc; i++){
markMe.insert(markMe.end(), node_to_elem[node_errs[i].second].begin(), node_to_elem[node_errs[i].second].end());
}
//mark those elements for refinement.
for(int i = 0; i < markMe.size(); i++){
if(!avoid_sides || (avoid_sides && !mesh.elem(markMe[i])->on_boundary()))
mesh.elem(markMe[i])->subdomain_id() = 1; //assuming HF regions marked with 1
}
//to test whether assignment matches matlab's
/*std::string stash_assign = "divvy_c_poke.txt";
std::ofstream output_dbg(stash_assign.c_str());
MeshBase::element_iterator elem_it = mesh.elements_begin();
const MeshBase::element_iterator elem_end = mesh.elements_end();
for (; elem_it != elem_end; ++elem_it){
Elem* elem = *elem_it;
if(output_dbg.is_open()){
output_dbg << elem->id() << " " << elem->subdomain_id() << "\n";
}
}
output_dbg.close();*/
#ifdef LIBMESH_HAVE_EXODUS_API
std::stringstream ss2;
ss2 << refIter + 1;
std::string str = ss2.str();
std::string write_divvy = "divvy" + str + ".exo";
ExodusII_IO (mesh).write_equation_systems(write_divvy,equation_systems); //DEBUG
#endif // #ifdef LIBMESH_HAVE_EXODUS_API
}
refIter += 1;
}
std::string stash_assign = "divvy_final.txt";
std::ofstream output_dbg(stash_assign.c_str());
MeshBase::element_iterator elem_it = mesh.elements_begin();
const MeshBase::element_iterator elem_end = mesh.elements_end();
double numMarked = 0.;
for (; elem_it != elem_end; ++elem_it){
Elem* elem = *elem_it;
numMarked += elem->subdomain_id();
if(output_dbg.is_open()){
output_dbg << elem->id() << " " << elem->subdomain_id() << "\n";
}
}
output_dbg.close();
std::cout << "\nRefinement concluded..." << std::endl;
std::cout << "Final refinement fraction: " << numMarked/system_mix.get_mesh().n_elem() << std::endl;
std::cout << "Final estimated relative error: " << relError << std::endl;
return 0; //done
} //end main
// Begin the main program. Note that the first
// statement in the program throws an error if
// you are in complex number mode, since this
// example is only intended to work with real
// numbers.
int main (int argc, char ** argv)
{
// Initialize libMesh.
LibMeshInit init (argc, argv);
#if !defined(LIBMESH_ENABLE_AMR)
libmesh_example_requires(false, "--enable-amr");
#else
libmesh_example_requires(libMesh::default_solver_package() == PETSC_SOLVERS, "--enable-petsc");
// Brief message to the user regarding the program name
// and command line arguments.
libMesh::out << "Running: " << argv[0];
for (int i=1; i<argc; i++)
libMesh::out << " " << argv[i];
libMesh::out << std::endl << std::endl;
// Skip this 2D example if libMesh was compiled as 1D-only.
libmesh_example_requires(2 <= LIBMESH_DIM, "2D support");
// Create a mesh, with dimension to be overridden later, distributed
// across the default MPI communicator.
Mesh mesh(init.comm());
// Create an equation systems object.
EquationSystems equation_systems (mesh);
MeshTools::Generation::build_square (mesh,
16,
16,
-1., 1.,
-1., 1.,
QUAD4);
LinearImplicitSystem & system =
equation_systems.add_system<LinearImplicitSystem>
("System");
// Adds the variable "u" to "System". "u"
// will be approximated using first-order approximation.
system.add_variable ("u", FIRST);
// Also, we need to add two vectors. The tensor matrix v*w^T of
// these two vectors will be part of the system matrix.
system.add_vector("v", false);
system.add_vector("w", false);
// We need an additional matrix to be used for preconditioning since
// a shell matrix is not suitable for that.
system.add_matrix("Preconditioner");
// Give the system a pointer to the matrix assembly function.
system.attach_assemble_function (assemble);
// Initialize the data structures for the equation system.
equation_systems.init ();
// Prints information about the system to the screen.
equation_systems.print_info();
equation_systems.parameters.set<unsigned int>
("linear solver maximum iterations") = 250;
equation_systems.parameters.set<Real>
("linear solver tolerance") = TOLERANCE;
// Refine arbitrarily some elements.
for (unsigned int i=0; i<2; i++)
{
MeshRefinement mesh_refinement(mesh);
MeshBase::element_iterator elem_it = mesh.elements_begin();
const MeshBase::element_iterator elem_end = mesh.elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem * elem = *elem_it;
if (elem->active())
{
if ((elem->id()%20)>8)
{
elem->set_refinement_flag(Elem::REFINE);
}
else
{
elem->set_refinement_flag(Elem::DO_NOTHING);
}
}
else
{
elem->set_refinement_flag(Elem::INACTIVE);
}
}
mesh_refinement.refine_elements();
equation_systems.reinit();
}
// Prints information about the system to the screen.
equation_systems.print_info();
// Before the assemblation of the matrix, we have to clear the two
// vectors that form the tensor matrix (since this is not performed
// automatically).
system.get_vector("v").init(system.n_dofs(), system.n_local_dofs());
system.get_vector("w").init(system.n_dofs(), system.n_local_dofs());
// We need a shell matrix to solve. There is currently no way to
// store the shell matrix in the system. We just create it locally
// here (a shell matrix does not occupy much memory).
SumShellMatrix<Number> shellMatrix(system.comm());
TensorShellMatrix<Number> shellMatrix0(system.get_vector("v"), system.get_vector("w"));
shellMatrix.matrices.push_back(&shellMatrix0);
SparseShellMatrix<Number> shellMatrix1(*system.matrix);
shellMatrix.matrices.push_back(&shellMatrix1);
// Attach that to the system.
system.attach_shell_matrix(&shellMatrix);
// Reset the preconditioning matrix to zero (for the system matrix,
// the same thing is done automatically).
system.get_matrix("Preconditioner").zero();
// Assemble & solve the linear system
system.solve();
// Detach the shell matrix from the system since it will go out of
// scope. Nobody should solve the system outside this function.
system.detach_shell_matrix();
// Print a nice message.
libMesh::out << "Solved linear system in "
<< system.n_linear_iterations()
<< " iterations, residual norm is "
<< system.final_linear_residual()
<< "."
<< std::endl;
#if defined(LIBMESH_HAVE_VTK) && !defined(LIBMESH_ENABLE_PARMESH)
// Write result to file.
VTKIO(mesh).write_equation_systems ("out.pvtu", equation_systems);
#endif // #ifdef LIBMESH_HAVE_VTK
#endif // #ifndef LIBMESH_ENABLE_AMR
return 0;
}
void
MultiAppNearestNodeTransfer::execute()
{
Moose::out << "Beginning NearestNodeTransfer " << _name << std::endl;
switch(_direction)
{
case TO_MULTIAPP:
{
FEProblem & from_problem = *_multi_app->problem();
MooseVariable & from_var = from_problem.getVariable(0, _from_var_name);
MeshBase * from_mesh = NULL;
if (_displaced_source_mesh && from_problem.getDisplacedProblem())
{
mooseError("Cannot use a NearestNode transfer from a displaced mesh to a MultiApp!");
from_mesh = &from_problem.getDisplacedProblem()->mesh().getMesh();
}
else
from_mesh = &from_problem.mesh().getMesh();
SystemBase & from_system_base = from_var.sys();
System & from_sys = from_system_base.system();
unsigned int from_sys_num = from_sys.number();
// Only works with a serialized mesh to transfer from!
mooseAssert(from_sys.get_mesh().is_serial(), "MultiAppNearestNodeTransfer only works with SerialMesh!");
unsigned int from_var_num = from_sys.variable_number(from_var.name());
// EquationSystems & from_es = from_sys.get_equation_systems();
//Create a serialized version of the solution vector
NumericVector<Number> * serialized_solution = NumericVector<Number>::build().release();
serialized_solution->init(from_sys.n_dofs(), false, SERIAL);
// Need to pull down a full copy of this vector on every processor so we can get values in parallel
from_sys.solution->localize(*serialized_solution);
for(unsigned int i=0; i<_multi_app->numGlobalApps(); i++)
{
if (_multi_app->hasLocalApp(i))
{
MPI_Comm swapped = Moose::swapLibMeshComm(_multi_app->comm());
// Loop over the master nodes and set the value of the variable
System * to_sys = find_sys(_multi_app->appProblem(i)->es(), _to_var_name);
if (!to_sys)
mooseError("Cannot find variable "<<_to_var_name<<" for "<<_name<<" Transfer");
unsigned int sys_num = to_sys->number();
unsigned int var_num = to_sys->variable_number(_to_var_name);
NumericVector<Real> & solution = _multi_app->appTransferVector(i, _to_var_name);
MeshBase * mesh = NULL;
if (_displaced_target_mesh && _multi_app->appProblem(i)->getDisplacedProblem())
mesh = &_multi_app->appProblem(i)->getDisplacedProblem()->mesh().getMesh();
else
mesh = &_multi_app->appProblem(i)->mesh().getMesh();
bool is_nodal = to_sys->variable_type(var_num).family == LAGRANGE;
if (is_nodal)
{
MeshBase::const_node_iterator node_it = mesh->local_nodes_begin();
MeshBase::const_node_iterator node_end = mesh->local_nodes_end();
for(; node_it != node_end; ++node_it)
{
Node * node = *node_it;
Point actual_position = *node+_multi_app->position(i);
if (node->n_dofs(sys_num, var_num) > 0) // If this variable has dofs at this node
{
// The zero only works for LAGRANGE!
dof_id_type dof = node->dof_number(sys_num, var_num, 0);
// Swap back
Moose::swapLibMeshComm(swapped);
Real distance = 0; // Just to satisfy the last argument
MeshBase::const_node_iterator from_nodes_begin = from_mesh->nodes_begin();
MeshBase::const_node_iterator from_nodes_end = from_mesh->nodes_end();
Node * nearest_node = NULL;
if (_fixed_meshes)
{
if (_node_map.find(node->id()) == _node_map.end()) // Haven't cached it yet
{
nearest_node = getNearestNode(actual_position, distance, from_nodes_begin, from_nodes_end);
_node_map[node->id()] = nearest_node;
_distance_map[node->id()] = distance;
}
else
{
nearest_node = _node_map[node->id()];
//distance = _distance_map[node->id()];
}
}
else
nearest_node = getNearestNode(actual_position, distance, from_nodes_begin, from_nodes_end);
// Assuming LAGRANGE!
dof_id_type from_dof = nearest_node->dof_number(from_sys_num, from_var_num, 0);
Real from_value = (*serialized_solution)(from_dof);
// Swap again
swapped = Moose::swapLibMeshComm(_multi_app->comm());
solution.set(dof, from_value);
}
}
}
else // Elemental
{
MeshBase::const_element_iterator elem_it = mesh->local_elements_begin();
MeshBase::const_element_iterator elem_end = mesh->local_elements_end();
for(; elem_it != elem_end; ++elem_it)
{
Elem * elem = *elem_it;
Point centroid = elem->centroid();
Point actual_position = centroid+_multi_app->position(i);
if (elem->n_dofs(sys_num, var_num) > 0) // If this variable has dofs at this elem
{
// The zero only works for LAGRANGE!
dof_id_type dof = elem->dof_number(sys_num, var_num, 0);
// Swap back
Moose::swapLibMeshComm(swapped);
Real distance = 0; // Just to satisfy the last argument
MeshBase::const_node_iterator from_nodes_begin = from_mesh->nodes_begin();
MeshBase::const_node_iterator from_nodes_end = from_mesh->nodes_end();
Node * nearest_node = NULL;
if (_fixed_meshes)
{
if (_node_map.find(elem->id()) == _node_map.end()) // Haven't cached it yet
{
nearest_node = getNearestNode(actual_position, distance, from_nodes_begin, from_nodes_end);
_node_map[elem->id()] = nearest_node;
_distance_map[elem->id()] = distance;
}
else
{
nearest_node = _node_map[elem->id()];
//distance = _distance_map[elem->id()];
}
}
else
nearest_node = getNearestNode(actual_position, distance, from_nodes_begin, from_nodes_end);
// Assuming LAGRANGE!
dof_id_type from_dof = nearest_node->dof_number(from_sys_num, from_var_num, 0);
Real from_value = (*serialized_solution)(from_dof);
// Swap again
swapped = Moose::swapLibMeshComm(_multi_app->comm());
solution.set(dof, from_value);
}
}
}
solution.close();
to_sys->update();
// Swap back
Moose::swapLibMeshComm(swapped);
}
}
delete serialized_solution;
break;
}
case FROM_MULTIAPP:
{
FEProblem & to_problem = *_multi_app->problem();
MooseVariable & to_var = to_problem.getVariable(0, _to_var_name);
SystemBase & to_system_base = to_var.sys();
System & to_sys = to_system_base.system();
NumericVector<Real> & to_solution = *to_sys.solution;
unsigned int to_sys_num = to_sys.number();
// Only works with a serialized mesh to transfer to!
mooseAssert(to_sys.get_mesh().is_serial(), "MultiAppNearestNodeTransfer only works with SerialMesh!");
unsigned int to_var_num = to_sys.variable_number(to_var.name());
// EquationSystems & to_es = to_sys.get_equation_systems();
MeshBase * to_mesh = NULL;
if (_displaced_target_mesh && to_problem.getDisplacedProblem())
to_mesh = &to_problem.getDisplacedProblem()->mesh().getMesh();
else
to_mesh = &to_problem.mesh().getMesh();
bool is_nodal = to_sys.variable_type(to_var_num) == FEType();
dof_id_type n_nodes = to_mesh->n_nodes();
dof_id_type n_elems = to_mesh->n_elem();
///// All of the following are indexed off to_node->id() or to_elem->id() /////
// Minimum distances from each node in the "to" mesh to a node in
std::vector<Real> min_distances;
// The node ids in the "from" mesh that this processor has found to be the minimum distances to the "to" nodes
std::vector<dof_id_type> min_nodes;
// After the call to maxloc() this will tell us which processor actually has the minimum
std::vector<unsigned int> min_procs;
// The global multiapp ID that this processor found had the minimum distance node in it.
std::vector<unsigned int> min_apps;
if (is_nodal)
{
min_distances.resize(n_nodes, std::numeric_limits<Real>::max());
min_nodes.resize(n_nodes);
min_procs.resize(n_nodes);
min_apps.resize(n_nodes);
}
else
{
min_distances.resize(n_elems, std::numeric_limits<Real>::max());
min_nodes.resize(n_elems);
min_procs.resize(n_elems);
min_apps.resize(n_elems);
}
for(unsigned int i=0; i<_multi_app->numGlobalApps(); i++)
{
if (!_multi_app->hasLocalApp(i))
continue;
MPI_Comm swapped = Moose::swapLibMeshComm(_multi_app->comm());
FEProblem & from_problem = *_multi_app->appProblem(i);
MooseVariable & from_var = from_problem.getVariable(0, _from_var_name);
SystemBase & from_system_base = from_var.sys();
System & from_sys = from_system_base.system();
// Only works with a serialized mesh to transfer from!
mooseAssert(from_sys.get_mesh().is_serial(), "MultiAppNearestNodeTransfer only works with SerialMesh!");
// unsigned int from_var_num = from_sys.variable_number(from_var.name());
// EquationSystems & from_es = from_sys.get_equation_systems();
MeshBase * from_mesh = NULL;
if (_displaced_source_mesh && from_problem.getDisplacedProblem())
from_mesh = &from_problem.getDisplacedProblem()->mesh().getMesh();
else
from_mesh = &from_problem.mesh().getMesh();
MeshTools::BoundingBox app_box = MeshTools::processor_bounding_box(*from_mesh, libMesh::processor_id());
Point app_position = _multi_app->position(i);
Moose::swapLibMeshComm(swapped);
if (is_nodal)
{
MeshBase::const_node_iterator to_node_it = to_mesh->nodes_begin();
MeshBase::const_node_iterator to_node_end = to_mesh->nodes_end();
for(; to_node_it != to_node_end; ++to_node_it)
{
Node * to_node = *to_node_it;
unsigned int to_node_id = to_node->id();
Real current_distance = 0;
MPI_Comm swapped = Moose::swapLibMeshComm(_multi_app->comm());
MeshBase::const_node_iterator from_nodes_begin = from_mesh->local_nodes_begin();
MeshBase::const_node_iterator from_nodes_end = from_mesh->local_nodes_end();
Node * nearest_node = NULL;
if (_fixed_meshes)
{
if (_node_map.find(to_node->id()) == _node_map.end()) // Haven't cached it yet
{
nearest_node = getNearestNode(*to_node-app_position, current_distance, from_nodes_begin, from_nodes_end);
_node_map[to_node->id()] = nearest_node;
_distance_map[to_node->id()] = current_distance;
}
else
{
nearest_node = _node_map[to_node->id()];
current_distance = _distance_map[to_node->id()];
}
}
else
nearest_node = getNearestNode(*to_node-app_position, current_distance, from_nodes_begin, from_nodes_end);
Moose::swapLibMeshComm(swapped);
// TODO: Logic bug when we are using caching. "current_distance" is set by a call to getNearestNode which is
// skipped in that case. We shouldn't be relying on it or stuffing it in another data structure
if (current_distance < min_distances[to_node->id()])
{
min_distances[to_node_id] = current_distance;
min_nodes[to_node_id] = nearest_node->id();
min_apps[to_node_id] = i;
}
}
}
else // Elemental
{
MeshBase::const_element_iterator to_elem_it = to_mesh->elements_begin();
MeshBase::const_element_iterator to_elem_end = to_mesh->elements_end();
for(; to_elem_it != to_elem_end; ++to_elem_it)
{
Elem * to_elem = *to_elem_it;
unsigned int to_elem_id = to_elem->id();
Point actual_position = to_elem->centroid()-app_position;
Real current_distance = 0;
MPI_Comm swapped = Moose::swapLibMeshComm(_multi_app->comm());
MeshBase::const_node_iterator from_nodes_begin = from_mesh->local_nodes_begin();
MeshBase::const_node_iterator from_nodes_end = from_mesh->local_nodes_end();
Node * nearest_node = NULL;
if (_fixed_meshes)
{
if (_node_map.find(to_elem->id()) == _node_map.end()) // Haven't cached it yet
{
nearest_node = getNearestNode(actual_position, current_distance, from_nodes_begin, from_nodes_end);
_node_map[to_elem->id()] = nearest_node;
_distance_map[to_elem->id()] = current_distance;
}
else
{
nearest_node = _node_map[to_elem->id()];
current_distance = _distance_map[to_elem->id()];
}
}
else
nearest_node = getNearestNode(actual_position, current_distance, from_nodes_begin, from_nodes_end);
Moose::swapLibMeshComm(swapped);
// TODO: Logic bug when we are using caching. "current_distance" is set by a call to getNearestNode which is
// skipped in that case. We shouldn't be relying on it or stuffing it in another data structure
if (current_distance < min_distances[to_elem->id()])
{
min_distances[to_elem_id] = current_distance;
min_nodes[to_elem_id] = nearest_node->id();
min_apps[to_elem_id] = i;
}
}
}
}
/*
// We're going to need serialized solution vectors for each app
// We could try to only do it for the apps that have mins in them...
// but it's tough because this is a collective operation... so that would have to be coordinated
std::vector<NumericVector<Number> *> serialized_from_solutions(_multi_app->numGlobalApps());
if (_multi_app->hasApp())
{
// Swap
MPI_Comm swapped = Moose::swapLibMeshComm(_multi_app->comm());
for(unsigned int i=0; i<_multi_app->numGlobalApps(); i++)
{
if (!_multi_app->hasLocalApp(i))
continue;
FEProblem & from_problem = *_multi_app->appProblem(i);
MooseVariable & from_var = from_problem.getVariable(0, _from_var_name);
SystemBase & from_system_base = from_var.sys();
System & from_sys = from_system_base.system();
//Create a serialized version of the solution vector
serialized_from_solutions[i] = NumericVector<Number>::build().release();
serialized_from_solutions[i]->init(from_sys.n_dofs(), false, SERIAL);
// Need to pull down a full copy of this vector on every processor so we can get values in parallel
from_sys.solution->localize(*serialized_from_solutions[i]);
}
// Swap back
Moose::swapLibMeshComm(swapped);
}
*/
// We've found the nearest nodes for this processor. We need to see which processor _actually_ found the nearest though
Parallel::minloc(min_distances, min_procs);
// Now loop through min_procs and see if _this_ processor had the actual minimum for any nodes.
// If it did then we're going to go get the value from that nearest node and transfer its value
processor_id_type proc_id = libMesh::processor_id();
for(unsigned int j=0; j<min_procs.size(); j++)
{
if (min_procs[j] == proc_id) // This means that this processor really did find the minumum so we need to transfer the value
{
// The zero only works for LAGRANGE!
dof_id_type to_dof = 0;
if (is_nodal)
{
Node & to_node = to_mesh->node(j);
to_dof = to_node.dof_number(to_sys_num, to_var_num, 0);
}
else
{
Elem & to_elem = *to_mesh->elem(j);
to_dof = to_elem.dof_number(to_sys_num, to_var_num, 0);
}
// The app that has the nearest node in it
unsigned int from_app_num = min_apps[j];
mooseAssert(_multi_app->hasLocalApp(from_app_num), "Something went very wrong!");
// Swap
MPI_Comm swapped = Moose::swapLibMeshComm(_multi_app->comm());
FEProblem & from_problem = *_multi_app->appProblem(from_app_num);
MooseVariable & from_var = from_problem.getVariable(0, _from_var_name);
SystemBase & from_system_base = from_var.sys();
System & from_sys = from_system_base.system();
unsigned int from_sys_num = from_sys.number();
unsigned int from_var_num = from_sys.variable_number(from_var.name());
// EquationSystems & from_es = from_sys.get_equation_systems();
MeshBase * from_mesh = NULL;
if (_displaced_source_mesh && from_problem.getDisplacedProblem())
from_mesh = &from_problem.getDisplacedProblem()->mesh().getMesh();
else
from_mesh = &from_problem.mesh().getMesh();
Node & from_node = from_mesh->node(min_nodes[j]);
// Assuming LAGRANGE!
dof_id_type from_dof = from_node.dof_number(from_sys_num, from_var_num, 0);
Real from_value = (*from_sys.solution)(from_dof);
// Swap back
Moose::swapLibMeshComm(swapped);
to_solution.set(to_dof, from_value);
}
}
to_solution.close();
to_sys.update();
break;
}
}
Moose::out << "Finished NearestNodeTransfer " << _name << std::endl;
}
void VTKIO::cells_to_vtk()
{
const MeshBase& mesh = MeshOutput<MeshBase>::mesh();
vtkSmartPointer<vtkCellArray> cells = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkIdList> pts = vtkSmartPointer<vtkIdList>::New();
std::vector<int> types(mesh.n_active_local_elem());
unsigned active_element_counter = 0;
vtkSmartPointer<vtkIntArray> elem_id = vtkSmartPointer<vtkIntArray>::New();
elem_id->SetName("libmesh_elem_id");
elem_id->SetNumberOfComponents(1);
vtkSmartPointer<vtkIntArray> subdomain_id = vtkSmartPointer<vtkIntArray>::New();
subdomain_id->SetName("subdomain_id");
subdomain_id->SetNumberOfComponents(1);
MeshBase::const_element_iterator it = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end = mesh.active_local_elements_end();
for (; it != end; ++it, ++active_element_counter)
{
Elem *elem = *it;
pts->SetNumberOfIds(elem->n_nodes());
// get the connectivity for this element
std::vector<dof_id_type> conn;
elem->connectivity(0, VTK, conn);
for (unsigned int i=0; i<conn.size(); ++i)
{
// If the node ID is not found in the _local_node_map, we'll
// add it to the _vtk_grid. NOTE[JWP]: none of the examples
// I have actually enters this section of code...
if (_local_node_map.find(conn[i]) == _local_node_map.end())
{
dof_id_type global_node_id = elem->node(i);
const Node* the_node = mesh.node_ptr(global_node_id);
// Error checking...
if (the_node == NULL)
{
libMesh::err << "Error getting pointer to node "
<< global_node_id
<< "!" << std::endl;
libmesh_error();
}
// InsertNextPoint accepts either a double or float array of length 3.
Real pt[3] = {0., 0., 0.};
for (unsigned int d=0; d<LIBMESH_DIM; ++d)
pt[d] = (*the_node)(d);
// Insert the point into the _vtk_grid
vtkIdType local = _vtk_grid->GetPoints()->InsertNextPoint(pt);
// Update the _local_node_map with the ID returned by VTK
_local_node_map[global_node_id] = local;
}
// Otherwise, the node ID was found in the _local_node_map, so
// insert it into the vtkIdList.
pts->InsertId(i, _local_node_map[conn[i]]);
}
vtkIdType vtkcellid = cells->InsertNextCell(pts);
types[active_element_counter] = this->get_elem_type(elem->type());
elem_id->InsertTuple1(vtkcellid, elem->id());
subdomain_id->InsertTuple1(vtkcellid, elem->subdomain_id());
} // end loop over active elements
_vtk_grid->SetCells(&types[0], cells);
_vtk_grid->GetCellData()->AddArray(elem_id);
_vtk_grid->GetCellData()->AddArray(subdomain_id);
}
void ParmetisPartitioner::assign_partitioning (MeshBase & mesh)
{
// This function must be run on all processors at once
libmesh_parallel_only(mesh.comm());
const dof_id_type
first_local_elem = _pmetis->vtxdist[mesh.processor_id()];
std::vector<std::vector<dof_id_type> >
requested_ids(mesh.n_processors()),
requests_to_fill(mesh.n_processors());
MeshBase::element_iterator elem_it = mesh.active_elements_begin();
MeshBase::element_iterator elem_end = mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem * elem = *elem_it;
// we need to get the index from the owning processor
// (note we cannot assign it now -- we are iterating
// over elements again and this will be bad!)
libmesh_assert_less (elem->processor_id(), requested_ids.size());
requested_ids[elem->processor_id()].push_back(elem->id());
}
// Trade with all processors (including self) to get their indices
for (processor_id_type pid=0; pid<mesh.n_processors(); pid++)
{
// Trade my requests with processor procup and procdown
const processor_id_type procup = (mesh.processor_id() + pid) % mesh.n_processors();
const processor_id_type procdown = (mesh.n_processors() +
mesh.processor_id() - pid) % mesh.n_processors();
mesh.comm().send_receive (procup, requested_ids[procup],
procdown, requests_to_fill[procdown]);
// we can overwrite these requested ids in-place.
for (std::size_t i=0; i<requests_to_fill[procdown].size(); i++)
{
const dof_id_type requested_elem_index =
requests_to_fill[procdown][i];
libmesh_assert(_global_index_by_pid_map.count(requested_elem_index));
const dof_id_type global_index_by_pid =
_global_index_by_pid_map[requested_elem_index];
const dof_id_type local_index =
global_index_by_pid - first_local_elem;
libmesh_assert_less (local_index, _pmetis->part.size());
libmesh_assert_less (local_index, mesh.n_active_local_elem());
const unsigned int elem_procid =
static_cast<unsigned int>(_pmetis->part[local_index]);
libmesh_assert_less (elem_procid, static_cast<unsigned int>(_pmetis->nparts));
requests_to_fill[procdown][i] = elem_procid;
}
// Trade back
mesh.comm().send_receive (procdown, requests_to_fill[procdown],
procup, requested_ids[procup]);
}
// and finally assign the partitioning.
// note we are iterating in exactly the same order
// used to build up the request, so we can expect the
// required entries to be in the proper sequence.
elem_it = mesh.active_elements_begin();
elem_end = mesh.active_elements_end();
for (std::vector<unsigned int> counters(mesh.n_processors(), 0);
elem_it != elem_end; ++elem_it)
{
Elem * elem = *elem_it;
const processor_id_type current_pid = elem->processor_id();
libmesh_assert_less (counters[current_pid], requested_ids[current_pid].size());
const processor_id_type elem_procid =
requested_ids[current_pid][counters[current_pid]++];
libmesh_assert_less (elem_procid, static_cast<unsigned int>(_pmetis->nparts));
elem->processor_id() = elem_procid;
}
}
void
MultiAppMeshFunctionTransfer::execute()
{
Moose::out << "Beginning MeshFunctionTransfer " << name() << std::endl;
getAppInfo();
/**
* For every combination of global "from" problem and local "to" problem, find
* which "from" bounding boxes overlap with which "to" elements. Keep track
* of which processors own bounding boxes that overlap with which elements.
* Build vectors of node locations/element centroids to send to other
* processors for mesh function evaluations.
*/
// Get the bounding boxes for the "from" domains.
std::vector<MeshTools::BoundingBox> bboxes = getFromBoundingBoxes();
// Figure out how many "from" domains each processor owns.
std::vector<unsigned int> froms_per_proc = getFromsPerProc();
std::vector<std::vector<Point> > outgoing_points(n_processors());
std::vector<std::map<std::pair<unsigned int, unsigned int>, unsigned int> > point_index_map(n_processors());
// point_index_map[i_to, element_id] = index
// outgoing_points[index] is the first quadrature point in element
for (unsigned int i_to = 0; i_to < _to_problems.size(); i_to++)
{
System * to_sys = find_sys(*_to_es[i_to], _to_var_name);
unsigned int sys_num = to_sys->number();
unsigned int var_num = to_sys->variable_number(_to_var_name);
MeshBase * to_mesh = & _to_meshes[i_to]->getMesh();
bool is_nodal = to_sys->variable_type(var_num).family == LAGRANGE;
if (is_nodal)
{
MeshBase::const_node_iterator node_it = to_mesh->local_nodes_begin();
MeshBase::const_node_iterator node_end = to_mesh->local_nodes_end();
for (; node_it != node_end; ++node_it)
{
Node * node = *node_it;
// Skip this node if the variable has no dofs at it.
if (node->n_dofs(sys_num, var_num) < 1)
continue;
// Loop over the "froms" on processor i_proc. If the node is found in
// any of the "froms", add that node to the vector that will be sent to
// i_proc.
unsigned int from0 = 0;
for (processor_id_type i_proc = 0;
i_proc < n_processors();
from0 += froms_per_proc[i_proc], i_proc++)
{
bool point_found = false;
for (unsigned int i_from = from0; i_from < from0 + froms_per_proc[i_proc] && ! point_found; i_from++)
{
if (bboxes[i_from].contains_point(*node + _to_positions[i_to]))
{
std::pair<unsigned int, unsigned int> key(i_to, node->id());
point_index_map[i_proc][key] = outgoing_points[i_proc].size();
outgoing_points[i_proc].push_back(*node + _to_positions[i_to]);
point_found = true;
}
}
}
}
}
else // Elemental
{
MeshBase::const_element_iterator elem_it = to_mesh->local_elements_begin();
MeshBase::const_element_iterator elem_end = to_mesh->local_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem * elem = *elem_it;
Point centroid = elem->centroid();
// Skip this element if the variable has no dofs at it.
if (elem->n_dofs(sys_num, var_num) < 1)
continue;
// Loop over the "froms" on processor i_proc. If the elem is found in
// any of the "froms", add that elem to the vector that will be sent to
// i_proc.
unsigned int from0 = 0;
for (processor_id_type i_proc = 0;
i_proc < n_processors();
from0 += froms_per_proc[i_proc], i_proc++)
{
bool point_found = false;
for (unsigned int i_from = from0; i_from < from0 + froms_per_proc[i_proc] && ! point_found; i_from++)
{
if (bboxes[i_from].contains_point(centroid + _to_positions[i_to]))
{
std::pair<unsigned int, unsigned int> key(i_to, elem->id());
point_index_map[i_proc][key] = outgoing_points[i_proc].size();
outgoing_points[i_proc].push_back(centroid + _to_positions[i_to]);
point_found = true;
}
}
}
}
}
}
/**
* Request point evaluations from other processors and handle requests sent to
* this processor.
*/
// Get the local bounding boxes.
std::vector<MeshTools::BoundingBox> local_bboxes(froms_per_proc[processor_id()]);
{
// Find the index to the first of this processor's local bounding boxes.
unsigned int local_start = 0;
for (processor_id_type i_proc = 0;
i_proc < n_processors() && i_proc != processor_id();
i_proc++)
{
local_start += froms_per_proc[i_proc];
}
// Extract the local bounding boxes.
for (unsigned int i_from = 0; i_from < froms_per_proc[processor_id()]; i_from++)
{
local_bboxes[i_from] = bboxes[local_start + i_from];
}
}
// Setup the local mesh functions.
std::vector<MooseSharedPointer<MeshFunction> > local_meshfuns;
for (unsigned int i_from = 0; i_from < _from_problems.size(); i_from++)
{
FEProblem & from_problem = *_from_problems[i_from];
MooseVariable & from_var = from_problem.getVariable(0, _from_var_name);
System & from_sys = from_var.sys().system();
unsigned int from_var_num = from_sys.variable_number(from_var.name());
MooseSharedPointer<MeshFunction> from_func;
//TODO: make MultiAppTransfer give me the right es
if (_displaced_source_mesh && from_problem.getDisplacedProblem())
from_func.reset(new MeshFunction(from_problem.getDisplacedProblem()->es(),
*from_sys.current_local_solution, from_sys.get_dof_map(), from_var_num));
else
from_func.reset(new MeshFunction(from_problem.es(),
*from_sys.current_local_solution, from_sys.get_dof_map(), from_var_num));
from_func->init(Trees::ELEMENTS);
from_func->enable_out_of_mesh_mode(OutOfMeshValue);
local_meshfuns.push_back(from_func);
}
// Send points to other processors.
std::vector<std::vector<Real> > incoming_evals(n_processors());
std::vector<std::vector<unsigned int> > incoming_app_ids(n_processors());
for (processor_id_type i_proc = 0; i_proc < n_processors(); i_proc++)
{
if (i_proc == processor_id())
continue;
_communicator.send(i_proc, outgoing_points[i_proc]);
}
// Recieve points from other processors, evaluate mesh frunctions at those
// points, and send the values back.
for (processor_id_type i_proc = 0; i_proc < n_processors(); i_proc++)
{
std::vector<Point> incoming_points;
if (i_proc == processor_id())
incoming_points = outgoing_points[i_proc];
else
_communicator.receive(i_proc, incoming_points);
std::vector<Real> outgoing_evals(incoming_points.size(), OutOfMeshValue);
std::vector<unsigned int> outgoing_ids(incoming_points.size(), -1); // -1 = largest unsigned int
for (unsigned int i_pt = 0; i_pt < incoming_points.size(); i_pt++)
{
Point pt = incoming_points[i_pt];
// Loop until we've found the lowest-ranked app that actually contains
// the quadrature point.
for (unsigned int i_from = 0; i_from < _from_problems.size() && outgoing_evals[i_pt] == OutOfMeshValue; i_from++)
{
if (local_bboxes[i_from].contains_point(pt))
{
outgoing_evals[i_pt] = (* local_meshfuns[i_from])(pt - _from_positions[i_from]);
if (_direction == FROM_MULTIAPP)
outgoing_ids[i_pt] = _local2global_map[i_from];
}
}
}
if (i_proc == processor_id())
{
incoming_evals[i_proc] = outgoing_evals;
if (_direction == FROM_MULTIAPP)
incoming_app_ids[i_proc] = outgoing_ids;
}
else
{
_communicator.send(i_proc, outgoing_evals);
if (_direction == FROM_MULTIAPP)
_communicator.send(i_proc, outgoing_ids);
}
}
/**
* Gather all of the evaluations, pick out the best ones for each point, and
* apply them to the solution vector. When we are transferring from
* multiapps, there may be multiple overlapping apps for a particular point.
* In that case, we'll try to use the value from the app with the lowest id.
*/
for (processor_id_type i_proc = 0; i_proc < n_processors(); i_proc++)
{
if (i_proc == processor_id())
continue;
_communicator.receive(i_proc, incoming_evals[i_proc]);
if (_direction == FROM_MULTIAPP)
_communicator.receive(i_proc, incoming_app_ids[i_proc]);
}
for (unsigned int i_to = 0; i_to < _to_problems.size(); i_to++)
{
System * to_sys = find_sys(*_to_es[i_to], _to_var_name);
unsigned int sys_num = to_sys->number();
unsigned int var_num = to_sys->variable_number(_to_var_name);
NumericVector<Real> * solution;
switch (_direction)
{
case TO_MULTIAPP:
solution = & getTransferVector(i_to, _to_var_name);
break;
case FROM_MULTIAPP:
solution = to_sys->solution.get();
break;
}
MeshBase * to_mesh = & _to_meshes[i_to]->getMesh();
bool is_nodal = to_sys->variable_type(var_num).family == LAGRANGE;
if (is_nodal)
{
MeshBase::const_node_iterator node_it = to_mesh->local_nodes_begin();
MeshBase::const_node_iterator node_end = to_mesh->local_nodes_end();
for (; node_it != node_end; ++node_it)
{
Node * node = *node_it;
// Skip this node if the variable has no dofs at it.
if (node->n_dofs(sys_num, var_num) < 1)
continue;
unsigned int lowest_app_rank = libMesh::invalid_uint;
Real best_val = 0.;
bool point_found = false;
for (unsigned int i_proc = 0; i_proc < incoming_evals.size(); i_proc++)
{
// Skip this proc if the node wasn't in it's bounding boxes.
std::pair<unsigned int, unsigned int> key(i_to, node->id());
if (point_index_map[i_proc].find(key) == point_index_map[i_proc].end())
continue;
unsigned int i_pt = point_index_map[i_proc][key];
// Ignore this proc if it's app has a higher rank than the
// previously found lowest app rank.
if (_direction == FROM_MULTIAPP)
{
if (incoming_app_ids[i_proc][i_pt] >= lowest_app_rank)
continue;
}
// Ignore this proc if the point was actually outside its meshes.
if (incoming_evals[i_proc][i_pt] == OutOfMeshValue)
continue;
best_val = incoming_evals[i_proc][i_pt];
point_found = true;
}
if (_error_on_miss && ! point_found)
mooseError("Point not found! " << *node + _to_positions[i_to]);
dof_id_type dof = node->dof_number(sys_num, var_num, 0);
solution->set(dof, best_val);
}
}
else // Elemental
{
MeshBase::const_element_iterator elem_it = to_mesh->local_elements_begin();
MeshBase::const_element_iterator elem_end = to_mesh->local_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem * elem = *elem_it;
// Skip this element if the variable has no dofs at it.
if (elem->n_dofs(sys_num, var_num) < 1)
continue;
unsigned int lowest_app_rank = libMesh::invalid_uint;
Real best_val = 0;
bool point_found = false;
for (unsigned int i_proc = 0; i_proc < incoming_evals.size(); i_proc++)
{
// Skip this proc if the elem wasn't in it's bounding boxes.
std::pair<unsigned int, unsigned int> key(i_to, elem->id());
if (point_index_map[i_proc].find(key) == point_index_map[i_proc].end())
continue;
unsigned int i_pt = point_index_map[i_proc][key];
// Ignore this proc if it's app has a higher rank than the
// previously found lowest app rank.
if (_direction == FROM_MULTIAPP)
{
if (incoming_app_ids[i_proc][i_pt] >= lowest_app_rank)
continue;
}
// Ignore this proc if the point was actually outside its meshes.
if (incoming_evals[i_proc][i_pt] == OutOfMeshValue)
continue;
best_val = incoming_evals[i_proc][i_pt];
point_found = true;
}
if (_error_on_miss && ! point_found)
mooseError("Point not found! " << elem->centroid() + _to_positions[i_to]);
dof_id_type dof = elem->dof_number(sys_num, var_num, 0);
solution->set(dof, best_val);
}
}
solution->close();
to_sys->update();
}
_console << "Finished MeshFunctionTransfer " << name() << std::endl;
}
void Partitioner::set_parent_processor_ids(MeshBase & mesh)
{
// Ignore the parameter when !LIBMESH_ENABLE_AMR
libmesh_ignore(mesh);
LOG_SCOPE("set_parent_processor_ids()", "Partitioner");
#ifdef LIBMESH_ENABLE_AMR
// If the mesh is serial we have access to all the elements,
// in particular all the active ones. We can therefore set
// the parent processor ids indirecly through their children, and
// set the subactive processor ids while examining their active
// ancestors.
// By convention a parent is assigned to the minimum processor
// of all its children, and a subactive is assigned to the processor
// of its active ancestor.
if (mesh.is_serial())
{
// Loop over all the active elements in the mesh
MeshBase::element_iterator it = mesh.active_elements_begin();
const MeshBase::element_iterator end = mesh.active_elements_end();
for ( ; it!=end; ++it)
{
Elem * child = *it;
// First set descendents
std::vector<const Elem *> subactive_family;
child->total_family_tree(subactive_family);
for (unsigned int i = 0; i != subactive_family.size(); ++i)
const_cast<Elem *>(subactive_family[i])->processor_id() = child->processor_id();
// Then set ancestors
Elem * parent = child->parent();
while (parent)
{
// invalidate the parent id, otherwise the min below
// will not work if the current parent id is less
// than all the children!
parent->invalidate_processor_id();
for (unsigned int c=0; c<parent->n_children(); c++)
{
child = parent->child_ptr(c);
libmesh_assert(child);
libmesh_assert(!child->is_remote());
libmesh_assert_not_equal_to (child->processor_id(), DofObject::invalid_processor_id);
parent->processor_id() = std::min(parent->processor_id(),
child->processor_id());
}
parent = parent->parent();
}
}
}
// When the mesh is parallel we cannot guarantee that parents have access to
// all their children.
else
{
// Setting subactive processor ids is easy: we can guarantee
// that children have access to all their parents.
// Loop over all the active elements in the mesh
MeshBase::element_iterator it = mesh.active_elements_begin();
const MeshBase::element_iterator end = mesh.active_elements_end();
for ( ; it!=end; ++it)
{
Elem * child = *it;
std::vector<const Elem *> subactive_family;
child->total_family_tree(subactive_family);
for (unsigned int i = 0; i != subactive_family.size(); ++i)
const_cast<Elem *>(subactive_family[i])->processor_id() = child->processor_id();
}
// When the mesh is parallel we cannot guarantee that parents have access to
// all their children.
// We will use a brute-force approach here. Each processor finds its parent
// elements and sets the parent pid to the minimum of its
// semilocal descendants.
// A global reduction is then performed to make sure the true minimum is found.
// As noted, this is required because we cannot guarantee that a parent has
// access to all its children on any single processor.
libmesh_parallel_only(mesh.comm());
libmesh_assert(MeshTools::n_elem(mesh.unpartitioned_elements_begin(),
mesh.unpartitioned_elements_end()) == 0);
const dof_id_type max_elem_id = mesh.max_elem_id();
std::vector<processor_id_type>
parent_processor_ids (std::min(communication_blocksize,
max_elem_id));
for (dof_id_type blk=0, last_elem_id=0; last_elem_id<max_elem_id; blk++)
{
last_elem_id =
std::min(static_cast<dof_id_type>((blk+1)*communication_blocksize),
max_elem_id);
const dof_id_type first_elem_id = blk*communication_blocksize;
std::fill (parent_processor_ids.begin(),
parent_processor_ids.end(),
DofObject::invalid_processor_id);
// first build up local contributions to parent_processor_ids
MeshBase::element_iterator not_it = mesh.ancestor_elements_begin();
const MeshBase::element_iterator not_end = mesh.ancestor_elements_end();
bool have_parent_in_block = false;
for ( ; not_it != not_end; ++not_it)
{
Elem * parent = *not_it;
const dof_id_type parent_idx = parent->id();
libmesh_assert_less (parent_idx, max_elem_id);
if ((parent_idx >= first_elem_id) &&
(parent_idx < last_elem_id))
{
have_parent_in_block = true;
processor_id_type parent_pid = DofObject::invalid_processor_id;
std::vector<const Elem *> active_family;
parent->active_family_tree(active_family);
for (unsigned int i = 0; i != active_family.size(); ++i)
parent_pid = std::min (parent_pid, active_family[i]->processor_id());
const dof_id_type packed_idx = parent_idx - first_elem_id;
libmesh_assert_less (packed_idx, parent_processor_ids.size());
parent_processor_ids[packed_idx] = parent_pid;
}
}
// then find the global minimum
mesh.comm().min (parent_processor_ids);
// and assign the ids, if we have a parent in this block.
if (have_parent_in_block)
for (not_it = mesh.ancestor_elements_begin();
not_it != not_end; ++not_it)
{
Elem * parent = *not_it;
const dof_id_type parent_idx = parent->id();
if ((parent_idx >= first_elem_id) &&
(parent_idx < last_elem_id))
{
const dof_id_type packed_idx = parent_idx - first_elem_id;
libmesh_assert_less (packed_idx, parent_processor_ids.size());
const processor_id_type parent_pid =
parent_processor_ids[packed_idx];
libmesh_assert_not_equal_to (parent_pid, DofObject::invalid_processor_id);
parent->processor_id() = parent_pid;
}
}
}
}
#endif // LIBMESH_ENABLE_AMR
}
void
MultiAppNearestNodeTransfer::execute()
{
_console << "Beginning NearestNodeTransfer " << name() << std::endl;
getAppInfo();
// Get the bounding boxes for the "from" domains.
std::vector<MeshTools::BoundingBox> bboxes = getFromBoundingBoxes();
// Figure out how many "from" domains each processor owns.
std::vector<unsigned int> froms_per_proc = getFromsPerProc();
////////////////////
// For every point in the local "to" domain, figure out which "from" domains
// might contain it's nearest neighbor, and send that point to the processors
// that own those "from" domains.
//
// How do we know which "from" domains might contain the nearest neighbor, you
// ask? Well, consider two "from" domains, A and B. If every point in A is
// closer than every point in B, then we know that B cannot possibly contain
// the nearest neighbor. Hence, we'll only check A for the nearest neighbor.
// We'll use the functions bboxMaxDistance and bboxMinDistance to figure out
// if every point in A is closer than every point in B.
////////////////////
// outgoing_qps = nodes/centroids we'll send to other processors.
std::vector<std::vector<Point> > outgoing_qps(n_processors());
// When we get results back, node_index_map will tell us which results go with
// which points
std::vector<std::map<std::pair<unsigned int, unsigned int>, unsigned int> > node_index_map(n_processors());
if (! _neighbors_cached)
{
for (unsigned int i_to = 0; i_to < _to_problems.size(); i_to++)
{
System * to_sys = find_sys(*_to_es[i_to], _to_var_name);
unsigned int sys_num = to_sys->number();
unsigned int var_num = to_sys->variable_number(_to_var_name);
MeshBase * to_mesh = & _to_meshes[i_to]->getMesh();
bool is_nodal = to_sys->variable_type(var_num).family == LAGRANGE;
if (is_nodal)
{
std::vector<Node *> target_local_nodes;
if (isParamValid("target_boundary"))
{
BoundaryID target_bnd_id = _to_meshes[i_to]->getBoundaryID(getParam<BoundaryName>("target_boundary"));
ConstBndNodeRange & bnd_nodes = *(_to_meshes[i_to])->getBoundaryNodeRange();
for (const auto & bnode : bnd_nodes)
if (bnode->_bnd_id == target_bnd_id && bnode->_node->processor_id() == processor_id())
target_local_nodes.push_back(bnode->_node);
}
else
{
target_local_nodes.resize(to_mesh->n_local_nodes());
MeshBase::const_node_iterator nodes_begin = to_mesh->local_nodes_begin();
MeshBase::const_node_iterator nodes_end = to_mesh->local_nodes_end();
unsigned int i = 0;
for (MeshBase::const_node_iterator nodes_it = nodes_begin; nodes_it != nodes_end; ++nodes_it, ++i)
target_local_nodes[i] = *nodes_it;
}
for (const auto & node : target_local_nodes)
{
// Skip this node if the variable has no dofs at it.
if (node->n_dofs(sys_num, var_num) < 1)
continue;
// Find which bboxes might have the nearest node to this point.
Real nearest_max_distance = std::numeric_limits<Real>::max();
for (const auto & bbox : bboxes)
{
Real distance = bboxMaxDistance(*node, bbox);
if (distance < nearest_max_distance)
nearest_max_distance = distance;
}
unsigned int from0 = 0;
for (processor_id_type i_proc = 0;
i_proc < n_processors();
from0 += froms_per_proc[i_proc], i_proc++)
{
bool qp_found = false;
for (unsigned int i_from = from0; i_from < from0 + froms_per_proc[i_proc] && ! qp_found; i_from++)
{
Real distance = bboxMinDistance(*node, bboxes[i_from]);
if (distance < nearest_max_distance || bboxes[i_from].contains_point(*node))
{
std::pair<unsigned int, unsigned int> key(i_to, node->id());
node_index_map[i_proc][key] = outgoing_qps[i_proc].size();
outgoing_qps[i_proc].push_back(*node + _to_positions[i_to]);
qp_found = true;
}
}
}
}
}
else // Elemental
{
MeshBase::const_element_iterator elem_it = to_mesh->local_elements_begin();
MeshBase::const_element_iterator elem_end = to_mesh->local_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem * elem = *elem_it;
Point centroid = elem->centroid();
// Skip this element if the variable has no dofs at it.
if (elem->n_dofs(sys_num, var_num) < 1)
continue;
// Find which bboxes might have the nearest node to this point.
Real nearest_max_distance = std::numeric_limits<Real>::max();
for (const auto & bbox : bboxes)
{
Real distance = bboxMaxDistance(centroid, bbox);
if (distance < nearest_max_distance)
nearest_max_distance = distance;
}
unsigned int from0 = 0;
for (processor_id_type i_proc = 0;
i_proc < n_processors();
from0 += froms_per_proc[i_proc], i_proc++)
{
bool qp_found = false;
for (unsigned int i_from = from0; i_from < from0 + froms_per_proc[i_proc] && ! qp_found; i_from++)
{
Real distance = bboxMinDistance(centroid, bboxes[i_from]);
if (distance < nearest_max_distance || bboxes[i_from].contains_point(centroid))
{
std::pair<unsigned int, unsigned int> key(i_to, elem->id());
node_index_map[i_proc][key] = outgoing_qps[i_proc].size();
outgoing_qps[i_proc].push_back(centroid + _to_positions[i_to]);
qp_found = true;
}
}
}
}
}
}
}
////////////////////
// Send local node/centroid positions off to the other processors and take
// care of points sent to this processor. We'll need to check the points
// against all of the "from" domains that this processor owns. For each
// point, we'll find the nearest node, then we'll send the value at that node
// and the distance between the node and the point back to the processor that
// requested that point.
////////////////////
std::vector<std::vector<Real> > incoming_evals(n_processors());
std::vector<Parallel::Request> send_qps(n_processors());
std::vector<Parallel::Request> send_evals(n_processors());
if (! _neighbors_cached)
{
for (processor_id_type i_proc = 0; i_proc < n_processors(); i_proc++)
{
if (i_proc == processor_id())
continue;
_communicator.send(i_proc, outgoing_qps[i_proc], send_qps[i_proc]);
}
// Build an array of pointers to all of this processor's local nodes. We
// need to do this to avoid the expense of using LibMesh iterators. This
// step also takes care of limiting the search to boundary nodes, if
// applicable.
std::vector< std::vector<Node *> > local_nodes(froms_per_proc[processor_id()]);
for (unsigned int i = 0; i < froms_per_proc[processor_id()]; i++)
{
getLocalNodes(_from_meshes[i], local_nodes[i]);
}
if (_fixed_meshes)
{
_cached_froms.resize(n_processors());
_cached_dof_ids.resize(n_processors());
}
for (processor_id_type i_proc = 0; i_proc < n_processors(); i_proc++)
{
std::vector<Point> incoming_qps;
if (i_proc == processor_id())
incoming_qps = outgoing_qps[i_proc];
else
_communicator.receive(i_proc, incoming_qps);
if (_fixed_meshes)
{
_cached_froms[i_proc].resize(incoming_qps.size());
_cached_dof_ids[i_proc].resize(incoming_qps.size());
}
std::vector<Real> outgoing_evals(2 * incoming_qps.size());
for (unsigned int qp = 0; qp < incoming_qps.size(); qp++)
{
Point qpt = incoming_qps[qp];
outgoing_evals[2*qp] = std::numeric_limits<Real>::max();
for (unsigned int i_local_from = 0; i_local_from < froms_per_proc[processor_id()]; i_local_from++)
{
MooseVariable & from_var = _from_problems[i_local_from]->getVariable(0, _from_var_name);
System & from_sys = from_var.sys().system();
unsigned int from_sys_num = from_sys.number();
unsigned int from_var_num = from_sys.variable_number(from_var.name());
for (unsigned int i_node = 0; i_node < local_nodes[i_local_from].size(); i_node++)
{
Real current_distance = (qpt - *(local_nodes[i_local_from][i_node]) - _from_positions[i_local_from]).norm();
if (current_distance < outgoing_evals[2*qp])
{
// Assuming LAGRANGE!
if (local_nodes[i_local_from][i_node]->n_dofs(from_sys_num, from_var_num) > 0)
{
dof_id_type from_dof = local_nodes[i_local_from][i_node]->dof_number(from_sys_num, from_var_num, 0);
outgoing_evals[2*qp] = current_distance;
outgoing_evals[2*qp + 1] = (*from_sys.solution)(from_dof);
if (_fixed_meshes)
{
// Cache the nearest nodes.
_cached_froms[i_proc][qp] = i_local_from;
_cached_dof_ids[i_proc][qp] = from_dof;
}
}
}
}
}
}
if (i_proc == processor_id())
incoming_evals[i_proc] = outgoing_evals;
else
_communicator.send(i_proc, outgoing_evals, send_evals[i_proc]);
}
}
else // We've cached the nearest nodes.
{
for (processor_id_type i_proc = 0; i_proc < n_processors(); i_proc++)
{
std::vector<Real> outgoing_evals(_cached_froms[i_proc].size());
for (unsigned int qp = 0; qp < outgoing_evals.size(); qp++)
{
MooseVariable & from_var = _from_problems[_cached_froms[i_proc][qp]]->getVariable(0, _from_var_name);
System & from_sys = from_var.sys().system();
dof_id_type from_dof = _cached_dof_ids[i_proc][qp];
//outgoing_evals[qp] = (*from_sys.solution)(_cached_dof_ids[i_proc][qp]);
outgoing_evals[qp] = (*from_sys.solution)(from_dof);
}
if (i_proc == processor_id())
incoming_evals[i_proc] = outgoing_evals;
else
_communicator.send(i_proc, outgoing_evals, send_evals[i_proc]);
}
}
////////////////////
// Gather all of the evaluations, find the nearest one for each node/element,
// and apply the values.
////////////////////
for (processor_id_type i_proc = 0; i_proc < n_processors(); i_proc++)
{
if (i_proc == processor_id())
continue;
_communicator.receive(i_proc, incoming_evals[i_proc]);
}
for (unsigned int i_to = 0; i_to < _to_problems.size(); i_to++)
{
// Loop over the master nodes and set the value of the variable
System * to_sys = find_sys(*_to_es[i_to], _to_var_name);
unsigned int sys_num = to_sys->number();
unsigned int var_num = to_sys->variable_number(_to_var_name);
NumericVector<Real> * solution = nullptr;
switch (_direction)
{
case TO_MULTIAPP:
solution = & getTransferVector(i_to, _to_var_name);
break;
case FROM_MULTIAPP:
solution = to_sys->solution.get();
break;
}
MeshBase * to_mesh = & _to_meshes[i_to]->getMesh();
bool is_nodal = to_sys->variable_type(var_num).family == LAGRANGE;
if (is_nodal)
{
std::vector<Node *> target_local_nodes;
if (isParamValid("target_boundary"))
{
BoundaryID target_bnd_id = _to_meshes[i_to]->getBoundaryID(getParam<BoundaryName>("target_boundary"));
ConstBndNodeRange & bnd_nodes = *(_to_meshes[i_to])->getBoundaryNodeRange();
for (const auto & bnode : bnd_nodes)
if (bnode->_bnd_id == target_bnd_id && bnode->_node->processor_id() == processor_id())
target_local_nodes.push_back(bnode->_node);
}
else
{
target_local_nodes.resize(to_mesh->n_local_nodes());
MeshBase::const_node_iterator nodes_begin = to_mesh->local_nodes_begin();
MeshBase::const_node_iterator nodes_end = to_mesh->local_nodes_end();
unsigned int i = 0;
for (MeshBase::const_node_iterator nodes_it = nodes_begin; nodes_it != nodes_end; ++nodes_it, ++i)
target_local_nodes[i] = *nodes_it;
}
for (const auto & node : target_local_nodes)
{
// Skip this node if the variable has no dofs at it.
if (node->n_dofs(sys_num, var_num) < 1)
continue;
Real best_val = 0;
if (! _neighbors_cached)
{
Real min_dist = std::numeric_limits<Real>::max();
for (unsigned int i_from = 0; i_from < incoming_evals.size(); i_from++)
{
std::pair<unsigned int, unsigned int> key(i_to, node->id());
if (node_index_map[i_from].find(key) == node_index_map[i_from].end())
continue;
unsigned int qp_ind = node_index_map[i_from][key];
if (incoming_evals[i_from][2*qp_ind] >= min_dist)
continue;
min_dist = incoming_evals[i_from][2*qp_ind];
best_val = incoming_evals[i_from][2*qp_ind + 1];
if (_fixed_meshes)
{
// Cache these indices.
_cached_from_inds[node->id()] = i_from;
_cached_qp_inds[node->id()] = qp_ind;
}
}
}
else
{
best_val = incoming_evals[_cached_from_inds[node->id()]][_cached_qp_inds[node->id()]];
}
dof_id_type dof = node->dof_number(sys_num, var_num, 0);
solution->set(dof, best_val);
}
}
else // Elemental
{
MeshBase::const_element_iterator elem_it = to_mesh->local_elements_begin();
MeshBase::const_element_iterator elem_end = to_mesh->local_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem * elem = *elem_it;
// Skip this element if the variable has no dofs at it.
if (elem->n_dofs(sys_num, var_num) < 1)
continue;
Real best_val = 0;
if (! _neighbors_cached)
{
Real min_dist = std::numeric_limits<Real>::max();
for (unsigned int i_from = 0; i_from < incoming_evals.size(); i_from++)
{
std::pair<unsigned int, unsigned int> key(i_to, elem->id());
if (node_index_map[i_from].find(key) == node_index_map[i_from].end())
continue;
unsigned int qp_ind = node_index_map[i_from][key];
if (incoming_evals[i_from][2*qp_ind] >= min_dist)
continue;
min_dist = incoming_evals[i_from][2*qp_ind];
best_val = incoming_evals[i_from][2*qp_ind + 1];
if (_fixed_meshes)
{
// Cache these indices.
_cached_from_inds[elem->id()] = i_from;
_cached_qp_inds[elem->id()] = qp_ind;
}
}
}
else
{
best_val = incoming_evals[_cached_from_inds[elem->id()]][_cached_qp_inds[elem->id()]];
}
dof_id_type dof = elem->dof_number(sys_num, var_num, 0);
solution->set(dof, best_val);
}
}
solution->close();
to_sys->update();
}
if (_fixed_meshes)
_neighbors_cached = true;
// Make sure all our sends succeeded.
for (processor_id_type i_proc = 0; i_proc < n_processors(); i_proc++)
{
if (i_proc == processor_id())
continue;
send_qps[i_proc].wait();
send_evals[i_proc].wait();
}
_console << "Finished NearestNodeTransfer " << name() << std::endl;
}
// we need to provide stress data for storing the data;
bool CMaterialInfo::StoreStressInfo()
{
cout<<STRING_WRITE_BEGIN << "store stress info" << endl;
MeshBase& mesh = d_es->get_mesh();
Mesh::element_iterator it_el = mesh.active_local_elements_begin();//mesh.elements_begin();
const Mesh::element_iterator it_last_el = mesh.active_local_elements_end();//mesh.elements_end();
int m= mesh.n_elem();
int n=9;
DenseMatrix<Number> stress_data(m,n); // this should come from initial case;
//
ExplicitSystem& stress_system = d_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");
std::vector<unsigned int> stress_dof_indices_var;
// need to put values from the file
for ( ; it_el != it_last_el ; ++it_el)
{
Elem* elem = *it_el;
int global_id= elem->id();
for (int irow = 0; irow<3; irow++)
{
for (int icol =0; icol<3; icol++)
{
stress_dof_map.dof_indices (elem, stress_dof_indices_var, sigma_vars[irow][icol]);
unsigned int 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, stress_data(global_id,irow*3+icol));
}
}
}
stress_dof_map.dof_indices (elem, stress_dof_indices_var, vonMises_var);
unsigned int 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, stress_data(global_id,9));
}
}
stress_system.solution->close();
stress_system.update();
cout<<STRING_WRITE_END << "store stress info" << endl;
return true;
}
void ParmetisPartitioner::build_graph (const MeshBase & mesh)
{
// build the graph in distributed CSR format. Note that
// the edges in the graph will correspond to
// face neighbors
const dof_id_type n_active_local_elem = mesh.n_active_local_elem();
// If we have boundary elements in this mesh, we want to account for
// the connectivity between them and interior elements. We can find
// interior elements from boundary elements, but we need to build up
// a lookup map to do the reverse.
typedef LIBMESH_BEST_UNORDERED_MULTIMAP<const Elem *, const Elem *>
map_type;
map_type interior_to_boundary_map;
{
MeshBase::const_element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::const_element_iterator elem_end = mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem * elem = *elem_it;
// If we don't have an interior_parent then there's nothing to look us
// up.
if ((elem->dim() >= LIBMESH_DIM) ||
!elem->interior_parent())
continue;
// get all relevant interior elements
std::set<const Elem *> neighbor_set;
elem->find_interior_neighbors(neighbor_set);
std::set<const Elem *>::iterator n_it = neighbor_set.begin();
for (; n_it != neighbor_set.end(); ++n_it)
{
// FIXME - non-const versions of the Elem set methods
// would be nice
Elem * neighbor = const_cast<Elem *>(*n_it);
#if defined(LIBMESH_HAVE_UNORDERED_MULTIMAP) || \
defined(LIBMESH_HAVE_TR1_UNORDERED_MAP) || \
defined(LIBMESH_HAVE_HASH_MAP) || \
defined(LIBMESH_HAVE_EXT_HASH_MAP)
interior_to_boundary_map.insert
(std::make_pair(neighbor, elem));
#else
interior_to_boundary_map.insert
(interior_to_boundary_map.begin(),
std::make_pair(neighbor, elem));
#endif
}
}
}
#ifdef LIBMESH_ENABLE_AMR
std::vector<const Elem *> neighbors_offspring;
#endif
std::vector<std::vector<dof_id_type> > graph(n_active_local_elem);
dof_id_type graph_size=0;
const dof_id_type first_local_elem = _pmetis->vtxdist[mesh.processor_id()];
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)
{
const Elem * elem = *elem_it;
libmesh_assert (_global_index_by_pid_map.count(elem->id()));
const dof_id_type global_index_by_pid =
_global_index_by_pid_map[elem->id()];
const dof_id_type local_index =
global_index_by_pid - first_local_elem;
libmesh_assert_less (local_index, n_active_local_elem);
std::vector<dof_id_type> & graph_row = graph[local_index];
// Loop over the element's neighbors. An element
// adjacency corresponds to a face neighbor
for (unsigned int ms=0; ms<elem->n_neighbors(); ms++)
{
const Elem * neighbor = elem->neighbor(ms);
if (neighbor != libmesh_nullptr)
{
// If the neighbor is active treat it
// as a connection
if (neighbor->active())
{
libmesh_assert(_global_index_by_pid_map.count(neighbor->id()));
const dof_id_type neighbor_global_index_by_pid =
_global_index_by_pid_map[neighbor->id()];
graph_row.push_back(neighbor_global_index_by_pid);
graph_size++;
}
#ifdef LIBMESH_ENABLE_AMR
// Otherwise we need to find all of the
// neighbor's children that are connected to
// us and add them
else
{
// The side of the neighbor to which
// we are connected
const unsigned int ns =
neighbor->which_neighbor_am_i (elem);
libmesh_assert_less (ns, neighbor->n_neighbors());
// Get all the active children (& grandchildren, etc...)
// of the neighbor
// FIXME - this is the wrong thing, since we
// should be getting the active family tree on
// our side only. But adding too many graph
// links may cause hanging nodes to tend to be
// on partition interiors, which would reduce
// communication overhead for constraint
// equations, so we'll leave it.
neighbor->active_family_tree (neighbors_offspring);
// Get all the neighbor's children that
// live on that side and are thus connected
// to us
for (unsigned int nc=0; nc<neighbors_offspring.size(); nc++)
{
const Elem * child =
neighbors_offspring[nc];
// This does not assume a level-1 mesh.
// Note that since children have sides numbered
// coincident with the parent then this is a sufficient test.
if (child->neighbor(ns) == elem)
{
libmesh_assert (child->active());
libmesh_assert (_global_index_by_pid_map.count(child->id()));
const dof_id_type child_global_index_by_pid =
_global_index_by_pid_map[child->id()];
graph_row.push_back(child_global_index_by_pid);
graph_size++;
}
}
}
#endif /* ifdef LIBMESH_ENABLE_AMR */
}
}
if ((elem->dim() < LIBMESH_DIM) &&
elem->interior_parent())
{
// get all relevant interior elements
std::set<const Elem *> neighbor_set;
elem->find_interior_neighbors(neighbor_set);
std::set<const Elem *>::iterator n_it = neighbor_set.begin();
for (; n_it != neighbor_set.end(); ++n_it)
{
// FIXME - non-const versions of the Elem set methods
// would be nice
Elem * neighbor = const_cast<Elem *>(*n_it);
const dof_id_type neighbor_global_index_by_pid =
_global_index_by_pid_map[neighbor->id()];
graph_row.push_back(neighbor_global_index_by_pid);
graph_size++;
}
}
// Check for any boundary neighbors
typedef map_type::iterator map_it_type;
std::pair<map_it_type, map_it_type>
bounds = interior_to_boundary_map.equal_range(elem);
for (map_it_type it = bounds.first; it != bounds.second; ++it)
{
const Elem * neighbor = it->second;
const dof_id_type neighbor_global_index_by_pid =
_global_index_by_pid_map[neighbor->id()];
graph_row.push_back(neighbor_global_index_by_pid);
graph_size++;
}
}
// Reserve space in the adjacency array
_pmetis->xadj.clear();
_pmetis->xadj.reserve (n_active_local_elem + 1);
_pmetis->adjncy.clear();
_pmetis->adjncy.reserve (graph_size);
for (std::size_t r=0; r<graph.size(); r++)
{
_pmetis->xadj.push_back(_pmetis->adjncy.size());
std::vector<dof_id_type> graph_row; // build this emtpy
graph_row.swap(graph[r]); // this will deallocate at the end of scope
_pmetis->adjncy.insert(_pmetis->adjncy.end(),
graph_row.begin(),
graph_row.end());
}
// The end of the adjacency array for the last elem
_pmetis->xadj.push_back(_pmetis->adjncy.size());
libmesh_assert_equal_to (_pmetis->xadj.size(), n_active_local_elem+1);
libmesh_assert_equal_to (_pmetis->adjncy.size(), graph_size);
}
void
BreakMeshByBlockManual_3Blocks::addInterfaceBoundary()
{
// construct boundary 100, which will contain the cohesive interface
Elem * elem;
BoundaryInfo & boundary_info = _mesh_ptr->getMesh().get_boundary_info();
SubdomainID interface_id = 100;
if (!_split_interface)
{
elem = _mesh_ptr->getMesh().elem_ptr(0);
boundary_info.add_side(elem->id(), 4, interface_id);
elem = _mesh_ptr->getMesh().elem_ptr(1);
boundary_info.add_side(elem->id(), 4, interface_id);
elem = _mesh_ptr->getMesh().elem_ptr(2);
boundary_info.add_side(elem->id(), 4, interface_id);
elem = _mesh_ptr->getMesh().elem_ptr(3);
boundary_info.add_side(elem->id(), 4, interface_id);
elem = _mesh_ptr->getMesh().elem_ptr(4);
boundary_info.add_side(elem->id(), 3, interface_id);
elem = _mesh_ptr->getMesh().elem_ptr(6);
boundary_info.add_side(elem->id(), 0, interface_id);
// rename the boundary
boundary_info.sideset_name(interface_id) = _interface_name;
}
else
{
elem = _mesh_ptr->getMesh().elem_ptr(0);
boundary_info.add_side(elem->id(), 4, 0);
elem = _mesh_ptr->getMesh().elem_ptr(2);
boundary_info.add_side(elem->id(), 4, 0);
elem = _mesh_ptr->getMesh().elem_ptr(3);
boundary_info.add_side(elem->id(), 4, 0);
// rename the boundary
boundary_info.sideset_name(0) = "Block1_Block2";
elem = _mesh_ptr->getMesh().elem_ptr(1);
boundary_info.add_side(elem->id(), 4, 4);
// rename the boundary
boundary_info.sideset_name(4) = "Block1_Block3";
elem = _mesh_ptr->getMesh().elem_ptr(4);
boundary_info.add_side(elem->id(), 3, 5);
elem = _mesh_ptr->getMesh().elem_ptr(6);
boundary_info.add_side(elem->id(), 0, 5);
// rename the boundary
boundary_info.sideset_name(5) = "Block2_Block3";
}
}
void LinearElasticityWithContact::move_mesh (MeshBase & input_mesh,
const NumericVector<Number> & input_solution)
{
// Maintain a set of node ids that we've encountered.
LIBMESH_BEST_UNORDERED_SET<dof_id_type> encountered_node_ids;
// Localize input_solution so that we have the data to move all
// elements (not just elements local to this processor).
UniquePtr< NumericVector<Number> > localized_input_solution =
NumericVector<Number>::build(input_solution.comm());
localized_input_solution->init (input_solution.size(), false, SERIAL);
input_solution.localize(*localized_input_solution);
MeshBase::const_element_iterator el = input_mesh.active_elements_begin();
const MeshBase::const_element_iterator end_el = input_mesh.active_elements_end();
for ( ; el != end_el; ++el)
{
Elem * elem = *el;
Elem * orig_elem = _sys.get_mesh().elem_ptr(elem->id());
for (unsigned int node_id=0; node_id<elem->n_nodes(); node_id++)
{
Node & node = elem->node_ref(node_id);
if (encountered_node_ids.find(node.id()) != encountered_node_ids.end())
continue;
encountered_node_ids.insert(node.id());
std::vector<std::string> uvw_names(3);
uvw_names[0] = "u";
uvw_names[1] = "v";
uvw_names[2] = "w";
{
const Point master_point = elem->master_point(node_id);
Point uvw;
for (unsigned int index=0; index<uvw_names.size(); index++)
{
const unsigned int var = _sys.variable_number(uvw_names[index]);
const FEType & fe_type = _sys.get_dof_map().variable_type(var);
FEComputeData data (_sys.get_equation_systems(), master_point);
FEInterface::compute_data(elem->dim(),
fe_type,
elem,
data);
std::vector<dof_id_type> dof_indices_var;
_sys.get_dof_map().dof_indices (orig_elem, dof_indices_var, var);
for (unsigned int i=0; i<dof_indices_var.size(); i++)
{
Number value = (*localized_input_solution)(dof_indices_var[i]) * data.shape[i];
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
// We explicitly store the real part in uvw
uvw(index) += value.real();
#else
uvw(index) += value;
#endif
}
}
// Update the node's location
node += uvw;
}
}
}
}
void unpack(std::vector<largest_id_type>::const_iterator in,
Elem** out,
MeshBase* mesh)
{
#ifndef NDEBUG
const std::vector<largest_id_type>::const_iterator original_in = in;
const largest_id_type incoming_header = *in++;
libmesh_assert_equal_to (incoming_header, elem_magic_header);
#endif
// int 0: level
const unsigned int level =
static_cast<unsigned int>(*in++);
#ifdef LIBMESH_ENABLE_AMR
// int 1: p level
const unsigned int p_level =
static_cast<unsigned int>(*in++);
// int 2: refinement flag
const int rflag = *in++;
libmesh_assert_greater_equal (rflag, 0);
libmesh_assert_less (rflag, Elem::INVALID_REFINEMENTSTATE);
const Elem::RefinementState refinement_flag =
static_cast<Elem::RefinementState>(rflag);
// int 3: p refinement flag
const int pflag = *in++;
libmesh_assert_greater_equal (pflag, 0);
libmesh_assert_less (pflag, Elem::INVALID_REFINEMENTSTATE);
const Elem::RefinementState p_refinement_flag =
static_cast<Elem::RefinementState>(pflag);
#else
in += 3;
#endif // LIBMESH_ENABLE_AMR
// int 4: element type
const int typeint = *in++;
libmesh_assert_greater_equal (typeint, 0);
libmesh_assert_less (typeint, INVALID_ELEM);
const ElemType type =
static_cast<ElemType>(typeint);
const unsigned int n_nodes =
Elem::type_to_n_nodes_map[type];
// int 5: processor id
const processor_id_type processor_id =
static_cast<processor_id_type>(*in++);
libmesh_assert (processor_id < mesh->n_processors() ||
processor_id == DofObject::invalid_processor_id);
// int 6: subdomain id
const subdomain_id_type subdomain_id =
static_cast<subdomain_id_type>(*in++);
// int 7: dof object id
const dof_id_type id =
static_cast<dof_id_type>(*in++);
libmesh_assert_not_equal_to (id, DofObject::invalid_id);
#ifdef LIBMESH_ENABLE_UNIQUE_ID
// int 8: dof object unique id
const unique_id_type unique_id =
static_cast<unique_id_type>(*in++);
#endif
#ifdef LIBMESH_ENABLE_AMR
// int 9: parent dof object id
const dof_id_type parent_id =
static_cast<dof_id_type>(*in++);
libmesh_assert (level == 0 || parent_id != DofObject::invalid_id);
libmesh_assert (level != 0 || parent_id == DofObject::invalid_id);
// int 10: local child id
const unsigned int which_child_am_i =
static_cast<unsigned int>(*in++);
#else
in += 2;
#endif // LIBMESH_ENABLE_AMR
// Make sure we don't miscount above when adding the "magic" header
// plus the real data header
libmesh_assert_equal_to (in - original_in, header_size + 1);
Elem *elem = mesh->query_elem(id);
// if we already have this element, make sure its
// properties match, and update any missing neighbor
// links, but then go on
if (elem)
{
libmesh_assert_equal_to (elem->level(), level);
libmesh_assert_equal_to (elem->id(), id);
//#ifdef LIBMESH_ENABLE_UNIQUE_ID
// No check for unqiue id sanity
//#endif
libmesh_assert_equal_to (elem->processor_id(), processor_id);
libmesh_assert_equal_to (elem->subdomain_id(), subdomain_id);
libmesh_assert_equal_to (elem->type(), type);
libmesh_assert_equal_to (elem->n_nodes(), n_nodes);
#ifndef NDEBUG
// All our nodes should be correct
for (unsigned int i=0; i != n_nodes; ++i)
libmesh_assert(elem->node(i) ==
static_cast<dof_id_type>(*in++));
#else
in += n_nodes;
#endif
#ifdef LIBMESH_ENABLE_AMR
libmesh_assert_equal_to (elem->p_level(), p_level);
libmesh_assert_equal_to (elem->refinement_flag(), refinement_flag);
libmesh_assert_equal_to (elem->p_refinement_flag(), p_refinement_flag);
libmesh_assert (!level || elem->parent() != NULL);
libmesh_assert (!level || elem->parent()->id() == parent_id);
libmesh_assert (!level || elem->parent()->child(which_child_am_i) == elem);
#endif
// Our neighbor links should be "close to" correct - we may have
// to update them, but we can check for some inconsistencies.
for (unsigned int n=0; n != elem->n_neighbors(); ++n)
{
const dof_id_type neighbor_id =
static_cast<dof_id_type>(*in++);
// If the sending processor sees a domain boundary here,
// we'd better agree.
if (neighbor_id == DofObject::invalid_id)
{
libmesh_assert (!(elem->neighbor(n)));
continue;
}
// If the sending processor has a remote_elem neighbor here,
// then all we know is that we'd better *not* have a domain
// boundary.
if (neighbor_id == remote_elem->id())
{
libmesh_assert(elem->neighbor(n));
continue;
}
Elem *neigh = mesh->query_elem(neighbor_id);
// The sending processor sees a neighbor here, so if we
// don't have that neighboring element, then we'd better
// have a remote_elem signifying that fact.
if (!neigh)
{
libmesh_assert_equal_to (elem->neighbor(n), remote_elem);
continue;
}
// The sending processor has a neighbor here, and we have
// that element, but that does *NOT* mean we're already
// linking to it. Perhaps we initially received both elem
// and neigh from processors on which their mutual link was
// remote?
libmesh_assert(elem->neighbor(n) == neigh ||
elem->neighbor(n) == remote_elem);
// If the link was originally remote, we should update it,
// and make sure the appropriate parts of its family link
// back to us.
if (elem->neighbor(n) == remote_elem)
{
elem->set_neighbor(n, neigh);
elem->make_links_to_me_local(n);
}
}
// FIXME: We should add some debug mode tests to ensure that the
// encoded indexing and boundary conditions are consistent.
}
else
{
// We don't already have the element, so we need to create it.
// Find the parent if necessary
Elem *parent = NULL;
#ifdef LIBMESH_ENABLE_AMR
// Find a child element's parent
if (level > 0)
{
// Note that we must be very careful to construct the send
// connectivity so that parents are encountered before
// children. If we get here and can't find the parent that
// is a fatal error.
parent = mesh->elem(parent_id);
}
// Or assert that the sending processor sees no parent
else
libmesh_assert_equal_to (parent_id, static_cast<dof_id_type>(-1));
#else
// No non-level-0 elements without AMR
libmesh_assert_equal_to (level, 0);
#endif
elem = Elem::build(type,parent).release();
libmesh_assert (elem);
#ifdef LIBMESH_ENABLE_AMR
if (level != 0)
{
// Since this is a newly created element, the parent must
// have previously thought of this child as a remote element.
libmesh_assert_equal_to (parent->child(which_child_am_i), remote_elem);
parent->add_child(elem, which_child_am_i);
}
// Assign the refinement flags and levels
elem->set_p_level(p_level);
elem->set_refinement_flag(refinement_flag);
elem->set_p_refinement_flag(p_refinement_flag);
libmesh_assert_equal_to (elem->level(), level);
// If this element definitely should have children, assign
// remote_elem to all of them for now, for consistency. Later
// unpacked elements may overwrite that.
if (!elem->active())
for (unsigned int c=0; c != elem->n_children(); ++c)
elem->add_child(const_cast<RemoteElem*>(remote_elem), c);
#endif // LIBMESH_ENABLE_AMR
// Assign the IDs
elem->subdomain_id() = subdomain_id;
elem->processor_id() = processor_id;
elem->set_id() = id;
#ifdef LIBMESH_ENABLE_UNIQUE_ID
elem->set_unique_id() = unique_id;
#endif
// Assign the connectivity
libmesh_assert_equal_to (elem->n_nodes(), n_nodes);
for (unsigned int n=0; n != n_nodes; n++)
elem->set_node(n) =
mesh->node_ptr
(static_cast<dof_id_type>(*in++));
for (unsigned int n=0; n<elem->n_neighbors(); n++)
{
const dof_id_type neighbor_id =
static_cast<dof_id_type>(*in++);
if (neighbor_id == DofObject::invalid_id)
continue;
// We may be unpacking an element that was a ghost element on the
// sender, in which case the element's neighbors may not all be
// known by the packed element. We'll have to set such
// neighbors to remote_elem ourselves and wait for a later
// packed element to give us better information.
if (neighbor_id == remote_elem->id())
{
elem->set_neighbor(n, const_cast<RemoteElem*>(remote_elem));
continue;
}
// If we don't have the neighbor element, then it's a
// remote_elem until we get it.
Elem *neigh = mesh->query_elem(neighbor_id);
if (!neigh)
{
elem->set_neighbor(n, const_cast<RemoteElem*>(remote_elem));
continue;
}
// If we have the neighbor element, then link to it, and
// make sure the appropriate parts of its family link back
// to us.
elem->set_neighbor(n, neigh);
elem->make_links_to_me_local(n);
}
elem->unpack_indexing(in);
}
in += elem->packed_indexing_size();
// If this is a coarse element,
// add any element side boundary condition ids
if (level == 0)
for (unsigned int s = 0; s != elem->n_sides(); ++s)
{
const int num_bcs = *in++;
libmesh_assert_greater_equal (num_bcs, 0);
for(int bc_it=0; bc_it < num_bcs; bc_it++)
mesh->boundary_info->add_side (elem, s, *in++);
}
// Return the new element
*out = elem;
}
int main (int argc, char** argv){
LibMeshInit init (argc, argv); //initialize libmesh library
std::cout << "Running " << argv[0];
for (int i=1; i<argc; i++)
std::cout << " " << argv[i];
std::cout << std::endl << std::endl;
Mesh mesh(init.comm());
//T-channel
//mesh.read("mesh.e");
//MeshRefinement meshRefinement(mesh);
//meshRefinement.uniformly_refine(0);
//1D - for debugging
//int n = 20;
//MeshTools::Generation::build_line(mesh, n, 0.0, 1.0, EDGE2); //n linear elements from 0 to 1
//nice geometry (straight channel)
MeshTools::Generation::build_square (mesh,
250, 50,
-0.0, 5.0,
-0.0, 1.0,
QUAD9);
//read in subdomain assignments
std::vector<double> prev_assign(mesh.n_elem(), 0.);
std::string read_assign = "do_divvy.txt";
if(FILE *fp=fopen(read_assign.c_str(),"r")){
int flag = 1;
int elemNum, assign;
int ind = 0;
while(flag != -1){
flag = fscanf(fp, "%d %d",&elemNum,&assign);
if(flag != -1){
prev_assign[ind] = assign;
ind += 1;
}
}
fclose(fp);
}
//to stash subdomain assignments
std::string stash_assign = "divvy.txt";
std::ofstream output(stash_assign.c_str());
MeshBase::element_iterator elem_it = mesh.elements_begin();
const MeshBase::element_iterator elem_end = mesh.elements_end();
for (; elem_it != elem_end; ++elem_it){
Elem* elem = *elem_it;
Point c = elem->centroid();
//Point cshift1(c(0)-0.63, c(1)-0.5);
elem->subdomain_id() = prev_assign[elem->id()];
//TEST/DEBUG
//if(fabs(c(0)-3.0) < 0.35 && fabs(c(1)-0.5) < 0.35)
// elem->subdomain_id() = 1;
if(output.is_open()){
output << elem->id() << " " << elem->subdomain_id() << "\n";
}
}
output.close();
EquationSystems equation_systems (mesh);
#ifdef LIBMESH_HAVE_EXODUS_API
ExodusII_IO (mesh).write_equation_systems("meep.exo",equation_systems);
#endif // #ifdef LIBMESH_HAVE_EXODUS_API
return 0;
} // end main
void UnstructuredMesh::find_neighbors (const bool reset_remote_elements,
const bool reset_current_list)
{
// We might actually want to run this on an empty mesh
// (e.g. the boundary mesh for a nonexistant bcid!)
// libmesh_assert_not_equal_to (this->n_nodes(), 0);
// libmesh_assert_not_equal_to (this->n_elem(), 0);
// This function must be run on all processors at once
parallel_object_only();
LOG_SCOPE("find_neighbors()", "Mesh");
const element_iterator el_end = this->elements_end();
//TODO:[BSK] This should be removed later?!
if (reset_current_list)
for (element_iterator el = this->elements_begin(); el != el_end; ++el)
{
Elem * e = *el;
for (unsigned int s=0; s<e->n_neighbors(); s++)
if (e->neighbor_ptr(s) != remote_elem ||
reset_remote_elements)
e->set_neighbor(s, libmesh_nullptr);
}
// Find neighboring elements by first finding elements
// with identical side keys and then check to see if they
// are neighbors
{
// data structures -- Use the hash_multimap if available
typedef unsigned int key_type;
typedef std::pair<Elem *, unsigned char> val_type;
typedef std::pair<key_type, val_type> key_val_pair;
typedef LIBMESH_BEST_UNORDERED_MULTIMAP<key_type, val_type> map_type;
// A map from side keys to corresponding elements & side numbers
map_type side_to_elem_map;
for (element_iterator el = this->elements_begin(); el != el_end; ++el)
{
Elem * element = *el;
for (unsigned char ms=0; ms<element->n_neighbors(); ms++)
{
next_side:
// If we haven't yet found a neighbor on this side, try.
// Even if we think our neighbor is remote, that
// information may be out of date.
if (element->neighbor_ptr(ms) == libmesh_nullptr ||
element->neighbor_ptr(ms) == remote_elem)
{
// Get the key for the side of this element
const unsigned int key = element->key(ms);
// Look for elements that have an identical side key
std::pair <map_type::iterator, map_type::iterator>
bounds = side_to_elem_map.equal_range(key);
// May be multiple keys, check all the possible
// elements which _might_ be neighbors.
if (bounds.first != bounds.second)
{
// Get the side for this element
const UniquePtr<Elem> my_side(element->side_ptr(ms));
// Look at all the entries with an equivalent key
while (bounds.first != bounds.second)
{
// Get the potential element
Elem * neighbor = bounds.first->second.first;
// Get the side for the neighboring element
const unsigned int ns = bounds.first->second.second;
const UniquePtr<Elem> their_side(neighbor->side_ptr(ns));
//libmesh_assert(my_side.get());
//libmesh_assert(their_side.get());
// If found a match with my side
//
// We need special tests here for 1D:
// since parents and children have an equal
// side (i.e. a node), we need to check
// ns != ms, and we also check level() to
// avoid setting our neighbor pointer to
// any of our neighbor's descendants
if( (*my_side == *their_side) &&
(element->level() == neighbor->level()) &&
((element->dim() != 1) || (ns != ms)) )
{
// So share a side. Is this a mixed pair
// of subactive and active/ancestor
// elements?
// If not, then we're neighbors.
// If so, then the subactive's neighbor is
if (element->subactive() ==
neighbor->subactive())
{
// an element is only subactive if it has
// been coarsened but not deleted
element->set_neighbor (ms,neighbor);
neighbor->set_neighbor(ns,element);
}
else if (element->subactive())
{
element->set_neighbor(ms,neighbor);
}
else if (neighbor->subactive())
{
neighbor->set_neighbor(ns,element);
}
side_to_elem_map.erase (bounds.first);
// get out of this nested crap
goto next_side;
}
++bounds.first;
}
}
// didn't find a match...
// Build the map entry for this element
key_val_pair kvp;
kvp.first = key;
kvp.second.first = element;
kvp.second.second = ms;
// use the lower bound as a hint for
// where to put it.
#if defined(LIBMESH_HAVE_UNORDERED_MAP) || defined(LIBMESH_HAVE_TR1_UNORDERED_MAP) || defined(LIBMESH_HAVE_HASH_MAP) || defined(LIBMESH_HAVE_EXT_HASH_MAP)
side_to_elem_map.insert (kvp);
#else
side_to_elem_map.insert (bounds.first,kvp);
#endif
}
}
}
}
#ifdef LIBMESH_ENABLE_AMR
/**
* Here we look at all of the child elements which
* don't already have valid neighbors.
*
* If a child element has a NULL neighbor it is
* either because it is on the boundary or because
* its neighbor is at a different level. In the
* latter case we must get the neighbor from the
* parent.
*
* If a child element has a remote_elem neighbor
* on a boundary it shares with its parent, that
* info may have become out-dated through coarsening
* of the neighbor's parent. In this case, if the
* parent's neighbor is active then the child should
* share it.
*
* Furthermore, that neighbor better be active,
* otherwise we missed a child somewhere.
*
*
* We also need to look through children ordered by increasing
* refinement level in order to add new interior_parent() links in
* boundary elements which have just been generated by refinement,
* and fix links in boundary elements whose previous
* interior_parent() has just been coarsened away.
*/
const unsigned int n_levels = MeshTools::n_levels(*this);
for (unsigned int level = 1; level < n_levels; ++level)
{
element_iterator end = this->level_elements_end(level);
for (element_iterator el = this->level_elements_begin(level);
el != end; ++el)
{
Elem * current_elem = *el;
libmesh_assert(current_elem);
Elem * parent = current_elem->parent();
libmesh_assert(parent);
const unsigned int my_child_num = parent->which_child_am_i(current_elem);
for (unsigned int s=0; s < current_elem->n_neighbors(); s++)
{
if (current_elem->neighbor_ptr(s) == libmesh_nullptr ||
(current_elem->neighbor_ptr(s) == remote_elem &&
parent->is_child_on_side(my_child_num, s)))
{
Elem * neigh = parent->neighbor_ptr(s);
// If neigh was refined and had non-subactive children
// made remote earlier, then a non-subactive elem should
// actually have one of those remote children as a
// neighbor
if (neigh && (neigh->ancestor()) && (!current_elem->subactive()))
{
#ifdef DEBUG
// Let's make sure that "had children made remote"
// situation is actually the case
libmesh_assert(neigh->has_children());
bool neigh_has_remote_children = false;
for (unsigned int c = 0; c != neigh->n_children(); ++c)
{
if (neigh->child_ptr(c) == remote_elem)
neigh_has_remote_children = true;
}
libmesh_assert(neigh_has_remote_children);
// And let's double-check that we don't have
// a remote_elem neighboring a local element
libmesh_assert_not_equal_to (current_elem->processor_id(),
this->processor_id());
#endif // DEBUG
neigh = const_cast<RemoteElem *>(remote_elem);
}
if (!current_elem->subactive())
current_elem->set_neighbor(s, neigh);
#ifdef DEBUG
if (neigh != libmesh_nullptr && neigh != remote_elem)
// We ignore subactive elements here because
// we don't care about neighbors of subactive element.
if ((!neigh->active()) && (!current_elem->subactive()))
{
libMesh::err << "On processor " << this->processor_id()
<< std::endl;
libMesh::err << "Bad element ID = " << current_elem->id()
<< ", Side " << s << ", Bad neighbor ID = " << neigh->id() << std::endl;
libMesh::err << "Bad element proc_ID = " << current_elem->processor_id()
<< ", Bad neighbor proc_ID = " << neigh->processor_id() << std::endl;
libMesh::err << "Bad element size = " << current_elem->hmin()
<< ", Bad neighbor size = " << neigh->hmin() << std::endl;
libMesh::err << "Bad element center = " << current_elem->centroid()
<< ", Bad neighbor center = " << neigh->centroid() << std::endl;
libMesh::err << "ERROR: "
<< (current_elem->active()?"Active":"Ancestor")
<< " Element at level "
<< current_elem->level() << std::endl;
libMesh::err << "with "
<< (parent->active()?"active":
(parent->subactive()?"subactive":"ancestor"))
<< " parent share "
<< (neigh->subactive()?"subactive":"ancestor")
<< " neighbor at level " << neigh->level()
<< std::endl;
NameBasedIO(*this).write ("bad_mesh.gmv");
libmesh_error_msg("Problematic mesh written to bad_mesh.gmv.");
}
#endif // DEBUG
}
}
// We can skip to the next element if we're full-dimension
// and therefore don't have any interior parents
if (current_elem->dim() >= LIBMESH_DIM)
continue;
// We have no interior parents unless we can find one later
current_elem->set_interior_parent(libmesh_nullptr);
Elem * pip = parent->interior_parent();
if (!pip)
continue;
// If there's no interior_parent children, whether due to a
// remote element or a non-conformity, then there's no
// children to search.
if (pip == remote_elem || pip->active())
{
current_elem->set_interior_parent(pip);
continue;
}
// For node comparisons we'll need a sensible tolerance
Real node_tolerance = current_elem->hmin() * TOLERANCE;
// Otherwise our interior_parent should be a child of our
// parent's interior_parent.
for (unsigned int c=0; c != pip->n_children(); ++c)
{
Elem * child = pip->child_ptr(c);
// If we have a remote_elem, that might be our
// interior_parent. We'll set it provisionally now and
// keep trying to find something better.
if (child == remote_elem)
{
current_elem->set_interior_parent
(const_cast<RemoteElem *>(remote_elem));
continue;
}
bool child_contains_our_nodes = true;
for (unsigned int n=0; n != current_elem->n_nodes();
++n)
{
bool child_contains_this_node = false;
for (unsigned int cn=0; cn != child->n_nodes();
++cn)
if (child->point(cn).absolute_fuzzy_equals
(current_elem->point(n), node_tolerance))
{
child_contains_this_node = true;
break;
}
if (!child_contains_this_node)
{
child_contains_our_nodes = false;
break;
}
}
if (child_contains_our_nodes)
{
current_elem->set_interior_parent(child);
break;
}
}
// We should have found *some* interior_parent at this
// point, whether semilocal or remote.
libmesh_assert(current_elem->interior_parent());
}
}
#endif // AMR
#ifdef DEBUG
MeshTools::libmesh_assert_valid_neighbors(*this,
!reset_remote_elements);
MeshTools::libmesh_assert_valid_amr_interior_parents(*this);
#endif
}