void GasRecombinationCatalyticWall<Chemistry>::init( const libMesh::FEMSystem& system )
{
libmesh_do_once(libmesh_deprecated());
const std::string r_var_name = std::string("w_"+this->_chemistry.species_name( this->_reactant_species_idx ) );
const std::string p_var_name = std::string("w_"+this->_chemistry.species_name( this->_product_species_idx ) );
libmesh_assert( system.has_variable( r_var_name ) );
libmesh_assert( system.has_variable( p_var_name ) );
this->_reactant_var_idx = system.variable_number( r_var_name );
this->_product_var_idx = system.variable_number( p_var_name );
}
/*
* FIXME: This is known to write nonsense on AMR meshes
* and it strips the imaginary parts of complex Numbers
*/
void VTKIO::system_vectors_to_vtk(const EquationSystems& es, vtkUnstructuredGrid*& grid)
{
if (MeshOutput<MeshBase>::mesh().processor_id() == 0)
{
std::map<std::string, std::vector<Number> > vecs;
for (unsigned int i=0; i<es.n_systems(); ++i)
{
const System& sys = es.get_system(i);
System::const_vectors_iterator v_end = sys.vectors_end();
System::const_vectors_iterator it = sys.vectors_begin();
for (; it!= v_end; ++it)
{
// for all vectors on this system
std::vector<Number> values;
// libMesh::out<<"it "<<it->first<<std::endl;
it->second->localize_to_one(values, 0);
// libMesh::out<<"finish localize"<<std::endl;
vecs[it->first] = values;
}
}
std::map<std::string, std::vector<Number> >::iterator it = vecs.begin();
for (; it!=vecs.end(); ++it)
{
vtkDoubleArray *data = vtkDoubleArray::New();
data->SetName(it->first.c_str());
libmesh_assert_equal_to (it->second.size(), es.get_mesh().n_nodes());
data->SetNumberOfValues(it->second.size());
for (unsigned int i=0; i<it->second.size(); ++i)
{
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
libmesh_do_once (libMesh::err << "Only writing the real part for complex numbers!\n"
<< "if you need this support contact " << LIBMESH_PACKAGE_BUGREPORT
<< std::endl);
data->SetValue(i, it->second[i].real());
#else
data->SetValue(i, it->second[i]);
#endif
}
grid->GetPointData()->AddArray(data);
data->Delete();
}
}
}
void GasRecombinationCatalyticWall<Chemistry>::apply_fluxes( AssemblyContext& context,
const CachedValues& cache,
const bool request_jacobian )
{
libmesh_do_once(libmesh_deprecated());
libMesh::FEGenericBase<libMesh::Real>* side_fe = NULL;
context.get_side_fe( _reactant_var_idx, side_fe );
// The number of local degrees of freedom in each variable.
const unsigned int n_var_dofs = context.get_dof_indices(_reactant_var_idx).size();
libmesh_assert_equal_to( n_var_dofs, context.get_dof_indices(_product_var_idx).size() );
// Element Jacobian * quadrature weight for side integration.
const std::vector<libMesh::Real> &JxW_side = side_fe->get_JxW();
// The var shape functions at side quadrature points.
const std::vector<std::vector<libMesh::Real> >& var_phi_side = side_fe->get_phi();
// Physical location of the quadrature points
const std::vector<libMesh::Point>& var_qpoint = side_fe->get_xyz();
// reactant residual
libMesh::DenseSubVector<libMesh::Number> &F_r_var = context.get_elem_residual(_reactant_var_idx);
// product residual
libMesh::DenseSubVector<libMesh::Number> &F_p_var = context.get_elem_residual(_product_var_idx);
unsigned int n_qpoints = context.get_side_qrule().n_points();
for (unsigned int qp=0; qp != n_qpoints; qp++)
{
libMesh::Real jac = JxW_side[qp];
if(Physics::is_axisymmetric())
{
const libMesh::Number r = var_qpoint[qp](0);
jac *= r;
}
const libMesh::Real rho = cache.get_cached_values(Cache::MIXTURE_DENSITY)[qp];
const libMesh::Real Y_r = cache.get_cached_vector_values(Cache::MASS_FRACTIONS)[qp][this->_reactant_species_idx];
const libMesh::Real T = cache.get_cached_values(Cache::TEMPERATURE)[qp];
const libMesh::Real r_value = this->compute_reactant_mass_flux(rho, Y_r, T);
const libMesh::Real p_value = -r_value;
for (unsigned int i=0; i != n_var_dofs; i++)
{
F_r_var(i) += r_value*var_phi_side[i][qp]*jac;
F_p_var(i) += p_value*var_phi_side[i][qp]*jac;
if( request_jacobian )
{
libmesh_not_implemented();
}
}
}
}
void VTKIO::write_nodal_data (const std::string & fname,
const std::vector<Number> & soln,
const std::vector<std::string> & names)
{
const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
// Warn that the .pvtu file extension should be used. Paraview
// recognizes this, and it works in both serial and parallel. Only
// warn about this once.
if (fname.substr(fname.rfind("."), fname.size()) != ".pvtu")
libmesh_do_once(libMesh::err << "The .pvtu extension should be used when writing VTK files in libMesh.");
// If there are variable names being written, the solution vector
// should not be empty, it should have been broadcast to all
// processors by the MeshOutput base class, since VTK is a parallel
// format. Verify this before going further.
if (!names.empty() && soln.empty())
libmesh_error_msg("Empty soln vector in VTKIO::write_nodal_data().");
// we only use Unstructured grids
_vtk_grid = vtkUnstructuredGrid::New();
vtkSmartPointer<vtkXMLPUnstructuredGridWriter> writer = vtkSmartPointer<vtkXMLPUnstructuredGridWriter>::New();
// add nodes to the grid and update _local_node_map
_local_node_map.clear();
this->nodes_to_vtk();
// add cells to the grid
this->cells_to_vtk();
// add nodal solutions to the grid, if solutions are given
if (names.size() > 0)
{
std::size_t num_vars = names.size();
dof_id_type num_nodes = mesh.n_nodes();
for (std::size_t variable=0; variable<num_vars; ++variable)
{
vtkSmartPointer<vtkDoubleArray> data = vtkSmartPointer<vtkDoubleArray>::New();
data->SetName(names[variable].c_str());
// number of local and ghost nodes
data->SetNumberOfValues(_local_node_map.size());
// loop over all nodes and get the solution for the current
// variable, if the node is in the current partition
for (dof_id_type k=0; k<num_nodes; ++k)
{
std::map<dof_id_type, dof_id_type>::iterator local_node_it = _local_node_map.find(k);
if (local_node_it == _local_node_map.end())
continue; // not a local node
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
libmesh_do_once (libMesh::err << "Only writing the real part for complex numbers!\n"
<< "if you need this support contact " << LIBMESH_PACKAGE_BUGREPORT
<< std::endl);
data->SetValue(local_node_it->second, soln[k*num_vars + variable].real());
#else
data->SetValue(local_node_it->second, soln[k*num_vars + variable]);
#endif
}
_vtk_grid->GetPointData()->AddArray(data);
}
}
// Tell the writer how many partitions exist and on which processor
// we are currently
writer->SetNumberOfPieces(MeshOutput<MeshBase>::mesh().n_processors());
writer->SetStartPiece(MeshOutput<MeshBase>::mesh().processor_id());
writer->SetEndPiece(MeshOutput<MeshBase>::mesh().processor_id());
// partitions overlap by one node
// FIXME: According to this document
// http://paraview.org/Wiki/images/5/51/SC07_tut107_ParaView_Handouts.pdf
// the ghosts are cells rather than nodes.
writer->SetGhostLevel(1);
// Not sure exactly when this changed, but SetInput() is not a
// method on vtkXMLPUnstructuredGridWriter as of VTK 6.1.0
#if VTK_VERSION_LESS_THAN(6,0,0)
writer->SetInput(_vtk_grid);
#else
writer->SetInputData(_vtk_grid);
#endif
writer->SetFileName(fname.c_str());
writer->SetDataModeToAscii();
// compress the output, if desired (switches also to binary)
if (this->_compress)
{
#if !VTK_VERSION_LESS_THAN(5,6,0)
writer->SetCompressorTypeToZLib();
#else
libmesh_do_once(libMesh::err << "Compression not implemented with old VTK libs!" << std::endl;);
void InfFE<Dim,T_radial,T_map>::init_shape_functions(const Elem * inf_elem)
{
libmesh_assert(inf_elem);
// Start logging the radial shape function initialization
START_LOG("init_shape_functions()", "InfFE");
// -----------------------------------------------------------------
// fast access to some const int's for the radial data
const unsigned int n_radial_mapping_sf =
cast_int<unsigned int>(radial_map.size());
const unsigned int n_radial_approx_sf =
cast_int<unsigned int>(mode.size());
const unsigned int n_radial_qp =
cast_int<unsigned int>(som.size());
// -----------------------------------------------------------------
// initialize most of the things related to mapping
// The element type and order to use in the base map
const Order base_mapping_order ( base_elem->default_order() );
const ElemType base_mapping_elem_type ( base_elem->type() );
// the number of base shape functions used to construct the map
// (Lagrange shape functions are used for mapping in the base)
unsigned int n_base_mapping_shape_functions = Base::n_base_mapping_sf(base_mapping_elem_type,
base_mapping_order);
const unsigned int n_total_mapping_shape_functions =
n_radial_mapping_sf * n_base_mapping_shape_functions;
// -----------------------------------------------------------------
// initialize most of the things related to physical approximation
unsigned int n_base_approx_shape_functions;
if (Dim > 1)
n_base_approx_shape_functions = base_fe->n_shape_functions();
else
n_base_approx_shape_functions = 1;
const unsigned int n_total_approx_shape_functions =
n_radial_approx_sf * n_base_approx_shape_functions;
// update class member field
_n_total_approx_sf = n_total_approx_shape_functions;
// The number of the base quadrature points.
const unsigned int n_base_qp = base_qrule->n_points();
// The total number of quadrature points.
const unsigned int n_total_qp = n_radial_qp * n_base_qp;
// update class member field
_n_total_qp = n_total_qp;
// -----------------------------------------------------------------
// initialize the node and shape numbering maps
{
// these vectors work as follows: the i-th entry stores
// the associated base/radial node number
_radial_node_index.resize (n_total_mapping_shape_functions);
_base_node_index.resize (n_total_mapping_shape_functions);
// similar for the shapes: the i-th entry stores
// the associated base/radial shape number
_radial_shape_index.resize (n_total_approx_shape_functions);
_base_shape_index.resize (n_total_approx_shape_functions);
const ElemType inf_elem_type (inf_elem->type());
// fill the node index map
for (unsigned int n=0; n<n_total_mapping_shape_functions; n++)
{
compute_node_indices (inf_elem_type,
n,
_base_node_index[n],
_radial_node_index[n]);
libmesh_assert_less (_base_node_index[n], n_base_mapping_shape_functions);
libmesh_assert_less (_radial_node_index[n], n_radial_mapping_sf);
}
// fill the shape index map
for (unsigned int n=0; n<n_total_approx_shape_functions; n++)
{
compute_shape_indices (this->fe_type,
inf_elem_type,
n,
_base_shape_index[n],
_radial_shape_index[n]);
libmesh_assert_less (_base_shape_index[n], n_base_approx_shape_functions);
libmesh_assert_less (_radial_shape_index[n], n_radial_approx_sf);
}
}
// -----------------------------------------------------------------
// resize the base data fields
dist.resize(n_base_mapping_shape_functions);
// -----------------------------------------------------------------
// resize the total data fields
// the phase term varies with xi, eta and zeta(v): store it for _all_ qp
//
// when computing the phase, we need the base approximations
// therefore, initialize the phase here, but evaluate it
// in combine_base_radial().
//
// the weight, though, is only needed at the radial quadrature points, n_radial_qp.
// but for a uniform interface to the protected data fields
// the weight data field (which are accessible from the outside) are expanded to n_total_qp.
weight.resize (n_total_qp);
dweightdv.resize (n_total_qp);
dweight.resize (n_total_qp);
dphase.resize (n_total_qp);
dphasedxi.resize (n_total_qp);
dphasedeta.resize (n_total_qp);
dphasedzeta.resize (n_total_qp);
// this vector contains the integration weights for the combined quadrature rule
_total_qrule_weights.resize(n_total_qp);
// -----------------------------------------------------------------
// InfFE's data fields phi, dphi, dphidx, phi_map etc hold the _total_
// shape and mapping functions, respectively
{
phi.resize (n_total_approx_shape_functions);
dphi.resize (n_total_approx_shape_functions);
dphidx.resize (n_total_approx_shape_functions);
dphidy.resize (n_total_approx_shape_functions);
dphidz.resize (n_total_approx_shape_functions);
dphidxi.resize (n_total_approx_shape_functions);
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
libmesh_do_once(libMesh::err << "Second derivatives for Infinite elements"
<< " are not yet implemented!"
<< std::endl);
d2phi.resize (n_total_approx_shape_functions);
d2phidx2.resize (n_total_approx_shape_functions);
d2phidxdy.resize (n_total_approx_shape_functions);
d2phidxdz.resize (n_total_approx_shape_functions);
d2phidy2.resize (n_total_approx_shape_functions);
d2phidydz.resize (n_total_approx_shape_functions);
d2phidz2.resize (n_total_approx_shape_functions);
d2phidxi2.resize (n_total_approx_shape_functions);
if (Dim > 1)
{
d2phidxideta.resize (n_total_approx_shape_functions);
d2phideta2.resize (n_total_approx_shape_functions);
}
if (Dim > 2)
{
d2phidetadzeta.resize (n_total_approx_shape_functions);
d2phidxidzeta.resize (n_total_approx_shape_functions);
d2phidzeta2.resize (n_total_approx_shape_functions);
}
#endif // ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
if (Dim > 1)
dphideta.resize (n_total_approx_shape_functions);
if (Dim == 3)
dphidzeta.resize (n_total_approx_shape_functions);
std::vector<std::vector<Real> > & phi_map = this->_fe_map->get_phi_map();
std::vector<std::vector<Real> > & dphidxi_map = this->_fe_map->get_dphidxi_map();
phi_map.resize (n_total_mapping_shape_functions);
dphidxi_map.resize (n_total_mapping_shape_functions);
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
std::vector<std::vector<Real> > & d2phidxi2_map = this->_fe_map->get_d2phidxi2_map();
d2phidxi2_map.resize (n_total_mapping_shape_functions);
if (Dim > 1)
{
std::vector<std::vector<Real> > & d2phidxideta_map = this->_fe_map->get_d2phidxideta_map();
std::vector<std::vector<Real> > & d2phideta2_map = this->_fe_map->get_d2phideta2_map();
d2phidxideta_map.resize (n_total_mapping_shape_functions);
d2phideta2_map.resize (n_total_mapping_shape_functions);
}
if (Dim == 3)
{
std::vector<std::vector<Real> > & d2phidxidzeta_map = this->_fe_map->get_d2phidxidzeta_map();
std::vector<std::vector<Real> > & d2phidetadzeta_map = this->_fe_map->get_d2phidetadzeta_map();
std::vector<std::vector<Real> > & d2phidzeta2_map = this->_fe_map->get_d2phidzeta2_map();
d2phidxidzeta_map.resize (n_total_mapping_shape_functions);
d2phidetadzeta_map.resize (n_total_mapping_shape_functions);
d2phidzeta2_map.resize (n_total_mapping_shape_functions);
}
#endif // ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
if (Dim > 1)
{
std::vector<std::vector<Real> > & dphideta_map = this->_fe_map->get_dphideta_map();
dphideta_map.resize (n_total_mapping_shape_functions);
}
if (Dim == 3)
{
std::vector<std::vector<Real> > & dphidzeta_map = this->_fe_map->get_dphidzeta_map();
dphidzeta_map.resize (n_total_mapping_shape_functions);
}
}
// -----------------------------------------------------------------
// collect all the for loops, where inner vectors are
// resized to the appropriate number of quadrature points
{
for (unsigned int i=0; i<n_total_approx_shape_functions; i++)
{
phi[i].resize (n_total_qp);
dphi[i].resize (n_total_qp);
dphidx[i].resize (n_total_qp);
dphidy[i].resize (n_total_qp);
dphidz[i].resize (n_total_qp);
dphidxi[i].resize (n_total_qp);
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
d2phi[i].resize (n_total_qp);
d2phidx2[i].resize (n_total_qp);
d2phidxdy[i].resize (n_total_qp);
d2phidxdz[i].resize (n_total_qp);
d2phidy2[i].resize (n_total_qp);
d2phidydz[i].resize (n_total_qp);
d2phidy2[i].resize (n_total_qp);
d2phidxi2[i].resize (n_total_qp);
if (Dim > 1)
{
d2phidxideta[i].resize (n_total_qp);
d2phideta2[i].resize (n_total_qp);
}
if (Dim > 2)
{
d2phidxidzeta[i].resize (n_total_qp);
d2phidetadzeta[i].resize (n_total_qp);
d2phidzeta2[i].resize (n_total_qp);
}
#endif // ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
if (Dim > 1)
dphideta[i].resize (n_total_qp);
if (Dim == 3)
dphidzeta[i].resize (n_total_qp);
}
for (unsigned int i=0; i<n_total_mapping_shape_functions; i++)
{
std::vector<std::vector<Real> > & phi_map = this->_fe_map->get_phi_map();
std::vector<std::vector<Real> > & dphidxi_map = this->_fe_map->get_dphidxi_map();
phi_map[i].resize (n_total_qp);
dphidxi_map[i].resize (n_total_qp);
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
std::vector<std::vector<Real> > & d2phidxi2_map = this->_fe_map->get_d2phidxi2_map();
d2phidxi2_map[i].resize (n_total_qp);
if (Dim > 1)
{
std::vector<std::vector<Real> > & d2phidxideta_map = this->_fe_map->get_d2phidxideta_map();
std::vector<std::vector<Real> > & d2phideta2_map = this->_fe_map->get_d2phideta2_map();
d2phidxideta_map[i].resize (n_total_qp);
d2phideta2_map[i].resize (n_total_qp);
}
if (Dim > 2)
{
std::vector<std::vector<Real> > & d2phidxidzeta_map = this->_fe_map->get_d2phidxidzeta_map();
std::vector<std::vector<Real> > & d2phidetadzeta_map = this->_fe_map->get_d2phidetadzeta_map();
std::vector<std::vector<Real> > & d2phidzeta2_map = this->_fe_map->get_d2phidzeta2_map();
d2phidxidzeta_map[i].resize (n_total_qp);
d2phidetadzeta_map[i].resize (n_total_qp);
d2phidzeta2_map[i].resize (n_total_qp);
}
#endif // ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
if (Dim > 1)
{
std::vector<std::vector<Real> > & dphideta_map = this->_fe_map->get_dphideta_map();
dphideta_map[i].resize (n_total_qp);
}
if (Dim == 3)
{
std::vector<std::vector<Real> > & dphidzeta_map = this->_fe_map->get_dphidzeta_map();
dphidzeta_map[i].resize (n_total_qp);
}
}
}
{
// -----------------------------------------------------------------
// (a) compute scalar values at _all_ quadrature points -- for uniform
// access from the outside to these fields
// (b) form a std::vector<Real> which contains the appropriate weights
// of the combined quadrature rule!
const std::vector<Point> & radial_qp = radial_qrule->get_points();
libmesh_assert_equal_to (radial_qp.size(), n_radial_qp);
const std::vector<Real> & radial_qw = radial_qrule->get_weights();
const std::vector<Real> & base_qw = base_qrule->get_weights();
libmesh_assert_equal_to (radial_qw.size(), n_radial_qp);
libmesh_assert_equal_to (base_qw.size(), n_base_qp);
for (unsigned int rp=0; rp<n_radial_qp; rp++)
for (unsigned int bp=0; bp<n_base_qp; bp++)
{
weight [ bp+rp*n_base_qp ] = Radial::D (radial_qp[rp](0));
dweightdv[ bp+rp*n_base_qp ] = Radial::D_deriv (radial_qp[rp](0));
_total_qrule_weights[ bp+rp*n_base_qp ] = radial_qw[rp] * base_qw[bp];
}
}
/**
* Stop logging the radial shape function initialization
*/
STOP_LOG("init_shape_functions()", "InfFE");
}