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#include <deal.II/base/quadrature_lib.h>
#include <deal.II/base/function.h>
#include <deal.II/base/parameter_handler.h>
#include <deal.II/base/function_parser.h>
#include <deal.II/base/utilities.h>
#include <deal.II/base/conditional_ostream.h>
#include <deal.II/lac/vector.h>
#include <deal.II/lac/sparsity_pattern.h>
#include <deal.II/grid/tria.h>
#include <deal.II/grid/grid_generator.h>
#include <deal.II/grid/grid_out.h>
#include <deal.II/grid/tria_accessor.h>
#include <deal.II/grid/tria_iterator.h>
#include <deal.II/grid/grid_in.h>
#include <deal.II/grid/tria_boundary_lib.h>
#include <deal.II/grid/manifold_lib.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/dofs/dof_accessor.h>
#include <deal.II/dofs/dof_tools.h>
#include <deal.II/dofs/dof_renumbering.h>
#include <deal.II/fe/fe_values.h>
#include <deal.II/fe/fe_system.h>
#include <deal.II/fe/mapping_q.h> //it used to be mapping_q1
#include <deal.II/fe/mapping_cartesian.h>
#include <deal.II/fe/fe_dgq.h>
#include <deal.II/fe/fe_dgp.h>
#include <deal.II/numerics/vector_tools.h>
#include <deal.II/numerics/solution_transfer.h>
#include <deal.II/numerics/matrix_tools.h>
#include <deal.II/lac/trilinos_sparse_matrix.h>
#include <deal.II/lac/trilinos_vector.h>
#include <deal.II/lac/trilinos_precondition.h>
#include <deal.II/lac/trilinos_solver.h>
#include <deal.II/lac/solver_gmres.h>
#include <deal.II/lac/sparse_direct.h>
#include <deal.II/lac/precondition_block.h>
#include <Sacado.hpp>
#include <iostream>
#include <fstream>
#include <vector>
#include <memory>
#include "claw.h"
#include "equation.h"
#include "ic.h"
#define Pi 3.1415926
// Coefficients for SSP-RK scheme
double ark[3];
unsigned int n_rk;
using namespace dealii;
//------------------------------------------------------------------------------
// @sect4{ConservationLaw::ConservationLaw}
//
// There is nothing much to say about
// the constructor. Essentially, it
// reads the input file and fills the
// parameter object with the parsed
// values:
//------------------------------------------------------------------------------
template <int dim>
ConservationLaw<dim>::ConservationLaw (const char *input_filename,
const unsigned int degree,
const FE_DGQArbitraryNodes<dim> &fe_scalar
/*const FE_DGQ<dim> &fe_scalar*/)
:
fe (fe_scalar, EulerEquations<dim>::n_components),
dof_handler (triangulation),
fe_cell (FE_DGQ<dim>(0)),
dh_cell (triangulation),
verbose_cout (std::cout, false)
{
read_parameters (input_filename);
// For MOOD method compute degree reduction matrices
if(parameters.solver == Parameters::Solver::mood)
compute_reduction_matrices ();
}
//------------------------------------------------------------------------------
// Constructor for Pk basis
//------------------------------------------------------------------------------
template <int dim>
ConservationLaw<dim>::ConservationLaw (const char *input_filename,
const unsigned int degree,
const FE_DGP<dim> &fe_scalar)
:
fe (fe_scalar, EulerEquations<dim>::n_components),
dof_handler (triangulation),
fe_cell (FE_DGQ<dim>(0)),
dh_cell (triangulation),
verbose_cout (std::cout, false)
{
read_parameters (input_filename);
// create map from dof index to total degree of basis function
index_to_degree.resize(fe.base_element(0).dofs_per_cell);
unsigned int c = 0;
if(dim==2)
{
for(unsigned int j=0; j<=degree; ++j)
for(unsigned int i=0; i<=degree-j; ++i)
{
index_to_degree[c++] = i+j;
}
}
else
{
AssertThrow(false, ExcMessage("Not implemented for dim=3"));
}
}
//------------------------------------------------------------------------------
// Read parameters from file and set some other parameters.
//------------------------------------------------------------------------------
template <int dim>
void ConservationLaw<dim>::read_parameters (const char *input_filename)
{
AssertThrow(dim == 2, ExcMessage("Only works for 2-D"));
ParameterHandler prm;
Parameters::AllParameters<dim>::declare_parameters (prm);
prm.read_input (input_filename);
parameters.parse_parameters (prm);
verbose_cout.set_condition (parameters.output == Parameters::Solver::verbose);
// Save all parameters in xml format
//std::ofstream xml_file ("input.xml");
//prm.print_parameters (xml_file, ParameterHandler::XML);
// Set coefficients for SSPRK
if(fe.degree == 0)
{
ark[0] = 0.0;
n_rk = 1;
}
else if(fe.degree==1)
{
ark[0] = 0.0;
ark[1] = 1.0/2.0;
n_rk = 2;
}
else
{
ark[0] = 0.0;
ark[1] = 3.0/4.0;
ark[2] = 1.0/3.0;
n_rk = 3;
}
}
//------------------------------------------------------------------------------
// Return mapping type based on selected type
//------------------------------------------------------------------------------
template <int dim>
const Mapping<dim,dim>& ConservationLaw<dim>::mapping() const
{
if(parameters.mapping_type == Parameters::AllParameters<dim>::q1)
{
static MappingQ1<dim> m;
return m;
}
else if(parameters.mapping_type == Parameters::AllParameters<dim>::q2)
{
static MappingQ<dim> m(2);
return m;
}
else if(parameters.mapping_type == Parameters::AllParameters<dim>::cartesian)
{
static MappingCartesian<dim> m;
return m;
}
else
{
AssertThrow (false, ExcMessage("Requested mapping type is unknown"));
static MappingQ1<dim> m;
return m;
}
}
//------------------------------------------------------------------------------
// Compute dx, dy, dz for cartesian meshes.
// At present it only checks that dx == dy
//------------------------------------------------------------------------------
template <int dim>
void ConservationLaw<dim>::compute_cartesian_mesh_size ()
{
const double geom_tol = 1.0e-12;
typename DoFHandler<dim>::active_cell_iterator
cell = dof_handler.begin_active(),
endc = dof_handler.end();
for (; cell!=endc; ++cell)
{
double xmin = 1.0e20, xmax = -1.0e20;
double ymin = 1.0e20, ymax = -1.0e20;
for (unsigned int f=0; f<GeometryInfo<dim>::faces_per_cell; ++f)
{
const Point<dim>& p = cell->face(f)->center();
xmin = std::min(xmin, p[0]);
xmax = std::max(xmax, p[0]);
ymin = std::min(ymin, p[1]);
ymax = std::max(ymax, p[1]);
}
double dx = xmax - xmin;
double dy = ymax - ymin;
AssertThrow(std::fabs(dx-dy) < geom_tol, ExcMessage("Cell is not square"));
}
}
//------------------------------------------------------------------------------
// Our nodal basis uses Gauss points and we use Gauss quadrature with degree+1
// nodes. Then the mass matrix is diagonal. The mass matrix is integrated exactly
// for Cartesian cells but not exact for general cells.
//------------------------------------------------------------------------------
template <int dim>
void ConservationLaw<dim>::compute_inv_mass_matrix ()
{
QGauss<dim> quadrature(fe.degree+1);
unsigned int n_q_points = quadrature.size();
FEValues<dim> fe_values(mapping(), fe, quadrature, update_values | update_JxW_values);
std::vector<unsigned int> dof_indices(fe.dofs_per_cell);
typename DoFHandler<dim>::active_cell_iterator
cell = dof_handler.begin_active(),
endc = dof_handler.end();
inv_mass_matrix.resize(triangulation.n_active_cells(),
Vector<double>(fe.dofs_per_cell));
for (; cell!=endc; ++cell)
{
unsigned int c = cell_number(cell);
cell->get_dof_indices (dof_indices);
fe_values.reinit(cell);
for(unsigned int i=0; i<fe.dofs_per_cell; ++i)
{
inv_mass_matrix[c][i] = 0.0;
for(unsigned int q=0; q<n_q_points; ++q)
inv_mass_matrix[c][i] += fe_values.shape_value(i,q) *
fe_values.shape_value(i,q) *
fe_values.JxW(q);
inv_mass_matrix[c][i] = 1.0 / inv_mass_matrix[c][i];
}
}
}
//------------------------------------------------------------------------------
// @sect4{ConservationLaw::setup_system}
//
// The following (easy) function is called
// each time the mesh is changed. All it
// does is to resize the Trilinos matrix
// according to a sparsity pattern that we
// generate as in all the previous tutorial
// programs.
//------------------------------------------------------------------------------
template <int dim>
void ConservationLaw<dim>::setup_system ()
{
//DoFRenumbering::Cuthill_McKee (dof_handler);
dof_handler.clear();
dof_handler.distribute_dofs (fe);
// Size all of the fields.
old_solution.reinit (dof_handler.n_dofs());
current_solution.reinit (dof_handler.n_dofs());
predictor.reinit (dof_handler.n_dofs());
right_hand_side.reinit (dof_handler.n_dofs());
cell_average.resize (triangulation.n_active_cells(),
Vector<double>(EulerEquations<dim>::n_components));
// Used for cell data like time step
dh_cell.clear();
dh_cell.distribute_dofs (fe_cell);
mu_shock.reinit (dh_cell.n_dofs());
shock_indicator.reinit (dh_cell.n_dofs());
jump_indicator.reinit (dh_cell.n_dofs());
// set cell index
unsigned int index=0;
for (typename Triangulation<dim>::active_cell_iterator cell=triangulation.begin_active();
cell!=triangulation.end(); ++cell, ++index)
cell->set_user_index(index);
if(parameters.implicit == false)
{
std::cout << "Creating mass matrix ...\n";
compute_inv_mass_matrix ();
}
else
{
DynamicSparsityPattern c_sparsity(dof_handler.n_dofs());
DoFTools::make_flux_sparsity_pattern (dof_handler, c_sparsity);
sparsity_pattern.copy_from(c_sparsity);
system_matrix.reinit (sparsity_pattern);
}
// Allocate memory for MOOD variables
if(parameters.solver == Parameters::Solver::mood)
{
min_mood_var.reinit(triangulation.n_active_cells());
max_mood_var.reinit(triangulation.n_active_cells());
work1.reinit (dof_handler.n_dofs());
}
cell_degree.resize(triangulation.n_active_cells());
re_update.resize(triangulation.n_active_cells());
for(unsigned int i=0; i<triangulation.n_active_cells(); ++i)
{
cell_degree[i] = fe.degree;
re_update[i] = true;
}
if(parameters.mapping_type == Parameters::AllParameters<dim>::cartesian)
compute_cartesian_mesh_size ();
if(parameters.mapping_type != Parameters::AllParameters<dim>::cartesian)
return;
// For each cell, find neighbourig cell
// This is needed for limiter
// CHECK: Should the size be n_active_cells() ?
lcell.resize(triangulation.n_cells());
rcell.resize(triangulation.n_cells());
bcell.resize(triangulation.n_cells());
tcell.resize(triangulation.n_cells());
const double EPS = 1.0e-10;
typename DoFHandler<dim>::active_cell_iterator
cell = dh_cell.begin_active(),
endc = dh_cell.end();
for (; cell!=endc; ++cell)
{
unsigned int c = cell_number(cell);
lcell[c] = endc;
rcell[c] = endc;
bcell[c] = endc;
tcell[c] = endc;
double dx = cell->diameter() / std::sqrt(1.0*dim);
for (unsigned int face_no=0; face_no<GeometryInfo<dim>::faces_per_cell; ++face_no)
if (! cell->at_boundary(face_no))
{
const typename DoFHandler<dim>::cell_iterator
neighbor = cell->neighbor(face_no);
Assert(neighbor->level() == cell->level() || neighbor->level() == cell->level()-1,
ExcInternalError());
Tensor<1,dim> dr = neighbor->center() - cell->center();
if(dr[0] < -0.5*dx)
lcell[c] = neighbor;
else if(dr[0] > 0.5*dx)
rcell[c] = neighbor;
else if(dr[1] < -0.5*dx)
bcell[c] = neighbor;
else if(dr[1] > 0.5*dx)
tcell[c] = neighbor;
else
{
std::cout << "Did not find all neighbours\n";
std::cout << "dx, dy = " << dr[0] << " " << dr[1] << std::endl;
exit(0);
}
}
}
// Visualize sparsity pattern
//std::ofstream out ("sparsity_pattern.1");
//sparsity_pattern.print_gnuplot (out);
//abort ();
}
//------------------------------------------------------------------------------
// Create mesh worker for implicit integration
//------------------------------------------------------------------------------
template <int dim>
void ConservationLaw<dim>::setup_mesh_worker (IntegratorImplicit<dim>& integrator)
{
const unsigned int n_gauss_points = fe.degree + 1;
integrator.info_box.initialize_gauss_quadrature(n_gauss_points,
n_gauss_points,
n_gauss_points);
integrator.info_box.initialize_update_flags ();
integrator.info_box.add_update_flags_all (update_values |
update_quadrature_points |
update_JxW_values);
integrator.info_box.add_update_flags_cell (update_gradients);
integrator.info_box.add_update_flags_boundary (update_normal_vectors | update_gradients);
integrator.info_box.add_update_flags_face (update_normal_vectors | update_gradients);
integrator.info_box.initialize (fe, mapping());
integrator.assembler.initialize (system_matrix, right_hand_side);
}
//------------------------------------------------------------------------------
// Create mesh worker for explicit integration
// This computes only the right hand side
//------------------------------------------------------------------------------
template <int dim>
void ConservationLaw<dim>::setup_mesh_worker (IntegratorExplicit<dim>& integrator)
{
const unsigned int n_gauss_points = fe.degree + 1;
integrator.info_box.initialize_gauss_quadrature(n_gauss_points,
n_gauss_points,
n_gauss_points);
integrator.info_box.initialize_update_flags ();
integrator.info_box.add_update_flags_all (update_values |
update_JxW_values);
integrator.info_box.add_update_flags_cell (update_gradients);
integrator.info_box.add_update_flags_boundary (update_normal_vectors | update_quadrature_points); // TODO:ADIFF
integrator.info_box.add_update_flags_face (update_normal_vectors); // TODO:ADIFF
integrator.info_box.initialize (fe, mapping());
AnyData rhs;
Vector<double>* data = &right_hand_side;
rhs.add<Vector<double>*> (data, "RHS");
integrator.assembler.initialize (rhs);
}
//------------------------------------------------------------------------------
// Compute local time step for each cell
// We compute speed at quadrature points and take maximum over these values.
// This speed is used to compute time step in each cell.
//------------------------------------------------------------------------------
template <int dim>
void
ConservationLaw<dim>::compute_time_step ()
{
// No need to compute time step for stationary flows
if(parameters.is_stationary == true)
return;
// Update size of dt array since adaptation might have been performed
dt.reinit (triangulation.n_cells());
// If time step given in input file, then use it. This is only for global time stepping
if(parameters.time_step_type == "global" && parameters.cfl <= 0.0)
{
dt = parameters.time_step;
global_dt = parameters.time_step;
return;
}
if(parameters.mapping_type == Parameters::AllParameters<dim>::cartesian)
compute_time_step_cartesian();
else
compute_time_step_q();
// For global time step, use the minimum value
if(parameters.time_step_type == "global")
{
if(global_dt > 0 && parameters.time_step > 0)
global_dt = std::min(global_dt, parameters.time_step);
if(elapsed_time + global_dt > parameters.final_time)
global_dt = parameters.final_time - elapsed_time;
dt = global_dt;
}
}
//------------------------------------------------------------------------------
// Compute local time step for each cell
// This function is specified to cartesian cells.
//------------------------------------------------------------------------------
template <int dim>
void
ConservationLaw<dim>::compute_time_step_cartesian ()
{
typename DoFHandler<dim>::active_cell_iterator
cell = dof_handler.begin_active(),
endc = dof_handler.end();
global_dt = 1.0e20;
for (; cell!=endc; ++cell)
{
const unsigned int c = cell_number (cell);
const double h = cell->diameter() / std::sqrt(1.0*dim);
const double sonic = EulerEquations<dim>::sound_speed(cell_average[c]);
const double density = cell_average[c][EulerEquations<dim>::density_component];
double max_eigenvalue = 0.0;
for (unsigned int d=0; d<dim; ++d)
max_eigenvalue += (sonic + std::fabs(cell_average[c][d]/density))/h;
dt(c) = parameters.cfl / max_eigenvalue / (2.0*fe.degree + 1.0);
global_dt = std::min(global_dt, dt(c));
}
}
//------------------------------------------------------------------------------
// Compute local time step for each cell
// We compute speed at quadrature points and take maximum over these values.
// This speed is used to compute time step in each cell.
//------------------------------------------------------------------------------
template <int dim>
void
ConservationLaw<dim>::compute_time_step_q ()
{
//QGaussLobatto<dim> quadrature_formula(fe.degree+1);
QIterated<dim> quadrature_formula(QTrapez<1>(), 3);
const unsigned int n_q_points = quadrature_formula.size();
FEValues<dim> fe_values (mapping(), fe,
quadrature_formula,
update_values);
std::vector<Vector<double> > solution_values(n_q_points,
Vector<double>(EulerEquations<dim>::n_components));
typename DoFHandler<dim>::active_cell_iterator
cell = dof_handler.begin_active(),
endc = dof_handler.end();
global_dt = 1.0e20;
for (; cell!=endc; ++cell)
{
fe_values.reinit (cell);
fe_values.get_function_values (current_solution, solution_values);
double max_eigenvalue = 0.0;
for (unsigned int q=0; q<n_q_points; ++q)
{
max_eigenvalue = std::max(max_eigenvalue,
EulerEquations<dim>::max_eigenvalue (solution_values[q]));
}
const unsigned int c = cell_number (cell);
const double h = cell->diameter() / std::sqrt(1.0*dim);
dt(c) = parameters.cfl * h / max_eigenvalue / (2.0*fe.degree + 1.0);
global_dt = std::min(global_dt, dt(c));
}
}
//------------------------------------------------------------------------------
// Compute cell average solution
//------------------------------------------------------------------------------
template <int dim>
void
ConservationLaw<dim>::compute_cell_average ()
{
QGauss<dim> quadrature_formula(fe.degree+1);
const unsigned int n_q_points = quadrature_formula.size();
FEValues<dim> fe_values (mapping(), fe,
quadrature_formula,
update_values | update_JxW_values);
std::vector<Vector<double> > solution_values(n_q_points,
Vector<double>(EulerEquations<dim>::n_components));
typename DoFHandler<dim>::active_cell_iterator
cell = dof_handler.begin_active(),
endc = dof_handler.end();
for (; cell!=endc; ++cell)
{
unsigned int cell_no = cell_number(cell);
if(re_update[cell_no])
{
fe_values.reinit (cell);
fe_values.get_function_values (current_solution, solution_values);
cell_average[cell_no] = 0.0;
for (unsigned int q=0; q<n_q_points; ++q)
for(unsigned int c=0; c<EulerEquations<dim>::n_components; ++c)
cell_average[cell_no][c] += solution_values[q][c] * fe_values.JxW(q);
cell_average[cell_no] /= cell->measure();
}
}
}
//------------------------------------------------------------------------------
// Computes total angular momentum in the computational domain
//------------------------------------------------------------------------------
template <int dim>
void
ConservationLaw<dim>::compute_angular_momentum ()
{
AssertThrow(dim==2, ExcNotImplemented());
QGauss<dim> quadrature_formula(fe.degree+1);
const unsigned int n_q_points = quadrature_formula.size();
FEValues<dim> fe_values (mapping(), fe,
quadrature_formula,
update_values | update_q_points | update_JxW_values);
const FEValuesExtractors::Vector momentum (0);
std::vector< Tensor<1,dim> > momentum_values(n_q_points);
double angular_momentum = 0;
typename DoFHandler<dim>::active_cell_iterator
cell = dof_handler.begin_active(),
endc = dof_handler.end();
for (; cell!=endc; ++cell)
{
fe_values.reinit(cell);
fe_values[momentum].get_function_values(current_solution, momentum_values);
const std::vector<Point<dim> >& qp = fe_values.get_quadrature_points();
for(unsigned int q=0; q<n_q_points; ++q)
{
double cross = qp[q][0] * momentum_values[q][1] - qp[q][1] * momentum_values[q][0];
angular_momentum += cross * fe_values.JxW(q);
}
}
printf("Total angular momentum: %18.8e %24.14e\n", elapsed_time, angular_momentum);
}
//------------------------------------------------------------------------------
// @sect4{ConservationLaw::solve}
//
// Here, we actually solve the linear system,
// using either of Trilinos' Aztec or Amesos
// linear solvers. The result of the
// computation will be written into the
// argument vector passed to this
// function. The result is a pair of number
// of iterations and the final linear
// residual.
//------------------------------------------------------------------------------
template <int dim>
std::pair<unsigned int, double>
ConservationLaw<dim>::solve (Vector<double> &newton_update,
double current_residual)
{
newton_update = 0;
switch (parameters.solver)
{
case Parameters::Solver::umfpack:
{
SparseDirectUMFPACK solver;
solver.initialize(system_matrix);
solver.vmult (newton_update, right_hand_side);
return std::pair<unsigned int, double> (1, 0);
}
case Parameters::Solver::gmres:
{
SolverControl solver_control (parameters.max_iterations,
parameters.linear_residual * current_residual);
SolverGMRES<>::AdditionalData gmres_data (30, true, true);
SolverGMRES<> solver (solver_control, gmres_data);
PreconditionBlockSSOR<SparseMatrix<double>, float> preconditioner;
preconditioner.initialize(system_matrix, fe.dofs_per_cell);
// If gmres does not converge, print message and continue
try
{
solver.solve (system_matrix,
newton_update,
right_hand_side,
preconditioner);
}
catch(...)
{
std::cout << " *** No convergence in gmres ... continuing ***\n";
}
return std::pair<unsigned int, double> (solver_control.last_step(),
solver_control.last_value());
}
// We have equation M*du/dt = rhs, where M = mass matrix
case Parameters::Solver::rk3:
case Parameters::Solver::mood:
{
// Multiply newton_update by time step dt
std::vector<unsigned int> dof_indices(fe.dofs_per_cell);
typename DoFHandler<dim>::active_cell_iterator
cell = dof_handler.begin_active(),
endc = dof_handler.end();
for (; cell!=endc; ++cell)
{
const unsigned int cell_no = cell_number (cell);
cell->get_dof_indices (dof_indices);
for(unsigned int i=0; i<fe.dofs_per_cell; ++i)
newton_update(dof_indices[i]) = dt(cell_no) *
right_hand_side(dof_indices[i]) *
inv_mass_matrix[cell_no][i];
}
return std::pair<unsigned int, double> (0,0);
}
default:
Assert (false, ExcNotImplemented());
}
return std::pair<unsigned int, double> (0,0);
}
//------------------------------------------------------------------------------
// Perform RK update
//------------------------------------------------------------------------------
template <int dim>
void ConservationLaw<dim>::iterate_explicit (IntegratorExplicit<dim>& integrator,
Vector<double>& newton_update,
double& res_norm0, double& res_norm)
{
// Loop for newton iterations or RK stages
for(unsigned int rk=0; rk<n_rk; ++rk)
{
// set time in boundary condition
// NOTE: We need to check if this is time accurate.
double bc_time;
if(rk==0)
bc_time = elapsed_time;
else
bc_time = elapsed_time + global_dt;
for (unsigned int boundary_id=0; boundary_id<Parameters::AllParameters<dim>::max_n_boundaries;
++boundary_id)
{
parameters.boundary_conditions[boundary_id].values.set_time(bc_time);
}
assemble_system (integrator);
res_norm = right_hand_side.l2_norm();
if(rk == 0) res_norm0 = res_norm;
std::pair<unsigned int, double> convergence
= solve (newton_update, res_norm);
// Forward euler step in case of explicit scheme
// In case of implicit scheme, this is the update
current_solution += newton_update;
// current_solution = ark*old_solution + (1-ark)*current_solution
current_solution.sadd (1.0-ark[rk], ark[rk], old_solution);
compute_cell_average ();
compute_shock_indicator ();
apply_limiter ();
if(parameters.pos_lim) apply_positivity_limiter ();
std::printf(" %-16.3e %04d %-5.2e\n",
res_norm, convergence.first, convergence.second);
}
}
//------------------------------------------------------------------------------
// Perform SSPRK step using MOOD method
//------------------------------------------------------------------------------
template <int dim>
void ConservationLaw<dim>::iterate_mood (IntegratorExplicit<dim>& integrator,
Vector<double>& newton_update,
double& res_norm0, double& res_norm)
{
std::pair<unsigned int, double> convergence;
// Loop for RK stages
for(unsigned int rk=0; rk<n_rk; ++rk)
{
std::cout << "RK stage " << rk+1 << std::endl;
std::cout << "\t Iter n_reduce n_re_update n_reset\n";
// set time in boundary condition
// NOTE: We need to check if this is time accurate.
for (unsigned int boundary_id=0; boundary_id<Parameters::AllParameters<dim>::max_n_boundaries;
++boundary_id)
{
parameters.boundary_conditions[boundary_id].values.set_time(elapsed_time);
}
compute_min_max_mood_var();
// iterate forward euler until DMP is satisfied
bool terminate = false;
unsigned int mood_iter = 0;
predictor = current_solution;
shock_indicator = 0;
while(!terminate)
{
assemble_system (integrator);
res_norm = right_hand_side.l2_norm();
if(rk == 0) res_norm0 = res_norm;
convergence = solve (newton_update, res_norm);
if(mood_iter == 0)
{
// In first iteration all cells must be updated
current_solution += newton_update;
work1 = current_solution;
}
else
{
// Update cells with re_update == true
std::vector<unsigned int> dof_indices(fe.dofs_per_cell);
typename DoFHandler<dim>::active_cell_iterator
cell = dof_handler.begin_active(),
endc = dof_handler.end();
for(; cell != endc; ++cell)
{
unsigned int c = cell_number(cell);
if(re_update[c] == true)
{
cell->get_dof_indices( dof_indices );
for(unsigned int i=0; i<fe.dofs_per_cell; ++i)
{
current_solution(dof_indices[i]) += newton_update(dof_indices[i]);
unsigned int base_i = fe.system_to_component_index(i).second;
if(index_to_degree[base_i] > cell_degree[c])
current_solution(dof_indices[i]) = 0.0;
work1(dof_indices[i]) = current_solution(dof_indices[i]);
}
}
}
}
compute_cell_average ();
unsigned int n_reduce=0, n_re_update=0, n_reset=0;
terminate = apply_mood (n_reduce, n_re_update, n_reset);
++mood_iter;
std::printf("%12d %12d %12d %12d\n", mood_iter, n_reduce, n_re_update, n_reset);
}
// Forward euler has been accepted.
// Now update rk stage.
current_solution = work1;
// current_solution = ark*old_solution + (1-ark)*current_solution
current_solution.sadd (1.0-ark[rk], ark[rk], old_solution);
// Reset degree and update flags
for(unsigned int i=0; i<triangulation.n_active_cells(); ++i)
{
cell_degree[i] = fe.degree;
re_update[i] = true;
}
compute_cell_average ();
apply_limiter();
if(parameters.pos_lim) apply_positivity_limiter ();
}
}
//------------------------------------------------------------------------------
// Perform one step of implicit scheme
//------------------------------------------------------------------------------
template <int dim>
void ConservationLaw<dim>::iterate_implicit (IntegratorImplicit<dim>& integrator,
Vector<double>& newton_update,
double& res_norm0, double& res_norm)
{
// set time in boundary condition
// NOTE: We need to check if this is time accurate.
for (unsigned int boundary_id=0; boundary_id<Parameters::AllParameters<dim>::max_n_boundaries;
++boundary_id)
{
parameters.boundary_conditions[boundary_id].values.set_time(elapsed_time);
}
unsigned int nonlin_iter = 0;
// Loop for newton iterations or RK stages
while(true)
{
assemble_system (integrator);
//print out the primal_matrix. just for test
/*
static int count = 0;
if(count == 0){
std::cout<<"writing primal matrix"<<std::endl;
std::ofstream out("primal matrix",std::ios::out);
out.precision(15);
system_matrix.print(out);
out.close();
count ++;
}
*/
res_norm = right_hand_side.l2_norm();
if(nonlin_iter == 0) res_norm0 = res_norm;
std::pair<unsigned int, double> convergence
= solve (newton_update, res_norm);
// Forward euler step in case of explicit scheme
// In case of implicit scheme, this is the update
current_solution += newton_update;
compute_cell_average ();
compute_shock_indicator ();
apply_limiter ();
if(parameters.pos_lim) apply_positivity_limiter ();
std::printf(" %-16.3e %04d %-5.2e\n",
res_norm, convergence.first, convergence.second);
++nonlin_iter;
// Check that newton iterations converged
if(parameters.solver == Parameters::Solver::gmres &&
nonlin_iter == parameters.max_nonlin_iter &&
std::fabs(res_norm) > 1.0e-10)
AssertThrow (nonlin_iter <= parameters.max_nonlin_iter,
ExcMessage ("No convergence in nonlinear solver"));
// check stopping criterion
if(parameters.solver == Parameters::Solver::gmres &&
(nonlin_iter == parameters.max_nonlin_iter ||
std::fabs(res_norm) <= 1.0e-10))
break;
else if(parameters.solver == Parameters::Solver::umfpack)
break;
}
}
//------------------------------------------------------------------------------
// @sect4{ConservationLaw::run}
// This function contains the top-level logic
// of this program: initialization, the time
// loop, and the inner Newton iteration.
//
// At the beginning, we read the mesh file
// specified by the parameter file, setup the
// DoFHandler and various vectors, and then
// interpolate the given initial conditions
// on this mesh. We then perform a number of
// mesh refinements, based on the initial
// conditions, to obtain a mesh that is
// already well adapted to the starting
// solution. At the end of this process, we
// output the initial solution.
//------------------------------------------------------------------------------
template <int dim>
void ConservationLaw<dim>::run ()
{
{
GridIn<dim> grid_in;
grid_in.attach_triangulation(triangulation);
std::ifstream input_file(parameters.mesh_filename.c_str());
Assert (input_file, ExcFileNotOpen(parameters.mesh_filename.c_str()));
if(parameters.mesh_type == "ucd")
grid_in.read_ucd(input_file);
else if(parameters.mesh_type == "gmsh")
grid_in.read_msh(input_file);
}
// {
// // Use this refine around corner in forward step
// unsigned int nrefine = 2;
// for(unsigned int i=0; i<nrefine; ++i)
// refine_forward_step ();
// }
/*
static const HyperBallBoundary<dim> boundary_description;
triangulation.set_boundary (1, boundary_description);
*/
//I add following lines to attach manifold to the boundary of the cylinder mesh