void
beam_PK1_dil_stress_function(TensorValue<double>& PP,
const TensorValue<double>& FF,
const libMesh::Point& /*X*/,
const libMesh::Point& /*s*/,
Elem* const /*elem*/,
const vector<NumericVector<double>*>& /*system_data*/,
double /*time*/,
void* /*ctx*/)
{
double J = FF.det();
J_dil_min = std::min(J, J_dil_min);
J_dil_max = std::max(J, J_dil_max);
PP.zero();
if (!MathUtilities<double>::equalEps(beta_s, 0.0))
{
const TensorValue<double> FF_inv_trans = tensor_inverse_transpose(FF, NDIM);
PP -= 2.0 * beta_s * log(FF.det()) * FF_inv_trans;
}
return;
} // beam_PK1_dil_stress_function
void
PK1_dil_stress_function(
TensorValue<double>& PP,
const TensorValue<double>& FF,
const libMesh::Point& /*X*/,
const libMesh::Point& /*s*/,
Elem* const /*elem*/,
const std::vector<NumericVector<double>*>& /*system_data*/,
double /*time*/,
void* /*ctx*/)
{
PP = 2.0*(-p0_s + beta_s*log(FF.det()))*tensor_inverse_transpose(FF, NDIM);
return;
}// PK1_dil_stress_function
void PK1_stress_function(TensorValue<double>& PP,
const TensorValue<double>& FF,
const libMesh::Point& /*x*/,
const libMesh::Point& /*X*/,
subdomain_id_type /*subdomain_id*/,
std::vector<double>& /*internal_vars*/,
double /*time*/,
void* /*ctx*/)
{
const TensorValue<double> FF_inv_trans = tensor_inverse_transpose(FF, NDIM);
const TensorValue<double> CC = FF.transpose() * FF;
PP = 2.0 * c1_s * FF;
if (!MathUtilities<double>::equalEps(p0_s, 0.0))
{
PP -= 2.0 * p0_s * FF_inv_trans;
}
if (!MathUtilities<double>::equalEps(beta_s, 0.0))
{
PP += beta_s * log(CC.det()) * FF_inv_trans;
}
return;
} // PK1_stress_function
/*******************************************************************************
* For each run, the input filename and restart information (if needed) must *
* be given on the command line. For non-restarted case, command line is: *
* *
* executable <input file name> *
* *
* For restarted run, command line is: *
* *
* executable <input file name> <restart directory> <restart number> *
* *
*******************************************************************************/
int
main(
int argc,
char* argv[])
{
// Initialize libMesh, PETSc, MPI, and SAMRAI.
LibMeshInit init(argc, argv);
SAMRAI_MPI::setCommunicator(PETSC_COMM_WORLD);
SAMRAI_MPI::setCallAbortInSerialInsteadOfExit();
SAMRAIManager::startup();
{// cleanup dynamically allocated objects prior to shutdown
// Parse command line options, set some standard options from the input
// file, initialize the restart database (if this is a restarted run),
// and enable file logging.
Pointer<AppInitializer> app_initializer = new AppInitializer(argc, argv, "IB.log");
Pointer<Database> input_db = app_initializer->getInputDatabase();
// Get various standard options set in the input file.
const bool dump_viz_data = app_initializer->dumpVizData();
const int viz_dump_interval = app_initializer->getVizDumpInterval();
const bool uses_visit = dump_viz_data && app_initializer->getVisItDataWriter();
const bool uses_exodus = dump_viz_data && !app_initializer->getExodusIIFilename().empty();
const string exodus_filename = app_initializer->getExodusIIFilename();
const bool dump_restart_data = app_initializer->dumpRestartData();
const int restart_dump_interval = app_initializer->getRestartDumpInterval();
const string restart_dump_dirname = app_initializer->getRestartDumpDirectory();
const bool dump_postproc_data = app_initializer->dumpPostProcessingData();
const int postproc_data_dump_interval = app_initializer->getPostProcessingDataDumpInterval();
const string postproc_data_dump_dirname = app_initializer->getPostProcessingDataDumpDirectory();
if (dump_postproc_data && (postproc_data_dump_interval > 0) && !postproc_data_dump_dirname.empty())
{
Utilities::recursiveMkdir(postproc_data_dump_dirname);
}
const bool dump_timer_data = app_initializer->dumpTimerData();
const int timer_dump_interval = app_initializer->getTimerDumpInterval();
// Create a simple FE mesh.
Mesh mesh(NDIM);
const double dx = input_db->getDouble("DX");
const double ds = input_db->getDouble("MFAC")*dx;
string elem_type = input_db->getString("ELEM_TYPE");
const double R = 0.2;
if (NDIM == 2 && (elem_type == "TRI3" || elem_type == "TRI6"))
{
const int num_circum_nodes = ceil(2.0*M_PI*R/ds);
for (int k = 0; k < num_circum_nodes; ++k)
{
const double theta = 2.0*M_PI*static_cast<double>(k)/static_cast<double>(num_circum_nodes);
mesh.add_point(libMesh::Point(R*cos(theta), R*sin(theta)));
}
TriangleInterface triangle(mesh);
triangle.triangulation_type() = TriangleInterface::GENERATE_CONVEX_HULL;
triangle.elem_type() = Utility::string_to_enum<ElemType>(elem_type);
triangle.desired_area() = 1.5*sqrt(3.0)/4.0*ds*ds;
triangle.insert_extra_points() = true;
triangle.smooth_after_generating() = true;
triangle.triangulate();
}
else
{
// NOTE: number of segments along boundary is 4*2^r.
const double num_circum_segments = 2.0*M_PI*R/ds;
const int r = log2(0.25*num_circum_segments);
MeshTools::Generation::build_sphere(mesh, R, r, Utility::string_to_enum<ElemType>(elem_type));
}
// Ensure nodes on the surface are on the analytic boundary.
MeshBase::element_iterator el_end = mesh.elements_end();
for (MeshBase::element_iterator el = mesh.elements_begin();
el != el_end; ++el)
{
Elem* const elem = *el;
for (unsigned int side = 0; side < elem->n_sides(); ++side)
{
const bool at_mesh_bdry = !elem->neighbor(side);
if (!at_mesh_bdry) continue;
for (unsigned int k = 0; k < elem->n_nodes(); ++k)
{
if (!elem->is_node_on_side(k,side)) continue;
Node& n = *elem->get_node(k);
n = R*n.unit();
}
}
}
mesh.prepare_for_use();
c1_s = input_db->getDouble("C1_S");
p0_s = input_db->getDouble("P0_S");
beta_s = input_db->getDouble("BETA_S");
// Create major algorithm and data objects that comprise the
// application. These objects are configured from the input database
// and, if this is a restarted run, from the restart database.
Pointer<INSHierarchyIntegrator> navier_stokes_integrator;
const string solver_type = app_initializer->getComponentDatabase("Main")->getString("solver_type");
if (solver_type == "STAGGERED")
{
navier_stokes_integrator = new INSStaggeredHierarchyIntegrator(
"INSStaggeredHierarchyIntegrator", app_initializer->getComponentDatabase("INSStaggeredHierarchyIntegrator"));
}
else if (solver_type == "COLLOCATED")
{
navier_stokes_integrator = new INSCollocatedHierarchyIntegrator(
"INSCollocatedHierarchyIntegrator", app_initializer->getComponentDatabase("INSCollocatedHierarchyIntegrator"));
}
else
{
TBOX_ERROR("Unsupported solver type: " << solver_type << "\n" <<
"Valid options are: COLLOCATED, STAGGERED");
}
Pointer<IBFEMethod> ib_method_ops = new IBFEMethod(
"IBFEMethod", app_initializer->getComponentDatabase("IBFEMethod"), &mesh, app_initializer->getComponentDatabase("GriddingAlgorithm")->getInteger("max_levels"));
Pointer<IBHierarchyIntegrator> time_integrator = new IBExplicitHierarchyIntegrator(
"IBHierarchyIntegrator", app_initializer->getComponentDatabase("IBHierarchyIntegrator"), ib_method_ops, navier_stokes_integrator);
Pointer<CartesianGridGeometry<NDIM> > grid_geometry = new CartesianGridGeometry<NDIM>(
"CartesianGeometry", app_initializer->getComponentDatabase("CartesianGeometry"));
Pointer<PatchHierarchy<NDIM> > patch_hierarchy = new PatchHierarchy<NDIM>(
"PatchHierarchy", grid_geometry);
Pointer<StandardTagAndInitialize<NDIM> > error_detector = new StandardTagAndInitialize<NDIM>(
"StandardTagAndInitialize", time_integrator, app_initializer->getComponentDatabase("StandardTagAndInitialize"));
Pointer<BergerRigoutsos<NDIM> > box_generator = new BergerRigoutsos<NDIM>();
Pointer<LoadBalancer<NDIM> > load_balancer = new LoadBalancer<NDIM>(
"LoadBalancer", app_initializer->getComponentDatabase("LoadBalancer"));
Pointer<GriddingAlgorithm<NDIM> > gridding_algorithm = new GriddingAlgorithm<NDIM>(
"GriddingAlgorithm", app_initializer->getComponentDatabase("GriddingAlgorithm"), error_detector, box_generator, load_balancer);
// Configure the IBFE solver.
ib_method_ops->registerInitialCoordinateMappingFunction(coordinate_mapping_function);
IBFEMethod::PK1StressFcnData PK1_dev_stress_data(PK1_dev_stress_function);
IBFEMethod::PK1StressFcnData PK1_dil_stress_data(PK1_dil_stress_function);
PK1_dev_stress_data.quad_order = Utility::string_to_enum<libMeshEnums::Order>(input_db->getStringWithDefault("PK1_DEV_QUAD_ORDER","THIRD"));
PK1_dil_stress_data.quad_order = Utility::string_to_enum<libMeshEnums::Order>(input_db->getStringWithDefault("PK1_DIL_QUAD_ORDER","FIRST"));
ib_method_ops->registerPK1StressFunction(PK1_dev_stress_data);
ib_method_ops->registerPK1StressFunction(PK1_dil_stress_data);
EquationSystems* equation_systems = ib_method_ops->getFEDataManager()->getEquationSystems();
// Set up post processor to recover computed stresses.
FEDataManager* fe_data_manager = ib_method_ops->getFEDataManager();
Pointer<IBFEPostProcessor> ib_post_processor = new IBFECentroidPostProcessor("IBFEPostProcessor", fe_data_manager);
ib_post_processor->registerTensorVariable(
"FF", MONOMIAL, CONSTANT, IBFEPostProcessor::FF_fcn);
std::pair<IBTK::TensorMeshFcnPtr,void*> PK1_dev_stress_fcn_data(PK1_dev_stress_function,static_cast<void*>(NULL));
ib_post_processor->registerTensorVariable(
"sigma_dev", MONOMIAL, CONSTANT,
IBFEPostProcessor::cauchy_stress_from_PK1_stress_fcn,
std::vector<unsigned int>(), &PK1_dev_stress_fcn_data);
std::pair<IBTK::TensorMeshFcnPtr,void*> PK1_dil_stress_fcn_data(PK1_dil_stress_function,static_cast<void*>(NULL));
ib_post_processor->registerTensorVariable(
"sigma_dil", MONOMIAL, CONSTANT,
IBFEPostProcessor::cauchy_stress_from_PK1_stress_fcn,
std::vector<unsigned int>(), &PK1_dil_stress_fcn_data);
ib_post_processor->registerInterpolatedScalarEulerianVariable(
"p_f", LAGRANGE, FIRST,
navier_stokes_integrator->getPressureVariable(),
navier_stokes_integrator->getCurrentContext());
// Create Eulerian initial condition specification objects.
if (input_db->keyExists("VelocityInitialConditions"))
{
Pointer<CartGridFunction> u_init = new muParserCartGridFunction(
"u_init", app_initializer->getComponentDatabase("VelocityInitialConditions"), grid_geometry);
navier_stokes_integrator->registerVelocityInitialConditions(u_init);
}
if (input_db->keyExists("PressureInitialConditions"))
{
Pointer<CartGridFunction> p_init = new muParserCartGridFunction(
"p_init", app_initializer->getComponentDatabase("PressureInitialConditions"), grid_geometry);
navier_stokes_integrator->registerPressureInitialConditions(p_init);
}
// Create Eulerian boundary condition specification objects (when necessary).
const IntVector<NDIM>& periodic_shift = grid_geometry->getPeriodicShift();
vector<RobinBcCoefStrategy<NDIM>*> u_bc_coefs(NDIM);
if (periodic_shift.min() > 0)
{
for (unsigned int d = 0; d < NDIM; ++d)
{
u_bc_coefs[d] = NULL;
}
}
else
{
for (unsigned int d = 0; d < NDIM; ++d)
{
ostringstream bc_coefs_name_stream;
bc_coefs_name_stream << "u_bc_coefs_" << d;
const string bc_coefs_name = bc_coefs_name_stream.str();
ostringstream bc_coefs_db_name_stream;
bc_coefs_db_name_stream << "VelocityBcCoefs_" << d;
const string bc_coefs_db_name = bc_coefs_db_name_stream.str();
u_bc_coefs[d] = new muParserRobinBcCoefs(
bc_coefs_name, app_initializer->getComponentDatabase(bc_coefs_db_name), grid_geometry);
}
navier_stokes_integrator->registerPhysicalBoundaryConditions(u_bc_coefs);
}
// Create Eulerian body force function specification objects.
if (input_db->keyExists("ForcingFunction"))
{
Pointer<CartGridFunction> f_fcn = new muParserCartGridFunction(
"f_fcn", app_initializer->getComponentDatabase("ForcingFunction"), grid_geometry);
time_integrator->registerBodyForceFunction(f_fcn);
}
// Set up visualization plot file writers.
Pointer<VisItDataWriter<NDIM> > visit_data_writer = app_initializer->getVisItDataWriter();
if (uses_visit)
{
time_integrator->registerVisItDataWriter(visit_data_writer);
}
AutoPtr<ExodusII_IO> exodus_io(uses_exodus ? new ExodusII_IO(mesh) : NULL);
// Initialize hierarchy configuration and data on all patches.
ib_method_ops->initializeFEData();
ib_post_processor->initializeFEData();
time_integrator->initializePatchHierarchy(patch_hierarchy, gridding_algorithm);
// Deallocate initialization objects.
app_initializer.setNull();
// Print the input database contents to the log file.
plog << "Input database:\n";
input_db->printClassData(plog);
// Write out initial visualization data.
int iteration_num = time_integrator->getIntegratorStep();
double loop_time = time_integrator->getIntegratorTime();
if (dump_viz_data)
{
pout << "\n\nWriting visualization files...\n\n";
if (uses_visit)
{
time_integrator->setupPlotData();
visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time);
}
if (uses_exodus)
{
ib_post_processor->postProcessData(loop_time);
exodus_io->write_timestep(exodus_filename, *equation_systems, iteration_num/viz_dump_interval+1, loop_time);
}
}
// Open streams to save volume of structure.
ofstream volume_stream;
if (SAMRAI_MPI::getRank() == 0)
{
volume_stream.open("volume.curve", ios_base::out | ios_base::trunc);
}
// Main time step loop.
double loop_time_end = time_integrator->getEndTime();
double dt = 0.0;
while (!MathUtilities<double>::equalEps(loop_time,loop_time_end) &&
time_integrator->stepsRemaining())
{
iteration_num = time_integrator->getIntegratorStep();
loop_time = time_integrator->getIntegratorTime();
pout << "\n";
pout << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n";
pout << "At beginning of timestep # " << iteration_num << "\n";
pout << "Simulation time is " << loop_time << "\n";
dt = time_integrator->getMaximumTimeStepSize();
time_integrator->advanceHierarchy(dt);
loop_time += dt;
pout << "\n";
pout << "At end of timestep # " << iteration_num << "\n";
pout << "Simulation time is " << loop_time << "\n";
pout << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n";
pout << "\n";
// At specified intervals, write visualization and restart files,
// print out timer data, and store hierarchy data for post
// processing.
iteration_num += 1;
const bool last_step = !time_integrator->stepsRemaining();
if (dump_viz_data && (iteration_num%viz_dump_interval == 0 || last_step))
{
pout << "\nWriting visualization files...\n\n";
if (uses_visit)
{
time_integrator->setupPlotData();
visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time);
}
if (uses_exodus)
{
ib_post_processor->postProcessData(loop_time);
exodus_io->write_timestep(exodus_filename, *equation_systems, iteration_num/viz_dump_interval+1, loop_time);
}
}
if (dump_restart_data && (iteration_num%restart_dump_interval == 0 || last_step))
{
pout << "\nWriting restart files...\n\n";
RestartManager::getManager()->writeRestartFile(restart_dump_dirname, iteration_num);
}
if (dump_timer_data && (iteration_num%timer_dump_interval == 0 || last_step))
{
pout << "\nWriting timer data...\n\n";
TimerManager::getManager()->print(plog);
}
if (dump_postproc_data && (iteration_num%postproc_data_dump_interval == 0 || last_step))
{
output_data(patch_hierarchy,
navier_stokes_integrator, mesh, equation_systems,
iteration_num, loop_time, postproc_data_dump_dirname);
}
// Compute the volume of the structure.
double J_integral = 0.0;
System& X_system = equation_systems->get_system<System>(IBFEMethod::COORDS_SYSTEM_NAME);
NumericVector<double>* X_vec = X_system.solution.get();
NumericVector<double>* X_ghost_vec = X_system.current_local_solution.get();
X_vec->localize(*X_ghost_vec);
DofMap& X_dof_map = X_system.get_dof_map();
std::vector<std::vector<unsigned int> > X_dof_indices(NDIM);
AutoPtr<FEBase> fe(FEBase::build(NDIM, X_dof_map.variable_type(0)));
AutoPtr<QBase> qrule = QBase::build(QGAUSS, NDIM, FIFTH);
fe->attach_quadrature_rule(qrule.get());
const std::vector<double>& JxW = fe->get_JxW();
const std::vector<std::vector<VectorValue<double> > >& dphi = fe->get_dphi();
TensorValue<double> FF;
boost::multi_array<double,2> X_node;
const MeshBase::const_element_iterator el_begin = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator el_end = mesh.active_local_elements_end();
for (MeshBase::const_element_iterator el_it = el_begin; el_it != el_end; ++el_it)
{
Elem* const elem = *el_it;
fe->reinit(elem);
for (unsigned int d = 0; d < NDIM; ++d)
{
X_dof_map.dof_indices(elem, X_dof_indices[d], d);
}
const int n_qp = qrule->n_points();
get_values_for_interpolation(X_node, *X_ghost_vec, X_dof_indices);
for (int qp = 0; qp < n_qp; ++qp)
{
jacobian(FF,qp,X_node,dphi);
J_integral += abs(FF.det())*JxW[qp];
}
}
J_integral = SAMRAI_MPI::sumReduction(J_integral);
if (SAMRAI_MPI::getRank() == 0)
{
volume_stream.precision(12);
volume_stream.setf(ios::fixed,ios::floatfield);
volume_stream << loop_time << " " << J_integral << endl;
}
}
// Close the logging streams.
if (SAMRAI_MPI::getRank() == 0)
{
volume_stream.close();
}
// Cleanup Eulerian boundary condition specification objects (when
// necessary).
for (unsigned int d = 0; d < NDIM; ++d) delete u_bc_coefs[d];
}// cleanup dynamically allocated objects prior to shutdown
SAMRAIManager::shutdown();
return 0;
}// main
/*******************************************************************************
* For each run, the input filename and restart information (if needed) must *
* be given on the command line. For non-restarted case, command line is: *
* *
* executable <input file name> *
* *
* For restarted run, command line is: *
* *
* executable <input file name> <restart directory> <restart number> *
* *
*******************************************************************************/
int
main(
int argc,
char* argv[])
{
// Initialize libMesh, PETSc, MPI, and SAMRAI.
LibMeshInit init(argc, argv);
SAMRAI_MPI::setCommunicator(PETSC_COMM_WORLD);
SAMRAI_MPI::setCallAbortInSerialInsteadOfExit();
SAMRAIManager::startup();
{// cleanup dynamically allocated objects prior to shutdown
// Parse command line options, set some standard options from the input
// file, initialize the restart database (if this is a restarted run),
// and enable file logging.
Pointer<AppInitializer> app_initializer = new AppInitializer(argc, argv, "IB.log");
Pointer<Database> input_db = app_initializer->getInputDatabase();
// Get various standard options set in the input file.
const bool dump_viz_data = app_initializer->dumpVizData();
const int viz_dump_interval = app_initializer->getVizDumpInterval();
const bool uses_visit = dump_viz_data && !app_initializer->getVisItDataWriter().isNull();
const bool uses_exodus = dump_viz_data && !app_initializer->getExodusIIFilename().empty();
const string exodus_filename = app_initializer->getExodusIIFilename();
const bool dump_restart_data = app_initializer->dumpRestartData();
const int restart_dump_interval = app_initializer->getRestartDumpInterval();
const string restart_dump_dirname = app_initializer->getRestartDumpDirectory();
const bool dump_postproc_data = app_initializer->dumpPostProcessingData();
const int postproc_data_dump_interval = app_initializer->getPostProcessingDataDumpInterval();
const string postproc_data_dump_dirname = app_initializer->getPostProcessingDataDumpDirectory();
if (dump_postproc_data && (postproc_data_dump_interval > 0) && !postproc_data_dump_dirname.empty())
{
Utilities::recursiveMkdir(postproc_data_dump_dirname);
}
const bool dump_timer_data = app_initializer->dumpTimerData();
const int timer_dump_interval = app_initializer->getTimerDumpInterval();
// Create a simple FE mesh with periodic boundary conditions in the "x"
// direction.
//
// Note that boundary condition data must be registered with each FE
// system before calling IBFEMethod::initializeFEData().
Mesh mesh(NDIM);
const double R = 0.25;
const double w = 0.0625;
const double dx0 = 1.0/64.0;
const double dx = input_db->getDouble("DX");
const double ds0 = input_db->getDouble("MFAC")*dx0;
string elem_type = input_db->getString("ELEM_TYPE");
MeshTools::Generation::build_square(mesh,
4*static_cast<int>((dx0/dx)*ceil(2.0*M_PI*R/ds0/4.0)), static_cast<int>((dx0/dx)*ceil(w/ds0)),
0.0, 2.0*M_PI*R,
0.0, w,
Utility::string_to_enum<ElemType>(elem_type));
VectorValue<double> boundary_translation(2.0*M_PI*R, 0.0, 0.0);
PeriodicBoundary pbc(boundary_translation);
pbc.myboundary = 3;
pbc.pairedboundary = 1;
// Configure stress tensor options.
smooth_case = input_db->getBool("SMOOTH_CASE");
// Create major algorithm and data objects that comprise the
// application. These objects are configured from the input database
// and, if this is a restarted run, from the restart database.
Pointer<INSHierarchyIntegrator> navier_stokes_integrator;
const string solver_type = app_initializer->getComponentDatabase("Main")->getString("solver_type");
if (solver_type == "STAGGERED")
{
navier_stokes_integrator = new INSStaggeredHierarchyIntegrator(
"INSStaggeredHierarchyIntegrator", app_initializer->getComponentDatabase("INSStaggeredHierarchyIntegrator"));
}
else if (solver_type == "COLLOCATED")
{
navier_stokes_integrator = new INSCollocatedHierarchyIntegrator(
"INSCollocatedHierarchyIntegrator", app_initializer->getComponentDatabase("INSCollocatedHierarchyIntegrator"));
}
else
{
TBOX_ERROR("Unsupported solver type: " << solver_type << "\n" <<
"Valid options are: COLLOCATED, STAGGERED");
}
Pointer<IBFEMethod> ib_method_ops = new IBFEMethod(
"IBFEMethod", app_initializer->getComponentDatabase("IBFEMethod"), &mesh, app_initializer->getComponentDatabase("GriddingAlgorithm")->getInteger("max_levels"));
Pointer<IBHierarchyIntegrator> time_integrator = new IBHierarchyIntegrator(
"IBHierarchyIntegrator", app_initializer->getComponentDatabase("IBHierarchyIntegrator"), ib_method_ops, navier_stokes_integrator);
Pointer<CartesianGridGeometry<NDIM> > grid_geometry = new CartesianGridGeometry<NDIM>(
"CartesianGeometry", app_initializer->getComponentDatabase("CartesianGeometry"));
Pointer<PatchHierarchy<NDIM> > patch_hierarchy = new PatchHierarchy<NDIM>(
"PatchHierarchy", grid_geometry);
Pointer<StandardTagAndInitialize<NDIM> > error_detector = new StandardTagAndInitialize<NDIM>(
"StandardTagAndInitialize", time_integrator, app_initializer->getComponentDatabase("StandardTagAndInitialize"));
Pointer<BergerRigoutsos<NDIM> > box_generator = new BergerRigoutsos<NDIM>();
Pointer<LoadBalancer<NDIM> > load_balancer = new LoadBalancer<NDIM>(
"LoadBalancer", app_initializer->getComponentDatabase("LoadBalancer"));
Pointer<GriddingAlgorithm<NDIM> > gridding_algorithm = new GriddingAlgorithm<NDIM>(
"GriddingAlgorithm", app_initializer->getComponentDatabase("GriddingAlgorithm"), error_detector, box_generator, load_balancer);
// Configure the IBFE solver.
ib_method_ops->registerInitialCoordinateMappingFunction(&coordinate_mapping_function);
ib_method_ops->registerPK1StressTensorFunction(&PK1_stress_function);
EquationSystems* equation_systems = ib_method_ops->getFEDataManager()->getEquationSystems();
for (unsigned int k = 0; k < equation_systems->n_systems(); ++k)
{
System& system = equation_systems->get_system(k);
system.get_dof_map().add_periodic_boundary(pbc);
}
// Create Eulerian initial condition specification objects. These
// objects also are used to specify exact solution values for error
// analysis.
Pointer<CartGridFunction> u_init = new muParserCartGridFunction(
"u_init", app_initializer->getComponentDatabase("VelocityInitialConditions"), grid_geometry);
navier_stokes_integrator->registerVelocityInitialConditions(u_init);
Pointer<CartGridFunction> p_init = new muParserCartGridFunction(
"p_init", app_initializer->getComponentDatabase("PressureInitialConditions"), grid_geometry);
navier_stokes_integrator->registerPressureInitialConditions(p_init);
// Create Eulerian boundary condition specification objects (when necessary).
const IntVector<NDIM>& periodic_shift = grid_geometry->getPeriodicShift();
TinyVector<RobinBcCoefStrategy<NDIM>*,NDIM> u_bc_coefs;
if (periodic_shift.min() > 0)
{
for (unsigned int d = 0; d < NDIM; ++d)
{
u_bc_coefs[d] = NULL;
}
}
else
{
for (unsigned int d = 0; d < NDIM; ++d)
{
ostringstream bc_coefs_name_stream;
bc_coefs_name_stream << "u_bc_coefs_" << d;
const string bc_coefs_name = bc_coefs_name_stream.str();
ostringstream bc_coefs_db_name_stream;
bc_coefs_db_name_stream << "VelocityBcCoefs_" << d;
const string bc_coefs_db_name = bc_coefs_db_name_stream.str();
u_bc_coefs[d] = new muParserRobinBcCoefs(
bc_coefs_name, app_initializer->getComponentDatabase(bc_coefs_db_name), grid_geometry);
}
navier_stokes_integrator->registerPhysicalBoundaryConditions(u_bc_coefs);
}
// Create Eulerian body force function specification objects.
if (input_db->keyExists("ForcingFunction"))
{
Pointer<CartGridFunction> f_fcn = new muParserCartGridFunction(
"f_fcn", app_initializer->getComponentDatabase("ForcingFunction"), grid_geometry);
time_integrator->registerBodyForceFunction(f_fcn);
}
// Set up visualization plot file writers.
Pointer<VisItDataWriter<NDIM> > visit_data_writer = app_initializer->getVisItDataWriter();
if (uses_visit)
{
time_integrator->registerVisItDataWriter(visit_data_writer);
}
AutoPtr<ExodusII_IO> exodus_io(uses_exodus ? new ExodusII_IO(mesh) : NULL);
// Initialize hierarchy configuration and data on all patches.
ib_method_ops->initializeFEData();
time_integrator->initializePatchHierarchy(patch_hierarchy, gridding_algorithm);
// Deallocate initialization objects.
app_initializer.setNull();
// Print the input database contents to the log file.
plog << "Input database:\n";
input_db->printClassData(plog);
// Setup data used to determine the accuracy of the computed solution.
VariableDatabase<NDIM>* var_db = VariableDatabase<NDIM>::getDatabase();
const Pointer<hier::Variable<NDIM> > u_var = navier_stokes_integrator->getVelocityVariable();
const Pointer<VariableContext> u_ctx = navier_stokes_integrator->getCurrentContext();
const int u_idx = var_db->mapVariableAndContextToIndex(u_var, u_ctx);
const int u_cloned_idx = var_db->registerClonedPatchDataIndex(u_var, u_idx);
const Pointer<hier::Variable<NDIM> > p_var = navier_stokes_integrator->getPressureVariable();
const Pointer<VariableContext> p_ctx = navier_stokes_integrator->getCurrentContext();
const int p_idx = var_db->mapVariableAndContextToIndex(p_var, p_ctx);
const int p_cloned_idx = var_db->registerClonedPatchDataIndex(p_var, p_idx);
visit_data_writer->registerPlotQuantity("P error", "SCALAR", p_cloned_idx);
const int coarsest_ln = 0;
const int finest_ln = patch_hierarchy->getFinestLevelNumber();
for (int ln = coarsest_ln; ln <= finest_ln; ++ln)
{
patch_hierarchy->getPatchLevel(ln)->allocatePatchData(u_cloned_idx);
patch_hierarchy->getPatchLevel(ln)->allocatePatchData(p_cloned_idx);
}
// Write out initial visualization data.
int iteration_num = time_integrator->getIntegratorStep();
double loop_time = time_integrator->getIntegratorTime();
if (dump_viz_data)
{
pout << "\n\nWriting visualization files...\n\n";
if (uses_visit)
{
time_integrator->setupPlotData();
visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time);
}
if (uses_exodus)
{
exodus_io->write_timestep(exodus_filename, *equation_systems, iteration_num/viz_dump_interval+1, loop_time);
}
}
// Open streams to save volume of structure.
ofstream volume_stream;
if (SAMRAI_MPI::getRank() == 0)
{
volume_stream.open("volume.curve", ios_base::out | ios_base::trunc);
}
// Main time step loop.
double loop_time_end = time_integrator->getEndTime();
double dt = 0.0;
while (!MathUtilities<double>::equalEps(loop_time,loop_time_end) &&
time_integrator->stepsRemaining())
{
iteration_num = time_integrator->getIntegratorStep();
loop_time = time_integrator->getIntegratorTime();
pout << "\n";
pout << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n";
pout << "At beginning of timestep # " << iteration_num << "\n";
pout << "Simulation time is " << loop_time << "\n";
dt = time_integrator->getTimeStepSize();
time_integrator->advanceHierarchy(dt);
loop_time += dt;
pout << "\n";
pout << "At end of timestep # " << iteration_num << "\n";
pout << "Simulation time is " << loop_time << "\n";
pout << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n";
pout << "\n";
// At specified intervals, write visualization and restart files,
// print out timer data, and store hierarchy data for post
// processing.
iteration_num += 1;
const bool last_step = !time_integrator->stepsRemaining();
if (dump_viz_data && (iteration_num%viz_dump_interval == 0 || last_step))
{
pout << "\nWriting visualization files...\n\n";
if (uses_visit)
{
time_integrator->setupPlotData();
visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time);
}
if (uses_exodus)
{
exodus_io->write_timestep(exodus_filename, *equation_systems, iteration_num/viz_dump_interval+1, loop_time);
}
}
if (dump_restart_data && (iteration_num%restart_dump_interval == 0 || last_step))
{
pout << "\nWriting restart files...\n\n";
RestartManager::getManager()->writeRestartFile(restart_dump_dirname, iteration_num);
}
if (dump_timer_data && (iteration_num%timer_dump_interval == 0 || last_step))
{
pout << "\nWriting timer data...\n\n";
TimerManager::getManager()->print(plog);
}
if (dump_postproc_data && (iteration_num%postproc_data_dump_interval == 0 || last_step))
{
pout << "\nWriting state data...\n\n";
output_data(patch_hierarchy,
navier_stokes_integrator, mesh, equation_systems,
iteration_num, loop_time, postproc_data_dump_dirname);
}
// Compute velocity and pressure error norms.
const int coarsest_ln = 0;
const int finest_ln = patch_hierarchy->getFinestLevelNumber();
for (int ln = coarsest_ln; ln <= finest_ln; ++ln)
{
Pointer<PatchLevel<NDIM> > level = patch_hierarchy->getPatchLevel(ln);
if (!level->checkAllocated(u_cloned_idx)) level->allocatePatchData(u_cloned_idx);
if (!level->checkAllocated(p_cloned_idx)) level->allocatePatchData(p_cloned_idx);
}
pout << "\n"
<< "+++++++++++++++++++++++++++++++++++++++++++++++++++\n"
<< "Computing error norms.\n\n";
u_init->setDataOnPatchHierarchy(u_cloned_idx, u_var, patch_hierarchy, loop_time);
p_init->setDataOnPatchHierarchy(p_cloned_idx, p_var, patch_hierarchy, loop_time-0.5*dt);
HierarchyMathOps hier_math_ops("HierarchyMathOps", patch_hierarchy);
hier_math_ops.setPatchHierarchy(patch_hierarchy);
hier_math_ops.resetLevels(coarsest_ln, finest_ln);
const double volume = hier_math_ops.getVolumeOfPhysicalDomain();
const int wgt_cc_idx = hier_math_ops.getCellWeightPatchDescriptorIndex();
const int wgt_sc_idx = hier_math_ops.getSideWeightPatchDescriptorIndex();
Pointer<CellVariable<NDIM,double> > u_cc_var = u_var;
if (!u_cc_var.isNull())
{
HierarchyCellDataOpsReal<NDIM,double> hier_cc_data_ops(patch_hierarchy, coarsest_ln, finest_ln);
hier_cc_data_ops.subtract(u_cloned_idx, u_idx, u_cloned_idx);
pout << "Error in u at time " << loop_time << ":\n"
<< " L1-norm: " << hier_cc_data_ops. L1Norm(u_cloned_idx,wgt_cc_idx) << "\n"
<< " L2-norm: " << hier_cc_data_ops. L2Norm(u_cloned_idx,wgt_cc_idx) << "\n"
<< " max-norm: " << hier_cc_data_ops.maxNorm(u_cloned_idx,wgt_cc_idx) << "\n";
}
Pointer<SideVariable<NDIM,double> > u_sc_var = u_var;
if (!u_sc_var.isNull())
{
HierarchySideDataOpsReal<NDIM,double> hier_sc_data_ops(patch_hierarchy, coarsest_ln, finest_ln);
hier_sc_data_ops.subtract(u_cloned_idx, u_idx, u_cloned_idx);
pout << "Error in u at time " << loop_time << ":\n"
<< " L1-norm: " << hier_sc_data_ops. L1Norm(u_cloned_idx,wgt_sc_idx) << "\n"
<< " L2-norm: " << hier_sc_data_ops. L2Norm(u_cloned_idx,wgt_sc_idx) << "\n"
<< " max-norm: " << hier_sc_data_ops.maxNorm(u_cloned_idx,wgt_sc_idx) << "\n";
}
HierarchyCellDataOpsReal<NDIM,double> hier_cc_data_ops(patch_hierarchy, coarsest_ln, finest_ln);
const double p_mean = (1.0/volume)*hier_cc_data_ops.integral(p_idx, wgt_cc_idx);
hier_cc_data_ops.addScalar(p_idx, p_idx, -p_mean);
const double p_cloned_mean = (1.0/volume)*hier_cc_data_ops.integral(p_cloned_idx, wgt_cc_idx);
hier_cc_data_ops.addScalar(p_cloned_idx, p_cloned_idx, -p_cloned_mean);
hier_cc_data_ops.subtract(p_cloned_idx, p_idx, p_cloned_idx);
pout << "Error in p at time " << loop_time-0.5*dt << ":\n"
<< " L1-norm: " << hier_cc_data_ops. L1Norm(p_cloned_idx,wgt_cc_idx) << "\n"
<< " L2-norm: " << hier_cc_data_ops. L2Norm(p_cloned_idx,wgt_cc_idx) << "\n"
<< " max-norm: " << hier_cc_data_ops.maxNorm(p_cloned_idx,wgt_cc_idx) << "\n"
<< "+++++++++++++++++++++++++++++++++++++++++++++++++++\n";
// Compute the volume of the structure.
double J_integral = 0.0;
System& X_system = equation_systems->get_system<System>(IBFEMethod::COORDS_SYSTEM_NAME);
NumericVector<double>* X_vec = X_system.solution.get();
NumericVector<double>* X_ghost_vec = X_system.current_local_solution.get();
X_vec->localize(*X_ghost_vec);
DofMap& X_dof_map = X_system.get_dof_map();
blitz::Array<std::vector<unsigned int>,1> X_dof_indices(NDIM);
AutoPtr<FEBase> fe(FEBase::build(NDIM, X_dof_map.variable_type(0)));
AutoPtr<QBase> qrule = QBase::build(QGAUSS, NDIM, FIFTH);
fe->attach_quadrature_rule(qrule.get());
const std::vector<double>& JxW = fe->get_JxW();
const std::vector<std::vector<VectorValue<double> > >& dphi = fe->get_dphi();
TensorValue<double> FF;
blitz::Array<double,2> X_node;
const MeshBase::const_element_iterator el_begin = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator el_end = mesh.active_local_elements_end();
for (MeshBase::const_element_iterator el_it = el_begin; el_it != el_end; ++el_it)
{
Elem* const elem = *el_it;
fe->reinit(elem);
for (unsigned int d = 0; d < NDIM; ++d)
{
X_dof_map.dof_indices(elem, X_dof_indices(d), d);
}
const int n_qp = qrule->n_points();
get_values_for_interpolation(X_node, *X_ghost_vec, X_dof_indices);
for (int qp = 0; qp < n_qp; ++qp)
{
jacobian(FF,qp,X_node,dphi);
J_integral += abs(FF.det())*JxW[qp];
}
}
J_integral = SAMRAI_MPI::sumReduction(J_integral);
if (SAMRAI_MPI::getRank() == 0)
{
volume_stream.precision(12);
volume_stream.setf(ios::fixed,ios::floatfield);
volume_stream << loop_time << " " << J_integral << endl;
}
}
// Close the logging streams.
if (SAMRAI_MPI::getRank() == 0)
{
volume_stream.close();
}
// Cleanup Eulerian boundary condition specification objects (when
// necessary).
for (unsigned int d = 0; d < NDIM; ++d) delete u_bc_coefs[d];
}// cleanup dynamically allocated objects prior to shutdown
SAMRAIManager::shutdown();
return 0;
}// main