/*******************************************************************************
* For each run, the input filename must be given on the command line. In all *
* cases, the command line is: *
* *
* executable <input file name> *
* *
*******************************************************************************/
int
main(int argc, char* argv[])
{
// Initialize PETSc, MPI, and SAMRAI.
PetscInitialize(&argc, &argv, NULL, NULL);
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, and enable file logging.
Pointer<AppInitializer> app_initializer = new AppInitializer(argc, argv, "vc_laplace.log");
Pointer<Database> input_db = app_initializer->getInputDatabase();
// Create major algorithm and data objects that comprise the
// application. These objects are configured from the input database.
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", NULL, 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);
// Create variables and register them with the variable database.
VariableDatabase<NDIM>* var_db = VariableDatabase<NDIM>::getDatabase();
Pointer<VariableContext> ctx = var_db->getContext("context");
Pointer<SideVariable<NDIM, double> > u_side_var = new SideVariable<NDIM, double>("u_side");
Pointer<SideVariable<NDIM, double> > f_side_var = new SideVariable<NDIM, double>("f_side");
Pointer<SideVariable<NDIM, double> > e_side_var = new SideVariable<NDIM, double>("e_side");
const int u_side_idx = var_db->registerVariableAndContext(u_side_var, ctx, IntVector<NDIM>(1));
const int f_side_idx = var_db->registerVariableAndContext(f_side_var, ctx, IntVector<NDIM>(1));
const int e_side_idx = var_db->registerVariableAndContext(e_side_var, ctx, IntVector<NDIM>(1));
Pointer<CellVariable<NDIM, double> > u_cell_var = new CellVariable<NDIM, double>("u_cell", NDIM);
Pointer<CellVariable<NDIM, double> > f_cell_var = new CellVariable<NDIM, double>("f_cell", NDIM);
Pointer<CellVariable<NDIM, double> > e_cell_var = new CellVariable<NDIM, double>("e_cell", NDIM);
const int u_cell_idx = var_db->registerVariableAndContext(u_cell_var, ctx, IntVector<NDIM>(0));
const int f_cell_idx = var_db->registerVariableAndContext(f_cell_var, ctx, IntVector<NDIM>(0));
const int e_cell_idx = var_db->registerVariableAndContext(e_cell_var, ctx, IntVector<NDIM>(0));
Pointer<NodeVariable<NDIM, double> > mu_node_var = new NodeVariable<NDIM, double>("mu_node");
const int mu_node_idx = var_db->registerVariableAndContext(mu_node_var, ctx, IntVector<NDIM>(1));
// Register variables for plotting.
Pointer<VisItDataWriter<NDIM> > visit_data_writer = app_initializer->getVisItDataWriter();
TBOX_ASSERT(visit_data_writer);
visit_data_writer->registerPlotQuantity(u_cell_var->getName(), "VECTOR", u_cell_idx);
for (unsigned int d = 0; d < NDIM; ++d)
{
ostringstream stream;
stream << d;
visit_data_writer->registerPlotQuantity(u_cell_var->getName() + stream.str(), "SCALAR", u_cell_idx, d);
}
visit_data_writer->registerPlotQuantity(f_cell_var->getName(), "VECTOR", f_cell_idx);
for (unsigned int d = 0; d < NDIM; ++d)
{
ostringstream stream;
stream << d;
visit_data_writer->registerPlotQuantity(f_cell_var->getName() + stream.str(), "SCALAR", f_cell_idx, d);
}
visit_data_writer->registerPlotQuantity(e_cell_var->getName(), "VECTOR", e_cell_idx);
for (unsigned int d = 0; d < NDIM; ++d)
{
ostringstream stream;
stream << d;
visit_data_writer->registerPlotQuantity(e_cell_var->getName() + stream.str(), "SCALAR", e_cell_idx, d);
}
visit_data_writer->registerPlotQuantity(mu_node_var->getName(), "SCALAR", mu_node_idx);
// Initialize the AMR patch hierarchy.
gridding_algorithm->makeCoarsestLevel(patch_hierarchy, 0.0);
int tag_buffer = 1;
int level_number = 0;
bool done = false;
while (!done && (gridding_algorithm->levelCanBeRefined(level_number)))
{
gridding_algorithm->makeFinerLevel(patch_hierarchy, 0.0, 0.0, tag_buffer);
done = !patch_hierarchy->finerLevelExists(level_number);
++level_number;
}
// Set the simulation time to be zero.
const double data_time = 0.0;
// Allocate data on each level of the patch hierarchy.
for (int ln = 0; ln <= patch_hierarchy->getFinestLevelNumber(); ++ln)
{
Pointer<PatchLevel<NDIM> > level = patch_hierarchy->getPatchLevel(ln);
level->allocatePatchData(u_side_idx, data_time);
level->allocatePatchData(f_side_idx, data_time);
level->allocatePatchData(e_side_idx, data_time);
level->allocatePatchData(u_cell_idx, data_time);
level->allocatePatchData(f_cell_idx, data_time);
level->allocatePatchData(e_cell_idx, data_time);
level->allocatePatchData(mu_node_idx, data_time);
}
// Setup exact solution data.
muParserCartGridFunction u_fcn("u", app_initializer->getComponentDatabase("u"), grid_geometry);
muParserCartGridFunction f_fcn("f", app_initializer->getComponentDatabase("f"), grid_geometry);
muParserCartGridFunction mu_fcn("mu", app_initializer->getComponentDatabase("mu"), grid_geometry);
u_fcn.setDataOnPatchHierarchy(u_side_idx, u_side_var, patch_hierarchy, data_time);
f_fcn.setDataOnPatchHierarchy(e_side_idx, e_side_var, patch_hierarchy, data_time);
mu_fcn.setDataOnPatchHierarchy(mu_node_idx, mu_node_var, patch_hierarchy, data_time);
// Create an object to communicate ghost cell data.
typedef HierarchyGhostCellInterpolation::InterpolationTransactionComponent InterpolationTransactionComponent;
InterpolationTransactionComponent u_transaction(u_side_idx, "CUBIC_COARSEN", "LINEAR");
InterpolationTransactionComponent mu_transaction(mu_node_idx, "CONSTANT_COARSEN", "LINEAR");
vector<InterpolationTransactionComponent> transactions(2);
transactions[0] = u_transaction;
transactions[1] = mu_transaction;
Pointer<HierarchyGhostCellInterpolation> bdry_fill_op = new HierarchyGhostCellInterpolation();
bdry_fill_op->initializeOperatorState(transactions, patch_hierarchy);
// Create the math operations object and get the patch data index for
// the side-centered weighting factor.
HierarchyMathOps hier_math_ops("hier_math_ops", patch_hierarchy);
const int dx_side_idx = hier_math_ops.getSideWeightPatchDescriptorIndex();
// Compute (f0,f1) := div mu (grad(u0,u1) + grad(u0,u1)^T).
hier_math_ops.vc_laplace(f_side_idx,
f_side_var,
1.0,
0.0,
mu_node_idx,
mu_node_var,
u_side_idx,
u_side_var,
bdry_fill_op,
data_time);
// Compute error and print error norms.
Pointer<HierarchyDataOpsReal<NDIM, double> > hier_side_data_ops =
HierarchyDataOpsManager<NDIM>::getManager()->getOperationsDouble(u_side_var, patch_hierarchy, true);
hier_side_data_ops->subtract(e_side_idx, e_side_idx, f_side_idx); // computes e := e - f
pout << "|e|_oo = " << hier_side_data_ops->maxNorm(e_side_idx, dx_side_idx) << "\n";
pout << "|e|_2 = " << hier_side_data_ops->L2Norm(e_side_idx, dx_side_idx) << "\n";
pout << "|e|_1 = " << hier_side_data_ops->L1Norm(e_side_idx, dx_side_idx) << "\n";
// Interpolate the side-centered data to cell centers for output.
static const bool synch_cf_interface = true;
hier_math_ops.interp(u_cell_idx, u_cell_var, u_side_idx, u_side_var, NULL, data_time, synch_cf_interface);
hier_math_ops.interp(f_cell_idx, f_cell_var, f_side_idx, f_side_var, NULL, data_time, synch_cf_interface);
hier_math_ops.interp(e_cell_idx, e_cell_var, e_side_idx, e_side_var, NULL, data_time, synch_cf_interface);
// Output data for plotting.
visit_data_writer->writePlotData(patch_hierarchy, 0, data_time);
} // cleanup dynamically allocated objects prior to shutdown
SAMRAIManager::shutdown();
PetscFinalize();
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 MPI and SAMRAI.
SAMRAI_MPI::init(&argc, &argv);
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, "advect.log");
Pointer<Database> input_db = app_initializer->getInputDatabase();
Pointer<Database> main_db = app_initializer->getComponentDatabase("Main");
// 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 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_timer_data = app_initializer->dumpTimerData();
const int timer_dump_interval = app_initializer->getTimerDumpInterval();
// Get solver configuration options.
bool using_refined_timestepping = false;
if (main_db->keyExists("timestepping"))
{
string timestepping_method = main_db->getString("timestepping");
if (timestepping_method == "SYNCHRONIZED")
{
using_refined_timestepping = false;
}
else
{
using_refined_timestepping = true;
}
}
if (using_refined_timestepping)
{
pout << "using subcycled timestepping.\n";
}
else
{
pout << "NOT using subcycled timestepping.\n";
}
// 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<AdvectorExplicitPredictorStrategy> explicit_predictor = new AdvectorExplicitPredictorStrategy(
"AdvectorExplicitPredictorStrategy", app_initializer->getComponentDatabase("AdvectorExplicitPredictorStrategy"));
Pointer<CartesianGridGeometry<NDIM> > grid_geometry = new CartesianGridGeometry<NDIM>(
"CartesianGeometry", app_initializer->getComponentDatabase("CartesianGeometry"));
Pointer<AdvectorPredictorCorrectorHyperbolicPatchOps> hyp_patch_ops = new AdvectorPredictorCorrectorHyperbolicPatchOps(
"AdvectorPredictorCorrectorHyperbolicPatchOps", app_initializer->getComponentDatabase("AdvectorPredictorCorrectorHyperbolicPatchOps"), explicit_predictor, grid_geometry);
Pointer<HyperbolicLevelIntegrator<NDIM> > hyp_level_integrator = new HyperbolicLevelIntegrator<NDIM>(
"HyperbolicLevelIntegrator", app_initializer->getComponentDatabase("HyperbolicLevelIntegrator"), hyp_patch_ops, true, using_refined_timestepping);
Pointer<PatchHierarchy<NDIM> > patch_hierarchy = new PatchHierarchy<NDIM>(
"PatchHierarchy", grid_geometry);
Pointer<StandardTagAndInitialize<NDIM> > error_detector = new StandardTagAndInitialize<NDIM>(
"StandardTagAndInitialize", hyp_level_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);
Pointer<TimeRefinementIntegrator<NDIM> > time_integrator = new TimeRefinementIntegrator<NDIM>(
"TimeRefinementIntegrator", app_initializer->getComponentDatabase("TimeRefinementIntegrator"), patch_hierarchy, hyp_level_integrator, gridding_algorithm);
// Setup the advection velocity.
const bool u_is_div_free = main_db->getBoolWithDefault("u_is_div_free", false);
if (u_is_div_free)
{
pout << "advection velocity u is discretely divergence free.\n";
}
else
{
pout << "advection velocity u is NOT discretely divergence free.\n";
}
Pointer<FaceVariable<NDIM,double> > u_var = new FaceVariable<NDIM,double>("u");
UFunction u_fcn("UFunction", grid_geometry, app_initializer->getComponentDatabase("UFunction"));
hyp_patch_ops->registerAdvectionVelocity(u_var);
hyp_patch_ops->setAdvectionVelocityIsDivergenceFree(u_var, u_is_div_free);
hyp_patch_ops->setAdvectionVelocityFunction(u_var, Pointer<CartGridFunction>(&u_fcn,false));
// Setup the advected quantity.
const ConvectiveDifferencingType difference_form =
IBAMR::string_to_enum<ConvectiveDifferencingType>(
main_db->getStringWithDefault(
"difference_form", IBAMR::enum_to_string<ConvectiveDifferencingType>(ADVECTIVE)));
pout << "solving the advection equation in "
<< enum_to_string<ConvectiveDifferencingType>(difference_form) << " form.\n";
Pointer<CellVariable<NDIM,double> > Q_var = new CellVariable<NDIM,double>("Q");
QInit Q_init("QInit", grid_geometry, app_initializer->getComponentDatabase("QInit"));
LocationIndexRobinBcCoefs<NDIM> physical_bc_coef(
"physical_bc_coef", app_initializer->getComponentDatabase("LocationIndexRobinBcCoefs"));
hyp_patch_ops->registerTransportedQuantity(Q_var);
hyp_patch_ops->setAdvectionVelocity(Q_var, u_var);
hyp_patch_ops->setConvectiveDifferencingType(Q_var, difference_form);
hyp_patch_ops->setInitialConditions(Q_var, Pointer<CartGridFunction>(&Q_init,false));
hyp_patch_ops->setPhysicalBcCoefs(Q_var, &physical_bc_coef);
// Set up visualization plot file writer.
Pointer<VisItDataWriter<NDIM> > visit_data_writer = app_initializer->getVisItDataWriter();
if (uses_visit) hyp_patch_ops->registerVisItDataWriter(visit_data_writer);
// Initialize hierarchy configuration and data on all patches.
double dt_now = time_integrator->initializeHierarchy();
// 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 && uses_visit)
{
pout << "\n\nWriting visualization files...\n\n";
visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time);
}
// Main time step loop.
double loop_time_end = time_integrator->getEndTime();
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";
double dt_new = time_integrator->advanceHierarchy(dt_now);
loop_time += dt_now;
dt_now = dt_new;
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,
// and print out timer data.
iteration_num += 1;
const bool last_step = !time_integrator->stepsRemaining();
if (dump_viz_data && uses_visit && (iteration_num%viz_dump_interval == 0 || last_step))
{
pout << "\nWriting visualization files...\n\n";
visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time);
}
if (dump_restart_data && (iteration_num%restart_dump_interval == 0 || last_step))
{
pout << "\nWriting restart files...\n\nn";
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);
}
}
// Determine the accuracy of the computed solution.
pout << "\n"
<< "+++++++++++++++++++++++++++++++++++++++++++++++++++\n"
<< "Computing error norms.\n\n";
VariableDatabase<NDIM>* var_db = VariableDatabase<NDIM>::getDatabase();
const Pointer<VariableContext> Q_ctx = hyp_level_integrator->getCurrentContext();
const int Q_idx = var_db->mapVariableAndContextToIndex(Q_var, Q_ctx);
const int Q_cloned_idx = var_db->registerClonedPatchDataIndex(Q_var, Q_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(Q_cloned_idx, loop_time);
}
Q_init.setDataOnPatchHierarchy(Q_cloned_idx, Q_var, patch_hierarchy, loop_time);
HierarchyMathOps hier_math_ops("HierarchyMathOps", patch_hierarchy);
hier_math_ops.setPatchHierarchy(patch_hierarchy);
hier_math_ops.resetLevels(coarsest_ln, finest_ln);
const int wgt_idx = hier_math_ops.getCellWeightPatchDescriptorIndex();
HierarchyCellDataOpsReal<NDIM,double> hier_cc_data_ops(patch_hierarchy, coarsest_ln, finest_ln);
hier_cc_data_ops.subtract(Q_idx, Q_idx, Q_cloned_idx);
pout << "Error in " << Q_var->getName() << " at time " << loop_time << ":\n"
<< " L1-norm: " << hier_cc_data_ops.L1Norm(Q_idx,wgt_idx) << "\n"
<< " L2-norm: " << hier_cc_data_ops.L2Norm(Q_idx,wgt_idx) << "\n"
<< " max-norm: " << hier_cc_data_ops.maxNorm(Q_idx,wgt_idx) << "\n"
<< "+++++++++++++++++++++++++++++++++++++++++++++++++++\n";
if (dump_viz_data && uses_visit)
{
visit_data_writer->writePlotData(patch_hierarchy, iteration_num+1, loop_time);
}
}// cleanup dynamically allocated objects prior to shutdown
SAMRAIManager::shutdown();
SAMRAI_MPI::finalize();
return 0;
}// main
/*******************************************************************************
* For each run, the input filename must be given on the command line. In all *
* cases, the command line is: *
* *
* executable <input file name> *
* *
*******************************************************************************/
int
main(int argc, char* argv[])
{
// Initialize PETSc, MPI, and SAMRAI.
PetscInitialize(&argc, &argv, NULL, NULL);
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, and enable file logging.
Pointer<AppInitializer> app_initializer = new AppInitializer(argc, argv, "sc_poisson.log");
Pointer<Database> input_db = app_initializer->getInputDatabase();
// Create major algorithm and data objects that comprise the
// application. These objects are configured from the input database.
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", NULL, 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);
// Create variables and register them with the variable database.
VariableDatabase<NDIM>* var_db = VariableDatabase<NDIM>::getDatabase();
Pointer<VariableContext> ctx = var_db->getContext("context");
Pointer<SideVariable<NDIM, double> > u_sc_var = new SideVariable<NDIM, double>("u_sc");
Pointer<SideVariable<NDIM, double> > f_sc_var = new SideVariable<NDIM, double>("f_sc");
Pointer<SideVariable<NDIM, double> > e_sc_var = new SideVariable<NDIM, double>("e_sc");
Pointer<SideVariable<NDIM, double> > r_sc_var = new SideVariable<NDIM, double>("r_sc");
const int u_sc_idx = var_db->registerVariableAndContext(u_sc_var, ctx, IntVector<NDIM>(1));
const int f_sc_idx = var_db->registerVariableAndContext(f_sc_var, ctx, IntVector<NDIM>(1));
const int e_sc_idx = var_db->registerVariableAndContext(e_sc_var, ctx, IntVector<NDIM>(1));
const int r_sc_idx = var_db->registerVariableAndContext(r_sc_var, ctx, IntVector<NDIM>(1));
Pointer<CellVariable<NDIM, double> > u_cc_var = new CellVariable<NDIM, double>("u_cc", NDIM);
Pointer<CellVariable<NDIM, double> > f_cc_var = new CellVariable<NDIM, double>("f_cc", NDIM);
Pointer<CellVariable<NDIM, double> > e_cc_var = new CellVariable<NDIM, double>("e_cc", NDIM);
Pointer<CellVariable<NDIM, double> > r_cc_var = new CellVariable<NDIM, double>("r_cc", NDIM);
const int u_cc_idx = var_db->registerVariableAndContext(u_cc_var, ctx, IntVector<NDIM>(0));
const int f_cc_idx = var_db->registerVariableAndContext(f_cc_var, ctx, IntVector<NDIM>(0));
const int e_cc_idx = var_db->registerVariableAndContext(e_cc_var, ctx, IntVector<NDIM>(0));
const int r_cc_idx = var_db->registerVariableAndContext(r_cc_var, ctx, IntVector<NDIM>(0));
// Register variables for plotting.
Pointer<VisItDataWriter<NDIM> > visit_data_writer = app_initializer->getVisItDataWriter();
TBOX_ASSERT(visit_data_writer);
visit_data_writer->registerPlotQuantity(u_cc_var->getName(), "VECTOR", u_cc_idx);
for (unsigned int d = 0; d < NDIM; ++d)
{
ostringstream stream;
stream << d;
visit_data_writer->registerPlotQuantity(u_cc_var->getName() + stream.str(), "SCALAR", u_cc_idx, d);
}
visit_data_writer->registerPlotQuantity(f_cc_var->getName(), "VECTOR", f_cc_idx);
for (unsigned int d = 0; d < NDIM; ++d)
{
ostringstream stream;
stream << d;
visit_data_writer->registerPlotQuantity(f_cc_var->getName() + stream.str(), "SCALAR", f_cc_idx, d);
}
visit_data_writer->registerPlotQuantity(e_cc_var->getName(), "VECTOR", e_cc_idx);
for (unsigned int d = 0; d < NDIM; ++d)
{
ostringstream stream;
stream << d;
visit_data_writer->registerPlotQuantity(e_cc_var->getName() + stream.str(), "SCALAR", e_cc_idx, d);
}
visit_data_writer->registerPlotQuantity(r_cc_var->getName(), "VECTOR", r_cc_idx);
for (unsigned int d = 0; d < NDIM; ++d)
{
ostringstream stream;
stream << d;
visit_data_writer->registerPlotQuantity(r_cc_var->getName() + stream.str(), "SCALAR", r_cc_idx, d);
}
// Initialize the AMR patch hierarchy.
gridding_algorithm->makeCoarsestLevel(patch_hierarchy, 0.0);
int tag_buffer = 1;
int level_number = 0;
bool done = false;
while (!done && (gridding_algorithm->levelCanBeRefined(level_number)))
{
gridding_algorithm->makeFinerLevel(patch_hierarchy, 0.0, 0.0, tag_buffer);
done = !patch_hierarchy->finerLevelExists(level_number);
++level_number;
}
// Allocate data on each level of the patch hierarchy.
for (int ln = 0; ln <= patch_hierarchy->getFinestLevelNumber(); ++ln)
{
Pointer<PatchLevel<NDIM> > level = patch_hierarchy->getPatchLevel(ln);
level->allocatePatchData(u_sc_idx, 0.0);
level->allocatePatchData(f_sc_idx, 0.0);
level->allocatePatchData(e_sc_idx, 0.0);
level->allocatePatchData(r_sc_idx, 0.0);
level->allocatePatchData(u_cc_idx, 0.0);
level->allocatePatchData(f_cc_idx, 0.0);
level->allocatePatchData(e_cc_idx, 0.0);
level->allocatePatchData(r_cc_idx, 0.0);
}
// Setup vector objects.
HierarchyMathOps hier_math_ops("hier_math_ops", patch_hierarchy);
const int h_sc_idx = hier_math_ops.getSideWeightPatchDescriptorIndex();
SAMRAIVectorReal<NDIM, double> u_vec("u", patch_hierarchy, 0, patch_hierarchy->getFinestLevelNumber());
SAMRAIVectorReal<NDIM, double> f_vec("f", patch_hierarchy, 0, patch_hierarchy->getFinestLevelNumber());
SAMRAIVectorReal<NDIM, double> e_vec("e", patch_hierarchy, 0, patch_hierarchy->getFinestLevelNumber());
SAMRAIVectorReal<NDIM, double> r_vec("r", patch_hierarchy, 0, patch_hierarchy->getFinestLevelNumber());
u_vec.addComponent(u_sc_var, u_sc_idx, h_sc_idx);
f_vec.addComponent(f_sc_var, f_sc_idx, h_sc_idx);
e_vec.addComponent(e_sc_var, e_sc_idx, h_sc_idx);
r_vec.addComponent(r_sc_var, r_sc_idx, h_sc_idx);
u_vec.setToScalar(0.0);
f_vec.setToScalar(0.0);
e_vec.setToScalar(0.0);
r_vec.setToScalar(0.0);
// Setup exact solutions.
muParserCartGridFunction u_fcn("u", app_initializer->getComponentDatabase("u"), grid_geometry);
muParserCartGridFunction f_fcn("f", app_initializer->getComponentDatabase("f"), grid_geometry);
u_fcn.setDataOnPatchHierarchy(e_sc_idx, e_sc_var, patch_hierarchy, 0.0);
f_fcn.setDataOnPatchHierarchy(f_sc_idx, f_sc_var, patch_hierarchy, 0.0);
// Setup the Poisson solver.
PoissonSpecifications poisson_spec("poisson_spec");
poisson_spec.setCConstant(0.0);
poisson_spec.setDConstant(-1.0);
vector<RobinBcCoefStrategy<NDIM>*> bc_coefs(NDIM, static_cast<RobinBcCoefStrategy<NDIM>*>(NULL));
SCLaplaceOperator laplace_op("laplace_op");
laplace_op.setPoissonSpecifications(poisson_spec);
laplace_op.setPhysicalBcCoefs(bc_coefs);
laplace_op.initializeOperatorState(u_vec, f_vec);
string solver_type = input_db->getString("solver_type");
Pointer<Database> solver_db = input_db->getDatabase("solver_db");
string precond_type = input_db->getString("precond_type");
Pointer<Database> precond_db = input_db->getDatabase("precond_db");
Pointer<PoissonSolver> poisson_solver = SCPoissonSolverManager::getManager()->allocateSolver(
solver_type, "poisson_solver", solver_db, "", precond_type, "poisson_precond", precond_db, "");
poisson_solver->setPoissonSpecifications(poisson_spec);
poisson_solver->setPhysicalBcCoefs(bc_coefs);
poisson_solver->initializeSolverState(u_vec, f_vec);
// Solve -L*u = f.
u_vec.setToScalar(0.0);
poisson_solver->solveSystem(u_vec, f_vec);
// Compute error and print error norms.
e_vec.subtract(Pointer<SAMRAIVectorReal<NDIM, double> >(&e_vec, false),
Pointer<SAMRAIVectorReal<NDIM, double> >(&u_vec, false));
pout << "|e|_oo = " << e_vec.maxNorm() << "\n";
pout << "|e|_2 = " << e_vec.L2Norm() << "\n";
pout << "|e|_1 = " << e_vec.L1Norm() << "\n";
// Compute the residual and print residual norms.
laplace_op.apply(u_vec, r_vec);
r_vec.subtract(Pointer<SAMRAIVectorReal<NDIM, double> >(&f_vec, false),
Pointer<SAMRAIVectorReal<NDIM, double> >(&r_vec, false));
pout << "|r|_oo = " << r_vec.maxNorm() << "\n";
pout << "|r|_2 = " << r_vec.L2Norm() << "\n";
pout << "|r|_1 = " << r_vec.L1Norm() << "\n";
// Interpolate the side-centered data to cell centers for output.
static const bool synch_cf_interface = true;
hier_math_ops.interp(u_cc_idx, u_cc_var, u_sc_idx, u_sc_var, NULL, 0.0, synch_cf_interface);
hier_math_ops.interp(f_cc_idx, f_cc_var, f_sc_idx, f_sc_var, NULL, 0.0, synch_cf_interface);
hier_math_ops.interp(e_cc_idx, e_cc_var, e_sc_idx, e_sc_var, NULL, 0.0, synch_cf_interface);
hier_math_ops.interp(r_cc_idx, r_cc_var, r_sc_idx, r_sc_var, NULL, 0.0, synch_cf_interface);
// Set invalid values on coarse levels (i.e., coarse-grid values that
// are covered by finer grid patches) to equal zero.
for (int ln = 0; ln <= patch_hierarchy->getFinestLevelNumber() - 1; ++ln)
{
Pointer<PatchLevel<NDIM> > level = patch_hierarchy->getPatchLevel(ln);
BoxArray<NDIM> refined_region_boxes;
Pointer<PatchLevel<NDIM> > next_finer_level = patch_hierarchy->getPatchLevel(ln + 1);
refined_region_boxes = next_finer_level->getBoxes();
refined_region_boxes.coarsen(next_finer_level->getRatioToCoarserLevel());
for (PatchLevel<NDIM>::Iterator p(level); p; p++)
{
Pointer<Patch<NDIM> > patch = level->getPatch(p());
const Box<NDIM>& patch_box = patch->getBox();
Pointer<CellData<NDIM, double> > e_cc_data = patch->getPatchData(e_cc_idx);
Pointer<CellData<NDIM, double> > r_cc_data = patch->getPatchData(r_cc_idx);
for (int i = 0; i < refined_region_boxes.getNumberOfBoxes(); ++i)
{
const Box<NDIM> refined_box = refined_region_boxes[i];
const Box<NDIM> intersection = Box<NDIM>::grow(patch_box, 1) * refined_box;
if (!intersection.empty())
{
e_cc_data->fillAll(0.0, intersection);
r_cc_data->fillAll(0.0, intersection);
}
}
}
}
// Output data for plotting.
visit_data_writer->writePlotData(patch_hierarchy, 0, 0.0);
} // cleanup dynamically allocated objects prior to shutdown
SAMRAIManager::shutdown();
PetscFinalize();
return 0;
} // main
/*******************************************************************************
* For each run, the input filename must be given on the command line. In all *
* cases, the command line is: *
* *
* executable <input file name> *
* *
*******************************************************************************/
bool
run_example(int argc, char* argv[])
{
// Initialize PETSc, MPI, and SAMRAI.
PetscInitialize(&argc, &argv, NULL, NULL);
SAMRAI_MPI::setCommunicator(PETSC_COMM_WORLD);
SAMRAI_MPI::setCallAbortInSerialInsteadOfExit();
SAMRAIManager::startup();
// Since SAMRAI and PETSc both require finalization routines we have to
// ensure that no SAMRAI or PETSc objects are active at the point where we
// call SAMRAIManager::shutdown() or PetscFinalize. Hence, to guarantee
// that all objects are cleaned up by that point, we put everything we use
// in an inner scope.
{
// Parse command line options, set some standard options from the input
// file, and enable file logging.
Pointer<AppInitializer> app_initializer = new AppInitializer(argc, argv, "cc_laplace.log");
Pointer<Database> input_db = app_initializer->getInputDatabase();
// Create major algorithm and data objects that comprise the
// application. These objects are configured from the input
// database. Nearly all SAMRAI applications (at least those in IBAMR)
// start by setting up the same half-dozen objects.
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", NULL, 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);
// Create variables and register them with the variable database.
VariableDatabase<NDIM>* var_db = VariableDatabase<NDIM>::getDatabase();
Pointer<VariableContext> ctx = var_db->getContext("context");
// We create a variable for every vector we ultimately declare,
// instead of creating and then cloning vectors. The rationale for
// this is given below.
Pointer<CellVariable<NDIM, double> > u_cc_var = new CellVariable<NDIM, double>("u_cc");
Pointer<CellVariable<NDIM, double> > f_cc_var = new CellVariable<NDIM, double>("f_cc");
Pointer<CellVariable<NDIM, double> > e_cc_var = new CellVariable<NDIM, double>("e_cc");
Pointer<CellVariable<NDIM, double> > f_approx_cc_var = new CellVariable<NDIM, double>("f_approx_cc");
// Internally, SAMRAI keeps track of variables (and their
// corresponding vectors, data, etc.) by converting them to
// indices. Here we get the indices after notifying the variable
// database about them.
const int u_cc_idx = var_db->registerVariableAndContext(u_cc_var, ctx, IntVector<NDIM>(1));
const int f_cc_idx = var_db->registerVariableAndContext(f_cc_var, ctx, IntVector<NDIM>(1));
const int e_cc_idx = var_db->registerVariableAndContext(e_cc_var, ctx, IntVector<NDIM>(1));
const int f_approx_cc_idx = var_db->registerVariableAndContext(f_approx_cc_var, ctx, IntVector<NDIM>(1));
// Register variables for plotting.
Pointer<VisItDataWriter<NDIM> > visit_data_writer = app_initializer->getVisItDataWriter();
TBOX_ASSERT(visit_data_writer);
visit_data_writer->registerPlotQuantity(u_cc_var->getName(), "SCALAR", u_cc_idx);
visit_data_writer->registerPlotQuantity(f_cc_var->getName(), "SCALAR", f_cc_idx);
visit_data_writer->registerPlotQuantity(f_approx_cc_var->getName(), "SCALAR", f_approx_cc_idx);
visit_data_writer->registerPlotQuantity(e_cc_var->getName(), "SCALAR", e_cc_idx);
// Initialize the AMR patch hierarchy. This sets up the coarsest level
// (level 0) as well as any other levels specified in the input
// file. We normally use the value tag_buffer to specify the number of
// cells between a patch on level N and a patch on level N - 2:
// however, SAMRAI ignores this value when setting up a hierarchy from
// an input file so we just set it to an invalid value.
gridding_algorithm->makeCoarsestLevel(patch_hierarchy, 0.0);
const int tag_buffer = std::numeric_limits<int>::max();
int level_number = 0;
while ((gridding_algorithm->levelCanBeRefined(level_number)))
{
gridding_algorithm->makeFinerLevel(patch_hierarchy, 0.0, 0.0, tag_buffer);
++level_number;
}
const int finest_level = patch_hierarchy->getFinestLevelNumber();
// Allocate data for each variable on each level of the patch
// hierarchy.
for (int ln = 0; ln <= finest_level; ++ln)
{
Pointer<PatchLevel<NDIM> > level = patch_hierarchy->getPatchLevel(ln);
level->allocatePatchData(u_cc_idx, 0.0);
level->allocatePatchData(f_cc_idx, 0.0);
level->allocatePatchData(e_cc_idx, 0.0);
level->allocatePatchData(f_approx_cc_idx, 0.0);
}
// By default, the norms defined on SAMRAI vectors are vectors in R^n:
// however, in IBAMR we almost always want to use a norm that
// corresponds to a numerical quadrature. To do this we have to
// associate each vector with a set of cell-centered volumes. Rather
// than set this up manually, we rely on an IBTK utility class that
// computes this (as well as many other things!). These values are
// known as `cell weights' in this context, so we get the ID of the
// associated data by asking for that. Behind the scenes
// HierarchyMathOps sets up the necessary cell-centered variables and
// registers them with the usual SAMRAI objects: all we need to do is
// ask for the ID. Due to the way SAMRAI works these calls must occur
HierarchyMathOps hier_math_ops("hier_math_ops", patch_hierarchy);
const int cv_cc_idx = hier_math_ops.getCellWeightPatchDescriptorIndex();
// SAMRAI patches do not store data as a single contiguous arrays;
// instead, each hierarchy contains several contiguous arrays. Hence,
// to do linear algebra, we rely on SAMRAI's own vector class which
// understands these relationships. We begin by initializing each
// vector with the patch hierarchy:
SAMRAIVectorReal<NDIM, double> u_vec("u", patch_hierarchy, 0, finest_level);
SAMRAIVectorReal<NDIM, double> f_vec("f", patch_hierarchy, 0, finest_level);
SAMRAIVectorReal<NDIM, double> f_approx_vec("f_approx", patch_hierarchy, 0, finest_level);
SAMRAIVectorReal<NDIM, double> e_vec("e", patch_hierarchy, 0, finest_level);
// and then associate them with, in each case, the relevant
// component. Note that adding the components in this way will
// register the vector with the visit data writer declared above and
// we will compute cell integrals over the entire domain with respect
// to the control volumes defined by cv_cc_idx.
u_vec.addComponent(u_cc_var, u_cc_idx, cv_cc_idx);
f_vec.addComponent(f_cc_var, f_cc_idx, cv_cc_idx);
f_approx_vec.addComponent(f_approx_cc_var, f_approx_cc_idx, cv_cc_idx);
e_vec.addComponent(e_cc_var, e_cc_idx, cv_cc_idx);
// By default, in SAMRAI, if we create another vector as
//
// SAMRAIVectorReal<NDIM, double> f_approx_vec("f_approx", patch_hierarchy, 0, finest_level);
//
// we will simply get a shallow copy of the u vector: put another way,
// the two vectors will have different names but refer to the same
// numerical values. Unfortunately cloning the vector doesn't work
// either: the following code
//
// tbox::Pointer<SAMRAIVectorReal<NDIM, double> > f_approx = u_vec.cloneVector("f_approx");
// SAMRAIVectorReal<NDIM, double> &f_approx_vec = *f_approx;
// f_approx_vec.setToScalar(0.0, false);
//
// crashes in SAMRAI 2.4.4 with a failed assertion referring to an
// unknown variable ID. While ambiguous, the error message is not
// wrong: we have to explicitly allocate data for each variable, so
// creating a new anonymous variable for a cloned vector does not make
// much sense.
// Zero the vectors, including possible ghost data:
u_vec.setToScalar(0.0, false);
f_vec.setToScalar(0.0, false);
f_approx_vec.setToScalar(0.0, false);
e_vec.setToScalar(0.0, false);
// Next, we use functions defined with muParser to set up the right
// hand side and solution. These functions are read from the input
// database and can be changed without recompiling.
{
muParserCartGridFunction u_fcn("u", app_initializer->getComponentDatabase("u"), grid_geometry);
muParserCartGridFunction f_fcn("f", app_initializer->getComponentDatabase("f"), grid_geometry);
u_fcn.setDataOnPatchHierarchy(u_cc_idx, u_cc_var, patch_hierarchy, 0.0);
f_fcn.setDataOnPatchHierarchy(f_cc_idx, f_cc_var, patch_hierarchy, 0.0);
}
// Compute -L*u = f.
PoissonSpecifications poisson_spec("poisson_spec");
poisson_spec.setCConstant(0.0);
poisson_spec.setDConstant(-1.0);
RobinBcCoefStrategy<NDIM>* bc_coef = NULL;
CCLaplaceOperator laplace_op("laplace op");
laplace_op.setPoissonSpecifications(poisson_spec);
laplace_op.setPhysicalBcCoef(bc_coef);
laplace_op.initializeOperatorState(u_vec, f_vec);
laplace_op.apply(u_vec, f_approx_vec);
// Compute error and print error norms. Here we create temporary smart
// pointers that will not delete the underlying object since the
// second argument to the constructor is false.
e_vec.subtract(Pointer<SAMRAIVectorReal<NDIM, double> >(&f_vec, false),
Pointer<SAMRAIVectorReal<NDIM, double> >(&f_approx_vec, false));
pout << "|e|_oo = " << e_vec.maxNorm() << "\n";
pout << "|e|_2 = " << e_vec.L2Norm() << "\n";
pout << "|e|_1 = " << e_vec.L1Norm() << "\n";
// Finally, we clean up the output by setting error values on patches
// on coarser levels which are covered by finer levels to zero.
for (int ln = 0; ln < finest_level; ++ln)
{
Pointer<PatchLevel<NDIM> > level = patch_hierarchy->getPatchLevel(ln);
Pointer<PatchLevel<NDIM> > next_finer_level = patch_hierarchy->getPatchLevel(ln + 1);
BoxArray<NDIM> refined_region_boxes = next_finer_level->getBoxes();
refined_region_boxes.coarsen(next_finer_level->getRatioToCoarserLevel());
for (PatchLevel<NDIM>::Iterator p(level); p; p++)
{
const Patch<NDIM>& patch = *level->getPatch(p());
const Box<NDIM>& patch_box = patch.getBox();
Pointer<CellData<NDIM, double> > e_cc_data = patch.getPatchData(e_cc_idx);
for (int i = 0; i < refined_region_boxes.getNumberOfBoxes(); ++i)
{
const Box<NDIM>& refined_box = refined_region_boxes[i];
// Box::operator* returns the intersection of two boxes.
const Box<NDIM>& intersection = patch_box * refined_box;
if (!intersection.empty())
{
e_cc_data->fillAll(0.0, intersection);
}
}
}
}
// Output data for plotting.
visit_data_writer->writePlotData(patch_hierarchy, 0, 0.0);
}
// At this point all SAMRAI, PETSc, and IBAMR objects have been cleaned
// up, so we shut things down in the opposite order of initialization:
SAMRAIManager::shutdown();
PetscFinalize();
return true;
} // run_example
