void
PenaltyIBMethod::preprocessIntegrateData(double current_time, double new_time, int num_cycles)
{
IBMethod::preprocessIntegrateData(current_time, new_time, num_cycles);
const int coarsest_ln = 0;
const int finest_ln = d_hierarchy->getFinestLevelNumber();
// Look-up or allocate Lagangian data.
d_K_data.resize(finest_ln + 1);
d_M_data.resize(finest_ln + 1);
d_Y_current_data.resize(finest_ln + 1);
d_Y_new_data.resize(finest_ln + 1);
d_V_current_data.resize(finest_ln + 1);
d_V_new_data.resize(finest_ln + 1);
for (int ln = coarsest_ln; ln <= finest_ln; ++ln)
{
if (!d_l_data_manager->levelContainsLagrangianData(ln)) continue;
d_K_data[ln] = d_l_data_manager->getLData("K", ln);
d_M_data[ln] = d_l_data_manager->getLData("M", ln);
d_Y_current_data[ln] = d_l_data_manager->getLData("Y", ln);
d_Y_new_data[ln] = d_l_data_manager->createLData("Y_new", ln, NDIM);
d_V_current_data[ln] = d_l_data_manager->getLData("V", ln);
d_V_new_data[ln] = d_l_data_manager->createLData("V_new", ln, NDIM);
// Initialize Y^{n+1} and V^{n+1} to equal Y^{n} and V^{n}.
int ierr;
ierr = VecCopy(d_Y_current_data[ln]->getVec(), d_Y_new_data[ln]->getVec());
IBTK_CHKERRQ(ierr);
ierr = VecCopy(d_V_current_data[ln]->getVec(), d_V_new_data[ln]->getVec());
IBTK_CHKERRQ(ierr);
}
return;
} // preprocessIntegrateData
void
IBImplicitModHelmholtzPETScLevelSolver::deallocateSolverState()
{
if (!d_is_initialized) return;
IBAMR_TIMER_START(t_deallocate_solver_state);
// Deallocate PETSc objects.
int ierr;
ierr = KSPDestroy(d_petsc_ksp); IBTK_CHKERRQ(ierr);
ierr = MatDestroy(d_petsc_mat); IBTK_CHKERRQ(ierr);
ierr = VecDestroy(d_petsc_x); IBTK_CHKERRQ(ierr);
ierr = VecDestroy(d_petsc_b); IBTK_CHKERRQ(ierr);
d_dof_index_fill.setNull();
d_petsc_ksp = PETSC_NULL;
d_petsc_mat = PETSC_NULL;
d_petsc_x = PETSC_NULL;
d_petsc_b = PETSC_NULL;
// Deallocate DOF index data.
Pointer<PatchLevel<NDIM> > level = d_hierarchy->getPatchLevel(d_level_num);
if (level->checkAllocated(d_dof_index_idx)) level->deallocatePatchData(d_dof_index_idx);
// Indicate that the solver is NOT initialized.
d_is_initialized = false;
IBAMR_TIMER_STOP(t_deallocate_solver_state);
return;
}// deallocateSolverState
void
PenaltyIBMethod::postprocessIntegrateData(double current_time, double new_time, int num_cycles)
{
IBMethod::postprocessIntegrateData(current_time, new_time, num_cycles);
const int coarsest_ln = 0;
const int finest_ln = d_hierarchy->getFinestLevelNumber();
// Reset time-dependent Lagrangian data.
for (int ln = coarsest_ln; ln <= finest_ln; ++ln)
{
if (!d_l_data_manager->levelContainsLagrangianData(ln)) continue;
int ierr;
ierr = VecSwap(d_Y_current_data[ln]->getVec(), d_Y_new_data[ln]->getVec());
IBTK_CHKERRQ(ierr);
ierr = VecSwap(d_V_current_data[ln]->getVec(), d_V_new_data[ln]->getVec());
IBTK_CHKERRQ(ierr);
}
// Deallocate Lagrangian scratch data.
d_K_data.clear();
d_M_data.clear();
d_Y_current_data.clear();
d_Y_new_data.clear();
d_V_current_data.clear();
d_V_new_data.clear();
return;
} // postprocessIntegrateData
void CCPoissonPETScLevelSolver::initializeSolverStateSpecialized(const SAMRAIVectorReal<NDIM, double>& x,
const SAMRAIVectorReal<NDIM, double>& /*b*/)
{
// Allocate DOF index data.
VariableDatabase<NDIM>* var_db = VariableDatabase<NDIM>::getDatabase();
const int x_idx = x.getComponentDescriptorIndex(0);
Pointer<CellDataFactory<NDIM, double> > x_fac = var_db->getPatchDescriptor()->getPatchDataFactory(x_idx);
const int depth = x_fac->getDefaultDepth();
Pointer<CellDataFactory<NDIM, int> > dof_index_fac =
var_db->getPatchDescriptor()->getPatchDataFactory(d_dof_index_idx);
dof_index_fac->setDefaultDepth(depth);
Pointer<PatchLevel<NDIM> > level = d_hierarchy->getPatchLevel(d_level_num);
if (!level->checkAllocated(d_dof_index_idx)) level->allocatePatchData(d_dof_index_idx);
// Setup PETSc objects.
int ierr;
PETScVecUtilities::constructPatchLevelDOFIndices(d_num_dofs_per_proc, d_dof_index_idx, level);
const int mpi_rank = SAMRAI_MPI::getRank();
ierr = VecCreateMPI(PETSC_COMM_WORLD, d_num_dofs_per_proc[mpi_rank], PETSC_DETERMINE, &d_petsc_x);
IBTK_CHKERRQ(ierr);
ierr = VecCreateMPI(PETSC_COMM_WORLD, d_num_dofs_per_proc[mpi_rank], PETSC_DETERMINE, &d_petsc_b);
IBTK_CHKERRQ(ierr);
PETScMatUtilities::constructPatchLevelCCLaplaceOp(
d_petsc_mat, d_poisson_spec, d_bc_coefs, d_solution_time, d_num_dofs_per_proc, d_dof_index_idx, level);
d_petsc_pc = d_petsc_mat;
d_petsc_ksp_ops_flag = SAME_PRECONDITIONER;
d_data_synch_sched = PETScVecUtilities::constructDataSynchSchedule(x_idx, level);
d_ghost_fill_sched = PETScVecUtilities::constructGhostFillSchedule(x_idx, level);
return;
} // initializeSolverStateSpecialized
PetscErrorCode IBImplicitStaggeredHierarchyIntegrator::compositeIBJacobianApply(Vec x, Vec f)
{
PetscErrorCode ierr;
const double half_time = d_integrator_time + 0.5 * d_current_dt;
Vec* component_sol_vecs;
Vec* component_rhs_vecs;
ierr = VecMultiVecGetSubVecs(x, &component_sol_vecs);
IBTK_CHKERRQ(ierr);
ierr = VecMultiVecGetSubVecs(f, &component_rhs_vecs);
IBTK_CHKERRQ(ierr);
Pointer<SAMRAIVectorReal<NDIM, double> > u =
PETScSAMRAIVectorReal::getSAMRAIVector(component_sol_vecs[0]);
Pointer<SAMRAIVectorReal<NDIM, double> > f_u =
PETScSAMRAIVectorReal::getSAMRAIVector(component_rhs_vecs[0]);
Pointer<Variable<NDIM> > u_var = d_ins_hier_integrator->getVelocityVariable();
const int u_idx = u->getComponentDescriptorIndex(0);
const int f_u_idx = f_u->getComponentDescriptorIndex(0);
Vec X = component_sol_vecs[1];
Vec R = component_rhs_vecs[1];
// Evaluate the Eulerian terms.
d_stokes_op->setHomogeneousBc(true);
d_stokes_op->apply(*u, *f_u);
d_ib_implicit_ops->computeLinearizedLagrangianForce(X, half_time);
if (d_enable_logging)
plog << d_object_name
<< "::integrateHierarchy(): spreading Lagrangian force to the Eulerian grid\n";
d_hier_velocity_data_ops->setToScalar(d_f_idx, 0.0);
d_u_phys_bdry_op->setPatchDataIndex(d_f_idx);
d_ib_implicit_ops->spreadLinearizedForce(d_f_idx,
d_u_phys_bdry_op,
getProlongRefineSchedules(d_object_name + "::f"),
half_time);
d_hier_velocity_data_ops->subtract(f_u_idx, f_u_idx, d_f_idx);
ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(component_rhs_vecs[0]));
IBTK_CHKERRQ(ierr);
// Evaluate the Lagrangian terms.
d_hier_velocity_data_ops->scale(d_u_idx, 0.5, u_idx);
d_u_phys_bdry_op->setPatchDataIndex(d_u_idx);
d_ib_implicit_ops->interpolateLinearizedVelocity(
d_u_idx,
getCoarsenSchedules(d_object_name + "::u::CONSERVATIVE_COARSEN"),
getGhostfillRefineSchedules(d_object_name + "::u"),
half_time);
d_ib_implicit_ops->computeLinearizedResidual(X, R);
// Ensure that PETSc sees that the state of the RHS vector has changed.
// This is a nasty hack.
ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(f));
IBTK_CHKERRQ(ierr);
return ierr;
} // compositeIBJacobianApply
bool
PETScKrylovLinearSolver::solveSystem(SAMRAIVectorReal<NDIM, double>& x, SAMRAIVectorReal<NDIM, double>& b)
{
IBTK_TIMER_START(t_solve_system);
#if !defined(NDEBUG)
TBOX_ASSERT(d_A);
#endif
int ierr;
// Initialize the solver, when necessary.
const bool deallocate_after_solve = !d_is_initialized;
if (deallocate_after_solve) initializeSolverState(x, b);
#if !defined(NDEBUG)
TBOX_ASSERT(d_petsc_ksp);
#endif
resetKSPOptions();
// Allocate scratch data.
d_b->allocateVectorData();
// Solve the system using a PETSc KSP object.
d_b->copyVector(Pointer<SAMRAIVectorReal<NDIM, double> >(&b, false));
d_A->setHomogeneousBc(d_homogeneous_bc);
d_A->modifyRhsForBcs(*d_b);
d_A->setHomogeneousBc(true);
PETScSAMRAIVectorReal::replaceSAMRAIVector(d_petsc_x, Pointer<SAMRAIVectorReal<NDIM, double> >(&x, false));
PETScSAMRAIVectorReal::replaceSAMRAIVector(d_petsc_b, d_b);
ierr = KSPSolve(d_petsc_ksp, d_petsc_b, d_petsc_x);
IBTK_CHKERRQ(ierr);
d_A->setHomogeneousBc(d_homogeneous_bc);
d_A->imposeSolBcs(x);
// Get iterations count and residual norm.
ierr = KSPGetIterationNumber(d_petsc_ksp, &d_current_iterations);
IBTK_CHKERRQ(ierr);
ierr = KSPGetResidualNorm(d_petsc_ksp, &d_current_residual_norm);
IBTK_CHKERRQ(ierr);
d_A->setHomogeneousBc(d_homogeneous_bc);
// Determine the convergence reason.
KSPConvergedReason reason;
ierr = KSPGetConvergedReason(d_petsc_ksp, &reason);
IBTK_CHKERRQ(ierr);
const bool converged = (static_cast<int>(reason) > 0);
if (d_enable_logging) reportKSPConvergedReason(reason, plog);
// Dealocate scratch data.
d_b->deallocateVectorData();
// Deallocate the solver, when necessary.
if (deallocate_after_solve) deallocateSolverState();
IBTK_TIMER_STOP(t_solve_system);
return converged;
} // solveSystem
bool
IBImplicitModHelmholtzPETScLevelSolver::solveSystem(
SAMRAIVectorReal<NDIM,double>& x,
SAMRAIVectorReal<NDIM,double>& b)
{
IBAMR_TIMER_START(t_solve_system);
int ierr;
if (d_enable_logging) plog << d_object_name << "::solveSystem():" << std::endl;
// Initialize the solver, when necessary.
const bool deallocate_after_solve = !d_is_initialized;
if (deallocate_after_solve) initializeSolverState(x,b);
#if 0 // XXXX
// Configure solver.
ierr = KSPSetTolerances(d_petsc_ksp, d_rel_residual_tol, d_abs_residual_tol, PETSC_DEFAULT, d_max_iterations); IBTK_CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(d_petsc_ksp, d_initial_guess_nonzero ? PETSC_TRUE : PETSC_FALSE); IBTK_CHKERRQ(ierr);
#endif
// Solve the system.
Pointer<PatchLevel<NDIM> > patch_level = d_hierarchy->getPatchLevel(d_level_num);
const int x_idx = x.getComponentDescriptorIndex(0);
Pointer<SideVariable<NDIM,double> > x_var = x.getComponentVariable(0);
const int b_idx = b.getComponentDescriptorIndex(0);
Pointer<SideVariable<NDIM,double> > b_var = b.getComponentVariable(0);
if (d_initial_guess_nonzero) PETScVecUtilities::copyToPatchLevelVec(d_petsc_x, x_idx, x_var, patch_level);
PETScVecUtilities::copyToPatchLevelVec(d_petsc_b, b_idx, b_var, patch_level);
PETScVecUtilities::constrainPatchLevelVec(d_petsc_b, d_dof_index_idx, d_dof_index_var, patch_level, d_dof_index_fill);
ierr = KSPSolve(d_petsc_ksp, d_petsc_b, d_petsc_x); IBTK_CHKERRQ(ierr);
PETScVecUtilities::copyFromPatchLevelVec(d_petsc_x, x_idx, x_var, patch_level);
typedef SideDataSynchronization::SynchronizationTransactionComponent SynchronizationTransactionComponent; // XXXX
SynchronizationTransactionComponent x_synch_transaction = SynchronizationTransactionComponent(x_idx, "CONSERVATIVE_COARSEN");
Pointer<SideDataSynchronization> side_synch_op = new SideDataSynchronization();
side_synch_op->initializeOperatorState(x_synch_transaction, x.getPatchHierarchy());
side_synch_op->synchronizeData(0.0);
// Log solver info.
KSPConvergedReason reason;
ierr = KSPGetConvergedReason(d_petsc_ksp, &reason); IBTK_CHKERRQ(ierr);
const bool converged = reason > 0;
if (d_enable_logging)
{
plog << d_object_name << "::solveSystem(): solver " << (converged ? "converged" : "diverged") << "\n"
<< "iterations = " << d_current_its << "\n"
<< "residual norm = " << d_current_residual_norm << std::endl;
}
// Deallocate the solver, when necessary.
if (deallocate_after_solve) deallocateSolverState();
IBAMR_TIMER_STOP(t_solve_system);
return converged;
}// solveSystem
PetscErrorCode
IBImplicitStaggeredHierarchyIntegrator::compositeIBPCApply_SAMRAI(PC pc, Vec x, Vec y)
{
PetscErrorCode ierr;
void* ctx;
ierr = PCShellGetContext(pc, &ctx);
IBTK_CHKERRQ(ierr);
IBImplicitStaggeredHierarchyIntegrator* ib_integrator =
static_cast<IBImplicitStaggeredHierarchyIntegrator*>(ctx);
ierr = ib_integrator->compositeIBPCApply(x, y);
IBTK_CHKERRQ(ierr);
return ierr;
} // compositeIBPCApply_SAMRAI
void GeneralizedIBMethod::preprocessIntegrateData(double current_time,
double new_time,
int num_cycles)
{
d_ib_force_and_torque_fcn_needs_init =
d_ib_force_fcn_needs_init || d_ib_force_and_torque_fcn_needs_init;
IBMethod::preprocessIntegrateData(current_time, new_time, num_cycles);
const int coarsest_ln = 0;
const int finest_ln = d_hierarchy->getFinestLevelNumber();
const double start_time = d_ib_solver->getStartTime();
if (d_ib_force_and_torque_fcn)
{
if (d_ib_force_and_torque_fcn_needs_init)
{
const bool initial_time =
MathUtilities<double>::equalEps(current_time, start_time);
resetLagrangianForceAndTorqueFunction(current_time, initial_time);
d_ib_force_and_torque_fcn_needs_init = false;
}
}
// Look-up or allocate Lagangian data.
d_D_current_data.resize(finest_ln + 1);
d_D_new_data.resize(finest_ln + 1);
d_N_current_data.resize(finest_ln + 1);
d_N_new_data.resize(finest_ln + 1);
d_W_current_data.resize(finest_ln + 1);
d_W_new_data.resize(finest_ln + 1);
for (int ln = coarsest_ln; ln <= finest_ln; ++ln)
{
if (!d_l_data_manager->levelContainsLagrangianData(ln)) continue;
d_D_current_data[ln] = d_l_data_manager->getLData("D", ln);
d_D_new_data[ln] = d_l_data_manager->createLData("D_new", ln, NDIM * NDIM);
d_N_current_data[ln] = d_l_data_manager->createLData("N", ln, NDIM);
d_N_new_data[ln] = d_l_data_manager->createLData("N_new", ln, NDIM);
d_W_current_data[ln] = d_l_data_manager->getLData("W", ln);
d_W_new_data[ln] = d_l_data_manager->createLData("W_new", ln, NDIM);
// Initialize D^{n+1} to equal D^{n}, and initialize W^{n+1} to equal
// W^{n}.
int ierr;
ierr = VecCopy(d_D_current_data[ln]->getVec(), d_D_new_data[ln]->getVec());
IBTK_CHKERRQ(ierr);
ierr = VecCopy(d_W_current_data[ln]->getVec(), d_W_new_data[ln]->getVec());
IBTK_CHKERRQ(ierr);
}
return;
} // preprocessIntegrateData
void StaggeredStokesPETScLevelSolver::initializeSolverStateSpecialized(
const SAMRAIVectorReal<NDIM, double>& x,
const SAMRAIVectorReal<NDIM, double>& /*b*/)
{
// Allocate DOF index data.
Pointer<PatchLevel<NDIM> > level = d_hierarchy->getPatchLevel(d_level_num);
if (!level->checkAllocated(d_u_dof_index_idx)) level->allocatePatchData(d_u_dof_index_idx);
if (!level->checkAllocated(d_p_dof_index_idx)) level->allocatePatchData(d_p_dof_index_idx);
// Setup PETSc objects.
int ierr;
StaggeredStokesPETScVecUtilities::constructPatchLevelDOFIndices(
d_num_dofs_per_proc, d_u_dof_index_idx, d_p_dof_index_idx, level);
const int mpi_rank = SAMRAI_MPI::getRank();
ierr = VecCreateMPI(
PETSC_COMM_WORLD, d_num_dofs_per_proc[mpi_rank], PETSC_DETERMINE, &d_petsc_x);
IBTK_CHKERRQ(ierr);
ierr = VecCreateMPI(
PETSC_COMM_WORLD, d_num_dofs_per_proc[mpi_rank], PETSC_DETERMINE, &d_petsc_b);
IBTK_CHKERRQ(ierr);
StaggeredStokesPETScMatUtilities::constructPatchLevelMACStokesOp(d_petsc_mat,
d_U_problem_coefs,
d_U_bc_coefs,
d_new_time,
d_num_dofs_per_proc,
d_u_dof_index_idx,
d_p_dof_index_idx,
level);
ierr = MatDuplicate(d_petsc_mat, MAT_COPY_VALUES, &d_petsc_pc);
IBTK_CHKERRQ(ierr);
HierarchyDataOpsManager<NDIM>* hier_ops_manager =
HierarchyDataOpsManager<NDIM>::getManager();
Pointer<HierarchyDataOpsInteger<NDIM> > hier_p_dof_index_ops =
hier_ops_manager->getOperationsInteger(d_p_dof_index_var, d_hierarchy, true);
hier_p_dof_index_ops->resetLevels(d_level_num, d_level_num);
const int min_p_idx = hier_p_dof_index_ops->min(
d_p_dof_index_idx); // NOTE: HierarchyDataOpsInteger::max() is broken
ierr = MatZeroRowsColumns(d_petsc_pc, 1, &min_p_idx, 1.0, NULL, NULL);
IBTK_CHKERRQ(ierr);
d_petsc_ksp_ops_flag = SAME_PRECONDITIONER;
const int u_idx = x.getComponentDescriptorIndex(0);
const int p_idx = x.getComponentDescriptorIndex(1);
d_data_synch_sched =
StaggeredStokesPETScVecUtilities::constructDataSynchSchedule(u_idx, p_idx, level);
d_ghost_fill_sched =
StaggeredStokesPETScVecUtilities::constructGhostFillSchedule(u_idx, p_idx, level);
return;
} // initializeSolverStateSpecialized
PetscErrorCode VecAYPX_SAMRAI(Vec y, const PetscScalar alpha, Vec x)
{
IBTK_TIMER_START(t_vec_aypx);
#if !defined(NDEBUG)
TBOX_ASSERT(x);
TBOX_ASSERT(y);
#endif
static const bool interior_only = false;
if (MathUtilities<double>::equalEps(alpha, 1.0))
{
PSVR_CAST2(y)->add(PSVR_CAST2(x), PSVR_CAST2(y), interior_only);
}
else if (MathUtilities<double>::equalEps(alpha, -1.0))
{
PSVR_CAST2(y)->subtract(PSVR_CAST2(x), PSVR_CAST2(y), interior_only);
}
else
{
PSVR_CAST2(y)->axpy(alpha, PSVR_CAST2(y), PSVR_CAST2(x), interior_only);
}
int ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(y));
IBTK_CHKERRQ(ierr);
IBTK_TIMER_STOP(t_vec_aypx);
PetscFunctionReturn(0);
} // VecAYPX
Pointer<SAMRAIVectorReal<NDIM, double> > PETScNewtonKrylovSolver::getFunctionVector() const
{
Vec petsc_f;
int ierr = SNESGetFunction(d_petsc_snes, &petsc_f, NULL, NULL);
IBTK_CHKERRQ(ierr);
return PETScSAMRAIVectorReal::getSAMRAIVector(petsc_f);
} // getFunctionVector
Pointer<SAMRAIVectorReal<NDIM, double> > PETScSNESJacobianJOWrapper::getBaseVector() const
{
Vec petsc_x;
int ierr = SNESGetSolution(d_petsc_snes, &petsc_x);
IBTK_CHKERRQ(ierr);
return PETScSAMRAIVectorReal::getSAMRAIVector(petsc_x);
} // getBaseVector
PetscErrorCode VecSetRandom_SAMRAI(Vec x, PetscRandom rctx)
{
IBTK_TIMER_START(t_vec_set_random);
#if !defined(NDEBUG)
TBOX_ASSERT(x);
#endif
PetscScalar lo, hi;
int ierr;
ierr = PetscRandomGetInterval(rctx, &lo, &hi);
IBTK_CHKERRQ(ierr);
PSVR_CAST2(x)->setRandomValues(hi - lo, lo);
ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(x));
IBTK_CHKERRQ(ierr);
IBTK_TIMER_STOP(t_vec_set_random);
PetscFunctionReturn(0);
} // VecSetRandom
PetscErrorCode
VecMAXPY_SAMRAI(
Vec y,
PetscInt nv,
const PetscScalar* alpha,
Vec* x)
{
IBTK_TIMER_START(t_vec_maxpy);
#ifdef DEBUG_CHECK_ASSERTIONS
TBOX_ASSERT(y != PETSC_NULL);
for (PetscInt i = 0; i < nv; ++i)
{
TBOX_ASSERT(x[i] != PETSC_NULL);
}
#endif
static const bool interior_only = false;
for (PetscInt i = 0; i < nv; ++i)
{
if (MathUtilities<double>::equalEps(alpha[i],1.0))
{
PSVR_CAST2(y)->add(PSVR_CAST2(x[i]), PSVR_CAST2(y), interior_only);
}
else if (MathUtilities<double>::equalEps(alpha[i],-1.0))
{
PSVR_CAST2(y)->subtract(PSVR_CAST2(y), PSVR_CAST2(x[i]), interior_only);
}
else
{
PSVR_CAST2(y)->axpy(alpha[i], PSVR_CAST2(x[i]), PSVR_CAST2(y), interior_only);
}
}
int ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(y)); IBTK_CHKERRQ(ierr);
IBTK_TIMER_STOP(t_vec_maxpy);
PetscFunctionReturn(0);
}// VecMAXPY
PetscErrorCode
VecWAXPY_SAMRAI(
Vec w,
PetscScalar alpha,
Vec x,
Vec y)
{
IBTK_TIMER_START(t_vec_waxpy);
#ifdef DEBUG_CHECK_ASSERTIONS
TBOX_ASSERT(x != PETSC_NULL);
TBOX_ASSERT(y != PETSC_NULL);
TBOX_ASSERT(w != PETSC_NULL);
#endif
static const bool interior_only = false;
if (MathUtilities<double>::equalEps(alpha,1.0))
{
PSVR_CAST2(w)->add(PSVR_CAST2(x), PSVR_CAST2(y), interior_only);
}
else if (MathUtilities<double>::equalEps(alpha,-1.0))
{
PSVR_CAST2(w)->subtract(PSVR_CAST2(y), PSVR_CAST2(x), interior_only);
}
else
{
PSVR_CAST2(w)->axpy(alpha, PSVR_CAST2(x), PSVR_CAST2(y), interior_only);
}
int ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(w)); IBTK_CHKERRQ(ierr);
IBTK_TIMER_STOP(t_vec_waxpy);
PetscFunctionReturn(0);
}// VecWAXPY
PetscErrorCode VecSwap_SAMRAI(Vec x, Vec y)
{
IBTK_TIMER_START(t_vec_swap);
#if !defined(NDEBUG)
TBOX_ASSERT(x);
TBOX_ASSERT(y);
#endif
PSVR_CAST2(x)->swapVectors(PSVR_CAST2(y));
int ierr;
ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(x));
IBTK_CHKERRQ(ierr);
ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(y));
IBTK_CHKERRQ(ierr);
IBTK_TIMER_STOP(t_vec_swap);
PetscFunctionReturn(0);
} // VecSwap
LData::LData(const std::string& name,
const unsigned int num_local_nodes,
const unsigned int depth,
const std::vector<int>& nonlocal_petsc_indices)
: d_name(name), d_global_node_count(0), d_local_node_count(0), d_ghost_node_count(0), d_depth(depth),
d_nonlocal_petsc_indices(nonlocal_petsc_indices), d_global_vec(NULL), d_managing_petsc_vec(true), d_array(NULL),
d_boost_array(NULL), d_boost_local_array(NULL), d_boost_vec_array(NULL), d_boost_local_vec_array(NULL),
d_ghosted_local_vec(NULL), d_ghosted_local_array(NULL), d_boost_ghosted_local_array(NULL),
d_boost_vec_ghosted_local_array(NULL)
{
// Create the PETSc Vec that provides storage for the Lagrangian data.
int ierr;
if (d_depth == 1)
{
ierr = VecCreateGhost(PETSC_COMM_WORLD,
num_local_nodes,
PETSC_DECIDE,
static_cast<int>(d_nonlocal_petsc_indices.size()),
d_nonlocal_petsc_indices.empty() ? NULL : &d_nonlocal_petsc_indices[0],
&d_global_vec);
IBTK_CHKERRQ(ierr);
}
else
{
ierr = VecCreateGhostBlock(PETSC_COMM_WORLD,
d_depth,
d_depth * num_local_nodes,
PETSC_DECIDE,
static_cast<int>(d_nonlocal_petsc_indices.size()),
d_nonlocal_petsc_indices.empty() ? NULL : &d_nonlocal_petsc_indices[0],
&d_global_vec);
IBTK_CHKERRQ(ierr);
}
int global_node_count;
ierr = VecGetSize(d_global_vec, &global_node_count);
IBTK_CHKERRQ(ierr);
#if !defined(NDEBUG)
TBOX_ASSERT(global_node_count >= 0);
#endif
d_global_node_count = global_node_count;
d_global_node_count /= d_depth;
d_local_node_count = num_local_nodes;
d_ghost_node_count = static_cast<int>(d_nonlocal_petsc_indices.size());
return;
} // LData
void GeneralizedIBMethod::computeLagrangianForce(const double data_time)
{
IBMethod::computeLagrangianForce(data_time);
const int coarsest_ln = 0;
const int finest_ln = d_hierarchy->getFinestLevelNumber();
int ierr;
std::vector<Pointer<LData> >* F_data = NULL;
std::vector<Pointer<LData> >* N_data = NULL;
std::vector<Pointer<LData> >* X_data = NULL;
std::vector<Pointer<LData> >* D_data = NULL;
if (MathUtilities<double>::equalEps(data_time, d_current_time))
{
d_F_current_needs_ghost_fill = true;
d_N_current_needs_ghost_fill = true;
F_data = &d_F_current_data;
N_data = &d_N_current_data;
X_data = &d_X_current_data;
D_data = &d_D_current_data;
}
else if (MathUtilities<double>::equalEps(data_time, d_half_time))
{
TBOX_ERROR(d_object_name << "::computeLagrangianForce():\n"
<< " time-stepping type MIDPOINT_RULE not supported by "
"class GeneralizedIBMethod;\n"
<< " use TRAPEZOIDAL_RULE instead.\n");
}
else if (MathUtilities<double>::equalEps(data_time, d_new_time))
{
d_F_new_needs_ghost_fill = true;
d_N_new_needs_ghost_fill = true;
F_data = &d_F_new_data;
N_data = &d_N_new_data;
X_data = &d_X_new_data;
D_data = &d_D_new_data;
}
for (int ln = coarsest_ln; ln <= finest_ln; ++ln)
{
if (!d_l_data_manager->levelContainsLagrangianData(ln)) continue;
ierr = VecSet((*N_data)[ln]->getVec(), 0.0);
IBTK_CHKERRQ(ierr);
if (d_ib_force_and_torque_fcn)
{
d_ib_force_and_torque_fcn->computeLagrangianForceAndTorque((*F_data)[ln],
(*N_data)[ln],
(*X_data)[ln],
(*D_data)[ln],
d_hierarchy,
ln,
data_time,
d_l_data_manager);
}
}
resetAnchorPointValues(*F_data, coarsest_ln, finest_ln);
resetAnchorPointValues(*N_data, coarsest_ln, finest_ln);
return;
} // computeLagrangianForce
PetscErrorCode IBImplicitStaggeredHierarchyIntegrator::compositeIBJacobianSetup(
SNES /*snes*/,
Vec x,
Mat* A,
Mat* /*B*/,
MatStructure* /*mat_structure*/)
{
PetscErrorCode ierr;
ierr = MatAssemblyBegin(*A, MAT_FINAL_ASSEMBLY);
IBTK_CHKERRQ(ierr);
ierr = MatAssemblyEnd(*A, MAT_FINAL_ASSEMBLY);
IBTK_CHKERRQ(ierr);
Vec* component_sol_vecs;
ierr = VecMultiVecGetSubVecs(x, &component_sol_vecs);
IBTK_CHKERRQ(ierr);
Vec X = component_sol_vecs[1];
d_ib_implicit_ops->setLinearizedPosition(X);
return 0;
} // compositeIBJacobianSetup
LData::~LData()
{
restoreArrays();
if (d_managing_petsc_vec)
{
const int ierr = VecDestroy(&d_global_vec);
IBTK_CHKERRQ(ierr);
}
return;
} // ~LData
void
VCSCViscousPETScLevelSolver::initializeSolverStateSpecialized(const SAMRAIVectorReal<NDIM, double>& x,
const SAMRAIVectorReal<NDIM, double>& /*b*/)
{
// Allocate DOF index data.
VariableDatabase<NDIM>* var_db = VariableDatabase<NDIM>::getDatabase();
const int x_idx = x.getComponentDescriptorIndex(0);
Pointer<SideDataFactory<NDIM, double> > x_fac = var_db->getPatchDescriptor()->getPatchDataFactory(x_idx);
const int depth = x_fac->getDefaultDepth();
Pointer<SideDataFactory<NDIM, int> > dof_index_fac =
var_db->getPatchDescriptor()->getPatchDataFactory(d_dof_index_idx);
dof_index_fac->setDefaultDepth(depth);
if (!d_level->checkAllocated(d_dof_index_idx)) d_level->allocatePatchData(d_dof_index_idx);
PETScVecUtilities::constructPatchLevelDOFIndices(d_num_dofs_per_proc, d_dof_index_idx, d_level);
// Setup PETSc objects.
int ierr;
const int mpi_rank = SAMRAI_MPI::getRank();
ierr = VecCreateMPI(PETSC_COMM_WORLD, d_num_dofs_per_proc[mpi_rank], PETSC_DETERMINE, &d_petsc_x);
IBTK_CHKERRQ(ierr);
ierr = VecCreateMPI(PETSC_COMM_WORLD, d_num_dofs_per_proc[mpi_rank], PETSC_DETERMINE, &d_petsc_b);
IBTK_CHKERRQ(ierr);
const double alpha = 1.0;
const double beta = 1.0;
PETScMatUtilities::constructPatchLevelVCSCViscousOp(d_petsc_mat,
d_poisson_spec,
alpha,
beta,
d_bc_coefs,
d_solution_time,
d_num_dofs_per_proc,
d_dof_index_idx,
d_level,
d_mu_interp_type);
d_petsc_pc = d_petsc_mat;
// Setup SAMRAI communication objects.
d_data_synch_sched = PETScVecUtilities::constructDataSynchSchedule(x_idx, d_level);
d_ghost_fill_sched = PETScVecUtilities::constructGhostFillSchedule(x_idx, d_level);
return;
} // initializeSolverStateSpecialized
PetscErrorCode
IBImplicitStaggeredHierarchyIntegrator::compositeIBJacobianApply_SAMRAI(Mat A, Vec x, Vec f)
{
PetscErrorCode ierr;
void* ctx;
ierr = MatShellGetContext(A, &ctx);
IBTK_CHKERRQ(ierr);
IBImplicitStaggeredHierarchyIntegrator* ib_integrator =
static_cast<IBImplicitStaggeredHierarchyIntegrator*>(ctx);
return ib_integrator->compositeIBJacobianApply(x, f);
} // compositeIBJacobianApply_SAMRAI
void LData::resetData(Vec vec, const std::vector<int>& nonlocal_petsc_indices, const bool manage_petsc_vec)
{
restoreArrays();
int ierr;
if (d_managing_petsc_vec)
{
ierr = VecDestroy(&d_global_vec);
IBTK_CHKERRQ(ierr);
}
// Take ownership of new Vec
d_global_vec = vec;
d_managing_petsc_vec = manage_petsc_vec;
int depth;
ierr = VecGetBlockSize(d_global_vec, &depth);
IBTK_CHKERRQ(ierr);
#if !defined(NDEBUG)
TBOX_ASSERT(depth >= 0);
#endif
d_depth = depth;
int global_node_count;
ierr = VecGetSize(d_global_vec, &global_node_count);
IBTK_CHKERRQ(ierr);
#if !defined(NDEBUG)
TBOX_ASSERT(global_node_count >= 0);
#endif
d_global_node_count = global_node_count;
d_global_node_count /= d_depth;
int local_node_count;
ierr = VecGetLocalSize(d_global_vec, &local_node_count);
IBTK_CHKERRQ(ierr);
#if !defined(NDEBUG)
TBOX_ASSERT(local_node_count >= 0);
#endif
d_local_node_count = local_node_count;
d_local_node_count /= d_depth;
d_nonlocal_petsc_indices = nonlocal_petsc_indices;
d_ghost_node_count = static_cast<int>(d_nonlocal_petsc_indices.size());
return;
} // resetData
PetscErrorCode
IBImplicitStaggeredHierarchyIntegrator::lagrangianSchurApply_SAMRAI(Mat A, Vec x, Vec y)
{
PetscErrorCode ierr;
void* ctx;
ierr = MatShellGetContext(A, &ctx);
IBTK_CHKERRQ(ierr);
IBImplicitStaggeredHierarchyIntegrator* ib_integrator =
static_cast<IBImplicitStaggeredHierarchyIntegrator*>(ctx);
ierr = ib_integrator->lagrangianSchurApply(x, y);
return ierr;
} // lagrangianSchurApply_SAMRAI
void PETScSNESFunctionGOWrapper::apply(SAMRAIVectorReal<NDIM, double>& x, SAMRAIVectorReal<NDIM, double>& y)
{
if (!d_is_initialized) initializeOperatorState(x, y);
// Update the PETSc Vec wrappers.
PETScSAMRAIVectorReal::replaceSAMRAIVector(d_petsc_x, Pointer<SAMRAIVectorReal<NDIM, double> >(&x, false));
PETScSAMRAIVectorReal::replaceSAMRAIVector(d_petsc_y, Pointer<SAMRAIVectorReal<NDIM, double> >(&y, false));
// Apply the operator.
int ierr = d_petsc_snes_form_func(d_petsc_snes, d_petsc_x, d_petsc_y, d_petsc_snes_func_ctx);
IBTK_CHKERRQ(ierr);
return;
} // apply
PetscErrorCode VecSet_SAMRAI(Vec x, PetscScalar alpha)
{
IBTK_TIMER_START(t_vec_set);
#if !defined(NDEBUG)
TBOX_ASSERT(x);
#endif
static const bool interior_only = false;
PSVR_CAST2(x)->setToScalar(alpha, interior_only);
int ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(x));
IBTK_CHKERRQ(ierr);
IBTK_TIMER_STOP(t_vec_set);
PetscFunctionReturn(0);
} // VecSet
void PETScSNESFunctionGOWrapper::initializeOperatorState(const SAMRAIVectorReal<NDIM, double>& in,
const SAMRAIVectorReal<NDIM, double>& out)
{
if (d_is_initialized) deallocateOperatorState();
d_x = in.cloneVector("");
d_y = out.cloneVector("");
MPI_Comm comm;
int ierr = PetscObjectGetComm(reinterpret_cast<PetscObject>(d_petsc_snes), &comm);
IBTK_CHKERRQ(ierr);
d_petsc_x = PETScSAMRAIVectorReal::createPETScVector(d_x, comm);
d_petsc_y = PETScSAMRAIVectorReal::createPETScVector(d_y, comm);
d_is_initialized = true;
return;
} // initializeOperatorState
bool
PETScPCLSWrapper::solveSystem(SAMRAIVectorReal<NDIM, double>& x, SAMRAIVectorReal<NDIM, double>& b)
{
if (!d_is_initialized) initializeSolverState(x, b);
// Update the PETSc Vec wrappers.
PETScSAMRAIVectorReal::replaceSAMRAIVector(d_petsc_x, Pointer<SAMRAIVectorReal<NDIM, double> >(&x, false));
PETScSAMRAIVectorReal::replaceSAMRAIVector(d_petsc_b, Pointer<SAMRAIVectorReal<NDIM, double> >(&b, false));
// Apply the preconditioner.
int ierr = PCApply(d_petsc_pc, d_petsc_x, d_petsc_b);
IBTK_CHKERRQ(ierr);
return true;
} // solveSystem
PetscErrorCode VecCopy_SAMRAI(Vec x, Vec y)
{
IBTK_TIMER_START(t_vec_copy);
#if !defined(NDEBUG)
TBOX_ASSERT(x);
TBOX_ASSERT(y);
#endif
static const bool interior_only = false;
PSVR_CAST2(y)->copyVector(PSVR_CAST2(x), interior_only);
int ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(y));
IBTK_CHKERRQ(ierr);
IBTK_TIMER_STOP(t_vec_copy);
PetscFunctionReturn(0);
} // VecCopy
