void createOuterPC(OuterContext* ctx) {
PCCreate(((ctx->data)->commAll), &(ctx->outerPC));
PCSetType(ctx->outerPC, PCSHELL);
PCShellSetName(ctx->outerPC, "RSD");
PCShellSetContext(ctx->outerPC, ctx);
PCShellSetApply(ctx->outerPC, &outerPCapply);
}
int main(int argc,char **args)
{
PC pc;
PetscErrorCode ierr;
PetscInt n = 5;
Mat mat;
ierr = PetscInitialize(&argc,&args,(char*)0,help);
if (ierr) return ierr;
ierr = PCCreate(PETSC_COMM_WORLD,&pc);
CHKERRQ(ierr);
ierr = PCSetType(pc,PCNONE);
CHKERRQ(ierr);
/* Vector and matrix must be set before calling PCSetUp */
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,n,n,3,NULL,&mat);
CHKERRQ(ierr);
ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = PCSetOperators(pc,mat,mat);
CHKERRQ(ierr);
ierr = PCSetUp(pc);
CHKERRQ(ierr);
ierr = MatDestroy(&mat);
CHKERRQ(ierr);
ierr = PCDestroy(&pc);
CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode DMCoarsen_AKKT_GAMG11(DM dm, Mat P0f0c, Mat *P1f1c_out) {
PetscErrorCode ierr;
DM_AKKT* kkt = (DM_AKKT*)(dm->data);
Mat Aff = kkt->Aff; /* fine-level KKT matrix */
Mat A1f0f; /* fine-level dual (constraint) Jacobian */
Mat A1f0c; /* = A1f0f*P0f0c coarsen only primal indices */
Mat B1f1f; /* = A1f0c'*A1f0c */
PC gamg11;/* Use PCGAMG internally to get access to some of its methods to operate on B1f1f = A1f0c*A1f0c', where A1f0c = A1f0f*P0f0c. */
PC_GAMG* pc_gamg11;
Mat G1f1f; /* = Graph(B1f1f) */
Mat P1f1c; /* = Prolongator(G1f1f); */
PetscCoarsenData *coarsening;
PetscFunctionBegin;
/*
What is faster:
- A0c1f = P0f0c'*A0f1f followed by B1f1f = A0c1f'*A0c1f, or
- A1f0c = A1f0f*P0f0c followed by B1f1f = A1f0c*A1f0c'?
My bet is on the latter:
- fewer transpositions inside MatMatMult and row indices are always local.
*/
ierr = MatGetSubMatrix(Aff, kkt->isf[1], kkt->isf[0], MAT_INITIAL_MATRIX, &A1f0f); CHKERRQ(ierr);
if(kkt->transposeP) {
ierr = MatMatTransposeMult(A1f0f,P0f0c,MAT_INITIAL_MATRIX, PETSC_DEFAULT, &A1f0c); CHKERRQ(ierr);
}
ierr = MatMatMult(A1f0f,P0f0c,MAT_INITIAL_MATRIX, PETSC_DEFAULT, &A1f0c); CHKERRQ(ierr);
ierr = MatMatTransposeMult(A1f0c, A1f0c, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &B1f1f); CHKERRQ(ierr);
/* We create PCGAMG here since it is only needed for coarsening and we don't want to have to carry the attendant data structures, if we don't need them. */
ierr = PCCreate(((PetscObject)dm)->comm, &gamg11); CHKERRQ(ierr);
/* This must be an aggregating GAMG. */
ierr = PCSetType(gamg11, PCGAMG); CHKERRQ(ierr);
ierr = PCGAMGSetSquareGraph(gamg11, PETSC_FALSE); CHKERRQ(ierr);
/*
Observe that we want to "square" A1f0c before passing it (B1f1f) to GAMG.
This is not because we are not sure how GAMG will deal with a (potentially) non-square matrix,
but rather because if we asked GAMG to square it, it would also smooth the resulting prolongator.
At least PC_GAMG_AGG would, and we need an unsmoothed prolongator.
*/
ierr = PCSetOperators(gamg11, B1f1f, B1f1f, DIFFERENT_NONZERO_PATTERN); CHKERRQ(ierr);
/* FIX: Currently there is no way to tell GAMG to coarsen onto a give comm, but it shouldn't be hard to hack that stuff in. */
pc_gamg11 = (PC_GAMG*)(gamg11->data);
ierr = pc_gamg11->graph(gamg11, B1f1f, &G1f1f); CHKERRQ(ierr);
ierr = pc_gamg11->coarsen(gamg11, &G1f1f, &coarsening); CHKERRQ(ierr);
ierr = pc_gamg11->prolongator(gamg11, B1f1f, G1f1f, coarsening, &P1f1c); CHKERRQ(ierr);
ierr = MatDestroy(&A1f0f); CHKERRQ(ierr);
ierr = MatDestroy(&A1f0c); CHKERRQ(ierr);
ierr = MatDestroy(&B1f1f); CHKERRQ(ierr);
ierr = MatDestroy(&G1f1f); CHKERRQ(ierr);
ierr = PCDestroy(&gamg11); CHKERRQ(ierr);
*P1f1c_out = P1f1c;
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat mat;
Vec b,u;
PC pc;
PetscErrorCode ierr;
PetscInt n = 5,i,col[3];
PetscScalar value[3];
PetscInitialize(&argc,&args,(char *)0,help);
/* Create vectors */
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&b);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&u);CHKERRQ(ierr);
/* Create and assemble matrix */
ierr = MatCreateSeqDense(PETSC_COMM_SELF,n,n,PETSC_NULL,&mat);CHKERRQ(ierr);
value[0] = -1.0; value[1] = 2.0; value[2] = -1.0;
for (i=1; i<n-1; i++) {
col[0] = i-1; col[1] = i; col[2] = i+1;
ierr = MatSetValues(mat,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
i = n - 1; col[0] = n - 2; col[1] = n - 1;
ierr = MatSetValues(mat,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
i = 0; col[0] = 0; col[1] = 1; value[0] = 2.0; value[1] = -1.0;
ierr = MatSetValues(mat,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Create PC context and set up data structures */
ierr = PCCreate(PETSC_COMM_WORLD,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCSOR);CHKERRQ(ierr);
ierr = PCSetFromOptions(pc);CHKERRQ(ierr);
ierr = PCSetOperators(pc,mat,mat,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = PCSetUp(pc);CHKERRQ(ierr);
value[0] = 1.0;
for (i=0; i<n; i++) {
ierr = VecSet(u,0.0);CHKERRQ(ierr);
ierr = VecSetValues(u,1,&i,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(u);CHKERRQ(ierr);
ierr = VecAssemblyEnd(u);CHKERRQ(ierr);
ierr = PCApply(pc,u,b);CHKERRQ(ierr);
ierr = VecView(b,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
}
/* Free data structures */
ierr = MatDestroy(&mat);CHKERRQ(ierr);
ierr = PCDestroy(&pc);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
MGSolver_PETScData* MultigridSolver_CreateCoarseSolver( MultigridSolver* self, Mat matrix ) {
//MatrixSolver* coarseSolver;
MGSolver_PETScData* courseSolver;
unsigned nProcs;
PC pc;
MPI_Comm_size( self->mgData->comm, (int*)&nProcs );
/*
coarseSolver = (MatrixSolver*)PETScMatrixSolver_New( "" );
PETScMatrixSolver_SetKSPType( coarseSolver,
PETScMatrixSolver_KSPType_PreOnly );
if( nProcs == 1 ) {
PETScMatrixSolver_SetPCType( coarseSolver,
PETScMatrixSolver_PCType_LU );
}
else {
PETScMatrixSolver_SetPCType( coarseSolver,
PETScMatrixSolver_PCType_RedundantLU );
}
MatrixSolver_SetMatrix( coarseSolver, matrix );
*/
if( nProcs == 1 ){
KSPCreate( MPI_COMM_WORLD, &courseSolver->ksp );
KSPSetType( courseSolver->ksp, KSPPREONLY );
KSPGetPC( courseSolver->ksp, &pc );
PCSetType( pc, PCLU );
}
else {
PCSetType( pc, PCREDUNDANT );
#if ((PETSC_VERSION_MAJOR>=3) && (PETSC_VERSION_MINOR>=2) )
PCCreate( MPI_COMM_WORLD, &pc);
PCRedundantGetKSP( pc, &courseSolver->ksp );
#else
KSPCreate( MPI_COMM_WORLD, &courseSolver->ksp );
KSPSetType( courseSolver->ksp, KSPPREONLY );
KSPGetPC( courseSolver->ksp, &pc );
PCRedundantGetPC( pc, &pc );
#endif
PCSetType( pc, PCLU );
}
if( courseSolver->matrix != PETSC_NULL ){
Stg_MatDestroy(&courseSolver->matrix );}
courseSolver->matrix = matrix;
Stg_KSPSetOperators( courseSolver->ksp, matrix, matrix, DIFFERENT_NONZERO_PATTERN );
return courseSolver;
}
int main(int argc,char **args)
{
Mat C,A;
PetscInt i,j;
PetscErrorCode ierr;
PetscScalar v;
PC pc;
Vec xtmp;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,3,3);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_WORLD,3,&xtmp);CHKERRQ(ierr);
i = 0; j = 0; v = 4;
ierr = MatSetValues(C,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
i = 0; j = 2; v = 1;
ierr = MatSetValues(C,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
i = 1; j = 0; v = 1;
ierr = MatSetValues(C,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
i = 1; j = 1; v = 4;
ierr = MatSetValues(C,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
i = 2; j = 1; v = 1;
ierr = MatSetValues(C,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PCCreate(PETSC_COMM_WORLD,&pc);CHKERRQ(ierr);
ierr = PCSetFromOptions(pc);CHKERRQ(ierr);
ierr = PCSetOperators(pc,C,C,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = PCSetUp(pc);CHKERRQ(ierr);
ierr = PCFactorGetMatrix(pc,&A);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PCDestroy(&pc);CHKERRQ(ierr);
ierr = VecDestroy(&xtmp);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
PC pc;
PetscErrorCode ierr;
PetscInt n = 5;
Mat mat;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = PCCreate(PETSC_COMM_WORLD,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCNONE);CHKERRQ(ierr);
/* Vector and matrix must be set before calling PCSetUp */
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,n,n,3,PETSC_NULL,&mat);CHKERRQ(ierr);
ierr = PCSetOperators(pc,mat,mat,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = PCSetUp(pc);CHKERRQ(ierr);
ierr = MatDestroy(&mat);CHKERRQ(ierr);
ierr = PCDestroy(&pc); CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
void PetscPreconditioner<T>::init ()
{
if(!this->_matrix)
{
libMesh::err << "ERROR: No matrix set for PetscPreconditioner, but init() called" << std::endl;
libmesh_error();
}
// Clear the preconditioner in case it has been created in the past
if (!this->_is_initialized)
{
// Should probably use PCReset(), but it's not working at the moment so we'll destroy instead
if (_pc)
{
int ierr = LibMeshPCDestroy(&_pc);
LIBMESH_CHKERRABORT(ierr);
}
int ierr = PCCreate(this->comm().get(),&_pc);
LIBMESH_CHKERRABORT(ierr);
PetscMatrix<T> * pmatrix = libmesh_cast_ptr<PetscMatrix<T>*, SparseMatrix<T> >(this->_matrix);
_mat = pmatrix->mat();
}
int ierr = PCSetOperators(_pc,_mat,_mat,SAME_NONZERO_PATTERN);
LIBMESH_CHKERRABORT(ierr);
// Set the PCType. Note: this used to be done *before* the call to
// PCSetOperators(), and only when !_is_initialized, but
// 1.) Some preconditioners (those employing sub-preconditioners,
// for example) have to call PCSetUp(), and can only do this after
// the operators have been set.
// 2.) It should be safe to call set_petsc_preconditioner_type()
// multiple times.
set_petsc_preconditioner_type(this->_preconditioner_type, _pc);
this->_is_initialized = true;
}
// =================================================
void PetscPreconditioner::init() {
if(!this->_matrix) {
std::cerr << "ERROR: No matrix set for PetscPreconditioner, but init() called" << std::endl;
abort();
}
//Clear the preconditioner in case it has been created in the past
if(!this->_is_initialized) {
//Create the preconditioning object
PCCreate(MPI_COMM_WORLD, &_pc);
//Set the PCType
set_petsc_preconditioner_type(this->_preconditioner_type, _pc);
// #ifdef LIBMESH_HAVE_PETSC_HYPRE
// if(this->_preconditioner_type == AMG_PRECOND)
// PCHYPRESetType(this->_pc, "boomerang");
// #endif
PetscMatrix * pmatrix = libmeshM_cast_ptr<PetscMatrix*, SparseMatrix >(this->_matrix);
_mat = pmatrix->mat();
}
//PCSetOperators(_pc,_mat,_mat,SAME_NONZERO_PATTERN);
PCSetOperators(_pc, _mat, _mat); //PETSC3p5
this->_is_initialized = true;
}
static PetscErrorCode PCCompositeAddPC_Composite(PC pc,PCType type)
{
PC_Composite *jac;
PC_CompositeLink next,ilink;
PetscErrorCode ierr;
PetscInt cnt = 0;
const char *prefix;
char newprefix[8];
PetscFunctionBegin;
ierr = PetscNewLog(pc,&ilink);CHKERRQ(ierr);
ilink->next = 0;
ierr = PCCreate(PetscObjectComm((PetscObject)pc),&ilink->pc);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)ilink->pc);CHKERRQ(ierr);
jac = (PC_Composite*)pc->data;
next = jac->head;
if (!next) {
jac->head = ilink;
ilink->previous = NULL;
} else {
cnt++;
while (next->next) {
next = next->next;
cnt++;
}
next->next = ilink;
ilink->previous = next;
}
ierr = PCGetOptionsPrefix(pc,&prefix);CHKERRQ(ierr);
ierr = PCSetOptionsPrefix(ilink->pc,prefix);CHKERRQ(ierr);
sprintf(newprefix,"sub_%d_",(int)cnt);
ierr = PCAppendOptionsPrefix(ilink->pc,newprefix);CHKERRQ(ierr);
/* type is set after prefix, because some methods may modify prefix, e.g. pcksp */
ierr = PCSetType(ilink->pc,type);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode PCBDDCNullSpaceAssembleCorrection(PC pc, PetscBool isdir, IS local_dofs)
{
PC_BDDC *pcbddc = (PC_BDDC*)pc->data;
PC_IS *pcis = (PC_IS*)pc->data;
Mat_IS* matis = (Mat_IS*)pc->pmat->data;
KSP local_ksp;
PC newpc;
NullSpaceCorrection_ctx shell_ctx;
Mat local_mat,local_pmat,small_mat,inv_small_mat;
Vec work1,work2;
const Vec *nullvecs;
VecScatter scatter_ctx;
IS is_aux;
MatFactorInfo matinfo;
PetscScalar *basis_mat,*Kbasis_mat,*array,*array_mat;
PetscScalar one = 1.0,zero = 0.0, m_one = -1.0;
PetscInt basis_dofs,basis_size,nnsp_size,i,k;
PetscBool nnsp_has_cnst;
PetscErrorCode ierr;
PetscFunctionBegin;
/* Infer the local solver */
ierr = ISGetSize(local_dofs,&basis_dofs);CHKERRQ(ierr);
if (isdir) {
/* Dirichlet solver */
local_ksp = pcbddc->ksp_D;
} else {
/* Neumann solver */
local_ksp = pcbddc->ksp_R;
}
ierr = KSPGetOperators(local_ksp,&local_mat,&local_pmat);CHKERRQ(ierr);
/* Get null space vecs */
ierr = MatNullSpaceGetVecs(pcbddc->NullSpace,&nnsp_has_cnst,&nnsp_size,&nullvecs);CHKERRQ(ierr);
basis_size = nnsp_size;
if (nnsp_has_cnst) {
basis_size++;
}
if (basis_dofs) {
/* Create shell ctx */
ierr = PetscNew(&shell_ctx);CHKERRQ(ierr);
/* Create work vectors in shell context */
ierr = VecCreate(PETSC_COMM_SELF,&shell_ctx->work_small_1);CHKERRQ(ierr);
ierr = VecSetSizes(shell_ctx->work_small_1,basis_size,basis_size);CHKERRQ(ierr);
ierr = VecSetType(shell_ctx->work_small_1,VECSEQ);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_small_1,&shell_ctx->work_small_2);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&shell_ctx->work_full_1);CHKERRQ(ierr);
ierr = VecSetSizes(shell_ctx->work_full_1,basis_dofs,basis_dofs);CHKERRQ(ierr);
ierr = VecSetType(shell_ctx->work_full_1,VECSEQ);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_full_1,&shell_ctx->work_full_2);CHKERRQ(ierr);
/* Allocate workspace */
ierr = MatCreateSeqDense(PETSC_COMM_SELF,basis_dofs,basis_size,NULL,&shell_ctx->basis_mat );CHKERRQ(ierr);
ierr = MatCreateSeqDense(PETSC_COMM_SELF,basis_dofs,basis_size,NULL,&shell_ctx->Kbasis_mat);CHKERRQ(ierr);
ierr = MatDenseGetArray(shell_ctx->basis_mat,&basis_mat);CHKERRQ(ierr);
ierr = MatDenseGetArray(shell_ctx->Kbasis_mat,&Kbasis_mat);CHKERRQ(ierr);
/* Restrict local null space on selected dofs (Dirichlet or Neumann)
and compute matrices N and K*N */
ierr = VecDuplicate(shell_ctx->work_full_1,&work1);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_full_1,&work2);CHKERRQ(ierr);
ierr = VecScatterCreate(pcis->vec1_N,local_dofs,work1,(IS)0,&scatter_ctx);CHKERRQ(ierr);
}
for (k=0;k<nnsp_size;k++) {
ierr = VecScatterBegin(matis->rctx,nullvecs[k],pcis->vec1_N,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(matis->rctx,nullvecs[k],pcis->vec1_N,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
if (basis_dofs) {
ierr = VecPlaceArray(work1,(const PetscScalar*)&basis_mat[k*basis_dofs]);CHKERRQ(ierr);
ierr = VecScatterBegin(scatter_ctx,pcis->vec1_N,work1,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(scatter_ctx,pcis->vec1_N,work1,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecPlaceArray(work2,(const PetscScalar*)&Kbasis_mat[k*basis_dofs]);CHKERRQ(ierr);
ierr = MatMult(local_mat,work1,work2);CHKERRQ(ierr);
ierr = VecResetArray(work1);CHKERRQ(ierr);
ierr = VecResetArray(work2);CHKERRQ(ierr);
}
}
if (basis_dofs) {
if (nnsp_has_cnst) {
ierr = VecPlaceArray(work1,(const PetscScalar*)&basis_mat[k*basis_dofs]);CHKERRQ(ierr);
ierr = VecSet(work1,one);CHKERRQ(ierr);
ierr = VecPlaceArray(work2,(const PetscScalar*)&Kbasis_mat[k*basis_dofs]);CHKERRQ(ierr);
ierr = MatMult(local_mat,work1,work2);CHKERRQ(ierr);
ierr = VecResetArray(work1);CHKERRQ(ierr);
ierr = VecResetArray(work2);CHKERRQ(ierr);
}
ierr = VecDestroy(&work1);CHKERRQ(ierr);
ierr = VecDestroy(&work2);CHKERRQ(ierr);
ierr = VecScatterDestroy(&scatter_ctx);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(shell_ctx->basis_mat,&basis_mat);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(shell_ctx->Kbasis_mat,&Kbasis_mat);CHKERRQ(ierr);
/* Assemble another Mat object in shell context */
ierr = MatTransposeMatMult(shell_ctx->basis_mat,shell_ctx->Kbasis_mat,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&small_mat);CHKERRQ(ierr);
ierr = MatFactorInfoInitialize(&matinfo);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,basis_size,0,1,&is_aux);CHKERRQ(ierr);
ierr = MatLUFactor(small_mat,is_aux,is_aux,&matinfo);CHKERRQ(ierr);
ierr = ISDestroy(&is_aux);CHKERRQ(ierr);
ierr = PetscMalloc1(basis_size*basis_size,&array_mat);CHKERRQ(ierr);
for (k=0;k<basis_size;k++) {
ierr = VecSet(shell_ctx->work_small_1,zero);CHKERRQ(ierr);
ierr = VecSetValue(shell_ctx->work_small_1,k,one,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(shell_ctx->work_small_1);CHKERRQ(ierr);
ierr = VecAssemblyEnd(shell_ctx->work_small_1);CHKERRQ(ierr);
ierr = MatSolve(small_mat,shell_ctx->work_small_1,shell_ctx->work_small_2);CHKERRQ(ierr);
ierr = VecGetArrayRead(shell_ctx->work_small_2,(const PetscScalar**)&array);CHKERRQ(ierr);
for (i=0;i<basis_size;i++) {
array_mat[i*basis_size+k]=array[i];
}
ierr = VecRestoreArrayRead(shell_ctx->work_small_2,(const PetscScalar**)&array);CHKERRQ(ierr);
}
ierr = MatCreateSeqDense(PETSC_COMM_SELF,basis_size,basis_size,array_mat,&inv_small_mat);CHKERRQ(ierr);
ierr = MatMatMult(shell_ctx->basis_mat,inv_small_mat,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&shell_ctx->Lbasis_mat);CHKERRQ(ierr);
ierr = PetscFree(array_mat);CHKERRQ(ierr);
ierr = MatDestroy(&inv_small_mat);CHKERRQ(ierr);
ierr = MatDestroy(&small_mat);CHKERRQ(ierr);
ierr = MatScale(shell_ctx->Kbasis_mat,m_one);CHKERRQ(ierr);
/* Rebuild local PC */
ierr = KSPGetPC(local_ksp,&shell_ctx->local_pc);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)shell_ctx->local_pc);CHKERRQ(ierr);
ierr = PCCreate(PETSC_COMM_SELF,&newpc);CHKERRQ(ierr);
ierr = PCSetOperators(newpc,local_mat,local_mat);CHKERRQ(ierr);
ierr = PCSetType(newpc,PCSHELL);CHKERRQ(ierr);
ierr = PCShellSetContext(newpc,shell_ctx);CHKERRQ(ierr);
ierr = PCShellSetApply(newpc,PCBDDCApplyNullSpaceCorrectionPC);CHKERRQ(ierr);
ierr = PCShellSetDestroy(newpc,PCBDDCDestroyNullSpaceCorrectionPC);CHKERRQ(ierr);
ierr = PCSetUp(newpc);CHKERRQ(ierr);
ierr = KSPSetPC(local_ksp,newpc);CHKERRQ(ierr);
ierr = PCDestroy(&newpc);CHKERRQ(ierr);
ierr = KSPSetUp(local_ksp);CHKERRQ(ierr);
}
/* test */
if (pcbddc->dbg_flag && basis_dofs) {
KSP check_ksp;
PC check_pc;
Mat test_mat;
Vec work3;
PetscReal test_err,lambda_min,lambda_max;
PetscBool setsym,issym=PETSC_FALSE;
PetscInt tabs;
ierr = PetscViewerASCIIGetTab(pcbddc->dbg_viewer,&tabs);CHKERRQ(ierr);
ierr = KSPGetPC(local_ksp,&check_pc);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_full_1,&work1);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_full_1,&work2);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_full_1,&work3);CHKERRQ(ierr);
ierr = VecSetRandom(shell_ctx->work_small_1,NULL);CHKERRQ(ierr);
ierr = MatMult(shell_ctx->basis_mat,shell_ctx->work_small_1,work1);CHKERRQ(ierr);
ierr = VecCopy(work1,work2);CHKERRQ(ierr);
ierr = MatMult(local_mat,work1,work3);CHKERRQ(ierr);
ierr = PCApply(check_pc,work3,work1);CHKERRQ(ierr);
ierr = VecAXPY(work1,m_one,work2);CHKERRQ(ierr);
ierr = VecNorm(work1,NORM_INFINITY,&test_err);CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"Subdomain %04d error for nullspace correction for ",PetscGlobalRank);CHKERRQ(ierr);
ierr = PetscViewerASCIIUseTabs(pcbddc->dbg_viewer,PETSC_FALSE);CHKERRQ(ierr);
if (isdir) {
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"Dirichlet ");CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"Neumann ");CHKERRQ(ierr);
}
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"solver is :%1.14e\n",test_err);CHKERRQ(ierr);
ierr = PetscViewerASCIISetTab(pcbddc->dbg_viewer,tabs);CHKERRQ(ierr);
ierr = PetscViewerASCIIUseTabs(pcbddc->dbg_viewer,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatTransposeMatMult(shell_ctx->Lbasis_mat,shell_ctx->Kbasis_mat,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&test_mat);CHKERRQ(ierr);
ierr = MatShift(test_mat,one);CHKERRQ(ierr);
ierr = MatNorm(test_mat,NORM_INFINITY,&test_err);CHKERRQ(ierr);
ierr = MatDestroy(&test_mat);CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"Subdomain %04d error for nullspace matrices is :%1.14e\n",PetscGlobalRank,test_err);CHKERRQ(ierr);
/* Create ksp object suitable for extreme eigenvalues' estimation */
ierr = KSPCreate(PETSC_COMM_SELF,&check_ksp);CHKERRQ(ierr);
ierr = KSPSetErrorIfNotConverged(check_ksp,pc->erroriffailure);CHKERRQ(ierr);
ierr = KSPSetOperators(check_ksp,local_mat,local_mat);CHKERRQ(ierr);
ierr = KSPSetTolerances(check_ksp,1.e-8,1.e-8,PETSC_DEFAULT,basis_dofs);CHKERRQ(ierr);
ierr = KSPSetComputeSingularValues(check_ksp,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatIsSymmetricKnown(pc->pmat,&setsym,&issym);CHKERRQ(ierr);
if (issym) {
ierr = KSPSetType(check_ksp,KSPCG);CHKERRQ(ierr);
}
ierr = KSPSetPC(check_ksp,check_pc);CHKERRQ(ierr);
ierr = KSPSetUp(check_ksp);CHKERRQ(ierr);
ierr = VecSetRandom(work1,NULL);CHKERRQ(ierr);
ierr = MatMult(local_mat,work1,work2);CHKERRQ(ierr);
ierr = KSPSolve(check_ksp,work2,work2);CHKERRQ(ierr);
ierr = VecAXPY(work2,m_one,work1);CHKERRQ(ierr);
ierr = VecNorm(work2,NORM_INFINITY,&test_err);CHKERRQ(ierr);
ierr = KSPComputeExtremeSingularValues(check_ksp,&lambda_max,&lambda_min);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(check_ksp,&k);CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"Subdomain %04d error for adapted KSP %1.14e (it %d, eigs %1.6e %1.6e)\n",PetscGlobalRank,test_err,k,lambda_min,lambda_max);CHKERRQ(ierr);
ierr = KSPDestroy(&check_ksp);CHKERRQ(ierr);
ierr = VecDestroy(&work1);CHKERRQ(ierr);
ierr = VecDestroy(&work2);CHKERRQ(ierr);
ierr = VecDestroy(&work3);CHKERRQ(ierr);
}
/* all processes shoud call this, even the void ones */
if (pcbddc->dbg_flag) {
ierr = PetscViewerFlush(pcbddc->dbg_viewer);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*MC
TSSUNDIALS - ODE solver using the LLNL CVODE/SUNDIALS package (now called SUNDIALS)
Options Database:
+ -ts_sundials_type <bdf,adams>
. -ts_sundials_gramschmidt_type <modified, classical> - type of orthogonalization inside GMRES
. -ts_sundials_atol <tol> - Absolute tolerance for convergence
. -ts_sundials_rtol <tol> - Relative tolerance for convergence
. -ts_sundials_linear_tolerance <tol>
. -ts_sundials_gmres_restart <restart> - Number of GMRES orthogonalization directions
. -ts_sundials_exact_final_time - Interpolate output to stop exactly at the final time
- -ts_sundials_monitor_steps - Monitor SUNDIALS internel steps
Notes: This uses its own nonlinear solver and Krylov method so PETSc SNES and KSP options do not apply
only PETSc PC options
Level: beginner
.seealso: TSCreate(), TS, TSSetType(), TSSundialsSetType(), TSSundialsSetGMRESRestart(), TSSundialsSetLinearTolerance(),
TSSundialsSetGramSchmidtType(), TSSundialsSetTolerance(), TSSundialsGetPC(), TSSundialsGetIterations(), TSSundialsSetExactFinalTime()
M*/
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "TSCreate_Sundials"
PetscErrorCode PETSCTS_DLLEXPORT TSCreate_Sundials(TS ts)
{
TS_Sundials *cvode;
PetscErrorCode ierr;
PetscFunctionBegin;
if (ts->problem_type != TS_NONLINEAR) {
SETERRQ(PETSC_ERR_SUP,"Only support for nonlinear problems");
}
ts->ops->destroy = TSDestroy_Sundials;
ts->ops->view = TSView_Sundials;
ts->ops->setup = TSSetUp_Sundials_Nonlinear;
ts->ops->step = TSStep_Sundials_Nonlinear;
ts->ops->setfromoptions = TSSetFromOptions_Sundials_Nonlinear;
ierr = PetscNewLog(ts,TS_Sundials,&cvode);CHKERRQ(ierr);
ierr = PCCreate(((PetscObject)ts)->comm,&cvode->pc);CHKERRQ(ierr);
ierr = PetscLogObjectParent(ts,cvode->pc);CHKERRQ(ierr);
ts->data = (void*)cvode;
cvode->cvode_type = SUNDIALS_BDF;
cvode->gtype = SUNDIALS_CLASSICAL_GS;
cvode->restart = 5;
cvode->linear_tol = .05;
cvode->exact_final_time = PETSC_TRUE;
cvode->monitorstep = PETSC_FALSE;
ierr = MPI_Comm_dup(((PetscObject)ts)->comm,&(cvode->comm_sundials));CHKERRQ(ierr);
/* set tolerance for Sundials */
cvode->reltol = 1e-6;
cvode->abstol = 1e-6;
ierr = PetscObjectComposeFunctionDynamic((PetscObject)ts,"TSSundialsSetType_C","TSSundialsSetType_Sundials",
TSSundialsSetType_Sundials);CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)ts,"TSSundialsSetGMRESRestart_C",
"TSSundialsSetGMRESRestart_Sundials",
TSSundialsSetGMRESRestart_Sundials);CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)ts,"TSSundialsSetLinearTolerance_C",
"TSSundialsSetLinearTolerance_Sundials",
TSSundialsSetLinearTolerance_Sundials);CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)ts,"TSSundialsSetGramSchmidtType_C",
"TSSundialsSetGramSchmidtType_Sundials",
TSSundialsSetGramSchmidtType_Sundials);CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)ts,"TSSundialsSetTolerance_C",
"TSSundialsSetTolerance_Sundials",
TSSundialsSetTolerance_Sundials);CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)ts,"TSSundialsGetPC_C",
"TSSundialsGetPC_Sundials",
TSSundialsGetPC_Sundials);CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)ts,"TSSundialsGetIterations_C",
"TSSundialsGetIterations_Sundials",
TSSundialsGetIterations_Sundials);CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)ts,"TSSundialsSetExactFinalTime_C",
"TSSundialsSetExactFinalTime_Sundials",
TSSundialsSetExactFinalTime_Sundials);CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)ts,"TSSundialsMonitorInternalSteps_C",
"TSSundialsMonitorInternalSteps_Sundials",
TSSundialsMonitorInternalSteps_Sundials);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat mat; /* matrix */
Vec b,ustar,u; /* vectors (RHS, exact solution, approx solution) */
PC pc; /* PC context */
KSP ksp; /* KSP context */
PetscErrorCode ierr;
PetscInt n = 10,i,its,col[3];
PetscScalar value[3];
PCType pcname;
KSPType kspname;
PetscReal norm,tol=1000.*PETSC_MACHINE_EPSILON;
PetscInitialize(&argc,&args,(char*)0,help);
/* Create and initialize vectors */
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&b);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&ustar);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&u);CHKERRQ(ierr);
ierr = VecSet(ustar,1.0);CHKERRQ(ierr);
ierr = VecSet(u,0.0);CHKERRQ(ierr);
/* Create and assemble matrix */
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,n,n,3,NULL,&mat);CHKERRQ(ierr);
value[0] = -1.0; value[1] = 2.0; value[2] = -1.0;
for (i=1; i<n-1; i++) {
col[0] = i-1; col[1] = i; col[2] = i+1;
ierr = MatSetValues(mat,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
i = n - 1; col[0] = n - 2; col[1] = n - 1;
ierr = MatSetValues(mat,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
i = 0; col[0] = 0; col[1] = 1; value[0] = 2.0; value[1] = -1.0;
ierr = MatSetValues(mat,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Compute right-hand-side vector */
ierr = MatMult(mat,ustar,b);CHKERRQ(ierr);
/* Create PC context and set up data structures */
ierr = PCCreate(PETSC_COMM_WORLD,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCNONE);CHKERRQ(ierr);
ierr = PCSetFromOptions(pc);CHKERRQ(ierr);
ierr = PCSetOperators(pc,mat,mat);CHKERRQ(ierr);
ierr = PCSetUp(pc);CHKERRQ(ierr);
/* Create KSP context and set up data structures */
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPRICHARDSON);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = PCSetOperators(pc,mat,mat);CHKERRQ(ierr);
ierr = KSPSetPC(ksp,pc);CHKERRQ(ierr);
ierr = KSPSetUp(ksp);CHKERRQ(ierr);
/* Solve the problem */
ierr = KSPGetType(ksp,&kspname);CHKERRQ(ierr);
ierr = PCGetType(pc,&pcname);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"Running %s with %s preconditioning\n",kspname,pcname);CHKERRQ(ierr);
ierr = KSPSolve(ksp,b,u);CHKERRQ(ierr);
ierr = VecAXPY(u,-1.0,ustar);CHKERRQ(ierr);
ierr = VecNorm(u,NORM_2,&norm);
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"2 norm of error %g Number of iterations %D\n",(double)norm,its);CHKERRQ(ierr);
}
/* Free data structures */
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&ustar);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = MatDestroy(&mat);CHKERRQ(ierr);
ierr = PCDestroy(&pc);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PETSC_EXTERN void PETSC_STDCALL pccreate_(MPI_Fint * comm,PC *newpc, int *__ierr ){
*__ierr = PCCreate(
MPI_Comm_f2c( *(comm) ),newpc);
}
