void PetscMatrix<Scalar>::alloc()
{
assert(this->pages != nullptr);
// calc nnz
int *nnz_array = malloc_with_check(this->size, this);
// fill in nnz_array
int aisize = this->get_num_indices();
int *ai = malloc_with_check(aisize, this);
// sort the indices and remove duplicities, insert into ai
int pos = 0;
for (unsigned int i = 0; i < this->size; i++)
{
nnz_array[i] = this->sort_and_store_indices(this->pages[i], ai + pos, ai + aisize);
pos += nnz_array[i];
}
// stote the number of nonzeros
nnz = pos;
free_with_check(this->pages; this->pages = nullptr);
free_with_check(ai);
//
MatCreateSeqAIJ(PETSC_COMM_SELF, this->size, this->size, 0, nnz_array, &matrix);
// MatSetOption(matrix, MAT_ROW_ORIENTED);
// MatSetOption(matrix, MAT_ROWS_SORTED);
free_with_check(nnz_array);
inited = true;
}
int main(int argc,char **args)
{
const PetscInt inds[] = {0,1};
PetscScalar avals[] = {2,3,5,7};
Mat S;
User user;
PetscErrorCode ierr;
Vec base;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscNew(&user);CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,2,2,2,NULL,&user->B);CHKERRQ(ierr);
ierr = MatSetUp(user->B);CHKERRQ(ierr);
ierr = MatSetValues(user->B,2,inds,2,inds,avals,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatCreateVecs(user->B,&base,NULL);CHKERRQ(ierr);
ierr = MatCreateShell(PETSC_COMM_WORLD,2,2,2,2,user,&S);CHKERRQ(ierr);
ierr = MatSetUp(S);CHKERRQ(ierr);
ierr = MatShellSetOperation(S,MATOP_MULT,(void (*)(void))MatMult_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S,MATOP_MULT_TRANSPOSE,(void (*)(void))MatMultTranspose_User);CHKERRQ(ierr);
ierr = MatShellTestMult(S,MyFunction,base,user,NULL);CHKERRQ(ierr);
ierr = MatShellTestMultTranspose(S,MyFunction,base,user,NULL);CHKERRQ(ierr);
ierr = VecDestroy(&base);CHKERRQ(ierr);
ierr = MatDestroy(&user->B);CHKERRQ(ierr);
ierr = MatDestroy(&S);CHKERRQ(ierr);
ierr = PetscFree(user);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
void PetscMatrix::alloc() {
_F_
#ifdef WITH_PETSC
assert(pages != NULL);
// calc nnz
int *nnz_array = new int[size];
MEM_CHECK(nnz_array);
// fill in nnz_array
int aisize = get_num_indices();
int *ai = new int[aisize];
MEM_CHECK(ai);
// sort the indices and remove duplicities, insert into ai
int pos = 0;
for (unsigned int i = 0; i < size; i++) {
nnz_array[i] = sort_and_store_indices(pages[i], ai + pos, ai + aisize);
pos += nnz_array[i];
}
// stote the number of nonzeros
nnz = pos;
delete [] pages; pages = NULL;
delete [] ai;
//
MatCreateSeqAIJ(PETSC_COMM_SELF, size, size, 0, nnz_array, &matrix);
// MatSetOption(matrix, MAT_ROW_ORIENTED);
// MatSetOption(matrix, MAT_ROWS_SORTED);
delete [] nnz_array;
inited = true;
#endif
}
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;
}
int main(int argc,char **argv) {
Mat A,B,As;
const PetscInt *ai,*aj;
PetscInt i,j,k,nz,n,asi[]={0,2,3,4,6,7};
PetscInt asj[]={0,4,1,2,3,4,4};
PetscScalar asa[7],*aa;
PetscRandom rctx;
PetscErrorCode ierr;
PetscMPIInt size;
PetscBool flg;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a uniprocessor example only!");
/* Create a aij matrix for checking */
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,5,5,2,PETSC_NULL,&A);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
k = 0;
for (i=0; i<5; i++) {
nz = asi[i+1] - asi[i]; /* length of i_th row of A */
for (j=0; j<nz; j++){
ierr = PetscRandomGetValue(rctx,&asa[k]);CHKERRQ(ierr);
ierr = MatSetValues(A,1,&i,1,&asj[k],&asa[k],INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(A,1,&i,1,&asj[k],&asa[k],INSERT_VALUES);CHKERRQ(ierr);
if (i != asj[k]){ /* insert symmetric entry */
ierr = MatSetValues(A,1,&asj[k],1,&i,&asa[k],INSERT_VALUES);CHKERRQ(ierr);
}
k++;
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Create a baij matrix using MatCreateSeqBAIJWithArrays() */
ierr = MatGetRowIJ(A,0,PETSC_FALSE,PETSC_FALSE,&n,&ai,&aj,&flg);CHKERRQ(ierr);
ierr = MatSeqAIJGetArray(A,&aa);CHKERRQ(ierr);
/* WARNING: This sharing is dangerous if either A or B is later assembled */
ierr = MatCreateSeqBAIJWithArrays(PETSC_COMM_SELF,1,5,5,(PetscInt*)ai,(PetscInt*)aj,aa,&B);CHKERRQ(ierr);
ierr = MatSeqAIJRestoreArray(A,&aa);CHKERRQ(ierr);
ierr = MatRestoreRowIJ(A,0,PETSC_FALSE,PETSC_FALSE,&n,&ai,&aj,&flg);CHKERRQ(ierr);
ierr = MatMultEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"MatMult(A,B) are NOT equal");
/* Create a sbaij matrix using MatCreateSeqSBAIJWithArrays() */
ierr = MatCreateSeqSBAIJWithArrays(PETSC_COMM_SELF,1,5,5,asi,asj,asa,&As);CHKERRQ(ierr);
ierr = MatMultEqual(A,As,10,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"MatMult(A,As) are NOT equal");
/* Free spaces */
ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&As);CHKERRQ(ierr);
ierr = PetscFinalize();
return(0);
}
PetscErrorCode InitializeProblem(AppCtx *user)
{
PetscErrorCode ierr;
PetscFunctionBegin;
user->n = 2;
ierr = VecCreateSeq(PETSC_COMM_SELF,user->n,&user->x);
CHKERRQ(ierr);
ierr = VecDuplicate(user->x,&user->xl);
CHKERRQ(ierr);
ierr = VecDuplicate(user->x,&user->xu);
CHKERRQ(ierr);
ierr = VecSet(user->x,0.0);
CHKERRQ(ierr);
ierr = VecSet(user->xl,-1.0);
CHKERRQ(ierr);
ierr = VecSet(user->xu,2.0);
CHKERRQ(ierr);
user->ne = 1;
ierr = VecCreateSeq(PETSC_COMM_SELF,user->ne,&user->ce);
CHKERRQ(ierr);
user->ni = 2;
ierr = VecCreateSeq(PETSC_COMM_SELF,user->ni,&user->ci);
CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,user->ne,user->n,user->n,NULL,&user->Ae);
CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,user->ni,user->n,user->n,NULL,&user->Ai);
CHKERRQ(ierr);
ierr = MatSetFromOptions(user->Ae);
CHKERRQ(ierr);
ierr = MatSetFromOptions(user->Ai);
CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,user->n,user->n,1,NULL,&user->H);
CHKERRQ(ierr);
ierr = MatSetFromOptions(user->H);
CHKERRQ(ierr);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void Field_solver::alloc_petsc_matrix_seqaij( Mat *A, PetscInt nrow,
PetscInt ncol, PetscInt nonzero_per_row )
{
PetscErrorCode ierr;
ierr = MatCreateSeqAIJ( PETSC_COMM_SELF, nrow, ncol,
nonzero_per_row, NULL, A ); CHKERRXX( ierr );
ierr = MatSetUp( *A ); CHKERRXX( ierr );
return;
}
int main(int argc,char **args)
{
Mat A,B,*Bsub;
PetscInt i,j,m = 6,n = 6,N = 36,Ii,J;
PetscErrorCode ierr;
PetscScalar v;
IS isrow;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,N,N,5,NULL,&A);CHKERRQ(ierr);
for (i=0; i<m; i++) {
for (j=0; j<n; j++) {
v = -1.0; Ii = j + n*i;
if (i>0) {J = Ii - n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (i<m-1) {J = Ii + n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j>0) {J = Ii - 1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j<n-1) {J = Ii + 1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
v = 4.0; ierr = MatSetValues(A,1,&Ii,1,&Ii,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
/* take the first diagonal block */
ierr = ISCreateStride(PETSC_COMM_WORLD,m,0,1,&isrow);CHKERRQ(ierr);
ierr = MatGetSubMatrices(A,1,&isrow,&isrow,MAT_INITIAL_MATRIX,&Bsub);CHKERRQ(ierr);
B = *Bsub;
ierr = PetscFree(Bsub);CHKERRQ(ierr);
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
/* take a strided block */
ierr = ISCreateStride(PETSC_COMM_WORLD,m,0,2,&isrow);CHKERRQ(ierr);
ierr = MatGetSubMatrices(A,1,&isrow,&isrow,MAT_INITIAL_MATRIX,&Bsub);CHKERRQ(ierr);
B = *Bsub;
ierr = PetscFree(Bsub);CHKERRQ(ierr);
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
/* take the last block */
ierr = ISCreateStride(PETSC_COMM_WORLD,m,N-m-1,1,&isrow);CHKERRQ(ierr);
ierr = MatGetSubMatrices(A,1,&isrow,&isrow,MAT_INITIAL_MATRIX,&Bsub);CHKERRQ(ierr);
B = *Bsub;
ierr = PetscFree(Bsub);CHKERRQ(ierr);
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
void FEMAssemble2DElasticity(MPI_Comm comm, Mesh *mesh, Mat &A, Vec &b,
PetscReal E, PetscReal mi, PetscReal(*dens)(Element *),
void(*f)(Element*, PetscReal, PetscReal*)) {
PetscInt rank;
MPI_Comm_rank(comm, &rank);
PetscInt size = mesh->vetrices.size();
MatCreateSeqAIJ(PETSC_COMM_SELF, size * 2, size * 2, 14, PETSC_NULL, &A);
VecCreateMPI(comm, size * 2, PETSC_DECIDE, &b);
for (std::map<PetscInt, Element*>::iterator e = mesh->elements.begin(); e
!= mesh->elements.end(); e++) {
Point* vetrices[3];
PetscInt vIndex[3];
for (int i = 0; i < 3; i++) {
vIndex[i] = e->second->vetrices[i];
vetrices[i] = mesh->vetrices[vIndex[i]];
}
PetscReal lStiff[36];
PetscReal bLoc[6];
//Local stiffness matrix and force vector assembly
PetscReal fs[2];
f(e->second, dens(e->second), fs);
elastLoc(vetrices, E, mi, fs, lStiff, bLoc);
PetscInt idx[6], idxLoc[6];
for (int i = 0; i < 3; i++) {
idx[i * 2] = vIndex[i] * 2;
idx[i * 2 + 1] = vIndex[i] * 2 + 1;
idxLoc[i * 2] = vIndex[i] * 2 - mesh->startIndexes[rank] * 2;
idxLoc[i * 2 + 1] = vIndex[i] * 2 + 1 - mesh->startIndexes[rank] * 2;
}
MatSetValues(A, 6, idxLoc, 6, idxLoc, lStiff, ADD_VALUES);
VecSetValues(b, 6, idx, bLoc, ADD_VALUES);
}
VecAssemblyBegin(b);
VecAssemblyEnd(b);
MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
}
int main(int argc,char **args)
{
const PetscScalar xvals[] = {11,13},yvals[] = {17,19};
const PetscInt inds[] = {0,1};
PetscScalar avals[] = {2,3,5,7};
Mat S1,S2;
Vec X,Y;
User user;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscNew(&user);CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,2,2,2,NULL,&user->A);CHKERRQ(ierr);
ierr = MatSetUp(user->A);CHKERRQ(ierr);
ierr = MatSetValues(user->A,2,inds,2,inds,avals,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_WORLD,2,&X);CHKERRQ(ierr);
ierr = VecSetValues(X,2,inds,xvals,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(X);CHKERRQ(ierr);
ierr = VecAssemblyEnd(X);CHKERRQ(ierr);
ierr = VecDuplicate(X,&Y);CHKERRQ(ierr);
ierr = VecSetValues(Y,2,inds,yvals,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(Y);CHKERRQ(ierr);
ierr = VecAssemblyEnd(Y);CHKERRQ(ierr);
ierr = MatCreateShell(PETSC_COMM_WORLD,2,2,2,2,user,&S1);CHKERRQ(ierr);
ierr = MatSetUp(S1);CHKERRQ(ierr);
ierr = MatShellSetOperation(S1,MATOP_MULT,(void (*)(void))MatMult_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S1,MATOP_COPY,(void (*)(void))MatCopy_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S1,MATOP_DESTROY,(void (*)(void))MatDestroy_User);CHKERRQ(ierr);
ierr = MatCreateShell(PETSC_COMM_WORLD,2,2,2,2,NULL,&S2);CHKERRQ(ierr);
ierr = MatSetUp(S2);CHKERRQ(ierr);
ierr = MatShellSetOperation(S2,MATOP_MULT,(void (*)(void))MatMult_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S2,MATOP_COPY,(void (*)(void))MatCopy_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S2,MATOP_DESTROY,(void (*)(void))MatDestroy_User);CHKERRQ(ierr);
ierr = MatScale(S1,31);CHKERRQ(ierr);
ierr = MatShift(S1,37);CHKERRQ(ierr);
ierr = MatDiagonalScale(S1,X,Y);CHKERRQ(ierr);
ierr = MatCopy(S1,S2,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatMult(S1,X,Y);CHKERRQ(ierr);
ierr = VecView(Y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatMult(S2,X,Y);CHKERRQ(ierr);
ierr = VecView(Y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&S1);CHKERRQ(ierr);
ierr = MatDestroy(&S2);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&Y);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode PadMatrix(Mat A,Vec v,PetscScalar c,Mat *B)
{
PetscErrorCode ierr;
PetscInt n = A->rmap->n,i,*cnt,*indices;
Mat_SeqAIJ *aij = (Mat_SeqAIJ*)A->data;
PetscScalar *vv;
PetscFunctionBegin;
ierr = VecGetArray(v,&vv);
CHKERRQ(ierr);
ierr = PetscMalloc(n*sizeof(PetscInt),&indices);
CHKERRQ(ierr);
for (i=0; i<n; i++) indices[i] = i;
/* determine number of nonzeros per row in the new matrix */
ierr = PetscMalloc((n+1)*sizeof(PetscInt),&cnt);
CHKERRQ(ierr);
for (i=0; i<n; i++) {
cnt[i] = aij->i[i+1] - aij->i[i] + (vv[i] != 0.0);
}
cnt[n] = 1;
for (i=0; i<n; i++) {
cnt[n] += (vv[i] != 0.0);
}
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,n+1,n+1,0,cnt,B);
CHKERRQ(ierr);
ierr = MatSetOption(*B,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE);
CHKERRQ(ierr);
/* copy over the matrix entries from the matrix and then the vector */
for (i=0; i<n; i++) {
ierr = MatSetValues(*B,1,&i,aij->i[i+1] - aij->i[i],aij->j + aij->i[i],aij->a + aij->i[i],INSERT_VALUES);
CHKERRQ(ierr);
}
ierr = MatSetValues(*B,1,&n,n,indices,vv,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatSetValues(*B,n,indices,1,&n,vv,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatSetValues(*B,1,&n,1,&n,&c,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = VecRestoreArray(v,&vv);
CHKERRQ(ierr);
ierr = PetscFree(cnt);
CHKERRQ(ierr);
ierr = PetscFree(indices);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode TaoPounders(AppCtx *user)
{
PetscErrorCode ierr;
Tao tao;
Vec X, F;
Mat J;
char buf[1024];
PetscFunctionBegin;
/* Set the values for the algorithm options we want to use */
sprintf(buf,"%d",user->nfmax);
ierr = PetscOptionsSetValue(NULL,"-tao_max_funcs",buf);CHKERRQ(ierr);
sprintf(buf,"%d",user->npmax);
ierr = PetscOptionsSetValue(NULL,"-tao_pounders_npmax",buf);CHKERRQ(ierr);
sprintf(buf,"%5.4e",user->delta);
ierr = PetscOptionsSetValue(NULL,"-tao_pounders_delta",buf);CHKERRQ(ierr);
/* Create the TAO objects and set the type */
ierr = TaoCreate(PETSC_COMM_SELF,&tao);CHKERRQ(ierr);
/* Create starting point and initialize */
ierr = VecCreateSeq(PETSC_COMM_SELF,user->n,&X);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)X,"X0");CHKERRQ(ierr);
ierr = PetscMatlabEngineGet(user->mengine,(PetscObject)X);CHKERRQ(ierr);
ierr = TaoSetInitialVector(tao,X);CHKERRQ(ierr);
/* Create residuals vector and set residual function */
ierr = VecCreateSeq(PETSC_COMM_SELF,user->m,&F);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)F,"F");CHKERRQ(ierr);
ierr = TaoSetResidualRoutine(tao,F,EvaluateResidual,(void*)user);CHKERRQ(ierr);
/* Create Jacobian matrix and set residual Jacobian routine */
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,user->m,user->n,user->n,NULL,&J);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)J,"J");CHKERRQ(ierr);
ierr = TaoSetResidualJacobianRoutine(tao,J,J,EvaluateJacobian,(void*)user);CHKERRQ(ierr);
/* Solve the problem */
ierr = TaoSetType(tao,TAOPOUNDERS);CHKERRQ(ierr);
ierr = TaoSetFromOptions(tao);CHKERRQ(ierr);
ierr = TaoSolve(tao);CHKERRQ(ierr);
/* Finish the problem */
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&F);CHKERRQ(ierr);
ierr = TaoDestroy(&tao);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int MatRead(char *fileA, PetscInt& n, Mat& A)
{
PetscInt *arrayIA, *arrayJA, // arrays of rows and columns of A
*nnzA, // number of nonzeros in each row
nzA; // number of nonzeros in matrix A
PetscScalar *arrayVA; // array of values of A
int read_error = 0;
if (readSparseMatrix(fileA, n, nzA, nnzA, arrayIA, arrayJA, arrayVA)) {
// read_error in reading in the vector, set read_error to 1
read_error = 1;
}
/*---------------------------------------------------------------------------
* set up the matrix A
*---------------------------------------------------------------------------*/
MatCreateSeqAIJ(MPI_COMM_SELF, n, n, nzA, nnzA, &A);
/*---------------------------------------------------------------------------
* set the values of matrix A
*---------------------------------------------------------------------------*/
/*
PetscMalloc1(n * sizeof(PetscInt), &idx);
for (PetscInt i = 0; i < n; ++i) {
idx[i] = i;
}
MatSetValues(A, n, idx, n, idx, arrayA, INSERT_VALUES);
*/
for (PetscInt i = 0; i < nzA; ++i) {
MatSetValue(A, arrayIA[i], arrayJA[i], arrayVA[i], INSERT_VALUES);
if (arrayIA[i] != arrayJA[i]) {
MatSetValue(A, arrayJA[i], arrayIA[i], arrayVA[i], INSERT_VALUES);
}
}
/*---------------------------------------------------------------------------
* assemble the matrix A
*---------------------------------------------------------------------------*/
MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
free(nnzA);
free(arrayIA);
free(arrayJA);
free(arrayVA);
}
PetscErrorCode AssemblePoissonPC2(int m, int n, Mat *A) {
PetscErrorCode ierr;
double *x, *y;
PetscFunctionBegin;
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF, m*n, m*n, 5, PETSC_NULL, A); CHKERRQ(ierr);
ierr = PetscMalloc2(m, double, &x, n, double, &y); CHKERRQ(ierr);
for (int i = 0; i < m; i++) x[i] = cos(i * PI / (m - 1));
for (int j = 0; j < n; j++) y[j] = cos(j * PI / (n - 1));
// Strong Dirichlet everywhere, then overwrite with correct values in the interior.
for (int I = 0; I < m*n; I++) {
ierr = MatSetValue(*A, I, I, 1.0, INSERT_VALUES); CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(*A,MAT_FLUSH_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*A,MAT_FLUSH_ASSEMBLY);CHKERRQ(ierr);
int J[5];
double v[5];
for (int i = 1; i < m - 1; i++) {
for (int j = 1; j < n - 1; j++) {
const int I = i * n + j;
const bool f = true;
// const double X = x[I], Y = y[I];
// J[0] = I - n; J[1] = I - 1; J[2] = I; J[3] = I + 1; J[4] = I + n;
int k=0;
if (f && i != 1) { J[k] = I-n; v[k++] = -1.0 / ((x[i-1] - x[i]) * (x[i-1] - x[i+1])); }
if (f && j != 1) { J[k] = I-1; v[k++] = -1.0 / ((y[j-1] - y[j]) * (y[j-1] - y[j+1])); }
J[k] = I; v[k++] = -( 1.0 / ((x[i] - x[i-1]) * (x[i] - x[i+1]))
+ 1.0 / ((y[j] - y[j-1]) * (y[j] - y[j+1])));
if (f && j != n-2) { J[k] = I+1; v[k++] = -1.0 / ((y[j+1] - y[j-1]) * (y[j+1] - y[j])); }
if (f && i != m-2) { J[k] = I+n; v[k++] = -1.0 / ((x[i+1] - x[i-1]) * (x[i+1] - x[i])); }
ierr = MatSetValues(*A, 1, &I, k, J, v, INSERT_VALUES); CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscFree2(x, y); CHKERRQ(ierr);
PetscFunctionReturn(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;
}
op_mat op_decl_mat( op_sparsity sparsity, int dim, char const * type, int type_size, char const * name )
{
assert( sparsity );
op_mat mat = op_decl_mat_core ( sparsity->rowmap->to, sparsity->colmap->to, dim, type, type_size, name );
Mat p_mat;
// Create a PETSc CSR sparse matrix and pre-allocate storage
MatCreateSeqAIJ(PETSC_COMM_SELF,
sparsity->nrows,
sparsity->ncols,
sparsity->max_nonzeros,
(const PetscInt*)sparsity->nnz,
&p_mat);
// Set the column indices (FIXME: benchmark if this is worth it)
MatSeqAIJSetColumnIndices(p_mat, (PetscInt*)sparsity->colidx);
MatZeroEntries(p_mat);
mat->mat = p_mat;
return mat;
}
PetscErrorCode Create1dLaplacian(PetscInt n,Mat *mat)
{
PetscScalar mone = -1.0,two = 2.0;
PetscInt i,idx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,n,n,3,NULL,mat);CHKERRQ(ierr);
idx = n-1;
ierr = MatSetValues(*mat,1,&idx,1,&idx,&two,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<n-1; i++) {
ierr = MatSetValues(*mat,1,&i,1,&i,&two,INSERT_VALUES);CHKERRQ(ierr);
idx = i+1;
ierr = MatSetValues(*mat,1,&idx,1,&i,&mone,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(*mat,1,&i,1,&idx,&mone,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat A;
PetscErrorCode ierr;
PetscInt m = 100,n = 11,js[11],i,j,cnt;
PetscScalar values[11];
PetscViewer view;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,m,n,20,0,&A);CHKERRQ(ierr);
for (i=0; i<n; i++) values[i] = (PetscReal)i;
for (i=0; i<m; i++) {
cnt = 0;
if (i % 2) {
for (j=0; j<n; j += 2) {
js[cnt++] = j;
}
} else {
;
}
ierr = MatSetValues(A,1,&i,cnt,js,values,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"rect",FILE_MODE_WRITE,&view);CHKERRQ(ierr);
ierr = MatView(A,view);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat C,A;
PetscInt i,j,m = 5,n = 5,Ii,J;
PetscErrorCode ierr;
PetscScalar v,five = 5.0,one = 1.0;
IS isrow,row,col;
Vec x,u,b;
PetscReal norm;
MatFactorInfo info;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,m*n,m*n,5,NULL,&C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
/* create the matrix for the five point stencil, YET AGAIN*/
for (i=0; i<m; i++) {
for (j=0; j<n; j++) {
v = -1.0; Ii = j + n*i;
if (i>0) {J = Ii - n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (i<m-1) {J = Ii + n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j>0) {J = Ii - 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j<n-1) {J = Ii + 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
v = 4.0; ierr = MatSetValues(C,1,&Ii,1,&Ii,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,(m*n)/2,0,2,&isrow);CHKERRQ(ierr);
ierr = MatZeroRowsIS(C,isrow,five,0,0);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,m*n,&u);CHKERRQ(ierr);
ierr = VecDuplicate(u,&x);CHKERRQ(ierr);
ierr = VecDuplicate(u,&b);CHKERRQ(ierr);
ierr = VecSet(u,one);CHKERRQ(ierr);
ierr = MatMultTranspose(C,u,b);CHKERRQ(ierr);
/* Set default ordering to be Quotient Minimum Degree; also read
orderings from the options database */
ierr = MatGetOrdering(C,MATORDERINGQMD,&row,&col);CHKERRQ(ierr);
ierr = MatFactorInfoInitialize(&info);CHKERRQ(ierr);
ierr = MatGetFactor(C,MATSOLVERPETSC,MAT_FACTOR_LU,&A);CHKERRQ(ierr);
ierr = MatLUFactorSymbolic(A,C,row,col,&info);CHKERRQ(ierr);
ierr = MatLUFactorNumeric(A,C,&info);CHKERRQ(ierr);
ierr = MatSolveTranspose(A,b,x);CHKERRQ(ierr);
ierr = ISView(row,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = VecAXPY(x,-1.0,u);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"Norm of error %g\n",(double)norm);CHKERRQ(ierr);
ierr = ISDestroy(&row);CHKERRQ(ierr);
ierr = ISDestroy(&col);CHKERRQ(ierr);
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat C;
PetscErrorCode ierr;
PetscInt i,m = 2,N,M,idx[4],Nsub1,Nsub2,ol=1,x1,x2;
PetscScalar Ke[16];
PetscReal x,y,h;
IS *is1,*is2;
PetscBool flg;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,PETSC_NULL);
CHKERRQ(ierr);
N = (m+1)*(m+1); /* dimension of matrix */
M = m*m; /* number of elements */
h = 1.0/m; /* mesh width */
x1= (m+1)/2;
x2= x1;
ierr = PetscOptionsGetInt(PETSC_NULL,"-x1",&x1,PETSC_NULL);
CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-x2",&x2,PETSC_NULL);
CHKERRQ(ierr);
/* create stiffness matrix */
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,9,PETSC_NULL,&C);
CHKERRQ(ierr);
/* forms the element stiffness for the Laplacian */
ierr = FormElementStiffness(h*h,Ke);
CHKERRQ(ierr);
for (i=0; i<M; i++) {
/* location of lower left corner of element */
x = h*(i % m);
y = h*(i/m);
/* node numbers for the four corners of element */
idx[0] = (m+1)*(i/m) + (i % m);
idx[1] = idx[0]+1;
idx[2] = idx[1] + m + 1;
idx[3] = idx[2] - 1;
ierr = MatSetValues(C,4,idx,4,idx,Ke,ADD_VALUES);
CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
for (ol=0; ol<m+2; ++ol) {
ierr = PCASMCreateSubdomains2D(m+1,m+1,x1,x2,1,0,&Nsub1,&is1);
CHKERRQ(ierr);
ierr = MatIncreaseOverlap(C,Nsub1,is1,ol);
CHKERRQ(ierr);
ierr = PCASMCreateSubdomains2D(m+1,m+1,x1,x2,1,ol,&Nsub2,&is2);
CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"flg == 1 => both index sets are same\n");
CHKERRQ(ierr);
if(Nsub1 != Nsub2) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: No of indes sets don't match\n");
CHKERRQ(ierr);
}
for (i=0; i<Nsub1; ++i) {
ierr = ISEqual(is1[i],is2[i],&flg);
CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"i = %D,flg = %d \n",i,(int)flg);
CHKERRQ(ierr);
}
for (i=0; i<Nsub1; ++i) {
ierr = ISDestroy(&&is1[i]);
CHKERRQ(ierr);
}
for (i=0; i<Nsub2; ++i) {
ierr = ISDestroy(&&is2[i]);
CHKERRQ(ierr);
}
ierr = PetscFree(is1);
CHKERRQ(ierr);
ierr = PetscFree(is2);
CHKERRQ(ierr);
}
ierr = MatDestroy(&C);
CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/*
GetElasticityMatrix - Forms 3D linear elasticity matrix.
*/
PetscErrorCode GetElasticityMatrix(PetscInt m,Mat *newmat)
{
PetscInt i,j,k,i1,i2,j_1,j2,k1,k2,h1,h2,shiftx,shifty,shiftz;
PetscInt ict,nz,base,r1,r2,N,*rowkeep,nstart;
PetscErrorCode ierr;
IS iskeep;
PetscReal **K,norm;
Mat mat,submat = 0,*submatb;
MatType type = MATSEQBAIJ;
m /= 2; /* This is done just to be consistent with the old example */
N = 3*(2*m+1)*(2*m+1)*(2*m+1);
ierr = PetscPrintf(PETSC_COMM_SELF,"m = %D, N=%D\n",m,N);CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,80,PETSC_NULL,&mat);CHKERRQ(ierr);
/* Form stiffness for element */
ierr = PetscMalloc(81*sizeof(PetscReal *),&K);CHKERRQ(ierr);
for (i=0; i<81; i++) {
ierr = PetscMalloc(81*sizeof(PetscReal),&K[i]);CHKERRQ(ierr);
}
ierr = Elastic20Stiff(K);CHKERRQ(ierr);
/* Loop over elements and add contribution to stiffness */
shiftx = 3; shifty = 3*(2*m+1); shiftz = 3*(2*m+1)*(2*m+1);
for (k=0; k<m; k++) {
for (j=0; j<m; j++) {
for (i=0; i<m; i++) {
h1 = 0;
base = 2*k*shiftz + 2*j*shifty + 2*i*shiftx;
for (k1=0; k1<3; k1++) {
for (j_1=0; j_1<3; j_1++) {
for (i1=0; i1<3; i1++) {
h2 = 0;
r1 = base + i1*shiftx + j_1*shifty + k1*shiftz;
for (k2=0; k2<3; k2++) {
for (j2=0; j2<3; j2++) {
for (i2=0; i2<3; i2++) {
r2 = base + i2*shiftx + j2*shifty + k2*shiftz;
ierr = AddElement(mat,r1,r2,K,h1,h2);CHKERRQ(ierr);
h2 += 3;
}
}
}
h1 += 3;
}
}
}
}
}
}
for (i=0; i<81; i++) {
ierr = PetscFree(K[i]);CHKERRQ(ierr);
}
ierr = PetscFree(K);CHKERRQ(ierr);
ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Exclude any superfluous rows and columns */
nstart = 3*(2*m+1)*(2*m+1);
ict = 0;
ierr = PetscMalloc((N-nstart)*sizeof(PetscInt),&rowkeep);CHKERRQ(ierr);
for (i=nstart; i<N; i++) {
ierr = MatGetRow(mat,i,&nz,0,0);CHKERRQ(ierr);
if (nz) rowkeep[ict++] = i;
ierr = MatRestoreRow(mat,i,&nz,0,0);CHKERRQ(ierr);
}
ierr = ISCreateGeneral(PETSC_COMM_SELF,ict,rowkeep,PETSC_COPY_VALUES,&iskeep);CHKERRQ(ierr);
ierr = MatGetSubMatrices(mat,1,&iskeep,&iskeep,MAT_INITIAL_MATRIX,&submatb);CHKERRQ(ierr);
submat = *submatb;
ierr = PetscFree(submatb);CHKERRQ(ierr);
ierr = PetscFree(rowkeep);CHKERRQ(ierr);
ierr = ISDestroy(&iskeep);CHKERRQ(ierr);
ierr = MatDestroy(&mat);CHKERRQ(ierr);
/* Convert storage formats -- just to demonstrate conversion to various
formats (in particular, block diagonal storage). This is NOT the
recommended means to solve such a problem. */
ierr = MatConvert(submat,type,MAT_INITIAL_MATRIX,newmat);CHKERRQ(ierr);
ierr = MatDestroy(&submat);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr);
ierr = MatView(*newmat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatNorm(*newmat,NORM_1,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"matrix 1 norm = %G\n",norm);CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
Mat C,Cperm;
PetscInt i,j,m = 5,n = 5,Ii,J,ncols;
PetscErrorCode ierr;
PetscScalar v;
PetscMPIInt size;
IS rperm,cperm,icperm;
const PetscInt *rperm_ptr,*cperm_ptr,*cols;
const PetscScalar *vals;
PetscBool TestMyorder=PETSC_FALSE;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);
CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a uniprocessor example only!");
/* create the matrix for the five point stencil, YET AGAIN */
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,m*n,m*n,5,NULL,&C);
ierr = MatSetUp(C);
CHKERRQ(ierr);
for (i=0; i<m; i++) {
for (j=0; j<n; j++) {
v = -1.0;
Ii = j + n*i;
if (i>0) {
J = Ii - n;
ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);
CHKERRQ(ierr);
}
if (i<m-1) {
J = Ii + n;
ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);
CHKERRQ(ierr);
}
if (j>0) {
J = Ii - 1;
ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);
CHKERRQ(ierr);
}
if (j<n-1) {
J = Ii + 1;
ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);
CHKERRQ(ierr);
}
v = 4.0;
ierr = MatSetValues(C,1,&Ii,1,&Ii,&v,INSERT_VALUES);
CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatGetOrdering(C,MATORDERINGND,&rperm,&cperm);
CHKERRQ(ierr);
ierr = ISView(rperm,PETSC_VIEWER_STDOUT_SELF);
CHKERRQ(ierr);
ierr = ISDestroy(&rperm);
CHKERRQ(ierr);
ierr = ISDestroy(&cperm);
CHKERRQ(ierr);
ierr = MatGetOrdering(C,MATORDERINGRCM,&rperm,&cperm);
CHKERRQ(ierr);
ierr = ISView(rperm,PETSC_VIEWER_STDOUT_SELF);
CHKERRQ(ierr);
ierr = ISDestroy(&rperm);
CHKERRQ(ierr);
ierr = ISDestroy(&cperm);
CHKERRQ(ierr);
ierr = MatGetOrdering(C,MATORDERINGQMD,&rperm,&cperm);
CHKERRQ(ierr);
ierr = ISView(rperm,PETSC_VIEWER_STDOUT_SELF);
CHKERRQ(ierr);
ierr = ISDestroy(&rperm);
CHKERRQ(ierr);
ierr = ISDestroy(&cperm);
CHKERRQ(ierr);
/* create Cperm = rperm*C*icperm */
ierr = PetscOptionsGetBool(NULL,"-testmyordering",&TestMyorder,NULL);
CHKERRQ(ierr);
if (TestMyorder) {
ierr = MatGetOrdering_myordering(C,MATORDERINGQMD,&rperm,&cperm);
CHKERRQ(ierr);
printf("myordering's rperm:\n");
ierr = ISView(rperm,PETSC_VIEWER_STDOUT_SELF);
CHKERRQ(ierr);
ierr = ISInvertPermutation(cperm,PETSC_DECIDE,&icperm);
CHKERRQ(ierr);
ierr = ISGetIndices(rperm,&rperm_ptr);
CHKERRQ(ierr);
ierr = ISGetIndices(icperm,&cperm_ptr);
CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,m*n,m*n,5,NULL,&Cperm);
CHKERRQ(ierr);
for (i=0; i<m*n; i++) {
ierr = MatGetRow(C,rperm_ptr[i],&ncols,&cols,&vals);
CHKERRQ(ierr);
for (j=0; j<ncols; j++) {
/* printf(" (%d %d %g)\n",i,cperm_ptr[cols[j]],vals[j]); */
ierr = MatSetValues(Cperm,1,&i,1,&cperm_ptr[cols[j]],&vals[j],INSERT_VALUES);
CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(Cperm,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(Cperm,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = ISRestoreIndices(rperm,&rperm_ptr);
CHKERRQ(ierr);
ierr = ISRestoreIndices(icperm,&cperm_ptr);
CHKERRQ(ierr);
ierr = ISDestroy(&rperm);
CHKERRQ(ierr);
ierr = ISDestroy(&cperm);
CHKERRQ(ierr);
ierr = ISDestroy(&icperm);
CHKERRQ(ierr);
ierr = MatDestroy(&Cperm);
CHKERRQ(ierr);
}
ierr = MatDestroy(&C);
CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
KSP ksp;
PC pc;
Mat A,M;
Vec X,B,D;
MPI_Comm comm;
PetscScalar v;
KSPConvergedReason reason;
PetscInt i,j,its;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr);
ierr = PetscOptionsSetValue("-options_left",PETSC_NULL);CHKERRQ(ierr);
comm = MPI_COMM_SELF;
/*
* Construct the Kershaw matrix
* and a suitable rhs / initial guess
*/
ierr = MatCreateSeqAIJ(comm,4,4,4,0,&A);CHKERRQ(ierr);
ierr = VecCreateSeq(comm,4,&B);CHKERRQ(ierr);
ierr = VecDuplicate(B,&X);CHKERRQ(ierr);
for (i=0; i<4; i++) {
v=3;
ierr = MatSetValues(A,1,&i,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
v=1;
ierr = VecSetValues(B,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecSetValues(X,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
}
i=0; v=0;
ierr = VecSetValues(X,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<3; i++) {
v=-2; j=i+1;
ierr = MatSetValues(A,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(A,1,&j,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
}
i=0; j=3; v=2;
ierr = MatSetValues(A,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(A,1,&j,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecAssemblyBegin(B);CHKERRQ(ierr);
ierr = VecAssemblyEnd(B);CHKERRQ(ierr);
printf("\nThe Kershaw matrix:\n\n"); MatView(A,0);
/*
* A Conjugate Gradient method
* with ILU(0) preconditioning
*/
ierr = KSPCreate(comm,&ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPCG);CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp,PETSC_TRUE);CHKERRQ(ierr);
/*
* ILU preconditioner;
* The iterative method will break down unless you comment in the SetShift
* line below, or use the -pc_factor_shift_positive_definite option.
* Run the code twice: once as given to see the negative pivot and the
* divergence behaviour, then comment in the Shift line, or add the
* command line option, and see that the pivots are all positive and
* the method converges.
*/
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCICC);CHKERRQ(ierr);
/* ierr = PCFactorSetShiftType(prec,MAT_SHIFT_POSITIVE_DEFINITE);CHKERRQ(ierr); */
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPSetUp(ksp);CHKERRQ(ierr);
/*
* Now that the factorisation is done, show the pivots;
* note that the last one is negative. This in itself is not an error,
* but it will make the iterative method diverge.
*/
ierr = PCFactorGetMatrix(pc,&M);CHKERRQ(ierr);
ierr = VecDuplicate(B,&D);CHKERRQ(ierr);
ierr = MatGetDiagonal(M,D);CHKERRQ(ierr);
printf("\nPivots:\n\n"); VecView(D,0);
/*
* Solve the system;
* without the shift this will diverge with
* an indefinite preconditioner
*/
ierr = KSPSolve(ksp,B,X);CHKERRQ(ierr);
ierr = KSPGetConvergedReason(ksp,&reason);CHKERRQ(ierr);
if (reason==KSP_DIVERGED_INDEFINITE_PC) {
printf("\nDivergence because of indefinite preconditioner;\n");
printf("Run the executable again but with -pc_factor_shift_positive_definite option.\n");
} else if (reason<0) {
printf("\nOther kind of divergence: this should not happen.\n");
} else {
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
printf("\nConvergence in %d iterations.\n",(int)its);
}
printf("\n");
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&B);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&D);CHKERRQ(ierr);
PetscFinalize();
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat C;
PetscErrorCode ierr;
PetscInt i,m = 2,N,M,its,idx[4],count,*rows;
PetscScalar val,Ke[16],r[4];
PetscReal x,y,h,norm,tol=1.e-14;
Vec u,ustar,b;
KSP ksp;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr);
N = (m+1)*(m+1); /* dimension of matrix */
M = m*m; /* number of elements */
h = 1.0/m; /* mesh width */
/* create stiffness matrix */
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,9,NULL,&C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
/* forms the element stiffness for the Laplacian */
ierr = FormElementStiffness(h*h,Ke);CHKERRQ(ierr);
for (i=0; i<M; i++) {
/* location of lower left corner of element */
x = h*(i % m); y = h*(i/m);
/* node numbers for the four corners of element */
idx[0] = (m+1)*(i/m) + (i % m);
idx[1] = idx[0]+1; idx[2] = idx[1] + m + 1; idx[3] = idx[2] - 1;
ierr = MatSetValues(C,4,idx,4,idx,Ke,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* create right hand side and solution */
ierr = VecCreateSeq(PETSC_COMM_SELF,N,&u);CHKERRQ(ierr);
ierr = VecDuplicate(u,&b);CHKERRQ(ierr);
ierr = VecDuplicate(b,&ustar);CHKERRQ(ierr);
ierr = VecSet(u,0.0);CHKERRQ(ierr);
ierr = VecSet(b,0.0);CHKERRQ(ierr);
for (i=0; i<M; i++) {
/* location of lower left corner of element */
x = h*(i % m); y = h*(i/m);
/* node numbers for the four corners of element */
idx[0] = (m+1)*(i/m) + (i % m);
idx[1] = idx[0]+1; idx[2] = idx[1] + m + 1; idx[3] = idx[2] - 1;
ierr = FormElementRhs(x,y,h*h,r);CHKERRQ(ierr);
ierr = VecSetValues(b,4,idx,r,ADD_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(b);CHKERRQ(ierr);
ierr = VecAssemblyEnd(b);CHKERRQ(ierr);
/* modify matrix and rhs for Dirichlet boundary conditions */
ierr = PetscMalloc1((4*m+1),&rows);CHKERRQ(ierr);
for (i=0; i<m+1; i++) {
rows[i] = i; /* bottom */
rows[3*m - 1 +i] = m*(m+1) + i; /* top */
}
count = m+1; /* left side */
for (i=m+1; i<m*(m+1); i+= m+1) rows[count++] = i;
count = 2*m; /* left side */
for (i=2*m+1; i<m*(m+1); i+= m+1) rows[count++] = i;
for (i=0; i<4*m; i++) {
x = h*(rows[i] % (m+1)); y = h*(rows[i]/(m+1));
val = y;
ierr = VecSetValues(u,1,&rows[i],&val,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecSetValues(b,1,&rows[i],&val,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatZeroRows(C,4*m,rows,1.0,0,0);CHKERRQ(ierr);
ierr = PetscFree(rows);CHKERRQ(ierr);
ierr = VecAssemblyBegin(u);CHKERRQ(ierr);
ierr = VecAssemblyEnd(u);CHKERRQ(ierr);
ierr = VecAssemblyBegin(b);CHKERRQ(ierr);
ierr = VecAssemblyEnd(b);CHKERRQ(ierr);
/* solve linear system */
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,C,C,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp,PETSC_TRUE);CHKERRQ(ierr);
ierr = KSPSolve(ksp,b,u);CHKERRQ(ierr);
/* check error */
for (i=0; i<N; i++) {
x = h*(i % (m+1)); y = h*(i/(m+1));
val = y;
ierr = VecSetValues(ustar,1,&i,&val,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(ustar);CHKERRQ(ierr);
ierr = VecAssemblyEnd(ustar);CHKERRQ(ierr);
ierr = VecAXPY(u,-1.0,ustar);CHKERRQ(ierr);
ierr = VecNorm(u,NORM_2,&norm);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of error %G Iterations %D\n",norm*h,its);CHKERRQ(ierr);
}
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = VecDestroy(&ustar);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Vec x,y,b;
Mat A; /* linear system matrix */
Mat sA,sC; /* symmetric part of the matrices */
PetscInt n,mbs=16,bs=1,nz=3,prob=1,i,j,col[3],block, row,Ii,J,n1,lvl;
PetscErrorCode ierr;
PetscMPIInt size;
PetscReal norm2,tol=1.e-10,err[10];
PetscScalar neg_one = -1.0,four=4.0,value[3];
IS perm,cperm;
PetscRandom rdm;
PetscBool reorder = PETSC_FALSE,displ = PETSC_FALSE;
MatFactorInfo factinfo;
PetscBool equal;
PetscBool TestAIJ = PETSC_FALSE,TestBAIJ = PETSC_TRUE;
PetscInt TestShift=0;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,1,"This is a uniprocessor example only!");
ierr = PetscOptionsGetInt(NULL,NULL,"-bs",&bs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-mbs",&mbs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-reorder",&reorder,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-testaij",&TestAIJ,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-testShift",&TestShift,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-displ",&displ,NULL);CHKERRQ(ierr);
n = mbs*bs;
if (TestAIJ) { /* A is in aij format */
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,n,n,nz,NULL,&A);CHKERRQ(ierr);
TestBAIJ = PETSC_FALSE;
} else { /* A is in baij format */
ierr =MatCreateSeqBAIJ(PETSC_COMM_WORLD,bs,n,n,nz,NULL,&A);CHKERRQ(ierr);
TestAIJ = PETSC_FALSE;
}
/* Assemble matrix */
if (bs == 1) {
ierr = PetscOptionsGetInt(NULL,NULL,"-test_problem",&prob,NULL);CHKERRQ(ierr);
if (prob == 1) { /* tridiagonal matrix */
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(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
i = n - 1; col[0]=0; col[1] = n - 2; col[2] = n - 1;
value[0]= 0.1; value[1]=-1; value[2]=2;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
i = 0; col[0] = 0; col[1] = 1; col[2]=n-1;
value[0] = 2.0; value[1] = -1.0; value[2]=0.1;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
} else if (prob ==2) { /* matrix for the five point stencil */
n1 = (PetscInt) (PetscSqrtReal((PetscReal)n) + 0.001);
if (n1*n1 - n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"sqrt(n) must be a positive interger!");
for (i=0; i<n1; i++) {
for (j=0; j<n1; j++) {
Ii = j + n1*i;
if (i>0) {
J = Ii - n1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
if (i<n1-1) {
J = Ii + n1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
if (j>0) {
J = Ii - 1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
if (j<n1-1) {
J = Ii + 1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatSetValues(A,1,&Ii,1,&Ii,&four,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
} else { /* bs > 1 */
for (block=0; block<n/bs; block++) {
/* diagonal blocks */
value[0] = -1.0; value[1] = 4.0; value[2] = -1.0;
for (i=1+block*bs; i<bs-1+block*bs; i++) {
col[0] = i-1; col[1] = i; col[2] = i+1;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
i = bs - 1+block*bs; col[0] = bs - 2+block*bs; col[1] = bs - 1+block*bs;
value[0]=-1.0; value[1]=4.0;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
i = 0+block*bs; col[0] = 0+block*bs; col[1] = 1+block*bs;
value[0]=4.0; value[1] = -1.0;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
/* off-diagonal blocks */
value[0]=-1.0;
for (i=0; i<(n/bs-1)*bs; i++) {
col[0]=i+bs;
ierr = MatSetValues(A,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
col[0]=i; row=i+bs;
ierr = MatSetValues(A,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
}
if (TestShift) {
/* set diagonals in the 0-th block as 0 for testing shift numerical factor */
for (i=0; i<bs; i++) {
row = i; col[0] = i; value[0] = 0.0;
ierr = MatSetValues(A,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Test MatConvert */
ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatConvert(A,MATSEQSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr);
ierr = MatMultEqual(A,sA,20,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"A != sA");
/* Test MatGetOwnershipRange() */
ierr = MatGetOwnershipRange(A,&Ii,&J);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(sA,&i,&j);CHKERRQ(ierr);
if (i-Ii || j-J) {
PetscPrintf(PETSC_COMM_SELF,"Error: MatGetOwnershipRange() in MatSBAIJ format\n");CHKERRQ(ierr);
}
/* Vectors */
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rdm);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = VecDuplicate(x,&y);CHKERRQ(ierr);
ierr = VecSetRandom(x,rdm);CHKERRQ(ierr);
/* Test MatReordering() - not work on sbaij matrix */
if (reorder) {
ierr = MatGetOrdering(A,MATORDERINGRCM,&perm,&cperm);CHKERRQ(ierr);
} else {
ierr = MatGetOrdering(A,MATORDERINGNATURAL,&perm,&cperm);CHKERRQ(ierr);
}
ierr = ISDestroy(&cperm);CHKERRQ(ierr);
/* initialize factinfo */
ierr = MatFactorInfoInitialize(&factinfo);CHKERRQ(ierr);
if (TestShift == 1) {
factinfo.shifttype = (PetscReal)MAT_SHIFT_NONZERO;
factinfo.shiftamount = 0.1;
} else if (TestShift == 2) {
factinfo.shifttype = (PetscReal)MAT_SHIFT_POSITIVE_DEFINITE;
}
/* Test MatCholeskyFactor(), MatICCFactor() */
/*------------------------------------------*/
/* Test aij matrix A */
if (TestAIJ) {
if (displ) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"AIJ: \n");CHKERRQ(ierr);
}
i = 0;
for (lvl=-1; lvl<10; lvl++) {
if (lvl==-1) { /* Cholesky factor */
factinfo.fill = 5.0;
ierr = MatGetFactor(A,MATSOLVERPETSC,MAT_FACTOR_CHOLESKY,&sC);CHKERRQ(ierr);
ierr = MatCholeskyFactorSymbolic(sC,A,perm,&factinfo);CHKERRQ(ierr);
} else { /* incomplete Cholesky factor */
factinfo.fill = 5.0;
factinfo.levels = lvl;
ierr = MatGetFactor(A,MATSOLVERPETSC,MAT_FACTOR_ICC,&sC);CHKERRQ(ierr);
ierr = MatICCFactorSymbolic(sC,A,perm,&factinfo);CHKERRQ(ierr);
}
ierr = MatCholeskyFactorNumeric(sC,A,&factinfo);CHKERRQ(ierr);
ierr = MatMult(A,x,b);CHKERRQ(ierr);
ierr = MatSolve(sC,b,y);CHKERRQ(ierr);
ierr = MatDestroy(&sC);CHKERRQ(ierr);
/* Check the error */
ierr = VecAXPY(y,neg_one,x);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&norm2);CHKERRQ(ierr);
if (displ) {
ierr = PetscPrintf(PETSC_COMM_WORLD," lvl: %D, error: %g\n", lvl,(double)norm2);CHKERRQ(ierr);
}
err[i++] = norm2;
}
}
/* Test baij matrix A */
if (TestBAIJ) {
if (displ) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"BAIJ: \n");CHKERRQ(ierr);
}
i = 0;
for (lvl=-1; lvl<10; lvl++) {
if (lvl==-1) { /* Cholesky factor */
factinfo.fill = 5.0;
ierr = MatGetFactor(A,MATSOLVERPETSC,MAT_FACTOR_CHOLESKY,&sC);CHKERRQ(ierr);
ierr = MatCholeskyFactorSymbolic(sC,A,perm,&factinfo);CHKERRQ(ierr);
} else { /* incomplete Cholesky factor */
factinfo.fill = 5.0;
factinfo.levels = lvl;
ierr = MatGetFactor(A,MATSOLVERPETSC,MAT_FACTOR_ICC,&sC);CHKERRQ(ierr);
ierr = MatICCFactorSymbolic(sC,A,perm,&factinfo);CHKERRQ(ierr);
}
ierr = MatCholeskyFactorNumeric(sC,A,&factinfo);CHKERRQ(ierr);
ierr = MatMult(A,x,b);CHKERRQ(ierr);
ierr = MatSolve(sC,b,y);CHKERRQ(ierr);
ierr = MatDestroy(&sC);CHKERRQ(ierr);
/* Check the error */
ierr = VecAXPY(y,neg_one,x);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&norm2);CHKERRQ(ierr);
if (displ) {
ierr = PetscPrintf(PETSC_COMM_WORLD," lvl: %D, error: %g\n", lvl,(double)norm2);CHKERRQ(ierr);
}
err[i++] = norm2;
}
}
/* Test sbaij matrix sA */
if (displ) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"SBAIJ: \n");CHKERRQ(ierr);
}
i = 0;
for (lvl=-1; lvl<10; lvl++) {
if (lvl==-1) { /* Cholesky factor */
factinfo.fill = 5.0;
ierr = MatGetFactor(sA,MATSOLVERPETSC,MAT_FACTOR_CHOLESKY,&sC);CHKERRQ(ierr);
ierr = MatCholeskyFactorSymbolic(sC,sA,perm,&factinfo);CHKERRQ(ierr);
} else { /* incomplete Cholesky factor */
factinfo.fill = 5.0;
factinfo.levels = lvl;
ierr = MatGetFactor(sA,MATSOLVERPETSC,MAT_FACTOR_ICC,&sC);CHKERRQ(ierr);
ierr = MatICCFactorSymbolic(sC,sA,perm,&factinfo);CHKERRQ(ierr);
}
ierr = MatCholeskyFactorNumeric(sC,sA,&factinfo);CHKERRQ(ierr);
if (lvl==0 && bs==1) { /* Test inplace ICC(0) for sbaij sA - does not work for new datastructure */
/*
Mat B;
ierr = MatDuplicate(sA,MAT_COPY_VALUES,&B);CHKERRQ(ierr);
ierr = MatICCFactor(B,perm,&factinfo);CHKERRQ(ierr);
ierr = MatEqual(sC,B,&equal);CHKERRQ(ierr);
if (!equal) {
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"in-place Cholesky factor != out-place Cholesky factor");
}
ierr = MatDestroy(&B);CHKERRQ(ierr);
*/
}
ierr = MatMult(sA,x,b);CHKERRQ(ierr);
ierr = MatSolve(sC,b,y);CHKERRQ(ierr);
/* Test MatSolves() */
if (bs == 1) {
Vecs xx,bb;
ierr = VecsCreateSeq(PETSC_COMM_SELF,n,4,&xx);CHKERRQ(ierr);
ierr = VecsDuplicate(xx,&bb);CHKERRQ(ierr);
ierr = MatSolves(sC,bb,xx);CHKERRQ(ierr);
ierr = VecsDestroy(xx);CHKERRQ(ierr);
ierr = VecsDestroy(bb);CHKERRQ(ierr);
}
ierr = MatDestroy(&sC);CHKERRQ(ierr);
/* Check the error */
ierr = VecAXPY(y,neg_one,x);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&norm2);CHKERRQ(ierr);
if (displ) {
ierr = PetscPrintf(PETSC_COMM_WORLD," lvl: %D, error: %g\n", lvl,(double)norm2);CHKERRQ(ierr);
}
err[i] -= norm2;
if (err[i] > tol) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_USER," level: %d, err: %g\n", lvl,(double)err[i]);
}
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&sA);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **args)
{
Mat A,B;
Vec xx,s1,s2,yy;
PetscErrorCode ierr;
PetscInt m=45,rows[2],cols[2],bs=1,i,row,col,*idx,M;
PetscScalar rval,vals1[4],vals2[4];
PetscRandom rdm;
IS is1,is2;
PetscReal s1norm,s2norm,rnorm,tol = 1.e-4;
PetscTruth flg;
MatFactorInfo info;
PetscInitialize(&argc,&args,(char *)0,help);
/* Test MatSetValues() and MatGetValues() */
ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_block_size",&bs,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_size",&m,PETSC_NULL);CHKERRQ(ierr);
M = m*bs;
ierr = MatCreateSeqBAIJ(PETSC_COMM_SELF,bs,M,M,1,PETSC_NULL,&A);CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,M,M,15,PETSC_NULL,&B);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rdm);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,M,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&yy);CHKERRQ(ierr);
/* For each row add atleast 15 elements */
for (row=0; row<M; row++) {
for (i=0; i<25*bs; i++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
col = (PetscInt)(PetscRealPart(rval)*M);
ierr = MatSetValues(A,1,&row,1,&col,&rval,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,1,&row,1,&col,&rval,INSERT_VALUES);CHKERRQ(ierr);
}
}
/* Now set blocks of values */
for (i=0; i<20*bs; i++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[0] = (PetscInt)(PetscRealPart(rval)*M);
vals1[0] = rval;
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[1] = (PetscInt)(PetscRealPart(rval)*M);
vals1[1] = rval;
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[0] = (PetscInt)(PetscRealPart(rval)*M);
vals1[2] = rval;
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[1] = (PetscInt)(PetscRealPart(rval)*M);
vals1[3] = rval;
ierr = MatSetValues(A,2,rows,2,cols,vals1,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,2,rows,2,cols,vals1,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Test MatNorm() */
ierr = MatNorm(A,NORM_FROBENIUS,&s1norm);CHKERRQ(ierr);
ierr = MatNorm(B,NORM_FROBENIUS,&s2norm);CHKERRQ(ierr);
rnorm = PetscAbsScalar(s2norm-s1norm)/s2norm;
if ( rnorm>tol ) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_FROBENIUS()- NormA=%16.14e NormB=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
ierr = MatNorm(A,NORM_INFINITY,&s1norm);CHKERRQ(ierr);
ierr = MatNorm(B,NORM_INFINITY,&s2norm);CHKERRQ(ierr);
rnorm = PetscAbsScalar(s2norm-s1norm)/s2norm;
if ( rnorm>tol ) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_INFINITY()- NormA=%16.14e NormB=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
ierr = MatNorm(A,NORM_1,&s1norm);CHKERRQ(ierr);
ierr = MatNorm(B,NORM_1,&s2norm);CHKERRQ(ierr);
rnorm = PetscAbsScalar(s2norm-s1norm)/s2norm;
if ( rnorm>tol ) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_NORM_1()- NormA=%16.14e NormB=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
/* MatShift() */
rval = 10*s1norm;
ierr = MatShift(A,rval);CHKERRQ(ierr);
ierr = MatShift(B,rval);CHKERRQ(ierr);
/* Test MatTranspose() */
ierr = MatTranspose(A,MAT_REUSE_MATRIX,&A);CHKERRQ(ierr);
ierr = MatTranspose(B,MAT_REUSE_MATRIX,&B);CHKERRQ(ierr);
/* Now do MatGetValues() */
for (i=0; i<30; i++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[0] = (PetscInt)(PetscRealPart(rval)*M);
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[1] = (PetscInt)(PetscRealPart(rval)*M);
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[0] = (PetscInt)(PetscRealPart(rval)*M);
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[1] = (PetscInt)(PetscRealPart(rval)*M);
ierr = MatGetValues(A,2,rows,2,cols,vals1);CHKERRQ(ierr);
ierr = MatGetValues(B,2,rows,2,cols,vals2);CHKERRQ(ierr);
ierr = PetscMemcmp(vals1,vals2,4*sizeof(PetscScalar),&flg);CHKERRQ(ierr);
if (!flg) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetValues bs = %D\n",bs);CHKERRQ(ierr);
}
}
/* Test MatMult(), MatMultAdd() */
for (i=0; i<40; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = VecSet(s2,0.0);CHKERRQ(ierr);
ierr = MatMult(A,xx,s1);CHKERRQ(ierr);
ierr = MatMultAdd(A,xx,s2,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"MatMult not equal to MatMultAdd Norm1=%e Norm2=%e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatMult() */
ierr = MatMultEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMult()\n");CHKERRQ(ierr);
}
/* Test MatMultAdd() */
ierr = MatMultAddEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMultAdd()\n");CHKERRQ(ierr);
}
/* Test MatMultTranspose() */
ierr = MatMultTransposeEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMultTranspose()\n");CHKERRQ(ierr);
}
/* Test MatMultTransposeAdd() */
ierr = MatMultTransposeAddEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMultTransposeAdd()\n");CHKERRQ(ierr);
}
/* Do LUFactor() on both the matrices */
ierr = PetscMalloc(M*sizeof(PetscInt),&idx);CHKERRQ(ierr);
for (i=0; i<M; i++) idx[i] = i;
ierr = ISCreateGeneral(PETSC_COMM_SELF,M,idx,&is1);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,M,idx,&is2);CHKERRQ(ierr);
ierr = PetscFree(idx);CHKERRQ(ierr);
ierr = ISSetPermutation(is1);CHKERRQ(ierr);
ierr = ISSetPermutation(is2);CHKERRQ(ierr);
ierr = MatFactorInfoInitialize(&info);CHKERRQ(ierr);
info.fill = 2.0;
info.dtcol = 0.0;
info.zeropivot = 1.e-14;
info.pivotinblocks = 1.0;
ierr = MatLUFactor(B,is1,is2,&info);CHKERRQ(ierr);
ierr = MatLUFactor(A,is1,is2,&info);CHKERRQ(ierr);
/* Test MatSolveAdd() */
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = VecSetRandom(yy,rdm);CHKERRQ(ierr);
ierr = MatSolveAdd(B,xx,yy,s2);CHKERRQ(ierr);
ierr = MatSolveAdd(A,xx,yy,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolveAdd - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatSolveAdd() when x = A'b +x */
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = VecSetRandom(s1,rdm);CHKERRQ(ierr);
ierr = VecCopy(s2,s1);CHKERRQ(ierr);
ierr = MatSolveAdd(B,xx,s2,s2);CHKERRQ(ierr);
ierr = MatSolveAdd(A,xx,s1,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolveAdd(same) - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatSolve() */
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = MatSolve(B,xx,s2);CHKERRQ(ierr);
ierr = MatSolve(A,xx,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolve - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatSolveTranspose() */
if (bs < 8) {
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = MatSolveTranspose(B,xx,s2);CHKERRQ(ierr);
ierr = MatSolveTranspose(A,xx,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolveTranspose - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
}
ierr = MatDestroy(A);CHKERRQ(ierr);
ierr = MatDestroy(B);CHKERRQ(ierr);
ierr = VecDestroy(xx);CHKERRQ(ierr);
ierr = VecDestroy(s1);CHKERRQ(ierr);
ierr = VecDestroy(s2);CHKERRQ(ierr);
ierr = VecDestroy(yy);CHKERRQ(ierr);
ierr = ISDestroy(is1);CHKERRQ(ierr);
ierr = ISDestroy(is2);CHKERRQ(ierr);
ierr = PetscRandomDestroy(rdm);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
PetscErrorCode testPTAPRectangular(void)
{
const int rows = 3;
const int cols = 5;
PetscErrorCode _ierr;
int i;
Mat A;
Mat P;
Mat C;
PetscFunctionBegin;
/* set up A */
_ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD, rows, rows,
1, PETSC_NULL, &A);
PETSc_CHKERRQ(_ierr);
for (i=0; i<rows; i++) {
_ierr = MatSetValue(A, i, i, 1.0, INSERT_VALUES);
PETSc_CHKERRQ(_ierr);
}
_ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
PETSc_CHKERRQ(_ierr);
_ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
PETSc_CHKERRQ(_ierr);
/* set up P */
_ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD, rows, cols,
5, PETSC_NULL, &P);
PETSc_CHKERRQ(_ierr);
_ierr = MatSetValue(P, 0, 0, 1.0, INSERT_VALUES);
PETSc_CHKERRQ(_ierr);
_ierr = MatSetValue(P, 0, 1, 2.0, INSERT_VALUES);
PETSc_CHKERRQ(_ierr);
_ierr = MatSetValue(P, 0, 2, 0.0, INSERT_VALUES);
PETSc_CHKERRQ(_ierr);
_ierr = MatSetValue(P, 0, 3, -1.0, INSERT_VALUES);
PETSc_CHKERRQ(_ierr);
_ierr = MatSetValue(P, 1, 0, 0.0, INSERT_VALUES);
PETSc_CHKERRQ(_ierr);
_ierr = MatSetValue(P, 1, 1, -1.0, INSERT_VALUES);
PETSc_CHKERRQ(_ierr);
_ierr = MatSetValue(P, 1, 2, 1.0, INSERT_VALUES);
PETSc_CHKERRQ(_ierr);
_ierr = MatSetValue(P, 2, 0, 3.0, INSERT_VALUES);
PETSc_CHKERRQ(_ierr);
_ierr = MatSetValue(P, 2, 1, 0.0, INSERT_VALUES);
PETSc_CHKERRQ(_ierr);
_ierr = MatSetValue(P, 2, 2, -3.0, INSERT_VALUES);
PETSc_CHKERRQ(_ierr);
_ierr = MatAssemblyBegin(P,MAT_FINAL_ASSEMBLY);
PETSc_CHKERRQ(_ierr);
_ierr = MatAssemblyEnd(P,MAT_FINAL_ASSEMBLY);
PETSc_CHKERRQ(_ierr);
/* compute C */
_ierr = MatPtAP( A, P, MAT_INITIAL_MATRIX, 1.0, &C);
PETSc_CHKERRQ(_ierr);
_ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);
PETSc_CHKERRQ(_ierr);
_ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);
PETSc_CHKERRQ(_ierr);
/* compare results */
/*
printf("C:\n");
_ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);PETSc_CHKERRQ(_ierr);
blitz::Array<double,2> actualC(cols, cols);
actualC = 0.0;
for (int i=0; i<cols; i++) {
for (int j=0; j<cols; j++) {
_ierr = MatGetValues(C, 1, &i, 1, &j, &actualC(i,j) );
PETSc_CHKERRQ(_ierr); ;
}
}
blitz::Array<double,2> expectedC(cols, cols);
expectedC = 0.0;
expectedC(0,0) = 10.0;
expectedC(0,1) = 2.0;
expectedC(0,2) = -9.0;
expectedC(0,3) = -1.0;
expectedC(1,0) = 2.0;
expectedC(1,1) = 5.0;
expectedC(1,2) = -1.0;
expectedC(1,3) = -2.0;
expectedC(2,0) = -9.0;
expectedC(2,1) = -1.0;
expectedC(2,2) = 10.0;
expectedC(2,3) = 0.0;
expectedC(3,0) = -1.0;
expectedC(3,1) = -2.0;
expectedC(3,2) = 0.0;
expectedC(3,3) = 1.0;
int check = areBlitzArrays2NumericallyEqual(actualC,expectedC);
validateEqualsWithParams3(check, -1 , "testPTAPRectangular()", check, actualC(check), expectedC(check));
*/
_ierr = MatDestroy(&A);
PETSc_CHKERRQ(_ierr);
_ierr = MatDestroy(&P);
PETSc_CHKERRQ(_ierr);
_ierr = MatDestroy(&C);
PETSc_CHKERRQ(_ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatLoad_BlockMat(Mat newmat, PetscViewer viewer)
{
PetscErrorCode ierr;
Mat tmpA;
PetscInt i,j,m,n,bs = 1,ncols,*lens,currentcol,mbs,**ii,*ilens,nextcol,*llens,cnt = 0;
const PetscInt *cols;
const PetscScalar *values;
PetscBool flg = PETSC_FALSE,notdone;
Mat_SeqAIJ *a;
Mat_BlockMat *amat;
PetscFunctionBegin;
ierr = MatCreate(PETSC_COMM_SELF,&tmpA);CHKERRQ(ierr);
ierr = MatSetType(tmpA,MATSEQAIJ);CHKERRQ(ierr);
ierr = MatLoad_SeqAIJ(tmpA,viewer);CHKERRQ(ierr);
ierr = MatGetLocalSize(tmpA,&m,&n);CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_SELF,NULL,"Options for loading BlockMat matrix 1","Mat");CHKERRQ(ierr);
ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-matload_symmetric","Store the matrix as symmetric","MatLoad",flg,&flg,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
/* Determine number of nonzero blocks for each block row */
a = (Mat_SeqAIJ*) tmpA->data;
mbs = m/bs;
ierr = PetscMalloc3(mbs,&lens,bs,&ii,bs,&ilens);CHKERRQ(ierr);
ierr = PetscMemzero(lens,mbs*sizeof(PetscInt));CHKERRQ(ierr);
for (i=0; i<mbs; i++) {
for (j=0; j<bs; j++) {
ii[j] = a->j + a->i[i*bs + j];
ilens[j] = a->i[i*bs + j + 1] - a->i[i*bs + j];
}
currentcol = -1;
notdone = PETSC_TRUE;
while (PETSC_TRUE) {
notdone = PETSC_FALSE;
nextcol = 1000000000;
for (j=0; j<bs; j++) {
while ((ilens[j] > 0 && ii[j][0]/bs <= currentcol)) {
ii[j]++;
ilens[j]--;
}
if (ilens[j] > 0) {
notdone = PETSC_TRUE;
nextcol = PetscMin(nextcol,ii[j][0]/bs);
}
}
if (!notdone) break;
if (!flg || (nextcol >= i)) lens[i]++;
currentcol = nextcol;
}
}
if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) {
ierr = MatSetSizes(newmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
}
ierr = MatBlockMatSetPreallocation(newmat,bs,0,lens);CHKERRQ(ierr);
if (flg) {
ierr = MatSetOption(newmat,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
}
amat = (Mat_BlockMat*)(newmat)->data;
/* preallocate the submatrices */
ierr = PetscMalloc1(bs,&llens);CHKERRQ(ierr);
for (i=0; i<mbs; i++) { /* loops for block rows */
for (j=0; j<bs; j++) {
ii[j] = a->j + a->i[i*bs + j];
ilens[j] = a->i[i*bs + j + 1] - a->i[i*bs + j];
}
currentcol = 1000000000;
for (j=0; j<bs; j++) { /* loop over rows in block finding first nonzero block */
if (ilens[j] > 0) {
currentcol = PetscMin(currentcol,ii[j][0]/bs);
}
}
notdone = PETSC_TRUE;
while (PETSC_TRUE) { /* loops over blocks in block row */
notdone = PETSC_FALSE;
nextcol = 1000000000;
ierr = PetscMemzero(llens,bs*sizeof(PetscInt));CHKERRQ(ierr);
for (j=0; j<bs; j++) { /* loop over rows in block */
while ((ilens[j] > 0 && ii[j][0]/bs <= currentcol)) { /* loop over columns in row */
ii[j]++;
ilens[j]--;
llens[j]++;
}
if (ilens[j] > 0) {
notdone = PETSC_TRUE;
nextcol = PetscMin(nextcol,ii[j][0]/bs);
}
}
if (cnt >= amat->maxnz) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Number of blocks found greater than expected %D",cnt);
if (!flg || currentcol >= i) {
amat->j[cnt] = currentcol;
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,bs,bs,0,llens,amat->a+cnt++);CHKERRQ(ierr);
}
if (!notdone) break;
currentcol = nextcol;
}
amat->ilen[i] = lens[i];
}
ierr = PetscFree3(lens,ii,ilens);CHKERRQ(ierr);
ierr = PetscFree(llens);CHKERRQ(ierr);
/* copy over the matrix, one row at a time */
for (i=0; i<m; i++) {
ierr = MatGetRow(tmpA,i,&ncols,&cols,&values);CHKERRQ(ierr);
ierr = MatSetValues(newmat,1,&i,ncols,cols,values,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatRestoreRow(tmpA,i,&ncols,&cols,&values);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatSetValues_BlockMat(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
{
Mat_BlockMat *a = (Mat_BlockMat*)A->data;
PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1;
PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen;
PetscInt *aj =a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol;
PetscErrorCode ierr;
PetscInt ridx,cidx;
PetscBool roworiented=a->roworiented;
MatScalar value;
Mat *ap,*aa = a->a;
PetscFunctionBegin;
for (k=0; k<m; k++) { /* loop over added rows */
row = im[k];
brow = row/bs;
if (row < 0) continue;
#if defined(PETSC_USE_DEBUG)
if (row >= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1);
#endif
rp = aj + ai[brow];
ap = aa + ai[brow];
rmax = imax[brow];
nrow = ailen[brow];
low = 0;
high = nrow;
for (l=0; l<n; l++) { /* loop over added columns */
if (in[l] < 0) continue;
#if defined(PETSC_USE_DEBUG)
if (in[l] >= A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->cmap->n-1);
#endif
col = in[l]; bcol = col/bs;
if (A->symmetric && brow > bcol) continue;
ridx = row % bs; cidx = col % bs;
if (roworiented) value = v[l + k*n];
else value = v[k + l*m];
if (col <= lastcol) low = 0;
else high = nrow;
lastcol = col;
while (high-low > 7) {
t = (low+high)/2;
if (rp[t] > bcol) high = t;
else low = t;
}
for (i=low; i<high; i++) {
if (rp[i] > bcol) break;
if (rp[i] == bcol) goto noinsert1;
}
if (nonew == 1) goto noinsert1;
if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
MatSeqXAIJReallocateAIJ(A,a->mbs,1,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,Mat);
N = nrow++ - 1; high++;
/* shift up all the later entries in this row */
for (ii=N; ii>=i; ii--) {
rp[ii+1] = rp[ii];
ap[ii+1] = ap[ii];
}
if (N>=i) ap[i] = 0;
rp[i] = bcol;
a->nz++;
A->nonzerostate++;
noinsert1:;
if (!*(ap+i)) {
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,bs,bs,0,0,ap+i);CHKERRQ(ierr);
}
ierr = MatSetValues(ap[i],1,&ridx,1,&cidx,&value,is);CHKERRQ(ierr);
low = i;
}
ailen[brow] = nrow;
}
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInitialize(&argc,&argv,(char*)0,help);
const int d = 2; // d = DOF
Mat A, Aminus;
// these are dense d x d sequential matrices, unrelated to the grid
// (each processor owns whole matrix)
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,d,d,d,NULL,&A); CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(A,"A_"); CHKERRQ(ierr);
ierr = MatSetFromOptions(A); CHKERRQ(ierr);
// fill A
double val[d][d], c = 3.0;
val[0][0] = 0.0; val[0][1] = c;
val[1][0] = c; val[1][1] = 0.0;
ierr = fillsmallmat(2,val,A); CHKERRQ(ierr);
// fill Aminus; see getAminus.m for computation of Aminus from A
ierr = MatDuplicate(A,MAT_SHARE_NONZERO_PATTERN,&Aminus); CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(Aminus,"Aminus_"); CHKERRQ(ierr);
val[0][0] = -1.5; val[0][1] = 1.5;
val[1][0] = 1.5; val[1][1] = -1.5;
ierr = fillsmallmat(2,val,Aminus); CHKERRQ(ierr);
// set up the grid
DM da;
ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC,
-50, // override with -da_grid_x or -da_refine
d, 1, NULL, // dof = 1 and stencil width = 1
&da); CHKERRQ(ierr);
// determine grid locations (cell-centered grid)
DMDALocalInfo info;
double L = 10.0, dx;
ierr = DMDAGetLocalInfo(da,&info); CHKERRQ(ierr);
dx = L / (double)(info.mx);
ierr = DMDASetUniformCoordinates(da,dx/2,L-dx/2,-1.0,-1.0,-1.0,-1.0);CHKERRQ(ierr);
// u = u(t_n), unew = u(t_n+1)
Vec u, unew, F;
ierr = DMCreateLocalVector(da,&u);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)u,"solution u"); CHKERRQ(ierr);
ierr = VecDuplicate(u,&F);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)F,"flux F"); CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&unew);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)unew,"updated solution unew"); CHKERRQ(ierr);
ierr = VecSet(unew,0.0); CHKERRQ(ierr);
// at each cell we will need to compute Fcell = A qleft + Aminus dq
Vec dq, qleft, tmp, Fcell;
ierr = VecCreateSeq(PETSC_COMM_WORLD,d,&dq); CHKERRQ(ierr);
ierr = VecDuplicate(dq,&qleft); CHKERRQ(ierr);
ierr = VecDuplicate(dq,&tmp); CHKERRQ(ierr);
ierr = VecDuplicate(dq,&Fcell); CHKERRQ(ierr);
// view the solution graphically; control with -draw_pause
PetscViewer viewer;
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,NULL,"solution u",
PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,&viewer); CHKERRQ(ierr);
/* time-stepping loop */
double t = 0.0, tf = 10.0, dt, nu;
int n, NN = 10;
dt = tf / NN;
nu = dt / dx;
for (n = 0; n < NN; ++n) {
ierr = PetscPrintf(PETSC_COMM_WORLD, " time[%3d]=%6g: \n", n, t); CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,unew,INSERT_VALUES,u); CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,unew,INSERT_VALUES,u); CHKERRQ(ierr);
ierr = VecView(u,viewer); CHKERRQ(ierr);
double **au, **aunew, **aF;
int j, p;
ierr = DMDAVecGetArrayDOF(da, u, &au);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da, F, &aF);CHKERRQ(ierr);
for (j=info.xs; j<info.xs+info.xm; j++) {
double *adq, *aqleft, *aFcell;
ierr = VecGetArray(dq,&adq); CHKERRQ(ierr);
ierr = VecGetArray(qleft,&aqleft); CHKERRQ(ierr);
for (p = 0; p < d; p++) {
adq[p] = au[j+1][p] - au[j][p];
aqleft[p] = au[j][p];
}
ierr = VecRestoreArray(dq,&adq); CHKERRQ(ierr);
ierr = VecRestoreArray(qleft,&aqleft); CHKERRQ(ierr);
// tmp = A qleft
// Fcell = tmp + Aminus dq
ierr = MatMult(A,qleft,tmp); CHKERRQ(ierr);
ierr = MatMultAdd(Aminus,dq,tmp,Fcell); CHKERRQ(ierr);
ierr = VecGetArray(Fcell,&aFcell); CHKERRQ(ierr);
for (p = 0; p < d; p++)
aF[j][p] = aFcell[p];
ierr = VecRestoreArray(Fcell,&aFcell); CHKERRQ(ierr);
}
ierr = DMDAVecRestoreArrayDOF(da, F, &aF);CHKERRQ(ierr);
ierr = DMLocalToLocalBegin(da,F,INSERT_VALUES,F); CHKERRQ(ierr);
ierr = DMLocalToLocalEnd(da,F,INSERT_VALUES,F); CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da, F, &aF);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da, unew, &aunew);CHKERRQ(ierr);
for (j=info.xs; j<info.xs+info.xm; j++) {
for (p = 0; p < d; p++)
aunew[j][p] = au[j][p] - nu * (aF[j+1][p] - aF[j][p]);
}
ierr = DMDAVecRestoreArrayDOF(da, u, &au);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da, F, &aF);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da, unew, &aunew);CHKERRQ(ierr);
t += dt;
}
// clean up
ierr = VecDestroy(&u); CHKERRQ(ierr);
ierr = VecDestroy(&unew); CHKERRQ(ierr);
ierr = VecDestroy(&F); CHKERRQ(ierr);
ierr = VecDestroy(&dq); CHKERRQ(ierr);
ierr = VecDestroy(&qleft); CHKERRQ(ierr);
ierr = VecDestroy(&tmp); CHKERRQ(ierr);
ierr = VecDestroy(&Fcell); CHKERRQ(ierr);
ierr = MatDestroy(&A); CHKERRQ(ierr);
ierr = MatDestroy(&Aminus); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
ierr = DMDestroy(&da); CHKERRQ(ierr);
ierr = PetscFinalize(); CHKERRQ(ierr);
return 0;
}
