void
PetscSparseMtrx :: times(const FloatMatrix &B, FloatMatrix &answer) const
{
if ( this->giveNumberOfColumns() != B.giveNumberOfRows() ) {
OOFEM_ERROR("Dimension mismatch");
}
#ifdef __PARALLEL_MODE
if ( emodel->isParallel() ) {
OOFEM_ERROR("PetscSparseMtrx :: times - Not implemented");
}
#endif
// I'm opting to work with a set of vectors, as i think it might be faster and more robust. / Mikael
int nr = this->giveNumberOfRows();
int nc = B.giveNumberOfColumns();
answer.resize(nr, nc);
double *aptr = answer.givePointer();
#if 0
// Approach using several vectors. Not sure if it is optimal, but it includes petsc calls which i suspect are inefficient. / Mikael
// UNTESTED!
Vec globX, globY;
VecCreate(PETSC_COMM_SELF, &globY);
VecSetType(globY, VECSEQ);
VecSetSizes(globY, PETSC_DECIDE, nr);
int nrB = B.giveNumberOfRows();
for (int k = 0; k < nc; k++) {
double colVals[nrB];
for (int i = 0; i < nrB; i++) colVals[i] = B(i,k); // B.copyColumn(Bk,k);
VecCreateSeqWithArray(PETSC_COMM_SELF, nrB, colVals, &globX);
MatMult(this->mtrx, globX, globY );
double *ptr;
VecGetArray(globY, &ptr);
for (int i = 0; i < nr; i++) *aptr++ = ptr[i]; // answer.setColumn(Ak,k);
VecRestoreArray(globY, &ptr);
VecDestroy(globX);
}
VecDestroy(globY);
#endif
Mat globB, globC;
MatCreateSeqDense(PETSC_COMM_SELF, B.giveNumberOfRows(), B.giveNumberOfColumns(), B.givePointer(), & globB);
MatMatMult(this->mtrx, globB, MAT_INITIAL_MATRIX, PETSC_DEFAULT, & globC);
const double *vals;
for ( int r = 0; r < nr; r++ ) {
MatGetRow(globC, r, NULL, NULL, & vals);
for ( int i = 0, i2 = r; i < nc; i++, i2 += nr ) {
aptr [ i2 ] = vals [ i ];
}
MatRestoreRow(globC, r, NULL, NULL, & vals);
}
MatDestroy(&globB);
MatDestroy(&globC);
}
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;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr; /* used to check for functions returning nonzeros */
Vec x, f; /* solution, function */
Mat J; /* Jacobian matrix */
Tao tao; /* Tao solver context */
PetscInt i; /* iteration information */
PetscReal hist[100],resid[100];
PetscInt lits[100];
AppCtx user; /* user-defined work context */
PetscInitialize(&argc,&argv,(char *)0,help);
/* Allocate vectors */
ierr = VecCreateSeq(MPI_COMM_SELF,NPARAMETERS,&x);CHKERRQ(ierr);
ierr = VecCreateSeq(MPI_COMM_SELF,NOBSERVATIONS,&f);CHKERRQ(ierr);
/* Create the Jacobian matrix. */
ierr = MatCreateSeqDense(MPI_COMM_SELF,NOBSERVATIONS,NPARAMETERS,NULL,&J);CHKERRQ(ierr);
for (i=0;i<NOBSERVATIONS;i++) user.idm[i] = i;
for (i=0;i<NPARAMETERS;i++) user.idn[i] = i;
/* Create TAO solver and set desired solution method */
ierr = TaoCreate(PETSC_COMM_SELF,&tao);CHKERRQ(ierr);
ierr = TaoSetType(tao,TAOPOUNDERS);CHKERRQ(ierr);
/* Set the function and Jacobian routines. */
ierr = InitializeData(&user);CHKERRQ(ierr);
ierr = FormStartingPoint(x);CHKERRQ(ierr);
ierr = TaoSetInitialVector(tao,x);CHKERRQ(ierr);
ierr = TaoSetSeparableObjectiveRoutine(tao,f,EvaluateFunction,(void*)&user);CHKERRQ(ierr);
ierr = TaoSetJacobianRoutine(tao, J, J, EvaluateJacobian, (void*)&user);CHKERRQ(ierr);
/* Check for any TAO command line arguments */
ierr = TaoSetFromOptions(tao);CHKERRQ(ierr);
ierr = TaoSetConvergenceHistory(tao,hist,resid,0,lits,100,PETSC_TRUE);CHKERRQ(ierr);
/* Perform the Solve */
ierr = TaoSolve(tao);CHKERRQ(ierr);
ierr = TaoView(tao,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
/* Free TAO data structures */
ierr = TaoDestroy(&tao);CHKERRQ(ierr);
/* Free PETSc data structures */
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&f);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A,C;
PetscErrorCode ierr;
PetscInt n = 10;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MatCreateSeqDense(PETSC_COMM_WORLD,n,n,NULL,&A);CHKERRQ(ierr);
ierr = MatConvert(A,MATSEQDENSE,MAT_INITIAL_MATRIX,&C);CHKERRQ(ierr);
ierr = MatView(C,NULL);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat A,Mat B,PetscReal fill,Mat *C)
{
PetscErrorCode ierr;
Mat_MPIAIJ *aij = (Mat_MPIAIJ*) A->data;
PetscInt nz = aij->B->cmap->n;
PetscContainer cont;
MPIAIJ_MPIDense *contents;
VecScatter ctx = aij->Mvctx;
VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata;
VecScatter_MPI_General *to = ( VecScatter_MPI_General*) ctx->todata;
PetscInt m=A->rmap->n,n=B->cmap->n;
PetscFunctionBegin;
ierr = MatCreate(((PetscObject)B)->comm,C);CHKERRQ(ierr);
ierr = MatSetSizes(*C,m,n,A->rmap->N,B->cmap->N);CHKERRQ(ierr);
ierr = MatSetType(*C,MATMPIDENSE);CHKERRQ(ierr);
ierr = MatAssemblyBegin(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscContainerCreate(((PetscObject)A)->comm,&cont);CHKERRQ(ierr);
ierr = PetscNew(MPIAIJ_MPIDense,&contents);CHKERRQ(ierr);
ierr = PetscContainerSetPointer(cont,contents);CHKERRQ(ierr);
ierr = PetscContainerSetUserDestroy(cont,MPIAIJ_MPIDenseDestroy);CHKERRQ(ierr);
/* Create work matrix used to store off processor rows of B needed for local product */
ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,B->cmap->N,PETSC_NULL,&contents->workB);CHKERRQ(ierr);
/* Create work arrays needed */
ierr = PetscMalloc4(B->cmap->N*from->starts[from->n],PetscScalar,&contents->rvalues,
B->cmap->N*to->starts[to->n],PetscScalar,&contents->svalues,
from->n,MPI_Request,&contents->rwaits,
to->n,MPI_Request,&contents->swaits);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject)(*C),"workB",(PetscObject)cont);CHKERRQ(ierr);
ierr = PetscContainerDestroy(cont);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void
PetscSparseMtrx :: timesT(const FloatMatrix &B, FloatMatrix &answer) const
{
if ( this->giveNumberOfRows() != B.giveNumberOfRows() ) {
OOFEM_ERROR("Dimension mismatch");
}
#ifdef __PARALLEL_MODE
if ( emodel->isParallel() ) {
OOFEM_ERROR("PetscSparseMtrx :: times - Not implemented");
}
#endif
int nr = this->giveNumberOfColumns();
int nc = B.giveNumberOfColumns();
answer.resize(nr, nc);
double *aptr = answer.givePointer();
// For some reason SEQAIJ and SEQDENSE are incompatible with each other for MatMatMultTranspose (MatMatMult is OK). I don't know why.
// Either way, this is not to bad, except for an extra transposition.
Mat globB, globC;
FloatMatrix BT;
BT.beTranspositionOf(B);
MatCreateSeqDense(PETSC_COMM_SELF, BT.giveNumberOfRows(), BT.giveNumberOfColumns(), BT.givePointer(), & globB);
MatMatMult(globB, this->mtrx, MAT_INITIAL_MATRIX, PETSC_DEFAULT, & globC);
const double *vals;
for ( int r = 0; r < nc; r++ ) {
MatGetRow(globC, r, NULL, NULL, & vals);
for ( int i = 0; i < nr; i++ ) {
* aptr++ = vals [ i ];
}
MatRestoreRow(globC, r, NULL, NULL, & vals);
}
MatDestroy(&globB);
MatDestroy(&globC);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
BV X;
Mat M;
Vec v,t,*C;
PetscInt i,j,n=20,k=8,nc=2;
PetscViewer view;
PetscBool verbose;
PetscReal norm;
PetscScalar alpha;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-k",&k,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-nc",&nc,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-verbose",&verbose);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Test BV orthogonalization with %D columns + %D constraints, of length %D.\n",k,nc,n);CHKERRQ(ierr);
/* Create template vector */
ierr = VecCreate(PETSC_COMM_WORLD,&t);CHKERRQ(ierr);
ierr = VecSetSizes(t,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(t);CHKERRQ(ierr);
/* Create BV object X */
ierr = BVCreate(PETSC_COMM_WORLD,&X);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)X,"X");CHKERRQ(ierr);
ierr = BVSetSizesFromVec(X,t,k);CHKERRQ(ierr);
ierr = BVSetFromOptions(X);CHKERRQ(ierr);
/* Generate constraints and attach them to X */
if (nc>0) {
ierr = VecDuplicateVecs(t,nc,&C);CHKERRQ(ierr);
for (j=0;j<nc;j++) {
for (i=0;i<=j;i++) {
ierr = VecSetValue(C[j],i,1.0,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(C[j]);CHKERRQ(ierr);
ierr = VecAssemblyEnd(C[j]);CHKERRQ(ierr);
}
ierr = BVInsertConstraints(X,&nc,C);CHKERRQ(ierr);
ierr = VecDestroyVecs(nc,&C);CHKERRQ(ierr);
}
/* Set up viewer */
ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&view);CHKERRQ(ierr);
if (verbose) {
ierr = PetscViewerPushFormat(view,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
}
/* Fill X entries */
for (j=0;j<k;j++) {
ierr = BVGetColumn(X,j,&v);CHKERRQ(ierr);
ierr = VecZeroEntries(v);CHKERRQ(ierr);
for (i=0;i<=n/2;i++) {
if (i+j<n) {
alpha = (3.0*i+j-2)/(2*(i+j+1));
ierr = VecSetValue(v,i+j,alpha,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = VecAssemblyBegin(v);CHKERRQ(ierr);
ierr = VecAssemblyEnd(v);CHKERRQ(ierr);
ierr = BVRestoreColumn(X,j,&v);CHKERRQ(ierr);
}
if (verbose) {
ierr = BVView(X,view);CHKERRQ(ierr);
}
/* Test BVOrthogonalizeColumn */
for (j=0;j<k;j++) {
ierr = BVOrthogonalizeColumn(X,j,NULL,&norm,NULL);CHKERRQ(ierr);
alpha = 1.0/norm;
ierr = BVScaleColumn(X,j,alpha);CHKERRQ(ierr);
}
if (verbose) {
ierr = BVView(X,view);CHKERRQ(ierr);
}
/* Check orthogonality */
ierr = MatCreateSeqDense(PETSC_COMM_SELF,k,k,NULL,&M);CHKERRQ(ierr);
ierr = BVDot(X,X,M);CHKERRQ(ierr);
ierr = MatShift(M,-1.0);CHKERRQ(ierr);
ierr = MatNorm(M,NORM_1,&norm);CHKERRQ(ierr);
if (norm<100*PETSC_MACHINE_EPSILON) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Level of orthogonality < 100*eps\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Level of orthogonality: %g\n",(double)norm);CHKERRQ(ierr);
}
ierr = MatDestroy(&M);CHKERRQ(ierr);
ierr = BVDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&t);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
PetscErrorCode DMCoarsen_Plex(DM dm, MPI_Comm comm, DM *dmCoarsened)
{
DM_Plex *mesh = (DM_Plex*) dm->data;
#ifdef PETSC_HAVE_PRAGMATIC
DM udm, coordDM;
DMLabel bd;
Mat A;
Vec coordinates, mb, mx;
PetscSection coordSection;
const PetscScalar *coords;
double *coarseCoords;
IS bdIS;
PetscReal *x, *y, *z, *eqns, *metric;
PetscReal coarseRatio = PetscSqr(0.5);
const PetscInt *faces;
PetscInt *cells, *bdFaces, *bdFaceIds;
PetscInt dim, numCorners, cStart, cEnd, numCells, numCoarseCells, c, vStart, vEnd, numVertices, numCoarseVertices, v, numBdFaces, f, maxConeSize, size, bdSize, coff;
#endif
PetscErrorCode ierr;
PetscFunctionBegin;
#ifdef PETSC_HAVE_PRAGMATIC
if (!mesh->coarseMesh) {
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &coordDM);CHKERRQ(ierr);
ierr = DMGetDefaultSection(coordDM, &coordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr);
ierr = DMPlexGetMaxSizes(udm, &maxConeSize, NULL);CHKERRQ(ierr);
numCells = cEnd - cStart;
numVertices = vEnd - vStart;
ierr = PetscCalloc5(numVertices, &x, numVertices, &y, numVertices, &z, numVertices*PetscSqr(dim), &metric, numCells*maxConeSize, &cells);CHKERRQ(ierr);
ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr);
for (v = vStart; v < vEnd; ++v) {
PetscInt off;
ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
x[v-vStart] = coords[off+0];
y[v-vStart] = coords[off+1];
if (dim > 2) z[v-vStart] = coords[off+2];
}
ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr);
for (c = 0, coff = 0; c < numCells; ++c) {
const PetscInt *cone;
PetscInt coneSize, cl;
ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr);
ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr);
for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart;
}
switch (dim) {
case 2:
pragmatic_2d_init(&numVertices, &numCells, cells, x, y);
break;
case 3:
pragmatic_3d_init(&numVertices, &numCells, cells, x, y, z);
break;
default:
SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic coarsening defined for dimension %d", dim);
}
/* Create boundary mesh */
ierr = DMLabelCreate("boundary", &bd);CHKERRQ(ierr);
ierr = DMPlexMarkBoundaryFaces(dm, bd);CHKERRQ(ierr);
ierr = DMLabelGetStratumIS(bd, 1, &bdIS);CHKERRQ(ierr);
ierr = DMLabelGetStratumSize(bd, 1, &numBdFaces);CHKERRQ(ierr);
ierr = ISGetIndices(bdIS, &faces);CHKERRQ(ierr);
for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
PetscInt *closure = NULL;
PetscInt closureSize, cl;
ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize;
}
ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
ierr = PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds);CHKERRQ(ierr);
for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
PetscInt *closure = NULL;
PetscInt closureSize, cl;
ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart;
}
/* TODO Fix */
bdFaceIds[f] = 1;
ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
ierr = ISDestroy(&bdIS);CHKERRQ(ierr);
ierr = DMLabelDestroy(&bd);CHKERRQ(ierr);
pragmatic_set_boundary(&numBdFaces, bdFaces, bdFaceIds);
/* Create metric */
size = (dim*(dim+1))/2;
ierr = PetscMalloc1(PetscSqr(size), &eqns);CHKERRQ(ierr);
ierr = MatCreateSeqDense(PETSC_COMM_SELF, size, size, eqns, &A);CHKERRQ(ierr);
ierr = MatCreateVecs(A, &mx, &mb);CHKERRQ(ierr);
ierr = VecSet(mb, 1.0);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {
const PetscScalar *sol;
PetscScalar *cellCoords = NULL;
PetscReal e[3], vol;
const PetscInt *cone;
PetscInt coneSize, cl, i, j, d, r;
ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);CHKERRQ(ierr);
/* Only works for simplices */
for (i = 0, r = 0; i < dim+1; ++i) {
for (j = 0; j < i; ++j, ++r) {
for (d = 0; d < dim; ++d) e[d] = cellCoords[i*dim+d] - cellCoords[j*dim+d];
/* FORTRAN ORDERING */
if (dim == 2) {
eqns[0*size+r] = PetscSqr(e[0]);
eqns[1*size+r] = 2.0*e[0]*e[1];
eqns[2*size+r] = PetscSqr(e[1]);
} else {
eqns[0*size+r] = PetscSqr(e[0]);
eqns[1*size+r] = 2.0*e[0]*e[1];
eqns[2*size+r] = 2.0*e[0]*e[2];
eqns[3*size+r] = PetscSqr(e[1]);
eqns[4*size+r] = 2.0*e[1]*e[2];
eqns[5*size+r] = PetscSqr(e[2]);
}
}
}
ierr = MatSetUnfactored(A);CHKERRQ(ierr);
ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);CHKERRQ(ierr);
ierr = MatLUFactor(A, NULL, NULL, NULL);CHKERRQ(ierr);
ierr = MatSolve(A, mb, mx);CHKERRQ(ierr);
ierr = VecGetArrayRead(mx, &sol);CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL);CHKERRQ(ierr);
ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr);
ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr);
for (cl = 0; cl < coneSize; ++cl) {
const PetscInt v = cone[cl] - vStart;
if (dim == 2) {
metric[v*4+0] += vol*coarseRatio*sol[0];
metric[v*4+1] += vol*coarseRatio*sol[1];
metric[v*4+2] += vol*coarseRatio*sol[1];
metric[v*4+3] += vol*coarseRatio*sol[2];
} else {
metric[v*9+0] += vol*coarseRatio*sol[0];
metric[v*9+1] += vol*coarseRatio*sol[1];
metric[v*9+3] += vol*coarseRatio*sol[1];
metric[v*9+2] += vol*coarseRatio*sol[2];
metric[v*9+6] += vol*coarseRatio*sol[2];
metric[v*9+4] += vol*coarseRatio*sol[3];
metric[v*9+5] += vol*coarseRatio*sol[4];
metric[v*9+7] += vol*coarseRatio*sol[4];
metric[v*9+8] += vol*coarseRatio*sol[5];
}
}
ierr = VecRestoreArrayRead(mx, &sol);CHKERRQ(ierr);
}
for (v = 0; v < numVertices; ++v) {
const PetscInt *support;
PetscInt supportSize, s;
PetscReal vol, totVol = 0.0;
ierr = DMPlexGetSupport(udm, v+vStart, &support);CHKERRQ(ierr);
ierr = DMPlexGetSupportSize(udm, v+vStart, &supportSize);CHKERRQ(ierr);
for (s = 0; s < supportSize; ++s) {ierr = DMPlexComputeCellGeometryFVM(dm, support[s], &vol, NULL, NULL);CHKERRQ(ierr); totVol += vol;}
for (s = 0; s < PetscSqr(dim); ++s) metric[v*PetscSqr(dim)+s] /= totVol;
}
ierr = VecDestroy(&mx);CHKERRQ(ierr);
ierr = VecDestroy(&mb);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = DMDestroy(&udm);CHKERRQ(ierr);
ierr = PetscFree(eqns);CHKERRQ(ierr);
pragmatic_set_metric(metric);
pragmatic_adapt();
/* Read out mesh */
pragmatic_get_info(&numCoarseVertices, &numCoarseCells);
ierr = PetscMalloc1(numCoarseVertices*dim, &coarseCoords);CHKERRQ(ierr);
switch (dim) {
case 2:
pragmatic_get_coords_2d(x, y);
numCorners = 3;
for (v = 0; v < numCoarseVertices; ++v) {coarseCoords[v*2+0] = x[v]; coarseCoords[v*2+1] = y[v];}
break;
case 3:
pragmatic_get_coords_3d(x, y, z);
numCorners = 4;
for (v = 0; v < numCoarseVertices; ++v) {coarseCoords[v*3+0] = x[v]; coarseCoords[v*3+1] = y[v]; coarseCoords[v*3+2] = z[v];}
break;
default:
SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic coarsening defined for dimension %d", dim);
}
pragmatic_get_elements(cells);
/* TODO Read out markers for boundary */
ierr = DMPlexCreateFromCellList(PetscObjectComm((PetscObject) dm), dim, numCoarseCells, numCoarseVertices, numCorners, PETSC_TRUE, cells, dim, coarseCoords, &mesh->coarseMesh);CHKERRQ(ierr);
pragmatic_finalize();
ierr = PetscFree5(x, y, z, metric, cells);CHKERRQ(ierr);
ierr = PetscFree2(bdFaces, bdFaceIds);CHKERRQ(ierr);
ierr = PetscFree(coarseCoords);CHKERRQ(ierr);
}
#endif
ierr = PetscObjectReference((PetscObject) mesh->coarseMesh);CHKERRQ(ierr);
*dmCoarsened = mesh->coarseMesh;
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);
}
EXTERN_C_BEGIN
void PETSC_STDCALL matcreateseqdense_(MPI_Comm *comm,PetscInt *m,PetscInt *n,PetscScalar *data,Mat *newmat,PetscErrorCode *ierr)
{
CHKFORTRANNULLSCALAR(data);
*ierr = MatCreateSeqDense(MPI_Comm_f2c(*(MPI_Fint *)&*comm),*m,*n,data,newmat);
}
For MATSEQDENSE matrix, the factorization is just a thin wrapper to LAPACK \n\n";
#include <petscmat.h>
#undef __FUNCT__
#define __FUNCT__ "main"
int main(int argc,char **argv)
{
Mat mat,F,RHS,SOLU;
MatInfo info;
PetscErrorCode ierr;
PetscInt m = 10,n = 10,i,j,rstart,rend,nrhs=2;
PetscScalar value = 1.0;
Vec x,y,b,ytmp;
PetscReal norm,tol=1.e-15;
PetscMPIInt size;
PetscScalar *rhs_array,*solu_array;
PetscRandom rand;
PetscScalar *array,rval;
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 single vectors */
ierr = VecCreate(PETSC_COMM_WORLD,&y);CHKERRQ(ierr);
ierr = VecSetSizes(y,PETSC_DECIDE,m);CHKERRQ(ierr);
ierr = VecSetFromOptions(y);CHKERRQ(ierr);
ierr = VecDuplicate(y,&x);CHKERRQ(ierr);
ierr = VecDuplicate(y,&ytmp);CHKERRQ(ierr);
ierr = VecSet(x,value);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecSetSizes(b,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(b);CHKERRQ(ierr);
/* create multiple vectors RHS and SOLU */
ierr = MatCreate(PETSC_COMM_WORLD,&RHS);CHKERRQ(ierr);
ierr = MatSetSizes(RHS,PETSC_DECIDE,PETSC_DECIDE,n,nrhs);CHKERRQ(ierr);
ierr = MatSetType(RHS,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(RHS);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(RHS,NULL);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = MatDenseGetArray(RHS,&array);CHKERRQ(ierr);
for (j=0; j<nrhs; j++) {
for (i=0; i<n; i++) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
array[n*j+i] = rval;
}
}
ierr = MatDenseRestoreArray(RHS,&array);CHKERRQ(ierr);
ierr = MatDuplicate(RHS,MAT_DO_NOT_COPY_VALUES,&SOLU);CHKERRQ(ierr);
/* create matrix */
ierr = MatCreateSeqDense(PETSC_COMM_WORLD,m,n,NULL,&mat);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(mat,&rstart,&rend);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
value = (PetscReal)i+1;
ierr = MatSetValues(mat,1,&i,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"matrix nonzeros = %D, allocated nonzeros = %D\n",
(PetscInt)info.nz_used,(PetscInt)info.nz_allocated);CHKERRQ(ierr);
/* Cholesky factorization - perm and factinfo are ignored by LAPACK */
/* in-place Cholesky */
ierr = MatMult(mat,x,b);CHKERRQ(ierr);
ierr = MatDuplicate(mat,MAT_COPY_VALUES,&F);CHKERRQ(ierr);
ierr = MatCholeskyFactor(F,0,0);CHKERRQ(ierr);
ierr = MatSolve(F,b,y);CHKERRQ(ierr);
ierr = MatDestroy(&F);CHKERRQ(ierr);
value = -1.0; ierr = VecAXPY(y,value,x);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: Norm of error for Cholesky %G\n",norm);CHKERRQ(ierr);
}
/* out-place Cholesky */
ierr = MatGetFactor(mat,MATSOLVERPETSC,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr);
ierr = MatCholeskyFactorSymbolic(F,mat,0,0);CHKERRQ(ierr);
ierr = MatCholeskyFactorNumeric(F,mat,0);CHKERRQ(ierr);
ierr = MatSolve(F,b,y);CHKERRQ(ierr);
value = -1.0; ierr = VecAXPY(y,value,x);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: Norm of error for Cholesky %G\n",norm);CHKERRQ(ierr);
}
ierr = MatDestroy(&F);CHKERRQ(ierr);
/* LU factorization - perms and factinfo are ignored by LAPACK */
i = m-1; value = 1.0;
ierr = MatSetValues(mat,1,&i,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatMult(mat,x,b);CHKERRQ(ierr);
ierr = MatDuplicate(mat,MAT_COPY_VALUES,&F);CHKERRQ(ierr);
/* in-place LU */
ierr = MatLUFactor(F,0,0,0);CHKERRQ(ierr);
ierr = MatSolve(F,b,y);CHKERRQ(ierr);
value = -1.0; ierr = VecAXPY(y,value,x);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: Norm of error for LU %G\n",norm);CHKERRQ(ierr);
}
ierr = MatMatSolve(F,RHS,SOLU);CHKERRQ(ierr);
ierr = MatDenseGetArray(SOLU,&solu_array);CHKERRQ(ierr);
ierr = MatDenseGetArray(RHS,&rhs_array);CHKERRQ(ierr);
for (j=0; j<nrhs; j++) {
ierr = VecPlaceArray(y,solu_array+j*m);CHKERRQ(ierr);
ierr = VecPlaceArray(b,rhs_array+j*m);CHKERRQ(ierr);
ierr = MatMult(mat,y,ytmp);CHKERRQ(ierr);
ierr = VecAXPY(ytmp,-1.0,b);CHKERRQ(ierr); /* ytmp = mat*SOLU[:,j] - RHS[:,j] */
ierr = VecNorm(ytmp,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: Norm of residual for LU %G\n",norm);CHKERRQ(ierr);
}
ierr = VecResetArray(b);CHKERRQ(ierr);
ierr = VecResetArray(y);CHKERRQ(ierr);
}
ierr = MatDenseRestoreArray(RHS,&rhs_array);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(SOLU,&solu_array);CHKERRQ(ierr);
ierr = MatDestroy(&F);CHKERRQ(ierr);
/* out-place LU */
ierr = MatGetFactor(mat,MATSOLVERPETSC,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
ierr = MatLUFactorSymbolic(F,mat,0,0,0);CHKERRQ(ierr);
ierr = MatLUFactorNumeric(F,mat,0);CHKERRQ(ierr);
ierr = MatSolve(F,b,y);CHKERRQ(ierr);
value = -1.0; ierr = VecAXPY(y,value,x);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: Norm of error for LU %G\n",norm);CHKERRQ(ierr);
}
/* free space */
ierr = MatDestroy(&F);CHKERRQ(ierr);
ierr = MatDestroy(&mat);CHKERRQ(ierr);
ierr = MatDestroy(&RHS);CHKERRQ(ierr);
ierr = MatDestroy(&SOLU);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = VecDestroy(&ytmp);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
TS ts;
SNES snes_alg;
PetscErrorCode ierr;
PetscMPIInt size;
Userctx user;
PetscViewer Xview,Ybusview;
Vec X;
Mat J;
PetscInt i;
ierr = PetscInitialize(&argc,&argv,"petscoptions",help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");
user.neqs_gen = 9*ngen; /* # eqs. for generator subsystem */
user.neqs_net = 2*nbus; /* # eqs. for network subsystem */
user.neqs_pgrid = user.neqs_gen + user.neqs_net;
/* Create indices for differential and algebraic equations */
PetscInt *idx2;
ierr = PetscMalloc1(7*ngen,&idx2);CHKERRQ(ierr);
for (i=0; i<ngen; i++) {
idx2[7*i] = 9*i; idx2[7*i+1] = 9*i+1; idx2[7*i+2] = 9*i+2; idx2[7*i+3] = 9*i+3;
idx2[7*i+4] = 9*i+6; idx2[7*i+5] = 9*i+7; idx2[7*i+6] = 9*i+8;
}
ierr = ISCreateGeneral(PETSC_COMM_WORLD,7*ngen,idx2,PETSC_COPY_VALUES,&user.is_diff);CHKERRQ(ierr);
ierr = ISComplement(user.is_diff,0,user.neqs_pgrid,&user.is_alg);CHKERRQ(ierr);
ierr = PetscFree(idx2);CHKERRQ(ierr);
/* Read initial voltage vector and Ybus */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"X.bin",FILE_MODE_READ,&Xview);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Ybus.bin",FILE_MODE_READ,&Ybusview);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&user.V0);CHKERRQ(ierr);
ierr = VecSetSizes(user.V0,PETSC_DECIDE,user.neqs_net);CHKERRQ(ierr);
ierr = VecLoad(user.V0,Xview);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&user.Ybus);CHKERRQ(ierr);
ierr = MatSetSizes(user.Ybus,PETSC_DECIDE,PETSC_DECIDE,user.neqs_net,user.neqs_net);CHKERRQ(ierr);
ierr = MatSetType(user.Ybus,MATBAIJ);CHKERRQ(ierr);
/* ierr = MatSetBlockSize(user.Ybus,2);CHKERRQ(ierr); */
ierr = MatLoad(user.Ybus,Ybusview);CHKERRQ(ierr);
/* Set run time options */
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Transient stability fault options","");CHKERRQ(ierr);
{
user.tfaulton = 1.0;
user.tfaultoff = 1.2;
user.Rfault = 0.0001;
user.faultbus = 8;
ierr = PetscOptionsReal("-tfaulton","","",user.tfaulton,&user.tfaulton,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tfaultoff","","",user.tfaultoff,&user.tfaultoff,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-faultbus","","",user.faultbus,&user.faultbus,NULL);CHKERRQ(ierr);
user.t0 = 0.0;
user.tmax = 5.0;
ierr = PetscOptionsReal("-t0","","",user.t0,&user.t0,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tmax","","",user.tmax,&user.tmax,NULL);CHKERRQ(ierr);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscViewerDestroy(&Xview);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&Ybusview);CHKERRQ(ierr);
/* Create DMs for generator and network subsystems */
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,user.neqs_gen,1,1,NULL,&user.dmgen);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(user.dmgen,"dmgen_");CHKERRQ(ierr);
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,user.neqs_net,1,1,NULL,&user.dmnet);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(user.dmnet,"dmnet_");CHKERRQ(ierr);
/* Create a composite DM packer and add the two DMs */
ierr = DMCompositeCreate(PETSC_COMM_WORLD,&user.dmpgrid);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(user.dmpgrid,"pgrid_");CHKERRQ(ierr);
ierr = DMCompositeAddDM(user.dmpgrid,user.dmgen);CHKERRQ(ierr);
ierr = DMCompositeAddDM(user.dmpgrid,user.dmnet);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user.dmpgrid,&X);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,user.neqs_pgrid,user.neqs_pgrid);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = PreallocateJacobian(J,&user);CHKERRQ(ierr);
/* Create matrix to save solutions at each time step */
user.stepnum = 0;
ierr = MatCreateSeqDense(PETSC_COMM_SELF,user.neqs_pgrid+1,1002,NULL,&user.Sol);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetEquationType(ts,TS_EQ_DAE_IMPLICIT_INDEX1);CHKERRQ(ierr);
ierr = TSARKIMEXSetFullyImplicit(ts,PETSC_TRUE);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,&user);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,J,J,(TSIJacobian)IJacobian,&user);CHKERRQ(ierr);
ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SetInitialGuess(X,&user);CHKERRQ(ierr);
/* Just to set up the Jacobian structure */
Vec Xdot;
MatStructure flg;
ierr = VecDuplicate(X,&Xdot);CHKERRQ(ierr);
ierr = IJacobian(ts,0.0,X,Xdot,0.0,J,J,&flg,&user);CHKERRQ(ierr);
ierr = VecDestroy(&Xdot);CHKERRQ(ierr);
/* Save initial solution */
PetscScalar *x,*mat;
PetscInt idx=user.stepnum*(user.neqs_pgrid+1);
ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecGetArray(X,&x);CHKERRQ(ierr);
mat[idx] = 0.0;
ierr = PetscMemcpy(mat+idx+1,x,user.neqs_pgrid*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecRestoreArray(X,&x);CHKERRQ(ierr);
user.stepnum++;
ierr = TSSetDuration(ts,1000,user.tfaulton);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,0.01);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSetPostStep(ts,SaveSolution);CHKERRQ(ierr);
user.alg_flg = PETSC_FALSE;
/* Prefault period */
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* Create the nonlinear solver for solving the algebraic system */
/* Note that although the algebraic system needs to be solved only for
Idq and V, we reuse the entire system including xgen. The xgen
variables are held constant by setting their residuals to 0 and
putting a 1 on the Jacobian diagonal for xgen rows
*/
Vec F_alg;
ierr = VecDuplicate(X,&F_alg);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&snes_alg);CHKERRQ(ierr);
ierr = SNESSetFunction(snes_alg,F_alg,AlgFunction,&user);CHKERRQ(ierr);
ierr = MatZeroEntries(J);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes_alg,J,J,AlgJacobian,&user);CHKERRQ(ierr);
ierr = SNESSetOptionsPrefix(snes_alg,"alg_");CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes_alg);CHKERRQ(ierr);
/* Apply disturbance - resistive fault at user.faultbus */
/* This is done by adding shunt conductance to the diagonal location
in the Ybus matrix */
PetscInt row_loc,col_loc;
PetscScalar val;
row_loc = 2*user.faultbus; col_loc = 2*user.faultbus+1; /* Location for G */
val = 1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
row_loc = 2*user.faultbus+1; col_loc = 2*user.faultbus; /* Location for G */
val = 1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
user.alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
/* Save fault-on solution */
idx = user.stepnum*(user.neqs_pgrid+1);
ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecGetArray(X,&x);CHKERRQ(ierr);
mat[idx] = user.tfaulton;
ierr = PetscMemcpy(mat+idx+1,x,user.neqs_pgrid*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecRestoreArray(X,&x);CHKERRQ(ierr);
user.stepnum++;
/* Disturbance period */
ierr = TSSetDuration(ts,1000,user.tfaultoff);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,user.tfaulton,.01);CHKERRQ(ierr);
user.alg_flg = PETSC_FALSE;
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* Remove the fault */
row_loc = 2*user.faultbus; col_loc = 2*user.faultbus+1;
val = -1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
row_loc = 2*user.faultbus+1; col_loc = 2*user.faultbus;
val = -1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatZeroEntries(J);CHKERRQ(ierr);
user.alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
/* Save tfault off solution */
idx = user.stepnum*(user.neqs_pgrid+1);
ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecGetArray(X,&x);CHKERRQ(ierr);
mat[idx] = user.tfaultoff;
ierr = PetscMemcpy(mat+idx+1,x,user.neqs_pgrid*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecRestoreArray(X,&x);CHKERRQ(ierr);
user.stepnum++;
/* Post-disturbance period */
ierr = TSSetDuration(ts,1000,user.tmax);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,user.tfaultoff,.01);CHKERRQ(ierr);
user.alg_flg = PETSC_TRUE;
ierr = TSSolve(ts,X);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user.Sol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user.Sol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
Mat A;
PetscScalar *amat;
ierr = MatCreateSeqDense(PETSC_COMM_SELF,user.neqs_pgrid+1,user.stepnum,NULL,&A);CHKERRQ(ierr);
ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = MatDenseGetArray(A,&amat);CHKERRQ(ierr);
ierr = PetscMemcpy(amat,mat,(user.stepnum*(user.neqs_pgrid+1))*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(A,&amat);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr);
PetscViewer viewer;
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"out.bin",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = MatView(A,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = SNESDestroy(&snes_alg);CHKERRQ(ierr);
ierr = VecDestroy(&F_alg);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = MatDestroy(&user.Ybus);CHKERRQ(ierr);
ierr = MatDestroy(&user.Sol);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&user.V0);CHKERRQ(ierr);
ierr = DMDestroy(&user.dmgen);CHKERRQ(ierr);
ierr = DMDestroy(&user.dmnet);CHKERRQ(ierr);
ierr = DMDestroy(&user.dmpgrid);CHKERRQ(ierr);
ierr = ISDestroy(&user.is_diff);CHKERRQ(ierr);
ierr = ISDestroy(&user.is_alg);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = PetscFinalize();
return(0);
}
int main(int argc,char **args)
{
const PetscScalar xvals[] = {11,13},yvals[] = {17,19},zvals[] = {23,29};
const PetscInt inds[] = {0,1};
PetscScalar avals[] = {2,3,5,7};
Mat A,S,D[4],N;
Vec X,Y,Z;
User user;
PetscInt i;
PetscErrorCode ierr;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,2,2,2,NULL,&A);
CHKERRQ(ierr);
ierr = MatSetUp(A);
CHKERRQ(ierr);
ierr = MatSetValues(A,2,inds,2,inds,avals,INSERT_VALUES);
CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_WORLD,2,&X);
CHKERRQ(ierr);
ierr = VecDuplicate(X,&Y);
CHKERRQ(ierr);
ierr = VecDuplicate(X,&Z);
CHKERRQ(ierr);
ierr = VecSetValues(X,2,inds,xvals,INSERT_VALUES);
CHKERRQ(ierr);
ierr = VecSetValues(Y,2,inds,yvals,INSERT_VALUES);
CHKERRQ(ierr);
ierr = VecSetValues(Z,2,inds,zvals,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = VecAssemblyBegin(X);
CHKERRQ(ierr);
ierr = VecAssemblyBegin(Y);
CHKERRQ(ierr);
ierr = VecAssemblyBegin(Z);
CHKERRQ(ierr);
ierr = VecAssemblyEnd(X);
CHKERRQ(ierr);
ierr = VecAssemblyEnd(Y);
CHKERRQ(ierr);
ierr = VecAssemblyEnd(Z);
CHKERRQ(ierr);
ierr = PetscNew(struct _n_User,&user);
CHKERRQ(ierr);
user->B = A;
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 = MatShellSetOperation(S,MATOP_GET_DIAGONAL,(void (*)(void))MatGetDiagonal_User);
CHKERRQ(ierr);
for (i=0; i<4; i++) {
ierr = MatCreateSeqDense(PETSC_COMM_WORLD,1,1,&avals[i],&D[i]);
CHKERRQ(ierr);
}
ierr = MatCreateNest(PETSC_COMM_WORLD,2,NULL,2,NULL,D,&N);
CHKERRQ(ierr);
ierr = MatSetUp(N);
CHKERRQ(ierr);
ierr = TestMatrix(S,X,Y,Z);
CHKERRQ(ierr);
ierr = TestMatrix(A,X,Y,Z);
CHKERRQ(ierr);
ierr = TestMatrix(N,X,Y,Z);
CHKERRQ(ierr);
for (i=0; i<4; i++) {
ierr = MatDestroy(&D[i]);
CHKERRQ(ierr);
}
ierr = MatDestroy(&A);
CHKERRQ(ierr);
ierr = MatDestroy(&S);
CHKERRQ(ierr);
ierr = MatDestroy(&N);
CHKERRQ(ierr);
ierr = VecDestroy(&X);
CHKERRQ(ierr);
ierr = VecDestroy(&Y);
CHKERRQ(ierr);
ierr = VecDestroy(&Z);
CHKERRQ(ierr);
ierr = PetscFree(user);
CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
Userctx user;
Vec p;
PetscScalar *x_ptr;
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt i,numDataBuses;
KSP ksp;
PC pc;
Tao tao;
TaoConvergedReason reason;
Vec lowerb,upperb;
PetscViewer viewer;
PetscScalar *proj_vec;
//PetscLogDouble t0,t1;
/* time the inversion process */
//ierr = PetscGetTime(&t0);CHKERRQ(ierr);
ierr = PetscInitialize(&argc,&argv,"petscoptions",help);CHKERRQ(ierr);
PetscFunctionBeginUser;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");
ierr = ModelSetup(&user);CHKERRQ(ierr);
/* hard code the data projection here - for now assume data at all buses */
ierr = VecCreateSeq(PETSC_COMM_WORLD,nbus,&user.proj);CHKERRQ(ierr);
/*ierr = VecCreateSeq(PETSC_COMM_WORLD,4,&user.proj);CHKERRQ(ierr);*/
ierr = VecGetArray(user.proj,&proj_vec);CHKERRQ(ierr);
for(i=0; i<nbus; i++) {
proj_vec[i]=i;
}
srand( time(NULL) + rand () );
//VecView(user.proj, PETSC_VIEWER_STDOUT_WORLD);
/* -- 2 5 6 8 */
/* -- proj_vec[0]=1; proj_vec[1]=4; proj_vec[2]=5; proj_vec[3]=7; */
ierr = VecRestoreArray(user.proj,&proj_vec);CHKERRQ(ierr);
/* allocate/set the prior mean and its standard deviation */
ierr = PetscMalloc(3*sizeof(PetscScalar), &user.prior_mean);
ierr = PetscMalloc(3*sizeof(PetscScalar), &user.prior_stddev);
/*{23.64,6.4,3.01};*/
user.prior_mean[0] = 24.0;
user.prior_mean[1] = 6.0;
user.prior_mean[2] = 3.1;
for(i=0; i<3; i++) user.prior_stddev[i] = user.prior_mean[i]*user.prior_noise;
/* Create matrix to store solution */
if(user.saveSol) {
ierr = MatCreateSeqDense(PETSC_COMM_SELF,
user.neqs_pgrid+1,
(PetscInt) round((user.tfinal-user.t0)/user.dt+1),
NULL,
&user.Sol);
CHKERRQ(ierr);
}
printf("Num cols=%d\n", (PetscInt) round((user.tfinal-user.t0)/user.dt+1));
/* *********************************
* Generate/load observations
**********************************/
ierr = VecGetSize(user.proj, &numDataBuses);CHKERRQ(ierr);
/* Create matrix to save solutions at each time step */
ierr = MatCreateSeqDense(PETSC_COMM_SELF,
2*numDataBuses,
//(PetscInt) round((user.tfinal-user.tdisturb)/user.data_dt)+1,
(PetscInt) round((user.tfinal-user.trestore)/user.data_dt)+1,
NULL,
&user.obs);
CHKERRQ(ierr);
ierr = InitializeData(H0, &user, user.data_noise, user.data_dt);CHKERRQ(ierr);
if(0==strlen(user.loadObsFile)) {
/* save observations */
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"obs-perturbed.bin",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = MatView(user.obs,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
printf("Observations generated.\n");
}
if(user.saveSol) {
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"out_pert.bin",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = MatView(user.Sol,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = MatDestroy(&user.Sol);CHKERRQ(ierr);
CHKERRQ(ierr);
}
if(user.outputCov) {
printf("The diagonal of the data noise covariance matrix (%g absolute noise) is:\n", user.data_noise);
for(i=0; i<2*numDataBuses; i++) printf("%18.12f ", user.data_stddev[i]*user.data_stddev[i]); printf("\n");
printf("The prior mean is: ");
for(i=0; i<3; i++) printf("%18.12f ", user.prior_mean[i]); printf("\n");
printf("The diagonal of the prior covariance matrix (%g relative noise) is:\n", user.prior_noise);
for(i=0; i<3; i++) printf("%18.12f ", user.prior_stddev[i]*user.prior_stddev[i]); printf("\n");
goto finalize;
}
/* ***************************************
* Optimization phase
* ***************************************/
/* Create TAO solver and set desired solution method */
ierr = TaoCreate(PETSC_COMM_WORLD,&tao);CHKERRQ(ierr);
ierr = TaoSetType(tao,TAOBLMVM);CHKERRQ(ierr);
/*
Optimization starts
*/
printf("Starting optimization...\n");
/* PetscScalar H_disturb[3]= {25.,6.4,3.01}; New inertia (after tdisturb) to be estimated */
/* Set initial solution guess */
ierr = VecCreateSeq(PETSC_COMM_WORLD,3,&p);CHKERRQ(ierr);
ierr = VecGetArray(p,&x_ptr);CHKERRQ(ierr);
//x_ptr[0] = H0[0]; x_ptr[1] = H0[1]; x_ptr[2] = H0[2];
x_ptr[0] = H0[0]*1.1; x_ptr[1] = H0[1]*1.1; x_ptr[2] = H0[2]*1.1;
ierr = VecRestoreArray(p,&x_ptr);CHKERRQ(ierr);
ierr = TaoSetInitialVector(tao,p);CHKERRQ(ierr);
/* Set routine for function and gradient evaluation */
//ierr = TaoSetObjectiveRoutine(tao,FormFunction,(void *)&user);CHKERRQ(ierr);
//ierr = TaoSetGradientRoutine(tao,TaoDefaultComputeGradient,(void *)&user);CHKERRQ(ierr);
/* Sets the cost and gradient evaluation routine for minimization */
ierr = TaoSetObjectiveAndGradientRoutine(tao,FormFunctionGradient,&user);CHKERRQ(ierr);
/* Set bounds for the optimization */
ierr = VecDuplicate(p,&lowerb);CHKERRQ(ierr);
ierr = VecDuplicate(p,&upperb);CHKERRQ(ierr);
ierr = VecGetArray(lowerb,&x_ptr);CHKERRQ(ierr);
x_ptr[0] = 20.64; x_ptr[1] = 5.4; x_ptr[2] = 2.01;
ierr = VecRestoreArray(lowerb,&x_ptr);CHKERRQ(ierr);
ierr = VecGetArray(upperb,&x_ptr);CHKERRQ(ierr);
x_ptr[0] = 25.64; x_ptr[1] = 7.4; x_ptr[2] = 4.01;
ierr = VecRestoreArray(upperb,&x_ptr);CHKERRQ(ierr);
ierr = TaoSetVariableBounds(tao,lowerb,upperb);
/* Check for any TAO command line options */
ierr = TaoSetFromOptions(tao);CHKERRQ(ierr);
ierr = TaoGetKSP(tao,&ksp);CHKERRQ(ierr);
if (ksp) {
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCNONE);CHKERRQ(ierr);
}
//ierr = TaoSetTolerances(tao,1e-8,1e-6,1e-8,1e-6,1e-4);
ierr = TaoSetTolerances(tao,1e-8,1e-8,1e-8,1e-8,1e-6);
//ierr = TaoSetGradientTolerances(tao,1e-8, 1e-6, 1e-6);
/* SOLVE the estimation problem */
ierr = TaoSolve(tao); CHKERRQ(ierr);
/* Get information on termination */
printf("--- optimization done\n");
/* time the inversion process */
//ierr = PetscGetTime(&t1);CHKERRQ(ierr);
//printf("elapsed_time %f seconds\n", t1 - t0);
ierr = TaoGetConvergedReason(tao,&reason);CHKERRQ(ierr);
if (reason <= 0){
ierr=PetscPrintf(MPI_COMM_WORLD, "Try another method! \n");CHKERRQ(ierr);
}
/*ierr = VecView(p,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);*/
ierr = VecGetArray(p,&x_ptr);CHKERRQ(ierr);
printf("inertia-out: %.12f %.12f %.12f\n", x_ptr[0], x_ptr[1], x_ptr[2]);
ierr = VecRestoreArray(p,&x_ptr);CHKERRQ(ierr);
//ierr = EvaluateHessianFD(tao, p, &user);CHKERRQ(ierr);
/* Free TAO data structures */
ierr = TaoDestroy(&tao);CHKERRQ(ierr);
ierr = VecDestroy(&lowerb);CHKERRQ(ierr);
ierr = VecDestroy(&upperb);CHKERRQ(ierr);
finalize:
ierr = MatDestroy(&user.obs);CHKERRQ(ierr);
ierr = VecDestroy(&user.X0_disturb);CHKERRQ(ierr);
ierr = PetscFree(user.data_stddev);CHKERRQ(ierr);
PetscFree(user.prior_mean);
PetscFree(user.prior_stddev);
ierr = DMDestroy(&user.dmgen);CHKERRQ(ierr);
ierr = DMDestroy(&user.dmnet);CHKERRQ(ierr);
ierr = DMDestroy(&user.dmpgrid);CHKERRQ(ierr);
ierr = ISDestroy(&user.is_diff);CHKERRQ(ierr);
ierr = ISDestroy(&user.is_alg);CHKERRQ(ierr);
ierr = MatDestroy(&user.J);CHKERRQ(ierr);
ierr = MatDestroy(&user.Jacp);CHKERRQ(ierr);
ierr = MatDestroy(&user.Ybus);CHKERRQ(ierr);
ierr = VecDestroy(&user.V0);CHKERRQ(ierr);
ierr = VecDestroy(&p);CHKERRQ(ierr);
ierr = PetscFinalize();
return(0);
}
/*
DMDAGetFaceInterpolation - Gets the interpolation for a face based coarse space
*/
PetscErrorCode DMDAGetFaceInterpolation(DM da,PC_Exotic *exotic,Mat Aglobal,MatReuse reuse,Mat *P)
{
PetscErrorCode ierr;
PetscInt dim,i,j,k,m,n,p,dof,Nint,Nface,Nwire,Nsurf,*Iint,*Isurf,cint = 0,csurf = 0,istart,jstart,kstart,*II,N,c = 0;
PetscInt mwidth,nwidth,pwidth,cnt,mp,np,pp,Ntotal,gl[6],*globals,Ng,*IIint,*IIsurf,Nt;
Mat Xint, Xsurf,Xint_tmp;
IS isint,issurf,is,row,col;
ISLocalToGlobalMapping ltg;
MPI_Comm comm;
Mat A,Aii,Ais,Asi,*Aholder,iAii;
MatFactorInfo info;
PetscScalar *xsurf,*xint;
#if defined(PETSC_USE_DEBUG_foo)
PetscScalar tmp;
#endif
PetscTable ht;
PetscFunctionBegin;
ierr = DMDAGetInfo(da,&dim,0,0,0,&mp,&np,&pp,&dof,0,0,0,0,0);
CHKERRQ(ierr);
if (dof != 1) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Only for single field problems");
if (dim != 3) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Only coded for 3d problems");
ierr = DMDAGetCorners(da,0,0,0,&m,&n,&p);
CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(da,&istart,&jstart,&kstart,&mwidth,&nwidth,&pwidth);
CHKERRQ(ierr);
istart = istart ? -1 : 0;
jstart = jstart ? -1 : 0;
kstart = kstart ? -1 : 0;
/*
the columns of P are the interpolation of each coarse grid point (one for each vertex and edge)
to all the local degrees of freedom (this includes the vertices, edges and faces).
Xint are the subset of the interpolation into the interior
Xface are the interpolation onto faces but not into the interior
Xsurf are the interpolation onto the vertices and edges (the surfbasket)
Xint
Symbolically one could write P = (Xface) after interchanging the rows to match the natural ordering on the domain
Xsurf
*/
N = (m - istart)*(n - jstart)*(p - kstart);
Nint = (m-2-istart)*(n-2-jstart)*(p-2-kstart);
Nface = 2*((m-2-istart)*(n-2-jstart) + (m-2-istart)*(p-2-kstart) + (n-2-jstart)*(p-2-kstart));
Nwire = 4*((m-2-istart) + (n-2-jstart) + (p-2-kstart)) + 8;
Nsurf = Nface + Nwire;
ierr = MatCreateSeqDense(MPI_COMM_SELF,Nint,6,NULL,&Xint);
CHKERRQ(ierr);
ierr = MatCreateSeqDense(MPI_COMM_SELF,Nsurf,6,NULL,&Xsurf);
CHKERRQ(ierr);
ierr = MatDenseGetArray(Xsurf,&xsurf);
CHKERRQ(ierr);
/*
Require that all 12 edges and 6 faces have at least one grid point. Otherwise some of the columns of
Xsurf will be all zero (thus making the coarse matrix singular).
*/
if (m-istart < 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Number of grid points per process in X direction must be at least 3");
if (n-jstart < 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Number of grid points per process in Y direction must be at least 3");
if (p-kstart < 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Number of grid points per process in Z direction must be at least 3");
cnt = 0;
for (j=1; j<n-1-jstart; j++) {
for (i=1; i<m-istart-1; i++) xsurf[cnt++ + 0*Nsurf] = 1;
}
for (k=1; k<p-1-kstart; k++) {
for (i=1; i<m-istart-1; i++) xsurf[cnt++ + 1*Nsurf] = 1;
for (j=1; j<n-1-jstart; j++) {
xsurf[cnt++ + 2*Nsurf] = 1;
/* these are the interior nodes */
xsurf[cnt++ + 3*Nsurf] = 1;
}
for (i=1; i<m-istart-1; i++) xsurf[cnt++ + 4*Nsurf] = 1;
}
for (j=1; j<n-1-jstart; j++) {
for (i=1; i<m-istart-1; i++) xsurf[cnt++ + 5*Nsurf] = 1;
}
#if defined(PETSC_USE_DEBUG_foo)
for (i=0; i<Nsurf; i++) {
tmp = 0.0;
for (j=0; j<6; j++) tmp += xsurf[i+j*Nsurf];
if (PetscAbsScalar(tmp-1.0) > 1.e-10) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Wrong Xsurf interpolation at i %D value %g",i,(double)PetscAbsScalar(tmp));
}
#endif
ierr = MatDenseRestoreArray(Xsurf,&xsurf);
CHKERRQ(ierr);
/* ierr = MatView(Xsurf,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);*/
/*
I are the indices for all the needed vertices (in global numbering)
Iint are the indices for the interior values, I surf for the surface values
(This is just for the part of the global matrix obtained with MatGetSubMatrix(), it
is NOT the local DMDA ordering.)
IIint and IIsurf are the same as the Iint, Isurf except they are in the global numbering
*/
#define Endpoint(a,start,b) (a == 0 || a == (b-1-start))
ierr = PetscMalloc3(N,&II,Nint,&Iint,Nsurf,&Isurf);
CHKERRQ(ierr);
ierr = PetscMalloc2(Nint,&IIint,Nsurf,&IIsurf);
CHKERRQ(ierr);
for (k=0; k<p-kstart; k++) {
for (j=0; j<n-jstart; j++) {
for (i=0; i<m-istart; i++) {
II[c++] = i + j*mwidth + k*mwidth*nwidth;
if (!Endpoint(i,istart,m) && !Endpoint(j,jstart,n) && !Endpoint(k,kstart,p)) {
IIint[cint] = i + j*mwidth + k*mwidth*nwidth;
Iint[cint++] = i + j*(m-istart) + k*(m-istart)*(n-jstart);
} else {
IIsurf[csurf] = i + j*mwidth + k*mwidth*nwidth;
Isurf[csurf++] = i + j*(m-istart) + k*(m-istart)*(n-jstart);
}
}
}
}
if (c != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"c != N");
if (cint != Nint) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"cint != Nint");
if (csurf != Nsurf) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"csurf != Nsurf");
ierr = DMGetLocalToGlobalMapping(da,<g);
CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApply(ltg,N,II,II);
CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApply(ltg,Nint,IIint,IIint);
CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApply(ltg,Nsurf,IIsurf,IIsurf);
CHKERRQ(ierr);
ierr = PetscObjectGetComm((PetscObject)da,&comm);
CHKERRQ(ierr);
ierr = ISCreateGeneral(comm,N,II,PETSC_COPY_VALUES,&is);
CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,Nint,Iint,PETSC_COPY_VALUES,&isint);
CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,Nsurf,Isurf,PETSC_COPY_VALUES,&issurf);
CHKERRQ(ierr);
ierr = PetscFree3(II,Iint,Isurf);
CHKERRQ(ierr);
ierr = ISSort(is);
CHKERRQ(ierr);
ierr = MatGetSubMatrices(Aglobal,1,&is,&is,MAT_INITIAL_MATRIX,&Aholder);
CHKERRQ(ierr);
A = *Aholder;
ierr = PetscFree(Aholder);
CHKERRQ(ierr);
ierr = MatGetSubMatrix(A,isint,isint,MAT_INITIAL_MATRIX,&Aii);
CHKERRQ(ierr);
ierr = MatGetSubMatrix(A,isint,issurf,MAT_INITIAL_MATRIX,&Ais);
CHKERRQ(ierr);
ierr = MatGetSubMatrix(A,issurf,isint,MAT_INITIAL_MATRIX,&Asi);
CHKERRQ(ierr);
/*
Solve for the interpolation onto the interior Xint
*/
ierr = MatMatMult(Ais,Xsurf,MAT_INITIAL_MATRIX,PETSC_DETERMINE,&Xint_tmp);
CHKERRQ(ierr);
ierr = MatScale(Xint_tmp,-1.0);
CHKERRQ(ierr);
if (exotic->directSolve) {
ierr = MatGetFactor(Aii,MATSOLVERPETSC,MAT_FACTOR_LU,&iAii);
CHKERRQ(ierr);
ierr = MatFactorInfoInitialize(&info);
CHKERRQ(ierr);
ierr = MatGetOrdering(Aii,MATORDERINGND,&row,&col);
CHKERRQ(ierr);
ierr = MatLUFactorSymbolic(iAii,Aii,row,col,&info);
CHKERRQ(ierr);
ierr = ISDestroy(&row);
CHKERRQ(ierr);
ierr = ISDestroy(&col);
CHKERRQ(ierr);
ierr = MatLUFactorNumeric(iAii,Aii,&info);
CHKERRQ(ierr);
ierr = MatMatSolve(iAii,Xint_tmp,Xint);
CHKERRQ(ierr);
ierr = MatDestroy(&iAii);
CHKERRQ(ierr);
} else {
Vec b,x;
PetscScalar *xint_tmp;
ierr = MatDenseGetArray(Xint,&xint);
CHKERRQ(ierr);
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,Nint,0,&x);
CHKERRQ(ierr);
ierr = MatDenseGetArray(Xint_tmp,&xint_tmp);
CHKERRQ(ierr);
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,Nint,0,&b);
CHKERRQ(ierr);
ierr = KSPSetOperators(exotic->ksp,Aii,Aii);
CHKERRQ(ierr);
for (i=0; i<6; i++) {
ierr = VecPlaceArray(x,xint+i*Nint);
CHKERRQ(ierr);
ierr = VecPlaceArray(b,xint_tmp+i*Nint);
CHKERRQ(ierr);
ierr = KSPSolve(exotic->ksp,b,x);
CHKERRQ(ierr);
ierr = VecResetArray(x);
CHKERRQ(ierr);
ierr = VecResetArray(b);
CHKERRQ(ierr);
}
ierr = MatDenseRestoreArray(Xint,&xint);
CHKERRQ(ierr);
ierr = MatDenseRestoreArray(Xint_tmp,&xint_tmp);
CHKERRQ(ierr);
ierr = VecDestroy(&x);
CHKERRQ(ierr);
ierr = VecDestroy(&b);
CHKERRQ(ierr);
}
ierr = MatDestroy(&Xint_tmp);
CHKERRQ(ierr);
#if defined(PETSC_USE_DEBUG_foo)
ierr = MatDenseGetArray(Xint,&xint);
CHKERRQ(ierr);
for (i=0; i<Nint; i++) {
tmp = 0.0;
for (j=0; j<6; j++) tmp += xint[i+j*Nint];
if (PetscAbsScalar(tmp-1.0) > 1.e-10) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Wrong Xint interpolation at i %D value %g",i,(double)PetscAbsScalar(tmp));
}
ierr = MatDenseRestoreArray(Xint,&xint);
CHKERRQ(ierr);
/* ierr =MatView(Xint,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */
#endif
/* total faces */
Ntotal = mp*np*(pp+1) + mp*pp*(np+1) + np*pp*(mp+1);
/*
For each vertex, edge, face on process (in the same orderings as used above) determine its local number including ghost points
*/
cnt = 0;
{
gl[cnt++] = mwidth+1;
}
{
{
gl[cnt++] = mwidth*nwidth+1;
}
{
gl[cnt++] = mwidth*nwidth + mwidth; /* these are the interior nodes */ gl[cnt++] = mwidth*nwidth + mwidth+m-istart-1;
}
{
gl[cnt++] = mwidth*nwidth+mwidth*(n-jstart-1)+1;
}
}
{
gl[cnt++] = mwidth*nwidth*(p-kstart-1) + mwidth+1;
}
/* PetscIntView(6,gl,PETSC_VIEWER_STDOUT_WORLD); */
/* convert that to global numbering and get them on all processes */
ierr = ISLocalToGlobalMappingApply(ltg,6,gl,gl);
CHKERRQ(ierr);
/* PetscIntView(6,gl,PETSC_VIEWER_STDOUT_WORLD); */
ierr = PetscMalloc1(6*mp*np*pp,&globals);
CHKERRQ(ierr);
ierr = MPI_Allgather(gl,6,MPIU_INT,globals,6,MPIU_INT,PetscObjectComm((PetscObject)da));
CHKERRQ(ierr);
/* Number the coarse grid points from 0 to Ntotal */
ierr = MatGetSize(Aglobal,&Nt,NULL);
CHKERRQ(ierr);
ierr = PetscTableCreate(Ntotal/3,Nt+1,&ht);
CHKERRQ(ierr);
for (i=0; i<6*mp*np*pp; i++) {
ierr = PetscTableAddCount(ht,globals[i]+1);
CHKERRQ(ierr);
}
ierr = PetscTableGetCount(ht,&cnt);
CHKERRQ(ierr);
if (cnt != Ntotal) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hash table size %D not equal to total number coarse grid points %D",cnt,Ntotal);
ierr = PetscFree(globals);
CHKERRQ(ierr);
for (i=0; i<6; i++) {
ierr = PetscTableFind(ht,gl[i]+1,&gl[i]);
CHKERRQ(ierr);
gl[i]--;
}
ierr = PetscTableDestroy(&ht);
CHKERRQ(ierr);
/* PetscIntView(6,gl,PETSC_VIEWER_STDOUT_WORLD); */
/* construct global interpolation matrix */
ierr = MatGetLocalSize(Aglobal,&Ng,NULL);
CHKERRQ(ierr);
if (reuse == MAT_INITIAL_MATRIX) {
ierr = MatCreateAIJ(PetscObjectComm((PetscObject)da),Ng,PETSC_DECIDE,PETSC_DECIDE,Ntotal,Nint+Nsurf,NULL,Nint,NULL,P);
CHKERRQ(ierr);
} else {
ierr = MatZeroEntries(*P);
CHKERRQ(ierr);
}
ierr = MatSetOption(*P,MAT_ROW_ORIENTED,PETSC_FALSE);
CHKERRQ(ierr);
ierr = MatDenseGetArray(Xint,&xint);
CHKERRQ(ierr);
ierr = MatSetValues(*P,Nint,IIint,6,gl,xint,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatDenseRestoreArray(Xint,&xint);
CHKERRQ(ierr);
ierr = MatDenseGetArray(Xsurf,&xsurf);
CHKERRQ(ierr);
ierr = MatSetValues(*P,Nsurf,IIsurf,6,gl,xsurf,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatDenseRestoreArray(Xsurf,&xsurf);
CHKERRQ(ierr);
ierr = MatAssemblyBegin(*P,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(*P,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = PetscFree2(IIint,IIsurf);
CHKERRQ(ierr);
#if defined(PETSC_USE_DEBUG_foo)
{
Vec x,y;
PetscScalar *yy;
ierr = VecCreateMPI(PetscObjectComm((PetscObject)da),Ng,PETSC_DETERMINE,&y);
CHKERRQ(ierr);
ierr = VecCreateMPI(PetscObjectComm((PetscObject)da),PETSC_DETERMINE,Ntotal,&x);
CHKERRQ(ierr);
ierr = VecSet(x,1.0);
CHKERRQ(ierr);
ierr = MatMult(*P,x,y);
CHKERRQ(ierr);
ierr = VecGetArray(y,&yy);
CHKERRQ(ierr);
for (i=0; i<Ng; i++) {
if (PetscAbsScalar(yy[i]-1.0) > 1.e-10) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Wrong p interpolation at i %D value %g",i,(double)PetscAbsScalar(yy[i]));
}
ierr = VecRestoreArray(y,&yy);
CHKERRQ(ierr);
ierr = VecDestroy(x);
CHKERRQ(ierr);
ierr = VecDestroy(y);
CHKERRQ(ierr);
}
#endif
ierr = MatDestroy(&Aii);
CHKERRQ(ierr);
ierr = MatDestroy(&Ais);
CHKERRQ(ierr);
ierr = MatDestroy(&Asi);
CHKERRQ(ierr);
ierr = MatDestroy(&A);
CHKERRQ(ierr);
ierr = ISDestroy(&is);
CHKERRQ(ierr);
ierr = ISDestroy(&isint);
CHKERRQ(ierr);
ierr = ISDestroy(&issurf);
CHKERRQ(ierr);
ierr = MatDestroy(&Xint);
CHKERRQ(ierr);
ierr = MatDestroy(&Xsurf);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
TS ts; /* ODE integrator */
Vec U; /* solution will be stored here */
Mat A; /* Jacobian matrix */
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt n = 2;
AppCtx user;
PetscScalar *u;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize program
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create necessary matrix and vectors
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatGetVecs(A,&U,PETSC_NULL);CHKERRQ(ierr);
/* Create wind speed data using Weibull distribution */
ierr = WindSpeeds(&user);CHKERRQ(ierr);
/* Set parameters for wind turbine and induction generator */
ierr = SetWindTurbineParams(&user);CHKERRQ(ierr);
ierr = SetInductionGeneratorParams(&user);CHKERRQ(ierr);
ierr = VecGetArray(U,&u);CHKERRQ(ierr);
u[0] = vwa;
u[1] = s;
ierr = VecRestoreArray(U,&u);CHKERRQ(ierr);
/* Create matrix to save solutions at each time step */
user.stepnum = 0;
ierr = MatCreateSeqDense(PETSC_COMM_SELF,3,2010,PETSC_NULL,&user.Sol);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,PETSC_NULL,(TSIFunction) IFunction,&user);CHKERRQ(ierr);
SNES snes;
ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,A,A,SNESDefaultComputeJacobian,PETSC_NULL);CHKERRQ(ierr);
/* ierr = TSSetIJacobian(ts,A,A,(TSIJacobian)IJacobian,&user);CHKERRQ(ierr); */
ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetSolution(ts,U);CHKERRQ(ierr);
/* Save initial solution */
PetscScalar *x,*mat;
PetscInt idx=3*user.stepnum;
ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecGetArray(U,&x);CHKERRQ(ierr);
mat[idx] = 0.0;
ierr = PetscMemcpy(mat+idx+1,x,2*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecRestoreArray(U,&x);CHKERRQ(ierr);
user.stepnum++;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set solver options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetDuration(ts,2000,20.0);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,.01);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSetPostStep(ts,SaveSolution);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSolve(ts,U);CHKERRQ(ierr);
Mat B;
PetscScalar *amat;
ierr = MatCreateSeqDense(PETSC_COMM_SELF,3,user.stepnum,PETSC_NULL,&B);CHKERRQ(ierr);
ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = MatDenseGetArray(B,&amat);CHKERRQ(ierr);
ierr = PetscMemcpy(amat,mat,user.stepnum*3*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(B,&amat);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr);
PetscViewer viewer;
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"out.bin",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = MatView(B,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = MatDestroy(&user.Sol);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecDestroy(&user.wind_data);CHKERRQ(ierr);
ierr = VecDestroy(&user.t_wind);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&U);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = PetscFinalize();
return(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
Vec t,v;
Mat B,M;
BV X;
PetscInt i,j,n=10,k=5,Istart,Iend,col[3];
PetscScalar value[3],alpha;
PetscReal nrm;
PetscViewer view;
PetscBool verbose,FirstBlock=PETSC_FALSE,LastBlock=PETSC_FALSE;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-k",&k,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-verbose",&verbose);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Test BV with non-standard inner product (n=%D, k=%D).\n",n,k);CHKERRQ(ierr);
/* Create inner product matrix */
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetSizes(B,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(B);CHKERRQ(ierr);
ierr = MatSetUp(B);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)B,"B");CHKERRQ(ierr);
ierr = MatGetOwnershipRange(B,&Istart,&Iend);CHKERRQ(ierr);
if (Istart==0) FirstBlock=PETSC_TRUE;
if (Iend==n) LastBlock=PETSC_TRUE;
value[0]=-1.0; value[1]=2.0; value[2]=-1.0;
for (i=(FirstBlock? Istart+1: Istart); i<(LastBlock? Iend-1: Iend); i++) {
col[0]=i-1; col[1]=i; col[2]=i+1;
ierr = MatSetValues(B,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (LastBlock) {
i=n-1; col[0]=n-2; col[1]=n-1;
ierr = MatSetValues(B,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (FirstBlock) {
i=0; col[0]=0; col[1]=1; value[0]=2.0; value[1]=-1.0;
ierr = MatSetValues(B,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatGetVecs(B,&t,NULL);CHKERRQ(ierr);
/* Create BV object X */
ierr = BVCreate(PETSC_COMM_WORLD,&X);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)X,"X");CHKERRQ(ierr);
ierr = BVSetSizesFromVec(X,t,k);CHKERRQ(ierr);
ierr = BVSetFromOptions(X);CHKERRQ(ierr);
ierr = BVSetMatrix(X,B,PETSC_FALSE);CHKERRQ(ierr);
/* Set up viewer */
ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&view);CHKERRQ(ierr);
if (verbose) {
ierr = PetscViewerPushFormat(view,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
}
/* Fill X entries */
for (j=0;j<k;j++) {
ierr = BVGetColumn(X,j,&v);CHKERRQ(ierr);
ierr = VecZeroEntries(v);CHKERRQ(ierr);
for (i=0;i<4;i++) {
if (i+j<n) {
ierr = VecSetValue(v,i+j,(PetscScalar)(3*i+j-2),INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = VecAssemblyBegin(v);CHKERRQ(ierr);
ierr = VecAssemblyEnd(v);CHKERRQ(ierr);
ierr = BVRestoreColumn(X,j,&v);CHKERRQ(ierr);
}
if (verbose) {
ierr = MatView(B,view);CHKERRQ(ierr);
ierr = BVView(X,view);CHKERRQ(ierr);
}
/* Test BVNormColumn */
ierr = BVNormColumn(X,0,NORM_2,&nrm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"B-Norm or X[0] = %g\n",(double)nrm);CHKERRQ(ierr);
/* Test BVOrthogonalizeColumn */
for (j=0;j<k;j++) {
ierr = BVOrthogonalizeColumn(X,j,NULL,&nrm,NULL);CHKERRQ(ierr);
alpha = 1.0/nrm;
ierr = BVScaleColumn(X,j,alpha);CHKERRQ(ierr);
}
if (verbose) {
ierr = BVView(X,view);CHKERRQ(ierr);
}
/* Check orthogonality */
ierr = MatCreateSeqDense(PETSC_COMM_SELF,k,k,NULL,&M);CHKERRQ(ierr);
ierr = BVDot(X,X,M);CHKERRQ(ierr);
ierr = MatShift(M,-1.0);CHKERRQ(ierr);
ierr = MatNorm(M,NORM_1,&nrm);CHKERRQ(ierr);
if (nrm<100*PETSC_MACHINE_EPSILON) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Level of orthogonality < 100*eps\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Level of orthogonality: %g\n",(double)nrm);CHKERRQ(ierr);
}
ierr = BVDestroy(&X);CHKERRQ(ierr);
ierr = MatDestroy(&M);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = VecDestroy(&t);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
Vec t,v;
Mat Q,M;
BV X,Y;
PetscInt i,j,n=10,kx=6,lx=3,ky=5,ly=2;
PetscScalar *q,*z;
PetscReal nrm;
PetscViewer view;
PetscBool verbose,trans;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-kx",&kx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-lx",&lx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-ky",&ky,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-ly",&ly,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-verbose",&verbose);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"First BV with %D active columns (%D leading columns) of dimension %D.\n",kx,lx,n);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Second BV with %D active columns (%D leading columns) of dimension %D.\n",ky,ly,n);CHKERRQ(ierr);
/* Create template vector */
ierr = VecCreate(PETSC_COMM_WORLD,&t);CHKERRQ(ierr);
ierr = VecSetSizes(t,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(t);CHKERRQ(ierr);
/* Create BV object X */
ierr = BVCreate(PETSC_COMM_WORLD,&X);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)X,"X");CHKERRQ(ierr);
ierr = BVSetSizesFromVec(X,t,kx+2);CHKERRQ(ierr); /* two extra columns to test active columns */
ierr = BVSetFromOptions(X);CHKERRQ(ierr);
ierr = BVSetActiveColumns(X,lx,kx);CHKERRQ(ierr);
/* Set up viewer */
ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&view);CHKERRQ(ierr);
if (verbose) {
ierr = PetscViewerPushFormat(view,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
}
/* Fill X entries */
for (j=0;j<kx+2;j++) {
ierr = BVGetColumn(X,j,&v);CHKERRQ(ierr);
ierr = VecZeroEntries(v);CHKERRQ(ierr);
for (i=0;i<4;i++) {
if (i+j<n) {
ierr = VecSetValue(v,i+j,(PetscScalar)(3*i+j-2),INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = VecAssemblyBegin(v);CHKERRQ(ierr);
ierr = VecAssemblyEnd(v);CHKERRQ(ierr);
ierr = BVRestoreColumn(X,j,&v);CHKERRQ(ierr);
}
if (verbose) {
ierr = BVView(X,view);CHKERRQ(ierr);
}
/* Create BV object Y */
ierr = BVCreate(PETSC_COMM_WORLD,&Y);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)Y,"Y");CHKERRQ(ierr);
ierr = BVSetSizesFromVec(Y,t,ky+1);CHKERRQ(ierr);
ierr = BVSetFromOptions(Y);CHKERRQ(ierr);
ierr = BVSetActiveColumns(Y,ly,ky);CHKERRQ(ierr);
/* Fill Y entries */
for (j=0;j<ky+1;j++) {
ierr = BVGetColumn(Y,j,&v);CHKERRQ(ierr);
ierr = VecSet(v,(PetscScalar)(j+1)/4.0);CHKERRQ(ierr);
ierr = BVRestoreColumn(Y,j,&v);CHKERRQ(ierr);
}
if (verbose) {
ierr = BVView(Y,view);CHKERRQ(ierr);
}
/* Create Mat */
ierr = MatCreateSeqDense(PETSC_COMM_SELF,kx,ky,NULL,&Q);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)Q,"Q");CHKERRQ(ierr);
ierr = MatDenseGetArray(Q,&q);CHKERRQ(ierr);
for (i=0;i<kx;i++)
for (j=0;j<ky;j++)
q[i+j*kx] = (i<j)? 2.0: -0.5;
ierr = MatDenseRestoreArray(Q,&q);CHKERRQ(ierr);
if (verbose) {
ierr = MatView(Q,NULL);CHKERRQ(ierr);
}
/* Test BVMult */
ierr = BVMult(Y,2.0,1.0,X,Q);CHKERRQ(ierr);
if (verbose) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"After BVMult - - - - - - - - -\n");CHKERRQ(ierr);
ierr = BVView(Y,view);CHKERRQ(ierr);
}
/* Test BVMultVec */
ierr = BVGetColumn(Y,0,&v);CHKERRQ(ierr);
ierr = PetscMalloc1(kx-lx,&z);CHKERRQ(ierr);
z[0] = 2.0;
for (i=1;i<kx-lx;i++) z[i] = -0.5*z[i-1];
ierr = BVMultVec(X,-1.0,1.0,v,z);CHKERRQ(ierr);
ierr = PetscFree(z);CHKERRQ(ierr);
ierr = BVRestoreColumn(Y,0,&v);CHKERRQ(ierr);
if (verbose) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"After BVMultVec - - - - - - -\n");CHKERRQ(ierr);
ierr = BVView(Y,view);CHKERRQ(ierr);
}
/* Test BVDot */
ierr = MatCreateSeqDense(PETSC_COMM_SELF,ky,kx,NULL,&M);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)M,"M");CHKERRQ(ierr);
ierr = BVDot(X,Y,M);CHKERRQ(ierr);
if (verbose) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"After BVDot - - - - - - - - -\n");CHKERRQ(ierr);
ierr = MatView(M,NULL);CHKERRQ(ierr);
}
/* Test BVDotVec */
ierr = BVGetColumn(Y,0,&v);CHKERRQ(ierr);
ierr = PetscMalloc1(kx-lx,&z);CHKERRQ(ierr);
ierr = BVDotVec(X,v,z);CHKERRQ(ierr);
ierr = BVRestoreColumn(Y,0,&v);CHKERRQ(ierr);
if (verbose) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"After BVDotVec - - - - - - -\n");CHKERRQ(ierr);
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,kx-lx,z,&v);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)v,"z");CHKERRQ(ierr);
ierr = VecView(v,view);CHKERRQ(ierr);
ierr = VecDestroy(&v);CHKERRQ(ierr);
}
ierr = PetscFree(z);CHKERRQ(ierr);
/* Test BVMultInPlace and BVScale */
ierr = PetscOptionsHasName(NULL,"-trans",&trans);CHKERRQ(ierr);
if (trans) {
Mat Qt;
ierr = MatTranspose(Q,MAT_INITIAL_MATRIX,&Qt);CHKERRQ(ierr);
ierr = BVMultInPlaceTranspose(X,Qt,lx+1,ky);CHKERRQ(ierr);
ierr = MatDestroy(&Qt);CHKERRQ(ierr);
} else {
ierr = BVMultInPlace(X,Q,lx+1,ky);CHKERRQ(ierr);
}
ierr = BVScale(X,2.0);CHKERRQ(ierr);
if (verbose) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"After BVMultInPlace - - - - -\n");CHKERRQ(ierr);
ierr = BVView(X,view);CHKERRQ(ierr);
}
/* Test BVNorm */
ierr = BVNormColumn(X,lx,NORM_2,&nrm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"2-Norm or X[%D] = %g\n",lx,(double)nrm);CHKERRQ(ierr);
ierr = BVNorm(X,NORM_FROBENIUS,&nrm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Frobenius Norm or X = %g\n",(double)nrm);CHKERRQ(ierr);
ierr = BVDestroy(&X);CHKERRQ(ierr);
ierr = BVDestroy(&Y);CHKERRQ(ierr);
ierr = MatDestroy(&Q);CHKERRQ(ierr);
ierr = MatDestroy(&M);CHKERRQ(ierr);
ierr = VecDestroy(&t);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
void FETI_Operations::set_null_space(const std::string& input_filename_base, int nb_of_vecs)
{
homemade_assert_msg(m_bNullVecsDimensionsSet,"Null vectors sizes not set yet!");
homemade_assert_msg(m_bScratchFolderSet,"Scratch folder not set yet!");
// Set the null vec arrays
m_null_nb_vecs = nb_of_vecs;
// Set the (dummy) coupling matrix pointer
Mat * coupling_matrix;
switch (m_RB_modes_system)
{
case RBModesSystem::MICRO :
coupling_matrix = &m_C_R_micro;
break;
case RBModesSystem::MACRO :
// TODO: Remove the error message below after the more general code was implemented
homemade_error_msg("Option not implemented yet!");
coupling_matrix = &m_C_R_BIG;
break;
}
// Matrix dimensions
// M x N
// coupling_matrix : n_med x n_sys
// m_null_vecs : n_sys x nb_of_vecs ( R ) -> nb_of_vecs vectors of dim n_sys
// m_null_coupled_vecs : n_med x nb_of_vecs ( RC ) -> nb_of_vecs vectors of dim n_coupl
// Set the first nullspace vectors
std::string input_filename = input_filename_base + "_0_n_" + std::to_string(m_null_nb_vecs) + ".petscvec";
VecCreate(m_comm.get(),&m_null_vecs[0]);
VecSetSizes(m_null_vecs[0],m_null_vecs_N_local,m_null_vecs_N);
read_PETSC_vector(m_null_vecs[0],input_filename, m_comm.get());
std::string output_filename = m_scratch_folder_path + "/rb_coupl_vector_0_n_" + std::to_string(m_null_nb_vecs) + ".petscvec";
VecCreate(m_comm.get(),&m_null_coupled_vecs[0]);
VecSetSizes(m_null_coupled_vecs[0],m_C_RR_M_local,m_C_RR_M);
VecSetFromOptions(m_null_coupled_vecs[0]);
MatMult(*coupling_matrix,m_null_vecs[0],m_null_coupled_vecs[0]);
write_PETSC_vector(m_null_coupled_vecs[0],output_filename,m_comm.rank(),m_comm.get());
// Read and calculate the rest of the nullspace vectors
for(int iii = 1; iii < m_null_nb_vecs; ++iii)
{
input_filename = input_filename_base + "_" + std::to_string(iii) + "_n_" + std::to_string(m_null_nb_vecs) + ".petscvec";
VecDuplicate(m_null_vecs[0],&m_null_vecs[iii]);
read_PETSC_vector(m_null_vecs[iii],input_filename, m_comm.get());
std::string output_filename = m_scratch_folder_path + "/rb_coupl_vector_" + std::to_string(iii) + "_n_" + std::to_string(m_null_nb_vecs) + ".petscvec";
VecDuplicate(m_null_coupled_vecs[0],&m_null_coupled_vecs[iii]);
MatMult(*coupling_matrix,m_null_vecs[iii],m_null_coupled_vecs[iii]);
write_PETSC_vector(m_null_coupled_vecs[iii],output_filename,m_comm.rank(),m_comm.get());
}
// Build the LOCAL dense matrix
std::vector<PetscScalar> dummy_vec_val(m_null_nb_vecs,0);
std::vector<PetscInt> dummy_vec_row(m_null_nb_vecs,0);
for(PetscInt iii = 0; iii < m_null_nb_vecs; ++iii)
{
dummy_vec_row[iii] = iii;
}
MatCreateSeqDense(PETSC_COMM_SELF,m_null_nb_vecs,m_null_nb_vecs,NULL,&m_RITRI_mat);
for(PetscInt iii = 0; iii < m_null_nb_vecs; ++iii)
{
VecMDot(m_null_coupled_vecs[iii],m_null_nb_vecs,m_null_coupled_vecs,dummy_vec_val.data());
MatSetValues(m_RITRI_mat,m_null_nb_vecs,dummy_vec_row.data(),1,&iii,dummy_vec_val.data(),INSERT_VALUES);
}
MatAssemblyBegin(m_RITRI_mat,MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(m_RITRI_mat,MAT_FINAL_ASSEMBLY);
PETSC_invert_dense_matrix(m_RITRI_mat,m_inv_RITRI_mat);
if(m_comm.rank() == 0)
{
write_PETSC_matrix(m_inv_RITRI_mat,m_scratch_folder_path + "/rb_inv_RITRI.petscmat",0,PETSC_COMM_SELF);
}
// Set up flag
m_bNullVecsSet = true;
m_binvRITRIMatSet = true;
// Cleanup
MatDestroy(&m_RITRI_mat);
}
static PetscErrorCode PCBDDCScalingSetUp_Deluxe_Private(PC pc)
{
PC_BDDC *pcbddc=(PC_BDDC*)pc->data;
PCBDDCDeluxeScaling deluxe_ctx=pcbddc->deluxe_ctx;
PCBDDCSubSchurs sub_schurs = pcbddc->sub_schurs;
PetscScalar *matdata,*matdata2;
PetscInt i,max_subset_size,cum,cum2;
const PetscInt *idxs;
PetscBool newsetup = PETSC_FALSE;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!sub_schurs) SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_PLIB,"Missing PCBDDCSubSchurs");
if (!sub_schurs->n_subs) PetscFunctionReturn(0);
/* Allocate arrays for subproblems */
if (!deluxe_ctx->seq_n) {
deluxe_ctx->seq_n = sub_schurs->n_subs;
ierr = PetscCalloc5(deluxe_ctx->seq_n,&deluxe_ctx->seq_scctx,deluxe_ctx->seq_n,&deluxe_ctx->seq_work1,deluxe_ctx->seq_n,&deluxe_ctx->seq_work2,deluxe_ctx->seq_n,&deluxe_ctx->seq_mat,deluxe_ctx->seq_n,&deluxe_ctx->seq_mat_inv_sum);CHKERRQ(ierr);
newsetup = PETSC_TRUE;
} else if (deluxe_ctx->seq_n != sub_schurs->n_subs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Number of deluxe subproblems %D is different from the sub_schurs %D",deluxe_ctx->seq_n,sub_schurs->n_subs);
/* the change of basis is just a reference to sub_schurs->change (if any) */
deluxe_ctx->change = sub_schurs->change;
deluxe_ctx->change_with_qr = sub_schurs->change_with_qr;
/* Create objects for deluxe */
max_subset_size = 0;
for (i=0;i<sub_schurs->n_subs;i++) {
PetscInt subset_size;
ierr = ISGetLocalSize(sub_schurs->is_subs[i],&subset_size);CHKERRQ(ierr);
max_subset_size = PetscMax(subset_size,max_subset_size);
}
if (newsetup) {
ierr = PetscMalloc1(2*max_subset_size,&deluxe_ctx->workspace);CHKERRQ(ierr);
}
cum = cum2 = 0;
ierr = ISGetIndices(sub_schurs->is_Ej_all,&idxs);CHKERRQ(ierr);
ierr = MatSeqAIJGetArray(sub_schurs->S_Ej_all,&matdata);CHKERRQ(ierr);
ierr = MatSeqAIJGetArray(sub_schurs->sum_S_Ej_all,&matdata2);CHKERRQ(ierr);
for (i=0;i<deluxe_ctx->seq_n;i++) {
PetscInt subset_size;
ierr = ISGetLocalSize(sub_schurs->is_subs[i],&subset_size);CHKERRQ(ierr);
if (newsetup) {
IS sub;
/* work vectors */
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,subset_size,deluxe_ctx->workspace,&deluxe_ctx->seq_work1[i]);CHKERRQ(ierr);
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,subset_size,deluxe_ctx->workspace+subset_size,&deluxe_ctx->seq_work2[i]);CHKERRQ(ierr);
/* scatters */
ierr = ISCreateGeneral(PETSC_COMM_SELF,subset_size,idxs+cum,PETSC_COPY_VALUES,&sub);CHKERRQ(ierr);
ierr = VecScatterCreate(pcbddc->work_scaling,sub,deluxe_ctx->seq_work1[i],NULL,&deluxe_ctx->seq_scctx[i]);CHKERRQ(ierr);
ierr = ISDestroy(&sub);CHKERRQ(ierr);
}
/* S_E_j */
ierr = MatDestroy(&deluxe_ctx->seq_mat[i]);CHKERRQ(ierr);
ierr = MatCreateSeqDense(PETSC_COMM_SELF,subset_size,subset_size,matdata+cum2,&deluxe_ctx->seq_mat[i]);CHKERRQ(ierr);
/* \sum_k S^k_E_j */
ierr = MatDestroy(&deluxe_ctx->seq_mat_inv_sum[i]);CHKERRQ(ierr);
ierr = MatCreateSeqDense(PETSC_COMM_SELF,subset_size,subset_size,matdata2+cum2,&deluxe_ctx->seq_mat_inv_sum[i]);CHKERRQ(ierr);
ierr = MatSetOption(deluxe_ctx->seq_mat_inv_sum[i],MAT_SPD,sub_schurs->is_posdef);CHKERRQ(ierr);
ierr = MatSetOption(deluxe_ctx->seq_mat_inv_sum[i],MAT_HERMITIAN,sub_schurs->is_hermitian);CHKERRQ(ierr);
if (sub_schurs->is_hermitian) {
ierr = MatCholeskyFactor(deluxe_ctx->seq_mat_inv_sum[i],NULL,NULL);CHKERRQ(ierr);
} else {
ierr = MatLUFactor(deluxe_ctx->seq_mat_inv_sum[i],NULL,NULL,NULL);CHKERRQ(ierr);
}
if (pcbddc->deluxe_singlemat) {
Mat X,Y;
if (!sub_schurs->is_hermitian) {
ierr = MatTranspose(deluxe_ctx->seq_mat[i],MAT_INITIAL_MATRIX,&X);CHKERRQ(ierr);
} else {
ierr = PetscObjectReference((PetscObject)deluxe_ctx->seq_mat[i]);CHKERRQ(ierr);
X = deluxe_ctx->seq_mat[i];
}
ierr = MatDuplicate(X,MAT_DO_NOT_COPY_VALUES,&Y);CHKERRQ(ierr);
if (!sub_schurs->is_hermitian) {
ierr = PCBDDCMatTransposeMatSolve_SeqDense(deluxe_ctx->seq_mat_inv_sum[i],X,Y);CHKERRQ(ierr);
} else {
ierr = MatMatSolve(deluxe_ctx->seq_mat_inv_sum[i],X,Y);CHKERRQ(ierr);
}
ierr = MatDestroy(&deluxe_ctx->seq_mat_inv_sum[i]);CHKERRQ(ierr);
ierr = MatDestroy(&deluxe_ctx->seq_mat[i]);CHKERRQ(ierr);
ierr = MatDestroy(&X);CHKERRQ(ierr);
if (deluxe_ctx->change) {
Mat C,CY;
if (!deluxe_ctx->change_with_qr) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only QR based change of basis");
ierr = KSPGetOperators(deluxe_ctx->change[i],&C,NULL);CHKERRQ(ierr);
ierr = MatMatMult(C,Y,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&CY);CHKERRQ(ierr);
ierr = MatMatTransposeMult(CY,C,MAT_REUSE_MATRIX,PETSC_DEFAULT,&Y);CHKERRQ(ierr);
ierr = MatDestroy(&CY);CHKERRQ(ierr);
}
ierr = MatTranspose(Y,MAT_INPLACE_MATRIX,&Y);CHKERRQ(ierr);
deluxe_ctx->seq_mat[i] = Y;
}
cum += subset_size;
cum2 += subset_size*subset_size;
}
ierr = ISRestoreIndices(sub_schurs->is_Ej_all,&idxs);CHKERRQ(ierr);
ierr = MatSeqAIJRestoreArray(sub_schurs->S_Ej_all,&matdata);CHKERRQ(ierr);
ierr = MatSeqAIJRestoreArray(sub_schurs->sum_S_Ej_all,&matdata2);CHKERRQ(ierr);
if (pcbddc->deluxe_singlemat) {
deluxe_ctx->change = NULL;
deluxe_ctx->change_with_qr = PETSC_FALSE;
}
if (deluxe_ctx->change && !deluxe_ctx->change_with_qr) {
for (i=0;i<deluxe_ctx->seq_n;i++) {
if (newsetup) {
PC pc;
ierr = KSPGetPC(deluxe_ctx->change[i],&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCLU);CHKERRQ(ierr);
ierr = KSPSetFromOptions(deluxe_ctx->change[i]);CHKERRQ(ierr);
}
ierr = KSPSetUp(deluxe_ctx->change[i]);CHKERRQ(ierr);
}
}
PetscFunctionReturn(0);
}
int main(int argc, char *argv[])
{
PetscMPIInt size;
TS ts;
Vec R;
Mat J;
Vec U,V;
PetscScalar *u,*v;
UserParams user = {/*Omega=*/ 1, /*Xi=*/ 0, /*u0=*/ 1, /*,v0=*/ 0};
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&argv,NULL,help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");
ierr = PetscOptionsBegin(PETSC_COMM_SELF,"","ex43 options","");CHKERRQ(ierr);
ierr = PetscOptionsReal("-frequency","Natual frequency",__FILE__,user.Omega,&user.Omega,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-damping","Damping coefficient",__FILE__,user.Xi,&user.Xi,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-initial_u","Initial displacement",__FILE__,user.u0,&user.u0,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-initial_v","Initial velocity",__FILE__,user.v0,&user.v0,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = TSCreate(PETSC_COMM_SELF,&ts);CHKERRQ(ierr);
ierr = TSSetType(ts,TSALPHA2);CHKERRQ(ierr);
ierr = TSSetMaxTime(ts,5*(2*PETSC_PI));CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
ierr = TSSetTimeStep(ts,0.01);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,1,&R);CHKERRQ(ierr);
ierr = VecSetUp(R);CHKERRQ(ierr);
ierr = MatCreateSeqDense(PETSC_COMM_SELF,1,1,NULL,&J);CHKERRQ(ierr);
ierr = MatSetUp(J);CHKERRQ(ierr);
if (user.Xi) {
ierr = TSSetI2Function(ts,R,Residual2,&user);CHKERRQ(ierr);
ierr = TSSetI2Jacobian(ts,J,J,Tangent2,&user);CHKERRQ(ierr);
} else {
ierr = TSSetIFunction(ts,R,Residual1,&user);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,J,J,Tangent1,&user);CHKERRQ(ierr);
}
ierr = VecDestroy(&R);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = TSSetSolutionFunction(ts,Solution,&user);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,1,&U);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,1,&V);CHKERRQ(ierr);
ierr = VecGetArray(U,&u);CHKERRQ(ierr);
ierr = VecGetArray(V,&v);CHKERRQ(ierr);
u[0] = user.u0;
v[0] = user.v0;
ierr = VecRestoreArray(U,&u);CHKERRQ(ierr);
ierr = VecRestoreArray(V,&v);CHKERRQ(ierr);
ierr = TS2SetSolution(ts,U,V);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSolve(ts,NULL);CHKERRQ(ierr);
ierr = VecDestroy(&U);CHKERRQ(ierr);
ierr = VecDestroy(&V);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
