void PETSc::Solve(void)
{
//start_clock("Before Assemble matrix and vector");
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
ierr = VecAssemblyBegin(x);
ierr = VecAssemblyEnd(x);
ierr = VecAssemblyBegin(b);
ierr = VecAssemblyEnd(b);
//stop_clock("After Assembly matrix and vector");
KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN);
KSPSetType(ksp,KSPBCGSL);
KSPBCGSLSetEll(ksp,2);
//KSPGetPC(ksp, &pc);
//PCSetType(pc, PCJACOBI);
KSPSetFromOptions(ksp);
KSPSetUp(ksp);
//start_clock("Before KSPSolve");
KSPSolve(ksp,b,x);
//stop_clock("After KSPSolve");
}
PetscErrorCode test_vec_ops( void )
{
Vec X, a,b;
Vec c,d,e,f;
PetscScalar val;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscPrintf( PETSC_COMM_WORLD, "\n\n============== %s ==============\n",PETSC_FUNCTION_NAME);
ierr = VecCreate( PETSC_COMM_WORLD, &X );CHKERRQ(ierr);
ierr = VecSetSizes( X, 2, 2 );CHKERRQ(ierr);
ierr = VecSetType( X, VECNEST );CHKERRQ(ierr);
ierr = VecCreate( PETSC_COMM_WORLD, &a );CHKERRQ(ierr);
ierr = VecSetSizes( a, 2, 2 );CHKERRQ(ierr);
ierr = VecSetType( a, VECNEST );CHKERRQ(ierr);
ierr = VecCreate( PETSC_COMM_WORLD, &b );CHKERRQ(ierr);
ierr = VecSetSizes( b, 2, 2 );CHKERRQ(ierr);
ierr = VecSetType( b, VECNEST );CHKERRQ(ierr);
/* assemble X */
ierr = VecNestSetSubVec( X, 0, a );CHKERRQ(ierr);
ierr = VecNestSetSubVec( X, 1, b );CHKERRQ(ierr);
ierr = VecAssemblyBegin(X);CHKERRQ(ierr);
ierr = VecAssemblyEnd(X);CHKERRQ(ierr);
ierr = VecCreate( PETSC_COMM_WORLD, &c );CHKERRQ(ierr);
ierr = VecSetSizes( c, 3, 3 );CHKERRQ(ierr);
ierr = VecSetType( c, VECSEQ );CHKERRQ(ierr);
ierr = VecDuplicate( c, &d );CHKERRQ(ierr);
ierr = VecDuplicate( c, &e );CHKERRQ(ierr);
ierr = VecDuplicate( c, &f );CHKERRQ(ierr);
ierr = VecSet( c, 1.0 );CHKERRQ(ierr);
ierr = VecSet( d, 2.0 );CHKERRQ(ierr);
ierr = VecSet( e, 3.0 );CHKERRQ(ierr);
ierr = VecSet( f, 4.0 );CHKERRQ(ierr);
/* assemble a */
ierr = VecNestSetSubVec( a, 0, c );CHKERRQ(ierr);
ierr = VecNestSetSubVec( a, 1, d );CHKERRQ(ierr);
ierr = VecAssemblyBegin(a);CHKERRQ(ierr);
ierr = VecAssemblyEnd(a);CHKERRQ(ierr);
/* assemble b */
ierr = VecNestSetSubVec( b, 0, e );CHKERRQ(ierr);
ierr = VecNestSetSubVec( b, 1, f );CHKERRQ(ierr);
ierr = VecAssemblyBegin(b);CHKERRQ(ierr);
ierr = VecAssemblyEnd(b);CHKERRQ(ierr);
//PetscPrintf( PETSC_COMM_WORLD, "X \n");
//VecView( X, PETSC_VIEWER_STDOUT_WORLD );
ierr = VecDot( X,X, &val );CHKERRQ(ierr);
PetscPrintf( PETSC_COMM_WORLD, "X.X = %f \n", val );
PetscFunctionReturn(0);
}
void PETSc::Solve_withPureNeumann_GMRES(void)
{
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
ierr = VecAssemblyBegin(x);
ierr = VecAssemblyEnd(x);
ierr = VecAssemblyBegin(b);
ierr = VecAssemblyEnd(b);
MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,PETSC_NULL,&nullsp);
KSPSetNullSpace(ksp,nullsp);
MatNullSpaceRemove(nullsp,b,PETSC_NULL);
KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN);
KSPSetType(ksp,KSPGMRES);
//KSPGetPC(ksp, &pc);
//PCSetType(pc, PCASM);
KSPSetFromOptions(ksp);
KSPSetUp(ksp);
//start_clock("Before Petsc Solve in pure neumann solver");
KSPSolve(ksp,b,x);
//stop_clock("After Petsc Solve in pure neumann solver");
}
PetscErrorCode formExactAndRHS(DM da, Vec uexact, Vec b) {
PetscErrorCode ierr;
DMDALocalInfo info;
PetscInt i;
PetscReal h, x, *ab, *auexact;
ierr = DMDAGetLocalInfo(da,&info); CHKERRQ(ierr);
h = 1.0/(info.mx-1);
ierr = DMDAVecGetArray(da, b, &ab);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da, uexact, &auexact);CHKERRQ(ierr);
for (i=info.xs; i<info.xs+info.xm; i++) {
x = i * h;
auexact[i] = x*x * (1.0 - x*x);
if ( (i>0) && (i<info.mx-1) )
ab[i] = h*h * (12.0 * x*x - 2.0);
else
ab[i] = 0.0;
}
ierr = DMDAVecRestoreArray(da, uexact, &auexact);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da, b, &ab); CHKERRQ(ierr);
ierr = VecAssemblyBegin(b); CHKERRQ(ierr);
ierr = VecAssemblyEnd(b); CHKERRQ(ierr);
ierr = VecAssemblyBegin(uexact); CHKERRQ(ierr);
ierr = VecAssemblyEnd(uexact); CHKERRQ(ierr);
return 0;
}
PetscErrorCode KSPBuildPressure_CB_Nullspace_BSSCR(KSP ksp)
{
KSP_BSSCR *bsscr = (KSP_BSSCR *)ksp->data;
FeEquationNumber *eq_num = bsscr->solver->st_sle->pSolnVec->feVariable->eqNum;
FeMesh *feMesh = bsscr->solver->st_sle->pSolnVec->feVariable->feMesh; /* is the pressure mesh */
unsigned ijk[3];
Vec t, v;
int numLocalNodes, globalNodeNumber, i, j, eq;
MatStokesBlockScaling BA = bsscr->BA;
PetscErrorCode ierr;
Mat Amat,Pmat, G;
MatStructure pflag;
PetscFunctionBegin;
/* get G matrix from Amat matrix operator on ksp */
ierr=Stg_PCGetOperators(ksp->pc,&Amat,&Pmat,&pflag);CHKERRQ(ierr);
MatNestGetSubMat( Amat, 0,1, &G );/* G should always exist */
/* now create Vecs t and v to match size of G: i.e. pressure */ /* NOTE: not using "h" vector from ksp->vec_rhs because this part of the block vector doesn't always exist */
MatGetVecs( G, &t, PETSC_NULL );/* t and v are destroyed in KSPDestroy_BSSCR */
MatGetVecs( G, &v, PETSC_NULL );/* t and v such that can do G*t */
numLocalNodes = Mesh_GetLocalSize( feMesh, MT_VERTEX); /* number of nodes on current proc not counting any shadow nodes */
for(j=0;j<numLocalNodes;j++){
i = globalNodeNumber = Mesh_DomainToGlobal( feMesh, MT_VERTEX, j);
RegularMeshUtils_Element_1DTo3D(feMesh, i, ijk);
eq = eq_num->destinationArray[j][0];/* get global equation number -- 2nd arg is always 0 because pressure has only one dof */
if(eq != -1){
if( (ijk[0]+ijk[1]+ijk[2])%2 ==0 ){
VecSetValue(t,eq,1.0,INSERT_VALUES);
}
else{
VecSetValue(v,eq,1.0,INSERT_VALUES); }}}
VecAssemblyBegin( t );
VecAssemblyEnd( t );
VecAssemblyBegin( v );
VecAssemblyEnd( v );
/* Scaling the null vectors here because it easier at the moment *//* maybe should do this in the original scaling function */
if( BA->scaling_exists == PETSC_TRUE ){
Vec R2;
/* Get the scalings out the block mat data */
VecNestGetSubVec( BA->Rz, 1, &R2 );
VecPointwiseDivide( t, t, R2); /* x <- x * 1/R2 */
VecPointwiseDivide( v, v, R2);
}
bsscr_writeVec( t, "t", "Writing t vector");
bsscr_writeVec( v, "v", "Writing v vector");
bsscr->t=t;
bsscr->v=v;
PetscFunctionReturn(0);
}
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;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt n = 9,bs = 3,indices[2],i;
PetscScalar values[6];
Vec x;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_SELF,1,"Must be run with one processor");
/* create vector */
ierr = VecCreate(PETSC_COMM_SELF,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,n,n);CHKERRQ(ierr);
ierr = VecSetBlockSize(x,bs);CHKERRQ(ierr);
ierr = VecSetType(x,VECSEQ);CHKERRQ(ierr);
for (i=0; i<6; i++) values[i] = 4.0*i;
indices[0] = 0;
indices[1] = 2;
ierr = VecSetValuesBlocked(x,2,indices,values,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
/*
Resulting vector should be 0 4 8 0 0 0 12 16 20
*/
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* test insertion with negative indices */
ierr = VecSetOption(x,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);CHKERRQ(ierr);
for (i=0; i<6; i++) values[i] = -4.0*i;
indices[0] = -1;
indices[1] = 2;
ierr = VecSetValuesBlocked(x,2,indices,values,ADD_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
/*
Resulting vector should be 0 4 8 0 0 0 0 0 0
*/
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
void PkStruct::finalize() {
VecAssemblyBegin(pkvec); VecAssemblyEnd(pkvec);
VecAssemblyBegin(nmodes); VecAssemblyEnd(nmodes);
VecAssemblyBegin(kvec); VecAssemblyEnd(kvec);
//Normalize and return
VecShift(nmodes, 1.e-20);
VecPointwiseDivide(pkvec, nmodes);
VecPointwiseDivide(kvec, nmodes);
VecGetArray(kvec, &_kvec);
VecGetArray(pkvec, &_pkvec);
VecGetArray(nmodes, &_nmodes);
}
/*@
KSPComputeExplicitOperator - Computes the explicit preconditioned operator.
Collective on KSP
Input Parameter:
. ksp - the Krylov subspace context
Output Parameter:
. mat - the explict preconditioned operator
Notes:
This computation is done by applying the operators to columns of the
identity matrix.
Currently, this routine uses a dense matrix format when 1 processor
is used and a sparse format otherwise. This routine is costly in general,
and is recommended for use only with relatively small systems.
Level: advanced
.keywords: KSP, compute, explicit, operator
.seealso: KSPComputeEigenvaluesExplicitly(), PCComputeExplicitOperator()
@*/
PetscErrorCode KSPComputeExplicitOperator(KSP ksp,Mat *mat)
{
Vec in,out;
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt i,M,m,*rows,start,end;
Mat A;
MPI_Comm comm;
PetscScalar *array,one = 1.0;
PetscFunctionBegin;
PetscValidHeaderSpecific(ksp,KSP_CLASSID,1);
PetscValidPointer(mat,2);
comm = ((PetscObject)ksp)->comm;
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = VecDuplicate(ksp->vec_sol,&in);CHKERRQ(ierr);
ierr = VecDuplicate(ksp->vec_sol,&out);CHKERRQ(ierr);
ierr = VecGetSize(in,&M);CHKERRQ(ierr);
ierr = VecGetLocalSize(in,&m);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(in,&start,&end);CHKERRQ(ierr);
ierr = PetscMalloc(m*sizeof(PetscInt),&rows);CHKERRQ(ierr);
for (i=0; i<m; i++) {rows[i] = start + i;}
ierr = MatCreate(comm,mat);CHKERRQ(ierr);
ierr = MatSetSizes(*mat,m,m,M,M);CHKERRQ(ierr);
if (size == 1) {
ierr = MatSetType(*mat,MATSEQDENSE);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(*mat,PETSC_NULL);CHKERRQ(ierr);
} else {
ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(*mat,0,PETSC_NULL,0,PETSC_NULL);CHKERRQ(ierr);
}
ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
if (!ksp->pc) {ierr = KSPGetPC(ksp,&ksp->pc);CHKERRQ(ierr);}
ierr = PCGetOperators(ksp->pc,&A,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
for (i=0; i<M; i++) {
ierr = VecSet(in,0.0);CHKERRQ(ierr);
ierr = VecSetValues(in,1,&i,&one,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(in);CHKERRQ(ierr);
ierr = VecAssemblyEnd(in);CHKERRQ(ierr);
ierr = KSP_MatMult(ksp,A,in,out);CHKERRQ(ierr);
ierr = KSP_PCApply(ksp,out,in);CHKERRQ(ierr);
ierr = VecGetArray(in,&array);CHKERRQ(ierr);
ierr = MatSetValues(*mat,m,rows,1,&i,array,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecRestoreArray(in,&array);CHKERRQ(ierr);
}
ierr = PetscFree(rows);CHKERRQ(ierr);
ierr = VecDestroy(&in);CHKERRQ(ierr);
ierr = VecDestroy(&out);CHKERRQ(ierr);
ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
Ensure(FFT, transforms_constant_into_delta_function)
{
Vec v;
DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,4,2,1,NULL,&da);
DMCreateGlobalVector(da, &v);
VecZeroEntries(v);
VecSetValue(v, 0, 0.7, INSERT_VALUES);
VecAssemblyBegin(v);
VecAssemblyEnd(v);
scFftCreate(da, &fft);
Vec x, y, z;
scFftCreateVecsFFTW(fft, &x, &y, &z);
scFftTransform(fft, v, 0, y);
const PetscScalar *arr;
VecGetArrayRead(y, &arr);
//assert_that_double(fabs(arr[0] - 0.7), is_less_than_double(1.0e-6));
assert_that(fabs(arr[1] - 0.0) < 1.0e-6, is_true);
assert_that(fabs(arr[1] - 0.7) < 1.0e-6, is_true);
assert_that(fabs(arr[2] - 0.0) < 1.0e-6, is_true);
assert_that(fabs(arr[3] - 0.7) < 1.0e-6, is_true);
assert_that(fabs(arr[4] - 0.0) < 1.0e-6, is_true);
VecRestoreArrayRead(y, &arr);
VecDestroy(&x);
VecDestroy(&y);
VecDestroy(&z);
VecDestroy(&v);
scFftDestroy(&fft);
DMDestroy(&da);
}
PetscErrorCode BSSPotR1Vec(BSS self, PF pot, Vec V) {
int order = self->order;
int nb = self->num_basis;
int ne = self->num_ele;
int nq = order*ne;
PetscErrorCode ierr;
ierr = BSSCheck(self); CHKERRQ(ierr);
PetscScalar *vs; PetscMalloc1(nq, &vs);
ierr = PFApply(pot, nq, self->Rrs, vs); CHKERRQ(ierr);
for(int i = 0; i < nb; i++) {
int k0, k1; Non0QuadIndex(i, i, order, nq, &k0, &k1);
PetscScalar v = 0.0;
for(int k = k0; k < k1; k++) {
//v += self->vals[k+i*nq] * self->ws[k] * vs[k];
v += self->vals[k+i*nq] * self->ws[k] * self->qrs[k] * vs[k];
}
ierr = VecSetValue(V, i, v, INSERT_VALUES); CHKERRQ(ierr);
}
PetscFree(vs);
VecAssemblyBegin(V);
VecAssemblyEnd(V);
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt n = 9,bs = 3,indices[2],i;
PetscScalar values[6];
Vec x;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(1,"Must be run with one processor");
/* create vector */
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&x);CHKERRQ(ierr);
ierr = VecSetBlockSize(x,bs);CHKERRQ(ierr);
for (i=0; i<6; i++) values[i] = 4.0*i;
indices[0] = 0; indices[1] = 2;
ierr = VecSetValuesBlocked(x,2,indices,values,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
/*
Resulting vector should be 0 4 8 0 0 0 12 16 20
*/
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
/*---------------------------------------------------------
Function to fill the rhs vector with
By + g values ****
---------------------------------------------------------*/
PetscErrorCode rhs(AppCtx *obj,PetscScalar *y, PetscInt nz, PetscScalar *z, PetscReal t)
{
PetscInt i,j,js,je,jj;
PetscScalar val,g[num_z],btri[num_z][3],add_term;
PetscErrorCode ierr;
for (i=0; i < nz-2; i++) {
for (j=0; j <= 2; j++) btri[i][j]=0.0;
g[i] = 0.0;
}
/* call femBg to set the tri-diagonal b matrix and vector g */
femBg(btri,g,nz,z,t);
/* setting the entries of the right hand side vector */
for (i=0; i < nz-2; i++) {
val = 0.0;
js = 0;
if (i == 0) js = 1;
je = 2;
if (i == nz-2) je = 1;
for (jj=js; jj <= je; jj++) {
j = i+jj-1;
val += (btri[i][jj])*(y[j]);
}
add_term = val + g[i];
ierr = VecSetValue(obj->ksp_rhs,(PetscInt)i,(PetscScalar)add_term,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(obj->ksp_rhs);CHKERRQ(ierr);
ierr = VecAssemblyEnd(obj->ksp_rhs);CHKERRQ(ierr);
/* return to main driver function */
return 0;
}
inline PetscErrorCode ScatIEMatMult(Mat mat,Vec xx,Vec yy)
{
PetscInt n,s,t;
PetscScalar tmp,v;
PetscInt xstart,xend;
PetscFunctionBegin;
VecGetOwnershipRange(xx,&xstart,&xend);
VecGetSize(yy,&n);
VecZeroEntries(yy);
for(s = 0; s <n ; s++)
{
tmp = 0;
for(t = xstart; t < xend; t++)
{
VecGetValues(xx,1,&t,&v);
tmp += ScatIE.CoefMatFast(s,t)*v;
}
VecSetValues(yy,1,&s,&tmp,ADD_VALUES);
}
VecAssemblyBegin(yy);
VecAssemblyEnd(yy);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt i,blocks[2],nlocal;
PetscMPIInt size,rank;
PetscScalar value;
Vec x,y;
IS is1,is2;
VecScatter ctx = 0;
PetscViewer subviewer;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
if (size != 2) SETERRQ(PETSC_COMM_SELF,1,"Must run with 2 processors");
/* create two vectors */
if (!rank) nlocal = 8;
else nlocal = 4;
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,nlocal,12);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&y);CHKERRQ(ierr);
ierr = VecSetSizes(y,8,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(y);CHKERRQ(ierr);
/* create two index sets */
if (!rank) {
blocks[0] = 0; blocks[1] = 2;
} else {
blocks[0] = 1; blocks[1] = 2;
}
ierr = ISCreateBlock(PETSC_COMM_SELF,4,2,blocks,PETSC_COPY_VALUES,&is1);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,8,0,1,&is2);CHKERRQ(ierr);
for (i=0; i<12; i++) {
value = i;
ierr = VecSetValues(x,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
ierr = VecScatterCreateWithData(x,is1,y,is2,&ctx);CHKERRQ(ierr);
ierr = VecScatterBegin(ctx,x,y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(ctx,x,y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterDestroy(&ctx);CHKERRQ(ierr);
ierr = PetscViewerGetSubViewer(PETSC_VIEWER_STDOUT_WORLD,PETSC_COMM_SELF,&subviewer);CHKERRQ(ierr);
ierr = VecView(y,subviewer);CHKERRQ(ierr);
ierr = PetscViewerRestoreSubViewer(PETSC_VIEWER_STDOUT_WORLD,PETSC_COMM_SELF,&subviewer);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = ISDestroy(&is1);CHKERRQ(ierr);
ierr = ISDestroy(&is2);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt n = 5,N,low,high,iglobal,i;
PetscMPIInt size,rank;
PetscScalar value,zero = 0.0;
Vec x,y;
IS is1,is2;
VecScatter ctx;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/* create two vectors */
N = size*n;
ierr = VecCreate(PETSC_COMM_WORLD,&y);CHKERRQ(ierr);
ierr = VecSetSizes(y,PETSC_DECIDE,N);CHKERRQ(ierr);
ierr = VecSetFromOptions(y);CHKERRQ(ierr);
if (!rank) {
ierr = VecCreateSeq(PETSC_COMM_SELF,N,&x);CHKERRQ(ierr);
} else {
ierr = VecCreateSeq(PETSC_COMM_SELF,0,&x);CHKERRQ(ierr);
}
/* create two index sets */
if (!rank) {
ierr = ISCreateStride(PETSC_COMM_SELF,N,0,1,&is1);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,N,0,1,&is2);CHKERRQ(ierr);
} else {
ierr = ISCreateStride(PETSC_COMM_SELF,0,0,1,&is1);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,0,0,1,&is2);CHKERRQ(ierr);
}
ierr = VecSet(x,zero);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(y,&low,&high);CHKERRQ(ierr);
for (i=0; i<n; i++) {
iglobal = i + low; value = (PetscScalar) (i + 10*rank);
ierr = VecSetValues(y,1,&iglobal,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(y);CHKERRQ(ierr);
ierr = VecAssemblyEnd(y);CHKERRQ(ierr);
ierr = VecView(y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecScatterCreate(y,is2,x,is1,&ctx);CHKERRQ(ierr);
ierr = VecScatterBegin(ctx,y,x,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(ctx,y,x,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterDestroy(&ctx);CHKERRQ(ierr);
if (!rank)
{printf("----\n"); ierr = VecView(x,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = ISDestroy(&is1);CHKERRQ(ierr);
ierr = ISDestroy(&is2);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode GetRadiusVec(Vec vecRad, int Nr, int Nz, double hr, int m)
{
PetscErrorCode ierr;
int i, j, ir, ic, ns, ne;
double value=1.0;
ierr = VecGetOwnershipRange(vecRad,&ns,&ne); CHKERRQ(ierr);
for(i=ns;i<ne; i++)
{
j = i;
ir = (j /= Nz) % Nr;
ic = (j /= Nr) % 3;
if (ic==0) value = (ir + 0.5)*hr;
if (ic==1) value = (ir + 0.0)*hr;
if (ic==2) value = (ir + 0.0)*hr + (ir==0)*(m==0)*hr/8;
VecSetValue(vecRad, i, value, INSERT_VALUES);
}
ierr = VecAssemblyBegin(vecRad); CHKERRQ(ierr);
ierr = VecAssemblyEnd(vecRad); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
FormInitialGuess - Computes an initial approximation to the solution.
Input Parameters:
. user - user-defined application context
. X - vector
Output Parameters:
X - vector
*/
PetscErrorCode FormInitialGuess(AppCtx *user,Vec X)
{
PetscErrorCode ierr;
PetscInt i, j, k, mx = user->mx, my = user->my;
PetscInt xs, ys, xm, ym, gxm, gym, gxs, gys, xe, ye;
PetscReal hx = 1.0/(mx+1), hy = 1.0/(my+1), temp, val;
PetscFunctionBegin;
/* Get local mesh boundaries */
ierr = DMDAGetCorners(user->dm,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(user->dm,&gxs,&gys,NULL,&gxm,&gym,NULL);CHKERRQ(ierr);
/* Compute initial guess over locally owned part of mesh */
xe = xs+xm;
ye = ys+ym;
for (j=ys; j<ye; j++) { /* for (j=0; j<my; j++) */
temp = PetscMin(j+1,my-j)*hy;
for (i=xs; i<xe; i++) { /* for (i=0; i<mx; i++) */
k = (j-gys)*gxm + i-gxs;
val = PetscMin((PetscMin(i+1,mx-i))*hx,temp);
ierr = VecSetValuesLocal(X,1,&k,&val,ADD_VALUES);CHKERRQ(ierr);
}
}
ierr = VecAssemblyBegin(X);CHKERRQ(ierr);
ierr = VecAssemblyEnd(X);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void operator| (PUP::er& p, Vec& v) {
PetscInt sz;
if (!p.isUnpacking()) {
VecGetSize(v, &sz);
}
p | sz;
if(p.isUnpacking()) {
VecCreateSeq(PETSC_COMM_WORLD, sz, &v);
VecSetFromOptions(v);
VecGetSize(v, &sz);
for (int i = 0; i < sz; i++) {
PetscScalar d;
p | d;
VecSetValue(v, i, d, INSERT_VALUES);
}
VecAssemblyBegin(v);
VecAssemblyEnd(v);
}
else {
for (int i = 0; i < sz; i++) {
PetscScalar d;
VecGetValues(v, 1, &i, &d);
p | d;
}
}
}
void Field_solver::set_solution_at_nodes_of_inner_regions( Spatial_mesh &spat_mesh,
Inner_region &inner_region )
{
int nx = spat_mesh.x_n_nodes;
int ny = spat_mesh.y_n_nodes;
int nz = spat_mesh.z_n_nodes;
std::vector<int> occupied_nodes_global_indices =
list_of_nodes_global_indices_in_matrix( inner_region.inner_nodes_not_at_domain_edge, nx, ny, nz );
PetscErrorCode ierr;
PetscInt num_of_elements_to_set = occupied_nodes_global_indices.size();
if( num_of_elements_to_set != 0 ){
std::vector<PetscScalar> phi_inside_region(num_of_elements_to_set);
std::fill( phi_inside_region.begin(), phi_inside_region.end(), inner_region.potential );
PetscInt *global_indices = &occupied_nodes_global_indices[0];
PetscScalar *values = &phi_inside_region[0];
ierr = VecSetValues( phi_vec, num_of_elements_to_set, global_indices,
values, INSERT_VALUES); CHKERRXX( ierr );
ierr = VecAssemblyBegin( phi_vec ); CHKERRXX( ierr );
ierr = VecAssemblyEnd( phi_vec ); CHKERRXX( ierr );
}
return;
}
PetscErrorCode gen_test_vector( MPI_Comm comm, PetscInt length, PetscInt start_value, PetscInt stride, Vec *_v )
{
int nproc;
Vec v;
PetscInt i;
PetscScalar vx;
PetscErrorCode ierr;
MPI_Comm_size( comm, &nproc );
ierr = VecCreate( comm, &v );CHKERRQ(ierr);
ierr = VecSetSizes( v, PETSC_DECIDE, length );CHKERRQ(ierr);
if ( nproc == 1 ) { ierr = VecSetType( v, VECSEQ );CHKERRQ(ierr); }
else { ierr = VecSetType( v, VECMPI );CHKERRQ(ierr); }
for ( i=0; i<length; i++ ) {
vx = (PetscScalar)( start_value + i * stride );
ierr = VecSetValue( v, i, vx, INSERT_VALUES );CHKERRQ(ierr);
}
ierr = VecAssemblyBegin( v );CHKERRQ(ierr);
ierr = VecAssemblyEnd( v );CHKERRQ(ierr);
*_v = v;
PetscFunctionReturn(0);
}
PetscErrorCode GetUnitVec(Vec ej, int pol, int N)
{
PetscErrorCode ierr;
int i, j, ns, ne, ic;
int Nc=3;
int Nxyz=N/6;
ierr = VecGetOwnershipRange(ej,&ns,&ne); CHKERRQ(ierr);
for(i=ns; i<ne; i++)
{
j=i;
ic = (j /= Nxyz) % Nc;
if (ic==pol)
VecSetValue(ej,i,1.0,INSERT_VALUES);
else
VecSetValue(ej,i,0.0,INSERT_VALUES);
}
ierr = VecAssemblyBegin(ej); CHKERRQ(ierr);
ierr = VecAssemblyEnd(ej); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void PETSc::Print_x(const char *filename)
{
ierr = VecAssemblyBegin(x);
ierr = VecAssemblyEnd(x);
PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_MATLAB);
VecView(x, PETSC_VIEWER_STDOUT_WORLD);
}
double Assembly_Mat_Vec(InterpolationDataStruct* pIData, int field, Mat M, Vec Fx, Vec Fy) {
double coord1[3],coord2[3],coord3[3], value1, value2, value3, Fx_values[3],Fy_values[3];
//Assembly
FIter fit = M_faceIter(pIData->m2);
while (pEntity entity = FIter_next(fit)){
//get the coordinates and the id's from the element's vertices
pEntity vertices[3] = {entity->get(0,0), entity->get(0,1), entity->get(0,2)};
int IDs[3] = {EN_id(vertices[0]), EN_id(vertices[1]), EN_id(vertices[2])};
int position[3] = {IDs[0]-1, IDs[1]-1, IDs[2]-1};
V_coord(vertices[0],coord1);
V_coord(vertices[1],coord2);
V_coord(vertices[2],coord3);
//calculate area
double At = F_area(coord1,coord2,coord3);
double At_by_6 = (double)(At/6.);
double At_by_12 = (double)(At/12.);
double M_values[9] = {At_by_6, At_by_12, At_by_12, At_by_12, At_by_6, At_by_12, At_by_12, At_by_12, At_by_6};
//get node values
pIData->pGetDblFunctions[field](IDs[0]-1,value1);
pIData->pGetDblFunctions[field](IDs[1]-1,value2);
pIData->pGetDblFunctions[field](IDs[2]-1,value3);
double CV[3] = {value1/6., value2/6., value3/6.};
//calculate the contributions
for(int i=0;i<3;i++){
Fx_values[i] = (coord2[1]-coord3[1])*CV[0] + (coord3[1]-coord1[1])*CV[1] + (coord1[1]-coord2[1])*CV[2];
Fy_values[i] = (coord3[0]-coord2[0])*CV[0] + (coord1[0]-coord3[0])*CV[1] + (coord2[0]-coord1[0])*CV[2];
}
VecSetValues(Fx,3,position,Fx_values, ADD_VALUES);
VecSetValues(Fy,3,position,Fy_values, ADD_VALUES);
MatSetValues(M,3,position,3,position,M_values, ADD_VALUES);
}
FIter_delete(fit);
PetscErrorCode ierr;
ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecAssemblyBegin(Fx);CHKERRQ(ierr);
ierr = VecAssemblyEnd(Fx);CHKERRQ(ierr);
ierr = VecAssemblyBegin(Fy);CHKERRQ(ierr);
ierr = VecAssemblyEnd(Fy);CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt i,j,n = 50,bs;
PetscScalar val,*vals,zero=0.0;
Vec x;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
bs = size;
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,n*bs);CHKERRQ(ierr);
ierr = VecSetBlockSize(x,bs);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
for (i=0; i<n*bs; i++) {
val = i*1.0;
ierr = VecSetValues(x,1,&i,&val,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Now do the blocksetvalues */
ierr = VecSet(x,zero);CHKERRQ(ierr);
ierr = PetscMalloc(bs*sizeof(PetscScalar),&vals);CHKERRQ(ierr);
for (i=0; i<n; i++) {
for (j=0; j<bs; j++) {
vals[j] = (i*bs+j)*1.0;
}
ierr = VecSetValuesBlocked(x,1,&i,vals,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = PetscFree(vals);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
void linearSystemPETSc<scalar>::zeroSolution()
{
if (_isAllocated) {
_try(VecAssemblyBegin(_x));
_try(VecAssemblyEnd(_x));
_try(VecZeroEntries(_x));
}
}
void linearSystemPETSc<scalar>::zeroRightHandSide()
{
if (_isAllocated) {
_try(VecAssemblyBegin(_b));
_try(VecAssemblyEnd(_b));
_try(VecZeroEntries(_b));
}
}
double linearSystemPETSc<scalar>::normInfRightHandSide() const
{
PetscReal nor;
VecAssemblyBegin(_b);
VecAssemblyEnd(_b);
_try(VecNorm(_b, NORM_INFINITY, &nor));
return nor;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscMPIInt rank;
PetscInt i,N;
PetscScalar one = 1.0;
Vec x;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/*
Create a parallel vector.
- In this case, we specify the size of each processor's local
portion, and PETSc computes the global size. Alternatively,
if we pass the global size and use PETSC_DECIDE for the
local size PETSc will choose a reasonable partition trying
to put nearly an equal number of elements on each processor.
*/
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,rank+1,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecGetSize(x,&N);CHKERRQ(ierr);
ierr = VecSet(x,one);CHKERRQ(ierr);
/*
Set the vector elements.
- Always specify global locations of vector entries.
- Each processor can contribute any vector entries,
regardless of which processor "owns" them; any nonlocal
contributions will be transferred to the appropriate processor
during the assembly process.
- In this example, the flag ADD_VALUES indicates that all
contributions will be added together.
*/
for (i=0; i<N-rank; i++) {
ierr = VecSetValues(x,1,&i,&one,ADD_VALUES);CHKERRQ(ierr);
}
/*
Assemble vector, using the 2-step process:
VecAssemblyBegin(), VecAssemblyEnd()
Computations can be done while messages are in transition
by placing code between these two statements.
*/
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
/*
View the vector; then destroy it.
*/
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
/*
#undef __FUNCT__
#define __FUNCT__ "phi2eval"
PetscErrorCode phi2eval(Vec *X, Vec *Phi, PetscInt n) {
PetscInt i,j,k,lo,hi;
PetscErrorCode ierr;
PetscReal sqrt2;
PetscFunctionBegin;
sqrt = PetscSqrtReal(2.0);
ierr = VecGetOwnershipRange(X,&lo,&hi);CHKERRQ(ierr);
PetscErrorCode phi2eval(PetscReal *x, PetscInt n, PetscReal *phi) {
// Phi = .5*[x(1)^2 sqrt(2)*x(1)*x(2) ... sqrt(2)*x(1)*x(n) ... x(2)^2 sqrt(2)*x(2)*x(3) .. x(n)^2]
PetscInt i,j,k;
PetscReal sqrt2 = PetscSqrtReal(2.0);
PetscFunctionBegin;
j=0;
for (i=0;i<n;i++) {
phi[j] = 0.5 * x[i]*x[i];
j++;
for (k=i+1;k<n;k++) {
phi[j] = x[i]*x[k]/sqrt2;
j++;
}
}
PetscFunctionReturn(0);
}*/
PetscErrorCode PoundersGramSchmidtReset(TAO_POUNDERS *mfqP, Vec *Q, PetscInt n)
{
PetscInt i;
for (i=0;i<n;i++) {
ierr = VecSet(Q[i],0.0);CHKERRQ(ierr);
ierr = VecSetValue(Q[i],i,1.0,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(Q[i]);CHKERRQ(ierr);
ierr = VecAssemblyEnd(Q[i]);CHKERRQ(ierr);
}
}
