/*---------------------------------------------------------
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;
}
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;
}
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);
}
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;
}
}
}
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;
}
/*@
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);
ierr = PetscObjectGetComm((PetscObject)ksp,&comm);CHKERRQ(ierr);
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 = PetscMalloc1(m,&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,NULL);CHKERRQ(ierr);
} else {
ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(*mat,0,NULL,0,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,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);
}
double linearSystemPETSc<scalar>::normInfRightHandSide() const
{
PetscReal nor;
VecAssemblyBegin(_b);
VecAssemblyEnd(_b);
_try(VecNorm(_b, NORM_INFINITY, &nor));
return nor;
}
void linearSystemPETSc<scalar>::zeroRightHandSide()
{
if (_isAllocated) {
_try(VecAssemblyBegin(_b));
_try(VecAssemblyEnd(_b));
_try(VecZeroEntries(_b));
}
}
void linearSystemPETSc<scalar>::zeroSolution()
{
if (_isAllocated) {
_try(VecAssemblyBegin(_x));
_try(VecAssemblyEnd(_x));
_try(VecZeroEntries(_x));
}
}
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;
}
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;
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);
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 = VecCreateSeq(PETSC_COMM_SELF,8,&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 = VecScatterCreate(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 = PetscSleep(2.0*rank);CHKERRQ(ierr);
ierr = VecView(y,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;
}
/*
#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);
}
}
-fout <file> : output file name\n\n";
#include <petscmat.h>
#undef __FUNCT__
#define __FUNCT__ "main"
int main(int argc,char **args)
{
Mat A;
Vec b;
char fileout[PETSC_MAX_PATH_LEN];
PetscInt i,j,m = 6,n = 6,N = 36,Ii,J;
PetscErrorCode ierr;
PetscScalar val,v;
PetscViewer view;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
for (i=0; i<m; i++) {
for (j=0; j<n; j++) {
v = -1.0; Ii = j + n*i;
if (i>0) {J = Ii - n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (i<m-1) {J = Ii + n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j>0) {J = Ii - 1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j<n-1) {J = Ii + 1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
v = 4.0; ierr = MatSetValues(A,1,&Ii,1,&Ii,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecSetSizes(b,PETSC_DECIDE,N);CHKERRQ(ierr);
ierr = VecSetFromOptions(b);CHKERRQ(ierr);
for (i=0; i<N; i++) {
val = i + 1;
ierr = VecSetValues(b,1,&i,&val,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(b);CHKERRQ(ierr);
ierr = VecAssemblyEnd(b);CHKERRQ(ierr);
ierr = PetscOptionsGetString(NULL,NULL,"-fout",fileout,PETSC_MAX_PATH_LEN,NULL);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,fileout,FILE_MODE_WRITE,&view);CHKERRQ(ierr);
ierr = MatView(A,view);CHKERRQ(ierr);
ierr = VecView(b,view);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/*@
MatComputeExplicitOperator - Computes the explicit matrix
Collective on Mat
Input Parameter:
. inmat - the matrix
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: Mat, compute, explicit, operator
@*/
PetscErrorCode MatComputeExplicitOperator(Mat inmat,Mat *mat)
{
Vec in,out;
PetscErrorCode ierr;
PetscInt i,m,n,M,N,*rows,start,end;
MPI_Comm comm;
PetscScalar *array,zero = 0.0,one = 1.0;
PetscMPIInt size;
PetscFunctionBegin;
PetscValidHeaderSpecific(inmat,MAT_CLASSID,1);
PetscValidPointer(mat,2);
ierr = PetscObjectGetComm((PetscObject)inmat,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = MatGetLocalSize(inmat,&m,&n);CHKERRQ(ierr);
ierr = MatGetSize(inmat,&M,&N);CHKERRQ(ierr);
ierr = MatGetVecs(inmat,&in,&out);CHKERRQ(ierr);
ierr = VecSetOption(in,VEC_IGNORE_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(out,&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,n,M,N);CHKERRQ(ierr);
if (size == 1) {
ierr = MatSetType(*mat,MATSEQDENSE);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(*mat,NULL);CHKERRQ(ierr);
} else {
ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(*mat,n,NULL,N-n,NULL);CHKERRQ(ierr);
}
for (i=0; i<N; i++) {
ierr = VecSet(in,zero);CHKERRQ(ierr);
ierr = VecSetValues(in,1,&i,&one,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(in);CHKERRQ(ierr);
ierr = VecAssemblyEnd(in);CHKERRQ(ierr);
ierr = MatMult(inmat,in,out);CHKERRQ(ierr);
ierr = VecGetArray(out,&array);CHKERRQ(ierr);
ierr = MatSetValues(*mat,m,rows,1,&i,array,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecRestoreArray(out,&array);CHKERRQ(ierr);
}
ierr = PetscFree(rows);CHKERRQ(ierr);
ierr = VecDestroy(&out);CHKERRQ(ierr);
ierr = VecDestroy(&in);CHKERRQ(ierr);
ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void FEMAssemble2DElasticity(MPI_Comm comm, Mesh *mesh, Mat &A, Vec &b,
PetscReal E, PetscReal mi, PetscReal(*dens)(Element *),
void(*f)(Element*, PetscReal, PetscReal*)) {
PetscInt rank;
MPI_Comm_rank(comm, &rank);
PetscInt size = mesh->vetrices.size();
MatCreateSeqAIJ(PETSC_COMM_SELF, size * 2, size * 2, 14, PETSC_NULL, &A);
VecCreateMPI(comm, size * 2, PETSC_DECIDE, &b);
for (std::map<PetscInt, Element*>::iterator e = mesh->elements.begin(); e
!= mesh->elements.end(); e++) {
Point* vetrices[3];
PetscInt vIndex[3];
for (int i = 0; i < 3; i++) {
vIndex[i] = e->second->vetrices[i];
vetrices[i] = mesh->vetrices[vIndex[i]];
}
PetscReal lStiff[36];
PetscReal bLoc[6];
//Local stiffness matrix and force vector assembly
PetscReal fs[2];
f(e->second, dens(e->second), fs);
elastLoc(vetrices, E, mi, fs, lStiff, bLoc);
PetscInt idx[6], idxLoc[6];
for (int i = 0; i < 3; i++) {
idx[i * 2] = vIndex[i] * 2;
idx[i * 2 + 1] = vIndex[i] * 2 + 1;
idxLoc[i * 2] = vIndex[i] * 2 - mesh->startIndexes[rank] * 2;
idxLoc[i * 2 + 1] = vIndex[i] * 2 + 1 - mesh->startIndexes[rank] * 2;
}
MatSetValues(A, 6, idxLoc, 6, idxLoc, lStiff, ADD_VALUES);
VecSetValues(b, 6, idx, bLoc, ADD_VALUES);
}
VecAssemblyBegin(b);
VecAssemblyEnd(b);
MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
}
int main(int argc,char **args)
{
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;
}
PetscErrorCode FEMAssembleTotal2DLaplace(MPI_Comm comm, Mesh *mesh, Mat &A,
Vec &b, PetscReal(*f)(Point), PetscReal(*K)(Point)) {
PetscErrorCode ierr;
PetscInt rank;
MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
PetscInt size = mesh->vetrices.size();
ierr
= MatCreateMPIAIJ(comm, size, size, PETSC_DECIDE, PETSC_DECIDE, 7, PETSC_NULL, 0, PETSC_NULL, &A);
CHKERRQ(ierr);
ierr = VecCreateMPI(comm, size, PETSC_DECIDE, &b);
CHKERRQ(ierr);
for (std::map<PetscInt, Element*>::iterator e = mesh->elements.begin(); e
!= mesh->elements.end(); e++) {
PetscScalar bl[3];
PetscScalar Al[9];
PetscReal R[4];
PetscInt elSize = e->second->numVetrices;
Point *vetrices = new Point[elSize];
PetscInt ixs[elSize];
for (int j = 0; j < elSize; j++) {
ixs[j] = e->second->vetrices[j];
vetrices[j] = *(mesh->vetrices[ixs[j]]);
}
R[0] = vetrices[1].x - vetrices[0].x;
R[2] = vetrices[1].y - vetrices[0].y;
R[1] = vetrices[2].x - vetrices[0].x;
R[3] = vetrices[2].y - vetrices[0].y;
Point center = getCenterOfSet(vetrices, elSize);
bLoc(R, bl, f(center));
ALoc(R, Al, K(center));
ierr = VecSetValues(b, elSize, ixs, bl, ADD_VALUES);
CHKERRQ(ierr);
ierr = MatSetValues(A, elSize, ixs, elSize, ixs, Al, ADD_VALUES);
CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(b);
CHKERRQ(ierr);
ierr = VecAssemblyEnd(b);
CHKERRQ(ierr);
ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
return ierr;
}
PetscErrorCode fill(Mat m, Vec v)
{
PetscInt idxn[3] = {0, 1, 2};
PetscInt localRows = 0;
PetscMPIInt rank,size;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(MPI_COMM_WORLD, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(MPI_COMM_WORLD, &size);CHKERRQ(ierr);
if (rank == 1 || rank == 2) localRows = 4;
if (size == 1) localRows = 8;
ierr = MatSetSizes(m, localRows, PETSC_DECIDE, PETSC_DECIDE, 3);CHKERRQ(ierr);
ierr = VecSetSizes(v, localRows, PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetFromOptions(m);CHKERRQ(ierr);
ierr = VecSetFromOptions(v);CHKERRQ(ierr);
ierr = MatSetUp(m);CHKERRQ(ierr);
if (size == 1) {
PetscInt idxm1[4] = {0, 1, 2, 3};
PetscScalar values1[12] = {1, 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 1};
PetscInt idxm2[4] = {4, 5, 6, 7};
PetscScalar values2[12] = {1, 2, 0, 1, 2, 1, 1, 3, 0, 1, 3, 1};
ierr = MatSetValues(m, 4, idxm1, 3, idxn, values1, INSERT_VALUES);CHKERRQ(ierr);
ierr = VecSetValue(v, 0, 1.1, INSERT_VALUES); VecSetValue(v, 1, 2.5, INSERT_VALUES);CHKERRQ(ierr);
ierr = VecSetValue(v, 2, 3, INSERT_VALUES); VecSetValue(v, 3, 4, INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(m, 4, idxm2, 3, idxn, values2, INSERT_VALUES);CHKERRQ(ierr);
ierr = VecSetValue(v, 4, 5, INSERT_VALUES); VecSetValue(v, 5, 6, INSERT_VALUES);CHKERRQ(ierr);
ierr = VecSetValue(v, 6, 7, INSERT_VALUES); VecSetValue(v, 7, 8, INSERT_VALUES);CHKERRQ(ierr);
} else if (rank == 1) {
PetscInt idxm[4] = {0, 1, 2, 3};
PetscScalar values[12] = {1, 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 1};
ierr = MatSetValues(m, 4, idxm, 3, idxn, values, INSERT_VALUES);CHKERRQ(ierr);
ierr = VecSetValue(v, 0, 1.1, INSERT_VALUES); VecSetValue(v, 1, 2.5, INSERT_VALUES);CHKERRQ(ierr);
ierr = VecSetValue(v, 2, 3, INSERT_VALUES); VecSetValue(v, 3, 4, INSERT_VALUES);CHKERRQ(ierr);
} else if (rank == 2) {
PetscInt idxm[4] = {4, 5, 6, 7};
PetscScalar values[12] = {1, 2, 0, 1, 2, 1, 1, 3, 0, 1, 3, 1};
ierr = MatSetValues(m, 4, idxm, 3, idxn, values, INSERT_VALUES);CHKERRQ(ierr);
ierr = VecSetValue(v, 4, 5, INSERT_VALUES); VecSetValue(v, 5, 6, INSERT_VALUES);CHKERRQ(ierr);
ierr = VecSetValue(v, 6, 7, INSERT_VALUES); VecSetValue(v, 7, 8, INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(m, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(m, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecAssemblyBegin(v);CHKERRQ(ierr);
ierr = VecAssemblyEnd(v);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static Vec op_create_vec ( const op_dat vec ) {
assert( vec );
Vec p_vec;
// Create a PETSc vector and pass it the user-allocated storage
VecCreateSeqWithArray(MPI_COMM_SELF,vec->dim * vec->set->size,(PetscScalar*)vec->data,&p_vec);
VecAssemblyBegin(p_vec);
VecAssemblyEnd(p_vec);
return p_vec;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt n = 5,i,idx2[3] = {0,2,3},idx1[3] = {0,1,2};
PetscMPIInt size,rank;
PetscScalar value;
Vec x,y;
IS is1,is2;
VecScatter ctx = 0;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/* create two vectors */
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,size*n);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&y);CHKERRQ(ierr);
/* create two index sets */
ierr = ISCreateGeneral(PETSC_COMM_SELF,3,idx1,PETSC_COPY_VALUES,&is1);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,3,idx2,PETSC_COPY_VALUES,&is2);CHKERRQ(ierr);
/* fill local part of parallel vector */
for (i=n*rank; i<n*(rank+1); i++) {
value = (PetscScalar) i;
ierr = VecSetValues(x,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecSet(y,-1.0);CHKERRQ(ierr);
ierr = VecScatterCreate(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);
if (!rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"scattered vector\n");CHKERRQ(ierr);
ierr = VecView(y,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
}
ierr = ISDestroy(&is1);CHKERRQ(ierr);
ierr = ISDestroy(&is2);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/*@
STComputeExplicitOperator - Computes the explicit operator associated
to the eigenvalue problem with the specified spectral transformation.
Collective on ST
Input Parameter:
. st - the spectral transform context
Output Parameter:
. mat - the explicit operator
Notes:
This routine builds a matrix containing the explicit operator. For
example, in generalized problems with shift-and-invert spectral
transformation the result would be matrix (A - s B)^-1 B.
This computation is done by applying the operator to columns of the
identity matrix. This is analogous to MatComputeExplicitOperator().
Level: advanced
.seealso: STApply()
@*/
PetscErrorCode STComputeExplicitOperator(ST st,Mat *mat)
{
PetscErrorCode ierr;
Vec in,out;
PetscInt i,M,m,*rows,start,end;
const PetscScalar *array;
PetscScalar one = 1.0;
PetscMPIInt size;
PetscFunctionBegin;
PetscValidHeaderSpecific(st,ST_CLASSID,1);
PetscValidPointer(mat,2);
STCheckMatrices(st,1);
if (st->nmat>2) SETERRQ(PetscObjectComm((PetscObject)st),PETSC_ERR_ARG_WRONGSTATE,"Can only be used with 1 or 2 matrices");
ierr = MPI_Comm_size(PetscObjectComm((PetscObject)st),&size);CHKERRQ(ierr);
ierr = MatGetVecs(st->A[0],&in,&out);CHKERRQ(ierr);
ierr = VecGetSize(out,&M);CHKERRQ(ierr);
ierr = VecGetLocalSize(out,&m);CHKERRQ(ierr);
ierr = VecSetOption(in,VEC_IGNORE_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(out,&start,&end);CHKERRQ(ierr);
ierr = PetscMalloc1(m,&rows);CHKERRQ(ierr);
for (i=0;i<m;i++) rows[i] = start + i;
ierr = MatCreate(PetscObjectComm((PetscObject)st),mat);CHKERRQ(ierr);
ierr = MatSetSizes(*mat,m,m,M,M);CHKERRQ(ierr);
if (size == 1) {
ierr = MatSetType(*mat,MATSEQDENSE);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(*mat,NULL);CHKERRQ(ierr);
} else {
ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(*mat,m,NULL,M-m,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 = STApply(st,in,out);CHKERRQ(ierr);
ierr = VecGetArrayRead(out,&array);CHKERRQ(ierr);
ierr = MatSetValues(*mat,m,rows,1,&i,array,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(out,&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);
}
PetscErrorCode SolveInit(FEMInf fem, int L, PetscScalar *e0, Vec *x) {
PetscErrorCode ierr;
Mat H, S;
ierr = CalcMat(fem, L, &H, &S); CHKERRQ(ierr);
EPS eps;
ierr = PrintTimeStamp(fem->comm, "EPS", NULL); CHKERRQ(ierr);
ierr = EPSCreate(fem->comm, &eps); CHKERRQ(ierr);
ierr = EPSSetTarget(eps, -0.6); CHKERRQ(ierr);
ierr = EPSSetWhichEigenpairs(eps, EPS_TARGET_MAGNITUDE); CHKERRQ(ierr);
ierr = EPSSetOperators(eps, H, S); CHKERRQ(ierr);
if(S == NULL) {
ierr = EPSSetProblemType(eps, EPS_NHEP); CHKERRQ(ierr);
} else {
ierr = EPSSetProblemType(eps, EPS_GNHEP); CHKERRQ(ierr);
}
Vec x0[1]; MatCreateVecs(H, &x0[0], NULL);
int num; FEMInfGetSize(fem, &num);
for(int i = 0; i < num; i++) {
VecSetValue(x0[0], i, 0.5, INSERT_VALUES);
}
VecAssemblyBegin(x0[0]); VecAssemblyEnd(x0[0]);
EPSSetInitialSpace(eps, 1, x0);
ierr = EPSSetFromOptions(eps); CHKERRQ(ierr);
ierr = EPSSolve(eps); CHKERRQ(ierr);
PetscInt nconv;
EPSGetConverged(eps, &nconv);
if(nconv == 0)
SETERRQ(fem->comm, 1, "Failed to digonalize in init state\n");
Vec x_ans;
MatCreateVecs(H, &x_ans, NULL);
EPSGetEigenpair(eps, 0, e0, NULL, x_ans, NULL);
EPSDestroy(&eps);
PetscScalar v[1]; PetscInt idx[1] = {1};
VecGetValues(x_ans, 1, idx, v);
PetscScalar scale_factor = v[0] / cabs(v[0]);
VecScale( x_ans, 1.0/scale_factor);
PetscScalar norm0;
Vec Sx; MatCreateVecs(S, &Sx, NULL);
MatMult(S, x_ans, Sx); VecDot(x_ans, Sx, &norm0);
VecScale(x_ans, 1.0/sqrt(norm0));
*x = x_ans;
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt n = 5,N,i;
PetscMPIInt size,rank;
PetscScalar value,zero = 0.0;
Vec x,y;
IS is1,is2;
VecScatter ctx = 0;
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,n,PETSC_DECIDE);CHKERRQ(ierr)
ierr = VecSetFromOptions(y);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,n,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
/* create two index sets */
ierr = ISCreateStride(PETSC_COMM_WORLD,n,n*rank,1,&is1);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_WORLD,n,(n*(rank+1))%N,1,&is2);CHKERRQ(ierr);
/* fill local part of parallel vector x */
value = (PetscScalar)(rank+1);
for (i=n*rank; i<n*(rank+1); i++) {
ierr = VecSetValues(x,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
ierr = VecSet(y,zero);CHKERRQ(ierr);
ierr = VecScatterCreate(x,is1,y,is2,&ctx);CHKERRQ(ierr);
ierr = VecScatterBegin(ctx,x,y,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(ctx,x,y,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterDestroy(ctx);CHKERRQ(ierr);
ierr = VecView(y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = VecDestroy(y);CHKERRQ(ierr);
ierr = ISDestroy(is1);CHKERRQ(ierr);
ierr = ISDestroy(is2);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
/*
FormHessian - Forms the Hessian matrix.
Input Parameters:
. tao - the Tao context
. X - the input vector
. ptr - optional user-defined context, as set by TaoSetHessian()
Output Parameters:
. H - Hessian matrix
. PrecH - optionally different preconditioning Hessian
. flag - flag indicating matrix structure
Notes:
This routine is intended simply as an example of the interface
to a Hessian evaluation routine. Since this example compute the
Hessian a column at a time, it is not particularly efficient and
is not recommended.
*/
PetscErrorCode FormHessian(Tao tao,Vec X,Mat H,Mat Hpre, void *ptr)
{
AppCtx *user = (AppCtx *) ptr;
PetscErrorCode ierr;
PetscInt i,j, ndim = user->ndim;
PetscReal *y, zero = 0.0, one = 1.0;
PetscBool assembled;
user->xvec = X;
/* Initialize Hessian entries and work vector to zero */
ierr = MatAssembled(H,&assembled);CHKERRQ(ierr);
if (assembled){ierr = MatZeroEntries(H); CHKERRQ(ierr);}
ierr = VecSet(user->s, zero);CHKERRQ(ierr);
/* Loop over matrix columns to compute entries of the Hessian */
for (j=0; j<ndim; j++) {
ierr = VecSetValues(user->s,1,&j,&one,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(user->s);CHKERRQ(ierr);
ierr = VecAssemblyEnd(user->s);CHKERRQ(ierr);
ierr = HessianProduct(ptr,user->s,user->y);CHKERRQ(ierr);
ierr = VecSetValues(user->s,1,&j,&zero,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(user->s);CHKERRQ(ierr);
ierr = VecAssemblyEnd(user->s);CHKERRQ(ierr);
ierr = VecGetArray(user->y,&y);CHKERRQ(ierr);
for (i=0; i<ndim; i++) {
if (y[i] != zero) {
ierr = MatSetValues(H,1,&i,1,&j,&y[i],ADD_VALUES);CHKERRQ(ierr);
}
}
ierr = VecRestoreArray(user->y,&y);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(H,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(H,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
return 0;
}
PetscErrorCode VecMerge(Vec r1, Vec r2, Vec r){
PetscErrorCode err;
PetscInt low, high, n1_local, n2_local;
PetscInt *n1_idx, *n2_idx;
PetscScalar *r1_array, *r2_array;
PetscInt n1;
int i;
//copy r1 to r
err = VecGetSize(r1, &n1); CHKERRQ(err);
err = VecGetOwnershipRange(r1, &low, &high); CHKERRQ(err);
err = VecGetLocalSize(r1, &n1_local); CHKERRQ(err);
err = PetscMalloc1(n1_local, &n1_idx); CHKERRQ(err);
for(i = 0; i < n1_local; i++)
n1_idx[i] = low + i;
err = VecGetArray(r1, &r1_array); CHKERRQ(err);
err = VecSetValues(r, n1_local, n1_idx, r1_array, INSERT_VALUES); CHKERRQ(err);
err = VecAssemblyBegin(r); CHKERRQ(err);
err = VecAssemblyEnd(r); CHKERRQ(err);
err = VecRestoreArray(r1, &r1_array); CHKERRQ(err);
err = PetscFree(n1_idx); CHKERRQ(err);
err = VecGetOwnershipRange(r2, &low, &high); CHKERRQ(err);
err = VecGetLocalSize(r2, &n2_local); CHKERRQ(err);
err = PetscMalloc1(n2_local, &n2_idx); CHKERRQ(err);
for(i = 0; i < n2_local; i++)
n2_idx[i] = low + i + n1;
err = VecGetArray(r2, &r2_array); CHKERRQ(err);
err = VecSetValues(r, n2_local, n2_idx, r2_array, INSERT_VALUES); CHKERRQ(err);
err = VecAssemblyBegin(r); CHKERRQ(err);
err = VecAssemblyEnd(r); CHKERRQ(err);
//err = VecRestoreArray(r1, &r1_array); CHKERRQ(err);
err = VecRestoreArray(r2, &r2_array); CHKERRQ(err);
err = PetscFree(n1_idx); CHKERRQ(err);
//err = PetscFree(n2_idx); CHKERRQ(err);
return err;
}
int main(int argc, char **args) {
PetscErrorCode ierr;
MPI_Comm comm = MPI_COMM_SELF;
FEMInf fem;
ViewerFunc viewer;
int n;
ierr = SlepcInitialize(&argc, &args, (char*)0, help); CHKERRQ(ierr);
// ==== Initialize ====
PrintTimeStamp(comm, "Init", NULL);
ierr = FEMInfCreate(comm, &fem); CHKERRQ(ierr);
ierr = ViewerFuncCreate(comm, &viewer); CHKERRQ(ierr);
// ==== Set values ====
PrintTimeStamp(comm, "Set", NULL);
PetscOptionsBegin(comm, "", "plot_basis.c options", "none");
ierr = FEMInfSetFromOptions(fem); CHKERRQ(ierr);
ierr = ViewerFuncSetFromOptions(viewer); CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL, "-n", &n, NULL); CHKERRQ(ierr);
PetscOptionsEnd();
// ==== Check input values ====
int num; FEMInfGetSize(fem, &num);
if(n < 0 || num <= n) {
SETERRQ(comm, 1, "n msut be zero or positive integer and smaller than size of FEM");
}
// ==== Calc ====
Vec c;
ierr = VecCreateSeq(comm, num, &c); CHKERRQ(ierr);
ierr = VecSet(c, 0.0); CHKERRQ(ierr);
int indices[1] = {n};
PetscScalar values[1] = {1.0};
ierr = VecSetValues(c, 1, indices, values, INSERT_VALUES); CHKERRQ(ierr);
ierr = VecAssemblyBegin(c); CHKERRQ(ierr);
ierr = VecAssemblyEnd(c); CHKERRQ(ierr);
FEMInfViewFunc(fem, c, viewer);
// ==== Finalize ====
ierr = SlepcFinalize(); CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscMPIInt size,rank;
PetscInt n = 5,i;
PetscScalar value;
Vec x,y;
IS is1,is2;
VecScatter ctx = 0;
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);
/* create two vectors */
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,size*n);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&y);CHKERRQ(ierr);
/* create two index sets */
ierr = ISCreateStride(PETSC_COMM_SELF,n,n*rank,1,&is1);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&is2);CHKERRQ(ierr);
/* each processor inserts the entire vector */
/* this is redundant but tests assembly */
for (i=0; i<n*size; i++) {
value = (PetscScalar) i;
ierr = VecSetValues(x,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecScatterCreate(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);
if (!rank) {
printf("----\n");
VecView(y,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 ierr;
}
PETSC_INTERN PetscErrorCode MatConvert_Shell(Mat oldmat, MatType newtype,MatReuse reuse,Mat *newmat)
{
Mat mat;
Vec in,out;
PetscErrorCode ierr;
PetscInt i,M,m,*rows,start,end;
MPI_Comm comm;
PetscScalar *array,zero = 0.0,one = 1.0;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)oldmat,&comm);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(oldmat,&start,&end);CHKERRQ(ierr);
ierr = VecCreateMPI(comm,end-start,PETSC_DECIDE,&in);CHKERRQ(ierr);
ierr = VecDuplicate(in,&out);CHKERRQ(ierr);
ierr = VecGetSize(in,&M);CHKERRQ(ierr);
ierr = VecGetLocalSize(in,&m);CHKERRQ(ierr);
ierr = PetscMalloc1(m+1,&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);
ierr = MatSetType(mat,newtype);CHKERRQ(ierr);
ierr = MatSetBlockSizesFromMats(mat,oldmat,oldmat);CHKERRQ(ierr);
ierr = MatSetUp(mat);CHKERRQ(ierr);
for (i=0; i<M; i++) {
ierr = VecSet(in,zero);CHKERRQ(ierr);
ierr = VecSetValues(in,1,&i,&one,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(in);CHKERRQ(ierr);
ierr = VecAssemblyEnd(in);CHKERRQ(ierr);
ierr = MatMult(oldmat,in,out);CHKERRQ(ierr);
ierr = VecGetArray(out,&array);CHKERRQ(ierr);
ierr = MatSetValues(mat,m,rows,1,&i,array,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecRestoreArray(out,&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);
if (reuse == MAT_INPLACE_MATRIX) {
ierr = MatHeaderReplace(oldmat,&mat);CHKERRQ(ierr);
} else {
*newmat = mat;
}
PetscFunctionReturn(0);
}
static PetscErrorCode VecAssemblyBegin_Nest(Vec v)
{
Vec_Nest *vs = (Vec_Nest*)v->data;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBegin;
for (i=0; i<vs->nb; i++) {
if (!vs->v[i]) SETERRQ(PetscObjectComm((PetscObject)v),PETSC_ERR_SUP,"Nest vector cannot contain NULL blocks");
ierr = VecAssemblyBegin(vs->v[i]);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
