PetscErrorCode RunTest(int nx, int ny, int nz, int loops, double *wt)
{
Vec x,f;
TS ts;
AppCtx _app,*app=&_app;
double t1,t2;
PetscErrorCode ierr;
PetscFunctionBegin;
app->nx = nx; app->h[0] = 1./(nx-1);
app->ny = ny; app->h[1] = 1./(ny-1);
app->nz = nz; app->h[2] = 1./(nz-1);
ierr = VecCreate(PETSC_COMM_SELF,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,nx*ny*nz,nx*ny*nz);CHKERRQ(ierr);
ierr = VecSetUp(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&f);CHKERRQ(ierr);
ierr = TSCreate(PETSC_COMM_SELF,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSTHETA);CHKERRQ(ierr);
ierr = TSThetaSetTheta(ts,1.0);CHKERRQ(ierr);
ierr = TSSetTimeStep(ts,0.01);CHKERRQ(ierr);
ierr = TSSetTime(ts,0.0);CHKERRQ(ierr);
ierr = TSSetDuration(ts,10,1.0);CHKERRQ(ierr);
ierr = TSSetSolution(ts,x);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,f,FormFunction,app);CHKERRQ(ierr);
ierr = PetscOptionsSetValue("-snes_mf","1");CHKERRQ(ierr);
{
SNES snes;
KSP ksp;
ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPCG);CHKERRQ(ierr);
}
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSetUp(ts);CHKERRQ(ierr);
*wt = 1e300;
while (loops-- > 0) {
ierr = FormInitial(0.0,x,app);CHKERRQ(ierr);
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
ierr = TSSolve(ts,x,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscGetTime(&t2);CHKERRQ(ierr);
*wt = PetscMin(*wt,t2-t1);
}
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&f);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode BSSCreateR1Vec(BSS self, Vec *v) {
PetscErrorCode ierr;
ierr = BSSCheck(self); CHKERRQ(ierr);
int nb = self->num_basis;
VecCreate(self->comm, v);
VecSetSizes(*v, PETSC_DECIDE, nb);
VecSetUp(*v);
return 0;
}
//-----------------------------------------------------------------
void PETScLinearSolver::VectorCreate(PetscInt m)
{
//PetscErrorCode ierr; // returned value from PETSc functions
VecCreate(PETSC_COMM_WORLD, &b);
////VecCreateMPI(PETSC_COMM_WORLD,m_size_loc, m, &b);
//VecSetSizes(b, m_size_loc, m);
VecSetSizes(b, PETSC_DECIDE, m);
VecSetFromOptions(b);
VecSetUp(b); //kg44 for PETSC 3.3
VecDuplicate(b, &x);
VecGetLocalSize(x, &m_size_loc);
//VecGetOwnershipRange(b, &i_start,&i_end);
}
int SFieldBeginRuns(SField sfv,
unsigned int N,
const unsigned int *nelem) {
mySField sf = static_cast<mySField>(sfv);
unsigned int j;
assert(!sf->running);
sf->maxN = N;
sf->running = 1;
sf->timeAssembly = 0;
sf->timeSolver = 0;
// Given k indices we need k*2^d variables
// Given N variables we need N / 2^d
// Now we are overestimating the number of modes.
sf->modes = sf->maxN;//(sf->N+ignored_modes) / (1 << sf->d) + ((sf->N+ignored_modes) % (1 << sf->d) != 0);
sf->N_multi_idx = new ind_t[sf->modes * sf->d];
GenTDSet(sf->d, 0, sf->N_multi_idx, sf->modes);
// Create sparse Matrix of size prod(mesh)
Mat J; Vec F; Vec U;
int s=1;
for (j=0;j < sf->d;j++){
sf->mesh[j] = nelem[j];
s *= sf->mesh[j];
}
MatCreate(PETSC_COMM_WORLD,&J);
MatSetSizes(J,s,s,s,s);
MatSetType(J,MATSEQAIJ);
MatSeqAIJSetPreallocation(J,1+2*sf->d,NULL);
MatSetFromOptions(J);
/* MatSetType(J,MATSEQDENSE); */
/* MatSeqDenseSetPreallocation(J,NULL); */
/* MatSetFromOptions(J); */
MatSetUp(J);
VecCreate(PETSC_COMM_WORLD,&F);
VecSetSizes(F,PETSC_DECIDE,s);
VecSetFromOptions(F);
VecSetUp(F);
VecDuplicate(F,&U);
KSP ksp;
KSPCreate(PETSC_COMM_WORLD,&ksp);
KSPSetFromOptions(ksp);
sf->J = J; sf->F = F; sf->U = U; sf->ksp = ksp;
return 0;
}
int main(int argc, char **argv)
{
PetscInt ierr;
PetscSF sf;
Vec A,Aout;
Vec B,Bout;
PetscScalar *bufA;
PetscScalar *bufAout;
PetscScalar *bufB;
PetscScalar *bufBout;
PetscMPIInt rank, size;
PetscInt nroots, nleaves;
PetscInt i;
PetscInt *ilocal;
PetscSFNode *iremote;
ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 2) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Only coded for two MPI processes\n");
ierr = PetscSFCreate(PETSC_COMM_WORLD,&sf);CHKERRQ(ierr);
ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr);
nleaves = 2;
nroots = 1;
ierr = PetscMalloc1(nleaves,&ilocal);CHKERRQ(ierr);
for (i = 0; i<nleaves; i++) {
ilocal[i] = i;
}
ierr = PetscMalloc1(nleaves,&iremote);CHKERRQ(ierr);
if (rank == 0) {
iremote[0].rank = 0;
iremote[0].index = 0;
iremote[1].rank = 1;
iremote[1].index = 0;
} else {
iremote[0].rank = 1;
iremote[0].index = 0;
iremote[1].rank = 0;
iremote[1].index = 0;
}
ierr = PetscSFSetGraph(sf,nroots,nleaves,ilocal,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr);
ierr = PetscSFSetUp(sf);CHKERRQ(ierr);
ierr = PetscSFView(sf,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = VecSetSizes(A,2,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(A);CHKERRQ(ierr);
ierr = VecSetUp(A);CHKERRQ(ierr);
ierr = VecDuplicate(A,&B);CHKERRQ(ierr);
ierr = VecDuplicate(A,&Aout);CHKERRQ(ierr);
ierr = VecDuplicate(A,&Bout);CHKERRQ(ierr);
ierr = VecGetArray(A,&bufA);CHKERRQ(ierr);
ierr = VecGetArray(B,&bufB);CHKERRQ(ierr);
for (i=0; i<2; i++) {
bufA[i] = (PetscScalar)rank;
bufB[i] = (PetscScalar)(rank) + 10.0;
}
ierr = VecRestoreArray(A,&bufA);CHKERRQ(ierr);
ierr = VecRestoreArray(B,&bufB);CHKERRQ(ierr);
ierr = VecGetArrayRead(A,(const PetscScalar**)&bufA);CHKERRQ(ierr);
ierr = VecGetArrayRead(B,(const PetscScalar**)&bufB);CHKERRQ(ierr);
ierr = VecGetArray(Aout,&bufAout);CHKERRQ(ierr);
ierr = VecGetArray(Bout,&bufBout);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(sf,MPIU_SCALAR,(const void*)bufA,(void *)bufAout);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(sf,MPIU_SCALAR,(const void*)bufB,(void *)bufBout);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(sf,MPIU_SCALAR,(const void*)bufA,(void *)bufAout);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(sf,MPIU_SCALAR,(const void*)bufB,(void *)bufBout);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(A,(const PetscScalar**)&bufA);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(B,(const PetscScalar**)&bufB);CHKERRQ(ierr);
ierr = VecRestoreArray(Aout,&bufAout);CHKERRQ(ierr);
ierr = VecRestoreArray(Bout,&bufBout);CHKERRQ(ierr);
ierr = VecView(Aout,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecView(Bout,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&B);CHKERRQ(ierr);
ierr = VecDestroy(&Aout);CHKERRQ(ierr);
ierr = VecDestroy(&Bout);CHKERRQ(ierr);
ierr = PetscSFDestroy(&sf);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
void PETSC_STDCALL vecsetup_(Vec v, int *__ierr ){
*__ierr = VecSetUp(
(Vec)PetscToPointer((v) ));
}
/*@
MatNullSpaceCreateRigidBody - create rigid body modes from coordinates
Collective on Vec
Input Argument:
. coords - block of coordinates of each node, must have block size set
Output Argument:
. sp - the null space
Level: advanced
Notes:
If you are solving an elasticity problems you should likely use this, in conjunction with ee MatSetNearNullspace(), to provide information that
the PCGAMG preconditioner can use to construct a much more efficient preconditioner.
If you are solving an elasticity problem with pure Neumann boundary conditions you can use this in conjunction with MatSetNullspace() to
provide this information to the linear solver so it can handle the null space appropriately in the linear solution.
.seealso: MatNullSpaceCreate(), MatSetNearNullspace(), MatSetNullspace()
@*/
PetscErrorCode MatNullSpaceCreateRigidBody(Vec coords,MatNullSpace *sp)
{
PetscErrorCode ierr;
const PetscScalar *x;
PetscScalar *v[6],dots[5];
Vec vec[6];
PetscInt n,N,dim,nmodes,i,j;
PetscReal sN;
PetscFunctionBegin;
ierr = VecGetBlockSize(coords,&dim);CHKERRQ(ierr);
ierr = VecGetLocalSize(coords,&n);CHKERRQ(ierr);
ierr = VecGetSize(coords,&N);CHKERRQ(ierr);
n /= dim;
N /= dim;
sN = 1./PetscSqrtReal((PetscReal)N);
switch (dim) {
case 1:
ierr = MatNullSpaceCreate(PetscObjectComm((PetscObject)coords),PETSC_TRUE,0,NULL,sp);CHKERRQ(ierr);
break;
case 2:
case 3:
nmodes = (dim == 2) ? 3 : 6;
ierr = VecCreate(PetscObjectComm((PetscObject)coords),&vec[0]);CHKERRQ(ierr);
ierr = VecSetSizes(vec[0],dim*n,dim*N);CHKERRQ(ierr);
ierr = VecSetBlockSize(vec[0],dim);CHKERRQ(ierr);
ierr = VecSetUp(vec[0]);CHKERRQ(ierr);
for (i=1; i<nmodes; i++) {ierr = VecDuplicate(vec[0],&vec[i]);CHKERRQ(ierr);}
for (i=0; i<nmodes; i++) {ierr = VecGetArray(vec[i],&v[i]);CHKERRQ(ierr);}
ierr = VecGetArrayRead(coords,&x);CHKERRQ(ierr);
for (i=0; i<n; i++) {
if (dim == 2) {
v[0][i*2+0] = sN;
v[0][i*2+1] = 0.;
v[1][i*2+0] = 0.;
v[1][i*2+1] = sN;
/* Rotations */
v[2][i*2+0] = -x[i*2+1];
v[2][i*2+1] = x[i*2+0];
} else {
v[0][i*3+0] = sN;
v[0][i*3+1] = 0.;
v[0][i*3+2] = 0.;
v[1][i*3+0] = 0.;
v[1][i*3+1] = sN;
v[1][i*3+2] = 0.;
v[2][i*3+0] = 0.;
v[2][i*3+1] = 0.;
v[2][i*3+2] = sN;
v[3][i*3+0] = x[i*3+1];
v[3][i*3+1] = -x[i*3+0];
v[3][i*3+2] = 0.;
v[4][i*3+0] = 0.;
v[4][i*3+1] = -x[i*3+2];
v[4][i*3+2] = x[i*3+1];
v[5][i*3+0] = x[i*3+2];
v[5][i*3+1] = 0.;
v[5][i*3+2] = -x[i*3+0];
}
}
for (i=0; i<nmodes; i++) {ierr = VecRestoreArray(vec[i],&v[i]);CHKERRQ(ierr);}
ierr = VecRestoreArrayRead(coords,&x);CHKERRQ(ierr);
for (i=dim; i<nmodes; i++) {
/* Orthonormalize vec[i] against vec[0:i-1] */
ierr = VecMDot(vec[i],i,vec,dots);CHKERRQ(ierr);
for (j=0; j<i; j++) dots[j] *= -1.;
ierr = VecMAXPY(vec[i],i,dots,vec);CHKERRQ(ierr);
ierr = VecNormalize(vec[i],NULL);CHKERRQ(ierr);
}
ierr = MatNullSpaceCreate(PetscObjectComm((PetscObject)coords),PETSC_FALSE,nmodes,vec,sp);CHKERRQ(ierr);
for (i=0; i<nmodes; i++) {ierr = VecDestroy(&vec[i]);CHKERRQ(ierr);}
}
PetscFunctionReturn(0);
}
/* Solves the specified ODE and computes the error if exact solution is available */
PetscErrorCode SolveODE(char* ptype, PetscReal dt, PetscReal tfinal, PetscInt maxiter, PetscReal *error, PetscBool *exact_flag)
{
PetscErrorCode ierr; /* Error code */
TS ts; /* time-integrator */
Vec Y; /* Solution vector */
Vec Yex; /* Exact solution */
PetscInt N; /* Size of the system of equations */
TSType time_scheme; /* Type of time-integration scheme */
Mat Jac = NULL; /* Jacobian matrix */
PetscFunctionBegin;
N = GetSize((const char *)&ptype[0]);
if (N < 0) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_SIZ,"Illegal problem specification.\n");
ierr = VecCreate(PETSC_COMM_WORLD,&Y);CHKERRQ(ierr);
ierr = VecSetSizes(Y,N,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetUp(Y);CHKERRQ(ierr);
ierr = VecSet(Y,0);CHKERRQ(ierr);
/* Initialize the problem */
ierr = Initialize(Y,&ptype[0]);
/* Create and initialize the time-integrator */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
/* Default time integration options */
ierr = TSSetType(ts,TSEULER);CHKERRQ(ierr);
ierr = TSSetDuration(ts,maxiter,tfinal);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr);
/* Read command line options for time integration */
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
/* Set solution vector */
ierr = TSSetSolution(ts,Y);CHKERRQ(ierr);
/* Specify left/right-hand side functions */
ierr = TSGetType(ts,&time_scheme);CHKERRQ(ierr);
if ((!strcmp(time_scheme,TSEULER)) || (!strcmp(time_scheme,TSRK)) || (!strcmp(time_scheme,TSSSP))) {
/* Explicit time-integration -> specify right-hand side function ydot = f(y) */
ierr = TSSetRHSFunction(ts,NULL,RHSFunction,&ptype[0]);CHKERRQ(ierr);
} else if ((!strcmp(time_scheme,TSBEULER)) || (!strcmp(time_scheme,TSARKIMEX))) {
/* Implicit time-integration -> specify left-hand side function ydot-f(y) = 0 */
/* and its Jacobian function */
ierr = TSSetIFunction(ts,NULL,IFunction,&ptype[0]);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&Jac);CHKERRQ(ierr);
ierr = MatSetSizes(Jac,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);
ierr = MatSetFromOptions(Jac);CHKERRQ(ierr);
ierr = MatSetUp(Jac);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,Jac,Jac,IJacobian,&ptype[0]);CHKERRQ(ierr);
}
/* Solve */
ierr = TSSolve(ts,Y);CHKERRQ(ierr);
/* Exact solution */
ierr = VecDuplicate(Y,&Yex);CHKERRQ(ierr);
ierr = ExactSolution(Yex,&ptype[0],tfinal,exact_flag);
/* Calculate Error */
ierr = VecAYPX(Yex,-1.0,Y);CHKERRQ(ierr);
ierr = VecNorm(Yex,NORM_2,error);CHKERRQ(ierr);
*error = PetscSqrtReal(((*error)*(*error))/N);
/* Clean up and finalize */
ierr = MatDestroy(&Jac);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = VecDestroy(&Yex);CHKERRQ(ierr);
ierr = VecDestroy(&Y);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
PetscInt ierr;
PetscSF sf;
Vec A,Aout;
PetscScalar *bufA;
PetscScalar *bufAout;
PetscMPIInt rank, size;
PetscInt nroots, nleaves;
PetscInt i;
PetscInt *ilocal;
PetscSFNode *iremote;
PetscBool test_dupped_type;
MPI_Datatype contig;
ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Only coded for one MPI process");
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","PetscSF type freeing options","none");CHKERRQ(ierr);
test_dupped_type = PETSC_FALSE;
ierr = PetscOptionsBool("-test_dupped_type", "Test dupped input type","",test_dupped_type,&test_dupped_type,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscSFCreate(PETSC_COMM_WORLD,&sf);CHKERRQ(ierr);
ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr);
nleaves = 1;
nroots = 1;
ierr = PetscMalloc1(nleaves,&ilocal);CHKERRQ(ierr);
for (i = 0; i<nleaves; i++) {
ilocal[i] = i;
}
ierr = PetscMalloc1(nleaves,&iremote);CHKERRQ(ierr);
iremote[0].rank = 0;
iremote[0].index = 0;
ierr = PetscSFSetGraph(sf,nroots,nleaves,ilocal,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr);
ierr = PetscSFSetUp(sf);CHKERRQ(ierr);
ierr = PetscSFView(sf,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = VecSetSizes(A,4,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(A);CHKERRQ(ierr);
ierr = VecSetUp(A);CHKERRQ(ierr);
ierr = VecDuplicate(A,&Aout);CHKERRQ(ierr);
ierr = VecGetArray(A,&bufA);CHKERRQ(ierr);
for (i=0; i<4; i++) {
bufA[i] = (PetscScalar)i;
}
ierr = VecRestoreArray(A,&bufA);CHKERRQ(ierr);
ierr = VecGetArrayRead(A,(const PetscScalar**)&bufA);CHKERRQ(ierr);
ierr = VecGetArray(Aout,&bufAout);CHKERRQ(ierr);
ierr = MPI_Type_contiguous(4, MPIU_SCALAR, &contig);CHKERRQ(ierr);
ierr = MPI_Type_commit(&contig);CHKERRQ(ierr);
if (test_dupped_type) {
MPI_Datatype tmp;
ierr = MPI_Type_dup(contig, &tmp);CHKERRQ(ierr);
ierr = MPI_Type_free(&contig);CHKERRQ(ierr);
contig = tmp;
}
for (i=0;i<10000;i++) {
ierr = PetscSFBcastBegin(sf,contig,bufA,bufAout);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(sf,contig,bufA,bufAout);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(A,(const PetscScalar**)&bufA);CHKERRQ(ierr);
ierr = VecRestoreArray(Aout,&bufAout);CHKERRQ(ierr);
ierr = VecView(Aout,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&Aout);CHKERRQ(ierr);
ierr = PetscSFDestroy(&sf);CHKERRQ(ierr);
ierr = MPI_Type_free(&contig);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/*@
MatCreateSubMatrix - Creates a composite matrix that acts as a submatrix
Collective on Mat
Input Parameters:
+ A - matrix that we will extract a submatrix of
. isrow - rows to be present in the submatrix
- iscol - columns to be present in the submatrix
Output Parameters:
. newmat - new matrix
Level: developer
Notes:
Most will use MatGetSubMatrix which provides a more efficient representation if it is available.
.seealso: MatGetSubMatrix(), MatSubMatrixUpdate()
@*/
PetscErrorCode MatCreateSubMatrix(Mat A,IS isrow,IS iscol,Mat *newmat)
{
Vec left,right;
PetscInt m,n;
Mat N;
Mat_SubMatrix *Na;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(A,MAT_CLASSID,1);
PetscValidHeaderSpecific(isrow,IS_CLASSID,2);
PetscValidHeaderSpecific(iscol,IS_CLASSID,3);
PetscValidPointer(newmat,4);
*newmat = 0;
ierr = MatCreate(PetscObjectComm((PetscObject)A),&N);CHKERRQ(ierr);
ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr);
ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr);
ierr = MatSetSizes(N,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)N,MATSUBMATRIX);CHKERRQ(ierr);
ierr = PetscNewLog(N,Mat_SubMatrix,&Na);CHKERRQ(ierr);
N->data = (void*)Na;
ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)isrow);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)iscol);CHKERRQ(ierr);
Na->A = A;
Na->isrow = isrow;
Na->iscol = iscol;
Na->scale = 1.0;
N->ops->destroy = MatDestroy_SubMatrix;
N->ops->mult = MatMult_SubMatrix;
N->ops->multadd = MatMultAdd_SubMatrix;
N->ops->multtranspose = MatMultTranspose_SubMatrix;
N->ops->multtransposeadd = MatMultTransposeAdd_SubMatrix;
N->ops->scale = MatScale_SubMatrix;
N->ops->diagonalscale = MatDiagonalScale_SubMatrix;
ierr = PetscLayoutSetBlockSize(N->rmap,A->rmap->bs);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(N->cmap,A->cmap->bs);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(N->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(N->cmap);CHKERRQ(ierr);
ierr = MatGetVecs(A,&Na->rwork,&Na->lwork);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)isrow),&left);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)iscol),&right);CHKERRQ(ierr);
ierr = VecSetSizes(left,m,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetSizes(right,n,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetUp(left);CHKERRQ(ierr);
ierr = VecSetUp(right);CHKERRQ(ierr);
ierr = VecScatterCreate(Na->lwork,isrow,left,NULL,&Na->lrestrict);CHKERRQ(ierr);
ierr = VecScatterCreate(right,NULL,Na->rwork,iscol,&Na->rprolong);CHKERRQ(ierr);
ierr = VecDestroy(&left);CHKERRQ(ierr);
ierr = VecDestroy(&right);CHKERRQ(ierr);
N->assembled = PETSC_TRUE;
ierr = MatSetUp(N);CHKERRQ(ierr);
*newmat = N;
PetscFunctionReturn(0);
}
int main(int argc, char** argv)
{
/* the total number of grid points in each spatial direction is (n+1) */
/* the total number of degrees-of-freedom in each spatial direction is (n-1) */
/* this version requires n to be a power of 2 */
if( argc < 2 ) {
printf("need a problem size\n");
return 1;
}
int n = atoi(argv[1]);
int m = n-1;
// Initialize Petsc
PetscInitialize(&argc,&argv,0,PETSC_NULL);
// Create our vector
Vec b;
VecCreate(PETSC_COMM_WORLD,&b);
VecSetSizes(b,m*m,PETSC_DECIDE);
VecSetFromOptions(b);
VecSetUp(b);
// Create our matrix
Mat A;
MatCreate(PETSC_COMM_WORLD,&A);
MatSetType(A,MATSEQAIJ);
MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,m*m,m*m);
MatSetUp(A);
// Create linear solver object
KSP ksp;
KSPCreate(PETSC_COMM_WORLD,&ksp);
// setup rhs
PetscInt low, high;
VecGetOwnershipRange(b,&low,&high);
PetscInt* inds = (PetscInt*)malloc((high-low)*sizeof(PetscInt));
double* vals = (double*)malloc((high-low)*sizeof(double));
double h = 1./(double)n;
for (int i=0;i<high-1;++i) {
inds[i] = low+i;
vals[i] = h*h;
}
VecSetValues(b,high-low,inds,vals,INSERT_VALUES);
free(inds);
free(vals);
// setup matrix
for (int i=0;i<m*m;++i) {
MatSetValue(A,i,i,4.f,INSERT_VALUES);
if (i%m != m-1)
MatSetValue(A,i,i+1,-1.f,INSERT_VALUES);
if (i%m)
MatSetValue(A,i,i-1,-1.f,INSERT_VALUES);
if (i > m)
MatSetValue(A,i,i-m,-1.f,INSERT_VALUES);
if (i < m*(m-1))
MatSetValue(A,i,i+m,-1.f,INSERT_VALUES);
}
// sync processes
VecAssemblyBegin(b);
VecAssemblyEnd(b);
MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
// solve
KSPSetType(ksp,"cg");
KSPSetTolerances(ksp,1.e-10,1.e-10,1.e6,10000);
KSPSetOperators(ksp,A,A,SAME_NONZERO_PATTERN);
PC pc;
KSPGetPC(ksp,&pc);
PCSetType(pc,"ilu");
PCSetFromOptions(pc);
PCSetUp(pc);
// setup solver
KSPSetFromOptions(ksp);
KSPSetUp(ksp);
Vec x;
VecDuplicate(b,&x);
KSPSolve(ksp,b,x);
double val;
VecNorm(x,NORM_INFINITY,&val);
printf (" umax = %e \n",val);
PetscFinalize();
return 0;
}
int testBSplinePsi() {
PetscErrorCode ierr;
PrintTimeStamp(PETSC_COMM_SELF, "Psi", NULL);
MPI_Comm comm = PETSC_COMM_SELF;
BPS bps; BPSCreate(comm, &bps); BPSSetLine(bps, 5.0, 6);
int order = 3;
BSS bss; BSSCreate(comm, &bss); BSSSetKnots(bss, order, bps);
BSSSetUp(bss);
int n; BSSGetSize(bss, &n);
if(n <= 0){
SETERRQ(comm, 1, "n is 0 or negative");
}
Vec c;
ierr = VecCreate(comm, &c); CHKERRQ(ierr);
ierr = VecSetSizes(c, PETSC_DECIDE, n);CHKERRQ(ierr);
ierr = VecSetUp(c); CHKERRQ(ierr);
PetscScalar *ptr_c;
ierr = VecGetArray(c, &ptr_c); CHKERRQ(ierr);
for(int i = 0; i < n; i++) {
ptr_c[i] = i + 0.1;
}
ierr = VecRestoreArray(c, &ptr_c); CHKERRQ(ierr);
PetscReal x = 1.1;
Vec xs; VecCreate(comm, &xs); VecSetSizes(xs, PETSC_DECIDE, 1);
ierr = VecSetUp(xs); CHKERRQ(ierr);
ierr = VecSetValue(xs, 0, x, INSERT_VALUES); CHKERRQ(ierr);
// Vec xs; VecCreate(comm, &xs); VecSetSizes(xs, PETSC_DEFAULT, 1);
// VecSetUp(xs);
// ierr = VecSetValue(xs, 0, x, INSERT_VALUES); CHKERRQ(ierr);
Vec ys;
ierr = VecDuplicate(xs, &ys); CHKERRQ(ierr);
ierr = BSSPsi(bss, c, xs, ys); CHKERRQ(ierr);
Vec dys;
ierr = VecDuplicate(xs, &dys); CHKERRQ(ierr);
ierr = BSSDerivPsi(bss, c, xs, dys); CHKERRQ(ierr);
PetscScalar y;
ierr = BSSPsiOne(bss, c, x, &y); CHKERRQ(ierr);
PetscScalar *ptr_y;
ierr = VecGetArray(ys, &ptr_y); CHKERRQ(ierr);
ASSERT_SCALAR_EQ(y, ptr_y[0]);
ierr = VecRestoreArray(ys, &ptr_y); CHKERRQ(ierr);
PetscScalar dy;
ierr = BSSDerivPsiOne(bss, c, x, &dy); CHKERRQ(ierr);
PetscScalar *ptr_dy;
ierr = VecGetArray(dys, &ptr_dy); CHKERRQ(ierr);
ASSERT_SCALAR_EQ(dy, ptr_dy[0]);
ierr = VecRestoreArray(dys, &ptr_dy); CHKERRQ(ierr);
BSSDestroy(&bss);
VecRestoreArray(c, &ptr_c);
VecDestroy(&c);
VecDestroy(&xs);
VecRestoreArray(ys, &ptr_y);
VecDestroy(&ys);
VecRestoreArray(dys, &ptr_dy);
VecDestroy(&dys);
return 0;
}
int main(int argc, char **argv)
{
Vec vec, tagged, untagged;
VecScatter taggedScatter, untaggedScatter;
PetscInt bs;
PetscInt n, nloc, nint, i, j, k, localStart, localEnd, ntagged, nuntagged;
MPI_Comm comm;
VecTagger tagger;
PetscScalar *array;
PetscRandom rand;
VecTaggerBox *defaultBox;
VecTaggerBox *boxes;
IS is, isBlockGlobal, isComp;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
n = 10.;
bs = 1;
comm = PETSC_COMM_WORLD;
ierr = PetscOptionsBegin(comm, "" , "VecTagger Test Options", "Vec");CHKERRQ(ierr);
ierr = PetscOptionsInt("-bs","The block size of the vector","ex1.c",bs,&bs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-n","The size of the vector (in blocks)","ex1.c",n,&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscRandomCreate(comm,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = VecCreate(comm,&vec);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)vec,"Vec to Tag");CHKERRQ(ierr);
ierr = VecSetBlockSize(vec,bs);CHKERRQ(ierr);
ierr = VecSetSizes(vec,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetUp(vec);CHKERRQ(ierr);
ierr = VecGetLocalSize(vec,&nloc);CHKERRQ(ierr);
ierr = VecGetArray(vec,&array);CHKERRQ(ierr);
for (i = 0; i < nloc; i++) {
PetscScalar val;
ierr = PetscRandomGetValue(rand,&val);CHKERRQ(ierr);
array[i] = val;
}
ierr = VecRestoreArray(vec,&array);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = VecViewFromOptions(vec,NULL,"-vec_view");CHKERRQ(ierr);
ierr = VecTaggerCreate(comm,&tagger);CHKERRQ(ierr);
ierr = VecTaggerSetBlockSize(tagger,bs);CHKERRQ(ierr);
ierr = VecTaggerSetType(tagger,VECTAGGERABSOLUTE);CHKERRQ(ierr);
ierr = PetscMalloc1(bs,&defaultBox);CHKERRQ(ierr);
for (i = 0; i < bs; i++) {
#if !defined(PETSC_USE_COMPLEX)
defaultBox[i].min = 0.1;
defaultBox[i].max = 1.5;
#else
defaultBox[i].min = PetscCMPLX(0.1,0.1);
defaultBox[i].max = PetscCMPLX(1.5,1.5);
#endif
}
ierr = VecTaggerAbsoluteSetBox(tagger,defaultBox);CHKERRQ(ierr);
ierr = PetscFree(defaultBox);CHKERRQ(ierr);
ierr = VecTaggerSetFromOptions(tagger);CHKERRQ(ierr);
ierr = VecTaggerSetUp(tagger);CHKERRQ(ierr);
ierr = PetscObjectViewFromOptions((PetscObject)tagger,NULL,"-vec_tagger_view");CHKERRQ(ierr);
ierr = VecTaggerGetBlockSize(tagger,&bs);CHKERRQ(ierr);
ierr = VecTaggerComputeBoxes(tagger,vec,&nint,&boxes);
if (ierr && ierr != PETSC_ERR_SUP) CHKERRQ(ierr);
else {
PetscViewer viewer = NULL;
ierr = PetscOptionsGetViewer(comm,NULL,NULL,"-vec_tagger_boxes_view",&viewer,NULL,NULL);CHKERRQ(ierr);
if (viewer) {
PetscBool iascii;
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr);
if (iascii) {
ierr = PetscViewerASCIIPrintf(viewer,"Num boxes: %D\n",nint);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
for (i = 0, k = 0; i < nint; i++) {
ierr = PetscViewerASCIIPrintf(viewer,"%D: ",i);CHKERRQ(ierr);
for (j = 0; j < bs; j++, k++) {
if (j) {ierr = PetscViewerASCIIPrintf(viewer," x ");CHKERRQ(ierr);}
#if !defined(PETSC_USE_COMPLEX)
ierr = PetscViewerASCIIPrintf(viewer,"[%g,%g]",(double)boxes[k].min,(double)boxes[k].max);CHKERRQ(ierr);
#else
ierr = PetscViewerASCIIPrintf(viewer,"[%g+%gi,%g+%gi]",(double)PetscRealPart(boxes[k].min),(double)PetscImaginaryPart(boxes[k].min),(double)PetscRealPart(boxes[k].max),(double)PetscImaginaryPart(boxes[k].max));CHKERRQ(ierr);
#endif
}
ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
}
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscFree(boxes);CHKERRQ(ierr);
}
ierr = VecTaggerComputeIS(tagger,vec,&is);CHKERRQ(ierr);
ierr = ISGetBlockGlobalIS(is,vec,bs,&isBlockGlobal);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)isBlockGlobal,"Tagged IS (block global)");CHKERRQ(ierr);
ierr = ISViewFromOptions(isBlockGlobal,NULL,"-tagged_is_view");CHKERRQ(ierr);
ierr = VecGetOwnershipRange(vec,&localStart,&localEnd);CHKERRQ(ierr);
ierr = ISComplement(isBlockGlobal,localStart,localEnd,&isComp);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)isComp,"Untagged IS (global)");CHKERRQ(ierr);
ierr = ISViewFromOptions(isComp,NULL,"-untagged_is_view");CHKERRQ(ierr);
ierr = ISGetLocalSize(isBlockGlobal,&ntagged);CHKERRQ(ierr);
ierr = ISGetLocalSize(isComp,&nuntagged);CHKERRQ(ierr);
ierr = VecCreate(comm,&tagged);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)tagged,"Tagged selection");CHKERRQ(ierr);
ierr = VecSetSizes(tagged,ntagged,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetUp(tagged);CHKERRQ(ierr);
ierr = VecCreate(comm,&untagged);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)untagged,"Untagged selection");CHKERRQ(ierr);
ierr = VecSetSizes(untagged,nuntagged,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetUp(untagged);CHKERRQ(ierr);
ierr = VecScatterCreate(vec,isBlockGlobal,tagged,NULL,&taggedScatter);CHKERRQ(ierr);
ierr = VecScatterCreate(vec,isComp,untagged,NULL,&untaggedScatter);CHKERRQ(ierr);
ierr = VecScatterBegin(taggedScatter,vec,tagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(taggedScatter,vec,tagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterBegin(untaggedScatter,vec,untagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(untaggedScatter,vec,untagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecViewFromOptions(tagged,NULL,"-tagged_vec_view");CHKERRQ(ierr);
ierr = VecViewFromOptions(untagged,NULL,"-untagged_vec_view");CHKERRQ(ierr);
ierr = VecScatterDestroy(&untaggedScatter);CHKERRQ(ierr);
ierr = VecScatterDestroy(&taggedScatter);CHKERRQ(ierr);
ierr = VecDestroy(&untagged);CHKERRQ(ierr);
ierr = VecDestroy(&tagged);CHKERRQ(ierr);
ierr = ISDestroy(&isComp);CHKERRQ(ierr);
ierr = ISDestroy(&isBlockGlobal);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
ierr = VecTaggerDestroy(&tagger);CHKERRQ(ierr);
ierr = VecDestroy(&vec);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc, char** argv)
{
PC pc;
PetscErrorCode ierr;
PetscInt m, nn, M, j, k, ne = 4;
PetscReal* coords;
Vec x, rhs;
Mat A;
KSP ksp;
PetscMPIInt npe, rank;
PetscInitialize(&argc, &argv, NULL, NULL);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &npe);
CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD, NULL, "Linear elasticity in 3D", "");
{
char nestring[256];
ierr = PetscSNPrintf(nestring, sizeof nestring, "number of elements in each direction, ne+1 must be a multiple of %D (sizes^{1/3})",
(PetscInt)(PetscPowReal((PetscReal)npe, 1.0 / 3.0) + 0.5));
ierr = PetscOptionsInt("-ne", nestring, "", ne, &ne, NULL);
}
ierr = PetscOptionsEnd();
CHKERRQ(ierr);
const HpddmOption* const opt = HpddmOptionGet();
{
HpddmOptionParse(opt, argc, argv, rank == 0);
if (rank) HpddmOptionRemove(opt, "verbosity");
}
nn = ne + 1;
M = 3 * nn * nn * nn;
if (npe == 2) {
if (rank == 1)
m = 0;
else
m = nn * nn * nn;
npe = 1;
}
else {
m = nn * nn * nn / npe;
if (rank == npe - 1) m = nn * nn * nn - (npe - 1) * m;
}
m *= 3;
ierr = KSPCreate(PETSC_COMM_WORLD, &ksp);
CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);
CHKERRQ(ierr);
int i;
{
PetscInt Istart, Iend, jj, ic;
const PetscInt NP = (PetscInt)(PetscPowReal((PetscReal)npe, 1.0 / 3.0) + 0.5);
const PetscInt ipx = rank % NP, ipy = (rank % (NP * NP)) / NP, ipz = rank / (NP * NP);
const PetscInt Ni0 = ipx * (nn / NP), Nj0 = ipy * (nn / NP), Nk0 = ipz * (nn / NP);
const PetscInt Ni1 = Ni0 + (m > 0 ? (nn / NP) : 0), Nj1 = Nj0 + (nn / NP), Nk1 = Nk0 + (nn / NP);
PetscInt *d_nnz, *o_nnz, osz[4] = {0, 9, 15, 19}, nbc;
if (npe != NP * NP * NP) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "npe=%d: npe^{1/3} must be integer", npe);
if (nn != NP * (nn / NP)) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "-ne %d: (ne+1)%(npe^{1/3}) must equal zero", ne);
ierr = PetscMalloc1(m + 1, &d_nnz);
CHKERRQ(ierr);
ierr = PetscMalloc1(m + 1, &o_nnz);
CHKERRQ(ierr);
for (i = Ni0, ic = 0; i < Ni1; i++) {
for (j = Nj0; j < Nj1; j++) {
for (k = Nk0; k < Nk1; k++) {
nbc = 0;
if (i == Ni0 || i == Ni1 - 1) nbc++;
if (j == Nj0 || j == Nj1 - 1) nbc++;
if (k == Nk0 || k == Nk1 - 1) nbc++;
for (jj = 0; jj < 3; jj++, ic++) {
d_nnz[ic] = 3 * (27 - osz[nbc]);
o_nnz[ic] = 3 * osz[nbc];
}
}
}
}
if (ic != m) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "ic %D does not equal m %D", ic, m);
ierr = MatCreate(PETSC_COMM_WORLD, &A);
CHKERRQ(ierr);
ierr = MatSetSizes(A, m, m, M, M);
CHKERRQ(ierr);
ierr = MatSetBlockSize(A, 3);
CHKERRQ(ierr);
ierr = MatSetType(A, MATAIJ);
CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(A, 0, d_nnz);
CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(A, 0, d_nnz, 0, o_nnz);
CHKERRQ(ierr);
ierr = PetscFree(d_nnz);
CHKERRQ(ierr);
ierr = PetscFree(o_nnz);
CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A, &Istart, &Iend);
CHKERRQ(ierr);
if (m != Iend - Istart) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "m %D does not equal Iend %D - Istart %D", m, Iend, Istart);
ierr = VecCreate(PETSC_COMM_WORLD, &x);
CHKERRQ(ierr);
ierr = VecSetSizes(x, m, M);
CHKERRQ(ierr);
ierr = VecSetBlockSize(x, 3);
CHKERRQ(ierr);
ierr = VecSetFromOptions(x);
CHKERRQ(ierr);
ierr = VecDuplicate(x, &rhs);
CHKERRQ(ierr);
ierr = PetscMalloc1(m + 1, &coords);
CHKERRQ(ierr);
coords[m] = -99.0;
PetscReal h = 1.0 / ne;
for (i = Ni0, ic = 0; i < Ni1; i++) {
for (j = Nj0; j < Nj1; j++) {
for (k = Nk0; k < Nk1; k++, ic++) {
coords[3 * ic] = h * (PetscReal)i;
coords[3 * ic + 1] = h * (PetscReal)j;
coords[3 * ic + 2] = h * (PetscReal)k;
}
}
}
}
PetscReal s_r[SIZE_ARRAY_R] = {30, 0.1, 20, 10};
PetscReal x_r[SIZE_ARRAY_R] = {0.5, 0.4, 0.4, 0.4};
PetscReal y_r[SIZE_ARRAY_R] = {0.5, 0.5, 0.4, 0.4};
PetscReal z_r[SIZE_ARRAY_R] = {0.5, 0.45, 0.4, 0.35};
PetscReal r[SIZE_ARRAY_R] = {0.5, 0.5, 0.4, 0.4};
AssembleSystem(A, rhs, s_r[0], x_r[0], y_r[0], z_r[0], r[0], ne, npe, rank, nn, m);
ierr = KSPSetOperators(ksp, A, A);
CHKERRQ(ierr);
MatNullSpace matnull;
Vec vec_coords;
PetscScalar* c;
ierr = VecCreate(MPI_COMM_WORLD, &vec_coords);
CHKERRQ(ierr);
ierr = VecSetBlockSize(vec_coords, 3);
CHKERRQ(ierr);
ierr = VecSetSizes(vec_coords, m, PETSC_DECIDE);
CHKERRQ(ierr);
ierr = VecSetUp(vec_coords);
CHKERRQ(ierr);
ierr = VecGetArray(vec_coords, &c);
CHKERRQ(ierr);
for (i = 0; i < m; i++) c[i] = coords[i];
ierr = VecRestoreArray(vec_coords, &c);
CHKERRQ(ierr);
ierr = MatNullSpaceCreateRigidBody(vec_coords, &matnull);
CHKERRQ(ierr);
ierr = MatSetNearNullSpace(A, matnull);
CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&matnull);
CHKERRQ(ierr);
ierr = VecDestroy(&vec_coords);
CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);
CHKERRQ(ierr);
MPI_Barrier(PETSC_COMM_WORLD);
double time = MPI_Wtime();
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
MPI_Barrier(PETSC_COMM_WORLD);
time = MPI_Wtime() - time;
ierr = PetscPrintf(PETSC_COMM_WORLD, "--- PC setup = %f\n", time);
CHKERRQ(ierr);
float t_time[SIZE_ARRAY_R];
int t_its[SIZE_ARRAY_R];
{
{
ierr = KSPSolve(ksp, rhs, x);
CHKERRQ(ierr);
ierr = KSPReset(ksp);
CHKERRQ(ierr);
ierr = KSPSetOperators(ksp, A, A);
CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);
CHKERRQ(ierr);
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
}
for (i = 0; i < SIZE_ARRAY_R; ++i) {
ierr = VecZeroEntries(x);
CHKERRQ(ierr);
MPI_Barrier(PETSC_COMM_WORLD);
time = MPI_Wtime();
ierr = KSPSolve(ksp, rhs, x);
CHKERRQ(ierr);
MPI_Barrier(PETSC_COMM_WORLD);
t_time[i] = MPI_Wtime() - time;
PetscInt its;
ierr = KSPGetIterationNumber(ksp, &its);
CHKERRQ(ierr);
t_its[i] = its;
ierr = ComputeError(A, rhs, x);
CHKERRQ(ierr);
if (i == (SIZE_ARRAY_R - 1))
AssembleSystem(A, rhs, s_r[0], x_r[0], y_r[0], z_r[0], r[0], ne, npe, rank, nn, m);
else
AssembleSystem(A, rhs, s_r[i + 1], x_r[i + 1], y_r[i + 1], z_r[i + 1], r[i + 1], ne, npe, rank, nn, m);
ierr = KSPSetOperators(ksp, A, A);
CHKERRQ(ierr);
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
}
for (i = 0; i < SIZE_ARRAY_R; ++i) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "%d\t%d\t%f\n", i + 1, t_its[i], t_time[i]);
CHKERRQ(ierr);
if (i > 0) {
t_its[0] += t_its[i];
t_time[0] += t_time[i];
}
}
if (SIZE_ARRAY_R > 1) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "------------------------\n\t%d\t%f\n", t_its[0], t_time[0]);
CHKERRQ(ierr);
}
}
{
ierr = KSPGetPC(ksp, &pc);
CHKERRQ(ierr);
HpddmCustomOperator H;
H._A = A;
H._M = pc;
H._mv = mv;
H._precond = precond;
H._b = rhs;
H._x = x;
int n;
MatGetLocalSize(A, &n, NULL);
{
ierr = VecZeroEntries(x);
K* pt_rhs;
K* pt_x;
VecGetArray(rhs, &pt_rhs);
VecGetArray(x, &pt_x);
int previous = HpddmOptionVal(opt, "verbosity");
if (previous > 0) HpddmOptionRemove(opt, "verbosity");
HpddmCustomOperatorSolve(&H, n, H._mv, H._precond, pt_rhs, pt_x, 1, &PETSC_COMM_WORLD);
if (previous > 0) {
char buffer[20];
snprintf(buffer, 20, "%d", previous);
char* concat = malloc(strlen("-hpddm_verbosity ") + strlen(buffer) + 1);
strcpy(concat, "-hpddm_verbosity ");
strcat(concat, buffer);
HpddmOptionParseString(opt, concat);
free(concat);
}
VecRestoreArray(x, &pt_x);
VecRestoreArray(rhs, &pt_rhs);
previous = HpddmOptionVal(opt, "krylov_method");
if(previous == 4 || previous == 5) HpddmDestroyRecycling();
ierr = KSPReset(ksp);
CHKERRQ(ierr);
ierr = KSPSetOperators(ksp, A, A);
CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);
CHKERRQ(ierr);
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
}
for (i = 0; i < SIZE_ARRAY_R; ++i) {
ierr = VecZeroEntries(x);
CHKERRQ(ierr);
K* pt_rhs;
K* pt_x;
VecGetArray(rhs, &pt_rhs);
VecGetArray(x, &pt_x);
MPI_Barrier(PETSC_COMM_WORLD);
time = MPI_Wtime();
t_its[i] = HpddmCustomOperatorSolve(&H, n, H._mv, H._precond, pt_rhs, pt_x, 1, &PETSC_COMM_WORLD);
MPI_Barrier(PETSC_COMM_WORLD);
t_time[i] = MPI_Wtime() - time;
VecRestoreArray(x, &pt_x);
VecRestoreArray(rhs, &pt_rhs);
ierr = ComputeError(A, rhs, x);
CHKERRQ(ierr);
if (i != (SIZE_ARRAY_R - 1)) {
AssembleSystem(A, rhs, s_r[i + 1], x_r[i + 1], y_r[i + 1], z_r[i + 1], r[i + 1], ne, npe, rank, nn, m);
ierr = KSPSetOperators(ksp, A, A);
CHKERRQ(ierr);
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
}
}
for (i = 0; i < SIZE_ARRAY_R; ++i) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "%d\t%d\t%f\n", i + 1, t_its[i], t_time[i]);
CHKERRQ(ierr);
if (i > 0) {
t_its[0] += t_its[i];
t_time[0] += t_time[i];
}
}
if (SIZE_ARRAY_R > 1) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "------------------------\n\t%d\t%f\n", t_its[0], t_time[0]);
CHKERRQ(ierr);
}
}
ierr = KSPDestroy(&ksp);
CHKERRQ(ierr);
ierr = VecDestroy(&x);
CHKERRQ(ierr);
ierr = VecDestroy(&rhs);
CHKERRQ(ierr);
ierr = MatDestroy(&A);
CHKERRQ(ierr);
ierr = PetscFree(coords);
CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
TS ts; /* ODE integrator */
Vec U; /* solution will be stored here */
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt n = 2;
PetscScalar *u;
AppCtx app;
PetscInt direction[2];
PetscBool terminate[2];
PetscBool rhs_form=PETSC_FALSE,hist=PETSC_TRUE;
TSAdapt adapt;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize program
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
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_WORLD,PETSC_ERR_SUP,"Only for sequential runs");
app.nbounces = 0;
app.maxbounces = 10;
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"ex40 options","");CHKERRQ(ierr);
ierr = PetscOptionsInt("-maxbounces","","",app.maxbounces,&app.maxbounces,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_adapthistory","","",hist,&hist,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set ODE routines
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
/* Users are advised against the following branching and code duplication.
For problems without a mass matrix like the one at hand, the RHSFunction
(and companion RHSJacobian) interface is enough to support both explicit
and implicit timesteppers. This tutorial example also deals with the
IFunction/IJacobian interface for demonstration and testing purposes. */
ierr = PetscOptionsGetBool(NULL,NULL,"-rhs-form",&rhs_form,NULL);CHKERRQ(ierr);
if (rhs_form) {
ierr = TSSetRHSFunction(ts,NULL,RHSFunction,NULL);CHKERRQ(ierr);
ierr = TSSetRHSJacobian(ts,NULL,NULL,RHSJacobian,NULL);CHKERRQ(ierr);
} else {
Mat A; /* Jacobian matrix */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = MatSetType(A,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,IFunction,NULL);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,A,A,IJacobian,NULL);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecCreate(PETSC_COMM_WORLD,&U);CHKERRQ(ierr);
ierr = VecSetSizes(U,n,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetUp(U);CHKERRQ(ierr);
ierr = VecGetArray(U,&u);CHKERRQ(ierr);
u[0] = 0.0;
u[1] = 20.0;
ierr = VecRestoreArray(U,&u);CHKERRQ(ierr);
ierr = TSSetSolution(ts,U);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set solver options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetSaveTrajectory(ts);CHKERRQ(ierr);
ierr = TSSetMaxTime(ts,30.0);CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
ierr = TSSetTimeStep(ts,0.1);CHKERRQ(ierr);
/* The adapative time step controller could take very large timesteps resulting in
the same event occuring multiple times in the same interval. A maximum step size
limit is enforced here to avoid this issue. */
ierr = TSGetAdapt(ts,&adapt);CHKERRQ(ierr);
ierr = TSAdaptSetStepLimits(adapt,0.0,0.5);CHKERRQ(ierr);
/* Set directions and terminate flags for the two events */
direction[0] = -1; direction[1] = -1;
terminate[0] = PETSC_FALSE; terminate[1] = PETSC_TRUE;
ierr = TSSetEventHandler(ts,2,direction,terminate,EventFunction,PostEventFunction,(void*)&app);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Run timestepping solver
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSolve(ts,U);CHKERRQ(ierr);
if (hist) { /* replay following history */
TSTrajectory tj;
PetscReal tf,t0,dt;
app.nbounces = 0;
ierr = TSGetTime(ts,&tf);CHKERRQ(ierr);
ierr = TSSetMaxTime(ts,tf);CHKERRQ(ierr);
ierr = TSSetStepNumber(ts,0);CHKERRQ(ierr);
ierr = TSRestartStep(ts);CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSGetAdapt(ts,&adapt);CHKERRQ(ierr);
ierr = TSAdaptSetType(adapt,TSADAPTHISTORY);CHKERRQ(ierr);
ierr = TSGetTrajectory(ts,&tj);CHKERRQ(ierr);
ierr = TSAdaptHistorySetTrajectory(adapt,tj,PETSC_FALSE);CHKERRQ(ierr);
ierr = TSAdaptHistoryGetStep(adapt,0,&t0,&dt);CHKERRQ(ierr);
/* this example fails with single (or smaller) precision */
#if defined(PETSC_USE_REAL_SINGLE) || defined(PETSC_USE_REAL__FP16)
ierr = TSAdaptSetType(adapt,TSADAPTBASIC);CHKERRQ(ierr);
ierr = TSAdaptSetStepLimits(adapt,0.0,0.5);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
#endif
ierr = TSSetTime(ts,t0);CHKERRQ(ierr);
ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr);
ierr = TSResetTrajectory(ts);CHKERRQ(ierr);
ierr = VecGetArray(U,&u);CHKERRQ(ierr);
u[0] = 0.0;
u[1] = 20.0;
ierr = VecRestoreArray(U,&u);CHKERRQ(ierr);
ierr = TSSolve(ts,U);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecDestroy(&U);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
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;
}