PetscErrorCode DMCreateInterpolation_Composite(DM coarse,DM fine,Mat *A,Vec *v)
{
PetscErrorCode ierr;
PetscInt m,n,M,N,nDM,i;
struct DMCompositeLink *nextc;
struct DMCompositeLink *nextf;
Vec gcoarse,gfine,*vecs;
DM_Composite *comcoarse = (DM_Composite*)coarse->data;
DM_Composite *comfine = (DM_Composite*)fine->data;
Mat *mats;
PetscFunctionBegin;
PetscValidHeaderSpecific(coarse,DM_CLASSID,1);
PetscValidHeaderSpecific(fine,DM_CLASSID,2);
ierr = DMSetUp(coarse);CHKERRQ(ierr);
ierr = DMSetUp(fine);CHKERRQ(ierr);
/* use global vectors only for determining matrix layout */
ierr = DMGetGlobalVector(coarse,&gcoarse);CHKERRQ(ierr);
ierr = DMGetGlobalVector(fine,&gfine);CHKERRQ(ierr);
ierr = VecGetLocalSize(gcoarse,&n);CHKERRQ(ierr);
ierr = VecGetLocalSize(gfine,&m);CHKERRQ(ierr);
ierr = VecGetSize(gcoarse,&N);CHKERRQ(ierr);
ierr = VecGetSize(gfine,&M);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(coarse,&gcoarse);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(fine,&gfine);CHKERRQ(ierr);
nDM = comfine->nDM;
if (nDM != comcoarse->nDM) SETERRQ2(((PetscObject)fine)->comm,PETSC_ERR_ARG_INCOMP,"Fine DMComposite has %D entries, but coarse has %D",nDM,comcoarse->nDM);
ierr = PetscMalloc(nDM*nDM*sizeof(Mat),&mats);CHKERRQ(ierr);
ierr = PetscMemzero(mats,nDM*nDM*sizeof(Mat));CHKERRQ(ierr);
if (v) {
ierr = PetscMalloc(nDM*sizeof(Vec),&vecs);CHKERRQ(ierr);
ierr = PetscMemzero(vecs,nDM*sizeof(Vec));CHKERRQ(ierr);
}
/* loop over packed objects, handling one at at time */
for (nextc=comcoarse->next,nextf=comfine->next,i=0; nextc; nextc=nextc->next,nextf=nextf->next,i++) {
if (!v) {
ierr = DMCreateInterpolation(nextc->dm,nextf->dm,&mats[i*nDM+i],PETSC_NULL);CHKERRQ(ierr);
} else {
ierr = DMCreateInterpolation(nextc->dm,nextf->dm,&mats[i*nDM+i],&vecs[i]);CHKERRQ(ierr);
}
}
ierr = MatCreateNest(((PetscObject)fine)->comm,nDM,PETSC_NULL,nDM,PETSC_NULL,mats,A);CHKERRQ(ierr);
if (v) {
ierr = VecCreateNest(((PetscObject)fine)->comm,nDM,PETSC_NULL,vecs,v);CHKERRQ(ierr);
}
for (i=0; i<nDM*nDM; i++) {ierr = MatDestroy(&mats[i]);CHKERRQ(ierr);}
ierr = PetscFree(mats);CHKERRQ(ierr);
if (v) {
for (i=0; i<nDM; i++) {ierr = VecDestroy(&vecs[i]);CHKERRQ(ierr);}
ierr = PetscFree(vecs);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
Mat A;
KSP ksp;
DM shell;
Vec *left, *right;
MPI_Comm c;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL, NULL);if (ierr) return ierr;
c = PETSC_COMM_WORLD;
ierr = MatCreate(c, &A); CHKERRQ(ierr);
ierr = MatSetSizes(A, 1, 1, PETSC_DECIDE, PETSC_DECIDE); CHKERRQ(ierr);
ierr = MatSetFromOptions(A); CHKERRQ(ierr);
ierr = MatSetUp(A); CHKERRQ(ierr);
ierr = KSPCreate(c, &ksp); CHKERRQ(ierr);
ierr = KSPSetOperators(ksp, A, A); CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp); CHKERRQ(ierr);
ierr = DMShellCreate(c, &shell); CHKERRQ(ierr);
ierr = DMSetFromOptions(shell); CHKERRQ(ierr);
ierr = DMSetUp(shell); CHKERRQ(ierr);
ierr = KSPSetDM(ksp, shell); CHKERRQ(ierr);
ierr = KSPCreateVecs(ksp, 1, &right, 1, &left); CHKERRQ(ierr);
ierr = VecView(right[0], PETSC_VIEWER_STDOUT_(c));CHKERRQ(ierr);
ierr = VecDestroyVecs(1,&right); CHKERRQ(ierr);
ierr = VecDestroyVecs(1,&left); CHKERRQ(ierr);
ierr = DMDestroy(&shell); CHKERRQ(ierr);
ierr = KSPDestroy(&ksp); CHKERRQ(ierr);
ierr = MatDestroy(&A); CHKERRQ(ierr);
PetscFinalize();
return 0;
}
PetscErrorCode SingleBodyPoints::createDMDA()
{
PetscErrorCode ierr;
DMDALocalInfo lclInfo;
PetscFunctionBeginUser;
ierr = DMDACreate1d(comm, DM_BOUNDARY_NONE, nPts, dim, 0, nullptr, &da);
CHKERRQ(ierr);
ierr = DMSetUp(da); CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da, &lclInfo); CHKERRQ(ierr);
// copy necessary local info
bgPt = lclInfo.xs;
nLclPts = lclInfo.xm;
edPt = bgPt + nLclPts;
// gather local info from other processes
ierr = MPI_Allgather(&nLclPts, 1, MPIU_INT, nLclAllProcs.data(), 1,
MPIU_INT, comm); CHKERRQ(ierr);
// each point has "dim" degree of freedom, so we have to multiply that
for (auto &it : nLclAllProcs) it *= dim;
// calculate the offset of the unpacked DM
for (PetscMPIInt r = mpiSize - 1; r > 0; r--)
offsetsAllProcs[r] = nLclAllProcs[r - 1];
for (PetscMPIInt r = 1; r < mpiSize; r++)
offsetsAllProcs[r] += offsetsAllProcs[r - 1];
PetscFunctionReturn(0);
} // createDMDA
PetscErrorCode DMDACreate2d(MPI_Comm comm,DMDABoundaryType bx,DMDABoundaryType by,DMDAStencilType stencil_type,
PetscInt M,PetscInt N,PetscInt m,PetscInt n,PetscInt dof,PetscInt s,const PetscInt lx[],const PetscInt ly[],DM *da)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMDACreate(comm, da);
CHKERRQ(ierr);
ierr = DMDASetDim(*da, 2);
CHKERRQ(ierr);
ierr = DMDASetSizes(*da, M, N, 1);
CHKERRQ(ierr);
ierr = DMDASetNumProcs(*da, m, n, PETSC_DECIDE);
CHKERRQ(ierr);
ierr = DMDASetBoundaryType(*da, bx, by, DMDA_BOUNDARY_NONE);
CHKERRQ(ierr);
ierr = DMDASetDof(*da, dof);
CHKERRQ(ierr);
ierr = DMDASetStencilType(*da, stencil_type);
CHKERRQ(ierr);
ierr = DMDASetStencilWidth(*da, s);
CHKERRQ(ierr);
ierr = DMDASetOwnershipRanges(*da, lx, ly, NULL);
CHKERRQ(ierr);
/* This violates the behavior for other classes, but right now users expect negative dimensions to be handled this way */
ierr = DMSetFromOptions(*da);
CHKERRQ(ierr);
ierr = DMSetUp(*da);
CHKERRQ(ierr);
ierr = DMViewFromOptions(*da,"-dm_view");
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
DM dm;
Vec X,Y;
PetscErrorCode ierr;
PetscInt dof = 10;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-dof",&dof,NULL);CHKERRQ(ierr);
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-128,-128,-128,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,dof,1,NULL,NULL,NULL,&dm);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = PetscMemoryTrace("DMDACreate3d ");CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dm,&X);CHKERRQ(ierr);
ierr = PetscMemoryTrace("DMCreateGlobalVector");
ierr = DMCreateGlobalVector(dm,&Y);CHKERRQ(ierr);
ierr = PetscMemoryTrace("DMCreateGlobalVector");CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&Y);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
KSP ksp;
DM da;
UserContext user;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC, DM_BOUNDARY_MIRROR,DMDA_STENCIL_STAR,11,11,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = KSPSetDM(ksp,(DM)da);CHKERRQ(ierr);
ierr = DMSetApplicationContext(da,&user);CHKERRQ(ierr);
user.uu = 1.0;
user.tt = 1.0;
ierr = KSPSetComputeRHS(ksp,ComputeRHS,&user);CHKERRQ(ierr);
ierr = KSPSetComputeOperators(ksp,ComputeJacobian,&user);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPSolve(ksp,NULL,NULL);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc, char **argv)
{
DM dm;
char typeString[256] = {'\0'};
PetscViewer viewer = NULL;
PetscBool flg;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
ierr = DMCreate(PETSC_COMM_WORLD, &dm);CHKERRQ(ierr);
ierr = PetscStrncpy(typeString,DMFOREST,256);CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"DM Forest example options",NULL);CHKERRQ(ierr);
ierr = PetscOptionsString("-dm_type","The type of the dm",NULL,DMFOREST,typeString,sizeof(typeString),NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = DMSetType(dm,(DMType) typeString);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(PETSC_COMM_WORLD,NULL,"-dm_view",&viewer,NULL,&flg);CHKERRQ(ierr);
if (flg) {
ierr = DMView(dm,viewer);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/*@C
DMCompositeRestoreAccess - Returns the vectors obtained with DMCompositeGetAccess()
representation.
Collective on DMComposite
Input Parameters:
+ dm - the packer object
. gvec - the global vector
- Vec* ... - the individual parallel vectors, PETSC_NULL for those that are not needed
Level: advanced
.seealso DMCompositeAddDM(), DMCreateGlobalVector(),
DMCompositeGather(), DMCompositeCreate(), DMCompositeGetISLocalToGlobalMappings(), DMCompositeScatter(),
DMCompositeRestoreAccess(), DMCompositeGetAccess()
@*/
PetscErrorCode DMCompositeRestoreAccess(DM dm,Vec gvec,...)
{
va_list Argp;
PetscErrorCode ierr;
struct DMCompositeLink *next;
DM_Composite *com = (DM_Composite*)dm->data;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscValidHeaderSpecific(gvec,VEC_CLASSID,2);
next = com->next;
if (!com->setup) {
ierr = DMSetUp(dm);CHKERRQ(ierr);
}
/* loop over packed objects, handling one at at time */
va_start(Argp,gvec);
while (next) {
Vec *vec;
vec = va_arg(Argp, Vec*);
if (vec) {
ierr = VecResetArray(*vec);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(next->dm,vec);CHKERRQ(ierr);
}
next = next->next;
}
va_end(Argp);
PetscFunctionReturn(0);
}
int main(int argc,char *argv[])
{
Mat M;
Vec x,y;
PetscErrorCode ierr;
DM da,daf;
ierr = PetscInitialize(&argc,&argv,0,help);if (ierr) return ierr;
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,4,5,PETSC_DECIDE,PETSC_DECIDE,41,1,0,0,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMRefine(da,PETSC_COMM_WORLD,&daf);CHKERRQ(ierr);
ierr = DMCreateInterpolation(da,daf,&M,NULL);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(daf,&y);CHKERRQ(ierr);
ierr = MatMult(M,x,y);CHKERRQ(ierr);
ierr = MatMultTranspose(M,y,x);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = DMDestroy(&daf);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = MatDestroy(&M);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode DMCoarsen_Composite(DM dmi,MPI_Comm comm,DM *fine)
{
PetscErrorCode ierr;
struct DMCompositeLink *next;
DM_Composite *com = (DM_Composite*)dmi->data;
DM dm;
PetscFunctionBegin;
PetscValidHeaderSpecific(dmi,DM_CLASSID,1);
ierr = DMSetUp(dmi);CHKERRQ(ierr);
if (comm == MPI_COMM_NULL) {
ierr = PetscObjectGetComm((PetscObject)dmi,&comm);CHKERRQ(ierr);
}
next = com->next;
ierr = DMCompositeCreate(comm,fine);CHKERRQ(ierr);
/* loop over packed objects, handling one at at time */
while (next) {
ierr = DMCoarsen(next->dm,comm,&dm);CHKERRQ(ierr);
ierr = DMCompositeAddDM(*fine,dm);CHKERRQ(ierr);
ierr = PetscObjectDereference((PetscObject)dm);CHKERRQ(ierr);
next = next->next;
}
PetscFunctionReturn(0);
}
void PetscDMNonlinearSolver<T>::init()
{
PetscErrorCode ierr;
DM dm;
this->PetscNonlinearSolver<T>::init();
// Attaching a DM with the function and Jacobian callbacks to SNES.
ierr = DMCreateLibMesh(libMesh::COMM_WORLD, this->system(), &dm); CHKERRABORT(libMesh::COMM_WORLD, ierr);
ierr = DMSetFromOptions(dm); CHKERRABORT(libMesh::COMM_WORLD, ierr);
ierr = DMSetUp(dm); CHKERRABORT(libMesh::COMM_WORLD, ierr);
ierr = SNESSetDM(this->_snes, dm); CHKERRABORT(libMesh::COMM_WORLD, ierr);
// SNES now owns the reference to dm.
ierr = DMDestroy(&dm); CHKERRABORT(libMesh::COMM_WORLD, ierr);
KSP ksp;
ierr = SNESGetKSP (this->_snes, &ksp); CHKERRABORT(libMesh::COMM_WORLD,ierr);
// Set the tolerances for the iterative solver. Use the user-supplied
// tolerance for the relative residual & leave the others at default values
ierr = KSPSetTolerances (ksp, this->initial_linear_tolerance, PETSC_DEFAULT,PETSC_DEFAULT, this->max_linear_iterations); CHKERRABORT(libMesh::COMM_WORLD,ierr);
// Set the tolerances for the non-linear solver.
ierr = SNESSetTolerances(this->_snes,
this->absolute_residual_tolerance,
this->relative_residual_tolerance,
this->absolute_step_tolerance,
this->max_nonlinear_iterations,
this->max_function_evaluations);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
//Pull in command-line options
KSPSetFromOptions(ksp);
SNESSetFromOptions(this->_snes);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
KSP ksp;
DM da,shell;
PetscInt levels;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,129,1,1,0,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = MyDMShellCreate(PETSC_COMM_WORLD,da,&shell);CHKERRQ(ierr);
/* these two lines are not needed but allow PCMG to automatically know how many multigrid levels the user wants */
ierr = DMGetRefineLevel(da,&levels);CHKERRQ(ierr);
ierr = DMSetRefineLevel(shell,levels);CHKERRQ(ierr);
ierr = KSPSetDM(ksp,shell);CHKERRQ(ierr);
ierr = KSPSetComputeRHS(ksp,ComputeRHS,NULL);CHKERRQ(ierr);
ierr = KSPSetComputeOperators(ksp,ComputeMatrix,NULL);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPSolve(ksp,NULL,NULL);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = DMDestroy(&shell);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
void petscSetupDM (NonlinearSystem & nl) {
#if !PETSC_VERSION_LESS_THAN(3,3,0)
PetscErrorCode ierr;
// Initialize the part of the DM package that's packaged with Moose; in the PETSc source tree this call would be in DMInitializePackage()
ierr = DMMooseRegisterAll();
CHKERRABORT(nl.comm().get(),ierr);
// Create and set up the DM that will consume the split options and deal with block matrices.
PetscNonlinearSolver<Number> *petsc_solver = dynamic_cast<PetscNonlinearSolver<Number> *>(nl.sys().nonlinear_solver.get());
SNES snes = petsc_solver->snes();
/* FIXME: reset the DM, do not recreate it anew every time? */
DM dm = PETSC_NULL;
ierr = DMCreateMoose(nl.comm().get(), nl, &dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = DMSetFromOptions(dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = DMSetUp(dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = SNESSetDM(snes,dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = DMDestroy(&dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = SNESSetUpdate(snes,SNESUpdateDMMoose);
CHKERRABORT(nl.comm().get(),ierr);
#endif
}
PetscErrorCode DMSetUp_Patch(DM dm)
{
DM_Patch *mesh = (DM_Patch*) dm->data;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
ierr = DMSetUp(mesh->dmCoarse);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv) {
PetscErrorCode ierr;
SNES snes;
KSP ksp;
Vec u, uexact;
FishCtx user;
DMDALocalInfo info;
double errnorm;
PetscInitialize(&argc,&argv,NULL,help);
user.printevals = PETSC_FALSE;
ierr = PetscOptionsBegin(PETSC_COMM_WORLD, "f3_", "options for fish3", ""); CHKERRQ(ierr);
ierr = PetscOptionsBool("-printevals","residual and Jacobian routines report grid",
"fish3.c",user.printevals,&user.printevals,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd(); CHKERRQ(ierr);
ierr = DMDACreate3d(COMM,
DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,
DMDA_STENCIL_STAR,
3,3,3,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,
1,1,
NULL,NULL,NULL,&(user.da)); CHKERRQ(ierr);
ierr = DMSetFromOptions(user.da); CHKERRQ(ierr);
ierr = DMSetUp(user.da); CHKERRQ(ierr);
ierr = DMSetApplicationContext(user.da,&user);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(user.da,&info); CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user.da,&u);CHKERRQ(ierr);
ierr = VecDuplicate(u,&uexact);CHKERRQ(ierr);
ierr = VecDuplicate(u,&(user.b));CHKERRQ(ierr);
ierr = formExactRHS(&info,uexact,user.b,&user); CHKERRQ(ierr);
ierr = SNESCreate(COMM,&snes); CHKERRQ(ierr);
ierr = SNESSetDM(snes,user.da); CHKERRQ(ierr);
ierr = DMDASNESSetFunctionLocal(user.da,INSERT_VALUES,
(DMDASNESFunction)FormFunctionLocal,&user); CHKERRQ(ierr);
ierr = DMDASNESSetJacobianLocal(user.da,
(DMDASNESJacobian)FormJacobianLocal,&user); CHKERRQ(ierr);
ierr = SNESGetKSP(snes,&ksp); CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPCG); CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes); CHKERRQ(ierr);
ierr = VecSet(u,0.0); CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,u); CHKERRQ(ierr);
ierr = VecAXPY(u,-1.0,uexact); CHKERRQ(ierr); // u <- u + (-1.0) uexact
ierr = VecNorm(u,NORM_INFINITY,&errnorm); CHKERRQ(ierr);
ierr = PetscPrintf(COMM,"on %d x %d x %d grid: error |u-uexact|_inf = %g\n",
info.mx,info.my,info.mz,errnorm); CHKERRQ(ierr);
VecDestroy(&u); VecDestroy(&uexact); VecDestroy(&(user.b));
SNESDestroy(&snes); DMDestroy(&(user.da));
PetscFinalize();
return 0;
}
/*@C
DMADDACreate - Creates and ADDA object that translate between coordinates
in a geometric grid of arbitrary dimension and data in a PETSc vector
distributed on several processors.
Collective on MPI_Comm
Input Parameters:
+ comm - MPI communicator
. dim - the dimension of the grid
. nodes - array with d entries that give the number of nodes in each dimension
. procs - array with d entries that give the number of processors in each dimension
(or NULL if to be determined automatically)
. dof - number of degrees of freedom per node
- periodic - array with d entries that, i-th entry is set to true iff dimension i is periodic
Output Parameters:
. adda - pointer to ADDA data structure that is created
Level: intermediate
@*/
PetscErrorCode DMADDACreate(MPI_Comm comm, PetscInt dim, PetscInt *nodes,PetscInt *procs,PetscInt dof, PetscBool *periodic,DM *dm_p)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMCreate(comm,dm_p);CHKERRQ(ierr);
ierr = DMSetType(*dm_p,DMADDA);CHKERRQ(ierr);
ierr = DMADDASetParameters(*dm_p,dim,nodes,procs,dof,periodic);CHKERRQ(ierr);
ierr = DMSetUp(*dm_p);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMShellCreate - Creates a shell DM object, used to manage user-defined problem data
Collective on MPI_Comm
Input Parameter:
. comm - the processors that will share the global vector
Output Parameters:
. shell - the shell DM
Level: advanced
.seealso DMDestroy(), DMCreateGlobalVector(), DMCreateLocalVector()
@*/
PetscErrorCode DMShellCreate(MPI_Comm comm,DM *dm)
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidPointer(dm,2);
ierr = DMCreate(comm,dm);CHKERRQ(ierr);
ierr = DMSetType(*dm,DMSHELL);CHKERRQ(ierr);
ierr = DMSetUp(*dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
DMCompositeGetISLocalToGlobalMappings - gets an ISLocalToGlobalMapping for each DM in the DMComposite, maps to the composite global space
Collective on DM
Input Parameter:
. dm - the packer object
Output Parameters:
. ltogs - the individual mappings for each packed vector. Note that this includes
all the ghost points that individual ghosted DMDA's may have.
Level: advanced
Notes:
Each entry of ltogs should be destroyed with ISLocalToGlobalMappingDestroy(), the ltogs array should be freed with PetscFree().
.seealso DMDestroy(), DMCompositeAddDM(), DMCreateGlobalVector(),
DMCompositeGather(), DMCompositeCreate(), DMCompositeGetAccess(), DMCompositeScatter(),
DMCompositeGetLocalVectors(), DMCompositeRestoreLocalVectors(),DMCompositeGetEntries()
@*/
PetscErrorCode DMCompositeGetISLocalToGlobalMappings(DM dm,ISLocalToGlobalMapping **ltogs)
{
PetscErrorCode ierr;
PetscInt i,*idx,n,cnt;
struct DMCompositeLink *next;
PetscMPIInt rank;
DM_Composite *com = (DM_Composite*)dm->data;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = PetscMalloc((com->nDM)*sizeof(ISLocalToGlobalMapping),ltogs);CHKERRQ(ierr);
next = com->next;
ierr = MPI_Comm_rank(((PetscObject)dm)->comm,&rank);CHKERRQ(ierr);
/* loop over packed objects, handling one at at time */
cnt = 0;
while (next) {
ISLocalToGlobalMapping ltog;
PetscMPIInt size;
const PetscInt *suboff,*indices;
Vec global;
/* Get sub-DM global indices for each local dof */
ierr = DMGetLocalToGlobalMapping(next->dm,<og);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetSize(ltog,&n);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetIndices(ltog,&indices);CHKERRQ(ierr);
ierr = PetscMalloc(n*sizeof(PetscInt),&idx);CHKERRQ(ierr);
/* Get the offsets for the sub-DM global vector */
ierr = DMGetGlobalVector(next->dm,&global);CHKERRQ(ierr);
ierr = VecGetOwnershipRanges(global,&suboff);CHKERRQ(ierr);
ierr = MPI_Comm_size(((PetscObject)global)->comm,&size);CHKERRQ(ierr);
/* Shift the sub-DM definition of the global space to the composite global space */
for (i=0; i<n; i++) {
PetscInt subi = indices[i],lo = 0,hi = size,t;
/* Binary search to find which rank owns subi */
while (hi-lo > 1) {
t = lo + (hi-lo)/2;
if (suboff[t] > subi) hi = t;
else lo = t;
}
idx[i] = subi - suboff[lo] + next->grstarts[lo];
}
ierr = ISLocalToGlobalMappingRestoreIndices(ltog,&indices);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingCreate(((PetscObject)dm)->comm,n,idx,PETSC_OWN_POINTER,&(*ltogs)[cnt]);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(next->dm,&global);CHKERRQ(ierr);
next = next->next;
cnt++;
}
PetscFunctionReturn(0);
}
/*@C
DMRedundantCreate - Creates a DM object, used to manage data for dense globally coupled variables
Collective on MPI_Comm
Input Parameter:
+ comm - the processors that will share the global vector
. rank - rank to own the redundant values
- N - total number of degrees of freedom
Output Parameters:
. red - the redundant DM
Level: advanced
.seealso DMDestroy(), DMCreateGlobalVector(), DMCreateMatrix(), DMCompositeAddDM(), DMREDUNDANT, DMSetType(), DMRedundantSetSize(), DMRedundantGetSize()
@*/
PetscErrorCode DMRedundantCreate(MPI_Comm comm,PetscInt rank,PetscInt N,DM *dm)
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidPointer(dm,2);
ierr = DMCreate(comm,dm);CHKERRQ(ierr);
ierr = DMSetType(*dm,DMREDUNDANT);CHKERRQ(ierr);
ierr = DMRedundantSetSize(*dm,rank,N);CHKERRQ(ierr);
ierr = DMSetUp(*dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode
PETScExternalSolverCreate(MPI_Comm comm, TS * ts)
{
DM da;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create distributed array (DMDA) to manage parallel grid and vectors
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMDACreate2d(comm,
DM_BOUNDARY_NONE,
DM_BOUNDARY_NONE,
DMDA_STENCIL_STAR,
11,
11,
PETSC_DECIDE,
PETSC_DECIDE,
1,
1,
NULL,
NULL,
&da);
CHKERRQ(ierr);
ierr = DMSetFromOptions(da);
CHKERRQ(ierr);
ierr = DMSetUp(da);
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(comm, ts);
CHKERRQ(ierr);
ierr = TSSetProblemType(*ts, TS_NONLINEAR);
CHKERRQ(ierr);
ierr = TSSetType(*ts, TSBEULER);
CHKERRQ(ierr);
ierr = TSSetDM(*ts, da);
CHKERRQ(ierr);
ierr = DMDestroy(&da);
CHKERRQ(ierr);
ierr = TSSetIFunction(*ts, NULL, FormIFunction, nullptr);
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set Jacobian evaluation routine
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetIJacobian(*ts, NULL, NULL, FormIJacobian, NULL);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMDAGetReducedDMDA - Gets the DMDA with the same layout but with fewer or more fields
Collective on DMDA
Input Parameters:
+ da - the distributed array
- nfields - number of fields in new DMDA
Output Parameter:
. nda - the new DMDA
Level: intermediate
.keywords: distributed array, get, corners, nodes, local indices, coordinates
.seealso: DMDAGetGhostCorners(), DMSetCoordinates(), DMDASetUniformCoordinates(), DMGetCoordinates(), DMDAGetGhostedCoordinates()
@*/
PetscErrorCode DMDAGetReducedDMDA(DM da,PetscInt nfields,DM *nda)
{
PetscErrorCode ierr;
DM_DA *dd = (DM_DA*)da->data;
PetscInt s,m,n,p,M,N,P,dim,Mo,No,Po;
const PetscInt *lx,*ly,*lz;
DMBoundaryType bx,by,bz;
DMDAStencilType stencil_type;
PetscInt ox,oy,oz;
PetscInt cl,rl;
PetscFunctionBegin;
dim = da->dim;
M = dd->M;
N = dd->N;
P = dd->P;
m = dd->m;
n = dd->n;
p = dd->p;
s = dd->s;
bx = dd->bx;
by = dd->by;
bz = dd->bz;
stencil_type = dd->stencil_type;
ierr = DMDAGetOwnershipRanges(da,&lx,&ly,&lz);CHKERRQ(ierr);
if (dim == 1) {
ierr = DMDACreate1d(PetscObjectComm((PetscObject)da),bx,M,nfields,s,dd->lx,nda);CHKERRQ(ierr);
} else if (dim == 2) {
ierr = DMDACreate2d(PetscObjectComm((PetscObject)da),bx,by,stencil_type,M,N,m,n,nfields,s,lx,ly,nda);CHKERRQ(ierr);
} else if (dim == 3) {
ierr = DMDACreate3d(PetscObjectComm((PetscObject)da),bx,by,bz,stencil_type,M,N,P,m,n,p,nfields,s,lx,ly,lz,nda);CHKERRQ(ierr);
}
ierr = DMSetUp(*nda);CHKERRQ(ierr);
if (da->coordinates) {
ierr = PetscObjectReference((PetscObject)da->coordinates);CHKERRQ(ierr);
(*nda)->coordinates = da->coordinates;
}
/* allow for getting a reduced DA corresponding to a domain decomposition */
ierr = DMDAGetOffset(da,&ox,&oy,&oz,&Mo,&No,&Po);CHKERRQ(ierr);
ierr = DMDASetOffset(*nda,ox,oy,oz,Mo,No,Po);CHKERRQ(ierr);
/* allow for getting a reduced DA corresponding to a coarsened DA */
ierr = DMGetCoarsenLevel(da,&cl);CHKERRQ(ierr);
ierr = DMGetRefineLevel(da,&rl);CHKERRQ(ierr);
(*nda)->levelup = rl;
(*nda)->leveldown = cl;
PetscFunctionReturn(0);
}
/*@
DMPlexUninterpolate - Take in a mesh with all intermediate faces, edges, etc. and return a cell-vertex mesh
Collective on DM
Input Parameter:
. dm - The complete DMPlex object
Output Parameter:
. dmUnint - The DMPlex object with only cells and vertices
Level: intermediate
.keywords: mesh
.seealso: DMPlexInterpolate(), DMPlexCreateFromCellList()
@*/
PetscErrorCode DMPlexUninterpolate(DM dm, DM *dmUnint)
{
DM udm;
PetscInt dim, vStart, vEnd, cStart, cEnd, c, maxConeSize = 0, *cone;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
if (dim <= 1) {
ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr);
*dmUnint = dm;
PetscFunctionReturn(0);
}
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMCreate(PetscObjectComm((PetscObject) dm), &udm);CHKERRQ(ierr);
ierr = DMSetType(udm, DMPLEX);CHKERRQ(ierr);
ierr = DMPlexSetDimension(udm, dim);CHKERRQ(ierr);
ierr = DMPlexSetChart(udm, cStart, vEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL, closureSize, cl, coneSize = 0;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
const PetscInt p = closure[cl];
if ((p >= vStart) && (p < vEnd)) ++coneSize;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexSetConeSize(udm, c, coneSize);CHKERRQ(ierr);
maxConeSize = PetscMax(maxConeSize, coneSize);
}
ierr = DMSetUp(udm);CHKERRQ(ierr);
ierr = PetscMalloc1(maxConeSize, &cone);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL, closureSize, cl, coneSize = 0;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
const PetscInt p = closure[cl];
if ((p >= vStart) && (p < vEnd)) cone[coneSize++] = p;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexSetCone(udm, c, cone);CHKERRQ(ierr);
}
ierr = PetscFree(cone);CHKERRQ(ierr);
ierr = DMPlexSymmetrize(udm);CHKERRQ(ierr);
ierr = DMPlexStratify(udm);CHKERRQ(ierr);
*dmUnint = udm;
PetscFunctionReturn(0);
}
/*
This takes as input the raw Hasse Diagram data
*/
PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
{
Vec coordinates;
PetscSection coordSection;
PetscScalar *coords;
PetscInt coordSize, firstVertex = numPoints[depth], pStart = 0, pEnd = 0, p, v, dim, d, off;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr);
}
ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr);
ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr);
}
ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
ierr = DMPlexStratify(dm);CHKERRQ(ierr);
/* Build coordinates */
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr);
for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) {
ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (v = 0; v < numPoints[0]; ++v) {
PetscInt off;
ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) {
coords[off+d] = vertexCoords[v*dim+d];
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMCreateLocalVector_Composite(DM dm,Vec *lvec)
{
PetscErrorCode ierr;
DM_Composite *com = (DM_Composite*)dm->data;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
if (!com->setup) {
ierr = DMSetUp(dm);CHKERRQ(ierr);
}
ierr = VecCreateSeq(((PetscObject)dm)->comm,com->nghost,lvec);CHKERRQ(ierr);
ierr = VecSetDM(*lvec, dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMLibMeshCreateDomainDecompositionDM(DM dm, PetscInt dnumber, PetscInt* dsizes, char*** dblocklists, DM* ddm)
{
PetscErrorCode ierr;
PetscBool islibmesh;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
ierr = PetscObjectTypeCompare((PetscObject)dm, DMLIBMESH,&islibmesh);
if(!islibmesh) SETERRQ2(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Got DM oftype %s, not of type %s", ((PetscObject)dm)->type_name, DMLIBMESH);
if(dnumber < 0) SETERRQ1(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Negative number %D of decomposition parts", dnumber);
PetscValidPointer(ddm,5);
DM_libMesh *dlm = (DM_libMesh *)(dm->data);
ierr = DMCreate(((PetscObject)dm)->comm, ddm); CHKERRQ(ierr);
ierr = DMSetType(*ddm, DMLIBMESH); CHKERRQ(ierr);
DM_libMesh *ddlm = (DM_libMesh *)((*ddm)->data);
ddlm->sys = dlm->sys;
ddlm->varids = dlm->varids;
ddlm->varnames = dlm->varnames;
ddlm->blockids = dlm->blockids;
ddlm->blocknames = dlm->blocknames;
ddlm->decomposition = new(std::vector<std::set<unsigned int> >);
ddlm->decomposition_type = DMLIBMESH_DOMAIN_DECOMPOSITION;
if(dnumber) {
for(PetscInt d = 0; d < dnumber; ++d) {
if(dsizes[d] < 0) SETERRQ2(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Negative size %D of decomposition part %D", dsizes[d],d);
ddlm->decomposition->push_back(std::set<unsigned int>());
for(PetscInt b = 0; b < dsizes[d]; ++b) {
std::string bname(dblocklists[d][b]);
std::map<std::string, unsigned int>::const_iterator bit = dlm->blockids->find(bname);
if(bit == dlm->blockids->end())
SETERRQ3(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Block %D on the %D-th list with name %s is not owned by this DM", b, d, dblocklists[d][b]);
unsigned int bid = bit->second;
(*ddlm->decomposition)[d].insert(bid);
}
}
}
else { /* Empty splits indicate default: split all blocks with one per split. */
PetscInt d = 0;
for(std::map<std::string, unsigned int>::const_iterator bit = ddlm->blockids->begin(); bit != ddlm->blockids->end(); ++bit) {
ddlm->decomposition->push_back(std::set<unsigned int>());
unsigned int bid = bit->second;
std::string bname = bit->first;
(*ddlm->decomposition)[d].insert(bid);
++d;
}
}
ierr = DMLibMeshSetUpName_Private(*ddm); CHKERRQ(ierr);
ierr = DMSetFromOptions(*ddm); CHKERRQ(ierr);
ierr = DMSetUp(*ddm); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMCreateFieldDecomposition_DA(DM dm, PetscInt *len,char ***namelist, IS **islist, DM** dmlist)
{
PetscInt i;
PetscErrorCode ierr;
DM_DA *dd = (DM_DA*)dm->data;
PetscInt dof = dd->w;
PetscFunctionBegin;
if(len) *len = dof;
if (islist) {
Vec v;
PetscInt rstart,n;
ierr = DMGetGlobalVector(dm,&v);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(v,&rstart,PETSC_NULL);CHKERRQ(ierr);
ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dm,&v);CHKERRQ(ierr);
ierr = PetscMalloc(dof*sizeof(IS),islist);CHKERRQ(ierr);
for (i=0; i<dof; i++) {
ierr = ISCreateStride(((PetscObject)dm)->comm,n/dof,rstart+i,dof,&(*islist)[i]);CHKERRQ(ierr);
}
}
if (namelist) {
ierr = PetscMalloc(dof*sizeof(const char *), namelist);CHKERRQ(ierr);
if (dd->fieldname) {
for (i=0; i<dof; i++) {
ierr = PetscStrallocpy(dd->fieldname[i],&(*namelist)[i]);CHKERRQ(ierr);
}
} else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Currently DMDA must have fieldnames");
}
if (dmlist) {
DM da;
ierr = DMDACreate(((PetscObject)dm)->comm, &da);CHKERRQ(ierr);
ierr = DMDASetDim(da, dd->dim);CHKERRQ(ierr);
ierr = DMDASetSizes(da, dd->M, dd->N, dd->P);CHKERRQ(ierr);
ierr = DMDASetNumProcs(da, dd->m, dd->n, dd->p);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, dd->bx, dd->by, dd->bz);CHKERRQ(ierr);
ierr = DMDASetDof(da, 1);CHKERRQ(ierr);
ierr = DMDASetStencilType(da, dd->stencil_type);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, dd->s);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = PetscMalloc(dof*sizeof(DM),dmlist);CHKERRQ(ierr);
for (i=0; i<dof-1; i++) {ierr = PetscObjectReference((PetscObject)da);CHKERRQ(ierr);}
for (i=0; i<dof; i++) (*dmlist)[i] = da;
}
PetscFunctionReturn(0);
}
static PetscErrorCode CreatePoints_Grid(DM dm, PetscInt *Np, PetscReal **pcoords, PetscBool *pointsAllProcs, AppCtx *ctx)
{
DM da;
DMDALocalInfo info;
PetscInt N = 3, n = 0, spaceDim, i, j, k, *ind, d;
PetscReal *h;
PetscMPIInt rank;
PetscErrorCode ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr);
ierr = DMGetCoordinateDim(dm, &spaceDim);CHKERRQ(ierr);
ierr = PetscCalloc1(spaceDim,&ind);CHKERRQ(ierr);
ierr = PetscCalloc1(spaceDim,&h);CHKERRQ(ierr);
h[0] = 1.0/(N-1); h[1] = 1.0/(N-1); h[2] = 1.0/(N-1);
ierr = DMDACreate(PetscObjectComm((PetscObject) dm), &da);CHKERRQ(ierr);
ierr = DMSetDimension(da, ctx->dim);CHKERRQ(ierr);
ierr = DMDASetSizes(da, N, N, N);CHKERRQ(ierr);
ierr = DMDASetDof(da, 1);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, 1);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da, &info);CHKERRQ(ierr);
*Np = info.xm * info.ym * info.zm;
ierr = PetscCalloc1(*Np * spaceDim, pcoords);CHKERRQ(ierr);
for (k = info.zs; k < info.zs + info.zm; ++k) {
ind[2] = k;
for (j = info.ys; j < info.ys + info.ym; ++j) {
ind[1] = j;
for (i = info.xs; i < info.xs + info.xm; ++i, ++n) {
ind[0] = i;
for (d = 0; d < spaceDim; ++d) (*pcoords)[n*spaceDim+d] = ind[d]*h[d];
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, "[%d]Point %D (", rank, n);CHKERRQ(ierr);
for (d = 0; d < spaceDim; ++d) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, "%g", (double)(*pcoords)[n*spaceDim+d]);CHKERRQ(ierr);
if (d < spaceDim-1) {ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, ", ");CHKERRQ(ierr);}
}
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, ")\n");CHKERRQ(ierr);
}
}
}
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD, NULL);CHKERRQ(ierr);
ierr = PetscFree(ind);CHKERRQ(ierr);
ierr = PetscFree(h);CHKERRQ(ierr);
*pointsAllProcs = PETSC_FALSE;
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscMPIInt rank;
PetscInt M = 10,N = 8,m = PETSC_DECIDE,n = PETSC_DECIDE;
PetscErrorCode ierr;
DM da;
PetscViewer viewer;
Vec local,global;
PetscScalar value;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",300,0,300,300,&viewer);CHKERRQ(ierr);
/* Read options */
ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-m",&m,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,m,n,1,1,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
value = -3.0;
ierr = VecSet(global,value);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
value = rank+1;
ierr = VecScale(local,value);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,local,ADD_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,local,ADD_VALUES,global);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMView(da,viewer);CHKERRQ(ierr);
/* Free memory */
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
PetscInt M = 5,N = 4,P = 3, m = PETSC_DECIDE,n = PETSC_DECIDE,p = PETSC_DECIDE,dim = 1;
PetscErrorCode ierr;
DM dac,daf;
DMBoundaryType bx = DM_BOUNDARY_NONE,by=DM_BOUNDARY_NONE,bz=DM_BOUNDARY_NONE;
DMDAStencilType stype = DMDA_STENCIL_BOX;
Mat A;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-P",&P,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-m",&m,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-p",&p,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-dim",&dim,NULL);CHKERRQ(ierr);
/* Create distributed array and get vectors */
if (dim == 1) {
ierr = DMDACreate1d(PETSC_COMM_WORLD,bx,M,1,1,NULL,&dac);CHKERRQ(ierr);
} else if (dim == 2) {
ierr = DMDACreate2d(PETSC_COMM_WORLD,bx,by,stype,M,N,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&dac);CHKERRQ(ierr);
} else if (dim == 3) {
ierr = DMDACreate3d(PETSC_COMM_WORLD,bx,by,bz,stype,M,N,P,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,NULL,&dac);CHKERRQ(ierr);
} else SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"dim must be 1,2, or 3");
ierr = DMSetFromOptions(dac);CHKERRQ(ierr);
ierr = DMSetUp(dac);CHKERRQ(ierr);
ierr = DMRefine(dac,PETSC_COMM_WORLD,&daf);CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(dac,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
if (dim == 1) {
ierr = SetCoordinates1d(daf);CHKERRQ(ierr);
} else if (dim == 2) {
ierr = SetCoordinates2d(daf);CHKERRQ(ierr);
} else if (dim == 3) {
ierr = SetCoordinates3d(daf);CHKERRQ(ierr);
}
ierr = DMCreateInterpolation(dac,daf,&A,0);CHKERRQ(ierr);
/* Free memory */
ierr = DMDestroy(&dac);CHKERRQ(ierr);
ierr = DMDestroy(&daf);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode DMGlobalToLocalBegin_Composite(DM dm,Vec gvec,InsertMode mode,Vec lvec)
{
PetscErrorCode ierr;
struct DMCompositeLink *next;
PetscInt cnt = 3;
PetscMPIInt rank;
PetscScalar *garray,*larray;
DM_Composite *com = (DM_Composite*)dm->data;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscValidHeaderSpecific(gvec,VEC_CLASSID,2);
next = com->next;
if (!com->setup) {
ierr = DMSetUp(dm);CHKERRQ(ierr);
}
ierr = MPI_Comm_rank(((PetscObject)dm)->comm,&rank);CHKERRQ(ierr);
ierr = VecGetArray(gvec,&garray);CHKERRQ(ierr);
ierr = VecGetArray(lvec,&larray);CHKERRQ(ierr);
/* loop over packed objects, handling one at at time */
while (next) {
Vec local,global;
PetscInt N;
ierr = DMGetGlobalVector(next->dm,&global);CHKERRQ(ierr);
ierr = VecGetLocalSize(global,&N);CHKERRQ(ierr);
ierr = VecPlaceArray(global,garray);CHKERRQ(ierr);
ierr = DMGetLocalVector(next->dm,&local);CHKERRQ(ierr);
ierr = VecPlaceArray(local,larray);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(next->dm,global,mode,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(next->dm,global,mode,local);CHKERRQ(ierr);
ierr = VecResetArray(global);CHKERRQ(ierr);
ierr = VecResetArray(local);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(next->dm,&global);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(next->dm,&local);CHKERRQ(ierr);
cnt++;
larray += next->nlocal;
next = next->next;
}
ierr = VecRestoreArray(gvec,PETSC_NULL);CHKERRQ(ierr);
ierr = VecRestoreArray(lvec,PETSC_NULL);CHKERRQ(ierr);
PetscFunctionReturn(0);
}