PetscErrorCode NavierStokesSolver::createVecs()
{
PetscErrorCode ierr;
ierr = DMCreateLocalVector(uda, &qxLocal); CHKERRQ(ierr);
ierr = DMCreateLocalVector(vda, &qyLocal); CHKERRQ(ierr);
//global vectors
ierr = DMCreateGlobalVector(qPack, &q); CHKERRQ(ierr); //velocity fluxes
ierr = VecDuplicate(q, &qStar); CHKERRQ(ierr); //intermediate velocity
ierr = VecDuplicate(q, &H); CHKERRQ(ierr); //convective term
ierr = VecDuplicate(q, &rn); CHKERRQ(ierr); //explicit term
ierr = VecDuplicate(q, &bc1); CHKERRQ(ierr); //B.C. from implicit terms
ierr = VecDuplicate(q, &rhs1); CHKERRQ(ierr); //rhs for intermediate solver
ierr = VecDuplicate(q, &MHat); CHKERRQ(ierr); // dialogal matrix
ierr = VecDuplicate(q, &RInv); CHKERRQ(ierr); // translation form velocity to flux
ierr = VecDuplicate(q, &BN); CHKERRQ(ierr); //approxiamte inverse of A
ierr = VecDuplicate(q, &temp); CHKERRQ(ierr); // ?
ierr = DMCreateGlobalVector(lambdaPack, &lambda); CHKERRQ(ierr); //pressure
ierr = VecDuplicate(lambda, &bc2); CHKERRQ(ierr);
ierr = VecDuplicate(lambda, &rhs2); CHKERRQ(ierr);
return 0;
}
/*@C
DMGetNamedLocalVector - get access to a named, persistent local vector
Not Collective
Input Arguments:
+ dm - DM to hold named vectors
- name - unique name for Vec
Output Arguments:
. X - named Vec
Level: developer
Note: If a Vec with the given name does not exist, it is created.
.seealso: DMGetNamedGlobalVector(),DMRestoreNamedLocalVector()
@*/
PetscErrorCode DMGetNamedLocalVector(DM dm,const char *name,Vec *X)
{
PetscErrorCode ierr;
DMNamedVecLink link;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscValidCharPointer(name,2);
PetscValidPointer(X,3);
for (link=dm->namedlocal; link; link=link->next) {
PetscBool match;
ierr = PetscStrcmp(name,link->name,&match);CHKERRQ(ierr);
if (match) {
if (link->status != DMVEC_STATUS_IN) SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_WRONGSTATE,"Vec name '%s' already checked out",name);
goto found;
}
}
/* Create the Vec */
ierr = PetscNew(&link);CHKERRQ(ierr);
ierr = PetscStrallocpy(name,&link->name);CHKERRQ(ierr);
ierr = DMCreateLocalVector(dm,&link->X);CHKERRQ(ierr);
link->next = dm->namedlocal;
dm->namedlocal = link;
found:
*X = link->X;
link->status = DMVEC_STATUS_OUT;
PetscFunctionReturn(0);
}
/*@
DMGetLocalVector - Gets a Seq PETSc vector that
may be used with the DMXXX routines. This vector has spaces for the ghost values.
Not Collective
Input Parameter:
. dm - the distributed array
Output Parameter:
. g - the local vector
Level: beginner
Note:
The vector values are NOT initialized and may have garbage in them, so you may need
to zero them.
The output parameter, g, is a regular PETSc vector that should be returned with
DMRestoreLocalVector() DO NOT call VecDestroy() on it.
VecStride*() operations can be useful when using DM with dof > 1
.keywords: distributed array, create, local, vector
.seealso: DMCreateGlobalVector(), VecDuplicate(), VecDuplicateVecs(),
DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMGlobalToLocalBegin(),
DMGlobalToLocalEnd(), DMLocalToGlobalBegin(), DMCreateLocalVector(), DMRestoreLocalVector(),
VecStrideMax(), VecStrideMin(), VecStrideNorm()
@*/
PetscErrorCode DMGetLocalVector(DM dm,Vec *g)
{
PetscErrorCode ierr,i;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscValidPointer(g,2);
for (i=0; i<DM_MAX_WORK_VECTORS; i++) {
if (dm->localin[i]) {
*g = dm->localin[i];
dm->localin[i] = NULL;
goto alldone;
}
}
ierr = DMCreateLocalVector(dm,g);CHKERRQ(ierr);
alldone:
for (i=0; i<DM_MAX_WORK_VECTORS; i++) {
if (!dm->localout[i]) {
dm->localout[i] = *g;
break;
}
}
PetscFunctionReturn(0);
}
EXTERN_C_END
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "MatDAADSetDA_AD"
PetscErrorCode MatDAADSetDA_AD(Mat A,DM da)
{
Mat_DAAD *a = (Mat_DAAD*)A->data;
PetscErrorCode ierr;
PetscInt nc,nx,ny,nz,Nx,Ny,Nz;
PetscFunctionBegin;
ierr = PetscObjectReference((PetscObject)da);
CHKERRQ(ierr);
if (a->da) {
ierr = DMDestroy(a->da);
CHKERRQ(ierr);
}
a->da = da;
ierr = DMDAGetInfo(da,0,&Nx,&Ny,&Nz,0,0,0,&nc,0,0,0);
CHKERRQ(ierr);
ierr = DMDAGetCorners(da,0,0,0,&nx,&ny,&nz);
CHKERRQ(ierr);
A->rmap->n = A->cmap->n = nc*nx*ny*nz;
A->rmap->N = A->cmap->N = nc*Nx*Ny*Nz;
ierr = DMCreateLocalVector(da,&a->localu);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode NavierStokesSolver :: createLocalToGlobalMappingsLambda()
{
PetscErrorCode ierr;
PetscInt m,n,i,j,mstart,nstart;
PetscReal **lp;
PetscInt localIdx;
ierr = VecGetOwnershipRange(lambda, &localIdx, NULL); CHKERRQ(ierr);
//populate local vector with global indices
//values outside the domain are never accessed and not set
//P
ierr = DMCreateLocalVector(pda, &pMapping); CHKERRQ(ierr);
ierr = DMDAVecGetArray(pda, pMapping, &lp); CHKERRQ(ierr);
ierr = DMDAGetCorners(pda, &mstart, &nstart, NULL, &m, &n, NULL); CHKERRQ(ierr);
for(j=nstart; j<nstart+n; j++)
{
for(i=mstart; i < mstart+m; i++)
{
lp[j][i] = localIdx;
localIdx++;
}
}
ierr = DMDAVecRestoreArray(pda, pMapping, &lp); CHKERRQ(ierr);
ierr = DMDALocalToLocalBegin(pda, pMapping, INSERT_VALUES, pMapping); CHKERRQ(ierr);
ierr = DMDALocalToLocalEnd(pda, pMapping, INSERT_VALUES, pMapping); CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
PetscInt dof = 2,M = 3,N = 3,m = PETSC_DECIDE,n = PETSC_DECIDE;
PetscErrorCode ierr;
DM da;
Vec global,local;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(0,"-dof",&dof,0);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,
M,N,m,n,dof,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = doit(da,global);CHKERRQ(ierr);
ierr = VecView(global,0);CHKERRQ(ierr);
/* Free memory */
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
static PetscErrorCode CreateLocalVector(DM shell,Vec *x)
{
PetscErrorCode ierr;
DM da;
ierr = DMShellGetContext(shell,(void**)&da);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,x);CHKERRQ(ierr);
ierr = VecSetDM(*x,shell);CHKERRQ(ierr);
return 0;
}
PetscErrorCode DMCreateLocalVector_Patch(DM dm, Vec *l)
{
DM_Patch *mesh = (DM_Patch*) dm->data;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
ierr = DMCreateLocalVector(mesh->dmCoarse, l);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetupMaterial(DM dm, DM dmAux, AppCtx *user)
{
void (*matFuncs[1])(const PetscReal x[], PetscScalar *u, void *ctx) = {nu_2d};
Vec nu;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMCreateLocalVector(dmAux, &nu);CHKERRQ(ierr);
ierr = DMPlexProjectFunctionLocal(dmAux, matFuncs, NULL, INSERT_ALL_VALUES, nu);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject) dm, "A", (PetscObject) nu);CHKERRQ(ierr);
ierr = VecDestroy(&nu);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscMPIInt rank;
PetscInt m = PETSC_DECIDE,n = PETSC_DECIDE,p = PETSC_DECIDE,M = 3,N = 5,P=3,s=1;
PetscInt *lx = NULL,*ly = NULL,*lz = NULL;
PetscErrorCode ierr;
PetscBool flg = PETSC_FALSE;
DM da;
Vec local,global,vslice;
PetscScalar value;
DMDABoundaryType wrap = DMDA_XYPERIODIC;
DMDAStencilType stencil_type = DMDA_STENCIL_BOX;
VecScatter scatter;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/* Read options */
ierr = PetscOptionsGetInt(NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-P",&P,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-p",&p,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-s",&s,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-star",&flg,NULL);CHKERRQ(ierr);
if (flg) stencil_type = DMDA_STENCIL_STAR;
/* Create distributed array and get vectors */
ierr = DMDACreate3d(PETSC_COMM_WORLD,wrap,stencil_type,M,N,P,m,n,p,1,s,
lx,ly,lz,&da);CHKERRQ(ierr);
ierr = DMView(da,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = GenerateSliceScatter(da,&scatter,&vslice);CHKERRQ(ierr);
/* Put the value rank+1 into all locations of vslice and transfer back to global vector */
value = 1.0 + rank;
ierr = VecSet(vslice,value);CHKERRQ(ierr);
ierr = VecScatterBegin(scatter,vslice,global,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterEnd(scatter,vslice,global,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 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)
{
PetscErrorCode ierr;
PetscInt M = -2, N = -3, P = 4,stencil_width = 1, dof = 1,m,n,p,xstart,ystart,zstart,i,j,k,c;
DM da;
Vec global,local;
PetscScalar ****vglobal;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
PetscFunctionBeginUser;
ierr = PetscOptionsGetInt(0,"-stencil_width",&stencil_width,0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(0,"-dof",&dof,0);CHKERRQ(ierr);
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_MIRROR,DM_BOUNDARY_MIRROR,DM_BOUNDARY_MIRROR,DMDA_STENCIL_STAR,M,N,P,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,dof,stencil_width,NULL,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xstart,&ystart,&zstart,&m,&n,&p);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,global,&vglobal);CHKERRQ(ierr);
for (k=zstart; k<zstart+p; k++) {
for (j=ystart; j<ystart+n; j++) {
for (i=xstart; i<xstart+m; i++) {
for (c=0; c<dof; c++) {
vglobal[k][j][i][c] = 1000*k + 100*j + 10*(i+1) + c;
}
}
}
}
ierr = DMDAVecRestoreArrayDOF(da,global,&vglobal);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = PetscSequentialPhaseBegin(PETSC_COMM_WORLD,1);CHKERRQ(ierr);
ierr = VecView(local,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = PetscSequentialPhaseEnd(PETSC_COMM_WORLD,1);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
static PetscErrorCode CreateAuxiliaryData(DM dm, DM *auxdm, Vec *la, AppCtx *user)
{
PetscErrorCode (**afuncs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *);
PetscInt dim, Nf, f;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr);
ierr = PetscMalloc1(Nf, &afuncs);CHKERRQ(ierr);
for (f = 0; f < Nf; ++f) afuncs[f] = linear;
ierr = DMClone(dm, auxdm);CHKERRQ(ierr);
ierr = SetupDiscretization(*auxdm, dim, user->cellSimplex, user);CHKERRQ(ierr);
ierr = DMCreateLocalVector(*auxdm, la);CHKERRQ(ierr);
ierr = DMProjectFunctionLocal(dm, 0.0, afuncs, NULL, INSERT_VALUES, *la);CHKERRQ(ierr);
ierr = VecViewFromOptions(*la, NULL, "-local_aux_view");CHKERRQ(ierr);
ierr = PetscFree(afuncs);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt M = 6,stencil_width = 1, dof = 1,m,xstart,i,j;
DM da;
Vec global,local;
PetscScalar **vglobal;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
PetscFunctionBeginUser;
ierr = PetscOptionsGetInt(0,"-stencil_width",&stencil_width,0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(0,"-dof",&dof,0);CHKERRQ(ierr);
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_MIRROR,M,dof,stencil_width,NULL,&da);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xstart,0,0,&m,0,0);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,global,&vglobal);CHKERRQ(ierr);
for (i=xstart; i<xstart+m; i++) {
for (j=0; j<dof; j++) {
vglobal[i][j] = 100*(i+1) + j;
}
}
ierr = DMDAVecRestoreArrayDOF(da,global,&vglobal);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = PetscSequentialPhaseBegin(PETSC_COMM_WORLD,1);CHKERRQ(ierr);
ierr = VecView(local,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = PetscSequentialPhaseEnd(PETSC_COMM_WORLD,1);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
static PetscErrorCode TestFields(DM dmstag)
{
PetscErrorCode ierr;
Vec vecLocal,vecGlobal;
PetscReal norm2;
PetscFunctionBeginUser;
ierr = DMCreateLocalVector(dmstag,&vecLocal);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dmstag,&vecGlobal);CHKERRQ(ierr);
ierr = VecSet(vecLocal,1.0);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dmstag,vecLocal,INSERT_VALUES,vecGlobal);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd (dmstag,vecLocal,INSERT_VALUES,vecGlobal);CHKERRQ(ierr);
ierr = VecSet(vecGlobal,2.0);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmstag,vecGlobal,INSERT_VALUES,vecLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd (dmstag,vecGlobal,INSERT_VALUES,vecLocal);CHKERRQ(ierr);
ierr = VecNorm(vecGlobal,NORM_2,&norm2);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"2 Norm of test vector: %g\n",(double)norm2);CHKERRQ(ierr);
ierr = VecDestroy(&vecLocal);CHKERRQ(ierr);
ierr = VecDestroy(&vecGlobal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscInt N = 3,M=2,P=4,dof=1,rstart,rend,i;
PetscInt stencil_width = 2;
PetscErrorCode ierr;
PetscMPIInt rank;
DMDABoundaryType bx = DMDA_BOUNDARY_NONE,by = DMDA_BOUNDARY_NONE,bz = DMDA_BOUNDARY_NONE;
DMDAStencilType stencil_type = DMDA_STENCIL_STAR;
DM da;
Vec global,local;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-P",&P,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-dof",&dof,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-stencil_width",&stencil_width,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-stencil_type",(PetscInt*)&stencil_type,NULL);CHKERRQ(ierr);
ierr = DMDACreate3d(PETSC_COMM_WORLD,bx,by,bz,stencil_type,M,N,P,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,dof,stencil_width,0,0,0,&da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(global,&rstart,&rend);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {ierr = VecSetValue(global,i,(PetscReal)(i + 100*rank),INSERT_VALUES);CHKERRQ(ierr);}
ierr = VecAssemblyBegin(global);CHKERRQ(ierr);
ierr = VecAssemblyEnd(global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = VecSet(local,-1);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
if (!rank) {ierr = VecView(local,0);CHKERRQ(ierr);}
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscInt M = 6,N = 5,P = 4, m = PETSC_DECIDE,n = PETSC_DECIDE,p = PETSC_DECIDE,i,j,k,is,js,ks,in,jen,kn;
PetscErrorCode ierr;
DM da;
Vec local,global;
PetscScalar ****l;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
/* Create distributed array and get vectors */
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,P,m,n,p,2,1,NULL,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);
ierr = DMDAGetCorners(da,&is,&js,&ks,&in,&jen,&kn);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,local,&l);CHKERRQ(ierr);
for (i=is; i<is+in; i++) {
for (j=js; j<js+jen; j++) {
for (k=ks; k<ks+kn; k++) {
l[k][j][i][0] = 2*(i + j*M + k*M*N);
l[k][j][i][1] = 2*(i + j*M + k*M*N) + 1;
}
}
}
ierr = DMDAVecRestoreArrayDOF(da,local,&l);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);
/* Free memory */
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
// Initialize the probe.
PetscErrorCode ProbePoint::init(const MPI_Comm &comm,
const YAML::Node &node,
const type::Mesh &mesh)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = ProbeBase::init(comm, node, mesh); CHKERRQ(ierr);
// only ASCII output format is supported
viewerType = PETSCVIEWERASCII;
// get location of the point to interpolate
loc = type::RealVec1D(3, 0.0);
for (PetscInt d = 0; d < mesh->dim; ++d)
loc[d] = node["loc"][d].as<PetscReal>();
// is the target point in on the current process sub-domain?
pointOnLocalProc = mesh->isPointOnLocalProc(loc, field);
// create a PETSc Viewer to output the data
// Note: as the target point belongs to only one sub-domain,
// we create a Viewer that involves only one process
ierr = PetscViewerCreate(PETSC_COMM_SELF, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, viewerType); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, path.c_str()); CHKERRQ(ierr);
if (pointOnLocalProc)
{
// create the interpolation object (2D: bi-linear, 3D: tri-linear)
ierr = createLinInterp(PETSC_COMM_SELF,
loc, mesh, field, interp); CHKERRQ(ierr);
}
// create a local vector that will have ghost-point values
ierr = DMCreateLocalVector(mesh->da[field], &svec); CHKERRQ(ierr);
PetscFunctionReturn(0);
} // ProbePoint::init
int main(int argc,char **argv)
{
PetscInt M = 6,N = 5,m = PETSC_DECIDE,n = PETSC_DECIDE,i,j,is,js,in,jen;
PetscErrorCode ierr;
DM da;
Vec local,global;
PetscScalar ***l;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,m,n,3,1,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&is,&js,0,&in,&jen,0);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,local,&l);CHKERRQ(ierr);
for (i=is; i<is+in; i++) {
for (j=js; j<js+jen; j++) {
l[j][i][0] = 3*(i + j*M);
l[j][i][1] = 3*(i + j*M) + 1;
l[j][i][2] = 3*(i + j*M) + 2;
}
}
ierr = DMDAVecRestoreArrayDOF(da,local,&l);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);
/* Free memory */
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscMPIInt rank,size;
PetscInt M = 14,time_steps = 20,w=1,s=1,localsize,j,i,mybase,myend,globalsize;
PetscErrorCode ierr;
DM da;
Vec global,local;
PetscScalar *globalptr,*localptr;
PetscReal h,k;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-time",&time_steps,NULL);CHKERRQ(ierr);
/* Set up the array */
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,M,w,s,NULL,&da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
/* Make copy of local array for doing updates */
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
/* determine starting point of each processor */
ierr = VecGetOwnershipRange(global,&mybase,&myend);CHKERRQ(ierr);
/* Initialize the Array */
ierr = VecGetLocalSize (global,&globalsize);CHKERRQ(ierr);
ierr = VecGetArray (global,&globalptr);CHKERRQ(ierr);
for (i=0; i<globalsize; i++) {
j = i + mybase;
globalptr[i] = PetscSinReal((PETSC_PI*j*6)/((PetscReal)M) + 1.2 * PetscSinReal((PETSC_PI*j*2)/((PetscReal)M))) * 4+4;
}
ierr = VecRestoreArray(global,&localptr);CHKERRQ(ierr);
/* Assign Parameters */
h= 1.0/M;
k= h*h/2.2;
ierr = VecGetLocalSize(local,&localsize);CHKERRQ(ierr);
for (j=0; j<time_steps; j++) {
/* Global to Local */
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
/*Extract local array */
ierr = VecGetArray(local,&localptr);CHKERRQ(ierr);
ierr = VecGetArray (global,&globalptr);CHKERRQ(ierr);
/* Update Locally - Make array of new values */
/* Note: I don't do anything for the first and last entry */
for (i=1; i< localsize-1; i++) {
globalptr[i-1] = localptr[i] + (k/(h*h)) * (localptr[i+1]-2.0*localptr[i]+localptr[i-1]);
}
ierr = VecRestoreArray (global,&globalptr);CHKERRQ(ierr);
ierr = VecRestoreArray(local,&localptr);CHKERRQ(ierr);
/* View Wave */
/* Set Up Display to Show Heat Graph */
#if defined(PETSC_USE_SOCKET_VIEWER)
ierr = VecView(global,PETSC_VIEWER_SOCKET_WORLD);CHKERRQ(ierr);
#endif
}
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscMPIInt rank, M, N, m, n, i;
PetscInt nx = 21, ny = 11;
const PetscInt *lxu, *lyu;
PetscInt *lxv, *lyv;
PetscInt *lxp, *lyp;
PetscErrorCode ierr;
DM uda, vda, pda;
Vec u;
ierr = PetscInitialize(&argc, &argv, NULL, NULL); CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank); CHKERRQ(ierr);
// Read options
ierr = PetscOptionsGetInt(NULL, "-nx", &nx, NULL); CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL, "-ny", &ny, NULL); CHKERRQ(ierr);
// Create distributed array and get vectors
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_STENCIL_BOX, nx-1, ny, PETSC_DECIDE, PETSC_DECIDE, 1, 1, NULL, NULL, &uda); CHKERRQ(ierr);
ierr = DMCreateLocalVector(uda, &u); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "\nCreated local distributed array U [DMDACreate2d, DMCreateLocalVector]"); CHKERRQ(ierr); hline();
ierr = PetscPrintf(PETSC_COMM_WORLD, "\nPrinting DA Info for U [DMDAGetInfo]"); CHKERRQ(ierr); hline();
ierr = DMDAGetInfo(uda, NULL, &M, &N, NULL, &m, &n, NULL, NULL, NULL, NULL, NULL, NULL, NULL); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Total size of array : M, N: %d, %d\n", M, N); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of processors: m, n: %d, %d\n", m, n); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "\nU-Node distribution along each direction [DMDAGetOwnershipRanges]"); CHKERRQ(ierr); hline();
ierr = DMDAGetOwnershipRanges(uda, &lxu, &lyu, NULL); CHKERRQ(ierr);
for(i=0; i<m; i++)
{
ierr = PetscPrintf(PETSC_COMM_WORLD, "%d\t", lxu[i]); CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHKERRQ(ierr);
for(i=0; i<n; i++)
{
ierr = PetscPrintf(PETSC_COMM_WORLD, "%d\t", lyu[i]); CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHKERRQ(ierr);
ierr = PetscMalloc(m*sizeof(*lxv), &lxv); CHKERRQ(ierr);
ierr = PetscMalloc(n*sizeof(*lyv), &lyv); CHKERRQ(ierr);
ierr = PetscMemcpy(lxv, lxu, m*sizeof(*lxv)); CHKERRQ(ierr);
ierr = PetscMemcpy(lyv, lyu, n*sizeof(*lyv)); CHKERRQ(ierr);
lxv[m-1]++;
lyv[n-1]--;
ierr = PetscPrintf(PETSC_COMM_WORLD, "\nV-Node distributed along each direction [Modified from U's info]"); CHKERRQ(ierr); hline();
for(i=0; i<m; i++)
{
ierr = PetscPrintf(PETSC_COMM_WORLD, "%d\t", lxv[i]); CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHKERRQ(ierr);
for(i=0; i<n; i++)
{
ierr = PetscPrintf(PETSC_COMM_WORLD, "%d\t", lyv[i]); CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "\nCreated and printing DA Info for V [DMDACreate2d, DMDAGetInfo]"); CHKERRQ(ierr); hline();
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_STENCIL_BOX, nx, ny-1, m, n, 1, 1, lxv, lyv, &vda); CHKERRQ(ierr);
ierr = DMDAGetInfo(vda, NULL, &M, &N, NULL, &m, &n, NULL, NULL, NULL, NULL, NULL, NULL, NULL); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "M, N: %d, %d\n", M, N); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "m, n: %d, %d\n", m, n); CHKERRQ(ierr);
ierr = PetscMalloc(m*sizeof(*lxp), &lxp); CHKERRQ(ierr);
ierr = PetscMalloc(n*sizeof(*lyp), &lyp); CHKERRQ(ierr);
ierr = PetscMemcpy(lxp, lxu, m*sizeof(*lxp)); CHKERRQ(ierr);
ierr = PetscMemcpy(lyp, lyu, n*sizeof(*lyp)); CHKERRQ(ierr);
lxp[m-1]++;
ierr = PetscPrintf(PETSC_COMM_WORLD, "\nCreated and printing DA Info for P [DMDACreate2d, DMDAGetInfo]"); CHKERRQ(ierr); hline();
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_STENCIL_STAR, nx, ny, m, n, 1, 1, lxp, lyp, &pda); CHKERRQ(ierr);
ierr = DMDAGetInfo(pda, NULL, &M, &N, NULL, &m, &n, NULL, NULL, NULL, NULL, NULL, NULL, NULL); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "M, N: %d, %d\n", M, N); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "m, n: %d, %d\n", m, n); CHKERRQ(ierr);
ierr = PetscFree(lxv); CHKERRQ(ierr);
ierr = PetscFree(lyv); CHKERRQ(ierr);
ierr = PetscFree(lxp); CHKERRQ(ierr);
ierr = PetscFree(lyp); CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = DMDestroy(&uda);CHKERRQ(ierr);
ierr = DMDestroy(&vda);CHKERRQ(ierr);
ierr = DMDestroy(&pda);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscMPIInt rank;
PetscErrorCode ierr;
PetscInt M = 10,N = 8,m = PETSC_DECIDE;
PetscInt s =2,w=2,n = PETSC_DECIDE,nloc,l,i,j,kk;
PetscInt Xs,Xm,Ys,Ym,iloc,*iglobal;
const PetscInt *ltog;
PetscInt *lx = NULL,*ly = NULL;
PetscBool testorder = PETSC_FALSE,flg;
DMBoundaryType bx = DM_BOUNDARY_NONE,by= DM_BOUNDARY_NONE;
DM da;
PetscViewer viewer;
Vec local,global;
PetscScalar value;
DMDAStencilType st = DMDA_STENCIL_BOX;
AO ao;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",300,0,400,400,&viewer);CHKERRQ(ierr);
/* Readoptions */
ierr = PetscOptionsGetInt(NULL,NULL,"-NX",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-NY",&N,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,"-s",&s,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-w",&w,NULL);CHKERRQ(ierr);
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-xperiodic",&flg,NULL);CHKERRQ(ierr); if (flg) bx = DM_BOUNDARY_PERIODIC;
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-yperiodic",&flg,NULL);CHKERRQ(ierr); if (flg) by = DM_BOUNDARY_PERIODIC;
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-xghosted",&flg,NULL);CHKERRQ(ierr); if (flg) bx = DM_BOUNDARY_GHOSTED;
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-yghosted",&flg,NULL);CHKERRQ(ierr); if (flg) by = DM_BOUNDARY_GHOSTED;
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-star",&flg,NULL);CHKERRQ(ierr); if (flg) st = DMDA_STENCIL_STAR;
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-box",&flg,NULL);CHKERRQ(ierr); if (flg) st = DMDA_STENCIL_BOX;
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-testorder",&testorder,NULL);CHKERRQ(ierr);
/*
Test putting two nodes in x and y on each processor, exact last processor
in x and y gets the rest.
*/
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-distribute",&flg,NULL);CHKERRQ(ierr);
if (flg) {
if (m == PETSC_DECIDE) SETERRQ(PETSC_COMM_WORLD,1,"Must set -m option with -distribute option");
ierr = PetscMalloc1(m,&lx);CHKERRQ(ierr);
for (i=0; i<m-1; i++) { lx[i] = 4;}
lx[m-1] = M - 4*(m-1);
if (n == PETSC_DECIDE) SETERRQ(PETSC_COMM_WORLD,1,"Must set -n option with -distribute option");
ierr = PetscMalloc1(n,&ly);CHKERRQ(ierr);
for (i=0; i<n-1; i++) { ly[i] = 2;}
ly[n-1] = N - 2*(n-1);
}
/* Create distributed array and get vectors */
ierr = DMDACreate2d(PETSC_COMM_WORLD,bx,by,st,M,N,m,n,w,s,lx,ly,&da);CHKERRQ(ierr);
ierr = PetscFree(lx);CHKERRQ(ierr);
ierr = PetscFree(ly);CHKERRQ(ierr);
ierr = DMView(da,viewer);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
/* Set global vector; send ghost points to local vectors */
value = 1;
ierr = VecSet(global,value);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
/* Scale local vectors according to processor rank; pass to global vector */
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
value = rank;
ierr = VecScale(local,value);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,local,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,local,INSERT_VALUES,global);CHKERRQ(ierr);
if (!testorder) { /* turn off printing when testing ordering mappings */
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nGlobal Vectors:\n");CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n\n");CHKERRQ(ierr);
}
/* Send ghost points to local vectors */
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-local_print",&flg,NULL);CHKERRQ(ierr);
if (flg) {
PetscViewer sviewer;
ierr = PetscViewerASCIIPushSynchronized(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\nLocal Vector: processor %d\n",rank);CHKERRQ(ierr);
ierr = PetscViewerGetSubViewer(PETSC_VIEWER_STDOUT_WORLD,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr);
ierr = VecView(local,sviewer);CHKERRQ(ierr);
ierr = PetscViewerRestoreSubViewer(PETSC_VIEWER_STDOUT_WORLD,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr);
ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscViewerASCIIPopSynchronized(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Tests mappings betweeen application/PETSc orderings */
if (testorder) {
ISLocalToGlobalMapping ltogm;
ierr = DMGetLocalToGlobalMapping(da,<ogm);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetSize(ltogm,&nloc);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetIndices(ltogm,<og);CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(da,&Xs,&Ys,NULL,&Xm,&Ym,NULL);CHKERRQ(ierr);
ierr = DMDAGetAO(da,&ao);CHKERRQ(ierr);
ierr = PetscMalloc1(nloc,&iglobal);CHKERRQ(ierr);
/* Set iglobal to be global indices for each processor's local and ghost nodes,
using the DMDA ordering of grid points */
kk = 0;
for (j=Ys; j<Ys+Ym; j++) {
for (i=Xs; i<Xs+Xm; i++) {
iloc = w*((j-Ys)*Xm + i-Xs);
for (l=0; l<w; l++) {
iglobal[kk++] = ltog[iloc+l];
}
}
}
/* Map this to the application ordering (which for DMDAs is just the natural ordering
that would be used for 1 processor, numbering most rapidly by x, then y) */
ierr = AOPetscToApplication(ao,nloc,iglobal);CHKERRQ(ierr);
/* Then map the application ordering back to the PETSc DMDA ordering */
ierr = AOApplicationToPetsc(ao,nloc,iglobal);CHKERRQ(ierr);
/* Verify the mappings */
kk=0;
for (j=Ys; j<Ys+Ym; j++) {
for (i=Xs; i<Xs+Xm; i++) {
iloc = w*((j-Ys)*Xm + i-Xs);
for (l=0; l<w; l++) {
if (iglobal[kk] != ltog[iloc+l]) {
ierr = PetscFPrintf(PETSC_COMM_SELF,stdout,"[%d] Problem with mapping: j=%D, i=%D, l=%D, petsc1=%D, petsc2=%D\n",rank,j,i,l,ltog[iloc+l],iglobal[kk]);CHKERRQ(ierr);
}
kk++;
}
}
}
ierr = PetscFree(iglobal);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingRestoreIndices(ltogm,<og);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)
{
SNES snes; /* nonlinear solver */
DM dm; /* problem definition */
Vec u,r; /* solution, residual vectors */
Mat A,J; /* Jacobian matrix */
MatNullSpace nullSpace; /* May be necessary for pressure */
AppCtx user; /* user-defined work context */
JacActionCtx userJ; /* context for Jacobian MF action */
PetscInt its; /* iterations for convergence */
PetscReal error = 0.0; /* L_2 error in the solution */
PetscInt numComponents = 0, f;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr);
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
ierr = SetupElement(dm, &user);CHKERRQ(ierr);
for (f = 0; f < NUM_FIELDS; ++f) {
PetscInt numComp;
ierr = PetscFEGetNumComponents(user.fe[f], &numComp);CHKERRQ(ierr);
numComponents += numComp;
}
ierr = PetscMalloc(NUM_FIELDS * sizeof(void (*)(const PetscReal[], PetscScalar *)), &user.exactFuncs);CHKERRQ(ierr);
user.fem.bcFuncs = (void (**)(const PetscReal[], PetscScalar *)) user.exactFuncs;
ierr = SetupExactSolution(dm, &user);CHKERRQ(ierr);
ierr = SetupSection(dm, &user);CHKERRQ(ierr);
ierr = DMPlexCreateClosureIndex(dm, NULL);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = DMSetMatType(dm,MATAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr);
if (user.jacobianMF) {
PetscInt M, m, N, n;
ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr);
ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr);
ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr);
ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr);
userJ.dm = dm;
userJ.J = J;
userJ.user = &user;
ierr = DMCreateLocalVector(dm, &userJ.u);CHKERRQ(ierr);
ierr = DMPlexProjectFunctionLocal(dm, user.fe, user.exactFuncs, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr);
ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr);
} else {
A = J;
}
ierr = CreatePressureNullSpace(dm, &user, &nullSpace);CHKERRQ(ierr);
ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr);
if (A != J) {
ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr);
}
ierr = DMSNESSetFunctionLocal(dm, (PetscErrorCode (*)(DM,Vec,Vec,void*))DMPlexComputeResidualFEM,&user);CHKERRQ(ierr);
ierr = DMSNESSetJacobianLocal(dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,MatStructure*,void*))DMPlexComputeJacobianFEM,&user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMPlexProjectFunction(dm, user.fe, user.exactFuncs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.runType == RUN_FULL) {
ierr = DMPlexProjectFunction(dm, user.fe, user.initialGuess, INSERT_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.debug) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %.3g\n", error);CHKERRQ(ierr);
if (user.showSolution) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr);
ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
} else {
PetscReal res = 0.0;
/* Check discretization error */
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr);
if (error >= 1.0e-11) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n", error);CHKERRQ(ierr);
}
/* Check residual */
ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr);
/* Check Jacobian */
{
Vec b;
MatStructure flag;
PetscBool isNull;
ierr = SNESComputeJacobian(snes, u, &A, &A, &flag);CHKERRQ(ierr);
ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr);
if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid.");
ierr = VecDuplicate(u, &b);CHKERRQ(ierr);
ierr = VecSet(r, 0.0);CHKERRQ(ierr);
ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr);
ierr = MatMult(A, u, r);CHKERRQ(ierr);
ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr);
}
}
if (user.runType == RUN_FULL) {
PetscViewer viewer;
Vec uLocal;
const char *name;
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "ex62_sol.vtk");CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &uLocal);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) u, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) uLocal, name);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = VecView(uLocal, viewer);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &uLocal);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr);
ierr = DestroyElement(&user);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
if (user.jacobianMF) {
ierr = VecDestroy(&userJ.u);CHKERRQ(ierr);
}
if (A != J) {
ierr = MatDestroy(&A);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscMPIInt rank;
PetscInt M = 13,s=1,dof=1;
DMDABoundaryType bx = DMDA_BOUNDARY_PERIODIC;
PetscErrorCode ierr;
DM da;
PetscViewer viewer;
Vec local,global;
PetscScalar value;
PetscDraw draw;
PetscBool flg = PETSC_FALSE;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
/* Create viewers */
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",280,480,600,200,&viewer);CHKERRQ(ierr);
ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
ierr = PetscDrawSetDoubleBuffer(draw);CHKERRQ(ierr);
/* Readoptions */
ierr = PetscOptionsGetInt(NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetEnum(NULL,"-wrap",DMDABoundaryTypes,(PetscEnum*)&bx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-dof",&dof,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-s",&s,NULL);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DMDACreate1d(PETSC_COMM_WORLD,bx,M,dof,s,NULL,&da);CHKERRQ(ierr);
ierr = DMView(da,viewer);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
/* Set global vector; send ghost points to local vectors */
value = 1;
ierr = VecSet(global,value);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
/* Scale local vectors according to processor rank; pass to global vector */
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
value = rank+1;
ierr = VecScale(local,value);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,local,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,local,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = VecView(global,viewer);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nGlobal Vector:\n");CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRQ(ierr);
/* Send ghost points to local vectors */
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-local_print",&flg,NULL);CHKERRQ(ierr);
if (flg) {
PetscViewer sviewer;
ISLocalToGlobalMapping is;
ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\nLocal Vector: processor %d\n",rank);CHKERRQ(ierr);
ierr = PetscViewerGetSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr);
ierr = VecView(local,sviewer);CHKERRQ(ierr);
ierr = PetscViewerRestoreSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr);
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\nLocal to global mapping: processor %d\n",rank);CHKERRQ(ierr);
ierr = PetscViewerGetSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr);
ierr = DMGetLocalToGlobalMapping(da,&is);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingView(is,sviewer);CHKERRQ(ierr);
ierr = PetscViewerRestoreSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr);
}
/* Free memory */
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
DM dm;
Vec vec,vecLocal1,vecLocal2;
PetscScalar *a,***a1,***a2,expected;
PetscInt startx,starty,nx,ny,i,j,d,is,js,dof0,dof1,dof2,dofTotal,stencilWidth,Nx,Ny;
DMBoundaryType boundaryTypex,boundaryTypey;
PetscMPIInt rank;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
dof0 = 1;
dof1 = 1;
dof2 = 1;
stencilWidth = 2;
ierr = DMStagCreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,DM_BOUNDARY_PERIODIC,4,4,PETSC_DECIDE,PETSC_DECIDE,dof0,dof1,dof2,DMSTAG_STENCIL_BOX,stencilWidth,NULL,NULL,&dm);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = DMStagGetDOF(dm,&dof0,&dof1,&dof2,NULL);CHKERRQ(ierr);
dofTotal = dof0 + 2*dof1 + dof2;
ierr = DMStagGetStencilWidth(dm,&stencilWidth);CHKERRQ(ierr);
ierr = DMCreateLocalVector(dm,&vecLocal1);CHKERRQ(ierr);
ierr = VecDuplicate(vecLocal1,&vecLocal2);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dm,&vec);CHKERRQ(ierr);
ierr = VecSet(vec,1.0);CHKERRQ(ierr);
ierr = VecSet(vecLocal1,0.0);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,vec,INSERT_VALUES,vecLocal1);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,vec,INSERT_VALUES,vecLocal1);CHKERRQ(ierr);
ierr = DMStagGetCorners(dm,&startx,&starty,NULL,&nx,&ny,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = DMStagVecGetArrayDOFRead(dm,vecLocal1,&a1);CHKERRQ(ierr);
ierr = DMStagVecGetArrayDOF(dm,vecLocal2,&a2);CHKERRQ(ierr);
for (j=starty; j<starty + ny; ++j) {
for (i=startx; i<startx + nx; ++i) {
for (d=0; d<dofTotal; ++d) {
if (a1[j][i][d] != 1.0) {
PetscPrintf(PETSC_COMM_SELF,"[%d] Unexpected value %g (expecting %g)\n",rank,a1[j][i][d],1.0);CHKERRQ(ierr);
}
a2[j][i][d] = 0.0;
for (js = -stencilWidth; js <= stencilWidth; ++js) {
for (is = -stencilWidth; is <= stencilWidth; ++is) {
a2[j][i][d] += a1[j+js][i+is][d];
}
}
}
}
}
ierr = DMStagVecRestoreArrayDOFRead(dm,vecLocal1,&a1);CHKERRQ(ierr);
ierr = DMStagVecRestoreArrayDOF(dm,vecLocal2,&a2);CHKERRQ(ierr);
DMLocalToGlobalBegin(dm,vecLocal2,INSERT_VALUES,vec);CHKERRQ(ierr);
DMLocalToGlobalEnd(dm,vecLocal2,INSERT_VALUES,vec);CHKERRQ(ierr);
/* For the all-periodic case, all values are the same . Otherwise, just check the local version */
ierr = DMStagGetBoundaryTypes(dm,&boundaryTypex,&boundaryTypey,NULL);CHKERRQ(ierr);
if (boundaryTypex == DM_BOUNDARY_PERIODIC && boundaryTypey == DM_BOUNDARY_PERIODIC) {
ierr = VecGetArray(vec,&a);CHKERRQ(ierr);
expected = 1.0; for(d=0;d<2;++d) expected *= (2*stencilWidth+1);
for (i=0; i<ny*nx*dofTotal; ++i) {
if (a[i] != expected) {
ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] Unexpected value %g (expecting %g)\n",rank,a[i],expected);CHKERRQ(ierr);
}
}
ierr = VecRestoreArray(vec,&a);CHKERRQ(ierr);
} else {
ierr = DMStagVecGetArrayDOFRead(dm,vecLocal2,&a2);CHKERRQ(ierr);
ierr = DMStagGetGlobalSizes(dm,&Nx,&Ny,NULL);CHKERRQ(ierr);
if (stencilWidth > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Non-periodic check implemented assuming stencilWidth = 1");
for (j=starty; j<starty + ny; ++j) {
for (i=startx; i<startx + nx; ++i) {
PetscInt dd,extra[2];
PetscBool bnd[2];
bnd[0] = (PetscBool)((i == 0 || i == Nx-1) && boundaryTypex != DM_BOUNDARY_PERIODIC);
bnd[1] = (PetscBool)((j == 0 || j == Ny-1) && boundaryTypey != DM_BOUNDARY_PERIODIC);
extra[0] = i == Nx-1 && boundaryTypex != DM_BOUNDARY_PERIODIC ? 1 : 0;
extra[1] = j == Ny-1 && boundaryTypey != DM_BOUNDARY_PERIODIC ? 1 : 0;
{ /* vertices */
PetscScalar expected = 1.0;
for (dd=0;dd<2;++dd) expected *= (bnd[dd] ? stencilWidth + 1 + extra[dd] : 2*stencilWidth + 1);
for (d=0; d<dof0; ++d) {
if (a2[j][i][d] != expected) {
ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] Element (%D,%D)[%D] Unexpected value %g (expecting %g)\n",rank,i,j,d,a2[j][i][d],expected);CHKERRQ(ierr);
}
}
}
{ /* down edges */
PetscScalar expected = (bnd[1] ? stencilWidth + 1 + extra[1] : 2*stencilWidth + 1);
expected *= ((bnd[0] ? 1 : 2) * stencilWidth + 1);
for (d=dof0; d<dof0+dof1; ++d) {
if (a2[j][i][d] != expected) {
ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] Element (%D,%D)[%D] Unexpected value %g (expecting %g)\n",rank,i,j,d,a2[j][i][d],expected);CHKERRQ(ierr);
}
}
}
{ /* left edges */
PetscScalar expected = (bnd[0] ? stencilWidth + 1 + extra[0] : 2*stencilWidth + 1);
expected *= ((bnd[1] ? 1 : 2) * stencilWidth + 1);
for (d=dof0+dof1; d<dof0+2*dof1; ++d) {
if (a2[j][i][d] != expected) {
ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] Element (%D,%D)[%D] Unexpected value %g (expecting %g)\n",rank,i,j,d,a2[j][i][d],expected);CHKERRQ(ierr);
}
}
}
{ /* elements */
PetscScalar expected = 1.0;
for (dd=0;dd<2;++dd) expected *= ((bnd[dd] ? 1 : 2) * stencilWidth + 1);
for (d=dofTotal-dof2; d<dofTotal; ++d) {
if (a2[j][i][d] != expected) {
ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] Element (%D,%D)[%D] Unexpected value %g (expecting %g)\n",rank,i,j,d,a2[j][i][d],expected);CHKERRQ(ierr);
}
}
}
}
}
ierr = DMStagVecRestoreArrayDOFRead(dm,vecLocal2,&a2);CHKERRQ(ierr);
}
ierr = VecDestroy(&vec);CHKERRQ(ierr);
ierr = VecDestroy(&vecLocal1);CHKERRQ(ierr);
ierr = VecDestroy(&vecLocal2);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt its,n,Nx=PETSC_DECIDE,Ny=PETSC_DECIDE,nlocal;
PetscMPIInt size;
PetscScalar one = 1.0;
PetscInt mx,my;
Mat A;
GridCtx fine_ctx;
KSP ksp;
PetscBool flg;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
/* set up discretization matrix for fine grid */
fine_ctx.mx = 9; fine_ctx.my = 9;
ierr = PetscOptionsGetInt(NULL,NULL,"-mx",&mx,&flg);CHKERRQ(ierr);
if (flg) fine_ctx.mx = mx;
ierr = PetscOptionsGetInt(NULL,NULL,"-my",&my,&flg);CHKERRQ(ierr);
if (flg) fine_ctx.my = my;
ierr = PetscPrintf(PETSC_COMM_WORLD,"Fine grid size %D by %D\n",fine_ctx.mx,fine_ctx.my);CHKERRQ(ierr);
n = fine_ctx.mx*fine_ctx.my;
MPI_Comm_size(PETSC_COMM_WORLD,&size);
ierr = PetscOptionsGetInt(NULL,NULL,"-Nx",&Nx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-Ny",&Ny,NULL);CHKERRQ(ierr);
/* Set up distributed array for fine grid */
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,fine_ctx.mx,
fine_ctx.my,Nx,Ny,1,1,NULL,NULL,&fine_ctx.da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(fine_ctx.da,&fine_ctx.x);CHKERRQ(ierr);
ierr = VecDuplicate(fine_ctx.x,&fine_ctx.b);CHKERRQ(ierr);
ierr = VecGetLocalSize(fine_ctx.x,&nlocal);CHKERRQ(ierr);
ierr = DMCreateLocalVector(fine_ctx.da,&fine_ctx.localX);CHKERRQ(ierr);
ierr = VecDuplicate(fine_ctx.localX,&fine_ctx.localF);CHKERRQ(ierr);
ierr = MatCreateAIJ(PETSC_COMM_WORLD,nlocal,nlocal,n,n,5,NULL,3,NULL,&A);CHKERRQ(ierr);
ierr = FormJacobian_Grid(&fine_ctx,&A);CHKERRQ(ierr);
/* create linear solver */
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
/* set values for rhs vector */
ierr = VecSet(fine_ctx.b,one);CHKERRQ(ierr);
/* set options, then solve system */
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); /* calls PCSetFromOptions_ML if 'pc_type=ml' */
ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr);
ierr = KSPSolve(ksp,fine_ctx.b,fine_ctx.x);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Number of iterations = %D\n",its);CHKERRQ(ierr);
/* free data structures */
ierr = VecDestroy(&fine_ctx.x);CHKERRQ(ierr);
ierr = VecDestroy(&fine_ctx.b);CHKERRQ(ierr);
ierr = DMDestroy(&fine_ctx.da);CHKERRQ(ierr);
ierr = VecDestroy(&fine_ctx.localX);CHKERRQ(ierr);
ierr = VecDestroy(&fine_ctx.localF);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInitialize(&argc,&argv,(char*)0,help);
const int d = 2; // d = DOF
Mat A, Aminus;
// these are dense d x d sequential matrices, unrelated to the grid
// (each processor owns whole matrix)
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,d,d,d,NULL,&A); CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(A,"A_"); CHKERRQ(ierr);
ierr = MatSetFromOptions(A); CHKERRQ(ierr);
// fill A
double val[d][d], c = 3.0;
val[0][0] = 0.0; val[0][1] = c;
val[1][0] = c; val[1][1] = 0.0;
ierr = fillsmallmat(2,val,A); CHKERRQ(ierr);
// fill Aminus; see getAminus.m for computation of Aminus from A
ierr = MatDuplicate(A,MAT_SHARE_NONZERO_PATTERN,&Aminus); CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(Aminus,"Aminus_"); CHKERRQ(ierr);
val[0][0] = -1.5; val[0][1] = 1.5;
val[1][0] = 1.5; val[1][1] = -1.5;
ierr = fillsmallmat(2,val,Aminus); CHKERRQ(ierr);
// set up the grid
DM da;
ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC,
-50, // override with -da_grid_x or -da_refine
d, 1, NULL, // dof = 1 and stencil width = 1
&da); CHKERRQ(ierr);
// determine grid locations (cell-centered grid)
DMDALocalInfo info;
double L = 10.0, dx;
ierr = DMDAGetLocalInfo(da,&info); CHKERRQ(ierr);
dx = L / (double)(info.mx);
ierr = DMDASetUniformCoordinates(da,dx/2,L-dx/2,-1.0,-1.0,-1.0,-1.0);CHKERRQ(ierr);
// u = u(t_n), unew = u(t_n+1)
Vec u, unew, F;
ierr = DMCreateLocalVector(da,&u);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)u,"solution u"); CHKERRQ(ierr);
ierr = VecDuplicate(u,&F);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)F,"flux F"); CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&unew);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)unew,"updated solution unew"); CHKERRQ(ierr);
ierr = VecSet(unew,0.0); CHKERRQ(ierr);
// at each cell we will need to compute Fcell = A qleft + Aminus dq
Vec dq, qleft, tmp, Fcell;
ierr = VecCreateSeq(PETSC_COMM_WORLD,d,&dq); CHKERRQ(ierr);
ierr = VecDuplicate(dq,&qleft); CHKERRQ(ierr);
ierr = VecDuplicate(dq,&tmp); CHKERRQ(ierr);
ierr = VecDuplicate(dq,&Fcell); CHKERRQ(ierr);
// view the solution graphically; control with -draw_pause
PetscViewer viewer;
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,NULL,"solution u",
PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,&viewer); CHKERRQ(ierr);
/* time-stepping loop */
double t = 0.0, tf = 10.0, dt, nu;
int n, NN = 10;
dt = tf / NN;
nu = dt / dx;
for (n = 0; n < NN; ++n) {
ierr = PetscPrintf(PETSC_COMM_WORLD, " time[%3d]=%6g: \n", n, t); CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,unew,INSERT_VALUES,u); CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,unew,INSERT_VALUES,u); CHKERRQ(ierr);
ierr = VecView(u,viewer); CHKERRQ(ierr);
double **au, **aunew, **aF;
int j, p;
ierr = DMDAVecGetArrayDOF(da, u, &au);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da, F, &aF);CHKERRQ(ierr);
for (j=info.xs; j<info.xs+info.xm; j++) {
double *adq, *aqleft, *aFcell;
ierr = VecGetArray(dq,&adq); CHKERRQ(ierr);
ierr = VecGetArray(qleft,&aqleft); CHKERRQ(ierr);
for (p = 0; p < d; p++) {
adq[p] = au[j+1][p] - au[j][p];
aqleft[p] = au[j][p];
}
ierr = VecRestoreArray(dq,&adq); CHKERRQ(ierr);
ierr = VecRestoreArray(qleft,&aqleft); CHKERRQ(ierr);
// tmp = A qleft
// Fcell = tmp + Aminus dq
ierr = MatMult(A,qleft,tmp); CHKERRQ(ierr);
ierr = MatMultAdd(Aminus,dq,tmp,Fcell); CHKERRQ(ierr);
ierr = VecGetArray(Fcell,&aFcell); CHKERRQ(ierr);
for (p = 0; p < d; p++)
aF[j][p] = aFcell[p];
ierr = VecRestoreArray(Fcell,&aFcell); CHKERRQ(ierr);
}
ierr = DMDAVecRestoreArrayDOF(da, F, &aF);CHKERRQ(ierr);
ierr = DMLocalToLocalBegin(da,F,INSERT_VALUES,F); CHKERRQ(ierr);
ierr = DMLocalToLocalEnd(da,F,INSERT_VALUES,F); CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da, F, &aF);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da, unew, &aunew);CHKERRQ(ierr);
for (j=info.xs; j<info.xs+info.xm; j++) {
for (p = 0; p < d; p++)
aunew[j][p] = au[j][p] - nu * (aF[j+1][p] - aF[j][p]);
}
ierr = DMDAVecRestoreArrayDOF(da, u, &au);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da, F, &aF);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da, unew, &aunew);CHKERRQ(ierr);
t += dt;
}
// clean up
ierr = VecDestroy(&u); CHKERRQ(ierr);
ierr = VecDestroy(&unew); CHKERRQ(ierr);
ierr = VecDestroy(&F); CHKERRQ(ierr);
ierr = VecDestroy(&dq); CHKERRQ(ierr);
ierr = VecDestroy(&qleft); CHKERRQ(ierr);
ierr = VecDestroy(&tmp); CHKERRQ(ierr);
ierr = VecDestroy(&Fcell); CHKERRQ(ierr);
ierr = MatDestroy(&A); CHKERRQ(ierr);
ierr = MatDestroy(&Aminus); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
ierr = DMDestroy(&da); CHKERRQ(ierr);
ierr = PetscFinalize(); CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
PetscMPIInt rank;
PetscInt M = -10,N = -8;
PetscErrorCode ierr;
PetscBool flg = PETSC_FALSE;
DM da;
PetscViewer viewer;
Vec local,global;
PetscScalar value;
DMBoundaryType bx = DM_BOUNDARY_NONE,by = DM_BOUNDARY_NONE;
DMDAStencilType stype = DMDA_STENCIL_BOX;
#if defined(PETSC_HAVE_MATLAB_ENGINE)
PetscViewer mviewer;
PetscMPIInt size;
#endif
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",300,0,300,300,&viewer);CHKERRQ(ierr);
#if defined(PETSC_HAVE_MATLAB_ENGINE)
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size == 1) {
ierr = PetscViewerMatlabOpen(PETSC_COMM_WORLD,"tmp.mat",FILE_MODE_WRITE,&mviewer);CHKERRQ(ierr);
}
#endif
ierr = PetscOptionsGetBool(NULL,NULL,"-star_stencil",&flg,NULL);CHKERRQ(ierr);
if (flg) stype = DMDA_STENCIL_STAR;
/* Create distributed array and get vectors */
ierr = DMDACreate2d(PETSC_COMM_WORLD,bx,by,stype,M,N,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&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);
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL, "-view_global", &flg,NULL);CHKERRQ(ierr);
if (flg) { /* view global vector in natural ordering */
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = DMView(da,viewer);CHKERRQ(ierr);
ierr = VecView(global,viewer);CHKERRQ(ierr);
#if defined(PETSC_HAVE_MATLAB_ENGINE)
if (size == 1) {
ierr = DMView(da,mviewer);CHKERRQ(ierr);
ierr = VecView(global,mviewer);CHKERRQ(ierr);
}
#endif
/* Free memory */
#if defined(PETSC_HAVE_MATLAB_ENGINE)
if (size == 1) {
ierr = PetscViewerDestroy(&mviewer);CHKERRQ(ierr);
}
#endif
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)
{
PetscMPIInt rank;
PetscInt M=8,dof=1,stencil_width=1,i,start,end,P=5,N = 6,m=PETSC_DECIDE,n=PETSC_DECIDE,p=PETSC_DECIDE,pt = 0,st = 0;
PetscErrorCode ierr;
PetscBool flg = PETSC_FALSE,flg2,flg3;
DMDABoundaryType periodic;
DMDAStencilType stencil_type;
DM da;
Vec local,global,local_copy;
PetscScalar value;
PetscReal norm,work;
PetscViewer viewer;
char filename[64];
FILE *file;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-dof",&dof,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-stencil_width",&stencil_width,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-periodic",&pt,NULL);CHKERRQ(ierr);
periodic = (DMDABoundaryType) pt;
ierr = PetscOptionsGetInt(NULL,"-stencil_type",&st,NULL);CHKERRQ(ierr);
stencil_type = (DMDAStencilType) st;
ierr = PetscOptionsHasName(NULL,"-2d",&flg2);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-3d",&flg3);CHKERRQ(ierr);
if (flg2) {
ierr = DMDACreate2d(PETSC_COMM_WORLD,periodic,periodic,stencil_type,M,N,m,n,dof,stencil_width,
NULL,NULL,&da);CHKERRQ(ierr);
} else if (flg3) {
ierr = DMDACreate3d(PETSC_COMM_WORLD,periodic,periodic,periodic,stencil_type,M,N,P,m,n,p,dof,stencil_width,
NULL,NULL,NULL,&da);CHKERRQ(ierr);
} else {
ierr = DMDACreate1d(PETSC_COMM_WORLD,periodic,M,dof,stencil_width,NULL,&da);CHKERRQ(ierr);
}
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = VecDuplicate(local,&local_copy);CHKERRQ(ierr);
/* zero out vectors so that ghostpoints are zero */
value = 0;
ierr = VecSet(local,value);CHKERRQ(ierr);
ierr = VecSet(local_copy,value);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(global,&start,&end);CHKERRQ(ierr);
for (i=start; i<end; i++) {
value = i + 1;
ierr = VecSetValues(global,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(global);CHKERRQ(ierr);
ierr = VecAssemblyEnd(global);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMDALocalToLocalBegin(da,local,INSERT_VALUES,local_copy);CHKERRQ(ierr);
ierr = DMDALocalToLocalEnd(da,local,INSERT_VALUES,local_copy);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-save",&flg,NULL);CHKERRQ(ierr);
if (flg) {
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
sprintf(filename,"local.%d",rank);
ierr = PetscViewerASCIIOpen(PETSC_COMM_SELF,filename,&viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIGetPointer(viewer,&file);CHKERRQ(ierr);
ierr = VecView(local,viewer);CHKERRQ(ierr);
fprintf(file,"Vector with correct ghost points\n");
ierr = VecView(local_copy,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = VecAXPY(local_copy,-1.0,local);CHKERRQ(ierr);
ierr = VecNorm(local_copy,NORM_MAX,&work);CHKERRQ(ierr);
ierr = MPI_Allreduce(&work,&norm,1,MPIU_REAL,MPIU_MAX,PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of difference %G should be zero\n",norm);CHKERRQ(ierr);
ierr = VecDestroy(&local_copy);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode SNESSetUp_NASM(SNES snes)
{
SNES_NASM *nasm = (SNES_NASM*)snes->data;
PetscErrorCode ierr;
DM dm,subdm;
DM *subdms;
PetscInt i;
const char *optionsprefix;
Vec F;
PetscMPIInt size;
KSP ksp;
PC pc;
PetscFunctionBegin;
if (!nasm->subsnes) {
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
if (dm) {
nasm->usesdm = PETSC_TRUE;
ierr = DMCreateDomainDecomposition(dm,&nasm->n,NULL,NULL,NULL,&subdms);CHKERRQ(ierr);
if (!subdms) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_WRONGSTATE,"DM has no default decomposition defined. Set subsolves manually with SNESNASMSetSubdomains().");
ierr = DMCreateDomainDecompositionScatters(dm,nasm->n,subdms,&nasm->iscatter,&nasm->oscatter,&nasm->gscatter);CHKERRQ(ierr);
ierr = SNESGetOptionsPrefix(snes, &optionsprefix);CHKERRQ(ierr);
ierr = PetscMalloc(nasm->n*sizeof(SNES),&nasm->subsnes);CHKERRQ(ierr);
for (i=0; i<nasm->n; i++) {
ierr = SNESCreate(PETSC_COMM_SELF,&nasm->subsnes[i]);CHKERRQ(ierr);
ierr = SNESAppendOptionsPrefix(nasm->subsnes[i],optionsprefix);CHKERRQ(ierr);
ierr = SNESAppendOptionsPrefix(nasm->subsnes[i],"sub_");CHKERRQ(ierr);
ierr = SNESSetDM(nasm->subsnes[i],subdms[i]);CHKERRQ(ierr);
ierr = MPI_Comm_size(PetscObjectComm((PetscObject)nasm->subsnes[i]),&size);CHKERRQ(ierr);
if (size == 1) {
ierr = SNESGetKSP(nasm->subsnes[i],&ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPPREONLY);CHKERRQ(ierr);
ierr = PCSetType(pc,PCLU);CHKERRQ(ierr);
}
ierr = SNESSetFromOptions(nasm->subsnes[i]);CHKERRQ(ierr);
ierr = DMDestroy(&subdms[i]);CHKERRQ(ierr);
}
ierr = PetscFree(subdms);CHKERRQ(ierr);
} else SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_WRONGSTATE,"Cannot construct local problems automatically without a DM!");
} else SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_WRONGSTATE,"Must set subproblems manually if there is no DM!");
/* allocate the global vectors */
if (!nasm->x) {
ierr = PetscMalloc(nasm->n*sizeof(Vec),&nasm->x);CHKERRQ(ierr);
ierr = PetscMemzero(nasm->x,nasm->n*sizeof(Vec));CHKERRQ(ierr);
}
if (!nasm->xl) {
ierr = PetscMalloc(nasm->n*sizeof(Vec),&nasm->xl);CHKERRQ(ierr);
ierr = PetscMemzero(nasm->xl,nasm->n*sizeof(Vec));CHKERRQ(ierr);
}
if (!nasm->y) {
ierr = PetscMalloc(nasm->n*sizeof(Vec),&nasm->y);CHKERRQ(ierr);
ierr = PetscMemzero(nasm->y,nasm->n*sizeof(Vec));CHKERRQ(ierr);
}
if (!nasm->b) {
ierr = PetscMalloc(nasm->n*sizeof(Vec),&nasm->b);CHKERRQ(ierr);
ierr = PetscMemzero(nasm->b,nasm->n*sizeof(Vec));CHKERRQ(ierr);
}
for (i=0; i<nasm->n; i++) {
ierr = SNESGetFunction(nasm->subsnes[i],&F,NULL,NULL);CHKERRQ(ierr);
if (!nasm->x[i]) {ierr = VecDuplicate(F,&nasm->x[i]);CHKERRQ(ierr);}
if (!nasm->y[i]) {ierr = VecDuplicate(F,&nasm->y[i]);CHKERRQ(ierr);}
if (!nasm->b[i]) {ierr = VecDuplicate(F,&nasm->b[i]);CHKERRQ(ierr);}
if (!nasm->xl[i]) {
ierr = SNESGetDM(nasm->subsnes[i],&subdm);CHKERRQ(ierr);
ierr = DMCreateLocalVector(subdm,&nasm->xl[i]);CHKERRQ(ierr);
}
ierr = DMGlobalToLocalHookAdd(subdm,DMGlobalToLocalSubDomainDirichletHook_Private,NULL,nasm->xl[i]);CHKERRQ(ierr);
}
if (nasm->finaljacobian) {
ierr = SNESSetUpMatrices(snes);CHKERRQ(ierr);
if (nasm->fjtype == 2) {
ierr = VecDuplicate(snes->vec_sol,&nasm->xinit);CHKERRQ(ierr);
}
for (i=0; i<nasm->n;i++) {
ierr = SNESSetUpMatrices(nasm->subsnes[i]);CHKERRQ(ierr);
}
}
PetscFunctionReturn(0);
}
