int main(int argc,char **argv)
{
PetscInt M = 14,dof = 1,s = 1,ratio = 2,dim = 2;
PetscErrorCode ierr;
DM da_c,da_f;
Vec v_c,v_f;
Mat I;
PetscScalar one = 1.0;
MPI_Comm comm_f, comm_c;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-dim",&dim,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-sw",&s,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-ratio",&ratio,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-dof",&dof,PETSC_NULL);CHKERRQ(ierr);
comm_f = PETSC_COMM_WORLD;
ierr = DMDASplitComm2d(comm_f,M,M,s,&comm_c);CHKERRQ(ierr);
/* Set up the array */
if (dim == 2) {
ierr = DMDACreate2d(comm_c,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,M,PETSC_DECIDE,PETSC_DECIDE,dof,s,PETSC_NULL,PETSC_NULL,&da_c);CHKERRQ(ierr);
M = ratio*(M-1) + 1;
ierr = DMDACreate2d(comm_f,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,M,PETSC_DECIDE,PETSC_DECIDE,dof,s,PETSC_NULL,PETSC_NULL,&da_f);CHKERRQ(ierr);
} else if (dim == 3) {
;
}
ierr = DMCreateGlobalVector(da_c,&v_c);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da_f,&v_f);CHKERRQ(ierr);
ierr = VecSet(v_c,one);CHKERRQ(ierr);
ierr = DMCreateInterpolation(da_c,da_f,&I,PETSC_NULL);CHKERRQ(ierr);
ierr = MatInterpolate(I,v_c,v_f);CHKERRQ(ierr);
ierr = VecView(v_f,PETSC_VIEWER_STDOUT_(comm_f));CHKERRQ(ierr);
ierr = MatRestrict(I,v_f,v_c);CHKERRQ(ierr);
ierr = VecView(v_c,PETSC_VIEWER_STDOUT_(comm_c));CHKERRQ(ierr);
ierr = MatDestroy(&I);CHKERRQ(ierr);
ierr = VecDestroy(&v_c);CHKERRQ(ierr);
ierr = DMDestroy(&da_c);CHKERRQ(ierr);
ierr = VecDestroy(&v_f);CHKERRQ(ierr);
ierr = DMDestroy(&da_f);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
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)
{
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;
}
inline void
DMCreate<2
>(MPI_Comm const& comm,
DMBoundaryTypeVector<2> const& boundaryTypes,
DMDAStencilType const& stencilType,
VectorDi<2> const& globalSize,
VectorDi<2> const& processorSize,
int const& dof,
int const& stencilWidth,
VectorDConstPetscIntPointer<2> const& localSizes,
DM* da) {
DMDACreate2d(comm,
boundaryTypes(0),
boundaryTypes(1),
stencilType,
globalSize(0),
globalSize(1),
processorSize(0),
processorSize(1),
dof,
stencilWidth,
localSizes(0).get(),
localSizes(1).get(),
da);
}
int main(int argc,char **argv)
{
KSP ksp;
DM da;
UserContext user;
PetscInt bc;
PetscErrorCode ierr;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-11,-11,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
ierr = KSPSetDM(ksp,(DM)da);
ierr = DMSetApplicationContext(da,&user);CHKERRQ(ierr);
user.uu = 1.0;
user.tt = 1.0;
bc = (PetscInt)NEUMANN; // Use Neumann Boundary Conditions
user.bcType = (BCType)bc;
ierr = KSPSetComputeRHS(ksp,ComputeRHS,&user);CHKERRQ(ierr);
ierr = KSPSetComputeOperators(ksp,ComputeJacobian,&user);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPSolve(ksp,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 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;
}
int main(int argc,char **argv)
{
SNES snes;
PetscErrorCode ierr;
PetscInt its,lits;
PetscReal litspit;
DM da;
PetscInitialize(&argc,&argv,PETSC_NULL,help);
/*
Set the DMDA (grid structure) for the grids.
*/
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-5,-5,PETSC_DECIDE,PETSC_DECIDE,1,1,0,0,&da);CHKERRQ(ierr);
ierr = DMDASNESSetFunctionLocal(da,INSERT_VALUES,(PetscErrorCode (*)(DMDALocalInfo*,void*,void*,void*))FormFunctionLocal,PETSC_NULL);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
ierr = SNESSetDM(snes,da);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = SNESSolve(snes,0,0);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
ierr = SNESGetLinearSolveIterations(snes,&lits);CHKERRQ(ierr);
litspit = ((PetscReal)lits)/((PetscReal)its);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Number of SNES iterations = %D\n",its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Number of Linear iterations = %D\n",lits);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Average Linear its / SNES = %e\n",litspit);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
KSP ksp;
DM da;
UserContext user;
const char *bcTypes[2] = {"dirichlet","neumann"};
PetscErrorCode ierr;
PetscInt bc;
Vec b,x;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);
CHKERRQ(ierr);
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-3,-3,PETSC_DECIDE,PETSC_DECIDE,1,1,0,0,&da);
CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(da,0,1,0,1,0,0);
CHKERRQ(ierr);
ierr = DMDASetFieldName(da,0,"Pressure");
CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD, "", "Options for the inhomogeneous Poisson equation", "DMqq");
user.rho = 1.0;
ierr = PetscOptionsReal("-rho", "The conductivity", "ex29.c", user.rho, &user.rho, PETSC_NULL);
CHKERRQ(ierr);
user.nu = 0.1;
ierr = PetscOptionsReal("-nu", "The width of the Gaussian source", "ex29.c", user.nu, &user.nu, PETSC_NULL);
CHKERRQ(ierr);
bc = (PetscInt)DIRICHLET;
ierr = PetscOptionsEList("-bc_type","Type of boundary condition","ex29.c",bcTypes,2,bcTypes[0],&bc,PETSC_NULL);
CHKERRQ(ierr);
user.bcType = (BCType)bc;
ierr = PetscOptionsEnd();
ierr = KSPSetComputeRHS(ksp,ComputeRHS,&user);
CHKERRQ(ierr);
ierr = KSPSetComputeOperators(ksp,ComputeMatrix,&user);
CHKERRQ(ierr);
ierr = KSPSetDM(ksp,da);
CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);
CHKERRQ(ierr);
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
ierr = KSPSolve(ksp,PETSC_NULL,PETSC_NULL);
CHKERRQ(ierr);
ierr = KSPGetSolution(ksp,&x);
CHKERRQ(ierr);
ierr = KSPGetRhs(ksp,&b);
CHKERRQ(ierr);
ierr = DMDestroy(&da);
CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);
CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PETSC_EXTERN void PETSC_STDCALL dmdacreate2d_(MPI_Comm *comm,DMBoundaryType *bx,DMBoundaryType *by,DMDAStencilType
*stencil_type,PetscInt *M,PetscInt *N,PetscInt *m,PetscInt *n,PetscInt *w,
PetscInt *s,PetscInt *lx,PetscInt *ly,DM *inra,PetscErrorCode *ierr)
{
CHKFORTRANNULLINTEGER(lx);
CHKFORTRANNULLINTEGER(ly);
*ierr = DMDACreate2d(MPI_Comm_f2c(*(MPI_Fint*)&*comm),*bx,*by,*stencil_type,*M,*N,*m,*n,*w,*s,lx,ly,inra);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
DM da2D;
PetscInt i,j,ixs, ixm, iys, iym;;
PetscViewer H5viewer;
PetscScalar xm=-1.0, xp=1.0;
PetscScalar ym=-1.0, yp=1.0;
PetscScalar value=1.0,dx,dy;
PetscInt Nx=40, Ny=40;
Vec gauss;
PetscScalar **gauss_ptr;
dx=(xp-xm)/(Nx-1);
dy=(yp-ym)/(Ny-1);
// Initialize the Petsc context
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
// Build of the DMDA
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,Nx,Ny,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da2D);CHKERRQ(ierr);
// Set the coordinates
DMDASetUniformCoordinates(da2D, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0);
// Declare gauss as a DMDA component
ierr = DMCreateGlobalVector(da2D,&gauss);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) gauss, "pressure");CHKERRQ(ierr);
// Initialize vector gauss with a constant value (=1)
ierr = VecSet(gauss,value);CHKERRQ(ierr);
// Get the coordinates of the corners for each process
ierr = DMDAGetCorners(da2D, &ixs, &iys, 0, &ixm, &iym, 0);CHKERRQ(ierr);
/* Build the gaussian profile (exp(-x^2-y^2)) */
ierr = DMDAVecGetArray(da2D,gauss,&gauss_ptr);CHKERRQ(ierr);
for (j=iys; j<iys+iym; j++){
for (i=ixs; i<ixs+ixm; i++){
gauss_ptr[j][i]=exp(-(xm+i*dx)*(xm+i*dx)-(ym+j*dy)*(ym+j*dy));
}
}
ierr = DMDAVecRestoreArray(da2D,gauss,&gauss_ptr);CHKERRQ(ierr);
// Create the HDF5 viewer
ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD,"gauss.h5",FILE_MODE_WRITE,&H5viewer);CHKERRQ(ierr);
// Write the H5 file
ierr = VecView(gauss,H5viewer);CHKERRQ(ierr);
// Cleaning stage
ierr = PetscViewerDestroy(&H5viewer);CHKERRQ(ierr);
ierr = VecDestroy(&gauss);CHKERRQ(ierr);
ierr = DMDestroy(&da2D);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode createDomain(DM *dm, int nx, int ny){
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,
DMDA_STENCIL_STAR,
nx, ny, PETSC_DECIDE, PETSC_DECIDE,
1, 1, PETSC_NULL, PETSC_NULL, dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void createArrays(simInfo *data)
{
PetscErrorCode ierr;
PetscInt *lx, *ly, m, n;
const PetscInt *lxu, *lyu;
// Create distributed array and get vectors
ierr = PetscPrintf(PETSC_COMM_WORLD, "\nCreate staggered U, V and P vectors [DMDACreate2d, DMDAGetInfo, DMDAGetOwnershipRanges, DMCreateGlobalVector]"); CHKERRV(ierr); hline();
ierr = DMCompositeCreate(PETSC_COMM_WORLD, &(data->pack)); CHKERRV(ierr);
// create u DA
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_STENCIL_BOX, data->nx-1, data->ny, PETSC_DECIDE, PETSC_DECIDE, 1, 1, NULL, NULL, &(data->uda)); CHKERRV(ierr);
ierr = DMCompositeAddDM(data->pack, data->uda); CHKERRV(ierr);
// determine process distribution of v
ierr = DMDAGetInfo(data->uda, NULL, NULL, NULL, NULL, &m, &n, NULL, NULL, NULL, NULL, NULL, NULL, NULL); CHKERRV(ierr);
ierr = DMDAGetOwnershipRanges(data->uda, &lxu, &lyu, NULL); CHKERRV(ierr);
ierr = PetscMalloc(m*sizeof(*lx), &lx); CHKERRV(ierr);
ierr = PetscMalloc(n*sizeof(*ly), &ly); CHKERRV(ierr);
ierr = PetscMemcpy(lx ,lxu, m*sizeof(*lx)); CHKERRV(ierr);
ierr = PetscMemcpy(ly ,lyu, n*sizeof(*ly)); CHKERRV(ierr);
lx[m-1]++;
// create v DA
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_STENCIL_STAR, data->nx, data->ny, m, n, 1, 1, lx, ly, &(data->pda)); CHKERRV(ierr);
// create vectors p and bc2
ierr = DMCreateGlobalVector(data->pda, &(data->pGlobal)); CHKERRV(ierr);
ierr = VecDuplicate(data->pGlobal, &(data->bc2)); CHKERRV(ierr);
ly[n-1]--;
// create p DA
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_STENCIL_BOX, data->nx, data->ny-1, m, n, 1, 1, lx, ly, &(data->vda)); CHKERRV(ierr);
ierr = DMCompositeAddDM(data->pack, data->vda); CHKERRV(ierr);
PetscFree(lx);
PetscFree(ly);
// create vector uPacked
ierr = DMCreateGlobalVector(data->pack, &(data->uPacked)); CHKERRV(ierr);
}
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);
}
int main(int argc, char **argv)
{
PetscErrorCode ierr;
Vec x; /* Solution vector */
TS ts; /* Time-stepping context */
AppCtx user; /* Application context */
Mat J;
PetscViewer viewer;
PetscInitialize(&argc,&argv,"petscopt_ex6", help);
/* Get physics and time parameters */
ierr = Parameter_settings(&user);CHKERRQ(ierr);
/* Create a 2D DA with dof = 1 */
ierr = DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&user.da);CHKERRQ(ierr);
/* Set x and y coordinates */
ierr = DMDASetUniformCoordinates(user.da,user.xmin,user.xmax,user.ymin,user.ymax,NULL,NULL);CHKERRQ(ierr);
/* Get global vector x from DM */
ierr = DMCreateGlobalVector(user.da,&x);CHKERRQ(ierr);
ierr = ini_bou(x,&user);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"ini_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = VecView(x,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
/* Get Jacobian matrix structure from the da */
ierr = DMSetMatType(user.da,MATAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(user.da,&J);CHKERRQ(ierr);
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,J,J,IJacobian,&user);CHKERRQ(ierr);
ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr);
ierr = TSSetDuration(ts,PETSC_DEFAULT,user.tmax);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,user.t0,.005);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSetPostStep(ts,PostStep);CHKERRQ(ierr);
ierr = TSSolve(ts,x);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fin_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = VecView(x,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = DMDestroy(&user.da);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
PetscFinalize();
return 0;
}
int main(int argc, char *argv[])
{
DM da, daX, daY;
DMDALocalInfo info;
MPI_Comm commX, commY;
Vec basisX, basisY;
PetscScalar **arrayX, **arrayY;
const PetscInt *lx, *ly;
PetscInt M = 3, N = 3;
PetscInt p = 1;
PetscInt numGP = 3;
PetscInt dof = 2*(p+1)*numGP;
PetscMPIInt rank, subsize, subrank;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr);
/* Create 2D DMDA */
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_STAR, M, N, PETSC_DECIDE, PETSC_DECIDE, 1, 1, NULL, NULL, &da);CHKERRQ(ierr);
/* Create 1D DMDAs along two directions */
ierr = DMDAGetOwnershipRanges(da, &lx, &ly, NULL);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da, &info);CHKERRQ(ierr);
ierr = DMDAGetProcessorSubsets(da, DMDA_X, &commX);CHKERRQ(ierr);
ierr = DMDAGetProcessorSubsets(da, DMDA_Y, &commY);CHKERRQ(ierr);
ierr = MPI_Comm_size(commX, &subsize);CHKERRQ(ierr);
ierr = MPI_Comm_rank(commX, &subrank);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "[%d]X subrank: %d subsize: %d\n", rank, subrank, subsize);
ierr = MPI_Comm_size(commY, &subsize);CHKERRQ(ierr);
ierr = MPI_Comm_rank(commY, &subrank);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "[%d]Y subrank: %d subsize: %d\n", rank, subrank, subsize);
ierr = DMDACreate1d(commX, DM_BOUNDARY_NONE, M, dof, 1, lx, &daX);CHKERRQ(ierr);
ierr = DMDACreate1d(commY, DM_BOUNDARY_NONE, N, dof, 1, ly, &daY);CHKERRQ(ierr);
/* Create 1D vectors for basis functions */
ierr = DMGetGlobalVector(daX, &basisX);CHKERRQ(ierr);
ierr = DMGetGlobalVector(daY, &basisY);CHKERRQ(ierr);
/* Extract basis functions */
ierr = DMDAVecGetArrayDOF(daX, basisX, &arrayX);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(daY, basisY, &arrayY);CHKERRQ(ierr);
/*arrayX[i][ndof]; */
/*arrayY[j][ndof]; */
ierr = DMDAVecRestoreArrayDOF(daX, basisX, &arrayX);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(daY, basisY, &arrayY);CHKERRQ(ierr);
/* Return basis vectors */
ierr = DMRestoreGlobalVector(daX, &basisX);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(daY, &basisY);CHKERRQ(ierr);
/* Cleanup */
ierr = DMDestroy(&daX);CHKERRQ(ierr);
ierr = DMDestroy(&daY);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/*
Sets up a monitor that will display He as a function of space and cluster size for each time step
*/
PetscErrorCode MyMonitorSetUp(TS ts)
{
DM da;
PetscErrorCode ierr;
PetscInt xi,xs,xm,*idx,M,xj,cnt = 0,dof = 3*N + N*N;
const PetscInt *lx;
Vec C;
MyMonitorCtx *ctx;
PetscBool flg;
IS is;
char ycoor[32];
PetscReal valuebounds[4] = {0, 1.2, 0, 1.2};
PetscFunctionBeginUser;
ierr = PetscOptionsHasName(PETSC_NULL,"-mymonitor",&flg);CHKERRQ(ierr);
if (!flg) PetscFunctionReturn(0);
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = PetscNew(MyMonitorCtx,&ctx);CHKERRQ(ierr);
ierr = PetscViewerDrawOpen(((PetscObject)da)->comm,PETSC_NULL,"",PETSC_DECIDE,PETSC_DECIDE,600,400,&ctx->viewer);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,PETSC_NULL,PETSC_NULL,&xm,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,PETSC_IGNORE,&M,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
ierr = DMDAGetOwnershipRanges(da,&lx,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
ierr = DMDACreate2d(((PetscObject)da)->comm,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,M,N,PETSC_DETERMINE,1,2,1,lx,PETSC_NULL,&ctx->da);CHKERRQ(ierr);
ierr = DMDASetFieldName(ctx->da,0,"He");CHKERRQ(ierr);
ierr = DMDASetFieldName(ctx->da,1,"V");CHKERRQ(ierr);
ierr = DMDASetCoordinateName(ctx->da,0,"X coordinate direction");CHKERRQ(ierr);
ierr = PetscSNPrintf(ycoor,32,"%D ... Cluster size ... 1",N);CHKERRQ(ierr);
ierr = DMDASetCoordinateName(ctx->da,1,ycoor);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(ctx->da,&ctx->He);CHKERRQ(ierr);
ierr = PetscMalloc(2*N*xm*sizeof(PetscInt),&idx);CHKERRQ(ierr);
cnt = 0;
for (xj=0; xj<N; xj++) {
for (xi=xs; xi<xs+xm; xi++) {
idx[cnt++] = dof*xi + xj;
idx[cnt++] = dof*xi + xj + N;
}
}
ierr = ISCreateGeneral(((PetscObject)ts)->comm,2*N*xm,idx,PETSC_OWN_POINTER,&is);CHKERRQ(ierr);
ierr = TSGetSolution(ts,&C);CHKERRQ(ierr);
ierr = VecScatterCreate(C,is,ctx->He,PETSC_NULL,&ctx->scatter);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
/* sets the bounds on the contour plot values so the colors mean the same thing for different timesteps */
ierr = PetscViewerDrawSetBounds(ctx->viewer,2,valuebounds);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,MyMonitorMonitor,ctx,MyMonitorDestroy);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
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;
DMDABoundaryType bx=DMDA_BOUNDARY_NONE,by=DMDA_BOUNDARY_NONE,bz=DMDA_BOUNDARY_NONE;
DMDAStencilType stype = DMDA_STENCIL_BOX;
Mat A;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
/* Read options */
ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-N",&N,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-P",&P,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-p",&p,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-dim",&dim,PETSC_NULL);CHKERRQ(ierr);
/* Create distributed array and get vectors */
if (dim == 1) {
ierr = DMDACreate1d(PETSC_COMM_WORLD,bx,M,1,1,PETSC_NULL,&dac);CHKERRQ(ierr);
} else if (dim == 2) {
ierr = DMDACreate2d(PETSC_COMM_WORLD,bx,by,stype,M,N,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_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,PETSC_NULL,PETSC_NULL,PETSC_NULL,&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);
ierr = MatViewFromOptions(A,"-mat_view");CHKERRQ(ierr);
/* Free memory */
ierr = DMDestroy(&dac);CHKERRQ(ierr);
ierr = DMDestroy(&daf);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc, char **argv)
{
PetscErrorCode ierr;
Vec x; /* Solution vector */
TS ts; /* Time-stepping context */
AppCtx user; /* Application context */
PetscViewer viewer;
PetscInitialize(&argc,&argv,"petscopt_ex7", help);
/* Get physics and time parameters */
ierr = Parameter_settings(&user);CHKERRQ(ierr);
/* Create a 2D DA with dof = 1 */
ierr = DMDACreate2d(PETSC_COMM_WORLD,user.bx,user.by,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,user.st_width,NULL,NULL,&user.da);CHKERRQ(ierr);
/* Set x and y coordinates */
ierr = DMDASetUniformCoordinates(user.da,user.xmin,user.xmax,user.ymin,user.ymax,0,0);CHKERRQ(ierr);
ierr = DMDASetCoordinateName(user.da,0,"X - the angle");
ierr = DMDASetCoordinateName(user.da,1,"Y - the speed");
/* Get global vector x from DM */
ierr = DMCreateGlobalVector(user.da,&x);CHKERRQ(ierr);
ierr = ini_bou(x,&user);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"ini_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = VecView(x,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetDM(ts,user.da);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr);
/* ierr = TSSetIJacobian(ts,NULL,NULL,IJacobian,&user);CHKERRQ(ierr); */
ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,.005);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSetPostStep(ts,PostStep);CHKERRQ(ierr);
ierr = TSSolve(ts,x);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fin_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = VecView(x,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = DMDestroy(&user.da);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
PetscFinalize();
return 0;
}
int main(int argc,char **argv) {
PetscErrorCode ierr;
SNES snes;
Vec u;
DMDALocalInfo info;
Ctx user;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = configureCtx(&user); CHKERRQ(ierr);
ierr = DMDACreate2d(PETSC_COMM_WORLD,
DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,
DMDA_STENCIL_STAR,
-3,-3,
PETSC_DECIDE,PETSC_DECIDE,
1,1,
NULL,NULL,
&user.da); CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(user.da,-1.0,1.0,-1.0,1.0,0.0,1.0); CHKERRQ(ierr);
ierr = DMSetApplicationContext(user.da,&user); CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(user.da,&info); CHKERRQ(ierr);
if ((info.mx < 2) || (info.my < 2)) {
SETERRQ(PETSC_COMM_WORLD,1,"grid too coarse ... require (mx,my) > (2,2)");
}
ierr = DMCreateGlobalVector(user.da,&u); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)u,"u_vec");CHKERRQ(ierr);
ierr = formInitial(&info,&user,u); CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&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 = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,u); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,
"done on %d x %d x %d grid with eps=%g ...\n",
info.mx,info.my,info.mz,user.eps); CHKERRQ(ierr);
VecDestroy(&u);
SNESDestroy(&snes); DMDestroy(&user.da);
ierr = PetscFinalize(); CHKERRQ(ierr);
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 = -8, N = -8,stencil_width = 1, dof = 1,m,n,xstart,ystart,i,j,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 = DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_MIRROR,DMDA_BOUNDARY_MIRROR,DMDA_STENCIL_STAR,M,N,PETSC_DECIDE,PETSC_DECIDE,dof,stencil_width,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xstart,&ystart,0,&m,&n,0);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,global,&vglobal);CHKERRQ(ierr);
for (j=ystart; j<ystart+n; j++) {
for (i=xstart; i<xstart+m; i++) {
for (c=0; c<dof; c++) {
vglobal[j][i][c] = 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;
}
int main(int argc,char **argv)
{
Vec u,xy;
DM da;
PetscErrorCode ierr;
PetscInt m = 10, n = 10, dof = 2;
PF pf;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);
CHKERRQ(ierr);
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,m,n,PETSC_DECIDE,PETSC_DECIDE,dof,1,0,0,&da);
CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,1.0);
CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&u);
CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&xy);
CHKERRQ(ierr);
ierr = DMDACreatePF(da,&pf);
CHKERRQ(ierr);
ierr = PFSet(pf,myfunction,0,0,0,0);
CHKERRQ(ierr);
ierr = PFSetFromOptions(pf);
CHKERRQ(ierr);
ierr = PFApplyVec(pf,xy,u);
CHKERRQ(ierr);
ierr = VecView(u,PETSC_VIEWER_DRAW_WORLD);
CHKERRQ(ierr);
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = PFDestroy(&pf);
CHKERRQ(ierr);
ierr = DMDestroy(&da);
CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
TS ts;
SNES snes;
SNESLineSearch linesearch;
Vec x;
AppCtx ctx;
PetscErrorCode ierr;
DM da;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = SetFromOptions(&ctx);CHKERRQ(ierr);
ierr = TSCreate(PETSC_COMM_WORLD, &ts);CHKERRQ(ierr);
ierr = TSSetType(ts,TSCN);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetIFunction(ts, NULL, FormIFunction, &ctx);CHKERRQ(ierr);
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,N_SPECIES,1,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr);
ierr = DMDASetFieldName(da,0,"species A");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,1,"species B");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,2,"species C");CHKERRQ(ierr);
ierr = DMSetApplicationContext(da,&ctx);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);
ierr = FormInitialGuess(da, &ctx, x);CHKERRQ(ierr);
ierr = TSSetDM(ts, da);CHKERRQ(ierr);
ierr = TSSetDuration(ts,10000,1000.0);CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,1.0);CHKERRQ(ierr);
ierr = TSSetSolution(ts,x);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
ierr = SNESGetLineSearch(snes,&linesearch);CHKERRQ(ierr);
ierr = SNESLineSearchSetPostCheck(linesearch, ReactingFlowPostCheck, (void*)&ctx);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = TSSolve(ts,x);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
PetscFunctionReturn(0);
}
static PetscErrorCode ComputeMapping(DomainData dd,ISLocalToGlobalMapping *isg2lmap)
{
PetscErrorCode ierr;
DM da;
AO ao;
DMBoundaryType bx = DM_BOUNDARY_NONE,by = DM_BOUNDARY_NONE, bz = DM_BOUNDARY_NONE;
DMDAStencilType stype = DMDA_STENCIL_BOX;
ISLocalToGlobalMapping temp_isg2lmap;
PetscInt i,j,k,ig,jg,kg,lindex,gindex,localsize;
PetscInt *global_indices;
PetscFunctionBeginUser;
/* Not an efficient mapping: this function computes a very simple lexicographic mapping
just to illustrate the creation of a MATIS object */
localsize = dd.xm_l*dd.ym_l*dd.zm_l;
ierr = PetscMalloc1(localsize,&global_indices);CHKERRQ(ierr);
for (k=0; k<dd.zm_l; k++) {
kg=dd.startz+k;
for (j=0; j<dd.ym_l; j++) {
jg=dd.starty+j;
for (i=0; i<dd.xm_l; i++) {
ig =dd.startx+i;
lindex =k*dd.xm_l*dd.ym_l+j*dd.xm_l+i;
gindex =kg*dd.xm*dd.ym+jg*dd.xm+ig;
global_indices[lindex]=gindex;
}
}
}
if (dd.dim==3) {
ierr = DMDACreate3d(dd.gcomm,bx,by,bz,stype,dd.xm,dd.ym,dd.zm,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,NULL,&da);CHKERRQ(ierr);
} else if (dd.dim==2) {
ierr = DMDACreate2d(dd.gcomm,bx,by,stype,dd.xm,dd.ym,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&da);CHKERRQ(ierr);
} else {
ierr = DMDACreate1d(dd.gcomm,bx,dd.xm,1,1,NULL,&da);CHKERRQ(ierr);
}
ierr = DMDASetAOType(da,AOMEMORYSCALABLE);CHKERRQ(ierr);
ierr = DMDAGetAO(da,&ao);CHKERRQ(ierr);
ierr = AOApplicationToPetsc(ao,dd.xm_l*dd.ym_l*dd.zm_l,global_indices);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingCreate(dd.gcomm,1,localsize,global_indices,PETSC_OWN_POINTER,&temp_isg2lmap);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
*isg2lmap = temp_isg2lmap;
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool interpolate = user->interpolate;
PetscReal refinementLimit = user->refinementLimit;
const char *partitioner = "chaco";
PetscErrorCode ierr;
PetscFunctionBegin;
if (user->simplex) {
DM refinedMesh = NULL;
DM distributedMesh = NULL;
ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr);
/* Refine mesh using a volume constraint */
ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr);
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, partitioner, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
ierr = PetscObjectSetName((PetscObject) *dm, "Simplical Mesh");CHKERRQ(ierr);
} else {
switch (user->dim) {
case 2:
ierr = DMDACreate2d(comm, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_STENCIL_BOX, -3, -3, PETSC_DETERMINE, PETSC_DETERMINE, 1, 1, NULL, NULL, dm);CHKERRQ(ierr);
ierr = DMDASetVertexCoordinates(*dm, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr);
break;
default:
SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cannot create structured mesh of dimension %d", dim);
}
ierr = PetscObjectSetName((PetscObject) *dm, "Hexahedral Mesh");CHKERRQ(ierr);
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
TS ts;
Vec x,c;
PetscErrorCode ierr;
DM da;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = TSCreate(PETSC_COMM_WORLD, &ts);CHKERRQ(ierr);
ierr = TSSetType(ts,TSCN);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr);
ierr = DMDASetFieldName(da,0,"Heat");CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);
ierr = FormInitialGuess(da,PETSC_NULL,x);CHKERRQ(ierr);
ierr = DMDATSSetIFunctionLocal(da,INSERT_VALUES,(PetscErrorCode (*)(DMDALocalInfo*,PetscReal,void*,void*,void*,void*))FormIFunctionLocal,PETSC_NULL);CHKERRQ(ierr);
/* set up the coefficient */
ierr = DMGetNamedGlobalVector(da,"coefficient",&c);CHKERRQ(ierr);
ierr = FormDiffusionCoefficient(da,PETSC_NULL,c);CHKERRQ(ierr);
ierr = DMRestoreNamedGlobalVector(da,"coefficient",&c);CHKERRQ(ierr);
ierr = DMCoarsenHookAdd(da,PETSC_NULL,CoefficientRestrictHook,ts);CHKERRQ(ierr);
ierr = DMSubDomainHookAdd(da,PETSC_NULL,CoefficientSubDomainRestrictHook,ts);CHKERRQ(ierr);
ierr = TSSetDM(ts, da);CHKERRQ(ierr);
ierr = TSSetDuration(ts,10000,1000.0);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,0.05);CHKERRQ(ierr);
ierr = TSSetSolution(ts,x);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSolve(ts,x);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
KSP ksp;
DM da;
Vec x, xNew;
UserContext user;
PetscErrorCode ierr;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,3,3,PETSC_DECIDE,PETSC_DECIDE,1,1,0,0,&da);CHKERRQ(ierr);
ierr = DMSetApplicationContext(da, &user);CHKERRQ(ierr);
ierr = KSPSetDM(ksp, da);CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD, "", "Options for PCICE", "DM");
user.phi = 0.5;
ierr = PetscOptionsScalar("-phi", "The time weighting parameter", "ex31.c", user.phi, &user.phi, NULL);CHKERRQ(ierr);
user.dt = 0.1;
ierr = PetscOptionsScalar("-dt", "The time step", "ex31.c", user.dt, &user.dt, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
ierr = CreateStructures(da, &user);CHKERRQ(ierr);
ierr = ComputePredictor(da, &user);CHKERRQ(ierr);
ierr = KSPSetComputeRHS(ksp,ComputeRHS,&user);CHKERRQ(ierr);
ierr = KSPSetComputeOperators(ksp,ComputeMatrix,&user);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPSolve(ksp, NULL, NULL);CHKERRQ(ierr);
ierr = KSPGetSolution(ksp, &x);CHKERRQ(ierr);
ierr = VecDuplicate(x, &xNew);CHKERRQ(ierr);
ierr = ComputeCorrector(da, x, xNew);CHKERRQ(ierr);
ierr = VecDestroy(&xNew);CHKERRQ(ierr);
ierr = DestroyStructures(da, &user);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscErrorCode ierr;
PetscFunctionBegin;
switch(dim) {
case 2:
ierr = DMDACreate2d(comm, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_STENCIL_STAR, -4, -4, PETSC_DECIDE, PETSC_DECIDE, 2, 1, PETSC_NULL, PETSC_NULL, dm);CHKERRQ(ierr);
break;
case 3:
ierr = DMDACreate3d(comm, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_STENCIL_STAR, -4, -4, -4, PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, 2, 1, PETSC_NULL, PETSC_NULL, PETSC_NULL, dm);CHKERRQ(ierr);
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Could not create mesh for dimension %d", dim);
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMDASetFieldName(*dm, 0, "velocity");CHKERRQ(ierr);
ierr = DMDASetFieldName(*dm, 1, "pressure");CHKERRQ(ierr);
user->dm = *dm;
PetscFunctionReturn(0);
}
int main(int argc,char *argv[])
{
PetscErrorCode ierr;
DM da;
PetscInt dim = 2,m,n,p,i;
const PetscInt *lx,*ly,*lz;
PetscMPIInt rank,size;
ierr = PetscInitialize(&argc,&argv,0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,0,"-dim",&dim,0);CHKERRQ(ierr);
switch (dim) {
case 2:
ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR, 3,5,PETSC_DECIDE,PETSC_DECIDE,2,1,NULL,NULL,&da);CHKERRQ(ierr);
break;
case 3:
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR, 3,5,7,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,2,1,NULL,NULL,NULL,&da);CHKERRQ(ierr);
break;
default: SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"No support for %D dimensions",dim);
}
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMDAGetInfo(da, 0, 0,0,0, &m,&n,&p, 0,0, 0,0,0,0);CHKERRQ(ierr);
ierr = DMDAGetOwnershipRanges(da,&lx,&ly,&lz);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
for (i=0; i<size; i++) {
ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
if (i == rank) {
ierr = PetscViewerASCIIPrintf(PETSC_VIEWER_STDOUT_SELF,"[%d] lx ly%s\n",rank,dim>2 ? " lz" : "");CHKERRQ(ierr);
ierr = PetscIntView(m,lx,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = PetscIntView(n,ly,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
if (dim > 2) {ierr = PetscIntView(n,lz,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
}
ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr);
}
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
