PetscErrorCode DMPatchCreateGrid(MPI_Comm comm, PetscInt dim, MatStencil patchSize, MatStencil commSize, MatStencil gridSize, DM *dm)
{
DM_Patch *mesh;
DM da;
PetscInt dof = 1, width = 1;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPatchCreate(comm, dm);CHKERRQ(ierr);
mesh = (DM_Patch*) (*dm)->data;
if (dim < 2) {
gridSize.j = 1;
patchSize.j = 1;
}
if (dim < 3) {
gridSize.k = 1;
patchSize.k = 1;
}
ierr = DMCreate(comm, &da);
ierr = DMSetType(da, DMDA);
ierr = DMDASetDim(da, dim);CHKERRQ(ierr);
ierr = DMDASetSizes(da, gridSize.i, gridSize.j, gridSize.k);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE);CHKERRQ(ierr);
ierr = DMDASetDof(da, dof);CHKERRQ(ierr);
ierr = DMDASetStencilType(da, DMDA_STENCIL_BOX);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, width);CHKERRQ(ierr);
mesh->dmCoarse = da;
ierr = DMPatchSetPatchSize(*dm, patchSize);CHKERRQ(ierr);
ierr = DMPatchSetCommSize(*dm, commSize);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMDACreate2d(MPI_Comm comm,DMDABoundaryType bx,DMDABoundaryType by,DMDAStencilType stencil_type,
PetscInt M,PetscInt N,PetscInt m,PetscInt n,PetscInt dof,PetscInt s,const PetscInt lx[],const PetscInt ly[],DM *da)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMDACreate(comm, da);
CHKERRQ(ierr);
ierr = DMDASetDim(*da, 2);
CHKERRQ(ierr);
ierr = DMDASetSizes(*da, M, N, 1);
CHKERRQ(ierr);
ierr = DMDASetNumProcs(*da, m, n, PETSC_DECIDE);
CHKERRQ(ierr);
ierr = DMDASetBoundaryType(*da, bx, by, DMDA_BOUNDARY_NONE);
CHKERRQ(ierr);
ierr = DMDASetDof(*da, dof);
CHKERRQ(ierr);
ierr = DMDASetStencilType(*da, stencil_type);
CHKERRQ(ierr);
ierr = DMDASetStencilWidth(*da, s);
CHKERRQ(ierr);
ierr = DMDASetOwnershipRanges(*da, lx, ly, NULL);
CHKERRQ(ierr);
/* This violates the behavior for other classes, but right now users expect negative dimensions to be handled this way */
ierr = DMSetFromOptions(*da);
CHKERRQ(ierr);
ierr = DMSetUp(*da);
CHKERRQ(ierr);
ierr = DMViewFromOptions(*da,"-dm_view");
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMCreateFieldDecomposition_DA(DM dm, PetscInt *len,char ***namelist, IS **islist, DM** dmlist)
{
PetscInt i;
PetscErrorCode ierr;
DM_DA *dd = (DM_DA*)dm->data;
PetscInt dof = dd->w;
PetscFunctionBegin;
if(len) *len = dof;
if (islist) {
Vec v;
PetscInt rstart,n;
ierr = DMGetGlobalVector(dm,&v);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(v,&rstart,PETSC_NULL);CHKERRQ(ierr);
ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dm,&v);CHKERRQ(ierr);
ierr = PetscMalloc(dof*sizeof(IS),islist);CHKERRQ(ierr);
for (i=0; i<dof; i++) {
ierr = ISCreateStride(((PetscObject)dm)->comm,n/dof,rstart+i,dof,&(*islist)[i]);CHKERRQ(ierr);
}
}
if (namelist) {
ierr = PetscMalloc(dof*sizeof(const char *), namelist);CHKERRQ(ierr);
if (dd->fieldname) {
for (i=0; i<dof; i++) {
ierr = PetscStrallocpy(dd->fieldname[i],&(*namelist)[i]);CHKERRQ(ierr);
}
} else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Currently DMDA must have fieldnames");
}
if (dmlist) {
DM da;
ierr = DMDACreate(((PetscObject)dm)->comm, &da);CHKERRQ(ierr);
ierr = DMDASetDim(da, dd->dim);CHKERRQ(ierr);
ierr = DMDASetSizes(da, dd->M, dd->N, dd->P);CHKERRQ(ierr);
ierr = DMDASetNumProcs(da, dd->m, dd->n, dd->p);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, dd->bx, dd->by, dd->bz);CHKERRQ(ierr);
ierr = DMDASetDof(da, 1);CHKERRQ(ierr);
ierr = DMDASetStencilType(da, dd->stencil_type);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, dd->s);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = PetscMalloc(dof*sizeof(DM),dmlist);CHKERRQ(ierr);
for (i=0; i<dof-1; i++) {ierr = PetscObjectReference((PetscObject)da);CHKERRQ(ierr);}
for (i=0; i<dof; i++) (*dmlist)[i] = da;
}
PetscFunctionReturn(0);
}
PetscErrorCode DMLoad_DA(DM da,PetscViewer viewer)
{
PetscErrorCode ierr;
PetscInt dim,m,n,p,dof,swidth;
DMDAStencilType stencil;
DMDABoundaryType bx,by,bz;
PetscInt classid = DM_FILE_CLASSID,subclassid = DMDA_FILE_CLASSID;
PetscBool coors;
DM dac;
Vec c;
PetscFunctionBegin;
ierr = PetscViewerBinaryRead(viewer,&classid,1,PETSC_INT);CHKERRQ(ierr);
if (classid != DM_FILE_CLASSID) SETERRQ(((PetscObject)da)->comm,PETSC_ERR_ARG_WRONG,"Not DM next in file");
ierr = PetscViewerBinaryRead(viewer,&subclassid,1,PETSC_INT);CHKERRQ(ierr);
if (subclassid != DMDA_FILE_CLASSID) SETERRQ(((PetscObject)da)->comm,PETSC_ERR_ARG_WRONG,"Not DM DA next in file");
ierr = PetscViewerBinaryRead(viewer,&dim,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&m,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&n,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&p,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&dof,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&swidth,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&bx,1,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&by,1,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&bz,1,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&stencil,1,PETSC_ENUM);CHKERRQ(ierr);
ierr = DMDASetDim(da, dim);CHKERRQ(ierr);
ierr = DMDASetSizes(da, m,n,p);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, bx, by, bz);CHKERRQ(ierr);
ierr = DMDASetDof(da, dof);CHKERRQ(ierr);
ierr = DMDASetStencilType(da, stencil);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, swidth);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&coors,1,PETSC_ENUM);CHKERRQ(ierr);
if (coors) {
ierr = DMDAGetCoordinateDA(da,&dac);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dac,&c);CHKERRQ(ierr);
ierr = VecLoad(c,viewer);CHKERRQ(ierr);
ierr = DMDASetCoordinates(da,c);CHKERRQ(ierr);
ierr = VecDestroy(&c);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
KSP ksp;
PC pc;
Vec x,b;
DM da;
Mat A;
PetscInt dof=1;
PetscBool flg;
PetscScalar zero=0.0;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = PetscOptionsGetInt(PETSC_NULL,"-dof",&dof,PETSC_NULL);CHKERRQ(ierr);
ierr = DMDACreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr);
ierr = DMDASetDim(da,3);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE);CHKERRQ(ierr);
ierr = DMDASetStencilType(da,DMDA_STENCIL_STAR);CHKERRQ(ierr);
ierr = DMDASetSizes(da,3,3,3);CHKERRQ(ierr);
ierr = DMDASetNumProcs(da,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = DMDASetDof(da,dof);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da,1);CHKERRQ(ierr);
ierr = DMDASetOwnershipRanges(da,PETSC_NULL,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&b);CHKERRQ(ierr);
ierr = DMCreateMatrix(da,MATAIJ,&A);CHKERRQ(ierr);
ierr = VecSet(b,zero);CHKERRQ(ierr);
/* Test sbaij matrix */
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(PETSC_NULL,"-test_sbaij",&flg,PETSC_NULL);CHKERRQ(ierr);
if (flg) {
Mat sA;
ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
A = sA;
}
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,A,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetDM(pc,(DM)da);CHKERRQ(ierr);
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
/* check final residual */
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(PETSC_NULL, "-check_final_residual", &flg,PETSC_NULL);CHKERRQ(ierr);
if (flg){
Vec b1;
PetscReal norm;
ierr = KSPGetSolution(ksp,&x);CHKERRQ(ierr);
ierr = VecDuplicate(b,&b1);CHKERRQ(ierr);
ierr = MatMult(A,x,b1);CHKERRQ(ierr);
ierr = VecAXPY(b1,-1.0,b);CHKERRQ(ierr);
ierr = VecNorm(b1,NORM_2,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Final residual %g\n",norm);CHKERRQ(ierr);
ierr = VecDestroy(&b1);CHKERRQ(ierr);
}
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode DMCoarsen_DA(DM da, MPI_Comm comm,DM *daref)
{
PetscErrorCode ierr;
PetscInt M,N,P,i;
DM da2;
DM_DA *dd = (DM_DA*)da->data,*dd2;
PetscFunctionBegin;
PetscValidHeaderSpecific(da,DM_CLASSID,1);
PetscValidPointer(daref,3);
if (dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0){
M = dd->M / dd->coarsen_x;
} else {
M = 1 + (dd->M - 1) / dd->coarsen_x;
}
if (dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0){
if (dd->dim > 1) {
N = dd->N / dd->coarsen_y;
} else {
N = 1;
}
} else {
N = 1 + (dd->N - 1) / dd->coarsen_y;
}
if (dd->bz == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0){
if (dd->dim > 2) {
P = dd->P / dd->coarsen_z;
} else {
P = 1;
}
} else {
P = 1 + (dd->P - 1) / dd->coarsen_z;
}
ierr = DMDACreate(((PetscObject)da)->comm,&da2);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(da2,((PetscObject)da)->prefix);CHKERRQ(ierr);
ierr = DMDASetDim(da2,dd->dim);CHKERRQ(ierr);
ierr = DMDASetSizes(da2,M,N,P);CHKERRQ(ierr);
ierr = DMDASetNumProcs(da2,dd->m,dd->n,dd->p);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da2,dd->bx,dd->by,dd->bz);CHKERRQ(ierr);
ierr = DMDASetDof(da2,dd->w);CHKERRQ(ierr);
ierr = DMDASetStencilType(da2,dd->stencil_type);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da2,dd->s);CHKERRQ(ierr);
if (dd->dim == 3) {
PetscInt *lx,*ly,*lz;
ierr = PetscMalloc3(dd->m,PetscInt,&lx,dd->n,PetscInt,&ly,dd->p,PetscInt,&lz);CHKERRQ(ierr);
ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_x,dd->m,dd->lx,lx);CHKERRQ(ierr);
ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_y,dd->n,dd->ly,ly);CHKERRQ(ierr);
ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->bz == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_z,dd->p,dd->lz,lz);CHKERRQ(ierr);
ierr = DMDASetOwnershipRanges(da2,lx,ly,lz);CHKERRQ(ierr);
ierr = PetscFree3(lx,ly,lz);CHKERRQ(ierr);
} else if (dd->dim == 2) {
PetscInt *lx,*ly;
ierr = PetscMalloc2(dd->m,PetscInt,&lx,dd->n,PetscInt,&ly);CHKERRQ(ierr);
ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_x,dd->m,dd->lx,lx);CHKERRQ(ierr);
ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_y,dd->n,dd->ly,ly);CHKERRQ(ierr);
ierr = DMDASetOwnershipRanges(da2,lx,ly,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscFree2(lx,ly);CHKERRQ(ierr);
} else if (dd->dim == 1) {
PetscInt *lx;
ierr = PetscMalloc(dd->m*sizeof(PetscInt),&lx);CHKERRQ(ierr);
ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_x,dd->m,dd->lx,lx);CHKERRQ(ierr);
ierr = DMDASetOwnershipRanges(da2,lx,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscFree(lx);CHKERRQ(ierr);
}
dd2 = (DM_DA*)da2->data;
/* allow overloaded (user replaced) operations to be inherited by refinement clones; why are only some inherited and not all? */
/* da2->ops->createinterpolation = da->ops->createinterpolation; copying this one causes trouble for DMSetVI */
da2->ops->creatematrix = da->ops->creatematrix;
da2->ops->getcoloring = da->ops->getcoloring;
dd2->interptype = dd->interptype;
/* copy fill information if given */
if (dd->dfill) {
ierr = PetscMalloc((dd->dfill[dd->w]+dd->w+1)*sizeof(PetscInt),&dd2->dfill);CHKERRQ(ierr);
ierr = PetscMemcpy(dd2->dfill,dd->dfill,(dd->dfill[dd->w]+dd->w+1)*sizeof(PetscInt));CHKERRQ(ierr);
}
if (dd->ofill) {
ierr = PetscMalloc((dd->ofill[dd->w]+dd->w+1)*sizeof(PetscInt),&dd2->ofill);CHKERRQ(ierr);
ierr = PetscMemcpy(dd2->ofill,dd->ofill,(dd->ofill[dd->w]+dd->w+1)*sizeof(PetscInt));CHKERRQ(ierr);
}
/* copy the refine information */
dd2->coarsen_x = dd2->refine_x = dd->coarsen_x;
dd2->coarsen_y = dd2->refine_y = dd->coarsen_y;
dd2->coarsen_z = dd2->refine_z = dd->coarsen_z;
/* copy vector type information */
ierr = PetscFree(da2->vectype);CHKERRQ(ierr);
ierr = PetscStrallocpy(da->vectype,(char**)&da2->vectype);CHKERRQ(ierr);
dd2->lf = dd->lf;
dd2->lj = dd->lj;
da2->leveldown = da->leveldown + 1;
da2->levelup = da->levelup;
ierr = DMSetFromOptions(da2);CHKERRQ(ierr);
ierr = DMSetUp(da2);CHKERRQ(ierr);
ierr = DMViewFromOptions(da2,"-dm_view");CHKERRQ(ierr);
/* inject coordinates if they are set on the fine grid */
if (da->coordinates) {
DM cdaf,cdac;
Vec coordsc,coordsf;
VecScatter inject;
ierr = DMGetCoordinateDM(da,&cdaf);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&coordsf);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da2,&cdac);CHKERRQ(ierr);
/* force creation of the coordinate vector */
ierr = DMDASetUniformCoordinates(da2,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
ierr = DMGetCoordinates(da2,&coordsc);CHKERRQ(ierr);
ierr = DMCreateInjection(cdac,cdaf,&inject);CHKERRQ(ierr);
ierr = VecScatterBegin(inject,coordsf,coordsc,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(inject ,coordsf,coordsc,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterDestroy(&inject);CHKERRQ(ierr);
}
for (i=0; i<da->bs; i++) {
const char *fieldname;
ierr = DMDAGetFieldName(da,i,&fieldname);CHKERRQ(ierr);
ierr = DMDASetFieldName(da2,i,fieldname);CHKERRQ(ierr);
}
*daref = da2;
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
KSP ksp;
PC pc;
Vec x,b;
DM da;
Mat A,Atrans;
PetscInt dof=1,M=-8;
PetscBool flg,trans=PETSC_FALSE;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = PetscOptionsGetInt(PETSC_NULL,"-dof",&dof,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(PETSC_NULL,"-trans",&trans,PETSC_NULL);CHKERRQ(ierr);
ierr = DMDACreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr);
ierr = DMDASetDim(da,3);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE);CHKERRQ(ierr);
ierr = DMDASetStencilType(da,DMDA_STENCIL_STAR);CHKERRQ(ierr);
ierr = DMDASetSizes(da,M,M,M);CHKERRQ(ierr);
ierr = DMDASetNumProcs(da,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = DMDASetDof(da,dof);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da,1);CHKERRQ(ierr);
ierr = DMDASetOwnershipRanges(da,PETSC_NULL,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&b);CHKERRQ(ierr);
ierr = ComputeRHS(da,b);CHKERRQ(ierr);
ierr = DMCreateMatrix(da,MATBAIJ,&A);CHKERRQ(ierr);
ierr = ComputeMatrix(da,A);CHKERRQ(ierr);
/* A is non-symmetric. Make A = 0.5*(A + Atrans) symmetric for testing icc and cholesky */
ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&Atrans);CHKERRQ(ierr);
ierr = MatAXPY(A,1.0,Atrans,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatScale(A,0.5);CHKERRQ(ierr);
ierr = MatDestroy(&Atrans);CHKERRQ(ierr);
/* Test sbaij matrix */
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(PETSC_NULL, "-test_sbaij1", &flg,PETSC_NULL);CHKERRQ(ierr);
if (flg){
Mat sA;
PetscBool issymm;
ierr = MatIsTranspose(A,A,0.0,&issymm);CHKERRQ(ierr);
if (issymm) {
ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
} else {
printf("Warning: A is non-symmetric\n");
}
ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
A = sA;
}
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,A,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetDM(pc,(DM)da);CHKERRQ(ierr);
if (trans) {
ierr = KSPSolveTranspose(ksp,b,x);CHKERRQ(ierr);
} else {
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
}
/* check final residual */
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(PETSC_NULL, "-check_final_residual", &flg,PETSC_NULL);CHKERRQ(ierr);
if (flg){
Vec b1;
PetscReal norm;
ierr = KSPGetSolution(ksp,&x);CHKERRQ(ierr);
ierr = VecDuplicate(b,&b1);CHKERRQ(ierr);
ierr = MatMult(A,x,b1);CHKERRQ(ierr);
ierr = VecAXPY(b1,-1.0,b);CHKERRQ(ierr);
ierr = VecNorm(b1,NORM_2,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Final residual %g\n",norm);CHKERRQ(ierr);
ierr = VecDestroy(&b1);CHKERRQ(ierr);
}
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PETSC_EXTERN void PETSC_STDCALL dmdasetdim_(DM da,PetscInt *dim, int *__ierr ){
*__ierr = DMDASetDim(
(DM)PetscToPointer((da) ),*dim);
}
PetscErrorCode DMRefine_DA(DM da,MPI_Comm comm,DM *daref)
{
PetscErrorCode ierr;
PetscInt M,N,P,i;
DM da2;
DM_DA *dd = (DM_DA*)da->data,*dd2;
PetscFunctionBegin;
PetscValidHeaderSpecific(da,DM_CLASSID,1);
PetscValidPointer(daref,3);
if (dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0) {
M = dd->refine_x*dd->M;
} else {
M = 1 + dd->refine_x*(dd->M - 1);
}
if (dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0) {
if (dd->dim > 1) {
N = dd->refine_y*dd->N;
} else {
N = 1;
}
} else {
N = 1 + dd->refine_y*(dd->N - 1);
}
if (dd->bz == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0) {
if (dd->dim > 2) {
P = dd->refine_z*dd->P;
} else {
P = 1;
}
} else {
P = 1 + dd->refine_z*(dd->P - 1);
}
ierr = DMDACreate(PetscObjectComm((PetscObject)da),&da2);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(da2,((PetscObject)da)->prefix);CHKERRQ(ierr);
ierr = DMDASetDim(da2,dd->dim);CHKERRQ(ierr);
ierr = DMDASetSizes(da2,M,N,P);CHKERRQ(ierr);
ierr = DMDASetNumProcs(da2,dd->m,dd->n,dd->p);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da2,dd->bx,dd->by,dd->bz);CHKERRQ(ierr);
ierr = DMDASetDof(da2,dd->w);CHKERRQ(ierr);
ierr = DMDASetStencilType(da2,dd->stencil_type);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da2,dd->s);CHKERRQ(ierr);
if (dd->dim == 3) {
PetscInt *lx,*ly,*lz;
ierr = PetscMalloc3(dd->m,&lx,dd->n,&ly,dd->p,&lz);CHKERRQ(ierr);
ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_x,dd->m,dd->lx,lx);CHKERRQ(ierr);
ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_y,dd->n,dd->ly,ly);CHKERRQ(ierr);
ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->bz == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_z,dd->p,dd->lz,lz);CHKERRQ(ierr);
ierr = DMDASetOwnershipRanges(da2,lx,ly,lz);CHKERRQ(ierr);
ierr = PetscFree3(lx,ly,lz);CHKERRQ(ierr);
} else if (dd->dim == 2) {
PetscInt *lx,*ly;
ierr = PetscMalloc2(dd->m,&lx,dd->n,&ly);CHKERRQ(ierr);
ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_x,dd->m,dd->lx,lx);CHKERRQ(ierr);
ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_y,dd->n,dd->ly,ly);CHKERRQ(ierr);
ierr = DMDASetOwnershipRanges(da2,lx,ly,NULL);CHKERRQ(ierr);
ierr = PetscFree2(lx,ly);CHKERRQ(ierr);
} else if (dd->dim == 1) {
PetscInt *lx;
ierr = PetscMalloc1(dd->m,&lx);CHKERRQ(ierr);
ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_x,dd->m,dd->lx,lx);CHKERRQ(ierr);
ierr = DMDASetOwnershipRanges(da2,lx,NULL,NULL);CHKERRQ(ierr);
ierr = PetscFree(lx);CHKERRQ(ierr);
}
dd2 = (DM_DA*)da2->data;
/* allow overloaded (user replaced) operations to be inherited by refinement clones */
da2->ops->creatematrix = da->ops->creatematrix;
/* da2->ops->createinterpolation = da->ops->createinterpolation; this causes problem with SNESVI */
da2->ops->getcoloring = da->ops->getcoloring;
dd2->interptype = dd->interptype;
/* copy fill information if given */
if (dd->dfill) {
ierr = PetscMalloc1((dd->dfill[dd->w]+dd->w+1),&dd2->dfill);CHKERRQ(ierr);
ierr = PetscMemcpy(dd2->dfill,dd->dfill,(dd->dfill[dd->w]+dd->w+1)*sizeof(PetscInt));CHKERRQ(ierr);
}
if (dd->ofill) {
ierr = PetscMalloc1((dd->ofill[dd->w]+dd->w+1),&dd2->ofill);CHKERRQ(ierr);
ierr = PetscMemcpy(dd2->ofill,dd->ofill,(dd->ofill[dd->w]+dd->w+1)*sizeof(PetscInt));CHKERRQ(ierr);
}
/* copy the refine information */
dd2->coarsen_x = dd2->refine_x = dd->refine_x;
dd2->coarsen_y = dd2->refine_y = dd->refine_y;
dd2->coarsen_z = dd2->refine_z = dd->refine_z;
/* copy vector type information */
ierr = DMSetVecType(da2,da->vectype);CHKERRQ(ierr);
dd2->lf = dd->lf;
dd2->lj = dd->lj;
da2->leveldown = da->leveldown;
da2->levelup = da->levelup + 1;
ierr = DMSetFromOptions(da2);CHKERRQ(ierr);
ierr = DMSetUp(da2);CHKERRQ(ierr);
/* interpolate coordinates if they are set on the coarse grid */
if (da->coordinates) {
DM cdaf,cdac;
Vec coordsc,coordsf;
Mat II;
ierr = DMGetCoordinateDM(da,&cdac);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&coordsc);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da2,&cdaf);CHKERRQ(ierr);
/* force creation of the coordinate vector */
ierr = DMDASetUniformCoordinates(da2,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
ierr = DMGetCoordinates(da2,&coordsf);CHKERRQ(ierr);
ierr = DMCreateInterpolation(cdac,cdaf,&II,NULL);CHKERRQ(ierr);
ierr = MatInterpolate(II,coordsc,coordsf);CHKERRQ(ierr);
ierr = MatDestroy(&II);CHKERRQ(ierr);
}
for (i=0; i<da->bs; i++) {
const char *fieldname;
ierr = DMDAGetFieldName(da,i,&fieldname);CHKERRQ(ierr);
ierr = DMDASetFieldName(da2,i,fieldname);CHKERRQ(ierr);
}
*daref = da2;
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
DM da;
/* Initialize the Petsc context */
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
/* Build of the DMDA -- 1D -- boundary_none */
ierr = PetscPrintf(PETSC_COMM_WORLD,"1D -- DMDA_BOUNDARY_NONE\n");CHKERRQ(ierr);
ierr = DMDACreate(PETSC_COMM_WORLD, &da);CHKERRQ(ierr);
ierr = DMDASetDim(da, 1);CHKERRQ(ierr);
ierr = DMDASetSizes(da, -8, 1, 1);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE);CHKERRQ(ierr);
ierr = DMDASetDof(da, 1);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, 1);CHKERRQ(ierr);
ierr = DMDASetOverlap(da,1,1,1);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(da,"n1d_");CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMView(da,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
/* Build of the DMDA -- 1D -- boundary_ghosted */
ierr = PetscPrintf(PETSC_COMM_WORLD,"1D -- DMDA_BOUNDARY_GHOSTED\n");CHKERRQ(ierr);
ierr = DMDACreate(PETSC_COMM_WORLD, &da);CHKERRQ(ierr);
ierr = DMDASetDim(da, 1);CHKERRQ(ierr);
ierr = DMDASetSizes(da, -8, 1, 1);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED);CHKERRQ(ierr);
ierr = DMDASetDof(da, 2);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, 1);CHKERRQ(ierr);
ierr = DMDASetOverlap(da,1,1,1);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(da,"g1d_");CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMView(da,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
/* Build of the DMDA -- 1D -- boundary_periodic */
ierr = PetscPrintf(PETSC_COMM_WORLD,"1D -- DMDA_BOUNDARY_PERIODIC\n");CHKERRQ(ierr);
ierr = DMDACreate(PETSC_COMM_WORLD, &da);CHKERRQ(ierr);
ierr = DMDASetDim(da, 1);CHKERRQ(ierr);
ierr = DMDASetSizes(da, -8, 1, 1);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, DMDA_BOUNDARY_PERIODIC, DMDA_BOUNDARY_PERIODIC, DMDA_BOUNDARY_PERIODIC);CHKERRQ(ierr);
ierr = DMDASetDof(da, 2);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, 1);CHKERRQ(ierr);
ierr = DMDASetOverlap(da,1,1,1);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(da,"p1d_");CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMView(da,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
/* Build of the DMDA -- 2D -- boundary_none */
ierr = PetscPrintf(PETSC_COMM_WORLD,"2D -- DMDA_BOUNDARY_NONE\n");CHKERRQ(ierr);
ierr = DMDACreate(PETSC_COMM_WORLD, &da);CHKERRQ(ierr);
ierr = DMDASetDim(da, 2);CHKERRQ(ierr);
ierr = DMDASetSizes(da, -8, -8, 1);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE);CHKERRQ(ierr);
ierr = DMDASetDof(da, 2);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, 1);CHKERRQ(ierr);
ierr = DMDASetOverlap(da,1,1,1);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(da,"n2d_");CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMView(da,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
/* Build of the DMDA -- 2D -- boundary_ghosted */
ierr = PetscPrintf(PETSC_COMM_WORLD,"2D -- DMDA_BOUNDARY_GHOSTED\n");CHKERRQ(ierr);
ierr = DMDACreate(PETSC_COMM_WORLD, &da);CHKERRQ(ierr);
ierr = DMDASetDim(da, 2);CHKERRQ(ierr);
ierr = DMDASetSizes(da, -8, -8, 1);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED);CHKERRQ(ierr);
ierr = DMDASetDof(da, 2);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, 1);CHKERRQ(ierr);
ierr = DMDASetOverlap(da,1,1,1);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(da,"g2d_");CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMView(da,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
/* Build of the DMDA -- 2D -- boundary_periodic */
ierr = PetscPrintf(PETSC_COMM_WORLD,"2D -- DMDA_BOUNDARY_PERIODIC\n");CHKERRQ(ierr);
ierr = DMDACreate(PETSC_COMM_WORLD, &da);CHKERRQ(ierr);
ierr = DMDASetDim(da, 2);CHKERRQ(ierr);
ierr = DMDASetSizes(da, -8, -8, 1);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, DMDA_BOUNDARY_PERIODIC, DMDA_BOUNDARY_PERIODIC, DMDA_BOUNDARY_PERIODIC);CHKERRQ(ierr);
ierr = DMDASetDof(da, 2);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, 1);CHKERRQ(ierr);
ierr = DMDASetOverlap(da,1,1,1);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(da,"p2d_");CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMView(da,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
/* Build of the DMDA -- 3D -- boundary_none */
ierr = PetscPrintf(PETSC_COMM_WORLD,"3D -- DMDA_BOUNDARY_NONE\n");CHKERRQ(ierr);
ierr = DMDACreate(PETSC_COMM_WORLD, &da);CHKERRQ(ierr);
ierr = DMDASetDim(da, 3);CHKERRQ(ierr);
ierr = DMDASetSizes(da, -8, -8, -8);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE);CHKERRQ(ierr);
ierr = DMDASetDof(da, 2);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, 1);CHKERRQ(ierr);
ierr = DMDASetOverlap(da,1,1,1);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(da,"n3d_");CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMView(da,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
/* Build of the DMDA -- 3D -- boundary_ghosted */
ierr = PetscPrintf(PETSC_COMM_WORLD,"3D -- DMDA_BOUNDARY_GHOSTED\n");CHKERRQ(ierr);
ierr = DMDACreate(PETSC_COMM_WORLD, &da);CHKERRQ(ierr);
ierr = DMDASetDim(da, 3);CHKERRQ(ierr);
ierr = DMDASetSizes(da, -8, -8, -8);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED);CHKERRQ(ierr);
ierr = DMDASetDof(da, 2);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, 1);CHKERRQ(ierr);
ierr = DMDASetOverlap(da,1,1,1);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(da,"g3d_");CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMView(da,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
/* Build of the DMDA -- 3D -- boundary_periodic */
ierr = PetscPrintf(PETSC_COMM_WORLD,"3D -- DMDA_BOUNDARY_PERIODIC\n");CHKERRQ(ierr);
ierr = DMDACreate(PETSC_COMM_WORLD, &da);CHKERRQ(ierr);
ierr = DMDASetDim(da, 3);CHKERRQ(ierr);
ierr = DMDASetSizes(da, -8, -8, -8);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, DMDA_BOUNDARY_PERIODIC, DMDA_BOUNDARY_PERIODIC, DMDA_BOUNDARY_PERIODIC);CHKERRQ(ierr);
ierr = DMDASetDof(da, 2);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, 1);CHKERRQ(ierr);
ierr = DMDASetOverlap(da,1,1,1);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(da,"p3d_");CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMView(da,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
/* test moving data in and out */
ierr = PetscFinalize();
return 0;
}
