PetscErrorCode FormCoordinates(DM da,AppCtx *user)
{
PetscErrorCode ierr;
Vec coords;
DM cda;
PetscInt mx,my,mz;
PetscInt i,j,k,xs,ys,zs,xm,ym,zm;
CoordField ***x;
PetscFunctionBegin;
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(cda,&coords);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&mx,&my,&mz,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,&ys,&zs,&xm,&ym,&zm);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,coords,&x);CHKERRQ(ierr);
for (k=zs; k<zs+zm; k++) {
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
PetscReal cx = ((PetscReal)i) / (((PetscReal)(mx-1)));
PetscReal cy = ((PetscReal)j) / (((PetscReal)(my-1)));
PetscReal cz = ((PetscReal)k) / (((PetscReal)(mz-1)));
PetscReal rad = user->rad + cy*user->height;
PetscReal ang = (cx - 0.5)*user->arc;
x[k][j][i][0] = rad*PetscSinReal(ang);
x[k][j][i][1] = rad*PetscCosReal(ang) - (user->rad + 0.5*user->height)*PetscCosReal(-0.5*user->arc);
x[k][j][i][2] = user->width*(cz - 0.5);
}
}
}
ierr = DMDAVecRestoreArray(da,coords,&x);CHKERRQ(ierr);
ierr = DMSetCoordinates(da,coords);CHKERRQ(ierr);
ierr = VecDestroy(&coords);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexClone - Creates a DMPlex object with the same mesh as the original.
Collective on MPI_Comm
Input Parameter:
. dm - The original DMPlex object
Output Parameter:
. newdm - The new DMPlex object
Level: beginner
.keywords: DMPlex, create
@*/
PetscErrorCode DMPlexClone(DM dm, DM *newdm)
{
DM_Plex *mesh;
Vec coords;
void *ctx;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
PetscValidPointer(newdm,2);
ierr = DMCreate(PetscObjectComm((PetscObject)dm), newdm);CHKERRQ(ierr);
ierr = PetscSFDestroy(&(*newdm)->sf);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject) dm->sf);CHKERRQ(ierr);
(*newdm)->sf = dm->sf;
mesh = (DM_Plex*) dm->data;
mesh->refct++;
(*newdm)->data = mesh;
ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr);
ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr);
ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr);
ierr = DMSetApplicationContext(*newdm, ctx);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coords);CHKERRQ(ierr);
if (coords) {
ierr = DMSetCoordinatesLocal(*newdm, coords);CHKERRQ(ierr);
} else {
ierr = DMGetCoordinates(dm, &coords);CHKERRQ(ierr);
if (coords) {ierr = DMSetCoordinates(*newdm, coords);CHKERRQ(ierr);}
}
PetscFunctionReturn(0);
}
PetscErrorCode DMCreateSubDM_DA(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm)
{
DM_DA *da = (DM_DA*) dm->data;
PetscSection section;
PetscErrorCode ierr;
PetscFunctionBegin;
if (subdm) {
PetscSF sf;
Vec coords;
void *ctx;
/* Cannot use DMClone since the dof stuff is mixed in. Ugh
ierr = DMClone(dm, subdm);CHKERRQ(ierr); */
ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr);
ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr);
ierr = DMSetPointSF(*subdm, sf);CHKERRQ(ierr);
ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr);
ierr = DMSetApplicationContext(*subdm, ctx);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coords);CHKERRQ(ierr);
if (coords) {
ierr = DMSetCoordinatesLocal(*subdm, coords);CHKERRQ(ierr);
} else {
ierr = DMGetCoordinates(dm, &coords);CHKERRQ(ierr);
if (coords) {ierr = DMSetCoordinates(*subdm, coords);CHKERRQ(ierr);}
}
ierr = DMSetType(*subdm, DMDA);CHKERRQ(ierr);
ierr = DMSetDimension(*subdm, dm->dim);CHKERRQ(ierr);
ierr = DMDASetSizes(*subdm, da->M, da->N, da->P);CHKERRQ(ierr);
ierr = DMDASetNumProcs(*subdm, da->m, da->n, da->p);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(*subdm, da->bx, da->by, da->bz);CHKERRQ(ierr);
ierr = DMDASetDof(*subdm, numFields);CHKERRQ(ierr);
ierr = DMDASetStencilType(*subdm, da->stencil_type);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(*subdm, da->s);CHKERRQ(ierr);
ierr = DMDASetOwnershipRanges(*subdm, da->lx, da->ly, da->lz);CHKERRQ(ierr);
}
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
if (section) {
ierr = DMCreateSubDM_Section_Private(dm, numFields, fields, is, subdm);CHKERRQ(ierr);
} else {
if (is) {
PetscInt *indices, cnt = 0, dof = da->w, i, j;
ierr = PetscMalloc1(da->Nlocal*numFields/dof, &indices);CHKERRQ(ierr);
for (i = da->base/dof; i < (da->base+da->Nlocal)/dof; ++i) {
for (j = 0; j < numFields; ++j) {
indices[cnt++] = dof*i + fields[j];
}
}
if (cnt != da->Nlocal*numFields/dof) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Count %d does not equal expected value %d", cnt, da->Nlocal*numFields/dof);
ierr = ISCreateGeneral(PetscObjectComm((PetscObject) dm), cnt, indices, PETSC_OWN_POINTER, is);CHKERRQ(ierr);
}
}
PetscFunctionReturn(0);
}
PETSC_INTERN PetscErrorCode DMStagSetUniformCoordinatesExplicit_1d(DM dm,PetscReal xmin,PetscReal xmax)
{
PetscErrorCode ierr;
DM_Stag *stagCoord;
DM dmCoord;
Vec coordLocal,coord;
PetscReal h,min;
PetscScalar **arr;
PetscInt ind,start,n,nExtra,s;
PetscInt ileft,ielement;
PetscFunctionBegin;
ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr);
stagCoord = (DM_Stag*) dmCoord->data;
for (s=0; s<2; ++s) {
if (stagCoord->dof[s] !=0 && stagCoord->dof[s] != 1) SETERRQ2(PetscObjectComm((PetscObject)dm),PETSC_ERR_PLIB,"Coordinate DM in 1 dimensions must have 0 or 1 dof on each stratum, but stratum %d has %d dof",s,stagCoord->dof[s]);
}
ierr = DMGetLocalVector(dmCoord,&coordLocal);CHKERRQ(ierr);
ierr = DMStagVecGetArrayDOF(dmCoord,coordLocal,&arr);CHKERRQ(ierr);
if (stagCoord->dof[0]) {
ierr = DMStagGetLocationSlot(dmCoord,DMSTAG_LEFT,0,&ileft);CHKERRQ(ierr);
}
if (stagCoord->dof[1]) {
ierr = DMStagGetLocationSlot(dmCoord,DMSTAG_ELEMENT,0,&ielement);CHKERRQ(ierr);
}
ierr = DMStagGetCorners(dmCoord,&start,NULL,NULL,&n,NULL,NULL,&nExtra,NULL,NULL);CHKERRQ(ierr);
min = xmin;
h = (xmax-xmin)/stagCoord->N[0];
for(ind=start; ind<start + n + nExtra; ++ind) {
if (stagCoord->dof[0]) {
const PetscReal off = 0.0;
arr[ind][ileft] = min + ((PetscReal)ind + off) * h;
}
if (stagCoord->dof[1]) {
const PetscReal off = 0.5;
arr[ind][ielement] = min + ((PetscReal)ind + off) * h;
}
}
ierr = DMStagVecRestoreArrayDOF(dmCoord,coordLocal,&arr);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dmCoord,&coord);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dmCoord,coordLocal,INSERT_VALUES,coord);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dmCoord,coordLocal,INSERT_VALUES,coord);CHKERRQ(ierr);
ierr = DMSetCoordinates(dm,coord);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)dm,(PetscObject)coord);CHKERRQ(ierr);
ierr = VecDestroy(&coord);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmCoord,&coordLocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMPlexCreateBoxMesh(comm, dim, user->simplex, user->cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr);
{
Parameter *param;
Vec coordinates;
PetscScalar *coords;
PetscReal alpha;
PetscInt cdim, N, bs, i;
ierr = DMGetCoordinateDim(*dm, &cdim);CHKERRQ(ierr);
ierr = DMGetCoordinates(*dm, &coordinates);CHKERRQ(ierr);
ierr = VecGetLocalSize(coordinates, &N);CHKERRQ(ierr);
ierr = VecGetBlockSize(coordinates, &bs);CHKERRQ(ierr);
if (bs != cdim) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Invalid coordinate blocksize %D != embedding dimension %D", bs, cdim);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
ierr = PetscBagGetData(user->bag, (void **) ¶m);CHKERRQ(ierr);
alpha = param->alpha;
for (i = 0; i < N; i += cdim) {
PetscScalar x = coords[i+0];
PetscScalar y = coords[i+1];
coords[i+0] = PetscCosReal(alpha)*x - PetscSinReal(alpha)*y;
coords[i+1] = PetscSinReal(alpha)*x + PetscCosReal(alpha)*y;
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinates(*dm, coordinates);CHKERRQ(ierr);
}
{
DM pdm = NULL;
PetscPartitioner part;
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
ierr = DMPlexDistribute(*dm, 0, NULL, &pdm);CHKERRQ(ierr);
if (pdm) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = pdm;
}
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMLoad_DA(DM da,PetscViewer viewer)
{
PetscErrorCode ierr;
PetscInt dim,m,n,p,dof,swidth;
DMDAStencilType stencil;
DMBoundaryType bx,by,bz;
PetscBool coors;
DM dac;
Vec c;
PetscFunctionBegin;
ierr = PetscViewerBinaryRead(viewer,&dim,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&m,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&n,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&p,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&dof,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&swidth,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&bx,1,NULL,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&by,1,NULL,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&bz,1,NULL,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&stencil,1,NULL,PETSC_ENUM);CHKERRQ(ierr);
ierr = DMSetDimension(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,NULL,PETSC_ENUM);CHKERRQ(ierr);
if (coors) {
ierr = DMGetCoordinateDM(da,&dac);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dac,&c);CHKERRQ(ierr);
ierr = VecLoad(c,viewer);CHKERRQ(ierr);
ierr = DMSetCoordinates(da,c);CHKERRQ(ierr);
ierr = VecDestroy(&c);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*@
DMDASetUniformCoordinates - Sets a DMDA coordinates to be a uniform grid
Collective on DMDA
Input Parameters:
+ da - the distributed array object
. xmin,xmax - extremes in the x direction
. ymin,ymax - extremes in the y direction (use NULL for 1 dimensional problems)
- zmin,zmax - extremes in the z direction (use NULL for 1 or 2 dimensional problems)
Level: beginner
.seealso: DMSetCoordinates(), DMGetCoordinates(), DMDACreate1d(), DMDACreate2d(), DMDACreate3d()
@*/
PetscErrorCode DMDASetUniformCoordinates(DM da,PetscReal xmin,PetscReal xmax,PetscReal ymin,PetscReal ymax,PetscReal zmin,PetscReal zmax)
{
MPI_Comm comm;
PetscSection section;
DM cda;
DMBoundaryType bx,by,bz;
Vec xcoor;
PetscScalar *coors;
PetscReal hx,hy,hz_;
PetscInt i,j,k,M,N,P,istart,isize,jstart,jsize,kstart,ksize,dim,cnt;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(da,DM_CLASSID,1);
ierr = DMDAGetInfo(da,&dim,&M,&N,&P,0,0,0,0,0,&bx,&by,&bz,0);CHKERRQ(ierr);
if (xmax <= xmin) SETERRQ2(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_INCOMP,"xmax must be larger than xmin %g %g",(double)xmin,(double)xmax);
if ((ymax <= ymin) && (dim > 1)) SETERRQ2(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_INCOMP,"ymax must be larger than ymin %g %g",(double)ymin,(double)ymax);
if ((zmax <= zmin) && (dim > 2)) SETERRQ2(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_INCOMP,"zmax must be larger than zmin %g %g",(double)zmin,(double)zmax);
ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);
ierr = DMGetDefaultSection(da,§ion);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&istart,&jstart,&kstart,&isize,&jsize,&ksize);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da, &cda);CHKERRQ(ierr);
if (section) {
/* This would be better as a vector, but this is compatible */
PetscInt numComp[3] = {1, 1, 1};
PetscInt numVertexDof[3] = {1, 1, 1};
ierr = DMDASetFieldName(cda, 0, "x");CHKERRQ(ierr);
if (dim > 1) {ierr = DMDASetFieldName(cda, 1, "y");CHKERRQ(ierr);}
if (dim > 2) {ierr = DMDASetFieldName(cda, 2, "z");CHKERRQ(ierr);}
ierr = DMDACreateSection(cda, numComp, numVertexDof, NULL, NULL);CHKERRQ(ierr);
}
ierr = DMCreateGlobalVector(cda, &xcoor);CHKERRQ(ierr);
if (section) {
PetscSection csection;
PetscInt vStart, vEnd;
ierr = DMGetDefaultGlobalSection(cda,&csection);CHKERRQ(ierr);
ierr = VecGetArray(xcoor,&coors);CHKERRQ(ierr);
ierr = DMDAGetHeightStratum(da, dim, &vStart, &vEnd);CHKERRQ(ierr);
if (bx == DM_BOUNDARY_PERIODIC) hx = (xmax-xmin)/(M+1);
else hx = (xmax-xmin)/(M ? M : 1);
if (by == DM_BOUNDARY_PERIODIC) hy = (ymax-ymin)/(N+1);
else hy = (ymax-ymin)/(N ? N : 1);
if (bz == DM_BOUNDARY_PERIODIC) hz_ = (zmax-zmin)/(P+1);
else hz_ = (zmax-zmin)/(P ? P : 1);
switch (dim) {
case 1:
for (i = 0; i < isize+1; ++i) {
PetscInt v = i+vStart, dof, off;
ierr = PetscSectionGetDof(csection, v, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(csection, v, &off);CHKERRQ(ierr);
if (off >= 0) {
coors[off] = xmin + hx*(i+istart);
}
}
break;
case 2:
for (j = 0; j < jsize+1; ++j) {
for (i = 0; i < isize+1; ++i) {
PetscInt v = j*(isize+1)+i+vStart, dof, off;
ierr = PetscSectionGetDof(csection, v, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(csection, v, &off);CHKERRQ(ierr);
if (off >= 0) {
coors[off+0] = xmin + hx*(i+istart);
coors[off+1] = ymin + hy*(j+jstart);
}
}
}
break;
case 3:
for (k = 0; k < ksize+1; ++k) {
for (j = 0; j < jsize+1; ++j) {
for (i = 0; i < isize+1; ++i) {
PetscInt v = (k*(jsize+1)+j)*(isize+1)+i+vStart, dof, off;
ierr = PetscSectionGetDof(csection, v, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(csection, v, &off);CHKERRQ(ierr);
if (off >= 0) {
coors[off+0] = xmin + hx*(i+istart);
coors[off+1] = ymin + hy*(j+jstart);
coors[off+2] = zmin + hz_*(k+kstart);
}
}
}
}
break;
default:
SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot create uniform coordinates for this dimension %D\n",dim);
}
ierr = VecRestoreArray(xcoor,&coors);CHKERRQ(ierr);
ierr = DMSetCoordinates(da,xcoor);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)da,(PetscObject)xcoor);CHKERRQ(ierr);
ierr = VecDestroy(&xcoor);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
if (dim == 1) {
if (bx == DM_BOUNDARY_PERIODIC) hx = (xmax-xmin)/M;
else hx = (xmax-xmin)/(M-1);
ierr = VecGetArray(xcoor,&coors);CHKERRQ(ierr);
for (i=0; i<isize; i++) {
coors[i] = xmin + hx*(i+istart);
}
ierr = VecRestoreArray(xcoor,&coors);CHKERRQ(ierr);
} else if (dim == 2) {
if (bx == DM_BOUNDARY_PERIODIC) hx = (xmax-xmin)/(M);
else hx = (xmax-xmin)/(M-1);
if (by == DM_BOUNDARY_PERIODIC) hy = (ymax-ymin)/(N);
else hy = (ymax-ymin)/(N-1);
ierr = VecGetArray(xcoor,&coors);CHKERRQ(ierr);
cnt = 0;
for (j=0; j<jsize; j++) {
for (i=0; i<isize; i++) {
coors[cnt++] = xmin + hx*(i+istart);
coors[cnt++] = ymin + hy*(j+jstart);
}
}
ierr = VecRestoreArray(xcoor,&coors);CHKERRQ(ierr);
} else if (dim == 3) {
if (bx == DM_BOUNDARY_PERIODIC) hx = (xmax-xmin)/(M);
else hx = (xmax-xmin)/(M-1);
if (by == DM_BOUNDARY_PERIODIC) hy = (ymax-ymin)/(N);
else hy = (ymax-ymin)/(N-1);
if (bz == DM_BOUNDARY_PERIODIC) hz_ = (zmax-zmin)/(P);
else hz_ = (zmax-zmin)/(P-1);
ierr = VecGetArray(xcoor,&coors);CHKERRQ(ierr);
cnt = 0;
for (k=0; k<ksize; k++) {
for (j=0; j<jsize; j++) {
for (i=0; i<isize; i++) {
coors[cnt++] = xmin + hx*(i+istart);
coors[cnt++] = ymin + hy*(j+jstart);
coors[cnt++] = zmin + hz_*(k+kstart);
}
}
}
ierr = VecRestoreArray(xcoor,&coors);CHKERRQ(ierr);
} else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot create uniform coordinates for this dimension %D\n",dim);
ierr = DMSetCoordinates(da,xcoor);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)da,(PetscObject)xcoor);CHKERRQ(ierr);
ierr = VecDestroy(&xcoor);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscInt main(PetscInt argc,char **args)
{
typedef enum {RANDOM, CONSTANT, TANH, NUM_FUNCS} FuncType;
const char *funcNames[NUM_FUNCS] = {"random", "constant", "tanh"};
Mat A, AA;
PetscMPIInt size;
PetscInt N,i, stencil=1,dof=1;
PetscInt dim[3] = {10,10,10}, ndim = 3;
Vec coords,x,y,z,xx,yy,zz;
PetscReal h[3];
PetscScalar s;
PetscRandom rdm;
PetscReal norm, enorm;
PetscInt func;
FuncType function = TANH;
DM da, coordsda;
PetscBool view_x = PETSC_FALSE, view_y = PETSC_FALSE, view_z = PETSC_FALSE;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP, "This is a uniprocessor example only!");
ierr = PetscOptionsBegin(PETSC_COMM_WORLD, NULL, "USFFT Options", "ex27");CHKERRQ(ierr);
ierr = PetscOptionsEList("-function", "Function type", "ex27", funcNames, NUM_FUNCS, funcNames[function], &func, NULL);CHKERRQ(ierr);
function = (FuncType) func;
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-view_x",&view_x,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-view_y",&view_y,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-view_z",&view_z,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetIntArray(NULL,NULL,"-dim",dim,&ndim,NULL);CHKERRQ(ierr);
ierr = DMDACreate3d(PETSC_COMM_SELF,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,dim[0], dim[1], dim[2],
PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE,dof, stencil,NULL, NULL, NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
/* Coordinates */
ierr = DMGetCoordinateDM(da, &coordsda);
ierr = DMGetGlobalVector(coordsda, &coords);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coords, "Grid coordinates");CHKERRQ(ierr);
for (i = 0, N = 1; i < 3; i++) {
h[i] = 1.0/dim[i];
PetscScalar *a;
ierr = VecGetArray(coords, &a);CHKERRQ(ierr);
PetscInt j,k,n = 0;
for (i = 0; i < 3; ++i) {
for (j = 0; j < dim[i]; ++j) {
for (k = 0; k < 3; ++k) {
a[n] = j*h[i]; /* coordinate along the j-th point in the i-th dimension */
++n;
}
}
}
ierr = VecRestoreArray(coords, &a);CHKERRQ(ierr);
}
ierr = DMSetCoordinates(da, coords);CHKERRQ(ierr);
/* Work vectors */
ierr = DMGetGlobalVector(da, &x);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) x, "Real space vector");CHKERRQ(ierr);
ierr = DMGetGlobalVector(da, &xx);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) xx, "Real space vector");CHKERRQ(ierr);
ierr = DMGetGlobalVector(da, &y);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) y, "USFFT frequency space vector");CHKERRQ(ierr);
ierr = DMGetGlobalVector(da, &yy);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) yy, "FFTW frequency space vector");CHKERRQ(ierr);
ierr = DMGetGlobalVector(da, &z);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) z, "USFFT reconstructed vector");CHKERRQ(ierr);
ierr = DMGetGlobalVector(da, &zz);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) zz, "FFTW reconstructed vector");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "%3-D: USFFT on vector of ");CHKERRQ(ierr);
for (i = 0, N = 1; i < 3; i++) {
ierr = PetscPrintf(PETSC_COMM_SELF, "dim[%d] = %d ",i,dim[i]);CHKERRQ(ierr);
N *= dim[i];
}
ierr = PetscPrintf(PETSC_COMM_SELF, "; total size %d \n",N);CHKERRQ(ierr);
if (function == RANDOM) {
ierr = PetscRandomCreate(PETSC_COMM_SELF, &rdm);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr);
ierr = VecSetRandom(x, rdm);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr);
} else if (function == CONSTANT) {
ierr = VecSet(x, 1.0);CHKERRQ(ierr);
} else if (function == TANH) {
PetscScalar *a;
ierr = VecGetArray(x, &a);CHKERRQ(ierr);
PetscInt j,k = 0;
for (i = 0; i < 3; ++i) {
for (j = 0; j < dim[i]; ++j) {
a[k] = tanh((j - dim[i]/2.0)*(10.0/dim[i]));
++k;
}
}
ierr = VecRestoreArray(x, &a);CHKERRQ(ierr);
}
if (view_x) {
ierr = VecView(x, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecCopy(x,xx);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "|x|_2 = %g\n",norm);CHKERRQ(ierr);
/* create USFFT object */
ierr = MatCreateSeqUSFFT(coords,da,&A);CHKERRQ(ierr);
/* create FFTW object */
ierr = MatCreateSeqFFTW(PETSC_COMM_SELF,3,dim,&AA);CHKERRQ(ierr);
/* apply USFFT and FFTW FORWARD "preemptively", so the fftw_plans can be reused on different vectors */
ierr = MatMult(A,x,z);CHKERRQ(ierr);
ierr = MatMult(AA,xx,zz);CHKERRQ(ierr);
/* Now apply USFFT and FFTW forward several (3) times */
for (i=0; i<3; ++i) {
ierr = MatMult(A,x,y);CHKERRQ(ierr);
ierr = MatMult(AA,xx,yy);CHKERRQ(ierr);
ierr = MatMultTranspose(A,y,z);CHKERRQ(ierr);
ierr = MatMultTranspose(AA,yy,zz);CHKERRQ(ierr);
}
if (view_y) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "y = \n");CHKERRQ(ierr);
ierr = VecView(y, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "yy = \n");CHKERRQ(ierr);
ierr = VecView(yy, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
if (view_z) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "z = \n");CHKERRQ(ierr);
ierr = VecView(z, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "zz = \n");CHKERRQ(ierr);
ierr = VecView(zz, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* compare x and z. USFFT computes an unnormalized DFT, thus z = N*x */
s = 1.0/(PetscReal)N;
ierr = VecScale(z,s);CHKERRQ(ierr);
ierr = VecAXPY(x,-1.0,z);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_1,&enorm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "|x-z| = %g\n",enorm);CHKERRQ(ierr);
/* compare xx and zz. FFTW computes an unnormalized DFT, thus zz = N*x */
s = 1.0/(PetscReal)N;
ierr = VecScale(zz,s);CHKERRQ(ierr);
ierr = VecAXPY(xx,-1.0,zz);CHKERRQ(ierr);
ierr = VecNorm(xx,NORM_1,&enorm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "|xx-zz| = %g\n",enorm);CHKERRQ(ierr);
/* compare y and yy: USFFT and FFTW results*/
ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr);
ierr = VecAXPY(y,-1.0,yy);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_1,&enorm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "|y|_2 = %g\n",norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "|y-yy| = %g\n",enorm);CHKERRQ(ierr);
/* compare z and zz: USFFT and FFTW results*/
ierr = VecNorm(z,NORM_2,&norm);CHKERRQ(ierr);
ierr = VecAXPY(z,-1.0,zz);CHKERRQ(ierr);
ierr = VecNorm(z,NORM_1,&enorm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "|z|_2 = %g\n",norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "|z-zz| = %g\n",enorm);CHKERRQ(ierr);
/* free spaces */
ierr = DMRestoreGlobalVector(da,&x);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(da,&xx);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(da,&y);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(da,&yy);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(da,&z);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(da,&zz);CHKERRQ(ierr);
ierr = VecDestroy(&coords);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
