PetscErrorCode ExactSolution(DM packer,Vec U)
{
PF pf;
Vec x,u_global;
PetscScalar *w;
DM da;
PetscErrorCode ierr;
PetscInt m;
PetscFunctionBeginUser;
ierr = DMCompositeGetEntries(packer,&m,&da);CHKERRQ(ierr);
ierr = PFCreate(PETSC_COMM_WORLD,1,2,&pf);CHKERRQ(ierr);
/* The cast through PETSC_UINTPTR_T is so that compilers will warn about casting to void * from void(*)(void) */
ierr = PFSetType(pf,PFQUICK,(void*)(PETSC_UINTPTR_T)u_solution);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&x);CHKERRQ(ierr);
if (!x) {
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&x);CHKERRQ(ierr);
}
ierr = DMCompositeGetAccess(packer,U,&w,&u_global,0);CHKERRQ(ierr);
if (w) w[0] = .25;
ierr = PFApplyVec(pf,x,u_global);CHKERRQ(ierr);
ierr = PFDestroy(&pf);CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(packer,U,&w,&u_global,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode OpSolution(Op op,DM dm,Vec U) {
PetscErrorCode ierr;
Vec X;
const PetscScalar *x;
PetscScalar *u;
PetscReal L[3];
PetscInt i,m,bs;
PetscFunctionBegin;
ierr = PetscLogEventBegin(OP_Solution,dm,U,0,0);CHKERRQ(ierr);
ierr = DMGetCoordinates(dm,&X);CHKERRQ(ierr);
ierr = VecStrideMax(X,0,NULL,&L[0]);CHKERRQ(ierr);
ierr = VecStrideMax(X,1,NULL,&L[1]);CHKERRQ(ierr);
ierr = VecStrideMax(X,2,NULL,&L[2]);CHKERRQ(ierr);
ierr = VecGetLocalSize(U,&m);CHKERRQ(ierr);
ierr = VecGetBlockSize(U,&bs);CHKERRQ(ierr);
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
ierr = VecGetArray(U,&u);CHKERRQ(ierr);
for (i=0; i<m/bs; i++) {
ierr = (op->PointwiseSolution)(op,&x[i*3],L,&u[i*bs]);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
ierr = VecRestoreArray(U,&u);CHKERRQ(ierr);
ierr = PetscLogEventEnd(OP_Solution,dm,U,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* Compute the values of the surface mass balance and ice hardness. */
PetscErrorCode FillDistributedParams(ExactCtx *exact, AppCtx *user)
{
PetscErrorCode ierr;
PetscInt i;
PetscReal dum1, dum2, *xstag, *Mstag, *Bstag;
DM coord_da;
Vec coord_x;
PetscFunctionBegin;
ierr = DMGetCoordinateDM(user->stagda, &coord_da); CHKERRQ(ierr);
ierr = DMGetCoordinates(user->stagda, &coord_x); CHKERRQ(ierr);
ierr = DMDAVecGetArray(coord_da,coord_x,&xstag);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->stagda,user->Mstag,&Mstag);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->stagda,user->Bstag,&Bstag);CHKERRQ(ierr);
for (i = user->xs; i < user->xs + user->xm - 1; i++) { /* note "-1" at end */
if (xstag[i] < exact->xg) {
ierr = exactBod(xstag[i], &dum1, &dum2, &(Mstag[i])); CHKERRQ(ierr);
ierr = exactBodBueler(xstag[i], &dum1, &(Bstag[i])); CHKERRQ(ierr);
} else {
Mstag[i] = exact->Mg;
Bstag[i] = exact->Bg;
}
}
ierr = DMDAVecRestoreArray(coord_da,coord_x,&xstag);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->stagda,user->Mstag,&Mstag);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->stagda,user->Bstag,&Bstag);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* Put a not-unreasonable initial guess in Hu. */
PetscErrorCode FillInitial(AppCtx *user, Vec *vHu)
{
PetscErrorCode ierr;
PetscInt i;
PetscReal *x;
Node *Hu;
const PetscReal
Hcguess = 300.0,
ucguess = (300.0/user->secpera),
Hslope = (Hcguess - user->Ha) / (user->xc - user->xa),
uslope = (ucguess - user->ua) / (user->xc - user->xa);
DM coord_da;
Vec coord_x;
PetscFunctionBegin;
ierr = DMGetCoordinateDM(user->da, &coord_da); CHKERRQ(ierr);
ierr = DMGetCoordinates(user->da, &coord_x); CHKERRQ(ierr);
ierr = DMDAVecGetArray(coord_da,coord_x,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,*vHu,&Hu);CHKERRQ(ierr);
for (i = user->xs; i < user->xs + user->xm; i++) {
/* use linear function which uses upstream Dirichlet b.c. but guesses
at calving-front values */
Hu[i].H = user->Ha + Hslope * (x[i] - user->xa);
Hu[i].u = user->ua + uslope * (x[i] - user->xa);
}
ierr = DMDAVecRestoreArray(coord_da,coord_x,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->da,*vHu,&Hu);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DADefineXLinearField2D(DM da,Vec field)
{
PetscErrorCode ierr;
PetscInt i,j;
PetscInt sx,nx,sy,ny;
Vec Gcoords;
DMDACoor2d **XX;
PetscScalar **FF;
DM cda;
PetscFunctionBeginUser;
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&Gcoords);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,Gcoords,&XX);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,field,&FF);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&sx,&sy,0,&nx,&ny,0);CHKERRQ(ierr);
for (i=sx; i<sx+nx; i++) {
for (j=sy; j<sy+ny; j++ ) {
FF[j][i] = 10.0 + 3.0 * XX[j][i].x + 5.5 * XX[j][i].y + 8.003 * XX[j][i].x * XX[j][i].y;
}
}
ierr = DMDAVecRestoreArray(da,field,&FF);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(cda,Gcoords,&XX);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetCoordinates1d(DM da)
{
PetscErrorCode ierr;
PetscInt i,start,m;
Vec gc,global;
PetscScalar *coors;
DM cda;
PetscFunctionBeginUser;
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&start,0,0,&m,0,0);CHKERRQ(ierr);
for (i=start; i<start+m; i++) {
if (i % 2) {
coors[i] = coors[i-1] + .1*(coors[i+1] - coors[i-1]);
}
}
ierr = DMDAVecRestoreArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&global);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(cda,gc,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(cda,gc,INSERT_VALUES,global);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetCoordinates2d(DM da)
{
PetscErrorCode ierr;
PetscInt i,j,mstart,m,nstart,n;
Vec local,global;
DMDACoor2d **coors,**coorslocal;
DM cda;
PetscFunctionBeginUser;
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&global);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(da,&local);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,global,&coors);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(cda,local,&coorslocal);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&mstart,&nstart,0,&m,&n,0);CHKERRQ(ierr);
for (i=mstart; i<mstart+m; i++) {
for (j=nstart; j<nstart+n; j++) {
if (i % 2) {
coors[j][i].x = coorslocal[j][i-1].x + .1*(coorslocal[j][i+1].x - coorslocal[j][i-1].x);
}
if (j % 2) {
coors[j][i].y = coorslocal[j-1][i].y + .3*(coorslocal[j+1][i].y - coorslocal[j-1][i].y);
}
}
}
ierr = DMDAVecRestoreArray(cda,global,&coors);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(cda,local,&coorslocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(cda,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(cda,global,INSERT_VALUES,local);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetCoordinates3d(DM da)
{
PetscErrorCode ierr;
PetscInt i,j,mstart,m,nstart,n,pstart,p,k;
Vec gc,global;
DMDACoor3d ***coors;
DM cda;
PetscFunctionBeginUser;
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&mstart,&nstart,&pstart,&m,&n,&p);CHKERRQ(ierr);
for (i=mstart; i<mstart+m; i++) {
for (j=nstart; j<nstart+n; j++) {
for (k=pstart; k<pstart+p; k++) {
if (i % 2) {
coors[k][j][i].x = coors[k][j][i-1].x + .1*(coors[k][j][i+1].x - coors[k][j][i-1].x);
}
if (j % 2) {
coors[k][j][i].y = coors[k][j-1][i].y + .3*(coors[k][j+1][i].y - coors[k][j-1][i].y);
}
if (k % 2) {
coors[k][j][i].z = coors[k-1][j][i].z + .4*(coors[k+1][j][i].z - coors[k-1][j][i].z);
}
}
}
}
ierr = DMDAVecRestoreArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&global);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(cda,gc,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(cda,gc,INSERT_VALUES,global);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormPsiAndInitialGuess(DM da,Vec U0,PetscBool feasible)
{
ObsCtx *user;
PetscErrorCode ierr;
PetscInt i,j,Mx,My,xs,ys,xm,ym;
DM coordDA;
Vec coordinates;
DMDACoor2d **coords;
PetscReal **psi, **u0, **uexact,
x, y, r,
afree = 0.69797, A = 0.68026, B = 0.47152, pi = 3.1415926;
PetscFunctionBeginUser;
ierr = DMGetApplicationContext(da,&user);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,PETSC_IGNORE,PETSC_IGNORE,
PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,
PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);
ierr = DMDAGetCorners(da,&xs,&ys,PETSC_NULL,&xm,&ym,PETSC_NULL);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da, &coordDA);CHKERRQ(ierr);
ierr = DMGetCoordinates(da, &coordinates);CHKERRQ(ierr);
ierr = DMDAVecGetArray(coordDA, coordinates, &coords);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da, user->psi, &psi);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da, U0, &u0);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da, user->uexact, &uexact);CHKERRQ(ierr);
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
x = coords[j][i].x;
y = coords[j][i].y;
r = sqrt(x * x + y * y);
if (r <= 1.0) {
psi[j][i] = sqrt(1.0 - r * r);
} else {
psi[j][i] = -1.0;
}
if (r <= afree) {
uexact[j][i] = psi[j][i]; /* on the obstacle */
} else {
uexact[j][i] = - A * log(r) + B; /* solves the laplace eqn */
}
if (feasible) {
if (i == 0 || j == 0 || i == Mx-1 || j == My-1) {
u0[j][i] = uexact[j][i];
} else {
/* initial guess is admissible: it is above the obstacle */
u0[j][i] = uexact[j][i] + cos(pi * x / 4) * cos(pi * y / 4);
}
} else {
u0[j][i] = 0.;
}
}
}
ierr = DMDAVecRestoreArray(da, user->psi, &psi);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da, U0, &u0);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da, user->uexact, &uexact);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(coordDA, coordinates, &coords);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* Compute the exact thickness and velocity on the regular grid, and
the staggered-grid ice hardness, over the locally-owned part of the grid. */
PetscErrorCode FillExactSoln(ExactCtx *exact, AppCtx *user)
{
PetscErrorCode ierr;
PetscInt i;
PetscReal dum1, *x;
Node *Hu;
DM coord_da;
Vec coord_x;
PetscFunctionBegin;
ierr = DMGetCoordinateDM(user->da, &coord_da); CHKERRQ(ierr);
ierr = DMGetCoordinates(user->da, &coord_x); CHKERRQ(ierr);
ierr = DMDAVecGetArray(coord_da,coord_x,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,exact->Hu,&Hu);CHKERRQ(ierr);
for (i = user->xs; i < user->xs + user->xm; i++) {
if (x[i] < exact->xg) {
/* grounded part: Bodvardsson formula */
ierr = exactBod(x[i], &(Hu[i].H), &(Hu[i].u), &dum1); CHKERRQ(ierr);
} else {
/* floating part: van der Veen formula */
ierr = exactVeen(x[i], exact->Mg, &(Hu[i].H), &(Hu[i].u));
if (ierr) PetscPrintf(PETSC_COMM_WORLD,"WARNING: exactVeen() returns error %d at i=%d, x[i]=%.3f km\n",
ierr,i,x[i]/1000.0);
}
}
ierr = DMDAVecRestoreArray(coord_da,coord_x,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->da,exact->Hu,&Hu);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormPsiAndExactSoln(DM da) {
ObsCtx *user;
PetscErrorCode ierr;
DMDALocalInfo info;
PetscInt i,j;
DM coordDA;
Vec coordinates;
DMDACoor2d **coords;
PetscReal **psi, **uexact, r;
const PetscReal afree = 0.69797, A = 0.68026, B = 0.47152;
PetscFunctionBeginUser;
ierr = DMGetApplicationContext(da,&user);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info); CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da, &coordDA);CHKERRQ(ierr);
ierr = DMGetCoordinates(da, &coordinates);CHKERRQ(ierr);
ierr = DMDAVecGetArray(coordDA, coordinates, &coords);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da, user->psi, &psi);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da, user->uexact, &uexact);CHKERRQ(ierr);
for (j=info.ys; j<info.ys+info.ym; j++) {
for (i=info.xs; i<info.xs+info.xm; i++) {
r = PetscSqrtReal(pow(coords[j][i].x,2) + pow(coords[j][i].y,2));
if (r <= 1.0) psi[j][i] = PetscSqrtReal(1.0 - r * r);
else psi[j][i] = -1.0;
if (r <= afree) uexact[j][i] = psi[j][i]; /* on the obstacle */
else uexact[j][i] = - A * PetscLogReal(r) + B; /* solves the laplace eqn */
}
}
ierr = DMDAVecRestoreArray(da, user->psi, &psi);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da, user->uexact, &uexact);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(coordDA, coordinates, &coords);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ini_bou(Vec X,AppCtx* user)
{
PetscErrorCode ierr;
DM cda;
DMDACoor2d **coors;
PetscScalar **p;
Vec gc;
PetscInt M,N,I,J;
PetscMPIInt rank;
PetscFunctionBeginUser;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = DMDAGetInfo(user->da,NULL,&M,&N,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
user->dx = (user->xmax - user->xmin)/(M-1); user->dy = (user->ymax - user->ymin)/(N-1);
ierr = DMGetCoordinateDM(user->da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinates(user->da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,X,&p);CHKERRQ(ierr);
/* Point mass at (mux,muy) */
ierr = PetscPrintf(PETSC_COMM_WORLD,"Original user->mux = %f, user->muy = %f\n",user->mux,user->muy);CHKERRQ(ierr);
ierr = DMDAGetLogicalCoordinate(user->da,user->mux,user->muy,0.0,&I,&J,NULL,&user->mux,&user->muy,NULL);CHKERRQ(ierr);
user->PM_min = user->Pmax*PetscSinScalar(user->mux);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Corrected user->mux = %f, user->muy = %f user->PM_min = %f,user->dx = %f\n",user->mux,user->muy,user->PM_min,user->dx);CHKERRQ(ierr);
if (I > -1 && J > -1) {
p[J][I] = 1.0;
}
ierr = DMDAVecRestoreArrayRead(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->da,X,&p);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
FormExactSolution2 - Forms initial approximation.
Input Parameters:
da - The DM
user - user-defined application context
Output Parameter:
X - vector
*/
PetscErrorCode FormExactSolution2(DM da, AppCtx *user, Vec U)
{
DM coordDA;
Vec coordinates;
DMDACoor2d **coords;
PetscScalar **u;
PetscReal x, y;
PetscInt xs, ys, xm, ym, i, j;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMDAGetCorners(da, &xs, &ys, NULL, &xm, &ym, NULL);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da, &coordDA);CHKERRQ(ierr);
ierr = DMGetCoordinates(da, &coordinates);CHKERRQ(ierr);
ierr = DMDAVecGetArray(coordDA, coordinates, &coords);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da, U, &u);CHKERRQ(ierr);
for (j = ys; j < ys+ym; ++j) {
for (i = xs; i < xs+xm; ++i) {
x = PetscRealPart(coords[j][i].x);
y = PetscRealPart(coords[j][i].y);
u[j][i] = PetscSinReal(PETSC_PI*x)*PetscSinReal(PETSC_PI*y);
}
}
ierr = DMDAVecRestoreArray(da, U, &u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(coordDA, coordinates, &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 ini_bou(Vec X,AppCtx* user)
{
PetscErrorCode ierr;
DM cda;
DMDACoor2d **coors;
PetscScalar **p;
Vec gc;
PetscInt i,j;
PetscInt xs,ys,xm,ym,M,N;
PetscScalar xi,yi;
PetscScalar sigmax=user->sigmax,sigmay=user->sigmay;
PetscScalar rho =user->rho;
PetscScalar mux =user->mux,muy=user->muy;
PetscMPIInt rank;
PetscScalar sum;
PetscFunctionBeginUser;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = DMDAGetInfo(user->da,NULL,&M,&N,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
user->dx = (user->xmax - user->xmin)/(M-1); user->dy = (user->ymax - user->ymin)/(N-1);
ierr = DMGetCoordinateDM(user->da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinates(user->da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,X,&p);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr);
/* mux and muy need to be grid points in the x and y-direction otherwise the solution goes unstable
muy is set by choosing the y domain, no. of grid points along y-direction so that muy is a grid point
in the y-direction. We only modify mux here
*/
mux = user->mux = coors[0][M/2+10].x; /* For -pi < x < pi, this should be some angle between 0 and pi/2 */
if (user->nonoiseinitial) {
for (i=xs; i < xs+xm; i++) {
for (j=ys; j < ys+ym; j++) {
xi = coors[j][i].x; yi = coors[j][i].y;
if ((xi == mux) && (yi == muy)) {
p[j][i] = 1.0;
}
}
}
} else {
/* Change PM_min accordingly */
user->PM_min = user->Pmax*sin(mux);
for (i=xs; i < xs+xm; i++) {
for (j=ys; j < ys+ym; j++) {
xi = coors[j][i].x; yi = coors[j][i].y;
p[j][i] = (0.5/(PETSC_PI*sigmax*sigmay*PetscSqrtScalar(1.0-rho*rho)))*PetscExpScalar(-0.5/(1-rho*rho)*(PetscPowScalar((xi-mux)/sigmax,2) + PetscPowScalar((yi-muy)/sigmay,2) - 2*rho*(xi-mux)*(yi-muy)/(sigmax*sigmay)));
}
}
}
ierr = DMDAVecRestoreArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->da,X,&p);CHKERRQ(ierr);
ierr = VecSum(X,&sum);CHKERRQ(ierr);
ierr = VecScale(X,1.0/sum);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DAApplyTrilinearMapping(DM da)
{
PetscErrorCode ierr;
PetscInt i,j,k;
PetscInt sx,nx,sy,ny,sz,nz;
Vec Gcoords;
DMDACoor3d ***XX;
PetscScalar xx,yy,zz;
DM cda;
PetscFunctionBeginUser;
ierr = DMDASetUniformCoordinates(da, -1.0,1.0, -1.0,1.0, -1.0,1.0 );CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&Gcoords);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,Gcoords,&XX);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&sx,&sy,&sz,&nx,&ny,&nz);CHKERRQ(ierr);
for (i=sx; i<sx+nx; i++) {
for (j=sy; j<sy+ny; j++ ) {
for (k=sz; k<sz+nz; k++ ) {
PetscScalar Ni[8];
PetscScalar xi = XX[k][j][i].x;
PetscScalar eta = XX[k][j][i].y;
PetscScalar zeta = XX[k][j][i].z;
PetscScalar xn[] = {0.0,2.0,0.2,3.5, 0.0,2.1,0.23,3.125 };
PetscScalar yn[] = {-1.3,0.0,2.0,4.0, -1.45,-0.1,2.24,3.79 };
PetscScalar zn[] = {0.0,0.3,-0.1,0.123, 0.956,1.32,1.12,0.798 };
PetscInt p;
Ni[0] = 0.125*(1.0-xi)*(1.0-eta)*(1.0-zeta);
Ni[1] = 0.125*(1.0+xi)*(1.0-eta)*(1.0-zeta);
Ni[2] = 0.125*(1.0-xi)*(1.0+eta)*(1.0-zeta);
Ni[3] = 0.125*(1.0+xi)*(1.0+eta)*(1.0-zeta);
Ni[4] = 0.125*(1.0-xi)*(1.0-eta)*(1.0+zeta);
Ni[5] = 0.125*(1.0+xi)*(1.0-eta)*(1.0+zeta);
Ni[6] = 0.125*(1.0-xi)*(1.0+eta)*(1.0+zeta);
Ni[7] = 0.125*(1.0+xi)*(1.0+eta)*(1.0+zeta);
xx = yy = zz = 0.0;
for (p=0; p<8; p++ ) {
xx += Ni[p]*xn[p];
yy += Ni[p]*yn[p];
zz += Ni[p]*zn[p];
}
XX[k][j][i].x = xx;
XX[k][j][i].y = yy;
XX[k][j][i].z = zz;
}
}
}
ierr = DMDAVecRestoreArray(cda,Gcoords,&XX);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);
}
/*@C
DMDARestoreCoordinateArray - Sets an array containing the coordinates of the DMDA
Not Collective
Input Parameter:
+ dm - the DM
- xc - the coordinates
Level: intermediate
.keywords: distributed array, get, component name
.seealso: DMDASetCoordinateName(), DMDASetFieldName(), DMDAGetFieldName(), DMDAGetCoordinateArray()
@*/
PetscErrorCode DMDARestoreCoordinateArray(DM dm,void *xc)
{
PetscErrorCode ierr;
DM cdm;
Vec x;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
ierr = DMGetCoordinates(dm,&x);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm,&cdm);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(cdm,x,xc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* FormFunctionLocalMMS2 - Evaluates nonlinear function, F(x) on local process patch */
PetscErrorCode FormFunctionLocalMMS2(DMDALocalInfo *info,PetscScalar **vx,PetscScalar **f,AppCtx *user)
{
PetscErrorCode ierr;
PetscInt i,j;
PetscReal lambda,hx,hy,hxdhy,hydhx;
PetscScalar u,ue,uw,un,us,uxx,uyy;
PetscReal x,y;
DM coordDA;
Vec coordinates;
DMDACoor2d **coords;
PetscFunctionBeginUser;
lambda = user->param;
hx = 1.0/(PetscReal)(info->mx-1);
hy = 1.0/(PetscReal)(info->my-1);
hxdhy = hx/hy;
hydhx = hy/hx;
/* Extract coordinates */
ierr = DMGetCoordinateDM(info->da, &coordDA);CHKERRQ(ierr);
ierr = DMGetCoordinates(info->da, &coordinates);CHKERRQ(ierr);
ierr = DMDAVecGetArray(coordDA, coordinates, &coords);CHKERRQ(ierr);
/* Compute function over the locally owned part of the grid */
for (j=info->ys; j<info->ys+info->ym; j++) {
for (i=info->xs; i<info->xs+info->xm; i++) {
if (i == 0 || j == 0 || i == info->mx-1 || j == info->my-1) {
f[j][i] = 2.0*(hydhx+hxdhy)*vx[j][i];
} else {
x = PetscRealPart(coords[j][i].x);
y = PetscRealPart(coords[j][i].y);
u = vx[j][i];
uw = vx[j][i-1];
ue = vx[j][i+1];
un = vx[j-1][i];
us = vx[j+1][i];
if (i-1 == 0) uw = 0.;
if (i+1 == info->mx-1) ue = 0.;
if (j-1 == 0) un = 0.;
if (j+1 == info->my-1) us = 0.;
uxx = (2.0*u - uw - ue)*hydhx;
uyy = (2.0*u - un - us)*hxdhy;
f[j][i] = uxx + uyy - hx*hy*(lambda*PetscExpScalar(u) + 2*PetscSqr(PETSC_PI)*PetscSinReal(PETSC_PI*x)*PetscSinReal(PETSC_PI*y) - lambda*exp(PetscSinReal(PETSC_PI*x)*PetscSinReal(PETSC_PI*y)));
}
}
}
ierr = DMDAVecRestoreArray(coordDA, coordinates, &coords);CHKERRQ(ierr);
ierr = PetscLogFlops(11.0*info->ym*info->xm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
DMDAGetLogicalCoordinate - Returns a the i,j,k logical coordinate for the closest mesh point to a x,y,z point in the coordinates of the DMDA
Collective on DMDA
Input Parameters:
+ da - the distributed array
- x,y,z - the physical coordinates
Output Parameters:
+ II, JJ, KK - the logical coordinate (-1 on processes that do not contain that point)
- X, Y, Z, - (optional) the coordinates of the located grid point
Level: advanced
Notes:
All processors that share the DMDA must call this with the same coordinate value
.keywords: distributed array, get, processor subset
@*/
PetscErrorCode DMDAGetLogicalCoordinate(DM da,PetscScalar x,PetscScalar y,PetscScalar z,PetscInt *II,PetscInt *JJ,PetscInt *KK,PetscScalar *X,PetscScalar *Y,PetscScalar *Z)
{
DM_DA *dd = (DM_DA*)da->data;
PetscErrorCode ierr;
Vec coors;
DM dacoors;
DMDACoor2d **c;
PetscInt i,j,xs,xm,ys,ym;
PetscReal d,D = PETSC_MAX_REAL,Dv;
PetscMPIInt rank,root;
PetscFunctionBegin;
if (dd->dim == 1) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot get point from 1d DMDA");
if (dd->dim == 3) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot get point from 3d DMDA");
*II = -1;
*JJ = -1;
ierr = DMGetCoordinateDM(da,&dacoors);CHKERRQ(ierr);
ierr = DMDAGetCorners(dacoors,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&coors);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dacoors,coors,&c);CHKERRQ(ierr);
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
d = PetscSqrtReal(PetscRealPart( (c[j][i].x - x)*(c[j][i].x - x) + (c[j][i].y - y)*(c[j][i].y - y) ));
if (d < D) {
D = d;
*II = i;
*JJ = j;
}
}
}
ierr = MPI_Allreduce(&D,&Dv,1,MPIU_REAL,MPI_MIN,PetscObjectComm((PetscObject)da));CHKERRQ(ierr);
if (D != Dv) {
*II = -1;
*JJ = -1;
rank = 0;
} else {
*X = c[*JJ][*II].x;
*Y = c[*JJ][*II].y;
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)da),&rank);CHKERRQ(ierr);
rank++;
}
ierr = MPI_Allreduce(&rank,&root,1,MPI_INT,MPI_SUM,PetscObjectComm((PetscObject)da));CHKERRQ(ierr);
root--;
ierr = MPI_Bcast(X,1,MPIU_SCALAR,root,PetscObjectComm((PetscObject)da));CHKERRQ(ierr);
ierr = MPI_Bcast(Y,1,MPIU_SCALAR,root,PetscObjectComm((PetscObject)da));CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dacoors,coors,&c);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 ini_bou(Vec X,AppCtx* user)
{
PetscErrorCode ierr;
DM cda;
DMDACoor2d **coors;
PetscScalar **p;
Vec gc;
PetscInt i,j;
PetscInt xs,ys,xm,ym,M,N;
PetscScalar xi,yi;
PetscScalar sigmax=user->sigmax,sigmay=user->sigmay;
PetscScalar rho =user->rho;
PetscScalar mux =user->mux,muy=user->muy;
PetscMPIInt rank;
PetscFunctionBeginUser;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
CHKERRQ(ierr);
ierr = DMDAGetInfo(user->da,NULL,&M,&N,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
user->dx = (user->xmax - user->xmin)/(M-1);
user->dy = (user->ymax - user->ymin)/(N-1);
ierr = DMGetCoordinateDM(user->da,&cda);
CHKERRQ(ierr);
ierr = DMGetCoordinates(user->da,&gc);
CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,gc,&coors);
CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,X,&p);
CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&xs,&ys,0,&xm,&ym,0);
CHKERRQ(ierr);
for (i=xs; i < xs+xm; i++) {
for (j=ys; j < ys+ym; j++) {
xi = coors[j][i].x;
yi = coors[j][i].y;
if (i == 0 || j == 0 || i == M-1 || j == N-1) p[j][i] = 0.0;
else p[j][i] = (0.5/(PETSC_PI*sigmax*sigmay*PetscSqrtScalar(1.0-rho*rho)))*PetscExpScalar(-0.5/(1-rho*rho)*(PetscPowScalar((xi-mux)/sigmax,2) + PetscPowScalar((yi-muy)/sigmay,2) - 2*rho*(xi-mux)*(yi-muy)/(sigmax*sigmay)));
}
}
/* p[N/2+N%2][M/2+M%2] = 1/(user->dx*user->dy); */
ierr = DMDAVecRestoreArray(cda,gc,&coors);
CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->da,X,&p);
CHKERRQ(ierr);
PetscFunctionReturn(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;
}
/*
FormFunctionLocal - Evaluates nonlinear function, F(x).
*/
PetscErrorCode FormFunctionLocal(DMDALocalInfo *info,PetscScalar **x,PetscScalar **f,AppCtx *user)
{
DM coordDA;
Vec coordinates;
DMDACoor2d **coords;
PetscScalar u, ux, uy, uxx, uyy;
PetscReal D, K, hx, hy, hxdhy, hydhx;
PetscInt i,j;
PetscErrorCode ierr;
PetscFunctionBeginUser;
D = user->D;
K = user->K;
hx = 1.0/(PetscReal)(info->mx-1);
hy = 1.0/(PetscReal)(info->my-1);
hxdhy = hx/hy;
hydhx = hy/hx;
/*
Compute function over the locally owned part of the grid
*/
ierr = DMGetCoordinateDM(info->da, &coordDA);CHKERRQ(ierr);
ierr = DMGetCoordinates(info->da, &coordinates);CHKERRQ(ierr);
ierr = DMDAVecGetArray(coordDA, coordinates, &coords);CHKERRQ(ierr);
for (j=info->ys; j<info->ys+info->ym; j++) {
for (i=info->xs; i<info->xs+info->xm; i++) {
if (i == 0 || j == 0 || i == info->mx-1 || j == info->my-1) f[j][i] = x[j][i];
else {
u = x[j][i];
ux = (x[j][i+1] - x[j][i])/hx;
uy = (x[j+1][i] - x[j][i])/hy;
uxx = (2.0*u - x[j][i-1] - x[j][i+1])*hydhx;
uyy = (2.0*u - x[j-1][i] - x[j+1][i])*hxdhy;
f[j][i] = D*(uxx + uyy) - (K*funcA(x[j][i], user)*PetscSqrtScalar(ux*ux + uy*uy) + funcU(&coords[j][i]))*hx*hy;
if (PetscIsInfOrNanScalar(f[j][i])) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FP, "Invalid residual: %g", PetscRealPart(f[j][i]));
}
}
}
ierr = DMDAVecRestoreArray(coordDA, coordinates, &coords);CHKERRQ(ierr);
ierr = PetscLogFlops(11*info->ym*info->xm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DADefineXLinearField3D(DM da,Vec field)
{
PetscErrorCode ierr;
PetscInt i,j,k;
PetscInt sx,nx,sy,ny,sz,nz;
Vec Gcoords;
DMDACoor3d ***XX;
PetscScalar ***FF;
DM cda;
PetscFunctionBeginUser;
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&Gcoords);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,Gcoords,&XX);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,field,&FF);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&sx,&sy,&sz,&nx,&ny,&nz);CHKERRQ(ierr);
for (k=sz; k<sz+nz; k++) {
for (j=sy; j<sy+ny; j++ ) {
for (i=sx; i<sx+nx; i++) {
FF[k][j][i] = 10.0
+ 4.05 * XX[k][j][i].x
+ 5.50 * XX[k][j][i].y
+ 1.33 * XX[k][j][i].z
+ 2.03 * XX[k][j][i].x * XX[k][j][i].y
+ 0.03 * XX[k][j][i].x * XX[k][j][i].z
+ 0.83 * XX[k][j][i].y * XX[k][j][i].z
+ 3.79 * XX[k][j][i].x * XX[k][j][i].y * XX[k][j][i].z;
}
}
}
ierr = DMDAVecRestoreArray(da,field,&FF);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(cda,Gcoords,&XX);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ComputeSolution(DM da,PetscGLL *gll,Vec u)
{
PetscErrorCode ierr;
PetscInt j,xs,xn;
PetscScalar *uu,*xx;
PetscReal xd;
Vec x;
PetscFunctionBegin;
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xn,NULL,NULL);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,x,&xx);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,u,&uu);CHKERRQ(ierr);
/* loop over local nodes */
for (j=xs; j<xs+xn; j++) {
xd = xx[j];
uu[j] = (xd*xd - 1.0)*PetscCosReal(5.*PETSC_PI*xd);
}
ierr = DMDAVecRestoreArray(da,x,&xx);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,u,&uu);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMDAGetLocalBoundingBox - Returns the local bounding box for the DMDA.
Not Collective
Input Parameter:
. dm - the DM
Output Parameters:
+ lmin - local minimum coordinates (length dim, optional)
- lmax - local maximim coordinates (length dim, optional)
Level: beginner
.keywords: distributed array, get, coordinates
.seealso: DMDAGetCoordinateDA(), DMGetCoordinates(), DMDAGetBoundingBox()
@*/
PetscErrorCode DMDAGetLocalBoundingBox(DM dm,PetscReal lmin[],PetscReal lmax[])
{
PetscErrorCode ierr;
Vec coords = NULL;
PetscInt dim,i,j;
const PetscScalar *local_coords;
PetscReal min[3]={PETSC_MAX_REAL,PETSC_MAX_REAL,PETSC_MAX_REAL},max[3]={PETSC_MIN_REAL,PETSC_MIN_REAL,PETSC_MIN_REAL};
PetscInt N,Ni;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
dim = dm->dim;
ierr = DMGetCoordinates(dm,&coords);CHKERRQ(ierr);
if (coords) {
ierr = VecGetArrayRead(coords,&local_coords);CHKERRQ(ierr);
ierr = VecGetLocalSize(coords,&N);CHKERRQ(ierr);
Ni = N/dim;
for (i=0; i<Ni; i++) {
for (j=0; j<3; j++) {
min[j] = j < dim ? PetscMin(min[j],PetscRealPart(local_coords[i*dim+j])) : 0;
max[j] = j < dim ? PetscMax(max[j],PetscRealPart(local_coords[i*dim+j])) : 0;
}
}
ierr = VecRestoreArrayRead(coords,&local_coords);CHKERRQ(ierr);
} else { /* Just use grid indices */
DMDALocalInfo info;
ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
min[0] = info.xs;
min[1] = info.ys;
min[2] = info.zs;
max[0] = info.xs + info.xm-1;
max[1] = info.ys + info.ym-1;
max[2] = info.zs + info.zm-1;
}
if (lmin) {ierr = PetscMemcpy(lmin,min,dim*sizeof(PetscReal));CHKERRQ(ierr);}
if (lmax) {ierr = PetscMemcpy(lmax,max,dim*sizeof(PetscReal));CHKERRQ(ierr);}
PetscFunctionReturn(0);
}
PetscErrorCode PostStep(TS ts)
{
PetscErrorCode ierr;
Vec X,gc;
AppCtx *user;
PetscScalar sum = 0,asum;
PetscReal t,**p;
DMDACoor2d **coors;
DM cda;
PetscInt i,j,xs,ys,xm,ym;
PetscFunctionBegin;
ierr = TSGetApplicationContext(ts,&user);CHKERRQ(ierr);
ierr = TSGetTime(ts,&t);CHKERRQ(ierr);
ierr = TSGetSolution(ts,&X);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(user->da,&cda);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr);
ierr = DMGetCoordinates(user->da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,X,&p);CHKERRQ(ierr);
for (i=xs; i < xs+xm; i++) {
for (j=ys; j < ys+ym; j++) {
// printf("i %d j %d y %g %g\n",i,j,coors[j][i].y,p[j][i]);
if (coors[j][i].y < 5) sum += p[j][i];
}
}
ierr = DMDAVecRestoreArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->da,X,&p);CHKERRQ(ierr);
ierr = MPI_Allreduce(&sum,&asum,1,MPIU_SCALAR,MPIU_SUM,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"sum(p)*dw*dtheta at t = %f = %f\n",(double)t,(double)(asum));CHKERRQ(ierr);
if (sum < 1.0e-2) {
ierr = TSSetConvergedReason(ts,TS_CONVERGED_USER);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Exiting TS as the integral of PDF is almost zero\n");CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode DisplayLine(SNES snes,Vec X)
{
PetscInt r,i,j=0,k=0,xs,xm,ys,ym,zs,zm,mx,my,mz;
PetscErrorCode ierr;
Field ***x;
CoordField ***c;
DM da,cda;
Vec C;
PetscMPIInt size,rank;
PetscFunctionBegin;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = SNESGetDM(snes,&da);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&mx,&my,&mz,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&C);CHKERRQ(ierr);
j = my / 2;
k = mz / 2;
ierr = DMDAGetCorners(da,&xs,&ys,&zs,&xm,&ym,&zm);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,X,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,C,&c);CHKERRQ(ierr);
for (r=0;r<size;r++) {
if (rank == r) {
if (j >= ys && j < ys+ym && k >= zs && k < zs+zm) {
for (i=xs; i<xs+xm; i++) {
ierr = PetscPrintf(PETSC_COMM_SELF,"%D %d %d: %f %f %f\n",i,0,0,(double)PetscRealPart(c[k][j][i][0] + x[k][j][i][0]),(double)PetscRealPart(c[k][j][i][1] + x[k][j][i][1]),(double)PetscRealPart(c[k][j][i][2] + x[k][j][i][2]));CHKERRQ(ierr);
}
}
}
ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr);
}
ierr = DMDAVecRestoreArray(da,X,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(cda,C,&c);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode DMDAVTKWriteAll_VTS(DM da,PetscViewer viewer)
{
#if defined(PETSC_USE_REAL_SINGLE)
const char precision[] = "Float32";
#elif defined(PETSC_USE_REAL_DOUBLE)
const char precision[] = "Float64";
#else
const char precision[] = "UnknownPrecision";
#endif
MPI_Comm comm = ((PetscObject)da)->comm;
PetscViewer_VTK *vtk = (PetscViewer_VTK*)viewer->data;
PetscViewerVTKObjectLink link;
FILE *fp;
PetscMPIInt rank,size,tag;
DMDALocalInfo info;
PetscInt dim,mx,my,mz,bs,boffset,maxnnodes,i,j,k,f,r;
PetscInt rloc[6],(*grloc)[6] = PETSC_NULL;
PetscScalar *array,*array2;
PetscReal gmin[3],gmax[3];
PetscErrorCode ierr;
PetscFunctionBegin;
#if defined(PETSC_USE_COMPLEX)
SETERRQ(comm,PETSC_ERR_SUP,"Complex values not supported");
#endif
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,&dim, &mx,&my,&mz, 0,0,0, &bs,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
ierr = DMDAGetBoundingBox(da,gmin,gmax);CHKERRQ(ierr);
ierr = PetscFOpen(comm,vtk->filename,"wb",&fp);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"<?xml version=\"1.0\"?>\n");CHKERRQ(ierr);
#ifdef PETSC_WORDS_BIGENDIAN
ierr = PetscFPrintf(comm,fp,"<VTKFile type=\"StructuredGrid\" version=\"0.1\" byte_order=\"BigEndian\">\n");CHKERRQ(ierr);
#else
ierr = PetscFPrintf(comm,fp,"<VTKFile type=\"StructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n");CHKERRQ(ierr);
#endif
ierr = PetscFPrintf(comm,fp," <StructuredGrid WholeExtent=\"%D %D %D %D %D %D\">\n",0,mx-1,0,my-1,0,mz-1);CHKERRQ(ierr);
if (!rank) {ierr = PetscMalloc(size*6*sizeof(PetscInt),&grloc);CHKERRQ(ierr);}
rloc[0] = info.xs;
rloc[1] = info.xm;
rloc[2] = info.ys;
rloc[3] = info.ym;
rloc[4] = info.zs;
rloc[5] = info.zm;
ierr = MPI_Gather(rloc,6,MPIU_INT,&grloc[0][0],6,MPIU_INT,0,comm);CHKERRQ(ierr);
/* Write XML header */
maxnnodes = 0; /* Used for the temporary array size on rank 0 */
boffset = 0; /* Offset into binary file */
for (r=0; r<size; r++) {
PetscInt xs=-1,xm=-1,ys=-1,ym=-1,zs=-1,zm=-1,nnodes = 0;
if (!rank) {
xs = grloc[r][0];
xm = grloc[r][1];
ys = grloc[r][2];
ym = grloc[r][3];
zs = grloc[r][4];
zm = grloc[r][5];
nnodes = xm*ym*zm;
}
maxnnodes = PetscMax(maxnnodes,nnodes);
#if 0
switch (dim) {
case 1:
ierr = PetscFPrintf(comm,fp," <Piece Extent=\"%D %D %D %D %D %D\">\n",xs,xs+xm-1,0,0,0,0);CHKERRQ(ierr);
break;
case 2:
ierr = PetscFPrintf(comm,fp," <Piece Extent=\"%D %D %D %D %D %D\">\n",xs,xs+xm,ys+ym-1,xs,xs+xm-1,0,0);CHKERRQ(ierr);
break;
case 3:
ierr = PetscFPrintf(comm,fp," <Piece Extent=\"%D %D %D %D %D %D\">\n",xs,xs+xm-1,ys,ys+ym-1,zs,zs+zm-1);CHKERRQ(ierr);
break;
default: SETERRQ1(((PetscObject)da)->comm,PETSC_ERR_SUP,"No support for dimension %D",dim);
}
#endif
ierr = PetscFPrintf(comm,fp," <Piece Extent=\"%D %D %D %D %D %D\">\n",xs,xs+xm-1,ys,ys+ym-1,zs,zs+zm-1);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," <Points>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," <DataArray type=\"%s\" Name=\"Position\" NumberOfComponents=\"3\" format=\"appended\" offset=\"%D\" />\n",precision,boffset);CHKERRQ(ierr);
boffset += 3*nnodes*sizeof(PetscScalar) + sizeof(int);
ierr = PetscFPrintf(comm,fp," </Points>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," <PointData Scalars=\"ScalarPointData\">\n");CHKERRQ(ierr);
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
const char *vecname = "";
if (((PetscObject)X)->name || link != vtk->link) { /* If the object is already named, use it. If it is past the first link, name it to disambiguate. */
ierr = PetscObjectGetName((PetscObject)X,&vecname);CHKERRQ(ierr);
}
for (i=0; i<bs; i++) {
char buf[256];
const char *fieldname;
ierr = DMDAGetFieldName(da,i,&fieldname);CHKERRQ(ierr);
if (!fieldname) {
ierr = PetscSNPrintf(buf,sizeof(buf),"Unnamed%D",i);CHKERRQ(ierr);
fieldname = buf;
}
ierr = PetscFPrintf(comm,fp," <DataArray type=\"%s\" Name=\"%s%s\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",precision,vecname,fieldname,boffset);CHKERRQ(ierr);
boffset += nnodes*sizeof(PetscScalar) + sizeof(int);
}
}
ierr = PetscFPrintf(comm,fp," </PointData>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," </Piece>\n");CHKERRQ(ierr);
}
ierr = PetscFPrintf(comm,fp," </StructuredGrid>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," <AppendedData encoding=\"raw\">\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"_");CHKERRQ(ierr);
/* Now write the arrays. */
tag = ((PetscObject)viewer)->tag;
ierr = PetscMalloc2(maxnnodes*PetscMax(3,bs),PetscScalar,&array,maxnnodes*3,PetscScalar,&array2);CHKERRQ(ierr);
for (r=0; r<size; r++) {
MPI_Status status;
PetscInt xs=-1,xm=-1,ys=-1,ym=-1,zs=-1,zm=-1,nnodes = 0;
if (!rank) {
xs = grloc[r][0];
xm = grloc[r][1];
ys = grloc[r][2];
ym = grloc[r][3];
zs = grloc[r][4];
zm = grloc[r][5];
nnodes = xm*ym*zm;
} else if (r == rank) {
nnodes = info.xm*info.ym*info.zm;
}
{ /* Write the coordinates */
Vec Coords;
ierr = DMGetCoordinates(da,&Coords);CHKERRQ(ierr);
if (Coords) {
const PetscScalar *coords;
ierr = VecGetArrayRead(Coords,&coords);CHKERRQ(ierr);
if (!rank) {
if (r) {
PetscMPIInt nn;
ierr = MPI_Recv(array,nnodes*dim,MPIU_SCALAR,r,tag,comm,&status);CHKERRQ(ierr);
ierr = MPI_Get_count(&status,MPIU_SCALAR,&nn);CHKERRQ(ierr);
if (nn != nnodes*dim) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Array size mismatch");
} else {
ierr = PetscMemcpy(array,coords,nnodes*dim*sizeof(PetscScalar));CHKERRQ(ierr);
}
/* Transpose coordinates to VTK (C-style) ordering */
for (k=0; k<zm; k++) {
for (j=0; j<ym; j++) {
for (i=0; i<xm; i++) {
PetscInt Iloc = i+xm*(j+ym*k);
array2[Iloc*3+0] = array[Iloc*dim + 0];
array2[Iloc*3+1] = dim > 1 ? array[Iloc*dim + 1] : 0;
array2[Iloc*3+2] = dim > 2 ? array[Iloc*dim + 2] : 0;
}
}
}
} else if (r == rank) {
ierr = MPI_Send((void*)coords,nnodes*dim,MPIU_SCALAR,0,tag,comm);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(Coords,&coords);CHKERRQ(ierr);
} else { /* Fabricate some coordinates using grid index */
for (k=0; k<zm; k++) {
for (j=0; j<ym; j++) {
for (i=0; i<xm; i++) {
PetscInt Iloc = i+xm*(j+ym*k);
array2[Iloc*3+0] = xs+i;
array2[Iloc*3+1] = ys+j;
array2[Iloc*3+2] = zs+k;
}
}
}
}
ierr = PetscViewerVTKFWrite(viewer,fp,array2,nnodes*3,PETSC_SCALAR);CHKERRQ(ierr);
}
/* Write each of the objects queued up for this file */
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
const PetscScalar *x;
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
if (!rank) {
if (r) {
PetscMPIInt nn;
ierr = MPI_Recv(array,nnodes*bs,MPIU_SCALAR,r,tag,comm,&status);CHKERRQ(ierr);
ierr = MPI_Get_count(&status,MPIU_SCALAR,&nn);CHKERRQ(ierr);
if (nn != nnodes*bs) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Array size mismatch receiving from rank %D",r);
} else {
ierr = PetscMemcpy(array,x,nnodes*bs*sizeof(PetscScalar));CHKERRQ(ierr);
}
for (f=0; f<bs; f++) {
/* Extract and transpose the f'th field */
for (k=0; k<zm; k++) {
for (j=0; j<ym; j++) {
for (i=0; i<xm; i++) {
PetscInt Iloc = i+xm*(j+ym*k);
array2[Iloc] = array[Iloc*bs + f];
}
}
}
ierr = PetscViewerVTKFWrite(viewer,fp,array2,nnodes,PETSC_SCALAR);CHKERRQ(ierr);
}
} else if (r == rank) {
ierr = MPI_Send((void*)x,nnodes*bs,MPIU_SCALAR,0,tag,comm);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
}
}
ierr = PetscFree2(array,array2);CHKERRQ(ierr);
ierr = PetscFree(grloc);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"\n </AppendedData>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"</VTKFile>\n");CHKERRQ(ierr);
ierr = PetscFClose(comm,fp);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
