PetscErrorCode SetVariableBounds(DM da,Vec xl,Vec xu)
{
PetscErrorCode ierr;
PetscScalar **l,**u;
PetscInt xs,xm;
PetscInt i;
PetscFunctionBeginUser;
ierr = DMDAVecGetArrayDOF(da,xl,&l);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,xu,&u);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
for (i=xs; i < xs+xm; i++) {
l[i][0] = -SNES_VI_INF;
l[i][1] = 0.0;
l[i][2] = 0.0;
u[i][0] = SNES_VI_INF;
u[i][1] = 1.0;
u[i][2] = 1.0;
}
ierr = DMDAVecRestoreArrayDOF(da,xl,&l);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da,xu,&u);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetVariableBounds(DM da,Vec xl,Vec xu)
{
PetscErrorCode ierr;
PetscScalar ***l,***u;
PetscInt xs,xm,ys,ym;
PetscInt j,i;
PetscFunctionBegin;
ierr = DMDAVecGetArrayDOF(da,xl,&l);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,xu,&u);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,&ys,PETSC_NULL,&xm,&ym,PETSC_NULL);CHKERRQ(ierr);
for(j=ys; j < ys+ym; j++) {
for(i=xs; i < xs+xm;i++) {
l[j][i][0] = -SNES_VI_INF;
l[j][i][1] = -1.0;
u[j][i][0] = SNES_VI_INF;
u[j][i][1] = 1.0;
}
}
ierr = DMDAVecRestoreArrayDOF(da,xl,&l);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da,xu,&u);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc, char *argv[])
{
DM da, daX, daY;
DMDALocalInfo info;
MPI_Comm commX, commY;
Vec basisX, basisY;
PetscScalar **arrayX, **arrayY;
const PetscInt *lx, *ly;
PetscInt M = 3, N = 3;
PetscInt p = 1;
PetscInt numGP = 3;
PetscInt dof = 2*(p+1)*numGP;
PetscMPIInt rank, subsize, subrank;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr);
/* Create 2D DMDA */
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_STAR, M, N, PETSC_DECIDE, PETSC_DECIDE, 1, 1, NULL, NULL, &da);CHKERRQ(ierr);
/* Create 1D DMDAs along two directions */
ierr = DMDAGetOwnershipRanges(da, &lx, &ly, NULL);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da, &info);CHKERRQ(ierr);
ierr = DMDAGetProcessorSubsets(da, DMDA_X, &commX);CHKERRQ(ierr);
ierr = DMDAGetProcessorSubsets(da, DMDA_Y, &commY);CHKERRQ(ierr);
ierr = MPI_Comm_size(commX, &subsize);CHKERRQ(ierr);
ierr = MPI_Comm_rank(commX, &subrank);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "[%d]X subrank: %d subsize: %d\n", rank, subrank, subsize);
ierr = MPI_Comm_size(commY, &subsize);CHKERRQ(ierr);
ierr = MPI_Comm_rank(commY, &subrank);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "[%d]Y subrank: %d subsize: %d\n", rank, subrank, subsize);
ierr = DMDACreate1d(commX, DM_BOUNDARY_NONE, M, dof, 1, lx, &daX);CHKERRQ(ierr);
ierr = DMDACreate1d(commY, DM_BOUNDARY_NONE, N, dof, 1, ly, &daY);CHKERRQ(ierr);
/* Create 1D vectors for basis functions */
ierr = DMGetGlobalVector(daX, &basisX);CHKERRQ(ierr);
ierr = DMGetGlobalVector(daY, &basisY);CHKERRQ(ierr);
/* Extract basis functions */
ierr = DMDAVecGetArrayDOF(daX, basisX, &arrayX);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(daY, basisY, &arrayY);CHKERRQ(ierr);
/*arrayX[i][ndof]; */
/*arrayY[j][ndof]; */
ierr = DMDAVecRestoreArrayDOF(daX, basisX, &arrayX);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(daY, basisY, &arrayY);CHKERRQ(ierr);
/* Return basis vectors */
ierr = DMRestoreGlobalVector(daX, &basisX);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(daY, &basisY);CHKERRQ(ierr);
/* Cleanup */
ierr = DMDestroy(&daX);CHKERRQ(ierr);
ierr = DMDestroy(&daY);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode SingleBodyPoints::calculateAvgForces(const Vec &f,
type::RealVec1D &fAvg) const
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
PetscReal **fArry;
type::RealVec1D fAvgLocal(dim, 0.0);
ierr = DMDAVecGetArrayDOF(da, f, &fArry); CHKERRQ(ierr);
for (PetscInt i = bgPt; i < edPt; ++i)
{
for (PetscInt dof = 0; dof < dim; ++dof)
{
fAvgLocal[dof] -=
fArry[i][dof]; // fArray is the force applied to fluid
}
}
ierr = MPI_Barrier(comm); CHKERRQ(ierr);
ierr = MPI_Allreduce(fAvgLocal.data(), fAvg.data(), dim, MPIU_REAL, MPI_SUM,
comm); CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da, f, &fArry); CHKERRQ(ierr);
PetscFunctionReturn(0);
} // calculateAvgForces
/*
Applies the second order centered difference diffusion operator on a one dimensional periodic domain
*/
static PetscErrorCode FormDiffusionFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
{
User user = (User)ptr;
PetscErrorCode ierr;
PetscScalar **f;
const PetscScalar **x;
DM dm;
PetscInt i,xs,xm,j,dof;
Vec Xlocal;
PetscReal idx;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMDAGetInfo(dm,NULL,NULL,NULL,NULL,NULL,NULL,NULL,&dof,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xlocal);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOFRead(dm,Xlocal,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(dm,F,&f);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
idx = 1.0*user->diffus/user->dx;
for (i=xs; i<xs+xm; i++) {
for (j=0; j<dof; j++) {
f[i][j] += idx*(x[i+1][j] - 2.0*x[i][j] + x[i-1][j]);
}
}
ierr = DMDAVecRestoreArrayDOFRead(dm,Xlocal,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(dm,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xlocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode FormRHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
{
User user = (User)ptr;
PetscErrorCode ierr;
PetscScalar **f;
const PetscScalar **x;
DM dm;
PetscInt i,xs,xm;
PetscFunctionBeginUser;
if (user->reactions) {
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOFRead(dm,X,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(dm,F,&f);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
for (i=xs; i<xs+xm; i++) {
ierr = PetscMemcpy(user->tchemwork,x[i],(user->Nspec+1)*sizeof(x[xs][0]));CHKERRQ(ierr);
user->tchemwork[0] *= user->Tini; /* Dimensionalize */
ierr = TC_getSrc(user->tchemwork,user->Nspec+1,f[i]);TCCHKERRQ(ierr);
f[i][0] /= user->Tini; /* Non-dimensionalize */
}
ierr = DMDAVecRestoreArrayDOFRead(dm,X,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(dm,F,&f);CHKERRQ(ierr);
} else {
ierr = VecZeroEntries(F);CHKERRQ(ierr);
}
if (user->diffusion) {
ierr = FormDiffusionFunction(ts,t,X,F,ptr);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode DMDAVecGenerateEntries(DM dm,Vec a)
{
PetscScalar ****LA_v;
PetscInt i,j,k,si,sj,sk,ni,nj,nk,M,N;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMDAGetInfo(dm,NULL,&M,&N,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&si,&sj,&sk,&ni,&nj,&nk);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(dm,a,&LA_v);CHKERRQ(ierr);
for (k=sk; k<sk+nk; k++) {
for (j=sj; j<sj+nj; j++) {
for (i=si; i<si+ni; i++) {
PetscScalar test_value_s;
test_value_s = dmda_i_val[i]*((PetscScalar)i) + dmda_j_val[j]*((PetscScalar)(i+j*M)) + dmda_k_val[k]*((PetscScalar)(i + j*M + k*M*N));
LA_v[k][j][i][0] = 3.0 * test_value_s;
LA_v[k][j][i][1] = 3.0 * test_value_s + 1.0;
LA_v[k][j][i][2] = 3.0 * test_value_s + 2.0;
}
}
}
ierr = DMDAVecRestoreArrayDOF(dm,a,&LA_v);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormInitialSolution(TS ts,Vec X,void *ctx)
{
PetscScalar **x,*xc;
PetscErrorCode ierr;
struct {const char *name; PetscReal massfrac;} initial[] = {
{"CH4", 0.0948178320887},
{"O2", 0.189635664177},
{"N2", 0.706766236705},
{"AR", 0.00878026702874}
};
PetscInt i,j,xs,xm;
DM dm;
PetscFunctionBeginUser;
ierr = VecZeroEntries(X);CHKERRQ(ierr);
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
ierr = DMDAGetCoordinateArray(dm,&xc);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(dm,X,&x);CHKERRQ(ierr);
for (i=xs; i<xs+xm; i++) {
x[i][0] = 1.0 + .05*PetscSinScalar(2.*PETSC_PI*xc[i]); /* Non-dimensionalized by user->Tini */
for (j=0; j<sizeof(initial)/sizeof(initial[0]); j++) {
int ispec = TC_getSpos(initial[j].name, strlen(initial[j].name));
if (ispec < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Could not find species %s",initial[j].name);
ierr = PetscPrintf(PETSC_COMM_SELF,"Species %d: %s %g\n",j,initial[j].name,initial[j].massfrac);CHKERRQ(ierr);
x[i][1+ispec] = initial[j].massfrac;
}
}
ierr = DMDAVecRestoreArrayDOF(dm,X,&x);CHKERRQ(ierr);
ierr = DMDARestoreCoordinateArray(dm,&xc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormInitialSolution(DM da,Vec U)
{
PetscErrorCode ierr;
PetscInt i,j,xs,ys,xm,ym,Mx,My;
PetscScalar ***u;
PetscReal hx,hy,x,y,r;
PetscFunctionBeginUser;
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);
hx = 1.0/(PetscReal)(Mx-1);
hy = 1.0/(PetscReal)(My-1);
/*
Get pointers to vector data
*/
ierr = DMDAVecGetArrayDOF(da,U,&u);CHKERRQ(ierr);
/*
Get local grid boundaries
*/
ierr = DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);
/*
Compute function over the locally owned part of the grid
*/
for (j=ys; j<ys+ym; j++) {
y = j*hy;
for (i=xs; i<xs+xm; i++) {
x = i*hx;
r = PetscSqrtReal((x-.5)*(x-.5) + (y-.5)*(y-.5));
if (r < .125) {
u[j][i][0] = PetscExpReal(-30.0*r*r*r);
u[j][i][1] = 0.0;
} else {
u[j][i][0] = 0.0;
u[j][i][1] = 0.0;
}
}
}
/*
Restore vectors
*/
ierr = DMDAVecRestoreArrayDOF(da,U,&u);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt M = -2, N = -3, P = 4,stencil_width = 1, dof = 1,m,n,p,xstart,ystart,zstart,i,j,k,c;
DM da;
Vec global,local;
PetscScalar ****vglobal;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
PetscFunctionBeginUser;
ierr = PetscOptionsGetInt(0,"-stencil_width",&stencil_width,0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(0,"-dof",&dof,0);CHKERRQ(ierr);
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_MIRROR,DM_BOUNDARY_MIRROR,DM_BOUNDARY_MIRROR,DMDA_STENCIL_STAR,M,N,P,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,dof,stencil_width,NULL,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xstart,&ystart,&zstart,&m,&n,&p);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,global,&vglobal);CHKERRQ(ierr);
for (k=zstart; k<zstart+p; k++) {
for (j=ystart; j<ystart+n; j++) {
for (i=xstart; i<xstart+m; i++) {
for (c=0; c<dof; c++) {
vglobal[k][j][i][c] = 1000*k + 100*j + 10*(i+1) + c;
}
}
}
}
ierr = DMDAVecRestoreArrayDOF(da,global,&vglobal);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = PetscSequentialPhaseBegin(PETSC_COMM_WORLD,1);CHKERRQ(ierr);
ierr = VecView(local,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = PetscSequentialPhaseEnd(PETSC_COMM_WORLD,1);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt M = 6,stencil_width = 1, dof = 1,m,xstart,i,j;
DM da;
Vec global,local;
PetscScalar **vglobal;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
PetscFunctionBeginUser;
ierr = PetscOptionsGetInt(0,"-stencil_width",&stencil_width,0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(0,"-dof",&dof,0);CHKERRQ(ierr);
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_MIRROR,M,dof,stencil_width,NULL,&da);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xstart,0,0,&m,0,0);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,global,&vglobal);CHKERRQ(ierr);
for (i=xstart; i<xstart+m; i++) {
for (j=0; j<dof; j++) {
vglobal[i][j] = 100*(i+1) + j;
}
}
ierr = DMDAVecRestoreArrayDOF(da,global,&vglobal);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = PetscSequentialPhaseBegin(PETSC_COMM_WORLD,1);CHKERRQ(ierr);
ierr = VecView(local,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = PetscSequentialPhaseEnd(PETSC_COMM_WORLD,1);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscInt M = 6,N = 5,P = 4, m = PETSC_DECIDE,n = PETSC_DECIDE,p = PETSC_DECIDE,i,j,k,is,js,ks,in,jen,kn;
PetscErrorCode ierr;
DM da;
Vec local,global;
PetscScalar ****l;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
/* Create distributed array and get vectors */
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,P,m,n,p,2,1,NULL,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&is,&js,&ks,&in,&jen,&kn);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,local,&l);CHKERRQ(ierr);
for (i=is; i<is+in; i++) {
for (j=js; j<js+jen; j++) {
for (k=ks; k<ks+kn; k++) {
l[k][j][i][0] = 2*(i + j*M + k*M*N);
l[k][j][i][1] = 2*(i + j*M + k*M*N) + 1;
}
}
}
ierr = DMDAVecRestoreArrayDOF(da,local,&l);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,local,ADD_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,local,ADD_VALUES,global);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Free memory */
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
PetscInt M = 6,N = 5,m = PETSC_DECIDE,n = PETSC_DECIDE,i,j,is,js,in,jen;
PetscErrorCode ierr;
DM da;
Vec local,global;
PetscScalar ***l;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,m,n,3,1,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&is,&js,0,&in,&jen,0);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,local,&l);CHKERRQ(ierr);
for (i=is; i<is+in; i++) {
for (j=js; j<js+jen; j++) {
l[j][i][0] = 3*(i + j*M);
l[j][i][1] = 3*(i + j*M) + 1;
l[j][i][2] = 3*(i + j*M) + 2;
}
}
ierr = DMDAVecRestoreArrayDOF(da,local,&l);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,local,ADD_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,local,ADD_VALUES,global);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Free memory */
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode InitialConditions(DM da,Vec U)
{
PetscErrorCode ierr;
PetscInt i,c,xs,xm,Mx,N;
PetscScalar **u;
PetscReal hx,x;
PetscFunctionBegin;
ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,&N,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
hx = 1.0/(PetscReal)(Mx-1);
/*
Get pointers to vector data
*/
ierr = DMDAVecGetArrayDOF(da,U,&u);CHKERRQ(ierr);
/*
Get local grid boundaries
*/
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
/*
Compute function over the locally owned part of the grid
*/
for (i=xs; i<xs+xm; i++) {
x = i*hx;
for (c=0; c<N; c++) u[i][c] = 0.0; /*PetscCosScalar(PETSC_PI*x);*/
}
/*
Restore vectors
*/
ierr = DMDAVecRestoreArrayDOF(da,U,&u);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode IJacobian(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal a,Mat *J,Mat *Jpre,MatStructure *str,void *ctx)
{
PetscErrorCode ierr;
PetscInt i,c,Mx,xs,xm,nc;
DM da;
MatStencil col[3],row;
PetscScalar vals[3],hx,sx;
AppCtx *user = (AppCtx*)ctx;
PetscInt N = user->N;
PetscScalar **u;
PetscFunctionBegin;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
hx = 1.0/(PetscReal)(Mx-1); sx = 1.0/(hx*hx);
ierr = DMDAVecGetArrayDOF(da,U,&u);CHKERRQ(ierr);
ierr = MatZeroEntries(*Jpre);CHKERRQ(ierr);
for (i=xs; i<xs+xm; i++) {
for (c=0; c<N; c++) {
nc = 0;
row.c = c; row.i = i;
col[nc].c = c; col[nc].i = i-1; vals[nc++] = -sx;
col[nc].c = c; col[nc].i = i; vals[nc++] = 2.0*sx + a;
col[nc].c = c; col[nc].i = i+1; vals[nc++] = -sx;
ierr = MatSetValuesStencil(*Jpre,1,&row,nc,col,vals,ADD_VALUES);CHKERRQ(ierr);
}
for (c=0; c<N/3; c++) {
nc = 0;
row.c = c; row.i = i;
col[nc].c = c; col[nc].i = i; vals[nc++] = 1000*u[i][c] + 500*u[i][c+1];
col[nc].c = c+1; col[nc].i = i; vals[nc++] = 500*u[i][c];
ierr = MatSetValuesStencil(*Jpre,1,&row,nc,col,vals,ADD_VALUES);CHKERRQ(ierr);
nc = 0;
row.c = c+1; row.i = i;
col[nc].c = c; col[nc].i = i; vals[nc++] = -1000*u[i][c] + 500*u[i][c+1];
col[nc].c = c+1; col[nc].i = i; vals[nc++] = 500*u[i][c];
ierr = MatSetValuesStencil(*Jpre,1,&row,nc,col,vals,ADD_VALUES);CHKERRQ(ierr);
nc = 0;
row.c = c+2; row.i = i;
col[nc].c = c; col[nc].i = i; vals[nc++] = -500*u[i][c+1];
col[nc].c = c+1; col[nc].i = i; vals[nc++] = -500*u[i][c];
ierr = MatSetValuesStencil(*Jpre,1,&row,nc,col,vals,ADD_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(*Jpre,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*Jpre,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (*J != *Jpre) {
ierr = MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
ierr = DMDAVecRestoreArrayDOF(da,U,&u);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
IFunction - Evaluates nonlinear function, F(U).
Input Parameters:
. ts - the TS context
. U - input vector
. ptr - optional user-defined context, as set by SNESSetFunction()
Output Parameter:
. F - function vector
*/
PetscErrorCode IFunction(TS ts,PetscReal ftime,Vec U,Vec Udot,Vec F,void *ptr)
{
DM da;
PetscErrorCode ierr;
PetscInt i,c,Mx,xs,xm,N;
PetscReal hx,sx,x;
PetscScalar uxx;
PetscScalar **u,**f,**udot;
Vec localU;
PetscFunctionBegin;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&localU);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,&N,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
hx = 1.0/(PetscReal)(Mx-1); sx = 1.0/(hx*hx);
/*
Scatter ghost points to local vector,using the 2-step process
DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
By placing code between these two statements, computations can be
done while messages are in transition.
*/
ierr = DMGlobalToLocalBegin(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
/*
Get pointers to vector data
*/
ierr = DMDAVecGetArrayDOF(da,localU,&u);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,Udot,&udot);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,F,&f);CHKERRQ(ierr);
/*
Get local grid boundaries
*/
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
/*
Compute function over the locally owned part of the grid
*/
for (i=xs; i<xs+xm; i++) {
x = i*hx;
/* diffusion term */
for (c=0; c<N; c++) {
uxx = (-2.0*u[i][c] + u[i-1][c] + u[i+1][c])*sx;
f[i][c] = udot[i][c] - uxx;
}
/* reaction terms */
for (c=0; c<N/3; c++) {
f[i][c] += 500*u[i][c]*u[i][c] + 500*u[i][c]*u[i][c+1];
f[i][c+1] += -500*u[i][c]*u[i][c] + 500*u[i][c]*u[i][c+1];
f[i][c+2] -= 500*u[i][c]*u[i][c+1];
}
/* forcing term */
f[i][0] -= 5*PetscExpScalar((1.0 - x)*(1.0 - x));
}
/*
Restore vectors
*/
ierr = DMDAVecRestoreArrayDOF(da,localU,&u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da,Udot,&udot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localU);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscInt M = 10,N = 8,dof=1,s=1,bx=0,by=0,i,n,j,k,m,wrap,xs,ys;
PetscErrorCode ierr;
DM da,dac;
PetscViewer viewer;
Vec local,global,coors;
PetscScalar ***xy,***aglobal;
PetscDraw draw;
char fname[16];
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
/* Create viewers */
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",PETSC_DECIDE,PETSC_DECIDE,600,200,&viewer);CHKERRQ(ierr);
ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
ierr = PetscDrawSetDoubleBuffer(draw);CHKERRQ(ierr);
/* Read options */
ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-dof",&dof,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-s",&s,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-periodic_x",&wrap,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-periodic_y",&wrap,NULL);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DMDACreate2d(PETSC_COMM_WORLD,(DMBoundaryType)bx,(DMBoundaryType)by,DMDA_STENCIL_BOX,M,N,PETSC_DECIDE,PETSC_DECIDE,dof,s,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,0.0);CHKERRQ(ierr);
for (i=0; i<dof; i++) {
sprintf(fname,"Field %d",(int)i);
ierr = DMDASetFieldName(da,i,fname);CHKERRQ(ierr);
}
ierr = DMView(da,viewer);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&coors);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&dac);CHKERRQ(ierr);
/* Set values into global vectors */
ierr = DMDAVecGetArrayDOFRead(dac,coors,&xy);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,global,&aglobal);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,&ys,0,&m,&n,0);CHKERRQ(ierr);
for (k=0; k<dof; k++) {
for (j=ys; j<ys+n; j++) {
for (i=xs; i<xs+m; i++) {
aglobal[j][i][k] = PetscSinScalar(2.0*PETSC_PI*(k+1)*xy[j][i][0]);
}
}
}
ierr = DMDAVecRestoreArrayDOF(da,global,&aglobal);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOFRead(dac,coors,&xy);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = VecSet(global,0.0);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,local,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,local,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecView(global,viewer);CHKERRQ(ierr);
/* Free memory */
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/*
FormFunction - Evaluates nonlinear function, F(x).
Input Parameters:
. ts - the TS context
. X - input vector
. ptr - optional user-defined context, as set by SNESSetFunction()
Output Parameter:
. F - function vector
*/
PetscErrorCode FormFunction(TS ts,PetscReal ftime,Vec X,Vec F,void *ptr)
{
DM da = (DM)ptr;
PetscErrorCode ierr;
PetscInt i,j,Mx,My,xs,ys,xm,ym;
PetscReal hx,hy,/*hxdhy,hydhx,*/ sx,sy;
PetscScalar u,uxx,uyy,v,***x,***f;
Vec localX;
PetscFunctionBeginUser;
ierr = DMGetLocalVector(da,&localX);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);
hx = 1.0/(PetscReal)(Mx-1); sx = 1.0/(hx*hx);
hy = 1.0/(PetscReal)(My-1); sy = 1.0/(hy*hy);
/*hxdhy = hx/hy;*/
/*hydhx = hy/hx;*/
/*
Scatter ghost points to local vector,using the 2-step process
DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
By placing code between these two statements, computations can be
done while messages are in transition.
*/
ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
/*
Get pointers to vector data
*/
ierr = DMDAVecGetArrayDOF(da,localX,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,F,&f);CHKERRQ(ierr);
/*
Get local grid boundaries
*/
ierr = DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);
/*
Compute function over the locally owned part of the grid
*/
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
if (i == 0 || j == 0 || i == Mx-1 || j == My-1) {
f[j][i][0] = x[j][i][0];
f[j][i][1] = x[j][i][1];
continue;
}
u = x[j][i][0];
v = x[j][i][1];
uxx = (-2.0*u + x[j][i-1][0] + x[j][i+1][0])*sx;
uyy = (-2.0*u + x[j-1][i][0] + x[j+1][i][0])*sy;
f[j][i][0] = v;
f[j][i][1] = uxx + uyy;
}
}
/*
Restore vectors
*/
ierr = DMDAVecRestoreArrayDOF(da,localX,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localX);CHKERRQ(ierr);
ierr = PetscLogFlops(11.0*ym*xm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInitialize(&argc,&argv,(char*)0,help);
const int d = 2; // d = DOF
Mat A, Aminus;
// these are dense d x d sequential matrices, unrelated to the grid
// (each processor owns whole matrix)
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,d,d,d,NULL,&A); CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(A,"A_"); CHKERRQ(ierr);
ierr = MatSetFromOptions(A); CHKERRQ(ierr);
// fill A
double val[d][d], c = 3.0;
val[0][0] = 0.0; val[0][1] = c;
val[1][0] = c; val[1][1] = 0.0;
ierr = fillsmallmat(2,val,A); CHKERRQ(ierr);
// fill Aminus; see getAminus.m for computation of Aminus from A
ierr = MatDuplicate(A,MAT_SHARE_NONZERO_PATTERN,&Aminus); CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(Aminus,"Aminus_"); CHKERRQ(ierr);
val[0][0] = -1.5; val[0][1] = 1.5;
val[1][0] = 1.5; val[1][1] = -1.5;
ierr = fillsmallmat(2,val,Aminus); CHKERRQ(ierr);
// set up the grid
DM da;
ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC,
-50, // override with -da_grid_x or -da_refine
d, 1, NULL, // dof = 1 and stencil width = 1
&da); CHKERRQ(ierr);
// determine grid locations (cell-centered grid)
DMDALocalInfo info;
double L = 10.0, dx;
ierr = DMDAGetLocalInfo(da,&info); CHKERRQ(ierr);
dx = L / (double)(info.mx);
ierr = DMDASetUniformCoordinates(da,dx/2,L-dx/2,-1.0,-1.0,-1.0,-1.0);CHKERRQ(ierr);
// u = u(t_n), unew = u(t_n+1)
Vec u, unew, F;
ierr = DMCreateLocalVector(da,&u);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)u,"solution u"); CHKERRQ(ierr);
ierr = VecDuplicate(u,&F);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)F,"flux F"); CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&unew);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)unew,"updated solution unew"); CHKERRQ(ierr);
ierr = VecSet(unew,0.0); CHKERRQ(ierr);
// at each cell we will need to compute Fcell = A qleft + Aminus dq
Vec dq, qleft, tmp, Fcell;
ierr = VecCreateSeq(PETSC_COMM_WORLD,d,&dq); CHKERRQ(ierr);
ierr = VecDuplicate(dq,&qleft); CHKERRQ(ierr);
ierr = VecDuplicate(dq,&tmp); CHKERRQ(ierr);
ierr = VecDuplicate(dq,&Fcell); CHKERRQ(ierr);
// view the solution graphically; control with -draw_pause
PetscViewer viewer;
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,NULL,"solution u",
PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,&viewer); CHKERRQ(ierr);
/* time-stepping loop */
double t = 0.0, tf = 10.0, dt, nu;
int n, NN = 10;
dt = tf / NN;
nu = dt / dx;
for (n = 0; n < NN; ++n) {
ierr = PetscPrintf(PETSC_COMM_WORLD, " time[%3d]=%6g: \n", n, t); CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,unew,INSERT_VALUES,u); CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,unew,INSERT_VALUES,u); CHKERRQ(ierr);
ierr = VecView(u,viewer); CHKERRQ(ierr);
double **au, **aunew, **aF;
int j, p;
ierr = DMDAVecGetArrayDOF(da, u, &au);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da, F, &aF);CHKERRQ(ierr);
for (j=info.xs; j<info.xs+info.xm; j++) {
double *adq, *aqleft, *aFcell;
ierr = VecGetArray(dq,&adq); CHKERRQ(ierr);
ierr = VecGetArray(qleft,&aqleft); CHKERRQ(ierr);
for (p = 0; p < d; p++) {
adq[p] = au[j+1][p] - au[j][p];
aqleft[p] = au[j][p];
}
ierr = VecRestoreArray(dq,&adq); CHKERRQ(ierr);
ierr = VecRestoreArray(qleft,&aqleft); CHKERRQ(ierr);
// tmp = A qleft
// Fcell = tmp + Aminus dq
ierr = MatMult(A,qleft,tmp); CHKERRQ(ierr);
ierr = MatMultAdd(Aminus,dq,tmp,Fcell); CHKERRQ(ierr);
ierr = VecGetArray(Fcell,&aFcell); CHKERRQ(ierr);
for (p = 0; p < d; p++)
aF[j][p] = aFcell[p];
ierr = VecRestoreArray(Fcell,&aFcell); CHKERRQ(ierr);
}
ierr = DMDAVecRestoreArrayDOF(da, F, &aF);CHKERRQ(ierr);
ierr = DMLocalToLocalBegin(da,F,INSERT_VALUES,F); CHKERRQ(ierr);
ierr = DMLocalToLocalEnd(da,F,INSERT_VALUES,F); CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da, F, &aF);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da, unew, &aunew);CHKERRQ(ierr);
for (j=info.xs; j<info.xs+info.xm; j++) {
for (p = 0; p < d; p++)
aunew[j][p] = au[j][p] - nu * (aF[j+1][p] - aF[j][p]);
}
ierr = DMDAVecRestoreArrayDOF(da, u, &au);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da, F, &aF);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da, unew, &aunew);CHKERRQ(ierr);
t += dt;
}
// clean up
ierr = VecDestroy(&u); CHKERRQ(ierr);
ierr = VecDestroy(&unew); CHKERRQ(ierr);
ierr = VecDestroy(&F); CHKERRQ(ierr);
ierr = VecDestroy(&dq); CHKERRQ(ierr);
ierr = VecDestroy(&qleft); CHKERRQ(ierr);
ierr = VecDestroy(&tmp); CHKERRQ(ierr);
ierr = VecDestroy(&Fcell); CHKERRQ(ierr);
ierr = MatDestroy(&A); CHKERRQ(ierr);
ierr = MatDestroy(&Aminus); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
ierr = DMDestroy(&da); CHKERRQ(ierr);
ierr = PetscFinalize(); CHKERRQ(ierr);
return 0;
}
PetscErrorCode CheckRedundancy(SNES snes, IS act, IS *outact, DM da)
{
PetscErrorCode ierr;
PetscScalar **uin,**uout;
Vec UIN, UOUT;
PetscInt xs,xm,*outindex;
const PetscInt *index;
PetscInt k,i,l,n,M,cnt=0;
PetscFunctionBeginUser;
ierr = DMDAGetInfo(da,0,&M,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMGetGlobalVector(da,&UIN);CHKERRQ(ierr);
ierr = VecSet(UIN,0.0);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&UOUT);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,UIN,&uin);CHKERRQ(ierr);
ierr = ISGetIndices(act,&index);CHKERRQ(ierr);
ierr = ISGetLocalSize(act,&n);CHKERRQ(ierr);
for (k=0; k<n; k++) {
l = index[k]%5;
i = index[k]/5;
uin[i][l]=1.0;
}
printf("Number of active constraints before applying redundancy %d\n",n);
ierr = ISRestoreIndices(act,&index);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da,UIN,&uin);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,UIN,INSERT_VALUES,UOUT);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,UIN,INSERT_VALUES,UOUT);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,UOUT,&uout);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
for (i=xs; i < xs+xm;i++) {
if (uout[i-1][1] && uout[i][1] && uout[i+1][1]) uout[i][0] = 1.0;
if (uout[i-1][3] && uout[i][3] && uout[i+1][3]) uout[i][2] = 1.0;
}
for (i=xs; i < xs+xm; i++) {
for (l=0; l < 5; l++) {
if (uout[i][l]) cnt++;
}
}
printf("Number of active constraints after applying redundancy %d\n",cnt);
ierr = PetscMalloc(cnt*sizeof(PetscInt),&outindex);CHKERRQ(ierr);
cnt = 0;
for (i=xs; i < xs+xm;i++) {
for (l=0;l<5;l++) {
if (uout[i][l]) outindex[cnt++] = 5*(i)+l;
}
}
ierr = ISCreateGeneral(PETSC_COMM_WORLD,cnt,outindex,PETSC_OWN_POINTER,outact);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(da,UOUT,&uout);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(da,&UIN);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&UOUT);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "DMConvert_DA_Mesh"
PetscErrorCode DMConvert_DA_Mesh(DM dm, const DMType newtype, DM *dmNew)
{
PetscSection section;
DM cda;
DMDALocalInfo info;
Vec coordinates;
PetscInt *cone, *coneO;
PetscInt dim, M, N, P, numCells, numGlobalCells, numCorners, numVertices, c = 0, v = 0;
PetscInt ye, ze;
PetscInt debug = 0;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscOptionsGetInt(PETSC_NULL, "-dm_mesh_debug", &debug, PETSC_NULL);CHKERRQ(ierr);
ierr = DMDAGetInfo(dm, &dim, &M, &N, &P, 0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm, &info);CHKERRQ(ierr);
if (info.sw > 1) SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_SUP, "Currently, only DMDAs with unti stencil width can be converted to DMMeshes.");
/* In order to get a partition of cells, rather than vertices, we give each process the cells between vertices it owns
and also higher numbered ghost vertices (vertices to the right and up) */
numCorners = 1 << dim;
numCells = ((info.gxm+info.gxs - info.xs) - 1);
if (dim > 1) {numCells *= ((info.gym+info.gys - info.ys) - 1);}
if (dim > 2) {numCells *= ((info.gzm+info.gzs - info.zs) - 1);}
numVertices = (info.gxm+info.gxs - info.xs);
if (dim > 1) {numVertices *= (info.gym+info.gys - info.ys);}
if (dim > 2) {numVertices *= (info.gzm+info.gzs - info.zs);}
numGlobalCells = M-1;
if (dim > 1) {numGlobalCells *= N-1;}
if (dim > 2) {numGlobalCells *= P-1;}
ALE::Obj<PETSC_MESH_TYPE> mesh = new PETSC_MESH_TYPE(((PetscObject) dm)->comm, info.dim, debug);
ALE::Obj<PETSC_MESH_TYPE::sieve_type> sieve = new PETSC_MESH_TYPE::sieve_type(((PetscObject) dm)->comm, 0, numCells+numVertices, debug);
PETSC_MESH_TYPE::renumbering_type renumbering;
mesh->setSieve(sieve);
/* Number each cell for the vertex in the lower left corner */
if (dim < 3) {ze = 1; P = 1;} else {ze = info.gzs+info.gzm-1;}
if (dim < 2) {ye = 1; N = 1;} else {ye = info.gys+info.gym-1;}
for(PetscInt k = info.zs; k < ze; ++k) {
for(PetscInt j = info.ys; j < ye; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm-1; ++i, ++c) {
PetscInt globalC = (k*(N-1) + j)*(M-1) + i;
renumbering[globalC] = c;
sieve->setConeSize(c, numCorners);
}
}
}
if (c != numCells) {SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Error in generated cell numbering, %d should be %d", c, numCells);}
/* Get vertex renumbering */
for(PetscInt k = info.zs; k < info.gzs+info.gzm; ++k) {
for(PetscInt j = info.ys; j < info.gys+info.gym; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i, ++v) {
PetscInt globalV = (k*N + j)*M + i + numGlobalCells;
renumbering[globalV] = v+numCells;
}
}
}
if (v != numVertices) {SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Error in generated vertex numbering, %d should be %d", v, numVertices);}
/* Calculate support sizes */
for(PetscInt k = info.zs; k < ze; ++k, ++c) {
for(PetscInt j = info.ys; j < ye; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm-1; ++i) {
for(PetscInt kp = k; kp <= k+(dim>2); ++kp) {
for(PetscInt jp = j; jp <= j+(dim>1); ++jp) {
for(PetscInt ip = i; ip <= i+1; ++ip) {
PetscInt globalV = (kp*N + jp)*M + ip + numGlobalCells;
sieve->addSupportSize(renumbering[globalV], 1);
}
}
}
}
}
}
sieve->allocate();
ierr = PetscMalloc2(numCorners,PetscInt,&cone,numCorners,PetscInt,&coneO);CHKERRQ(ierr);
for(PetscInt v = 0; v < numCorners; ++v) {
coneO[v] = 1;
}
for(PetscInt k = info.zs; k < ze; ++k) {
for(PetscInt j = info.ys; j < ye; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm-1; ++i) {
PetscInt globalC = (k*(N-1) + j)*(M-1) + i;
PetscInt v = 0;
cone[v++] = renumbering[(k*N + j)*M + i+0 + numGlobalCells];
cone[v++] = renumbering[(k*N + j)*M + i+1 + numGlobalCells];
if (dim > 1) {
cone[v++] = renumbering[(k*N + j+1)*M + i+0 + numGlobalCells];
cone[v++] = renumbering[(k*N + j+1)*M + i+1 + numGlobalCells];
}
if (dim > 2) {
cone[v++] = renumbering[((k+1)*N + j+0)*M + i+0 + numGlobalCells];
cone[v++] = renumbering[((k+1)*N + j+0)*M + i+1 + numGlobalCells];
cone[v++] = renumbering[((k+1)*N + j+1)*M + i+0 + numGlobalCells];
cone[v++] = renumbering[((k+1)*N + j+1)*M + i+1 + numGlobalCells];
}
sieve->setCone(cone, renumbering[globalC]);
sieve->setConeOrientation(coneO, renumbering[globalC]);
}
}
}
ierr = PetscFree2(cone,coneO);CHKERRQ(ierr);
sieve->symmetrize();
mesh->stratify();
/* Create boundary marker */
{
const Obj<PETSC_MESH_TYPE::label_type>& boundary = mesh->createLabel("marker");
for(PetscInt k = info.zs; k < info.gzs+info.gzm; ++k) {
for(PetscInt j = info.ys; j < info.gys+info.gym; ++j) {
if (info.xs == 0) {
PetscInt globalV = (k*N + j)*M + info.xs + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
if (info.gxs+info.gxm-1 == M-1) {
PetscInt globalV = (k*N + j)*M + info.gxs+info.gxm-1 + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
}
}
if (dim > 1) {
for(PetscInt k = info.zs; k < info.gzs+info.gzm; ++k) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i) {
if (info.ys == 0) {
PetscInt globalV = (k*N + info.ys)*M + i + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
if (info.gys+info.gym-1 == N-1) {
PetscInt globalV = (k*N + info.gys+info.gym-1)*M + i + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
}
}
}
if (dim > 2) {
for(PetscInt j = info.ys; j < info.gys+info.gym; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i) {
if (info.zs == 0) {
PetscInt globalV = (info.zs*N + j)*M + i + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
if (info.gzs+info.gzm-1 == P-1) {
PetscInt globalV = ((info.gzs+info.gzm-1)*N + j)*M + i + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
}
}
}
}
/* Create new DM */
ierr = DMMeshCreate(((PetscObject) dm)->comm, dmNew);CHKERRQ(ierr);
ierr = DMMeshSetMesh(*dmNew, mesh);CHKERRQ(ierr);
/* Set coordinates */
ierr = PetscSectionCreate(((PetscObject) dm)->comm, §ion);CHKERRQ(ierr);
ierr = PetscSectionSetChart(section, numCells, numCells+numVertices);CHKERRQ(ierr);
for(PetscInt v = numCells; v < numCells+numVertices; ++v) {
ierr = PetscSectionSetDof(section, v, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(section);CHKERRQ(ierr);
ierr = DMMeshSetCoordinateSection(*dmNew, section);CHKERRQ(ierr);
ierr = DMDAGetCoordinateDA(dm, &cda);CHKERRQ(ierr);
ierr = DMDAGetGhostedCoordinates(dm, &coordinates);CHKERRQ(ierr);
{
Obj<PETSC_MESH_TYPE::real_section_type> coordSection = mesh->getRealSection("coordinates");
switch(dim) {
case 1:
{
PetscScalar **coords;
ierr = DMDAVecGetArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i) {
PetscInt globalV = i + numGlobalCells;
coordSection->updatePoint(renumbering[globalV], coords[i]);
}
ierr = DMDAVecRestoreArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
break;
}
case 2:
{
PetscScalar ***coords;
ierr = DMDAVecGetArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
for(PetscInt j = info.ys; j < info.gys+info.gym; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i) {
PetscInt globalV = j*M + i + numGlobalCells;
coordSection->updatePoint(renumbering[globalV], coords[j][i]);
}
}
ierr = DMDAVecRestoreArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
break;
}
case 3:
{
PetscScalar ****coords;
ierr = DMDAVecGetArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
for(PetscInt k = info.zs; k < info.gzs+info.gzm; ++k, ++v) {
for(PetscInt j = info.ys; j < info.gys+info.gym; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i) {
PetscInt globalV = (k*N + j)*M + i + numGlobalCells;
coordSection->updatePoint(renumbering[globalV], coords[k][j][i]);
}
}
}
ierr = DMDAVecRestoreArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
break;
}
default:
SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid DMDA dimension %d", dim);
}
}
/* Get overlap for interdomain communication */
{
typedef PETSC_MESH_TYPE::point_type point_type;
PETSc::Log::Event("CreateOverlap").begin();
ALE::Obj<PETSC_MESH_TYPE::send_overlap_type> sendParallelMeshOverlap = mesh->getSendOverlap();
ALE::Obj<PETSC_MESH_TYPE::recv_overlap_type> recvParallelMeshOverlap = mesh->getRecvOverlap();
// Can I figure this out in a nicer way?
ALE::SetFromMap<std::map<point_type,point_type> > globalPoints(renumbering);
ALE::OverlapBuilder<>::constructOverlap(globalPoints, renumbering, sendParallelMeshOverlap, recvParallelMeshOverlap);
if (debug) {
sendParallelMeshOverlap->view("Send Overlap");
recvParallelMeshOverlap->view("Recieve Overlap");
}
mesh->setCalculatedOverlap(true);
PETSc::Log::Event("CreateOverlap").end();
}
PetscFunctionReturn(0);
}