static PetscErrorCode CreateSpectralPlanes(DM dm, PetscInt numPlanes, const PetscInt planeDir[], const PetscReal planeCoord[], AppCtx *user)
{
PetscSection coordSection;
Vec coordinates;
const PetscScalar *coords;
PetscInt dim, p, vStart, vEnd, v;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr);
for (p = 0; p < numPlanes; ++p) {
DMLabel label;
char name[PETSC_MAX_PATH_LEN];
ierr = PetscSNPrintf(name, PETSC_MAX_PATH_LEN, "spectral_plane_%D", p);CHKERRQ(ierr);
ierr = DMCreateLabel(dm, name);CHKERRQ(ierr);
ierr = DMGetLabel(dm, name, &label);CHKERRQ(ierr);
ierr = DMLabelAddStratum(label, 1);CHKERRQ(ierr);
for (v = vStart; v < vEnd; ++v) {
PetscInt off;
ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
if (PetscAbsReal(planeCoord[p] - PetscRealPart(coords[off+planeDir[p]])) < PETSC_SMALL) {
ierr = DMLabelSetValue(label, v, 1);CHKERRQ(ierr);
}
}
}
ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode RHSJacobian(TS ts,PetscReal t,Vec X,Mat A,Mat B,void *ctx)
{
PetscErrorCode ierr;
User user = (User)ctx;
PetscReal mu = user->mu;
PetscInt rowcol[] = {0,1};
PetscScalar J[2][2];
const PetscScalar *x;
PetscFunctionBeginUser;
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
J[0][0] = 0;
J[1][0] = -2.*mu*x[1]*x[0]-1;
J[0][1] = 1.0;
J[1][1] = mu*(1.0-x[0]*x[0]);
ierr = MatSetValues(A,2,rowcol,2,rowcol,&J[0][0],INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (A != B) {
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode PCApply_Redistribute(PC pc,Vec b,Vec x)
{
PC_Redistribute *red = (PC_Redistribute*)pc->data;
PetscErrorCode ierr;
PetscInt dcnt = red->dcnt,i;
const PetscInt *drows = red->drows;
PetscScalar *xwork;
const PetscScalar *bwork,*diag = red->diag;
PetscFunctionBegin;
if (!red->work) {
ierr = VecDuplicate(b,&red->work);CHKERRQ(ierr);
}
/* compute the rows of solution that have diagonal entries only */
ierr = VecSet(x,0.0);CHKERRQ(ierr); /* x = diag(A)^{-1} b */
ierr = VecGetArray(x,&xwork);CHKERRQ(ierr);
ierr = VecGetArrayRead(b,&bwork);CHKERRQ(ierr);
for (i=0; i<dcnt; i++) {
xwork[drows[i]] = diag[i]*bwork[drows[i]];
}
ierr = PetscLogFlops(dcnt);CHKERRQ(ierr);
ierr = VecRestoreArray(red->work,&xwork);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(b,&bwork);CHKERRQ(ierr);
/* update the right hand side for the reduced system with diagonal rows (and corresponding columns) removed */
ierr = MatMult(pc->pmat,x,red->work);CHKERRQ(ierr);
ierr = VecAYPX(red->work,-1.0,b);CHKERRQ(ierr); /* red->work = b - A x */
ierr = VecScatterBegin(red->scatter,red->work,red->b,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(red->scatter,red->work,red->b,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = KSPSolve(red->ksp,red->b,red->x);CHKERRQ(ierr);
ierr = VecScatterBegin(red->scatter,red->x,x,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterEnd(red->scatter,red->x,x,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode StokesWriteSolution(Stokes *s)
{
PetscMPIInt size;
PetscInt n,i,j;
const PetscScalar *array;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* write data (*warning* only works sequential) */
MPI_Comm_size(MPI_COMM_WORLD,&size);
/*ierr = PetscPrintf(PETSC_COMM_WORLD," number of processors = %D\n",size);CHKERRQ(ierr);*/
if (size == 1) {
PetscViewer viewer;
ierr = VecGetArrayRead(s->x, &array);CHKERRQ(ierr);
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD, "solution.dat", &viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "# x, y, u, v, p\n");CHKERRQ(ierr);
for (j = 0; j < s->ny; j++) {
for (i = 0; i < s->nx; i++) {
n = j*s->nx+i;
ierr = PetscViewerASCIIPrintf(viewer, "%.12g %.12g %.12g %.12g %.12g\n", (double)(i*s->hx+s->hx/2),(double)(j*s->hy+s->hy/2), (double)PetscRealPart(array[n]), (double)PetscRealPart(array[n+s->nx*s->ny]),(double)PetscRealPart(array[n+2*s->nx*s->ny]));CHKERRQ(ierr);
}
}
ierr = VecRestoreArrayRead(s->x, &array);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode MatSolve_LUSOL(Mat A,Vec b,Vec x)
{
Mat_LUSOL *lusol=(Mat_LUSOL*)A->spptr;
double *xx;
const double *bb;
int mode=5;
PetscErrorCode ierr;
int i,m,n,nnz,status;
PetscFunctionBegin;
ierr = VecGetArray(x, &xx);CHKERRQ(ierr);
ierr = VecGetArrayRead(b, &bb);CHKERRQ(ierr);
m = n = lusol->n;
nnz = lusol->nnz;
for (i = 0; i < m; i++) lusol->mnsv[i] = bb[i];
LU6SOL(&mode, &m, &n, lusol->mnsv, xx, &nnz,
lusol->luparm, lusol->parmlu, lusol->data,
lusol->indc, lusol->indr, lusol->ip, lusol->iq,
lusol->lenc, lusol->lenr, lusol->locc, lusol->locr, &status);
if (status) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"solve failed, error code %d",status);
ierr = VecRestoreArray(x, &xx);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(b, &bb);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode CostIntegrand(TS ts,PetscReal t,Vec U,Vec R,Userctx *user)
{
PetscErrorCode ierr;
PetscScalar *r;
const PetscScalar *u;
PetscInt idx;
Vec Xgen,Xnet;
PetscScalar *xgen;
PetscInt i;
PetscFunctionBegin;
ierr = DMCompositeGetLocalVectors(user->dmpgrid,&Xgen,&Xnet);CHKERRQ(ierr);
ierr = DMCompositeScatter(user->dmpgrid,U,Xgen,Xnet);CHKERRQ(ierr);
ierr = VecGetArray(Xgen,&xgen);CHKERRQ(ierr);
ierr = VecGetArrayRead(U,&u);CHKERRQ(ierr);
ierr = VecGetArray(R,&r);CHKERRQ(ierr);
r[0] = 0.;
idx = 0;
for (i=0;i<ngen;i++) {
r[0] += PetscPowScalarInt(PetscMax(0.,PetscMax(xgen[idx+3]/(2.*PETSC_PI)-user->freq_u,user->freq_l-xgen[idx+3]/(2.*PETSC_PI))),user->pow);
idx += 9;
}
ierr = VecRestoreArray(R,&r);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(U,&u);CHKERRQ(ierr);
ierr = DMCompositeRestoreLocalVectors(user->dmpgrid,&Xgen,&Xnet);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode VecMax_Seq(Vec xin,PetscInt* idx,PetscReal * z)
{
PetscInt i,j=0,n = xin->map->n;
PetscReal max,tmp;
const PetscScalar *xx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = VecGetArrayRead(xin,&xx);CHKERRQ(ierr);
if (!n) {
max = PETSC_MIN_REAL;
j = -1;
} else {
#if defined(PETSC_USE_COMPLEX)
max = PetscRealPart(*xx++); j = 0;
#else
max = *xx++; j = 0;
#endif
for (i=1; i<n; i++) {
#if defined(PETSC_USE_COMPLEX)
if ((tmp = PetscRealPart(*xx++)) > max) { j = i; max = tmp;}
#else
if ((tmp = *xx++) > max) { j = i; max = tmp; }
#endif
}
}
*z = max;
if (idx) *idx = j;
ierr = VecRestoreArrayRead(xin,&xx);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void SetJacobian(Geometry geo, Mat J, Vec v, int jc, int jr, int jh){
// use jc = -1 for last 2 columns, and jc = -2 for blocks (all jc)
AssembleVec(v);
int ns, ne, i;
VecGetOwnershipRange(v, &ns, &ne);
const double *vals;
VecGetArrayRead(v, &vals);
for(i=ns; i<ne; i++){
if( Last2(geo, i) || vals[i-ns] == 0.0) continue;
int col, offset = jh*(Nxyzcr(geo)+2),
ij = i%(Nxyzcr(geo)+2);
Point p;
CreatePoint_i(&p, ij, &geo->gN);
if(jc == -1) //columns
col = Nxyzcr(geo)+jr;
else if(jc == -2) //blocks
col = jr*Nxyzc(geo) + xyzc(&p);
else // tensors
col = jr*Nxyzc(geo) + jc*Nxyz(geo) + xyz(&p);
MatSetValue(J, i, col+offset, vals[i-ns], ADD_VALUES);
}
VecRestoreArrayRead(v, &vals);
}
void CollectVec(Geometry geo, Vec vN, Vec vM){
VecSet(vM, 0.0);
Vecfun f;
CreateVecfun(&f, geo->vf);
const double *vals;
VecGetArrayRead(vN, &vals);
int ns, ne;
VecGetOwnershipRange(vN, &ns, &ne);
if( ne > Nxyzcr(geo)-2) ne = Nxyzcr(geo)-2;
int i;
for(i=ns; i<ne; i++){
if( valr(&f, i) == 0.0) continue;
// skip if gain profile zero here
Point p;
CreatePoint_i(&p, i, &geo->gN);
if( projectmedium(&p, &geo->gM, geo->LowerPML) )
VecSetValue(vM, xyz(&p), vals[i-ns], ADD_VALUES);
}
VecRestoreArrayRead(vN, &vals);
DestroyVecfun(&f);
AssembleVec(vM);
}
PetscErrorCode MatBackwardSolve_SeqBAIJ_1_NaturalOrdering(Mat A,Vec bb,Vec xx)
{
Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data;
PetscErrorCode ierr;
const PetscInt n = a->mbs,*aj = a->j,*adiag = a->diag,*vi;
PetscScalar *x,sum;
const PetscScalar *b;
const MatScalar *aa = a->a,*v;
PetscInt i,nz;
PetscFunctionBegin;
if (!n) PetscFunctionReturn(0);
ierr = VecGetArrayRead(bb,&b);CHKERRQ(ierr);
ierr = VecGetArray(xx,&x);CHKERRQ(ierr);
/* backward solve the upper triangular */
for (i=n-1; i>=0; i--) {
v = aa + adiag[i+1] + 1;
vi = aj + adiag[i+1] + 1;
nz = adiag[i] - adiag[i+1]-1;
sum = b[i];
PetscSparseDenseMinusDot(sum,x,v,vi,nz);
x[i] = sum*v[nz]; /* x[i]=aa[adiag[i]]*sum; v++; */
}
ierr = PetscLogFlops(2.0*a->nz - A->cmap->n);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(bb,&b);CHKERRQ(ierr);
ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode IJacobian(TS ts,PetscReal t,Vec X,Vec Xdot,PetscReal a,Mat A,Mat B,void *ptr)
{
PetscErrorCode ierr;
User user = (User)ptr;
PetscReal mu = user->mu;
PetscInt rowcol[] = {0,1};
PetscScalar J[2][2];
const PetscScalar *x;
PetscFunctionBegin;
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
J[0][0] = a;
J[0][1] = 0;
J[1][0] = (2.*x[0]*x[1]+1.)/mu;
J[1][1] = a - (1. - x[0]*x[0])/mu;
ierr = MatSetValues(B,2,rowcol,2,rowcol,&J[0][0],INSERT_VALUES);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (A != B) {
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode MatForwardSolve_SeqBAIJ_1_NaturalOrdering(Mat A,Vec bb,Vec xx)
{
Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data;
PetscErrorCode ierr;
const PetscInt n = a->mbs,*ai = a->i,*aj = a->j,*vi;
PetscScalar *x,sum;
const PetscScalar *b;
const MatScalar *aa = a->a,*v;
PetscInt i,nz;
PetscFunctionBegin;
if (!n) PetscFunctionReturn(0);
ierr = VecGetArrayRead(bb,&b);CHKERRQ(ierr);
ierr = VecGetArray(xx,&x);CHKERRQ(ierr);
/* forward solve the lower triangular */
x[0] = b[0];
v = aa;
vi = aj;
for (i=1; i<n; i++) {
nz = ai[i+1] - ai[i];
sum = b[i];
PetscSparseDenseMinusDot(sum,x,v,vi,nz);
v += nz;
vi += nz;
x[i] = sum;
}
ierr = PetscLogFlops(a->nz - A->cmap->n);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(bb,&b);CHKERRQ(ierr);
ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode FormIJacobian(TS ts,PetscReal t,Vec U, Vec Udot, PetscReal a, Mat J,Mat Jpre,void *ctx)
{
PetscErrorCode ierr;
AppCtx *user = (AppCtx *)ctx;
PetscScalar v;
const PetscScalar *x;
PetscInt i,col;
PetscFunctionBegin;
ierr = VecGetArrayRead(U,&x);
CHKERRQ(ierr);
for(i=0; i < user->mx; i++) {
v = a - 1. + 3.*x[i]*x[i];
col = i;
ierr = MatSetValues(J,1,&i,1,&col,&v,INSERT_VALUES);
CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(U,&x);
CHKERRQ(ierr);
ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
if (J != Jpre) {
ierr = MatAssemblyBegin(Jpre,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(Jpre,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
}
/* MatView(J,PETSC_VIEWER_STDOUT_WORLD);*/
PetscFunctionReturn(0);
}
static PetscErrorCode RHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
{
PetscErrorCode ierr;
AppCtx *user = (AppCtx*)ptr;
PetscScalar *f;
const PetscScalar *x;
PetscInt i,mx;
PetscReal hx,eps;
PetscFunctionBegin;
mx = user->mx;
eps = user->param;
hx = (user->xright-user->xleft)/(mx-1);
ierr = VecGetArrayRead(X,&x);
CHKERRQ(ierr);
ierr = VecGetArray(F,&f);
CHKERRQ(ierr);
f[0] = 2.*eps*(x[1]-x[0])/(hx*hx); /*boundary*/
for(i=1; i<mx-1; i++) {
f[i]= eps*(x[i+1]-2.*x[i]+x[i-1])/(hx*hx);
}
f[mx-1] = 2.*eps*(x[mx-2]- x[mx-1])/(hx*hx); /*boundary*/
ierr = VecRestoreArrayRead(X,&x);
CHKERRQ(ierr);
ierr = VecRestoreArray(F,&f);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode KSPMonitorRange_Private(KSP ksp,PetscInt it,PetscReal *per)
{
PetscErrorCode ierr;
Vec resid;
PetscReal rmax,pwork;
PetscInt i,n,N;
const PetscScalar *r;
PetscFunctionBegin;
ierr = KSPBuildResidual(ksp,NULL,NULL,&resid);
CHKERRQ(ierr);
ierr = VecNorm(resid,NORM_INFINITY,&rmax);
CHKERRQ(ierr);
ierr = VecGetLocalSize(resid,&n);
CHKERRQ(ierr);
ierr = VecGetSize(resid,&N);
CHKERRQ(ierr);
ierr = VecGetArrayRead(resid,&r);
CHKERRQ(ierr);
pwork = 0.0;
for (i=0; i<n; i++) pwork += (PetscAbsScalar(r[i]) > .20*rmax);
ierr = VecRestoreArrayRead(resid,&r);
CHKERRQ(ierr);
ierr = VecDestroy(&resid);
CHKERRQ(ierr);
ierr = MPIU_Allreduce(&pwork,per,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)ksp));
CHKERRQ(ierr);
*per = *per/N;
PetscFunctionReturn(0);
}
/*
FormFunctionFortran - Evaluates nonlinear function, F(x) in Fortran.
*/
int FormFunctionFortran(SNES snes,Vec X,Vec F,void *ptr)
{
AppCtx *user = (AppCtx*)ptr;
int ierr;
PetscScalar *f;
const PetscScalar *x;
/*
Process 0 has to wait for all other processes to get here
before proceeding to write in the shared vector
*/
ierr = PetscBarrier((PetscObject)snes);CHKERRQ(ierr);
if (!user->rank) {
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
ierr = VecGetArray(F,&f);CHKERRQ(ierr);
applicationfunctionfortran_(&user->param,&user->mx,&user->my,x,f,&ierr);
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&f);CHKERRQ(ierr);
ierr = PetscLogFlops(11.0*(user->mx-2)*(user->my-2))CHKERRQ(ierr);
}
/*
All the non-busy processors have to wait here for process 0 to finish
evaluating the function; otherwise they will start using the vector values
before they have been computed
*/
ierr = PetscBarrier((PetscObject)snes);CHKERRQ(ierr);
return 0;
}
PetscErrorCode IFunction(TS ts,PetscReal t, Vec X, Vec Xdot, Vec F, Userctx *user)
{
PetscErrorCode ierr;
SNES snes;
PetscScalar *f;
const PetscScalar *xdot;
PetscInt i;
PetscFunctionBegin;
user->t = t;
ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
ierr = ResidualFunction(snes,X,F,user);CHKERRQ(ierr);
ierr = VecGetArray(F,&f);
ierr = VecGetArrayRead(Xdot,&xdot);CHKERRQ(ierr);
for (i=0;i < ngen;i++) {
f[9*i] += xdot[9*i];
f[9*i+1] += xdot[9*i+1];
f[9*i+2] += xdot[9*i+2];
f[9*i+3] += xdot[9*i+3];
f[9*i+6] += xdot[9*i+6];
f[9*i+7] += xdot[9*i+7];
f[9*i+8] += xdot[9*i+8];
}
ierr = VecRestoreArray(F,&f);
ierr = VecRestoreArrayRead(Xdot,&xdot);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void Save(Vec u, const char* filename) {
int n, rank;
MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
VecGetSize(u, &n);
Vec uloc;
VecCreateSeq(PETSC_COMM_SELF, n, &uloc);
VecScatter ctx;
VecScatterCreateToZero(u, &ctx, &uloc);
VecScatterBegin(ctx, u, uloc, INSERT_VALUES, SCATTER_FORWARD);
VecScatterEnd(ctx, u, uloc, INSERT_VALUES, SCATTER_FORWARD);
const PetscScalar *pu;
VecGetArrayRead(uloc, &pu);
if (rank==0) {
int sq = sqrt(n);
std::ofstream out(filename);
for (size_t i=0; i<n; i++) {
out << pu[i] << std::endl;
if ((i+1)%sq == 0) out << std::endl;
}
}
VecRestoreArrayRead(uloc, &pu);
VecScatterDestroy(&ctx);
VecDestroy(&uloc);
}
static
PetscErrorCode krylov_petsc_apply_aij( Mat A, Vec x, Vec y )
{
void *ctx;
PetscErrorCode ierr;
krylov_pc_ctx_t* kct;
const double* px;
double* py;
/* PetscFunctionBegin; */
ierr = MatShellGetContext( A, &ctx ); CHKERRQ(ierr);
kct = (krylov_pc_ctx_t *)ctx;
ierr = VecGetArrayRead( x, &px ); CHKERRQ(ierr);
ierr = VecGetArray( y, &py ); CHKERRQ(ierr);
problem_data_t* vecs = kct->vecs;
weakeqn_ptrs_t* fcns = kct->fcns;
p4est_t* p4est = kct->p4est;
p4est_ghost_t* ghost = *kct->ghost;
element_data_t* ghost_data = *kct->ghost_data;
dgmath_jit_dbase_t* dgmath_jit_dbase = kct->dgmath_jit_dbase;
problem_data_t vecs_for_aij;
problem_data_copy_ptrs(vecs, &vecs_for_aij);
vecs_for_aij.u = (double*)px;
vecs_for_aij.Au = py;
fcns->apply_lhs(p4est, ghost, ghost_data, &vecs_for_aij, dgmath_jit_dbase);
ierr = VecRestoreArrayRead( x, &px ); CHKERRQ(ierr);
ierr = VecRestoreArray( y, &py ); CHKERRQ(ierr);
return ierr;
}
static PetscErrorCode IJacobian(TS ts,PetscReal t,Vec X,Vec Xdot,PetscReal a,Mat A,Mat B,void *ctx)
{
PetscErrorCode ierr;
User user = (User)ctx;
PetscInt rowcol[] = {0,1};
PetscScalar J[2][2];
const PetscScalar *x;
PetscFunctionBeginUser;
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
J[0][0] = a; J[0][1] = -1.0;
J[1][0] = c21*a + user->mu*(1.0 + 2.0*x[0]*x[1]); J[1][1] = -c21 + a - user->mu*(1.0-x[0]*x[0]);
ierr = MatSetValues(B,2,rowcol,2,rowcol,&J[0][0],INSERT_VALUES);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (B && A != B) {
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/**
divide the the solution by the density
*/
PetscErrorCode ReformatSolution(Vec solution, Vec solution_unscaled, User user)
{
PetscScalar *x;
const PetscScalar *xold;
PetscInt cStart, cEnd, cEndInterior = user->cEndInterior, c;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMPlexGetHeightStratum(user->dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = VecGetArrayRead(solution, &xold);CHKERRQ(ierr);
ierr = VecGetArray(solution_unscaled, &x);CHKERRQ(ierr);
for (c = cStart; c < cEndInterior; ++c) {
PetscScalar *xc, *xcold;
ierr = DMPlexPointGlobalRef(user->dm,c,x,&xc);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRead(user->dm,c,xold,&xcold);CHKERRQ(ierr);
if (xc) {
xc[0] = xcold[0]; // Density
xc[1] = xcold[1]/xcold[0]; // Velocity u (the x-direction)
xc[2] = xcold[2]/xcold[0]; // Velocity v (the y-direction)
xc[3] = xcold[3]/xcold[0]; // Velocity w (the z-direction)
xc[4] = xcold[4]/xcold[0]; // Total energy E
}
}
ierr = VecRestoreArrayRead(solution, &xold);CHKERRQ(ierr);
ierr = VecRestoreArray(solution_unscaled, &x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormJacobian(SNES snes,Vec x,Mat jac,Mat B,void *ctx){
Solver_ctx *sol_ctx = (Solver_ctx*)ctx;
ASL *asl=(ASL*)(sol_ctx->asl);
const PetscScalar *xx; /* Variable vector*/
PetscScalar A[nzc]; /* Temporary storage for Jacobian Calc. */
PetscErrorCode ierr; /* PETSc Error code */
int err; /* ASL Error code */
unsigned long int i; /* Constraint index */
cgrad *cg; /* Constraint gradient information */
/* Compute Jacobian entries and insert into matrix. */
ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr);
jacval((real*)xx,(real*)A,&err);
ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr);
for(i=n_conjac[0];i<n_conjac[1]; ++i){ /*i is constraint index */
cg = Cgrad[i];
while(cg!=NULL){
MatSetValue(B, i, cg->varno, A[cg->goff],INSERT_VALUES);
cg=cg->next;
}
}
/* Assemble matrix */
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
return 0;
}
/*
Use the first order upwind scheme to compute the flux
*/
PetscErrorCode CaculateLocalMassFunction(DM dm, Vec locX, Vec F, User user)
{
PetscErrorCode ierr;
const PetscScalar *x;
PetscScalar *f;
PetscInt cStart, cell;
// Physics phys = user->model->physics;
PetscFunctionBeginUser;
ierr = VecGetArrayRead(locX,&x);CHKERRQ(ierr);
ierr = VecGetArray(F,&f);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, NULL);CHKERRQ(ierr);
for (cell = cStart; cell < user->cEndInterior; cell++) {
PetscInt i;
PetscScalar *fref;
const PetscScalar *xref;
ierr = DMPlexPointGlobalRead(dm,cell,x,&xref);CHKERRQ(ierr); /*For the unkown variables*/
ierr = DMPlexPointGlobalRef(dm,cell,f,&fref);CHKERRQ(ierr);
// if (!fref){ PetscPrintf(PETSC_COMM_WORLD,"%d, %d\n", cell, user->cEndInterior);}
if (fref){
fref[0] = xref[0];/*the density*/
for (i=1; i<DIM+1; i++) {
fref[i] = xref[0]*xref[i];
}/*viscosity*/
fref[DIM+1] = user->R/(user->adiabatic - 1)*xref[0]*xref[DIM+1];/*Energy*/
}
}
ierr = VecRestoreArrayRead(locX,&x);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&f);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode RHSfunction(TS ts,PetscReal t,Vec globalin,Vec globalout,void *ctx)
{
PetscErrorCode ierr;
AppCtx *obj = (AppCtx*)ctx;
PetscScalar soln[num_z];
const PetscScalar *soln_ptr;
PetscInt i,nz=obj->nz;
PetscReal time;
/* get the previous solution to compute updated system */
ierr = VecGetArrayRead(globalin,&soln_ptr);CHKERRQ(ierr);
for (i=0; i < num_z-2; i++) soln[i] = soln_ptr[i];
ierr = VecRestoreArrayRead(globalin,&soln_ptr);CHKERRQ(ierr);
soln[num_z-1] = 0.0;
soln[num_z-2] = 0.0;
/* clear out the matrix and rhs for ksp to keep things straight */
ierr = VecSet(obj->ksp_rhs,(PetscScalar)0.0);CHKERRQ(ierr);
time = t;
/* get the updated system */
rhs(obj,soln,nz,obj->z,time); /* setup of the By+g rhs */
/* do a ksp solve to get the rhs for the ts problem */
if (obj->useAlhs) {
/* ksp_sol = ksp_rhs */
ierr = VecCopy(obj->ksp_rhs,globalout);CHKERRQ(ierr);
} else {
/* ksp_sol = inv(Amat)*ksp_rhs */
ierr = Petsc_KSPSolve(obj);CHKERRQ(ierr);CHKERRQ(ierr);
ierr = VecCopy(obj->ksp_sol,globalout);CHKERRQ(ierr);
}
return 0;
}
/* Monitor timesteps and use interpolation to output at integer multiples of 0.1 */
static PetscErrorCode Monitor(TS ts,PetscInt step,PetscReal t,Vec X,void *ctx)
{
PetscErrorCode ierr;
const PetscScalar *x;
PetscReal tfinal, dt;
User user = (User)ctx;
Vec interpolatedX;
PetscFunctionBeginUser;
ierr = TSGetTimeStep(ts,&dt);CHKERRQ(ierr);
ierr = TSGetDuration(ts,NULL,&tfinal);CHKERRQ(ierr);
while (user->next_output <= t && user->next_output <= tfinal) {
ierr = VecDuplicate(X,&interpolatedX);CHKERRQ(ierr);
ierr = TSInterpolate(ts,user->next_output,interpolatedX);CHKERRQ(ierr);
ierr = VecGetArrayRead(interpolatedX,&x);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%.1f] %D TS %.6f (dt = %.6f) X % 12.6e % 12.6e\n",
user->next_output,step,t,dt,(double)PetscRealPart(x[0]),
(double)PetscRealPart(x[1]));CHKERRQ(ierr);
ierr = VecRestoreArrayRead(interpolatedX,&x);CHKERRQ(ierr);
ierr = VecDestroy(&interpolatedX);CHKERRQ(ierr);
user->next_output += 0.1;
}
PetscFunctionReturn(0);
}
/*
Defines the Jacobian of the ODE passed to the ODE solver. See TSSetIJacobian() for the meaning of a and the Jacobian.
*/
static PetscErrorCode RHSJacobian(TS ts,PetscReal t,Vec U,Mat A,Mat B,AppCtx *ctx)
{
PetscErrorCode ierr;
PetscInt rowcol[] = {0,1};
PetscScalar J[2][2],Pmax;
const PetscScalar *u;
PetscFunctionBegin;
ierr = VecGetArrayRead(U,&u);CHKERRQ(ierr);
if ((t > ctx->tf) && (t < ctx->tcl)) Pmax = 0.0; /* A short-circuit on the generator terminal that drives the electrical power output (Pmax*sin(delta)) to 0 */
else Pmax = ctx->Pmax;
J[0][0] = 0; J[0][1] = ctx->omega_b;
J[1][1] = -ctx->D*ctx->omega_s/(2.0*ctx->H); J[1][0] = -Pmax*PetscCosScalar(u[0])*ctx->omega_s/(2.0*ctx->H);
ierr = MatSetValues(B,2,rowcol,2,rowcol,&J[0][0],INSERT_VALUES);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(U,&u);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (A != B) {
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode ComputeExactSolution(DM dm, PetscReal time, Vec X, User user)
{
DM dmCell;
const PetscScalar *cellgeom;
PetscScalar *x;
PetscInt cStart, cEnd, cEndInterior = user->cEndInterior, c;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = VecGetDM(user->cellgeom, &dmCell);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->cellgeom, &cellgeom);CHKERRQ(ierr);
ierr = VecGetArray(X, &x);CHKERRQ(ierr);
for (c = cStart; c < cEndInterior; ++c) {
const CellGeom *cg;
PetscScalar *xc;
ierr = DMPlexPointLocalRead(dmCell,c,cellgeom,&cg);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dm,c,x,&xc);CHKERRQ(ierr);
if (xc) {ierr = ExactSolution(time, cg->centroid, xc, user);CHKERRQ(ierr);}
}
ierr = VecRestoreArrayRead(user->cellgeom, &cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArray(X, &x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode VecView_Seq_Draw_LG(Vec xin,PetscViewer v)
{
PetscDraw draw;
PetscBool isnull;
PetscDrawLG lg;
PetscErrorCode ierr;
PetscInt i,c,bs = PetscAbs(xin->map->bs),n = xin->map->n/bs;
const PetscScalar *xv;
PetscReal *xx,*yy;
int colors[] = {PETSC_DRAW_RED};
PetscFunctionBegin;
ierr = PetscViewerDrawGetDraw(v,0,&draw);CHKERRQ(ierr);
ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr);
if (isnull) PetscFunctionReturn(0);
ierr = PetscMalloc2(n,&xx,n,&yy);CHKERRQ(ierr);
ierr = VecGetArrayRead(xin,&xv);CHKERRQ(ierr);
for (c=0; c<bs; c++) {
ierr = PetscViewerDrawGetDrawLG(v,c,&lg);CHKERRQ(ierr);
ierr = PetscDrawLGReset(lg);CHKERRQ(ierr);
ierr = PetscDrawLGSetDimension(lg,1);CHKERRQ(ierr);
ierr = PetscDrawLGSetColors(lg,colors);CHKERRQ(ierr);
for (i=0; i<n; i++) {
xx[i] = (PetscReal)i;
yy[i] = PetscRealPart(xv[c + i*bs]);
}
ierr = PetscDrawLGAddPoints(lg,n,&xx,&yy);CHKERRQ(ierr);
ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
ierr = PetscDrawLGSave(lg);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(xin,&xv);CHKERRQ(ierr);
ierr = PetscFree2(xx,yy);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode VecGetArray_Nest(Vec X,PetscScalar **x)
{
Vec_Nest *bx = (Vec_Nest*)X->data;
PetscInt i,m,rstart,rend;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = VecGetOwnershipRange(X,&rstart,&rend);CHKERRQ(ierr);
ierr = VecGetLocalSize(X,&m);CHKERRQ(ierr);
ierr = PetscMalloc1(m,x);CHKERRQ(ierr);
for (i=0; i<bx->nb; i++) {
Vec subvec = bx->v[i];
IS isy = bx->is[i];
PetscInt j,sm;
const PetscInt *ixy;
const PetscScalar *y;
ierr = VecGetLocalSize(subvec,&sm);CHKERRQ(ierr);
ierr = VecGetArrayRead(subvec,&y);CHKERRQ(ierr);
ierr = ISGetIndices(isy,&ixy);CHKERRQ(ierr);
for (j=0; j<sm; j++) {
PetscInt ix = ixy[j];
if (ix < rstart || rend <= ix) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for getting array from nonlocal subvec");
(*x)[ix-rstart] = y[j];
}
ierr = ISRestoreIndices(isy,&ixy);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(subvec,&y);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);
}