static PetscErrorCode DMPlexTSSetupGradient(DM dm, PetscFV fvm, DMTS_Plex *dmplexts)
{
DM dmFace, dmCell;
PetscScalar *fgeom, *cgeom;
PetscSection sectionGrad;
PetscInt dim, pdim, cStart, cEnd, cEndInterior, c;
PetscErrorCode ierr;
PetscFunctionBegin;
if (dmplexts->setupGrad) PetscFunctionReturn(0);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = PetscFVGetNumComponents(fvm, &pdim);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
/* Construct the interpolant corresponding to each face from the leat-square solution over the cell neighborhood */
ierr = VecGetDM(dmplexts->facegeom, &dmFace);CHKERRQ(ierr);
ierr = VecGetDM(dmplexts->cellgeom, &dmCell);CHKERRQ(ierr);
ierr = VecGetArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
ierr = VecGetArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
ierr = BuildGradientReconstruction(dm, fvm, dmFace, fgeom, dmCell, cgeom);CHKERRQ(ierr);
ierr = VecRestoreArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
ierr = VecRestoreArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
/* Create storage for gradients */
ierr = DMClone(dm, &dmplexts->dmGrad);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionGrad);CHKERRQ(ierr);
ierr = PetscSectionSetChart(sectionGrad, cStart, cEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionGrad, c, pdim*dim);CHKERRQ(ierr);}
ierr = PetscSectionSetUp(sectionGrad);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dmplexts->dmGrad, sectionGrad);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionGrad);CHKERRQ(ierr);
dmplexts->setupGrad = PETSC_TRUE;
PetscFunctionReturn(0);
}
/*@
DMShellSetLocalVector - sets a template local vector associated with the DMShell
Logically Collective on DM
Input Arguments:
+ dm - shell DM
- X - template vector
Level: advanced
.seealso: DMCreateLocalVector(), DMShellSetMatrix(), DMShellSetCreateLocalVector()
@*/
PetscErrorCode DMShellSetLocalVector(DM dm,Vec X)
{
DM_Shell *shell = (DM_Shell*)dm->data;
PetscErrorCode ierr;
PetscBool isshell;
DM vdm;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscValidHeaderSpecific(X,VEC_CLASSID,2);
ierr = PetscObjectTypeCompare((PetscObject)dm,DMSHELL,&isshell);
CHKERRQ(ierr);
if (!isshell) PetscFunctionReturn(0);
ierr = VecGetDM(X,&vdm);
CHKERRQ(ierr);
/*
if the vector proposed as the new base global vector for the DM is a DM vector associated
with the same DM then the current base global vector for the DM is ok and if we replace it with the new one
we get a circular dependency that prevents the DM from being destroy when it should be.
This occurs when SNESSet/GetNPC() is used with a SNES that does not have a user provided
DM attached to it since the inner SNES (which shares the DM with the outer SNES) tries
to set its input vector (which is associated with the DM) as the base global vector.
Thanks to Juan P. Mendez Granado Re: [petsc-maint] Nonlinear conjugate gradien
for pointing out the problem.
*/
if (vdm == dm) PetscFunctionReturn(0);
ierr = PetscObjectReference((PetscObject)X);
CHKERRQ(ierr);
ierr = VecDestroy(&shell->Xlocal);
CHKERRQ(ierr);
shell->Xlocal = X;
PetscFunctionReturn(0);
}
/*
Caculate the source term of the equations, which includes all
terms except convetion term, diffusion term, and timedependent term.
*/
PetscErrorCode CaculateLocalSourceTerm(DM dm, Vec locX, Vec F, User user)
{
PetscErrorCode ierr;
DM dmGrad = user->dmGrad;
const PetscScalar *x;
PetscScalar *f;
PetscInt cStart, cell;
const PetscScalar *cellgeom;
const CellGeom *cg;
Vec locGrad, Grad;
const PetscScalar *grad;
DM dmCell;
PetscFunctionBeginUser;
ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr);
ierr = VecGetArrayRead(locX,&x);CHKERRQ(ierr);
ierr = VecGetArray(F,&f);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, NULL);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = DMGetGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = DMGetLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = VecGetArrayRead(locGrad,&grad);CHKERRQ(ierr);
for (cell = cStart; cell < user->cEndInterior; cell++) {
PetscScalar *fref;
const PetscScalar *xref;
PetscScalar *cgrad;
ierr = DMPlexPointLocalRead(dmCell,cell,cellgeom,&cg);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm,cell,x,&xref);CHKERRQ(ierr); /*For the unkown variables*/
ierr = DMPlexPointGlobalRef(dm,cell,f,&fref);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad,cell,grad,&cgrad);CHKERRQ(ierr);
// if (!fref){ PetscPrintf(PETSC_COMM_WORLD,"%d, %d\n", cell, user->cEndInterior);}
if (fref){
fref[0] += SourceRho(user, cgrad, xref, cg->centroid);/*the continuity equation*/
fref[1] += SourceU(user, cgrad, xref, cg->centroid); /*Momentum U*/
fref[2] += SourceV(user, cgrad, xref, cg->centroid); /*Momentum V*/
fref[3] += SourceW(user, cgrad, xref, cg->centroid); /*Momentum W*/
fref[4] += SourceE(user, cgrad, xref, cg->centroid);/*Energy*/
}
}
ierr = VecRestoreArrayRead(locX,&x);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&f);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetInitialCondition(DM dm, 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 = InitialCondition(0.0, cg->centroid, xc, user);CHKERRQ(ierr);
}
}
ierr = VecRestoreArrayRead(user->cellgeom, &cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArray(X, &x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Evaluates FU = Gradiant(L(w,u,lambda))
This local function acts on the ghosted version of U (accessed via DMCompositeGetLocalVectors() and
DMCompositeScatter()) BUT the global, nonghosted version of FU (via DMCompositeGetAccess()).
*/
PetscErrorCode ComputeFunction(SNES snes,Vec U,Vec FU,void *ctx)
{
PetscErrorCode ierr;
PetscInt xs,xm,i,N;
ULambda *u_lambda,*fu_lambda;
PetscScalar d,h,*w,*fw;
Vec vw,vfw,vu_lambda,vfu_lambda;
DM packer,red,da;
PetscFunctionBeginUser;
ierr = VecGetDM(U, &packer);CHKERRQ(ierr);
ierr = DMCompositeGetEntries(packer,&red,&da);CHKERRQ(ierr);
ierr = DMCompositeGetLocalVectors(packer,&vw,&vu_lambda);CHKERRQ(ierr);
ierr = DMCompositeScatter(packer,U,vw,vu_lambda);CHKERRQ(ierr);
ierr = DMCompositeGetAccess(packer,FU,&vfw,&vfu_lambda);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&N,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
ierr = VecGetArray(vw,&w);CHKERRQ(ierr);
ierr = VecGetArray(vfw,&fw);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,vu_lambda,&u_lambda);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,vfu_lambda,&fu_lambda);CHKERRQ(ierr);
d = N-1.0;
h = 1.0/d;
/* derivative of L() w.r.t. w */
if (xs == 0) { /* only first processor computes this */
fw[0] = -2.0*d*u_lambda[0].lambda;
}
/* derivative of L() w.r.t. u */
for (i=xs; i<xs+xm; i++) {
if (i == 0) fu_lambda[0].lambda = h*u_lambda[0].u + 2.*d*u_lambda[0].lambda - d*u_lambda[1].lambda;
else if (i == 1) fu_lambda[1].lambda = 2.*h*u_lambda[1].u + 2.*d*u_lambda[1].lambda - d*u_lambda[2].lambda;
else if (i == N-1) fu_lambda[N-1].lambda = h*u_lambda[N-1].u + 2.*d*u_lambda[N-1].lambda - d*u_lambda[N-2].lambda;
else if (i == N-2) fu_lambda[N-2].lambda = 2.*h*u_lambda[N-2].u + 2.*d*u_lambda[N-2].lambda - d*u_lambda[N-3].lambda;
else fu_lambda[i].lambda = 2.*h*u_lambda[i].u - d*(u_lambda[i+1].lambda - 2.0*u_lambda[i].lambda + u_lambda[i-1].lambda);
}
/* derivative of L() w.r.t. lambda */
for (i=xs; i<xs+xm; i++) {
if (i == 0) fu_lambda[0].u = 2.0*d*(u_lambda[0].u - w[0]);
else if (i == N-1) fu_lambda[N-1].u = 2.0*d*u_lambda[N-1].u;
else fu_lambda[i].u = -(d*(u_lambda[i+1].u - 2.0*u_lambda[i].u + u_lambda[i-1].u) - 2.0*h);
}
ierr = VecRestoreArray(vw,&w);CHKERRQ(ierr);
ierr = VecRestoreArray(vfw,&fw);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,vu_lambda,&u_lambda);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,vfu_lambda,&fu_lambda);CHKERRQ(ierr);
ierr = DMCompositeRestoreLocalVectors(packer,&vw,&vu_lambda);CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(packer,FU,&vfw,&vfu_lambda);CHKERRQ(ierr);
ierr = PetscLogFlops(13.0*N);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode VecDuplicate_MPI_DA(Vec g,Vec* gg)
{
PetscErrorCode ierr;
DM da;
PetscFunctionBegin;
ierr = VecGetDM(g, &da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,gg);CHKERRQ(ierr);
ierr = PetscLayoutReference(g->map,&(*gg)->map);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/**
This function is for the explicit method, that is the right hand side
of the system: du/dt = F(u)
*/
PetscErrorCode MyRHSFunction(TS ts,PetscReal time,Vec in,Vec out,void *ctx)
{
User user = (User)ctx;
DM dm, dmFace, dmCell;
PetscSection section;
Vec inLocal;
PetscErrorCode ierr;
PetscFunctionBeginUser;
{
PetscReal norm;
PetscInt size;
ierr = VecNorm(in,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = VecGetSize(in, &size);CHKERRQ(ierr);
norm = norm/size;
if (norm>1.e5) {
SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_LIB,
"The norm of the solution is: %f (current time: %f). The explicit method is going to DIVERGE!!!", norm, time);
}
}
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = VecGetDM(user->facegeom,&dmFace);CHKERRQ(ierr);
ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&inLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr);
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
ierr = ApplyBC(dm, time, inLocal, user);CHKERRQ(ierr);
ierr = ConstructCellCentriodGradient(user->dm, dmFace, dmCell, time, inLocal, out, user);CHKERRQ(ierr);
ierr = VecZeroEntries(out);CHKERRQ(ierr);
if (user->second_order){
ierr = CaculateLocalFunction_LS(user->dm, dmFace, dmCell, time, inLocal, out, user);CHKERRQ(ierr);
}else{
ierr = CaculateLocalFunction_Upwind(user->dm, dmFace, dmCell, time, inLocal, out, user);CHKERRQ(ierr);
}
ierr = DMRestoreLocalVector(dm,&inLocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode VecDuplicate_MPI_DA(Vec g,Vec *gg)
{
PetscErrorCode ierr;
DM da;
PetscLayout map;
PetscFunctionBegin;
ierr = VecGetDM(g, &da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,gg);CHKERRQ(ierr);
ierr = VecGetLayout(g,&map);CHKERRQ(ierr);
ierr = VecSetLayout(*gg,map);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "VecView_DMComposite"
PetscErrorCode VecView_DMComposite(Vec gvec,PetscViewer viewer)
{
DM dm;
PetscErrorCode ierr;
struct DMCompositeLink *next;
PetscBool isdraw;
DM_Composite *com;
PetscFunctionBegin;
ierr = VecGetDM(gvec, &dm);CHKERRQ(ierr);
if (!dm) SETERRQ(((PetscObject)gvec)->comm,PETSC_ERR_ARG_WRONG,"Vector not generated from a DMComposite");
com = (DM_Composite*)dm->data;
next = com->next;
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr);
if (!isdraw) {
/* do I really want to call this? */
ierr = VecView_MPI(gvec,viewer);CHKERRQ(ierr);
} else {
PetscInt cnt = 0;
/* loop over packed objects, handling one at at time */
while (next) {
Vec vec;
PetscScalar *array;
PetscInt bs;
/* Should use VecGetSubVector() eventually, but would need to forward the DM for that to work */
ierr = DMGetGlobalVector(next->dm,&vec);CHKERRQ(ierr);
ierr = VecGetArray(gvec,&array);CHKERRQ(ierr);
ierr = VecPlaceArray(vec,array+next->rstart);CHKERRQ(ierr);
ierr = VecRestoreArray(gvec,&array);CHKERRQ(ierr);
ierr = VecView(vec,viewer);CHKERRQ(ierr);
ierr = VecGetBlockSize(vec,&bs);CHKERRQ(ierr);
ierr = VecResetArray(vec);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(next->dm,&vec);CHKERRQ(ierr);
ierr = PetscViewerDrawBaseAdd(viewer,bs);CHKERRQ(ierr);
cnt += bs;
next = next->next;
}
ierr = PetscViewerDrawBaseAdd(viewer,-cnt);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode SetInitialCondition(DM dm, 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 = InitialCondition(0.0, cg->centroid, xc, user);CHKERRQ(ierr);
}
}
ierr = VecRestoreArrayRead(user->cellgeom, &cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArray(X, &x);CHKERRQ(ierr);
{ //Apply the Boundary condition for the intial condition
Vec XLocal;
ierr = DMGetLocalVector(user->dm, &XLocal);CHKERRQ(ierr);
ierr = VecSet(XLocal, 0);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user->dm, X, INSERT_VALUES, XLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user->dm, X, INSERT_VALUES, XLocal);CHKERRQ(ierr);
ierr = ApplyBC(user->dm, user->current_time, XLocal, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(user->dm, XLocal, INSERT_VALUES, X);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(user->dm, XLocal, INSERT_VALUES, X);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*@C
SNESMonitorDefaultField - Monitors progress of the SNES solvers, separated into fields.
Collective on SNES
Input Parameters:
+ snes - the SNES context
. its - iteration number
. fgnorm - 2-norm of residual
- ctx - the PetscViewer
Notes:
This routine uses the DM attached to the residual vector
Level: intermediate
.keywords: SNES, nonlinear, field, monitor, norm
.seealso: SNESMonitorSet(), SNESMonitorSolution(), SNESMonitorDefault(), SNESMonitorDefaultShort()
@*/
PetscErrorCode SNESMonitorDefaultField(SNES snes, PetscInt its, PetscReal fgnorm, void *ctx)
{
PetscViewer viewer = (PetscViewer) ctx;
Vec r;
DM dm;
PetscReal res[256];
PetscInt tablevel;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,4);
ierr = SNESGetFunction(snes, &r, NULL, NULL);CHKERRQ(ierr);
ierr = VecGetDM(r, &dm);CHKERRQ(ierr);
if (!dm) {ierr = SNESMonitorDefault(snes, its, fgnorm, ctx);CHKERRQ(ierr);}
else {
PetscSection s, gs;
PetscInt Nf, f;
ierr = DMGetDefaultSection(dm, &s);CHKERRQ(ierr);
ierr = DMGetDefaultGlobalSection(dm, &gs);CHKERRQ(ierr);
if (!s || !gs) {ierr = SNESMonitorDefault(snes, its, fgnorm, ctx);CHKERRQ(ierr);}
ierr = PetscSectionGetNumFields(s, &Nf);CHKERRQ(ierr);
if (Nf > 256) SETERRQ1(PetscObjectComm((PetscObject) snes), PETSC_ERR_SUP, "Do not support %d fields > 256", Nf);
ierr = PetscSectionVecNorm(s, gs, r, NORM_2, res);CHKERRQ(ierr);
ierr = PetscObjectGetTabLevel((PetscObject) snes, &tablevel);CHKERRQ(ierr);
ierr = PetscViewerASCIIAddTab(viewer, tablevel);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);CHKERRQ(ierr);
for (f = 0; f < Nf; ++f) {
if (f) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);}
ierr = PetscViewerASCIIPrintf(viewer, "%14.12e", res[f]);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, "] \n");CHKERRQ(ierr);
ierr = PetscViewerASCIISubtractTab(viewer, tablevel);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode VecView_MPI_Draw_DA1d(Vec xin,PetscViewer v)
{
DM da;
PetscErrorCode ierr;
PetscMPIInt rank,size,tag1,tag2;
PetscInt i,n,N,step,istart,isize,j,nbounds;
MPI_Status status;
PetscReal coors[4],ymin,ymax,min,max,xmin = 0.0,xmax = 0.0,tmp = 0.0,xgtmp = 0.0;
const PetscScalar *array,*xg;
PetscDraw draw;
PetscBool isnull,showpoints = PETSC_FALSE;
MPI_Comm comm;
PetscDrawAxis axis;
Vec xcoor;
DMBoundaryType bx;
const PetscReal *bounds;
PetscInt *displayfields;
PetscInt k,ndisplayfields;
PetscBool hold;
PetscFunctionBegin;
ierr = PetscViewerDrawGetDraw(v,0,&draw);CHKERRQ(ierr);
ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0);
ierr = PetscViewerDrawGetBounds(v,&nbounds,&bounds);CHKERRQ(ierr);
ierr = VecGetDM(xin,&da);CHKERRQ(ierr);
if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
ierr = PetscOptionsGetBool(NULL,"-draw_vec_mark_points",&showpoints,NULL);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&N,0,0,0,0,0,&step,0,&bx,0,0,0);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&istart,0,0,&isize,0,0);CHKERRQ(ierr);
ierr = VecGetArrayRead(xin,&array);CHKERRQ(ierr);
ierr = VecGetLocalSize(xin,&n);CHKERRQ(ierr);
n = n/step;
/* get coordinates of nodes */
ierr = DMGetCoordinates(da,&xcoor);CHKERRQ(ierr);
if (!xcoor) {
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,0.0,0.0,0.0);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&xcoor);CHKERRQ(ierr);
}
ierr = VecGetArrayRead(xcoor,&xg);CHKERRQ(ierr);
ierr = PetscObjectGetComm((PetscObject)xin,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
/*
Determine the min and max x coordinate in plot
*/
if (!rank) {
xmin = PetscRealPart(xg[0]);
}
if (rank == size-1) {
xmax = PetscRealPart(xg[n-1]);
}
ierr = MPI_Bcast(&xmin,1,MPIU_REAL,0,comm);CHKERRQ(ierr);
ierr = MPI_Bcast(&xmax,1,MPIU_REAL,size-1,comm);CHKERRQ(ierr);
ierr = DMDASelectFields(da,&ndisplayfields,&displayfields);CHKERRQ(ierr);
for (k=0; k<ndisplayfields; k++) {
j = displayfields[k];
ierr = PetscViewerDrawGetDraw(v,k,&draw);CHKERRQ(ierr);
ierr = PetscDrawCheckResizedWindow(draw);CHKERRQ(ierr);
/*
Determine the min and max y coordinate in plot
*/
min = 1.e20; max = -1.e20;
for (i=0; i<n; i++) {
if (PetscRealPart(array[j+i*step]) < min) min = PetscRealPart(array[j+i*step]);
if (PetscRealPart(array[j+i*step]) > max) max = PetscRealPart(array[j+i*step]);
}
if (min + 1.e-10 > max) {
min -= 1.e-5;
max += 1.e-5;
}
if (j < nbounds) {
min = PetscMin(min,bounds[2*j]);
max = PetscMax(max,bounds[2*j+1]);
}
ierr = MPI_Reduce(&min,&ymin,1,MPIU_REAL,MPIU_MIN,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&max,&ymax,1,MPIU_REAL,MPIU_MAX,0,comm);CHKERRQ(ierr);
ierr = PetscViewerDrawGetHold(v,&hold);CHKERRQ(ierr);
if (!hold) {
ierr = PetscDrawSynchronizedClear(draw);CHKERRQ(ierr);
}
ierr = PetscViewerDrawGetDrawAxis(v,k,&axis);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)draw,(PetscObject)axis);CHKERRQ(ierr);
if (!rank) {
const char *title;
ierr = PetscDrawAxisSetLimits(axis,xmin,xmax,ymin,ymax);CHKERRQ(ierr);
ierr = PetscDrawAxisDraw(axis);CHKERRQ(ierr);
ierr = PetscDrawGetCoordinates(draw,coors,coors+1,coors+2,coors+3);CHKERRQ(ierr);
ierr = DMDAGetFieldName(da,j,&title);CHKERRQ(ierr);
if (title) {ierr = PetscDrawSetTitle(draw,title);CHKERRQ(ierr);}
}
ierr = MPI_Bcast(coors,4,MPIU_REAL,0,comm);CHKERRQ(ierr);
if (rank) {
ierr = PetscDrawSetCoordinates(draw,coors[0],coors[1],coors[2],coors[3]);CHKERRQ(ierr);
}
/* draw local part of vector */
ierr = PetscObjectGetNewTag((PetscObject)xin,&tag1);CHKERRQ(ierr);
ierr = PetscObjectGetNewTag((PetscObject)xin,&tag2);CHKERRQ(ierr);
if (rank < size-1) { /*send value to right */
ierr = MPI_Send((void*)&array[j+(n-1)*step],1,MPIU_REAL,rank+1,tag1,comm);CHKERRQ(ierr);
ierr = MPI_Send((void*)&xg[n-1],1,MPIU_REAL,rank+1,tag1,comm);CHKERRQ(ierr);
}
if (!rank && bx == DM_BOUNDARY_PERIODIC && size > 1) { /* first processor sends first value to last */
ierr = MPI_Send((void*)&array[j],1,MPIU_REAL,size-1,tag2,comm);CHKERRQ(ierr);
}
for (i=1; i<n; i++) {
ierr = PetscDrawLine(draw,PetscRealPart(xg[i-1]),PetscRealPart(array[j+step*(i-1)]),PetscRealPart(xg[i]),PetscRealPart(array[j+step*i]),PETSC_DRAW_RED);CHKERRQ(ierr);
if (showpoints) {
ierr = PetscDrawPoint(draw,PetscRealPart(xg[i-1]),PetscRealPart(array[j+step*(i-1)]),PETSC_DRAW_BLACK);CHKERRQ(ierr);
}
}
if (rank) { /* receive value from left */
ierr = MPI_Recv(&tmp,1,MPIU_REAL,rank-1,tag1,comm,&status);CHKERRQ(ierr);
ierr = MPI_Recv(&xgtmp,1,MPIU_REAL,rank-1,tag1,comm,&status);CHKERRQ(ierr);
ierr = PetscDrawLine(draw,xgtmp,tmp,PetscRealPart(xg[0]),PetscRealPart(array[j]),PETSC_DRAW_RED);CHKERRQ(ierr);
if (showpoints) {
ierr = PetscDrawPoint(draw,xgtmp,tmp,PETSC_DRAW_BLACK);CHKERRQ(ierr);
}
}
if (rank == size-1 && bx == DM_BOUNDARY_PERIODIC && size > 1) {
ierr = MPI_Recv(&tmp,1,MPIU_REAL,0,tag2,comm,&status);CHKERRQ(ierr);
/* If the mesh is not uniform we do not know the mesh spacing between the last point on the right and the first ghost point */
ierr = PetscDrawLine(draw,PetscRealPart(xg[n-1]),PetscRealPart(array[j+step*(n-1)]),PetscRealPart(xg[n-1]+(xg[n-1]-xg[n-2])),tmp,PETSC_DRAW_RED);CHKERRQ(ierr);
if (showpoints) {
ierr = PetscDrawPoint(draw,PetscRealPart(xg[n-2]),PetscRealPart(array[j+step*(n-1)]),PETSC_DRAW_BLACK);CHKERRQ(ierr);
}
}
ierr = PetscDrawSynchronizedFlush(draw);CHKERRQ(ierr);
ierr = PetscDrawPause(draw);CHKERRQ(ierr);
}
ierr = PetscFree(displayfields);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(xcoor,&xg);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(xin,&array);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode DMPlexVTKWriteAll_ASCII(DM dm, PetscViewer viewer)
{
MPI_Comm comm;
PetscViewer_VTK *vtk = (PetscViewer_VTK*) viewer->data;
FILE *fp;
PetscViewerVTKObjectLink link;
PetscSection coordSection, globalCoordSection;
PetscLayout vLayout;
Vec coordinates;
PetscReal lengthScale;
PetscInt vMax, totVertices, totCells;
PetscBool hasPoint = PETSC_FALSE, hasCell = PETSC_FALSE, writePartition = PETSC_FALSE;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = PetscFOpen(comm, vtk->filename, "wb", &fp);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "# vtk DataFile Version 2.0\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "Simplicial Mesh Example\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "ASCII\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "DATASET UNSTRUCTURED_GRID\n");CHKERRQ(ierr);
/* Vertices */
ierr = DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionCreateGlobalSection(coordSection, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalCoordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, NULL, NULL, NULL, &vMax);CHKERRQ(ierr);
if (vMax >= 0) {
PetscInt pStart, pEnd, p, localSize = 0;
ierr = PetscSectionGetChart(globalCoordSection, &pStart, &pEnd);CHKERRQ(ierr);
pEnd = PetscMin(pEnd, vMax);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof;
ierr = PetscSectionGetDof(globalCoordSection, p, &dof);CHKERRQ(ierr);
if (dof > 0) ++localSize;
}
ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &vLayout);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(vLayout, localSize);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr);
} else {
ierr = PetscSectionGetPointLayout(PetscObjectComm((PetscObject)dm), globalCoordSection, &vLayout);CHKERRQ(ierr);
}
ierr = PetscLayoutGetSize(vLayout, &totVertices);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "POINTS %d double\n", totVertices);CHKERRQ(ierr);
ierr = DMPlexVTKWriteSection_ASCII(dm, coordSection, globalCoordSection, coordinates, fp, 3, PETSC_DETERMINE, lengthScale);CHKERRQ(ierr);
/* Cells */
ierr = DMPlexVTKWriteCells_ASCII(dm, fp, &totCells);CHKERRQ(ierr);
/* Vertex fields */
for (link = vtk->link; link; link = link->next) {
if ((link->ft == PETSC_VTK_POINT_FIELD) || (link->ft == PETSC_VTK_POINT_VECTOR_FIELD)) hasPoint = PETSC_TRUE;
if ((link->ft == PETSC_VTK_CELL_FIELD) || (link->ft == PETSC_VTK_CELL_VECTOR_FIELD)) hasCell = PETSC_TRUE;
}
if (hasPoint) {
ierr = PetscFPrintf(comm, fp, "POINT_DATA %d\n", totVertices);CHKERRQ(ierr);
for (link = vtk->link; link; link = link->next) {
Vec X = (Vec) link->vec;
DM dmX;
PetscSection section, globalSection, newSection = NULL;
const char *name;
PetscInt enforceDof = PETSC_DETERMINE;
if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
if (link->ft == PETSC_VTK_POINT_VECTOR_FIELD) enforceDof = 3;
ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
if (dmX) {
DMLabel subpointMap, subpointMapX;
PetscInt dim, dimX, pStart, pEnd, qStart, qEnd;
ierr = DMGetDefaultSection(dmX, §ion);CHKERRQ(ierr);
/* Here is where we check whether dmX is a submesh of dm */
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetDimension(dmX, &dimX);CHKERRQ(ierr);
ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
ierr = DMPlexGetChart(dmX, &qStart, &qEnd);CHKERRQ(ierr);
ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr);
ierr = DMPlexGetSubpointMap(dmX, &subpointMapX);CHKERRQ(ierr);
if (((dim != dimX) || ((pEnd-pStart) < (qEnd-qStart))) && subpointMap && !subpointMapX) {
const PetscInt *ind = NULL;
IS subpointIS;
PetscInt n = 0, q;
ierr = PetscSectionGetChart(section, &qStart, &qEnd);CHKERRQ(ierr);
ierr = DMPlexCreateSubpointIS(dm, &subpointIS);CHKERRQ(ierr);
if (subpointIS) {
ierr = ISGetLocalSize(subpointIS, &n);CHKERRQ(ierr);
ierr = ISGetIndices(subpointIS, &ind);CHKERRQ(ierr);
}
ierr = PetscSectionCreate(comm, &newSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(newSection, pStart, pEnd);CHKERRQ(ierr);
for (q = qStart; q < qEnd; ++q) {
PetscInt dof, off, p;
ierr = PetscSectionGetDof(section, q, &dof);CHKERRQ(ierr);
if (dof) {
ierr = PetscFindInt(q, n, ind, &p);CHKERRQ(ierr);
if (p >= pStart) {
ierr = PetscSectionSetDof(newSection, p, dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, q, &off);CHKERRQ(ierr);
ierr = PetscSectionSetOffset(newSection, p, off);CHKERRQ(ierr);
}
}
}
if (subpointIS) {
ierr = ISRestoreIndices(subpointIS, &ind);CHKERRQ(ierr);
ierr = ISDestroy(&subpointIS);CHKERRQ(ierr);
}
/* No need to setup section */
section = newSection;
}
} else {
ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) §ion);CHKERRQ(ierr);
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
}
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
if (newSection) {ierr = PetscSectionDestroy(&newSection);CHKERRQ(ierr);}
}
}
/* Cell Fields */
ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_view_partition", &writePartition, NULL);CHKERRQ(ierr);
if (hasCell || writePartition) {
ierr = PetscFPrintf(comm, fp, "CELL_DATA %d\n", totCells);CHKERRQ(ierr);
for (link = vtk->link; link; link = link->next) {
Vec X = (Vec) link->vec;
DM dmX;
PetscSection section, globalSection;
const char *name;
PetscInt enforceDof = PETSC_DETERMINE;
if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
if (link->ft == PETSC_VTK_CELL_VECTOR_FIELD) enforceDof = 3;
ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
if (dmX) {
ierr = DMGetDefaultSection(dmX, §ion);CHKERRQ(ierr);
} else {
PetscContainer c;
ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) &c);CHKERRQ(ierr);
if (!c) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscContainerGetPointer(c, (void**) §ion);CHKERRQ(ierr);
}
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
}
if (writePartition) {
ierr = PetscFPrintf(comm, fp, "SCALARS partition int 1\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "LOOKUP_TABLE default\n");CHKERRQ(ierr);
ierr = DMPlexVTKWritePartition_ASCII(dm, fp);CHKERRQ(ierr);
}
}
/* Cleanup */
ierr = PetscSectionDestroy(&globalCoordSection);CHKERRQ(ierr);
ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr);
ierr = PetscFClose(comm, fp);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ApplyBC(DM dm, PetscReal time, Vec locX, User user)
{
const char *name = "Face Sets"; /*Set up in the function DMPlexCreateExodus. is the side set*/
DM dmFace;
IS idIS;
const PetscInt *ids;
PetscScalar *x;
const PetscScalar *facegeom;
PetscInt numFS, fs;
PetscErrorCode ierr;
PetscMPIInt rank;
PetscFunctionBeginUser;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = VecGetDM(user->facegeom,&dmFace);CHKERRQ(ierr);
ierr = DMPlexGetLabelIdIS(dm, name, &idIS);CHKERRQ(ierr);
// ISView(idIS, PETSC_VIEWER_STDOUT_SELF);
if (!idIS) PetscFunctionReturn(0);
ierr = ISGetLocalSize(idIS, &numFS);CHKERRQ(ierr);
ierr = ISGetIndices(idIS, &ids);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->facegeom, &facegeom);CHKERRQ(ierr);
ierr = VecGetArray(locX, &x);CHKERRQ(ierr);
for (fs = 0; fs < numFS; ++fs) {
IS faceIS;
const PetscInt *faces;
PetscInt numFaces, f;
ierr = DMPlexGetStratumIS(dm, name, ids[fs], &faceIS);CHKERRQ(ierr);
ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr);
ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr);
for (f = 0; f < numFaces; ++f) {
// PetscPrintf(PETSC_COMM_SELF, "rank[%d]: ids[%d] = %d, faceIS[%d] = %d, numFaces = %d\n", rank, fs, ids[fs], f, faces[f], numFaces);
const PetscInt face = faces[f], *cells;
const PetscScalar *xI; /*Inner point*/
PetscScalar *xG; /*Ghost point*/
const FaceGeom *fg;
ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr);
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm, cells[0], x, &xI);CHKERRQ(ierr);
ierr = DMPlexPointLocalRef(dm, cells[1], x, &xG);CHKERRQ(ierr);
if (ids[fs]==1){
//PetscPrintf(PETSC_COMM_SELF, "Set Inlfow Boundary Condition! \n");
ierr = BoundaryInflow(time, fg->centroid, fg->normal, xI, xG, user);CHKERRQ(ierr);
// DM dmCell;
// const PetscScalar *cellgeom;
// const CellGeom *cgL, *cgR;
// ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr);
// ierr = VecGetArrayRead(user->cellgeom, &cellgeom);CHKERRQ(ierr);
// ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr);
// ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr);
// ierr = PetscPrintf(PETSC_COMM_WORLD,"cells[0] = (%f, %f, %f), cells[1] = (%f, %f, %f)\n",cgL->centroid[0], cgL->centroid[1], cgL->centroid[2],cgR->centroid[0], cgR->centroid[1], cgR->centroid[2]);CHKERRQ(ierr);
}else if (ids[fs]==2){
//PetscPrintf(PETSC_COMM_SELF, "Set Outlfow Boundary Condition! \n");
ierr = BoundaryOutflow(time, fg->centroid, fg->normal, xI, xG, user);CHKERRQ(ierr);
}else if (ids[fs]==3){
//PetscPrintf(PETSC_COMM_SELF, "Set Wall Boundary Condition! \n");
ierr = BoundaryWallflow(time, fg->centroid, fg->normal, xI, xG, user);CHKERRQ(ierr);
}else {
SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Wrong type of boundary condition setup!!! \n The set up of the boundary should be: 1 for the inflow, 2 for the outflow, and 3 for the wallflow");
}
}
// PetscPrintf(PETSC_COMM_SELF, " \n");
ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr);
ierr = ISDestroy(&faceIS);CHKERRQ(ierr);
}
ierr = VecRestoreArray(locX, &x);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = ISRestoreIndices(idIS, &ids);CHKERRQ(ierr);
ierr = ISDestroy(&idIS);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/**
Compute the gadient of the cell center gradient obtained by the least-square method
*/
PetscErrorCode GradientGradientJacobian(DM dm, Vec locX, PetscScalar elemMat[], void *ctx)
{
User user = (User) ctx;
Physics phys = user->model->physics;
PetscInt dof = phys->dof;
const PetscScalar *facegeom, *cellgeom,*x;
PetscErrorCode ierr;
DM dmFace, dmCell;
DM dmGrad = user->dmGrad;
PetscInt fStart, fEnd, face, cStart;
Vec Grad;
/*here the localGradLimiter refers to the gradient that has been multiplied by the limiter function.
The locGradLimiter is used to construct the uL and uR, and the locGrad is used to caculate the diffusion term*/
Vec TempVec; /*a temperal vec for the vector restore*/
PetscFunctionBeginUser;
ierr = VecGetDM(user->facegeom,&dmFace);CHKERRQ(ierr);
ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr);
ierr = DMGetGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = VecZeroEntries(Grad);CHKERRQ(ierr);
ierr = VecDuplicate(Grad, &TempVec);CHKERRQ(ierr);
ierr = VecCopy(Grad, TempVec);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(locX,&x);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, NULL);CHKERRQ(ierr);
{
PetscScalar *grad;
ierr = VecGetArray(TempVec,&grad);CHKERRQ(ierr);
/* Reconstruct gradients */
for (face=fStart; face<fEnd; face++) {
const PetscInt *cells;
const PetscScalar *cx[2];
const FaceGeom *fg;
PetscScalar *cgrad[2];
PetscInt i,j;
PetscBool ghost;
ierr = IsExteriorGhostFace(dm,face,&ghost);CHKERRQ(ierr);
if (ghost) continue;
ierr = DMPlexGetSupport(dm,face,&cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmFace,face,facegeom,&fg);CHKERRQ(ierr);
for (i=0; i<2; i++) {
ierr = DMPlexPointLocalRead(dm,cells[i],x,&cx[i]);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dmGrad,cells[i],grad,&cgrad[i]);CHKERRQ(ierr);
}
for (i=0; i<dof; i++) {
PetscScalar delta = cx[1][i] - cx[0][i];
for (j=0; j<DIM; j++) {
if (cgrad[0]) cgrad[0][i*DIM+j] += fg->grad[0][j] * delta;
if (cgrad[1]) cgrad[1][i*DIM+j] -= fg->grad[1][j] * delta;
}
}
for (i=0; i<phys->dof; i++) {
for (j=0; j<phys->dof; j++) {
if(cells[0]<user->cEndInterior) elemMat[cells[0]*dof*dof + i*dof + j] -= cells[0]*1.0;
if(cells[1]<user->cEndInterior) elemMat[cells[1]*dof*dof + i*dof + j] += cells[1]*1.2;
}
}
}
ierr = VecRestoreArray(TempVec,&grad);CHKERRQ(ierr);
}
ierr = DMRestoreGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locX,&x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ComputeJacobian_LS(DM dm, Vec locX, PetscInt cell, PetscScalar CellValues[], void *ctx)
{
User user = (User) ctx;
Physics phys = user->model->physics;
PetscInt dof = phys->dof;
const PetscScalar *facegeom, *cellgeom,*x;
PetscErrorCode ierr;
DM dmFace, dmCell;
DM dmGrad = user->dmGrad;
PetscInt fStart, fEnd, face, cStart;
Vec locGrad, locGradLimiter, Grad;
/*here the localGradLimiter refers to the gradient that has been multiplied by the limiter function.
The locGradLimiter is used to construct the uL and uR, and the locGrad is used to caculate the diffusion term*/
Vec TempVec; /*a temperal vec for the vector restore*/
PetscFunctionBeginUser;
ierr = VecGetDM(user->facegeom,&dmFace);CHKERRQ(ierr);
ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr);
ierr = DMGetGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = VecDuplicate(Grad, &TempVec);CHKERRQ(ierr);
ierr = VecCopy(Grad, TempVec);CHKERRQ(ierr);
/*Backup the original vector and use it to restore the value of dmGrad,
because I do not want to change the values of the cell gradient*/
ierr = VecGetArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(locX,&x);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, NULL);CHKERRQ(ierr);
{
PetscScalar *grad;
ierr = VecGetArray(Grad,&grad);CHKERRQ(ierr);
/* Limit interior gradients. Using cell-based loop because it generalizes better to vector limiters. */
const PetscInt *faces;
PetscInt numFaces,f;
PetscReal *cellPhi; /* Scalar limiter applied to each component separately */
const PetscScalar *cx;
const CellGeom *cg;
PetscScalar *cgrad;
PetscInt i;
ierr = PetscMalloc(phys->dof*sizeof(PetscScalar),&cellPhi);CHKERRQ(ierr);
ierr = DMPlexGetConeSize(dm,cell,&numFaces);CHKERRQ(ierr);
ierr = DMPlexGetCone(dm,cell,&faces);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm,cell,x,&cx);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell,cell,cellgeom,&cg);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dmGrad,cell,grad,&cgrad);CHKERRQ(ierr);
/* Limiter will be minimum value over all neighbors */
for (i=0; i<dof; i++) {
cellPhi[i] = PETSC_MAX_REAL;
}
for (f=0; f<numFaces; f++) {
const PetscScalar *ncx;
const CellGeom *ncg;
const PetscInt *fcells;
PetscInt face = faces[f],ncell;
PetscScalar v[DIM];
PetscBool ghost;
ierr = IsExteriorGhostFace(dm,face,&ghost);CHKERRQ(ierr);
if (ghost) continue;
ierr = DMPlexGetSupport(dm,face,&fcells);CHKERRQ(ierr);
ncell = cell == fcells[0] ? fcells[1] : fcells[0]; /*The expression (x ? y : z) has the value of y if x is nonzero, z otherwise */
ierr = DMPlexPointLocalRead(dm,ncell,x,&ncx);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell,ncell,cellgeom,&ncg);CHKERRQ(ierr);
Waxpy2(-1, cg->centroid, ncg->centroid, v);
for (i=0; i<dof; i++) {
/* We use the symmetric slope limited form of Berger, Aftosmis, and Murman 2005 */
PetscScalar phi,flim = 0.5 * (ncx[i] - cx[i]) / Dot2(&cgrad[i*DIM],v);
phi = (*user->LimitGrad)(flim);
cellPhi[i] = PetscMin(cellPhi[i],phi);
}
}
/* Apply limiter to gradient */
for (i=0; i<dof; i++) Scale2(cellPhi[i],&cgrad[i*DIM],&cgrad[i*DIM]);
ierr = PetscFree(cellPhi);CHKERRQ(ierr);
ierr = VecRestoreArray(Grad,&grad);CHKERRQ(ierr);
}
ierr = DMGetLocalVector(dmGrad,&locGradLimiter);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmGrad,Grad,INSERT_VALUES,locGradLimiter);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dmGrad,Grad,INSERT_VALUES,locGradLimiter);CHKERRQ(ierr);
ierr = VecCopy(TempVec, Grad);CHKERRQ(ierr);/*Restore the vector*/
ierr = DMGetLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = VecDestroy(&TempVec);CHKERRQ(ierr);
{
const PetscScalar *grad, *gradlimiter;
ierr = VecGetArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = VecGetArrayRead(locGradLimiter,&gradlimiter);CHKERRQ(ierr);
for (face=fStart; face<fEnd; face++) {
const PetscInt *cells;
PetscInt ghost,i,j;
PetscScalar *fluxcon, *fluxdiff, *fx[2];
const FaceGeom *fg;
const CellGeom *cg[2];
const PetscScalar *cx[2],*cgrad[2], *cgradlimiter[2];
PetscScalar *uL, *uR;
PetscReal FaceArea;
ierr = PetscMalloc(phys->dof * phys->dof * sizeof(PetscScalar), &fluxcon);CHKERRQ(ierr); /*For the convection terms*/
ierr = PetscMalloc(phys->dof * phys->dof * sizeof(PetscScalar), &fluxdiff);CHKERRQ(ierr); /*For the diffusion terms*/
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &uL);CHKERRQ(ierr);
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &uR);CHKERRQ(ierr);
fx[0] = uL; fx[1] = uR;
ierr = DMPlexGetLabelValue(dm, "ghost", face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmFace,face,facegeom,&fg);CHKERRQ(ierr);
for (i=0; i<2; i++) {
PetscScalar dx[DIM];
ierr = DMPlexPointLocalRead(dmCell,cells[i],cellgeom,&cg[i]);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm,cells[i],x,&cx[i]);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad,cells[i],gradlimiter,&cgradlimiter[i]);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad,cells[i],grad,&cgrad[i]);CHKERRQ(ierr);
Waxpy2(-1,cg[i]->centroid,fg->centroid,dx);
for (j=0; j<dof; j++) {
fx[i][j] = cx[i][j] + Dot2(cgradlimiter[i],dx);
}
/*fx[0] and fx[1] are the value of the variables on the left and right
side of the face, respectively, that is u_L and u_R.*/
}
ierr = RiemannSolver_Rusanov_Jacobian(user, cgrad[0], cgrad[1], fg->centroid, cg[0]->centroid, cg[1]->centroid, fg->normal,
fx[0], fx[1], fluxcon, fluxdiff);CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dm, face, &FaceArea, NULL, NULL);CHKERRQ(ierr);
/*Compute the face area*/
for (i=0; i<phys->dof; i++) {
for (j=0; j<phys->dof; j++) {
if(cells[0]<user->cEndInterior) CellValues[cells[0]*dof*dof + i*dof + j] -= cells[0]*1.0;
if(cells[1]<user->cEndInterior) CellValues[cells[1]*dof*dof + i*dof + j] += cells[1]*1.2;
}
}
// ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRQ(ierr);
ierr = PetscFree(fluxcon);CHKERRQ(ierr);
ierr = PetscFree(fluxdiff);CHKERRQ(ierr);
ierr = PetscFree(uL);CHKERRQ(ierr);
ierr = PetscFree(uR);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locGradLimiter,&gradlimiter);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locX,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmGrad,&locGradLimiter);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/**
Creates \f$ f_n \f$ part of time-stepping scheme.
For ODE solvers (aka time-stepping schemes), you think of your problem as \f$ y' = f(y) \f$ and
Note that this actually returns something more like \f$ -f_n \f$.
*/
PetscErrorCode FormTimeStepFunction(User user, Algebra algebra, Vec in, Vec out)
{
PetscErrorCode ierr;
PetscMPIInt rank;
Vec inLocal;
DM dmFace, dmCell;
PetscFunctionBegin;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = VecSet(out, 0.0);CHKERRQ(ierr);
// ierr = VecView(in, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
/*Since the DMPlexVecSetClosure only works on the local vectors,
we need to create a local vector and scatter the global
vector to the local vector and insert the values,
and then scatter the local updated vectors back to the global vector.*/
ierr = DMGetLocalVector(user->dm, &inLocal);CHKERRQ(ierr);
ierr = VecSet(inLocal, 0);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user->dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user->dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr);
ierr = ApplyBC(user->dm, user->current_time, inLocal, user);CHKERRQ(ierr);
ierr = VecGetDM(user->facegeom,&dmFace);CHKERRQ(ierr);
ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr);
ierr = ConstructCellCentriodGradient(user->dm, dmFace, dmCell, user->current_time, inLocal, out, user);CHKERRQ(ierr);
/*Construct the cell gradient at the current time
and save it into the user->dmGrad. If you want
to use the cell gradient, following these:
ierr = DMGetGlobalVector(user->dmGrad,&Grad);CHKERRQ(ierr); or
ierr = DMGetLocalVector(user->dmGrad,&Grad);CHKERRQ(ierr);
*/
if (user->second_order){
ierr = CaculateLocalFunction_LS(user->dm, dmFace, dmCell, user->current_time, inLocal, out, user);CHKERRQ(ierr);
}else{
ierr = CaculateLocalFunction_Upwind(user->dm, dmFace, dmCell, user->current_time, inLocal, out, user);CHKERRQ(ierr);
}
ierr = CaculateLocalSourceTerm(user->dm, inLocal, out, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(user->dm, inLocal, INSERT_VALUES, in);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(user->dm, inLocal, INSERT_VALUES, in);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(user->dm, &inLocal);CHKERRQ(ierr);
//VecView(in,PETSC_VIEWER_STDOUT_WORLD);
//VecView(out,PETSC_VIEWER_STDOUT_WORLD);
if (0){
PetscViewer viewer;
PetscReal fnnorm;
ierr = VecNorm(out,NORM_INFINITY,&fnnorm);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, "function.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(out, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with founction norm = %g \n",
user->current_step, user->current_time, fnnorm);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc, char *argv[])
{
PetscErrorCode ierr;
DM dm;
PetscBool interpolate = PETSC_TRUE;
PetscInt dim;
PetscInt pStart, pEnd;
PetscInt vStart, vEnd;
PetscInt eStart, eEnd;
PetscInt cStart, cEnd;
PetscSection s;
ierr = PetscInitialize(&argc, &argv, (char*)0, help); CHKERRQ(ierr);
ierr = DMPlexCreateGmshFromFile(MPI_COMM_WORLD, argv[1], interpolate, &dm); CHKERRQ(ierr);
ierr = DMGetDimension(dm, &dim); CHKERRQ(ierr);
printf("dim = %d\n", dim);
ierr = DMPlexGetChart(dm, &pStart, &pEnd); CHKERRQ(ierr);
printf("chart: pstart, pend = %d %d\n", pStart, pEnd);
// vertices
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd); CHKERRQ(ierr);
printf("Depth 0: vstart, vend, len = %d %d %d\n", vStart, vEnd, vEnd-vStart);
// edges
ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd); CHKERRQ(ierr);
printf("Depth 1: estart, eend, len = %d %d %d\n", eStart, eEnd, eEnd-eStart);
// cells
ierr = DMPlexGetDepthStratum(dm, 2, &cStart, &cEnd); CHKERRQ(ierr);
printf("Depth 2: cstart, cend, len = %d %d %d\n", cStart, cEnd, cEnd-cStart);
// cells adjacent to face
{
FILE * fid = fopen("face_nbr.txt","w");
for(PetscInt e=eStart; e<eEnd; ++e)
{
PetscInt nbr;
ierr = DMPlexGetSupportSize(dm, e, &nbr); CHKERRQ(ierr);
const PetscInt *nbcells;
ierr = DMPlexGetSupport(dm, e, &nbcells); CHKERRQ(ierr);
if(nbr == 1) // boundary face
fprintf(fid, "%d %d\n",e-eStart+1,nbcells[0]-cStart+1);
else if(nbr == 2) // interior face
fprintf(fid, "%d %d %d\n",e-eStart+1,nbcells[0]-cStart+1,nbcells[1]-cStart+1);
else
{
printf("nbr is not 1 or 2\n");
exit(0);
}
}
fclose(fid);
}
// point coordinates
{
Vec coordinates;
ierr = DMGetCoordinatesLocal(dm, &coordinates); CHKERRQ(ierr);
const PetscScalar *coords;
ierr = VecGetArrayRead(coordinates, &coords); CHKERRQ(ierr);
DM dmCoord;
ierr = DMGetCoordinateDM(dm, &dmCoord); CHKERRQ(ierr);
FILE * fid = fopen("vertices.txt","w");
for(PetscInt v=vStart; v<vEnd; ++v)
{
PetscScalar *vertex;
ierr = DMPlexPointLocalRead(dmCoord, v, coords, &vertex); CHKERRQ(ierr);
fprintf(fid, "%f %f\n", vertex[0], vertex[1]);
}
fclose(fid);
ierr = VecRestoreArrayRead(coordinates, &coords); CHKERRQ(ierr);
}
// compute cell and face geometry
{
Vec cellgeom, facegeom;
ierr = DMPlexComputeGeometryFVM(dm, &cellgeom, &facegeom); CHKERRQ(ierr);
// cell information
DM dmCell;
ierr = VecGetDM(cellgeom, &dmCell); CHKERRQ(ierr);
const PetscScalar *cgeom;
ierr = VecGetArrayRead(cellgeom, &cgeom); CHKERRQ(ierr);
FILE * fid = fopen("cells.txt","w");
for(PetscInt c=cStart; c<cEnd; ++c)
{
// cell properties like volume, centroid
PetscFVCellGeom *cg;
ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg); CHKERRQ(ierr);
fprintf(fid, "%d %f %f %f\n", c-cStart+1, cg->volume,
cg->centroid[0], cg->centroid[1]);
}
fclose(fid);
ierr = VecRestoreArrayRead(cellgeom, &cgeom); CHKERRQ(ierr);
// face information
DM dmFace;
ierr = VecGetDM(facegeom, &dmFace); CHKERRQ(ierr);
const PetscScalar *fgeom;
ierr = VecGetArrayRead(facegeom, &fgeom); CHKERRQ(ierr);
fid = fopen("faces.txt","w");
for(PetscInt e=eStart; e<eEnd; ++e)
{
// face properties like area normal, centroid
PetscFVFaceGeom *fg;
ierr = DMPlexPointLocalRead(dmFace, e, fgeom, &fg); CHKERRQ(ierr);
fprintf(fid, "%d %f %f %f %f\n", e-eStart+1, fg->normal[0], fg->normal[1],
fg->centroid[0], fg->centroid[1]);
}
fclose(fid);
ierr = VecRestoreArrayRead(facegeom, &fgeom); CHKERRQ(ierr);
}
// create section with one variable in each cell
ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &s); CHKERRQ(ierr);
ierr = PetscSectionSetChart(s, pStart, pEnd); CHKERRQ(ierr);
for(PetscInt c=cStart; c<cEnd; ++c)
{
ierr = PetscSectionSetDof(s, c, 1); CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(s); CHKERRQ(ierr);
// create vector to store solution
Vec lv, gv;
ierr = DMSetDefaultSection(dm, s); CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &lv); CHKERRQ(ierr);
ierr = DMGetGlobalVector(dm, &gv); CHKERRQ(ierr);
}
static PetscErrorCode TSComputeRHSFunction_DMPlex(TS ts, PetscReal time, Vec X, Vec F, void *ctx)
{
DM dm;
DMTS_Plex *dmplexts = (DMTS_Plex *) ctx;
void (*riemann)(const PetscReal[], const PetscReal[], const PetscScalar[], const PetscScalar[], PetscScalar[], void *) = dmplexts->riemann;
PetscFV fvm;
PetscLimiter lim;
Vec faceGeometry = dmplexts->facegeom;
Vec cellGeometry = dmplexts->cellgeom;
Vec Grad = NULL, locGrad, locX;
DM dmFace, dmCell;
DMLabel ghostLabel;
PetscCellGeometry fgeom, cgeom;
const PetscScalar *facegeom, *cellgeom, *x, *lgrad;
PetscScalar *grad, *f, *uL, *uR, *fluxL, *fluxR;
PetscReal *centroid, *normal, *vol, *cellPhi;
PetscBool computeGradients;
PetscInt Nf, dim, pdim, fStart, fEnd, numFaces = 0, face, iface, cell, cStart, cEnd, cEndInterior;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(ts,TS_CLASSID,1);
PetscValidHeaderSpecific(X,VEC_CLASSID,3);
PetscValidHeaderSpecific(F,VEC_CLASSID,5);
ierr = TSGetDM(ts, &dm);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr);
ierr = VecZeroEntries(locX);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr);
ierr = VecZeroEntries(F);CHKERRQ(ierr);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr);
ierr = DMGetField(dm, 0, (PetscObject *) &fvm);CHKERRQ(ierr);
ierr = PetscFVGetLimiter(fvm, &lim);CHKERRQ(ierr);
ierr = PetscFVGetNumComponents(fvm, &pdim);CHKERRQ(ierr);
ierr = PetscFVGetComputeGradients(fvm, &computeGradients);CHKERRQ(ierr);
if (computeGradients) {
ierr = DMGetGlobalVector(dmplexts->dmGrad, &Grad);CHKERRQ(ierr);
ierr = VecZeroEntries(Grad);CHKERRQ(ierr);
ierr = VecGetArray(Grad, &grad);CHKERRQ(ierr);
}
ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr);
ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr);
ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr);
/* Count faces and reconstruct gradients */
for (face = fStart; face < fEnd; ++face) {
const PetscInt *cells;
const FaceGeom *fg;
const PetscScalar *cx[2];
PetscScalar *cgrad[2];
PetscBool boundary;
PetscInt ghost, c, pd, d;
ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
++numFaces;
if (!computeGradients) continue;
ierr = DMPlexIsBoundaryPoint(dm, face, &boundary);CHKERRQ(ierr);
if (boundary) continue;
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr);
for (c = 0; c < 2; ++c) {
ierr = DMPlexPointLocalRead(dm, cells[c], x, &cx[c]);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dmplexts->dmGrad, cells[c], grad, &cgrad[c]);CHKERRQ(ierr);
}
for (pd = 0; pd < pdim; ++pd) {
PetscScalar delta = cx[1][pd] - cx[0][pd];
for (d = 0; d < dim; ++d) {
if (cgrad[0]) cgrad[0][pd*dim+d] += fg->grad[0][d] * delta;
if (cgrad[1]) cgrad[1][pd*dim+d] -= fg->grad[1][d] * delta;
}
}
}
/* Limit interior gradients (using cell-based loop because it generalizes better to vector limiters) */
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
ierr = DMGetWorkArray(dm, pdim, PETSC_REAL, &cellPhi);CHKERRQ(ierr);
for (cell = computeGradients && lim ? cStart : cEnd; cell < cEndInterior; ++cell) {
const PetscInt *faces;
const PetscScalar *cx;
const CellGeom *cg;
PetscScalar *cgrad;
PetscInt coneSize, f, pd, d;
ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr);
ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm, cell, x, &cx);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cell, cellgeom, &cg);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dmplexts->dmGrad, cell, grad, &cgrad);CHKERRQ(ierr);
if (!cgrad) continue; /* Unowned overlap cell, we do not compute */
/* Limiter will be minimum value over all neighbors */
for (d = 0; d < pdim; ++d) cellPhi[d] = PETSC_MAX_REAL;
for (f = 0; f < coneSize; ++f) {
const PetscScalar *ncx;
const CellGeom *ncg;
const PetscInt *fcells;
PetscInt face = faces[f], ncell, ghost;
PetscReal v[3];
PetscBool boundary;
ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
ierr = DMPlexIsBoundaryPoint(dm, face, &boundary);CHKERRQ(ierr);
if ((ghost >= 0) || boundary) continue;
ierr = DMPlexGetSupport(dm, face, &fcells);CHKERRQ(ierr);
ncell = cell == fcells[0] ? fcells[1] : fcells[0];
ierr = DMPlexPointLocalRead(dm, ncell, x, &ncx);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, ncell, cellgeom, &ncg);CHKERRQ(ierr);
WaxpyD(dim, -1, cg->centroid, ncg->centroid, v);
for (d = 0; d < pdim; ++d) {
/* We use the symmetric slope limited form of Berger, Aftosmis, and Murman 2005 */
PetscReal phi, flim = 0.5 * PetscRealPart(ncx[d] - cx[d]) / DotD(dim, &cgrad[d*dim], v);
ierr = PetscLimiterLimit(lim, flim, &phi);CHKERRQ(ierr);
cellPhi[d] = PetscMin(cellPhi[d], phi);
}
}
/* Apply limiter to gradient */
for (pd = 0; pd < pdim; ++pd)
/* Scalar limiter applied to each component separately */
for (d = 0; d < dim; ++d) cgrad[pd*dim+d] *= cellPhi[pd];
}
ierr = DMRestoreWorkArray(dm, pdim, PETSC_REAL, &cellPhi);CHKERRQ(ierr);
ierr = DMPlexInsertBoundaryValuesFVM_Static(dm, fvm, time, locX, Grad, dmplexts);CHKERRQ(ierr);
if (computeGradients) {
ierr = VecRestoreArray(Grad, &grad);CHKERRQ(ierr);
ierr = DMGetLocalVector(dmplexts->dmGrad, &locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmplexts->dmGrad, Grad, INSERT_VALUES, locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dmplexts->dmGrad, Grad, INSERT_VALUES, locGrad);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dmplexts->dmGrad, &Grad);CHKERRQ(ierr);
ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr);
}
ierr = PetscMalloc7(numFaces*dim,¢roid,numFaces*dim,&normal,numFaces*2,&vol,numFaces*pdim,&uL,numFaces*pdim,&uR,numFaces*pdim,&fluxL,numFaces*pdim,&fluxR);CHKERRQ(ierr);
/* Read out values */
for (face = fStart, iface = 0; face < fEnd; ++face) {
const PetscInt *cells;
const FaceGeom *fg;
const CellGeom *cgL, *cgR;
const PetscScalar *xL, *xR, *gL, *gR;
PetscInt ghost, d;
ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr);
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm, cells[0], x, &xL);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm, cells[1], x, &xR);CHKERRQ(ierr);
if (computeGradients) {
PetscReal dxL[3], dxR[3];
ierr = DMPlexPointLocalRead(dmplexts->dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmplexts->dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr);
WaxpyD(dim, -1, cgL->centroid, fg->centroid, dxL);
WaxpyD(dim, -1, cgR->centroid, fg->centroid, dxR);
for (d = 0; d < pdim; ++d) {
uL[iface*pdim+d] = xL[d] + DotD(dim, &gL[d*dim], dxL);
uR[iface*pdim+d] = xR[d] + DotD(dim, &gR[d*dim], dxR);
}
} else {
for (d = 0; d < pdim; ++d) {
uL[iface*pdim+d] = xL[d];
uR[iface*pdim+d] = xR[d];
}
}
for (d = 0; d < dim; ++d) {
centroid[iface*dim+d] = fg->centroid[d];
normal[iface*dim+d] = fg->normal[d];
}
vol[iface*2+0] = cgL->volume;
vol[iface*2+1] = cgR->volume;
++iface;
}
if (computeGradients) {
ierr = VecRestoreArrayRead(locGrad,&lgrad);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmplexts->dmGrad, &locGrad);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr);
fgeom.v0 = centroid;
fgeom.n = normal;
cgeom.vol = vol;
/* Riemann solve */
ierr = PetscFVIntegrateRHSFunction(fvm, numFaces, Nf, &fvm, 0, fgeom, cgeom, uL, uR, riemann, fluxL, fluxR, dmplexts->rhsfunctionlocalctx);CHKERRQ(ierr);
/* Insert fluxes */
ierr = VecGetArray(F, &f);CHKERRQ(ierr);
for (face = fStart, iface = 0; face < fEnd; ++face) {
const PetscInt *cells;
PetscScalar *fL, *fR;
PetscInt ghost, d;
ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dm, cells[0], f, &fL);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dm, cells[1], f, &fR);CHKERRQ(ierr);
for (d = 0; d < pdim; ++d) {
if (fL) fL[d] -= fluxL[iface*pdim+d];
if (fR) fR[d] += fluxR[iface*pdim+d];
}
++iface;
}
ierr = VecRestoreArray(F, &f);CHKERRQ(ierr);
ierr = PetscFree7(centroid,normal,vol,uL,uR,fluxL,fluxR);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode DMPlexInsertBoundaryValuesFVM_Static(DM dm, PetscFV fvm, PetscReal time, Vec locX, Vec Grad, DMTS_Plex *dmplexts)
{
Vec faceGeometry = dmplexts->facegeom;
Vec cellGeometry = dmplexts->cellgeom;
DM dmFace, dmCell;
const PetscScalar *facegeom, *cellgeom, *grad;
PetscScalar *x, *fx;
PetscInt numBd, b, dim, pdim, fStart, fEnd;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = PetscFVGetNumComponents(fvm, &pdim);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr);
if (Grad) {
ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr);
ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr);
ierr = DMGetWorkArray(dm, pdim, PETSC_SCALAR, &fx);CHKERRQ(ierr);
ierr = VecGetArrayRead(Grad, &grad);CHKERRQ(ierr);
}
ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr);
ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr);
ierr = VecGetArray(locX, &x);CHKERRQ(ierr);
for (b = 0; b < numBd; ++b) {
PetscErrorCode (*func)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*);
DMLabel label;
const char *labelname;
const PetscInt *ids;
PetscInt numids, i;
void *ctx;
ierr = DMPlexGetBoundary(dm, b, NULL, NULL, &labelname, NULL, (void (**)()) &func, &numids, &ids, &ctx);CHKERRQ(ierr);
ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr);
for (i = 0; i < numids; ++i) {
IS faceIS;
const PetscInt *faces;
PetscInt numFaces, f;
ierr = DMLabelGetStratumIS(label, ids[i], &faceIS);CHKERRQ(ierr);
if (!faceIS) continue; /* No points with that id on this process */
ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr);
ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr);
for (f = 0; f < numFaces; ++f) {
const PetscInt face = faces[f], *cells;
const FaceGeom *fg;
if ((face < fStart) || (face >= fEnd)) continue; /* Refinement adds non-faces to labels */
ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr);
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
if (Grad) {
const CellGeom *cg;
const PetscScalar *cx, *cgrad;
PetscScalar *xG;
PetscReal dx[3];
PetscInt d;
ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cg);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm, cells[0], x, &cx);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmplexts->dmGrad, cells[0], grad, &cgrad);CHKERRQ(ierr);
ierr = DMPlexPointLocalRef(dm, cells[1], x, &xG);CHKERRQ(ierr);
WaxpyD(dim, -1, cg->centroid, fg->centroid, dx);
for (d = 0; d < pdim; ++d) fx[d] = cx[d] + DotD(dim, &cgrad[d*dim], dx);
ierr = (*func)(time, fg->centroid, fg->normal, fx, xG, ctx);CHKERRQ(ierr);
} else {
const PetscScalar *xI;
PetscScalar *xG;
ierr = DMPlexPointLocalRead(dm, cells[0], x, &xI);CHKERRQ(ierr);
ierr = DMPlexPointLocalRef(dm, cells[1], x, &xG);CHKERRQ(ierr);
ierr = (*func)(time, fg->centroid, fg->normal, xI, xG, ctx);CHKERRQ(ierr);
}
}
ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr);
ierr = ISDestroy(&faceIS);CHKERRQ(ierr);
}
}
ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr);
ierr = VecRestoreArray(locX, &x);CHKERRQ(ierr);
if (Grad) {
ierr = DMRestoreWorkArray(dm, pdim, PETSC_SCALAR, &fx);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(Grad, &grad);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
