/*
Compute the gradient of the variables at the center of the cell
by the least-square reconstruction method based on the function
BuildLeastSquares.
*/
PetscErrorCode ConstructCellCentriodGradient(DM dm,DM dmFace,DM dmCell,PetscReal time,Vec locX,Vec F,User user)
{
DM dmGrad = user->dmGrad;
Model mod = user->model;
Physics phys = mod->physics;
const PetscInt dof = phys->dof;
PetscErrorCode ierr;
const PetscScalar *facegeom, *cellgeom, *x;
PetscInt fStart, fEnd, face, cStart;
Vec Grad;
PetscFunctionBeginUser;
ierr = DMGetGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = VecZeroEntries(Grad);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(Grad,&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;
}
}
}
ierr = VecRestoreArray(Grad,&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);
}
static PetscErrorCode ReadData2D(DM dm, Vec u, AppCtx *user)
{
PetscInt cStart, cEnd, cell;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
for (cell = cStart; cell < cEnd; ++cell) {
PetscScalar *closure = NULL;
PetscInt closureSize, ki, kj, f, c, foff = 0, o = 0;
ierr = DMPlexVecGetClosure(dm, NULL, u, cell, &closureSize, &closure);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "Cell %D\n", cell);CHKERRQ(ierr);
for (f = 0; f < user->Nf; ++f) {
ierr = PetscPrintf(PETSC_COMM_SELF, " Field %D\n", f);CHKERRQ(ierr);
for (kj = user->k[f]; kj >= 0; --kj) {
for (ki = 0; ki <= user->k[f]; ++ki) {
if (ki > 0) {ierr = PetscPrintf(PETSC_COMM_SELF, " ");CHKERRQ(ierr);}
for (c = 0; c < user->Nc[f]; ++c) {
if (c > 0) ierr = PetscPrintf(PETSC_COMM_SELF, ",");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "%2.0f", closure[(kj*(user->k[f]+1) + ki)*user->Nc[f]+c + foff]);CHKERRQ(ierr);
}
}
ierr = PetscPrintf(PETSC_COMM_SELF, "\n");CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_SELF, "\n\n");CHKERRQ(ierr);
foff += PetscSqr(user->k[f]+1);
}
ierr = DMPlexVecRestoreClosure(dm, NULL, u, cell, &closureSize, &closure);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "\n\n");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);
}
/**
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);
}
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);
}
/*
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 CheckMesh(DM dm, AppCtx *user)
{
PetscReal detJ, J[9], refVol = 1.0;
PetscReal vol;
PetscInt dim, depth, d, cStart, cEnd, c;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) {
refVol *= 2.0;
}
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, NULL, J, NULL, &detJ);CHKERRQ(ierr);
if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %d is inverted, |J| = %g", c, detJ);
if (user->debug) {PetscPrintf(PETSC_COMM_SELF, "FEM Volume: %g\n", detJ*refVol);CHKERRQ(ierr);}
if (depth > 1) {
ierr = DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL);CHKERRQ(ierr);
if (vol <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %d is inverted, vol = %g", c, vol);
if (user->debug) {PetscPrintf(PETSC_COMM_SELF, "FVM Volume: %g\n", vol);CHKERRQ(ierr);}
}
}
PetscFunctionReturn(0);
}
PetscErrorCode CompareCones(DM dm, DM idm)
{
PetscInt cStart, cEnd, c, vStart, vEnd, v;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
const PetscInt *cone;
PetscInt *points = NULL, numPoints, p, numVertices = 0, coneSize;
ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr);
ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr);
ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
for (p = 0; p < numPoints*2; p += 2) {
const PetscInt point = points[p];
if ((point >= vStart) && (point < vEnd)) points[numVertices++] = point;
}
if (numVertices != coneSize) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "In cell %d, cone size %d != %d vertices in closure", c, coneSize, numVertices);
for (v = 0; v < numVertices; ++v) {
if (cone[v] != points[v]) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "In cell %d, cone point %d is %d != %d vertex in closure", c, v, cone[v], points[v]);
}
ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
}
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);
}
static PetscErrorCode TestCone(DM dm, AppCtx *user)
{
PetscInt numRuns, cStart, cEnd, c, i;
PetscReal maxTimePerRun = user->maxConeTime;
PetscLogStage stage;
PetscLogEvent event;
PetscEventPerfInfo eventInfo;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogStageRegister("DMPlex Cone Test", &stage);CHKERRQ(ierr);
ierr = PetscLogEventRegister("Cone", PETSC_OBJECT_CLASSID, &event);CHKERRQ(ierr);
ierr = PetscLogStagePush(stage);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = PetscLogEventBegin(event,0,0,0,0);CHKERRQ(ierr);
for (i = 0; i < user->iterations; ++i) {
for (c = cStart; c < cEnd; ++c) {
const PetscInt *cone;
ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr);
}
}
ierr = PetscLogEventEnd(event,0,0,0,0);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogEventGetPerfInfo(stage, event, &eventInfo);CHKERRQ(ierr);
numRuns = (cEnd-cStart) * user->iterations;
if (eventInfo.count != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event calls %d should be %d", eventInfo.count, 1);
if ((PetscInt) eventInfo.flops != 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event flops %d should be %d", (PetscInt) eventInfo.flops, 0);
if (eventInfo.time > maxTimePerRun * numRuns) {
ierr = PetscPrintf(PETSC_COMM_SELF, "Cones: %d Average time per cone: %gs standard: %gs\n", numRuns, eventInfo.time/numRuns, maxTimePerRun);
if (user->errors) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Average time for cone %g > standard %g", eventInfo.time/numRuns, maxTimePerRun);
}
PetscFunctionReturn(0);
}
static PetscErrorCode TestLocation(DM dm, AppCtx *user)
{
PetscInt dim = user->dim;
PetscInt cStart, cEnd, c;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
/* Locate all centroids */
for (c = cStart; c < cEnd; ++c) {
Vec v;
IS is;
PetscScalar *a;
PetscReal centroid[3];
PetscInt *cells, n, d;
ierr = DMPlexComputeCellGeometryFVM(dm, c, NULL, centroid, NULL);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF, dim, &v);CHKERRQ(ierr);
ierr = VecSetBlockSize(v, dim);CHKERRQ(ierr);
ierr = VecGetArray(v, &a);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) a[d] = centroid[d];
ierr = VecRestoreArray(v, &a);CHKERRQ(ierr);
ierr = DMLocatePoints(dm, v, &is);CHKERRQ(ierr);
ierr = VecDestroy(&v);CHKERRQ(ierr);
ierr = ISGetLocalSize(is, &n);CHKERRQ(ierr);
ierr = ISGetIndices(is, &cells);CHKERRQ(ierr);
if (n != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Found %d cells instead %d", n, 1);
if (cells[0] != c) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not locate centroid of cell %d, instead found %d", c, cells[0]);
ierr = ISRestoreIndices(is, &cells);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
DM dm, dmAdapt;
DMLabel adaptLabel;
PetscInt dim, nfaces, cStart, cEnd;
PetscBool interpolate;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
dim = 2;
nfaces = 3;
interpolate = PETSC_TRUE;
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"ex20",NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim","domain dimension",NULL,dim,&dim,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-nfaces","number of faces per dimension",NULL,nfaces,&nfaces,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD,dim,nfaces,interpolate,&dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)dm,"Pre Adaptation Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(dm,NULL,"-pre_adapt_dm_view");CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr);
ierr = DMLabelCreate("adapt",&adaptLabel);CHKERRQ(ierr);
ierr = DMLabelSetDefaultValue(adaptLabel,DM_ADAPT_COARSEN);CHKERRQ(ierr);
if (cEnd > cStart) {ierr = DMLabelSetValue(adaptLabel,cStart,DM_ADAPT_REFINE);CHKERRQ(ierr);}
ierr = DMAdaptLabel(dm,adaptLabel,&dmAdapt);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)dmAdapt,"Post Adaptation Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(dmAdapt,NULL,"-post_adapt_dm_view");CHKERRQ(ierr);
ierr = DMDestroy(&dmAdapt);CHKERRQ(ierr);
ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
static PetscErrorCode DMPlexGetVTKConnectivity(DM dm,PieceInfo *piece,PetscVTKInt **oconn,PetscVTKInt **ooffsets,PetscVTKType **otypes)
{
PetscErrorCode ierr;
PetscVTKInt *conn,*offsets;
PetscVTKType *types;
PetscInt dim,vStart,vEnd,cStart,cEnd,pStart,pEnd,cellHeight,cMax,numLabelCells,hasLabel,c,v,countcell,countconn;
PetscFunctionBegin;
ierr = PetscMalloc3(piece->nconn,PetscVTKInt,&conn,piece->ncells,PetscVTKInt,&offsets,piece->ncells,PetscVTKType,&types);CHKERRQ(ierr);
ierr = DMPlexGetDimension(dm,&dim);CHKERRQ(ierr);
ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr);
ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr);
if (cMax >= 0) cEnd = PetscMin(cEnd, cMax);
ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr);
hasLabel = numLabelCells > 0 ? PETSC_TRUE : PETSC_FALSE;
countcell = 0;
countconn = 0;
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize,nverts,celltype,startoffset,nC=0;
if (hasLabel) {
PetscInt value;
ierr = DMPlexGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
startoffset = countconn;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
conn[countconn++] = closure[v] - vStart;
++nC;
}
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexInvertCell(dim, nC, &conn[countconn-nC]);CHKERRQ(ierr);
offsets[countcell] = countconn;
nverts = countconn - startoffset;
ierr = DMPlexVTKGetCellType(dm,dim,nverts,&celltype);CHKERRQ(ierr);
types[countcell] = celltype;
countcell++;
}
if (countcell != piece->ncells) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Inconsistent cell count");
if (countconn != piece->nconn) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Inconsistent connectivity count");
*oconn = conn;
*ooffsets = offsets;
*otypes = types;
PetscFunctionReturn(0);
}
static PetscErrorCode BuildGradientReconstruction(DM dm, PetscFV fvm, DM dmFace, PetscScalar *fgeom, DM dmCell, PetscScalar *cgeom)
{
DMLabel ghostLabel;
PetscScalar *dx, *grad, **gref;
PetscInt dim, cStart, cEnd, c, cEndInterior, maxNumFaces;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
ierr = DMPlexGetMaxSizes(dm, &maxNumFaces, NULL);CHKERRQ(ierr);
ierr = PetscFVLeastSquaresSetMaxFaces(fvm, maxNumFaces);CHKERRQ(ierr);
ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
ierr = PetscMalloc3(maxNumFaces*dim, &dx, maxNumFaces*dim, &grad, maxNumFaces, &gref);CHKERRQ(ierr);
for (c = cStart; c < cEndInterior; c++) {
const PetscInt *faces;
PetscInt numFaces, usedFaces, f, d;
const CellGeom *cg;
PetscBool boundary;
PetscInt ghost;
ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr);
ierr = DMPlexGetConeSize(dm, c, &numFaces);CHKERRQ(ierr);
ierr = DMPlexGetCone(dm, c, &faces);CHKERRQ(ierr);
if (numFaces < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cell %D has only %D faces, not enough for gradient reconstruction", c, numFaces);
for (f = 0, usedFaces = 0; f < numFaces; ++f) {
const CellGeom *cg1;
FaceGeom *fg;
const PetscInt *fcells;
PetscInt ncell, side;
ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr);
ierr = DMPlexIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr);
if ((ghost >= 0) || boundary) continue;
ierr = DMPlexGetSupport(dm, faces[f], &fcells);CHKERRQ(ierr);
side = (c != fcells[0]); /* c is on left=0 or right=1 of face */
ncell = fcells[!side]; /* the neighbor */
ierr = DMPlexPointLocalRef(dmFace, faces[f], fgeom, &fg);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, ncell, cgeom, &cg1);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) dx[usedFaces*dim+d] = cg1->centroid[d] - cg->centroid[d];
gref[usedFaces++] = fg->grad[side]; /* Gradient reconstruction term will go here */
}
if (!usedFaces) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_USER, "Mesh contains isolated cell (no neighbors). Is it intentional?");
ierr = PetscFVComputeGradient(fvm, usedFaces, dx, grad);CHKERRQ(ierr);
for (f = 0, usedFaces = 0; f < numFaces; ++f) {
ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr);
ierr = DMPlexIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr);
if ((ghost >= 0) || boundary) continue;
for (d = 0; d < dim; ++d) gref[usedFaces][d] = grad[usedFaces*dim+d];
++usedFaces;
}
}
ierr = PetscFree3(dx, grad, gref);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexTSComputeIFunctionFEM - Form the local residual F from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
. locX_t - Local solution time derivative, or NULL
- user - The user context
Output Parameter:
. locF - Local output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeIFunctionFEM(DM dm, PetscReal time, Vec locX, Vec locX_t, Vec locF, void *user)
{
PetscInt cStart, cEnd, cEndInterior;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMPlexComputeResidual_Internal(dm, cStart, cEnd, time, locX, locX_t, locF, user);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexUninterpolate - Take in a mesh with all intermediate faces, edges, etc. and return a cell-vertex mesh
Collective on DM
Input Parameter:
. dm - The complete DMPlex object
Output Parameter:
. dmUnint - The DMPlex object with only cells and vertices
Level: intermediate
.keywords: mesh
.seealso: DMPlexInterpolate(), DMPlexCreateFromCellList()
@*/
PetscErrorCode DMPlexUninterpolate(DM dm, DM *dmUnint)
{
DM udm;
PetscInt dim, vStart, vEnd, cStart, cEnd, c, maxConeSize = 0, *cone;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
if (dim <= 1) {
ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr);
*dmUnint = dm;
PetscFunctionReturn(0);
}
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMCreate(PetscObjectComm((PetscObject) dm), &udm);CHKERRQ(ierr);
ierr = DMSetType(udm, DMPLEX);CHKERRQ(ierr);
ierr = DMPlexSetDimension(udm, dim);CHKERRQ(ierr);
ierr = DMPlexSetChart(udm, cStart, vEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL, closureSize, cl, coneSize = 0;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
const PetscInt p = closure[cl];
if ((p >= vStart) && (p < vEnd)) ++coneSize;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexSetConeSize(udm, c, coneSize);CHKERRQ(ierr);
maxConeSize = PetscMax(maxConeSize, coneSize);
}
ierr = DMSetUp(udm);CHKERRQ(ierr);
ierr = PetscMalloc1(maxConeSize, &cone);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL, closureSize, cl, coneSize = 0;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
const PetscInt p = closure[cl];
if ((p >= vStart) && (p < vEnd)) cone[coneSize++] = p;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexSetCone(udm, c, cone);CHKERRQ(ierr);
}
ierr = PetscFree(cone);CHKERRQ(ierr);
ierr = DMPlexSymmetrize(udm);CHKERRQ(ierr);
ierr = DMPlexStratify(udm);CHKERRQ(ierr);
*dmUnint = udm;
PetscFunctionReturn(0);
}
/*@
DMNetworkLayoutSetUp - Sets up the bare layout (graph) for the network
Collective on DM
Input Parameters
. DM - the dmnetwork object
Notes:
This routine should be called after the network sizes and edgelists have been provided. It creates
the bare layout of the network and sets up the network to begin insertion of components.
All the components should be registered before calling this routine.
Level: intermediate
.seealso: DMNetworkSetSizes, DMNetworkSetEdgeList
@*/
PetscErrorCode DMNetworkLayoutSetUp(DM dm)
{
PetscErrorCode ierr;
DM_Network *network = (DM_Network*) dm->data;
PetscInt dim = 1; /* One dimensional network */
PetscInt numCorners=2;
PetscInt spacedim=2;
double *vertexcoords=NULL;
PetscInt i;
PetscInt ndata;
PetscFunctionBegin;
if (network->nNodes) {
ierr = PetscMalloc1(numCorners*network->nNodes,&vertexcoords);CHKERRQ(ierr);
}
ierr = DMPlexCreateFromCellList(PetscObjectComm((PetscObject)dm),dim,network->nEdges,network->nNodes,numCorners,PETSC_FALSE,network->edges,spacedim,vertexcoords,&network->plex);CHKERRQ(ierr);
if (network->nNodes) {
ierr = PetscFree(vertexcoords);CHKERRQ(ierr);
}
ierr = DMPlexGetChart(network->plex,&network->pStart,&network->pEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(network->plex,0,&network->eStart,&network->eEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(network->plex,1,&network->vStart,&network->vEnd);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm),&network->DataSection);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm),&network->DofSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(network->DataSection,network->pStart,network->pEnd);CHKERRQ(ierr);
ierr = PetscSectionSetChart(network->DofSection,network->pStart,network->pEnd);CHKERRQ(ierr);
network->dataheadersize = sizeof(struct _p_DMNetworkComponentHeader)/sizeof(DMNetworkComponentGenericDataType);
ierr = PetscMalloc1(network->pEnd-network->pStart,&network->header);CHKERRQ(ierr);
for (i = network->pStart; i < network->pEnd; i++) {
network->header[i].ndata = 0;
ndata = network->header[i].ndata;
ierr = PetscSectionAddDof(network->DataSection,i,network->dataheadersize);CHKERRQ(ierr);
network->header[i].offset[ndata] = 0;
}
ierr = PetscMalloc1(network->pEnd-network->pStart,&network->cvalue);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode CheckMesh(DM dm)
{
PetscReal detJ, J[9];
PetscInt cStart, cEnd, c;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
ierr = DMPlexComputeCellGeometry(dm, c, NULL, J, NULL, &detJ);CHKERRQ(ierr);
if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %d is inverted, |J| = %g", c, detJ);
}
PetscFunctionReturn(0);
}
static PetscErrorCode ScrambleOrientation(DM dm, AppCtx *user)
{
PetscInt h, cStart, cEnd, c;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMPlexGetVTKCellHeight(dm, &h);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, h, &cStart, &cEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {
/* Could use PetscRand instead */
if (c%2) {ierr = DMPlexReverseCell(dm, c);CHKERRQ(ierr);}
}
PetscFunctionReturn(0);
}
PetscErrorCode TestVecClosure(DM dm, AppCtx *user)
{
PetscSection s;
Vec v;
PetscInt numRuns, cStart, cEnd, c, i;
PetscScalar tmpArray[64];
PetscScalar *userArray = user->reuseArray ? tmpArray : NULL;
PetscReal maxTimePerRun = user->maxVecClosureTime;
PetscStageLog stageLog;
PetscEventPerfLog eventLog;
PetscInt stage;
PetscLogEvent event;
PetscEventPerfInfo eventInfo;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogStageRegister("DMPlex Vector Closure Test", &stage);CHKERRQ(ierr);
ierr = PetscLogEventRegister("VecClosure", PETSC_OBJECT_CLASSID, &event);CHKERRQ(ierr);
ierr = PetscLogStagePush(stage);CHKERRQ(ierr);
ierr = DMPlexCreateSection(dm, user->dim, user->numFields, user->numComponents, user->numDof, 0, NULL, NULL, &s);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dm, s);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&s);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &v);CHKERRQ(ierr);
ierr = PetscLogEventBegin(event,0,0,0,0);CHKERRQ(ierr);
for (i = 0; i < user->iterations; ++i) {
for (c = cStart; c < cEnd; ++c) {
PetscScalar *closure = userArray;
PetscInt closureSize = 64;;
ierr = DMPlexVecGetClosure(dm, s, v, c, &closureSize, &closure);CHKERRQ(ierr);
if (!user->reuseArray) {ierr = DMPlexVecRestoreClosure(dm, s, v, c, &closureSize, &closure);CHKERRQ(ierr);}
}
}
ierr = PetscLogEventEnd(event,0,0,0,0);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &v);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogGetStageLog(&stageLog);
ierr = PetscStageLogGetEventPerfLog(stageLog, stage, &eventLog);
numRuns = (cEnd-cStart) * user->iterations;
eventInfo = eventLog->eventInfo[event];
if (eventInfo.count != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event calls %d should be %d", eventInfo.count, 1);
if ((PetscInt) eventInfo.flops != 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event flops %d should be %d", (PetscInt) eventInfo.flops, 0);
if (eventInfo.time > maxTimePerRun * numRuns) {
ierr = PetscPrintf(PETSC_COMM_SELF, "VecClosures: %d Average time per cone: %gs standard: %gs\n", numRuns, eventInfo.time/numRuns, maxTimePerRun);
if (user->errors) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Average time for vector closure %g > standard %g", eventInfo.time/numRuns, maxTimePerRun);
}
PetscFunctionReturn(0);
}
/*@
DMNetworkDistribute - Distributes the network and moves associated component data.
Collective
Input Parameter:
+ oldDM - the original DMNetwork object
- overlap - The overlap of partitions, 0 is the default
Output Parameter:
. distDM - the distributed DMNetwork object
Notes:
This routine should be called only when using multiple processors.
Distributes the network with <overlap>-overlapping partitioning of the edges.
Level: intermediate
.seealso: DMNetworkCreate
@*/
PetscErrorCode DMNetworkDistribute(DM oldDM, PetscInt overlap,DM *distDM)
{
PetscErrorCode ierr;
DM_Network *oldDMnetwork = (DM_Network*)oldDM->data;
PetscSF pointsf;
DM newDM;
DM_Network *newDMnetwork;
PetscFunctionBegin;
ierr = DMNetworkCreate(PetscObjectComm((PetscObject)oldDM),&newDM);CHKERRQ(ierr);
newDMnetwork = (DM_Network*)newDM->data;
newDMnetwork->dataheadersize = sizeof(struct _p_DMNetworkComponentHeader)/sizeof(DMNetworkComponentGenericDataType);
/* Distribute plex dm and dof section */
ierr = DMPlexDistribute(oldDMnetwork->plex,overlap,&pointsf,&newDMnetwork->plex);CHKERRQ(ierr);
/* Distribute dof section */
ierr = PetscSectionCreate(PetscObjectComm((PetscObject)oldDM),&newDMnetwork->DofSection);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(pointsf,oldDMnetwork->DofSection,NULL,newDMnetwork->DofSection);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject)oldDM),&newDMnetwork->DataSection);CHKERRQ(ierr);
/* Distribute data and associated section */
ierr = DMPlexDistributeData(newDMnetwork->plex,pointsf,oldDMnetwork->DataSection,MPI_INT,(void*)oldDMnetwork->componentdataarray,newDMnetwork->DataSection,(void**)&newDMnetwork->componentdataarray);CHKERRQ(ierr);
/* Destroy point SF */
ierr = PetscSFDestroy(&pointsf);CHKERRQ(ierr);
ierr = PetscSectionGetChart(newDMnetwork->DataSection,&newDMnetwork->pStart,&newDMnetwork->pEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(newDMnetwork->plex,0, &newDMnetwork->eStart,&newDMnetwork->eEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(newDMnetwork->plex,1,&newDMnetwork->vStart,&newDMnetwork->vEnd);CHKERRQ(ierr);
newDMnetwork->nEdges = newDMnetwork->eEnd - newDMnetwork->eStart;
newDMnetwork->nNodes = newDMnetwork->vEnd - newDMnetwork->vStart;
newDMnetwork->NNodes = oldDMnetwork->NNodes;
newDMnetwork->NEdges = oldDMnetwork->NEdges;
/* Set Dof section as the default section for dm */
ierr = DMSetDefaultSection(newDMnetwork->plex,newDMnetwork->DofSection);CHKERRQ(ierr);
ierr = DMGetDefaultGlobalSection(newDMnetwork->plex,&newDMnetwork->GlobalDofSection);CHKERRQ(ierr);
*distDM = newDM;
PetscFunctionReturn(0);
}
/*@
DMPlexTSComputeIJacobianFEM - Form the local Jacobian J from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
. locX_t - Local solution time derivative, or NULL
. X_tshift - The multiplicative parameter for dF/du_t
- user - The user context
Output Parameter:
. locF - Local output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeIJacobianFEM(DM dm, PetscReal time, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user)
{
PetscInt cStart, cEnd, cEndInterior;
DM plex;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMTSConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMPlexComputeJacobian_Internal(plex, cStart, cEnd, time, X_tShift, locX, locX_t, Jac, JacP, user);CHKERRQ(ierr);
ierr = DMDestroy(&plex);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMPlexPreallocateOperator_2(DM dm, PetscInt bs, PetscSection section, PetscSection sectionGlobal, PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[], Mat A, PetscBool fillMatrix)
{
PetscInt *tmpClosure,*tmpAdj,*visits;
PetscInt c,cStart,cEnd,pStart,pEnd;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr);
maxClosureSize = 2*PetscMax(PetscPowInt(mesh->maxConeSize,depth+1),PetscPowInt(mesh->maxSupportSize,depth+1));
ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr);
npoints = pEnd - pStart;
ierr = PetscMalloc3(maxClosureSize,&tmpClosure,npoints,&lvisits,npoints,&visits);CHKERRQ(ierr);
ierr = PetscMemzero(lvisits,(pEnd-pStart)*sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemzero(visits,(pEnd-pStart)*sizeof(PetscInt));CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
for (c=cStart; c<cEnd; c++) {
PetscInt *support = tmpClosure;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_FALSE, &supportSize, (PetscInt**)&support);CHKERRQ(ierr);
for (p=0; p<supportSize; p++) lvisits[support[p]]++;
}
ierr = PetscSFReduceBegin(sf,MPIU_INT,lvisits,visits,MPI_SUM);CHKERRQ(ierr);
ierr = PetscSFReduceEnd (sf,MPIU_INT,lvisits,visits,MPI_SUM);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(sf,MPIU_INT,visits,lvisits);CHKERRQ(ierr);
ierr = PetscSFBcastEnd (sf,MPIU_INT,visits,lvisits);CHKERRQ(ierr);
ierr = PetscSFGetRanks();CHKERRQ(ierr);
ierr = PetscMalloc2(maxClosureSize*maxClosureSize,&cellmat,npoints,&owner);CHKERRQ(ierr);
for (c=cStart; c<cEnd; c++) {
ierr = PetscMemzero(cellmat,maxClosureSize*maxClosureSize*sizeof(PetscInt));CHKERRQ(ierr);
/*
Depth-first walk of transitive closure.
At each leaf frame f of transitive closure that we see, add 1/visits[f] to each pair (p,q) not marked as done in cellmat.
This contribution is added to dnz if owning ranks of p and q match, to onz otherwise.
*/
}
ierr = PetscSFReduceBegin(sf,MPIU_INT,ldnz,dnz,MPI_SUM);CHKERRQ(ierr);
ierr = PetscSFReduceEnd (sf,MPIU_INT,lonz,onz,MPI_SUM);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexTSComputeRHSFunctionFVM - Form the local forcing F from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
- user - The user context
Output Parameter:
. F - Global output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeRHSFunctionFVM(DM dm, PetscReal time, Vec locX, Vec F, void *user)
{
Vec locF;
PetscInt cStart, cEnd, cEndInterior;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMGetLocalVector(dm, &locF);CHKERRQ(ierr);
ierr = VecZeroEntries(locF);CHKERRQ(ierr);
ierr = DMPlexComputeResidual_Internal(dm, cStart, cEnd, time, locX, NULL, locF, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm, locF, INSERT_VALUES, F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm, locF, INSERT_VALUES, F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locF);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMPlexVTKWritePartition_ASCII(DM dm, FILE *fp)
{
MPI_Comm comm;
PetscInt numCells = 0, cellHeight;
PetscInt numLabelCells, cMax, cStart, cEnd, c;
PetscMPIInt numProcs, rank, proc, tag;
PetscBool hasLabel;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = PetscCommGetNewTag(comm, &tag);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr);
if (cMax >= 0) cEnd = PetscMin(cEnd, cMax);
ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr);
hasLabel = numLabelCells > 0 ? PETSC_TRUE : PETSC_FALSE;
for (c = cStart; c < cEnd; ++c) {
if (hasLabel) {
PetscInt value;
ierr = DMPlexGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
++numCells;
}
if (!rank) {
for (c = 0; c < numCells; ++c) {ierr = PetscFPrintf(comm, fp, "%d\n", rank);CHKERRQ(ierr);}
for (proc = 1; proc < numProcs; ++proc) {
MPI_Status status;
ierr = MPI_Recv(&numCells, 1, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {ierr = PetscFPrintf(comm, fp, "%d\n", proc);CHKERRQ(ierr);}
}
} else {
ierr = MPI_Send(&numCells, 1, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode TestTransitiveClosure(DM dm, AppCtx *user)
{
PetscInt numRuns, cStart, cEnd, c, i;
PetscReal maxTimePerRun = user->maxClosureTime;
PetscStageLog stageLog;
PetscEventPerfLog eventLog;
PetscInt stage;
PetscLogEvent event;
PetscEventPerfInfo eventInfo;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogStageRegister("DMPlex Transitive Closure Test", &stage);CHKERRQ(ierr);
ierr = PetscLogEventRegister("TransitiveClosure", PETSC_OBJECT_CLASSID, &event);CHKERRQ(ierr);
ierr = PetscLogStagePush(stage);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = PetscLogEventBegin(event,0,0,0,0);CHKERRQ(ierr);
for (i = 0; i < user->iterations; ++i) {
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
}
ierr = PetscLogEventEnd(event,0,0,0,0);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogGetStageLog(&stageLog);
ierr = PetscStageLogGetEventPerfLog(stageLog, stage, &eventLog);
numRuns = (cEnd-cStart) * user->iterations;
eventInfo = eventLog->eventInfo[event];
if (eventInfo.count != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event calls %d should be %d", eventInfo.count, 1);
if ((PetscInt) eventInfo.flops != 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event flops %d should be %d", (PetscInt) eventInfo.flops, 0);
if (eventInfo.time > maxTimePerRun * numRuns) {
ierr = PetscPrintf(PETSC_COMM_SELF, "Closures: %d Average time per cone: %gs standard: %gs\n", numRuns, eventInfo.time/numRuns, maxTimePerRun);
if (user->errors) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Average time for closure %g > standard %g", eventInfo.time/numRuns, maxTimePerRun);
}
PetscFunctionReturn(0);
}
/*@
DMPlexTSComputeRHSFunctionFVM - Form the local forcing F from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
- user - The user context
Output Parameter:
. F - Global output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeRHSFunctionFVM(DM dm, PetscReal time, Vec locX, Vec F, void *user)
{
Vec locF;
PetscInt cStart, cEnd, cEndInterior;
DM plex;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMTSConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMGetLocalVector(plex, &locF);CHKERRQ(ierr);
ierr = VecZeroEntries(locF);CHKERRQ(ierr);
ierr = DMPlexComputeResidual_Internal(plex, cStart, cEnd, time, locX, NULL, time, locF, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(plex, locF, ADD_VALUES, F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(plex, locF, ADD_VALUES, F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(plex, &locF);CHKERRQ(ierr);
ierr = DMDestroy(&plex);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);
}
static PetscErrorCode CreatePoints_Centroid(DM dm, PetscInt *Np, PetscReal **pcoords, PetscBool *pointsAllProcs, AppCtx *ctx)
{
PetscSection coordSection;
Vec coordsLocal;
PetscInt spaceDim, p;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = DMGetCoordinateDim(dm, &spaceDim);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, NULL, Np);CHKERRQ(ierr);
ierr = PetscCalloc1(*Np * spaceDim, pcoords);CHKERRQ(ierr);
for (p = 0; p < *Np; ++p) {
PetscScalar *coords = NULL;
PetscInt size, num, n, d;
ierr = DMPlexVecGetClosure(dm, coordSection, coordsLocal, p, &size, &coords);CHKERRQ(ierr);
num = size/spaceDim;
for (n = 0; n < num; ++n) {
for (d = 0; d < spaceDim; ++d) (*pcoords)[p*spaceDim+d] += PetscRealPart(coords[n*spaceDim+d]) / num;
}
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, "[%d]Point %D (", rank, p);CHKERRQ(ierr);
for (d = 0; d < spaceDim; ++d) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, "%g", (double)(*pcoords)[p*spaceDim+d]);CHKERRQ(ierr);
if (d < spaceDim-1) {ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, ", ");CHKERRQ(ierr);}
}
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, ")\n");CHKERRQ(ierr);
ierr = DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, p, &num, &coords);CHKERRQ(ierr);
}
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD, NULL);CHKERRQ(ierr);
*pointsAllProcs = PETSC_FALSE;
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
DM dm;
PetscSection section;
PetscFE fe;
PetscInt cells[3] = {2, 2, 2},dim = 2,c,cStart,cEnd,tmp;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Spectral/tensor element restrictions",NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim","Topological dimension",NULL,dim,&dim,NULL);CHKERRQ(ierr);
tmp = dim;
ierr = PetscOptionsIntArray("-cells","Number of cells per dimension",NULL,cells,&tmp,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD,dim,PETSC_FALSE,cells,NULL,NULL,NULL,PETSC_TRUE,&dm);CHKERRQ(ierr);
ierr = PetscFECreateDefault(PETSC_COMM_SELF,dim,1,PETSC_FALSE,NULL,PETSC_DETERMINE,&fe);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
ierr = DMAddField(dm,NULL,(PetscObject)fe);CHKERRQ(ierr);
ierr = DMCreateDS(dm);CHKERRQ(ierr);
ierr = DMPlexSetClosurePermutationTensor(dm,PETSC_DETERMINE,NULL);CHKERRQ(ierr);
ierr = DMGetDefaultSection(dm,§ion);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr);
for (c=cStart; c<cEnd; c++) {
PetscInt numindices,*indices;
ierr = DMPlexGetClosureIndices(dm,section,section,c,&numindices,&indices,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"Element #%D\n",c-cStart);CHKERRQ(ierr);
ierr = PetscIntView(numindices,indices,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = DMPlexRestoreClosureIndices(dm,section,section,c,&numindices,&indices,NULL);CHKERRQ(ierr);
}
ierr = PetscFEDestroy(&fe);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}