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);
}
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 CheckFVMGeometry(DM dm, PetscInt cell, PetscInt spaceDim, PetscReal centroidEx[], PetscReal normalEx[], PetscReal volEx)
{
PetscReal centroid[3], normal[3], vol;
PetscInt d;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexComputeCellGeometryFVM(dm, cell, &vol, centroid, normal);CHKERRQ(ierr);
for (d = 0; d < spaceDim; ++d) {
if (fabs(centroid[d] - centroidEx[d]) > 1.0e-9) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid centroid[%d]: %g != %g", d, centroid[d], centroidEx[d]);
if (fabs(normal[d] - normalEx[d]) > 1.0e-9) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid normal[%d]: %g != %g", d, normal[d], normalEx[d]);
}
if (fabs(volEx - vol) > 1.0e-9) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid volume = %g != %g", vol, volEx);
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);
}
/**
Caculate the flux using the Monotonic Upstream-Centered Scheme for Conservation Laws (van Leer, 1979)
*/
PetscErrorCode CaculateLocalFunction_LS(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;
PetscScalar *f;
PetscInt fStart, fEnd, face, cStart, cell;
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 = 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);
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);
// Limit interior gradients. Using cell-based loop because it generalizes better to vector limiters.
for (cell=cStart; cell<user->cEndInterior; cell++) {
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);
if (!cgrad) continue; // ghost cell, we don't compute
// 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->Limit)(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;
const PetscInt *cells;
PetscInt ghost,i,j;
PetscScalar *fluxcon, *fluxdiff, *fx[2],*cf[2];
const FaceGeom *fg;
const CellGeom *cg[2];
const PetscScalar *cx[2],*cgrad[2], *cgradlimiter[2];
PetscScalar *uL, *uR;
PetscReal FaceArea;
ierr = VecGetArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = VecGetArrayRead(locGradLimiter,&gradlimiter);CHKERRQ(ierr);
ierr = VecGetArray(F,&f);CHKERRQ(ierr);
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &fluxcon);CHKERRQ(ierr); // For the convection terms
ierr = PetscMalloc(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);// Please do not put the Malloc function into a for loop!!!!
for (face=fStart; face<fEnd; face++) {
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);
ierr = DMPlexPointGlobalRef(dm,cells[i],f,&cf[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(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++) {
if (cf[0]) cf[0][i] -= FaceArea*(fluxcon[i] + fluxdiff[i])/cg[0]->volume;
if (cf[1]) cf[1][i] += FaceArea*(fluxcon[i] + fluxdiff[i])/cg[1]->volume;
// The flux on the interface, for the cell[0], it is an outcome flux and for the cell[1], it is
// an income flux.
}
// ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locGradLimiter,&gradlimiter);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&f);CHKERRQ(ierr);
ierr = PetscFree(fluxcon);CHKERRQ(ierr);
ierr = PetscFree(fluxdiff);CHKERRQ(ierr);
ierr = PetscFree(uL);CHKERRQ(ierr);
ierr = PetscFree(uR);CHKERRQ(ierr);
// VecView(F,PETSC_VIEWER_STDOUT_WORLD);
}
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);
}
/*
Use the first order upwind scheme to compute the flux
*/
PetscErrorCode CaculateLocalFunction_Upwind(DM dm,DM dmFace,DM dmCell,PetscReal time,Vec locX,Vec F,User user)
{
Physics phys = user->model->physics;
DM dmGrad = user->dmGrad;
PetscErrorCode ierr;
const PetscScalar *facegeom, *cellgeom, *x;
PetscScalar *f;
PetscInt fStart, fEnd, face;
Vec locGrad, Grad;
PetscFunctionBeginUser;
ierr = VecGetArrayRead(user->facegeom, &facegeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->cellgeom, &cellgeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr);
ierr = VecGetArray(F, &f);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);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);
const PetscScalar *grad;
ierr = VecGetArrayRead(locGrad, &grad);CHKERRQ(ierr);
{
const PetscInt *cells;
PetscInt i,ghost;
PetscScalar *fluxcon, *fluxdiff, *fL,*fR;
const FaceGeom *fg;
const CellGeom *cgL,*cgR;
const PetscScalar *xL,*xR;
const PetscScalar *cgrad[2];
PetscReal FaceArea;
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &fluxcon);CHKERRQ(ierr); /*For the convection terms*/
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &fluxdiff);CHKERRQ(ierr); /*For the diffusion terms*/
for (face = fStart; face < fEnd; ++face) {
ierr = DMPlexGetLabelValue(dm, "ghost", face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);/*The support of a face is the cells (two cells)*/
ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr);/*Read the data from "facegeom" for the point "face"*/
ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr);
/*
PetscPrintf(PETSC_COMM_SELF, "face[%d]:(%f, %f, %f), cgL:(%f, %f, %f), cgR:(%f, %f, %f), fnorm:(%f, %f, %f)\n",
face, fg->centroid[0], fg->centroid[1], fg->centroid[2],
cgL->centroid[0], cgL->centroid[1], cgL->centroid[2], cgR->centroid[0], cgR->centroid[1], cgR->centroid[2],
fg->normal[0], fg->normal[1], fg->normal[2]);
*/
ierr = DMPlexPointLocalRead(dm, cells[0], x, &xL);CHKERRQ(ierr); /*For the unkown variables*/
ierr = DMPlexPointLocalRead(dm, cells[1], x, &xR);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dm, cells[0], f, &fL);CHKERRQ(ierr); /*For the functions*/
ierr = DMPlexPointGlobalRef(dm, cells[1], f, &fR);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad, cells[0], grad, &cgrad[0]);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad, cells[1], grad, &cgrad[1]);CHKERRQ(ierr);
ierr = RiemannSolver_Rusanov(user, cgrad[0], cgrad[1], fg->centroid, cgL->centroid, cgR->centroid, fg->normal, xL, xR, fluxcon, fluxdiff);CHKERRQ(ierr);
/*Caculate the flux*/
ierr = DMPlexComputeCellGeometryFVM(dm, face, &FaceArea, NULL, NULL);CHKERRQ(ierr);
//PetscPrintf(PETSC_COMM_SELF, "FaceArea=%f, Volume=%f\n",FaceArea,cgL->volume);
/*Compute the face area*/
// FaceArea = 0.0;
for (i=0; i<phys->dof; i++) {
/*
PetscPrintf(PETSC_COMM_SELF, "face[%d]:(%f, %f, %f), GradL[%d] = (%f, %f, %f), GradR[%d] = (%f, %f, %f), fluxcon[%d] = %f\n",
face, fg->centroid[0], fg->centroid[1], fg->centroid[2],
i, cgrad[0][DIM*i], cgrad[0][DIM*i + 1], cgrad[0][DIM*i + 2],
i, cgrad[1][DIM*i], cgrad[1][DIM*i + 1], cgrad[1][DIM*i + 2], i, fluxcon[i]);
*/
if (fL) {
fL[i] -= FaceArea*(fluxcon[i] + fluxdiff[i])/cgL->volume;
// if (fL) PetscPrintf(PETSC_COMM_SELF, "x=%g, y=%g, z=%g,fluxcon[i]=%g, FaceArea=%g, volume=%g, fLc=%g, fL=%g\n",fg->centroid[0], fg->centroid[1], fg->centroid[2],fluxcon[i],FaceArea,cgL->volume,FaceArea*(fluxcon[i] + fluxdiff[i])/cgL->volume,fL[i]);
}
if (fR) fR[i] += FaceArea*(fluxcon[i] + fluxdiff[i])/cgR->volume;
}
}
ierr = PetscFree(fluxcon);CHKERRQ(ierr);
ierr = PetscFree(fluxdiff);CHKERRQ(ierr);
}
// VecView(F,PETSC_VIEWER_STDOUT_WORLD);
ierr = VecRestoreArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locX,&x);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&f);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode DMPlexTSSetupGeometry(DM dm, PetscFV fvm, DMTS_Plex *dmplexts)
{
DM dmFace, dmCell;
DMLabel ghostLabel;
PetscSection sectionFace, sectionCell;
PetscSection coordSection;
Vec coordinates;
PetscReal minradius;
PetscScalar *fgeom, *cgeom;
PetscInt dim, cStart, cEnd, cEndInterior, c, fStart, fEnd, f;
PetscErrorCode ierr;
PetscFunctionBegin;
if (dmplexts->setupGeom) PetscFunctionReturn(0);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
/* Make cell centroids and volumes */
ierr = DMClone(dm, &dmCell);CHKERRQ(ierr);
ierr = DMSetCoordinateSection(dmCell, coordSection);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionCell);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, sizeof(CellGeom)/sizeof(PetscScalar));CHKERRQ(ierr);}
ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr);
ierr = DMCreateLocalVector(dmCell, &dmplexts->cellgeom);CHKERRQ(ierr);
ierr = VecGetArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
for (c = cStart; c < cEndInterior; ++c) {
CellGeom *cg;
ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr);
ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dmCell, c, &cg->volume, cg->centroid, NULL);CHKERRQ(ierr);
}
/* Compute face normals and minimum cell radius */
ierr = DMClone(dm, &dmFace);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionFace);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
ierr = PetscSectionSetChart(sectionFace, fStart, fEnd);CHKERRQ(ierr);
for (f = fStart; f < fEnd; ++f) {ierr = PetscSectionSetDof(sectionFace, f, sizeof(FaceGeom)/sizeof(PetscScalar));CHKERRQ(ierr);}
ierr = PetscSectionSetUp(sectionFace);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dmFace, sectionFace);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionFace);CHKERRQ(ierr);
ierr = DMCreateLocalVector(dmFace, &dmplexts->facegeom);CHKERRQ(ierr);
ierr = VecGetArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
minradius = PETSC_MAX_REAL;
for (f = fStart; f < fEnd; ++f) {
FaceGeom *fg;
PetscReal area;
PetscInt ghost, d;
ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexPointLocalRef(dmFace, f, fgeom, &fg);CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dm, f, &area, fg->centroid, fg->normal);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) fg->normal[d] *= area;
/* Flip face orientation if necessary to match ordering in support, and Update minimum radius */
{
CellGeom *cL, *cR;
const PetscInt *cells;
PetscReal *lcentroid, *rcentroid;
PetscReal v[3];
ierr = DMPlexGetSupport(dm, f, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cL);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[1], cgeom, &cR);CHKERRQ(ierr);
lcentroid = cells[0] >= cEndInterior ? fg->centroid : cL->centroid;
rcentroid = cells[1] >= cEndInterior ? fg->centroid : cR->centroid;
WaxpyD(dim, -1, lcentroid, rcentroid, v);
if (DotRealD(dim, fg->normal, v) < 0) {
for (d = 0; d < dim; ++d) fg->normal[d] = -fg->normal[d];
}
if (DotRealD(dim, fg->normal, v) <= 0) {
if (dim == 2) SETERRQ5(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed, normal (%g,%g) v (%g,%g)", f, (double) fg->normal[0], (double) fg->normal[1], (double) v[0], (double) v[1]);
if (dim == 3) SETERRQ7(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed, normal (%g,%g,%g) v (%g,%g,%g)", f, (double) fg->normal[0], (double) fg->normal[1], (double) fg->normal[2], (double) v[0], (double) v[1], (double) v[2]);
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed", f);
}
if (cells[0] < cEndInterior) {
WaxpyD(dim, -1, fg->centroid, cL->centroid, v);
minradius = PetscMin(minradius, NormD(dim, v));
}
if (cells[1] < cEndInterior) {
WaxpyD(dim, -1, fg->centroid, cR->centroid, v);
minradius = PetscMin(minradius, NormD(dim, v));
}
}
}
ierr = MPI_Allreduce(&minradius, &dmplexts->minradius, 1, MPIU_REAL, MPI_MIN, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr);
/* Compute centroids of ghost cells */
for (c = cEndInterior; c < cEnd; ++c) {
FaceGeom *fg;
const PetscInt *cone, *support;
PetscInt coneSize, supportSize, s;
ierr = DMPlexGetConeSize(dmCell, c, &coneSize);CHKERRQ(ierr);
if (coneSize != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Ghost cell %d has cone size %d != 1", c, coneSize);
ierr = DMPlexGetCone(dmCell, c, &cone);CHKERRQ(ierr);
ierr = DMPlexGetSupportSize(dmCell, cone[0], &supportSize);CHKERRQ(ierr);
if (supportSize != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %d has support size %d != 1", cone[0], supportSize);
ierr = DMPlexGetSupport(dmCell, cone[0], &support);CHKERRQ(ierr);
ierr = DMPlexPointLocalRef(dmFace, cone[0], fgeom, &fg);CHKERRQ(ierr);
for (s = 0; s < 2; ++s) {
/* Reflect ghost centroid across plane of face */
if (support[s] == c) {
const CellGeom *ci;
CellGeom *cg;
PetscReal c2f[3], a;
ierr = DMPlexPointLocalRead(dmCell, support[(s+1)%2], cgeom, &ci);CHKERRQ(ierr);
WaxpyD(dim, -1, ci->centroid, fg->centroid, c2f); /* cell to face centroid */
a = DotRealD(dim, c2f, fg->normal)/DotRealD(dim, fg->normal, fg->normal);
ierr = DMPlexPointLocalRef(dmCell, support[s], cgeom, &cg);CHKERRQ(ierr);
WaxpyD(dim, 2*a, fg->normal, ci->centroid, cg->centroid);
cg->volume = ci->volume;
}
}
}
ierr = VecRestoreArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
ierr = VecRestoreArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
ierr = DMDestroy(&dmCell);CHKERRQ(ierr);
ierr = DMDestroy(&dmFace);CHKERRQ(ierr);
dmplexts->setupGeom = PETSC_TRUE;
PetscFunctionReturn(0);
}
PetscErrorCode DMCoarsen_Plex(DM dm, MPI_Comm comm, DM *dmCoarsened)
{
DM_Plex *mesh = (DM_Plex*) dm->data;
#ifdef PETSC_HAVE_PRAGMATIC
DM udm, coordDM;
DMLabel bd;
Mat A;
Vec coordinates, mb, mx;
PetscSection coordSection;
const PetscScalar *coords;
double *coarseCoords;
IS bdIS;
PetscReal *x, *y, *z, *eqns, *metric;
PetscReal coarseRatio = PetscSqr(0.5);
const PetscInt *faces;
PetscInt *cells, *bdFaces, *bdFaceIds;
PetscInt dim, numCorners, cStart, cEnd, numCells, numCoarseCells, c, vStart, vEnd, numVertices, numCoarseVertices, v, numBdFaces, f, maxConeSize, size, bdSize, coff;
#endif
PetscErrorCode ierr;
PetscFunctionBegin;
#ifdef PETSC_HAVE_PRAGMATIC
if (!mesh->coarseMesh) {
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &coordDM);CHKERRQ(ierr);
ierr = DMGetDefaultSection(coordDM, &coordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr);
ierr = DMPlexGetMaxSizes(udm, &maxConeSize, NULL);CHKERRQ(ierr);
numCells = cEnd - cStart;
numVertices = vEnd - vStart;
ierr = PetscCalloc5(numVertices, &x, numVertices, &y, numVertices, &z, numVertices*PetscSqr(dim), &metric, numCells*maxConeSize, &cells);CHKERRQ(ierr);
ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr);
for (v = vStart; v < vEnd; ++v) {
PetscInt off;
ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
x[v-vStart] = coords[off+0];
y[v-vStart] = coords[off+1];
if (dim > 2) z[v-vStart] = coords[off+2];
}
ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr);
for (c = 0, coff = 0; c < numCells; ++c) {
const PetscInt *cone;
PetscInt coneSize, cl;
ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr);
ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr);
for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart;
}
switch (dim) {
case 2:
pragmatic_2d_init(&numVertices, &numCells, cells, x, y);
break;
case 3:
pragmatic_3d_init(&numVertices, &numCells, cells, x, y, z);
break;
default:
SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic coarsening defined for dimension %d", dim);
}
/* Create boundary mesh */
ierr = DMLabelCreate("boundary", &bd);CHKERRQ(ierr);
ierr = DMPlexMarkBoundaryFaces(dm, bd);CHKERRQ(ierr);
ierr = DMLabelGetStratumIS(bd, 1, &bdIS);CHKERRQ(ierr);
ierr = DMLabelGetStratumSize(bd, 1, &numBdFaces);CHKERRQ(ierr);
ierr = ISGetIndices(bdIS, &faces);CHKERRQ(ierr);
for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
PetscInt *closure = NULL;
PetscInt closureSize, cl;
ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize;
}
ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
ierr = PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds);CHKERRQ(ierr);
for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
PetscInt *closure = NULL;
PetscInt closureSize, cl;
ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart;
}
/* TODO Fix */
bdFaceIds[f] = 1;
ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
ierr = ISDestroy(&bdIS);CHKERRQ(ierr);
ierr = DMLabelDestroy(&bd);CHKERRQ(ierr);
pragmatic_set_boundary(&numBdFaces, bdFaces, bdFaceIds);
/* Create metric */
size = (dim*(dim+1))/2;
ierr = PetscMalloc1(PetscSqr(size), &eqns);CHKERRQ(ierr);
ierr = MatCreateSeqDense(PETSC_COMM_SELF, size, size, eqns, &A);CHKERRQ(ierr);
ierr = MatCreateVecs(A, &mx, &mb);CHKERRQ(ierr);
ierr = VecSet(mb, 1.0);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {
const PetscScalar *sol;
PetscScalar *cellCoords = NULL;
PetscReal e[3], vol;
const PetscInt *cone;
PetscInt coneSize, cl, i, j, d, r;
ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);CHKERRQ(ierr);
/* Only works for simplices */
for (i = 0, r = 0; i < dim+1; ++i) {
for (j = 0; j < i; ++j, ++r) {
for (d = 0; d < dim; ++d) e[d] = cellCoords[i*dim+d] - cellCoords[j*dim+d];
/* FORTRAN ORDERING */
if (dim == 2) {
eqns[0*size+r] = PetscSqr(e[0]);
eqns[1*size+r] = 2.0*e[0]*e[1];
eqns[2*size+r] = PetscSqr(e[1]);
} else {
eqns[0*size+r] = PetscSqr(e[0]);
eqns[1*size+r] = 2.0*e[0]*e[1];
eqns[2*size+r] = 2.0*e[0]*e[2];
eqns[3*size+r] = PetscSqr(e[1]);
eqns[4*size+r] = 2.0*e[1]*e[2];
eqns[5*size+r] = PetscSqr(e[2]);
}
}
}
ierr = MatSetUnfactored(A);CHKERRQ(ierr);
ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);CHKERRQ(ierr);
ierr = MatLUFactor(A, NULL, NULL, NULL);CHKERRQ(ierr);
ierr = MatSolve(A, mb, mx);CHKERRQ(ierr);
ierr = VecGetArrayRead(mx, &sol);CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL);CHKERRQ(ierr);
ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr);
ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr);
for (cl = 0; cl < coneSize; ++cl) {
const PetscInt v = cone[cl] - vStart;
if (dim == 2) {
metric[v*4+0] += vol*coarseRatio*sol[0];
metric[v*4+1] += vol*coarseRatio*sol[1];
metric[v*4+2] += vol*coarseRatio*sol[1];
metric[v*4+3] += vol*coarseRatio*sol[2];
} else {
metric[v*9+0] += vol*coarseRatio*sol[0];
metric[v*9+1] += vol*coarseRatio*sol[1];
metric[v*9+3] += vol*coarseRatio*sol[1];
metric[v*9+2] += vol*coarseRatio*sol[2];
metric[v*9+6] += vol*coarseRatio*sol[2];
metric[v*9+4] += vol*coarseRatio*sol[3];
metric[v*9+5] += vol*coarseRatio*sol[4];
metric[v*9+7] += vol*coarseRatio*sol[4];
metric[v*9+8] += vol*coarseRatio*sol[5];
}
}
ierr = VecRestoreArrayRead(mx, &sol);CHKERRQ(ierr);
}
for (v = 0; v < numVertices; ++v) {
const PetscInt *support;
PetscInt supportSize, s;
PetscReal vol, totVol = 0.0;
ierr = DMPlexGetSupport(udm, v+vStart, &support);CHKERRQ(ierr);
ierr = DMPlexGetSupportSize(udm, v+vStart, &supportSize);CHKERRQ(ierr);
for (s = 0; s < supportSize; ++s) {ierr = DMPlexComputeCellGeometryFVM(dm, support[s], &vol, NULL, NULL);CHKERRQ(ierr); totVol += vol;}
for (s = 0; s < PetscSqr(dim); ++s) metric[v*PetscSqr(dim)+s] /= totVol;
}
ierr = VecDestroy(&mx);CHKERRQ(ierr);
ierr = VecDestroy(&mb);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = DMDestroy(&udm);CHKERRQ(ierr);
ierr = PetscFree(eqns);CHKERRQ(ierr);
pragmatic_set_metric(metric);
pragmatic_adapt();
/* Read out mesh */
pragmatic_get_info(&numCoarseVertices, &numCoarseCells);
ierr = PetscMalloc1(numCoarseVertices*dim, &coarseCoords);CHKERRQ(ierr);
switch (dim) {
case 2:
pragmatic_get_coords_2d(x, y);
numCorners = 3;
for (v = 0; v < numCoarseVertices; ++v) {coarseCoords[v*2+0] = x[v]; coarseCoords[v*2+1] = y[v];}
break;
case 3:
pragmatic_get_coords_3d(x, y, z);
numCorners = 4;
for (v = 0; v < numCoarseVertices; ++v) {coarseCoords[v*3+0] = x[v]; coarseCoords[v*3+1] = y[v]; coarseCoords[v*3+2] = z[v];}
break;
default:
SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic coarsening defined for dimension %d", dim);
}
pragmatic_get_elements(cells);
/* TODO Read out markers for boundary */
ierr = DMPlexCreateFromCellList(PetscObjectComm((PetscObject) dm), dim, numCoarseCells, numCoarseVertices, numCorners, PETSC_TRUE, cells, dim, coarseCoords, &mesh->coarseMesh);CHKERRQ(ierr);
pragmatic_finalize();
ierr = PetscFree5(x, y, z, metric, cells);CHKERRQ(ierr);
ierr = PetscFree2(bdFaces, bdFaceIds);CHKERRQ(ierr);
ierr = PetscFree(coarseCoords);CHKERRQ(ierr);
}
#endif
ierr = PetscObjectReference((PetscObject) mesh->coarseMesh);CHKERRQ(ierr);
*dmCoarsened = mesh->coarseMesh;
PetscFunctionReturn(0);
}
