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); }
static PetscErrorCode CreateAuxiliaryData(DM dm, DM *auxdm, Vec *la, AppCtx *user) { PetscErrorCode (**afuncs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *); PetscInt dim, Nf, f; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); ierr = PetscMalloc1(Nf, &afuncs);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) afuncs[f] = linear; ierr = DMClone(dm, auxdm);CHKERRQ(ierr); ierr = SetupDiscretization(*auxdm, dim, user->cellSimplex, user);CHKERRQ(ierr); ierr = DMCreateLocalVector(*auxdm, la);CHKERRQ(ierr); ierr = DMProjectFunctionLocal(dm, 0.0, afuncs, NULL, INSERT_VALUES, *la);CHKERRQ(ierr); ierr = VecViewFromOptions(*la, NULL, "-local_aux_view");CHKERRQ(ierr); ierr = PetscFree(afuncs);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc,char **args) { Mat Amat; PetscErrorCode ierr; SNES snes; KSP ksp; MPI_Comm comm; PetscMPIInt npe,rank; PetscLogStage stage[7]; PetscBool test_nonzero_cols=PETSC_FALSE,use_nearnullspace=PETSC_TRUE; Vec xx,bb; PetscInt iter,i,N,dim=3,cells[3]={1,1,1},max_conv_its,local_sizes[7],run_type=1; DM dm,distdm,basedm; PetscBool flg; char convType[256]; PetscReal Lx,mdisp[10],err[10]; const char * const options[10] = {"-ex56_dm_refine 0", "-ex56_dm_refine 1", "-ex56_dm_refine 2", "-ex56_dm_refine 3", "-ex56_dm_refine 4", "-ex56_dm_refine 5", "-ex56_dm_refine 6", "-ex56_dm_refine 7", "-ex56_dm_refine 8", "-ex56_dm_refine 9"}; PetscFunctionBeginUser; ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr; comm = PETSC_COMM_WORLD; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &npe);CHKERRQ(ierr); /* options */ ierr = PetscOptionsBegin(comm,NULL,"3D bilinear Q1 elasticity options","");CHKERRQ(ierr); { i = 3; ierr = PetscOptionsIntArray("-cells", "Number of (flux tube) processor in each dimension", "ex56.c", cells, &i, NULL);CHKERRQ(ierr); Lx = 1.; /* or ne for rod */ max_conv_its = 3; ierr = PetscOptionsInt("-max_conv_its","Number of iterations in convergence study","",max_conv_its,&max_conv_its,NULL);CHKERRQ(ierr); if (max_conv_its<=0 || max_conv_its>7) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_USER, "Bad number of iterations for convergence test (%D)",max_conv_its); ierr = PetscOptionsReal("-lx","Length of domain","",Lx,&Lx,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-alpha","material coefficient inside circle","",s_soft_alpha,&s_soft_alpha,NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-test_nonzero_cols","nonzero test","",test_nonzero_cols,&test_nonzero_cols,NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-use_mat_nearnullspace","MatNearNullSpace API test","",use_nearnullspace,&use_nearnullspace,NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-run_type","0: twisting load on cantalever, 1: 3rd order accurate convergence test","",run_type,&run_type,NULL);CHKERRQ(ierr); i = 3; ierr = PetscOptionsInt("-mat_block_size","","",i,&i,&flg);CHKERRQ(ierr); if (!flg || i!=3) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_USER, "'-mat_block_size 3' must be set (%D) and = 3 (%D)",flg,flg? i : 3); } ierr = PetscOptionsEnd();CHKERRQ(ierr); ierr = PetscLogStageRegister("Mesh Setup", &stage[6]);CHKERRQ(ierr); ierr = PetscLogStageRegister("1st Setup", &stage[0]);CHKERRQ(ierr); ierr = PetscLogStageRegister("1st Solve", &stage[1]);CHKERRQ(ierr); /* create DM, Plex calls DMSetup */ ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr); ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr); { DMLabel label; IS is; ierr = DMCreateLabel(dm, "boundary");CHKERRQ(ierr); ierr = DMGetLabel(dm, "boundary", &label);CHKERRQ(ierr); ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr); if (run_type==0) { ierr = DMGetStratumIS(dm, "boundary", 1, &is);CHKERRQ(ierr); ierr = DMCreateLabel(dm,"Faces");CHKERRQ(ierr); if (is) { PetscInt d, f, Nf; const PetscInt *faces; PetscInt csize; PetscSection cs; Vec coordinates ; DM cdm; ierr = ISGetLocalSize(is, &Nf);CHKERRQ(ierr); ierr = ISGetIndices(is, &faces);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); ierr = DMGetDefaultSection(cdm, &cs);CHKERRQ(ierr); /* Check for each boundary face if any component of its centroid is either 0.0 or 1.0 */ for (f = 0; f < Nf; ++f) { PetscReal faceCoord; PetscInt b,v; PetscScalar *coords = NULL; PetscInt Nv; ierr = DMPlexVecGetClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr); Nv = csize/dim; /* Calculate mean coordinate vector */ for (d = 0; d < dim; ++d) { faceCoord = 0.0; for (v = 0; v < Nv; ++v) faceCoord += PetscRealPart(coords[v*dim+d]); faceCoord /= Nv; for (b = 0; b < 2; ++b) { if (PetscAbs(faceCoord - b) < PETSC_SMALL) { /* domain have not been set yet, still [0,1]^3 */ ierr = DMSetLabelValue(dm, "Faces", faces[f], d*2+b+1);CHKERRQ(ierr); } } } ierr = DMPlexVecRestoreClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr); } ierr = ISRestoreIndices(is, &faces);CHKERRQ(ierr); } ierr = ISDestroy(&is);CHKERRQ(ierr); ierr = DMGetLabel(dm, "Faces", &label);CHKERRQ(ierr); ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr); } } { PetscInt dimEmbed, i; PetscInt nCoords; PetscScalar *coords,bounds[] = {0,Lx,-.5,.5,-.5,.5,}; /* x_min,x_max,y_min,y_max */ Vec coordinates; if (run_type==1) { for (i = 0; i < 2*dim; i++) bounds[i] = (i%2) ? 1 : 0; } ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr); ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr); if (dimEmbed != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"dimEmbed != dim %D",dimEmbed);CHKERRQ(ierr); ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr); if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size");CHKERRQ(ierr); ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr); for (i = 0; i < nCoords; i += dimEmbed) { PetscInt j; PetscScalar *coord = &coords[i]; for (j = 0; j < dimEmbed; j++) { coord[j] = bounds[2 * j] + coord[j] * (bounds[2 * j + 1] - bounds[2 * j]); } } ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr); } /* convert to p4est, and distribute */ ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr); ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format (should not be Plex!)","ex56.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr); ierr = PetscOptionsEnd(); if (flg) { DM newdm; ierr = DMConvert(dm,convType,&newdm);CHKERRQ(ierr); if (newdm) { const char *prefix; PetscBool isForest; ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject)newdm,prefix);CHKERRQ(ierr); ierr = DMIsForest(newdm,&isForest);CHKERRQ(ierr); if (isForest) { } else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Converted to non Forest?"); ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = newdm; } else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Convert failed?"); } else { /* Plex Distribute mesh over processes */ ierr = DMPlexDistribute(dm, 0, NULL, &distdm);CHKERRQ(ierr); if (distdm) { const char *prefix; ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject)distdm,prefix);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = distdm; } } ierr = PetscLogStagePop();CHKERRQ(ierr); basedm = dm; dm = NULL; for (iter=0 ; iter<max_conv_its ; iter++) { ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr); /* make new DM */ ierr = DMClone(basedm, &dm);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, "ex56_");CHKERRQ(ierr); ierr = PetscObjectSetName( (PetscObject)dm,"Mesh");CHKERRQ(ierr); ierr = PetscOptionsClearValue(NULL,"-ex56_dm_refine");CHKERRQ(ierr); ierr = PetscOptionsInsertString(NULL,options[iter]);CHKERRQ(ierr); ierr = DMSetFromOptions(dm);CHKERRQ(ierr); /* refinement done here in Plex, p4est */ /* snes */ ierr = SNESCreate(comm, &snes);CHKERRQ(ierr); ierr = SNESSetDM(snes, dm);CHKERRQ(ierr); /* fem */ { const PetscInt Ncomp = dim; const PetscInt components[] = {0,1,2}; const PetscInt Nfid = 1, Npid = 1; const PetscInt fid[] = {1}; /* The fixed faces (x=0) */ const PetscInt pid[] = {2}; /* The faces with loading (x=L_x) */ PetscFE fe; PetscDS prob; DM cdm = dm; ierr = PetscFECreateDefault(dm, dim, dim, PETSC_FALSE, NULL, PETSC_DECIDE, &fe);CHKERRQ(ierr); /* elasticity */ ierr = PetscObjectSetName((PetscObject) fe, "deformation");CHKERRQ(ierr); /* FEM prob */ ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe);CHKERRQ(ierr); /* setup problem */ if (run_type==1) { ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d);CHKERRQ(ierr); ierr = PetscDSSetResidual(prob, 0, f0_u_x4, f1_u_3d);CHKERRQ(ierr); } else { ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d_alpha);CHKERRQ(ierr); ierr = PetscDSSetResidual(prob, 0, f0_u, f1_u_3d_alpha);CHKERRQ(ierr); ierr = PetscDSSetBdResidual(prob, 0, f0_bd_u_3d, f1_bd_u);CHKERRQ(ierr); } /* bcs */ if (run_type==1) { PetscInt id = 1; ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "boundary", 0, 0, NULL, (void (*)()) zero, 1, &id, NULL);CHKERRQ(ierr); } else { ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "fixed", "Faces", 0, Ncomp, components, (void (*)()) zero, Nfid, fid, NULL);CHKERRQ(ierr); ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL, "traction", "Faces", 0, Ncomp, components, NULL, Npid, pid, NULL);CHKERRQ(ierr); } while (cdm) { ierr = DMSetDS(cdm,prob);CHKERRQ(ierr); ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr); } ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); } /* vecs & mat */ ierr = DMCreateGlobalVector(dm,&xx);CHKERRQ(ierr); ierr = VecDuplicate(xx, &bb);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) bb, "b");CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) xx, "u");CHKERRQ(ierr); ierr = DMCreateMatrix(dm, &Amat);CHKERRQ(ierr); ierr = VecGetSize(bb,&N);CHKERRQ(ierr); local_sizes[iter] = N; ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d global equations, %d vertices\n",rank,PETSC_FUNCTION_NAME,N,N/dim);CHKERRQ(ierr); if (use_nearnullspace && N/dim > 1) { /* Set up the near null space (a.k.a. rigid body modes) that will be used by the multigrid preconditioner */ DM subdm; MatNullSpace nearNullSpace; PetscInt fields = 0; PetscObject deformation; ierr = DMCreateSubDM(dm, 1, &fields, NULL, &subdm);CHKERRQ(ierr); ierr = DMPlexCreateRigidBody(subdm, &nearNullSpace);CHKERRQ(ierr); ierr = DMGetField(dm, 0, &deformation);CHKERRQ(ierr); ierr = PetscObjectCompose(deformation, "nearnullspace", (PetscObject) nearNullSpace);CHKERRQ(ierr); ierr = DMDestroy(&subdm);CHKERRQ(ierr); ierr = MatNullSpaceDestroy(&nearNullSpace);CHKERRQ(ierr); /* created by DM and destroyed by Mat */ } ierr = DMPlexSetSNESLocalFEM(dm,NULL,NULL,NULL);CHKERRQ(ierr); ierr = SNESSetJacobian(snes, Amat, Amat, NULL, NULL);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = DMSetUp(dm);CHKERRQ(ierr); ierr = PetscLogStagePop();CHKERRQ(ierr); ierr = PetscLogStagePush(stage[0]);CHKERRQ(ierr); /* ksp */ ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr); /* test BCs */ ierr = VecZeroEntries(xx);CHKERRQ(ierr); if (test_nonzero_cols) { if (rank==0) ierr = VecSetValue(xx,0,1.0,INSERT_VALUES);CHKERRQ(ierr); ierr = VecAssemblyBegin(xx);CHKERRQ(ierr); ierr = VecAssemblyEnd(xx);CHKERRQ(ierr); } ierr = VecZeroEntries(bb);CHKERRQ(ierr); ierr = VecGetSize(bb,&i);CHKERRQ(ierr); local_sizes[iter] = i; ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d equations in vector, %d vertices\n",rank,PETSC_FUNCTION_NAME,i,i/dim);CHKERRQ(ierr); /* setup solver, dummy solve to really setup */ if (0) { ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,1);CHKERRQ(ierr); ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr); ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,50);CHKERRQ(ierr); ierr = VecZeroEntries(xx);CHKERRQ(ierr); } ierr = PetscLogStagePop();CHKERRQ(ierr); /* solve */ ierr = PetscLogStagePush(stage[1]);CHKERRQ(ierr); ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr); ierr = PetscLogStagePop();CHKERRQ(ierr); ierr = VecNorm(xx,NORM_INFINITY,&mdisp[iter]);CHKERRQ(ierr); ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); { PetscViewer viewer = NULL; PetscViewerFormat fmt; ierr = PetscOptionsGetViewer(comm,"ex56_","-vec_view",&viewer,&fmt,&flg);CHKERRQ(ierr); if (flg) { ierr = PetscViewerPushFormat(viewer,fmt);CHKERRQ(ierr); ierr = VecView(xx,viewer);CHKERRQ(ierr); ierr = VecView(bb,viewer);CHKERRQ(ierr); ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); } ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } /* Free work space */ ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = VecDestroy(&xx);CHKERRQ(ierr); ierr = VecDestroy(&bb);CHKERRQ(ierr); ierr = MatDestroy(&Amat);CHKERRQ(ierr); } ierr = DMDestroy(&basedm);CHKERRQ(ierr); if (run_type==1) { err[0] = 59.975208 - mdisp[0]; /* error with what I think is the exact solution */ } else { err[0] = 171.038 - mdisp[0]; } for (iter=1 ; iter<max_conv_its ; iter++) { if (run_type==1) { err[iter] = 59.975208 - mdisp[iter]; } else { err[iter] = 171.038 - mdisp[iter]; } PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %D) N=%12D, max displ=%9.7e, disp diff=%9.2e, error=%4.3e, rate=%3.2g\n", rank,PETSC_FUNCTION_NAME,iter,local_sizes[iter],mdisp[iter], mdisp[iter]-mdisp[iter-1],err[iter],log(err[iter-1]/err[iter])/log(2.)); } ierr = PetscFinalize(); return ierr; }
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); }
int main(int argc, char **argv) { DM dm; /* Problem specification */ DM dmAux; /* Material specification */ SNES snes; /* nonlinear solver */ Vec u,r; /* solution, residual vectors */ Mat A,J; /* Jacobian matrix */ MatNullSpace nullSpace; /* May be necessary for Neumann conditions */ AppCtx user; /* user-defined work context */ JacActionCtx userJ; /* context for Jacobian MF action */ PetscInt its; /* iterations for convergence */ PetscReal error = 0.0; /* L_2 error in the solution */ PetscInt numComponents; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr); ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); ierr = SNESSetDM(snes, dm);CHKERRQ(ierr); ierr = DMSetApplicationContext(dm, &user);CHKERRQ(ierr); user.fem.fe = user.fe; ierr = PetscFECreateDefault(dm, user.dim, 1, PETSC_TRUE, NULL, -1, &user.fe[0]);CHKERRQ(ierr); if (user.bcType != NEUMANN) { user.fem.feBd = NULL; user.feBd[0] = NULL; } else { user.fem.feBd = user.feBd; ierr = PetscFECreateDefault(dm, user.dim-1, 1, PETSC_TRUE, "bd_", -1, &user.feBd[0]);CHKERRQ(ierr); } ierr = PetscFEGetNumComponents(user.fe[0], &numComponents);CHKERRQ(ierr); ierr = PetscMalloc(NUM_FIELDS * sizeof(void (*)(const PetscReal[], PetscScalar *, void *)), &user.exactFuncs);CHKERRQ(ierr); ierr = SetupProblem(dm, &user);CHKERRQ(ierr); ierr = SetupSection(dm, &user);CHKERRQ(ierr); /* Setup Material */ ierr = DMClone(dm, &dmAux);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(dm, dmAux);CHKERRQ(ierr); if (user.variableCoefficient != COEFF_FIELD) { user.fem.feAux = NULL; user.feAux[0] = NULL; } else { PetscQuadrature q; user.fem.feAux = user.feAux; ierr = PetscFECreateDefault(dmAux, user.dim, 1, PETSC_TRUE, "mat_", -1, &user.feAux[0]);CHKERRQ(ierr); ierr = PetscFEGetQuadrature(user.fe[0], &q);CHKERRQ(ierr); ierr = PetscFESetQuadrature(user.feAux[0], q);CHKERRQ(ierr); } ierr = SetupMaterialSection(dmAux, &user);CHKERRQ(ierr); ierr = SetupMaterial(dm, dmAux, &user);CHKERRQ(ierr); ierr = DMDestroy(&dmAux);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) u, "potential");CHKERRQ(ierr); ierr = VecDuplicate(u, &r);CHKERRQ(ierr); ierr = DMSetMatType(dm,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); if (user.jacobianMF) { PetscInt M, m, N, n; ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr); ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr); ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr); ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr); ierr = MatSetUp(A);CHKERRQ(ierr); #if 0 ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr); #endif userJ.dm = dm; userJ.J = J; userJ.user = &user; ierr = DMCreateLocalVector(dm, &userJ.u);CHKERRQ(ierr); ierr = DMPlexProjectFunctionLocal(dm, user.fe, user.exactFuncs, NULL, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr); ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr); } else { A = J; } if (user.bcType == NEUMANN) { ierr = MatNullSpaceCreate(PetscObjectComm((PetscObject) dm), PETSC_TRUE, 0, NULL, &nullSpace);CHKERRQ(ierr); ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr); if (A != J) { ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr); } } ierr = DMSNESSetFunctionLocal(dm, (PetscErrorCode (*)(DM,Vec,Vec,void*)) DMPlexComputeResidualFEM, &user);CHKERRQ(ierr); ierr = DMSNESSetJacobianLocal(dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,void*)) DMPlexComputeJacobianFEM, &user);CHKERRQ(ierr); ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = DMPlexProjectFunction(dm, user.fe, user.exactFuncs, NULL, INSERT_ALL_VALUES, u);CHKERRQ(ierr); if (user.checkpoint) { #if defined(PETSC_HAVE_HDF5) ierr = PetscViewerHDF5PushGroup(user.checkpoint, "/fields");CHKERRQ(ierr); ierr = VecLoad(u, user.checkpoint);CHKERRQ(ierr); ierr = PetscViewerHDF5PopGroup(user.checkpoint);CHKERRQ(ierr); #endif } ierr = PetscViewerDestroy(&user.checkpoint);CHKERRQ(ierr); if (user.showInitial) { Vec lv; ierr = DMGetLocalVector(dm, &lv);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, u, INSERT_VALUES, lv);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, u, INSERT_VALUES, lv);CHKERRQ(ierr); ierr = DMPrintLocalVec(dm, "Local function", 1.0e-10, lv);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &lv);CHKERRQ(ierr); } if (user.runType == RUN_FULL) { void (*initialGuess[numComponents])(const PetscReal x[], PetscScalar *, void *ctx); PetscInt c; for (c = 0; c < numComponents; ++c) initialGuess[c] = zero; ierr = DMPlexProjectFunction(dm, user.fe, initialGuess, NULL, INSERT_VALUES, u);CHKERRQ(ierr); if (user.debug) { ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr); ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr); ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, NULL, u, &error);CHKERRQ(ierr); if (error < 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);} if (user.showSolution) { ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr); ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } } else if (user.runType == RUN_PERF) { PetscReal res = 0.0; ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); } else { PetscReal res = 0.0; /* Check discretization error */ ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, NULL, u, &error);CHKERRQ(ierr); if (error < 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);} /* Check residual */ ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); /* Check Jacobian */ { Vec b; ierr = SNESComputeJacobian(snes, u, A, A);CHKERRQ(ierr); ierr = VecDuplicate(u, &b);CHKERRQ(ierr); ierr = VecSet(r, 0.0);CHKERRQ(ierr); ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr); ierr = MatMult(A, u, r);CHKERRQ(ierr); ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr); } } ierr = VecViewFromOptions(u, NULL, "-vec_view");CHKERRQ(ierr); if (user.bcType == NEUMANN) { ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); } if (user.jacobianMF) { ierr = VecDestroy(&userJ.u);CHKERRQ(ierr); } if (A != J) {ierr = MatDestroy(&A);CHKERRQ(ierr);} ierr = PetscFEDestroy(&user.fe[0]);CHKERRQ(ierr); ierr = PetscFEDestroy(&user.feBd[0]);CHKERRQ(ierr); ierr = PetscFEDestroy(&user.feAux[0]);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc, char **argv) { DM dm; /* Problem specification */ SNES snes; /* Nonlinear solver */ Vec u; /* Solutions */ AppCtx user; /* User-defined work context */ PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); /* Primal system */ ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); ierr = SNESSetDM(snes, dm);CHKERRQ(ierr); ierr = SetupDiscretization(dm, "potential", SetupPrimalProblem, &user);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr); ierr = VecSet(u, 0.0);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) u, "potential");CHKERRQ(ierr); ierr = DMPlexSetSNESLocalFEM(dm, &user, &user, &user);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr); ierr = SNESGetSolution(snes, &u);CHKERRQ(ierr); ierr = VecViewFromOptions(u, NULL, "-potential_view");CHKERRQ(ierr); if (user.spectral) { PetscInt planeDir[2] = {0, 1}; PetscReal planeCoord[2] = {0., 1.}; ierr = ComputeSpectral(dm, u, 2, planeDir, planeCoord, &user);CHKERRQ(ierr); } /* Adjoint system */ if (user.adjoint) { DM dmAdj; SNES snesAdj; Vec uAdj; ierr = SNESCreate(PETSC_COMM_WORLD, &snesAdj);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject) snesAdj, "adjoint_");CHKERRQ(ierr); ierr = DMClone(dm, &dmAdj);CHKERRQ(ierr); ierr = SNESSetDM(snesAdj, dmAdj);CHKERRQ(ierr); ierr = SetupDiscretization(dmAdj, "adjoint", SetupAdjointProblem, &user);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dmAdj, &uAdj);CHKERRQ(ierr); ierr = VecSet(uAdj, 0.0);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) uAdj, "adjoint");CHKERRQ(ierr); ierr = DMPlexSetSNESLocalFEM(dmAdj, &user, &user, &user);CHKERRQ(ierr); ierr = SNESSetFromOptions(snesAdj);CHKERRQ(ierr); ierr = SNESSolve(snesAdj, NULL, uAdj);CHKERRQ(ierr); ierr = SNESGetSolution(snesAdj, &uAdj);CHKERRQ(ierr); ierr = VecViewFromOptions(uAdj, NULL, "-adjoint_view");CHKERRQ(ierr); /* Error representation */ { DM dmErr, dmErrAux, dms[2]; Vec errorEst, errorL2, uErr, uErrLoc, uAdjLoc, uAdjProj; IS *subis; PetscReal errorEstTot, errorL2Norm, errorL2Tot; PetscInt N, i; PetscErrorCode (*funcs[1])(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *) = {trig_u}; void (*identity[1])(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]) = {f0_identityaux_u}; void *ctxs[1] = {0}; ctxs[0] = &user; ierr = DMClone(dm, &dmErr);CHKERRQ(ierr); ierr = SetupDiscretization(dmErr, "error", SetupErrorProblem, &user);CHKERRQ(ierr); ierr = DMGetGlobalVector(dmErr, &errorEst);CHKERRQ(ierr); ierr = DMGetGlobalVector(dmErr, &errorL2);CHKERRQ(ierr); /* Compute auxiliary data (solution and projection of adjoint solution) */ ierr = DMGetLocalVector(dmAdj, &uAdjLoc);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dmAdj, uAdj, INSERT_VALUES, uAdjLoc);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dmAdj, uAdj, INSERT_VALUES, uAdjLoc);CHKERRQ(ierr); ierr = DMGetGlobalVector(dm, &uAdjProj);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "dmAux", (PetscObject) dmAdj);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "A", (PetscObject) uAdjLoc);CHKERRQ(ierr); ierr = DMProjectField(dm, 0.0, u, identity, INSERT_VALUES, uAdjProj);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "dmAux", NULL);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "A", NULL);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dmAdj, &uAdjLoc);CHKERRQ(ierr); /* Attach auxiliary data */ dms[0] = dm; dms[1] = dm; ierr = DMCreateSuperDM(dms, 2, &subis, &dmErrAux);CHKERRQ(ierr); if (0) { PetscSection sec; ierr = DMGetSection(dms[0], &sec);CHKERRQ(ierr); ierr = PetscSectionView(sec, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = DMGetSection(dms[1], &sec);CHKERRQ(ierr); ierr = PetscSectionView(sec, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = DMGetSection(dmErrAux, &sec);CHKERRQ(ierr); ierr = PetscSectionView(sec, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = DMViewFromOptions(dmErrAux, NULL, "-dm_err_view");CHKERRQ(ierr); ierr = ISViewFromOptions(subis[0], NULL, "-super_is_view");CHKERRQ(ierr); ierr = ISViewFromOptions(subis[1], NULL, "-super_is_view");CHKERRQ(ierr); ierr = DMGetGlobalVector(dmErrAux, &uErr);CHKERRQ(ierr); ierr = VecViewFromOptions(u, NULL, "-map_vec_view");CHKERRQ(ierr); ierr = VecViewFromOptions(uAdjProj, NULL, "-map_vec_view");CHKERRQ(ierr); ierr = VecViewFromOptions(uErr, NULL, "-map_vec_view");CHKERRQ(ierr); ierr = VecISCopy(uErr, subis[0], SCATTER_FORWARD, u);CHKERRQ(ierr); ierr = VecISCopy(uErr, subis[1], SCATTER_FORWARD, uAdjProj);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dm, &uAdjProj);CHKERRQ(ierr); for (i = 0; i < 2; ++i) {ierr = ISDestroy(&subis[i]);CHKERRQ(ierr);} ierr = PetscFree(subis);CHKERRQ(ierr); ierr = DMGetLocalVector(dmErrAux, &uErrLoc);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, uErr, INSERT_VALUES, uErrLoc);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, uErr, INSERT_VALUES, uErrLoc);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dmErrAux, &uErr);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dmAdj, "dmAux", (PetscObject) dmErrAux);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dmAdj, "A", (PetscObject) uErrLoc);CHKERRQ(ierr); /* Compute cellwise error estimate */ ierr = VecSet(errorEst, 0.0);CHKERRQ(ierr); ierr = DMPlexComputeCellwiseIntegralFEM(dmAdj, uAdj, errorEst, &user);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dmAdj, "dmAux", NULL);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dmAdj, "A", NULL);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dmErrAux, &uErrLoc);CHKERRQ(ierr); ierr = DMDestroy(&dmErrAux);CHKERRQ(ierr); /* Plot cellwise error vector */ ierr = VecViewFromOptions(errorEst, NULL, "-error_view");CHKERRQ(ierr); /* Compute ratio of estimate (sum over cells) with actual L_2 error */ ierr = DMComputeL2Diff(dm, 0.0, funcs, ctxs, u, &errorL2Norm);CHKERRQ(ierr); ierr = DMPlexComputeL2DiffVec(dm, 0.0, funcs, ctxs, u, errorL2);CHKERRQ(ierr); ierr = VecViewFromOptions(errorL2, NULL, "-l2_error_view");CHKERRQ(ierr); ierr = VecNorm(errorL2, NORM_INFINITY, &errorL2Tot);CHKERRQ(ierr); ierr = VecNorm(errorEst, NORM_INFINITY, &errorEstTot);CHKERRQ(ierr); ierr = VecGetSize(errorEst, &N);CHKERRQ(ierr); ierr = VecPointwiseDivide(errorEst, errorEst, errorL2);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) errorEst, "Error ratio");CHKERRQ(ierr); ierr = VecViewFromOptions(errorEst, NULL, "-error_ratio_view");CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "N: %D L2 error: %g Error Ratio: %g/%g = %g\n", N, (double) errorL2Norm, (double) errorEstTot, (double) PetscSqrtReal(errorL2Tot), (double) errorEstTot/PetscSqrtReal(errorL2Tot));CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dmErr, &errorEst);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dmErr, &errorL2);CHKERRQ(ierr); ierr = DMDestroy(&dmErr);CHKERRQ(ierr); } ierr = DMDestroy(&dmAdj);CHKERRQ(ierr); ierr = VecDestroy(&uAdj);CHKERRQ(ierr); ierr = SNESDestroy(&snesAdj);CHKERRQ(ierr); } /* Cleanup */ ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode SetupDiscretization(DM dm, AppCtx *user) { DM cdm = dm; const PetscInt dim = user->dim; const PetscInt id = 1; PetscFE feAux = NULL; PetscFE feBd = NULL; PetscFE feCh = NULL; PetscFE fe; PetscDS prob; PetscErrorCode ierr; PetscFunctionBeginUser; /* Create finite element */ ierr = PetscFECreateDefault(dm, dim, 1, PETSC_TRUE, NULL, -1, &fe);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe, "potential");CHKERRQ(ierr); if (user->bcType == NEUMANN) { ierr = PetscFECreateDefault(dm, dim-1, 1, PETSC_TRUE, "bd_", -1, &feBd);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) feBd, "potential");CHKERRQ(ierr); } if (user->variableCoefficient == COEFF_FIELD) { PetscQuadrature q; ierr = PetscFECreateDefault(dm, dim, 1, PETSC_TRUE, "mat_", -1, &feAux);CHKERRQ(ierr); ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); ierr = PetscFESetQuadrature(feAux, q);CHKERRQ(ierr); } if (user->check) {ierr = PetscFECreateDefault(dm, dim, 1, PETSC_TRUE, "ch_", -1, &feCh);CHKERRQ(ierr);} /* Set discretization and boundary conditions for each mesh */ while (cdm) { ierr = DMGetDS(cdm, &prob);CHKERRQ(ierr); ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe);CHKERRQ(ierr); ierr = PetscDSSetBdDiscretization(prob, 0, (PetscObject) feBd);CHKERRQ(ierr); if (feAux) { DM dmAux; PetscDS probAux; ierr = DMClone(cdm, &dmAux);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(cdm, dmAux);CHKERRQ(ierr); ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); ierr = PetscDSSetDiscretization(probAux, 0, (PetscObject) feAux);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "dmAux", (PetscObject) dmAux);CHKERRQ(ierr); ierr = SetupMaterial(cdm, dmAux, user);CHKERRQ(ierr); ierr = DMDestroy(&dmAux);CHKERRQ(ierr); } if (feCh) { DM dmCh; PetscDS probCh; ierr = DMClone(cdm, &dmCh);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(cdm, dmCh);CHKERRQ(ierr); ierr = DMGetDS(dmCh, &probCh);CHKERRQ(ierr); ierr = PetscDSSetDiscretization(probCh, 0, (PetscObject) feCh);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "dmCh", (PetscObject) dmCh);CHKERRQ(ierr); ierr = DMDestroy(&dmCh);CHKERRQ(ierr); } ierr = SetupProblem(cdm, user);CHKERRQ(ierr); ierr = DMPlexAddBoundary(cdm, user->bcType == DIRICHLET, "wall", user->bcType == NEUMANN ? "boundary" : "marker", 0, user->exactFuncs[0], 1, &id, user);CHKERRQ(ierr); ierr = DMPlexGetCoarseDM(cdm, &cdm);CHKERRQ(ierr); } ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); ierr = PetscFEDestroy(&feBd);CHKERRQ(ierr); ierr = PetscFEDestroy(&feAux);CHKERRQ(ierr); ierr = PetscFEDestroy(&feCh);CHKERRQ(ierr); PetscFunctionReturn(0); }