static PetscErrorCode CreateMesh(MPI_Comm comm, DM *dm, AppCtx *ctx) { DM pdm = NULL; const PetscInt dim = ctx->dim; PetscInt cells[3] = {1, 1, 1}; /* coarse mesh is one cell; refine from there */ PetscBool hasLabel; PetscErrorCode ierr; PetscFunctionBeginUser; if (ctx->simplex) { ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, PETSC_TRUE, dm); CHKERRQ(ierr); } else { ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm); CHKERRQ(ierr); } ierr = PetscObjectSetName((PetscObject) *dm, "Mesh"); CHKERRQ(ierr); /* If no boundary marker exists, mark the whole boundary */ ierr = DMHasLabel(*dm, "marker", &hasLabel); CHKERRQ(ierr); if (!hasLabel) { ierr = CreateBCLabel(*dm, "marker"); CHKERRQ(ierr); } /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, 0, NULL, &pdm); CHKERRQ(ierr); if (pdm) { ierr = DMDestroy(dm); CHKERRQ(ierr); *dm = pdm; } ierr = DMSetFromOptions(*dm); CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view"); CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool interpolate = user->interpolate; PetscReal refinementLimit = user->refinementLimit; PetscBool cellSimplex = user->cellSimplex; const char *filename = user->filename; PetscInt triSizes_n2[2] = {4, 4}; PetscInt triPoints_n2[8] = {3, 5, 6, 7, 0, 1, 2, 4}; PetscInt triSizes_n8[8] = {1, 1, 1, 1, 1, 1, 1, 1}; PetscInt triPoints_n8[8] = {0, 1, 2, 3, 4, 5, 6, 7}; PetscInt quadSizes[2] = {2, 2}; PetscInt quadPoints[4] = {2, 3, 0, 1}; const PetscInt cells[3] = {2, 2, 2}; size_t len; PetscMPIInt rank, numProcs; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) {ierr = DMPlexCreateFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr);} else if (cellSimplex) {ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, interpolate, dm);CHKERRQ(ierr);} else {ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm);CHKERRQ(ierr);} { DM refinedMesh = NULL; DM distributedMesh = NULL; if (user->testPartition) { const PetscInt *sizes = NULL; const PetscInt *points = NULL; PetscPartitioner part; if (!rank) { if (dim == 2 && cellSimplex && numProcs == 2) { sizes = triSizes_n2; points = triPoints_n2; } else if (dim == 2 && cellSimplex && numProcs == 8) { sizes = triSizes_n8; points = triPoints_n8; } else if (dim == 2 && !cellSimplex && numProcs == 2) { sizes = quadSizes; points = quadPoints; } } ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr); ierr = PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);CHKERRQ(ierr); ierr = PetscPartitionerShellSetPartition(part, numProcs, sizes, points);CHKERRQ(ierr); } /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } /* Refine mesh using a volume constraint */ ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr); ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr); ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = refinedMesh; } } ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); if (user->overlap) { DM overlapMesh = NULL; /* Add the level-1 overlap to refined mesh */ ierr = DMPlexDistributeOverlap(*dm, 1, NULL, &overlapMesh);CHKERRQ(ierr); if (overlapMesh) { ierr = DMView(overlapMesh, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = overlapMesh; } } ierr = PetscObjectSetName((PetscObject) *dm, "Simplicial Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); user->dm = *dm; 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; }
int main(int argc, char **argv) { DM dm; PetscSection s; Vec u; AppCtx user; PetscInt cells[3] = {2, 2, 2}; PetscInt size = 0, cStart, cEnd, cell, c, f, i, j; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); ierr = DMPlexCreateHexBoxMesh(PETSC_COMM_WORLD, user.dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr); ierr = DMSetFromOptions(dm);CHKERRQ(ierr); /* Create a section for SEM order k */ { PetscInt *numDof, d; ierr = PetscMalloc1(user.Nf*(user.dim+1), &numDof);CHKERRQ(ierr); for (f = 0; f < user.Nf; ++f) { for (d = 0; d <= user.dim; ++d) numDof[f*(user.dim+1)+d] = PetscPowInt(user.k[f]-1, d)*user.Nc[f]; size += PetscPowInt(user.k[f]+1, d)*user.Nc[f]; } ierr = DMPlexCreateSection(dm, user.dim, user.Nf, user.Nc, numDof, 0, NULL, NULL, NULL, NULL, &s);CHKERRQ(ierr); ierr = SetSymmetries(dm, s, &user);CHKERRQ(ierr); ierr = PetscFree(numDof);CHKERRQ(ierr); } ierr = DMSetDefaultSection(dm, s);CHKERRQ(ierr); /* Create spectral ordering and load in data */ ierr = DMPlexCreateSpectralClosurePermutation(dm, NULL);CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &u);CHKERRQ(ierr); switch (user.dim) { case 2: ierr = LoadData2D(dm, 2, 2, size, u, &user);CHKERRQ(ierr);break; case 3: ierr = LoadData3D(dm, 2, 2, 2, size, u, &user);CHKERRQ(ierr);break; } /* Remove ordering and check some values */ ierr = PetscSectionSetClosurePermutation(s, (PetscObject) dm, NULL);CHKERRQ(ierr); switch (user.dim) { case 2: ierr = CheckPoint(dm, u, 0, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 13, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 15, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 19, &user);CHKERRQ(ierr); break; case 3: ierr = CheckPoint(dm, u, 0, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 13, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 15, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 19, &user);CHKERRQ(ierr); break; } /* Recreate spectral ordering and read out data */ ierr = DMPlexCreateSpectralClosurePermutation(dm, s);CHKERRQ(ierr); switch (user.dim) { case 2: ierr = ReadData2D(dm, u, &user);CHKERRQ(ierr);break; case 3: ierr = ReadData3D(dm, u, &user);CHKERRQ(ierr);break; } ierr = DMRestoreLocalVector(dm, &u);CHKERRQ(ierr); ierr = PetscSectionDestroy(&s);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFree(user.Nc);CHKERRQ(ierr); ierr = PetscFree(user.k);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { DM dmDist = NULL; PetscInt dim = user->dim; PetscBool cellSimplex = user->cellSimplex; const char *filename = user->filename; const PetscInt cells[3] = {2, 2, 2}; size_t len; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) {ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, dm);CHKERRQ(ierr);} else if (cellSimplex) {ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_TRUE, dm);CHKERRQ(ierr);} else {ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm);CHKERRQ(ierr);} if (user->testPartition) { PetscPartitioner part; const PetscInt *sizes = NULL; const PetscInt *points = NULL; PetscMPIInt rank, numProcs; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr); if (!rank) { if (dim == 2 && cellSimplex && numProcs == 2) { switch (user->testNum) { case 0: { PetscInt triSizes_p2[2] = {4, 4}; PetscInt triPoints_p2[8] = {3, 5, 6, 7, 0, 1, 2, 4}; sizes = triSizes_p2; points = triPoints_p2;break;} case 1: { PetscInt triSizes_p2[2] = {6, 2}; PetscInt triPoints_p2[8] = {1, 2, 3, 4, 6, 7, 0, 5}; sizes = triSizes_p2; points = triPoints_p2;break;} default: SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for triangular mesh on 2 procs", user->testNum); } } else if (dim == 2 && cellSimplex && numProcs == 3) { PetscInt triSizes_p3[3] = {3, 3, 2}; PetscInt triPoints_p3[8] = {1, 2, 4, 3, 6, 7, 0, 5}; sizes = triSizes_p3; points = triPoints_p3; } else if (dim == 2 && !cellSimplex && numProcs == 2) { PetscInt quadSizes_p2[2] = {2, 2}; PetscInt quadPoints_p2[4] = {2, 3, 0, 1}; sizes = quadSizes_p2; points = quadPoints_p2; } else SETERRQ3(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test partition dim: %D simplex: %D numProcs: %D", dim, (PetscInt) cellSimplex, (PetscInt) numProcs); } ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr); ierr = PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);CHKERRQ(ierr); ierr = PetscPartitionerShellSetPartition(part, numProcs, sizes, points);CHKERRQ(ierr); } ierr = DMPlexDistribute(*dm, 0, NULL, &dmDist);CHKERRQ(ierr); if (dmDist) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = dmDist; } ierr = PetscObjectSetName((PetscObject) *dm, cellSimplex ? "Simplicial Mesh" : "Tensor Product Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode CreateMesh(MPI_Comm comm, PetscInt testNum, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool cellSimplex = user->cellSimplex; PetscBool useGenerator = user->useGenerator; const char *filename = user->filename; size_t len; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) { ierr = DMPlexCreateFromFile(comm, filename, PETSC_FALSE, dm);CHKERRQ(ierr); ierr = DMGetDimension(*dm, &dim);CHKERRQ(ierr); } else if (useGenerator) { if (cellSimplex) { ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, PETSC_FALSE, dm);CHKERRQ(ierr); } else { const PetscInt cells[3] = {2, 2, 2}; ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, PETSC_FALSE, PETSC_FALSE, PETSC_FALSE, dm);CHKERRQ(ierr); } } else { ierr = DMCreate(comm, dm);CHKERRQ(ierr); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); switch (dim) { case 2: if (cellSimplex) { ierr = CreateSimplex_2D(comm, *dm);CHKERRQ(ierr); } else { ierr = CreateQuad_2D(comm, testNum, *dm);CHKERRQ(ierr); } break; case 3: if (cellSimplex) { ierr = CreateSimplex_3D(comm, *dm);CHKERRQ(ierr); } else { ierr = CreateHex_3D(comm, *dm);CHKERRQ(ierr); } break; default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); } } { DM interpolatedMesh = NULL; ierr = CheckMesh(*dm, user);CHKERRQ(ierr); ierr = DMPlexInterpolate(*dm, &interpolatedMesh);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(*dm, interpolatedMesh);CHKERRQ(ierr); ierr = CompareCones(*dm, interpolatedMesh);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = interpolatedMesh; } { DM distributedMesh = NULL; /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMViewFromOptions(distributedMesh, NULL, "-dm_view");CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } } ierr = PetscObjectSetName((PetscObject) *dm, "Interpolated Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); user->dm = *dm; PetscFunctionReturn(0); }
int main(int argc, char **argv) { MPI_Comm comm; DM base, preForest, postForest; PetscInt dim = 2; PetscInt preCount, postCount; Vec preVec, postVecTransfer, postVecExact; PetscErrorCode (*funcs[1]) (PetscInt,PetscReal,const PetscReal [],PetscInt,PetscScalar [], void *) = {MultiaffineFunction}; void *ctxs[1] = {NULL}; const PetscInt cells[] = {3, 3, 3}; PetscReal diff, tol = PETSC_SMALL; PetscBool linear = PETSC_FALSE; PetscBool useFV = PETSC_FALSE; PetscDS ds; bc_func_ctx bcCtx; DMLabel adaptLabel; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; comm = PETSC_COMM_WORLD; ierr = PetscOptionsBegin(comm, "", "DMForestTransferVec() Test Options", "DMFOREST");CHKERRQ(ierr); ierr = PetscOptionsInt("-dim", "The dimension (2 or 3)", "ex2.c", dim, &dim, NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-linear","Transfer a simple linear function", "ex2.c", linear, &linear, NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-use_fv","Use a finite volume approximation", "ex2.c", useFV, &useFV, NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); if (linear) { funcs[0] = LinearFunction; } bcCtx.func = funcs[0]; bcCtx.dim = dim; bcCtx.Nf = 1; bcCtx.ctx = NULL; /* the base mesh */ ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &base);CHKERRQ(ierr); if (useFV) { PetscFV fv; PetscLimiter limiter; DM baseFV; ierr = DMPlexConstructGhostCells(base,NULL,NULL,&baseFV);CHKERRQ(ierr); ierr = DMDestroy(&base);CHKERRQ(ierr); base = baseFV; ierr = PetscFVCreate(comm, &fv);CHKERRQ(ierr); ierr = PetscFVSetSpatialDimension(fv,dim);CHKERRQ(ierr); ierr = PetscFVSetType(fv,PETSCFVLEASTSQUARES);CHKERRQ(ierr); ierr = PetscFVSetNumComponents(fv,1);CHKERRQ(ierr); ierr = PetscLimiterCreate(comm,&limiter);CHKERRQ(ierr); ierr = PetscLimiterSetType(limiter,PETSCLIMITERNONE);CHKERRQ(ierr); ierr = PetscFVSetLimiter(fv,limiter);CHKERRQ(ierr); ierr = PetscLimiterDestroy(&limiter);CHKERRQ(ierr); ierr = PetscFVSetFromOptions(fv);CHKERRQ(ierr); ierr = DMSetField(base,0,(PetscObject)fv);CHKERRQ(ierr); ierr = PetscFVDestroy(&fv);CHKERRQ(ierr); } else { PetscFE fe; ierr = PetscFECreateDefault(base,dim,1,PETSC_FALSE,NULL,PETSC_DEFAULT,&fe);CHKERRQ(ierr); ierr = DMSetField(base,0,(PetscObject)fe);CHKERRQ(ierr); ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); } { PetscDS prob; PetscInt comps[] = {0}; PetscInt ids[] = {1, 2, 3, 4, 5, 6}; ierr = DMGetDS(base,&prob);CHKERRQ(ierr); ierr = PetscDSAddBoundary(prob,PETSC_TRUE, "bc", "marker", 0, 1, comps, useFV ? (void(*)()) bc_func_fv : (void(*)()) funcs[0], 2 * dim, ids, useFV ? (void *) &bcCtx : NULL);CHKERRQ(ierr); } ierr = AddIdentityLabel(base);CHKERRQ(ierr); ierr = DMViewFromOptions(base,NULL,"-dm_base_view");CHKERRQ(ierr); /* the pre adaptivity forest */ ierr = DMCreate(comm,&preForest);CHKERRQ(ierr); ierr = DMSetType(preForest,(dim == 2) ? DMP4EST : DMP8EST);CHKERRQ(ierr); ierr = DMGetDS(base,&ds);CHKERRQ(ierr); ierr = DMSetDS(preForest,ds);CHKERRQ(ierr); ierr = DMForestSetBaseDM(preForest,base);CHKERRQ(ierr); ierr = DMForestSetMinimumRefinement(preForest,1);CHKERRQ(ierr); ierr = DMForestSetInitialRefinement(preForest,1);CHKERRQ(ierr); ierr = DMSetFromOptions(preForest);CHKERRQ(ierr); ierr = DMSetUp(preForest);CHKERRQ(ierr); ierr = DMViewFromOptions(preForest,NULL,"-dm_pre_view");CHKERRQ(ierr); /* the pre adaptivity field */ ierr = DMCreateGlobalVector(preForest,&preVec);CHKERRQ(ierr); ierr = DMProjectFunction(preForest,0.,funcs,ctxs,INSERT_VALUES,preVec);CHKERRQ(ierr); ierr = VecViewFromOptions(preVec,NULL,"-vec_pre_view");CHKERRQ(ierr); ierr = PetscObjectGetReference((PetscObject)preForest,&preCount);CHKERRQ(ierr); /* adapt */ ierr = CreateAdaptivityLabel(preForest,&adaptLabel);CHKERRQ(ierr); ierr = DMForestTemplate(preForest,comm,&postForest);CHKERRQ(ierr); ierr = DMForestSetMinimumRefinement(postForest,0);CHKERRQ(ierr); ierr = DMForestSetInitialRefinement(postForest,0);CHKERRQ(ierr); ierr = DMForestSetAdaptivityLabel(postForest,adaptLabel);CHKERRQ(ierr); ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr); ierr = DMSetUp(postForest);CHKERRQ(ierr); ierr = DMViewFromOptions(postForest,NULL,"-dm_post_view");CHKERRQ(ierr); /* transfer */ ierr = DMCreateGlobalVector(postForest,&postVecTransfer);CHKERRQ(ierr); ierr = DMForestTransferVec(preForest,preVec,postForest,postVecTransfer,PETSC_TRUE,0.0);CHKERRQ(ierr); ierr = VecViewFromOptions(postVecTransfer,NULL,"-vec_post_transfer_view");CHKERRQ(ierr); /* the exact post adaptivity field */ ierr = DMCreateGlobalVector(postForest,&postVecExact);CHKERRQ(ierr); ierr = DMProjectFunction(postForest,0.,funcs,ctxs,INSERT_VALUES,postVecExact);CHKERRQ(ierr); ierr = VecViewFromOptions(postVecExact,NULL,"-vec_post_exact_view");CHKERRQ(ierr); /* compare */ ierr = VecAXPY(postVecTransfer,-1.,postVecExact);CHKERRQ(ierr); ierr = VecViewFromOptions(postVecTransfer,NULL,"-vec_diff_view");CHKERRQ(ierr); ierr = VecNorm(postVecTransfer,NORM_2,&diff);CHKERRQ(ierr); /* output */ if (diff < tol) { ierr = PetscPrintf(comm,"DMForestTransferVec() passes.\n");CHKERRQ(ierr); } else { ierr = PetscPrintf(comm,"DMForestTransferVec() fails with error %g and tolerance %g\n",diff,tol);CHKERRQ(ierr); } /* disconnect preForest from postForest */ ierr = DMForestSetAdaptivityForest(postForest,NULL);CHKERRQ(ierr); ierr = PetscObjectGetReference((PetscObject)preForest,&postCount);CHKERRQ(ierr); if (postCount != preCount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Adaptation not memory neutral: reference count increase from %d to %d\n",preCount,postCount); /* cleanup */ ierr = VecDestroy(&postVecExact);CHKERRQ(ierr); ierr = VecDestroy(&postVecTransfer);CHKERRQ(ierr); ierr = DMDestroy(&postForest);CHKERRQ(ierr); ierr = VecDestroy(&preVec);CHKERRQ(ierr); ierr = DMDestroy(&preForest);CHKERRQ(ierr); ierr = DMDestroy(&base);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode CreateMesh(MPI_Comm comm, PetscInt testNum, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool cellSimplex = user->cellSimplex; PetscBool useGenerator = user->useGenerator; const char *filename = user->filename; const char *partitioner = "chaco"; size_t len; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) { #if defined(PETSC_HAVE_EXODUSII) int CPU_word_size = 0, IO_word_size = 0, exoid = -1; float version; if (!rank) { exoid = ex_open(filename, EX_READ, &CPU_word_size, &IO_word_size, &version); if (exoid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "ex_open(\"%s\",...) did not return a valid file ID", filename); } ierr = DMPlexCreateExodus(comm, exoid, PETSC_FALSE, dm);CHKERRQ(ierr); if (!rank) {ierr = ex_close(exoid);CHKERRQ(ierr);} ierr = DMPlexGetDimension(*dm, &dim);CHKERRQ(ierr); #else SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires ExodusII support. Reconfigure using --download-exodusii"); #endif } else if (useGenerator) { if (cellSimplex) { ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_FALSE, dm);CHKERRQ(ierr); } else { ierr = DMPlexCreateHexBoxMesh(comm, dim, PETSC_FALSE, dm);CHKERRQ(ierr); } } else { ierr = DMCreate(comm, dm);CHKERRQ(ierr); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr); switch (dim) { case 2: if (cellSimplex) { ierr = CreateSimplex_2D(comm, *dm);CHKERRQ(ierr); } else { ierr = CreateQuad_2D(comm, testNum, *dm);CHKERRQ(ierr); } break; case 3: if (cellSimplex) { ierr = CreateSimplex_3D(comm, *dm);CHKERRQ(ierr); } else { ierr = CreateHex_3D(comm, *dm);CHKERRQ(ierr); } break; default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); } } { DM interpolatedMesh = NULL; ierr = CheckMesh(*dm);CHKERRQ(ierr); ierr = DMPlexInterpolate(*dm, &interpolatedMesh);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(*dm, interpolatedMesh);CHKERRQ(ierr); ierr = CompareCones(*dm, interpolatedMesh);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = interpolatedMesh; } { DM distributedMesh = NULL; /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, partitioner, 0, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } } ierr = PetscObjectSetName((PetscObject) *dm, "Interpolated Mesh");CHKERRQ(ierr); ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); user->dm = *dm; PetscFunctionReturn(0); }
PETSC_EXTERN void PETSC_STDCALL dmplexcreatehexboxmesh_(MPI_Fint * comm,PetscInt *dim, PetscInt cells[],DMBoundaryType *periodicX,DMBoundaryType *periodicY,DMBoundaryType *periodicZ,DM *dm, int *__ierr ){ *__ierr = DMPlexCreateHexBoxMesh( MPI_Comm_f2c( *(comm) ),*dim,cells,*periodicX,*periodicY,*periodicZ,dm); }
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool interpolate = user->interpolate; PetscBool refinementUniform = user->refinementUniform; PetscReal refinementLimit = user->refinementLimit; PetscBool cellSimplex = user->cellSimplex; const char *filename = user->filename; const char *partitioner = "chaco"; size_t len; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) { #if defined(PETSC_HAVE_CGNS) int cgid = -1; if (!rank) { ierr = cg_open(filename, CG_MODE_READ, &cgid);CHKERRQ(ierr); if (cgid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "cg_open(\"%s\",...) did not return a valid file ID", filename); } ierr = DMPlexCreateCGNS(comm, cgid, interpolate, dm);CHKERRQ(ierr); if (!rank) {ierr = cg_close(cgid);CHKERRQ(ierr);} #else SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires CGNS support. Reconfigure using --with-cgns-dir"); #endif } else if (cellSimplex) { ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr); } else { const PetscInt cells[3] = {2, 2, 2}; ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, dm);CHKERRQ(ierr); } { DM refinedMesh = NULL; DM distributedMesh = NULL; /* Refine mesh using a volume constraint */ ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr); ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr); ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = refinedMesh; } /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, partitioner, 0, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } if (refinementUniform) { ierr = DMPlexSetRefinementUniform(*dm, refinementUniform);CHKERRQ(ierr); ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = refinedMesh; } } } ierr = PetscObjectSetName((PetscObject) *dm, "Simplical Mesh");CHKERRQ(ierr); ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); user->dm = *dm; PetscFunctionReturn(0); }