PetscErrorCode SetupDiscretization(DM dm, AppCtx *user) { DM cdm = dm; const PetscInt dim = 2; PetscFE fe[3]; PetscQuadrature q; PetscInt f; MPI_Comm comm; PetscErrorCode ierr; PetscFunctionBeginUser; /* Create finite element */ ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); ierr = PetscFECreateDefault(comm, dim, 1, PETSC_TRUE, "potential_", -1, &fe[0]);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe[0], "potential");CHKERRQ(ierr); ierr = PetscFEGetQuadrature(fe[0], &q);CHKERRQ(ierr); ierr = PetscFECreateDefault(comm, dim, 1, PETSC_TRUE, "charge_", -1, &fe[1]);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe[1], "charge");CHKERRQ(ierr); ierr = PetscFESetQuadrature(fe[1], q);CHKERRQ(ierr); ierr = PetscFECreateDefault(comm, dim, 1, PETSC_TRUE, "multiplier_", -1, &fe[2]);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe[2], "multiplier");CHKERRQ(ierr); ierr = PetscFESetQuadrature(fe[2], q);CHKERRQ(ierr); /* Set discretization and boundary conditions for each mesh */ for (f = 0; f < 3; ++f) {ierr = DMSetField(dm, f, NULL, (PetscObject) fe[f]);CHKERRQ(ierr);} ierr = DMCreateDS(cdm);CHKERRQ(ierr); ierr = SetupProblem(dm, user);CHKERRQ(ierr); while (cdm) { ierr = DMCopyDisc(dm, cdm);CHKERRQ(ierr); ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr); } for (f = 0; f < 3; ++f) {ierr = PetscFEDestroy(&fe[f]);CHKERRQ(ierr);} PetscFunctionReturn(0); }
PetscErrorCode SetupDiscretization(DM dm, AppCtx *user) { DM cdm = dm; const PetscInt dim = user->dim; PetscFE fe[2]; PetscQuadrature q; Parameter *param; MPI_Comm comm; PetscErrorCode ierr; PetscFunctionBeginUser; /* Create finite element */ ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); ierr = PetscFECreateDefault(comm, dim, dim, user->simplex, "vel_", PETSC_DEFAULT, &fe[0]);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe[0], "velocity");CHKERRQ(ierr); ierr = PetscFEGetQuadrature(fe[0], &q);CHKERRQ(ierr); ierr = PetscFECreateDefault(comm, dim, 1, user->simplex, "pres_", PETSC_DEFAULT, &fe[1]);CHKERRQ(ierr); ierr = PetscFESetQuadrature(fe[1], q);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe[1], "pressure");CHKERRQ(ierr); /* Set discretization and boundary conditions for each mesh */ ierr = DMSetField(dm, 0, NULL, (PetscObject) fe[0]);CHKERRQ(ierr); ierr = DMSetField(dm, 1, NULL, (PetscObject) fe[1]);CHKERRQ(ierr); ierr = DMCreateDS(dm);CHKERRQ(ierr); ierr = SetupProblem(dm, user);CHKERRQ(ierr); ierr = PetscBagGetData(user->bag, (void **) ¶m);CHKERRQ(ierr); while (cdm) { ierr = DMCopyDisc(dm, cdm);CHKERRQ(ierr); ierr = DMPlexCreateBasisRotation(cdm, param->alpha, 0.0, 0.0);CHKERRQ(ierr); ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr); } ierr = PetscFEDestroy(&fe[0]);CHKERRQ(ierr); ierr = PetscFEDestroy(&fe[1]);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode SetupFE(DM dm, PetscInt Nc, PetscBool simplex, const char name[], PetscErrorCode (*setup)(DM, AppCtx *), void *ctx) { AppCtx *user = (AppCtx *) ctx; DM cdm = dm; PetscFE fe; char prefix[PETSC_MAX_PATH_LEN]; PetscInt dim; PetscErrorCode ierr; PetscFunctionBegin; /* Create finite element */ ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = PetscSNPrintf(prefix, PETSC_MAX_PATH_LEN, "%s_", name);CHKERRQ(ierr); ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) dm), dim, Nc, simplex, name ? prefix : NULL, -1, &fe);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe, name);CHKERRQ(ierr); /* Set discretization and boundary conditions for each mesh */ ierr = DMSetField(dm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr); ierr = DMCreateDS(dm);CHKERRQ(ierr); ierr = (*setup)(dm, user);CHKERRQ(ierr); while (cdm) { ierr = DMCopyDisc(dm, cdm);CHKERRQ(ierr); if (user->useNearNullspace) {ierr = DMSetNearNullSpaceConstructor(cdm, 0, CreateElasticityNullSpace);CHKERRQ(ierr);} /* TODO: Check whether the boundary of coarse meshes is marked */ ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr); } ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode SetupDiscretization(DM dm, AppCtx* ctx) { DM cdm = dm; const PetscInt dim = ctx->dim; const PetscInt id = 1; PetscDS prob; PetscFE fe; PetscErrorCode ierr; PetscFunctionBeginUser; /* Create finite element */ ierr = PetscFECreateDefault(dm, dim, 1, ctx->simplex, "temp_", -1, &fe); CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe, "temperature"); CHKERRQ(ierr); /* Set discretization and boundary conditions for each mesh */ ierr = DMGetDS(dm, &prob); CHKERRQ(ierr); ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe); CHKERRQ(ierr); ierr = SetupProblem(prob, ctx); CHKERRQ(ierr); while (cdm) { PetscBool hasLabel; ierr = DMSetDS(cdm, prob); CHKERRQ(ierr); ierr = DMHasLabel(cdm, "marker", &hasLabel); CHKERRQ(ierr); if (!hasLabel) { ierr = CreateBCLabel(cdm, "marker"); CHKERRQ(ierr); } ierr = DMGetCoarseDM(cdm, &cdm); CHKERRQ(ierr); } ierr = PetscFEDestroy(&fe); CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode SetupDiscretization(DM dm, AppCtx *user) { DM cdm = dm; const PetscInt dim = 2; PetscFE fe[3]; PetscQuadrature q; PetscInt f; PetscErrorCode ierr; PetscFunctionBeginUser; /* Create finite element */ ierr = PetscFECreateDefault(dm, dim, 1, PETSC_TRUE, "potential_", -1, &fe[0]);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe[0], "potential");CHKERRQ(ierr); ierr = PetscFEGetQuadrature(fe[0], &q);CHKERRQ(ierr); ierr = PetscFECreateDefault(dm, dim, 1, PETSC_TRUE, "conductivity_", -1, &fe[1]);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe[1], "conductivity");CHKERRQ(ierr); ierr = PetscFESetQuadrature(fe[1], q);CHKERRQ(ierr); ierr = PetscFECreateDefault(dm, dim, 1, PETSC_TRUE, "multiplier_", -1, &fe[2]);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe[2], "multiplier");CHKERRQ(ierr); ierr = PetscFESetQuadrature(fe[2], q);CHKERRQ(ierr); /* Set discretization and boundary conditions for each mesh */ while (cdm) { const PetscInt id = 1; PetscDS prob; ierr = DMGetDS(cdm, &prob);CHKERRQ(ierr); for (f = 0; f < 3; ++f) {ierr = PetscDSSetDiscretization(prob, f, (PetscObject) fe[f]);CHKERRQ(ierr);} ierr = SetupProblem(cdm, user);CHKERRQ(ierr); ierr = DMAddBoundary(cdm, PETSC_TRUE, "wall", "marker", 0, 0, NULL, (void (*)()) user->exactFuncs[0], 1, &id, user);CHKERRQ(ierr); ierr = DMAddBoundary(cdm, PETSC_TRUE, "wall", "marker", 1, 0, NULL, (void (*)()) user->exactFuncs[1], 1, &id, user);CHKERRQ(ierr); ierr = DMAddBoundary(cdm, PETSC_TRUE, "wall", "marker", 2, 0, NULL, (void (*)()) user->exactFuncs[2], 1, &id, user);CHKERRQ(ierr); ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr); } for (f = 0; f < 3; ++f) {ierr = PetscFEDestroy(&fe[f]);CHKERRQ(ierr);} PetscFunctionReturn(0); }
static PetscErrorCode SetupDiscretization(DM dm, const char name[], PetscErrorCode (*setup)(DM, AppCtx *), AppCtx *user) { DM cdm = dm; PetscFE fe; char prefix[PETSC_MAX_PATH_LEN]; PetscErrorCode ierr; PetscFunctionBeginUser; /* Create finite element */ ierr = PetscSNPrintf(prefix, PETSC_MAX_PATH_LEN, "%s_", name);CHKERRQ(ierr); ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) dm), user->dim, 1, user->simplex, name ? prefix : NULL, -1, &fe);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fe, name);CHKERRQ(ierr); /* Set discretization and boundary conditions for each mesh */ ierr = DMSetField(dm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr); ierr = DMCreateDS(dm);CHKERRQ(ierr); ierr = (*setup)(dm, user);CHKERRQ(ierr); while (cdm) { ierr = DMCopyDisc(dm,cdm);CHKERRQ(ierr); /* TODO: Check whether the boundary of coarse meshes is marked */ ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr); } ierr = PetscFEDestroy(&fe);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 TestCellShape(DM dm) { PetscMPIInt rank; PetscInt dim, c, cStart, cEnd, count = 0; ex1_stats_t stats, globalStats; PetscReal *J, *invJ, min = 0, max = 0, mean = 0, stdev = 0; MPI_Comm comm = PetscObjectComm((PetscObject)dm); DM dmCoarse; PetscErrorCode ierr; PetscFunctionBegin; stats.min = PETSC_MAX_REAL; stats.max = PETSC_MIN_REAL; stats.sum = stats.squaresum = 0.; stats.count = 0; ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); ierr = PetscMalloc2(dim * dim, &J, dim * dim, &invJ);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr); for (c = cStart; c < cEnd; c++) { PetscInt i; PetscReal frobJ = 0., frobInvJ = 0., cond2, cond, detJ; ierr = DMPlexComputeCellGeometryAffineFEM(dm,c,NULL,J,invJ,&detJ);CHKERRQ(ierr); for (i = 0; i < dim * dim; i++) { frobJ += J[i] * J[i]; frobInvJ += invJ[i] * invJ[i]; } cond2 = frobJ * frobInvJ; cond = PetscSqrtReal(cond2); stats.min = PetscMin(stats.min,cond); stats.max = PetscMax(stats.max,cond); stats.sum += cond; stats.squaresum += cond2; stats.count++; } { PetscMPIInt blockLengths[2] = {4,1}; MPI_Aint blockOffsets[2] = {offsetof(ex1_stats_t,min),offsetof(ex1_stats_t,count)}; MPI_Datatype blockTypes[2] = {MPIU_REAL,MPIU_INT}, statType; MPI_Op statReduce; ierr = MPI_Type_create_struct(2,blockLengths,blockOffsets,blockTypes,&statType);CHKERRQ(ierr); ierr = MPI_Type_commit(&statType);CHKERRQ(ierr); ierr = MPI_Op_create(ex1_stats_reduce, PETSC_TRUE, &statReduce);CHKERRQ(ierr); ierr = MPI_Reduce(&stats,&globalStats,1,statType,statReduce,0,comm);CHKERRQ(ierr); ierr = MPI_Op_free(&statReduce);CHKERRQ(ierr); ierr = MPI_Type_free(&statType);CHKERRQ(ierr); } ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); if (!rank) { count = globalStats.count; min = globalStats.min; max = globalStats.max; mean = globalStats.sum / globalStats.count; stdev = PetscSqrtReal(globalStats.squaresum / globalStats.count - mean * mean); } ierr = PetscPrintf(comm,"Mesh with %d cells, shape condition numbers: min = %g, max = %g, mean = %g, stddev = %g\n", count, (double) min, (double) max, (double) mean, (double) stdev); ierr = PetscFree2(J,invJ);CHKERRQ(ierr); ierr = DMGetCoarseDM(dm,&dmCoarse);CHKERRQ(ierr); if (dmCoarse) { ierr = TestCellShape(dmCoarse);CHKERRQ(ierr); } PetscFunctionReturn(0); }