示例#1
0
static PetscErrorCode CreateElasticityNullSpace(DM dm, PetscInt dummy, MatNullSpace *nullspace)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMPlexCreateRigidBody(dm, nullspace);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
示例#2
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;
}