C++ PetscMalloc1函数代码示例

/* get adjacencies due to point-to-point constraints that can't be found with DMPlexGetAdjacency() */
static PetscErrorCode DMPlexComputeAnchorAdjacencies(DM dm, PetscSection section, PetscSection sectionGlobal, PetscSection *anchorSectionAdj, PetscInt *anchorAdj[])
{
  PetscInt       pStart, pEnd;
  PetscSection   adjSec, aSec;
  IS             aIS;
  PetscErrorCode ierr;

  PetscFunctionBegin;

  ierr = PetscSectionCreate(PetscObjectComm((PetscObject)section),&adjSec);CHKERRQ(ierr);
  ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(adjSec,pStart,pEnd);CHKERRQ(ierr);

  ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr);
  if (aSec) {
    const PetscInt *anchors;
    PetscInt       p, q, a, aSize, *offsets, aStart, aEnd, *inverse, iSize, *adj, adjSize;
    PetscInt       *tmpAdjP = NULL, *tmpAdjQ = NULL;
    PetscSection   inverseSec;

    /* invert the constraint-to-anchor map */
    ierr = PetscSectionCreate(PetscObjectComm((PetscObject)aSec),&inverseSec);CHKERRQ(ierr);
    ierr = PetscSectionSetChart(inverseSec,pStart,pEnd);CHKERRQ(ierr);
    ierr = ISGetLocalSize(aIS, &aSize);CHKERRQ(ierr);
    ierr = ISGetIndices(aIS, &anchors);CHKERRQ(ierr);

    for (p = 0; p < aSize; p++) {
      PetscInt a = anchors[p];

      ierr = PetscSectionAddDof(inverseSec,a,1);CHKERRQ(ierr);
    }
    ierr = PetscSectionSetUp(inverseSec);CHKERRQ(ierr);
    ierr = PetscSectionGetStorageSize(inverseSec,&iSize);CHKERRQ(ierr);
    ierr = PetscMalloc1(iSize,&inverse);CHKERRQ(ierr);
    ierr = PetscCalloc1(pEnd-pStart,&offsets);CHKERRQ(ierr);
    ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr);
    for (p = aStart; p < aEnd; p++) {
      PetscInt dof, off;

      ierr = PetscSectionGetDof(aSec, p, &dof);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(aSec, p, &off);CHKERRQ(ierr);

      for (q = 0; q < dof; q++) {
        PetscInt iOff;

        a = anchors[off + q];
        ierr = PetscSectionGetOffset(inverseSec, a, &iOff);CHKERRQ(ierr);
        inverse[iOff + offsets[a-pStart]++] = p;
      }
    }
    ierr = ISRestoreIndices(aIS, &anchors);CHKERRQ(ierr);
    ierr = PetscFree(offsets);CHKERRQ(ierr);

    /* construct anchorAdj and adjSec
     *
     * loop over anchors:
     *   construct anchor adjacency
     *   loop over constrained:
     *     construct constrained adjacency
     *     if not in anchor adjacency, add to dofs
     * setup adjSec, allocate anchorAdj
     * loop over anchors:
     *   construct anchor adjacency
     *   loop over constrained:
     *     construct constrained adjacency
     *     if not in anchor adjacency
     *       if not already in list, put in list
     *   sort, unique, reduce dof count
     * optional: compactify
     */
    for (p = pStart; p < pEnd; p++) {
      PetscInt iDof, iOff, i, r, s, numAdjP = PETSC_DETERMINE;

      ierr = PetscSectionGetDof(inverseSec,p,&iDof);CHKERRQ(ierr);
      if (!iDof) continue;
      ierr = PetscSectionGetOffset(inverseSec,p,&iOff);CHKERRQ(ierr);
      ierr = DMPlexGetAdjacency(dm,p,&numAdjP,&tmpAdjP);CHKERRQ(ierr);
      for (i = 0; i < iDof; i++) {
        PetscInt iNew = 0, qAdj, qAdjDof, qAdjCDof, numAdjQ = PETSC_DETERMINE;

        q = inverse[iOff + i];
        ierr = DMPlexGetAdjacency(dm,q,&numAdjQ,&tmpAdjQ);CHKERRQ(ierr);
        for (r = 0; r < numAdjQ; r++) {
          qAdj = tmpAdjQ[r];
          if ((qAdj < pStart) || (qAdj >= pEnd)) continue;
          for (s = 0; s < numAdjP; s++) {
            if (qAdj == tmpAdjP[s]) break;
          }
          if (s < numAdjP) continue;
          ierr  = PetscSectionGetDof(section,qAdj,&qAdjDof);CHKERRQ(ierr);
          ierr  = PetscSectionGetConstraintDof(section,qAdj,&qAdjCDof);CHKERRQ(ierr);
          iNew += qAdjDof - qAdjCDof;
        }
        ierr = PetscSectionAddDof(adjSec,p,iNew);CHKERRQ(ierr);
      }
    }

    ierr = PetscSectionSetUp(adjSec);CHKERRQ(ierr);
    ierr = PetscSectionGetStorageSize(adjSec,&adjSize);CHKERRQ(ierr);
//.........这里部分代码省略.........

PetscErrorCode MatSetUpMultiply_MPIAIJ(Mat mat)
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  Mat_SeqAIJ     *B   = (Mat_SeqAIJ*)(aij->B->data);
  PetscErrorCode ierr;
  PetscInt       i,j,*aj = B->j,ec = 0,*garray;
  IS             from,to;
  Vec            gvec;
#if defined(PETSC_USE_CTABLE)
  PetscTable         gid1_lid1;
  PetscTablePosition tpos;
  PetscInt           gid,lid;
#else
  PetscInt N = mat->cmap->N,*indices;
#endif

  PetscFunctionBegin;
  if (!aij->garray) {
#if defined(PETSC_USE_CTABLE)
    /* use a table */
    ierr = PetscTableCreate(aij->B->rmap->n,mat->cmap->N+1,&gid1_lid1);CHKERRQ(ierr);
    for (i=0; i<aij->B->rmap->n; i++) {
      for (j=0; j<B->ilen[i]; j++) {
        PetscInt data,gid1 = aj[B->i[i] + j] + 1;
        ierr = PetscTableFind(gid1_lid1,gid1,&data);CHKERRQ(ierr);
        if (!data) {
          /* one based table */
          ierr = PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);CHKERRQ(ierr);
        }
      }
    }
    /* form array of columns we need */
    ierr = PetscMalloc1(ec+1,&garray);CHKERRQ(ierr);
    ierr = PetscTableGetHeadPosition(gid1_lid1,&tpos);CHKERRQ(ierr);
    while (tpos) {
      ierr = PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);CHKERRQ(ierr);
      gid--;
      lid--;
      garray[lid] = gid;
    }
    ierr = PetscSortInt(ec,garray);CHKERRQ(ierr); /* sort, and rebuild */
    ierr = PetscTableRemoveAll(gid1_lid1);CHKERRQ(ierr);
    for (i=0; i<ec; i++) {
      ierr = PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr);
    }
    /* compact out the extra columns in B */
    for (i=0; i<aij->B->rmap->n; i++) {
      for (j=0; j<B->ilen[i]; j++) {
        PetscInt gid1 = aj[B->i[i] + j] + 1;
        ierr = PetscTableFind(gid1_lid1,gid1,&lid);CHKERRQ(ierr);
        lid--;
        aj[B->i[i] + j] = lid;
      }
    }
    aij->B->cmap->n = aij->B->cmap->N = ec;
    aij->B->cmap->bs = 1;

    ierr = PetscLayoutSetUp((aij->B->cmap));CHKERRQ(ierr);
    ierr = PetscTableDestroy(&gid1_lid1);CHKERRQ(ierr);
#else
    /* Make an array as long as the number of columns */
    /* mark those columns that are in aij->B */
    ierr = PetscCalloc1(N+1,&indices);CHKERRQ(ierr);
    for (i=0; i<aij->B->rmap->n; i++) {
      for (j=0; j<B->ilen[i]; j++) {
        if (!indices[aj[B->i[i] + j]]) ec++;
        indices[aj[B->i[i] + j]] = 1;
      }
    }

    /* form array of columns we need */
    ierr = PetscMalloc1(ec+1,&garray);CHKERRQ(ierr);
    ec   = 0;
    for (i=0; i<N; i++) {
      if (indices[i]) garray[ec++] = i;
    }

    /* make indices now point into garray */
    for (i=0; i<ec; i++) {
      indices[garray[i]] = i;
    }

    /* compact out the extra columns in B */
    for (i=0; i<aij->B->rmap->n; i++) {
      for (j=0; j<B->ilen[i]; j++) {
        aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
      }
    }
    aij->B->cmap->n = aij->B->cmap->N = ec;
    aij->B->cmap->bs = 1;

    ierr = PetscLayoutSetUp((aij->B->cmap));CHKERRQ(ierr);
    ierr = PetscFree(indices);CHKERRQ(ierr);
#endif
  } else {
    garray = aij->garray;
  }

  if (!aij->lvec) {
    /* create local vector that is used to scatter into */
//.........这里部分代码省略.........

//.........这里部分代码省略.........
  VecAssemblyEnd(fin);
/*    VecView(fin,PETSC_VIEWER_STDOUT_WORLD); */


  VecGetArray(fin,&x_arr);
  VecGetArray(fout1,&z_arr);
  VecGetArray(fout,&y_arr);

  fplan=fftw_mpi_plan_dft_r2c_3d(N0,N1,N2,(double*)x_arr,(fftw_complex*)y_arr,PETSC_COMM_WORLD,FFTW_ESTIMATE);
  bplan=fftw_mpi_plan_dft_c2r_3d(N0,N1,N2,(fftw_complex*)y_arr,(double*)z_arr,PETSC_COMM_WORLD,FFTW_ESTIMATE);

  fftw_execute(fplan);
  fftw_execute(bplan);

  VecRestoreArray(fin,&x_arr);
  VecRestoreArray(fout1,&z_arr);
  VecRestoreArray(fout,&y_arr);


/*    a = 1.0/(PetscReal)N_factor; */
/*    ierr = VecScale(fout1,a);CHKERRQ(ierr); */
  VecCreate(PETSC_COMM_WORLD,&ini);
  VecCreate(PETSC_COMM_WORLD,&final);
  VecSetSizes(ini,local_n0*N1*N2,N_factor);
  VecSetSizes(final,local_n0*N1*N2,N_factor);
/*    VecSetSizes(ini,PETSC_DECIDE,N_factor); */
/*    VecSetSizes(final,PETSC_DECIDE,N_factor); */
  VecSetFromOptions(ini);
  VecSetFromOptions(final);

  if (N2%2==0) NM=N2+2;
  else NM=N2+1;

  ierr = VecGetOwnershipRange(fin,&low,NULL);
  printf("The local index is %d from %d\n",low,rank);
  ierr = PetscMalloc1(local_n0*N1*N2,&indx3);
  ierr = PetscMalloc1(local_n0*N1*N2,&indx4);
  for (i=0; i<local_n0; i++) {
    for (j=0;j<N1;j++) {
      for (k=0;k<N2;k++) {
        tempindx  = i*N1*N2 + j*N2 + k;
        tempindx1 = i*N1*NM + j*NM + k;

        indx3[tempindx]=local_0_start*N1*N2+tempindx;
        indx4[tempindx]=low+tempindx1;
      }
      /*          printf("index3 %d from proc %d is \n",indx3[tempindx],rank); */
      /*          printf("index4 %d from proc %d is \n",indx4[tempindx],rank); */
    }
  }
  VecGetValues(fin,local_n0*N1*N2,indx4,x_arr);
  VecSetValues(ini,local_n0*N1*N2,indx3,x_arr,INSERT_VALUES);
  VecAssemblyBegin(ini);
  VecAssemblyEnd(ini);

  VecGetValues(fout1,local_n0*N1*N2,indx4,y_arr);
  VecSetValues(final,local_n0*N1*N2,indx3,y_arr,INSERT_VALUES);
  VecAssemblyBegin(final);
  VecAssemblyEnd(final);

  printf("The local index value is %ld from %d",local_n0*N1*N2,rank);
/*
  for (i=0;i<N0;i++) {
     for (j=0;j<N1;j++) {
        indx=i*N1*NM+j*NM;
        ISCreateStride(PETSC_COMM_WORLD,N2,indx,1,&indx1);
        indx=i*N1*N2+j*N2;
        ISCreateStride(PETSC_COMM_WORLD,N2,indx,1,&indx2);
        VecScatterCreate(fin,indx1,ini,indx2,&vecscat);
        VecScatterBegin(vecscat,fin,ini,INSERT_VALUES,SCATTER_FORWARD);
        VecScatterEnd(vecscat,fin,ini,INSERT_VALUES,SCATTER_FORWARD);
        VecScatterCreate(fout1,indx1,final,indx2,&vecscat1);
        VecScatterBegin(vecscat1,fout1,final,INSERT_VALUES,SCATTER_FORWARD);
        VecScatterEnd(vecscat1,fout1,final,INSERT_VALUES,SCATTER_FORWARD);
     }
  }
*/
  a    = 1.0/(PetscReal)N_factor;
  ierr = VecScale(fout1,a);CHKERRQ(ierr);
  ierr = VecScale(final,a);CHKERRQ(ierr);

  VecAssemblyBegin(ini);
  VecAssemblyEnd(ini);

  VecAssemblyBegin(final);
  VecAssemblyEnd(final);

/*    VecView(final,PETSC_VIEWER_STDOUT_WORLD); */
  ierr = VecAXPY(final,-1.0,ini);CHKERRQ(ierr);
  ierr = VecNorm(final,NORM_1,&enorm);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"  Error norm of |x - z|  = %e\n",enorm);CHKERRQ(ierr);
  fftw_destroy_plan(fplan);
  fftw_destroy_plan(bplan);
  fftw_free(in1); ierr = VecDestroy(&fin);CHKERRQ(ierr);
  fftw_free(out); ierr = VecDestroy(&fout);CHKERRQ(ierr);
  fftw_free(in2); ierr = VecDestroy(&fout1);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return ierr;
}

int main(int argc, char **argv)
{
  PetscInt    ierr;
  PetscSF     sf;
  Vec         A,Aout;
  Vec         B,Bout;
  PetscScalar *bufA;
  PetscScalar *bufAout;
  PetscScalar *bufB;
  PetscScalar *bufBout;
  PetscMPIInt rank, size;
  PetscInt    nroots, nleaves;
  PetscInt    i;
  PetscInt    *ilocal;
  PetscSFNode *iremote;

  ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);

  if (size != 2) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Only coded for two MPI processes\n");

  ierr = PetscSFCreate(PETSC_COMM_WORLD,&sf);CHKERRQ(ierr);
  ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr);

  nleaves = 2;
  nroots = 1;
  ierr = PetscMalloc1(nleaves,&ilocal);CHKERRQ(ierr);

  for (i = 0; i<nleaves; i++) {
    ilocal[i] = i;
  }

  ierr = PetscMalloc1(nleaves,&iremote);CHKERRQ(ierr);
  if (rank == 0) {
    iremote[0].rank = 0;
    iremote[0].index = 0;
    iremote[1].rank = 1;
    iremote[1].index = 0;
  } else {
    iremote[0].rank = 1;
    iremote[0].index = 0;
    iremote[1].rank = 0;
    iremote[1].index = 0;
  }
  ierr = PetscSFSetGraph(sf,nroots,nleaves,ilocal,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr);
  ierr = PetscSFSetUp(sf);CHKERRQ(ierr);
  ierr = PetscSFView(sf,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = VecSetSizes(A,2,PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(A);CHKERRQ(ierr);
  ierr = VecSetUp(A);CHKERRQ(ierr);

  ierr = VecDuplicate(A,&B);CHKERRQ(ierr);
  ierr = VecDuplicate(A,&Aout);CHKERRQ(ierr);
  ierr = VecDuplicate(A,&Bout);CHKERRQ(ierr);
  ierr = VecGetArray(A,&bufA);CHKERRQ(ierr);
  ierr = VecGetArray(B,&bufB);CHKERRQ(ierr);
  for (i=0; i<2; i++) {
    bufA[i] = (PetscScalar)rank;
    bufB[i] = (PetscScalar)(rank) + 10.0;
  }
  ierr = VecRestoreArray(A,&bufA);CHKERRQ(ierr);
  ierr = VecRestoreArray(B,&bufB);CHKERRQ(ierr);

  ierr = VecGetArrayRead(A,(const PetscScalar**)&bufA);CHKERRQ(ierr);
  ierr = VecGetArrayRead(B,(const PetscScalar**)&bufB);CHKERRQ(ierr);
  ierr = VecGetArray(Aout,&bufAout);CHKERRQ(ierr);
  ierr = VecGetArray(Bout,&bufBout);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(sf,MPIU_SCALAR,(const void*)bufA,(void *)bufAout);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(sf,MPIU_SCALAR,(const void*)bufB,(void *)bufBout);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(sf,MPIU_SCALAR,(const void*)bufA,(void *)bufAout);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(sf,MPIU_SCALAR,(const void*)bufB,(void *)bufBout);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(A,(const PetscScalar**)&bufA);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(B,(const PetscScalar**)&bufB);CHKERRQ(ierr);
  ierr = VecRestoreArray(Aout,&bufAout);CHKERRQ(ierr);
  ierr = VecRestoreArray(Bout,&bufBout);CHKERRQ(ierr);

  ierr = VecView(Aout,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecView(Bout,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecDestroy(&A);CHKERRQ(ierr);
  ierr = VecDestroy(&B);CHKERRQ(ierr);
  ierr = VecDestroy(&Aout);CHKERRQ(ierr);
  ierr = VecDestroy(&Bout);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&sf);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return ierr;
}

/* Version for when blocks are 4 by 4  */
PetscErrorCode MatCholeskyFactorNumeric_SeqSBAIJ_4(Mat C,Mat A,const MatFactorInfo *info)
{
  Mat_SeqSBAIJ   *a   = (Mat_SeqSBAIJ*)A->data,*b = (Mat_SeqSBAIJ*)C->data;
  IS             perm = b->row;
  PetscErrorCode ierr;
  const PetscInt *ai,*aj,*perm_ptr,mbs=a->mbs,*bi=b->i,*bj=b->j;
  PetscInt       i,j,*a2anew,k,k1,jmin,jmax,*jl,*il,vj,nexti,ili;
  MatScalar      *ba = b->a,*aa,*ap,*dk,*uik;
  MatScalar      *u,*diag,*rtmp,*rtmp_ptr;
  PetscBool      pivotinblocks = b->pivotinblocks;
  PetscReal      shift         = info->shiftamount;
  PetscBool      allowzeropivot,zeropivotdetected=PETSC_FALSE;

  PetscFunctionBegin;
  /* initialization */
  allowzeropivot = PetscNot(A->erroriffailure);
  ierr = PetscCalloc1(16*mbs,&rtmp);CHKERRQ(ierr);
  ierr = PetscMalloc2(mbs,&il,mbs,&jl);CHKERRQ(ierr);
  il[0] = 0;
  for (i=0; i<mbs; i++) jl[i] = mbs; 
  
  ierr = PetscMalloc2(16,&dk,16,&uik);CHKERRQ(ierr);
  ierr = ISGetIndices(perm,&perm_ptr);CHKERRQ(ierr);

  /* check permutation */
  if (!a->permute) {
    ai = a->i; aj = a->j; aa = a->a;
  } else {
    ai   = a->inew; aj = a->jnew;
    ierr = PetscMalloc1(16*ai[mbs],&aa);CHKERRQ(ierr);
    ierr = PetscMemcpy(aa,a->a,16*ai[mbs]*sizeof(MatScalar));CHKERRQ(ierr);
    ierr = PetscMalloc1(ai[mbs],&a2anew);CHKERRQ(ierr);
    ierr = PetscMemcpy(a2anew,a->a2anew,(ai[mbs])*sizeof(PetscInt));CHKERRQ(ierr);

    for (i=0; i<mbs; i++) {
      jmin = ai[i]; jmax = ai[i+1];
      for (j=jmin; j<jmax; j++) {
        while (a2anew[j] != j) {
          k = a2anew[j]; a2anew[j] = a2anew[k]; a2anew[k] = k;
          for (k1=0; k1<16; k1++) {
            dk[k1]      = aa[k*16+k1];
            aa[k*16+k1] = aa[j*16+k1];
            aa[j*16+k1] = dk[k1];
          }
        }
        /* transform columnoriented blocks that lie in the lower triangle to roworiented blocks */
        if (i > aj[j]) {
          /* printf("change orientation, row: %d, col: %d\n",i,aj[j]); */
          ap = aa + j*16;                     /* ptr to the beginning of j-th block of aa */
          for (k=0; k<16; k++) dk[k] = ap[k]; /* dk <- j-th block of aa */
          for (k=0; k<4; k++) {               /* j-th block of aa <- dk^T */
            for (k1=0; k1<4; k1++) *ap++ = dk[k + 4*k1];
          }
        }
      }
    }
    ierr = PetscFree(a2anew);CHKERRQ(ierr);
  }

  /* for each row k */
  for (k = 0; k<mbs; k++) {

    /*initialize k-th row with elements nonzero in row perm(k) of A */
    jmin = ai[perm_ptr[k]]; jmax = ai[perm_ptr[k]+1];
    if (jmin < jmax) {
      ap = aa + jmin*16;
      for (j = jmin; j < jmax; j++) {
        vj       = perm_ptr[aj[j]];   /* block col. index */
        rtmp_ptr = rtmp + vj*16;
        for (i=0; i<16; i++) *rtmp_ptr++ = *ap++;
      }
    }

    /* modify k-th row by adding in those rows i with U(i,k) != 0 */
    ierr = PetscMemcpy(dk,rtmp+k*16,16*sizeof(MatScalar));CHKERRQ(ierr);
    i    = jl[k]; /* first row to be added to k_th row  */

    while (i < mbs) {
      nexti = jl[i]; /* next row to be added to k_th row */

      /* compute multiplier */
      ili = il[i];  /* index of first nonzero element in U(i,k:bms-1) */

      /* uik = -inv(Di)*U_bar(i,k) */
      diag = ba + i*16;
      u    = ba + ili*16;

      uik[0] = -(diag[0]*u[0] + diag[4]*u[1] + diag[8]*u[2] + diag[12]*u[3]);
      uik[1] = -(diag[1]*u[0] + diag[5]*u[1] + diag[9]*u[2] + diag[13]*u[3]);
      uik[2] = -(diag[2]*u[0] + diag[6]*u[1] + diag[10]*u[2]+ diag[14]*u[3]);
      uik[3] = -(diag[3]*u[0] + diag[7]*u[1] + diag[11]*u[2]+ diag[15]*u[3]);

      uik[4] = -(diag[0]*u[4] + diag[4]*u[5] + diag[8]*u[6] + diag[12]*u[7]);
      uik[5] = -(diag[1]*u[4] + diag[5]*u[5] + diag[9]*u[6] + diag[13]*u[7]);
      uik[6] = -(diag[2]*u[4] + diag[6]*u[5] + diag[10]*u[6]+ diag[14]*u[7]);
      uik[7] = -(diag[3]*u[4] + diag[7]*u[5] + diag[11]*u[6]+ diag[15]*u[7]);

      uik[8] = -(diag[0]*u[8] + diag[4]*u[9] + diag[8]*u[10] + diag[12]*u[11]);
      uik[9] = -(diag[1]*u[8] + diag[5]*u[9] + diag[9]*u[10] + diag[13]*u[11]);
//.........这里部分代码省略.........

int main(int argc,char **argv)
{
  TS                ts;         /* time integrator */
  TSAdapt           adapt;
  Vec               X;          /* solution vector */
  Mat               J;          /* Jacobian matrix */
  PetscInt          steps,maxsteps,ncells,xs,xm,i;
  PetscErrorCode    ierr;
  PetscReal         ftime,dt;
  char              chemfile[PETSC_MAX_PATH_LEN] = "chem.inp",thermofile[PETSC_MAX_PATH_LEN] = "therm.dat";
  struct _User      user;
  TSConvergedReason reason;
  PetscBool         showsolutions = PETSC_FALSE;
  char              **snames,*names;
  Vec               lambda;     /* used with TSAdjoint for sensitivities */

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Chemistry solver options","");CHKERRQ(ierr);
  ierr = PetscOptionsString("-chem","CHEMKIN input file","",chemfile,chemfile,sizeof(chemfile),NULL);CHKERRQ(ierr);
  ierr = PetscOptionsString("-thermo","NASA thermo input file","",thermofile,thermofile,sizeof(thermofile),NULL);CHKERRQ(ierr);
  user.pressure = 1.01325e5;    /* Pascal */
  ierr = PetscOptionsReal("-pressure","Pressure of reaction [Pa]","",user.pressure,&user.pressure,NULL);CHKERRQ(ierr);
  user.Tini   = 1550;
  ierr = PetscOptionsReal("-Tini","Initial temperature [K]","",user.Tini,&user.Tini,NULL);CHKERRQ(ierr);
  user.diffus = 100;
  ierr = PetscOptionsReal("-diffus","Diffusion constant","",user.diffus,&user.diffus,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsBool("-draw_solution","Plot the solution for each cell","",showsolutions,&showsolutions,NULL);CHKERRQ(ierr);
  user.diffusion = PETSC_TRUE;
  ierr = PetscOptionsBool("-diffusion","Have diffusion","",user.diffusion,&user.diffusion,NULL);CHKERRQ(ierr);
  user.reactions = PETSC_TRUE;
  ierr = PetscOptionsBool("-reactions","Have reactions","",user.reactions,&user.reactions,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsEnd();CHKERRQ(ierr);

  ierr = TC_initChem(chemfile, thermofile, 0, 1.0);TCCHKERRQ(ierr);
  user.Nspec = TC_getNspec();
  user.Nreac = TC_getNreac();

  ierr    = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,-1,user.Nspec+1,1,NULL,&user.dm);CHKERRQ(ierr);
  ierr    = DMDAGetInfo(user.dm,NULL,&ncells,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
  user.dx = 1.0/ncells;  /* Set the coordinates of the cell centers; note final ghost cell is at x coordinate 1.0 */
  ierr    = DMDASetUniformCoordinates(user.dm,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);

  /* set the names of each field in the DMDA based on the species name */
  ierr = PetscMalloc1((user.Nspec+1)*LENGTHOFSPECNAME,&names);CHKERRQ(ierr);
  ierr = PetscStrcpy(names,"Temp");CHKERRQ(ierr);
  TC_getSnames(user.Nspec,names+LENGTHOFSPECNAME);CHKERRQ(ierr);
  ierr = PetscMalloc1((user.Nspec+2),&snames);CHKERRQ(ierr);
  for (i=0; i<user.Nspec+1; i++) snames[i] = names+i*LENGTHOFSPECNAME;
  snames[user.Nspec+1] = NULL;
  ierr = DMDASetFieldNames(user.dm,(const char * const *)snames);CHKERRQ(ierr);
  ierr = PetscFree(snames);CHKERRQ(ierr);
  ierr = PetscFree(names);CHKERRQ(ierr);


  ierr = DMCreateMatrix(user.dm,&J);CHKERRQ(ierr);
  ierr = DMCreateGlobalVector(user.dm,&X);CHKERRQ(ierr);

  ierr = PetscMalloc3(user.Nspec+1,&user.tchemwork,PetscSqr(user.Nspec+1),&user.Jdense,user.Nspec+1,&user.rows);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetDM(ts,user.dm);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr);
  ierr = TSARKIMEXSetFullyImplicit(ts,PETSC_TRUE);CHKERRQ(ierr);
  ierr = TSARKIMEXSetType(ts,TSARKIMEX4);CHKERRQ(ierr);
  ierr = TSSetRHSFunction(ts,NULL,FormRHSFunction,&user);CHKERRQ(ierr);
  ierr = TSSetRHSJacobian(ts,J,J,FormRHSJacobian,&user);CHKERRQ(ierr);

  ftime    = 1.0;
  maxsteps = 10000;
  ierr     = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr);
  ierr     = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = FormInitialSolution(ts,X,&user);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,X);CHKERRQ(ierr);
  dt   = 1e-10;                 /* Initial time step */
  ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);
  ierr = TSGetAdapt(ts,&adapt);CHKERRQ(ierr);
  ierr = TSAdaptSetStepLimits(adapt,1e-12,1e-4);CHKERRQ(ierr); /* Also available with -ts_adapt_dt_min/-ts_adapt_dt_max */
  ierr = TSSetMaxSNESFailures(ts,-1);CHKERRQ(ierr);            /* Retry step an unlimited number of times */


  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Pass information to graphical monitoring routine
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  if (showsolutions) {
    ierr = DMDAGetCorners(user.dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
    for (i=xs;i<xs+xm;i++) {
      ierr = MonitorCell(ts,&user,i);CHKERRQ(ierr);
    }
  }

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set runtime options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
//.........这里部分代码省略.........

PetscErrorCode PCGAMGCreateGraph(const Mat Amat, Mat *a_Gmat)
{
  PetscErrorCode ierr;
  PetscInt       Istart,Iend,Ii,jj,kk,ncols,nloc,NN,MM,bs;
  PetscMPIInt    rank, size;
  MPI_Comm       comm;
  Mat            Gmat;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  ierr = MatGetOwnershipRange(Amat, &Istart, &Iend);CHKERRQ(ierr);
  ierr = MatGetSize(Amat, &MM, &NN);CHKERRQ(ierr);
  ierr = MatGetBlockSize(Amat, &bs);CHKERRQ(ierr);
  nloc = (Iend-Istart)/bs;

#if defined PETSC_GAMG_USE_LOG
  ierr = PetscLogEventBegin(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr);
#endif
  if (bs > 1) {
    const PetscScalar *vals;
    const PetscInt    *idx;
    PetscInt          *d_nnz, *o_nnz;
    /* count nnz, there is sparcity in here so this might not be enough */
    ierr = PetscMalloc1(nloc, &d_nnz);CHKERRQ(ierr);
    ierr = PetscMalloc1(nloc, &o_nnz);CHKERRQ(ierr);
    for (Ii = Istart, jj = 0; Ii < Iend; Ii += bs, jj++) {
      d_nnz[jj] = 0;
      for (kk=0; kk<bs; kk++) {
        ierr = MatGetRow(Amat,Ii+kk,&ncols,0,0);CHKERRQ(ierr);
        if (ncols > d_nnz[jj]) {
          d_nnz[jj] = ncols; /* very pessimistic but could be too low in theory */
          o_nnz[jj] = ncols;
          if (d_nnz[jj] > nloc) d_nnz[jj] = nloc;
          if (o_nnz[jj] > (NN/bs-nloc)) o_nnz[jj] = NN/bs-nloc;
        }
        ierr = MatRestoreRow(Amat,Ii+kk,&ncols,0,0);CHKERRQ(ierr);
      }
    }

    /* get scalar copy (norms) of matrix -- AIJ specific!!! */
    ierr = MatCreateAIJ(comm, nloc, nloc, PETSC_DETERMINE, PETSC_DETERMINE,0, d_nnz, 0, o_nnz, &Gmat);CHKERRQ(ierr);

    ierr = PetscFree(d_nnz);CHKERRQ(ierr);
    ierr = PetscFree(o_nnz);CHKERRQ(ierr);

    for (Ii = Istart; Ii < Iend; Ii++) {
      PetscInt dest_row = Ii/bs;
      ierr = MatGetRow(Amat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr);
      for (jj=0; jj<ncols; jj++) {
        PetscInt    dest_col = idx[jj]/bs;
        PetscScalar sv       = PetscAbs(PetscRealPart(vals[jj]));
        ierr = MatSetValues(Gmat,1,&dest_row,1,&dest_col,&sv,ADD_VALUES);CHKERRQ(ierr);
      }
      ierr = MatRestoreRow(Amat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr);
    }
    ierr = MatAssemblyBegin(Gmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(Gmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  } else {
    /* just copy scalar matrix - abs() not taken here but scaled later */
    ierr = MatDuplicate(Amat, MAT_COPY_VALUES, &Gmat);CHKERRQ(ierr);
  }

#if defined PETSC_GAMG_USE_LOG
  ierr = PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr);
#endif

  *a_Gmat = Gmat;
  PetscFunctionReturn(0);
}

/*@C
   PetscBinaryRead - Reads from a binary file.

   Not Collective

   Input Parameters:
+  fd - the file descriptor
.  num  - the maximum number of items to read
-  type - the type of items to read (PETSC_INT, PETSC_REAL, PETSC_SCALAR, etc.)

   Output Parameters:
+  data - the buffer
-  count - the number of items read, optional



   Level: developer

   Notes:
   If count is not provided and the number of items read is less than
   the maximum number of items to read, then this routine errors.

   PetscBinaryRead() uses byte swapping to work on all machines; the files
   are written to file ALWAYS using big-endian ordering. On small-endian machines the numbers
   are converted to the small-endian format when they are read in from the file.
   When PETSc is ./configure with --with-64bit-indices the integers are written to the
   file as 64 bit integers, this means they can only be read back in when the option --with-64bit-indices
   is used.

   Concepts: files^reading binary
   Concepts: binary files^reading

.seealso: PetscBinaryWrite(), PetscBinaryOpen(), PetscBinaryClose(), PetscViewerBinaryGetDescriptor(), PetscBinarySynchronizedWrite(),
          PetscBinarySynchronizedRead(), PetscBinarySynchronizedSeek()
@*/
PetscErrorCode  PetscBinaryRead(int fd,void *data,PetscInt num,PetscInt *count,PetscDataType type)
{
  size_t            typesize, m = (size_t) num, n = 0, maxblock = 65536;
  char              *p = (char*)data;
#if defined(PETSC_USE_REAL___FLOAT128)
  PetscBool         readdouble = PETSC_FALSE;
  double            *pdouble;
#endif
  void              *ptmp = data;
  char              *fname = NULL;
  PetscErrorCode    ierr;

  PetscFunctionBegin;
  if (count) *count = 0;
  if (num < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Trying to read a negative amount of data %D",num);
  if (!num) PetscFunctionReturn(0);

  if (type == PETSC_FUNCTION) {
    m     = 64;
    type  = PETSC_CHAR;
    fname = (char*)malloc(m*sizeof(char));
    p     = (char*)fname;
    ptmp  = (void*)fname;
    if (!fname) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_MEM,"Cannot allocate space for function name");
  }
  if (type == PETSC_BIT_LOGICAL) m = PetscBTLength(m);

  ierr = PetscDataTypeGetSize(type,&typesize);CHKERRQ(ierr);

#if defined(PETSC_USE_REAL___FLOAT128)
  ierr = PetscOptionsGetBool(NULL,NULL,"-binary_read_double",&readdouble,NULL);CHKERRQ(ierr);
  /* If using __float128 precision we still read in doubles from file */
  if ((type == PETSC_REAL || type == PETSC_COMPLEX) && readdouble) {
    PetscInt cnt = num * ((type == PETSC_REAL) ? 1 : 2);
    ierr = PetscMalloc1(cnt,&pdouble);CHKERRQ(ierr);
    p = (char*)pdouble;
    typesize /= 2;
  }
#endif

  m *= typesize;

  while (m) {
    size_t len = (m < maxblock) ? m : maxblock;
    int    ret = (int)read(fd,p,len);
    if (ret < 0 && errno == EINTR) continue;
    if (!ret && len > 0) break; /* Proxy for EOF */
    if (ret < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FILE_READ,"Error reading from file, errno %d",errno);
    m -= ret;
    p += ret;
    n += ret;
  }
  if (m && !count) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_READ,"Read past end of file");

  num = (PetscInt)(n/typesize); /* Should we require `n % typesize == 0` ? */
  if (count) *count = num;      /* TODO: This is most likely wrong for PETSC_BIT_LOGICAL */

#if defined(PETSC_USE_REAL___FLOAT128)
  if ((type == PETSC_REAL || type == PETSC_COMPLEX) && readdouble) {
    PetscInt  i, cnt = num * ((type == PETSC_REAL) ? 1 : 2);
    PetscReal *preal = (PetscReal*)data;
    if (!PetscBinaryBigEndian()) {ierr = PetscByteSwapDouble(pdouble,cnt);CHKERRQ(ierr);}
    for (i=0; i<cnt; i++) preal[i] = pdouble[i];
    ierr = PetscFree(pdouble);CHKERRQ(ierr);
    PetscFunctionReturn(0);
//.........这里部分代码省略.........

//.........这里部分代码省略.........
    ierr = VecScatterEnd(matis->rctx,nullvecs[k],pcis->vec1_N,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    if (basis_dofs) {
      ierr = VecPlaceArray(work1,(const PetscScalar*)&basis_mat[k*basis_dofs]);CHKERRQ(ierr);
      ierr = VecScatterBegin(scatter_ctx,pcis->vec1_N,work1,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
      ierr = VecScatterEnd(scatter_ctx,pcis->vec1_N,work1,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
      ierr = VecPlaceArray(work2,(const PetscScalar*)&Kbasis_mat[k*basis_dofs]);CHKERRQ(ierr);
      ierr = MatMult(local_mat,work1,work2);CHKERRQ(ierr);
      ierr = VecResetArray(work1);CHKERRQ(ierr);
      ierr = VecResetArray(work2);CHKERRQ(ierr);
    }
  }

  if (basis_dofs) {
    if (nnsp_has_cnst) {
      ierr = VecPlaceArray(work1,(const PetscScalar*)&basis_mat[k*basis_dofs]);CHKERRQ(ierr);
      ierr = VecSet(work1,one);CHKERRQ(ierr);
      ierr = VecPlaceArray(work2,(const PetscScalar*)&Kbasis_mat[k*basis_dofs]);CHKERRQ(ierr);
      ierr = MatMult(local_mat,work1,work2);CHKERRQ(ierr);
      ierr = VecResetArray(work1);CHKERRQ(ierr);
      ierr = VecResetArray(work2);CHKERRQ(ierr);
    }
    ierr = VecDestroy(&work1);CHKERRQ(ierr);
    ierr = VecDestroy(&work2);CHKERRQ(ierr);
    ierr = VecScatterDestroy(&scatter_ctx);CHKERRQ(ierr);
    ierr = MatDenseRestoreArray(shell_ctx->basis_mat,&basis_mat);CHKERRQ(ierr);
    ierr = MatDenseRestoreArray(shell_ctx->Kbasis_mat,&Kbasis_mat);CHKERRQ(ierr);

    /* Assemble another Mat object in shell context */
    ierr = MatTransposeMatMult(shell_ctx->basis_mat,shell_ctx->Kbasis_mat,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&small_mat);CHKERRQ(ierr);
    ierr = MatFactorInfoInitialize(&matinfo);CHKERRQ(ierr);
    ierr = ISCreateStride(PETSC_COMM_SELF,basis_size,0,1,&is_aux);CHKERRQ(ierr);
    ierr = MatLUFactor(small_mat,is_aux,is_aux,&matinfo);CHKERRQ(ierr);
    ierr = ISDestroy(&is_aux);CHKERRQ(ierr);
    ierr = PetscMalloc1(basis_size*basis_size,&array_mat);CHKERRQ(ierr);
    for (k=0;k<basis_size;k++) {
      ierr = VecSet(shell_ctx->work_small_1,zero);CHKERRQ(ierr);
      ierr = VecSetValue(shell_ctx->work_small_1,k,one,INSERT_VALUES);CHKERRQ(ierr);
      ierr = VecAssemblyBegin(shell_ctx->work_small_1);CHKERRQ(ierr);
      ierr = VecAssemblyEnd(shell_ctx->work_small_1);CHKERRQ(ierr);
      ierr = MatSolve(small_mat,shell_ctx->work_small_1,shell_ctx->work_small_2);CHKERRQ(ierr);
      ierr = VecGetArrayRead(shell_ctx->work_small_2,(const PetscScalar**)&array);CHKERRQ(ierr);
      for (i=0;i<basis_size;i++) {
        array_mat[i*basis_size+k]=array[i];
      }
      ierr = VecRestoreArrayRead(shell_ctx->work_small_2,(const PetscScalar**)&array);CHKERRQ(ierr);
    }
    ierr = MatCreateSeqDense(PETSC_COMM_SELF,basis_size,basis_size,array_mat,&inv_small_mat);CHKERRQ(ierr);
    ierr = MatMatMult(shell_ctx->basis_mat,inv_small_mat,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&shell_ctx->Lbasis_mat);CHKERRQ(ierr);
    ierr = PetscFree(array_mat);CHKERRQ(ierr);
    ierr = MatDestroy(&inv_small_mat);CHKERRQ(ierr);
    ierr = MatDestroy(&small_mat);CHKERRQ(ierr);
    ierr = MatScale(shell_ctx->Kbasis_mat,m_one);CHKERRQ(ierr);

    /* Rebuild local PC */
    ierr = KSPGetPC(local_ksp,&shell_ctx->local_pc);CHKERRQ(ierr);
    ierr = PetscObjectReference((PetscObject)shell_ctx->local_pc);CHKERRQ(ierr);
    ierr = PCCreate(PETSC_COMM_SELF,&newpc);CHKERRQ(ierr);
    ierr = PCSetOperators(newpc,local_mat,local_mat);CHKERRQ(ierr);
    ierr = PCSetType(newpc,PCSHELL);CHKERRQ(ierr);
    ierr = PCShellSetContext(newpc,shell_ctx);CHKERRQ(ierr);
    ierr = PCShellSetApply(newpc,PCBDDCApplyNullSpaceCorrectionPC);CHKERRQ(ierr);
    ierr = PCShellSetDestroy(newpc,PCBDDCDestroyNullSpaceCorrectionPC);CHKERRQ(ierr);
    ierr = PCSetUp(newpc);CHKERRQ(ierr);
    ierr = KSPSetPC(local_ksp,newpc);CHKERRQ(ierr);
    ierr = PCDestroy(&newpc);CHKERRQ(ierr);
    ierr = KSPSetUp(local_ksp);CHKERRQ(ierr);

PetscErrorCode PCBDDCNullSpaceAssembleCoarse(PC pc, Mat coarse_mat, MatNullSpace* CoarseNullSpace)
{
  PC_BDDC        *pcbddc = (PC_BDDC*)pc->data;
  Mat_IS         *matis = (Mat_IS*)pc->pmat->data;
  MatNullSpace   tempCoarseNullSpace=NULL;
  const Vec      *nsp_vecs;
  Vec            *coarse_nsp_vecs,local_vec,local_primal_vec,wcoarse_vec,wcoarse_rhs;
  PetscInt       nsp_size,coarse_nsp_size,i;
  PetscBool      nsp_has_cnst;
  PetscReal      test_null;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  tempCoarseNullSpace = 0;
  coarse_nsp_size = 0;
  coarse_nsp_vecs = 0;
  ierr = MatNullSpaceGetVecs(pcbddc->NullSpace,&nsp_has_cnst,&nsp_size,&nsp_vecs);CHKERRQ(ierr);
  if (coarse_mat) {
    ierr = PetscMalloc1(nsp_size+1,&coarse_nsp_vecs);CHKERRQ(ierr);
    for (i=0;i<nsp_size+1;i++) {
      ierr = MatCreateVecs(coarse_mat,&coarse_nsp_vecs[i],NULL);CHKERRQ(ierr);
    }
    if (pcbddc->dbg_flag) {
      ierr = MatCreateVecs(coarse_mat,&wcoarse_vec,&wcoarse_rhs);CHKERRQ(ierr);
    }
  }
  ierr = MatCreateVecs(pcbddc->ConstraintMatrix,&local_vec,&local_primal_vec);CHKERRQ(ierr);
  if (nsp_has_cnst) {
    ierr = VecSet(local_vec,1.0);CHKERRQ(ierr);
    ierr = MatMult(pcbddc->ConstraintMatrix,local_vec,local_primal_vec);CHKERRQ(ierr);
    ierr = VecScatterBegin(pcbddc->coarse_loc_to_glob,local_primal_vec,pcbddc->coarse_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = VecScatterEnd(pcbddc->coarse_loc_to_glob,local_primal_vec,pcbddc->coarse_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    if (coarse_mat) {
      PetscScalar *array_out;
      const PetscScalar *array_in;
      PetscInt lsize;
      if (pcbddc->dbg_flag) {
        PetscViewer dbg_viewer = PETSC_VIEWER_STDOUT_(PetscObjectComm((PetscObject)coarse_mat));
        ierr = MatMult(coarse_mat,wcoarse_vec,wcoarse_rhs);CHKERRQ(ierr);
        ierr = VecNorm(wcoarse_rhs,NORM_INFINITY,&test_null);CHKERRQ(ierr);
        ierr = PetscViewerASCIIPrintf(dbg_viewer,"Constant coarse null space error % 1.14e\n",test_null);CHKERRQ(ierr);
        ierr = PetscViewerFlush(dbg_viewer);CHKERRQ(ierr);
      }
      ierr = VecGetLocalSize(pcbddc->coarse_vec,&lsize);CHKERRQ(ierr);
      ierr = VecGetArrayRead(pcbddc->coarse_vec,&array_in);CHKERRQ(ierr);
      ierr = VecGetArray(coarse_nsp_vecs[coarse_nsp_size],&array_out);CHKERRQ(ierr);
      ierr = PetscMemcpy(array_out,array_in,lsize*sizeof(PetscScalar));CHKERRQ(ierr);
      ierr = VecRestoreArray(coarse_nsp_vecs[coarse_nsp_size],&array_out);CHKERRQ(ierr);
      ierr = VecRestoreArrayRead(pcbddc->coarse_vec,&array_in);CHKERRQ(ierr);
      coarse_nsp_size++;
    }
  }
  for (i=0;i<nsp_size;i++)  {
    ierr = VecScatterBegin(matis->rctx,nsp_vecs[i],local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = VecScatterEnd(matis->rctx,nsp_vecs[i],local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = MatMult(pcbddc->ConstraintMatrix,local_vec,local_primal_vec);CHKERRQ(ierr);
    ierr = VecScatterBegin(pcbddc->coarse_loc_to_glob,local_primal_vec,pcbddc->coarse_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = VecScatterEnd(pcbddc->coarse_loc_to_glob,local_primal_vec,pcbddc->coarse_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    if (coarse_mat) {
      PetscScalar *array_out;
      const PetscScalar *array_in;
      PetscInt lsize;
      if (pcbddc->dbg_flag) {
        PetscViewer dbg_viewer = PETSC_VIEWER_STDOUT_(PetscObjectComm((PetscObject)coarse_mat));
        ierr = MatMult(coarse_mat,wcoarse_vec,wcoarse_rhs);CHKERRQ(ierr);
        ierr = VecNorm(wcoarse_rhs,NORM_2,&test_null);CHKERRQ(ierr);
        ierr = PetscViewerASCIIPrintf(dbg_viewer,"Vec %d coarse null space error % 1.14e\n",i,test_null);CHKERRQ(ierr);
        ierr = PetscViewerFlush(dbg_viewer);CHKERRQ(ierr);
      }
      ierr = VecGetLocalSize(pcbddc->coarse_vec,&lsize);CHKERRQ(ierr);
      ierr = VecGetArrayRead(pcbddc->coarse_vec,&array_in);CHKERRQ(ierr);
      ierr = VecGetArray(coarse_nsp_vecs[coarse_nsp_size],&array_out);CHKERRQ(ierr);
      ierr = PetscMemcpy(array_out,array_in,lsize*sizeof(PetscScalar));CHKERRQ(ierr);
      ierr = VecRestoreArray(coarse_nsp_vecs[coarse_nsp_size],&array_out);CHKERRQ(ierr);
      ierr = VecRestoreArrayRead(pcbddc->coarse_vec,&array_in);CHKERRQ(ierr);
      coarse_nsp_size++;
    }
  }
  if (coarse_nsp_size > 0) {
    ierr = PCBDDCOrthonormalizeVecs(coarse_nsp_size,coarse_nsp_vecs);CHKERRQ(ierr);
    ierr = MatNullSpaceCreate(PetscObjectComm((PetscObject)coarse_mat),PETSC_FALSE,coarse_nsp_size,coarse_nsp_vecs,&tempCoarseNullSpace);CHKERRQ(ierr);
    for (i=0;i<nsp_size+1;i++) {
      ierr = VecDestroy(&coarse_nsp_vecs[i]);CHKERRQ(ierr);
    }
  }
  if (coarse_mat) {
    ierr = PetscFree(coarse_nsp_vecs);CHKERRQ(ierr);
    if (pcbddc->dbg_flag) {
      ierr = VecDestroy(&wcoarse_vec);CHKERRQ(ierr);
      ierr = VecDestroy(&wcoarse_rhs);CHKERRQ(ierr);
    }
  }
  ierr = VecDestroy(&local_vec);CHKERRQ(ierr);
  ierr = VecDestroy(&local_primal_vec);CHKERRQ(ierr);
  *CoarseNullSpace = tempCoarseNullSpace;
  PetscFunctionReturn(0);
}

PetscErrorCode MatISGetMPIXAIJ_IS(Mat mat, MatReuse reuse, Mat *M)
{
  Mat_IS         *matis = (Mat_IS*)(mat->data);
  Mat            local_mat;
  /* info on mat */
  PetscInt       bs,rows,cols,lrows,lcols;
  PetscInt       local_rows,local_cols;
  PetscBool      isdense,issbaij,isseqaij;
  PetscMPIInt    nsubdomains;
  /* values insertion */
  PetscScalar    *array;
  /* work */
  PetscErrorCode ierr;

  PetscFunctionBegin;
  /* get info from mat */
  ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&nsubdomains);CHKERRQ(ierr);
  if (nsubdomains == 1) {
    if (reuse == MAT_INITIAL_MATRIX) {
      ierr = MatDuplicate(matis->A,MAT_COPY_VALUES,&(*M));CHKERRQ(ierr);
    } else {
      ierr = MatCopy(matis->A,*M,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
    }
    PetscFunctionReturn(0);
  }
  ierr = MatGetSize(mat,&rows,&cols);CHKERRQ(ierr);
  ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr);
  ierr = MatGetLocalSize(mat,&lrows,&lcols);CHKERRQ(ierr);
  ierr = MatGetSize(matis->A,&local_rows,&local_cols);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQDENSE,&isdense);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQAIJ,&isseqaij);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQSBAIJ,&issbaij);CHKERRQ(ierr);

  if (reuse == MAT_INITIAL_MATRIX) {
    MatType     new_mat_type;
    PetscBool   issbaij_red;

    /* determining new matrix type */
    ierr = MPIU_Allreduce(&issbaij,&issbaij_red,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
    if (issbaij_red) {
      new_mat_type = MATSBAIJ;
    } else {
      if (bs>1) {
        new_mat_type = MATBAIJ;
      } else {
        new_mat_type = MATAIJ;
      }
    }

    ierr = MatCreate(PetscObjectComm((PetscObject)mat),M);CHKERRQ(ierr);
    ierr = MatSetSizes(*M,lrows,lcols,rows,cols);CHKERRQ(ierr);
    ierr = MatSetBlockSize(*M,bs);CHKERRQ(ierr);
    ierr = MatSetType(*M,new_mat_type);CHKERRQ(ierr);
    ierr = MatISSetMPIXAIJPreallocation_Private(mat,*M,PETSC_FALSE);CHKERRQ(ierr);
  } else {
    PetscInt mbs,mrows,mcols,mlrows,mlcols;
    /* some checks */
    ierr = MatGetBlockSize(*M,&mbs);CHKERRQ(ierr);
    ierr = MatGetSize(*M,&mrows,&mcols);CHKERRQ(ierr);
    ierr = MatGetLocalSize(*M,&mlrows,&mlcols);CHKERRQ(ierr);
    if (mrows != rows) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of rows (%d != %d)",rows,mrows);
    if (mcols != cols) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of cols (%d != %d)",cols,mcols);
    if (mlrows != lrows) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of local rows (%d != %d)",lrows,mlrows);
    if (mlcols != lcols) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of local cols (%d != %d)",lcols,mlcols);
    if (mbs != bs) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong block size (%d != %d)",bs,mbs);
    ierr = MatZeroEntries(*M);CHKERRQ(ierr);
  }

  if (issbaij) {
    ierr = MatConvert(matis->A,MATSEQBAIJ,MAT_INITIAL_MATRIX,&local_mat);CHKERRQ(ierr);
  } else {
    ierr = PetscObjectReference((PetscObject)matis->A);CHKERRQ(ierr);
    local_mat = matis->A;
  }

  /* Set values */
  ierr = MatSetLocalToGlobalMapping(*M,mat->rmap->mapping,mat->cmap->mapping);CHKERRQ(ierr);
  if (isdense) { /* special case for dense local matrices */
    PetscInt i,*dummy_rows,*dummy_cols;

    if (local_rows != local_cols) {
      ierr = PetscMalloc2(local_rows,&dummy_rows,local_cols,&dummy_cols);CHKERRQ(ierr);
      for (i=0;i<local_rows;i++) dummy_rows[i] = i;
      for (i=0;i<local_cols;i++) dummy_cols[i] = i;
    } else {
      ierr = PetscMalloc1(local_rows,&dummy_rows);CHKERRQ(ierr);
      for (i=0;i<local_rows;i++) dummy_rows[i] = i;
      dummy_cols = dummy_rows;
    }
    ierr = MatSetOption(*M,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr);
    ierr = MatDenseGetArray(local_mat,&array);CHKERRQ(ierr);
    ierr = MatSetValuesLocal(*M,local_rows,dummy_rows,local_cols,dummy_cols,array,ADD_VALUES);CHKERRQ(ierr);
    ierr = MatDenseRestoreArray(local_mat,&array);CHKERRQ(ierr);
    if (dummy_rows != dummy_cols) {
      ierr = PetscFree2(dummy_rows,dummy_cols);CHKERRQ(ierr);
    } else {
      ierr = PetscFree(dummy_rows);CHKERRQ(ierr);
    }
  } else if (isseqaij) {
    PetscInt  i,nvtxs,*xadj,*adjncy;
//.........这里部分代码省略.........

PETSC_EXTERN PetscErrorCode MatISSetMPIXAIJPreallocation_Private(Mat A, Mat B, PetscBool maxreduce)
{
  Mat_IS          *matis = (Mat_IS*)(A->data);
  PetscInt        *my_dnz,*my_onz,*dnz,*onz,*mat_ranges,*row_ownership;
  const PetscInt  *global_indices_r,*global_indices_c;
  PetscInt        i,j,bs,rows,cols;
  PetscInt        lrows,lcols;
  PetscInt        local_rows,local_cols;
  PetscMPIInt     nsubdomains;
  PetscBool       isdense,issbaij;
  PetscErrorCode  ierr;

  PetscFunctionBegin;
  ierr = MPI_Comm_size(PetscObjectComm((PetscObject)A),&nsubdomains);CHKERRQ(ierr);
  ierr = MatGetSize(A,&rows,&cols);CHKERRQ(ierr);
  ierr = MatGetBlockSize(A,&bs);CHKERRQ(ierr);
  ierr = MatGetSize(matis->A,&local_rows,&local_cols);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQDENSE,&isdense);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQSBAIJ,&issbaij);CHKERRQ(ierr);
  ierr = ISLocalToGlobalMappingGetIndices(A->rmap->mapping,&global_indices_r);CHKERRQ(ierr);
  if (A->rmap->mapping != A->cmap->mapping) {
    ierr = ISLocalToGlobalMappingGetIndices(A->rmap->mapping,&global_indices_c);CHKERRQ(ierr);
  } else {
    global_indices_c = global_indices_r;
  }

  if (issbaij) {
    ierr = MatGetRowUpperTriangular(matis->A);CHKERRQ(ierr);
  }
  /*
     An SF reduce is needed to sum up properly on shared rows.
     Note that generally preallocation is not exact, since it overestimates nonzeros
  */
  if (!matis->sf) { /* setup SF if not yet created and allocate rootdata and leafdata */
    ierr = MatISComputeSF_Private(A);CHKERRQ(ierr);
  }
  ierr = MatGetLocalSize(A,&lrows,&lcols);CHKERRQ(ierr);
  ierr = MatPreallocateInitialize(PetscObjectComm((PetscObject)A),lrows,lcols,dnz,onz);CHKERRQ(ierr);
  /* All processes need to compute entire row ownership */
  ierr = PetscMalloc1(rows,&row_ownership);CHKERRQ(ierr);
  ierr = MatGetOwnershipRanges(A,(const PetscInt**)&mat_ranges);CHKERRQ(ierr);
  for (i=0;i<nsubdomains;i++) {
    for (j=mat_ranges[i];j<mat_ranges[i+1];j++) {
      row_ownership[j] = i;
    }
  }

  /*
     my_dnz and my_onz contains exact contribution to preallocation from each local mat
     then, they will be summed up properly. This way, preallocation is always sufficient
  */
  ierr = PetscCalloc2(local_rows,&my_dnz,local_rows,&my_onz);CHKERRQ(ierr);
  /* preallocation as a MATAIJ */
  if (isdense) { /* special case for dense local matrices */
    for (i=0;i<local_rows;i++) {
      PetscInt index_row = global_indices_r[i];
      for (j=i;j<local_rows;j++) {
        PetscInt owner = row_ownership[index_row];
        PetscInt index_col = global_indices_c[j];
        if (index_col > mat_ranges[owner]-1 && index_col < mat_ranges[owner+1] ) { /* diag block */
          my_dnz[i] += 1;
        } else { /* offdiag block */
          my_onz[i] += 1;
        }
        /* same as before, interchanging rows and cols */
        if (i != j) {
          owner = row_ownership[index_col];
          if (index_row > mat_ranges[owner]-1 && index_row < mat_ranges[owner+1] ) {
            my_dnz[j] += 1;
          } else {
            my_onz[j] += 1;
          }
        }
      }
    }
  } else { /* TODO: this could be optimized using MatGetRowIJ */
    for (i=0;i<local_rows;i++) {
      const PetscInt *cols;
      PetscInt       ncols,index_row = global_indices_r[i];
      ierr = MatGetRow(matis->A,i,&ncols,&cols,NULL);CHKERRQ(ierr);
      for (j=0;j<ncols;j++) {
        PetscInt owner = row_ownership[index_row];
        PetscInt index_col = global_indices_c[cols[j]];
        if (index_col > mat_ranges[owner]-1 && index_col < mat_ranges[owner+1] ) { /* diag block */
          my_dnz[i] += 1;
        } else { /* offdiag block */
          my_onz[i] += 1;
        }
        /* same as before, interchanging rows and cols */
        if (issbaij && index_col != index_row) {
          owner = row_ownership[index_col];
          if (index_row > mat_ranges[owner]-1 && index_row < mat_ranges[owner+1] ) {
            my_dnz[cols[j]] += 1;
          } else {
            my_onz[cols[j]] += 1;
          }
        }
      }
      ierr = MatRestoreRow(matis->A,i,&ncols,&cols,NULL);CHKERRQ(ierr);
    }
//.........这里部分代码省略.........

static PetscErrorCode PCBDDCScalingSetUp_Deluxe_Private(PC pc)
{
  PC_BDDC                *pcbddc=(PC_BDDC*)pc->data;
  PCBDDCDeluxeScaling    deluxe_ctx=pcbddc->deluxe_ctx;
  PCBDDCSubSchurs        sub_schurs = pcbddc->sub_schurs;
  PetscScalar            *matdata,*matdata2;
  PetscInt               i,max_subset_size,cum,cum2;
  const PetscInt         *idxs;
  PetscBool              newsetup = PETSC_FALSE;
  PetscErrorCode         ierr;

  PetscFunctionBegin;
  if (!sub_schurs) SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_PLIB,"Missing PCBDDCSubSchurs");
  if (!sub_schurs->n_subs) PetscFunctionReturn(0);

  /* Allocate arrays for subproblems */
  if (!deluxe_ctx->seq_n) {
    deluxe_ctx->seq_n = sub_schurs->n_subs;
    ierr = PetscCalloc5(deluxe_ctx->seq_n,&deluxe_ctx->seq_scctx,deluxe_ctx->seq_n,&deluxe_ctx->seq_work1,deluxe_ctx->seq_n,&deluxe_ctx->seq_work2,deluxe_ctx->seq_n,&deluxe_ctx->seq_mat,deluxe_ctx->seq_n,&deluxe_ctx->seq_mat_inv_sum);CHKERRQ(ierr);
    newsetup = PETSC_TRUE;
  } else if (deluxe_ctx->seq_n != sub_schurs->n_subs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Number of deluxe subproblems %D is different from the sub_schurs %D",deluxe_ctx->seq_n,sub_schurs->n_subs);

  /* the change of basis is just a reference to sub_schurs->change (if any) */
  deluxe_ctx->change         = sub_schurs->change;
  deluxe_ctx->change_with_qr = sub_schurs->change_with_qr;

  /* Create objects for deluxe */
  max_subset_size = 0;
  for (i=0;i<sub_schurs->n_subs;i++) {
    PetscInt subset_size;
    ierr = ISGetLocalSize(sub_schurs->is_subs[i],&subset_size);CHKERRQ(ierr);
    max_subset_size = PetscMax(subset_size,max_subset_size);
  }
  if (newsetup) {
    ierr = PetscMalloc1(2*max_subset_size,&deluxe_ctx->workspace);CHKERRQ(ierr);
  }
  cum = cum2 = 0;
  ierr = ISGetIndices(sub_schurs->is_Ej_all,&idxs);CHKERRQ(ierr);
  ierr = MatSeqAIJGetArray(sub_schurs->S_Ej_all,&matdata);CHKERRQ(ierr);
  ierr = MatSeqAIJGetArray(sub_schurs->sum_S_Ej_all,&matdata2);CHKERRQ(ierr);
  for (i=0;i<deluxe_ctx->seq_n;i++) {
    PetscInt     subset_size;

    ierr = ISGetLocalSize(sub_schurs->is_subs[i],&subset_size);CHKERRQ(ierr);
    if (newsetup) {
      IS  sub;
      /* work vectors */
      ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,subset_size,deluxe_ctx->workspace,&deluxe_ctx->seq_work1[i]);CHKERRQ(ierr);
      ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,subset_size,deluxe_ctx->workspace+subset_size,&deluxe_ctx->seq_work2[i]);CHKERRQ(ierr);

      /* scatters */
      ierr = ISCreateGeneral(PETSC_COMM_SELF,subset_size,idxs+cum,PETSC_COPY_VALUES,&sub);CHKERRQ(ierr);
      ierr = VecScatterCreate(pcbddc->work_scaling,sub,deluxe_ctx->seq_work1[i],NULL,&deluxe_ctx->seq_scctx[i]);CHKERRQ(ierr);
      ierr = ISDestroy(&sub);CHKERRQ(ierr);
    }

    /* S_E_j */
    ierr = MatDestroy(&deluxe_ctx->seq_mat[i]);CHKERRQ(ierr);
    ierr = MatCreateSeqDense(PETSC_COMM_SELF,subset_size,subset_size,matdata+cum2,&deluxe_ctx->seq_mat[i]);CHKERRQ(ierr);

    /* \sum_k S^k_E_j */
    ierr = MatDestroy(&deluxe_ctx->seq_mat_inv_sum[i]);CHKERRQ(ierr);
    ierr = MatCreateSeqDense(PETSC_COMM_SELF,subset_size,subset_size,matdata2+cum2,&deluxe_ctx->seq_mat_inv_sum[i]);CHKERRQ(ierr);
    ierr = MatSetOption(deluxe_ctx->seq_mat_inv_sum[i],MAT_SPD,sub_schurs->is_posdef);CHKERRQ(ierr);
    ierr = MatSetOption(deluxe_ctx->seq_mat_inv_sum[i],MAT_HERMITIAN,sub_schurs->is_hermitian);CHKERRQ(ierr);
    if (sub_schurs->is_hermitian) {
      ierr = MatCholeskyFactor(deluxe_ctx->seq_mat_inv_sum[i],NULL,NULL);CHKERRQ(ierr);
    } else {
      ierr = MatLUFactor(deluxe_ctx->seq_mat_inv_sum[i],NULL,NULL,NULL);CHKERRQ(ierr);
    }
    if (pcbddc->deluxe_singlemat) {
      Mat X,Y;
      if (!sub_schurs->is_hermitian) {
        ierr = MatTranspose(deluxe_ctx->seq_mat[i],MAT_INITIAL_MATRIX,&X);CHKERRQ(ierr);
      } else {
        ierr = PetscObjectReference((PetscObject)deluxe_ctx->seq_mat[i]);CHKERRQ(ierr);
        X    = deluxe_ctx->seq_mat[i];
      }
      ierr = MatDuplicate(X,MAT_DO_NOT_COPY_VALUES,&Y);CHKERRQ(ierr);
      if (!sub_schurs->is_hermitian) {
        ierr = PCBDDCMatTransposeMatSolve_SeqDense(deluxe_ctx->seq_mat_inv_sum[i],X,Y);CHKERRQ(ierr);
      } else {
        ierr = MatMatSolve(deluxe_ctx->seq_mat_inv_sum[i],X,Y);CHKERRQ(ierr);
      }

      ierr = MatDestroy(&deluxe_ctx->seq_mat_inv_sum[i]);CHKERRQ(ierr);
      ierr = MatDestroy(&deluxe_ctx->seq_mat[i]);CHKERRQ(ierr);
      ierr = MatDestroy(&X);CHKERRQ(ierr);
      if (deluxe_ctx->change) {
        Mat C,CY;

        if (!deluxe_ctx->change_with_qr) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only QR based change of basis");
        ierr = KSPGetOperators(deluxe_ctx->change[i],&C,NULL);CHKERRQ(ierr);
        ierr = MatMatMult(C,Y,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&CY);CHKERRQ(ierr);
        ierr = MatMatTransposeMult(CY,C,MAT_REUSE_MATRIX,PETSC_DEFAULT,&Y);CHKERRQ(ierr);
        ierr = MatDestroy(&CY);CHKERRQ(ierr);
      }
      ierr = MatTranspose(Y,MAT_INPLACE_MATRIX,&Y);CHKERRQ(ierr);
      deluxe_ctx->seq_mat[i] = Y;
    }
//.........这里部分代码省略.........

int main(int argc,char **argv)
{
  PetscMPIInt      rank;
  PetscErrorCode   ierr;
  PetscInt         M = 10,N = 8,m = PETSC_DECIDE;
  PetscInt         s =2,w=2,n = PETSC_DECIDE,nloc,l,i,j,kk;
  PetscInt         Xs,Xm,Ys,Ym,iloc,*iglobal;
  const PetscInt   *ltog;
  PetscInt         *lx       = NULL,*ly = NULL;
  PetscBool        testorder = PETSC_FALSE,flg;
  DMBoundaryType   bx        = DM_BOUNDARY_NONE,by= DM_BOUNDARY_NONE;
  DM               da;
  PetscViewer      viewer;
  Vec              local,global;
  PetscScalar      value;
  DMDAStencilType  st = DMDA_STENCIL_BOX;
  AO               ao;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",300,0,400,400,&viewer);CHKERRQ(ierr);

  /* Readoptions */
  ierr = PetscOptionsGetInt(NULL,NULL,"-NX",&M,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-NY",&N,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-m",&m,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-s",&s,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-w",&w,NULL);CHKERRQ(ierr);

  flg  = PETSC_FALSE;
  ierr = PetscOptionsGetBool(NULL,NULL,"-xperiodic",&flg,NULL);CHKERRQ(ierr); if (flg) bx = DM_BOUNDARY_PERIODIC;
  flg  = PETSC_FALSE;
  ierr = PetscOptionsGetBool(NULL,NULL,"-yperiodic",&flg,NULL);CHKERRQ(ierr); if (flg) by = DM_BOUNDARY_PERIODIC;
  flg  = PETSC_FALSE;
  ierr = PetscOptionsGetBool(NULL,NULL,"-xghosted",&flg,NULL);CHKERRQ(ierr); if (flg) bx = DM_BOUNDARY_GHOSTED;
  flg  = PETSC_FALSE;
  ierr = PetscOptionsGetBool(NULL,NULL,"-yghosted",&flg,NULL);CHKERRQ(ierr); if (flg) by = DM_BOUNDARY_GHOSTED;
  flg  = PETSC_FALSE;
  ierr = PetscOptionsGetBool(NULL,NULL,"-star",&flg,NULL);CHKERRQ(ierr); if (flg) st = DMDA_STENCIL_STAR;
  flg  = PETSC_FALSE;
  ierr = PetscOptionsGetBool(NULL,NULL,"-box",&flg,NULL);CHKERRQ(ierr); if (flg) st = DMDA_STENCIL_BOX;
  flg  = PETSC_FALSE;
  ierr = PetscOptionsGetBool(NULL,NULL,"-testorder",&testorder,NULL);CHKERRQ(ierr);
  /*
      Test putting two nodes in x and y on each processor, exact last processor
      in x and y gets the rest.
  */
  flg  = PETSC_FALSE;
  ierr = PetscOptionsGetBool(NULL,NULL,"-distribute",&flg,NULL);CHKERRQ(ierr);
  if (flg) {
    if (m == PETSC_DECIDE) SETERRQ(PETSC_COMM_WORLD,1,"Must set -m option with -distribute option");
    ierr = PetscMalloc1(m,&lx);CHKERRQ(ierr);
    for (i=0; i<m-1; i++) { lx[i] = 4;}
    lx[m-1] = M - 4*(m-1);
    if (n == PETSC_DECIDE) SETERRQ(PETSC_COMM_WORLD,1,"Must set -n option with -distribute option");
    ierr = PetscMalloc1(n,&ly);CHKERRQ(ierr);
    for (i=0; i<n-1; i++) { ly[i] = 2;}
    ly[n-1] = N - 2*(n-1);
  }


  /* Create distributed array and get vectors */
  ierr = DMDACreate2d(PETSC_COMM_WORLD,bx,by,st,M,N,m,n,w,s,lx,ly,&da);CHKERRQ(ierr);
  ierr = PetscFree(lx);CHKERRQ(ierr);
  ierr = PetscFree(ly);CHKERRQ(ierr);

  ierr = DMView(da,viewer);CHKERRQ(ierr);
  ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
  ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);

  /* Set global vector; send ghost points to local vectors */
  value = 1;
  ierr = VecSet(global,value);CHKERRQ(ierr);
  ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);

  /* Scale local vectors according to processor rank; pass to global vector */
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
  value = rank;
  ierr = VecScale(local,value);CHKERRQ(ierr);
  ierr = DMLocalToGlobalBegin(da,local,INSERT_VALUES,global);CHKERRQ(ierr);
  ierr = DMLocalToGlobalEnd(da,local,INSERT_VALUES,global);CHKERRQ(ierr);

  if (!testorder) { /* turn off printing when testing ordering mappings */
    ierr = PetscPrintf(PETSC_COMM_WORLD,"\nGlobal Vectors:\n");CHKERRQ(ierr);
    ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
    ierr = PetscPrintf(PETSC_COMM_WORLD,"\n\n");CHKERRQ(ierr);
  }

  /* Send ghost points to local vectors */
  ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);

  flg  = PETSC_FALSE;
  ierr = PetscOptionsGetBool(NULL,NULL,"-local_print",&flg,NULL);CHKERRQ(ierr);
  if (flg) {
    PetscViewer sviewer;

    ierr = PetscViewerASCIIPushSynchronized(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
    ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\nLocal Vector: processor %d\n",rank);CHKERRQ(ierr);
//.........这里部分代码省略.........

PetscErrorCode PCGAMGFilterGraph(Mat *a_Gmat,const PetscReal vfilter,const PetscBool symm,const PetscInt verbose)
{
  PetscErrorCode    ierr;
  PetscInt          Istart,Iend,Ii,jj,ncols,nnz0,nnz1, NN, MM, nloc;
  PetscMPIInt       rank, size;
  Mat               Gmat  = *a_Gmat, tGmat, matTrans;
  MPI_Comm          comm;
  const PetscScalar *vals;
  const PetscInt    *idx;
  PetscInt          *d_nnz, *o_nnz;
  Vec               diag;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)Gmat,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr);
  nloc = Iend - Istart;
  ierr = MatGetSize(Gmat, &MM, &NN);CHKERRQ(ierr);
#if defined PETSC_GAMG_USE_LOG
  ierr = PetscLogEventBegin(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr);
#endif
  /* scale Gmat so filter works */
  ierr = MatGetVecs(Gmat, &diag, 0);CHKERRQ(ierr);
  ierr = MatGetDiagonal(Gmat, diag);CHKERRQ(ierr);
  ierr = VecReciprocal(diag);CHKERRQ(ierr);
  ierr = VecSqrtAbs(diag);CHKERRQ(ierr);
  ierr = MatDiagonalScale(Gmat, diag, diag);CHKERRQ(ierr);
  ierr = VecDestroy(&diag);CHKERRQ(ierr);

  if (symm) {
    ierr = MatTranspose(Gmat, MAT_INITIAL_MATRIX, &matTrans);CHKERRQ(ierr);
  }

  /* filter - dup zeros out matrix */
  ierr = PetscMalloc1(nloc, &d_nnz);CHKERRQ(ierr);
  ierr = PetscMalloc1(nloc, &o_nnz);CHKERRQ(ierr);
  for (Ii = Istart, jj = 0; Ii < Iend; Ii++, jj++) {
    ierr      = MatGetRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
    d_nnz[jj] = ncols;
    o_nnz[jj] = ncols;
    ierr      = MatRestoreRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
    if (symm) {
      ierr       = MatGetRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
      d_nnz[jj] += ncols;
      o_nnz[jj] += ncols;
      ierr       = MatRestoreRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
    }
    if (d_nnz[jj] > nloc) d_nnz[jj] = nloc;
    if (o_nnz[jj] > (MM-nloc)) o_nnz[jj] = MM - nloc;
  }
  ierr = MatCreateAIJ(comm, nloc, nloc, MM, MM, 0, d_nnz, 0, o_nnz, &tGmat);CHKERRQ(ierr);
  ierr = PetscFree(d_nnz);CHKERRQ(ierr);
  ierr = PetscFree(o_nnz);CHKERRQ(ierr);
  if (symm) {
    ierr = MatDestroy(&matTrans);CHKERRQ(ierr);
  }

  for (Ii = Istart, nnz0 = nnz1 = 0; Ii < Iend; Ii++) {
    ierr = MatGetRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr);
    for (jj=0; jj<ncols; jj++,nnz0++) {
      PetscScalar sv = PetscAbs(PetscRealPart(vals[jj]));
      if (PetscRealPart(sv) > vfilter) {
        nnz1++;
        if (symm) {
          sv  *= 0.5;
          ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr);
          ierr = MatSetValues(tGmat,1,&idx[jj],1,&Ii,&sv,ADD_VALUES);CHKERRQ(ierr);
        } else {
          ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr);
        }
      }
    }
    ierr = MatRestoreRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr);
  }
  ierr = MatAssemblyBegin(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

#if defined PETSC_GAMG_USE_LOG
  ierr = PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr);
#endif

  if (verbose) {
    if (verbose == 1) {
      ierr = PetscPrintf(comm,"\t[%d]%s %g%% nnz after filtering, with threshold %g, %g nnz ave. (N=%d)\n",rank,__FUNCT__,
                         100.*(double)nnz1/(double)nnz0,vfilter,(double)nnz0/(double)nloc,MM);CHKERRQ(ierr);
    } else {
      PetscInt nnz[2],out[2];
      nnz[0] = nnz0; nnz[1] = nnz1;
      ierr   = MPI_Allreduce(nnz, out, 2, MPIU_INT, MPI_SUM, comm);CHKERRQ(ierr);
      ierr   = PetscPrintf(comm,"\t[%d]%s %g%% nnz after filtering, with threshold %g, %g nnz ave. (N=%d)\n",rank,__FUNCT__,
                           100.*(double)out[1]/(double)out[0],vfilter,(double)out[0]/(double)MM,MM);CHKERRQ(ierr);
    }
  }
  ierr    = MatDestroy(&Gmat);CHKERRQ(ierr);
  *a_Gmat = tGmat;
  PetscFunctionReturn(0);
}