xref: /petsc/src/dm/impls/da/fdda.c (revision b06ff27eac5114371f4ff10d36699518dda77a85)

#include <petsc/private/dmdaimpl.h> /*I      "petscdmda.h"     I*/
#include <petscmat.h>

extern PetscErrorCode DMCreateColoring_DA_1d_MPIAIJ(DM,ISColoringType,ISColoring*);
extern PetscErrorCode DMCreateColoring_DA_2d_MPIAIJ(DM,ISColoringType,ISColoring*);
extern PetscErrorCode DMCreateColoring_DA_2d_5pt_MPIAIJ(DM,ISColoringType,ISColoring*);
extern PetscErrorCode DMCreateColoring_DA_3d_MPIAIJ(DM,ISColoringType,ISColoring*);

/*
   For ghost i that may be negative or greater than the upper bound this
  maps it into the 0:m-1 range using periodicity
*/
#define SetInRange(i,m) ((i < 0) ? m+i : ((i >= m) ? i-m : i))

static PetscErrorCode DMDASetBlockFills_Private(const PetscInt *dfill,PetscInt w,PetscInt **rfill)
{
  PetscErrorCode ierr;
  PetscInt       i,j,nz,*fill;

  PetscFunctionBegin;
  if (!dfill) PetscFunctionReturn(0);

  /* count number nonzeros */
  nz = 0;
  for (i=0; i<w; i++) {
    for (j=0; j<w; j++) {
      if (dfill[w*i+j]) nz++;
    }
  }
  ierr = PetscMalloc1(nz + w + 1,&fill);CHKERRQ(ierr);
  /* construct modified CSR storage of nonzero structure */
  /*  fill[0 -- w] marks starts of each row of column indices (and end of last row)
   so fill[1] - fill[0] gives number of nonzeros in first row etc */
  nz = w + 1;
  for (i=0; i<w; i++) {
    fill[i] = nz;
    for (j=0; j<w; j++) {
      if (dfill[w*i+j]) {
        fill[nz] = j;
        nz++;
      }
    }
  }
  fill[w] = nz;

  *rfill = fill;
  PetscFunctionReturn(0);
}

/*@
    DMDASetBlockFills - Sets the fill pattern in each block for a multi-component problem
    of the matrix returned by DMCreateMatrix().

    Logically Collective on DMDA

    Input Parameter:
+   da - the distributed array
.   dfill - the fill pattern in the diagonal block (may be NULL, means use dense block)
-   ofill - the fill pattern in the off-diagonal blocks


    Level: developer

    Notes: This only makes sense when you are doing multicomponent problems but using the
       MPIAIJ matrix format

           The format for dfill and ofill is a 2 dimensional dof by dof matrix with 1 entries
       representing coupling and 0 entries for missing coupling. For example
$             dfill[9] = {1, 0, 0,
$                         1, 1, 0,
$                         0, 1, 1}
       means that row 0 is coupled with only itself in the diagonal block, row 1 is coupled with
       itself and row 0 (in the diagonal block) and row 2 is coupled with itself and row 1 (in the
       diagonal block).

     DMDASetGetMatrix() allows you to provide general code for those more complicated nonzero patterns then
     can be represented in the dfill, ofill format

   Contributed by Glenn Hammond

.seealso DMCreateMatrix(), DMDASetGetMatrix(), DMSetMatrixPreallocateOnly()

@*/
PetscErrorCode  DMDASetBlockFills(DM da,const PetscInt *dfill,const PetscInt *ofill)
{
  DM_DA          *dd = (DM_DA*)da->data;
  PetscErrorCode ierr;
  PetscInt       i,k,cnt = 1;

  PetscFunctionBegin;
  ierr = DMDASetBlockFills_Private(dfill,dd->w,&dd->dfill);CHKERRQ(ierr);
  ierr = DMDASetBlockFills_Private(ofill,dd->w,&dd->ofill);CHKERRQ(ierr);

  /* ofillcount tracks the columns of ofill that have any nonzero in thems; the value in each location is the number of
   columns to the left with any nonzeros in them plus 1 */
  ierr = PetscCalloc1(dd->w,&dd->ofillcols);CHKERRQ(ierr);
  for (i=0; i<dd->w; i++) {
    for (k=dd->ofill[i]; k<dd->ofill[i+1]; k++) dd->ofillcols[dd->ofill[k]] = 1;
  }
  for (i=0; i<dd->w; i++) {
    if (dd->ofillcols[i]) {
      dd->ofillcols[i] = cnt++;
    }
  }
  PetscFunctionReturn(0);
}


PetscErrorCode  DMCreateColoring_DA(DM da,ISColoringType ctype,ISColoring *coloring)
{
  PetscErrorCode   ierr;
  PetscInt         dim,m,n,p,nc;
  DMBoundaryType bx,by,bz;
  MPI_Comm         comm;
  PetscMPIInt      size;
  PetscBool        isBAIJ;
  DM_DA            *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  /*
                                  m
          ------------------------------------------------------
         |                                                     |
         |                                                     |
         |               ----------------------                |
         |               |                    |                |
      n  |           yn  |                    |                |
         |               |                    |                |
         |               .---------------------                |
         |             (xs,ys)     xn                          |
         |            .                                        |
         |         (gxs,gys)                                   |
         |                                                     |
          -----------------------------------------------------
  */

  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  ierr = DMDAGetInfo(da,&dim,0,0,0,&m,&n,&p,&nc,0,&bx,&by,&bz,0);CHKERRQ(ierr);

  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  if (ctype == IS_COLORING_LOCAL) {
    if (size == 1) {
      ctype = IS_COLORING_GLOBAL;
    } else if (dim > 1) {
      if ((m==1 && bx == DM_BOUNDARY_PERIODIC) || (n==1 && by == DM_BOUNDARY_PERIODIC) || (p==1 && bz == DM_BOUNDARY_PERIODIC)) {
        SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"IS_COLORING_LOCAL cannot be used for periodic boundary condition having both ends of the domain  on the same process");
      }
    }
  }

  /* Tell the DMDA it has 1 degree of freedom per grid point so that the coloring for BAIJ
     matrices is for the blocks, not the individual matrix elements  */
  ierr = PetscStrcmp(da->mattype,MATBAIJ,&isBAIJ);CHKERRQ(ierr);
  if (!isBAIJ) {ierr = PetscStrcmp(da->mattype,MATMPIBAIJ,&isBAIJ);CHKERRQ(ierr);}
  if (!isBAIJ) {ierr = PetscStrcmp(da->mattype,MATSEQBAIJ,&isBAIJ);CHKERRQ(ierr);}
  if (isBAIJ) {
    dd->w  = 1;
    dd->xs = dd->xs/nc;
    dd->xe = dd->xe/nc;
    dd->Xs = dd->Xs/nc;
    dd->Xe = dd->Xe/nc;
  }

  /*
     We do not provide a getcoloring function in the DMDA operations because
   the basic DMDA does not know about matrices. We think of DMDA as being more
   more low-level then matrices.
  */
  if (dim == 1) {
    ierr = DMCreateColoring_DA_1d_MPIAIJ(da,ctype,coloring);CHKERRQ(ierr);
  } else if (dim == 2) {
    ierr =  DMCreateColoring_DA_2d_MPIAIJ(da,ctype,coloring);CHKERRQ(ierr);
  } else if (dim == 3) {
    ierr =  DMCreateColoring_DA_3d_MPIAIJ(da,ctype,coloring);CHKERRQ(ierr);
  } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Not done for %D dimension, send us mail petsc-maint@mcs.anl.gov for code",dim);
  if (isBAIJ) {
    dd->w  = nc;
    dd->xs = dd->xs*nc;
    dd->xe = dd->xe*nc;
    dd->Xs = dd->Xs*nc;
    dd->Xe = dd->Xe*nc;
  }
  PetscFunctionReturn(0);
}

/* ---------------------------------------------------------------------------------*/

PetscErrorCode DMCreateColoring_DA_2d_MPIAIJ(DM da,ISColoringType ctype,ISColoring *coloring)
{
  PetscErrorCode   ierr;
  PetscInt         xs,ys,nx,ny,i,j,ii,gxs,gys,gnx,gny,m,n,M,N,dim,s,k,nc,col;
  PetscInt         ncolors;
  MPI_Comm         comm;
  DMBoundaryType bx,by;
  DMDAStencilType  st;
  ISColoringValue  *colors;
  DM_DA            *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  ierr = DMDAGetInfo(da,&dim,&m,&n,0,&M,&N,0,&nc,&s,&bx,&by,0,&st);CHKERRQ(ierr);
  col  = 2*s + 1;
  ierr = DMDAGetCorners(da,&xs,&ys,0,&nx,&ny,0);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,&gys,0,&gnx,&gny,0);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  /* special case as taught to us by Paul Hovland */
  if (st == DMDA_STENCIL_STAR && s == 1) {
    ierr = DMCreateColoring_DA_2d_5pt_MPIAIJ(da,ctype,coloring);CHKERRQ(ierr);
  } else {

    if (bx == DM_BOUNDARY_PERIODIC && (m % col)) SETERRQ2(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"For coloring efficiency ensure number of grid points in X (%d) is divisible\n\
                                                            by 2*stencil_width + 1 (%d)\n", m, col);
    if (by == DM_BOUNDARY_PERIODIC && (n % col)) SETERRQ2(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"For coloring efficiency ensure number of grid points in Y (%d) is divisible\n\
                                                            by 2*stencil_width + 1 (%d)\n", n, col);
    if (ctype == IS_COLORING_GLOBAL) {
      if (!dd->localcoloring) {
        ierr = PetscMalloc1(nc*nx*ny,&colors);CHKERRQ(ierr);
        ii   = 0;
        for (j=ys; j<ys+ny; j++) {
          for (i=xs; i<xs+nx; i++) {
            for (k=0; k<nc; k++) {
              colors[ii++] = k + nc*((i % col) + col*(j % col));
            }
          }
        }
        ncolors = nc + nc*(col-1 + col*(col-1));
        ierr    = ISColoringCreate(comm,ncolors,nc*nx*ny,colors,PETSC_OWN_POINTER,&dd->localcoloring);CHKERRQ(ierr);
      }
      *coloring = dd->localcoloring;
    } else if (ctype == IS_COLORING_LOCAL) {
      if (!dd->ghostedcoloring) {
        ierr = PetscMalloc1(nc*gnx*gny,&colors);CHKERRQ(ierr);
        ii   = 0;
        for (j=gys; j<gys+gny; j++) {
          for (i=gxs; i<gxs+gnx; i++) {
            for (k=0; k<nc; k++) {
              /* the complicated stuff is to handle periodic boundaries */
              colors[ii++] = k + nc*((SetInRange(i,m) % col) + col*(SetInRange(j,n) % col));
            }
          }
        }
        ncolors = nc + nc*(col - 1 + col*(col-1));
        ierr    = ISColoringCreate(comm,ncolors,nc*gnx*gny,colors,PETSC_OWN_POINTER,&dd->ghostedcoloring);CHKERRQ(ierr);
        /* PetscIntView(ncolors,(PetscInt*)colors,0); */

        ierr = ISColoringSetType(dd->ghostedcoloring,IS_COLORING_LOCAL);CHKERRQ(ierr);
      }
      *coloring = dd->ghostedcoloring;
    } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Unknown ISColoringType %d",(int)ctype);
  }
  ierr = ISColoringReference(*coloring);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/* ---------------------------------------------------------------------------------*/

PetscErrorCode DMCreateColoring_DA_3d_MPIAIJ(DM da,ISColoringType ctype,ISColoring *coloring)
{
  PetscErrorCode   ierr;
  PetscInt         xs,ys,nx,ny,i,j,gxs,gys,gnx,gny,m,n,p,dim,s,k,nc,col,zs,gzs,ii,l,nz,gnz,M,N,P;
  PetscInt         ncolors;
  MPI_Comm         comm;
  DMBoundaryType bx,by,bz;
  DMDAStencilType  st;
  ISColoringValue  *colors;
  DM_DA            *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  ierr = DMDAGetInfo(da,&dim,&m,&n,&p,&M,&N,&P,&nc,&s,&bx,&by,&bz,&st);CHKERRQ(ierr);
  col  = 2*s + 1;
  if (bx == DM_BOUNDARY_PERIODIC && (m % col)) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"For coloring efficiency ensure number of grid points in X is divisible\n\
                                                         by 2*stencil_width + 1\n");
  if (by == DM_BOUNDARY_PERIODIC && (n % col)) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"For coloring efficiency ensure number of grid points in Y is divisible\n\
                                                         by 2*stencil_width + 1\n");
  if (bz == DM_BOUNDARY_PERIODIC && (p % col)) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"For coloring efficiency ensure number of grid points in Z is divisible\n\
                                                         by 2*stencil_width + 1\n");

  ierr = DMDAGetCorners(da,&xs,&ys,&zs,&nx,&ny,&nz);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,&gys,&gzs,&gnx,&gny,&gnz);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  /* create the coloring */
  if (ctype == IS_COLORING_GLOBAL) {
    if (!dd->localcoloring) {
      ierr = PetscMalloc1(nc*nx*ny*nz,&colors);CHKERRQ(ierr);
      ii   = 0;
      for (k=zs; k<zs+nz; k++) {
        for (j=ys; j<ys+ny; j++) {
          for (i=xs; i<xs+nx; i++) {
            for (l=0; l<nc; l++) {
              colors[ii++] = l + nc*((i % col) + col*(j % col) + col*col*(k % col));
            }
          }
        }
      }
      ncolors = nc + nc*(col-1 + col*(col-1)+ col*col*(col-1));
      ierr    = ISColoringCreate(comm,ncolors,nc*nx*ny*nz,colors,PETSC_OWN_POINTER,&dd->localcoloring);CHKERRQ(ierr);
    }
    *coloring = dd->localcoloring;
  } else if (ctype == IS_COLORING_LOCAL) {
    if (!dd->ghostedcoloring) {
      ierr = PetscMalloc1(nc*gnx*gny*gnz,&colors);CHKERRQ(ierr);
      ii   = 0;
      for (k=gzs; k<gzs+gnz; k++) {
        for (j=gys; j<gys+gny; j++) {
          for (i=gxs; i<gxs+gnx; i++) {
            for (l=0; l<nc; l++) {
              /* the complicated stuff is to handle periodic boundaries */
              colors[ii++] = l + nc*((SetInRange(i,m) % col) + col*(SetInRange(j,n) % col) + col*col*(SetInRange(k,p) % col));
            }
          }
        }
      }
      ncolors = nc + nc*(col-1 + col*(col-1)+ col*col*(col-1));
      ierr    = ISColoringCreate(comm,ncolors,nc*gnx*gny*gnz,colors,PETSC_OWN_POINTER,&dd->ghostedcoloring);CHKERRQ(ierr);
      ierr    = ISColoringSetType(dd->ghostedcoloring,IS_COLORING_LOCAL);CHKERRQ(ierr);
    }
    *coloring = dd->ghostedcoloring;
  } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Unknown ISColoringType %d",(int)ctype);
  ierr = ISColoringReference(*coloring);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/* ---------------------------------------------------------------------------------*/

PetscErrorCode DMCreateColoring_DA_1d_MPIAIJ(DM da,ISColoringType ctype,ISColoring *coloring)
{
  PetscErrorCode   ierr;
  PetscInt         xs,nx,i,i1,gxs,gnx,l,m,M,dim,s,nc,col;
  PetscInt         ncolors;
  MPI_Comm         comm;
  DMBoundaryType bx;
  ISColoringValue  *colors;
  DM_DA            *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  ierr = DMDAGetInfo(da,&dim,&m,0,0,&M,0,0,&nc,&s,&bx,0,0,0);CHKERRQ(ierr);
  col  = 2*s + 1;

  if (bx == DM_BOUNDARY_PERIODIC && (m % col)) SETERRQ2(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"For coloring efficiency ensure number of grid points %d is divisible\n\
                                                          by 2*stencil_width + 1 %d\n",(int)m,(int)col);

  ierr = DMDAGetCorners(da,&xs,0,0,&nx,0,0);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,0,0,&gnx,0,0);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  /* create the coloring */
  if (ctype == IS_COLORING_GLOBAL) {
    if (!dd->localcoloring) {
      ierr = PetscMalloc1(nc*nx,&colors);CHKERRQ(ierr);
      if (dd->ofillcols) {
        PetscInt tc = 0;
        for (i=0; i<nc; i++) tc += (PetscInt) (dd->ofillcols[i] > 0);
        i1 = 0;
        for (i=xs; i<xs+nx; i++) {
          for (l=0; l<nc; l++) {
            if (dd->ofillcols[l] && (i % col)) {
              colors[i1++] =  nc - 1 + tc*((i % col) - 1) + dd->ofillcols[l];
            } else {
              colors[i1++] = l;
            }
          }
        }
        ncolors = nc + 2*s*tc;
      } else {
        i1 = 0;
        for (i=xs; i<xs+nx; i++) {
          for (l=0; l<nc; l++) {
            colors[i1++] = l + nc*(i % col);
          }
        }
        ncolors = nc + nc*(col-1);
      }
      ierr = ISColoringCreate(comm,ncolors,nc*nx,colors,PETSC_OWN_POINTER,&dd->localcoloring);CHKERRQ(ierr);
    }
    *coloring = dd->localcoloring;
  } else if (ctype == IS_COLORING_LOCAL) {
    if (!dd->ghostedcoloring) {
      ierr = PetscMalloc1(nc*gnx,&colors);CHKERRQ(ierr);
      i1   = 0;
      for (i=gxs; i<gxs+gnx; i++) {
        for (l=0; l<nc; l++) {
          /* the complicated stuff is to handle periodic boundaries */
          colors[i1++] = l + nc*(SetInRange(i,m) % col);
        }
      }
      ncolors = nc + nc*(col-1);
      ierr    = ISColoringCreate(comm,ncolors,nc*gnx,colors,PETSC_OWN_POINTER,&dd->ghostedcoloring);CHKERRQ(ierr);
      ierr    = ISColoringSetType(dd->ghostedcoloring,IS_COLORING_LOCAL);CHKERRQ(ierr);
    }
    *coloring = dd->ghostedcoloring;
  } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Unknown ISColoringType %d",(int)ctype);
  ierr = ISColoringReference(*coloring);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode DMCreateColoring_DA_2d_5pt_MPIAIJ(DM da,ISColoringType ctype,ISColoring *coloring)
{
  PetscErrorCode   ierr;
  PetscInt         xs,ys,nx,ny,i,j,ii,gxs,gys,gnx,gny,m,n,dim,s,k,nc;
  PetscInt         ncolors;
  MPI_Comm         comm;
  DMBoundaryType bx,by;
  ISColoringValue  *colors;
  DM_DA            *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  ierr = DMDAGetInfo(da,&dim,&m,&n,0,0,0,0,&nc,&s,&bx,&by,0,0);CHKERRQ(ierr);
  ierr = DMDAGetCorners(da,&xs,&ys,0,&nx,&ny,0);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,&gys,0,&gnx,&gny,0);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  if (bx == DM_BOUNDARY_PERIODIC && (m % 5)) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"For coloring efficiency ensure number of grid points in X is divisible by 5\n");
  if (by == DM_BOUNDARY_PERIODIC && (n % 5)) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"For coloring efficiency ensure number of grid points in Y is divisible by 5\n");

  /* create the coloring */
  if (ctype == IS_COLORING_GLOBAL) {
    if (!dd->localcoloring) {
      ierr = PetscMalloc1(nc*nx*ny,&colors);CHKERRQ(ierr);
      ii   = 0;
      for (j=ys; j<ys+ny; j++) {
        for (i=xs; i<xs+nx; i++) {
          for (k=0; k<nc; k++) {
            colors[ii++] = k + nc*((3*j+i) % 5);
          }
        }
      }
      ncolors = 5*nc;
      ierr    = ISColoringCreate(comm,ncolors,nc*nx*ny,colors,PETSC_OWN_POINTER,&dd->localcoloring);CHKERRQ(ierr);
    }
    *coloring = dd->localcoloring;
  } else if (ctype == IS_COLORING_LOCAL) {
    if (!dd->ghostedcoloring) {
      ierr = PetscMalloc1(nc*gnx*gny,&colors);CHKERRQ(ierr);
      ii = 0;
      for (j=gys; j<gys+gny; j++) {
        for (i=gxs; i<gxs+gnx; i++) {
          for (k=0; k<nc; k++) {
            colors[ii++] = k + nc*((3*SetInRange(j,n) + SetInRange(i,m)) % 5);
          }
        }
      }
      ncolors = 5*nc;
      ierr    = ISColoringCreate(comm,ncolors,nc*gnx*gny,colors,PETSC_OWN_POINTER,&dd->ghostedcoloring);CHKERRQ(ierr);
      ierr    = ISColoringSetType(dd->ghostedcoloring,IS_COLORING_LOCAL);CHKERRQ(ierr);
    }
    *coloring = dd->ghostedcoloring;
  } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Unknown ISColoringType %d",(int)ctype);
  PetscFunctionReturn(0);
}

/* =========================================================================== */
extern PetscErrorCode DMCreateMatrix_DA_1d_MPIAIJ(DM,Mat);
extern PetscErrorCode DMCreateMatrix_DA_1d_MPIAIJ_Fill(DM,Mat);
extern PetscErrorCode DMCreateMatrix_DA_2d_MPIAIJ(DM,Mat);
extern PetscErrorCode DMCreateMatrix_DA_2d_MPIAIJ_Fill(DM,Mat);
extern PetscErrorCode DMCreateMatrix_DA_3d_MPIAIJ(DM,Mat);
extern PetscErrorCode DMCreateMatrix_DA_3d_MPIAIJ_Fill(DM,Mat);
extern PetscErrorCode DMCreateMatrix_DA_2d_MPIBAIJ(DM,Mat);
extern PetscErrorCode DMCreateMatrix_DA_3d_MPIBAIJ(DM,Mat);
extern PetscErrorCode DMCreateMatrix_DA_2d_MPISBAIJ(DM,Mat);
extern PetscErrorCode DMCreateMatrix_DA_3d_MPISBAIJ(DM,Mat);

/*@C
   MatSetupDM - Sets the DMDA that is to be used by the HYPRE_StructMatrix PETSc matrix

   Logically Collective on Mat

   Input Parameters:
+  mat - the matrix
-  da - the da

   Level: intermediate

@*/
PetscErrorCode MatSetupDM(Mat mat,DM da)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(mat,MAT_CLASSID,1);
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  ierr = PetscTryMethod(mat,"MatSetupDM_C",(Mat,DM),(mat,da));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode  MatView_MPI_DA(Mat A,PetscViewer viewer)
{
  DM                da;
  PetscErrorCode    ierr;
  const char        *prefix;
  Mat               Anatural;
  AO                ao;
  PetscInt          rstart,rend,*petsc,i;
  IS                is;
  MPI_Comm          comm;
  PetscViewerFormat format;

  PetscFunctionBegin;
  /* Check whether we are just printing info, in which case MatView() already viewed everything we wanted to view */
  ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr);
  if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) PetscFunctionReturn(0);

  ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr);
  ierr = MatGetDM(A, &da);CHKERRQ(ierr);
  if (!da) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Matrix not generated from a DMDA");

  ierr = DMDAGetAO(da,&ao);CHKERRQ(ierr);
  ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
  ierr = PetscMalloc1(rend-rstart,&petsc);CHKERRQ(ierr);
  for (i=rstart; i<rend; i++) petsc[i-rstart] = i;
  ierr = AOApplicationToPetsc(ao,rend-rstart,petsc);CHKERRQ(ierr);
  ierr = ISCreateGeneral(comm,rend-rstart,petsc,PETSC_OWN_POINTER,&is);CHKERRQ(ierr);

  /* call viewer on natural ordering */
  ierr = MatCreateSubMatrix(A,is,is,MAT_INITIAL_MATRIX,&Anatural);CHKERRQ(ierr);
  ierr = ISDestroy(&is);CHKERRQ(ierr);
  ierr = PetscObjectGetOptionsPrefix((PetscObject)A,&prefix);CHKERRQ(ierr);
  ierr = PetscObjectSetOptionsPrefix((PetscObject)Anatural,prefix);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject)Anatural,((PetscObject)A)->name);CHKERRQ(ierr);
  ierr = MatView(Anatural,viewer);CHKERRQ(ierr);
  ierr = MatDestroy(&Anatural);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode  MatLoad_MPI_DA(Mat A,PetscViewer viewer)
{
  DM             da;
  PetscErrorCode ierr;
  Mat            Anatural,Aapp;
  AO             ao;
  PetscInt       rstart,rend,*app,i,m,n,M,N;
  IS             is;
  MPI_Comm       comm;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr);
  ierr = MatGetDM(A, &da);CHKERRQ(ierr);
  if (!da) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Matrix not generated from a DMDA");

  /* Load the matrix in natural ordering */
  ierr = MatCreate(PetscObjectComm((PetscObject)A),&Anatural);CHKERRQ(ierr);
  ierr = MatSetType(Anatural,((PetscObject)A)->type_name);CHKERRQ(ierr);
  ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr);
  ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
  ierr = MatSetSizes(Anatural,m,n,M,N);CHKERRQ(ierr);
  ierr = MatLoad(Anatural,viewer);CHKERRQ(ierr);

  /* Map natural ordering to application ordering and create IS */
  ierr = DMDAGetAO(da,&ao);CHKERRQ(ierr);
  ierr = MatGetOwnershipRange(Anatural,&rstart,&rend);CHKERRQ(ierr);
  ierr = PetscMalloc1(rend-rstart,&app);CHKERRQ(ierr);
  for (i=rstart; i<rend; i++) app[i-rstart] = i;
  ierr = AOPetscToApplication(ao,rend-rstart,app);CHKERRQ(ierr);
  ierr = ISCreateGeneral(comm,rend-rstart,app,PETSC_OWN_POINTER,&is);CHKERRQ(ierr);

  /* Do permutation and replace header */
  ierr = MatCreateSubMatrix(Anatural,is,is,MAT_INITIAL_MATRIX,&Aapp);CHKERRQ(ierr);
  ierr = MatHeaderReplace(A,&Aapp);CHKERRQ(ierr);
  ierr = ISDestroy(&is);CHKERRQ(ierr);
  ierr = MatDestroy(&Anatural);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode DMCreateMatrix_DA(DM da, Mat *J)
{
  PetscErrorCode ierr;
  PetscInt       dim,dof,nx,ny,nz,dims[3],starts[3],M,N,P;
  Mat            A;
  MPI_Comm       comm;
  MatType        Atype;
  PetscSection   section, sectionGlobal;
  void           (*aij)(void)=NULL,(*baij)(void)=NULL,(*sbaij)(void)=NULL;
  MatType        mtype;
  PetscMPIInt    size;
  DM_DA          *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  ierr = MatInitializePackage();CHKERRQ(ierr);
  mtype = da->mattype;

  ierr = DMGetDefaultSection(da, &section);CHKERRQ(ierr);
  if (section) {
    PetscInt  bs = -1;
    PetscInt  localSize;
    PetscBool isShell, isBlock, isSeqBlock, isMPIBlock, isSymBlock, isSymSeqBlock, isSymMPIBlock, isSymmetric;

    ierr = DMGetDefaultGlobalSection(da, &sectionGlobal);CHKERRQ(ierr);
    ierr = PetscSectionGetConstrainedStorageSize(sectionGlobal, &localSize);CHKERRQ(ierr);
    ierr = MatCreate(PetscObjectComm((PetscObject)da), J);CHKERRQ(ierr);
    ierr = MatSetSizes(*J, localSize, localSize, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr);
    ierr = MatSetType(*J, mtype);CHKERRQ(ierr);
    ierr = MatSetFromOptions(*J);CHKERRQ(ierr);
    ierr = PetscStrcmp(mtype, MATSHELL, &isShell);CHKERRQ(ierr);
    ierr = PetscStrcmp(mtype, MATBAIJ, &isBlock);CHKERRQ(ierr);
    ierr = PetscStrcmp(mtype, MATSEQBAIJ, &isSeqBlock);CHKERRQ(ierr);
    ierr = PetscStrcmp(mtype, MATMPIBAIJ, &isMPIBlock);CHKERRQ(ierr);
    ierr = PetscStrcmp(mtype, MATSBAIJ, &isSymBlock);CHKERRQ(ierr);
    ierr = PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock);CHKERRQ(ierr);
    ierr = PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock);CHKERRQ(ierr);
    /* Check for symmetric storage */
    isSymmetric = (PetscBool) (isSymBlock || isSymSeqBlock || isSymMPIBlock);
    if (isSymmetric) {
      ierr = MatSetOption(*J, MAT_IGNORE_LOWER_TRIANGULAR, PETSC_TRUE);CHKERRQ(ierr);
    }
    if (!isShell) {
      PetscInt *dnz, *onz, *dnzu, *onzu, bsLocal;

      if (bs < 0) {
        if (isBlock || isSeqBlock || isMPIBlock || isSymBlock || isSymSeqBlock || isSymMPIBlock) {
          PetscInt pStart, pEnd, p, dof;

          ierr = PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);CHKERRQ(ierr);
          for (p = pStart; p < pEnd; ++p) {
            ierr = PetscSectionGetDof(sectionGlobal, p, &dof);CHKERRQ(ierr);
            if (dof) {
              bs = dof;
              break;
            }
          }
        } else {
          bs = 1;
        }
        /* Must have same blocksize on all procs (some might have no points) */
        bsLocal = bs;
        ierr    = MPIU_Allreduce(&bsLocal, &bs, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)da));CHKERRQ(ierr);
      }
      ierr = PetscCalloc4(localSize/bs, &dnz, localSize/bs, &onz, localSize/bs, &dnzu, localSize/bs, &onzu);CHKERRQ(ierr);
      /* ierr = DMPlexPreallocateOperator(dm, bs, section, sectionGlobal, dnz, onz, dnzu, onzu, *J, fillMatrix);CHKERRQ(ierr); */
      ierr = PetscFree4(dnz, onz, dnzu, onzu);CHKERRQ(ierr);
    }
  }
  /*
                                  m
          ------------------------------------------------------
         |                                                     |
         |                                                     |
         |               ----------------------                |
         |               |                    |                |
      n  |           ny  |                    |                |
         |               |                    |                |
         |               .---------------------                |
         |             (xs,ys)     nx                          |
         |            .                                        |
         |         (gxs,gys)                                   |
         |                                                     |
          -----------------------------------------------------
  */

  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  M   = dd->M;
  N   = dd->N;
  P   = dd->P;
  dim = da->dim;
  dof = dd->w;
  /* ierr = DMDAGetInfo(da,&dim,&M,&N,&P,0,0,0,&dof,0,0,0,0,0);CHKERRQ(ierr); */
  ierr = DMDAGetCorners(da,0,0,0,&nx,&ny,&nz);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);
  ierr = MatCreate(comm,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,dof*nx*ny*nz,dof*nx*ny*nz,dof*M*N*P,dof*M*N*P);CHKERRQ(ierr);
  ierr = MatSetType(A,mtype);CHKERRQ(ierr);
  ierr = MatSetDM(A,da);CHKERRQ(ierr);
  if (da->structure_only) {
    ierr = MatSetOption(A,MAT_STRUCTURE_ONLY,PETSC_TRUE);CHKERRQ(ierr);
  }
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatGetType(A,&Atype);CHKERRQ(ierr);
  /*
     We do not provide a getmatrix function in the DMDA operations because
   the basic DMDA does not know about matrices. We think of DMDA as being more
   more low-level than matrices. This is kind of cheating but, cause sometimes
   we think of DMDA has higher level than matrices.

     We could switch based on Atype (or mtype), but we do not since the
   specialized setting routines depend only the particular preallocation
   details of the matrix, not the type itself.
  */
  ierr = PetscObjectQueryFunction((PetscObject)A,"MatMPIAIJSetPreallocation_C",&aij);CHKERRQ(ierr);
  if (!aij) {
    ierr = PetscObjectQueryFunction((PetscObject)A,"MatSeqAIJSetPreallocation_C",&aij);CHKERRQ(ierr);
  }
  if (!aij) {
    ierr = PetscObjectQueryFunction((PetscObject)A,"MatMPIBAIJSetPreallocation_C",&baij);CHKERRQ(ierr);
    if (!baij) {
      ierr = PetscObjectQueryFunction((PetscObject)A,"MatSeqBAIJSetPreallocation_C",&baij);CHKERRQ(ierr);
    }
    if (!baij) {
      ierr = PetscObjectQueryFunction((PetscObject)A,"MatMPISBAIJSetPreallocation_C",&sbaij);CHKERRQ(ierr);
      if (!sbaij) {
        ierr = PetscObjectQueryFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C",&sbaij);CHKERRQ(ierr);
      }
    }
  }
  if (aij) {
    if (dim == 1) {
      if (dd->ofill) {
        ierr = DMCreateMatrix_DA_1d_MPIAIJ_Fill(da,A);CHKERRQ(ierr);
      } else {
        ierr = DMCreateMatrix_DA_1d_MPIAIJ(da,A);CHKERRQ(ierr);
      }
    } else if (dim == 2) {
      if (dd->ofill) {
        ierr = DMCreateMatrix_DA_2d_MPIAIJ_Fill(da,A);CHKERRQ(ierr);
      } else {
        ierr = DMCreateMatrix_DA_2d_MPIAIJ(da,A);CHKERRQ(ierr);
      }
    } else if (dim == 3) {
      if (dd->ofill) {
        ierr = DMCreateMatrix_DA_3d_MPIAIJ_Fill(da,A);CHKERRQ(ierr);
      } else {
        ierr = DMCreateMatrix_DA_3d_MPIAIJ(da,A);CHKERRQ(ierr);
      }
    }
  } else if (baij) {
    if (dim == 2) {
      ierr = DMCreateMatrix_DA_2d_MPIBAIJ(da,A);CHKERRQ(ierr);
    } else if (dim == 3) {
      ierr = DMCreateMatrix_DA_3d_MPIBAIJ(da,A);CHKERRQ(ierr);
    } else SETERRQ3(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Not implemented for %D dimension and Matrix Type: %s in %D dimension! Send mail to petsc-maint@mcs.anl.gov for code",dim,Atype,dim);
  } else if (sbaij) {
    if (dim == 2) {
      ierr = DMCreateMatrix_DA_2d_MPISBAIJ(da,A);CHKERRQ(ierr);
    } else if (dim == 3) {
      ierr = DMCreateMatrix_DA_3d_MPISBAIJ(da,A);CHKERRQ(ierr);
    } else SETERRQ3(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Not implemented for %D dimension and Matrix Type: %s in %D dimension! Send mail to petsc-maint@mcs.anl.gov for code",dim,Atype,dim);
  } else {
    ISLocalToGlobalMapping ltog;
    ierr = DMGetLocalToGlobalMapping(da,&ltog);CHKERRQ(ierr);
    ierr = MatSetUp(A);CHKERRQ(ierr);
    ierr = MatSetLocalToGlobalMapping(A,ltog,ltog);CHKERRQ(ierr);
  }
  ierr = DMDAGetGhostCorners(da,&starts[0],&starts[1],&starts[2],&dims[0],&dims[1],&dims[2]);CHKERRQ(ierr);
  ierr = MatSetStencil(A,dim,dims,starts,dof);CHKERRQ(ierr);
  ierr = MatSetDM(A,da);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  if (size > 1) {
    /* change viewer to display matrix in natural ordering */
    ierr = MatShellSetOperation(A, MATOP_VIEW, (void (*)(void))MatView_MPI_DA);CHKERRQ(ierr);
    ierr = MatShellSetOperation(A, MATOP_LOAD, (void (*)(void))MatLoad_MPI_DA);CHKERRQ(ierr);
  }
  *J = A;
  PetscFunctionReturn(0);
}

/* ---------------------------------------------------------------------------------*/
PetscErrorCode DMCreateMatrix_DA_2d_MPIAIJ(DM da,Mat J)
{
  PetscErrorCode         ierr;
  PetscInt               xs,ys,nx,ny,i,j,slot,gxs,gys,gnx,gny,m,n,dim,s,*cols = NULL,k,nc,*rows = NULL,col,cnt,l,p,M,N;
  PetscInt               lstart,lend,pstart,pend,*dnz,*onz;
  MPI_Comm               comm;
  PetscScalar            *values;
  DMBoundaryType         bx,by;
  ISLocalToGlobalMapping ltog;
  DMDAStencilType        st;
  PetscBool              removedups = PETSC_FALSE;

  PetscFunctionBegin;
  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  ierr = DMDAGetInfo(da,&dim,&m,&n,&M,&N,0,0,&nc,&s,&bx,&by,0,&st);CHKERRQ(ierr);
  col  = 2*s + 1;
  /*
       With one processor in periodic domains in a skinny dimension the code will label nonzero columns multiple times
       because of "wrapping" around the end of the domain hitting an entry already counted in the other direction.
  */
  if (M == 1 && 2*s >= m) removedups = PETSC_TRUE;
  if (N == 1 && 2*s >= n) removedups = PETSC_TRUE;
  ierr = DMDAGetCorners(da,&xs,&ys,0,&nx,&ny,0);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,&gys,0,&gnx,&gny,0);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  ierr = PetscMalloc2(nc,&rows,col*col*nc*nc,&cols);CHKERRQ(ierr);
  ierr = DMGetLocalToGlobalMapping(da,&ltog);CHKERRQ(ierr);

  ierr = MatSetBlockSize(J,nc);CHKERRQ(ierr);
  /* determine the matrix preallocation information */
  ierr = MatPreallocateInitialize(comm,nc*nx*ny,nc*nx*ny,dnz,onz);CHKERRQ(ierr);
  for (i=xs; i<xs+nx; i++) {

    pstart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
    pend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));

    for (j=ys; j<ys+ny; j++) {
      slot = i - gxs + gnx*(j - gys);

      lstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
      lend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));

      cnt = 0;
      for (k=0; k<nc; k++) {
        for (l=lstart; l<lend+1; l++) {
          for (p=pstart; p<pend+1; p++) {
            if ((st == DMDA_STENCIL_BOX) || (!l || !p)) {  /* entries on star have either l = 0 or p = 0 */
              cols[cnt++] = k + nc*(slot + gnx*l + p);
            }
          }
        }
        rows[k] = k + nc*(slot);
      }
      if (removedups) {
        ierr = MatPreallocateSetLocalRemoveDups(ltog,nc,rows,ltog,cnt,cols,dnz,onz);CHKERRQ(ierr);
      } else {
        ierr = MatPreallocateSetLocal(ltog,nc,rows,ltog,cnt,cols,dnz,onz);CHKERRQ(ierr);
      }
    }
  }
  ierr = MatSetBlockSize(J,nc);CHKERRQ(ierr);
  ierr = MatSeqAIJSetPreallocation(J,0,dnz);CHKERRQ(ierr);
  ierr = MatMPIAIJSetPreallocation(J,0,dnz,0,onz);CHKERRQ(ierr);
  ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);

  ierr = MatSetLocalToGlobalMapping(J,ltog,ltog);CHKERRQ(ierr);

  /*
    For each node in the grid: we get the neighbors in the local (on processor ordering
    that includes the ghost points) then MatSetValuesLocal() maps those indices to the global
    PETSc ordering.
  */
  if (!da->prealloc_only) {
    ierr = PetscCalloc1(col*col*nc*nc,&values);CHKERRQ(ierr);
    for (i=xs; i<xs+nx; i++) {

      pstart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
      pend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));

      for (j=ys; j<ys+ny; j++) {
        slot = i - gxs + gnx*(j - gys);

        lstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
        lend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));

        cnt = 0;
        for (k=0; k<nc; k++) {
          for (l=lstart; l<lend+1; l++) {
            for (p=pstart; p<pend+1; p++) {
              if ((st == DMDA_STENCIL_BOX) || (!l || !p)) {  /* entries on star have either l = 0 or p = 0 */
                cols[cnt++] = k + nc*(slot + gnx*l + p);
              }
            }
          }
          rows[k] = k + nc*(slot);
        }
        ierr = MatSetValuesLocal(J,nc,rows,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
      }
    }
    ierr = PetscFree(values);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  }
  ierr = PetscFree2(rows,cols);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode DMCreateMatrix_DA_2d_MPIAIJ_Fill(DM da,Mat J)
{
  PetscErrorCode         ierr;
  PetscInt               xs,ys,nx,ny,i,j,slot,gxs,gys,gnx,gny;
  PetscInt               m,n,dim,s,*cols,k,nc,row,col,cnt,maxcnt = 0,l,p,M,N;
  PetscInt               lstart,lend,pstart,pend,*dnz,*onz;
  DM_DA                  *dd = (DM_DA*)da->data;
  PetscInt               ifill_col,*ofill = dd->ofill, *dfill = dd->dfill;
  MPI_Comm               comm;
  PetscScalar            *values;
  DMBoundaryType         bx,by;
  ISLocalToGlobalMapping ltog;
  DMDAStencilType        st;
  PetscBool              removedups = PETSC_FALSE;

  PetscFunctionBegin;
  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  ierr = DMDAGetInfo(da,&dim,&m,&n,&M,&N,0,0,&nc,&s,&bx,&by,0,&st);CHKERRQ(ierr);
  col  = 2*s + 1;
  /*
       With one processor in periodic domains in a skinny dimension the code will label nonzero columns multiple times
       because of "wrapping" around the end of the domain hitting an entry already counted in the other direction.
  */
  if (M == 1 && 2*s >= m) removedups = PETSC_TRUE;
  if (N == 1 && 2*s >= n) removedups = PETSC_TRUE;
  ierr = DMDAGetCorners(da,&xs,&ys,0,&nx,&ny,0);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,&gys,0,&gnx,&gny,0);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  ierr = PetscMalloc1(col*col*nc,&cols);CHKERRQ(ierr);
  ierr = DMGetLocalToGlobalMapping(da,&ltog);CHKERRQ(ierr);

  ierr = MatSetBlockSize(J,nc);CHKERRQ(ierr);
  /* determine the matrix preallocation information */
  ierr = MatPreallocateInitialize(comm,nc*nx*ny,nc*nx*ny,dnz,onz);CHKERRQ(ierr);
  for (i=xs; i<xs+nx; i++) {

    pstart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
    pend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));

    for (j=ys; j<ys+ny; j++) {
      slot = i - gxs + gnx*(j - gys);

      lstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
      lend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));

      for (k=0; k<nc; k++) {
        cnt = 0;
        for (l=lstart; l<lend+1; l++) {
          for (p=pstart; p<pend+1; p++) {
            if (l || p) {
              if ((st == DMDA_STENCIL_BOX) || (!l || !p)) {  /* entries on star */
                for (ifill_col=ofill[k]; ifill_col<ofill[k+1]; ifill_col++) cols[cnt++] = ofill[ifill_col] + nc*(slot + gnx*l + p);
              }
            } else {
              if (dfill) {
                for (ifill_col=dfill[k]; ifill_col<dfill[k+1]; ifill_col++) cols[cnt++] = dfill[ifill_col] + nc*(slot + gnx*l + p);
              } else {
                for (ifill_col=0; ifill_col<nc; ifill_col++) cols[cnt++] = ifill_col + nc*(slot + gnx*l + p);
              }
            }
          }
        }
        row    = k + nc*(slot);
        maxcnt = PetscMax(maxcnt,cnt);
        if (removedups) {
          ierr   = MatPreallocateSetLocalRemoveDups(ltog,1,&row,ltog,cnt,cols,dnz,onz);CHKERRQ(ierr);
        } else {
          ierr   = MatPreallocateSetLocal(ltog,1,&row,ltog,cnt,cols,dnz,onz);CHKERRQ(ierr);
        }
      }
    }
  }
  ierr = MatSeqAIJSetPreallocation(J,0,dnz);CHKERRQ(ierr);
  ierr = MatMPIAIJSetPreallocation(J,0,dnz,0,onz);CHKERRQ(ierr);
  ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);
  ierr = MatSetLocalToGlobalMapping(J,ltog,ltog);CHKERRQ(ierr);

  /*
    For each node in the grid: we get the neighbors in the local (on processor ordering
    that includes the ghost points) then MatSetValuesLocal() maps those indices to the global
    PETSc ordering.
  */
  if (!da->prealloc_only) {
    ierr = PetscCalloc1(maxcnt,&values);CHKERRQ(ierr);
    for (i=xs; i<xs+nx; i++) {

      pstart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
      pend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));

      for (j=ys; j<ys+ny; j++) {
        slot = i - gxs + gnx*(j - gys);

        lstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
        lend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));

        for (k=0; k<nc; k++) {
          cnt = 0;
          for (l=lstart; l<lend+1; l++) {
            for (p=pstart; p<pend+1; p++) {
              if (l || p) {
                if ((st == DMDA_STENCIL_BOX) || (!l || !p)) {  /* entries on star */
                  for (ifill_col=ofill[k]; ifill_col<ofill[k+1]; ifill_col++) cols[cnt++] = ofill[ifill_col] + nc*(slot + gnx*l + p);
                }
              } else {
                if (dfill) {
                  for (ifill_col=dfill[k]; ifill_col<dfill[k+1]; ifill_col++) cols[cnt++] = dfill[ifill_col] + nc*(slot + gnx*l + p);
                } else {
                  for (ifill_col=0; ifill_col<nc; ifill_col++) cols[cnt++] = ifill_col + nc*(slot + gnx*l + p);
                }
              }
            }
          }
          row  = k + nc*(slot);
          ierr = MatSetValuesLocal(J,1,&row,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
        }
      }
    }
    ierr = PetscFree(values);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  }
  ierr = PetscFree(cols);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/* ---------------------------------------------------------------------------------*/

PetscErrorCode DMCreateMatrix_DA_3d_MPIAIJ(DM da,Mat J)
{
  PetscErrorCode         ierr;
  PetscInt               xs,ys,nx,ny,i,j,slot,gxs,gys,gnx,gny;
  PetscInt               m,n,dim,s,*cols = NULL,k,nc,*rows = NULL,col,cnt,l,p,*dnz = NULL,*onz = NULL;
  PetscInt               istart,iend,jstart,jend,kstart,kend,zs,nz,gzs,gnz,ii,jj,kk,M,N,P;
  MPI_Comm               comm;
  PetscScalar            *values;
  DMBoundaryType         bx,by,bz;
  ISLocalToGlobalMapping ltog;
  DMDAStencilType        st;
  PetscBool              removedups = PETSC_FALSE;

  PetscFunctionBegin;
  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  ierr = DMDAGetInfo(da,&dim,&m,&n,&p,&M,&N,&P,&nc,&s,&bx,&by,&bz,&st);CHKERRQ(ierr);
  col  = 2*s + 1;

  /*
       With one processor in periodic domains in a skinny dimension the code will label nonzero columns multiple times
       because of "wrapping" around the end of the domain hitting an entry already counted in the other direction.
  */
  if (M == 1 && 2*s >= m) removedups = PETSC_TRUE;
  if (N == 1 && 2*s >= n) removedups = PETSC_TRUE;
  if (P == 1 && 2*s >= p) removedups = PETSC_TRUE;

  ierr = DMDAGetCorners(da,&xs,&ys,&zs,&nx,&ny,&nz);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,&gys,&gzs,&gnx,&gny,&gnz);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  ierr = PetscMalloc2(nc,&rows,col*col*col*nc*nc,&cols);CHKERRQ(ierr);
  ierr = DMGetLocalToGlobalMapping(da,&ltog);CHKERRQ(ierr);

  ierr = MatSetBlockSize(J,nc);CHKERRQ(ierr);
  /* determine the matrix preallocation information */
  ierr = MatPreallocateInitialize(comm,nc*nx*ny*nz,nc*nx*ny*nz,dnz,onz);CHKERRQ(ierr);
  for (i=xs; i<xs+nx; i++) {
    istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
    iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
    for (j=ys; j<ys+ny; j++) {
      jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
      jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
      for (k=zs; k<zs+nz; k++) {
        kstart = (bz == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-k));
        kend   = (bz == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,p-k-1));

        slot = i - gxs + gnx*(j - gys) + gnx*gny*(k - gzs);

        cnt = 0;
        for (l=0; l<nc; l++) {
          for (ii=istart; ii<iend+1; ii++) {
            for (jj=jstart; jj<jend+1; jj++) {
              for (kk=kstart; kk<kend+1; kk++) {
                if ((st == DMDA_STENCIL_BOX) || ((!ii && !jj) || (!jj && !kk) || (!ii && !kk))) {/* entries on star*/
                  cols[cnt++] = l + nc*(slot + ii + gnx*jj + gnx*gny*kk);
                }
              }
            }
          }
          rows[l] = l + nc*(slot);
        }
        if (removedups) {
          ierr = MatPreallocateSetLocalRemoveDups(ltog,nc,rows,ltog,cnt,cols,dnz,onz);CHKERRQ(ierr);
        } else {
          ierr = MatPreallocateSetLocal(ltog,nc,rows,ltog,cnt,cols,dnz,onz);CHKERRQ(ierr);
        }
      }
    }
  }
  ierr = MatSetBlockSize(J,nc);CHKERRQ(ierr);
  ierr = MatSeqAIJSetPreallocation(J,0,dnz);CHKERRQ(ierr);
  ierr = MatMPIAIJSetPreallocation(J,0,dnz,0,onz);CHKERRQ(ierr);
  ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);
  ierr = MatSetLocalToGlobalMapping(J,ltog,ltog);CHKERRQ(ierr);

  /*
    For each node in the grid: we get the neighbors in the local (on processor ordering
    that includes the ghost points) then MatSetValuesLocal() maps those indices to the global
    PETSc ordering.
  */
  if (!da->prealloc_only) {
    ierr = PetscCalloc1(col*col*col*nc*nc*nc,&values);CHKERRQ(ierr);
    for (i=xs; i<xs+nx; i++) {
      istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
      iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
      for (j=ys; j<ys+ny; j++) {
        jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
        jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
        for (k=zs; k<zs+nz; k++) {
          kstart = (bz == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-k));
          kend   = (bz == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,p-k-1));

          slot = i - gxs + gnx*(j - gys) + gnx*gny*(k - gzs);

          cnt = 0;
          for (l=0; l<nc; l++) {
            for (ii=istart; ii<iend+1; ii++) {
              for (jj=jstart; jj<jend+1; jj++) {
                for (kk=kstart; kk<kend+1; kk++) {
                  if ((st == DMDA_STENCIL_BOX) || ((!ii && !jj) || (!jj && !kk) || (!ii && !kk))) {/* entries on star*/
                    cols[cnt++] = l + nc*(slot + ii + gnx*jj + gnx*gny*kk);
                  }
                }
              }
            }
            rows[l] = l + nc*(slot);
          }
          ierr = MatSetValuesLocal(J,nc,rows,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
        }
      }
    }
    ierr = PetscFree(values);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  }
  ierr = PetscFree2(rows,cols);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/* ---------------------------------------------------------------------------------*/

PetscErrorCode DMCreateMatrix_DA_1d_MPIAIJ_Fill(DM da,Mat J)
{
  PetscErrorCode         ierr;
  DM_DA                  *dd = (DM_DA*)da->data;
  PetscInt               xs,nx,i,j,gxs,gnx,row,k,l;
  PetscInt               m,dim,s,*cols = NULL,nc,cnt,maxcnt = 0,*ocols;
  PetscInt               *ofill = dd->ofill,*dfill = dd->dfill;
  PetscScalar            *values;
  DMBoundaryType         bx;
  ISLocalToGlobalMapping ltog;
  PetscMPIInt            rank,size;

  PetscFunctionBegin;
  if (dd->bx == DM_BOUNDARY_PERIODIC) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"With fill provided not implemented with periodic boundary conditions");
  ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)da),&rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(PetscObjectComm((PetscObject)da),&size);CHKERRQ(ierr);

  /*
         nc - number of components per grid point

  */
  ierr = DMDAGetInfo(da,&dim,&m,0,0,0,0,0,&nc,&s,&bx,0,0,0);CHKERRQ(ierr);
  ierr = DMDAGetCorners(da,&xs,0,0,&nx,0,0);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,0,0,&gnx,0,0);CHKERRQ(ierr);

  ierr = MatSetBlockSize(J,nc);CHKERRQ(ierr);
  ierr = PetscCalloc2(nx*nc,&cols,nx*nc,&ocols);CHKERRQ(ierr);

  /*
        note should be smaller for first and last process with no periodic
        does not handle dfill
  */
  cnt = 0;
  /* coupling with process to the left */
  for (i=0; i<s; i++) {
    for (j=0; j<nc; j++) {
      ocols[cnt] = ((!rank) ? 0 : (s - i)*(ofill[j+1] - ofill[j]));
      cols[cnt]  = dfill[j+1] - dfill[j] + (s + i)*(ofill[j+1] - ofill[j]);
      maxcnt = PetscMax(maxcnt,ocols[cnt]+cols[cnt]);
      cnt++;
    }
  }
  for (i=s; i<nx-s; i++) {
    for (j=0; j<nc; j++) {
      cols[cnt] = dfill[j+1] - dfill[j] + 2*s*(ofill[j+1] - ofill[j]);
      maxcnt = PetscMax(maxcnt,ocols[cnt]+cols[cnt]);
      cnt++;
    }
  }
  /* coupling with process to the right */
  for (i=nx-s; i<nx; i++) {
    for (j=0; j<nc; j++) {
      ocols[cnt] = ((rank == (size-1)) ? 0 : (i - nx + s + 1)*(ofill[j+1] - ofill[j]));
      cols[cnt]  = dfill[j+1] - dfill[j] + (s + nx - i - 1)*(ofill[j+1] - ofill[j]);
      maxcnt = PetscMax(maxcnt,ocols[cnt]+cols[cnt]);
      cnt++;
    }
  }

  ierr = MatSeqAIJSetPreallocation(J,0,cols);CHKERRQ(ierr);
  ierr = MatMPIAIJSetPreallocation(J,0,cols,0,ocols);CHKERRQ(ierr);
  ierr = PetscFree2(cols,ocols);CHKERRQ(ierr);

  ierr = DMGetLocalToGlobalMapping(da,&ltog);CHKERRQ(ierr);
  ierr = MatSetLocalToGlobalMapping(J,ltog,ltog);CHKERRQ(ierr);

  /*
    For each node in the grid: we get the neighbors in the local (on processor ordering
    that includes the ghost points) then MatSetValuesLocal() maps those indices to the global
    PETSc ordering.
  */
  if (!da->prealloc_only) {
    ierr = PetscCalloc2(maxcnt,&values,maxcnt,&cols);CHKERRQ(ierr);

    row = xs*nc;
    /* coupling with process to the left */
    for (i=xs; i<xs+s; i++) {
      for (j=0; j<nc; j++) {
        cnt = 0;
        if (rank) {
          for (l=0; l<s; l++) {
            for (k=ofill[j]; k<ofill[j+1]; k++) cols[cnt++] = (i - s + l)*nc + ofill[k];
          }
        }
        if (dfill) {
          for (k=dfill[j]; k<dfill[j+1]; k++) {
            cols[cnt++] = i*nc + dfill[k];
          }
        } else {
          for (k=0; k<nc; k++) {
            cols[cnt++] = i*nc + k;
          }
        }
        for (l=0; l<s; l++) {
          for (k=ofill[j]; k<ofill[j+1]; k++) cols[cnt++] = (i + s - l)*nc + ofill[k];
        }
        ierr = MatSetValues(J,1,&row,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
        row++;
      }
    }
    for (i=xs+s; i<xs+nx-s; i++) {
      for (j=0; j<nc; j++) {
        cnt = 0;
        for (l=0; l<s; l++) {
          for (k=ofill[j]; k<ofill[j+1]; k++) cols[cnt++] = (i - s + l)*nc + ofill[k];
        }
        if (dfill) {
          for (k=dfill[j]; k<dfill[j+1]; k++) {
            cols[cnt++] = i*nc + dfill[k];
          }
        } else {
          for (k=0; k<nc; k++) {
            cols[cnt++] = i*nc + k;
          }
        }
        for (l=0; l<s; l++) {
          for (k=ofill[j]; k<ofill[j+1]; k++) cols[cnt++] = (i + s - l)*nc + ofill[k];
        }
        ierr = MatSetValues(J,1,&row,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
        row++;
      }
    }
    /* coupling with process to the right */
    for (i=xs+nx-s; i<xs+nx; i++) {
      for (j=0; j<nc; j++) {
        cnt = 0;
        for (l=0; l<s; l++) {
          for (k=ofill[j]; k<ofill[j+1]; k++) cols[cnt++] = (i - s + l)*nc + ofill[k];
        }
        if (dfill) {
          for (k=dfill[j]; k<dfill[j+1]; k++) {
            cols[cnt++] = i*nc + dfill[k];
          }
        } else {
          for (k=0; k<nc; k++) {
            cols[cnt++] = i*nc + k;
          }
        }
        if (rank < size-1) {
          for (l=0; l<s; l++) {
            for (k=ofill[j]; k<ofill[j+1]; k++) cols[cnt++] = (i + s - l)*nc + ofill[k];
          }
        }
        ierr = MatSetValues(J,1,&row,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
        row++;
      }
    }
    ierr = PetscFree2(values,cols);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

/* ---------------------------------------------------------------------------------*/

PetscErrorCode DMCreateMatrix_DA_1d_MPIAIJ(DM da,Mat J)
{
  PetscErrorCode         ierr;
  PetscInt               xs,nx,i,i1,slot,gxs,gnx;
  PetscInt               m,dim,s,*cols = NULL,nc,*rows = NULL,col,cnt,l;
  PetscInt               istart,iend;
  PetscScalar            *values;
  DMBoundaryType         bx;
  ISLocalToGlobalMapping ltog;

  PetscFunctionBegin;
  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  ierr = DMDAGetInfo(da,&dim,&m,0,0,0,0,0,&nc,&s,&bx,0,0,0);CHKERRQ(ierr);
  col  = 2*s + 1;

  ierr = DMDAGetCorners(da,&xs,0,0,&nx,0,0);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,0,0,&gnx,0,0);CHKERRQ(ierr);

  ierr = MatSetBlockSize(J,nc);CHKERRQ(ierr);
  ierr = MatSeqAIJSetPreallocation(J,col*nc,0);CHKERRQ(ierr);
  ierr = MatMPIAIJSetPreallocation(J,col*nc,0,col*nc,0);CHKERRQ(ierr);

  ierr = DMGetLocalToGlobalMapping(da,&ltog);CHKERRQ(ierr);
  ierr = MatSetLocalToGlobalMapping(J,ltog,ltog);CHKERRQ(ierr);

  /*
    For each node in the grid: we get the neighbors in the local (on processor ordering
    that includes the ghost points) then MatSetValuesLocal() maps those indices to the global
    PETSc ordering.
  */
  if (!da->prealloc_only) {
    ierr = PetscMalloc2(nc,&rows,col*nc*nc,&cols);CHKERRQ(ierr);
    ierr = PetscCalloc1(col*nc*nc,&values);CHKERRQ(ierr);
    for (i=xs; i<xs+nx; i++) {
      istart = PetscMax(-s,gxs - i);
      iend   = PetscMin(s,gxs + gnx - i - 1);
      slot   = i - gxs;

      cnt = 0;
      for (l=0; l<nc; l++) {
        for (i1=istart; i1<iend+1; i1++) {
          cols[cnt++] = l + nc*(slot + i1);
        }
        rows[l] = l + nc*(slot);
      }
      ierr = MatSetValuesLocal(J,nc,rows,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
    }
    ierr = PetscFree(values);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
    ierr = PetscFree2(rows,cols);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode DMCreateMatrix_DA_2d_MPIBAIJ(DM da,Mat J)
{
  PetscErrorCode         ierr;
  PetscInt               xs,ys,nx,ny,i,j,slot,gxs,gys,gnx,gny;
  PetscInt               m,n,dim,s,*cols,nc,col,cnt,*dnz,*onz;
  PetscInt               istart,iend,jstart,jend,ii,jj;
  MPI_Comm               comm;
  PetscScalar            *values;
  DMBoundaryType         bx,by;
  DMDAStencilType        st;
  ISLocalToGlobalMapping ltog;

  PetscFunctionBegin;
  /*
     nc - number of components per grid point
     col - number of colors needed in one direction for single component problem
  */
  ierr = DMDAGetInfo(da,&dim,&m,&n,0,0,0,0,&nc,&s,&bx,&by,0,&st);CHKERRQ(ierr);
  col  = 2*s + 1;

  ierr = DMDAGetCorners(da,&xs,&ys,0,&nx,&ny,0);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,&gys,0,&gnx,&gny,0);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  ierr = PetscMalloc1(col*col*nc*nc,&cols);CHKERRQ(ierr);

  ierr = DMGetLocalToGlobalMapping(da,&ltog);CHKERRQ(ierr);

  /* determine the matrix preallocation information */
  ierr = MatPreallocateInitialize(comm,nx*ny,nx*ny,dnz,onz);CHKERRQ(ierr);
  for (i=xs; i<xs+nx; i++) {
    istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
    iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
    for (j=ys; j<ys+ny; j++) {
      jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
      jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
      slot   = i - gxs + gnx*(j - gys);

      /* Find block columns in block row */
      cnt = 0;
      for (ii=istart; ii<iend+1; ii++) {
        for (jj=jstart; jj<jend+1; jj++) {
          if (st == DMDA_STENCIL_BOX || !ii || !jj) { /* BOX or on the STAR */
            cols[cnt++] = slot + ii + gnx*jj;
          }
        }
      }
      ierr = MatPreallocateSetLocalBlock(ltog,1,&slot,ltog,cnt,cols,dnz,onz);CHKERRQ(ierr);
    }
  }
  ierr = MatSeqBAIJSetPreallocation(J,nc,0,dnz);CHKERRQ(ierr);
  ierr = MatMPIBAIJSetPreallocation(J,nc,0,dnz,0,onz);CHKERRQ(ierr);
  ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);

  ierr = MatSetLocalToGlobalMapping(J,ltog,ltog);CHKERRQ(ierr);

  /*
    For each node in the grid: we get the neighbors in the local (on processor ordering
    that includes the ghost points) then MatSetValuesLocal() maps those indices to the global
    PETSc ordering.
  */
  if (!da->prealloc_only) {
    ierr = PetscCalloc1(col*col*nc*nc,&values);CHKERRQ(ierr);
    for (i=xs; i<xs+nx; i++) {
      istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
      iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
      for (j=ys; j<ys+ny; j++) {
        jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
        jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
        slot = i - gxs + gnx*(j - gys);
        cnt  = 0;
        for (ii=istart; ii<iend+1; ii++) {
          for (jj=jstart; jj<jend+1; jj++) {
            if (st == DMDA_STENCIL_BOX || !ii || !jj) { /* BOX or on the STAR */
              cols[cnt++] = slot + ii + gnx*jj;
            }
          }
        }
        ierr = MatSetValuesBlockedLocal(J,1,&slot,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
      }
    }
    ierr = PetscFree(values);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  }
  ierr = PetscFree(cols);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode DMCreateMatrix_DA_3d_MPIBAIJ(DM da,Mat J)
{
  PetscErrorCode         ierr;
  PetscInt               xs,ys,nx,ny,i,j,slot,gxs,gys,gnx,gny;
  PetscInt               m,n,dim,s,*cols,k,nc,col,cnt,p,*dnz,*onz;
  PetscInt               istart,iend,jstart,jend,kstart,kend,zs,nz,gzs,gnz,ii,jj,kk;
  MPI_Comm               comm;
  PetscScalar            *values;
  DMBoundaryType         bx,by,bz;
  DMDAStencilType        st;
  ISLocalToGlobalMapping ltog;

  PetscFunctionBegin;
  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  ierr = DMDAGetInfo(da,&dim,&m,&n,&p,0,0,0,&nc,&s,&bx,&by,&bz,&st);CHKERRQ(ierr);
  col  = 2*s + 1;

  ierr = DMDAGetCorners(da,&xs,&ys,&zs,&nx,&ny,&nz);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,&gys,&gzs,&gnx,&gny,&gnz);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  ierr = PetscMalloc1(col*col*col,&cols);CHKERRQ(ierr);

  ierr = DMGetLocalToGlobalMapping(da,&ltog);CHKERRQ(ierr);

  /* determine the matrix preallocation information */
  ierr = MatPreallocateInitialize(comm,nx*ny*nz,nx*ny*nz,dnz,onz);CHKERRQ(ierr);
  for (i=xs; i<xs+nx; i++) {
    istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
    iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
    for (j=ys; j<ys+ny; j++) {
      jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
      jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
      for (k=zs; k<zs+nz; k++) {
        kstart = (bz == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-k));
        kend   = (bz == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,p-k-1));

        slot = i - gxs + gnx*(j - gys) + gnx*gny*(k - gzs);

        /* Find block columns in block row */
        cnt = 0;
        for (ii=istart; ii<iend+1; ii++) {
          for (jj=jstart; jj<jend+1; jj++) {
            for (kk=kstart; kk<kend+1; kk++) {
              if ((st == DMDA_STENCIL_BOX) || ((!ii && !jj) || (!jj && !kk) || (!ii && !kk))) {/* entries on star*/
                cols[cnt++] = slot + ii + gnx*jj + gnx*gny*kk;
              }
            }
          }
        }
        ierr = MatPreallocateSetLocalBlock(ltog,1,&slot,ltog,cnt,cols,dnz,onz);CHKERRQ(ierr);
      }
    }
  }
  ierr = MatSeqBAIJSetPreallocation(J,nc,0,dnz);CHKERRQ(ierr);
  ierr = MatMPIBAIJSetPreallocation(J,nc,0,dnz,0,onz);CHKERRQ(ierr);
  ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);

  ierr = MatSetLocalToGlobalMapping(J,ltog,ltog);CHKERRQ(ierr);

  /*
    For each node in the grid: we get the neighbors in the local (on processor ordering
    that includes the ghost points) then MatSetValuesLocal() maps those indices to the global
    PETSc ordering.
  */
  if (!da->prealloc_only) {
    ierr = PetscCalloc1(col*col*col*nc*nc,&values);CHKERRQ(ierr);
    for (i=xs; i<xs+nx; i++) {
      istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
      iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
      for (j=ys; j<ys+ny; j++) {
        jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
        jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
        for (k=zs; k<zs+nz; k++) {
          kstart = (bz == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-k));
          kend   = (bz == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,p-k-1));

          slot = i - gxs + gnx*(j - gys) + gnx*gny*(k - gzs);

          cnt = 0;
          for (ii=istart; ii<iend+1; ii++) {
            for (jj=jstart; jj<jend+1; jj++) {
              for (kk=kstart; kk<kend+1; kk++) {
                if ((st == DMDA_STENCIL_BOX) || ((!ii && !jj) || (!jj && !kk) || (!ii && !kk))) {/* entries on star*/
                  cols[cnt++] = slot + ii + gnx*jj + gnx*gny*kk;
                }
              }
            }
          }
          ierr = MatSetValuesBlockedLocal(J,1,&slot,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
        }
      }
    }
    ierr = PetscFree(values);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  }
  ierr = PetscFree(cols);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
  This helper is for of SBAIJ preallocation, to discard the lower-triangular values which are difficult to
  identify in the local ordering with periodic domain.
*/
static PetscErrorCode L2GFilterUpperTriangular(ISLocalToGlobalMapping ltog,PetscInt *row,PetscInt *cnt,PetscInt col[])
{
  PetscErrorCode ierr;
  PetscInt       i,n;

  PetscFunctionBegin;
  ierr = ISLocalToGlobalMappingApplyBlock(ltog,1,row,row);CHKERRQ(ierr);
  ierr = ISLocalToGlobalMappingApplyBlock(ltog,*cnt,col,col);CHKERRQ(ierr);
  for (i=0,n=0; i<*cnt; i++) {
    if (col[i] >= *row) col[n++] = col[i];
  }
  *cnt = n;
  PetscFunctionReturn(0);
}

PetscErrorCode DMCreateMatrix_DA_2d_MPISBAIJ(DM da,Mat J)
{
  PetscErrorCode         ierr;
  PetscInt               xs,ys,nx,ny,i,j,slot,gxs,gys,gnx,gny;
  PetscInt               m,n,dim,s,*cols,nc,col,cnt,*dnz,*onz;
  PetscInt               istart,iend,jstart,jend,ii,jj;
  MPI_Comm               comm;
  PetscScalar            *values;
  DMBoundaryType         bx,by;
  DMDAStencilType        st;
  ISLocalToGlobalMapping ltog;

  PetscFunctionBegin;
  /*
     nc - number of components per grid point
     col - number of colors needed in one direction for single component problem
  */
  ierr = DMDAGetInfo(da,&dim,&m,&n,0,0,0,0,&nc,&s,&bx,&by,0,&st);CHKERRQ(ierr);
  col  = 2*s + 1;

  ierr = DMDAGetCorners(da,&xs,&ys,0,&nx,&ny,0);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,&gys,0,&gnx,&gny,0);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  ierr = PetscMalloc1(col*col*nc*nc,&cols);CHKERRQ(ierr);

  ierr = DMGetLocalToGlobalMapping(da,&ltog);CHKERRQ(ierr);

  /* determine the matrix preallocation information */
  ierr = MatPreallocateInitialize(comm,nx*ny,nx*ny,dnz,onz);CHKERRQ(ierr);
  for (i=xs; i<xs+nx; i++) {
    istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
    iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
    for (j=ys; j<ys+ny; j++) {
      jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
      jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
      slot   = i - gxs + gnx*(j - gys);

      /* Find block columns in block row */
      cnt = 0;
      for (ii=istart; ii<iend+1; ii++) {
        for (jj=jstart; jj<jend+1; jj++) {
          if (st == DMDA_STENCIL_BOX || !ii || !jj) {
            cols[cnt++] = slot + ii + gnx*jj;
          }
        }
      }
      ierr = L2GFilterUpperTriangular(ltog,&slot,&cnt,cols);CHKERRQ(ierr);
      ierr = MatPreallocateSymmetricSetBlock(slot,cnt,cols,dnz,onz);CHKERRQ(ierr);
    }
  }
  ierr = MatSeqSBAIJSetPreallocation(J,nc,0,dnz);CHKERRQ(ierr);
  ierr = MatMPISBAIJSetPreallocation(J,nc,0,dnz,0,onz);CHKERRQ(ierr);
  ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);

  ierr = MatSetLocalToGlobalMapping(J,ltog,ltog);CHKERRQ(ierr);

  /*
    For each node in the grid: we get the neighbors in the local (on processor ordering
    that includes the ghost points) then MatSetValuesLocal() maps those indices to the global
    PETSc ordering.
  */
  if (!da->prealloc_only) {
    ierr = PetscCalloc1(col*col*nc*nc,&values);CHKERRQ(ierr);
    for (i=xs; i<xs+nx; i++) {
      istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
      iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
      for (j=ys; j<ys+ny; j++) {
        jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
        jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
        slot   = i - gxs + gnx*(j - gys);

        /* Find block columns in block row */
        cnt = 0;
        for (ii=istart; ii<iend+1; ii++) {
          for (jj=jstart; jj<jend+1; jj++) {
            if (st == DMDA_STENCIL_BOX || !ii || !jj) {
              cols[cnt++] = slot + ii + gnx*jj;
            }
          }
        }
        ierr = L2GFilterUpperTriangular(ltog,&slot,&cnt,cols);CHKERRQ(ierr);
        ierr = MatSetValuesBlocked(J,1,&slot,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
      }
    }
    ierr = PetscFree(values);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  }
  ierr = PetscFree(cols);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode DMCreateMatrix_DA_3d_MPISBAIJ(DM da,Mat J)
{
  PetscErrorCode         ierr;
  PetscInt               xs,ys,nx,ny,i,j,slot,gxs,gys,gnx,gny;
  PetscInt               m,n,dim,s,*cols,k,nc,col,cnt,p,*dnz,*onz;
  PetscInt               istart,iend,jstart,jend,kstart,kend,zs,nz,gzs,gnz,ii,jj,kk;
  MPI_Comm               comm;
  PetscScalar            *values;
  DMBoundaryType         bx,by,bz;
  DMDAStencilType        st;
  ISLocalToGlobalMapping ltog;

  PetscFunctionBegin;
  /*
     nc - number of components per grid point
     col - number of colors needed in one direction for single component problem
  */
  ierr = DMDAGetInfo(da,&dim,&m,&n,&p,0,0,0,&nc,&s,&bx,&by,&bz,&st);CHKERRQ(ierr);
  col  = 2*s + 1;

  ierr = DMDAGetCorners(da,&xs,&ys,&zs,&nx,&ny,&nz);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,&gys,&gzs,&gnx,&gny,&gnz);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  /* create the matrix */
  ierr = PetscMalloc1(col*col*col,&cols);CHKERRQ(ierr);

  ierr = DMGetLocalToGlobalMapping(da,&ltog);CHKERRQ(ierr);

  /* determine the matrix preallocation information */
  ierr = MatPreallocateInitialize(comm,nx*ny*nz,nx*ny*nz,dnz,onz);CHKERRQ(ierr);
  for (i=xs; i<xs+nx; i++) {
    istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
    iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
    for (j=ys; j<ys+ny; j++) {
      jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
      jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
      for (k=zs; k<zs+nz; k++) {
        kstart = (bz == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-k));
        kend   = (bz == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,p-k-1));

        slot = i - gxs + gnx*(j - gys) + gnx*gny*(k - gzs);

        /* Find block columns in block row */
        cnt = 0;
        for (ii=istart; ii<iend+1; ii++) {
          for (jj=jstart; jj<jend+1; jj++) {
            for (kk=kstart; kk<kend+1; kk++) {
              if ((st == DMDA_STENCIL_BOX) || (!ii && !jj) || (!jj && !kk) || (!ii && !kk)) {
                cols[cnt++] = slot + ii + gnx*jj + gnx*gny*kk;
              }
            }
          }
        }
        ierr = L2GFilterUpperTriangular(ltog,&slot,&cnt,cols);CHKERRQ(ierr);
        ierr = MatPreallocateSymmetricSetBlock(slot,cnt,cols,dnz,onz);CHKERRQ(ierr);
      }
    }
  }
  ierr = MatSeqSBAIJSetPreallocation(J,nc,0,dnz);CHKERRQ(ierr);
  ierr = MatMPISBAIJSetPreallocation(J,nc,0,dnz,0,onz);CHKERRQ(ierr);
  ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);

  ierr = MatSetLocalToGlobalMapping(J,ltog,ltog);CHKERRQ(ierr);

  /*
    For each node in the grid: we get the neighbors in the local (on processor ordering
    that includes the ghost points) then MatSetValuesLocal() maps those indices to the global
    PETSc ordering.
  */
  if (!da->prealloc_only) {
    ierr = PetscCalloc1(col*col*col*nc*nc,&values);CHKERRQ(ierr);
    for (i=xs; i<xs+nx; i++) {
      istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
      iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
      for (j=ys; j<ys+ny; j++) {
        jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
        jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
        for (k=zs; k<zs+nz; k++) {
          kstart = (bz == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-k));
          kend   = (bz == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,p-k-1));

          slot = i - gxs + gnx*(j - gys) + gnx*gny*(k - gzs);

          cnt = 0;
          for (ii=istart; ii<iend+1; ii++) {
            for (jj=jstart; jj<jend+1; jj++) {
              for (kk=kstart; kk<kend+1; kk++) {
                if ((st == DMDA_STENCIL_BOX) || (!ii && !jj) || (!jj && !kk) || (!ii && !kk)) {
                  cols[cnt++] = slot + ii + gnx*jj + gnx*gny*kk;
                }
              }
            }
          }
          ierr = L2GFilterUpperTriangular(ltog,&slot,&cnt,cols);CHKERRQ(ierr);
          ierr = MatSetValuesBlocked(J,1,&slot,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
        }
      }
    }
    ierr = PetscFree(values);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  }
  ierr = PetscFree(cols);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/* ---------------------------------------------------------------------------------*/

PetscErrorCode DMCreateMatrix_DA_3d_MPIAIJ_Fill(DM da,Mat J)
{
  PetscErrorCode         ierr;
  PetscInt               xs,ys,nx,ny,i,j,slot,gxs,gys,gnx,gny;
  PetscInt               m,n,dim,s,*cols,k,nc,row,col,cnt, maxcnt = 0,l,p,*dnz,*onz;
  PetscInt               istart,iend,jstart,jend,kstart,kend,zs,nz,gzs,gnz,ii,jj,kk,M,N,P;
  DM_DA                  *dd = (DM_DA*)da->data;
  PetscInt               ifill_col,*dfill = dd->dfill,*ofill = dd->ofill;
  MPI_Comm               comm;
  PetscScalar            *values;
  DMBoundaryType         bx,by,bz;
  ISLocalToGlobalMapping ltog;
  DMDAStencilType        st;
  PetscBool              removedups = PETSC_FALSE;

  PetscFunctionBegin;
  /*
         nc - number of components per grid point
         col - number of colors needed in one direction for single component problem

  */
  ierr = DMDAGetInfo(da,&dim,&m,&n,&p,&M,&N,&P,&nc,&s,&bx,&by,&bz,&st);CHKERRQ(ierr);
  col  = 2*s + 1;
  if (bx == DM_BOUNDARY_PERIODIC && (m % col)) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"For coloring efficiency ensure number of grid points in X is divisible\n\
                 by 2*stencil_width + 1\n");
  if (by == DM_BOUNDARY_PERIODIC && (n % col)) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"For coloring efficiency ensure number of grid points in Y is divisible\n\
                 by 2*stencil_width + 1\n");
  if (bz == DM_BOUNDARY_PERIODIC && (p % col)) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"For coloring efficiency ensure number of grid points in Z is divisible\n\
                 by 2*stencil_width + 1\n");

  /*
       With one processor in periodic domains in a skinny dimension the code will label nonzero columns multiple times
       because of "wrapping" around the end of the domain hitting an entry already counted in the other direction.
  */
  if (M == 1 && 2*s >= m) removedups = PETSC_TRUE;
  if (N == 1 && 2*s >= n) removedups = PETSC_TRUE;
  if (P == 1 && 2*s >= p) removedups = PETSC_TRUE;

  ierr = DMDAGetCorners(da,&xs,&ys,&zs,&nx,&ny,&nz);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(da,&gxs,&gys,&gzs,&gnx,&gny,&gnz);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)da,&comm);CHKERRQ(ierr);

  ierr = PetscMalloc1(col*col*col*nc,&cols);CHKERRQ(ierr);
  ierr = DMGetLocalToGlobalMapping(da,&ltog);CHKERRQ(ierr);

  /* determine the matrix preallocation information */
  ierr = MatPreallocateInitialize(comm,nc*nx*ny*nz,nc*nx*ny*nz,dnz,onz);CHKERRQ(ierr);

  ierr = MatSetBlockSize(J,nc);CHKERRQ(ierr);
  for (i=xs; i<xs+nx; i++) {
    istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
    iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
    for (j=ys; j<ys+ny; j++) {
      jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
      jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
      for (k=zs; k<zs+nz; k++) {
        kstart = (bz == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-k));
        kend   = (bz == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,p-k-1));

        slot = i - gxs + gnx*(j - gys) + gnx*gny*(k - gzs);

        for (l=0; l<nc; l++) {
          cnt = 0;
          for (ii=istart; ii<iend+1; ii++) {
            for (jj=jstart; jj<jend+1; jj++) {
              for (kk=kstart; kk<kend+1; kk++) {
                if (ii || jj || kk) {
                  if ((st == DMDA_STENCIL_BOX) || ((!ii && !jj) || (!jj && !kk) || (!ii && !kk))) {/* entries on star*/
                    for (ifill_col=ofill[l]; ifill_col<ofill[l+1]; ifill_col++) cols[cnt++] = ofill[ifill_col] + nc*(slot + ii + gnx*jj + gnx*gny*kk);
                  }
                } else {
                  if (dfill) {
                    for (ifill_col=dfill[l]; ifill_col<dfill[l+1]; ifill_col++) cols[cnt++] = dfill[ifill_col] + nc*(slot + ii + gnx*jj + gnx*gny*kk);
                  } else {
                    for (ifill_col=0; ifill_col<nc; ifill_col++) cols[cnt++] = ifill_col + nc*(slot + ii + gnx*jj + gnx*gny*kk);
                  }
                }
              }
            }
          }
          row  = l + nc*(slot);
          maxcnt = PetscMax(maxcnt,cnt);
          if (removedups) {
            ierr = MatPreallocateSetLocalRemoveDups(ltog,1,&row,ltog,cnt,cols,dnz,onz);CHKERRQ(ierr);
          } else {
            ierr = MatPreallocateSetLocal(ltog,1,&row,ltog,cnt,cols,dnz,onz);CHKERRQ(ierr);
          }
        }
      }
    }
  }
  ierr = MatSeqAIJSetPreallocation(J,0,dnz);CHKERRQ(ierr);
  ierr = MatMPIAIJSetPreallocation(J,0,dnz,0,onz);CHKERRQ(ierr);
  ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);
  ierr = MatSetLocalToGlobalMapping(J,ltog,ltog);CHKERRQ(ierr);

  /*
    For each node in the grid: we get the neighbors in the local (on processor ordering
    that includes the ghost points) then MatSetValuesLocal() maps those indices to the global
    PETSc ordering.
  */
  if (!da->prealloc_only) {
    ierr = PetscCalloc1(maxcnt,&values);CHKERRQ(ierr);
    for (i=xs; i<xs+nx; i++) {
      istart = (bx == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-i));
      iend   = (bx == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,m-i-1));
      for (j=ys; j<ys+ny; j++) {
        jstart = (by == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-j));
        jend   = (by == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,n-j-1));
        for (k=zs; k<zs+nz; k++) {
          kstart = (bz == DM_BOUNDARY_PERIODIC) ? -s : (PetscMax(-s,-k));
          kend   = (bz == DM_BOUNDARY_PERIODIC) ?  s : (PetscMin(s,p-k-1));

          slot = i - gxs + gnx*(j - gys) + gnx*gny*(k - gzs);

          for (l=0; l<nc; l++) {
            cnt = 0;
            for (ii=istart; ii<iend+1; ii++) {
              for (jj=jstart; jj<jend+1; jj++) {
                for (kk=kstart; kk<kend+1; kk++) {
                  if (ii || jj || kk) {
                    if ((st == DMDA_STENCIL_BOX) || ((!ii && !jj) || (!jj && !kk) || (!ii && !kk))) {/* entries on star*/
                      for (ifill_col=ofill[l]; ifill_col<ofill[l+1]; ifill_col++) cols[cnt++] = ofill[ifill_col] + nc*(slot + ii + gnx*jj + gnx*gny*kk);
                    }
                  } else {
                    if (dfill) {
                      for (ifill_col=dfill[l]; ifill_col<dfill[l+1]; ifill_col++) cols[cnt++] = dfill[ifill_col] + nc*(slot + ii + gnx*jj + gnx*gny*kk);
                    } else {
                      for (ifill_col=0; ifill_col<nc; ifill_col++) cols[cnt++] = ifill_col + nc*(slot + ii + gnx*jj + gnx*gny*kk);
                    }
                  }
                }
              }
            }
            row  = l + nc*(slot);
            ierr = MatSetValuesLocal(J,1,&row,cnt,cols,values,INSERT_VALUES);CHKERRQ(ierr);
          }
        }
      }
    }
    ierr = PetscFree(values);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  }
  ierr = PetscFree(cols);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}