xref: /petsc/src/dm/impls/da/da3.c (revision d461ba9780c55a0df6dc85ac9e4e0589fbf99e79)

/*
   Code for manipulating distributed regular 3d arrays in parallel.
   File created by Peter Mell  7/14/95
 */

#include <private/daimpl.h>     /*I   "petscdmda.h"    I*/

#undef __FUNCT__
#define __FUNCT__ "DMView_DA_3d"
PetscErrorCode DMView_DA_3d(DM da,PetscViewer viewer)
{
  PetscErrorCode ierr;
  PetscMPIInt    rank;
  PetscBool      iascii,isdraw,isbinary;
  DM_DA          *dd = (DM_DA*)da->data;
#if defined(PETSC_HAVE_MATLAB_ENGINE)
  PetscBool      ismatlab;
#endif

  PetscFunctionBegin;
  ierr = MPI_Comm_rank(((PetscObject)da)->comm,&rank);CHKERRQ(ierr);

  ierr = PetscTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr);
  ierr = PetscTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr);
  ierr = PetscTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr);
#if defined(PETSC_HAVE_MATLAB_ENGINE)
  ierr = PetscTypeCompare((PetscObject)viewer,PETSCVIEWERMATLAB,&ismatlab);CHKERRQ(ierr);
#endif
  if (iascii) {
    PetscViewerFormat format;

    ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);CHKERRQ(ierr);
    ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr);
    if (format != PETSC_VIEWER_ASCII_VTK && format != PETSC_VIEWER_ASCII_VTK_CELL) {
      DMDALocalInfo info;
      ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
      ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Processor [%d] M %D N %D P %D m %D n %D p %D w %D s %D\n",rank,dd->M,dd->N,dd->P,dd->m,dd->n,dd->p,dd->w,dd->s);CHKERRQ(ierr);
      ierr = PetscViewerASCIISynchronizedPrintf(viewer,"X range of indices: %D %D, Y range of indices: %D %D, Z range of indices: %D %D\n",
                                                info.xs,info.xs+info.xm,info.ys,info.ys+info.ym,info.zs,info.zs+info.zm);CHKERRQ(ierr);
#if !defined(PETSC_USE_COMPLEX)
      if (dd->coordinates) {
        PetscInt        last;
        const PetscReal *coors;
        ierr = VecGetArrayRead(dd->coordinates,&coors);CHKERRQ(ierr);
        ierr = VecGetLocalSize(dd->coordinates,&last);CHKERRQ(ierr);
        last = last - 3;
        ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Lower left corner %G %G %G : Upper right %G %G %G\n",coors[0],coors[1],coors[2],coors[last],coors[last+1],coors[last+2]);CHKERRQ(ierr);
        ierr = VecRestoreArrayRead(dd->coordinates,&coors);CHKERRQ(ierr);
      }
#endif
      ierr = PetscViewerFlush(viewer);CHKERRQ(ierr);
      ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_FALSE);CHKERRQ(ierr);
    } else {
      ierr = DMView_DA_VTK(da,viewer);CHKERRQ(ierr);
    }
  } else if (isdraw) {
    PetscDraw       draw;
    PetscReal     ymin = -1.0,ymax = (PetscReal)dd->N;
    PetscReal     xmin = -1.0,xmax = (PetscReal)((dd->M+2)*dd->P),x,y,ycoord,xcoord;
    PetscInt        k,plane,base,*idx;
    char       node[10];
    PetscBool  isnull;

    ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
    ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0);
    ierr = PetscDrawSetCoordinates(draw,xmin,ymin,xmax,ymax);CHKERRQ(ierr);
    ierr = PetscDrawSynchronizedClear(draw);CHKERRQ(ierr);

    /* first processor draw all node lines */
    if (!rank) {
      for (k=0; k<dd->P; k++) {
        ymin = 0.0; ymax = (PetscReal)(dd->N - 1);
        for (xmin=(PetscReal)(k*(dd->M+1)); xmin<(PetscReal)(dd->M+(k*(dd->M+1))); xmin++) {
          ierr = PetscDrawLine(draw,xmin,ymin,xmin,ymax,PETSC_DRAW_BLACK);CHKERRQ(ierr);
        }

        xmin = (PetscReal)(k*(dd->M+1)); xmax = xmin + (PetscReal)(dd->M - 1);
        for (ymin=0; ymin<(PetscReal)dd->N; ymin++) {
          ierr = PetscDrawLine(draw,xmin,ymin,xmax,ymin,PETSC_DRAW_BLACK);CHKERRQ(ierr);
        }
      }
    }
    ierr = PetscDrawSynchronizedFlush(draw);CHKERRQ(ierr);
    ierr = PetscDrawPause(draw);CHKERRQ(ierr);

    for (k=0; k<dd->P; k++) {  /*Go through and draw for each plane*/
      if ((k >= dd->zs) && (k < dd->ze)) {
        /* draw my box */
        ymin = dd->ys;
        ymax = dd->ye - 1;
        xmin = dd->xs/dd->w    + (dd->M+1)*k;
        xmax =(dd->xe-1)/dd->w + (dd->M+1)*k;

        ierr = PetscDrawLine(draw,xmin,ymin,xmax,ymin,PETSC_DRAW_RED);CHKERRQ(ierr);
        ierr = PetscDrawLine(draw,xmin,ymin,xmin,ymax,PETSC_DRAW_RED);CHKERRQ(ierr);
        ierr = PetscDrawLine(draw,xmin,ymax,xmax,ymax,PETSC_DRAW_RED);CHKERRQ(ierr);
        ierr = PetscDrawLine(draw,xmax,ymin,xmax,ymax,PETSC_DRAW_RED);CHKERRQ(ierr);

        xmin = dd->xs/dd->w;
        xmax =(dd->xe-1)/dd->w;

        /* put in numbers*/
        base = (dd->base+(dd->xe-dd->xs)*(dd->ye-dd->ys)*(k-dd->zs))/dd->w;

        /* Identify which processor owns the box */
        sprintf(node,"%d",rank);
        ierr = PetscDrawString(draw,xmin+(dd->M+1)*k+.2,ymin+.3,PETSC_DRAW_RED,node);CHKERRQ(ierr);

        for (y=ymin; y<=ymax; y++) {
          for (x=xmin+(dd->M+1)*k; x<=xmax+(dd->M+1)*k; x++) {
            sprintf(node,"%d",(int)base++);
            ierr = PetscDrawString(draw,x,y,PETSC_DRAW_BLACK,node);CHKERRQ(ierr);
          }
        }

      }
    }
    ierr = PetscDrawSynchronizedFlush(draw);CHKERRQ(ierr);
    ierr = PetscDrawPause(draw);CHKERRQ(ierr);

    for (k=0-dd->s; k<dd->P+dd->s; k++) {
      /* Go through and draw for each plane */
      if ((k >= dd->Zs) && (k < dd->Ze)) {

        /* overlay ghost numbers, useful for error checking */
        base = (dd->Xe-dd->Xs)*(dd->Ye-dd->Ys)*(k-dd->Zs); idx = dd->idx;
        plane=k;
        /* Keep z wrap around points on the dradrawg */
        if (k<0)    { plane=dd->P+k; }
        if (k>=dd->P) { plane=k-dd->P; }
        ymin = dd->Ys; ymax = dd->Ye;
        xmin = (dd->M+1)*plane*dd->w;
        xmax = (dd->M+1)*plane*dd->w+dd->M*dd->w;
        for (y=ymin; y<ymax; y++) {
          for (x=xmin+dd->Xs; x<xmin+dd->Xe; x+=dd->w) {
            sprintf(node,"%d",(int)(idx[base]/dd->w));
            ycoord = y;
            /*Keep y wrap around points on drawing */
            if (y<0)      { ycoord = dd->N+y; }

            if (y>=dd->N) { ycoord = y-dd->N; }
            xcoord = x;   /* Keep x wrap points on drawing */

            if (x<xmin)  { xcoord = xmax - (xmin-x); }
            if (x>=xmax) { xcoord = xmin + (x-xmax); }
            ierr = PetscDrawString(draw,xcoord/dd->w,ycoord,PETSC_DRAW_BLUE,node);CHKERRQ(ierr);
            base+=dd->w;
          }
        }
      }
    }
    ierr = PetscDrawSynchronizedFlush(draw);CHKERRQ(ierr);
    ierr = PetscDrawPause(draw);CHKERRQ(ierr);
  } else if (isbinary){
    ierr = DMView_DA_Binary(da,viewer);CHKERRQ(ierr);
#if defined(PETSC_HAVE_MATLAB_ENGINE)
  } else if (ismatlab) {
    ierr = DMView_DA_Matlab(da,viewer);CHKERRQ(ierr);
#endif
  } else SETERRQ1(((PetscObject)da)->comm,PETSC_ERR_SUP,"Viewer type %s not supported for DMDA 1d",((PetscObject)viewer)->type_name);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMSetUp_DA_3D"
PetscErrorCode  DMSetUp_DA_3D(DM da)
{
  DM_DA                  *dd           = (DM_DA*)da->data;
  const PetscInt         M            = dd->M;
  const PetscInt         N            = dd->N;
  const PetscInt         P            = dd->P;
  PetscInt               m            = dd->m;
  PetscInt               n            = dd->n;
  PetscInt               p            = dd->p;
  const PetscInt         dof          = dd->w;
  const PetscInt         s            = dd->s;
  const DMDABoundaryType bx         = dd->bx;
  const DMDABoundaryType by         = dd->by;
  const DMDABoundaryType bz         = dd->bz;
  const DMDAStencilType  stencil_type = dd->stencil_type;
  PetscInt               *lx           = dd->lx;
  PetscInt               *ly           = dd->ly;
  PetscInt               *lz           = dd->lz;
  MPI_Comm               comm;
  PetscMPIInt            rank,size;
  PetscInt               xs = 0,xe,ys = 0,ye,zs = 0,ze,x = 0,y = 0,z = 0;
  PetscInt               Xs,Xe,Ys,Ye,Zs,Ze,IXs,IXe,IYs,IYe,IZs,IZe,start,end,pm;
  PetscInt               left,right,up,down,bottom,top,i,j,k,*idx,*idx_cpy,nn;
  const PetscInt         *idx_full;
  PetscInt               n0,n1,n2,n3,n4,n5,n6,n7,n8,n9,n10,n11,n12,n14;
  PetscInt               n15,n16,n17,n18,n19,n20,n21,n22,n23,n24,n25,n26;
  PetscInt               *bases,*ldims,base,x_t,y_t,z_t,s_t,count,s_x,s_y,s_z;
  PetscInt               sn0 = 0,sn1 = 0,sn2 = 0,sn3 = 0,sn5 = 0,sn6 = 0,sn7 = 0;
  PetscInt               sn8 = 0,sn9 = 0,sn11 = 0,sn15 = 0,sn24 = 0,sn25 = 0,sn26 = 0;
  PetscInt               sn17 = 0,sn18 = 0,sn19 = 0,sn20 = 0,sn21 = 0,sn23 = 0;
  Vec                    local,global;
  VecScatter             ltog,gtol;
  IS                     to,from,ltogis;
  PetscErrorCode         ierr;

  PetscFunctionBegin;
  if (dof < 1) SETERRQ1(((PetscObject)da)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Must have 1 or more degrees of freedom per node: %D",dof);
  if (s < 0) SETERRQ1(((PetscObject)da)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Stencil width cannot be negative: %D",s);

  ierr = PetscObjectGetComm((PetscObject) da, &comm);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);

  dd->dim = 3;
  ierr = PetscMalloc(dof*sizeof(char*),&dd->fieldname);CHKERRQ(ierr);
  ierr = PetscMemzero(dd->fieldname,dof*sizeof(char*));CHKERRQ(ierr);

  if (m != PETSC_DECIDE) {
    if (m < 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Non-positive number of processors in X direction: %D",m);
    else if (m > size) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Too many processors in X direction: %D %d",m,size);
  }
  if (n != PETSC_DECIDE) {
    if (n < 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Non-positive number of processors in Y direction: %D",n);
    else if (n > size)  SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Too many processors in Y direction: %D %d",n,size);
  }
  if (p != PETSC_DECIDE) {
    if (p < 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Non-positive number of processors in Z direction: %D",p);
    else if (p > size) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Too many processors in Z direction: %D %d",p,size);
  }
  if ((m > 0) && (n > 0) && (p > 0) && (m*n*p != size)) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"m %D * n %D * p %D != size %d",m,n,p,size);

  /* Partition the array among the processors */
  if (m == PETSC_DECIDE && n != PETSC_DECIDE && p != PETSC_DECIDE) {
    m = size/(n*p);
  } else if (m != PETSC_DECIDE && n == PETSC_DECIDE && p != PETSC_DECIDE) {
    n = size/(m*p);
  } else if (m != PETSC_DECIDE && n != PETSC_DECIDE && p == PETSC_DECIDE) {
    p = size/(m*n);
  } else if (m == PETSC_DECIDE && n == PETSC_DECIDE && p != PETSC_DECIDE) {
    /* try for squarish distribution */
    m = (int)(0.5 + sqrt(((double)M)*((double)size)/((double)N*p)));
    if (!m) m = 1;
    while (m > 0) {
      n = size/(m*p);
      if (m*n*p == size) break;
      m--;
    }
    if (!m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"bad p value: p = %D",p);
    if (M > N && m < n) {PetscInt _m = m; m = n; n = _m;}
  } else if (m == PETSC_DECIDE && n != PETSC_DECIDE && p == PETSC_DECIDE) {
    /* try for squarish distribution */
    m = (int)(0.5 + sqrt(((double)M)*((double)size)/((double)P*n)));
    if (!m) m = 1;
    while (m > 0) {
      p = size/(m*n);
      if (m*n*p == size) break;
      m--;
    }
    if (!m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"bad n value: n = %D",n);
    if (M > P && m < p) {PetscInt _m = m; m = p; p = _m;}
  } else if (m != PETSC_DECIDE && n == PETSC_DECIDE && p == PETSC_DECIDE) {
    /* try for squarish distribution */
    n = (int)(0.5 + sqrt(((double)N)*((double)size)/((double)P*m)));
    if (!n) n = 1;
    while (n > 0) {
      p = size/(m*n);
      if (m*n*p == size) break;
      n--;
    }
    if (!n) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"bad m value: m = %D",n);
    if (N > P && n < p) {PetscInt _n = n; n = p; p = _n;}
  } else if (m == PETSC_DECIDE && n == PETSC_DECIDE && p == PETSC_DECIDE) {
    /* try for squarish distribution */
    n = (PetscInt)(0.5 + pow(((double)N*N)*((double)size)/((double)P*M),(double)(1./3.)));
    if (!n) n = 1;
    while (n > 0) {
      pm = size/n;
      if (n*pm == size) break;
      n--;
    }
    if (!n) n = 1;
    m = (PetscInt)(0.5 + sqrt(((double)M)*((double)size)/((double)P*n)));
    if (!m) m = 1;
    while (m > 0) {
      p = size/(m*n);
      if (m*n*p == size) break;
      m--;
    }
    if (M > P && m < p) {PetscInt _m = m; m = p; p = _m;}
  } else if (m*n*p != size) SETERRQ(((PetscObject)da)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Given Bad partition");

  if (m*n*p != size) SETERRQ(((PetscObject)da)->comm,PETSC_ERR_PLIB,"Could not find good partition");
  if (M < m) SETERRQ2(((PetscObject)da)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Partition in x direction is too fine! %D %D",M,m);
  if (N < n) SETERRQ2(((PetscObject)da)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Partition in y direction is too fine! %D %D",N,n);
  if (P < p) SETERRQ2(((PetscObject)da)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Partition in z direction is too fine! %D %D",P,p);

  /*
     Determine locally owned region
     [x, y, or z]s is the first local node number, [x, y, z] is the number of local nodes
  */

  if (!lx) {
    ierr = PetscMalloc(m*sizeof(PetscInt), &dd->lx);CHKERRQ(ierr);
    lx = dd->lx;
    for (i=0; i<m; i++) {
      lx[i] = M/m + ((M % m) > (i % m));
    }
  }
  x  = lx[rank % m];
  xs = 0;
  for (i=0; i<(rank%m); i++) { xs += lx[i];}
  if ((x < s) && ((m > 1) || (bx == DMDA_BOUNDARY_PERIODIC))) {
    SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local x-width of domain x %D is smaller than stencil width s %D",x,s);
  }

  if (!ly) {
    ierr = PetscMalloc(n*sizeof(PetscInt), &dd->ly);CHKERRQ(ierr);
    ly = dd->ly;
    for (i=0; i<n; i++) {
      ly[i] = N/n + ((N % n) > (i % n));
    }
  }
  y  = ly[(rank % (m*n))/m];
  if ((y < s) && ((n > 1) || (by == DMDA_BOUNDARY_PERIODIC))) {
    SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local y-width of domain y %D is smaller than stencil width s %D",y,s);
  }
  ys = 0;
  for (i=0; i<(rank % (m*n))/m; i++) { ys += ly[i];}

  if (!lz) {
    ierr = PetscMalloc(p*sizeof(PetscInt), &dd->lz);CHKERRQ(ierr);
    lz = dd->lz;
    for (i=0; i<p; i++) {
      lz[i] = P/p + ((P % p) > (i % p));
    }
  }
  z  = lz[rank/(m*n)];

  /* note this is different than x- and y-, as we will handle as an important special
   case when p=P=1 and DMDA_BOUNDARY_PERIODIC and s > z.  This is to deal with 2D problems
   in a 3D code.  Additional code for this case is noted with "2d case" comments */
  if ((z < s) && ((p > 1) || ((P > 1) && bz == DMDA_BOUNDARY_PERIODIC))) {
    SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local z-width of domain z %D is smaller than stencil width s %D",z,s);
  }
  zs = 0;
  for (i=0; i<(rank/(m*n)); i++) { zs += lz[i];}
  ye = ys + y;
  xe = xs + x;
  ze = zs + z;

  /* determine ghost region */
  /* Assume No Periodicity */
  if (xs-s > 0) { Xs = xs - s; IXs = xs - s; } else { Xs = 0; IXs = 0; }
  if (xe+s <= M) { Xe = xe + s; IXe = xe + s; } else { Xe = M; IXe = M; }
  if (ys-s > 0) { Ys = ys - s; IYs = ys - s; } else { Ys = 0; IYs = 0; }
  if (ye+s <= N) { Ye = ye + s; IYe = ye + s; } else { Ye = N; IYe = N; }
  if (zs-s > 0) { Zs = zs - s; IZs = zs - s; } else { Zs = 0; IZs = 0; }
  if (ze+s <= P) { Ze = ze + s; IZe = ze + s; } else { Ze = P; IZe = P; }

  /* fix for periodicity/ghosted */
  if (bx) { Xs = xs - s; Xe = xe + s; }
  if (bx == DMDA_BOUNDARY_PERIODIC) { IXs = xs - s; IXe = xe + s; }
  if (by) { Ys = ys - s; Ye = ye + s; }
  if (by == DMDA_BOUNDARY_PERIODIC) { IYs = ys - s; IYe = ye + s; }
  if (bz) { Zs = zs - s; Ze = ze + s; }
  if (bz == DMDA_BOUNDARY_PERIODIC) { IZs = zs - s; IZe = ze + s; }

  /* Resize all X parameters to reflect w */
  s_x = s;
  s_y  = s;
  s_z  = s;

  /* determine starting point of each processor */
  nn       = x*y*z;
  ierr     = PetscMalloc2(size+1,PetscInt,&bases,size,PetscInt,&ldims);CHKERRQ(ierr);
  ierr     = MPI_Allgather(&nn,1,MPIU_INT,ldims,1,MPIU_INT,comm);CHKERRQ(ierr);
  bases[0] = 0;
  for (i=1; i<=size; i++) {
    bases[i] = ldims[i-1];
  }
  for (i=1; i<=size; i++) {
    bases[i] += bases[i-1];
  }
  base = bases[rank]*dof;

  /* allocate the base parallel and sequential vectors */
  dd->Nlocal = x*y*z*dof;
  ierr = VecCreateMPIWithArray(comm,dd->Nlocal,PETSC_DECIDE,0,&global);CHKERRQ(ierr);
  ierr = VecSetBlockSize(global,dof);CHKERRQ(ierr);
  dd->nlocal = (Xe-Xs)*(Ye-Ys)*(Ze-Zs)*dof;
  ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,dd->nlocal,0,&local);CHKERRQ(ierr);
  ierr = VecSetBlockSize(local,dof);CHKERRQ(ierr);

  /* generate appropriate vector scatters */
  /* local to global inserts non-ghost point region into global */
  ierr = VecGetOwnershipRange(global,&start,&end);CHKERRQ(ierr);
  ierr = ISCreateStride(comm,x*y*z*dof,start,1,&to);CHKERRQ(ierr);

  count = x*y*z;
  ierr = PetscMalloc(x*y*z*sizeof(PetscInt),&idx);CHKERRQ(ierr);
  left   = xs - Xs; right = left + x;
  bottom = ys - Ys; top = bottom + y;
  down   = zs - Zs; up  = down + z;
  count  = 0;
  for (i=down; i<up; i++) {
    for (j=bottom; j<top; j++) {
      for (k=left; k<right; k++) {
        idx[count++] = (i*(Ye-Ys) + j)*(Xe-Xs) + k;
      }
    }
  }

  ierr = ISCreateBlock(comm,dof,count,idx,PETSC_OWN_POINTER,&from);CHKERRQ(ierr);
  ierr = VecScatterCreate(local,from,global,to,&ltog);CHKERRQ(ierr);
  ierr = PetscLogObjectParent(da,ltog);CHKERRQ(ierr);
  ierr = ISDestroy(&from);CHKERRQ(ierr);
  ierr = ISDestroy(&to);CHKERRQ(ierr);

  /* global to local must include ghost points within the domain,
     but not ghost points outside the domain that aren't periodic */
  if (stencil_type == DMDA_STENCIL_BOX) {
    count = (IXe-IXs)*(IYe-IYs)*(IZe-IZs);
    ierr  = PetscMalloc(count*sizeof(PetscInt),&idx);CHKERRQ(ierr);

    left   = IXs - Xs; right = left + (IXe-IXs);
    bottom = IYs - Ys; top = bottom + (IYe-IYs);
    down   = IZs - Zs; up  = down + (IZe-IZs);
    count = 0;
    for (i=down; i<up; i++) {
      for (j=bottom; j<top; j++) {
        for (k=left; k<right; k++) {
          idx[count++] = (i*(Ye-Ys) + j)*(Xe-Xs) + k;
        }
      }
    }
    ierr = ISCreateBlock(comm,dof,count,idx,PETSC_OWN_POINTER,&to);CHKERRQ(ierr);

  } else {
    /* This is way ugly! We need to list the funny cross type region */
    count = ((ys-IYs) + (IYe-ye))*x*z + ((xs-IXs) + (IXe-xe))*y*z + ((zs-IZs) + (IZe-ze))*x*y + x*y*z;
    ierr   = PetscMalloc(count*sizeof(PetscInt),&idx);CHKERRQ(ierr);

    left   = xs - Xs; right = left + x;
    bottom = ys - Ys; top = bottom + y;
    down   = zs - Zs;   up  = down + z;
    count  = 0;
    /* the bottom chunck */
    for (i=(IZs-Zs); i<down; i++) {
      for (j=bottom; j<top; j++) {
        for (k=left; k<right; k++) idx[count++] = (i*(Ye-Ys) + j)*(Xe-Xs) + k;
      }
    }
    /* the middle piece */
    for (i=down; i<up; i++) {
      /* front */
      for (j=(IYs-Ys); j<bottom; j++) {
        for (k=left; k<right; k++) idx[count++] = (i*(Ye-Ys) + j)*(Xe-Xs) + k;
      }
      /* middle */
      for (j=bottom; j<top; j++) {
        for (k=IXs-Xs; k<IXe-Xs; k++) idx[count++] = (i*(Ye-Ys) + j)*(Xe-Xs) + k;
      }
      /* back */
      for (j=top; j<top+IYe-ye; j++) {
        for (k=left; k<right; k++) idx[count++] = (i*(Ye-Ys) + j)*(Xe-Xs) + k;
      }
    }
    /* the top piece */
    for (i=up; i<up+IZe-ze; i++) {
      for (j=bottom; j<top; j++) {
        for (k=left; k<right; k++) idx[count++] = (i*(Ye-Ys) + j)*(Xe-Xs) + k;
      }
    }
    ierr = ISCreateBlock(comm,dof,count,idx,PETSC_OWN_POINTER,&to);CHKERRQ(ierr);
  }

  /* determine who lies on each side of use stored in    n24 n25 n26
                                                         n21 n22 n23
                                                         n18 n19 n20

                                                         n15 n16 n17
                                                         n12     n14
                                                         n9  n10 n11

                                                         n6  n7  n8
                                                         n3  n4  n5
                                                         n0  n1  n2
  */

  /* Solve for X,Y, and Z Periodic Case First, Then Modify Solution */
  /* Assume Nodes are Internal to the Cube */
  n0  = rank - m*n - m - 1;
  n1  = rank - m*n - m;
  n2  = rank - m*n - m + 1;
  n3  = rank - m*n -1;
  n4  = rank - m*n;
  n5  = rank - m*n + 1;
  n6  = rank - m*n + m - 1;
  n7  = rank - m*n + m;
  n8  = rank - m*n + m + 1;

  n9  = rank - m - 1;
  n10 = rank - m;
  n11 = rank - m + 1;
  n12 = rank - 1;
  n14 = rank + 1;
  n15 = rank + m - 1;
  n16 = rank + m;
  n17 = rank + m + 1;

  n18 = rank + m*n - m - 1;
  n19 = rank + m*n - m;
  n20 = rank + m*n - m + 1;
  n21 = rank + m*n - 1;
  n22 = rank + m*n;
  n23 = rank + m*n + 1;
  n24 = rank + m*n + m - 1;
  n25 = rank + m*n + m;
  n26 = rank + m*n + m + 1;

  /* Assume Pieces are on Faces of Cube */

  if (xs == 0) { /* First assume not corner or edge */
    n0  = rank       -1 - (m*n);
    n3  = rank + m   -1 - (m*n);
    n6  = rank + 2*m -1 - (m*n);
    n9  = rank       -1;
    n12 = rank + m   -1;
    n15 = rank + 2*m -1;
    n18 = rank       -1 + (m*n);
    n21 = rank + m   -1 + (m*n);
    n24 = rank + 2*m -1 + (m*n);
   }

  if (xe == M) { /* First assume not corner or edge */
    n2  = rank -2*m +1 - (m*n);
    n5  = rank - m  +1 - (m*n);
    n8  = rank      +1 - (m*n);
    n11 = rank -2*m +1;
    n14 = rank - m  +1;
    n17 = rank      +1;
    n20 = rank -2*m +1 + (m*n);
    n23 = rank - m  +1 + (m*n);
    n26 = rank      +1 + (m*n);
  }

  if (ys==0) { /* First assume not corner or edge */
    n0  = rank + m * (n-1) -1 - (m*n);
    n1  = rank + m * (n-1)    - (m*n);
    n2  = rank + m * (n-1) +1 - (m*n);
    n9  = rank + m * (n-1) -1;
    n10 = rank + m * (n-1);
    n11 = rank + m * (n-1) +1;
    n18 = rank + m * (n-1) -1 + (m*n);
    n19 = rank + m * (n-1)    + (m*n);
    n20 = rank + m * (n-1) +1 + (m*n);
  }

  if (ye == N) { /* First assume not corner or edge */
    n6  = rank - m * (n-1) -1 - (m*n);
    n7  = rank - m * (n-1)    - (m*n);
    n8  = rank - m * (n-1) +1 - (m*n);
    n15 = rank - m * (n-1) -1;
    n16 = rank - m * (n-1);
    n17 = rank - m * (n-1) +1;
    n24 = rank - m * (n-1) -1 + (m*n);
    n25 = rank - m * (n-1)    + (m*n);
    n26 = rank - m * (n-1) +1 + (m*n);
  }

  if (zs == 0) { /* First assume not corner or edge */
    n0 = size - (m*n) + rank - m - 1;
    n1 = size - (m*n) + rank - m;
    n2 = size - (m*n) + rank - m + 1;
    n3 = size - (m*n) + rank - 1;
    n4 = size - (m*n) + rank;
    n5 = size - (m*n) + rank + 1;
    n6 = size - (m*n) + rank + m - 1;
    n7 = size - (m*n) + rank + m ;
    n8 = size - (m*n) + rank + m + 1;
  }

  if (ze == P) { /* First assume not corner or edge */
    n18 = (m*n) - (size-rank) - m - 1;
    n19 = (m*n) - (size-rank) - m;
    n20 = (m*n) - (size-rank) - m + 1;
    n21 = (m*n) - (size-rank) - 1;
    n22 = (m*n) - (size-rank);
    n23 = (m*n) - (size-rank) + 1;
    n24 = (m*n) - (size-rank) + m - 1;
    n25 = (m*n) - (size-rank) + m;
    n26 = (m*n) - (size-rank) + m + 1;
  }

  if ((xs==0) && (zs==0)) { /* Assume an edge, not corner */
    n0 = size - m*n + rank + m-1 - m;
    n3 = size - m*n + rank + m-1;
    n6 = size - m*n + rank + m-1 + m;
  }

  if ((xs==0) && (ze==P)) { /* Assume an edge, not corner */
    n18 = m*n - (size - rank) + m-1 - m;
    n21 = m*n - (size - rank) + m-1;
    n24 = m*n - (size - rank) + m-1 + m;
  }

  if ((xs==0) && (ys==0)) { /* Assume an edge, not corner */
    n0  = rank + m*n -1 - m*n;
    n9  = rank + m*n -1;
    n18 = rank + m*n -1 + m*n;
  }

  if ((xs==0) && (ye==N)) { /* Assume an edge, not corner */
    n6  = rank - m*(n-1) + m-1 - m*n;
    n15 = rank - m*(n-1) + m-1;
    n24 = rank - m*(n-1) + m-1 + m*n;
  }

  if ((xe==M) && (zs==0)) { /* Assume an edge, not corner */
    n2 = size - (m*n-rank) - (m-1) - m;
    n5 = size - (m*n-rank) - (m-1);
    n8 = size - (m*n-rank) - (m-1) + m;
  }

  if ((xe==M) && (ze==P)) { /* Assume an edge, not corner */
    n20 = m*n - (size - rank) - (m-1) - m;
    n23 = m*n - (size - rank) - (m-1);
    n26 = m*n - (size - rank) - (m-1) + m;
  }

  if ((xe==M) && (ys==0)) { /* Assume an edge, not corner */
    n2  = rank + m*(n-1) - (m-1) - m*n;
    n11 = rank + m*(n-1) - (m-1);
    n20 = rank + m*(n-1) - (m-1) + m*n;
  }

  if ((xe==M) && (ye==N)) { /* Assume an edge, not corner */
    n8  = rank - m*n +1 - m*n;
    n17 = rank - m*n +1;
    n26 = rank - m*n +1 + m*n;
  }

  if ((ys==0) && (zs==0)) { /* Assume an edge, not corner */
    n0 = size - m + rank -1;
    n1 = size - m + rank;
    n2 = size - m + rank +1;
  }

  if ((ys==0) && (ze==P)) { /* Assume an edge, not corner */
    n18 = m*n - (size - rank) + m*(n-1) -1;
    n19 = m*n - (size - rank) + m*(n-1);
    n20 = m*n - (size - rank) + m*(n-1) +1;
  }

  if ((ye==N) && (zs==0)) { /* Assume an edge, not corner */
    n6 = size - (m*n-rank) - m * (n-1) -1;
    n7 = size - (m*n-rank) - m * (n-1);
    n8 = size - (m*n-rank) - m * (n-1) +1;
  }

  if ((ye==N) && (ze==P)) { /* Assume an edge, not corner */
    n24 = rank - (size-m) -1;
    n25 = rank - (size-m);
    n26 = rank - (size-m) +1;
  }

  /* Check for Corners */
  if ((xs==0)   && (ys==0) && (zs==0)) { n0  = size -1;}
  if ((xs==0)   && (ys==0) && (ze==P)) { n18 = m*n-1;}
  if ((xs==0)   && (ye==N) && (zs==0)) { n6  = (size-1)-m*(n-1);}
  if ((xs==0)   && (ye==N) && (ze==P)) { n24 = m-1;}
  if ((xe==M) && (ys==0) && (zs==0)) { n2  = size-m;}
  if ((xe==M) && (ys==0) && (ze==P)) { n20 = m*n-m;}
  if ((xe==M) && (ye==N) && (zs==0)) { n8  = size-m*n;}
  if ((xe==M) && (ye==N) && (ze==P)) { n26 = 0;}

  /* Check for when not X,Y, and Z Periodic */

  /* If not X periodic */
  if (bx != DMDA_BOUNDARY_PERIODIC) {
    if (xs==0)   {n0  = n3  = n6  = n9  = n12 = n15 = n18 = n21 = n24 = -2;}
    if (xe==M) {n2  = n5  = n8  = n11 = n14 = n17 = n20 = n23 = n26 = -2;}
  }

  /* If not Y periodic */
  if (by != DMDA_BOUNDARY_PERIODIC) {
    if (ys==0)   {n0  = n1  = n2  = n9  = n10 = n11 = n18 = n19 = n20 = -2;}
    if (ye==N)   {n6  = n7  = n8  = n15 = n16 = n17 = n24 = n25 = n26 = -2;}
  }

  /* If not Z periodic */
  if (bz != DMDA_BOUNDARY_PERIODIC) {
    if (zs==0)   {n0  = n1  = n2  = n3  = n4  = n5  = n6  = n7  = n8  = -2;}
    if (ze==P)   {n18 = n19 = n20 = n21 = n22 = n23 = n24 = n25 = n26 = -2;}
  }

  ierr = PetscMalloc(27*sizeof(PetscInt),&dd->neighbors);CHKERRQ(ierr);
  dd->neighbors[0] = n0;
  dd->neighbors[1] = n1;
  dd->neighbors[2] = n2;
  dd->neighbors[3] = n3;
  dd->neighbors[4] = n4;
  dd->neighbors[5] = n5;
  dd->neighbors[6] = n6;
  dd->neighbors[7] = n7;
  dd->neighbors[8] = n8;
  dd->neighbors[9] = n9;
  dd->neighbors[10] = n10;
  dd->neighbors[11] = n11;
  dd->neighbors[12] = n12;
  dd->neighbors[13] = rank;
  dd->neighbors[14] = n14;
  dd->neighbors[15] = n15;
  dd->neighbors[16] = n16;
  dd->neighbors[17] = n17;
  dd->neighbors[18] = n18;
  dd->neighbors[19] = n19;
  dd->neighbors[20] = n20;
  dd->neighbors[21] = n21;
  dd->neighbors[22] = n22;
  dd->neighbors[23] = n23;
  dd->neighbors[24] = n24;
  dd->neighbors[25] = n25;
  dd->neighbors[26] = n26;

  /* If star stencil then delete the corner neighbors */
  if (stencil_type == DMDA_STENCIL_STAR) {
     /* save information about corner neighbors */
     sn0 = n0; sn1 = n1; sn2 = n2; sn3 = n3; sn5 = n5; sn6 = n6; sn7 = n7;
     sn8 = n8; sn9 = n9; sn11 = n11; sn15 = n15; sn17 = n17; sn18 = n18;
     sn19 = n19; sn20 = n20; sn21 = n21; sn23 = n23; sn24 = n24; sn25 = n25;
     sn26 = n26;
     n0  = n1  = n2  = n3  = n5  = n6  = n7  = n8  = n9  = n11 =
     n15 = n17 = n18 = n19 = n20 = n21 = n23 = n24 = n25 = n26 = -1;
  }


  ierr = PetscMalloc((Xe-Xs)*(Ye-Ys)*(Ze-Zs)*sizeof(PetscInt),&idx);CHKERRQ(ierr);
  ierr = PetscLogObjectMemory(da,(Xe-Xs)*(Ye-Ys)*(Ze-Zs)*sizeof(PetscInt));CHKERRQ(ierr);

  nn = 0;
  /* Bottom Level */
  for (k=0; k<s_z; k++) {
    for (i=1; i<=s_y; i++) {
      if (n0 >= 0) { /* left below */
        x_t = lx[n0 % m];
        y_t = ly[(n0 % (m*n))/m];
        z_t = lz[n0 / (m*n)];
        s_t = bases[n0] + x_t*y_t*z_t - (s_y-i)*x_t - s_x - (s_z-k-1)*x_t*y_t;
        if (s_t < 0) {s_t = bases[n0] + x_t*y_t*z_t - (s_y-i)*x_t - s_x;} /* 2D case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
      if (n1 >= 0) { /* directly below */
        x_t = x;
        y_t = ly[(n1 % (m*n))/m];
        z_t = lz[n1 / (m*n)];
        s_t = bases[n1] + x_t*y_t*z_t - (s_y+1-i)*x_t - (s_z-k-1)*x_t*y_t;
        if (s_t < 0) {s_t = bases[n1] + x_t*y_t*z_t - (s_y+1-i)*x_t;} /* 2D case */
        for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
      }
      if (n2 >= 0) { /* right below */
        x_t = lx[n2 % m];
        y_t = ly[(n2 % (m*n))/m];
        z_t = lz[n2 / (m*n)];
        s_t = bases[n2] + x_t*y_t*z_t - (s_y+1-i)*x_t - (s_z-k-1)*x_t*y_t;
        if (s_t < 0) {s_t = bases[n2] + x_t*y_t*z_t - (s_y+1-i)*x_t;} /* 2D case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
    }

    for (i=0; i<y; i++) {
      if (n3 >= 0) { /* directly left */
        x_t = lx[n3 % m];
        y_t = y;
        z_t = lz[n3 / (m*n)];
        s_t = bases[n3] + (i+1)*x_t - s_x + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
        if (s_t < 0) {s_t = bases[n3] + (i+1)*x_t - s_x + x_t*y_t*z_t - x_t*y_t;} /* 2D case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }

      if (n4 >= 0) { /* middle */
        x_t = x;
        y_t = y;
        z_t = lz[n4 / (m*n)];
        s_t = bases[n4] + i*x_t + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
        if (s_t < 0) {s_t = bases[n4] + i*x_t + x_t*y_t*z_t - x_t*y_t;} /* 2D case */
        for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
      }

      if (n5 >= 0) { /* directly right */
        x_t = lx[n5 % m];
        y_t = y;
        z_t = lz[n5 / (m*n)];
        s_t = bases[n5] + i*x_t + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
        if (s_t < 0) {s_t = bases[n5] + i*x_t + x_t*y_t*z_t - x_t*y_t;} /* 2D case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
    }

    for (i=1; i<=s_y; i++) {
      if (n6 >= 0) { /* left above */
        x_t = lx[n6 % m];
        y_t = ly[(n6 % (m*n))/m];
        z_t = lz[n6 / (m*n)];
        s_t = bases[n6] + i*x_t - s_x + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
        if (s_t < 0) {s_t = bases[n6] + i*x_t - s_x + x_t*y_t*z_t - x_t*y_t;} /* 2D case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
      if (n7 >= 0) { /* directly above */
        x_t = x;
        y_t = ly[(n7 % (m*n))/m];
        z_t = lz[n7 / (m*n)];
        s_t = bases[n7] + (i-1)*x_t + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
        if (s_t < 0) {s_t = bases[n7] + (i-1)*x_t + x_t*y_t*z_t - x_t*y_t;} /* 2D case */
        for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
      }
      if (n8 >= 0) { /* right above */
        x_t = lx[n8 % m];
        y_t = ly[(n8 % (m*n))/m];
        z_t = lz[n8 / (m*n)];
        s_t = bases[n8] + (i-1)*x_t + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
        if (s_t < 0) {s_t = bases[n8] + (i-1)*x_t + x_t*y_t*z_t - x_t*y_t;} /* 2D case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
    }
  }

  /* Middle Level */
  for (k=0; k<z; k++) {
    for (i=1; i<=s_y; i++) {
      if (n9 >= 0) { /* left below */
        x_t = lx[n9 % m];
        y_t = ly[(n9 % (m*n))/m];
        /* z_t = z; */
        s_t = bases[n9] - (s_y-i)*x_t -s_x + (k+1)*x_t*y_t;
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
      if (n10 >= 0) { /* directly below */
        x_t = x;
        y_t = ly[(n10 % (m*n))/m];
        /* z_t = z; */
        s_t = bases[n10] - (s_y+1-i)*x_t + (k+1)*x_t*y_t;
        for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
      }
      if (n11 >= 0) { /* right below */
        x_t = lx[n11 % m];
        y_t = ly[(n11 % (m*n))/m];
        /* z_t = z; */
        s_t = bases[n11] - (s_y+1-i)*x_t + (k+1)*x_t*y_t;
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
    }

    for (i=0; i<y; i++) {
      if (n12 >= 0) { /* directly left */
        x_t = lx[n12 % m];
        y_t = y;
        /* z_t = z; */
        s_t = bases[n12] + (i+1)*x_t - s_x + k*x_t*y_t;
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }

      /* Interior */
      s_t = bases[rank] + i*x + k*x*y;
      for (j=0; j<x; j++) { idx[nn++] = s_t++;}

      if (n14 >= 0) { /* directly right */
        x_t = lx[n14 % m];
        y_t = y;
        /* z_t = z; */
        s_t = bases[n14] + i*x_t + k*x_t*y_t;
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
    }

    for (i=1; i<=s_y; i++) {
      if (n15 >= 0) { /* left above */
        x_t = lx[n15 % m];
        y_t = ly[(n15 % (m*n))/m];
        /* z_t = z; */
        s_t = bases[n15] + i*x_t - s_x + k*x_t*y_t;
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
      if (n16 >= 0) { /* directly above */
        x_t = x;
        y_t = ly[(n16 % (m*n))/m];
        /* z_t = z; */
        s_t = bases[n16] + (i-1)*x_t + k*x_t*y_t;
        for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
      }
      if (n17 >= 0) { /* right above */
        x_t = lx[n17 % m];
        y_t = ly[(n17 % (m*n))/m];
        /* z_t = z; */
        s_t = bases[n17] + (i-1)*x_t + k*x_t*y_t;
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
    }
  }

  /* Upper Level */
  for (k=0; k<s_z; k++) {
    for (i=1; i<=s_y; i++) {
      if (n18 >= 0) { /* left below */
        x_t = lx[n18 % m];
        y_t = ly[(n18 % (m*n))/m];
        /* z_t = lz[n18 / (m*n)]; */
        s_t = bases[n18] - (s_y-i)*x_t -s_x + (k+1)*x_t*y_t;
        if (s_t >= x*y*z) {s_t = bases[n18] - (s_y-i)*x_t -s_x + x_t*y_t;} /* 2d case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
      if (n19 >= 0) { /* directly below */
        x_t = x;
        y_t = ly[(n19 % (m*n))/m];
        /* z_t = lz[n19 / (m*n)]; */
        s_t = bases[n19] - (s_y+1-i)*x_t + (k+1)*x_t*y_t;
        if (s_t >= x*y*z) {s_t = bases[n19] - (s_y+1-i)*x_t + x_t*y_t;} /* 2d case */
        for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
      }
      if (n20 >= 0) { /* right below */
        x_t = lx[n20 % m];
        y_t = ly[(n20 % (m*n))/m];
        /* z_t = lz[n20 / (m*n)]; */
        s_t = bases[n20] - (s_y+1-i)*x_t + (k+1)*x_t*y_t;
        if (s_t >= x*y*z) {s_t = bases[n20] - (s_y+1-i)*x_t + x_t*y_t;} /* 2d case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
    }

    for (i=0; i<y; i++) {
      if (n21 >= 0) { /* directly left */
        x_t = lx[n21 % m];
        y_t = y;
        /* z_t = lz[n21 / (m*n)]; */
        s_t = bases[n21] + (i+1)*x_t - s_x + k*x_t*y_t;
        if (s_t >= x*y*z) {s_t = bases[n21] + (i+1)*x_t - s_x;}  /* 2d case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }

      if (n22 >= 0) { /* middle */
        x_t = x;
        y_t = y;
        /* z_t = lz[n22 / (m*n)]; */
        s_t = bases[n22] + i*x_t + k*x_t*y_t;
        if (s_t >= x*y*z) {s_t = bases[n22] + i*x_t;} /* 2d case */
        for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
      }

      if (n23 >= 0) { /* directly right */
        x_t = lx[n23 % m];
        y_t = y;
        /* z_t = lz[n23 / (m*n)]; */
        s_t = bases[n23] + i*x_t + k*x_t*y_t;
        if (s_t >= x*y*z) {s_t = bases[n23] + i*x_t;} /* 2d case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
    }

    for (i=1; i<=s_y; i++) {
      if (n24 >= 0) { /* left above */
        x_t = lx[n24 % m];
        y_t = ly[(n24 % (m*n))/m];
        /* z_t = lz[n24 / (m*n)]; */
        s_t = bases[n24] + i*x_t - s_x + k*x_t*y_t;
        if (s_t >= x*y*z) {s_t = bases[n24] + i*x_t - s_x;} /* 2d case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
      if (n25 >= 0) { /* directly above */
        x_t = x;
        y_t = ly[(n25 % (m*n))/m];
        /* z_t = lz[n25 / (m*n)]; */
        s_t = bases[n25] + (i-1)*x_t + k*x_t*y_t;
        if (s_t >= x*y*z) {s_t = bases[n25] + (i-1)*x_t;} /* 2d case */
        for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
      }
      if (n26 >= 0) { /* right above */
        x_t = lx[n26 % m];
        y_t = ly[(n26 % (m*n))/m];
        /* z_t = lz[n26 / (m*n)]; */
        s_t = bases[n26] + (i-1)*x_t + k*x_t*y_t;
        if (s_t >= x*y*z) {s_t = bases[n26] + (i-1)*x_t;} /* 2d case */
        for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
      }
    }
  }

  ierr = ISCreateBlock(comm,dof,nn,idx,PETSC_COPY_VALUES,&from);CHKERRQ(ierr);
  ierr = VecScatterCreate(global,from,local,to,&gtol);CHKERRQ(ierr);
  ierr = PetscLogObjectParent(da,gtol);CHKERRQ(ierr);
  ierr = ISDestroy(&to);CHKERRQ(ierr);
  ierr = ISDestroy(&from);CHKERRQ(ierr);

  if (stencil_type == DMDA_STENCIL_STAR) {
    n0  = sn0;  n1  = sn1;  n2  = sn2;  n3  = sn3;  n5  = sn5;  n6  = sn6; n7 = sn7;
    n8  = sn8;  n9  = sn9;  n11 = sn11; n15 = sn15; n17 = sn17; n18 = sn18;
    n19 = sn19; n20 = sn20; n21 = sn21; n23 = sn23; n24 = sn24; n25 = sn25;
    n26 = sn26;
  }

  if ((stencil_type == DMDA_STENCIL_STAR) ||
      (bx != DMDA_BOUNDARY_PERIODIC && bx) ||
      (by != DMDA_BOUNDARY_PERIODIC && by) ||
      (bz != DMDA_BOUNDARY_PERIODIC && bz)) {
    /*
        Recompute the local to global mappings, this time keeping the
      information about the cross corner processor numbers.
    */
    nn = 0;
    /* Bottom Level */
    for (k=0; k<s_z; k++) {
      for (i=1; i<=s_y; i++) {
        if (n0 >= 0) { /* left below */
          x_t = lx[n0 % m];
          y_t = ly[(n0 % (m*n))/m];
          z_t = lz[n0 / (m*n)];
          s_t = bases[n0] + x_t*y_t*z_t - (s_y-i)*x_t - s_x - (s_z-k-1)*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (Xs-xs < 0 && Ys-ys < 0 && Zs-zs < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
        if (n1 >= 0) { /* directly below */
          x_t = x;
          y_t = ly[(n1 % (m*n))/m];
          z_t = lz[n1 / (m*n)];
          s_t = bases[n1] + x_t*y_t*z_t - (s_y+1-i)*x_t - (s_z-k-1)*x_t*y_t;
          for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
        } else if (Ys-ys < 0 && Zs-zs < 0) {
          for (j=0; j<x; j++) { idx[nn++] = -1;}
        }
        if (n2 >= 0) { /* right below */
          x_t = lx[n2 % m];
          y_t = ly[(n2 % (m*n))/m];
          z_t = lz[n2 / (m*n)];
          s_t = bases[n2] + x_t*y_t*z_t - (s_y+1-i)*x_t - (s_z-k-1)*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (xe-Xe < 0 && Ys-ys < 0 && Zs-zs < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
      }

      for (i=0; i<y; i++) {
        if (n3 >= 0) { /* directly left */
          x_t = lx[n3 % m];
          y_t = y;
          z_t = lz[n3 / (m*n)];
          s_t = bases[n3] + (i+1)*x_t - s_x + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (Xs-xs < 0 && Zs-zs < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }

        if (n4 >= 0) { /* middle */
          x_t = x;
          y_t = y;
          z_t = lz[n4 / (m*n)];
          s_t = bases[n4] + i*x_t + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
          for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
        } else if (Zs-zs < 0) {
          for (j=0; j<x; j++) { idx[nn++] = -1;}
        }

        if (n5 >= 0) { /* directly right */
          x_t = lx[n5 % m];
          y_t = y;
          z_t = lz[n5 / (m*n)];
          s_t = bases[n5] + i*x_t + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (xe-Xe < 0 && Zs-zs < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
      }

      for (i=1; i<=s_y; i++) {
        if (n6 >= 0) { /* left above */
          x_t = lx[n6 % m];
          y_t = ly[(n6 % (m*n))/m];
          z_t = lz[n6 / (m*n)];
          s_t = bases[n6] + i*x_t - s_x + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (Xs-xs < 0 && ye-Ye < 0 && Zs-zs < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
        if (n7 >= 0) { /* directly above */
          x_t = x;
          y_t = ly[(n7 % (m*n))/m];
          z_t = lz[n7 / (m*n)];
          s_t = bases[n7] + (i-1)*x_t + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
          for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
        } else if (ye-Ye < 0 && Zs-zs < 0) {
          for (j=0; j<x; j++) { idx[nn++] = -1;}
        }
        if (n8 >= 0) { /* right above */
          x_t = lx[n8 % m];
          y_t = ly[(n8 % (m*n))/m];
          z_t = lz[n8 / (m*n)];
          s_t = bases[n8] + (i-1)*x_t + x_t*y_t*z_t - (s_z-k)*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (xe-Xe < 0 && ye-Ye < 0 && Zs-zs < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
      }
    }

    /* Middle Level */
    for (k=0; k<z; k++) {
      for (i=1; i<=s_y; i++) {
        if (n9 >= 0) { /* left below */
          x_t = lx[n9 % m];
          y_t = ly[(n9 % (m*n))/m];
          /* z_t = z; */
          s_t = bases[n9] - (s_y-i)*x_t -s_x + (k+1)*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (Xs-xs < 0 && Ys-ys < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
        if (n10 >= 0) { /* directly below */
          x_t = x;
          y_t = ly[(n10 % (m*n))/m];
          /* z_t = z; */
          s_t = bases[n10] - (s_y+1-i)*x_t + (k+1)*x_t*y_t;
          for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
        } else if (Ys-ys < 0) {
          for (j=0; j<x; j++) { idx[nn++] = -1;}
        }
        if (n11 >= 0) { /* right below */
          x_t = lx[n11 % m];
          y_t = ly[(n11 % (m*n))/m];
          /* z_t = z; */
          s_t = bases[n11] - (s_y+1-i)*x_t + (k+1)*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (xe-Xe < 0 && Ys-ys < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
      }

      for (i=0; i<y; i++) {
        if (n12 >= 0) { /* directly left */
          x_t = lx[n12 % m];
          y_t = y;
          /* z_t = z; */
          s_t = bases[n12] + (i+1)*x_t - s_x + k*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (Xs-xs < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }

        /* Interior */
        s_t = bases[rank] + i*x + k*x*y;
        for (j=0; j<x; j++) { idx[nn++] = s_t++;}

        if (n14 >= 0) { /* directly right */
          x_t = lx[n14 % m];
          y_t = y;
          /* z_t = z; */
          s_t = bases[n14] + i*x_t + k*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (xe-Xe < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
      }

      for (i=1; i<=s_y; i++) {
        if (n15 >= 0) { /* left above */
          x_t = lx[n15 % m];
          y_t = ly[(n15 % (m*n))/m];
          /* z_t = z; */
          s_t = bases[n15] + i*x_t - s_x + k*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (Xs-xs < 0 && ye-Ye < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
        if (n16 >= 0) { /* directly above */
          x_t = x;
          y_t = ly[(n16 % (m*n))/m];
          /* z_t = z; */
          s_t = bases[n16] + (i-1)*x_t + k*x_t*y_t;
          for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
        } else if (ye-Ye < 0) {
          for (j=0; j<x; j++) { idx[nn++] = -1;}
        }
        if (n17 >= 0) { /* right above */
          x_t = lx[n17 % m];
          y_t = ly[(n17 % (m*n))/m];
          /* z_t = z; */
          s_t = bases[n17] + (i-1)*x_t + k*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (xe-Xe < 0 && ye-Ye < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
      }
    }

    /* Upper Level */
    for (k=0; k<s_z; k++) {
      for (i=1; i<=s_y; i++) {
        if (n18 >= 0) { /* left below */
          x_t = lx[n18 % m];
          y_t = ly[(n18 % (m*n))/m];
          /* z_t = lz[n18 / (m*n)]; */
          s_t = bases[n18] - (s_y-i)*x_t -s_x + (k+1)*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (Xs-xs < 0 && Ys-ys < 0 && ze-Ze < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
        if (n19 >= 0) { /* directly below */
          x_t = x;
          y_t = ly[(n19 % (m*n))/m];
          /* z_t = lz[n19 / (m*n)]; */
          s_t = bases[n19] - (s_y+1-i)*x_t + (k+1)*x_t*y_t;
          for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
        } else if (Ys-ys < 0 && ze-Ze < 0) {
          for (j=0; j<x; j++) { idx[nn++] = -1;}
        }
        if (n20 >= 0) { /* right below */
          x_t = lx[n20 % m];
          y_t = ly[(n20 % (m*n))/m];
          /* z_t = lz[n20 / (m*n)]; */
          s_t = bases[n20] - (s_y+1-i)*x_t + (k+1)*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (xe-Xe < 0 && Ys-ys < 0 && ze-Ze < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
      }

      for (i=0; i<y; i++) {
        if (n21 >= 0) { /* directly left */
          x_t = lx[n21 % m];
          y_t = y;
          /* z_t = lz[n21 / (m*n)]; */
          s_t = bases[n21] + (i+1)*x_t - s_x + k*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (Xs-xs < 0 && ze-Ze < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }

        if (n22 >= 0) { /* middle */
          x_t = x;
          y_t = y;
          /* z_t = lz[n22 / (m*n)]; */
          s_t = bases[n22] + i*x_t + k*x_t*y_t;
          for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
        } else if (ze-Ze < 0) {
          for (j=0; j<x; j++) { idx[nn++] = -1;}
        }

        if (n23 >= 0) { /* directly right */
          x_t = lx[n23 % m];
          y_t = y;
          /* z_t = lz[n23 / (m*n)]; */
          s_t = bases[n23] + i*x_t + k*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (xe-Xe < 0 && ze-Ze < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
      }

      for (i=1; i<=s_y; i++) {
        if (n24 >= 0) { /* left above */
          x_t = lx[n24 % m];
          y_t = ly[(n24 % (m*n))/m];
          /* z_t = lz[n24 / (m*n)]; */
          s_t = bases[n24] + i*x_t - s_x + k*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (Xs-xs < 0 && ye-Ye < 0 && ze-Ze < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
        if (n25 >= 0) { /* directly above */
          x_t = x;
          y_t = ly[(n25 % (m*n))/m];
          /* z_t = lz[n25 / (m*n)]; */
          s_t = bases[n25] + (i-1)*x_t + k*x_t*y_t;
          for (j=0; j<x_t; j++) { idx[nn++] = s_t++;}
        } else if (ye-Ye < 0 && ze-Ze < 0) {
          for (j=0; j<x; j++) { idx[nn++] = -1;}
        }
        if (n26 >= 0) { /* right above */
          x_t = lx[n26 % m];
          y_t = ly[(n26 % (m*n))/m];
          /* z_t = lz[n26 / (m*n)]; */
          s_t = bases[n26] + (i-1)*x_t + k*x_t*y_t;
          for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
        } else if (xe-Xe < 0 && ye-Ye < 0 && ze-Ze < 0) {
          for (j=0; j<s_x; j++) { idx[nn++] = -1;}
        }
      }
    }
  }
  /*
     Set the local to global ordering in the global vector, this allows use
     of VecSetValuesLocal().
  */
  ierr = ISCreateBlock(comm,dof,nn,idx,PETSC_OWN_POINTER,&ltogis);CHKERRQ(ierr);
  ierr = PetscMalloc(nn*dof*sizeof(PetscInt),&idx_cpy);CHKERRQ(ierr);
  ierr = PetscLogObjectMemory(da,nn*dof*sizeof(PetscInt));CHKERRQ(ierr);
  ierr = ISGetIndices(ltogis, &idx_full);
  ierr = PetscMemcpy(idx_cpy,idx_full,nn*dof*sizeof(PetscInt));CHKERRQ(ierr);
  ierr = ISRestoreIndices(ltogis, &idx_full);
  ierr = ISLocalToGlobalMappingCreateIS(ltogis,&da->ltogmap);CHKERRQ(ierr);
  ierr = PetscLogObjectParent(da,da->ltogmap);CHKERRQ(ierr);
  ierr = ISDestroy(&ltogis);CHKERRQ(ierr);
  ierr = ISLocalToGlobalMappingBlock(da->ltogmap,dd->w,&da->ltogmapb);CHKERRQ(ierr);
  ierr = PetscLogObjectParent(da,da->ltogmap);CHKERRQ(ierr);

  ierr = PetscFree2(bases,ldims);CHKERRQ(ierr);
  dd->m  = m;  dd->n  = n;  dd->p  = p;
  /* note petsc expects xs/xe/Xs/Xe to be multiplied by #dofs in many places */
  dd->xs = xs*dof; dd->xe = xe*dof; dd->ys = ys; dd->ye = ye; dd->zs = zs; dd->ze = ze;
  dd->Xs = Xs*dof; dd->Xe = Xe*dof; dd->Ys = Ys; dd->Ye = Ye; dd->Zs = Zs; dd->Ze = Ze;

  ierr = VecDestroy(&local);CHKERRQ(ierr);
  ierr = VecDestroy(&global);CHKERRQ(ierr);

  dd->gtol      = gtol;
  dd->ltog      = ltog;
  dd->idx       = idx_cpy;
  dd->Nl        = nn*dof;
  dd->base      = base;
  da->ops->view = DMView_DA_3d;
  dd->ltol = PETSC_NULL;
  dd->ao   = PETSC_NULL;

  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "DMDACreate3d"
/*@C
   DMDACreate3d - Creates an object that will manage the communication of three-dimensional
   regular array data that is distributed across some processors.

   Collective on MPI_Comm

   Input Parameters:
+  comm - MPI communicator
.  bx,by,bz - type of ghost nodes the array have.
         Use one of DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_PERIODIC.
.  stencil_type - Type of stencil (DMDA_STENCIL_STAR or DMDA_STENCIL_BOX)
.  M,N,P - global dimension in each direction of the array (use -M, -N, and or -P to indicate that it may be set to a different value
            from the command line with -da_grid_x <M> -da_grid_y <N> -da_grid_z <P>)
.  m,n,p - corresponding number of processors in each dimension
           (or PETSC_DECIDE to have calculated)
.  dof - number of degrees of freedom per node
.  lx, ly, lz - arrays containing the number of nodes in each cell along
          the x, y, and z coordinates, or PETSC_NULL. If non-null, these
          must be of length as m,n,p and the corresponding
          m,n, or p cannot be PETSC_DECIDE. Sum of the lx[] entries must be M, sum of
          the ly[] must N, sum of the lz[] must be P
-  s - stencil width

   Output Parameter:
.  da - the resulting distributed array object

   Options Database Key:
+  -da_view - Calls DMView() at the conclusion of DMDACreate3d()
.  -da_grid_x <nx> - number of grid points in x direction, if M < 0
.  -da_grid_y <ny> - number of grid points in y direction, if N < 0
.  -da_grid_z <nz> - number of grid points in z direction, if P < 0
.  -da_processors_x <MX> - number of processors in x direction
.  -da_processors_y <MY> - number of processors in y direction
.  -da_processors_z <MZ> - number of processors in z direction
.  -da_refine_x <rx> - refinement ratio in x direction
.  -da_refine_y <ry> - refinement ratio in y direction
.  -da_refine_z <rz>- refinement ratio in z directio
-  -da_refine <n> - refine the DMDA n times before creating it, , if M, N, or P < 0

   Level: beginner

   Notes:
   The stencil type DMDA_STENCIL_STAR with width 1 corresponds to the
   standard 7-pt stencil, while DMDA_STENCIL_BOX with width 1 denotes
   the standard 27-pt stencil.

   The array data itself is NOT stored in the DMDA, it is stored in Vec objects;
   The appropriate vector objects can be obtained with calls to DMCreateGlobalVector()
   and DMCreateLocalVector() and calls to VecDuplicate() if more are needed.

.keywords: distributed array, create, three-dimensional

.seealso: DMDestroy(), DMView(), DMDACreate1d(), DMDACreate2d(), DMGlobalToLocalBegin(), DMDAGetRefinementFactor(),
          DMGlobalToLocalEnd(), DMLocalToGlobalBegin(), DMDALocalToLocalBegin(), DMDALocalToLocalEnd(), DMDASetRefinementFactor(),
          DMDAGetInfo(), DMCreateGlobalVector(), DMCreateLocalVector(), DMDACreateNaturalVector(), DMLoad(), DMDAGetOwnershipRanges()

@*/
PetscErrorCode  DMDACreate3d(MPI_Comm comm,DMDABoundaryType bx,DMDABoundaryType by,DMDABoundaryType bz,DMDAStencilType stencil_type,PetscInt M,
               PetscInt N,PetscInt P,PetscInt m,PetscInt n,PetscInt p,PetscInt dof,PetscInt s,const PetscInt lx[],const PetscInt ly[],const PetscInt lz[],DM *da)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMDACreate(comm, da);CHKERRQ(ierr);
  ierr = DMDASetDim(*da, 3);CHKERRQ(ierr);
  ierr = DMDASetSizes(*da, M, N, P);CHKERRQ(ierr);
  ierr = DMDASetNumProcs(*da, m, n, p);CHKERRQ(ierr);
  ierr = DMDASetBoundaryType(*da, bx, by, bz);CHKERRQ(ierr);
  ierr = DMDASetDof(*da, dof);CHKERRQ(ierr);
  ierr = DMDASetStencilType(*da, stencil_type);CHKERRQ(ierr);
  ierr = DMDASetStencilWidth(*da, s);CHKERRQ(ierr);
  ierr = DMDASetOwnershipRanges(*da, lx, ly, lz);CHKERRQ(ierr);
  /* This violates the behavior for other classes, but right now users expect negative dimensions to be handled this way */
  ierr = DMSetFromOptions(*da);CHKERRQ(ierr);
  ierr = DMSetUp(*da);CHKERRQ(ierr);
  ierr = DMView_DA_Private(*da);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}