impls/da/da2.c

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

#undef __FUNCT__
#define __FUNCT__ "DMView_DA_2d"
PetscErrorCode DMView_DA_2d(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 = 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 = PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);CHKERRQ(ierr);
      ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Processor [%d] M %D N %D m %D n %D w %D s %D\n",rank,dd->M,dd->N,dd->m,dd->n,dd->w,dd->s);CHKERRQ(ierr);
      ierr = PetscViewerASCIISynchronizedPrintf(viewer,"X range of indices: %D %D, Y range of indices: %D %D\n",info.xs,info.xs+info.xm,info.ys,info.ys+info.ym);CHKERRQ(ierr);
      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;
    double     ymin = -1*dd->s-1,ymax = dd->N+dd->s;
    double     xmin = -1*dd->s-1,xmax = dd->M+dd->s;
    double     x,y;
    PetscInt   base,*idx;
    char       node[10];
    PetscBool  isnull;

    ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
    ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0);
    if (!dd->coordinates) {
      ierr = PetscDrawSetCoordinates(draw,xmin,ymin,xmax,ymax);CHKERRQ(ierr);
    }
    ierr = PetscDrawSynchronizedClear(draw);CHKERRQ(ierr);

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

    /* draw my box */
    ymin = dd->ys; ymax = dd->ye - 1; xmin = dd->xs/dd->w;
    xmax =(dd->xe-1)/dd->w;
    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);

    /* put in numbers */
    base = (dd->base)/dd->w;
    for (y=ymin; y<=ymax; y++) {
      for (x=xmin; x<=xmax; 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);
    /* overlay ghost numbers, useful for error checking */
    /* put in numbers */

    base = 0; idx = dd->idx;
    ymin = dd->Ys; ymax = dd->Ye; xmin = dd->Xs; xmax = dd->Xe;
    for (y=ymin; y<ymax; y++) {
      for (x=xmin; x<xmax; x++) {
        if ((base % dd->w) == 0) {
          sprintf(node,"%d",(int)(idx[base]/dd->w));
          ierr = PetscDrawString(draw,x/dd->w,y,PETSC_DRAW_BLUE,node);CHKERRQ(ierr);
        }
        base++;
      }
    }
    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);
}

/*
      M is number of grid points
      m is number of processors

*/
#undef __FUNCT__
#define __FUNCT__ "DMDASplitComm2d"
PetscErrorCode  DMDASplitComm2d(MPI_Comm comm,PetscInt M,PetscInt N,PetscInt sw,MPI_Comm *outcomm)
{
  PetscErrorCode ierr;
  PetscInt       m,n = 0,x = 0,y = 0;
  PetscMPIInt    size,csize,rank;

  PetscFunctionBegin;
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);

  csize = 4*size;
  do {
    if (csize % 4) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cannot split communicator of size %d tried %d %D %D",size,csize,x,y);
    csize   = csize/4;

    m = (PetscInt)(0.5 + sqrt(((double)M)*((double)csize)/((double)N)));
    if (!m) m = 1;
    while (m > 0) {
      n = csize/m;
      if (m*n == csize) break;
      m--;
    }
    if (M > N && m < n) {PetscInt _m = m; m = n; n = _m;}

    x = M/m + ((M % m) > ((csize-1) % m));
    y = (N + (csize-1)/m)/n;
  } while ((x < 4 || y < 4) && csize > 1);
  if (size != csize) {
    MPI_Group    entire_group,sub_group;
    PetscMPIInt  i,*groupies;

    ierr = MPI_Comm_group(comm,&entire_group);CHKERRQ(ierr);
    ierr = PetscMalloc(csize*sizeof(PetscInt),&groupies);CHKERRQ(ierr);
    for (i=0; i<csize; i++) {
      groupies[i] = (rank/csize)*csize + i;
    }
    ierr = MPI_Group_incl(entire_group,csize,groupies,&sub_group);CHKERRQ(ierr);
    ierr = PetscFree(groupies);CHKERRQ(ierr);
    ierr = MPI_Comm_create(comm,sub_group,outcomm);CHKERRQ(ierr);
    ierr = MPI_Group_free(&entire_group);CHKERRQ(ierr);
    ierr = MPI_Group_free(&sub_group);CHKERRQ(ierr);
    ierr = PetscInfo1(0,"DMDASplitComm2d:Creating redundant coarse problems of size %d\n",csize);CHKERRQ(ierr);
  } else {
    *outcomm = comm;
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAFunction"
static PetscErrorCode DMDAFunction(DM dm,Vec x,Vec F)
{
  PetscErrorCode ierr;
  Vec            localX;

  PetscFunctionBegin;
  ierr = DMGetLocalVector(dm,&localX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalBegin(dm,x,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(dm,x,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = DMDAComputeFunction1(dm,localX,F,dm->ctx);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(dm,&localX);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDASetLocalFunction"
/*@C
       DMDASetLocalFunction - Caches in a DM a local function.

   Logically Collective on DMDA

   Input Parameter:
+  da - initial distributed array
-  lf - the local function

   Level: intermediate

   Notes:
      If you used SNESSetFunction(snes,r,SNESDMDAComputeFunction,ctx); then the context passed to your function is the ctx set here.

      If you use SNESSetDM() and did not use SNESSetFunction() then the context passed to your function is the context set with DMSetApplicationContext()

   Developer Notes: It is possibly confusing which context is passed to the user function, it would be nice to unify them somehow.

.keywords:  distributed array, refine

.seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMDestroy(), DMDAGetLocalFunction(), DMDASetLocalFunctioni()
@*/
PetscErrorCode  DMDASetLocalFunction(DM da,DMDALocalFunction1 lf)
{
  PetscErrorCode ierr;
  DM_DA          *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  ierr = DMSetFunction(da,DMDAFunction);CHKERRQ(ierr);
  dd->lf       = lf;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDASetLocalFunctioni"
/*@C
       DMDASetLocalFunctioni - Caches in a DM a local function that evaluates a single component

   Logically Collective on DMDA

   Input Parameter:
+  da - initial distributed array
-  lfi - the local function

   Level: intermediate

.keywords:  distributed array, refine

.seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMDestroy(), DMDAGetLocalFunction(), DMDASetLocalFunction()
@*/
PetscErrorCode  DMDASetLocalFunctioni(DM da,PetscErrorCode (*lfi)(DMDALocalInfo*,MatStencil*,void*,PetscScalar*,void*))
{
  DM_DA          *dd = (DM_DA*)da->data;
  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  dd->lfi = lfi;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDASetLocalFunctionib"
/*@C
       DMDASetLocalFunctionib - Caches in a DM a block local function that evaluates a single component

   Logically Collective on DMDA

   Input Parameter:
+  da - initial distributed array
-  lfi - the local function

   Level: intermediate

.keywords:  distributed array, refine

.seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMDestroy(), DMDAGetLocalFunction(), DMDASetLocalFunction()
@*/
PetscErrorCode  DMDASetLocalFunctionib(DM da,PetscErrorCode (*lfi)(DMDALocalInfo*,MatStencil*,void*,PetscScalar*,void*))
{
  DM_DA          *dd = (DM_DA*)da->data;
  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  dd->lfib = lfi;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDASetLocalAdicFunction_Private"
PetscErrorCode DMDASetLocalAdicFunction_Private(DM da,DMDALocalFunction1 ad_lf)
{
  DM_DA          *dd = (DM_DA*)da->data;
  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  dd->adic_lf = ad_lf;
  PetscFunctionReturn(0);
}

/*MC
       DMDASetLocalAdicFunctioni - Caches in a DM a local functioni computed by ADIC/ADIFOR

   Synopsis:
   PetscErrorCode DMDASetLocalAdicFunctioni(DM da,PetscInt (ad_lf*)(DMDALocalInfo*,MatStencil*,void*,void*,void*)

   Logically Collective on DMDA

   Input Parameter:
+  da - initial distributed array
-  ad_lfi - the local function as computed by ADIC/ADIFOR

   Level: intermediate

.keywords:  distributed array, refine

.seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMDestroy(), DMDAGetLocalFunction(), DMDASetLocalFunction(),
          DMDASetLocalJacobian(), DMDASetLocalFunctioni()
M*/

#undef __FUNCT__
#define __FUNCT__ "DMDASetLocalAdicFunctioni_Private"
PetscErrorCode DMDASetLocalAdicFunctioni_Private(DM da,PetscErrorCode (*ad_lfi)(DMDALocalInfo*,MatStencil*,void*,void*,void*))
{
  DM_DA          *dd = (DM_DA*)da->data;
  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  dd->adic_lfi = ad_lfi;
  PetscFunctionReturn(0);
}

/*MC
       DMDASetLocalAdicMFFunctioni - Caches in a DM a local functioni computed by ADIC/ADIFOR

   Synopsis:
   PetscErrorCode  DMDASetLocalAdicFunctioni(DM da,int (ad_lf*)(DMDALocalInfo*,MatStencil*,void*,void*,void*)

   Logically Collective on DMDA

   Input Parameter:
+  da - initial distributed array
-  admf_lfi - the local matrix-free function as computed by ADIC/ADIFOR

   Level: intermediate

.keywords:  distributed array, refine

.seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMDestroy(), DMDAGetLocalFunction(), DMDASetLocalFunction(),
          DMDASetLocalJacobian(), DMDASetLocalFunctioni()
M*/

#undef __FUNCT__
#define __FUNCT__ "DMDASetLocalAdicMFFunctioni_Private"
PetscErrorCode DMDASetLocalAdicMFFunctioni_Private(DM da,PetscErrorCode (*admf_lfi)(DMDALocalInfo*,MatStencil*,void*,void*,void*))
{
  DM_DA          *dd = (DM_DA*)da->data;
  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  dd->adicmf_lfi = admf_lfi;
  PetscFunctionReturn(0);
}

/*MC
       DMDASetLocalAdicFunctionib - Caches in a DM a block local functioni computed by ADIC/ADIFOR

   Synopsis:
   PetscErrorCode DMDASetLocalAdicFunctionib(DM da,PetscInt (ad_lf*)(DMDALocalInfo*,MatStencil*,void*,void*,void*)

   Logically Collective on DMDA

   Input Parameter:
+  da - initial distributed array
-  ad_lfi - the local function as computed by ADIC/ADIFOR

   Level: intermediate

.keywords:  distributed array, refine

.seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMDestroy(), DMDAGetLocalFunction(), DMDASetLocalFunction(),
          DMDASetLocalJacobian(), DMDASetLocalFunctionib()
M*/

#undef __FUNCT__
#define __FUNCT__ "DMDASetLocalAdicFunctionib_Private"
PetscErrorCode DMDASetLocalAdicFunctionib_Private(DM da,PetscErrorCode (*ad_lfi)(DMDALocalInfo*,MatStencil*,void*,void*,void*))
{
  DM_DA          *dd = (DM_DA*)da->data;
  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  dd->adic_lfib = ad_lfi;
  PetscFunctionReturn(0);
}

/*MC
       DMDASetLocalAdicMFFunctionib - Caches in a DM a block local functioni computed by ADIC/ADIFOR

   Synopsis:
   PetscErrorCode  DMDASetLocalAdicFunctionib(DM da,int (ad_lf*)(DMDALocalInfo*,MatStencil*,void*,void*,void*)

   Logically Collective on DMDA

   Input Parameter:
+  da - initial distributed array
-  admf_lfi - the local matrix-free function as computed by ADIC/ADIFOR

   Level: intermediate

.keywords:  distributed array, refine

.seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMDestroy(), DMDAGetLocalFunction(), DMDASetLocalFunction(),
          DMDASetLocalJacobian(), DMDASetLocalFunctionib()
M*/

#undef __FUNCT__
#define __FUNCT__ "DMDASetLocalAdicMFFunctionib_Private"
PetscErrorCode DMDASetLocalAdicMFFunctionib_Private(DM da,PetscErrorCode (*admf_lfi)(DMDALocalInfo*,MatStencil*,void*,void*,void*))
{
  DM_DA          *dd = (DM_DA*)da->data;
  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  dd->adicmf_lfib = admf_lfi;
  PetscFunctionReturn(0);
}

/*MC
       DMDASetLocalAdicMFFunction - Caches in a DM a local function computed by ADIC/ADIFOR

   Synopsis:
   PetscErrorCode DMDASetLocalAdicMFFunction(DM da,DMDALocalFunction1 ad_lf)

   Logically Collective on DMDA

   Input Parameter:
+  da - initial distributed array
-  ad_lf - the local function as computed by ADIC/ADIFOR

   Level: intermediate

.keywords:  distributed array, refine

.seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMDestroy(), DMDAGetLocalFunction(), DMDASetLocalFunction(),
          DMDASetLocalJacobian()
M*/

#undef __FUNCT__
#define __FUNCT__ "DMDASetLocalAdicMFFunction_Private"
PetscErrorCode DMDASetLocalAdicMFFunction_Private(DM da,DMDALocalFunction1 ad_lf)
{
  DM_DA          *dd = (DM_DA*)da->data;
  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  dd->adicmf_lf = ad_lf;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAJacobianDefaultLocal"
PetscErrorCode DMDAJacobianLocal(DM dm,Vec x,Mat A,Mat B, MatStructure *str)
{
  PetscErrorCode ierr;
  Vec            localX;

  PetscFunctionBegin;
  ierr = DMGetLocalVector(dm,&localX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalBegin(dm,x,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(dm,x,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = MatFDColoringApply(B,dm->fd,localX,str,dm);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(dm,&localX);CHKERRQ(ierr);
  /* Assemble true Jacobian; if it is different */
  if (A != B) {
    ierr  = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr  = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  }
  ierr  = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  *str = SAME_NONZERO_PATTERN;
  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "DMDAJacobian"
static PetscErrorCode DMDAJacobian(DM dm,Vec x,Mat A,Mat B, MatStructure *str)
{
  PetscErrorCode ierr;
  Vec            localX;

  PetscFunctionBegin;
  ierr = DMGetLocalVector(dm,&localX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalBegin(dm,x,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(dm,x,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = DMDAComputeJacobian1(dm,localX,B,dm->ctx);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(dm,&localX);CHKERRQ(ierr);
  /* Assemble true Jacobian; if it is different */
  if (A != B) {
    ierr  = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr  = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  }
  ierr  = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  *str = SAME_NONZERO_PATTERN;
  PetscFunctionReturn(0);
}

/*@C
       DMDASetLocalJacobian - Caches in a DM a local Jacobian computation function

   Logically Collective on DMDA


   Input Parameter:
+  da - initial distributed array
-  lj - the local Jacobian

   Level: intermediate

   Notes: The routine SNESDMDAComputeFunction() uses this the cached function to evaluate the user provided function.

.keywords:  distributed array, refine

.seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMDestroy(), DMDAGetLocalFunction(), DMDASetLocalFunction()
@*/
#undef __FUNCT__
#define __FUNCT__ "DMDASetLocalJacobian"
PetscErrorCode  DMDASetLocalJacobian(DM da,DMDALocalFunction1 lj)
{
  PetscErrorCode ierr;
  DM_DA          *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  ierr = DMSetJacobian(da,DMDAJacobian);CHKERRQ(ierr);
  dd->lj    = lj;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAGetLocalFunction"
/*@C
       DMDAGetLocalFunction - Gets from a DM a local function and its ADIC/ADIFOR Jacobian

   Note Collective

   Input Parameter:
.  da - initial distributed array

   Output Parameter:
.  lf - the local function

   Level: intermediate

.keywords:  distributed array, refine

.seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMDestroy(), DMDAGetLocalJacobian(), DMDASetLocalFunction()
@*/
PetscErrorCode  DMDAGetLocalFunction(DM da,DMDALocalFunction1 *lf)
{
  DM_DA *dd = (DM_DA*)da->data;
  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  if (lf) *lf = dd->lf;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAGetLocalJacobian"
/*@C
       DMDAGetLocalJacobian - Gets from a DM a local jacobian

   Not Collective

   Input Parameter:
.  da - initial distributed array

   Output Parameter:
.  lj - the local jacobian

   Level: intermediate

.keywords:  distributed array, refine

.seealso: DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMDestroy(), DMDAGetLocalFunction(), DMDASetLocalJacobian()
@*/
PetscErrorCode  DMDAGetLocalJacobian(DM da,DMDALocalFunction1 *lj)
{
  DM_DA *dd = (DM_DA*)da->data;
  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  if (lj) *lj = dd->lj;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAComputeFunction"
/*@
    DMDAComputeFunction - Evaluates a user provided function on each processor that
        share a DMDA

   Input Parameters:
+    da - the DM that defines the grid
.    vu - input vector
.    vfu - output vector
-    w - any user data

    Notes: Does NOT do ghost updates on vu upon entry

           This should eventually replace DMDAComputeFunction1

    Level: advanced

.seealso: DMDAComputeJacobian1WithAdic()

@*/
PetscErrorCode  DMDAComputeFunction(DM da,PetscErrorCode (*lf)(void),Vec vu,Vec vfu,void *w)
{
  PetscErrorCode ierr;
  void           *u,*fu;
  DMDALocalInfo  info;
  PetscErrorCode (*f)(DMDALocalInfo*,void*,void*,void*) = (PetscErrorCode (*)(DMDALocalInfo*,void*,void*,void*))lf;

  PetscFunctionBegin;
  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,vu,&u);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,vfu,&fu);CHKERRQ(ierr);

  ierr = (*f)(&info,u,fu,w);CHKERRQ(ierr);

  ierr = DMDAVecRestoreArray(da,vu,&u);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArray(da,vfu,&fu);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAComputeFunctionLocal"
/*@C
   DMDAComputeFunctionLocal - This is a universal function evaluation routine for
   a local DM function.

   Collective on DMDA

   Input Parameters:
+  da - the DM context
.  func - The local function
.  X - input vector
.  F - function vector
-  ctx - A user context

   Level: intermediate

.seealso: DMDASetLocalFunction(), DMDASetLocalJacobian(), DMDASetLocalAdicFunction(), DMDASetLocalAdicMFFunction(),
          SNESSetFunction(), SNESSetJacobian()

@*/
PetscErrorCode  DMDAComputeFunctionLocal(DM da, DMDALocalFunction1 func, Vec X, Vec F, void *ctx)
{
  Vec            localX;
  DMDALocalInfo  info;
  void           *u;
  void           *fu;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMGetLocalVector(da,&localX);CHKERRQ(ierr);
  /*
     Scatter ghost points to local vector, using the 2-step process
        DMGlobalToLocalBegin(), DMGlobalToLocalEnd().
  */
  ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,localX,&u);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,F,&fu);CHKERRQ(ierr);
  ierr = (*func)(&info,u,fu,ctx);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArray(da,localX,&u);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArray(da,F,&fu);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(da,&localX);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAComputeFunctionLocalGhost"
/*@C
   DMDAComputeFunctionLocalGhost - This is a universal function evaluation routine for
   a local DM function, but the ghost values of the output are communicated and added.

   Collective on DMDA

   Input Parameters:
+  da - the DM context
.  func - The local function
.  X - input vector
.  F - function vector
-  ctx - A user context

   Level: intermediate

.seealso: DMDASetLocalFunction(), DMDASetLocalJacobian(), DMDASetLocalAdicFunction(), DMDASetLocalAdicMFFunction(),
          SNESSetFunction(), SNESSetJacobian()

@*/
PetscErrorCode  DMDAComputeFunctionLocalGhost(DM da, DMDALocalFunction1 func, Vec X, Vec F, void *ctx)
{
  Vec            localX, localF;
  DMDALocalInfo  info;
  void           *u;
  void           *fu;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMGetLocalVector(da,&localX);CHKERRQ(ierr);
  ierr = DMGetLocalVector(da,&localF);CHKERRQ(ierr);
  /*
     Scatter ghost points to local vector, using the 2-step process
        DMGlobalToLocalBegin(), DMGlobalToLocalEnd().
  */
  ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = VecSet(F, 0.0);CHKERRQ(ierr);
  ierr = VecSet(localF, 0.0);CHKERRQ(ierr);
  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,localX,&u);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,localF,&fu);CHKERRQ(ierr);
  ierr = (*func)(&info,u,fu,ctx);CHKERRQ(ierr);
  ierr = DMLocalToGlobalBegin(da,localF,ADD_VALUES,F);CHKERRQ(ierr);
  ierr = DMLocalToGlobalEnd(da,localF,ADD_VALUES,F);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArray(da,localX,&u);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArray(da,localF,&fu);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(da,&localX);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(da,&localF);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAComputeFunction1"
/*@
    DMDAComputeFunction1 - Evaluates a user provided function on each processor that
        share a DMDA

   Input Parameters:
+    da - the DM that defines the grid
.    vu - input vector
.    vfu - output vector
-    w - any user data

    Notes: Does NOT do ghost updates on vu upon entry

    Level: advanced

.seealso: DMDAComputeJacobian1WithAdic()

@*/
PetscErrorCode  DMDAComputeFunction1(DM da,Vec vu,Vec vfu,void *w)
{
  PetscErrorCode ierr;
  void           *u,*fu;
  DMDALocalInfo  info;
  DM_DA          *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  if (!dd->lf) SETERRQ(((PetscObject)da)->comm,PETSC_ERR_ARG_NULL,"DMDASetLocalFunction() never called");
  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,vu,&u);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,vfu,&fu);CHKERRQ(ierr);

  CHKMEMQ;
  ierr = (*dd->lf)(&info,u,fu,w);CHKERRQ(ierr);
  CHKMEMQ;

  ierr = DMDAVecRestoreArray(da,vu,&u);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArray(da,vfu,&fu);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAComputeFunctioniTest1"
PetscErrorCode  DMDAComputeFunctioniTest1(DM da,void *w)
{
  Vec            vu,fu,fui;
  PetscErrorCode ierr;
  PetscInt       i,n;
  PetscScalar    *ui;
  PetscRandom    rnd;
  PetscReal      norm;

  PetscFunctionBegin;
  ierr = DMGetLocalVector(da,&vu);CHKERRQ(ierr);
  ierr = PetscRandomCreate(PETSC_COMM_SELF,&rnd);CHKERRQ(ierr);
  ierr = PetscRandomSetFromOptions(rnd);CHKERRQ(ierr);
  ierr = VecSetRandom(vu,rnd);CHKERRQ(ierr);
  ierr = PetscRandomDestroy(&rnd);CHKERRQ(ierr);

  ierr = DMGetGlobalVector(da,&fu);CHKERRQ(ierr);
  ierr = DMGetGlobalVector(da,&fui);CHKERRQ(ierr);

  ierr = DMDAComputeFunction1(da,vu,fu,w);CHKERRQ(ierr);

  ierr = VecGetArray(fui,&ui);CHKERRQ(ierr);
  ierr = VecGetLocalSize(fui,&n);CHKERRQ(ierr);
  for (i=0; i<n; i++) {
    ierr = DMDAComputeFunctioni1(da,i,vu,ui+i,w);CHKERRQ(ierr);
  }
  ierr = VecRestoreArray(fui,&ui);CHKERRQ(ierr);

  ierr = VecAXPY(fui,-1.0,fu);CHKERRQ(ierr);
  ierr = VecNorm(fui,NORM_2,&norm);CHKERRQ(ierr);
  ierr = PetscPrintf(((PetscObject)da)->comm,"Norm of difference in vectors %G\n",norm);CHKERRQ(ierr);
  ierr = VecView(fu,0);CHKERRQ(ierr);
  ierr = VecView(fui,0);CHKERRQ(ierr);

  ierr = DMRestoreLocalVector(da,&vu);CHKERRQ(ierr);
  ierr = DMRestoreGlobalVector(da,&fu);CHKERRQ(ierr);
  ierr = DMRestoreGlobalVector(da,&fui);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAComputeFunctioni1"
/*@
    DMDAComputeFunctioni1 - Evaluates a user provided point-wise function

   Input Parameters:
+    da - the DM that defines the grid
.    i - the component of the function we wish to compute (must be local)
.    vu - input vector
.    vfu - output value
-    w - any user data

    Notes: Does NOT do ghost updates on vu upon entry

    Level: advanced

.seealso: DMDAComputeJacobian1WithAdic()

@*/
PetscErrorCode  DMDAComputeFunctioni1(DM da,PetscInt i,Vec vu,PetscScalar *vfu,void *w)
{
  PetscErrorCode ierr;
  void           *u;
  DMDALocalInfo  info;
  MatStencil     stencil;
  DM_DA          *dd = (DM_DA*)da->data;

  PetscFunctionBegin;

  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,vu,&u);CHKERRQ(ierr);

  /* figure out stencil value from i */
  stencil.c = i % info.dof;
  stencil.i = (i % (info.xm*info.dof))/info.dof;
  stencil.j = (i % (info.xm*info.ym*info.dof))/(info.xm*info.dof);
  stencil.k = i/(info.xm*info.ym*info.dof);

  ierr = (*dd->lfi)(&info,&stencil,u,vfu,w);CHKERRQ(ierr);

  ierr = DMDAVecRestoreArray(da,vu,&u);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAComputeFunctionib1"
/*@
    DMDAComputeFunctionib1 - Evaluates a user provided point-block function

   Input Parameters:
+    da - the DM that defines the grid
.    i - the component of the function we wish to compute (must be local)
.    vu - input vector
.    vfu - output value
-    w - any user data

    Notes: Does NOT do ghost updates on vu upon entry

    Level: advanced

.seealso: DMDAComputeJacobian1WithAdic()

@*/
PetscErrorCode  DMDAComputeFunctionib1(DM da,PetscInt i,Vec vu,PetscScalar *vfu,void *w)
{
  PetscErrorCode ierr;
  void           *u;
  DMDALocalInfo  info;
  MatStencil     stencil;
  DM_DA          *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,vu,&u);CHKERRQ(ierr);

  /* figure out stencil value from i */
  stencil.c = i % info.dof;
  if (stencil.c) SETERRQ(((PetscObject)da)->comm,PETSC_ERR_ARG_WRONG,"Point-block functions can only be called for the entire block");
  stencil.i = (i % (info.xm*info.dof))/info.dof;
  stencil.j = (i % (info.xm*info.ym*info.dof))/(info.xm*info.dof);
  stencil.k = i/(info.xm*info.ym*info.dof);

  ierr = (*dd->lfib)(&info,&stencil,u,vfu,w);CHKERRQ(ierr);

  ierr = DMDAVecRestoreArray(da,vu,&u);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#if defined(new)
#undef __FUNCT__
#define __FUNCT__ "DMDAGetDiagonal_MFFD"
/*
  DMDAGetDiagonal_MFFD - Gets the diagonal for a matrix free matrix where local
    function lives on a DMDA

        y ~= (F(u + ha) - F(u))/h,
  where F = nonlinear function, as set by SNESSetFunction()
        u = current iterate
        h = difference interval
*/
PetscErrorCode DMDAGetDiagonal_MFFD(DM da,Vec U,Vec a)
{
  PetscScalar    h,*aa,*ww,v;
  PetscReal      epsilon = PETSC_SQRT_MACHINE_EPSILON,umin = 100.0*PETSC_SQRT_MACHINE_EPSILON;
  PetscErrorCode ierr;
  PetscInt       gI,nI;
  MatStencil     stencil;
  DMDALocalInfo  info;

  PetscFunctionBegin;
  ierr = (*ctx->func)(0,U,a,ctx->funcctx);CHKERRQ(ierr);
  ierr = (*ctx->funcisetbase)(U,ctx->funcctx);CHKERRQ(ierr);

  ierr = VecGetArray(U,&ww);CHKERRQ(ierr);
  ierr = VecGetArray(a,&aa);CHKERRQ(ierr);

  nI = 0;
    h  = ww[gI];
    if (h == 0.0) h = 1.0;
#if !defined(PETSC_USE_COMPLEX)
    if (h < umin && h >= 0.0)      h = umin;
    else if (h < 0.0 && h > -umin) h = -umin;
#else
    if (PetscAbsScalar(h) < umin && PetscRealPart(h) >= 0.0)     h = umin;
    else if (PetscRealPart(h) < 0.0 && PetscAbsScalar(h) < umin) h = -umin;
#endif
    h     *= epsilon;

    ww[gI] += h;
    ierr          = (*ctx->funci)(i,w,&v,ctx->funcctx);CHKERRQ(ierr);
    aa[nI]  = (v - aa[nI])/h;
    ww[gI] -= h;
    nI++;
  }
  ierr = VecRestoreArray(U,&ww);CHKERRQ(ierr);
  ierr = VecRestoreArray(a,&aa);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
#endif

#if defined(PETSC_HAVE_ADIC)
EXTERN_C_BEGIN
#include <adic/ad_utils.h>
EXTERN_C_END

#undef __FUNCT__
#define __FUNCT__ "DMDAComputeJacobian1WithAdic"
/*@C
    DMDAComputeJacobian1WithAdic - Evaluates a adiC provided Jacobian function on each processor that
        share a DMDA

   Input Parameters:
+    da - the DM that defines the grid
.    vu - input vector (ghosted)
.    J - output matrix
-    w - any user data

   Level: advanced

    Notes: Does NOT do ghost updates on vu upon entry

.seealso: DMDAComputeFunction1()

@*/
PetscErrorCode  DMDAComputeJacobian1WithAdic(DM da,Vec vu,Mat J,void *w)
{
  PetscErrorCode ierr;
  PetscInt       gtdof,tdof;
  PetscScalar    *ustart;
  DMDALocalInfo  info;
  void           *ad_u,*ad_f,*ad_ustart,*ad_fstart;
  ISColoring     iscoloring;

  PetscFunctionBegin;
  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);

  PetscADResetIndep();

  /* get space for derivative objects.  */
  ierr = DMDAGetAdicArray(da,PETSC_TRUE,&ad_u,&ad_ustart,&gtdof);CHKERRQ(ierr);
  ierr = DMDAGetAdicArray(da,PETSC_FALSE,&ad_f,&ad_fstart,&tdof);CHKERRQ(ierr);
  ierr = VecGetArray(vu,&ustart);CHKERRQ(ierr);
  ierr = DMCreateColoring(da,IS_COLORING_GHOSTED,MATAIJ,&iscoloring);CHKERRQ(ierr);

  PetscADSetValueAndColor(ad_ustart,gtdof,iscoloring->colors,ustart);

  ierr = VecRestoreArray(vu,&ustart);CHKERRQ(ierr);
  ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
  ierr = PetscADIncrementTotalGradSize(iscoloring->n);CHKERRQ(ierr);
  PetscADSetIndepDone();

  ierr = PetscLogEventBegin(DMDA_LocalADFunction,0,0,0,0);CHKERRQ(ierr);
  ierr = (*dd->adic_lf)(&info,ad_u,ad_f,w);CHKERRQ(ierr);
  ierr = PetscLogEventEnd(DMDA_LocalADFunction,0,0,0,0);CHKERRQ(ierr);

  /* stick the values into the matrix */
  ierr = MatSetValuesAdic(J,(PetscScalar**)ad_fstart);CHKERRQ(ierr);

  /* return space for derivative objects.  */
  ierr = DMDARestoreAdicArray(da,PETSC_TRUE,&ad_u,&ad_ustart,&gtdof);CHKERRQ(ierr);
  ierr = DMDARestoreAdicArray(da,PETSC_FALSE,&ad_f,&ad_fstart,&tdof);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAMultiplyByJacobian1WithAdic"
/*@C
    DMDAMultiplyByJacobian1WithAdic - Applies an ADIC-provided Jacobian function to a vector on
    each processor that shares a DMDA.

    Input Parameters:
+   da - the DM that defines the grid
.   vu - Jacobian is computed at this point (ghosted)
.   v - product is done on this vector (ghosted)
.   fu - output vector = J(vu)*v (not ghosted)
-   w - any user data

    Notes:
    This routine does NOT do ghost updates on vu upon entry.

   Level: advanced

.seealso: DMDAComputeFunction1()

@*/
PetscErrorCode  DMDAMultiplyByJacobian1WithAdic(DM da,Vec vu,Vec v,Vec f,void *w)
{
  PetscErrorCode ierr;
  PetscInt       i,gtdof,tdof;
  PetscScalar    *avu,*av,*af,*ad_vustart,*ad_fstart;
  DMDALocalInfo  info;
  void           *ad_vu,*ad_f;

  PetscFunctionBegin;
  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);

  /* get space for derivative objects.  */
  ierr = DMDAGetAdicMFArray(da,PETSC_TRUE,&ad_vu,&ad_vustart,&gtdof);CHKERRQ(ierr);
  ierr = DMDAGetAdicMFArray(da,PETSC_FALSE,&ad_f,&ad_fstart,&tdof);CHKERRQ(ierr);

  /* copy input vector into derivative object */
  ierr = VecGetArray(vu,&avu);CHKERRQ(ierr);
  ierr = VecGetArray(v,&av);CHKERRQ(ierr);
  for (i=0; i<gtdof; i++) {
    ad_vustart[2*i]   = avu[i];
    ad_vustart[2*i+1] = av[i];
  }
  ierr = VecRestoreArray(vu,&avu);CHKERRQ(ierr);
  ierr = VecRestoreArray(v,&av);CHKERRQ(ierr);

  PetscADResetIndep();
  ierr = PetscADIncrementTotalGradSize(1);CHKERRQ(ierr);
  PetscADSetIndepDone();

  ierr = (*dd->adicmf_lf)(&info,ad_vu,ad_f,w);CHKERRQ(ierr);

  /* stick the values into the vector */
  ierr = VecGetArray(f,&af);CHKERRQ(ierr);
  for (i=0; i<tdof; i++) {
    af[i] = ad_fstart[2*i+1];
  }
  ierr = VecRestoreArray(f,&af);CHKERRQ(ierr);

  /* return space for derivative objects.  */
  ierr = DMDARestoreAdicMFArray(da,PETSC_TRUE,&ad_vu,&ad_vustart,&gtdof);CHKERRQ(ierr);
  ierr = DMDARestoreAdicMFArray(da,PETSC_FALSE,&ad_f,&ad_fstart,&tdof);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
#endif

#undef __FUNCT__
#define __FUNCT__ "DMDAComputeJacobian1"
/*@
    DMDAComputeJacobian1 - Evaluates a local Jacobian function on each processor that
        share a DMDA

   Input Parameters:
+    da - the DM that defines the grid
.    vu - input vector (ghosted)
.    J - output matrix
-    w - any user data

    Notes: Does NOT do ghost updates on vu upon entry

    Level: advanced

.seealso: DMDAComputeFunction1()

@*/
PetscErrorCode  DMDAComputeJacobian1(DM da,Vec vu,Mat J,void *w)
{
  PetscErrorCode ierr;
  void           *u;
  DMDALocalInfo  info;
  DM_DA          *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,vu,&u);CHKERRQ(ierr);
  ierr = (*dd->lj)(&info,u,J,w);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArray(da,vu,&u);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "DMDAComputeJacobian1WithAdifor"
/*
    DMDAComputeJacobian1WithAdifor - Evaluates a ADIFOR provided Jacobian local function on each processor that
        share a DMDA

   Input Parameters:
+    da - the DM that defines the grid
.    vu - input vector (ghosted)
.    J - output matrix
-    w - any user data

    Notes: Does NOT do ghost updates on vu upon entry

.seealso: DMDAComputeFunction1()

*/
PetscErrorCode  DMDAComputeJacobian1WithAdifor(DM da,Vec vu,Mat J,void *w)
{
  PetscErrorCode  ierr;
  PetscInt        i,Nc,N;
  ISColoringValue *color;
  DMDALocalInfo   info;
  PetscScalar     *u,*g_u,*g_f,*f = 0,*p_u;
  ISColoring      iscoloring;
  DM_DA          *dd = (DM_DA*)da->data;
  void            (*lf)(PetscInt*,DMDALocalInfo*,PetscScalar*,PetscScalar*,PetscInt*,PetscScalar*,PetscScalar*,PetscInt*,void*,PetscErrorCode*) =
                  (void (*)(PetscInt*,DMDALocalInfo*,PetscScalar*,PetscScalar*,PetscInt*,PetscScalar*,PetscScalar*,PetscInt*,void*,PetscErrorCode*))*dd->adifor_lf;

  PetscFunctionBegin;
  ierr = DMCreateColoring(da,IS_COLORING_GHOSTED,MATAIJ,&iscoloring);CHKERRQ(ierr);
  Nc   = iscoloring->n;
  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
  N    = info.gxm*info.gym*info.gzm*info.dof;

  /* get space for derivative objects.  */
  ierr  = PetscMalloc(Nc*info.gxm*info.gym*info.gzm*info.dof*sizeof(PetscScalar),&g_u);CHKERRQ(ierr);
  ierr  = PetscMemzero(g_u,Nc*info.gxm*info.gym*info.gzm*info.dof*sizeof(PetscScalar));CHKERRQ(ierr);
  p_u   = g_u;
  color = iscoloring->colors;
  for (i=0; i<N; i++) {
    p_u[*color++] = 1.0;
    p_u          += Nc;
  }
  ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
  ierr = PetscMalloc2(Nc*info.xm*info.ym*info.zm*info.dof,PetscScalar,&g_f,info.xm*info.ym*info.zm*info.dof,PetscScalar,&f);CHKERRQ(ierr);

  /* Seed the input array g_u with coloring information */

  ierr = VecGetArray(vu,&u);CHKERRQ(ierr);
  (lf)(&Nc,&info,u,g_u,&Nc,f,g_f,&Nc,w,&ierr);CHKERRQ(ierr);
  ierr = VecRestoreArray(vu,&u);CHKERRQ(ierr);

  /* stick the values into the matrix */
  /* PetscScalarView(Nc*info.xm*info.ym,g_f,0); */
  ierr = MatSetValuesAdifor(J,Nc,g_f);CHKERRQ(ierr);

  /* return space for derivative objects.  */
  ierr = PetscFree(g_u);CHKERRQ(ierr);
  ierr = PetscFree2(g_f,f);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAFormJacobianLocal"
/*@C
   DMDAFormjacobianLocal - This is a universal Jacobian evaluation routine for
   a local DM function.

   Collective on DMDA

   Input Parameters:
+  da - the DM context
.  func - The local function
.  X - input vector
.  J - Jacobian matrix
-  ctx - A user context

   Level: intermediate

.seealso: DMDASetLocalFunction(), DMDASetLocalJacobian(), DMDASetLocalAdicFunction(), DMDASetLocalAdicMFFunction(),
          SNESSetFunction(), SNESSetJacobian()

@*/
PetscErrorCode  DMDAFormJacobianLocal(DM da, DMDALocalFunction1 func, Vec X, Mat J, void *ctx)
{
  Vec            localX;
  DMDALocalInfo  info;
  void           *u;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMGetLocalVector(da,&localX);CHKERRQ(ierr);
  /*
     Scatter ghost points to local vector, using the 2-step process
        DMGlobalToLocalBegin(), DMGlobalToLocalEnd().
  */
  ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,localX,&u);CHKERRQ(ierr);
  ierr = (*func)(&info,u,J,ctx);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArray(da,localX,&u);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(da,&localX);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAMultiplyByJacobian1WithAD"
/*@C
    DMDAMultiplyByJacobian1WithAD - Applies a Jacobian function supplied by ADIFOR or ADIC
    to a vector on each processor that shares a DMDA.

   Input Parameters:
+    da - the DM that defines the grid
.    vu - Jacobian is computed at this point (ghosted)
.    v - product is done on this vector (ghosted)
.    fu - output vector = J(vu)*v (not ghosted)
-    w - any user data

    Notes:
    This routine does NOT do ghost updates on vu and v upon entry.

    Automatically calls DMDAMultiplyByJacobian1WithAdifor() or DMDAMultiplyByJacobian1WithAdic()
    depending on whether DMDASetLocalAdicMFFunction() or DMDASetLocalAdiforMFFunction() was called.

   Level: advanced

.seealso: DMDAComputeFunction1(), DMDAMultiplyByJacobian1WithAdifor(), DMDAMultiplyByJacobian1WithAdic()

@*/
PetscErrorCode  DMDAMultiplyByJacobian1WithAD(DM da,Vec u,Vec v,Vec f,void *w)
{
  PetscErrorCode ierr;
  DM_DA          *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  if (dd->adicmf_lf) {
#if defined(PETSC_HAVE_ADIC)
    ierr = DMDAMultiplyByJacobian1WithAdic(da,u,v,f,w);CHKERRQ(ierr);
#else
    SETERRQ(((PetscObject)da)->comm,PETSC_ERR_SUP_SYS,"Requires ADIC to be installed and cannot use complex numbers");
#endif
  } else if (dd->adiformf_lf) {
    ierr = DMDAMultiplyByJacobian1WithAdifor(da,u,v,f,w);CHKERRQ(ierr);
  } else {
    SETERRQ(((PetscObject)da)->comm,PETSC_ERR_ORDER,"Must call DMDASetLocalAdiforMFFunction() or DMDASetLocalAdicMFFunction() before using");
  }
  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "DMDAMultiplyByJacobian1WithAdifor"
/*@C
    DMDAMultiplyByJacobian1WithAdifor - Applies a ADIFOR provided Jacobian function on each processor that
        share a DM to a vector

   Input Parameters:
+    da - the DM that defines the grid
.    vu - Jacobian is computed at this point (ghosted)
.    v - product is done on this vector (ghosted)
.    fu - output vector = J(vu)*v (not ghosted)
-    w - any user data

    Notes: Does NOT do ghost updates on vu and v upon entry

   Level: advanced

.seealso: DMDAComputeFunction1()

@*/
PetscErrorCode  DMDAMultiplyByJacobian1WithAdifor(DM da,Vec u,Vec v,Vec f,void *w)
{
  PetscErrorCode ierr;
  PetscScalar    *au,*av,*af,*awork;
  Vec            work;
  DMDALocalInfo  info;
  DM_DA          *dd = (DM_DA*)da->data;
  void           (*lf)(DMDALocalInfo*,PetscScalar*,PetscScalar*,PetscScalar*,PetscScalar*,void*,PetscErrorCode*) =
                 (void (*)(DMDALocalInfo*,PetscScalar*,PetscScalar*,PetscScalar*,PetscScalar*,void*,PetscErrorCode*))*dd->adiformf_lf;

  PetscFunctionBegin;
  ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);

  ierr = DMGetGlobalVector(da,&work);CHKERRQ(ierr);
  ierr = VecGetArray(u,&au);CHKERRQ(ierr);
  ierr = VecGetArray(v,&av);CHKERRQ(ierr);
  ierr = VecGetArray(f,&af);CHKERRQ(ierr);
  ierr = VecGetArray(work,&awork);CHKERRQ(ierr);
  (lf)(&info,au,av,awork,af,w,&ierr);CHKERRQ(ierr);
  ierr = VecRestoreArray(u,&au);CHKERRQ(ierr);
  ierr = VecRestoreArray(v,&av);CHKERRQ(ierr);
  ierr = VecRestoreArray(f,&af);CHKERRQ(ierr);
  ierr = VecRestoreArray(work,&awork);CHKERRQ(ierr);
  ierr = DMRestoreGlobalVector(da,&work);CHKERRQ(ierr);

  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMSetUp_DA_2D"
PetscErrorCode  DMSetUp_DA_2D(DM da)
{
  DM_DA                  *dd = (DM_DA*)da->data;
  const PetscInt         M            = dd->M;
  const PetscInt         N            = dd->N;
  PetscInt               m            = dd->m;
  PetscInt               n            = dd->n;
  const PetscInt         dof          = dd->w;
  const PetscInt         s            = dd->s;
  const DMDABoundaryType bx         = dd->bx;
  const DMDABoundaryType by         = dd->by;
  const DMDAStencilType  stencil_type = dd->stencil_type;
  PetscInt               *lx           = dd->lx;
  PetscInt               *ly           = dd->ly;
  MPI_Comm               comm;
  PetscMPIInt            rank,size;
  PetscInt               xs,xe,ys,ye,x,y,Xs,Xe,Ys,Ye,start,end,IXs,IXe,IYs,IYe;
  PetscInt               up,down,left,right,i,n0,n1,n2,n3,n5,n6,n7,n8,*idx,nn,*idx_cpy;
  const PetscInt         *idx_full;
  PetscInt               xbase,*bases,*ldims,j,x_t,y_t,s_t,base,count;
  PetscInt               s_x,s_y; /* s proportionalized to w */
  PetscInt               sn0 = 0,sn2 = 0,sn6 = 0,sn8 = 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);
#if !defined(PETSC_USE_64BIT_INDICES)
  if (((Petsc64bitInt) M)*((Petsc64bitInt) N)*((Petsc64bitInt) dof) > (Petsc64bitInt) PETSC_MPI_INT_MAX) SETERRQ3(comm,PETSC_ERR_INT_OVERFLOW,"Mesh of %D by %D by %D (dof) is too large for 32 bit indices",M,N,dof);
#endif

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

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

  dd->dim         = 2;
  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(comm,PETSC_ERR_ARG_OUTOFRANGE,"Non-positive number of processors in X direction: %D",m);
    else if (m > size) SETERRQ2(comm,PETSC_ERR_ARG_OUTOFRANGE,"Too many processors in X direction: %D %d",m,size);
  }
  if (n != PETSC_DECIDE) {
    if (n < 1) SETERRQ1(comm,PETSC_ERR_ARG_OUTOFRANGE,"Non-positive number of processors in Y direction: %D",n);
    else if (n > size) SETERRQ2(comm,PETSC_ERR_ARG_OUTOFRANGE,"Too many processors in Y direction: %D %d",n,size);
  }

  if (m == PETSC_DECIDE || n == PETSC_DECIDE) {
    if (n != PETSC_DECIDE) {
      m = size/n;
    } else if (m != PETSC_DECIDE) {
      n = size/m;
    } else {
      /* try for squarish distribution */
      m = (PetscInt)(0.5 + sqrt(((double)M)*((double)size)/((double)N)));
      if (!m) m = 1;
      while (m > 0) {
	n = size/m;
	if (m*n == size) break;
	m--;
      }
      if (M > N && m < n) {PetscInt _m = m; m = n; n = _m;}
    }
    if (m*n != size) SETERRQ(comm,PETSC_ERR_PLIB,"Unable to create partition, check the size of the communicator and input m and n ");
  } else if (m*n != size) SETERRQ(comm,PETSC_ERR_ARG_OUTOFRANGE,"Given Bad partition");

  if (M < m) SETERRQ2(comm,PETSC_ERR_ARG_OUTOFRANGE,"Partition in x direction is too fine! %D %D",M,m);
  if (N < n) SETERRQ2(comm,PETSC_ERR_ARG_OUTOFRANGE,"Partition in y direction is too fine! %D %D",N,n);

  /*
     Determine locally owned region
     xs is the first local node number, x 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);
    }
  }
  x  = lx[rank % m];
  xs = 0;
  for (i=0; i<(rank % m); i++) {
    xs += lx[i];
  }
#if defined(PETSC_USE_DEBUG)
  left = xs;
  for (i=(rank % m); i<m; i++) {
    left += lx[i];
  }
  if (left != M) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Sum of lx across processors not equal to M: %D %D",left,M);
#endif

  /*
     Determine locally owned region
     ys is the first local node number, y is the number of local nodes
  */
  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);
    }
  }
  y  = ly[rank/m];
  ys = 0;
  for (i=0; i<(rank/m); i++) {
    ys += ly[i];
  }
#if defined(PETSC_USE_DEBUG)
  left = ys;
  for (i=(rank/m); i<n; i++) {
    left += ly[i];
  }
  if (left != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Sum of ly across processors not equal to N: %D %D",left,N);
#endif

  /*
   check if the scatter requires more than one process neighbor or wraps around
   the domain more than once
  */
  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 ((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);
  }
  xe = xs + x;
  ye = ys + y;

  /* determine ghost region (Xs) and region scattered into (IXs)  */
  /* 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; }

  /* 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; }

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

  /* determine starting point of each processor */
  nn    = x*y;
  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*dof;
  ierr = VecCreateMPIWithArray(comm,dof,dd->Nlocal,PETSC_DECIDE,0,&global);CHKERRQ(ierr);
  dd->nlocal = (Xe-Xs)*(Ye-Ys)*dof;
  ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,dof,dd->nlocal,0,&local);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*dof,start,1,&to);CHKERRQ(ierr);

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

  ierr = ISCreateBlock(comm,dof,count,idx,PETSC_OWN_POINTER,&from);CHKERRQ(ierr);
  ierr = VecScatterCreate(local,from,global,to,&ltog);CHKERRQ(ierr);
  ierr = PetscLogObjectParent(dd,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);
    ierr  = PetscMalloc(count*sizeof(PetscInt),&idx);CHKERRQ(ierr);

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

  } else {
    /* must drop into cross shape region */
    /*       ---------|
            |  top    |
         |---         ---| up
         |   middle      |
         |               |
         ----         ---- down
            | bottom  |
            -----------
         Xs xs        xe Xe */
    count = (ys-IYs)*x + y*(IXe-IXs) + (IYe-ye)*x;
    ierr  = PetscMalloc(count*sizeof(PetscInt),&idx);CHKERRQ(ierr);

    left = xs - Xs; right = left + x;
    down = ys - Ys; up = down + y;
    count = 0;
    /* bottom */
    for (i=(IYs-Ys); i<down; i++) {
      for (j=left; j<right; j++) {
        idx[count++] = j + i*(Xe-Xs);
      }
    }
    /* middle */
    for (i=down; i<up; i++) {
      for (j=(IXs-Xs); j<(IXe-Xs); j++) {
        idx[count++] = j + i*(Xe-Xs);
      }
    }
    /* top */
    for (i=up; i<up+IYe-ye; i++) {
      for (j=left; j<right; j++) {
        idx[count++] = j + i*(Xe-Xs);
      }
    }
    ierr = ISCreateBlock(comm,dof,count,idx,PETSC_OWN_POINTER,&to);CHKERRQ(ierr);
  }


  /* determine who lies on each side of us stored in    n6 n7 n8
                                                        n3    n5
                                                        n0 n1 n2
  */

  /* Assume the Non-Periodic Case */
  n1 = rank - m;
  if (rank % m) {
    n0 = n1 - 1;
  } else {
    n0 = -1;
  }
  if ((rank+1) % m) {
    n2 = n1 + 1;
    n5 = rank + 1;
    n8 = rank + m + 1; if (n8 >= m*n) n8 = -1;
  } else {
    n2 = -1; n5 = -1; n8 = -1;
  }
  if (rank % m) {
    n3 = rank - 1;
    n6 = n3 + m; if (n6 >= m*n) n6 = -1;
  } else {
    n3 = -1; n6 = -1;
  }
  n7 = rank + m; if (n7 >= m*n) n7 = -1;

  if (bx == DMDA_BOUNDARY_PERIODIC && by == DMDA_BOUNDARY_PERIODIC) {
  /* Modify for Periodic Cases */
    /* Handle all four corners */
    if ((n6 < 0) && (n7 < 0) && (n3 < 0)) n6 = m-1;
    if ((n8 < 0) && (n7 < 0) && (n5 < 0)) n8 = 0;
    if ((n2 < 0) && (n5 < 0) && (n1 < 0)) n2 = size-m;
    if ((n0 < 0) && (n3 < 0) && (n1 < 0)) n0 = size-1;

    /* Handle Top and Bottom Sides */
    if (n1 < 0) n1 = rank + m * (n-1);
    if (n7 < 0) n7 = rank - m * (n-1);
    if ((n3 >= 0) && (n0 < 0)) n0 = size - m + rank - 1;
    if ((n3 >= 0) && (n6 < 0)) n6 = (rank%m)-1;
    if ((n5 >= 0) && (n2 < 0)) n2 = size - m + rank + 1;
    if ((n5 >= 0) && (n8 < 0)) n8 = (rank%m)+1;

    /* Handle Left and Right Sides */
    if (n3 < 0) n3 = rank + (m-1);
    if (n5 < 0) n5 = rank - (m-1);
    if ((n1 >= 0) && (n0 < 0)) n0 = rank-1;
    if ((n1 >= 0) && (n2 < 0)) n2 = rank-2*m+1;
    if ((n7 >= 0) && (n6 < 0)) n6 = rank+2*m-1;
    if ((n7 >= 0) && (n8 < 0)) n8 = rank+1;
  } else if (by == DMDA_BOUNDARY_PERIODIC) {  /* Handle Top and Bottom Sides */
    if (n1 < 0) n1 = rank + m * (n-1);
    if (n7 < 0) n7 = rank - m * (n-1);
    if ((n3 >= 0) && (n0 < 0)) n0 = size - m + rank - 1;
    if ((n3 >= 0) && (n6 < 0)) n6 = (rank%m)-1;
    if ((n5 >= 0) && (n2 < 0)) n2 = size - m + rank + 1;
    if ((n5 >= 0) && (n8 < 0)) n8 = (rank%m)+1;
  } else if (bx == DMDA_BOUNDARY_PERIODIC) { /* Handle Left and Right Sides */
    if (n3 < 0) n3 = rank + (m-1);
    if (n5 < 0) n5 = rank - (m-1);
    if ((n1 >= 0) && (n0 < 0)) n0 = rank-1;
    if ((n1 >= 0) && (n2 < 0)) n2 = rank-2*m+1;
    if ((n7 >= 0) && (n6 < 0)) n6 = rank+2*m-1;
    if ((n7 >= 0) && (n8 < 0)) n8 = rank+1;
  }

  ierr = PetscMalloc(9*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] = rank;
  dd->neighbors[5] = n5;
  dd->neighbors[6] = n6;
  dd->neighbors[7] = n7;
  dd->neighbors[8] = n8;

  if (stencil_type == DMDA_STENCIL_STAR) {
    /* save corner processor numbers */
    sn0 = n0; sn2 = n2; sn6 = n6; sn8 = n8;
    n0 = n2 = n6 = n8 = -1;
  }

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

  nn = 0;
  xbase = bases[rank];
  for (i=1; i<=s_y; i++) {
    if (n0 >= 0) { /* left below */
      x_t = lx[n0 % m];
      y_t = ly[(n0/m)];
      s_t = bases[n0] + x_t*y_t - (s_y-i)*x_t - s_x;
      for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
    }
    if (n1 >= 0) { /* directly below */
      x_t = x;
      y_t = ly[(n1/m)];
      s_t = bases[n1] + x_t*y_t - (s_y+1-i)*x_t;
      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)];
      s_t = bases[n2] + x_t*y_t - (s_y+1-i)*x_t;
      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; */
      s_t = bases[n3] + (i+1)*x_t - s_x;
      for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
    }

    for (j=0; j<x; j++) { idx[nn++] = xbase++; } /* interior */

    if (n5 >= 0) { /* directly right */
      x_t = lx[n5 % m];
      /* y_t = y; */
      s_t = bases[n5] + (i)*x_t;
      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)]; */
      s_t = bases[n6] + (i)*x_t - s_x;
      for (j=0; j<s_x; j++) { idx[nn++] = s_t++;}
    }
    if (n7 >= 0) { /* directly above */
      x_t = x;
      /* y_t = ly[(n7/m)]; */
      s_t = bases[n7] + (i-1)*x_t;
      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)]; */
      s_t = bases[n8] + (i-1)*x_t;
      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; n2 = sn2; n6 = sn6; n8 = sn8;
  }

  if ((stencil_type == DMDA_STENCIL_STAR) ||
      (bx && bx != DMDA_BOUNDARY_PERIODIC) ||
      (by && by != DMDA_BOUNDARY_PERIODIC)) {
    /*
        Recompute the local to global mappings, this time keeping the
      information about the cross corner processor numbers and any ghosted
      but not periodic indices.
    */
    nn = 0;
    xbase = bases[rank];
    for (i=1; i<=s_y; i++) {
      if (n0 >= 0) { /* left below */
        x_t = lx[n0 % m];
        y_t = ly[(n0/m)];
        s_t = bases[n0] + x_t*y_t - (s_y-i)*x_t - s_x;
        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 (n1 >= 0) { /* directly below */
        x_t = x;
        y_t = ly[(n1/m)];
        s_t = bases[n1] + x_t*y_t - (s_y+1-i)*x_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 (n2 >= 0) { /* right below */
        x_t = lx[n2 % m];
        y_t = ly[(n2/m)];
        s_t = bases[n2] + x_t*y_t - (s_y+1-i)*x_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 (n3 >= 0) { /* directly left */
        x_t = lx[n3 % m];
        /* y_t = y; */
        s_t = bases[n3] + (i+1)*x_t - s_x;
        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;}
      }

      for (j=0; j<x; j++) { idx[nn++] = xbase++; } /* interior */

      if (n5 >= 0) { /* directly right */
        x_t = lx[n5 % m];
        /* y_t = y; */
        s_t = bases[n5] + (i)*x_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 (n6 >= 0) { /* left above */
        x_t = lx[n6 % m];
        /* y_t = ly[(n6/m)]; */
        s_t = bases[n6] + (i)*x_t - s_x;
        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 (n7 >= 0) { /* directly above */
        x_t = x;
        /* y_t = ly[(n7/m)]; */
        s_t = bases[n7] + (i-1)*x_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 (n8 >= 0) { /* right above */
        x_t = lx[n8 % m];
        /* y_t = ly[(n8/m)]; */
        s_t = bases[n8] + (i-1)*x_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;}
      }
    }
  }
  /*
     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;
  /* 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 = 0; dd->ze = 1;
  dd->Xs = Xs*dof; dd->Xe = Xe*dof; dd->Ys = Ys; dd->Ye = Ye; dd->Zs = 0; dd->Ze = 1;

  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_2d;
  dd->ltol = PETSC_NULL;
  dd->ao   = PETSC_NULL;

  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDACreate2d"
/*@C
   DMDACreate2d -  Creates an object that will manage the communication of  two-dimensional
   regular array data that is distributed across some processors.

   Collective on MPI_Comm

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

   Output Parameter:
.  da - the resulting distributed array object

   Options Database Key:
+  -da_view - Calls DMView() at the conclusion of DMDACreate2d()
.  -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_processors_x <nx> - number of processors in x direction
.  -da_processors_y <ny> - number of processors in y direction
.  -da_refine_x <rx> - refinement ratio in x direction
.  -da_refine_y <ry> - refinement ratio in y direction
-  -da_refine <n> - refine the DMDA n times before creating, if M or N < 0


   Level: beginner

   Notes:
   The stencil type DMDA_STENCIL_STAR with width 1 corresponds to the
   standard 5-pt stencil, while DMDA_STENCIL_BOX with width 1 denotes
   the standard 9-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, two-dimensional

.seealso: DMDestroy(), DMView(), DMDACreate1d(), DMDACreate3d(), DMGlobalToLocalBegin(), DMDAGetRefinementFactor(),
          DMGlobalToLocalEnd(), DMLocalToGlobalBegin(), DMDALocalToLocalBegin(), DMDALocalToLocalEnd(), DMDASetRefinementFactor(),
          DMDAGetInfo(), DMCreateGlobalVector(), DMCreateLocalVector(), DMDACreateNaturalVector(), DMLoad(), DMDAGetOwnershipRanges()

@*/

PetscErrorCode  DMDACreate2d(MPI_Comm comm,DMDABoundaryType bx,DMDABoundaryType by,DMDAStencilType stencil_type,
                          PetscInt M,PetscInt N,PetscInt m,PetscInt n,PetscInt dof,PetscInt s,const PetscInt lx[],const PetscInt ly[],DM *da)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMDACreate(comm, da);CHKERRQ(ierr);
  ierr = DMDASetDim(*da, 2);CHKERRQ(ierr);
  ierr = DMDASetSizes(*da, M, N, 1);CHKERRQ(ierr);
  ierr = DMDASetNumProcs(*da, m, n, PETSC_DECIDE);CHKERRQ(ierr);
  ierr = DMDASetBoundaryType(*da, bx, by, DMDA_BOUNDARY_NONE);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, PETSC_NULL);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);
}