xref: /petsc/src/dm/impls/da/dalocal.c (revision e4d69e081bcf8bbabfb8a3c65677035c2cd07561)

/*
  Code for manipulating distributed regular arrays in parallel.
*/

#include <petsc-private/dmdaimpl.h>    /*I   "petscdmda.h"   I*/
#include <petscsf.h>
#include <petscfe.h>

/*
   This allows the DMDA vectors to properly tell MATLAB their dimensions
*/
#if defined(PETSC_HAVE_MATLAB_ENGINE)
#include <engine.h>   /* MATLAB include file */
#include <mex.h>      /* MATLAB include file */
#undef __FUNCT__
#define __FUNCT__ "VecMatlabEnginePut_DA2d"
static PetscErrorCode  VecMatlabEnginePut_DA2d(PetscObject obj,void *mengine)
{
  PetscErrorCode ierr;
  PetscInt       n,m;
  Vec            vec = (Vec)obj;
  PetscScalar    *array;
  mxArray        *mat;
  DM             da;

  PetscFunctionBegin;
  ierr = VecGetDM(vec, &da);CHKERRQ(ierr);
  if (!da) SETERRQ(PetscObjectComm((PetscObject)vec),PETSC_ERR_ARG_WRONGSTATE,"Vector not associated with a DMDA");
  ierr = DMDAGetGhostCorners(da,0,0,0,&m,&n,0);CHKERRQ(ierr);

  ierr = VecGetArray(vec,&array);CHKERRQ(ierr);
#if !defined(PETSC_USE_COMPLEX)
  mat = mxCreateDoubleMatrix(m,n,mxREAL);
#else
  mat = mxCreateDoubleMatrix(m,n,mxCOMPLEX);
#endif
  ierr = PetscMemcpy(mxGetPr(mat),array,n*m*sizeof(PetscScalar));CHKERRQ(ierr);
  ierr = PetscObjectName(obj);CHKERRQ(ierr);
  engPutVariable((Engine*)mengine,obj->name,mat);

  ierr = VecRestoreArray(vec,&array);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
#endif


#undef __FUNCT__
#define __FUNCT__ "DMCreateLocalVector_DA"
PetscErrorCode  DMCreateLocalVector_DA(DM da,Vec *g)
{
  PetscErrorCode ierr;
  DM_DA          *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  PetscValidPointer(g,2);
  if (da->defaultSection) {
    ierr = DMCreateLocalVector_Section_Private(da,g);CHKERRQ(ierr);
  } else {
    ierr = VecCreate(PETSC_COMM_SELF,g);CHKERRQ(ierr);
    ierr = VecSetSizes(*g,dd->nlocal,PETSC_DETERMINE);CHKERRQ(ierr);
    ierr = VecSetBlockSize(*g,dd->w);CHKERRQ(ierr);
    ierr = VecSetType(*g,da->vectype);CHKERRQ(ierr);
    ierr = VecSetDM(*g, da);CHKERRQ(ierr);
#if defined(PETSC_HAVE_MATLAB_ENGINE)
    if (dd->w == 1  && dd->dim == 2) {
      ierr = PetscObjectComposeFunction((PetscObject)*g,"PetscMatlabEnginePut_C",VecMatlabEnginePut_DA2d);CHKERRQ(ierr);
    }
#endif
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAGetNumCells"
PetscErrorCode DMDAGetNumCells(DM dm, PetscInt *numCellsX, PetscInt *numCellsY, PetscInt *numCellsZ, PetscInt *numCells)
{
  DM_DA          *da = (DM_DA*) dm->data;
  const PetscInt dim = da->dim;
  const PetscInt mx  = (da->Xe - da->Xs)/da->w, my = da->Ye - da->Ys, mz = da->Ze - da->Zs;
  const PetscInt nC  = (mx)*(dim > 1 ? (my)*(dim > 2 ? (mz) : 1) : 1);

  PetscFunctionBegin;
  if (numCellsX) {
    PetscValidIntPointer(numCellsX,2);
    *numCellsX = mx;
  }
  if (numCellsY) {
    PetscValidIntPointer(numCellsX,3);
    *numCellsY = my;
  }
  if (numCellsZ) {
    PetscValidIntPointer(numCellsX,4);
    *numCellsZ = mz;
  }
  if (numCells) {
    PetscValidIntPointer(numCells,5);
    *numCells = nC;
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAGetNumVertices"
PetscErrorCode DMDAGetNumVertices(DM dm, PetscInt *numVerticesX, PetscInt *numVerticesY, PetscInt *numVerticesZ, PetscInt *numVertices)
{
  DM_DA          *da = (DM_DA*) dm->data;
  const PetscInt dim = da->dim;
  const PetscInt mx  = (da->Xe - da->Xs)/da->w, my = da->Ye - da->Ys, mz = da->Ze - da->Zs;
  const PetscInt nVx = mx+1;
  const PetscInt nVy = dim > 1 ? (my+1) : 1;
  const PetscInt nVz = dim > 2 ? (mz+1) : 1;
  const PetscInt nV  = nVx*nVy*nVz;

  PetscFunctionBegin;
  if (numVerticesX) {
    PetscValidIntPointer(numVerticesX,2);
    *numVerticesX = nVx;
  }
  if (numVerticesY) {
    PetscValidIntPointer(numVerticesY,3);
    *numVerticesY = nVy;
  }
  if (numVerticesZ) {
    PetscValidIntPointer(numVerticesZ,4);
    *numVerticesZ = nVz;
  }
  if (numVertices) {
    PetscValidIntPointer(numVertices,5);
    *numVertices = nV;
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAGetNumFaces"
PetscErrorCode DMDAGetNumFaces(DM dm, PetscInt *numXFacesX, PetscInt *numXFaces, PetscInt *numYFacesY, PetscInt *numYFaces, PetscInt *numZFacesZ, PetscInt *numZFaces)
{
  DM_DA          *da = (DM_DA*) dm->data;
  const PetscInt dim = da->dim;
  const PetscInt mx  = (da->Xe - da->Xs)/da->w, my = da->Ye - da->Ys, mz = da->Ze - da->Zs;
  const PetscInt nxF = (dim > 1 ? (my)*(dim > 2 ? (mz) : 1) : 1);
  const PetscInt nXF = (mx+1)*nxF;
  const PetscInt nyF = mx*(dim > 2 ? mz : 1);
  const PetscInt nYF = dim > 1 ? (my+1)*nyF : 0;
  const PetscInt nzF = mx*(dim > 1 ? my : 0);
  const PetscInt nZF = dim > 2 ? (mz+1)*nzF : 0;

  PetscFunctionBegin;
  if (numXFacesX) {
    PetscValidIntPointer(numXFacesX,2);
    *numXFacesX = nxF;
  }
  if (numXFaces) {
    PetscValidIntPointer(numXFaces,3);
    *numXFaces = nXF;
  }
  if (numYFacesY) {
    PetscValidIntPointer(numYFacesY,4);
    *numYFacesY = nyF;
  }
  if (numYFaces) {
    PetscValidIntPointer(numYFaces,5);
    *numYFaces = nYF;
  }
  if (numZFacesZ) {
    PetscValidIntPointer(numZFacesZ,6);
    *numZFacesZ = nzF;
  }
  if (numZFaces) {
    PetscValidIntPointer(numZFaces,7);
    *numZFaces = nZF;
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAGetHeightStratum"
PetscErrorCode DMDAGetHeightStratum(DM dm, PetscInt height, PetscInt *pStart, PetscInt *pEnd)
{
  DM_DA          *da = (DM_DA*) dm->data;
  const PetscInt dim = da->dim;
  PetscInt       nC, nV, nXF, nYF, nZF;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (pStart) PetscValidIntPointer(pStart,3);
  if (pEnd)   PetscValidIntPointer(pEnd,4);
  ierr = DMDAGetNumCells(dm, NULL, NULL, NULL, &nC);CHKERRQ(ierr);
  ierr = DMDAGetNumVertices(dm, NULL, NULL, NULL, &nV);CHKERRQ(ierr);
  ierr = DMDAGetNumFaces(dm, NULL, &nXF, NULL, &nYF, NULL, &nZF);CHKERRQ(ierr);
  if (height == 0) {
    /* Cells */
    if (pStart) *pStart = 0;
    if (pEnd)   *pEnd   = nC;
  } else if (height == 1) {
    /* Faces */
    if (pStart) *pStart = nC+nV;
    if (pEnd)   *pEnd   = nC+nV+nXF+nYF+nZF;
  } else if (height == dim) {
    /* Vertices */
    if (pStart) *pStart = nC;
    if (pEnd)   *pEnd   = nC+nV;
  } else if (height < 0) {
    /* All points */
    if (pStart) *pStart = 0;
    if (pEnd)   *pEnd   = nC+nV+nXF+nYF+nZF;
  } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No points of height %d in the DA", height);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAGetDepthStratum"
PetscErrorCode DMDAGetDepthStratum(DM dm, PetscInt depth, PetscInt *pStart, PetscInt *pEnd)
{
  DM_DA         *da  = (DM_DA*) dm->data;
  const PetscInt dim = da->dim;
  PetscInt       nC, nV, nXF, nYF, nZF;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (pStart) PetscValidIntPointer(pStart,3);
  if (pEnd)   PetscValidIntPointer(pEnd,4);
  ierr = DMDAGetNumCells(dm, NULL, NULL, NULL, &nC);CHKERRQ(ierr);
  ierr = DMDAGetNumVertices(dm, NULL, NULL, NULL, &nV);CHKERRQ(ierr);
  ierr = DMDAGetNumFaces(dm, NULL, &nXF, NULL, &nYF, NULL, &nZF);CHKERRQ(ierr);
  if (depth == dim) {
    /* Cells */
    if (pStart) *pStart = 0;
    if (pEnd)   *pEnd   = nC;
  } else if (depth == dim-1) {
    /* Faces */
    if (pStart) *pStart = nC+nV;
    if (pEnd)   *pEnd   = nC+nV+nXF+nYF+nZF;
  } else if (depth == 0) {
    /* Vertices */
    if (pStart) *pStart = nC;
    if (pEnd)   *pEnd   = nC+nV;
  } else if (depth < 0) {
    /* All points */
    if (pStart) *pStart = 0;
    if (pEnd)   *pEnd   = nC+nV+nXF+nYF+nZF;
  } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No points of depth %d in the DA", depth);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAGetConeSize"
PetscErrorCode DMDAGetConeSize(DM dm, PetscInt p, PetscInt *coneSize)
{
  DM_DA         *da  = (DM_DA*) dm->data;
  const PetscInt dim = da->dim;
  PetscInt       nC, nV, nXF, nYF, nZF;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  *coneSize = 0;
  ierr = DMDAGetNumCells(dm, NULL, NULL, NULL, &nC);CHKERRQ(ierr);
  ierr = DMDAGetNumVertices(dm, NULL, NULL, NULL, &nV);CHKERRQ(ierr);
  ierr = DMDAGetNumFaces(dm, NULL, &nXF, NULL, &nYF, NULL, &nZF);CHKERRQ(ierr);
  switch (dim) {
  case 2:
    if (p >= 0) {
      if (p < nC) {
        *coneSize = 4;
      } else if (p < nC+nV) {
        *coneSize = 0;
      } else if (p < nC+nV+nXF+nYF+nZF) {
        *coneSize = 2;
      } else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Point %d should be in [0, %d)", p, nC+nV+nXF+nYF+nZF);
    } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Negative point %d is invalid", p);
    break;
  case 3:
    SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Too lazy to do 3D");
    break;
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAGetCone"
PetscErrorCode DMDAGetCone(DM dm, PetscInt p, PetscInt *cone[])
{
  DM_DA         *da  = (DM_DA*) dm->data;
  const PetscInt dim = da->dim;
  PetscInt       nCx, nCy, nCz, nC, nVx, nVy, nVz, nV, nxF, nyF, nzF, nXF, nYF, nZF;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (!cone) {ierr = DMGetWorkArray(dm, 6, PETSC_INT, cone);CHKERRQ(ierr);}
  ierr = DMDAGetNumCells(dm, &nCx, &nCy, &nCz, &nC);CHKERRQ(ierr);
  ierr = DMDAGetNumVertices(dm, &nVx, &nVy, &nVz, &nV);CHKERRQ(ierr);
  ierr = DMDAGetNumFaces(dm, &nxF, &nXF, &nyF, &nYF, &nzF, &nZF);CHKERRQ(ierr);
  switch (dim) {
  case 2:
    if (p >= 0) {
      if (p < nC) {
        const PetscInt cy = p / nCx;
        const PetscInt cx = p % nCx;

        (*cone)[0] = cy*nxF + cx + nC+nV;
        (*cone)[1] = cx*nyF + cy + nyF + nC+nV+nXF;
        (*cone)[2] = cy*nxF + cx + nxF + nC+nV;
        (*cone)[3] = cx*nyF + cy + nC+nV+nXF;
        SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Too lazy to do cell cones");
      } else if (p < nC+nV) {
      } else if (p < nC+nV+nXF) {
        const PetscInt fy = (p - nC+nV) / nxF;
        const PetscInt fx = (p - nC+nV) % nxF;

        (*cone)[0] = fy*nVx + fx + nC;
        (*cone)[1] = fy*nVx + fx + 1 + nC;
      } else if (p < nC+nV+nXF+nYF) {
        const PetscInt fx = (p - nC+nV+nXF) / nyF;
        const PetscInt fy = (p - nC+nV+nXF) % nyF;

        (*cone)[0] = fy*nVx + fx + nC;
        (*cone)[1] = fy*nVx + fx + nVx + nC;
      } else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Point %d should be in [0, %d)", p, nC+nV+nXF+nYF+nZF);
    } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Negative point %d is invalid", p);
    break;
  case 3:
    SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Too lazy to do 3D");
    break;
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDARestoreCone"
PetscErrorCode DMDARestoreCone(DM dm, PetscInt p, PetscInt *cone[])
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMGetWorkArray(dm, 6, PETSC_INT, cone);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDACreateSection"
/*@C
  DMDACreateSection - Create a PetscSection inside the DMDA that describes data layout. This allows multiple fields with
  different numbers of dofs on vertices, cells, and faces in each direction.

  Input Parameters:
+ dm- The DMDA
. numFields - The number of fields
. numComp - The number of components in each field
. numDof - The number of dofs per dimension for each field
. numFaceDof - The number of dofs per face for each field and direction, or NULL

  Level: developer

  Note:
  The default DMDA numbering is as follows:

    - Cells:    [0,             nC)
    - Vertices: [nC,            nC+nV)
    - X-Faces:  [nC+nV,         nC+nV+nXF)         normal is +- x-dir
    - Y-Faces:  [nC+nV+nXF,     nC+nV+nXF+nYF)     normal is +- y-dir
    - Z-Faces:  [nC+nV+nXF+nYF, nC+nV+nXF+nYF+nZF) normal is +- z-dir

  We interpret the default DMDA partition as a cell partition, and the data assignment as a cell assignment.
@*/
PetscErrorCode DMDACreateSection(DM dm, PetscInt numComp[], PetscInt numDof[], PetscInt numFaceDof[], PetscSection *s)
{
  DM_DA            *da  = (DM_DA*) dm->data;
  PetscSection      section;
  const PetscInt    dim = da->dim;
  PetscInt          numFields, numVertexTotDof = 0, numCellTotDof = 0, numFaceTotDof[3] = {0, 0, 0};
  PetscSF           sf;
  PetscMPIInt       rank;
  const PetscMPIInt *neighbors;
  PetscInt          *localPoints;
  PetscSFNode       *remotePoints;
  PetscInt          nleaves = 0,  nleavesCheck = 0, nL = 0;
  PetscInt          nC, nVx, nVy, nVz, nV, nxF, nXF, nyF, nYF, nzF, nZF;
  PetscInt          pStart, pEnd, cStart, cEnd, vStart, vEnd, fStart, fEnd, xfStart, xfEnd, yfStart, yfEnd, zfStart, zfEnd;
  PetscInt          f, v, c, xf, yf, zf, xn, yn, zn;
  PetscErrorCode    ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(s, 4);
  ierr    = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
  ierr    = DMDAGetNumCells(dm, NULL, NULL, NULL, &nC);CHKERRQ(ierr);
  ierr    = DMDAGetNumVertices(dm, &nVx, &nVy, &nVz, &nV);CHKERRQ(ierr);
  ierr    = DMDAGetNumFaces(dm, &nxF, &nXF, &nyF, &nYF, &nzF, &nZF);CHKERRQ(ierr);
  ierr    = DMDAGetHeightStratum(dm, -1,  &pStart, &pEnd);CHKERRQ(ierr);
  ierr    = DMDAGetHeightStratum(dm, 0,   &cStart, &cEnd);CHKERRQ(ierr);
  ierr    = DMDAGetHeightStratum(dm, 1,   &fStart, &fEnd);CHKERRQ(ierr);
  ierr    = DMDAGetHeightStratum(dm, dim, &vStart, &vEnd);CHKERRQ(ierr);
  xfStart = vEnd;  xfEnd = xfStart+nXF;
  yfStart = xfEnd; yfEnd = yfStart+nYF;
  zfStart = yfEnd; zfEnd = zfStart+nZF;
  if (zfEnd != fEnd) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid face end %d, should be %d", zfEnd, fEnd);
  /* Create local section */
  ierr = DMDAGetInfo(dm, 0,0,0,0,0,0,0, &numFields, 0,0,0,0,0);CHKERRQ(ierr);
  for (f = 0; f < numFields; ++f) {
    numVertexTotDof  += numDof[f*(dim+1)+0];
    numCellTotDof    += numDof[f*(dim+1)+dim];
    numFaceTotDof[0] += dim > 0 ? (numFaceDof ? numFaceDof[f*dim+0] : numDof[f*(dim+1)+dim-1]) : 0;
    numFaceTotDof[1] += dim > 1 ? (numFaceDof ? numFaceDof[f*dim+1] : numDof[f*(dim+1)+dim-1]) : 0;
    numFaceTotDof[2] += dim > 2 ? (numFaceDof ? numFaceDof[f*dim+2] : numDof[f*(dim+1)+dim-1]) : 0;
  }
  ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &section);CHKERRQ(ierr);
  if (numFields > 0) {
    ierr = PetscSectionSetNumFields(section, numFields);CHKERRQ(ierr);
    for (f = 0; f < numFields; ++f) {
      const char *name;

      ierr = DMDAGetFieldName(dm, f, &name);CHKERRQ(ierr);
      ierr = PetscSectionSetFieldName(section, f, name ? name : "Field");CHKERRQ(ierr);
      if (numComp) {
        ierr = PetscSectionSetFieldComponents(section, f, numComp[f]);CHKERRQ(ierr);
      }
    }
  }
  ierr = PetscSectionSetChart(section, pStart, pEnd);CHKERRQ(ierr);
  for (v = vStart; v < vEnd; ++v) {
    for (f = 0; f < numFields; ++f) {
      ierr = PetscSectionSetFieldDof(section, v, f, numDof[f*(dim+1)+0]);CHKERRQ(ierr);
    }
    ierr = PetscSectionSetDof(section, v, numVertexTotDof);CHKERRQ(ierr);
  }
  for (xf = xfStart; xf < xfEnd; ++xf) {
    for (f = 0; f < numFields; ++f) {
      ierr = PetscSectionSetFieldDof(section, xf, f, numFaceDof ? numFaceDof[f*dim+0] : numDof[f*(dim+1)+dim-1]);CHKERRQ(ierr);
    }
    ierr = PetscSectionSetDof(section, xf, numFaceTotDof[0]);CHKERRQ(ierr);
  }
  for (yf = yfStart; yf < yfEnd; ++yf) {
    for (f = 0; f < numFields; ++f) {
      ierr = PetscSectionSetFieldDof(section, yf, f, numFaceDof ? numFaceDof[f*dim+1] : numDof[f*(dim+1)+dim-1]);CHKERRQ(ierr);
    }
    ierr = PetscSectionSetDof(section, yf, numFaceTotDof[1]);CHKERRQ(ierr);
  }
  for (zf = zfStart; zf < zfEnd; ++zf) {
    for (f = 0; f < numFields; ++f) {
      ierr = PetscSectionSetFieldDof(section, zf, f, numFaceDof ? numFaceDof[f*dim+2] : numDof[f*(dim+1)+dim-1]);CHKERRQ(ierr);
    }
    ierr = PetscSectionSetDof(section, zf, numFaceTotDof[2]);CHKERRQ(ierr);
  }
  for (c = cStart; c < cEnd; ++c) {
    for (f = 0; f < numFields; ++f) {
      ierr = PetscSectionSetFieldDof(section, c, f, numDof[f*(dim+1)+dim]);CHKERRQ(ierr);
    }
    ierr = PetscSectionSetDof(section, c, numCellTotDof);CHKERRQ(ierr);
  }
  ierr = PetscSectionSetUp(section);CHKERRQ(ierr);
  /* Create mesh point SF */
  ierr = DMDAGetNeighbors(dm, &neighbors);CHKERRQ(ierr);
  for (zn = 0; zn < (dim > 2 ? 3 : 1); ++zn) {
    for (yn = 0; yn < (dim > 1 ? 3 : 1); ++yn) {
      for (xn = 0; xn < 3; ++xn) {
        const PetscInt xp       = xn-1, yp = dim > 1 ? yn-1 : 0, zp = dim > 2 ? zn-1 : 0;
        const PetscInt neighbor = neighbors[(zn*3+yn)*3+xn];

        if (neighbor >= 0 && neighbor < rank) {
          nleaves += (!xp ? nVx : 1) * (!yp ? nVy : 1) * (!zp ? nVz : 1); /* vertices */
          if (xp && !yp && !zp) {
            nleaves += nxF; /* x faces */
          } else if (yp && !zp && !xp) {
            nleaves += nyF; /* y faces */
          } else if (zp && !xp && !yp) {
            nleaves += nzF; /* z faces */
          }
        }
      }
    }
  }
  ierr = PetscMalloc2(nleaves,&localPoints,nleaves,&remotePoints);CHKERRQ(ierr);
  for (zn = 0; zn < (dim > 2 ? 3 : 1); ++zn) {
    for (yn = 0; yn < (dim > 1 ? 3 : 1); ++yn) {
      for (xn = 0; xn < 3; ++xn) {
        const PetscInt xp       = xn-1, yp = dim > 1 ? yn-1 : 0, zp = dim > 2 ? zn-1 : 0;
        const PetscInt neighbor = neighbors[(zn*3+yn)*3+xn];
        PetscInt       xv, yv, zv;

        if (neighbor >= 0 && neighbor < rank) {
          if (xp < 0) { /* left */
            if (yp < 0) { /* bottom */
              if (zp < 0) { /* back */
                const PetscInt localVertex  = (      0*nVy +     0)*nVx +     0 + nC;
                const PetscInt remoteVertex = ((nVz-1)*nVy + nVy-1)*nVx + nVx-1 + nC; /* TODO: Correct this for neighbor sizes */
                nleavesCheck += 1; /* left bottom back vertex */

                localPoints[nL]        = localVertex;
                remotePoints[nL].rank  = neighbor;
                remotePoints[nL].index = remoteVertex;
                ++nL;
              } else if (zp > 0) { /* front */
                const PetscInt localVertex  = ((nVz-1)*nVy +     0)*nVx +     0 + nC;
                const PetscInt remoteVertex = (      0*nVy + nVy-1)*nVx + nVx-1 + nC; /* TODO: Correct this for neighbor sizes */
                nleavesCheck += 1; /* left bottom front vertex */

                localPoints[nL]        = localVertex;
                remotePoints[nL].rank  = neighbor;
                remotePoints[nL].index = remoteVertex;
                ++nL;
              } else {
                nleavesCheck += nVz; /* left bottom vertices */
                for (zv = 0; zv < nVz; ++zv, ++nL) {
                  const PetscInt localVertex  = (zv*nVy +     0)*nVx +     0 + nC;
                  const PetscInt remoteVertex = (zv*nVy + nVy-1)*nVx + nVx-1 + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              }
            } else if (yp > 0) { /* top */
              if (zp < 0) { /* back */
                const PetscInt localVertex  = (      0*nVy + nVy-1)*nVx +     0 + nC;
                const PetscInt remoteVertex = ((nVz-1)*nVy +     0)*nVx + nVx-1 + nC; /* TODO: Correct this for neighbor sizes */
                nleavesCheck += 1; /* left top back vertex */

                localPoints[nL]        = localVertex;
                remotePoints[nL].rank  = neighbor;
                remotePoints[nL].index = remoteVertex;
                ++nL;
              } else if (zp > 0) { /* front */
                const PetscInt localVertex  = ((nVz-1)*nVy + nVy-1)*nVx +     0 + nC;
                const PetscInt remoteVertex = (      0*nVy +     0)*nVx + nVx-1 + nC; /* TODO: Correct this for neighbor sizes */
                nleavesCheck += 1; /* left top front vertex */

                localPoints[nL]        = localVertex;
                remotePoints[nL].rank  = neighbor;
                remotePoints[nL].index = remoteVertex;
                ++nL;
              } else {
                nleavesCheck += nVz; /* left top vertices */
                for (zv = 0; zv < nVz; ++zv, ++nL) {
                  const PetscInt localVertex  = (zv*nVy + nVy-1)*nVx +     0 + nC;
                  const PetscInt remoteVertex = (zv*nVy +     0)*nVx + nVx-1 + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              }
            } else {
              if (zp < 0) { /* back */
                nleavesCheck += nVy; /* left back vertices */
                for (yv = 0; yv < nVy; ++yv, ++nL) {
                  const PetscInt localVertex  = (      0*nVy + yv)*nVx +     0 + nC;
                  const PetscInt remoteVertex = ((nVz-1)*nVy + yv)*nVx + nVx-1 + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              } else if (zp > 0) { /* front */
                nleavesCheck += nVy; /* left front vertices */
                for (yv = 0; yv < nVy; ++yv, ++nL) {
                  const PetscInt localVertex  = ((nVz-1)*nVy + yv)*nVx +     0 + nC;
                  const PetscInt remoteVertex = (      0*nVy + yv)*nVx + nVx-1 + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              } else {
                nleavesCheck += nVy*nVz; /* left vertices */
                for (zv = 0; zv < nVz; ++zv) {
                  for (yv = 0; yv < nVy; ++yv, ++nL) {
                    const PetscInt localVertex  = (zv*nVy + yv)*nVx +     0 + nC;
                    const PetscInt remoteVertex = (zv*nVy + yv)*nVx + nVx-1 + nC; /* TODO: Correct this for neighbor sizes */

                    localPoints[nL]        = localVertex;
                    remotePoints[nL].rank  = neighbor;
                    remotePoints[nL].index = remoteVertex;
                  }
                }
                nleavesCheck += nxF;     /* left faces */
                for (xf = 0; xf < nxF; ++xf, ++nL) {
                  /* THIS IS WRONG */
                  const PetscInt localFace  = 0 + nC+nV;
                  const PetscInt remoteFace = 0 + nC+nV;

                  localPoints[nL]        = localFace;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteFace;
                }
              }
            }
          } else if (xp > 0) { /* right */
            if (yp < 0) { /* bottom */
              if (zp < 0) { /* back */
                const PetscInt localVertex  = (      0*nVy +     0)*nVx + nVx-1 + nC;
                const PetscInt remoteVertex = ((nVz-1)*nVy + nVy-1)*nVx +     0 + nC; /* TODO: Correct this for neighbor sizes */
                nleavesCheck += 1; /* right bottom back vertex */

                localPoints[nL]        = localVertex;
                remotePoints[nL].rank  = neighbor;
                remotePoints[nL].index = remoteVertex;
                ++nL;
              } else if (zp > 0) { /* front */
                const PetscInt localVertex  = ((nVz-1)*nVy +     0)*nVx + nVx-1 + nC;
                const PetscInt remoteVertex = (      0*nVy + nVy-1)*nVx +     0 + nC; /* TODO: Correct this for neighbor sizes */
                nleavesCheck += 1; /* right bottom front vertex */

                localPoints[nL]        = localVertex;
                remotePoints[nL].rank  = neighbor;
                remotePoints[nL].index = remoteVertex;
                ++nL;
              } else {
                nleavesCheck += nVz; /* right bottom vertices */
                for (zv = 0; zv < nVz; ++zv, ++nL) {
                  const PetscInt localVertex  = (zv*nVy +     0)*nVx + nVx-1 + nC;
                  const PetscInt remoteVertex = (zv*nVy + nVy-1)*nVx +     0 + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              }
            } else if (yp > 0) { /* top */
              if (zp < 0) { /* back */
                const PetscInt localVertex  = (      0*nVy + nVy-1)*nVx + nVx-1 + nC;
                const PetscInt remoteVertex = ((nVz-1)*nVy +     0)*nVx +     0 + nC; /* TODO: Correct this for neighbor sizes */
                nleavesCheck += 1; /* right top back vertex */

                localPoints[nL]        = localVertex;
                remotePoints[nL].rank  = neighbor;
                remotePoints[nL].index = remoteVertex;
                ++nL;
              } else if (zp > 0) { /* front */
                const PetscInt localVertex  = ((nVz-1)*nVy + nVy-1)*nVx + nVx-1 + nC;
                const PetscInt remoteVertex = (      0*nVy +     0)*nVx +     0 + nC; /* TODO: Correct this for neighbor sizes */
                nleavesCheck += 1; /* right top front vertex */

                localPoints[nL]        = localVertex;
                remotePoints[nL].rank  = neighbor;
                remotePoints[nL].index = remoteVertex;
                ++nL;
              } else {
                nleavesCheck += nVz; /* right top vertices */
                for (zv = 0; zv < nVz; ++zv, ++nL) {
                  const PetscInt localVertex  = (zv*nVy + nVy-1)*nVx + nVx-1 + nC;
                  const PetscInt remoteVertex = (zv*nVy +     0)*nVx +     0 + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              }
            } else {
              if (zp < 0) { /* back */
                nleavesCheck += nVy; /* right back vertices */
                for (yv = 0; yv < nVy; ++yv, ++nL) {
                  const PetscInt localVertex  = (      0*nVy + yv)*nVx + nVx-1 + nC;
                  const PetscInt remoteVertex = ((nVz-1)*nVy + yv)*nVx +     0 + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              } else if (zp > 0) { /* front */
                nleavesCheck += nVy; /* right front vertices */
                for (yv = 0; yv < nVy; ++yv, ++nL) {
                  const PetscInt localVertex  = ((nVz-1)*nVy + yv)*nVx + nVx-1 + nC;
                  const PetscInt remoteVertex = (      0*nVy + yv)*nVx +     0 + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              } else {
                nleavesCheck += nVy*nVz; /* right vertices */
                for (zv = 0; zv < nVz; ++zv) {
                  for (yv = 0; yv < nVy; ++yv, ++nL) {
                    const PetscInt localVertex  = (zv*nVy + yv)*nVx + nVx-1 + nC;
                    const PetscInt remoteVertex = (zv*nVy + yv)*nVx + 0     + nC; /* TODO: Correct this for neighbor sizes */

                    localPoints[nL]        = localVertex;
                    remotePoints[nL].rank  = neighbor;
                    remotePoints[nL].index = remoteVertex;
                  }
                }
                nleavesCheck += nxF;     /* right faces */
                for (xf = 0; xf < nxF; ++xf, ++nL) {
                  /* THIS IS WRONG */
                  const PetscInt localFace  = 0 + nC+nV;
                  const PetscInt remoteFace = 0 + nC+nV;

                  localPoints[nL]        = localFace;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteFace;
                }
              }
            }
          } else {
            if (yp < 0) { /* bottom */
              if (zp < 0) { /* back */
                nleavesCheck += nVx; /* bottom back vertices */
                for (xv = 0; xv < nVx; ++xv, ++nL) {
                  const PetscInt localVertex  = (      0*nVy +     0)*nVx + xv + nC;
                  const PetscInt remoteVertex = ((nVz-1)*nVy + nVy-1)*nVx + xv + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              } else if (zp > 0) { /* front */
                nleavesCheck += nVx; /* bottom front vertices */
                for (xv = 0; xv < nVx; ++xv, ++nL) {
                  const PetscInt localVertex  = ((nVz-1)*nVy +     0)*nVx + xv + nC;
                  const PetscInt remoteVertex = (      0*nVy + nVy-1)*nVx + xv + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              } else {
                nleavesCheck += nVx*nVz; /* bottom vertices */
                for (zv = 0; zv < nVz; ++zv) {
                  for (xv = 0; xv < nVx; ++xv, ++nL) {
                    const PetscInt localVertex  = (zv*nVy +     0)*nVx + xv + nC;
                    const PetscInt remoteVertex = (zv*nVy + nVy-1)*nVx + xv + nC; /* TODO: Correct this for neighbor sizes */

                    localPoints[nL]        = localVertex;
                    remotePoints[nL].rank  = neighbor;
                    remotePoints[nL].index = remoteVertex;
                  }
                }
                nleavesCheck += nyF;     /* bottom faces */
                for (yf = 0; yf < nyF; ++yf, ++nL) {
                  /* THIS IS WRONG */
                  const PetscInt localFace  = 0 + nC+nV;
                  const PetscInt remoteFace = 0 + nC+nV;

                  localPoints[nL]        = localFace;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteFace;
                }
              }
            } else if (yp > 0) { /* top */
              if (zp < 0) { /* back */
                nleavesCheck += nVx; /* top back vertices */
                for (xv = 0; xv < nVx; ++xv, ++nL) {
                  const PetscInt localVertex  = (      0*nVy + nVy-1)*nVx + xv + nC;
                  const PetscInt remoteVertex = ((nVz-1)*nVy +     0)*nVx + xv + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              } else if (zp > 0) { /* front */
                nleavesCheck += nVx; /* top front vertices */
                for (xv = 0; xv < nVx; ++xv, ++nL) {
                  const PetscInt localVertex  = ((nVz-1)*nVy + nVy-1)*nVx + xv + nC;
                  const PetscInt remoteVertex = (      0*nVy +     0)*nVx + xv + nC; /* TODO: Correct this for neighbor sizes */

                  localPoints[nL]        = localVertex;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteVertex;
                }
              } else {
                nleavesCheck += nVx*nVz; /* top vertices */
                for (zv = 0; zv < nVz; ++zv) {
                  for (xv = 0; xv < nVx; ++xv, ++nL) {
                    const PetscInt localVertex  = (zv*nVy + nVy-1)*nVx + xv + nC;
                    const PetscInt remoteVertex = (zv*nVy +     0)*nVx + xv + nC; /* TODO: Correct this for neighbor sizes */

                    localPoints[nL]        = localVertex;
                    remotePoints[nL].rank  = neighbor;
                    remotePoints[nL].index = remoteVertex;
                  }
                }
                nleavesCheck += nyF;     /* top faces */
                for (yf = 0; yf < nyF; ++yf, ++nL) {
                  /* THIS IS WRONG */
                  const PetscInt localFace  = 0 + nC+nV;
                  const PetscInt remoteFace = 0 + nC+nV;

                  localPoints[nL]        = localFace;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteFace;
                }
              }
            } else {
              if (zp < 0) { /* back */
                nleavesCheck += nVx*nVy; /* back vertices */
                for (yv = 0; yv < nVy; ++yv) {
                  for (xv = 0; xv < nVx; ++xv, ++nL) {
                    const PetscInt localVertex  = (      0*nVy + yv)*nVx + xv + nC;
                    const PetscInt remoteVertex = ((nVz-1)*nVy + yv)*nVx + xv + nC; /* TODO: Correct this for neighbor sizes */

                    localPoints[nL]        = localVertex;
                    remotePoints[nL].rank  = neighbor;
                    remotePoints[nL].index = remoteVertex;
                  }
                }
                nleavesCheck += nzF;     /* back faces */
                for (zf = 0; zf < nzF; ++zf, ++nL) {
                  /* THIS IS WRONG */
                  const PetscInt localFace  = 0 + nC+nV;
                  const PetscInt remoteFace = 0 + nC+nV;

                  localPoints[nL]        = localFace;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteFace;
                }
              } else if (zp > 0) { /* front */
                nleavesCheck += nVx*nVy; /* front vertices */
                for (yv = 0; yv < nVy; ++yv) {
                  for (xv = 0; xv < nVx; ++xv, ++nL) {
                    const PetscInt localVertex  = ((nVz-1)*nVy + yv)*nVx + xv + nC;
                    const PetscInt remoteVertex = (      0*nVy + yv)*nVx + xv + nC; /* TODO: Correct this for neighbor sizes */

                    localPoints[nL]        = localVertex;
                    remotePoints[nL].rank  = neighbor;
                    remotePoints[nL].index = remoteVertex;
                  }
                }
                nleavesCheck += nzF;     /* front faces */
                for (zf = 0; zf < nzF; ++zf, ++nL) {
                  /* THIS IS WRONG */
                  const PetscInt localFace  = 0 + nC+nV;
                  const PetscInt remoteFace = 0 + nC+nV;

                  localPoints[nL]        = localFace;
                  remotePoints[nL].rank  = neighbor;
                  remotePoints[nL].index = remoteFace;
                }
              } else {
                /* Nothing is shared from the interior */
              }
            }
          }
        }
      }
    }
  }
  /* TODO: Remove duplication in leaf determination */
  if (nleaves != nleavesCheck) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "The number of leaves %d did not match the number of remote leaves %d", nleaves, nleavesCheck);
  ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), &sf);CHKERRQ(ierr);
  ierr = PetscSFSetGraph(sf, pEnd, nleaves, localPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr);
  ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&sf);CHKERRQ(ierr);
  *s = section;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDASetVertexCoordinates"
PetscErrorCode DMDASetVertexCoordinates(DM dm, PetscReal xl, PetscReal xu, PetscReal yl, PetscReal yu, PetscReal zl, PetscReal zu)
{
  DM_DA         *da = (DM_DA *) dm->data;
  Vec            coordinates;
  PetscSection   section;
  PetscScalar   *coords;
  PetscReal      h[3];
  PetscInt       dim, size, M, N, P, nVx, nVy, nVz, nV, vStart, vEnd, v, i, j, k;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  ierr = DMDAGetInfo(dm, &dim, &M, &N, &P, 0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
  h[0] = (xu - xl)/M;
  h[1] = (yu - yl)/N;
  h[2] = (zu - zl)/P;
  ierr = DMDAGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
  ierr = DMDAGetNumVertices(dm, &nVx, &nVy, &nVz, &nV);CHKERRQ(ierr);
  ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), &section);CHKERRQ(ierr);
  ierr = PetscSectionSetNumFields(section, 1);CHKERRQ(ierr);
  ierr = PetscSectionSetFieldComponents(section, 0, dim);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(section, vStart, vEnd);CHKERRQ(ierr);
  for (v = vStart; v < vEnd; ++v) {
    ierr = PetscSectionSetDof(section, v, dim);CHKERRQ(ierr);
  }
  ierr = PetscSectionSetUp(section);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(section, &size);CHKERRQ(ierr);
  ierr = VecCreateSeq(PETSC_COMM_SELF, size, &coordinates);CHKERRQ(ierr);
  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  for (k = 0; k < nVz; ++k) {
    PetscInt ind[3], d, off;

    ind[0] = 0;
    ind[1] = 0;
    ind[2] = k + da->zs;
    for (j = 0; j < nVy; ++j) {
      ind[1] = j + da->ys;
      for (i = 0; i < nVx; ++i) {
        const PetscInt vertex = (k*nVy + j)*nVx + i + vStart;

        ierr = PetscSectionGetOffset(section, vertex, &off);CHKERRQ(ierr);
        ind[0] = i + da->xs;
        for (d = 0; d < dim; ++d) {
          coords[off+d] = h[d]*ind[d];
        }
      }
    }
  }
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = DMSetCoordinateSection(dm, section);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&section);CHKERRQ(ierr);
  ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAProjectFunctionLocal"
PetscErrorCode DMDAProjectFunctionLocal(DM dm, PetscFE fe[], void (**funcs)(const PetscReal [], PetscScalar *), InsertMode mode, Vec localX)
{
  PetscDualSpace *sp;
  PetscQuadrature q;
  PetscSection    section;
  PetscScalar    *values;
  PetscReal      *v0, *J, *detJ;
  PetscInt        numFields, numComp, dim, spDim, totDim = 0, numValues, cStart, cEnd, f, c, v, d;
  PetscErrorCode  ierr;

  PetscFunctionBegin;
  ierr = DMGetDefaultSection(dm, &section);CHKERRQ(ierr);
  ierr = PetscFEGetQuadrature(fe[0], &q);CHKERRQ(ierr);
  ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr);
  ierr = PetscMalloc(numFields * sizeof(PetscDualSpace), &sp);CHKERRQ(ierr);
  for (f = 0; f < numFields; ++f) {
    ierr = PetscFEGetDualSpace(fe[f], &sp[f]);CHKERRQ(ierr);
    ierr = PetscFEGetNumComponents(fe[f], &numComp);CHKERRQ(ierr);
    ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr);
    totDim += spDim*numComp;
  }
  ierr = DMDAGetInfo(dm, &dim,0,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
  ierr = DMDAGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
  ierr = DMDAVecGetClosure(dm, section, localX, cStart, &numValues, NULL);CHKERRQ(ierr);
  if (numValues != totDim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The section cell closure size %d != dual space dimension %d", numValues, totDim);
  ierr = DMGetWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr);
  ierr = PetscMalloc3(dim*q.numPoints,&v0,dim*dim*q.numPoints,&J,q.numPoints,&detJ);CHKERRQ(ierr);
  for (c = cStart; c < cEnd; ++c) {
    PetscCellGeometry geom;

    ierr = DMDAComputeCellGeometry(dm, c, &q, v0, J, NULL, detJ);CHKERRQ(ierr);
    geom.v0   = v0;
    geom.J    = J;
    geom.detJ = detJ;
    for (f = 0, v = 0; f < numFields; ++f) {
      ierr = PetscFEGetNumComponents(fe[f], &numComp);CHKERRQ(ierr);
      ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr);
      for (d = 0; d < spDim; ++d) {
        ierr = PetscDualSpaceApply(sp[f], d, geom, numComp, funcs[f], &values[v]);CHKERRQ(ierr);
        v += numComp;
      }
    }
    ierr = DMDAVecSetClosure(dm, section, localX, c, values, mode);CHKERRQ(ierr);
  }
  ierr = DMRestoreWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr);
  ierr = PetscFree3(v0,J,detJ);CHKERRQ(ierr);
  ierr = PetscFree(sp);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAProjectFunction"
/*@C
  DMDAProjectFunction - This projects the given function into the function space provided.

  Input Parameters:
+ dm      - The DM
. fe      - The PetscFE associated with the field
. funcs   - The coordinate functions to evaluate
- mode    - The insertion mode for values

  Output Parameter:
. X - vector

  Level: developer

.seealso: DMDAComputeL2Diff()
@*/
PetscErrorCode DMDAProjectFunction(DM dm, PetscFE fe[], void (**funcs)(const PetscReal [], PetscScalar *), InsertMode mode, Vec X)
{
  Vec            localX;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr);
  ierr = DMDAProjectFunctionLocal(dm, fe, funcs, mode, localX);CHKERRQ(ierr);
  ierr = DMLocalToGlobalBegin(dm, localX, mode, X);CHKERRQ(ierr);
  ierr = DMLocalToGlobalEnd(dm, localX, mode, X);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDAComputeL2Diff"
/*@C
  DMDAComputeL2Diff - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h.

  Input Parameters:
+ dm    - The DM
. fe    - The PetscFE object for each field
. funcs - The functions to evaluate for each field component
- X     - The coefficient vector u_h

  Output Parameter:
. diff - The diff ||u - u_h||_2

  Level: developer

.seealso: DMDAProjectFunction()
@*/
PetscErrorCode DMDAComputeL2Diff(DM dm, PetscFE fe[], void (**funcs)(const PetscReal [], PetscScalar *), Vec X, PetscReal *diff)
{
  const PetscInt  debug = 0;
  PetscSection    section;
  PetscQuadrature quad;
  Vec             localX;
  PetscScalar    *funcVal;
  PetscReal      *coords, *v0, *J, *invJ, detJ;
  PetscReal       localDiff = 0.0;
  PetscInt        dim, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset, comp;
  PetscErrorCode  ierr;

  PetscFunctionBegin;
  ierr = DMDAGetInfo(dm, &dim,0,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
  ierr = DMGetDefaultSection(dm, &section);CHKERRQ(ierr);
  ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr);
  ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr);
  for (field = 0; field < numFields; ++field) {
    PetscInt Nc;

    ierr = PetscFEGetNumComponents(fe[field], &Nc);CHKERRQ(ierr);
    numComponents += Nc;
  }
  /* There are no BC values in DAs right now: ierr = DMDAProjectFunctionLocal(dm, fe, funcs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); */
  ierr = PetscMalloc5(numComponents,&funcVal,dim,&coords,dim,&v0,dim*dim,&J,dim*dim,&invJ);CHKERRQ(ierr);
  ierr = DMDAGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
  ierr = PetscFEGetQuadrature(fe[0], &quad);CHKERRQ(ierr);
  for (c = cStart; c < cEnd; ++c) {
    PetscScalar *x = NULL;
    PetscReal    elemDiff = 0.0;

    ierr = DMDAComputeCellGeometry(dm, c, &quad, v0, J, invJ, &detJ);CHKERRQ(ierr);
    if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c);
    ierr = DMDAVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr);

    for (field = 0, comp = 0, fieldOffset = 0; field < numFields; ++field) {
      const PetscInt   numQuadPoints = quad.numPoints;
      const PetscReal *quadPoints    = quad.points;
      const PetscReal *quadWeights   = quad.weights;
      PetscReal       *basis;
      PetscInt         numBasisFuncs, numBasisComps, q, d, e, fc, f;

      ierr = PetscFEGetDimension(fe[field], &numBasisFuncs);CHKERRQ(ierr);
      ierr = PetscFEGetNumComponents(fe[field], &numBasisComps);CHKERRQ(ierr);
      ierr = PetscFEGetDefaultTabulation(fe[field], &basis, NULL, NULL);CHKERRQ(ierr);
      if (debug) {
        char title[1024];
        ierr = PetscSNPrintf(title, 1023, "Solution for Field %d", field);CHKERRQ(ierr);
        ierr = DMPrintCellVector(c, title, numBasisFuncs*numBasisComps, &x[fieldOffset]);CHKERRQ(ierr);
      }
      for (q = 0; q < numQuadPoints; ++q) {
        for (d = 0; d < dim; d++) {
          coords[d] = v0[d];
          for (e = 0; e < dim; e++) {
            coords[d] += J[d*dim+e]*(quadPoints[q*dim+e] + 1.0);
          }
        }
        (*funcs[field])(coords, funcVal);
        for (fc = 0; fc < numBasisComps; ++fc) {
          PetscScalar interpolant = 0.0;

          for (f = 0; f < numBasisFuncs; ++f) {
            const PetscInt fidx = f*numBasisComps+fc;
            interpolant += x[fieldOffset+fidx]*basis[q*numBasisFuncs*numBasisComps+fidx];
          }
          if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, "    elem %d field %d diff %g\n", c, field, PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ);CHKERRQ(ierr);}
          elemDiff += PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ;
        }
      }
      comp        += numBasisComps;
      fieldOffset += numBasisFuncs*numBasisComps;
    }
    ierr = DMDAVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr);
    if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, "  elem %d diff %g\n", c, elemDiff);CHKERRQ(ierr);}
    localDiff += elemDiff;
  }
  ierr  = PetscFree5(funcVal,coords,v0,J,invJ);CHKERRQ(ierr);
  ierr  = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr);
  ierr  = MPI_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPI_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr);
  *diff = PetscSqrtReal(*diff);
  PetscFunctionReturn(0);
}

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

#undef __FUNCT__
#define __FUNCT__ "DMDAGetArray"
/*@C
     DMDAGetArray - Gets a work array for a DMDA

    Input Parameter:
+    da - information about my local patch
-    ghosted - do you want arrays for the ghosted or nonghosted patch

    Output Parameters:
.    vptr - array data structured

    Note:  The vector values are NOT initialized and may have garbage in them, so you may need
           to zero them.

  Level: advanced

.seealso: DMDARestoreArray()

@*/
PetscErrorCode  DMDAGetArray(DM da,PetscBool ghosted,void *vptr)
{
  PetscErrorCode ierr;
  PetscInt       j,i,xs,ys,xm,ym,zs,zm;
  char           *iarray_start;
  void           **iptr = (void**)vptr;
  DM_DA          *dd    = (DM_DA*)da->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  if (ghosted) {
    for (i=0; i<DMDA_MAX_WORK_ARRAYS; i++) {
      if (dd->arrayghostedin[i]) {
        *iptr                 = dd->arrayghostedin[i];
        iarray_start          = (char*)dd->startghostedin[i];
        dd->arrayghostedin[i] = NULL;
        dd->startghostedin[i] = NULL;

        goto done;
      }
    }
    xs = dd->Xs;
    ys = dd->Ys;
    zs = dd->Zs;
    xm = dd->Xe-dd->Xs;
    ym = dd->Ye-dd->Ys;
    zm = dd->Ze-dd->Zs;
  } else {
    for (i=0; i<DMDA_MAX_WORK_ARRAYS; i++) {
      if (dd->arrayin[i]) {
        *iptr          = dd->arrayin[i];
        iarray_start   = (char*)dd->startin[i];
        dd->arrayin[i] = NULL;
        dd->startin[i] = NULL;

        goto done;
      }
    }
    xs = dd->xs;
    ys = dd->ys;
    zs = dd->zs;
    xm = dd->xe-dd->xs;
    ym = dd->ye-dd->ys;
    zm = dd->ze-dd->zs;
  }

  switch (dd->dim) {
  case 1: {
    void *ptr;

    ierr = PetscMalloc(xm*sizeof(PetscScalar),&iarray_start);CHKERRQ(ierr);

    ptr   = (void*)(iarray_start - xs*sizeof(PetscScalar));
    *iptr = (void*)ptr;
    break;
  }
  case 2: {
    void **ptr;

    ierr = PetscMalloc((ym+1)*sizeof(void*)+xm*ym*sizeof(PetscScalar),&iarray_start);CHKERRQ(ierr);

    ptr = (void**)(iarray_start + xm*ym*sizeof(PetscScalar) - ys*sizeof(void*));
    for (j=ys; j<ys+ym; j++) ptr[j] = iarray_start + sizeof(PetscScalar)*(xm*(j-ys) - xs);
    *iptr = (void*)ptr;
    break;
  }
  case 3: {
    void ***ptr,**bptr;

    ierr = PetscMalloc((zm+1)*sizeof(void**)+(ym*zm+1)*sizeof(void*)+xm*ym*zm*sizeof(PetscScalar),&iarray_start);CHKERRQ(ierr);

    ptr  = (void***)(iarray_start + xm*ym*zm*sizeof(PetscScalar) - zs*sizeof(void*));
    bptr = (void**)(iarray_start + xm*ym*zm*sizeof(PetscScalar) + zm*sizeof(void**));
    for (i=zs; i<zs+zm; i++) ptr[i] = bptr + ((i-zs)*ym - ys);
    for (i=zs; i<zs+zm; i++) {
      for (j=ys; j<ys+ym; j++) {
        ptr[i][j] = iarray_start + sizeof(PetscScalar)*(xm*ym*(i-zs) + xm*(j-ys) - xs);
      }
    }
    *iptr = (void*)ptr;
    break;
  }
  default:
    SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Dimension %D not supported",dd->dim);
  }

done:
  /* add arrays to the checked out list */
  if (ghosted) {
    for (i=0; i<DMDA_MAX_WORK_ARRAYS; i++) {
      if (!dd->arrayghostedout[i]) {
        dd->arrayghostedout[i] = *iptr;
        dd->startghostedout[i] = iarray_start;
        break;
      }
    }
  } else {
    for (i=0; i<DMDA_MAX_WORK_ARRAYS; i++) {
      if (!dd->arrayout[i]) {
        dd->arrayout[i] = *iptr;
        dd->startout[i] = iarray_start;
        break;
      }
    }
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMDARestoreArray"
/*@C
     DMDARestoreArray - Restores an array of derivative types for a DMDA

    Input Parameter:
+    da - information about my local patch
.    ghosted - do you want arrays for the ghosted or nonghosted patch
-    vptr - array data structured to be passed to ad_FormFunctionLocal()

     Level: advanced

.seealso: DMDAGetArray()

@*/
PetscErrorCode  DMDARestoreArray(DM da,PetscBool ghosted,void *vptr)
{
  PetscInt i;
  void     **iptr = (void**)vptr,*iarray_start = 0;
  DM_DA    *dd    = (DM_DA*)da->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  if (ghosted) {
    for (i=0; i<DMDA_MAX_WORK_ARRAYS; i++) {
      if (dd->arrayghostedout[i] == *iptr) {
        iarray_start           = dd->startghostedout[i];
        dd->arrayghostedout[i] = NULL;
        dd->startghostedout[i] = NULL;
        break;
      }
    }
    for (i=0; i<DMDA_MAX_WORK_ARRAYS; i++) {
      if (!dd->arrayghostedin[i]) {
        dd->arrayghostedin[i] = *iptr;
        dd->startghostedin[i] = iarray_start;
        break;
      }
    }
  } else {
    for (i=0; i<DMDA_MAX_WORK_ARRAYS; i++) {
      if (dd->arrayout[i] == *iptr) {
        iarray_start    = dd->startout[i];
        dd->arrayout[i] = NULL;
        dd->startout[i] = NULL;
        break;
      }
    }
    for (i=0; i<DMDA_MAX_WORK_ARRAYS; i++) {
      if (!dd->arrayin[i]) {
        dd->arrayin[i] = *iptr;
        dd->startin[i] = iarray_start;
        break;
      }
    }
  }
  PetscFunctionReturn(0);
}