snes/utils/dmplexsnes.c

#include <petsc/private/dmpleximpl.h>   /*I "petscdmplex.h" I*/
#include <petsc/private/snesimpl.h>     /*I "petscsnes.h"   I*/
#include <petscds.h>
#include <petscblaslapack.h>
#include <petsc/private/petscimpl.h>
#include <petsc/private/petscfeimpl.h>

/************************** Interpolation *******************************/

static PetscErrorCode DMSNESConvertPlex(DM dm, DM *plex, PetscBool copy)
{
  PetscBool      isPlex;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);CHKERRQ(ierr);
  if (isPlex) {
    *plex = dm;
    ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr);
  } else {
    ierr = PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);CHKERRQ(ierr);
    if (!*plex) {
      ierr = DMConvert(dm,DMPLEX,plex);CHKERRQ(ierr);
      ierr = PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);CHKERRQ(ierr);
      if (copy) {
        PetscInt    i;
        PetscObject obj;
        const char *comps[3] = {"A","dmAux","dmCh"};

        ierr = DMCopyDMSNES(dm, *plex);CHKERRQ(ierr);
        for (i = 0; i < 3; i++) {
          ierr = PetscObjectQuery((PetscObject) dm, comps[i], &obj);CHKERRQ(ierr);
          ierr = PetscObjectCompose((PetscObject) *plex, comps[i], obj);CHKERRQ(ierr);
        }
      }
    } else {
      ierr = PetscObjectReference((PetscObject) *plex);CHKERRQ(ierr);
    }
  }
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationCreate - Creates a DMInterpolationInfo context

  Collective

  Input Parameter:
. comm - the communicator

  Output Parameter:
. ctx - the context

  Level: beginner

.seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationDestroy()
@*/
PetscErrorCode DMInterpolationCreate(MPI_Comm comm, DMInterpolationInfo *ctx)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidPointer(ctx, 2);
  ierr = PetscNew(ctx);CHKERRQ(ierr);

  (*ctx)->comm   = comm;
  (*ctx)->dim    = -1;
  (*ctx)->nInput = 0;
  (*ctx)->points = NULL;
  (*ctx)->cells  = NULL;
  (*ctx)->n      = -1;
  (*ctx)->coords = NULL;
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationSetDim - Sets the spatial dimension for the interpolation context

  Not collective

  Input Parameters:
+ ctx - the context
- dim - the spatial dimension

  Level: intermediate

.seealso: DMInterpolationGetDim(), DMInterpolationEvaluate(), DMInterpolationAddPoints()
@*/
PetscErrorCode DMInterpolationSetDim(DMInterpolationInfo ctx, PetscInt dim)
{
  PetscFunctionBegin;
  if ((dim < 1) || (dim > 3)) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension for points: %D", dim);
  ctx->dim = dim;
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationGetDim - Gets the spatial dimension for the interpolation context

  Not collective

  Input Parameter:
. ctx - the context

  Output Parameter:
. dim - the spatial dimension

  Level: intermediate

.seealso: DMInterpolationSetDim(), DMInterpolationEvaluate(), DMInterpolationAddPoints()
@*/
PetscErrorCode DMInterpolationGetDim(DMInterpolationInfo ctx, PetscInt *dim)
{
  PetscFunctionBegin;
  PetscValidIntPointer(dim, 2);
  *dim = ctx->dim;
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationSetDof - Sets the number of fields interpolated at a point for the interpolation context

  Not collective

  Input Parameters:
+ ctx - the context
- dof - the number of fields

  Level: intermediate

.seealso: DMInterpolationGetDof(), DMInterpolationEvaluate(), DMInterpolationAddPoints()
@*/
PetscErrorCode DMInterpolationSetDof(DMInterpolationInfo ctx, PetscInt dof)
{
  PetscFunctionBegin;
  if (dof < 1) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of components: %D", dof);
  ctx->dof = dof;
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationGetDof - Gets the number of fields interpolated at a point for the interpolation context

  Not collective

  Input Parameter:
. ctx - the context

  Output Parameter:
. dof - the number of fields

  Level: intermediate

.seealso: DMInterpolationSetDof(), DMInterpolationEvaluate(), DMInterpolationAddPoints()
@*/
PetscErrorCode DMInterpolationGetDof(DMInterpolationInfo ctx, PetscInt *dof)
{
  PetscFunctionBegin;
  PetscValidIntPointer(dof, 2);
  *dof = ctx->dof;
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationAddPoints - Add points at which we will interpolate the fields

  Not collective

  Input Parameters:
+ ctx    - the context
. n      - the number of points
- points - the coordinates for each point, an array of size n * dim

  Note: The coordinate information is copied.

  Level: intermediate

.seealso: DMInterpolationSetDim(), DMInterpolationEvaluate(), DMInterpolationCreate()
@*/
PetscErrorCode DMInterpolationAddPoints(DMInterpolationInfo ctx, PetscInt n, PetscReal points[])
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (ctx->dim < 0) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set");
  if (ctx->points)  SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "Cannot add points multiple times yet");
  ctx->nInput = n;

  ierr = PetscMalloc1(n*ctx->dim, &ctx->points);CHKERRQ(ierr);
  ierr = PetscArraycpy(ctx->points, points, n*ctx->dim);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationSetUp - Computea spatial indices that add in point location during interpolation

  Collective on ctx

  Input Parameters:
+ ctx - the context
. dm  - the DM for the function space used for interpolation
- redundantPoints - If PETSC_TRUE, all processes are passing in the same array of points. Otherwise, points need to be communicated among processes.

  Level: intermediate

.seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate()
@*/
PetscErrorCode DMInterpolationSetUp(DMInterpolationInfo ctx, DM dm, PetscBool redundantPoints)
{
  MPI_Comm          comm = ctx->comm;
  PetscScalar       *a;
  PetscInt          p, q, i;
  PetscMPIInt       rank, size;
  PetscErrorCode    ierr;
  Vec               pointVec;
  PetscSF           cellSF;
  PetscLayout       layout;
  PetscReal         *globalPoints;
  PetscScalar       *globalPointsScalar;
  const PetscInt    *ranges;
  PetscMPIInt       *counts, *displs;
  const PetscSFNode *foundCells;
  const PetscInt    *foundPoints;
  PetscMPIInt       *foundProcs, *globalProcs;
  PetscInt          n, N, numFound;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  if (ctx->dim < 0) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set");
  /* Locate points */
  n = ctx->nInput;
  if (!redundantPoints) {
    ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr);
    ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr);
    ierr = PetscLayoutSetLocalSize(layout, n);CHKERRQ(ierr);
    ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr);
    ierr = PetscLayoutGetSize(layout, &N);CHKERRQ(ierr);
    /* Communicate all points to all processes */
    ierr = PetscMalloc3(N*ctx->dim,&globalPoints,size,&counts,size,&displs);CHKERRQ(ierr);
    ierr = PetscLayoutGetRanges(layout, &ranges);CHKERRQ(ierr);
    for (p = 0; p < size; ++p) {
      counts[p] = (ranges[p+1] - ranges[p])*ctx->dim;
      displs[p] = ranges[p]*ctx->dim;
    }
    ierr = MPI_Allgatherv(ctx->points, n*ctx->dim, MPIU_REAL, globalPoints, counts, displs, MPIU_REAL, comm);CHKERRQ(ierr);
  } else {
    N = n;
    globalPoints = ctx->points;
    counts = displs = NULL;
    layout = NULL;
  }
#if 0
  ierr = PetscMalloc3(N,&foundCells,N,&foundProcs,N,&globalProcs);CHKERRQ(ierr);
  /* foundCells[p] = m->locatePoint(&globalPoints[p*ctx->dim]); */
#else
#if defined(PETSC_USE_COMPLEX)
  ierr = PetscMalloc1(N*ctx->dim,&globalPointsScalar);CHKERRQ(ierr);
  for (i=0; i<N*ctx->dim; i++) globalPointsScalar[i] = globalPoints[i];
#else
  globalPointsScalar = globalPoints;
#endif
  ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, ctx->dim, N*ctx->dim, globalPointsScalar, &pointVec);CHKERRQ(ierr);
  ierr = PetscMalloc2(N,&foundProcs,N,&globalProcs);CHKERRQ(ierr);
  for (p = 0; p < N; ++p) {foundProcs[p] = size;}
  cellSF = NULL;
  ierr = DMLocatePoints(dm, pointVec, DM_POINTLOCATION_REMOVE, &cellSF);CHKERRQ(ierr);
  ierr = PetscSFGetGraph(cellSF,NULL,&numFound,&foundPoints,&foundCells);CHKERRQ(ierr);
#endif
  for (p = 0; p < numFound; ++p) {
    if (foundCells[p].index >= 0) foundProcs[foundPoints ? foundPoints[p] : p] = rank;
  }
  /* Let the lowest rank process own each point */
  ierr   = MPIU_Allreduce(foundProcs, globalProcs, N, MPI_INT, MPI_MIN, comm);CHKERRQ(ierr);
  ctx->n = 0;
  for (p = 0; p < N; ++p) {
    if (globalProcs[p] == size) SETERRQ4(comm, PETSC_ERR_PLIB, "Point %d: %g %g %g not located in mesh", p, (double)globalPoints[p*ctx->dim+0], (double)(ctx->dim > 1 ? globalPoints[p*ctx->dim+1] : 0.0), (double)(ctx->dim > 2 ? globalPoints[p*ctx->dim+2] : 0.0));
    else if (globalProcs[p] == rank) ctx->n++;
  }
  /* Create coordinates vector and array of owned cells */
  ierr = PetscMalloc1(ctx->n, &ctx->cells);CHKERRQ(ierr);
  ierr = VecCreate(comm, &ctx->coords);CHKERRQ(ierr);
  ierr = VecSetSizes(ctx->coords, ctx->n*ctx->dim, PETSC_DECIDE);CHKERRQ(ierr);
  ierr = VecSetBlockSize(ctx->coords, ctx->dim);CHKERRQ(ierr);
  ierr = VecSetType(ctx->coords,VECSTANDARD);CHKERRQ(ierr);
  ierr = VecGetArray(ctx->coords, &a);CHKERRQ(ierr);
  for (p = 0, q = 0, i = 0; p < N; ++p) {
    if (globalProcs[p] == rank) {
      PetscInt d;

      for (d = 0; d < ctx->dim; ++d, ++i) a[i] = globalPoints[p*ctx->dim+d];
      ctx->cells[q] = foundCells[q].index;
      ++q;
    }
  }
  ierr = VecRestoreArray(ctx->coords, &a);CHKERRQ(ierr);
#if 0
  ierr = PetscFree3(foundCells,foundProcs,globalProcs);CHKERRQ(ierr);
#else
  ierr = PetscFree2(foundProcs,globalProcs);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&cellSF);CHKERRQ(ierr);
  ierr = VecDestroy(&pointVec);CHKERRQ(ierr);
#endif
  if ((void*)globalPointsScalar != (void*)globalPoints) {ierr = PetscFree(globalPointsScalar);CHKERRQ(ierr);}
  if (!redundantPoints) {ierr = PetscFree3(globalPoints,counts,displs);CHKERRQ(ierr);}
  ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationGetCoordinates - Gets a Vec with the coordinates of each interpolation point

  Collective on ctx

  Input Parameter:
. ctx - the context

  Output Parameter:
. coordinates  - the coordinates of interpolation points

  Note: The local vector entries correspond to interpolation points lying on this process, according to the associated DM. This is a borrowed vector that the user should not destroy.

  Level: intermediate

.seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate()
@*/
PetscErrorCode DMInterpolationGetCoordinates(DMInterpolationInfo ctx, Vec *coordinates)
{
  PetscFunctionBegin;
  PetscValidPointer(coordinates, 2);
  if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup.");
  *coordinates = ctx->coords;
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationGetVector - Gets a Vec which can hold all the interpolated field values

  Collective on ctx

  Input Parameter:
. ctx - the context

  Output Parameter:
. v  - a vector capable of holding the interpolated field values

  Note: This vector should be returned using DMInterpolationRestoreVector().

  Level: intermediate

.seealso: DMInterpolationRestoreVector(), DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate()
@*/
PetscErrorCode DMInterpolationGetVector(DMInterpolationInfo ctx, Vec *v)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidPointer(v, 2);
  if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup.");
  ierr = VecCreate(ctx->comm, v);CHKERRQ(ierr);
  ierr = VecSetSizes(*v, ctx->n*ctx->dof, PETSC_DECIDE);CHKERRQ(ierr);
  ierr = VecSetBlockSize(*v, ctx->dof);CHKERRQ(ierr);
  ierr = VecSetType(*v,VECSTANDARD);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationRestoreVector - Returns a Vec which can hold all the interpolated field values

  Collective on ctx

  Input Parameters:
+ ctx - the context
- v  - a vector capable of holding the interpolated field values

  Level: intermediate

.seealso: DMInterpolationGetVector(), DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate()
@*/
PetscErrorCode DMInterpolationRestoreVector(DMInterpolationInfo ctx, Vec *v)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidPointer(v, 2);
  if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup.");
  ierr = VecDestroy(v);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Triangle_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v)
{
  PetscReal      *v0, *J, *invJ, detJ;
  const PetscScalar *coords;
  PetscScalar    *a;
  PetscInt       p;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr);
  ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr);
  ierr = VecGetArray(v, &a);CHKERRQ(ierr);
  for (p = 0; p < ctx->n; ++p) {
    PetscInt     c = ctx->cells[p];
    PetscScalar *x = NULL;
    PetscReal    xi[4];
    PetscInt     d, f, comp;

    ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr);
    if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D", (double)detJ, c);
    ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr);
    for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp];

    for (d = 0; d < ctx->dim; ++d) {
      xi[d] = 0.0;
      for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]);
      for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[(d+1)*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d];
    }
    ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr);
  }
  ierr = VecRestoreArray(v, &a);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr);
  ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Tetrahedron_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v)
{
  PetscReal      *v0, *J, *invJ, detJ;
  const PetscScalar *coords;
  PetscScalar    *a;
  PetscInt       p;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr);
  ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr);
  ierr = VecGetArray(v, &a);CHKERRQ(ierr);
  for (p = 0; p < ctx->n; ++p) {
    PetscInt       c = ctx->cells[p];
    const PetscInt order[3] = {2, 1, 3};
    PetscScalar   *x = NULL;
    PetscReal      xi[4];
    PetscInt       d, f, comp;

    ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr);
    if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D", (double)detJ, c);
    ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr);
    for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp];

    for (d = 0; d < ctx->dim; ++d) {
      xi[d] = 0.0;
      for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]);
      for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[order[d]*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d];
    }
    ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr);
  }
  ierr = VecRestoreArray(v, &a);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr);
  ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PETSC_STATIC_INLINE PetscErrorCode QuadMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx)
{
  const PetscScalar *vertices = (const PetscScalar*) ctx;
  const PetscScalar x0        = vertices[0];
  const PetscScalar y0        = vertices[1];
  const PetscScalar x1        = vertices[2];
  const PetscScalar y1        = vertices[3];
  const PetscScalar x2        = vertices[4];
  const PetscScalar y2        = vertices[5];
  const PetscScalar x3        = vertices[6];
  const PetscScalar y3        = vertices[7];
  const PetscScalar f_1       = x1 - x0;
  const PetscScalar g_1       = y1 - y0;
  const PetscScalar f_3       = x3 - x0;
  const PetscScalar g_3       = y3 - y0;
  const PetscScalar f_01      = x2 - x1 - x3 + x0;
  const PetscScalar g_01      = y2 - y1 - y3 + y0;
  const PetscScalar *ref;
  PetscScalar       *real;
  PetscErrorCode    ierr;

  PetscFunctionBegin;
  ierr = VecGetArrayRead(Xref,  &ref);CHKERRQ(ierr);
  ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr);
  {
    const PetscScalar p0 = ref[0];
    const PetscScalar p1 = ref[1];

    real[0] = x0 + f_1 * p0 + f_3 * p1 + f_01 * p0 * p1;
    real[1] = y0 + g_1 * p0 + g_3 * p1 + g_01 * p0 * p1;
  }
  ierr = PetscLogFlops(28);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(Xref,  &ref);CHKERRQ(ierr);
  ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#include <petsc/private/dmimpl.h>
PETSC_STATIC_INLINE PetscErrorCode QuadJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx)
{
  const PetscScalar *vertices = (const PetscScalar*) ctx;
  const PetscScalar x0        = vertices[0];
  const PetscScalar y0        = vertices[1];
  const PetscScalar x1        = vertices[2];
  const PetscScalar y1        = vertices[3];
  const PetscScalar x2        = vertices[4];
  const PetscScalar y2        = vertices[5];
  const PetscScalar x3        = vertices[6];
  const PetscScalar y3        = vertices[7];
  const PetscScalar f_01      = x2 - x1 - x3 + x0;
  const PetscScalar g_01      = y2 - y1 - y3 + y0;
  const PetscScalar *ref;
  PetscErrorCode    ierr;

  PetscFunctionBegin;
  ierr = VecGetArrayRead(Xref,  &ref);CHKERRQ(ierr);
  {
    const PetscScalar x       = ref[0];
    const PetscScalar y       = ref[1];
    const PetscInt    rows[2] = {0, 1};
    PetscScalar       values[4];

    values[0] = (x1 - x0 + f_01*y) * 0.5; values[1] = (x3 - x0 + f_01*x) * 0.5;
    values[2] = (y1 - y0 + g_01*y) * 0.5; values[3] = (y3 - y0 + g_01*x) * 0.5;
    ierr      = MatSetValues(J, 2, rows, 2, rows, values, INSERT_VALUES);CHKERRQ(ierr);
  }
  ierr = PetscLogFlops(30);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(Xref,  &ref);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Quad_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v)
{
  DM             dmCoord;
  PetscFE        fem = NULL;
  SNES           snes;
  KSP            ksp;
  PC             pc;
  Vec            coordsLocal, r, ref, real;
  Mat            J;
  PetscTabulation    T;
  const PetscScalar *coords;
  PetscScalar    *a;
  PetscReal      xir[2];
  PetscInt       Nf, p;
  const PetscInt dof = ctx->dof;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr);
  if (Nf) {ierr = DMGetField(dm, 0, NULL, (PetscObject *) &fem);CHKERRQ(ierr);}
  ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr);
  ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr);
  ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr);
  ierr = SNESSetOptionsPrefix(snes, "quad_interp_");CHKERRQ(ierr);
  ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr);
  ierr = VecSetSizes(r, 2, 2);CHKERRQ(ierr);
  ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr);
  ierr = VecDuplicate(r, &ref);CHKERRQ(ierr);
  ierr = VecDuplicate(r, &real);CHKERRQ(ierr);
  ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr);
  ierr = MatSetSizes(J, 2, 2, 2, 2);CHKERRQ(ierr);
  ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr);
  ierr = MatSetUp(J);CHKERRQ(ierr);
  ierr = SNESSetFunction(snes, r, QuadMap_Private, NULL);CHKERRQ(ierr);
  ierr = SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);CHKERRQ(ierr);
  ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr);
  ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr);
  ierr = PCSetType(pc, PCLU);CHKERRQ(ierr);
  ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);

  ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr);
  ierr = VecGetArray(v, &a);CHKERRQ(ierr);
  ierr = PetscFECreateTabulation(fem, 1, 1, xir, 0, &T);CHKERRQ(ierr);
  for (p = 0; p < ctx->n; ++p) {
    PetscScalar *x = NULL, *vertices = NULL;
    PetscScalar *xi;
    PetscInt     c = ctx->cells[p], comp, coordSize, xSize;

    /* Can make this do all points at once */
    ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr);
    if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %d", coordSize, 4*2);
    ierr   = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr);
    ierr   = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr);
    ierr   = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr);
    ierr   = VecGetArray(real, &xi);CHKERRQ(ierr);
    xi[0]  = coords[p*ctx->dim+0];
    xi[1]  = coords[p*ctx->dim+1];
    ierr   = VecRestoreArray(real, &xi);CHKERRQ(ierr);
    ierr   = SNESSolve(snes, real, ref);CHKERRQ(ierr);
    ierr   = VecGetArray(ref, &xi);CHKERRQ(ierr);
    xir[0] = PetscRealPart(xi[0]);
    xir[1] = PetscRealPart(xi[1]);
    if (4*dof != xSize) {
      PetscInt d;

      xir[0] = 2.0*xir[0] - 1.0; xir[1] = 2.0*xir[1] - 1.0;
      ierr = PetscFEComputeTabulation(fem, 1, xir, 0, T);CHKERRQ(ierr);
      for (comp = 0; comp < dof; ++comp) {
        a[p*dof+comp] = 0.0;
        for (d = 0; d < xSize/dof; ++d) {
          a[p*dof+comp] += x[d*dof+comp]*T->T[0][d*dof+comp];
        }
      }
    } else {
      for (comp = 0; comp < dof; ++comp)
        a[p*dof+comp] = x[0*dof+comp]*(1 - xir[0])*(1 - xir[1]) + x[1*dof+comp]*xir[0]*(1 - xir[1]) + x[2*dof+comp]*xir[0]*xir[1] + x[3*dof+comp]*(1 - xir[0])*xir[1];
    }
    ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr);
    ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr);
    ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr);
  }
  ierr = PetscTabulationDestroy(&T);CHKERRQ(ierr);
  ierr = VecRestoreArray(v, &a);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr);

  ierr = SNESDestroy(&snes);CHKERRQ(ierr);
  ierr = VecDestroy(&r);CHKERRQ(ierr);
  ierr = VecDestroy(&ref);CHKERRQ(ierr);
  ierr = VecDestroy(&real);CHKERRQ(ierr);
  ierr = MatDestroy(&J);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx)
{
  const PetscScalar *vertices = (const PetscScalar*) ctx;
  const PetscScalar x0        = vertices[0];
  const PetscScalar y0        = vertices[1];
  const PetscScalar z0        = vertices[2];
  const PetscScalar x1        = vertices[9];
  const PetscScalar y1        = vertices[10];
  const PetscScalar z1        = vertices[11];
  const PetscScalar x2        = vertices[6];
  const PetscScalar y2        = vertices[7];
  const PetscScalar z2        = vertices[8];
  const PetscScalar x3        = vertices[3];
  const PetscScalar y3        = vertices[4];
  const PetscScalar z3        = vertices[5];
  const PetscScalar x4        = vertices[12];
  const PetscScalar y4        = vertices[13];
  const PetscScalar z4        = vertices[14];
  const PetscScalar x5        = vertices[15];
  const PetscScalar y5        = vertices[16];
  const PetscScalar z5        = vertices[17];
  const PetscScalar x6        = vertices[18];
  const PetscScalar y6        = vertices[19];
  const PetscScalar z6        = vertices[20];
  const PetscScalar x7        = vertices[21];
  const PetscScalar y7        = vertices[22];
  const PetscScalar z7        = vertices[23];
  const PetscScalar f_1       = x1 - x0;
  const PetscScalar g_1       = y1 - y0;
  const PetscScalar h_1       = z1 - z0;
  const PetscScalar f_3       = x3 - x0;
  const PetscScalar g_3       = y3 - y0;
  const PetscScalar h_3       = z3 - z0;
  const PetscScalar f_4       = x4 - x0;
  const PetscScalar g_4       = y4 - y0;
  const PetscScalar h_4       = z4 - z0;
  const PetscScalar f_01      = x2 - x1 - x3 + x0;
  const PetscScalar g_01      = y2 - y1 - y3 + y0;
  const PetscScalar h_01      = z2 - z1 - z3 + z0;
  const PetscScalar f_12      = x7 - x3 - x4 + x0;
  const PetscScalar g_12      = y7 - y3 - y4 + y0;
  const PetscScalar h_12      = z7 - z3 - z4 + z0;
  const PetscScalar f_02      = x5 - x1 - x4 + x0;
  const PetscScalar g_02      = y5 - y1 - y4 + y0;
  const PetscScalar h_02      = z5 - z1 - z4 + z0;
  const PetscScalar f_012     = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7;
  const PetscScalar g_012     = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7;
  const PetscScalar h_012     = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7;
  const PetscScalar *ref;
  PetscScalar       *real;
  PetscErrorCode    ierr;

  PetscFunctionBegin;
  ierr = VecGetArrayRead(Xref,  &ref);CHKERRQ(ierr);
  ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr);
  {
    const PetscScalar p0 = ref[0];
    const PetscScalar p1 = ref[1];
    const PetscScalar p2 = ref[2];

    real[0] = x0 + f_1*p0 + f_3*p1 + f_4*p2 + f_01*p0*p1 + f_12*p1*p2 + f_02*p0*p2 + f_012*p0*p1*p2;
    real[1] = y0 + g_1*p0 + g_3*p1 + g_4*p2 + g_01*p0*p1 + g_01*p0*p1 + g_12*p1*p2 + g_02*p0*p2 + g_012*p0*p1*p2;
    real[2] = z0 + h_1*p0 + h_3*p1 + h_4*p2 + h_01*p0*p1 + h_01*p0*p1 + h_12*p1*p2 + h_02*p0*p2 + h_012*p0*p1*p2;
  }
  ierr = PetscLogFlops(114);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(Xref,  &ref);CHKERRQ(ierr);
  ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx)
{
  const PetscScalar *vertices = (const PetscScalar*) ctx;
  const PetscScalar x0        = vertices[0];
  const PetscScalar y0        = vertices[1];
  const PetscScalar z0        = vertices[2];
  const PetscScalar x1        = vertices[9];
  const PetscScalar y1        = vertices[10];
  const PetscScalar z1        = vertices[11];
  const PetscScalar x2        = vertices[6];
  const PetscScalar y2        = vertices[7];
  const PetscScalar z2        = vertices[8];
  const PetscScalar x3        = vertices[3];
  const PetscScalar y3        = vertices[4];
  const PetscScalar z3        = vertices[5];
  const PetscScalar x4        = vertices[12];
  const PetscScalar y4        = vertices[13];
  const PetscScalar z4        = vertices[14];
  const PetscScalar x5        = vertices[15];
  const PetscScalar y5        = vertices[16];
  const PetscScalar z5        = vertices[17];
  const PetscScalar x6        = vertices[18];
  const PetscScalar y6        = vertices[19];
  const PetscScalar z6        = vertices[20];
  const PetscScalar x7        = vertices[21];
  const PetscScalar y7        = vertices[22];
  const PetscScalar z7        = vertices[23];
  const PetscScalar f_xy      = x2 - x1 - x3 + x0;
  const PetscScalar g_xy      = y2 - y1 - y3 + y0;
  const PetscScalar h_xy      = z2 - z1 - z3 + z0;
  const PetscScalar f_yz      = x7 - x3 - x4 + x0;
  const PetscScalar g_yz      = y7 - y3 - y4 + y0;
  const PetscScalar h_yz      = z7 - z3 - z4 + z0;
  const PetscScalar f_xz      = x5 - x1 - x4 + x0;
  const PetscScalar g_xz      = y5 - y1 - y4 + y0;
  const PetscScalar h_xz      = z5 - z1 - z4 + z0;
  const PetscScalar f_xyz     = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7;
  const PetscScalar g_xyz     = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7;
  const PetscScalar h_xyz     = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7;
  const PetscScalar *ref;
  PetscErrorCode    ierr;

  PetscFunctionBegin;
  ierr = VecGetArrayRead(Xref,  &ref);CHKERRQ(ierr);
  {
    const PetscScalar x       = ref[0];
    const PetscScalar y       = ref[1];
    const PetscScalar z       = ref[2];
    const PetscInt    rows[3] = {0, 1, 2};
    PetscScalar       values[9];

    values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0;
    values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0;
    values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0;
    values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0;
    values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0;
    values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0;
    values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0;
    values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0;
    values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0;

    ierr = MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);CHKERRQ(ierr);
  }
  ierr = PetscLogFlops(152);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(Xref,  &ref);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v)
{
  DM             dmCoord;
  SNES           snes;
  KSP            ksp;
  PC             pc;
  Vec            coordsLocal, r, ref, real;
  Mat            J;
  const PetscScalar *coords;
  PetscScalar    *a;
  PetscInt       p;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr);
  ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr);
  ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr);
  ierr = SNESSetOptionsPrefix(snes, "hex_interp_");CHKERRQ(ierr);
  ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr);
  ierr = VecSetSizes(r, 3, 3);CHKERRQ(ierr);
  ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr);
  ierr = VecDuplicate(r, &ref);CHKERRQ(ierr);
  ierr = VecDuplicate(r, &real);CHKERRQ(ierr);
  ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr);
  ierr = MatSetSizes(J, 3, 3, 3, 3);CHKERRQ(ierr);
  ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr);
  ierr = MatSetUp(J);CHKERRQ(ierr);
  ierr = SNESSetFunction(snes, r, HexMap_Private, NULL);CHKERRQ(ierr);
  ierr = SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);CHKERRQ(ierr);
  ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr);
  ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr);
  ierr = PCSetType(pc, PCLU);CHKERRQ(ierr);
  ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);

  ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr);
  ierr = VecGetArray(v, &a);CHKERRQ(ierr);
  for (p = 0; p < ctx->n; ++p) {
    PetscScalar *x = NULL, *vertices = NULL;
    PetscScalar *xi;
    PetscReal    xir[3];
    PetscInt     c = ctx->cells[p], comp, coordSize, xSize;

    /* Can make this do all points at once */
    ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr);
    if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %d", coordSize, 8*3);
    ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr);
    if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %D should be %D", xSize, 8*ctx->dof);
    ierr   = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr);
    ierr   = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr);
    ierr   = VecGetArray(real, &xi);CHKERRQ(ierr);
    xi[0]  = coords[p*ctx->dim+0];
    xi[1]  = coords[p*ctx->dim+1];
    xi[2]  = coords[p*ctx->dim+2];
    ierr   = VecRestoreArray(real, &xi);CHKERRQ(ierr);
    ierr   = SNESSolve(snes, real, ref);CHKERRQ(ierr);
    ierr   = VecGetArray(ref, &xi);CHKERRQ(ierr);
    xir[0] = PetscRealPart(xi[0]);
    xir[1] = PetscRealPart(xi[1]);
    xir[2] = PetscRealPart(xi[2]);
    for (comp = 0; comp < ctx->dof; ++comp) {
      a[p*ctx->dof+comp] =
        x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) +
        x[3*ctx->dof+comp]*    xir[0]*(1-xir[1])*(1-xir[2]) +
        x[2*ctx->dof+comp]*    xir[0]*    xir[1]*(1-xir[2]) +
        x[1*ctx->dof+comp]*(1-xir[0])*    xir[1]*(1-xir[2]) +
        x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*   xir[2] +
        x[5*ctx->dof+comp]*    xir[0]*(1-xir[1])*   xir[2] +
        x[6*ctx->dof+comp]*    xir[0]*    xir[1]*   xir[2] +
        x[7*ctx->dof+comp]*(1-xir[0])*    xir[1]*   xir[2];
    }
    ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr);
    ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr);
    ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr);
  }
  ierr = VecRestoreArray(v, &a);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr);

  ierr = SNESDestroy(&snes);CHKERRQ(ierr);
  ierr = VecDestroy(&r);CHKERRQ(ierr);
  ierr = VecDestroy(&ref);CHKERRQ(ierr);
  ierr = VecDestroy(&real);CHKERRQ(ierr);
  ierr = MatDestroy(&J);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationEvaluate - Using the input from dm and x, calculates interpolated field values at the interpolation points.

  Input Parameters:
+ ctx - The DMInterpolationInfo context
. dm  - The DM
- x   - The local vector containing the field to be interpolated

  Output Parameters:
. v   - The vector containing the interpolated values

  Note: A suitable v can be obtained using DMInterpolationGetVector().

  Level: beginner

.seealso: DMInterpolationGetVector(), DMInterpolationAddPoints(), DMInterpolationCreate()
@*/
PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v)
{
  PetscInt       dim, coneSize, n;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 2);
  PetscValidHeaderSpecific(x, VEC_CLASSID, 3);
  PetscValidHeaderSpecific(v, VEC_CLASSID, 4);
  ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr);
  if (n != ctx->n*ctx->dof) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid input vector size %D should be %D", n, ctx->n*ctx->dof);
  if (n) {
    ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
    ierr = DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);CHKERRQ(ierr);
    if (dim == 2) {
      if (coneSize == 3) {
        ierr = DMInterpolate_Triangle_Private(ctx, dm, x, v);CHKERRQ(ierr);
      } else if (coneSize == 4) {
        ierr = DMInterpolate_Quad_Private(ctx, dm, x, v);CHKERRQ(ierr);
      } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %D for point interpolation", dim);
    } else if (dim == 3) {
      if (coneSize == 4) {
        ierr = DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);CHKERRQ(ierr);
      } else {
        ierr = DMInterpolate_Hex_Private(ctx, dm, x, v);CHKERRQ(ierr);
      }
    } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %D for point interpolation", dim);
  }
  PetscFunctionReturn(0);
}

/*@C
  DMInterpolationDestroy - Destroys a DMInterpolationInfo context

  Collective on ctx

  Input Parameter:
. ctx - the context

  Level: beginner

.seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate()
@*/
PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidPointer(ctx, 2);
  ierr = VecDestroy(&(*ctx)->coords);CHKERRQ(ierr);
  ierr = PetscFree((*ctx)->points);CHKERRQ(ierr);
  ierr = PetscFree((*ctx)->cells);CHKERRQ(ierr);
  ierr = PetscFree(*ctx);CHKERRQ(ierr);
  *ctx = NULL;
  PetscFunctionReturn(0);
}

/*@C
  SNESMonitorFields - Monitors the residual for each field separately

  Collective on SNES

  Input Parameters:
+ snes   - the SNES context
. its    - iteration number
. fgnorm - 2-norm of residual
- vf  - PetscViewerAndFormat of type ASCII

  Notes:
  This routine prints the residual norm at each iteration.

  Level: intermediate

.seealso: SNESMonitorSet(), SNESMonitorDefault()
@*/
PetscErrorCode SNESMonitorFields(SNES snes, PetscInt its, PetscReal fgnorm, PetscViewerAndFormat *vf)
{
  PetscViewer        viewer = vf->viewer;
  Vec                res;
  DM                 dm;
  PetscSection       s;
  const PetscScalar *r;
  PetscReal         *lnorms, *norms;
  PetscInt           numFields, f, pStart, pEnd, p;
  PetscErrorCode     ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,4);
  ierr = SNESGetFunction(snes, &res, NULL, NULL);CHKERRQ(ierr);
  ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr);
  ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr);
  ierr = PetscSectionGetNumFields(s, &numFields);CHKERRQ(ierr);
  ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr);
  ierr = PetscCalloc2(numFields, &lnorms, numFields, &norms);CHKERRQ(ierr);
  ierr = VecGetArrayRead(res, &r);CHKERRQ(ierr);
  for (p = pStart; p < pEnd; ++p) {
    for (f = 0; f < numFields; ++f) {
      PetscInt fdof, foff, d;

      ierr = PetscSectionGetFieldDof(s, p, f, &fdof);CHKERRQ(ierr);
      ierr = PetscSectionGetFieldOffset(s, p, f, &foff);CHKERRQ(ierr);
      for (d = 0; d < fdof; ++d) lnorms[f] += PetscRealPart(PetscSqr(r[foff+d]));
    }
  }
  ierr = VecRestoreArrayRead(res, &r);CHKERRQ(ierr);
  ierr = MPIU_Allreduce(lnorms, norms, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr);
  ierr = PetscViewerPushFormat(viewer,vf->format);CHKERRQ(ierr);
  ierr = PetscViewerASCIIAddTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);CHKERRQ(ierr);
  for (f = 0; f < numFields; ++f) {
    if (f > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);}
    ierr = PetscViewerASCIIPrintf(viewer, "%14.12e", (double) PetscSqrtReal(norms[f]));CHKERRQ(ierr);
  }
  ierr = PetscViewerASCIIPrintf(viewer, "]\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIISubtractTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr);
  ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
  ierr = PetscFree2(lnorms, norms);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/********************* Residual Computation **************************/

/*@
  DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user

  Input Parameters:
+ dm - The mesh
. X  - Local solution
- user - The user context

  Output Parameter:
. F  - Local output vector

  Level: developer

.seealso: DMPlexComputeJacobianAction()
@*/
PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user)
{
  DM             plex;
  IS             allcellIS;
  PetscInt       Nds, s, depth;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMGetNumDS(dm, &Nds);CHKERRQ(ierr);
  ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr);
  ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr);
  ierr = DMGetStratumIS(plex, "dim", depth, &allcellIS);CHKERRQ(ierr);
  if (!allcellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &allcellIS);CHKERRQ(ierr);}
  for (s = 0; s < Nds; ++s) {
    PetscDS ds;
    DMLabel label;
    IS      cellIS;

    ierr = DMGetRegionNumDS(dm, s, &label, NULL, &ds);CHKERRQ(ierr);
    if (!label) {
      ierr = PetscObjectReference((PetscObject) allcellIS);CHKERRQ(ierr);
      cellIS = allcellIS;
    } else {
      IS pointIS;

      ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr);
      ierr = ISIntersect_Caching_Internal(allcellIS, pointIS, &cellIS);CHKERRQ(ierr);
      ierr = ISDestroy(&pointIS);CHKERRQ(ierr);
    }
    ierr = DMPlexComputeResidual_Internal(plex, cellIS, PETSC_MIN_REAL, X, NULL, 0.0, F, user);CHKERRQ(ierr);
    ierr = ISDestroy(&cellIS);CHKERRQ(ierr);
  }
  ierr = ISDestroy(&allcellIS);CHKERRQ(ierr);
  ierr = DMDestroy(&plex);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@
  DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X

  Input Parameters:
+ dm - The mesh
- user - The user context

  Output Parameter:
. X  - Local solution

  Level: developer

.seealso: DMPlexComputeJacobianAction()
@*/
PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user)
{
  DM             plex;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr);
  ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);CHKERRQ(ierr);
  ierr = DMDestroy(&plex);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@
  DMPlexComputeJacobianAction - Form the local portion of the Jacobian action Z = J(X) Y at the local solution X using pointwise functions specified by the user.

  Input Parameters:
+ dm - The mesh
. cellIS -
. t  - The time
. X_tShift - The multiplier for the Jacobian with repsect to X_t
. X  - Local solution vector
. X_t  - Time-derivative of the local solution vector
. Y  - Local input vector
- user - The user context

  Output Parameter:
. Z - Local output vector

  Note:
  We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator,
  like a GPU, or vectorize on a multicore machine.

  Level: developer

.seealso: FormFunctionLocal()
@*/
PetscErrorCode DMPlexComputeJacobianAction(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Vec Y, Vec Z, void *user)
{
  DM_Plex          *mesh  = (DM_Plex *) dm->data;
  const char       *name  = "Jacobian";
  DM                dmAux, plex, plexAux = NULL;
  DMEnclosureType   encAux;
  Vec               A;
  PetscDS           prob, probAux = NULL;
  PetscQuadrature   quad;
  PetscSection      section, globalSection, sectionAux;
  PetscScalar      *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z;
  PetscInt          Nf, fieldI, fieldJ;
  PetscInt          totDim, totDimAux = 0;
  const PetscInt   *cells;
  PetscInt          cStart, cEnd, numCells, c;
  PetscBool         hasDyn;
  DMField           coordField;
  PetscErrorCode    ierr;

  PetscFunctionBegin;
  ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr);
  ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr);
  if (!cellIS) {
    PetscInt depth;

    ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr);
    ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr);
    if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);}
  } else {
    ierr = PetscObjectReference((PetscObject) cellIS);CHKERRQ(ierr);
  }
  ierr = DMGetLocalSection(dm, &section);CHKERRQ(ierr);
  ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr);
  ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr);
  ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr);
  ierr = DMGetCellDS(dm, cells ? cells[cStart] : cStart, &prob);CHKERRQ(ierr);
  ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr);
  ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr);
  ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr);
  hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE;
  ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr);
  ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr);
  if (dmAux) {
    ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr);
    ierr = DMConvert(dmAux, DMPLEX, &plexAux);CHKERRQ(ierr);
    ierr = DMGetLocalSection(plexAux, &sectionAux);CHKERRQ(ierr);
    ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr);
    ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr);
  }
  ierr = VecSet(Z, 0.0);CHKERRQ(ierr);
  ierr = PetscMalloc6(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim*totDim,&elemMat,hasDyn ? numCells*totDim*totDim : 0, &elemMatD,numCells*totDim,&y,totDim,&z);CHKERRQ(ierr);
  if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);}
  ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr);
  for (c = cStart; c < cEnd; ++c) {
    const PetscInt cell = cells ? cells[c] : c;
    const PetscInt cind = c - cStart;
    PetscScalar   *x = NULL,  *x_t = NULL;
    PetscInt       i;

    ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr);
    for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i];
    ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr);
    if (X_t) {
      ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr);
      for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i];
      ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr);
    }
    if (dmAux) {
      PetscInt subcell;
      ierr = DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);CHKERRQ(ierr);
      ierr = DMPlexVecGetClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr);
      for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i];
      ierr = DMPlexVecRestoreClosure(plexAux, sectionAux, A, subcell, NULL, &x);CHKERRQ(ierr);
    }
    ierr = DMPlexVecGetClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr);
    for (i = 0; i < totDim; ++i) y[cind*totDim+i] = x[i];
    ierr = DMPlexVecRestoreClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr);
  }
  ierr = PetscArrayzero(elemMat, numCells*totDim*totDim);CHKERRQ(ierr);
  if (hasDyn)  {ierr = PetscArrayzero(elemMatD, numCells*totDim*totDim);CHKERRQ(ierr);}
  for (fieldI = 0; fieldI < Nf; ++fieldI) {
    PetscFE  fe;
    PetscInt Nb;
    /* Conforming batches */
    PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
    /* Remainder */
    PetscInt Nr, offset, Nq;
    PetscQuadrature qGeom = NULL;
    PetscInt    maxDegree;
    PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL;

    ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr);
    ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr);
    ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr);
    ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr);
    ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr);
    if (maxDegree <= 1) {ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr);}
    if (!qGeom) {
      ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr);
      ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr);
    }
    ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr);
    ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr);
    blockSize = Nb;
    batchSize = numBlocks * blockSize;
    ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr);
    numChunks = numCells / (numBatches*batchSize);
    Ne        = numChunks*numBatches*batchSize;
    Nr        = numCells % (numBatches*batchSize);
    offset    = numCells - Nr;
    ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr);
    ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr);
    for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
      ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr);
      ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr);
      if (hasDyn) {
        ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr);
        ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatD[offset*totDim*totDim]);CHKERRQ(ierr);
      }
    }
    ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr);
    ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr);
    ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr);
    ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr);
  }
  if (hasDyn) {
    for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];
  }
  for (c = cStart; c < cEnd; ++c) {
    const PetscInt     cell = cells ? cells[c] : c;
    const PetscInt     cind = c - cStart;
    const PetscBLASInt M = totDim, one = 1;
    const PetscScalar  a = 1.0, b = 0.0;

    PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[cind*totDim*totDim], &M, &y[cind*totDim], &one, &b, z, &one));
    if (mesh->printFEM > 1) {
      ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);
      ierr = DMPrintCellVector(c, "Y",  totDim, &y[cind*totDim]);CHKERRQ(ierr);
      ierr = DMPrintCellVector(c, "Z",  totDim, z);CHKERRQ(ierr);
    }
    ierr = DMPlexVecSetClosure(dm, section, Z, cell, z, ADD_VALUES);CHKERRQ(ierr);
  }
  ierr = PetscFree6(u,u_t,elemMat,elemMatD,y,z);CHKERRQ(ierr);
  if (mesh->printFEM) {
    ierr = PetscPrintf(PetscObjectComm((PetscObject)Z), "Z:\n");CHKERRQ(ierr);
    ierr = VecView(Z, NULL);CHKERRQ(ierr);
  }
  ierr = PetscFree(a);CHKERRQ(ierr);
  ierr = ISDestroy(&cellIS);CHKERRQ(ierr);
  ierr = DMDestroy(&plexAux);CHKERRQ(ierr);
  ierr = DMDestroy(&plex);CHKERRQ(ierr);
  ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@
  DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user.

  Input Parameters:
+ dm - The mesh
. X  - Local input vector
- user - The user context

  Output Parameter:
. Jac  - Jacobian matrix

  Note:
  We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator,
  like a GPU, or vectorize on a multicore machine.

  Level: developer

.seealso: FormFunctionLocal()
@*/
PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user)
{
  DM             plex;
  IS             allcellIS;
  PetscBool      hasJac, hasPrec;
  PetscInt       Nds, s, depth;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMGetNumDS(dm, &Nds);CHKERRQ(ierr);
  ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr);
  ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr);
  ierr = DMGetStratumIS(plex, "dim", depth, &allcellIS);CHKERRQ(ierr);
  if (!allcellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &allcellIS);CHKERRQ(ierr);}
  for (s = 0; s < Nds; ++s) {
    PetscDS ds;
    DMLabel label;
    IS      cellIS;

    ierr = DMGetRegionNumDS(dm, s, &label, NULL, &ds);CHKERRQ(ierr);
    if (!label) {
      ierr = PetscObjectReference((PetscObject) allcellIS);CHKERRQ(ierr);
      cellIS = allcellIS;
    } else {
      IS pointIS;

      ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr);
      ierr = ISIntersect_Caching_Internal(allcellIS, pointIS, &cellIS);CHKERRQ(ierr);
      ierr = ISDestroy(&pointIS);CHKERRQ(ierr);
    }
    if (!s) {
      ierr = PetscDSHasJacobian(ds, &hasJac);CHKERRQ(ierr);
      ierr = PetscDSHasJacobianPreconditioner(ds, &hasPrec);CHKERRQ(ierr);
      if (hasJac && hasPrec) {ierr = MatZeroEntries(Jac);CHKERRQ(ierr);}
      ierr = MatZeroEntries(JacP);CHKERRQ(ierr);
    }
    ierr = DMPlexComputeJacobian_Internal(plex, cellIS, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr);
    ierr = ISDestroy(&cellIS);CHKERRQ(ierr);
  }
  ierr = ISDestroy(&allcellIS);CHKERRQ(ierr);
  ierr = DMDestroy(&plex);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
     MatComputeNeumannOverlap - Computes an unassembled (Neumann) local overlapping Mat in nonlinear context.

   Input Parameters:
+     X - SNES linearization point
.     ovl - index set of overlapping subdomains

   Output Parameter:
.     J - unassembled (Neumann) local matrix

   Level: intermediate

.seealso: DMCreateNeumannOverlap(), MATIS, PCHPDDMSetAuxiliaryMat()
*/
static PetscErrorCode MatComputeNeumannOverlap_Plex(Mat J, PetscReal t, Vec X, Vec X_t, PetscReal s, IS ovl, void *ctx)
{
  SNES           snes;
  Mat            pJ;
  DM             ovldm,origdm;
  DMSNES         sdm;
  PetscErrorCode (*bfun)(DM,Vec,void*);
  PetscErrorCode (*jfun)(DM,Vec,Mat,Mat,void*);
  void           *bctx,*jctx;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Overlap_HPDDM_MATIS",(PetscObject*)&pJ);CHKERRQ(ierr);
  if (!pJ) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Missing overlapping Mat");CHKERRQ(ierr);
  ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Original_HPDDM",(PetscObject*)&origdm);CHKERRQ(ierr);
  if (!origdm) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Missing original DM");CHKERRQ(ierr);
  ierr = MatGetDM(pJ,&ovldm);CHKERRQ(ierr);
  ierr = DMSNESGetBoundaryLocal(origdm,&bfun,&bctx);CHKERRQ(ierr);
  ierr = DMSNESSetBoundaryLocal(ovldm,bfun,bctx);CHKERRQ(ierr);
  ierr = DMSNESGetJacobianLocal(origdm,&jfun,&jctx);CHKERRQ(ierr);
  ierr = DMSNESSetJacobianLocal(ovldm,jfun,jctx);CHKERRQ(ierr);
  ierr = PetscObjectQuery((PetscObject)ovl,"_DM_Overlap_HPDDM_SNES",(PetscObject*)&snes);CHKERRQ(ierr);
  if (!snes) {
    ierr = SNESCreate(PetscObjectComm((PetscObject)ovl),&snes);CHKERRQ(ierr);
    ierr = SNESSetDM(snes,ovldm);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject)ovl,"_DM_Overlap_HPDDM_SNES",(PetscObject)snes);CHKERRQ(ierr);
    ierr = PetscObjectDereference((PetscObject)snes);CHKERRQ(ierr);
  }
  ierr = DMGetDMSNES(ovldm,&sdm);CHKERRQ(ierr);
  ierr = VecLockReadPush(X);CHKERRQ(ierr);
  PetscStackPush("SNES user Jacobian function");
  ierr = (*sdm->ops->computejacobian)(snes,X,pJ,pJ,sdm->jacobianctx);CHKERRQ(ierr);
  PetscStackPop;
  ierr = VecLockReadPop(X);CHKERRQ(ierr);
  /* this is a no-hop, just in case we decide to change the placeholder for the local Neumann matrix */
  {
    Mat locpJ;

    ierr = MatISGetLocalMat(pJ,&locpJ);CHKERRQ(ierr);
    ierr = MatCopy(locpJ,J,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

/*@
  DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian.

  Input Parameters:
+ dm - The DM object
. boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see PetscDSAddBoundary())
. residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual())
- jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian())

  Level: developer
@*/
PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);CHKERRQ(ierr);
  ierr = DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);CHKERRQ(ierr);
  ierr = DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)dm,"MatComputeNeumannOverlap_C",MatComputeNeumannOverlap_Plex);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  DMSNESCheckDiscretization - Check the discretization error of the exact solution

  Input Parameters:
+ snes - the SNES object
. dm   - the DM
. t    - the time
. u    - a DM vector
- tol  - A tolerance for the check, or -1 to print the results instead

  Output Parameters:
. error - An array which holds the discretization error in each field, or NULL

  Note: The user must call PetscDSSetExactSolution() beforehand

  Level: developer

.seealso: DNSNESCheckFromOptions(), DMSNESCheckResidual(), DMSNESCheckJacobian(), PetscDSSetExactSolution()
@*/
PetscErrorCode DMSNESCheckDiscretization(SNES snes, DM dm, PetscReal t, Vec u, PetscReal tol, PetscReal error[])
{
  PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx);
  void            **ectxs;
  PetscReal        *err;
  MPI_Comm          comm;
  PetscInt          Nf, f;
  PetscErrorCode    ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(snes, SNES_CLASSID, 1);
  PetscValidHeaderSpecific(dm, DM_CLASSID, 2);
  PetscValidHeaderSpecific(u, VEC_CLASSID, 3);
  if (error) PetscValidRealPointer(error, 6);

  ierr = DMComputeExactSolution(dm, t, u, NULL);CHKERRQ(ierr);
  ierr = VecViewFromOptions(u, NULL, "-vec_view");CHKERRQ(ierr);

  ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr);
  ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr);
  ierr = PetscCalloc3(Nf, &exacts, Nf, &ectxs, PetscMax(1, Nf), &err);CHKERRQ(ierr);
  {
    PetscInt Nds, s;

    ierr = DMGetNumDS(dm, &Nds);CHKERRQ(ierr);
    for (s = 0; s < Nds; ++s) {
      PetscDS         ds;
      DMLabel         label;
      IS              fieldIS;
      const PetscInt *fields;
      PetscInt        dsNf, f;

      ierr = DMGetRegionNumDS(dm, s, &label, &fieldIS, &ds);CHKERRQ(ierr);
      ierr = PetscDSGetNumFields(ds, &dsNf);CHKERRQ(ierr);
      ierr = ISGetIndices(fieldIS, &fields);CHKERRQ(ierr);
      for (f = 0; f < dsNf; ++f) {
        const PetscInt field = fields[f];
        ierr = PetscDSGetExactSolution(ds, field, &exacts[field], &ectxs[field]);CHKERRQ(ierr);
      }
      ierr = ISRestoreIndices(fieldIS, &fields);CHKERRQ(ierr);
    }
  }
  if (Nf > 1) {
    ierr = DMComputeL2FieldDiff(dm, t, exacts, ectxs, u, err);CHKERRQ(ierr);
    if (tol >= 0.0) {
      for (f = 0; f < Nf; ++f) {
        if (err[f] > tol) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "L_2 Error %g for field %D exceeds tolerance %g", (double) err[f], f, (double) tol);
      }
    } else if (error) {
      for (f = 0; f < Nf; ++f) error[f] = err[f];
    } else {
      ierr = PetscPrintf(comm, "L_2 Error: [");CHKERRQ(ierr);
      for (f = 0; f < Nf; ++f) {
        if (f) {ierr = PetscPrintf(comm, ", ");CHKERRQ(ierr);}
        ierr = PetscPrintf(comm, "%g", (double)err[f]);CHKERRQ(ierr);
      }
      ierr = PetscPrintf(comm, "]\n");CHKERRQ(ierr);
    }
  } else {
    ierr = DMComputeL2Diff(dm, t, exacts, ectxs, u, &err[0]);CHKERRQ(ierr);
    if (tol >= 0.0) {
      if (err[0] > tol) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "L_2 Error %g exceeds tolerance %g", (double) err[0], (double) tol);
    } else if (error) {
      error[0] = err[0];
    } else {
      ierr = PetscPrintf(comm, "L_2 Error: %g\n", (double) err[0]);CHKERRQ(ierr);
    }
  }
  ierr = PetscFree3(exacts, ectxs, err);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  DMSNESCheckResidual - Check the residual of the exact solution

  Input Parameters:
+ snes - the SNES object
. dm   - the DM
. u    - a DM vector
- tol  - A tolerance for the check, or -1 to print the results instead

  Output Parameters:
. residual - The residual norm of the exact solution, or NULL

  Level: developer

.seealso: DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckJacobian()
@*/
PetscErrorCode DMSNESCheckResidual(SNES snes, DM dm, Vec u, PetscReal tol, PetscReal *residual)
{
  MPI_Comm       comm;
  Vec            r;
  PetscReal      res;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(snes, SNES_CLASSID, 1);
  PetscValidHeaderSpecific(dm, DM_CLASSID, 2);
  PetscValidHeaderSpecific(u, VEC_CLASSID, 3);
  if (residual) PetscValidRealPointer(residual, 5);
  ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr);
  ierr = DMComputeExactSolution(dm, 0.0, u, NULL);CHKERRQ(ierr);
  ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
  ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr);
  ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
  if (tol >= 0.0) {
    if (res > tol) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "L_2 Residual %g exceeds tolerance %g", (double) res, (double) tol);
  } else if (residual) {
    *residual = res;
  } else {
    ierr = PetscPrintf(comm, "L_2 Residual: %g\n", (double)res);CHKERRQ(ierr);
    ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
    ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr);
    ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr);
    ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr);
  }
  ierr = VecDestroy(&r);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  DMSNESCheckJacobian - Check the Jacobian of the exact solution against the residual using the Taylor Test

  Input Parameters:
+ snes - the SNES object
. dm   - the DM
. u    - a DM vector
- tol  - A tolerance for the check, or -1 to print the results instead

  Output Parameters:
+ isLinear - Flag indicaing that the function looks linear, or NULL
- convRate - The rate of convergence of the linear model, or NULL

  Level: developer

.seealso: DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckResidual()
@*/
PetscErrorCode DMSNESCheckJacobian(SNES snes, DM dm, Vec u, PetscReal tol, PetscBool *isLinear, PetscReal *convRate)
{
  MPI_Comm       comm;
  PetscDS        ds;
  Mat            J, M;
  MatNullSpace   nullspace;
  PetscReal      slope, intercept;
  PetscBool      hasJac, hasPrec, isLin = PETSC_FALSE;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(snes, SNES_CLASSID, 1);
  PetscValidHeaderSpecific(dm, DM_CLASSID, 2);
  PetscValidHeaderSpecific(u, VEC_CLASSID, 3);
  if (isLinear) PetscValidBoolPointer(isLinear, 5);
  if (convRate) PetscValidRealPointer(convRate, 5);
  ierr = PetscObjectGetComm((PetscObject) snes, &comm);CHKERRQ(ierr);
  ierr = DMComputeExactSolution(dm, 0.0, u, NULL);CHKERRQ(ierr);
  /* Create and view matrices */
  ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr);
  ierr = DMGetDS(dm, &ds);CHKERRQ(ierr);
  ierr = PetscDSHasJacobian(ds, &hasJac);CHKERRQ(ierr);
  ierr = PetscDSHasJacobianPreconditioner(ds, &hasPrec);CHKERRQ(ierr);
  if (hasJac && hasPrec) {
    ierr = DMCreateMatrix(dm, &M);CHKERRQ(ierr);
    ierr = SNESComputeJacobian(snes, u, J, M);CHKERRQ(ierr);
    ierr = PetscObjectSetName((PetscObject) M, "Preconditioning Matrix");CHKERRQ(ierr);
    ierr = PetscObjectSetOptionsPrefix((PetscObject) M, "jacpre_");CHKERRQ(ierr);
    ierr = MatViewFromOptions(M, NULL, "-mat_view");CHKERRQ(ierr);
    ierr = MatDestroy(&M);CHKERRQ(ierr);
  } else {
    ierr = SNESComputeJacobian(snes, u, J, J);CHKERRQ(ierr);
  }
  ierr = PetscObjectSetName((PetscObject) J, "Jacobian");CHKERRQ(ierr);
  ierr = PetscObjectSetOptionsPrefix((PetscObject) J, "jac_");CHKERRQ(ierr);
  ierr = MatViewFromOptions(J, NULL, "-mat_view");CHKERRQ(ierr);
  /* Check nullspace */
  ierr = MatGetNullSpace(J, &nullspace);CHKERRQ(ierr);
  if (nullspace) {
    PetscBool isNull;
    ierr = MatNullSpaceTest(nullspace, J, &isNull);CHKERRQ(ierr);
    if (!isNull) SETERRQ(comm, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid.");
  }
  ierr = MatNullSpaceDestroy(&nullspace);CHKERRQ(ierr);
  /* Taylor test */
  {
    PetscRandom rand;
    Vec         du, uhat, r, rhat, df;
    PetscReal   h;
    PetscReal  *es, *hs, *errors;
    PetscReal   hMax = 1.0, hMin = 1e-6, hMult = 0.1;
    PetscInt    Nv, v;

    /* Choose a perturbation direction */
    ierr = PetscRandomCreate(comm, &rand);CHKERRQ(ierr);
    ierr = VecDuplicate(u, &du);CHKERRQ(ierr);
    ierr = VecSetRandom(du, rand);CHKERRQ(ierr);
    ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
    ierr = VecDuplicate(u, &df);CHKERRQ(ierr);
    ierr = MatMult(J, du, df);CHKERRQ(ierr);
    /* Evaluate residual at u, F(u), save in vector r */
    ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
    ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr);
    /* Look at the convergence of our Taylor approximation as we approach u */
    for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv);
    ierr = PetscCalloc3(Nv, &es, Nv, &hs, Nv, &errors);CHKERRQ(ierr);
    ierr = VecDuplicate(u, &uhat);CHKERRQ(ierr);
    ierr = VecDuplicate(u, &rhat);CHKERRQ(ierr);
    for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv) {
      ierr = VecWAXPY(uhat, h, du, u);CHKERRQ(ierr);
      /* F(\hat u) \approx F(u) + J(u) (uhat - u) = F(u) + h * J(u) du */
      ierr = SNESComputeFunction(snes, uhat, rhat);CHKERRQ(ierr);
      ierr = VecAXPBYPCZ(rhat, -1.0, -h, 1.0, r, df);CHKERRQ(ierr);
      ierr = VecNorm(rhat, NORM_2, &errors[Nv]);CHKERRQ(ierr);

      es[Nv] = PetscLog10Real(errors[Nv]);
      hs[Nv] = PetscLog10Real(h);
    }
    ierr = VecDestroy(&uhat);CHKERRQ(ierr);
    ierr = VecDestroy(&rhat);CHKERRQ(ierr);
    ierr = VecDestroy(&df);CHKERRQ(ierr);
    ierr = VecDestroy(&r);CHKERRQ(ierr);
    ierr = VecDestroy(&du);CHKERRQ(ierr);
    for (v = 0; v < Nv; ++v) {
      if ((tol >= 0) && (errors[v] > tol)) break;
      else if (errors[v] > PETSC_SMALL)    break;
    }
    if (v == Nv) isLin = PETSC_TRUE;
    ierr = PetscLinearRegression(Nv, hs, es, &slope, &intercept);CHKERRQ(ierr);
    ierr = PetscFree3(es, hs, errors);CHKERRQ(ierr);
    /* Slope should be about 2 */
    if (tol >= 0) {
      if (!isLin && PetscAbsReal(2 - slope) > tol) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Taylor approximation convergence rate should be 2, not %0.2f", (double) slope);
    } else if (isLinear || convRate) {
      if (isLinear) *isLinear = isLin;
      if (convRate) *convRate = slope;
    } else {
      if (!isLin) {ierr = PetscPrintf(comm, "Taylor approximation converging at order %3.2f\n", (double) slope);CHKERRQ(ierr);}
      else        {ierr = PetscPrintf(comm, "Function appears to be linear\n");CHKERRQ(ierr);}
    }
  }
  ierr = MatDestroy(&J);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode DMSNESCheck_Internal(SNES snes, DM dm, Vec u)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMSNESCheckDiscretization(snes, dm, 0.0, u, -1.0, NULL);CHKERRQ(ierr);
  ierr = DMSNESCheckResidual(snes, dm, u, -1.0, NULL);CHKERRQ(ierr);
  ierr = DMSNESCheckJacobian(snes, dm, u, -1.0, NULL, NULL);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  DMSNESCheckFromOptions - Check the residual and Jacobian functions using the exact solution by outputting some diagnostic information

  Input Parameters:
+ snes - the SNES object
- u    - representative SNES vector

  Note: The user must call PetscDSSetExactSolution() beforehand

  Level: developer
@*/
PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u)
{
  DM             dm;
  Vec            sol;
  PetscBool      check;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr);
  if (!check) PetscFunctionReturn(0);
  ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr);
  ierr = VecDuplicate(u, &sol);CHKERRQ(ierr);
  ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr);
  ierr = DMSNESCheck_Internal(snes, dm, sol);CHKERRQ(ierr);
  ierr = VecDestroy(&sol);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}