static char help[] = "Demonstrates adjoint sensitivity analysis for Reaction-Diffusion Equations.\n";

/*
  See ex5.c for details on the equation.
  This code demonestrates the TSAdjoint interface to a system of time-dependent partial differential equations.
  It computes the sensitivity of a component in the final solution, which locates in the center of the 2D domain, w.r.t. the initial conditions.
  The user does not need to provide any additional functions. The required functions in the original simulation are reused in the adjoint run.

  Runtime options:
    -forwardonly  - run the forward simulation without adjoint
    -implicitform - provide IFunction and IJacobian to TS, if not set, RHSFunction and RHSJacobian will be used
    -aijpc        - set the preconditioner matrix to be aij (the Jacobian matrix can be of a different type such as ELL)
*/

#include <petscsys.h>
#include <petscdm.h>
#include <petscdmda.h>
#include <petscts.h>

typedef struct {
  PetscScalar u,v;
} Field;

typedef struct {
  PetscReal D1,D2,gamma,kappa;
  PetscBool aijpc;
} AppCtx;

/*
   User-defined routines
*/
PetscErrorCode RHSFunction(TS,PetscReal,Vec,Vec,void*);
PetscErrorCode InitialConditions(DM,Vec);
PetscErrorCode RHSJacobian(TS,PetscReal,Vec,Mat,Mat,void*);
PetscErrorCode IFunction(TS,PetscReal,Vec,Vec,Vec,void*);
PetscErrorCode IJacobian(TS,PetscReal,Vec,Vec,PetscReal,Mat,Mat,void*);

PetscErrorCode InitializeLambda(DM da,Vec lambda,PetscReal x,PetscReal y)
{
   PetscInt i,j,Mx,My,xs,ys,xm,ym;
   PetscErrorCode ierr;
   Field **l;
   PetscFunctionBegin;

   ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
   /* locate the global i index for x and j index for y */
   i = (PetscInt)(x*(Mx-1));
   j = (PetscInt)(y*(My-1));
   ierr = DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);

   if (xs <= i && i < xs+xm && ys <= j && j < ys+ym) {
     /* the i,j vertex is on this process */
     ierr = DMDAVecGetArray(da,lambda,&l);CHKERRQ(ierr);
     l[j][i].u = 1.0;
     l[j][i].v = 1.0;
     ierr = DMDAVecRestoreArray(da,lambda,&l);CHKERRQ(ierr);
   }
   PetscFunctionReturn(0);
}

int main(int argc,char **argv)
{
  TS             ts;                  /* ODE integrator */
  Vec            x;                   /* solution */
  PetscErrorCode ierr;
  DM             da;
  AppCtx         appctx;
  Vec            lambda[1];
  PetscBool      forwardonly=PETSC_FALSE,implicitform=PETSC_TRUE;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = PetscOptionsGetBool(NULL,NULL,"-forwardonly",&forwardonly,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetBool(NULL,NULL,"-implicitform",&implicitform,NULL);CHKERRQ(ierr);
  appctx.aijpc = PETSC_FALSE;
  ierr = PetscOptionsGetBool(NULL,NULL,"-aijpc",&appctx.aijpc,NULL);CHKERRQ(ierr);

  appctx.D1    = 8.0e-5;
  appctx.D2    = 4.0e-5;
  appctx.gamma = .024;
  appctx.kappa = .06;

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create distributed array (DMDA) to manage parallel grid and vectors
  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,DM_BOUNDARY_PERIODIC,DMDA_STENCIL_STAR,64,64,PETSC_DECIDE,PETSC_DECIDE,2,1,NULL,NULL,&da);CHKERRQ(ierr);
  ierr = DMSetFromOptions(da);CHKERRQ(ierr);
  ierr = DMSetUp(da);CHKERRQ(ierr);
  ierr = DMDASetFieldName(da,0,"u");CHKERRQ(ierr);
  ierr = DMDASetFieldName(da,1,"v");CHKERRQ(ierr);

  /*  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Extract global vectors from DMDA; then duplicate for remaining
     vectors that are the same types
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetDM(ts,da);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetEquationType(ts,TS_EQ_ODE_EXPLICIT);CHKERRQ(ierr); /* less Jacobian evaluations when adjoint BEuler is used, otherwise no effect */
  if (!implicitform) {
    ierr = TSSetType(ts,TSRK);CHKERRQ(ierr);
    ierr = TSSetRHSFunction(ts,NULL,RHSFunction,&appctx);CHKERRQ(ierr);
    ierr = TSSetRHSJacobian(ts,NULL,NULL,RHSJacobian,&appctx);CHKERRQ(ierr);
  } else {
    ierr = TSSetType(ts,TSCN);CHKERRQ(ierr);
    ierr = TSSetIFunction(ts,NULL,IFunction,&appctx);CHKERRQ(ierr);
    if (appctx.aijpc) {
      Mat                    A,B;

      ierr = DMSetMatType(da,MATSELL);CHKERRQ(ierr);
      ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr);
      ierr = MatConvert(A,MATAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);
      /* FIXME do we need to change viewer to display matrix in natural ordering as DMCreateMatrix_DA does? */
      ierr = TSSetIJacobian(ts,A,B,IJacobian,&appctx);CHKERRQ(ierr);
      ierr = MatDestroy(&A);CHKERRQ(ierr);
      ierr = MatDestroy(&B);CHKERRQ(ierr);
    } else {
      ierr = TSSetIJacobian(ts,NULL,NULL,IJacobian,&appctx);CHKERRQ(ierr);
    }
  }

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = InitialConditions(da,x);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,x);CHKERRQ(ierr);

  /*
    Have the TS save its trajectory so that TSAdjointSolve() may be used
  */
  if (!forwardonly) { ierr = TSSetSaveTrajectory(ts);CHKERRQ(ierr); }

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set solver options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetMaxTime(ts,200.0);CHKERRQ(ierr);
  ierr = TSSetTimeStep(ts,0.5);CHKERRQ(ierr);
  ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve ODE system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,x);CHKERRQ(ierr);
  if (!forwardonly) {
    /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
       Start the Adjoint model
       - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    ierr = VecDuplicate(x,&lambda[0]);CHKERRQ(ierr);
    /*   Reset initial conditions for the adjoint integration */
    ierr = InitializeLambda(da,lambda[0],0.5,0.5);CHKERRQ(ierr);
    ierr = TSSetCostGradients(ts,1,lambda,NULL);CHKERRQ(ierr);
    ierr = TSAdjointSolve(ts);CHKERRQ(ierr);
    ierr = VecDestroy(&lambda[0]);CHKERRQ(ierr);
  }
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.  All PETSc objects should be destroyed when they
     are no longer needed.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = DMDestroy(&da);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}

/* ------------------------------------------------------------------- */
/*
   RHSFunction - Evaluates nonlinear function, F(x).

   Input Parameters:
.  ts - the TS context
.  X - input vector
.  ptr - optional user-defined context, as set by TSSetRHSFunction()

   Output Parameter:
.  F - function vector
 */
PetscErrorCode RHSFunction(TS ts,PetscReal ftime,Vec U,Vec F,void *ptr)
{
  AppCtx         *appctx = (AppCtx*)ptr;
  DM             da;
  PetscErrorCode ierr;
  PetscInt       i,j,Mx,My,xs,ys,xm,ym;
  PetscReal      hx,hy,sx,sy;
  PetscScalar    uc,uxx,uyy,vc,vxx,vyy;
  Field          **u,**f;
  Vec            localU;

  PetscFunctionBegin;
  ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
  ierr = DMGetLocalVector(da,&localU);CHKERRQ(ierr);
  ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
  hx = 2.50/(PetscReal)Mx; sx = 1.0/(hx*hx);
  hy = 2.50/(PetscReal)My; sy = 1.0/(hy*hy);

  /*
     Scatter ghost points to local vector,using the 2-step process
        DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
     By placing code between these two statements, computations can be
     done while messages are in transition.
  */
  ierr = DMGlobalToLocalBegin(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);

  /*
     Get pointers to vector data
  */
  ierr = DMDAVecGetArrayRead(da,localU,&u);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,F,&f);CHKERRQ(ierr);

  /*
     Get local grid boundaries
  */
  ierr = DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);

  /*
     Compute function over the locally owned part of the grid
  */
  for (j=ys; j<ys+ym; j++) {
    for (i=xs; i<xs+xm; i++) {
      uc        = u[j][i].u;
      uxx       = (-2.0*uc + u[j][i-1].u + u[j][i+1].u)*sx;
      uyy       = (-2.0*uc + u[j-1][i].u + u[j+1][i].u)*sy;
      vc        = u[j][i].v;
      vxx       = (-2.0*vc + u[j][i-1].v + u[j][i+1].v)*sx;
      vyy       = (-2.0*vc + u[j-1][i].v + u[j+1][i].v)*sy;
      f[j][i].u = appctx->D1*(uxx + uyy) - uc*vc*vc + appctx->gamma*(1.0 - uc);
      f[j][i].v = appctx->D2*(vxx + vyy) + uc*vc*vc - (appctx->gamma + appctx->kappa)*vc;
    }
  }
  ierr = PetscLogFlops(16.0*xm*ym);CHKERRQ(ierr);

  /*
     Restore vectors
  */
  ierr = DMDAVecRestoreArrayRead(da,localU,&u);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(da,&localU);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/* ------------------------------------------------------------------- */
PetscErrorCode InitialConditions(DM da,Vec U)
{
  PetscErrorCode ierr;
  PetscInt       i,j,xs,ys,xm,ym,Mx,My;
  Field          **u;
  PetscReal      hx,hy,x,y;

  PetscFunctionBegin;
  ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);

  hx = 2.5/(PetscReal)Mx;
  hy = 2.5/(PetscReal)My;

  /*
     Get pointers to vector data
  */
  ierr = DMDAVecGetArray(da,U,&u);CHKERRQ(ierr);

  /*
     Get local grid boundaries
  */
  ierr = DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);

  /*
     Compute function over the locally owned part of the grid
  */
  for (j=ys; j<ys+ym; j++) {
    y = j*hy;
    for (i=xs; i<xs+xm; i++) {
      x = i*hx;
      if (PetscGTE(x,1.0) && PetscLTE(x,1.5) && PetscGTE(y,1.0) && PetscLTE(y,1.5)) u[j][i].v = PetscPowReal(PetscSinReal(4.0*PETSC_PI*x),2.0)*PetscPowReal(PetscSinReal(4.0*PETSC_PI*y),2.0)/4.0;
      else u[j][i].v = 0.0;

      u[j][i].u = 1.0 - 2.0*u[j][i].v;
    }
  }

  /*
     Restore vectors
  */
  ierr = DMDAVecRestoreArray(da,U,&u);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode RHSJacobian(TS ts,PetscReal t,Vec U,Mat A,Mat BB,void *ctx)
{
  AppCtx         *appctx = (AppCtx*)ctx;     /* user-defined application context */
  DM             da;
  PetscErrorCode ierr;
  PetscInt       i,j,Mx,My,xs,ys,xm,ym;
  PetscReal      hx,hy,sx,sy;
  PetscScalar    uc,vc;
  Field          **u;
  Vec            localU;
  MatStencil     stencil[6],rowstencil;
  PetscScalar    entries[6];

  PetscFunctionBegin;
  ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
  ierr = DMGetLocalVector(da,&localU);CHKERRQ(ierr);
  ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);

  hx = 2.50/(PetscReal)Mx; sx = 1.0/(hx*hx);
  hy = 2.50/(PetscReal)My; sy = 1.0/(hy*hy);

  /*
     Scatter ghost points to local vector,using the 2-step process
        DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
     By placing code between these two statements, computations can be
     done while messages are in transition.
  */
  ierr = DMGlobalToLocalBegin(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);

  /*
     Get pointers to vector data
  */
  ierr = DMDAVecGetArrayRead(da,localU,&u);CHKERRQ(ierr);

  /*
     Get local grid boundaries
  */
  ierr = DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);

  stencil[0].k = 0;
  stencil[1].k = 0;
  stencil[2].k = 0;
  stencil[3].k = 0;
  stencil[4].k = 0;
  stencil[5].k = 0;
  rowstencil.k = 0;
  /*
     Compute function over the locally owned part of the grid
  */
  for (j=ys; j<ys+ym; j++) {

    stencil[0].j = j-1;
    stencil[1].j = j+1;
    stencil[2].j = j;
    stencil[3].j = j;
    stencil[4].j = j;
    stencil[5].j = j;
    rowstencil.k = 0; rowstencil.j = j;
    for (i=xs; i<xs+xm; i++) {
      uc = u[j][i].u;
      vc = u[j][i].v;

      /*      uxx       = (-2.0*uc + u[j][i-1].u + u[j][i+1].u)*sx;
      uyy       = (-2.0*uc + u[j-1][i].u + u[j+1][i].u)*sy;

      vxx       = (-2.0*vc + u[j][i-1].v + u[j][i+1].v)*sx;
      vyy       = (-2.0*vc + u[j-1][i].v + u[j+1][i].v)*sy;
       f[j][i].u = appctx->D1*(uxx + uyy) - uc*vc*vc + appctx->gamma*(1.0 - uc);*/

      stencil[0].i = i; stencil[0].c = 0; entries[0] = appctx->D1*sy;
      stencil[1].i = i; stencil[1].c = 0; entries[1] = appctx->D1*sy;
      stencil[2].i = i-1; stencil[2].c = 0; entries[2] = appctx->D1*sx;
      stencil[3].i = i+1; stencil[3].c = 0; entries[3] = appctx->D1*sx;
      stencil[4].i = i; stencil[4].c = 0; entries[4] = -2.0*appctx->D1*(sx + sy) - vc*vc - appctx->gamma;
      stencil[5].i = i; stencil[5].c = 1; entries[5] = -2.0*uc*vc;
      rowstencil.i = i; rowstencil.c = 0;

      ierr = MatSetValuesStencil(A,1,&rowstencil,6,stencil,entries,INSERT_VALUES);CHKERRQ(ierr);
      if (appctx->aijpc) {
        ierr = MatSetValuesStencil(BB,1,&rowstencil,6,stencil,entries,INSERT_VALUES);CHKERRQ(ierr);
      }
      stencil[0].c = 1; entries[0] = appctx->D2*sy;
      stencil[1].c = 1; entries[1] = appctx->D2*sy;
      stencil[2].c = 1; entries[2] = appctx->D2*sx;
      stencil[3].c = 1; entries[3] = appctx->D2*sx;
      stencil[4].c = 1; entries[4] = -2.0*appctx->D2*(sx + sy) + 2.0*uc*vc - appctx->gamma - appctx->kappa;
      stencil[5].c = 0; entries[5] = vc*vc;
      rowstencil.c = 1;

      ierr = MatSetValuesStencil(A,1,&rowstencil,6,stencil,entries,INSERT_VALUES);CHKERRQ(ierr);
      if (appctx->aijpc) {
        ierr = MatSetValuesStencil(BB,1,&rowstencil,6,stencil,entries,INSERT_VALUES);CHKERRQ(ierr);
      }
      /* f[j][i].v = appctx->D2*(vxx + vyy) + uc*vc*vc - (appctx->gamma + appctx->kappa)*vc; */
    }
  }

  /*
     Restore vectors
  */
  ierr = PetscLogFlops(19.0*xm*ym);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArrayRead(da,localU,&u);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(da,&localU);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  if (appctx->aijpc) {
    ierr = MatAssemblyBegin(BB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(BB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(BB,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  }

  PetscFunctionReturn(0);
}

/*
   IFunction - Evaluates implicit nonlinear function, xdot - F(x).

   Input Parameters:
.  ts - the TS context
.  U - input vector
.  Udot - input vector
.  ptr - optional user-defined context, as set by TSSetRHSFunction()

   Output Parameter:
.  F - function vector
 */
PetscErrorCode IFunction(TS ts,PetscReal ftime,Vec U,Vec Udot,Vec F,void *ptr)
{
  AppCtx         *appctx = (AppCtx*)ptr;
  DM             da;
  PetscErrorCode ierr;
  PetscInt       i,j,Mx,My,xs,ys,xm,ym;
  PetscReal      hx,hy,sx,sy;
  PetscScalar    uc,uxx,uyy,vc,vxx,vyy;
  Field          **u,**f,**udot;
  Vec            localU;

  PetscFunctionBegin;
  ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
  ierr = DMGetLocalVector(da,&localU);CHKERRQ(ierr);
  ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
  hx = 2.50/(PetscReal)Mx; sx = 1.0/(hx*hx);
  hy = 2.50/(PetscReal)My; sy = 1.0/(hy*hy);

  /*
     Scatter ghost points to local vector,using the 2-step process
        DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
     By placing code between these two statements, computations can be
     done while messages are in transition.
  */
  ierr = DMGlobalToLocalBegin(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);

  /*
     Get pointers to vector data
  */
  ierr = DMDAVecGetArrayRead(da,localU,&u);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(da,F,&f);CHKERRQ(ierr);
  ierr = DMDAVecGetArrayRead(da,Udot,&udot);CHKERRQ(ierr);

  /*
     Get local grid boundaries
  */
  ierr = DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);

  /*
     Compute function over the locally owned part of the grid
  */
  for (j=ys; j<ys+ym; j++) {
    for (i=xs; i<xs+xm; i++) {
      uc        = u[j][i].u;
      uxx       = (-2.0*uc + u[j][i-1].u + u[j][i+1].u)*sx;
      uyy       = (-2.0*uc + u[j-1][i].u + u[j+1][i].u)*sy;
      vc        = u[j][i].v;
      vxx       = (-2.0*vc + u[j][i-1].v + u[j][i+1].v)*sx;
      vyy       = (-2.0*vc + u[j-1][i].v + u[j+1][i].v)*sy;
      f[j][i].u = udot[j][i].u - ( appctx->D1*(uxx + uyy) - uc*vc*vc + appctx->gamma*(1.0 - uc));
      f[j][i].v = udot[j][i].v - ( appctx->D2*(vxx + vyy) + uc*vc*vc - (appctx->gamma + appctx->kappa)*vc);
    }
  }
  ierr = PetscLogFlops(16.0*xm*ym);CHKERRQ(ierr);

  /*
     Restore vectors
  */
  ierr = DMDAVecRestoreArrayRead(da,localU,&u);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArrayRead(da,Udot,&udot);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(da,&localU);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode IJacobian(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal a,Mat A,Mat BB,void *ctx)
{
  AppCtx         *appctx = (AppCtx*)ctx;     /* user-defined application context */
  DM             da;
  PetscErrorCode ierr;
  PetscInt       i,j,Mx,My,xs,ys,xm,ym;
  PetscReal      hx,hy,sx,sy;
  PetscScalar    uc,vc;
  Field          **u;
  Vec            localU;
  MatStencil     stencil[6],rowstencil;
  PetscScalar    entries[6];

  PetscFunctionBegin;
  ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
  ierr = DMGetLocalVector(da,&localU);CHKERRQ(ierr);
  ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);

  hx = 2.50/(PetscReal)Mx; sx = 1.0/(hx*hx);
  hy = 2.50/(PetscReal)My; sy = 1.0/(hy*hy);

  /*
     Scatter ghost points to local vector,using the 2-step process
        DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
     By placing code between these two statements, computations can be
     done while messages are in transition.
  */
  ierr = DMGlobalToLocalBegin(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);

  /*
     Get pointers to vector data
  */
  ierr = DMDAVecGetArrayRead(da,localU,&u);CHKERRQ(ierr);

  /*
     Get local grid boundaries
  */
  ierr = DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);

  stencil[0].k = 0;
  stencil[1].k = 0;
  stencil[2].k = 0;
  stencil[3].k = 0;
  stencil[4].k = 0;
  stencil[5].k = 0;
  rowstencil.k = 0;
  /*
     Compute function over the locally owned part of the grid
  */
  for (j=ys; j<ys+ym; j++) {

    stencil[0].j = j-1;
    stencil[1].j = j+1;
    stencil[2].j = j;
    stencil[3].j = j;
    stencil[4].j = j;
    stencil[5].j = j;
    rowstencil.k = 0; rowstencil.j = j;
    for (i=xs; i<xs+xm; i++) {
      uc = u[j][i].u;
      vc = u[j][i].v;

      /*      uxx       = (-2.0*uc + u[j][i-1].u + u[j][i+1].u)*sx;
      uyy       = (-2.0*uc + u[j-1][i].u + u[j+1][i].u)*sy;

      vxx       = (-2.0*vc + u[j][i-1].v + u[j][i+1].v)*sx;
      vyy       = (-2.0*vc + u[j-1][i].v + u[j+1][i].v)*sy;
       f[j][i].u = appctx->D1*(uxx + uyy) - uc*vc*vc + appctx->gamma*(1.0 - uc);*/

      stencil[0].i = i; stencil[0].c = 0; entries[0] = -appctx->D1*sy;
      stencil[1].i = i; stencil[1].c = 0; entries[1] = -appctx->D1*sy;
      stencil[2].i = i-1; stencil[2].c = 0; entries[2] = -appctx->D1*sx;
      stencil[3].i = i+1; stencil[3].c = 0; entries[3] = -appctx->D1*sx;
      stencil[4].i = i; stencil[4].c = 0; entries[4] = 2.0*appctx->D1*(sx + sy) + vc*vc + appctx->gamma + a;
      stencil[5].i = i; stencil[5].c = 1; entries[5] = 2.0*uc*vc;
      rowstencil.i = i; rowstencil.c = 0;

      ierr = MatSetValuesStencil(A,1,&rowstencil,6,stencil,entries,INSERT_VALUES);CHKERRQ(ierr);
      if (appctx->aijpc) {
        ierr = MatSetValuesStencil(BB,1,&rowstencil,6,stencil,entries,INSERT_VALUES);CHKERRQ(ierr);
      }
      stencil[0].c = 1; entries[0] = -appctx->D2*sy;
      stencil[1].c = 1; entries[1] = -appctx->D2*sy;
      stencil[2].c = 1; entries[2] = -appctx->D2*sx;
      stencil[3].c = 1; entries[3] = -appctx->D2*sx;
      stencil[4].c = 1; entries[4] = 2.0*appctx->D2*(sx + sy) - 2.0*uc*vc + appctx->gamma + appctx->kappa + a;
      stencil[5].c = 0; entries[5] = -vc*vc;
      rowstencil.c = 1;

      ierr = MatSetValuesStencil(A,1,&rowstencil,6,stencil,entries,INSERT_VALUES);CHKERRQ(ierr);
      if (appctx->aijpc) {
        ierr = MatSetValuesStencil(BB,1,&rowstencil,6,stencil,entries,INSERT_VALUES);CHKERRQ(ierr);
      }
      /* f[j][i].v = appctx->D2*(vxx + vyy) + uc*vc*vc - (appctx->gamma + appctx->kappa)*vc; */
    }
  }

  /*
     Restore vectors
  */
  ierr = PetscLogFlops(19.0*xm*ym);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArrayRead(da,localU,&u);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(da,&localU);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  if (appctx->aijpc) {
    ierr = MatAssemblyBegin(BB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(BB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatSetOption(BB,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

/*TEST

   build:
      requires: !complex !single

   test:
      args: -ts_max_steps 10 -ts_monitor -ts_adjoint_monitor -da_grid_x 20 -da_grid_y 20
      output_file: output/ex5adj_1.out

   test:
      suffix: 2
      nsize: 2
      args: -ts_max_steps 10 -ts_dt 10 -ts_monitor -ts_adjoint_monitor -ksp_monitor_short -da_grid_x 20 -da_grid_y 20 -ts_trajectory_dirname Test-dir -ts_trajectory_file_template test-%06D.cp

   test:
      suffix: 3
      nsize: 2
      args: -ts_max_steps 10 -ts_dt 10 -ts_adjoint_monitor_draw_sensi

   test:
      suffix: 4
      nsize: 2
      args: -ts_max_steps 10 -ts_dt 10 -ts_monitor -ts_adjoint_monitor -ksp_monitor_short -da_grid_x 20 -da_grid_y 20 -snes_fd_color
      output_file: output/ex5adj_2.out

   test:
      suffix: 5
      nsize: 2
      args: -ts_max_steps 10 -implicitform 0 -ts_type rk -ts_rk_type 4 -ts_monitor -ts_adjoint_monitor -da_grid_x 20 -da_grid_y 20 -snes_fd_color
      output_file: output/ex5adj_1.out

   test:
      suffix: knl
      args: -ts_max_steps 10 -ts_monitor -ts_adjoint_monitor -ts_trajectory_type memory -ts_trajectory_solution_only 0 -malloc_hbw -ts_trajectory_use_dram 1
      output_file: output/ex5adj_3.out
      requires: knl

   test:
      suffix: sell
      nsize: 4
      args: -forwardonly -ts_max_steps 10 -ts_monitor -snes_monitor_short -dm_mat_type sell -pc_type none
      output_file: output/ex5adj_sell_1.out

   test:
      suffix: aijsell
      nsize: 4
      args: -forwardonly -ts_max_steps 10 -ts_monitor -snes_monitor_short -dm_mat_type aijsell -pc_type none
      output_file: output/ex5adj_sell_1.out

   test:
      suffix: sell2
      nsize: 4
      args: -forwardonly -ts_max_steps 10 -ts_monitor -snes_monitor_short -dm_mat_type sell -pc_type mg -pc_mg_levels 2 -mg_coarse_pc_type sor
      output_file: output/ex5adj_sell_2.out

   test:
      suffix: aijsell2
      nsize: 4
      args: -forwardonly -ts_max_steps 10 -ts_monitor -snes_monitor_short -dm_mat_type aijsell -pc_type mg -pc_mg_levels 2 -mg_coarse_pc_type sor
      output_file: output/ex5adj_sell_2.out

   test:
      suffix: sell3
      nsize: 4
      args: -forwardonly -ts_max_steps 10 -ts_monitor -snes_monitor_short -dm_mat_type sell -pc_type mg -pc_mg_levels 2 -mg_coarse_pc_type bjacobi -mg_levels_pc_type bjacobi
      output_file: output/ex5adj_sell_3.out

   test:
      suffix: sell4
      nsize: 4
      args: -forwardonly -implicitform -ts_max_steps 10 -ts_monitor -snes_monitor_short -dm_mat_type sell -pc_type mg -pc_mg_levels 2 -mg_coarse_pc_type bjacobi -mg_levels_pc_type bjacobi
      output_file: output/ex5adj_sell_4.out

   test:
      suffix: sell5
      nsize: 4
      args: -forwardonly -ts_max_steps 10 -ts_monitor -snes_monitor_short -dm_mat_type sell -aijpc
      output_file: output/ex5adj_sell_5.out

   test:
      suffix: aijsell5
      nsize: 4
      args: -forwardonly -ts_max_steps 10 -ts_monitor -snes_monitor_short -dm_mat_type aijsell
      output_file: output/ex5adj_sell_5.out

   test:
      suffix: sell6
      args: -ts_max_steps 10 -ts_monitor -ts_adjoint_monitor -ts_trajectory_type memory -ts_trajectory_solution_only 0 -dm_mat_type sell -pc_type jacobi
      output_file: output/ex5adj_sell_6.out

   test:
      suffix: gamg1
      args: -pc_type gamg -pc_mg_levels 2 -mg_levels_pc_type jacobi -ksp_monitor_short -ts_max_steps 2 -ts_monitor -ts_adjoint_monitor -ts_trajectory_type memory
      output_file: output/ex5adj_gamg_1.out

   test:
      suffix: gamg2
      args: -pc_type gamg -pc_mg_levels 2 -mg_levels_pc_type jacobi -ksp_monitor_short -ts_max_steps 2 -ts_monitor -ts_adjoint_monitor -ts_trajectory_type memory -ksp_use_explicittranspose
      output_file: output/ex5adj_gamg_2.out
TEST*/