static char help[] = "Newton method to solve u'' + u^{2} = f, sequentially.\n\
This example employs a user-defined monitoring routine.\n\n";

/*T
   Concepts: SNES^basic uniprocessor example
   Concepts: SNES^setting a user-defined monitoring routine
   Processors: 1
T*/



/*
   Include "petscdraw.h" so that we can use PETSc drawing routines.
   Include "petscsnes.h" so that we can use SNES solvers.  Note that this
   file automatically includes:
     petscsys.h       - base PETSc routines   petscvec.h - vectors
     petscmat.h - matrices
     petscis.h     - index sets            petscksp.h - Krylov subspace methods
     petscviewer.h - viewers               petscpc.h  - preconditioners
     petscksp.h   - linear solvers
*/

#include <petscsnes.h>

/*
   User-defined routines
*/
extern PetscErrorCode FormJacobian(SNES,Vec,Mat,Mat,void*);
extern PetscErrorCode FormFunction(SNES,Vec,Vec,void*);
extern PetscErrorCode FormInitialGuess(Vec);
extern PetscErrorCode Monitor(SNES,PetscInt,PetscReal,void*);

extern PetscErrorCode FormFunction_SNES(SNES snes,Vec x, Vec r,void* ctx){
  FormFunction(snes,x,r,ctx);
  return 0;
}

extern PetscErrorCode FormFunction_MFFD(void*snes_ctx,Vec x, Vec r){
  SNES snes = (SNES) snes_ctx;
  void *ctx;
  SNESGetFunction(snes,NULL,NULL,&ctx);
  FormFunction(snes,x,r,ctx);
  return 0;
}

PETSC_EXTERN PetscErrorCode MatAssemblyEnd_MFFD(Mat,MatAssemblyType);
PETSC_EXTERN PetscErrorCode MatMFFDSetBase_MFFD(Mat,Vec,Vec);
PetscErrorCode MatAssemblyEnd_SNESMF(Mat J,MatAssemblyType mt)
{
  PetscErrorCode ierr;
  SNES           snes;
  Vec            u,f;

  PetscFunctionBegin;
  ierr = MatAssemblyEnd_MFFD(J,mt);CHKERRQ(ierr);
  ierr = MatSNESMFGetSNES(J,&snes);CHKERRQ(ierr);
  ierr = SNESGetSolution(snes,&u);CHKERRQ(ierr);
  ierr = SNESGetFunction(snes,&f,NULL,NULL);CHKERRQ(ierr);
  ierr = MatMFFDSetBase_MFFD(J,u,f);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}


/*
   User-defined context for monitoring
*/
typedef struct {
  PetscViewer viewer;
} MonitorCtx;

int main(int argc,char **argv)
{
  SNES           snes;                   /* SNES context */
  Vec            x,r,F,U;             /* vectors */
  Mat            J;                      /* Jacobian matrix */
  MonitorCtx     monP;                   /* monitoring context */
  PetscErrorCode ierr;
  PetscInt       its,n = 5,i,maxit,maxf;
  PetscMPIInt    size;
  PetscScalar    h,xp,v,none = -1.0;
  PetscReal      abstol,rtol,stol,norm;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  if (size != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"This is a uniprocessor example only!");
  ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
  h    = 1.0/(n-1);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create nonlinear solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

  ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create vector data structures; set function evaluation routine
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  /*
     Note that we form 1 vector from scratch and then duplicate as needed.
  */
  ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
  ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
  ierr = VecSetFromOptions(x);CHKERRQ(ierr);
  ierr = VecDuplicate(x,&r);CHKERRQ(ierr);
  ierr = VecDuplicate(x,&F);CHKERRQ(ierr);
  ierr = VecDuplicate(x,&U);CHKERRQ(ierr);

  /*
     Set function evaluation routine and vector
  */
  ierr = SNESSetFunction(snes,r,FormFunction_SNES,(void*)F);CHKERRQ(ierr);


  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create matrix data structure; set Jacobian evaluation routine
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

  ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
  ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
  ierr = MatSetFromOptions(J);CHKERRQ(ierr);
  ierr = MatSeqAIJSetPreallocation(J,3,NULL);CHKERRQ(ierr);

  /*
     Set Jacobian matrix data structure and default Jacobian evaluation
     routine. User can override with:
     -snes_fd : default finite differencing approximation of Jacobian
     -snes_mf : matrix-free Newton-Krylov method with no preconditioning
                (unless user explicitly sets preconditioner)
     -snes_mf_operator : form preconditioning matrix as set by the user,
                         but use matrix-free approx for Jacobian-vector
                         products within Newton-Krylov method
  */

  ierr = SNESSetJacobian(snes,NULL,J,FormJacobian,NULL);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Customize nonlinear solver; set runtime options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

  /*
     Set an optional user-defined monitoring routine
  */
  ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,0,0,0,400,400,&monP.viewer);CHKERRQ(ierr);
  /*ierr = SNESMonitorSet(snes,Monitor,&monP,0);CHKERRQ(ierr);*/

  /*
     Set names for some vectors to facilitate monitoring (optional)
  */
  ierr = PetscObjectSetName((PetscObject)x,"Approximate Solution");CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject)U,"Exact Solution");CHKERRQ(ierr);

  /*
     Set SNES/KSP/KSP/PC runtime options, e.g.,
         -snes_view -snes_monitor -ksp_type <ksp> -pc_type <pc>
  */
  ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);

  ierr = SNESSetUp(snes);CHKERRQ(ierr);

  Mat Jacobian;

  ierr = SNESGetJacobian(snes,&Jacobian,NULL,NULL,NULL);CHKERRQ(ierr);

  ierr = MatMFFDSetFunction(Jacobian,FormFunction_MFFD,(void*)snes);CHKERRQ(ierr);
  ierr = MatShellSetOperation(Jacobian,MATOP_ASSEMBLY_END,(void (*)(void))MatAssemblyEnd_SNESMF);CHKERRQ(ierr);
                              
  /*
     Print parameters used for convergence testing (optional) ... just
     to demonstrate this routine; this information is also printed with
     the option -snes_view
  */
  ierr = SNESGetTolerances(snes,&abstol,&rtol,&stol,&maxit,&maxf);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"atol=%g, rtol=%g, stol=%g, maxit=%D, maxf=%D\n",(double)abstol,(double)rtol,(double)stol,maxit,maxf);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize application:
     Store right-hand-side of PDE and exact solution
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

  xp = 0.0;
  for (i=0; i<n; i++) {
    v    = 6.0*xp + PetscPowScalar(xp+1.e-12,6.0); /* +1.e-12 is to prevent 0^6 */
    ierr = VecSetValues(F,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
    v    = xp*xp*xp;
    ierr = VecSetValues(U,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
    xp  += h;
  }

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Evaluate initial guess; then solve nonlinear system
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  /*
     Note: The user should initialize the vector, x, with the initial guess
     for the nonlinear solver prior to calling SNESSolve().  In particular,
     to employ an initial guess of zero, the user should explicitly set
     this vector to zero by calling VecSet().
  */
  ierr = FormInitialGuess(x);CHKERRQ(ierr);
  ierr = SNESSolve(snes,NULL,x);CHKERRQ(ierr);
  ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"number of SNES iterations = %D\n\n",its);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Check solution and clean up
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

  /*
     Check the error
  */
  ierr = VecAXPY(x,none,U);CHKERRQ(ierr);
  ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of error %g, Iterations %D\n",(double)norm,its);CHKERRQ(ierr);


  /*
     Free work space.  All PETSc objects should be destroyed when they
     are no longer needed.
  */
  ierr = VecDestroy(&x);CHKERRQ(ierr);  ierr = VecDestroy(&r);CHKERRQ(ierr);
  ierr = VecDestroy(&U);CHKERRQ(ierr);  ierr = VecDestroy(&F);CHKERRQ(ierr);
  ierr = MatDestroy(&J);CHKERRQ(ierr);  ierr = SNESDestroy(&snes);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&monP.viewer);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
/* ------------------------------------------------------------------- */
/*
   FormInitialGuess - Computes initial guess.

   Input/Output Parameter:
.  x - the solution vector
*/
PetscErrorCode FormInitialGuess(Vec x)
{
  PetscErrorCode ierr;
  PetscScalar    pfive = .50;
  ierr = VecSet(x,pfive);CHKERRQ(ierr);
  return 0;
}
/* ------------------------------------------------------------------- */
/*
   FormFunction - Evaluates nonlinear function, F(x).

   Input Parameters:
.  snes - the SNES context
.  x - input vector
.  ctx - optional user-defined context, as set by SNESSetFunction()

   Output Parameter:
.  f - function vector

   Note:
   The user-defined context can contain any application-specific data
   needed for the function evaluation (such as various parameters, work
   vectors, and grid information).  In this program the context is just
   a vector containing the right-hand-side of the discretized PDE.
 */

PetscErrorCode FormFunction(SNES snes,Vec x,Vec f,void *ctx)
{
  Vec               g = (Vec)ctx;
  const PetscScalar *xx,*gg;
  PetscScalar       *ff,d;
  PetscErrorCode    ierr;
  PetscInt          i,n;

  ierr = PetscPrintf(PETSC_COMM_WORLD," FormFunction is called \n");CHKERRQ(ierr);

  /*
     Get pointers to vector data.
       - For default PETSc vectors, VecGetArray() returns a pointer to
         the data array.  Otherwise, the routine is implementation dependent.
       - You MUST call VecRestoreArray() when you no longer need access to
         the array.
  */
  ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr);
  ierr = VecGetArray(f,&ff);CHKERRQ(ierr);
  ierr = VecGetArrayRead(g,&gg);CHKERRQ(ierr);

  /*
     Compute function
  */
  ierr  = VecGetSize(x,&n);CHKERRQ(ierr);
  d     = (PetscReal)(n - 1); d = d*d;
  ff[0] = xx[0];
  for (i=1; i<n-1; i++) ff[i] = d*(xx[i-1] - 2.0*xx[i] + xx[i+1]) + xx[i]*xx[i] - gg[i];
  ff[n-1] = xx[n-1] - 1.0;

  /*
     Restore vectors
  */
  ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr);
  ierr = VecRestoreArray(f,&ff);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(g,&gg);CHKERRQ(ierr);
  return 0;
}
/* ------------------------------------------------------------------- */
/*
   FormJacobian - Evaluates Jacobian matrix.

   Input Parameters:
.  snes - the SNES context
.  x - input vector
.  dummy - optional user-defined context (not used here)

   Output Parameters:
.  jac - Jacobian matrix
.  B - optionally different preconditioning matrix

*/

PetscErrorCode FormJacobian(SNES snes,Vec x,Mat jac,Mat B,void *dummy)
{
  const PetscScalar *xx;
  PetscScalar       A[3],d;
  PetscErrorCode    ierr;
  PetscInt          i,n,j[3];

  /*
     Get pointer to vector data
  */
  ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr);

  /*
     Compute Jacobian entries and insert into matrix.
      - Note that in this case we set all elements for a particular
        row at once.
  */
  ierr = VecGetSize(x,&n);CHKERRQ(ierr);
  d    = (PetscReal)(n - 1); d = d*d;

  /*
     Interior grid points
  */
  for (i=1; i<n-1; i++) {
    j[0] = i - 1; j[1] = i; j[2] = i + 1;
    A[0] = A[2] = d; A[1] = -2.0*d + 2.0*xx[i];
    ierr = MatSetValues(B,1,&i,3,j,A,INSERT_VALUES);CHKERRQ(ierr);
  }

  /*
     Boundary points
  */
  i = 0;   A[0] = 1.0;

  ierr = MatSetValues(B,1,&i,1,&i,A,INSERT_VALUES);CHKERRQ(ierr);

  i = n-1; A[0] = 1.0;

  ierr = MatSetValues(B,1,&i,1,&i,A,INSERT_VALUES);CHKERRQ(ierr);

  /*
     Restore vector
  */
  ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr);

  /*
     Assemble matrix
  */
  ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  if (jac != B) {
    ierr = MatAssemblyBegin(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  }
  return 0;
}
/* ------------------------------------------------------------------- */
/*
   Monitor - User-defined monitoring routine that views the
   current iterate with an x-window plot.

   Input Parameters:
   snes - the SNES context
   its - iteration number
   norm - 2-norm function value (may be estimated)
   ctx - optional user-defined context for private data for the
         monitor routine, as set by SNESMonitorSet()

   Note:
   See the manpage for PetscViewerDrawOpen() for useful runtime options,
   such as -nox to deactivate all x-window output.
 */
PetscErrorCode Monitor(SNES snes,PetscInt its,PetscReal fnorm,void *ctx)
{
  PetscErrorCode ierr;
  MonitorCtx     *monP = (MonitorCtx*) ctx;
  Vec            x;

  ierr = PetscPrintf(PETSC_COMM_WORLD,"iter = %D, SNES Function norm %g\n",its,(double)fnorm);CHKERRQ(ierr);
  ierr = SNESGetSolution(snes,&x);CHKERRQ(ierr);
  /*ierr = VecView(x,monP->viewer);CHKERRQ(ierr);*/
  return 0;
}


/*TEST

   test:
      args: -nox -snes_monitor_cancel -snes_monitor_short -snes_view -pc_type jacobi -ksp_gmres_cgs_refinement_type refine_always

   test:
      suffix: 2
      args: -nox -snes_monitor_cancel -snes_monitor_short -snes_type newtontr -snes_view
      requires: !single

   test:
      suffix: 3
      args: -nox -snes_monitor_cancel -snes_monitor_short -malloc no -snes_view -pc_type jacobi -ksp_gmres_cgs_refinement_type refine_always

TEST*/