static char help[] = "Pseudotransient continuation to solve a many-variable system that comes from the 2 variable Rosenbrock function + trivial.\n\n";

#include <petscts.h>

static PetscErrorCode FormIJacobian(TS, PetscReal, Vec, Vec, PetscReal, Mat, Mat, void *);
static PetscErrorCode FormIFunction(TS, PetscReal, Vec, Vec, Vec, void *);
static PetscErrorCode MonitorObjective(TS, PetscInt, PetscReal, Vec, void *);

typedef struct {
  PetscInt  n;
  PetscBool monitor_short;
} Ctx;

int main(int argc, char **argv)
{
  TS           ts; /* time integration context */
  Vec          X;  /* solution, residual vectors */
  Mat          J;  /* Jacobian matrix */
  PetscScalar *x;
  PetscReal    ftime;
  PetscInt     i, steps, nits, lits;
  PetscBool    view_final;
  Ctx          ctx;

  PetscFunctionBeginUser;
  PetscCall(PetscInitialize(&argc, &argv, NULL, help));
  ctx.n = 3;
  PetscCall(PetscOptionsGetInt(NULL, NULL, "-n", &ctx.n, NULL));
  PetscCheck(ctx.n >= 2, PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "The dimension specified with -n must be at least 2");

  view_final = PETSC_FALSE;
  PetscCall(PetscOptionsGetBool(NULL, NULL, "-view_final", &view_final, NULL));

  ctx.monitor_short = PETSC_FALSE;
  PetscCall(PetscOptionsGetBool(NULL, NULL, "-monitor_short", &ctx.monitor_short, NULL));

  /*
     Create Jacobian matrix data structure and state vector
  */
  PetscCall(MatCreate(PETSC_COMM_WORLD, &J));
  PetscCall(MatSetSizes(J, PETSC_DECIDE, PETSC_DECIDE, ctx.n, ctx.n));
  PetscCall(MatSetFromOptions(J));
  PetscCall(MatSetUp(J));
  PetscCall(MatCreateVecs(J, &X, NULL));

  /* Create time integration context */
  PetscCall(TSCreate(PETSC_COMM_WORLD, &ts));
  PetscCall(TSSetType(ts, TSPSEUDO));
  PetscCall(TSSetIFunction(ts, NULL, FormIFunction, &ctx));
  PetscCall(TSSetIJacobian(ts, J, J, FormIJacobian, &ctx));
  PetscCall(TSSetMaxSteps(ts, 1000));
  PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER));
  PetscCall(TSSetTimeStep(ts, 1e-3));
  PetscCall(TSMonitorSet(ts, MonitorObjective, &ctx, NULL));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Customize time integrator; set runtime options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(TSSetFromOptions(ts));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Evaluate initial guess; then solve nonlinear system
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(VecSet(X, 0.0));
  PetscCall(VecGetArray(X, &x));
#if 1
  x[0] = 5.;
  x[1] = -5.;
  for (i = 2; i < ctx.n; i++) x[i] = 5.;
#else
  x[0] = 1.0;
  x[1] = 15.0;
  for (i = 2; i < ctx.n; i++) x[i] = 10.0;
#endif
  PetscCall(VecRestoreArray(X, &x));

  PetscCall(TSSolve(ts, X));
  PetscCall(TSGetSolveTime(ts, &ftime));
  PetscCall(TSGetStepNumber(ts, &steps));
  PetscCall(TSGetSNESIterations(ts, &nits));
  PetscCall(TSGetKSPIterations(ts, &lits));
  PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Time integrator took (%" PetscInt_FMT ",%" PetscInt_FMT ",%" PetscInt_FMT ") iterations to reach final time %g\n", steps, nits, lits, (double)ftime));
  if (view_final) PetscCall(VecView(X, PETSC_VIEWER_STDOUT_WORLD));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.  All PETSc objects should be destroyed when they
     are no longer needed.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

  PetscCall(VecDestroy(&X));
  PetscCall(MatDestroy(&J));
  PetscCall(TSDestroy(&ts));
  PetscCall(PetscFinalize());
  return 0;
}

static PetscErrorCode MonitorObjective(TS ts, PetscInt step, PetscReal t, Vec X, void *ictx)
{
  Ctx               *ctx = (Ctx *)ictx;
  const PetscScalar *x;
  PetscScalar        f;
  PetscReal          dt, gnorm;
  PetscInt           i, snesit, linit;
  SNES               snes;
  Vec                Xdot, F;

  PetscFunctionBeginUser;
  /* Compute objective functional */
  PetscCall(VecGetArrayRead(X, &x));
  f = 0;
  for (i = 0; i < ctx->n - 1; i++) f += PetscSqr(1. - x[i]) + 100. * PetscSqr(x[i + 1] - PetscSqr(x[i]));
  PetscCall(VecRestoreArrayRead(X, &x));

  /* Compute norm of gradient */
  PetscCall(VecDuplicate(X, &Xdot));
  PetscCall(VecDuplicate(X, &F));
  PetscCall(VecZeroEntries(Xdot));
  PetscCall(FormIFunction(ts, t, X, Xdot, F, ictx));
  PetscCall(VecNorm(F, NORM_2, &gnorm));
  PetscCall(VecDestroy(&Xdot));
  PetscCall(VecDestroy(&F));

  PetscCall(TSGetTimeStep(ts, &dt));
  PetscCall(TSGetSNES(ts, &snes));
  PetscCall(SNESGetIterationNumber(snes, &snesit));
  PetscCall(SNESGetLinearSolveIterations(snes, &linit));
  PetscCall(PetscPrintf(PETSC_COMM_WORLD, ctx->monitor_short ? "%3" PetscInt_FMT " t=%10.1e  dt=%10.1e  f=%10.1e  df=%10.1e  it=(%2" PetscInt_FMT ",%3" PetscInt_FMT ")\n" : "%3" PetscInt_FMT " t=%10.4e  dt=%10.4e  f=%10.4e  df=%10.4e  it=(%2" PetscInt_FMT ",%3" PetscInt_FMT ")\n", step, (double)t, (double)dt, (double)PetscRealPart(f), (double)gnorm, snesit, linit));
  PetscFunctionReturn(PETSC_SUCCESS);
}

/* ------------------------------------------------------------------- */
/*
   FormIFunction - Evaluates nonlinear function, F(X,Xdot) = Xdot + grad(objective(X))

   Input Parameters:
+  ts   - the TS context
.  t - time
.  X    - input vector
.  Xdot - time derivative
-  ctx  - optional user-defined context

   Output Parameter:
.  F - function vector
 */
static PetscErrorCode FormIFunction(TS ts, PetscReal t, Vec X, Vec Xdot, Vec F, void *ictx)
{
  const PetscScalar *x;
  PetscScalar       *f;
  PetscInt           i;
  Ctx               *ctx = (Ctx *)ictx;

  PetscFunctionBeginUser;
  /*
    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.
  */
  PetscCall(VecGetArrayRead(X, &x));
  PetscCall(VecZeroEntries(F));
  PetscCall(VecGetArray(F, &f));

  /* Compute gradient of objective */
  for (i = 0; i < ctx->n - 1; i++) {
    PetscScalar a, a0, a1;
    a  = x[i + 1] - PetscSqr(x[i]);
    a0 = -2. * x[i];
    a1 = 1.;
    f[i] += -2. * (1. - x[i]) + 200. * a * a0;
    f[i + 1] += 200. * a * a1;
  }
  /* Restore vectors */
  PetscCall(VecRestoreArrayRead(X, &x));
  PetscCall(VecRestoreArray(F, &f));
  PetscCall(VecAXPY(F, 1.0, Xdot));
  PetscFunctionReturn(PETSC_SUCCESS);
}
/* ------------------------------------------------------------------- */
/*
   FormIJacobian - Evaluates Jacobian matrix.

   Input Parameters:
+  ts - the TS context
.  t - pseudo-time
.  X - input vector
.  Xdot - time derivative
.  shift - multiplier for mass matrix
.  dummy - user-defined context

   Output Parameters:
.  J - Jacobian matrix
.  B - optionally different preconditioning matrix
.  flag - flag indicating matrix structure
*/
static PetscErrorCode FormIJacobian(TS ts, PetscReal t, Vec X, Vec Xdot, PetscReal shift, Mat J, Mat B, void *ictx)
{
  const PetscScalar *x;
  PetscInt           i;
  Ctx               *ctx = (Ctx *)ictx;

  PetscFunctionBeginUser;
  PetscCall(MatZeroEntries(B));
  /*
     Get pointer to vector data
  */
  PetscCall(VecGetArrayRead(X, &x));

  /*
     Compute Jacobian entries and insert into matrix.
  */
  for (i = 0; i < ctx->n - 1; i++) {
    PetscInt    rowcol[2];
    PetscScalar v[2][2], a, a0, a1, a00, a01, a10, a11;
    rowcol[0] = i;
    rowcol[1] = i + 1;
    a         = x[i + 1] - PetscSqr(x[i]);
    a0        = -2. * x[i];
    a00       = -2.;
    a01       = 0.;
    a1        = 1.;
    a10       = 0.;
    a11       = 0.;
    v[0][0]   = 2. + 200. * (a * a00 + a0 * a0);
    v[0][1]   = 200. * (a * a01 + a1 * a0);
    v[1][0]   = 200. * (a * a10 + a0 * a1);
    v[1][1]   = 200. * (a * a11 + a1 * a1);
    PetscCall(MatSetValues(B, 2, rowcol, 2, rowcol, &v[0][0], ADD_VALUES));
  }
  for (i = 0; i < ctx->n; i++) PetscCall(MatSetValue(B, i, i, (PetscScalar)shift, ADD_VALUES));

  PetscCall(VecRestoreArrayRead(X, &x));

  /*
     Assemble matrix
  */
  PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
  PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
  if (J != B) {
    PetscCall(MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY));
    PetscCall(MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY));
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

/*TEST

    test:
      requires: !single

    test:
      args: -pc_type lu -ts_dt 1e-5 -ts_max_time 1e5 -n 50 -monitor_short -snes_max_it 5 -snes_type newtonls -ts_max_snes_failures unlimited
      requires: !single
      suffix: 2

TEST*/
