static char help[] = "Solves the van der Pol equation and demonstrate IMEX.\n\
Input parameters include:\n\
      -mu : stiffness parameter\n\n";

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

   This program solves the van der Pol equation
       y'' - \mu ((1-y^2)*y' - y) = 0        (1)
   on the domain 0 <= x <= 1, with the boundary conditions
       y(0) = 2, y'(0) = - 2/3 +10/(81*\mu) - 292/(2187*\mu^2),
   This is a nonlinear equation. The well prepared initial condition gives errors that are not dominated by the first few steps of the method when \mu is large.

   Notes:
   This code demonstrates the TS solver interface to two variants of
   linear problems, u_t = f(u,t), namely turning (1) into a system of
   first order differential equations,

   [ y' ] = [          z            ]
   [ z' ]   [ \mu ((1 - y^2) z - y) ]

   which then we can write as a vector equation

   [ u_1' ] = [             u_2           ]  (2)
   [ u_2' ]   [ \mu (1 - u_1^2) u_2 - u_1 ]

   which is now in the desired form of u_t = f(u,t). One way that we
   can split f(u,t) in (2) is to split by component,

   [ u_1' ] = [ u_2 ] + [            0                ]
   [ u_2' ]   [  0  ]   [ \mu ((1 - u_1^2) u_2 - u_1) ]

   where

   [ G(u,t) ] = [ u_2 ]
                [  0  ]

   and

   [ F(u',u,t) ] = [ u_1' ] - [            0                ]
                   [ u_2' ]   [ \mu ((1 - u_1^2) u_2 - u_1) ]

   Using the definition of the Jacobian of F (from the PETSc user manual),
   in the equation F(u',u,t) = G(u,t),

              dF   dF
   J(F) = a * -- - --
              du'  du

   where d is the partial derivative. In this example,

   dF   [ 1 ; 0 ]
   -- = [       ]
   du'  [ 0 ; 1 ]

   dF   [       0             ;         0        ]
   -- = [                                        ]
   du   [ -\mu (2*u_1*u_2 + 1);  \mu (1 - u_1^2) ]

   Hence,

          [      a             ;          0          ]
   J(F) = [                                          ]
          [ \mu (2*u_1*u_2 + 1); a - \mu (1 - u_1^2) ]

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

#include <petscts.h>

typedef struct _n_User *User;
struct _n_User {
  PetscReal mu;
  PetscBool imex;
  PetscReal next_output;
};

/*
   User-defined routines
*/
static PetscErrorCode RHSFunction(TS ts, PetscReal t, Vec X, Vec F, PetscCtx ctx)
{
  User               user = (User)ctx;
  PetscScalar       *f;
  const PetscScalar *x;

  PetscFunctionBeginUser;
  PetscCall(VecGetArrayRead(X, &x));
  PetscCall(VecGetArray(F, &f));
  f[0] = (user->imex ? x[1] : 0);
  f[1] = 0.0;
  PetscCall(VecRestoreArrayRead(X, &x));
  PetscCall(VecRestoreArray(F, &f));
  PetscFunctionReturn(PETSC_SUCCESS);
}

static PetscErrorCode IFunction(TS ts, PetscReal t, Vec X, Vec Xdot, Vec F, PetscCtx ctx)
{
  User               user = (User)ctx;
  const PetscScalar *x, *xdot;
  PetscScalar       *f;

  PetscFunctionBeginUser;
  PetscCall(VecGetArrayRead(X, &x));
  PetscCall(VecGetArrayRead(Xdot, &xdot));
  PetscCall(VecGetArray(F, &f));
  f[0] = xdot[0] + (user->imex ? 0 : x[1]);
  f[1] = xdot[1] - user->mu * ((1. - x[0] * x[0]) * x[1] - x[0]);
  PetscCall(VecRestoreArrayRead(X, &x));
  PetscCall(VecRestoreArrayRead(Xdot, &xdot));
  PetscCall(VecRestoreArray(F, &f));
  PetscFunctionReturn(PETSC_SUCCESS);
}

static PetscErrorCode IJacobian(TS ts, PetscReal t, Vec X, Vec Xdot, PetscReal a, Mat A, Mat B, PetscCtx ctx)
{
  User               user     = (User)ctx;
  PetscReal          mu       = user->mu;
  PetscInt           rowcol[] = {0, 1};
  const PetscScalar *x;
  PetscScalar        J[2][2];

  PetscFunctionBeginUser;
  PetscCall(VecGetArrayRead(X, &x));
  J[0][0] = a;
  J[0][1] = (user->imex ? 0 : 1.);
  J[1][0] = mu * (2. * x[0] * x[1] + 1.);
  J[1][1] = a - mu * (1. - x[0] * x[0]);
  PetscCall(MatSetValues(B, 2, rowcol, 2, rowcol, &J[0][0], INSERT_VALUES));
  PetscCall(VecRestoreArrayRead(X, &x));

  PetscCall(MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY));
  PetscCall(MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY));
  if (A != B) {
    PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
    PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

static PetscErrorCode RegisterMyARK2(void)
{
  PetscFunctionBeginUser;
  {
    const PetscReal A[3][3] =
      {
        {0,                      0,    0},
        {0.41421356237309504880, 0,    0},
        {0.75,                   0.25, 0}
    },
                    At[3][3] = {{0, 0, 0}, {0.12132034355964257320, 0.29289321881345247560, 0}, {0.20710678118654752440, 0.50000000000000000000, 0.29289321881345247560}}, *bembedt = NULL, *bembed = NULL;
    PetscCall(TSARKIMEXRegister("myark2", 2, 3, &At[0][0], NULL, NULL, &A[0][0], NULL, NULL, bembedt, bembed, 0, NULL, NULL));
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

/* Monitor timesteps and use interpolation to output at integer multiples of 0.1 */
static PetscErrorCode Monitor(TS ts, PetscInt step, PetscReal t, Vec X, PetscCtx ctx)
{
  const PetscScalar *x;
  PetscReal          tfinal, dt;
  User               user = (User)ctx;
  Vec                interpolatedX;

  PetscFunctionBeginUser;
  PetscCall(TSGetTimeStep(ts, &dt));
  PetscCall(TSGetMaxTime(ts, &tfinal));

  while (user->next_output <= t && user->next_output <= tfinal) {
    PetscCall(VecDuplicate(X, &interpolatedX));
    PetscCall(TSInterpolate(ts, user->next_output, interpolatedX));
    PetscCall(VecGetArrayRead(interpolatedX, &x));
    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "[%.1f] %" PetscInt_FMT " TS %.6f (dt = %.6f) X % 12.6e % 12.6e\n", (double)user->next_output, step, (double)t, (double)dt, (double)PetscRealPart(x[0]), (double)PetscRealPart(x[1])));
    PetscCall(VecRestoreArrayRead(interpolatedX, &x));
    PetscCall(VecDestroy(&interpolatedX));

    user->next_output += 0.1;
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

int main(int argc, char **argv)
{
  TS             ts; /* nonlinear solver */
  Vec            x;  /* solution, residual vectors */
  Mat            A;  /* Jacobian matrix */
  PetscInt       steps;
  PetscReal      ftime   = 0.5;
  PetscBool      monitor = PETSC_FALSE;
  PetscScalar   *x_ptr;
  PetscMPIInt    size;
  struct _n_User user;

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize program
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscFunctionBeginUser;
  PetscCall(PetscInitialize(&argc, &argv, NULL, help));
  PetscCallMPI(MPI_Comm_size(PETSC_COMM_WORLD, &size));
  PetscCheck(size == 1, PETSC_COMM_WORLD, PETSC_ERR_WRONG_MPI_SIZE, "This is a uniprocessor example only!");

  PetscCall(RegisterMyARK2());

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Set runtime options
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  user.mu          = 1000.0;
  user.imex        = PETSC_TRUE;
  user.next_output = 0.0;

  PetscCall(PetscOptionsGetReal(NULL, NULL, "-mu", &user.mu, NULL));
  PetscCall(PetscOptionsGetBool(NULL, NULL, "-imex", &user.imex, NULL));
  PetscCall(PetscOptionsGetBool(NULL, NULL, "-monitor", &monitor, NULL));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Create necessary matrix and vectors, solve same ODE on every process
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(MatCreate(PETSC_COMM_WORLD, &A));
  PetscCall(MatSetSizes(A, PETSC_DECIDE, PETSC_DECIDE, 2, 2));
  PetscCall(MatSetFromOptions(A));
  PetscCall(MatSetUp(A));
  PetscCall(MatCreateVecs(A, &x, NULL));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(TSCreate(PETSC_COMM_WORLD, &ts));
  PetscCall(TSSetType(ts, TSBEULER));
  PetscCall(TSSetRHSFunction(ts, NULL, RHSFunction, &user));
  PetscCall(TSSetIFunction(ts, NULL, IFunction, &user));
  PetscCall(TSSetIJacobian(ts, A, A, IJacobian, &user));
  PetscCall(TSSetMaxTime(ts, ftime));
  PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER));
  if (monitor) PetscCall(TSMonitorSet(ts, Monitor, &user, NULL));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(VecGetArray(x, &x_ptr));
  x_ptr[0] = 2.0;
  x_ptr[1] = -2.0 / 3.0 + 10.0 / (81.0 * user.mu) - 292.0 / (2187.0 * user.mu * user.mu);
  PetscCall(VecRestoreArray(x, &x_ptr));
  PetscCall(TSSetTimeStep(ts, 0.01));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set runtime options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(TSSetFromOptions(ts));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve nonlinear system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(TSSolve(ts, x));
  PetscCall(TSGetSolveTime(ts, &ftime));
  PetscCall(TSGetStepNumber(ts, &steps));
  PetscCall(PetscPrintf(PETSC_COMM_WORLD, "mu %g, steps %" PetscInt_FMT ", ftime %g\n", (double)user.mu, steps, (double)ftime));
  PetscCall(VecView(x, PETSC_VIEWER_STDOUT_WORLD));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.  All PETSc objects should be destroyed when they
     are no longer needed.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(MatDestroy(&A));
  PetscCall(VecDestroy(&x));
  PetscCall(TSDestroy(&ts));

  PetscCall(PetscFinalize());
  return 0;
}

/*TEST

    test:
      args: -ts_type arkimex -ts_arkimex_type myark2 -ts_adapt_type none
      requires: !single

TEST*/
