/*
       The Problem:
           Solve the convection-diffusion equation:

             u_t+a*(u_x+u_y)=epsilon*(u_xx+u_yy)
             u=0   at x=0, y=0
             u_x=0 at x=1
             u_y=0 at y=1
             u = exp(-20.0*(pow(x-0.5,2.0)+pow(y-0.5,2.0))) at t=0

       This program tests the routine of computing the Jacobian by the
       finite difference method as well as PETSc.

*/

static char help[] = "Solve the convection-diffusion equation. \n\n";

#include <petscts.h>

typedef struct {
  PetscInt  m;       /* the number of mesh points in x-direction */
  PetscInt  n;       /* the number of mesh points in y-direction */
  PetscReal dx;      /* the grid space in x-direction */
  PetscReal dy;      /* the grid space in y-direction */
  PetscReal a;       /* the convection coefficient    */
  PetscReal epsilon; /* the diffusion coefficient     */
  PetscReal tfinal;
} Data;

extern PetscErrorCode Monitor(TS, PetscInt, PetscReal, Vec, void *);
extern PetscErrorCode Initial(Vec, void *);
extern PetscErrorCode RHSFunction(TS, PetscReal, Vec, Vec, void *);
extern PetscErrorCode RHSJacobian(TS, PetscReal, Vec, Mat, Mat, void *);
extern PetscErrorCode PostStep(TS);

int main(int argc, char **argv)
{
  PetscInt      time_steps = 100, iout, NOUT = 1;
  Vec           global;
  PetscReal     dt, ftime, ftime_original;
  TS            ts;
  PetscViewer   viewfile;
  Mat           J = 0;
  Vec           x;
  Data          data;
  PetscInt      mn;
  PetscBool     flg;
  MatColoring   mc;
  ISColoring    iscoloring;
  MatFDColoring matfdcoloring        = 0;
  PetscBool     fd_jacobian_coloring = PETSC_FALSE;
  SNES          snes;
  KSP           ksp;
  PC            pc;

  PetscFunctionBeginUser;
  PetscCall(PetscInitialize(&argc, &argv, NULL, help));

  /* set data */
  data.m       = 9;
  data.n       = 9;
  data.a       = 1.0;
  data.epsilon = 0.1;
  data.dx      = 1.0 / (data.m + 1.0);
  data.dy      = 1.0 / (data.n + 1.0);
  mn           = (data.m) * (data.n);
  PetscCall(PetscOptionsGetInt(NULL, NULL, "-time", &time_steps, NULL));

  /* set initial conditions */
  PetscCall(VecCreate(PETSC_COMM_WORLD, &global));
  PetscCall(VecSetSizes(global, PETSC_DECIDE, mn));
  PetscCall(VecSetFromOptions(global));
  PetscCall(Initial(global, &data));
  PetscCall(VecDuplicate(global, &x));

  /* create timestep context */
  PetscCall(TSCreate(PETSC_COMM_WORLD, &ts));
  PetscCall(TSMonitorSet(ts, Monitor, &data, NULL));
  PetscCall(TSSetType(ts, TSEULER));
  dt             = 0.1;
  ftime_original = data.tfinal = 1.0;

  PetscCall(TSSetTimeStep(ts, dt));
  PetscCall(TSSetMaxSteps(ts, time_steps));
  PetscCall(TSSetMaxTime(ts, ftime_original));
  PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER));
  PetscCall(TSSetSolution(ts, global));

  /* set user provided RHSFunction and RHSJacobian */
  PetscCall(TSSetRHSFunction(ts, NULL, RHSFunction, &data));
  PetscCall(MatCreate(PETSC_COMM_WORLD, &J));
  PetscCall(MatSetSizes(J, PETSC_DECIDE, PETSC_DECIDE, mn, mn));
  PetscCall(MatSetFromOptions(J));
  PetscCall(MatSeqAIJSetPreallocation(J, 5, NULL));
  PetscCall(MatMPIAIJSetPreallocation(J, 5, NULL, 5, NULL));

  PetscCall(PetscOptionsHasName(NULL, NULL, "-ts_fd", &flg));
  if (!flg) {
    PetscCall(TSSetRHSJacobian(ts, J, J, RHSJacobian, &data));
  } else {
    PetscCall(TSGetSNES(ts, &snes));
    PetscCall(PetscOptionsHasName(NULL, NULL, "-fd_color", &fd_jacobian_coloring));
    if (fd_jacobian_coloring) { /* Use finite differences with coloring */
      /* Get data structure of J */
      PetscBool pc_diagonal;
      PetscCall(PetscOptionsHasName(NULL, NULL, "-pc_diagonal", &pc_diagonal));
      if (pc_diagonal) { /* the preconditioner of J is a diagonal matrix */
        PetscInt    rstart, rend, i;
        PetscScalar zero = 0.0;
        PetscCall(MatGetOwnershipRange(J, &rstart, &rend));
        for (i = rstart; i < rend; i++) PetscCall(MatSetValues(J, 1, &i, 1, &i, &zero, INSERT_VALUES));
        PetscCall(MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY));
        PetscCall(MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY));
      } else {
        /* Fill the structure using the expensive SNESComputeJacobianDefault. Temporarily set up the TS so we can call this function */
        PetscCall(TSSetType(ts, TSBEULER));
        PetscCall(TSSetUp(ts));
        PetscCall(SNESComputeJacobianDefault(snes, x, J, J, ts));
      }

      /* create coloring context */
      PetscCall(MatColoringCreate(J, &mc));
      PetscCall(MatColoringSetType(mc, MATCOLORINGSL));
      PetscCall(MatColoringSetFromOptions(mc));
      PetscCall(MatColoringApply(mc, &iscoloring));
      PetscCall(MatColoringDestroy(&mc));
      PetscCall(MatFDColoringCreate(J, iscoloring, &matfdcoloring));
      PetscCall(MatFDColoringSetFunction(matfdcoloring, (MatFDColoringFn *)SNESTSFormFunction, ts));
      PetscCall(MatFDColoringSetFromOptions(matfdcoloring));
      PetscCall(MatFDColoringSetUp(J, iscoloring, matfdcoloring));
      PetscCall(SNESSetJacobian(snes, J, J, SNESComputeJacobianDefaultColor, matfdcoloring));
      PetscCall(ISColoringDestroy(&iscoloring));
    } else { /* Use finite differences (slow) */
      PetscCall(SNESSetJacobian(snes, J, J, SNESComputeJacobianDefault, NULL));
    }
  }

  /* Pick up a PETSc preconditioner */
  /* one can always set method or preconditioner during the run time */
  PetscCall(TSGetSNES(ts, &snes));
  PetscCall(SNESGetKSP(snes, &ksp));
  PetscCall(KSPGetPC(ksp, &pc));
  PetscCall(PCSetType(pc, PCJACOBI));
  PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER));

  PetscCall(TSSetFromOptions(ts));
  PetscCall(TSSetUp(ts));

  /* Test TSSetPostStep() */
  PetscCall(PetscOptionsHasName(NULL, NULL, "-test_PostStep", &flg));
  if (flg) PetscCall(TSSetPostStep(ts, PostStep));

  PetscCall(PetscOptionsGetInt(NULL, NULL, "-NOUT", &NOUT, NULL));
  for (iout = 1; iout <= NOUT; iout++) {
    PetscCall(TSSetMaxSteps(ts, time_steps));
    PetscCall(TSSetMaxTime(ts, iout * ftime_original / NOUT));
    PetscCall(TSSolve(ts, global));
    PetscCall(TSGetSolveTime(ts, &ftime));
    PetscCall(TSSetTime(ts, ftime));
    PetscCall(TSSetTimeStep(ts, dt));
  }
  /* Interpolate solution at tfinal */
  PetscCall(TSGetSolution(ts, &global));
  PetscCall(TSInterpolate(ts, ftime_original, global));

  PetscCall(PetscOptionsHasName(NULL, NULL, "-matlab_view", &flg));
  if (flg) { /* print solution into a MATLAB file */
    PetscCall(PetscViewerASCIIOpen(PETSC_COMM_WORLD, "out.m", &viewfile));
    PetscCall(PetscViewerPushFormat(viewfile, PETSC_VIEWER_ASCII_MATLAB));
    PetscCall(VecView(global, viewfile));
    PetscCall(PetscViewerPopFormat(viewfile));
    PetscCall(PetscViewerDestroy(&viewfile));
  }

  /* free the memories */
  PetscCall(TSDestroy(&ts));
  PetscCall(VecDestroy(&global));
  PetscCall(VecDestroy(&x));
  PetscCall(MatDestroy(&J));
  if (fd_jacobian_coloring) PetscCall(MatFDColoringDestroy(&matfdcoloring));
  PetscCall(PetscFinalize());
  return 0;
}

/* -------------------------------------------------------------------*/
/* the initial function */
PetscReal f_ini(PetscReal x, PetscReal y)
{
  PetscReal f;

  f = PetscExpReal(-20.0 * (PetscPowRealInt(x - 0.5, 2) + PetscPowRealInt(y - 0.5, 2)));
  return f;
}

PetscErrorCode Initial(Vec global, PetscCtx ctx)
{
  Data        *data = (Data *)ctx;
  PetscInt     m, row, col;
  PetscReal    x, y, dx, dy;
  PetscScalar *localptr;
  PetscInt     i, mybase, myend, locsize;

  PetscFunctionBeginUser;
  /* make the local  copies of parameters */
  m  = data->m;
  dx = data->dx;
  dy = data->dy;

  /* determine starting point of each processor */
  PetscCall(VecGetOwnershipRange(global, &mybase, &myend));
  PetscCall(VecGetLocalSize(global, &locsize));

  /* Initialize the array */
  PetscCall(VecGetArrayWrite(global, &localptr));

  for (i = 0; i < locsize; i++) {
    row         = 1 + (mybase + i) - ((mybase + i) / m) * m;
    col         = (mybase + i) / m + 1;
    x           = dx * row;
    y           = dy * col;
    localptr[i] = f_ini(x, y);
  }

  PetscCall(VecRestoreArrayWrite(global, &localptr));
  PetscFunctionReturn(PETSC_SUCCESS);
}

PetscErrorCode Monitor(TS ts, PetscInt step, PetscReal time, Vec global, PetscCtx ctx)
{
  VecScatter         scatter;
  IS                 from, to;
  PetscInt           i, n, *idx, nsteps, maxsteps;
  Vec                tmp_vec;
  const PetscScalar *tmp;

  PetscFunctionBeginUser;
  PetscCall(TSGetStepNumber(ts, &nsteps));
  /* display output at selected time steps */
  PetscCall(TSGetMaxSteps(ts, &maxsteps));
  if (nsteps % 10 != 0) PetscFunctionReturn(PETSC_SUCCESS);

  /* Get the size of the vector */
  PetscCall(VecGetSize(global, &n));

  /* Set the index sets */
  PetscCall(PetscMalloc1(n, &idx));
  for (i = 0; i < n; i++) idx[i] = i;

  /* Create local sequential vectors */
  PetscCall(VecCreateSeq(PETSC_COMM_SELF, n, &tmp_vec));

  /* Create scatter context */
  PetscCall(ISCreateGeneral(PETSC_COMM_SELF, n, idx, PETSC_COPY_VALUES, &from));
  PetscCall(ISCreateGeneral(PETSC_COMM_SELF, n, idx, PETSC_COPY_VALUES, &to));
  PetscCall(VecScatterCreate(global, from, tmp_vec, to, &scatter));
  PetscCall(VecScatterBegin(scatter, global, tmp_vec, INSERT_VALUES, SCATTER_FORWARD));
  PetscCall(VecScatterEnd(scatter, global, tmp_vec, INSERT_VALUES, SCATTER_FORWARD));

  PetscCall(VecGetArrayRead(tmp_vec, &tmp));
  PetscCall(PetscPrintf(PETSC_COMM_WORLD, "At t[%" PetscInt_FMT "] =%14.2e u= %14.2e at the center \n", nsteps, (double)time, (double)PetscRealPart(tmp[n / 2])));
  PetscCall(VecRestoreArrayRead(tmp_vec, &tmp));

  PetscCall(PetscFree(idx));
  PetscCall(ISDestroy(&from));
  PetscCall(ISDestroy(&to));
  PetscCall(VecScatterDestroy(&scatter));
  PetscCall(VecDestroy(&tmp_vec));
  PetscFunctionReturn(PETSC_SUCCESS);
}

PetscErrorCode RHSJacobian(TS ts, PetscReal t, Vec x, Mat A, Mat BB, void *ptr)
{
  Data       *data = (Data *)ptr;
  PetscScalar v[5];
  PetscInt    idx[5], i, j, row;
  PetscInt    m, n, mn;
  PetscReal   dx, dy, a, epsilon, xc, xl, xr, yl, yr;

  PetscFunctionBeginUser;
  m       = data->m;
  n       = data->n;
  mn      = m * n;
  dx      = data->dx;
  dy      = data->dy;
  a       = data->a;
  epsilon = data->epsilon;

  xc = -2.0 * epsilon * (1.0 / (dx * dx) + 1.0 / (dy * dy));
  xl = 0.5 * a / dx + epsilon / (dx * dx);
  xr = -0.5 * a / dx + epsilon / (dx * dx);
  yl = 0.5 * a / dy + epsilon / (dy * dy);
  yr = -0.5 * a / dy + epsilon / (dy * dy);

  row    = 0;
  v[0]   = xc;
  v[1]   = xr;
  v[2]   = yr;
  idx[0] = 0;
  idx[1] = 2;
  idx[2] = m;
  PetscCall(MatSetValues(A, 1, &row, 3, idx, v, INSERT_VALUES));

  row    = m - 1;
  v[0]   = 2.0 * xl;
  v[1]   = xc;
  v[2]   = yr;
  idx[0] = m - 2;
  idx[1] = m - 1;
  idx[2] = m - 1 + m;
  PetscCall(MatSetValues(A, 1, &row, 3, idx, v, INSERT_VALUES));

  for (i = 1; i < m - 1; i++) {
    row    = i;
    v[0]   = xl;
    v[1]   = xc;
    v[2]   = xr;
    v[3]   = yr;
    idx[0] = i - 1;
    idx[1] = i;
    idx[2] = i + 1;
    idx[3] = i + m;
    PetscCall(MatSetValues(A, 1, &row, 4, idx, v, INSERT_VALUES));
  }

  for (j = 1; j < n - 1; j++) {
    row    = j * m;
    v[0]   = xc;
    v[1]   = xr;
    v[2]   = yl;
    v[3]   = yr;
    idx[0] = j * m;
    idx[1] = j * m;
    idx[2] = j * m - m;
    idx[3] = j * m + m;
    PetscCall(MatSetValues(A, 1, &row, 4, idx, v, INSERT_VALUES));

    row    = j * m + m - 1;
    v[0]   = xc;
    v[1]   = 2.0 * xl;
    v[2]   = yl;
    v[3]   = yr;
    idx[0] = j * m + m - 1;
    idx[1] = j * m + m - 1 - 1;
    idx[2] = j * m + m - 1 - m;
    idx[3] = j * m + m - 1 + m;
    PetscCall(MatSetValues(A, 1, &row, 4, idx, v, INSERT_VALUES));

    for (i = 1; i < m - 1; i++) {
      row    = j * m + i;
      v[0]   = xc;
      v[1]   = xl;
      v[2]   = xr;
      v[3]   = yl;
      v[4]   = yr;
      idx[0] = j * m + i;
      idx[1] = j * m + i - 1;
      idx[2] = j * m + i + 1;
      idx[3] = j * m + i - m;
      idx[4] = j * m + i + m;
      PetscCall(MatSetValues(A, 1, &row, 5, idx, v, INSERT_VALUES));
    }
  }

  row    = mn - m;
  v[0]   = xc;
  v[1]   = xr;
  v[2]   = 2.0 * yl;
  idx[0] = mn - m;
  idx[1] = mn - m + 1;
  idx[2] = mn - m - m;
  PetscCall(MatSetValues(A, 1, &row, 3, idx, v, INSERT_VALUES));

  row    = mn - 1;
  v[0]   = xc;
  v[1]   = 2.0 * xl;
  v[2]   = 2.0 * yl;
  idx[0] = mn - 1;
  idx[1] = mn - 2;
  idx[2] = mn - 1 - m;
  PetscCall(MatSetValues(A, 1, &i, 3, idx, v, INSERT_VALUES));

  for (i = 1; i < m - 1; i++) {
    row    = mn - m + i;
    v[0]   = xl;
    v[1]   = xc;
    v[2]   = xr;
    v[3]   = 2.0 * yl;
    idx[0] = mn - m + i - 1;
    idx[1] = mn - m + i;
    idx[2] = mn - m + i + 1;
    idx[3] = mn - m + i - m;
    PetscCall(MatSetValues(A, 1, &row, 4, idx, v, INSERT_VALUES));
  }

  PetscCall(MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY));
  PetscCall(MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY));
  PetscFunctionReturn(PETSC_SUCCESS);
}

/* globalout = -a*(u_x+u_y) + epsilon*(u_xx+u_yy) */
PetscErrorCode RHSFunction(TS ts, PetscReal t, Vec globalin, Vec globalout, PetscCtx ctx)
{
  Data              *data = (Data *)ctx;
  PetscInt           m, n, mn;
  PetscReal          dx, dy;
  PetscReal          xc, xl, xr, yl, yr;
  PetscReal          a, epsilon;
  PetscScalar       *outptr;
  const PetscScalar *inptr;
  PetscInt           i, j, len;
  IS                 from, to;
  PetscInt          *idx;
  VecScatter         scatter;
  Vec                tmp_in, tmp_out;

  PetscFunctionBeginUser;
  m       = data->m;
  n       = data->n;
  mn      = m * n;
  dx      = data->dx;
  dy      = data->dy;
  a       = data->a;
  epsilon = data->epsilon;

  xc = -2.0 * epsilon * (1.0 / (dx * dx) + 1.0 / (dy * dy));
  xl = 0.5 * a / dx + epsilon / (dx * dx);
  xr = -0.5 * a / dx + epsilon / (dx * dx);
  yl = 0.5 * a / dy + epsilon / (dy * dy);
  yr = -0.5 * a / dy + epsilon / (dy * dy);

  /* Get the length of parallel vector */
  PetscCall(VecGetSize(globalin, &len));

  /* Set the index sets */
  PetscCall(PetscMalloc1(len, &idx));
  for (i = 0; i < len; i++) idx[i] = i;

  /* Create local sequential vectors */
  PetscCall(VecCreateSeq(PETSC_COMM_SELF, len, &tmp_in));
  PetscCall(VecDuplicate(tmp_in, &tmp_out));

  /* Create scatter context */
  PetscCall(ISCreateGeneral(PETSC_COMM_SELF, len, idx, PETSC_COPY_VALUES, &from));
  PetscCall(ISCreateGeneral(PETSC_COMM_SELF, len, idx, PETSC_COPY_VALUES, &to));
  PetscCall(VecScatterCreate(globalin, from, tmp_in, to, &scatter));
  PetscCall(VecScatterBegin(scatter, globalin, tmp_in, INSERT_VALUES, SCATTER_FORWARD));
  PetscCall(VecScatterEnd(scatter, globalin, tmp_in, INSERT_VALUES, SCATTER_FORWARD));
  PetscCall(VecScatterDestroy(&scatter));

  /*Extract income array - include ghost points */
  PetscCall(VecGetArrayRead(tmp_in, &inptr));

  /* Extract outcome array*/
  PetscCall(VecGetArrayWrite(tmp_out, &outptr));

  outptr[0]     = xc * inptr[0] + xr * inptr[1] + yr * inptr[m];
  outptr[m - 1] = 2.0 * xl * inptr[m - 2] + xc * inptr[m - 1] + yr * inptr[m - 1 + m];
  for (i = 1; i < m - 1; i++) outptr[i] = xc * inptr[i] + xl * inptr[i - 1] + xr * inptr[i + 1] + yr * inptr[i + m];

  for (j = 1; j < n - 1; j++) {
    outptr[j * m]         = xc * inptr[j * m] + xr * inptr[j * m + 1] + yl * inptr[j * m - m] + yr * inptr[j * m + m];
    outptr[j * m + m - 1] = xc * inptr[j * m + m - 1] + 2.0 * xl * inptr[j * m + m - 1 - 1] + yl * inptr[j * m + m - 1 - m] + yr * inptr[j * m + m - 1 + m];
    for (i = 1; i < m - 1; i++) outptr[j * m + i] = xc * inptr[j * m + i] + xl * inptr[j * m + i - 1] + xr * inptr[j * m + i + 1] + yl * inptr[j * m + i - m] + yr * inptr[j * m + i + m];
  }

  outptr[mn - m] = xc * inptr[mn - m] + xr * inptr[mn - m + 1] + 2.0 * yl * inptr[mn - m - m];
  outptr[mn - 1] = 2.0 * xl * inptr[mn - 2] + xc * inptr[mn - 1] + 2.0 * yl * inptr[mn - 1 - m];
  for (i = 1; i < m - 1; i++) outptr[mn - m + i] = xc * inptr[mn - m + i] + xl * inptr[mn - m + i - 1] + xr * inptr[mn - m + i + 1] + 2 * yl * inptr[mn - m + i - m];

  PetscCall(VecRestoreArrayRead(tmp_in, &inptr));
  PetscCall(VecRestoreArrayWrite(tmp_out, &outptr));

  PetscCall(VecScatterCreate(tmp_out, from, globalout, to, &scatter));
  PetscCall(VecScatterBegin(scatter, tmp_out, globalout, INSERT_VALUES, SCATTER_FORWARD));
  PetscCall(VecScatterEnd(scatter, tmp_out, globalout, INSERT_VALUES, SCATTER_FORWARD));

  /* Destroy idx and scatter */
  PetscCall(VecDestroy(&tmp_in));
  PetscCall(VecDestroy(&tmp_out));
  PetscCall(ISDestroy(&from));
  PetscCall(ISDestroy(&to));
  PetscCall(VecScatterDestroy(&scatter));

  PetscCall(PetscFree(idx));
  PetscFunctionReturn(PETSC_SUCCESS);
}

PetscErrorCode PostStep(TS ts)
{
  PetscReal t;

  PetscFunctionBeginUser;
  PetscCall(TSGetTime(ts, &t));
  PetscCall(PetscPrintf(PETSC_COMM_SELF, "  PostStep, t: %g\n", (double)t));
  PetscFunctionReturn(PETSC_SUCCESS);
}

/*TEST

    test:
      args: -ts_fd -ts_type beuler
      output_file: output/ex4.out

    test:
      suffix: 2
      args: -ts_fd -ts_type beuler
      nsize: 2
      output_file: output/ex4.out

    test:
      suffix: 3
      args: -ts_fd -ts_type cn

    test:
      suffix: 4
      args: -ts_fd -ts_type cn
      output_file: output/ex4_3.out
      nsize: 2

    test:
      suffix: 5
      args: -ts_type beuler -ts_fd -fd_color -mat_coloring_type sl
      output_file: output/ex4.out

    test:
      suffix: 6
      args: -ts_type beuler -ts_fd -fd_color -mat_coloring_type sl
      output_file: output/ex4.out
      nsize: 2

    test:
      suffix: 7
      requires: !single
      args: -ts_fd -ts_type beuler -test_PostStep -ts_time_step .1

    test:
      suffix: 8
      requires: !single
      args: -ts_type rk -ts_rk_type 5dp -ts_time_step .01 -ts_adapt_type none -ts_view

TEST*/