snes/tutorials/ex30.c

static const char help[] = "Steady-state 2D subduction flow, pressure and temperature solver.\n\
       The flow is driven by the subducting slab.\n\
---------------------------------ex30 help---------------------------------\n\
  -OPTION <DEFAULT> = (UNITS) DESCRIPTION.\n\n\
  -width <320> = (km) width of domain.\n\
  -depth <300> = (km) depth of domain.\n\
  -slab_dip <45> = (degrees) dip angle of the slab (determines the grid aspect ratio).\n\
  -lid_depth <35> = (km) depth of the static conductive lid.\n\
  -fault_depth <35> = (km) depth of slab-wedge mechanical coupling\n\
     (fault dept >= lid depth).\n\
\n\
  -ni <82> = grid cells in x-direction. (nj adjusts to accommodate\n\
      the slab dip & depth). DO NOT USE -da_grid_x option!!!\n\
  -ivisc <3> = rheology option.\n\
      0 --- constant viscosity.\n\
      1 --- olivine diffusion creep rheology (T&P-dependent, newtonian).\n\
      2 --- olivine dislocation creep rheology (T&P-dependent, non-newtonian).\n\
      3 --- Full mantle rheology, combination of 1 & 2.\n\
\n\
  -slab_velocity <5> = (cm/year) convergence rate of slab into subduction zone.\n\
  -slab_age <50> = (million yrs) age of slab for thermal profile boundary condition.\n\
  -lid_age <50> = (million yrs) age of lid for thermal profile boundary condition.\n\
\n\
  FOR OTHER PARAMETER OPTIONS AND THEIR DEFAULT VALUES, see SetParams() in ex30.c.\n\
---------------------------------ex30 help---------------------------------\n";

/*F-----------------------------------------------------------------------

    This PETSc 2.2.0 example by Richard F. Katz
    http://www.ldeo.columbia.edu/~katz/

    The problem is modeled by the partial differential equation system

\begin{eqnarray}
         -\nabla P + \nabla \cdot [\eta (\nabla v + \nabla v^T)] & = & 0  \\
                                           \nabla \cdot v & = & 0   \\
                    dT/dt + \nabla \cdot (vT) - 1/Pe \triangle^2(T) & = & 0  \\
\end{eqnarray}

 \begin{eqnarray}
        \eta(T,Eps\_dot) &  = & \hbox{constant                        }    \hbox{if ivisc} ==0  \\
                      &  = & \hbox{diffusion creep (T,P-dependent)    }     \hbox{if ivisc} ==1  \\
                      &  = & \hbox{dislocation creep (T,P,v-dependent)}  \hbox{if ivisc} ==2  \\
                      &  = & \hbox{mantle viscosity (difn and disl)   }  \hbox{if ivisc} ==3
\end{eqnarray}

    which is uniformly discretized on a staggered mesh:
                      -------$w_{ij}$------
                  $u_{i-1j}$    $P,T_{ij}$   $u_{ij}$
                      ------$w_{ij-1}$-----

  ------------------------------------------------------------------------F*/

#include <petscsnes.h>
#include <petscdm.h>
#include <petscdmda.h>

#define VISC_CONST   0
#define VISC_DIFN    1
#define VISC_DISL    2
#define VISC_FULL    3
#define CELL_CENTER  0
#define CELL_CORNER  1
#define BC_ANALYTIC  0
#define BC_NOSTRESS  1
#define BC_EXPERMNT  2
#define ADVECT_FV    0
#define ADVECT_FROMM 1
#define PLATE_SLAB   0
#define PLATE_LID    1
#define EPS_ZERO     0.00000001

typedef struct { /* holds the variables to be solved for */
  PetscScalar u, w, p, T;
} Field;

typedef struct { /* parameters needed to compute viscosity */
  PetscReal A, n, Estar, Vstar;
} ViscParam;

typedef struct { /* physical and miscelaneous parameters */
  PetscReal width, depth, scaled_width, scaled_depth, peclet, potentialT;
  PetscReal slab_dip, slab_age, slab_velocity, kappa, z_scale;
  PetscReal c, d, sb, cb, skt, visc_cutoff, lid_age, eta0, continuation;
  PetscReal L, V, lid_depth, fault_depth;
  ViscParam diffusion, dislocation;
  PetscInt  ivisc, adv_scheme, ibound, output_ivisc;
  PetscBool quiet, param_test, output_to_file, pv_analytic;
  PetscBool interrupted, stop_solve, toggle_kspmon, kspmon;
  char      filename[PETSC_MAX_PATH_LEN];
} Parameter;

typedef struct { /* grid parameters */
  DMBoundaryType  bx, by;
  DMDAStencilType stencil;
  PetscInt        corner, ni, nj, jlid, jfault, inose;
  PetscInt        dof, stencil_width, mglevels;
  PetscReal       dx, dz;
} GridInfo;

typedef struct { /* application context */
  Vec        x, Xguess;
  Parameter *param;
  GridInfo  *grid;
} AppCtx;

/* Callback functions (static interface) */
extern PetscErrorCode FormFunctionLocal(DMDALocalInfo *, Field **, Field **, void *);

/* Main routines */
extern PetscErrorCode SetParams(Parameter *, GridInfo *);
extern PetscErrorCode ReportParams(Parameter *, GridInfo *);
extern PetscErrorCode Initialize(DM);
extern PetscErrorCode UpdateSolution(SNES, AppCtx *, PetscInt *);
extern PetscErrorCode DoOutput(SNES, PetscInt);

/* Post-processing & misc */
extern PetscErrorCode ViscosityField(DM, Vec, Vec);
extern PetscErrorCode StressField(DM);
extern PetscErrorCode SNESConverged_Interactive(SNES, PetscInt, PetscReal, PetscReal, PetscReal, SNESConvergedReason *, void *);
extern PetscErrorCode InteractiveHandler(int, void *);

int main(int argc, char **argv) {
  SNES      snes;
  AppCtx   *user; /* user-defined work context */
  Parameter param;
  GridInfo  grid;
  PetscInt  nits;
  MPI_Comm  comm;
  DM        da;

  PetscFunctionBeginUser;
  PetscCall(PetscInitialize(&argc, &argv, (char *)0, help));
  PetscOptionsSetValue(NULL, "-file", "ex30_output");
  PetscOptionsSetValue(NULL, "-snes_monitor_short", NULL);
  PetscOptionsSetValue(NULL, "-snes_max_it", "20");
  PetscOptionsSetValue(NULL, "-ksp_max_it", "1500");
  PetscOptionsSetValue(NULL, "-ksp_gmres_restart", "300");
  PetscOptionsInsert(NULL, &argc, &argv, NULL);

  comm = PETSC_COMM_WORLD;

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set up the problem parameters.
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(SetParams(&param, &grid));
  PetscCall(ReportParams(&param, &grid));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(SNESCreate(comm, &snes));
  PetscCall(DMDACreate2d(comm, grid.bx, grid.by, grid.stencil, grid.ni, grid.nj, PETSC_DECIDE, PETSC_DECIDE, grid.dof, grid.stencil_width, 0, 0, &da));
  PetscCall(DMSetFromOptions(da));
  PetscCall(DMSetUp(da));
  PetscCall(SNESSetDM(snes, da));
  PetscCall(DMDASetFieldName(da, 0, "x-velocity"));
  PetscCall(DMDASetFieldName(da, 1, "y-velocity"));
  PetscCall(DMDASetFieldName(da, 2, "pressure"));
  PetscCall(DMDASetFieldName(da, 3, "temperature"));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create user context, set problem data, create vector data structures.
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(PetscNew(&user));
  user->param = &param;
  user->grid  = &grid;
  PetscCall(DMSetApplicationContext(da, user));
  PetscCall(DMCreateGlobalVector(da, &(user->Xguess)));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set up the SNES solver with callback functions.
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(DMDASNESSetFunctionLocal(da, INSERT_VALUES, (PetscErrorCode(*)(DMDALocalInfo *, void *, void *, void *))FormFunctionLocal, (void *)user));
  PetscCall(SNESSetFromOptions(snes));

  PetscCall(SNESSetConvergenceTest(snes, SNESConverged_Interactive, (void *)user, NULL));
  PetscCall(PetscPushSignalHandler(InteractiveHandler, (void *)user));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize and solve the nonlinear system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(Initialize(da));
  PetscCall(UpdateSolution(snes, user, &nits));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Output variables.
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(DoOutput(snes, nits));

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscCall(VecDestroy(&user->Xguess));
  PetscCall(VecDestroy(&user->x));
  PetscCall(PetscFree(user));
  PetscCall(SNESDestroy(&snes));
  PetscCall(DMDestroy(&da));
  PetscCall(PetscPopSignalHandler());
  PetscCall(PetscFinalize());
  return 0;
}

/*=====================================================================
  PETSc INTERACTION FUNCTIONS (initialize & call SNESSolve)
  =====================================================================*/

/*  manages solve: adaptive continuation method  */
PetscErrorCode UpdateSolution(SNES snes, AppCtx *user, PetscInt *nits) {
  KSP                 ksp;
  PC                  pc;
  SNESConvergedReason reason    = SNES_CONVERGED_ITERATING;
  Parameter          *param     = user->param;
  PetscReal           cont_incr = 0.3;
  PetscInt            its;
  PetscBool           q = PETSC_FALSE;
  DM                  dm;

  PetscFunctionBeginUser;
  PetscCall(SNESGetDM(snes, &dm));
  PetscCall(DMCreateGlobalVector(dm, &user->x));
  PetscCall(SNESGetKSP(snes, &ksp));
  PetscCall(KSPGetPC(ksp, &pc));
  PetscCall(KSPSetComputeSingularValues(ksp, PETSC_TRUE));

  *nits = 0;

  /* Isoviscous solve */
  if (param->ivisc == VISC_CONST && !param->stop_solve) {
    param->ivisc = VISC_CONST;

    PetscCall(SNESSolve(snes, 0, user->x));
    PetscCall(SNESGetConvergedReason(snes, &reason));
    PetscCall(SNESGetIterationNumber(snes, &its));
    *nits += its;
    PetscCall(VecCopy(user->x, user->Xguess));
    if (param->stop_solve) goto done;
  }

  /* Olivine diffusion creep */
  if (param->ivisc >= VISC_DIFN && !param->stop_solve) {
    if (!q) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Computing Variable Viscosity Solution\n"));

    /* continuation method on viscosity cutoff */
    for (param->continuation = 0.0;; param->continuation += cont_incr) {
      if (!q) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " Continuation parameter = %g\n", (double)param->continuation));

      /* solve the non-linear system */
      PetscCall(VecCopy(user->Xguess, user->x));
      PetscCall(SNESSolve(snes, 0, user->x));
      PetscCall(SNESGetConvergedReason(snes, &reason));
      PetscCall(SNESGetIterationNumber(snes, &its));
      *nits += its;
      if (!q) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " SNES iterations: %" PetscInt_FMT ", Cumulative: %" PetscInt_FMT "\n", its, *nits));
      if (param->stop_solve) goto done;

      if (reason < 0) {
        /* NOT converged */
        cont_incr = -PetscAbsReal(cont_incr) / 2.0;
        if (PetscAbsReal(cont_incr) < 0.01) goto done;

      } else {
        /* converged */
        PetscCall(VecCopy(user->x, user->Xguess));
        if (param->continuation >= 1.0) goto done;
        if (its <= 3) cont_incr = 0.30001;
        else if (its <= 8) cont_incr = 0.15001;
        else cont_incr = 0.10001;

        if (param->continuation + cont_incr > 1.0) cont_incr = 1.0 - param->continuation;
      } /* endif reason<0 */
    }
  }
done:
  if (param->stop_solve && !q) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "USER SIGNAL: stopping solve.\n"));
  if (reason < 0 && !q) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "FAILED TO CONVERGE: stopping solve.\n"));
  PetscFunctionReturn(0);
}

/*=====================================================================
  PHYSICS FUNCTIONS (compute the discrete residual)
  =====================================================================*/

static inline PetscScalar UInterp(Field **x, PetscInt i, PetscInt j) {
  return 0.25 * (x[j][i].u + x[j + 1][i].u + x[j][i + 1].u + x[j + 1][i + 1].u);
}

static inline PetscScalar WInterp(Field **x, PetscInt i, PetscInt j) {
  return 0.25 * (x[j][i].w + x[j + 1][i].w + x[j][i + 1].w + x[j + 1][i + 1].w);
}

static inline PetscScalar PInterp(Field **x, PetscInt i, PetscInt j) {
  return 0.25 * (x[j][i].p + x[j + 1][i].p + x[j][i + 1].p + x[j + 1][i + 1].p);
}

static inline PetscScalar TInterp(Field **x, PetscInt i, PetscInt j) {
  return 0.25 * (x[j][i].T + x[j + 1][i].T + x[j][i + 1].T + x[j + 1][i + 1].T);
}

/*  isoviscous analytic solution for IC */
static inline PetscScalar HorizVelocity(PetscInt i, PetscInt j, AppCtx *user) {
  Parameter  *param = user->param;
  GridInfo   *grid  = user->grid;
  PetscScalar st, ct, th, c = param->c, d = param->d;
  PetscReal   x, z, r;

  x  = (i - grid->jlid) * grid->dx;
  z  = (j - grid->jlid - 0.5) * grid->dz;
  r  = PetscSqrtReal(x * x + z * z);
  st = z / r;
  ct = x / r;
  th = PetscAtanReal(z / x);
  return ct * (c * th * st + d * (st + th * ct)) + st * (c * (st - th * ct) + d * th * st);
}

/*  isoviscous analytic solution for IC */
static inline PetscScalar VertVelocity(PetscInt i, PetscInt j, AppCtx *user)

{
  Parameter  *param = user->param;
  GridInfo   *grid  = user->grid;
  PetscScalar st, ct, th, c = param->c, d = param->d;
  PetscReal   x, z, r;

  x  = (i - grid->jlid - 0.5) * grid->dx;
  z  = (j - grid->jlid) * grid->dz;
  r  = PetscSqrtReal(x * x + z * z);
  st = z / r;
  ct = x / r;
  th = PetscAtanReal(z / x);
  return st * (c * th * st + d * (st + th * ct)) - ct * (c * (st - th * ct) + d * th * st);
}

/*  isoviscous analytic solution for IC */
static inline PetscScalar Pressure(PetscInt i, PetscInt j, AppCtx *user) {
  Parameter  *param = user->param;
  GridInfo   *grid  = user->grid;
  PetscScalar x, z, r, st, ct, c = param->c, d = param->d;

  x  = (i - grid->jlid - 0.5) * grid->dx;
  z  = (j - grid->jlid - 0.5) * grid->dz;
  r  = PetscSqrtReal(x * x + z * z);
  st = z / r;
  ct = x / r;
  return (-2.0 * (c * ct - d * st) / r);
}

/*  computes the second invariant of the strain rate tensor */
static inline PetscScalar CalcSecInv(Field **x, PetscInt i, PetscInt j, PetscInt ipos, AppCtx *user) {
  Parameter  *param = user->param;
  GridInfo   *grid  = user->grid;
  PetscInt    ilim = grid->ni - 1, jlim = grid->nj - 1;
  PetscScalar uN, uS, uE, uW, wN, wS, wE, wW;
  PetscScalar eps11, eps12, eps22;

  if (i < j) return EPS_ZERO;
  if (i == ilim) i--;
  if (j == jlim) j--;

  if (ipos == CELL_CENTER) { /* on cell center */
    if (j <= grid->jlid) return EPS_ZERO;

    uE = x[j][i].u;
    uW = x[j][i - 1].u;
    wN = x[j][i].w;
    wS = x[j - 1][i].w;
    wE = WInterp(x, i, j - 1);
    if (i == j) {
      uN = param->cb;
      wW = param->sb;
    } else {
      uN = UInterp(x, i - 1, j);
      wW = WInterp(x, i - 1, j - 1);
    }

    if (j == grid->jlid + 1) uS = 0.0;
    else uS = UInterp(x, i - 1, j - 1);

  } else { /* on CELL_CORNER */
    if (j < grid->jlid) return EPS_ZERO;

    uN = x[j + 1][i].u;
    uS = x[j][i].u;
    wE = x[j][i + 1].w;
    wW = x[j][i].w;
    if (i == j) {
      wN = param->sb;
      uW = param->cb;
    } else {
      wN = WInterp(x, i, j);
      uW = UInterp(x, i - 1, j);
    }

    if (j == grid->jlid) {
      uE = 0.0;
      uW = 0.0;
      uS = -uN;
      wS = -wN;
    } else {
      uE = UInterp(x, i, j);
      wS = WInterp(x, i, j - 1);
    }
  }

  eps11 = (uE - uW) / grid->dx;
  eps22 = (wN - wS) / grid->dz;
  eps12 = 0.5 * ((uN - uS) / grid->dz + (wE - wW) / grid->dx);

  return PetscSqrtReal(0.5 * (eps11 * eps11 + 2.0 * eps12 * eps12 + eps22 * eps22));
}

/*  computes the shear viscosity */
static inline PetscScalar Viscosity(PetscScalar T, PetscScalar eps, PetscScalar z, Parameter *param) {
  PetscReal   result = 0.0;
  ViscParam   difn = param->diffusion, disl = param->dislocation;
  PetscInt    iVisc     = param->ivisc;
  PetscScalar eps_scale = param->V / (param->L * 1000.0);
  PetscScalar strain_power, v1, v2, P;
  PetscScalar rho_g = 32340.0, R = 8.3144;

  P = rho_g * (z * param->L * 1000.0); /* Pa */

  if (iVisc == VISC_CONST) {
    /* constant viscosity */
    return 1.0;
  } else if (iVisc == VISC_DIFN) {
    /* diffusion creep rheology */
    result = PetscRealPart((difn.A * PetscExpScalar((difn.Estar + P * difn.Vstar) / R / (T + 273.0)) / param->eta0));
  } else if (iVisc == VISC_DISL) {
    /* dislocation creep rheology */
    strain_power = PetscPowScalar(eps * eps_scale, (1.0 - disl.n) / disl.n);

    result = PetscRealPart(disl.A * PetscExpScalar((disl.Estar + P * disl.Vstar) / disl.n / R / (T + 273.0)) * strain_power / param->eta0);
  } else if (iVisc == VISC_FULL) {
    /* dislocation/diffusion creep rheology */
    strain_power = PetscPowScalar(eps * eps_scale, (1.0 - disl.n) / disl.n);

    v1 = difn.A * PetscExpScalar((difn.Estar + P * difn.Vstar) / R / (T + 273.0)) / param->eta0;
    v2 = disl.A * PetscExpScalar((disl.Estar + P * disl.Vstar) / disl.n / R / (T + 273.0)) * strain_power / param->eta0;

    result = PetscRealPart(1.0 / (1.0 / v1 + 1.0 / v2));
  }

  /* max viscosity is param->eta0 */
  result = PetscMin(result, 1.0);
  /* min viscosity is param->visc_cutoff */
  result = PetscMax(result, param->visc_cutoff);
  /* continuation method */
  result = PetscPowReal(result, param->continuation);
  return result;
}

/*  computes the residual of the x-component of eqn (1) above */
static inline PetscScalar XMomentumResidual(Field **x, PetscInt i, PetscInt j, AppCtx *user) {
  Parameter  *param = user->param;
  GridInfo   *grid  = user->grid;
  PetscScalar dx = grid->dx, dz = grid->dz;
  PetscScalar etaN, etaS, etaE, etaW, epsN = 0.0, epsS = 0.0, epsE = 0.0, epsW = 0.0;
  PetscScalar TE = 0.0, TN = 0.0, TS = 0.0, TW = 0.0, dPdx, residual, z_scale;
  PetscScalar dudxW, dudxE, dudzN, dudzS, dwdxN, dwdxS;
  PetscInt    jlim = grid->nj - 1;

  z_scale = param->z_scale;

  if (param->ivisc == VISC_DIFN || param->ivisc >= VISC_DISL) { /* viscosity is T-dependent */
    TS = param->potentialT * TInterp(x, i, j - 1) * PetscExpScalar((j - 1.0) * dz * z_scale);
    if (j == jlim) TN = TS;
    else TN = param->potentialT * TInterp(x, i, j) * PetscExpScalar(j * dz * z_scale);
    TW = param->potentialT * x[j][i].T * PetscExpScalar((j - 0.5) * dz * z_scale);
    TE = param->potentialT * x[j][i + 1].T * PetscExpScalar((j - 0.5) * dz * z_scale);
    if (param->ivisc >= VISC_DISL) { /* olivine dislocation creep */
      epsN = CalcSecInv(x, i, j, CELL_CORNER, user);
      epsS = CalcSecInv(x, i, j - 1, CELL_CORNER, user);
      epsE = CalcSecInv(x, i + 1, j, CELL_CENTER, user);
      epsW = CalcSecInv(x, i, j, CELL_CENTER, user);
    }
  }
  etaN = Viscosity(TN, epsN, dz * (j + 0.5), param);
  etaS = Viscosity(TS, epsS, dz * (j - 0.5), param);
  etaW = Viscosity(TW, epsW, dz * j, param);
  etaE = Viscosity(TE, epsE, dz * j, param);

  dPdx = (x[j][i + 1].p - x[j][i].p) / dx;
  if (j == jlim) dudzN = etaN * (x[j][i].w - x[j][i + 1].w) / dx;
  else dudzN = etaN * (x[j + 1][i].u - x[j][i].u) / dz;
  dudzS = etaS * (x[j][i].u - x[j - 1][i].u) / dz;
  dudxE = etaE * (x[j][i + 1].u - x[j][i].u) / dx;
  dudxW = etaW * (x[j][i].u - x[j][i - 1].u) / dx;

  residual = -dPdx /* X-MOMENTUM EQUATION*/
           + (dudxE - dudxW) / dx + (dudzN - dudzS) / dz;

  if (param->ivisc != VISC_CONST) {
    dwdxN = etaN * (x[j][i + 1].w - x[j][i].w) / dx;
    dwdxS = etaS * (x[j - 1][i + 1].w - x[j - 1][i].w) / dx;

    residual += (dudxE - dudxW) / dx + (dwdxN - dwdxS) / dz;
  }

  return residual;
}

/*  computes the residual of the z-component of eqn (1) above */
static inline PetscScalar ZMomentumResidual(Field **x, PetscInt i, PetscInt j, AppCtx *user)

{
  Parameter  *param = user->param;
  GridInfo   *grid  = user->grid;
  PetscScalar dx = grid->dx, dz = grid->dz;
  PetscScalar etaN = 0.0, etaS = 0.0, etaE = 0.0, etaW = 0.0, epsN = 0.0, epsS = 0.0, epsE = 0.0, epsW = 0.0;
  PetscScalar TE = 0.0, TN = 0.0, TS = 0.0, TW = 0.0, dPdz, residual, z_scale;
  PetscScalar dudzE, dudzW, dwdxW, dwdxE, dwdzN, dwdzS;
  PetscInt    ilim = grid->ni - 1;

  /* geometric and other parameters */
  z_scale = param->z_scale;

  /* viscosity */
  if (param->ivisc == VISC_DIFN || param->ivisc >= VISC_DISL) { /* viscosity is T-dependent */
    TN = param->potentialT * x[j + 1][i].T * PetscExpScalar((j + 0.5) * dz * z_scale);
    TS = param->potentialT * x[j][i].T * PetscExpScalar((j - 0.5) * dz * z_scale);
    TW = param->potentialT * TInterp(x, i - 1, j) * PetscExpScalar(j * dz * z_scale);
    if (i == ilim) TE = TW;
    else TE = param->potentialT * TInterp(x, i, j) * PetscExpScalar(j * dz * z_scale);
    if (param->ivisc >= VISC_DISL) { /* olivine dislocation creep */
      epsN = CalcSecInv(x, i, j + 1, CELL_CENTER, user);
      epsS = CalcSecInv(x, i, j, CELL_CENTER, user);
      epsE = CalcSecInv(x, i, j, CELL_CORNER, user);
      epsW = CalcSecInv(x, i - 1, j, CELL_CORNER, user);
    }
  }
  etaN = Viscosity(TN, epsN, dz * (j + 1.0), param);
  etaS = Viscosity(TS, epsS, dz * (j + 0.0), param);
  etaW = Viscosity(TW, epsW, dz * (j + 0.5), param);
  etaE = Viscosity(TE, epsE, dz * (j + 0.5), param);

  dPdz  = (x[j + 1][i].p - x[j][i].p) / dz;
  dwdzN = etaN * (x[j + 1][i].w - x[j][i].w) / dz;
  dwdzS = etaS * (x[j][i].w - x[j - 1][i].w) / dz;
  if (i == ilim) dwdxE = etaE * (x[j][i].u - x[j + 1][i].u) / dz;
  else dwdxE = etaE * (x[j][i + 1].w - x[j][i].w) / dx;
  dwdxW = 2.0 * etaW * (x[j][i].w - x[j][i - 1].w) / dx;

  /* Z-MOMENTUM */
  residual = -dPdz /* constant viscosity terms */
           + (dwdzN - dwdzS) / dz + (dwdxE - dwdxW) / dx;

  if (param->ivisc != VISC_CONST) {
    dudzE = etaE * (x[j + 1][i].u - x[j][i].u) / dz;
    dudzW = etaW * (x[j + 1][i - 1].u - x[j][i - 1].u) / dz;

    residual += (dwdzN - dwdzS) / dz + (dudzE - dudzW) / dx;
  }

  return residual;
}

/*  computes the residual of eqn (2) above */
static inline PetscScalar ContinuityResidual(Field **x, PetscInt i, PetscInt j, AppCtx *user) {
  GridInfo   *grid = user->grid;
  PetscScalar uE, uW, wN, wS, dudx, dwdz;

  uW   = x[j][i - 1].u;
  uE   = x[j][i].u;
  dudx = (uE - uW) / grid->dx;
  wS   = x[j - 1][i].w;
  wN   = x[j][i].w;
  dwdz = (wN - wS) / grid->dz;

  return dudx + dwdz;
}

/*  computes the residual of eqn (3) above */
static inline PetscScalar EnergyResidual(Field **x, PetscInt i, PetscInt j, AppCtx *user) {
  Parameter  *param = user->param;
  GridInfo   *grid  = user->grid;
  PetscScalar dx = grid->dx, dz = grid->dz;
  PetscInt    ilim = grid->ni - 1, jlim = grid->nj - 1, jlid = grid->jlid;
  PetscScalar TE, TN, TS, TW, residual;
  PetscScalar uE, uW, wN, wS;
  PetscScalar fN, fS, fE, fW, dTdxW, dTdxE, dTdzN, dTdzS;

  dTdzN = (x[j + 1][i].T - x[j][i].T) / dz;
  dTdzS = (x[j][i].T - x[j - 1][i].T) / dz;
  dTdxE = (x[j][i + 1].T - x[j][i].T) / dx;
  dTdxW = (x[j][i].T - x[j][i - 1].T) / dx;

  residual = ((dTdzN - dTdzS) / dz + /* diffusion term */
              (dTdxE - dTdxW) / dx) *
             dx * dz / param->peclet;

  if (j <= jlid && i >= j) {
    /* don't advect in the lid */
    return residual;
  } else if (i < j) {
    /* beneath the slab sfc */
    uW = uE = param->cb;
    wS = wN = param->sb;
  } else {
    /* advect in the slab and wedge */
    uW = x[j][i - 1].u;
    uE = x[j][i].u;
    wS = x[j - 1][i].w;
    wN = x[j][i].w;
  }

  if (param->adv_scheme == ADVECT_FV || i == ilim - 1 || j == jlim - 1 || i == 1 || j == 1) {
    /* finite volume advection */
    TS = (x[j][i].T + x[j - 1][i].T) / 2.0;
    TN = (x[j][i].T + x[j + 1][i].T) / 2.0;
    TE = (x[j][i].T + x[j][i + 1].T) / 2.0;
    TW = (x[j][i].T + x[j][i - 1].T) / 2.0;
    fN = wN * TN * dx;
    fS = wS * TS * dx;
    fE = uE * TE * dz;
    fW = uW * TW * dz;

  } else {
    /* Fromm advection scheme */
    fE = (uE * (-x[j][i + 2].T + 5.0 * (x[j][i + 1].T + x[j][i].T) - x[j][i - 1].T) / 8.0 - PetscAbsScalar(uE) * (-x[j][i + 2].T + 3.0 * (x[j][i + 1].T - x[j][i].T) + x[j][i - 1].T) / 8.0) * dz;
    fW = (uW * (-x[j][i + 1].T + 5.0 * (x[j][i].T + x[j][i - 1].T) - x[j][i - 2].T) / 8.0 - PetscAbsScalar(uW) * (-x[j][i + 1].T + 3.0 * (x[j][i].T - x[j][i - 1].T) + x[j][i - 2].T) / 8.0) * dz;
    fN = (wN * (-x[j + 2][i].T + 5.0 * (x[j + 1][i].T + x[j][i].T) - x[j - 1][i].T) / 8.0 - PetscAbsScalar(wN) * (-x[j + 2][i].T + 3.0 * (x[j + 1][i].T - x[j][i].T) + x[j - 1][i].T) / 8.0) * dx;
    fS = (wS * (-x[j + 1][i].T + 5.0 * (x[j][i].T + x[j - 1][i].T) - x[j - 2][i].T) / 8.0 - PetscAbsScalar(wS) * (-x[j + 1][i].T + 3.0 * (x[j][i].T - x[j - 1][i].T) + x[j - 2][i].T) / 8.0) * dx;
  }

  residual -= (fE - fW + fN - fS);

  return residual;
}

/*  computes the shear stress---used on the boundaries */
static inline PetscScalar ShearStress(Field **x, PetscInt i, PetscInt j, PetscInt ipos, AppCtx *user) {
  Parameter  *param = user->param;
  GridInfo   *grid  = user->grid;
  PetscInt    ilim = grid->ni - 1, jlim = grid->nj - 1;
  PetscScalar uN, uS, wE, wW;

  if (j <= grid->jlid || i < j || i == ilim || j == jlim) return EPS_ZERO;

  if (ipos == CELL_CENTER) { /* on cell center */

    wE = WInterp(x, i, j - 1);
    if (i == j) {
      wW = param->sb;
      uN = param->cb;
    } else {
      wW = WInterp(x, i - 1, j - 1);
      uN = UInterp(x, i - 1, j);
    }
    if (j == grid->jlid + 1) uS = 0.0;
    else uS = UInterp(x, i - 1, j - 1);

  } else { /* on cell corner */

    uN = x[j + 1][i].u;
    uS = x[j][i].u;
    wW = x[j][i].w;
    wE = x[j][i + 1].w;
  }

  return (uN - uS) / grid->dz + (wE - wW) / grid->dx;
}

/*  computes the normal stress---used on the boundaries */
static inline PetscScalar XNormalStress(Field **x, PetscInt i, PetscInt j, PetscInt ipos, AppCtx *user) {
  Parameter  *param = user->param;
  GridInfo   *grid  = user->grid;
  PetscScalar dx = grid->dx, dz = grid->dz;
  PetscInt    ilim = grid->ni - 1, jlim = grid->nj - 1, ivisc;
  PetscScalar epsC = 0.0, etaC, TC, uE, uW, pC, z_scale;
  if (i < j || j <= grid->jlid) return EPS_ZERO;

  ivisc   = param->ivisc;
  z_scale = param->z_scale;

  if (ipos == CELL_CENTER) { /* on cell center */

    TC = param->potentialT * x[j][i].T * PetscExpScalar((j - 0.5) * dz * z_scale);
    if (ivisc >= VISC_DISL) epsC = CalcSecInv(x, i, j, CELL_CENTER, user);
    etaC = Viscosity(TC, epsC, dz * j, param);

    uW = x[j][i - 1].u;
    uE = x[j][i].u;
    pC = x[j][i].p;

  } else { /* on cell corner */
    if (i == ilim || j == jlim) return EPS_ZERO;

    TC = param->potentialT * TInterp(x, i, j) * PetscExpScalar(j * dz * z_scale);
    if (ivisc >= VISC_DISL) epsC = CalcSecInv(x, i, j, CELL_CORNER, user);
    etaC = Viscosity(TC, epsC, dz * (j + 0.5), param);

    if (i == j) uW = param->sb;
    else uW = UInterp(x, i - 1, j);
    uE = UInterp(x, i, j);
    pC = PInterp(x, i, j);
  }

  return 2.0 * etaC * (uE - uW) / dx - pC;
}

/*  computes the normal stress---used on the boundaries */
static inline PetscScalar ZNormalStress(Field **x, PetscInt i, PetscInt j, PetscInt ipos, AppCtx *user) {
  Parameter  *param = user->param;
  GridInfo   *grid  = user->grid;
  PetscScalar dz    = grid->dz;
  PetscInt    ilim = grid->ni - 1, jlim = grid->nj - 1, ivisc;
  PetscScalar epsC = 0.0, etaC, TC;
  PetscScalar pC, wN, wS, z_scale;
  if (i < j || j <= grid->jlid) return EPS_ZERO;

  ivisc   = param->ivisc;
  z_scale = param->z_scale;

  if (ipos == CELL_CENTER) { /* on cell center */

    TC = param->potentialT * x[j][i].T * PetscExpScalar((j - 0.5) * dz * z_scale);
    if (ivisc >= VISC_DISL) epsC = CalcSecInv(x, i, j, CELL_CENTER, user);
    etaC = Viscosity(TC, epsC, dz * j, param);
    wN   = x[j][i].w;
    wS   = x[j - 1][i].w;
    pC   = x[j][i].p;

  } else { /* on cell corner */
    if ((i == ilim) || (j == jlim)) return EPS_ZERO;

    TC = param->potentialT * TInterp(x, i, j) * PetscExpScalar(j * dz * z_scale);
    if (ivisc >= VISC_DISL) epsC = CalcSecInv(x, i, j, CELL_CORNER, user);
    etaC = Viscosity(TC, epsC, dz * (j + 0.5), param);
    if (i == j) wN = param->sb;
    else wN = WInterp(x, i, j);
    wS = WInterp(x, i, j - 1);
    pC = PInterp(x, i, j);
  }

  return 2.0 * etaC * (wN - wS) / dz - pC;
}

/*=====================================================================
  INITIALIZATION, POST-PROCESSING AND OUTPUT FUNCTIONS
  =====================================================================*/

/* initializes the problem parameters and checks for
   command line changes */
PetscErrorCode SetParams(Parameter *param, GridInfo *grid) {
  PetscReal SEC_PER_YR                     = 3600.00 * 24.00 * 365.2500;
  PetscReal alpha_g_on_cp_units_inverse_km = 4.0e-5 * 9.8;

  /* domain geometry */
  param->slab_dip    = 45.0;
  param->width       = 320.0; /* km */
  param->depth       = 300.0; /* km */
  param->lid_depth   = 35.0;  /* km */
  param->fault_depth = 35.0;  /* km */

  PetscCall(PetscOptionsGetReal(NULL, NULL, "-slab_dip", &(param->slab_dip), NULL));
  PetscCall(PetscOptionsGetReal(NULL, NULL, "-width", &(param->width), NULL));
  PetscCall(PetscOptionsGetReal(NULL, NULL, "-depth", &(param->depth), NULL));
  PetscCall(PetscOptionsGetReal(NULL, NULL, "-lid_depth", &(param->lid_depth), NULL));
  PetscCall(PetscOptionsGetReal(NULL, NULL, "-fault_depth", &(param->fault_depth), NULL));

  param->slab_dip = param->slab_dip * PETSC_PI / 180.0; /* radians */

  /* grid information */
  PetscCall(PetscOptionsGetInt(NULL, NULL, "-jfault", &(grid->jfault), NULL));
  grid->ni = 82;
  PetscCall(PetscOptionsGetInt(NULL, NULL, "-ni", &(grid->ni), NULL));

  grid->dx     = param->width / ((PetscReal)(grid->ni - 2)); /* km */
  grid->dz     = grid->dx * PetscTanReal(param->slab_dip);   /* km */
  grid->nj     = (PetscInt)(param->depth / grid->dz + 3.0);  /* gridpoints*/
  param->depth = grid->dz * (grid->nj - 2);                  /* km */
  grid->inose  = 0;                                          /* gridpoints*/
  PetscCall(PetscOptionsGetInt(NULL, NULL, "-inose", &(grid->inose), NULL));
  grid->bx            = DM_BOUNDARY_NONE;
  grid->by            = DM_BOUNDARY_NONE;
  grid->stencil       = DMDA_STENCIL_BOX;
  grid->dof           = 4;
  grid->stencil_width = 2;
  grid->mglevels      = 1;

  /* boundary conditions */
  param->pv_analytic = PETSC_FALSE;
  param->ibound      = BC_NOSTRESS;
  PetscCall(PetscOptionsGetInt(NULL, NULL, "-ibound", &(param->ibound), NULL));

  /* physical constants */
  param->slab_velocity = 5.0;       /* cm/yr */
  param->slab_age      = 50.0;      /* Ma */
  param->lid_age       = 50.0;      /* Ma */
  param->kappa         = 0.7272e-6; /* m^2/sec */
  param->potentialT    = 1300.0;    /* degrees C */

  PetscCall(PetscOptionsGetReal(NULL, NULL, "-slab_velocity", &(param->slab_velocity), NULL));
  PetscCall(PetscOptionsGetReal(NULL, NULL, "-slab_age", &(param->slab_age), NULL));
  PetscCall(PetscOptionsGetReal(NULL, NULL, "-lid_age", &(param->lid_age), NULL));
  PetscCall(PetscOptionsGetReal(NULL, NULL, "-kappa", &(param->kappa), NULL));
  PetscCall(PetscOptionsGetReal(NULL, NULL, "-potentialT", &(param->potentialT), NULL));

  /* viscosity */
  param->ivisc        = 3;    /* 0=isovisc, 1=difn creep, 2=disl creep, 3=full */
  param->eta0         = 1e24; /* Pa-s */
  param->visc_cutoff  = 0.0;  /* factor of eta_0 */
  param->continuation = 1.0;

  /* constants for diffusion creep */
  param->diffusion.A     = 1.8e7; /* Pa-s */
  param->diffusion.n     = 1.0;   /* dim'less */
  param->diffusion.Estar = 375e3; /* J/mol */
  param->diffusion.Vstar = 5e-6;  /* m^3/mol */

  /* constants for param->dislocationocation creep */
  param->dislocation.A     = 2.8969e4; /* Pa-s */
  param->dislocation.n     = 3.5;      /* dim'less */
  param->dislocation.Estar = 530e3;    /* J/mol */
  param->dislocation.Vstar = 14e-6;    /* m^3/mol */

  PetscCall(PetscOptionsGetInt(NULL, NULL, "-ivisc", &(param->ivisc), NULL));
  PetscCall(PetscOptionsGetReal(NULL, NULL, "-visc_cutoff", &(param->visc_cutoff), NULL));

  param->output_ivisc = param->ivisc;

  PetscCall(PetscOptionsGetInt(NULL, NULL, "-output_ivisc", &(param->output_ivisc), NULL));
  PetscCall(PetscOptionsGetReal(NULL, NULL, "-vstar", &(param->dislocation.Vstar), NULL));

  /* output options */
  param->quiet      = PETSC_FALSE;
  param->param_test = PETSC_FALSE;

  PetscCall(PetscOptionsHasName(NULL, NULL, "-quiet", &(param->quiet)));
  PetscCall(PetscOptionsHasName(NULL, NULL, "-test", &(param->param_test)));
  PetscCall(PetscOptionsGetString(NULL, NULL, "-file", param->filename, sizeof(param->filename), &(param->output_to_file)));

  /* advection */
  param->adv_scheme = ADVECT_FROMM; /* advection scheme: 0=finite vol, 1=Fromm */

  PetscCall(PetscOptionsGetInt(NULL, NULL, "-adv_scheme", &(param->adv_scheme), NULL));

  /* misc. flags */
  param->stop_solve    = PETSC_FALSE;
  param->interrupted   = PETSC_FALSE;
  param->kspmon        = PETSC_FALSE;
  param->toggle_kspmon = PETSC_FALSE;

  /* derived parameters for slab angle */
  param->sb = PetscSinReal(param->slab_dip);
  param->cb = PetscCosReal(param->slab_dip);
  param->c  = param->slab_dip * param->sb / (param->slab_dip * param->slab_dip - param->sb * param->sb);
  param->d  = (param->slab_dip * param->cb - param->sb) / (param->slab_dip * param->slab_dip - param->sb * param->sb);

  /* length, velocity and time scale for non-dimensionalization */
  param->L = PetscMin(param->width, param->depth);      /* km */
  param->V = param->slab_velocity / 100.0 / SEC_PER_YR; /* m/sec */

  /* other unit conversions and derived parameters */
  param->scaled_width = param->width / param->L;                   /* dim'less */
  param->scaled_depth = param->depth / param->L;                   /* dim'less */
  param->lid_depth    = param->lid_depth / param->L;               /* dim'less */
  param->fault_depth  = param->fault_depth / param->L;             /* dim'less */
  grid->dx            = grid->dx / param->L;                       /* dim'less */
  grid->dz            = grid->dz / param->L;                       /* dim'less */
  grid->jlid          = (PetscInt)(param->lid_depth / grid->dz);   /* gridcells */
  grid->jfault        = (PetscInt)(param->fault_depth / grid->dz); /* gridcells */
  param->lid_depth    = grid->jlid * grid->dz;                     /* dim'less */
  param->fault_depth  = grid->jfault * grid->dz;                   /* dim'less */
  grid->corner        = grid->jlid + 1;                            /* gridcells */
  param->peclet       = param->V                                   /* m/sec */
                * param->L * 1000.0                                /* m */
                / param->kappa;                                    /* m^2/sec */
  param->z_scale = param->L * alpha_g_on_cp_units_inverse_km;
  param->skt     = PetscSqrtReal(param->kappa * param->slab_age * SEC_PER_YR);
  PetscCall(PetscOptionsGetReal(NULL, NULL, "-peclet", &(param->peclet), NULL));

  return 0;
}

/*  prints a report of the problem parameters to stdout */
PetscErrorCode ReportParams(Parameter *param, GridInfo *grid) {
  char date[30];

  PetscCall(PetscGetDate(date, 30));

  if (!(param->quiet)) {
    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "---------------------BEGIN ex30 PARAM REPORT-------------------\n"));
    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Domain: \n"));
    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "  Width = %g km,         Depth = %g km\n", (double)param->width, (double)param->depth));
    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "  Slab dip = %g degrees,  Slab velocity = %g cm/yr\n", (double)(param->slab_dip * 180.0 / PETSC_PI), (double)param->slab_velocity));
    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "  Lid depth = %5.2f km,   Fault depth = %5.2f km\n", (double)(param->lid_depth * param->L), (double)(param->fault_depth * param->L)));

    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nGrid: \n"));
    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "  [ni,nj] = %" PetscInt_FMT ", %" PetscInt_FMT "       [dx,dz] = %g, %g km\n", grid->ni, grid->nj, (double)(grid->dx * param->L), (double)(grid->dz * param->L)));
    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "  jlid = %3" PetscInt_FMT "              jfault = %3" PetscInt_FMT " \n", grid->jlid, grid->jfault));
    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "  Pe = %g\n", (double)param->peclet));

    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nRheology:"));
    if (param->ivisc == VISC_CONST) {
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "                 Isoviscous \n"));
      if (param->pv_analytic) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "                          Pressure and Velocity prescribed! \n"));
    } else if (param->ivisc == VISC_DIFN) {
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "                 Diffusion Creep (T-Dependent Newtonian) \n"));
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "                          Viscosity range: %g--%g Pa-sec \n", (double)param->eta0, (double)(param->visc_cutoff * param->eta0)));
    } else if (param->ivisc == VISC_DISL) {
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "                 Dislocation Creep (T-Dependent Non-Newtonian) \n"));
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "                          Viscosity range: %g--%g Pa-sec \n", (double)param->eta0, (double)(param->visc_cutoff * param->eta0)));
    } else if (param->ivisc == VISC_FULL) {
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "                 Full Rheology \n"));
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "                          Viscosity range: %g--%g Pa-sec \n", (double)param->eta0, (double)(param->visc_cutoff * param->eta0)));
    } else {
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "                 Invalid! \n"));
      return 1;
    }

    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Boundary condition:"));
    if (param->ibound == BC_ANALYTIC) {
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "       Isoviscous Analytic Dirichlet \n"));
    } else if (param->ibound == BC_NOSTRESS) {
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "       Stress-Free (normal & shear stress)\n"));
    } else if (param->ibound == BC_EXPERMNT) {
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "       Experimental boundary condition \n"));
    } else {
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "       Invalid! \n"));
      return 1;
    }

    if (param->output_to_file) {
#if defined(PETSC_HAVE_MATLAB_ENGINE)
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Output Destination:       Mat file \"%s\"\n", param->filename));
#else
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Output Destination:       PETSc binary file \"%s\"\n", param->filename));
#endif
    }
    if (param->output_ivisc != param->ivisc) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "                          Output viscosity: -ivisc %" PetscInt_FMT "\n", param->output_ivisc));

    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "---------------------END ex30 PARAM REPORT---------------------\n"));
  }
  if (param->param_test) PetscEnd();
  return 0;
}

/* ------------------------------------------------------------------- */
/*  generates an initial guess using the analytic solution for isoviscous
    corner flow */
PetscErrorCode Initialize(DM da)
/* ------------------------------------------------------------------- */
{
  AppCtx    *user;
  Parameter *param;
  GridInfo  *grid;
  PetscInt   i, j, is, js, im, jm;
  Field    **x;
  Vec        Xguess;

  /* Get the fine grid */
  PetscCall(DMGetApplicationContext(da, &user));
  Xguess = user->Xguess;
  param  = user->param;
  grid   = user->grid;
  PetscCall(DMDAGetCorners(da, &is, &js, NULL, &im, &jm, NULL));
  PetscCall(DMDAVecGetArray(da, Xguess, (void **)&x));

  /* Compute initial guess */
  for (j = js; j < js + jm; j++) {
    for (i = is; i < is + im; i++) {
      if (i < j) x[j][i].u = param->cb;
      else if (j <= grid->jlid) x[j][i].u = 0.0;
      else x[j][i].u = HorizVelocity(i, j, user);

      if (i <= j) x[j][i].w = param->sb;
      else if (j <= grid->jlid) x[j][i].w = 0.0;
      else x[j][i].w = VertVelocity(i, j, user);

      if (i < j || j <= grid->jlid) x[j][i].p = 0.0;
      else x[j][i].p = Pressure(i, j, user);

      x[j][i].T = PetscMin(grid->dz * (j - 0.5), 1.0);
    }
  }

  /* Restore x to Xguess */
  PetscCall(DMDAVecRestoreArray(da, Xguess, (void **)&x));

  return 0;
}

/*  controls output to a file */
PetscErrorCode DoOutput(SNES snes, PetscInt its) {
  AppCtx     *user;
  Parameter  *param;
  GridInfo   *grid;
  PetscInt    ivt;
  PetscMPIInt rank;
  PetscViewer viewer;
  Vec         res, pars;
  MPI_Comm    comm;
  DM          da;

  PetscCall(SNESGetDM(snes, &da));
  PetscCall(DMGetApplicationContext(da, &user));
  param = user->param;
  grid  = user->grid;
  ivt   = param->ivisc;

  param->ivisc = param->output_ivisc;

  /* compute final residual and final viscosity/strain rate fields */
  PetscCall(SNESGetFunction(snes, &res, NULL, NULL));
  PetscCall(ViscosityField(da, user->x, user->Xguess));

  /* get the communicator and the rank of the processor */
  PetscCall(PetscObjectGetComm((PetscObject)snes, &comm));
  PetscCallMPI(MPI_Comm_rank(comm, &rank));

  if (param->output_to_file) { /* send output to binary file */
    PetscCall(VecCreate(comm, &pars));
    if (rank == 0) { /* on processor 0 */
      PetscCall(VecSetSizes(pars, 20, PETSC_DETERMINE));
      PetscCall(VecSetFromOptions(pars));
      PetscCall(VecSetValue(pars, 0, (PetscScalar)(grid->ni), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 1, (PetscScalar)(grid->nj), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 2, (PetscScalar)(grid->dx), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 3, (PetscScalar)(grid->dz), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 4, (PetscScalar)(param->L), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 5, (PetscScalar)(param->V), INSERT_VALUES));
      /* skipped 6 intentionally */
      PetscCall(VecSetValue(pars, 7, (PetscScalar)(param->slab_dip), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 8, (PetscScalar)(grid->jlid), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 9, (PetscScalar)(param->lid_depth), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 10, (PetscScalar)(grid->jfault), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 11, (PetscScalar)(param->fault_depth), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 12, (PetscScalar)(param->potentialT), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 13, (PetscScalar)(param->ivisc), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 14, (PetscScalar)(param->visc_cutoff), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 15, (PetscScalar)(param->ibound), INSERT_VALUES));
      PetscCall(VecSetValue(pars, 16, (PetscScalar)(its), INSERT_VALUES));
    } else { /* on some other processor */
      PetscCall(VecSetSizes(pars, 0, PETSC_DETERMINE));
      PetscCall(VecSetFromOptions(pars));
    }
    PetscCall(VecAssemblyBegin(pars));
    PetscCall(VecAssemblyEnd(pars));

    /* create viewer */
#if defined(PETSC_HAVE_MATLAB_ENGINE)
    PetscCall(PetscViewerMatlabOpen(PETSC_COMM_WORLD, param->filename, FILE_MODE_WRITE, &viewer));
#else
    PetscCall(PetscViewerBinaryOpen(PETSC_COMM_WORLD, param->filename, FILE_MODE_WRITE, &viewer));
#endif

    /* send vectors to viewer */
    PetscCall(PetscObjectSetName((PetscObject)res, "res"));
    PetscCall(VecView(res, viewer));
    PetscCall(PetscObjectSetName((PetscObject)user->x, "out"));
    PetscCall(VecView(user->x, viewer));
    PetscCall(PetscObjectSetName((PetscObject)(user->Xguess), "aux"));
    PetscCall(VecView(user->Xguess, viewer));
    PetscCall(StressField(da)); /* compute stress fields */
    PetscCall(PetscObjectSetName((PetscObject)(user->Xguess), "str"));
    PetscCall(VecView(user->Xguess, viewer));
    PetscCall(PetscObjectSetName((PetscObject)pars, "par"));
    PetscCall(VecView(pars, viewer));

    /* destroy viewer and vector */
    PetscCall(PetscViewerDestroy(&viewer));
    PetscCall(VecDestroy(&pars));
  }

  param->ivisc = ivt;
  return 0;
}

/* ------------------------------------------------------------------- */
/* Compute both the second invariant of the strain rate tensor and the viscosity, at both cell centers and cell corners */
PetscErrorCode ViscosityField(DM da, Vec X, Vec V)
/* ------------------------------------------------------------------- */
{
  AppCtx    *user;
  Parameter *param;
  GridInfo  *grid;
  Vec        localX;
  Field    **v, **x;
  PetscReal  eps, /* dx,*/ dz, T, epsC, TC;
  PetscInt   i, j, is, js, im, jm, ilim, jlim, ivt;

  PetscFunctionBeginUser;
  PetscCall(DMGetApplicationContext(da, &user));
  param        = user->param;
  grid         = user->grid;
  ivt          = param->ivisc;
  param->ivisc = param->output_ivisc;

  PetscCall(DMGetLocalVector(da, &localX));
  PetscCall(DMGlobalToLocalBegin(da, X, INSERT_VALUES, localX));
  PetscCall(DMGlobalToLocalEnd(da, X, INSERT_VALUES, localX));
  PetscCall(DMDAVecGetArray(da, localX, (void **)&x));
  PetscCall(DMDAVecGetArray(da, V, (void **)&v));

  /* Parameters */
  /* dx = grid->dx; */ dz = grid->dz;

  ilim = grid->ni - 1;
  jlim = grid->nj - 1;

  /* Compute real temperature, strain rate and viscosity */
  PetscCall(DMDAGetCorners(da, &is, &js, NULL, &im, &jm, NULL));
  for (j = js; j < js + jm; j++) {
    for (i = is; i < is + im; i++) {
      T = PetscRealPart(param->potentialT * x[j][i].T * PetscExpScalar((j - 0.5) * dz * param->z_scale));
      if (i < ilim && j < jlim) {
        TC = PetscRealPart(param->potentialT * TInterp(x, i, j) * PetscExpScalar(j * dz * param->z_scale));
      } else {
        TC = T;
      }
      eps  = PetscRealPart((CalcSecInv(x, i, j, CELL_CENTER, user)));
      epsC = PetscRealPart(CalcSecInv(x, i, j, CELL_CORNER, user));

      v[j][i].u = eps;
      v[j][i].w = epsC;
      v[j][i].p = Viscosity(T, eps, dz * (j - 0.5), param);
      v[j][i].T = Viscosity(TC, epsC, dz * j, param);
    }
  }
  PetscCall(DMDAVecRestoreArray(da, V, (void **)&v));
  PetscCall(DMDAVecRestoreArray(da, localX, (void **)&x));
  PetscCall(DMRestoreLocalVector(da, &localX));

  param->ivisc = ivt;
  PetscFunctionReturn(0);
}

/* ------------------------------------------------------------------- */
/* post-processing: compute stress everywhere */
PetscErrorCode StressField(DM da)
/* ------------------------------------------------------------------- */
{
  AppCtx  *user;
  PetscInt i, j, is, js, im, jm;
  Vec      locVec;
  Field  **x, **y;

  PetscCall(DMGetApplicationContext(da, &user));

  /* Get the fine grid of Xguess and X */
  PetscCall(DMDAGetCorners(da, &is, &js, NULL, &im, &jm, NULL));
  PetscCall(DMDAVecGetArray(da, user->Xguess, (void **)&x));

  PetscCall(DMGetLocalVector(da, &locVec));
  PetscCall(DMGlobalToLocalBegin(da, user->x, INSERT_VALUES, locVec));
  PetscCall(DMGlobalToLocalEnd(da, user->x, INSERT_VALUES, locVec));
  PetscCall(DMDAVecGetArray(da, locVec, (void **)&y));

  /* Compute stress on the corner points */
  for (j = js; j < js + jm; j++) {
    for (i = is; i < is + im; i++) {
      x[j][i].u = ShearStress(y, i, j, CELL_CENTER, user);
      x[j][i].w = ShearStress(y, i, j, CELL_CORNER, user);
      x[j][i].p = XNormalStress(y, i, j, CELL_CENTER, user);
      x[j][i].T = ZNormalStress(y, i, j, CELL_CENTER, user);
    }
  }

  /* Restore the fine grid of Xguess and X */
  PetscCall(DMDAVecRestoreArray(da, user->Xguess, (void **)&x));
  PetscCall(DMDAVecRestoreArray(da, locVec, (void **)&y));
  PetscCall(DMRestoreLocalVector(da, &locVec));
  return 0;
}

/*=====================================================================
  UTILITY FUNCTIONS
  =====================================================================*/

/* returns the velocity of the subducting slab and handles fault nodes for BC */
static inline PetscScalar SlabVel(char c, PetscInt i, PetscInt j, AppCtx *user) {
  Parameter *param = user->param;
  GridInfo  *grid  = user->grid;

  if (c == 'U' || c == 'u') {
    if (i < j - 1) return param->cb;
    else if (j <= grid->jfault) return 0.0;
    else return param->cb;

  } else {
    if (i < j) return param->sb;
    else if (j <= grid->jfault) return 0.0;
    else return param->sb;
  }
}

/*  solution to diffusive half-space cooling model for BC */
static inline PetscScalar PlateModel(PetscInt j, PetscInt plate, AppCtx *user) {
  Parameter  *param = user->param;
  PetscScalar z;
  if (plate == PLATE_LID) z = (j - 0.5) * user->grid->dz;
  else z = (j - 0.5) * user->grid->dz * param->cb; /* PLATE_SLAB */
#if defined(PETSC_HAVE_ERF)
  return (PetscReal)(erf((double)PetscRealPart(z * param->L / 2.0 / param->skt)));
#else
  (*PetscErrorPrintf)("erf() not available on this machine\n");
  MPI_Abort(PETSC_COMM_SELF, 1);
#endif
}

/*=====================================================================
  INTERACTIVE SIGNAL HANDLING
  =====================================================================*/

/* ------------------------------------------------------------------- */
PetscErrorCode SNESConverged_Interactive(SNES snes, PetscInt it, PetscReal xnorm, PetscReal snorm, PetscReal fnorm, SNESConvergedReason *reason, void *ctx)
/* ------------------------------------------------------------------- */
{
  AppCtx    *user  = (AppCtx *)ctx;
  Parameter *param = user->param;
  KSP        ksp;

  PetscFunctionBeginUser;
  if (param->interrupted) {
    param->interrupted = PETSC_FALSE;
    PetscCall(PetscPrintf(PETSC_COMM_WORLD, "USER SIGNAL: exiting SNES solve. \n"));
    *reason = SNES_CONVERGED_FNORM_ABS;
    PetscFunctionReturn(0);
  } else if (param->toggle_kspmon) {
    param->toggle_kspmon = PETSC_FALSE;

    PetscCall(SNESGetKSP(snes, &ksp));

    if (param->kspmon) {
      PetscCall(KSPMonitorCancel(ksp));

      param->kspmon = PETSC_FALSE;
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "USER SIGNAL: deactivating ksp singular value monitor. \n"));
    } else {
      PetscViewerAndFormat *vf;
      PetscCall(PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &vf));
      PetscCall(KSPMonitorSet(ksp, (PetscErrorCode(*)(KSP, PetscInt, PetscReal, void *))KSPMonitorSingularValue, vf, (PetscErrorCode(*)(void **))PetscViewerAndFormatDestroy));

      param->kspmon = PETSC_TRUE;
      PetscCall(PetscPrintf(PETSC_COMM_WORLD, "USER SIGNAL: activating ksp singular value monitor. \n"));
    }
  }
  PetscCall(SNESConvergedDefault(snes, it, xnorm, snorm, fnorm, reason, ctx));
  PetscFunctionReturn(0);
}

/* ------------------------------------------------------------------- */
#include <signal.h>
PetscErrorCode InteractiveHandler(int signum, void *ctx)
/* ------------------------------------------------------------------- */
{
  AppCtx    *user  = (AppCtx *)ctx;
  Parameter *param = user->param;

  if (signum == SIGILL) {
    param->toggle_kspmon = PETSC_TRUE;
#if !defined(PETSC_MISSING_SIGCONT)
  } else if (signum == SIGCONT) {
    param->interrupted = PETSC_TRUE;
#endif
#if !defined(PETSC_MISSING_SIGURG)
  } else if (signum == SIGURG) {
    param->stop_solve = PETSC_TRUE;
#endif
  }
  return 0;
}

/*  main call-back function that computes the processor-local piece of the residual */
PetscErrorCode FormFunctionLocal(DMDALocalInfo *info, Field **x, Field **f, void *ptr) {
  AppCtx     *user  = (AppCtx *)ptr;
  Parameter  *param = user->param;
  GridInfo   *grid  = user->grid;
  PetscScalar mag_w, mag_u;
  PetscInt    i, j, mx, mz, ilim, jlim;
  PetscInt    is, ie, js, je, ibound; /* ,ivisc */

  PetscFunctionBeginUser;
  /* Define global and local grid parameters */
  mx   = info->mx;
  mz   = info->my;
  ilim = mx - 1;
  jlim = mz - 1;
  is   = info->xs;
  ie   = info->xs + info->xm;
  js   = info->ys;
  je   = info->ys + info->ym;

  /* Define geometric and numeric parameters */
  /* ivisc = param->ivisc; */ ibound = param->ibound;

  for (j = js; j < je; j++) {
    for (i = is; i < ie; i++) {
      /************* X-MOMENTUM/VELOCITY *************/
      if (i < j) f[j][i].u = x[j][i].u - SlabVel('U', i, j, user);
      else if (j <= grid->jlid || (j < grid->corner + grid->inose && i < grid->corner + grid->inose)) {
        /* in the lithospheric lid */
        f[j][i].u = x[j][i].u - 0.0;
      } else if (i == ilim) {
        /* on the right side boundary */
        if (ibound == BC_ANALYTIC) {
          f[j][i].u = x[j][i].u - HorizVelocity(i, j, user);
        } else {
          f[j][i].u = XNormalStress(x, i, j, CELL_CENTER, user) - EPS_ZERO;
        }

      } else if (j == jlim) {
        /* on the bottom boundary */
        if (ibound == BC_ANALYTIC) {
          f[j][i].u = x[j][i].u - HorizVelocity(i, j, user);
        } else if (ibound == BC_NOSTRESS) {
          f[j][i].u = XMomentumResidual(x, i, j, user);
        } else {
          /* experimental boundary condition */
        }

      } else {
        /* in the mantle wedge */
        f[j][i].u = XMomentumResidual(x, i, j, user);
      }

      /************* Z-MOMENTUM/VELOCITY *************/
      if (i <= j) {
        f[j][i].w = x[j][i].w - SlabVel('W', i, j, user);

      } else if (j <= grid->jlid || (j < grid->corner + grid->inose && i < grid->corner + grid->inose)) {
        /* in the lithospheric lid */
        f[j][i].w = x[j][i].w - 0.0;

      } else if (j == jlim) {
        /* on the bottom boundary */
        if (ibound == BC_ANALYTIC) {
          f[j][i].w = x[j][i].w - VertVelocity(i, j, user);
        } else {
          f[j][i].w = ZNormalStress(x, i, j, CELL_CENTER, user) - EPS_ZERO;
        }

      } else if (i == ilim) {
        /* on the right side boundary */
        if (ibound == BC_ANALYTIC) {
          f[j][i].w = x[j][i].w - VertVelocity(i, j, user);
        } else if (ibound == BC_NOSTRESS) {
          f[j][i].w = ZMomentumResidual(x, i, j, user);
        } else {
          /* experimental boundary condition */
        }

      } else {
        /* in the mantle wedge */
        f[j][i].w = ZMomentumResidual(x, i, j, user);
      }

      /************* CONTINUITY/PRESSURE *************/
      if (i < j || j <= grid->jlid || (j < grid->corner + grid->inose && i < grid->corner + grid->inose)) {
        /* in the lid or slab */
        f[j][i].p = x[j][i].p;

      } else if ((i == ilim || j == jlim) && ibound == BC_ANALYTIC) {
        /* on an analytic boundary */
        f[j][i].p = x[j][i].p - Pressure(i, j, user);

      } else {
        /* in the mantle wedge */
        f[j][i].p = ContinuityResidual(x, i, j, user);
      }

      /************* TEMPERATURE *************/
      if (j == 0) {
        /* on the surface */
        f[j][i].T = x[j][i].T + x[j + 1][i].T + PetscMax(PetscRealPart(x[j][i].T), 0.0);

      } else if (i == 0) {
        /* slab inflow boundary */
        f[j][i].T = x[j][i].T - PlateModel(j, PLATE_SLAB, user);

      } else if (i == ilim) {
        /* right side boundary */
        mag_u     = 1.0 - PetscPowRealInt((1.0 - PetscMax(PetscMin(PetscRealPart(x[j][i - 1].u) / param->cb, 1.0), 0.0)), 5);
        f[j][i].T = x[j][i].T - mag_u * x[j - 1][i - 1].T - (1.0 - mag_u) * PlateModel(j, PLATE_LID, user);

      } else if (j == jlim) {
        /* bottom boundary */
        mag_w     = 1.0 - PetscPowRealInt((1.0 - PetscMax(PetscMin(PetscRealPart(x[j - 1][i].w) / param->sb, 1.0), 0.0)), 5);
        f[j][i].T = x[j][i].T - mag_w * x[j - 1][i - 1].T - (1.0 - mag_w);

      } else {
        /* in the mantle wedge */
        f[j][i].T = EnergyResidual(x, i, j, user);
      }
    }
  }
  PetscFunctionReturn(0);
}

/*TEST

   build:
      requires: !complex erf

   test:
      args: -ni 18
      filter: grep -v Destination
      requires: !single

TEST*/