/*
   SNESSetFromOptions_VINEWTONSSLS - Sets various parameters for the SNESVI method.

   Input Parameter:
.  snes - the SNES context

   Application Interface Routine: SNESSetFromOptions()
*/
static PetscErrorCode SNESSetFromOptions_VINEWTONSSLS(PetscOptionItems *PetscOptionsObject,SNES snes)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = SNESSetFromOptions_VI(PetscOptionsObject,snes);CHKERRQ(ierr);
  ierr = PetscOptionsHead(PetscOptionsObject,"SNES semismooth method options");CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode TaoSetFromOptions_BLMVM(PetscOptionItems* PetscOptionsObject,Tao tao)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"Limited-memory variable-metric method for bound constrained optimization");CHKERRQ(ierr);
  ierr = TaoLineSearchSetFromOptions(tao->linesearch);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode KSPSetFromOptions_PGMRES(KSP ksp)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = KSPSetFromOptions_GMRES(ksp);CHKERRQ(ierr);
  ierr = PetscOptionsHead("KSP pipelined GMRES Options");CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode TaoSetFromOptions_BMRM(PetscOptionItems *PetscOptionsObject,Tao tao)
{
  PetscErrorCode ierr;
  TAO_BMRM*      bmrm = (TAO_BMRM*)tao->data;

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"BMRM for regularized risk minimization");CHKERRQ(ierr);
  ierr = PetscOptionsReal("-tao_bmrm_lambda", "regulariser weight","", 100,&bmrm->lambda,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode KSPSetFromOptions_Chebyshev(PetscOptions *PetscOptionsObject,KSP ksp)
{
  KSP_Chebyshev  *cheb = (KSP_Chebyshev*)ksp->data;
  PetscErrorCode ierr;
  PetscInt       neigarg = 2, nestarg = 4;
  PetscReal      eminmax[2] = {0., 0.};
  PetscReal      tform[4] = {PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE};
  PetscBool      flgeig, flgest;

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"KSP Chebyshev Options");CHKERRQ(ierr);
  ierr = PetscOptionsInt("-ksp_chebyshev_esteig_steps","Number of est steps in Chebyshev","",cheb->eststeps,&cheb->eststeps,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsRealArray("-ksp_chebyshev_eigenvalues","extreme eigenvalues","KSPChebyshevSetEigenvalues",eminmax,&neigarg,&flgeig);CHKERRQ(ierr);
  if (flgeig) {
    if (neigarg != 2) SETERRQ(PetscObjectComm((PetscObject)ksp),PETSC_ERR_ARG_INCOMP,"-ksp_chebyshev_eigenvalues: must specify 2 parameters, min and max eigenvalues");
    ierr = KSPChebyshevSetEigenvalues(ksp, eminmax[1], eminmax[0]);CHKERRQ(ierr);
  }
  ierr = PetscOptionsRealArray("-ksp_chebyshev_esteig","estimate eigenvalues using a Krylov method, then use this transform for Chebyshev eigenvalue bounds","KSPChebyshevEstEigSet",tform,&nestarg,&flgest);CHKERRQ(ierr);
  if (flgest) {
    switch (nestarg) {
    case 0:
      ierr = KSPChebyshevEstEigSet(ksp,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
      break;
    case 2:                     /* Base everything on the max eigenvalues */
      ierr = KSPChebyshevEstEigSet(ksp,PETSC_DECIDE,tform[0],PETSC_DECIDE,tform[1]);CHKERRQ(ierr);
      break;
    case 4:                     /* Use the full 2x2 linear transformation */
      ierr = KSPChebyshevEstEigSet(ksp,tform[0],tform[1],tform[2],tform[3]);CHKERRQ(ierr);
      break;
    default: SETERRQ(PetscObjectComm((PetscObject)ksp),PETSC_ERR_ARG_INCOMP,"Must specify either 0, 2, or 4 parameters for eigenvalue estimation");
    }
  }

  /* We need to estimate eigenvalues; need to set this here so that KSPSetFromOptions() is called on the estimator */
  if ((cheb->emin == 0. || cheb->emax == 0.) && !cheb->kspest) {
   ierr = KSPChebyshevEstEigSet(ksp,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
  }

  if (cheb->kspest) {
    ierr = PetscOptionsBool("-ksp_chebyshev_esteig_random","Use random right hand side for estimate","KSPChebyshevEstEigSetUseRandom",cheb->userandom,&cheb->userandom,NULL);CHKERRQ(ierr);
    if (cheb->userandom) {
      const char  *ksppre;
      if (!cheb->random) {
        ierr = PetscRandomCreate(PetscObjectComm((PetscObject)ksp),&cheb->random);CHKERRQ(ierr);
      }
      ierr = KSPGetOptionsPrefix(cheb->kspest, &ksppre);CHKERRQ(ierr);
      ierr = PetscObjectSetOptionsPrefix((PetscObject)cheb->random,ksppre);CHKERRQ(ierr);
      ierr = PetscRandomSetFromOptions(cheb->random);CHKERRQ(ierr);
    }
    ierr = KSPSetFromOptions(cheb->kspest);CHKERRQ(ierr);
  }
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode TSSetFromOptions_RK(TS ts)
{
  TS_RK          *rk = (TS_RK*)ts->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscOptionsHead("RK ODE solver options");CHKERRQ(ierr);
    ierr = PetscOptionsReal("-ts_rk_tol","Tolerance for convergence","TSRKSetTolerance",rk->tolerance,&rk->tolerance,PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
   MatMFFDSetFromOptions_WP - Looks in the options database for 
     any options appropriate for this method

  Input Parameter:
.  ctx - the matrix free context

*/
static PetscErrorCode MatMFFDSetFromOptions_WP(MatMFFD ctx)
{
  PetscErrorCode ierr;
  MatMFFD_WP     *hctx = (MatMFFD_WP*)ctx->hctx;

  PetscFunctionBegin;
  ierr = PetscOptionsHead("Walker-Pernice options");CHKERRQ(ierr);
    ierr = PetscOptionsBool("-mat_mffd_compute_normu","Compute the norm of u","MatMFFDWPSetComputeNormU", hctx->computenormU,&hctx->computenormU,0);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode SNESSetFromOptions_Test(SNES snes)
{
  SNES_Test      *ls = (SNES_Test*)snes->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscOptionsHead("Hand-coded Jacobian tester options");CHKERRQ(ierr);
  ierr = PetscOptionsBool("-snes_test_display","Display difference between hand-coded and finite difference Jacobians","None",ls->complete_print,&ls->complete_print,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode PCSetFromOptions_Redundant(PetscOptionItems *PetscOptionsObject,PC pc)
{
  PetscErrorCode ierr;
  PC_Redundant   *red = (PC_Redundant*)pc->data;

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"Redundant options");CHKERRQ(ierr);
  ierr = PetscOptionsInt("-pc_redundant_number","Number of redundant pc","PCRedundantSetNumber",red->nsubcomm,&red->nsubcomm,0);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode PFSetFromOptions_Constant(PF pf)
{
  PetscErrorCode ierr;
  PetscScalar    *value = (PetscScalar*)pf->data;

  PetscFunctionBegin;
  ierr = PetscOptionsHead("Constant function options");CHKERRQ(ierr);
  ierr = PetscOptionsScalar("-pf_constant","The constant value","None",*value,value,0);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
   MatMFFDSetFromOptions_DS - Looks in the options database for
   any options appropriate for this method.

   Input Parameter:
.  ctx - the matrix free context

*/
static PetscErrorCode MatMFFDSetFromOptions_DS(PetscOptionItems *PetscOptionsObject,MatMFFD ctx)
{
  PetscErrorCode ierr;
  MatMFFD_DS     *hctx = (MatMFFD_DS*)ctx->hctx;

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"Finite difference matrix free parameters");CHKERRQ(ierr);
  ierr = PetscOptionsReal("-mat_mffd_umin","umin","MatMFFDDSSetUmin",hctx->umin,&hctx->umin,0);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscSFSetFromOptions_Window(PetscOptionItems *PetscOptionsObject,PetscSF sf)
{
  PetscSF_Window *w = (PetscSF_Window*)sf->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"PetscSF Window options");CHKERRQ(ierr);
  ierr = PetscOptionsEnum("-sf_window_sync","synchronization type to use for PetscSF Window communication","PetscSFWindowSetSyncType",PetscSFWindowSyncTypes,(PetscEnum)w->sync,(PetscEnum*)&w->sync,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatColoringSetFromOptions_JP(PetscOptionItems *PetscOptionsObject,MatColoring mc)
{
  PetscErrorCode ierr;
  MC_JP          *jp = (MC_JP*)mc->data;

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"JP options");CHKERRQ(ierr);
  ierr = PetscOptionsBool("-mat_coloring_jp_local","Do an initial coloring of local columns","",jp->local,&jp->local,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode KSPSetFromOptions_STCG(KSP ksp)
{
  PetscErrorCode ierr;
  KSP_STCG       *cg = (KSP_STCG*)ksp->data;

  PetscFunctionBegin;
  ierr = PetscOptionsHead("KSP STCG options");CHKERRQ(ierr);
  ierr = PetscOptionsReal("-ksp_stcg_radius", "Trust Region Radius", "KSPSTCGSetRadius", cg->radius, &cg->radius, NULL);CHKERRQ(ierr);
  ierr = PetscOptionsEList("-ksp_stcg_dtype", "Norm used for direction", "", DType_Table, STCG_DIRECTION_TYPES, DType_Table[cg->dtype], &cg->dtype, NULL);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
   TSAdaptSetFromOptions - Sets various TSAdapt parameters from user options.

   Collective on TSAdapt

   Input Parameter:
.  adapt - the TSAdapt context

   Options Database Keys:
+  -ts_adapt_type <type> - algorithm to use for adaptivity
.  -ts_adapt_always_accept - always accept steps regardless of error/stability goals
.  -ts_adapt_safety <safety> - safety factor relative to target error/stability goal
.  -ts_adapt_reject_safety <safety> - extra safety factor to apply if the last step was rejected
.  -ts_adapt_clip <low,high> - admissible time step decrease and increase factors
.  -ts_adapt_dt_min <min> - minimum timestep to use
.  -ts_adapt_dt_max <max> - maximum timestep to use
.  -ts_adapt_scale_solve_failed <scale> - scale timestep by this factor if a solve fails
.  -ts_adapt_wnormtype <2 or infinity> - type of norm for computing error estimates
-  -ts_adapt_time_step_increase_delay - number of timesteps to delay increasing the time step after it has been decreased due to failed solver

   Level: advanced

   Notes:
   This function is automatically called by TSSetFromOptions()

.keywords: TS, TSGetAdapt(), TSAdaptSetType(), TSAdaptSetStepLimits()

.seealso: TSGetAdapt(), TSAdaptSetType(), TSAdaptSetAlwaysAccept(), TSAdaptSetSafety(),
          TSAdaptSetClip(), TSAdaptSetStepLimits(), TSAdaptSetMonitor()
*/
PetscErrorCode  TSAdaptSetFromOptions(PetscOptionItems *PetscOptionsObject,TSAdapt adapt)
{
  PetscErrorCode ierr;
  char           type[256] = TSADAPTBASIC;
  PetscReal      safety,reject_safety,clip[2],hmin,hmax;
  PetscBool      set,flg;
  PetscInt       two;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(adapt,TSADAPT_CLASSID,1);
  /* This should use PetscOptionsBegin() if/when this becomes an object used outside of TS, but currently this
   * function can only be called from inside TSSetFromOptions()  */
  ierr = PetscOptionsHead(PetscOptionsObject,"TS Adaptivity options");CHKERRQ(ierr);
  ierr = PetscOptionsFList("-ts_adapt_type","Algorithm to use for adaptivity","TSAdaptSetType",TSAdaptList,((PetscObject)adapt)->type_name ? ((PetscObject)adapt)->type_name : type,type,sizeof(type),&flg);CHKERRQ(ierr);
  if (flg || !((PetscObject)adapt)->type_name) {
    ierr = TSAdaptSetType(adapt,type);CHKERRQ(ierr);
  }

  ierr = PetscOptionsBool("-ts_adapt_always_accept","Always accept the step","TSAdaptSetAlwaysAccept",adapt->always_accept,&flg,&set);CHKERRQ(ierr);
  if (set) {ierr = TSAdaptSetAlwaysAccept(adapt,flg);CHKERRQ(ierr);}

  safety = adapt->safety; reject_safety = adapt->reject_safety;
  ierr = PetscOptionsReal("-ts_adapt_safety","Safety factor relative to target error/stability goal","TSAdaptSetSafety",safety,&safety,&set);CHKERRQ(ierr);
  ierr = PetscOptionsReal("-ts_adapt_reject_safety","Extra safety factor to apply if the last step was rejected","TSAdaptSetSafety",reject_safety,&reject_safety,&flg);CHKERRQ(ierr);
  if (set || flg) {ierr = TSAdaptSetSafety(adapt,safety,reject_safety);CHKERRQ(ierr);}

  two = 2; clip[0] = adapt->clip[0]; clip[1] = adapt->clip[1];
  ierr = PetscOptionsRealArray("-ts_adapt_clip","Admissible decrease/increase factor in step size","TSAdaptSetClip",clip,&two,&set);CHKERRQ(ierr);
  if (set && (two != 2)) SETERRQ(PetscObjectComm((PetscObject)adapt),PETSC_ERR_ARG_OUTOFRANGE,"Must give exactly two values to -ts_adapt_clip");
  if (set) {ierr = TSAdaptSetClip(adapt,clip[0],clip[1]);CHKERRQ(ierr);}

  hmin = adapt->dt_min; hmax = adapt->dt_max;
  ierr = PetscOptionsReal("-ts_adapt_dt_min","Minimum time step considered","TSAdaptSetStepLimits",hmin,&hmin,&set);CHKERRQ(ierr);
  ierr = PetscOptionsReal("-ts_adapt_dt_max","Maximum time step considered","TSAdaptSetStepLimits",hmax,&hmax,&flg);CHKERRQ(ierr);
  if (set || flg) {ierr = TSAdaptSetStepLimits(adapt,hmin,hmax);CHKERRQ(ierr);}

  ierr = PetscOptionsReal("-ts_adapt_max_ignore","Adaptor ignores (absolute) solution values smaller than this value","",adapt->ignore_max,&adapt->ignore_max,&set);CHKERRQ(ierr);
  ierr = PetscOptionsBool("-ts_adapt_glee_use_local","GLEE adaptor uses local error estimation for step control","",adapt->glee_use_local,&adapt->glee_use_local,&set);CHKERRQ(ierr);

  ierr = PetscOptionsReal("-ts_adapt_scale_solve_failed","Scale step by this factor if solve fails","",adapt->scale_solve_failed,&adapt->scale_solve_failed,NULL);CHKERRQ(ierr);

  ierr = PetscOptionsEnum("-ts_adapt_wnormtype","Type of norm computed for error estimation","",NormTypes,(PetscEnum)adapt->wnormtype,(PetscEnum*)&adapt->wnormtype,NULL);CHKERRQ(ierr);
  if (adapt->wnormtype != NORM_2 && adapt->wnormtype != NORM_INFINITY) SETERRQ(PetscObjectComm((PetscObject)adapt),PETSC_ERR_SUP,"Only 2-norm and infinite norm supported");

  ierr = PetscOptionsInt("-ts_adapt_time_step_increase_delay","Number of timesteps to delay increasing the time step after it has been decreased due to failed solver","TSAdaptSetTimeStepIncreaseDelay",adapt->timestepjustdecreased_delay,&adapt->timestepjustdecreased_delay,NULL);CHKERRQ(ierr);

  ierr = PetscOptionsBool("-ts_adapt_monitor","Print choices made by adaptive controller","TSAdaptSetMonitor",adapt->monitor ? PETSC_TRUE : PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
  if (set) {ierr = TSAdaptSetMonitor(adapt,flg);CHKERRQ(ierr);}

  if (adapt->ops->setfromoptions) {ierr = (*adapt->ops->setfromoptions)(PetscOptionsObject,adapt);CHKERRQ(ierr);}
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode DMSetFromOptions_Patch(PetscOptionItems *PetscOptionsObject,DM dm)
{
  /* DM_Patch      *mesh = (DM_Patch*) dm->data; */
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  ierr = PetscOptionsHead(PetscOptionsObject,"DMPatch Options");CHKERRQ(ierr);
  /* Handle associated vectors */
  /* Handle viewing */
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatSetFromOptions_SchurComplement(PetscOptions *PetscOptionsObject,Mat N)
{
  Mat_SchurComplement *Na = (Mat_SchurComplement*)N->data;
  PetscErrorCode      ierr;

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"MatSchurComplementOptions");CHKERRQ(ierr);
  Na->ainvtype = MAT_SCHUR_COMPLEMENT_AINV_DIAG;
  ierr = PetscOptionsEnum("-mat_schur_complement_ainv_type","Type of approximation for inv(A00) used when assembling Sp = A11 - A10 inv(A00) A01","MatSchurComplementSetAinvType",MatSchurComplementAinvTypes,(PetscEnum)Na->ainvtype,(PetscEnum*)&Na->ainvtype,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  ierr = KSPSetFromOptions(Na->ksp);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode PCSetFromOptions_KSP(PetscOptionItems *PetscOptionsObject,PC pc)
{
  PC_KSP         *jac = (PC_KSP*)pc->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"PC KSP options");CHKERRQ(ierr);
  if (jac->ksp) {
    ierr = KSPSetFromOptions(jac->ksp);CHKERRQ(ierr);
   }
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode TaoSetFromOptions_OWLQN(Tao tao)
{
  TAO_OWLQN      *lmP = (TAO_OWLQN *)tao->data;
  PetscBool      flg;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscOptionsHead("Orthant-Wise Limited-memory method for Quasi-Newton unconstrained optimization");CHKERRQ(ierr);
  ierr = PetscOptionsReal("-tao_owlqn_lambda", "regulariser weight","", 100,&lmP->lambda,&flg); CHKERRQ(ierr);
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  ierr = TaoLineSearchSetFromOptions(tao->linesearch);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode PCSetFromOptions_LSC(PetscOptions *PetscOptionsObject,PC pc)
{
  PC_LSC         *lsc = (PC_LSC*)pc->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"LSC options");CHKERRQ(ierr);
  {
    ierr = PetscOptionsBool("-pc_lsc_scale_diag","Use diagonal of velocity block (A) for scaling","None",lsc->scalediag,&lsc->scalediag,NULL);CHKERRQ(ierr);
  }
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}