cleans up a few names in writing checkpoint/vis files; stops use of p…

…k name in tag

src/pks/flow/constitutive_relations/wrm/wrm_implicit_permafrost_model.cc

@@ -358,17 +358,19 @@ WRMImplicitPermafrostModel::si_frozen_unsaturated_nospline_(double pc_liq,
   int max_it(max_it_);
 
   if (solver_ == "bisection") {
-    Errors::Message emsg("WRMImplicitPermafrostModel:: invalid solver method \"bisection\", use \"brent\"");
+    Errors::Message emsg(
+      "WRMImplicitPermafrostModel:: invalid solver method \"bisection\", use \"brent\"");
     Exceptions::amanzi_throw(emsg);
   } else if (solver_ == "toms") {
-    Errors::Message emsg("WRMImplicitPermafrostModel:: invalid solver method \"bisection\", use \"brent\"");
+    Errors::Message emsg(
+      "WRMImplicitPermafrostModel:: invalid solver method \"bisection\", use \"brent\"");
     Exceptions::amanzi_throw(emsg);
   } else if (solver_ == "brent") {
     result = Utils::findRootBrent(func, left, right, eps_, &max_it);
   } else {
     Errors::Message emsg;
-    emsg << "WRMImplicitPermafrostModel: invalid solver method \""
-         << solver_ << "\", use \"brent\"";
+    emsg << "WRMImplicitPermafrostModel: invalid solver method \"" << solver_
+         << "\", use \"brent\"";
     Exceptions::amanzi_throw(emsg);
   }
 
@@ -378,8 +380,8 @@ WRMImplicitPermafrostModel::si_frozen_unsaturated_nospline_(double pc_liq,
   if (max_it >= max_it_) {
     // did not converge?  May be ABS converged but not REL converged!
     std::cerr << "WRMImplicitPermafrostModel did not converge, " << max_it
-             << " iterations, error = " << func(si) << ", s_i = " << si
-             << ", PC_{lg,il} = " << pc_liq << "," << pc_ice << std::endl;
+              << " iterations, error = " << func(si) << ", s_i = " << si
+              << ", PC_{lg,il} = " << pc_liq << "," << pc_ice << std::endl;
     if (throw_ok) { Exceptions::amanzi_throw(Errors::CutTimeStep()); }
   }
   return si;

src/pks/flow/predictor_delegate_bc_flux.cc

@@ -104,8 +104,8 @@ PredictorDelegateBCFlux::CreateFunctor_(int f, const Teuchos::Ptr<const Composit
 
 int
 PredictorDelegateBCFlux::CalculateLambda_(int f,
-        const Teuchos::Ptr<const CompositeVector>& pres,
-        double& lambda)
+                                          const Teuchos::Ptr<const CompositeVector>& pres,
+                                          double& lambda)
 {
 #if DEBUG_FLAG
   std::cout << " Flux correcting face " << f << ": q = " << (*bc_values_)[f] << std::endl;

src/pks/pk_bdf_default.cc

@@ -39,11 +39,11 @@ PK_BDF_Default::Setup()
     // check if continuation method and require continuation parameter
     // -- ETC Note this needs fixed if more than one continuation method used
     if (bdf_plist.isSublist("continuation parameters")) {
-      S_->Require<double>("continuation_parameter", Tag(name_), name_);
+      S_->Require<double>(Keys::cleanName(name_) + "_continuation_parameter", Tags::DEFAULT, name_);
     }
 
     // require data for checkpointing timestep size
-    S_->Require<double>("dt_internal", Tag(name_), name_);
+    S_->Require<double>(Keys::cleanName(name_) + "_dt_internal", Tags::DEFAULT, name_);
   }
 };
 
@@ -67,13 +67,15 @@ PK_BDF_Default::Initialize()
       Teuchos::rcp(new BDF1_TI<TreeVector, TreeVectorSpace>(*this, bdf_plist, solution_, S_));
 
     double dt_init = time_stepper_->initial_timestep();
-    S_->Assign("dt_internal", Tag(name_), name_, dt_init);
-    S_->GetRecordW("dt_internal", Tag(name_), name_).set_initialized();
+    S_->Assign(Keys::cleanName(name_) + "_dt_internal", Tags::DEFAULT, name_, dt_init);
+    S_->GetRecordW(Keys::cleanName(name_) + "_dt_internal", Tags::DEFAULT, name_).set_initialized();
 
     // -- initialize continuation parameter if needed.
-    if (S_->HasRecord("continuation_parameter", Tag(name_))) {
-      S_->Assign("continuation_parameter", Tag(name_), name_, (double)1.);
-      S_->GetRecordW("continuation_parameter", Tag(name_), name_).set_initialized();
+    if (S_->HasRecord(Keys::cleanName(name_) + "_continuation_parameter", Tags::DEFAULT)) {
+      S_->Assign(
+        Keys::cleanName(name_) + "_continuation_parameter", Tags::DEFAULT, name_, (double)1.);
+      S_->GetRecordW(Keys::cleanName(name_) + "_continuation_parameter", Tags::DEFAULT, name_)
+        .set_initialized();
     }
 
     // -- initialize time derivative
@@ -93,15 +95,16 @@ double
 PK_BDF_Default::get_dt()
 {
   if (!strongly_coupled_)
-    return S_->Get<double>("dt_internal", Tag(name_));
+    return S_->Get<double>(Keys::cleanName(name_) + "_dt_internal", Tags::DEFAULT);
   else
     return -1.;
 }
 
 void
 PK_BDF_Default::set_dt(double dt)
 {
-  if (!strongly_coupled_) S_->Assign("dt_internal", Tag(name_), name_, dt);
+  if (!strongly_coupled_)
+    S_->Assign(Keys::cleanName(name_) + "_dt_internal", Tags::DEFAULT, name_, dt);
 }
 
 // -- Commit any secondary (dependent) variables.
@@ -139,7 +142,7 @@ PK_BDF_Default::AdvanceStep(double t_old, double t_new, bool reinit)
   // --  dt is the requested timestep size.  It must be less than or equal to...
   // --  dt_internal is the max valid dt, and is set by physics/solvers
   // --  dt_solver is what the solver wants to do
-  double dt_internal = S_->Get<double>("dt_internal", Tag(name_));
+  double dt_internal = S_->Get<double>(Keys::cleanName(name_) + "_dt_internal", Tags::DEFAULT);
 
   // NOTE, still a bug in amanzi#685, despite fixes in amanzi#694, so this assertion still fails --ETC
   // AMANZI_ASSERT(dt <= dt_internal + 2.e-8); // roundoff
@@ -175,7 +178,7 @@ PK_BDF_Default::AdvanceStep(double t_old, double t_new, bool reinit)
       dt_internal = dt_solver;
     }
 
-    S_->Assign("dt_internal", Tag(name_), name_, dt_internal);
+    S_->Assign(Keys::cleanName(name_) + "_dt_internal", Tags::DEFAULT, name_, dt_internal);
   } catch (Errors::TimeStepCrash& e) {
     // inject more information into the crash message
     std::stringstream msg_str;
@@ -196,7 +199,7 @@ PK_BDF_Default::AdvanceStep(double t_old, double t_new, bool reinit)
 void
 PK_BDF_Default::UpdateContinuationParameter(double lambda)
 {
-  S_->Assign("continuation_parameter", Tag(name_), name_, lambda);
+  S_->Assign(Keys::cleanName(name_) + "_continuation_parameter", Tags::DEFAULT, name_, lambda);
   ChangedSolution();
 }
 

src/pks/surface_balance/constitutive_relations/land_cover/albedo_threecomponent_evaluator.cc

@@ -51,9 +51,7 @@ AlbedoThreeComponentEvaluator::AlbedoThreeComponentEvaluator(Teuchos::ParameterL
   a_ice_ = plist_.get<double>("albedo ice [-]", 0.44);
   a_water_ = plist_.get<double>("albedo water [-]", 0.1168);
   is_constant_snow_albedo_ = plist_.isParameter("albedo snow [-]");
-  if (is_constant_snow_albedo_) {
-    a_snow_ = plist_.get<double>("albedo snow [-]");
-  }
+  if (is_constant_snow_albedo_) { a_snow_ = plist_.get<double>("albedo snow [-]"); }
 
   e_ice_ = plist_.get<double>("emissivity ice [-]", 0.98);
   e_water_ = plist_.get<double>("emissivity water [-]", 0.995);
@@ -88,7 +86,8 @@ AlbedoThreeComponentEvaluator::Evaluate_(const State& S,
 
     for (auto c : lc_ids) {
       // albedo of the snow
-      albedo[2][c] = is_constant_snow_albedo_ ? a_snow_ : Relations::CalcAlbedoSnow((*snow_dens)[0][c]); 
+      albedo[2][c] =
+        is_constant_snow_albedo_ ? a_snow_ : Relations::CalcAlbedoSnow((*snow_dens)[0][c]);
 
       // a and e of water
       albedo[1][c] = unfrozen_fraction[0][c] * a_water_ + (1 - unfrozen_fraction[0][c]) * a_ice_;

src/pks/surface_balance/constitutive_relations/land_cover/albedo_twocomponent_evaluator.cc

@@ -55,9 +55,7 @@ AlbedoTwoComponentEvaluator::AlbedoTwoComponentEvaluator(Teuchos::ParameterList&
   a_ice_ = plist_.get<double>("albedo ice [-]", 0.44);
   a_water_ = plist_.get<double>("albedo water [-]", 0.1168);
   is_constant_snow_albedo_ = plist_.isParameter("albedo snow [-]");
-  if (is_constant_snow_albedo_) {
-    a_snow_ = plist_.get<double>("albedo snow [-]");
-  }
+  if (is_constant_snow_albedo_) { a_snow_ = plist_.get<double>("albedo snow [-]"); }
 
   e_ice_ = plist_.get<double>("emissivity ice [-]", 0.98);
   e_water_ = plist_.get<double>("emissivity water [-]", 0.995);
@@ -92,7 +90,8 @@ AlbedoTwoComponentEvaluator::Evaluate_(const State& S, const std::vector<Composi
 
     for (auto c : lc_ids) {
       // albedo of the snow
-      albedo[1][c] = is_constant_snow_albedo_ ? a_snow_ : Relations::CalcAlbedoSnow((*snow_dens)[0][c]); 
+      albedo[1][c] =
+        is_constant_snow_albedo_ ? a_snow_ : Relations::CalcAlbedoSnow((*snow_dens)[0][c]);
 
       double albedo_water =
         unfrozen_fraction[0][c] * a_water_ + (1 - unfrozen_fraction[0][c]) * a_ice_;

src/pks/surface_balance/constitutive_relations/land_cover/seb_physics_funcs.cc

@@ -403,17 +403,18 @@ DetermineSnowTemperature(const GroundProperties& surf,
   int max_it(my_max_it);
   double result(0.);
   if (method == "bisection") {
-    Errors::Message msg("SurfaceEnergyBalance: root finding method \"bisection\" is not longer supported -- use \"brent\"");
+    Errors::Message msg("SurfaceEnergyBalance: root finding method \"bisection\" is not longer "
+                        "supported -- use \"brent\"");
     Exceptions::amanzi_throw(msg);
   } else if (method == "toms") {
-    Errors::Message msg("SurfaceEnergyBalance: root finding method \"bisection\" is not longer supported -- use \"brent\"");
+    Errors::Message msg("SurfaceEnergyBalance: root finding method \"bisection\" is not longer "
+                        "supported -- use \"brent\"");
     Exceptions::amanzi_throw(msg);
   } else if (method == "brent") {
     result = Utils::findRootBrent(func, left, right, ENERGY_BALANCE_TOL, &max_it);
   } else {
     Errors::Message emsg;
-    emsg << "SurfaceEnergyBalance: invalid solver method \""
-         << method << "\", use \"brent\"";
+    emsg << "SurfaceEnergyBalance: invalid solver method \"" << method << "\", use \"brent\"";
     Exceptions::amanzi_throw(emsg);
   }