Merge pull request #114 from cticenhour/fixup-precheck

include/actions/ChemicalReactionsBase.h

@@ -92,7 +92,7 @@ class ChemicalReactionsBase : public Action
   unsigned int _num_constant_reactions;
 
   bool _mole_factor;
-  Real N_A; 
+  Real N_A;
   Real _rate_factor;
 
   std::string _interpolation_type;

include/materials/ADEEDFRateConstantTownsend.h

@@ -25,7 +25,7 @@ class ADEEDFRateConstantTownsend : public ADMaterial
   virtual void computeQpProperties();
 
   SplineInterpolation _coefficient_interpolation;
-  
+
   std::string _coefficient_format;
   ADMaterialProperty<Real> & _townsend_coefficient;
   const MaterialProperty<Real> & _massIncident;

problems/e5_plot.py

@@ -20,8 +20,8 @@
 data = np.genfromtxt(file, dtype=float, delimiter=',', skip_header=1)
 data2 = np.genfromtxt(file2, dtype=float, delimiter=',', skip_header=1)
 data3 = np.genfromtxt(file3, dtype=float, delimiter=',', skip_header=1)
-names =['Ar','Ar+','Production2','Production0','Production3','e'] 
-names2 =['Ar','Ar+','e','Ar+ and e Production rate','Ar+ + e Recombination rate','test 1-Body Production rate'] 
+names =['Ar','Ar+','Production2','Production0','Production3','e']
+names2 =['Ar','Ar+','e','Ar+ and e Production rate','Ar+ + e Recombination rate','test 1-Body Production rate']
 names3 =['N','N+','N2','N2+','N2A','N2B','N2C','N2a1','N3+','N4+','Te','Teff','e','rate0','rate1','rate10','rate11','rate12','rate13','rate14','rate15','rate16','rate17','rate18','rate19','rate2','rate20','rate21','rate22','rate23','rate24','rate25','rate26','rate27','rate28','rate29','rate3','rate30','rate31','rate32','rate33','rate4','rate5','rate6','rate7','rate8','rate9']
 print(data3)
 

problems/e5_track.i

@@ -49,7 +49,7 @@
     sampling_variable = 'reduced_field'
     track_rates = true
     # Add reactions here
-    reactions = 'e + Ar -> e + e + Ar+   : EEDF 
+    reactions = 'e + Ar -> e + e + Ar+   : EEDF
                  e + Ar+ + Ar -> Ar + Ar : 1e-25
                  Ar+ -> Ar+ : 1e-14
 '

problems/first_order_example/lieberman_ex1.i

@@ -1,9 +1,9 @@
 # This input file describes a simple system of two first-order reactions
 #
-# Based on the example shown in the textbook: 
+# Based on the example shown in the textbook:
 #
-# Lieberman, Michael A. and Lichtenberg, Allan J. "Principles of Plasma 
-# Discharges and Materials Processing." Second Edition. John Wiley & Sons, Inc. 
+# Lieberman, Michael A. and Lichtenberg, Allan J. "Principles of Plasma
+# Discharges and Materials Processing." Second Edition. John Wiley & Sons, Inc.
 # (2005)
 #
 # Chapter 9, Section 2, "First-Order Consecutive Reactions)
@@ -12,7 +12,7 @@
 [Mesh]
   # 'Dummy' mesh - a mesh is always needed to run MOOSE, but
   # scalar variables do not exist on a mesh.
-  # When you're doing a 0D problem you just need to give MOOSE 
+  # When you're doing a 0D problem you just need to give MOOSE
   # a single element to work with.
   type = GeneratedMesh
   dim = 1
@@ -104,8 +104,8 @@
   []
 
   # This next one is optional, but highly recommended.
-  # Without this, scalar variables are printed on the terminal as the 
-  # simulation runs. 
+  # Without this, scalar variables are printed on the terminal as the
+  # simulation runs.
   # It's best to keep this on to prevent things from being cluttered.
   [console]
     type = Console

problems/first_order_example/lieberman_ex1_comp.py

@@ -19,7 +19,7 @@ def exact_solution(time, n0, KA, KB):
     Equations 9.2.5 (nA), 9.2.6 (nB), 9.2.8 (nC)
     '''
     nA = n0 * np.exp(-KA * time)
-    
+
     nB = n0 * KA / (KB - KA) * (np.exp(-KA * time) - np.exp(-KB * time))
 
     nC = n0 * (1. + 1./(KA - KB) * (KB * np.exp(-KA * time) - KA * np.exp(-KB * time)))

scripts/fixup_headers.py

@@ -176,4 +176,4 @@ def checkAndUpdatePython(filename):
     parser.add_option("-f", "--force", action="store_true", dest="force", default=False)
 
     (global_options, args) = parser.parse_args()
-    fixupHeader()
+    fixupHeader()

src/actions/AddGeneralReactions.C

@@ -288,7 +288,7 @@ AddGeneralReactions::act()
       // if (_energy_change[i] == true)
       // {
       // Gas temperature is almost in place, but not finished yet.
-      // std::cout << "WARNING: energy dependence is not yet implemented." << std::endl;
+      // mooseError("Energy dependence is not yet implemented.");
       // }
     }
   }
@@ -346,7 +346,6 @@ AddGeneralReactions::act()
           reactant_kernel_name += "Log";
         }
       }
-      // std::cout << energy_kernel_name << ", " << _energy_change[i] << std::endl;
 
       // if (_energy_change[i] && _rate_type[i] == "EEDF")
       // {
@@ -557,8 +556,6 @@ AddGeneralReactions::act()
               InputParameters params = _factory.getValidParams(reactant_kernel_name);
               params.set<NonlinearVariableName>("variable") = _species[j];
               params.set<Real>("coefficient") = _species_count[i][j];
-              // std::cout << getParam<std::vector<SubdomainName>>("block")[0] << ", " <<
-              // _species_count[i][j] << std::endl; mooseError("TESTING");
               params.set<std::string>("reaction") = _reaction[i];
               if (find_other || find_aux)
               {
@@ -670,8 +667,6 @@ AddGeneralReactions::act()
               // If a species is not tracked, it is treated as a background gas.
               for (unsigned int k = 0; k < _reactants[i].size(); ++k)
               {
-                // std::cout << _reaction[i] << ": \n" << "  " << _reactants[i][k] << ", " <<
-                // include_species[k] << std::endl;
                 if (include_species[k])
                 {
                   params.set<std::vector<VariableName>>(other_variables[k]) = {_reactants[i][k]};

src/actions/AddZapdosReactions.C

@@ -299,7 +299,7 @@ AddZapdosReactions::act()
       // First all EEDF-based reactions are added.
       for (unsigned int i = 0; i < _num_eedf_reactions; ++i)
       {
-        std::cout << _ad_prepend + "ReactionRateEEDF" + _townsend_append + _log_append << std::endl;
+        mooseInfo(_ad_prepend, "ReactionRateEEDF", _townsend_append, _log_append);
         if (_coefficient_format == "townsend")
           addAuxRate(_ad_prepend + "ReactionRateEEDF" + _townsend_append + _log_append,
                      _eedf_reaction_number[i],

src/actions/ChemicalReactions.C

@@ -235,7 +235,7 @@ ChemicalReactions::ChemicalReactions(const InputParameters & params)
       //////////
       // if (_rate_equation_string[i].find("Tgas") != std::string::npos)
       // {
-      //   std::cout << "found!" << std::endl;
+      //   mooseInfo("found!");
       // }
       //////////
 
@@ -245,7 +245,7 @@ ChemicalReactions::ChemicalReactions(const InputParameters & params)
       // std::string token;
       // while (std::getline(iss >> std::ws, token,'/'))
       // {
-      //   std::cout << token << std::endl;
+      //   mooseInfo(token);
       // }
     }
     else
@@ -528,11 +528,7 @@ ChemicalReactions::act()
 
   if (gas_tracking)
   {
-    // mooseError("Functionality for tracking neutral gas densities and temperatures is under
-    // development.");
-    std::cout
-        << "WARNING: Functionality for tracking neutral gas densities is still under development."
-        << std::endl;
+    mooseError("Functionality for tracking neutral gas densities is still under development.");
   }
 
   else if (_current_task == "add_function" && _scalar_problem == false)
@@ -741,8 +737,7 @@ ChemicalReactions::act()
       }
       else if (_rate_type[i] == "Equation")
       {
-        std::cout << "WARNING: CRANE cannot yet handle equation-based equations." << std::endl;
-        // This should be a mooseError...but I'm using it for testing purposes.
+        mooseError("CRANE cannot yet handle equation-based equations.");
       }
       else if (_superelastic_reaction[i] == true)
       {
@@ -788,7 +783,7 @@ ChemicalReactions::act()
       if (_energy_change == true)
       {
         // Gas temperature is almost in place, but not finished yet.
-        std::cout << "WARNING: energy dependence is not yet implemented." << std::endl;
+        mooseError("Energy dependence is not yet implemented.");
       }
     }
   }
@@ -801,7 +796,6 @@ ChemicalReactions::act()
     std::vector<Real> rxn_coeff = getParam<std::vector<Real>>("reaction_coefficient");
     for (unsigned int i = 0; i < _num_reactions; ++i)
     {
-      // std::cout << rxn_coeff[i] << std::endl;
       if (_reactants[i].size() == 1)
       {
         product_kernel_name = "Product1BodyScalar";
@@ -881,8 +875,6 @@ ChemicalReactions::act()
 
           if (_species_count[i][j] > 0)
           {
-            // std::cout << _species_count[i][j] << std::endl;
-            // std::cout <<
             InputParameters params = _factory.getValidParams(product_kernel_name);
             params.set<NonlinearVariableName>("variable") = _species[j];
             // params.set<Real>("n_gas") = 3.219e24;

src/actions/ChemicalReactionsBase.C

@@ -357,7 +357,7 @@ ChemicalReactionsBase::ChemicalReactionsBase(const InputParameters & params)
       //////////
       // if (_rate_equation_string[i].find("Tgas") != std::string::npos)
       // {
-      //   std::cout << "found!" << std::endl;
+      //   mooseInfo("found!");
       // }
       //////////
 
@@ -367,7 +367,7 @@ ChemicalReactionsBase::ChemicalReactionsBase(const InputParameters & params)
       // std::string token;
       // while (std::getline(iss >> std::ws, token,'/'))
       // {
-      //   std::cout << token << std::endl;
+      //   mooseInfo(token);
       // }
     }
     else
@@ -388,7 +388,7 @@ ChemicalReactionsBase::ChemicalReactionsBase(const InputParameters & params)
       }
       catch (const std::out_of_range &)
       {
-        std::cerr << "Argument out of range for a double\n";
+        mooseError("Argument out of range for a double\n");
         throw;
       }
       // _rate_coefficient[i] = std::stod(rate_coefficient_string[i]);
@@ -730,15 +730,6 @@ ChemicalReactionsBase::ChemicalReactionsBase(const InputParameters & params)
   }
 
   _num_reactions += superelastic_reactions;
-  // for (unsigned int i=0; i<_num_reactions; ++i)
-  // {
-  //   std::cout << _reaction[i] << std::endl;
-  //   for (unsigned int j=0; j<_species.size(); ++j)
-  //   {
-  //     std::cout << _species[j] << ", " << _species_count[i][j] << std::endl;
-  //   }
-  // }
-  // mooseError("TEST");
   _reaction_coefficient_name.resize(_num_reactions);
   // Find the unique species across all reaction pathways
   // Note that this also accounts for species that are not tracked in case
@@ -910,11 +901,16 @@ ChemicalReactionsBase::ChemicalReactionsBase(const InputParameters & params)
     }
     if (unbalanced)
     {
-      std::cout << "WARNING: The following equations are unbalanced." << std::endl;
+      std:string error_str;
       for (unsigned int i = 0; i < faulty_reaction.size(); ++i)
-        std::cout << "    " << faulty_reaction[i] << std::endl;
+      {
+        error_str.append("    ");
+        error_str.append(faulty_reaction[i]);
+        error_str.append("\n");
+      }
 
-      mooseError("Fix unbalanced reactions or particle conservation will not be enforced.");
+      mooseError("The following equations are unbalanced:\n", error_str,
+                 "Fix unbalanced reactions or particle conservation will not be enforced.");
     }
   }
 

src/auxkernels/BolsigValueScalar.C

@@ -35,9 +35,6 @@ BolsigValueScalar::BolsigValueScalar(const InputParameters & parameters)
 Real
 BolsigValueScalar::computeValue()
 {
-  // std::cout << _data.test(0) << std::endl;
-  // return 0.0;
-
   if (_data_type == "diffusivity")
   {
     mooseError("No diffusivity function yet! Whoops!");

src/auxkernels/EEDFRateCoefficientScalar.C

@@ -35,8 +35,6 @@ EEDFRateCoefficientScalar::EEDFRateCoefficientScalar(const InputParameters & par
 Real
 EEDFRateCoefficientScalar::computeValue()
 {
-  // std::cout << _data.test(0) << std::endl;
-  // return 0.0;
   Real val;
   if (_sample_value)
   {
@@ -49,7 +47,6 @@ EEDFRateCoefficientScalar::computeValue()
     {
       return val;
     }
-    // return _data.coefficient_sample(_reaction_number, _sampler_var[0]/1e-21);
   }
   else
   {

src/auxkernels/ParsedScalarRateCoefficient.C

@@ -69,7 +69,6 @@ ParsedScalarRateCoefficient::ParsedScalarRateCoefficient(const InputParameters &
   // {
     // Real extra_value = _data.electron_temperature(7.7e-20);
     // _constant_names.push_back(getParam<std::vector<std::string>>("file_value")[0]);
-    // std::cout << _reduced_field[_i] << std::endl;
     // if (isCoupledScalar("reduced_field"))
       // _constant_expressions.push_back(std::to_string(_data.electron_temperature(_reduced_field[_i])));
     // else

src/auxkernels/VariableSum.C

@@ -33,9 +33,6 @@ VariableSum::computeValue()
   Real variable_sum = 0;
   for (unsigned int i = 0; i < _nargs; ++i)
   {
-    // variables += (i == 0 ? "" : ",") + getScalarVar("args", i)->name();
-    // _args[i] = &coupledScalarValue("args", i);
-    // std::cout << (*_args[i])[_i] << std::endl;
     variable_sum += coupledScalarValue("args", i)[_i];
   }
   return variable_sum;

src/auxkernels/VariableSumLog.C

@@ -33,9 +33,6 @@ VariableSumLog::computeValue()
   Real variable_sum = 0;
   for (unsigned int i = 0; i < _nargs; ++i)
   {
-    // variables += (i == 0 ? "" : ",") + getScalarVar("args", i)->name();
-    // _args[i] = &coupledScalarValue("args", i);
-    // std::cout << (*_args[i])[_i] << std::endl;
     variable_sum += std::exp(coupledScalarValue("args", i)[_i]);
   }
   return std::log(variable_sum);

src/kernels/ReactionSecondOrder.C

@@ -235,8 +235,6 @@ ReactionSecondOrder::computeQpOffDiagJacobian(unsigned int jvar)
   }
   else
   {
-    // std::cout << getParam<std::string>("reaction") << ": " << _v_eq_u << ", " << _w_eq_u <<
-    // std::endl;
     mooseError("ReactionSecondOrder, computeQpOffDiagJacobian: this is not yet implemented for the "
                "current case.");
   }*/

src/materials/SuperelasticReactionRate.C

@@ -95,5 +95,4 @@ SuperelasticReactionRate::computeQpProperties()
   (delta_a[4]/20.0)*std::pow(_Tgas[_qp], 4.0) - delta_a[5]*std::pow(_Tgas[_qp], -1.0) + delta_a[6]);
 
   _reaction_rate[_qp] = _reversible_rate[_qp] / _equilibrium_constant;
-  // std::cout << _reversible_rate[_qp] << std::endl;
 }