Merge pull request #2522 from renchao-lu/SmallFixesPhreeqcInterface

Fixed a few cppcheck/clang-tidy warnings in chemistry library

ChemistryLib/CreateOutput.cpp

@@ -7,7 +7,9 @@
  *
  */
 
+#include <algorithm>
 #include <numeric>
+
 #include "CreateOutput.h"
 
 namespace ChemistryLib
@@ -21,20 +23,16 @@ std::unique_ptr<Output> createOutput(
     // Mark which phreeqc output items will be held.
     std::vector<OutputItem> accepted_items{{"pH", ItemType::pH},
                                            {"pe", ItemType::pe}};
-    for (auto const& component : components)
-    {
-        accepted_items.emplace_back(component.name, ItemType::Component);
-    }
-    for (auto const& equilibrium_phase : equilibrium_phases)
-    {
-        accepted_items.emplace_back(equilibrium_phase.name,
-                                    ItemType::EquilibriumPhase);
-    }
-    for (auto const& kinetic_reactant : kinetic_reactants)
-    {
-        accepted_items.emplace_back(kinetic_reactant.name,
-                                    ItemType::KineticReactant);
-    }
+
+    auto accepted_item = [](auto const& item) {
+        return OutputItem(item.name, item.item_type);
+    };
+    std::transform(components.begin(), components.end(),
+                   std::back_inserter(accepted_items), accepted_item);
+    std::transform(equilibrium_phases.begin(), equilibrium_phases.end(),
+                   std::back_inserter(accepted_items), accepted_item);
+    std::transform(kinetic_reactants.begin(), kinetic_reactants.end(),
+                   std::back_inserter(accepted_items), accepted_item);
 
     // Record ids of which phreeqc output items will be dropped.
     BasicOutputSetups basic_output_setups(project_file_name);
@@ -58,7 +56,7 @@ std::unique_ptr<Output> createOutput(
         dvalue_item_id += 2 * (i + 1);
     }
 
-    return std::make_unique<Output>(basic_output_setups,
+    return std::make_unique<Output>(std::move(basic_output_setups),
                                     std::move(accepted_items),
                                     std::move(dropped_item_ids));
 }

ChemistryLib/Output.h

@@ -76,10 +76,10 @@ struct OutputItem
 
 struct Output
 {
-    Output(BasicOutputSetups basic_output_setups_,
+    Output(BasicOutputSetups&& basic_output_setups_,
            std::vector<OutputItem>&& accepted_items_,
            std::vector<int>&& dropped_item_ids_)
-        : basic_output_setups(basic_output_setups_),
+        : basic_output_setups(std::move(basic_output_setups_)),
           accepted_items(std::move(accepted_items_)),
           dropped_item_ids(std::move(dropped_item_ids_))
     {

ChemistryLib/PhreeqcIO.h

@@ -80,6 +80,6 @@ private:
     std::unique_ptr<Output> const _output;
     std::vector<std::pair<int, std::string>> const&
         _process_id_to_component_name_map;
-    double _dt;
+    double _dt = std::numeric_limits<double>::quiet_NaN();
 };
 }  // namespace ChemistryLib

ChemistryLib/PhreeqcIOData/AqueousSolution.h

@@ -13,6 +13,8 @@
 #include <string>
 #include <vector>
 
+#include "ChemistryLib/Output.h"
+
 namespace ChemistryLib
 {
 struct Component
@@ -20,7 +22,8 @@ struct Component
     explicit Component(std::string name_) : name(std::move(name_)) {}
 
     std::string const name;
-    double amount;
+    double amount = std::numeric_limits<double>::quiet_NaN();
+    static const ItemType item_type = ItemType::Component;
 };
 
 enum class MeansOfAdjustingCharge
@@ -50,7 +53,7 @@ struct AqueousSolution
 
     double temperature;
     double pressure;
-    double pH;
+    double pH = std::numeric_limits<double>::quiet_NaN();
     double pe;
     std::vector<Component> components;
     MeansOfAdjustingCharge const means_of_adjusting_charge;

ChemistryLib/PhreeqcIOData/CreateReactionRate.cpp

@@ -29,17 +29,18 @@ std::vector<ReactionRate> createReactionRates(
             //! \ogs_file_param{prj__chemical_system__rates__rate__kinetic_reactant}
             rate_config.getConfigParameter<std::string>("kinetic_reactant");
 
-        std::vector<std::string> expression_statements;
         auto const expression_config =
             //! \ogs_file_param{prj__chemical_system__rates__rate__expression}
             rate_config.getConfigSubtree("expression");
-        for (
-            auto const& expression_statement :
+        auto const& statements =
             //! \ogs_file_param{prj__chemical_system__rates__rate__expression__statement}
-            expression_config.getConfigParameterList<std::string>("statement"))
-        {
-            expression_statements.push_back(expression_statement);
-        }
+            expression_config.getConfigParameterList<std::string>("statement");
+
+        std::vector<std::string> expression_statements;
+        expression_statements.reserve(statements.size());
+        std::copy(begin(statements),
+                  end(statements),
+                  back_inserter(expression_statements));
 
         reaction_rates.emplace_back(std::move(kinetic_reactant),
                                     std::move(expression_statements));

ChemistryLib/PhreeqcIOData/EquilibriumPhase.h

@@ -13,6 +13,8 @@
 #include <string>
 #include <vector>
 
+#include "ChemistryLib/Output.h"
+
 namespace BaseLib
 {
 class ConfigTree;
@@ -38,5 +40,6 @@ struct EquilibriumPhase
     std::string const name;
     double amount;
     double const saturation_index;
+    static const ItemType item_type = ItemType::EquilibriumPhase;
 };
 }  // namespace ChemistryLib

ChemistryLib/PhreeqcIOData/KineticReactant.h

@@ -14,6 +14,8 @@
 #include <string>
 #include <vector>
 
+#include "ChemistryLib/Output.h"
+
 namespace ChemistryLib
 {
 struct KineticReactant
@@ -36,5 +38,6 @@ struct KineticReactant
     std::string const name;
     double amount;
     std::vector<double> const parameters;
+    static const ItemType item_type = ItemType::KineticReactant;
 };
 }  // namespace ChemistryLib