clang-format ChemistryLib

ChemistryLib/Common/CreateChargeBalance.cpp

@@ -9,6 +9,7 @@
  */
 
 #include "CreateChargeBalance.h"
+
 #include "BaseLib/ConfigTree.h"
 #include "BaseLib/Error.h"
 #include "ChargeBalance.h"

ChemistryLib/PhreeqcIO.cpp

@@ -243,14 +243,14 @@ void PhreeqcIO::initializeChemicalSystemConcrete(
 
     for (auto& kinetic_reactant : _chemical_system->kinetic_reactants)
     {
-        initializeReactantMolality(kinetic_reactant, chemical_system_id, medium, pos,
-                            t);
+        initializeReactantMolality(kinetic_reactant, chemical_system_id, medium,
+                                   pos, t);
     }
 
     for (auto& equilibrium_reactant : _chemical_system->equilibrium_reactants)
     {
-        initializeReactantMolality(equilibrium_reactant, chemical_system_id, medium,
-                            pos, t);
+        initializeReactantMolality(equilibrium_reactant, chemical_system_id,
+                                   medium, pos, t);
     }
 }
 

ChemistryLib/PhreeqcIOData/AqueousSolution.cpp

@@ -8,10 +8,11 @@
  *
  */
 
+#include "AqueousSolution.h"
+
 #include <cmath>
 #include <ostream>
 
-#include "AqueousSolution.h"
 #include "ChemistryLib/Common/ChargeBalance.h"
 #include "MeshLib/PropertyVector.h"
 

ChemistryLib/PhreeqcIOData/ChemicalSystem.cpp

@@ -9,8 +9,8 @@
  */
 
 #include "ChemicalSystem.h"
-#include "AqueousSolution.h"
 
+#include "AqueousSolution.h"
 #include "MathLib/LinAlg/MatrixVectorTraits.h"
 #include "MathLib/LinAlg/UnifiedMatrixSetters.h"
 

ChemistryLib/PhreeqcIOData/CreateAqueousSolution.cpp

@@ -9,6 +9,7 @@
  */
 
 #include "CreateAqueousSolution.h"
+
 #include "AqueousSolution.h"
 #include "BaseLib/ConfigTree.h"
 #include "ChemistryLib/Common/CreateChargeBalance.h"

ChemistryLib/PhreeqcIOData/CreateChemicalSystem.cpp

@@ -9,6 +9,7 @@
  */
 
 #include "CreateChemicalSystem.h"
+
 #include "BaseLib/ConfigTree.h"
 #include "ChemicalSystem.h"
 #include "CreateAqueousSolution.h"

ChemistryLib/PhreeqcIOData/CreateEquilibriumReactants.cpp

@@ -53,8 +53,11 @@ std::vector<EquilibriumReactant> createEquilibriumReactants(
             mesh, name + "_avg", MeshLib::MeshItemType::Cell, 1);
         mesh_prop_molality->resize(mesh.getNumberOfElements());
 
-        equilibrium_reactants.emplace_back(
-            std::move(name), molality, volume_fraction, mesh_prop_molality, saturation_index);
+        equilibrium_reactants.emplace_back(std::move(name),
+                                           molality,
+                                           volume_fraction,
+                                           mesh_prop_molality,
+                                           saturation_index);
     }
 
     return equilibrium_reactants;

ChemistryLib/PhreeqcIOData/CreateKnobs.cpp

@@ -9,6 +9,7 @@
  */
 
 #include "CreateKnobs.h"
+
 #include "BaseLib/ConfigTree.h"
 #include "Knobs.h"
 

ChemistryLib/PhreeqcIOData/CreateOutput.cpp

@@ -8,12 +8,13 @@
  *
  */
 
+#include "CreateOutput.h"
+
 #include <algorithm>
 #include <numeric>
 
 #include "AqueousSolution.h"
 #include "ChemicalSystem.h"
-#include "CreateOutput.h"
 #include "KineticReactant.h"
 #include "UserPunch.h"
 

ChemistryLib/PhreeqcIOData/CreateSolutionComponent.cpp

@@ -9,6 +9,7 @@
  */
 
 #include "CreateSolutionComponent.h"
+
 #include "AqueousSolution.h"
 #include "BaseLib/ConfigTree.h"
 

ChemistryLib/PhreeqcIOData/Dump.cpp

@@ -8,21 +8,24 @@
  *
  */
 
-#include <iostream>
-
 #include "Dump.h"
 
+#include <iostream>
+
 namespace ChemistryLib
 {
 namespace PhreeqcIOData
 {
 void Dump::print(std::ostream& os, std::size_t const num_chemical_systems) const
 {
-    os << "DUMP" << "\n";
+    os << "DUMP"
+       << "\n";
     os << "-file " << dump_file << "\n";
-    os << "-append false" << "\n";
+    os << "-append false"
+       << "\n";
     os << "-solution 1-" << num_chemical_systems << "\n";
-    os << "END" << "\n";
+    os << "END"
+       << "\n";
 }
 
 void Dump::readDumpFile(std::istream& in,

ChemistryLib/PhreeqcIOData/EquilibriumReactant.cpp

@@ -8,10 +8,10 @@
  *
  */
 
-#include <ostream>
-
 #include "EquilibriumReactant.h"
 
+#include <ostream>
+
 namespace ChemistryLib
 {
 namespace PhreeqcIOData

ChemistryLib/PhreeqcIOData/KineticReactant.cpp

@@ -8,10 +8,10 @@
  *
  */
 
-#include <ostream>
-
 #include "KineticReactant.h"
 
+#include <ostream>
+
 namespace ChemistryLib
 {
 namespace PhreeqcIOData

ChemistryLib/PhreeqcIOData/Knobs.cpp

@@ -8,17 +8,18 @@
  *
  */
 
-#include <ostream>
-
 #include "Knobs.h"
 
+#include <ostream>
+
 namespace ChemistryLib
 {
 namespace PhreeqcIOData
 {
 std::ostream& operator<<(std::ostream& os, Knobs const& knobs)
 {
-    os << "KNOBS" << "\n";
+    os << "KNOBS"
+       << "\n";
     os << "-iterations " << knobs.max_iterations << "\n";
     os << "-convergence_tolerance " << knobs.relative_convergence_tolerance
        << "\n";

ChemistryLib/PhreeqcIOData/Output.cpp

@@ -8,10 +8,10 @@
  *
  */
 
-#include <ostream>
-
 #include "Output.h"
 
+#include <ostream>
+
 namespace ChemistryLib
 {
 namespace PhreeqcIOData
@@ -19,7 +19,8 @@ namespace PhreeqcIOData
 std::ostream& operator<<(std::ostream& os,
                          BasicOutputSetups const& basic_output_setups)
 {
-    os << "SELECTED_OUTPUT" << "\n";
+    os << "SELECTED_OUTPUT"
+       << "\n";
     os << "-file " << basic_output_setups.output_file << "\n";
     os << "-high_precision " << std::boolalpha
        << basic_output_setups.use_high_precision << "\n";

ChemistryLib/PhreeqcIOData/ReactionRate.cpp

@@ -8,10 +8,10 @@
  *
  */
 
-#include <ostream>
-
 #include "ReactionRate.h"
 
+#include <ostream>
+
 namespace ChemistryLib
 {
 namespace PhreeqcIOData
@@ -19,14 +19,16 @@ namespace PhreeqcIOData
 std::ostream& operator<<(std::ostream& os, ReactionRate const& reaction_rate)
 {
     os << reaction_rate.kinetic_reactant << "\n";
-    os << "-start" << "\n";
+    os << "-start"
+       << "\n";
     int line_number = 1;
     for (auto const& expression_statement : reaction_rate.expression_statements)
     {
         os << line_number << " " << expression_statement << "\n";
         ++line_number;
     }
-    os << "-end" << "\n";
+    os << "-end"
+       << "\n";
 
     return os;
 }

ChemistryLib/PhreeqcIOData/Surface.cpp

@@ -8,10 +8,10 @@
  *
  */
 
-#include <ostream>
-
 #include "Surface.h"
 
+#include <ostream>
+
 namespace ChemistryLib
 {
 namespace PhreeqcIOData

ChemistryLib/PhreeqcIOData/UserPunch.cpp

@@ -9,6 +9,7 @@
  */
 
 #include "UserPunch.h"
+
 #include "BaseLib/ConfigTreeUtil.h"
 
 namespace ChemistryLib
@@ -25,7 +26,8 @@ void UserPunch::initialize(std::size_t const num_chemical_systems)
 
 std::ostream& operator<<(std::ostream& os, UserPunch const& user_punch)
 {
-    os << "USER_PUNCH" << "\n";
+    os << "USER_PUNCH"
+       << "\n";
     os << "-headings ";
     auto const& secondary_variables = user_punch.secondary_variables;
     for (auto& secondary_variable : secondary_variables)
@@ -34,14 +36,16 @@ std::ostream& operator<<(std::ostream& os, UserPunch const& user_punch)
     }
     os << "\n";
 
-    os << "-start" << "\n";
+    os << "-start"
+       << "\n";
     int line_number = 1;
     for (auto const& statement : user_punch.statements)
     {
         os << line_number << " " << statement << "\n";
         ++line_number;
     }
-    os << "-end" << "\n";
+    os << "-end"
+       << "\n";
 
     return os;
 }

ChemistryLib/PhreeqcKernelData/CreateInitialAqueousSolution.cpp

@@ -9,6 +9,7 @@
  */
 
 #include "CreateInitialAqueousSolution.h"
+
 #include "BaseLib/ConfigTree.h"
 #include "BaseLib/Error.h"
 #include "ChemistryLib/Common/ChargeBalance.h"

ChemistryLib/PhreeqcKernelData/KineticReactant.cpp

@@ -8,10 +8,10 @@
  *
  */
 
-#include <algorithm>
-
 #include "KineticReactant.h"
 
+#include <algorithm>
+
 namespace ChemistryLib
 {
 namespace PhreeqcKernelData