feat(reaclib): working on building efficient reaclib tooling for general nuclear network

this commit primarily adds a more robust ability to cull reactions that are not needed from the generated header

assets/static/atomic/meson.build

@@ -1,4 +1,15 @@
+required_headers = [
+    'atomicSpecies.h',
+]
+
+foreach h : required_headers
+    if not cpp.has_header(h, include_directories: include_directories('include'))
+        error('SERiF requires the header file ' + h + ' to be present in the assets/static/atomic/include directory.')
+    endif
+endforeach
+
 species_weight_dep = declare_dependency(
     include_directories: include_directories('include'),
 )
+
 message('✅ SERiF species_weight dependency declared')

src/composition/private/composition.cpp

@@ -33,11 +33,11 @@
 
 namespace serif::composition {
 
-    CompositionEntry::CompositionEntry() : m_symbol("H-1"), m_isotope(chemSpecies::species.at("H-1")),
+    CompositionEntry::CompositionEntry() : m_symbol("H-1"), m_isotope(serif::atomic::species.at("H-1")),
                                            m_initialized(false) {
     }
 
-    CompositionEntry::CompositionEntry(const std::string& symbol, const bool massFracMode) : m_symbol(symbol), m_isotope(chemSpecies::species.at(symbol)), m_massFracMode(massFracMode) {
+    CompositionEntry::CompositionEntry(const std::string& symbol, const bool massFracMode) : m_symbol(symbol), m_isotope(serif::atomic::species.at(symbol)), m_massFracMode(massFracMode) {
         setSpecies(symbol);
     }
 
@@ -54,11 +54,11 @@ namespace serif::composition {
         if (m_initialized) {
             throw std::runtime_error("Composition entry is already initialized.");
         }
-        if (chemSpecies::species.count(symbol) == 0) {
+        if (serif::atomic::species.count(symbol) == 0) {
             throw std::runtime_error("Invalid symbol.");
         }
         m_symbol = symbol;
-        m_isotope = chemSpecies::species.at(symbol);
+        m_isotope = serif::atomic::species.at(symbol);
         m_initialized = true;
     }
 
@@ -99,7 +99,7 @@ namespace serif::composition {
         return m_relAbundance;
     }
 
-    chemSpecies::Species CompositionEntry::isotope() const {
+    serif::atomic::Species CompositionEntry::isotope() const {
         return m_isotope;
     }
 
@@ -256,7 +256,7 @@ namespace serif::composition {
     }
 
     bool Composition::isValidSymbol(const std::string& symbol) {
-        return chemSpecies::species.contains(symbol);
+        return serif::atomic::species.contains(symbol);
     }
 
     double Composition::setMassFraction(const std::string& symbol, const double& mass_fraction) {

src/composition/public/composition.h

@@ -63,7 +63,7 @@ namespace serif::composition {
      */
     struct CompositionEntry {
         std::string m_symbol; ///< The chemical symbol of the species.
-        chemSpecies::Species m_isotope; ///< The isotope of the species.
+        serif::atomic::Species m_isotope; ///< The isotope of the species.
         bool m_massFracMode = true; ///< The mode of the composition entry. True if mass fraction, false if number fraction.   
 
         double m_massFraction = 0.0; ///< The mass fraction of the species.
@@ -142,7 +142,7 @@ namespace serif::composition {
          * @brief Gets the isotope of the species.
          * @return The isotope of the species.
          */
-        chemSpecies::Species isotope() const;
+        serif::atomic::Species isotope() const;
 
         /**
          * @brief Gets the mode of the composition entry.

tests/composition/compositionTest.cpp

@@ -18,10 +18,10 @@ class compositionTest : public ::testing::Test {};
  * @brief Test the constructor of the composition class.
  */
 TEST_F(compositionTest, isotopeMasses) {
-    EXPECT_NO_THROW(chemSpecies::species.at("H-1"));
-    EXPECT_DOUBLE_EQ(chemSpecies::species.at("H-1").mass(), 1.007825031898);
-    EXPECT_DOUBLE_EQ(chemSpecies::species.at("He-3").mass(), 3.0160293219700001);
-    EXPECT_DOUBLE_EQ(chemSpecies::species.at("He-4").mass(),4.0026032541300003);
+    EXPECT_NO_THROW(serif::atomic::species.at("H-1"));
+    EXPECT_DOUBLE_EQ(serif::atomic::species.at("H-1").mass(), 1.007825031898);
+    EXPECT_DOUBLE_EQ(serif::atomic::species.at("He-3").mass(), 3.0160293219700001);
+    EXPECT_DOUBLE_EQ(serif::atomic::species.at("He-4").mass(),4.0026032541300003);
 }
 
 TEST_F(compositionTest, constructor) {
@@ -135,7 +135,7 @@ TEST_F(compositionTest, getComposition) {
     comp.setMassFraction("He-4", 0.4);
     EXPECT_NO_THROW(comp.finalize());
 
-    auto compositionEntry = comp.getComposition("H-1");
+    const auto compositionEntry = comp.getComposition("H-1");
     EXPECT_DOUBLE_EQ(compositionEntry.first.mass_fraction(), 0.6);
     EXPECT_DOUBLE_EQ(compositionEntry.second.meanParticleMass, 1.4382769310381101);
     EXPECT_DOUBLE_EQ(compositionEntry.second.specificNumberDensity, 1.0/1.4382769310381101);