fix(standard_compositions.cpp): found and fixed h and he leaking out of the composition data

added a check for H and He getting added to SpeciesObject and cleaned up some variable names  and filenames

src/composition/include/fourdst/composition/io/StandardMetalFractionsBinary.h

@@ -2,7 +2,7 @@
 
 #include <cstddef>
 
-const unsigned char StandardAbundances[] = {
+const unsigned char StandardMetalFractions[] = {
     0x53, 0x45, 0x43, 0x54, 0x49, 0x4f, 0x4e, 0x53, 0x20, 0x5b, 0x61, 0x62, 0x75, 0x6e, 0x64, 0x61, 
     0x6e, 0x63, 0x65, 0x20, 0x64, 0x61, 0x74, 0x61, 0x2c, 0x20, 0x69, 0x73, 0x6f, 0x74, 0x6f, 0x70, 
     0x69, 0x63, 0x20, 0x70, 0x65, 0x72, 0x63, 0x65, 0x6e, 0x74, 0x61, 0x67, 0x65, 0x5d, 0x0a, 0x43, 
@@ -1458,4 +1458,4 @@ const unsigned char StandardAbundances[] = {
     0x65, 0x6e, 0x74, 0x61, 0x67, 0x65, 0x0a, 
 };
 
-const size_t StandardAbundances_len = sizeof(StandardAbundances);
+const size_t StandardMetalFractions_len = sizeof(StandardMetalFractions);

src/composition/lib/io/standard_compositions.cpp

@@ -1,5 +1,5 @@
 #include "fourdst/composition/io/standard_compositions.h"
-#include "fourdst/composition/io/StandardAbundancesBinary.h"
+#include "fourdst/composition/io/StandardMetalFractionsBinary.h"
 
 #include "fourdst/composition/composition.h"
 #include "fourdst/atomic/atomicSpecies.h"
@@ -252,13 +252,13 @@ namespace fourdst::composition {
         std::vector<char> data;
 
         io::ChemicalFileParser parser;
-        io::CompositionData compositions;
+        io::CompositionData metals;
 
         io::IsotopicPercentage isotopes;
 
-        data = std::ranges::to<std::vector<char>>(StandardAbundances);
+        data = std::ranges::to<std::vector<char>>(StandardMetalFractions);
 
-        compositions = parser.parse_compositon_data(data,metal_fraction_scheme);
+        metals = parser.parse_compositon_data(data,metal_fraction_scheme);
         isotopes = parser.parse_isotopic_percentage(data,isotopic_percentage_scheme);
 
         std::string name;
@@ -267,7 +267,7 @@ namespace fourdst::composition {
 
         // construct name of the isotopes for all elements
         for (const auto [E,A] : std::ranges::views::zip(isotopes.elements, isotopes.mass_numbers)){
-            if (std::ranges::contains(compositions.elements,E)) {
+            if (std::ranges::contains(metals.elements,E ) || E == "H" || E == "He") {
                 name = std::format("{}-{}",E,A);
                 auto SpeciesObject = atomic::species.at(name);
                 species.push_back(SpeciesObject);
@@ -297,7 +297,7 @@ namespace fourdst::composition {
 
         // multiply by atomic weight if needed
 
-        if (compositions.requires_atomic_weight){
+        if (metals.requires_atomic_weight){
             // get isotope with max abundance for each metal
             // and store the corresponding mass number
             auto element_atomic_weight = [&isotopes]() {
@@ -316,7 +316,7 @@ namespace fourdst::composition {
                 return elem_info;
             }();
 
-            for (const auto [E,A] : std::ranges::views::zip(compositions.elements, compositions.abundances)) {
+            for (const auto [E,A] : std::ranges::views::zip(metals.elements, metals.abundances)) {
                 // std::println("element: {}", E);
                 auto name = std::format("{}-{}",E,element_atomic_weight.at(E).second);
                 // std::println("{}", name);
@@ -326,7 +326,7 @@ namespace fourdst::composition {
                 // std::println("End");
             }
         } else {
-            for (const auto [E,A] : std::ranges::views::zip(compositions.elements, compositions.abundances)) {
+            for (const auto [E,A] : std::ranges::views::zip(metals.elements, metals.abundances)) {
                 metal_fractions.emplace(E,A);
             }
         }

src/composition/meson.build

@@ -6,7 +6,7 @@ required_headers = [
     'fourdst/composition/composition_abstract.h',
     'fourdst/composition/exceptions/exceptions_composition.h',
     'fourdst/composition/io/standard_compositions.h',
-    'fourdst/composition/io/StandardAbundancesBinary.h'
+    'fourdst/composition/io/StandardMetalFractionsBinary.h'
 ]
 
 foreach h : required_headers
@@ -56,7 +56,7 @@ composition_headers = files(
   'include/fourdst/composition/composition.h',
   'include/fourdst/composition/composition_abstract.h',
   'include/fourdst/composition/io/standard_compositions.h',
-  'include/fourdst/composition/io/StandardAbundancesBinary.h'
+  'include/fourdst/composition/io/StandardMetalFractionsBinary.h'
 
 )
 install_headers(composition_headers, subdir : 'fourdst/fourdst/composition')

tests/composition/sandbox/sandbox.cpp

@@ -1,21 +1,12 @@
 #include "fourdst/composition/io/standard_compositions.h"
-#include "fourdst/composition/io/StandardAbundancesBinary.h"
-
 #include "fourdst/composition/composition.h"
-#include "fourdst/atomic/atomicSpecies.h"
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
 
 #include <string>
 #include <vector>
-#include <algorithm>
-#include <fstream>
 #include <numeric>
-#include <stdexcept>
 #include <unordered_map>
-#include <print>
 #include <ranges>
-#include <algorithm>
 #include "CLI/CLI.hpp"
 
 int main(int argc, char** argv) {
@@ -32,7 +23,7 @@ int main(int argc, char** argv) {
     
     CLI::App app("Example App To Load Solar Composition");
     app.add_option("-z,--initial_z", initial_z, "Initial Z")->required();
-    app.add_option("-c,--solar-composition", metal_fraction_scheme)->
+    app.add_option("-c,--metal-fraction-scheme", metal_fraction_scheme)->
         check(
             CLI::IsMember(
                 keys,
@@ -46,7 +37,6 @@ int main(int argc, char** argv) {
 
     // the following four should be user input
     // initial_y can be optional
-    // initial_z = 0.02;
     initial_y = 0.24 + 2*initial_z;
     isotopic_percentage_scheme = "L03_data";