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docs(docs): added robust docs

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This commit is contained in:
Emily Boudreaux
2025-07-24 09:35:52 -04:00
parent 1905e642ab
commit 9f5ef7fd6a
452 changed files with 578689 additions and 218 deletions
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18
src/composition/lib/composition.cpp
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@@ -31,7 +31,6 @@
#include "fourdst/composition/atomicSpecies.h"
#include "fourdst/composition/species.h"
#include "fourdst/composition/composition.h"
#include "fourdst/constants/const.h"
#include "fourdst/composition/exceptions/exceptions_composition.h"
namespace fourdst::composition {
@@ -39,7 +38,7 @@ namespace fourdst::composition {
CompositionEntry::CompositionEntry() :
m_symbol("H-1"),
m_isotope(fourdst::atomic::species.at("H-1")),
m_initialized(false) {}
m_initialized(false) {} // Note: Default entry is uninitialized, must be explicitly set.
CompositionEntry::CompositionEntry(const std::string& symbol, const bool massFracMode) : m_symbol(symbol), m_isotope(fourdst::atomic::species.at(symbol)), m_massFracMode(massFracMode) {
setSpecies(symbol);
@@ -81,6 +80,8 @@ namespace fourdst::composition {
if (m_massFracMode) {
return m_massFraction;
}
// Convert from number fraction to mass fraction using: X_i = n_i * A_i / <A>
// where m_relAbundance is n_i * A_i and meanMolarMass is <A>.
return m_relAbundance / meanMolarMass;
}
@@ -94,6 +95,8 @@ namespace fourdst::composition {
double CompositionEntry::number_fraction(const double totalMoles) const {
if (m_massFracMode) {
// Convert from mass fraction to number fraction using: n_i = (X_i / A_i) / sum(X_j / A_j)
// where m_relAbundance is X_i / A_i and totalMoles is sum(X_j / A_j).
return m_relAbundance / totalMoles;
}
return m_numberFraction;
@@ -425,6 +428,7 @@ namespace fourdst::composition {
m_finalized = false;
return false;
}
// After validation, calculate the specific number density (total moles per unit mass).
for (const auto &entry: m_compositions | std::views::values) {
m_specificNumberDensity += entry.rel_abundance();
}
@@ -458,6 +462,7 @@ namespace fourdst::composition {
m_finalized = false;
return false;
}
// After validation, calculate the mean particle mass.
for (const auto &entry: m_compositions | std::views::values) {
m_meanParticleMass += entry.rel_abundance();
}
@@ -477,7 +482,7 @@ namespace fourdst::composition {
}
std::set<std::string> mixedSymbols = other.getRegisteredSymbols();
// Get the union of the two sets
// Get the union of the two sets of symbols to ensure all species are included in the new composition.
mixedSymbols.insert(m_registeredSymbols.begin(), m_registeredSymbols.end());
Composition mixedComposition(mixedSymbols);
@@ -487,6 +492,7 @@ namespace fourdst::composition {
const double thisMassFrac = hasSymbol(symbol) ? getMassFraction(symbol) : 0.0;
otherMassFrac = other.hasSymbol(symbol) ? other.getMassFraction(symbol) : 0.0;
// The mixing formula is a linear interpolation of mass fractions.
double massFraction = fraction * thisMassFrac + otherMassFrac * (1-fraction);
mixedComposition.setMassFraction(symbol, massFraction);
}
@@ -502,7 +508,7 @@ namespace fourdst::composition {
if (!m_compositions.contains(symbol)) {
LOG_ERROR(m_logger, "Symbol {} is not in the composition.", symbol);
std::string currentSymbols;
int count = 0;
size_t count = 0;
for (const auto& sym : m_compositions | std::views::keys) {
currentSymbols += sym;
if (count < m_compositions.size() - 2) {
@@ -622,9 +628,11 @@ namespace fourdst::composition {
// Loop through all registered species in the composition.
for (const auto &val: m_compositions | std::views::values) {
// Sum of (X_i * Z_i / A_i)
zSum += (val.mass_fraction() * val.m_isotope.z())/val.m_isotope.a();
}
// Calculate mean atomic number <Z> = <A> * sum(X_i * Z_i / A_i)
const double mean_A = m_meanParticleMass * zSum;
return mean_A;
}
@@ -763,7 +771,7 @@ namespace fourdst::composition {
std::ostream& operator<<(std::ostream& os, const Composition& composition) {
os << "Composition(finalized: " << (composition.m_finalized ? "true" : "false") << ", " ;
int count = 0;
size_t count = 0;
for (const auto &entry: composition.m_compositions | std::views::values) {
os << entry;
if (count < composition.m_compositions.size() - 1) {