diff --git a/docs/html/atomic_8dox.html b/docs/html/atomic_8dox.html new file mode 100644 index 0000000..94f0dcf --- /dev/null +++ b/docs/html/atomic_8dox.html @@ -0,0 +1,131 @@ + + +
+ + + + +|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
Documentation for the fourdst::atomic namespace. +More...
++Namespaces | |
| namespace | fourdst::atomic |
| Contains canonical information about atomic species and elements used by 4D-STAR. | |
Documentation for the fourdst::atomic namespace.
+ +Definition in file atomic.dox.
+|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
This is the complete list of members for CompositionAbstract, including all inherited members.
+| contains(const fourdst::atomic::Species &species) const noexcept=0 | CompositionAbstract | pure virtual |
| contains(const std::string &symbol) const =0 | CompositionAbstract | pure virtual |
| getElectronAbundance() const noexcept=0 | CompositionAbstract | pure virtual |
| getMassFraction() const noexcept=0 | CompositionAbstract | pure virtual |
| getMassFraction(const std::string &symbol) const =0 | CompositionAbstract | pure virtual |
| getMassFraction(const fourdst::atomic::Species &species) const =0 | CompositionAbstract | pure virtual |
| getMassFractionVector() const noexcept=0 | CompositionAbstract | pure virtual |
| getMeanParticleMass() const noexcept=0 | CompositionAbstract | pure virtual |
| getMolarAbundance(const std::string &symbol) const =0 | CompositionAbstract | pure virtual |
| getMolarAbundance(const fourdst::atomic::Species &species) const =0 | CompositionAbstract | pure virtual |
| getMolarAbundanceVector() const noexcept=0 | CompositionAbstract | pure virtual |
| getNumberFraction() const noexcept=0 | CompositionAbstract | pure virtual |
| getNumberFraction(const std::string &symbol) const =0 | CompositionAbstract | pure virtual |
| getNumberFraction(const fourdst::atomic::Species &species) const =0 | CompositionAbstract | pure virtual |
| getNumberFractionVector() const noexcept=0 | CompositionAbstract | pure virtual |
| getRegisteredSpecies() const noexcept=0 | CompositionAbstract | pure virtual |
| getRegisteredSymbols() const noexcept=0 | CompositionAbstract | pure virtual |
| getSpeciesAtIndex(size_t index) const =0 | CompositionAbstract | pure virtual |
| getSpeciesIndex(const std::string &symbol) const =0 | CompositionAbstract | pure virtual |
| getSpeciesIndex(const fourdst::atomic::Species &species) const =0 | CompositionAbstract | pure virtual |
| size() const noexcept=0 | CompositionAbstract | pure virtual |
| ~CompositionAbstract()=default | CompositionAbstract | virtual |
|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
Abstract base class for chemical composition representations. + More...
+ +#include <composition_abstract.h>
+Public Member Functions | |
| virtual | ~CompositionAbstract ()=default |
| Virtual destructor. | |
| virtual bool | contains (const fourdst::atomic::Species &species) const noexcept=0 |
| Check if the composition contains the given species. | |
| virtual bool | contains (const std::string &symbol) const =0 |
| Check if the composition contains the given species. | |
| virtual size_t | size () const noexcept=0 |
| virtual std::set< std::string > | getRegisteredSymbols () const noexcept=0 |
| Get all registered chemical symbols in the composition. | |
| virtual const std::set< fourdst::atomic::Species > & | getRegisteredSpecies () const noexcept=0 |
| Get all registered atomic species in the composition. | |
| virtual std::unordered_map< fourdst::atomic::Species, double > | getMassFraction () const noexcept=0 |
| Get the mass fraction for all registered symbols. | |
| virtual std::unordered_map< fourdst::atomic::Species, double > | getNumberFraction () const noexcept=0 |
| Get the number fraction for all registered symbols. | |
| virtual double | getMassFraction (const std::string &symbol) const =0 |
| Get the mass fraction for a given symbol. | |
| virtual double | getMassFraction (const fourdst::atomic::Species &species) const =0 |
| Get the mass fraction for a given species. | |
| virtual double | getNumberFraction (const std::string &symbol) const =0 |
| Get the number fraction for a given symbol. | |
| virtual double | getNumberFraction (const fourdst::atomic::Species &species) const =0 |
| Get the number fraction for a given species. | |
| virtual double | getMolarAbundance (const std::string &symbol) const =0 |
| Get the molar abundance for a given symbol. | |
| virtual double | getMolarAbundance (const fourdst::atomic::Species &species) const =0 |
| Get the molar abundance for a given species. | |
| virtual double | getMeanParticleMass () const noexcept=0 |
| Get the mean particle mass of the composition. | |
| virtual double | getElectronAbundance () const noexcept=0 |
| Get the electron abundance of the composition. | |
| virtual std::vector< double > | getMassFractionVector () const noexcept=0 |
| Get the mass fraction as a vector. | |
| virtual std::vector< double > | getNumberFractionVector () const noexcept=0 |
| Get the number fraction as a vector. | |
| virtual std::vector< double > | getMolarAbundanceVector () const noexcept=0 |
| Get the molar abundance as a vector. | |
| virtual size_t | getSpeciesIndex (const std::string &symbol) const =0 |
| Get the index of a species by symbol. | |
| virtual size_t | getSpeciesIndex (const fourdst::atomic::Species &species) const =0 |
| Get the index of a species. | |
| virtual fourdst::atomic::Species | getSpeciesAtIndex (size_t index) const =0 |
| Get the species at a given index. | |
Abstract base class for chemical composition representations.
+The purpose of this class is to define a standard interface for all composition types. Children of this class are responsible for implementing the setter methods, but any object that is a child of CompositionAbstract will always have these getter methods.
+This ensures that all derived composition classes provide a consistent API for querying composition properties, regardless of how the data is set or stored.
+Definition at line 33 of file composition_abstract.h.
+
+
|
+ +virtualdefault | +
Virtual destructor.
+ +
+
|
+ +nodiscardpure virtualnoexcept | +
Check if the composition contains the given species.
+| species | The atomic species to check. |
Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtual | +
Check if the composition contains the given species.
+| symbol | The symbol of the atomic species to check. |
Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtualnoexcept | +
Get the electron abundance of the composition.
+Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtualnoexcept | +
Get the mass fraction for all registered symbols.
+Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtual | +
Get the mass fraction for a given species.
+| species | The atomic species. |
Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtual | +
Get the mass fraction for a given symbol.
+| symbol | The chemical symbol. |
Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtualnoexcept | +
Get the mass fraction as a vector.
+Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtualnoexcept | +
Get the mean particle mass of the composition.
+Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtual | +
Get the molar abundance for a given species.
+| species | The atomic species. |
Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtual | +
Get the molar abundance for a given symbol.
+| symbol | The chemical symbol. |
Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtualnoexcept | +
Get the molar abundance as a vector.
+Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtualnoexcept | +
Get the number fraction for all registered symbols.
+Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtual | +
Get the number fraction for a given species.
+| species | The atomic species. |
Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtual | +
Get the number fraction for a given symbol.
+| symbol | The chemical symbol. |
Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtualnoexcept | +
Get the number fraction as a vector.
+Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtualnoexcept | +
Get all registered atomic species in the composition.
+Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtualnoexcept | +
Get all registered chemical symbols in the composition.
+Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtual | +
Get the species at a given index.
+| index | The index of the species. |
Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtual | +
Get the index of a species.
+| species | The atomic species. |
Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtual | +
Get the index of a species by symbol.
+| symbol | The chemical symbol. |
Implemented in fourdst::composition::Composition.
+ +
+
|
+ +nodiscardpure virtualnoexcept | +
Implemented in fourdst::composition::Composition.
+ +|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
This is the complete list of members for fourdst::composition::exceptions::SpeciesError, including all inherited members.
+| m_message | fourdst::composition::exceptions::SpeciesError | protected |
| SpeciesError(const std::string &message) | fourdst::composition::exceptions::SpeciesError | inlineexplicit |
| what() const noexcept override | fourdst::composition::exceptions::SpeciesError | inline |
|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
Base class for exceptions related to atomic species. + More...
+ +#include <exceptions_composition.h>
+Public Member Functions | |
| SpeciesError (const std::string &message) | |
| const char * | what () const noexcept override |
+Protected Attributes | |
| std::string | m_message |
Base class for exceptions related to atomic species.
+ +Definition at line 59 of file exceptions_composition.h.
+
+
|
+ +inlineexplicit | +
Definition at line 63 of file exceptions_composition.h.
+ +
+
|
+ +inlineoverridenoexcept | +
Definition at line 66 of file exceptions_composition.h.
+ +
+
|
+ +protected | +
Definition at line 61 of file exceptions_composition.h.
+ +|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
This is the complete list of members for fourdst::composition::exceptions::UnknownSymbolError, including all inherited members.
+| m_message | fourdst::composition::exceptions::SpeciesError | protected |
| SpeciesError(const std::string &message) | fourdst::composition::exceptions::UnknownSymbolError | inlineexplicitprivate |
| what() const noexcept override | fourdst::composition::exceptions::SpeciesError | inline |
|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
Exception thrown when an unknown symbol is encountered. + More...
+ +#include <exceptions_composition.h>
+Private Member Functions | |
| SpeciesError (const std::string &message) | |
+Additional Inherited Members | |
Public Member Functions inherited from fourdst::composition::exceptions::SpeciesError | |
| SpeciesError (const std::string &message) | |
| const char * | what () const noexcept override |
Protected Attributes inherited from fourdst::composition::exceptions::SpeciesError | |
| std::string | m_message |
Exception thrown when an unknown symbol is encountered.
+This typically occurs when a symbol does not correspond to any known atomic species.
+ +Definition at line 77 of file exceptions_composition.h.
+
+
|
+ +inlineexplicitprivate | +
Definition at line 63 of file exceptions_composition.h.
+ +|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
High-level documentation for the fourdst::composition namespace. +More...
++Namespaces | |
| namespace | fourdst::composition |
| Utilities and types for representing and manipulating chemical compositions. | |
High-level documentation for the fourdst::composition namespace.
+This file provides namespace-level Doxygen documentation for the composition module. It summarizes the public API (classes, utilities, and exceptions) and shows small examples demonstrating typical usage patterns.
+ +Definition in file composition.dox.
+|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
#include "fourdst/atomic/atomicSpecies.h"#include <string>#include <unordered_map>#include <set>#include <vector>Go to the source code of this file.
++Classes | |
| class | CompositionAbstract |
| Abstract base class for chemical composition representations. More... | |
|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
| File in src/composition/include/fourdst/composition | Includes file in src/composition/include/fourdst/atomic |
|---|---|
| composition.h | atomicSpecies.h |
| composition_abstract.h | atomicSpecies.h |
| utils.h | atomicSpecies.h |
|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
| File in src/composition/lib | Includes file in src/composition/include |
|---|---|
| composition.cpp | fourdst / atomic / atomicSpecies.h |
| composition.cpp | fourdst / composition / composition.h |
| composition.cpp | fourdst / composition / exceptions / exceptions_composition.h |
| composition.cpp | fourdst / atomic / species.h |
| utils.cpp | fourdst / atomic / atomicSpecies.h |
| utils.cpp | fourdst / composition / composition.h |
| utils.cpp | fourdst / composition / exceptions / exceptions_composition.h |
| utils.cpp | fourdst / atomic / species.h |
| utils.cpp | fourdst / composition / utils.h |
|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
+Files | |
| atomicSpecies.h | |
| elements.h | |
| Provides mappings between atomic numbers and element symbols for the periodic table. | |
| species.h | |
|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
Provides mappings between atomic numbers and element symbols for the periodic table. +More...
+#include <unordered_map>#include <cstdint>#include <string>Go to the source code of this file.
++Namespaces | |
| namespace | fourdst |
| namespace | fourdst::atomic |
| Contains canonical information about atomic species and elements used by 4D-STAR. | |
+Variables | |
| static const std::unordered_map< uint8_t, std::string > | fourdst::atomic::element_symbol_map |
| Maps atomic number (Z) to element symbol. | |
| static const std::unordered_map< std::string, uint8_t > | fourdst::atomic::symbol_element_map |
| Maps element symbol to atomic number (Z). | |
Provides mappings between atomic numbers and element symbols for the periodic table.
+This header defines lookup tables for converting between atomic numbers (Z) and their corresponding chemical element symbols, and vice versa. These maps are useful for parsing, displaying, or validating chemical compositions in scientific applications.
+ +Definition in file elements.h.
+|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
This page explains how to interpret the graphs that are generated by doxygen.
+Consider the following example:
This will result in the following graph:
+The boxes in the above graph have the following meaning:
+The arrows have the following meaning:
+|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
This is the complete list of members for fourdst::composition::Composition::CompositionCache, including all inherited members.
+|
+ fourdst::libcomposition v2.0.1
+
+ Robust atomic species information library
+ |
+
Caches computed properties of the composition to avoid redundant calculations. + More...
++Public Member Functions | |
| void | clear () |
| Clears all cached values. | |
| bool | is_clear () const |
| Checks if the cache is clear (i.e., all cached values are empty). | |
+Public Attributes | |
| std::optional< CanonicalComposition > | canonicalComp |
| Cached canonical composition data. | |
| std::optional< std::vector< double > > | massFractions |
| Cached vector of mass fractions. | |
| std::optional< std::vector< double > > | numberFractions |
| Cached vector of number fractions. | |
| std::optional< std::vector< double > > | molarAbundances |
| Cached vector of molar abundances. | |
| std::optional< std::vector< atomic::Species > > | sortedSpecies |
| Cached vector of sorted species (by mass). | |
| std::optional< std::vector< std::string > > | sortedSymbols |
| Cached vector of sorted species (by mass). | |
| std::optional< double > | Ye |
| Cached electron abundance. | |
Caches computed properties of the composition to avoid redundant calculations.
+This struct holds optional cached values for various computed properties of the composition, such as canonical composition, mass fractions, number fractions, molar abundances, sorted species, sorted symbols, and electron abundance. The cache can be cleared when the composition is modified.
+ +Definition at line 106 of file composition.h.
+
+
|
+ +inline | +
Clears all cached values.
+ +Definition at line 118 of file composition.h.
+ +
+
|
+ +inlinenodiscard | +
Checks if the cache is clear (i.e., all cached values are empty).
+Definition at line 132 of file composition.h.
+ +| std::optional<CanonicalComposition> fourdst::composition::Composition::CompositionCache::canonicalComp | +
Cached canonical composition data.
+ +Definition at line 107 of file composition.h.
+ +| std::optional<std::vector<double> > fourdst::composition::Composition::CompositionCache::massFractions | +
Cached vector of mass fractions.
+ +Definition at line 108 of file composition.h.
+ +| std::optional<std::vector<double> > fourdst::composition::Composition::CompositionCache::molarAbundances | +
Cached vector of molar abundances.
+ +Definition at line 110 of file composition.h.
+ +| std::optional<std::vector<double> > fourdst::composition::Composition::CompositionCache::numberFractions | +
Cached vector of number fractions.
+ +Definition at line 109 of file composition.h.
+ +| std::optional<std::vector<atomic::Species> > fourdst::composition::Composition::CompositionCache::sortedSpecies | +
Cached vector of sorted species (by mass).
+ +Definition at line 111 of file composition.h.
+ +| std::optional<std::vector<std::string> > fourdst::composition::Composition::CompositionCache::sortedSymbols | +
Cached vector of sorted species (by mass).
+ +Definition at line 112 of file composition.h.
+ +| std::optional<double> fourdst::composition::Composition::CompositionCache::Ye | +
Cached electron abundance.
+ +Definition at line 113 of file composition.h.
+ +