#include "cdstd.h"
#include "cddefines.h"
#include "deuterium.h"
#include "elementnames.h"
#include "h2.h"
#include "hmi.h"
#include "dense.h"
#include "grainvar.h"
#include "trace.h"
#include "abund.h"
#include "mole_priv.h"
#include "mole.h"
#include "parse_species.h"

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Namespaces
namespace	mole_priv

Typedefs
typedef map< string, size_t >::iterator	chem_nuclide_i

Enumerations
enum	spectype { MOLECULE , OTHER }

Functions
STATIC void	read_species_file (string filename, bool lgCreateIsotopologues=true)

STATIC void	newelement (const char label[], int ipion)

STATIC void	newisotope (const shared_ptr< chem_element > &el, int massNumberA, realnum mass_amu, double frac)

STATIC realnum	MeanMassOfElement (const shared_ptr< chem_element > &el)

STATIC molecule *	newspecies (const char label[], enum spectype type, enum mole_state state, realnum form_enthalpy)

STATIC molecule *	newspecies (const char label[], enum spectype type, enum mole_state state, realnum form_enthalpy, bool lgCreateIsotopologues)

STATIC bool	isactive (const molecule &mol)

STATIC bool	ispassive (const molecule &mol)

STATIC void	SetIsotopeFractions (const vector< bool > &lgResolveNelem)

void	mole_make_list ()

void	create_isotopologues (ChemNuclideList &atoms, vector< int > &numNuclides, string atom_old, string atom_new, string embellishments, vector< string > &newLabels)

void	create_isotopologues_one_position (unsigned position, ChemNuclideList &atoms, vector< int > &numNuclides, string atom_old, string atom_new, string embellishments, string &newLabel)

bool	parse_species_label (const char label[], ChemNuclideList &nuclidesLeftToRight, vector< int > &numNuclides, string &embellishments)

bool	parse_species_label (const char label[], ChemNuclideList &nuclidesLeftToRight, vector< int > &numNuclides, string &embellishments, bool &lgExcit, int &charge, bool &lgGas_Phase)

bool	lgDifferByExcitation (const molecule &mol1, const molecule &mol2)

molecule *	findspecies (const char buf[])

molecule *	findspecies_validate (const char buf[])

molezone *	findspecieslocal (const char buf[])

molezone *	findspecieslocal_validate (const char buf[])

shared_ptr< chem_nuclide >	findnuclide (const char buf[])

void	mole_update_species_cache (void)

realnum	mole_return_cached_species (const GroupMap &)

void	total_molecule_deut (realnum &total_f)

void	total_molecule_elems (realnum total[LIMELM])

realnum	total_molecules (void)

realnum	total_molecules_gasphase (void)

realnum	species_gasphase_density (const string &chSpecies)

void	mole_make_groups (void)

bool	isSpecies (const string &chSpecies)

bool	isMolecule (const string &chSpecies)

void	test_isMolecule ()

void	getMolecules (vector< string > &allMolecules)

Variables
map< string, size_t >	nuclidetab

molecule *	null_mole

molezone *	null_molezone

molezone	null_molezone_impl

chem_nuclide *	null_nuclide

chem_nuclide	null_nuclide_impl

ChemElementList	element_list

ChemNuclideList	nuclide_list

vector< molecule * >	groupspecies

Typedef Documentation

◆ chem_nuclide_i

typedef map<string,size_t>::iterator chem_nuclide_i

Enumeration Type Documentation

◆ spectype

enum spectype

Enumerator
MOLECULE
OTHER

Function Documentation

◆ create_isotopologues()

void create_isotopologues	(	ChemNuclideList &	atoms,
		vector< int > &	numNuclides,
		string	atom_old,
		string	atom_new,
		string	embellishments,
		vector< string > &	newLabels )

References atoms, create_isotopologues_one_position(), DEBUG_ENTRY, and fixit.

Referenced by mole_generate_isotopologue_reactions(), and newspecies().

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◆ create_isotopologues_one_position()

void create_isotopologues_one_position	(	unsigned	position,
		ChemNuclideList &	atoms,
		vector< int > &	numNuclides,
		string	atom_old,
		string	atom_new,
		string	embellishments,
		string &	newLabel )

References ASSERT, atoms, and DEBUG_ENTRY.

Referenced by create_isotopologues(), and mole_generate_isotopologue_reactions().

◆ findnuclide()

shared_ptr< chem_nuclide > findnuclide ( const char buf[] )

References DEBUG_ENTRY, nuclide_list, nuclidetab, and NULL.

Referenced by mole_effects(), mole_generate_isotopologue_reactions(), mole_h_rate_diagnostics(), parse_species_label(), and PrtZone().

◆ findspecies()

molecule * findspecies ( const char buf[] )

version for species we know are valid, but may not be present in calculation

References DEBUG_ENTRY, null_mole, and mole_priv::spectab.

Referenced by t_mole_local::chem_heat(), ConvBase(), CoolHeatError(), database_readin(), t_mole_local::dissoc_rate(), findspecieslocal(), diatomics::init(), isMolecule(), iso_allocate(), isSpecies(), lgElemsConserved(), lgNetEdenSrcSmall(), t_mole_global::make_species(), mole_make_list(), mole_save(), parse_reaction(), parse_udfa(), prt_smooth_predictions(), radius_increment(), SaveDo(), t_mole_local::sink_rate_tot(), t_mole_local::source_rate_tot(), species_gasphase_density(), and states_nelemfill().

◆ findspecies_validate()

molecule * findspecies_validate ( const char buf[] )

version for user-supplied species which may not be valid

References cdEXIT, DEBUG_ENTRY, EXIT_FAILURE, fprintf(), ioQQQ, and mole_priv::spectab.

Referenced by findspecieslocal_validate().

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◆ findspecieslocal()

molezone * findspecieslocal ( const char buf[] )

version for species we know are valid, but may not be present in calculation

References DEBUG_ENTRY, findspecies(), molecule::index, mole, null_mole, and null_molezone.

Referenced by AgeCheck(), t_gaunt::brems_sum_ions(), cdColm(), check_co_ion_converge(), ConvBase(), CoolEvaluate(), dBaseAbund(), DynaPunchTimeDep(), getLevelsGeneric(), GrainCollHeating(), diatomics::H2_PunchDo(), diatomics::H2_X_coll_rate_evaluate(), HeatSum(), InitSimPostparse(), IonHydro(), iso_level(), iter_end_check(), IterRestart(), lines_molecules(), mole_effects(), diatomics::mole_H2_form(), mole_h_fixup(), mole_h_rate_diagnostics(), mole_h_reactions(), OpacityAddTotal(), PrtAllTau(), PrtComment(), PrtZone(), radius_increment(), radius_next(), RT_continuum(), RT_OTS(), RT_tau_inc(), SaveDo(), SaveLineData(), SecIoniz(), t_mole_local::set_ion_locations(), and ShowMe().

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◆ findspecieslocal_validate()

molezone * findspecieslocal_validate ( const char buf[] )

version for user-supplied species which may not be valid

References DEBUG_ENTRY, findspecies_validate(), molecule::index, and mole.

Referenced by iter_end_check(), radius_first(), and radius_next().

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◆ getMolecules()

void getMolecules ( vector< string > & allMolecules )

getMolecules - Get a list of all active molecules.

Parameters

allMolecules [in,out] List of molecule strings.

References DEBUG_ENTRY, isMolecule(), and mole_global.

Referenced by t_mean::setup_molecules(), and test_cdTemp_molecules().

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◆ isactive()

STATIC bool isactive ( const molecule & mol )

References DEBUG_ENTRY, MOLE_ACTIVE, molecule::state, and STATIC.

Referenced by mole_make_list().

◆ isMolecule()

bool isMolecule ( const string & chSpecies )

isMolecule - Tell if the input string corresponds to a valid & active molecule.

Parameters

chSpecies [in] Species string

Returns: bool value: true, if a valid molecule; false, otherwise

References chSpecies, DEBUG_ENTRY, findspecies(), molecule::isMolecule(), molecule::label, and null_mole.

Referenced by cdTemp(), getMolecules(), and test_isMolecule().

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◆ ispassive()

STATIC bool ispassive ( const molecule & mol )

References DEBUG_ENTRY, MOLE_PASSIVE, molecule::state, and STATIC.

Referenced by mole_make_list().

◆ isSpecies()

bool isSpecies ( const string & chSpecies )

isSpecies - Tell if the input string corresponds to a valid & active species.

Parameters

chSpecies [in] Species string

Returns: bool value: true, if a valid species; false, otherwise

References chSpecies, DEBUG_ENTRY, findspecies(), molecule::isMolecule(), molecule::isMonatomic(), molecule::label, and null_mole.

Referenced by cdTemp().

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◆ lgDifferByExcitation()

bool lgDifferByExcitation	(	const molecule &	mol1,
		const molecule &	mol2 )

References molecule::label.

Referenced by register_reaction_vectors().

◆ MeanMassOfElement()

STATIC realnum MeanMassOfElement ( const shared_ptr< chem_element > & el )

References ASSERT, DEBUG_ENTRY, dense, fp_equal(), and STATIC.

Referenced by t_mole_global::make_species().

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◆ mole_make_groups()

void mole_make_groups ( void )

References ASSERT, DEBUG_ENTRY, groupspecies, LIMELM, and mole_global.

Referenced by t_mole_global::init().

◆ mole_make_list()

void mole_make_list ( void )

References ASSERT, molecule::charge, DEBUG_ENTRY, findspecies(), molecule::index, isactive(), molecule::isMonatomic(), ispassive(), molecule::lgGas_Phase, mole_global, molecule::nNuclide, t_mole_global::sort(), and mole_priv::spectab.

Referenced by t_mole_global::init().

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◆ mole_return_cached_species()

realnum mole_return_cached_species ( const GroupMap & MoleMap )

References ASSERT, dense, deut, frac(), lgElemsConserved(), mole, MOLE_ACTIVE, mole_global, NULL, and SDIV().

Referenced by mole_solve().

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◆ mole_update_species_cache()

void mole_update_species_cache ( void )

References ASSERT, DEBUG_ENTRY, fprintf(), gv, ioQQQ, mole, mole_global, and NULL.

Referenced by diatomics::H2_LevelPops(), mole_drive(), and mole_update_sources().

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◆ newelement()

STATIC void newelement	(	const char	label[],
		int	ipion )

References DEBUG_ENTRY, element_list, mole_priv::elemtab, exists(), and STATIC.

Referenced by t_mole_global::make_species().

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◆ newisotope()

STATIC void newisotope	(	const shared_ptr< chem_element > &	el,
		int	massNumberA,
		realnum	mass_amu,
		double	frac )

References ASSERT, DEBUG_ENTRY, frac(), LIMELM, nuclide_list, nuclidetab, and STATIC.

Referenced by t_mole_global::make_species(), and SetIsotopeFractions().

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◆ newspecies() [1/2]

STATIC molecule * newspecies	(	const char	label[],
		enum spectype	type,
		enum mole_state	state,
		realnum	form_enthalpy )

References newspecies(), and STATIC.

Referenced by t_mole_global::make_species(), newspecies(), newspecies(), and read_species_file().

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◆ newspecies() [2/2]

STATIC molecule * newspecies	(	const char	label[],
		enum spectype	type,
		enum mole_state	state,
		realnum	form_enthalpy,
		bool	lgCreateIsotopologues )

References ASSERT, multi_arr< T, d, ALLOC, lgBC >::begin(), create_isotopologues(), DEBUG_ENTRY, exists(), fprintf(), ioQQQ, ipHYDROGEN, MOLE_ACTIVE, mole_global, MOLE_NULL, MOLECULE, newspecies(), NULL, molecule::parentLabel, parse_species_label(), speciesOff(), mole_priv::spectab, STATIC, and trace.

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◆ parse_species_label() [1/2]

bool parse_species_label	(	const char	label[],
		ChemNuclideList &	nuclidesLeftToRight,
		vector< int > &	numNuclides,
		string &	embellishments )

References parse_species_label().

Referenced by mole_generate_isotopologue_reactions(), newspecies(), and parse_species_label().

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◆ parse_species_label() [2/2]

bool parse_species_label	(	const char	label[],
		ChemNuclideList &	nuclidesLeftToRight,
		vector< int > &	numNuclides,
		string &	embellishments,
		bool &	lgExcit,
		int &	charge,
		bool &	lgGas_Phase )