#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
	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

typedef map<string,size_t >::iterator chem_nuclide_i

Enumeration Type Documentation

enum spectype

Enumerator
MOLECULE
OTHER

Function Documentation

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

References create_isotopologues_one_position(), DEBUG_ENTRY, and fixit.

Referenced by mole_generate_isotopologue_reactions(), and newspecies().

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

References ASSERT, and DEBUG_ENTRY.

Referenced by create_isotopologues(), and mole_generate_isotopologue_reactions().

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().

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().

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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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_molezone, and t_mole_local::species.

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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molezone* findspecieslocal_validate ( const char buf[] )

version for user-supplied species which may not be valid

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

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

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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(), t_mole_global::list, and mole_global.

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

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STATIC bool isactive ( const molecule & mol )

References DEBUG_ENTRY, MOLE_ACTIVE, and molecule::state.

Referenced by mole_make_list().

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 DEBUG_ENTRY, findspecies(), molecule::isMolecule(), and molecule::label.

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

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STATIC bool ispassive ( const molecule & mol )

References DEBUG_ENTRY, MOLE_PASSIVE, and molecule::state.

Referenced by mole_make_list().

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

Referenced by cdTemp().

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

References molecule::label.

Referenced by register_reaction_vectors().

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

References ASSERT, t_dense::AtomicWeight, DEBUG_ENTRY, dense, and fp_equal().

Referenced by t_mole_global::make_species().

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void mole_make_groups ( void )

References ASSERT, DEBUG_ENTRY, groupspecies, LIMELM, t_mole_global::list, mole_global, t_mole_global::num_calc, and t_mole_global::num_compacted.

Referenced by t_mole_global::init().

void mole_make_list ( void )

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

Referenced by t_mole_global::init().

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realnum mole_return_cached_species ( const GroupMap & )

References ASSERT, dense, deut, t_mole_local::elec, frac(), t_dense::gas_phase, lgElemsConserved(), t_mole_global::list, mole, MOLE_ACTIVE, mole_global, NULL, t_mole_global::num_calc, t_mole_global::num_total, SDIV(), t_mole_local::species, t_deuterium::updateXMolecules(), and t_dense::updateXMolecules().

Referenced by mole_solve().

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void mole_update_species_cache ( void )

References ASSERT, GrainVar::bin, DEBUG_ENTRY, fprintf(), t_mole_local::grain_area, t_mole_local::grain_density, t_mole_local::grain_saturation, gv, ioQQQ, GrainVar::lgDustOn(), t_mole_global::list, mole, mole_global, NULL, t_mole_global::num_total, t_mole_local::set_isotope_abundances(), and t_mole_local::species.

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

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

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

Referenced by t_mole_global::make_species().

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

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

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

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

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

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

References ASSERT, create_isotopologues(), DEBUG_ENTRY, exists(), fprintf(), ioQQQ, ipHYDROGEN, t_mole_global::lgNoHeavyMole, t_mole_global::lgNoMole, t_trace::lgTraceMole, t_mole_global::lgTreatIsotopes, MOLE_ACTIVE, mole_global, MOLE_NULL, MOLECULE, newspecies(), NULL, t_mole_global::num_calc, t_mole_global::num_total, molecule::parentLabel, parse_species_label(), speciesOff(), mole_priv::spectab, and trace.

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

Referenced by mole_generate_isotopologue_reactions(), and newspecies().

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