#include "cddefines.h"
#include "species.h"
#include "taulines.h"
#include "input.h"
#include "dense.h"
#include "atmdat.h"
#include "elementnames.h"
#include "version.h"
#include "save.h"
#include "mole.h"
#include "service.h"
#include "parser.h"
#include "parse_species.h"
#include "prt.h"
#include "warnings.h"

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Functions
STATIC void	states_popfill (void)

STATIC void	states_nelemfill (void)

STATIC void	database_prep (int)

STATIC void	trim_levels (long)

STATIC void	set_fractionation (species *sp)

STATIC void	states_propprint (void)

void	db_basename_to_spectral (const string &chBasename, string &chElement, char *chSpecLabel)

void	database_readin (void)

void	parsespect (const char *chLabel, long &nelem, long &IonStg)

bool	isAtomicIonValid (const long element_index, const long spCharge)

bool	isBareNucleus (const long element_index, const long spCharge)

string	makeChemical (long nelem, long ion)

void	makeChemical (char *chLabelChemical, long nelem, long ion)

STATIC void	spectral_to_chemical (char chLabelChemical, const char chLabel, long &nelem, long &IonStg)

void	spectral_to_chemical (char chLabelChemical, const char chLabel)

void	spectral_to_chemical (string &chemicalLabel, const char *chLabel)

bool	parse_chemical (const string &chLabelChem, string &chElemMol, long &spCharge)

void	chemical_to_spectral (const string &chLabelChem, string &chLabelSpec)

bool	isSpeciesActive (const string &chLabelChem)

Variables
static const bool	DEBUGSTATE = false

Function Documentation

◆ chemical_to_spectral()

void chemical_to_spectral	(	const string &	chLabelChem,
		string &	chLabelSpec )

chemical_to_spectral - Convert a chemical label to spectral.

Parameters

chLabelChem[in]	Chemical label, e.g., "C+"
chLabelSpec[out]	Spectral label, e.g., "C 2"

References DEBUG_ENTRY, elem_symbol_to_index(), isAtomicIonValid(), isBareNucleus(), isElementSym(), and parse_chemical().

Referenced by SaveAllSpeciesLabelsLevels(), SaveSpeciesLines(), and band_emission::setup().

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◆ database_prep()

STATIC void database_prep ( int intSpIndex )

References atmdat, BIGFLOAT, dBaseSpecies, dBaseStates, dBaseTrans, DEBUG_ENTRY, ipCRD, ipCRDW, ipIRON, ipPRD, SMALLFLOAT, and STATIC.

Referenced by database_readin().

◆ database_readin()

void database_readin ( void )

References AllTransitions, ASSERT, atmdat, atmdat_CHIANTI_readin(), atmdat_LAMDA_readin(), atmdat_STOUT_readin(), AtmolCollRateCoeff, AtmolCollSplines, CHARS_SPECIES, DataParser::checkEOL(), DataParser::checkMagic(), cpu, database_prep(), db_basename_to_spectral(), dBaseSpecies, dBaseStates, dBaseTrans, DEBUG_ENTRY, DEBUGSTATE, elementnames, DataParser::errorAbort(), ES_NONE, findspecies(), fixit, fprintf(), DataParser::getline(), DataParser::getToken(), DataParser::getTokenOptional(), Singleton< t_version >::Inst(), ioQQQ, ipdBaseTrans, ipNCOLLIDER, LIMELM, notein(), nSpecies, null_mole, DataParser::open(), prt, save, set_fractionation(), speciesCheck(), states_nelemfill(), states_popfill(), states_propprint(), StoutCollData, TotalInsanity(), trim_levels(), and trimTrailingWhiteSpace().

Referenced by atmdat_readin().

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◆ db_basename_to_spectral()

void db_basename_to_spectral	(	const string &	chBasename,
		string &	chElement,
		char *	chSpecLabel )

db_basename_to_spectral - Convert the species basename in Stout or Chianti to a spectral label.

Parameters

chBasename[in]	File basename, e.g., "c_2"
chElement[out]	Extracted element name, e.g., "C"
chSpecLabel[out]	Spectral label, e.g., "C 2"

References ASSERT, DEBUG_ENTRY, toupper(), and uncaps().

Referenced by database_readin().

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◆ isAtomicIonValid()

bool isAtomicIonValid	(	const long	element_index,
		const long	spCharge )

isAtomicIonValid - Tell if an atomic ion is has a charge consistent with its atomic number.

Parameters

element_index[in]	Zero-offset index for element; 0 for H, 29 for Zn
spCharge[in]	Species charge

Returns: bool True, if ion is valid; false, otherwise.

References ASSERT, and DEBUG_ENTRY.

Referenced by cdTemp(), and chemical_to_spectral().

◆ isBareNucleus()

bool isBareNucleus	(	const long	element_index,
		const long	spCharge )

isBareNucleus - Tell if the given ion is a bare nucleus.

Parameters

element_index[in]	Zero-offset index for element; 0 for H, 29 for Zn
spCharge[in]	Species charge

Returns: bool True, if ion is bare nucleus; false, otherwise.

References ASSERT, and DEBUG_ENTRY.

Referenced by chemical_to_spectral().

◆ isSpeciesActive()

bool isSpeciesActive ( const string & chSpecLabel )

isSpeciesActive - Tell if the species is enabled

An atomic/ionic species may be inactive if the relevant element is disabled. Likewise, a molecular species may be inactive if one of its constituents elements is disabled. This function reports on the given species. If not found, the result is false.

Parameters

chLabelChem [in] Chemical label, e.g., "C+2", or "HCl"

Returns: bool True, if species active; false, otherwise.

References DEBUG_ENTRY, mole, mole_global, and NULL.

Referenced by SpeciesBandsCreate().

◆ makeChemical() [1/2]

void makeChemical	(	char *	chLabelChemical,
		long	nelem,
		long	ion )

References CHARS_SPECIES, DEBUG_ENTRY, and makeChemical().

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◆ makeChemical() [2/2]

string makeChemical	(	long	nelem,
		long	ion )

References DEBUG_ENTRY, and elementnames.

Referenced by InitCoreloadPostparse(), iso_allocate(), iso_level(), lines(), makeChemical(), ParseSave(), save_opacity(), setProperties(), and spectral_to_chemical().

◆ parse_chemical()

bool parse_chemical	(	const string &	chLabelChem,
		string &	chElemMol,
		long &	spCharge )

parse_chemical - Parse the element and charge of a chemical label.

Parameters

chLabelChem[in]	Chemical label, e.g., "C+2", or "HCl"
chElemMol[out]	Element or molecule, e.g., "C", or "HCl"
spCharge[out]	Species charge, e.g., 2, or 0

Returns: bool True, if successful; false, otherwise.

References DEBUG_ENTRY, fprintf(), and ioQQQ.

Referenced by cdTemp(), and chemical_to_spectral().

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◆ parsespect()

void parsespect	(	const char *	chLabel,
		long &	nelem,
		long &	IonStg )

References DEBUG_ENTRY, elementnames, and LIMELM.

Referenced by lines(), setProperties(), and spectral_to_chemical().

◆ set_fractionation()

STATIC void set_fractionation ( species * sp )

References species::chLabel, DEBUG_ENTRY, fixit, species::fracIsotopologue, species::fracType, and STATIC.

Referenced by database_readin().

◆ spectral_to_chemical() [1/3]

void spectral_to_chemical	(	char *	chLabelSpec,
		const char *	chLabelChem )

spectral_to_chemical - Convert a spectral label to chemical.

Parameters

chLabelSpec[in]	Spectral label, e.g., "C 2"
chLabelChem[out]	Chemical label, e.g., "C+"

References DEBUG_ENTRY, and spectral_to_chemical().

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◆ spectral_to_chemical() [2/3]

STATIC void spectral_to_chemical	(	char *	chLabelChemical,
		const char *	chLabel,
		long &	nelem,
		long &	IonStg )

References ASSERT, cdEXIT, DEBUG_ENTRY, elementnames, EXIT_FAILURE, fprintf(), ioQQQ, LIMELM, makeChemical(), NISO, parsespect(), and STATIC.

Referenced by atmdat_CHIANTI_readin(), atmdat_STOUT_readin(), Atom_LevelN::operator()(), spectral_to_chemical(), spectral_to_chemical(), and states_nelemfill().

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◆ spectral_to_chemical() [3/3]

void spectral_to_chemical	(	string &	chLabelSpec,
		const char *	chLabelChem )

spectral_to_chemical - Convert a spectral label to chemical.

Parameters

chLabelSpec[in]	Spectral label, e.g., "C 2"
chLabelChem[out]	Chemical label, e.g., "C+"

References DEBUG_ENTRY, NCHLAB, and spectral_to_chemical().

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◆ states_nelemfill()

STATIC void states_nelemfill ( void )

References atmdat, CHARS_SPECIES, dBaseSpecies, dBaseStates, dBaseTrans, DEBUG_ENTRY, dense, findspecies(), fixit, fprintf(), molecule::index, ioQQQ, ipHYDROGEN, mole, nSpecies, null_mole, prt, save, spectral_to_chemical(), STATIC, and TotalInsanity().

Referenced by database_readin().

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◆ states_popfill()

STATIC void states_popfill ( void )

References dBaseSpecies, dBaseStates, DEBUG_ENTRY, nSpecies, and STATIC.

Referenced by database_readin().

◆ states_propprint()

STATIC void states_propprint ( void )

References dBaseSpecies, dBaseStates, DEBUG_ENTRY, energy(), nSpecies, and STATIC.

Referenced by database_readin().

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◆ trim_levels()

STATIC void trim_levels ( long ipSpecies )

trim_levels: Trim the highest energy levels until there is a transition out of the highest level with an Aul value that is not the default. The default value of 1e-30 is used when no Aul is given in the database.

References atmdat, EmissionProxy::Aul(), cdEXIT, dBaseSpecies, dBaseStates, dBaseTrans, DEBUG_ENTRY, DEBUGSTATE, TransitionProxy::Emis(), EXIT_FAILURE, fprintf(), ioQQQ, ipdBaseTrans, and STATIC.

Referenced by database_readin().

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Variable Documentation

◆ DEBUGSTATE

const bool DEBUGSTATE = false

static

Functions

Variables

Function Documentation

◆ chemical_to_spectral()

◆ database_prep()

◆ database_readin()

◆ db_basename_to_spectral()

◆ isAtomicIonValid()

◆ isBareNucleus()

◆ isSpeciesActive()

◆ makeChemical() [1/2]

◆ makeChemical() [2/2]

◆ parse_chemical()

◆ parsespect()

◆ set_fractionation()

◆ spectral_to_chemical() [1/3]

◆ spectral_to_chemical() [2/3]

◆ spectral_to_chemical() [3/3]

◆ states_nelemfill()

◆ states_popfill()

◆ states_propprint()

◆ trim_levels()

Variable Documentation

◆ DEBUGSTATE