#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

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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STATIC void database_prep ( int intSpIndex )

References atmdat, BIGFLOAT, dBaseSpecies, dBaseStates, dBaseTrans, DEBUG_ENTRY, ipCRD, ipCRDW, ipIRON, ipPRD, t_atmdat::ipSpecIon, and SMALLFLOAT.

Referenced by database_readin().

void database_readin ( void )

References AllTransitions, ASSERT, atmdat, atmdat_CHIANTI_readin(), atmdat_LAMDA_readin(), atmdat_STOUT_readin(), AtmolCollRateCoeff, AtmolCollSplines, CHARS_SPECIES, t_atmdat::chCloudyChiantiFile, t_atmdat::chdBaseSources, t_cpu_i::chDirSeparator(), DataParser::checkEOL(), DataParser::checkMagic(), t_elementnames::chElementSym, t_atmdat::chLamdaFile, t_atmdat::chStoutFile, t_atmdat::chVersion, 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(), t_cpu::i(), Singleton< t_version >::Inst(), ioQQQ, ipdBaseTrans, ipNCOLLIDER, t_save::ipSDSFile, t_atmdat::lgCalpgmOn, t_atmdat::lgChiantiOn, t_atmdat::lgdBaseSourceExists, t_atmdat::lgLamdaOn, t_prt::lgPrintTime, t_save::lgSDSOn, t_atmdat::lgStoutOn, 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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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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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().

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().

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, t_mole_global::list, mole, mole_global, NULL, and t_mole_local::species.

Referenced by SpeciesBandsCreate().

string makeChemical	(	long	nelem,
		long	ion
	)

References t_elementnames::chElementSym, DEBUG_ENTRY, and elementnames.

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

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

References CHARS_SPECIES, DEBUG_ENTRY, and makeChemical().

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

References t_elementnames::chElementSym, DEBUG_ENTRY, elementnames, and LIMELM.

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

STATIC void set_fractionation ( species * sp )

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

Referenced by database_readin().

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

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

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

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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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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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STATIC void states_nelemfill ( void )

References atmdat, t_dense::AtomicWeight, CHARS_SPECIES, dBaseSpecies, dBaseStates, dBaseTrans, DEBUG_ENTRY, dense, findspecies(), fixit, fprintf(), t_save::img_matrix, molecule::index, ioQQQ, ipHYDROGEN, t_atmdat::ipSpecIon, t_atmdat::lgChiantiHybrid, t_dense::lgElmtOn, t_dense::lgIonChiantiOn, t_dense::lgIonStoutOn, t_atmdat::lgStoutHybrid, t_prt::matrix, t_dense::maxWN, mole, nSpecies, null_mole, prt, save, t_prt_matrix::species, t_mole_local::species, spectral_to_chemical(), and TotalInsanity().

Referenced by database_readin().

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STATIC void states_popfill ( void )

References dBaseSpecies, dBaseStates, DEBUG_ENTRY, and nSpecies.

Referenced by database_readin().

STATIC void states_propprint ( void )

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

Referenced by database_readin().

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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, t_atmdat::aulThreshold, cdEXIT, dBaseSpecies, dBaseStates, dBaseTrans, DEBUG_ENTRY, DEBUGSTATE, EXIT_FAILURE, fprintf(), ioQQQ, ipdBaseTrans, t_atmdat::lgChiantiPrint, t_atmdat::lgLamdaPrint, and t_atmdat::lgStoutPrint.

Referenced by database_readin().

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Variable Documentation

const bool DEBUGSTATE = false

static

Referenced by database_readin(), and trim_levels().

Functions

Variables

Function Documentation

Variable Documentation