#include "cdstd.h"
#include <cctype>
#include <string.h>
#include <algorithm>
#include <stdlib.h>
#include "cddefines.h"
#include "co.h"
#include "colden.h"
#include "conv.h"
#include "deuterium.h"
#include "doppvel.h"
#include "elementnames.h"
#include "h2.h"
#include "iso.h"
#include "phycon.h"
#include "physconst.h"
#include "mole.h"
#include "mole_priv.h"
#include "hmi.h"
#include "radius.h"
#include "rfield.h"
#include "rt.h"
#include "secondaries.h"
#include "dense.h"
#include "ionbal.h"
#include "grainvar.h"
#include "timesc.h"
#include "taulines.h"
#include "trace.h"
#include <functional>

Include dependency graph for mole_species.cpp:

Namespaces
namespace	mole_priv

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 count_ptr< chem_element > &el, int massNumberA, realnum mass_amu, double frac)

STATIC realnum	MeanMassOfElement (const count_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 count_ptr< chem_atom >	findatom (const char buf[])

STATIC bool	isactive (const molecule &mol)

STATIC bool	ispassive (const molecule &mol)

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

void	mole_make_list ()

void	create_isotopologues_one (ChemAtomList &atoms, vector< int > &numAtoms, string atom_old, string atom_new, string embellishments, vector< string > &newLabels)

bool	parse_species_label (const char label[], ChemAtomList &atomsLeftToRight, vector< int > &numAtoms, string &embellishments)

bool	parse_species_label (const char label[], ChemAtomList &atomsLeftToRight, vector< int > &numAtoms, string &embellishments, bool &lgExcit, int &charge, bool &lgGas_Phase)

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

molecule *	findspecies (const char buf[])

molezone *	findspecieslocal (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])

void	total_network_elems (double total[LIMELM])

realnum	total_molecules (void)

realnum	total_molecules_gasphase (void)

void	mole_make_groups (void)

Variables
molecule *	null_mole

molezone *	null_molezone

chem_element *	null_element

chem_atom *	null_atom

vector< count_ptr< chem_element > >	element_list

ChemAtomList	unresolved_atom_list

ChemAtomList	atom_list

molecule **	groupspecies

Enumeration Type Documentation

◆ spectype

enum spectype

Enumerator
MOLECULE
OTHER

Definition at line 40 of file mole_species.cpp.

Function Documentation

◆ create_isotopologues_one()

void create_isotopologues_one	(	ChemAtomList &	atoms,
		vector< int > &	numAtoms,
		string	atom_old,
		string	atom_new,
		string	embellishments,
		vector< string > &	newLabels
	)

Definition at line 387 of file mole_species.cpp.

References ASSERT, atoms, and fixit().

Referenced by mole_generate_isotopologue_reactions(), and newspecies().

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◆ findatom()

STATIC count_ptr< chem_atom > findatom ( const char buf[] )

Definition at line 852 of file mole_species.cpp.

References mole_priv::atomtab, and DEBUG_ENTRY.

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

◆ findspecies()

molecule * findspecies ( const char buf[] )

Definition at line 814 of file mole_species.cpp.

References DEBUG_ENTRY, null_mole, and mole_priv::spectab.

Referenced by t_mole_local::chem_heat(), database_readin(), t_mole_local::dissoc_rate(), diatomics::init(), iso_allocate(), lgElemsConserved(), lgNetEdenSrcSmall(), t_mole_global::make_species(), mole_make_list(), mole_punch(), parse_reaction(), parse_udfa(), prt_smooth_predictions(), radius_increment(), SaveDo(), SaveSpecies(), t_mole_local::sink_rate_tot(), t_mole_local::source_rate_tot(), and states_nelemfill().

◆ findspecieslocal()

molezone * findspecieslocal ( const char buf[] )

◆ isactive()

STATIC bool isactive ( const molecule & mol )

Definition at line 792 of file mole_species.cpp.

References DEBUG_ENTRY, MOLE_ACTIVE, and molecule::state.

Referenced by mole_make_list().

◆ ispassive()

STATIC bool ispassive ( const molecule & mol )

Definition at line 797 of file mole_species.cpp.

References DEBUG_ENTRY, MOLE_PASSIVE, and molecule::state.

Referenced by mole_make_list().

◆ lgDifferByExcitation()

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

Definition at line 804 of file mole_species.cpp.

References molecule::label.

Referenced by register_reaction_vectors().

◆ MeanMassOfElement()

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

Definition at line 515 of file mole_species.cpp.

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

Referenced by t_mole_global::make_species().

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◆ mole_make_groups()

void mole_make_groups ( void )

Definition at line 1142 of file mole_species.cpp.

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

Referenced by t_mole_global::init().

◆ mole_make_list()

void mole_make_list ( void )

Definition at line 296 of file mole_species.cpp.

References ASSERT, molecule::charge, DEBUG_ENTRY, findspecies(), molecule::index, isactive(), molecule::isMonatomic(), ispassive(), molecule::lgGas_Phase, t_mole_global::list, mole_global, molecule::nAtom, 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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◆ mole_return_cached_species()

realnum mole_return_cached_species ( const GroupMap & MoleMap )

Definition at line 935 of file mole_species.cpp.

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

Referenced by mole_solve().

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◆ mole_update_species_cache()

void mole_update_species_cache ( void )

Definition at line 866 of file mole_species.cpp.

References ASSERT, GrainVar::bin, DEBUG_ENTRY, 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, 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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◆ newelement()

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

Definition at line 461 of file mole_species.cpp.

References auto_vec< T >::data(), DEBUG_ENTRY, element_list, and mole_priv::elemtab.

Referenced by t_mole_global::make_species().

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◆ newisotope()

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

Definition at line 487 of file mole_species.cpp.

References ASSERT, atom_list, mole_priv::atomtab, DEBUG_ENTRY, count_ptr< T >::get_ptr(), LIMELM, and unresolved_atom_list.

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

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◆ newspecies() [1/2]

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

Definition at line 534 of file mole_species.cpp.

References newspecies(), and state.

Referenced by t_mole_global::make_species(), 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
	)

Definition at line 544 of file mole_species.cpp.

References ASSERT, ATOMIC_MASS_UNIT, count_ptr< T >::compare(), create_isotopologues_one(), auto_vec< T >::data(), DEBUG_ENTRY, 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(), t_mole_global::num_calc, t_mole_global::num_total, molecule::parentLabel, parse_species_label(), mole_priv::spectab, state, and trace.

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◆ parse_species_label() [1/2]

bool parse_species_label	(	const char	label[],
		ChemAtomList &	atomsLeftToRight,
		vector< int > &	numAtoms,
		string &	embellishments
	)

Definition at line 678 of file mole_species.cpp.

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[],
		ChemAtomList &	atomsLeftToRight,
		vector< int > &	numAtoms,
		string &	embellishments,
		bool &	lgExcit,
		int &	charge,
		bool &	lgGas_Phase
	)