/home66/gary/public_html/cloudy/c13_branch/source/mole_species.cpp File Reference

#include "cdstd.h"
#include <cctype>
#include <string.h>
#include <algorithm>
#include <stdlib.h>
#include "cddefines.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>

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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 (void)
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

enum spectype

Enumerator:

MOLECULE
OTHER

Definition at line 39 of file mole_species.cpp.

Function Documentation

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

Definition at line 361 of file mole_species.cpp.

References ASSERT, and fixit().

Referenced by mole_generate_isotopologue_reactions(), and newspecies().

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

Definition at line 825 of file mole_species.cpp.

References mole_priv::atomtab, and DEBUG_ENTRY.

Referenced by parse_species_label().

molecule* findspecies ( const char buf[] )

Definition at line 787 of file mole_species.cpp.

References DEBUG_ENTRY, and mole_priv::spectab.

Referenced by t_mole_local::chem_heat(), database_readin(), t_mole_local::dissoc_rate(), diatomics::init(), 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().

molezone* findspecieslocal ( const char buf[] )

STATIC bool isactive ( const molecule & mol )

Definition at line 765 of file mole_species.cpp.

References DEBUG_ENTRY, MOLE_ACTIVE, and molecule::state.

Referenced by mole_make_list().

STATIC bool ispassive ( const molecule & mol )

Definition at line 770 of file mole_species.cpp.

References DEBUG_ENTRY, MOLE_PASSIVE, and molecule::state.

Referenced by mole_make_list().

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

Definition at line 777 of file mole_species.cpp.

References molecule::label.

Referenced by register_reaction_vectors().

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

Definition at line 489 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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void mole_make_groups ( void )

Definition at line 1112 of file mole_species.cpp.

References ASSERT, DEBUG_ENTRY, 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().

void mole_make_list ( void )

Definition at line 270 of file mole_species.cpp.

References ASSERT, molecule::charge, DEBUG_ENTRY, findspecies(), 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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realnum mole_return_cached_species ( void )

Definition at line 908 of file mole_species.cpp.

References ASSERT, dense, deut, t_mole_local::elec, 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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void mole_update_species_cache ( void )

Definition at line 839 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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STATIC void newelement	(	const char	label[],
		int	ipion
	)

Definition at line 435 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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STATIC void newisotope	(	const count_ptr< chem_element > &	el,
		int	massNumberA,
		realnum	mass_amu,
		double	frac
	)

Definition at line 461 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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STATIC molecule * newspecies	(	const char	label[],
		enum spectype	type,
		enum mole_state	state,
		realnum	form_enthalpy,
		bool	lgCreateIsotopologues
	)

Definition at line 518 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, and trace.

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

Definition at line 508 of file mole_species.cpp.

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

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