#include "count_ptr.h"
#include "module.h"

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Data Structures
class	chem_element

class	chem_nuclide

class	element_pointer_value_less

class	molecule

class	t_mole_global

class	molezone

class	t_mole_local

Macros
#define	SMALLABUND 1e-24

Typedefs
typedef map< int, count_ptr < chem_nuclide > >::iterator	isotopes_i

typedef vector< count_ptr < chem_nuclide > >	ChemNuclideList

typedef vector< count_ptr < chem_element > >	ChemElementList

typedef molecule::nNucsMap::iterator	nNucs_i

typedef molecule::nNucsMap::reverse_iterator	nNucs_ri

typedef molecule::nNucsMap::const_reverse_iterator	nNucs_cri

Enumerations
enum	mole_state { MOLE_NULL, MOLE_PASSIVE, MOLE_ACTIVE }

Functions
bool	operator< (const chem_nuclide &a, const chem_nuclide &b)

bool	operator> (const chem_nuclide &a, const chem_nuclide &b)

bool	operator<= (const chem_nuclide &a, const chem_nuclide &b)

bool	operator>= (const chem_nuclide &a, const chem_nuclide &b)

bool	operator== (const chem_nuclide &a, const chem_nuclide &b)

bool	operator!= (const chem_nuclide &a, const chem_nuclide &b)

void	mole_drive (void)

void	mole_create_react (void)

mole_reaction *	mole_findrate_s (const char buf[])

bool	exists (const molecule *m)

molecule *	findspecies (const char buf[])

molecule *	findspecies_validate (const char buf[])

molezone *	findspecieslocal (const char buf[])

molezone *	findspecieslocal_validate (const char buf[])

count_ptr< chem_nuclide >	findnuclide (const char buf[])

bool	exists (const molezone *m)

void	total_molecule_elems (realnum total[LIMELM])

void	total_molecule_deut (realnum &total)

realnum	total_molecules (void)

realnum	total_molecules_gasphase (void)

void	mole_make_list (void)

void	mole_make_groups (void)

void	mole_cmp_num_in_out_reactions (void)

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

void	mole_update_species_cache (void)

void	mole_update_sources (void)

void	mole_rk_bigchange (void)

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

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

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

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

double	hmrate4 (double a, double b, double c, double te)

void	ParseChemistry (Parser &p)

Variables
ChemNuclideList	nuclide_list

ChemElementList	element_list

chem_element *	null_element

chem_nuclide *	null_nuclide

molecule *	null_mole

t_mole_global	mole_global

molezone *	null_molezone

t_mole_local	mole

Macro Definition Documentation

#define SMALLABUND 1e-24

Definition at line 17 of file mole.h.

Referenced by newton_step().

Typedef Documentation

typedef vector< count_ptr<chem_element> > ChemElementList

Definition at line 126 of file mole.h.

typedef vector< count_ptr<chem_nuclide> > ChemNuclideList

Definition at line 124 of file mole.h.

typedef map<int, count_ptr<chem_nuclide> >::iterator isotopes_i

Definition at line 39 of file mole.h.

typedef molecule::nNucsMap::const_reverse_iterator nNucs_cri

Definition at line 244 of file mole.h.

typedef molecule::nNucsMap::iterator nNucs_i

Definition at line 242 of file mole.h.

typedef molecule::nNucsMap::reverse_iterator nNucs_ri

Definition at line 243 of file mole.h.

Enumeration Type Documentation

enum mole_state

Enumerator
MOLE_NULL
MOLE_PASSIVE
MOLE_ACTIVE

Definition at line 19 of file mole.h.

Function Documentation

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

Definition at line 337 of file mole_species.cpp.

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 > &	numAtoms,
		string	atom_old,
		string	atom_new,
		string	embellishments,
		string &	newLabel
	)

Definition at line 362 of file mole_species.cpp.

References ASSERT, and DEBUG_ENTRY.

Referenced by create_isotopologues(), and mole_generate_isotopologue_reactions().

bool exists ( const molecule * m )

inline

Definition at line 258 of file mole.h.

References null_mole.

Referenced by dBaseAbund(), mole_check_reverse_reactions(), newelement(), newreact(), newspecies(), and specBandsExists().

bool exists ( const molezone * m )

inline

Definition at line 477 of file mole.h.

References null_molezone.

count_ptr<chem_nuclide> findnuclide ( const char buf[] )

Definition at line 850 of file mole_species.cpp.

References DEBUG_ENTRY, nuclide_list, and nuclidetab.

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

Definition at line 787 of file mole_species.cpp.

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(), iso_allocate(), 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(), and states_nelemfill().

molecule* findspecies_validate ( const char buf[] )

version for user-supplied species which may not be valid

Definition at line 806 of file mole_species.cpp.

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

Definition at line 829 of file mole_species.cpp.

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

Definition at line 841 of file mole_species.cpp.

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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double hmrate4	(	double	a,
		double	b,
		double	c,
		double	te
	)

inline

Definition at line 537 of file mole.h.

References pow(), and sexp().

Referenced by ChargTranEval(), and ion_photo().

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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().

void mole_cmp_num_in_out_reactions ( void )

Definition at line 2307 of file mole_reactions.cpp.

References CHARS_SPECIES, DEBUG_ENTRY, fprintf(), molecule::index, ioQQQ, t_mole_global::list, mole_global, mole_reaction::nproducts, mole_reaction::nreactants, t_mole_global::num_total, mole_reaction::products, mole_priv::reactab, and mole_reaction::reactants.

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void mole_create_react ( void )

mole_create_react build reaction structures

Definition at line 1722 of file mole_reactions.cpp.

References canonicalize_reaction_label(), cdEXIT, DEBUG_ENTRY, dense, deut, EXIT_FAILURE, fixit, fprintf(), hmi, ipHELIUM, t_deuterium::lgElmtOn, t_dense::lgElmtOn, t_mole_global::lgFederman, t_hmi::lgLeiden_Keep_ipMH2s, t_mole_global::lgLeidenHack, t_mole_global::lgProtElim, mole, mole_check_reverse_reactions(), mole_generate_isotopologue_reactions(), mole_global, newreact(), nuclide_list, t_mole_global::offReactions, t_mole_local::old_zone, parse_base(), parse_udfa(), plot_sparsity(), pow(), mole_priv::reactab, t_mole_local::reaction_rks, read_data(), register_reaction_vectors(), and UDFA.

Referenced by InitSimPostparse().

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void mole_drive ( void )

mole_drive main driver for chemical equilibrium routines

Definition at line 29 of file mole_drive.cpp.

References DEBUG_ENTRY, mole_effects(), mole_ion_trim(), mole_solve(), mole_update_limiting_reactants(), mole_update_rks(), mole_update_species_cache(), and MOLETOLER.

Referenced by ConvBase().

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mole_reaction* mole_findrate_s ( const char buf[] )

Definition at line 4123 of file mole_reactions.cpp.

References canonicalize_reaction_label(), DEBUG_ENTRY, and mole_priv::reactab.

Referenced by t_mole_local::findrate(), t_mole_local::findrk(), mole_get_equilibrium_condition(), and t_mole_local::sink_rate().

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void mole_make_groups ( void )

Definition at line 1135 of file mole_species.cpp.

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 )

Definition at line 246 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::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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void mole_rk_bigchange ( void )

Definition at line 3023 of file mole_reactions.cpp.

References ASSERT, DEBUG_ENTRY, fprintf(), mole_reaction::index, ioQQQ, mole_reaction::label, mole, nzone, t_mole_local::old_reaction_rks, t_mole_local::old_zone, mole_priv::reactab, and t_mole_local::reaction_rks.

Referenced by ZoneEnd().

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void mole_update_sources ( void )

Definition at line 55 of file mole_drive.cpp.

References DEBUG_ENTRY, mole_eval_sources(), mole_global, mole_update_species_cache(), and t_mole_global::num_total.

Referenced by ConvBase().

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void mole_update_species_cache ( void )

Definition at line 864 of file mole_species.cpp.

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, 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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bool operator!=	(	const chem_nuclide &	a,
		const chem_nuclide &	b
	)

inline

Definition at line 119 of file mole.h.

bool operator<	(	const chem_nuclide &	a,
		const chem_nuclide &	b
	)

inline

Definition at line 99 of file mole.h.

References chem_nuclide::compare().

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bool operator<=	(	const chem_nuclide &	a,
		const chem_nuclide &	b
	)

inline

Definition at line 107 of file mole.h.

References chem_nuclide::compare().

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bool operator==	(	const chem_nuclide &	a,
		const chem_nuclide &	b
	)

inline

Definition at line 115 of file mole.h.

References chem_nuclide::compare().

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bool operator>	(	const chem_nuclide &	a,
		const chem_nuclide &	b
	)

inline

Definition at line 103 of file mole.h.

References chem_nuclide::compare().

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bool operator>=	(	const chem_nuclide &	a,
		const chem_nuclide &	b
	)

inline

Definition at line 111 of file mole.h.

References chem_nuclide::compare().

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

Definition at line 653 of file mole_species.cpp.

References parse_species_label().

Referenced by mole_generate_isotopologue_reactions(), newspecies(), and parse_species_label().

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