#include "module.h"
#include "container_classes.h"

Include dependency graph for mole.h:

This graph shows which files directly or indirectly include this file:

Classes
class	chem_element

class	chem_nuclide

class	element_pointer_value_less

class	molecule

class	t_mole_global

class	molezone

class	t_mole_local

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

typedef vector< shared_ptr < chem_nuclide > >	ChemNuclideList

typedef vector< shared_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[])

shared_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)

realnum	species_gasphase_density (const string &chSpecies)

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)

bool	isSpecies (const string &chSpecies)

bool	isMolecule (const string &chSpecies)

void	test_isMolecule ()

void	getMolecules (vector< string > &allMolecules)

Variables
static const double	SMALLABUND = 1e-24

ChemNuclideList	nuclide_list

ChemElementList	element_list

chem_nuclide *	null_nuclide

molecule *	null_mole

t_mole_global	mole_global

molezone *	null_molezone

t_mole_local	mole

Typedef Documentation

typedef vector< shared_ptr<chem_element> > ChemElementList

typedef vector< shared_ptr<chem_nuclide> > ChemNuclideList

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

typedef molecule::nNucsMap::const_reverse_iterator nNucs_cri

typedef molecule::nNucsMap::iterator nNucs_i

typedef molecule::nNucsMap::reverse_iterator nNucs_ri

Enumeration Type Documentation

enum mole_state

Enumerator
MOLE_NULL
MOLE_PASSIVE
MOLE_ACTIVE

Function Documentation

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

References create_isotopologues_one_position(), DEBUG_ENTRY, and fixit.

Referenced by mole_generate_isotopologue_reactions(), and newspecies().

Here is the call graph for this function:

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

References ASSERT, and DEBUG_ENTRY.

Referenced by create_isotopologues(), and mole_generate_isotopologue_reactions().

bool exists ( const molecule * m )

inline

References null_mole.

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

bool exists ( const molezone * m )

inline

References null_molezone.

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

References DEBUG_ENTRY, nuclide_list, nuclidetab, and NULL.

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

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(), isMolecule(), iso_allocate(), isSpecies(), 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(), species_gasphase_density(), and states_nelemfill().

molecule* findspecies_validate ( const char buf[] )

version for user-supplied species which may not be valid

References cdEXIT, DEBUG_ENTRY, EXIT_FAILURE, fprintf(), ioQQQ, and mole_priv::spectab.

Referenced by findspecieslocal_validate().

Here is the call graph for this function:

molezone* findspecieslocal ( const char buf[] )

version for species we know are valid, but may not be present in calculation

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().

Here is the call graph for this function:

molezone* findspecieslocal_validate ( const char buf[] )

version for user-supplied species which may not be valid

References DEBUG_ENTRY, findspecies_validate(), molecule::index, mole, and t_mole_local::species.

Referenced by iter_end_check(), radius_first(), and radius_next().

Here is the call graph for this function:

void getMolecules ( vector< string > & allMolecules )

getMolecules - Get a list of all active molecules.

Parameters

allMolecules [in,out] List of molecule strings.

References DEBUG_ENTRY, isMolecule(), t_mole_global::list, and mole_global.

Referenced by t_mean::setup_molecules(), and test_cdTemp_molecules().

Here is the call graph for this function:

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

inline

References min(), pow(), and sexp().

Referenced by ChargTranEval(), and ion_photo().

Here is the call graph for this function:

bool isMolecule ( const string & chSpecies )

isMolecule - Tell if the input string corresponds to a valid & active molecule.

Parameters

chSpecies [in] Species string

Returns: bool value: true, if a valid molecule; false, otherwise

References DEBUG_ENTRY, findspecies(), molecule::isMolecule(), and molecule::label.

Referenced by cdTemp(), getMolecules(), and test_isMolecule().

Here is the call graph for this function:

bool isSpecies ( const string & chSpecies )

isSpecies - Tell if the input string corresponds to a valid & active species.

Parameters

chSpecies [in] Species string

Returns: bool value: true, if a valid species; false, otherwise

References DEBUG_ENTRY, findspecies(), molecule::isMolecule(), molecule::isMonatomic(), and molecule::label.

Referenced by cdTemp().

Here is the call graph for this function:

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

References molecule::label.

Referenced by register_reaction_vectors().

void mole_cmp_num_in_out_reactions ( void )

References CHARS_SPECIES, DEBUG_ENTRY, fprintf(), ioQQQ, t_mole_global::list, mole_global, t_mole_global::num_total, and mole_priv::reactab.

Here is the call graph for this function:

void mole_create_react ( void )

mole_create_react build reaction structures

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().

Here is the call graph for this function:

void mole_drive ( void )

mole_drive main driver for chemical equilibrium routines

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().

Here is the call graph for this function:

mole_reaction* mole_findrate_s ( const char buf[] )

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

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

Here is the call graph for this function:

void mole_make_groups ( void )

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 )

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().

Here is the call graph for this function:

void mole_rk_bigchange ( void )

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().

Here is the call graph for this function:

void mole_update_sources ( void )

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

Referenced by ConvBase().

Here is the call graph for this function:

void mole_update_species_cache ( void )

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, NULL, 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().

Here is the call graph for this function:

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

inline

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

inline

References chem_nuclide::compare().

Here is the call graph for this function:

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

inline

References chem_nuclide::compare().

Here is the call graph for this function:

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

inline

References chem_nuclide::compare().

Here is the call graph for this function:

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

inline

References chem_nuclide::compare().

Here is the call graph for this function:

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

inline

References chem_nuclide::compare().

Here is the call graph for this function:

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

Referenced by mole_generate_isotopologue_reactions(), and newspecies().

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