#include "count_ptr.h"
#include "elementnames.h"
#include "transition.h"

Include dependency graph for mole.h:

Data Structures
class	chem_element

class	chem_atom

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_atom > >::iterator	isotopes_i

typedef vector< count_ptr< chem_atom > >	ChemAtomList

typedef molecule::nAtomsMap::iterator	nAtoms_i

typedef molecule::nAtomsMap::reverse_iterator	nAtoms_ri

typedef molecule::nAtomsMap::const_reverse_iterator	nAtoms_cri

Enumerations
enum	mole_state { MOLE_NULL , MOLE_PASSIVE , MOLE_ACTIVE }

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

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

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

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

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

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

void	mole_drive (void)

void	mole_create_react (void)

mole_reaction *	mole_findrate_s (const char buf[])

void	mole_print_species_reactions (molecule *speciesToPrint)

molecule *	findspecies (const char buf[])

molezone *	findspecieslocal (const char buf[])

void	mole_punch (FILE *punit, const char speciesname[], const char args[], bool lgHeader, bool lgData, double depth)

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

Variables
ChemAtomList	atom_list

ChemAtomList	unresolved_atom_list

chem_element *	null_element

chem_atom *	null_atom

molecule *	null_mole

t_mole_global	mole_global

molezone *	null_molezone

t_mole_local	mole

Macro Definition Documentation

◆ SMALLABUND

#define SMALLABUND 1e-24

Definition at line 13 of file mole.h.

Typedef Documentation

◆ ChemAtomList

typedef vector< count_ptr<chem_atom> > ChemAtomList

Definition at line 115 of file mole.h.

◆ isotopes_i

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

Definition at line 35 of file mole.h.

◆ nAtoms_cri

typedef molecule::nAtomsMap::const_reverse_iterator nAtoms_cri

Definition at line 216 of file mole.h.

◆ nAtoms_i

typedef molecule::nAtomsMap::iterator nAtoms_i

Definition at line 214 of file mole.h.

◆ nAtoms_ri

typedef molecule::nAtomsMap::reverse_iterator nAtoms_ri

Definition at line 215 of file mole.h.

Enumeration Type Documentation

◆ mole_state

enum mole_state

Enumerator
MOLE_NULL
MOLE_PASSIVE
MOLE_ACTIVE

Definition at line 15 of file mole.h.

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().

Here is the call graph for this function:

◆ 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[] )

◆ 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().

◆ mole_cmp_num_in_out_reactions()

void mole_cmp_num_in_out_reactions ( void )

Definition at line 2183 of file mole_reactions.cpp.

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

◆ mole_create_react()

void mole_create_react ( void )

mole_create_react build reaction structures

Definition at line 1665 of file mole_reactions.cpp.

References DEBUG_ENTRY, dense, deut, fixit(), ipHELIUM, t_dense::lgElmtOn, t_deuterium::lgElmtOn, t_mole_global::lgFederman, t_mole_global::lgLeidenHack, t_mole_global::lgProtElim, mole, mole_check_reverse_reactions(), mole_generate_isotopologue_reactions(), mole_global, newreact(), t_mole_local::old_zone, parse_base(), parse_udfa(), plot_sparsity(), mole_priv::reactab, t_mole_local::reaction_rks, read_data(), register_reaction_vectors(), SAHA, source, UDFA, and unresolved_atom_list.

Referenced by InitSimPostparse().

Here is the call graph for this function:

◆ mole_drive()

void mole_drive ( void )

mole_drive main driver for chemical equilibrium routines

Definition at line 41 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().

Here is the call graph for this function:

◆ mole_findrate_s()

mole_reaction * mole_findrate_s ( const char buf[] )

Definition at line 3872 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_constant(), and t_mole_local::sink_rate().

Here is the call graph for this function:

◆ 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().

Here is the call graph for this function:

◆ mole_print_species_reactions()

void mole_print_species_reactions ( molecule * speciesToPrint )

Definition at line 316 of file newton_step.cpp.

References molecule::index, mole_reaction::index, ioQQQ, molecule::label, mole_reaction::label, mole, mole_reaction::nproducts, mole_reaction::nreactants, mole_reaction::products, mole_reaction::pvector, mole_priv::reactab, mole_reaction::reactants, t_mole_local::reaction_rks, mole_reaction::rvector, and t_mole_local::species.

Referenced by lgElemsConserved(), and mole_system_error().

◆ mole_punch()

void mole_punch	(	FILE *	punit,
		const char	speciesname[],
		const char	args[],
		bool	lgHeader,
		bool	lgData,
		double	depth
	)

Definition at line 4221 of file mole_reactions.cpp.

References DEBUG_ENTRY, findspecies(), molecule::index, mole_reaction::index, mole_reaction::label, mole, mole_reaction::nproducts, mole_reaction::nreactants, mole_reaction::products, mole_reaction::pvector, mole_reaction::pvector_excit, mole_priv::reactab, mole_reaction::reactants, t_mole_local::reaction_rks, mole_reaction::rvector, mole_reaction::rvector_excit, and t_mole_local::species.

Referenced by SaveDo().

Here is the call graph for this function:

◆ mole_rk_bigchange()

void mole_rk_bigchange ( void )

Definition at line 2866 of file mole_reactions.cpp.

References ASSERT, DEBUG_ENTRY, 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().

◆ mole_update_sources()

void mole_update_sources ( void )

Definition at line 106 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().

Here is the call graph for this function:

◆ 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().

Here is the call graph for this function:

◆ operator!=()

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

inline

Definition at line 110 of file mole.h.

◆ operator<()

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

inline

Definition at line 90 of file mole.h.

References chem_atom::compare().

Here is the call graph for this function:

◆ operator<=()

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

inline

Definition at line 98 of file mole.h.

References chem_atom::compare().

Here is the call graph for this function:

◆ operator==()

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

inline

Definition at line 106 of file mole.h.

References chem_atom::compare().

Here is the call graph for this function:

◆ operator>()

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

inline

Definition at line 94 of file mole.h.

References chem_atom::compare().

Here is the call graph for this function:

◆ operator>=()

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

inline

Definition at line 102 of file mole.h.

References chem_atom::compare().

Here is the call graph for this function:

◆ 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().

Here is the call graph for this function:

◆ parse_species_label() [2/2]

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