mole.h File Reference

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

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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)
	Computes the UMIST rate coefficient for a reaction as a function of temperature.
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

ChemElementList

typedef vector< shared_ptr<chem_element> > ChemElementList

ChemNuclideList

typedef vector< shared_ptr<chem_nuclide> > ChemNuclideList

isotopes_i

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

nNucs_cri

typedef molecule::nNucsMap::const_reverse_iterator nNucs_cri

nNucs_i

typedef molecule::nNucsMap::iterator nNucs_i

nNucs_ri

typedef molecule::nNucsMap::reverse_iterator nNucs_ri

Enumeration Type Documentation

mole_state

enum mole_state

Enumerator
MOLE_NULL
MOLE_PASSIVE
MOLE_ACTIVE

Function Documentation

create_isotopologues()

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

References atoms, create_isotopologues_one_position(), DEBUG_ENTRY, and fixit.

Referenced by mole_generate_isotopologue_reactions(), and newspecies().

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create_isotopologues_one_position()

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

References ASSERT, atoms, and DEBUG_ENTRY.

Referenced by create_isotopologues(), and mole_generate_isotopologue_reactions().

exists() [1/2]

bool exists ( const molecule * m )

inline

References null_mole.

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

exists() [2/2]

bool exists ( const molezone * m )

inline

References null_molezone.

findnuclide()

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

extern

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().

findspecies()

molecule * findspecies ( const char buf[] )

extern

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().

findspecies_validate()

molecule * findspecies_validate ( const char buf[] )

extern

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().

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findspecieslocal()

molezone * findspecieslocal ( const char buf[] )

extern

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

References DEBUG_ENTRY, findspecies(), molecule::index, mole, null_mole, and null_molezone.

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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findspecieslocal_validate()

molezone * findspecieslocal_validate ( const char buf[] )

extern

version for user-supplied species which may not be valid

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

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

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getMolecules()

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(), and mole_global.

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

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hmrate4()

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

inline

Computes the UMIST rate coefficient for a reaction as a function of temperature.

This function evaluates the rate coefficient using the UMIST formula: k(T) = a * (T/300)^b * exp(-c/T) with safeguards to prevent extrapolation outside the intended temperature range.

• For b > 0, temperature is capped at 5000 K to avoid unphysical rates at high T.
• For b < 0 or c < 0, temperature is floored at 10 K to avoid unphysical rates at low T.
• If both b and c are zero, returns a constant rate.

Parameters

a	Pre-exponential factor (rate coefficient at reference temperature).
b	Temperature exponent.
c	Activation energy (in temperature units).
te	Gas temperature (in Kelvin).

Returns

The computed rate coefficient.

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

Referenced by ChargTranEval(), and ion_photo().

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isMolecule()

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 chSpecies, DEBUG_ENTRY, findspecies(), molecule::isMolecule(), molecule::label, and null_mole.

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

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isSpecies()

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

Referenced by cdTemp().

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lgDifferByExcitation()

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

References molecule::label.

Referenced by register_reaction_vectors().

mole_cmp_num_in_out_reactions()

void mole_cmp_num_in_out_reactions

(

void

)

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

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mole_create_react()

void mole_create_react ( void )

extern

mole_create_react build reaction structures

References canonicalize_reaction_label(), cdEXIT, DEBUG_ENTRY, dense, deut, EXIT_FAILURE, fixit, fprintf(), hmi, ipHELIUM, mole, mole_check_reverse_reactions(), mole_generate_isotopologue_reactions(), mole_global, newreact(), nuclide_list, parse_base(), parse_udfa(), plot_sparsity(), mole_priv::reactab, read_data(), register_reaction_vectors(), and UDFA.

Referenced by InitSimPostparse().

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mole_drive()

void mole_drive ( void )

extern

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().

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mole_findrate_s()

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().

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mole_make_groups()

void mole_make_groups ( void )

extern

References ASSERT, DEBUG_ENTRY, groupspecies, LIMELM, and mole_global.

Referenced by t_mole_global::init().

mole_make_list()

void mole_make_list ( void )

extern

References ASSERT, molecule::charge, DEBUG_ENTRY, findspecies(), molecule::index, isactive(), molecule::isMonatomic(), ispassive(), molecule::lgGas_Phase, mole_global, molecule::nNuclide, t_mole_global::sort(), and mole_priv::spectab.

Referenced by t_mole_global::init().

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mole_rk_bigchange()

void mole_rk_bigchange

(

void

)

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

Referenced by ZoneEnd().

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mole_update_sources()

void mole_update_sources

(

void

)

References DEBUG_ENTRY, mole_eval_sources(), mole_global, and mole_update_species_cache().

Referenced by ConvBase().

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mole_update_species_cache()

void mole_update_species_cache ( void )

extern

References ASSERT, DEBUG_ENTRY, fprintf(), gv, ioQQQ, mole, mole_global, and NULL.

Referenced by diatomics::H2_LevelPops(), mole_drive(), and mole_update_sources().

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operator!=()

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

inline

operator<()

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

inline

References chem_nuclide::compare().

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operator<=()

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

inline

References chem_nuclide::compare().

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operator==()

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

inline

References chem_nuclide::compare().

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operator>()

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

inline

References chem_nuclide::compare().

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operator>=()

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

inline

References chem_nuclide::compare().

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parse_species_label() [1/2]

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

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

References ASSERT, CHARS_ISOTOPE_SYM, dense, findnuclide(), fprintf(), ioQQQ, NULL, and trace.

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ParseChemistry()

void ParseChemistry

(

Parser &

p

)

References cdEXIT, DEBUG_ENTRY, Symbol::EOSTAT, Symbol::ERROR, EXIT_FAILURE, fprintf(), Parser::getSymbol(), ioQQQ, mole_global, Symbol::NAME, Symbol::OPERATOR, Symbol::STRING, Symbol::toktype, and Symbol::value.

Referenced by ParseCommands().

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species_gasphase_density()

realnum species_gasphase_density

(

const string &

chSpecies

)

species_gasphase_density - Report gas phase density of requested species

Parameters

chSpecies

[in] species to process

Returns

density of species in the current zone

References chSpecies, DEBUG_ENTRY, findspecies(), molecule::index, mole, and null_mole.

Referenced by t_mean::MeanInc().

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test_isMolecule()

void test_isMolecule

(

)

test_isMolecule() - Test function isMolecule()

References cdEXIT, DEBUG_ENTRY, EXIT_SUCCESS, fprintf(), ioQQQ, isMolecule(), and mole_global.

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total_molecule_deut()

void total_molecule_deut ( realnum & total )

extern

References DEBUG_ENTRY, deut, mole, mole_global, and NULL.

Referenced by t_deuterium::updateXMolecules().

total_molecule_elems()

void total_molecule_elems ( realnum total[LIMELM] )

extern

References ASSERT, DEBUG_ENTRY, ipHYDROGEN, LIMELM, mole, mole_global, and NULL.

Referenced by t_dense::updateXMolecules().

total_molecules()

realnum total_molecules ( void )

extern

References DEBUG_ENTRY, mole, mole_global, and NULL.

total_molecules_gasphase()

realnum total_molecules_gasphase ( void )

extern

References DEBUG_ENTRY, mole, mole_global, and NULL.

Referenced by SumDensities().

Variable Documentation

element_list

ChemElementList element_list

extern

Referenced by t_mole_global::make_species(), newelement(), and SetIsotopeFractions().

mole

t_mole_local mole

extern

Referenced by AbundChange(), t_gaunt::brems_sum_ions(), ChemImportance(), ConvBase(), ConvIterCheck(), CoolEvaluate(), DynaStartZone(), eden_sum(), ElectronFractions(), fill_array(), fill_ext_src_and_snk(), find_solution(), findspecieslocal(), findspecieslocal_validate(), funjac(), diatomics::H2_LevelPops(), diatomics::H2_PunchDo(), diatomics::H2_X_sink_and_source(), HomogeneousSource(), diatomics::init(), t_mole_global::init(), InitSimPostparse(), iso_allocate(), iso_level(), isSpeciesActive(), iter_end_check(), IterRestart(), IterStart(), lgNetEdenSrcSmall(), lgNucleiConserved(), lines(), lines_molecules(), molecule::local(), matchGeneric(), t_mean::MeanMoleculeTemp(), molcol(), mole_create_react(), mole_dominant_rates(), mole_effects(), mole_eval_balance(), mole_eval_dynamic_balance(), mole_eval_sources(), diatomics::mole_H2_form(), mole_h_fixup(), mole_h_rate_diagnostics(), mole_print_species_reactions(), mole_return_cached_species(), mole_rk_bigchange(), mole_save(), mole_solve(), mole_update_limiting_reactants(), mole_update_rks(), mole_update_species_cache(), PrintRates(), PrtComment(), PrtZone(), radius_increment(), radius_next(), RT_tau_reset(), SaveDo(), SaveSpecies(), ScaleAllDensities(), GroupMap::setup(), species_gasphase_density(), states_nelemfill(), total_molecule_deut(), total_molecule_elems(), total_molecules(), total_molecules_gasphase(), GroupMap::updateMolecules(), and zero().

mole_global

t_mole_global mole_global

extern

Referenced by AbundChange(), atmdat_readin(), t_gaunt::brems_sum_ions(), ChargTranEval(), ChemImportance(), diatomics::Cont_Diss_Heat_Rate(), ConvBase(), ConvInitSolution(), ConvIterCheck(), CoolEvaluate(), DynaCreateArrays(), DynaIonize(), DynaNewStep(), DynaSaveLast(), DynaStartZone(), eden_sum(), ElectronFractions(), funjac(), getMolecules(), molezone::global(), grouped_elems(), diatomics::H2_X_sink_and_source(), diatomics::init(), init_struc(), InitSimPostparse(), ion_photo(), ion_trim(), ion_trim2(), isSpeciesActive(), iter_end_check(), IterRestart(), IterStart(), lgNucleiConserved(), t_mole_global::make_species(), matchGeneric(), diatomics::Mol_Photo_Diss_Rates(), molcol(), mole_cmp_num_in_out_reactions(), mole_create_react(), mole_effects(), mole_eval_balance(), mole_eval_dynamic_balance(), mole_h_fixup(), mole_h_rate_diagnostics(), mole_h_reactions(), mole_make_groups(), mole_make_list(), mole_return_cached_species(), mole_solve(), mole_update_limiting_reactants(), mole_update_sources(), mole_update_species_cache(), newreact(), newspecies(), OpacityAddTotal(), OpacityCreateAll(), ParseChemistry(), ParseCommands(), ParseDont(), ParseElement(), ParseSet(), ParseSpecies(), plot_sparsity(), PrtComment(), PrtZone(), radius_increment(), radius_next(), RT_tau_reset(), SaveDo(), SaveSpecies(), ScaleAllDensities(), t_mole_local::set_ion_locations(), setProperties(), GroupMap::setup(), speciesCheck(), speciesOff(), test_isMolecule(), total_molecule_deut(), total_molecule_elems(), total_molecules(), total_molecules_gasphase(), GroupMap::updateMolecules(), and t_mole_local::zero().

nuclide_list

ChemNuclideList nuclide_list

extern

Referenced by findnuclide(), funjac(), grouped_elems(), lgElemsConserved(), lgNucleiConserved(), t_mole_global::make_species(), mole_create_react(), mole_eval_sources(), mole_h_rate_diagnostics(), mole_ion_trim(), mole_solve(), newisotope(), t_mole_local::set_ion_locations(), t_mole_local::set_isotope_abundances(), GroupMap::setup(), and GroupMap::updateMolecules().

null_mole

molecule* null_mole

extern

Referenced by database_readin(), t_mole_local::dissoc_rate(), exists(), findspecies(), findspecieslocal(), molezone::global(), diatomics::init(), isMolecule(), iso_allocate(), isSpecies(), t_mole_global::make_species(), mole_save(), parse_reaction(), parse_udfa(), SaveDo(), species_gasphase_density(), and states_nelemfill().

null_molezone

molezone* null_molezone

extern

Referenced by exists(), findspecieslocal(), getLevelsGeneric(), genericState::isSpecies(), lgCheckMonitors(), molecule::local(), t_mole_global::make_species(), matchGeneric(), SaveAllSpeciesLabelsLevels(), SaveSpecies(), and SaveSpeciesLines().

null_nuclide

chem_nuclide* null_nuclide

extern

Referenced by molecule::heavyAtom(), IterRestart(), t_mole_global::make_species(), molcol(), mole_update_limiting_reactants(), and molezone::zero().

SMALLABUND

const double SMALLABUND = 1e-24

static