mole_priv.h File Reference

#include "count_ptr.h"

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Data Structures
class	GroupMap
class	mole_reaction

Namespaces
	mole_priv

Macros
#define	MAXREACTANTS   3
#define	MAXPRODUCTS   4

Typedefs
typedef map< string, count_ptr< mole_reaction > >::iterator	mole_reaction_i
typedef map< string, count_ptr< mole_reaction > >::const_iterator	mole_reaction_ci
typedef map< string, count_ptr< molecule > >::iterator	molecule_i
typedef map< string, count_ptr< chem_element > >::iterator	chem_element_i
typedef map< string, count_ptr< chem_atom > >::iterator	chem_atom_i

Enumerations
enum	udfastate { ABSENT, CORRECT, CONFLICT }

Functions
void	mole_dominant_rates (const molecule *debug_species, FILE *ioOut)
void	mole_eval_balance (long int n, double *b, bool lgJac, multi_arr< double, 2 > &c)
double	mole_solve (void)
void	mole_eval_sources (long int num_total)
realnum	mole_return_cached_species (const GroupMap &MoleMap)
double	frac_H2star_hminus ()
void	mole_update_rks (void)

Variables
map< string, count_ptr< molecule > >	mole_priv::spectab
map< string, count_ptr< mole_reaction > >	mole_priv::reactab
map< string, count_ptr< chem_element > >	mole_priv::elemtab
map< string, count_ptr< chem_atom > >	mole_priv::atomtab
map< string, count_ptr< mole_reaction > >	mole_priv::functab
molecule **	groupspecies

Macro Definition Documentation

MAXPRODUCTS

#define MAXPRODUCTS   4

Definition at line 46 of file mole_priv.h.

Referenced by compare_udfa(), parse_reaction(), and parse_udfa().

MAXREACTANTS

#define MAXREACTANTS   3

Definition at line 45 of file mole_priv.h.

Referenced by compare_udfa(), mole_dominant_rates(), mole_eval_balance(), mole_eval_sources(), parse_reaction(), and parse_udfa().

Typedef Documentation

chem_atom_i

typedef map<string,count_ptr<chem_atom> >::iterator chem_atom_i

Definition at line 41 of file mole_priv.h.

chem_element_i

typedef map<string,count_ptr<chem_element> >::iterator chem_element_i

Definition at line 40 of file mole_priv.h.

mole_reaction_ci

typedef map<string,count_ptr<mole_reaction> >::const_iterator mole_reaction_ci

Definition at line 38 of file mole_priv.h.

mole_reaction_i

typedef map<string,count_ptr<mole_reaction> >::iterator mole_reaction_i

Definition at line 37 of file mole_priv.h.

molecule_i

typedef map<string,count_ptr<molecule> >::iterator molecule_i

Definition at line 39 of file mole_priv.h.

Enumeration Type Documentation

udfastate

enum udfastate

Enumerator
ABSENT
CORRECT
CONFLICT

Definition at line 69 of file mole_priv.h.

Function Documentation

frac_H2star_hminus()

double frac_H2star_hminus

(

)

Definition at line 690 of file mole_reactions.cpp.

References mole_reaction::a, t_phycon::alogte, ASSERT, atmdat, diatomics::Average_A, diatomics::Average_collH2_deexcit, diatomics::Average_collH2_dissoc_g, diatomics::Average_collH2_dissoc_s, diatomics::Average_collH2_excit, diatomics::Average_collH_deexcit, diatomics::Average_collH_dissoc_g, diatomics::Average_collH_dissoc_s, diatomics::Average_collH_excit, t_atmdat::CharExcIonOf, t_atmdat::CharExcRecTo, conv, t_secondaries::csupra, dense, t_dense::eden, t_hmi::exphmi, t_iso_sp::fb, findspecieslocal(), fixit(), fp_equal(), GammaK(), t_mole_local::grain_area, gv, h2, t_hmi::H2_forms_grains, t_hmi::H2_forms_hminus, t_hmi::H2_H2g_to_H2s_rate_used, t_hmi::H2_photodissoc_used_H2g, t_hmi::H2_photodissoc_used_H2s, t_hmi::H2_Solomon_dissoc_rate_used_H2g, t_hmi::H2_Solomon_dissoc_rate_used_H2s, t_hmi::H2star_forms_grains, t_hmi::H2star_forms_hminus, hd, hmi, t_hmi::HMinus_induc_rec_rate, t_hmi::HMinus_photo_rate, hmirat(), HMRATE, t_opac::ih2pnt, t_opac::ih2pof, ipH1s, ipH2p, ipH2s, ipH3d, ipH3p, ipH3s, ipH_LIKE, ipHYDROGEN, ipOXYGEN, iso_photo(), iso_sp, diatomics::lgEnabled, diatomics::lgEvaluated, t_hmi::lgH2_Chemistry_BigH2, t_mole_global::lgLeidenHack, MAX2, MIN2, mole, mole_get_equilibrium_constant(), mole_global, t_conv::nTotalIoniz, opac, diatomics::photodissoc_BigH2_H2g, diatomics::photoionize_rate, phycon, powi(), GrainVar::rate_h2_form_grains_used_total, t_hmi::rel_pop_LTE_H2g, t_hmi::rel_pop_LTE_H2s, t_hmi::rel_pop_LTE_Hmin, SAHA, SDIV(), secondaries, sexp(), diatomics::Solomon_dissoc_rate_g, diatomics::spon_diss_tot, t_phycon::sqrte, t_iso_sp::st, t_phycon::te, t_phycon::te05, t_phycon::te30, t_phycon::te90, t_phycon::tesqrd, t_secondaries::x12tot, and t_dense::xIonDense.

Referenced by mole_h_rate_diagnostics().

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mole_dominant_rates()

void mole_dominant_rates	(	const molecule *	debug_species,
		FILE *	ioOut
	)

Definition at line 335 of file mole_eval_balance.cpp.

References mole_reaction::index, molecule::index, mole_reaction::label, molecule::label, MAXREACTANTS, mole, mole_reaction::nproducts, mole_reaction::nreactants, null_mole, 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 SaveDo().

mole_eval_balance()

void mole_eval_balance	(	long int	n,
		double *	b,
		bool	lgJac,
		multi_arr< double, 2 > &	c
	)

mole_eval_balance

Definition at line 37 of file mole_eval_balance.cpp.

References ASSERT, DEBUG_ENTRY, mole_reaction::index, molecule::index, ioQQQ, mole_reaction::label, lgNucleiConserved(), t_trace::lgTrace, t_mole_global::list, MAXREACTANTS, mole, mole_global, mole_reaction::nproducts, mole_reaction::nreactants, t_mole_global::num_calc, mole_reaction::products, mole_reaction::pvector, mole_priv::reactab, mole_reaction::reactants, t_mole_local::reaction_rks, mole_reaction::rvector, t_mole_local::species, trace, and multi_arr< T, d, ALLOC, lgBC >::zero().

Referenced by mole_eval_dynamic_balance().

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mole_eval_sources()

void mole_eval_sources

(

long int

num_total

)

Definition at line 149 of file mole_eval_balance.cpp.

References atmdat, molecule::charge, DEBUG_ENTRY, dense, mole_reaction::index, molecule::index, molecule::isMonatomic(), t_atmdat::lgCTOn, t_dense::lgElmtOn, LIMELM, MAXREACTANTS, mole, molecule::nAtom, 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, t_mole_local::sink, t_mole_local::source, t_mole_local::species, unresolved_atom_list, and t_mole_local::xMoleChTrRate.

Referenced by mole_effects(), and mole_update_sources().

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mole_return_cached_species()

realnum mole_return_cached_species

(

const GroupMap &

MoleMap

)

Definition at line 935 of file mole_species.cpp.

References ASSERT, dense, deut, t_mole_local::elec, t_dense::gas_phase, 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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mole_solve()

double mole_solve

(

void

)

mole_solve fills in matrix for heavy elements molecular routines

Definition at line 49 of file mole_solve.cpp.

References ASSERT, atom_list, BIGFLOAT, check_co_ion_converge(), conv, DEBUG_ENTRY, dense, t_dense::eden, fixit(), fnzone, funjac(), get_ptr(), t_hmi::H2_frac_abund_set, hmi, t_conv::incrementCounter(), ionbal, t_conv::IonizErrorAllowed, ioQQQ, ipHYDROGEN, lgElemsConserved(), t_trace::lgTrace, mole, mole_global, mole_h_fixup(), mole_return_cached_species(), MOLE_SOLVE, MOLE_SOLVE_STEPS, newton_step(), t_mole_global::num_calc, t_mole_global::num_compacted, nzone, phycon, t_ionbal::RateIonizTot(), t_ionbal::RateRecomTot, SDIV(), t_conv::setConvIonizFail(), t_mole_local::sink, SMALLABUND, t_mole_local::source, t_mole_local::species, t_phycon::te, trace, and t_dense::xIonDense.

Referenced by mole_drive().

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mole_update_rks()

void mole_update_rks

(

void

)

mole_update_rks update rate coefficients, only temp part

Definition at line 2840 of file mole_reactions.cpp.

References mole_reaction::a, DEBUG_ENTRY, mole_reaction::index, ioQQQ, mole_reaction::label, mole, mole_h2_grain_form(), mole_h_reactions(), mole_priv::reactab, t_mole_local::reaction_rks, and mole_reaction::rk().

Referenced by mole_drive().

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Variable Documentation

groupspecies

molecule** groupspecies

Definition at line 72 of file mole_species.cpp.

Referenced by funjac(), grouped_elems(), mole_make_groups(), mole_system_error(), newton_step(), GroupMap::setup(), and GroupMap::updateMolecules().