#include "cdstd.h"
#include <stdlib.h>
#include "cddefines.h"
#include "colden.h"
#include "physconst.h"
#include "mole.h"
#include "version.h"
#include "mole_priv.h"
#include "hmi.h"
#include "conv.h"
#include "dense.h"
#include "thermal.h"
#include "gammas.h"
#include "grainvar.h"
#include "ionbal.h"
#include "opacity.h"
#include "path.h"
#include "radius.h"
#include "atmdat.h"
#include "taulines.h"
#include "trace.h"
#include "deuterium.h"
#include "phycon.h"
#include "doppvel.h"
#include "rfield.h"
#include "secondaries.h"
#include "hextra.h"
#include "rt.h"
#include "iso.h"
#include "h2.h"

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Macros
#define	gzopen(file, mode) fopen(file,mode)

#define	gzgets(fp, buf, siz) fgets(buf,siz,fp)

#define	gzclose(fp) fclose(fp)

#define	gzFile FILE

#define	FLTEQ(a, b) (fabs((a)-(b)) <= 1e-6*fabs((a)+(b)))

Enumerations
enum	{ UDFA = 0 }

enum	{ BUFSIZE =256 }

Functions
STATIC void	newreact (const char label[], const char fun[], double a, double b, double c)

STATIC long	parse_reaction (count_ptr< mole_reaction > &rate, const char label[])

STATIC string	canonicalize_reaction_label (const char label[])

STATIC void	canonicalize_reaction (count_ptr< mole_reaction > &rate)

STATIC void	register_reaction_vectors (count_ptr< mole_reaction > rate)

STATIC void	mole_check_reverse_reactions (void)

STATIC double	mole_get_equilibrium_constant (const char buf[])

STATIC double	mole_partition_function (const molecule *const sp)

STATIC void	mole_generate_isotopologue_reactions (string atom_old, string atom_new)

STATIC void	plot_sparsity (void)

STATIC bool	lgReactBalance (const count_ptr< mole_reaction > &rate)

STATIC void	read_data (const char file[], void(parse)(char s))

STATIC void	parse_base (char *s)

STATIC void	parse_udfa (char *s)

STATIC void	compare_udfa (const count_ptr< mole_reaction > &rate)

double	frac_H2star_hminus (void)

double	hmirat (double te)

STATIC void	mole_h2_grain_form (void)

STATIC void	mole_h_reactions (void)

void	mole_create_react (void)

void	mole_cmp_num_in_out_reactions ()

STATIC char *	getcsvfield (char **s, char c)

void	mole_update_rks (void)

void	mole_rk_bigchange (void)

mole_reaction *	mole_findrate_s (const char buf[])

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

Variables
static realnum	albedo = 0.5

static map< formula_species, struct udfa_reaction_s * >	udfatab

Macro Definition Documentation

◆ FLTEQ

#define FLTEQ	(	a,
		b
	)	(fabs((a)-(b)) <= 1e-6*fabs((a)+(b)))

Definition at line 2685 of file mole_reactions.cpp.

◆ gzclose

#define gzclose ( fp ) fclose(fp)

Definition at line 2621 of file mole_reactions.cpp.

◆ gzFile

#define gzFile FILE

Definition at line 2622 of file mole_reactions.cpp.

◆ gzgets

#define gzgets	(	fp,
		buf,
		siz
	)	fgets(buf,siz,fp)

Definition at line 2620 of file mole_reactions.cpp.

◆ gzopen

#define gzopen	(	file,
		mode
	)	fopen(file,mode)

Definition at line 2619 of file mole_reactions.cpp.

Enumeration Type Documentation

◆ anonymous enum

anonymous enum

Enumerator
UDFA

Definition at line 49 of file mole_reactions.cpp.

◆ anonymous enum

anonymous enum

Enumerator
BUFSIZE

Definition at line 2625 of file mole_reactions.cpp.

Function Documentation

◆ canonicalize_reaction()

STATIC void canonicalize_reaction ( count_ptr< mole_reaction > & rate )

Definition at line 2387 of file mole_reactions.cpp.

References DEBUG_ENTRY, and t_mole_global::sort().

Referenced by canonicalize_reaction_label(), and newreact().

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◆ canonicalize_reaction_label()

STATIC string canonicalize_reaction_label ( const char label[] )

Definition at line 2371 of file mole_reactions.cpp.

References canonicalize_reaction(), DEBUG_ENTRY, and parse_reaction().

Referenced by mole_findrate_s(), and mole_generate_isotopologue_reactions().

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◆ compare_udfa()

STATIC void compare_udfa ( const count_ptr< mole_reaction > & rate )

Definition at line 2794 of file mole_reactions.cpp.

References CONFLICT, CORRECT, FLTEQ, MAXPRODUCTS, MAXREACTANTS, and udfatab.

Referenced by newreact().

◆ frac_H2star_hminus()

double frac_H2star_hminus ( void )

Definition at line 690 of file mole_reactions.cpp.

References h2, t_hmi::H2_forms_hminus, t_hmi::H2star_forms_hminus, hmi, diatomics::lgEnabled, diatomics::lgEvaluated, t_hmi::lgH2_Chemistry_BigH2, and SDIV().

Referenced by mole_h_rate_diagnostics().

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◆ getcsvfield()

STATIC char * getcsvfield	(	char **	s,
		char	c
	)

Definition at line 2782 of file mole_reactions.cpp.

Referenced by parse_base(), and parse_udfa().

◆ hmirat()

double hmirat ( double te )

hmirat computes radiative association rate for H-

Parameters

te

Definition at line 1581 of file mole_reactions.cpp.

References DEBUG_ENTRY, phycon, t_phycon::sqrte, t_phycon::te001, t_phycon::te003, t_phycon::te01, t_phycon::te03, t_phycon::te10, t_phycon::te20, and t_phycon::te70.

Referenced by mole_h_reactions().

◆ lgReactBalance()

STATIC bool lgReactBalance ( const count_ptr< mole_reaction > & rate )

Definition at line 2574 of file mole_reactions.cpp.

References sign().

Referenced by newreact().

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◆ mole_check_reverse_reactions()

STATIC void mole_check_reverse_reactions ( void )

Definition at line 2084 of file mole_reactions.cpp.

References DEBUG_ENTRY, fixit(), ioQQQ, t_trace::lgTraceMole, mole_priv::reactab, and trace.

Referenced by mole_create_react().

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◆ 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().

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◆ 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().

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◆ mole_generate_isotopologue_reactions()

STATIC void mole_generate_isotopologue_reactions	(	string	atom_old,
		string	atom_new
	)

Definition at line 1935 of file mole_reactions.cpp.

References ASSERT, ATOMIC_MASS_UNIT, canonicalize_reaction_label(), create_isotopologues_one(), DEBUG_ENTRY, fixit(), ioQQQ, newreact(), parse_species_label(), and mole_priv::reactab.

Referenced by mole_create_react().

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◆ mole_get_equilibrium_constant()

STATIC double mole_get_equilibrium_constant ( const char buf[] )

Definition at line 2127 of file mole_reactions.cpp.

References BIGFLOAT, DEBUG_ENTRY, MIN2, mole_findrate_s(), mole_partition_function(), mole_reaction::nproducts, mole_reaction::nreactants, mole_reaction::products, and mole_reaction::reactants.

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◆ mole_h2_grain_form()

STATIC void mole_h2_grain_form ( void )

Todo:: 2 - put in actual composition dependent Tad - this is only valid for bare surfaces - not ice - for ice Tad is 555K hmi.Tad is binding energy expressed as a temperature note that hmi.Tad is set to 800. in zero tau_nu the first equation in section 2.5 equation one paragraph before equation 2 at low grain temperatures all end in para, J=0

Definition at line 2925 of file mole_reactions.cpp.

References ASSERT, t_dense::AtomicWeight, GrainVar::bin, t_hmi::chJura, dense, fixit(), fnzone, t_dense::gas_phase, GetAveVelocity(), GrainDrive(), gv, h2, hmi, ipHYDROGEN, GrainVar::lgDustOn(), GrainVar::lgGrainPhysicsOn, diatomics::lgH2_grain_deexcitation, MALLOC, MAT_CAR, MAT_CAR2, MAT_SIL, MAT_SIL2, NQGRID, phycon, POW2, qheat(), diatomics::rate_grain_J1_to_J0, diatomics::rate_grain_op_conserve, t_hmi::rate_h2_form_grains_set, GrainVar::rate_h2_form_grains_used_total, t_hmi::ScaleJura, SDIV(), sexp(), t_phycon::sqrte, t_hmi::Tad, and t_phycon::te.