mole_reactions.cpp File Reference

#include "cdstd.h"
#include "cddefines.h"
#include "prt.h"
#include "version.h"
#include "hmi.h"
#include "conv.h"
#include "thermal.h"
#include "grainvar.h"
#include "ionbal.h"
#include "opacity.h"
#include "radius.h"
#include "atmdat.h"
#include "trace.h"
#include "deuterium.h"
#include "grains.h"
#include "mole_priv.h"
#include "gammas.h"
#include "mole.h"
#include "freebound.h"
#include "dense.h"
#include "ipoint.h"
#include "phycon.h"
#include "doppvel.h"
#include "rfield.h"
#include "secondaries.h"
#include "hextra.h"
#include "rt_escprob.h"
#include "iso.h"
#include "h2.h"

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Macros
#define	FLTEQ(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 (shared_ptr< mole_reaction > &rate, const char label[])
STATIC string	canonicalize_reaction_label (const char label[])
STATIC void	canonicalize_reaction (shared_ptr< mole_reaction > &rate)
STATIC bool	lgReactionTrivial (shared_ptr< mole_reaction > &rate)
STATIC void	register_reaction_vectors (shared_ptr< mole_reaction > rate)
STATIC void	mole_check_reverse_reactions (void)
STATIC double	mole_get_equilibrium_condition (const char buf[])
STATIC double	mole_get_equilibrium_condition (const mole_reaction *const rate)
STATIC double	mole_partition_function (const molecule *const sp)
STATIC void	mole_generate_isotopologue_reactions (string atom_old, string atom_new)
STATIC double	sticking_probability_H_func (double T_gas, double T_grain)
STATIC double	sticking_probability_H_HM79 (double T_gas, double T_grain)
STATIC void	plot_sparsity (void)
STATIC bool	lgReactBalance (const shared_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 shared_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[])

Variables
static realnum	albedo = 0.5
static map< formula_species, shared_ptr< udfa_reaction > >	udfatab

Macro Definition Documentation

FLTEQ

#define FLTEQ	(		a,
			b )

Value:

(fabs((a)-(b)) <= 1e-6*fabs((a)+(b)))

Referenced by compare_udfa(), and parse_udfa().

Enumeration Type Documentation

anonymous enum

anonymous enum

set UDFA = 1 to make UDFA comparison and stop http://udfa.ajmarkwick.net/index.php

Enumerator
UDFA

anonymous enum

anonymous enum

Enumerator
BUFSIZE

Function Documentation

canonicalize_reaction()

STATIC void canonicalize_reaction

(

shared_ptr< mole_reaction > &

rate

)

References DEBUG_ENTRY, t_mole_global::sort(), and STATIC.

Referenced by canonicalize_reaction_label(), and newreact().

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canonicalize_reaction_label()

STATIC string canonicalize_reaction_label

(

const char

label[]

)

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

Referenced by mole_create_react(), mole_findrate_s(), and mole_generate_isotopologue_reactions().

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compare_udfa()

STATIC void compare_udfa

(

const shared_ptr< mole_reaction > &

rate

)

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

Referenced by newreact().

frac_H2star_hminus()

double frac_H2star_hminus

(

void

)

References h2, hmi, and SDIV().

Referenced by mole_h_rate_diagnostics().

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getcsvfield()

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

References STATIC.

Referenced by parse_base(), and parse_udfa().

hmirat()

double hmirat

(

double

te

)

hmirat computes radiative association rate for H-

Parameters

te

References DEBUG_ENTRY, and phycon.

Referenced by mole_h_reactions().

lgReactBalance()

STATIC bool lgReactBalance

(

const shared_ptr< mole_reaction > &

rate

)

References fprintf(), ioQQQ, sign(), and STATIC.

Referenced by newreact().

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lgReactionTrivial()

STATIC bool lgReactionTrivial

(

shared_ptr< mole_reaction > &

rate

)

References DEBUG_ENTRY, and STATIC.

Referenced by newreact().

mole_check_reverse_reactions()

STATIC void mole_check_reverse_reactions

(

void

)

References DEBUG_ENTRY, exists(), fixit, fprintf(), ioQQQ, NULL, mole_priv::reactab, STATIC, 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

)

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

)

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(), pow(), mole_priv::reactab, read_data(), register_reaction_vectors(), and UDFA.

Referenced by InitSimPostparse().

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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_generate_isotopologue_reactions()

STATIC void mole_generate_isotopologue_reactions	(	string	atom_old,
		string	atom_new )

References ASSERT, canonicalize_reaction_label(), create_isotopologues(), create_isotopologues_one_position(), DEBUG_ENTRY, findnuclide(), fixit, fprintf(), ioQQQ, newreact(), parse_species_label(), mole_priv::reactab, STATIC, and TotalInsanity().

Referenced by mole_create_react().

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mole_get_equilibrium_condition() [1/2]

STATIC double mole_get_equilibrium_condition

(

const char

buf[]

)

References DEBUG_ENTRY, mole_findrate_s(), mole_get_equilibrium_condition(), and STATIC.

Referenced by mole_get_equilibrium_condition().

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mole_get_equilibrium_condition() [2/2]

STATIC double mole_get_equilibrium_condition

(

const mole_reaction *const

rate

)

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

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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

References ASSERT, DEBUG_ENTRY, dense, ENABLE_QUANTUM_HEATING, fixit, fnzone, fprintf(), GetAveVelocity(), GrainDrive(), gv, h2, hmi, ioQQQ, ipHYDROGEN, MAT_CAR, MAT_CAR2, MAT_PAH, MAT_PAH2, MAT_SIC, MAT_SIL, MAT_SIL2, NQGRID, phycon, POW2, qheat(), SDIV(), sexp(), STATIC, and sticking_probability_H_func().

Referenced by mole_update_rks().

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mole_h_reactions()

STATIC void mole_h_reactions

(

void

)

hmole_reactions - evaluates hydrogen chemistry reactions

Todo

2 following always true, why? either remove test or use it - it is here to save time - this step routine is called very often

Todo

2 this should be done with new populations after converged soln

References ASSERT, atmdat, molezone::column, conv, DEBUG_ENTRY, molezone::den, dense, diatoms, esc_PRD_1side(), findspecieslocal(), fixit, fnzone, fp_equal(), fprintf(), GammaBn(), GammaPrt(), GetDopplerWidth(), h2, hd, t_phoHeat::HeatNet, hmi, hmirat(), ioQQQ, ipHELIUM, ipHYDROGEN, ipoint(), iteration, MAX2, mole_global, nzone, opac, phycon, pow(), POW2, radius, rfield, secondaries, sexp(), SMALLFLOAT, STATIC, and TotalInsanity().

Referenced by mole_update_rks().

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mole_partition_function()

STATIC double mole_partition_function

(

const molecule *const

sp

)

References ASSERT, BIGFLOAT, DEBUG_ENTRY, dsexp(), fixit, molecule::form_enthalpy, molecule::label, molecule::mole_mass, phycon, powpq(), and STATIC.

Referenced by mole_get_equilibrium_condition().

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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_rks()

void mole_update_rks

(

void

)

mole_update_rks update rate coefficients, only temp part

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

Referenced by mole_drive().

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newreact()

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

References ABSENT, ASSERT, canonicalize_reaction(), cdEXIT, compare_udfa(), DEBUG_ENTRY, exists(), EXIT_FAILURE, fprintf(), Singleton< t_version >::Inst(), ioQQQ, lgReactBalance(), lgReactionTrivial(), mole_global, NULL, parse_reaction(), phycon, prt, mole_priv::reactab, STATIC, and UDFA.

Referenced by mole_create_react(), mole_generate_isotopologue_reactions(), and parse_base().

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parse_base()

STATIC void parse_base

(

char *

s

)

References getcsvfield(), newreact(), and STATIC.

Referenced by mole_create_react().

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parse_reaction()

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

References ASSERT, cdEXIT, DEBUG_ENTRY, EXIT_FAILURE, findspecies(), fprintf(), ioQQQ, molecule::isEnabled, MAXPRODUCTS, MAXREACTANTS, NULL, null_mole, STATIC, and trace.

Referenced by canonicalize_reaction_label(), and newreact().

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parse_udfa()

STATIC void parse_udfa

(

char *

s

)

References ASSERT, findspecies(), FLTEQ, fprintf(), getcsvfield(), MAXPRODUCTS, MAXREACTANTS, NULL, null_mole, t_mole_global::sort(), STATIC, and udfatab.

Referenced by mole_create_react().

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plot_sparsity()

STATIC void plot_sparsity

(

void

)

References fprintf(), molecule::index, mole_global, mole_reaction::nproducts, mole_reaction::nreactants, NULL, open_data(), mole_reaction::products, mole_reaction::pvector, mole_priv::reactab, mole_reaction::reactants, mole_reaction::rvector, and STATIC.

Referenced by mole_create_react().

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read_data()

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

References BUFSIZE, cdEXIT, DEBUG_ENTRY, EXIT_FAILURE, fixit, fprintf(), open_data(), and STATIC.

Referenced by mole_create_react().

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register_reaction_vectors()

STATIC void register_reaction_vectors

(

shared_ptr< mole_reaction >

rate

)

References DEBUG_ENTRY, lgDifferByExcitation(), NULL, and STATIC.

Referenced by mole_create_react().

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sticking_probability_H_func()

STATIC double sticking_probability_H_func	(	double	T_gas,
		double	T_grain )

References DEBUG_ENTRY, S, STATIC, and sticking_probability_H_HM79().

Referenced by mole_h2_grain_form().

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sticking_probability_H_HM79()

STATIC double sticking_probability_H_HM79	(	double	T_gas,
		double	T_grain )

References DEBUG_ENTRY, S, and STATIC.

Referenced by sticking_probability_H_func().

Variable Documentation

albedo

realnum albedo = 0.5

static

udfatab

map<formula_species,shared_ptr<udfa_reaction> > udfatab

static

Referenced by compare_udfa(), and parse_udfa().