mole.h File Reference

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Data Structures

struct t_co

struct t_mole

struct molecule

Enumerations

enum { CHARS_SPECIES = 7 }

Functions

void CO_drive (void)

void CO_zero (void)

void CO_create_react (void)

void CO_Init (void)

void CO_update_rks (void)

void CO_update_species_cache (void)

double CO_sink_rate (const char species[])

double CO_source_rate (const char species[])

double CO_dissoc_rate (const char species[])

struct COmole_rate_s * CO_findrate_s (const char buf[])

double CO_findrk (const char buf[])

double CO_findrate (const char buf[])

struct molecule * findspecies (const char buf[])

void CO_punch_mol (FILE *punit, const char species[], char header[], double depth)

Variables

EXTERN struct t_co co

EXTERN struct t_mole mole

EXTERN struct molecule ** COmole

Enumeration Type Documentation

anonymous enum

Enumerator:

CHARS_SPECIES

Definition at line 486 of file mole.h.

Function Documentation

void CO_create_react ( void )

CO_create_react build reaction structures

Definition at line 54 of file mole_co_reactions.cpp.

References ASSERT, co, co_lnu_c_o_lnu(), coreactions, crnurate(), DEBUG_ENTRY, DEBUG_EXIT, E, ele_ion_ladder(), grn_abs(), gv, h_hnc_hcn_h(), hmi, hmrate(), t_gv::lgDustOn, t_co::lgFederman, t_mole::lgGrain_mole_deplete, t_hmi::lgLeiden_Keep_ipMH2s, t_co::lgProtElim, t_co::lgUMISTrates, t_coreactions::list, makeplist(), MALLOC, mole, mole_priv, t_coreactions::n, newreact(), oh_c2h2_co_ch3(), mole_priv_s::reactab, th85rate(), th85rate_co(), and vib_evap().

Referenced by cloudy().

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double CO_dissoc_rate ( const char species[] )

Referenced by CO_solve().

void CO_drive ( void )

CO_drive main driver for heavy molecular equilibrium routines

Definition at line 44 of file mole_co_drive.cpp.

References ASSERT, t_conv::BadConvIoniz, t_CoolHeavy::C12O16Rot, C12O16Rotate, t_CoolHeavy::C13O16Rot, C13O16Rotate, called, t_conv::chConvIoniz, co, CO_findrate_s(), t_co::co_nzone, CO_solve(), CO_update_rks(), CO_update_species_cache(), CO_zero(), CODEBUG, t_co::CODissHeat, COmole, conv, ConvFail(), EmLine::cool, CoolHeavy, t_CoolHeavy::dC12O16Rot, t_CoolHeavy::dC13O16Rot, DEBUG_ENTRY, DEBUG_EXIT, dense, findspecies(), fnzone, t_dense::gas_phase, t_hmi::H2_total, h2lim, EmLine::heat, t_thermal::heating, molecule::hevmol, hmi, t_dense::IonLow, ioQQQ, ipCARBON, ipHYDROGEN, ipIRON, ipLITHIUM, ipMAGNESIUM, ipOXYGEN, ipSILICON, ipSULPHUR, iteration, t_co::iteration_co, t_co::lgCODoCalc, t_conv::lgConvIoniz, t_conv::lgConvPops, t_dense::lgElmtOn, lgMolecAver(), lgMoleZeroed, t_co::lgNoCOMole, t_hmi::lgNoH2Mole, t_conv::lgSearch, t_called::lgTalk, LIMELM, LUPMAX_CODRIV, mole, nCORotate, t_trace::nTrConvg, t_mole::num_comole_calc, nzone, EmLine::phots, phycon, EmLine::PopHi, EmLine::PopLo, EmLine::PopOpc, COmole_rate_s::rate_species, COmole_rate_s::rk, SDIV(), t_mole::sink, t_mole::source, t_phycon::te, thermal, TorF(), trace, EmLine::xIntensity, t_dense::xIonDense, and t_mole::xMoleChTrRate.

Referenced by ConvBase().

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double CO_findrate ( const char buf[] )

Definition at line 571 of file mole_co_etc.cpp.

References CO_findrate_s(), DEBUG_ENTRY, DEBUG_EXIT, molecule::hevmol, COmole_rate_s::nrates, COmole_rate_s::rate_species, and COmole_rate_s::rk.

Referenced by CO_solve(), CoolOxyg(), and lines_lv1_li_ne().

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struct COmole_rate_s* CO_findrate_s ( const char buf[] ) [read]

Definition at line 538 of file mole_co_etc.cpp.

References DEBUG_ENTRY, DEBUG_EXIT, lookup(), mole_priv, data_u::p, and mole_priv_s::reactab.

Referenced by CO_drive(), CO_findrate(), and CO_findrk().

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double CO_findrk ( const char buf[] )

Definition at line 553 of file mole_co_etc.cpp.

References ASSERT, CO_findrate_s(), DEBUG_ENTRY, DEBUG_EXIT, isnan, and COmole_rate_s::rk.

Referenced by hmole_step(), IonIron(), IonMagne(), and PunchDo().

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void CO_Init ( void )

called from cdInit to initialized co routines

Definition at line 45 of file mole_co_etc.cpp.

References molecule::active, ACTIVE, t_mole::amat, ASSERT, t_mole::b, t_mole::c, co, t_co::co_nzone, COmole, DEBUG_ENTRY, DEBUG_EXIT, dense, t_dense::eden_f, ELECTRON_MASS, mole_priv_s::elemtab, gv, molecule::hevcol, molecule::hevmol, hmi, t_hmi::Hmolec, molecule::index, ipCARBON, ipCHLORINE, ipHELIUM, ipHYDROGEN, ipIRON, ipiv, ipMAGNESIUM, ipMH2g, ipMH2p, ipMH2s, ipMH3p, ipMHm, chem_element_s::ipMl, chem_element_s::ipMlP, ipNITROGEN, ipOXYGEN, ipSILICON, ipSULPHUR, isactive(), isCOnet(), ispassive(), t_co::iteration_co, t_gv::lgDustOn, t_mole::lgElem_in_chemistry, t_mole::lgGrain_mole_deplete, LIMELM, makeplist(), MALLOC, mole, molecule::mole_mass, mole_priv, MOLECULE, molecule::n_nuclei, molecule::nElec, molecule::nelem_hevmol, newelement(), newhash(), newspecies(), null_mole, t_mole::num_comole_calc, t_mole::num_comole_tot, t_mole::num_elements, OTHER, PASSIVE, mole_priv_s::reactab, mole_priv_s::spectab, tot_ion, and t_dense::xIonDense.

Referenced by cloudy().

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void CO_punch_mol	(	FILE *	punit,
		const char	species[],
		char	header[],
		double	depth
	)

Definition at line 782 of file mole_co_etc.cpp.

References coreactions, DEBUG_ENTRY, DEBUG_EXIT, findspecies(), molecule::hevmol, COmole_rate_s::label, t_coreactions::list, t_coreactions::n, COmole_rate_s::nproducts, COmole_rate_s::nrates, COmole_rate_s::products, COmole_rate_s::rate_species, and COmole_rate_s::rk.

Referenced by PunchDo().

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double CO_sink_rate ( const char species[] )

Referenced by iso_ionize_recombine().

double CO_source_rate ( const char species[] )

void CO_update_rks ( void )

CO_update_rks update rate coefficients, only temp part

Definition at line 680 of file mole_co_etc.cpp.

References COmole_rate_s::a, coreactions, DEBUG_ENTRY, DEBUG_EXIT, COmole_rate_s::fun, t_coreactions::list, t_coreactions::n, and COmole_rate_s::rk.

Referenced by CO_drive(), and ConvBase().

void CO_update_species_cache ( void )

Definition at line 594 of file mole_co_etc.cpp.

References ASSERT, COmole, DEBUG_ENTRY, DEBUG_EXIT, dense, t_dense::eden, t_dense::eden_f, molecule::hevmol, isnan, molecule::location, mole, and t_mole::num_comole_tot.

Referenced by CO_drive(), and ConvBase().

void CO_zero ( void )

CO_zero allocate + initialize workspace

Definition at line 853 of file mole_co_etc.cpp.

References t_timesc::AgeCOMoleDest, cdEXIT(), COmole, DEBUG_ENTRY, DEBUG_EXIT, molecule::hevcol, molecule::hevmol, ioQQQ, lgFirstCall, MALLOC, mole, t_mole::num_comole_calc, t_mole::num_comole_tot, timesc, and molecule::xMoleFracMax.

Referenced by cloudy(), and CO_drive().

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struct molecule* findspecies ( const char buf[] ) [read]

Definition at line 506 of file mole_co_etc.cpp.

References DEBUG_ENTRY, DEBUG_EXIT, lookup(), mole_priv, null_mole, data_u::p, and mole_priv_s::spectab.

Referenced by AgeCheck(), cdColm(), CO_dissoc_rate(), CO_drive(), CO_punch_mol(), CO_sink_rate(), CO_solve(), CO_source_rate(), DynaPunchTimeDep(), GrainCollHeating(), HeatSum(), HeLikeLevel(), hmole_step(), iter_end_check(), lgMolecAver(), newreact(), OpacityAddTotal(), prt_smooth_predictions(), PrtZone(), PunchDo(), radius_increment(), and radius_next().

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Variable Documentation

EXTERN struct molecule ** COmole

EXTERN struct t_mole mole

Referenced by atmdat_readin(), CO_create_react(), CO_drive(), CO_Init(), CO_solve(), CO_step(), CO_update_species_cache(), CO_zero(), ConvBase(), ConvInitSolution(), ConvIterCheck(), DynaCreateArrays(), DynaIonize(), DynaNewStep(), DynaSaveLast(), DynaStartZone(), eden_sum(), H2_Accel(), H2_collid_rates(), H2_ContPoint(), H2_Cooling(), H2_Create(), H2_gs_rates(), H2_Init(), H2_InterEnergy(), H2_Level_low_matrix(), H2_LevelPops(), H2_LineZero(), H2_Prt_line_tau(), H2_Punch_line_data(), H2_PunchDo(), H2_PunchLineStuff(), H2_RadPress(), H2_Reset(), H2_RT_OTS(), H2_RT_tau_inc(), H2_RT_tau_reset(), H2_RTMake(), H2_Solomon_rate(), H2_X_coll_rate_evaluate(), H2_Zero(), H2_zero_pops_too_low(), HeatSum(), hmole(), hmole_step(), ion_solver(), ion_trim(), iter_end_check(), IterRestart(), IterStart(), lgMolecAver(), molcol(), mole_H2_LTE(), newspecies(), ParseAtomH2(), ParseDont(), ParseElement(), ParsePunch(), PressureChange(), PresTotCurrent(), PrtComment(), PunchDo(), radius_increment(), radius_next(), RT_tau_reset(), state_get_put(), and zero().


Data Structures
struct	t_co
struct	t_mole
struct	molecule
Enumerations
enum	{ CHARS_SPECIES = 7 }
Functions
void	CO_drive (void)
void	CO_zero (void)
void	CO_create_react (void)
void	CO_Init (void)
void	CO_update_rks (void)
void	CO_update_species_cache (void)
double	CO_sink_rate (const char species[])
double	CO_source_rate (const char species[])
double	CO_dissoc_rate (const char species[])
struct COmole_rate_s *	CO_findrate_s (const char buf[])
double	CO_findrk (const char buf[])
double	CO_findrate (const char buf[])
struct molecule *	findspecies (const char buf[])
void	CO_punch_mol (FILE *punit, const char species[], char header[], double depth)
Variables
EXTERN struct t_co	co
EXTERN struct t_mole	mole
EXTERN struct molecule **	COmole