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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 |
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().
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().
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().
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().
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().
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().
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().
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().
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().
>>chng 03 feb 09, rm ipH3P_hev, since not used, and decrement NUM_HEAVY_MOLEC to 17 >>chng 03 aug 04, rm ipCTWO and ipC2P from hevmol since not included in balance, and always finds zero column density, so NUM_HEAVY_MOLEC from 17 to 15 >>chng 03 aug 05, rm ch2 and ch3, so n from 15 to 13 >>chng 03 nov 14 add Si chemistry & CH3+, so that now every reaction that is in the TH85 chemical network is also included in Cloudy. Additionally, there are also reactions taken from other papers (mostly Hollenbach and McKee...see co.c). In all 20 molecular species are calculated, along with the atomic and first ionization stages of C, O, and Si >>chng 04 May 13, Nick Abel. Add CH3, CH4, CH4+, and CH5+ to network in order to get the same chemical abundances vs. depth as other PDR codes in the Leiden meeting. With changes we now can predict molecular abundances for 24 C, O, and Si bearing molecules. >>chng 04 jul 13, Nick Abel. Add nitrogen and sulphur bearing molecules to the chemical network. First added to generate a chemical model for eta carinae, but is applicable to all molecular clouds >>chng 05 mar 11, Nick Abel. Add C2 and C2+ to chemistry, reactions involving these species affects the abundance of C >>chng 05 mar 23, Nick Abel. Add Chlorine to chemistry
Referenced by advection_set_detault(), ChargTranEval(), CO_create_react(), CO_drive(), CO_Init(), CO_PopsEmisCool(), CO_solve(), ConvBase(), ConvIoniz(), CoolCarb(), eden_sum(), H2_PunchDo(), H2_X_coll_rate_evaluate(), hmole_reactions(), hmole_step(), IonCarbo(), IonIron(), IonMagne(), IonNitro(), IonOxyge(), IonSilic(), IonSulph(), iso_ionize_recombine(), IterStart(), lgMolecAver(), lines_lv1_li_ne(), lines_molecules(), map_do(), noneq_offset(), ParseCommands(), ParseDont(), ParseElement(), ParseSet(), PrtComment(), radius_next(), th85rate(), and zero().
Referenced by CO_drive(), CO_Init(), CO_solve(), CO_update_species_cache(), CO_zero(), ConvBase(), ConvInitSolution(), ConvIterCheck(), DynaStartZone(), eden_sum(), HeatSum(), hmole(), hmole_step(), iter_end_check(), IterRestart(), IterStart(), lgMolecAver(), molcol(), ParsePunch(), PressureChange(), PresTotCurrent(), PrtComment(), PunchDo(), radius_increment(), radius_next(), and RT_tau_reset().
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().