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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 chSpecies[]) |
| double | CO_source_rate (const char chSpecies[]) |
| double | CO_dissoc_rate (const char chSpecies[]) |
| 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 chSpecies[], char header[], double depth) |
Variables | |
| struct molecule | null_mole |
| 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, ele_ion_ladder(), grn_abs(), gv, h_hnc_hcn_h(), hmi, hmrate(), GrainVar::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 InitSimPostparse().
| double CO_dissoc_rate | ( | const char | chSpecies[] | ) |
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, 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(), DEBUG_ENTRY, dense, findspecies(), fnzone, t_dense::gas_phase, t_hmi::H2_total, h2lim, 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, t_trace::nTrConvg, t_mole::num_comole_calc, nzone, phycon, COmole_rate_s::rate_species, COmole_rate_s::rk, SDIV(), t_mole::sink, t_mole::source, t_phycon::te, thermal, TorF(), trace, t_dense::xIonDense, and t_mole::xMoleChTrRate.
Referenced by ConvBase().
| double CO_findrate | ( | const char | buf[] | ) |
Definition at line 569 of file mole_co_etc.cpp.
References CO_findrate_s(), DEBUG_ENTRY, 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 540 of file mole_co_etc.cpp.
References DEBUG_ENTRY, 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, isnan, and COmole_rate_s::rk.
Referenced by hmole_step(), IonIron(), IonMagne(), and SaveDo().
| void CO_Init | ( | void | ) |
called from cdInit to initialized co routines
Definition at line 44 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, 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, GrainVar::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 InitSimPostparse().
| void CO_punch_mol | ( | FILE * | punit, | |
| const char | chSpecies[], | |||
| char | header[], | |||
| double | depth | |||
| ) |
Definition at line 767 of file mole_co_etc.cpp.
References cdEXIT, coreactions, DEBUG_ENTRY, findspecies(), molecule::hevmol, ioQQQ, COmole_rate_s::label, t_coreactions::list, t_coreactions::n, COmole_rate_s::nproducts, COmole_rate_s::nrates, null_mole, COmole_rate_s::products, COmole_rate_s::rate_species, and COmole_rate_s::rk.
Referenced by SaveDo().
| double CO_sink_rate | ( | const char | chSpecies[] | ) |
Referenced by iso_ionize_recombine().
| double CO_source_rate | ( | const char | chSpecies[] | ) |
Referenced by iso_ionize_recombine().
| void CO_update_rks | ( | void | ) |
CO_update_rks update rate coefficients, only temp part
Definition at line 671 of file mole_co_etc.cpp.
References COmole_rate_s::a, coreactions, DEBUG_ENTRY, 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 589 of file mole_co_etc.cpp.
References ASSERT, COmole, DEBUG_ENTRY, dense, t_dense::eden, t_dense::eden_f, molecule::hevmol, isnan, molecule::location, MAX_DENSITY, 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 842 of file mole_co_etc.cpp.
References t_timesc::AgeCOMoleDest, cdEXIT, COmole, DEBUG_ENTRY, molecule::hevcol, molecule::hevmol, ioQQQ, lgFirstCall, MALLOC, mole, t_mole::num_comole_calc, t_mole::num_comole_tot, timesc, and molecule::xMoleFracMax.
Referenced by CO_drive(), and InitSimPostparse().
| struct molecule* findspecies | ( | const char | buf[] | ) | [read] |
Definition at line 507 of file mole_co_etc.cpp.
References DEBUG_ENTRY, 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(), database_readin(), dBase_solve(), DynaPunchTimeDep(), GrainCollHeating(), hmole_step(), iso_level(), iter_end_check(), lgMolecAver(), newreact(), OpacityAddTotal(), prt_smooth_predictions(), PrtZone(), radius_increment(), radius_next(), and SaveDo().
Referenced by advection_set_default(), ChargTranEval(), CO_create_react(), CO_drive(), CO_Init(), CO_solve(), ConvBase(), CoolCarb(), eden_sum(), H2_PunchDo(), H2_X_coll_rate_evaluate(), hmole_reactions(), hmole_step(), IonCarbo(), IonIron(), IonMagne(), IterStart(), lgMolecAver(), lines_lv1_li_ne(), lines_molecules(), map_do(), noneq_offset(), ParseCommands(), ParseDont(), ParseElement(), ParseSet(), PrtComment(), radius_next(), th85rate(), and zero().
Referenced by ChemImportance(), CO_drive(), CO_Init(), CO_solve(), CO_update_species_cache(), CO_zero(), ConvBase(), ConvIterCheck(), DynaStartZone(), eden_sum(), HeatSum(), hmole(), iter_end_check(), IterRestart(), IterStart(), lgMolecAver(), molcol(), PressureChange(), PresTotCurrent(), PrtComment(), radius_increment(), radius_next(), RT_tau_reset(), and SaveDo().
Referenced by atmdat_readin(), ChemImportance(), CO_create_react(), CO_drive(), CO_Init(), CO_solve(), CO_step(), CO_update_species_cache(), CO_zero(), ConvBase(), ConvIterCheck(), DynaCreateArrays(), DynaIonize(), DynaNewStep(), DynaSaveLast(), DynaStartZone(), eden_sum(), fill_array(), find_solution(), H2_Accel(), H2_CollidRateEvalAll(), H2_CollidRateEvalOne(), H2_CollidRateRead(), H2_ContPoint(), H2_Cooling(), H2_Create(), H2_gs_rates(), H2_Init(), 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_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(), InitCoreload(), InitDefaultsPreparse(), ion_trim(), iso_level(), iter_end_check(), IterRestart(), IterStart(), lgMolecAver(), lgOH_ChargeTransferDominant(), molcol(), mole_H2_LTE(), newspecies(), ParseAtomH2(), ParseDont(), ParseElement(), ParseSet(), PressureChange(), PresTotCurrent(), PrintRates(), PrtComment(), radius_increment(), radius_next(), RT_tau_reset(), SaveDo(), state_get_put(), and zero().
>>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
this includes the atomic and first ionized species of each element that can combine to form molecules. This is the number of molecules, ions, and atoms that the co network uses This is used in comole to improve the calculation, as deep in molecular regions reactions with molecules can be important to the ionization balance
Definition at line 40 of file mole_co_etc.cpp.
Referenced by cdColm(), CO_Init(), CO_punch_mol(), database_readin(), dBase_solve(), findspecies(), and newreact().
1.6.1