#include <mole.h>
>>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
Definition at line 65 of file mole.h.
double t_co::C_H3OP_HCOP_H2_1 |
double t_co::C_OH_CO_H_1 |
double t_co::CHP_H2O_HCOP_H2_1 |
double t_co::CHP_OH_COP_H2_1 |
long t_co::co_nzone |
Definition at line 131 of file mole.h.
Referenced by CO_drive(), CO_Init(), CO_solve(), and lgMolecAver().
double t_co::COCoolBigFrac |
flag saying what fraction of total cooling was carried by CO
Definition at line 75 of file mole.h.
Referenced by IterStart(), lines_molecules(), PrtComment(), and zero().
float t_co::codfrc |
total heating integrated over cloud
Definition at line 69 of file mole.h.
Referenced by IterStart(), lines_molecules(), PrtComment(), and zero().
float t_co::CODissHeat |
CODissHeat is CO Photodissociation heating largest fraction of total heating
Definition at line 69 of file mole.h.
Referenced by CO_drive(), CO_solve(), lines_molecules(), and zero().
float t_co::codtot |
Definition at line 69 of file mole.h.
Referenced by IterStart(), lines_molecules(), PrtComment(), and zero().
double t_co::comole_eden |
total electron density in molecules
Definition at line 134 of file mole.h.
Referenced by ConvBase(), ConvIoniz(), and eden_sum().
double t_co::CP_H2O_HCOP_H_1 |
double t_co::CP_OH_CO_HP_1 |
double t_co::CP_OH_COP_H_1 |
double t_co::crnu_CH3_CH2_H |
double t_co::crnu_CH3_CH_H2 |
double t_co::crnu_CH4_CH2_H2 |
double t_co::crnu_CH_C_H |
double t_co::crnu_CHP_CP_H |
double t_co::crnu_H2O_OH_H |
double t_co::crnu_OH_O_H |
double t_co::crnu_SiH_Si_H |
double t_co::e_CH2P_C_H2 |
double t_co::e_CH2P_C_H_H |
double t_co::e_CH2P_CH_H |
double t_co::e_CH3P_C_H2_H |
double t_co::e_CH3P_CH2_H |
double t_co::e_CH3P_CH_H2 |
double t_co::e_CH3P_CH_H_H |
double t_co::e_CH4P_CH2_H_H |
double t_co::e_CH4P_CH3_H |
double t_co::e_CH5P_CH3_H2 |
double t_co::e_CH5P_CH4_H |
double t_co::e_CHP_C_H |
double t_co::e_H2OP_O_H2 |
double t_co::e_H2OP_O_H_H |
double t_co::e_H2OP_OH_H |
double t_co::e_H3OP_H2O_H |
double t_co::e_H3OP_O_H2_H |
double t_co::e_H3OP_OH_H2 |
double t_co::e_H3OP_OH_H_H |
double t_co::e_HCOP_CO_H |
double t_co::e_OHP_O_H |
double t_co::e_SiH2P_Si_H2 |
double t_co::e_SiH2P_Si_H_H |
double t_co::e_SiH2P_SiH_H |
double t_co::e_SiOHP_SiO_H |
double t_co::H2_C2HP_C2H2P_H |
double t_co::H2_C2P_C2HP_H |
double t_co::H2_C3P_C3HP_H |
double t_co::H2_C_CH2_nu |
double t_co::H2_C_CH_H |
double t_co::H2_CH2_CH3_H |
double t_co::H2_CH2P_CH3P_H |
double t_co::H2_CH3_CH4_H |
double t_co::H2_CH3P_CH5P_nu |
double t_co::H2_CH4P_CH5P_H |
double t_co::H2_CH_C_H2_H |
double t_co::H2_CH_CH2_H |
double t_co::H2_CH_CH3_nu |
double t_co::H2_CHP_CH2P_H |
double t_co::H2_ClP_HClP_H |
double t_co::H2_CN_HCN_H |
double t_co::H2_CNP_HCNP_H |
double t_co::H2_COP_HCOP_H |
double t_co::H2_CP_CH2P_nu |
double t_co::H2_CP_CHP_H |
double t_co::H2_CSP_HCSP_H |
double t_co::H2_H2O_OH_H2_H |
double t_co::H2_H2OP_H3OP_H |
double t_co::H2_HClP_H2ClP_H |
double t_co::H2_HCNP_HCNHP_H |
double t_co::H2_N_NH_H |
double t_co::H2_NH2_NH3_H |
double t_co::H2_NH2P_NH3P_H |
double t_co::H2_NH3P_NH4P_H |
double t_co::H2_NH_NH2_H |
double t_co::H2_NHP_N_H3P |
double t_co::H2_NHP_NH2P_H |
double t_co::H2_NP_NHP_H |
double t_co::H2_O2_O_O_H2 |
double t_co::H2_O2_OH_OH |
double t_co::H2_O_OH_H |
double t_co::H2_OH_H2O_H |
double t_co::H2_OH_O_H2_H |
double t_co::H2_OHP_H2OP_H |
double t_co::H2_OP_OHP_H |
double t_co::H2_S_HS_H |
double t_co::H2_SiOP_SiOHP_H |
double t_co::H2_SiP_SiH2P_nu |
double t_co::H2_SP_HSP_H |
double t_co::h2lim |
double t_co::H2P_C2_C2HP_H |
double t_co::H2P_C2_C2P_H2 |
double t_co::H2P_C2H2_C2H2P_H2 |
double t_co::H2P_C2H2_C2H3P_H |
double t_co::H2P_C2H_C2H2P_H |
double t_co::H2P_C2H_C2HP_H2 |
double t_co::H2P_C_CHP_H |
double t_co::H2P_CH2_CH2P_H2 |
double t_co::H2P_CH2_CH3P_H |
double t_co::H2P_CH4_CH3P_H2 |
double t_co::H2P_CH4_CH4P_H2 |
double t_co::H2P_CH4_CH5P_H |
double t_co::H2P_CH_CH2P_H |
double t_co::H2P_CH_CHP_H2 |
double t_co::H2P_CN_CNP_H2 |
double t_co::H2P_CN_HCNP_H |
double t_co::H2P_CO_COP_H2 |
double t_co::H2P_CO_HCOP_H |
double t_co::H2P_H2O_H2OP_H2 |
double t_co::H2P_H2O_H3OP_H |
double t_co::H2P_HCN_HCNP_H2 |
double t_co::H2P_N_NHP_H |
double t_co::H2P_NH2_NH2P_H2 |
double t_co::H2P_NH3_NH3P_H2 |
double t_co::H2P_NH_NH2P_H |
double t_co::H2P_NH_NHP_H2 |
double t_co::H2P_NO_HNOP_H |
double t_co::H2P_NO_NOP_H2 |
double t_co::H2P_O2_O2P_H2 |
double t_co::H2P_O_OHP_H |
double t_co::H2P_OH_H2OP_H |
double t_co::H2P_OH_OHP_H2 |
double t_co::H2s_C_CH_H |
double t_co::H2s_CH2_CH3_H |
double t_co::H2s_CH3_CH4_H |
double t_co::H2s_CH_C_H2_H |
double t_co::H2s_CH_CH2_H |
double t_co::H2s_CH_CH3_nu |
double t_co::H2s_CP_CHP_H |
double t_co::H2s_H2O_OH_H2_H |
double t_co::H2s_O2_O_O_H2 |
double t_co::H2s_O_OH_H |
double t_co::H2s_OH_H2O_H |
double t_co::H2s_OH_O_H2_H |
double t_co::H2s_OP_OHP_H |
double t_co::H3P_C2_C2HP_H2 |
double t_co::H3P_C2H2_C2H3P_H2 |
double t_co::H3P_C2H_C2H2P_H2 |
double t_co::H3P_C3_C3HP_H2 |
double t_co::H3P_C_CHP_H2 |
double t_co::H3P_CH2_CH3P_H2 |
double t_co::H3P_CH3_CH4P_H2 |
double t_co::H3P_CH4_CH5P_H2 |
double t_co::H3P_CH_CH2P_H2 |
double t_co::H3P_Cl_HClP_H2 |
double t_co::H3P_CN_HCNP_H2 |
double t_co::H3P_CO_HCOP_H2 |
double t_co::H3P_CS_HCSP_H2 |
double t_co::H3P_H2O_H3OP_H2 |
double t_co::H3P_HCl_H2ClP_H2 |
double t_co::H3P_HCN_HCNHP_H2 |
double t_co::H3P_NH2_NH3P_H2 |
double t_co::H3P_NH3_NH4P_H2 |
double t_co::H3P_NH_NH2P_H2 |
double t_co::H3P_NO2_NOP_OH_H2 |
double t_co::H3P_NO_HNOP_H2 |
double t_co::H3P_O_OHP_H2 |
double t_co::H3P_OH_H2OP_H2 |
double t_co::H3P_S_HSP_H2 |
double t_co::H3P_SiH_SiH2P_H2 |
double t_co::H3P_SiO_SiOHP_H2 |
double t_co::H_C2H3P_C2H2P_H2 |
double t_co::H_C_CH_nu |
double t_co::H_CH2_CH_H2 |
double t_co::H_CH3_CH2_H2 |
double t_co::H_CH3P_CH2P_H2 |
double t_co::H_CH4P_CH3P_H2 |
double t_co::H_CH5P_CH4P_H2 |
double t_co::H_CH_C_H2 |
double t_co::H_CH_C_H_H |
These reactions and included in hmole_step as formation and destruction processes
Definition at line 149 of file mole.h.
Referenced by hmole_step().
double t_co::H_CHP_CP_H2 |
double t_co::H_CNP_CN_HP |
double t_co::H_COP_CO_HP |
double t_co::H_CP_CHP_nu |
double t_co::H_H2O_OH_H2 |
double t_co::H_H2O_OH_H_H |
double t_co::H_HCNP_HCN_HP |
double t_co::H_HNC_HCN_H |
double t_co::H_HSP_SP_H2 |
double t_co::H_N2P_N2_HP |
double t_co::H_OH_H2O_nu |
double t_co::H_OH_O_H2 |
double t_co::H_OH_O_H_H |
double t_co::HeP_CH2_CHP_He_H |
double t_co::HeP_CH2_CP_He_H2 |
double t_co::HeP_CH_CP_He_H |
float t_co::hep_destroy |
The following are rates used in determining the ionization balance of helium
Definition at line 145 of file mole.h.
Referenced by iso_ionize_recombine().
double t_co::HeP_H2O_OH_He_HP |
double t_co::HeP_H2O_OHP_He_H |
double t_co::HeP_OH_OP_He_H |
double t_co::HeP_SiH_SiP_He_H |
double t_co::Hminus_C_CH_e |
double t_co::Hminus_CH2_CH3_e |
double t_co::Hminus_CH3_CH4_e |
double t_co::Hminus_CH_CH2_e |
double t_co::Hminus_H3OP_H2O_H2 |
double t_co::Hminus_H3OP_OH_H2_H |
double t_co::Hminus_HCOP_CO_H2 |
double t_co::Hminus_NH4P_NH3_H2 |
double t_co::Hminus_NP_N_H |
double t_co::Hminus_O_OH_e |
double t_co::Hminus_OH_H2O_e |
double t_co::hmole_mass[N_H_MOLEC+1] |
double t_co::HP_C2_C2P_H |
double t_co::HP_C2H2_C2H2P_H |
double t_co::HP_C2H2_C2HP_H2 |
double t_co::HP_C2H_C2HP_H |
double t_co::HP_C2H_C2P_H2 |
double t_co::HP_C3_C3P_H |
double t_co::HP_C3H_C3HP_H |
double t_co::HP_C3H_C3P_H2 |
double t_co::HP_CH2_CH2P_H |
double t_co::HP_CH2_CHP_H2 |
double t_co::HP_CH3_CH3P_H |
double t_co::HP_CH4_CH3P_H2 |
double t_co::HP_CH4_CH4P_H |
double t_co::HP_CH_CHP_H |
double t_co::HP_CS_CSP_H |
double t_co::HP_H2O_H2OP_H |
double t_co::HP_HCl_HClP_H |
double t_co::HP_HCN_HCNP_H |
double t_co::HP_HNC_HCN_HP |
double t_co::HP_HNO_NOP_H2 |
double t_co::HP_HS_HSP_H |
double t_co::HP_HS_SP_H2 |
double t_co::HP_NH2_NH2P_H |
double t_co::HP_NH3_NH3P_H |
double t_co::HP_NH_NHP_H |
double t_co::HP_NO_NOP_H |
double t_co::HP_NS_NSP_H |
double t_co::HP_O2_O2P_H |
double t_co::HP_OCS_OCSP_H |
double t_co::HP_OH_OHP_H |
double t_co::HP_S2_S2P_H |
double t_co::HP_SiH_SiP_H2 |
double t_co::HP_SiN_SiNP_H |
double t_co::HP_SiO_SiOP_H |
double t_co::HP_SO_SOP_H |
float t_co::hydro_sink[8] |
molecules of the heavy elements. order must exactly match that in hevcolumn number of molecules in heavy element network the density (cm-3) of each species these are source and sink terms for the hydrogen molecular network that appear in co.c
Definition at line 93 of file mole.h.
Referenced by hmole_step().
float t_co::hydro_source[8] |
long t_co::iteration_co |
Definition at line 131 of file mole.h.
Referenced by CO_drive(), CO_Init(), lgMolecAver(), and map_do().
bool t_co::lgCOCoolCaped |
flag saying CO is important but lines capped by highest level
Definition at line 78 of file mole.h.
Referenced by CO_PopsEmisCool(), IterStart(), PrtComment(), and zero().
bool t_co::lgCODoCalc |
This lets the code know if the CO network is turned on
Definition at line 84 of file mole.h.
Referenced by CO_drive().
bool t_co::lgFederman |
bool t_co::lgH2Ozer |
flag set true if H2O destruction rate went to zero
Definition at line 107 of file mole.h.
Referenced by PrtComment(), and zero().
bool t_co::lgNeutrals |
option to not include neutrals in the non-equilibrium scheme >> refer Federman, S. R. & Zsargo, J. 2003, ApJ, 589, 319 By default, this is false - changed with set chemistry command
Definition at line 127 of file mole.h.
Referenced by noneq_offset(), ParseSet(), and zero().
bool t_co::lgNoCOMole |
flag to turn off CO molecules, set with no molecules command
Definition at line 81 of file mole.h.
Referenced by advection_set_detault(), CO_drive(), IonIron(), IonMagne(), ParseCommands(), ParseDont(), ParseElement(), and zero().
bool t_co::lgNonEquilChem |
option to use effective temperature as defined in >> refer Federman, S. R. & Zsargo, J. 2003, ApJ, 589, 319 By default, this is false - changed with set chemistry command
Definition at line 117 of file mole.h.
Referenced by noneq_offset(), ParseSet(), and zero().
bool t_co::lgProtElim |
option to set proton elimination rates to zero >>refer CO chemistry Huntress, W. T., 1977, ApJS, 33, 495 By default, this is false - changed with set chemistry command
Definition at line 122 of file mole.h.
Referenced by CO_create_react(), ParseSet(), and zero().
bool t_co::lgUMISTrates |
set rates to that in UMIST
Definition at line 110 of file mole.h.
Referenced by ChargTranEval(), CO_create_react(), H2_X_coll_rate_evaluate(), hmole_reactions(), hmole_step(), IonCarbo(), ParseSet(), radius_next(), th85rate(), and zero().
double t_co::N2_H3P_N2HP_H2 |
float t_co::nitro_dissoc_rate |
double t_co::nu_CH2_CH_H |
double t_co::nu_CH2P_CHP_H |
double t_co::nu_CH3_CH2_H |
double t_co::nu_CH3_CH_H2 |
double t_co::nu_CH3P_CH2P_H |
double t_co::nu_CH3P_CHP_H2 |
double t_co::nu_CH4_CH2_H2 |
double t_co::nu_CH4_CH3_H |
double t_co::nu_CH4_CH_H2 |
double t_co::nu_CH_C_H |
double t_co::nu_CHP_CP_H |
double t_co::nu_H2O_OH_H |
double t_co::nu_OH_O_H |
double t_co::nu_OHP_O_HP |
double t_co::nu_SiH_Si_H |
double t_co::O_CH2_CO_H2_1 |
double t_co::O_CH2_CO_H_H_1 |
double t_co::O_CH2P_HCOP_H_1 |
double t_co::O_CH3P_HCOP_H2_1 |
double t_co::O_CH_CO_H_1 |
double t_co::O_CHP_COP_H_1 |
double t_co::O_H2OP_O2P_H2_1 |
double t_co::O_OH_O2_H_1 |
double t_co::O_OHP_O2P_H_1 |
double t_co::O_SiH2P_SiOHP_H_1 |
double t_co::O_SiH_SiO_H_1 |
double t_co::OP_CH_COP_H_1 |
double t_co::OP_OH_O2P_H_1 |
abundance ratio C12O16 to C13O16, init in zero.c
Definition at line 104 of file mole.h.
Referenced by CO_solve(), CoolCarb(), ParseSet(), and zero().
double t_co::Si_OH_SiO_H_1 |
double t_co::SiP_H2O_SiOHP_H_1 |
double t_co::SiP_OH_SiOP_H_1 |