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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 "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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#define FLTEQ(a, b)   (fabs((a)-(b)) <= 1e-6*fabs((a)+(b)))


enum  { UDFA = 0 }
enum  { BUFSIZE =256 }


STATIC void newreact (const char label[], const char fun[], double a, double b, double c)
STATIC long parse_reaction (count_ptr< mole_reaction > &rate, const char label[])
STATIC string canonicalize_reaction_label (const char label[])
STATIC void canonicalize_reaction (count_ptr< mole_reaction > &rate)
STATIC bool lgReactionTrivial (count_ptr< mole_reaction > &rate)
STATIC void register_reaction_vectors (count_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 count_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 count_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_reactionmole_findrate_s (const char buf[])


static realnum albedo = 0.5
static map< formula_species,
count_ptr< udfa_reaction > > 

Macro Definition Documentation

#define FLTEQ (   a,
)    (fabs((a)-(b)) <= 1e-6*fabs((a)+(b)))

Definition at line 2851 of file mole_reactions.cpp.

Referenced by compare_udfa(), and parse_udfa().

Enumeration Type Documentation

anonymous enum

Definition at line 46 of file mole_reactions.cpp.

anonymous enum

Definition at line 2790 of file mole_reactions.cpp.

anonymous enum

Definition at line 1715 of file mole_reactions.cpp.

Function Documentation

STATIC void canonicalize_reaction ( count_ptr< mole_reaction > &  rate)
STATIC string canonicalize_reaction_label ( const char  label[])

Definition at line 2519 of file mole_reactions.cpp.

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

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

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STATIC void compare_udfa ( const count_ptr< mole_reaction > &  rate)
double frac_H2star_hminus ( void  )

Definition at line 699 of file mole_reactions.cpp.

References h2, t_hmi::H2_forms_hminus, t_hmi::H2star_forms_hminus, hmi, diatomics::lgEnabled, diatomics::lgEvaluated, t_hmi::lgH2_Chemistry_BigH2, and SDIV().

Referenced by mole_h_rate_diagnostics().

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

Definition at line 2941 of file mole_reactions.cpp.

Referenced by parse_base(), and parse_udfa().

double hmirat ( double  te)

hmirat computes radiative association rate for H-


Definition at line 1632 of file mole_reactions.cpp.

References DEBUG_ENTRY, phycon, t_phycon::sqrte, t_phycon::te001, t_phycon::te003, t_phycon::te01, t_phycon::te03, t_phycon::te10, t_phycon::te20, and t_phycon::te70.

Referenced by mole_h_reactions().

STATIC bool lgReactBalance ( const count_ptr< mole_reaction > &  rate)
STATIC bool lgReactionTrivial ( count_ptr< mole_reaction > &  rate)
STATIC void mole_check_reverse_reactions ( void  )

Definition at line 2201 of file mole_reactions.cpp.

References DEBUG_ENTRY, exists(), fixit, fprintf(), ioQQQ, t_trace::lgTraceMole, mole_priv::reactab, and trace.

Referenced by mole_create_react().

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void mole_cmp_num_in_out_reactions ( void  )
void mole_create_react ( void  )
mole_reaction* mole_findrate_s ( const char  buf[])
STATIC void mole_generate_isotopologue_reactions ( string  atom_old,
string  atom_new 
STATIC double mole_get_equilibrium_condition ( const char  buf[])

Definition at line 2243 of file mole_reactions.cpp.

References DEBUG_ENTRY, and mole_findrate_s().

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STATIC double mole_get_equilibrium_condition ( const mole_reaction *const  rate)
STATIC void mole_h2_grain_form ( void  )
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

Definition at line 3081 of file mole_reactions.cpp.

References ASSERT, t_dense::AtomicWeight, GrainVar::bin, t_hmi::chJura, DEBUG_ENTRY, dense, ENABLE_QUANTUM_HEATING, fixit, fnzone, fprintf(), t_dense::gas_phase, GetAveVelocity(), GrainDrive(), gv, h2, hmi, ioQQQ, ipHYDROGEN, GrainVar::lgDustOn(), GrainVar::lgGrainPhysicsOn, diatomics::lgH2_grain_deexcitation, MAT_CAR, MAT_CAR2, MAT_PAH, MAT_PAH2, MAT_SIC, MAT_SIL, MAT_SIL2, NQGRID, phycon, POW2, qheat(), diatomics::rate_grain_J1_to_J0, diatomics::rate_grain_op_conserve, t_hmi::rate_h2_form_grains_set, GrainVar::rate_h2_form_grains_used_total, t_hmi::ScaleJura, SDIV(), sexp(), t_phycon::sqrte, sticking_probability_H_func(), t_hmi::Tad, and t_phycon::te.

Referenced by mole_update_rks().

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STATIC void mole_h_reactions ( void  )

hmole_reactions - evaluates hydrogen chemistry reactions

2 following always true, why? either remove test or use it - it is here to save time - this step routine is called very often
2 this should be done with new populations after converged soln

Definition at line 3515 of file mole_reactions.cpp.

References t_mesh::anu(), ASSERT, t_dense::AtomicWeight, t_hmi::chH2_small_model_type, molezone::column, t_rfield::ConInterOut, diatomics::Cont_Dissoc_Rate_H2g, diatomics::Cont_Dissoc_Rate_H2s, conv, DEBUG_ENTRY, molezone::den, dense, diatoms, t_dense::eden, esc_PRD_1side(), t_hmi::exphmi, t_rfield::extin_mag_V_point, t_iso_sp::fb, findspecieslocal(), fixit, t_rfield::flux, fnzone, fp_equal(), fprintf(), GammaBn(), GammaPrt(), GetDopplerWidth(), diatomics::gs_rate(), h2, t_hmi::H2_H2g_to_H2s_rate_BD96, t_hmi::H2_H2g_to_H2s_rate_BHT90, t_hmi::H2_H2g_to_H2s_rate_ELWERT, t_hmi::H2_H2g_to_H2s_rate_TH85, t_hmi::H2_H2g_to_H2s_rate_used, t_hmi::H2_photodissoc_BHT90, t_hmi::H2_photodissoc_ELWERT_H2g, t_hmi::H2_photodissoc_ELWERT_H2s, t_hmi::H2_photodissoc_TH85, t_hmi::H2_photodissoc_used_H2g, t_hmi::H2_photodissoc_used_H2s, t_hmi::H2_Solomon_dissoc_rate_BD96_H2g, t_hmi::H2_Solomon_dissoc_rate_BD96_H2s, t_hmi::H2_Solomon_dissoc_rate_BHT90_H2g, t_hmi::H2_Solomon_dissoc_rate_BHT90_H2s, t_hmi::H2_Solomon_dissoc_rate_ELWERT_H2g, t_hmi::H2_Solomon_dissoc_rate_ELWERT_H2s, t_hmi::H2_Solomon_dissoc_rate_TH85_H2g, t_hmi::H2_Solomon_dissoc_rate_TH85_H2s, t_hmi::H2_Solomon_dissoc_rate_used_H2g, t_hmi::H2_Solomon_dissoc_rate_used_H2s, t_hmi::H2Opacity, hd, t_phoHeat::HeatNet, hmi, t_hmi::hmicol, t_hmi::HMinus_induc_rec_cooling, t_hmi::HMinus_induc_rec_rate, t_hmi::HMinus_photo_heat, t_hmi::HMinus_photo_rate, hmirat(), ioQQQ, t_rfield::ip1000A, t_rfield::ipG0_DB96_hi, t_rfield::ipG0_DB96_lo, t_rfield::ipG0_spec_hi, t_rfield::ipG0_spec_lo, t_rfield::ipG0_TH85_hi, t_rfield::ipG0_TH85_lo, ipHE_LIKE, ipHELIUM, t_hmi::iphmin, t_opac::iphmop, ipHYDROGEN, iso_sp, iteration, diatomics::lgEnabled, diatomics::lgEvaluated, t_hmi::lgH2_Chemistry_BigH2, t_hmi::lgLeidenCRHack, t_mole_global::lgLeidenHack, t_mole_global::lgStancil, MAX2, mole_global, t_conv::nPres2Ioniz, t_conv::nTotalIoniz, nzone, opac, t_rfield::outlin, t_rfield::outlin_noplot, diatomics::photodissoc_BigH2_H2g, diatomics::photodissoc_BigH2_H2s, phycon, pow(), POW2, t_radius::r1r0sq, radius, diatomics::rel_pop_LTE_g, t_hmi::rel_pop_LTE_H2g, t_hmi::rel_pop_LTE_H2p, t_hmi::rel_pop_LTE_H2s, t_hmi::rel_pop_LTE_H3p, t_hmi::rel_pop_LTE_Hmin, diatomics::rel_pop_LTE_s, rfield, secondaries, sexp(), SMALLFLOAT, diatomics::Solomon_dissoc_rate_g, diatomics::Solomon_dissoc_rate_s, t_opac::TauAbsFace, t_phycon::te, t_phycon::te32, TotalInsanity(), t_hmi::UV_Cont_rel2_Draine_DB96_depth, t_hmi::UV_Cont_rel2_Draine_DB96_face, t_hmi::UV_Cont_rel2_Habing_spec_depth, t_hmi::UV_Cont_rel2_Habing_TH85_depth, t_hmi::UV_Cont_rel2_Habing_TH85_face, and t_secondaries::x12tot.

Referenced by mole_update_rks().

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STATIC double mole_partition_function ( const molecule *const  sp)

Definition at line 2282 of file mole_reactions.cpp.

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

Referenced by mole_get_equilibrium_condition().

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void mole_rk_bigchange ( void  )
void mole_update_rks ( void  )

mole_update_rks update rate coefficients, only temp part

Definition at line 2997 of file mole_reactions.cpp.

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, t_mole_local::reaction_rks, and mole_reaction::rk().

Referenced by mole_drive().

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

Definition at line 2344 of file mole_reactions.cpp.

References getcsvfield(), and newreact().

Referenced by mole_create_react().

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STATIC long parse_reaction ( count_ptr< mole_reaction > &  rate,
const char  label[] 
STATIC void parse_udfa ( char *  s)

Definition at line 2852 of file mole_reactions.cpp.

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

Referenced by mole_create_react().

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

Definition at line 2830 of file mole_reactions.cpp.

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

Referenced by mole_create_react().

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STATIC void register_reaction_vectors ( count_ptr< mole_reaction rate)
STATIC double sticking_probability_H_func ( double  T_gas,
double  T_grain 

Definition at line 4453 of file mole_reactions.cpp.

References DEBUG_ENTRY, S, and sticking_probability_H_HM79().

Referenced by mole_h2_grain_form().

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STATIC double sticking_probability_H_HM79 ( double  T_gas,
double  T_grain 

Definition at line 4460 of file mole_reactions.cpp.

References DEBUG_ENTRY, and S.

Referenced by sticking_probability_H_func().

Variable Documentation

realnum albedo = 0.5

Definition at line 82 of file mole_reactions.cpp.

map<formula_species,count_ptr<udfa_reaction> > udfatab

Definition at line 2828 of file mole_reactions.cpp.