#include "cdstd.h"
#include <stdlib.h>
#include "cddefines.h"
#include "colden.h"
#include "physconst.h"
#include "mole.h"
#include "version.h"
#include "mole_priv.h"
#include "hmi.h"
#include "conv.h"
#include "dense.h"
#include "thermal.h"
#include "gammas.h"
#include "grainvar.h"
#include "ionbal.h"
#include "opacity.h"
#include "path.h"
#include "radius.h"
#include "atmdat.h"
#include "taulines.h"
#include "trace.h"
#include "deuterium.h"
#include "phycon.h"
#include "doppvel.h"
#include "rfield.h"
#include "secondaries.h"
#include "hextra.h"
#include "rt.h"
#include "iso.h"
#include "h2.h"
Go to the source code of this file.
Defines | |
#define | gzopen(file, mode) fopen(file,mode) |
#define | gzgets(fp, buf, siz) fgets(buf,siz,fp) |
#define | gzclose(fp) fclose(fp) |
#define | gzFile FILE |
#define | FLTEQ(a, b) (fabs((a)-(b)) <= 1e-6*fabs((a)+(b))) |
Enumerations | |
enum | { UDFA = 0 } |
enum | |
enum | { BUFSIZE = 256 } |
Functions | |
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 void | register_reaction_vectors (count_ptr< mole_reaction > rate) |
STATIC void | mole_check_reverse_reactions (void) |
STATIC double | mole_get_equilibrium_constant (const char buf[]) |
STATIC double | mole_partition_function (const molecule *const sp) |
STATIC void | mole_generate_isotopologue_reactions (string atom_old, string atom_new) |
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_reaction * | mole_findrate_s (const char buf[]) |
void | mole_punch (FILE *punit, const char speciesname[], const char args[], bool lgHeader, bool lgData, double depth) |
Variables | |
static realnum | albedo = 0.5 |
static map< formula_species, struct udfa_reaction_s * > | udfatab |
#define FLTEQ | ( | a, | |||
b | ) | (fabs((a)-(b)) <= 1e-6*fabs((a)+(b))) |
Definition at line 2694 of file mole_reactions.cpp.
Referenced by compare_udfa(), and parse_udfa().
#define gzclose | ( | fp | ) | fclose(fp) |
Definition at line 2630 of file mole_reactions.cpp.
#define gzFile FILE |
Definition at line 2631 of file mole_reactions.cpp.
#define gzgets | ( | fp, | |||
buf, | |||||
siz | ) | fgets(buf,siz,fp) |
Definition at line 2629 of file mole_reactions.cpp.
#define gzopen | ( | file, | |||
mode | ) | fopen(file,mode) |
Definition at line 2628 of file mole_reactions.cpp.
anonymous enum |
Definition at line 47 of file mole_reactions.cpp.
anonymous enum |
Definition at line 2634 of file mole_reactions.cpp.
anonymous enum |
Definition at line 1678 of file mole_reactions.cpp.
STATIC void canonicalize_reaction | ( | count_ptr< mole_reaction > & | rate | ) |
Definition at line 2396 of file mole_reactions.cpp.
References DEBUG_ENTRY, and t_mole_global::sort().
Referenced by canonicalize_reaction_label(), and newreact().
STATIC string canonicalize_reaction_label | ( | const char | label[] | ) |
Definition at line 2380 of file mole_reactions.cpp.
References canonicalize_reaction(), DEBUG_ENTRY, and parse_reaction().
Referenced by mole_findrate_s(), and mole_generate_isotopologue_reactions().
STATIC void compare_udfa | ( | const count_ptr< mole_reaction > & | rate | ) |
Definition at line 2803 of file mole_reactions.cpp.
References CONFLICT, CORRECT, and FLTEQ.
Referenced by newreact().
double frac_H2star_hminus | ( | void | ) |
Definition at line 688 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().
STATIC char * getcsvfield | ( | char ** | s, | |
char | c | |||
) |
Definition at line 2791 of file mole_reactions.cpp.
Referenced by parse_base(), and parse_udfa().
double hmirat | ( | double | te | ) |
hmirat computes radiative association rate for H-
te |
Definition at line 1601 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 | ) |
Definition at line 2583 of file mole_reactions.cpp.
References sign().
Referenced by newreact().
STATIC void mole_check_reverse_reactions | ( | void | ) |
Definition at line 2104 of file mole_reactions.cpp.
References DEBUG_ENTRY, fixit(), ioQQQ, t_trace::lgTraceMole, mole_priv::reactab, and trace.
Referenced by mole_create_react().
void mole_cmp_num_in_out_reactions | ( | void | ) |
Definition at line 2192 of file mole_reactions.cpp.
References CHARS_SPECIES, DEBUG_ENTRY, ioQQQ, t_mole_global::list, mole_global, t_mole_global::num_total, and mole_priv::reactab.
void mole_create_react | ( | void | ) |
mole_create_react build reaction structures
Definition at line 1685 of file mole_reactions.cpp.
References DEBUG_ENTRY, dense, deut, fixit(), ipHELIUM, t_deuterium::lgElmtOn, t_dense::lgElmtOn, t_mole_global::lgFederman, t_mole_global::lgLeidenHack, t_mole_global::lgProtElim, mole, mole_check_reverse_reactions(), mole_generate_isotopologue_reactions(), mole_global, newreact(), t_mole_local::old_zone, parse_base(), parse_udfa(), plot_sparsity(), pow(), mole_priv::reactab, t_mole_local::reaction_rks, read_data(), register_reaction_vectors(), SAHA, source, UDFA, and unresolved_atom_list.
Referenced by InitSimPostparse().
mole_reaction* mole_findrate_s | ( | const char | buf[] | ) |
Definition at line 3880 of file mole_reactions.cpp.
References canonicalize_reaction_label(), DEBUG_ENTRY, and mole_priv::reactab.
Referenced by t_mole_local::findrate(), t_mole_local::findrk(), mole_get_equilibrium_constant(), and t_mole_local::sink_rate().
STATIC void mole_generate_isotopologue_reactions | ( | string | atom_old, | |
string | atom_new | |||
) |
Definition at line 1955 of file mole_reactions.cpp.
References ASSERT, ATOMIC_MASS_UNIT, canonicalize_reaction_label(), create_isotopologues_one(), DEBUG_ENTRY, fixit(), ioQQQ, newreact(), parse_species_label(), and mole_priv::reactab.
Referenced by mole_create_react().
STATIC double mole_get_equilibrium_constant | ( | const char | buf[] | ) |
Definition at line 2147 of file mole_reactions.cpp.
References DEBUG_ENTRY, mole_findrate_s(), mole_partition_function(), mole_reaction::nproducts, mole_reaction::nreactants, mole_reaction::products, and mole_reaction::reactants.
STATIC void mole_h2_grain_form | ( | void | ) |
Definition at line 2934 of file mole_reactions.cpp.
References ASSERT, t_dense::AtomicWeight, GrainVar::bin, t_hmi::chJura, dense, fixit(), fnzone, t_dense::gas_phase, GetAveVelocity(), GrainDrive(), gv, h2, hmi, ipHYDROGEN, GrainVar::lgDustOn(), GrainVar::lgGrainPhysicsOn, diatomics::lgH2_grain_deexcitation, MALLOC, MAT_CAR, MAT_CAR2, 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, t_hmi::Tad, and t_phycon::te.
Referenced by mole_update_rks().
STATIC void mole_h_reactions | ( | void | ) |
hmole_reactions - evaluates hydrogen chemistry reactions
Definition at line 3277 of file mole_reactions.cpp.
References t_rfield::anu, ASSERT, t_dense::AtomicWeight, t_hmi::chH2_small_model_type, t_colden::colden, colden, t_rfield::ConInterOut, diatomics::Cont_Dissoc_Rate_H2g, diatomics::Cont_Dissoc_Rate_H2s, conv, DEBUG_ENTRY, molezone::den, dense, diatoms, t_dense::eden, EN1RYD, esc_PRD_1side(), t_hmi::exphmi, t_rfield::extin_mag_V_point, t_iso_sp::fb, findspecieslocal(), fixit(), t_rfield::flux, fnzone, fp_equal(), 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, 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, ipCOL_H2g, ipCOL_H2s, 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, 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, SAHA, 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().
STATIC double mole_partition_function | ( | const molecule *const | sp | ) |
Definition at line 2167 of file mole_reactions.cpp.
References ASSERT, AVOGADRO, BIGFLOAT, BOLTZMANN, DEBUG_ENTRY, dsexp(), ELECTRON_MASS, fixit(), molecule::form_enthalpy, HION_LTE_POP, molecule::label, molecule::mole_mass, phycon, pow(), and t_phycon::te.
Referenced by mole_get_equilibrium_constant().
void mole_punch | ( | FILE * | punit, | |
const char | speciesname[], | |||
const char | args[], | |||
bool | lgHeader, | |||
bool | lgData, | |||
double | depth | |||
) |
Definition at line 4229 of file mole_reactions.cpp.
References DEBUG_ENTRY, findspecies(), molecule::index, mole_reaction::index, mole_reaction::label, mole, mole_reaction::nproducts, mole_reaction::nreactants, mole_reaction::products, mole_reaction::pvector, mole_reaction::pvector_excit, mole_priv::reactab, mole_reaction::reactants, t_mole_local::reaction_rks, mole_reaction::rvector, mole_reaction::rvector_excit, and t_mole_local::species.
Referenced by SaveDo().
void mole_rk_bigchange | ( | void | ) |
Definition at line 2875 of file mole_reactions.cpp.
References ASSERT, DEBUG_ENTRY, mole_reaction::index, ioQQQ, mole_reaction::label, mole, nzone, t_mole_local::old_reaction_rks, t_mole_local::old_zone, mole_priv::reactab, and t_mole_local::reaction_rks.
Referenced by ZoneEnd().
void mole_update_rks | ( | void | ) |
mole_update_rks update rate coefficients, only temp part
Definition at line 2849 of file mole_reactions.cpp.
References mole_reaction::a, DEBUG_ENTRY, 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().
STATIC void newreact | ( | const char | label[], | |
const char | fun[], | |||
double | a, | |||
double | b, | |||
double | c | |||
) |
Definition at line 2246 of file mole_reactions.cpp.
References ABSENT, ASSERT, canonicalize_reaction(), cdEXIT, compare_udfa(), DEBUG_ENTRY, EXIT_FAILURE, Singleton< t_version >::Inst(), ioQQQ, lgReactBalance(), t_version::lgRelease, t_version::nBetaVer, parse_reaction(), mole_priv::reactab, source, and UDFA.
Referenced by mole_create_react(), mole_generate_isotopologue_reactions(), and parse_base().
STATIC void parse_base | ( | char * | s | ) |
Definition at line 2229 of file mole_reactions.cpp.
References getcsvfield(), and newreact().
Referenced by mole_create_react().
STATIC long parse_reaction | ( | count_ptr< mole_reaction > & | rate, | |
const char | label[] | |||
) |
Definition at line 2307 of file mole_reactions.cpp.
References ASSERT, cdEXIT, DEBUG_ENTRY, EXIT_FAILURE, findspecies(), ioQQQ, molecule::isEnabled, t_trace::lgTraceMole, MAXPRODUCTS, MAXREACTANTS, null_mole, and trace.
Referenced by canonicalize_reaction_label(), and newreact().
STATIC void parse_udfa | ( | char * | s | ) |
Definition at line 2695 of file mole_reactions.cpp.
References ASSERT, findspecies(), FLTEQ, getcsvfield(), MALLOC, null_mole, and t_mole_global::sort().
Referenced by mole_create_react().
STATIC void plot_sparsity | ( | void | ) |
Definition at line 2510 of file mole_reactions.cpp.
References molecule::index, MALLOC, mole_global, mole_reaction::nproducts, mole_reaction::nreactants, t_mole_global::num_total, mole_reaction::products, mole_reaction::pvector, mole_priv::reactab, mole_reaction::reactants, and mole_reaction::rvector.
Referenced by mole_create_react().
STATIC void read_data | ( | const char | file[], | |
void(*)(char *s) | parse | |||
) |
Definition at line 2673 of file mole_reactions.cpp.
References BUFSIZE, fixit(), and open_data().
Referenced by mole_create_react().
STATIC void register_reaction_vectors | ( | count_ptr< mole_reaction > | rate | ) |
Definition at line 2428 of file mole_reactions.cpp.
References DEBUG_ENTRY, and lgDifferByExcitation().
Referenced by mole_create_react().
Definition at line 75 of file mole_reactions.cpp.
map<formula_species,struct udfa_reaction_s *> udfatab [static] |
Definition at line 2671 of file mole_reactions.cpp.