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Data Structures | |
class | chem_element |
class | chem_atom |
class | element_pointer_value_less |
class | molecule |
class | t_mole_global |
class | molezone |
class | t_mole_local |
Macros | |
#define | SMALLABUND 1e-24 |
Typedefs | |
typedef map< int, count_ptr< chem_atom > >::iterator | isotopes_i |
typedef vector< count_ptr< chem_atom > > | ChemAtomList |
typedef molecule::nAtomsMap::iterator | nAtoms_i |
typedef molecule::nAtomsMap::reverse_iterator | nAtoms_ri |
typedef molecule::nAtomsMap::const_reverse_iterator | nAtoms_cri |
Enumerations | |
enum | mole_state { MOLE_NULL , MOLE_PASSIVE , MOLE_ACTIVE } |
Functions | |
bool | operator< (const chem_atom &a, const chem_atom &b) |
bool | operator> (const chem_atom &a, const chem_atom &b) |
bool | operator<= (const chem_atom &a, const chem_atom &b) |
bool | operator>= (const chem_atom &a, const chem_atom &b) |
bool | operator== (const chem_atom &a, const chem_atom &b) |
bool | operator!= (const chem_atom &a, const chem_atom &b) |
void | mole_drive (void) |
void | mole_create_react (void) |
mole_reaction * | mole_findrate_s (const char buf[]) |
void | mole_print_species_reactions (molecule *speciesToPrint) |
molecule * | findspecies (const char buf[]) |
molezone * | findspecieslocal (const char buf[]) |
void | mole_punch (FILE *punit, const char speciesname[], const char args[], bool lgHeader, bool lgData, double depth) |
void | total_molecule_elems (realnum total[LIMELM]) |
void | total_molecule_deut (realnum &total) |
realnum | total_molecules (void) |
realnum | total_molecules_gasphase (void) |
void | mole_make_list (void) |
void | mole_make_groups (void) |
void | mole_cmp_num_in_out_reactions (void) |
bool | lgDifferByExcitation (const molecule &mol1, const molecule &mol2) |
void | mole_update_species_cache (void) |
void | mole_update_sources (void) |
void | mole_rk_bigchange (void) |
void | create_isotopologues_one (ChemAtomList &atoms, vector< int > &numAtoms, string atom_old, string atom_new, string embellishments, vector< string > &newLabels) |
bool | parse_species_label (const char label[], ChemAtomList &atomsLeftToRight, vector< int > &numAtoms, string &embellishments) |
bool | parse_species_label (const char mylab[], ChemAtomList &atomsLeftToRight, vector< int > &numAtoms, string &embellishments, bool &lgExcit, int &charge, bool &lgGas_Phase) |
#define SMALLABUND 1e-24 |
Definition at line 13 of file mole.h.
Referenced by mole_solve(), newton_step(), and GroupMap::setup().
typedef vector< count_ptr<chem_atom> > ChemAtomList |
typedef map<int,count_ptr<chem_atom>>::iterator isotopes_i |
typedef molecule::nAtomsMap::const_reverse_iterator nAtoms_cri |
enum mole_state |
void create_isotopologues_one | ( | ChemAtomList & | atoms, |
vector< int > & | numAtoms, | ||
string | atom_old, | ||
string | atom_new, | ||
string | embellishments, | ||
vector< string > & | newLabels ) |
Definition at line 387 of file mole_species.cpp.
References ASSERT, atoms, and fixit().
Referenced by mole_generate_isotopologue_reactions(), and newspecies().
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Definition at line 814 of file mole_species.cpp.
References DEBUG_ENTRY, null_mole, and mole_priv::spectab.
Referenced by t_mole_local::chem_heat(), database_readin(), t_mole_local::dissoc_rate(), diatomics::init(), iso_allocate(), lgElemsConserved(), lgNetEdenSrcSmall(), t_mole_global::make_species(), mole_make_list(), mole_punch(), parse_reaction(), parse_udfa(), prt_smooth_predictions(), radius_increment(), SaveDo(), SaveSpecies(), t_mole_local::sink_rate_tot(), t_mole_local::source_rate_tot(), and states_nelemfill().
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Definition at line 833 of file mole_species.cpp.
References DEBUG_ENTRY, mole, null_molezone, and mole_priv::spectab.
Referenced by AgeCheck(), cdColm(), check_co_ion_converge(), ConvBase(), CoolCarb(), CoolEvaluate(), CoolNeon(), dBase_solve(), DynaPunchTimeDep(), GrainCollHeating(), diatomics::H2_PunchDo(), diatomics::H2_X_coll_rate_evaluate(), HeatSum(), InitSimPostparse(), IonHydro(), iso_level(), iter_end_check(), IterRestart(), lines_molecules(), mole_effects(), diatomics::mole_H2_form(), mole_h_fixup(), mole_h_rate_diagnostics(), mole_h_reactions(), OpacityAddTotal(), PrtZone(), radius_increment(), radius_next(), RT_OTS(), RT_tau_inc(), SaveDo(), SaveLineData(), SaveSpecies(), and ShowMe().
Definition at line 804 of file mole_species.cpp.
References molecule::label.
Referenced by register_reaction_vectors().
void mole_cmp_num_in_out_reactions | ( | void | ) |
Definition at line 2183 of file mole_reactions.cpp.
References CHARS_SPECIES, DEBUG_ENTRY, ioQQQ, mole_global, and mole_priv::reactab.
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mole_create_react build reaction structures
Definition at line 1665 of file mole_reactions.cpp.
References DEBUG_ENTRY, dense, deut, fixit(), ipHELIUM, mole, mole_check_reverse_reactions(), mole_generate_isotopologue_reactions(), mole_global, newreact(), parse_base(), parse_udfa(), plot_sparsity(), mole_priv::reactab, read_data(), register_reaction_vectors(), SAHA, source, UDFA, and unresolved_atom_list.
Referenced by InitSimPostparse().
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mole_drive main driver for chemical equilibrium routines
Definition at line 41 of file mole_drive.cpp.
References DEBUG_ENTRY, mole_effects(), mole_ion_trim(), mole_solve(), mole_update_limiting_reactants(), mole_update_rks(), mole_update_species_cache(), and MOLETOLER.
Referenced by ConvBase().
mole_reaction * mole_findrate_s | ( | const char | buf[] | ) |
Definition at line 3872 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().
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Definition at line 1142 of file mole_species.cpp.
References ASSERT, DEBUG_ENTRY, groupspecies, LIMELM, MALLOC, mole_global, and REALLOC.
Referenced by t_mole_global::init().
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Definition at line 296 of file mole_species.cpp.
References ASSERT, molecule::charge, DEBUG_ENTRY, findspecies(), molecule::index, isactive(), molecule::isMonatomic(), ispassive(), molecule::lgGas_Phase, mole_global, molecule::nAtom, t_mole_global::sort(), and mole_priv::spectab.
Referenced by t_mole_global::init().
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Definition at line 316 of file newton_step.cpp.
References mole_reaction::index, molecule::index, ioQQQ, mole_reaction::label, molecule::label, mole, mole_reaction::nproducts, mole_reaction::nreactants, mole_reaction::products, mole_reaction::pvector, mole_priv::reactab, mole_reaction::reactants, and mole_reaction::rvector.
Referenced by lgElemsConserved(), and mole_system_error().
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Definition at line 4221 of file mole_reactions.cpp.
References DEBUG_ENTRY, findspecies(), mole_reaction::index, molecule::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, mole_reaction::rvector, and mole_reaction::rvector_excit.
Referenced by SaveDo().
void mole_rk_bigchange | ( | void | ) |
Definition at line 2866 of file mole_reactions.cpp.
References ASSERT, DEBUG_ENTRY, mole_reaction::index, ioQQQ, mole_reaction::label, mole, nzone, and mole_priv::reactab.
Referenced by ZoneEnd().
void mole_update_sources | ( | void | ) |
Definition at line 106 of file mole_drive.cpp.
References DEBUG_ENTRY, mole_eval_sources(), mole_global, and mole_update_species_cache().
Referenced by ConvBase().
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Definition at line 866 of file mole_species.cpp.
References ASSERT, DEBUG_ENTRY, gv, ioQQQ, mole, and mole_global.
Referenced by diatomics::H2_LevelPops(), mole_drive(), and mole_update_sources().
Definition at line 90 of file mole.h.
References chem_atom::compare().
Definition at line 98 of file mole.h.
References chem_atom::compare().
Definition at line 106 of file mole.h.
References chem_atom::compare().
Definition at line 94 of file mole.h.
References chem_atom::compare().
Definition at line 102 of file mole.h.
References chem_atom::compare().
bool parse_species_label | ( | const char | label[], |
ChemAtomList & | atomsLeftToRight, | ||
vector< int > & | numAtoms, | ||
string & | embellishments ) |
Definition at line 678 of file mole_species.cpp.
References parse_species_label().
Referenced by mole_generate_isotopologue_reactions(), newspecies(), and parse_species_label().
bool parse_species_label | ( | const char | mylab[], |
ChemAtomList & | atomsLeftToRight, | ||
vector< int > & | numAtoms, | ||
string & | embellishments, | ||
bool & | lgExcit, | ||
int & | charge, | ||
bool & | lgGas_Phase ) |
Definition at line 685 of file mole_species.cpp.
References ASSERT, CHARS_ISOTOPE_SYM, CHARS_SPECIES, dense, findatom(), count_ptr< T >::get_ptr(), ioQQQ, and trace.
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Definition at line 1034 of file mole_species.cpp.
References DEBUG_ENTRY, deut, mole, and mole_global.
Referenced by mole_return_cached_species(), and SetDeuteriumIonization().
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Definition at line 1063 of file mole_species.cpp.
References ASSERT, DEBUG_ENTRY, ipHYDROGEN, LIMELM, mole, and mole_global.
Referenced by t_dense::updateXMolecules().
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Definition at line 1109 of file mole_species.cpp.
References DEBUG_ENTRY, mole, and mole_global.
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Definition at line 1124 of file mole_species.cpp.
References DEBUG_ENTRY, mole, and mole_global.
Referenced by SumDensities().
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Definition at line 71 of file mole_species.cpp.
Referenced by funjac(), grouped_elems(), lgElemsConserved(), lgNucleiConserved(), mole_solve(), newisotope(), GroupMap::setup(), and GroupMap::updateMolecules().
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Definition at line 7 of file mole.cpp.
Referenced by AbundChange(), ChemImportance(), ConvBase(), ConvIterCheck(), CoolEvaluate(), CoolOxyg(), DynaStartZone(), eden_sum(), fill_array(), find_solution(), findspecieslocal(), funjac(), diatomics::H2_LevelPops(), diatomics::H2_X_sink_and_source(), HeatSum(), HomogeneousSource(), diatomics::init(), t_mole_global::init(), InitSimPostparse(), iso_allocate(), iso_level(), iter_end_check(), IterRestart(), IterStart(), lgNetEdenSrcSmall(), lgNucleiConserved(), lgOH_ChargeTransferDominant(), lines_lv1_li_ne(), lines_molecules(), molcol(), mole_create_react(), mole_dominant_rates(), mole_effects(), mole_eval_balance(), mole_eval_dynamic_balance(), mole_eval_sources(), diatomics::mole_H2_form(), mole_h_fixup(), mole_h_rate_diagnostics(), mole_print_species_reactions(), mole_punch(), mole_return_cached_species(), mole_rk_bigchange(), mole_solve(), mole_update_limiting_reactants(), mole_update_rks(), mole_update_species_cache(), OpacityAddTotal(), PrintRates(), PrtColumns(), PrtComment(), PrtZone(), radius_increment(), radius_next(), RT_diffuse(), RT_tau_reset(), SaveDo(), SaveSpecies(), SaveSpeciesOne(), ScaleAllDensities(), SetDeuteriumIonization(), GroupMap::setup(), states_nelemfill(), total_molecule_deut(), total_molecule_elems(), total_molecules(), total_molecules_gasphase(), total_network_elems(), GroupMap::updateMolecules(), t_mole_global::zero(), and zero().
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Definition at line 6 of file mole.cpp.
Referenced by AbundChange(), atmdat_readin(), ChargTranEval(), ChemImportance(), diatomics::Cont_Diss_Heat_Rate(), ConvBase(), ConvInitSolution(), ConvIterCheck(), CoolEvaluate(), DynaCreateArrays(), DynaIonize(), DynaNewStep(), DynaSaveLast(), DynaStartZone(), eden_sum(), funjac(), grouped_elems(), diatomics::H2_X_sink_and_source(), HeatSum(), diatomics::init(), t_mole_global::init(), InitSimPostparse(), ion_photo(), ion_trim(), iter_end_check(), IterRestart(), IterStart(), lgNucleiConserved(), t_mole_global::make_species(), diatomics::Mol_Photo_Diss_Rates(), molcol(), mole_cmp_num_in_out_reactions(), mole_create_react(), mole_effects(), mole_eval_balance(), mole_eval_dynamic_balance(), mole_h_fixup(), mole_h_rate_diagnostics(), mole_h_reactions(), mole_make_groups(), mole_make_list(), mole_return_cached_species(), mole_solve(), mole_update_limiting_reactants(), mole_update_sources(), mole_update_species_cache(), newspecies(), OpacityAddTotal(), OpacityCreateAll(), ParseCommands(), ParseDont(), ParseSet(), plot_sparsity(), PrtColumns(), PrtComment(), PrtZone(), radius_increment(), radius_next(), RT_diffuse(), RT_tau_reset(), SaveDo(), SaveSpecies(), SaveSpeciesOne(), ScaleAllDensities(), t_mole_local::set_location(), GroupMap::setup(), state_get_put(), total_molecule_deut(), total_molecule_elems(), total_molecules(), total_molecules_gasphase(), total_network_elems(), GroupMap::updateMolecules(), t_mole_global::zero(), and zero().
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Definition at line 68 of file mole_species.cpp.
Referenced by molecule::heavyAtom(), t_mole_global::make_species(), and molcol().
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Definition at line 67 of file mole_species.cpp.
Referenced by t_mole_global::make_species().
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Definition at line 65 of file mole_species.cpp.
Referenced by database_readin(), t_mole_local::dissoc_rate(), findspecies(), diatomics::init(), iso_allocate(), t_mole_global::make_species(), mole_dominant_rates(), parse_reaction(), parse_udfa(), SaveDo(), SaveSpeciesOne(), and states_nelemfill().
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Definition at line 66 of file mole_species.cpp.
Referenced by dBase_solve(), findspecieslocal(), t_mole_global::make_species(), SaveSpecies(), and SaveSpeciesOne().
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Definition at line 70 of file mole_species.cpp.
Referenced by ChemImportance(), iter_end_check(), t_mole_global::make_species(), mole_create_react(), mole_effects(), mole_eval_dynamic_balance(), mole_eval_sources(), mole_h_rate_diagnostics(), mole_ion_trim(), newisotope(), PrtZone(), t_mole_local::set_isotope_abundances(), and t_mole_local::set_location().