cloudy trunk
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#include "cdstd.h"
#include <cctype>
#include <string.h>
#include <algorithm>
#include <stdlib.h>
#include "cddefines.h"
#include "co.h"
#include "colden.h"
#include "conv.h"
#include "deuterium.h"
#include "doppvel.h"
#include "elementnames.h"
#include "h2.h"
#include "iso.h"
#include "phycon.h"
#include "physconst.h"
#include "mole.h"
#include "mole_priv.h"
#include "hmi.h"
#include "radius.h"
#include "rfield.h"
#include "rt.h"
#include "secondaries.h"
#include "dense.h"
#include "ionbal.h"
#include "grainvar.h"
#include "timesc.h"
#include "taulines.h"
#include "trace.h"
#include <functional>
Go to the source code of this file.
Namespaces | |
namespace | mole_priv |
Enumerations | |
enum | spectype { MOLECULE , OTHER } |
Functions | |
STATIC void | read_species_file (string filename, bool lgCreateIsotopologues=true) |
STATIC void | newelement (const char label[], int ipion) |
STATIC void | newisotope (const count_ptr< chem_element > &el, int massNumberA, realnum mass_amu, double frac) |
STATIC realnum | MeanMassOfElement (const count_ptr< chem_element > &el) |
STATIC molecule * | newspecies (const char label[], enum spectype type, enum mole_state state, realnum form_enthalpy) |
STATIC molecule * | newspecies (const char label[], enum spectype type, enum mole_state state, realnum form_enthalpy, bool lgCreateIsotopologues) |
STATIC count_ptr< chem_atom > | findatom (const char buf[]) |
STATIC bool | isactive (const molecule &mol) |
STATIC bool | ispassive (const molecule &mol) |
STATIC void | ReadIsotopeFractions (const vector< bool > &lgResolveNelem) |
void | mole_make_list () |
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 label[], ChemAtomList &atomsLeftToRight, vector< int > &numAtoms, string &embellishments, bool &lgExcit, int &charge, bool &lgGas_Phase) |
bool | lgDifferByExcitation (const molecule &mol1, const molecule &mol2) |
molecule * | findspecies (const char buf[]) |
molezone * | findspecieslocal (const char buf[]) |
void | mole_update_species_cache (void) |
realnum | mole_return_cached_species (const GroupMap &) |
void | total_molecule_deut (realnum &total_f) |
void | total_molecule_elems (realnum total[LIMELM]) |
void | total_network_elems (double total[LIMELM]) |
realnum | total_molecules (void) |
realnum | total_molecules_gasphase (void) |
void | mole_make_groups (void) |
Variables | |
molecule * | null_mole |
molezone * | null_molezone |
chem_element * | null_element |
chem_atom * | null_atom |
vector< count_ptr< chem_element > > | element_list |
ChemAtomList | unresolved_atom_list |
ChemAtomList | atom_list |
molecule ** | groupspecies |
enum spectype |
Enumerator | |
---|---|
MOLECULE | |
OTHER |
Definition at line 40 of file mole_species.cpp.
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().
Definition at line 852 of file mole_species.cpp.
References mole_priv::atomtab, DEBUG_ENTRY, and STATIC.
Referenced by t_mole_global::make_species(), and parse_species_label().
molecule * findspecies | ( | const char | buf[] | ) |
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().
molezone * findspecieslocal | ( | const char | buf[] | ) |
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 792 of file mole_species.cpp.
References DEBUG_ENTRY, MOLE_ACTIVE, molecule::state, and STATIC.
Referenced by mole_make_list().
Definition at line 797 of file mole_species.cpp.
References DEBUG_ENTRY, MOLE_PASSIVE, molecule::state, and STATIC.
Referenced by mole_make_list().
Definition at line 804 of file mole_species.cpp.
References molecule::label.
Referenced by register_reaction_vectors().
STATIC realnum MeanMassOfElement | ( | const count_ptr< chem_element > & | el | ) |
Definition at line 515 of file mole_species.cpp.
References ASSERT, DEBUG_ENTRY, dense, fp_equal(), and STATIC.
Referenced by t_mole_global::make_species().
void mole_make_groups | ( | void | ) |
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().
void mole_make_list | ( | void | ) |
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().
Definition at line 935 of file mole_species.cpp.
References ASSERT, dense, deut, lgElemsConserved(), mole, MOLE_ACTIVE, mole_global, SDIV(), and total_molecule_deut().
Referenced by mole_solve().
void mole_update_species_cache | ( | void | ) |
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().
STATIC void newelement | ( | const char | label[], |
int | ipion ) |
Definition at line 461 of file mole_species.cpp.
References auto_vec< T >::data(), DEBUG_ENTRY, element_list, mole_priv::elemtab, and STATIC.
Referenced by t_mole_global::make_species().
STATIC void newisotope | ( | const count_ptr< chem_element > & | el, |
int | massNumberA, | ||
realnum | mass_amu, | ||
double | frac ) |
Definition at line 487 of file mole_species.cpp.
References ASSERT, atom_list, mole_priv::atomtab, DEBUG_ENTRY, count_ptr< T >::get_ptr(), LIMELM, STATIC, and unresolved_atom_list.
Referenced by t_mole_global::make_species(), and ReadIsotopeFractions().
STATIC molecule * newspecies | ( | const char | label[], |
enum spectype | type, | ||
enum mole_state | state, | ||
realnum | form_enthalpy ) |
Definition at line 534 of file mole_species.cpp.
References newspecies(), state, and STATIC.
Referenced by t_mole_global::make_species(), newspecies(), newspecies(), and read_species_file().
STATIC molecule * newspecies | ( | const char | label[], |
enum spectype | type, | ||
enum mole_state | state, | ||
realnum | form_enthalpy, | ||
bool | lgCreateIsotopologues ) |
Definition at line 544 of file mole_species.cpp.
References ASSERT, ATOMIC_MASS_UNIT, multi_arr< T, d, ALLOC, lgBC >::begin(), create_isotopologues_one(), auto_vec< T >::data(), DEBUG_ENTRY, ioQQQ, ipHYDROGEN, MOLE_ACTIVE, mole_global, MOLE_NULL, MOLECULE, newspecies(), molecule::parentLabel, parse_species_label(), mole_priv::spectab, state, STATIC, and trace.
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 | label[], |
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.
Definition at line 359 of file mole_species.cpp.
References ASSERT, DEBUG_ENTRY, mode_r, MOLE_ACTIVE, MOLECULE, newspecies(), open_data(), and STATIC.
Referenced by t_mole_global::make_species().
Definition at line 104 of file mole_species.cpp.
References ASSERT, DEBUG_ENTRY, element_list, FFmtRead(), fixit(), INPUT_LINE_LENGTH, ipCARBON, newisotope(), open_data(), read_whole_line(), and STATIC.
Referenced by t_mole_global::make_species().
void total_molecule_deut | ( | realnum & | total_f | ) |
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().
void total_molecule_elems | ( | realnum | total[LIMELM] | ) |
Definition at line 1063 of file mole_species.cpp.
References ASSERT, DEBUG_ENTRY, ipHYDROGEN, LIMELM, mole, and mole_global.
Referenced by t_dense::updateXMolecules().
realnum total_molecules | ( | void | ) |
Definition at line 1109 of file mole_species.cpp.
References DEBUG_ENTRY, mole, and mole_global.
realnum total_molecules_gasphase | ( | void | ) |
Definition at line 1124 of file mole_species.cpp.
References DEBUG_ENTRY, mole, and mole_global.
Referenced by SumDensities().
void total_network_elems | ( | double | total[LIMELM] | ) |
Definition at line 1087 of file mole_species.cpp.
References DEBUG_ENTRY, ipHYDROGEN, LIMELM, mole, and mole_global.
ChemAtomList atom_list |
Definition at line 71 of file mole_species.cpp.
Referenced by funjac(), grouped_elems(), lgElemsConserved(), lgNucleiConserved(), mole_solve(), newisotope(), GroupMap::setup(), and GroupMap::updateMolecules().
vector< count_ptr <chem_element> > element_list |
Definition at line 69 of file mole_species.cpp.
Referenced by t_mole_global::make_species(), newelement(), and ReadIsotopeFractions().
molecule** groupspecies |
Definition at line 72 of file mole_species.cpp.
Referenced by funjac(), grouped_elems(), mole_make_groups(), mole_system_error(), newton_step(), GroupMap::setup(), and GroupMap::updateMolecules().
chem_atom* null_atom |
Definition at line 68 of file mole_species.cpp.
Referenced by molecule::heavyAtom(), t_mole_global::make_species(), and molcol().
chem_element* null_element |
Definition at line 67 of file mole_species.cpp.
Referenced by t_mole_global::make_species().
molecule* null_mole |
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().
molezone* null_molezone |
Definition at line 66 of file mole_species.cpp.
Referenced by dBase_solve(), findspecieslocal(), t_mole_global::make_species(), SaveSpecies(), and SaveSpeciesOne().
ChemAtomList unresolved_atom_list |
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().