cloudy trunk
Loading...
Searching...
No Matches
mole.h File Reference
#include "count_ptr.h"
#include "elementnames.h"
#include "transition.h"
Include dependency graph for mole.h:

Go to the source code of this file.

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_reactionmole_findrate_s (const char buf[])
void mole_print_species_reactions (molecule *speciesToPrint)
moleculefindspecies (const char buf[])
molezonefindspecieslocal (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)

Variables

ChemAtomList atom_list
ChemAtomList unresolved_atom_list
chem_elementnull_element
chem_atomnull_atom
moleculenull_mole
t_mole_global mole_global
molezonenull_molezone
t_mole_local mole

Macro Definition Documentation

◆ SMALLABUND

#define SMALLABUND   1e-24

Definition at line 13 of file mole.h.

Referenced by mole_solve(), newton_step(), and GroupMap::setup().

Typedef Documentation

◆ ChemAtomList

typedef vector< count_ptr<chem_atom> > ChemAtomList

Definition at line 115 of file mole.h.

◆ isotopes_i

Definition at line 35 of file mole.h.

◆ nAtoms_cri

typedef molecule::nAtomsMap::const_reverse_iterator nAtoms_cri

Definition at line 216 of file mole.h.

◆ nAtoms_i

typedef molecule::nAtomsMap::iterator nAtoms_i

Definition at line 214 of file mole.h.

◆ nAtoms_ri

typedef molecule::nAtomsMap::reverse_iterator nAtoms_ri

Definition at line 215 of file mole.h.

Enumeration Type Documentation

◆ mole_state

enum mole_state
Enumerator
MOLE_NULL 
MOLE_PASSIVE 
MOLE_ACTIVE 

Definition at line 15 of file mole.h.

Function Documentation

◆ create_isotopologues_one()

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().

Here is the call graph for this function:

◆ findspecies()

◆ findspecieslocal()

◆ lgDifferByExcitation()

bool lgDifferByExcitation ( const molecule & mol1,
const molecule & mol2 )

Definition at line 804 of file mole_species.cpp.

References molecule::label.

Referenced by register_reaction_vectors().

◆ mole_cmp_num_in_out_reactions()

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.

◆ mole_create_react()

void mole_create_react ( void )
extern

◆ mole_drive()

void mole_drive ( void )
extern

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().

Here is the call graph for this function:

◆ mole_findrate_s()

mole_reaction * mole_findrate_s ( const char buf[])

◆ mole_make_groups()

void mole_make_groups ( void )
extern

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().

◆ mole_make_list()

void mole_make_list ( void )
extern

◆ mole_print_species_reactions()

◆ mole_punch()

void mole_punch ( FILE * punit,
const char speciesname[],
const char args[],
bool lgHeader,
bool lgData,
double depth )
extern

◆ mole_rk_bigchange()

void mole_rk_bigchange ( void )

◆ mole_update_sources()

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().

Here is the call graph for this function:

◆ mole_update_species_cache()

void mole_update_species_cache ( void )
extern

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().

◆ operator!=()

bool operator!= ( const chem_atom & a,
const chem_atom & b )
inline

Definition at line 110 of file mole.h.

◆ operator<()

bool operator< ( const chem_atom & a,
const chem_atom & b )
inline

Definition at line 90 of file mole.h.

References chem_atom::compare().

Here is the call graph for this function:

◆ operator<=()

bool operator<= ( const chem_atom & a,
const chem_atom & b )
inline

Definition at line 98 of file mole.h.

References chem_atom::compare().

Here is the call graph for this function:

◆ operator==()

bool operator== ( const chem_atom & a,
const chem_atom & b )
inline

Definition at line 106 of file mole.h.

References chem_atom::compare().

Here is the call graph for this function:

◆ operator>()

bool operator> ( const chem_atom & a,
const chem_atom & b )
inline

Definition at line 94 of file mole.h.

References chem_atom::compare().

Here is the call graph for this function:

◆ operator>=()

bool operator>= ( const chem_atom & a,
const chem_atom & b )
inline

Definition at line 102 of file mole.h.

References chem_atom::compare().

Here is the call graph for this function:

◆ parse_species_label() [1/2]

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().

Here is the call graph for this function:

◆ parse_species_label() [2/2]

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.

Here is the call graph for this function:

◆ total_molecule_deut()

void total_molecule_deut ( realnum & total)
extern

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().

◆ total_molecule_elems()

void total_molecule_elems ( realnum total[LIMELM])
extern

Definition at line 1063 of file mole_species.cpp.

References ASSERT, DEBUG_ENTRY, ipHYDROGEN, LIMELM, mole, and mole_global.

Referenced by t_dense::updateXMolecules().

◆ total_molecules()

realnum total_molecules ( void )
extern

Definition at line 1109 of file mole_species.cpp.

References DEBUG_ENTRY, mole, and mole_global.

◆ total_molecules_gasphase()

realnum total_molecules_gasphase ( void )
extern

Definition at line 1124 of file mole_species.cpp.

References DEBUG_ENTRY, mole, and mole_global.

Referenced by SumDensities().

Variable Documentation

◆ atom_list

◆ mole

◆ mole_global

t_mole_global mole_global
extern

◆ null_atom

chem_atom* null_atom
extern

Definition at line 68 of file mole_species.cpp.

Referenced by molecule::heavyAtom(), t_mole_global::make_species(), and molcol().

◆ null_element

chem_element* null_element
extern

Definition at line 67 of file mole_species.cpp.

Referenced by t_mole_global::make_species().

◆ null_mole

◆ null_molezone

molezone* null_molezone
extern

◆ unresolved_atom_list