/home66/gary/public_html/cloudy/c13_branch/source/mole.h File Reference

#include "count_ptr.h"
#include "elementnames.h"
#include "transition.h"
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Data Structures

class  chem_element
class  chem_atom
class  element_pointer_value_less
class  molecule
class  t_mole_global
class  t_mole_local
class  molezone

Defines

#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
t_mole_local mole
molezonenull_molezone

Define Documentation

#define SMALLABUND   1e-24

Definition at line 13 of file mole.h.

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


Typedef Documentation

typedef vector< count_ptr<chem_atom> > ChemAtomList

Definition at line 115 of file mole.h.

typedef map<int, count_ptr<chem_atom> >::iterator isotopes_i

Definition at line 35 of file mole.h.

typedef molecule::nAtomsMap::const_reverse_iterator nAtoms_cri

Definition at line 216 of file mole.h.

typedef molecule::nAtomsMap::iterator nAtoms_i

Definition at line 214 of file mole.h.

typedef molecule::nAtomsMap::reverse_iterator nAtoms_ri

Definition at line 215 of file mole.h.


Enumeration Type Documentation

enum mole_state
Enumerator:
MOLE_NULL 
MOLE_PASSIVE 
MOLE_ACTIVE 

Definition at line 15 of file mole.h.


Function Documentation

void create_isotopologues_one ( ChemAtomList atoms,
vector< int > &  numAtoms,
string  atom_old,
string  atom_new,
string  embellishments,
vector< string > &  newLabels 
)

Definition at line 361 of file mole_species.cpp.

References ASSERT, and fixit().

Referenced by mole_generate_isotopologue_reactions(), and newspecies().

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molecule* findspecies ( const char  buf[]  ) 
molezone* findspecieslocal ( const char  buf[]  ) 
bool lgDifferByExcitation ( const molecule mol1,
const molecule mol2 
)

Definition at line 777 of file mole_species.cpp.

References molecule::label.

Referenced by register_reaction_vectors().

void mole_cmp_num_in_out_reactions ( void   ) 
void mole_create_react ( void   ) 
void mole_drive ( void   ) 

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().

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mole_reaction* mole_findrate_s ( const char  buf[]  ) 
void mole_make_groups ( void   ) 
void mole_make_list ( void   ) 
void mole_print_species_reactions ( molecule speciesToPrint  ) 
void mole_punch ( FILE *  punit,
const char  speciesname[],
const char  args[],
bool  lgHeader,
bool  lgData,
double  depth 
)
void mole_rk_bigchange ( void   ) 
void mole_update_sources ( void   ) 

Definition at line 106 of file mole_drive.cpp.

References DEBUG_ENTRY, mole_eval_sources(), mole_global, mole_update_species_cache(), and t_mole_global::num_total.

Referenced by ConvBase().

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void mole_update_species_cache ( void   ) 
bool operator!= ( const chem_atom a,
const chem_atom b 
) [inline]

Definition at line 110 of file mole.h.

bool operator< ( const chem_atom a,
const chem_atom b 
) [inline]

Definition at line 90 of file mole.h.

References chem_atom::compare().

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

Definition at line 98 of file mole.h.

References chem_atom::compare().

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bool operator== ( const chem_atom a,
const chem_atom b 
) [inline]

Definition at line 106 of file mole.h.

References chem_atom::compare().

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bool operator> ( const chem_atom a,
const chem_atom b 
) [inline]

Definition at line 94 of file mole.h.

References chem_atom::compare().

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

Definition at line 102 of file mole.h.

References chem_atom::compare().

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bool parse_species_label ( const char  mylab[],
ChemAtomList atomsLeftToRight,
vector< int > &  numAtoms,
string &  embellishments,
bool &  lgExcit,
int &  charge,
bool &  lgGas_Phase 
)

Definition at line 659 of file mole_species.cpp.

References ASSERT, CHARS_ISOTOPE_SYM, CHARS_SPECIES, dense, findatom(), count_ptr< T >::get_ptr(), ioQQQ, t_dense::lgElmtOn, t_trace::lgTraceMole, and trace.

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bool parse_species_label ( const char  label[],
ChemAtomList atomsLeftToRight,
vector< int > &  numAtoms,
string &  embellishments 
)

Definition at line 652 of file mole_species.cpp.

References parse_species_label().

Referenced by mole_generate_isotopologue_reactions(), newspecies(), and parse_species_label().

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void total_molecule_deut ( realnum total  ) 
void total_molecule_elems ( realnum  total[LIMELM]  ) 
realnum total_molecules ( void   ) 
realnum total_molecules_gasphase ( void   ) 

Variable Documentation

Definition at line 67 of file mole_species.cpp.

Referenced by molcol().

Definition at line 66 of file mole_species.cpp.

Definition at line 65 of file mole_species.cpp.

Referenced by dBase_solve(), SaveSpecies(), and SaveSpeciesOne().

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