t_mole_global Class Reference

#include <mole.h>

Inheritance diagram for t_mole_global:

Collaboration diagram for t_mole_global:

Public Types
typedef vector< shared_ptr< molecule > >	MoleculeList

Public Member Functions
const char *	chName () const
void	zero ()
void	comment (t_warnings &)
void	init (void)
void	make_species (void)
Public Member Functions inherited from module
	module ()
virtual	~module ()

Static Public Member Functions
static void	sort (MoleculeList::iterator start, MoleculeList::iterator end)
static void	sort (molecule **start, molecule **end)

Public Attributes
bool	lgNoMole
bool	lgNoHeavyMole
bool	lgH2Ozer
bool	lgLeidenHack
bool	lgFederman
bool	lgStancil
bool	lgNonEquilChem
bool	lgProtElim
bool	lgNeutrals
bool	lgGrain_mole_deplete
vector< bool >	lgTreatIsotopes
int	num_total
int	num_calc
int	num_compacted
MoleculeList	list
map< string, bool >	offReactions
map< string, Properties >	speciesProperties

Member Typedef Documentation

MoleculeList

typedef vector<shared_ptr<molecule> > t_mole_global::MoleculeList

Member Function Documentation

chName()

const char * t_mole_global::chName ( ) const

inlinevirtual

Implements module.

comment()

void t_mole_global::comment ( t_warnings & )

inlinevirtual

Implements module.

init()

void t_mole_global::init

(

void

)

mole_zero allocate + initialize workspace

References cdEXIT, DEBUG_ENTRY, EXIT_FAILURE, fprintf(), ioQQQ, make_species(), mole, mole_make_groups(), mole_make_list(), and num_total.

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make_species()

void t_mole_global::make_species

(

void

)

References molecule::charge, CHARS_ION_STAGE, CHARS_ISOTOPE_SYM, DEBUG_ENTRY, dense, deut, element_list, elementnames, findspecies(), fixit, frac(), gv, h2, hmi, InitDeuteriumIonization(), ipHYDROGEN, lgTreatIsotopes, LIMELM, MeanMassOfElement(), MOLE_ACTIVE, mole_global, molecule::mole_mass, MOLE_NULL, MOLE_PASSIVE, MOLECULE, newelement(), newisotope(), newspecies(), nuclide_list, NULL, null_mole, null_molezone, null_molezone_impl, null_nuclide, null_nuclide_impl, OTHER, read_species_file(), SetDeuteriumFractionation(), SetGasPhaseDeuterium(), SetIsotopeFractions(), and TotalInsanity().

Referenced by init().

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sort() [1/2]

void t_mole_global::sort ( molecule ** start, molecule ** end )

static

References start().

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sort() [2/2]

static void t_mole_global::sort ( MoleculeList::iterator start, MoleculeList::iterator end )

static

References start().

Referenced by canonicalize_reaction(), mole_make_list(), and parse_udfa().

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zero()

void t_mole_global::zero ( void )

virtual

option to set proton elimination rates to zero

>refer CO chemistry Huntress, W. T., 1977, ApJS, 33, 495 By default, this is false - changed with set chemistry command

option to not include neutrals in the non-equilibrium scheme

refer Federman, S. R. & Zsargo, J. 2003, ApJ, 589, 319 By default, this is false - changed with set chemistry command

Implements module.

References DEBUG_ENTRY, lgFederman, lgGrain_mole_deplete, lgH2Ozer, lgLeidenHack, lgNeutrals, lgNoHeavyMole, lgNoMole, lgNonEquilChem, lgProtElim, lgStancil, lgTreatIsotopes, and LIMELM.

Member Data Documentation

lgFederman

bool t_mole_global::lgFederman

option to use diffuse cloud chemical rates from Table 8 of

refer Federman, S. R. & Zsargo, J. 2003, ApJ, 589, 319 By default, this is true - changed with set chemistry command these rates are in both mole_co_federman.dat and mole_co_base.dat, latter based on UMIST

Referenced by zero().

lgGrain_mole_deplete

bool t_mole_global::lgGrain_mole_deplete

do we include capture of molecules onto grain surfaces? default is true, turned off with NO GRAIN MOLECULES command

Referenced by zero().

lgH2Ozer

bool t_mole_global::lgH2Ozer

flag set true if H2O destruction rate went to zero

Referenced by zero().

lgLeidenHack

bool t_mole_global::lgLeidenHack

option to turn on the original UMIST rates rather than the corrected network adopted in the Leiden PDR meeting, by deffault false, set true with the set UMIST rates command, these rates are from mole_co_umisthack.dat and also in mole_co_base.dat (UMIST)

Referenced by zero().

lgNeutrals

bool t_mole_global::lgNeutrals

option to not include neutrals in the non-equilibrium scheme

refer Federman, S. R. & Zsargo, J. 2003, ApJ, 589, 319 By default, this is false - changed with set chemistry command

Referenced by zero().

lgNoHeavyMole

bool t_mole_global::lgNoHeavyMole

flag to turn off heavy molecules, set with no heavy molecules command

Referenced by zero().

lgNoMole

bool t_mole_global::lgNoMole

flag to turn off all molecules, set with no molecules command

Referenced by zero().

lgNonEquilChem

bool t_mole_global::lgNonEquilChem

option to use effective temperature as defined in

refer Federman, S. R. & Zsargo, J. 2003, ApJ, 589, 319 By default, this is false - changed with set chemistry command

Referenced by zero().

lgProtElim

bool t_mole_global::lgProtElim

option to set proton elimination rates to zero

>refer CO chemistry Huntress, W. T., 1977, ApJS, 33, 495 By default, this is false - changed with set chemistry command

Referenced by zero().

lgStancil

bool t_mole_global::lgStancil

Referenced by zero().

lgTreatIsotopes

vector<bool> t_mole_global::lgTreatIsotopes

Referenced by make_species(), and zero().

list

MoleculeList t_mole_global::list

num_calc

int t_mole_global::num_calc

num_compacted

int t_mole_global::num_compacted

num_total

int t_mole_global::num_total

flag saying whether an element is in the chemistry network

Referenced by init().

offReactions

map<string,bool> t_mole_global::offReactions

speciesProperties

map<string,Properties > t_mole_global::speciesProperties

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The documentation for this class was generated from the following files:

• mole.h
• mole.cpp
• mole_species.cpp