#include <mole.h>

Inheritance diagram for t_mole_global:

Collaboration diagram for t_mole_global:

Public Types
typedef vector< count_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)

Data Fields
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

Detailed Description

Definition at line 310 of file mole.h.

Member Typedef Documentation

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

Definition at line 364 of file mole.h.

Member Function Documentation

const char* t_mole_global::chName ( ) const

inlinevirtual

Implements module.

Definition at line 313 of file mole.h.

void t_mole_global::comment ( t_warnings & )

inlinevirtual

Implements module.

Definition at line 318 of file mole.h.

void t_mole_global::init ( void )

mole_zero allocate + initialize workspace

Definition at line 52 of file mole.cpp.

References cdEXIT, DEBUG_ENTRY, t_mole_local::elec, EXIT_FAILURE, fprintf(), ioQQQ, make_species(), mole_make_groups(), mole_make_list(), num_total, and t_mole_local::species.

Referenced by InitSimPostparse().

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void t_mole_global::make_species ( void )

Definition at line 111 of file mole_species.cpp.

References molecule::charge, CHARS_ION_STAGE, CHARS_ISOTOPE_SYM, t_elementnames::chElementSym, DEBUG_ENTRY, molezone::den, dense, deut, element_list, elementnames, diatomics::ENERGY_H2_STAR, findspecies(), fixit, frac(), t_dense::gas_phase, gv, h2, hmi, molecule::index, InitDeuteriumIonization(), ipHYDROGEN, GrainVar::lgDustOn(), t_deuterium::lgElmtOn, lgGrain_mole_deplete, t_hmi::lgLeiden_Keep_ipMH2s, lgLeidenHack, lgTreatIsotopes, LIMELM, MeanMassOfElement(), MOLE_ACTIVE, mole_global, molecule::mole_mass, MOLE_NULL, MOLE_PASSIVE, MOLECULE, newelement(), newisotope(), newspecies(), nuclide_list, null_mole, num_calc, num_total, OTHER, read_species_file(), SetDeuteriumFractionation(), SetGasPhaseDeuterium(), SetIsotopeFractions(), and TotalInsanity().

Referenced by init().

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

static

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

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

static

Definition at line 82 of file mole_species.cpp.

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.

Definition at line 10 of file mole.cpp.

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

Field Documentation

bool t_mole_global::lgFederman

Definition at line 336 of file mole.h.

Referenced by mole_create_react(), ParseSet(), and zero().

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

Definition at line 356 of file mole.h.

Referenced by make_species(), ParseDont(), and zero().

bool t_mole_global::lgH2Ozer

flag set true if H2O destruction rate went to zero

Definition at line 331 of file mole.h.

Referenced by PrtComment(), and zero().

bool t_mole_global::lgLeidenHack

set rates to that in UMIST

Definition at line 334 of file mole.h.

Referenced by ChargTranEval(), ion_photo(), make_species(), mole_create_react(), mole_h_reactions(), ParseSet(), radius_next(), and zero().

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

Definition at line 352 of file mole.h.

Referenced by ParseSet(), and zero().

bool t_mole_global::lgNoHeavyMole

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

Definition at line 328 of file mole.h.

Referenced by newspecies(), ParseDont(), and zero().

bool t_mole_global::lgNoMole

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

Definition at line 325 of file mole.h.

Referenced by ConvInitSolution(), CoolEvaluate(), ion_trim(), ion_trim2(), newspecies(), ParseCommands(), ParseDont(), and zero().

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

Definition at line 342 of file mole.h.

Referenced by ParseSet(), and zero().

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

Definition at line 347 of file mole.h.

Referenced by mole_create_react(), ParseSet(), and zero().

bool t_mole_global::lgStancil

Definition at line 337 of file mole.h.

Referenced by diatomics::Cont_Diss_Heat_Rate(), CoolEvaluate(), diatomics::H2_X_sink_and_source(), diatomics::init(), diatomics::Mol_Photo_Diss_Rates(), mole_h_reactions(), OpacityAddTotal(), OpacityCreateAll(), ParseSet(), and zero().