t_mole_global Class Reference

#include <mole.h>

Collaboration diagram for t_mole_global:

Public Types
typedef vector< count_ptr < molecule > >	MoleculeList
Public Member Functions
void	init (void)
void	make_species (void)
void	zero (void)
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

Detailed Description

>>chng 03 feb 09, rm ipH3P_hev, since not used, and decrement NUM_HEAVY_MOLEC to 17 
 >>chng 03 aug 04, rm ipCTWO and ipC2P from den since not included in balance,
 and always finds zero column density, so NUM_HEAVY_MOLEC from 17 to 15 
 >>chng 03 aug 05, rm ch2 and ch3, so n from 15 to 13 
 >>chng 03 nov 14  add Si chemistry & CH3+, so that now every
     reaction that is in the TH85 chemical network is also included
     in Cloudy.  Additionally, there are also reactions taken from other
     papers (mostly Hollenbach and McKee...see co.c).  In all 20 molecular
     species are calculated, along with the atomic and first ionization 
	 stages of C, O, and Si
 >>chng 04 May 13, Nick Abel.  Add CH3, CH4, CH4+, and CH5+ to network in order 
	to get the same chemical abundances vs. depth as other PDR codes in the Leiden
	meeting.  With changes we now can predict molecular abundances for 24 C, O, 
	and Si bearing molecules. 

 >>chng 04 jul 13, Nick Abel.  Add nitrogen and sulphur bearing molecules
    to the chemical network.  First added to generate a chemical model for
    eta carinae, but is applicable to all molecular clouds 

 >>chng 05 mar 11, Nick Abel.  Add C2 and C2+ to chemistry, reactions 
    involving these species affects the abundance of C

 >>chng 05 mar 23, Nick Abel.  Add Chlorine to chemistry

this includes the atomic and first ionized species of each element that can combine to form molecules. This is the number of molecules, ions, and atoms that the co network uses This is used in comole to improve the calculation, as deep in molecular regions reactions with molecules can be important to the ionization balance

Definition at line 266 of file mole.h.

Member Typedef Documentation

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

Definition at line 316 of file mole.h.

Member Function Documentation

void t_mole_global::init ( void )

Definition at line 11 of file mole.cpp.

References DEBUG_ENTRY, 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 139 of file mole_species.cpp.

References ASSERT, molecule::charge, CHARS_ION_STAGE, CHARS_ISOTOPE_SYM, t_elementnames::chElementSym, DEBUG_ENTRY, molezone::den, dense, deut, ELECTRON_MASS, element_list, elementnames, findspecies(), fixit(), t_dense::gas_phase, gv, 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(), num_calc, num_total, OTHER, read_species_file(), ReadIsotopeFractions(), SetDeuteriumFractionation(), SetGasPhaseDeuterium(), and unresolved_atom_list.

Referenced by init().

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void t_mole_global::sort	(	molecule **	start,
		molecule **	end
	)			`[static]`

Definition at line 98 of file mole_species.cpp.

References sort().

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

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

void t_mole_global::zero ( void )

mole_zero allocate + initialize workspace

Definition at line 36 of file mole.cpp.

References cdEXIT, DEBUG_ENTRY, EXIT_FAILURE, ioQQQ, num_total, and t_mole_local::species.

Referenced by InitSimPostparse().

Field Documentation

bool t_mole_global::lgFederman

Definition at line 288 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 308 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 283 of file mole.h.

Referenced by PrtComment(), and zero().

bool t_mole_global::lgLeidenHack

set rates to that in UMIST

Definition at line 286 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 304 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 280 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 277 of file mole.h.

Referenced by ConvInitSolution(), CoolEvaluate(), ion_trim(), 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 294 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 299 of file mole.h.

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

bool t_mole_global::lgStancil

Definition at line 289 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().