#include <mole.h>

Collaboration diagram for t_mole_global:

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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

◆ MoleculeList

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

Definition at line 316 of file mole.h.

Member Function Documentation

◆ init()

void t_mole_global::init ( void )

Definition at line 11 of file mole.cpp.

References DEBUG_ENTRY, make_species(), mole, mole_global, mole_make_groups(), mole_make_list(), num_total, and t_mole_local::species.

Referenced by InitSimPostparse().

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◆ make_species()

void t_mole_global::make_species ( void )

Definition at line 140 of file mole_species.cpp.

References ASSERT, t_co::C12_C13_isotope_ratio, t_co::C12_C13_isotope_ratio_parsed, molecule::charge, CHARS_ION_STAGE, CHARS_ISOTOPE_SYM, t_elementnames::chElementSym, co, DEBUG_ENTRY, molezone::den, dense, deut, ELECTRON_MASS, element_list, elementnames, diatomics::ENERGY_H2_STAR, findatom(), findspecies(), fixit(), t_dense::gas_phase, gv, h2, hmi, molecule::index, InitDeuteriumIonization(), ipCARBON, ipHYDROGEN, KJMOL1CM, 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(), null_atom, null_element, null_mole, null_molezone, num_calc, num_total, OTHER, read_species_file(), ReadIsotopeFractions(), SDIV(), SetDeuteriumFractionation(), SetGasPhaseDeuterium(), and unresolved_atom_list.

Referenced by init().

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◆ sort() [1/2]

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

static

Definition at line 99 of file mole_species.cpp.

References start().

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◆ sort() [2/2]

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

static

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

◆ zero()

void t_mole_global::zero ( void )

mole_zero allocate + initialize workspace

Definition at line 36 of file mole.cpp.

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

Referenced by InitSimPostparse().

Field Documentation

◆ lgFederman

bool t_mole_global::lgFederman

Definition at line 288 of file mole.h.

Referenced by mole_create_react(), ParseSet(), and 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

Definition at line 308 of file mole.h.

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

◆ lgH2Ozer

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().

◆ lgLeidenHack

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().

◆ 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

Definition at line 304 of file mole.h.

Referenced by ParseSet(), and zero().

◆ lgNoHeavyMole

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().

◆ lgNoMole

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().

◆ 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

Definition at line 294 of file mole.h.

Referenced by ParseSet(), and 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

Definition at line 299 of file mole.h.

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

◆ lgStancil

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().

◆ lgTreatIsotopes

vector<bool> t_mole_global::lgTreatIsotopes

Definition at line 311 of file mole.h.

Referenced by make_species(), newspecies(), ParseSet(), and zero().

◆ list

◆ num_calc

int t_mole_global::num_calc

Definition at line 314 of file mole.h.

Referenced by atmdat_readin(), ChemImportance(), ConvBase(), ConvIterCheck(), CoolEvaluate(), DynaCreateArrays(), DynaIonize(), DynaNewStep(), DynaSaveLast(), DynaStartZone(), eden_sum(), funjac(), HeatSum(), iter_end_check(), IterRestart(), IterStart(), lgNucleiConserved(), make_species(), molcol(), mole_eval_balance(), mole_eval_dynamic_balance(), mole_h_fixup(), mole_h_rate_diagnostics(), mole_make_groups(), mole_make_list(), mole_return_cached_species(), mole_solve(), mole_update_limiting_reactants(), newspecies(), OpacityAddTotal(), PrtColumns(), PrtComment(), PrtZone(), radius_increment(), radius_next(), RT_diffuse(), RT_tau_reset(), SaveDo(), state_get_put(), total_molecule_deut(), total_molecule_elems(), total_molecules(), total_molecules_gasphase(), total_network_elems(), and GroupMap::updateMolecules().

◆ num_compacted

int t_mole_global::num_compacted

Definition at line 314 of file mole.h.

Referenced by funjac(), grouped_elems(), mole_make_groups(), mole_solve(), GroupMap::setup(), and GroupMap::updateMolecules().

◆ num_total

int t_mole_global::num_total

flag saying whether an element is in the chemistry network

Definition at line 314 of file mole.h.

Referenced by AbundChange(), atmdat_readin(), funjac(), init(), make_species(), mole_cmp_num_in_out_reactions(), mole_effects(), mole_make_list(), mole_return_cached_species(), mole_update_sources(), mole_update_species_cache(), newspecies(), plot_sparsity(), ScaleAllDensities(), t_mole_local::set_location(), GroupMap::setup(), and zero().

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

/home/iurt/rpmbuild/BUILD/c13.05/source/mole.h
/home/iurt/rpmbuild/BUILD/c13.05/source/mole.cpp
/home/iurt/rpmbuild/BUILD/c13.05/source/mole_species.cpp

Public Types

Public Member Functions

Static Public Member Functions

Data Fields

Detailed Description

Member Typedef Documentation

◆ MoleculeList

Member Function Documentation

◆ init()

◆ make_species()

◆ sort() [1/2]

◆ sort() [2/2]

◆ zero()

Field Documentation

◆ lgFederman

◆ lgGrain_mole_deplete

◆ lgH2Ozer

◆ lgLeidenHack

◆ lgNeutrals

◆ lgNoHeavyMole

◆ lgNoMole

◆ lgNonEquilChem

◆ lgProtElim

◆ lgStancil

◆ lgTreatIsotopes

◆ list

◆ num_calc

◆ num_compacted

◆ num_total