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Data Structures
struct	t_atoms

Functions
void	AtomSeqBeryllium (double cs12, double cs13, double cs23, const TransitionProxy &t, double a30)

void	AtomSeqBoron (const TransitionProxy &t21, const TransitionProxy &t31, const TransitionProxy &t41, const TransitionProxy &t32, const TransitionProxy &t42, const TransitionProxy &t52, double cs51, double cs43, double cs53, double cd54, double pump_rate, const char *chLabel)

void	atom_level2 (const TransitionProxy &t)

void	atom_level3 (const TransitionProxy &t10, const TransitionProxy &t21, const TransitionProxy &t20)

double	atom_pop2 (double omega, double g1, double g2, double a21, double bltz, double abund)

double	atom_pop3 (double g1, double g2, double g3, double o12, double o13, double o23, double a21, double a31, double a32, double Tex12, double Tex23, realnum *pop2, double abund, double gam2, double r12, double r13)

void	atom_pop5 (const double g[], const double ex[], double cs12, double cs13, double cs14, double cs15, double cs23, double cs24, double cs25, double cs34, double cs35, double cs45, double a21, double a31, double a41, double a51, double a32, double a42, double a52, double a43, double a53, double a54, double p[], realnum abund, double Cooling, double CoolingDeriv, double pump12, double pump13, double pump14, double pump15)

void	atom_levelN (long int nlev, realnum abund, const double g[], const double ex[], char chExUnits, double pops[], double depart[], double *AulEscp, double col_str, double AulDest, double AulPump, double *CollRate, const double create[], const double destroy[], bool lgCollRateDone, double cooltl, double coolder, const char chLabel, int nNegPop, bool lgZeroPop, bool lgDeBug, bool lgLTE=false, multi_arr< double, 2 > Cool=NULL, multi_arr< double, 2 > dCooldT=NULL)

void	atom_oi_calc (double *coloi)

Variables
const int	N_OI_LEVELS = 6

const long	LIMLEVELN = 20L

t_atoms	atoms

Function Documentation

◆ atom_level2()

void atom_level2 ( const TransitionProxy & t )

atom_level2 do level population and cooling for two level atom

Parameters

t

Definition at line 17 of file atom_level2.cpp.

References ASSERT, atoms, EmissionProxy::Aul(), t_dense::cdsqte, chIonLbl(), CollisionProxy::col_str(), TransitionProxy::Coll(), EmissionProxy::ColOvTot(), t_rfield::ContBoltz, CollisionProxy::cool(), CoolAdd(), t_thermal::dCooldT, DEBUG_ENTRY, dense, t_atoms::DepLTELevels, TransitionProxy::Emis(), TransitionProxy::EnergyErg(), TransitionProxy::EnergyK(), g, t_thermal::halfte, CollisionProxy::heat(), TransitionProxy::Hi(), TransitionProxy::ipCont(), TransitionProxy::Lo(), EmissionProxy::ots(), EmissionProxy::Pdest(), EmissionProxy::Pelec_esc(), EmissionProxy::Pesc(), EmissionProxy::phots(), phycon, t_atoms::PopLevels, EmissionProxy::PopOpc(), EmissionProxy::pump(), rfield, sexp(), t_phycon::te, thermal, t_thermal::tsq1, TransitionProxy::WLAng(), EmissionProxy::xIntensity(), and t_dense::xIonDense.

Referenced by atom_level3(), CoolAlum(), CoolArgo(), CoolCalc(), CoolCarb(), CoolChlo(), CoolCoba(), CoolDima(), CoolEvaluate(), CoolIron(), CoolMagn(), CoolNeon(), CoolNitr(), CoolOxyg(), CoolPhos(), CoolPota(), CoolScan(), CoolSili(), CoolSodi(), CoolSulf(), and Fe2_cooling().

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◆ atom_level3()

void atom_level3	(	const TransitionProxy &	t10,
		const TransitionProxy &	t21,
		const TransitionProxy &	t20
	)

atom_level3 compute three level atom, 10, 21, and 20 are line

Parameters

t10
t21
t20

Todo:: 2 test on c checks whether collisions are possible at this temperature, should add photo excitation

Todo:: 2 these pops ARE NOT defined below

Definition at line 15 of file atom_level3.cpp.

References ASSERT, atom_level2(), atoms, EmissionProxy::Aul(), cdEXIT, t_dense::cdsqte, chIonLbl(), chLineLbl(), CollisionProxy::col_str(), TransitionProxy::Coll(), EmissionProxy::ColOvTot(), CollisionProxy::cool(), CoolAdd(), t_thermal::dCooldT, DEBUG_ENTRY, dense, t_atoms::DepLTELevels, t_dense::eden, TransitionProxy::Emis(), EN1RYD, TransitionProxy::EnergyErg(), TransitionProxy::EnergyK(), EXIT_FAILURE, fp_equal(), g, t_thermal::halfte, CollisionProxy::heat(), TransitionProxy::Hi(), ioQQQ, TransitionProxy::ipCont(), TransitionProxy::Lo(), MAX2, EmissionProxy::Pdest(), EmissionProxy::Pelec_esc(), EmissionProxy::Pesc(), EmissionProxy::phots(), phycon, t_rfield::plsfrq, t_atoms::PopLevels, EmissionProxy::PopOpc(), EmissionProxy::pump(), rfield, RT_OTS_AddLine(), ShowMe(), t_phycon::te, t_phycon::teinv, thermal, TotalInsanity(), t_thermal::tsq1, TransitionProxy::WLAng(), EmissionProxy::xIntensity(), and t_dense::xIonDense.

Referenced by CoolAlum(), CoolArgo(), CoolCarb(), CoolChlo(), CoolIron(), CoolMagn(), CoolNeon(), CoolNick(), CoolNitr(), CoolOxyg(), CoolPhos(), CoolPota(), CoolSili(), CoolSodi(), and CoolSulf().

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◆ atom_levelN()

void atom_levelN	(	long int	nlev,
		realnum	abund,
		const double	g[],
		const double	ex[],
		char	chExUnits,
		double	pops[],
		double	depart[],
		double ***	AulEscp,
		double ***	col_str,
		double ***	AulDest,
		double ***	AulPump,
		double ***	CollRate,
		const double	create[],
		const double	destroy[],
		bool	lgCollRateDone,
		double *	cooltl,
		double *	coolder,
		const char *	chLabel,
		int *	nNegPop,
		bool *	lgZeroPop,
		bool	lgDeBug,
		bool	lgLTE = `false`,
		multi_arr< double, 2 > *	Cool = `NULL`,
		multi_arr< double, 2 > *	dCooldT = `NULL`
	)

atom_levelN - compute populations of arbitrary n-level atom

Parameters

nlev	nlev is the number of levels to compute
abund	ABUND is total abundance of species, used for nth equation
g[]	G(ndim) is stat weight of levels
ex[]	EX(ndim) is excitation potential of levels, either wn or deg K 0 for first one, NOT d(ENER), but energy rel to ground
chExUnits	this is 'K' for above ex[] as Kelvin deg, is 'w' for wavenumbers
pops[]	populations of each level as deduced here
depart[]	departure coefficient derived here
AulEscp	net transition rate, A * esc prob, s-1
col_str	col str rom up to low
AulDest	AulDest(ilo,ihi) is destruction rate, from up to low, A * dest prob, [s-1], asserts confirm that ihi,lo is zero
AulPump	AulPump(lo, hi) is pumping rate, A * occ num, (hi,lo) must be zero, [s-1]
CollRate	collision rates, evaluated here and returned for cooling by calling function, unless following flag is true. If true then calling function has already filled in these rates. CollRate[i][j] is rate from i to j
create	this is an additional creation rate, normally zero, units cm-3 s-1
destroy[]	this is an additional destruction rate to continuum, normally zero, units s-1
lgCollRateDone	flag saying whether CollRate already done, or we need to do it here
cooltl	total cooling, set here but nothing done with it
coolder	derivative of cooling, set here but nothing done with it
chLabel	string used to identify calling program in case of error
lgNegPop	lgNegPop flag indicating what we have done positive if negative populations occurred zero if normal calculation done negative if too cold (for some atoms other routine will be called in this case)
lgZeroPop	true if populations are zero, either due to zero abundance of very low temperature
lgDeBug	option to print matrices for debugging

Postcondition: atoms.PopLevels[n], atoms.DepLTELevels[n] are set lines added to ots array

Definition at line 15 of file atom_leveln.cpp.

References abund, amat, ASSERT, AulDest, AulEscp, AulPump, BOLTZMANN, cdEXIT, t_dense::cdsqte, col_str, CollRate, conv, DEBUG_ENTRY, dense, depart, dsexp(), dynamics, ex, EXIT_FAILURE, g, t_thermal::halfte, ioQQQ, iteration, t_dynamics::lgAdvection, t_conv::lgSearch, t_trace::lgTrace, t_trace::lgTrLevN, MAX2, t_dynamics::n_initial_relax, phycon, pops, pow2(), sink, SMALLFLOAT, solve_system(), source, T1CM, t_phycon::te, t_phycon::te_wn, thermal, t_dynamics::timestep, TorF(), TotalInsanity(), trace, and t_thermal::tsq1.

Referenced by AtomSeqBoron(), dBase_solve(), Fe2_cooling(), Fe3Lev14(), Fe4Lev12(), and diatomics::H2_Level_low_matrix().

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◆ atom_oi_calc()

void atom_oi_calc ( double * coloi )

atom_oi drive the solution of OI level populations, Ly-beta pumping

Parameters

coloi

Todo:: 2 following needed to get badbugs/bug5.in to work

Definition at line 23 of file atom_oi.cpp.

References t_dense::AtomicWeight, atoms, EmissionProxy::Aul(), DEBUG_ENTRY, dense, TransitionList::Emis(), TransitionProxy::Emis(), fixit(), GetDopplerWidth(), ioQQQ, ipH1s, ipH3p, ipH_LIKE, ipHYDROGEN, ipOXYGEN, ipT1039, ipT1304, ipT4368, ipT8446, ipTO1025, ipTOI11, ipTOI13, ipTOI29, ipTOI46, iso_sp, t_rfield::lgInducProcess, t_trace::lgTr8446, t_trace::lgTrace, MAX2, MIN2, oi_level_pops(), EmissionProxy::Pelec_esc(), EmissionProxy::Pesc(), t_atoms::pmpo15, t_atoms::pmpo51, t_atoms::popoi, rfield, t_iso_sp::st, TauLines, trace, t_iso_sp::trans(), and t_dense::xIonDense.

Referenced by CoolOxyg().

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◆ atom_pop2()

double atom_pop2	(	double	omega,
		double	g1,
		double	g2,
		double	a21,
		double	bltz,
		double	abund
	)

atom_pop2 do level population for simple two level atom, no radiative transfer

Parameters

omega
g1
g2
a21
bltz
abund

Definition at line 9 of file atom_pop2.cpp.

References abund, ASSERT, t_dense::cdsqte, DEBUG_ENTRY, dense, phycon, and t_phycon::teinv.

Referenced by CoolChro(), CoolIron(), CoolMagn(), CoolNeon(), CoolScan(), CoolSili(), and ion_photo().

◆ atom_pop3()

double atom_pop3	(	double	g1,
		double	g2,
		double	g3,
		double	o12,
		double	o13,
		double	o23,
		double	a21,
		double	a31,
		double	a32,
		double	Tex12,
		double	Tex23,
		realnum *	pop2,
		double	abund,
		double	gam2,
		double	r12,
		double	r13
	)

atom_pop3 return value is population for 3-level atom, cm^-3

Parameters

g1	statictical weights of level 1
g2	statictical weights of level 2
g3	statictical weights of level 3
o12	collision strengths between three levels
o13	collision strengths between three levels
o23	collision strengths between three levels
a21	transition probabilities between three levels
a31	transition probabilities between three levels
a32	transition probabilities between three levels
Tex12	excitation energy in Kelvin
Tex23	excitation energy in Kelvin
*pop2	returned population of level 2, cm^-3
abund	incoming total abundance of ion
gam2	possible photodestruction of level 2, normally 0
r12	excitation rates (s-1) due to "other" processes
r13	excitation rates (s-1) due to "other" processes

Definition at line 10 of file atom_pop3.cpp.

References abund, ASSERT, atoms, t_atoms::c12, t_atoms::c13, t_dense::cdsqte, DEBUG_ENTRY, dense, ex, phycon, SMALLFLOAT, and t_phycon::te.

Referenced by CoolAlum(), CoolArgo(), CoolCarb(), CoolChlo(), CoolChro(), CoolNeon(), CoolNitr(), CoolOxyg(), CoolPhos(), CoolScan(), CoolSili(), CoolSodi(), and CoolSulf().

◆ atom_pop5()

void atom_pop5	(	const double	g[],
		const double	ex[],
		double	cs12,
		double	cs13,
		double	cs14,
		double	cs15,
		double	cs23,
		double	cs24,
		double	cs25,
		double	cs34,
		double	cs35,
		double	cs45,
		double	a21,
		double	a31,
		double	a41,
		double	a51,
		double	a32,
		double	a42,
		double	a52,
		double	a43,
		double	a53,
		double	a54,
		double	p[],
		realnum	abund,
		double *	Cooling,
		double *	CoolingDeriv,
		double	pump12,
		double	pump13,
		double	pump14,
		double	pump15
	)

atom_pop5 do populations and cooling for five level atom

Parameters

g[]
ex[]
cs12
cs13
cs14
cs15
cs23
cs24
cs25
cs34
cs35
cs45
a21
a31
a41
a51
a32
a42
a52
a43
a53
a54
p[]
abund
cooling
cooling	derivative
pump12
pump13
pump14
pump15

Definition at line 13 of file atom_pop5.cpp.

References abund, amat, ASSERT, cdEXIT, t_dense::cdsqte, DEBUG_ENTRY, dense, ERG1CM, EXIT_FAILURE, g, getrf_wrapper(), getrs_wrapper(), t_thermal::halfte, ioQQQ, MAX2, phycon, sexp(), T1CM, t_phycon::te, thermal, and t_thermal::tsq1.

Referenced by CoolArgo(), CoolCalc(), CoolChlo(), CoolNitr(), CoolOxyg(), and CoolSulf().

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◆ AtomSeqBeryllium()

void AtomSeqBeryllium	(	double	cs12,
		double	cs13,
		double	cs23,
		const TransitionProxy &	t,
		double	a30
	)

AtomSeqBeryllium compute level populations and emissivity for Be-sequence ions

Parameters

cs12
cs13
cs23
t
a30

Definition at line 13 of file atom_seq_beryllium.cpp.

References amat, ASSERT, atoms, EmissionProxy::Aul(), cdEXIT, t_dense::cdsqte, chIonLbl(), CollisionProxy::col_str(), TransitionProxy::Coll(), EmissionProxy::ColOvTot(), CollisionProxy::cool(), CoolAdd(), t_thermal::dCooldT, DEBUG_ENTRY, dense, t_atoms::DepLTELevels, TransitionProxy::Emis(), TransitionProxy::EnergyErg(), TransitionProxy::EnergyK(), EXIT_FAILURE, getrf_wrapper(), getrs_wrapper(), t_thermal::halfte, CollisionProxy::heat(), TransitionProxy::Hi(), ioQQQ, TransitionProxy::Lo(), EmissionProxy::Pdest(), EmissionProxy::Pelec_esc(), EmissionProxy::Pesc(), EmissionProxy::phots(), phycon, t_atoms::PopLevels, EmissionProxy::PopOpc(), EmissionProxy::pump(), t_phycon::te, thermal, t_thermal::tsq1, TransitionProxy::WLAng(), EmissionProxy::xIntensity(), and t_dense::xIonDense.

Referenced by CoolAlum(), CoolCarb(), CoolNeon(), CoolNitr(), CoolOxyg(), CoolSili(), and CoolSulf().

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◆ AtomSeqBoron()

void AtomSeqBoron	(	const TransitionProxy &	t21,
		const TransitionProxy &	t31,
		const TransitionProxy &	t41,
		const TransitionProxy &	t32,
		const TransitionProxy &	t42,
		const TransitionProxy &	t52,
		double	cs51,
		double	cs43,
		double	cs53,
		double	cd54,
		double	pump_rate,
		const char *	chLabel
	)

AtomSeqBoron compute cooling from 5-level boron sequence model atom

Parameters

t21
t31
t41
t32
t42
t52
cs51
cs43
cs53
cd54
pump_rate	pump rate due to UV permitted lines
chLabel	string used to identify calling program in case of error

Todo:: 2 use transition::Zero here

Definition at line 11 of file atom_seq_boron.cpp.

References ASSERT, atom_levelN(), atoms, EmissionProxy::Aul(), AulDest, AulEscp, AulPump, CollisionProxy::col_str(), col_str, TransitionProxy::Coll(), CollRate, EmissionProxy::ColOvTot(), CollisionProxy::cool(), CoolAdd(), t_thermal::dCooldT, DEBUG_ENTRY, dense, depart, t_atoms::DepLTELevels, TransitionProxy::Emis(), TransitionProxy::EnergyErg(), TransitionProxy::EnergyK(), g, t_thermal::halfte, CollisionProxy::heat(), TransitionProxy::Hi(), lgFirst, LIMLEVELN, TransitionProxy::Lo(), MALLOC, N_SEQ_BORON, EmissionProxy::Pdest(), EmissionProxy::Pelec_esc(), EmissionProxy::Pesc(), EmissionProxy::phots(), t_atoms::PopLevels, EmissionProxy::PopOpc(), pops, EmissionProxy::pump(), SDIV(), thermal, t_thermal::tsq1, TransitionProxy::WLAng(), EmissionProxy::xIntensity(), and t_dense::xIonDense.

Referenced by CoolCarb(), CoolNitr(), CoolOxyg(), CoolSili(), and CoolSulf().

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Variable Documentation

◆ atoms

t_atoms atoms

extern

Definition at line 5 of file atoms.cpp.

Referenced by atom_level2(), atom_level3(), atom_oi_calc(), atom_pop3(), AtomSeqBeryllium(), AtomSeqBoron(), ContCreatePointers(), CoolAlum(), CoolCarb(), CoolMagn(), CoolNeon(), CoolNitr(), CoolOxyg(), CoolSili(), CoolSulf(), create_isotopologues_one(), Fe2_cooling(), Fe3Lev14(), Fe4Lev12(), GrainsInit(), InitSimPostparse(), ion_photo(), IterRestart(), IterStart(), lines_lv1_li_ne(), oi_level_pops(), OpacityAddTotal(), PrtComment(), and zero().

◆ LIMLEVELN

const long LIMLEVELN = 20L

Definition at line 237 of file atoms.h.

Referenced by AtomSeqBoron(), Fe2_cooling(), Fe3Lev14(), and Fe4Lev12().

◆ N_OI_LEVELS

const int N_OI_LEVELS = 6

number of levels in OI atom

Definition at line 236 of file atoms.h.

Referenced by IterStart(), and zero().

Data Structures

Functions

Variables

Function Documentation

◆ atom_level2()

◆ atom_level3()

◆ atom_levelN()

◆ atom_oi_calc()

◆ atom_pop2()

◆ atom_pop3()

◆ atom_pop5()

◆ AtomSeqBeryllium()

◆ AtomSeqBoron()

Variable Documentation

◆ atoms

◆ LIMLEVELN

◆ N_OI_LEVELS