Atom Class Reference

Inherits object.

Public Member Functions
def	__init__
def	getOmega
def	getCollRates
def	getTransition
def	printTransition (self, wave)
def	printSources (self)
def	getSources (self)
def	getA
def	getPopulations
def	getLowDensRatio
def	getHighDensRatio
def	getDensityRange
def	getCritDensity
def	getEmissivity
def	getTemDen
def	getIonAbundance
def	printIonic
def	printTemDen
def	plotEmiss
def	plotGrotrian
def	__repr__ (self)

Public Attributes
	log_
	type
	is_valid
	atom
	elem
	spec
	name
	Z
	IP
	IP_up
	calling
	NLevels
	atomFileType
	AtomData
	atomFile
	atomPath
	atomFitsFile
	atomFitsPath
	wave_Ang
	getStatWeight
	getEnergy
	atomNLevels
	collFileType
	CollData
	CollHeader
	getOmegaArray
	getTemArray
	collFile
	collPath
	collFitsFile
	collFitsPath
	collNLevels
	tem_units
	gs
	AtomHeader
	NIST
	lineList
	energy_Ryd
	energy_eV
	EnergyNLevels
	source

Detailed Description

Define the atom object, fill it with data, explore the data, and 
compute quantities such as level populations and line emissivities.

Constructor & Destructor Documentation

def __init__	(		self,
			elem = None,
			spec = None,
			atom = None,
			OmegaInterp = 'Linear',
			noExtrapol = False,
			NLevels = None
	)

Atom constructor

Parameters:
    - elem          symbol of the selected element
    - spec          ionization stage in spectroscopic notation (I = 1, II = 2, etc.)
    - atom          ion (e.g. 'O3').
    - OmegaInterp   one of ('Cheb', 'Linear'). Default is Linear. "Cheb" works only for fits files. 
    - noExtrapol    if set to False (default), Omega will be extrapolated above and below
            the highest and lowest temperatures where it is defined. If set to True
            a NaN will be return.
    
Usage:
    O3 = pn.Atom('O',3)
    N2 = pn.Atom(atom='N2')
    S2 = pn.Atom(atom='S2', OmegaInterp='Linear')

Member Function Documentation

def __repr__

(

self

)

def getA	(		self,
			lev_i = -1,
			lev_j = -1,
			wave = -1
	)

Return the transition probability data. 
If no arguments are given, the whole array of A is returned.
A specific A value can be obtained by giving either the upper and lower levels or 
    the wavelength of the transition (keyword wave).
    
Usage:
    A_O3 = O3.getA()          # The whole A array is stored in A_O3
    O3.getA(4, 2)      # A(4, 2) of the O3 atom is printed
    O3.getA(2, 4)      # Returns 0
    O3.getA(wave=4959)      

Parameters:
    - lev_i  upper level of transition (default= -1, returns complete array)
    - lev_j  lower level of transition (default= -1, returns complete array)
    - wave   wavelength of transition. Takes precedence on lev_i and lev_j. Ignored if not set.

def getCollRates	(		self,
			tem,
			NLevels = None
	)

Return (n_levels x n_levels) array of collision rates at given temperature. 

Usage:
    O3.getCollRates(tem=10000)
    O3.getCollRates([8e3, 1e4, 1.2e4])

Parameters:
    - tem     electronic temperature in K. May be an array.

def getCritDensity	(		self,
			tem,
			level = -1
	)

Return the critical density of selected level at given temperature. 
If no transition is selected, return complete array.

Usage:
    O3.getCritDensity(12000)
    O3.getCritDensity(12000, 4)

Parameters:
    - tem    electronic temperature in K. May be an array.
    - level  selected atomic level (default= -1)

def getDensityRange	(		self,
			lev_i1 = -1,
			lev_i2 = -1,
			lev_j1 = -1,
			lev_j2 = -1,
			wave1 = -1,
			wave2 = -1,
			to_eval = None,
			tol = 0.1,
			tem = 1e4
	)

Return the range of density where a given line ratio is between 10% and 90% of the low and high density limits

def getEmissivity	(		self,
			tem,
			den,
			lev_i = -1,
			lev_j = -1,
			wave = -1,
			product = True
	)

Return the line emissivity of selected transition or complete array of emissivities
The transition is selected by the argument wave (if given); 
if wave is not supplied, it is selected by the upper and lower levels (lev_i and lev_j); 
if neither is given, the whole array is computed

Usage:      
    O3.getEmissivity(12000, 100, 4, 2)         # (4, 2) transition
    O3.getEmissivity(10000, 10000, wave=5007)  # (4, 2) transition
    O3.getEmissivity(12000, 100)               # all transitions
    O3.getEmissivity([10000, 12000], [100, 500], 4, 2)
    O3.getEmissivity([10000, 12000], [100, 500])
    
Parameters:
    - tem      electronic temperature in K. May be an array.
    - den      electronic density in cm^-3. May be an array.
    - lev_i    upper level (default= -1)
    - lev_j    lower level (default= -1)
    - wave     wavelength of transition. Takes precedence on lev_i and lev_j if set, 
        ignored otherwise. It can also be a blend label.
    - product  Boolean. If True (default), all the combination of (tem, den) are used. 
         If False, tem and den must have the same size and are joined.

def getHighDensRatio	(		self,
			lev_i1 = -1,
			lev_i2 = -1,
			lev_j1 = -1,
			lev_j2 = -1,
			wave1 = -1,
			wave2 = -1,
			to_eval = None
	)

Return the value of a diagostic ratio at the high density limit
S2.getHighDensRatio(lev_i1 = 3, lev_i2 = 2)
S2.getHighDensRatio(wave1 = 6716, wave2 = 6731)
S2.getHighDensRatio(to_eval = 'L(6716)/L(6731)')

def getIonAbundance	(		self,
			int_ratio,
			tem,
			den,
			lev_i = -1,
			lev_j = -1,
			wave = -1,
			to_eval = None,
			Hbeta = 100.
	)

Compute the ionic abundance relative to H+ given the intensity of a line or sum of lines, 
the temperature, and the density. 
The line can be specified as a transition (i.e., giving the two atomic level involved), 
as a wavelength, or as an algebraic expression. In the last case, a sum of lines 
can also be supplied.

Usage:
    O3.getIonAbundance(100, 1.5e4, 100., wave=5007)
    O3.getIonAbundance(130, 1.5e4, 100., to_eval='I(4,3) + I(4,2)')
    O3.getIonAbundance(np.array([100, 150]), np.array([1.5e4, 1.2e4]), np.array([100., 120]), 
wave=5007)
    O2.getIonAbundance(int_ratio=100, tem=1.5e4, den=100., to_eval='L(3726)+L(3729)')

    
Parameters:
    - int_ratio    relative line intensity (default normalization: Hbeta = 100). 
            May be an array.
    - tem          electronic temperature in K. May be an array.
    - den          electronic density in cm^-3. May be an array.
    - lev_i        upper level of transition
    - lev_j        lower level of transition
    - wave         wavelength of transition. Takes precedence on lev_i and lev_j if set, 
            ignored otherwise 
    - to_eval      expression to be evaluated. Takes precedence on wave if set, 
            ignored otherwise.
    - Hbeta        line intensity normalization at Hbeta (default Hbeta = 100)

def getLowDensRatio	(		self,
			lev_i1 = -1,
			lev_i2 = -1,
			wave1 = -1,
			wave2 = -1,
			to_eval = None
	)

Return the value of a diagostic ratio at the low density limit
S2.getLowDensRatio(lev_i1 = 3, lev_i2 = 2)
S2.getLowDensRatio(wave1 = 6716, wave2 = 6731)
S2.getLowDensRatio(to_eval = 'L(6716)/L(6731)')

def getOmega	(		self,
			tem,
			lev_i = -1,
			lev_j = -1,
			wave = -1
	)

Return interpolated value of the collision strength value at the given temperature 
    for the complete array or a specified transition.
If kappa is not None (non-maxwellian distribution of e-velocities), the collision 
    strength is corrected as in Mendoza & Bautista, 2014 ApJ 785, 91.

Usage:
    O3.getOmega(15000.)
    O3.getOmega([8e3, 1e4, 1.2e4])
    O3.getOmega([8e3, 1e4, 1.2e4], 5, 4)

Parameters:
    - tem    electronic temperature in K. May be an array.
    - lev_i  upper level
    - lev_j  lower level

def getPopulations	(		self,
			tem,
			den,
			product = True,
			NLevels = None
	)

Return array of populations at given temperature and density.
The method returns a 1-, 2- or 3-D array containing the population of each level 
    for all temperatures and densities specified in the input vectors tem and den 
    (which can be n-element or 1-element vectors).
If either quantity (tem or den) is a 1-element vector -that is, a single value-, 
    the resulting population array is collapsed along that dimension; 
    as a result, the result population array can be a 1-D, 2-D or 3-D array 
    (the three cases corresponding to situations in which both tem and den are single values; 
    one of them is a single value and the other an n-element vector; or both are multielement 
    vectors, respectively). In the general case, the level index is the first 
    [WARNING! It is not in physical unit, i.e. ground level = 0; to be normalized], 
    followed by the temperature index (if it exists) and the density index. 

Usage:
    O3.getPopulations(1e4, 1e2)
    tem=np.array([10000., 12000., 15000., 20000]) # An array of four temperatures
    den=np.array([600., 800., 1000])      # An array of three densities
    O3.getPopulations(tem, den)           # is a (6, 4, 3) array
    O3.getPopulations(tem, den)[0,2,1]    # Returns the population of level 1 for T = 15000 
                                    and Ne = 800
    tem = 20000                           # tem is no longer an array
    O3.getPopulations(tem, den)[0,2,1]  # Crashes: one index too much
    O3.getPopulations(tem, den)[0,1]    # Returns the population of level 1 for T = 20000 
                                    and Ne = 800 [see warning]
    tem=np.array([10000., 15000., 20000]) # An array of three temperatures
    O3.getPopulations(tem, den, product = False)# is a (6, 3) array, tem and den beeing 
                                            taken 2 by 2.

Parameters:
    - tem       electronic temperature in K
    - den       electronic density in cm^-3
    - product   operate on all possible combinations of temperature and density 
      (product = True, default case) or on those resulting from combining 
      the i-th value of tem with the i-th value of den (product = False).
      If product = False, then tem and den must be the same size.

def getSources

(

self

)

def getTemDen	(		self,
			int_ratio,
			tem = -1,
			den = -1,
			lev_i1 = -1,
			lev_j1 = -1,
			lev_i2 = -1,
			lev_j2 = -1,
			wave1 = -1,
			wave2 = -1,
			maxError = 1.e-3,
			method = 'nsect_recur',
			log = True,
			start_x = -1,
			end_x = -1,
			to_eval = None,
			nCut = 30,
			maxIter = 20
	)

Return either the temperature or the density given the other variable for a selected line ratio 
    of known intensity.
The line ratio can involve two or more than two lines. 
In the first case (only two lines), it can be specified giving either two transitions 
    (four atomic levels, i.e. two for each transition), or two wavelengths.
In the general case (any number of lines), it can be specified as an algebraic expression 
    to be evaluated, involving either atomic levels or wavelengths.
An array of values, rather than a single value, can also be given, in which case the result 
    will also be an array.
    
Usage: 
    O3.getTemDen(150., den=100., wave1=5007, wave2=4363, maxError=1.e-2)
    O3.getTemDen(150., den=100., to_eval = '(I(4,3) + I(4,2) + I(4,1)) / I(5,4)')
    N2.getTemDen(150., den=100., to_eval = '(L(6584) + L(6548)) / L(5755)')
    O3.getTemDen([0.02, 0.04], den=[1.e4, 1.1e4], to_eval="I(5, 4) / (I(4, 3) + I(4, 2))")

Parameters:
    - int_ratio    intensity ratio of the selected transition
    - tem          electronic temperature
    - den          electronic density
    - lev_i1       upper level of 1st transition
    - lev_j1       lower level of 1st transition
    - lev_i2       upper level of 2nd transition
    - lev_j2       lower level of 2nd transition
    - wave1        wavelength of 1st transition
    - wave2        wavelength of 2nd transition
    - maxError     tolerance on difference between input and computed ratio 
    - method       numerical method for finding the root (nsect_recur, nsect_iter)
    - log          switch of log (default = True). start_x and end_x are using this parameter.
    - start_x      lower end of the interval to explore. (default: lower end of collision 
            strength temperature array for temperature, 1 if density)
    - end_x        higher end of the interval to explore. (default: higher end of collision 
            strength temperature array for temperature, 1e8 if density)
    - to_eval      expression to be evaluated, using either I (for transitions identified 
            through atomic levels) or L (for transitions identified through wavelengths)
    - nCut        number of sections in which each step is cut. 2 would be dichotomy.
    - maxIter     maximum number of iterations

def getTransition	(		self,
			wave,
			maxErrorA = 5.e-3,
			maxErrorm = 5.e-2
	)

Return the indexes (upper level, lower level) of a transition for a given atom 
    from the wavelength.

Usage:
    O3.getTransition(4959)
    
Parameters:
    - wave      wavelength in Angstrom (a float or a label: e.g., 5007, '5007A') 
or in micron (a label: '51.5m')
    - maxErrorA: tolerance if the input wavelength is in Angstrom
    - maxErrorm: tolerance if the input wavelength is in micron

def plotEmiss	(		self,
			tem_min = 1000,
			tem_max = 30000,
			ionic_abund = 1.0,
			den = 1e3,
			style = '-',
			legend_loc = 4,
			temLog = False,
			plot_total = False,
			plot_only_total = False,
			legend = True,
			total_color = 'black',
			total_label = 'TOTAL',
			ax = None
	)

Plot the emissivity as a function of temperature of all the lines of the selected atom.  

Usage: 
    O3.plotEmiss(tem_min=10000, tem_max=20000)

Parameters:
    - tem_min         minimum value of the temperature range to span (default=1000)
    - tem_max         maximum value of the temperature range to span (default=30000)
    - ionic_abund     relative ionic abundance (default = 1.0)
    - den             electron density
    - style           line style of the plot (default: '-' [solid line])
    - legend_loc      localization of the legend (default: 4 = lower right; see plt.legend 
                for more details)
    - temLog          linear (False) or logarithmic temperature axis (default = False)
    - plot_total      flag to also plot total emissivity (default = False)
    - plot_only_total flag to only plot total emissivity (default = False)
    - legend          flag to place legend (default = True)
    - total_color     color of the total emissivity (default = 'black')
    - total_label     label of the total emissivity (default = 'TOTAL')
    - ax              axis where to send the plot. If None, a new axis is done

def plotGrotrian	(		self,
			tem = 1e4,
			den = 1e2,
			thresh_int = 1e-3,
			unit = 'eV',
			detailed = False,
			ax = None
	)

Draw a Grotrian plot of the selected atom, labelling only lines above a
pecified intensity threshold (relative to the most intense line). 
For ground state levels, the Russell-Saunders term symbol is also given.

Usage:
    O3.plotGrotrian()

Parameters:
    - tem          temperature at which the intensity threshold is to be computed 
    - den          density at which the intensity threshold is to be computed 
    - thresh_int   intensity threshold (relative to the most intense line, default: 1.e-3)
    - unit         one of 'eV' (default), '1/Ang' or 'Ryd'
    - ax           axis where to plot the result

def printIonic	(		self,
			tem = None,
			den = None,
			printA = False,
			printPop = True,
			printCrit = True
	)

Print miscellaneous information (wavelengths, level populations, emissivities, 
    critical densities) for given physical conditions.
If an electron temperature is given, level critical densities can be printed 
    (using printCrit=True)
If an electron density is also given, line emissivities (also for Hbeta) are printed and level 
    populations can be printed (using printPop=True)

Usage:
    O3.printIonic()
    O3.printIonic(printA=True)
    O3.printIonic(tem=10000., printCrit=True)
    O3.printIonic(tem=10000., den=1e3, printA=True, printPop=True, printCrit=True)

Parameters:
    - tem          temperature
    - den          density
    - printA       also print transition probabilities (default=False)
    - printPop     also print level populations (needs tem and den)
    - printCrit    also print critical densities (needs tem)

def printSources

(

self

)

def printTemDen	(		self,
			int_ratio,
			tem = -1,
			den = -1,
			lev_i1 = -1,
			lev_j1 = -1,
			lev_i2 = -1,
			lev_j2 = -1,
			wave1 = -1,
			wave2 = -1,
			maxError = 1.e-3,
			method = 'nsect_recur',
			log = True,
			start_x = -1,
			end_x = -1,
			to_eval = None,
			nCut = 30,
			maxIter = 20
	)

Print result of getTemDen function. See getTemDen for more details.

Usage:
    O3.printTemDen(100, tem=10000, wave1=5007, wave2=4363)

Parameters:
    - int_ratio    intensity ratio of the selected transition
    - tem          electronic temperature
    - den          electronic density
    - lev_i1       upper level of 1st transition
    - lev_j1       lower level of 1st transition
    - lev_i2       upper level of 2nd transition
    - lev_j2       lower level of 2nd transition
    - wave1        wavelength of 1st transition
    - wave2        wavelength of 2nd transition
    - maxError     tolerance on difference between input and computed ratio 
    - method       numerical method for finding the root (nsect_recur, nsect_iter)
    - log          log switch (default = True)
    - start_x      lower end of the interval to explore (default: lower end of collision 
            strength temperature array)
    - end_x        higher end of the interval to explore (default: higher end of collision 
            strength temperature array)
    - to_eval      expression to be evaluated, using either I (for transitions identified through 
            atomic levels) or L (for transitions identified through wavelengths)
    - nCut        number of sections in which each step is cut. 2 would be dichotomy.
    - maxIter     maximum number of iterations

def printTransition	(		self,
			wave
	)

Print info on transition associated to input wavelength.

Usage:
    O3.printTransition(4959)
    
Parameters:
    - wave      wavelength in Angstrom (a float or a label: e.g., 5007, '5007A') 
or in micron (a label: '51.5m')

Member Data Documentation

atom

AtomData

atomFile

atomFileType

atomFitsFile

atomFitsPath

AtomHeader

atomNLevels

atomPath

calling

CollData

collFile

collFileType

collFitsFile

collFitsPath

CollHeader

collNLevels

collPath

elem

energy_eV

energy_Ryd

EnergyNLevels

getEnergy

getOmegaArray

getStatWeight

getTemArray

gs

IP

IP_up

is_valid

lineList

log_

name

NIST

NLevels

source

spec

tem_units

type

wave_Ang

Z