atomdb module

This modules is designed to interact with the main atomic database, extracting real values of coefficients and so on.

The atomdb module contains several routines for interfacing with the AtomDB database to extract useful physical quantities, line lists, write new fits files and more. It is currently a dump of everything I’ve done with AtomDB. This should all be considered unstable and possibly susceptible to being wrong. It will be fixed, including moving many routines out of this library, as time goes on.

Version 0.1 - initial release Adam Foster July 17th 2015

Version 0.2 - added PI reading routines and get_data online enhancements. Adam Foster August 17th 2015

Version 0.3 - added RRC generation routines Adam Foster August 28th 2015

pyatomdb.atomdb.calc_rad_rec_cont(Z, z1, z1_drv, T, ebins, abund=1.0, ion_pop=1.0, settings=False, datacache=False)[source]

Calculate the radiative recombination continuum for an ion at temperature T

Parameters:

Zint: nuclear charge
z1int: recombined ion charge+1
z1_drvint: recombining ion charge+1
Tfloat: temperautre (K)
ebinsarray(float): energy bins (in keV) on which to caclulate the spectrum
abundfloat: elemental abundance, relative to hydrogen
ion_popfloat: the ion’s population fraction of that element (i.e. sum of all ion_pop for an element = 1)

Returns:

array(float): RRC in photons cm^3 s^-1 bin^-1, in an array of length(ebins)-1
array(float): Recombination rates into the excited levels, in s-1

pyatomdb.atomdb.calc_rrc(Z, z1, eedges, Te, lev, xstardat=False, xstarlevfinal=1, settings=False, datacache=False, returntotal=False)[source]

Calculate the radiative recombination continuum for a given ion

Parameters:

Zint: Atomic number
z1int: recombined ion charge
eedgesarray(float): the bin edges for the spectrum to be calculated on (keV)
Tefloat: The electron temperature (K)
levint: The level of the ion for the recombination to be calculated into
xstardatdict or HDUList: The xstar PI data. This can be an already sorted dictionary, as returned by sort_xstar_data, or the raw results of opening the PI file
xstarlevfinalint: If you need to identify the recombining level, you can do so here. Should normally be 1.
settingsdict: See description in read_data
datacachedict: See description in read_data
returntotalbool: If true, return the total recombination rate as well

Returns:

array(float): The rrc in photons cm^3 s^-1 keV^-1
optional float: If returntotal is set, also return total RRC calculated by separate integral from the ionization edge to infinity.

pyatomdb.atomdb.calc_two_phot(wavelength, einstein_a, lev_pop, ebins)[source]

Calculate two photon spectrum

Parameters:

wavelengthfloat: Wavelength of the transition (Angstroms)
einstein_afloat: The Einstein_A paramater for the transition
lev_popfloat: The level population for the upper level
ebinsarray(float): The bin edges for the spectrum (in keV)

Returns:

array(float): The flux in photons cm-3 s-1 bin-1 array is one element shorter than ebins.

pyatomdb.atomdb.format_level(level)[source]

Take the output of a level from a level file and format it nicely

Parameters:

levelarray: The single line from an atomdb LV file corresponding to a level

Returns:

str: The formatted string.

pyatomdb.atomdb.get_abundance(abundfile=False, abundset='AG89', element=[-1], datacache=False, settings=False, show=False)[source]

Get the elemental abundances, relative to H (H=1.0)

Parameters:

abundfilestring

special abundance file, if not using the default from filemap

abundsetstring

Abundance set. To list those available, set to one that doesn’t exist (suggest “list”). Available:

Allen: Allen, C. W. Astrophysical Quantities, 3rd Ed., 1973 (London: Athlone Press)
AG89: Anders, E. and Grevesse, N. 1989, Geochimica et Cosmochimica Acta, 53, 197
GA88: Grevesse, N, and Anders, E.1988, Cosmic abundances of matter, ed. C. J. Waddington, AIP Conference, Minneapolis, MN
Feldman: Feldman, U., Mandelbaum, P., Seely, J.L., Doschek, G.A.,Gursky H., 1992, ApJSS, 81,387

Default is AG89

elementlist of int

Elements to find abundance for. If not specified, return all.

datacachedict

See get_data

settingssettings

See get_data

showbool

If set to true, print available abundances and their references to the screen.

Returns:

dict

abundances in dictionary, i.e :

{1: 1.0,

2: 0.097723722095581111,

3: 1.4454397707459272e-11,

4: 1.4125375446227541e-11,

5: 3.9810717055349735e-10,

6: 0.00036307805477010178,…

pyatomdb.atomdb.get_data(Z, z1, ftype, datacache=False, settings=False, indexzero=False, offline=False)[source]

Read AtomDB data of type ftype for ion rmJ of element Z.

If settings are set, the filemap can be overwritten (see below), otherwise $ATOMDB/filemap will be used to locate the file. If indexzero is set, all levels will have 1 subtracted from them (AtomDB indexes lines from 1, but python and C index arrays from 0, so this can be useful)

Parameters:

Zint

Element nuclear charge

rmJint

Ion charge +1 (e.g. 5 for C^{4+}, a.k.a. C V)

ftypestring

type of data to read. Currently available

‘IR’ - ionization and recombination
‘LV’ - energy levels
‘LA’ - radiative transition data (lambda and A-values)
‘EC’ - electron collision data
‘PC’ - proton collision data
‘DR’ - dielectronic recombination satellite line data
‘PI’ - XSTAR photoionization data
‘AI’ - autoionization data
‘ALL’ - reads all of the above. Does not return anything. Used for bulk downloading.

Or, for non-ion-specific data (abundances and bremstrahlung coeffts) * ‘ABUND’ - abundance tables * ‘HBREMS’ - Hummer bremstrahlung coefficients * ‘RBREMS’ - relativistic bremstrahlung coefficitients * ‘IONBAL’ - ionization balance tables * ‘EIGEN’ - eigenvalue files

filemapstring

The filemap to use, if you do not want to use the default one.

settingsdict

This will let you override some standard inputs for get_data:

settings[‘filemap’]: the filemap to use if you do not want to use the default $ATOMDB/filemap
settings[‘atomdbroot’]: If you have files in non-standard locations you can replace $ATOMDB with this value

datacachedict

This variable will hold the results of the read in a dictionary. It will also be checked to see if the requested data has already been cached here before re-reading from the disk. If you have not yet read in any data but want to start caching, provide it as an empty dictionary i.e. mydatacache={}

2 parts of the data ares stored here:

Settings[‘data’] will store a copy of the data you read in. This means that if your code ends up calling for the same file multiple times, rather than re-reading from the disk, it will just point to this data already in memory. To clear the read files, just reset the data dictionary (e.g. settings[‘data’] ={})
settings[‘datasums’] stores the datasum when read in. Can be used later to check files are the same.

Both data and datasums store the data in identical trees, e.g.: settings[‘data’][Z][z1][ftype] will have the data.

indexzero: bool

If True, subtract 1 from all level indexes as python indexes from 0, while AtomDB indexes from 1.

offline: bool

If True, do not search online to download data files - just return as if data does not exist

Returns:

HDUlist: the opened pyfits hdulist if succesful. False if file doesn’t exist

pyatomdb.atomdb.get_filemap_file(ftype, Z, z1, fmapfile='$ATOMDB/filemap', atomdbroot='$ATOMDB', quiet=False, misc=False)[source]

Find the correct file from the database for atomic data of type ftype for ion with nuclear charge Z and ioncharge+1 = z1

Parameters:

ftypestr

‘ir’ = ionization & recombination data
‘lv’ = energy levels
‘la’ = wavelength and transition probabilities (lambda & a-values)
‘ec’ = electron collision rates
‘pc’ = proton collision rates
‘dr’ = dielectronic recombination satellite line information
‘ai’ = autoionization rate data
‘pi’ = XSTAR photoionization data
‘em’ = emission feature data (currently unused)

Zint

Element atomic number (=6 for C+4)

z1int

Ion charge +1 (=5 for C+4)

fmapfilestr

Specific filemap to use. Otherwise defaults to atomdbroot+’/filemap’

atomdbrootstr

Location of ATOMDB database. Defaults to ATOMDB environment variable. all $ATOMDB in the filemap will be expanded to this value

quietbool

If true, suppress warnings about files not being present for certain ions

miscbool

If requesting “misc” data, i.e. the Bremsstrahlung inputs, use this. This is for non ion-specific data, therefore Z,z1 are ignored. types are: 10 or ‘abund’: elemental abundances 11 or ‘hbrems’: Hummer bremstrahlung gaunt factor coefficients 13 or ‘rbrems’: Relativistic bremstrahlung gaunt factor coefficients

Returns:

str: The filename for the relevant file, with all $ATOMDB expanded. If no file exists, returns zero length string.

pyatomdb.atomdb.get_ionpot(Z, z1, settings=False, datacache=False)[source]

Get the ionization potential of an ion in eV

Parameters:

Zint: The atomic number of the element
z1int: The ion charge + 1 of the ion
settingsdict: See description in get_data
datacachedict: Used for caching the data. See description in get_data

Returns:

float: The ionization potential of the ion in eV.

pyatomdb.atomdb.get_ionrec_rate(Te_in, irdat_in=False, lvdat_in=False, Te_unit='K', lvdatp1_in=False, ionpot=False, separate=False, Z=-1, z1=-1, settings=False, datacache=False, extrap=True)[source]

Get the ionization and recombination rates at temperture(s) Te from ionization and recombination rate data file irdat.

Parameters:

Te_infloat or arr(float): electron temperature in K (default), eV, or keV
irdat_inHDUList: ionization and recombination rate data, if already open
lvdat_inHDUList: level data for ion with lower charge (i.e. ionizing ion or recombined ion)
Te_unit{‘K’ , ‘keV’ , ‘eV’}: temperature unit
lvdatp1_inHDUList: level data for the ion with higher charge (i.e ionized or recombining ion)
ionpotfloat: ionization potential of ion (eV).
separatebool: if set, return DR, RR, EA and CI rates seperately. (DR = dielectronic recombination, RR = radiative recombination, EA = excitaiton autoionization, CI = collisional ionization) Note that EA & CI are not stored separately in all cases, so may return zeros for EA as the data is incorporated into CI rates.
Zint: Element charge to get rates for (ignores “irdat_in”)
z1int: Ion charge +1 to get rates for (ignores “irdat_in”) e.g. Z=6,z1=4 for C IV (C 3+)
settingsdict: See description in read_data
datacachedict: See description in read_data
extrapbool: Extrappolate rates to Te ranges which are off the provided scale

Returns:

float, float:: (ionization rate coeff., recombination rate coeff.) in cm^3 s^-1 unless separate is set, in which case:
float, float, float, float:: (CI, EA, RR, DR rate coeffs) in cm^3 s^-1 Note that these assume low density & to get the real rates you need to multiply by N_e N_ion.

pyatomdb.atomdb.get_maxwell_rate(Te, colldata=False, index=-1, lvdata=False, Te_unit='K', lvdatap1=False, ionpot=False, force_extrap=False, silent=True, finallev=False, initlev=False, Z=-1, z1=-1, dtype=False, exconly=False, datacache=False, settings=False, ladat=False)[source]

Get the maxwellian rate for a transition from a file, typically for ionization, recombination or excitation.

Parameters:

Tefloat

electron temperature(s), in K by default

colldataHDUList

If provided, the HDUList for the collisional data

indexint

The line in the HDUList to do the calculation for. Indexed from 0.

lvdataHDUList

the hdulist for the energy level file (as returned by pyfits.open(‘file’))

Te_unit{‘K’ , ‘eV’ , ‘keV’}

Units of temperature grid.

lvdatap1HDUList

The level data for the recombining or ionized data.

ionpotfloat

The ionization potential in eV (required for some calculations, if not provided, it will be looked up)

force_extrapbool

Force extrappolation to occur for rates outside the nominal range of the input data

silentbool

Turn off notifications

finallevint

Instead of specifying the index, can use upperlev, lowerlev instead.

initlevint

Instead of specifying the index, can use upperlev, lowerlev instead

Zint

Instead of providing colldata, can provide Z & z1. Z is the atomic number of the element.

z1int

Instead of providing colldata, can provide Z & z1. z1 is the ion charge +1 for the initial ion

dtypestr

data type. One of:

‘EC’ : electron impact excitation

‘PC’ : proton impact excitation

‘CI’ : collisional ionization

‘EA’ : excitation-autoionization

‘XI’ : excluded ionization

‘XR’ : excluded recombination

‘RR’ : radiative recombination

‘DR’ : dielectronic recombination

exconlybool

For collisional excitation, return only the excitation rate, not the de-excitation rate.

settingsdict

See description in read_data

datacachedict

See description in read_data

Returns:

float or array(float): Maxwellian rate coefficient, in units of cm^3 s^-1 For collisional excitation (proton or electron) returns excitation, dexcitation rates

Examples

>>> Te = numpy.logspace(4,9,20)

>>> # (1) Get excitation rates for row 12 of an Fe XVII file
>>> colldata = pyatomdb.atomdb.get_data(26,17,'EC')
>>> exc, dex = get_maxwell_rate(Te, colldata=colldata, index=12)

>>> # (2) Get excitation rates for row 12 of an Fe XVII file
>>> exc, dex = get_maxwell_rate(Te, Z=26,z1=17, index=12)

>>>  (3) Get excitation rates for transitions from level 1 to 15 of FE XVII
>>> exc, dex = get_maxwell_rate(Te, Z=26, z1=17, dtype='EC', finallev=15, initlev=1)

pyatomdb.atomdb.get_oscillator_strength(Z, z1, upperlev, lowerlev, datacache=False)[source]

Get the oscillator strength f_{ij} of a transition

Parameters:

Zint: The atomic number of the element
z1int: The ion charge + 1 of the ion
upperlevint: The upper level, indexed from 1
lowerlevint: The lower level, indexed from 1
datacachedict: Used for caching the data. See description in get_data

Returns:

float: The oscillator strength. Returns 0 if transition not found. If transition is not found but the inverse transition is present the oscillator strength is calculated for this instead.

pyatomdb.atomdb.make_lorentz(version=False, do_all=True, cie=False, power=False, stronglines=False, neicsd=False, neilines=False, neicont=False, levpop=False)[source]

This makes all the Lorentz data comparison files from the Astrophysical Collisional Plasma Test Suite, version 0.4.0

Parameters:

versionstring (optional): e.g. “3.0.7” to run the suite for v3.0.7. Otherwise uses latest version.

Returns:

none

pyatomdb.atomdb.read_filemap(filemap='$ATOMDB/filemap', atomdbroot='$ATOMDB')[source]

Reads the AtomDB filemap file in to memory. By default, tries to read $ATOMDB/filemap, replacing all instances of $ATOMDB in the filemap file with the value of the environment variable $ATOMDB

Parameters:

filemap: str: the filemap file to read
atomdbroot: str: location of files, if not $ATOMDB.

pyatomdb.atomdb.rrc_ph_value(E, Z, z1, rrc_ph_factor, IonE, kT, levdat, xstardata=False, xstarfinallev=False)[source]

Returns RRC in photons cm3 s-1 keV-1

Parameters:

E:

Z: int

Atomic number of element (i.e. 8 for Oxygen)

z1: int

Ion charge +1 e.g. 5 for C+4, a.k.a. C V

rrc_ph_factor: float

Conversion factor for RRC.

IonE: float

Ionization potential of ion

kT: float

Temperature (keV)

levdat: lvdat line

Line from the lvdat file

xstardatadict, str or HDUList

if the data is XSTAR data (pi_type=3), supply the xstardata. This can be a dictionary with 2 arrays, one “Energy”, one “sigma”, the file name, or the entire PI file (already loaded):

# load level data
lvdata = atomdb.get_data(26, 24, 'LV', settings)

# load XSTAR PI data if it exists
pidata = atomdb.get_data(26, 24, 'PI', settings)

# get pi xsection at energy E for the ground state to ground state
sigma_photoion(E,
               lvdata[1].data['pi_type'][0],
               lvdata[1].data['pi_param'][0],
               xstardata=pidata,
               xstarfinallev=1)

xstarfinallev: the level to ionize in to. Defaults to 1.

Returns:

float: The RRC in photons cm3 s-1 keV-1 at energy(ies) E.

pyatomdb.atomdb.sigma_photoion(E, Z, z1, pi_type, pi_coeffts, xstardata=False, xstarfinallev=1)[source]

Returns the photoionization cross section at E, given an input of sig_coeffts.

Parameters:

E: float or array of floats

Energy/ies to find PI cross section at (keV)

Z: int

Atomic number of element (i.e. 8 for Oxygen)

pi_typeint

the “PI_TYPE” from the energy level file for this level, can be:

-1. No PI data 0. Hydrogenic 1. Clark 2. Verner 3. XSTAR

pi_coefftsarray(float)

the “PI_PARAM” array for this level from the LV file

xstardatadict, str or HDUList

if the data is XSTAR data (pi_type=3), supply the xstardata. This can be a dictionary with 2 arrays, one “Energy”, one “sigma”, the file name, or the entire PI file (already loaded):

# load level data
lvdata = atomdb.get_data(26, 24, 'LV', settings)

# load XSTAR PI data if it exists
pidata = atomdb.get_data(26, 24, 'PI', settings)

# get pi xsection at energy E for the ground state to ground state
sigma_photoion(E,
               lvdata[1].data['pi_type'][0],
               lvdata[1].data['pi_param'][0],
               xstardata=pidata,
               xstarfinallev=1)

xstarfinallev: the level to ionize in to. Defaults to 1.

Returns:

array(float): pi cross section in cm^2 at energy E.

pyatomdb.atomdb.write_filemap(d, filemap, atomdbroot='')[source]

Write filemap to file

Parameters:

ddict: Dictionary with filemap data in it. Structure defined as return value from read_filemap.
filemapstr: Name of filemap file to read. If zero length, use “$ATOMDB/filemap”
atomdbrootstr: Replace any $ATOMDB in the file names with this. If not provided, use “ATOMDB” environment variable instead

Returns:

none