1. acx2 module class reference

class acx2.ACXDonorModel(donor, donor_linefile=None, donor_contfile=None, donor_crosssectionfile=None, abundset='AG89', elements=None, acxmodel=8, recombtype=1, collisiontype=1)

A model of the ACX Donor

Parameters:

  • donor (string) – The donor symbol (e.g. “H”)

  • donor_linefile (string) – The file with the donor line emision

  • donor_contfile (string) – The file with the donor continuum emision

  • donor_crosssectionfile (string) – The cross section file for donor

  • abundset (optional, {"AG89"}) – The abundance set. Only AG89 works currently

  • elements (optional, array-like int) – The recombining element atomic numbers. Default is all.

  • acxmodel (optional, int, default=8) – The acx model l, n distribution to fall back on.

linedata

The data in the donor_linefile

Type:

HDUList

contdata

The data in the donor_contfile

Type:

HDUList

crosssectiondata

The data in the donor_crosssectionfile

Type:

HDUList

donorAbundance

The donor abundance. Defaults to 1.0. Intended for correctly mixing donors, e.g. in 10%He, 90%H donor plasma, set to 0.1 and 0.9 respectively, though no normalization is checked for.

Type:

float

donormass

mass of the donor in a.m.u.

Type:

float

abund

abundance of each element, relative to abundset. e.g. abund[6] = 2.0 means 2x solar C

Type:

dict of float

ionfrac_from_temperature

was the ionfracance calculated from the temperature

Type:

bool

temperature

the temperature in keV

Type:

float

ionfrac

the ionization fraction, normalized to 1 for each element, e.g. ionfrac[2] = ndarray([0.01,0.1,0.89])

Type:

dict of arrays of float

calc_crosssection(collparam)

Calculate the total and partial cross sections by n, l, S.

Parameters:

collparam (float) – Collision energy, or velocity, as determined by set_collisiontype, in kev/u, cm/s or km/s

Return type:

TBD

calc_line_emissivity(Z, z1_in, up, lo, collvalue=None)

Calculate the emissivity of a specific line.

Parameters:

  • collvalue (float) – The collision parameter (kev/u or cm/s, depending) to calculate the spectrum

  • Z (int) – element charge

  • z1 (int) – recombining ion charge +1.

  • up (int) – upper level of transition

  • lo (int) – lower level of transition

Returns:

ret – The spectrum, in ph cm^3 s-1 bin-1

Return type:

array(float)

calc_linelist(collparam, specrange, specunit='A', redshift=0.0)

Calculate the spectrum we want

Parameters:

  • collparam (float) – Collision energy, or velocity, as determined by set_collisiontype, in kev/u, cm/s or km/s

  • specrange ([float, float]) – Minimum and maximum values for interval in which to search

  • specunit ({'Angstrom','keV'}) – Units for specrange (default A)

Returns:

linelist – Numpy array of lines and emissivity, custom dtype

Return type:

numpy.array

calc_spectrum(collparam, Tbroaden, vbroaden, ebroaden)

Calculate the spectrum we want

Parameters:

collparam (float) – Collision energy, or velocity, as determined by set_collisiontype, in kev/u, cm/s or km/s

Returns:

self.emiss – The emissivity in photons cm^3 bin-1 s-1

Return type:

array(float)

find_crosssection_type(Z, z1)

Find the cross section type, to assign correct CXIonSpectrum type

Parameters:

  • Z (int) – element charge

  • z1 (int) – recombining ion charge +1.

Returns:

  • resolution (string) – The coupling, currently N, NLS or ACX1 (returned in upper case)

  • ihdu (int) – The HDU with the cross section data for the ion. Set to -1 for none.

hashlib = <module 'hashlib' from '/home/docs/.asdf/installs/python/3.11.12/lib/python3.11/hashlib.py'>
initialize_CXIonspectrum()

Called to ensure that all the ion spectra exist and are ready to use

numpy = <module 'numpy' from '/home/docs/checkouts/readthedocs.org/user_builds/acx2/envs/latest/lib/python3.11/site-packages/numpy/__init__.py'>
os = <module 'os' (frozen)>
set_abund(abund, elements=None)

Set the elemental abundance, also in each donor model

Parameters:

abund (array(float)) – Abundances, relative to defulat

Return type:

None

set_abundset(abundstring)

Set the abundance set.

Parameters:

abundstring (string) – The abundance string (e.g. “AG89”, “uniform”). Case insensitive. See atomdb.get_abundance for list of possible abundances

Returns:

updates self.abundset and self.abundsetvector.

Return type:

none

set_acxmodel(acxmodel)

Set the ACX spectrum type

Parameters:

acxmodel (int) – The acxmodel (between 1 and 8)

set_collisionparam(collisionparam)

Set the collision velocity or energy

Parameters:

collisionparam (float) – The collision velocity or energy. Units and parameter type are set in ACXModel.set_collisiontype

Return type:

None

set_collisiontype(colltype, collunits='default')

Set the collision type and units

Parameters:

  • colltype (int) – Parameter for provided collision type Collision type - 1=energy/mass of center of mass Collision type - 2=velocity of center of mass Collision type - 3=velocity of donor Collision type - 4=velocity of receiver

  • collunits (string, optional) – Units of collision paramter. Defaults to “kev/u” for colltype=1, “cm/s” for others

Return type:

None

set_donorabund(abund)

Set the donor abundance

Parameters:

abund (float) – The abundance of the donor.

set_ebins(ebins, ebins_checksum=False)

Set the energy bins for the spectrum being returned.

Parameters:

  • ebins (array(float)) – Energy bin edges (keV)

  • ebins_checksum (string, optional) – The hex digest of the md5 sum of ebins. Used to check for changes.

set_ionfrac(ionfrac)

Recalculate the ionization balance based on equilibrium electron temperature

Parameters:

ionfrac (dict of arrays) – ionization fraction, e.g. ionfrac[8]=numpy.array([0.0, 0.0, 0.0, 0.0, 0.1, 0.3, 0.4, 0.2, 0.0])

Return type:

None

set_recombtype(recombtype)

Set the recombination type

Parameters:

recombtype (int) – The type of recombination (1=single, 2=all the way to neutral, 3 = same as 2, but renomalized by total cross section)

set_temperature(temperature)

Recalculate the ionization balance based on equilibrium electron temperature

Parameters:

temperature (float) – electron temperature in keV

Return type:

None

class acx2.CXIonSpectrum(Z, z1, ebins, crosssectiondata, linedata, contdata, cxdata)

Class to store and prepare each ion’s spectrum. Will have a subset of CXShellSpectrum for each shell. Can provide it a set of energy bins and get a spectrum back. This will store all the emissivity data.

expand_E_grid(eedges, Econt_in_full, cont_in_full)

Code to expand the compressed continuum onto a series of bins.

Parameters:

  • eedges (float(array)) – The bin edges for the spectrum to be calculated on, in units of keV

  • Econt_in_full (float(array)) – The compressed continuum energies (keV)

  • cont_in_full (float(array)) – The compressed continuum emissivities (ph cm3 s-1 keV-1)

Returns:

len(bins)-1 array of continuum emission, in units of photons cm^3 s^-1 bin^-1

Return type:

float(array)

hashlib = <module 'hashlib' from '/home/docs/.asdf/installs/python/3.11.12/lib/python3.11/hashlib.py'>
numpy = <module 'numpy' from '/home/docs/checkouts/readthedocs.org/user_builds/acx2/envs/latest/lib/python3.11/site-packages/numpy/__init__.py'>
os = <module 'os' (frozen)>
set_acxmodel(acxmodel)

Set the ACX spectrum type

Parameters:

acxmodel (int) – The acxmodel (between 1 and 8)

set_ebins(ebins, ebins_checksum=False)

Set the energy bins for the spectrum being returned.

Parameters:

  • ebins (array(float)) – Energy bin edges (keV)

  • ebins_checksum (string, optional) – The hex digest of the md5 sum of ebins. Used to check for changes.

set_recombtype(recombtype)

Set the energy bins, also in each donor model

Parameters:

ebins (array(float)) – The energy bins in keV for the spectrum

Return type:

None

class acx2.CXIonSpectrum_ACX1(Z, z1, crosssectionhdu, linedata, contdata, acxmodel=8, donor=False, receivermass=False, donormass=False)

This is a class for ACX1 model data

ebins

The energy bin in keV

Type:

array(float)

ebins_m5sum

hex digest of ebins

Type:

md5hash

calc_crosssection(collenergy)

Calculate cross sections

calc_linelist(collenergy, collvelocity, specrange, specunit='A', redshift=0.0)

Calculate the spectrum of the data

Parameters:

  • ebins (array(float)) – The energy bins (in keV) to calcualte the spectrum on

  • collenergy (flaot) – The collision energy (keV/amu)

  • collvelocity (float) – The velocity of the center of mass (cm/s)

  • specrange ([float, float]) – Minimum and maximum values for interval in which to search

  • specunit ({'Angstrom','keV'}) – Units for specrange (default A)

Returns:

emissivity – Emissivity * velocity in photons cm4 s-2

Return type:

array(float)

calc_spectrum(collenergy, collvelocity, Tbroaden, vbroaden, ebroaden)

Calculate the spectrum of the data

Parameters:

  • ebins (array(float)) – The energy bins (in keV) to calcualte the spectrum on

  • collenergy (flaot) – The collision energy (keV/amu)

  • collvelocity (float) – The velocity of the center of mass (cm/s)

  • linedata (hdulist) – The line emissivity data

  • contdata (hdulist) – The continuum emissivity data

  • acxmodel (int) – n, l shell distribution, between 1 and 8:

Returns:

emissivity – Emissivity * velocity in photons cm4 s-2

Return type:

array(float)

hashlib = <module 'hashlib' from '/home/docs/.asdf/installs/python/3.11.12/lib/python3.11/hashlib.py'>
numpy = <module 'numpy' from '/home/docs/checkouts/readthedocs.org/user_builds/acx2/envs/latest/lib/python3.11/site-packages/numpy/__init__.py'>
os = <module 'os' (frozen)>
set_ebins(ebins, ebins_checksum=False)

Set the energy bins, also in each donor model

Parameters:

ebins (array(float)) – The energy bins in keV for the spectrum

Return type:

None

class acx2.CXIonSpectrum_N(Z, z1, crosssectiondata, linedata, contdata, acxmodel=8, donor=False, receivermass=False, donormass=False)

This is a class for n resolved Kronos data

calc_linelist(collenergy, collvelocity, specrange, specunit='A')

Calculate the spectrum of the data

Parameters:

  • ebins (array(float)) – The energy bins (in keV) to calcualte the spectrum on

  • collenergy (flaot) – The collision energy (keV/amu)

  • collvelocity (float) – The velocity of the center of mass (cm/s)

  • specrange ([float, float]) – Minimum and maximum values for interval in which to search

  • specunit ({'Angstrom','keV'}) – Units for specrange (default A)

Returns:

emissivity – Emissivity * velocity in photons cm4 s-2

Return type:

array(float)

calc_spectrum(collenergy, collvelocity, Tbroaden, vbroaden, ebroaden)

Calculate the spectrum of the data

Parameters:

  • ebins (array(float)) – The energy bins (in keV) to calcualte the spectrum on

  • collenergy (flaot) – The collision energy (keV/amu)

  • collvelocity (float) – The velocity of the center of mass (cm/s)

  • linedata (hdulist) – The line emissivity data

  • contdata (hdulist) – The continuum emissivity data

  • acxmodel (int) – n, l shell distribution, between 1 and 8

Returns:

emissivity – Emissivity * velocity in photons cm4 s-2

Return type:

array(float)

hashlib = <module 'hashlib' from '/home/docs/.asdf/installs/python/3.11.12/lib/python3.11/hashlib.py'>
numpy = <module 'numpy' from '/home/docs/checkouts/readthedocs.org/user_builds/acx2/envs/latest/lib/python3.11/site-packages/numpy/__init__.py'>
os = <module 'os' (frozen)>
set_ebins(ebins, ebins_checksum=False)

Set the energy bins, also in each donor model

Parameters:

ebins (array(float)) – The energy bins in keV for the spectrum

Return type:

None

class acx2.CXIonSpectrum_NLS(Z, z1, crosssectiondata, linedata, contdata, donor=False, receivermass=False, donormass=False)

This is a class for nls resolved Kronos data

calc_linelist(collenergy, collvelocity, specrange, specunit='A')

Calculate the spectrum of the data

Parameters:

  • ebins (array(float)) – The energy bins (in keV) to calcualte the spectrum on

  • collenergy (flaot) – The collision energy (keV/amu)

  • collvelocity (float) – The velocity of the center of mass (cm/s)

  • specrange ([float, float]) – Minimum and maximum values for interval in which to search

  • specunit ({'Angstrom','keV'}) – Units for specrange (default A)

Returns:

emissivity – Emissivity * velocity in photons cm4 s-2

Return type:

array(float)

calc_spectrum(collenergy, collvelocity, Tbroaden, vbroaden, ebroaden)

Calculate the spectrum of the data

Parameters:

  • ebins (array(float)) – The energy bins (in keV) to calcualte the spectrum on

  • collenergy (flaot) – The collision energy (keV/amu)

  • collvelocity (float) – The velocity of the center of mass (cm/s)

  • linedata (hdulist) – The line emissivity data

  • contdata (hdulist) – The continuum emissivity data

  • acxmodel (int) – n, l shell distribution, between 1 and 8

Returns:

emissivity – Emissivity * velocity in photons cm4 s-2

Return type:

array(float)

hashlib = <module 'hashlib' from '/home/docs/.asdf/installs/python/3.11.12/lib/python3.11/hashlib.py'>
numpy = <module 'numpy' from '/home/docs/checkouts/readthedocs.org/user_builds/acx2/envs/latest/lib/python3.11/site-packages/numpy/__init__.py'>
os = <module 'os' (frozen)>
set_ebins(ebins, ebins_checksum=False)

Set the energy bins, also in each donor model

Parameters:

ebins (array(float)) – The energy bins in keV for the spectrum

Return type:

None

class acx2.CXShellSpectrum(Z, z1, n, l, linedata, contdata, s=False)

Holds a single n, l, shell spectrum

expand_E_grid(eedges, Econt_in_full, cont_in_full)

Code to expand the compressed continuum onto a series of bins.

Parameters:

  • eedges (float(array)) – The bin edges for the spectrum to be calculated on, in units of keV

  • Econt_in_full (float(array)) – The compressed continuum energies (keV)

  • cont_in_full (float(array)) – The compressed continuum emissivities (ph cm3 s-1 keV-1)

Returns:

len(bins)-1 array of continuum emission, in units of photons cm^3 s^-1 bin^-1

Return type:

float(array)

hashlib = <module 'hashlib' from '/home/docs/.asdf/installs/python/3.11.12/lib/python3.11/hashlib.py'>
numpy = <module 'numpy' from '/home/docs/checkouts/readthedocs.org/user_builds/acx2/envs/latest/lib/python3.11/site-packages/numpy/__init__.py'>
os = <module 'os' (frozen)>
scipy = <module 'scipy' from '/home/docs/checkouts/readthedocs.org/user_builds/acx2/envs/latest/lib/python3.11/site-packages/scipy/__init__.py'>
set_ebins(ebins, ebins_checksum)

Set the energy bins, also in each donor model

Parameters:

ebins (array(float)) – The energy bins in keV for the spectrum

Return type:

None

class acx2.DummyCXShellSpectrum(Z, z1, n, l, s=False)

Placeholder for a blank spectrum

calc_spectrum(ebins, ebins_checksum, Tbroaden, vbroaden, ebroaden)

Return zeros

Parameters:

  • ebinshash (string) – md5 sum of ebins

  • ebins (array(float)) – array of floats

Returns:

0.0

Return type:

there is no data here, so return zero.

set_ebins(ebins, ebins_checksum=False)

Dummy

Parameters:

  • ebinshash (string) – md5 sum of ebins

  • ebins (array(float)) – array of floats

Return type:

None

acx2.download_acx_emissivity_files(adbroot, userid, version, donor)

Download the AtomDB CX model emissivity files for AtomDB”

This code will go to the AtomDB FTP site and download the necessary files. It will then unpack them into a directory adbroot. It will not overwrite existing files with the same md5sum (to avoid pointless updates) but it will not know this until it has downloaded and unzipped the main file.

Parameters:

  • adbroot (string) – The location to install the data. Typically should match $ATOMDB

  • userid (string) – An 8 digit ID number. Usually passed as a string, but integer is also fine (provided it is all numbers)

  • version (string) – The version string, including donors for the release, e.g. “2_1_0-h_he”

Return type:

None

acx2.get_full_line_info(linelist, filemap='$ATOMDB/filemap_acx', atomdbroot='$ATOMDB')

Gets the data for the full linelist

acx2.loginterp(newx, x, y, offset=1e-40)

Interpolation helper function. Interpolates linearly on a log-log grid If newx < x[0], return x[0]. If newx > x[-1], extrapolate slope of last 2 points, unless y[-1] ==0 in which case return 0.

Parameters:

  • newx (float) – The new X parameters (energy, kev/amu)

  • x (array(float)) – The x parameters (energy, kev/amu)

  • y (array(float)) – The y parameters (cross section, cm2)

  • offset (float (optional)) – An offset to apply before interpolation. Prevents log(0) issues.

Returns:

newy – The interpolated cross section. Minimum of 0 in case of numerical issues.

Return type:

float