Kurucz spectrum

[menasrac]

Description

PR for the 2023 GSOC project : Common API for large molecular databases. This PR includes the implementation of the Kurucz database to Radis with an example to plot spectrum using Spectrum Factory and all the related changes to the API or other sections of the code Follows PR #579 and adds broadening, a spectrum factory based example for Kurucz, also fixes minor requested changes.

Fixes #<Issue Number>

[menasrac]

Reviewed kuruczapi.py and partfunc.py. Main comment: there are some duplicates and I don't understand why

A global answer to all these comments : @minouHub The key structure will be modified to stick to the conventions when I introduce the species notations, I'm already working on it. The SiJ0 function and partfcn function in the API are not used because the int is added by radis but I let it for the moment to compare the results with the version of the code which adds int to the def ( see the #int in the read_kurucz methods). I will also remove it when we are satisfied with the physics. I will check what I can do for the hardcoded arrays and indeed load_atomic data is not needed any longer so I will remove it

[codecov-commenter]

Codecov Report

Merging #601 (4a08a8b) into develop (460640b) will increase coverage by 0.07%. The diff coverage is 78.24%.

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Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #601      +/-   ##
===========================================
+ Coverage    73.15%   73.22%   +0.07%     
===========================================
  Files          143      147       +4     
  Lines        20046    20360     +314     
===========================================
+ Hits         14665    14909     +244     
- Misses        5381     5451      +70     

[dcmvdbekerom]

@menasrac I believe the issue with test_gascomp.py is on Cantera's end, see also this issue I opened there: https://github.com/Cantera/cantera/issues/1607 For the moment, I would suggest to set - cantera>=2.5.1, <3.0.0 in environment.yml

[menasrac]

@menasrac I believe the issue with test_gascomp.py is on Cantera's end, see also this issue I opened there: Cantera/cantera#1607 For the moment, I would suggest to set - cantera>=2.5.1, <3.0.0 in environment.yml

I tried your suggestion, the test passed indeed but other tests in calc.py and broadening.py failed after this modification @dcmvdbekerom

[minouHub]

A few issues remaining, sorted in order of priority

• [ ] the file plot_Kurucz.py is still not running (see below)
• [ ] There is no test of SpectrumFactory using atoms
• [ ] fetch_databank() is not implemented for atoms (see below)
• [ ] the calc_spectrum function is not compatible with atomic spectra

---- fetchdatabank() ----

from radis import SpectrumFactory
from astropy import units as u
sf = SpectrumFactory(wavelength_min=4165 * u.nm,
                     wavelength_max=4200 * u.nm,
                     species='Fe_I',
                     medium='air',
                     verbose=1,    # more for more details
                     )
sf.fetch_databank()

---- plot_kurucz.py ---- output

Traceback (most recent call last):

  File C:\Anaconda\envs\radis-Kurucz\lib\site-packages\spyder_kernels\py3compat.py:356 in compat_exec
    exec(code, globals, locals)

  File c:\users\nicolas minesi\python\examples\plot_kurucz.py:6
    hdf5_path = fetch_kurucz('Fe_I')[0] # replace 'Fe_I' with atom and ionization_state

  File c:\users\nicolas minesi\python\radis\io\kurucz.py:21 in fetch_kurucz
    kurucz = AdBKurucz(species)

  File c:\users\nicolas minesi\python\radis\api\kuruczapi.py:36 in __init__
    self.pfTdat, self.pfdat = self.load_pf_Barklem2016()

  File c:\users\nicolas minesi\python\radis\api\kuruczapi.py:99 in load_pf_Barklem2016
    with open(file_path, "r") as file:

FileNotFoundError: [Errno 2] No such file or directory: 'radis/levels/pfTKurucz_values.txt'

[menasrac]

A few issues remaining, sorted in order of priority

• [ ] the file plot_Kurucz.py is still not running (see below)
• [ ] There is no test of SpectrumFactory using atoms
• [ ] fetch_databank() is not implemented for atoms (see below)
• [ ] the calc_spectrum function is not compatible with atomic spectra

---- fetchdatabank() ----

from radis import SpectrumFactory
from astropy import units as u
sf = SpectrumFactory(wavelength_min=4165 * u.nm,
                     wavelength_max=4200 * u.nm,
                     species='Fe_I',
                     medium='air',
                     verbose=1,    # more for more details
                     )
sf.fetch_databank()

---- plot_kurucz.py ---- output

Traceback (most recent call last):

  File C:\Anaconda\envs\radis-Kurucz\lib\site-packages\spyder_kernels\py3compat.py:356 in compat_exec
    exec(code, globals, locals)

  File c:\users\nicolas minesi\python\examples\plot_kurucz.py:6
    hdf5_path = fetch_kurucz('Fe_I')[0] # replace 'Fe_I' with atom and ionization_state

  File c:\users\nicolas minesi\python\radis\io\kurucz.py:21 in fetch_kurucz
    kurucz = AdBKurucz(species)

  File c:\users\nicolas minesi\python\radis\api\kuruczapi.py:36 in __init__
    self.pfTdat, self.pfdat = self.load_pf_Barklem2016()

  File c:\users\nicolas minesi\python\radis\api\kuruczapi.py:99 in load_pf_Barklem2016
    with open(file_path, "r") as file:

FileNotFoundError: [Errno 2] No such file or directory: 'radis/levels/pfTKurucz_values.txt'

Fetch databank is not implemented for atoms, however load_databank works with atoms as in the plot_kurucz examples. You have to mention sf.load_databank(path=hdf5_path, format='kurucz',parfuncfmt='kurucz') @minouHub

[menasrac]

A few issues remaining, sorted in order of priority

• [ ] the file plot_Kurucz.py is still not running (see below)
• [ ] There is no test of SpectrumFactory using atoms
• [ ] fetch_databank() is not implemented for atoms (see below)
• [ ] the calc_spectrum function is not compatible with atomic spectra

---- fetchdatabank() ----

from radis import SpectrumFactory
from astropy import units as u
sf = SpectrumFactory(wavelength_min=4165 * u.nm,
                     wavelength_max=4200 * u.nm,
                     species='Fe_I',
                     medium='air',
                     verbose=1,    # more for more details
                     )
sf.fetch_databank()

---- plot_kurucz.py ---- output

Traceback (most recent call last):

  File C:\Anaconda\envs\radis-Kurucz\lib\site-packages\spyder_kernels\py3compat.py:356 in compat_exec
    exec(code, globals, locals)

  File c:\users\nicolas minesi\python\examples\plot_kurucz.py:6
    hdf5_path = fetch_kurucz('Fe_I')[0] # replace 'Fe_I' with atom and ionization_state

  File c:\users\nicolas minesi\python\radis\io\kurucz.py:21 in fetch_kurucz
    kurucz = AdBKurucz(species)

  File c:\users\nicolas minesi\python\radis\api\kuruczapi.py:36 in __init__
    self.pfTdat, self.pfdat = self.load_pf_Barklem2016()

  File c:\users\nicolas minesi\python\radis\api\kuruczapi.py:99 in load_pf_Barklem2016
    with open(file_path, "r") as file:

FileNotFoundError: [Errno 2] No such file or directory: 'radis/levels/pfTKurucz_values.txt'

Fetch databank is not implemented for atoms, however load_databank works with atoms as in the plot_kurucz examples. You have to mention sf.load_databank(path=hdf5_path, format='kurucz',parfuncfmt='kurucz') @minouHub

I have also added a test for fetch_kurucz. Though it is not directly a test for load_databank, it still asserts that the df which will be used by calc_spectrum contains all the required columns

[erwanp]

@menasrac please add a runnable test code in the PR main text so we can test it

[minouHub]

New work on this branch - see #652