JWST pack files

[alexmaragko]

JWST science pack files in ipac format, based on JWST simulations of the Orion's Bar ionization front (see https://pdrs4all.org/publications/ for details).

• JWST_pack_file.ipac coveres lines and dust features between 0.7 and 27.8 microns. Features in the overlap wavelengths between NIRspec and MIRI-MRS are those measured in the MIRI wavelenths.
• JWST_pack_file_NIRspec.ipac covers lines and dust features between 0.7 and 5.26 microns.
• JWST_pack_file_MIRI-MRS.ipac covers lines and dust features between 4.69 and 27.8 microns.

Emission lines and dust features were fitted with Gaussian1D and Drude1D models/profiles respectively, at separate smaller wavelength regions (not in one go of the entire NIR/MIR simulated spectra.)

• A height/sigma threshold was used for emission line identification. Below are some example of lines identified and fitted, and non-identified lines. Subsequently, the number of lines in the pack files depend on the threshold applied. Refinement of the lines and packs will be done with actual JWST spectra.

• Identified lines were then cross-correlated with the species from provided tables, as CLOUDY computed lines in the simulations are in general expected to be more than those resolved in actual observations.
• Currently, emission lines have the species name only. This will be updated to include a wavelength string, based on the lines central wavelength given in the table.

Notes on PAHFIT fitting

• Dummy uncertainties 10% of the flux were used for the fitting.
• Fitting the entire 0.7 - 27.8 micron spectrum (~22300 wavelength elements!) required ~ 1 hour on a core-i5 without giving a successful fit. Perhaps partial fitting in smaller regions is required.
• Using the entire pack file in smaller/subset wavelength regions is ~ 4x more time consuming compared to when trimming the pack file to the input wavelength range.

Example fitting on the 5 - 15 micron region of the simulations.

• No details because of the single points from the very narrow emission lines.
• Zooming in.
• Using 4000 fit_maxiter.

[codecov-commenter]

Codecov Report

Merging #224 (b2df3af) into master (920af78) will decrease coverage by 8.64%. The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #224      +/-   ##
==========================================
- Coverage   52.56%   43.91%   -8.65%     
==========================================
  Files           9       12       +3     
  Lines         605      822     +217     
==========================================
+ Hits          318      361      +43     
- Misses        287      461     +174     

Impacted Files	Coverage Δ
pahfit/errors.py	100.00% <0.00%> (ø)
pahfit/features/features_format.py	33.33% <0.00%> (ø)
pahfit/features/__init__.py	100.00% <0.00%> (ø)
pahfit/features/features.py	15.55% <0.00%> (ø)

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[alexmaragko]

Here is a brute fit (no redshift correction or proper unit conversion) and comparison between the different packs on the 5-15 micron JWST data of galaxy VV114.

• JWST_pack_file_MIRI-MRS.ipac
• ISO_SWS_pack_file_R_1600.ipac from #215
• scipack_ExGal_SpitzerIRSSLLL.ipac

[ThomasSYLai]

We should be able to fit the emission lines by properly shifting the spectrum back to the rest frame. The redshift of VV114 is 0.02007.

[alexmaragko]

Indeed things are improving with redshift correction.

• JWST_pack_file_MIRI-MRS.ipac
• ISO_SWS_pack_file_R_1600.ipac
• scipack_ExGal_SpitzerIRSSLLL.ipac

With the JWST pack the fit is using a larger number of emission lines than required for the galaxy. The ISO pack, which includes ~ 100 less emission lines than the JWST pack, gives a better result.

[alexmaragko]

To give a better description of the above, looking at the large number of emission lines e.g. in the 7 - 7.5 um region when fitting the galaxy with the JWST pack is because these lines are there in the simulations. In the plot below I'm zooming-in in the simulation spectrum at that region.

So these lines are included in the JWST pack file and PAHFIT is using them.

[alexmaragko]

Added new JWST packs based on the PDR dissociation front (DF) simulations.

• Fit to the 5-15 micron region of the DF simulations using the JWST_PDR_DF_MIRI-MRS_pack_file.ipac pack file.
• Fit to the 5-15 micron JWST data of galaxy VV114 using the JWST_PDR_DF_MIRI-MRS_pack_file.ipac pack file.

[jdtsmith]

I'm going to close this for now since our pack format has diverged since this was written. Definitely still interested in improvements and the birth of a pdr.yaml science pack. Probably starting small and building lines in as you go is the right approach.