AtomNeb (IDL)
AtomNeb - IDL/GDL Library for Atomic Data of Ionized Nebulae
Description
AtomNeb-idl is a library written in Interactive Data Language (IDL)/GNU Data Language (GDL) for reading atomic data from AtomNeb, which is a database containing atomic data stored in the Flexible Image Transport System (FITS) file format for collisionally excited lines and recombination lines typically observed in spectra of ionized gaseous nebulae. The AtomNeb database were generated for use in proEQUIB, pyEQUIB, and other nebular spectral analysis tools.
Collisionally Excited Lines
AtomNeb for collisionally excited lines contains sets of atomic datasets, which include energy levels (Ej), collision strengths (Ωij), and transition probabilities (Aij) of the most ions commonly observed in ionized nebulae.
The atomic datasets for collisionally excited lines are as follows:
- Collection from the National Institute of Standards and Technology (NIST) Atomic Spectra Database, the CHIANTI atomic database, and some improved atomic data from Cloudy v13.04 and pyNeb v1.0. This collection was compiled according to the atomic data used in pyNeb v1.0.
- Chianti52 from the CHIANTI atomic database version 5.2. This dataset was compiled according to the atomic data used in MOCASSIN.
- Chianti60 from the CHIANTI atomic database version 6.0. This dataset was compiled according to the atomic data used in MOCASSIN.
- Chianti70 from the CHIANTI atomic database version 7.0. This dataset was compiled according to the atomic data used in MOCASSIN.
- Chianti90 from the CHIANTI atomic database version 9.0. This dataset was compiled according to the atomic data used in NEAT.
Each dataset contains the following atomic data FITS files: AtomElj.fits for Energy Levels (Ej), AtomOmij.fits for Collision Strengths (Ωij), and AtomAij.fits for Transition Probabilities (Aij).
Recombination Lines
AtomNeb for recombination lines contains sets of effective recombination coefficients (αeff) of recombination lines of H I, He I, He II, C I, C II, C III, C VI, N II, N III, N IV, N V, N VI, N VII, O II, O III, O IV, O V, O VI, O VIII, and Ne II ions typically observed in ionized nebulae, as well as Branching ratios (Br) of O II and N II lines.
The atomic datasets for recombination lines are as follows:
- RC Collection, effective recombination coefficients for C II (Davey et al. 2000), N II (Escalante and Victor 1990), O II (Storey 1994; Liu et al. 1995), and Ne II ions (Kisielius et al. 1998), including Branching ratios (Br) for O II and N II ions. This collection was compiled according to the atomic data used in MOCASSIN.
- SH95 Collection, hydrogenic ions for Z=1 to 8, namely H I, He II, Li III, Be IV, B V, C VI, N VII, and O VIII ions from Storey and Hummer (1995).
- PPB91 Collection, effective recombination coefficients for H, He, C, N, O, Ne ions from Pequignot, Petitjean and Boisson (1991).
- PFSD12 He I data, effective He I recombination coefficients from Porter et al (2012) and (2013a).
- FSL13 N II data, effective N II recombination coefficients (corrigendum) from Fang, Storey and Liu (2011) and (2013b).
- SSB17 O II data, effective O II recombination coefficients of 8889 recombination lines for Cases A, B, and C, and 2433 optical (3500-9000Å) recombination lines for Case B from Storey, Sochi and Bastin (2017).
Installation
Dependent IDL Packages
This package requires the following packages:
- To get this package with all the dependent packages, you can simply use git command as follows:
git clone --recursive https://github.com/atomneb/AtomNeb-idl
- If you plan to use the recent O II recombination coefficients (Storey, Sochi and Bastin 2017), you need to unpack them:
cd AtomNeb-idl/atomic-data-rc/ tar -xvf *.fits.tar.gz
Installation in IDL
- To install the AtomNeb database and its API library in the Interactive Data Language (IDL), you need to add the path of this package directory to your IDL path. or more information about the path management in IDL, read the tips for customizing IDL program path provided by Harris Geospatial Solutions or the IDL library installation note by David Fanning in the Coyote IDL Library.
- This package requires IDL version 7.1 or later.
Installation in GDL
You can install the GNU Data Language (GDL) if you do not have it on your machine:
- Linux (Fedora):
sudo dnf install gdl
- Linux (Ubuntu):
sudo apt-get install gnudatalanguage
- OS X (brew):
brew tap brewsci/science brew install gnudatalanguage
- OS X (macports):
sudo port selfupdate sudo port upgrade libtool sudo port install gnudatalanguage
- Windows: You can use the GNU Data Language for Win32 (Unofficial Version) or you can compile the GitHub source using Visual Studio 2015 as shown in appveyor.yml.
To install the AtomNeb database and its API library in GDL, you need to add the path of this package directory to your .gdl_startup file in your home directory:
!PATH=!PATH + ':/home/AtomNeb-idl/pro/' !PATH=!PATH + ':/home/AtomNeb-idl/externals/astron/pro/'
You may also need to set GDL_STARTUP if you have not done in .bashrc (bash):
export GDL_STARTUP=~/.gdl_startup
or in .tcshrc (cshrc):
setenv GDL_STARTUP ~/.gdl_startup
This package requires GDL version 0.9.8 or later.
How to Use
The Documentation of the IDL functions provides in detail in the API Documentation (atomneb.github.io/AtomNeb-idl/doc). There are two main categories: collisionally excited lines (CEL) and recombination lines (RC).
See Jupyter Notebooks: Notebooks.ipynb
Run Jupyter Notebooks on Binder:
The atomic data for collisionally excited lines (CEL) contain Energy Levels (Ej), Collision Strengths (Ωij), and Transition Probabilities (Aij). We have four atomic datasets for them: collection, chianti52, chianti60, and chianti70.
You need to load the atomneb object class, and choose either collection, chianti52, chianti60 or chianti70 as follows:
atm=obj_new('atomneb') atm->set_data_cel,'chianti70'
Now you have access to:
Energy Levels (Ej):
atom='o' ion='iii' oiii_elj_data=atm->read_elj(atom, ion, level_num=6) print,oiii_elj_data.J_v print,oiii_elj_data.Ej
which gives:
0.00000 1.00000 2.00000 2.00000 0.00000 2.00000 0.00000 113.200 306.200 20273.30 43185.69 60324.80
Collision Strengths (Ωij):
atom='o' ion='iii' oiii_omij_data=atm->read_omij(atom, ion) print,oiii_omij_data.level1 print,oiii_omij_data.level2 print,oiii_omij_data[0].strength
which gives:
0 1 1 1 1 ... 0 2 3 4 5 ... 100.0 158.50 251.20 398.10 631.0 ...
Transition Probabilities (Aij):
atom='o' ion='iii' oiii_aij_data=atm->read_aij(atom, ion) print,oiii_aij_data.Aij[*,*]
which gives:
0.0000 2.5969e-05 0.0000 2.3220e-06 ...
The atomic data for recombination lines (RC) contain effective recombination coefficients (αeff) of emission lines from different collections: RC Collection, SH95 Collection, PPB91 Collection, PFSD12 He I data, FSL13 N II data, and SSB17 O II data.
You need to load the atomneb object class:
atm=obj_new('atomneb')
Now you have access to effective recombination coefficients (αeff) of the following collections:
RC Collection:
atom='c' ion='iii' cii_rc_data=atm->read_aeff_collection(atom, ion) n_line=size(cii_rc_data.Wavelength,/DIMENSIONS) for i=0,n_line[0]-1 do print,cii_rc_data[i].Wavelength, cii_rc_data[i].a, $ cii_rc_data[i].b, cii_rc_data[i].c, $ cii_rc_data[i].d, cii_rc_data[i].f
which gives:
914.00000 0.69280000 0.021400000 -0.016300000 -0.24310000 -0.88000000 962.00000 1.0998000 -0.0042000000 -0.027900000 -0.22940000 -0.96560000 997.00000 0.78210000 -0.36840000 0.00030000000 -0.12170000 -0.78740000 ...
SH95 Collection:
atom='h' ion='ii' hi_rc_data=atm->read_aeff_sh95(atom, ion) print,hi_rc_data[0].Aeff
which gives:
100.00000 500.00000 0.0000000 4.2140000e-27 1.7560000e-27 1.0350000e-27 ...
PPB91 Collection:
atom='c' ion='iii' cii_rc_data=atm->read_aeff_ppb91(atom, ion) n_line=size(cii_rc_data.Wavelength,/DIMENSIONS) for i=0,n_line[0]-1 do print,cii_rc_data[i].Ion,cii_rc_data[i].Case1, $ cii_rc_data[i].Wavelength, cii_rc_data[i].a, $ cii_rc_data[i].b, cii_rc_data[i].c, $ cii_rc_data[i].d, cii_rc_data[i].br, $ cii_rc_data[i].Q, cii_rc_data[i].y
which gives:
C2+A 9903.4600 0.69700000 -0.78400000 4.2050000 0.72000000 1.0000000 1.6210000 C2+A 4267.1500 1.0110000 -0.75400000 2.5870000 0.71900000 0.95000000 2.7950000 ...
PFSD12 He I data:
atom='he' ion='ii' hei_rc_data=atm->read_aeff_he_i_pfsd12(atom, ion) hei_rc_data_wave=atm->read_aeff_he_i_pfsd12(atom, ion, /wavelength) print,hei_rc_data[0].Aeff
which gives:
5000.0000 10.000000 -25.379540 -25.058970 -25.948440 -24.651820 -25.637660 ...
FSL13 N II data:
atom='n' ion='iii' wavelength_range=[4400.0, 7100.0] nii_rc_data=atm->read_aeff_n_ii_fsl13(atom, ion, wavelength_range) nii_rc_data_wave=atm->read_aeff_n_ii_fsl13(atom, ion, wavelength_range, /wavelength) print,nii_rc_data[0].Aeff n_line=size(nii_rc_data_wave.Wavelength,/DIMENSIONS) for i=0,n_line[0]-1 do print,nii_rc_data_wave[i].Wavelength, nii_rc_data_wave[i].Tr, nii_rc_data_wave[i].Trans
which gives:
255.000 79.5000 47.3000 12.5000 6.20000 4.00000 2.86000 258.000 54.4000 29.7000 7.92000 4.11000 2.72000 2.00000 310.000 48.1000 23.7000 5.19000 2.55000 1.65000 1.21000 434.000 50.3000 23.2000 4.71000 2.26000 1.45000 1.05000 6413.23 6g - 4f2p6g G[9/2]o4 - 2p4f F[7/2]e3 6556.32 6g - 4f2p6g G[9/2]o5 - 2p4f G[7/2]e4 6456.97 6g - 4f2p6g G[9/2]o5 - 2p4f F[7/2]e4 6446.53 6g - 4f2p6g F[7/2]o3 - 2p4f D[5/2]e2 6445.34 6g - 4f2p6g F[7/2]o4 - 2p4f D[5/2]e3 ...
SSB17 O II data: You first need to unpack rc_o_iii_SSB17_orl_case_b.fits.tar.gz, e.g.:
tar -xvf rc_o_iii_SSB17_orl_case_b.fits.tar.gz
If you need to have access to the full dataset (entire wavelengths, case A and B):
tar -xvf rc_o_iii_SSB17.fits.tar.gz
To use the full dataset:
atm->set_Atom_RC_O_III_SSB17, /full_data
Please note that using the entire atomic data will make your program very slow and you may need to have a higher memory on your system. Without the above comment, as default, the cose uses rc_o_iii_SSB17_orl_case_b.fits:
atom='o' ion='iii' case1='B' wavelength_range=[5320.0, 5330.0] oii_rc_data=atm->read_aeff_o_ii_ssb17(atom, ion, case1, wavelength_range) oii_rc_data_wave=atm->read_aeff_o_ii_ssb17(atom, ion, case1, wavelength_range, /wavelength) print,oii_rc_data[0].Aeff n_line=size(oii_rc_data_wave.Wavelength,/DIMENSIONS) for i=0,n_line[0]-1 do print,oii_rc_data_wave[i].Wavelength, oii_rc_data_wave[i].lower_term, oii_rc_data_wave[i].upper_term
which gives:
1.64100e-30 1.60000e-30 1.56400e-30 1.54100e-30 1.52100e-30 1.50900e-30 ... 5327.17 2s22p2(1S)3p 2Po 5325.42 2s22p2(1S)3p 2Po 5327.18 2s22p2(1D)3d 2Ge 5326.84 2s22p2(1D)3d 2Ge ...
Documentation
For more information on how to use the API functions from the AtomNeb IDL libray, please read the API Documentation published on atomneb.github.io/AtomNeb-idl.
References
- Danehkar, A. (2020). AtomNeb Python Package, an addendum to AtomNeb: IDL Library for Atomic Data of Ionized Nebulae. J. Open Source Softw., 5, 2797. doi:10.21105/joss.02797 ads:2020JOSS....5.2797D.
- Danehkar, A. (2019). AtomNeb: IDL Library for Atomic Data of Ionized Nebulae. J. Open Source Softw., 4, 898. doi:10.21105/joss.00898 ads:2019JOSS....4..898D.
Citation
Using the AtomNeb IDL library in a scholarly publication? Please cite these papers:
@article{Danehkar2019, author = {{Danehkar}, Ashkbiz}, title = {AtomNeb: IDL Library for Atomic Data of Ionized Nebulae}, journal = {Journal of Open Source Software}, volume = {4}, number = {35}, pages = {898}, year = {2019}, doi = {10.21105/joss.00898} }
and if you use the AtomNeb Python package:
@article{Danehkar2020, author = {{Danehkar}, Ashkbiz}, title = {AtomNeb Python Package, an addendum to AtomNeb: IDL Library for Atomic Data of Ionized Nebulae}, journal = {Journal of Open Source Software}, volume = {5}, number = {55}, pages = {2797}, year = {2020}, doi = {10.21105/joss.02797} }
Learn More
| Documentation | https://atomneb.github.io/AtomNeb-idl/doc/ |
| Repository | https://github.com/atomneb/AtomNeb-idl |
| Issues & Ideas | https://github.com/atomneb/AtomNeb-idl/issues |
| DOI | 10.21105/joss.00898 |
| Archive | 10.5281/zenodo.2584419 |