# PyAtomDB: Extending the AtomDB Atomic Database to Model New Plasma Processes and Uncertainties

^{*}

## Abstract

**:**

`ACX`models for non-Maxwellian and Charge-Exchange plasmas respectively. In addition, PyAtomDB allows for full open access to the

`apec`code, which underlies all of the AtomDB spectra and has enabled the development of a module for estimating the sensitivity of emission lines and diagnostic line ratios to uncertainties in the underlying atomic data. We present these publicly available tools and results for several X-ray diagnostics of Fe L-shell ions and He-like ions as examples.

## 1. History of the AtomDB Project

`PyAtomDB`(https://github.com/AtomDB/pyatomdb), which now underpins all aspects of the AtomDB project.

`PyAtomDB`project, the new data formats created for non-equilibrium modeling, the new models which this has enabled for charge exchange (CX), non-Maxwellian electrons (Kappa), and the ability to perform uncertainty studies.

#### 1.1. The Astrophysical Plasma Emission Database (APED)

`$ATOMDB/APED/he/he_1/`. There are up to eight different file types for each ion, as listed in Table 1. In addition, APED contains several multi-element files, which hold data covering many ions together, as described in Table 2.

#### 1.2. The Astrophysical Plasma Emission Code (APEC)

`line`file contains the ${\epsilon}_{ij}$, wavelength, ion and transition identification for each line above a set ${\epsilon}_{ij}$ (by default, ${10}^{-20}$ ph cm

^{3}s

^{−1}). The

`coco`files contain the continuum emissivities from bremsstrahlung, radiative recombination and two photon decay, in ph cm

^{3}keV

^{−1}s

^{−1}, compressed onto an emissivity vs energy grid by an algorithm [9] which ensures that when the table is linearly interpolated the result is within 1% of the original emissivity value at every point. This is stored on an element by element basis, assuming equilibrium ionization fractions. The

`coco`file also contains the sum of the emission from weak lines not contained in the

`line`file, known as the pseudocontinuum, which is compressed in the same way as the continuum. Within these two files, both of which are standard FITS files, the first Header/Data Unit (HDU) is the list of temperatures, then each subsequent HDU contains the line or continuum emission for one of these temperatures. This data can then be rapidly read by fitting codes such as XSPEC and used to analyze data, interpolating between neighboring temperatures in $log\left(T\right)-log\left(\epsilon \right)$ space.

`nei`versions of the same data files that do not have this factor included in their emissivity, and for each line and continuum component specify the driving ion which created the feature, as opposed to just the element or ion of the line. For example, the forbidden line of He-like O can originate from the excitation of O

^{6+}, ionization of O

^{5+}, or recombination of O

^{7+}. Creating a model spectrum then involves calculating the ionization fraction for the plasma in question and then multiplying the tabulated emissivities by this to the result to obtain the final emissivity for the model.

#### 1.3. PyAtomDB

`PyAtomDB`now uses. This conversion enables several long term goals of the project: Users can now run the code themselves, direct access to the APED is possible for those wishing to integrate atomic data lookups into their code, and spectral models based on APED can be developed by users and integrated easily into analysis tools. The resulting six different modules of the PyAtomDB package are listed in Table 3.

`PyAtomDB`is beyond the scope of this paper. We will instead highlight some of the capabilities of the spectrum module, creating spectra of interest to end users, and extensions to it for modeling different, non-standard plasma types and investigating the effects of uncertainties on atomic data.

## 2. Spectral Modeling with PyAtomDB

`spectrum`module in PyAtomDB contains routines for creating collisional ionization equilibrium (CIE) spectra of thermal plasmas, complete with applying instrument responses. These tools are also provided with wrappers, allowing them to be used in PyXspec (https://heasarc.gsfc.nasa.gov/xanadu/xspec/python/html/).

#### 2.1. Non-Equilibrium Ionization Modeling

^{−3}s. The ionizing case is dominated by He-like lines of Si and Ne, while the recombining case shows significant emission from He- and H-like Fe, as well as the H-like Si and Mg ions.

`rnei`model in XSPEC, but has additional flexibility such as allowing the user to identify strong lines in a selected wavelength region of a non-equilibrium plasma. There is a similar model for a plane-parallel shock (

`pshock`) [12].

#### 2.2. Non-Maxwellian Modeling

#### 2.3. Charge Exchange

#### 2.4. Cross Section Data Selection

`nlS`selective cross sections for collisions with a hydrogen donor and a H-like recombining ion, and also for the bare recombining ion of C, N, O, and Ne. For all other bare ions, and for He as the donor, data is only resolved to the

`n`shell.

`nlS`resolved data, the total capture into all the states which match the

`nlS`is split evenly. For

`n`resolved data the

`l`shell distribution is handled by one of the analytical distribution functions described for ACX version 1 (the user may choose which one). For all other ions, where there is no data in the Kronos database, the model falls back to the ACX 1 models, with the total cross section fixed at $3\times {10}^{-15}$ cm

^{2}.

#### 2.5. Spectral Generation

^{25+}. This is beyond the AtomDB holdings, which stop at $n=10$ for He- and H-like ions and at $n\le $ 7 for all other ions. For these cases we have topped up the existing AtomDB A-values and wavelengths using calculations from Autostructure [28]. Where possible, the wavelengths for these calculations have been shifted to match the NIST ASD [29] values. The new energy levels were matched to the existing AtomDB levels using energy-order, symmetry, and degeneracy matching. For the Li-, He-, and H- like ions these matches were relatively trivial, though in the middle of the Fe L shell ions this matching becomes more problematic. Fortunately, the inaccuracies introduced by poor wavelengths at high energies in these complex ions can be largely discounted due to the fact that the sheer number of lines prevents any one line from producing a strong spectral signature. By contrast, a simple ion such as O

^{7+}has a straightforward series of lines with well established wavelengths, and therefore discrepancies would be more pronounced.

## 3. Estimating the Impact of Uncertainties with PyAtomDB

#### Varying Atomic Data

`variableapec`(https://github.com/AtomDB/variableapec) module, which makes use of routines in

`PyAtomDB`to identify which atomic processes most strongly affect the resulting spectra. The user can vary any fundamental atomic data in the AtomDB database by a set amount and re-run emissivity calculations to identify which lines are sensitive to the changed parameter. This allows users to investigate the sensitivity of line and line ratio emissivities over a range of temperatures and densities. The module also checks for other lines affected from perturbing a single line.

`variableapec`can also apply uncertainties for more complicated line ratios, such as the G and R ratios in the $n=2\to 1$ transition lines of He-like ions [33]. These are the ratios of the forbidden plus intercombination lines to the resonance lines (G) and the forbidden to intercombination (R) lines, which are temperature and density dependent respectively. It adds the same uncertainty to the forbidden, intercombination, and resonance lines and then calculates the error propagation on the individual rate changes to produce an error on the final line ratio. Figure 5 and Figure 6 show the effect of perturbing these key emission lines for the O vii R ratio and Fe xxv G ratio respectively. We applied a constant error over a temperature or density range, however the errors on the underlying data can be significantly temperature dependent, e.g., effective collision strengths. Future steps include recalculating line emissivities and line ratios with representative temperature-dependent errors.

## 4. Summary

## Author Contributions

`PyAtomDB`. K.H. developed the

`variableapec`module. All authors have read and agreed to the published version of the manuscript.

## Funding

## Conflicts of Interest

## Appendix A. Summary of Filetypes in APED

#### Appendix A.1. Ion-by-Ion Files

**Table A1.**APED IR (ionization and recombination rate) file definition. Excluded data types (XI, XR, and XD) are used to populate excited levels of ions but are not used when calculating the charge state distribution. The effect of these rates is included in the CI, EA, DR, and RR total rates used for calculating the charge state distribution. Notable header keywords: IONPOT contains the ionization potential in eV.

Name | Format | Description |
---|---|---|

Element | 1J | Atomic Number |

Ion_init | 1J | z1 of initial ion |

Ion_final | 1J | z1 of final ion |

Level_init | 1J | level process starts in |

Level_final | 1J | level process finished at |

TR_Type | 2A | Transition type. One of: |

CI : Collisional Ionization | ||

EA : Excitation Autoionization | ||

XI : eXcluded Ionization | ||

DR : Dielectronic Recombination | ||

RR : Radiative Recombination | ||

XR : eXcluded Radiative recombination | ||

XD : eXcluded Dielectronic recombination | ||

TR_Index | 1J | Line index in file (starting from 1) |

Par_Type | 1J | Parameter type. Defines meaning of Temperature and IonRec_Par |

51: CI: Coefficients from Younger [35]. | ||

61: EA: Lithium coefficients from Arnaud & Rothenflug [36]. | ||

62: EA: Other coefficients from Arnaud & Rothenflug [36]. | ||

63: EA: Coefficients from Mazzotta [37]. | ||

71: RR: Coefficients from Shull & Van Steenberg [38]. | ||

72: RR: Coefficients from Verner & Ferland [39]. | ||

73: RR: Coefficients from Arnaud & Raymond [40]. | ||

74: RR: Coefficients from Badnell [41]. | ||

81: DR: Coefficients from Mazzotta [37]. | ||

82: DR: Coefficients from Badnell [42]. | ||

100: CI: Coefficients from Dere [43]. | ||

Interpolatable arrays of N Rate Coefficients (cm^{3} s^{−1}): | ||

300+N: include both left and right boundary | ||

350+N: include neither boundary | ||

700+N: include only minimum boundary | ||

750+N: include only maximum boundary | ||

900+N: CI: Interpolatable array of N ${\rm Y}$ effective ionization coefficients. | ||

Min_Temp | 1E | Minimum Temperature for which data is valid (K) |

Max_Temp | 1E | Maximum Temperature for which data is valid (K) |

Temperature | 20E | Array of up to 20 temperatures (K) |

IonRec_Par | 20E | Array of up to 20 rate coefficients (cm^{3} s^{−1}) |

or coefficients as Par_Type indicates. | ||

Wavelen | 1E | Deprecated |

Wave_Obs | 1E | Deprecated |

Wave_Err | 1E | Deprecated |

BR_Ratio | 1E | Deprecated |

BR_Rat_Err | 1E | Deprecated |

Label | 20A | Deprecated |

Rate_Ref | 20A | Bibcode of reference for rates |

Wave_Ref | 20A | Deprecated |

Wv_Obs_Ref | 20A | Deprecated |

Br_Rat_Ref | 20A | Deprecated |

Name | Format | Description |
---|---|---|

Elec_Config | 40A | Electron Configuration |

Energy | 1E | Energy above ground of level (eV) |

E_Error | 1E | Error on Energy (eV) |

N_Quan | 1J | Maximum n shell of configuration |

L_Quan | 1J | Total orbital angular momentum (L) |

S_Quan | 1E | Total spin angular momentum (S) |

Lev_Deg | 1J | Level degeneracy (=$2J+1)$ |

Phot_Type | 1J | Format of photo-ionization data stored for level: |

−1 : None | ||

0 : Hydrogenic [44] | ||

1 : Clark [45] | ||

2 : Verner & Yakolev [46] | ||

3 : Table from XSTAR [47] | ||

Phot_Par | 20E | Photoionization Parameters |

AAut_Tot | 1E | Total autoionization rate from the level (s^{−1}) |

ARad_Tot | 1E | Total radiative rate from the level (s^{−1}) |

Energy_Ref | 20A | Bibcode of reference for energy |

Phot_Ref | 20A | Bibcode of reference for photoionization rate |

AAut_Ref | 20A | Bibcode of reference for autoionization sum |

ARad_Ref | 20A | Bibcode of reference for radiative sum |

Name | Format | Description |
---|---|---|

Upper_Lev | 1J | Upper (initial) level index |

Lower_Lev | 1J | Lower (final) level index |

Wavelen | 1E | Wavelength (Å) |

Wave_Obs | 1E | Observed wavelength (if not NULL, use instead of Wavelen) (Å) |

Wave_Err | 1E | Error on wavelength (Å) |

Einstein_A | 1E | Spontaneous emission coefficient (s^{−1}) |

Ein_A_Err | 1E | Error on Spontaneous emission coefficient (s^{−1}) |

Wave_Ref | 20A | Bibcode of reference for wavelength |

Wv_Obs_Ref | 20A | Bibcode of reference for observed wavelength |

Ein_A_Ref | 20A | Bibcode of reference for spontaneous emission coefficient |

Name | Format | Description |
---|---|---|

Lower_Lev | 1J | Lower (initial) level index |

Upper_Lev | 1J | Upper (final) level index |

Coeff_Type | 1J | Parameter type. Defines meaning of Temperature and EffCollStrPar |

1 : Burgess-Tully type data [48] | ||

11–16: CHIANTI 5 point spline data of types 1 to 6. | ||

21–26: CHIANTI 9 point spline data of types 1 to 6. | ||

31: S-type He-like Data from Sampson, Goett and Clark [49] | ||

32: P-type He-like Data from Sampson, Goett and Clark [49] | ||

33: S-type H-like Data from Sampson, Goett and Clark [49] | ||

41: Eqn 6 from Kato and Nakazaki [50] | ||

42: Eqns 10–12 from Kato and Nakazaki [50] | ||

100+N : Interpolable ${\rm Y}$, include both left and right boundary | ||

150+N : Interpolable ${\rm Y}$, include neither boundary | ||

500+N : Interpolable ${\rm Y}$, include only minimum boundary | ||

550+N : Interpolable ${\rm Y}$, include only maximum boundary | ||

300+N : Interpolable rate coefficient, include both left and right boundary | ||

350+N : Interpolable rate coefficient, include neither boundary | ||

700+N : Interpolable rate coefficient, include only minimum boundary | ||

750+N : Interpolable rate coefficient, include only maximum boundary | ||

Min_Temp | 1E | Minimum Temperature coefficients are valid for (K) |

Max_Temp | 1E | Maximum Temperature coefficients are valid for (K) |

Temperature | 20E | Temperature Grid (K) |

EffCollStrPar | 20E | Effective collision strength parameters |

Inf_Limit | 1E | Infinite temperature limit for extrapolations |

Reference | 20A | Bibcode for data. |

Name | Format | Description |
---|---|---|

Lower_Lev | 1J | Lower (initial) level index |

Upper_Lev | 1J | Upper (final) level index |

Coeff_Type | 1J | Parameter type. Defines meaning of Temperature and Coeff_Om |

200+N : Interpolable Y, include both left and right boundary | ||

250+N : Interpolable Y, include neither boundary | ||

600+N : Interpolable Y, include only minimum boundary | ||

650+N : Interpolable Y, include only maximum boundary | ||

400+N : Interpolable rate coefficient, include both left and right boundary | ||

450+N : Interpolable rate coefficient, include neither boundary | ||

400+N : Interpolable rate coefficient, include only minimum boundary | ||

450+N : Interpolable rate coefficient, include only maximum boundary | ||

1001 : Burgess-Tully proton excitation rate data [48] | ||

Min_Temp | 1E | Minimum Temperature coefficients are valid for (K) |

Max_Temp | 1E | Maximum Temperature coefficients are valid for (K) |

Temperature | 20E | Temperature Grid (K) |

Coeff_Om | 20E | Effective collision strength parameters |

Reference | 20A | Bibcode for data. |

Name | Format | Description |
---|---|---|

Upper_Lev | 1J | Upper (initial) level index |

Lower_Lev | 1J | Lower (final) level index |

Wavelen | 1E | Wavelength (Å) |

Wave_Obs | 1E | Observed wavelength (if not NULL, use instead of Wavelen) (Å) |

Wave_Err | 1E | Error on wavelength (Å) |

DR_Type | 1J | Type of DR data stored: |

1: Romanik [51] | ||

2: Safranova [52] | ||

E_Excite | 1E | Excitation Energy (keV) |

EExc_Err | 1E | Error on Excitation Energy (keV) |

SatelInt | 1E | Satellite line intensity (s^{−1}) |

SatIntErr | 1E | Error on satellite line intensity (s^{−1}) |

Params | 10E | DR line parameters |

DRRate_Ref | 20A | Bibcode for DR rate |

Wave_Ref | 20A | Bibcode of reference for wavelength |

Wv_Obs_Ref | 20A | Bibcode of reference for observed wavelength |

**Table A7.**APED PI (photoionization) file definition. This is used to store tabulated XSTAR style data.

Name | Format | Description |
---|---|---|

HDU 1 | ||

Ion_init | 1J | z1 of initial ion |

Lev_init | 1J | level process starts in |

Ion_final | 1J | z1 of final ion |

Lev_final | 1J | level process finished at |

PI_Type | 1J | Type of XSTAR data: |

10,000+N: XSTAR Type 49 data at N points | ||

20,000+N: XSTAR Type 53 data at N points | ||

G_Ratio | 1E | Degeneracy ratio of the levels |

Energy | 40E | Energy grid (eV) |

PI_Param | 40E | Photoionization cross section (Mb) |

Reference | 20A | Bibcode of reference for data |

HDU 2: XSTAR Level file | ||

Elec_Config | 40A | Electron Configuration |

Energy | 1E | Energy above ground of level (eV) |

E_Error | 1E | Error on Energy (eV) |

N_Quan | 1J | Maximum n shell of configuration |

L_Quan | 1J | Total orbital angular momentum (L) |

S_Quan | 1E | Total spin angular momentum (S) |

Lev_Deg | 1J | Level degeneracy (=$2J+1)$ |

Phot_Type | 1J | Format of photo-ionization data stored for level (should be 3): |

−1 : None | ||

0 : Hydrogenic [44] | ||

1 : Clark [45] | ||

2 : Verner & Yakolev [46] | ||

3 : Table from XSTAR [47] | ||

Phot_Par | 20E | Photoionization Parameters |

Name | Format | Description |
---|---|---|

Ion_init | 1J | z1 of initial ion |

Ion_final | 1J | z1 of final ion |

Lev_init | 1J | level process starts in |

Lev_final | 1J | level process finished at |

Auto_Rate | 1E | Autoionization rate s^{−1} |

Auto_Err | 1E | Error on autoionization rate s^{−1} |

Auto_Ref | 20A | Bibcode of reference for data |

#### Appendix A.2. All Ion Files

**Table A9.**APED abundance file definition. Each source refers to a different published data table. Descriptions matching them to publications can be found in the headers.

Name | Format | Description |
---|---|---|

Source | 10A | description of source |

H | 1D | Abundance of H in $log\left(12\right)$ notation |

He | 1D | Abundance of He in $log\left(12\right)$ notation |

Li | 1D | Abundance of Li in $log\left(12\right)$ notation |

Be | 1D | Abundance of Be in $log\left(12\right)$ notation |

B | 1D | Abundance of B in $log\left(12\right)$ notation |

⋮ | ⋮ | ⋮ |

Ni | 1D | Abundance of Ni in $log\left(12\right)$ notation |

Cu | 1D | Abundance of Cu in $log\left(12\right)$ notation |

Zn | 1D | Abundance of Zn in $log\left(12\right)$ notation |

**Table A10.**APED eigenvector file definition. These can be in separate file for each ion or a separate Header Data Unit (HDU) in the same file for each. Data is stored at 1251 temperatures from ${10}^{4}$ to ${10}^{9}$ K, logarithmically spaced. Eigenvector and eigenvalue data is stored for solving non-equilibrium ionization balances, using the method of [53].

Name | Format | Description |
---|---|---|

FEQB | (Z+1)D | Equilibrium ionization fraction for each ion (Z = atomic number of element) |

EIG | (Z)D | Eigenvalues for each ion |

VR | Z^{2} | Right eigenvectors for each ion |

VL | Z^{2} | Left eigenvectors for each ion |

**Table A11.**APED filemap file definition. This is a text file which denotes which files were used in an APEC run to create the emissivity files. It is used to identify the current recommended data in the database. Each line indicates another file, with the contents of each line being four columns, in the format “I2XI2XI2XS”. I2 is a two character integer, S is a string of unspecified length, and X is a white space character. Each column represents, from left to right:

Name | Format | Description |
---|---|---|

Filetype | I2 | 1: IR |

2: LV | ||

3: LA | ||

4: EC | ||

5: PC | ||

6: DR | ||

8: PI | ||

9: AI | ||

10: Abundances | ||

11: Bremsstrahlung coefficients from [54] | ||

13: Bremsstrahlung coefficients from [55] | ||

Z | I2 | : Element charge. 0 indicates non-element-specific data. |

z1 | I2 | : Ion charge plus 1. −1 indicates irrelevant (e.g., for non-element specific data) |

Filename | S | The path and name of the file to open |

#### Appendix A.3. APEC Emissivity Files

**Table A12.**APEC Line Emission file definition. HDU 1 lists the plasma parameters for each HDU, HDU 2+ are the spectrum for each of those plasams defined in HDU 1.

Name | Format | Description |
---|---|---|

HDU 1: parameters | ||

kT | 1E | Temperature for each HDU (keV) |

EDensity | 1E | Electron Density (cm^{−3}) |

Time | 1E | Time elapsed from equilibrium (s) (not used) |

Nelement | 1J | Number of elements in the HDU |

Nline | 1J | Number of lines in the HDU |

HDU 2+: emissivity | ||

Lambda | 1E | Line wavelength (Å) |

Lambda_Err | 1E | Error on line wavelength (Å) |

Epsilon | 1E | Line emissivity (ph cm^{3} s^{−1}) |

Epsilon_Err | 1E | Error on line emissivity (photons cm^{3} s^{−1}) |

Element | 1J | Atomic number of element |

Elem_drv | 1J | Atomic number of driving element (NEI only) |

Ion | 1J | z1 of ion |

Ion_drv | 1J | z1 of driving ion (NEI only) |

UpperLev | 1J | Upper level of transition |

LowerLev | 1J | Lower level of transition |

**Table A13.**APEC Continuum Emission file definition. HDU 1 lists the plasma parameters for each HDU, HDU 2+ are the spectrum for each of those plasmas defined in HDU 1. Note that for the E_Cont, Cont, E_Pseudo, and Pseudo variables, the size of the array is set to the maximum length (N_Cont or N_Pseudo) of every ion in the HDU. However all values above the relevant N_Cont or N_Pseudo are ignored when using the data.

Name | Format | Description |
---|---|---|

HDU 1: parameters | ||

kT | 1E | Temperature for each HDU (keV) |

EDensity | 1E | Electron Density (cm^{−3}) |

Time | 1E | Time elapsed from equilibrium (s) (not used) |

Nelement | 1J | Number of elements in the HDU |

NCont | 1J | Max length continuum entries in the HDU |

NPseudo | 1J | Max length of pseudocontinuum entries in the HDU |

HDU 2+: emissivity | ||

Z | 1J | Atomic number of element |

rmJ | 1J | z1 of driving ion. 0 if equilibrium |

N_Cont | 1J | Length of continuum entry for ion |

E_Cont | N_Cont*E | Energies for each continuum point (keV) |

Continuum | max(N_Cont)*E | Emissivity at each continuum point (ph cm^{−3} s^{−1} keV^{−1}) |

Cont_Err | max(N_Cont)*E | Error on emissivity at each continuum point (ph cm^{−3} s^{−1} keV^{−1}) |

N_Pseudo | 1J | Length of pseudocontinuum entry for ion |

E_Pseuso | max(N_Pseudo)*E | Energies for each pseudocontinuum point (keV) |

Pseudo | max(N_Pseudo)*E | Emissivity at each pseudocontinuum point (ph cm^{−3} s^{−1} keV^{−1}) |

Pseudo_Err | N_Pseudo*E | Error on emissivity at each pseudocontinuum point (ph cm^{−3} s^{−1} keV^{−1}) |

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**Figure 1.**Emission from $k{T}_{e}=0.7$ keV plasmas in equilibrium, ionizing (from $k{T}_{e}=0.07$ keV) and recombining (from $k{T}_{e}=7.0$ keV). The ionization timescale is ${n}_{e}t={10}^{10}$ cm

^{−3}s for both non-equilibrium cases. Spectra have been folded though the Chandra ACIS-S/HETG +1 order response from Cycle 22.

**Figure 2.**Ionization and recombination rate coefficients of oxygen in a kT = 0.2 keV, $\kappa $ = 2.0 plasma. Top: The total rate coefficients for the $\kappa $ and Maxwellian case. Middle: The ratio of the $\kappa =2.0$ ionization (red) and recombination (blue) rates to their Maxwellian equivalent. The different shades represents the contribution of each Maxwellian component from the decomposition method of [18]. Bottom: The resulting emission in the O

^{6+}He-$\alpha $ triplet. The components of the Maxwellian decomposition are again shown in different colors. Note that the Maxwellian total emissivity, marked with the red line, is larger due to the charge state distribution having more O

^{6+}in the Maxwellian case.

**Figure 3.**Fe xvii emission lines in the range of 10–20 Å sensitive to a ±30% change in A value at ${T}_{e}=4\times {10}^{6}$ K and low density. Black points denote the emissivity change for the transition varied while colored points denote other transitions affected for each perturbed line.

**Figure 4.**Fe xvii 3C/3D line ratio at low density as a function of temperature with a ±15% uncertainty on the direct excitation rates of both the 3C and 3D lines. The final error on the line ratio is ∼30% for the entire temperature range plotted.

**Figure 5.**O vii R ratio with a ±15% uncertainty on the direct excitation rates of the forbidden, resonance, and intercombination lines at three different plasma temperatures.

**Figure 6.**Fe xxv G ratio with a ±15% uncertainty on the direct excitation rates of the forbidden, resonance, and intercombination lines at low density. The final error on the line ratio is ∼15% for the entire temperature range plotted.

**Figure 7.**Blended Fe xiii line ratio (209.62 + 209.92) Å/213.77 Å versus density at Te = 200 eV. The final error on the line ratio is ∼16% for the entire temperature range plotted.

Type | Short Description | Details |
---|---|---|

IR | Ionization & recombination | Ionization from and recombination into the ion. |

LV | Energy levels | Energy levels and photoionization cross section data. |

LA | Lambda & A-values | Wavelengths and Einstein-A probabilities of transitions. |

EC | Electron collisions | Electron-impact excitation rate coefficients or effective |

collision strengths. | ||

PC | Proton collisions | Proton-impact excitation rate coefficients or effective |

collision strengths. | ||

DR | Dielectronic recombination | DR Satellite line wavelengths and intensities. |

PI | Photoionization | Photoionization cross sections for ions with data from XSTAR. |

AI | Autoionization | Final state selective autoionization transition probabilities. |

**Table 2.**File types for global atomic data in APED. A full description of the data files and formats is included in Appendix A.

Type | Short Description | Details |
---|---|---|

abund | Elemental abundance | Abundance relative to solar for elements $Z\le 30$ |

ionbal | Ionization balance | Equilibrium ionization balance and non-equilibrium |

eigenvectors for each element | ||

filemap | List of filenames | The data files used to create the latest release of the |

Astrophysical Plasma Emission Code (APEC) model |

**Table 3.**Modules within PyAtomDB and their purpose. A full description is provided in the code documentation (https://atomdb.readthedocs.io).

Module | Purpose |
---|---|

atomdb | Accessing the database, returning atomic data |

apec | Thermal plasma model |

spectrum | Creating spectra from apec outputs |

atomic | Basic atomic data (element names, etc.) |

const | Physical and code related constants |

util | Utilities and helper routines |

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**MDPI and ACS Style**

Foster, A.R.; Heuer, K.
PyAtomDB: Extending the AtomDB Atomic Database to Model New Plasma Processes and Uncertainties. *Atoms* **2020**, *8*, 49.
https://doi.org/10.3390/atoms8030049

**AMA Style**

Foster AR, Heuer K.
PyAtomDB: Extending the AtomDB Atomic Database to Model New Plasma Processes and Uncertainties. *Atoms*. 2020; 8(3):49.
https://doi.org/10.3390/atoms8030049

**Chicago/Turabian Style**

Foster, Adam R., and Keri Heuer.
2020. "PyAtomDB: Extending the AtomDB Atomic Database to Model New Plasma Processes and Uncertainties" *Atoms* 8, no. 3: 49.
https://doi.org/10.3390/atoms8030049