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

Round 1

Reviewer 1 Report

An accuracy of physical parameters and chemical abundances of astrophysical objects depends largely on completeness and accuracy of existing atomic and molecular data and adequate treatment of the physical processes that affect the emergent radiation. The paper describes the software package PyAtomDB, which provides the atomic data and the tools for modelling the theoretical X-ray and EUV spectra of optically thin, hot plasma, which are applicable to a variety of astrophysical objects, such as coronas of the Sun and cool stars, stellar winds, supernova remnants, interstellar and intergalactic gas. PyAtomDB is an extension of the widely known AtomDB project, and it allows for (i) direct access to the atomic database APED, (ii) creating the new models which enable for charge exchange and non-Maxwellian electron energy distribution, and (iii) estimating the effects of uncertainties in the used atomic data on diagnostic line ratios.

The paper opens new opportunities for all the researchers dealing with analysis of the X-ray and EUV astrophysical spectra. I recommend the paper for publication, however, have a few minor remarks. I would be happy the authors to address them.

1. In the text, there are no references to Figures 4 and 6.

2. Page 3, string 82: One needs to decrypt the abbreviation HDU, when it is first used.

3. Pages 10 and 11: What is meant by G and R ratios?

4. Typos on string 155 and caption of Table A13.

Author Response

We thank the reviewer for their comments. We have made all the changes requested and have marked in bold any changes to the text (excluding typo corrections)

1. In the text, there are no references to Figures 4 and 6.

We have now added references to these figures in the relevant section [DEFINE]

2. Page 3, string 82: One needs to decrypt the abbreviation HDU, when it is first used.

This is part of the FITS (Flexible Image Transfer System) definition, admittedly a very old standard not used much outside of astrophysics today.  We have added the definition of the Header/Data Unit.

3. Pages 10 and 11: What is meant by G and R ratios?

We have added a sentence to this description. Further information is provided in the reference provided.

4. Typos on string 155 and caption of Table A13.

These have been fixed, as have several others.

 

Reviewer 2 Report

The AtomDB package has been available for many years.  Every few years, it is updated and extended as described in Section 1.  The present paper describes a further extension and improvement over earlier versions. As part of that improvement, the new version is written in Python

The paper describes the various extensions and shows some examples of how those extensions can be implemented. It also points users to ways in which their own work can be improved by the use of this new version of the package.  It is of particular value to the astronomy/astrophysics community.

It represents a significant enhancement of a well-established database project and merits publication.

Author Response

We thank the reviewer for their comments.

Reviewer 3 Report

Atoms #893270 referee report The article presents a detailed description of the new software package, PyAtomDB, for synthesis of EUV and X-ray spectra of optically thin, collisionally-dominated astronomical sources. New tools for non-Maxwellian and Charge-exchange plasmas are added. I applaud the authors' efforts put into such modelling, as well as the fact that the package is written in Python. In addition, the package contains several useful features, such as tools to evaluate the atomic data precision on the resulting spectra, and allows for including ionization and recombination into excited levels. The manuscript can be recommended for acceptance; however I would like to offer few minor remarks for the authors' consideration. MINOR REMARKS 1. page 1, line 18: The authors should be clear if by "collision strenghts" they mean the Omegas themselves, or the effective collision strengths (Maxwellian-integrated). 2. page 4, lines 118-120: The authors should provide more details on the physical conditions leading to ionizing and recombining spectra. These should be described in the text, and not in the caption of Figure 1. 3. page 7, line 152: The formulation "foreground CX emission adds an additional background ..." should be rephrased. 4. Section 3.1, p. 9, lines 225-227: The authors should explain what the "fractional change in emissivity" is. If the A-value for the 3E transition is changed by 30%, surely the emissivity of the line must change by a similar amount. The valuee of "fractional change in emissivity greater than 0.01%" is confusing. 5. The authors should discuss the relative magnitude of atomic data uncertainties chosen. For example, a change in A-value of 30% for well-observed lines seems excessive. 6. Figures 5-7 are small and the labels are barely readable.

Author Response

1. page 1, line 18: The authors should be clear if by "collision strenghts" they mean the Omegas themselves, or the effective collision strengths (Maxwellian-integrated).

We meant the effective collision strengths. This has been added to the text.

2. page 4, lines 118-120: The authors should provide more details on the physical conditions leading to ionizing and recombining spectra. These should be described in the text, and not in the caption of Figure 1.

We have added in a new section 2.1 detailing NEI spectra and their origins.

3. page 7, line 152: The formulation "foreground CX emission adds an additional background ..." should be rephrased.

Background has been changed to “nuisance component”

4. Section 3.1, p. 9, lines 225-227: The authors should explain what the "fractional change in emissivity" is. If the A-value for the 3E transition is changed by 30%, surely the emissivity of the line must change by a similar amount. The valuee of "fractional change in emissivity greater than 0.01%" is confusing.

Adam’s version:

The A values do not lead to 30% change in the emissivity as , in the low density case, it is limited by the process populating the level. So a 30% change in the effective collision strength from the ground would lead to a ~30% change in the emissivity. We have added text to this effect.

We have revised the sentence “fractional change in emissivity greater than 0.01%” to say “Throughout this work we provide errors as the mean value of the positive and negative uncertainties for the fractional emissivity change. Line ratio errors are half the range of the maximum and minimum ratios obtained when applying both positive and negative uncertainties to the individual atomic data.”

 We also revised our error calculations to show the +/- error, rather than give the error as a fraction of the full error range over the original emissivity value in the previous draft. We have updated all plots to reflect this new definition. 

5. The authors should discuss the relative magnitude of atomic data uncertainties chosen. For example, a change in A-value of 30% for well-observed lines seems excessive.

This is a deliberately large number for demonstration purposes, though it is at least consistent with the uncertainties in NIST and found in Bernit 2012. We have added some explanation to the text.

6. Figures 5-7 are small and the labels are barely readable.

We have enlarged the text on these figures