Issues Reproducing CsPbI₃ Static Structure Factor Tutorial and Missing Example Files in dynasor Documentation

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Hello everyone,

I am a graduate student currently learning to use ‘dynasor’ for analyzing MD trajectories and comparing them with scattering experiments. First of all, I would like to express my sincere appreciation for this excellent tool and the valuable work behind it.

While studying the tutorials on the official dynasor documentation and GitHub page, I encountered several issues that I hope you could help me with.

  1. Unable to reproduce “Static structure factor in CsPbI₃” tutorial

I followed the steps exactly as described, but I was unable to reproduce the results shown on the tutorial page. It would be very helpful if you could provide:

  • the exact trajectory or dataset used in the example,
  • or any additional settings/parameters that are required but not explicitly shown.
  1. Missing example files in several tutorial sections**

I noticed that some parts of the documentation do not include the full runnable example files needed to carry out the calculations. The sections where I encountered missing datasets or scripts are:

  • Spectral energy density (SED)
  • Peak fitting
  • Autocorrelation functions and FFTs

Would it be possible to share the input files, datasets, or minimal working examples for these sections? Having access to the original files would greatly help me understand the correct workflow and verify that my setup is consistent with the intended usage.

Thank you very much in advance!

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Hi Vead917

Thank you for you post. Concerning your questions, the files needed for the tutorial on the computation of the static structure factor are provided on zenodo and can be retrieved via wget as shown in the tutorial. The MD output files are provided as a tar.gz archive that needs to be extracted as well. On the Linux (or OSX) command line this can be done by running tar xfz md_runs.tar.gz or in two steps via gunzip md_runs.tar.gz && tar xf md_runs.tar. The notebook only mentions the first step of the latter combination. This will be fixed via a merge request soon.

The input files for the other tutorials you mention are part of the repository, which you can find on GitLab, see, e.g.:

We will add more explicit links to the tutorials.

1 Like
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You can now find updated versions of the tutorial notebooks in the current master version, the documentation of which can be found at dynasor – Correlations for everyone — dynasor documentation

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Thank you very much for your detailed explanation and guidance. After following your instructions, I was able to successfully retrieve and extract the files, and now I can fully reproduce the tutorial results. The additional links to the ACF, DHO, and SED examples were also extremely helpful.

My issues are completely resolved now. I really appreciate your assistance and the effort you and the team put into maintaining dynasor.

Thanks again!