DOC: add xps to howto

[superstar54]

This PR adds the doc for XPS calculation using the plugin_workchain branch of aiidalab-qe.

I also improved the XPS plugin by:

• Added an upload button for the experimental data.
• Add the offset correction into the workflow so that the user don't need to correct the binding energy manually.

[codecov]

Codecov Report

Attention: Patch coverage is 8.57143% with 32 lines in your changes are missing coverage. Please review.

Project coverage is 75.79%. Comparing base (979f2e4) to head (c4a8241).

Files	Patch %	Lines
src/aiidalab_qe/plugins/xps/result.py	8.82%	31 Missing ⚠️
src/aiidalab_qe/plugins/xps/workchain.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #438      +/-   ##
==========================================
- Coverage   75.83%   75.79%   -0.05%     
==========================================
  Files          60       60              
  Lines        4295     4300       +5     
==========================================
+ Hits         3257     3259       +2     
- Misses       1038     1041       +3     

Flag	Coverage Δ
python-3.10	75.79% <8.57%> (-0.05%)	⬇️
python-3.8	75.82% <8.57%> (-0.05%)	⬇️
python-3.9	75.82% <8.57%> (-0.05%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[PNOGillespie]

Hi @superstar54, good work putting together a simple documentation set.

I've added some suggested some minor changes to fix typos and grammar in some places.

The more substantive changes are:

1. Step 2 is missing a picture of the XPS Settings tab.
2. There are parts towards the end which talk about the offset energies and the spin-orbit splitting, but lacks a prior step which explains how to export the data (beyond reading the value from the Plotly widget)
3. The real world example of ETFA doesn't seem to give much useful information for the user about the plugin (see the relevant comment for more information).

[PNOGillespie]

This section here could be useful, but (unless I'm mistaken) there is no way to extract the exact binding energy values from AiiDALab-QE.

If there is a way to do this, then please update some part of the text with instructions on how to do so, otherwise this doesn't provide much utility and should be removed for simplicity.

[superstar54]

Thanks for pointing out this. I add the detail text to tell user how to find the exact binding energies.

[PNOGillespie]

This last example doesn't seem to provide much for the user's benefit, for a few reasons:

1. The calculated and experimental spectra aren't plotted together for comparison.
2. Without a set of instructions, or source for the structure, the user can't use this like some sort of complex "real-world" example as an extension of the documentation and so it doesn't really add much.

I would suggest either removing the section or replacing the example with one for Phenacetylene, which we have tested already and can provide figures/data for.

[superstar54]

Thanks for the suggestions. I added the ETFA molecule into the example so users can use it. also, add a tip to tell users how to run the calculation.
Currently, the app does not provide the functionality to add experimental data to the plot. But one can also compare the two plots together. I don't plot them manually because I don't want to give the user the impression that this can be done in the app directly.
Instead of giving an example that the calculated values match the experiment very well, the real example here shows the difference between calculated values and the experimental values. This is important that, the user knows our app is powerful, but there are still some limitations due to the underlying method.

[superstar54]

@PNOGillespie thanks for the review. I revised the page based on your suggestions.

Step 2 is missing a picture of the XPS Settings tab.

I added a picture.

There are parts towards the end which talk about the offset energies and the spin-orbit splitting, but lacks a prior step which explains how to export the data (beyond reading the value from the Plotly widget)

I added a detailed instruction.

The real world example of ETFA doesn't seem to give much useful information for the user about the plugin (see the relevant comment for more information).

I replied after your comment.

Please have a second review.

[PNOGillespie]

Hi @superstar54. Looks good for the most part, particularly in providing a contrast between ETFA and Phenylacetylene. Just a few proofreading changes to make, then I think this is good to go.

Since you have added a spectrum upload tool (which seems to work fine, from what i can see) I would suggest (in a different PR) one improvement, which would be to add a UI element to scale the intensities of the computed XPS traces so as to make it easier to compare the profile of (in particular) the total XPS to the experimental data.

Again, I would just suggest you open an improvements issue for that and address that at a later time.

[superstar54]

Thanks @PNOGillespie . I made the changes and also created an issue as you suggested. #627

[PNOGillespie]

Good to go. Nice work @superstar54! Thanks also for adding the issue page.