Add plugin: XPS #518
Add plugin: XPS #518
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## main #518 +/- ##
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- Coverage 77.48% 75.82% -1.67%
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Files 55 60 +5
Lines 4011 4277 +266
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+ Hits 3108 3243 +135
- Misses 903 1034 +131
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@PNOGillespie, Please review this PR. Thanks! |
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It seems that the plugins still use the default pseudo family from pw workchain. |
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Hi @superstar54, I've had a look at the code and, generally speaking, it looks good. I've left some suggested changes here and there to improve readability and clean up commented-out blocks of code.
The only important change IMO is a selection widget for the element to display in the Result panel - see the relevant comment for discussion.
| voigt_profile_help = ipw.HTML( | ||
| """<div style="line-height: 140%; padding-top: 10px; padding-bottom: 10px"> | ||
| The Voigt function: | ||
| </div>""" | ||
| ) |
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Was there meant to be a description of the Voigt function here? I would suggest adding something for the user's benefit, at least just to tell them what the two slider values are.
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I added a description for the parameters and also a link to Wikipedia.
| for element, data in spectra.items(): | ||
| # print(element, data) | ||
| for site, d in data.items(): | ||
| g.add_scatter(x=d[0], y=d[1], fill="tozeroy", name=f"{element}_{site}") |
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Would it be possible to add a dropdown/selection widget to change between different elements? (e.g. like what the XAS plugin has)
On the one hand, the user should know that XPS spectra from different elements aren't comparable and to look at the different elements separately. On the other hand, it would tidy up the UI a lot - particularly when considering a structure with many inequivalent atoms (e.g. a complex molecule)
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Thanks! I added the selection dropdown for different elements, like in the XAS plugin.
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| pseudo_title = ipw.HTML( | ||
| """<div style="padding-top: 0px; padding-bottom: 0px"> | ||
| <h4>Pseudopotential</h4></div>""" |
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Just to make things easier to read:
| <h4>Pseudopotential</h4></div>""" | |
| <h4>Core-Hole pseudopotential group</h4></div>""" |
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I changed as you suggested.
| peak_title = ipw.HTML( | ||
| """<div style="padding-top: 0px; padding-bottom: 0px"> | ||
| <h4>Select peak</h4></div>""" | ||
| ) | ||
| peak_help = ipw.HTML( | ||
| """<div style="line-height: 140%; padding-top: 6px; padding-bottom: 0px"> | ||
| The list of peaks to be considered for analysis. | ||
| </div>""" | ||
| ) |
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Would something like this make sense for readability? "Core-Hole" or "Core-Level" seems like it would be more intuitive, but if "Peak" is the correct technical term in this case then don't worry.
| peak_title = ipw.HTML( | |
| """<div style="padding-top: 0px; padding-bottom: 0px"> | |
| <h4>Select peak</h4></div>""" | |
| ) | |
| peak_help = ipw.HTML( | |
| """<div style="line-height: 140%; padding-top: 6px; padding-bottom: 0px"> | |
| The list of peaks to be considered for analysis. | |
| </div>""" | |
| ) | |
| peak_title = ipw.HTML( | |
| """<div style="padding-top: 0px; padding-bottom: 0px"> | |
| <h4>Select core-level</h4></div>""" | |
| ) | |
| peak_help = ipw.HTML( | |
| """<div style="line-height: 140%; padding-top: 6px; padding-bottom: 0px"> | |
| The list of core-levels to be considered for analysis. | |
| </div>""" | |
| ) |
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Thanks! I change it to core-level
| # self.core_hole_treatment_title, | ||
| # self.core_hole_treatment_help, | ||
| # self.core_hole_treatment, | ||
| self.pseudo_title, | ||
| self.pseudo_help, | ||
| self.pseudo_group, | ||
| self.peak_title, | ||
| self.peak_help, | ||
| ipw.HBox( | ||
| [self.peak_list], | ||
| ), | ||
| # self.supercell_title, | ||
| # self.supercell_help, | ||
| # ipw.HBox( | ||
| # [self.supercell_min_parameter], | ||
| # ), |
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There are quite a few commented-out sections here which should be cleaned up if possible:
| # self.core_hole_treatment_title, | |
| # self.core_hole_treatment_help, | |
| # self.core_hole_treatment, | |
| self.pseudo_title, | |
| self.pseudo_help, | |
| self.pseudo_group, | |
| self.peak_title, | |
| self.peak_help, | |
| ipw.HBox( | |
| [self.peak_list], | |
| ), | |
| # self.supercell_title, | |
| # self.supercell_help, | |
| # ipw.HBox( | |
| # [self.supercell_min_parameter], | |
| # ), | |
| self.pseudo_title, | |
| self.pseudo_help, | |
| self.pseudo_group, | |
| self.peak_title, | |
| self.peak_help, | |
| ipw.HBox( | |
| [self.peak_list], | |
| ), |
Does this also mean (based on the fact that supercell_min_parameter is not used) that the supercell size used in calculation is defined entirely by the protocol?
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Yes. This would be more user friendly
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@PNOGillespie Thanks for your review. I made the changes as you suggested. I added the dropdown button to select the spectrum for different elements. I also added a table to show the offset energies, which are used to calibrate the calculated binding energy. |
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Hi @superstar54. Code looks good for the most part. I've added a few final changes, after which I think this PR is complete.
| g.add_scatter( | ||
| x=d["x"], y=d["y"], fill=fill.value, name=d["site"] | ||
| ) |
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This section here causes a crash because you're calling the value from the UI element rather than converting it to a type of fill method (e.g. "tozeroy"):
| g.add_scatter( | |
| x=d["x"], y=d["y"], fill=fill.value, name=d["site"] | |
| ) | |
| if fill.value: | |
| fill_type = "tozeroy" | |
| else: | |
| fill_type = None | |
| g.add_scatter( | |
| x=d["x"], y=d["y"], fill=fill_type, name=d["site"] | |
| ) |
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thanks! I changed it.
| correction_energies_table = ipw.HTML( | ||
| """<h4>Offset Energies (δ)</h4> | ||
| <div>The binding energies should be corrected by these constant offsets. These offsets mainly depend on chemical element and core level, and are determined by comparing the calculated core electron binding energy to the experimental one.</div> | ||
| <table><tr><th>Core-level</th><th>Value (eV)</th></tr>""" | ||
| ) |
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The first sentence should remind the user how the correction energies are used in practice:
| correction_energies_table = ipw.HTML( | |
| """<h4>Offset Energies (δ)</h4> | |
| <div>The binding energies should be corrected by these constant offsets. These offsets mainly depend on chemical element and core level, and are determined by comparing the calculated core electron binding energy to the experimental one.</div> | |
| <table><tr><th>Core-level</th><th>Value (eV)</th></tr>""" | |
| ) | |
| correction_energies_table = ipw.HTML( | |
| """<h4>Offset Energies (δ)</h4> | |
| <div>When comparing binding energies reported by AiiDALab-QE to experimental data, these should be corrected by the given offset listed below</div> | |
| <table><tr><th>Core-level</th><th>Value (eV)</th></tr>""" | |
| ) |
I would also recommend moving the second sentence (or maybe the relevant concept or description) to the documentation since this is not really needed here.
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thanks! I made the changes.
| for core_level, value in correction_energies.items(): | ||
| element = core_level.split("_")[0] | ||
| if element not in self.spectrum_select_options: | ||
| continue | ||
| exp = value["exp"] | ||
| correction_energies_table.value += ( | ||
| f"<tr><td>{core_level}</td><td>{exp}</td></tr>" | ||
| ) | ||
| return correction_energies_table |
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Just a little addition to make things clearer:
| for core_level, value in correction_energies.items(): | |
| element = core_level.split("_")[0] | |
| if element not in self.spectrum_select_options: | |
| continue | |
| exp = value["exp"] | |
| correction_energies_table.value += ( | |
| f"<tr><td>{core_level}</td><td>{exp}</td></tr>" | |
| ) | |
| return correction_energies_table | |
| for core_level, value in correction_energies.items(): | |
| element = core_level.split("_")[0] | |
| if element not in self.spectrum_select_options: | |
| continue | |
| exp = value["exp"] | |
| if exp >= 0.0: | |
| sign = "+" | |
| elif exp < 0: | |
| sign = "" | |
| correction_energies_table.value += ( | |
| f"<tr><td>{core_level}</td><td>{sign}{exp}</td></tr>" | |
| ) | |
| return correction_energies_table |
If the values can be positive or negative, then it's usually a good idea to give the sign explicitly even if the number is positive.
The string for the core level name should probably also have the underscore removed, since this doesn't format so well in non-monospace text. I understand this is also the way that the labels for the core levels are written in the Setting panel, but I wouldn't worry about changing those at this stage.
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thanks! The sign is indeed very important. I just noticed reverse the sign for all values.
Co-authored-by: Peter Gillespie <55498719+PNOGillespie@users.noreply.github.com>
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@PNOGillespie, thanks for your review and very useful suggestions! I made all the changes as suggested. |
This PR adds a plugin for calculating X-ray Photoelectron Spectroscopy (XPS) spectra using the
XpsWorkChainof aiida-quantumespresso package.Setting Panel
The Setting panel allows users to
Results Panel
The Result panel displays the final XPS spectrum.
Pseudopotentials
XPS calculations in QE require core-hole pseudopotentials. We supply a set of pseudopotentials specific to XPS calculations in the XPS Pseudopotential Repository. This repository provides the core-hole pseudopotentials as an AiiDA archive file. There are two kind of pseudopotentials available:
WorkChain
To make the setting as simple as possible for user. The following default setting are used.
core_hole_treatment.fullfor moleculexch_smearfor metalxch_fixedfor insulatorsupercell_min_parameterupdated based onprotocol.