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aiidalab / aiidalab-qe

AiiDAlab App for Quantum ESPRESSO
https://aiidalab-qe.readthedocs.io/
MIT License
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Example structure SiO2 has extra tags #617

Closed superstar54 closed 6 months ago

superstar54 commented 8 months ago

Describe the bug Feedback from a PSI user: I tried calculating XAS spectra for SiO2 (from the example structures). The SiO2 structure gives me the error < ValueError: Error occurred validating port 'inputs.pw': The pseudos specified and structure kinds do not match: {'O', 'O1', 'Si', 'X'} vs {'O', 'Si', 'X'} >

Additional context We should remove the tag of the SiO2 structure.

PNOGillespie commented 8 months ago

Hi @superstar54. Just wanted to add a few things here:

  1. I would be interested to try re-creating the error, since I'm fairly sure something like this should be fixed by (https://github.com/aiidateam/aiida-quantumespresso/pull/969) but I'd like to make sure this is the case.
  2. Why does the structure have this special marker for oxygen anyway? I'm just curious about that.

SiO2 is also used in the XSpectra literature (section A of the 2009 paper), and their past tutorials, as an example for Si and O K-edge calculations. The structure used there is hexagonal, rather than the one currently in the examples which is tetragonal, so I could provide a replacement for the structure already in the AiiDALab-QE examples if we want to do that.

Let me know your thoughts on that.

superstar54 commented 6 months ago

The tag is removed in #518.

The structure used there is hexagonal, rather than the one currently in the examples which is tetragonal, so I could provide a replacement for the structure already in the AiiDALab-QE examples if we want to do that.

Thanks @PNOGillespie. Some structures in the example are incorrect, and @cpignedoli is working on it.