Handling fractional coordinates from Quantum Espresso

NOMAD and FAIRmat
1

Hi
Using fractional coordinates in Quantum Espresso via the “ATOMIC_POSITIONS (Crystal)” tag results in wrong structure display once uploaded to NOMAD. It looks like the parser cannot handle fractional coordinates from QE.
If I use the “ATOMIC_POSITIONS (Angstrom)” tag, then the structure is correctly displayed.
Has anyone observed this behaviour?
Thanks

2

Thanks for your report. It is very well possible that this is a problem with our parser indeed. We will investigate and let you know: Factional coordinates in QA results in wrong structure in NOMAD (#1222) · Issues · nomad-lab / nomad-FAIR · GitLab

1 Like
3

Hi,
Thank you for reporting the error. The parser seems to handle units for the atomic positions. Currently, unit can either be alat, a_0, bohr, angstrom or 2 pi/alat. It is possible that the unit was incorrectly parsed. In order to probe this further, can you please send an example output that I can work on? Thank you.

4

Is the crystal tag supposed to be similar to alat?

5

Hi,

Thanks for looking into this!
I can’t attach files. Could you drop me an email to briqul01 @ matthey.com and I’ll share the file with you.

Both “alat” and “crystal” are types of fractional coordinates. “alat” is a bit peculiar as it uses the lattice coordinate A or celldm(1) as units. “crystal” is the traditional fractional coordinates (ie relative to the primitive lattice vectors) as used in other DFT software such as VASP

6

Fix has been implemented.

7

This means the fix is merged to the develop branch of our source code repository. It is not yet in a released image and also not available on nomad. Currently it will be only available in NOMAD Oases using the “develop” tagged nomad image. We will make an official release soon. I’ll let you know.

8

Thanks for the update and for fixing the bug!