nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2024-02-15T13:59:36Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1665Use runschema def for archive section run2024-02-15T13:59:36ZAlvin Noe LadinesUse runschema def for archive section runFix error in loading archive as a result of not explicitly defining archive section run using the new schema.Fix error in loading archive as a result of not explicitly defining archive section run using the new schema.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1664fixed active orbital error2024-02-09T12:35:36ZJoseph Rudzinskifixed active orbital errorCloses #1884
@ndaelman this may not be the most elegant solution (please make another suggestion if you'd like), but the old code/check:
```
active_orbitals_run = [
param.core_hole for param in atom_params if hasa...Closes #1884
@ndaelman this may not be the most elegant solution (please make another suggestion if you'd like), but the old code/check:
```
active_orbitals_run = [
param.core_hole for param in atom_params if hasattr(param, 'core_hole')
]
```
returns a list of None's in every case and always throws an errorJoseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1663Draft: Resolve "rework elabftw parser"2024-03-15T10:08:24ZAmir GolparvarDraft: Resolve "rework elabftw parser"Closes #1882Closes #1882Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1662Resolve "plotly config dictionary can't be fed in from normalize function"2024-02-22T13:00:07ZMohammad NakhaeeResolve "plotly config dictionary can't be fed in from normalize function"Closes #1857Closes #1857Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1661Do not lazy load schema plugin2024-02-08T10:46:03ZAlvin Noe LadinesDo not lazy load schema pluginIndeed the problem was caused by lazy loading the schemas. Disabled it now.Indeed the problem was caused by lazy loading the schemas. Disabled it now.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1660Resolve "Remove Perovskite Solar Cell Database Files"2024-02-09T15:01:06ZYaru WangResolve "Remove Perovskite Solar Cell Database Files"Closes #1870Closes #1870https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1659Fixed CP2K2024-02-06T12:30:54ZJose PizarroFixed CP2KCloses #1879Closes #1879Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1658Update parser ref2024-02-05T16:41:11ZAlvin Noe LadinesUpdate parser refAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1657Update plugin refs2024-02-02T17:19:56ZAlvin Noe LadinesUpdate plugin refsAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1656Resolve "Special group 'all'"2024-02-12T11:02:29ZSascha KlawohnResolve "Special group 'all'"- Make it possible to add 'all' to upload reviewer groups
- Raise error when adding 'all' to upload coauthor groups
- Adjust tests
- Add upload/entry with 'all' reviewer group to test data
- Test adding all to reviewer groups / coaut...- Make it possible to add 'all' to upload reviewer groups
- Raise error when adding 'all' to upload coauthor groups
- Adjust tests
- Add upload/entry with 'all' reviewer group to test data
- Test adding all to reviewer groups / coauthor groups (fails)
Closes #1868Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1655Draft: Resolve "Generic xml parser"2024-02-01T04:50:32ZAlvin Noe LadinesDraft: Resolve "Generic xml parser"Closes #1875Closes #1875Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1654Added default values for process status both in the pydantic model as well as...2024-02-01T11:44:29ZLauri HimanenAdded default values for process status both in the pydantic model as well as...Added default values for process status both in the pydantic model as well as in the mongo document schema.
Closes #1841Added default values for process status both in the pydantic model as well as in the mongo document schema.
Closes #1841Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1653New Atomic Descriptors2024-02-05T10:41:34ZJames DarbyNew Atomic DescriptorsHi,
I've updated the atomic descriptors that are computed. The old approach was to store 4 different variations of the SOAP power spectrum, 2 descriptor vectors for each atom in the system and then 2 structure-wise-averaged descriptor ...Hi,
I've updated the atomic descriptors that are computed. The old approach was to store 4 different variations of the SOAP power spectrum, 2 descriptor vectors for each atom in the system and then 2 structure-wise-averaged descriptor vectors. Instead of this, the new approach is to store 2 structure-wise-averaged descriptor vectors only. One of these is an element-agnostic, radially scaled variant of the SOAP power spectrum and the second is the descriptor extracted from the recent MACE-MP-0 foundation model.
Questions/Discussion points:
1. Total storage requirement is now greatly reduced to 296 floats per system. With 13 million structures currently in NOMAD I make this about 16 GB of data. Is this acceptable?
2. Adding the MACE descriptors has introduced new dependencies via [mace-torch](https://github.com/ACEsuit/mace/tree/88d49f9ed6925dec07d1777043a36e1fe4872ff3?tab=readme-ov-file#installation). mace-torch is pip installable so I'm hoping this won't cause any issues. I haven't updated requirement.txt etc. Should I do this?
3. The MACE descriptors are computed using the MACE-MP-0 foundation model. The model file (42 MB) gets automatically downloaded to ~/.cache/mace/ the first time it is called. Think we need to be careful with how this will work with multiple different "workers" running in parallel. Will they try to write to the same file?
4. Loading the MACE model takes much longer than computing the MACE descriptor. Currently the model is loaded once per system, I don't see a great way of avoiding this but worth being aware of.
5. The current schema for SOAP descriptors (shown below) includes entries for the parameters that were used to generate the descriptors e.g. `r_cut`, `n_max` etc. These will be the same for all structures in the database so this seems inefficient? My proposal is to put this information into the quantity definition of the soap_descriptor itself (see image) so the same data isn't duplicated for each structure. Thoughts?
![image](/uploads/c9c58f497f8e66fda43360f74956d74d/image.png)Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1652Resolve "tabular parser should set the file name correctly"2024-01-30T09:20:49ZAmir GolparvarResolve "tabular parser should set the file name correctly"Closes #1871Closes #1871Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1651Resolve "Update electronicparsers"2024-01-29T13:17:50ZLauri HimanenResolve "Update electronicparsers"Closes #1869Closes #1869Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1650Resolve "Celery Task ID sometimes none causing error"2024-01-26T13:52:31ZTheodore ChangResolve "Celery Task ID sometimes none causing error"Closes #1841Closes #1841Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1649Add coauthor, reviewer groups2024-01-29T13:47:24ZSascha KlawohnAdd coauthor, reviewer groups- Add user groups, API `/groups`
- Add coauthor, reviewer groups
- Add writer, viewer groups
- Add groups to ES owner query
- Add tests for groups, uploads, search
Closes #1760- Add user groups, API `/groups`
- Add coauthor, reviewer groups
- Add writer, viewer groups
- Add groups to ES owner query
- Add tests for groups, uploads, search
Closes #1760Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1648Resolve "Add documetation about how units work in NOMAD"2024-01-26T06:18:29ZLauri HimanenResolve "Add documetation about how units work in NOMAD"Closes #1855Closes #1855Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1647Resolve "Problem with material overview card"2024-01-26T08:37:26ZLauri HimanenResolve "Problem with material overview card"Closes #1861Closes #1861Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1646Resolve "Config option to disable optimade API."2024-02-26T11:46:23ZMarkus ScheidgenResolve "Config option to disable optimade API."Closes #1866Closes #1866