nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-08-29T08:18:05Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1453Updated ref to electronic-parsers with CP2K fix2023-08-29T08:18:05ZJose PizarroUpdated ref to electronic-parsers with CP2K fixhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1450Added oasis registration link to the docs.2023-08-24T12:03:59ZMarkus ScheidgenAdded oasis registration link to the docs.Changelog: AddedChangelog: Addedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1332Resolve "Mongo and elasticsearch authentication"2023-09-01T12:03:47ZMarkus ScheidgenResolve "Mongo and elasticsearch authentication"Closes #1526Closes #1526https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1446Resolve "Reviewer not counting for max number of uploads"2023-08-23T12:32:39ZMarkus ScheidgenResolve "Reviewer not counting for max number of uploads"Closes #1651Closes #1651https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1439JSONSchema for nomad schemas2023-08-23T09:17:03ZAhmed IlyasJSONSchema for nomad schemasAhmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1233Allow for command line forced parser matching2023-08-22T13:08:55ZNathan DaelmanAllow for command line forced parser matchingAllow the user to enforce a parser choice via the command line `nomad parse`.
To respect the interface with other components, this is done by adding the flag `--force_parser`, i.e.
```
nomad parse --parser parser/vasp --force_parser <p...Allow the user to enforce a parser choice via the command line `nomad parse`.
To respect the interface with other components, this is done by adding the flag `--force_parser`, i.e.
```
nomad parse --parser parser/vasp --force_parser <path to auxiliary output>
```
The description in `nomad parse --help` has been updated to
- distinguish both flags
- give examples on parser name formatting
- warn the user of the risks
Closes #1435Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1448fixed2023-08-17T15:43:35ZJoseph RudzinskifixedCloses #1661Closes #1661Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1413Merging TB with TightBinding and Projection2023-08-17T12:03:47ZJose PizarroMerging TB with TightBinding and ProjectionThis is to be merged into #1251. @mnakh when you want, check it out and we can merge into your branch.
I did some normalization to directly populate `results.method`.
I also modified the FilterMenus in the GUI to add the menu `TB` und...This is to be merged into #1251. @mnakh when you want, check it out and we can merge into your branch.
I did some normalization to directly populate `results.method`.
I also modified the FilterMenus in the GUI to add the menu `TB` under DFT in the explore page.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1385Refactored Substance Base Sections2023-08-16T06:09:25ZHampus NaesstroemRefactored Substance Base SectionsSeparates out `Substance` properties to a `SubstanceSection` class
Adds `SubstanceComponent` with `SubstanceSection` sub section
Moves `system` quantity from `Component` to inheriting `SystemComponent` class
Adds `PubChemSubstanceSect...Separates out `Substance` properties to a `SubstanceSection` class
Adds `SubstanceComponent` with `SubstanceSection` sub section
Moves `system` quantity from `Component` to inheriting `SystemComponent` class
Adds `PubChemSubstanceSection` which queries PubChem for substance information
Adds `PubChemSubstanceComponent` and `PubChemSubstance` analogous to `Substance`
Closes #1585https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1444Read all once2023-08-14T19:48:53ZTheodore ChangRead all onceTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1442Updating ref to electronicparsers for hotfix on Wannier90 parser2023-08-14T11:54:32ZJose PizarroUpdating ref to electronicparsers for hotfix on Wannier90 parserHotfix on Wannier90 parser.Hotfix on Wannier90 parser.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1437fixed storage of times in archive_to_universe, and recoded Rg value calc and...2023-08-11T15:56:57ZJoseph Rudzinskifixed storage of times in archive_to_universe, and recoded Rg value calc and...fixed storage of times in archive_to_universe, and recoded Rg value calc and storage in workflow normalizer
Closes #1643fixed storage of times in archive_to_universe, and recoded Rg value calc and storage in workflow normalizer
Closes #1643Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1397Adds styling to H5web and small bug fixes in Nexus browsing2023-08-11T10:13:56ZSherjeel ShabihAdds styling to H5web and small bug fixes in Nexus browsingThis tries to get our current version of H5Web themed up to look better with Nomad.
Note: This branch can benefit from updating pynxtools submodule.This tries to get our current version of H5Web themed up to look better with Nomad.
Note: This branch can benefit from updating pynxtools submodule.Sherjeel ShabihSherjeel Shabihhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1441Use bulk insert2023-08-10T14:35:32ZTheodore ChangUse bulk insertCloses #1396Closes #1396Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1433Resolve "Better handling of dynamic filters in SearchContext"2023-08-07T13:00:08ZLauri HimanenResolve "Better handling of dynamic filters in SearchContext"Closes #1645Closes #1645Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1435Resolve "Digicert RFC3161 timestamp service cannot be reached"2023-08-07T12:11:21ZLauri HimanenResolve "Digicert RFC3161 timestamp service cannot be reached"Closes #1649Closes #1649https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1427Update development docs2023-08-04T17:42:13ZSascha KlawohnUpdate development docsFix typos, unify names, clean up formatting.
Closes #1628Fix typos, unify names, clean up formatting.
Closes #1628Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1428Resolve "Shared upload delete warning and shared upload icon"2023-08-03T08:11:43ZLauri HimanenResolve "Shared upload delete warning and shared upload icon"Closes #1633Closes #1633Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1429Add config key to mount external volumes into north tool2023-08-03T07:52:21ZFlorian DobenerAdd config key to mount external volumes into north toolThis basically readds a feature to mount external folders into a north tools container. It was removed during the refactoring of the north config (see https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/b0e28fa7fd3f47fcd538f33bd84b...This basically readds a feature to mount external folders into a north tools container. It was removed during the refactoring of the north config (see https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/b0e28fa7fd3f47fcd538f33bd84bad659ee6549a#0c8c279f7dd1dae6be962aa1e764f2e07e029710_272_142).
Example config (under north):
```
north:
external_mounts:
- host_path: /mnt/pcshare
bind: pcshare
mode: ro
- host_path: /scratch/localDataStore:
bind: localDataStore
mode: rw
```https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1423Resolve "ELN metainfo load problem"2023-07-31T10:34:20ZAhmed IlyasResolve "ELN metainfo load problem"Closes #1632Closes #1632Ahmed IlyasAhmed Ilyas