nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-01-13T23:18:13Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/963Compare DOS for integrals, not means2023-01-13T23:18:13ZNathan DaelmanCompare DOS for integrals, not meansUpdates `test_dos_magnitude` which compares Si DOS from VASP, FHIaims and _exciting_ to use the integral over the occupied valence states rather than the mean.
The result is a unanimous answer of 8 electrons, with deviations of up to 0.0...Updates `test_dos_magnitude` which compares Si DOS from VASP, FHIaims and _exciting_ to use the integral over the occupied valence states rather than the mean.
The result is a unanimous answer of 8 electrons, with deviations of up to 0.05 electron charge, instead of unintelligible values into the 1e46, where the order of deviation is much larger.
Closes #1201Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/962Resolve "GUI Breaks when using create Archive"2022-12-14T16:17:03ZMohammad NakhaeeResolve "GUI Breaks when using create Archive"Closes #1192Closes #1192Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/961Fixes in perovskite database2022-11-28T06:57:51ZJose Marquez PrietoFixes in perovskite databaseIt contains two fixes for the Perovskite Database schema and ELN Publication reference base section:
- Write 'perovskite' in `material.symmetry.structure_name` and removes it from `material.material_name`
- Makes sure that the DOIs add...It contains two fixes for the Perovskite Database schema and ELN Publication reference base section:
- Write 'perovskite' in `material.symmetry.structure_name` and removes it from `material.material_name`
- Makes sure that the DOIs added manually through the ELN can be navigated in `metadata.references` by adding the correct prefix if the string starts with '10.'
Changes `results.properties.optoelectronic.band_gap` to `band_gap_optical`. After merging this would require re-processing of solar cell entries in prod:
- Perovskite Solar Cell Database upload and all unpublished uploads with `solar_cell`shttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/959Add support of complex2022-12-08T06:25:10ZTheodore ChangAdd support of complexCloses #1126Closes #1126Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/958Add section defs2022-12-09T08:15:20ZTheodore ChangAdd section defsCloses #1190Closes #1190Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/957New workflow visualizer2023-02-11T00:06:53ZAlvin Noe LadinesNew workflow visualizerImplementation of visualizer following the new workflow schema.Implementation of visualizer following the new workflow schema.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/956Refactor: change terminology from installationUrl to deploymentUrl, and2022-11-22T09:21:23ZDavid SikterRefactor: change terminology from installationUrl to deploymentUrl, andRefactor: change terminology from installationUrl to deploymentUrl, and deployment_id -> deployment_url, etc.Refactor: change terminology from installationUrl to deploymentUrl, and deployment_id -> deployment_url, etc.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/955Refactor bundle functionality2022-12-14T09:56:47ZDavid SikterRefactor bundle functionalityRefactoring and improvements related to bundle functionality, part of #1181.
The bundle functionality is modularized, broken out into a new module `bundles.py`, and CLI commands are introduced for import and exporting bundles. The setti...Refactoring and improvements related to bundle functionality, part of #1181.
The bundle functionality is modularized, broken out into a new module `bundles.py`, and CLI commands are introduced for import and exporting bundles. The settings are reorganized, and importing bundles through the api is by default disabled for now (previously, it was enabled by default). The bundle file format is essentially unchanged, except for renaming `export_options` to `export_settings` for more consistency. Also made some improvements to related code, to make sure the GUI doesn't crash and that the user can always delete uploads where the import failed.
As before, importing is done by first creating a "skeleton upload" and then running a process (locally or on the worker) on this upload to do the main part of the work. Unlike before, the process is now focused on importing the parsed archive files, not reprocessing the raw files (reprocessing is still possible, but disabled by default).David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/954Resolve "Add Rg plots to overview GUI page for molecular dynamics trajectories"2022-12-13T13:44:54ZJoseph RudzinskiResolve "Add Rg plots to overview GUI page for molecular dynamics trajectories"Closes #1157Closes #1157Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/952Resolve "Add RFC 3161 timestamps to entry metadata"2022-12-03T01:00:02ZTheodore ChangResolve "Add RFC 3161 timestamps to entry metadata"Closes #1179Closes #1179Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/951Added if statement to include the right prefix for the DOIs2022-11-18T10:28:50ZJose Marquez PrietoAdded if statement to include the right prefix for the DOIsCloses #1183Closes #1183https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/950Archive browser data links2022-11-18T08:56:02ZTheodore ChangArchive browser data linksCloses #999Closes #999Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/949Resolve "GW metainfo and parsing for exciting and FHIaims"2022-12-15T12:56:41ZJose PizarroResolve "GW metainfo and parsing for exciting and FHIaims"Closes #1131Closes #1131Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/948Resolve "Survey 3rd-party ELNs for integration"2023-01-03T10:37:08ZAmir GolparvarResolve "Survey 3rd-party ELNs for integration"Related #896Related #896Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/946Adds test for nexus parsing error2022-11-16T05:56:40ZFlorian DobenerAdds test for nexus parsing errorhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/945DOS normalization (FHIaims, VASP, exciting)2022-12-22T09:55:49ZNathan DaelmanDOS normalization (FHIaims, VASP, exciting)This MR resolves https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/728 and https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/868.
It is accompanied by https://github.com/nomad-coe/electronic-parsers/pull/16 on the parser ...This MR resolves https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/728 and https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/868.
It is accompanied by https://github.com/nomad-coe/electronic-parsers/pull/16 on the parser side.
Basically, the DOS in FHIaims, VASP, exciting were incorrectly scaled at the parser side:
they no longer lead to integer electrons when integrating over a band.
Moreover, the total DOS in older FHIaims versions was off by a factor of 2 (regardless of spin).
Projected DOS or bands were not affected.
This MR updates the parsers and adds the new metadata entry `raw_data_normalization_factor`, to store the original FHIaims DOS without any correction.
Up to now, this metadata only applies to FHIaims, so I could also move it to that parser's specific metadata.Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/944Decreased the size limit for processing topology, skipped topology tests2022-11-11T14:05:49ZLauri HimanenDecreased the size limit for processing topology, skipped topology testsA hotfix for #1174.A hotfix for #1174.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/943Switched to updated matid version with fix for empty prototype cell.2022-11-11T12:51:33ZLauri HimanenSwitched to updated matid version with fix for empty prototype cell.Closes #1173Closes #1173Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/942Resolve "Reprocessing fails without add_matched_entries_to_published"2022-11-11T08:37:18ZMarkus ScheidgenResolve "Reprocessing fails without add_matched_entries_to_published"Closes #1175Closes #1175https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/941Update README.md2022-11-11T16:15:55ZMarkus ScheidgenUpdate README.md