nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2019-05-07T08:26:04Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/43Occasional merge towards v0.4.42019-05-07T08:26:04ZMarkus ScheidgenOccasional merge towards v0.4.4repo/archive consolidationMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/6Offline2018-09-27T12:32:17ZMarkus ScheidgenOfflinehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/381Openmx parser2021-09-08T12:03:29ZAlvin Noe LadinesOpenmx parserAdded openmx in parser modules.Added openmx in parser modules.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/116Optimade2020-06-08T14:20:48ZAlvin Noe LadinesOptimadeIntegrate implemented optimade endpoints and metainfo m_xpath functionality.Integrate implemented optimade endpoints and metainfo m_xpath functionality.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/232Optimade fixes #4502021-01-07T08:01:20ZMarkus ScheidgenOptimade fixes #450https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/754Optimade search quantity (#848)2022-07-14T07:19:50ZMohammad NakhaeeOptimade search quantity (#848)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/59OptimadeTest2019-10-11T12:46:33ZAlvin Noe LadinesOptimadeTesthttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/565Optimize ArchiveReader read disk performance2022-02-23T07:22:20ZTheodore ChangOptimize ArchiveReader read disk performanceCloses #751Closes #751Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1225Optimizing w2dynamics parser2023-04-20T09:50:28ZJose PizarroOptimizing w2dynamics parserCloses #1429Closes #1429Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1028ordering of residues fixed2023-01-16T12:30:30ZJoseph Rudzinskiordering of residues fixedCloses #1273Closes #1273Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/255Overview2021-02-08T09:48:24ZLauri HimanenOverviewLatest version of the overview page with the new two-column layout. I will keep working on this branch so let's not delete it for now.Latest version of the overview page with the new two-column layout. I will keep working on this branch so let's not delete it for now.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/262Overview alternative2021-02-22T12:48:24ZLauri HimanenOverview alternativeNow includes the changes as discussed in our meeting on monday and in issue #495.
Also I added improved handling of margins: there is a new `fixedMargins` flag, which when set instructs the plots to compute the margins automatically onc...Now includes the changes as discussed in our meeting on monday and in issue #495.
Also I added improved handling of margins: there is a new `fixedMargins` flag, which when set instructs the plots to compute the margins automatically once on startup, after which they are not recomputed until the data changes. This together with some padding make for a nice behaviour even on scrolling and zooming. Only if the user scrolls super much, the labels will start to overlap with titles. But I think this is acceptable considering the benefits.
Things you should note and check:
- I put the encyclopedia button inside the material card as a `text`-variant with blue color, as discussed. The api button is at the bottom right of the left panel with blue color, but with the `contained`-variant. We were discussing to use the `text`-variant also there, but to me it looked very weird.. Also the `contained`-variant against the gray background is consistent with the buttons on the search page. Change as you see fit.
- The legend is now at top left, with a slightly transparent background. Change as you see fit.
- I picked the `ViewList` icon for the links to the data in the Archive. Change as you see fit.
![Screenshot_2021-02-19_NOMAD](/uploads/65f7918f77f60b3b471c141f78096db2/Screenshot_2021-02-19_NOMAD.png)
![Screenshot_2021-02-19_NOMAD_1_](/uploads/38176c7dde821261d90f012d3f6273fe/Screenshot_2021-02-19_NOMAD_1_.png)Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/260Overview improvements2021-02-11T14:25:29ZLauri HimanenOverview improvementsContains several improvements and fixes to the overview page:
- Added new "NoData" component so that the same layout can be retained even if some data is missing.
- Fixed issues with trying to access missing SCCS, methods, or systems
- A...Contains several improvements and fixes to the overview page:
- Added new "NoData" component so that the same layout can be retained even if some data is missing.
- Fixed issues with trying to access missing SCCS, methods, or systems
- Added direct communication between plots/structures through RxJS Subjects. After researching what other people have done in a similar situation, this approach popped up in multiple locations. Essentially it is just the PubSub pattern. Bypassing the rendering with this approach seems to give a nice performance boost to Plot interactivity. @mscheidg: I think this is quite a clean and versatile approach, but if you can suggest any improvements they are certainly welcome.
- Modified the ToggleButton text opacity a bit so that it does not look like it is disabled.
- Improved the initial translation/orientation of structures shown by the Structure component so that systems have a more "natural" initial state in the overview page.
- Changed the order of Material and API access buttons.
Before merging I would suggest that you check and modify the `NoData` component visuals to your liking.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/251Overview page2021-02-08T09:01:31ZLauri HimanenOverview pageContains the first version of the overview page. Has the following "cards":
- material
- method
- entry
- electronic properties
- geometry optimization
- vibrational properties
It would be good to get some comments for the layout/cards ...Contains the first version of the overview page. Has the following "cards":
- material
- method
- entry
- electronic properties
- geometry optimization
- vibrational properties
It would be good to get some comments for the layout/cards before we publish to production.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/314Overview page and electronic structure handling improvements2021-04-19T05:52:29ZLauri HimanenOverview page and electronic structure handling improvements- Now placeholders are always shown while loading the data that is indicated to be present in `searchable_quantities`. Also improved the detection of `searchable_quantities` within processing for `electronic_dos`, `electronic_band_struct...- Now placeholders are always shown while loading the data that is indicated to be present in `searchable_quantities`. Also improved the detection of `searchable_quantities` within processing for `electronic_dos`, `electronic_band_structure`, `phonon_dos`, `phonon_band_structure` (this will show up only after re-processing).
- Added correct shifts in the BS/DOS plots shown in the GUI, added a horizontal line + legend that indicates the highest occupied energy in the plots ([example](https://nomad-lab.eu/prod/rae/beta/gui/entry/id/_ijarO1hQCqsTpOyb62WXw/w5ae2QjYUDfZKLal4Dvbmd-mdG6U)). If normalization cannot be detected, a small warning icon will be shown with a tooltip ([example](https://nomad-lab.eu/prod/rae/beta/gui/entry/id/BU_f9jJnRdOGtZ9pj_QQ9w/vSmPRh6yDFmjGu0BuGR-6nazwTs-)).
- Fixed issue with plotting spin-polarized band structures and band structures with discontinuous segments.
- Modified the geometry optimization card to only show the energy convergence plot. The energy convergence now shows the absolute energy change (+convergence threshold if available) on a separate logarithmic y-axis ([example](https://nomad-lab.eu/prod/rae/beta/gui/entry/id/Xx-8c6huQNO6PwefMksdcg/gBAzpgQEeU68haCHfUN_pJM1znoN)) (related to #517)
- Fixed incorrect band/dos shifts in exciting and FHI-aims (related to #521)
- Fixed GW parsing in exciting (#323)
There are still examples where the placeholders will not show up until reprocessing is done. E.g. [here](https://nomad-lab.eu/prod/rae/beta/gui/entry/id/Xx-8c6huQNO6PwefMksdcg/QDbMQ7Kn6GrNGhdOZ7u55c6bjyQL) there is no `electronic_dos` in searchable quantities because of old processing.
@mscheidg: When you have the time, can you check that these changes are OK? When this is merged to v0.10.3, I could also rebase dev-newentry to v0.10.3.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/933Overview reference card2022-11-14T14:20:08ZTheodore ChangOverview reference cardTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/274Overview small fixes2021-03-09T07:56:33ZLauri HimanenOverview small fixesContains fixes to issues discussed in #505. Please see attached screenshots to see how the new alerts look like before emerging. The new alerts are based on the `Alert`-component from MUI with different `severity`.
- New alert for loadi...Contains fixes to issues discussed in #505. Please see attached screenshots to see how the new alerts look like before emerging. The new alerts are based on the `Alert`-component from MUI with different `severity`.
- New alert for loading large system: ![Screenshot_2021-03-08_NOMAD](/uploads/4a5932a5d47178a5b4916b563d298f85/Screenshot_2021-03-08_NOMAD.png)
- New error alert style: ![Screenshot_2021-03-08_NOMAD_1_](/uploads/df3a4b7a16248feb95f733fb50f8fc99/Screenshot_2021-03-08_NOMAD_1_.png)Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/157Parallel archive client2020-08-21T18:48:58ZMarkus ScheidgenParallel archive clientFixed parallel archive access issues. #350Fixed parallel archive access issues. #350https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/190parser_dos_bands2020-10-02T11:47:08ZCuauhtemoc Salazartemok@physik.hu-berlin.deparser_dos_bands`parser_dos_bands`
- DOS support for ABINIT parser (`dos_values` & `dos_integrated_values`)
- tiny fix in `exciting_parser_dos.py` to a bug that was causing an error when the Fermi energy was `None` (line 113).`parser_dos_bands`
- DOS support for ABINIT parser (`dos_values` & `dos_integrated_values`)
- tiny fix in `exciting_parser_dos.py` to a bug that was causing an error when the Fermi energy was `None` (line 113).https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/471Parser fix2021-12-02T07:27:08ZAlvin Noe LadinesParser fixImplemented resolution of hybrid and metagga functionals in vasp parser Should solve #675Implemented resolution of hybrid and metagga functionals in vasp parser Should solve #675Markus ScheidgenMarkus Scheidgen