nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-09-19T13:56:26Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1452CLI utility to export archive data2023-09-19T13:56:26ZMarkus ScheidgenCLI utility to export archive data... e.g. for use in machine learning.... e.g. for use in machine learning.https://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/1449New DOS schema2023-10-31T09:36:36ZJose PizarroNew DOS schemaAdded a new dos_electronic schema in run and results.Added a new dos_electronic schema in run and results.Jose PizarroJose Pizarrohttps://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/1447Updating all files and submodule for stm integration.2023-08-31T13:00:04ZRubel MozumderUpdating all files and submodule for stm integration.https://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/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/1441Use bulk insert2023-08-10T14:35:32ZTheodore ChangUse bulk insertCloses #1396Closes #1396Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1440eDMFT parser and revisit DMFT metainfo2023-09-05T13:33:21ZJose PizarroeDMFT parser and revisit DMFT metainfoI've been working in a new parser for DMFT calculations. This is the first parser without using tight-binding models (unlike w2dynamics and solid_dmft), but instead is based on having a DFT Wien2k calculation, and doing a DMFT on top of ...I've been working in a new parser for DMFT calculations. This is the first parser without using tight-binding models (unlike w2dynamics and solid_dmft), but instead is based on having a DFT Wien2k calculation, and doing a DMFT on top of it. They can do a Maximum Entropy analytical continuation to compare DFT vs DMFT results (hence the name MaxEnt in the metadata).
The associated new parser (initially reviewed by @ladinesa) can be found in https://github.com/nomad-coe/electronic-parsers/pull/144
These are the first set of changes to allocate for the new metainfo.
* I polished the current `run.method.dmft` and `run.calculation.greens_functions` metadata.
* I also defined `maxent_analytical_continuation` as a boolean in the `results.method.simulation.dmft` to indicate if the MaxEnt was performed or not.
* I defined a new workflow, `MaxEnt`, which groups DMFT and MaxEnt (which only calculated Σ(ω), hence the name 'MaxEnt Sigma') SinglePoint entries. This workflow also contains the calculation of the G(ω) and the DOS.
* I extended the metadata schema of `results.properties.electronic.greens_function` , and change the fact that only real or imaginary parts were written down; now the hole complex number is available.
* I added a new util function, `extract_section`. I felt `traverse_reverse` was not the best when resolving multiple calculation sections, as it resolves everything. This function is very useful, I am using widely in the parsers and here can be nice to do it so. But please, let me know if it is good enough for the general utils or not.
There are some issues and todos beyond the scope of this merge request:
* [x] I have to fix and create some testing.
* [x] Right now, the plotting of Green's function is broken. In one hand, some entries will have different quantities. For now, I want to keep it simple and show only Σ(iωn) if this quantity is present (i.e. delete `regtau` plotting).
On the other hand, I tried defining `greens_functions_tau.re` and `self_energy_iw.im` in the Js module, but it didn't work; instead is showing the following plots:
![Screenshot from 2023-08-10 14-23-51.png](/uploads/ccd5b1df2ac05849f95644cf6d785261/Screenshot_from_2023-08-10_14-23-51.png){width=338 height=305}
I would like to fix this first, before continuing with more changes into the plotting. @himanel1 can you help me with this simple thing?
* [x] I have to define the full DFT+DMFT workflow. This can will contain the following tasks: or DFT+(Projection)+DMFT+(MaxEnt). I will do this in a next merge.
* [ ] And after that, I will tackle the full design of the Green's functions plotting section. @wojasadr gave some suggestions and I'd like to try them out; namely, make collapsable plots (at the end, there are going to be so many quantities in the most general workflow entry, so it would be nice if these can be collapse such that the user don't get overwhelm by the amount of plots).
If it looks nice, this could be then use in other cases.
Closes #1450Jose PizarroJose Pizarrohttps://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/1438Resolve "Aggregations for custom quantities"2023-09-20T12:13:23ZLauri HimanenResolve "Aggregations for custom quantities"Closes #1502Closes #1502Lauri HimanenLauri Himanenhttps://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/1436Resolve "Some Tabular parser features to revise or add"2023-10-05T06:59:58ZAmir GolparvarResolve "Some Tabular parser features to revise or add"Closes #1637Closes #1637Amir GolparvarAmir Golparvarhttps://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/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/1432GitHub PR: Remove docker image which doesn't seem to be available anymore2023-12-21T08:53:59ZMarkus ScheidgenGitHub PR: Remove docker image which doesn't seem to be available anymoreOriginal pull request on GitHub: https://github.com/nomad-coe/nomad/pull/79Original pull request on GitHub: https://github.com/nomad-coe/nomad/pull/79https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1431Resolve "draft for heterogeneous catalysis app"2023-10-16T12:11:31ZJulia SchumannResolve "draft for heterogeneous catalysis app"Closes #1592
Additions to results.py and to gui files to prepare a new search app for Heterogeneous Catalysis.
The schemas to generate the relevant entries are seperate in a plugin published here: https://github.com/schumannj/nomad-s...Closes #1592
Additions to results.py and to gui files to prepare a new search app for Heterogeneous Catalysis.
The schemas to generate the relevant entries are seperate in a plugin published here: https://github.com/schumannj/nomad-schema-plugin-fhi-catalysis
I attach a datafile for the Activity Test entry, from which the reactivity quantities such as products/names are taken.
[MoVOx_C2_performance_cleared_NaN.xlsx](/uploads/9d06b02bfb6df599672638b830a84389/MoVOx_C2_performance_cleared_NaN.xlsx)Julia SchumannJulia Schumannhttps://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/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 Himanen