nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-09-01T12:03:47Zhttps://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/1316Spectra normalizer2023-07-28T08:29:15ZJose PizarroSpectra normalizerList of changes #1506:
- Changed `ParticleHoleExcitations` to `XS` workflow name.
- Added `methodology` in `ElectronicStructureProvenance`.
- Added `intensities_units` for `Spectra`.
- Added `SpectraNormalizer`.
- Added provenance fo...List of changes #1506:
- Changed `ParticleHoleExcitations` to `XS` workflow name.
- Added `methodology` in `ElectronicStructureProvenance`.
- Added `intensities_units` for `Spectra`.
- Added `SpectraNormalizer`.
- Added provenance for spectra pointing to the specific `method.photon` section.
- Added provenance for spectra in case of being in an XS workflow pointing to `method.bse` section of each corresponding task.
- New result class for `results.properties.spectroscopic.Spectra`. This contains:
- `type` to identify the type of spectra obtained.
- `label` to differentiate between experiment or computation.
- `n_energies`, `energies`, `intensities`, `intensities_units` as the axes of the data.
- `provenance` pointing to `SpectraProvenance(ProvenanceTracker)`. This contains two sub sections, `eels`, `electronic_structure`. The idea would be to extend this.
- Moved certain definitions and normalization from the EELSDB parser to here (https://github.com/nomad-coe/nomad-parser-eelsdb/pull/7).
- Added `resolve_spectra` and `xs_workflow_properties` in ResultsNormalizer.
- Modified the visualization side to get the new `results.properties.spectroscopic.spectra` data. Also modified names from EELS to Spectroscopic.
This MR is dependent on the merge of !1261.
The current `SpectraNormalizer` looks a bit empty right now, but my plan is to extend it soon.
Should I move the EELSDB normalization to there?
In any case, let me know what you think; maybe there is a better / more convenient solution for this.
TODO:
- [x] Fix testing and clean up.
- [x] Define a normalization similar to the plot for DOS.
- [x] ~~Move `label` inside provenance.~~ No, `provenance.label` contains other information that cannot be overwritten.
- [x] Use `label` to identify each line or plot: `comp. 1` or `exp. 1`.
- [x] Use `type` to title each plot.
- [x] ~~Populate `results.properties.X` where `X=electronic, vibrational, structural` according to the `type` of spectra (e.g., `XAS` should be repeated in `electronic`, `XRD` in `structural`, etc.). This is something I talked with Luca.~~ TODO in another merge request.
- [x] ~~Define FilterMenu `Spectroscopic` and move `EELS` below it. `Spectroscopic` will be clickable and contain `label` inside. I need some feedback here.~~ TODO in another merge request.
- [x] ~~Develop ref for plot labels pointing to the specific provenance of the property (if available).~~ TODO in another merge request.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1307Draft: Resolve "Survey 3rd-party ELNs for integration"2023-06-20T07:53:12ZAmir GolparvarDraft: Resolve "Survey 3rd-party ELNs for integration"Closes #896Closes #896Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1304DMFT workflow2023-07-20T09:45:59ZJose PizarroDMFT workflowCloses #1445Closes #1445Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1294Resolve "MOF normalizer"2023-06-19T07:55:07ZDinga WonankeResolve "MOF normalizer"Closes #1464
Created a new mofnormalizer
1) Identify whether an input is a MOF
2) Check for the presence of guest molecules and if yes, remove it before computing the properties of the MOFs
3) Compute geometric properties of MOFs such a...Closes #1464
Created a new mofnormalizer
1) Identify whether an input is a MOF
2) Check for the presence of guest molecules and if yes, remove it before computing the properties of the MOFs
3) Compute geometric properties of MOFs such as PLD, LCD, AV, ASA, void fraction and number of channels. This is computed using a probe of radius 1.86 corresponding to the atomic radii of nitrogen and runs for 5000 cycles. In the future, users should be able to use their own properties.
4) Deconstruct the MOF into their unique building units. This include the metal secondary building unit, organic secondary building unit and organic ligandDinga WonankeDinga Wonankehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1285Resolve "Add Tight Binding Studio parser"2023-11-20T11:31:52ZMohammad NakhaeeResolve "Add Tight Binding Studio parser"Closes #1251Closes #1251Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1272Going up from folder DMFT2023-05-11T10:03:32ZJose PizarroGoing up from folder DMFTMinor change updating the ref to electronic parsers for w2dynamics after talking with developer.
- Going up instead of down in the folder directory scanning for Wannier90 files in w2dynamics parser
Closes #1445Minor change updating the ref to electronic parsers for w2dynamics after talking with developer.
- Going up instead of down in the folder directory scanning for Wannier90 files in w2dynamics parser
Closes #1445Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1264Restructure metainfo for clearer semantic connection between `BasisSet` and...2023-05-14T10:34:45ZNathan DaelmanRestructure metainfo for clearer semantic connection between `BasisSet` and...Restructure metainfo for clearer semantic connection between `BasisSet` and `AtomParameters` + TODO: fix wrongfulmapping of `muffin-tin core` and `local orbital`
Closes #1449Restructure metainfo for clearer semantic connection between `BasisSet` and `AtomParameters` + TODO: fix wrongfulmapping of `muffin-tin core` and `local orbital`
Closes #1449Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1249Use modern stmp impl2023-05-02T07:18:17ZTheodore ChangUse modern stmp implTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1248Resolve "Fallback to old archive versions"2023-05-02T11:00:11ZMarkus ScheidgenResolve "Fallback to old archive versions"Closes #1460Closes #1460https://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/1232Added implementation and tests for m_setdefault.2023-04-24T08:53:35ZLauri HimanenAdded implementation and tests for m_setdefault.Closes #1442Closes #1442Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1218Resolve "Warning when deleting uploads or entries that are referenced"2023-05-11T13:06:18ZMohammad NakhaeeResolve "Warning when deleting uploads or entries that are referenced"Closes #1383Closes #1383Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1209Resolve "Serialize subsections as dictionaries"2023-05-24T14:14:15ZTheodore ChangResolve "Serialize subsections as dictionaries"Closes #1416Closes #1416Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1206GW and BSE method normalizer2023-04-27T08:32:17ZJose PizarroGW and BSE method normalizerMethod normalization related with #1316.
Main changes:
- Added `ExcitedState` in results. Base class for results.method GW and BSE.
- Added method normalization for BSE and DFT+BSE, as well as generalizing GW and DFT+GW.
List of change...Method normalization related with #1316.
Main changes:
- Added `ExcitedState` in results. Base class for results.method GW and BSE.
- Added method normalization for BSE and DFT+BSE, as well as generalizing GW and DFT+GW.
List of changes:
- Grouping GW and BSE as much as possible into base classes with names `ExcitedState`. This will be further useful when parsing TDDFT calculations.
- `MethodNormalizer` has been changed: new defined abstract class for ElectronicMethod, with the method `to_simulation`. This populates `results.simulation.method` for each specific electronic technique we currently have (DFT, GW/BSE, Projection, DMFT).
- Included BSE FilterMenu for the GUI under GW. This contains both `BSE.type` and `BSE.solver` as well as DFT+BSE and DFT+GW+BSE[^1] metainfo (XC functionals, basis set names, GW Hedin type).
____
[^1]: Thought there is currently not this DFT+GW+BSE workflow being defined or parsed, this is in my TODO list. For now I kept it as a possibility in the metainfo, but will revisit it soon.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1203Use process based implementation for file matching2023-08-10T19:39:48ZTheodore ChangUse process based implementation for file matchingCloses #1396Closes #1396Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1199Rework GW and BSE method2023-04-04T14:08:20ZJose PizarroRework GW and BSE methodThere are several changes affecting GW and BSE.
1. Added `ExcitedStateMethodology` in Method as base class for GW, BSE.
2. Added `Screening` as step to be callable as sub-section in GW and BSE.
3. Fixed some issues with appending and `m...There are several changes affecting GW and BSE.
1. Added `ExcitedStateMethodology` in Method as base class for GW, BSE.
2. Added `Screening` as step to be callable as sub-section in GW and BSE.
3. Fixed some issues with appending and `m_add_sub_section` in workflow.py.
4. Added a condition for adding inputs in `TaskReference` normalizer. This was causing that inputs and outputs were repeated.
With this I will move into the normalizer for BSE and Spectra as explained in #1316.
@ladinesa do you mind reviewing this? It is related with the changes in the parsers. Thanks!Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1166Draft: Resolve "Parser matching is too slow"2023-04-02T21:08:33ZTheodore ChangDraft: Resolve "Parser matching is too slow"Closes #1396Closes #1396Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1162Draft: Resolve "Parser matching is too slow"2023-04-02T21:08:31ZTheodore ChangDraft: Resolve "Parser matching is too slow"Closes #1396Closes #1396https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1161Draft: Resolve "Parser matching is too slow"2023-04-02T21:08:27ZTheodore ChangDraft: Resolve "Parser matching is too slow"Closes #1396Closes #1396