nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-10-31T09:36:36Zhttps://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/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/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/1378Resolve "Plot support refactor"2023-10-17T14:37:35ZMohammad NakhaeeResolve "Plot support refactor"Closes #1554Closes #1554Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1377Resolve "Refactoring tabular parser"2023-07-19T12:43:09ZAmir GolparvarResolve "Refactoring tabular parser"Closes #1531
Closes #1583Closes #1531
Closes #1583Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1367Resolve "ELN for integration (elabFTW, labfolder, chemotion)"2023-07-27T12:17:13ZAmir GolparvarResolve "ELN for integration (elabFTW, labfolder, chemotion)"Related #896Related #896Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1344Merge EELS to spectra2023-06-09T08:40:04ZJose PizarroMerge EELS to spectraMerging EELSDB data with computational data for a class in results in `results.properties.spectroscopic.spectra`.Merging EELSDB data with computational data for a class in results in `results.properties.spectroscopic.spectra`.https://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/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 Nakhaee