nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2020-09-14T10:42:50Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/172V0.8.92020-09-14T10:42:50ZMarkus ScheidgenV0.8.9https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/173Implemented new lammps parser2020-09-16T06:33:53ZAlvin Noe LadinesImplemented new lammps parserNew lammps parser using metainfo. Added metainfo quantities to accommodate lammps outputsNew lammps parser using metainfo. Added metainfo quantities to accommodate lammps outputsMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/174Implemented fixes and tests to workflow2020-09-16T20:37:33ZAlvin Noe LadinesImplemented fixes and tests to workflowTests are now available for workflows. Changed Relaxation to GeometryOptimization.
Fixed bug in workflow GeometryOptimization and lammpsparser and elasticparser.Tests are now available for workflows. Changed Relaxation to GeometryOptimization.
Fixed bug in workflow GeometryOptimization and lammpsparser and elasticparser.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/175K8s dbs2020-09-17T07:19:34ZMarkus ScheidgenK8s dbshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/177DOS analysis: added Jupyter notebook2020-09-17T14:02:02ZCuauhtemoc Salazartemok@physik.hu-berlin.deDOS analysis: added Jupyter notebookAdded a notebook to compare DOS output from different DFT codes. DOS data is fetched from NOMAD's repository.Added a notebook to compare DOS output from different DFT codes. DOS data is fetched from NOMAD's repository.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/178Many minor GUI tweaks.2020-12-18T16:07:59ZMarkus ScheidgenMany minor GUI tweaks.Minro GUI tweaks.Minro GUI tweaks.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/179Fixes issue # 4232020-09-21T06:47:57ZMarkus ScheidgenFixes issue # 423https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/181Fixed issue with searching materials that contain both band structure and DOS...2020-09-23T06:31:32ZLauri HimanenFixed issue with searching materials that contain both band structure and DOS. Removed accidental comment.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/180Added component for viewing the Brillouin Zone, added a uniform way of dealin...2020-09-23T06:32:45ZLauri HimanenAdded component for viewing the Brillouin Zone, added a uniform way of dealing with exceptions through React error boundaries (ErrorHandler.js), fixed small issues with plots and structureviewer.Before merging you can check the functionality at: [https://labdev-nomad.esc.rzg.mpg.de/dev/nomad/brillouin-zone/gui/entry/id/0w6CbOiCRg2sqWzTjO1Bew/skkhFDTWZHGcgva081IiIfts_Hh7/archive/section_run/section_single_configuration_calculatio...Before merging you can check the functionality at: [https://labdev-nomad.esc.rzg.mpg.de/dev/nomad/brillouin-zone/gui/entry/id/0w6CbOiCRg2sqWzTjO1Bew/skkhFDTWZHGcgva081IiIfts_Hh7/archive/section_run/section_single_configuration_calculation:0/section_k_band](https://labdev-nomad.esc.rzg.mpg.de/dev/nomad/brillouin-zone/gui/entry/id/0w6CbOiCRg2sqWzTjO1Bew/skkhFDTWZHGcgva081IiIfts_Hh7/archive/section_run/section_single_configuration_calculation:0/section_k_band)
I went with a radio button for toggling between the band structure plot and the Brillouin zone viewer. Radio buttons are a fairly standard way to switch between exclusive options so I felt it to be a better fit than a simple button or switch. What do you think?Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/182Bugfixes2020-09-23T07:41:15ZMarkus ScheidgenBugfixeshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/183Refactored the Encyclopedia API. The complex aggregations are now prefiltered...2020-09-24T11:16:01ZLauri HimanenRefactored the Encyclopedia API. The complex aggregations are now prefiltered correctly according to the user query and the maximum result set size has been lowered.I reordered the search logic a bit and included a bit better filtering before the costly aggregations are run. Also lowered the maximum result size from 5M to 500k. If this does not improve the situation, we can still lower the query siz...I reordered the search logic a bit and included a bit better filtering before the costly aggregations are run. Also lowered the maximum result size from 5M to 500k. If this does not improve the situation, we can still lower the query size. But I would not spend much more time optimizing these queries as they will anyways go away once we get the materials index up.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/184Added a fixed Pint unit and constant file, added CLI command for creating uni...2020-09-29T06:42:07ZLauri HimanenAdded a fixed Pint unit and constant file, added CLI command for creating unit conversion data for the GUI, added new React component for changing the units in the ArchiveBrowser.The CLI command `nomad dev units` outputs a Javascript source file that is automatically created from the currently used Pint units. This command is also run in the Dockerfile.
I added a menu for choosing the units in the ArchiveBrowser...The CLI command `nomad dev units` outputs a Javascript source file that is automatically created from the currently used Pint units. This command is also run in the Dockerfile.
I added a menu for choosing the units in the ArchiveBrowser. You can either select SI units, atomic units, or a custom selection for a selection of quantities. By default, a custom selection is used (eV instead of Joule, angstrom instead of meter, otherwise default SI units). This can be changed based on what we think is reasonable.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/185Bugfixes2020-09-29T06:42:28ZMarkus ScheidgenBugfixeshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/186Fixed issue with the Pint data files not ending up in the package installation.2020-09-29T11:38:39ZLauri HimanenFixed issue with the Pint data files not ending up in the package installation.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/187Bugfixes2020-09-29T13:38:09ZMarkus ScheidgenBugfixeshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/188V0.9.02020-10-01T05:46:04ZMarkus ScheidgenV0.9.0https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/189V0.9.12020-10-01T08:45:20ZMarkus ScheidgenV0.9.1https://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/192V0.9.22020-10-06T06:37:10ZMarkus ScheidgenV0.9.2https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/191PEP8 on ABINIT parser2020-10-06T08:03:21ZCuauhtemoc Salazartemok@physik.hu-berlin.dePEP8 on ABINIT parserBranch `parser_abinit_PEP8` branched off from `v0.9.2` an hour ago (so it's up to date with Friday's state)
The main file of the ABINIT parser
```
dependencies/parsers/abinit/abinitparser/parser.py
```
had inhomogeneous indentations, r...Branch `parser_abinit_PEP8` branched off from `v0.9.2` an hour ago (so it's up to date with Friday's state)
The main file of the ABINIT parser
```
dependencies/parsers/abinit/abinitparser/parser.py
```
had inhomogeneous indentations, ranging from 4-, 3-, and single-space indentations; this caused problems when editing the code. The indentation was fixed using the `autopep8` tool.
I ran the tests and DOS cases again and they produce the same archive outcome.
---
There is also a minor fix to the block of code that finds the DOS file: the parser was reporting "multiple DOS files found" when there isn't any DOS file.