nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-12-20T16:25:56Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1541Add timer2023-12-20T16:25:56ZTheodore ChangAdd timerTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1540Small fixes2023-11-07T23:37:13ZTheodore ChangSmall fixesTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1539Improvement excited state workflows MethodNormalizer2023-11-07T10:28:48ZJose PizarroImprovement excited state workflows MethodNormalizerIn a recent merge for the `SimulationWorkflow.normalize()`, a different ordering was introduced for writting the inputs. I then adapted the MethodNormalizer part handling GW, BSE, XS workflows to handle these potential issues, such that ...In a recent merge for the `SimulationWorkflow.normalize()`, a different ordering was introduced for writting the inputs. I then adapted the MethodNormalizer part handling GW, BSE, XS workflows to handle these potential issues, such that now it scans the inputs and searches for one having the keyword `'method'` in the name.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1538Draft: Resolve "Restructure parser plug ins"2024-02-26T11:31:14ZAlvin Noe LadinesDraft: Resolve "Restructure parser plug ins"Closes #1536Closes #1536Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1537Resolve "MOF App"2023-11-03T12:12:32ZDinga WonankeResolve "MOF App"Closes #1766
We have built a MOF app by adding quantities to config/model.py, which is a simple layout for exploring MOFs and properties in NOMAD. The app currently
1. displays a periodic table containing all atoms and their number of i...Closes #1766
We have built a MOF app by adding quantities to config/model.py, which is a simple layout for exploring MOFs and properties in NOMAD. The app currently
1. displays a periodic table containing all atoms and their number of instances in the MOF subset
2. displays a table illustrating the type of metal SBUs and the number of each present.
3. four histograms displaying
i. pore limiting diameter
ii. largest cavity diameter
iii. accessible surface area
iv. void fractions.
We still need to have a discussion about the following.
1. Whether to create two apps, one for experimental data and the other for computed data or merge everything into a single MOF app.
2. Add scatter plots for preliminary analysis. The main issue is that quantities extracted from the porosity normalisers are stored in topology meanwhile scattered plots can currently be done only on quantities found in data. A plan discussion will be made at some point in the future.Dinga WonankeDinga Wonankehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1535Provide possibility to return msection from xpath2023-11-03T11:07:13ZAlvin Noe LadinesProvide possibility to return msection from xpathAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1534Resolve "Searching from Upload does not behave as expected"2023-11-07T06:23:51ZLauri HimanenResolve "Searching from Upload does not behave as expected"Closes #1756Closes #1756Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1533Resolve "Cannot plot a Datetime Quantity"2023-11-17T13:47:56ZMohammad NakhaeeResolve "Cannot plot a Datetime Quantity"Closes #1754Closes #1754Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1532Resolve "Wrong entry type"2023-11-23T12:55:28ZMohammad NakhaeeResolve "Wrong entry type"Closes #1764Closes #1764Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1531Use ruff as linter2023-11-06T10:47:12ZAhmed IlyasUse ruff as linterThis replaces `pylint` with `ruff-pylint`. I have removed the `pylint` checks in CI and QA and updated the docs.
Once this is merged, I can also post on `nomad-developers` and recommend people to get the `ruff` extensions for vscode/py...This replaces `pylint` with `ruff-pylint`. I have removed the `pylint` checks in CI and QA and updated the docs.
Once this is merged, I can also post on `nomad-developers` and recommend people to get the `ruff` extensions for vscode/pycharm etc. That would also give people some time to transition towards using `ruff` tooling.Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1530Resolve "DataTextParser inheriting from TextParser"2023-11-03T12:29:07ZAlvin Noe LadinesResolve "DataTextParser inheriting from TextParser"Closes #1655Closes #1655Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1528Resolve "Some tabular parser modifications to make it more flexible"2023-11-07T11:35:21ZAmir GolparvarResolve "Some tabular parser modifications to make it more flexible"Closes #1741Closes #1741Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1527Resolve "Incorrect unit for geometry optimization final energy difference"2023-11-01T09:52:20ZAlvin Noe LadinesResolve "Incorrect unit for geometry optimization final energy difference"Closes #1762Closes #1762Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1526Resolve "Add bond list and generalize interactions in gromacs and lammps"2023-11-07T07:35:52ZJoseph RudzinskiResolve "Add bond list and generalize interactions in gromacs and lammps"Closes #1761
@ladinesa See also corresponding PR in atomistic parsersCloses #1761
@ladinesa See also corresponding PR in atomistic parsersJoseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1525w2dynamics support of Wannier90 config filenames2023-10-30T12:07:45ZJose Pizarrow2dynamics support of Wannier90 config filenamesQuick implementation for w2dynamics parser support of Wannier90 config filenames as specified in the w2dynamics HDF5 mainfile.Quick implementation for w2dynamics parser support of Wannier90 config filenames as specified in the w2dynamics HDF5 mainfile.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1524Added explanation documentation for processing.2023-11-11T15:01:21ZMarkus ScheidgenAdded explanation documentation for processing.Changelog: AddedChangelog: Addedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1523Fixed issue with periodic table size not updating.2023-11-01T06:44:39ZLauri HimanenFixed issue with periodic table size not updating.Closes #1757Closes #1757Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1522Resolve "Add Entity History Card"2023-12-21T08:58:31ZJose Marquez PrietoResolve "Add Entity History Card"Closes #1695Closes #1695Jose Marquez PrietoJose Marquez Prietohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1521Resolve "View Data in the Archive Button in plots does not work"2023-11-08T13:29:13ZMohammad NakhaeeResolve "View Data in the Archive Button in plots does not work"Closes #1748Closes #1748Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1520Fixed issue with unsupported mapping types, added tests for loading plugin...2023-10-26T13:50:22ZLauri HimanenFixed issue with unsupported mapping types, added tests for loading plugin...Fixed issue with unsupported mapping types, added tests for loading plugin values into search quantities.
Closes #1753Fixed issue with unsupported mapping types, added tests for loading plugin values into search quantities.
Closes #1753Lauri HimanenLauri Himanen