nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-10-20T13:02:58Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1455Resolve "Basesections Should Populate Workflow Section"2023-10-20T13:02:58ZHampus NaesstroemResolve "Basesections Should Populate Workflow Section"Closes #1658Closes #1658Hampus NaesstroemHampus Naesstroemhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1454Resolve "ReadableIdentifiers Normalizers Fails"2023-09-08T09:07:13ZHampus NaesstroemResolve "ReadableIdentifiers Normalizers Fails"Closes #1670
Closes #1594Closes #1670
Closes #1594Hampus NaesstroemHampus Naesstroemhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1385Refactored Substance Base Sections2023-08-16T06:09:25ZHampus NaesstroemRefactored Substance Base SectionsSeparates out `Substance` properties to a `SubstanceSection` class
Adds `SubstanceComponent` with `SubstanceSection` sub section
Moves `system` quantity from `Component` to inheriting `SystemComponent` class
Adds `PubChemSubstanceSect...Separates out `Substance` properties to a `SubstanceSection` class
Adds `SubstanceComponent` with `SubstanceSection` sub section
Moves `system` quantity from `Component` to inheriting `SystemComponent` class
Adds `PubChemSubstanceSection` which queries PubChem for substance information
Adds `PubChemSubstanceComponent` and `PubChemSubstance` analogous to `Substance`
Closes #1585https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1295Move ELN Base Sections2023-06-01T07:52:05ZHampus NaesstroemMove ELN Base SectionsMoved base sections from `eln` to `basesections`
Closes #1494Moved base sections from `eln` to `basesections`
Closes #1494Hampus NaesstroemHampus Naesstroemhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/16011547-add-support-for-h5md-files2024-01-17T15:11:47ZJoseph Rudzinski1547-add-support-for-h5md-filespartner changes to dev of h5md parser: https://github.com/nomad-coe/atomistic-parsers/pull/71
Closes #1547partner changes to dev of h5md parser: https://github.com/nomad-coe/atomistic-parsers/pull/71
Closes #1547Joseph RudzinskiJoseph Rudzinskihttps://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/1466Resolve "New thermostat metadata needed for OpenMX parsing of MD data"2023-09-21T14:26:10ZJoseph RudzinskiResolve "New thermostat metadata needed for OpenMX parsing of MD data"Closes #1684
I have simply added repeats to the sections ThermostatParameters and BarostatParameters here and added 1 enum value for thermostat type.Closes #1684
I have simply added repeats to the sections ThermostatParameters and BarostatParameters here and added 1 enum value for thermostat type.Joseph RudzinskiJoseph Rudzinskihttps://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/1286new Rg tests for MD workflow2023-05-16T11:16:43ZJoseph Rudzinskinew Rg tests for MD workflowCloses #1490
@ladinesa This should fix your memory issues for the workflow tests for MD. Once you confirm, I will merge and also remove the corresponding issues in the atomistic parser.Closes #1490
@ladinesa This should fix your memory issues for the workflow tests for MD. Once you confirm, I will merge and also remove the corresponding issues in the atomistic parser.Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1225Optimizing w2dynamics parser2023-04-20T09:50:28ZJose PizarroOptimizing w2dynamics parserCloses #1429Closes #1429Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1172Resolve "molecular dynamics support for fhiaims"2023-04-05T12:38:41ZJoseph RudzinskiResolve "molecular dynamics support for fhiaims"Closes #1377Closes #1377Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1168Highlighted atoms in material visualizer2023-03-27T12:16:44ZJose PizarroHighlighted atoms in material visualizer@himanel1 would you mind reviewing these changes?
I am not sure what is the best procedure about `[showBonds, setShowBonds]`. I added a line to check whether the method is 'parser/hightlight', but there might be a better option.
Close...@himanel1 would you mind reviewing these changes?
I am not sure what is the best procedure about `[showBonds, setShowBonds]`. I added a line to check whether the method is 'parser/hightlight', but there might be a better option.
Closes #1373Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1158GW in VASP2023-03-16T16:05:19ZJose PizarroGW in VASPI implemented GW in VASP and generalized a bit further the `run.method.gw` metainfo.
Closes #1290I implemented GW in VASP and generalized a bit further the `run.method.gw` metainfo.
Closes #1290Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1139Modified GW method metainfo2023-03-13T09:58:02ZJose PizarroModified GW method metainfo@ladinesa What do you think?
These changes are then reflected in the modifications for exciting, FHIaims and ABINIT in the submodule.@ladinesa What do you think?
These changes are then reflected in the modifications for exciting, FHIaims and ABINIT in the submodule.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1078Hotfix GW workflow method section2023-02-09T14:04:49ZJose PizarroHotfix GW workflow method sectionFixed method normalizer to get starting_point and basis_set metainfo ONLY in the GW workflow entry
Deleted starting_point metainfo from GW run.methodFixed method normalizer to get starting_point and basis_set metainfo ONLY in the GW workflow entry
Deleted starting_point metainfo from GW run.methodJose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1042added atom types to archive_to_universe from method.atom_parameters2023-01-23T11:18:00ZJoseph Rudzinskiadded atom types to archive_to_universe from method.atom_parametersCloses #1288Closes #1288https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1039HubbardModel to HubbardKanamoriModel renaming2023-01-18T12:00:04ZJose PizarroHubbardModel to HubbardKanamoriModel renamingI think it makes sense if you also review it here, @ndaelman
Closes #1285I think it makes sense if you also review it here, @ndaelman
Closes #1285Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1029change Lammps mainfile_contents_re2023-01-13T14:47:49ZJoseph Rudzinskichange Lammps mainfile_contents_reCloses #1276
@ladinesa - I changed the Lammps regex matcher to include the data after. Typical log file looks like this: LAMMPS (12 Dec 2018). Not sure if this is completely general, but it works for all the test data I can see, and it...Closes #1276
@ladinesa - I changed the Lammps regex matcher to include the data after. Typical log file looks like this: LAMMPS (12 Dec 2018). Not sure if this is completely general, but it works for all the test data I can see, and it avoids the other files which simply print "LAMMPS" at the beginning of the line in the header.Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1028ordering of residues fixed2023-01-16T12:30:30ZJoseph Rudzinskiordering of residues fixedCloses #1273Closes #1273Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1020Resolve "Generalization of MD workflow2 results"2023-01-10T09:26:11ZJoseph RudzinskiResolve "Generalization of MD workflow2 results"Closes #1265Closes #1265