nomad-FAIR issueshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues2023-12-21T16:06:51Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1523Integrate GIMS (as a NORTH tool)2023-12-21T16:06:51ZMarkus ScheidgenIntegrate GIMS (as a NORTH tool)The "Graphical Interface for Materials Simulations" (GIMS) is a Python-based web-enabled tool to visualize fhi-aims and exciting output.
It is imaginable that we could containerise this and offer it as a NORTH tool on NOMAD. So if you ...The "Graphical Interface for Materials Simulations" (GIMS) is a Python-based web-enabled tool to visualize fhi-aims and exciting output.
It is imaginable that we could containerise this and offer it as a NORTH tool on NOMAD. So if you uploaded some exciting or aims data, you can run this to have a look.
If the tool provides value, we can think about improving it.
GIMS gitlab: https://gitlab.com/gims-developers/gims
GIMS docs: https://gims-developers.gitlab.io/gims/developerManual/developerManual.htmlhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1409Elemental Composition in Results2023-05-11T08:56:30ZJose Marquez PrietoElemental Composition in ResultsFor many experimental applications and apps, we need to have a place in `results` to store the elemental composition of a sample or a material.
My proposal would be to have it under `results.material` and under each system in `results.m...For many experimental applications and apps, we need to have a place in `results` to store the elemental composition of a sample or a material.
My proposal would be to have it under `results.material` and under each system in `results.material.topology`.
The section would have the following form, which is adapted from the one in our eln `System` base class that @hnaesstroem designed:
```
class ElementalComposition(MSection):
'''A section for describing the elemental composition of a system, i.e. the element
and its atomic fraction.
'''
m_def = Section(label_quantity='element')
element = Quantity(
type=MEnum(chemical_symbols[1:]),
description='''
The symbol of the element, e.g. 'Pb'.
''')
atomic_fraction = Quantity(
type=np.float64,
description='''
The atomic fraction of the element in the system it is contained within.
Per definition a positive value less than or equal to 1.
'''
)
```
This will allow us to search these values, use these in search widgets like the Scatter Plot once #1325 gets fixed, and build new widgets like ternary plot diagrams (important for #1296).
We will also update the Formula normalizer to populate this automatically from the formulas so that upon reprocessing the entries everything gets populated too.
@lucamghi, @himanel1 and Team C (@jrudz, @pizarroj and @ndaelman). Please do let us know as soon as possible if you have any objections to this. We would need this to be implemented with high priority for several upcoming presentations and use cases.Jose Marquez PrietoJose Marquez Prietohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1747Change management strategies and policies2023-12-21T15:40:08ZMohammad NakhaeeChange management strategies and policiesI think at the moment we have lack of cahnge mangement. These are some conducting strategies that comes to my mind for user onboarding
- Warning when using deprecated features in a not published upload (If it is publishe we can show the...I think at the moment we have lack of cahnge mangement. These are some conducting strategies that comes to my mind for user onboarding
- Warning when using deprecated features in a not published upload (If it is publishe we can show the feature without any warning)
- Warning or even preventing publishing of outdated features
- Warnings or even preventing publishing of Beta version features
We had the same problem about tabular parser that changed a lot before approaching this version and hopefully we did not have any published schema.
In the case of plot functuionality I would say
- plotly_graph_object annotation [official feature]
- python PlotSection [official feature]
- plotly_express annotation [beta feature]
- plotly_subplot annotation [beta feature]
- plot annotation [deprecated feature]
@mscheidg @himanel1https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1735Files with filenames starting with a number cannot be opened2023-10-23T12:12:02ZMichael KriegerFiles with filenames starting with a number cannot be openedWhen a filename starts with a number (e.g. "1.txt"), the file cannot be opened from the FILES page in an upload. The error message shown ("ERROR The item ":1.txt" could not be found.") indicates that a colon is added before the actual fi...When a filename starts with a number (e.g. "1.txt"), the file cannot be opened from the FILES page in an upload. The error message shown ("ERROR The item ":1.txt" could not be found.") indicates that a colon is added before the actual filename; this only happends if the filename starts with a number.Markus ScheidgenMarkus Scheidgen