GUI (explore/entries and explore/materials menus) cleanup

@mscheidg @himanel1 @ndaelman @pizarroj @jrudz @ladinesa .

GUI cleanup

General features

• This list of changes has been thoroughly discussed in Area C. The main idea is to remove everything that contains wrong values or denominations, unless we see easy fixes, in which case, we describe what should be changed.
• This applies to explore/entries and explore/materials views, but other apps that use similar menus may consider to adapt (e.g, solar cells)
• There will be no changes in "results" metadata section, all changes in the GUI itself.
• Allow for subscripts for chemical formulas (Lauri: tracked in issue #1272) and (optional) Strukturbericht Designation. This is in the visualization. The search string should be still in line e.g., "C3PO4" or "L10" rather than any tricky way to write the subscripts on the fly. There is no ambiguity in having the subscripts in formulas and Strukturbericht in line, but in the visualization, it makes it appear way more professional.
• The comments are based on what one sees in beta version as of today, December 23, 2022.
• In the future, I propose that changes in NOMAD that reflect into changes in the GUI main page (explore/entries "app", and also explore/materials as the layout of the menus is the same, except for the Combine results from several entries option) should be submitted to coordinators (at least ABC) for approval. Also for the beta version, inasmuch it is a version easily publicly accessible from the FAIRmat/NOMAD pages
• Some of the entries may spawn dedicated issues in order to keep the discussion here tidy. In that case, we should add a link to the dedicated issue in the list below.
• Individual entries need to be assigned, probably we meet early next year to discuss who does what and deadlines?

List of changes

• Material

  • structural type, rename into Dimensionality. Again: no change in the metadata name at this point, but eventually we should consider renaming when necessary. E.g., structural type really tells nothing about what one may find as options.
    • Check: structural type = 2d, there are no data? It seems that in the prod version there are data under this class. Lauri: Fixed in #1256 (closed)
    • In the near future: check structural type = unavailable; In principle there should be no unassigned entries according to dimensionality. In particular, to be checked: liquids and solvent in liquids are categorized as? Lauri: Things can be unassigned, as structural_type != dimensionality. Structural type has additional checks that go beyond dimensionality. For now I'm simply hiding the value unavailable from the menu.
  • functional type, remove. [These are from Springer-Materials. It is unclear if we can tell it explicitly, due to copyrights, and also the assignment is often questionable. IMPORTANT: Ask Pepe about "solar cell" (suggestion: only in app) ]
  • compound type, remove [It needs rethinking. E.g, "chemical element" should be elemental system? "Intermetallic" is not just something containing d-metals; maybe oxide, nitride,and so on are fine, but let's remove it and then work later to make it publishable]
  • material name -> remove. [it is just the chemical formula in words, not the name of the material. E.g., carbon is not a material. So, the label "material name" is misleading.]

• element formula

  • chemical formula anonymous: show by default the statistics so that one can see what are the possible search values. Also, improve the description, as at the moment it is unclear what/how to search for. Lauri: now the placeholder shows examples, improved the metainfo description.
  • IMPORTANTLY: add IUPAC chemical formula. I.e., order elements by electronegativity (e.g., Pauling). [This is the only change that requires a normalizer and a new metadata item, but it is long due. This should be also the default formula shown in the Formula column in the listed results.] Lauri: now added IUPAC formula as defined in IUPAC nomenclature of inorganic chemistry 2005. The chemical proportion numbers are not NOT reduced. Note that we should not make the table column shown this formula before most of the entries have it (requires reprocessing or some manual ES scripting.).
  • Add chemical formula reduced. This is already created upon normalization, I believe, but it should be made searchable. Note: probably, since the stoichiometric number now would be rational numbers, not necessarily integers, the searched formula should be parsed up to a pre-fixed precision (e.g., 2 decimal points). Lauri: Now added with examples in the placeholder. We follow the OPTIMADE definition that only allows integer stoichiometry. There is also a bug associated with the reduced formula that is tracked in #1259 (closed) and #879 (closed) that will be fixed here.

• symmetry

  • structure name, remove [It needs revision, it is not clear what kind of classification this is and how it is assigned and in general the class names are a heterogeneous lot] Lauri: As discussed, I merged the Pnma and cubic perovskite definitions into one structure_name=perovskite option. This also fixes #520 (closed). In the GUI I'm temporarily hiding the cubic perovskite option. This filter is otherwise kept as it is, since it is very useful. Renaming is of course possible.
  • space group symbol: move it to 3rd place, after Bravais Lattice and crystal system. Also add statistics by default in order to show options. Lauri: Reordered, now the placeholder shows examples.
  • Not the highest priority: correct Strukturbericht Designation entries, i.e., with subscripts where necessary. See https://aflowlib.org/prototype-encyclopedia/strukturberichts.html or https://en.wikipedia.org/wiki/Strukturbericht_designation for the correct symbol. Lauri: tracked in issues #1274
  • Prototype aflow, show statistics by default to suggest options. Lauri: now the placeholder shows examples.

• Method

  • Remove method name and workflow name. This implies that method is no longer a menu, just a header of the items below it (simulation, etc.).

• DFT

  • Remove xc functional type and substitute with Jacob's ladder Lauri: this is tracked separately in issue #1167 (closed).

• EELS

  • check Electron Energy Loss Spectrum (EELS) Max Energy (eV) entries. Apparently, one wrong entry is making the scale unreasonable. In general, for the future: define expected ranges for values to catch bogus entries at parsing/normalization time. It is better to have one/few entry/ies unlisted than having the ranges screwed to accommodate wrong values. There is already an issue about this in #814. I think the best way to handle this is to not ignore such data but instead sanitize the aggregations by default with some sensible limits.

• Properties.

  • remove Optoelectronic. [It is a copy of solar cell properties in solar cell app, where it belongs]
  • remove Spectroscopy. [It is not a property and it is a copy of Experiment / EELS]
  • remove from properties Thermodynamics and Geometry Optimization (see next point, where this are moved to)

• Add new section Workflow with items:

  • Geometry Optimization, which is the current Geometry Optimization from Properties, just moved here.
  • Molecular Dynamics, which is the current Thermodynamics from Properties

• For the future: Optimade should rather be an option in the search bar. This belongs into a larger topic of supporting more complex search queries in the search bar, including the optimade language and possibly some other alternatives as well.