Provide categorized example structures. (#1019)

[x] Provide categorized example structures, and only the respective examples are shown when the button is clicked. 
[x] The example catalog is extensible by the plugins.
[x] Remove the "Primitive cell" from everywhere, as done below, as we should always ONLY provide the primitive cell):
[x] For gold, replace the current one with its primitive cell.
[x] For Cobalt, remove it and replace with Nickel FCC.

docs/source/tutorials/advanced.rst

@@ -5,14 +5,14 @@ Advanced Tutorial
 Overview
 --------
 
-Calculations probing more intricate properties often require additional computational resources. In this tutorial, we will again compute a band structure, but this time, we will do it for a magnetic system, namely bulk cobalt. As such, will set up our environment to submit to a remote machine capable of handling the calculation.
+Calculations probing more intricate properties often require additional computational resources. In this tutorial, we will again compute a band structure, but this time, we will do it for a magnetic system, namely bulk nickel. As such, will set up our environment to submit to a remote machine capable of handling the calculation.
 
 Start
 -----
 
 .. admonition:: Goal
 
-   To submit a band structure calculation for magnetic cobalt on a remote machine.
+   To submit a band structure calculation for magnetic nickel on a remote machine.
 
 To start, go ahead and :doc:`launch </installation/launch>` the app, then follow the steps below.
 
@@ -23,12 +23,12 @@ To start, go ahead and :doc:`launch </installation/launch>` the app, then follow
 Step 1: Select a structure
 **************************
 
-Select `Cobalt (hcp)` from the `From examples` tab and click `Confirm`.
+Select `Nickel (hcp)` from the `From examples` tab and click `Confirm`.
 
 Step 2: Configure the workflow
 ******************************
 
-Select `Full geometry` to relax the structure. As we are looking at magnetic cobalt, we also want to turn on `Magnetism`. Go ahead and do so now.
+Select `Full geometry` to relax the structure. As we are looking at magnetic nickel, we also want to turn on `Magnetism`. Go ahead and do so now.
 
 Select both `Band structure` and `Projected density of states` as the properties of interest.
 

setup.cfg

@@ -52,6 +52,8 @@ aiidalab_qe.app.static.styles = *.css
 aiidalab_qe.app.static.templates = *.jinja
 aiidalab_qe.app.structure.examples = *
 aiidalab_qe.plugins.xas = pseudo_toc.yaml
+aiidalab_qe.plugins.xps.structure_examples = *
+aiidalab_qe.plugins.xas.structure_examples = *
 
 [options.entry_points]
 aiidalab_qe.properties =

src/aiidalab_qe/app/structure/__init__.py

@@ -15,10 +15,10 @@
     LazyLoadedStructureBrowser,
 )
 from aiidalab_qe.common.infobox import InAppGuide
+from aiidalab_qe.common.widgets import CategorizedStructureExamplesWidget
 from aiidalab_widgets_base import (
     BasicCellEditor,
     BasicStructureEditor,
-    StructureExamplesWidget,
     StructureManagerWidget,
     StructureUploadWidget,
     WizardAppWidgetStep,
@@ -28,16 +28,13 @@
 # StructureExamplesWidget.
 file_path = pathlib.Path(__file__).parent
 Examples = [
-    ("Bulk silicon (primitive cell)", file_path / "examples" / "Si.cif"),
-    ("Silicon oxide (alpha quartz)", file_path / "examples" / "SiO2.cif"),
-    ("Diamond (primitive cell)", file_path / "examples" / "Diamond.cif"),
-    ("Gallium arsenide (primitive cell)", file_path / "examples" / "GaAs.cif"),
-    ("Gold (conventional cell)", file_path / "examples" / "Au.cif"),
-    ("Cobalt (primitive cell)", file_path / "examples" / "Co.cif"),
-    ("Lithium carbonate", file_path / "examples" / "Li2CO3.cif"),
-    ("Phenylacetylene molecule", file_path / "examples" / "Phenylacetylene.xyz"),
-    ("ETFA molecule", file_path / "examples" / "ETFA.xyz"),
+    ("Bulk silicon", file_path / "examples" / "Si.cif"),
+    ("Diamond", file_path / "examples" / "Diamond.cif"),
+    ("Gallium arsenide", file_path / "examples" / "GaAs.cif"),
+    ("Gold", file_path / "examples" / "Au.cif"),
+    ("Nickel", file_path / "examples" / "Ni.cif"),
     ("LiCoO2", file_path / "examples" / "LiCoO2.cif"),
+    ("Silicon oxide (alpha quartz)", file_path / "examples" / "SiO2.cif"),
 ]
 
 
@@ -73,11 +70,22 @@ def render(self):
         if self.rendered:
             return
 
+        examples_by_category = {"Simple crystals": Examples}
+        plugin_structure_examples = {
+            item["title"]: item["structures"]
+            for item in get_entry_items(
+                "aiidalab_qe.properties", "structure_examples"
+            ).values()
+        }
+        examples_by_category.update(plugin_structure_examples)
+
         importers = [
             StructureUploadWidget(title="Upload file"),
             LazyLoadedOptimade(title="OPTIMADE"),
             LazyLoadedStructureBrowser(title="AiiDA database"),
-            StructureExamplesWidget(title="From Examples", examples=Examples),
+            CategorizedStructureExamplesWidget(
+                title="From Examples", examples_by_category=examples_by_category
+            ),
         ]
 
         plugin_importers = get_entry_items("aiidalab_qe.properties", "importer")

src/aiidalab_qe/app/structure/examples/Au.cif

@@ -1,12 +1,12 @@
 data_image0
-_chemical_formula_structural       Au4
-_chemical_formula_sum              "Au4"
-_cell_length_a       4.078
-_cell_length_b       4.078
-_cell_length_c       4.078
-_cell_angle_alpha    90
-_cell_angle_beta     90
-_cell_angle_gamma    90
+_chemical_formula_structural       Au
+_chemical_formula_sum              "Au1"
+_cell_length_a       2.885
+_cell_length_b       2.885
+_cell_length_c       2.885
+_cell_angle_alpha    60
+_cell_angle_beta     60
+_cell_angle_gamma    60
 
 _space_group_name_H-M_alt    "P 1"
 _space_group_IT_number       1
@@ -24,6 +24,3 @@ loop_
   _atom_site_fract_z
   _atom_site_occupancy
   Au  Au1       1.0  0.00000  0.00000  0.00000  1.0000
-  Au  Au2       1.0  0.00000  0.50000  0.50000  1.0000
-  Au  Au3       1.0  0.50000  0.00000  0.50000  1.0000
-  Au  Au4       1.0  0.50000  0.50000  0.00000  1.0000

src/aiidalab_qe/app/structure/examples/Ni.cif

@@ -0,0 +1,26 @@
+data_image0
+_chemical_formula_structural       Ni
+_chemical_formula_sum              "Ni1"
+_cell_length_a       2.48902
+_cell_length_b       2.48902
+_cell_length_c       2.48902
+_cell_angle_alpha    60
+_cell_angle_beta     60
+_cell_angle_gamma    60
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_type_symbol
+  _atom_site_label
+  _atom_site_symmetry_multiplicity
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_occupancy
+  Ni  Ni1       1.0  0.00000  0.00000  0.00000  1.0000

src/aiidalab_qe/common/widgets.py

@@ -19,7 +19,7 @@
 
 from aiida.orm import CalcJobNode, load_code, load_node
 from aiida.orm import Data as orm_Data
-from aiidalab_widgets_base import ComputationalResourcesWidget
+from aiidalab_widgets_base import ComputationalResourcesWidget, StructureExamplesWidget
 from aiidalab_widgets_base.utils import (
     StatusHTML,
     list_to_string_range,
@@ -1065,3 +1065,29 @@ def _get_widget(self):
                 HubbardStructureData,
             ),
         )
+
+
+class CategorizedStructureExamplesWidget(StructureExamplesWidget):
+    """Extended widget to provide categorized example structures."""
+
+    def __init__(self, examples_by_category, title="", **kwargs):
+        self.examples_by_category = examples_by_category
+        self._category_buttons = ipw.ToggleButtons(
+            options=list(examples_by_category.keys()),
+            description="Category:",
+        )
+        self._category_buttons.observe(self._on_category_change, names="value")
+
+        # Initialize with the first category
+        initial_category = next(iter(examples_by_category.keys()))
+        super().__init__(
+            examples=examples_by_category[initial_category], title=title, **kwargs
+        )
+
+        self.children = [self._category_buttons, *list(self.children)]
+
+    def _on_category_change(self, change):
+        """Update the dropdown when the category changes."""
+        new_category = change["new"]
+        new_examples = self.examples_by_category.get(new_category, [])
+        self._select_structure.options = self.get_example_structures(new_examples)

src/aiidalab_qe/plugins/xas/__init__.py

@@ -9,6 +9,7 @@
 from .resources import XasResourceSettingsModel, XasResourceSettingsPanel
 from .result import XasResultsModel, XasResultsPanel
 from .setting import XasConfigurationSettingsPanel
+from .structure_examples import structure_examples
 from .workchain import workchain_and_builder
 
 PSEUDO_TOC = yaml.safe_load(
@@ -25,6 +26,7 @@ class XasPluginOutline(PluginOutline):
 
 xas = {
     "outline": XasPluginOutline,
+    "structure_examples": structure_examples,
     "configuration": {
         "panel": XasConfigurationSettingsPanel,
         "model": XasConfigurationSettingsModel,

src/aiidalab_qe/plugins/xas/structure_examples/__init__.py

@@ -0,0 +1,10 @@
+import pathlib
+
+file_path = pathlib.Path(__file__).parent
+
+structure_examples = {
+    "title": "XAS examples",
+    "structures": [
+        ("Lithium carbonate", file_path / "Li2CO3.cif"),
+    ],
+}

src/aiidalab_qe/plugins/xps/__init__.py

@@ -3,6 +3,7 @@
 from .model import XpsConfigurationSettingsModel
 from .result import XpsResultsModel, XpsResultsPanel
 from .setting import XpsConfigurationSettingsPanel
+from .structure_examples import structure_examples
 from .workchain import workchain_and_builder
 
 
@@ -12,6 +13,7 @@ class XpsPluginOutline(PluginOutline):
 
 xps = {
     "outline": XpsPluginOutline,
+    "structure_examples": structure_examples,
     "configuration": {
         "panel": XpsConfigurationSettingsPanel,
         "model": XpsConfigurationSettingsModel,

src/aiidalab_qe/plugins/xps/structure_examples/__init__.py

@@ -0,0 +1,10 @@
+import pathlib
+
+file_path = pathlib.Path(__file__).parent
+structure_examples = {
+    "title": "XPS examples",
+    "structures": [
+        ("Phenylacetylene molecule", file_path / "Phenylacetylene.xyz"),
+        ("ETFA molecule", file_path / "ETFA.xyz"),
+    ],
+}