Fix structure.kind-related bugs

src/aiidalab_qe/app/configuration/advanced/hubbard/model.py

@@ -102,7 +102,7 @@ def _update_defaults(self, which):
                     ),
                     [
                         Element(symbol)
-                        for symbol in self.input_structure.get_kind_names()
+                        for symbol in self.input_structure.get_symbols_set()
                     ],
                 )
             ]
@@ -124,13 +124,16 @@ def _get_default_eigenvalues(self):
         return deepcopy(self._defaults["eigenvalues"])
 
     def _get_labels(self):
-        symbols = self.input_structure.get_kind_names()
         hubbard_manifold_list = [
-            self._get_manifold(Element(symbol)) for symbol in symbols
+            self._get_manifold(Element(kind.symbol))
+            for kind in self.input_structure.kinds
         ]
         return [
-            f"{symbol} - {manifold}"
-            for symbol, manifold in zip(symbols, hubbard_manifold_list)
+            f"{kind_name} - {manifold}"
+            for kind_name, manifold in zip(
+                self.input_structure.get_kind_names(),
+                hubbard_manifold_list,
+            )
         ]
 
     def _get_manifold(self, element):

src/aiidalab_qe/app/configuration/advanced/pseudos/model.py

@@ -169,14 +169,12 @@ def update_default_cutoffs(self):
                 </div>
             """
         else:
-            symbols = (
-                self.input_structure.get_kind_names() if self.input_structure else []
-            )
+            kinds = self.input_structure.kinds if self.input_structure else []
 
         ecutwfc_list = []
         ecutrho_list = []
-        for symbol in symbols:
-            cutoff = cutoff_dict.get(symbol, {})
+        for kind in kinds:
+            cutoff = cutoff_dict.get(kind.symbol, {})
             ecutrho, ecutwfc = (
                 U.Quantity(v, current_unit).to("Ry").to_tuple()[0]
                 for v in cutoff.values()

src/aiidalab_qe/app/configuration/advanced/pseudos/pseudos.py

@@ -287,22 +287,18 @@ def _build_setter_widgets(self):
 
         children = []
 
-        elements = (
-            self._model.input_structure.get_kind_names()
-            if self._model.input_structure
-            else []
-        )
+        kinds = self._model.input_structure.kinds if self._model.input_structure else []
 
-        for index, element in enumerate(elements):
-            upload_widget = PseudoUploadWidget(element=element)
+        for index, kind in enumerate(kinds):
+            upload_widget = PseudoUploadWidget(kind_name=kind.name)
             pseudo_link = ipw.link(
                 (self._model, "dictionary"),
                 (upload_widget, "pseudo"),
                 [
-                    lambda d, element=element: orm.load_node(d.get(element)),
-                    lambda v, element=element: {
+                    lambda d, symbol=kind.symbol: orm.load_node(d.get(symbol)),
+                    lambda v, symbol=kind.symbol: {
                         **self._model.dictionary,
-                        element: v.uuid,
+                        symbol: v.uuid,
                     },
                 ],
             )
@@ -345,13 +341,13 @@ class PseudoUploadWidget(ipw.HBox):
     cutoffs = tl.List(tl.Float(), [])
     error_message = tl.Unicode(allow_none=True)
 
-    def __init__(self, element, **kwargs):
+    def __init__(self, kind_name, **kwargs):
         super().__init__(
             children=[LoadingWidget("Loading pseudopotential uploader")],
             **kwargs,
         )
 
-        self.element = element
+        self.kind_name = kind_name
 
         self.rendered = False
 
@@ -363,7 +359,7 @@ def render(self):
             description="Upload",
             multiple=False,
         )
-        self.pseudo_text = ipw.Text(description=self.element)
+        self.pseudo_text = ipw.Text(description=self.kind_name)
         self.file_upload.observe(self._on_file_upload, "value")
 
         cutoffs_message_template = """
@@ -413,9 +409,9 @@ def _on_file_upload(self, change=None):
             self.pseudo.store()
 
             # check if element is matched with the pseudo
-            element = "".join([i for i in self.element if not i.isdigit()])
+            element = "".join([i for i in self.kind_name if not i.isdigit()])
             if element != self.pseudo.element:
-                self.error_message = f"""<div class="alert alert-danger"> ERROR: Element {self.element} is not matched with the pseudo {self.pseudo.element}</div>"""
+                self.error_message = f"""<div class="alert alert-danger"> ERROR: Element {self.kind_name} is not matched with the pseudo {self.pseudo.element}</div>"""
                 self._reset()
             else:
                 self.pseudo_text.value = filename

tests/test_pseudo.py

@@ -228,15 +228,15 @@ def test_pseudo_upload_widget(generate_upf_data):
     # the widget initialize with the pseudo as input to mock how it will
     # be used in PseudoSetter when the pseudo family is set.
     old_pseudo = generate_upf_data("O", "O_old.upf")
-    w = PseudoUploadWidget(element="O1")
+    w = PseudoUploadWidget(kind_name="O1")
     w.pseudo = old_pseudo
     w.cutoffs = [30, 240]
     w.render()
 
     message = "Recommended ecutwfc: <b>{ecutwfc} Ry</b> ecutrho: <b>{ecutrho} Ry</b>"
 
     assert w.pseudo.filename == "O_old.upf"
-    assert w.element == "O1"
+    assert w.kind_name == "O1"
     assert message.format(ecutwfc=30.0, ecutrho=240.0) in w.cutoff_message.value
     assert w.error_message is None
 
@@ -253,7 +253,7 @@ def test_pseudo_upload_widget(generate_upf_data):
     )
 
     assert w.pseudo.filename == "O_new.upf"
-    assert w.element == "O1"
+    assert w.kind_name == "O1"
     assert w.error_message is None
 
     # test upload a invalid pseudo of other element