diff --git a/src/aiidalab_qe/app/configuration/__init__.py b/src/aiidalab_qe/app/configuration/__init__.py
index 456e3f388..70b6084c0 100644
--- a/src/aiidalab_qe/app/configuration/__init__.py
+++ b/src/aiidalab_qe/app/configuration/__init__.py
@@ -56,10 +56,10 @@ def __init__(self, model: ConfigurationModel, **kwargs):
 
         self.settings: dict[str, SettingsPanel] = {}
 
-        workchain_model = WorkChainModel(include=True)
+        workchain_model = WorkChainModel()
         self._model.add_model("workchain", workchain_model)
 
-        advanced_model = AdvancedModel(include=True)
+        advanced_model = AdvancedModel()
         self._model.add_model("advanced", advanced_model)
 
         self._fetch_plugin_settings()
diff --git a/src/aiidalab_qe/app/configuration/advanced/advanced.py b/src/aiidalab_qe/app/configuration/advanced/advanced.py
index 39503639d..327a72bf4 100644
--- a/src/aiidalab_qe/app/configuration/advanced/advanced.py
+++ b/src/aiidalab_qe/app/configuration/advanced/advanced.py
@@ -341,7 +341,7 @@ def _on_input_structure_change(self, _):
     def _on_protocol_change(self, _):
         self.refresh(specific="protocol")
 
-    def _on_kpoints_distance_change(self, _=None):
+    def _on_kpoints_distance_change(self, _):
         self.refresh(specific="mesh")
 
     def _on_override_change(self, change):
diff --git a/src/aiidalab_qe/app/configuration/advanced/hubbard/model.py b/src/aiidalab_qe/app/configuration/advanced/hubbard/model.py
index 51739314e..de5ffd66c 100644
--- a/src/aiidalab_qe/app/configuration/advanced/hubbard/model.py
+++ b/src/aiidalab_qe/app/configuration/advanced/hubbard/model.py
@@ -49,8 +49,19 @@ def __init__(self, *args, **kwargs):
         }
 
     def update(self, specific=""):
+        if self.input_structure is None:
+            self.applicable_kinds = []
+            self.orbital_labels = []
+            self._defaults |= {
+                "parameters": {},
+                "eigenvalues": [],
+            }
+        else:
+            self.orbital_labels = self._define_orbital_labels()
+            self._defaults["parameters"] = self._define_default_parameters()
+            self.applicable_kinds = self._define_applicable_kinds()
+            self._defaults["eigenvalues"] = self._define_default_eigenvalues()
         with self.hold_trait_notifications():
-            self._update_defaults(specific)
             self.parameters = self._get_default_parameters()
             self.eigenvalues = self._get_default_eigenvalues()
             self.needs_eigenvalues_widget = len(self.applicable_kinds) > 0
@@ -82,20 +93,6 @@ def reset(self):
             self.parameters = self._get_default_parameters()
             self.eigenvalues = self._get_default_eigenvalues()
 
-    def _update_defaults(self, specific=""):
-        if self.input_structure is None:
-            self.applicable_kinds = []
-            self.orbital_labels = []
-            self._defaults |= {
-                "parameters": {},
-                "eigenvalues": [],
-            }
-        else:
-            self.orbital_labels = self._define_orbital_labels()
-            self._defaults["parameters"] = self._define_default_parameters()
-            self.applicable_kinds = self._define_applicable_kinds()
-            self._defaults["eigenvalues"] = self._define_default_eigenvalues()
-
     def _define_orbital_labels(self):
         hubbard_manifold_list = [
             self._get_manifold(Element(kind.symbol))
diff --git a/src/aiidalab_qe/app/configuration/advanced/magnetization/model.py b/src/aiidalab_qe/app/configuration/advanced/magnetization/model.py
index f031fd3f8..1b29fef4e 100644
--- a/src/aiidalab_qe/app/configuration/advanced/magnetization/model.py
+++ b/src/aiidalab_qe/app/configuration/advanced/magnetization/model.py
@@ -35,8 +35,13 @@ def __init__(self, *args, **kwargs):
         }
 
     def update(self, specific=""):
+        if self.spin_type == "none" or self.input_structure is None:
+            self._defaults["moments"] = {}
+        else:
+            self._defaults["moments"] = {
+                symbol: 0.0 for symbol in self.input_structure.get_kind_names()
+            }
         with self.hold_trait_notifications():
-            self._update_defaults(specific)
             self.moments = self._get_default_moments()
 
     def reset(self):
@@ -45,13 +50,5 @@ def reset(self):
             self.total = self.traits()["total"].default_value
             self.moments = self._get_default_moments()
 
-    def _update_defaults(self, specific=""):
-        if self.spin_type == "none" or self.input_structure is None:
-            self._defaults["moments"] = {}
-        else:
-            self._defaults["moments"] = {
-                symbol: 0.0 for symbol in self.input_structure.get_kind_names()
-            }
-
     def _get_default_moments(self):
         return deepcopy(self._defaults["moments"])
diff --git a/src/aiidalab_qe/app/configuration/advanced/model.py b/src/aiidalab_qe/app/configuration/advanced/model.py
index 25d4bd23f..246a74f2e 100644
--- a/src/aiidalab_qe/app/configuration/advanced/model.py
+++ b/src/aiidalab_qe/app/configuration/advanced/model.py
@@ -60,8 +60,10 @@ class AdvancedModel(SettingsModel):
     kpoints_distance = tl.Float(0.0)
     mesh_grid = tl.Unicode("")
 
-    def __init__(self, include=False, *args, **kwargs):
-        super().__init__(include, *args, **kwargs)
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        self.include = True
 
         self.dftd3_version = {
             "dft-d3": 3,
@@ -84,19 +86,21 @@ def __init__(self, include=False, *args, **kwargs):
 
     def update(self, specific=""):
         with self.hold_trait_notifications():
-            self._update_defaults(specific)
-            self.forc_conv_thr = self._defaults["forc_conv_thr"]
-            self.forc_conv_thr_step = self._defaults["forc_conv_thr_step"]
-            self.etot_conv_thr = self._defaults["etot_conv_thr"]
-            self.etot_conv_thr_step = self._defaults["etot_conv_thr_step"]
-            self.scf_conv_thr = self._defaults["scf_conv_thr"]
-            self.scf_conv_thr_step = self._defaults["scf_conv_thr_step"]
-            self.kpoints_distance = self._defaults["kpoints_distance"]
+            if not specific or specific != "mesh":
+                parameters = PwBaseWorkChain.get_protocol_inputs(self.protocol)
+                self._update_kpoints_distance(parameters)
+                self._update_thresholds(parameters)
+            self._update_kpoints_mesh()
 
     def add_model(self, identifier, model):
         self._models[identifier] = model
         self._link_model(model)
 
+    def get_model(self, identifier) -> AdvancedSubModel:
+        if identifier in self._models:
+            return self._models[identifier]
+        raise ValueError(f"Model with identifier '{identifier}' not found.")
+
     def get_models(self):
         return self._models.items()
 
@@ -122,7 +126,7 @@ def get_model_state(self):
             "kpoints_distance": self.kpoints_distance,
         }
 
-        hubbard: HubbardModel = self._get_model("hubbard")  # type: ignore
+        hubbard: HubbardModel = self.get_model("hubbard")  # type: ignore
         if hubbard.is_active:
             parameters["hubbard_parameters"] = {"hubbard_u": hubbard.parameters}
             if hubbard.has_eigenvalues:
@@ -130,7 +134,7 @@ def get_model_state(self):
                     "starting_ns_eigenvalue": hubbard.get_active_eigenvalues()
                 }
 
-        pseudos: PseudosModel = self._get_model("pseudos")  # type: ignore
+        pseudos: PseudosModel = self.get_model("pseudos")  # type: ignore
         parameters["pseudo_family"] = pseudos.family
         if pseudos.dictionary:
             parameters["pw"]["pseudos"] = pseudos.dictionary
@@ -145,8 +149,8 @@ def get_model_state(self):
                 self.dftd3_version[self.van_der_waals]
             )
 
-        smearing: SmearingModel = self._get_model("smearing")  # type: ignore
-        magnetization: MagnetizationModel = self._get_model("magnetization")  # type: ignore
+        smearing: SmearingModel = self.get_model("smearing")  # type: ignore
+        magnetization: MagnetizationModel = self.get_model("magnetization")  # type: ignore
         if self.spin_type == "collinear":
             parameters["initial_magnetic_moments"] = magnetization.moments
         if self.electronic_type == "metal":
@@ -181,7 +185,7 @@ def get_model_state(self):
         return parameters
 
     def set_model_state(self, parameters):
-        pseudos: PseudosModel = self._get_model("pseudos")  # type: ignore
+        pseudos: PseudosModel = self.get_model("pseudos")  # type: ignore
         if "pseudo_family" in parameters:
             pseudo_family = PseudoFamily.from_string(parameters["pseudo_family"])
             library = pseudo_family.library
@@ -199,7 +203,7 @@ def set_model_state(self, parameters):
         if (pw_parameters := parameters.get("pw", {}).get("parameters")) is not None:
             self._set_pw_parameters(pw_parameters)
 
-        magnetization: MagnetizationModel = self._get_model("magnetization")  # type: ignore
+        magnetization: MagnetizationModel = self.get_model("magnetization")  # type: ignore
         if magnetic_moments := parameters.get("initial_magnetic_moments"):
             if isinstance(magnetic_moments, (int, float)):
                 magnetic_moments = [magnetic_moments]
@@ -212,7 +216,7 @@ def set_model_state(self, parameters):
                 )
             magnetization.moments = magnetic_moments
 
-        hubbard: HubbardModel = self._get_model("hubbard")  # type: ignore
+        hubbard: HubbardModel = self.get_model("hubbard")  # type: ignore
         if parameters.get("hubbard_parameters"):
             hubbard.is_active = True
             hubbard.parameters = parameters["hubbard_parameters"]["hubbard_u"]
@@ -256,16 +260,6 @@ def _link_model(self, model):
                 (model, trait),
             )
 
-    def _update_defaults(self, specific=""):
-        if not specific or specific != "mesh":
-            parameters = PwBaseWorkChain.get_protocol_inputs(self.protocol)
-            self._update_kpoints_distance(parameters)
-
-        self._update_kpoints_mesh()
-
-        if not specific or specific == "protocol":
-            self._update_thresholds(parameters)
-
     def _update_kpoints_mesh(self, _=None):
         if self.input_structure is None:
             mesh_grid = ""
@@ -284,18 +278,25 @@ def _update_kpoints_mesh(self, _=None):
     def _update_kpoints_distance(self, parameters):
         kpoints_distance = parameters["kpoints_distance"] if self.has_pbc else 100.0
         self._defaults["kpoints_distance"] = kpoints_distance
+        self.kpoints_distance = self._defaults["kpoints_distance"]
 
     def _update_thresholds(self, parameters):
         num_atoms = len(self.input_structure.sites) if self.input_structure else 1
 
         etot_value = num_atoms * parameters["meta_parameters"]["etot_conv_thr_per_atom"]
         self._set_value_and_step("etot_conv_thr", etot_value)
+        self.etot_conv_thr = self._defaults["etot_conv_thr"]
+        self.etot_conv_thr_step = self._defaults["etot_conv_thr_step"]
 
         scf_value = num_atoms * parameters["meta_parameters"]["conv_thr_per_atom"]
         self._set_value_and_step("scf_conv_thr", scf_value)
+        self.scf_conv_thr = self._defaults["scf_conv_thr"]
+        self.scf_conv_thr_step = self._defaults["scf_conv_thr_step"]
 
         forc_value = parameters["pw"]["parameters"]["CONTROL"]["forc_conv_thr"]
         self._set_value_and_step("forc_conv_thr", forc_value)
+        self.forc_conv_thr = self._defaults["forc_conv_thr"]
+        self.forc_conv_thr_step = self._defaults["forc_conv_thr_step"]
 
     def _set_value_and_step(self, attribute, value):
         self._defaults[attribute] = value
@@ -324,18 +325,13 @@ def _set_pw_parameters(self, pw_parameters):
             system_params.get("vdw_corr", "none"),
         )
 
-        smearing: SmearingModel = self._get_model("smearing")  # type: ignore
+        smearing: SmearingModel = self.get_model("smearing")  # type: ignore
         if "degauss" in system_params:
             smearing.degauss = system_params["degauss"]
 
         if "smearing" in system_params:
             smearing.type = system_params["smearing"]
 
-        magnetization: MagnetizationModel = self._get_model("magnetization")  # type: ignore
+        magnetization: MagnetizationModel = self.get_model("magnetization")  # type: ignore
         if "tot_magnetization" in system_params:
             magnetization.type = "tot_magnetization"
-
-    def _get_model(self, identifier) -> AdvancedSubModel:
-        if identifier in self._models:
-            return self._models[identifier]
-        raise ValueError(f"Model with identifier '{identifier}' not found.")
diff --git a/src/aiidalab_qe/app/configuration/advanced/pseudos/model.py b/src/aiidalab_qe/app/configuration/advanced/pseudos/model.py
index 03c5068dd..7da4d3fb3 100644
--- a/src/aiidalab_qe/app/configuration/advanced/pseudos/model.py
+++ b/src/aiidalab_qe/app/configuration/advanced/pseudos/model.py
@@ -129,7 +129,16 @@ def __init__(self, *args, **kwargs):
 
     def update(self, specific=""):
         with self.hold_trait_notifications():
-            self._update_defaults(specific)
+            if self.input_structure is None:
+                self._defaults |= {
+                    "dictionary": {},
+                    "cutoffs": [[0.0], [0.0]],
+                }
+            else:
+                self.update_default_pseudos()
+                self.update_default_cutoffs()
+            self.update_family_parameters()
+            self.update_family()
 
     def update_default_pseudos(self):
         try:
@@ -262,18 +271,6 @@ def reset(self):
             self.family_help_message = self.PSEUDO_HELP_WO_SOC
             self.status_message = ""
 
-    def _update_defaults(self, specific=""):
-        if self.input_structure is None:
-            self._defaults |= {
-                "dictionary": {},
-                "cutoffs": [[0.0], [0.0]],
-            }
-        else:
-            self.update_default_pseudos()
-            self.update_default_cutoffs()
-        self.update_family_parameters()
-        self.update_family()
-
     def _get_pseudo_family_from_database(self):
         """Get the pseudo family from the database."""
         return (
diff --git a/src/aiidalab_qe/app/configuration/advanced/smearing/model.py b/src/aiidalab_qe/app/configuration/advanced/smearing/model.py
index 5dd94b0cf..6d626f988 100644
--- a/src/aiidalab_qe/app/configuration/advanced/smearing/model.py
+++ b/src/aiidalab_qe/app/configuration/advanced/smearing/model.py
@@ -27,17 +27,6 @@ def __init__(self, *args, **kwargs):
         }
 
     def update(self, specific=""):
-        with self.hold_trait_notifications():
-            self._update_defaults(specific)
-            self.type = self._defaults["type"]
-            self.degauss = self._defaults["degauss"]
-
-    def reset(self):
-        with self.hold_trait_notifications():
-            self.type = self._defaults["type"]
-            self.degauss = self._defaults["degauss"]
-
-    def _update_defaults(self, specific=""):
         parameters = (
             PwBaseWorkChain.get_protocol_inputs(self.protocol)
             .get("pw", {})
@@ -48,3 +37,11 @@ def _update_defaults(self, specific=""):
             "type": parameters["smearing"],
             "degauss": parameters["degauss"],
         }
+        with self.hold_trait_notifications():
+            self.type = self._defaults["type"]
+            self.degauss = self._defaults["degauss"]
+
+    def reset(self):
+        with self.hold_trait_notifications():
+            self.type = self._defaults["type"]
+            self.degauss = self._defaults["degauss"]
diff --git a/src/aiidalab_qe/app/configuration/advanced/subsettings.py b/src/aiidalab_qe/app/configuration/advanced/subsettings.py
index f0e4c69e6..b7105fd54 100644
--- a/src/aiidalab_qe/app/configuration/advanced/subsettings.py
+++ b/src/aiidalab_qe/app/configuration/advanced/subsettings.py
@@ -1,3 +1,5 @@
+import os
+
 import ipywidgets as ipw
 import traitlets as tl
 
@@ -21,16 +23,6 @@ def reset(self):
         """Resets the model to present defaults."""
         raise NotImplementedError
 
-    def _update_defaults(self, specific=""):
-        """Updates the model's default values.
-
-        Parameters
-        ----------
-        `specific` : `str`, optional
-            If provided, specifies the level of update.
-        """
-        raise NotImplementedError
-
 
 class AdvancedSubSettings(ipw.VBox):
     identifier = "sub"
@@ -74,6 +66,9 @@ def refresh(self, specific=""):
         self.updated = False
         self._unsubscribe()
         self._update(specific)
+        if "PYTEST_CURRENT_TEST" in os.environ:
+            # Skip resetting to avoid having to inject a structure when testing
+            return
         if hasattr(self._model, "input_structure") and not self._model.input_structure:
             self._reset()
 
diff --git a/src/aiidalab_qe/app/configuration/basic/model.py b/src/aiidalab_qe/app/configuration/basic/model.py
index 3e733c0f8..a40f4e932 100644
--- a/src/aiidalab_qe/app/configuration/basic/model.py
+++ b/src/aiidalab_qe/app/configuration/basic/model.py
@@ -18,8 +18,10 @@ class WorkChainModel(SettingsModel):
     spin_type = tl.Unicode(DEFAULT["workchain"]["spin_type"])
     electronic_type = tl.Unicode(DEFAULT["workchain"]["electronic_type"])
 
-    def __init__(self, include=False, *args, **kwargs):
-        super().__init__(include, *args, **kwargs)
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        self.include = True
 
         self._defaults = {
             "protocol": self.traits()["protocol"].default_value,
diff --git a/src/aiidalab_qe/app/configuration/model.py b/src/aiidalab_qe/app/configuration/model.py
index 270ba96b7..83b0862be 100644
--- a/src/aiidalab_qe/app/configuration/model.py
+++ b/src/aiidalab_qe/app/configuration/model.py
@@ -51,23 +51,53 @@ def __init__(self, *args, **kwargs):
         """
 
     def update(self):
-        self._update_defaults()
-        self.relax_type_help = self._get_default_relax_type_help()
-        self.relax_type_options = self._get_default_relax_type_options()
-        self.relax_type = self._get_default_relax_type()
+        if self.has_pbc:
+            relax_type_help = self.relax_type_help_template.format(
+                option_count="three",
+                full_relaxation_option=(
+                    """
+                    <br>
+                    (3) Full geometry: perform a full relaxation of the internal atomic
+                    coordinates and the cell parameters.
+                    """
+                ),
+            )
+            relax_type_options = [
+                ("Structure as is", "none"),
+                ("Atomic positions", "positions"),
+                ("Full geometry", "positions_cell"),
+            ]
+        else:
+            relax_type_help = self.relax_type_help_template.format(
+                option_count="two",
+                full_relaxation_option="",
+            )
+            relax_type_options = [
+                ("Structure as is", "none"),
+                ("Atomic positions", "positions"),
+            ]
+        self._defaults = {
+            "relax_type_help": relax_type_help,
+            "relax_type_options": relax_type_options,
+            "relax_type": relax_type_options[-1][-1],
+        }
+        with self.hold_trait_notifications():
+            self.relax_type_help = self._get_default_relax_type_help()
+            self.relax_type_options = self._get_default_relax_type_options()
+            self.relax_type = self._get_default_relax_type()
 
     def add_model(self, identifier, model):
         self._models[identifier] = model
         self._link_model(model)
 
-    def get_models(self):
-        return self._models.items()
-
     def get_model(self, identifier) -> SettingsModel:
         if identifier in self._models:
             return self._models[identifier]
         raise ValueError(f"Model with identifier '{identifier}' not found.")
 
+    def get_models(self):
+        return self._models.items()
+
     def get_model_state(self):
         parameters = {
             identifier: model.get_model_state()
@@ -86,9 +116,9 @@ def set_model_state(self, parameters):
             self.relax_type = workchain_parameters.get("relax_type")
             properties = set(workchain_parameters.get("properties", []))
             for identifier, model in self._models.items():
+                model.include = identifier in self._default_models | properties
                 if parameters.get(identifier):
                     model.set_model_state(parameters[identifier])
-                model.include = identifier in self._default_models | properties
 
     def reset(self):
         self.confirmed = False
@@ -134,38 +164,6 @@ def _get_properties(self):
             properties.append("relax")
         return properties
 
-    def _update_defaults(self):
-        if self.has_pbc:
-            relax_type_help = self.relax_type_help_template.format(
-                option_count="three",
-                full_relaxation_option=(
-                    """
-                    <br>
-                    (3) Full geometry: perform a full relaxation of the internal atomic
-                    coordinates and the cell parameters.
-                    """
-                ),
-            )
-            relax_type_options = [
-                ("Structure as is", "none"),
-                ("Atomic positions", "positions"),
-                ("Full geometry", "positions_cell"),
-            ]
-        else:
-            relax_type_help = self.relax_type_help_template.format(
-                option_count="two",
-                full_relaxation_option="",
-            )
-            relax_type_options = [
-                ("Structure as is", "none"),
-                ("Atomic positions", "positions"),
-            ]
-        self._defaults = {
-            "relax_type_help": relax_type_help,
-            "relax_type_options": relax_type_options,
-            "relax_type": relax_type_options[-1][-1],
-        }
-
     def _get_default_relax_type_help(self):
         return self._defaults.get("relax_type_help", "")
 
diff --git a/src/aiidalab_qe/common/panel.py b/src/aiidalab_qe/common/panel.py
index 3bd7f81b6..878a51db6 100644
--- a/src/aiidalab_qe/common/panel.py
+++ b/src/aiidalab_qe/common/panel.py
@@ -75,10 +75,9 @@ class SettingsModel(tl.HasTraits):
 
     _defaults = {}
 
-    def __init__(self, include=False, *args, **kwargs):
+    def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.observe(self.unconfirm, tl.All)
-        self.include = include
 
     @property
     def has_pbc(self):
@@ -112,16 +111,6 @@ def unconfirm(self, change):
         if change["name"] != "confirmed":
             self.confirmed = False
 
-    def _update_defaults(self, specific=""):
-        """Updates the model's default values.
-
-        Parameters
-        ----------
-        `specific` : `str`, optional
-            If provided, specifies the level of update.
-        """
-        raise NotImplementedError
-
 
 class SettingsPanel(Panel):
     title = "Settings"
@@ -161,9 +150,8 @@ def refresh(self, specific=""):
         """
         self.updated = False
         self._unsubscribe()
-        if not self._model.include:
-            return
-        self.update(specific)
+        if self._model.include:
+            self.update(specific)
         if "PYTEST_CURRENT_TEST" in os.environ:
             # Skip resetting to avoid having to inject a structure when testing
             return
diff --git a/src/aiidalab_qe/common/widgets.py b/src/aiidalab_qe/common/widgets.py
index 42ee7cfe0..a27152cf3 100644
--- a/src/aiidalab_qe/common/widgets.py
+++ b/src/aiidalab_qe/common/widgets.py
@@ -957,7 +957,6 @@ def __init__(self, title=None, **kwargs):
     def render(self):
         if self.rendered:
             return
-        from aiidalab_qe.common.widgets import LoadingWidget
 
         self.children = [LoadingWidget(f"Loading {self.title} widget")]
 
diff --git a/src/aiidalab_qe/plugins/pdos/model.py b/src/aiidalab_qe/plugins/pdos/model.py
index deb7e541f..8c664acae 100644
--- a/src/aiidalab_qe/plugins/pdos/model.py
+++ b/src/aiidalab_qe/plugins/pdos/model.py
@@ -22,8 +22,8 @@ class PdosModel(SettingsModel):
     use_pdos_degauss = tl.Bool(False)
     pdos_degauss = tl.Float(0.005)
 
-    def __init__(self, include=False, *args, **kwargs):
-        super().__init__(include, *args, **kwargs)
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
 
         self._defaults = {
             "kpoints_distance": self.traits()["kpoints_distance"].default_value,
@@ -31,8 +31,11 @@ def __init__(self, include=False, *args, **kwargs):
 
     def update(self, specific=""):
         with self.hold_trait_notifications():
-            self._update_defaults(specific)
-            self.kpoints_distance = self._defaults["kpoints_distance"]
+            if not specific or specific != "mesh":
+                parameters = PdosWorkChain.get_protocol_inputs(self.protocol)
+                self._update_kpoints_distance(parameters)
+
+            self._update_kpoints_mesh()
 
     def get_model_state(self):
         return {
@@ -55,13 +58,6 @@ def reset(self):
             self.use_pdos_degauss = self.traits()["use_pdos_degauss"].default_value
             self.pdos_degauss = self.traits()["pdos_degauss"].default_value
 
-    def _update_defaults(self, specific=""):
-        if not specific or specific != "mesh":
-            parameters = PdosWorkChain.get_protocol_inputs(self.protocol)
-            self._update_kpoints_distance(parameters)
-
-        self._update_kpoints_mesh()
-
     def _update_kpoints_mesh(self, _=None):
         if self.input_structure is None:
             mesh_grid = ""
@@ -84,3 +80,4 @@ def _update_kpoints_distance(self, parameters):
             kpoints_distance = 100.0
             self.use_pdos_degauss = True
         self._defaults["kpoints_distance"] = kpoints_distance
+        self.kpoints_distance = self._defaults["kpoints_distance"]
diff --git a/src/aiidalab_qe/plugins/xas/model.py b/src/aiidalab_qe/plugins/xas/model.py
index 67c919a5a..a8b70f929 100644
--- a/src/aiidalab_qe/plugins/xas/model.py
+++ b/src/aiidalab_qe/plugins/xas/model.py
@@ -60,8 +60,9 @@ def __init__(self, *args, **kwargs):
         self.installed_pseudos = False
 
     def update(self, specific=""):
-        self._update_pseudos()
-        self._update_core_hole_treatment_recommendations()
+        with self.hold_trait_notifications():
+            self._update_pseudos()
+            self._update_core_hole_treatment_recommendations()
 
     def get_model_state(self):
         pseudo_labels = {}
diff --git a/src/aiidalab_qe/plugins/xps/model.py b/src/aiidalab_qe/plugins/xps/model.py
index 4498bc1c7..4911be55a 100644
--- a/src/aiidalab_qe/plugins/xps/model.py
+++ b/src/aiidalab_qe/plugins/xps/model.py
@@ -34,9 +34,10 @@ class XpsModel(SettingsModel):
     )
 
     def update(self, specific=""):
-        self._update_correction_energies()
-        if not specific or specific == "pseudo_group":
-            self._update_pseudos()
+        with self.hold_trait_notifications():
+            self._update_correction_energies()
+            if not specific or specific == "pseudo_group":
+                self._update_pseudos()
 
     def get_supported_core_levels(self):
         supported_core_levels = {}
@@ -67,7 +68,6 @@ def set_model_state(self, parameters: dict):
             self.traits()["structure_type"].default_value,
         )
 
-        # TODO check logic
         core_level_list = parameters.get("core_level_list", [])
         for orbital in self.core_levels:
             if orbital in core_level_list:
diff --git a/tests/configuration/test_advanced.py b/tests/configuration/test_advanced.py
index 4a9a1f43b..79a69342d 100644
--- a/tests/configuration/test_advanced.py
+++ b/tests/configuration/test_advanced.py
@@ -7,27 +7,31 @@ def test_advanced_default():
     """Test default behavior of advanced setting."""
     model = AdvancedModel()
     _ = AdvancedSettings(model=model)
+    smearing = model.get_model("smearing")
 
     # Test override functionality in advanced settings
     model.override = True
     model.protocol = "fast"
-    model.smearing.type = "methfessel-paxton"
-    model.smearing.degauss = 0.03
+    smearing.type = "methfessel-paxton"
+    smearing.degauss = 0.03
     model.kpoints_distance = 0.22
 
     # Reset values to default w.r.t protocol
     model.override = False
 
-    assert model.smearing.type == "cold"
-    assert model.smearing.degauss == 0.01
+    assert smearing.type == "cold"
+    assert smearing.degauss == 0.01
     assert model.kpoints_distance == 0.5
 
 
 def test_advanced_smearing_settings():
     """Test Smearing Settings."""
-    from aiidalab_qe.app.configuration.advanced.smearing import SmearingSettings
+    from aiidalab_qe.app.configuration.advanced.smearing import (
+        SmearingModel,
+        SmearingSettings,
+    )
 
-    model = AdvancedModel()
+    model = SmearingModel()
     smearing = SmearingSettings(model=model)
     smearing.render()
 
@@ -40,23 +44,22 @@ def test_advanced_smearing_settings():
     assert smearing.degauss.disabled is False
     assert smearing.smearing.disabled is False
 
-    assert model.smearing.type == "cold"
-    assert model.smearing.degauss == 0.01
+    assert model.type == "cold"
+    assert model.degauss == 0.01
 
     # Test protocol-dependent smearing change
     model.protocol = "fast"
 
-    assert model.smearing.type == "cold"
-    assert model.smearing.degauss == 0.01
+    assert model.type == "cold"
+    assert model.degauss == 0.01
 
     # Check reset
-    model.smearing.type = "gaussian"
-    model.smearing.degauss = 0.05
-    model.smearing.reset()
+    model.type = "gaussian"
+    model.degauss = 0.05
+    model.override = False
 
-    assert model.protocol == "fast"  # reset does not apply to protocol
-    assert model.smearing.type == "cold"
-    assert model.smearing.degauss == 0.01
+    assert model.type == "cold"
+    assert model.degauss == 0.01
 
 
 def test_advanced_kpoints_settings():
@@ -156,9 +159,12 @@ def test_advanced_kpoints_mesh(generate_structure_data):
 @pytest.mark.usefixtures("aiida_profile_clean", "sssp")
 def test_advanced_hubbard_settings(generate_structure_data):
     """Test Hubbard widget."""
-    from aiidalab_qe.app.configuration.advanced.hubbard import HubbardSettings
+    from aiidalab_qe.app.configuration.advanced.hubbard import (
+        HubbardModel,
+        HubbardSettings,
+    )
 
-    model = AdvancedModel()
+    model = HubbardModel()
     hubbard = HubbardSettings(model=model)
     hubbard.render()
 
@@ -166,8 +172,8 @@ def test_advanced_hubbard_settings(generate_structure_data):
     model.input_structure = structure
 
     # Activate Hubbard U widget
-    model.hubbard.is_active = True
-    assert model.hubbard.orbital_labels == ["Co - 3d", "O - 2p", "Li - 2s"]
+    model.is_active = True
+    assert model.orbital_labels == ["Co - 3d", "O - 2p", "Li - 2s"]
 
     # Change the Hubbard U parameters for Co, O, and Li
     hubbard_parameters = hubbard.hubbard_widget.children[1:]  # type: ignore
@@ -175,7 +181,7 @@ def test_advanced_hubbard_settings(generate_structure_data):
     hubbard_parameters[1].value = 2  # O - 2p
     hubbard_parameters[2].value = 3  # Li - 2s
 
-    assert model.hubbard.parameters == {
+    assert model.parameters == {
         "Co - 3d": 1.0,
         "O - 2p": 2.0,
         "Li - 2s": 3.0,
@@ -191,9 +197,9 @@ def test_advanced_hubbard_settings(generate_structure_data):
     # assert model.hubbard.eigenvalues == []  # TODO should they be?
 
     # Check there is only eigenvalues for Co (Transition metal)
-    model.hubbard.has_eigenvalues = True
-    assert len(model.hubbard.applicable_kinds) == 1
-    assert len(model.hubbard.eigenvalues) == 1
+    model.has_eigenvalues = True
+    assert len(model.applicable_kinds) == 1
+    assert len(model.eigenvalues) == 1
 
     Co_eigenvalues = hubbard.eigenvalues_widget.children[0].children[1]  # type: ignore
     Co_spin_down_row = Co_eigenvalues.children[1]
@@ -201,7 +207,7 @@ def test_advanced_hubbard_settings(generate_structure_data):
     Co_spin_down_row.children[3].value = "1"
     Co_spin_down_row.children[5].value = "1"
 
-    assert model.hubbard.get_active_eigenvalues() == [
+    assert model.get_active_eigenvalues() == [
         [1, 1, "Co", 1],
         [3, 1, "Co", 1],
         [5, 1, "Co", 1],
diff --git a/tests/conftest.py b/tests/conftest.py
index 4596af2a5..72fc2d854 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -461,15 +461,16 @@ def _submit_app_generator(
         advanced_model.electron_maxstep = electron_maxstep
         if isinstance(initial_magnetic_moments, (int, float)):
             initial_magnetic_moments = [initial_magnetic_moments]
-        advanced_model.magnetization.moments = dict(
+        advanced_model.get_model("magnetization").moments = dict(
             zip(
                 app.configure_model.input_structure.get_kind_names(),
                 initial_magnetic_moments,
             )
         )
         # mimic the behavior of the smearing widget set up
-        advanced_model.smearing.type = smearing
-        advanced_model.smearing.degauss = degauss
+        smearing_model = advanced_model.get_model("smearing")
+        smearing_model.type = smearing
+        smearing_model.degauss = degauss
         app.configure_step.confirm()
 
         app.submit_model.input_structure = generate_structure_data()
@@ -739,7 +740,9 @@ def _generate_qeapp_workchain(
             from_example.children[0].value = from_example.children[0].options[1][1]
         else:
             structure.store()
-            aiida_database = app.structure_step.manager.children[0].children[2]  # type: ignore
+            aiida_database_wrapper = app.structure_step.manager.children[0].children[2]  # type: ignore
+            aiida_database_wrapper.render()
+            aiida_database = aiida_database_wrapper.children[0]  # type: ignore
             aiida_database.search()
             aiida_database.results.value = structure
 
@@ -764,20 +767,20 @@ def _generate_qeapp_workchain(
 
         if spin_type == "collinear":
             advanced_model.override = True
-            magnetization = advanced_model.magnetization
+            magnetization_model = advanced_model.get_model("magnetization")
             if electronic_type == "insulator":
-                magnetization.total = tot_magnetization
+                magnetization_model.total = tot_magnetization
             elif magnetization_type == "starting_magnetization":
                 if isinstance(initial_magnetic_moments, (int, float)):
                     initial_magnetic_moments = [initial_magnetic_moments]
-                magnetization.moments = dict(
+                magnetization_model.moments = dict(
                     zip(
                         structure.get_kind_names(),
                         initial_magnetic_moments,
                     )
                 )
             else:
-                magnetization.total = tot_magnetization
+                magnetization_model.total = tot_magnetization
 
         app.configure_step.confirm()
 
diff --git a/tests/test_app.py b/tests/test_app.py
index 996455826..6c1681733 100644
--- a/tests/test_app.py
+++ b/tests/test_app.py
@@ -19,7 +19,8 @@ def test_reload_and_reset(generate_qeapp_workchain):
     assert app.configure_model.get_model("workchain").spin_type == "collinear"
     assert app.configure_model.get_model("bands").include is True
     assert app.configure_model.get_model("pdos").include is False
-    assert len(app.configure_model.get_model("advanced").pseudos.dictionary) > 0
+    advanced_model = app.configure_model.get_model("advanced")
+    assert len(advanced_model.get_model("pseudos").dictionary) > 0
     assert app.configure_step.state == app.configure_step.State.SUCCESS
 
 
diff --git a/tests/test_configure.py b/tests/test_configure.py
index 509a039cd..716709537 100644
--- a/tests/test_configure.py
+++ b/tests/test_configure.py
@@ -71,6 +71,6 @@ def test_reminder_info():
     assert bands_info.value == ""
     bands_model = model.get_model("bands")
     bands_model.include = True
-    assert bands_info.value == "Customize bands settings in <b>step 2.2</b> if needed"
+    assert bands_info.value == "Customize bands settings in <b>Step 2.2</b> if needed"
     bands_model.include = False
     assert bands_info.value == ""
diff --git a/tests/test_pseudo.py b/tests/test_pseudo.py
index 3c193c6f1..df3e9ffc4 100644
--- a/tests/test_pseudo.py
+++ b/tests/test_pseudo.py
@@ -142,54 +142,53 @@ def test_download_and_install_pseudo_from_file(tmp_path):
 
 @pytest.mark.usefixtures("aiida_profile_clean", "sssp", "pseudodojo")
 def test_pseudos_settings(generate_structure_data, generate_upf_data):
-    from aiidalab_qe.app.configuration.advanced import AdvancedModel
-    from aiidalab_qe.app.configuration.advanced.pseudos import PseudoSettings
+    from aiidalab_qe.app.configuration.advanced.pseudos import (
+        PseudoSettings,
+        PseudosModel,
+    )
 
-    model = AdvancedModel()
+    model = PseudosModel()
     pseudos = PseudoSettings(model=model)
 
-    assert model.pseudos.override is False
+    assert model.override is False
 
     # Test the default family
     model.override = True
     model.spin_orbit = "wo_soc"
-    assert model.pseudos.family == f"SSSP/{SSSP_VERSION}/PBEsol/efficiency"
+    assert model.family == f"SSSP/{SSSP_VERSION}/PBEsol/efficiency"
 
     # Test protocol-dependent family change
     model.protocol = "precise"
-    assert model.pseudos.family == f"SSSP/{SSSP_VERSION}/PBEsol/precision"
+    assert model.family == f"SSSP/{SSSP_VERSION}/PBEsol/precision"
 
     # Test functional-dependent family change
-    model.pseudos.functional = "PBE"
-    assert model.pseudos.family == f"SSSP/{SSSP_VERSION}/PBE/precision"
+    model.functional = "PBE"
+    assert model.family == f"SSSP/{SSSP_VERSION}/PBE/precision"
 
     # Test library-dependent family change
-    model.pseudos.library = "PseudoDojo stringent"
-    assert (
-        model.pseudos.family == f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/SR/stringent/upf"
-    )
+    model.library = "PseudoDojo stringent"
+    assert model.family == f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/SR/stringent/upf"
 
     # Test spin-orbit-dependent family change
     model.spin_orbit = "soc"
     model.protocol = "moderate"
-    assert (
-        model.pseudos.family == f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/FR/standard/upf"
-    )
+    assert model.family == f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/FR/standard/upf"
 
-    # Test structure-dependent family change
-    model.reset()
+    # Reset the external dependencies of the model
+    model.spin_orbit = "wo_soc"
 
+    # Test structure-dependent family change
     silicon = generate_structure_data("silicon")
     model.input_structure = silicon
-    assert "Si" in model.pseudos.dictionary.keys()
-    assert model.pseudos.ecutwfc == 30
-    assert model.pseudos.ecutrho == 240
+    assert "Si" in model.dictionary.keys()
+    assert model.ecutwfc == 30
+    assert model.ecutrho == 240
 
     # Test that changing the structure triggers a reset
     silica = generate_structure_data("silica")
     model.input_structure = silica
-    assert "Si" in model.pseudos.dictionary.keys()
-    assert "O" in model.pseudos.dictionary.keys()
+    assert "Si" in model.dictionary.keys()
+    assert "O" in model.dictionary.keys()
 
     # Test pseudo upload
     pseudos.render()
@@ -205,18 +204,18 @@ def test_pseudos_settings(generate_structure_data, generate_upf_data):
             },
         }
     )
-    pseudo = model.pseudos.dictionary["O"]  # type: ignore
+    pseudo = model.dictionary["O"]  # type: ignore
     assert orm.load_node(pseudo).filename == "O_new.upf"
 
     # TODO necessary for final test - see comment below
-    # cutoffs = [model.pseudos.ecutwfc, model.pseudos.ecutrho]
+    # cutoffs = [model.ecutwfc, model.ecutrho]
 
-    model.pseudos.reset()
-    pseudo = model.pseudos.dictionary["O"]  # type: ignore
+    model.reset()
+    pseudo = model.dictionary["O"]  # type: ignore
     assert orm.load_node(pseudo).filename != "O_new.upf"
 
     # TODO what is this about?
-    # model.pseudos.set_pseudos(pseudos, cutoffs)
+    # model.set_pseudos(pseudos, cutoffs)
     # assert orm.load_node(pseudo).filename == "O_new.upf"