Lazy loading refactoring (#105)

Adapt plugin for lazy loading (Refactoring of the Plugin)
 Create model for Settings Panel
 Create model for the Code Panel
 Create widget/model logic for Results Panel
 Create widget/model logic for Phonons Results
 Create widget/model logic for IR/Raman Results
 Create widget/model logic for Dielectric Results
 Create widget/model logic for INS Results (This part was not completed)

We observed an issue with the INS Results, there is need of of refactoring the widget for visualisation
Co-author with @mikibonacci

pyproject.toml

@@ -20,12 +20,11 @@ requires-python = ">=3.8"
 dependencies = [
     "aiida-vibroscopy>=1.0.2",
     "aiida-phonopy>=1.1.3",
-    "phonopy",
-    #"euphonic==1.1.0",
+    "phonopy=2.25.0",
     "pre-commit",
     "euphonic",
     "kaleido",
-    "weas-widget==0.1.15",
+    "weas-widget==0.1.19",
 ]
 
 [tool.ruff.lint]

src/aiidalab_qe_vibroscopy/app/__init__.py

@@ -1,43 +1,34 @@
-from aiidalab_qe_vibroscopy.app.settings import Setting
-from aiidalab_qe_vibroscopy.app.workchain import workchain_and_builder
-from aiidalab_qe_vibroscopy.app.result import Result
-from aiidalab_qe.common.panel import OutlinePanel
+from aiidalab_qe.common.panel import PluginOutline
 
-from aiidalab_qe.common.widgets import (
-    QEAppComputationalResourcesWidget,
-    PwCodeResourceSetupWidget,
+from aiidalab_qe_vibroscopy.app.model import VibroConfigurationSettingsModel
+from aiidalab_qe_vibroscopy.app.settings import VibroConfigurationSettingPanel
+from aiidalab_qe_vibroscopy.app.code import (
+    VibroResourceSettingsModel,
+    VibroResourcesSettingsPanel,
 )
+from aiidalab_qe_vibroscopy.app.result.result import VibroResultsPanel
+from aiidalab_qe_vibroscopy.app.result.model import VibroResultsModel
 
+from aiidalab_qe_vibroscopy.app.workchain import workchain_and_builder
 
-class Outline(OutlinePanel):
-    title = "Vibrational properties"
-    # description = "IR and Raman spectra; you may also select phononic and dielectric properties"
 
+class VibroPluginOutline(PluginOutline):
+    title = "Vibrational Spectroscopy (VIBRO)"
 
-PhononWorkChainPwCode = PwCodeResourceSetupWidget(
-    description="pw.x for phonons",  # code for the PhononWorkChain workflow",
-    default_calc_job_plugin="quantumespresso.pw",
-)
-
-# The finite electric field does not support npools (does not work with npools>1), so we just set it as QEAppComputationalResourcesWidget
-DielectricWorkChainPwCode = QEAppComputationalResourcesWidget(
-    description="pw.x for dielectric",  # code for the DielectricWorChain workflow",
-    default_calc_job_plugin="quantumespresso.pw",
-)
-
-PhonopyCalculationCode = QEAppComputationalResourcesWidget(
-    description="phonopy",  # code for the PhonopyCalculation calcjob",
-    default_calc_job_plugin="phonopy.phonopy",
-)
 
 property = {
-    "outline": Outline,
+    "outline": VibroPluginOutline,
+    "configuration": {
+        "panel": VibroConfigurationSettingPanel,
+        "model": VibroConfigurationSettingsModel,
+    },
     "code": {
-        "phonon": PhononWorkChainPwCode,
-        "dielectric": DielectricWorkChainPwCode,
-        "phonopy": PhonopyCalculationCode,
+        "panel": VibroResourcesSettingsPanel,
+        "model": VibroResourceSettingsModel,
+    },
+    "result": {
+        "panel": VibroResultsPanel,
+        "model": VibroResultsModel,
     },
-    "setting": Setting,
     "workchain": workchain_and_builder,
-    "result": Result,
 }

src/aiidalab_qe_vibroscopy/app/code.py

@@ -0,0 +1,29 @@
+from aiidalab_qe.common.code.model import CodeModel, PwCodeModel
+from aiidalab_qe.common.panel import ResourceSettingsModel, ResourceSettingsPanel
+
+
+class VibroResourceSettingsModel(ResourceSettingsModel):
+    """Resource settings for the vibroscopy calculations."""
+
+    codes = {
+        "phonon": PwCodeModel(
+            description="pw.x for phonons",
+            default_calc_job_plugin="quantumespresso.pw",
+        ),
+        "dielectric": PwCodeModel(
+            description="pw.x for dielectric",
+            default_calc_job_plugin="quantumespresso.pw",
+        ),
+        "phonopy": CodeModel(
+            name="phonopy",
+            description="phonopy",
+            default_calc_job_plugin="phonopy.phonopy",
+        ),
+    }
+
+
+class VibroResourcesSettingsPanel(ResourceSettingsPanel[VibroResourceSettingsModel]):
+    """Panel for the resource settings for the vibroscopy calculations."""
+
+    title = "Vibronic"
+    identifier = identifier = "vibronic"

src/aiidalab_qe_vibroscopy/app/model.py

@@ -0,0 +1,221 @@
+import traitlets as tl
+
+import numpy as np
+from aiidalab_qe.common.mixins import HasInputStructure
+from aiidalab_qe.common.panel import ConfigurationSettingsModel
+
+from aiida_phonopy.data.preprocess import PreProcessData
+from aiida.plugins import DataFactory
+import sys
+import os
+
+HubbardStructureData = DataFactory("quantumespresso.hubbard_structure")
+from aiida_vibroscopy.calculations.spectra_utils import get_supercells_for_hubbard
+from aiida_vibroscopy.workflows.phonons.base import get_supercell_hubbard_structure
+
+# spinner for waiting time (supercell estimations)
+spinner_html = """
+<style>
+@keyframes spin {
+  0% { transform: rotate(0deg); }
+  100% { transform: rotate(360deg); }
+}
+
+.spinner {
+  display: inline-block;
+  width: 15px;
+  height: 15px;
+}
+
+.spinner div {
+  width: 100%;
+  height: 100%;
+  border: 4px solid #f3f3f3;
+  border-top: 4px solid #3498db;
+  border-radius: 50%;
+  animation: spin 1s linear infinite;
+}
+</style>
+<div class="spinner">
+  <div></div>
+</div>
+"""
+
+
+def disable_print(func):
+    def wrapper(*args, **kwargs):
+        # Save the current standard output
+        original_stdout = sys.stdout
+        # Redirect standard output to os.devnull
+        sys.stdout = open(os.devnull, "w")
+        try:
+            # Call the function
+            result = func(*args, **kwargs)
+        finally:
+            # Restore the original standard output
+            sys.stdout.close()
+            sys.stdout = original_stdout
+        return result
+
+    return wrapper
+
+
+class VibroConfigurationSettingsModel(ConfigurationSettingsModel, HasInputStructure):
+    dependencies = [
+        "input_structure",
+    ]
+
+    simulation_type_options = tl.List(
+        trait=tl.List(tl.Union([tl.Unicode(), tl.Int()])),
+        default_value=[
+            ("IR/Raman, Phonon, Dielectric, INS properties", 1),
+            ("IR/Raman and Dielectric in Primitive Cell Approach", 2),
+            ("Phonons for non-polar materials and INS", 3),
+            ("Dielectric properties", 4),
+        ],
+    )
+    simulation_type = tl.Int(1)
+
+    symmetry_symprec = tl.Float(1e-5)
+    supercell_x = tl.Int(2)
+    supercell_y = tl.Int(2)
+    supercell_z = tl.Int(2)
+
+    # Control for disable the supercell widget
+
+    disable_x = tl.Bool(False)
+    disable_y = tl.Bool(False)
+    disable_z = tl.Bool(False)
+
+    supercell = tl.List(
+        trait=tl.Int(),
+        default_value=[2, 2, 2],
+    )
+    supercell_number_estimator = tl.Unicode(
+        "Click the button to estimate the supercell size."
+    )
+
+    def get_model_state(self):
+        return {
+            "simulation_type": self.simulation_type,
+            "symmetry_symprec": self.symmetry_symprec,
+            "supercell": self.supercell,
+        }
+
+    def set_model_state(self, parameters: dict):
+        self.simulation_type = parameters.get("simulation_type", 1)
+        self.symmetry_symprec = parameters.get("symmetry_symprec", 1e-5)
+        self.supercell = parameters.get("supercell", [2, 2, 2])
+        self.supercell_x, self.supercell_y, self.supercell_z = self.supercell
+
+    def reset(self):
+        with self.hold_trait_notifications():
+            self.simulation_type = 1
+            self.symmetry_symprec = self._get_default("symmetry_symprec")
+            self.supercell = [2, 2, 2]
+            self.supercell_x, self.supercell_y, self.supercell_z = self.supercell
+            self.supercell_number_estimator = self._get_default(
+                "supercell_number_estimator"
+            )
+
+    def _get_default(self, trait):
+        return self._defaults.get(trait, self.traits()[trait].default_value)
+
+    def on_input_structure_change(self, _=None):
+        if not self.input_structure:
+            self.reset()
+
+        else:
+            self.disable_x, self.disable_y, self.disable_z = True, True, True
+            pbc = self.input_structure.pbc
+
+            if pbc == (False, False, False):
+                # No periodicity; fully disable and reset supercell
+                self.supercell_x = self.supercell_y = self.supercell_z = 1
+            elif pbc == (True, False, False):
+                self.supercell_y = self.supercell_z = 1
+                self.disable_x = False
+                self.symmetry_symprec = 1e-3
+            elif pbc == (True, True, False):
+                self.supercell_z = 1
+                self.disable_x = self.disable_y = False
+            elif pbc == (True, True, True):
+                self.disable_x = self.disable_y = self.disable_z = False
+
+            self.supercell = [self.supercell_x, self.supercell_y, self.supercell_z]
+
+    def suggest_supercell(self, _=None):
+        """
+        minimal supercell size for phonons, imposing a minimum lattice parameter of 15 A.
+        """
+        if self.input_structure and self.input_structure.pbc != (False, False, False):
+            ase_structure = self.input_structure.get_ase()
+            suggested_3D = 15 // np.array(ase_structure.cell.cellpar()[:3]) + 1
+
+            # Update only dimensions that are not disabled
+            if not self.disable_x:
+                self.supercell_x = int(suggested_3D[0])
+            if not self.disable_y:
+                self.supercell_y = int(suggested_3D[1])
+            if not self.disable_z:
+                self.supercell_z = int(suggested_3D[2])
+
+            # Sync the updated values to the supercell list
+            self.supercell = [self.supercell_x, self.supercell_y, self.supercell_z]
+
+        else:
+            return
+
+    def supercell_reset(self, _=None):
+        if not self.disable_x:
+            self.supercell_x = self._get_default("supercell_x")
+        if not self.disable_y:
+            self.supercell_y = self._get_default("supercell_x")
+        if not self.disable_z:
+            self.supercell_z = self._get_default("supercell_x")
+        self.supercell = [self.supercell_x, self.supercell_y, self.supercell_z]
+
+    def reset_symprec(self, _=None):
+        self.symmetry_symprec = (
+            self._get_default("symmetry_symprec")
+            if self.input_structure.pbc != (True, False, False)
+            else 1e-3
+        )
+        self.supercell_number_estimator = self._get_default(
+            "supercell_number_estimator"
+        )
+
+    @disable_print
+    def _estimate_supercells(self, _=None):
+        if self.input_structure:
+            self.supercell_number_estimator = spinner_html
+
+            preprocess_data = PreProcessData(
+                structure=self.input_structure,
+                supercell_matrix=[
+                    [self.supercell_x, 0, 0],
+                    [0, self.supercell_y, 0],
+                    [0, 0, self.supercell_z],
+                ],
+                symprec=self.symmetry_symprec,
+                distinguish_kinds=False,
+                is_symmetry=True,
+            )
+
+            if isinstance(self.input_structure, HubbardStructureData):
+                supercell = get_supercell_hubbard_structure(
+                    self.input_structure,
+                    self.input_structure,
+                    metadata={"store_provenance": False},
+                )
+                supercells = get_supercells_for_hubbard(
+                    preprocess_data=preprocess_data,
+                    ref_structure=supercell,
+                    metadata={"store_provenance": False},
+                )
+            else:
+                supercells = preprocess_data.get_supercells_with_displacements()
+
+            self.supercell_number_estimator = f"{len(supercells)}"
+
+        return