For INS in low dimensional systems, parsing the band path from the Wo…

…rkChain inputs (#93)

* For INS in low dimensional systems, parsing the band path from the WorkChain inputs

This fix #69

* Bug fixing the q_path in Result panel.

* Pre-commit fixings

* Adding a check for emin and emax

and a loading spinner for INS data initialization.

* Adding an on-the-fly test for emin, emax.

src/aiidalab_qe_vibroscopy/app/result.py

@@ -211,7 +211,9 @@ def _update_view(self):
 
         # euphonic
         if ins_data:
-            intensity_maps = EuphonicSuperWidget(fc=ins_data["fc"])
+            intensity_maps = EuphonicSuperWidget(
+                fc=ins_data["fc"], q_path=ins_data["q_path"]
+            )
             children_result_widget += (intensity_maps,)
             tab_titles.append("Inelastic Neutrons")
 

src/aiidalab_qe_vibroscopy/utils/euphonic/__init__.py

@@ -18,6 +18,34 @@
 
 ###### START for detached app:
 
+# 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>
+"""
+
 
 # Upload buttons
 class UploadPhonopyYamlWidget(ipw.FileUpload):
@@ -111,7 +139,34 @@ class EuphonicSuperWidget(ipw.VBox):
     In between, we trigger the initialization of plots via a button.
     """
 
-    def __init__(self, mode="aiidalab-qe app plugin", fc=None):
+    def __init__(self, mode="aiidalab-qe app plugin", fc=None, q_path=None):
+        """
+        Initialize the Euphonic utility class.
+        Parameters:
+        -----------
+        mode : str, optional
+            The mode of operation, default is "aiidalab-qe app plugin".
+        fc : optional
+            Force constants, default is None.
+        q_path : optional
+            Q-path for phonon calculations, default is None. If Low-D system, this can be provided.
+            It is the same path obtained for the PhonopyCalculation of the phonopy_bands.
+        Attributes:
+        -----------
+        mode : str
+            The mode of operation.
+        upload_widget : UploadPhonopyWidget
+            Widget for uploading phonopy files.
+        fc_hdf5_content : None
+            Content of the force constants HDF5 file.
+        tab_widget : ipw.Tab
+            Tab widget for different views.
+        plot_button : ipw.Button
+            Button to initialize INS data.
+        fc : optional
+            Force constants if provided.
+        """
+
         self.mode = mode
 
         self.upload_widget = UploadPhonopyWidget()
@@ -128,6 +183,8 @@ def __init__(self, mode="aiidalab-qe app plugin", fc=None):
         if fc:
             self.fc = fc
 
+        self.q_path = q_path
+
         self.plot_button = ipw.Button(
             description="Initialise INS data",
             icon="pencil",
@@ -137,6 +194,11 @@ def __init__(self, mode="aiidalab-qe app plugin", fc=None):
         )
         self.plot_button.on_click(self._on_first_plot_button_clicked)
 
+        self.loading_widget = ipw.HTML(
+            value=spinner_html,
+        )
+        self.loading_widget.layout.display = "none"
+
         if self.mode == "aiidalab-qe app plugin":
             self.upload_widget.layout.display = "none"
             self.plot_button.disabled = False
@@ -148,6 +210,7 @@ def __init__(self, mode="aiidalab-qe app plugin", fc=None):
             children=[
                 self.upload_widget,
                 self.plot_button,
+                self.loading_widget,
                 self.tab_widget,
             ],
         )
@@ -203,10 +266,13 @@ def _generate_force_constants(
     def _on_first_plot_button_clicked(self, change=None):
         # It creates the widgets
         self.plot_button.layout.display = "none"
+
+        self.loading_widget.layout.display = "block"
+
         self.fc = self._generate_force_constants()
 
         # I first initialise this widget, to then have the 0K ref for the other two.
-        singlecrystalwidget = SingleCrystalFullWidget(self.fc)
+        singlecrystalwidget = SingleCrystalFullWidget(self.fc, self.q_path)
 
         self.tab_widget.children = (
             singlecrystalwidget,
@@ -218,6 +284,8 @@ def _on_first_plot_button_clicked(self, change=None):
             ),
         )
 
+        self.loading_widget.layout.display = "none"
+
         self.tab_widget.layout.display = "block"
 
 

src/aiidalab_qe_vibroscopy/utils/euphonic/euphonic_single_crystal_widgets.py

@@ -2,6 +2,7 @@
 from IPython.display import display
 
 import numpy as np
+import copy
 import ipywidgets as ipw
 import plotly.graph_objects as go
 import plotly.io as pio
@@ -196,11 +197,13 @@ class SingleCrystalFullWidget(ipw.VBox):
     and are from Sears (1992) Neutron News 3(3) pp26--37.
     """
 
-    def __init__(self, fc, **kwargs):
+    def __init__(self, fc, q_path, **kwargs):
         self.fc = fc
+        self.q_path = q_path
 
         self.spectra, self.parameters = produce_bands_weigthed_data(
             fc=self.fc,
+            linear_path=self.q_path,
             plot=False,  # CHANGED
         )
 
@@ -248,7 +251,9 @@ def _on_plot_button_clicked(self, change=None):
                 "delta_q": parameters_["q_spacing"],
             }
         else:
-            linear_path = None
+            linear_path = copy.deepcopy(self.q_path)
+            if linear_path:
+                linear_path["delta_q"] = parameters_["q_spacing"]
 
         self.spectra, self.parameters = produce_bands_weigthed_data(
             params=parameters_,

src/aiidalab_qe_vibroscopy/utils/euphonic/intensity_maps.py

@@ -299,6 +299,21 @@ def produce_bands_weigthed_data(
         x_tick_labels = get_qpoint_labels(
             modes.qpts, cell=modes.crystal.to_spglib_cell()
         )
+
+    # duplication from euphonic/cli/utils.py
+    if args.e_min is None:
+        # Subtract small amount from min frequency - otherwise due to unit
+        # conversions binning of this frequency can vary with different
+        # architectures/lib versions, making it difficult to test
+        emin_room = 1e-5 * ureg("meV").to(modes.frequencies.units).magnitude
+        args.e_min = min(np.min(modes.frequencies.magnitude - emin_room), 0.0)
+    if args.e_max is None:
+        args.e_max = np.max(modes.frequencies.magnitude) * 1.05
+    if args.e_min >= args.e_max:
+        raise ValueError(
+            f"Maximum energy ({args.e_max}) should be greater than minimum ({args.e_min}). "
+        )
+
     modes.frequencies_unit = args.energy_unit
     ebins = _get_energy_bins(modes, args.ebins + 1, emin=args.e_min, emax=args.e_max)
 
@@ -753,12 +768,36 @@ def export_euphonic_data(node, fermi_energy=None):
 
     output_set = node.outputs.vibronic.phonon_bands
 
+    if any(not element for element in node.inputs.structure.pbc):
+        vibro_bands = node.inputs.vibronic.phonopy_bands_dict.get_dict()
+        # Group the band and band_labels
+        band = vibro_bands["band"]
+        band_labels = vibro_bands["band_labels"]
+
+        grouped_bands = [
+            item
+            for sublist in [band_labels[i : i + 2] for i in range(len(band_labels) - 1)]
+            for item in sublist
+        ]
+        grouped_q = [
+            [tuple(band[i : i + 3]), tuple(band[i + 3 : i + 6])]
+            for i in range(0, len(band) - 3, 3)
+        ]
+        q_path = {
+            "coordinates": grouped_q,
+            "labels": grouped_bands,
+            "delta_q": 0.01,  # 1/A
+        }
+    else:
+        q_path = None
+
     phonopy_calc = output_set.creator
     fc = generate_force_constant_instance(phonopy_calc)
     # bands = compute_bands(fc)
     # pdos = compute_pdos(fc)
     return {
         "fc": fc,
+        "q_path": q_path,
     }  # "bands": bands, "pdos": pdos, "thermal": None}