Adding Symprec Widget

src/aiidalab_qe_vibroscopy/app/result.py

@@ -94,7 +94,6 @@ def _update_view(self):
                 _bands_plot_view_class.update_layout(
                     yaxis=dict(autorange=True),  # Automatically scale the y-axis
                 )
-
 
                 # the data (bands and pdos) are the first element of the lists phonon_data["bands"] and phonon_data["pdos"]!
                 downloadBandsPdos_widget = DownloadBandsPdosWidget(
@@ -209,14 +208,13 @@ def _update_view(self):
             dielectric_results = DielectricResults(dielectric_data)
             children_result_widget += (dielectric_results,)
             tab_titles.append("Dielectric properties")
-            
+
         # euphonic
         if ins_data:
             intensity_maps = EuphonicSuperWidget(fc=ins_data["fc"])
             children_result_widget += (intensity_maps,)
             tab_titles.append("Inelastic Neutrons")
 
-
         self.result_tabs = ipw.Tab(children=children_result_widget)
 
         for title_index in range(len(tab_titles)):

src/aiidalab_qe_vibroscopy/app/settings.py

@@ -143,6 +143,13 @@ def change_supercell(_=None):
         self.supercell_widget.layout.display = "block"
         # end Supercell.
 
+        self.symmetry_symprec = ipw.FloatText(
+            value=1e-5,
+            description="Symmetry tolerance (symprec):",
+            style={"description_width": "initial"},
+            layout={"width": "300px"},
+        )
+
         self.children = [
             ipw.VBox(
                 [
@@ -167,6 +174,7 @@ def change_supercell(_=None):
                 ],
             ),
             self.supercell_widget,
+            self.symmetry_symprec,
         ]
 
         super().__init__(**kwargs)
@@ -208,16 +216,19 @@ def get_panel_value(self):
         return {
             "simulation_mode": self.calc_options.value,
             "supercell_selector": self.supercell,
+            "symmetry_symprec": self.symmetry_symprec.value,
         }
 
     def set_panel_value(self, input_dict):
         """Load a dictionary with the input parameters for the plugin."""
         self.calc_options.value = input_dict.get("simulation_mode", 1)
         self.supercell = input_dict.get("supercell_selector", [2, 2, 2])
+        self.symmetry_symprec.value = input_dict.get("symmetry_symprec", 1e-5)
         self._sc_x.value, self._sc_y.value, self._sc_z.value = self.supercell
 
     def reset(self):
         """Reset the panel"""
         self.calc_options.value = 1
         self.supercell = [2, 2, 2]
+        self.symmetry_symprec.value = 1e-5
         self._sc_x.value, self._sc_y.value, self._sc_z.value = self.supercell

src/aiidalab_qe_vibroscopy/app/workchain.py

@@ -56,6 +56,7 @@ def get_builder(codes, structure, parameters):
             "supercell_matrix": supercell_matrix,
         },
         "dielectric": {"scf": deepcopy(parameters["advanced"])},
+        "symmetry": {"symprec": parameters["vibronic"]["symmetry_symprec"]},
     }
 
     # Update code information with resource configurations

src/aiidalab_qe_vibroscopy/workflows/vibroworkchain.py

@@ -439,18 +439,24 @@ def get_builder_from_protocol(
                 if structure.pbc == (True, False, False):
                     builder.phonopy_bands_dict = Dict(
                         dict={
-                            "symmetry_tolerance": 1e-3,
+                            "symmetry_tolerance": overrides["symmetry"]["symprec"],
                             "band": [0, 0, 0, 1 / 2, 0, 0],
                             "band_points": 100,
                             "band_labels": [GAMMA, "$\\mathrm{X}$"],
                         }
                     )
                     # change symprec for 1D materials to 1e-3
-                    builder.phonopy_pdos_dict["symmetry_tolerance"] = 1e-3
-                    builder.phonopy_thermo_dict["symmetry_tolerance"] = 1e-3
-                    builder.harmonic.symmetry.symprec = orm.Float(1e-3)
+                    builder.phonopy_pdos_dict["symmetry_tolerance"] = overrides[
+                        "symmetry"
+                    ]["symprec"]  # 1e-3
+                    builder.phonopy_thermo_dict["symmetry_tolerance"] = overrides[
+                        "symmetry"
+                    ]["symprec"]  # 1e-3
+                    builder.harmonic.symmetry.symprec = orm.Float(
+                        overrides["symmetry"]["symprec"]
+                    )
                     builder.harmonic.phonon.phonopy.parameters = orm.Dict(
-                        {"symmetry_tolerance": 1e-3}
+                        {"symmetry_tolerance": overrides["symmetry"]["symprec"]}
                     )
 
                 elif structure.pbc == (True, True, False):
@@ -475,8 +481,12 @@ def get_builder_from_protocol(
                     )
             else:
                 builder.phonopy_bands_dict = Dict(dict=PhononProperty.BANDS.value)
+                builder.phonopy_bands_dict["symmetry_tolerance"] = overrides[
+                    "symmetry"
+                ]["symprec"]
                 builder.phonopy_pdos_dict = Dict(
                     dict={
+                        "symmetry_tolerance": overrides["symmetry"]["symprec"],
                         "pdos": "auto",
                         "mesh": 150,  # 1000 is too heavy
                         "write_mesh": False,
@@ -485,6 +495,7 @@ def get_builder_from_protocol(
 
             builder.phonopy_thermo_dict = Dict(
                 dict={
+                    "symmetry_tolerance": overrides["symmetry"]["symprec"],
                     "tprop": True,
                     "mesh": 200,  # 1000 is too heavy
                     "write_mesh": False,
@@ -517,9 +528,11 @@ def get_builder_from_protocol(
                 builder_iraman.dielectric.pop("kpoints_parallel_distance", None)
 
                 if structure.pbc == (True, False, False):
-                    builder_iraman.symmetry.symprec = orm.Float(1e-3)
+                    builder_iraman.symmetry.symprec = orm.Float(
+                        overrides["symmetry"]["symprec"]
+                    )
                     builder_iraman.phonon.phonopy.parameters = orm.Dict(
-                        {"symmetry_tolerance": 1e-3}
+                        {"symmetry_tolerance": overrides["symmetry"]["symprec"]}
                     )
 
             builder.iraman = builder_iraman
@@ -544,9 +557,8 @@ def get_builder_from_protocol(
             builder_phonon.phonopy.settings = Dict(dict={"keep_phonopy_yaml": True})
 
             # MBO: I do not understand why I have to do this, but it works
-            symmetry = builder_phonon.pop("symmetry")
             builder.phonon = builder_phonon
-            builder.phonon.symmetry = symmetry
+            builder.phonon.symmetry = overrides["symmetry"]
 
             # Adding the bands and pdos inputs.
             if structure.pbc != (True, True, True):
@@ -574,18 +586,24 @@ def get_builder_from_protocol(
                 if structure.pbc == (True, False, False):
                     builder.phonopy_bands_dict = Dict(
                         dict={
-                            "symmetry_tolerance": 1e-3,
+                            "symmetry_tolerance": overrides["symmetry"]["symprec"],
                             "band": [0, 0, 0, 1 / 2, 0, 0],
                             "band_points": 100,
                             "band_labels": [GAMMA, "$\\mathrm{X}$"],
                         }
                     )
                     # change symprec for 1D materials to 1e-3
-                    builder.phonopy_pdos_dict["symmetry_tolerance"] = 1e-3
-                    builder.phonopy_thermo_dict["symmetry_tolerance"] = 1e-3
-                    builder.phonon.symmetry.symprec = orm.Float(1e-3)
+                    builder.phonopy_pdos_dict["symmetry_tolerance"] = overrides[
+                        "symmetry"
+                    ]["symprec"]
+                    builder.phonopy_thermo_dict["symmetry_tolerance"] = overrides[
+                        "symmetry"
+                    ]["symprec"]
+                    builder.phonon.symmetry.symprec = orm.Float(
+                        overrides["symmetry"]["symprec"]
+                    )
                     builder.phonon.phonopy.parameters = orm.Dict(
-                        {"symmetry_tolerance": 1e-3}
+                        {"symmetry_tolerance": overrides["symmetry"]["symprec"]}
                     )
 
                 elif structure.pbc == (True, True, False):
@@ -610,8 +628,12 @@ def get_builder_from_protocol(
                     )
             else:
                 builder.phonopy_bands_dict = Dict(dict=PhononProperty.BANDS.value)
+                builder.phonopy_bands_dict["symmetry_tolerance"] = overrides[
+                    "symmetry"
+                ]["symprec"]
                 builder.phonopy_pdos_dict = Dict(
                     dict={
+                        "symmetry_tolerance": overrides["symmetry"]["symprec"],
                         "pdos": "auto",
                         "mesh": 150,  # 1000 is too heavy
                         "write_mesh": False,
@@ -620,6 +642,7 @@ def get_builder_from_protocol(
 
             builder.phonopy_thermo_dict = Dict(
                 dict={
+                    "symmetry_tolerance": overrides["symmetry"]["symprec"],
                     "tprop": True,
                     "mesh": 200,  # 1000 is too heavy
                     "write_mesh": False,
@@ -635,12 +658,10 @@ def get_builder_from_protocol(
                 **kwargs,
             )
 
-            # MBO: I do not understand why I have to do this, but it works. maybe related with excludes.
-            symmetry = builder_dielectric.pop("symmetry")
             if structure.pbc != (True, True, True):
                 builder_dielectric.pop("kpoints_parallel_distance", None)
             builder.dielectric = builder_dielectric
-            builder.dielectric.symmetry = symmetry
+            builder.dielectric.symmetry = overrides["symmetry"]
             builder.dielectric.property = dielectric_property
 
         # Deleting the not needed parts of the builder:
@@ -659,7 +680,9 @@ def get_builder_from_protocol(
             "num_mpiprocs_per_machine": 1,
         }
         if structure.pbc == (True, False, False):
-            builder.phonopy_calc.parameters = orm.Dict({"symmetry_tolerance": 1e-3})
+            builder.phonopy_calc.parameters = orm.Dict(
+                {"symmetry_tolerance": overrides["symmetry"]["symprec"]}
+            )
         builder.structure = structure
 
         return builder

tests/conftest.py

@@ -48,14 +48,15 @@ def _fixture_code(entry_point_name):
 def generate_structure_data():
     """generate a `StructureData` object."""
 
-    def _generate_structure_data(name="silicon", pbc=(True, True, True)):
+    def _generate_structure_data(name="silicon"):
         if name == "silicon":
             structure = orm.StructureData(
                 cell=[
                     [3.84737, 0.0, 0.0],
                     [1.923685, 3.331920, 0.0],
                     [1.923685, 1.110640, 3.141364],
-                ]
+                ],
+                pbc=(True, True, True),
             )
             structure.append_atom(position=(0.0, 0.0, 0.0), symbols="Si")
             structure.append_atom(position=(1.923685, 1.110640, 0.785341), symbols="Si")
@@ -65,7 +66,8 @@ def _generate_structure_data(name="silicon", pbc=(True, True, True)):
                     [4.18, 0.0, 0.0],
                     [0.0, 4.18, 0.0],
                     [0.0, 0.0, 2.66],
-                ]
+                ],
+                pbc=(True, True, True),
             )
             structure.append_atom(position=(0.0, 0.0, 0.0), symbols="Si")
             structure.append_atom(position=(2.09, 2.09, 1.33), symbols="Si")
@@ -88,11 +90,23 @@ def _generate_structure_data(name="silicon", pbc=(True, True, True)):
                 ["O", "O", (0, 0, 10.201532881212)],
                 ["Li", "Li", (0, 0, 6.9018028772754)],
             ]
-            structure = orm.StructureData(cell=cell)
+            structure = orm.StructureData(cell=cell, pbc=(True, True, True))
 
             for site in sites:
                 structure.append_atom(position=site[2], symbols=site[0], name=site[1])
-        structure.pbc = pbc
+
+        elif name == "2D-xy-arsenic":
+            cell = [[3.61, 0, 0], [-1.80, 3.13, 0], [0, 0, 21.3]]
+            structure = orm.StructureData(cell=cell, pbc=(True, True, False))
+            structure.append_atom(
+                position=(1.804, 1.042, 11.352), symbols="As", name="As"
+            )
+            structure.append_atom(position=(0, 2.083, 9.960), symbols="As", name="As")
+
+        elif name == "1D-x-carbon":
+            cell = [[4.2, 0, 0], [0, 20, 0], [0, 0, 20]]
+            structure = orm.StructureData(cell=cell, pbc=(True, False, False))
+            structure.append_atom(position=(0, 0, 0), symbols="C", name="C")
 
         return structure
 

tests/test_settings.py

@@ -47,3 +47,31 @@ def test_settings():
     parameters = configure_step.settings["vibronic"].get_panel_value()
     assert parameters["simulation_mode"] == 1
     assert parameters["supercell_selector"] == [2, 2, 2]
+
+
+@pytest.mark.usefixtures("sssp")
+def test_xy_settings(generate_structure_data):
+    """Test the settings of the vibroscopy app."""
+
+    from aiidalab_qe.app.configuration import ConfigureQeAppWorkChainStep
+
+    configure_step = ConfigureQeAppWorkChainStep()
+    structure = generate_structure_data("2D-xy-arsenic")
+    configure_step.input_structure = structure
+    configure_step.workchain_settings.properties["vibronic"].run.value = True
+    parameters = configure_step.settings["vibronic"].get_panel_value()
+    assert parameters["supercell_selector"] == [2, 2, 1]
+
+
+@pytest.mark.usefixtures("sssp")
+def test_x_settings(generate_structure_data):
+    """Test the settings of the vibroscopy app."""
+
+    from aiidalab_qe.app.configuration import ConfigureQeAppWorkChainStep
+
+    configure_step = ConfigureQeAppWorkChainStep()
+    structure = generate_structure_data("1D-x-carbon")
+    configure_step.input_structure = structure
+    configure_step.workchain_settings.properties["vibronic"].run.value = True
+    parameters = configure_step.settings["vibronic"].get_panel_value()
+    assert parameters["supercell_selector"] == [2, 1, 1]

tests/test_submit.py

@@ -37,7 +37,7 @@ def test_create_builder_default(
     submit_step.codes["dielectric"].value = pw_code.uuid
     submit_step.codes["phonopy"].value = phonopy_code.uuid
 
-    submit_step.codes["pw"].num_cpus.value = 10
+    submit_step.codes["pw"].num_cpus.value = 8
     submit_step.codes["phonon"].num_cpus.value = 2
     submit_step.codes["dielectric"].num_cpus.value = 3
 

tests/test_submit/test_create_builder_default.yml

@@ -39,18 +39,19 @@ codes:
     nodes: 1
     ntasks_per_node: 1
   pw:
-    cpus: 10
+    cpus: 8
     cpus_per_task: 1
     max_wallclock_seconds: 43200
     nodes: 1
-    ntasks_per_node: 10
+    ntasks_per_node: 8
     parallelization: {}
 vibronic:
   simulation_mode: 1
   supercell_selector:
   - 2
   - 2
   - 2
+  symmetry_symprec: 1.0e-05
 workchain:
   electronic_type: metal
   properties: