Symprec parameter

src/aiidalab_qe_vibroscopy/app/workchain.py

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

src/aiidalab_qe_vibroscopy/workflows/vibroworkchain.py

@@ -481,8 +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,
@@ -491,6 +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,
@@ -552,9 +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):
@@ -624,8 +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,
@@ -634,6 +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,
@@ -649,12 +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:

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/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: