Feature Spin-Orbit coupling (#708)

* Feature Spin-Orbit coupling

src/aiidalab_qe/app/configuration/advanced.py

@@ -209,6 +209,21 @@ def __init__(self, default_protocol=None, **kwargs):
             (self.etot_conv_thr, "disabled"),
             lambda override: not override,
         )
+        # Spin-Orbit calculation
+        self.spin_orbit = ipw.ToggleButtons(
+            options=[
+                ("Off", "wo_soc"),
+                ("On", "soc"),
+            ],
+            description="Spin-Orbit:",
+            value="wo_soc",
+            style={"description_width": "initial"},
+        )
+        ipw.dlink(
+            (self.override, "value"),
+            (self.spin_orbit, "disabled"),
+            lambda override: not override,
+        )
 
         self.pseudo_family_selector = PseudoFamilySelector()
         self.pseudo_setter = PseudoSetter()
@@ -217,6 +232,12 @@ def __init__(self, default_protocol=None, **kwargs):
             (self.pseudo_setter, "pseudo_family"),
         )
         self.kpoints_distance.observe(self._display_mesh, "value")
+
+        # Link with PseudoWidget
+        ipw.dlink(
+            (self.spin_orbit, "value"),
+            (self.pseudo_family_selector, "spin_orbit"),
+        )
         self.children = [
             self.title,
             ipw.HBox(
@@ -245,6 +266,8 @@ def __init__(self, default_protocol=None, **kwargs):
             self.kpoints_description,
             ipw.HBox([self.kpoints_distance, self.mesh_grid]),
             self.hubbard_widget,
+            # Spin-Orbit calculation
+            self.spin_orbit,
             self.pseudo_family_selector,
             self.pseudo_setter,
         ]
@@ -436,6 +459,12 @@ def get_panel_value(self):
             self.etot_conv_thr.value
         )
 
+        # Spin-Orbit calculation
+        if self.spin_orbit.value == "soc":
+            parameters["pw"]["parameters"]["SYSTEM"]["lspinorb"] = True
+            parameters["pw"]["parameters"]["SYSTEM"]["noncolin"] = True
+            parameters["pw"]["parameters"]["SYSTEM"]["nspin"] = 4
+
         return parameters
 
     def set_insulator_magnetization(self, parameters):
@@ -483,6 +512,10 @@ def set_panel_value(self, parameters):
             self.total_charge.value = parameters["pw"]["parameters"]["SYSTEM"].get(
                 "tot_charge", 0
             )
+            if "lspinorb" in system:
+                self.spin_orbit.value = "soc"
+            else:
+                self.spin_orbit.value = "wo_soc"
             # van der waals correction
             self.van_der_waals.value = self.dftd3_version.get(
                 system.get("dftd3_version"),

src/aiidalab_qe/app/configuration/pseudos.py

@@ -30,6 +30,20 @@ class PseudoFamilySelector(ipw.VBox):
         """<div style="padding-top: 0px; padding-bottom: 10px">
         <h4>Accuracy and precision</h4></div>"""
     )
+    PSEUDO_HELP_SOC = """<div style="line-height: 140%; padding-top: 10px; padding-bottom: 0px; opacity:0.5;">
+            Spin-orbit coupling (SOC) calculations are supported exclusively with PseudoDojo pseudopotentials.
+            PseudoDojo offers these pseudopotentials in two versions: standard and stringent.
+            Here, we utilize the FR (fully relativistic) type from PseudoDojo.
+            Please ensure you choose appropriate cutoff values for your calculations.
+        </div>"""
+
+    PSEUDO_HELP_WO_SOC = """<div style="line-height: 140%; padding-top: 10px; padding-bottom: 0px; opacity:0.5;">
+        If you are unsure, select 'SSSP efficiency', which for
+        most calculations will produce sufficiently accurate results at
+        comparatively small computational costs. If your calculations require a
+        higher accuracy, select 'SSSP accuracy' or 'PseudoDojo stringent', which will be computationally
+        more expensive. SSSP is the standard solid-state pseudopotentials.
+        The PseudoDojo used here has the SR relativistic type.</div>"""
 
     description = ipw.HTML(
         """<div style="line-height: 140%; padding-top: 0px; padding-bottom: 10px">
@@ -45,15 +59,7 @@ class PseudoFamilySelector(ipw.VBox):
         <b><a href="https://www.materialscloud.org/discover/sssp/table/efficiency"
         target="_blank">Pseudopotential family</b></div>"""
     )
-    pseudo_family_help = ipw.HTML(
-        """<div style="line-height: 140%; padding-top: 10px; padding-bottom: 0px; opacity:0.5;">
-        If you are unsure, select 'SSSP efficiency', which for
-        most calculations will produce sufficiently accurate results at
-        comparatively small computational costs. If your calculations require a
-        higher accuracy, select 'SSSP accuracy' or 'PseudoDojo stringent', which will be computationally
-        more expensive. SSSP is the standard solid-state pseudopotentials.
-        The PseudoDojo used here has the SR relativistic type.</div>"""
-    )
+    pseudo_family_help = ipw.HTML(PSEUDO_HELP_WO_SOC)
 
     dft_functional_prompt = ipw.HTML(
         """
@@ -68,6 +74,7 @@ class PseudoFamilySelector(ipw.VBox):
     )
     protocol = tl.Unicode(allow_none=True)
     disabled = tl.Bool()
+    spin_orbit = tl.Unicode()
 
     # output pseudo family widget which is the string of the pseudo family (of the AiiDA group).
     value = tl.Unicode(allow_none=True)
@@ -150,9 +157,14 @@ def set_value(self, _=None):
         functional = self.dft_functional.value
         # XXX (jusong.yu): a validator is needed to check the family string is consistent with the list of pseudo families defined in the setup_pseudos.py
         if library == "PseudoDojo":
-            pseudo_family_string = (
-                f"PseudoDojo/{PSEUDODOJO_VERSION}/{functional}/SR/{accuracy}/upf"
-            )
+            if self.spin_orbit == "soc":
+                pseudo_family_string = (
+                    f"PseudoDojo/{PSEUDODOJO_VERSION}/{functional}/FR/{accuracy}/upf"
+                )
+            else:
+                pseudo_family_string = (
+                    f"PseudoDojo/{PSEUDODOJO_VERSION}/{functional}/SR/{accuracy}/upf"
+                )
         elif library == "SSSP":
             pseudo_family_string = f"SSSP/{SSSP_VERSION}/{functional}/{accuracy}"
         else:
@@ -190,6 +202,24 @@ def reset(self):
         # stay the same while xc selection is changed.
         self._update_settings_from_protocol(self.protocol)
 
+    @tl.observe("spin_orbit")
+    def _update_library_selection(self, _):
+        """Update the library selection according to the spin orbit value."""
+        if self.spin_orbit == "soc":
+            self.library_selection.options = [
+                "PseudoDojo standard",
+                "PseudoDojo stringent",
+            ]
+            self.pseudo_family_help.value = self.PSEUDO_HELP_SOC
+        else:
+            self.library_selection.options = [
+                "SSSP efficiency",
+                "SSSP precision",
+                "PseudoDojo standard",
+                "PseudoDojo stringent",
+            ]
+            self.pseudo_family_help.value = self.PSEUDO_HELP_WO_SOC
+
     @tl.observe("protocol")
     def _protocol_changed(self, _):
         """Input protocol changed, update the value of widgets."""
@@ -198,9 +228,17 @@ def _protocol_changed(self, _):
     def _update_settings_from_protocol(self, protocol):
         """Update the widget values from the given protocol, and trigger the callback."""
         # FIXME: this rely on the aiida-quantumespresso, which is not ideal
-        pseudo_family_string = PwBaseWorkChain.get_protocol_inputs(protocol)[
-            "pseudo_family"
-        ]
+
+        if self.spin_orbit == "soc":
+            if protocol in ["fast", "moderate"]:
+                pseudo_family_string = "PseudoDojo/0.4/PBE/FR/standard/upf"
+            else:
+                pseudo_family_string = "PseudoDojo/0.4/PBE/FR/stringent/upf"
+        else:
+            pseudo_family_string = PwBaseWorkChain.get_protocol_inputs(protocol)[
+                "pseudo_family"
+            ]
+
         pseudo_family = PseudoFamily.from_string(pseudo_family_string)
 
         self.load_from_pseudo_family(pseudo_family)

src/aiidalab_qe/app/result/summary_viewer.py

@@ -124,6 +124,9 @@ def generate_report_parameters(qeapp_wc):
         qeapp_wc.inputs.structure.pbc, "xyz"
     )
 
+    # Spin-Oribit coupling
+    report["spin_orbit"] = pw_parameters["SYSTEM"].get("lspinorb", False)
+
     # DFT+U
     hubbard_dict = ui_parameters["advanced"].pop("hubbard_parameters", None)
     if hubbard_dict:

src/aiidalab_qe/app/static/workflow_summary.jinja

@@ -122,6 +122,13 @@
         <td>{{ hubbard_u }}</td>
       </tr>
       {% endif %}
+      {% if spin_orbit %}
+      <tr>
+        <td>Spin-Orbit</td>
+        <td>{{ spin_orbit }}</td>
+      </tr>
+      {% endif %}
+
     </table>
   </div>
 </div>

src/aiidalab_qe/common/setup_pseudos.py

@@ -28,6 +28,10 @@
     f"PseudoDojo/{PSEUDODOJO_VERSION}/PBEsol/SR/standard/upf",
     f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/SR/stringent/upf",
     f"PseudoDojo/{PSEUDODOJO_VERSION}/PBEsol/SR/stringent/upf",
+    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/FR/standard/upf",
+    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBEsol/FR/standard/upf",
+    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/FR/stringent/upf",
+    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBEsol/FR/stringent/upf",
 }
 
 

src/aiidalab_qe/workflows/__init__.py

@@ -20,6 +20,8 @@
 # because we want to decouple the workflows from the app, so I copied it here
 # instead of importing it.
 # load entry points
+
+
 def get_entries(entry_point_name="aiidalab_qe.property"):
     from importlib.metadata import entry_points
 
@@ -190,15 +192,6 @@ def get_builder_from_protocol(
         relax_builder.pop("base_final_scf", None)  # never run a final scf
         builder.relax = relax_builder
 
-        # remove starting magnetization if tot_magnetization is set
-        if (
-            relax_builder["base"]["pw"]["parameters"]["SYSTEM"].get("tot_magnetization")
-            is not None
-        ):
-            builder.relax["base"]["pw"]["parameters"]["SYSTEM"].pop(
-                "starting_magnetization", None
-            )
-
         if properties is None:
             properties = []
         builder.properties = orm.List(list=properties)
@@ -211,7 +204,6 @@ def get_builder_from_protocol(
                 plugin_builder = entry_point["get_builder"](
                     codes, builder.structure, copy.deepcopy(parameters), **kwargs
                 )
-                # check if the plugin has a clean_workdir input
                 plugin_workchain = entry_point["workchain"]
                 if plugin_workchain.spec().has_input("clean_workdir"):
                     plugin_builder.clean_workdir = clean_workdir

tests/test_pseudo.py

@@ -104,7 +104,7 @@ def test_setup_pseudos_cmd(tmp_path):
 def test_pseudos_installation():
     """Test install_pseudos"""
     # Test by compare the pseudos_to_install before and after the installation
-    assert len(pseudos_to_install()) == 8
+    assert len(pseudos_to_install()) == 12
     EXPECTED_PSEUDOS = {
         f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/SR/standard/upf",
         f"SSSP/{SSSP_VERSION}/PBE/efficiency",
@@ -114,13 +114,13 @@ def test_pseudos_installation():
     [_ for _ in _install_pseudos(EXPECTED_PSEUDOS)]
 
     # Two pseudos are installed
-    assert len(pseudos_to_install()) == 6
+    assert len(pseudos_to_install()) == 10
 
 
 @pytest.mark.usefixtures("aiida_profile_clean")
 def test_download_and_install_pseudo_from_file(tmp_path):
     """Test download and install pseudo from file."""
-    assert len(pseudos_to_install()) == 8
+    assert len(pseudos_to_install()) == 12
     EXPECTED_PSEUDOS = {
         f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/SR/standard/upf",
         f"SSSP/{SSSP_VERSION}/PBE/efficiency",
@@ -129,14 +129,14 @@ def test_download_and_install_pseudo_from_file(tmp_path):
     # Download the pseudos to the tmp_path but not install
     [_ for _ in _install_pseudos(EXPECTED_PSEUDOS, download_only=True, cwd=tmp_path)]
 
-    assert len(pseudos_to_install()) == 8
+    assert len(pseudos_to_install()) == 12
     assert len(list(tmp_path.iterdir())) == 2
 
     # Install the pseudos from the tmp_path
     [_ for _ in _install_pseudos(EXPECTED_PSEUDOS, cwd=tmp_path)]
 
     # Two pseudos are installed
-    assert len(pseudos_to_install()) == 6
+    assert len(pseudos_to_install()) == 10
 
 
 def test_pseudos_family_selector_widget():
@@ -147,7 +147,7 @@ def test_pseudos_family_selector_widget():
     assert w.override.value is False
 
     w.override.value = True
-
+    w.spin_orbit = "wo_soc"
     # test the default value
     assert w.value == f"SSSP/{SSSP_VERSION}/PBEsol/efficiency"
 
@@ -163,6 +163,12 @@ def test_pseudos_family_selector_widget():
     w.library_selection.value = "PseudoDojo stringent"
     assert w.value == f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/SR/stringent/upf"
 
+    # Test spin-orbit change will update
+
+    w.spin_orbit = "soc"
+    w.protocol = "moderate"
+    assert w.value == f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/FR/standard/upf"
+
 
 @pytest.mark.usefixtures("sssp")
 def test_pseudos_setter_widget(generate_structure_data, generate_upf_data):

tests/test_result/test_summary_report.yml

@@ -26,6 +26,7 @@ relax_method: positions_cell
 relaxed: positions_cell
 scf_kpoints_distance: 0.5
 smearing: cold
+spin_orbit: false
 tot_charge: 0.0
 tot_magnetization: false
 vdw_corr: none

tests_integration/test_image.py

@@ -26,4 +26,4 @@ def test_pseudos_families_are_installed(aiidalab_exec, nb_user):
     assert "PseudoDojo" in output
 
     # Two lines of header, 8 pseudos
-    assert len(output.splitlines()) == 10
+    assert len(output.splitlines()) == 14