Adding Van del Waals Correction widget (Adv Setting) (#620)

src/aiidalab_qe/app/configuration/advanced.py

@@ -38,6 +38,12 @@ class AdvancedSettings(Panel):
         Tick the box to override the default, smaller is more accurate and costly. </div>"""
     )
 
+    dftd3_version = {
+        "dft-d3": 3,
+        "dft-d3bj": 4,
+        "dft-d3m": 5,
+        "dft-d3mbj": 6,
+    }
     # protocol interface
     protocol = tl.Unicode(allow_none=True)
     input_structure = tl.Instance(orm.StructureData, allow_none=True)
@@ -121,6 +127,28 @@ def __init__(self, default_protocol=None, **kwargs):
         )
         self.total_charge.observe(self._callback_value_set, "value")
 
+        # Van der Waals setting widget
+        self.van_der_waals = ipw.Dropdown(
+            options=[
+                ("None", "none"),
+                ("Grimme-D3", "dft-d3"),
+                ("Grimme-D3BJ", "dft-d3bj"),
+                ("Grimme-D3M", "dft-d3m"),
+                ("Grimme-D3MBJ", "dft-d3mbj"),
+                ("Tkatchenko-Scheffler", "ts-vdw"),
+            ],
+            description="Van der Waals correction:",
+            value="none",
+            disabled=False,
+            style={"description_width": "initial"},
+        )
+
+        ipw.dlink(
+            (self.override, "value"),
+            (self.van_der_waals, "disabled"),
+            lambda override: not override,
+        )
+
         self.magnetization = MagnetizationSettings()
         ipw.dlink(
             (self.override, "value"),
@@ -146,6 +174,8 @@ def __init__(self, default_protocol=None, **kwargs):
             ),
             # total charge setting widget
             self.total_charge,
+            # van der waals setting widget
+            self.van_der_waals,
             # magnetization setting widget
             self.magnetization,
             # smearing setting widget
@@ -245,6 +275,17 @@ def get_panel_value(self):
             ] = self.pseudo_setter.ecutrho
         # if override is not ticked, use the default value
         parameters["pw"]["parameters"]["SYSTEM"]["tot_charge"] = self.total_charge.value
+
+        if self.van_der_waals.value in ["none", "ts-vdw"]:
+            parameters["pw"]["parameters"]["SYSTEM"][
+                "vdw_corr"
+            ] = self.van_der_waals.value
+        else:
+            parameters["pw"]["parameters"]["SYSTEM"]["vdw_corr"] = "dft-d3"
+            parameters["pw"]["parameters"]["SYSTEM"][
+                "dftd3_version"
+            ] = self.dftd3_version[self.van_der_waals.value]
+
         # there are two choose, use link or parent
         if self.spin_type == "collinear":
             parameters[
@@ -290,6 +331,12 @@ def set_panel_value(self, parameters):
             self.total_charge.value = parameters["pw"]["parameters"]["SYSTEM"].get(
                 "tot_charge", 0
             )
+            # van der waals correction
+            self.van_der_waals.value = self.dftd3_version.get(
+                system.get("dftd3_version"),
+                parameters["pw"]["parameters"]["SYSTEM"].get("vdw_corr", "none"),
+            )
+
         if parameters.get("initial_magnetic_moments"):
             self.magnetization._set_magnetization_values(
                 parameters.get("initial_magnetic_moments")
@@ -308,6 +355,9 @@ def reset(self):
             # reset total charge
             self.total_charge.value = DEFAULT_PARAMETERS["advanced"]["tot_charge"]
 
+            # reset the van der waals correction
+            self.van_der_waals.value = DEFAULT_PARAMETERS["advanced"]["vdw_corr"]
+
             # reset the override checkbox
             self.override.value = False
             self.smearing.reset()

src/aiidalab_qe/app/parameters/qeapp.yaml

@@ -21,6 +21,7 @@ advanced:
         functional: PBEsol
         accuracy: efficiency
     tot_charge: 0
+    vdw_corr: none
 
 ## Codes
 codes:

src/aiidalab_qe/app/result/summary_viewer.py

@@ -24,6 +24,15 @@
     (True, False, False): "x",
 }
 
+VDW_CORRECTION_VERSION = {
+    3: "Grimme-D3",
+    4: "Grimme-D3BJ",
+    5: "Grimme-D3M",
+    6: "Grimme-D3MBJ",
+    "ts-vdw": "Tkatchenko-Scheffler",
+    "none": "None",
+}
+
 
 def generate_report_parameters(qeapp_wc):
     """Generate the report parameters from the ui parameters and workchain's input.
@@ -107,6 +116,10 @@ def generate_report_parameters(qeapp_wc):
         report["degauss"] = pw_parameters["SYSTEM"]["degauss"]
         report["smearing"] = pw_parameters["SYSTEM"]["smearing"]
     report["tot_charge"] = pw_parameters["SYSTEM"].get("tot_charge", 0.0)
+    report["vdw_corr"] = VDW_CORRECTION_VERSION.get(
+        pw_parameters["SYSTEM"].get("dftd3_version"),
+        pw_parameters["SYSTEM"].get("vdw_corr", "none"),
+    )
     report["periodicity"] = PERIODICITY_MAPPING.get(
         qeapp_wc.inputs.structure.pbc, "xyz"
     )

src/aiidalab_qe/app/static/workflow_summary.jinja

@@ -100,6 +100,10 @@
         <td>Total Charge</td>
         <td>{{ tot_charge }}</td>
       </tr>
+      <tr>
+        <td>Van der Waals Correction</td>
+        <td>{{ vdw_corr }}</td>
+      </tr>
       <tr>
         <td>Initial Magnetic Moments</td>
         <td>{{ initial_magnetic_moments }}</td>

tests/conftest.py

@@ -336,6 +336,7 @@ def _submit_app_generator(
         smearing="methfessel-paxton",
         degauss=0.015,
         tot_charge=0.0,
+        vdw_corr="none",
         initial_magnetic_moments=0.0,
     ):
         configure_step = app.configure_step
@@ -354,6 +355,7 @@ def _submit_app_generator(
         # Advanced settings
         configure_step.advanced_settings.override.value = True
         configure_step.advanced_settings.total_charge.value = tot_charge
+        configure_step.advanced_settings.van_der_waals.value = vdw_corr
         configure_step.advanced_settings.kpoints_distance.value = kpoints_distance
         configure_step.advanced_settings.magnetization._set_magnetization_values(
             initial_magnetic_moments

tests/test_result/test_summary_report.yml

@@ -27,3 +27,4 @@ relaxed: positions_cell
 scf_kpoints_distance: 0.5
 smearing: cold
 tot_charge: 0.0
+vdw_corr: none

tests/test_submit_qe_workchain.py

@@ -62,6 +62,7 @@ def test_create_builder_advanced_settings(
         electronic_type="metal",
         spin_type="collinear",
         tot_charge=1.0,
+        vdw_corr="dft-d3bj",
         initial_magnetic_moments=0.1,
         properties=["bands", "pdos"],
     )
@@ -80,6 +81,8 @@ def test_create_builder_advanced_settings(
         got["pdos"]["nscf"],
     ]:
         assert parameters["pw"]["parameters"]["SYSTEM"]["tot_charge"] == 1.0
+        assert parameters["pw"]["parameters"]["SYSTEM"]["vdw_corr"] == "dft-d3"
+        assert parameters["pw"]["parameters"]["SYSTEM"]["dftd3_version"] == 4
 
     # test initial_magnetic_moments set 'starting_magnetization' in pw.in
     assert (

tests/test_submit_qe_workchain/test_create_builder_default.yml

@@ -26,6 +26,7 @@ bands:
           occupations: smearing
           smearing: cold
           tot_charge: 0.0
+          vdw_corr: none
       pseudos:
         Si: Si.upf
   bands_kpoints_distance: 0.025
@@ -55,6 +56,7 @@ bands:
           occupations: smearing
           smearing: methfessel-paxton
           tot_charge: 0.0
+          vdw_corr: none
       pseudos:
         Si: Si.upf
 clean_workdir: false
@@ -87,6 +89,7 @@ pdos:
           nosym: true
           occupations: tetrahedra
           tot_charge: 0.0
+          vdw_corr: none
       pseudos:
         Si: Si.upf
   projwfc:
@@ -123,6 +126,7 @@ pdos:
           occupations: smearing
           smearing: methfessel-paxton
           tot_charge: 0.0
+          vdw_corr: none
       pseudos:
         Si: Si.upf
 properties:
@@ -158,6 +162,7 @@ relax:
           occupations: smearing
           smearing: methfessel-paxton
           tot_charge: 0.0
+          vdw_corr: none
       pseudos:
         Si: Si.upf
   base_final_scf: