From 0e6c72082c1179aedb55a2936ce9416332092d9d Mon Sep 17 00:00:00 2001
From: AndresOrtegaGuerrero <oandresg15@gmail.com>
Date: Fri, 31 Mar 2023 07:32:59 +0000
Subject: [PATCH 1/6] adding a intslider (tot_charge) to select the total
 charge

---
 aiidalab_qe/parameters/qeapp.yaml |  2 ++
 aiidalab_qe/steps.py              | 29 +++++++++++++++++++++++++++++
 2 files changed, 31 insertions(+)

diff --git a/aiidalab_qe/parameters/qeapp.yaml b/aiidalab_qe/parameters/qeapp.yaml
index 16bc9518..9b62a57b 100644
--- a/aiidalab_qe/parameters/qeapp.yaml
+++ b/aiidalab_qe/parameters/qeapp.yaml
@@ -19,3 +19,5 @@ electronic_type: metal
 protocol: moderate
 kpoints_distance_override:
 pseudo_family: SSSP/1.2/PBEsol/efficiency
+
+tot_charge: 0
diff --git a/aiidalab_qe/steps.py b/aiidalab_qe/steps.py
index c86dd9b0..bb018001 100644
--- a/aiidalab_qe/steps.py
+++ b/aiidalab_qe/steps.py
@@ -108,6 +108,14 @@ def __init__(self, **kwargs):
             style={"description_width": "initial"},
         )
 
+        # tot_charge: total charge of the simulations
+        self.tot_charge = ipw.IntSlider(
+            value=DEFAULT_PARAMETERS["tot_charge"],
+            min=-2,
+            max=2,
+            step=1,
+        )
+
         # Checkbox to see if the band structure should be calculated
         self.bands_run = ipw.Checkbox(
             description="",
@@ -159,6 +167,17 @@ def __init__(self, **kwargs):
                         self.spin_type,
                     ]
                 ),
+                ipw.HBox(
+                    children=[
+                        ipw.Label(
+                            "Total charge:",
+                            layout=ipw.Layout(
+                                justify_content="flex-start", width="120px"
+                            ),
+                        ),
+                        self.tot_charge,
+                    ]
+                ),
                 self.properties_title,
                 ipw.HTML("Select which properties to calculate:"),
                 ipw.HBox(children=[ipw.HTML("<b>Band structure</b>"), self.bands_run]),
@@ -404,6 +423,7 @@ def set_input_parameters(self, parameters):
             self.workchain_settings.bands_run.value = parameters["run_bands"]
             self.workchain_settings.pdos_run.value = parameters["run_pdos"]
             self.workchain_settings.workchain_protocol.value = parameters["protocol"]
+            self.workchain_settings.tot_charge.value = parameters["tot_charge"]
 
             # Advanced settings
             self.pseudo_family_selector.value = parameters["pseudo_family"]
@@ -774,6 +794,7 @@ def get_input_parameters(self):
             run_bands=self.workchain_settings.bands_run.value,
             run_pdos=self.workchain_settings.pdos_run.value,
             protocol=self.workchain_settings.workchain_protocol.value,
+            tot_charge=self.workchain_settings.total_charge.value,
             # Codes
             pw_code=self.pw_code.value,
             dos_code=self.dos_code.value,
@@ -856,6 +877,14 @@ def update_builder(buildy, resources, npools):
             electronic_type=ElectronicType(parameters["electronic_type"]),
         )
 
+        # Updating tot_charge of the builder
+        builder.relax.base.pw.parameters['SYSTEM']['tot_charge'] = parameters["tot_charge"]
+        builder.bands.bands.pw.parameters['SYSTEM']['tot_charge'] = parameters["tot_charge"]
+        builder.bands.scf.pw.parameters['SYSTEM']['tot_charge'] = parameters["tot_charge"]
+        builder.pdos.scf.pw.parameters['SYSTEM']['tot_charge'] = parameters["tot_charge"]
+        builder.pdos.nscf.pw.parameters['SYSTEM']['tot_charge'] = parameters["tot_charge"]
+
+
         if "kpoints_distance_override" in parameters:
             builder.kpoints_distance_override = Float(
                 parameters["kpoints_distance_override"]

From 644a2fbc2597d26cb7a05f1d2840d7568003540f Mon Sep 17 00:00:00 2001
From: AndresOrtegaGuerrero <oandresg15@gmail.com>
Date: Fri, 31 Mar 2023 07:36:40 +0000
Subject: [PATCH 2/6] adding the tot_charge to the final report

---
 aiidalab_qe/report.py                     | 1 +
 aiidalab_qe/static/workflow_summary.jinja | 6 +++++-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/aiidalab_qe/report.py b/aiidalab_qe/report.py
index b7646c92..8b181d41 100644
--- a/aiidalab_qe/report.py
+++ b/aiidalab_qe/report.py
@@ -42,6 +42,7 @@ def _generate_report_dict(qeapp_wc: WorkChainNode):
     # Material settings
     yield "material_magnetic", builder_parameters["spin_type"]
     yield "electronic_type", builder_parameters["electronic_type"]
+    yield "tot_charge", builder_parameters["tot_charge"]
 
     # Calculation settings
     yield "protocol", builder_parameters["protocol"]
diff --git a/aiidalab_qe/static/workflow_summary.jinja b/aiidalab_qe/static/workflow_summary.jinja
index ba317a40..c556c845 100644
--- a/aiidalab_qe/static/workflow_summary.jinja
+++ b/aiidalab_qe/static/workflow_summary.jinja
@@ -32,7 +32,11 @@
         <td>Electronic type</td>
         <td>{{ electronic_type }}</td>
       </tr>
-
+      <tr>
+        <td>Total Charge</td>
+        <td>{{ tot_charge }}</td>
+      </tr>
+      
     </table>
   </div>
   <div class="column">

From a02923c5136b67dab9f95b9b4021ef99ffe5022b Mon Sep 17 00:00:00 2001
From: AndresOrtegaGuerrero <oandresg15@gmail.com>
Date: Fri, 31 Mar 2023 08:03:24 +0000
Subject: [PATCH 3/6] pre-commit fix

---
 aiidalab_qe/static/workflow_summary.jinja |  2 +-
 aiidalab_qe/steps.py                      | 21 +++++++++++++++------
 2 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/aiidalab_qe/static/workflow_summary.jinja b/aiidalab_qe/static/workflow_summary.jinja
index c556c845..b8d0b26e 100644
--- a/aiidalab_qe/static/workflow_summary.jinja
+++ b/aiidalab_qe/static/workflow_summary.jinja
@@ -36,7 +36,7 @@
         <td>Total Charge</td>
         <td>{{ tot_charge }}</td>
       </tr>
-      
+
     </table>
   </div>
   <div class="column">
diff --git a/aiidalab_qe/steps.py b/aiidalab_qe/steps.py
index bb018001..9ab763d5 100644
--- a/aiidalab_qe/steps.py
+++ b/aiidalab_qe/steps.py
@@ -878,12 +878,21 @@ def update_builder(buildy, resources, npools):
         )
 
         # Updating tot_charge of the builder
-        builder.relax.base.pw.parameters['SYSTEM']['tot_charge'] = parameters["tot_charge"]
-        builder.bands.bands.pw.parameters['SYSTEM']['tot_charge'] = parameters["tot_charge"]
-        builder.bands.scf.pw.parameters['SYSTEM']['tot_charge'] = parameters["tot_charge"]
-        builder.pdos.scf.pw.parameters['SYSTEM']['tot_charge'] = parameters["tot_charge"]
-        builder.pdos.nscf.pw.parameters['SYSTEM']['tot_charge'] = parameters["tot_charge"]
-
+        builder.relax.base.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
+            "tot_charge"
+        ]
+        builder.bands.bands.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
+            "tot_charge"
+        ]
+        builder.bands.scf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
+            "tot_charge"
+        ]
+        builder.pdos.scf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
+            "tot_charge"
+        ]
+        builder.pdos.nscf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
+            "tot_charge"
+        ]
 
         if "kpoints_distance_override" in parameters:
             builder.kpoints_distance_override = Float(

From 397835a9505ba1e5e55af552e23523ab6d386f3d Mon Sep 17 00:00:00 2001
From: AndresOrtegaGuerrero <oandresg15@gmail.com>
Date: Thu, 6 Apr 2023 09:30:47 +0000
Subject: [PATCH 4/6] adding tot_charge in advanced tab

---
 aiidalab_qe/steps.py | 103 ++++++++++++++++++++++++++++++++++++-------
 1 file changed, 88 insertions(+), 15 deletions(-)

diff --git a/aiidalab_qe/steps.py b/aiidalab_qe/steps.py
index 9ab763d5..ce5ba0ab 100644
--- a/aiidalab_qe/steps.py
+++ b/aiidalab_qe/steps.py
@@ -196,6 +196,66 @@ def __init__(self, **kwargs):
             **kwargs,
         )
 
+class PwAdvancedSettings(ipw.VBox):
+
+    title = ipw.HTML(
+        """<div style="padding-top: 0px; padding-bottom: 10px">
+        <h4>Pw Advanced Settings</h4></div>"""
+    )
+    pw_advanced_settings = ipw.HTML(
+        """Select the advanced settings for the <b>pw.x</b> code."""
+    )
+    #set here defaul values for the advanced settings
+    tot_charge_default = 0
+
+    def __init__(self, **kwargs):
+        self.override_pw_advanced_settings = ipw.Checkbox(
+            description="Override",
+            indent=False,
+            value=False,
+        )
+        self.override_tot_charge = ipw.Checkbox(
+            description ="",
+            indent=False,
+            value=False,
+        )
+        
+        self.tot_charge = ipw.IntSlider(
+            value=0,
+            min=-2,
+            max=2,
+            step=1,
+            disabled=False,
+            description="Total charge:",
+            style={"description_width": "initial"},
+        )
+        ipw.dlink(
+            (self.override_pw_advanced_settings, "value"),
+            (self.override_tot_charge, "disabled"),
+            lambda override: not override,
+        )
+        ipw.dlink(
+            (self.override_tot_charge, "value"),
+            (self.tot_charge, "disabled"),
+            lambda override: not override,
+        )
+        self.tot_charge.observe(self.set_pw_settings, "value")
+        self.override_pw_advanced_settings.observe(self.set_pw_settings, "value")
+        super().__init__(
+            children=[
+                self.title,
+                ipw.HBox([self.pw_advanced_settings, self.override_pw_advanced_settings,],layout=ipw.Layout(justify_content="space-between"),),
+                ipw.HBox([self.tot_charge, self.override_tot_charge], layout=ipw.Layout(justify_content="space-between")),
+            ],
+            **kwargs,
+        )
+    def set_pw_settings(self, _=None):
+        self.tot_charge.value = (
+            self.tot_charge.value 
+            if self.pw_advanced_settings.value and self.override_tot_charge.value
+            else self.tot_charge_default
+        )
+
 
 class SmearingSettings(ipw.VBox):
 
@@ -330,6 +390,7 @@ class ConfigureQeAppWorkChainStep(ipw.VBox, WizardAppWidgetStep):
     workchain_settings = traitlets.Instance(WorkChainSettings, allow_none=True)
     kpoints_settings = traitlets.Instance(KpointSettings, allow_none=True)
     smearing_settings = traitlets.Instance(SmearingSettings, allow_none=True)
+    pw_advanced_settings = traitlets.Instance(PwAdvancedSettings, allow_none=True)
     pseudo_family_selector = traitlets.Instance(PseudoFamilySelector, allow_none=True)
 
     def __init__(self, **kwargs):
@@ -341,6 +402,7 @@ def __init__(self, **kwargs):
 
         self.kpoints_settings = KpointSettings()
         self.smearing_settings = SmearingSettings()
+        self.pw_advanced_settings = PwAdvancedSettings()
         self.pseudo_family_selector = PseudoFamilySelector()
 
         ipw.dlink(
@@ -372,6 +434,7 @@ def __init__(self, **kwargs):
                 self.workchain_settings,
                 ipw.VBox(
                     children=[
+                        self.pw_advanced_settings,
                         self.pseudo_family_selector,
                         self.kpoints_settings,
                         self.smearing_settings,
@@ -495,6 +558,7 @@ class SubmitQeAppWorkChainStep(ipw.VBox, WizardAppWidgetStep):
     previous_step_state = traitlets.UseEnum(WizardAppWidgetStep.State)
     workchain_settings = traitlets.Instance(WorkChainSettings, allow_none=True)
     kpoints_settings = traitlets.Instance(KpointSettings, allow_none=True)
+    pw_advanced_settings = traitlets.Instance(PwAdvancedSettings, allow_none=True)
     smearing_settings = traitlets.Instance(SmearingSettings, allow_none=True)
     pseudo_family_selector = traitlets.Instance(PseudoFamilySelector, allow_none=True)
     _submission_blockers = traitlets.List(traitlets.Unicode)
@@ -802,6 +866,14 @@ def get_input_parameters(self):
             # Advanced settings
             pseudo_family=self.pseudo_family_selector.value,
         )
+        #Should we make this logic in the class of advanced settings?
+        if self.pw_advanced_settings.override_protocol_settings.value:
+            parameters["override"] = {"pw": {"parameters": {"SYSTEM": {}}},}
+            if self.pw_advanced_settings.override_tot_charge.value:
+                parameters["override"]["pw"]["parameters"]["SYSTEM"]["tot_charge"] = self.pw_advanced_settings.total_charge.value
+        else:
+            parameters["override"] = None
+
         if self.kpoints_settings.override_protocol_kpoints.value:
             parameters[
                 "kpoints_distance_override"
@@ -871,6 +943,7 @@ def update_builder(buildy, resources, npools):
             dos_code=load_code(parameters["dos_code"]),
             projwfc_code=load_code(parameters["projwfc_code"]),
             protocol=parameters["protocol"],
+            overrides=parameters["override"],
             pseudo_family=parameters["pseudo_family"],
             relax_type=RelaxType(parameters["relax_type"]),
             spin_type=SpinType(parameters["spin_type"]),
@@ -878,21 +951,21 @@ def update_builder(buildy, resources, npools):
         )
 
         # Updating tot_charge of the builder
-        builder.relax.base.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
-            "tot_charge"
-        ]
-        builder.bands.bands.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
-            "tot_charge"
-        ]
-        builder.bands.scf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
-            "tot_charge"
-        ]
-        builder.pdos.scf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
-            "tot_charge"
-        ]
-        builder.pdos.nscf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
-            "tot_charge"
-        ]
+        # builder.relax.base.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
+        #     "tot_charge"
+        # ]
+        # builder.bands.bands.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
+        #     "tot_charge"
+        # ]
+        # builder.bands.scf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
+        #     "tot_charge"
+        # ]
+        # builder.pdos.scf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
+        #     "tot_charge"
+        # ]
+        # builder.pdos.nscf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
+        #     "tot_charge"
+        # ]
 
         if "kpoints_distance_override" in parameters:
             builder.kpoints_distance_override = Float(

From 59ed8957494e3f3bbcd1e8a0277622439435e6e5 Mon Sep 17 00:00:00 2001
From: AndresOrtegaGuerrero <oandresg15@gmail.com>
Date: Thu, 6 Apr 2023 12:43:59 +0000
Subject: [PATCH 5/6] updating tot_charge settings and tot_charge in advanced
 report

---
 aiidalab_qe/parameters/qeapp.yaml         |  1 -
 aiidalab_qe/report.py                     |  4 +-
 aiidalab_qe/static/workflow_summary.jinja |  9 ++-
 aiidalab_qe/steps.py                      | 73 +++++++++--------------
 qe.ipynb                                  |  1 +
 5 files changed, 37 insertions(+), 51 deletions(-)

diff --git a/aiidalab_qe/parameters/qeapp.yaml b/aiidalab_qe/parameters/qeapp.yaml
index 9b62a57b..1af57544 100644
--- a/aiidalab_qe/parameters/qeapp.yaml
+++ b/aiidalab_qe/parameters/qeapp.yaml
@@ -20,4 +20,3 @@ protocol: moderate
 kpoints_distance_override:
 pseudo_family: SSSP/1.2/PBEsol/efficiency
 
-tot_charge: 0
diff --git a/aiidalab_qe/report.py b/aiidalab_qe/report.py
index 8b181d41..f5ca5956 100644
--- a/aiidalab_qe/report.py
+++ b/aiidalab_qe/report.py
@@ -42,7 +42,9 @@ def _generate_report_dict(qeapp_wc: WorkChainNode):
     # Material settings
     yield "material_magnetic", builder_parameters["spin_type"]
     yield "electronic_type", builder_parameters["electronic_type"]
-    yield "tot_charge", builder_parameters["tot_charge"]
+   
+    #Advanced settings
+    yield "tot_charge", builder_parameters.get("tot_charge", None)
 
     # Calculation settings
     yield "protocol", builder_parameters["protocol"]
diff --git a/aiidalab_qe/static/workflow_summary.jinja b/aiidalab_qe/static/workflow_summary.jinja
index b8d0b26e..6c835144 100644
--- a/aiidalab_qe/static/workflow_summary.jinja
+++ b/aiidalab_qe/static/workflow_summary.jinja
@@ -32,11 +32,6 @@
         <td>Electronic type</td>
         <td>{{ electronic_type }}</td>
       </tr>
-      <tr>
-        <td>Total Charge</td>
-        <td>{{ tot_charge }}</td>
-      </tr>
-
     </table>
   </div>
   <div class="column">
@@ -90,6 +85,10 @@
         <td>{{ nscf_kpoints_distance }} &#8491;<sup>-1</sup></td>
       </tr>
       {% endif %}
+      {% if tot_charge %}
+        <td>Total Charge</td>
+        <td>{{ tot_charge }}</td>
+      {% endif %}
     </table>
   </div>
 </div>
diff --git a/aiidalab_qe/steps.py b/aiidalab_qe/steps.py
index ce5ba0ab..b8aa739e 100644
--- a/aiidalab_qe/steps.py
+++ b/aiidalab_qe/steps.py
@@ -108,14 +108,6 @@ def __init__(self, **kwargs):
             style={"description_width": "initial"},
         )
 
-        # tot_charge: total charge of the simulations
-        self.tot_charge = ipw.IntSlider(
-            value=DEFAULT_PARAMETERS["tot_charge"],
-            min=-2,
-            max=2,
-            step=1,
-        )
-
         # Checkbox to see if the band structure should be calculated
         self.bands_run = ipw.Checkbox(
             description="",
@@ -167,17 +159,6 @@ def __init__(self, **kwargs):
                         self.spin_type,
                     ]
                 ),
-                ipw.HBox(
-                    children=[
-                        ipw.Label(
-                            "Total charge:",
-                            layout=ipw.Layout(
-                                justify_content="flex-start", width="120px"
-                            ),
-                        ),
-                        self.tot_charge,
-                    ]
-                ),
                 self.properties_title,
                 ipw.HTML("Select which properties to calculate:"),
                 ipw.HBox(children=[ipw.HTML("<b>Band structure</b>"), self.bands_run]),
@@ -202,7 +183,7 @@ class PwAdvancedSettings(ipw.VBox):
         """<div style="padding-top: 0px; padding-bottom: 10px">
         <h4>Pw Advanced Settings</h4></div>"""
     )
-    pw_advanced_settings = ipw.HTML(
+    description = ipw.HTML(
         """Select the advanced settings for the <b>pw.x</b> code."""
     )
     #set here defaul values for the advanced settings
@@ -244,7 +225,7 @@ def __init__(self, **kwargs):
         super().__init__(
             children=[
                 self.title,
-                ipw.HBox([self.pw_advanced_settings, self.override_pw_advanced_settings,],layout=ipw.Layout(justify_content="space-between"),),
+                ipw.HBox([self.description, self.override_pw_advanced_settings,],layout=ipw.Layout(justify_content="space-between"),),
                 ipw.HBox([self.tot_charge, self.override_tot_charge], layout=ipw.Layout(justify_content="space-between")),
             ],
             **kwargs,
@@ -252,7 +233,7 @@ def __init__(self, **kwargs):
     def set_pw_settings(self, _=None):
         self.tot_charge.value = (
             self.tot_charge.value 
-            if self.pw_advanced_settings.value and self.override_tot_charge.value
+            if self.override_pw_advanced_settings.value and self.override_tot_charge.value
             else self.tot_charge_default
         )
 
@@ -486,7 +467,6 @@ def set_input_parameters(self, parameters):
             self.workchain_settings.bands_run.value = parameters["run_bands"]
             self.workchain_settings.pdos_run.value = parameters["run_pdos"]
             self.workchain_settings.workchain_protocol.value = parameters["protocol"]
-            self.workchain_settings.tot_charge.value = parameters["tot_charge"]
 
             # Advanced settings
             self.pseudo_family_selector.value = parameters["pseudo_family"]
@@ -858,7 +838,7 @@ def get_input_parameters(self):
             run_bands=self.workchain_settings.bands_run.value,
             run_pdos=self.workchain_settings.pdos_run.value,
             protocol=self.workchain_settings.workchain_protocol.value,
-            tot_charge=self.workchain_settings.total_charge.value,
+            
             # Codes
             pw_code=self.pw_code.value,
             dos_code=self.dos_code.value,
@@ -867,10 +847,32 @@ def get_input_parameters(self):
             pseudo_family=self.pseudo_family_selector.value,
         )
         #Should we make this logic in the class of advanced settings?
-        if self.pw_advanced_settings.override_protocol_settings.value:
-            parameters["override"] = {"pw": {"parameters": {"SYSTEM": {}}},}
+        if self.pw_advanced_settings.override_pw_advanced_settings.value:
+            pw_base = {"pw": {"parameters": {"SYSTEM": {}}},}
+
             if self.pw_advanced_settings.override_tot_charge.value:
-                parameters["override"]["pw"]["parameters"]["SYSTEM"]["tot_charge"] = self.pw_advanced_settings.total_charge.value
+                pw_base["pw"]["parameters"]["SYSTEM"]["tot_charge"] = self.pw_advanced_settings.tot_charge.value
+                parameters["tot_charge"] = self.pw_advanced_settings.tot_charge.value # This to be placed in the builder and also for report
+  
+            parameters["override"] = {
+                "relax": {
+                    "base": pw_base,
+                    "base_final_scf": pw_base,
+                },
+                "bands": {
+                    "relax": {
+                        "base": pw_base,
+                        "base_final_scf": pw_base,
+                    },
+                    "scf": pw_base,
+                    "bands": pw_base,
+                },
+                "pdos": {
+                    "scf": pw_base,
+                    "nscf": pw_base,
+                },
+                        
+            }
         else:
             parameters["override"] = None
 
@@ -950,23 +952,6 @@ def update_builder(buildy, resources, npools):
             electronic_type=ElectronicType(parameters["electronic_type"]),
         )
 
-        # Updating tot_charge of the builder
-        # builder.relax.base.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
-        #     "tot_charge"
-        # ]
-        # builder.bands.bands.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
-        #     "tot_charge"
-        # ]
-        # builder.bands.scf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
-        #     "tot_charge"
-        # ]
-        # builder.pdos.scf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
-        #     "tot_charge"
-        # ]
-        # builder.pdos.nscf.pw.parameters["SYSTEM"]["tot_charge"] = parameters[
-        #     "tot_charge"
-        # ]
-
         if "kpoints_distance_override" in parameters:
             builder.kpoints_distance_override = Float(
                 parameters["kpoints_distance_override"]
diff --git a/qe.ipynb b/qe.ipynb
index 729cfa74..9ed6d329 100644
--- a/qe.ipynb
+++ b/qe.ipynb
@@ -83,6 +83,7 @@
     "ipw.dlink((configure_qe_app_work_chain_step, 'state'), (submit_qe_app_work_chain_step, 'previous_step_state'))\n",
     "ipw.dlink((configure_qe_app_work_chain_step, 'workchain_settings'), (submit_qe_app_work_chain_step, 'workchain_settings'))\n",
     "ipw.dlink((configure_qe_app_work_chain_step, 'kpoints_settings'), (submit_qe_app_work_chain_step, 'kpoints_settings'))\n",
+    "ipw.dlink((configure_qe_app_work_chain_step, 'pw_advanced_settings'), (submit_qe_app_work_chain_step, 'pw_advanced_settings'))\n",
     "ipw.dlink((configure_qe_app_work_chain_step, 'smearing_settings'), (submit_qe_app_work_chain_step, 'smearing_settings'))\n",
     "ipw.dlink((configure_qe_app_work_chain_step, 'pseudo_family_selector'), (submit_qe_app_work_chain_step, 'pseudo_family_selector'))\n",
     "\n",

From 4b056952b10f06d414921a2ff14eda63b0e18f55 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 6 Apr 2023 12:44:20 +0000
Subject: [PATCH 6/6] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 aiidalab_qe/parameters/qeapp.yaml |  1 -
 aiidalab_qe/report.py             |  4 +--
 aiidalab_qe/steps.py              | 50 ++++++++++++++++++++-----------
 3 files changed, 35 insertions(+), 20 deletions(-)

diff --git a/aiidalab_qe/parameters/qeapp.yaml b/aiidalab_qe/parameters/qeapp.yaml
index 1af57544..16bc9518 100644
--- a/aiidalab_qe/parameters/qeapp.yaml
+++ b/aiidalab_qe/parameters/qeapp.yaml
@@ -19,4 +19,3 @@ electronic_type: metal
 protocol: moderate
 kpoints_distance_override:
 pseudo_family: SSSP/1.2/PBEsol/efficiency
-
diff --git a/aiidalab_qe/report.py b/aiidalab_qe/report.py
index f5ca5956..d4f8f918 100644
--- a/aiidalab_qe/report.py
+++ b/aiidalab_qe/report.py
@@ -42,8 +42,8 @@ def _generate_report_dict(qeapp_wc: WorkChainNode):
     # Material settings
     yield "material_magnetic", builder_parameters["spin_type"]
     yield "electronic_type", builder_parameters["electronic_type"]
-   
-    #Advanced settings
+
+    # Advanced settings
     yield "tot_charge", builder_parameters.get("tot_charge", None)
 
     # Calculation settings
diff --git a/aiidalab_qe/steps.py b/aiidalab_qe/steps.py
index b8aa739e..287f2f97 100644
--- a/aiidalab_qe/steps.py
+++ b/aiidalab_qe/steps.py
@@ -177,16 +177,15 @@ def __init__(self, **kwargs):
             **kwargs,
         )
 
+
 class PwAdvancedSettings(ipw.VBox):
 
     title = ipw.HTML(
         """<div style="padding-top: 0px; padding-bottom: 10px">
         <h4>Pw Advanced Settings</h4></div>"""
     )
-    description = ipw.HTML(
-        """Select the advanced settings for the <b>pw.x</b> code."""
-    )
-    #set here defaul values for the advanced settings
+    description = ipw.HTML("""Select the advanced settings for the <b>pw.x</b> code.""")
+    # set here defaul values for the advanced settings
     tot_charge_default = 0
 
     def __init__(self, **kwargs):
@@ -196,11 +195,11 @@ def __init__(self, **kwargs):
             value=False,
         )
         self.override_tot_charge = ipw.Checkbox(
-            description ="",
+            description="",
             indent=False,
             value=False,
         )
-        
+
         self.tot_charge = ipw.IntSlider(
             value=0,
             min=-2,
@@ -225,15 +224,26 @@ def __init__(self, **kwargs):
         super().__init__(
             children=[
                 self.title,
-                ipw.HBox([self.description, self.override_pw_advanced_settings,],layout=ipw.Layout(justify_content="space-between"),),
-                ipw.HBox([self.tot_charge, self.override_tot_charge], layout=ipw.Layout(justify_content="space-between")),
+                ipw.HBox(
+                    [
+                        self.description,
+                        self.override_pw_advanced_settings,
+                    ],
+                    layout=ipw.Layout(justify_content="space-between"),
+                ),
+                ipw.HBox(
+                    [self.tot_charge, self.override_tot_charge],
+                    layout=ipw.Layout(justify_content="space-between"),
+                ),
             ],
             **kwargs,
         )
+
     def set_pw_settings(self, _=None):
         self.tot_charge.value = (
-            self.tot_charge.value 
-            if self.override_pw_advanced_settings.value and self.override_tot_charge.value
+            self.tot_charge.value
+            if self.override_pw_advanced_settings.value
+            and self.override_tot_charge.value
             else self.tot_charge_default
         )
 
@@ -838,7 +848,6 @@ def get_input_parameters(self):
             run_bands=self.workchain_settings.bands_run.value,
             run_pdos=self.workchain_settings.pdos_run.value,
             protocol=self.workchain_settings.workchain_protocol.value,
-            
             # Codes
             pw_code=self.pw_code.value,
             dos_code=self.dos_code.value,
@@ -846,14 +855,22 @@ def get_input_parameters(self):
             # Advanced settings
             pseudo_family=self.pseudo_family_selector.value,
         )
-        #Should we make this logic in the class of advanced settings?
+        # Should we make this logic in the class of advanced settings?
         if self.pw_advanced_settings.override_pw_advanced_settings.value:
-            pw_base = {"pw": {"parameters": {"SYSTEM": {}}},}
+            pw_base = {
+                "pw": {"parameters": {"SYSTEM": {}}},
+            }
 
             if self.pw_advanced_settings.override_tot_charge.value:
-                pw_base["pw"]["parameters"]["SYSTEM"]["tot_charge"] = self.pw_advanced_settings.tot_charge.value
-                parameters["tot_charge"] = self.pw_advanced_settings.tot_charge.value # This to be placed in the builder and also for report
-  
+                pw_base["pw"]["parameters"]["SYSTEM"][
+                    "tot_charge"
+                ] = self.pw_advanced_settings.tot_charge.value
+                parameters[
+                    "tot_charge"
+                ] = (
+                    self.pw_advanced_settings.tot_charge.value
+                )  # This to be placed in the builder and also for report
+
             parameters["override"] = {
                 "relax": {
                     "base": pw_base,
@@ -871,7 +888,6 @@ def get_input_parameters(self):
                     "scf": pw_base,
                     "nscf": pw_base,
                 },
-                        
             }
         else:
             parameters["override"] = None