From 2c5ca5543ed3f63707936e3dcc2b3610774b46c8 Mon Sep 17 00:00:00 2001
From: AndresOrtegaGuerrero
<34098967+AndresOrtegaGuerrero@users.noreply.github.com>
Date: Fri, 5 Apr 2024 14:43:53 +0200
Subject: [PATCH] Fix tot magnetization (#512)
* updating Magnetization widget, and including logic for insulator
* adapting logic of bands and pdos for bandspdoswidget
* starting_magnetization as default
---
src/aiidalab_qe/app/configuration/advanced.py | 146 ++++++++++++++----
src/aiidalab_qe/app/result/summary_viewer.py | 4 +
.../app/static/workflow_summary.jinja | 8 +
src/aiidalab_qe/common/bandpdoswidget.py | 115 +++++++++++---
src/aiidalab_qe/plugins/bands/workchain.py | 5 +
src/aiidalab_qe/plugins/pdos/workchain.py | 7 +
src/aiidalab_qe/workflows/__init__.py | 9 ++
tests/conftest.py | 20 ++-
tests/test_result.py | 2 +-
tests/test_result/test_summary_report.yml | 1 +
10 files changed, 260 insertions(+), 57 deletions(-)
diff --git a/src/aiidalab_qe/app/configuration/advanced.py b/src/aiidalab_qe/app/configuration/advanced.py
index 0140685f2..ad2b33264 100644
--- a/src/aiidalab_qe/app/configuration/advanced.py
+++ b/src/aiidalab_qe/app/configuration/advanced.py
@@ -211,6 +211,11 @@ def _update_input_structure(self, change):
self.magnetization.input_structure = None
self.pseudo_setter.structure = None
+ @tl.observe("electronic_type")
+ def _electronic_type_changed(self, change):
+ """Input electronic_type changed, update the widget values."""
+ self.magnetization.electronic_type = change["new"]
+
@tl.observe("protocol")
def _protocol_changed(self, _):
"""Input protocol changed, update the widget values."""
@@ -255,17 +260,16 @@ def get_panel_value(self):
# XXX: start from parameters = {} and then bundle the settings by purposes (e.g. pw, bands, etc.)
parameters = {
"initial_magnetic_moments": None,
- "pw": {
- "parameters": {
- "SYSTEM": {},
- },
- },
+ "pw": {"parameters": {"SYSTEM": {}}},
+ "clean_workdir": self.clean_workdir.value,
+ "pseudo_family": self.pseudo_family_selector.value,
+ "kpoints_distance": self.value.get("kpoints_distance"),
}
- # add clean_workdir to the parameters
- parameters["clean_workdir"] = self.clean_workdir.value
- # add the pseudo_family to the parameters
- parameters["pseudo_family"] = self.pseudo_family_selector.value
+ # Set total charge
+ parameters["pw"]["parameters"]["SYSTEM"]["tot_charge"] = self.total_charge.value
+
+ # Set the pseudos
if self.pseudo_setter.pseudos:
parameters["pw"]["pseudos"] = self.pseudo_setter.pseudos
parameters["pw"]["parameters"]["SYSTEM"]["ecutwfc"] = (
@@ -303,8 +307,35 @@ def get_panel_value(self):
self.smearing.degauss_value
)
+ # Set tot_magnetization for collinear simulations.
+ if self.spin_type == "collinear":
+ # Conditions for metallic systems. Select the magnetization type and set the value if override is True
+ if self.electronic_type == "metal" and self.override.value is True:
+ self.set_metallic_magnetization(parameters)
+ # Conditions for insulator systems. Default value is 0.0
+ elif self.electronic_type == "insulator":
+ self.set_insulator_magnetization(parameters)
+
return parameters
+ def set_insulator_magnetization(self, parameters):
+ """Set the parameters for collinear insulator calculation. Total magnetization."""
+ parameters["pw"]["parameters"]["SYSTEM"]["tot_magnetization"] = (
+ self.magnetization.tot_magnetization.value
+ )
+
+ def set_metallic_magnetization(self, parameters):
+ """Set the parameters for magnetization calculation in metals"""
+ magnetization_type = self.magnetization.magnetization_type.value
+ if magnetization_type == "tot_magnetization":
+ parameters["pw"]["parameters"]["SYSTEM"]["tot_magnetization"] = (
+ self.magnetization.tot_magnetization.value
+ )
+ else:
+ parameters["initial_magnetic_moments"] = (
+ self.magnetization.get_magnetization()
+ )
+
def set_panel_value(self, parameters):
"""Set the panel value from the given parameters."""
@@ -338,11 +369,18 @@ def set_panel_value(self, parameters):
parameters["pw"]["parameters"]["SYSTEM"].get("vdw_corr", "none"),
)
+ # Logic to set the magnetization
if parameters.get("initial_magnetic_moments"):
self.magnetization._set_magnetization_values(
parameters.get("initial_magnetic_moments")
)
+ if "tot_magnetization" in parameters["pw"]["parameters"]["SYSTEM"]:
+ self.magnetization.magnetization_type.value = "tot_magnetization"
+ self.magnetization._set_tot_magnetization(
+ parameters["pw"]["parameters"]["SYSTEM"]["tot_magnetization"]
+ )
+
def reset(self):
"""Reset the widget and the traitlets"""
@@ -363,7 +401,11 @@ def reset(self):
self.override.value = False
self.smearing.reset()
# reset the pseudo setter
- self.pseudo_setter._reset()
+ if self.input_structure is None:
+ self.pseudo_setter.structure = None
+ self.pseudo_setter._reset()
+ else:
+ self.pseudo_setter._reset()
# reset the magnetization
self.magnetization.reset()
# reset mesh grid
@@ -387,10 +429,13 @@ def _display_mesh(self, _=None):
class MagnetizationSettings(ipw.VBox):
- """Widget to set the initial magnetic moments for each kind names defined in the StructureData (StructureDtaa.get_kind_names())
+ """Widget to set the type of magnetization used in the calculation:
+ 1) Tot_magnetization: Total majority spin charge - minority spin charge.
+ 2) Starting magnetization: Starting spin polarization on atomic type 'i' in a spin polarized (LSDA or noncollinear/spin-orbit) calculation.
+
+ For Starting magnetization you can set each kind names defined in the StructureData (StructureDtaa.get_kind_names())
Usually these are the names of the elements in the StructureData
(For example 'C' , 'N' , 'Fe' . However the StructureData can have defined kinds like 'Fe1' and 'Fe2')
-
The widget generate a dictionary that can be used to set initial_magnetic_moments in the builder of PwBaseWorkChain
Attributes:
@@ -398,30 +443,45 @@ class MagnetizationSettings(ipw.VBox):
"""
input_structure = tl.Instance(orm.StructureData, allow_none=True)
-
+ electronic_type = tl.Unicode()
disabled = tl.Bool()
+ _DEFAULT_TOT_MAGNETIZATION = 0.0
+ _DEFAULT_DESCRIPTION = "Magnetization: Input structure not confirmed"
def __init__(self, **kwargs):
self.input_structure = orm.StructureData()
self.input_structure_labels = []
- self.description = ipw.HTML(
- "Define magnetization: Input structure not confirmed"
+ self.tot_magnetization = ipw.BoundedIntText(
+ min=0,
+ max=100,
+ step=1,
+ value=self._DEFAULT_TOT_MAGNETIZATION,
+ disabled=True,
+ description="Total magnetization:",
+ style={"description_width": "initial"},
+ )
+ self.magnetization_type = ipw.ToggleButtons(
+ options=[
+ ("Starting Magnetization", "starting_magnetization"),
+ ("Tot. Magnetization", "tot_magnetization"),
+ ],
+ value="starting_magnetization",
+ style={"description_width": "initial"},
)
+ self.description = ipw.HTML(self._DEFAULT_DESCRIPTION)
self.kinds = self.create_kinds_widget()
self.kinds_widget_out = ipw.Output()
+ self.magnetization_out = ipw.Output()
+ self.magnetization_type.observe(self._render, "value")
super().__init__(
children=[
- ipw.HBox(
- [
- self.description,
- self.kinds_widget_out,
- ],
- ),
+ self.description,
+ self.magnetization_out,
+ self.kinds_widget_out,
],
layout=ipw.Layout(justify_content="space-between"),
**kwargs,
)
- self.display_kinds()
@tl.observe("disabled")
def _disabled_changed(self, _):
@@ -429,19 +489,19 @@ def _disabled_changed(self, _):
if hasattr(self.kinds, "children") and self.kinds.children:
for i in range(len(self.kinds.children)):
self.kinds.children[i].disabled = self.disabled
+ self.tot_magnetization.disabled = self.disabled
+ self.magnetization_type.disabled = self.disabled
def reset(self):
self.disabled = True
+ self.tot_magnetization.value = self._DEFAULT_TOT_MAGNETIZATION
+ #
if self.input_structure is None:
- self.description.value = (
- "Define magnetization: Input structure not confirmed"
- )
+ self.description.value = self._DEFAULT_DESCRIPTION
self.kinds = None
- with self.kinds_widget_out:
- clear_output()
-
else:
- self.update_kinds_widget()
+ self.description.value = "Magnetization"
+ self.kinds = self.create_kinds_widget()
def create_kinds_widget(self):
if self.input_structure_labels:
@@ -462,11 +522,30 @@ def create_kinds_widget(self):
return kinds_widget
+ @tl.observe("electronic_type")
+ def _electronic_type_changed(self, change):
+ with self.magnetization_out:
+ clear_output()
+ if change["new"] == "metal":
+ display(self.magnetization_type)
+ self._render({"new": self.magnetization_type.value})
+ else:
+ display(self.tot_magnetization)
+ with self.kinds_widget_out:
+ clear_output()
+
def update_kinds_widget(self):
self.input_structure_labels = self.input_structure.get_kind_names()
self.kinds = self.create_kinds_widget()
- self.description.value = "Define magnetization: "
- self.display_kinds()
+ self.description.value = "Magnetization"
+
+ def _render(self, value):
+ if value["new"] == "tot_magnetization":
+ with self.kinds_widget_out:
+ clear_output()
+ display(self.tot_magnetization)
+ else:
+ self.display_kinds()
def display_kinds(self):
if "PYTEST_CURRENT_TEST" not in os.environ and self.kinds:
@@ -477,6 +556,7 @@ def display_kinds(self):
def _update_widget(self, change):
self.input_structure = change["new"]
self.update_kinds_widget()
+ self.display_kinds()
def get_magnetization(self):
"""Method to generate the dictionary with the initial magnetic moments"""
@@ -497,6 +577,10 @@ def _set_magnetization_values(self, magnetic_moments):
else:
self.kinds.children[i].value = magnetic_moments
+ def _set_tot_magnetization(self, tot_magnetization):
+ """Set the total magnetization"""
+ self.tot_magnetization.value = tot_magnetization
+
class SmearingSettings(ipw.VBox):
# accept protocol as input and set the values
diff --git a/src/aiidalab_qe/app/result/summary_viewer.py b/src/aiidalab_qe/app/result/summary_viewer.py
index 59f12e2c6..95840dd00 100644
--- a/src/aiidalab_qe/app/result/summary_viewer.py
+++ b/src/aiidalab_qe/app/result/summary_viewer.py
@@ -123,6 +123,10 @@ def generate_report_parameters(qeapp_wc):
report["periodicity"] = PERIODICITY_MAPPING.get(
qeapp_wc.inputs.structure.pbc, "xyz"
)
+ report["tot_magnetization"] = pw_parameters["SYSTEM"].get(
+ "tot_magnetization", False
+ )
+
# hard code bands and pdos
if "bands" in qeapp_wc.inputs:
report["bands_kpoints_distance"] = PwBandsWorkChain.get_protocol_inputs(
diff --git a/src/aiidalab_qe/app/static/workflow_summary.jinja b/src/aiidalab_qe/app/static/workflow_summary.jinja
index 33630127d..dd54e3718 100644
--- a/src/aiidalab_qe/app/static/workflow_summary.jinja
+++ b/src/aiidalab_qe/app/static/workflow_summary.jinja
@@ -104,10 +104,18 @@
| Van der Waals Correction |
{{ vdw_corr }} |
+
+ {% if tot_magnetization %}
+
+ | Total magnetization |
+ {{ tot_magnetization }} |
+
+ {% else %}
| Initial Magnetic Moments |
{{ initial_magnetic_moments }} |
+ {% endif %}
diff --git a/src/aiidalab_qe/common/bandpdoswidget.py b/src/aiidalab_qe/common/bandpdoswidget.py
index 540c2c647..04d43a1b5 100644
--- a/src/aiidalab_qe/common/bandpdoswidget.py
+++ b/src/aiidalab_qe/common/bandpdoswidget.py
@@ -43,12 +43,21 @@ def __init__(self, bands_data=None, pdos_data=None):
self._dos_yaxis = self._dos_yaxis()
def _get_fermi_energy(self):
- fermi_energy = (
- self.pdos_data["fermi_energy"]
- if self.pdos_data
- else self.bands_data["fermi_energy"]
- )
- return fermi_energy
+ """Function to return the Fermi energy information depending on the data available."""
+ fermi_data = {}
+ if self.pdos_data:
+ if "fermi_energy_up" in self.pdos_data:
+ fermi_data["fermi_energy_up"] = self.pdos_data["fermi_energy_up"]
+ fermi_data["fermi_energy_down"] = self.pdos_data["fermi_energy_down"]
+ else:
+ fermi_data["fermi_energy"] = self.pdos_data["fermi_energy"]
+ else:
+ if "fermi_energy_up" in self.bands_data:
+ fermi_data["fermi_energy_up"] = self.bands_data["fermi_energy_up"]
+ fermi_data["fermi_energy_down"] = self.bands_data["fermi_energy_down"]
+ else:
+ fermi_data["fermi_energy"] = self.bands_data["fermi_energy"]
+ return fermi_data
def _band_xaxis(self):
"""Function to return the xaxis for the bands plot."""
@@ -267,7 +276,7 @@ def _add_band_traces(self, fig, paths, plot_type):
scatter_objects.append(
go.Scatter(
x=band["x"],
- y=bands_np - self.fermi_energy,
+ y=bands_np - self.fermi_energy["fermi_energy"],
mode="lines",
line=dict(
color=self.SETTINGS["bands_linecolor"],
@@ -286,16 +295,15 @@ def _add_band_traces(self, fig, paths, plot_type):
color_first_half = self.SETTINGS["bands_up_linecolor"]
# Blue line for the Spin down
color_second_half = self.SETTINGS["bands_down_linecolor"]
-
- for bands, color in zip(
- (first_half, second_half), (color_first_half, color_second_half)
- ):
- for band_values in bands:
- bands_np = np.array(band_values)
+ if "fermi_energy" in self.fermi_energy:
+ for bands, color in zip(
+ (first_half, second_half), (color_first_half, color_second_half)
+ ):
+ bands_np = np.array(bands)
scatter_objects.append(
go.Scatter(
x=band["x"],
- y=bands_np - self.fermi_energy,
+ y=bands_np - self.fermi_energy["fermi_energy"],
mode="lines",
line=dict(
color=color,
@@ -305,6 +313,30 @@ def _add_band_traces(self, fig, paths, plot_type):
showlegend=False,
)
)
+ else:
+ for bands, color, fermi_energy in zip(
+ (first_half, second_half),
+ (color_first_half, color_second_half),
+ (
+ self.fermi_energy["fermi_energy_up"],
+ self.fermi_energy["fermi_energy_down"],
+ ),
+ ):
+ for band_values in bands:
+ bands_np = np.array(band_values)
+ scatter_objects.append(
+ go.Scatter(
+ x=band["x"],
+ y=bands_np - fermi_energy,
+ mode="lines",
+ line=dict(
+ color=color,
+ shape="spline",
+ smoothing=1.3,
+ ),
+ showlegend=False,
+ )
+ )
if plot_type == "bands_only":
fig.add_traces(scatter_objects)
@@ -325,12 +357,41 @@ def _add_dos_traces(self, fig, plot_type):
for i, trace in enumerate(dos_data):
dos_np = np.array(trace["x"])
fill = "tozerox" if plot_type == "combined" else "tozeroy"
- x_data = (
- trace["y"] if plot_type == "combined" else dos_np - self.fermi_energy
- )
- y_data = (
- dos_np - self.fermi_energy if plot_type == "combined" else trace["y"]
- )
+
+ if "fermi_energy" in self.fermi_energy:
+ y_data = (
+ dos_np - self.fermi_energy["fermi_energy"]
+ if plot_type == "combined"
+ else trace["y"]
+ )
+ x_data = (
+ trace["y"]
+ if plot_type == "combined"
+ else dos_np - self.fermi_energy["fermi_energy"]
+ )
+ else:
+ if trace["label"].endswith("(↑)"):
+ y_data = (
+ dos_np - self.fermi_energy["fermi_energy_up"]
+ if plot_type == "combined"
+ else trace["y"]
+ )
+ x_data = (
+ trace["y"]
+ if plot_type == "combined"
+ else dos_np - self.fermi_energy["fermi_energy_up"]
+ )
+ else:
+ y_data = (
+ dos_np - self.fermi_energy["fermi_energy_down"]
+ if plot_type == "combined"
+ else trace["y"]
+ )
+ x_data = (
+ trace["y"]
+ if plot_type == "combined"
+ else dos_np - self.fermi_energy["fermi_energy_down"]
+ )
scatter_objects[i] = go.Scatter(
x=x_data,
y=y_data,
@@ -632,9 +693,15 @@ def get_pdos_data(pdos, group_tag, plot_tag, selected_atoms):
)
data_dict = {
- "fermi_energy": pdos.nscf.output_parameters["fermi_energy"],
"dos": dos,
}
+ if "fermi_energy_up" in pdos.nscf.output_parameters:
+ data_dict["fermi_energy_up"] = pdos.nscf.output_parameters["fermi_energy_up"]
+ data_dict["fermi_energy_down"] = pdos.nscf.output_parameters[
+ "fermi_energy_down"
+ ]
+ else:
+ data_dict["fermi_energy"] = pdos.nscf.output_parameters["fermi_energy"]
return json.loads(json.dumps(data_dict))
@@ -802,7 +869,11 @@ def export_bands_data(outputs, fermi_energy=None):
data = json.loads(outputs.band_structure._exportcontent("json", comments=False)[0])
# The fermi energy from band calculation is not robust.
- data["fermi_energy"] = outputs.band_parameters["fermi_energy"] or fermi_energy
+ if "fermi_energy_up" in outputs.band_parameters:
+ data["fermi_energy_up"] = outputs.band_parameters["fermi_energy_up"]
+ data["fermi_energy_down"] = outputs.band_parameters["fermi_energy_down"]
+ else:
+ data["fermi_energy"] = outputs.band_parameters["fermi_energy"] or fermi_energy
data["pathlabels"] = get_bands_labeling(data)
return data
diff --git a/src/aiidalab_qe/plugins/bands/workchain.py b/src/aiidalab_qe/plugins/bands/workchain.py
index 484ec082f..e60c611f4 100644
--- a/src/aiidalab_qe/plugins/bands/workchain.py
+++ b/src/aiidalab_qe/plugins/bands/workchain.py
@@ -217,6 +217,11 @@ def get_builder(codes, structure, parameters, **kwargs):
bands.pop("relax")
bands.pop("structure", None)
bands.pop("clean_workdir", None)
+
+ if scf_overrides["pw"]["parameters"]["SYSTEM"].get("tot_magnetization") is not None:
+ bands.scf["pw"]["parameters"]["SYSTEM"].pop("starting_magnetization", None)
+ bands.bands["pw"]["parameters"]["SYSTEM"].pop("starting_magnetization", None)
+
return bands
diff --git a/src/aiidalab_qe/plugins/pdos/workchain.py b/src/aiidalab_qe/plugins/pdos/workchain.py
index bd9915f2e..b0c8325e7 100644
--- a/src/aiidalab_qe/plugins/pdos/workchain.py
+++ b/src/aiidalab_qe/plugins/pdos/workchain.py
@@ -66,6 +66,13 @@ def get_builder(codes, structure, parameters, **kwargs):
# pop the inputs that are exclueded from the expose_inputs
pdos.pop("structure", None)
pdos.pop("clean_workdir", None)
+
+ if (
+ scf_overrides["pw"]["parameters"]["SYSTEM"].get("tot_magnetization")
+ is not None
+ ):
+ pdos.scf["pw"]["parameters"]["SYSTEM"].pop("starting_magnetization", None)
+ pdos.nscf["pw"]["parameters"]["SYSTEM"].pop("starting_magnetization", None)
else:
raise ValueError("The dos_code and projwfc_code are required.")
return pdos
diff --git a/src/aiidalab_qe/workflows/__init__.py b/src/aiidalab_qe/workflows/__init__.py
index ac292cb4a..c2d002815 100644
--- a/src/aiidalab_qe/workflows/__init__.py
+++ b/src/aiidalab_qe/workflows/__init__.py
@@ -146,6 +146,15 @@ 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)
diff --git a/tests/conftest.py b/tests/conftest.py
index a83ac32cf..cca1ed0d0 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -603,7 +603,10 @@ def _generate_qeapp_workchain(
run_bands=True,
run_pdos=True,
spin_type="none",
+ electronic_type="metal",
+ magnetization_type="starting_magnetization", # Options: "starting_magnetization", "tot_magnetization"
initial_magnetic_moments=0.0,
+ tot_magnetization=0.0,
):
from copy import deepcopy
@@ -635,9 +638,20 @@ def _generate_qeapp_workchain(
s2.workchain_settings.properties["pdos"].run.value = run_pdos
s2.workchain_settings.workchain_protocol.value = "fast"
s2.workchain_settings.spin_type.value = spin_type
- s2.advanced_settings.magnetization._set_magnetization_values(
- initial_magnetic_moments
- )
+ s2.workchain_settings.electronic_type.value = electronic_type
+ if spin_type == "collinear":
+ s2.advanced_settings.override.value = True
+ magnetization_values = (
+ initial_magnetic_moments
+ if magnetization_type == "starting_magnetization"
+ else tot_magnetization
+ )
+ s2.advanced_settings.magnetization._set_tot_magnetization(
+ tot_magnetization
+ ) if electronic_type == "insulator" else s2.advanced_settings.magnetization._set_magnetization_values(
+ magnetization_values
+ )
+
s2.confirm()
# step 3 setup code and resources
s3: SubmitQeAppWorkChainStep = app.submit_step
diff --git a/tests/test_result.py b/tests/test_result.py
index 7fca7ba85..c6e087d17 100644
--- a/tests/test_result.py
+++ b/tests/test_result.py
@@ -34,7 +34,7 @@ def test_summary_report_advanced_settings(data_regression, generate_qeapp_workch
from aiidalab_qe.app.result.summary_viewer import SummaryView
wkchain = generate_qeapp_workchain(
- spin_type="collinear", initial_magnetic_moments=0.1
+ spin_type="collinear", electronic_type="metal", initial_magnetic_moments=0.1
)
viewer = SummaryView(wkchain.node)
report = viewer.report
diff --git a/tests/test_result/test_summary_report.yml b/tests/test_result/test_summary_report.yml
index 734ec9e11..d41f91b10 100644
--- a/tests/test_result/test_summary_report.yml
+++ b/tests/test_result/test_summary_report.yml
@@ -27,4 +27,5 @@ relaxed: positions_cell
scf_kpoints_distance: 0.5
smearing: cold
tot_charge: 0.0
+tot_magnetization: false
vdw_corr: none