From f64607c601f0f468902050e167b5617d415a37db Mon Sep 17 00:00:00 2001
From: AndresOrtegaGuerrero
<34098967+AndresOrtegaGuerrero@users.noreply.github.com>
Date: Thu, 15 Feb 2024 15:25:41 +0100
Subject: [PATCH] Adding Van del Waals Correction widget (Adv Setting) (#620)
---
src/aiidalab_qe/app/configuration/advanced.py | 50 +++++++++++++++++++
src/aiidalab_qe/app/parameters/qeapp.yaml | 1 +
src/aiidalab_qe/app/result/summary_viewer.py | 13 +++++
.../app/static/workflow_summary.jinja | 4 ++
tests/conftest.py | 2 +
tests/test_result/test_summary_report.yml | 1 +
tests/test_submit_qe_workchain.py | 3 ++
.../test_create_builder_default.yml | 5 ++
8 files changed, 79 insertions(+)
diff --git a/src/aiidalab_qe/app/configuration/advanced.py b/src/aiidalab_qe/app/configuration/advanced.py
index df75c76d9..99becc4fd 100644
--- a/src/aiidalab_qe/app/configuration/advanced.py
+++ b/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. """
)
+ 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()
diff --git a/src/aiidalab_qe/app/parameters/qeapp.yaml b/src/aiidalab_qe/app/parameters/qeapp.yaml
index 024e1ec6c..616f4286c 100644
--- a/src/aiidalab_qe/app/parameters/qeapp.yaml
+++ b/src/aiidalab_qe/app/parameters/qeapp.yaml
@@ -21,6 +21,7 @@ advanced:
functional: PBEsol
accuracy: efficiency
tot_charge: 0
+ vdw_corr: none
## Codes
codes:
diff --git a/src/aiidalab_qe/app/result/summary_viewer.py b/src/aiidalab_qe/app/result/summary_viewer.py
index 45880cbc8..1340eefcd 100644
--- a/src/aiidalab_qe/app/result/summary_viewer.py
+++ b/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"
)
diff --git a/src/aiidalab_qe/app/static/workflow_summary.jinja b/src/aiidalab_qe/app/static/workflow_summary.jinja
index 5ff5d32d8..33630127d 100644
--- a/src/aiidalab_qe/app/static/workflow_summary.jinja
+++ b/src/aiidalab_qe/app/static/workflow_summary.jinja
@@ -100,6 +100,10 @@
| Total Charge |
{{ tot_charge }} |
+
+ | Van der Waals Correction |
+ {{ vdw_corr }} |
+
| Initial Magnetic Moments |
{{ initial_magnetic_moments }} |
diff --git a/tests/conftest.py b/tests/conftest.py
index 076ac04c8..a83ac32cf 100644
--- a/tests/conftest.py
+++ b/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
diff --git a/tests/test_result/test_summary_report.yml b/tests/test_result/test_summary_report.yml
index da8360942..734ec9e11 100644
--- a/tests/test_result/test_summary_report.yml
+++ b/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
diff --git a/tests/test_submit_qe_workchain.py b/tests/test_submit_qe_workchain.py
index 9f71ffb4d..5bde299c2 100644
--- a/tests/test_submit_qe_workchain.py
+++ b/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 (
diff --git a/tests/test_submit_qe_workchain/test_create_builder_default.yml b/tests/test_submit_qe_workchain/test_create_builder_default.yml
index b2af426fc..868198e3b 100644
--- a/tests/test_submit_qe_workchain/test_create_builder_default.yml
+++ b/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: