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Adding Symprec Widget (#85)
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* Adding Symprec Widget
---------

Co-authored-by: mikibonacci <[email protected]>
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@AndresOrtegaGuerrero @mikibonacci
AndresOrtegaGuerrero and mikibonacci authored Sep 23, 2024
1 parent 7ec2adb commit 9881c23
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Showing 8 changed files with 105 additions and 29 deletions.
4 changes: 1 addition & 3 deletions src/aiidalab_qe_vibroscopy/app/result.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,6 @@ def _update_view(self):
_bands_plot_view_class.update_layout(
yaxis=dict(autorange=True), # Automatically scale the y-axis
)


# the data (bands and pdos) are the first element of the lists phonon_data["bands"] and phonon_data["pdos"]!
downloadBandsPdos_widget = DownloadBandsPdosWidget(
Expand Down Expand Up @@ -209,14 +208,13 @@ def _update_view(self):
dielectric_results = DielectricResults(dielectric_data)
children_result_widget += (dielectric_results,)
tab_titles.append("Dielectric properties")

# euphonic
if ins_data:
intensity_maps = EuphonicSuperWidget(fc=ins_data["fc"])
children_result_widget += (intensity_maps,)
tab_titles.append("Inelastic Neutrons")


self.result_tabs = ipw.Tab(children=children_result_widget)

for title_index in range(len(tab_titles)):
Expand Down
11 changes: 11 additions & 0 deletions src/aiidalab_qe_vibroscopy/app/settings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -143,6 +143,13 @@ def change_supercell(_=None):
self.supercell_widget.layout.display = "block"
# end Supercell.

self.symmetry_symprec = ipw.FloatText(
value=1e-5,
description="Symmetry tolerance (symprec):",
style={"description_width": "initial"},
layout={"width": "300px"},
)

self.children = [
ipw.VBox(
[
Expand All @@ -167,6 +174,7 @@ def change_supercell(_=None):
],
),
self.supercell_widget,
self.symmetry_symprec,
]

super().__init__(**kwargs)
Expand Down Expand Up @@ -208,16 +216,19 @@ def get_panel_value(self):
return {
"simulation_mode": self.calc_options.value,
"supercell_selector": self.supercell,
"symmetry_symprec": self.symmetry_symprec.value,
}

def set_panel_value(self, input_dict):
"""Load a dictionary with the input parameters for the plugin."""
self.calc_options.value = input_dict.get("simulation_mode", 1)
self.supercell = input_dict.get("supercell_selector", [2, 2, 2])
self.symmetry_symprec.value = input_dict.get("symmetry_symprec", 1e-5)
self._sc_x.value, self._sc_y.value, self._sc_z.value = self.supercell

def reset(self):
"""Reset the panel"""
self.calc_options.value = 1
self.supercell = [2, 2, 2]
self.symmetry_symprec.value = 1e-5
self._sc_x.value, self._sc_y.value, self._sc_z.value = self.supercell
1 change: 1 addition & 0 deletions src/aiidalab_qe_vibroscopy/app/workchain.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,7 @@ def get_builder(codes, structure, parameters):
"supercell_matrix": supercell_matrix,
},
"dielectric": {"scf": deepcopy(parameters["advanced"])},
"symmetry": {"symprec": parameters["vibronic"]["symmetry_symprec"]},
}

# Update code information with resource configurations
Expand Down
59 changes: 41 additions & 18 deletions src/aiidalab_qe_vibroscopy/workflows/vibroworkchain.py
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Original file line number Diff line number Diff line change
Expand Up @@ -439,18 +439,24 @@ def get_builder_from_protocol(
if structure.pbc == (True, False, False):
builder.phonopy_bands_dict = Dict(
dict={
"symmetry_tolerance": 1e-3,
"symmetry_tolerance": overrides["symmetry"]["symprec"],
"band": [0, 0, 0, 1 / 2, 0, 0],
"band_points": 100,
"band_labels": [GAMMA, "$\\mathrm{X}$"],
}
)
# change symprec for 1D materials to 1e-3
builder.phonopy_pdos_dict["symmetry_tolerance"] = 1e-3
builder.phonopy_thermo_dict["symmetry_tolerance"] = 1e-3
builder.harmonic.symmetry.symprec = orm.Float(1e-3)
builder.phonopy_pdos_dict["symmetry_tolerance"] = overrides[
"symmetry"
]["symprec"] # 1e-3
builder.phonopy_thermo_dict["symmetry_tolerance"] = overrides[
"symmetry"
]["symprec"] # 1e-3
builder.harmonic.symmetry.symprec = orm.Float(
overrides["symmetry"]["symprec"]
)
builder.harmonic.phonon.phonopy.parameters = orm.Dict(
{"symmetry_tolerance": 1e-3}
{"symmetry_tolerance": overrides["symmetry"]["symprec"]}
)

elif structure.pbc == (True, True, False):
Expand All @@ -475,8 +481,12 @@ def get_builder_from_protocol(
)
else:
builder.phonopy_bands_dict = Dict(dict=PhononProperty.BANDS.value)
builder.phonopy_bands_dict["symmetry_tolerance"] = overrides[
"symmetry"
]["symprec"]
builder.phonopy_pdos_dict = Dict(
dict={
"symmetry_tolerance": overrides["symmetry"]["symprec"],
"pdos": "auto",
"mesh": 150, # 1000 is too heavy
"write_mesh": False,
Expand All @@ -485,6 +495,7 @@ def get_builder_from_protocol(

builder.phonopy_thermo_dict = Dict(
dict={
"symmetry_tolerance": overrides["symmetry"]["symprec"],
"tprop": True,
"mesh": 200, # 1000 is too heavy
"write_mesh": False,
Expand Down Expand Up @@ -517,9 +528,11 @@ def get_builder_from_protocol(
builder_iraman.dielectric.pop("kpoints_parallel_distance", None)

if structure.pbc == (True, False, False):
builder_iraman.symmetry.symprec = orm.Float(1e-3)
builder_iraman.symmetry.symprec = orm.Float(
overrides["symmetry"]["symprec"]
)
builder_iraman.phonon.phonopy.parameters = orm.Dict(
{"symmetry_tolerance": 1e-3}
{"symmetry_tolerance": overrides["symmetry"]["symprec"]}
)

builder.iraman = builder_iraman
Expand All @@ -544,9 +557,8 @@ def get_builder_from_protocol(
builder_phonon.phonopy.settings = Dict(dict={"keep_phonopy_yaml": True})

# MBO: I do not understand why I have to do this, but it works
symmetry = builder_phonon.pop("symmetry")
builder.phonon = builder_phonon
builder.phonon.symmetry = symmetry
builder.phonon.symmetry = overrides["symmetry"]

# Adding the bands and pdos inputs.
if structure.pbc != (True, True, True):
Expand Down Expand Up @@ -574,18 +586,24 @@ def get_builder_from_protocol(
if structure.pbc == (True, False, False):
builder.phonopy_bands_dict = Dict(
dict={
"symmetry_tolerance": 1e-3,
"symmetry_tolerance": overrides["symmetry"]["symprec"],
"band": [0, 0, 0, 1 / 2, 0, 0],
"band_points": 100,
"band_labels": [GAMMA, "$\\mathrm{X}$"],
}
)
# change symprec for 1D materials to 1e-3
builder.phonopy_pdos_dict["symmetry_tolerance"] = 1e-3
builder.phonopy_thermo_dict["symmetry_tolerance"] = 1e-3
builder.phonon.symmetry.symprec = orm.Float(1e-3)
builder.phonopy_pdos_dict["symmetry_tolerance"] = overrides[
"symmetry"
]["symprec"]
builder.phonopy_thermo_dict["symmetry_tolerance"] = overrides[
"symmetry"
]["symprec"]
builder.phonon.symmetry.symprec = orm.Float(
overrides["symmetry"]["symprec"]
)
builder.phonon.phonopy.parameters = orm.Dict(
{"symmetry_tolerance": 1e-3}
{"symmetry_tolerance": overrides["symmetry"]["symprec"]}
)

elif structure.pbc == (True, True, False):
Expand All @@ -610,8 +628,12 @@ def get_builder_from_protocol(
)
else:
builder.phonopy_bands_dict = Dict(dict=PhononProperty.BANDS.value)
builder.phonopy_bands_dict["symmetry_tolerance"] = overrides[
"symmetry"
]["symprec"]
builder.phonopy_pdos_dict = Dict(
dict={
"symmetry_tolerance": overrides["symmetry"]["symprec"],
"pdos": "auto",
"mesh": 150, # 1000 is too heavy
"write_mesh": False,
Expand All @@ -620,6 +642,7 @@ def get_builder_from_protocol(

builder.phonopy_thermo_dict = Dict(
dict={
"symmetry_tolerance": overrides["symmetry"]["symprec"],
"tprop": True,
"mesh": 200, # 1000 is too heavy
"write_mesh": False,
Expand All @@ -635,12 +658,10 @@ def get_builder_from_protocol(
**kwargs,
)

# MBO: I do not understand why I have to do this, but it works. maybe related with excludes.
symmetry = builder_dielectric.pop("symmetry")
if structure.pbc != (True, True, True):
builder_dielectric.pop("kpoints_parallel_distance", None)
builder.dielectric = builder_dielectric
builder.dielectric.symmetry = symmetry
builder.dielectric.symmetry = overrides["symmetry"]
builder.dielectric.property = dielectric_property

# Deleting the not needed parts of the builder:
Expand All @@ -659,7 +680,9 @@ def get_builder_from_protocol(
"num_mpiprocs_per_machine": 1,
}
if structure.pbc == (True, False, False):
builder.phonopy_calc.parameters = orm.Dict({"symmetry_tolerance": 1e-3})
builder.phonopy_calc.parameters = orm.Dict(
{"symmetry_tolerance": overrides["symmetry"]["symprec"]}
)
builder.structure = structure

return builder
Expand Down
24 changes: 19 additions & 5 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,14 +48,15 @@ def _fixture_code(entry_point_name):
def generate_structure_data():
"""generate a `StructureData` object."""

def _generate_structure_data(name="silicon", pbc=(True, True, True)):
def _generate_structure_data(name="silicon"):
if name == "silicon":
structure = orm.StructureData(
cell=[
[3.84737, 0.0, 0.0],
[1.923685, 3.331920, 0.0],
[1.923685, 1.110640, 3.141364],
]
],
pbc=(True, True, True),
)
structure.append_atom(position=(0.0, 0.0, 0.0), symbols="Si")
structure.append_atom(position=(1.923685, 1.110640, 0.785341), symbols="Si")
Expand All @@ -65,7 +66,8 @@ def _generate_structure_data(name="silicon", pbc=(True, True, True)):
[4.18, 0.0, 0.0],
[0.0, 4.18, 0.0],
[0.0, 0.0, 2.66],
]
],
pbc=(True, True, True),
)
structure.append_atom(position=(0.0, 0.0, 0.0), symbols="Si")
structure.append_atom(position=(2.09, 2.09, 1.33), symbols="Si")
Expand All @@ -88,11 +90,23 @@ def _generate_structure_data(name="silicon", pbc=(True, True, True)):
["O", "O", (0, 0, 10.201532881212)],
["Li", "Li", (0, 0, 6.9018028772754)],
]
structure = orm.StructureData(cell=cell)
structure = orm.StructureData(cell=cell, pbc=(True, True, True))

for site in sites:
structure.append_atom(position=site[2], symbols=site[0], name=site[1])
structure.pbc = pbc

elif name == "2D-xy-arsenic":
cell = [[3.61, 0, 0], [-1.80, 3.13, 0], [0, 0, 21.3]]
structure = orm.StructureData(cell=cell, pbc=(True, True, False))
structure.append_atom(
position=(1.804, 1.042, 11.352), symbols="As", name="As"
)
structure.append_atom(position=(0, 2.083, 9.960), symbols="As", name="As")

elif name == "1D-x-carbon":
cell = [[4.2, 0, 0], [0, 20, 0], [0, 0, 20]]
structure = orm.StructureData(cell=cell, pbc=(True, False, False))
structure.append_atom(position=(0, 0, 0), symbols="C", name="C")

return structure

Expand Down
28 changes: 28 additions & 0 deletions tests/test_settings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,3 +47,31 @@ def test_settings():
parameters = configure_step.settings["vibronic"].get_panel_value()
assert parameters["simulation_mode"] == 1
assert parameters["supercell_selector"] == [2, 2, 2]


@pytest.mark.usefixtures("sssp")
def test_xy_settings(generate_structure_data):
"""Test the settings of the vibroscopy app."""

from aiidalab_qe.app.configuration import ConfigureQeAppWorkChainStep

configure_step = ConfigureQeAppWorkChainStep()
structure = generate_structure_data("2D-xy-arsenic")
configure_step.input_structure = structure
configure_step.workchain_settings.properties["vibronic"].run.value = True
parameters = configure_step.settings["vibronic"].get_panel_value()
assert parameters["supercell_selector"] == [2, 2, 1]


@pytest.mark.usefixtures("sssp")
def test_x_settings(generate_structure_data):
"""Test the settings of the vibroscopy app."""

from aiidalab_qe.app.configuration import ConfigureQeAppWorkChainStep

configure_step = ConfigureQeAppWorkChainStep()
structure = generate_structure_data("1D-x-carbon")
configure_step.input_structure = structure
configure_step.workchain_settings.properties["vibronic"].run.value = True
parameters = configure_step.settings["vibronic"].get_panel_value()
assert parameters["supercell_selector"] == [2, 1, 1]
2 changes: 1 addition & 1 deletion tests/test_submit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ def test_create_builder_default(
submit_step.codes["dielectric"].value = pw_code.uuid
submit_step.codes["phonopy"].value = phonopy_code.uuid

submit_step.codes["pw"].num_cpus.value = 10
submit_step.codes["pw"].num_cpus.value = 8
submit_step.codes["phonon"].num_cpus.value = 2
submit_step.codes["dielectric"].num_cpus.value = 3

Expand Down
5 changes: 3 additions & 2 deletions tests/test_submit/test_create_builder_default.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,18 +39,19 @@ codes:
nodes: 1
ntasks_per_node: 1
pw:
cpus: 10
cpus: 8
cpus_per_task: 1
max_wallclock_seconds: 43200
nodes: 1
ntasks_per_node: 10
ntasks_per_node: 8
parallelization: {}
vibronic:
simulation_mode: 1
supercell_selector:
- 2
- 2
- 2
symmetry_symprec: 1.0e-05
workchain:
electronic_type: metal
properties:
Expand Down

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