Bump SSSP to 1.3 (#578)

docs/source/development/architecture.rst

@@ -46,7 +46,7 @@ The dictionary has the following structure:
                 },
                 "pseudos": {"Si": "eaef3352-2b0e-4205-b404-e6565a88aec8"},
             },
-            "pseudo_family": "SSSP/1.2/PBEsol/efficiency",
+            "pseudo_family": "SSSP/1.3/PBEsol/efficiency",
             "kpoints_distance": 0.5,
         },
         "bands": {"kpath_2d": "hexagonal"},

docs/source/development/plugin.rst

@@ -206,7 +206,7 @@ The `parameters` passed to the `get_builder` function has the following structur
                 },
                 "pseudos": {"Si": "eaef3352-2b0e-4205-b404-e6565a88aec8"},
             },
-            "pseudo_family": "SSSP/1.2/PBEsol/efficiency",
+            "pseudo_family": "SSSP/1.3/PBEsol/efficiency",
             "kpoints_distance": 0.5,
         },
         "bands": {"kpath_2d": "hexagonal"},

post_install

@@ -2,9 +2,10 @@
 
 # This script is executed after the app installation completes
 # triggered by the post install hook implemented in https://github.com/aiidalab/aiidalab/pull/295
+# TODO: this script is not yet properly tested. The integration tests are run from the qeapp docker image, this script is executed when the app is installed by `aiidalab install`. Therefore, we need to bring original di test (which removed in https://github.com/aiidalab/aiidalab-qe/pull/449/files#diff-83993fe9ad162677c85ae244400df2469b6d666c2a28d7b8d179785e87beb7f3) back.
 
 echo "Starting installation of QE..."
 python -m aiidalab_qe install-qe & disown
 
 echo "Starting installation of pseudo-potentials..."
-python -m aiidalab_qe install-sssp & disown
+python -m aiidalab_qe install-pseudos & disown

qe.ipynb

@@ -97,7 +97,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.9.13"
   },
   "vscode": {
    "interpreter": {

src/aiidalab_qe/app/configuration/advanced.py

@@ -196,6 +196,10 @@ def _update_settings_from_protocol(self, protocol):
 
         self.kpoints_distance.value = parameters["kpoints_distance"]
 
+        # The pseudo_family read from the protocol (aiida-quantumespresso plugin settings)
+        # we override it with the value from the pseudo_family_selector widget
+        parameters["pseudo_family"] = self.pseudo_family_selector.value
+
     def _callback_value_set(self, _=None):
         """Callback function to set the parameters"""
         settings = {
@@ -299,10 +303,7 @@ def reset(self):
             self._update_settings_from_protocol(self.protocol)
 
             # reset the pseudo family
-            pseudo_family_dict = DEFAULT_PARAMETERS["advanced"]["pseudo_family"]
-            pseudo_family = PseudoFamily(**pseudo_family_dict)
-
-            self.pseudo_family_selector.load_from_pseudo_family(pseudo_family)
+            self.pseudo_family_selector.reset()
 
             # reset total charge
             self.total_charge.value = DEFAULT_PARAMETERS["advanced"]["tot_charge"]

src/aiidalab_qe/app/configuration/pseudos.py

@@ -78,7 +78,6 @@ def __init__(self, **kwargs):
         self.override = ipw.Checkbox(
             description="",
             indent=False,
-            value=False,
             layout=ipw.Layout(max_width="10%"),
         )
         self.set_pseudo_family_box = ipw.HBox(
@@ -140,6 +139,7 @@ def __init__(self, **kwargs):
         # this will trigger the callback to set the value of widgets to the default
         self._default_protocol = DEFAULT_PARAMETERS["workchain"]["protocol"]
         self.protocol = self._default_protocol
+        self.override.value = False
 
     def set_value(self, _=None):
         """The callback when the selection of pseudo family or dft functional is changed.
@@ -197,6 +197,7 @@ def _protocol_changed(self, _):
 
     def _update_settings_from_protocol(self, protocol):
         """Update the widget values from the given protocol, and trigger the callback."""
+        # FIXME: this rely on the aiida-quantumespresso, which is not ideal
         pseudo_family_string = PwBaseWorkChain.get_protocol_inputs(protocol)[
             "pseudo_family"
         ]

src/aiidalab_qe/app/parameters/qeapp.yaml

@@ -17,7 +17,7 @@ workchain:
 advanced:
     pseudo_family:
         library: SSSP
-        version: 1.2
+        version: 1.3
         functional: PBEsol
         accuracy: efficiency
     tot_charge: 0

src/aiidalab_qe/common/setup_pseudos.py

@@ -16,7 +16,7 @@
 
 from aiidalab_qe.common.widgets import ProgressBar
 
-SSSP_VERSION = "1.2"
+SSSP_VERSION = "1.3"
 PSEUDODOJO_VERSION = "0.4"
 
 EXPECTED_PSEUDOS = {

src/aiidalab_qe/plugins/bands/workchain.py

@@ -177,13 +177,18 @@ def get_builder(codes, structure, parameters, **kwargs):
     pw_code = codes.get("pw")
     protocol = parameters["workchain"]["protocol"]
     scf_overrides = deepcopy(parameters["advanced"])
+    relax_overrides = {
+        "base": deepcopy(parameters["advanced"]),
+        "base_final_scf": deepcopy(parameters["advanced"]),
+    }
     bands_overrides = deepcopy(parameters["advanced"])
     bands_overrides.pop("kpoints_distance", None)
     bands_overrides["pw"]["parameters"]["SYSTEM"].pop("smearing", None)
     bands_overrides["pw"]["parameters"]["SYSTEM"].pop("degauss", None)
     overrides = {
         "scf": scf_overrides,
         "bands": bands_overrides,
+        "relax": relax_overrides,
     }
     bands = PwBandsWorkChain.get_builder_from_protocol(
         code=pw_code,

src/aiidalab_qe/workflows/__init__.py

@@ -124,7 +124,10 @@ def get_builder_from_protocol(
         # Set the structure.
         builder.structure = structure
         # relax
-        relax_overrides = {"base": parameters["advanced"]}
+        relax_overrides = {
+            "base": parameters["advanced"],
+            "base_final_scf": parameters["advanced"],
+        }
         protocol = parameters["workchain"]["protocol"]
         relax_builder = PwRelaxWorkChain.get_builder_from_protocol(
             code=codes.get("pw"),

tests/conftest.py

@@ -7,6 +7,8 @@
 import pytest
 from aiida import orm
 
+from aiidalab_qe.common.setup_pseudos import SSSP_VERSION
+
 pytest_plugins = ["aiida.manage.tests.pytest_fixtures"]
 
 
@@ -214,7 +216,7 @@ def sssp(aiida_profile, generate_upf_data):
                 "cutoff_rho": 240.0,
             }
 
-        label = "SSSP/1.2/PBEsol/efficiency"
+        label = f"SSSP/{SSSP_VERSION}/PBEsol/efficiency"
         family = SsspFamily.create_from_folder(dirpath, label)
 
     family.set_cutoffs(cutoffs, stringency, unit="Ry")
@@ -423,11 +425,21 @@ def _generate_pdos_workchain(structure, spin_type="none"):
         from aiida.orm import Dict, FolderData, RemoteData
         from aiida_quantumespresso.workflows.pdos import PdosWorkChain
 
+        pseudo_family = f"SSSP/{SSSP_VERSION}/PBEsol/efficiency"
+
         inputs = {
             "pw_code": fixture_code("quantumespresso.pw"),
             "dos_code": fixture_code("quantumespresso.dos"),
             "projwfc_code": fixture_code("quantumespresso.projwfc"),
             "structure": structure,
+            "overrides": {
+                "scf": {
+                    "pseudo_family": pseudo_family,
+                },
+                "nscf": {
+                    "pseudo_family": pseudo_family,
+                },
+            },
         }
         builder = PdosWorkChain.get_builder_from_protocol(**inputs)
         inputs = builder._inputs()
@@ -515,9 +527,7 @@ def _generate_pdos_workchain(structure, spin_type="none"):
 
 @pytest.fixture
 def generate_bands_workchain(
-    fixture_localhost,
     fixture_code,
-    generate_xy_data,
     generate_bands_data,
     generate_workchain,
 ):
@@ -530,9 +540,27 @@ def _generate_bands_workchain(structure):
         from aiida.orm import Dict
         from aiida_quantumespresso.workflows.pw.bands import PwBandsWorkChain
 
+        pseudo_family = f"SSSP/{SSSP_VERSION}/PBEsol/efficiency"
+
         inputs = {
             "code": fixture_code("quantumespresso.pw"),
             "structure": structure,
+            "overrides": {
+                "scf": {
+                    "pseudo_family": pseudo_family,
+                },
+                "bands": {
+                    "pseudo_family": pseudo_family,
+                },
+                "relax": {
+                    "base": {
+                        "pseudo_family": pseudo_family,
+                    },
+                    "base_final_scf": {
+                        "pseudo_family": pseudo_family,
+                    },
+                },
+            },
         }
         builder = PwBandsWorkChain.get_builder_from_protocol(**inputs)
         inputs = builder._inputs()
@@ -579,6 +607,8 @@ def _generate_qeapp_workchain(
 
         from aiida.orm.utils.serialize import serialize
 
+        from aiidalab_qe.app.configuration import ConfigureQeAppWorkChainStep
+        from aiidalab_qe.app.submission import SubmitQeAppWorkChainStep
         from aiidalab_qe.workflows import QeAppWorkChain
 
         # Step 1: select structure from example
@@ -595,7 +625,7 @@ def _generate_qeapp_workchain(
         s1.confirm()
         structure = s1.confirmed_structure
         # step 2 configure
-        s2 = app.configure_step
+        s2: ConfigureQeAppWorkChainStep = app.configure_step
         s2.workchain_settings.relax_type.value = relax_type
         # In order to parepare a complete inputs, I set all the properties to true
         # this can be overrided later
@@ -608,7 +638,7 @@ def _generate_qeapp_workchain(
         )
         s2.confirm()
         # step 3 setup code and resources
-        s3 = app.submit_step
+        s3: SubmitQeAppWorkChainStep = app.submit_step
         s3.resources_config.num_cpus.value = 4
         builder = s3._create_builder()
         inputs = builder._inputs()

tests/test_configure.py

@@ -1,3 +1,6 @@
+from aiidalab_qe.common.setup_pseudos import PSEUDODOJO_VERSION, SSSP_VERSION
+
+
 def test_protocol():
     """Test the protocol.
     The protocol from workchain_settings will trigger the
@@ -31,12 +34,14 @@ def test_set_configuration_parameters():
     wg = ConfigureQeAppWorkChainStep()
     parameters = wg.get_configuration_parameters()
     parameters["workchain"]["relax_type"] = "positions"
-    parameters["advanced"]["pseudo_family"] = "SSSP/1.2/PBE/efficiency"
+    parameters["advanced"]["pseudo_family"] = f"SSSP/{SSSP_VERSION}/PBE/efficiency"
     wg.set_configuration_parameters(parameters)
     new_parameters = wg.get_configuration_parameters()
     assert parameters == new_parameters
     # test pseudodojo
-    parameters["advanced"]["pseudo_family"] = "PseudoDojo/0.4/PBEsol/SR/standard/upf"
+    parameters["advanced"][
+        "pseudo_family"
+    ] = f"PseudoDojo/{PSEUDODOJO_VERSION}/PBEsol/SR/standard/upf"
     wg.set_configuration_parameters(parameters)
     new_parameters = wg.get_configuration_parameters()
     assert parameters == new_parameters

tests/test_pseudo.py

@@ -75,7 +75,10 @@ def test_setup_pseudos_cmd(tmp_path):
     assert "--from-download" not in cmd
 
     # mock the source file
-    source_file = tmp_path / "PseudoDojo_0.4_PBEsol_SR_standard_upf.aiida_pseudo"
+    source_file = (
+        tmp_path
+        / f"PseudoDojo_{PSEUDODOJO_VERSION}_PBEsol_SR_standard_upf.aiida_pseudo"
+    )
     source_file.touch()
     cmd = _construct_cmd(pseudo_family, cwd=tmp_path)
     assert cmd == [
@@ -85,15 +88,15 @@ def test_setup_pseudos_cmd(tmp_path):
         "--functional",
         "PBEsol",
         "--version",
-        "0.4",
+        f"{PSEUDODOJO_VERSION}",
         "-p",
         "standard",
         "--relativistic",
         "SR",
         "--pseudo-format",
         "upf",
         "--from-download",
-        f"{str(tmp_path)}/PseudoDojo_0.4_PBEsol_SR_standard_upf.aiida_pseudo",
+        f"{str(tmp_path)}/PseudoDojo_{PSEUDODOJO_VERSION}_PBEsol_SR_standard_upf.aiida_pseudo",
     ]
 
 
@@ -146,19 +149,19 @@ def test_pseudos_family_selector_widget():
     w.override.value = True
 
     # test the default value
-    assert w.value == "SSSP/1.2/PBEsol/efficiency"
+    assert w.value == f"SSSP/{SSSP_VERSION}/PBEsol/efficiency"
 
     # Test if the protocol change the value will be updated
     w.protocol = "precise"
-    assert w.value == "SSSP/1.2/PBEsol/precision"
+    assert w.value == f"SSSP/{SSSP_VERSION}/PBEsol/precision"
 
     # test the functional change will update the value
     w.dft_functional.value = "PBE"
-    assert w.value == "SSSP/1.2/PBE/precision"
+    assert w.value == f"SSSP/{SSSP_VERSION}/PBE/precision"
 
     # Test if selecet new pseudo library the value will be updated
     w.library_selection.value = "PseudoDojo stringent"
-    assert w.value == "PseudoDojo/0.4/PBE/SR/stringent/upf"
+    assert w.value == f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/SR/stringent/upf"
 
 
 @pytest.mark.usefixtures("sssp")
@@ -168,7 +171,9 @@ def test_pseudos_setter_widget(generate_structure_data, generate_upf_data):
 
     # test the widget is set with the elements of the structure
     silicon = generate_structure_data("silicon")
-    w = PseudoSetter(structure=silicon, pseudo_family="SSSP/1.2/PBEsol/efficiency")
+    w = PseudoSetter(
+        structure=silicon, pseudo_family=f"SSSP/{SSSP_VERSION}/PBEsol/efficiency"
+    )
 
     assert "Si" in w.pseudos.keys()
     assert w.ecutwfc == 30

tests/test_result/test_summary_report.yml

@@ -17,11 +17,11 @@ properties:
 - pdos
 - relax
 protocol: fast
-pseudo_family: SSSP/1.2/PBEsol/efficiency
+pseudo_family: SSSP/1.3/PBEsol/efficiency
 pseudo_library: SSSP
 pseudo_link: https://www.materialscloud.org/discover/sssp/table/efficiency
 pseudo_protocol: efficiency
-pseudo_version: '1.2'
+pseudo_version: '1.3'
 relax_method: positions_cell
 relaxed: positions_cell
 scf_kpoints_distance: 0.5

tests/test_submit_qe_workchain.py

@@ -1,3 +1,7 @@
+import pytest
+
+
+@pytest.mark.usefixtures("sssp")
 def test_create_builder_default(
     data_regression,
     submit_app_generator,
@@ -19,6 +23,7 @@ def test_create_builder_default(
     data_regression.check(got)
 
 
+@pytest.mark.usefixtures("sssp")
 def test_create_builder_insulator(
     submit_app_generator,
 ):
@@ -41,6 +46,7 @@ def test_create_builder_insulator(
     assert "smearing" not in got["bands"]["scf"]["pw"]["parameters"]["SYSTEM"]
 
 
+@pytest.mark.usefixtures("sssp")
 def test_create_builder_advanced_settings(
     submit_app_generator,
 ):