HubbardStructureData: add compatibility for <3D structures

The `HubbardStructureData.append_hubbard_parameter()` method currently fails for
structures that don't have 3-dimensional periodic boundary conditions. This is caused
by a restriction in the StructureData.get_pymatgen_structure()` method, which raises a
`ValueError` if the periodic boundary conditions are not (True, True, True). This has
been fixed in a recent commit on `aiida-core`:

aiidateam/aiida-core@adcce4b

But this will take some time to be released and would restrict our compatibility to
`aiida-core>=2.6.0`.

Here we directly construct a list of `PeriodicSite` objects from the `sites` list of the
object obtained from `StructureData.get_pymatgen()`, which can be both either a
pymatgen `Structure` or `Molecule`, depending on the dimensionality of the structure.

Co-authored-by: AndresOrtegaGuerrero <[email protected]>

src/aiida_quantumespresso/data/hubbard_structure.py

@@ -5,6 +5,7 @@
 
 from aiida.orm import StructureData
 import numpy as np
+from pymatgen.core import Lattice, PeriodicSite
 
 from aiida_quantumespresso.common.hubbard import Hubbard, HubbardParameters
 
@@ -110,8 +111,11 @@ def append_hubbard_parameter(
         :param hubbard_type: hubbard type (U, V, J, ...), defaults to 'Ueff'
             (see :class:`~aiida_quantumespresso.common.hubbard.Hubbard` for full allowed values)
         """
-        pymat = self.get_pymatgen_structure()
-        sites = pymat.sites
+        sites = [
+            PeriodicSite(
+                species=site.species, coords=site.coords, lattice=Lattice(self.cell), coords_are_cartesian=True
+            ) for site in self.get_pymatgen().sites
+        ]
 
         if any((atom_index > len(sites) - 1, neighbour_index > len(sites) - 1)):
             raise ValueError(

tests/data/test_hubbard_structure.py

@@ -62,7 +62,7 @@ def test_from_structure(generate_structure, generate_hubbard):
 
 
 @pytest.mark.usefixtures('aiida_profile')
-@pytest.mark.parametrize('structure_name', ('silicon',))
+@pytest.mark.parametrize('structure_name', ('silicon', '2D-xy-arsenic'))
 @pytest.mark.parametrize(
     'parameters', (
         ((0, '1s', 0, '1s', 5.0, (0, 0, 0), 'Ueff'),),
@@ -88,13 +88,14 @@ def test_append_hubbard_parameters(data_regression, generate_structure, structur
     assert len(hubbard_structure.hubbard.parameters) == len(set(parameters))
 
 
+@pytest.mark.parametrize('structure_name', ('cobalt-prim', '1D-x-carbon'))
 @pytest.mark.parametrize('parameter', (
     (0, '1s', 1, '1s', 5.0, None, 'V'),
     (0, '1s', 1, '1s', 5.0, (0, 0, 0), 'V'),
 ))
-def test_append_hubbard_parameters_invalid_index(generate_structure, parameter):
+def test_append_hubbard_parameters_invalid_index(generate_structure, structure_name, parameter):
     """Test the `append_hubbard_parameters` method with invalid index."""
-    hubbard_structure = HubbardStructureData.from_structure(generate_structure('cobalt-prim'))
+    hubbard_structure = HubbardStructureData.from_structure(generate_structure(structure_name))
 
     with pytest.raises(ValueError, match='atom_index and neighbour_index must be within the range'):
         hubbard_structure.append_hubbard_parameter(*parameter)

tests/data/test_hubbard_structure/test_append_hubbard_parameters_parameters0_2D_xy_arsenic_.yml

@@ -0,0 +1,9 @@
+- - 0
+  - 1s
+  - 0
+  - 1s
+  - 5.0
+  - - 0
+    - 0
+    - 0
+  - Ueff

tests/data/test_hubbard_structure/test_append_hubbard_parameters_parameters1_2D_xy_arsenic_.yml

@@ -0,0 +1,9 @@
+- - 0
+  - 1s
+  - 1
+  - 1s
+  - 5.0
+  - - 0
+    - 0
+    - 0
+  - V

tests/data/test_hubbard_structure/test_append_hubbard_parameters_parameters2_2D_xy_arsenic_.yml

@@ -0,0 +1,9 @@
+- - 0
+  - 1s
+  - 0
+  - 1s
+  - 5.0
+  - - 0
+    - 0
+    - 0
+  - Ueff

tests/data/test_hubbard_structure/test_append_hubbard_parameters_parameters3_2D_xy_arsenic_.yml

@@ -0,0 +1,18 @@
+- - 0
+  - 1s
+  - 0
+  - 1s
+  - 5.0
+  - - 0
+    - 0
+    - 0
+  - Ueff
+- - 0
+  - 1s
+  - 1
+  - 1s
+  - 5.0
+  - - 0
+    - 1
+    - 0
+  - V