seekpath_structure_analysis: HubbardStructureData compatibility

src/aiida_quantumespresso/calculations/functions/seekpath_structure_analysis.py

@@ -3,6 +3,8 @@
 from aiida.engine import calcfunction
 from aiida.orm import Data
 
+from aiida_quantumespresso.data.hubbard_structure import HubbardStructureData
+
 
 @calcfunction
 def seekpath_structure_analysis(structure, **kwargs):
@@ -28,4 +30,31 @@
     # All keyword arugments should be `Data` node instances of base type and so should have the `.value` attribute
     unwrapped_kwargs = {key: node.value for key, node in kwargs.items() if isinstance(node, Data)}
 
-    return get_explicit_kpoints_path(structure, **unwrapped_kwargs)
+    result = get_explicit_kpoints_path(structure, **unwrapped_kwargs)
+
+    if isinstance(structure, HubbardStructureData):
+        result['primitive_structure'] = update_structure_with_hubbard(result['primitive_structure'], structure)
+        result['conv_structure'] = update_structure_with_hubbard(result['conv_structure'], structure)
+
+    return result
+
+
+def update_structure_with_hubbard(structure, orig_structure):
+    """Update the structure based on Hubbard parameters if the input structure is a HubbardStructureData."""
+    from aiida_quantumespresso.utils.hubbard import is_intersite_hubbard
+
+    hubbard_structure = HubbardStructureData.from_structure(structure)
+
+    if is_intersite_hubbard(orig_structure.hubbard):
+        raise NotImplementedError('Intersite Hubbard parameters are not yet supported.')
+
+    for parameter in orig_structure.hubbard.parameters:
+        hubbard_structure.initialize_onsites_hubbard(
+            atom_name=orig_structure.sites[parameter.atom_index].kind_name,
+            atom_manifold=parameter.atom_manifold,
+            value=parameter.value,
+            hubbard_type=parameter.hubbard_type,
+            use_kinds=True,
+        )
+
+    return hubbard_structure

tests/calculations/functions/test_seekpath_analysis.py

@@ -0,0 +1,69 @@
+# -*- coding: utf-8 -*-
+"""Tests for the `seekpath_structure_analysis` function for HubbbardStructureData."""
+import pytest
+
+from aiida_quantumespresso.calculations.functions.seekpath_structure_analysis import seekpath_structure_analysis
+from aiida_quantumespresso.data.hubbard_structure import HubbardStructureData
+
+
+# pylint: disable=W0621
+@pytest.mark.usefixtures('aiida_profile')
+def test_seekpath_analysis(data_regression):
+    """Test the `seekpath_structure_analysis` calculation function for HubbardStructureData."""
+    cell = [[5.43, 0.0, 0.0], [0.0, 5.43, 0.0], [0.0, 0.0, 5.43]]
+    sites = (
+        ('Co', 'Co0', (0.0, 0.0, 0.0)),
+        ('Co', 'Co0', (0.0, 2.715, 2.715)),
+        ('Co', 'Co1', (2.715, 0.0, 2.715)),
+        ('Co', 'Co1', (2.715, 2.715, 0.0)),
+    )
+    orig_structure = HubbardStructureData(cell=cell, sites=sites)
+
+    for hubbard_parameter in [
+        ('Co0', '3d', 4.0, 'Ueff', True),
+        ('Co1', '3d', 3.0, 'U', True),
+    ]:
+        orig_structure.initialize_onsites_hubbard(*hubbard_parameter)
+
+    result = seekpath_structure_analysis(orig_structure)
+
+    prim_structure = result['primitive_structure']
+    conv_structure = result['conv_structure']
+
+    assert isinstance(prim_structure, HubbardStructureData), 'Primitive structure should be a HubbardStructureData'
+    assert isinstance(conv_structure, HubbardStructureData), 'Conventional structure should be a HubbardStructureData'
+
+    assert prim_structure.hubbard.parameters != orig_structure.hubbard.parameters, \
+        'Primitive parameters should be different'
+    assert len(prim_structure.hubbard.parameters) == len(orig_structure.hubbard.parameters), \
+        'Primitive parameters should have the same length as original parameters'
+    assert all(
+        prim_param.atom_manifold == orig_param.atom_manifold
+        for prim_param, orig_param in zip(prim_structure.hubbard.parameters, orig_structure.hubbard.parameters)
+    ), 'Primitive cell parameter atom manifolds should match the original'
+
+    data_regression.check({
+        'primitive': {
+            'cell': prim_structure.cell,
+            'kinds': prim_structure.get_site_kindnames(),
+            'positions': [site.position for site in prim_structure.sites],
+            'hubbard': prim_structure.hubbard.to_list(),
+        },
+        'conventional': {
+            'cell': conv_structure.cell,
+            'kinds': conv_structure.get_site_kindnames(),
+            'positions': [site.position for site in conv_structure.sites],
+            'hubbard': conv_structure.hubbard.to_list(),
+        }
+    })
+
+
+# pylint: disable=W0621
+@pytest.mark.usefixtures('aiida_profile')
+def test_seekpath_analysis_intersite(generate_structure):
+    """Test that the `seekpath_structure_analysis` with intersite hubbard corrections fails."""
+    orig_structure = HubbardStructureData.from_structure(generate_structure('silicon-kinds'))
+    orig_structure.initialize_intersites_hubbard('Si0', '2p', 'Si1', '2p', 4.0, 'V', True)
+
+    with pytest.raises(NotImplementedError, match='Intersite Hubbard parameters are not yet supported.'):
+        seekpath_structure_analysis(orig_structure)

tests/calculations/functions/test_seekpath_analysis/test_seekpath_analysis.yml

@@ -0,0 +1,80 @@
+conventional:
+  cell:
+  - - 3.839589821843
+    - 0.0
+    - 0.0
+  - - 0.0
+    - 3.839589821843
+    - 0.0
+  - - 0.0
+    - 0.0
+    - 5.43
+  hubbard:
+  - - 0
+    - 3d
+    - 0
+    - 3d
+    - 4.0
+    - - 0
+      - 0
+      - 0
+    - Ueff
+  - - 1
+    - 3d
+    - 1
+    - 3d
+    - 3.0
+    - - 0
+      - 0
+      - 0
+    - U
+  kinds:
+  - Co0
+  - Co1
+  positions:
+  - - 0.0
+    - 0.0
+    - 0.0
+  - - 1.9197949109215
+    - 1.9197949109215
+    - 2.715
+primitive:
+  cell:
+  - - 3.839589821843
+    - 0.0
+    - 0.0
+  - - 0.0
+    - 3.839589821843
+    - 0.0
+  - - 0.0
+    - 0.0
+    - 5.43
+  hubbard:
+  - - 0
+    - 3d
+    - 0
+    - 3d
+    - 4.0
+    - - 0
+      - 0
+      - 0
+    - Ueff
+  - - 1
+    - 3d
+    - 1
+    - 3d
+    - 3.0
+    - - 0
+      - 0
+      - 0
+    - U
+  kinds:
+  - Co0
+  - Co1
+  positions:
+  - - 0.0
+    - 0.0
+    - 0.0
+  - - 1.9197949109215
+    - 1.9197949109215
+    - 2.715