seekpath_structure_analysis: make compatible with `HubbardStructure…

…Data`

MESSAGE

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 +30,47 @@ def seekpath_structure_analysis(structure, **kwargs):
     # 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 the input structure was a HubbardStructureData, update the primitive structure with Hubbard parameters
+    if isinstance(structure, HubbardStructureData):
+        update_structure_with_hubbard(structure, result)
+
+    return result
+
+
+def update_structure_with_hubbard(structure, result):
+    """Update the structure based on Hubbard parameters if the input structure is a HubbardStructureData."""
+    hubbard_parameters = structure.hubbard.parameters
+    if not hubbard_parameters:
+        return
+
+    hubbard_structure = HubbardStructureData.from_structure(result['primitive_structure'])
+
+    for parameter in hubbard_parameters:
+        atom_index = parameter.atom_index
+        atom_name = structure.sites[atom_index].kind_name
+
+        if parameter.hubbard_type != 'V':
+            hubbard_structure.initialize_onsites_hubbard(
+                atom_name=atom_name,
+                atom_manifold=parameter.atom_manifold,
+                value=parameter.value,
+                hubbard_type=parameter.hubbard_type,
+                use_kinds=True,
+            )
+        else:
+            neighbour_index = parameter.neighbour_index
+            neighbour_name = structure.sites[neighbour_index].kind_name
+
+            hubbard_structure.initialize_intersites_hubbard(
+                atom_name=atom_name,
+                atom_manifold=parameter.atom_manifold,
+                neighbour_name=neighbour_name,
+                neighbour_manifold=parameter.neighbour_manifold,
+                value=parameter.value,
+                hubbard_type=parameter.hubbard_type,
+                use_kinds=True,
+            )
+
+    result['primitive_structure'] = hubbard_structure

tests/calculations/functions/test_seekpath_analysis.py

@@ -0,0 +1,89 @@
+# -*- 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
+
+
+@pytest.fixture
+def generate_hubbardstructure_conv():
+    """Return a `HubbardStructureData` instance in conventional cell."""
+
+    def _generate_hubbardstructure_conv():
+        cell = [[7.96416, 0.0, 4.87664153e-16], [-4.87664153e-16, 7.96416, 4.87664153e-16], [0.0, 0.0, 7.96416]]
+        sites = [['Li', 'Li', (2.98656, 0.99552, 6.96864)], ['Li', 'Li', (6.96864, 6.96864, 4.9776)],
+                 ['Li', 'Li', (0.99552, 0.99552, 4.9776)], ['Li', 'Li', (4.9776, 6.96864, 6.96864)],
+                 ['Li', 'Li', (2.98656, 4.9776, 2.98656)], ['Li', 'Li', (6.96864, 2.98656, 0.99552)],
+                 ['Li', 'Li', (0.99552, 4.9776, 0.99552)], ['Li', 'Li', (4.9776, 2.98656, 2.98656)],
+                 ['Li', 'Li', (6.96864, 0.99552, 2.98656)], ['Li', 'Li', (2.98656, 6.96864, 0.99552)],
+                 ['Li', 'Li', (4.9776, 0.99552, 0.99552)], ['Li', 'Li', (0.99552, 6.96864, 2.98656)],
+                 ['Li', 'Li', (6.96864, 4.9776, 6.96864)], ['Li', 'Li', (2.98656, 2.98656, 4.9776)],
+                 ['Li', 'Li', (4.9776, 4.9776, 4.9776)], ['Li', 'Li', (0.99552, 2.98656, 6.96864)],
+                 ['Co', 'Co', (2.98656, 6.96864, 4.9776)], ['Co', 'Co', (0.99552, 6.96864, 6.96864)],
+                 ['Co', 'Co', (0.99552, 4.9776, 4.9776)], ['Co', 'Co', (2.98656, 4.9776, 6.96864)],
+                 ['Co', 'Co', (2.98656, 2.98656, 0.99552)], ['Co', 'Co', (0.99552, 2.98656, 2.98656)],
+                 ['Co', 'Co', (0.99552, 0.99552, 0.99552)], ['Co', 'Co', (2.98656, 0.99552, 2.98656)],
+                 ['Co', 'Co', (6.96864, 6.96864, 0.99552)], ['Co', 'Co', (4.9776, 6.96864, 2.98656)],
+                 ['Co', 'Co', (4.9776, 4.9776, 0.99552)], ['Co', 'Co', (6.96864, 4.9776, 2.98656)],
+                 ['Co', 'Co', (6.96864, 2.98656, 4.9776)], ['Co', 'Co', (4.9776, 2.98656, 6.96864)],
+                 ['Co', 'Co', (4.9776, 0.99552, 4.9776)], ['Co', 'Co', (6.96864, 0.99552, 6.96864)],
+                 ['O', 'O', (3.06333, 0.91875, 4.90083)], ['O', 'O', (0.91875, 3.06333, 4.90083)],
+                 ['O', 'O', (3.06333, 3.06333, 7.04541)], ['O', 'O', (0.91875, 0.91875, 7.04541)],
+                 ['O', 'O', (5.05437, 1.07229, 6.89187)], ['O', 'O', (2.90979, 6.89187, 6.89187)],
+                 ['O', 'O', (1.07229, 6.89187, 5.05437)], ['O', 'O', (6.89187, 1.07229, 5.05437)],
+                 ['O', 'O', (3.06333, 4.90083, 0.91875)], ['O', 'O', (0.91875, 7.04541, 0.91875)],
+                 ['O', 'O', (3.06333, 7.04541, 3.06333)], ['O', 'O', (0.91875, 4.90083, 3.06333)],
+                 ['O', 'O', (5.05437, 5.05437, 2.90979)], ['O', 'O', (2.90979, 2.90979, 2.90979)],
+                 ['O', 'O', (1.07229, 2.90979, 1.07229)], ['O', 'O', (6.89187, 5.05437, 1.07229)],
+                 ['O', 'O', (7.04541, 0.91875, 0.91875)], ['O', 'O', (4.90083, 3.06333, 0.91875)],
+                 ['O', 'O', (7.04541, 3.06333, 3.06333)], ['O', 'O', (4.90083, 0.91875, 3.06333)],
+                 ['O', 'O', (1.07229, 1.07229, 2.90979)], ['O', 'O', (6.89187, 6.89187, 2.90979)],
+                 ['O', 'O', (5.05437, 6.89187, 1.07229)], ['O', 'O', (2.90979, 1.07229, 1.07229)],
+                 ['O', 'O', (7.04541, 4.90083, 4.90083)], ['O', 'O', (4.90083, 7.04541, 4.90083)],
+                 ['O', 'O', (7.04541, 7.04541, 7.04541)], ['O', 'O', (4.90083, 4.90083, 7.04541)],
+                 ['O', 'O', (1.07229, 5.05437, 6.89187)], ['O', 'O', (6.89187, 2.90979, 6.89187)],
+                 ['O', 'O', (5.05437, 2.90979, 5.05437)], ['O', 'O', (2.90979, 5.05437, 5.05437)]]
+        structure = HubbardStructureData(cell=cell, sites=sites)
+
+        initializations = [
+            ('Co', '3d', 3.0, 'U', True),
+            ('O', '2p', 2.0, 'U', True),
+            ('Li', '2s', 1.5, 'U', True),
+        ]
+
+        for atom_name, atom_manifold, value, hubbard_type, use_kinds in initializations:
+            structure.initialize_onsites_hubbard(
+                atom_name=atom_name,
+                atom_manifold=atom_manifold,
+                value=value,
+                hubbard_type=hubbard_type,
+                use_kinds=use_kinds,
+            )
+
+        return structure
+
+    return _generate_hubbardstructure_conv
+
+
+# pylint: disable=W0621
+@pytest.mark.usefixtures('aiida_profile')
+def test_seekpath_analysis(generate_hubbardstructure_conv):
+    """Test the `seekpath_structure_analysis` calculation function for HubbardStructureData."""
+    structure = generate_hubbardstructure_conv()
+    conventional_parameters = structure.hubbard.parameters
+
+    result = seekpath_structure_analysis(structure)
+    primitive_parameters = result['primitive_structure'].hubbard.parameters
+
+    assert isinstance(
+        result['primitive_structure'], HubbardStructureData
+    ), 'Primitive structure should be a HubbardStructureData'
+    assert conventional_parameters != primitive_parameters, 'Primitive parameters should be different'
+    assert len(primitive_parameters) == len(
+        conventional_parameters
+    ), 'Primitive parameters should have the same length as conventional parameters'
+    assert all(
+        conv_param.atom_manifold == prim_param.atom_manifold
+        for conv_param, prim_param in zip(conventional_parameters, primitive_parameters)
+    ), 'Atom manifold should match in primitive'