From 9cb1cfa8a70d19af7aaa1b624cf17c8babe93f41 Mon Sep 17 00:00:00 2001 From: Marnik Bercx Date: Mon, 19 Feb 2024 14:56:25 +0100 Subject: [PATCH] `seekpath_structure_analysis`: `HubbardStructureData` compatibility The current implementation of the `seekpath_structure_analysis` calculation function is not compatible with the `HubbardStructureData` data class. Although the function runs without errors, the returned primitive structure is now simply a `StructureData` instance, and hence we lose all information related to the Hubbard parameters. Here we adapt the `seekpath_structure_analysis` calculation function so that it checks if the provided input `structure` is a `HubbardStructureData` instance. If so, the resulting primitive and conventional structures are converted into `HubbardStructureData` instances with the same _onsite_ Hubbard parameters as the input structure. Intersite parameters are much more challenging to preserve correctly when primitivizing the structure, since they cannot simply be defined in terms of the kinds of the structure. Rather, they are defined on pairs of site indices and transations, which the `get_explicit_kpoints_path` does not consider when primitivizing the structure. Hence, the `seekpath_structure_analysis` function currently does not support intersite parameters and will raise if the input `structure` has any defined. Co-authored-by: AndresOrtegaGuerrero <34098967+AndresOrtegaGuerrero@users.noreply.github.com> --- .../functions/seekpath_structure_analysis.py | 31 ++++++- .../functions/test_seekpath_analysis.py | 69 ++++++++++++++++ .../test_seekpath_analysis.yml | 80 +++++++++++++++++++ 3 files changed, 179 insertions(+), 1 deletion(-) create mode 100644 tests/calculations/functions/test_seekpath_analysis.py create mode 100644 tests/calculations/functions/test_seekpath_analysis/test_seekpath_analysis.yml diff --git a/src/aiida_quantumespresso/calculations/functions/seekpath_structure_analysis.py b/src/aiida_quantumespresso/calculations/functions/seekpath_structure_analysis.py index 4237342be..5d89dc64d 100644 --- a/src/aiida_quantumespresso/calculations/functions/seekpath_structure_analysis.py +++ b/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 @@ 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 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 diff --git a/tests/calculations/functions/test_seekpath_analysis.py b/tests/calculations/functions/test_seekpath_analysis.py new file mode 100644 index 000000000..cbf150d71 --- /dev/null +++ b/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) diff --git a/tests/calculations/functions/test_seekpath_analysis/test_seekpath_analysis.yml b/tests/calculations/functions/test_seekpath_analysis/test_seekpath_analysis.yml new file mode 100644 index 000000000..859ac81d5 --- /dev/null +++ b/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