From 97e649f245c06ec76b63efca7580a05178a4740f Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Tue, 2 Aug 2022 15:13:32 +0200 Subject: [PATCH 01/63] Modify nomad/normalizing/material.py to include classification of 2D and surfaces to results.material.topology. Also added the unit test for that functionality and reference data for the unit test --- nomad/normalizing/material.py | 2 +- .../surface_2D_subsystem_classification.json | 5395 +++++++++++++++++ 2 files changed, 5396 insertions(+), 1 deletion(-) create mode 100644 tests/data/classification/surface_2D_subsystem_classification.json diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index 3ec39c80a..b347397ff 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -18,7 +18,6 @@ from typing import Union, Dict, List, Tuple, Optional from nptyping import NDArray -from collections import defaultdict import re import ase.data from ase import Atoms @@ -34,6 +33,7 @@ from nomad import atomutils from nomad.utils import hash + class MaterialNormalizer(): def __init__( self, diff --git a/tests/data/classification/surface_2D_subsystem_classification.json b/tests/data/classification/surface_2D_subsystem_classification.json new file mode 100644 index 000000000..db8bd8cb3 --- /dev/null +++ b/tests/data/classification/surface_2D_subsystem_classification.json @@ -0,0 +1,5395 @@ +{ + "5BZbNJgzr0hqEwBFL0tzhCYVlfRb": { + "topology": [ + { + "atoms": { + "labels": [ + "N", + "N", + "C", + "C", + "B", + "B" + ], + "species": [ + 7, + 7, + 6, + 6, + 5, + 5 + ], + "positions": [ + [ + 0.0, + 0.0, + 0.0 + ], + [ + 0.0, + 0.0, + 6.207700540042802 + ], + [ + -7.734710224832942e-18, + 1.4385198970702377, + 3.1033148311789057 + ], + [ + 7.734710224832942e-18, + 2.8770398372960724, + 3.1044161012110054 + ], + [ + -7.734710224832942e-18, + 1.4385198970702377, + 9.248229259962613e-4 + ], + [ + 7.734710224832942e-18, + 2.8770398372960724, + 6.206744562579172 + ] + ], + "lattice_vectors": [ + [ + 1.24579479260285, + 2.157779867183155, + 0.0 + ], + [ + -1.24579479260285, + 2.157779867183155, + 0.0 + ], + [ + 0.0, + 0.0, + 9.527381539056982 + ] + ], + "periodic": [ + true, + true, + true + ] + }, + "description": "A representative system chosen from the 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"subsystem", + "elements": [ + "H", + "C" + ], + "formula_hill": "H10C16", + "parent": "0", + "indices": [ + 27, + 28, + 29, + 30, + 31, + 32, + 33, + 34, + 35, + 36, + 37, + 38, + 39, + 40, + 41, + 42, + 43, + 44, + 45, + 46, + 47, + 48, + 49, + 50, + 51, + 52 + ], + "structural_type": "molecule / cluster" + }, + { + "description": "Automatically detected subsystem.", + "id": "8", + "methode": "matid", + "label": "subsystem", + "elements": [ + "Mo", + "S" + ], + "formula_hill": "Mo9S18", + "parent": "0", + "indices": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15, + 16, + 17, + 18, + 19, + 20, + 21, + 22, + 23, + 24, + 25, + 26 + ], + "structural_type": "2D" + } + ] + } +} \ No newline at end of file -- GitLab From c2965a1b08ab7f22e810dbdd1ea7d764f34c3180 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Tue, 2 Aug 2022 15:42:18 +0200 Subject: [PATCH 02/63] Modify nomad/normalizing/material.py to include classification of 2D and surfaces to results.material.topology. Also added the unit test for that functionality and reference data for the unit test --- tests/normalizing/test_material.py | 78 ++++++++++++++++++++---------- 1 file changed, 52 insertions(+), 26 deletions(-) diff --git a/tests/normalizing/test_material.py b/tests/normalizing/test_material.py index b1fbd0376..18a685538 100644 --- a/tests/normalizing/test_material.py +++ b/tests/normalizing/test_material.py @@ -62,7 +62,8 @@ def assert_structure(structure, has_cell=True, has_wyckoff=False): assert structure.species[0].chemical_symbols if has_cell: assert len(structure.dimension_types) == 3 - assert np.sum(structure.dimension_types) == structure.nperiodic_dimensions + assert np.sum( + structure.dimension_types) == structure.nperiodic_dimensions assert structure.lattice_vectors.shape == (3, 3) a = structure.lattice_parameters.a b = structure.lattice_parameters.b @@ -145,9 +146,11 @@ def test_material_1d(one_d): assert conv.n_sites == 4 assert conv.species_at_sites == ["C", "C", "H", "H"] assert np.array_equal(conv.dimension_types, [1, 0, 0]) - assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(2.459, abs=1e-3) + assert conv.lattice_parameters.a.to( + ureg.angstrom).magnitude == pytest.approx(2.459, abs=1e-3) assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == 0 - assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == pytest.approx(2.890, abs=1e-3) + assert conv.lattice_parameters.c.to( + ureg.angstrom).magnitude == pytest.approx(2.890, abs=1e-3) assert conv.lattice_parameters.alpha is None assert conv.lattice_parameters.beta.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.gamma is None @@ -182,12 +185,15 @@ def test_material_2d(two_d): assert conv.n_sites == 2 assert conv.species_at_sites == ["C", "C"] assert np.array_equal(conv.dimension_types, [1, 1, 0]) - assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) - assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) + assert conv.lattice_parameters.a.to( + ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) + assert conv.lattice_parameters.b.to( + ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == 0 assert conv.lattice_parameters.alpha is None assert conv.lattice_parameters.beta is None - assert conv.lattice_parameters.gamma.magnitude == pytest.approx(120 / 180 * np.pi) + assert conv.lattice_parameters.gamma.magnitude == pytest.approx( + 120 / 180 * np.pi) # Original structure assert_structure(two_d.results.properties.structures.structure_original) @@ -232,11 +238,15 @@ def test_material_bulk(bulk): conv = bulk.results.properties.structures.structure_conventional assert_structure(conv, has_wyckoff=True) assert conv.n_sites == 8 - assert conv.species_at_sites == ["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"] + assert conv.species_at_sites == [ + "Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"] assert np.array_equal(conv.dimension_types, [1, 1, 1]) - assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) - assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) - assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.a.to( + ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.b.to( + ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.c.to( + ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) assert conv.lattice_parameters.alpha.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.beta.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.gamma.magnitude == pytest.approx(np.pi / 2) @@ -281,7 +291,8 @@ def test_1d_material_identification(): pos = nanotube4.get_positions() pos += 0.2 * np.random.rand(pos.shape[0], pos.shape[1]) nanotube4.set_positions(pos) - hash4 = get_template_for_structure(nanotube4).results.material.material_id + hash4 = get_template_for_structure( + nanotube4).results.material.material_id assert hash4 == hash1 # Too distorted copy should not match @@ -303,7 +314,8 @@ def test_2d_material_identification(): indices=[0, 1] )] space_group_number = 191 - norm_hash_string = atomutils.get_symmetry_string(space_group_number, wyckoff_sets, is_2d=True) + norm_hash_string = atomutils.get_symmetry_string( + space_group_number, wyckoff_sets, is_2d=True) graphene_material_id = hash(norm_hash_string) # Graphene orthogonal cell @@ -322,13 +334,15 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure(graphene).results.material.material_id + material_id = get_template_for_structure( + graphene).results.material.material_id assert material_id == graphene_material_id # Graphene orthogonal supercell graphene2 = graphene.copy() graphene2 *= [2, 1, 2] - material_id = get_template_for_structure(graphene2).results.material.material_id + material_id = get_template_for_structure( + graphene2).results.material.material_id assert material_id == graphene_material_id # Graphene primitive cell @@ -345,7 +359,8 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure(graphene3).results.material.material_id + material_id = get_template_for_structure( + graphene3).results.material.material_id assert material_id == graphene_material_id # Slightly distorted system should match @@ -355,7 +370,8 @@ def test_2d_material_identification(): pos = graphene4.get_positions() pos += 0.05 * np.random.rand(pos.shape[0], pos.shape[1]) graphene4.set_positions(pos) - material_id = get_template_for_structure(graphene4).results.material.material_id + material_id = get_template_for_structure( + graphene4).results.material.material_id assert material_id == graphene_material_id # Too distorted system should not match @@ -364,7 +380,8 @@ def test_2d_material_identification(): np.random.seed(4) pos += 1 * np.random.rand(pos.shape[0], pos.shape[1]) graphene5.set_positions(pos) - material_id = get_template_for_structure(graphene5).results.material.material_id + material_id = get_template_for_structure( + graphene5).results.material.material_id assert material_id != graphene_material_id # Expected information for MoS2. MoS2 has finite thichkness unlike @@ -388,7 +405,8 @@ def test_2d_material_identification(): ) ] space_group_number = 11 - norm_hash_string = atomutils.get_symmetry_string(space_group_number, wyckoff_sets, is_2d=True) + norm_hash_string = atomutils.get_symmetry_string( + space_group_number, wyckoff_sets, is_2d=True) mos2_material_id = hash(norm_hash_string) # MoS2 orthogonal cell @@ -409,30 +427,36 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure(atoms).results.material.material_id + material_id = get_template_for_structure( + atoms).results.material.material_id assert material_id == mos2_material_id # MoS2 orthogonal supercell atoms *= [2, 3, 1] - material_id = get_template_for_structure(atoms).results.material.material_id + material_id = get_template_for_structure( + atoms).results.material.material_id assert material_id == mos2_material_id def test_bulk_material_identification(): # Original system - wurtzite = ase.build.bulk("SiC", crystalstructure="wurtzite", a=3.086, c=10.053) - material_id_wurtzite = get_template_for_structure(wurtzite).results.material.material_id + wurtzite = ase.build.bulk( + "SiC", crystalstructure="wurtzite", a=3.086, c=10.053) + material_id_wurtzite = get_template_for_structure( + wurtzite).results.material.material_id # Rotated wurtzite2 = wurtzite.copy() wurtzite2.rotate(90, "z", rotate_cell=True) - material_id = get_template_for_structure(wurtzite2).results.material.material_id + material_id = get_template_for_structure( + wurtzite2).results.material.material_id assert material_id == material_id_wurtzite # Supercell wurtzite3 = wurtzite.copy() wurtzite3 *= [2, 3, 1] - materia_id = get_template_for_structure(wurtzite3).results.material.material_id + materia_id = get_template_for_structure( + wurtzite3).results.material.material_id assert materia_id == material_id_wurtzite # Slightly distorted system should match @@ -442,7 +466,8 @@ def test_bulk_material_identification(): pos = wurtzite4.get_positions() pos += 0.05 * np.random.rand(pos.shape[0], pos.shape[1]) wurtzite4.set_positions(pos) - material_id = get_template_for_structure(wurtzite4).results.material.material_id + material_id = get_template_for_structure( + wurtzite4).results.material.material_id assert material_id == material_id_wurtzite # Too distorted system should not match @@ -451,7 +476,8 @@ def test_bulk_material_identification(): np.random.seed(4) pos += 1 * np.random.rand(pos.shape[0], pos.shape[1]) wurtzite5.set_positions(pos) - material_id = get_template_for_structure(wurtzite5).results.material.material_id + material_id = get_template_for_structure( + wurtzite5).results.material.material_id assert material_id != material_id_wurtzite -- GitLab From c3248172c19976e261626c94d699b6e8759b58f9 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Tue, 2 Aug 2022 16:16:42 +0200 Subject: [PATCH 03/63] Revert "Modify nomad/normalizing/material.py to include classification of 2D and surfaces to results.material.topology. Also added the unit test for that functionality and reference data for the unit test" This reverts commit 624f94080ce4fa94cf22c29adad1231cc65a6b29. --- nomad/normalizing/material.py | 2 +- tests/normalizing/test_material.py | 78 ++++++++++-------------------- 2 files changed, 27 insertions(+), 53 deletions(-) diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index b347397ff..e62e88a15 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -640,7 +640,7 @@ class MaterialNormalizer(): topology can be extracted. ''' try: - structure_original = self.properties.structures.structure_original + groups = self.entry_archive.run[0].system[0].atoms_group except Exception: return None diff --git a/tests/normalizing/test_material.py b/tests/normalizing/test_material.py index 18a685538..b1fbd0376 100644 --- a/tests/normalizing/test_material.py +++ b/tests/normalizing/test_material.py @@ -62,8 +62,7 @@ def assert_structure(structure, has_cell=True, has_wyckoff=False): assert structure.species[0].chemical_symbols if has_cell: assert len(structure.dimension_types) == 3 - assert np.sum( - structure.dimension_types) == structure.nperiodic_dimensions + assert np.sum(structure.dimension_types) == structure.nperiodic_dimensions assert structure.lattice_vectors.shape == (3, 3) a = structure.lattice_parameters.a b = structure.lattice_parameters.b @@ -146,11 +145,9 @@ def test_material_1d(one_d): assert conv.n_sites == 4 assert conv.species_at_sites == ["C", "C", "H", "H"] assert np.array_equal(conv.dimension_types, [1, 0, 0]) - assert conv.lattice_parameters.a.to( - ureg.angstrom).magnitude == pytest.approx(2.459, abs=1e-3) + assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(2.459, abs=1e-3) assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == 0 - assert conv.lattice_parameters.c.to( - ureg.angstrom).magnitude == pytest.approx(2.890, abs=1e-3) + assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == pytest.approx(2.890, abs=1e-3) assert conv.lattice_parameters.alpha is None assert conv.lattice_parameters.beta.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.gamma is None @@ -185,15 +182,12 @@ def test_material_2d(two_d): assert conv.n_sites == 2 assert conv.species_at_sites == ["C", "C"] assert np.array_equal(conv.dimension_types, [1, 1, 0]) - assert conv.lattice_parameters.a.to( - ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) - assert conv.lattice_parameters.b.to( - ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) + assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) + assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == 0 assert conv.lattice_parameters.alpha is None assert conv.lattice_parameters.beta is None - assert conv.lattice_parameters.gamma.magnitude == pytest.approx( - 120 / 180 * np.pi) + assert conv.lattice_parameters.gamma.magnitude == pytest.approx(120 / 180 * np.pi) # Original structure assert_structure(two_d.results.properties.structures.structure_original) @@ -238,15 +232,11 @@ def test_material_bulk(bulk): conv = bulk.results.properties.structures.structure_conventional assert_structure(conv, has_wyckoff=True) assert conv.n_sites == 8 - assert conv.species_at_sites == [ - "Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"] + assert conv.species_at_sites == ["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"] assert np.array_equal(conv.dimension_types, [1, 1, 1]) - assert conv.lattice_parameters.a.to( - ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) - assert conv.lattice_parameters.b.to( - ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) - assert conv.lattice_parameters.c.to( - ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) assert conv.lattice_parameters.alpha.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.beta.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.gamma.magnitude == pytest.approx(np.pi / 2) @@ -291,8 +281,7 @@ def test_1d_material_identification(): pos = nanotube4.get_positions() pos += 0.2 * np.random.rand(pos.shape[0], pos.shape[1]) nanotube4.set_positions(pos) - hash4 = get_template_for_structure( - nanotube4).results.material.material_id + hash4 = get_template_for_structure(nanotube4).results.material.material_id assert hash4 == hash1 # Too distorted copy should not match @@ -314,8 +303,7 @@ def test_2d_material_identification(): indices=[0, 1] )] space_group_number = 191 - norm_hash_string = atomutils.get_symmetry_string( - space_group_number, wyckoff_sets, is_2d=True) + norm_hash_string = atomutils.get_symmetry_string(space_group_number, wyckoff_sets, is_2d=True) graphene_material_id = hash(norm_hash_string) # Graphene orthogonal cell @@ -334,15 +322,13 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure( - graphene).results.material.material_id + material_id = get_template_for_structure(graphene).results.material.material_id assert material_id == graphene_material_id # Graphene orthogonal supercell graphene2 = graphene.copy() graphene2 *= [2, 1, 2] - material_id = get_template_for_structure( - graphene2).results.material.material_id + material_id = get_template_for_structure(graphene2).results.material.material_id assert material_id == graphene_material_id # Graphene primitive cell @@ -359,8 +345,7 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure( - graphene3).results.material.material_id + material_id = get_template_for_structure(graphene3).results.material.material_id assert material_id == graphene_material_id # Slightly distorted system should match @@ -370,8 +355,7 @@ def test_2d_material_identification(): pos = graphene4.get_positions() pos += 0.05 * np.random.rand(pos.shape[0], pos.shape[1]) graphene4.set_positions(pos) - material_id = get_template_for_structure( - graphene4).results.material.material_id + material_id = get_template_for_structure(graphene4).results.material.material_id assert material_id == graphene_material_id # Too distorted system should not match @@ -380,8 +364,7 @@ def test_2d_material_identification(): np.random.seed(4) pos += 1 * np.random.rand(pos.shape[0], pos.shape[1]) graphene5.set_positions(pos) - material_id = get_template_for_structure( - graphene5).results.material.material_id + material_id = get_template_for_structure(graphene5).results.material.material_id assert material_id != graphene_material_id # Expected information for MoS2. MoS2 has finite thichkness unlike @@ -405,8 +388,7 @@ def test_2d_material_identification(): ) ] space_group_number = 11 - norm_hash_string = atomutils.get_symmetry_string( - space_group_number, wyckoff_sets, is_2d=True) + norm_hash_string = atomutils.get_symmetry_string(space_group_number, wyckoff_sets, is_2d=True) mos2_material_id = hash(norm_hash_string) # MoS2 orthogonal cell @@ -427,36 +409,30 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure( - atoms).results.material.material_id + material_id = get_template_for_structure(atoms).results.material.material_id assert material_id == mos2_material_id # MoS2 orthogonal supercell atoms *= [2, 3, 1] - material_id = get_template_for_structure( - atoms).results.material.material_id + material_id = get_template_for_structure(atoms).results.material.material_id assert material_id == mos2_material_id def test_bulk_material_identification(): # Original system - wurtzite = ase.build.bulk( - "SiC", crystalstructure="wurtzite", a=3.086, c=10.053) - material_id_wurtzite = get_template_for_structure( - wurtzite).results.material.material_id + wurtzite = ase.build.bulk("SiC", crystalstructure="wurtzite", a=3.086, c=10.053) + material_id_wurtzite = get_template_for_structure(wurtzite).results.material.material_id # Rotated wurtzite2 = wurtzite.copy() wurtzite2.rotate(90, "z", rotate_cell=True) - material_id = get_template_for_structure( - wurtzite2).results.material.material_id + material_id = get_template_for_structure(wurtzite2).results.material.material_id assert material_id == material_id_wurtzite # Supercell wurtzite3 = wurtzite.copy() wurtzite3 *= [2, 3, 1] - materia_id = get_template_for_structure( - wurtzite3).results.material.material_id + materia_id = get_template_for_structure(wurtzite3).results.material.material_id assert materia_id == material_id_wurtzite # Slightly distorted system should match @@ -466,8 +442,7 @@ def test_bulk_material_identification(): pos = wurtzite4.get_positions() pos += 0.05 * np.random.rand(pos.shape[0], pos.shape[1]) wurtzite4.set_positions(pos) - material_id = get_template_for_structure( - wurtzite4).results.material.material_id + material_id = get_template_for_structure(wurtzite4).results.material.material_id assert material_id == material_id_wurtzite # Too distorted system should not match @@ -476,8 +451,7 @@ def test_bulk_material_identification(): np.random.seed(4) pos += 1 * np.random.rand(pos.shape[0], pos.shape[1]) wurtzite5.set_positions(pos) - material_id = get_template_for_structure( - wurtzite5).results.material.material_id + material_id = get_template_for_structure(wurtzite5).results.material.material_id assert material_id != material_id_wurtzite -- GitLab From 3c2fccb1e816ab8fb69ef4c8c4780d2c0e49d520 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Tue, 2 Aug 2022 16:17:55 +0200 Subject: [PATCH 04/63] Revert "Modify nomad/normalizing/material.py to include classification of 2D and surfaces to results.material.topology. Also added the unit test for that functionality and reference data for the unit test" This reverts commit da5df4f4f0e7624ddba0aa0eb3c258e34c8aa2cc. --- nomad/normalizing/material.py | 6 +- .../surface_2D_subsystem_classification.json | 5395 ----------------- 2 files changed, 1 insertion(+), 5400 deletions(-) delete mode 100644 tests/data/classification/surface_2D_subsystem_classification.json diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index e62e88a15..b970a8e5f 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -18,22 +18,18 @@ from typing import Union, Dict, List, Tuple, Optional from nptyping import NDArray +from collections import defaultdict import re import ase.data from ase import Atoms -from ase.geometry.cell import complete_cell import numpy as np import matid.geometry -from matid.classification.structureclusterer import StructureClusterer -from matid import Classifier -from matid.classifications import Class0D, Atom, Class1D, Material2D, Surface, Class3D, Unknown from nomad.datamodel.results import Symmetry, Material, System, Cell, Relation, StructureOriginal from nomad import atomutils from nomad.utils import hash - class MaterialNormalizer(): def __init__( self, diff --git a/tests/data/classification/surface_2D_subsystem_classification.json b/tests/data/classification/surface_2D_subsystem_classification.json deleted file mode 100644 index db8bd8cb3..000000000 --- a/tests/data/classification/surface_2D_subsystem_classification.json +++ /dev/null @@ -1,5395 +0,0 @@ -{ - "5BZbNJgzr0hqEwBFL0tzhCYVlfRb": { - "topology": [ - { - "atoms": { - "labels": [ - "N", - "N", - "C", - "C", - "B", - "B" - ], - "species": [ - 7, - 7, - 6, - 6, - 5, - 5 - ], - "positions": [ - [ - 0.0, - 0.0, - 0.0 - ], - [ - 0.0, - 0.0, - 6.207700540042802 - ], - [ - -7.734710224832942e-18, - 1.4385198970702377, - 3.1033148311789057 - ], - [ - 7.734710224832942e-18, - 2.8770398372960724, - 3.1044161012110054 - ], - [ - -7.734710224832942e-18, - 1.4385198970702377, - 9.248229259962613e-4 - ], - [ - 7.734710224832942e-18, - 2.8770398372960724, - 6.206744562579172 - ] - ], - "lattice_vectors": [ - [ - 1.24579479260285, - 2.157779867183155, - 0.0 - ], - [ - -1.24579479260285, - 2.157779867183155, - 0.0 - ], - [ - 0.0, - 0.0, - 9.527381539056982 - ] - ], - "periodic": [ - true, - true, - true - ] - }, - "description": "A representative system chosen from the original simulation.", - "id": "0", - "method": "parser", - "label": "original", - "structural_type": "unavailable", - "elements": [ - "B", - "C", - "N" - ], - "formula_hill": "C2B2N2", - "children": [ - 1, - 2, - 3 - ] - }, - { - "description": "Automatically detected subsystem.", - "id": "1", - "methode": "matid", - "label": "subsystem", - "elements": [ - "B", - "N" - ], - "formula_hill": "BN", - "parent": "0", - "indices": [ - 1, - 5 - ], - "structural_type": "2D" - }, - { - "description": "Automatically detected subsystem.", - "id": "2", - "methode": "matid", - "label": "subsystem", - "elements": [ - "C" - ], - "formula_hill": "C2", - "parent": "0", - "indices": [ - 2, - 3 - ], - "structural_type": "2D" - }, - { - "description": "Automatically detected subsystem.", - "id": "3", - "methode": "matid", - "label": "subsystem", - "elements": [ - "B", - "N" - ], - "formula_hill": "BN", - "parent": "0", - "indices": [ - 0, - 4 - ], - "structural_type": "2D" - } - ] - }, - "6-UUp1KpacX4OikAFWrv64TJqV_L": { - "topology": [ - { - "atoms": { - "labels": [ - "Ba", - "Ba", - "O", - "O", - "O", - "O", - "O", - "O", - "Sn", - "Sn", - "Ba", - "Ba", - "O", - "O", - "O", - "O", - "O", - "O", - "Sn", - "Sn", - "Ba", - "Ba", - "O", - "O", - "O", - "O", - "O", - "O", - "Sn", - "Sn", - "Ba", - "Ba", - "O", - "O", - "O", - "O", - "Sn", - "Sn", - "O", - "O", - "Ba", - "Ba", - "O", - "O", - "O", - "O", - "Sn", - "Sn", - "O", - "O", - "O", - "O", - "Ba", - "Ba", - "O", - "O", - "Sn", - "Sn", - "O", - "O", - "O", - "O", - "Ba", - "Ba", - "O", - "O", - "Sn", - "Sn", - "O", - "O", - "O", - "O", - "Ba", - "Ba", - "O", - "O", - "Sn", - "Sn", - "O", - "O", - "Ba", - "Ba", - "O", - "O", - "O", - "O", - "Sn", - "Sn", - "O", - "O", - "Ba", - "Ba", - "O", - "O", - "O", - "O", - "Sn", - 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Added unit test for classifucation --- nomad/normalizing/material.py | 7 + .../surface_2D_subsystem_classification.json | 5395 +++++++++++++++++ 2 files changed, 5402 insertions(+) create mode 100644 tests/data/normalizers/classification/surface_2D_subsystem_classification.json diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index b970a8e5f..b48bd947a 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -22,8 +22,12 @@ from collections import defaultdict import re import ase.data from ase import Atoms +from ase.geometry.cell import complete_cell import numpy as np import matid.geometry +from matid.classification.structureclusterer import StructureClusterer +from matid import Classifier +from matid.classifications import Class0D, Atom, Class1D, Material2D, Surface, Class3D, Unknown from nomad.datamodel.results import Symmetry, Material, System, Cell, Relation, StructureOriginal from nomad import atomutils @@ -404,6 +408,7 @@ class MaterialNormalizer(): ''' # Use the calculation topology primarily topology_calc = self.topology_calculation(material) + if topology_calc: return topology_calc topology_matid = self.topology_matid(material) @@ -444,6 +449,7 @@ class MaterialNormalizer(): try: formula = atomutils.Formula(group.composition_formula) except Exception: + print('520') formula_hill = None formula_anonymous = None formula_reduced = None @@ -525,6 +531,7 @@ class MaterialNormalizer(): try: formula = atomutils.Formula(symbols) except Exception: + print('602') pass else: top.formula_hill = formula.format('hill') diff --git a/tests/data/normalizers/classification/surface_2D_subsystem_classification.json b/tests/data/normalizers/classification/surface_2D_subsystem_classification.json new file mode 100644 index 000000000..db8bd8cb3 --- /dev/null +++ b/tests/data/normalizers/classification/surface_2D_subsystem_classification.json @@ -0,0 +1,5395 @@ +{ + "5BZbNJgzr0hqEwBFL0tzhCYVlfRb": { + "topology": [ + { + "atoms": 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9.486358919170467, + 0.0, + 0.0 + ], + [ + -4.74267984964827, + 8.215719540366331, + 0.0 + ], + [ + 0.0, + 0.0, + 14.999998923476708 + ] + ], + "periodic": [ + true, + true, + true + ] + }, + "description": "A representative system chosen from the original simulation.", + "id": "0", + "method": "parser", + "label": "original", + "structural_type": "unavailable", + "elements": [ + "C", + "H", + "Mo", + "S" + ], + "formula_hill": "C16H10Mo9S18", + "children": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15, + 16, + 17, + 18, + 19, + 20, + 21, + 22, + 23, + 24, + 25, + 26, + 27 + ] + }, + { + "description": "Automatically detected subsystem.", + "id": "1", + "methode": "matid", + "label": "subsystem", + "elements": [ + "H", + "C" + ], + "formula_hill": "H10C16", + "parent": "0", + "indices": [ + 27, + 28, + 29, + 30, + 31, + 32, + 33, + 34, + 35, + 36, + 37, + 38, + 39, + 40, + 41, + 42, + 43, + 44, + 45, + 46, + 47, + 48, + 49, + 50, + 51, + 52 + ], + "structural_type": "molecule / cluster" + }, + { + "description": "Automatically detected subsystem.", + "id": "8", + "methode": "matid", + "label": "subsystem", + "elements": [ + "Mo", + "S" + ], + "formula_hill": "Mo9S18", + "parent": "0", + "indices": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15, + 16, + 17, + 18, + 19, + 20, + 21, + 22, + 23, + 24, + 25, + 26 + ], + "structural_type": "2D" + } + ] + } +} \ No newline at end of file -- GitLab From 679fe943096f68e7be898ee88e43ccb9e8504de0 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Tue, 9 Aug 2022 16:40:20 +0200 Subject: [PATCH 06/63] refactored the topology functions so that there is a seperate function for topologies retrieved from the simulation itself and for topologies calculated by MatID --- nomad/normalizing/material.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index b48bd947a..33a30358f 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -408,7 +408,6 @@ class MaterialNormalizer(): ''' # Use the calculation topology primarily topology_calc = self.topology_calculation(material) - if topology_calc: return topology_calc topology_matid = self.topology_matid(material) @@ -432,7 +431,6 @@ class MaterialNormalizer(): topology, original, structure_original = self._init_orig_topology(material) if structure_original is None: return [] - top_id = 0 top_id_original = f'/results/material/topology/{top_id}' top_id += 1 @@ -596,7 +594,7 @@ class MaterialNormalizer(): return list(topology.values()) - def _init_orig_topology(self, material: Material) -> Tuple[Dict[str, System], System, StructureOriginal]: + def _init_orig_topology(self, material: Material) -> Tuple[System, StructureOriginal, Dict[str, System]]: topology: Dict[str, System] = {} structure_original = self._check_original_structure() @@ -647,9 +645,13 @@ class MaterialNormalizer(): except Exception: return None + # TODO: It still needs to be decided what this limit should be. + n_atoms = len(structure_original.species_at_sites) + if n_atoms > 500: + return None return structure_original - def _perform_matid_clustering(self, structure_original: StructureOriginal) -> list: + def _perform_MatID_clustering(self, structure_original: StructureOriginal) -> list: ''' Creates an ase.atoms and performs the clustering with MatID ''' -- GitLab From 6da4ffc2c19ff3286581ad85b6d1d8e95c844be0 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Mon, 15 Aug 2022 15:42:06 +0200 Subject: [PATCH 07/63] Added test of periodicity to prevent periodic_finder from analyzing systems without any periodicity --- nomad/normalizing/material.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index 33a30358f..ba0e3b22b 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -645,6 +645,9 @@ class MaterialNormalizer(): except Exception: return None + if structure_original.nperiodic_dimensions == 0: + return None + # TODO: It still needs to be decided what this limit should be. n_atoms = len(structure_original.species_at_sites) if n_atoms > 500: -- GitLab From d17e0f0c3ae4e0a19fd0029da8792a5d099bb49f Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Fri, 12 Aug 2022 16:14:49 +0200 Subject: [PATCH 08/63] Extracted the largest (in respect of number of atoms) region from each cluster that corresponds to a surface, calculated the symmetri information for that region with matids SymmetryAnalyzer and added the conventional cell as sub-system to that cluster. However, there are still some visualization problems in the gui. And a little cleanup is necessary --- nomad/normalizing/material.py | 92 +++++++++++++++++++++++++++++++---- 1 file changed, 82 insertions(+), 10 deletions(-) diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index ba0e3b22b..0688a464d 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -28,7 +28,7 @@ import matid.geometry from matid.classification.structureclusterer import StructureClusterer from matid import Classifier from matid.classifications import Class0D, Atom, Class1D, Material2D, Surface, Class3D, Unknown - +from matid.symmetry.symmetryanalyzer import SymmetryAnalyzer from nomad.datamodel.results import Symmetry, Material, System, Cell, Relation, StructureOriginal from nomad import atomutils from nomad.utils import hash @@ -411,6 +411,22 @@ class MaterialNormalizer(): if topology_calc: return topology_calc topology_matid = self.topology_matid(material) + + #============================== + # import json + # topology_json = {'topology': []} + # for top_counter, top in enumerate(topology_matid): + # try: + # if top.symmetry: + # top.symmetry = top.symmetry.m_to_json() + # topology_json['topology'] = [top.m_to_json()] + + # except: + # import pdb; pdb.set_trace() + # with open('test_topology.json', 'w') as f: + # json.dump(topology_json, f) + # import pdb; pdb.set_trace() + #============================== if topology_matid: return topology_matid @@ -551,6 +567,7 @@ class MaterialNormalizer(): if material.structural_type not in {'2D', 'surface', 'unavailable'}: return None topology, original, structure_original = self._init_orig_topology(material) + if structure_original is None: return None if structure_original.nperiodic_dimensions == 0: @@ -572,14 +589,21 @@ class MaterialNormalizer(): if system_type not in {"2D", "surface"}: continue subsystem = self._create_subsystem(structure_original, indices, system_type, top_id) - topology[top_id_str] = subsystem - parent_children = original.child_systems if original.child_systems else [] - parent_children.append(top_id_str) - original.child_systems = parent_children + parent_children_original = original.child_systems if original.child_systems else [] + parent_children_original.append(top_id_str) + original.child_systems = parent_children_original + parent_system = f'/results/material/topology/{top_id}' top_id += 1 - top_id_str = f'/results/material/topology/{top_id}' - + if system_type == 'surface': + top_id_str = f'/results/material/topology/{top_id}' + symmsystem = self._create_symmsystem(symm, top_id_str, parent_system, subsystem) + topology[top_id_str] = symmsystem + parent_children_subsystem = subsystem.child_systems if subsystem.child_systems else [] + parent_children_subsystem.append(top_id_str) + subsystem.child_systems = parent_children_subsystem + top_id += 1 + top_id_str = f'/results/material/topology/{top_id}' # TODO: Analyze the connected cells # (matid.core.linkedunits.LinkedUnitCollection) in the subsystem to # figure out the structure type, conventional cell, orientation, @@ -602,7 +626,7 @@ class MaterialNormalizer(): return None, None, None top_id = 0 - original = self._add_orig_topology_as_root(material, top_id) + original, top_id_str = self._add_orig_topology_as_root(material, top_id) if structure_original: original.cell = self._create_cell(structure_original) @@ -713,8 +737,20 @@ class MaterialNormalizer(): for cluster in filtered_cluster: indices = list(cluster.indices) cluster_indices_list += [indices] - - return cluster_indices_list + # ======================================== + regions = cluster.regions + number_of_atoms = [] + for region in regions: + if region: + number_of_atoms += [region.cell.get_number_of_atoms()] + + # TODO: What happens when there are 2 regions that have the same size? + largest_region_index = number_of_atoms.index(max(number_of_atoms)) + largest_region_system = regions[largest_region_index].cell + # TODO: only SymmetryAnalyzer for 2D and surface + symm = SymmetryAnalyzer(largest_region_system) + cluster_symmetries += [symm] + return cluster_indices_list, cluster_symmetries def _system_type_analysis(self, structure_original: StructureOriginal, indices: List[int]) -> matid.classifications: ''' @@ -779,3 +815,39 @@ class MaterialNormalizer(): n_atoms=len(indices) ) return subsystem + + def _create_symmsystem(self, symm, top_id_str, parent_system, parent_subsystem): + """ + Creates the subsystem with the symmetry information of the conventional cell + """ + subsystem = System( + system_id=top_id_str, + method='matid', + label='conventional cell', + description='This is the calulated conventional cell of the bulk material to which the surface belongs.', + system_relation=Relation(type='subsystem'), + parent_system=parent_system, + symmetry=Symmetry() + ) + space_group_number = symm.get_space_group_number() + hall_number = symm.get_hall_number() + hall_symbol = symm.get_hall_symbol() + international_short = symm.get_space_group_international_short() + crystal_system = symm.get_crystal_system() + bravais_lattice = symm.get_bravais_lattice() + point_group = symm.get_point_group() + transform = symm._get_spglib_transformation_matrix() + origin_shift = symm._get_spglib_origin_shift() + + sec_symmetry = subsystem.symmetry + sec_symmetry.symmetry_method = 'MatID' + sec_symmetry.space_group_number = space_group_number + sec_symmetry.hall_number = hall_number + sec_symmetry.hall_symbol = hall_symbol + sec_symmetry.international_short_symbol = international_short + sec_symmetry.point_group = point_group + sec_symmetry.crystal_system = crystal_system + sec_symmetry.bravais_lattice = bravais_lattice + sec_symmetry.origin_shift = origin_shift + sec_symmetry.transformation_matrix = transform + return subsystem -- GitLab From 42eed70631eccdd59c1108af8fa793619b317de9 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Fri, 12 Aug 2022 16:14:49 +0200 Subject: [PATCH 09/63] Extracted the largest (in respect of number of atoms) region from each cluster that corresponds to a surface, calculated the symmetri information for that region with matids SymmetryAnalyzer and added the conventional cell as sub-system to that cluster. However, there are still some visualization problems in the gui. And a little cleanup is necessary --- nomad/normalizing/material.py | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index 0688a464d..9cae82060 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -851,3 +851,39 @@ class MaterialNormalizer(): sec_symmetry.origin_shift = origin_shift sec_symmetry.transformation_matrix = transform return subsystem + + def _create_symmsystem(self, symm, top_id_str, parent_system, parent_subsystem): + """ + Creates the subsystem with the symmetry information of the conventional cell + """ + subsystem = System( + system_id=top_id_str, + method='matid', + label='conventional cell', + description='This is the calulated conventional cell of the bulk material to which the surface belongs.', + system_relation=Relation(type='subsystem'), + parent_system=parent_system, + symmetry=Symmetry() + ) + space_group_number = symm.get_space_group_number() + hall_number = symm.get_hall_number() + hall_symbol = symm.get_hall_symbol() + international_short = symm.get_space_group_international_short() + crystal_system = symm.get_crystal_system() + bravais_lattice = symm.get_bravais_lattice() + point_group = symm.get_point_group() + transform = symm._get_spglib_transformation_matrix() + origin_shift = symm._get_spglib_origin_shift() + + sec_symmetry = subsystem.symmetry + sec_symmetry.symmetry_method = 'MatID' + sec_symmetry.space_group_number = space_group_number + sec_symmetry.hall_number = hall_number + sec_symmetry.hall_symbol = hall_symbol + sec_symmetry.international_short_symbol = international_short + sec_symmetry.point_group = point_group + sec_symmetry.crystal_system = crystal_system + sec_symmetry.bravais_lattice = bravais_lattice + sec_symmetry.origin_shift = origin_shift + sec_symmetry.transformation_matrix = transform + return subsystem -- GitLab From f36897baf33f425ba3b39d782390040722d318f4 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Fri, 19 Aug 2022 21:57:43 +0200 Subject: [PATCH 10/63] Refactoring and clean up --- nomad/normalizing/material.py | 116 ++++++++++++++++++---------------- 1 file changed, 63 insertions(+), 53 deletions(-) diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index 9cae82060..54a39b37f 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -19,6 +19,7 @@ from typing import Union, Dict, List, Tuple, Optional from nptyping import NDArray from collections import defaultdict +from math import pi import re import ase.data from ase import Atoms @@ -28,8 +29,9 @@ import matid.geometry from matid.classification.structureclusterer import StructureClusterer from matid import Classifier from matid.classifications import Class0D, Atom, Class1D, Material2D, Surface, Class3D, Unknown +from matid.core.system import System as CorSystem from matid.symmetry.symmetryanalyzer import SymmetryAnalyzer -from nomad.datamodel.results import Symmetry, Material, System, Cell, Relation, StructureOriginal +from nomad.datamodel.results import Symmetry, Material, System, Cell, Relation, StructureOriginal, Prototype from nomad import atomutils from nomad.utils import hash @@ -412,21 +414,6 @@ class MaterialNormalizer(): return topology_calc topology_matid = self.topology_matid(material) - #============================== - # import json - # topology_json = {'topology': []} - # for top_counter, top in enumerate(topology_matid): - # try: - # if top.symmetry: - # top.symmetry = top.symmetry.m_to_json() - # topology_json['topology'] = [top.m_to_json()] - - # except: - # import pdb; pdb.set_trace() - # with open('test_topology.json', 'w') as f: - # json.dump(topology_json, f) - # import pdb; pdb.set_trace() - #============================== if topology_matid: return topology_matid @@ -590,14 +577,10 @@ class MaterialNormalizer(): continue subsystem = self._create_subsystem(structure_original, indices, system_type, top_id) topology[top_id_str] = subsystem - parent_children_original = original.child_systems if original.child_systems else [] - parent_children_original.append(top_id_str) - original.child_systems = parent_children_original - parent_system = f'/results/material/topology/{top_id}' - top_id += 1 + original = self._add_child_system(original, top_id_str) if system_type == 'surface': - top_id_str = f'/results/material/topology/{top_id}' - symmsystem = self._create_symmsystem(symm, top_id_str, parent_system, subsystem) + symmsystem = self._create_conv_cell_system(symm) + top_id_str = f'/results/material/topology/{self.top_id}' topology[top_id_str] = symmsystem parent_children_subsystem = subsystem.child_systems if subsystem.child_systems else [] parent_children_subsystem.append(top_id_str) @@ -625,8 +608,8 @@ class MaterialNormalizer(): if structure_original is None: return None, None, None - top_id = 0 - original, top_id_str = self._add_orig_topology_as_root(material, top_id) + self.top_id = 0 + original, top_id_str = self._add_orig_topology_as_root(material) if structure_original: original.cell = self._create_cell(structure_original) @@ -706,15 +689,15 @@ class MaterialNormalizer(): Creates a Cell from the given structure. ''' cell = Cell( - a=structure_original.lattice_parameters.a, - b=structure_original.lattice_parameters.b, - c=structure_original.lattice_parameters.c, - alpha=structure_original.lattice_parameters.alpha, - beta=structure_original.lattice_parameters.beta, - gamma=structure_original.lattice_parameters.gamma, - volume=structure_original.cell_volume, - atomic_density=structure_original.atomic_density, - mass_density=structure_original.mass_density, + a=cell_params['a'], + b=cell_params['b'], + c=cell_params['c'], + alpha=cell_params['alpha'], + beta=cell_params['beta'], + gamma=cell_params['gamma'], + volume=cell_params['volume'], + atomic_density=cell_params['atomic_density'], + mass_density=cell_params['mass_density'], ) return cell @@ -737,7 +720,7 @@ class MaterialNormalizer(): for cluster in filtered_cluster: indices = list(cluster.indices) cluster_indices_list += [indices] - # ======================================== + regions = cluster.regions number_of_atoms = [] for region in regions: @@ -752,6 +735,31 @@ class MaterialNormalizer(): cluster_symmetries += [symm] return cluster_indices_list, cluster_symmetries + def _create_system_params(self, label: str, parent_system: str) -> Dict: + systemparams_subsystem = {} + if label is 'subsystem': + systemparams_subsystem = { + 'method': 'matid', + 'label': 'subsystem', + 'description': 'Automatically detected subsystem.', + 'system_relation': Relation(type='subsystem'), + 'parent_system': f'/results/material/topology/0' + } + elif label is 'conventional cell': + systemparams_subsystem = { + 'method': 'matid', + 'label': 'conventional cell', + 'description': 'This is the calulated conventional cell of the bulk material to which the surface belongs.', + 'system_relation': Relation(type='subsystem'), + 'structural_type': None, + 'indices': None, + 'parent_system': parent_system + } + else: + self.logger.error( + 'Creation of system parameters failed because the label is neither subsystem nor conventional cell') + return systemparams_subsystem + def _system_type_analysis(self, structure_original: StructureOriginal, indices: List[int]) -> matid.classifications: ''' Classifies ase.atoms and returns the MatID system type as a string. @@ -797,16 +805,16 @@ class MaterialNormalizer(): formula_anonymous = formula.format('anonymous') formula_reduced = formula.format('reduce') elements = formula.elements() - top_id_str = f'/results/material/topology/{top_id}' + top_id_str = f'/results/material/topology/{self.top_id}' subsystem = System( system_id=top_id_str, - method='matid', - label='subsystem', - description='Automatically detected subsystem.', - structural_type=system_type, - indices=[indices], - system_relation=Relation(type='subsystem'), + method=systemparams['method'], + label=systemparams['label'], + description=systemparams['description'], + structural_type=systemparams['structural_type'], + indices=systemparams['indices'], + system_relation=systemparams['system_relation'], formula_hill=formula_hill, formula_anonymous=formula_anonymous, formula_reduced=formula_reduced, @@ -816,19 +824,21 @@ class MaterialNormalizer(): ) return subsystem - def _create_symmsystem(self, symm, top_id_str, parent_system, parent_subsystem): + def _create_symmsystem(self, symm: SymmetryAnalyzer, subsystem: System) -> System: """ Creates the subsystem with the symmetry information of the conventional cell """ - subsystem = System( - system_id=top_id_str, - method='matid', - label='conventional cell', - description='This is the calulated conventional cell of the bulk material to which the surface belongs.', - system_relation=Relation(type='subsystem'), - parent_system=parent_system, - symmetry=Symmetry() - ) + conv_system = symm.get_conventional_system() + cell_params = self._extract_cell_params(conv_system) + cell = self._create_cell(cell_params) + subsystem.cell = cell + symmetry = self._create_symmetry(subsystem, symm) + subsystem.symmetry = symmetry + prototype = self._create_prototype(symm, conv_system) + subsystem.prototype = prototype + return subsystem + + def _create_symmetry(self, subsystem: System, symm: SymmetryAnalyzer) -> Symmetry: space_group_number = symm.get_space_group_number() hall_number = symm.get_hall_number() hall_symbol = symm.get_hall_symbol() @@ -839,7 +849,7 @@ class MaterialNormalizer(): transform = symm._get_spglib_transformation_matrix() origin_shift = symm._get_spglib_origin_shift() - sec_symmetry = subsystem.symmetry + sec_symmetry = Symmetry() sec_symmetry.symmetry_method = 'MatID' sec_symmetry.space_group_number = space_group_number sec_symmetry.hall_number = hall_number -- GitLab From a77f682be2da34c74e64a9a451a5ca7e340e3d90 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Tue, 2 Aug 2022 15:13:32 +0200 Subject: [PATCH 11/63] Modify nomad/normalizing/material.py to include classification of 2D and surfaces to results.material.topology. Also added the unit test for that functionality and reference data for the unit test --- nomad/normalizing/material.py | 1 + .../surface_2D_subsystem_classification.json | 5395 +++++++++++++++++ 2 files changed, 5396 insertions(+) create mode 100644 tests/data/classification/surface_2D_subsystem_classification.json diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index 54a39b37f..2e4b857df 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -36,6 +36,7 @@ from nomad import atomutils from nomad.utils import hash + class MaterialNormalizer(): def __init__( self, diff --git a/tests/data/classification/surface_2D_subsystem_classification.json b/tests/data/classification/surface_2D_subsystem_classification.json new file mode 100644 index 000000000..db8bd8cb3 --- /dev/null +++ b/tests/data/classification/surface_2D_subsystem_classification.json @@ -0,0 +1,5395 @@ +{ + "5BZbNJgzr0hqEwBFL0tzhCYVlfRb": { + "topology": [ + { + "atoms": { + "labels": [ + "N", + "N", + "C", + "C", + "B", + "B" + ], + "species": [ + 7, + 7, + 6, + 6, + 5, + 5 + ], + "positions": [ + [ + 0.0, + 0.0, + 0.0 + ], + [ + 0.0, + 0.0, + 6.207700540042802 + ], + [ + -7.734710224832942e-18, + 1.4385198970702377, + 3.1033148311789057 + ], + [ + 7.734710224832942e-18, + 2.8770398372960724, + 3.1044161012110054 + ], + [ + -7.734710224832942e-18, + 1.4385198970702377, + 9.248229259962613e-4 + ], + [ + 7.734710224832942e-18, + 2.8770398372960724, + 6.206744562579172 + ] + ], + "lattice_vectors": [ + [ + 1.24579479260285, + 2.157779867183155, + 0.0 + ], + [ + -1.24579479260285, + 2.157779867183155, + 0.0 + ], + [ + 0.0, + 0.0, + 9.527381539056982 + ] + ], + "periodic": [ + true, + true, + true + ] + }, + "description": "A representative system chosen from the original simulation.", + "id": "0", + "method": "parser", + "label": "original", + "structural_type": "unavailable", + "elements": [ + "B", + "C", + "N" + ], + "formula_hill": "C2B2N2", + "children": 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"structural_type": "molecule / cluster" + }, + { + "description": "Automatically detected subsystem.", + "id": "8", + "methode": "matid", + "label": "subsystem", + "elements": [ + "Mo", + "S" + ], + "formula_hill": "Mo9S18", + "parent": "0", + "indices": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15, + 16, + 17, + 18, + 19, + 20, + 21, + 22, + 23, + 24, + 25, + 26 + ], + "structural_type": "2D" + } + ] + } +} \ No newline at end of file -- GitLab From a938c8d53cc325830475f06652ea39b327fddfc6 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Tue, 2 Aug 2022 15:42:18 +0200 Subject: [PATCH 12/63] Modify nomad/normalizing/material.py to include classification of 2D and surfaces to results.material.topology. Also added the unit test for that functionality and reference data for the unit test --- tests/normalizing/test_material.py | 78 ++++++++++++++++++++---------- 1 file changed, 52 insertions(+), 26 deletions(-) diff --git a/tests/normalizing/test_material.py b/tests/normalizing/test_material.py index b1fbd0376..18a685538 100644 --- a/tests/normalizing/test_material.py +++ b/tests/normalizing/test_material.py @@ -62,7 +62,8 @@ def assert_structure(structure, has_cell=True, has_wyckoff=False): assert structure.species[0].chemical_symbols if has_cell: assert len(structure.dimension_types) == 3 - assert np.sum(structure.dimension_types) == structure.nperiodic_dimensions + assert np.sum( + structure.dimension_types) == structure.nperiodic_dimensions assert structure.lattice_vectors.shape == (3, 3) a = structure.lattice_parameters.a b = structure.lattice_parameters.b @@ -145,9 +146,11 @@ def test_material_1d(one_d): assert conv.n_sites == 4 assert conv.species_at_sites == ["C", "C", "H", "H"] assert np.array_equal(conv.dimension_types, [1, 0, 0]) - assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(2.459, abs=1e-3) + assert conv.lattice_parameters.a.to( + ureg.angstrom).magnitude == pytest.approx(2.459, abs=1e-3) assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == 0 - assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == pytest.approx(2.890, abs=1e-3) + assert conv.lattice_parameters.c.to( + ureg.angstrom).magnitude == pytest.approx(2.890, abs=1e-3) assert conv.lattice_parameters.alpha is None assert conv.lattice_parameters.beta.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.gamma is None @@ -182,12 +185,15 @@ def test_material_2d(two_d): assert conv.n_sites == 2 assert conv.species_at_sites == ["C", "C"] assert np.array_equal(conv.dimension_types, [1, 1, 0]) - assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) - assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) + assert conv.lattice_parameters.a.to( + ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) + assert conv.lattice_parameters.b.to( + ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == 0 assert conv.lattice_parameters.alpha is None assert conv.lattice_parameters.beta is None - assert conv.lattice_parameters.gamma.magnitude == pytest.approx(120 / 180 * np.pi) + assert conv.lattice_parameters.gamma.magnitude == pytest.approx( + 120 / 180 * np.pi) # Original structure assert_structure(two_d.results.properties.structures.structure_original) @@ -232,11 +238,15 @@ def test_material_bulk(bulk): conv = bulk.results.properties.structures.structure_conventional assert_structure(conv, has_wyckoff=True) assert conv.n_sites == 8 - assert conv.species_at_sites == ["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"] + assert conv.species_at_sites == [ + "Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"] assert np.array_equal(conv.dimension_types, [1, 1, 1]) - assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) - assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) - assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.a.to( + ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.b.to( + ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.c.to( + ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) assert conv.lattice_parameters.alpha.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.beta.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.gamma.magnitude == pytest.approx(np.pi / 2) @@ -281,7 +291,8 @@ def test_1d_material_identification(): pos = nanotube4.get_positions() pos += 0.2 * np.random.rand(pos.shape[0], pos.shape[1]) nanotube4.set_positions(pos) - hash4 = get_template_for_structure(nanotube4).results.material.material_id + hash4 = get_template_for_structure( + nanotube4).results.material.material_id assert hash4 == hash1 # Too distorted copy should not match @@ -303,7 +314,8 @@ def test_2d_material_identification(): indices=[0, 1] )] space_group_number = 191 - norm_hash_string = atomutils.get_symmetry_string(space_group_number, wyckoff_sets, is_2d=True) + norm_hash_string = atomutils.get_symmetry_string( + space_group_number, wyckoff_sets, is_2d=True) graphene_material_id = hash(norm_hash_string) # Graphene orthogonal cell @@ -322,13 +334,15 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure(graphene).results.material.material_id + material_id = get_template_for_structure( + graphene).results.material.material_id assert material_id == graphene_material_id # Graphene orthogonal supercell graphene2 = graphene.copy() graphene2 *= [2, 1, 2] - material_id = get_template_for_structure(graphene2).results.material.material_id + material_id = get_template_for_structure( + graphene2).results.material.material_id assert material_id == graphene_material_id # Graphene primitive cell @@ -345,7 +359,8 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure(graphene3).results.material.material_id + material_id = get_template_for_structure( + graphene3).results.material.material_id assert material_id == graphene_material_id # Slightly distorted system should match @@ -355,7 +370,8 @@ def test_2d_material_identification(): pos = graphene4.get_positions() pos += 0.05 * np.random.rand(pos.shape[0], pos.shape[1]) graphene4.set_positions(pos) - material_id = get_template_for_structure(graphene4).results.material.material_id + material_id = get_template_for_structure( + graphene4).results.material.material_id assert material_id == graphene_material_id # Too distorted system should not match @@ -364,7 +380,8 @@ def test_2d_material_identification(): np.random.seed(4) pos += 1 * np.random.rand(pos.shape[0], pos.shape[1]) graphene5.set_positions(pos) - material_id = get_template_for_structure(graphene5).results.material.material_id + material_id = get_template_for_structure( + graphene5).results.material.material_id assert material_id != graphene_material_id # Expected information for MoS2. MoS2 has finite thichkness unlike @@ -388,7 +405,8 @@ def test_2d_material_identification(): ) ] space_group_number = 11 - norm_hash_string = atomutils.get_symmetry_string(space_group_number, wyckoff_sets, is_2d=True) + norm_hash_string = atomutils.get_symmetry_string( + space_group_number, wyckoff_sets, is_2d=True) mos2_material_id = hash(norm_hash_string) # MoS2 orthogonal cell @@ -409,30 +427,36 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure(atoms).results.material.material_id + material_id = get_template_for_structure( + atoms).results.material.material_id assert material_id == mos2_material_id # MoS2 orthogonal supercell atoms *= [2, 3, 1] - material_id = get_template_for_structure(atoms).results.material.material_id + material_id = get_template_for_structure( + atoms).results.material.material_id assert material_id == mos2_material_id def test_bulk_material_identification(): # Original system - wurtzite = ase.build.bulk("SiC", crystalstructure="wurtzite", a=3.086, c=10.053) - material_id_wurtzite = get_template_for_structure(wurtzite).results.material.material_id + wurtzite = ase.build.bulk( + "SiC", crystalstructure="wurtzite", a=3.086, c=10.053) + material_id_wurtzite = get_template_for_structure( + wurtzite).results.material.material_id # Rotated wurtzite2 = wurtzite.copy() wurtzite2.rotate(90, "z", rotate_cell=True) - material_id = get_template_for_structure(wurtzite2).results.material.material_id + material_id = get_template_for_structure( + wurtzite2).results.material.material_id assert material_id == material_id_wurtzite # Supercell wurtzite3 = wurtzite.copy() wurtzite3 *= [2, 3, 1] - materia_id = get_template_for_structure(wurtzite3).results.material.material_id + materia_id = get_template_for_structure( + wurtzite3).results.material.material_id assert materia_id == material_id_wurtzite # Slightly distorted system should match @@ -442,7 +466,8 @@ def test_bulk_material_identification(): pos = wurtzite4.get_positions() pos += 0.05 * np.random.rand(pos.shape[0], pos.shape[1]) wurtzite4.set_positions(pos) - material_id = get_template_for_structure(wurtzite4).results.material.material_id + material_id = get_template_for_structure( + wurtzite4).results.material.material_id assert material_id == material_id_wurtzite # Too distorted system should not match @@ -451,7 +476,8 @@ def test_bulk_material_identification(): np.random.seed(4) pos += 1 * np.random.rand(pos.shape[0], pos.shape[1]) wurtzite5.set_positions(pos) - material_id = get_template_for_structure(wurtzite5).results.material.material_id + material_id = get_template_for_structure( + wurtzite5).results.material.material_id assert material_id != material_id_wurtzite -- GitLab From 11e0d22e6dc7926a41a7b01f312aaf0a77ea72cb Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Tue, 2 Aug 2022 16:16:42 +0200 Subject: [PATCH 13/63] Revert "Modify nomad/normalizing/material.py to include classification of 2D and surfaces to results.material.topology. Also added the unit test for that functionality and reference data for the unit test" This reverts commit 624f94080ce4fa94cf22c29adad1231cc65a6b29. --- tests/normalizing/test_material.py | 78 ++++++++++-------------------- 1 file changed, 26 insertions(+), 52 deletions(-) diff --git a/tests/normalizing/test_material.py b/tests/normalizing/test_material.py index 18a685538..b1fbd0376 100644 --- a/tests/normalizing/test_material.py +++ b/tests/normalizing/test_material.py @@ -62,8 +62,7 @@ def assert_structure(structure, has_cell=True, has_wyckoff=False): assert structure.species[0].chemical_symbols if has_cell: assert len(structure.dimension_types) == 3 - assert np.sum( - structure.dimension_types) == structure.nperiodic_dimensions + assert np.sum(structure.dimension_types) == structure.nperiodic_dimensions assert structure.lattice_vectors.shape == (3, 3) a = structure.lattice_parameters.a b = structure.lattice_parameters.b @@ -146,11 +145,9 @@ def test_material_1d(one_d): assert conv.n_sites == 4 assert conv.species_at_sites == ["C", "C", "H", "H"] assert np.array_equal(conv.dimension_types, [1, 0, 0]) - assert conv.lattice_parameters.a.to( - ureg.angstrom).magnitude == pytest.approx(2.459, abs=1e-3) + assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(2.459, abs=1e-3) assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == 0 - assert conv.lattice_parameters.c.to( - ureg.angstrom).magnitude == pytest.approx(2.890, abs=1e-3) + assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == pytest.approx(2.890, abs=1e-3) assert conv.lattice_parameters.alpha is None assert conv.lattice_parameters.beta.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.gamma is None @@ -185,15 +182,12 @@ def test_material_2d(two_d): assert conv.n_sites == 2 assert conv.species_at_sites == ["C", "C"] assert np.array_equal(conv.dimension_types, [1, 1, 0]) - assert conv.lattice_parameters.a.to( - ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) - assert conv.lattice_parameters.b.to( - ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) + assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) + assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == pytest.approx(2.461, abs=1e-3) assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == 0 assert conv.lattice_parameters.alpha is None assert conv.lattice_parameters.beta is None - assert conv.lattice_parameters.gamma.magnitude == pytest.approx( - 120 / 180 * np.pi) + assert conv.lattice_parameters.gamma.magnitude == pytest.approx(120 / 180 * np.pi) # Original structure assert_structure(two_d.results.properties.structures.structure_original) @@ -238,15 +232,11 @@ def test_material_bulk(bulk): conv = bulk.results.properties.structures.structure_conventional assert_structure(conv, has_wyckoff=True) assert conv.n_sites == 8 - assert conv.species_at_sites == [ - "Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"] + assert conv.species_at_sites == ["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"] assert np.array_equal(conv.dimension_types, [1, 1, 1]) - assert conv.lattice_parameters.a.to( - ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) - assert conv.lattice_parameters.b.to( - ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) - assert conv.lattice_parameters.c.to( - ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.a.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.b.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) + assert conv.lattice_parameters.c.to(ureg.angstrom).magnitude == pytest.approx(5.431, abs=1e-3) assert conv.lattice_parameters.alpha.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.beta.magnitude == pytest.approx(np.pi / 2) assert conv.lattice_parameters.gamma.magnitude == pytest.approx(np.pi / 2) @@ -291,8 +281,7 @@ def test_1d_material_identification(): pos = nanotube4.get_positions() pos += 0.2 * np.random.rand(pos.shape[0], pos.shape[1]) nanotube4.set_positions(pos) - hash4 = get_template_for_structure( - nanotube4).results.material.material_id + hash4 = get_template_for_structure(nanotube4).results.material.material_id assert hash4 == hash1 # Too distorted copy should not match @@ -314,8 +303,7 @@ def test_2d_material_identification(): indices=[0, 1] )] space_group_number = 191 - norm_hash_string = atomutils.get_symmetry_string( - space_group_number, wyckoff_sets, is_2d=True) + norm_hash_string = atomutils.get_symmetry_string(space_group_number, wyckoff_sets, is_2d=True) graphene_material_id = hash(norm_hash_string) # Graphene orthogonal cell @@ -334,15 +322,13 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure( - graphene).results.material.material_id + material_id = get_template_for_structure(graphene).results.material.material_id assert material_id == graphene_material_id # Graphene orthogonal supercell graphene2 = graphene.copy() graphene2 *= [2, 1, 2] - material_id = get_template_for_structure( - graphene2).results.material.material_id + material_id = get_template_for_structure(graphene2).results.material.material_id assert material_id == graphene_material_id # Graphene primitive cell @@ -359,8 +345,7 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure( - graphene3).results.material.material_id + material_id = get_template_for_structure(graphene3).results.material.material_id assert material_id == graphene_material_id # Slightly distorted system should match @@ -370,8 +355,7 @@ def test_2d_material_identification(): pos = graphene4.get_positions() pos += 0.05 * np.random.rand(pos.shape[0], pos.shape[1]) graphene4.set_positions(pos) - material_id = get_template_for_structure( - graphene4).results.material.material_id + material_id = get_template_for_structure(graphene4).results.material.material_id assert material_id == graphene_material_id # Too distorted system should not match @@ -380,8 +364,7 @@ def test_2d_material_identification(): np.random.seed(4) pos += 1 * np.random.rand(pos.shape[0], pos.shape[1]) graphene5.set_positions(pos) - material_id = get_template_for_structure( - graphene5).results.material.material_id + material_id = get_template_for_structure(graphene5).results.material.material_id assert material_id != graphene_material_id # Expected information for MoS2. MoS2 has finite thichkness unlike @@ -405,8 +388,7 @@ def test_2d_material_identification(): ) ] space_group_number = 11 - norm_hash_string = atomutils.get_symmetry_string( - space_group_number, wyckoff_sets, is_2d=True) + norm_hash_string = atomutils.get_symmetry_string(space_group_number, wyckoff_sets, is_2d=True) mos2_material_id = hash(norm_hash_string) # MoS2 orthogonal cell @@ -427,36 +409,30 @@ def test_2d_material_identification(): ], pbc=True ) - material_id = get_template_for_structure( - atoms).results.material.material_id + material_id = get_template_for_structure(atoms).results.material.material_id assert material_id == mos2_material_id # MoS2 orthogonal supercell atoms *= [2, 3, 1] - material_id = get_template_for_structure( - atoms).results.material.material_id + material_id = get_template_for_structure(atoms).results.material.material_id assert material_id == mos2_material_id def test_bulk_material_identification(): # Original system - wurtzite = ase.build.bulk( - "SiC", crystalstructure="wurtzite", a=3.086, c=10.053) - material_id_wurtzite = get_template_for_structure( - wurtzite).results.material.material_id + wurtzite = ase.build.bulk("SiC", crystalstructure="wurtzite", a=3.086, c=10.053) + material_id_wurtzite = get_template_for_structure(wurtzite).results.material.material_id # Rotated wurtzite2 = wurtzite.copy() wurtzite2.rotate(90, "z", rotate_cell=True) - material_id = get_template_for_structure( - wurtzite2).results.material.material_id + material_id = get_template_for_structure(wurtzite2).results.material.material_id assert material_id == material_id_wurtzite # Supercell wurtzite3 = wurtzite.copy() wurtzite3 *= [2, 3, 1] - materia_id = get_template_for_structure( - wurtzite3).results.material.material_id + materia_id = get_template_for_structure(wurtzite3).results.material.material_id assert materia_id == material_id_wurtzite # Slightly distorted system should match @@ -466,8 +442,7 @@ def test_bulk_material_identification(): pos = wurtzite4.get_positions() pos += 0.05 * np.random.rand(pos.shape[0], pos.shape[1]) wurtzite4.set_positions(pos) - material_id = get_template_for_structure( - wurtzite4).results.material.material_id + material_id = get_template_for_structure(wurtzite4).results.material.material_id assert material_id == material_id_wurtzite # Too distorted system should not match @@ -476,8 +451,7 @@ def test_bulk_material_identification(): np.random.seed(4) pos += 1 * np.random.rand(pos.shape[0], pos.shape[1]) wurtzite5.set_positions(pos) - material_id = get_template_for_structure( - wurtzite5).results.material.material_id + material_id = get_template_for_structure(wurtzite5).results.material.material_id assert material_id != material_id_wurtzite -- GitLab From 0914e18dfc68401cc805a9114e286646075915de Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Tue, 2 Aug 2022 16:17:55 +0200 Subject: [PATCH 14/63] Revert "Modify nomad/normalizing/material.py to include classification of 2D and surfaces to results.material.topology. Also added the unit test for that functionality and reference data for the unit test" This reverts commit da5df4f4f0e7624ddba0aa0eb3c258e34c8aa2cc. --- nomad/normalizing/material.py | 2 - .../surface_2D_subsystem_classification.json | 5395 ----------------- 2 files changed, 5397 deletions(-) delete mode 100644 tests/data/classification/surface_2D_subsystem_classification.json diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index 2e4b857df..f339593e4 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -23,7 +23,6 @@ from math import pi import re import ase.data from ase import Atoms -from ase.geometry.cell import complete_cell import numpy as np import matid.geometry from matid.classification.structureclusterer import StructureClusterer @@ -36,7 +35,6 @@ from nomad import atomutils from nomad.utils import hash - class MaterialNormalizer(): def __init__( self, diff --git a/tests/data/classification/surface_2D_subsystem_classification.json b/tests/data/classification/surface_2D_subsystem_classification.json deleted file mode 100644 index db8bd8cb3..000000000 --- a/tests/data/classification/surface_2D_subsystem_classification.json +++ /dev/null @@ -1,5395 +0,0 @@ -{ - "5BZbNJgzr0hqEwBFL0tzhCYVlfRb": { - "topology": [ - { - "atoms": { - "labels": [ - "N", - "N", - "C", - "C", - "B", - "B" - ], - "species": [ - 7, - 7, - 6, - 6, - 5, - 5 - ], - "positions": [ - [ - 0.0, - 0.0, - 0.0 - ], - [ - 0.0, - 0.0, - 6.207700540042802 - ], - [ - -7.734710224832942e-18, - 1.4385198970702377, - 3.1033148311789057 - ], - [ - 7.734710224832942e-18, - 2.8770398372960724, - 3.1044161012110054 - ], - [ - -7.734710224832942e-18, - 1.4385198970702377, - 9.248229259962613e-4 - ], - [ - 7.734710224832942e-18, - 2.8770398372960724, - 6.206744562579172 - ] - ], - "lattice_vectors": [ - [ - 1.24579479260285, - 2.157779867183155, - 0.0 - ], - [ - -1.24579479260285, - 2.157779867183155, - 0.0 - ], - [ - 0.0, - 0.0, - 9.527381539056982 - ] - ], - "periodic": [ - true, - true, - true - ] - }, - "description": "A representative system chosen from the original simulation.", - "id": "0", - "method": "parser", - "label": "original", - "structural_type": "unavailable", - "elements": [ - 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"children": [ - 1, - 2, - 3, - 4, - 5, - 6, - 7, - 8, - 9, - 10, - 11, - 12, - 13, - 14, - 15, - 16, - 17, - 18, - 19, - 20, - 21, - 22, - 23, - 24, - 25, - 26, - 27 - ] - }, - { - "description": "Automatically detected subsystem.", - "id": "1", - "methode": "matid", - "label": "subsystem", - "elements": [ - "H", - "C" - ], - "formula_hill": "H10C16", - "parent": "0", - "indices": [ - 27, - 28, - 29, - 30, - 31, - 32, - 33, - 34, - 35, - 36, - 37, - 38, - 39, - 40, - 41, - 42, - 43, - 44, - 45, - 46, - 47, - 48, - 49, - 50, - 51, - 52 - ], - "structural_type": "molecule / cluster" - }, - { - "description": "Automatically detected subsystem.", - "id": "8", - "methode": "matid", - "label": "subsystem", - "elements": [ - "Mo", - "S" - ], - "formula_hill": "Mo9S18", - "parent": "0", - "indices": [ - 0, - 1, - 2, - 3, - 4, - 5, - 6, - 7, - 8, - 9, - 10, - 11, - 12, - 13, - 14, - 15, - 16, - 17, - 18, - 19, - 20, - 21, - 22, - 23, - 24, - 25, - 26 - ], - "structural_type": "2D" - } - ] - } -} \ No newline at end of file -- GitLab From c50b01df245d26bc5aaf7cca8170f08976554cc9 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Mon, 8 Aug 2022 11:13:22 +0200 Subject: [PATCH 15/63] Modified material.py to add the new topological and its classification. Added unit test for classifucation --- nomad/normalizing/material.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index f339593e4..c86e8d82f 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -23,6 +23,7 @@ from math import pi import re import ase.data from ase import Atoms +from ase.geometry.cell import complete_cell import numpy as np import matid.geometry from matid.classification.structureclusterer import StructureClusterer @@ -409,6 +410,7 @@ class MaterialNormalizer(): ''' # Use the calculation topology primarily topology_calc = self.topology_calculation(material) + if topology_calc: return topology_calc topology_matid = self.topology_matid(material) -- GitLab From ca37073cc907b75444812da02d78bcc92e02915d Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Fri, 12 Aug 2022 16:14:49 +0200 Subject: [PATCH 16/63] Extracted the largest (in respect of number of atoms) region from each cluster that corresponds to a surface, calculated the symmetri information for that region with matids SymmetryAnalyzer and added the conventional cell as sub-system to that cluster. However, there are still some visualization problems in the gui. And a little cleanup is necessary --- nomad/normalizing/material.py | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index c86e8d82f..1391b075e 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -898,3 +898,39 @@ class MaterialNormalizer(): sec_symmetry.origin_shift = origin_shift sec_symmetry.transformation_matrix = transform return subsystem + + def _create_symmsystem(self, symm, top_id_str, parent_system, parent_subsystem): + """ + Creates the subsystem with the symmetry information of the conventional cell + """ + subsystem = System( + system_id=top_id_str, + method='matid', + label='conventional cell', + description='This is the calulated conventional cell of the bulk material to which the surface belongs.', + system_relation=Relation(type='subsystem'), + parent_system=parent_system, + symmetry=Symmetry() + ) + space_group_number = symm.get_space_group_number() + hall_number = symm.get_hall_number() + hall_symbol = symm.get_hall_symbol() + international_short = symm.get_space_group_international_short() + crystal_system = symm.get_crystal_system() + bravais_lattice = symm.get_bravais_lattice() + point_group = symm.get_point_group() + transform = symm._get_spglib_transformation_matrix() + origin_shift = symm._get_spglib_origin_shift() + + sec_symmetry = subsystem.symmetry + sec_symmetry.symmetry_method = 'MatID' + sec_symmetry.space_group_number = space_group_number + sec_symmetry.hall_number = hall_number + sec_symmetry.hall_symbol = hall_symbol + sec_symmetry.international_short_symbol = international_short + sec_symmetry.point_group = point_group + sec_symmetry.crystal_system = crystal_system + sec_symmetry.bravais_lattice = bravais_lattice + sec_symmetry.origin_shift = origin_shift + sec_symmetry.transformation_matrix = transform + return subsystem -- GitLab From dab3b0d7c45085a1497c987a3a7dc8d92f4f2c9b Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Fri, 12 Aug 2022 16:14:49 +0200 Subject: [PATCH 17/63] Extracted the largest (in respect of number of atoms) region from each cluster that corresponds to a surface, calculated the symmetri information for that region with matids SymmetryAnalyzer and added the conventional cell as sub-system to that cluster. However, there are still some visualization problems in the gui. And a little cleanup is necessary --- nomad/normalizing/material.py | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index 1391b075e..03f600d32 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -934,3 +934,39 @@ class MaterialNormalizer(): sec_symmetry.origin_shift = origin_shift sec_symmetry.transformation_matrix = transform return subsystem + + def _create_symmsystem(self, symm, top_id_str, parent_system, parent_subsystem): + """ + Creates the subsystem with the symmetry information of the conventional cell + """ + subsystem = System( + system_id=top_id_str, + method='matid', + label='conventional cell', + description='This is the calulated conventional cell of the bulk material to which the surface belongs.', + system_relation=Relation(type='subsystem'), + parent_system=parent_system, + symmetry=Symmetry() + ) + space_group_number = symm.get_space_group_number() + hall_number = symm.get_hall_number() + hall_symbol = symm.get_hall_symbol() + international_short = symm.get_space_group_international_short() + crystal_system = symm.get_crystal_system() + bravais_lattice = symm.get_bravais_lattice() + point_group = symm.get_point_group() + transform = symm._get_spglib_transformation_matrix() + origin_shift = symm._get_spglib_origin_shift() + + sec_symmetry = subsystem.symmetry + sec_symmetry.symmetry_method = 'MatID' + sec_symmetry.space_group_number = space_group_number + sec_symmetry.hall_number = hall_number + sec_symmetry.hall_symbol = hall_symbol + sec_symmetry.international_short_symbol = international_short + sec_symmetry.point_group = point_group + sec_symmetry.crystal_system = crystal_system + sec_symmetry.bravais_lattice = bravais_lattice + sec_symmetry.origin_shift = origin_shift + sec_symmetry.transformation_matrix = transform + return subsystem -- GitLab From d218c26846e644037bb41b2472d1332ea7487998 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Fri, 19 Aug 2022 21:57:43 +0200 Subject: [PATCH 18/63] Refactoring and clean up --- nomad/normalizing/material.py | 55 ++++++++++++++++++++++++++++------- 1 file changed, 44 insertions(+), 11 deletions(-) diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index 03f600d32..b69c24ed1 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -939,15 +939,17 @@ class MaterialNormalizer(): """ Creates the subsystem with the symmetry information of the conventional cell """ - subsystem = System( - system_id=top_id_str, - method='matid', - label='conventional cell', - description='This is the calulated conventional cell of the bulk material to which the surface belongs.', - system_relation=Relation(type='subsystem'), - parent_system=parent_system, - symmetry=Symmetry() - ) + conv_system = symm.get_conventional_system() + cell_params = self._extract_cell_params(conv_system) + cell = self._create_cell(cell_params) + subsystem.cell = cell + symmetry = self._create_symmetry(subsystem, symm) + subsystem.symmetry = symmetry + prototype = self._create_prototype(symm, conv_system) + subsystem.prototype = prototype + return subsystem + + def _create_symmetry(self, subsystem: System, symm: SymmetryAnalyzer) -> Symmetry: space_group_number = symm.get_space_group_number() hall_number = symm.get_hall_number() hall_symbol = symm.get_hall_symbol() @@ -958,7 +960,7 @@ class MaterialNormalizer(): transform = symm._get_spglib_transformation_matrix() origin_shift = symm._get_spglib_origin_shift() - sec_symmetry = subsystem.symmetry + sec_symmetry = Symmetry() sec_symmetry.symmetry_method = 'MatID' sec_symmetry.space_group_number = space_group_number sec_symmetry.hall_number = hall_number @@ -969,4 +971,35 @@ class MaterialNormalizer(): sec_symmetry.bravais_lattice = bravais_lattice sec_symmetry.origin_shift = origin_shift sec_symmetry.transformation_matrix = transform - return subsystem + return sec_symmetry + + def _create_prototype(self, symm: SymmetryAnalyzer, conv_system: System) -> Prototype: + spg_number = symm.get_space_group_number() + atom_species = conv_system.get_atomic_numbers() + wyckoffs = conv_system.wyckoff_letters + norm_wyckoff = atomutils.get_normalized_wyckoff(atom_species, wyckoffs) + protoDict = atomutils.search_aflow_prototype(spg_number, norm_wyckoff) + + if protoDict is not None: + aflow_prototype_id = protoDict["aflow_prototype_id"] + aflow_prototype_url = protoDict["aflow_prototype_url"] + aflow_prototype_notes = protoDict["Notes"] + aflow_prototype_name = protoDict["Prototype"] + aflow_strukturbericht_designation = protoDict["Strukturbericht Designation"] + prototype_label = '%d-%s-%s' % ( + spg_number, + aflow_prototype_name, + protoDict.get("Pearsons Symbol", "-") + ) + prototype = Prototype() + prototype.label = prototype_label + prototype.aflow_id = aflow_prototype_id + prototype.aflow_url = aflow_prototype_url + prototype.assignment_method = "normalized-wyckoff" + prototype.m_cache["prototype_notes"] = aflow_prototype_notes + prototype.m_cache["prototype_name"] = aflow_prototype_name + if aflow_strukturbericht_designation != "None": + prototype.m_cache["strukturbericht_designation"] = aflow_strukturbericht_designation + else: + prototype = None + return prototype -- GitLab From c0d71a0b79f7e8bc0ecffa002d0cefe64cfc28b5 Mon Sep 17 00:00:00 2001 From: Thea Denell Date: Tue, 2 Aug 2022 15:13:32 +0200 Subject: [PATCH 19/63] Modify nomad/normalizing/material.py to include classification of 2D and surfaces to results.material.topology. Also added the unit test for that functionality and reference data for the unit test --- nomad/normalizing/material.py | 2 +- .../surface_2D_subsystem_classification.json | 5395 +++++++++++++++++ 2 files changed, 5396 insertions(+), 1 deletion(-) create mode 100644 tests/data/classification/surface_2D_subsystem_classification.json diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py index b69c24ed1..c24d5b41b 100644 --- a/nomad/normalizing/material.py +++ b/nomad/normalizing/material.py @@ -19,7 +19,6 @@ from typing import Union, Dict, List, Tuple, Optional from nptyping import NDArray from collections import defaultdict -from math import pi import re import ase.data from ase import Atoms @@ -36,6 +35,7 @@ from nomad import atomutils from nomad.utils import hash + class MaterialNormalizer(): def __init__( self, diff --git a/tests/data/classification/surface_2D_subsystem_classification.json b/tests/data/classification/surface_2D_subsystem_classification.json new file mode 100644 index 000000000..db8bd8cb3 --- /dev/null +++ b/tests/data/classification/surface_2D_subsystem_classification.json @@ -0,0 +1,5395 @@ +{ + "5BZbNJgzr0hqEwBFL0tzhCYVlfRb": { + "topology": [ + { + "atoms": { + "labels": [ + "N", + "N", + "C", + "C", + "B", + "B" + ], + "species": [ + 7, + 7, + 6, + 6, + 5, + 5 + ], + "positions": [ + [ + 0.0, + 0.0, + 0.0 + ], + [ + 0.0, + 0.0, + 6.207700540042802 + ], + [ + -7.734710224832942e-18, + 1.4385198970702377, + 3.1033148311789057 + ], + [ + 7.734710224832942e-18, + 2.8770398372960724, + 3.1044161012110054 + ], + [ + -7.734710224832942e-18, + 1.4385198970702377, + 9.248229259962613e-4 + ], + [ + 7.734710224832942e-18, + 2.8770398372960724, + 6.206744562579172 + ] + ], + "lattice_vectors": [ + [ + 1.24579479260285, + 2.157779867183155, + 0.0 + ], + [ + -1.24579479260285, + 2.157779867183155, + 0.0 + ], + [ + 0.0, + 0.0, + 9.527381539056982 + ] + ], + "periodic": [ + true, + true, + true + ] + }, + "description": "A representative 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