From 6041506dc6371e5de15476983354245e4ae98329 Mon Sep 17 00:00:00 2001 From: Sean Kavanagh Date: Wed, 20 Nov 2024 22:16:36 -0500 Subject: [PATCH] Update `closest_site_info` to be robust for very very weird structure inputs (e.g. mp-674158, mp-1208561) --- doped/core.py | 2 +- doped/generation.py | 143 +++++++++++++--------- doped/utils/efficiency.py | 6 +- tests/data/CdTe_defect_gen.json | 2 +- tests/data/N_diamond_defect_gen.json | 2 +- tests/data/agcu_defect_gen.json | 2 +- tests/data/cd_i_supercell_defect_gen.json | 2 +- tests/data/cu_defect_gen.json | 2 +- tests/data/lmno_defect_gen.json | 2 +- tests/data/ytos_defect_gen.json | 2 +- tests/data/ytos_defect_gen_supercell.json | 2 +- tests/test_generation.py | 20 +-- 12 files changed, 111 insertions(+), 76 deletions(-) diff --git a/doped/core.py b/doped/core.py index 7546c3e7..c29b0432 100644 --- a/doped/core.py +++ b/doped/core.py @@ -2175,7 +2175,7 @@ def __eq__(self, other) -> bool: loose ``stol`` used in ``pymatgen-analysis-defects``) and much more efficient. """ - if not isinstance(other, (self, core.Defect)): + if not isinstance(other, (type(self), core.Defect)): raise TypeError("Can only compare `Defect`s with `Defect`s!") if self.defect_type != other.defect_type: diff --git a/doped/generation.py b/doped/generation.py index e99af887..da90d76f 100644 --- a/doped/generation.py +++ b/doped/generation.py @@ -3,6 +3,7 @@ calculations. """ +import contextlib import copy import logging import operator @@ -28,7 +29,7 @@ from pymatgen.core import IStructure, Structure from pymatgen.core.composition import Composition, Element from pymatgen.core.periodic_table import DummySpecies -from pymatgen.core.structure import PeriodicSite +from pymatgen.core.structure import PeriodicNeighbor, PeriodicSite from pymatgen.entries.computed_entries import ComputedStructureEntry from pymatgen.transformations.advanced_transformations import CubicSupercellTransformation from pymatgen.util.typing import PathLike @@ -199,10 +200,15 @@ def closest_site_info( be at least 0.02 Å further away than the n-1th site. """ if isinstance(defect_entry_or_defect, (DefectEntry, thermo.DefectEntry)): - defect = defect_entry_or_defect.defect - # use defect_supercell_site if attribute exists, otherwise use sc_defect_frac_coords: - defect_supercell_site = parsing._get_defect_supercell_site(defect_entry_or_defect) - defect_supercell = parsing._get_defect_supercell(defect_entry_or_defect) + site = None + with contextlib.suppress(Exception): + defect = defect_entry_or_defect.defect + site = defect.site + structure = defect.structure + if site is None: + # use defect_supercell_site if attribute exists, otherwise use sc_defect_frac_coords: + site = parsing._get_defect_supercell_site(defect_entry_or_defect) + structure = parsing._get_bulk_supercell(defect_entry_or_defect) elif isinstance(defect_entry_or_defect, (Defect, core.Defect)): if isinstance(defect_entry_or_defect, core.Defect): @@ -210,20 +216,9 @@ def closest_site_info( else: defect = defect_entry_or_defect - req_sc_mat = np.eye(3) * np.ceil((5 * np.sqrt(n)) / min(defect.defect_structure.lattice.abc)) - if np.all(req_sc_mat == np.eye(3)): # just defect is fine - defect_supercell = defect.defect_structure - defect_supercell_site = defect.site + site = defect.site + structure = defect.structure - else: - ( - defect_supercell, - defect_supercell_site, - _equivalent_supercell_sites, - ) = defect.get_supercell_structure( - sc_mat=req_sc_mat, - return_sites=True, - ) else: raise TypeError( f"defect_entry_or_defect must be a DefectEntry or Defect object, not " @@ -233,43 +228,68 @@ def closest_site_info( if element_list is None: element_list = _get_element_list(defect) - distance_matrix = defect_supercell.lattice.get_all_distances( - defect_supercell.frac_coords, - defect_supercell_site.frac_coords, - ) - if distance_matrix.shape[1] == 1: # Check if it is (X, 1) - distance_matrix = distance_matrix.ravel() - - # ensure the defect site itself is excluded, and ignore sites further than 5*sqrt(n) Å away - possible_close_site_indices = np.where((distance_matrix > 0.05) & (distance_matrix < 5 * np.sqrt(n)))[ - 0 - ] - - site_distances = sorted( # Could make this faster using caching if it was becoming a bottleneck - [ - ( - distance_matrix[i], - defect_supercell.sites[i].specie.symbol, - ) - for i in possible_close_site_indices - ], - key=lambda x: (symmetry._custom_round(x[0], 2), _list_index_or_val(element_list, x[1]), x[1]), - ) - - # prune site_distances to remove any tuples with distances within 0.02 Å of the previous entry: - site_distances = [ - site_distances[i] - for i in range(len(site_distances)) - if i == 0 - or abs(site_distances[i][0] - site_distances[i - 1][0]) > 0.02 - or site_distances[i][1] != site_distances[i - 1][1] - ] + def _get_site_distances_and_symbols( + site: PeriodicSite, + structure: Structure, + n: int, + element_list: list[str], + dist_tol_prefactor: float = 3.0, + ): + """ + Get a list of sorted tuples of (distance, element) for the closest + sites to the input site in the input structure, and the last used + ``dist_tol_prefactor``. + + Dynamically increases ``dist_tol_prefactor`` until at least one other + site is found within the distance tolerance. Function defined and used + here to allow dynamic upscaling of the distance tolerance for weird + structures (e.g. mp-674158, mp-1208561). + """ + neighbours: list[PeriodicNeighbor] = [] + while not neighbours: # for efficiency, ignore sites further than dist_tol*sqrt(n) Å away: + neighbours_w_site_itself = structure.get_sites_in_sphere( + site.coords, dist_tol_prefactor * np.sqrt(n) + ) # exclude defect site itself: + neighbours = sorted(neighbours_w_site_itself, key=lambda x: x.nn_distance)[1:] + dist_tol_prefactor += 0.5 # increase the distance tolerance if no other sites are found + if dist_tol_prefactor > 40: + warnings.warn( + "No other sites found within 40*sqrt(n) Å of the defect site, indicating a very " + "weird structure..." + ) + break + if not neighbours: + return [], dist_tol_prefactor - if site_distances: - min_distance, closest_site = site_distances[n - 1] - return f"{closest_site}{symmetry._custom_round(min_distance, 2):.2f}" + site_distances = sorted( # Could make this faster using caching if it was becoming a bottleneck + [ + ( + neigh.nn_distance, + neigh.specie.symbol, + ) + for neigh in neighbours + ], + key=lambda x: (symmetry._custom_round(x[0], 2), _list_index_or_val(element_list, x[1]), x[1]), + ) + return [ # prune site_distances to remove any with distances within 0.02 Å of the previous n: + site_distances[i] + for i in range(len(site_distances)) + if i == 0 + or abs(site_distances[i][0] - site_distances[i - 1][0]) > 0.02 + or site_distances[i][1] != site_distances[i - 1][1] + ], dist_tol_prefactor + + site_distances, dist_tol_prefactor = _get_site_distances_and_symbols(site, structure, n, element_list) + while len(site_distances) < n: + if dist_tol_prefactor > 40: + return "" # already warned + + site_distances, dist_tol_prefactor = _get_site_distances_and_symbols( + site, structure, n, element_list, dist_tol_prefactor + 2 + ) - return "" # hypothetical case of very weird structure with no sites within 5*sqrt(n) Å... + min_distance, closest_site = site_distances[n - 1] + return f"{closest_site}{symmetry._custom_round(min_distance, 2):.2f}" def get_defect_name_from_defect( @@ -2497,12 +2517,21 @@ def get_Voronoi_interstitial_sites( f"only the following keys are supported: {supported_interstitial_gen_kwargs}" ) top = DopedTopographyAnalyzer(host_structure) + if not top.vnodes: + warnings.warn("No interstitial sites found in host structure!") + return [] + sites_list = [v.frac_coords for v in top.vnodes] - sites_list = remove_collisions( - sites_list, structure=host_structure, min_dist=interstitial_gen_kwargs.get("min_dist", 0.9) - ) + min_dist = interstitial_gen_kwargs.get("min_dist", 0.9) + sites_array = remove_collisions(sites_list, structure=host_structure, min_dist=min_dist) + if sites_array.size == 0: + warnings.warn( + f"No interstitial sites found after removing those within {min_dist} Å of host atoms!" + ) + return [] + site_frac_coords_array: np.array = _doped_cluster_frac_coords( - sites_list, + sites_array, host_structure, tol=interstitial_gen_kwargs.get("clustering_tol", 0.55), symmetry_preference=interstitial_gen_kwargs.get("symmetry_preference", 0.1), diff --git a/doped/utils/efficiency.py b/doped/utils/efficiency.py index 6ed98363..87c13d42 100644 --- a/doped/utils/efficiency.py +++ b/doped/utils/efficiency.py @@ -457,8 +457,12 @@ def _doped_cluster_frac_coords( Returns: np.typing.NDArray: Clustered fractional coordinates """ - if len(fcoords) <= 1: + if len(fcoords) == 0: return None + if len(fcoords) == 1: + return symmetry._vectorized_custom_round( + np.mod(symmetry._vectorized_custom_round(fcoords, 5), 1), 4 + ) # to unit cell lattice = structure.lattice sga = symmetry.get_sga(structure, symprec=0.1) # for getting symmetries of different sites diff --git a/tests/data/CdTe_defect_gen.json b/tests/data/CdTe_defect_gen.json index a4496d62..1b7f68a8 100644 --- a/tests/data/CdTe_defect_gen.json +++ b/tests/data/CdTe_defect_gen.json @@ -1 +1 @@ -{"@module": "doped.generation", "@class": "DefectsGenerator", "defects": {"vacancies": [{"@module": "doped.core", "@class": "Vacancy", "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0.0, "lattice": {"matrix": [[0.0, 3.27033, 3.27033], [3.27033, 0.0, 3.27033], [3.27033, 3.27033, 0.0]], "pbc": [true, true, true], "a": 4.6249450394356035, "b": 4.6249450394356035, "c": 4.6249450394356035, "alpha": 59.99999999999999, "beta": 59.99999999999999, "gamma": 59.99999999999999, "volume": 69.95274007868987}, "properties": {}, "sites": [{"species": [{"element": "Cd", "oxidation_state": 2, "spin": null, "occu": 1.0}], "abc": [0.0, 0.0, 0.0], "properties": {}, "label": "Cd", "xyz": [0.0, 0.0, 0.0]}, {"species": [{"element": "Te", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.25, 0.25, 0.25], "properties": {}, "label": "Te", "xyz": [1.635165, 1.635165, 1.635165]}], "@version": null}, "site": {"species": [{"element": "Cd", "occu": 1.0}], "abc": [0.0, 0.0, 0.0], "lattice": {"@module": "pymatgen.core.lattice", "@class": "Lattice", "matrix": [[0.0, 3.27033, 3.27033], [3.27033, 0.0, 3.27033], [3.27033, 3.27033, 0.0]], "pbc": [true, true, true]}, "@module": "pymatgen.core.sites", "@class": "PeriodicSite", "properties": {}, "label": "Cd", "@version": null}, "symprec": 0.01, "angle_tolerance": 5, "multiplicity": 1, "equivalent_sites": [{"species": [{"element": "Cd", "occu": 1.0}], "abc": [0.0, 0.0, 0.0], "lattice": {"@module": "pymatgen.core.lattice", "@class": "Lattice", "matrix": [[0.0, 3.27033, 3.27033], [3.27033, 0.0, 3.27033], [3.27033, 3.27033, 0.0]], "pbc": [true, true, true]}, "@module": "pymatgen.core.sites", "@class": "PeriodicSite", "properties": {}, "label": "Cd", "@version": null}], "user_charges": [], "oxi_state": -2, "_defect_site": {"@module": "pymatgen.core.structure", "@class": "PeriodicNeighbor", "@version": null, "species": {"Cd2+": 1.0}, "coords": {"@module": "numpy", "@class": "array", "dtype": "float64", "data": [0.0, 0.0, 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newline at end of file diff --git a/tests/data/agcu_defect_gen.json b/tests/data/agcu_defect_gen.json index ac59c13e..e6d6965e 100644 --- a/tests/data/agcu_defect_gen.json +++ b/tests/data/agcu_defect_gen.json @@ -1 +1 @@ -{"@module": "doped.generation", "@class": "DefectsGenerator", "defects": {"vacancies": [{"@module": "doped.core", "@class": "Vacancy", "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0.0, "lattice": {"matrix": [[1.805, 0.0, 1.805], [1.805, -1.805, 0.0], [3.61, 1.805, -1.805]], "pbc": [true, true, true], "a": 2.5526554800834367, "b": 2.5526554800834367, "c": 4.421328985723637, "alpha": 73.22134511903964, "beta": 73.22134511903964, "gamma": 60.00000000000001, "volume": 23.5229405}, "properties": {}, "sites": [{"species": [{"element": "Cu", "oxidation_state": 0, "spin": null, "occu": 1.0}], "abc": [0.0, 0.0, 0.0], "properties": {}, "label": "Cu", "xyz": [0.0, 0.0, 0.0]}, {"species": [{"element": "Ag", "oxidation_state": 0, "spin": 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[{"element": "O", "occu": 1.0}], "abc": [0.5, 0.5, 0.5], "properties": {}, "label": "O", "xyz": [1.878454, 1.878454, 11.41966]}, {"species": [{"element": "O", "occu": 1.0}], "abc": [0.0, 0.5, 0.098983], "properties": {}, "label": "O", "xyz": [0.0, 1.878454, 2.26070441156]}, {"species": [{"element": "O", "occu": 1.0}], "abc": [0.5, 0.0, 0.098983], "properties": {}, "label": "O", "xyz": [1.878454, 0.0, 2.26070441156]}, {"species": [{"element": "O", "occu": 1.0}], "abc": [0.0, 0.5, 0.401017], "properties": {}, "label": "O", "xyz": [0.0, 1.878454, 9.158955588440001]}, {"species": [{"element": "O", "occu": 1.0}], "abc": [0.5, 0.0, 0.401017], "properties": {}, "label": "O", "xyz": [1.878454, 0.0, 9.158955588440001]}, {"species": [{"element": "O", "occu": 1.0}], "abc": [0.0, 0.5, 0.598983], "properties": {}, "label": "O", "xyz": [0.0, 1.878454, 13.680364411560001]}, {"species": [{"element": "O", "occu": 1.0}], "abc": [0.5, 0.0, 0.598983], "properties": {}, "label": "O", "xyz": [1.878454, 0.0, 13.680364411560001]}, {"species": [{"element": "O", "occu": 1.0}], "abc": [0.0, 0.5, 0.901017], "properties": {}, "label": "O", "xyz": [0.0, 1.878454, 20.578615588439998]}, {"species": [{"element": "O", "occu": 1.0}], "abc": [0.5, 0.0, 0.901017], "properties": {}, "label": "O", "xyz": [1.878454, 0.0, 20.578615588439998]}], "@version": null}, "_BilbaoCS_conv_cell_vector_mapping": [0, 1, 2], "@version": null} \ No newline at end of file diff --git a/tests/test_generation.py b/tests/test_generation.py index eb0133d0..a801d742 100644 --- a/tests/test_generation.py +++ b/tests/test_generation.py @@ -736,23 +736,23 @@ def setUp(self): Interstitials Guessed Charges Conv. Cell Coords Wyckoff --------------- --------------------------- ------------------- --------- +Si_i_C1_Sb2.48 [+4,+3,+2,+1,0] [0.347,0.348,0.457] 18f Si_i_C1_Si2.21 [+4,+3,+2,+1,0] [0.158,0.359,0.167] 18f -Si_i_C1_Si2.48 [+4,+3,+2,+1,0] [0.347,0.348,0.457] 18f Si_i_C1_Te2.44 [+4,+3,+2,+1,0] [0.001,0.336,0.289] 18f -Si_i_C3_Sb2.41 [+4,+3,+2,+1,0] [0.000,0.000,0.050] 6c Si_i_C3_Si2.64 [+4,+3,+2,+1,0] [0.000,0.000,0.318] 6c +Si_i_C3_Te2.41 [+4,+3,+2,+1,0] [0.000,0.000,0.050] 6c Si_i_C3i_Te2.81 [+4,+3,+2,+1,0] [0.000,0.000,0.000] 3a +Sb_i_C1_Sb2.48 [+5,+4,+3,+2,+1,0,-1,-2,-3] [0.347,0.348,0.457] 18f Sb_i_C1_Si2.21 [+5,+4,+3,+2,+1,0,-1,-2,-3] [0.158,0.359,0.167] 18f -Sb_i_C1_Si2.48 [+5,+4,+3,+2,+1,0,-1,-2,-3] [0.347,0.348,0.457] 18f Sb_i_C1_Te2.44 [+5,+4,+3,+2,+1,0,-1,-2,-3] [0.001,0.336,0.289] 18f -Sb_i_C3_Sb2.41 [+5,+4,+3,+2,+1,0,-1,-2,-3] [0.000,0.000,0.050] 6c Sb_i_C3_Si2.64 [+5,+4,+3,+2,+1,0,-1,-2,-3] [0.000,0.000,0.318] 6c +Sb_i_C3_Te2.41 [+5,+4,+3,+2,+1,0,-1,-2,-3] [0.000,0.000,0.050] 6c Sb_i_C3i_Te2.81 [+5,+4,+3,+2,+1,0,-1,-2,-3] [0.000,0.000,0.000] 3a +Te_i_C1_Sb2.48 [+4,+3,+2,+1,0,-1,-2] [0.347,0.348,0.457] 18f Te_i_C1_Si2.21 [+4,+3,+2,+1,0,-1,-2] [0.158,0.359,0.167] 18f -Te_i_C1_Si2.48 [+4,+3,+2,+1,0,-1,-2] [0.347,0.348,0.457] 18f Te_i_C1_Te2.44 [+4,+3,+2,+1,0,-1,-2] [0.001,0.336,0.289] 18f -Te_i_C3_Sb2.41 [+4,+3,+2,+1,0,-1,-2] [0.000,0.000,0.050] 6c Te_i_C3_Si2.64 [+4,+3,+2,+1,0,-1,-2] [0.000,0.000,0.318] 6c +Te_i_C3_Te2.41 [+4,+3,+2,+1,0,-1,-2] [0.000,0.000,0.050] 6c Te_i_C3i_Te2.81 [+4,+3,+2,+1,0,-1,-2] [0.000,0.000,0.000] 3a \n""" "The number in the Wyckoff label is the site multiplicity/degeneracy of that defect " @@ -854,7 +854,9 @@ def _general_defect_gen_check(self, defect_gen, charge_states_removed=False): set(Poscar(structure).site_symbols) ) # no duplicates - assert np.isclose(defect_gen.min_image_distance, get_min_image_distance(defect_gen.bulk_supercell)) + assert np.isclose( + defect_gen.min_image_distance, get_min_image_distance(defect_gen.bulk_supercell), atol=1e-2 + ) print("Checking Defect/DefectEntry types") assert all(defect.defect_type == DefectType.Vacancy for defect in defect_gen.defects["vacancies"]) @@ -1854,7 +1856,7 @@ def test_supercell_gen_kwargs(self): ) # gives 4x conventional cell assert self.CdTe_defect_gen_info in output self._general_defect_gen_check(CdTe_defect_gen) - assert CdTe_defect_gen.min_image_distance == 26.1626 + assert np.isclose(CdTe_defect_gen.min_image_distance, 26.1626, atol=1e-2) assert len(CdTe_defect_gen.bulk_supercell) == 512 assert CdTe_defect_gen.supercell_gen_kwargs["min_image_distance"] == 20 assert CdTe_defect_gen.supercell_gen_kwargs["force_cubic"] is True @@ -3372,7 +3374,7 @@ def Sn5O6_defect_gen_check(self, defect_gen, manual_oxi=False): "v_O_C1_Sn2.09 [+2,+1,0,-1] [0.642,0.323,0.461] 4e", "Sn_Sn_C1_O2.08O2.11O2.14b [+2,+1,0,-1] [0.101,0.502,0.319] 4e", "Sn_Sn_C1_O2.08Sn3.28O3.69a [+1,0,-1] [0.500,0.500,0.500] 2b", - "Sn_i_C1_Sn2.33O2.33O2.39d [+4,+3,+2,+1,0] [0.273,0.460,0.248] 4e", + "Sn_i_C1_Sn2.33O2.39O2.60d [+4,+3,+2,+1,0] [0.273,0.460,0.248] 4e", "O_i_C1_O1.83Sn1.99Sn2.09a [0,-1,-2] [0.567,0.320,0.205] 4e", ] assert set(defect_gen._bulk_oxi_states.composition.elements) == {