Merge pull request #2724 from materialsproject/gh-2723

Fix TypeError in SpacegroupAnalyzer.get_symmetrized_structure() if spglib returns no symmetries

.pre-commit-config.yaml

@@ -42,7 +42,7 @@ repos:
         additional_dependencies: [flake8-bugbear]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.981
+    rev: v0.982
     hooks:
       - id: mypy
 

pymatgen/io/lobster/inputs.py

@@ -11,14 +11,15 @@
 import itertools
 import os
 import warnings
-from typing import Any, Dict, List, Sequence
+from typing import Any, Sequence
 
 import numpy as np
 import spglib
 from monty.io import zopen
 from monty.json import MSONable
 from monty.serialization import loadfn
 
+from pymatgen.core.composition import Composition
 from pymatgen.core.structure import Structure
 from pymatgen.io.vasp import Vasprun
 from pymatgen.io.vasp.inputs import Incar, Kpoints, Potcar
@@ -27,7 +28,7 @@
 __author__ = "Janine George, Marco Esters"
 __copyright__ = "Copyright 2017, The Materials Project"
 __version__ = "0.2"
-__maintainer__ = "Janine George, Marco Esters "
+__maintainer__ = "Janine George, Marco Esters"
 __email__ = "janine.george@uclouvain.be, esters@uoregon.edu"
 __date__ = "Dec 13, 2017"
 
@@ -135,7 +136,7 @@ def __setitem__(self, key, val):
 
     def __getitem__(self, item):
         """
-        implements getitem from dict to avoid problems with cases
+        Implements getitem from dict to avoid problems with cases
         """
         found = False
         for key_here in self:
@@ -152,8 +153,10 @@ def diff(self, other):
         """
         Diff function for lobsterin. Compares two lobsterin and indicates which parameters are the same.
         Similar to the diff in INCAR.
+
         Args:
             other (Lobsterin): Lobsterin object to compare to
+
         Returns:
             dict with differences and similarities
         """
@@ -209,12 +212,12 @@ def diff(self, other):
 
     def _get_nbands(self, structure: Structure):
         """
-        get number of nbands
+        Get number of bands.
         """
         if self.get("basisfunctions") is None:
             raise OSError("No basis functions are provided. The program cannot calculate nbands.")
 
-        basis_functions = []  # type: List[str]
+        basis_functions: list[str] = []
         for string_basis in self["basisfunctions"]:
             # string_basis.lstrip()
             string_basis_raw = string_basis.strip().split(" ")
@@ -238,7 +241,8 @@ def _get_nbands(self, structure: Structure):
 
     def write_lobsterin(self, path="lobsterin", overwritedict=None):
         """
-        writes a lobsterin file
+        Writes a lobsterin file
+
         Args:
             path (str): filename of the lobsterin file that will be written
             overwritedict (dict): dict that can be used to overwrite lobsterin, e.g. {"skipdos": True}
@@ -302,6 +306,7 @@ def write_INCAR(
         """
         Will only make the run static, insert nbands, make ISYM=-1, set LWAVE=True and write a new INCAR.
         You have to check for the rest.
+
         Args:
             incar_input (str): path to input INCAR
             incar_output (str): path to output INCAR
@@ -335,11 +340,13 @@ def get_basis(
         address_basis_file: str = None,
     ):
         """
-        will get the basis from given potcar_symbols (e.g., ["Fe_pv","Si"]
+        Will get the basis from given potcar_symbols (e.g., ["Fe_pv","Si"]
         #include this in lobsterin class
+
         Args:
             structure (Structure): Structure object
             potcar_symbols: list of potcar symbols
+
         Returns:
             returns basis
         """
@@ -415,7 +422,8 @@ def write_POSCAR_with_standard_primitive(
         POSCAR_input="POSCAR", POSCAR_output="POSCAR.lobster", symprec: float = 0.01
     ):
         """
-        writes a POSCAR with the standard primitive cell. This is needed to arrive at the correct kpath
+        Writes a POSCAR with the standard primitive cell. This is needed to arrive at the correct kpath
+
         Args:
             POSCAR_input (str): filename of input POSCAR
             POSCAR_output (str): filename of output POSCAR
@@ -439,7 +447,8 @@ def write_KPOINTS(
         symprec: float = 0.01,
     ):
         """
-        writes a KPOINT file for lobster (only ISYM=-1 and ISYM=0 are possible), grids are gamma centered
+        Writes a KPOINT file for lobster (only ISYM=-1 and ISYM=0 are possible), grids are gamma centered
+
         Args:
             POSCAR_input (str): path to POSCAR
             KPOINTS_output (str): path to output KPOINTS
@@ -463,7 +472,7 @@ def write_KPOINTS(
         # we need to switch off symmetry here
         latt = structure.lattice.matrix
         positions = structure.frac_coords
-        unique_species = []  # type: List[Any]
+        unique_species: list[Composition] = []
         zs = []
         magmoms = []
 
@@ -572,7 +581,7 @@ def from_file(cls, lobsterin: str):
             data = f.read().split("\n")
         if len(data) == 0:
             raise OSError("lobsterin file contains no data.")
-        Lobsterindict = {}  # type: Dict
+        Lobsterindict: dict[str, Any] = {}
 
         for datum in data:
             # will remove all comments to avoid complications
@@ -608,9 +617,11 @@ def from_file(cls, lobsterin: str):
     @staticmethod
     def _get_potcar_symbols(POTCAR_input: str) -> list:
         """
-        will return the name of the species in the POTCAR
+        Will return the name of the species in the POTCAR
+
         Args:
-         POTCAR_input(str): string to potcar file
+            POTCAR_input(str): string to potcar file
+
         Returns:
             list of the names of the species in string format
         """
@@ -650,7 +661,7 @@ def standard_calculations_from_vasp_files(
         option: str = "standard",
     ):
         """
-        will generate Lobsterin with standard settings
+        Will generate Lobsterin with standard settings
 
         Args:
             POSCAR_input(str): path to POSCAR
@@ -694,7 +705,7 @@ def standard_calculations_from_vasp_files(
         ]:
             raise ValueError("The option is not valid!")
 
-        Lobsterindict = {}  # type: Dict[Any,Any]
+        Lobsterindict: dict[str, Any] = {}
         # this basis set covers most elements
         Lobsterindict["basisSet"] = "pbeVaspFit2015"
         # energies around e-fermi

pymatgen/symmetry/analyzer.py

@@ -217,6 +217,11 @@ def _get_symmetry(self):
             vectors in scaled positions.
         """
         d = spglib.get_symmetry(self._cell, symprec=self._symprec, angle_tolerance=self._angle_tol)
+        if d is None:
+            raise ValueError(
+                f"Symmetry detection failed for structure with formula {self._structure.formula}. "
+                f"Try setting symprec={self._symprec} to a different value."
+            )
         # Sometimes spglib returns small translation vectors, e.g.
         # [1e-4, 2e-4, 1e-4]
         # (these are in fractional coordinates, so should be small denominator

pymatgen/symmetry/tests/test_analyzer.py

@@ -124,6 +124,18 @@ def test_get_symmetry_dataset(self):
         ds = self.sg.get_symmetry_dataset()
         assert ds["international"] == "Pnma"
 
+    def test_get_symmetry(self):
+        # see discussion in https://github.com/materialsproject/pymatgen/pull/2724
+        Co8 = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "Co8.cif"))
+        symprec = 1e-1
+
+        with pytest.raises(
+            ValueError,
+            match=f"Symmetry detection failed for structure with formula {Co8.formula}. "
+            f"Try setting {symprec=} to a different value.",
+        ):
+            SpacegroupAnalyzer(Co8, symprec=symprec)._get_symmetry()
+
     def test_get_crystal_system(self):
         crystal_system = self.sg.get_crystal_system()
         assert "orthorhombic" == crystal_system

setup.py

@@ -112,7 +112,7 @@
             "coveralls",
             "doc2dash",
             "flake8",
-            "mypy",
+            "mypy==0.982",
             "pre-commit",
             "pydocstyle",
             "pylint",

test_files/Co8.cif

@@ -0,0 +1,34 @@
+# generated using pymatgen
+data_Co
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   3.70701825
+_cell_length_b   3.70701825
+_cell_length_c   7.98790154
+_cell_angle_alpha   103.38852320
+_cell_angle_beta   103.38852320
+_cell_angle_gamma   89.96878549
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Co
+_chemical_formula_sum   Co8
+_cell_volume   103.72064306
+_cell_formula_units_Z   8
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Co  Co0  1  0.62683200  0.62683200  0.25354400  1.0
+  Co  Co1  1  0.37316800  0.37316800  0.74645600  1.0
+  Co  Co2  1  0.50000000  0.00000000  0.00000000  1.0
+  Co  Co3  1  0.00000000  0.50000000  0.00000000  1.0
+  Co  Co4  1  0.74993500  0.25006500  0.50000000  1.0
+  Co  Co5  1  0.25006500  0.74993500  0.50000000  1.0
+  Co  Co6  1  0.87978400  0.87978400  0.75931100  1.0
+  Co  Co7  1  0.12021600  0.12021600  0.24068900  1.0