Skip another failing Phonopy test in Windows after NumPy bumped to 2 in CI

[DanielYang59]

Skip another failing phonopy test in Windows after NumPy bumped to 2 in CI

• numpy._core._exceptions.MemoryError in Windows NumPy 2 phonopy/phonopy#476

I could recreate this in my Windows PC, all four tests failing for the same reason:

Python 3.10.0

phonopy==2.33.0
numpy==2.0.2

$ pytest tests/io/test_phonopy.py 
....FFFF...                                                                                                                                                       [100%]
=============================================================================== FAILURES ===============================================================================
_______________________________________________________ TestGetDisplacedStructures.test_get_displaced_structures _______________________________________________________

self = <tests.io.test_phonopy.TestGetDisplacedStructures testMethod=test_get_displaced_structures>

    def test_get_displaced_structures(self):
        pmg_s = Structure.from_file(f"{TEST_DIR}/POSCAR-unitcell", primitive=False)
        supercell_matrix = np.diag((2, 1, 2))
>       structures = get_displaced_structures(pmg_structure=pmg_s, atom_disp=0.01, supercell_matrix=supercell_matrix)

D:\pymatgen\tests\io\test_phonopy.py:134:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\monty\dev.py:216: in decorated
    return _callable(*args, **kwargs)
D:\pymatgen\src\pymatgen\io\phonopy.py:260: in get_displaced_structures
    phonon = Phonopy(unitcell=ph_structure, supercell_matrix=supercell_matrix)
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\api_phonopy.py:293: in __init__
    self._build_primitive_cell()
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\api_phonopy.py:4146: in _build_primitive_cell
    self._primitive = get_primitive(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:886: in get_primitive
    return Primitive(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:386: in __init__
    self._run(supercell, positions_to_reorder=positions_to_reorder)
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:554: in _run
    (self._smallest_vectors, self._multiplicity) = self._get_smallest_vectors(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:650: in _get_smallest_vectors
    svecs, multi = get_smallest_vectors(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1098: in get_smallest_vectors
    spairs = ShortestPairs(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1165: in __init__
    svecs, multi = self._run_dense()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  

self = <phonopy.structure.cells.ShortestPairs object at 0x0000027AFBAD2B60>

    def _run_dense(self):
        """Find shortest atomic pair vectors.

        Returns
        -------
        shortest_vectors : ndarray
            Shortest vectors in supercell coordinates.
            shape=(sum(multiplicities[:, :, 0], 3), dtype='double'
        multiplicities : ndarray
            Number of equidistance shortest vectors. The last dimension
            indicates [0] multipliticy at the pair of atoms in the supercell
            and primitive cell, and [1] integral of multiplicities to
            this pair, i.e., which indicates address used in
            `shortest_vectors`.
            shape=(size_super, size_prim, 2), dtype='int_'

        """
        (
            lattice_points,
            supercell_fracs,
            primitive_fracs,
            trans_mat_inv,
            reduced_bases,
        ) = self._transform_cell_basis("int_")

        # Phase1 : Set multiplicity.
        # shortest_vectors is a dummy array.
        shortest_vectors = np.zeros((1, 3), dtype="double", order="C")
        multiplicity = np.zeros(
            (len(supercell_fracs), len(primitive_fracs), 2), dtype="int_", order="C"
        )
        import phonopy._phonopy as phonoc

        phonoc.gsv_set_smallest_vectors_dense(
            shortest_vectors,
            multiplicity,
            supercell_fracs,
            primitive_fracs,
            lattice_points,
            np.array(reduced_bases.T, dtype="double", order="C"),
            np.array(trans_mat_inv.T, dtype="int_", order="C"),
            1,
            self._symprec,
        )

        # Phase 2 : Set shortest_vectors.
>       shortest_vectors = np.zeros(
            (np.sum(multiplicity[:, :, 0]), 3), dtype="double", order="C"
        )
E       numpy._core._exceptions._ArrayMemoryError: Unable to allocate 2.14 EiB for an array with shape (102803044411911591, 3) and data type float64

C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1239: MemoryError
_________________________________________________ TestPhonopyFromForceConstants.test_get_phonon_band_structure_from_fc _________________________________________________ 

self = <tests.io.test_phonopy.TestPhonopyFromForceConstants testMethod=test_get_phonon_band_structure_from_fc>

    def test_get_phonon_band_structure_from_fc(self):
>       bs = get_phonon_band_structure_from_fc(
            self.structure,
            self.supercell_matrix,
            self.force_constants,
            mesh_density=10.0,
        )

tests\io\test_phonopy.py:187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\monty\dev.py:216: in decorated
    return _callable(*args, **kwargs)
src\pymatgen\io\phonopy.py:362: in get_phonon_band_structure_from_fc
    phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix, **kwargs)
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\api_phonopy.py:293: in __init__
    self._build_primitive_cell()
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\api_phonopy.py:4146: in _build_primitive_cell
    self._primitive = get_primitive(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:886: in get_primitive
    return Primitive(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:386: in __init__
    self._run(supercell, positions_to_reorder=positions_to_reorder)
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:554: in _run
    (self._smallest_vectors, self._multiplicity) = self._get_smallest_vectors(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:650: in _get_smallest_vectors
    svecs, multi = get_smallest_vectors(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1098: in get_smallest_vectors
    spairs = ShortestPairs(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1165: in __init__
    svecs, multi = self._run_dense()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  

self = <phonopy.structure.cells.ShortestPairs object at 0x0000027AFC82BB20>

    def _run_dense(self):
        """Find shortest atomic pair vectors.

        Returns
        -------
        shortest_vectors : ndarray
            Shortest vectors in supercell coordinates.
            shape=(sum(multiplicities[:, :, 0], 3), dtype='double'
        multiplicities : ndarray
            Number of equidistance shortest vectors. The last dimension
            indicates [0] multipliticy at the pair of atoms in the supercell
            and primitive cell, and [1] integral of multiplicities to
            this pair, i.e., which indicates address used in
            `shortest_vectors`.
            shape=(size_super, size_prim, 2), dtype='int_'

        """
        (
            lattice_points,
            supercell_fracs,
            primitive_fracs,
            trans_mat_inv,
            reduced_bases,
        ) = self._transform_cell_basis("int_")

        # Phase1 : Set multiplicity.
        # shortest_vectors is a dummy array.
        shortest_vectors = np.zeros((1, 3), dtype="double", order="C")
        multiplicity = np.zeros(
            (len(supercell_fracs), len(primitive_fracs), 2), dtype="int_", order="C"
        )
        import phonopy._phonopy as phonoc

        phonoc.gsv_set_smallest_vectors_dense(
            shortest_vectors,
            multiplicity,
            supercell_fracs,
            primitive_fracs,
            lattice_points,
            np.array(reduced_bases.T, dtype="double", order="C"),
            np.array(trans_mat_inv.T, dtype="int_", order="C"),
            1,
            self._symprec,
        )

        # Phase 2 : Set shortest_vectors.
>       shortest_vectors = np.zeros(
            (np.sum(multiplicity[:, :, 0]), 3), dtype="double", order="C"
        )
E       numpy._core._exceptions._ArrayMemoryError: Unable to allocate 45.7 PiB for an array with shape (2143661127108530, 3) and data type float64

C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1239: MemoryError
____________________________________________ TestPhonopyFromForceConstants.test_get_phonon_band_structure_symm_line_from_fc ____________________________________________ 

self = <tests.io.test_phonopy.TestPhonopyFromForceConstants testMethod=test_get_phonon_band_structure_symm_line_from_fc>

    def test_get_phonon_band_structure_symm_line_from_fc(self):
>       bs = get_phonon_band_structure_symm_line_from_fc(
            self.structure,
            self.supercell_matrix,
            self.force_constants,
            line_density=5.0,
        )

tests\io\test_phonopy.py:200:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\monty\dev.py:216: in decorated
    return _callable(*args, **kwargs)
src\pymatgen\io\phonopy.py:396: in get_phonon_band_structure_symm_line_from_fc
    phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix, symprec=symprec, **kwargs)
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\api_phonopy.py:293: in __init__
    self._build_primitive_cell()
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\api_phonopy.py:4146: in _build_primitive_cell
    self._primitive = get_primitive(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:886: in get_primitive
    return Primitive(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:386: in __init__
    self._run(supercell, positions_to_reorder=positions_to_reorder)
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:554: in _run
    (self._smallest_vectors, self._multiplicity) = self._get_smallest_vectors(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:650: in _get_smallest_vectors
    svecs, multi = get_smallest_vectors(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1098: in get_smallest_vectors
    spairs = ShortestPairs(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1165: in __init__
    svecs, multi = self._run_dense()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  

self = <phonopy.structure.cells.ShortestPairs object at 0x0000027AFA9AF4C0>

    def _run_dense(self):
        """Find shortest atomic pair vectors.

        Returns
        -------
        shortest_vectors : ndarray
            Shortest vectors in supercell coordinates.
            shape=(sum(multiplicities[:, :, 0], 3), dtype='double'
        multiplicities : ndarray
            Number of equidistance shortest vectors. The last dimension
            indicates [0] multipliticy at the pair of atoms in the supercell
            and primitive cell, and [1] integral of multiplicities to
            this pair, i.e., which indicates address used in
            `shortest_vectors`.
            shape=(size_super, size_prim, 2), dtype='int_'

        """
        (
            lattice_points,
            supercell_fracs,
            primitive_fracs,
            trans_mat_inv,
            reduced_bases,
        ) = self._transform_cell_basis("int_")

        # Phase1 : Set multiplicity.
        # shortest_vectors is a dummy array.
        shortest_vectors = np.zeros((1, 3), dtype="double", order="C")
        multiplicity = np.zeros(
            (len(supercell_fracs), len(primitive_fracs), 2), dtype="int_", order="C"
        )
        import phonopy._phonopy as phonoc

        phonoc.gsv_set_smallest_vectors_dense(
            shortest_vectors,
            multiplicity,
            supercell_fracs,
            primitive_fracs,
            lattice_points,
            np.array(reduced_bases.T, dtype="double", order="C"),
            np.array(trans_mat_inv.T, dtype="int_", order="C"),
            1,
            self._symprec,
        )

        # Phase 2 : Set shortest_vectors.
>       shortest_vectors = np.zeros(
            (np.sum(multiplicity[:, :, 0]), 3), dtype="double", order="C"
        )
E       numpy._core._exceptions._ArrayMemoryError: Unable to allocate 45.7 PiB for an array with shape (2143661127108530, 3) and data type float64

C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1239: MemoryError
______________________________________________________ TestPhonopyFromForceConstants.test_get_phonon_dos_from_fc _______________________________________________________ 

self = <tests.io.test_phonopy.TestPhonopyFromForceConstants testMethod=test_get_phonon_dos_from_fc>

    def test_get_phonon_dos_from_fc(self):
>       dos = get_phonon_dos_from_fc(
            self.structure,
            self.supercell_matrix,
            self.force_constants,
            mesh_density=10.0,
        )

tests\io\test_phonopy.py:174:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\monty\dev.py:216: in decorated
    return _callable(*args, **kwargs)
src\pymatgen\io\phonopy.py:315: in get_phonon_dos_from_fc
    phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix, **kwargs)
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\api_phonopy.py:293: in __init__
    self._build_primitive_cell()
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\api_phonopy.py:4146: in _build_primitive_cell
    self._primitive = get_primitive(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:886: in get_primitive
    return Primitive(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:386: in __init__
    self._run(supercell, positions_to_reorder=positions_to_reorder)
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:554: in _run
    (self._smallest_vectors, self._multiplicity) = self._get_smallest_vectors(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:650: in _get_smallest_vectors
    svecs, multi = get_smallest_vectors(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1098: in get_smallest_vectors
    spairs = ShortestPairs(
C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1165: in __init__
    svecs, multi = self._run_dense()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  

self = <phonopy.structure.cells.ShortestPairs object at 0x0000027AFBAD02E0>

    def _run_dense(self):
        """Find shortest atomic pair vectors.

        Returns
        -------
        shortest_vectors : ndarray
            Shortest vectors in supercell coordinates.
            shape=(sum(multiplicities[:, :, 0], 3), dtype='double'
        multiplicities : ndarray
            Number of equidistance shortest vectors. The last dimension
            indicates [0] multipliticy at the pair of atoms in the supercell
            and primitive cell, and [1] integral of multiplicities to
            this pair, i.e., which indicates address used in
            `shortest_vectors`.
            shape=(size_super, size_prim, 2), dtype='int_'

        """
        (
            lattice_points,
            supercell_fracs,
            primitive_fracs,
            trans_mat_inv,
            reduced_bases,
        ) = self._transform_cell_basis("int_")

        # Phase1 : Set multiplicity.
        # shortest_vectors is a dummy array.
        shortest_vectors = np.zeros((1, 3), dtype="double", order="C")
        multiplicity = np.zeros(
            (len(supercell_fracs), len(primitive_fracs), 2), dtype="int_", order="C"
        )
        import phonopy._phonopy as phonoc

        phonoc.gsv_set_smallest_vectors_dense(
            shortest_vectors,
            multiplicity,
            supercell_fracs,
            primitive_fracs,
            lattice_points,
            np.array(reduced_bases.T, dtype="double", order="C"),
            np.array(trans_mat_inv.T, dtype="int_", order="C"),
            1,
            self._symprec,
        )

        # Phase 2 : Set shortest_vectors.
>       shortest_vectors = np.zeros(
            (np.sum(multiplicity[:, :, 0]), 3), dtype="double", order="C"
        )
E       numpy._core._exceptions._ArrayMemoryError: Unable to allocate 45.7 PiB for an array with shape (2143661127108530, 3) and data type float64

C:\Users\Yang\anaconda3\envs\py310\lib\site-packages\phonopy\structure\cells.py:1239: MemoryError
========================================================================= slowest 30 durations ========================================================================= 
24.93s call     tests/io/test_phonopy.py::TestGruneisen::test_gruneisen_parameter
8.58s call     tests/io/test_phonopy.py::TestGruneisen::test_ph_bs_symm_line
4.29s call     tests/io/test_phonopy.py::TestPhonopyParser::test_get_ph_bs
1.11s call     tests/io/test_phonopy.py::TestThermalDisplacementMatrices::test_get_thermal_displacement_matrix
0.51s call     tests/io/test_phonopy.py::TestGetDisplacedStructures::test_get_displaced_structures
0.12s call     tests/io/test_phonopy.py::TestPhonopyParser::test_get_complete_dos
0.03s call     tests/io/test_phonopy.py::TestPhonopyFromForceConstants::test_get_phonon_dos_from_fc
0.03s call     tests/io/test_phonopy.py::TestPhonopyFromForceConstants::test_get_phonon_band_structure_symm_line_from_fc
0.03s call     tests/io/test_phonopy.py::TestPhonopyFromForceConstants::test_get_phonon_band_structure_from_fc
0.01s call     tests/io/test_phonopy.py::TestStructureConversion::test_structure_conversion
0.01s setup    tests/io/test_phonopy.py::TestPhonopyParser::test_get_ph_bs

(19 durations < 0.005s hidden.  Use -vv to show these durations.)
4 failed, 7 passed in 42.69s