symfc 1.2.1__tar.gz → 1.2.2__tar.gz

{symfc-1.2.1/src/symfc.egg-info → symfc-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: symfc
-Version: 1.2.1
+Version: 1.2.2
 Summary: This is the symfc module.
 Author-email: Atsuto Seko <seko@cms.mtl.kyoto-u.ac.jp>
 Maintainer-email: Atsushi Togo <atztogo@gmail.com>

{symfc-1.2.1 → symfc-1.2.2}/src/symfc/utils/utils.py

@@ -57,7 +57,7 @@ def argsort_positions(positions: np.ndarray, tol: float = 1e-13, decimals: int =
 def _find_optimal_decimals(positions: np.ndarray, tol: float = 1e-13):
     """Find optimal value of decimals used for sorting atoms."""
     n_atom = positions.shape[0]
-    for decimals in range(1, 15):
+    for decimals in range(3, 15):
         positions_round = round_positions(positions, tol=tol, decimals=decimals)
         n_atom_uniq = len(set([tuple(pos) for pos in positions_round]))
         if n_atom_uniq == n_atom:
@@ -115,7 +115,7 @@ def compute_sg_permutations(
         )
         if np.allclose(sorted_trans_positions - sorted_positions, 0.0):
             tp = np.zeros(n_atom, dtype=int)
-            tp[sorted_ids] = sorted_trans_ids
+            tp[sorted_trans_ids] = sorted_ids
         else:
             diffs = positions[None, :, :] - trans_positions[:, None, :]
             diffs -= np.rint(diffs)

{symfc-1.2.1 → symfc-1.2.2}/src/symfc/version.py

@@ -1,3 +1,3 @@
 """Version number of the package."""
 
-__version__ = "1.2.1"
+__version__ = "1.2.2"

{symfc-1.2.1 → symfc-1.2.2/src/symfc.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: symfc
-Version: 1.2.1
+Version: 1.2.2
 Summary: This is the symfc module.
 Author-email: Atsuto Seko <seko@cms.mtl.kyoto-u.ac.jp>
 Maintainer-email: Atsushi Togo <atztogo@gmail.com>

symfc-1.2.2/tests/utils/test_utils.py

@@ -0,0 +1,408 @@
+"""Tests of matrix manipulating functions."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+import numpy as np
+import pytest
+
+from symfc.spg_reps import SpgRepsBase
+from symfc.utils.utils import (
+    SymfcAtoms,
+    compute_sg_permutations,
+    compute_sg_permutations_stable,
+    get_indep_atoms_by_lat_trans,
+)
+
+cwd = Path(__file__).parent
+
+
+def test_get_indep_atoms_by_lattice_translation(
+    ph_nacl_222: tuple[SymfcAtoms, np.ndarray, np.ndarray],
+):
+    """Test of get_indep_atoms_by_lattice_translation."""
+    supercell, _, _ = ph_nacl_222
+    sym_op_reps = SpgRepsBase(supercell)
+    trans_perms = sym_op_reps.translation_permutations
+    assert trans_perms.shape == (32, 64)
+    indep_atoms = get_indep_atoms_by_lat_trans(trans_perms)
+    np.testing.assert_array_equal(indep_atoms, [0, 32])
+
+
+def test_compute_sg_permutations(
+    ph_gan_222: tuple[SymfcAtoms, np.ndarray, np.ndarray], cell_gan_111: SymfcAtoms
+):
+    """Test compute_sg_permutations."""
+    pytest.importorskip("spglib", minversion="2.5")
+    from spglib import spglib
+
+    supercell, _, _ = ph_gan_222
+    primitive = cell_gan_111
+    dataset = spglib.get_symmetry_dataset(supercell.totuple())
+    primitive_dataset = spglib.get_symmetry_dataset(primitive.totuple())
+    perms = compute_sg_permutations(
+        primitive.scaled_positions,
+        primitive_dataset.rotations,
+        primitive_dataset.translations,
+        primitive.cell,
+    )
+    ref_perms = [
+        [0, 1, 2, 3],
+        [1, 0, 3, 2],
+        [0, 1, 2, 3],
+        [1, 0, 3, 2],
+        [0, 1, 2, 3],
+        [1, 0, 3, 2],
+        [1, 0, 3, 2],
+        [0, 1, 2, 3],
+        [1, 0, 3, 2],
+        [0, 1, 2, 3],
+        [1, 0, 3, 2],
+        [0, 1, 2, 3],
+    ]
+    np.testing.assert_array_equal(ref_perms, perms)
+
+    perms_super = compute_sg_permutations(
+        supercell.scaled_positions,
+        dataset.rotations,
+        dataset.translations,
+        supercell.cell,
+    )
+    # np.savetxt("perms_super.dat", perms_super, fmt="%d")
+    perms_super_ref = np.loadtxt(cwd / ".." / "perms_super.dat", dtype=int)
+    np.testing.assert_array_equal(perms_super_ref, perms_super)
+
+
+def test_compute_sg_permutations_compare_stable():
+    """Test compute_sg_permutations and compare with compute_sg_permutations_stable."""
+    pytest.importorskip("spglib", minversion="2.5")
+    from spglib import spglib
+
+    axis = np.array([[0.0, 1.0, 1.0], [7.0, 6.0, 7.0], [8.0, 8.0, 8.0]])
+    positions = np.array(
+        [
+            [0.000000000000000, 0.000000000000000, 0.000000000000000],
+            [0.000000000000000, 0.000000000000000, 0.125000000000000],
+            [0.000000000000000, 0.000000000000000, 0.250000000000000],
+            [0.000000000000000, 0.000000000000000, 0.375000000000000],
+            [0.000000000000000, 0.000000000000000, 0.500000000000000],
+            [0.000000000000000, 0.000000000000000, 0.625000000000000],
+            [0.000000000000000, 0.000000000000000, 0.750000000000000],
+            [0.000000000000000, 0.000000000000000, 0.875000000000000],
+        ]
+    )
+    types = np.zeros(8, dtype=int)
+
+    cell = axis, positions, types
+    dataset = spglib.get_symmetry_dataset(cell)
+    perms = compute_sg_permutations(
+        positions,
+        dataset.rotations,
+        dataset.translations,
+        axis,
+    )
+    perms_stable = compute_sg_permutations_stable(
+        positions,
+        dataset.rotations,
+        dataset.translations,
+        axis,
+    )
+    ref_perms = [
+        [0, 1, 2, 3, 4, 5, 6, 7],
+        [0, 7, 6, 5, 4, 3, 2, 1],
+        [0, 7, 6, 5, 4, 3, 2, 1],
+        [0, 1, 2, 3, 4, 5, 6, 7],
+        [0, 1, 2, 3, 4, 5, 6, 7],
+        [0, 7, 6, 5, 4, 3, 2, 1],
+        [0, 7, 6, 5, 4, 3, 2, 1],
+        [0, 1, 2, 3, 4, 5, 6, 7],
+        [0, 7, 6, 5, 4, 3, 2, 1],
+        [0, 1, 2, 3, 4, 5, 6, 7],
+        [0, 1, 2, 3, 4, 5, 6, 7],
+        [0, 7, 6, 5, 4, 3, 2, 1],
+        [1, 2, 3, 4, 5, 6, 7, 0],
+        [1, 0, 7, 6, 5, 4, 3, 2],
+        [1, 0, 7, 6, 5, 4, 3, 2],
+        [1, 2, 3, 4, 5, 6, 7, 0],
+        [1, 2, 3, 4, 5, 6, 7, 0],
+        [1, 0, 7, 6, 5, 4, 3, 2],
+        [1, 0, 7, 6, 5, 4, 3, 2],
+        [1, 2, 3, 4, 5, 6, 7, 0],
+        [1, 0, 7, 6, 5, 4, 3, 2],
+        [1, 2, 3, 4, 5, 6, 7, 0],
+        [1, 2, 3, 4, 5, 6, 7, 0],
+        [1, 0, 7, 6, 5, 4, 3, 2],
+        [2, 3, 4, 5, 6, 7, 0, 1],
+        [2, 1, 0, 7, 6, 5, 4, 3],
+        [2, 1, 0, 7, 6, 5, 4, 3],
+        [2, 3, 4, 5, 6, 7, 0, 1],
+        [2, 3, 4, 5, 6, 7, 0, 1],
+        [2, 1, 0, 7, 6, 5, 4, 3],
+        [2, 1, 0, 7, 6, 5, 4, 3],
+        [2, 3, 4, 5, 6, 7, 0, 1],
+        [2, 1, 0, 7, 6, 5, 4, 3],
+        [2, 3, 4, 5, 6, 7, 0, 1],
+        [2, 3, 4, 5, 6, 7, 0, 1],
+        [2, 1, 0, 7, 6, 5, 4, 3],
+        [3, 4, 5, 6, 7, 0, 1, 2],
+        [3, 2, 1, 0, 7, 6, 5, 4],
+        [3, 2, 1, 0, 7, 6, 5, 4],
+        [3, 4, 5, 6, 7, 0, 1, 2],
+        [3, 4, 5, 6, 7, 0, 1, 2],
+        [3, 2, 1, 0, 7, 6, 5, 4],
+        [3, 2, 1, 0, 7, 6, 5, 4],
+        [3, 4, 5, 6, 7, 0, 1, 2],
+        [3, 2, 1, 0, 7, 6, 5, 4],
+        [3, 4, 5, 6, 7, 0, 1, 2],
+        [3, 4, 5, 6, 7, 0, 1, 2],
+        [3, 2, 1, 0, 7, 6, 5, 4],
+        [4, 5, 6, 7, 0, 1, 2, 3],
+        [4, 3, 2, 1, 0, 7, 6, 5],
+        [4, 3, 2, 1, 0, 7, 6, 5],
+        [4, 5, 6, 7, 0, 1, 2, 3],
+        [4, 5, 6, 7, 0, 1, 2, 3],
+        [4, 3, 2, 1, 0, 7, 6, 5],
+        [4, 3, 2, 1, 0, 7, 6, 5],
+        [4, 5, 6, 7, 0, 1, 2, 3],
+        [4, 3, 2, 1, 0, 7, 6, 5],
+        [4, 5, 6, 7, 0, 1, 2, 3],
+        [4, 5, 6, 7, 0, 1, 2, 3],
+        [4, 3, 2, 1, 0, 7, 6, 5],
+        [5, 6, 7, 0, 1, 2, 3, 4],
+        [5, 4, 3, 2, 1, 0, 7, 6],
+        [5, 4, 3, 2, 1, 0, 7, 6],
+        [5, 6, 7, 0, 1, 2, 3, 4],
+        [5, 6, 7, 0, 1, 2, 3, 4],
+        [5, 4, 3, 2, 1, 0, 7, 6],
+        [5, 4, 3, 2, 1, 0, 7, 6],
+        [5, 6, 7, 0, 1, 2, 3, 4],
+        [5, 4, 3, 2, 1, 0, 7, 6],
+        [5, 6, 7, 0, 1, 2, 3, 4],
+        [5, 6, 7, 0, 1, 2, 3, 4],
+        [5, 4, 3, 2, 1, 0, 7, 6],
+        [6, 7, 0, 1, 2, 3, 4, 5],
+        [6, 5, 4, 3, 2, 1, 0, 7],
+        [6, 5, 4, 3, 2, 1, 0, 7],
+        [6, 7, 0, 1, 2, 3, 4, 5],
+        [6, 7, 0, 1, 2, 3, 4, 5],
+        [6, 5, 4, 3, 2, 1, 0, 7],
+        [6, 5, 4, 3, 2, 1, 0, 7],
+        [6, 7, 0, 1, 2, 3, 4, 5],
+        [6, 5, 4, 3, 2, 1, 0, 7],
+        [6, 7, 0, 1, 2, 3, 4, 5],
+        [6, 7, 0, 1, 2, 3, 4, 5],
+        [6, 5, 4, 3, 2, 1, 0, 7],
+        [7, 0, 1, 2, 3, 4, 5, 6],
+        [7, 6, 5, 4, 3, 2, 1, 0],
+        [7, 6, 5, 4, 3, 2, 1, 0],
+        [7, 0, 1, 2, 3, 4, 5, 6],
+        [7, 0, 1, 2, 3, 4, 5, 6],
+        [7, 6, 5, 4, 3, 2, 1, 0],
+        [7, 6, 5, 4, 3, 2, 1, 0],
+        [7, 0, 1, 2, 3, 4, 5, 6],
+        [7, 6, 5, 4, 3, 2, 1, 0],
+        [7, 0, 1, 2, 3, 4, 5, 6],
+        [7, 0, 1, 2, 3, 4, 5, 6],
+        [7, 6, 5, 4, 3, 2, 1, 0],
+    ]
+    np.testing.assert_array_equal(perms, perms_stable)
+    np.testing.assert_array_equal(perms, ref_perms)
+
+
+def test_compute_sg_permutations_compare_stable_nacl(
+    ph_nacl_222: tuple[SymfcAtoms, np.ndarray, np.ndarray],
+):
+    """Test of compute_sg_permutations for NaCl."""
+    pytest.importorskip("spglib", minversion="2.5")
+    from spglib import spglib
+
+    supercell, _, _ = ph_nacl_222
+    dataset = spglib.get_symmetry_dataset(supercell.totuple())
+    perms = compute_sg_permutations(
+        supercell.scaled_positions,
+        dataset.rotations,
+        dataset.translations,
+        supercell.cell,
+    )
+    perms_stable = compute_sg_permutations_stable(
+        supercell.scaled_positions,
+        dataset.rotations,
+        dataset.translations,
+        supercell.cell,
+    )
+    np.testing.assert_array_equal(perms, perms_stable)
+
+
+def test_compute_sg_permutations_compare_stable_sio2(
+    ph_sio2_221: tuple[SymfcAtoms, np.ndarray, np.ndarray],
+):
+    """Test of compute_sg_permutations for SiO2."""
+    pytest.importorskip("spglib", minversion="2.5")
+    from spglib import spglib
+
+    supercell, _, _ = ph_sio2_221
+    dataset = spglib.get_symmetry_dataset(supercell.totuple())
+    perms = compute_sg_permutations(
+        supercell.scaled_positions,
+        dataset.rotations,
+        dataset.translations,
+        supercell.cell,
+    )
+    perms_stable = compute_sg_permutations_stable(
+        supercell.scaled_positions,
+        dataset.rotations,
+        dataset.translations,
+        supercell.cell,
+    )
+    np.testing.assert_array_equal(perms, perms_stable)
+
+
+def test_compute_sg_permutations_compare_stable_baal2o4():
+    """Test compute_sg_permutations for BaAl2O4."""
+    pytest.importorskip("spglib", minversion="2.5")
+    from spglib import spglib
+
+    types = np.zeros(8, dtype=int)
+    axis = np.array(
+        [
+            [10.4020522437529994, 0.0000000000000000, 0.0000000000000000],
+            [-5.2010261218764997, 9.0084414945829998, 0.0000000000000000],
+            [0.00000000000000000, 0.0000000000000000, 17.8057491600000013],
+        ]
+    )
+    types = np.hstack(
+        [np.zeros(16, dtype=int), np.ones(32, dtype=int), np.ones(64, dtype=int) * 2]
+    )
+    positions = np.array(
+        [
+            [0.0000000000000000, 0.0000000000000000, 0.1250000000000000],
+            [0.5000000000000000, 0.0000000000000000, 0.1250000000000000],
+            [0.0000000000000050, 0.5000000000000000, 0.1250000000000000],
+            [0.4999999999999950, 0.5000000000000000, 0.1250000000000000],
+            [0.0000000000000000, 0.0000000000000000, 0.6250000000000000],
+            [0.5000000000000000, 0.0000000000000000, 0.6250000000000000],
+            [0.0000000000000050, 0.5000000000000000, 0.6250000000000000],
+            [0.4999999999999950, 0.5000000000000000, 0.6250000000000000],
+            [0.0000000000000000, 0.0000000000000000, 0.3750000000000000],
+            [0.5000000000000000, 0.0000000000000000, 0.3750000000000000],
+            [0.0000000000000050, 0.5000000000000000, 0.3750000000000000],
+            [0.4999999999999950, 0.5000000000000000, 0.3750000000000000],
+            [0.0000000000000000, 0.0000000000000000, 0.8750000000000000],
+            [0.5000000000000000, 0.0000000000000000, 0.8750000000000000],
+            [0.0000000000000050, 0.5000000000000000, 0.8750000000000000],
+            [0.4999999999999950, 0.5000000000000000, 0.8750000000000000],
+            [0.1666666666666690, 0.3333333333333370, 0.2768253700000010],
+            [0.6666666666666690, 0.3333333333333370, 0.2768253700000010],
+            [0.1666666666666730, 0.8333333333333370, 0.2768253700000010],
+            [0.6666666666666640, 0.8333333333333370, 0.2768253700000010],
+            [0.1666666666666690, 0.3333333333333370, 0.7768253699999890],
+            [0.6666666666666690, 0.3333333333333370, 0.7768253699999890],
+            [0.1666666666666730, 0.8333333333333370, 0.7768253699999890],
+            [0.6666666666666640, 0.8333333333333370, 0.7768253699999890],
+            [0.3333333333333270, 0.1666666666666630, 0.0268253700000010],
+            [0.8333333333333270, 0.1666666666666630, 0.0268253700000010],
+            [0.3333333333333320, 0.6666666666666630, 0.0268253700000010],
+            [0.8333333333333310, 0.6666666666666630, 0.0268253700000010],
+            [0.3333333333333270, 0.1666666666666630, 0.5268253700000010],
+            [0.8333333333333270, 0.1666666666666630, 0.5268253700000010],
+            [0.3333333333333320, 0.6666666666666630, 0.5268253700000010],
+            [0.8333333333333310, 0.6666666666666630, 0.5268253700000010],
+            [0.3333333333333270, 0.1666666666666630, 0.2231746299999990],
+            [0.8333333333333270, 0.1666666666666630, 0.2231746299999990],
+            [0.3333333333333320, 0.6666666666666630, 0.2231746299999990],
+            [0.8333333333333310, 0.6666666666666630, 0.2231746299999990],
+            [0.3333333333333270, 0.1666666666666630, 0.7231746300000110],
+            [0.8333333333333270, 0.1666666666666630, 0.7231746300000110],
+            [0.3333333333333320, 0.6666666666666630, 0.7231746300000110],
+            [0.8333333333333310, 0.6666666666666630, 0.7231746300000110],
+            [0.1666666666666690, 0.3333333333333370, 0.4731746299999990],
+            [0.6666666666666690, 0.3333333333333370, 0.4731746299999990],
+            [0.1666666666666730, 0.8333333333333370, 0.4731746299999990],
+            [0.6666666666666640, 0.8333333333333370, 0.4731746299999990],
+            [0.1666666666666690, 0.3333333333333370, 0.9731746300000110],
+            [0.6666666666666690, 0.3333333333333370, 0.9731746300000110],
+            [0.1666666666666730, 0.8333333333333370, 0.9731746300000110],
+            [0.6666666666666640, 0.8333333333333370, 0.9731746300000110],
+            [0.1749127449999990, 0.1749127449999980, 0.2500000000000000],
+            [0.6749127449999970, 0.1749127449999980, 0.2500000000000000],
+            [0.1749127450000020, 0.6749127449999980, 0.2500000000000000],
+            [0.6749127450000020, 0.6749127449999980, 0.2500000000000000],
+            [0.1749127449999990, 0.1749127449999980, 0.7500000000000000],
+            [0.6749127449999970, 0.1749127449999980, 0.7500000000000000],
+            [0.1749127450000020, 0.6749127449999980, 0.7500000000000000],
+            [0.6749127450000020, 0.6749127449999980, 0.7500000000000000],
+            [0.0000000000000030, 0.3250872550000020, 0.2500000000000000],
+            [0.5000000000000030, 0.3250872550000020, 0.2500000000000000],
+            [0.9999999999999990, 0.8250872550000020, 0.2500000000000000],
+            [0.5000000000000010, 0.8250872550000020, 0.2500000000000000],
+            [0.0000000000000030, 0.3250872550000020, 0.7500000000000000],
+            [0.5000000000000030, 0.3250872550000020, 0.7500000000000000],
+            [0.9999999999999990, 0.8250872550000020, 0.7500000000000000],
+            [0.5000000000000010, 0.8250872550000020, 0.7500000000000000],
+            [0.9999999999999990, 0.1749127449999980, 0.0000000000000000],
+            [0.5000000000000010, 0.1749127449999980, 0.0000000000000000],
+            [0.9999999999999970, 0.6749127449999980, 0.0000000000000000],
+            [0.4999999999999970, 0.6749127449999980, 0.0000000000000000],
+            [0.9999999999999990, 0.1749127449999980, 0.5000000000000000],
+            [0.5000000000000010, 0.1749127449999980, 0.5000000000000000],
+            [0.9999999999999970, 0.6749127449999980, 0.5000000000000000],
+            [0.4999999999999970, 0.6749127449999980, 0.5000000000000000],
+            [0.1666666666666690, 0.3333333333333370, 0.3750000000000000],
+            [0.6666666666666690, 0.3333333333333370, 0.3750000000000000],
+            [0.1666666666666730, 0.8333333333333370, 0.3750000000000000],
+            [0.6666666666666640, 0.8333333333333370, 0.3750000000000000],
+            [0.1666666666666690, 0.3333333333333370, 0.8750000000000000],
+            [0.6666666666666690, 0.3333333333333370, 0.8750000000000000],
+            [0.1666666666666730, 0.8333333333333370, 0.8750000000000000],
+            [0.6666666666666640, 0.8333333333333370, 0.8750000000000000],
+            [0.3250872549999980, 0.3250872550000020, 0.0000000000000000],
+            [0.8250872549999980, 0.3250872550000020, 0.0000000000000000],
+            [0.3250872550000010, 0.8250872550000020, 0.0000000000000000],
+            [0.8250872550000030, 0.8250872550000020, 0.0000000000000000],
+            [0.3250872549999980, 0.3250872550000020, 0.5000000000000000],
+            [0.8250872549999980, 0.3250872550000020, 0.5000000000000000],
+            [0.3250872550000010, 0.8250872550000020, 0.5000000000000000],
+            [0.8250872550000030, 0.8250872550000020, 0.5000000000000000],
+            [0.3250872550000040, 0.0000000000000000, 0.2500000000000000],
+            [0.8250872550000040, 0.0000000000000000, 0.2500000000000000],
+            [0.3250872550000020, 0.5000000000000000, 0.2500000000000000],
+            [0.8250872550000000, 0.5000000000000000, 0.2500000000000000],
+            [0.3250872550000040, 0.0000000000000000, 0.7500000000000000],
+            [0.8250872550000040, 0.0000000000000000, 0.7500000000000000],
+            [0.3250872550000020, 0.5000000000000000, 0.7500000000000000],
+            [0.8250872550000000, 0.5000000000000000, 0.7500000000000000],
+            [0.3333333333333270, 0.1666666666666630, 0.1250000000000000],
+            [0.8333333333333270, 0.1666666666666630, 0.1250000000000000],
+            [0.3333333333333320, 0.6666666666666630, 0.1250000000000000],
+            [0.8333333333333310, 0.6666666666666630, 0.1250000000000000],
+            [0.3333333333333270, 0.1666666666666630, 0.6250000000000000],
+            [0.8333333333333270, 0.1666666666666630, 0.6250000000000000],
+            [0.3333333333333320, 0.6666666666666630, 0.6250000000000000],
+            [0.8333333333333310, 0.6666666666666630, 0.6250000000000000],
+            [0.1749127449999960, 0.0000000000000000, 0.0000000000000000],
+            [0.6749127449999960, 0.0000000000000000, 0.0000000000000000],
+            [0.1749127449999980, 0.5000000000000000, 0.0000000000000000],
+            [0.6749127450000000, 0.5000000000000000, 0.0000000000000000],
+            [0.1749127449999960, 0.0000000000000000, 0.5000000000000000],
+            [0.6749127449999960, 0.0000000000000000, 0.5000000000000000],
+            [0.1749127449999980, 0.5000000000000000, 0.5000000000000000],
+            [0.6749127450000000, 0.5000000000000000, 0.5000000000000000],
+        ]
+    )
+
+    cell = axis, positions, types
+    dataset = spglib.get_symmetry_dataset(cell)
+    perms = compute_sg_permutations(
+        positions,
+        dataset.rotations,
+        dataset.translations,
+        axis,
+    )
+    perms_stable = compute_sg_permutations_stable(
+        positions,
+        dataset.rotations,
+        dataset.translations,
+        axis,
+    )
+    np.testing.assert_array_equal(perms, perms_stable)

symfc-1.2.1/tests/utils/test_utils.py

@@ -1,73 +0,0 @@
-"""Tests of matrix manipulating functions."""
-
-from __future__ import annotations
-
-from pathlib import Path
-
-import numpy as np
-import pytest
-
-from symfc.spg_reps import SpgRepsBase
-from symfc.utils.utils import (
-    SymfcAtoms,
-    compute_sg_permutations,
-    get_indep_atoms_by_lat_trans,
-)
-
-cwd = Path(__file__).parent
-
-
-def test_get_indep_atoms_by_lattice_translation(
-    ph_nacl_222: tuple[SymfcAtoms, np.ndarray, np.ndarray],
-):
-    """Test of get_indep_atoms_by_lattice_translation."""
-    supercell, _, _ = ph_nacl_222
-    sym_op_reps = SpgRepsBase(supercell)
-    trans_perms = sym_op_reps.translation_permutations
-    assert trans_perms.shape == (32, 64)
-    indep_atoms = get_indep_atoms_by_lat_trans(trans_perms)
-    np.testing.assert_array_equal(indep_atoms, [0, 32])
-
-
-def test_compute_sg_permutations(
-    ph_gan_222: tuple[SymfcAtoms, np.ndarray, np.ndarray], cell_gan_111: SymfcAtoms
-):
-    """Test compute_sg_permutations."""
-    pytest.importorskip("spglib", minversion="2.5")
-    from spglib import spglib
-
-    supercell, _, _ = ph_gan_222
-    primitive = cell_gan_111
-    dataset = spglib.get_symmetry_dataset(supercell.totuple())
-    primitive_dataset = spglib.get_symmetry_dataset(primitive.totuple())
-    perms = compute_sg_permutations(
-        primitive.scaled_positions,
-        primitive_dataset.rotations,
-        primitive_dataset.translations,
-        primitive.cell,
-    )
-    ref_perms = [
-        [0, 1, 2, 3],
-        [1, 0, 3, 2],
-        [0, 1, 2, 3],
-        [1, 0, 3, 2],
-        [0, 1, 2, 3],
-        [1, 0, 3, 2],
-        [1, 0, 3, 2],
-        [0, 1, 2, 3],
-        [1, 0, 3, 2],
-        [0, 1, 2, 3],
-        [1, 0, 3, 2],
-        [0, 1, 2, 3],
-    ]
-    np.testing.assert_array_equal(ref_perms, perms)
-
-    perms_super = compute_sg_permutations(
-        supercell.scaled_positions,
-        dataset.rotations,
-        dataset.translations,
-        supercell.cell,
-    )
-    # np.savetxt("perms_super.dat", perms_super, fmt="%d")
-    perms_super_ref = np.loadtxt(cwd / ".." / "perms_super.dat", dtype=int)
-    np.testing.assert_array_equal(perms_super_ref, perms_super)