Ensure decohesive slabs stay right-handed for LAMMPS.

Swap a↔b when det([a,b,c]) ≤ 0 after slab construction so left-handed cells from odd axis permutations do not fail dpdata/LAMMPS conversion.

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: Zikkying

apex/core/property/Decohesive.py

@@ -268,13 +268,40 @@ def __gen_slab_pmg(
         self.is_flip = c_vec[2] < 0
         elong_scale = 1 + (abs(vacuum_size) / slab_height)
 
-        new_lattice = [a_vec, b_vec, elong_scale * c_vec]
+        new_lattice = np.array([a_vec, b_vec, elong_scale * c_vec], dtype=float)
         new_frac_coords = []
         for frac in sorted_frac_coords:
-            coord = frac.copy()
+            coord = np.array(frac, dtype=float)
             coord[2] = coord[2] / elong_scale
             new_frac_coords.append(coord)
 
+        # LAMMPS requires a right-handed box: det([a, b, c]) > 0.
+        # Slab construction (odd axis permutations / mirroring) can produce a
+        # left-handed cell; swapping a↔b restores chirality without changing
+        # the physical slab.
+        new_lattice, new_frac_coords = _ensure_right_handed_cell(
+            new_lattice, new_frac_coords
+        )
+
         return Structure(
-            lattice=np.array(new_lattice), coords=new_frac_coords, species=sorted_species
+            lattice=new_lattice, coords=new_frac_coords, species=sorted_species
+        )
+
+
+def _ensure_right_handed_cell(lattice, frac_coords):
+    """Swap a↔b when det([a, b, c]) ≤ 0 so the cell is right-handed."""
+    lattice = np.array(lattice, dtype=float)
+    det = np.linalg.det(lattice)
+    if det > 0:
+        return lattice, [np.array(fc, dtype=float) for fc in frac_coords]
+    if abs(det) <= np.finfo(float).eps:
+        raise RuntimeError(
+            "Generated slab has a singular lattice (det ≈ 0); cannot convert to LAMMPS"
         )
+    lattice = lattice[[1, 0, 2]]
+    fixed_frac = []
+    for frac in frac_coords:
+        coord = np.array(frac, dtype=float)
+        coord[0], coord[1] = coord[1], coord[0]
+        fixed_frac.append(coord)
+    return lattice, fixed_frac

tests/test_decohesive.py

@@ -128,9 +128,45 @@ def test_make_confs_with_c_vector_not_aligned_to_z(self):
             1.0,
             places=8,
         )
-    
+
+    def test_make_confs_bcc_110_is_finite_and_right_handed(self):
+        bcc_mo = Structure(
+            Lattice.cubic(3.16),
+            ["Mo", "Mo"],
+            [[0, 0, 0], [0.5, 0.5, 0.5]],
+        )
+        bcc_mo.to(filename=os.path.join(self.equi_path, "CONTCAR"), fmt="poscar")
+        parameter = {
+            "type": "decohesive",
+            "min_slab_size": 25,
+            "max_vacuum_size": 2,
+            "vacuum_size_step": 1,
+            "miller_index": [1, 1, 0],
+            "cal_type": "static",
+        }
+
+        tasks = Decohesive(parameter).make_confs(self.target_path, self.equi_path)
+        for task in tasks:
+            slab = Structure.from_file(os.path.join(task, "POSCAR.tmp"))
+            self.assertTrue(np.isfinite(slab.lattice.matrix).all())
+            self.assertGreater(np.linalg.det(slab.lattice.matrix), 0.0)
+
+    def test_ensure_right_handed_cell_swaps_ab(self):
+        from apex.core.property.Decohesive import _ensure_right_handed_cell
+
+        left_handed = np.array(
+            [[0.0, 3.0, 0.0], [3.0, 0.0, 0.0], [0.0, 0.0, 3.0]], dtype=float
+        )
+        self.assertLess(np.linalg.det(left_handed), 0.0)
+        fixed, frac = _ensure_right_handed_cell(
+            left_handed, [np.array([0.1, 0.2, 0.3])]
+        )
+        self.assertGreater(np.linalg.det(fixed), 0.0)
+        np.testing.assert_allclose(frac[0], [0.2, 0.1, 0.3])
+
     def __gen_slab_pmg(self, structure: Structure,
                        plane_miller, slab_size, vacuum_size) -> Structure:
+        from apex.core.property.Decohesive import _ensure_right_handed_cell
 
         # Generate slab via Pymatgen
         slabGen = SlabGenerator(structure, miller_index=plane_miller,
@@ -150,19 +186,20 @@ def __gen_slab_pmg(self, structure: Structure,
             sorted_species.append(species)
         # add vacuum layer to the slab with height unit of angstrom
         a_vec, b_vec, c_vec = slab.lattice.matrix
-        slab_height = abs(c_vec[2])
+        slab_height = np.linalg.norm(c_vec)
         elong_scale = 1 + (abs(vacuum_size) / slab_height)
-        new_lattice = [a_vec, b_vec, elong_scale * c_vec]
+        new_lattice = np.array([a_vec, b_vec, elong_scale * c_vec], dtype=float)
         new_frac_coords = []
         for frac in sorted_frac_coords:
-            coord = frac.copy()
+            coord = np.array(frac, dtype=float)
             coord[2] = coord[2] / elong_scale
             new_frac_coords.append(coord)
-        slab_new = Structure(
-            lattice=np.array(new_lattice), coords=new_frac_coords, species=sorted_species
+        new_lattice, new_frac_coords = _ensure_right_handed_cell(
+            new_lattice, new_frac_coords
+        )
+        return Structure(
+            lattice=new_lattice, coords=new_frac_coords, species=sorted_species
         )
-
-        return slab_new
 
 class TestDecohesiveReport(unittest.TestCase):
     def setUp(self):