Update build_slab tool

Author: ahxbcn

src/abacusagent/modules/structure_editor.py

@@ -10,10 +10,9 @@ def build_slab(stru_file: Path,
                stru_type: Literal["cif", "poscar", "abacus/stru"] = "cif",
                miller_indices: Tuple[int, int, int] = (1, 0, 0),
                layers: int = 3,
-               supercell_2d: Tuple[int, int] = (1, 1),
-               vacuum: float = 10.0,
-               vacuum_direction: Literal['a', 'b', 'c'] = 'b'
-):
+               surface_supercell: Tuple[int, int] = (1, 1),
+               vacuum: float = 15.0,
+               vacuum_direction: Literal['a', 'b', 'c'] = 'b'):
     """
     Build slab from given structure file.
 
@@ -22,14 +21,14 @@ def build_slab(stru_file: Path,
         stru_type (Literal["cif", "poscar", "abacus/stru"]): Type of structure file. Defaults to "cif".
         miller_indices (Tuple[int, int, int]): Miller indices of the surface. Defaults to (1, 0, 0), which means (100) surface of the structure.
         layers (int, optional): Number of layers of the surface. Note that the layers is number of equivalent layers, not number of layers of atoms. Defaults to 3.
-        supercell_2d (Tuple[int, int], optional): Supercell size of the surface. Default is (1, 1), which means no supercell.
-        vacuum (float, optional): Vacuum space along on both sides of the cleaved surface. The total vacuum size will be twice this value. Units in Angstrom. Defaults to 10.0. 
+        surface_supercell (Tuple[int, int], optional): Supercell size of the surface. Default is (1, 1), which means no supercell.
+        vacuum (float, optional): Vacuum space between the cleaved surface and its periodic image. The total vacuum size will be twice this value. Units in Angstrom. Defaults to 15.0. 
         vacuum_direction (Literal['a', 'b', 'c']): The direction of the vacuum space. Defaults to 'b'.
     Returns:
         A dictionary containing the path to the surface structure file.
         Keys:
-            - surface_stru_file: Path to the surface structure file.
+            - surface_stru_file: Path to the surface structure file. The format of the generated structure file depends on the input structure file.
     Raises:
         ValueError: If stru_type is not supported.
     """
-    return _build_slab(stru_file, stru_type, miller_indices, layers, supercell_2d, vacuum, vacuum_direction)
+    return _build_slab(stru_file, stru_type, miller_indices, layers, surface_supercell, vacuum, vacuum_direction)

src/abacusagent/modules/submodules/structure_editor.py

@@ -10,8 +10,8 @@ def build_slab(stru_file: Path,
                stru_type: Literal["cif", "poscar", "abacus/stru"] = "cif",
                miller_indices: Tuple[int, int, int] = (1, 0, 0),
                layers: int = 3,
-               supercell_2d: Tuple[int, int] = (1, 1),
-               vacuum: float = 10.0,
+               surface_supercell: Tuple[int, int] = (1, 1),
+               vacuum: float = 15.0,
                vacuum_direction: Literal['a', 'b', 'c'] = 'b'):
     """
     Build slab from given structure file.
@@ -21,13 +21,13 @@ def build_slab(stru_file: Path,
         stru_type (Literal["cif", "poscar", "abacus/stru"]): Type of structure file. Defaults to "cif".
         miller_indices (Tuple[int, int, int]): Miller indices of the surface. Defaults to (1, 0, 0), which means (100) surface of the structure.
         layers (int, optional): Number of layers of the surface. Note that the layers is number of equivalent layers, not number of layers of atoms. Defaults to 3.
-        supercell_2d (Tuple[int, int], optional): Supercell size of the surface. Default is (1, 1), which means no supercell.
-        vacuum (float, optional): Vacuum space along on both sides of the cleaved surface. The total vacuum size will be twice this value. Units in Angstrom. Defaults to 10.0. 
+        surface_supercell (Tuple[int, int], optional): Supercell size of the surface. Default is (1, 1), which means no supercell.
+        vacuum (float, optional): Vacuum space between the cleaved surface and its periodic image. The total vacuum size will be twice this value. Units in Angstrom. Defaults to 15.0. 
         vacuum_direction (Literal['a', 'b', 'c']): The direction of the vacuum space. Defaults to 'b'.
     Returns:
         A dictionary containing the path to the surface structure file.
         Keys:
-            - surface_stru_file: Path to the surface structure file.
+            - surface_stru_file: Path to the surface structure file. The format of the generated structure file depends on the input structure file.
     Raises:
         ValueError: If stru_type is not supported.
     """
@@ -39,8 +39,8 @@ def build_slab(stru_file: Path,
     else:
         raise ValueError(f"Unsupported structure file type: {stru_type}")
 
-    stru_surface = surface(stru_ase, miller_indices, layers, vacuum=vacuum, periodic=True)
-    stru_surface = make_supercell(stru_surface, [[supercell_2d[0], 0, 0], [0, supercell_2d[1], 0], [0, 0, 1]])
+    stru_surface = surface(stru_ase, miller_indices, layers, vacuum=vacuum/2, periodic=True)
+    stru_surface = make_supercell(stru_surface, [[surface_supercell[0], 0, 0], [0, surface_supercell[1], 0], [0, 0, 1]])
     stru_surface_abacusstru = AbacusSTRU.from_ase(stru_surface, metadata={
                 "lattice_constant": A2BOHR,
                 "atom_type": "cartesian",
@@ -49,16 +49,14 @@ def build_slab(stru_file: Path,
 
     # Permute axis to set vacuum direction along given axis. The vacuum direction create by ase.build.surface is always along z axis.
     if vacuum_direction == "a":
-        stru_surface_abacusstru.permute_lat_vec(mode="cab")
-        stru_surface_abacusstru.permute_coord(mode="zxy")
+        stru_surface_abacusstru.permute_lat_vec(mode="cab", rotate_cart_coord=True)
     elif vacuum_direction == "b":
-        stru_surface_abacusstru.permute_lat_vec(mode="bca")
-        stru_surface_abacusstru.permute_coord(mode="yzx")
+        stru_surface_abacusstru.permute_lat_vec(mode="bca", rotate_cart_coord=True)
     elif vacuum_direction == "c":
         pass
 
     h, k, l = miller_indices
     surface_stru_file = Path(f"./{stru_file.stem}_{h}{k}{l}_{layers}layer.STRU").absolute()
-    stru_surface_abacusstru.write(surface_stru_file, fmt="stru")
+    stru_surface_abacusstru.write(surface_stru_file, fmt=stru_type)
 
     return {'surface_stru_file': surface_stru_file}