diff --git a/deepmd/pt/model/model/transform_output.py b/deepmd/pt/model/model/transform_output.py
index f0f7cc967d..e8afab15c4 100644
--- a/deepmd/pt/model/model/transform_output.py
+++ b/deepmd/pt/model/model/transform_output.py
@@ -108,14 +108,6 @@ def get_leading_dims(
     return list(vshape[: (len(vshape) - len(vdef.shape))])
 
 
-def get_atom_axis(
-    vdef: torch.Tensor,
-):
-    """Get the axis of atoms."""
-    atom_axis = -(len(vdef.shape) + 1)
-    return atom_axis
-
-
 def take_deriv(
     vv: torch.Tensor,
     svv: torch.Tensor,
diff --git a/deepmd/pt/utils/preprocess.py b/deepmd/pt/utils/preprocess.py
index af49b51d5a..7d5b0cf314 100644
--- a/deepmd/pt/utils/preprocess.py
+++ b/deepmd/pt/utils/preprocess.py
@@ -1,231 +1,11 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 import logging
-from typing import (
-    Union,
-)
 
 import torch
 
-from deepmd.pt.utils import (
-    env,
-)
-
 log = logging.getLogger(__name__)
 
 
-class Region3D:
-    def __init__(self, boxt):
-        """Construct a simulation box."""
-        boxt = boxt.reshape([3, 3])
-        self.boxt = boxt  # convert physical coordinates to internal ones
-        self.rec_boxt = torch.linalg.inv(
-            self.boxt
-        )  # convert internal coordinates to physical ones
-
-        self.volume = torch.linalg.det(self.boxt)  # compute the volume
-
-        # boxt = boxt.permute(1, 0)
-        c_yz = torch.cross(boxt[1], boxt[2])
-        self._h2yz = self.volume / torch.linalg.norm(c_yz)
-        c_zx = torch.cross(boxt[2], boxt[0])
-        self._h2zx = self.volume / torch.linalg.norm(c_zx)
-        c_xy = torch.cross(boxt[0], boxt[1])
-        self._h2xy = self.volume / torch.linalg.norm(c_xy)
-
-    def phys2inter(self, coord):
-        """Convert physical coordinates to internal ones."""
-        return coord @ self.rec_boxt
-
-    def inter2phys(self, coord):
-        """Convert internal coordinates to physical ones."""
-        return coord @ self.boxt
-
-    def get_face_distance(self):
-        """Return face distinces to each surface of YZ, ZX, XY."""
-        return torch.stack([self._h2yz, self._h2zx, self._h2xy])
-
-
-def normalize_coord(coord, region: Region3D, nloc: int):
-    """Move outer atoms into region by mirror.
-
-    Args:
-    - coord: shape is [nloc*3]
-    """
-    tmp_coord = coord.clone()
-    inter_cood = torch.remainder(region.phys2inter(tmp_coord), 1.0)
-    tmp_coord = region.inter2phys(inter_cood)
-    return tmp_coord
-
-
-def compute_serial_cid(cell_offset, ncell):
-    """Tell the sequential cell ID in its 3D space.
-
-    Args:
-    - cell_offset: shape is [3]
-    - ncell: shape is [3]
-    """
-    cell_offset[:, 0] *= ncell[1] * ncell[2]
-    cell_offset[:, 1] *= ncell[2]
-    return cell_offset.sum(-1)
-
-
-def compute_pbc_shift(cell_offset, ncell):
-    """Tell shift count to move the atom into region."""
-    shift = torch.zeros_like(cell_offset)
-    shift = shift + (cell_offset < 0) * -(
-        torch.div(cell_offset, ncell, rounding_mode="floor")
-    )
-    shift = shift + (cell_offset >= ncell) * -(
-        torch.div((cell_offset - ncell), ncell, rounding_mode="floor") + 1
-    )
-    assert torch.all(cell_offset + shift * ncell >= 0)
-    assert torch.all(cell_offset + shift * ncell < ncell)
-    return shift
-
-
-def build_inside_clist(coord, region: Region3D, ncell):
-    """Build cell list on atoms inside region.
-
-    Args:
-    - coord: shape is [nloc*3]
-    - ncell: shape is [3]
-    """
-    loc_ncell = int(torch.prod(ncell))  # num of local cells
-    nloc = coord.numel() // 3  # num of local atoms
-    inter_cell_size = 1.0 / ncell
-
-    inter_cood = region.phys2inter(coord.view(-1, 3))
-    cell_offset = torch.floor(inter_cood / inter_cell_size).to(torch.long)
-    # numerical error brought by conversion from phys to inter back and force
-    # may lead to negative value
-    cell_offset[cell_offset < 0] = 0
-    delta = cell_offset - ncell
-    a2c = compute_serial_cid(cell_offset, ncell)  # cell id of atoms
-    arange = torch.arange(0, loc_ncell, 1)  # pylint: disable=no-explicit-dtype,no-explicit-device
-    cellid = a2c == arange.unsqueeze(-1)  # one hot cellid
-    c2a = cellid.nonzero()
-    lst = []
-    cnt = 0
-    bincount = torch.bincount(a2c, minlength=loc_ncell)
-    for i in range(loc_ncell):
-        n = bincount[i]
-        lst.append(c2a[cnt : cnt + n, 1])
-        cnt += n
-    return a2c, lst
-
-
-def append_neighbors(coord, region: Region3D, atype, rcut: float):
-    """Make ghost atoms who are valid neighbors.
-
-    Args:
-    - coord: shape is [nloc*3]
-    - atype: shape is [nloc]
-    """
-    to_face = region.get_face_distance()
-
-    # compute num and size of local cells
-    ncell = torch.floor(to_face / rcut).to(torch.long)
-    ncell[ncell == 0] = 1
-    cell_size = to_face / ncell
-    ngcell = (
-        torch.floor(rcut / cell_size).to(torch.long) + 1
-    )  # num of cells out of local, which contain ghost atoms
-
-    # add ghost atoms
-    a2c, c2a = build_inside_clist(coord, region, ncell)
-    xi = torch.arange(-ngcell[0], ncell[0] + ngcell[0], 1)  # pylint: disable=no-explicit-dtype,no-explicit-device
-    yi = torch.arange(-ngcell[1], ncell[1] + ngcell[1], 1)  # pylint: disable=no-explicit-dtype,no-explicit-device
-    zi = torch.arange(-ngcell[2], ncell[2] + ngcell[2], 1)  # pylint: disable=no-explicit-dtype,no-explicit-device
-    xyz = xi.view(-1, 1, 1, 1) * torch.tensor([1, 0, 0], dtype=torch.long)  # pylint: disable=no-explicit-device
-    xyz = xyz + yi.view(1, -1, 1, 1) * torch.tensor([0, 1, 0], dtype=torch.long)  # pylint: disable=no-explicit-device
-    xyz = xyz + zi.view(1, 1, -1, 1) * torch.tensor([0, 0, 1], dtype=torch.long)  # pylint: disable=no-explicit-device
-    xyz = xyz.view(-1, 3)
-    mask_a = (xyz >= 0).all(dim=-1)
-    mask_b = (xyz < ncell).all(dim=-1)
-    mask = ~torch.logical_and(mask_a, mask_b)
-    xyz = xyz[mask]  # cell coord
-    shift = compute_pbc_shift(xyz, ncell)
-    coord_shift = region.inter2phys(shift.to(env.GLOBAL_PT_FLOAT_PRECISION))
-    mirrored = shift * ncell + xyz
-    cid = compute_serial_cid(mirrored, ncell)
-
-    n_atoms = coord.shape[0]
-    aid = [c2a[ci] + i * n_atoms for i, ci in enumerate(cid)]
-    aid = torch.cat(aid)
-    tmp = torch.div(aid, n_atoms, rounding_mode="trunc")
-    aid = aid % n_atoms
-    tmp_coord = coord[aid] - coord_shift[tmp]
-    tmp_atype = atype[aid]
-
-    # merge local and ghost atoms
-    merged_coord = torch.cat([coord, tmp_coord])
-    merged_coord_shift = torch.cat([torch.zeros_like(coord), coord_shift[tmp]])
-    merged_atype = torch.cat([atype, tmp_atype])
-    merged_mapping = torch.cat([torch.arange(atype.numel()), aid])  # pylint: disable=no-explicit-dtype,no-explicit-device
-    return merged_coord_shift, merged_atype, merged_mapping
-
-
-def build_neighbor_list(
-    nloc: int, coord, atype, rcut: float, sec, mapping, type_split=True, min_check=False
-):
-    """For each atom inside region, build its neighbor list.
-
-    Args:
-    - coord: shape is [nall*3]
-    - atype: shape is [nall]
-    """
-    nall = coord.numel() // 3
-    coord = coord.float()
-    nlist = [[] for _ in range(nloc)]
-    coord_l = coord.view(-1, 1, 3)[:nloc]
-    coord_r = coord.view(1, -1, 3)
-    distance = coord_l - coord_r
-    distance = torch.linalg.norm(distance, dim=-1)
-    DISTANCE_INF = distance.max().detach() + rcut
-    distance[:nloc, :nloc] += torch.eye(nloc, dtype=torch.bool) * DISTANCE_INF  # pylint: disable=no-explicit-device
-    if min_check:
-        if distance.min().abs() < 1e-6:
-            raise RuntimeError("Atom dist too close!")
-    if not type_split:
-        sec = sec[-1:]
-    lst = []
-    nlist = torch.zeros((nloc, sec[-1].item())).long() - 1  # pylint: disable=no-explicit-dtype,no-explicit-device
-    nlist_loc = torch.zeros((nloc, sec[-1].item())).long() - 1  # pylint: disable=no-explicit-dtype,no-explicit-device
-    nlist_type = torch.zeros((nloc, sec[-1].item())).long() - 1  # pylint: disable=no-explicit-dtype,no-explicit-device
-    for i, nnei in enumerate(sec):
-        if i > 0:
-            nnei = nnei - sec[i - 1]
-        if not type_split:
-            tmp = distance
-        else:
-            mask = atype.unsqueeze(0) == i
-            tmp = distance + (~mask) * DISTANCE_INF
-        if tmp.shape[1] >= nnei:
-            _sorted, indices = torch.topk(tmp, nnei, dim=1, largest=False)
-        else:
-            # when nnei > nall
-            indices = torch.zeros((nloc, nnei)).long() - 1  # pylint: disable=no-explicit-dtype,no-explicit-device
-            _sorted = torch.ones((nloc, nnei)).long() * DISTANCE_INF  # pylint: disable=no-explicit-dtype,no-explicit-device
-            _sorted_nnei, indices_nnei = torch.topk(
-                tmp, tmp.shape[1], dim=1, largest=False
-            )
-            _sorted[:, : tmp.shape[1]] = _sorted_nnei
-            indices[:, : tmp.shape[1]] = indices_nnei
-        mask = (_sorted < rcut).to(torch.long)
-        indices_loc = mapping[indices]
-        indices = indices * mask + -1 * (1 - mask)  # -1 for padding
-        indices_loc = indices_loc * mask + -1 * (1 - mask)  # -1 for padding
-        if i == 0:
-            start = 0
-        else:
-            start = sec[i - 1]
-        end = min(sec[i], start + indices.shape[1])
-        nlist[:, start:end] = indices[:, :nnei]
-        nlist_loc[:, start:end] = indices_loc[:, :nnei]
-        nlist_type[:, start:end] = atype[indices[:, :nnei]] * mask + -1 * (1 - mask)
-    return nlist, nlist_loc, nlist_type
-
-
 def compute_smooth_weight(distance, rmin: float, rmax: float):
     """Compute smooth weight for descriptor elements."""
     if rmin >= rmax:
@@ -236,70 +16,3 @@ def compute_smooth_weight(distance, rmin: float, rmax: float):
     uu = (distance - rmin) / (rmax - rmin)
     vv = uu * uu * uu * (-6 * uu * uu + 15 * uu - 10) + 1
     return vv * mid_mask + min_mask
-
-
-def make_env_mat(
-    coord,
-    atype,
-    region,
-    rcut: Union[float, list],
-    sec,
-    pbc=True,
-    type_split=True,
-    min_check=False,
-):
-    """Based on atom coordinates, return environment matrix.
-
-    Returns
-    -------
-    nlist: nlist, [nloc, nnei]
-    merged_coord_shift: shift on nall atoms, [nall, 3]
-    merged_mapping: mapping from nall index to nloc index, [nall]
-    """
-    # move outer atoms into cell
-    hybrid = isinstance(rcut, list)
-    _rcut = rcut
-    if hybrid:
-        _rcut = max(rcut)
-    if pbc:
-        merged_coord_shift, merged_atype, merged_mapping = append_neighbors(
-            coord, region, atype, _rcut
-        )
-        merged_coord = coord[merged_mapping] - merged_coord_shift
-        if merged_coord.shape[0] <= coord.shape[0]:
-            log.warning("No ghost atom is added for system ")
-    else:
-        merged_coord_shift = torch.zeros_like(coord)
-        merged_atype = atype.clone()
-        merged_mapping = torch.arange(atype.numel())  # pylint: disable=no-explicit-dtype,no-explicit-device
-        merged_coord = coord.clone()
-
-    # build nlist
-    if not hybrid:
-        nlist, nlist_loc, nlist_type = build_neighbor_list(
-            coord.shape[0],
-            merged_coord,
-            merged_atype,
-            rcut,
-            sec,
-            merged_mapping,
-            type_split=type_split,
-            min_check=min_check,
-        )
-    else:
-        nlist, nlist_loc, nlist_type = [], [], []
-        for ii, single_rcut in enumerate(rcut):
-            nlist_tmp, nlist_loc_tmp, nlist_type_tmp = build_neighbor_list(
-                coord.shape[0],
-                merged_coord,
-                merged_atype,
-                single_rcut,
-                sec[ii],
-                merged_mapping,
-                type_split=type_split,
-                min_check=min_check,
-            )
-            nlist.append(nlist_tmp)
-            nlist_loc.append(nlist_loc_tmp)
-            nlist_type.append(nlist_type_tmp)
-    return nlist, nlist_loc, nlist_type, merged_coord_shift, merged_mapping
diff --git a/deepmd/pt/utils/region.py b/deepmd/pt/utils/region.py
index 9d811acb9b..6fa77125aa 100644
--- a/deepmd/pt/utils/region.py
+++ b/deepmd/pt/utils/region.py
@@ -68,17 +68,6 @@ def to_face_distance(
     return dist.view(list(cshape[:-2]) + [3])  # noqa:RUF005
 
 
-def _to_face_distance(cell):
-    volume = torch.linalg.det(cell)
-    c_yz = torch.cross(cell[1], cell[2])
-    _h2yz = volume / torch.linalg.norm(c_yz)
-    c_zx = torch.cross(cell[2], cell[0])
-    _h2zx = volume / torch.linalg.norm(c_zx)
-    c_xy = torch.cross(cell[0], cell[1])
-    _h2xy = volume / torch.linalg.norm(c_xy)
-    return torch.stack([_h2yz, _h2zx, _h2xy])
-
-
 def b_to_face_distance(cell):
     volume = torch.linalg.det(cell)
     c_yz = torch.cross(cell[:, 1], cell[:, 2], dim=-1)
diff --git a/source/tests/pt/model/test_region.py b/source/tests/pt/model/test_region.py
index fa01f5f9bb..f92fb24f52 100644
--- a/source/tests/pt/model/test_region.py
+++ b/source/tests/pt/model/test_region.py
@@ -4,12 +4,6 @@
 import numpy as np
 import torch
 
-from deepmd.pt.utils import (
-    env,
-)
-from deepmd.pt.utils.preprocess import (
-    Region3D,
-)
 from deepmd.pt.utils.region import (
     inter2phys,
     to_face_distance,
@@ -60,29 +54,3 @@ def test_to_face_dist(self):
                 torch.testing.assert_close(
                     dists[ii][jj], expected, rtol=self.prec, atol=self.prec
                 )
-
-
-class TestLegacyRegion(unittest.TestCase):
-    def setUp(self):
-        self.cell = torch.tensor(
-            [[1, 0, 0], [0.4, 0.8, 0], [0.1, 0.3, 2.1]], dtype=dtype, device=env.DEVICE
-        )
-        self.prec = 1e-6
-
-    def test_inter_to_phys(self):
-        generator = torch.Generator(device=env.DEVICE).manual_seed(GLOBAL_SEED)
-        inter = torch.rand([3, 3], dtype=dtype, device=env.DEVICE, generator=generator)
-        reg = Region3D(self.cell)
-        phys = reg.inter2phys(inter)
-        expected_phys = torch.matmul(inter, self.cell)
-        torch.testing.assert_close(phys, expected_phys, rtol=self.prec, atol=self.prec)
-
-    def test_inter_to_inter(self):
-        generator = torch.Generator(device=env.DEVICE).manual_seed(GLOBAL_SEED)
-        inter = torch.rand([3, 3], dtype=dtype, device=env.DEVICE, generator=generator)
-        reg = Region3D(self.cell)
-        new_inter = reg.phys2inter(reg.inter2phys(inter))
-        torch.testing.assert_close(inter, new_inter, rtol=self.prec, atol=self.prec)
-
-    def test_to_face_dist(self):
-        pass