add ut for the open boundary condition. fix bugs

deepmd/model_format/make_model.py

@@ -44,18 +44,26 @@ def call(
             box: Optional[np.ndarray] = None,
             do_atomic_virial: bool = False,
         ) -> Dict[str, np.ndarray]:
-            """Return total energy of the system.
-            Args:
-            - coord: Atom coordinates with shape [nframes, natoms[1]*3].
-            - atype: Atom types with shape [nframes, natoms[1]].
-            - natoms: Atom statisics with shape [self.ntypes+2].
-            - box: Simulation box with shape [nframes, 9].
-            - atomic_virial: Whether or not compoute the atomic virial.
+            """Return predictions of a model.
+
+            Parameters
+            ----------
+            coord
+                The coordinates of the atoms.
+                shape: nf x (nloc x 3)
+            atype
+                The type of atoms. shape: nf x nloc
+            box
+                The simulation box. shape: nf x 9
+            do_atomic_virial
+                If calculate the atomic virial.
 
             Returns
             -------
-            - energy: Energy per atom.
-            - force: XYZ force per atom.
+            ret_dict
+                The result dict of type Dict[str,np.ndarray].
+                The keys are defined by the `ModelOutputDef`.
+
             """
             nframes, nloc = atype.shape[:2]
             if box is not None:
@@ -64,7 +72,7 @@ def call(
                     box.reshape(nframes, 3, 3),
                 )
             else:
-                coord_normalized = coord.clone()
+                coord_normalized = coord.copy()
             extended_coord, extended_atype, mapping = extend_coord_with_ghosts(
                 coord_normalized, atype, box, self.get_rcut()
             )

deepmd/model_format/nlist.py

@@ -40,7 +40,7 @@ def build_neighbor_list(
     rr = rr[:, :, 1:]
     nlist = nlist[:, :, 1:]
     nnei = rr.shape[2]
-    if nsel != nnei:
+    if nsel <= nnei:
         rr = rr[:, :, :nsel]
         nlist = nlist[:, :, :nsel]
     else:

deepmd/model_format/region.py

@@ -57,6 +57,8 @@ def normalize_coord(
     ----------
     coord : np.ndarray
         orignal coordinates of shape [*, na, 3].
+    cell : np.ndarray
+        simulation cell shape [*, 3, 3].
 
     Returns
     -------

source/tests/pt/test_dp_mode.py

@@ -110,6 +110,36 @@ def test_dp_consistency(self):
             to_numpy_array(ret1["energy_redu"]),
         )
 
+    def test_dp_consistency_nopbc(self):
+        nf, nloc = self.atype.shape
+        ds = DPDescrptSeA(
+            self.rcut,
+            self.rcut_smth,
+            self.sel,
+        )
+        ft = DPInvarFitting(
+            "energy",
+            self.nt,
+            ds.get_dim_out(),
+            1,
+            distinguish_types=ds.distinguish_types(),
+        )
+        type_map = ["foo", "bar"]
+        md0 = DPDPModel(ds, ft, type_map=type_map)
+        md1 = DPModel.deserialize(md0.serialize()).to(env.DEVICE)
+        args0 = [self.coord, self.atype]
+        args1 = [to_torch_tensor(ii) for ii in [self.coord, self.atype]]
+        ret0 = md0.call(*args0)
+        ret1 = md1.forward_common(*args1)
+        np.testing.assert_allclose(
+            ret0["energy"],
+            to_numpy_array(ret1["energy"]),
+        )
+        np.testing.assert_allclose(
+            ret0["energy_redu"],
+            to_numpy_array(ret1["energy_redu"]),
+        )
+
 
 class TestDPModelLower(unittest.TestCase, TestCaseSingleFrameWithNlist):
     def setUp(self):