breaking: pt: unify the output of descriptors.

deepmd/model_format/se_e2_a.py

@@ -223,7 +223,18 @@ def call(
         Returns
         -------
         descriptor
-            The descriptor. shape: nf x nloc x ng x axis_neuron
+            The descriptor. shape: nf x nloc x (ng x axis_neuron)
+        gr
+            The rotationally equivariant and permutationally invariant single particle
+            representation. shape: nf x nloc x ng x 3
+        g2
+            The rotationally invariant pair-partical representation.
+            this descriptor returns None
+        h2
+            The rotationally equivariant pair-partical representation.
+            this descriptor returns None
+        sw
+            The smooth switch function.
         """
         # nf x nloc x nnei x 4
         rr, ww = self.env_mat.call(coord_ext, atype_ext, nlist, self.davg, self.dstd)
@@ -238,15 +249,17 @@ def call(
             gg = self.cal_g(ss, tt)
             # nf x nloc x ng x 4
             gr += np.einsum("flni,flnj->flij", gg, tr)
+        # nf x nloc x ng x 4
         gr /= self.nnei
         gr1 = gr[:, :, : self.axis_neuron, :]
         # nf x nloc x ng x ng1
         grrg = np.einsum("flid,fljd->flij", gr, gr1)
         # nf x nloc x (ng x ng1)
         grrg = grrg.reshape(nf, nloc, ng * self.axis_neuron)
-        return grrg
+        return grrg, gr[..., 1:], None, None, ww
 
     def serialize(self) -> dict:
+        """Serialize the descriptor to dict."""
         return {
             "rcut": self.rcut,
             "rcut_smth": self.rcut_smth,
@@ -271,6 +284,7 @@ def serialize(self) -> dict:
 
     @classmethod
     def deserialize(cls, data: dict) -> "DescrptSeA":
+        """Deserialize from dict."""
         data = copy.deepcopy(data)
         variables = data.pop("@variables")
         embeddings = data.pop("embeddings")

deepmd/pt/model/descriptor/dpa1.py

@@ -135,12 +135,42 @@ def forward(
         nlist: torch.Tensor,
         mapping: Optional[torch.Tensor] = None,
     ):
+        """Compute the descriptor.
+
+        Parameters
+        ----------
+        coord_ext
+            The extended coordinates of atoms. shape: nf x (nallx3)
+        atype_ext
+            The extended aotm types. shape: nf x nall
+        nlist
+            The neighbor list. shape: nf x nloc x nnei
+        mapping
+            The index mapping, not required by this descriptor.
+
+        Returns
+        -------
+        descriptor
+            The descriptor. shape: nf x nloc x (ng x axis_neuron)
+        gr
+            The rotationally equivariant and permutationally invariant single particle
+            representation. shape: nf x nloc x ng x 3
+        g2
+            The rotationally invariant pair-partical representation.
+            shape: nf x nloc x nnei x ng
+        h2
+            The rotationally equivariant pair-partical representation.
+            shape: nf x nloc x nnei x 3
+        sw
+            The smooth switch function. shape: nf x nloc x nnei
+
+        """
         del mapping
         nframes, nloc, nnei = nlist.shape
         nall = extended_coord.view(nframes, -1).shape[1] // 3
         g1_ext = self.type_embedding(extended_atype)
         g1_inp = g1_ext[:, :nloc, :]
-        g1, env_mat, diff, rot_mat, sw = self.se_atten(
+        g1, g2, h2, rot_mat, sw = self.se_atten(
             nlist,
             extended_coord,
             extended_atype,
@@ -149,4 +179,5 @@ def forward(
         )
         if self.concat_output_tebd:
             g1 = torch.cat([g1, g1_inp], dim=-1)
-        return g1, env_mat, diff, rot_mat, sw
+
+        return g1, rot_mat, g2, h2, sw

deepmd/pt/model/descriptor/dpa2.py

@@ -329,6 +329,36 @@ def forward(
         nlist: torch.Tensor,
         mapping: Optional[torch.Tensor] = None,
     ):
+        """Compute the descriptor.
+
+        Parameters
+        ----------
+        coord_ext
+            The extended coordinates of atoms. shape: nf x (nallx3)
+        atype_ext
+            The extended aotm types. shape: nf x nall
+        nlist
+            The neighbor list. shape: nf x nloc x nnei
+        mapping
+            The index mapping, mapps extended region index to local region.
+
+        Returns
+        -------
+        descriptor
+            The descriptor. shape: nf x nloc x (ng x axis_neuron)
+        gr
+            The rotationally equivariant and permutationally invariant single particle
+            representation. shape: nf x nloc x ng x 3
+        g2
+            The rotationally invariant pair-partical representation.
+            shape: nf x nloc x nnei x ng
+        h2
+            The rotationally equivariant pair-partical representation.
+            shape: nf x nloc x nnei x 3
+        sw
+            The smooth switch function. shape: nf x nloc x nnei
+
+        """
         nframes, nloc, nnei = nlist.shape
         nall = extended_coord.view(nframes, -1).shape[1] // 3
         # nlists
@@ -372,4 +402,4 @@ def forward(
         )
         if self.concat_output_tebd:
             g1 = torch.cat([g1, g1_inp], dim=-1)
-        return g1, g2, h2, rot_mat, sw
+        return g1, rot_mat, g2, h2, sw

deepmd/pt/model/descriptor/repformers.py

@@ -256,7 +256,7 @@ def forward(
         # (nb x nloc) x ng2 x 3
         rot_mat = torch.permute(h2g2, (0, 1, 3, 2))
 
-        return g1, g2, h2, rot_mat.view(-1, self.dim_emb, 3), sw
+        return g1, g2, h2, rot_mat.view(-1, nloc, self.dim_emb, 3), sw
 
     def compute_input_stats(self, merged):
         """Update mean and stddev for descriptor elements."""

deepmd/pt/model/descriptor/se_a.py

@@ -115,12 +115,42 @@ def get_data_process_key(cls, config):
 
     def forward(
         self,
-        extended_coord: torch.Tensor,
-        extended_atype: torch.Tensor,
+        coord_ext: torch.Tensor,
+        atype_ext: torch.Tensor,
         nlist: torch.Tensor,
         mapping: Optional[torch.Tensor] = None,
     ):
-        return self.sea.forward(nlist, extended_coord, extended_atype, None, mapping)
+        """Compute the descriptor.
+
+        Parameters
+        ----------
+        coord_ext
+            The extended coordinates of atoms. shape: nf x (nallx3)
+        atype_ext
+            The extended aotm types. shape: nf x nall
+        nlist
+            The neighbor list. shape: nf x nloc x nnei
+        mapping
+            The index mapping, not required by this descriptor.
+
+        Returns
+        -------
+        descriptor
+            The descriptor. shape: nf x nloc x (ng x axis_neuron)
+        gr
+            The rotationally equivariant and permutationally invariant single particle
+            representation. shape: nf x nloc x ng x 3
+        g2
+            The rotationally invariant pair-partical representation.
+            this descriptor returns None
+        h2
+            The rotationally equivariant pair-partical representation.
+            this descriptor returns None
+        sw
+            The smooth switch function.
+
+        """
+        return self.sea.forward(nlist, coord_ext, atype_ext, None, mapping)
 
     def set_stat_mean_and_stddev(
         self,
@@ -389,7 +419,7 @@ def forward(
         del extended_atype_embd, mapping
         nloc = nlist.shape[1]
         atype = extended_atype[:, :nloc]
-        dmatrix, diff, _ = prod_env_mat_se_a(
+        dmatrix, diff, sw = prod_env_mat_se_a(
             extended_coord,
             nlist,
             atype,
@@ -438,12 +468,14 @@ def forward(
         result = torch.matmul(
             xyz_scatter_1, xyz_scatter_2
         )  # shape is [nframes*nall, self.filter_neuron[-1], self.axis_neuron]
+        result = result.view(-1, nloc, self.filter_neuron[-1] * self.axis_neuron)
+        rot_mat = rot_mat.view([-1, nloc] + list(rot_mat.shape[1:]))  # noqa:RUF005
         return (
-            result.view(-1, nloc, self.filter_neuron[-1] * self.axis_neuron),
-            None,
-            None,
+            result,
+            rot_mat,
             None,
             None,
+            sw,
         )
 
 

deepmd/pt/model/descriptor/se_atten.py

@@ -281,9 +281,8 @@ def forward(
             self.rcut,
             self.rcut_smth,
         )
-        dmatrix = dmatrix.view(
-            -1, self.ndescrpt
-        )  # shape is [nframes*nall, self.ndescrpt]
+        # [nfxnlocxnnei, self.ndescrpt]
+        dmatrix = dmatrix.view(-1, self.ndescrpt)
         nlist_mask = nlist != -1
         nlist[nlist == -1] = 0
         sw = torch.squeeze(sw, -1)
@@ -328,7 +327,7 @@ def forward(
         return (
             result.view(-1, nloc, self.filter_neuron[-1] * self.axis_neuron),
             ret.view(-1, nloc, self.nnei, self.filter_neuron[-1]),
-            diff,
+            dmatrix.view(-1, nloc, self.nnei, 4)[..., 1:],
             rot_mat.view(-1, self.filter_neuron[-1], 3),
             sw,
         )

deepmd/pt/model/model/dp_atomic_model.py

@@ -14,7 +14,6 @@
     Descriptor,
 )
 from deepmd.pt.model.task import (
-    DenoiseNet,
     Fitting,
 )
 
@@ -93,40 +92,20 @@ def __init__(
             sampled=sampled,
         )
 
-        # Fitting
-        if fitting_net:
-            fitting_net["type"] = fitting_net.get("type", "ener")
-            if self.descriptor_type not in ["se_e2_a"]:
-                fitting_net["ntypes"] = 1
-            else:
-                fitting_net["ntypes"] = self.descriptor.get_ntype()
-                fitting_net["use_tebd"] = False
-            fitting_net["embedding_width"] = self.descriptor.dim_out
-
-            self.grad_force = "direct" not in fitting_net["type"]
-            if not self.grad_force:
-                fitting_net["out_dim"] = self.descriptor.dim_emb
-                if "ener" in fitting_net["type"]:
-                    fitting_net["return_energy"] = True
-            self.fitting_net = Fitting(**fitting_net)
+        fitting_net["type"] = fitting_net.get("type", "ener")
+        if self.descriptor_type not in ["se_e2_a"]:
+            fitting_net["ntypes"] = 1
         else:
-            self.fitting_net = None
-            self.grad_force = False
-            if not self.split_nlist:
-                self.coord_denoise_net = DenoiseNet(
-                    self.descriptor.dim_out, self.ntypes - 1, self.descriptor.dim_emb
-                )
-            elif self.combination:
-                self.coord_denoise_net = DenoiseNet(
-                    self.descriptor.dim_out,
-                    self.ntypes - 1,
-                    self.descriptor.dim_emb_list,
-                    self.prefactor,
-                )
-            else:
-                self.coord_denoise_net = DenoiseNet(
-                    self.descriptor.dim_out, self.ntypes - 1, self.descriptor.dim_emb
-                )
+            fitting_net["ntypes"] = self.descriptor.get_ntype()
+            fitting_net["use_tebd"] = False
+        fitting_net["embedding_width"] = self.descriptor.dim_out
+
+        self.grad_force = "direct" not in fitting_net["type"]
+        if not self.grad_force:
+            fitting_net["out_dim"] = self.descriptor.dim_emb
+            if "ener" in fitting_net["type"]:
+                fitting_net["return_energy"] = True
+        self.fitting_net = Fitting(**fitting_net)
 
     def get_fitting_output_def(self) -> FittingOutputDef:
         """Get the output def of the fitting net."""
@@ -178,31 +157,13 @@ def forward_atomic(
         atype = extended_atype[:, :nloc]
         if self.do_grad():
             extended_coord.requires_grad_(True)
-        descriptor, env_mat, diff, rot_mat, sw = self.descriptor(
+        descriptor, rot_mat, g2, h2, sw = self.descriptor(
             extended_coord,
             extended_atype,
             nlist,
             mapping=mapping,
         )
         assert descriptor is not None
         # energy, force
-        if self.fitting_net is not None:
-            fit_ret = self.fitting_net(
-                descriptor, atype, atype_tebd=None, rot_mat=rot_mat
-            )
-        # denoise
-        else:
-            nlist_list = [nlist]
-            if not self.split_nlist:
-                nnei_mask = nlist != -1
-            elif self.combination:
-                nnei_mask = []
-                for item in nlist_list:
-                    nnei_mask_item = item != -1
-                    nnei_mask.append(nnei_mask_item)
-            else:
-                env_mat = env_mat[-1]
-                diff = diff[-1]
-                nnei_mask = nlist_list[-1] != -1
-            fit_ret = self.coord_denoise_net(env_mat, diff, nnei_mask, descriptor, sw)
+        fit_ret = self.fitting_net(descriptor, atype, atype_tebd=None, rot_mat=rot_mat)
         return fit_ret

deepmd/pt/model/task/ener.py

@@ -207,8 +207,11 @@ def forward(
                 inputs
             )  # Shape is [nframes, nloc, m1]
             assert list(vec_out.size()) == [nframes, nloc, self.out_dim]
+            # (nf x nloc) x 1 x od
             vec_out = vec_out.view(-1, 1, self.out_dim)
             assert rot_mat is not None
+            # (nf x nloc) x od x 3
+            rot_mat = rot_mat.view(-1, self.out_dim, 3)
             vec_out = (
                 torch.bmm(vec_out, rot_mat).squeeze(-2).view(nframes, nloc, 3)
             )  # Shape is [nframes, nloc, 3]

source/tests/common/test_model_format_utils.py

@@ -367,4 +367,5 @@ def test_self_consistency(
         em1 = DescrptSeA.deserialize(em0.serialize())
         mm0 = em0.call(self.coord_ext, self.atype_ext, self.nlist)
         mm1 = em1.call(self.coord_ext, self.atype_ext, self.nlist)
-        np.testing.assert_allclose(mm0, mm1)
+        for ii in [0, 1, 4]:
+            np.testing.assert_allclose(mm0[ii], mm1[ii])

source/tests/pt/test_permutation_denoise.py

@@ -66,6 +66,7 @@ def test(
         )
 
 
+@unittest.skip("support of the denoise is temporally disabled")
 class TestDenoiseModelDPA1(unittest.TestCase, PermutationDenoiseTest):
     def setUp(self):
         model_params = copy.deepcopy(model_dpa1)
@@ -74,6 +75,7 @@ def setUp(self):
         self.model = get_model(model_params, sampled).to(env.DEVICE)
 
 
+@unittest.skip("support of the denoise is temporally disabled")
 class TestDenoiseModelDPA2(unittest.TestCase, PermutationDenoiseTest):
     def setUp(self):
         model_params_sample = copy.deepcopy(model_dpa2)

source/tests/pt/test_rot_denoise.py

@@ -97,6 +97,7 @@ def test(
         )
 
 
+@unittest.skip("support of the denoise is temporally disabled")
 class TestDenoiseModelDPA1(unittest.TestCase, RotDenoiseTest):
     def setUp(self):
         model_params = copy.deepcopy(model_dpa1)
@@ -105,6 +106,7 @@ def setUp(self):
         self.model = get_model(model_params, sampled).to(env.DEVICE)
 
 
+@unittest.skip("support of the denoise is temporally disabled")
 class TestDenoiseModelDPA2(unittest.TestCase, RotDenoiseTest):
     def setUp(self):
         model_params_sample = copy.deepcopy(model_dpa2)