breaking: pt: remove data preprocess from data stat

deepmd/pt/model/descriptor/dpa1.py

@@ -112,7 +112,7 @@ def distinguish_types(self) -> bool:
         """Returns if the descriptor requires a neighbor list that distinguish different
         atomic types or not.
         """
-        return False
+        return self.se_atten.distinguish_types()
 
     @property
     def dim_out(self):

deepmd/pt/model/descriptor/hybrid.py

@@ -103,6 +103,14 @@ def get_dim_in(self) -> int:
     def get_dim_emb(self):
         return self.dim_emb
 
+    def distinguish_types(self) -> bool:
+        """Returns if the descriptor requires a neighbor list that distinguish different
+        atomic types or not.
+        """
+        return True in [
+            descriptor.distinguish_types() for descriptor in self.descriptor_list
+        ]
+
     @property
     def dim_out(self):
         """Returns the output dimension of this descriptor."""

deepmd/pt/model/descriptor/repformers.py

@@ -21,7 +21,7 @@
     env,
 )
 from deepmd.pt.utils.nlist import (
-    build_neighbor_list,
+    process_input,
 )
 from deepmd.pt.utils.utils import (
     get_activation_fn,
@@ -178,6 +178,12 @@
         """Returns the embedding dimension g2."""
         return self.g2_dim
 
+    def distinguish_types(self) -> bool:
+        """Returns if the descriptor requires a neighbor list that distinguish different
+        atomic types or not.
+        """
+        return False
+
     @property
     def dim_out(self):
         """Returns the output dimension of this descriptor."""
@@ -272,44 +278,41 @@
         suma2 = []
         mixed_type = "real_natoms_vec" in merged[0]
         for system in merged:
-            index = system["mapping"].unsqueeze(-1).expand(-1, -1, 3)
-            extended_coord = torch.gather(system["coord"], dim=1, index=index)
-            extended_coord = extended_coord - system["shift"]
-            index = system["mapping"]
-            extended_atype = torch.gather(system["atype"], dim=1, index=index)
-            nloc = system["atype"].shape[-1]
-            #######################################################
-            # dirty hack here! the interface of dataload should be
-            # redesigned to support descriptors like dpa2
-            #######################################################
-            nlist = build_neighbor_list(
-                extended_coord,
-                extended_atype,
-                nloc,
-                self.rcut,
+            coord, atype, box, natoms = (
+                system["coord"],
+                system["atype"],
+                system["box"],
+                system["natoms"],
+            )
+            extended_coord, extended_atype, mapping, nlist = process_input(
+                coord,
+                atype,
+                self.get_rcut(),
                 self.get_sel(),
-                distinguish_types=False,
+                distinguish_types=self.distinguish_types(),
+                box=box,
             )
             env_mat, _, _ = prod_env_mat_se_a(
                 extended_coord,
                 nlist,
-                system["atype"],
+                atype,
                 self.mean,
                 self.stddev,
                 self.rcut,
                 self.rcut_smth,
             )
             if not mixed_type:
                 sysr, sysr2, sysa, sysa2, sysn = analyze_descrpt(
-                    env_mat.detach().cpu().numpy(), ndescrpt, system["natoms"]
+                    env_mat.detach().cpu().numpy(), ndescrpt, natoms
                 )
             else:
+                real_natoms_vec = system["real_natoms_vec"]
                 sysr, sysr2, sysa, sysa2, sysn = analyze_descrpt(
                     env_mat.detach().cpu().numpy(),
                     ndescrpt,
-                    system["real_natoms_vec"],
+                    real_natoms_vec,
                     mixed_type=mixed_type,
-                    real_atype=system["atype"].detach().cpu().numpy(),
+                    real_atype=atype.detach().cpu().numpy(),
                 )
             sumr.append(sysr)
             suma.append(sysa)

deepmd/pt/model/descriptor/se_a.py

@@ -37,6 +37,11 @@
 from deepmd.pt.model.network.network import (
     TypeFilter,
 )
+from deepmd.pt.utils.nlist import (
+    process_input,
+)
+
+log = logging.getLogger(__name__)
 
 log = logging.getLogger(__name__)
 
@@ -100,7 +105,7 @@
         """Returns if the descriptor requires a neighbor list that distinguish different
         atomic types or not.
         """
-        return True
+        return self.sea.distinguish_types()
 
     @property
     def dim_out(self):
@@ -347,6 +352,12 @@
         """Returns the input dimension."""
         return self.dim_in
 
+    def distinguish_types(self) -> bool:
+        """Returns if the descriptor requires a neighbor list that distinguish different
+        atomic types or not.
+        """
+        return True
+
     @property
     def dim_out(self):
         """Returns the output dimension of this descriptor."""
@@ -381,20 +392,31 @@
         sumr2 = []
         suma2 = []
         for system in merged:
-            index = system["mapping"].unsqueeze(-1).expand(-1, -1, 3)
-            extended_coord = torch.gather(system["coord"], dim=1, index=index)
-            extended_coord = extended_coord - system["shift"]
+            coord, atype, box, natoms = (
+                system["coord"],
+                system["atype"],
+                system["box"],
+                system["natoms"],
+            )
+            extended_coord, extended_atype, mapping, nlist = process_input(
+                coord,
+                atype,
+                self.get_rcut(),
+                self.get_sel(),
+                distinguish_types=self.distinguish_types(),
+                box=box,
+            )
             env_mat, _, _ = prod_env_mat_se_a(
                 extended_coord,
-                system["nlist"],
-                system["atype"],
+                nlist,
+                atype,
                 self.mean,
                 self.stddev,
                 self.rcut,
                 self.rcut_smth,
             )
             sysr, sysr2, sysa, sysa2, sysn = analyze_descrpt(
-                env_mat.detach().cpu().numpy(), self.ndescrpt, system["natoms"]
+                env_mat.detach().cpu().numpy(), self.ndescrpt, natoms
             )
             sumr.append(sysr)
             suma.append(sysa)

deepmd/pt/model/descriptor/se_atten.py

@@ -21,6 +21,9 @@
 from deepmd.pt.utils import (
     env,
 )
+from deepmd.pt.utils.nlist import (
+    process_input,
+)
 
 
 @DescriptorBlock.register("se_atten")
@@ -161,6 +164,12 @@
         """Returns the output dimension of embedding."""
         return self.filter_neuron[-1]
 
+    def distinguish_types(self) -> bool:
+        """Returns if the descriptor requires a neighbor list that distinguish different
+        atomic types or not.
+        """
+        return False
+
     @property
     def dim_out(self):
         """Returns the output dimension of this descriptor."""
@@ -185,29 +194,41 @@
         suma2 = []
         mixed_type = "real_natoms_vec" in merged[0]
         for system in merged:
-            index = system["mapping"].unsqueeze(-1).expand(-1, -1, 3)
-            extended_coord = torch.gather(system["coord"], dim=1, index=index)
-            extended_coord = extended_coord - system["shift"]
+            coord, atype, box, natoms = (
+                system["coord"],
+                system["atype"],
+                system["box"],
+                system["natoms"],
+            )
+            extended_coord, extended_atype, mapping, nlist = process_input(
+                coord,
+                atype,
+                self.get_rcut(),
+                self.get_sel(),
+                distinguish_types=self.distinguish_types(),
+                box=box,
+            )
             env_mat, _, _ = prod_env_mat_se_a(
                 extended_coord,
-                system["nlist"],
-                system["atype"],
+                nlist,
+                atype,
                 self.mean,
                 self.stddev,
                 self.rcut,
                 self.rcut_smth,
             )
             if not mixed_type:
                 sysr, sysr2, sysa, sysa2, sysn = analyze_descrpt(
-                    env_mat.detach().cpu().numpy(), self.ndescrpt, system["natoms"]
+                    env_mat.detach().cpu().numpy(), self.ndescrpt, natoms
                 )
             else:
+                real_natoms_vec = system["real_natoms_vec"]
                 sysr, sysr2, sysa, sysa2, sysn = analyze_descrpt(
                     env_mat.detach().cpu().numpy(),
                     self.ndescrpt,
-                    system["real_natoms_vec"],
+                    real_natoms_vec,
                     mixed_type=mixed_type,
-                    real_atype=system["atype"].detach().cpu().numpy(),
+                    real_atype=atype.detach().cpu().numpy(),
                 )
             sumr.append(sysr)
             suma.append(sysa)

deepmd/pt/model/model/make_model.py

@@ -14,12 +14,8 @@
     fit_output_to_model_output,
 )
 from deepmd.pt.utils.nlist import (
-    build_neighbor_list,
-    extend_coord_with_ghosts,
     nlist_distinguish_types,
-)
-from deepmd.pt.utils.region import (
-    normalize_coord,
+    process_input,
 )
 
 
@@ -93,26 +89,14 @@ def forward_common(
                 The keys are defined by the `ModelOutputDef`.
 
             """
-            nframes, nloc = atype.shape[:2]
-            if box is not None:
-                coord_normalized = normalize_coord(
-                    coord.view(nframes, nloc, 3),
-                    box.reshape(nframes, 3, 3),
-                )
-            else:
-                coord_normalized = coord.clone()
-            extended_coord, extended_atype, mapping = extend_coord_with_ghosts(
-                coord_normalized, atype, box, self.get_rcut()
-            )
-            nlist = build_neighbor_list(
-                extended_coord,
-                extended_atype,
-                nloc,
+            extended_coord, extended_atype, mapping, nlist = process_input(
+                coord,
+                atype,
                 self.get_rcut(),
                 self.get_sel(),
                 distinguish_types=self.distinguish_types(),
+                box=box,
             )
-            extended_coord = extended_coord.view(nframes, -1, 3)
             model_predict_lower = self.forward_common_lower(
                 extended_coord,
                 extended_atype,

deepmd/pt/utils/dataloader.py

@@ -267,26 +267,7 @@ def collate_batch(batch):
     example = batch[0]
     result = example.copy()
     for key in example.keys():
-        if key == "shift" or key == "mapping":
-            natoms_extended = max([d[key].shape[0] for d in batch])
-            n_frames = len(batch)
-            list = []
-            for x in range(n_frames):
-                list.append(batch[x][key])
-            if key == "shift":
-                result[key] = torch.zeros(
-                    (n_frames, natoms_extended, 3),
-                    dtype=env.GLOBAL_PT_FLOAT_PRECISION,
-                )
-            else:
-                result[key] = torch.zeros(
-                    (n_frames, natoms_extended),
-                    dtype=torch.long,
-                )
-            for i in range(len(batch)):
-                natoms_tmp = list[i].shape[0]
-                result[key][i, :natoms_tmp] = list[i]
-        elif "find_" in key:
+        if "find_" in key:
             result[key] = batch[0][key]
         else:
             if batch[0][key] is None: