feat(jax/array-api): DPA-2 (#4294)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Introduced new classes for enhanced descriptor functionality,
including `DescrptDPA2`, `DescrptBlockRepformers`, and
`DescrptBlockSeTTebd`.
- Added serialization and deserialization methods for better state
management of descriptor objects.

- **Improvements**
- Enhanced compatibility with various array backends through the
integration of `array_api_compat`.
- Refactored existing methods to utilize new array API functions for
improved performance.
- Updated documentation to reflect JAX as a supported backend alongside
PyTorch.

- **Bug Fixes**
- Updated handling of attributes in several classes to ensure correct
deserialization and type safety.

- **Tests**
- Enhanced testing capabilities for JAX and Array API Strict backend
integration, including conditional imports and new evaluation methods.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>

deepmd/dpmodel/descriptor/dpa2.py

@@ -4,11 +4,18 @@
     Union,
 )
 
+import array_api_compat
 import numpy as np
 
 from deepmd.dpmodel import (
     NativeOP,
 )
+from deepmd.dpmodel.array_api import (
+    xp_take_along_axis,
+)
+from deepmd.dpmodel.common import (
+    to_numpy_array,
+)
 from deepmd.dpmodel.utils import (
     EnvMat,
     NetworkCollection,
@@ -787,9 +794,10 @@ def call(
             The smooth switch function. shape: nf x nloc x nnei
 
         """
+        xp = array_api_compat.array_namespace(coord_ext, atype_ext, nlist)
         use_three_body = self.use_three_body
         nframes, nloc, nnei = nlist.shape
-        nall = coord_ext.reshape(nframes, -1).shape[1] // 3
+        nall = xp.reshape(coord_ext, (nframes, -1)).shape[1] // 3
         # nlists
         nlist_dict = build_multiple_neighbor_list(
             coord_ext,
@@ -798,7 +806,10 @@ def call(
             self.nsel_list,
         )
         # repinit
-        g1_ext = self.type_embedding.call()[atype_ext]
+        g1_ext = xp.reshape(
+            xp.take(self.type_embedding.call(), xp.reshape(atype_ext, [-1]), axis=0),
+            (nframes, nall, self.tebd_dim),
+        )
         g1_inp = g1_ext[:, :nloc, :]
         g1, _, _, _, _ = self.repinit(
             nlist_dict[
@@ -823,16 +834,18 @@ def call(
                 g1_ext,
                 mapping,
             )
-            g1 = np.concatenate([g1, g1_three_body], axis=-1)
+            g1 = xp.concat([g1, g1_three_body], axis=-1)
         # linear to change shape
         g1 = self.g1_shape_tranform(g1)
         if self.add_tebd_to_repinit_out:
             assert self.tebd_transform is not None
             g1 = g1 + self.tebd_transform(g1_inp)
         # mapping g1
         assert mapping is not None
-        mapping_ext = np.tile(mapping.reshape(nframes, nall, 1), (1, 1, g1.shape[-1]))
-        g1_ext = np.take_along_axis(g1, mapping_ext, axis=1)
+        mapping_ext = xp.tile(
+            xp.reshape(mapping, (nframes, nall, 1)), (1, 1, g1.shape[-1])
+        )
+        g1_ext = xp_take_along_axis(g1, mapping_ext, axis=1)
         # repformer
         g1, g2, h2, rot_mat, sw = self.repformers(
             nlist_dict[
@@ -846,7 +859,7 @@ def call(
             mapping,
         )
         if self.concat_output_tebd:
-            g1 = np.concatenate([g1, g1_inp], axis=-1)
+            g1 = xp.concat([g1, g1_inp], axis=-1)
         return g1, rot_mat, g2, h2, sw
 
     def serialize(self) -> dict:
@@ -883,8 +896,8 @@ def serialize(self) -> dict:
             "embeddings": repinit.embeddings.serialize(),
             "env_mat": EnvMat(repinit.rcut, repinit.rcut_smth).serialize(),
             "@variables": {
-                "davg": repinit["davg"],
-                "dstd": repinit["dstd"],
+                "davg": to_numpy_array(repinit["davg"]),
+                "dstd": to_numpy_array(repinit["dstd"]),
             },
         }
         if repinit.tebd_input_mode in ["strip"]:
@@ -896,8 +909,8 @@ def serialize(self) -> dict:
             "repformer_layers": [layer.serialize() for layer in repformers.layers],
             "env_mat": EnvMat(repformers.rcut, repformers.rcut_smth).serialize(),
             "@variables": {
-                "davg": repformers["davg"],
-                "dstd": repformers["dstd"],
+                "davg": to_numpy_array(repformers["davg"]),
+                "dstd": to_numpy_array(repformers["dstd"]),
             },
         }
         data.update(
@@ -913,8 +926,8 @@ def serialize(self) -> dict:
                     repinit_three_body.rcut, repinit_three_body.rcut_smth
                 ).serialize(),
                 "@variables": {
-                    "davg": repinit_three_body["davg"],
-                    "dstd": repinit_three_body["dstd"],
+                    "davg": to_numpy_array(repinit_three_body["davg"]),
+                    "dstd": to_numpy_array(repinit_three_body["dstd"]),
                 },
             }
             if repinit_three_body.tebd_input_mode in ["strip"]: