feat(jax/array-api): se_e3 (#4286)

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

- **New Features**
- Introduced a new descriptor class `DescrptSeT` for enhanced
compatibility with array APIs.
- Added support for JAX as a backend option for the `"se_e3"`
descriptor.

- **Bug Fixes**
- Improved array handling in the `clear` method of the `NN` class to
ensure compatibility across different array implementations.

- **Documentation**
	- Updated the module exports to include the new `DescrptSeT` class.
- Expanded documentation to reflect JAX as a supported backend for the
`"se_e3"` descriptor.

- **Tests**
- Enhanced the test suite to support additional computational backends
and added new evaluation methods.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <[email protected]>

Author: njzjz

deepmd/dpmodel/descriptor/se_t.py

@@ -6,13 +6,18 @@
     Union,
 )
 
+import array_api_compat
 import numpy as np
 
 from deepmd.dpmodel import (
     DEFAULT_PRECISION,
     PRECISION_DICT,
     NativeOP,
 )
+from deepmd.dpmodel.common import (
+    get_xp_precision,
+    to_numpy_array,
+)
 from deepmd.dpmodel.utils import (
     EmbeddingNet,
     EnvMat,
@@ -25,9 +30,6 @@
 from deepmd.dpmodel.utils.update_sel import (
     UpdateSel,
 )
-from deepmd.env import (
-    GLOBAL_NP_FLOAT_PRECISION,
-)
 from deepmd.utils.data_system import (
     DeepmdDataSystem,
 )
@@ -122,26 +124,28 @@ def __init__(
         # order matters, placed after the assignment of self.ntypes
         self.reinit_exclude(exclude_types)
         self.trainable = trainable
+        self.sel_cumsum = [0, *np.cumsum(self.sel).tolist()]
 
         in_dim = 1  # not considiering type embedding
-        self.embeddings = NetworkCollection(
+        embeddings = NetworkCollection(
             ntypes=self.ntypes,
             ndim=2,
             network_type="embedding_network",
         )
         for ii, embedding_idx in enumerate(
-            itertools.product(range(self.ntypes), repeat=self.embeddings.ndim)
+            itertools.product(range(self.ntypes), repeat=embeddings.ndim)
         ):
-            self.embeddings[embedding_idx] = EmbeddingNet(
+            embeddings[embedding_idx] = EmbeddingNet(
                 in_dim,
                 self.neuron,
                 self.activation_function,
                 self.resnet_dt,
                 self.precision,
                 seed=child_seed(self.seed, ii),
             )
+        self.embeddings = embeddings
         self.env_mat = EnvMat(self.rcut, self.rcut_smth, protection=self.env_protection)
-        self.nnei = np.sum(self.sel)
+        self.nnei = sum(self.sel)
         self.davg = np.zeros(
             [self.ntypes, self.nnei, 4], dtype=PRECISION_DICT[self.precision]
         )
@@ -299,20 +303,22 @@ def call(
             The smooth switch function.
         """
         del mapping
+        xp = array_api_compat.array_namespace(coord_ext, atype_ext, nlist)
         # nf x nloc x nnei x 4
         rr, diff, ww = self.env_mat.call(
             coord_ext, atype_ext, nlist, self.davg, self.dstd
         )
         nf, nloc, nnei, _ = rr.shape
-        sec = np.append([0], np.cumsum(self.sel))
+        sec = self.sel_cumsum
 
         ng = self.neuron[-1]
-        result = np.zeros([nf * nloc, ng], dtype=PRECISION_DICT[self.precision])
+        result = xp.zeros([nf * nloc, ng], dtype=get_xp_precision(xp, self.precision))
         exclude_mask = self.emask.build_type_exclude_mask(nlist, atype_ext)
         # merge nf and nloc axis, so for type_one_side == False,
         # we don't require atype is the same in all frames
-        exclude_mask = exclude_mask.reshape(nf * nloc, nnei)
-        rr = rr.reshape(nf * nloc, nnei, 4)
+        exclude_mask = xp.reshape(exclude_mask, (nf * nloc, nnei))
+        rr = xp.reshape(rr, (nf * nloc, nnei, 4))
+        rr = xp.astype(rr, get_xp_precision(xp, self.precision))
 
         for embedding_idx in itertools.product(
             range(self.ntypes), repeat=self.embeddings.ndim
@@ -325,23 +331,26 @@ def call(
                 # nfnl x nt_i x 3
                 rr_i = rr[:, sec[ti] : sec[ti + 1], 1:]
                 mm_i = exclude_mask[:, sec[ti] : sec[ti + 1]]
-                rr_i = rr_i * mm_i[:, :, None]
+                rr_i = rr_i * xp.astype(mm_i[:, :, None], rr_i.dtype)
                 # nfnl x nt_j x 3
                 rr_j = rr[:, sec[tj] : sec[tj + 1], 1:]
                 mm_j = exclude_mask[:, sec[tj] : sec[tj + 1]]
-                rr_j = rr_j * mm_j[:, :, None]
+                rr_j = rr_j * xp.astype(mm_j[:, :, None], rr_j.dtype)
                 # nfnl x nt_i x nt_j
-                env_ij = np.einsum("ijm,ikm->ijk", rr_i, rr_j)
+                # env_ij = np.einsum("ijm,ikm->ijk", rr_i, rr_j)
+                env_ij = xp.sum(rr_i[:, :, None, :] * rr_j[:, None, :, :], axis=-1)
                 # nfnl x nt_i x nt_j x 1
                 env_ij_reshape = env_ij[:, :, :, None]
                 # nfnl x nt_i x nt_j x ng
                 gg = self.embeddings[embedding_idx].call(env_ij_reshape)
                 # nfnl x nt_i x nt_j x ng
-                res_ij = np.einsum("ijk,ijkm->im", env_ij, gg)
+                # res_ij = np.einsum("ijk,ijkm->im", env_ij, gg)
+                res_ij = xp.sum(env_ij[:, :, :, None] * gg, axis=(1, 2))
                 res_ij = res_ij * (1.0 / float(nei_type_i) / float(nei_type_j))
                 result += res_ij
         # nf x nloc x ng
-        result = result.reshape(nf, nloc, ng).astype(GLOBAL_NP_FLOAT_PRECISION)
+        result = xp.reshape(result, (nf, nloc, ng))
+        result = xp.astype(result, get_xp_precision(xp, "global"))
         return result, None, None, None, ww
 
     def serialize(self) -> dict:
@@ -369,8 +378,8 @@ def serialize(self) -> dict:
             "exclude_types": self.exclude_types,
             "env_protection": self.env_protection,
             "@variables": {
-                "davg": self.davg,
-                "dstd": self.dstd,
+                "davg": to_numpy_array(self.davg),
+                "dstd": to_numpy_array(self.dstd),
             },
             "type_map": self.type_map,
             "trainable": self.trainable,

deepmd/dpmodel/utils/network.py

@@ -572,11 +572,12 @@ def call(self, x):
         def clear(self):
             """Clear the network parameters to zero."""
             for layer in self.layers:
-                layer.w.fill(0.0)
+                xp = array_api_compat.array_namespace(layer.w)
+                layer.w = xp.zeros_like(layer.w)
                 if layer.b is not None:
-                    layer.b.fill(0.0)
+                    layer.b = xp.zeros_like(layer.b)
                 if layer.idt is not None:
-                    layer.idt.fill(0.0)
+                    layer.idt = xp.zeros_like(layer.idt)
 
     return NN
 

deepmd/jax/descriptor/__init__.py

@@ -11,10 +11,14 @@
 from deepmd.jax.descriptor.se_e2_r import (
     DescrptSeR,
 )
+from deepmd.jax.descriptor.se_t import (
+    DescrptSeT,
+)
 
 __all__ = [
     "DescrptSeA",
     "DescrptSeR",
+    "DescrptSeT",
     "DescrptDPA1",
     "DescrptHybrid",
 ]

deepmd/jax/descriptor/se_t.py

@@ -0,0 +1,42 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+from typing import (
+    Any,
+)
+
+from deepmd.dpmodel.descriptor.se_t import DescrptSeT as DescrptSeTDP
+from deepmd.jax.common import (
+    ArrayAPIVariable,
+    flax_module,
+    to_jax_array,
+)
+from deepmd.jax.descriptor.base_descriptor import (
+    BaseDescriptor,
+)
+from deepmd.jax.utils.exclude_mask import (
+    PairExcludeMask,
+)
+from deepmd.jax.utils.network import (
+    NetworkCollection,
+)
+
+
+@BaseDescriptor.register("se_e3")
+@BaseDescriptor.register("se_at")
+@BaseDescriptor.register("se_a_3be")
+@flax_module
+class DescrptSeT(DescrptSeTDP):
+    def __setattr__(self, name: str, value: Any) -> None:
+        if name in {"dstd", "davg"}:
+            value = to_jax_array(value)
+            if value is not None:
+                value = ArrayAPIVariable(value)
+        elif name in {"embeddings"}:
+            if value is not None:
+                value = NetworkCollection.deserialize(value.serialize())
+        elif name == "env_mat":
+            # env_mat doesn't store any value
+            pass
+        elif name == "emask":
+            value = PairExcludeMask(value.ntypes, value.exclude_types)
+
+        return super().__setattr__(name, value)

doc/model/train-se-e3.md

@@ -1,7 +1,7 @@
-# Descriptor `"se_e3"` {{ tensorflow_icon }} {{ pytorch_icon }} {{ dpmodel_icon }}
+# Descriptor `"se_e3"` {{ tensorflow_icon }} {{ pytorch_icon }} {{ jax_icon }} {{ dpmodel_icon }}
 
 :::{note}
-**Supported backends**: TensorFlow {{ tensorflow_icon }}, PyTorch {{ pytorch_icon }}, DP {{ dpmodel_icon }}
+**Supported backends**: TensorFlow {{ tensorflow_icon }}, PyTorch {{ pytorch_icon }}, JAX {{ jax_icon }}, DP {{ dpmodel_icon }}
 :::
 
 The notation of `se_e3` is short for three-body embedding DeepPot-SE, which incorporates embedded bond-angle information.

source/tests/array_api_strict/descriptor/se_t.py

@@ -0,0 +1,32 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+from typing import (
+    Any,
+)
+
+from deepmd.dpmodel.descriptor.se_t import DescrptSeT as DescrptSeTDP
+
+from ..common import (
+    to_array_api_strict_array,
+)
+from ..utils.exclude_mask import (
+    PairExcludeMask,
+)
+from ..utils.network import (
+    NetworkCollection,
+)
+
+
+class DescrptSeT(DescrptSeTDP):
+    def __setattr__(self, name: str, value: Any) -> None:
+        if name in {"dstd", "davg"}:
+            value = to_array_api_strict_array(value)
+        elif name in {"embeddings"}:
+            if value is not None:
+                value = NetworkCollection.deserialize(value.serialize())
+        elif name == "env_mat":
+            # env_mat doesn't store any value
+            pass
+        elif name == "emask":
+            value = PairExcludeMask(value.ntypes, value.exclude_types)
+
+        return super().__setattr__(name, value)

source/tests/consistent/descriptor/test_se_t.py

@@ -12,6 +12,8 @@
 )
 
 from ..common import (
+    INSTALLED_ARRAY_API_STRICT,
+    INSTALLED_JAX,
     INSTALLED_PT,
     INSTALLED_TF,
     CommonTest,
@@ -29,6 +31,14 @@
     from deepmd.tf.descriptor.se_t import DescrptSeT as DescrptSeTTF
 else:
     DescrptSeTTF = None
+if INSTALLED_JAX:
+    from deepmd.jax.descriptor.se_t import DescrptSeT as DescrptSeTJAX
+else:
+    DescrptSeTJAX = None
+if INSTALLED_ARRAY_API_STRICT:
+    from ...array_api_strict.descriptor.se_t import DescrptSeT as DescrptSeTStrict
+else:
+    DescrptSeTStrict = None
 from deepmd.utils.argcheck import (
     descrpt_se_t_args,
 )
@@ -91,9 +101,14 @@ def skip_tf(self) -> bool:
         ) = self.param
         return env_protection != 0.0 or excluded_types
 
+    skip_array_api_strict = not INSTALLED_ARRAY_API_STRICT
+    skip_jax = not INSTALLED_JAX
+
     tf_class = DescrptSeTTF
     dp_class = DescrptSeTDP
     pt_class = DescrptSeTPT
+    jax_class = DescrptSeTJAX
+    array_api_strict_class = DescrptSeTStrict
     args = descrpt_se_t_args()
 
     def setUp(self):
@@ -168,6 +183,24 @@ def eval_pt(self, pt_obj: Any) -> Any:
             self.box,
         )
 
+    def eval_jax(self, jax_obj: Any) -> Any:
+        return self.eval_jax_descriptor(
+            jax_obj,
+            self.natoms,
+            self.coords,
+            self.atype,
+            self.box,
+        )
+
+    def eval_array_api_strict(self, array_api_strict_obj: Any) -> Any:
+        return self.eval_array_api_strict_descriptor(
+            array_api_strict_obj,
+            self.natoms,
+            self.coords,
+            self.atype,
+            self.box,
+        )
+
     def extract_ret(self, ret: Any, backend) -> tuple[np.ndarray, ...]:
         return (ret[0],)