feat(jax/array-api): se_e3 #4286
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Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
📝 WalkthroughWalkthroughThe pull request introduces several modifications primarily to the Changes
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Actionable comments posted: 4
🧹 Outside diff range and nitpick comments (4)
source/tests/array_api_strict/descriptor/se_t.py (2)
20-20: Add return type hint and docstring.The
__setattr__method should include a return type hint and documentation explaining its purpose and behavior for different attributes.- def __setattr__(self, name: str, value: Any) -> None: + def __setattr__(self, name: str, value: Any) -> None: + """Custom attribute setter for handling special attributes. + + Args: + name: Attribute name + value: Value to set + """
32-32: Consider MRO implications.The use of
super().__setattr__is correct, but in case of future multiple inheritance, it would be helpful to document that this class participates in Python's method resolution order (MRO).source/tests/consistent/descriptor/test_se_t.py (1)
195-202: Consider adding docstrings for consistency.While the implementation is correct, consider adding docstrings to match the documentation style of other evaluation methods in the class.
def eval_array_api_strict(self, array_api_strict_obj: Any) -> Any: + """Evaluate Array API Strict descriptor. + + Parameters + ---------- + array_api_strict_obj : Any + The descriptor object to evaluate + + Returns + ------- + Any + The evaluation result + """ return self.eval_array_api_strict_descriptor( array_api_strict_obj, self.natoms, self.coords, self.atype, self.box, )deepmd/jax/descriptor/se_t.py (1)
33-35: Reevaluate the serialize-deserialize process for 'embeddings'Serializing and immediately deserializing 'embeddings' may introduce unnecessary overhead. Consider assigning the value directly or ensuring this process is required for proper initialization.
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📒 Files selected for processing (6)
deepmd/dpmodel/descriptor/se_t.py(5 hunks)deepmd/dpmodel/utils/network.py(1 hunks)deepmd/jax/descriptor/__init__.py(1 hunks)deepmd/jax/descriptor/se_t.py(1 hunks)source/tests/array_api_strict/descriptor/se_t.py(1 hunks)source/tests/consistent/descriptor/test_se_t.py(4 hunks)
🔇 Additional comments (19)
deepmd/jax/descriptor/__init__.py (2)
11-13: LGTM! Clean import statement.
The import follows the project's conventions and is properly grouped with other descriptor imports.
18-18: LGTM! Proper export declaration.
The DescrptSeT class is correctly added to __all__ list, maintaining alphabetical order and consistency with the module's public interface.
source/tests/array_api_strict/descriptor/se_t.py (2)
1-16: LGTM! Well-organized imports and proper licensing.
The imports are logically grouped and all are necessary for the implementation. The LGPL license header is correctly included.
26-28: Verify the env_mat handling.
The explicit pass for env_mat seems suspicious. If this attribute truly doesn't store any value, it might be better to prevent setting it altogether or document why this behavior is necessary.
✅ Verification successful
Based on the code analysis, I can now provide a definitive response about the env_mat handling:
The pass for env_mat is intentional and correct.
The env_mat attribute is used as a placeholder in the descriptor implementations (TF/PyTorch/JAX) but does not need to store any actual value. This is because:
- The
env_matobject is only used for serialization purposes to maintain compatibility between different implementations - The actual environment matrix calculations are handled internally by the respective framework-specific operations
- All three implementations (TF/PyTorch/JAX) explicitly handle this case by having a special case in
__setattr__that just passes when settingenv_mat
🏁 Scripts executed
The following scripts were executed for the analysis:
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#!/bin/bash
# Search for env_mat usage in the codebase to understand its purpose
rg -A 5 "env_mat" --type python
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rg -A 5 "env_mat"
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source/tests/consistent/descriptor/test_se_t.py (5)
15-16: LGTM: New backend availability flags.
The new imports follow the existing pattern for backend availability flags.
34-41: LGTM: Backend class imports are well-structured.
The conditional imports for JAX and Array API Strict backends follow the established pattern, with appropriate null fallbacks.
104-105: LGTM: Skip properties for new backends.
The skip properties are correctly implemented using their respective INSTALLED_* flags.
110-111: LGTM: Backend class assignments.
The new backend class variables are properly integrated with existing backend class assignments.
186-193: Verify parent class implementation of JAX descriptor evaluation.
The method appears correct but relies on eval_jax_descriptor from the parent class.
✅ Verification successful
Let me gather more context about the parent class implementation to ensure it's complete and properly handles the parameters.
Let me get the complete implementation to ensure it properly handles all parameters and returns the expected result.
Parent class implementation of JAX descriptor evaluation is complete and correct
The parent class DescriptorTest properly implements eval_jax_descriptor with:
- Correct parameter handling (natoms, coords, atype, box)
- Ghost atom coordination via
extend_coord_with_ghosts - Neighbor list construction with
build_neighbor_list - Proper JAX array conversion and return value handling
🏁 Scripts executed
The following scripts were executed for the analysis:
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#!/bin/bash
# Check if the parent class (DescriptorTest) implements the required method
rg -A 5 "def eval_jax_descriptor" "source/tests/consistent/descriptor/common.py"
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rg -A 15 "def eval_jax_descriptor" "source/tests/consistent/descriptor/common.py"
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rg -B 2 -A 25 "def eval_jax_descriptor" "source/tests/consistent/descriptor/common.py"
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deepmd/dpmodel/utils/network.py (1)
575-580: LGTM! Improved array backend compatibility
The changes correctly implement array backend compatibility by using array_api_compat.array_namespace and zeros_like operations. This ensures consistent array types across different backends.
deepmd/jax/descriptor/se_t.py (2)
28-32: Proper handling of 'dstd' and 'davg' attributes
The conversion of 'dstd' and 'davg' to JAX arrays and wrapping with ArrayAPIVariable ensures compatibility with the array API standards.
39-40: Correct handling of 'emask' attribute
The creation of a PairExcludeMask using value.ntypes and value.exclude_types appropriately initializes the exclusion mask.
deepmd/dpmodel/descriptor/se_t.py (7)
9-9: Approved: Correct import of array_api_compat
The import statement is necessary for array API compatibility, allowing the code to operate seamlessly across different array backends.
17-20: Approved: Importing utility functions for precision handling and serialization
The functions get_xp_precision and to_numpy_array are correctly imported from deepmd.dpmodel.common and are essential for managing array precision and serialization throughout the code.
127-127: Approved: Proper initialization of cumulative sum for sel_cumsum
The computation of self.sel_cumsum correctly initializes the cumulative sum of self.sel, which is used for indexing purposes later in the code.
130-146: Verify the initialization of embeddings with correct dimensions and seed management
The embeddings object is initialized as a NetworkCollection with ntypes and ndim=2, which is appropriate for the descriptor's requirements. The loop over itertools.product correctly assigns an EmbeddingNet to each index combination. Ensure that in_dim is correctly set to 1 since type embedding is not considered. Also, verify that child_seed(self.seed, ii) provides consistent and reproducible seeds for each embedding net.
306-321: Approved: Consistent use of array API namespace and precision handling
The code appropriately obtains the array namespace xp using array_api_compat, ensuring compatibility across different array libraries. The reshaping and type casting of arrays using xp.reshape and xp.astype are correctly implemented, and the use of get_xp_precision(xp, self.precision) ensures that array operations adhere to the specified precision.
352-353: Approved: Final reshaping and casting of the result
The result is correctly reshaped to (nf, nloc, ng) and cast to the global precision using xp.astype, ensuring consistency in the output data type.
381-382: Approved: Serialization of davg and dstd using to_numpy_array
The serialize method properly converts self.davg and self.dstd to NumPy arrays using to_numpy_array, which is essential for accurately storing these arrays in the serialization process.
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
doc/model/train-se-e3.md (1)
Line range hint
1-100: Consider enhancing the documentation.While the documentation is comprehensive, consider these improvements:
- Add a version compatibility note specifying which JAX versions are supported
- Include a small code example demonstrating JAX-specific usage
- Add a link to JAX-specific configuration options, if any exist
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## devel #4286 +/- ##
==========================================
+ Coverage 84.29% 84.31% +0.01%
==========================================
Files 553 554 +1
Lines 51820 51853 +33
Branches 3052 3052
==========================================
+ Hits 43683 43718 +35
+ Misses 7177 7176 -1
+ Partials 960 959 -1 ☔ View full report in Codecov by Sentry. |
<!-- 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 <jinzhe.zeng@rutgers.edu>
Summary by CodeRabbit
New Features
DescrptSeTfor enhanced compatibility with array APIs."se_e3"descriptor.Bug Fixes
clearmethod of theNNclass to ensure compatibility across different array implementations.Documentation
DescrptSeTclass."se_e3"descriptor.Tests