refact: the DPA2 descriptor

[iProzd]

• Refact the DPA2 descriptor in PyTorch with clearer interface
• Support residual
• Remove bn
• Add numpy implement

Summary by CodeRabbit

• New Features

  • Added a new descriptor class DescrptDPA2 implementing DPA-2 functionality for computing descriptors and representations based on input coordinates and atom types.
  • Expanded supported backends for DPA-2 descriptor to include DP in addition to PyTorch.

• Documentation

  • Updated the supported backends information in the documentation for the DPA-2 descriptor to reflect the addition of DP backend support.
  • Added a reference to the model implementation and a training example link in the DPA-2 descriptor documentation.

• Tests

  • Introduced test cases for the DescrptDPA2 class in different frameworks like TensorFlow, PyTorch, and DeepMD to cover various parameters and configurations.
  • Validated the functionality of the DescrptDPA2 descriptor class for deep learning models in the test case class TestDescrptDPA2.

[coderabbitai]

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Commits

Files that changed from the base of the PR and between f17f40f and e223336.

Walkthrough

The recent updates focus on enhancing the deepmd module by refining documentation, optimizing imports, and enriching class functionalities. These changes aim to improve clarity, functionality, and compatibility within the module, including method descriptions, class replacements, and support for new modes and functionalities.

Changes

Files	Summary of Changes
deepmd/pt/model/descriptor/dpa2.py	- Introduces DescrptDPA2 class for DPA-2 descriptor functionality. - Adds properties dim_out and dim_emb. - Updates imports and includes new modules and classes.
deepmd/pt/model/descriptor/repformers.py	- Replaces SimpleLinear with MLPLayer. - Updates se_repformer class parameters and forward method implementation.
deepmd/utils/argcheck.py	- Adds env_protection argument with optional default value and updates related functions' documentation.
doc/model/dpa2.md	- Expands supported backends for DPA-2 descriptor to include DP in addition to PyTorch. - Updates model references and training examples.
source/tests/common/dpmodel/test_descriptor_dpa2.py, source/tests/consistent/descriptor/test_dpa2.py	- Introduces test classes and methods to validate DescrptDPA2 functionality across different frameworks. - Adds setups for testing various scenarios and defining tolerances.

This summary condenses the changes across different files for a more concise overview.

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[github-advanced-security]

CodeQL found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.

[coderabbitai]

Actionable comments posted: 11

Out of diff range and nitpick comments (1)

deepmd/pt/model/descriptor/repformer_layer.py (1)

271-290: Review the initialization parameters of Atten2Map.

Consider adding default values for parameters such as has_gate and smooth in the Atten2Map class to enhance usability and avoid potential errors if these parameters are not provided.

[coderabbitai]

Actionable comments posted: 5

Out of diff range and nitpick comments (2)

deepmd/pt/model/descriptor/repformer_layer.py (2)

32-67: Consider adding type hints for _scale and _mode in the get_residual function to improve code readability and maintainability.

---

494-494: Plan to refactor grrg for reuse across descriptors.

The method grrg could be reused in different descriptors. Plan a refactoring in a future PR to improve code reuse and maintainability.

[coderabbitai]

Actionable comments posted: 7

[coderabbitai]

Actionable comments posted: 0

Out of diff range and nitpick comments (1)

deepmd/pt/model/descriptor/repformer_layer.py (1)

32-67: Consider adding type hints for all parameters in the get_residual function to enhance code readability and maintainability.