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deepmodeling / deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics
https://docs.deepmodeling.com/projects/deepmd/
GNU Lesser General Public License v3.0
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feat(dp/pt): refactor `se_e3` descriptor #3813

Closed iProzd closed 1 month ago

iProzd commented 1 month ago

Note:

  1. exclude_types is supported only for pt/dp.
  2. Note that an exsiting bug in TF is fixed in deepmd/tf/env.py, when resnet_dt is True for se_e3.

Summary by CodeRabbit

coderabbitai[bot] commented 1 month ago

Walkthrough

The recent changes introduce a new class DescrptSeT across multiple files, representing a DeepPot-SE descriptor for atomic configurations. This class incorporates angular and radial information, provides methods for computing descriptors, managing parameters, serialization, and updating selections for neighbor statistics. Additionally, test cases for consistency and JIT compilation have been added, and the env_protection parameter has been integrated into the descriptor initialization and related methods.

Changes

Files/Groups Change Summary
deepmd/dpmodel/descriptor/se_t.py, deepmd/pt/model/descriptor/se_t.py, deepmd/tf/descriptor/se_t.py Introduced DescrptSeT class with methods for descriptor computation, parameter management, serialization, and updating selections. Added env_protection parameter in the __init__ method.
deepmd/pt/model/descriptor/se_a.py Modified __init__ method to include trainable parameter and removed ntypes and **kwargs. Added logic to raise NotImplementedError if spin is not None.
source/tests/pt/model/test_se_t.py Added test cases for DescrptSeT functionality, including consistency checks and JIT compilation testing.
source/tests/consistent/descriptor/test_se_t.py Introduced test cases for DescrptSeT descriptor class across different deep learning frameworks, ensuring consistency across frameworks.

Sequence Diagram(s) (Beta)

sequenceDiagram
    participant User
    participant DescrptSeT
    participant DeepPot-SE Frameworks

    User->>DescrptSeT: Initialize with parameters
    DescrptSeT->>DeepPot-SE Frameworks: Compute descriptor
    DeepPot-SE Frameworks-->>DescrptSeT: Return descriptor
    DescrptSeT-->>User: Provide descriptor

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codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 82.74336% with 78 lines in your changes are missing coverage. Please review.

Project coverage is 82.53%. Comparing base (dd7f27a) to head (0ac65d6).

Files Patch % Lines
deepmd/pt/model/descriptor/se_t.py 78.24% 47 Missing :warning:
deepmd/dpmodel/descriptor/se_t.py 85.92% 19 Missing :warning:
deepmd/tf/descriptor/se_t.py 88.29% 11 Missing :warning:
deepmd/pt/model/descriptor/se_a.py 66.66% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #3813 +/- ## ======================================== Coverage 82.53% 82.53% ======================================== Files 513 515 +2 Lines 49040 49492 +452 Branches 2985 2985 ======================================== + Hits 40473 40849 +376 - Misses 7656 7732 +76 Partials 911 911 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

iProzd commented 1 month ago

A UT is needed for testing consistency between results using exclude_types and results from masked nlist. I opened an issue https://github.com/deepmodeling/deepmd-kit/issues/3830 and a seperate PR needed, after finding inconsistencies in some of the existing descriptors.