Feat: add `se_atten_v2`to PyTorch and DP #3840

Chengqian-Zhang · 2024-05-30T07:36:35Z

add se_atten_v2 to PyTorch and DP
add document equation for se_attn_v2

Summary by CodeRabbit

New Features
- Introduced a new descriptor class with enhanced configuration options and methods for serialization and deserialization.
- Added new configurable parameters to the descriptor setup for improved flexibility.
Documentation
- Updated function documentation to reflect new arguments and usage instructions.
Bug Fixes
- Refined serialization logic to handle new parameters and class types more accurately.
- Improved error messages for better clarity during serialization processes.

coderabbitai · 2024-05-30T07:36:46Z

Walkthrough

The updates introduce a new descriptor class DescrptSeAttenV2 across multiple files, enhancing the existing DescrptDPA1 class with additional parameters and methods for configuration, serialization, and deserialization. Changes also include refining serialization logic and updating argument checking functions to support new parameters.

Changes

File Path	Change Summary
`.../descriptor/se_atten_v2.py`	Introduced `DescrptSeAttenV2` class with new parameters and serialization methods.
`.../pt/model/descriptor/se_atten_v2.py`	Added `DescrptSeAttenV2` class with extended constructor parameters from `DescrptDPA1`.
`.../descriptor/se_atten.py`	Adjusted serialization logic and error messages for `DescrptSeAtten` and related classes.
`.../utils/argcheck.py`	Added new arguments to `descrpt_se_atten_v2_args()` function, updating its documentation accordingly.

Sequence Diagram(s) (Beta)

sequenceDiagram
    participant User
    participant DescrptSeAttenV2
    participant Serializer
    User->>DescrptSeAttenV2: Initialize with extended parameters
    DescrptSeAttenV2->>Serializer: Call serialize method
    Serializer-->>DescrptSeAttenV2: Serialized data
    DescrptSeAttenV2-->>User: Return serialized data

Recent review details

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Review profile: CHILL

Commits

Files that changed from the base of the PR and between c982d0e and 38fc569.

Files selected for processing (1)

deepmd/utils/argcheck.py (1 hunks)

Files skipped from review as they are similar to previous changes (1)

deepmd/utils/argcheck.py

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coderabbitai

Actionable comments posted: 1

deepmd/dpmodel/descriptor/dpa1.py

codecov · 2024-05-30T07:50:55Z

Codecov Report

Attention: Patch coverage is 79.48718% with 24 lines in your changes missing coverage. Please review.

Project coverage is 82.66%. Comparing base (eb474d4) to head (38fc569).
Report is 120 commits behind head on devel.

Files with missing lines	Patch %	Lines
deepmd/tf/descriptor/se_atten_v2.py	14.28%	24 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #3840      +/-   ##
==========================================
- Coverage   82.67%   82.66%   -0.01%     
==========================================
  Files         515      517       +2     
  Lines       49549    49662     +113     
  Branches     2989     2985       -4     
==========================================
+ Hits        40965    41055      +90     
- Misses       7673     7696      +23     
  Partials      911      911

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coderabbitai

Actionable comments posted: 1

deepmd/pt/model/descriptor/__init__.py

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deepmd/dpmodel/descriptor/dpa1.py

deepmd/pt/model/descriptor/se_atten_v2.py

source/tests/pt/model/test_se_attn_v2.py

Chengqian-Zhang · 2024-05-30T11:17:10Z

@iProzd thinks there is no need to redirect dpa1 to se_atten_v2. dpa1 is equivalent to se_atten from original definition, while se_atten_v2 is a special case of dpa1 to use strip structure. So I'm not redirecting it for now.

coderabbitai

Actionable comments posted: 1

deepmd/dpmodel/descriptor/dpa1.py

njzjz · 2024-05-30T23:50:47Z

Do you want to update the documentation in #3828 or in this PR??

Co-authored-by: Duo <[email protected]> Signed-off-by: Chenqqian Zhang <[email protected]>

coderabbitai

Actionable comments posted: 2

deepmd/pt/model/descriptor/se_atten_v2.py

deepmd/utils/argcheck.py

Solve deepmodeling#3831 and deepmodeling#3139 - add `se_atten_v2` to PyTorch and DP - add document equation for `se_attn_v2`  ## Summary by CodeRabbit - **New Features** - Introduced a new descriptor class with enhanced configuration options and methods for serialization and deserialization. - Added new configurable parameters to the descriptor setup for improved flexibility. - **Documentation** - Updated function documentation to reflect new arguments and usage instructions. - **Bug Fixes** - Refined serialization logic to handle new parameters and class types more accurately. - Improved error messages for better clarity during serialization processes.  --------- Signed-off-by: Chenqqian Zhang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Duo <[email protected]>

Chengqian-Zhang added 2 commits May 30, 2024 07:08

Add se_attn_v2 in pt

2e8396e

Add se_attn_v2 in dp

87c3561

Chengqian-Zhang marked this pull request as draft May 30, 2024 07:36

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Chengqian-Zhang and others added 6 commits May 30, 2024 08:02

Delete redirect to dpa1

95696ee

Merge branch '3831' of github.com:Chengqian-Zhang/deepmd-kit into 3831

e55a891

[pre-commit.ci] auto fixes from pre-commit.com hooks

08bf55a

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Change se_attn_v2 impl in dp and pt

999adc8

Fix conflict

0e27dc8

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c08f61d

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Chengqian-Zhang and others added 3 commits May 30, 2024 11:10

Add UT

59269f2

[pre-commit.ci] auto fixes from pre-commit.com hooks

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Fix bug

46783e3

Chengqian-Zhang marked this pull request as ready for review May 30, 2024 11:14

Chengqian-Zhang changed the title ~~Feat: add se_atten_v2to PyTorch and DP and redirect dpa1 to se_atten_v2~~ Feat: add se_atten_v2to PyTorch and DP May 30, 2024

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Chengqian-Zhang requested review from njzjz, iProzd and wanghan-iapcm May 30, 2024 11:19

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njzjz linked an issue May 30, 2024 that may be closed by this pull request

[Feature Request] add se_atten_v2 and redirect dpa1 to se_atten_v2 #3831

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Chengqian-Zhang and others added 2 commits June 4, 2024 18:28

Update deepmd/pt/model/descriptor/se_atten_v2.py

ef94c04

Co-authored-by: Duo <[email protected]> Signed-off-by: Chenqqian Zhang <[email protected]>

Update deepmd/utils/argcheck.py

b39fcce

Co-authored-by: Duo <[email protected]> Signed-off-by: Chenqqian Zhang <[email protected]>

Chengqian-Zhang requested a review from iProzd June 4, 2024 10:31

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Chengqian-Zhang and others added 3 commits June 5, 2024 12:30

Merge branch 'devel' into 3831

c982d0e

Delete doc_stripped_type_embedding

c3892f4

Merge branch '3831' of github.com:Chengqian-Zhang/deepmd-kit into 3831

38fc569

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Merged via the queue into deepmodeling:devel with commit c71ece3 Jun 6, 2024
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This was referenced Oct 22, 2024

docs: fix parameter links #4239

Merged

fix(tf): fix compress suffix in DescrptDPA1Compat #4243

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docs: document JAX backend #4259

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coderabbitai bot mentioned this pull request Oct 30, 2024

feat(jax/array-api): se_atten_v2 #4289

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This was referenced Nov 7, 2024

fix: consistent DPA-1 model #4320

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docs: improve docs, examples, and error messages #4338

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coderabbitai bot mentioned this pull request Nov 20, 2024

docs: document more differences among different backends #4388

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coderabbitai bot mentioned this pull request Dec 23, 2024

[WIP] pd: update paddle doc #4489

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Feat: add `se_atten_v2`to PyTorch and DP #3840

Feat: add `se_atten_v2`to PyTorch and DP #3840

Chengqian-Zhang commented May 30, 2024 •

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Feat: add se_atten_v2to PyTorch and DP #3840

Feat: add se_atten_v2to PyTorch and DP #3840

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Feat: add `se_atten_v2`to PyTorch and DP #3840

Feat: add `se_atten_v2`to PyTorch and DP #3840

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