search

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
1.41k stars 487 forks source link

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

Closed Chengqian-Zhang closed 1 month ago

Chengqian-Zhang commented 1 month ago

Solve #3831 and #3139

Summary by CodeRabbit

coderabbitai[bot] commented 1 month ago
Walkthrough ## 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) ```mermaid 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 **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between c982d0e8409eb6bb9b9541421ead7aa3921ae795 and 38fc569abdbefb40aeeebc21803d633262438f95.
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
--- Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?
Share - [X](https://twitter.com/intent/tweet?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A&url=https%3A//coderabbit.ai) - [Mastodon](https://mastodon.social/share?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A%20https%3A%2F%2Fcoderabbit.ai) - [Reddit](https://www.reddit.com/submit?title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&text=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code.%20Check%20it%20out%3A%20https%3A//coderabbit.ai) - [LinkedIn](https://www.linkedin.com/sharing/share-offsite/?url=https%3A%2F%2Fcoderabbit.ai&mini=true&title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&summary=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code)
Tips ### Chat There are 3 ways to chat with [CodeRabbit](https://coderabbit.ai): - Review comments: Directly reply to a review comment made by CodeRabbit. Example: - `I pushed a fix in commit .` - `Generate unit testing code for this file.` - `Open a follow-up GitHub issue for this discussion.` - Files and specific lines of code (under the "Files changed" tab): Tag `@coderabbitai` in a new review comment at the desired location with your query. Examples: - `@coderabbitai generate unit testing code for this file.` - `@coderabbitai modularize this function.` - PR comments: Tag `@coderabbitai` in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples: - `@coderabbitai generate interesting stats about this repository and render them as a table.` - `@coderabbitai show all the console.log statements in this repository.` - `@coderabbitai read src/utils.ts and generate unit testing code.` - `@coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.` - `@coderabbitai help me debug CodeRabbit configuration file.` Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. ### CodeRabbit Commands (invoked as PR comments) - `@coderabbitai pause` to pause the reviews on a PR. - `@coderabbitai resume` to resume the paused reviews. - `@coderabbitai review` to trigger an incremental review. This is useful when automatic reviews are disabled for the repository. - `@coderabbitai full review` to do a full review from scratch and review all the files again. - `@coderabbitai summary` to regenerate the summary of the PR. - `@coderabbitai resolve` resolve all the CodeRabbit review comments. - `@coderabbitai configuration` to show the current CodeRabbit configuration for the repository. - `@coderabbitai help` to get help. Additionally, you can add `@coderabbitai ignore` anywhere in the PR description to prevent this PR from being reviewed. ### CodeRabbit Configration File (`.coderabbit.yaml`) - You can programmatically configure CodeRabbit by adding a `.coderabbit.yaml` file to the root of your repository. - Please see the [configuration documentation](https://docs.coderabbit.ai/guides/configure-coderabbit) for more information. - If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: `# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json` ### Documentation and Community - Visit our [Documentation](https://coderabbit.ai/docs) for detailed information on how to use CodeRabbit. - Join our [Discord Community](https://discord.com/invite/GsXnASn26c) to get help, request features, and share feedback. - Follow us on [X/Twitter](https://twitter.com/coderabbitai) for updates and announcements.
codecov[bot] commented 1 month ago

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).

Files Patch % Lines
deepmd/tf/descriptor/se_atten_v2.py 14.28% 24 Missing :warning:
Additional details and impacted files ```diff @@ 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 ```

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

Chengqian-Zhang commented 1 month ago

@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.

njzjz commented 1 month ago

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

Chengqian-Zhang commented 1 month ago

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

I think it is better to update the documentation in this PR.

Chengqian-Zhang commented 1 month ago

could you please provide consistency UT like the se_atten descriptor?

I do not add tf "se_atten_v2" consistency UT, because the implementation of smooth_type_embedding is different between tf and pt/dp. But smooth_type_embedding is always true in descriptor "se_atten_v2".

njzjz commented 1 month ago

@iProzd could you take a look at the unit test failure?