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
1.46k stars 504 forks source link

fix(pt): fix global bias stat with different natom #3944

Closed iProzd closed 3 months ago

iProzd commented 3 months ago

polar/dipole need further check from @anyangml

Summary by CodeRabbit

coderabbitai[bot] commented 3 months ago
Walkthrough ## Walkthrough The recent changes focus on improving how model predictions are computed and processed in the `deepmd` package. Adjustments were made to handle global predictions by summing over atomic dimensions and concatenating frames within systems, along with the removal of a redundant summation axis. Additionally, testing functions in `test_finetune.py` were updated to handle energy calculations for multiple frames with varying atom numbers, including scaling atom data. ## Changes | File | Change Summary | |------|----------------| | `deepmd/pt/utils/stat.py` | Adjusted handling of model predictions by summing over atomic dimensions and concatenating frames within systems. Removed an unnecessary summation line. | | `source/tests/pt/test_finetune.py` | Modified `test_finetune_change_out_bias` to sample multiple frames with different atom numbers, scale atom data, and concatenate energy calculations. | ## Sequence Diagram(s) ```mermaid sequenceDiagram participant A as Model Predictions participant B as Atomic Dimensions participant C as Frames within Systems participant D as Testing Function A->>B: Sum over atomic dimensions A->>C: Concatenate frames Note right of A: Remove redundant summation D->>A: Sample multiple frames with different atom numbers D->>A: Scale atom data D->>A: Concatenate energy calculations ```

[!TIP]

AI model upgrade ## `gpt-4o` model for reviews and chat is now live OpenAI claims that this model is better at understanding and generating code than the previous models. Please join our [Discord Community](https://discord.com/invite/GsXnASn26c) to provide any feedback or to report any issues.
Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between f2223fbfccc49ea282ee9c9d288d4acef99c3e82 and 58910aad2f95a21e6cab79b6461843b2ed152e4b.
Files selected for processing (2) * deepmd/pt/utils/stat.py (3 hunks) * source/tests/pt/test_finetune.py (2 hunks)
Files skipped from review due to trivial changes (1) * source/tests/pt/test_finetune.py
Additional comments not posted (2)
deepmd/pt/utils/stat.py (2)
`316-318`: **Ensure correct handling of global predictions.** The code sums the model predictions over the atomic dimension. Ensure that this change correctly handles the global predictions and does not introduce any inconsistencies. --- `333-335`: **Verify concatenation of frames within systems.** The code concatenates frames within systems for global predictions. Ensure that this change correctly handles the concatenation and does not introduce any inconsistencies.
--- 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 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 82.86%. Comparing base (f2223fb) to head (58910aa). Report is 108 commits behind head on devel.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #3944 +/- ## ======================================= Coverage 82.85% 82.86% ======================================= Files 520 520 Lines 50805 50804 -1 Branches 3015 3015 ======================================= + Hits 42096 42097 +1 + Misses 7774 7772 -2 Partials 935 935 ```

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