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

docs: improve se_atten documentation #3832

Closed njzjz closed 1 month ago

njzjz commented 1 month ago
  1. add dpmodel icon to se_atten;
  2. merge TF and PT example. There are no differences between them, so only having one is easy to maintain.
  3. move data system section in se_atten to the data section, considering dpa2 also uses it.

Summary by CodeRabbit

coderabbitai[bot] commented 1 month ago
Walkthrough ## Walkthrough The recent changes introduce a new `mixed_type` system format to handle frame-sparse systems by grouping frames with the same total number of atoms, including virtual atoms with type `-1`. Additionally, the DPA-2 model now supports this new format, and the `se_atten` descriptor has expanded backend support to include DP, with recommendations for using the updated `se_atten_v2` descriptor. ## Changes | File(s) | Change Summary | |----------------------------------|--------------------------------------------------------------------------------------------------------| | `doc/data/system.md` | Introduced `mixed_type` system format for handling frame-sparse systems with virtual atoms. | | `doc/model/dpa2.md` | Added support for the `mixed_type` data format in the DPA-2 model. | | `doc/model/train-se-atten.md` | Expanded backend support for `se_atten` descriptor to include DP and recommended using `se_atten_v2`. | ## Sequence Diagram(s) (Beta) ```mermaid sequenceDiagram participant User participant SystemFormat participant DPA2Model participant SEAttenDescriptor User->>SystemFormat: Define `mixed_type` format SystemFormat-->>User: Format defined with virtual atoms User->>DPA2Model: Use `mixed_type` format DPA2Model-->>User: Model supports `mixed_type` User->>SEAttenDescriptor: Use `se_atten` with DP backend SEAttenDescriptor-->>User: Backend support expanded User->>SEAttenDescriptor: Use `se_atten_v2` descriptor SEAttenDescriptor-->>User: Recommended parameters for `se_atten_v2` ```
Recent Review Details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between 0afe8bf7c7c6b0fdb0f0bfbec14d13db7d3c3405 and f1dcea8bbfd2697425feed60e9a02c559c21ef45.
Files selected for processing (3) * doc/data/system.md (1 hunks) * doc/model/dpa2.md (1 hunks) * doc/model/train-se-atten.md (4 hunks)
Additional Context Used
Markdownlint (26)
doc/data/system.md (11)
62: null Fenced code blocks should have a language specified --- 17: Expected: 7; Actual: 6; Too few cells, row will be missing data Table column count --- 19: Expected: 7; Actual: 6; Too few cells, row will be missing data Table column count --- 20: Expected: 7; Actual: 6; Too few cells, row will be missing data Table column count --- 27: Expected: 6; Actual: 5; Too few cells, row will be missing data Table column count --- 28: Expected: 6; Actual: 5; Too few cells, row will be missing data Table column count --- 30: Expected: 6; Actual: 5; Too few cells, row will be missing data Table column count --- 31: Expected: 6; Actual: 5; Too few cells, row will be missing data Table column count --- 32: Expected: 6; Actual: 5; Too few cells, row will be missing data Table column count --- 33: Expected: 6; Actual: 5; Too few cells, row will be missing data Table column count --- 36: Expected: 6; Actual: 5; Too few cells, row will be missing data Table column count
doc/model/dpa2.md (1)
7: null Bare URL used
doc/model/train-se-atten.md (14)
87: Column: 1 Hard tabs --- 88: Column: 18 Hard tabs --- 89: Column: 23 Hard tabs --- 90: Column: 18 Hard tabs --- 91: Column: 17 Hard tabs --- 92: Column: 20 Hard tabs --- 93: Column: 25 Hard tabs --- 94: Column: 23 Hard tabs --- 95: Column: 18 Hard tabs --- 96: Column: 24 Hard tabs --- 97: Column: 23 Hard tabs --- 98: Column: 23 Hard tabs --- 99: Column: 18 Hard tabs --- 100: Column: 1 Hard tabs
Additional comments not posted (4)
doc/model/dpa2.md (2)
Line range hint `3-3`: Add a reference or link to the DP model documentation for clarity. --- `13-13`: The clarification on data format support is well-documented and clear.
doc/model/train-se-atten.md (2)
`4-4`: The update to include DP in the supported backends is accurate and aligns with the documentation improvements. --- `163-163`: The update on data format support is consistent and well-integrated with related documentation.
--- 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

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

Project coverage is 82.48%. Comparing base (0afe8bf) to head (f1dcea8).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #3832 +/- ## ========================================== + Coverage 82.30% 82.48% +0.17% ========================================== Files 513 513 Lines 48993 48993 Branches 2985 2985 ========================================== + Hits 40326 40411 +85 + Misses 7756 7671 -85 Partials 911 911 ```

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