Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

docs: document plugin mechanisms and deepmd-gnn #4345

Merged
merged 1 commit into from
Nov 13, 2024

Conversation

njzjz
Copy link
Member

@njzjz njzjz commented Nov 12, 2024

Summary by CodeRabbit

  • New Features

    • Introduced plugin mechanisms for external models in the DeePMD-kit.
    • Added comprehensive instructions for creating models using PyTorch and a framework-independent backend.
  • Documentation

    • Enhanced organization of the third-party documentation for better clarity and navigability.

@njzjz njzjz requested a review from wanghan-iapcm November 12, 2024 23:51
@github-actions github-actions bot added the Docs label Nov 12, 2024
Copy link
Contributor

coderabbitai bot commented Nov 12, 2024

📝 Walkthrough

Walkthrough

The changes in this pull request involve updates to several documentation files related to the DeePMD-kit. The README.md file introduces a new feature for plugin mechanisms for external models, enhancing the software's extensibility. The create-a-model-pt.md document expands instructions for creating models, particularly focusing on the integration of PyTorch and a framework-independent backend. Lastly, the out-of-deepmd-kit.md document undergoes structural reorganization to improve clarity and navigability of plugin-related content.

Changes

File Change Summary
README.md Added new feature: "Plugin mechanisms for external models" in version "v3" section.
doc/development/create-a-model-pt.md Updated to include instructions for creating models in PyTorch and dpmodel, detailing descriptors and fitting networks. Added methods and classes for new model implementation.
doc/third-party/out-of-deepmd-kit.md Reorganized sections and titles for clarity, consolidating plugin-related content under broader categories.

Possibly related PRs

Suggested labels

Docs

Suggested reviewers

  • wanghan-iapcm
  • iProzd

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
🪧 Tips

Chat

There are 3 ways to chat with CodeRabbit:

  • Review comments: Directly reply to a review comment made by CodeRabbit. Example:
    • I pushed a fix in commit <commit_id>, please review it.
    • 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 gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
    • @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 using 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.

Other keywords and placeholders

  • Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
  • Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
  • Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration 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 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 for detailed information on how to use CodeRabbit.
  • Join our Discord Community to get help, request features, and share feedback.
  • Follow us on X/Twitter for updates and announcements.

Copy link
Contributor

@coderabbitai coderabbitai bot left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (6)
doc/third-party/out-of-deepmd-kit.md (2)

7-11: LGTM! Consider adding installation instructions.

The new section clearly introduces the GNN models integration. However, it would be helpful to add basic installation instructions or link to them.

Consider adding:

 It has interfaced with [MACE](https://github.com/ACEsuit/mace) (PyTorch version) and [NequIP](https://github.com/mir-group/nequip) (PyTorch version).
 It is also the first example to the DeePMD-kit [plugin mechanism](../development/create-a-model-pt.md#package-new-codes).
+
+For installation instructions, please refer to the [DeePMD-GNN documentation](https://github.com/njzjz/deepmd-gnn#installation).

42-42: Minor grammar improvement needed.

Change "in the local or remote server" to "on the local or remote server" for better English usage.

-[DP-GEN](https://github.com/deepmodeling/dpgen) provides a workflow to generate accurate DP models by calling DeePMD-kit's command line interface (CLI) in the local or remote server.
+[DP-GEN](https://github.com/deepmodeling/dpgen) provides a workflow to generate accurate DP models by calling DeePMD-kit's command line interface (CLI) on the local or remote server.
🧰 Tools
🪛 LanguageTool

[uncategorized] ~42-~42: The preposition “on” seems more likely in this position than the preposition “in”.
Context: ...ePMD-kit's command line interface (CLI) in the local or remote server. Details can...

(AI_EN_LECTOR_REPLACEMENT_PREPOSITION_IN_ON)

README.md (1)

77-77: Consider expanding the plugin mechanisms documentation.

While the addition is appropriate, consider enhancing it with:

  • A brief description of what plugin mechanisms are available
  • A link to detailed documentation (e.g., in doc/third-party/out-of-deepmd-kit.md)

Example enhancement:

-- Plugin mechanisms for external models.
+- Plugin mechanisms for external models, allowing integration of custom model implementations. See [plugin documentation](doc/third-party/out-of-deepmd-kit.md) for details.
doc/development/create-a-model-pt.md (3)

Line range hint 37-82: Enhance the descriptor code example with documentation and implementation details.

While the code structure is correct, consider enhancing the example by:

  1. Adding docstrings for each abstract method explaining their purpose and return values
  2. Including a basic implementation example for at least one method
  3. Adding error handling examples, especially for input validation

Here's an example enhancement for one method:

def get_rcut(self) -> float:
    """Returns the cutoff radius used by this descriptor.
    
    Returns
    -------
    float
        The cutoff radius in length unit
    """
    return self._rcut  # Example implementation

Line range hint 84-117: Enhance model implementation examples with practical details.

The code structure is correct, but the examples would be more helpful with:

  1. Documentation of input/output tensor shapes for forward and forward_atomic methods
  2. Examples of batch processing
  3. Common use case implementations

Example enhancement:

def forward_atomic(
    self,
    descriptor: torch.Tensor,  # Shape: [batch_size, n_atoms, descriptor_dim]
    atype: torch.Tensor,       # Shape: [batch_size, n_atoms]
) -> torch.Tensor:            # Shape: [batch_size, n_atoms, output_dim]
    """Process atomic descriptors to predict atomic properties.
    
    Args:
        descriptor: Atomic descriptor tensor
        atype: Atom type tensor
        
    Returns:
        Atomic property predictions
    """
    # Example implementation
    batch_size = descriptor.shape[0]
    # ... processing logic

Also applies to: 119-134


Line range hint 1-182: Consider adding troubleshooting guidance.

The documentation is comprehensive and well-structured. Consider enhancing it with:

  1. A troubleshooting section covering common issues and their solutions
  2. A list of common pitfalls to avoid when implementing new models
  3. Performance optimization tips
📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 7416c9f and 633de8e.

📒 Files selected for processing (3)
  • README.md (1 hunks)
  • doc/development/create-a-model-pt.md (1 hunks)
  • doc/third-party/out-of-deepmd-kit.md (2 hunks)
🧰 Additional context used
🪛 LanguageTool
doc/third-party/out-of-deepmd-kit.md

[uncategorized] ~42-~42: The preposition “on” seems more likely in this position than the preposition “in”.
Context: ...ePMD-kit's command line interface (CLI) in the local or remote server. Details can...

(AI_EN_LECTOR_REPLACEMENT_PREPOSITION_IN_ON)

🔇 Additional comments (2)
doc/third-party/out-of-deepmd-kit.md (1)

5-6: LGTM! Clear and logical reorganization.

The new structure improves navigation by grouping related interfaces under appropriate categories.

Also applies to: 13-14, 38-38

doc/development/create-a-model-pt.md (1)

183-183: Verify the DeePMD-GNN example link and relevance.

Please ensure that:

  1. The GitHub repository link is accessible and maintained
  2. The example demonstrates the concepts discussed in this documentation

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants