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docs: document plugin mechanisms and deepmd-gnn #4345
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Signed-off-by: Jinzhe Zeng <[email protected]>
📝 WalkthroughWalkthroughThe changes in this pull request involve updates to several documentation files related to the DeePMD-kit. The Changes
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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:
- Adding docstrings for each abstract method explaining their purpose and return values
- Including a basic implementation example for at least one method
- 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:
- Documentation of input/output tensor shapes for
forward
andforward_atomic
methods- Examples of batch processing
- 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 logicAlso applies to: 119-134
Line range hint
1-182
: Consider adding troubleshooting guidance.The documentation is comprehensive and well-structured. Consider enhancing it with:
- A troubleshooting section covering common issues and their solutions
- A list of common pitfalls to avoid when implementing new models
- Performance optimization tips
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📒 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:
- The GitHub repository link is accessible and maintained
- The example demonstrates the concepts discussed in this documentation
Summary by CodeRabbit
New Features
Documentation