docs: fix quick_start.ipynb #4392
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Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
📝 WalkthroughWalkthroughThe changes involve updates to a Jupyter Notebook titled "quick_start.ipynb," which serves as a tutorial for using the DeePMD-kit software. The modifications include adding new sections for better structure, enhancing text clarity, incorporating new code cells and outputs, and improving visual formatting. The aim is to make the tutorial more comprehensive and user-friendly without altering any public or exported entities. Changes
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🧹 Outside diff range and nitpick comments (4)
doc/getting-started/quick_start.ipynb (4)
Line range hint
1-100: Documentation and setup section looks good but could be enhancedThe initial documentation and setup section provides good context but could benefit from:
- Adding version requirements for key dependencies (DeePMD-kit, LAMMPS, etc.)
- Including a brief overview of hardware requirements
- Mentioning expected runtime for different hardware configurations
Line range hint
401-700: Model configuration needs documentation improvementsThe model configuration section using input.json is comprehensive but could be improved:
- Add comments explaining key hyperparameters and their impact
- Document the rationale behind the chosen network architecture
- Consider extracting configuration to a separate file for better maintainability
Line range hint
701-900: Training process monitoring could be enhancedThe training section has good basic functionality but could benefit from:
- Adding early stopping based on validation metrics
- Implementing learning rate scheduling
- Adding training progress visualization during training
The model testing code looks solid with appropriate metrics being calculated.
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1-1100: Overall architecture feedbackThe notebook provides a good introduction to DeePMD-kit but could be improved with:
- Better modularization of code into reusable functions
- Addition of proper logging throughout the pipeline
- Implementation of configuration management
- More extensive error handling and input validation
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🔇 Additional comments (2)
doc/getting-started/quick_start.ipynb (2)
Line range hint 101-400: Data preparation code needs error handling
The data preparation section using dpdata has good functionality but lacks error handling:
# Add error handling
try:
data = dpdata.LabeledSystem("DeePMD-kit_Tutorial/00.data/abacus_md", fmt="abacus/md")
except Exception as e:
print(f"Error loading data: {e}")
raiseAlso recommend adding validation checks for the training/validation split ratios and data integrity.
Line range hint 901-1100: LAMMPS integration needs better error checking
The LAMMPS integration section should include:
- Verification that LAMMPS is properly installed with DeePMD-kit support
- Checks for model file existence before running
- Validation of LAMMPS input parameters
It seems this file is not rendered correctly, even in
r2... The reason is that<>is not escaped. I fix it in deepmodeling/dargs#85.Summary by CodeRabbit