search

deepmodeling / dpgen2

2nd generation of the Deep Potential GENerator
https://docs.deepmodeling.com/projects/dpgen2/
GNU Lesser General Public License v3.0
33 stars 26 forks source link

Fix bugs related to lammps PIMD #266

Closed zjgemi closed 1 month ago

zjgemi commented 1 month ago

Summary by CodeRabbit

coderabbitai[bot] commented 1 month ago

[!CAUTION]

Review failed

The head commit changed during the review from 7c36020d403284ea9ff98e4936ed8d86e401e2b2 to 041f9e16c8e2576c105e3713aabba734c7b036c0.

📝 Walkthrough
📝 Walkthrough
📝 Walkthrough ## Walkthrough The changes in this pull request involve modifications to the `RunLmp` class in `dpgen2/op/run_lmp.py`, the `SelectConfs` class in `dpgen2/op/select_confs.py`, and the `CollectData` class in `dpgen2/op/collect_data.py`. In `run_lmp.py`, the `merge_pimd_files()` function call's indentation was adjusted to ensure it executes within a specific context, improving control flow during LAMMPS task execution. In `select_confs.py`, the `validate_trajs` method's conditional check for `optional_outputs` was enhanced to ensure it contains non-None values, along with corrected indentation for better readability. Additionally, in `collect_data.py`, checks were added to ensure operations involving file existence only occur when `ii` is truthy. ## Changes | File Path | Change Summary | |-----------------------------------|------------------------------------------------------------------------------------------------------------------------| | dpgen2/op/run_lmp.py | Adjusted indentation for `merge_pimd_files()` call in `execute` method to ensure it runs within `with set_directory(...)`. Added a newline for readability. | | dpgen2/op/select_confs.py | Updated conditional check in `validate_trajs` method to ensure `optional_outputs` contains at least one non-None value. Corrected indentation for clarity. | | dpgen2/op/collect_data.py | Introduced checks for `ii` before executing operations involving `rglob`. Updated conditions for file existence checks to ensure `ii` is truthy. | ## Possibly related PRs - #263: The changes in this PR involve enhancements related to PIMD (Path Integral Molecular Dynamics) tasks, which are directly relevant to the modifications made in the `merge_pimd_files()` function in the main PR, as both involve handling PIMD files and improving file management for LAMMPS tasks. ## Suggested reviewers - wanghan-iapcm

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 , 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](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](http://discord.gg/coderabbit) 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 83.70%. Comparing base (850eb22) to head (041f9e1). Report is 1 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #266 +/- ## ========================================== - Coverage 83.72% 83.70% -0.02% ========================================== Files 104 104 Lines 6015 6015 ========================================== - Hits 5036 5035 -1 - Misses 979 980 +1 ```

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