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

CP2K support for dpgen2 #238

Closed Andy6M closed 4 months ago

Andy6M commented 5 months ago

Summary by CodeRabbit

coderabbitai[bot] commented 5 months ago

[!WARNING]

Rate limit exceeded

@Andy6M has exceeded the limit for the number of commits or files that can be reviewed per hour. Please wait 20 minutes and 31 seconds before requesting another review.

How to resolve this issue? After the wait time has elapsed, a review can be triggered using the `@coderabbitai review` command as a PR comment. Alternatively, push new commits to this PR. We recommend that you space out your commits to avoid hitting the rate limit.
How do rate limits work? CodeRabbit enforces hourly rate limits for each developer per organization. Our paid plans have higher rate limits than the trial, open-source and free plans. In all cases, we re-allow further reviews after a brief timeout. Please see our [FAQ](https://coderabbit.ai/docs/faq) for further information.
Commits Files that changed from the base of the PR and between 36ac09496553394664729a94f529abe9f0fcec57 and c2784d63d4fcadb7b7396902216ba807d743b9ff.

Walkthrough

The changes introduce support for interfacing with CP2K simulations. This includes new classes and methods to handle CP2K inputs and executions, additional test cases, and updates to configuration files to integrate CP2K operations into larger workflows. The update also removes unnecessary arguments from existing methods and adds dependencies in pyproject.toml to support the new functionalities.

Changes

File(s) Change Summary
dpgen2/fp/__init__.py Imported FpOpCp2kInputs, PrepFpOpCp2k, RunFpOpCp2k and added "fpop_cp2k" entry in the dictionary.
dpgen2/fp/cp2k.py Introduced classes FpOpCp2kInputs, PrepFpOpCp2k, RunFpOpCp2k, static method args, and get_run_type.
dpgen2/fp/abacus.py Removed the out argument from the args method in Abacus's execute function.
pyproject.toml Added cp2kdata dependency.
tests/fp/data.cp2k/**/* Added various test input data files for CP2K such as cell parameters, coordinates, and configuration settings.
tests/fp/test_cp2k.py Added TestFpOpCp2k class to test CP2K operations, with methods for setup, teardown, and workflow execution validation.
examples/water/input_dpgen_abacus.json Added configuration file for water simulation tool specifying parameters for training and calculations.
examples/water/input_dpgen_cp2k.json Added configuration file for water simulation tool involving CP2K operations.
tests/check_examples.py Added new input files for water simulations in the test checks.
tests/test_check_examples.py Added test cases for different scenarios using various input JSON files.

Sequence Diagram(s)

sequenceDiagram
    participant Tester as TestFpOpCp2k
    participant CP2KModule as dpgen2.fp.cp2k
    participant Config as Configuration Files
    participant Executor as Execution Engine

    Tester->>+Config: Load CP2K configuration
    Config-->>Tester: Configuration settings
    Tester->>+CP2KModule: Prepare CP2K inputs
    CP2KModule-->>Tester: Prepared inputs
    Tester->>+Executor: Execute CP2K operation
    Executor-->>Tester: Execution status and results
    Tester->>Tester: Validate workflow execution and outputs

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 5 months ago

Codecov Report

Attention: Patch coverage is 44.70588% with 47 lines in your changes missing coverage. Please review.

Project coverage is 83.84%. Comparing base (e2c2470) to head (c2784d6). Report is 23 commits behind head on master.

Files with missing lines Patch % Lines
dpgen2/fp/cp2k.py 44.57% 46 Missing :warning:
dpgen2/fp/abacus.py 0.00% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #238 +/- ## ========================================== - Coverage 84.46% 83.84% -0.62% ========================================== Files 96 97 +1 Lines 5285 5368 +83 ========================================== + Hits 4464 4501 +37 - Misses 821 867 +46 ```

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

Andy6M commented 4 months ago

Could you please add an example, showcasing how to use cp2k in dpgen2?

Thank you for your suggestion. Two example files, examples/water/input_dpgen_abacus.json and examples/water/input_dpgen_cp2k.json, have been uploaded with the assistance of @zjgemi.