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deepmodeling / dpgen2

2nd generation of the Deep Potential GENerator
https://docs.deepmodeling.com/projects/dpgen2/
GNU Lesser General Public License v3.0
32 stars 24 forks source link

Add DiffCSP as a new exploration engine #251

Closed zjgemi closed 3 weeks ago

zjgemi commented 3 weeks ago

Summary by CodeRabbit

coderabbitai[bot] commented 3 weeks ago
Walkthrough ## Walkthrough The recent modifications enhance the `dpgen2` package by integrating the new "DiffCSP" exploration style, which includes the addition of various classes and functions for managing configuration filters, task groups, and relaxation processes. Comprehensive test frameworks have also been introduced, boosting the robustness of the codebase and improving the management of complex computational workflows. ## Changes | Files Changed | Change Summary | |---------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------| | `dpgen2/entrypoint/.../args.py` | Introduced `variant_filter`, updated `lmp_args`, `caly_args`, and added `run_diffcsp_args` and `diffcsp_args` for handling configuration filters in DiffCSP. | | `dpgen2/entrypoint/showkey.py` | Modified `showkey` function to include additional keys for enhanced output. | | `dpgen2/entrypoint/.../submit.py` | Added support for DiffCSP exploration style with new functions and classes, improving task management and configuration handling. | | `dpgen2/exploration/render/traj_render_lammps.py` | Updated `get_confs` to utilize `conf_filters` for filtering configurations. | | `dpgen2/exploration/selector/.../__init__.py` | Imported `DistanceConfFilter` and defined `conf_filter_styles` for distance-based filtering. | | `dpgen2/exploration/selector/.../conf_filter.py` | Modified `check` function to handle atom types by converting them to NumPy arrays for better processing. | | `dpgen2/exploration/selector/.../distance_conf_filter.py` | Implemented `DistanceConfFilter` class to validate configurations based on distance criteria. | | `dpgen2/exploration/task/.../__init__.py` | Added new imports for functionalities related to DiffCSP task groups. | | `dpgen2/exploration/task/.../diffcsp_task_group.py` | Defined `DiffCSPTaskGroup` class for managing DiffCSP-specific tasks. | | `dpgen2/exploration/task/.../make_task_group_from_config.py` | Introduced functions for creating and normalizing DiffCSP task groups. | | `dpgen2/op/.../__init__.py` | New imports for classes related to DiffCSP operations added. | | `dpgen2/op/.../diffcsp_gen.py` | Added functionality to convert model outputs to CIF format and defined the `DiffCSPGen` class. | | `dpgen2/op/.../prep_relax.py` | Introduced `PrepRelax` class for managing relaxation tasks. | | `dpgen2/op/run_relax.py` | Defined `RunRelax` class to execute relaxation operations effectively. | | `dpgen2/superop/.../__init__.py` | Imported `PrepRunDiffCSP` to support new workflows. | | `dpgen2/superop/.../prep_run_diffcsp.py` | Implemented `PrepRunDiffCSP` class for orchestrating multi-step workflows involving DiffCSP processes. | | `examples/diffcsp/dpgen.json` | Introduced a comprehensive configuration for managing DiffCSP computational tasks. | | `tests/exploration/.../test_distance_conf_filter.py` | Added unit tests for `DistanceConfFilter` to validate atomic configuration checks. | | `tests/op/.../test_diffcsp_gen.py` | Created tests for the `DiffCSPGen` class to ensure proper CIF generation from model outputs. | | `tests/op/.../test_prep_relax.py` | Implemented tests for `PrepRelax`, focusing on task generation from CIF files. | | `tests/op/.../test_run_relax.py` | Developed tests for `RunRelax` to validate relaxation task executions. | | `tests/.../test_prep_run_diffcsp.py` | Introduced tests for the `PrepRunDiffCSP` workflow to ensure integration of multiple components works as intended. |
Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between dea89da07320c7396a9932969893ce6532a84864 and 4b42e38dd45dc1ed5d77144ed9546bad4e421507.
Files selected for processing (1) * dpgen2/op/diffcsp_gen.py (1 hunks)
Additional context used
Ruff
dpgen2/op/diffcsp_gen.py
92-92: Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling (B904)
Additional comments not posted (2)
dpgen2/op/diffcsp_gen.py (2)
`92-92`: **Enhance exception handling with context.** Use `raise ... from None` to distinguish exceptions raised in the `except` block from those occurring elsewhere. This comment has already been made in previous reviews.
Tools
Ruff
92-92: Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling (B904)
--- `93-93`: **Verify the existence of `model_path`.** Ensure that `model_path` exists before proceeding with file operations. Consider adding a check to confirm the existence of `model_path` and handle the case where it does not exist.
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codecov[bot] commented 3 weeks ago

Codecov Report

Attention: Patch coverage is 85.90604% with 42 lines in your changes missing coverage. Please review.

Project coverage is 84.05%. Comparing base (44d3fd1) to head (4b42e38). Report is 1 commits behind head on master.

Files Patch % Lines
dpgen2/entrypoint/submit.py 5.26% 18 Missing :warning:
...n2/exploration/task/make_task_group_from_config.py 23.52% 13 Missing :warning:
dpgen2/superop/prep_run_diffcsp.py 90.74% 5 Missing :warning:
dpgen2/op/run_relax.py 95.12% 4 Missing :warning:
dpgen2/op/diffcsp_gen.py 96.61% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #251 +/- ## ========================================== + Coverage 83.87% 84.05% +0.17% ========================================== Files 98 103 +5 Lines 5433 5725 +292 ========================================== + Hits 4557 4812 +255 - Misses 876 913 +37 ```

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zjgemi commented 3 weeks ago

I would recommend cherry-picking the implementation of diffcsp, so this pr is decoupled from #250

There are conf-filter related modifications in diffcsp. We can handle this PR after #250.