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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
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Add CP2K support for dpgen2 #190

Closed Cloudac7 closed 2 months ago

Cloudac7 commented 6 months ago

As described in #180 , dpgen2 did not support CP2K. This PR add RunCp2k and is tested to be OK to generate fp tasks.

Thus solved #180.

Summary by CodeRabbit

codecov[bot] commented 6 months ago

Codecov Report

Attention: Patch coverage is 91.36691% with 12 lines in your changes are missing coverage. Please review.

Project coverage is 87.69%. Comparing base (76c9657) to head (3ccfe50).

:exclamation: Current head 3ccfe50 differs from pull request most recent head 61fbc00

Please upload reports for the commit 61fbc00 to get more accurate results.

Files Patch % Lines
dpgen2/fp/cp2k_input.py 92.85% 7 Missing :warning:
dpgen2/fp/cp2k.py 87.50% 5 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #190 +/- ## ========================================== + Coverage 84.63% 87.69% +3.06% ========================================== Files 94 85 -9 Lines 5140 4322 -818 ========================================== - Hits 4350 3790 -560 + Misses 790 532 -258 ```

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Andy6M commented 3 months ago

It seems that only the three elements C, N, and H and the corresponding pseudopotentials are considered in the code, and once there are other elements in the system, the code may be incorrect.

Cloudac7 commented 3 months ago

It seems that only the three elements C, N, and H and the corresponding pseudopotentials are considered in the code, and once there are other elements in the system, the code may be incorrect.

No, it is just a default dict as placeholder. This PR would be soon refactored.

coderabbitai[bot] commented 3 months ago
Walkthrough ## Walkthrough The changes introduce functionalities for integrating CP2K, a computational chemistry software package, into the `dpgen2` framework. This integration includes adding new classes for preparing and running CP2K tasks, generating CP2K input files, and handling structural data. Additionally, new test cases are created to ensure the correctness of these functionalities. The updates enhance the capability of `dpgen2` to support CP2K simulations, making it more versatile for computational chemistry applications. ## Changes | Files/Paths | Change Summary | |-------------------------------------|-------------------------------------------------------------------------------| | `dpgen2/fp/__init__.py` | Added imports for CP2K-related classes and a dictionary entry for "cp2k". | | `dpgen2/fp/cp2k.py` | Introduced `PrepCp2k` and `RunCp2k` classes with methods for CP2K task preparation and execution. | | `dpgen2/fp/cp2k_input.py` | Added functionality for generating CP2K input files, including dictionary updates and structural data handling. | | `tests/fp/data.cp2k/coord_n_cell.inc` | Introduced coordinate and cell information for Na atoms in a crystal structure. | | `tests/fp/data.cp2k/input.inp` | Added configuration settings for a CP2K simulation, including global settings, DFT parameters, and atomic details. | | `tests/fp/data.cp2k/input.json` | Defined parameters for a CP2K simulation in JSON format. | | `tests/fp/data.cp2k/sys-2/type.raw` | Included type information for a system. | | `tests/fp/data.cp2k/sys-2/type_map.raw` | Introduced type mapping for Na. | | `tests/fp/test_cp2k.py` | Added test cases for `Cp2kInputs` and `RunCp2k` classes to validate CP2K input generation and task execution. |
Recent Review Details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between 76c96571a879132aea4fd4e1fbdb6ad2803b3e6c and 61fbc00317d9d7107a1fd9843e026ae7d1d19c63.
Files selected for processing (9) * dpgen2/fp/__init__.py (2 hunks) * dpgen2/fp/cp2k.py (1 hunks) * dpgen2/fp/cp2k_input.py (1 hunks) * tests/fp/data.cp2k/coord_n_cell.inc (1 hunks) * tests/fp/data.cp2k/input.inp (1 hunks) * tests/fp/data.cp2k/input.json (1 hunks) * tests/fp/data.cp2k/sys-2/type.raw (1 hunks) * tests/fp/data.cp2k/sys-2/type_map.raw (1 hunks) * tests/fp/test_cp2k.py (1 hunks)
Files skipped from review due to trivial changes (4) * tests/fp/data.cp2k/coord_n_cell.inc * tests/fp/data.cp2k/input.json * tests/fp/data.cp2k/sys-2/type.raw * tests/fp/data.cp2k/sys-2/type_map.raw
Additional Context Used
Ruff (31)
dpgen2/fp/cp2k.py (14)
6-6: `typing.Dict` imported but unused --- 8-8: `typing.Optional` imported but unused --- 9-9: `typing.Set` imported but unused --- 11-11: `typing.Union` imported but unused --- 15-15: `numpy` imported but unused --- 18-18: `dargs.ArgumentEncoder` imported but unused --- 19-19: `dargs.Variant` imported but unused --- 20-20: `dargs.dargs` imported but unused --- 23-23: `dflow.python.OP` imported but unused --- 24-24: `dflow.python.OPIO` imported but unused --- 25-25: `dflow.python.Artifact` imported but unused --- 26-26: `dflow.python.BigParameter` imported but unused --- 27-27: `dflow.python.FatalError` imported but unused --- 28-28: `dflow.python.OPIOSign` imported but unused
dpgen2/fp/cp2k_input.py (8)
2-2: `pathlib.Path` imported but unused --- 6-6: `typing.List` imported but unused --- 8-8: `typing.Set` imported but unused --- 9-9: `typing.Tuple` imported but unused --- 10-10: `typing.Union` imported but unused --- 17-17: `dargs.ArgumentEncoder` imported but unused --- 18-18: `dargs.Variant` imported but unused --- 19-19: `dargs.dargs` imported but unused
tests/fp/test_cp2k.py (9)
1-1: `glob` imported but unused --- 2-2: `json` imported but unused --- 3-3: `os` imported but unused --- 4-4: `shutil` imported but unused --- 5-5: `sys` imported but unused --- 6-6: `textwrap` imported but unused --- 17-17: `numpy` imported but unused --- 21-21: `.context.dpgen2` imported but unused --- 33-33: Redefinition of unused `json` from line 2
Additional comments not posted (5)
tests/fp/data.cp2k/input.inp (1)
`1-52`: The CP2K configuration file is well-structured and aligns with the standard practices for setting up simulations. Good job on maintaining clarity and organization in the file.
dpgen2/fp/__init__.py (1)
`6-10`: The addition of CP2K classes to the imports and the `fp_styles` dictionary is correctly implemented. This setup enables the framework to handle CP2K tasks effectively. Also applies to: 48-52
tests/fp/test_cp2k.py (1)
`31-93`: The test cases for CP2K input generation and task execution are comprehensive and well-implemented. These tests should effectively validate the CP2K integration.
dpgen2/fp/cp2k.py (1)
`55-164`: The implementations of `PrepCp2k` and `RunCp2k` classes are robust and well-documented. These classes are crucial for integrating CP2K support into the framework.
dpgen2/fp/cp2k_input.py (1)
`51-211`: The functions `update_dict` and `iterdict`, along with the class `Cp2kInputs`, are well-implemented and crucial for generating CP2K input files. These implementations are essential for the CP2K support in the framework.
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Andy6M commented 2 months ago

Hi @Cloudac7 :

Could you please provide the following example files:

An example of the CP2K inp file. A corresponding input.json file for dpgen2.

These example files would be incredibly helpful for us to quickly get started and verify the new functionality.

Thank you very much!

zjgemi commented 2 months ago

https://github.com/deepmodeling/dpgen2/pull/238

zjgemi commented 2 months ago

https://github.com/deepmodeling/dpgen2/pull/238 CP2K support is implemented with FPOP. Please feed back if there is any question. I will close this PR.