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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
31 stars 22 forks source link

Calypso speedup by refactorizing model deviation. #217

Closed wangzyphysics closed 2 months ago

wangzyphysics commented 2 months ago
  1. add a slice when running op run_caly_model_devi
  2. support distanceofion in dict format, e.g. distanceofion = {"Mg": 0.8, "Al": 0.9}, the value denotes the radius of each element, and the mindistance of different element is equal to the sum of value of element Mg and Al and multipy 0.7.
  3. support providing a list of list format name_of_element, e.g. name_of_element = [["Mg", "Al", "Cu", "Li"], ["La", "Ce", "Ca", "Li"], ["H"]], code will randomly choose one of element in each list to set up a input file of calypso.

Summary by CodeRabbit

coderabbitai[bot] commented 2 months ago
Walkthrough ## Walkthrough The recent updates to the `dpgen2` project focus on enhancing Calypso task generation and management, introducing a new operation for preparing model deviations, and refining error handling and logging. These changes include adding new classes, modifying function parameters, and improving task group configurations and testing to streamline processes and enhance flexibility in task parameter handling. ## Changes | File Path | Change Summary | |-----------------------------------------------|--------------------------------------------------------------------------------------------------| | `dpgen2/entrypoint/submit.py` | Added `PrepCalyModelDevi` operation and updated imports. | | `dpgen2/exploration/task/caly_task_group.py` | Updated task parameters handling, including changes to types and optional status of arguments. | | `dpgen2/exploration/task/calypso/caly_input.py` | Updated `atomic_number` parameter's type annotation. | | `dpgen2/exploration/task/make_task_group_from_config.py` | Updated arguments in `caly_task_grp_args` function. | | `dpgen2/op/collect_run_caly.py` | Improved logic for running `calypso`, error handling, and logging. | | `dpgen2/op/prep_caly_dp_optim.py` | Changed logic for determining `group_size` based on dictionary key presence. | | `dpgen2/op/prep_caly_model_devi.py` | Introduced `PrepCalyModelDevi` class for organizing model deviations. | | `dpgen2/superop/prep_run_calypso.py` | Added steps and parameters related to `prep_caly_model_devi_op`. | | `tests/exploration/test_exploration_group.py` | Enhanced testing with new configurations and test methods. | | `tests/mocked_ops.py` | Streamlined logic in the `execute` function for better clarity. | | `tests/op/test_prep_caly_model_devi.py` | Introduced unit tests for the `PrepCalyModelDevi` class. | | `tests/op/test_run_caly_model_devi.py` | Added imports and a new test method for slicing Calypso model deviations. |
Recent Review Details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between 7f0c7e59a6b51ae6b98ac53d5cc8d1833e9b2a3a and 6e447e9b3f9f8c283a400f7d1683847da1dc9da2.
Files selected for processing (4) * dpgen2/entrypoint/submit.py (4 hunks) * dpgen2/exploration/task/caly_task_group.py (4 hunks) * dpgen2/superop/prep_run_calypso.py (5 hunks) * tests/op/test_run_caly_model_devi.py (3 hunks)
Additional Context Used
Ruff (64)
dpgen2/entrypoint/submit.py (34)
2-2: `glob` imported but unused --- 6-6: `pickle` imported but unused --- 16-16: `typing.Type` imported but unused --- 17-17: `typing.Union` imported but unused --- 20-20: `dpdata` imported but unused --- 23-23: `dflow.InputArtifact` imported but unused --- 24-24: `dflow.InputParameter` imported but unused --- 25-25: `dflow.Inputs` imported but unused --- 26-26: `dflow.OutputArtifact` imported but unused --- 27-27: `dflow.OutputParameter` imported but unused --- 28-28: `dflow.Outputs` imported but unused --- 31-31: `dflow.Steps` imported but unused --- 33-33: `dflow.argo_range` imported but unused --- 34-34: `dflow.download_artifact` imported but unused --- 38-38: `dflow.python.OP` imported but unused --- 39-39: `dflow.python.OPIO` imported but unused --- 40-40: `dflow.python.Artifact` imported but unused --- 41-41: `dflow.python.FatalError` imported but unused --- 42-42: `dflow.python.OPIOSign` imported but unused --- 43-43: `dflow.python.PythonOPTemplate` imported but unused --- 44-44: `dflow.python.TransientError` imported but unused --- 45-45: `dflow.python.upload_packages` imported but unused --- 52-52: `dpgen2.constants.default_host` imported but unused --- 65-65: `dpgen2.exploration.report.ExplorationReportTrustLevelsRandom` imported but unused --- 76-76: `dpgen2.exploration.task.CustomizedLmpTemplateTaskGroup` imported but unused --- 78-78: `dpgen2.exploration.task.ExplorationTask` imported but unused --- 79-79: `dpgen2.exploration.task.LmpTemplateTaskGroup` imported but unused --- 80-80: `dpgen2.exploration.task.NPTTaskGroup` imported but unused --- 116-116: `dpgen2.utils.bohrium_config_from_dict` imported but unused --- 117-117: `dpgen2.utils.dump_object_to_file` imported but unused --- 119-119: `dpgen2.utils.load_object_from_file` imported but unused --- 123-123: `dpgen2.utils.workflow_config_from_dict` imported but unused --- 435-435: Local variable `default_config` is assigned to but never used --- 533-533: f-string without any placeholders
dpgen2/exploration/task/caly_task_group.py (1)
126-126: f-string without any placeholders
dpgen2/superop/prep_run_calypso.py (13)
6-6: `pathlib.Path` imported but unused --- 22-22: `dflow.OutputParameter` imported but unused --- 26-26: `dflow.Workflow` imported but unused --- 27-27: `dflow.argo_len` imported but unused --- 28-28: `dflow.argo_range` imported but unused --- 29-29: `dflow.argo_sequence` imported but unused --- 30-30: `dflow.download_artifact` imported but unused --- 31-31: `dflow.upload_artifact` imported but unused --- 35-35: `dflow.python.OPIO` imported but unused --- 36-36: `dflow.python.Artifact` imported but unused --- 37-37: `dflow.python.OPIOSign` imported but unused --- 43-43: `dpgen2.constants.calypso_index_pattern` imported but unused --- 51-51: `.caly_evo_step.CalyEvoStep` imported but unused
tests/op/test_run_caly_model_devi.py (16)
1-1: `os` imported but unused --- 5-5: `ast.Slice` imported but unused --- 11-11: `unittest.mock.Mock` imported but unused --- 12-12: `unittest.mock.call` imported but unused --- 16-16: `numpy` imported but unused --- 24-24: `dflow.Step` imported but unused --- 27-27: `dflow.python.OP` imported but unused --- 29-29: `dflow.python.Artifact` imported but unused --- 30-30: `dflow.python.OPIOSign` imported but unused --- 31-31: `dflow.python.PythonOPTemplate` imported but unused --- 32-32: `dflow.python.TransientError` imported but unused --- 36-36: `dpgen2.constants.calypso_input_file` imported but unused --- 37-37: `dpgen2.constants.calypso_log_name` imported but unused --- 46-46: `dpgen2.utils.BinaryFileInput` imported but unused --- 55-55: `deepmd` imported but unused --- 58-58: Do not use bare `except`
Additional comments not posted (6)
tests/op/test_run_caly_model_devi.py (5)
`1-1`: Remove unused import `os`. --- `5-5`: Remove unused import `Slice`. --- `24-24`: Remove unused import `Step`. --- `31-31`: Remove unused import `PythonOPTemplate`. --- `32-32`: Remove unused import `TransientError`.
dpgen2/exploration/task/caly_task_group.py (1)
`126-126`: The error message in the exception uses an f-string without placeholders, which is redundant. Consider simplifying the string or correctly utilizing the f-string if dynamic data is intended to be included.
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codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 94.50549% with 5 lines in your changes are missing coverage. Please review.

Project coverage is 84.98%. Comparing base (8bdea14) to head (6e447e9).

Files Patch % Lines
dpgen2/entrypoint/submit.py 0.00% 3 Missing :warning:
dpgen2/exploration/task/caly_task_group.py 94.73% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #217 +/- ## ========================================== + Coverage 84.82% 84.98% +0.15% ========================================== Files 93 94 +1 Lines 5034 5114 +80 ========================================== + Hits 4270 4346 +76 - Misses 764 768 +4 ```

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