fix dplr: support initializing from a restart file #4084
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Outside diff range, codebase verification and nitpick comments (2)
source/lmp/fix_dplr.h (1)
47-47: Incomplete Renaming DetectedThe method
post_integrate()is still being referenced insource/lmp/fix_dplr.cpp. Please ensure that all occurrences ofpost_integrate()are updated toend_of_step()to maintain consistency across the codebase.
- File:
source/lmp/fix_dplr.cpp- Line: Reference found in
min_pre_exchange()method.Analysis chain
Method Renaming Approved
The renaming of
post_integrate()toend_of_step()is appropriate for the described functionality. Ensure that all references to this method in the codebase are updated accordingly.The code changes are approved.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all references to `post_integrate` are updated to `end_of_step`. # Test: Search for the old function name. Expect: No occurrences. rg --type cpp -A 5 $'post_integrate'Length of output: 375
source/lmp/fix_dplr.cpp (1)
402-402: Incomplete Renaming DetectedThe function
post_integrateis still being referenced in themin_pre_exchangemethod withinsource/lmp/fix_dplr.cpp. Please update all occurrences ofpost_integratetoend_of_stepto ensure consistency and prevent potential errors.
- File:
source/lmp/fix_dplr.cpp- Line:
void FixDPLR::min_pre_exchange() { post_integrate(); }Analysis chain
Method Implementation and Renaming Approved
The implementation of
end_of_step()correctly updates the WC positions as intended. Ensure that all references to this method in the codebase are updated accordingly.The code changes are approved.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all references to `post_integrate` are updated to `end_of_step`. # Test: Search for the old function name. Expect: No occurrences. rg --type cpp -A 5 $'post_integrate'Length of output: 375
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #4084 +/- ##
==========================================
- Coverage 84.40% 84.07% -0.33%
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Files 570 570
Lines 53071 53099 +28
Branches 3054 3059 +5
==========================================
- Hits 44794 44643 -151
- Misses 7318 7494 +176
- Partials 959 962 +3 ☔ View full report in Codecov by Sentry. |
Yi-FanLi
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deepmd/dpmodel/descriptor/dpa1.py
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| variables = data.pop("@variables") | ||
| embeddings = data.pop("embeddings") | ||
| attention_layers = data.pop("attention_layers") | ||
| env_mat = data.pop("env_mat") |
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| data.pop("type") | ||
| variables = data.pop("@variables") | ||
| embeddings = data.pop("embeddings") | ||
| env_mat = data.pop("env_mat") |
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deepmd/dpmodel/utils/seed.py
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deepmd/infer/deep_property.py
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| def eval( | ||
| self, | ||
| coords: np.ndarray, | ||
| cells: Optional[np.ndarray], | ||
| atom_types: Union[list[int], np.ndarray], | ||
| atomic: bool = False, | ||
| fparam: Optional[np.ndarray] = None, | ||
| aparam: Optional[np.ndarray] = None, | ||
| mixed_type: bool = False, | ||
| **kwargs: dict[str, Any], | ||
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deepmd/infer/model_devi.py
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| real_f: Optional[np.ndarray] = None, | |||
| relative: Optional[float] = None, | |||
| atomic: Literal[False] = ..., | |||
| ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]: ... | |||
| ) -> tuple[np.ndarray, np.ndarray, np.ndarray]: ... | |||
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deepmd/jax/common.py
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deepmd/jax/common.py
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deepmd/jax/infer/deep_eval.py
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deepmd/jax/utils/serialization.py
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| elif model_file.endswith(".hlo"): | ||
| model = BaseModel.deserialize(data["model"]) | ||
| model_def_script = data["model_def_script"] |
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deepmd/pt/model/descriptor/dpa2.py
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| if data["repinit"].use_three_body: | ||
| # deserialize repinit_three_body | ||
| statistic_repinit_three_body = repinit_three_body_variable.pop("@variables") | ||
| env_mat = repinit_three_body_variable.pop("env_mat") |
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Thie PR aims at fixing #3679.
The
get_valid_pairswill raise an error whenThe origin is that the check in
get_valid_pairsis too strict for the initialization process. The check requires that a pair of real and virtual atoms found by iterating over the bondlist to be the local atoms of the same processor. This requirement is automatically satisfied during the running of MD because the positions of virtual atoms are set equal to those of real atoms before rebuilding bondlists. However, during initialization (Verlet::setup(int flag)), the bondlist is built based on the initial configuration provided by the user. If the user provides a configuration in which the virtual atoms are placed at the Wannier centroids, it is possible that a bond formed by a pair of real and virtual atoms are between a local and a ghost atom, which triggers this error.This PR loosens the requirement on the initial configuration provided by the user. In the
setup_post_neighborfunction, theget_valid_pairsfunction searches for bonded pairs but skips the aforementioned check. It sets the coordinates of the virtual atoms to the coordinates of the real atoms, and then rebuilds the bondlist. Afterwards, the check can be passed.Summary by CodeRabbit
post_integratemethod topre_exchangeto better reflect its role in the simulation process.