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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
33 stars 26 forks source link

Optimize set operations in ExplorationReport #262

Closed zjgemi closed 2 months ago

zjgemi commented 2 months ago

set.union becomes slow significantly when set size large than 100k. Test with

from tqdm import tqdm
s = set()
for i in tqdm(range(200000)):
    s = s.union([i])

in comparison to

from tqdm import tqdm
s = set()
for i in tqdm(range(200000)):
    s.update([i])

Summary by CodeRabbit

coderabbitai[bot] commented 2 months ago
Walkthrough ## Walkthrough The pull request modifies the `record` function in the `report_adaptive_lower.py` file by replacing the `union` method with the `update` method for the `self.accur` attribute. This change alters how accuracy values are aggregated, allowing for in-place updates to the existing set instead of creating a new set. The overall logic of the function remains unchanged. ## Changes | Files | Change Summary | |---------------------------------------------|------------------------------------------------------------------------------------------------| | dpgen2/exploration/report/report_adaptive_lower.py | Replaced `union` method with `update` method for `self.accur` to improve efficiency in accuracy aggregation. | ## Sequence Diagram(s) ```mermaid sequenceDiagram participant A as User participant B as report_adaptive_lower A->>B: Call record function B->>B: Update self.accur using update method B->>A: Return updated accuracy ```
Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between a8ca7f03d397d11e9f0f1f836852865ced8350b1 and 9c6d48729efc3953111882bdb945a80ae8452729.
Files selected for processing (1) * dpgen2/exploration/report/report_adaptive_lower.py (1 hunks)
Additional comments not posted (15)
dpgen2/exploration/report/report_adaptive_lower.py (15)
Line range hint `1-121`: **LGTM!** The `__init__` function is correctly implemented and initializes the attributes appropriately. --- Line range hint `123-143`: **LGTM!** The `doc` function correctly generates the class documentation. --- Line range hint `145-205`: **LGTM!** The `args` function correctly returns the list of `Argument` objects. --- Line range hint `207-217`: **LGTM!** The `clear` function correctly resets the state of the object. --- `242-242`: **LGTM!** The change from `self.accur = self.accur.union(add_accur)` to `self.accur.update(add_accur)` is an optimization that improves performance by updating the existing set in-place instead of creating a new set. --- Line range hint `280-315`: **LGTM!** The `_record_one_traj` function correctly processes a single trajectory and updates the state of the object. --- Line range hint `317-326`: **LGTM!** The `_sequence_conv` function correctly checks if a sequence has converged based on the convergence tolerance. --- Line range hint `328-343`: **LGTM!** The `converged` function correctly checks if the exploration has converged based on the convergence criteria. --- Line range hint `345-349`: **LGTM!** The `failed_ratio` function correctly calculates the ratio of failed frames. --- Line range hint `351-355`: **LGTM!** The `accurate_ratio` function correctly calculates the ratio of accurate frames. --- Line range hint `357-361`: **LGTM!** The `candidate_ratio` function correctly calculates the ratio of candidate frames. --- Line range hint `363-373`: **LGTM!** The `get_candidate_ids` function correctly returns a list of candidate frame IDs for each trajectory. --- Line range hint `375-386`: **LGTM!** The `_get_candidates` function correctly selects candidate frames based on the specified selection method. --- Line range hint `388-413`: **LGTM!** The `_get_candidates_uniform` function correctly selects candidate frames uniformly. --- Line range hint `415-443`: **LGTM!** The `_get_candidates_inv_pop_f` function correctly selects candidate frames based on the inverse population in force model deviation statistics.
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codecov[bot] commented 2 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 83.65%. Comparing base (a8ca7f0) to head (9c6d487). Report is 1 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #262 +/- ## ======================================= Coverage 83.65% 83.65% ======================================= Files 104 104 Lines 5990 5990 ======================================= Hits 5011 5011 Misses 979 979 ```

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