Closed kenko911 closed 4 months ago
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The _compute_3body
function in src/matgl/graph/compute.py
has been significantly optimized for performance. Key improvements include the efficient counting of bonds per atom using np.bincount
and streamlined generation of triple_bond_indices
with numpy operations. The management of three_body_id
and max_three_body_id
has also been revised for efficiency. Additionally, the return value has been simplified to return only l_g
.
File | Change Summary |
---|---|
src/matgl/graph/compute.py |
Optimized _compute_3body function, removed unnecessary parameters, streamlined return type. |
sequenceDiagram
participant Caller
participant Compute as compute.py
Caller->>Compute: _compute_3body(g)
Compute->>Compute: Count bonds per atom using np.bincount
Compute->>Compute: Generate triple_bond_indices via numpy operations
Compute->>Compute: Handle three_body_id and max_three_body_id efficiently
Compute-->>Caller: Return l_g
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Summary
The new implementation of _compute_3body accelerates the calculation of counting 3-body indices. Based on my preliminary benchmarking, the new implementation for simulating thousands of atoms improves by around 15-20% speed compared to the current implementation.
Checklist
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