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OPTIMIZATION.md

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Micro-Optimization Sprint

Objective

Thoroughly scan the codebase one file at a time, analyzing every function individually. For each function, we define:

  1. Functionality: What does the function do?
  2. Analysis: Is there anything redundant, slow, or incorrect?
  3. Optimization: Apply surgical improvements to maximize performance and code quality.

Progress Tracking

[X] src/topology.py

  • Function: generate_topology
    • Status: Optimized.
    • Changes: Moved imports to top-level, removed dead code (get_bond_type), and replaced manual NumPy geometric calculations with optimized RDKit rdMolTransforms C++ routines.

[X] src/simulation.py

  • Status: Optimized.
  • Changes: Hoisted CHONS_DEFAULTS to module-level, refactored generate_input_file to use list joining for better efficiency, and implemented streaming stdout in run_simulation using subprocess.Popen to prevent memory bloat and provide real-time feedback. Added configurable gpus support.

[X] src/analysis.py

  • Status: Optimized.
  • Changes: Refactored analyze_results and calculate_encapsulation_efficiency to use memory-efficient file reading. Replaced readlines() with line-by-line parsing for logs and implemented a seeking-from-end strategy for dump files to handle large trajectories (GB+) without memory exhaustion.

[X] src/visualization.py

  • Status: Optimized.
  • Changes: Implemented element-specific Van der Waals radii (CHONS) for realistic particle sizing. Added dynamic frame sampling (max_frames) to prevent massive GIF generation and reduce render times. Refined AmbientOcclusion and ColorCoding for better visual depth and molecule distinction.

Sprint Complete

All core modules (topology, simulation, analysis, visualization) have been individually analyzed and optimized for performance, memory efficiency, and code quality.