Compressing molecular dynamics trajectories: Breaking the one-bit-per-sample barrier.
2016
Molecular dynamics simulations yield large amounts of trajectory data. For their durable storage and accessibility an efficient compression algorithm is paramount. State of the art domain-specific algorithms combine quantization, Huffman encoding and occasionally domain knowledge. We propose the high resolution trajectory compression scheme (HRTC) that relies on piecewise linear functions to approximate quantized trajectories. By splitting the error budget between quantization and approximation, our approach beats the current state of the art by several orders of magnitude given the same error tolerance. It allows storing samples at far less than one bit per sample. It is simple and fast enough to be integrated into the inner simulation loop, store every time step, and become the primary representation of trajectory data.
Keywords:
- Computational chemistry
- Quantization (signal processing)
- Mathematical optimization
- Quantization (physics)
- Trajectory
- Data compression
- Huffman coding
- Compression (physics)
- Molecular dynamics
- Piecewise linear function
- Computer science
- Domain knowledge
- Real-time computing
- Algorithm
- Orders of magnitude (numbers)
- Theoretical computer science
- Correction
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