Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Time-series well performance prediction based on Long Short-Term Memory (LSTM) neural network model

Pore structure and its fractal dimensions of transitional shale: A cross-section from east margin of the Ordos Basin, China

Performance of fractured horizontal well with stimulated reservoir volume in unconventional gas reservoir

Fracture network and fractured porous media as well as their transport properties have received great attentions in many fields from engineering application and basic theoretical researches. Fracture will dynamically extend in length and aperture to form complex fracture network under some external conditions such as percussion drilling, wave propagation, desiccation and hydrofracturing. The complexity of fracture network can be well quantitatively characterized by fractal dimension. In this work, the dynamic characterization of fracture network extension in porous media under drying process is measured by the improved box-counting technique, and fractal dimensions of fracture network are respectively related to drying time, average aperture, moisture content and fracture porosity. The fractal dimension increases exponentially with drying time and average aperture, and decreases with moisture content in the form of power law. Specially, the fractal dimension is approximatively increased with porosity in t...

Yulong Zhao

Papers

Performance of fractured horizontal well with stimulated reservoir volume in unconventional gas reservoir

Performance analysis for a model of a multi-wing hydraulically fractured vertical well in a coalbed methane gas reservoir

“Triple porosity” modeling of transient well test and rate decline analysis for multi-fractured horizontal well in shale gas reservoirs

Gibbs free energy of gaseous phosphorus dimer

Prediction of entropy and Gibbs free energy for nitrogen