کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
501801 | 863651 | 2011 | 9 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Efficient parallel implementation of Ewald summation in molecular dynamics simulations on multi-core platforms
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موضوعات مرتبط
مهندسی و علوم پایه
شیمی
شیمی تئوریک و عملی
پیش نمایش صفحه اول مقاله
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چکیده انگلیسی
We present a multi-step computation method to implement the Ewald summation for long-range electrostatic interactions in molecular dynamic simulations on a multi-core machine. Our methodology is based on the OpenMP programming model. It partitions computations of real-space summation among threads so that the global force of a single particle cannot be modified by more than one thread simultaneously. It requires neither a private copy of the force array for each thread nor an inspector at runtime. Compared with some other methods that can parallelise reduction operations on a force-array, our method achieves relatively higher speedups and lower L2 cache miss and bus utilisation ratios.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Computer Physics Communications - Volume 182, Issue 5, May 2011, Pages 1111–1119
Journal: Computer Physics Communications - Volume 182, Issue 5, May 2011, Pages 1111–1119
نویسندگان
Yali Liu, Changjun Hu, Chongchong Zhao,