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基于MPI+CUDA环境的静电相互作用能并行求解 被引量:1
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作者 刘青昆 马名威 +1 位作者 杨荣杰 宫利东 《计算机应用与软件》 CSCD 北大核心 2012年第11期35-38,共4页
ABEEMσπ(Atom-Bond Electronegativity EqualizationσπModel)模型中,原串行程序求静电相互作用能的方法非常耗时,致使研究问题的效率降低。针对原程序中多个循环相互嵌套的求解部分,采用带状卷帘存储迭代分配的MPI(Message Passing ... ABEEMσπ(Atom-Bond Electronegativity EqualizationσπModel)模型中,原串行程序求静电相互作用能的方法非常耗时,致使研究问题的效率降低。针对原程序中多个循环相互嵌套的求解部分,采用带状卷帘存储迭代分配的MPI(Message Passing Inter-face)并行化处理;对体系中所有原子、σ键、孤对电子、π键位点之间的静电相互作用能采用多线程CUDA(Computer Unified DeviceArchitecture)并行化处理。传统MPI+CUDA环境中,GPU和CPU之间的数据传输开销大,导致整体性能下降以及各种粒子间计算串行调用CUDA,致使时间浪费。针对上述情况,使用GPU核心的缓存机制解决传输开销大的问题,并利用多CUDA流技术实现多个循环异步进行计算,从而缩短了运行时间。然后选取多个不同类型的大分子体系进行测试,结果表明,利用改进的MPI+CUDA并行模型进行动力学模拟,并行加速比显著提高,大幅度缩减了求解静电相互作用能的时间,并得到与串行一致的结果。 展开更多
关键词 原子-键电负性均衡σπ模型 静电子相互作用能 并行计算 消息传递接口 统一计算设备架构
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Effective polarization energy of the naphthalene molecular crystal: a study on the polarizable force field
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作者 XU Tao YIN ShiWei 《Science China Chemistry》 SCIE EI CAS 2014年第10期1375-1382,共8页
Apparent polarization energy of the localized charge in organic solids consists of electronic polarization energy, permanent electrostatic interactions, and inter/intra molecular relaxation energies. The effective ele... Apparent polarization energy of the localized charge in organic solids consists of electronic polarization energy, permanent electrostatic interactions, and inter/intra molecular relaxation energies. The effective electronic polarization energies for an electron/hole carrier were successfully estimated by AMOEBA polarizable force field in naphthalene molecular crystals. Both electronic polarization energy and permanent electrostatic interaction were in agreement with the preview experimental values. In addition, the influence of the multipoles from different distributed mutipole analysis (DMA) fitting options on the electro- static interactions are discussed in this paper. We found that the multipoles obtained from Gauss-Hermite quadrature without diffuse function or grid-based quadrature with 0.325 A H atomic radius will give reasonable electronic polarization energies and permanent interactions for electron and hole carriers. 展开更多
关键词 polarization energy organic molecular crystal AMOEBA
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