Embedded divide-and-conquer algorithm on hierarchical real-space grids: parallel molecular dynamics simulation based on linear-scaling density functional theory
Embedded divide-and-conquer algorithm on hierarchical real-space grids: parallel molecular dynamics simulation based on linear-scaling density functional theory
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DOI：
10.1016/j.cpc.2005.01.005
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发表时间：
2005-05
期刊：
影响因子：
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通讯作者：
F. Shimojo;R. Kalia;A. Nakano;P. Vashishta
中科院分区：
文献类型：
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作者：
F. Shimojo;R. Kalia;A. Nakano;P. Vashishta
线性标度算法已被开发用于进行大规模分子动力学（MD）模拟，其中原子间力在密度泛函理论的框架中以量子力学的方式计算。分而治之的算法被用来计算电子结构，其中非添加剂的动能的贡献包括与嵌入式集群计划。电子波函数表示在一个真实的空间网格，这是增强与粗多重网格，以加速迭代解的收敛和原子周围的自适应细网格，以准确地计算离子赝势。采用空间分解的方法，在大规模并行计算机上实现了层次网格算法。在512个IBM POWER4处理器上，对32，768个原子的非晶CdSe系统的电子结构问题进行了收敛求解.在分子动力学模拟过程中，总能量是很好的保存液体Rb，显示该算法的适用性的第一性原理分子动力学模拟。对于65，536个原子的CdSe系统，在128个Intel Xeon处理器上的并行效率为0.985。
A linear-scaling algorithm has been developed to perform large-scale molecular-dynamics (MD) simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory. A divide-and-conquer algorithm is used to compute the electronic structure, where non-additive contribution to the kinetic energy is included with an embedded cluster scheme. Electronic wave functions are represented on a real-space grid, which is augmented with coarse multigrids to accelerate the convergence of iterative solutions and adaptive fine grids around atoms to accurately calculate ionic pseudopotentials. Spatial decomposition is employed to implement the hierarchical-grid algorithm on massively parallel computers. A converged solution to the electronic-structure problem is obtained for a 32,768-atom amorphous CdSe system on 512 IBM POWER4 processors. The total energy is well conserved during MD simulations of liquid Rb, showing the applicability of this algorithm to first principles MD simulations. The parallel efficiency is 0.985 on 128 Intel Xeon processors for a 65,536-atom CdSe system.