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首页> 外文期刊>RSC Advances >Introducing DDEC6 atomic population analysis: part 4. Efficient parallel computation of net atomic charges, atomic spin moments, bond orders, and more
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Introducing DDEC6 atomic population analysis: part 4. Efficient parallel computation of net atomic charges, atomic spin moments, bond orders, and more

机译：DDEC6原子填充分析简介：第4部分。净原子电荷，原子自旋矩，键序等的高效并行计算

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The DDEC6 method is one of the most accurate and broadly applicable atomic population analysis methods. It works for a broad range of periodic and non-periodic materials with no magnetism, collinear magnetism, and non-collinear magnetism irrespective of the basis set type. First, we show DDEC6 charge partitioning to assign net atomic charges corresponds to solving a series of 14 Lagrangians in order. Then, we provide flow diagrams for overall DDEC6 analysis, spin partitioning, and bond order calculations. We wrote an OpenMP parallelized Fortran code to provide efficient computations. We show that by storing large arrays as shared variables in cache line friendly order, memory requirements are independent of the number of parallel computing cores and false sharing is minimized. We show that both total memory required and the computational time scale linearly with increasing numbers of atoms in the unit cell. Using the presently chosen uniform grids, computational times of ～9 to 94 seconds per atom were required to perform DDEC6 analysis on a single computing core in an Intel Xeon E5 multi-processor unit. Parallelization efficiencies were usually >50% for computations performed on 2 to 16 cores of a cache coherent node. As examples we study a B-DNA decamer, nickel metal, supercells of hexagonal ice crystals, six X@C60 endohedral fullerene complexes, a water dimer, a Mn12-acetate single molecule magnet exhibiting collinear magnetism, a Fe4O12N4C40H52 single molecule magnet exhibiting non-collinear magnetism, and several spin states of an ozone molecule. Efficient parallel computation was achieved for systems containing as few as one and as many as >8000 atoms in a unit cell. We varied many calculation factors (e.g., grid spacing, code design, thread arrangement, etc.) and report their effects on calculation speed and precision. We make recommendations for excellent performance.
机译：DDEC6方法是最准确，应用最广泛的原子人口分析方法之一。它适用于范围广泛的周期性和非周期性材料，而没有磁性，共线磁性和非共线磁性，而与基集类型无关。首先，我们显示DDEC6电荷分配以分配净原子电荷对应于按顺序求解一系列14个拉格朗日数。然后，我们提供了用于总体DDEC6分析，自旋分区和键合顺序计算的流程图。我们编写了OpenMP并行化的Fortran代码以提供有效的计算。我们展示了通过以缓存行友好顺序将大型数组存储为共享变量，内存需求与并行计算核心的数量无关，并且错误共享得以最小化。我们表明，所需的总存储量和计算时间都随着晶胞中原子数量的增加而线性变化。使用当前选择的均匀网格，在Intel Xeon E5多处理器单元中的单个计算核心上执行DDEC6分析所需的计算时间为每个原子约9至94秒。对于在缓存一致性节点的2到16个核心上执行的计算，并行效率通常> 50％。例如，我们研究了B-DNA十聚体，镍金属，六角形冰晶的超晶胞，六个X @ C 60 内面富勒烯络合物，水二聚体，Mn 12 -醋酸单分子磁体，显示共线磁性，Fe 4 O 12 N 4 C 40 H 52 <表现出非共线磁性和臭氧分子的几种自旋态的单分子磁体。对于在一个晶胞中包含少至一个和多达> 8000个原子的系统，可以实现有效的并行计算。我们更改了许多计算因素（例如 ，网格间距，代码设计，线程排列，等），并报告了它们对计算速度和精度的影响。我们提出了出色的性能建议。

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