Introducing DDEC6 atomic population analysis: part 4. Efficient parallel computation of net atomic charges, atomic spin moments, bond orders, and more.
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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DOI：
10.1039/c7ra11829e
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发表时间：
2018-01-09
期刊：
影响因子：
3.9
通讯作者：
Manz, Thomas A.
中科院分区：
文献类型：
--
作者：
Limas, Nidia Gabaldon;Manz, Thomas A.
DDEC6方法是最准确、应用最广泛的原子居数分析方法之一。它适用于广泛的周期和非周期材料，无磁性，共线磁性和非共线磁性，而不考虑基集类型。首先，我们证明了分配净原子电荷的DDEC6电荷划分对应于按顺序求解一系列14个拉格朗日量。然后，我们提供了总体DDEC6分析、自旋划分和键序计算的流程图。我们编写了一个OpenMP并行Fortran代码来提供高效的计算。我们表明，通过以缓存线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，并且将错误共享最小化。我们表明，所需的总内存和计算时间都与单元胞中原子数量的增加呈线性关系。使用目前选择的均匀网格，在Intel至强E5多处理器单元的单个计算核心上执行DDEC6分析需要每个原子的计算时间为~ 9到94秒。对于在缓存相干节点的2到16核上执行的计算，并行化效率通常为50%。作为例子，我们研究了一个B-DNA十聚体、金属镍、六方冰晶的超级细胞、六个X@C60内嵌富勒烯配合物、一个水二聚体、一个具有共线磁性的mn12 -乙酸单分子磁铁、一个具有非共线磁性的Fe4O12N4C40H52单分子磁铁和一个臭氧分子的几个自旋态。在单个晶胞中包含少至1个原子，多至bb0 8000个原子的系统中，实现了高效的并行计算。我们改变了许多计算因素（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。我们对表现优异的人进行推荐。我们将DDEC6方法并行化，以有效地计算不同材料中的净原子电荷、原子自旋矩和键序。
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. We parallelize the DDEC6 method to efficiently compute net atomic charges, atomic spin moments, and bond orders in diverse materials.
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影响因子：
3.7
作者：
Kresse, G;Furthmuller, J
通讯作者：
Furthmuller, J
影响因子：
4.4
作者：
BECKE, AD
通讯作者：
BECKE, AD
DOI：
10.1007/bf00549096
发表时间：
1977-01-01
期刊：
THEORETICA CHIMICA ACTA
影响因子：
--
作者：
HIRSHFELD, FL
通讯作者：
HIRSHFELD, FL
影响因子：
56.9
作者：
BILLAS, IML;CHATELAIN, A;DEHEER, WA
通讯作者：
DEHEER, WA
影响因子：
9.1
作者：
Gates, TS;Odegard, GM;Clancy, TC
通讯作者：
Clancy, TC