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用于计算材料中原子极化率和色散系数的新标度关系:第2部分。线性标度计算算法与并行化

New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization.

作者信息

Manz Thomas A, Chen Taoyi

机构信息

Department of Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-8001 USA

出版信息

RSC Adv. 2019 Oct 17;9(57):33310-33336. doi: 10.1039/c9ra01983a. eCollection 2019 Oct 15.

Abstract

We present two algorithms to compute system-specific polarizabilities and dispersion coefficients such that required memory and computational time scale linearly with increasing number of atoms in the unit cell for large systems. The first algorithm computes the atom-in-material (AIM) static polarizability tensors, force-field polarizabilities, and , , , dispersion coefficients using the MCLF method. The second algorithm computes the AIM polarizability tensors and coefficients using the TS-SCS method. Linear-scaling computational cost is achieved using a dipole interaction cutoff length function combined with iterative methods that avoid large dense matrix multiplies and large matrix inversions. For MCLF, Richardson extrapolation of the screening increments is used. For TS-SCS, a failproof conjugate residual (FCR) algorithm is introduced that solves any linear equation system having Hermitian coefficients matrix. These algorithms have mathematically provable stable convergence that resists round-off errors. We parallelized these methods to provide rapid computation on multi-core computers. Excellent parallelization efficiencies were obtained, and adding parallel processors does not significantly increase memory requirements. This enables system-specific polarizabilities and dispersion coefficients to be readily computed for materials containing millions of atoms in the unit cell. The largest example studied herein is an ice crystal containing >2 million atoms in the unit cell. For this material, the FCR algorithm solved a linear equation system containing >6 million rows, 7.57 billion interacting atom pairs, 45.4 billion stored non-negligible matrix components used in each large matrix-vector multiplication, and ∼19 million unknowns per frequency point (>300 million total unknowns).

摘要

我们提出了两种算法来计算特定系统的极化率和色散系数,以便对于大型系统,所需内存和计算时间随晶胞中原子数的增加呈线性增长。第一种算法使用MCLF方法计算材料中原子(AIM)的静态极化率张量、力场极化率以及 、 、 、 色散系数。第二种算法使用TS - SCS方法计算AIM极化率张量和 系数。通过结合偶极相互作用截止长度函数与迭代方法实现线性缩放计算成本,该迭代方法避免了大型密集矩阵乘法和大型矩阵求逆。对于MCLF,使用筛选增量的理查森外推法。对于TS - SCS,引入了一种万无一失共轭残差(FCR)算法,该算法可求解任何具有厄米特系数矩阵的线性方程组。这些算法在数学上具有可证明的稳定收敛性,可抵抗舍入误差。我们将这些方法并行化,以便在多核计算机上进行快速计算。获得了出色的并行化效率,并且添加并行处理器不会显著增加内存需求。这使得能够轻松计算晶胞中包含数百万个原子的材料的特定系统极化率和色散系数。本文研究的最大示例是一个晶胞中包含超过200万个原子的冰晶。对于这种材料,FCR算法求解了一个包含超过600万行、75.7亿个相互作用原子对、每个大型矩阵 - 向量乘法中使用的454亿个存储的不可忽略矩阵分量以及每个频率点约190万个未知数(总计超过3亿个未知数)的线性方程组。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1eb/9073276/521cc36482cc/c9ra01983a-f1.jpg

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