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PyBERTHART:一种基于Python原型技术的相对论实时四分量含时密度泛函理论实现方法。

PyBERTHART: A Relativistic Real-Time Four-Component TDDFT Implementation Using Prototyping Techniques Based on Python.

作者信息

De Santis Matteo, Storchi Loriano, Belpassi Leonardo, Quiney Harry M, Tarantelli Francesco

机构信息

Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy.

Istituto di Scienze e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy.

出版信息

J Chem Theory Comput. 2020 Apr 14;16(4):2410-2429. doi: 10.1021/acs.jctc.0c00053. Epub 2020 Mar 9.

Abstract

We present a real-time time-dependent four-component Dirac-Kohn-Sham (RT-TDDKS) implementation based on the BERTHA code. This new implementation takes advantage of modern software engineering, including the prototyping techniques. The software design follows a three step approach: (i) the prototype implementation of a time-propagation algorithm in nonrelativistic real-time TDDFT within the Psi4NumPy framework, which provides a suitable environment for the creation of a clear, readable, and easy to test reference code in Python, (ii) the design of an original Python application programming interface for the relativistic four-component code BERTHA (PyBERTHA), which has an efficient computational kernel for relativistic integrals written in FORTRAN, and (iii) the porting of the time-propagation scheme enveloped within the Psi4NumPy framework to PyBERTHA. The propagation scheme consequently resides in a single readable Python computer code that is easy to maintain and in which the key quantities, such as the Dirac-Kohn-Sham and dipole matrices, can be accessed directly from the PyBERTHA module. For linear algebra operations (matrix-matrix multiplications and diagonalization) we use the highly optimized procedures implemented in the popular NumPy library. The overhead introduced by the Python interface to BERTHA is almost negligible (less than 1% evaluated on the SCF procedure), and the interoperability between different programming languages (FORTRAN, C, and Python) does not affect the numerical stability of the time-propagation scheme. Our new RT-TDDKS implementation has been employed to investigate the stability of the time-propagation procedure in combination with a density-fitting algorithm (both for the Coulomb and for the exchange-correlation matrix construction), which are employed in BERTHA to speed up the Dirac-Kohn-Sham matrix evaluation. On the basis of systematic calculations, employing several density-fitting basis sets of increasing accuracy, we showed that quantitative agreement can be achieved in combination with extended-fitting basis sets, with an error in the Coulomb energy below 1 μ-hartree. Convergence of the transition energies increasing of quality of the fitting basis sets has been also observed. Our data suggest that the error in the Coulomb energy may also represent a good estimate of the fitting basis set quality for real-time electron dynamics simulations. Further, we study the applicability of the RT-TDDKS method in combination with both weak- and extreme strong-field regime. Numerical results of excited-state transitions for the Group 12 atoms are reported and compared with a previous real-time Dirac-Kohn-Sham implementation (Repisky et al. 2015, 11, 980-991). Finally, calculations of high harmonic generation in the hydrogen molecule and Au dimer have been also carried out. We were able to generate high harmonics with relatively well-defined peaks up to the 21st and 13th order in the case of H and Au, respectively. Our findings show that the four-component structure of the Dirac-Kohn-Sham Hamiltonian provides a suitable theoretical framework, with no intrinsic unfavorable features, to study molecules in the strong-field regime.

摘要

我们展示了一种基于BERTHA代码的实时含时四分量狄拉克-科恩-沙姆(RT-TDDKS)实现。这种新实现利用了现代软件工程,包括原型技术。软件设计遵循三步方法:(i)在Psi4NumPy框架内的非相对论实时含时密度泛函理论(TDDFT)中对时间传播算法进行原型实现,该框架为在Python中创建清晰、可读且易于测试的参考代码提供了合适的环境;(ii)为相对论四分量代码BERTHA设计一个原始的Python应用程序编程接口(PyBERTHA),它具有用于以FORTRAN编写的相对论积分的高效计算内核;(iii)将Psi4NumPy框架内的时间传播方案移植到PyBERTHA。因此,传播方案驻留在一个易于维护的单一可读Python计算机代码中,并且关键量(如狄拉克-科恩-沙姆矩阵和偶极矩阵)可以直接从PyBERTHA模块访问。对于线性代数运算(矩阵-矩阵乘法和对角化),我们使用流行的NumPy库中实现的高度优化的过程。Python接口引入到BERTHA的开销几乎可以忽略不计(在自洽场(SCF)过程中评估小于1%),并且不同编程语言(FORTRAN、C和Python)之间的互操作性不会影响时间传播方案的数值稳定性。我们新的RT-TDDKS实现已被用于结合密度拟合算法(用于库仑和交换-相关矩阵构建)研究时间传播过程的稳定性,这些算法在BERTHA中用于加速狄拉克-科恩-沙姆矩阵评估。基于系统计算,使用了几个精度不断提高的密度拟合基组,我们表明结合扩展拟合基组可以实现定量一致性,库仑能量误差低于1微哈特里。还观察到随着拟合基组质量的提高,跃迁能量的收敛情况。我们的数据表明,库仑能量的误差也可能代表实时电子动力学模拟中拟合基组质量的良好估计。此外,我们研究了RT-TDDKS方法在弱场和超强场区域的适用性。报告了第12族原子激发态跃迁的数值结果,并与先前的实时狄拉克-科恩-沙姆实现进行了比较(Repisky等人,2015年,11卷,980 - 991页)。最后,还对氢分子和金二聚体中的高次谐波产生进行了计算。在氢和金的情况下,我们分别能够生成高达第21阶和第13阶的具有相对明确峰值的高次谐波。我们的研究结果表明,狄拉克-科恩-沙姆哈密顿量的四分量结构为研究强场区域的分子提供了一个合适的理论框架,没有内在的不利特征。

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