DynaPhoPy: A code for extracting phonon quasiparticles from molecular dynamics simulations
DynaPhoPy: A code for extracting phonon quasiparticles from molecular dynamics simulations
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DOI：
10.1016/j.cpc.2017.08.017
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发表时间：
2017-12-01
影响因子：
6.3
通讯作者：
Tanaka, Isao
中科院分区：
文献类型：
--
作者：
Carreras, Abel;Togo, Atsushi;Tanaka, Isao
我们开发了一种计算代码 DYNAPHOPY，它允许我们使用 Sun 等人提出的简正模式分解技术从分子动力学 (MD) 模拟中提取微观非谐声子特性。 （2014）。使用此代码，我们使用第一原理和 Tersoff 经验势方法计算了不同温度下晶体硅的准粒子声子频率和线宽。在这项工作中，我们使用这两种方法展示了这些特性对温度的依赖性，并将它们与拉曼光谱获得的报告实验数据进行比较（Balkanski et al., 1983; Tsu and Hernandez, 1982）。 程序摘要手稿标题：DynaPhoPy：从分子动力学模拟中提取声子准粒子的代码作者：Abel Carreras、Atsushi Togo 和 Isao Tanaka 程序标题： DynaPhoPyJournal 参考文献：目录标识符：许可规定：MIT 许可证编程语言：Python 和 C 计算机：PC 和集群计算机操作系统：UNIX/OSXRAM：很大程度上取决于输入数据的数量（几 GB）使用的处理器数量：1-16 补充材料：关键字：非谐性、声子、线宽、频移、分子动力学分类：7.8 结构和晶格Dynamics外部例程/库：phonopy、numpy、matplotlib、scipy 和 h5py python 模块。可选：FFTW 和 Cuda 使用的子程序：先前版本的目录标识符：*先前版本的期刊参考：*新版本是否取代先前版本？：*问题的性质：温度升高，晶体电势开始偏离谐波状态，非谐波性变得明显 [1]。为了处理非谐性，微扰方法通常成功地描述了声子寿命和晶格热导率等现象。然而，当系统包含大的原子位移时，它会失败。解决方法：使用正常模式分解技术从分子动力学（MD）模拟中提取声子准粒子。新版本的原因：*修订摘要：*限制：不考虑晶格动力学的量子效应。不寻常的功能：附加注释：运行时间：它高度依赖于所请求的计算类型。它主要取决于原胞中原子的数量、MD模拟的时间步数以及计算功率谱的方法。目前 DyaPhoPy 中实现了两种方法：傅立叶变换和最大熵方法。傅立叶变换方法缩放至 O [N-2]，最大熵方法缩放至 O [N x M]，其中 N 是时间步数，M 是系数数量。 (C) 2017 Elsevier B.V. 保留所有权利。
We have developed a computational code, DYNAPHOPY, that allows us to extract the microscopic anharmonic phonon properties from molecular dynamics (MD) simulations using the normal-mode decomposition technique as presented by Sun et al. (2014). Using this code we calculated the quasiparticle phonon frequencies and linewidths of crystalline silicon at different temperatures using both of first principles and the Tersoff empirical potential approaches. In this work we show the dependence of these properties on the temperature using both approaches and compare them with reported experimental data obtained by Raman spectroscopy (Balkanski et al., 1983; Tsu and Hernandez, 1982).Program summaryManuscript Title: DynaPhoPy: A code for extracting phonon quasiparticles from molecular dynamics simulationsAuthors: Abel Carreras, Atsushi Togo and Isao TanakaProgram Title: DynaPhoPyJournal Reference:Catalogue identifier:Licensing provisions: MIT LicenseProgramming language: Python and CComputer: PC and cluster computersOperating system: UNIX/OSXRAM: Depends strongly on number of input data (several Gb)Number of processors used: 1-16Supplementary material:Keywords: anharmonicity, phonon, linewidth, frequency shift, molecular dynamicsClassification: 7.8 Structure and Lattice DynamicsExternal routines/libraries: phonopy, numpy, matplotlib, scipy and h5py python modules. Optional: FFTW and CudaSubprograms used:Catalogue identifier of previous version:*Journal reference of previous version:*Does the new version supersede the previous version?:*Nature of problem:Increasing temperature, a crystal potential starts to deviate from the harmonic regime and anharmonicity is getting to be evident [1]. To treat anharmonicity, perturbation approach often describes successfully phenomena such as phonon lifetime and lattice thermal conductivity. However it fails when the system contains large atomic displacements.Solution method:Extracting the phonon quasiparticles from molecular dynamics (MD) simulations using the normal mode-decomposition technique.Reasons for the new version:*Summary of revisions:*Restrictions:Quantum effects of lattice dynamics are not considered.Unusual features:Additional comments:Running time:It is highly dependent on the type of calculation requested. It depends mainly on the number of atoms in the primitive cell, the number of time steps of the MD simulation and the method employed to calculate the power spectra. Currently two methods are implemented in DyaPhoPy: The Fourier transform and the maximum entropy methods. The Fourier transform method scales to O [N-2] and the maximum entropy method scales to O [N x M] where N is the number of time steps and M is the number of coefficients. (C) 2017 Elsevier B.V. All rights reserved.