Phonon dispersion measured directly from molecular dynamics simulations
Phonon dispersion measured directly from molecular dynamics simulations
复制标题
直接通过分子动力学模拟测量声子色散
DOI：
10.1016/j.cpc.2011.04.019
复制
发表时间：
2011-10-01
影响因子：
6.3
通讯作者：
Kong, Ling Ti
中科院分区：
文献类型：
--
作者：
Kong, Ling Ti
提出并实现了一种基于分子动力学模拟的晶体声子色散测量方法，作为对开放源代码经典分子动力学模拟程序LAMMPS的扩展。该方法利用涨落耗散理论，通过观察分子动力学模拟过程中原子的位移来构造动力学矩阵。然后，动力学矩阵可以用来计算声子谱，通过评估其本征值。结果表明，该方法能够准确地计算声子色散，同时考虑了声子的非谐效应。该实现是在LAMMPS的修复的风格，它被设计为并行运行，并利用LAMMPS提供的功能，测量的动力学矩阵可以被传递到一个辅助的后处理代码来评估声子。http://cpc.cs.qub.ac.uk/summaries/AEJB_v1_0.htmlProgram爱尔兰许可条款：GNU通用公共许可证编号。分布式程序中的行，包括测试数据等：105 393号分布式程序的字节数，包括测试数据等：3 231 800分发格式：tar. gz编程语言：C++计算机：全部操作系统：Linux代码是否已矢量化或并行化？：是的可以使用1到N个处理器RAM：取决于问题，大约1 kB到几MB分类：7.8外部例程：MPI，FIT，LAMMPS版本15，2010年1月（http：//lammps.sandia.gov/）问题的性质：固体中的原子围绕其平衡位置不断振动，集体振动形成允许波长和振幅的波。这种晶格振动的量子被称为声子，而所谓的“晶格动力学”是寻找这些振动的正常模式的研究领域。换句话说，晶格动力学检查声子频率和波矢量之间的关系，即，声子色散声子色散的计算需要构造动力学矩阵。在原子尺度模型中，动力学矩阵通常是通过推导所用力场的导数来构造的，这不能解释温度对声子的影响，除了冗长的“准谐波”过程。我们提出了一种直接从分子动力学模拟中构造动力学矩阵的方法，简单地通过观察系统中原子的位移，从而使得动力学矩阵的构建成为一项简单的任务。此外，在分子动力学模拟中自然地考虑了非谐效应，因此得到的声子同时反映了有限温度效应。限制：一个定义良好的晶格是必要的，采用所提出的方法以及实施的代码来评估声子色散。换句话说，所研究的系统应该处于固态，原子在其平衡位置附近振动。此外，预期没有晶格的漂移。该方法最适合于周期性系统，尽管具有超晶胞方法的非周期性系统也是可能的，但是当单位晶胞包含太多原子时，它将变得低效。附加说明：我们鼓励读者访问http://code.google.com/p/fix-phonon以获取后续的代码更新以及相关的后处理代码，从而跟上LAMMPS的最新版本。运行时间：运行时间取决于系统大小、使用的处理器数量以及力场的复杂性，就像典型的分子动力学模拟一样。对于本文中显示的第三个示例，在Intel Xeon X3220架构（2.4G，四核）上花费了大约2.5小时。
A method to measure the phonon dispersion of a crystal based on molecular dynamics simulation is proposed and implemented as an extension to an open source classical molecular dynamics simulation code LAMMPS. In the proposed method, the dynamical matrix is constructed by observing the displacements of atoms during molecular dynamics simulation, making use of the fluctuation-dissipation theory. The dynamical matrix can then be employed to compute the phonon spectra by evaluating its eigenvalues. It is found that the proposed method is capable of yielding the phonon dispersion accurately, while taking into account the anharmonic effect on phonons simultaneously. The implementation is done in the style of fix of LAMMPS, which is designed to run in parallel and to exploit the functions provided by LAMMPS; the measured dynamical matrices could be passed to an auxiliary postprocessing code to evaluate the phonons.Program summaryProgram title: FixPhonon, version 1.0Catalogue identifier: AEJB_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJB_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU General Public licenseNo. of lines in distributed program, including test data, etc.: 105 393No. of bytes in distributed program, including test data, etc.: 3 231 800Distribution format: tar.gzProgramming language: C++Computer: AllOperating system: LinuxHas the code been vectorized or parallelized?: Yes. 1 to N processors may be usedRAM: Depends on problem, approximate to 1 kB to several MBClassification: 7.8External routines: MPI, FIT, LAMMPS version 15, January 2010 (http://lammps.sandia.gov/)Nature of problem: Atoms in solids make ceaseless vibrations about their equilibrium positions, and a collective vibration forms a wave of allowed wavelength and amplitude. The quantum of such lattice vibration is called the phonon, and the so-called "lattice dynamics" is the field of study to find the normal modes of these vibrations. In other words, lattice dynamics examines the relationship between the frequencies of phonons and the wave vectors, i.e., the phonon dispersion. The evaluation of the phonon dispersion requires the construction of the dynamical matrix. In atomic scale modeling, the dynamical matrices are usually constructed by deriving the derivatives of the force field employed, which cannot account for the effect of temperature on phonons, with an exception of the tedious "quasi-harmonic" procedure.Solution method: We propose here a method to construct the dynamical matrix directly from molecular dynamics simulations, simply by observing the displacements of atoms in the system thus making the constructing of the dynamical matrix a straightforward task. Moreover, the anharmonic effect was taken into account in molecular dynamics simulations naturally, the resultant phonons therefore reflect the finite temperature effect simultaneously.Restrictions: A well defined lattice is necessary to employ the proposed method as well as the implemented code to evaluate the phonon dispersion. In other words, the system under study should be in solid state where atoms vibrate about their equilibrium positions. Besides, no drifting of the lattice is expected. The method is best suited for periodic systems, although non-periodic system with a supercell approach is also possible, it will however become inefficient when the unit cell contains too many atoms. Additional comments: The readers are encouraged to visit http://code.google.com/p/fix-phonon for subsequent update of the code as well as the associated postprocessing code, so as to keep up with the latest version of LAMMPS.Running time: Running time depends on the system size, the numbers of processors used, and the complexity of the force field, like a typical molecular dynamics simulation. For the third example shown in this paper, it took about 2.5 hours on an Intel Xeon X3220 architecture (2.4G, quadcore).