dynasor—A Tool for Extracting Dynamical Structure Factors and Current Correlation Functions from Molecular Dynamics Simulations,Advanced Theory and Simulations

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dynasor—A Tool for Extracting Dynamical Structure Factors and Current Correlation Functions from Molecular Dynamics Simulations
Advanced Theory and Simulations ( IF 2.9 ) Pub Date : 2021-01-22 , DOI: 10.1002/adts.202000240
Erik Fransson ₁ , Mattias Slabanja ₁ , Paul Erhart ₁ , Göran Wahnström ₁

Affiliation

Perturbative treatments of the lattice dynamics are widely successful for many crystalline materials; however, their applicability is limited for strongly anharmonic systems, metastable crystal structures and liquids. The full dynamics of these systems can, however, be accessed via molecular dynamics (MD) simulations using correlation functions, which includes dynamical structure factors providing a direct bridge to experiment. To simplify the analysis of correlation functions, here the dynasor package is presented as a flexible and efficient tool that enables the calculation of static and dynamical structure factors, current correlation functions as well as their partial counterparts from MD trajectories. The dynasor code can handle input from several major open source MD packages and thanks to its C/Python structure can be readily extended to support additional codes. The utility of dynasor is demonstrated via examples for both solid and liquid single and multi‐component systems. In particular, the possibility to extract the full temperature dependence of phonon frequencies and lifetimes is emphasized.

中文翻译：

dynasor-一种从分子动力学模拟中提取动力学结构因子和电流相关函数的工具

晶格动力学的微扰处理在许多晶体材料中都非常成功。但是，它们的应用仅限于强非谐系统，亚稳态晶体结构和液体。但是，可以通过使用相关函数的分子动力学（MD）仿真来访问这些系统的完整动力学，其中包括相关的动力学结构因素，这些动力学因素为实验提供了直接的桥梁。为了简化相关函数的分析，在这里提出了dynasor软件包，它是一种灵活而有效的工具，可以计算静态和动态结构因子，当前相关函数以及它们从MD轨迹得到的部分对应函数。该dynasor代码可以处理来自几个主要的开源MD包的输入，并且由于其C / Python结构，可以轻松扩展以支持其他代码。通过对固体和液体单组分和多组分系统的实例证明了Dynasor的实用性。特别地，强调了提取声子频率和寿命的全温度依赖性的可能性。

更新日期：2021-02-04

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