LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

Neutron scattering is a powerful experimental technique for characterizing the structure and dynamics of materials on the atomic or molecular scale. However, the interpretation of experimental data from neutron scattering is oftentimes not trivial, partly because scattering methods probe ensemble-averaged information in the reciprocal space. Therefore, computer simulations, such as classical and ab initio molecular dynamics, are frequently used to unravel the time-dependent atomistic configurations that can reproduce the scattering patterns and thus assist in the understanding of the microscopic origin of certain properties of materials. LiquidLib is a post-processing package for analyzing the trajectory of atomistic simulations of liquids and liquid-like matter with application to neutron scattering experiments. From an atomistic simulation, LiquidLib provides the computation of various statistical quantities including the pair distribution function, the weighted and unweighted structure factors, the mean squared displacement, the non-Gaussian parameter, the four-point correlation function, the velocity auto correlation function, the self and collective van Hove correlation functions, the self and collective intermediate scattering functions, and the bond orientational order parameter. LiquidLib analyzes atomistic trajectories generated from packages such as LAMMPS, GROMACS, and VASP. It also offers an extendable platform to conveniently integrate new quantities into the library and integrate simulation trajectories of other file formats for analysis. Weighting the quantities by element-specific neutron-scattering lengths provides results directly comparable to neutron scattering measurements. Lastly, LiquidLib is independent of dimensionality, which allows analysis of trajectories in two, three, and higher dimensions. The code is beginning to find worldwide use.

中子散射（Neutron scattering）是一种用于在原子或分子尺度上表征材料结构与动力学行为的强大实验技术。然而，对中子散射实验数据的解析往往并非易事，部分原因在于散射方法探测的是倒易空间中的系综平均信息。因此，诸如经典分子动力学与从头算分子动力学（ab initio molecular dynamics）这类计算机模拟方法常被用于解析可复现散射图样的随时间演化的原子构型，从而助力理解材料特定属性的微观起源。LiquidLib是一款后处理工具包，用于分析液体及类液体物质的原子级模拟轨迹，可应用于中子散射实验相关研究。基于原子级模拟轨迹，LiquidLib可计算多种统计量，包括对分布函数（pair distribution function）、加权与未加权结构因子（structure factors）、均方位移（mean squared displacement）、非高斯参数（non-Gaussian parameter）、四点关联函数（four-point correlation function）、速度自关联函数（velocity auto correlation function）、自关联与集体关联范霍夫关联函数（van Hove correlation functions）、自关联与集体关联中间散射函数（intermediate scattering functions），以及键取向序参数（bond orientational order parameter）。LiquidLib可分析由LAMMPS、GROMACS及VASP等模拟软件生成的原子级轨迹。该工具包还提供了可扩展平台，便于将新的统计量集成至库中，同时支持导入其他文件格式的模拟轨迹以供分析。通过元素特异性中子散射长度对统计量进行加权处理，可得到可直接与中子散射实验测量结果相比较的计算值。此外，LiquidLib不受维度限制，可用于分析二维、三维及更高维度的模拟轨迹。目前，该代码已开始在全球范围内得到应用。