LiquidLib by Z Lab

Purpose

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

Introduction

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 factor, 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 function, the self and collective intermediate scattering function, 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.

More details are provided in our publication [DOI].

Capabilities

LiquidLib provides computation the following quantities:

Pair Distribution Function
Weighted and Unweighted Structure Factor
Mean Squared Displacement
Non-Gaussian Parameter
Four-point Correlation Function
Velocity Auto Correlation Function
Self van Hove Correlation Function
Collective van Hove Correlation Function
Self Intermediate Scattering Function
Collective Intermediate Scattering Function
Bond Orientational Order Parameter
Current Correlation Function
Electric Current Correlation Function
All quantities support center of mass calculation

Since the publication of the original LiquidLib, we have also added MPI parallelization, current correlation function, electric current correlation function, and fixed several bugs. The center of mass calculation are also enable for all quantities. These additions will be published in an extension paper soon and can currently be found in the stable version.

We are keeping adding new features to LiquidLib in the develop version. For instance, CUDA acceleration for the calculation with NVIDIA GPU can be found in the develop version. We will merge them into the stable version once the new features are testified to be stable.

Reference

If used, please cite the following reference:

N. P. Walter, A. Jaiswal, Z. Cai, and Y. Zhang, “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,” Computational Physics Communications, vol. 228, pp. 209–218, 2018. [ DOI ]

Contact

This project is developed and maintained by Z Lab. Current active developers:

Shao-Chun Lee (2019 - Present)

Previous developers:

Yanqin Zhai (2018 - 2023)
Zhixia Li (2018 - 2021)
Nathan Walter (2015 - 2020)
Zhikun Cai (2015 - 2020)
Abhishek Jaiswal (2015 - 2017)

For obtaining user support please contact us at Z Lab.