AMEP: The active matter evaluation package for Python

The Active Matter Evaluation Package (AMEP) is a Python library for analyzing simulation data of particle-based and continuum simulations. It provides a powerful and simple interface for handling large data sets and for calculating and visualizing a broad variety of observables that are relevant to active matter systems. Examples range from the mean-square displacement and the structure factor to cluster-size distributions, binder cumulants, and growth exponents. AMEP is written in pure Python and is based on powerful libraries such as NumPy, SciPy, Matplotlib, and scikit-image. Computationally expensive methods are parallelized and optimized to run efficiently on workstations, laptops, and high-performance computing architectures, and an HDF5-based data format is used in the backend to store and handle simulation data as well as analysis results. AMEP provides the first comprehensive framework for analyzing simulation results of both particle-based and continuum simulations (as well as experimental data) of active matter systems. In particular, AMEP also allows it to analyze simulations that combine particle-based and continuum techniques such as used to study the motion of bacteria in chemical fields or for modeling particle motion in a flow field for example.主动物质评估套件（Active Matter Evaluation Package，简称AMEP）是一款用于分析粒子模拟与连续介质模拟数据的Python库。该套件提供简洁高效的接口，可处理大规模数据集，并能计算与可视化主动物质（active matter）系统相关的各类可观测量。此类可观测量的示例涵盖均方位移、结构因子、团簇尺寸分布、Binder累积量以及生长指数等。AMEP采用纯Python编写，依托NumPy、SciPy、Matplotlib及scikit-image等高性能开源库实现功能。对于计算成本较高的方法，套件进行了并行化与优化处理，可在工作站、笔记本电脑以及高性能计算架构上高效运行；其后端采用基于HDF5的数据格式存储与管理模拟数据及分析结果。AMEP是首个可全面分析主动物质系统的粒子模拟、连续介质模拟（乃至实验数据）结果的综合性框架。尤为关键的是，AMEP还支持分析融合粒子与连续介质技术的模拟场景，例如用于研究化学场中细菌运动，或是模拟流场内粒子运动的相关场景。