LUNAR: Automated input generation and analysis for reactive LAMMPS simulations input and output files

Generating molecular models for the LAMMPS molecular dynamics (MD) simulation software package is a difficult task and is an impediment to the more widespread and efficient use of MD in materials design and development. Fixed-bond force fields generally require manual assignment of atom types, bonded interactions, charges, and simulation domain sizes. A new LAMMPS pre- and post-processing toolkit (LUNAR) is presented that efficiently builds molecular systems for LAMMPS. LUNAR automatically assigns atom types, generates bonded interactions, assigns charges, and provides initial configuration methods to generate large molecular systems. LUNAR can also incorporate chemical reactivity into simulations using fixed-bond force fields by facilitating the use of the REACTER protocol. Additionally, LUNAR provides post-processing for free volume calculations, cure characterization calculations, and property predictions from LAMMPS thermodynamic outputs. LUNAR has been validated via building and si..., The data was collected using LAMMPS version April 7th, 2022, , # LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations Input and Output files [https://doi.org/10.5061/dryad.h18931zv1](https://doi.org/10.5061/dryad.h18931zv1) This dataset contains all LAMMPS output data files generated during the benchmarking of the LUNAR software. ## Description of the data and file structure The naming of the files should provide enough guidance on what each file is. Here are a few notes about the naming convention: * The \"pxld\" stands for percent crosslinked where the trailing number is the crosslinking percent (i.e. \"pxld_10\", means 10% crosslinked). * The \"replicate\" stands for the replicate identifier (i.e. \"replicate_1\", means it is replicate 1 from the manuscript). * The \"initial_configuration\" means this file was input to LAMMPS to start the first MD simulation with LAMMPS. * All \".data\" file extensions are LAMMPS data files * All \".script\" extensions are LAMMPS input files * All \".lmpmol\" extensions are LAMMPS mole...为LAMMPS分子动力学（Molecular Dynamics, MD）模拟软件包生成分子模型是一项极具挑战性的工作，也是制约MD在材料设计与开发中更广泛、高效应用的核心阻碍。固定键合力场通常需要手动指派原子类型、键合相互作用、电荷以及模拟计算域尺寸。本文提出一款全新的LAMMPS前后处理工具集（LUNAR），可高效为LAMMPS构建分子系统。LUNAR能够自动完成原子类型指派、键合相互作用生成、电荷分配，并提供可生成大规模分子系统的初始构型方案。通过便捷调用REACTER协议，LUNAR还可在固定键合力场的模拟中融入化学反应特性。此外，LUNAR还支持基于LAMMPS热力学输出结果的后处理工作，涵盖自由体积计算、固化表征计算以及材料性能预测。研究团队已通过构建与[...]完成了LUNAR的验证，本次数据集采用2022年4月7日版本的LAMMPS进行采集。 # LUNAR：面向反应式LAMMPS模拟的自动化输入生成与分析工具 输入与输出文件 [https://doi.org/10.5061/dryad.h18931zv1](https://doi.org/10.5061/dryad.h18931zv1) 本数据集包含了LUNAR软件基准测试过程中生成的全部LAMMPS输出数据文件。 ## 数据与文件结构说明 文件名的命名规则已足以说明各文件的用途，以下为命名约定的几点说明： * "pxld"代表交联百分比，后缀数字即代表交联率（例如"pxld_10"表示交联度为10%）。 * "replicate"代表重复实验标识符（例如"replicate_1"对应论文中的第1组重复实验）。 * "initial_configuration"表示该文件作为LAMMPS的输入文件，用于启动首次分子动力学模拟。 * 所有扩展名为".data"的文件均为LAMMPS数据文件 * 所有扩展名为".script"的文件均为LAMMPS输入脚本文件 * 所有扩展名为".lmpmol"的文件均为LAMMPS分子[...]