Data for: "Filler-induced heterogeneous nucleation of polymer crystals investigated by molecular dynamics simulations"

All of the simulations for this publication were performed with LAMMPS version lammps/intel-2020.4/29Sep2021 This dataset contains the input files for the publication "Filler-induced heterogeneous nucleation of polymer crystals investigated by molecular dynamics simulations" The folder structure splits into - two_wall_systems (contains surfaces (wall) potentials top and bottom of the simulation cell) and - bulk_systems (fully periodic without surfaces). Within each of these, there are "cooling" and "heating" subfolders, and these are further subdivided into cooling/heating rates. The subfolders include one or more of the following: 0.25Gamma0, 0.5Gamma0, Gamma0, 2Gamma0, 10Gamma0 which correspond to the rates in the paper, labelled similarly. The bulk_systems were only performed at the Gamma0 cooling and heating rate. In the bulk_systems, the folders are further subdivided indicating different chain stiffnesses, including - k1 (chain stiffness of ktheta=1) - k2 (chain stiffness of ktheta=2) - k2.4 (chain stiffness of ktheta=2.4) - k3 (chain stiffness of ktheta=3) - k4 (chain stiffness of ktheta=4) In the two_wall_systems, these folders are further subdivided indicating the chain stiffness and the wall interaction strength, for example: - k2.4_wall090 (chain stiffness of ktheta=2.4, wall strength epsilon_w=0.9) - k2.4_wall180 (chain stiffness of ktheta=2.4, wall strength epsilon_w=1.8) - k2.4_wall270 (chain stiffness of ktheta=2.4, wall strength epsilon_w=2.7) Note that for the surface simulations only systems with a chain stiffness of ktheta-2.4 were simulated. All simulations only require two files to run: 1) input file, named in.* 2) molecule template file, named *.txt or a data file named data.* The input file details simulation box dimensions, geometry and forcefield potentials as well as which ensemble to perform the molecular dynamics simulations in. The molecule template file details the coordinates of all beads that make up a single polymer chain. A data file will be generated at the end of the simulation. A lammps trajectory file will also be produced using unwrapped coordinates. For example, to find the files corresponding to a bulk system with a chain stiffness of k=3, cooling down at a rate of Gamma0, the directory path is: bulk_systems > cooling > Gamma0 > k3 > {chainfinaltest.txt, in.cool} where in.cool is the input file and chainfinaltest.txt is the molecule template file. As a second example, to find the files corresponding to a surface system with a chain stiffness of k=2.4 and a wall strength of 1.8, heating at a rate of 2Gamma0, the directory path is: two_wall_systems > heating > 2Gamma0 > k2.4_wall180 > {data.quench_npt, in.heat} where in.heat is the input file and data.quench_npt is the data file.

本论文的所有模拟均通过LAMMPS版本lammps/intel-2020.4/29Sep2021完成。本数据集包含论文《基于分子动力学模拟的填料诱导聚合物晶体异质形核研究》（原英文标题："Filler-induced heterogeneous nucleation of polymer crystals investigated by molecular dynamics simulations"）的输入文件。
文件夹结构分为两大类别：
1. two_wall_systems（双壁体系）：包含模拟盒上下壁面的势函数文件；
2. bulk_systems（体相体系）：无表面、采用全周期性边界条件的体系。
每个类别下均设有"cooling（冷却）"与"heating（升温）"子文件夹，二者进一步按冷却/升温速率细分。子文件夹包含以下一种或多种速率组别：0.25Gamma0、0.5Gamma0、Gamma0、2Gamma0、10Gamma0，与论文中标记的速率一一对应。
体相体系仅在Gamma0的冷却与升温速率下开展模拟。体相体系的文件夹还会按不同的链刚度进一步细分，涵盖：
- k1（键角刚度k_θ=1）
- k2（键角刚度k_θ=2）
- k2.4（键角刚度k_θ=2.4）
- k3（键角刚度k_θ=3）
- k4（键角刚度k_θ=4）
双壁体系的文件夹则同时按链刚度与壁面相互作用强度细分，示例如下：
- k2.4_wall090（链刚度k_θ=2.4，壁面作用强度ε_w=0.9）
- k2.4_wall180（链刚度k_θ=2.4，壁面作用强度ε_w=1.8）
- k2.4_wall270（链刚度k_θ=2.4，壁面作用强度ε_w=2.7）
需注意，表面模拟仅采用了链刚度为k_θ=2.4的体系。
所有模拟仅需两个文件即可运行：
1. 输入文件，命名格式为in.*；
2. 分子模板文件，命名为*.txt，或数据文件命名为data.*。
输入文件用于指定模拟盒尺寸、几何结构、力场势函数以及分子动力学模拟所用的系综；分子模板文件用于描述单条聚合物链所有珠子的坐标。模拟结束后将生成数据文件，同时还会输出采用未包裹坐标的LAMMPS轨迹文件。
示例1：若需查找链刚度为k=3、以Gamma0速率冷却的体相体系对应文件，其目录路径为：bulk_systems > cooling > Gamma0 > k3 > {chainfinaltest.txt, in.cool}，其中in.cool为输入文件，chainfinaltest.txt为分子模板文件。
示例2：若需查找链刚度k=2.4、壁面作用强度1.8、以2Gamma0速率升温的表面体系对应文件，其目录路径为：two_wall_systems > heating > 2Gamma0 > k2.4_wall180 > {data.quench_npt, in.heat}，其中in.heat为输入文件，data.quench_npt为数据文件。