An open-source implementation of a quasi harmonic approach to compute the intramolecular entropy of particle systems

The implementation of a quasi harmonic approach to determine the intramolecular entropy of particle systems in an open-source python code is presented. The code makes use of platform-independent tools and can be readily transferred to any computer platform which can run python. It is straightforward to incorporate the code into the LAMMPS software as well as into other molecular simulation programs. In the computational part of this work, we evaluate the intramolecular entropy of atactic polystyrene and polyethylene melts in an all atom as well as in a coarse grained (CG) resolution at five temperatures between 400 and 450 K. For both polymers, coarse graining with its reduced system degrees of freedom and its softened bonded radial potential, causes a strong reduction of the entropy. However, the averaged entropy per degree of freedom in the CG case exceeds the one under atomistic resolution. Also the temperature dependence of the intramolecular entropy becomes weaker in the transition from an atomistic to a coarse grained description. The larger entropy of polyethylene in comparison to polystyrene under both resolutions is a consequence of its longer chain length. To simplify a comparison of the two polymers in the two considered resolutions, we analyze the total intramolecular entropy as well as its temperature gradient via a scaling of both quantities by the number of degrees of freedom. In the two studied systems and for both levels of resolution, a linear dependence of the intramolecular entropy on the temperature is identified.本研究介绍了一种准谐波（quasi harmonic）方法的开源Python实现，用于计算粒子系统的分子内熵。该代码采用与平台无关的工具开发，可便捷移植至任意支持Python运行的计算机平台，且可轻松集成至LAMMPS软件及其他分子模拟程序中。在本研究的计算部分，我们针对400 K至450 K范围内的五个温度点，分别以全原子（all atom）和粗粒度（CG）两种分辨率，计算了无规立构聚苯乙烯与聚乙烯熔体的分子内熵。对于两种聚合物而言，粗粒度建模通过缩减系统自由度、软化成键径向势能，会导致熵值显著降低。但粗粒度模型下，单位自由度的平均熵却高于全原子分辨率下的结果。此外，从全原子描述转向粗粒度描述时，分子内熵的温度依赖性会减弱。在两种分辨率下，聚乙烯的熵值均高于聚苯乙烯，这源于其更长的分子链长度。为简化两种聚合物在两种分辨率下的对比分析，我们通过将总分子内熵及其温度梯度按自由度数目进行尺度归一化，对二者展开了分析。在本次研究的两个体系以及两种分辨率下，均发现分子内熵与温度呈线性相关关系。