An open-source implementation of a quasi harmonic approach to compute the intramolecular entropy of particle systems
| Autor: | Michael C. Böhm, Evangelos Voyiatzis |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
Particle system
Physics Quantitative Biology::Biomolecules Computation NumPy Degrees of freedom (statistics) General Physics and Astronomy 01 natural sciences 010305 fluids & plasmas Molecular dynamics Hardware and Architecture Intramolecular force 0103 physical sciences Statistical physics Granularity 010306 general physics Scaling computer computer.programming_language |
| Zdroj: | Computer Physics Communications. 234:286-293 |
| ISSN: | 0010-4655 |
| Popis: | 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. Program summary Program title: IEtool Program Files doi: http://dx.doi.org/10.17632/xn3ccj6kym.1 Licensing provisions: GNU General Public License 3 (GPL) Programming language: Python Dependencies: NumPy Nature of problem: Computation of the intramolecular entropy of particle systems studied by molecular simulations. Solution method: We have implemented a quasi harmonic approach to compute the intramolecular entropy in a Python code. The code is easily integrated into the LAMMPS software [1]. References: 1. S. Plimpton, J. Comput. Phys. 117 (1995) 1–19. Link: http://lammps.sandia.gov/ |
| Databáze: | OpenAIRE |
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