Ran Y A, Sharma S, Balestra S R G, Li Z, Calero S, Vlugt T J H, Snurr R Q, Dubbeldam D
Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands.
J Chem Phys. 2024 Sep 21;161(11). doi: 10.1063/5.0226249.
We present RASPA3, a molecular simulation code for computing adsorption and diffusion in nanoporous materials and thermodynamic and transport properties of fluids. It implements force field based classical Monte Carlo/molecular dynamics in various ensembles. In this article, we introduce the new additions and changes compared to RASPA2. RASPA3 is rewritten from the ground up in C++23 with speed and code readability in mind. Transition-matrix Monte Carlo is added to compute the density of states and free energies. The Monte Carlo code for rigid molecules is based on quaternions, and the atomic positions needed in the energy evaluation are recreated from the center of mass position and quaternion orientation. The expanded ensemble methodology for fractional molecules, with a scaling parameter λ between 0 and 1, now also keeps track of analytic expressions of dU/dλ, allowing independent verification of the chemical potential using thermodynamic integration. The source code is freely available under the MIT license on GitHub. Using this code, we compare four Monte Carlo (MC) insertion/deletion techniques: unbiased Metropolis MC, Configurational-Bias Monte Carlo (CBMC), Continuous Fractional Component MC (CFCMC), and CB/CFCMC. We compare particle distribution shapes, acceptance ratios, accuracy and speed of isotherm computation, enthalpies of adsorption, and chemical potentials, over a wide range of loadings and systems, for the grand canonical ensemble and for the Gibbs ensemble.
我们展示了RASPA3，这是一个用于计算纳米多孔材料中吸附和扩散以及流体热力学和传输性质的分子模拟代码。它在各种系综中实现了基于力场的经典蒙特卡罗/分子动力学。在本文中，我们介绍了与RASPA2相比的新增加内容和变化。RASPA3是用C++23从头开始重写的，兼顾了速度和代码可读性。添加了跃迁矩阵蒙特卡罗来计算态密度和自由能。刚性分子的蒙特卡罗代码基于四元数，能量评估所需的原子位置从质心位置和四元数取向重新创建。分数分子的扩展系综方法，其缩放参数λ在0到1之间，现在还跟踪dU/dλ的解析表达式，允许使用热力学积分独立验证化学势。源代码在GitHub上根据MIT许可免费提供。使用此代码，我们比较了四种蒙特卡罗（MC）插入/删除技术：无偏Metropolis MC、构型偏置蒙特卡罗（CBMC）、连续分数组分MC（CFCMC）和CB/CFCMC。我们在广泛的负载和系统范围内，针对巨正则系综和吉布斯系综，比较了粒子分布形状、接受率、等温线计算的准确性和速度、吸附焓以及化学势。
