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Pilgrim: A thermal rate constant calculator and a chemical kinetics simulator
Computer Physics Communications ( IF 6.3 ) Pub Date : 2020-11-01 , DOI: 10.1016/j.cpc.2020.107457
David Ferro-Costas , Donald G. Truhlar , Antonio Fernández-Ramos

Abstract Pilgrim is a program written in Python and designed to use direct dynamics in the calculation of thermal rate constants of chemical reactions by the variational transition state theory (VTST), based on electronic structure calculations for the potential energy surface. Pilgrim can also simulate reaction mechanisms using kinetic Monte Carlo (KMC). For reaction processes with many elementary steps, the rate constant of each of these steps can be calculated by means of conventional transition state theory (TST) or by using VTST. In the current version, Pilgrim can evaluate thermal rates using the canonical version of reaction-path VTST, which requires the calculation of the minimum energy path (MEP) associated with each elementary step or transition structure. Multi-dimensional quantum effects can be incorporated through the small-curvature tunneling (SCT) approximation. These methodologies are available both for reactions involving a single structure of the reactants and the transition state and also for reactions involving flexible molecules with multiple conformations of the reactant and/or of the transition state. For systems with many conformers, the program can evaluate each of the elementary reaction rate constants by multipath canonical VTST or multi-structural VTST. Moreover, the reactant can be unimolecular or bimolecular. Torsional anharmonicity can be incorporated through either the MSTor or the Q2DTor programs. Dual-level calculations are also available in Pilgrim: automatic high-level single-point energies can be used to correct the energy of reactants, transition states, products, and MEP points using the interpolated single-point energies (ISPE) algorithm. When the rate constants of all the chemical processes of interest are known, by means of their calculation using Pilgrim or alternatively through analytical fits to the rate constants as functions of temperature, it is possible to simulate a multistep mechanism under specified laboratory conditions using KMC. This algorithm allows performing a kinetic simulation to monitor the evolution of each chemical species with time and obtain the product yields. Program summary Program Title: Pilgrim CPC Library link to program files: http://dx.doi.org/10.17632/24cj4dwxvg.1 Developer’s repository link: https://github.com/cathedralpkg/pilgrim/releases ; https://comp.chem.umn.edu/pilgrim ; https://conservancy.umn.edu/handle/11299/166578 Licensing provisions: MIT Programming language: Python 3 Nature of problem: Calculation of thermal rate constants for bimolecular and unimolecular chemical reactions and simulation of reaction mechanisms Solution method: The program uses variational transition state theory to calculate thermal rate constants and kinetic Monte Carlo to simulate reaction mechanisms. Restrictions and unusual features: The program cannot treat reactions without saddle points. Unimolecular reactions are calculated only in the high-pressure limit. Direct dynamics calculations with Pilgrim require an electronic structure package to be supplied by the user; currently, Pilgrim supports the G a u s s i a n [Frisch et al. (2003), Frisch et al. (2016a), Frisch et al. (2016b)] and O r c a [Neese (2011)] electronic structure packages. Pilgrim has an especially powerful suite of options for handling torsional anharmonicity and multistructural effects.

中文翻译:

Pilgrim:热速率常数计算器和化学动力学模拟器

摘要 Pilgrim 是一个用 Python 编写的程序,旨在通过变分过渡态理论 (VTST) 使用直接动力学计算化学反应的热速率常数,基于势能面的电子结构计算。Pilgrim 还可以使用动力学蒙特卡罗 (KMC) 模拟反应机制。对于具有许多基本步骤的反应过程,可以通过常规过渡态理论 (TST) 或使用 VTST 计算每个步骤的速率常数。在当前版本中,Pilgrim 可以使用标准版本的反应路径 VTST 来评估热速率,这需要计算与每个基本步骤或过渡结构相关的最小能量路径 (MEP)。可以通过小曲率隧穿 (SCT) 近似来合并多维量子效应。这些方法既可用于涉及单一结构的反应物和过渡态的反应,也可用于涉及具有多种反应物和/或过渡态构象的柔性分子的反应。对于具有许多构象异构体的系统,该程序可以通过多路径规范 VTST 或多结构 VTST 评估每个基本反应速率常数。此外,反应物可以是单分子的或双分子的。扭转非谐性可以通过 MSTor 或 Q2DTor 程序合并。Pilgrim 还提供双能级计算:自动高能级单点能量可用于校正反应物、过渡态、产物、和 MEP 点使用插值单点能量 (ISPE) 算法。当所有感兴趣的化学过程的速率常数已知时,通过使用 Pilgrim 进行计算,或者通过对作为温度函数的速率常数进行分析拟合,可以使用 KMC 在指定的实验室条件下模拟多步机制。该算法允许执行动力学模拟以监测每种化学物质随时间的演变并获得产品产率。程序摘要程序名称: Pilgrim CPC 库程序文件链接:http://dx.doi.org/10.17632/24cj4dwxvg.1 开发者存储库链接:https://github.com/cathedralpkg/pilgrim/releases ;https://comp.chem.umn.edu/pilgrim ; https://conservancy.umn.edu/handle/11299/166578 许可条款:MIT 编程语言:Python 3 问题性质:计算双分子和单分子化学反应的热速率常数并模拟反应机理 求解方法:程序使用变分过渡态理论计算热速率常数,使用动力学蒙特卡罗来模拟反应机理。限制和异常功能:该程序无法处理没有鞍点的反应。单分子反应仅在高压极限下计算。Pilgrim 的直接动力学计算需要用户提供电子结构包;目前,Pilgrim 支持 G aussian [Frisch 等人。(2003),弗里施等。(2016a),弗里施等人。(2016b)] 和 Orca [Neese (2011)] 电子结构封装。
更新日期:2020-11-01
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