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Apr. 20, 2020

Pilgrim 2.0: A thermal rate constant calculator and a chemical kinetics simulator

David Ferro-Costas [a], Donald G. Truhlar [b], Antonio Fernandez Ramos [a]
[a] Universidade de Santiago de Compostela, Santiago, Spain
[b]University of Minnesota, Minneapolis, Minnesota 55455, USA

Pilgrim status:

Currently available version at this site: version 2.0
Date of manuscript describing v2.0 (available below): April 20, 2020
Date of manual for v2.0 (available below): Feb. 6, 2020

Pilgrim 2.0 description:

        Pilgrim is a program for direct dynamics calculations of thermal rate constants of chemical reactions and simulations of chemical kinetics mechanisms. For reaction processes with many elementary steps, each of the steps can be calculated using conventional transition state theory (TST) or variational transition state theory (VTST), in particular canonical variation theory (CVT) with the small-curvature tunneling approximation (SCT), which involves the calculation of minimum-energy paths (MEPs).
        The above methodologies are available for reactions involving a single structure and for reactions involving flexible molecules with multiple conformations of the reactants and/or transition states. In particular, for systems with many conformers the program can evaluate each of the elementary reactions by multi-path canonical variational transition state theory (MP-CVT) or multi-structural VTST (MS-VTST). Torsional anharmonicity can be also incorporated through the MSTor and Q2DTor programs.
        Pilgrim can also performs dual-level calculations automatically. For this option, the first step is a low-level calculation, and the second step involves higher-level single-point energy calculations of the reactants, transition state, points along the MEP, and products. The low-level calculations are corrected with the high-level single point energies using the interpolated single-point energies (ISPE) algorithm.
        When all the rate constants of the chemical processes of interest are known, by means of their calculation using Pilgrim or by using an analytical rate constant expression, Pilgrim can simulate a complex reaction process using kinetic Monte Carlo (KMC). This algorithm performs a kinetics simulation, monitors the evolution of each chemical species with time, and provides the chemical yields.

Pilgrim citation:

We request that publications of work carried out with Pilgrim give the first reference below and optionally also the second.

1. D. Ferro-Costas , D. G. Truhlar, and A. Fernández-Ramos, Pilgrim: A Thermal Rate Constant Calculator and a Chemical Kinetics Simulator, Computer Physics Communications 256, 107457/133 (2020). doi.org/10.1016/j.cpc.2020.107457
2. D. Ferro-Costas, D. G. Truhlar, and A. Feranndez-Ramos, Pilgrim-version 2.0; University of Minneapolis, Minnesota, MN, USA and Universidade de Santiago de Compostela, Santiago, Spain; 2019. https://comp.chem.umn.edu/pilgrim and https://github.com/daferro/Pilgrim

We request that publications of work carried out with modified versions of Pilgrim state that the work was done with a modified version of Pilgrim and give the first reference above.

Pilgrim license:

Pilgrim is distributed under the MIT license. See https://mit-license.org

To obtain Pilgrim:

Users can obtain version 2.0 of Pilgrim from the CPC library at https://dx.doi.org/10.17632/24cj4dwxvg.1
The latest version can be obtained at https://github.com/cathedralpkg/Pilgrim/releases

Pilgrim manuscript:

Download Pilgrim manuscript

Pilgrim manual:

Download Pilgrim manual

Links to other pages of interest:

This document last modified on Oct. 20, 2022
Updated by:  Software Manager