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MANUAL Polyrate 2016-2A

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MANUAL Polyrate 2016-2A MANUAL Polyrate 2016-2A Jingjing Zheng, Junwei Lucas Bao, Rubén Meana-Pañeda, Shuxia Zhang, Benjamin J. Lynch, José C. Corchado, Yao-Yuan Chuang, Patton L. Fast, Wei-Ping Hu, Yi-Ping Liu, Gillian C. Lynch, Kiet A. Nguyen, Charles F. Jackels, Antonio Fernandez Ramos, Benjamin A. Ellingson, Vasilios S. Melissas, Jordi Villà, Ivan Rossi, Elena. L. Coitiño, Jingzhi Pu, Titus V. Albu Department of Chemistry Chemical Theory Center, and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455 Artur Ratkiewicz Institute of Chemistry University of Bialystok, Poland Rozeanne Steckler Northwest Alliance for Computational Science & Engineering Oregon State University, Corvallis, Oregon 97331 Bruce C. Garrett Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory, Richland, Washington 99352 Alan D. Isaacson Department of Chemistry and Biochemistry Miami University, Oxford, Ohio 45056 and Donald G. Truhlar Department of Chemistry, Chemical Theory Center, and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455 Program version: 2016-2A Program version date: Nov. 29, 2016 Manual version date: Nov. 29, 2016 Copyright 1989 – 2016 Executive summary: Polyrate is a computer program for the calculation of chemical reaction rates of polyatomic species (and also atoms and diatoms as special cases) by variational transition state theory (VTST); conventional transition state theory is also supported. Bimolecular and unimolecular reactions and gas-phase, solid-state, and gas-solid-interface reactions are all included. Polyrate can perform variational transition state theory (VTST) calculations on reactions with both tight and loose transition states. For tight transition states it uses reaction-path (RP) variational transition state theory of Garret and Truhlar, and for loose transition states it uses variable-reaction-coordinate (VRC) variational transition state theory of Georgievskii and Klippenstein. For RP calculations there are Sept. 3, 2016 POLYRATE–V2016 1 options to use curvilinear coordinates along a minimum energy path or a variationally optimized reaction path and to add multidimensional tunneling contributions by means of a transmission coefficient; the treatment of loose transition states is based on variable- reaction-coordinate VTST with single-faceted and multifaceted dividing surfaces. The methods used for tight transition states are conventional transition state theory, canonical variational transition state theory (CVT), and microcanonical variational transition state theory ( µVT) with multidimensional semiclassical approximations for tunneling and nonclassical reflection. The tunneling approximations available are zero- curvature tunneling (ZCT), small-curvature tunneling (SSCT), large-curvature- tunneling (LCT), and optimized multidimensional tunneling (OMT). The SCT option is the centrifugal dominant semiclassical adiabatic ground-state tunneling, and the LCT options include both LC3 and LC4 including tunneling into excited states. One may also treat specific vibrational states of selected modes with translational, rotational, and other vibrational modes treated thermally. Pressure-dependent rate constants for elementary reactions can be computed using system-specific quantum RRK theory (SS-QRRK) with the information obtained from high-pressure-limit VTST calculation as input by using the SS-QRRK utility code. The SS-QRRK utility program is part of the POLYRATE distribution, and its usage is described in a separate manual. For tight transition states, several options are available for reaction paths, vibrations transverse to the reaction path, and transition state dividing surfaces. Reaction paths may be calculated by the Euler steepest-descent, Euler stabilization, Page-McIver, or variational reaction path algorithms. Vibrations away from the reaction path may be defined by rectilinear, nonredundant curvilinear, or redundant curvilinear coordinates. Generalized-transition-state dividing surfaces may be defined on the basis of gradient directions or by the re-orientation of the dividing surface algorithm. Vibrational frequencies may be scaled or unscaled. For loose transition states, rate constants may be calculated for canonical or microcanonical ensembles or energy and total angular momentum resolved microcanonical ensembles. For loose transition states in barrierless association reactions, single-faceted or multifaceted dividing surfaces based on a variable reaction coordinate are used. Potential energy surfaces may be analytic functions evaluated by subroutines, or they may be implicit surfaces defined by electronic structure input files containing energies, gradients, and force constants (Hessians) at selected points on a reaction path. The use of electronic structure calculations to calculate rate constants or other dynamical quantities without an analytic potential energy surface is called direct dynamics. Analytic surfaces may be used for variational transition state theory and any of the types of tunneling calculations, single-level and dual-level calculations based solely on electronic structure input files may be used for variational transition state theory and zero-curvature or small-curvature tunneling, and dual-level calculations based on using an analytic potential energy surface as the lower level and using an electronic structure Sept. 3, 2016 POLYRATE–V2016 2 input file as the higher level may be used for variational transition state theory and any of the types of tunneling calculations. Polyrate supports six options for direct dynamics, namely (i) straight single-level direct dynamics, (ii) zero-order interpolated variational transition state theory (IVTST-0), (iii) first-order interpolated variational transition state theory (IVTST-1), (iv) interpolated variational transition state theory by mapping (IVTST-M), (v) variational transition state theory with interpolated single-point energies (VTST-ISPE), and (vi) variational transition state theory with interpolated optimized corrections (VTST-IOC). VTST-IOC and VTST-ISPE are examples of dual-level direct dynamics; and VTST-IOC is also called triple-slash dynamics (///), where the triple slash denotes higher-order corrections of the geometries at which energetic and Hessian corrections are calculated. Dual-level methods may be applied with electronic structure data for both levels (dual-level direct dynamics), or it may be applied with an analytical potential energy surface for the lower level and electronic structure data for the higher level. When dual-level methods are employed with electronic structure data for both levels, the lower level may be either straight direct dynamics or IVTST-M. This version of Polyrate contains 112 test runs, and 46 of these are for direct dynamics calculations; 85 of the test runs are single-level runs, and 27 are dual-level calculations. Polyrate is designed to be used in conjunction with interfaces to electronic structure calculations for direct dynamics. Currently the following interfaces are available: Electronic structure package Interface CHARMM with CHARMMRATE CRATE GAMESS (or with GAMESSPLUS) GAMESSPLUSRATE GAUSSIAN 09/GAUSSIAN 03 GAUSSRATE JAGUAR JAGUARATE MC-TINKER MC-TINKERATE MORATE MOPAC MULTILEVEL MULTILEVELRATE NWCHEM NWCHEMRATE Sept. 3, 2016 POLYRATE–V2016 3 CONTENTS TITLE PAGE AND EXECUTIVE SUMMARY ................................................................1 CONTENTS .................................................................................................................................... 4 MANUAL ........................................................................................................................................ 1 PART I GENERAL INFORMATION ....................................................................................... 13 1. INTRODUCTION .........................................................................................................13 2. REFERENCES ...............................................................................................................22 2.A. RECOMMENDED CITATION AND OTHER Polyrate REFERENCES ...........22 2.B. REFERENCES FOR INCORPORATED CODE ..................................................23 3. AVAILABILITY AND LICENSING ............................................................................24 4. POLYRATE SPECIFICS ....................................................................................................25 4.A. Polyrate authors .....................................................................................................25 4.B. Hardware platforms ................................................................................................27 4.C. Compiler versions ..................................................................................................30 5. PROGRAM AND MANUAL DESCRIPTION .............................................................33 5.A. Code description, portability, and special files ......................................................33 5.B. Description of the manual ......................................................................................33 5.B.1. Referencing conventions .................................................................................34 5.B.2. Book chapters ..................................................................................................35 PART II THEORY BACKGROUND AND CALCULATION DETAILS ON RP-VTST .... 36 6. THEORETICAL BACKGROUND ON RP-VTST .........................................................36
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