POLYRATE 6.5: A New Version of a Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics
Rozeanne STECKLER,a Wei-Ping HU,b Yi-Ping LIU,b Gillian C. LYNCH,b Bruce C. GARRETT,c Alan D. ISAACSON,d Vasilios S. MELISSAS,b Da-hong LU,b Thanh N. TRUONG,b Sachchida N. RAI,b Gene C. HANCOCK,b J. G. LAUDERDALE,b Tomi JOSEPH,b and Donald G. TRUHLARb
aSan Diego Supercomputer Center, P.O. Box 85608, San Diego, CA 92186-9784, USA
bDepartment of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, MN 55455-0431, USA
cEnvironmental Molecular Sciences Laboratory, Pacific Northwest Laboratory, Richland, WA 99352, USA
dDepartment of Chemistry, Miami University, Oxford, OH 45056, USA
Abstract. POLYRATE is a computer program for the calculation of chemical reaction rates of polyatomic species (and also atoms and diatoms as special cases). Version 1.1 was submitted to the CPC Program Library in 1987, and version 4.0.1 was submitted in 1992. Since that time many new capabilities have been added, old ones have been improved, and the code has been made more portable and user-friendly, resulting in the present improved version 6.5. The methods used are variational or conventional transition state theory and multidimensional semiclassical adiabatic and large-curvature approximations for tunneling and nonclassical reflection. Rate constants may be calculated for canonical or microcanonical ensembles or for specific vibrational states of selected modes with translational, rotational, and other vibrational modes treated thermally. Bimolecular and unimolecular reactions and gas- phase, solid-state, and gas-solid interface reactions are all included. Potential energy surfaces may be global analytic functions or implicit functions defined by interpolation from input energies, gradients, and force constants (hessian matrices) at selected points on a reaction path. The data needed for the dynamics calculations may also be calculated from a global potential energy surface with more accurate calculations at stationary points. The program calculates reaction paths by the Euler, Euler stabilization, or Page- McIver methods. Variational transition states are optimized from among a one-parameter sequence of generalized transition states orthogonal to the reaction path. Tunneling probabilities are calculated by numerical quadrature, using either the centrifugal-dominant-small-curvature approximation, the large-curvature-version-3 approximation, and/or optimized multidimensional tunneling approximations. In the large-curvature case the tunneling probabilities may be summed over final vibrational states for exoergic reactions or initial vibrational states for endoergic reactions.
New Version Summary
Title of program: POLYRATE; version: 6.5
Catalogue number: to be assigned by CPC
Program obtainable from: Academic and other non-profit users may obtain the program from an anonymous FTP site at San Diego Supercomputer Center (ftp.sdsc.edu in the directory /pub/sdsc/polyrate), from Quantum Chemistry Program Exchange (Indiana University, Bloomington, IN, U.S.A., program number QCPE 601), or from the CPC Program Library, Queen's University of Belfast, N. Ireland (see application form in this issue). Commercial users may obtain the code from the principal investigator (D.G.T.).
References in CPC for earlier versions of program:
 A. D. Isaacson, D. G. Truhlar, S. N. Rai, R. Steckler, G. C. Hancock, B. C. Garrett, and M. J. Redmon, Computer Physics Communications 47 (1987) 91 (version 1.1).
 D.-h. Lu, T. N. Truong, V. S. Melissas, G. C. Lynch, Y.-P. Liu, B. C. Garrett, R. Steckler, A. D. Isaacson, S. N. Rai, G. C. Hancock, J. G. Lauderdale, T. Joseph, and D. G. Truhlar, Computer Physics Communications 71 (1992) 235 (version 4.0.1).
Catalogue numbers of previous versions: ABBD (version 1.1), ACJC (version 4.0.1)
Does the new version supersede the previous ones: yes
Licensing provisions: Both non-profit and commercial users may obtain license forms and licensing instructions by anonymous FTP from ftp.sdsc.edu (San Diego Supercomputer Center). Licenses and a README file are located in the directory /pub/sdsc/polyrate. There is no license fee for non-profit users; QCPE and CPC apply handling charges, but distribution to non-profit users from the anonymous FTP site is free. Commercial license fees are specified on the license. When requesting a copy of the program from any of the authorized distributors (SDSC, QCPE, or CPC for non-profit use or D.G.T. for commercial use), please supply a signed license by fax or mail.
Computers on which this or another recent version has been tested: Cray- 2, Cray X- MP- EA/4- 64, Cray C90, Silicon Graphics IRIS Indigo R4000, Sun SPARCStation IPX, IBM RS/6000- 550, DEC Alpha Model ?
Operating systems under which the new version has been tested: UNICOS 7.0.5 (Cray-2) UNICOS 7.C.3 (Cray X-MP-EA and Cray C90), IRIX System V.4 Release 5.2 (IRIS), SunOS 4.1.2 (SPARCStation), AIX 3.2.5 (IBM RS/6000), DEC Alpha (?)
Installations: Department of Chemistry, University of Minnesota (IBM RS/6000); University of Minnesota Supercomputing Institute (Cray-2, Cray X-MP-EA, Cray C90, IRIS, and Sun); San Diego Supercomputer Center (Cray C90, Sun, IRIS, and DEC Alpha)
Program language used: ANSI-standard FORTRAN 77 with the INCLUDE and DO WHILE extensions. Exception to standard: subroutine names are in lower case for convenience in using FSPLIT.
Memory required to execute with typical data: 0.6-1.6 Megawords (Cray) or 3-11 Megabytes (workstations)
No. of bits in a word: The program is written in double precision (two 32-bit words), but on the Cray computers it is run with the "disable precision" option, which causes the program to run with single precision. We coded the precision in this way because single precision on Cray computers is 64 bits. Thus the code runs with REAL*8 floating point arithmetic on all machines.
Memory required to execute largest test run: 1.6 Megawords (Cray) or 11.5 Megabytes (workstations)
Peripherals used: disk for input/output
No. of processors used: one
No. of lines in -
FORTRAN and C files: 46,433 manual (Postscript): 119,690 C shell scripts: 4,589 data files for test potentials, utility programs, and test runs: 9,128 output for test runs:  30781 total: 210,621Keywords: chemical reaction rates, activation energy, stationary-point analysis, reaction path, variational transition state theory, small-curvature tunneling, large-curvature tunneling, kinetics, surface science
Nature of the physical problem
The program calculates unimolecular and bimolecular chemical reaction rates of polyatomic species (and also of atoms and diatoms as special cases). Rate constants may be calculated for canonical or microcanonical ensembles and for reactions in the gas phase or solid state or at gas-solid interfaces. In addition, rates may be calculated for adiabatic and diabatic reactions in which one or more of the vibrational modes is restricted to the ground state or to the first excited state, while the translational, rotational, and remaining vibrational modes are treated thermally. The program may also be used to find stationary geometries of reactants, products, and transition states and to calculate reaction paths, Arrhenius parameters, and equilibrium constants.
Method of solution
Energies, gradients, and hessians are obtained from analytic potential energy functions or electronic structure input data. A number of methods are available for calculating the reaction path. Generalized normal mode coordinates are obtained in Cartesian coordinates in the subspace orthogonal to translations, rotations, and the gradient. Anharmonicity may be included under the assumption of independent generalized normal modes. Rate constants may be calculated using either conventional or variational transition state theory [1,2]. Small-curvature, large-curvature, and optimized multidimensional semiclassical tunneling methods [3-5] are available as options to calculate tunneling contributions to transmission coefficients.
Reasons for the new version
To improve stability and efficiency, add new capabilities, and make input preparation more user-friendly.
Summary of revisions
The most important new capabilities since version 4.0.1 (the previous version described in CPC) are
1. The tunneling calculations have been made more stable and efficient. 2. The large-curvature tunneling method has been generalized to allow for a well on the product side of the reaction path in the exoergic direction. 3. Dimension management has been made easier. 4. The VTST-IC method (dual-level direct dynamics) [6,7] has been added. 5. Input has been converted to keyword form. 6. The canonical and microcanonical optimized multidimensional tunneling approximations have been included. 7. An option has been added to allow quantization of the reaction-coordinate motion for unimolecular reactions. 8. Output has been cleaned up and reformatted. 9. The scripts for compilation and job submission have been improved. 10. The manual has been improved and indexed.A complete revision history is given in the manual. Versions 4.1-5.1 were prepared primarily by Yi-Ping Liu, Gillian Lynch, Wei-Ping Hu, Vasilios Melissas, Rozeanne Steckler, Bruce Garrett, Alan Isaacson, and Donald Truhlar. Versions 6.0-6.5 were prepared primarily by Rozeanne Steckler, Wei-Ping Hu, Alan Isaacson, and Donald Truhlar.
Restrictions on the complexity of the problem
The program has PARAMETER control for the maximum number of atoms and maximum number of save points at which reaction-path information is saved; these are set in one of the INCLUDE files, and several sample settings are included in the distributed version. Large-curvature tunneling is available only for thermal rate constants in the harmonic approximation and with analytic potential energy functions. The hindered-internal-rotator anharmonicity option is also supported in runs employing analytic potential energy functions or using the IVTST- 0 method or both.
Typical running times
The running time varies quite a bit, depending mainly on the number of atoms, complexity of the potential, range of reaction coordinate examined, step sizes, and options for anharmonicity and tunneling. The range of computer times in seconds for the 35 gas-phase test runs distributed with the program, the average computer time for these 35 runs, and the range of computer times for the two gas-solid interface test runs distributed with the program on the seven computers tested (in all cases, the code was compiled with optimization "on" at the highest "safe" level, and times refer to execution on a single processor) are given in the following table:
gas-phase gas-phase gas-solid (range) (average) (average) Cray-2 0.7-149 27 338 Cray C90 0.2-94 14 155 Cray X-MP-EA 0.4-195 28 201 IBM RS/6000 1.0-360 39 351 IRIS 0.6-911 98 694 SPARCStation 1.3-1883 204 1688 DEC Alpha 0.5-296 35 347Unusual features of the program
 B. C. Garrett, D. G. Truhlar, R. S. Grev, and A. W. Magnuson, J. Chem. Phys. 84 (1980) 1730.
 D. G. Truhlar, A. D. Isaacson, and B. C. Garrett, in: Theory of Chemical Reaction Dynamics, Vol. 4, ed. M. Baer (CRC Press, Boca Raton, FL, 1985) pp. 65-137.
 D.-h. Lu, T. N. Truong, V. S. Melissas, G. C. Lynch, Y.-P. Liu, B. C. Garrett, R. Steckler, A. D. Isaacson, S. N. Rai, G. C. Hancock, J. G. Lauderdale, T. Joseph, and D. G. Truhlar, Computer Physics Communications 71 (1992) 235.
 Y.-P. Liu, G. C. Lynch, T. N. Truong, D.-h. Lu, D. G. Truhlar, and B. C. Garrett, J. Amer. Chem. Soc. 115 (1993) 2408.
 Y.-P. Liu, D.-h. Lu, A. Gonzalez-Lafont, D. G. Truhlar, and B. C. Garrett, J. Amer. Chem. Soc. 115 (1993) 7806.
 W.-P. Hu, Y.-P. Liu, and D. G. Truhlar, J. Chem. Soc. Faraday Trans. 90 (1994) 715.
 J. C. Corchado, J. Espinosa-Garcia, W.-P. Hu, I. Rossi, and D. G. Truhlar, J. Phys. Chem. 99 (1995) 687.