POLYRATE is a computer program for calculating unimolecular and bimolecular chemical reaction rates of polyatomic species (and also of atoms and diatoms as special cases) from analytic potential energy functions or electronic structure input data. Rate constants are calculated by conventional or variational transition state theory, and tunneling contributions may be estimated by semiclassical small-curvature, large-curvature, and optimized multidimensional tunneling approximations. 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.
A new version of POLYRATE (QCPE 601) is now available. The new version, 6.5, is described in the updated program announcement below. The major changes as compared to the previous version distributed by QCPE (version 5.0.1) are as follows:
1. Modular keyword input has been introduced.
2. A new way to interface dynamics with electronic structure theory and global potential energy functions, variational transition state theory with interpolated corrections (VTST-IC), has been implemented.
3. The canonical and microcanonical optimized tunneling approximations have been implemented.
4. An option has been added to allow quantization of the reaction-coordinate motion for unimolecular reactions.
5. Output has been cleaned up and reformatted.
6. The scripts for compilation and job submission have been improved, and a script for checking test run results has been added.
7. Several minor bugs have been corrected.
8. The manual has been improved and indexed.
The new version of POLYRATE will retain the QCPE catalog number 601.
At this time QCPE will also begin to distribute POLYRATE's sister program, MORATE. (MORATE was previously distributed only by Computer Physics Communications Program Library and by the authors.) MORATE is an interface of POLYRATE with MOPAC-version 5.05mn. The latter is a very portable version of MOPAC developed and enhanced at the University of Minnesota. Whereas POLYRATE obtains the required energy, gradient, and hessian data for its dynamics calculations from analytic potential energy surfaces or electronic structure input files, MORATE calculates all energies, gradients, and hessians "on the fly" by carrying out MINDO/3, MNDO, AM1, PM3, or NDDO-SRP calculations as required. This makes it particularly convenient for studying organic reactions. The interested reader is referred to a published paper describing an earlier version (4.5) of MORATE (Ref. 1) and three prototype application papers (Refs. 2 and 3):
1. T. N. Truong, D.-h. Lu, G. C. Lynch, Y.- P. Liu, V. S. Melissas, J. J. P. Stewart, R. Steckler, B. C. Garrett, A. D. Isaacson, A. Gonzalez-Lafont, S. N. Rai, G. C. Hancock, T. Joseph, and D. G. Truhlar, Computer Physics Communications 75 (1993) 143.
2. 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.
3. Y.-P. Liu, D.-h. Lu, A. Gonzalez-Lafont, D. G. Truhlar, and B. C. Garrett, J. Amer. Chem. Soc. 115 (1993) 7806.
4. J. C. Corchado, J. Espinosa-Garcia, W.-P. Hu, I. Rossi, and D. G. Truhlar, J. Phys. Chem. 99 (1995) 687.
The present version of MORATE is called 6.5/P6.5-M5.05 or, for short, 6.5. The longer designation indicates that MORATE 6.5 is based on POLYRATE 6.5 and MOPAC 5.05mn.
Both codes are copyrighted and licensed. QCPE is an authorized distributor for non-profit licenses. (Commercial licensing is handled by the principal investigator, D.G.T.) QCPE can supply copies of the license by fax or e-mail, and the license is also available on the QCPE internet server. QCPE distribution fees are computed from the standard QCPE rate schedule.
The program listing for MORATE is given at the end of this bulletin in the new programs section. An updating listing for the new version of POLYRATE is given below.
Updated Program Listing for POLYRATE
601. POLYRATE: A Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics (version 6.5)
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
bDepartment of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-043l
cEnvironmental Molecular Sciences Laboratory, Battelle Pacific Northwest Laboratories, Richland, WA 99352
dDepartment of Chemistry, Miami University, Oxford, OH 45056
POLYRATE is a computer program for the calculation of chemical reaction rates of polyatomic species and also atoms and diatoms as special cases.1,2 The methods used are variational or conventional transition state theory3,4 and multidimensional semiclassical approximations for tunneling and nonclassical reflection. The tunneling methods in version 6.5 include the centrifugal-dominant small-curvature adiabatic approximation,2,5 the large-curvature, version-3 approximation, including tunneling into excited states in the exoergic direction,2 and the canonical and microcanonical optimized multidimensional tunneling approximations.6 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 interface7 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 (hessians) at selected points on a reaction path. 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. Various anharmonicity options are available.
The program is completely described in a manual which is distributed as a Postscript file as part of the program package. The dimensions are easily adjustable to allow the user to create the smallest possible executable file for a given computational need.
POLYRATE-version 6.5 requires a license. Copies of the non-profit license may be obtained from QCPE, the principal investigator (Donald G. Truhlar), or Rozeanne Steckler and must be signed and returned to QCPE with the program order. There is no additional fee above the usual QCPE service charge for the license if the program is to be used for non-profit or academic research. Persons who want to obtain a commercial license should contact the principal investigator directly.
References:
1. 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) 91-102. (version 1.1)
2. 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) 235-262. (version 4.0.1)
3. B. C. Garrett, D. G. Truhlar, R. S. Grev, and A. W. Magnuson, J. Phys. Chem. 84 (1980) 1730-1748.
4. 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.
5. 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) 2408-2415.
6. Y.-P. Liu, D.-h. Lu, A. Gonzalez-Lafont, D. G. Truhlar, and B. C. Garrett, J. Amer. Chem. Soc. 115 (1993) 7806-7817.
7. S. E. Wonchoba and D. G. Truhlar, J. Chem. Phys. 99 (1993) 9637-9651.
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ANSI-standard FORTRAN77 (except that subroutine names are lower case) with the INCLUDE and DO WHILE extensions. Tested successfully on Cray C90, Cray X-MP-EA, and Cray-2 under UNICOS 7.0.5 and 7.C.3, IBM RS/6000- 550 under AIX 3.2.5, Silicon Graphics IRIS Indigo R4000 under IRIX System V.4 Release 5.2, and Sun SPARCStation IPX under SunOS 4.1.2
Lines of code, including FORTRAN source, Postscript manual, input and partial output for 37 test runs, and C shell scripts for making Unix command files: 210,621