Subject: polyrate

From: <[email-masked]>
Date: Wed, 8 Feb 95 19:15:38 CST

With respect to:

>I am trying to model the chemical reactions of some polyatomic
>gases on the polysilicon surface. Firstly, I want to calculate the reaction
>constants of those reactions and I found that the QCPE program "Polyrate"
>would fit this purpose. Is there any other possibilities?
>And does anybody know the contact point(fax or e-mail) of Donald G. Truhlar
>who is one of authors of "Polyrate"?
>Any suggestions shall be greatly appreciated.
>Bye.
>
>Jai K. Shin

We (Rozeanne Steckler, Wei-Ping Hu, Ivan Rossi, and myself) have just 
completed POLYRATE 6.5, and we are finishing a few small details on the 
documentation.  We also expect to have MORATE 6.5 done very soon.

I do not recommend using older versions.  Versions 6.5 have a new form for
the keyword input, which I hope will be stable over a reasonable period of
time.  However, the input differs from previous input so new users will want to
start with 6.5 rather than start with an older version and then convert.

I am preparing a mailing describing the new versions and explaining the 
licensing, distribution, etc.  I plan to send the mailing out by postal
mail (i.e., the kind that uses stamps and envelopes) before the end of 
the month.

The new versions of both codes will be distributed by San Diego Supercomputer 
Center, by QCPE, and through the Computer Physics Communication Program 
Library.  Further details will be available soon in my mailing and also in the
May issue of QCPE Bulletin.

If you would like to receive the mailing when it is ready, please send me your 
name and mailing address, and I will send you a personal copy when everything
is ready.

Background:

     POLYRATE (version 4.0.1 is described in Ref. 1) 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 variational transition state theory (Ref. 2), 
and tunneling contributions may be estimated by semiclassical small-curvature 
and large-curvature 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.

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 data in 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 (or Si chemistry).  The interested reader is referred to a 
published paper describing an earlier version (4.5) of MORATE (Ref. 3) and 
two prototype application papers (Refs. 4 and 5):

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.

2.  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.

3.  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.

4.  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.

5.  Y.-P. Liu, D.-h. Lu, A. Gonzalez-Lafont, D. G. Truhlar, and B. C. 
Garrett, J. Amer. Chem. Soc. 115 (1993) 7806.

POLYRATE is written in portable FORTRAN 77 with the INCLUDE and DO WHILE
extensions.  It is tested on Cray, IBM, Silicon Graphics, and Sun computers.

Don Truhlar
[email-masked]