Copyright © 2002–2016 by A. Miyoshi
GPOP reference manual - tstrate
[Top]

GPOP reference manual - tstrate

Synopsis

tstrate basename

Description

  The program tstrate reads a reaction input file, basename.rxn, and GPOP-format files for molecules or atoms described in the reaction input.   Rate constants and/or equilibrium constants are calculated and results are written in a CSV file, basename.csv.
* Note that the vibrational frequencies are scaled when GPOP detects known method for calculation. See Frequency scaling and zero-point energy in gpop1scf reference manual. However, the imaginary frequency for the tunneling correction, it is used UNSCALED.

Input

  The program expects following input files in the current directory.
1) A reaction input file, basename.rxn.
2) GPOP-format files (*.gpo).
  Note: The .gpo files should be pre-processed by gpop3tst before using tstrate.   Even in the case that no modification is needed, it must be pre-processed with a null .mod file.   The energetics is the one of the most important property in the rate constant calculation.   The energy of the reactants and the TS (and/or the products) must be specified either explicitly in the .rxn file, or should have been specified by energyTST in the .mod file.
Reaction input file format
  The reaction input file, basename.rxn, should contain a reactants block and at least one of a products block or a transitionState block.   If a reactants and a products block are found, the program calculates the equilibrium constants for the reaction.   An example reaction input for calculating equilibrium constants for C2H5 → C2H4 + H is shown below.
reactants{
  file ethyl500
}
products{
  file etln500 hatom50
}
Each block should contain at least one file key, specifying the '.gpo' file(s) to be read.   If a reactants and a transitionState block are found, the program calculates the rate constants for the reaction. If all three blocks, reactants, transitionState, and products blocks, are found, the rate constants as well as the equilibrium constants are calculated.   Since the tunneling correction to the rate constants using an asymmetric Eckart potential requires the energy for products, this correction is only made when all three blocks are found.   An example of a reaction input with three blocks is shown below.
reactants{
  file etp500
}
transitionState{
  file tsho501
}
products{
  file hoo500 etln500
}
All valid keys in the blocks or the outside the blocks will be described in detail below.
Keys valid outside the blocks
energyUnit unit
  Changes the unit for energy key in the blocks. Note that this NEVER override the unit of energyTST key in '.gpo' files, which is always hartree. Values may be one of 'hartree' (default), 'kJ/mol', and 'cm-1'.
tempRange T_start T_end T_step
tempRecipRange numer start end step
tempGauChebGrd T_min T_max nT
tempList T1 T2 T3 ...
  Temperatures for calculation. Either tempRange or tempList can be used. Same as these keys in the temperature file format in gpop4thf.
fileType ftyp
  The file type for molecular property input. Valid values are 'gpo' (default) and 'tst'. This is retained for older compatibility.
Keys valid in the blocks
energy engy
  This key overrides the sum of the energies in the molecules (or atoms) in the block. The unit of the energy may be changed by 'energyUnit' key outside the block.
imagFreqTS imgfrq
  This key is valid only in a transitionState block, and is used to override the imaginary frequency used for tunneling corrections. Note that the value should be real and positive, that is, the absolute figure of the imaginary frequency in cm–1 unit.

Output

  The results are written to a csv-format file, basename.csv. An output from the sample input EtO2concHO2elim.rxn is shown below.
The units for equilibrium constants (Keq) and rate constants (k) are in (molecule cm−3), s–1 units. The 'k+Eck' and 'corrEck' are the rate constants corrected for tunneling by assuming asymmetric Eckart potential [4], and the corresponding correction factor. Similarly, 'k+Sh' and 'corrSh' denote those by Shavitt's correction [5].

References

[4] B. C. Garrett and D .G. Truhlar, J. Phys. Chem. 83, 2921 (1979).
[5] I. Shavitt, J. Chem. Phys. 31, 1359 (1959).