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GPOP reference manual - gpop3tst
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GPOP reference manual - gpop3tst

Synopsis

gpop3tst basename [-tst/-ath]

Description

  gpop3tst makes modifications to a GPOP-format file, basename.gpo, according to the modification information file, basename.mod, before the thermodynamic and/or rate constant calculations.
  The corrections or additions that it can make are: electronic degeneracy, low energy electronic states, rotational symmetry number, number of isomers, the energy for rate constant calculation, intramolecular rotations, and the flag indicate transition state.

Input

  The program expects following two input files in the current directory.
1) A GPOP-format file, basename.gpo.
2) A modification information file, basename.mod.
The program gpop1scf creates a template modification file, basename.mod (or basename_.mod). For example, if the sample Gaussian output, ethyl500.log, is processes, the newly created modification template file, ethyl500.mod (or ethyl500_.mod), looks like;
! gElec 2
! rotSymNbr 1
! numIsomers 1
! isTS false
! energyTST #
! setIntRotor idVib nSym moi1 moi2 V0 comment
Any characters from an exclamation mark '!' to the end of the line are comments. The template file include typical keys and value as comments.
  The values for gElec (degeneracy of the elctronic state), rotSymNbr (rotational symmetry number), numIsomers (number of isomers), and isTS (flag indicates transition state) are the default that are already set in the GPOP-format file. Thus, if these values are correct, leave them commented out, but if any value is wrong, remove '!' and a white space follows, and type correct value. See below for the other keys.
Valid Keys in .mod file
gElec degeneracy
  Degeneracy of the electronic state including both the electronic spin degeneracy and the electronic angular momentum degeneracy.
default: determined from the output (Gaussian, note-1; MOLPRO, note-2)
pntGrp point_group
  Point group of the molecule.
default: determined from the output (Gaussian), or "C1" (MOLPRO, note-2)
elState state_sym
  Symmetry of the electronic state.
default: determined from the output (Gaussian), or "A" (MOLPRO, note-2)
eStates nEstates (g energy)*nEstates
  Fine elctronic states specification. If this key is specified, the gElec key is completely ignored. nEstates is the number of electronic states, followed by nEstates pairs of (g energy) where g and energy are the degeneracy and the energy (in cm–1 unit) of each state. Below is an example for the OH radical with 2Π3/2 and 2Π1/2 spin-orbit states;
eStates 2 2 0. 2 139.21
rotSymNbr sigma
  Rotational symmetry number.
default: determined from the output (Gaussian, note-3), or "1" (MOLPRO, note-2)
numIsomers nIsomers
  Number of isomers.
default: determined from the output (Gaussian, note-4), or "1" (MOLPRO, note-2)
isomStates nIsomSts (n energy)*nIsomSts
  Isomeric species specifications. If this key is specified, the numIsomers key is ignored. nIsomSts is the number of isomeric species, followed by nIsomSts pairs of (n energy) where n and energy are the number of occurrence and the energy (in cm–1 unit) of each isomeric species.
isTS flag
  A flag indicates the transition state. The value flag must be either of 'true' or 'false'.
default: determined from the Gaussian output (note-5)
energyTST energy
  Energy (in hartree unit) for rate constant calculation, and should correspond to the internal energy at 0 K. Since only the differences (between reactants and transition states, etc.) are significant, the energy can be defined from any zero point, which, however, should be common for all relevant molecules or atoms.
useSCFenergy+ZPE
  This key (without any value followed) tell the program to use SCF level energy corrected for ZPE for rate constant calculations.
scaleFactVib factor
  Change the vibrational-frequency scaling factor to factor.
scaleFactZPE factor
  This key tells the program to use, factor, for the scaling of vibrational frequencies in the zero-point energy calculation.   This affects the results when used with useSCFenergy+ZPE and/or setIntRotor.
setIntRotor idVib nSym moi1 moi2 V0 comment
  Definition of a intramolecular rotor. idVib is the index of the vibrational mode which is treated as a hindered internal rotor. If this index is set to 0 or negative value, gpop3tst automatically detects the most similar vibrational mode (note-6). nSym is the symmetry number of the internal rotation. moi1 and moi2 inputs specifies the intramolecular rotation and the format for these are the same as that in gpop6irt program. V0 is the height of the hindrance potential. if a positive V0 input is found, the value is used for calculation. If V0 is zero, it is treated as a free rotor. If V0 is negative, V0 is calculated from the eq. (2) below. comment is an optional comment field. The vibrational frequency is scaled by scaleFactZPE for the quantum mechanical correction and for the estimation of V0, in order to keep the consistency of zero-point energy.
Notes
note-1 (gElec)
Since the Gaussian often fails to determine the degenerated electronic states of highly symmetric molecules, the angular momentum degeneracy must be carefully considered by the user.
note-2
These parameters cannot be properly set by gpop2mlp.  These parameters should be carefully investigated and set manually.
note-3 (rotSymNbr)
The rotational symmetry number is determined by the point group identified by the Gaussian. Note that the point group identification by Gaussian is done from the initial geometry specification, and the only slightly asymetric input results in the lower symmetry and thus, the incorrectly small symmetry number.
note-4 (numIsomers)
Only the number of the optical isomers, which is easily determined by the molecular symmetry, is set as the number of isomers by default. This default is not appropriate for hydrocarbon molecules with many rotational conformers. Usually, as far as it is possible to guess the energy of rotational conformers, the use of isomStates key is recommended instead of numIsomers.
note-5 (isTS)
The default is set 'true' if at least one imaginary vibrational frequency was found. This may not be correct for very loose transition states for variational calculations.
note-6 (setIntRotor)
This automatic detection is not always safe. If the corresponding vibrational motion is fairly localized, the result of autodetection is satisfactory, but if it couples strongly with other vibrational mode(s), the results may be inappropriate. See the manual of gpop6mrt for further discussion on this problem.

Output

  The GPOP-format file, basename.gpo, is rewritten.   With "-ath" option in the command line, a template file for the auxiliary thermodynamic input, basename.ath, is also created. (See the manual for gpop4thf for details.)

Calculation details

Intramolecular rotations
  The intramolecular rotor specified by setIntRotor is treated as a sinusoidally hindered rotor with a potential energy curve,
      (1)
where V0 is barrier height, n is the symmetry number of rotation (nSym in setIntRotor), and θ is angle of rotation.   Its partition function and thermodynamic functions are calculated by using Pitzer-Gwin approximation [1] in the programs tstrate and gpop4thf.   The potential barrier height, V0, is estimated from the harmonic frequency of corresponding vibrational mode, ν, as,

  or
      (2)
where B is the reduced rotational constant of the rotor, h is the Planck constant, and  is the wavenumber corresponding to the vibrational frequency.   The barrier height estimation by Eq. (2) is a fairly good approximation for symmetric rotors with moderate barrier height, such as methyl group (–CH3).

Fig. 1.   Sinusoidal potential (n = 3).
Application of this method for asymmetric rotors may be even worse than the harmonic oscillator approximation and must be done carefully.   BEx1D program may be useful for precise analysis of asymmetric rotors, though it requires a few more points of quantum chemical calculations along the rotational coordinate.

References

[1] K. S. Pitzer and W. D. Gwinn, J. Chem. Phys. 10, 428 (1942).