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GPOP reference manual - gpop3tst

GPOP reference manual - gpop3tst

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GPOP reference manual - **gpop3tst**

Synopsis

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, . |

2) | A modification information file, . |

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 !' and
a white space follows, and type correct value. See below for the other
keys.

`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 'Valid Keys in .mod file

Degeneracy of the electronic state including both the electronic
spin degeneracy and the electronic angular momentum degeneracy.

Point group of the molecule.

Symmetry of the electronic state.

Fine elctronic states specification. If this key is specified,
the ^{–1} unit) of each state. Below is an example for
the OH radical with ^{2}Π_{3/2} and
^{2}Π_{1/2} spin-orbit states;

`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
cmeStates 2 2 0. 2 139.21

Rotational symmetry number.

Number of isomers.

Isomeric species specifications. If this key is specified, the
^{–1} unit) of each isomeric species.

`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
A flag indicates the transition state. The value

*flag*

must be either of '`true`

'
or '`false`

'.
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.

This key (without any value followed) tell the program to use
SCF level energy corrected for ZPE for rate constant calculations.

Change the vibrational-frequency scaling factor to

*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`

.
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, **gpop4thf**
for details.)

*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 Intramolecular rotations

The intramolecular rotor specified by *V*_{0} is barrier height, *n* is the
symmetry number of rotation (*θ* is angle of rotation.
Its partition
function and thermodynamic functions are calculated by using
Pitzer-Gwin
approximation [1] in the programs
*V*_{0},
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 (–CH_{3}).

`setIntRotor`

is treated as a sinusoidally hindered rotor with a potential energy
curve,
(1)

where `nSym`

in
`setIntRotor`

), and `tstrate`

and `gpop4thf`

.
The potential barrier height, or

(2)

Fig. 1. Sinusoidal potential (

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). |