Synopsis
Description
gpop1scf serves as a pre-processor for other programs
in GPOP. It reads in a Gaussian output file containing a
frequency job, extracts essential informations needed for thermodynamic and
rate constants calculations, and stores them in a GPOP-format file named
basename.gpo.
The name of a Gaussian output file should be specified as the first
command-line argument. If the name does not contain any
'.' (dot), a default extension, '.log', is assumed.
An optional second argument, '-csv', '-xyz',
'-txt', or '-all',
controls the additional outputs.
Input
basename.gpo output file for first use, even if the
program seems to terminate normally.
Output
basename.gpo and basename.mod.
If a file named basename.mod already exists in
the current directory, basename_.mod is created
instead.
basename.gpo is a file containing the essentail
results of quantum chemical calculations needed for other programs in
GPOP. As it being a text file with a readable format, users may view
or edit it by text editors if necessary.
basename.mod (or
basename_.mod) is a sample modification file used by
gpop3tst. (See the reference manual for gpop3tst
for details.)
basename.csv, will be
created when either -csv or -all option is
specified. It contains essentially the same information as
basename.gpo, but in comma-delimited format, which
is useful for some manual post precessing with spread-sheet softwares
such as Excel.
basename.xyz, will be
created when either -xyz or -all option is
specified. It may be useful to export optimized geometries to
other quantum chemical calculation packages and molecular viewer
programs.
basename.txt, will be
created when either -txt or -all option is
specified. It contains essential summary of the Gaussian output
in the text format. This option was added for my ad-hoc purpose,
but I myself found it useful for making the calculation summaries
in various formats. Users may also customize the output
by slightly editing the codes in gpop1scf.cc only.
-all option, four files with extensions,
'.frq', '.geo', '.tst', and
'.zpe', will be generated
in addition to the '.gpo', '.mod',
'.csv', and '.xyz' files described above.
These files are in the format of obsolete ancestor software to GPOP,
and this option is preserved for compatibility and diagnostic purposes
only. All of these files are text files.
Calculation details
gpop1scf, it
automatically sets three types of preferred frequency scaling factors.
The first is the preferred scaling factor for (1 ↔ 0) vibrational
transition ( f VIB), the second is the preferred
scaling factor for zero-point energy ( f ZPE),
and the third is the scaling factor for zero-point energy
defined in the procedures of Gaussian Theories, or Complete Basis Set
Methods ( f GT). If the mothod or the basis set is unknown, all three scaling
factors are set to unity (= 1.0).
In basename.gpo, the program prints three
types of zero-point energies,
(1) unscaled, (2) scaled by preferred factor for ZPE, and (3) scaled
as in the Gaussian Theories (or CBS methods), both in the wavenumber
(cm-1) unit and atomic unit (hatreee).
gpop1scf, and automatic scaling is done
in thermodynamic function calculations (gpop4thf) and
TST calculations (tstrate).
| method | f VIB | f ZPE | f GT |
|---|---|---|---|
HF/6-31G(D) |
0.8929 | 0.9135 | 1 / 1.12 (~0.8929) |
MP2/6-311G(D,P) |
0.945 | 0.970 | 0.970 |
B3LYP/6-31G(D) |
0.9613 | 0.9804 | 0.96 |
B3LYP/6-311G(D,P) |
0.97 | 0.99 | 0.99 |
B3LYP/CBSB7 |
0.97 | 0.99 | 0.99 |
B3LYP/6-311G(2D,D,P) |
0.97 | 0.99 | 0.99 |
WB97XD/6-311G(D,P) |
0.949 | 0.974 | 0.974 |
APFD/6-311G(D,P) |
0.97 | 0.99 | 0.99 |
RS2/CC-PVTZ |
0.97 | 0.99 | 0.99 |
RS2/CC-PVDZ |
0.96 | 0.98 | 0.98 |
zpe_GT) written in the '.gpo' file,
and never affect any other calculations. The f ZPE
is used when useSCFenergy+ZPE key is specified in
'.mod' file (see the manual for gpop3tst),
and in the hindered rotor calculations.
The f VIB affects all calculations which
include vibratinal partition function calculations, that is, rate constants
equilibrium constants, and thermodynamic functions.
scaleFactZPE and/or scaleFactVib key(s)
in the '.mod' file.
A more systematic method to customize the scaling factors
is to use methods.dat file. An example file can
be found in the gpop/sample/library directory and
a part of it is shown below.
tableOfMethods{ 4
! slightly changed according to Scott&Radom J.Phys.Chem. 100,16502(1996)
HF/6-31G(d) 0.8953 0.9135 0.892857142857143 ! =1/1.12
B3LYP/6-31G(d) 0.9614 0.9806 0.96
! changed according to Irikura et al. J.Phys.Chem.A 109,8430(2005)
B3LYP/6-311G(d,p) 0.9669 0.99 0.99
B3LYP/CBSB7 0.9669 0.99 0.99
}tableOfMethods
When GPOP components found methods.dat in the current directory
or in the path specified by the GPOP_LIB environment variable,
the content of methods.dat is appended after the default
list shown in Table 1. Since a search is done from the bottom
of the list, the appended part overwrites the default when same methods
were found in the appended part. The file methods.dat
can contain as many number of scaling factors as you want.
The gpop/sample/library directory also contains sample
shell scripts and MS-DOS batch file to set GPOP_LIB
environment variable.