Copyright © 2002–2016 by A. Miyoshi
GPOP reference manual - gpop1scf
[Top]

GPOP reference manual - gpop1scf

Synopsis

gpop1scf basename[.ext] [-csv/-xyz/-txt/-all]

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

  The input file should contain the output of at least one frequency calculation job.   Although the program has been used and tested for Gaussian 94, 98, 03, and 09 jobs, but has not been tested for all possible options of Gaussian.   It is recommended to check the basename.gpo output file for first use, even if the program seems to terminate normally.

Output

Default output
  By default, the program creates two new files named as 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.)
CSV output
  CSV-format output, 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.
XYZ output
  XYZ-format output, 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.
TXT output
  Text format output, 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.
Other output
  With the -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

Frequency scaling and zero-point energy
  If the method for quantum chemical calculation and the basis set used match with those registered inside of 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).
  Currently, following four types of SCF calculations are recognized by gpop1scf, and automatic scaling is done in thermodynamic function calculations (gpop4thf) and TST calculations (tstrate).
Table 1. Methods recognized by GPOP
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
[CBSB7 = 6-311G(2D,D,P)]
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
Note that the f GT only affects the zero-point energy (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.
  The scaling factors can be changed by using 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.