- DISCOVER
The file names for DISCOVER files can be file_name.car
,
file_name.cor
, or file_name.arc
. The base name is used to
construct the file name file_name.hessian
(the file with frequencies
and normal coordinates). All necessary data are extracted from these files.
- DMOL/DSOLID/DMOL3
The necessary data are collected from the .outmol
file.
- GAMESS
GAMESS output files are first checked for the occurrence of the string
GAMESS
. If it is found the necessary data are collected from this file.
- GAUSSIAN 9X
Gaussian output files are first checked for the occurrence of the string
Entering Gaussian System
. If it is found the necessary
data are collected from this file. To use the wave function related topics in
VIEWMOL with GAUSSIAN outputs GAUSSIAN must run with
GFPRINT
and Iop(5/33=1)
3 to print basis set and MO coefficients. Due to the vastly different
outputs created by the GAUSSIAN 9X series of programs, it is not guaranteed
that a particular output can be successfully read. The common types of output have
been tested, but non-default routes through the program might have generated
output which cannot be read.
- MOPAC/Vamp
VIEWMOL first checks for the presence of a file with the extension .gpt
and the same basename as the MOPAC output file. This file is generated if
MOPAC has been run with the keyword GRAPH
. If such a file is found
coordinates, basis functions, and MO coefficients are read from this file. If such
a file does not exist, coordinates are read from the MOPAC output file under
the header CARTESIAN COORDINATES
. Finally, vibrational frequencies and normal
modes are read from the MOPAC output file, if present.
- PDB files
Only the cartesian coordinates and atomic symbols are read from this file,
the connectivity information is ignored and will be determined by VIEWMOL
itself.
- PQS
Coordinates are read from the section identified by Coordinates (Angstroms)
.
Forces, the energy, vibrational frequencies, and normal modes are collected from
the corresponding sections of the output.
- TURBOMOLE
The program reads the following data groups from the control
file:
$atoms
$basis
$pople
The basis functions are read from these data groups. These data will be read
only if they are available.
$closed shells
, $alpha shells
, $beta shells
These data group are read to determine which molecular orbitals are occupied
by how many electrons. The data is necessary for the calculation of electron
densities.
$coord
The cartesian coordinates of the molecule calculated. This data group
must be available.
$grad
The cartesian coordinates and gradients of all previous steps of a geometry
optimization. This data group will be read only if it is available.
$scfmo
The symmetry labels, energies, and MO coefficients for closed shells are read
from this data group. These data will be read if they are available and if the
file contains either converged or first order molecular orbitals.
$uhfmo_alpha
$uhfmo_beta
The symmetry labels, energies, and MO coefficients for open shells are read
from this data group. These data will be read if they are available and if
the file contains either converged or first order molecular orbitals.
$symmetry
The point group of the molecule. This data group will be read only if it is
available.
$title
The title of the calculation. This data group will be read only if it is
available.
$vibrational spectrum
$vibrational normal modes
The results of a force constant calculation. These two data groups will be read
only if they are available.
Footnotes
- ...
Iop(5/33=1)
3
- GAUSSIAN 98 seems to have
a bug with respect to this option - no MO coefficients are printed anymore.
Use Iop(5/33=2) instead which, unfortunately, also prints the density
matrix.
Jörg-Rüdiger Hill Fri Oct 31 14:19:21 CET 2003