control file:
$atoms
$basis
$pople$closed shell$coord$grad$rundimensions$scfmo$symmetry$title$vibrational spectrum
$vibrational normal modes-g.
The file is opened and the occurence of the string Entering Gaussian System
is checked. 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)
to print basis set and MO coefficients.
-d.
This file name can be file_name.car, file_name.cor or the base
name file_name only. The base name is used to construct the file names
file_name.cor (the coordinate file), file_name.frq (the file with
frequencies and normal coordinates) and file_name.out (the output of a
DISCOVER run where the intensities can be found in). All necessary data are
extracted from these files. You can specify one of the two file names mentioned
above or only the base name without extension at the command line. If you use
file_name.car no information about the vibrational spectrum is read, even
if the .frq and .out files are present.
-o.
The extension .outmol is optional and will be appended to the file
name automatically if it is not present.
-m.
The programme first reads from this file the title (hopefully in the 16th line of
the file) and the cartesian coordinates from the block entitled
MOLECULAR BASIS SET (the atomic symbols are set using the atomic
numbers in this block).
Then it looks whether informations from a geometry optimization are available
(OPTIMIZATION CONVERGED and Point n where n is an integer).
The corresponding data are read in (energies from the line following
FINAL VALUES OF TOTAL ENERGY AND ELECTRONIC ENERGY ARE,
gradients
from the lines following GRADIENT OF THE ENERGY). When all optimization data
were read in, the final geometry replaces the geometry read from
MOLECULAR BASIS SET and the gradient norms are calculated for each
step of the geometry optimization.
Then the programme searches for NORMAL MODES AND VIBRATIONAL FREQUENCIES
in the file. The data following this line are read in. All vibrations are taken
to be IR as well Raman active, the intensities for the IR active modes are set
to 100 %, and the symmetry of the mode to A1.
-p.
Only the cartesian coordinates and atomic symbols are read from this file,
the connectivity information is ignored and will be determined by VIEWMOL
itself.
The programme displays the molecule according to the coordinates in a window. Following manipulations are possible:
All rotations are carried out in a molecule fixed coordinate system.
or down
the molecule will be enlarged and by pressing
the molecule will be made smaller.
Geometry
menu items or repeat the steps above. Clicking with the left mouse
button on an atom may be also necessary for setting or selecting some
atom specific values (vide infra).
$symmetry is
not C
, TURBOMOLE's moloch programme must be available (vide infra,
p. 
) and only basis functions, occupied MO's, and electron densities
can be drawn in this case. Since TURBOMOLE can handle up to g functions
and GAUSSIAN can handle up to f functions the same limitations apply
to VIEWMOL.
If any wave function related drawing is displayed and the scaling of the
molecule is changed (by pressing either or )
the drawing disappears and the recalculation has to be explicitly demanded
by selecting this menu item again, since large molecules require significant
time for the recalculation. A change of the grid granularity also requires
recalculation. A change of the isosurface or the interpolation method, however,
can be done without recalculation. They are therefore much faster.
Figure 1: The dialogue box for setting options for
wave function related topics.
At the top of this dialogue box are five buttons which can be used to select the property which shall be shown.
viewmolrc
file (vide infra, p. ). At the bottom of the dialogue box there
is another slider with can be used to set the granularity of the grid. As
higher the number selected here as finer the grid and as smoother the
resulting surface, but the calculation time goes with the third power of
this number. Default is 10, but this can be overwritten in the viewmolrc
file (vide infra, p. ).
$scfmo must be available.
and to the right
one can see how the geometry optimization works.
Alternatively, the red cross can be dragged with the mouse.
This topic is not available using DISCOVER outputs. In
TURBOMOLE outputs the data group $grad must be available.
viewmolrc
file (these properties hold for sticks as well as for balls or cups). This
topic is not available if the graphics adapter was configured in double
buffered colour map mode.
Surface, see above will not be available in this mode), but in contrast
to the single buffered RGB mode, the molecule can be moved without flickering.
This option is thought for running VIEWMOL on 8-bit graphics adapters,
which do not support the double buffered RGB mode (IBM).
vm_plot.hp. This topic is not available if
the drawing is done with sticks, balls, or cups. If molecular orbitals are drawn
this topic is only available if the MO is drawn with lines.
vm_image.tiff. If
normal modes are animated while this option is selected a series of 24 TIFF
files will be written out, each contains a single frame of the animation. By
using standard image manipulation tools available on the Internet it is
possible to generate a video file (MPEG) from these TIFF files which can be
included in multimedia documents (vide infra, p. ).
Wire model. If, however, a molecular orbital is drawn, while the molecule
is drawn as wire model, this topic is available and will produce a stick model
of the molecule in the ray tracing. A submenu is provided with the topics
vm_rayshade.ray)
and then the scene description is written to this file. If normal modes are animated
while this option is selected a series of 24 input files for RAYSHADE will be
written out, each contains a single frame of the animation, and a shell script
raytrace is created which contains the commands necessary to do the raytracing
for all 24 files.
Generate file are performed. Then the RAYSHADE
programme is called in background (in case of an animation of normal modes the
raytrace shell script is started). This topic is only available if the
viewmolrc file contains the path name to this programme. The raytracing
will continue to run, even if VIEWMOL is quit.
).
viewmolrc
file to be able to read the manual. This topic is only available if the
file viewmol.html was found in the location $VIEWMOLPATH/man.
Choosing Spectrum from the menu will result in a new
window showing the calculated spectrum for the molecule.
In this window the mouse acts as follows:
Figure 2: The dialogue box for setting options for the
spectrum
The menu contains the following topics:
All modes, IR active modes, Ramanactive modes, and Inelastic neutron scattering can be used to
select the type of spectrum desired. IR active modes are the default.
Animate and Draw arrows can be used to select
whether the normal modes are to be shown animated or with arrows.
Animation is the default.
Line spectrum and Gaussian spectrum can be used
to select whether the spectrum is drawn as simple line spectrum or
whether a Gaussian band shape [1] should be applied. Line spectrum is
the default.
Table and Plot buttons one can select whether selecting
Hardcopy from the spectrum menu produces a table of the wave numbers
or a hardcopy of the spectrum. Both outputs are written in a form suitable
for LaTeX. Activating the Create header option adds a header (preamble:
\documentstyle ...) to the file so that it can be processed by
LaTeX without further modifications (note: The \textwidth and
\textheight macros are defined for an A4 page). Plot without header is
the default.
OK button all weights are drawn at the atoms in the main window
and you can set an atom's weight just by clicking on it with the left mouse button.
All weights are set initially to zero, so that selecting Inelastic neutron scattering
as spectrum type produces nothing.
Draw Arrows
was chosen as normal mode representation.
).
).
Settings for spectrum.
A file selection box will appear for selecting the file
name, the default is vm_spectrum.tex.
vm_image.tiff.
and ,
respectively
Choosing Optimization history from the menu will result in
a new window showing the energy and gradient norm in dependence
of the step number of the geometry optimization. In this window
the mouse acts as follows:
and to the right
, respectively.
Figure 3: The dialogue box for setting options for the
optimization history
The menu contains the following topics (the letters in brackets can be used to activate a topic from the keyboard):
).
).
).
vm_image.tiff.
Choosing Energy level diagram from the menu will result in
a new window showing the calculated MO energies in an energy
level diagram. In this window the mouse acts as follows:
and down , respectively.
Figure 4: The dialogue box for setting the energy units for the
MO energy level diagram
The menu contains the following topics (the letters in brackets can be used to activate a topic from the keyboard):
.
viewmolrc
file (vide infra, p. ).
).
).
vm_elevel.hp.
This topic is not available if a MO is selected or if the transition option is
activated.
vm_image.tiff.