Geometry
menu items or repeat the steps above. Clicking with the left mouse
button on an atom may also be necessary for setting or selecting some
atom specific values (vide infra).
viewmolrc file (cf. p.
).
Coordinates and bond information are passed to the corresponding output filter which
writes the file. Currently, the only output formats provided are Accelrys car-files,
MDL mol-files, and TURBOMOLE.
).
).
All and can be used to change the currently
selected molecule. Other possibilities to select a molecule consist
of clicking on the molecule (preferably while holding the shift key down)
or pressing the Tab key, which cycles through all entries in the
Select molecule submenu.
) is
reversed. All geometry changes are buffered in the undo buffer and can be reversed one
by one by repeatedly using this menu item. Geometry changes can also be reversed through
the molecule editor.
).
$symmetry is not C1, TURBOMOLE's moloch program
must be available (vide supra, 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 grid resolution is changed 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.
At the top of this dialog box are five buttons which can be used to select the property which shall be shown.Next to these buttons there is a slider which can be used to select the value of the isosurface used to draw the property selected. Following this slider another three buttons allow the selection of the interpolation method used in drawing the property.
). Following is another
slider with can be used to set the resolution 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 20, but this can be overwritten in the resource file (vide infra,
p.
). At the bottom of the dialog box is a toggle button
which can be used to turn automatic recalculation of MOs etc. on whenever the
energy level is changed. Since these calculations can be quite time consuming,
this button is off by default, but this can be overwritten in the resource file
(vide infra, p.
).
$scfmo or the data
groups $uhfmo_alpha and $uhfmo_beta must be available.
The screen for a molecule shows the title of that molecule on top. Underneath
the molecular mass (in g/mol), the symmetry number, and either the rotational
constants (for molecules in cm-1) or the density (for solids in g/cm3)
are displayed on the left hand side. On the right hand side there is a
popup menu which allows the user to select whether this molecule should be
a reactant or a product in a reaction, or whether it is not involved in a
reaction at all. The last item in this popup menu, All reactions,
will force VIEWMOL to determine a linear independent set of possible
reactions between all molecules where this item has been selected.
The remainder of the screen shows thermodynamical data for the molecule. On the left hand side there are a number of buttons which can be used to select which contributions (translation, pV, rotation, vibration) to include in the total which is used to calculate thermodynamical data for a reaction. The enthalphy, entropy, Gibbs energy, and heat capacity are listed to the right, split into contributions from translation, pV, rotation, and vibration.
The screen for reactions (not shown) shows the reaction equation on top. Underneath the values of reaction enthalphy, entropy, Gibbs energy, heat capacity, and the (decadic) logarithm of the equilibrium constant are listed. The electronic and statistical-mechanic contributions to the reaction enthalphy are listed separately.
At the bottom all screens share a popup menu for selecting the units to be used (Joules, calories, or thermochemical calories) and two sliders. The top slider can be used to select the temperature at which the thermodynamical data are to be calculated, the bottom slider serves the same purpose for the pressure.
visible, allows to turn the
display of the unit cell on or off. The three sliders on the left hand side
can be used to increase or decrease the number of unit cells displayed in each
crystallographic direction. By default between one and five unit cells can be
selected.
The first button on the right, Show Miller plane, allows to turn the
display of Miller planes on or off. The three sliders underneath this button
can be used to select the Miller plane to be displayed. By default, all
combinations between -5 and 5 for the Miller indices are possible.
viewmolrc
file (these properties hold for sticks as well as for balls or CPKs).
).
).
Select ... which allows the user to run arbitrary Python scripts.
).
viewmol.html can be accessed in the location
$VIEWMOLPATH/doc.
Viewmol from the directory $VIEWMOLPATH/locale/X where
X stands for a language identifier. The four text input fields can be
used to specify the location of helper programs VIEWMOL needs for some
of its operations. If the corresponding program was found in the path the
dialog box will already show the correct information. If the programs specified
here need file names as parameters, put %s as a place holder for the
file name in the command.
A the bottom is a button Save which allows the information entered in
this dialog as well as some other settings to be stored as resources in
$HOME/.Xdefaults. The following settings are saved: position and
size of all open windows, window colors, selected model, selected drawing
mode, selected bond type, setting of ``lines while rotating", selected
interpolation mode, resolution of spheres, line width, selected isosurface,
selected resolution for density of states, setting of ``automatic recalculation",
paper size, and hydrogen bond threshold. Note: On Linux
the setting of resources is kept across different invocations of the
program. Saving the configuration and restarting VIEWMOL will
therefore apparently not work. To get rid of the old resource settings
issue the command xrdb -remove $HOME/.Xdefaults or log out and
in again.