Geometrymenu 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).
viewmolrcfile (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.
Alland 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
Tabkey, which cycles through all entries in the
$symmetryis 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.
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.
$scfmoor the data groups
$uhfmo_betamust 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,
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.
viewmolrcfile (these properties hold for sticks as well as for balls or CPKs).
Select ...which allows the user to run arbitrary Python scripts.
viewmol.htmlcan be accessed in the location
Viewmolfrom the directory
Xstands 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
%sas 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
$HOME/.Xdefaults or log out and