Visualisation with the CCP1GUI
The GUI does not yet have a user manual, but the following sections
should provide some help in trying out the code and seeing what
is there now.
In many cases context-sensitive help is available using the F1 key.
Please read through the bugs and limitations
help avoid frustration when you try to run something which is not
yet implemented, and work through the examples in the order given
as information is not repeated.
Structure of a molecule
In the data directory you will find a file ch3oh_potential.pun
which you can read in with the File->Open.
For each "object" (this general classification includes both molecules
and numerical data fields) in the data file there will be an option on
the Views menu.
The first entry on this menu, labelled "Methanol" will be portrayed
in a bold font, denoting the fact that an image of this object is
being displayed. A submenu will provide the option of removing the
image "Hide.." and changing the settings for the image "Adjust..".
Using the panel that comes up when you use the Adjust... option
you can add sphere, stick, and label representations.
After each change, press Update to rebuild the images.
Clicking right-mouse on an atom will cause the atom
details (bond lengths and angles) to be printed. The output will
appear in the window from which the GUI was started, unless you
have opened the Idle Shell (Shell menu). The Idle shell is
not yet available if you are using Python 2.3.
Charge Density, Potential and Orbitals
The remaining objects are data fields, the values of scalar
data fields at a grid of points (a 51x51x51 3D grid in this case).
By default, no default view of data fields is generated, "Orbital
View" for the HOMO and LUMO. For the density, you can use the
"Density View", to get a simple isosurface. You can create multiple
surfaces by repeating the operation and setting different contour
heights using the "Adjust ..." option and make the outer ones partially
transparent by reducing the Opacity.
To examine the potential, first try colouring an isosurface
representation of the charge density. View the Density with the
colour surface view, and then adjust this to set the colour field to
"potential". You adjust the parameters to change the view, for example
change the way potential is mapped to colour using the colourmapping
entry boxes which indicate which potential values correspond to the low
and high ends of the rainbow colourmap.
Then try the Cut Slice View on the potential sub-menu. A control panel
will appear, increae the value of the X Scale and Y Scale slides to
the cut slice grid to take a large slice, and move it through the
space around the molecule using the translate and rotate options.
Vibrational Modes of Ethane
Open the file examples/ethane_vib.pun. The Views menu will now contain
an entry for each vibration labelled by the frequence in wavenumbers,
-ve values denoting the imaginary frequencies. In each case the
relevant submenu will have a single entry, which will create an
animation of that mode. You may want to hide the view of the
molecule before starting the animation using the button on the
Viewing a Periodic Structure
The file examples/sodalite.c provides a suitable example to try out
the Extend option on the Edit menu, which will allow a number of
unit cells to be visualised using the molecule visualiser.
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