Introduction
GDIS is a free(GPL) chemical visualization program. It is primarily aimed
at displaying molecular and periodic systems - such as surface slabs and
crystal unit cells. It also acts as an interface to external compuational
packages in order to perform energy minimization and other tasks.
Loading structures
The primary way of utilizing GDIS is to load up some structure(s). See elsewhere in this
manual for a list of supported filetypes. Once the open model icon
is clicked, or the
File->Open menu item is selected, a directory browsing dialog is presented.
By default, this shows all supported files in the current directory that GDIS believes it
can load. In the bottom right hand corner is a pull down menu that can be used to filter for
the desired filetype. For example, selecting GULP would then only show files in the current
directory that end with .gin/.res. (input) or .got/.gout (ouput) extensions.
Files can be loaded by double clicking on their name entry in the dialog, or by selecting
(single click) the file and hitting the open button. Filenames can be manually typed
into the box in the bottom left corner of the dialog as well; in this case hitting
the ENTER key or the OPEN button will load up the model. Note that the extension of a
file name is a mandatory part of file format determination and must always be present
when loading
and saving
files.
Basic Interaction
GDIS was designed with a three button mouse in mind.
Left button
The left button is used to create
selections of subsets within the model. This can be acheived by clicking on atoms, in which
case some information will appear in the atom properties box in the left pane of the main window.
If the left button is held and the mouse is dragged, then a selection box will be drawn. When
the mouse button is released, all atoms in the box become part of the selection.
Single clicking on an empty part of the graphical display will clear the selection.
If the shift key is held then atoms may be appended to an existing selection.
Selected atoms can be deleted by pressing the delete key or through the
Edit->Delete menu. Selected atoms can be cut and pasted into other models,
hidden, or have their colour modified by employing the appropriate option in the
Edit menu.
Middle button
The default action when the middle button is held and the mouse moved is to translate the
model as a whole. Note that holding down the control key will result in only the
selected atoms of the model being translated. Also, if the shift button is pressed,
this will transform the mouse motion into a scaling operation.
Right mouse button
Holding down the right mouse button, coupled with mouse motion will rotate the model as
a whole. Mouse motion in the x and y direction produces rotation about two of the three
spatial axes. If the shift key is held, then the right mouse button will only
rotate around the third axis. In similar fashion to the middle button, if the
control key is held, then only the selected atoms will be rotated.
Operational modes
By default, GDIS operates in normal mode. The behaviour of this mode is described by the
previous section on Basic Interaction. However, other modes exist that modify how GDIS
responds to mouse input. Note that the current operational mode is always displayed in the
bottom right hand corner of the graphical window. Also, normal mode operation can readily
be returned to by clicking on the toolbar icon
.
Adding and deleting objects
When the Tools->Model editing menu option, or the corresponding icon
is clicked, then a new dialog
will be presented. Note that this will only happen if a model is already loaded (or created
through the File->New), since you can't edit a model if you haven't opened
one yet! Two of the buttons on the Objects tab of this dialog are for adding and deleting atoms.
If these are clicked, then the left mouse button can no longer be used for creating and
modifying selections. Instead, single clicking will perform the desired task. Note that when
adding atoms, the atom properties pane can be used to modify the element, charge, and even
position of the new atom. Buttons for switching to other operation modes, such as adding
and deleting bonds, are present and will be dealt with in more detail in future updates to
this manual.
Measurements
The
icon or the
View->Measurements menu option brings up the measurements dialog. If one of the
manual methods are selected, then the operational mode will change accordingly. However,
the mode will also indicate that it expects a number of atoms to be specified in order to
perform the required task. For example, if measure angles is selected, then the mode will
reflect how many atoms have been clicked on already, and how many it requires in total.
When the latter number is satisfied the measurement is drawn and displayed in the dialog.
Measurements can also be made using the search panel. Here, the component atoms can be
either any atom, part of the selection, or a specific element/atom label type. The Atom 1,
Atom 2, etc. pulldown entries can be changed to a preset value, or modified manually
to provide a search filtering pattern for the desired measurements. Cutoff limits may
also be specified. Once a number of measurements are made, they may also be removed by
clicking on their entry in the dialog and then on the Delete button. If the model name
in the measurements dialog is selected, then all measurements are removed.