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.