Atoms Window
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This window shows the atomic structure with lines or vectors attached to each atom showing the displacement in the selected vibrational mode. It appears or is refreshed after a calculation if the Atoms Plot box is checked in the Control Window.

See the complete list of Menu options

The dialog bar on the left edge of the Atoms Window allows manipulating the structure image in the window in several ways. For more elaborate ways of rotating the image, see the dialogs in the Rotation menu.

At the top of the dialog bar is a small sketch of the current orientation of the original structure axes. These are called a, b and c, which are equivalent to x, y and z for a molecule using a Cartesian coordinate system. The letters are attached to the positive ends of the axes, and the end of the axis which points out of the screen (towards the observer) is drawn with a heavy line.

Below this are buttons for instantaneous rotation on the x, y and z Cartesian reference axes, from top to bottom. The amount of rotation, in degrees, is given in the edit box below the buttons. The default angle value can be set in the Basic Parameters dialog (Setting menu).

Below this is the scale factor which is applied to atomic displacements. This factor is applied only in this window. Other factors which affect the magnitude of the atomic-motion vectors are set in the Basic Parameters dialog (Setting menu). The displacements as printed in the Output window, and as used to derive the spectral intensities, need to be small to satisfy the assumptions of the calculations, so it is normally necessary to supply a large magnification factor in this Atoms Window, on the order of 50-100.

The Replot button is needed after changing the Scale or Parameters (below).

The Parameters button brings up the Atoms Plot Parameters dialog (Settings menu), for setting several aspects of the appearance of the plot.

The Print button causes printing of the Atoms image. Since the Print option in the File menu prints different things depending on which window is active (Output file Text window; Spectra; Atoms), using this button insures that the Atoms image is printed.

The Mode button brings up a dialog which allows selection of the particular mode which is being viewed. There is an automatic replot when the mode is changed.

Clicking on an atom in the window itself will bring up the Generated Atom Data dialog or if atoms are superimposed, the Atoms at Cursor dialog. These dialogs give information about the specific atom.

Cursor Mode radio buttons. In Atom ID (identification) mode, clicking on the left mouse button will identify atoms - see Atoms at Cursor. The cursor in this mode is a cross. In Rotation mode, clicking and dragging rotates the structure. The cursor in this mode is a circular arrow. Clicking and dragging in most of the window will rotate around the y and z Cartesian axes, in the plane of the screen. Clicking and dragging near the left or upper edges will rotate about the z axis, perpendicular to the screen.

The atomic motions shown in this window are those of the main isotope configuration, not any other isotope configurations. To see which modes in isotope configurations correspond to these, it may be necessary to refer to the "Main" column in the mode lists for isotope configurations near the end of the text output, since the order of modes may be different in different isotope configurations.