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Basic commands

The eFFview visualizer is run from the command line, and can be used to display both .cfg input files as a single frame, or .eff output files as a multi-frame animation (see Chapter 1 for information on the command line options):
  effview [.cfg or .eff file] [number of frames] /off (optional)
Once started, eFFview displays the nuclei and electrons together on the main screen (Figure 4.1). The nuclei or electrons can be displayed alone by pressing the n or e key.

The nuclei are represented as balls and sticks, where bonds connect atoms that are within a threshold distance of each other:

$\displaystyle \mathrm{solid\ line}$   $\displaystyle \mathrm{if\ } r_{ij} < 1.5 \cdot (r_{i} + r_{j})$  
$\displaystyle \mathrm{else\ dotted\ line}$   $\displaystyle \mathrm{if\ } r_{ij} < 1.8 \cdot (r_{i} + r_{j})$  

where $ r$ is the covalent radius of the atom.

Figure 4.1: By default, eFF overlays nuclei and electrons together, but pressing n or e causes the nuclei or electrons to be displayed alone.

The electrons are displayed as translucent spheres whose radii are the widths of the wave packets defined in the eFF equations. Thus electrons that are more diffuse are larger. Electrons with a radius greater than 5 bohr are displayed separately as ionized electrons in the lower right-hand section of the screen (Figure 4.2).

Figure 4.2: Electrons above a threshold size are displayed separately as ionized electrons.

Up spin electrons are colored red and down spin electrons are colored blue. eFFview tries to detect when opposite-spin electrons are spin-paired ( $ \Delta r <$ 0.1 bohr, $ \Delta s <$ 0.1 bohr), so that spin-unpolarized regions are colored a uniform gray, and the eye-catching red and blue colors are reserved for spin-polarized regions of space. The spin-pairing option may be toggled by pressing the s key.

Periodic boundary conditions are automatically detected by eFFview and drawn appropriately (Figure 4.3). Nuclei and electrons that bisect a boundary plane are made visible on both sides, and clipped so that the circular intersection their spherical forms make with the plane is evident. 1D, 2D, and 3D boundary planes are shown using lines and cross-hatching that make clear which dimensions are periodic while not obstructing the particle view.

Figure 4.3: Periodic boundary display. The left side shows how 1D, 2D, and 3D periodic boundary planes are depicted in eFF. The right side shows an example of a 3D periodic system, etching of a diamond film by a dense hydrogen plasma.

The mouse controls the view (Figure 4.4). Dragging the left mouse button manipulates a virtual trackball - moving inside the trackball region rotates the model along the XY screen plane, while moving outside the region rotates the model about the Z axis. Dragging with the right mouse button translates the model, and rolling the scroll wheel up and down zooms the model in and out. The +/- keys can also be used to zoom in and out if a scroll wheel is not available.

Figure 4.4: Mouse controls in eFFview: dragging with the left button rotates, dragging with the right button translates, and rolling the scroll wheel up and down zooms in and out.

eFFview displays .eff multi-frame files as animations, controlled using the timer bar which appears when the mouse is in the upper part of the window (Figure 4.5). The timer bar shows the overall progress of the animation, both graphically, as the shaded portion of the bar, and as text, by the frame number and by the absolute time when available. A left click on the bar plays or pauses the animation, while a right click in the bar jumps to a particular frame.

Figure 4.5: The timer bar appears when the mouse is in the upper part of the screen, and controls the animation of multi-frame .eff files.

Several options are available which can help to clarify the display, as shown in Figure 4.6. The electron sizes can be scaled using the keys 1, 2, 3, and 4, corresponding to scalings of 1.0, 0.5, 0.2, and 0.1 respectively. This can be useful for distinguishing electrons that are spaced closely together.

Figure 4.6: Example eFFview keystrokes applied to a frame from a core-ionized diamondoid trajectory. By changing electron sizes, separating spin pairs, and adding velocity vectors, more subtle details are the Auger process are made visible.

Pressing s toggles the spin-pairing procedure which colors electron pairs gray. This can help to resolve small spin polarizations that would otherwise be obscured by the spin-pairing algorithm. It is often used together with the electron shrinking options.

The key v toggles the display of velocity vectors on fast-moving nuclei. This is useful for indicating motion in still frames.

Finally, pressing b switches the display of bonds off or on. This option is rarely used, as the lines drawn between nuclei are an important visual aid. However, the bonds are laborious to compute and so for large systems, turning the bond display off will improve the rate at which the visualizer can display frames. In such cases it can also help to draw the system using a lower level of detail (Figure 4.7), which tells eFFview to use a style of drawing with fewer polygons that provides improved performance.

Figure 4.7: Different levels of detail are selected using the keys F1 (lowest) through F5 (highest); or Shift-1 through Shift-5, if the function keys are disabled. Lower levels of detail are faster to render.

next up previous contents index
Next: Saving snapshots and movies Up: The eFFview visualizer Previous: The eFFview visualizer   Contents   Index
Julius 2008-04-29