STIGMA Screenshots
Well, not really screenshots of STIGMA itself – that would be pretty boring, just a bunch of text from a terminal. No, what we have here are images crafted by GrayMatter using data from STIGMA!
GrayMatter has several methods for representing tunneling height/current in images it creates. Here we see the "false-color" mode, where height/current maps to distinct colors. This image also includes a lateral scale bar at the bottom of the image and the dependent scale bar at the left edge.
This image also shows GrayMatter's overlay capabilities: atomic positions and two text labels (top-left corner of the image) in this case.
This is a more classical STM image: tip height rendered as a grayscale level. The system in question was a cluster model of the Si (100) surface in the 2x1 reconstruction; two neighboring dimer rows are present, with one "passivated" by hydrogenation. Note that the scale bars can be placed left- or right-aligned or centered on any edge of the image.
Beyond simple grayscale, GrayMatter also allows you to colorize a grayscale image. Grayscale uses the HSB (Hue, Saturation, Brightness) color space with varying brightness according to dependent variable. Colorization simply makes use of a non-zero saturation and a hue angle (e.g. hue of 0° is red).
Here we see a constant-height image of an isolated benzene molecule. The hydrogens of C6H6 were present in the system, but GrayMatter allows one to selectively overlay only those atoms that are deemed noteworthy.
The three images here show the Image, Range, and Scale configuration tabs available in a GrayMatter document window. By default, when GrayMatter is started it will create a window containing data that can be thought of as a constant-height image of a perfectly spherical isodensity surface. Hopefully, such a surface should be easily imagined by the end-user, and thus the nature of each configuration option can be understood as it relates to this simplistic surface.
