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A input file should be a text file. The data are arranged in columns. Each column represents coordinates of atoms, type of atom, color, radius, velocity or force. Not all of these quantities are required. Only coordinates for atoms are must-needed. Velocity and force are needed in your input file only when you want visualize the velocity field and the force field. Color and radius of atoms could be used to visualize other physical quantities, for example, the temperature field or potentials of atoms. If no color or radius information input, VisAtoms uses default values for them. In VisAtoms, RGB mode is used for color. Atoms could be given types. For example, in simulation the deposition of clusters on surface, you could set atoms of substrate as type 1, and atoms of clusters as type 2 etc.

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Click File-Open menu, you can load an input file. The following dialog box will appear:

One can check Open continuously in the dialog box. You can open files and render the scene without stopping if your files have number as their extensions. Click File-Next menu or File-Previous to invoke this process.

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Click Option-Background menu. Change the components of R, G, B.

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The default size of box is assumed to be unit, i.e., the coordinate range is (–0.5, 0.5). Thus, after loading the data, you may find the graphics created is too large(if you use A or lattice unit for the coordinates of atoms) or too small (if you use cm for the coordinates of atoms). You can fit graphics into the viewport by click Edit-Normalization menu:

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Click Action-Rotation- menus and Action-Scroll objec menus or corresponding toolbar to set the object at a suitable position to have a better view point:

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The atoms could be drawn in dots, circles, wire spheres or solid spheres. To change the drawing style by clicking Edit-Drawing style menu, The following dialog box popup.

You can draw an atom by the properties (color and style) of its kind if you check Draw by property of subsample. A subsample here is a group of atoms of the same kind. In this way, atoms of different kind could be drawn in different style. You can also draw atoms by their own properties if you Draw by property of each atom. In this case, all the atoms have the same style (dot is the default style) but could have different color or radii even for atoms of the same kind if input color or radius for each atom have input (see also INPUT FILE).

Following is the results of Draw by property of subsample. The atoms of type 1 are drawn in circle, type 2 and type 3 drawn in solid sphere.

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The size of the atoms are too small in this figure, thus you can make them bigger (or smaller) by click Action-Zoom-Make sphere larger (Action-Zoom-Make sphere smaller) or tool bar:

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Click File-Save image menu to save the current graphics.

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You can select an atom or a group of atoms in different picking mode, by clicking an atom. Click an atom twice, you can move the atom or the group atoms of its kind around by mouse. The picked atom(s) could be hidden, deleted, copy etc by click Edit-... menu.

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Another way to modify the configurations of a sample is to make subsample. Click Edit-Make cluster the following dialog box popup:

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Click File-Save configuration menu to save the coordinates of atoms that have been modified.

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Comments or suggestions and error reports are welcome.