Molecular systems


The NanoLanguage Scripter	Periodic systems

1. Open the Atomic Manipulator

The first step in constructing a model for a nanoscale system is to define its atomic geometry. For this purpose, we use the tool Atomic Manipulator: To open the tool, double-click the corresponding icon in the VNL Toolbar.

	Note
	If you open an Atomic Manipulator which has been used before, the tool remembers the last used configuration.

In the Atomic Manipulator, it is possible to

to import existing molecules from your file system.
build molecules by hand, simply by inserting the atoms at their positions.

For convenience, you can define groups of atoms, which will be moved or rotated together as one single object. For complicated systems, the grouping of atoms provides a very handy way of defining different parts of the system separately (such as side-groups), and then putting them all together without distorting the internal configuration of the groups.

The different groups are called molecules in the interface, but note that when saving the system, the entire system will be treated as a single molecule. By default, the Atomic Manipulator always contains at least one (empty) molecule. To insert or delete molecules

right-click the left gray area
choose Insert new molecule or Delete new molecule from the context menu

Molecules can also be renamed from the context menu.

2. Insert two hydrogen atoms

Atoms are inserted into a specific molecule groups by

right-clicking the white area belonging to the molecule, and choosing Insert Atom from the context menu.

To delete an atom from a group,

right-click on the corresponding line and select Delete Atom from the context menu.

To create the hydrogen molecule, insert two hydrogen atoms (by default, new atoms are always inserted at the origin). The interatomic distance in a hydrogen molecule has experimentally been determined to be 0.741 Å, so specify this as the X-value for one of the atoms, and let the other one remain at the origin.

Note

It is of course completely arbitrary whether we choose the X, Y, or Z direction as the molecular axis, but it is highly recommended to always align the molecular geometry symmetrically with respect the coordinate axes. If not, it becomes complicated to plot quantities such as the electron density as a contour plane in the Nanoscope, since this type of plot requires the specification of the normal surface. Generally, the contour surface normal should be related to the molecular symmetry directions — if not, the plots can be very difficult to interpret.

Using the Atomic Manipulator for creating a hydrogen molecule. hydrogen molecule The context menu shows where to click in order to insert or delete molecules.

Figure 25: Using the Atomic Manipulator for creating a hydrogen molecule. The context menu shows where to click in order to insert or delete molecules.

The 3D representation of the molecule in the Preview window to the right can be zoomed, rotated, and panned by using the mouse in the same way as in the Nanoscope. In order to rotate, zoom, or pan the camera, however, it is necessary to click on a part of the preview area which does not contain any atoms (i.e. the background). If you instead click on an atom and then move the mouse, the camera will be fixed while the molecule is rotated (or translated, if the Shift button is held down). This can, in principle, be used to position or orient a group, but it is difficult to achieve high precision by using this method with just the mouse.

A more controlled way of positioning the groups is offered either by the entries Translate and Rotate from the context menu, or directly by specifying the origin and orientation of the group in the corresponding boxes above the atom list for each group. We will discuss these features a bit later on.

3. Save the configuration

Save the hydrogen molecule to a NanoLanguage script by clicking the button Save/Save As. It is a good idea to name the file with a descriptive name such as hydrogen.py or H2.py.