GAMGI Interfaces: Cell Link

# Cell Link

- Object
- Position
- Occupancy
- Packing

Link cells to other objects, for example to build crystals and glasses.

### Hierarchy

Cells can be linked to objects above or below, in the Gamgi hierarchy. Pressing the button Below (the default), the Objects menu shows the classes of objects that can be owned by cells: Cluster, Molecule, Group, Plane, Direction, Atom, Orbital and Text. Pressing the button Above, the same menu shows the classes of objects that can own cells: Layer and Assembly. When the chosen Hierarchy is Above, the link methods designed to add multiple objects to cells are disabled: Independent, Automatic and Random.

### Object

Gamgi expects users to identify first the cell or list of cells and then the object to link. When the Cell entry is active and empty, clicking the mouse over a cell, on the current layer (local selection), its identification is transported to the Cell entry. Gamgi is now expecting users to click on a object of the class currently selected in the Object menu. This object can be in a different layer or even in a different window (global selection).

To select a visible object in a different layer, in the same window, just press the mouse over the object, as if it was in the current layer. To select objects without visual representation, as layers and lights, press the mouse over the graphic area in the window, to create a menu with all the objects of that class in the window, which can then be selected. To select an object in a different window, with the mouse, use exactly the same procedure, in that window.

### Method

Gamgi suppports three linking modes for cell objects: Object, Crystallographic and Random.

The Object method (the default), links a cell to a single Object. When the Hierarchy is Above, the cell is unlinked from its current parent and linked to the object. When the cell is moved to a different layer, all its bonds to other objects are autmatically removed. When the Hierarchy is Below, the object is unlinked from its current parent and linked to the cell. An error is issued when the parent already owned the child object. After the linking operation, Gamgi always puts on top the window and layer containing the linked objects.

The Crystallographic method is used to link the selected Object to the various cell nodes, in order to build crystals, liquids and other nanostructures. The linked objects can be handled independently of the cell: they can be rotated, scaled, moved, removed, copied, as if the cell did not exist, for example to create defect crystals. Users can specificy patterns of occupation for the cell nodes, for example to create mixtures of different liquids, or to build multi-layer arbitrary nanostructures.

The Random method is an implementation of the Jodrey algorithm to build a Random Close Packing (RCP) structure: the cell volume is randomly packed with atoms copied from the template atom selected as Object. The RCP structure has the highest volume density among amorphous structures (0.62 - 0.64), which compares with the highest volume density among crystalline structures (0.74). The RCP structure is particularly suitable to describe metallic glasses, due to the nondirectional nature of metallic bonding combined with the absence of local charge-neutrality requirements.
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