GAMGI Interfaces: Cell Link

# Cell Link

- Object
- Shift
- Position
- Change
- Occupancy
- Packing

Link a cell or a list of cells to other objects, for example to build crystals and glasses.

### Hierarchy

Atoms can be linked to objects above or below, in the Gamgi hierarchy. Pressing the button Below (the default), the class menu shows the classes of objects that can be owned by cells. Pressing the button Above, the same menu shows the classes of objects that can own cells.

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

To select a visible object, just press the mouse over the object, in its window. To select objects without visual representation, such 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.

When the chosen Hierarchy is Above, methods designed to add multiple objects to cells are disabled: Crystal and Random.

### Method

Gamgi suppports three methods to link cells: Object, Crystal and Random. The last two are designed to add multiple objects to cells, so they are disabled when Hierarchy is set to Above.

The Object method links a cell or a list of cells to a single object, Above or Below.

When the Hierarchy is Above, the cell is unlinked from its current parent and linked to the new object. When the cell is moved to a different layer, its bonds are automatically removed. When the Hierarchy is Below, the child 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.

When linking a list of cells Above, all cells in the list are unlinked and linked to the parent object. When linking a list of cells Below, the child object is replicated as many times as necessary to link each cell in the list to a different replica.

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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