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<title>GAMGI Interfaces: Cell Link</title>
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<h1>Cell Link</h1>
<div id="notebook">
<ul>
<li><span>Object</span></li>
<li><a href="link_shift.html">Shift</a></li>
<li><a href="link_position.html">Position</a></li>
<li><a href="link_change.html">Change</a></li>
<li><a href="link_occupancy.html">Occupancy</a></li>
<li><a href="link_packing.html">Packing</a></li>
</ul>
</div>
<div class="contents">
Link a cell or a list of cells to other objects,
for example to build crystals and glasses.
<h3>Hierarchy</h3>
Atoms can be linked to objects above or below, in the Gamgi hierarchy.
Pressing the button <b>Below</b> (the default), the class menu
shows the classes of objects that can be owned by cells. Pressing
the button <b>Above</b>, the same menu shows the classes of objects
that can own cells.
<p/>
Gamgi expects users to identify first the cell or list of cells
and then the object to link. When the <b>Atom</b> entry is active
and empty, clicking the mouse over a cell, on the current layer
(local selection), its identification is transported to the <b>Atom</b>
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).
<p/>
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.
<p/>
When the chosen <b>Hierarchy</b> is <b>Above</b>,
methods designed to add multiple objects to cells are disabled:
<b>Crystal</b> and <b>Random</b>.
<h3>Method</h3>
Gamgi suppports three methods to link cells: <b>Object</b>,
<b>Crystal</b> and <b>Random</b>. The last two are designed to add
multiple objects to cells, so they are disabled when <b>Hierarchy</b>
is set to <b>Above</b>.
<p/>
The <b>Object</b> method links a cell or a list of cells to
a single object, <b>Above</b> or <b>Below</b>.
<p/>
When the <b>Hierarchy</b> is <b>Above</b>, 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 <b>Hierarchy</b> is <b>Below</b>, 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.
<p/>
After the linking operation, Gamgi always puts on top
the window and layer containing the linked objects.
<p/>
When linking a list of cells <b>Above</b>, all cells in the list
are unlinked and linked to the parent object. When linking a list
of cells <b>Below</b>, the child object is replicated as many times
as necessary to link each cell in the list to a different replica.
<p/>
The <b>Crystallographic</b> method is used to link the selected
<b>Object</b> 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.
<p/>
The <b>Random</b> 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
<b>Object</b>.
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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