Define here the criterium used to create new bonds.
Direct
Selecting the 
Direct, the 
Atom entries become active, 
to enter the name and number of two atoms. If GAMGI identifies the 
atoms, a bond is created between them, after pressing 
Ok.
An easy technique to select an atom is to click the mouse over its 
visual representation: if GAMGI recognises the atom (it must be in 
the current layer), its identification is transported to the first 
empty 
Atom entry. If both entries were occupied before, the 
mouse action is ignored. If both entries are occupied after, GAMGI 
tries to create the bond.
The writing and clicking techniques can be combined. For example, the 
user can write an atom identification in the second 
Atom entry
and then click on the visual representation of the other atom: GAMGI 
writes its identification in the first 
Atom entry, previously 
empty, and attempts to create the bond.
The only information that matters is the information writen in the 
dialog when the 
Ok button is pressed. For example, if a user 
clicks on an atom to get its identification (in the first 
Atom       
entry), then writes another atom in the second 
Atom entry and 
finally deletes the first atom identification before pressing 
Ok, 
an error is shown, as the first atom is not found.
Length
This method is based only on the distance between atoms and the 
elements of the atoms, thus 
Element and 
Length entries 
become active and 
Atom entries become inactive. If both 
Element and 
Length entries are left empty, GAMGI 
attempts to create bonds for all atoms, using the following procedures.
For each atom pair, GAMGI checks whether specific minimum and maximum 
bond length limits have been configured. If the atoms distance is in 
the configured interval, a new bond is created. To configure bond length 
limits for specific element pairs, select 
Bond->Config.
If no bond length interval has been configured for this element pair, 
GAMGI attempts to calculate automatic minimum and maximum limits, summing 
the two atom radius and multiplying by lower and upper factors (currently
0.80 and 1.10 by default). If the atoms distance is in the calculated 
interval, a new bond is created. To configure these lower and upper 
factors, valid for all element pairs, select 
Bond->Config.
If no radius is defined for at least one of the elements, then no bond 
is created. To configure the atom radius, for specific elements, select 
Atom->Config.
When both 
Element entries are occupied, GAMGI tries to identify 
its contents as valid element names, which can be, for example,
"
Si", "
 Si", "
Si " but not "
si",
"
S i" or "
14". When both elements are recognized, minimum 
and maximum bond length limits for this element pair - calculated according 
to the rules described above - are automatically writen in the 
Length 
entries, otherwise these entries are set empty.
After pressing 
Ok, if both elements are recognized, GAMGI attempts 
to create bonds only between atoms of these elements, using the bond length 
limits writen in the 
Length entries (if the elements are invalid, 
an error is shown). If the 
Length entries are empty, GAMGI uses the 
default minimum and maximum limits for this element pair, calculated as 
described above.
If the 
Element entries are empty when the user presses the 
Ok 
button, but the 
Length entries are not, GAMGI attempts to create 
bonds between all atoms, independently of its elements, using the bond 
length limits writen in the 
Length entries. The values writen in 
the 
Length entries must be valid lengths, and the minimum value 
cannot excede the maximum, otherwise an error is shown.
In all cases, when pressing 
Ok, the 
Element entries must 
be both empty or valid and the 
Length entries must be both empty 
or valid, otherwise an error dialog is shown.
Delaunay
In this method, a Voronoi polyhedron is determined for each atom, 
and bonds are created between atoms whose polyhedrons share a common 
face, forming a Delaunay connection.
The 
Delaunay method is based on topological considerations only, 
so 
Element, 
Length and 
Atom entries are disabled.
Bonds that already exist are never created again: in 
Length 
and 
Delaunay methods, these cases are silently ignored, while 
in the 
Direct method an error is produced.