Set here the method used to create new bonds.
Atoms
Selecting this method, 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 shown.