min, max, element1, element2
One of the methods available to automatically create
new bonds is to calculate the distance between the two atoms
and to check whether it fits inside the bond length range
previously defined for that atom pair. Users can set explicit
values for the default minimum and maximum length limits, for
each element pair, using the
min,
max parameters,
coupled with the
element1,
element2 parameters,
to define the elements.
Explicitly defined bond length ranges become immediately active
and constitute the first priority when using the bond length criterium
to create new bonds. These parameters can thus be changed several times
in the same file, to handle blocks of data with different bonding characteristics.
As
min,
max parameters are specific for a given
element pair, the attributes
element1,
element2
must be included. When
element1,
element2 are present,
but
min,
max are not, an error is also shown,
because the only purpose of
element1,
element2
parameters is to set
min,
max values.
Example: <bond min="1.4720" max="2.0240" element1="Si" element2="O"/> (default)
(calculated from default Si, O radius and lower, upper parameters)
Allowed values: positive reals, element names (optional)
lower, upper
When explicit bond length ranges are not defined for a given element pair,
GAMGI attempts to create default minimum and maximum bond length limits by
summing the two atom radius and multiplying the sum by
lower and
upper factors. These
lower,
upper parameters are common
to all atom pairs and provide thus a method much less accurate (but
much more easy) to determine bonds than
min,
max.
When at least one of the atom radius is undefined, no bond is created
using the length criterium.
Example: <bond lower="0.80" upper="1.10"/> (default)
(defined in GAMGI_CHEM_BOND_LOWER and GAMGI_CHEM_BOND_UPPER)
Allowed values: positive reals, lower upper (optional)