Select here the main parameters controlling the Voronoi tesselation.
Boundaries
GAMGI supports two methods to handle the tesselation
in the boundaries,
Planar and
Periodic.
The
Planar method defines six outer planes, forming a closed space
that includes all the seeds. Conceptually, this is equivalent to
create six virtual seeds around each real seed, positioned in such
a way that they define six planes at half-distance, common for all
seeds, forming a closed background.
The
Periodic method applies periodic boundary conditions,
using the extended image convention, which means to create 26 virtual
systems around the central system (as 26 boxes around the central one,
in a 3x3x3 arrangement). The minimum image convention, often used in
Molecular Mechanics simulations, is not suitable in Voronoi tesselation,
because it considers only the nearest neighbours, while Voronoi tesselation
requires all the 26 nearest neighbours.
The
Offset parameter defines the border width between: 1)
the seeds and the outer planes, in the
Planar method; 2)
the central system and the other 26 around, in the
Periodic
method.
Offset cannot be 0 in the
Planar method, because
virtual seeds would coincide with real seeds, producing an error.
Offset can be 0 in the
Periodic method, if real and
virtual seeds do not coincide, otherwise an error is flagged.
An error is also produced when two real seeds coincide (current
tolerance: 1.0E-4).
Weights
By default, GAMGI calculates the normal Voronoi partition,
so all atoms are given the same weight, corresponding to
Variancy equal to zero. However GAMGI can partition
the space giving different weights to different atoms (Radical
Tesselation), according to their radius. In general, if
d
is the distance between seed 0 and neighbour 1, the plane between
them passes at a distance
d * fraction from the seed, where
fraction is given by:
r0 = radius0 * variancy
r1 = radius1 * variancy
fraction = 1/2 [1 + (r0**2 - r1**2)/d**2]
When
Variancy is 0,
fraction is 1/2 (normal Voronoi),
whereas when
Variancy is 1, unscaled atomic radius are
used to determine
fraction.
Variancy can vary
continuously from 0 to a given limit,
GAMGI_PHYS_VORONOI_VARIANCY,
currently 10.0.
When
Variancy is 0, the tesselation can always be obtained (as long
as there are no atoms with essentially the same coordinates). When
Variancy
increases, the tesselation becomes progressively more restrictive. The atoms must
be far enough from each other, particularly when the radius are quite different,
otherwise the tesselation cannot be determined and and error is shown.