style
Set how the atom is shown: a
solid sphere
or a
wired cross. When not indicated, GAMGI uses
the default. To change the default select
Atom->Config
and read
Help->Topics->Formats->Config->Atom.
The sphere provides the highest visual quality and is recommended
to produce final images of structures, together with lights. A sphere uses
considerable screen space though and is time consuming because it is simulated
by numerous 2D polygons, so many vertices and normal vectors (to calculate light)
must be allocated and calculated all the time. The cross is designed for atomistic
modelling work. Both screen space and computing time are kept to a minimum.
Moreover, when atoms are bonded, the crosses are not represented and atoms are
identified just by the ends of the lines representing bonds, thus decreasing
even further computation needs. However, because lines do not have a 3D
representation, diffuse and specular lights are not reflected by these objects,
and they become almost invisible when using lights with an ambient component
lower than (0.4, 0.4, 0.4).
Example: <atom style="wired"/> (default)
Allowed values: wired, solid (optional)
variancy
The intrinsic size of a solid (spherical) atom in GAMGI is calculated according
to the equation:
intrinsic = size x [variancy x radius + (1 - variancy) x min],
where
radius is the element radius currently defined and
min is by
default the H covalent radius, as defined in GAMGI (0.37).
In
wired mode,
variancy is always
0.0 so all atom crosses
have a constant size, given by
size x
min. In
solid mode,
when
variancy is
0.0 the atom spheres have all the same size,
when
variancy is
1.0 the atom spheres are scaled directly by
the atom radius. To change the default select
Atom->Config and read
Help->Topics->Formats->Config->Atom.
Example: <atom variancy="0.0"/> (default)
Allowed values: 0.0 - 1.0 (optional)
size
Sets the size of a spherical atom, in
solid mode. Combining atom
size
and
variancy with bond
size, it is possible to obtain a wide range
of styles to represent atomic structures.
The default is to represent atoms as constant spheres,
slightly larger than the bonds:
Example: <atom variancy="0.0" size="0.8"/><bond size="0.5"/>
An elegant style is to represent atoms with constant spheres
and the same
size as bonds:
Example: <atom variancy="0.0" size="0.5"/><bond size="0.5"/>
To show atoms in real size, atom
size and
variancy must
be set to
1.0. This is often required in compact cristalline structures,
to be consistent with cell dimensions, and in molecules, to emphasize the atomic
radius and electronic distribution:
Example: <atom variancy="1.0" size="1.0"/>
To change the default
size, select
Atom->Config
and read
Help->Topics->Formats->Config->Atom.
Example: <atom size="0.8"/> (default)
Allowed values: positive real (optional)
red, green, blue
Set the atom color. When not indicated, GAMGI uses the default for the atom
element. The default colors are essentially a superset of the CPK color scheme
introduced by Corey, Pauling and Koltun.
To see the default, just select the Periodic Table
from
Atom->Create,
Atom->Modify or
Atom->Config,
and choose the element. To change the default select
Atom->Config
and read
Help->Topics->Formats->Config->Atom.
Example: <atom red="1.0" green="1.0" blue="0.0" element="Si"/> (default Si color)
Allowed values: 0.0 - 1.0, element name
(optional, coupled)
scale
Change the atom size, including its child objects. Atom objects are
scaled around the atom center. The visual representation of an object
is always scaled by its own scale factor multiplied by the scale factor
of all its parent objects until layer, inclusive.
Example: <atom ... scale="1.0"/> (default)
(defined in GAMGI_MESA_SCALE)
Allowed values: positive real (optional)