element
Identifies the element to which other properties apply, thus
it must be coupled with
mass,
radius or
red,
green,
blue parameters. It must be a valid element name,
or a Dummy atom, represented as
Du. Accepted values are
"
Si", "
Si", "
Si " but not
"
SI", "
si", "
S i" or "
14".
mass
Coupled with the
element parameter, the
mass
parameter can be used to change the default mass for each element.
The new value replaces the old one everywhere in GAMGI interfaces,
including the periodic table.
It might be useful, sometimes, to change this parameter
several times in the same file, to handle blocks of data
with different atomic characteristics (in isotopic studies,
for example).
Default: <atom mass="15.9994" element="O"/> (default O mass)
Allowed values: positive real, element name (optional)
radius
The covalent radius used by default in GAMGI were obtained from
http://www.webelements.com/.
Coupled with the
element parameter, the
radius
parameter can be used to change the default radius for each element.
The new value replaces the old one everywhere in GAMGI interfaces,
including the periodic table.
We note that the new radius becomes immediately active, and
might be used together with the
lower, upper bond configuration
parameters, to calculate bond length ranges, when creating new
bonds automatically.
Default: <atom radius="0.7300" element="O"/> (default O radius)
Allowed values: positive real, element name (optional)
red, green, blue
Coupled with the
element parameter,
red,
green,
blue
can be used to change the default color for an element. The new values
replaces the old ones everywhere, including the periodic table.
Default: <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)
style
Controls which
style is applied by default when creating a new atom.
Default: <atom style="wired"/> (defined in
GAMGI_MESA_ATOM_DRAW)
Allowed values: wired, solid (optional)
variancy
The intrinsic size of a solid (spherical) atom 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 the minimum
radius, by default the H covalent radius.
In
wired mode,
variancy is always
0.0 so
all atom crosses have a constant size, given by
size x
min.
In
solid mode,
variancy controls how the
size of the atom spheres is affected by the atom radius.
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.
Default: <atom variancy="0.0"/> (defined in
GAMGI_CHEM_ATOM_VARIANCY)
Allowed values: 0.0 - 1.0 (optional)
size
In
solid mode, controls the size of the atom spheres.
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:
<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:
<atom variancy="0.0" size="0.5"/><bond size="0.5"/>
To represent compact cristalline structures, atom
size
and
variancy must be
1.0, to be consistent with
cell dimensions:
<atom variancy="1.0" size="1.0"/>
This style can also be used to represent molecules, in order
to emphasize the atomic radius and electronic distribution.
Default: <atom size="0.8"/> (defined in
GAMGI_CHEM_ATOM_SIZE)
Allowed values: positive real (optional)
min
In
solid mode, defines the radius used by default to represent atoms,
when variancy is set to 0.0 and all atoms are represented with the same size,
as described above. By default it is the smallest radius available, the
Hydrogen radius.
Default: <atom min="0.3700"/> (defined in GAMGI_CHEM_ATOM_MIN)
Allowed values: positive real (optional)
slices
In
solid mode, controls the number of fragments used to represent
curved surfaces such as atom spheres and bond cylinders, thus controlling
the visual quality of these objects. Increasing the number of fragments
improves noticeably the visual quality but also decreases performance
substantially.
Default: <atom slices="16"/> (defined in
GAMGI_MESA_ATOM_SLICES)
Allowed values: 10...100 (defined in
GAMGI_MESA_ATOM_SLICES_MIN
and GAMGI_MESA_ATOM_SLICES_MAX) (optional)
width
In
wired mode, controls the line width used to draw atoms and bonds.
Default: <atom width="2"/> (defined in
GAMGI_MESA_ATOM_WIDTH)
Allowed values: 1...5 (defined in
GAMGI_MESA_ATOM_WIDTH_MIN and
GAMGI_MESA_ATOM_WIDTH_MAX) (optional)