GAMGI Formats: Atom Config

Atom Config

### 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)

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