GAMGI Formats: Atom Create

# Atom Create

- Type
- Property
- Analysis
- Position
- View

### 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)

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