GAMGI Formats: Bond Config

# Bond Config

- Length
- View

### min, max, element1, element2

One of the methods available to automatically create new bonds is to calculate the distance between the two atoms and to check whether it fits inside the bond length range previously defined for that atom pair. Users can set explicit values for the default minimum and maximum length limits, for each element pair, using the min, max parameters, coupled with the element1, element2 parameters, to define the elements.

Explicitly defined bond length ranges become immediately active and constitute the first priority when using the bond length criterium to create new bonds. These parameters can thus be changed several times in the same file, to handle blocks of data with different bonding characteristics.

As min, max parameters are specific for a given element pair, the attributes element1, element2 must be included. When element1, element2 are present, but min, max are not, an error is also shown, because the only purpose of element1, element2 parameters is to set min, max values.

    Example: <bond min="1.4720" max="2.0240" element1="Si" element2="O"/> (default)
    (calculated from default Si, O radius and lower, upper parameters)
    Allowed values: positive reals, element names (optional)

### lower, upper

When explicit bond length ranges are not defined for a given element pair, GAMGI attempts to create default minimum and maximum bond length limits by summing the two atom radius and multiplying the sum by lower and upper factors. These lower, upper parameters are common to all atom pairs and provide thus a method much less accurate (but much more easy) to determine bonds than min, max. When at least one of the atom radius is undefined, no bond is created using the length criterium.

    Example: <bond lower="0.80" upper="1.10"/> (default)
    (defined in GAMGI_CHEM_BOND_LOWER and GAMGI_CHEM_BOND_UPPER)
    Allowed values: positive reals, lower < upper (optional)

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