Enlarge Unit Cell

Description

Add atoms outside the unit cell by different criteria.

Input Ports

structure_in MoleculeType Molecular structure data. It must contains unit cell definition data.

Parameters

Criteria for addition radio buttons Set the criteria used to add atoms outside the unit cell. Possible values are:
Fixed percentage
The unit cell is enlarged on both sides by a given percentage of the basis vector lenght.
Within distance
Atoms within a given distance from atoms in the unit cell are added.
Only bonded
Will be added atoms that have at least one bond with atoms in the unit cell.
Enlarge a (or b or c) slider Percentage of the corresponding basis vector that is added to the two opposite sides of the unit cell. The percentage is restricted in the interval 0 .. 50%. Those controls are active only when the "Fixed percentage" criteria is selected.
Distance slider Allowable distance from any atom inside the unit cell for an atom to be added to the enlarged unit cell. The distance is restricted in the interval 0 .. 5.0. This control is active only when the "Within distance" criteria is selected.
H bonds toggle Enable computation of H bonds.
Greedy bonding toggle Ignore the maximum number of bonds for each atom.
Bonding Range Adjustment slider Percentage of variation of the maximum distance between atoms to form a bond.
H Bonding Range Adjustment slider Percentage of variation of the maximum distance between H and an atom to form a bond.
H Bond Max Distance slider Maximum lenght of an H bond.
H Bond Max Angle slider Maximum angle HXY (in X__H..Y where .. is the H bond) to form an H bond.

Output Ports

structure_out MoleculeType Molecular structure data with border atoms removed.
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