Scale system

Description

This function scales the entire system by a factor scale_factor relative to a reference point ref. The operation performed is:

 x = x + scale_factor * (x - ref)

Two types of scaling are available, determined by the scale_mode input:

  • atom-based: Each atom is scaled individually.

  • component-based: Scaling is applied only to the center of mass of each component in the system.

The system cell can also be scaled along with the atomic positions. If this option is not selected and periodic boundary conditions (PBCs) are not applied, atoms may end up outside the cell. However, if PBC is enabled, the center of mass of each component is wrapped into the system cell. It is the user’s responsibility to ensure that the scaling operation does not cause atoms to become too close to each other.

Latest version

Allowed number of parents: 1

Parameter Description Value type Value restrictions Default value Units

Scale factor

Scaling factor to scale the system.

float

>0

0.0

N/A

Scale mode

How to scale the system: atom-based or component-based. In the first approach each atom is scaled individually, whereas in the second the scaling is only applied to the center of mass of each component.

selector

“atom-based”, “component-based”

atom-based

N/A

Reference point for the scaling

Indicates with respect to which reference point the scaling is calculated. Refers to the atoms of the entire system, e.g. min is the minimum value of the coordinates among all atoms of the system. Except origin that is the origin of the system.

selector

min, max, geocen, origin

[min, min, min]

N/A

Scale the cell

Indicates whether the cell shall as well be scaled (in x, y, z)

boolean

True, False

True

N/A

Periodic boundary conditions

Indicates whether we have periodic boundary conditions in x, y and z

boolean

True, False

[True, True,True]

N/A